Search

Highlights: [•] The development of the mammalian nervous system is accompanied by sequential changes in BAF chromatin remodeling complexes. [•] Recapitulating the micro-RNA/BAF chromatin remodeling complex switch is instructive for the conversion of human fibroblasts to neurons. [•] Mutations in BAF subunits have genetically dominant roles in human intellectual disability and neurodegeneration. [Copyright &y& Elsevier]

Mammalian neural development has been traditionally studied in the context of evolutionarily conserved signaling pathways and neurogenic transcription factors. Recent studies suggest that microRNAs, a group of highly conserved noncoding regulatory small RNAs also play essential roles in neural development and neuronal function. A part of their action in the developing nervous system is to regulate subunit compositions of BAF complexes (ATP-dependent chromatin remodeling complexes), which appear to have dedicated functions during neural development. Intriguingly, ectopic expression of a set of brain-enriched microRNAs, miR-9/9* and miR-124 that promote the assembly of neuron-specific BAF complexes, converts the nonneuronal fate of human dermal fibroblasts towards postmitotic neurons, thereby revealing a previously unappreciated instructive role of these microRNAs. In addition to these global effects, accumulating evidence indicates that many microRNAs could also function locally, such as at the growth cone or at synapses modulating synaptic activity and neuronal connectivity. Here we discuss some of the recent findings about microRNAs’ activity in regulating various developmental stages of neurons. [ABSTRACT FROM AUTHOR]

Summary: Recent exon sequencing studies have revealed that over 20% of human tumors have mutations in subunits of mSWI/SNF (BAF) complexes. To investigate the underlying mechanism, we studied human synovial sarcoma (SS), in which transformation results from the translocation of exactly 78 amino acids of SSX to the SS18 subunit of BAF complexes. We demonstrate that the SS18-SSX fusion protein competes for assembly with wild-type SS18, forming an altered complex lacking the tumor suppressor BAF47 (hSNF5). The altered complex binds the Sox2 locus and reverses polycomb-mediated repression, resulting in Sox2 activation. Sox2 is uniformly expressed in SS tumors and is essential for proliferation. Increasing the concentration of wild-type SS18 leads to reassembly of wild-type complexes retargeted away from the Sox2 locus, polycomb-mediated repression of Sox2, and cessation of proliferation. This mechanism of transformation depends on only two amino acids of SSX, providing a potential foundation for therapeutic intervention. [ABSTRACT FROM AUTHOR]

A central goal of chromatin biology is to reveal how posttranslational histone marks modulate gene expression; however, relatively little is known about the spatial or temporal dynamics of these marks. We previously showed that a dynamic model of histone mark nucleation, propagation, and turnover fits the mean enrichment profiles from 99% of noncentromeric histone H3 lysine 9 trimethylation (H3K9me3) domains in mouse embryonic stem cells without the need for boundary or insulator elements. Here we report the full details of this "inherently bounded" model of histone modification dynamics and describe several dynamic features of the model using H3K9me3 as a paradigm. By analyzing the kinetic and structural constraints that drive formation of inherently bounded domains, we find that such domains are optimized when the rates of marking and turnover are comparable. Additionally, we find that to establish such domains, propagation of the histone marks must occur primarily through local contacts. [ABSTRACT FROM AUTHOR]

New methods for the genome-wide analysis of chromatin are providing insight into its roles in development and their underlying mechanisms. Current studies indicate that chromatin is dynamic, with its structure and its histone modifications undergoing global changes during transitions in development and in response to extracellular cues. In addition to DNA methylation and histone modification, ATP-dependent enzymes that remodel chromatin are important controllers of chromatin structure and assembly, and are major contributors to the dynamic nature of chromatin. Evidence is emerging that these chromatin-remodelling enzymes have instructive and programmatic roles during development. Particularly intriguing are the findings that specialized assemblies of ATP-dependent remodellers are essential for establishing and maintaining pluripotent and multipotent states in cells. [ABSTRACT FROM AUTHOR]

Recent advances have revealed that modification of chromatin structure is an important determinant of cell fate and function. DNA methylation and covalent modifications of histone tails contribute to changes in chromatin architectures, either enhancing or repressing gene expression. Another mechanism underlying the modification of chromatin structure relies on the activity of the SWI/SNF-related ATP-dependent chromatin remodeling complexes that control the accessibility of DNA sequences to transcription factors. There is increasing evidence that ATP-dependent chromatin remodeling complexes based on the alternative DNA-dependent ATPases, Brg1 and Brm, plays essential roles during neural development in both vertebrates and invertebrates. This remodeling complex has dedicated functions at different stages of neural development that appear to arise by combinatorial assembly of its subunits. [Copyright &y& Elsevier]

Protein aggregation is involved in the pathogenesis of neurodegenerative diseases and hence is considered an attractive target for therapeutic intervention. However, protein-protein interactions are exceedingly difficult to inhibit. Small molecules lack sufficient steric bulk to prevent interactions between large peptide surfaces. To yield potent inhibitors of β-amyloid (Aβ) aggregation, we synthesized small molecules that increase their steric bulk by binding to chaperones but also have a moiety available for interaction with Aβ. This strategy yields potent inhibitors of Aβ aggregation and could lead to therapeutics for Alzheimer's disease and other forms of neurodegeneration. [ABSTRACT FROM AUTHOR]

Focuses on the role of NFAT signaling in the development of cell-to-cell interaction. Mechanisms of NFAT signaling; Stimulation of phosphatase calcineurin by calcium signaling; Degradation of nuclear import by kinases.

Transcriptional control is generally thought to operate as a binary switch, a behavior that might explain observations such as monoallelic gene expression, stochastic phenotypic changes and bimodal gene activation kinetics. By measuring the activity of the single-copy GAL1 promoter in single cells, we found that changes in the activities of either the transcriptional activator, Ga14 (by simple recruitment with synthetic ligands), or the transcriptional repressor, Migi, generated graded (non-binary) changes in gene expression that were proportional to signal intensity. However, in the context of the endogenous glucose- responsive signaling pathway, these transcription factors formed part of a binary transcriptional response. Genetic studies demonstrated that this binary response resulted from regulation of a second repressor, Ga180, whereas regulation of Migi by a distinct signaling pathway generated graded changes in GAL1 promoter activity. Surprisingly, isogenetic cells can respond to glucose with either binary or graded changes in gene expression, depending on growth conditions. Our studies demonstrate that a given promoter can adapt either binary or graded behavior, and identify the Migi and Ga180 genes as necessary for binary versus graded behavior of the Gall pro- moter. [ABSTRACT FROM AUTHOR]

Studies the mechanisms underlying the specificity of signaling through calcium/calcineurin and the NF-AT transcription complex. Tissue-specific expression of NF-AT family members; Discrimination of calcium signals; Cellular context as a determinant of specificity; Structure of the NF-AT complex.

Chromatin presents a significant obstacle to transcription, but two means of overcoming its repressive effects, histone acetylation and the activities of the Swi—Snf complex, have been proposed. Histone acetylation and Swi—Snf activity have been shown to be crucial for transcriptional induction and to facilitate binding of transcription factors to DNA. By regulating the activity of the Swi—Snf complex in vivo, we found that active transcription requires continuous Swi—Snf function, demonstrating a role for this complex beyond the induction of transcription. Despite the presumably generalized packaging of genes into chromatin, previous studies have indicated that the transcriptional requirements for the histone acetyltransferase, Gcn5, and the Swi—Snf complex are limited to a handful of genes. However, inactivating Swi—Snf function in cells also lacking GCN5 revealed defects in transcription of several genes previously thought to be SWI—SNF-and GCN5-independent. These findings suggest that chromatin remodeling plays a widespread role in gene expression and that these two chromatin remodeling activities perform independent and overlapping functions during transcriptional activation. [ABSTRACT FROM AUTHOR]

Investigates the potential of induced proximity in mediating intracellular signaling. Natural molecules appearing to have arisen to bring two proteins together; Illustration of how such mechanism can be used to control biological processes.

Describes the calcium signalling in T cells stimulated by a cyclophilin B-binding protein. Activity of cyclosporin A when bound to cyclophilin; Identification of potential homologues; Calcium-signal modulating cyclophilin ligand (CAML).

Examines the emerging role of the actin cytoskeleton as an integral component of lymphocyte activation. Caps and supramolecular activation clusters; Molecular forces driving actin reorganization; Role of actin-dependent structures in T cell activation; Mechanism of actin-dependent receptor clustering.

Analysis of human mutation rates and the number of genes required for human intellectual and emotional fitness indicates that we are almost certainly losing these abilities. If so, how did we get them in the first place, and when did things begin to change? [Copyright &y& Elsevier]

New developments in genetics, anthropology, and neurobiology predict that a very large number of genes underlie our intellectual and emotional abilities, making these abilities genetically surprisingly fragile. [Copyright &y& Elsevier]

The article discusses the role of transcription factor Foxp3 for T cell function. Foxp3 inhibits the transcriptional activity. The transcription complexes are formed by the association of cytoplasmic subunits with nuclear partners to produce specific complexes on DNA. Consensus forkhead binding domains were identified in the promoters of genes encoding cytokines.

Reports that the over expression of calcineurin in Jurkat cells renders them more resistant to the effects of CsA and FK506 and augments both NFAT- and NFIL2A-dependent transcription. The immunosuppressive drugs cyclosporin A and FK506 and their interference with a Ca2+-sensitive T-cell transduction pathway; More.

The ability of hemopoietic stem cells to self-renew and differentiate into downstream lineages is dependent on specialized chromatin environments that establish and maintain stage-specific patterns of gene expression. However, the epigenetic factors responsible for mediating these regulatory events remain poorly defined. Here we provide evidence that BAF45a/PHF10, a subunit of SWI/SNF-like chromatin remodeling complexes, is essential for adult hemopoietic stem cell maintenance and myeloid lineage development. Deletion of BAF45a in the mouse is embryonic lethal. Acute deletion of BAF45a in the adult hemopoietic system causes a dose-dependent decrease in the frequency of long-term repopulating hemopoietic stem cells and committed myeloid progenitors without affecting their rate of proliferation. BAF45a- deficient hemopoietic stem cells and myeloid progenitors are selectively lost from mixed bone marrow chimeras, indicating their impaired function even in an intact microenvironment. Together, these studies suggest that the BAF45a subunit of SWI/SNF-like chromatin remodeling complexes plays nonredundant and specialized roles within the developing hemopoietic tissue. [ABSTRACT FROM AUTHOR]

The article discusses the study by J. K. Takeuchi and B. G. Bruneau on the role of chromatin-remodelling complexes in the developing heart. The study found out that the integration of Barrier-to-Autointegration Factor (BAF) 60 complexes and cardiogenic transcription factor Gata4 induces gene expression that contributes to heart development. However, it contends that the details of the cardiogenic BAF complex for generating tissue may work better if the researchers could reduce Baf60 subunits.

Sustained calcium signaling in T cells is critical for development and activation. In this issue of Immunity, demonstrate that the huge scaffold protein, AHNAK1, interacts with L-type calcium channels, regulates Ca2+ influx, and defends against Leishmania major infection. [Copyright &y& Elsevier]

The article presents a comment on exploiting protein destruction for constructive use. Discovering the biological roles of a protein is best accomplished by observing the consequences of its removal. In case of genetic experiments, including those dealing with knockout mice, gene functions in one tissue type are often disguised by deleterious phenotypes, including lethality, in another.

The article discusses the study which shows an exciting new mechanism underlying coordination of rapid changes in cell shape, involving interactions between the actin cytoskeleton and a protein that regulates gene expression, called MAL, a myocardin family transcriptional coactivator for serum. The study likewise shows that MAL is regulated by nuclear G-actin, which is a monomeric actin, at multiple steps. The authors of the study also discover that changes in the cell's cytoskeleton affect gene expression by a signaling circuit that involves regulation of cofactor transport and function by actin in the nucleus.

The article reports that Calcium ions (Ca 2+) may be the most widely used second messenger molecules in biology. Indeed, Ca 2+ is essential for early development of organisms, immune responses, and even for remembering what you are about to read. The diverse tasks of Ca 2+ raise the question of the molecular origins of specific Ca 2+ responses. Researchers identify new players that regulate the movement of Ca 2+ into and out of cells, providing a more complete understanding of Ca 2+ responses in the immune system. Activation of the T cell receptor by ligand initiates a rapid influx of Ca sup 2+ into T cells.

Discusses ways of controlling the regulators of gene transcription. How histone proteins compress DNA and DNA-bound proteins into a compact structure called chromatin; Discussion of regulatory enzymes including histone deacetylase (HDAC) enzymes which regulate transcription by removing acetyl groups from histone proteins bound to DNA; Process of converting an unspecialized muscle cell to a skeletal muscle fiber, or myogenesis.

Provides information on two reports which dealt with the nuclear counterparts of inositol signaling pathways in the cytoplasm. Identification of yeast genes that contribute to the nuclear export of messenger RNA (mRNA); How inositol hexakisphosphate may facilitate mRNA export in yeast; Function of inositol polyphosphate kinase (IPK2p) in IPK2-dependent processes.

Reports on research into the role of the Oct transcription factors which control cell type-specific expression of immunoglobulins. Discovery of the octamer sequence; Octamer sequences role; Research into an accessory protein, named BOB in this research, Questions raised as to BOBs location in T cells that do not activate their immunoglobulin genes; Questions raised by research.

The article discusses the ability of an enucleated frog egg to reprogram the nucleus of a somatic cell to a pluripotent state. Three transcription factors are required to transform skin cell into a pluripotent cell namely "Oct4," "Sox2," and "Klf4." John Gurdon of Gurdon Institute in Cambridge, Great Britain chose to examine Oct4 and they discovered that the initiation of Oct4 expression involved unexpected proteins. The author mentions the ability of the egg to reset a nucleus into a pluripotent state lies in these unexpected proteins.

Calcineurin (Cn), a phosphatase important for synaptic plasticity and neuronal development, has been implicated in the etiology and pathophysiology of neuropsychiatric disorders, including schizophrenia, intellectual disability, autism spectrum disorders, epilepsy, and Alzheimer's disease. Forebrain-specific conditional Cn knockout mice have been known to exhibit multiple behavioral phenotypes related to these disorders. In this study, we investigated whether Cn mutant mice show pseudo-immaturity of the dentate gyrus (iDG) in the hippocampus, which we have proposed as an endophenotype shared by these disorders. Expression of calbindin and GluA1, typical markers for mature DG granule cells (GCs), was decreased and that of doublecortin, calretinin, phospho-CREB, and dopamine D1 receptor (Drd1), markers for immature GC, was increased in Cn mutants. Phosphorylation of cAMP-dependent protein kinase (PKA) substrates (GluA1, ERK2, DARPP-32, PDE4) was increased and showed higher sensitivity to SKF81297, a Drd1-like agonist, in Cn mutants than in controls. While cAMP/PKA signaling is increased in the iDG of Cn mutants, chronic treatment with rolipram, a selective PDE4 inhibitor that increases intracellular cAMP, ameliorated the iDG phenotype significantly and nesting behavior deficits with nominal significance. Chronic rolipram administration also decreased the phosphorylation of CREB, but not the other four PKA substrates examined, in Cn mutants. These results suggest that Cn deficiency induces pseudo-immaturity of GCs and that cAMP signaling increases to compensate for this maturation abnormality. This study further supports the idea that iDG is an endophenotype shared by certain neuropsychiatric disorders. [ABSTRACT FROM AUTHOR]

A recent article in the journal Science discusses the development of a new pharmacological strategy for targeting cancer cells. The researchers focused on cyclin-dependent kinases (CDKs) that regulate transcription, which are promising therapeutic targets in cancer. Instead of inhibiting or degrading CDKs, the researchers developed bivalent molecules that relocalized the activity of transcriptional kinases to activate cell death genes. These molecules were found to be highly potent and specific in killing cancer cells, while being less toxic to normal cells. The study suggests that relocalizing kinase activity could be a promising approach for cancer therapy. [Extracted from the article]

The development of the vertebrate nervous system requires a switch of ATP-dependent chromatin remodeling mechanisms, which occurs by substituting subunits within these complexes near cell cycle exit. This switching involves a triple negative genetic circuitry in which REST represses miR-9 and miR-124, which in turn repress BAF53a, which in turn repress the homologous neuron-specific BAF53b. Recapitulation of this microRNA/chromatin switch in human fibroblasts converts them to neurons. The genes involved in this fate-determining chromatin switch play genetically dominant roles in several human neurologic diseases suggesting that they are rate-limiting for aspects of human neural development. We review how this switch in ATP-dependent chromatin complexes might interface with traditional ideas about neural determination and reprogramming. [ABSTRACT FROM AUTHOR]

Recent genome-sequencing studies in human neurodevelopmental and psychiatric disorders have uncovered mutations in many chromatin regulators. These human genetic studies, along with studies in model organisms, are providing insight into chromatin regulatory mechanisms in neural development and how alterations to these mechanisms can cause cognitive deficits, such as intellectual disability. We discuss several implicated chromatin regulators, including BAF (also known as SWI/SNF) and CHD8 chromatin remodellers, HDAC4 and the Polycomb component EZH2. Interestingly, mutations in EZH2 and certain BAF complex components have roles in both neurodevelopmental disorders and cancer, and overlapping point mutations are suggesting functionally important residues and domains. We speculate on the contribution of these similar mutations to disparate disorders. [ABSTRACT FROM AUTHOR]

Recent studies indicate that chromatin regulatory complexes produce biological specificity in the way that letters produce meanings by combinations into words. Combinatorial assembly of chromatin regulatory complexes may be critical for maximizing the information content provided by arrays of histone modifications. [Copyright &y& Elsevier]

Ca2+ signals control a variety of lymphocyte responses, ranging from short-term cytoskeletal modifications to long-term changes in gene expression. The identification of molecules and channels that modulate Ca2+ entry into T and B lymphocytes has both provided details of the molecular events leading to immune responses and raised controversy. Here we review studies of the pathways that allow Ca2+ entry, the function of Ca2+ in the regulation of cell polarity and motility and the principles by which Ca2+-dependent transcription regulates lymphocyte function. [ABSTRACT FROM AUTHOR]

The modulation of intracellular calcium ion concentration, [Ca2+]i, is a common signalling mechanism used in many biological systems. B and T lymphocytes rely on Ca2+ signalling to initiate both developmental and activation programs. Recent data has shed new light on the initiation of this signalling pathway, the connection between the release of intracellular Ca2+ stores and the influx of extracellular Ca2+, and the molecular identity of the elusive Ca2+ release-activated Ca2+ (CRAC) channel. In addition, recent gene profiling of T lymphocytes has identified the genes that are controlled by [Ca2+]i and the Ca2+-dependent phosphatase calcineurin. [Copyright &y& Elsevier]

The existence and function of actin in the nucleus has been hotly debated for forty years. Recently, β-actin was found to be a component of mammalian SWI/SNF-like BAF chromatin remodeling complexes and still more recently other SWI/SNF-related chromatin remodeling complexes in yeast, flies, and man. Although the function of actin in these chromatin remodeling complexes is only starting to be explored, the fact that actin is one of the most regulated proteins in the cell suggests that control of nuclear actin may be a critical regulatory point in the control of chromatin remodeling. Actin rapidly shuttles between the nucleus and the cytoplasm offering additional sites and modes of regulation. In addition, actin-related proteins (Arps) are also components of these chromatin remodeling complexes and have been implicated in transcriptional control in yeast. The observation that the BAF chromatin remodeling complex in which actin was originally identified, is also a human tumor suppressor complex necessary for the actions of the retinoblastoma protein indicates that the study of nuclear actin is likely to contribute to understanding cell growth control. [ABSTRACT FROM AUTHOR]

Discusses the events in eukaryotic signal transduction processes that involve dimerization. Overview of the underlying strategies in protein dimerization; Examples of dimerization in signal transduction; Regulation of biological responses using small synthetic ligands that promote protein association.

Discusses two studies, which showed that several adenosine triphosphate-dependent chromatin remodeling complexes are subject to control by phosphoinositols. Classes of chromatin-regulating activities; Role of inositol polyphosphates in regulating the activity of the Swi/Snf complex; Description of the small molecule control of chromatin structure; Requirements for the transcription of PHO5.

The chromatin remodeler CHD8 is among the most frequently mutated genes in autism spectrum disorder (ASD). CHD8 has a dosagesensitive role in ASD, but when and how it becomes critical to human social function is unclear. Here, we conducted genomic analyses of heterozygous and homozygous Chd8 mouse embryonic stem cells and differentiated neural progenitors. We identify dosage-sensitive CHD8 transcriptional targets, sites of regulated accessibility, and an unexpected cooperation with SOX transcription factors. Collectively, our findings reveal that CHD8 negatively regulates expression of neuronal genes to maintain pluripotency and also during differentiation. Thus, CHD8 is essential for both the maintenance of pluripotency and neural differentiation, providing mechanistic insight into its function with potential implications for ASD. [ABSTRACT FROM AUTHOR]

One action of cyclosporin A thought to be central to many of its immunosuppressive effects is its ability to inhibit the early events of T lymphocyte activation such as lymphokine gene transcription in response to signals initiated at the antigen receptor. Cyclosporin A was found to specifically inhibit the appearance of DNA binding activity of NF-AT, AP-3, and to a lesser extent NF-kB, nuclear proteins that appear to be important in the transcriptional activation of the genes for interleukin-2 and its receptor, as well as several other lymphokines. In addition, cyclosporin A abolished the ability of the NF-AT binding site to activate a linked promoter in transfected mitogen-stimulated T lymphocytes and in lymphocytes from transgenic mice. These results indicate that cyclosporin A either directly inhibits the function of nuclear proteins critical to T lymphocyte activation or inhibits the action of a more proximal member of the signal transmission cascade leading from the antigen receptor to the nucleus. [ABSTRACT FROM AUTHOR]

Dynamic control of gene expression is essential for the development of a totipotent zygote into an embryo with defined cell lineages. The accessibility of genes responsible for cell specification to transcriptional machinery is dependent on chromatin remodelling complexes such as the SWI\SNF (BAF) complex. However, the role of the BAF complex in early mouse development has remained unclear. Here, we demonstrate that BAF155, a major BAF complex subunit, regulates the assembly of the BAF complex in vivo and regulates lineage specification of the mouse blastocyst. We find that associations of BAF155 with other BAF complex subunits become enriched in extra-embryonic lineages just prior to implantation. This enrichment is attributed to decreased mobility of BAF155 in extraembryonic compared with embryonic lineages. Downregulation of BAF155 leads to increased expression of the pluripotency marker Nanog and its ectopic expression in extra-embryonic lineages, whereas upregulation of BAF155 leads to the upregulation of differentiation markers. Finally, we show that the arginine methyltransferase CARM1 methylates BAF155, which differentially influences assembly of the BAF complex between the lineages and the expression of pluripotency markers. Together, our results indicate a novel role of BAF-dependent chromatin remodelling in mouse development via regulation of lineage specification. [ABSTRACT FROM AUTHOR]

In mammals, combinatorial assembly of alternative families of subunits confers functional specificity to adenosine triphosphate (ATP)-dependent SWI/SNF-like Brg/Brm-associated factor (BAF) chromatin remodeling complexes by creating distinct polymorphic surfaces for interaction with regulatory elements and DNA-binding factors. Although redundant in terms of biochemical activity, the core ATPase subunits, BRG/ SMARCA4 and BRM/SM ARCA2. are functionally distinct and may contribute to complex specificity. Here we show using quantitative proteomics that BAF complexes expressed in leukemia are specifically assembled around the BRG ATPase. Moreover, using a mouse model of acute myeloid leukemia, we demonstrate that BRG is essential for leukemia maintenance, as leukemic cells lacking BRG rapidly undergo cell-cycle arrest and apoptosis. Most importantly, we show that BRG is dispensable for the maintenance of immunophenotypic long-term repopulating hematopoietic stem cells, suggesting that adroit targeting of BRG in leukemia may have potent and specific therapeutic effects. [ABSTRACT FROM AUTHOR]

A correction to the article "From neural development to cognition: unexpected roles for chromatin" that was published in the May 2013 issue is presented.

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease whose causes are still poorly understood. To identify additional genetic risk factors, we assessed the role of de novo mutations in ALS by sequencing the exomes of 47 ALS patients and both of their unaffected parents (n = 141 exomes). We found that amino acid-altering de novo mutations were enriched in genes encoding chromatin regulators, including the neuronal chromatin remodeling complex (nBAF) component SS18L1 (also known as CREST). CREST mutations inhibited activity-dependent neurite outgrowth in primary neurons, and CREST associated with the ALS protein FUS. These findings expand our understanding of the ALS genetic landscape and provide a resource for future studies into the pathogenic mechanisms contributing to sporadic ALS. [ABSTRACT FROM AUTHOR]