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Centromeres, the chromosomal loci where spindle fibers attach during cell division to segregate chromosomes, are typically found within satellite arrays in plants and animals. Satellite arrays have been difficult to analyze because they comprise megabases of tandem head-to-tail highly repeated DNA sequences. Much evidence suggests that centromeres are epigenetically defined by the location of nucleosomes containing the centromere-specific histone H3 variant cenH3, independently of the DNA sequences where they are located; however, the reason that cenH3 nucleosomes are generally found on rapidly evolving satellite arrays has remained unclear. Recently, long read sequencing technology has clarified the structures of satellite arrays and sparked rethinking of how they evolve, while new experiments and analyses have helped bring both understanding and further speculation about the role these highly repeated sequences play in centromere identification.

Alpha satellite DNA is a major DNA component of primate centromeres. We previously reported that Azara's owl monkey has two types of alpha satellite DNA, OwlAlp1 and OwlAlp2. OwlAlp2 (344 bp) exhibits a sequence similarity throughout its entire length with alpha satellite DNA of closely related species. OwlAlp1 (185 bp) corresponds to the part of OwlAlp2. Based on the observation that the CENP-A protein binds to OwlAlp1, we proposed that OwlAlp1 is a relatively new repetitive DNA that replaced OwlAlp2 as the centromeric satellite DNA. However, a detailed picture of the evolutionary process of this centromere DNA replacement remains largely unknown. Here, we performed a phylogenetic analysis of OwlAlp1 and OwlAlp2 sequences, and also compared our results to alpha satellite DNA sequences of other primate species. We found that: (i) OwlAlp1 exhibits a higher similarity to OwlAlp2 than to alpha satellite DNA of other species, (ii) OwlAlp1 has a single origin, and (iii) sequence variation is lower in OwlAlp1 than in OwlAlp2. We conclude that OwlAlp1 underwent a recent and rapid expansion in the owl monkey lineage. This centromere DNA replacement could have been facilitated by the heterochromatin reorganization that is associated with the adaptation of owl monkeys to a nocturnal lifestyle.

The interest in Robertsonian fusion chromosomes (Rb fusions), sometimes referred to as Robertsonian translocations, derives from their impact on mammalian karyotype evolution, as well from their influence on fertility and disease. The formation of a Rb chromosome necessitates the occurrence of double strand breaks in the pericentromeric regions of two chromosomes in the satellite DNA (satDNA) sequences. Here, we report on the fine-scale molecular analysis of the centromeric satDNA families in the Rb(1;29) translocation of domestic cattle and six antelope species of the subfamily Bovinae. We do so from two perspectives: its occurrence as a chromosomal abnormality in cattle and, secondly, as a fixed evolutionarily rearrangement in spiral-horned antelope (Tragelaphini). By analysing the reorganization of satDNAs in the centromeric regions of translocated chromosomes, we show that Rb fusions are multistep, complex rearrangements which entail the precise elimination and reorganization of specific (peri)centromeric satDNA sequences. Importantly, these structural changes do not influence the centromeric activity of the satellite DNAs that provide segregation stability to the translocated chromosome. Our results suggest a common mechanism for Rb fusions in these bovids and, more widely, for mammals in general.

Vector-borne parasites often manipulate hosts to attract uninfected vectors. For example, parasites causing malaria alter host odor to attract mosquitoes. Here, we discuss the ecology and evolution of fruit-colonizing yeast in a tripartite symbiosis—the so-called “killer yeast” system. “Killer yeast” consists of Saccharomyces cerevisiae yeast hosting two double-stranded RNA viruses (M satellite dsRNAs, L-A dsRNA helper virus). When both dsRNA viruses occur in a yeast cell, the yeast converts to lethal toxin‑producing “killer yeast” phenotype that kills uninfected yeasts. Yeasts on ephemeral fruits attract insect vectors to colonize new habitats. As the viruses have no extracellular stage, they depend on the same insect vectors as yeast for their dispersal. Viruses also benefit from yeast dispersal as this promotes yeast to reproduce sexually, which is how viruses can transmit to uninfected yeast strains. We tested whether insect vectors are more attracted to killer yeasts than to non‑killer yeasts. In our field experiment, we found that killer yeasts were more attractive to Drosophila than non-killer yeasts. This suggests that vectors foraging on yeast are more likely to transmit yeast with a killer phenotype, allowing the viruses to colonize those uninfected yeast strains that engage in sexual reproduction with the killer yeast. Beyond insights into the basic ecology of the killer yeast system, our results suggest that viruses could increase transmission success by manipulating the insect vectors of their host., Ecology and Evolution, 11 (11), ISSN:2045-7758

Bacteria persist under constant threat of predation by bacterial viruses (phages). Bacteria-phage conflicts result in evolutionary arms races often driven by mobile genetic elements (MGEs). One such MGE, a phage satellite in Vibrio cholerae called PLE, provides specific and robust defense against a pervasive lytic phage, ICP1. The interplay between PLE and ICP1 has revealed strategies for molecular parasitism allowing PLE to hijack ICP1 processes in order to mobilize. Here, we describe the mechanism of PLE-mediated transcriptional manipulation of ICP1 structural gene transcription. PLE encodes a novel DNA binding protein, CapR, that represses ICP1’s capsid morphogenesis operon. Although CapR is sufficient for the degree of capsid repression achieved by PLE, its activity does not hinder the ICP1 lifecycle. We explore the consequences of repression of this operon, demonstrating that more stringent repression achieved through CRISPRi restricts both ICP1 and PLE. We also discover that PLE transduces in modified ICP1-like particles. Examination of CapR homologs led to the identification of a suite of ICP1-encoded homing endonucleases, providing a putative origin for the satellite-encoded repressor. This work unveils a facet of the delicate balance of satellite-mediated inhibition aimed at blocking phage production while successfully mobilizing in a phage-derived particle.

Summary Methyl-CpG binding protein 2 (MeCP2) has historically been linked to heterochromatin organization, and in mouse cells it accumulates at pericentric heterochromatin (PCH), closely following major satellite (MajSat) DNA distribution. However, little is known about the specific function of MeCP2 in these regions. We describe the first evidence of a role in neurons for MeCP2 and MajSat forward (MajSat-fw) RNA in reciprocal targeting to PCH through their physical interaction. Moreover, MeCP2 contributes to maintenance of PCH by promoting deposition of H3K9me3 and H4K20me3. We highlight that the MeCP2B isoform is required for correct higher-order PCH organization, and underline involvement of the methyl-binding and transcriptional repression domains. The T158 residue, which is commonly mutated in Rett patients, is directly involved in this process. Our findings support the hypothesis that MeCP2 and the MajSat-fw transcript are mutually dependent for PCH organization, and contribute to clarify MeCP2 function in the regulation of chromatin architecture., Graphical Abstract, Highlights • MeCP2 and MajSat-fw transcript targeting to chromocenters is mutually dependent • MeCP2B and its MBD domain are required for correct higher-order PCH organization • The TRD domain of the MeCP2 protein binds the MajSat-fw transcript • The Rett syndrome T158M mutation of MeCP2 impairs higher-order PCH organization, Della Ragione and colleagues describe a novel function of MeCP2 and MajSat forward transcript in terms of their reciprocal targeting to chromocenters in neurons through their physical interaction. Moreover, MeCP2B has a prominent role in higher-order PCH organization, with both its MBD and TRD involved in this process. These findings further clarify MeCP2 function in the regulation of chromatin architecture.

Betasatellites are single-stranded DNA molecules associated with most monopartite begomoviruses of family Geminiviridae. They are symptoms modulating molecules and depend on their helper viruses for replication, encapsidation and movement. To investigate the genetic diversity of cotton leaf curl Multan betasatellite (CLCuMuB), different Pakistani isolates of betasatellites were retrieved from the NCBI data bank. The sequences were compared to all available sequences of CLCuMuB in the database, identified from cotton in Pakistan, India and China. Phylogenetic and recombination analysis showed the sequences are separated into five major groups. This is primarily based on recombination within the satellite conserved region (SCR) of the betasatellite genome. The first group consists of sequences of the original betasatellite associated with the first epidemic of cotton leaf curl disease (CLCuD) in the 1990s, while the second group consists of recombinant betasatellites associated with the second epidemic of CLCuD, containing a short fragment of tomato leaf curl betasatellite (ToLCB) DNA in the “satellite conserved region (SCR)”. The third group contains a short fragment of papaya leaf curl betasatellite (PaLCuB), while the fourth group contains a short fragment of tobacco curly shoot betasatellite (TbCSB) in the SCR region. The fifth group consists of sequences of betasatellite associated with the recent begomovirus disease complex identified from Vehari. This betasatellite contains a short fragment of sequences in the SCR region of a defective betasatellite (KT228331) from India. This new strain of CLCuMuB is named CLCuMuBVeh. Here, the significance of the evolution of CLCuMuB with respect to the CLCuD complex is discussed.

Summary Muscle satellite cells are normally quiescent but are rapidly activated following muscle damage. Here, we investigated whether damaged myofibers influence the activation of satellite cells. Our findings revealed that satellite cells are directly activated by damaged-myofiber-derived factors (DMDFs). DMDFs induced satellite cells to enter the cell cycle; however, the cells stayed at the G1 phase and did not undergo S phase, and these cells were reversible to the quiescent-like state. Proteome analysis identified metabolic enzymes, including GAPDH, as DMDFs, whose recombinant proteins stimulated the activation of satellite cells. Satellite cells pre-exposed to the DMDFs demonstrated accelerated proliferation ex vivo. Treatment with recombinant GAPDH prior to muscle injury promoted expansion of the satellite cell population in vivo. Thus, our results indicate that DMDFs are not only a set of biomarkers for muscle damage, but also act as moonlighting proteins involved in satellite cell activation at the initial step of muscle regeneration., Graphical Abstract, Highlights • Damaged-myofiber-derived factors (DMDFs) activate satellite cells • DMDFs induce activation, but not proliferation, of satellite cells • Satellite cells activated by DMDFs are reversible to the quiescent-like state • DMDFs play an important role in the initial step of muscle regeneration, In this article, Tsuchiya et al. demonstrate that muscle satellite cells are directly activated by damaged-myofiber-derived factors (DMDFs). DMDFs promote population expansion of satellite cells during muscle regeneration. DMDFs are not only a set of biomarkers for muscle damage, but also act as functional proteins involved in satellite cell activation at the initial step of muscle regeneration.

Made available in DSpace on 2020-12-12T01:26:10Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-09-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) A common characteristic of sex chromosomes is the accumulation of repetitive DNA, which accounts for their diversification and degeneration. In grasshoppers, the X0 sex-determining system in males is considered ancestral. However, in some species, derived variants like neo-XY in males evolved several times independently by Robertsonian translocation. This is the case of Ronderosia bergii, in which further large pericentromeric inversion in the neo-Y also took place, making this species particularly interesting for investigating sex chromosome evolution. Here, we characterized the satellite DNAs (satDNAs) and transposable elements (TEs) of the species to investigate the quantitative differences in repeat composition between male and female genomes putatively associated with sex chromosomes. We found a total of 53 satDNA families and 56 families of TEs. The satDNAs were 13.5% more abundant in males than in females, while TEs were just 1.02% more abundant in females. These results imply differential amplification of satDNAs on neo-Y chromosome and a minor role of TEs in sex chromosome differentiation. We showed highly differentiated neo-XY sex chromosomes owing to major amplification of satDNAs in neo-Y. Furthermore, chromosomal mapping of satDNAs suggests high turnover of neo-sex chromosomes in R. bergii at the intrapopulation level, caused by multiple paracentric inversions, amplifications, and transpositions. Finally, the species is an example of the action of repetitive DNAs in the generation of variability for sex chromosomes after the suppression of recombination, and helps understand sex chromosome evolution at the intrapopulation level. Departamento de Biologia Geral e Aplicada UNESP-Univ Estadual Paulista Instituto de Biociências/IB Department of Organismal Biology Uppsala University Evolutionary Biology Centre Department of Ecology and Genetics Uppsala University Evolutionary Biology Centre Departamento de Biologia Geral e Aplicada UNESP-Univ Estadual Paulista Instituto de Biociências/IB

Satellite DNA is the main component of functional centromeres and forms the main structural constituent of heterochromatin. The presence of alkali-labile sites (ALSs) is a feature inherent to chromatin structure. Here we aimed to characterize ALSs in different satellite DNA loci in cervical epithelial cells using DNA breakage detection coupled with fluorescence in situ hybridization (DBD–FISH). Cervical epithelial cells embedded in an agarose matrix were deproteinized and exposed to alkaline denaturation, which generated single-stranded DNA (ssDNA) starting from the ends of spontaneous basal DNA breaks and ALSs. The amount of ssDNA produced within a specific sequence area could be detected by DBD–FISH using specific probes. The DBD–FISH signals, which were corrected for respective FISH signals during metaphase, were remarkably stronger in the 5 bp classical satellite DNA domains analyzed (D1Z1, D9Z3, and D16Z3) compared with alphoid satellite regions (D3Z1, D8Z2, and DXZ1). D1Z1 locus of chromome-1 being the most affected by alkali denaturation, and contrary, D3Z1 locus of chromosome–3 was the least sensitive to alkali treatment. These findings suggest a high density of constitutive ALSs—probably abasic sites—within the 5 bp satellite DNA sequences in cervical epithelial cells. The presence and relative abundance of ALSs might help explain the high frequency of spontaneous breakage and rearrangements in the pericentromeric heterochromatin of chromosomes 1, 9, and 16 when this chromatin region is undercondensed spontaneously or via induction, such as following viral infections. ALSs in these sequences could be useful tools to monitor DNA damage in cases of cervical carcinogenesis. ALSs on these sequences could be useful tools to monitor DNA damage in cases of cervical carcinogenesis.

Our recent ability to sequence entire genomes, along with all of their transcribed RNAs, has led to the surprising finding that only ∼1% of the human genome is used to encode proteins. This finding has led to vigorous debate over the functional importance of the transcribed but untranslated portions of the genome. Currently, scientists tend to assume coding genes are functional until proven not to be, while the opposite is true for noncoding genes. This review takes a new look at the evidence for and against widespread noncoding gene functionality. We focus in particular on long noncoding RNA (noncoding RNAs longer than 200 nucleotides) genes and their 'junk' associates, transposable elements, and satellite repeats. Taken together, the suggestion put forward is that more of this junk DNA may be functional than nonfunctional and that noncoding RNAs and transposable elements act symbiotically to drive evolution.

Transmissible plasmids spread genes encoding antibiotic resistance and other traits to new bacterial species. Here we report that laboratory populations of Escherichia coli with a newly acquired IncQ plasmid often evolve ‘satellite plasmids’ with deletions of accessory genes and genes required for plasmid replication. Satellite plasmids are molecular parasites: their presence reduces the copy number of the full-length plasmid on which they rely for their continued replication. Cells with satellite plasmids gain an immediate fitness advantage from reducing burdensome expression of accessory genes. Yet, they maintain copies of these genes and the complete plasmid, which potentially enables them to benefit from and transmit the traits they encode in the future. Evolution of satellite plasmids is transient. Cells that entirely lose accessory gene function or plasmid mobility dominate in the long run. Satellite plasmids also evolve in Snodgrassella alvi colonizing the honey bee gut, suggesting that this mechanism may broadly contribute to the importance of IncQ plasmids as agents of bacterial gene transfer in nature., Newly acquired plasmids are frequently lost due to fitness costs. Here, Zhang et al. show that the evolution of satellite plasmids with gene deletions can reduce fitness costs by driving down the copy number of full plasmids and thus favor maintenance of the full plasmid and its novel accessory genes.

Skeletal muscle from meat-producing livestock such as cattle is a major source of food for humans. To improve skeletal muscle growth efficiency or quality in cattle, it is necessary to understand the genetic and physiological mechanisms that govern skeletal muscle composition, development, and growth. Satellite cells are the myogenic progenitor cells in postnatal skeletal muscle. In this study we analyzed the composition of bovine satellite cells with single-cell RNA sequencing (scRNA-seq). We isolated satellite cells from a 2-week-old male calf, cultured them in growth medium for a week, and performed scRNA-seq using the 10x Genomics platform. Deep sequencing of two scRNA-seq libraries constructed from cultured bovine satellite cells yielded 860 million reads. Cell calling analyses revealed that these reads were sequenced from 19,096 individual cells. Clustering analyses indicated that these reads represented 15 cell clusters that differed in gene expression profile. Based on the enriched expression of markers of satellite cells (PAX7 and PAX3), markers of myoblasts (MYOD1, MYF5), and markers of differentiated myoblasts or myocytes (MYOG), three clusters were determined to be satellite cells, two clusters myoblasts, and two clusters myocytes. Gene ontology and trajectory inference analyses indicated that cells in these myogenic clusters differed in proliferation rate and differentiation stage. Two of the remaining clusters were enriched with PDGFRA, a marker of fibro-adipogenic (FAP) cells, the progenitor cells for intramuscular fat, and are therefore considered to be FAP cells. Gene ontology analyses indicated active lipogenesis in one of these two clusters. The identity of the remaining six clusters could not be defined. Overall, the results of this study support the hypothesis that bovine satellite cells are composed of subpopulations that differ in transcriptional and myogenic state. The results of this study also support the hypothesis that intramuscular fat in cattle originates from fibro-adipogenic cells. Published version

Newly hatched poults and chicks have immature thermoregulatory systems and are not able to maintain a constant body temperature when exposed to hot or cold ambient temperatures. During the immediate posthatch period during handling and transport, poults and chicks are commonly exposed to acute thermal conditions. This immediate posthatch period is when satellite cells, adult myoblasts, have their highest period of mitotic activity and are sensitive to extrinsic stimuli including ambient temperature. Variable temperatures can have long-lasting positive or negative effects on skeletal muscle growth. Satellite cells are a self-renewing multipotential stem cell population located between the basement membrane and sarcolemma of muscle fibers. They are responsible for all posthatch growth of muscle through muscle fiber hypertrophy. Results have shown that satellite cells are more sensitive to thermal stress during the period of satellite cell proliferation than during differentiation into multinucleated myotubes, and that pectoralis major muscle satellite cells from growth-selected lines of chickens and turkeys are more sensitive to temperature. Recent findings have shown that the rapamycin, mTOR, signaling pathway which is involved in muscle growth through hypertrophy is differentially affected by thermal stress in a growth-dependent manner. Since satellite cells are a stem cell population, they can also transdifferentiate into other cellular lineages. Anaerobic muscles like the pectoralis major muscle are more prone to converting to an adipogenic lineage compared to aerobic muscles like the biceps femoris. Thus, variable temperatures can impact the intramuscular fat content of the breast muscle. Taken together, changes in ambient temperature alter satellite cell function causing long-term effects on growth, morphological organization, and composition of the pectoralis major, breast, muscle.

Neotropical fishes have highly diversified karyotypic and genomic characteristics and present many diverse sex chromosome systems, with various degrees of sex chromosome differentiation. Knowledge on their sex-specific composition and evolution, however, is still limited. Satellite DNAs (satDNAs) are tandemly repeated sequences with pervasive genomic distribution and distinctive evolutionary pathways, and investigating satDNA content might shed light into how genome architecture is organized in fishes and in their sex chromosomes. The present study investigated the satellitome of Megaleporinus elongatus, a freshwater fish with a proposed Z1Z1Z2Z2/Z1W1Z2W2 multiple sex chromosome system that encompasses a highly heterochromatic and differentiated W1 chromosome. The species satellitome comprises of 140 different satDNA families, including previously isolated sequences and new families found in this study. This diversity is remarkable considering the relatively low proportion that satDNAs generally account for the M. elongatus genome (around only 5%). Differences between the sexes in regards of satDNA content were also evidenced, as these sequences are 14% more abundant in the female genome. The occurrence of sex-biased signatures of satDNA evolution in the species is tightly linked to satellite enrichment associated with W1 in females. Although both sexes share practically all satDNAs, the overall massive amplification of only a few of them accompanied the W1 differentiation. We also investigated the expansion and diversification of the two most abundant satDNAs of M. elongatus, MelSat01-36 and MelSat02-26, both highly amplified sequences in W1 and, in MelSat02-26’s case, also harbored by Z2 and W2 chromosomes. We compared their occurrences in M. elongatus and the sister species M. macrocephalus (with a standard ZW sex chromosome system) and concluded that both satDNAs have led to the formation of highly amplified arrays in both species; however, they formed species-specific organization on female-restricted sex chromosomes. Our results show how satDNA composition is highly diversified in M. elongatus, in which their accumulation is significantly contributing to W1 differentiation and not satDNA diversity per se. Also, the evolutionary behavior of these repeats may be associated with genome plasticity and satDNA variability between the sexes and between closely related species, influencing how seemingly homeologous heteromorphic sex chromosomes undergo independent satDNA evolution.

Satellite cells support adult skeletal muscle fiber adaptations to loading in numerous ways. The fusion of satellite cells, driven by cell-autonomous and/or extrinsic factors, contributes new myonuclei to muscle fibers, associates with load-induced hypertrophy, and may support focal membrane damage repair and long-term myonuclear transcriptional output. Recent studies have also revealed that satellite cells communicate within their niche to mediate muscle remodeling in response to resistance exercise, regulating the activity of numerous cell types through various mechanisms such as secretory signaling and cell-cell contact. Muscular adaptation to resistance and endurance activity can be initiated and sustained for a period of time in the absence of satellite cells, but satellite cell participation is ultimately required to achieve full adaptive potential, be it growth, function, or proprioceptive coordination. While significant progress has been made in understanding the roles of satellite cells in adult muscle over the last few decades, many conclusions have been extrapolated from regeneration studies. This review highlights our current understanding of satellite cell behavior and contributions to adaptation outside of regeneration in adult muscle, as well as the roles of satellite cells beyond fusion and myonuclear accretion, which are gaining broader recognition.

The vast majority of viruses consist of a nucleic acid surrounded by a protective icosahedral protein shell called the capsid. During viral infection of a host cell, the timing and efficiency of the assembly process is important for ensuring the production of infectious new progeny virus particles. In the class of single-stranded RNA (ssRNA) viruses, the assembly of the capsid takes place in tandem with packaging of the ssRNA genome in a highly cooperative co-assembly process. In simple ssRNA viruses such as the bacteriophage MS2 and small RNA plant viruses such as STNV, this cooperative process results from multiple interactions between the protein shell and sites in the RNA genome which have been termed packaging signals. Using a stochastic assembly algorithm which includes cooperative interactions between the protein shell and packaging signals in the RNA genome, we demonstrate that highly efficient assembly of STNV capsids arises from a set of simple local rules. Altering the local assembly rules results in different nucleation scenarios with varying assembly efficiencies, which in some cases depend strongly on interactions with RNA packaging signals. Our results provide a potential simple explanation based on local assembly rules for the ability of some ssRNA viruses to spontaneously assemble around charged polymers and other non-viral RNAs in vitro., Author Summary Assembly in single-stranded RNA plant viruses takes place via a highly cooperative process in which capsid proteins co-assemble around ssRNA. In the small satellite plant virus STNV, small hairpins present in the genome, termed packaging signals, bind to capsid proteins during assembly and allow for efficient formation of the capsid shell. Although these hairpins have been visualised in X-ray crystallography, the local rules of their interaction with the capsid proteins and how they ensure an efficient assembly process is somewhat unknown. Here we test several assembly scenarios involving different local rules for the protein-protein and RNA-protein interactions and find that assembly efficiency is highly dependent on the local assembly rules. Interestingly, while certain local assembly rules are consistent with a packaging signal mediated assembly model, some local rules predict reasonable assembly efficiency independent of packaging signal distribution. This may explain the ability to package charged polymer materials in some plant viruses.

Zanthoxylum armatum is an important woody crop with multiple applications in pharmaceutics, cosmetics, and food industries. With continuous increases in the plantation area, integrated pest management is required for scale production when diseases caused by biotic factors such as pests and pathogens have become new problems, one of which is the infectious flower yellowing disease (FYD). Here, isolates of a new illarvirus (3) and a new nepovirus-associated subviral satellite RNA (12) were identified in Z. armatum, in addition to 38 new isolates of four previously reported RNA viruses. Sequence variation can be observed in viral/subviral quasispecies and among predominant isolates from the same or different samples and geographic origins. Intriguingly, RNA sequencing of different diseased trees invariably showed an extraordinary pattern of particularly high reads accumulation of the green Sichuan pepper-nepovirus (GSPNeV) and the satellite RNA in symptomatic tissues. In addition, we also examined small RNAs of the satellite RNA, which show similar patterns to those of coinfecting viruses. This study provides further evidence to support association of the FYD with viral/subviral infections and deepens our understanding of the diversity and molecular characteristics of the viruses and satellite, as well as their interactions with the host.

Significance Cholera toxin, the principal virulence factor of Vibrio cholerae, is encoded in the genome of an integrative mobile element exploiting Xer (IMEX), CTXΦ. Nontoxigenic strains generally lack a suitable CTXΦ attachment site. In addition, CTXΦ integration is intrinsically irreversible. Nevertheless, new epidemic clones carrying potentially more potent toxins are constantly created by CTXΦ excision and reintegration cycles. Previous studies suggested that these cycles depended on another IMEX, TLCΦ, whose integration corrected the attachment site of nontoxigenic strains and whose excision promoted the joint elimination of CTXΦ copies. Our work brings molecular understanding to the role played by TLCΦ and suggests how similar IMEXs might participate in the evolution of other pathogenic bacteria., The circular chromosomes of bacteria can be concatenated into dimers by homologous recombination. Dimers are solved by the addition of a cross-over at a specific chromosomal site, dif, by 2 related tyrosine recombinases, XerC and XerD. Each enzyme catalyzes the exchange of a specific pair of strands. Some plasmids exploit the Xer machinery for concatemer resolution. Other mobile elements exploit it to integrate into the genome of their host. Chromosome dimer resolution is initiated by XerD. The reaction is under the control of a cell-division protein, FtsK, which activates XerD by a direct contact. Most mobile elements exploit FtsK-independent Xer recombination reactions initiated by XerC. The only notable exception is the toxin-linked cryptic satellite phage of Vibrio cholerae, TLCΦ, which integrates into and excises from the dif site of the primary chromosome of its host by a reaction initiated by XerD. However, the reaction remains independent of FtsK. Here, we show that TLCΦ carries a Xer recombination activation factor, XafT. We demonstrate in vitro that XafT activates XerD catalysis. Correspondingly, we found that XafT specifically interacts with XerD. We further show that integrative mobile elements exploiting Xer (IMEXs) encoding a XafT-like protein are widespread in gamma- and beta-proteobacteria, including human, animal, and plant pathogens.

As a class of parasitic, non-coding RNAs, satellite RNAs (satRNAs) have to compete with their helper virus for limited amounts of viral and/or host resources for efficient replication, by which they usually reduce viral accumulation and symptom expression. Here, we report a cucumber mosaic virus (CMV)-associated satRNA (sat-T1) that ameliorated CMV-induced symptoms, accompanied with a significant reduction in the accumulation of viral genomic RNAs 1 and 2, which encode components of the viral replicase. Intrans replication assays suggest that the reduced accumulation is the outcome of replication competition. The structural basis of sat-T1 responsible for the inhibition of viral RNA accumulation was determined to be a three-way branched secondary structure that contains two biologically important hairpins. One is indispensable for the helper virus inhibition, and the other engages in formation of a tertiary pseudoknot structure that is essential for sat-T1 survival. The secondary structure containing the pseudoknot is the first RNA element with a biological phenotype experimentally identified in CMV satRNAs, and it is structurally conserved in most CMV satRNAs. Thus, this may be a generic method for CMV satRNAs to inhibit the accumulation of the helper virus via the newly-identified RNA structure.

Satellite repeats are a structural component of centromeres and telomeres, and in some instances their divergence is known to drive speciation. Due to their highly repetitive nature, satellite sequences have been understudied and underrepresented in genome assemblies. To investigate their turnover in great apes, we studied satellite repeats of unit sizes up to 50 bp in human, chimpanzee, bonobo, gorilla, and Sumatran and Bornean orangutans, using unassembled short and long sequencing reads. The density of satellite repeats, as identified from accurate short reads (Illumina), varied greatly among great ape genomes. These were dominated by a handful of abundant repeated motifs, frequently shared among species, which formed two groups: (1) the (AATGG)nrepeat (critical for heat shock response) and its derivatives; and (2) subtelomeric 32-mers involved in telomeric metabolism. Using the densities of abundant repeats, individuals could be classified into species. However clustering did not reproduce the accepted species phylogeny, suggesting rapid repeat evolution. Several abundant repeats were enriched in males vs. females; using Y chromosome assemblies or FIuorescent In Situ Hybridization, we validated their location on the Y. Finally, applying a novel computational tool, we identified many satellite repeats completely embedded within long Oxford Nanopore and Pacific Biosciences reads. Such repeats were up to 59 kb in length and consisted of perfect repeats interspersed with other similar sequences. Our results based on sequencing reads generated with three different technologies provide the first detailed characterization of great ape satellite repeats, and open new avenues for exploring their functions.

The purpose of this study was to test the hypothesis that macrophage polarization is altered in old compared to young skeletal muscle, possibly contributing to the poor satellite cell response observed in older muscle tissue. Muscle biopsies were collected prior to and at 3, 24, and 72 h following a muscle-damaging exercise in young and old individuals. Immunohistochemistry was used to measure i.m. macrophage content and phenotype, and cell culture experiments tested macrophage behavior and influence on primary myoblasts from older individuals. We found that macrophage infiltration was similar between groups at 24 (young: 3712 ± 2407

Many fungal viruses or mycoviruses have multi-segmented, rather than single-segmented, genomes. This multi-segment nature is frequently possessed by double-stranded RNA viruses, which include members of the Chrysoviridae, Quadriviridae, Megabirnaviridae, Partitiviridae, and Reoviridae families, and unassigned groups. Their genome segments are often packaged separately with the exception of mycoreoviruses, which are multi-segmented but mono-particulate viruses. These multi-segmented fungal dsRNA viruses, as exemplified by reoviruses, have been extensively studied among structural biologists, and contributed to discoveries of novel virion structures. Multi-component systems, interactions of viruses with subviral agents such as satellite and defective RNAs as typified by the yeast killer, and the rule-breaking neo-virus lifestyle exhibited by a capsidless single-stranded RNA virus hosted in an unrelated double-stranded RNA virus are also discussed. Fungal multi-segmented viruses and multicomponent virus systems would continue to provide virologists with interesting future challenges.

Summary Adult muscle stem cells (satellite cells) are required for adult skeletal muscle regeneration. A proper balance between quiescence, proliferation, and differentiation is essential for the maintenance of the satellite cell pool and their regenerative function. Although the ubiquitin-proteasome is required for most protein degradation in mammalian cells, how its dysfunction affects tissue stem cells remains unclear. Here, we investigated the function of the proteasome in satellite cells using mice lacking the crucial proteasomal component, Rpt3. Ablation of Rpt3 in satellite cells decreased proteasome activity. Proteasome dysfunction in Rpt3-deficient satellite cells impaired their ability to proliferate, survive and differentiate, resulting in defective muscle regeneration. We found that inactivation of proteasomal activity induced proliferation defects and apoptosis in satellite cells. Mechanistically, insufficient proteasomal activity upregulated the p53 pathway, which caused cell-cycle arrest. Our findings delineate a critical function of the proteasome system in maintaining satellite cells in adult muscle., Graphical Abstract, Highlights • Ablation of Rpt3 in satellite cells leads to decreased proteasome activity • Proteasome dysfunction in satellite cells results in defective muscle regeneration • Proteasome dysfunction induces proliferation defects and apoptosis • Inhibition of p53 rescues Rpt3-mediated defects in proliferation, It is not clear how proteasome insufficiency affects tissue stem cells. Kitajima et al. demonstrate that the proteasome system is indispensable for the maintenance of muscle stem cells. Proteasome dysfunction in Rpt3-deficient satellite cells impairs their ability to proliferate, survive and differentiate, resulting in defective muscle regeneration.

Vector-borne parasites often manipulate hosts to attract uninfected vectors. For example, parasites causing malaria alter host odor to attract mosquitoes. Here we discuss the ecology and evolution of fruit-colonizing yeast in a tripartite symbiosis – the so-called “killer yeast” system. “Killer yeast” consists of Saccharomyces cerevisiae yeast hosting two double stranded RNA viruses (M satellite dsRNAs, L-A dsRNA helper virus). When both dsRNA viruses occur in a yeast cell, the yeast converts to lethal toxin‑producing “killer yeast” phenotype that kills uninfected yeasts. Yeasts on ephemeral fruits attract insect vectors to colonize new habitats. As the viruses have no extracellular stage, they depend on the same insect vectors as yeast for their dispersal. Viruses also benefit from yeast dispersal as this promotes yeast to reproduce sexually, which is how viruses can transmit to uninfected yeast strains. We tested whether insect vectors are more attracted to killer yeasts than to non‑killer yeasts. In our field experiment, we found that killer yeasts were more attractive to Drosophila than non-killer yeasts. This suggests that vectors foraging on yeast are more likely to transmit yeast with a killer phenotype, allowing the viruses to colonize those uninfected yeast strains that engage in sexual reproduction with the killer yeast. Beyond insights into the basic ecology of the killer yeast system, our results suggest that viruses could increase transmission success by manipulating the insect vectors of their host.

Single Cell RNA-sequencing (scRNA-seq) is a powerful technique to deconvolute gene expression of various subset of cells intermingled within a complex tissue, such as the skeletal muscle. We first used scRNA-seq to understand dynamics of cell populations and their gene expression during muscle regeneration in murine limb muscles. This leads to the identification of a subset of satellite cells (the resident stem cells of skeletal muscles) with immune gene signatures in regenerating muscles. Next, we used scRNA-seq to examine gene expression dynamics of satellite cells at various status: quiescence, activation, proliferation, differentiation and self-renewal. This analysis uncovers stage-dependent changes in expression of genes related to lipid metabolism. Further analyses lead to the discovery of previously unappreciated dynamics of lipid droplets in satellite cells; and demonstrate that the abundance of the lipid droplets in newly divided satellite daughter cells is linked to cell fate segregation into differentiation versus self-renewal. Perturbation of lipid droplet dynamics through blocking lipolysis disrupts cell fate homeostasis and impairs muscle regeneration. Finally, we show that lipid metabolism regulates the function of satellite cells through two mechanisms. On one hand, lipid metabolism functions as an energy source through fatty acid oxidation (FAO), and blockage of FAO reduces energy production that is critical for satellite cell function. On the other hand, lipid metabolism generates bioactive molecules that influence signaling transduction and gene expression. In this scenario, lipid metabolism and FAO regulate the intracellular levels of acetyl-coA and selective acetylation of PAX7, a pivotal transcriptional factor underlying function of satellite cells. These results together reveal for the first time a critical role of lipid metabolism and lipid droplet dynamics in muscle satellite cell fate determination and regenerative function; and underscore a potential role of dietary fatty acids in satellite cell-dependent muscle development, growth and regeneration.

Suffolk ewes (n = 26) were blocked by body condition and weight, and randomly divided into two breeding groups (n = 13/group). One group was bred to a Texel ram and the other to a Suffolk ram. Ewes were confirmed pregnant by ultrasound and went to term. Male lambs (n = 4/sire/time) were harvested on d 2, 14, and 203 of age for muscle characterization and satellite cell isolation. From d 2 to 14, body weight increased (P < 0.01) by 80%, weight of the longissimus increased by 160%, and longissimus muscle area increased by 100%. Between d 14 and 203 lamb weight and weight of the longissimus increased by 350%, while longissimus area only increased by 100%. Sire breed did not alter lamb weight or weight of the longissimus (P > 0.10). Longissimus muscle area tended (P < 0.10) to be increased for Texel sired lambs when compared to Suffolk sired lambs. The total number of satellite cells isolated were not different by sire breed but did differ by animal age (P < 0.01). Satellite cell populations per gram of tissue increased between d 2 and 14 and decreased from d 14 to 203. Due to the large changes in growth from d2 to 14, satellite cell proliferation was examined at d 2 of age. Satellite cell proliferation capacity was altered by sire breed at d 2 of age potentially contributing to the increased longissimus muscle area. Advancing animal age and development alters satellite cell population numbers and potentially supports a high capacity for growth.

Summary Regeneration of skeletal muscle requires resident stem cells called satellite cells. Here, we report that the chromatin remodeler CHD4, a member of the nucleosome remodeling and deacetylase (NuRD) repressive complex, is essential for the expansion and regenerative functions of satellite cells. We show that conditional deletion of the Chd4 gene in satellite cells results in failure to regenerate muscle after injury. This defect is principally associated with increased stem cell plasticity and lineage infidelity during the expansion of satellite cells, caused by de-repression of non-muscle-cell lineage genes in the absence of Chd4. Thus, CHD4 ensures that a transcriptional program that safeguards satellite cell identity during muscle regeneration is maintained. Given the therapeutic potential of muscle stem cells in diverse neuromuscular pathologies, CHD4 constitutes an attractive target for satellite cell-based therapies., Graphical abstract, Highlights • CHD4/NuRD regulates satellite cell (SC) fate commitment • CHD4 deficiency blocks SC proliferation and disrupts skeletal muscle regeneration • CHD4/NuRD repress myogenic differentiation genes during SC proliferative expansion • CHD4/NuRD represses genes associated with other fates (brain, heart) in SCs, In this article, Sreenivasan and colleagues show that the chromatin-remodeling complex CHD4/NuRD is required to maintain muscle stem cell (satellite cell) identity. CHD4 represses the skeletal muscle differentiation gene program during satellite cell proliferation and maintains genes from other lineages (brain, heart) silent, being essential for proper skeletal muscle regeneration.

This study describes a new mycovirus infecting a strain from the Fusarium incarnatum-equiseti species complex. Based on phylogenetic and genomic analyses, this virus belongs to the recently proposed genus "Zetapartitivirus" in the family Partitiviridae. The name "Fusarium equiseti partitivirus 1″ (FePV1) is therefore suggested for this novel viral species. Similar to other partitiviruses, FePV1 genome is composed by two dsRNA segments that exhibit each one large ORF encoding for an RdRp and a CP, respectively. A smaller dsRNA was also detected in infected mycelium and could be a satellite RNA of FePV1. In addition to characterized zetapartitiviruses, other FePV1-related sequences were retrieved from online databases and their significance is discussed. Following conidial isolation, an FePV1-free isogenic line of the fungal host was obtained. In comparison with the original infected strain, this line showed higher growth, biomass production and pathogenicity on tomato, advocating that FePV1 induces hypovirulence on its host.

Background Trimethylation of histone H3 on lysine 9 (H3K9me3) at satellite DNA sequences has been primarily studied at (peri)centromeric regions, where its level shows differences associated with various processes such as development and malignant transformation. However, the dynamics of H3K9me3 at distal satellite DNA repeats has not been thoroughly investigated. Results We exploit the sets of publicly available data derived from chromatin immunoprecipitation combined with massively parallel DNA sequencing (ChIP-Seq), produced by the The Encyclopedia of DNA Elements (ENCODE) project, to analyze H3K9me3 at assembled satellite DNA repeats in genomes of human cell lines and during mouse fetal development. We show that annotated satellite elements are generally enriched for H3K9me3, but its level in cancer cell lines is on average lower than in normal cell lines. We find 407 satellite DNA instances with differential H3K9me3 enrichment between cancer and normal cells including a large 115-kb cluster of GSATII elements on chromosome 12. Differentially enriched regions are not limited to satellite DNA instances, but instead encompass a wider region of flanking sequences. We found no correlation between the levels of H3K9me3 and noncoding RNA at corresponding satellite DNA loci. The analysis of data derived from multiple tissues identified 864 instances of satellite DNA sequences in the mouse reference genome that are differentially enriched between fetal developmental stages. Conclusions Our study reveals significant differences in H3K9me3 level at a subset of satellite repeats between biological states and as such contributes to understanding of the role of satellite DNA repeats in epigenetic regulation during development and carcinogenesis.

Geminiviridae is one of the most important families in plant viruses with a single-stranded DNA genome comprises one or two genomes (DNA-A and DNA-B) of 2.5–5.2Kb. These viruses infect economically important food and fiber crops worldwide. Till to date nine genera (Mastrevirus, Curtovirus, Becurtovirus, Turncurtovirus, Begomovirus, Capulavirus, Topocuvirus, Eragrovirus, and Grablovirus) have been reported which are transmitted by four insect vectors (whiteflies, leafhoppers, aphids, and treehoppers). DNA-A encodes replication-associated protein, coat protein, replication enhancer protein, transcriptional activator protein, AV2, AC4, and AC5 while DNA-B encodes nuclear shuttle protein and movement protein. Satellite molecules have also been reported to be associated with the family Geminiviridae that includes alphasatellite, betasatellite which encode alpha rep and βC1 gene respectively. A non-coding deltasatellite has also been reported to be associated with geminivirus infections. Geminivirus encoded proteins interact with host proteins to perform a variety of functions which include reprogramming of cell cycle, inhibition of cell death pathways, transcriptional control of multiple genes, interference with cell signaling pathways and overcoming host defense response. Our current knowledge regarding interactions of geminivirus encoded proteins with the host has been described in the following chapter.

Apoptosis is programmed cell death that can be stimulated by external stress or nutrition restrictions. Lysine (Lys) is an essential amino acid for pig growth, and the relationship between Lys deficiency caused apoptosis and inhibition of skeletal muscle growth remains unknown. The objective of this study was to investigate whether apoptosis could be regulated by Lys supplementation and the potential mechanism. In current work, 30 male Duroc × Landrace × Large weaned piglets were divided randomly into 3 groups: control group (Lys 1.30%), Lys deficiency group (Lys 0.86%), and Lys rescue group (Lys 0.86%, 0-14d; 1.30%,15–28 d). The experiment lasted for 28 days, and on the morning of 29 d, piglets were slaughtered to collect samples. Isobaric tag for relative and absolute quantification (iTRAQ) proteomics analysis of the longissimus dorsi muscle showed that Janus family tyrosine kinase (JAK)-signal transducer and activator of transcription (STAT) pathway was involved in Lys deficiency-induced apoptosis and inhibited skeletal muscle growth. Meanwhile, western blotting results of the longissimus dorsi muscle demonstrated that Lys deficiency caused apoptosis (P < 0.05) with the JAK2-STAT3 pathway inhibition (P < 0.05). Interestingly, apoptosis was suppressed (P < 0.05), and the JAK2-STAT3 pathway was reactivated (P < 0.05) after Lys re-supplementation in longissimus dorsi muscle. In addition, results of satellite cells (SCs) isolated from the longissimus dorsi muscle of 5-day-old Landrace piglets showed that Lys deficiency-induced apoptosis (P < 0.05) was mediated by the JAK2-STAT3 pathway inhibition (P < 0.05). Moreover, the JAK2-STAT3 pathway was reactivated (P < 0.05) by Lys re-supplementation and suppressed apoptosis in SCs (P < 0.05), and this effect was blocked (P < 0.05) after SCs treated with AG-490 (a specific inhibitor of JAK2). Collectively, Lys inhibited apoptosis in SCs to govern skeletal muscle growth via the JAK2-STAT3 pathway.

Centromeres are defined by the location of Centromeric Histone H3 (CENP-A/CENH3) which interacts with DNA to define the locations and sizes of functional centromeres. An analysis of 26 maize genomes including 110 fully assembled centromeric regions revealed positive relationships between centromere size and genome size. These effects are independent of variation in the amounts of the major centromeric satellite sequence CentC. We also backcrossed known centromeres into two different lines with larger genomes and observed consistent increases in functional centromere sizes for multiple centromeres. Although changes in centromere size involve changes in bound CENH3, we could not mimic the effect by overexpressing CENH3 by threefold. Literature from other fields demonstrate that changes in genome size affect protein levels, organelle size and cell size. Our data demonstrate that centromere size is among these scalable features, and that multiple limiting factors together contribute to a stable centromere size equilibrium.

We report a rare case of a 14-month-old male child who was referred for developmental delay. Clinical examination revealed a hypotonic infant with speech delay and no dysmorphic features. The banding cytogenetics revealed a small supernumerary marker chromosome. Upon silver staining, the marker showed the presence of satellite regions on either ends. Further, analysis using fluorescence in situ hybridization on marker chromosome revealed its origin from chromosome 15.

Geminiviruses can infect a wide range of plant hosts worldwide and have hence become an emerging global agroeconomic threat. The association of these viruses with satellite molecules and highly efficient insect vectors such as whiteflies further prime their devastating impacts. Plants elicit a strong antiviral immune response to restrict the invasion of these destructive pathogens. Phytohormones help plants to mount this response and occupy a key position in combating these biotrophs. These defense hormones not only inhibit geminiviral propagation but also hamper viral transmission by compromising the performance of their insect vectors. Nonetheless, geminiviruses have co-evolved to have a few multitasking virulence factors that readily remodel host cellular machineries to circumvent the phytohormone-mediated manifestation of the immune response. Furthermore, these obligate parasites exploit plant growth hormones to produce a cellular environment permissive for virus replication. In this review, we outline the current understanding of the roles and regulation of phytohormones in geminiviral pathogenesis.

Satellite DNA is a class of repetitive sequences that are organized in long arrays of tandemly repeated units in most eukaryotes. Long considered as selfish DNA, satellite sequences are now proposed to contribute to genome integrity. Despite their potential impact on the architecture and evolution of the genome, satellite DNAs have not been investigated in oomycetes due to the paucity of genomic data and the difficulty of assembling highly conserved satellite arrays. Yet gaining knowledge on the structure and evolution of genomes of oomycete pathogens is crucial to understanding the mechanisms underlying adaptation to their environment and to proposing efficient disease control strategies. A de novo assembly of the genome of Phytophthora parasitica, an important oomycete plant pathogen, led to the identification of several families of tandemly repeated sequences varying in size, copy number, and sequence conservation. Among them, two abundant families, designated as PpSat1 and PpSat2, displayed typical features of satellite DNA and were collectively designated as PpSat. These two satellite families differ by their length, sequence, organization, genomic environment, and evolutionary dynamics. PpSat1, but not PpSat2, presented homologs among oomycetes. This observation, as well as the characterization of transcripts of PpSat families, suggested that these satellite DNA families likely play a conserved role within this important group of pathogens.

Begomoviruses belong to the family Geminiviridae are single-stranded circular DNA viruses with either monopartite (DNA-A genome of about 2.7 kb), encoding six open reading frames or bipartite genomes (DNA-A and DNA-B genomes of 2.5–2.6 kb) encapsulated in twinned particles. They are efficiently transmitted by the vector whitefly (Bemisia tabaci) to dicotyledonous plants. The DNA-A component of the bipartite begomoviruses is involved in replication and production of virions, but requires the DNA-B component for nuclear localization, systemic infection, host-range determination, and symptom expression. Begomoviruses are known to have satellite molecules known as betasatellites and alphasatellites. Plant virology in Saudi Arabia is in its infancy; very little information is available about the plant viruses causing diseases in important crops. This chapter summarizes the major developments and current status of begomovirus research and future prospects, especially in the area of begomovirus research, in Saudi Arabia.

Repetitive DNA is a major organizational component of eukaryotic genomes, being intrinsically related with their architecture and evolution. Tandemly repeated satellite DNAs (satDNAs) can be found clustered in specific heterochromatin-rich chromosomal regions, building vital structures like functional centromeres and also dispersed within euchromatin. Interestingly, despite their association to critical chromosomal structures, satDNAs are widely variable among species due to their high turnover rates. This dynamic behavior has been associated with genome plasticity and chromosome rearrangements, leading to the reshaping of genomes. Here we present the current knowledge regarding satDNAs in the light of new genomic technologies, and the challenges in the study of these sequences. Furthermore, we discuss how these sequences, together with other repeats, influence genome architecture, impacting its evolution and association with disease.

Wnt/β-catenin plays a crucial role in skeletal muscle growth, but its specific mechanism still unclear. In this study, due to the distinct role of lysine in pig industry, we provided it as an entry point to investigate the role of Wnt/β-catenin in governing skeletal muscle growth. Firstly, total 18 weaned piglets were divided into three groups: control group, lysine deficiency group and lysine re-supplementation group (lysine levels added from 0.83% to 1.31% at 14 d). After 28 d experiment, all pigs were slaughtered to measure the change of Wnt/β-catenin in skeletal muscle. Secondly, satellite cell (SC) was isolated and cultured with Wnt activator, such as Wnt3a and WRN (Wnt3a, R-spondin1, Noggin) after lysine deficiency for 48 h to investigate cell proliferation and differentiation ability and the level of Wnt/β-catenin in different conditions. The results showed that compared with the control group, lysine deficiency significantly reduced longissimus dorsi muscle weight and Pax7 positive SC, and inhibited Wnt/β-catenin (P < 0.05). Fortunately, these restrictions were rescued to the control levels by lysine re-supplementation (P > 0.05). Meanwhile, compared with the lysine deficiency group, the MTT and western blotting assay showed cell proliferation ability was significantly increased with re-activated Wnt/β-catenin by re-supplemented lysine, Wnt3a or WRN (P < 0.05), respectively. Moreover, under the condition of cell differentiation, compared with the control group, cell fusion index was significantly decreased in the lysine deficiency group (P < 0.05), whereas it was significantly increased with lysine re-supplementation group, Wnt3a or WRN respective supplementation group in comparison with the lysine deficiency group (P < 0.05). In addition, compared with the lysine deficiency group, the protein levels of myogenic regulatory factors and Wnt/β-catenin pathway were also re-activated by re-supplemented lysine, Wnt3a or WRN (P < 0.05). Collectively, we found Wnt/β-catenin activation is required for porcine SC proliferation and differentiation to promote skeletal muscle growth.

Summary Satellite cells function as precursor cells in mature skeletal muscle homeostasis and regeneration. In healthy tissue, these cells are maintained in a state of quiescence by a microenvironment formed by myofibers and basement membrane in which LAMININs (LMs) form a major component. In the present study, we evaluated the satellite cell microenvironment in vivo and found that these cells are encapsulated by LMα2–5. We sought to recapitulate this satellite cell niche in vitro by culturing satellite cells in the presence of recombinant LM-E8 fragments. We show that treatment with LM-E8 promotes proliferation of satellite cells in an undifferentiated state, through reduced phosphorylation of JNK and p38. On transplantation into injured muscle tissue, satellite cells cultured with LM-E8 promoted the regeneration of skeletal muscle. These findings represent an efficient method of culturing satellite cells for use in transplantation through the recapitulation of the satellite cell niche using recombinant LM-E8 fragments., Graphical Abstract, Highlights • Satellite cells are encapsulated by LMα2–5 • LM-E8 promotes proliferation of satellite cells in an undifferentiated state • Satellite cells cultured with LM-E8 enhanced the regeneration of skeletal muscle, In this study, examination of the satellite cell microenvironment in vivo revealed that these cells are encapsulated by LMα2–5. We find that reconstitution of the satellite cell niche with recombinant LM-E8 fragments promotes the proliferation and maintains satellite cells in an undifferentiated state.

Repetitive DNA, represented by transposons and satellite DNA, constitutes a large portion of eukaryotic genomes, being the major component of constitutive heterochromatin. There is a growing body of evidence that it regulates several nuclear functions including chromatin state and the proper functioning of centromeres and telomeres. The 1.688 satellite is one of the most abundant repetitive sequences in Drosophila melanogaster, with the longest array being located in the pericentromeric region of the X-chromosome. Short arrays of 1.688 repeats are widespread within the euchromatic part of the X-chromosome, and these arrays were recently suggested to assist in recognition of the X-chromosome by the dosage compensation male-specific lethal complex. We discovered that a short array of 1.688 satellite repeats is essential for recruitment of the protein POF to a previously described site on the X-chromosome (PoX2) and to various transgenic constructs. On an isolated target, i.e., an autosomic transgene consisting of a gene upstream of 1.688 satellite repeats, POF is recruited to the transgene in both males and females. The sequence of the satellite, as well as its length and position within the recruitment element, are the major determinants of targeting. Moreover, the 1.688 array promotes POF targeting to the roX1-proximal PoX1 site in trans. Finally, binding of POF to the 1.688-related satellite-enriched sequences is conserved in evolution. We hypothesize that the 1.688 satellite functioned in an ancient dosage compensation system involving POF targeting to the X-chromosome.

Trace minerals are vital for the health and growth of livestock, supporting multiple biochemical processes in the body. There are several different signaling pathways that may be affected by trace minerals, ultimately altering growth of skeletal muscle. However, it is currently unknown how trace minerals specifically impact growth of skeletal muscle. As such, the objective of this study was to determine how zinc (Zn) and manganese (Mn) affect proliferation and protein synthesis of primary bovine satellite cell (BSC) cultures. Cultures were grown to 80% confluency and treated in 1% fetal bovine serum (control), 0.05, 0.10 or 0.25 µM of Mn, or 10, 20 or 40 µM of Zn to assess proliferation. Additionally, the above treatments were applied to fused BSC cultures in serum free media (control) to measure protein synthesis. The trace mineral concentrations chosen were based off known ranges of circulating concentrations of Zn or Mn. A series of contrasts were constructed to determine whether growth of BSC cultures was different between the treated and control cultures. Treatment with 10 µM Zn increased (P = 0.03) proliferation when compared to control cultures. However, treatment with Mn at the tested concentration did not (P > 0.12) result in proliferation rates that were different than the control cultures. Treatment with 10 µM Zn, 20 µM Zn, or 0.5 µM Mn increased (P < 0.05) protein synthesis compared to control cultures. These results indicate Zn is capable of increasing proliferation and both Zn and Mn increase protein synthesis of BSC cultures. Additional research is needed to couple trace mineral nutrition with knowledge of BSC biology to elucidate the molecular mechanisms by which trace minerals may function to support bovine skeletal muscle growth.

The type of myofiber is important for porcine meat quality. Meanwhile, the nt/Ca2+ pathway has been showed multiple roles in skeletal muscle formation; however, the distinct mechanism is still unclear. In this study, the weaned piglets and satellite cells were designed into the control group, lysine deficiency group and lysine rescue group to investigate the function of Wnt/Ca2+ pathway in governing skeletal muscle typing. After we confirm the growth of weaned piglets was controlled by lysine, the isobaric tag for relative and absolute quantification (iTRAQ) analysis of skeletal muscle detected that Wnt/Ca2+ pathway was involved in the transition of fast and slow fiber. Then, we found the ratio of type I myofiber in Semimembranous (fast muscle) was significantly increased after lysine deficiency (P < 0.05), and decreased by lysine rescue (P < 0.05). In contrast, the ratio of type I myofiber in Semitendinous muscle (slow muscle) was significantly decreased in the lysine deficiency group, and increased in the lysine rescue group (P < 0.05). Furthermore, the Wnt/Ca2+ pathway was significantly increased in Semimembranous muscle, while decreased in Semitendinous muscle with lysine deficiency, and this phenomenon was inversed after lysine rescue (P < 0.05). Meanwhile, the Wnt/Ca2+ pathway was stronger in satellite cells isolated from Semitendinous muscle (StSCs) than that of Semimembranous satellite cell (SmSCs) (P < 0.05). And we also found the StSCs enter in differentiation is more easily than SmSCs (P < 0.05). Besides, the ratio of type I myofiber originated from StSCs showed greater than StSCs (P < 0.05). In summary, we conclude that satellite cells participate in the Wnt/Ca2+ pathway controlled porcine myofiber determination.

Transcription factors (TFs) are key regulators of gene expression during cell differentiation. Four TFs including Myf5, MyoD, MyoG and Myf6 have been identified as key myogenic regulatory factors (MYFs) that regulate gene transcription during myogenesis. Satellite cells (SCs) are the myogenic precursor cells in adult skeletal muscle. The objective of this study was to identify additional TFs that control the differentiation of bovine satellite cells. Bovine satellite cells (bSCs) were isolated from 4 crossbred steers and were initially cultured in growth medium for 12 days to expand and then in differentiation medium for 48 hours to differentiate. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) was performed to identify chromatin regions marked with acetylation of histone H3 on lysine 27 (H3K27ac). This ChIP-seq analysis revealed 3,348 and 38,800 H3K27ac-associated chromatin regions in bSCs before and after differentiation, respectively. A motif enrichment analysis of the H3K27ac-marked chromatin regions from the differentiated bSCs indicated the enrichment of binding sites for the 4 MYFs and many other TFs including Fos and FosB. RNA-sequencing revealed the upregulation of Fos and FosB mRNAs in bSCs from growth to differentiation. To verify the roles of Fos and FosB in bSC differentiation, their expressions in bSCs were reduced by siRNA-induced knockdown. Based on qRT-PCR analyses, expressions of MYH2, MYH3, MYOG, and CKM mRNAs, which were selected as markers of muscle cell differentiation, were increased (P < 0.05) in bSCs from growth to differentiation, but the increases in at least three of them were reversed (P < 0.05) by Fos or FosB knockdown. Taken together, these results establish Fos and FosB as transcriptional regulators of bovine satellite cell differentiation.

The biological function of chromatin bases on its spatial organization and dynamic activities in different situations. Labeling and tracing of genomic sequences has been a huge challenge in studying the spatial dynamics of chromatin. We reported the development of 'all-in-one Casilio system (Aio-Casilio)', a new system that enables the labeling of endogenous genomic loci. The Aio-Casilio system consists of the dCas9 protein, mClover fused with the Pumilio and FBF proteins RNA-binding domain (PUF domain) and an U6-sgRNA appended with multiple PUF-binding site(s). Here we showed that the Aio-Casilio system is robust tool for imaging of repetitive elements in telomeres and major satellite in N2A cells. Furthermore, we developed a PBTon-Aio-Casilio System, which enables the visualization of repetitive sequences in mES cells. However, this system failed to establish a labeled ES cell line when we attempted to establish a stable labeling cell line for living cell image. This Aio-Casilio imaging tool has potential to significantly improve the capacity to study the conformation of chromosomes in living cells.