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The human transcriptome contains many types of noncoding RNAs, which rival the number of protein‐coding species. From long noncoding RNAs (lncRNAs) that are over 200 nucleotides long to piwi‐interacting RNAs (piRNAs) of only 20 nucleotides, noncoding RNAs play important roles in regulating transcription, epigenetic modifications, translation, and cell signaling. Roles for noncoding RNAs in disease mechanisms are also being uncovered, and several species have been identified as potential drug targets. On May 11–14, 2021, the Keystone eSymposium "Noncoding RNAs: Biology and Applications" brought together researchers working in RNA biology, structure, and technologies to accelerate both the understanding of RNA basic biology and the translation of those findings into clinical applications. [ABSTRACT FROM AUTHOR]

The American black bear undergoes a 3-5 month winter hibernation during which time bears do not eat, drink, defecate, or urinate. During hibernation renal function ( GFR) is 16-50% of normal but urine is reabsorbed across the urinary bladder ( UB) urothelium thus enabling metabolic recycling of all urinary constituents. To elucidate the mechanism(s) whereby urine is reabsorbed, we examined the UBs of five nonhibernating wild bears using light, electron ( EM), and confocal immunofluorescent ( IF) microscopy-concentrating on two components of the urothelial permeability barrier - the umbrella cell apical membranes and tight junctions ( TJ). Bear UB has the same tissue layers (serosa, muscularis, lamina propria, urothelia) and its urothelia has the same cell layers (basal, intermediate, umbrella cells) as other mammalians. By EM, the bear apical membrane demonstrated a typical mammalian scalloped appearance with hinge and plaque regions - the latter containing an asymmetric trilaminar membrane and, on IF, uroplakins Ia, IIIa, and IIIb. The umbrella cell TJs appeared similar to those in other mammals and also contained TJ proteins occludin and claudin - 4, and not claudin -2. Thus, we were unable to demonstrate urothelial apical membrane or TJ differences between active black bears and other mammals. Expression and localization of UT-B, AQP-1 and -3, and Na+, K+- ATPase on bear urothelial membranes was similar to that of other mammals. Similar studies of urothelia of hibernating bears, including evaluation of the apical membrane lipid bilayer and GAGs layer are warranted to elucidate the mechanism(s) whereby hibernating bears reabsorb their daily urine output and thus ensure successful hibernation. [ABSTRACT FROM AUTHOR]

A firm may induce some customers to sign exclusive contracts in order to deprive a rival of the minimum viable size, exclude it from the market, and enjoy increased market power. This strategy may result in socially inefficient exclusion even if the excluded firm is present at the contracting stage and can make counteroffers. In addition, allowing for breach penalty clauses decreases firms' incentives to exclude rivals, because such clauses allow a firm to use customers as a conduit for the transfer of another firm's profits. [ABSTRACT FROM AUTHOR]

A growing number of long nuclear-retained non-coding RNAs (ncRNAs) have recently been described. However, few functions have been elucidated for these ncRNAs. Here, we have characterized the function of one such ncRNA, identified as metastasis-associated lung adenocarcinoma transcript 1 (Malat1). Malat1 RNA is expressed in numerous tissues and is highly abundant in neurons. It is enriched in nuclear speckles only when RNA polymerase II-dependent transcription is active. Knock-down studies revealed that Malat1 modulates the recruitment of SR family pre-mRNA-splicing factors to the transcription site of a transgene array. DNA microarray analysis in Malat1-depleted neuroblastoma cells indicates that Malat1 controls the expression of genes involved not only in nuclear processes, but also in synapse function. In cultured hippocampal neurons, knock-down of Malat1 decreases synaptic density, whereas its over-expression results in a cell-autonomous increase in synaptic density. Our results suggest that Malat1 regulates synapse formation by modulating the expression of genes involved in synapse formation and/or maintenance. [ABSTRACT FROM AUTHOR]

The interphase nucleus exists as a highly dynamic system, the physical properties of which have functional importance in gene regulation. Not only can gene expression be influenced by the local sequence context, but also by the architecture of the nucleus in three-dimensions (3D), and by the interactions between these levels via chromatin modifications. A challenging task is to resolve the complex interplay between sequence- and genome structure-based control mechanisms. Here, we created a collection of 277 Arabidopsis lines that allow the visual tracking of individual loci in living plants while comparing gene expression potential at these locations, via an identical reporter cassette. Our studies revealed regional gene silencing near a heterochromatin island, via DNA methylation, that is correlated with mobility constraint and nucleolar association. We also found an example of nucleolar association that does not correlate with gene suppression, suggesting that distinct mechanisms exist that can mediate interactions between chromatin and the nucleolus. These studies demonstrate the utility of this novel resource in unifying structural and functional studies towards a more comprehensive model of how global chromatin organization may coordinate gene expression over large scales. [ABSTRACT FROM AUTHOR]

The initiation of DNA replication in S phase requires the prior assembly of an origin recognition complex (ORC)-dependent pre-replicative complex on chromatin during G1 phase of the cell division cycle. In human cells, the Orc2 subunit localized to the nucleus as expected, but it also localized to centrosomes throughout the entire cell cycle. Furthermore, Orc2 was tightly bound to heterochromatin and heterochromatin protein 1a (HP1a) and HP1ß in G1 and early S phase, but during late S, G2 and M phases tight chromatin association was restricted to centromeres. Depletion of Orc2 by siRNA caused multiple phenotypes. A population of cells showed an S-phase defect with little proliferating cell nuclear antigen (PCNA) on chromatin, although MCM proteins remained. Orc2 depletion also disrupted HP1 localization, but not histone-H3-lysine-9 methylation at prominent heterochromatic foci. Another subset of Orc2-depleted cells containing replicated DNA arrested with abnormally condensed chromosomes, failed chromosome congression and multiple centrosomes. These results implicate Orc2 protein in chromosome duplication, chromosome structure and centrosome copy number control, suggesting that it coordinates all stages of the chromosome inheritance cycle. [ABSTRACT FROM AUTHOR]

Most healthy individuals have been exposed to human cytomegalovirus (HCMV) and harbor the virus in a dormant form. However, in situations of immune compromise, HCMV infection is associated with high mortality rates in recipients of bone marrow transplants and with significant morbidity in recipients of solid organ transplants. Conventional vaccination with attenuated HCMV or HCMV proteins fails to prime protective immune responses, presumably because the antigens fail to be presented effectively in vivo. Dendritic cells (DC) are professional antigen-presenting cells that can be genetically engineered to direct their ability to induce immune responses toward immunodominant HCMV antigens. DC are a distinct lineage of leukocytes whose function is most notable for their ability to form clusters with T cells and stimulate vigorous cytotoxic T lymphocyte responses. We hypothesize that in this capacity, DC engineered to express HCMV antigens are uniquely positioned to control immunity against HCMV. [ABSTRACT FROM AUTHOR]

Over the course of two and a half days, hypotheses and results about the organization and function of the eukaryotic nucleus were discussed intensely in the congenial atmosphere of this meeting. The topics covered ranged from DNA repair to nuclear actin, from nuclear assembly to the deposition of histone variants, and from technical aspects of fluorescence signal separation to the analysis of chromatin dynamics in living cells. New ways to monitor dynamics, paired with the fact that nuclear organization now attracts experts from a wide range of fields, left participants uniformly excited about the potential offered by the marriage of live fluorescence imaging and molecular genetics.

Components of the pre-mRNA splicing machinery are localized in interchromatin granule clusters (IGCs) and perichromatin fibrils (PFs). Here we report the biochemical purification of IGCs. Approximately 75 enriched proteins were present in the IGC fraction. Protein identification employing a novel mass spectrometry strategy and peptide microsequencing identified 33 known proteins, many of which have been linked to pre-mRNA splicing, as well as numerous uncharacterized proteins. Thus far, three new protein constituents of the IGCs have been identified. One of these, a 137 kDa protein, has a striking sequence similarity over its entire length to UV-damaged DNA-binding protein, a protein associated with the hereditary disease xeroderma pigmentosum group E, and to the 160 kDa subunit of cleavage polyadenylation specificity factor. Overall, these results provide a key framework that will enable the biological functions associated with the IGCs to be elucidated. [ABSTRACT FROM AUTHOR]

Correction to: The EMBO Journal (2004) 23, 2651-2663. doi:10.1038/sj.emboj.7600255 [ABSTRACT FROM AUTHOR]

Genes are expressed as a result of the concerted processes of transcription, mRNA processing, messenger ribonucleoprotein particle (mRNP) export and translation. The majority of protein-coding mRNAs are transported into the cytoplasm shortly after synthesis. Earlier studies from our laboratory identified a nuclear population of RNA that is not chased into the cytoplasm upon termination of transcription. We have been interested in identifying and characterizing the RNA species in this nuclear population. As several of these RNAs are not diffusely distributed throughout the nucleoplasm we were also interested in identifying the nuclear domains to which they are localized. Candidate RNAs were identified from a sub-nuclear cDNA library or by bioinformatics analysis. One of the identified clones, CTN-RNA localized to a nuclear domain termed paraspeckles and was part of a p54nrb/PSP1 containing RNP complex (Prasanth et al. 2005). CTN-RNA is transcribed from the protein-coding m̱ouse C̱ationic A̱mino acid Transporter 2 (mCAT2) gene through alternative promoter and poly(A) site usage. The 3'UTR of CTN-RNA contains elements for adenosine-to-inosine editing, involved in its nuclear retention. Under stress CTN-RNA is post-transcriptionally cleaved to produce protein-coding mCAT2 mRNA. These findings reveal a role of the cell nucleus in harboring RNA molecules that are not immediately needed to produce proteins, but whose cytoplasmic presence is rapidly required upon stress. This mechanism of action highlights an important paradigm for the role of a nuclear retained RNA transcript in regulating gene expression. Further bioinformatics analyses have identified several additional nuclear retained RNAs. The localization and characterization of these RNAs will be discussed. [ABSTRACT FROM AUTHOR]