Dietary nutrients interact with gene networks to orchestrate adaptive responses during metabolic stress. Here, we identify Baf60a as a diet-sensitive subunit of the SWI/SNF chromatin-remodeling complexes in the mouse liver that links the consumption of fat- and cholesterol-rich diet to elevated plasma cholesterol levels. Baf60a expression was elevated in the liver following feeding with a western diet. Hepatocyte-specific inactivation of Baf60a reduced bile acid production and cholesterol absorption, and attenuated diet-induced hypercholesterolemia and atherosclerosis in mice. Baf60a stimulates expression of genes involved in bile acid synthesis, modification, and transport through a CAR/Baf60a feedforward regulatory loop. Baf60a is required for the recruitment of the SWI/SNF chromatin-remodeling complexes to facilitate an activating epigenetic switch on target genes. These studies elucidate a regulatory pathway that mediates the hyperlipidemic and atherogenic effects of western diet ...

Excellgen Brahma-related Gene 1 protein, wild type, BRG1, SMARCA4 [RP-22] - Product Name Brahma-related Gene 1, BRG1, SMARCA4 Size 5,000 U Description The wild type human brahma-related gene 1 (Brg1) encodes a protein of 1,647 amino acids that contains a conserved domain of the SWI2/SNF2 family necessary for normal mitotic growth and transcription regulation (1-3). BRG1 is an essential component of the SWI/SNF chromatin remodeling complexes

One of the longest standing problems in DNA repair is how cells relax chromatin in order to make DNA lesions accessible for global nucleotide excision repair (NER). Since chromatin has to be relaxed for efficient lesion detection, the key question is whether chromatin relaxation precedes lesion detection or vice versa. Chromatin accessibility factors have been proposed but not yet identified. Here we show that p53 acts as a chromatin accessibility factor, mediating UV-induced global chromatin relaxation. Using localized subnuclear UV irradiation, we demonstrate that chromatin relaxation is extended over the whole nucleus and that this process requires p53. We show that the sequence for initiation of global NER is as follows: transcription-associated lesion detection; p53-mediated global chromatin relaxation; and global lesion detection. The tumour suppressor p53 is crucial for genomic stability, a role partially explained by its pro-apoptotic capacity. We demonstrate here that p53 is also a ...

Beijing, China - Chromatin remodeling proteins (chromatin remodelers) are essential and powerful regulators for critical DNA-templated cellular processes, such as DNA replication, recombination, gene transcription/repression, and DNA damage repair. These molecular and genetic processes are important for a wide spectrum of cellular functions, including cell cycle, death, differentiation, pluripotency, and genome integrity. Recently, many scientific reports have shown that chromatin remodeling proteins could be promising new targets for the treatment of human malignancy.. This is a hot and exciting research topic for cancer researchers, and our article provides an updated understanding on the functions and mechanisms of chromatin remodelers in human cancers, says Dr. Chun Zhang, the principle investigator of the Department of Nuclear Medicine of Beijing Chao-Yang Hospital and Capital Medical University of China.. Chromatin remodeling is an energy-driven process in which chromatin remodelers use ...

Core component of the BAF (hSWI/SNF) complex. This ATP-dependent chromatin-remodeling complex plays important roles in cell proliferation and differentiation, in cellular antiviral activities and inhibition of tumor formation. The BAF complex is able to create a stable, altered form of chromatin that constrains fewer negative supercoils than normal. This change in supercoiling would be due to the conversion of up to one-half of the nucleosomes on polynucleosomal arrays into asymmetric structures, termed altosomes, each composed of 2 histones octamers. Stimulates in vitro the remodeling activity of SMARCA4/BRG1/BAF190A. Involved in activation of CSF1 promoter. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a postmitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The

ATP-dependent chromatin-remodeling complexes (remodelers) modulate gene transcription by regulating the accessibility of highly packaged genomic DNA. However, the molecular mechanisms involved at the nucleosomal level in this process remain controversial. Here, we monitor the real-time activity of single ySWI/SNF or RSC complexes on single, stretched nucleosomal templates under tensions above 1 pN forces. We find that these remodelers can translocate along DNA at rates of approximately 13 bp/s and generate forces up to approximately 12 pN, producing DNA loops of a broad range of sizes (20-1200 bp, average approximately 100 bp) in a nucleosome-dependent manner. This nucleosome-specific activity differs significantly from that on bare DNA observed under low tensions and suggests a nucleosome-remodeling mechanism through intranucleosomal DNA loop formation. Such loop formation may provide a molecular basis for the biological functions of remodelers.

CHD8 (Chromodomain-Helicase-DNA binding protein 8) is a member of the chromodomain helicase DNA-binding (CHD) subfamily of enzymes, which also belongs to the SNF2 family of ATP-dependent chromatin remodelers ...

The DDT has been named after the better characterised DNA-binding homeobox- containing proteins and the Different Transcription and chromatin remodelling factors in which it is found. It is a domain of about 60 amino acids which is exclusively associated with nuclear domains like AT-Hook, PHD finger, methyl-CpG-binding domain, bromodomain and DNA-binding homeodomain.. The DDT domain is characterised by a number of conserved aromatic and charged residues and is predicted to consist of three alpha helices. A DNA-binding function for the DDT domain has been proposed [ (PUBMED:11246006) ]. ...

MS Thesis: EXPRESSION AND FUNCTION OF WILLIAMS SYNDROME TRANSCRIPTION FACTOR (WSTF) IN THE NEURAL DEVELOPMENT OF XENOPUS LAEVIS Imitation Switch (ISWI) is a member of the SWI2/SNF2 superfamily of ATP-dependent chromatin remodelers. Twenty different ISWI complexes have been identified so far in yeast, Drosophila, Xenopus and mammals. Three ISWI-containing complexes, WICH, ACF and CHRAC, have been characterized in Xenopus. Loss of ISWI function in Xenopus embryos results in severe defects in neural and eye development, including loss of retinal differentiation and formation of cataracts. We have begun to dissect the contributions of individual ISWI-dependent complexes to development, by using in situ hybridization and antisense morpholino knockdowns against subunits unique to different ISWI-containing complexes. Here I have investigated the WICH complex in Xenopus and have targeted the WSTF subunit. Whole mount in situ hybridization shows WSTF localized in the neural tissue including eye, brain, ...

TY - JOUR. T1 - Mutant-IDH1-dependent chromatin state reprogramming, reversibility, and persistence. AU - Turcan, Sevin. AU - Makarov, Vladimir. AU - Taranda, Julian. AU - Wang, Yuxiang. AU - Fabius, Armida W.M.. AU - Wu, Wei. AU - Zheng, Yupeng. AU - El-Amine, Nour. AU - Haddock, Sara. AU - Nanjangud, Gouri. AU - Lekaye, H. Carl. AU - Brennan, Cameron. AU - Cross, Justin. AU - Huse, Jason T.. AU - Kelleher, Neil L.. AU - Osten, Pavel. AU - Thompson, Craig B.. AU - Chan, Timothy A.. N1 - Funding Information: We thank the members of the Chan and Thompson laboratories for helpful discussions. This work was supported in part by the US National Institutes of Health (NIH; R01 CA177828) (T.A.C. and C.B.T.), the MSKCC Brain Tumor Center (S.T. and T.A.C.), the Sontag Foundation (T.A.C.), the PaineWebber Chair Endowment (T.A.C.), NIH T32 grant 5T32CA160001 (S.T.), the MSKCC Society (T.A.C.), the NIH (R01 MH096946) (P.O.), and NIH Cancer Center Support Grant P30CA008748 (G.N.). This research was carried ...

PubMed Central Canada (PMC Canada) provides free access to a stable and permanent online digital archive of full-text, peer-reviewed health and life sciences research publications. It builds on PubMed Central (PMC), the U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature and is a member of the broader PMC International (PMCI) network of e-repositories.

Estrogen receptor α (ER) is a member of the family of nuclear receptors and functions as a transcriptional factor to induce gene expression by binding to specific DNA sequences upon hormone treatment. It regulates cell growth, development and metabolic homeostasis in multi-cellular organisms. Estrogen-mediated transcription has been intensively studied genome-wide as well as on a small number of specific endogenous target promoters. However, the exact mechanism by which ER coordinates the activities of chromatin remodeling complexes and coactivators to facilitate initiation of transcription remains elusive. Here, we show the molecular mechanisms of the recruitment of the SWI/SNF chromatin remodeling complex by Fli-I, and recruitment of Tip60, a histone acetyltransferase.; Fli-I can bind directly to both ER and BAF53, an actin-related component of the SWI/SNF complex, suggesting that Fli-I may recruit SWI/SNF to ER target genes via interaction with BAF53. Depletion of endogenous Fli-I or BAF53 ...

Activation of HO in yeast involves recruitment of transcription factors in two waves. The first is triggered by inactivation of Cdk1 at the end of mitosis, which promotes import into the nucleus of the Swi5 transcription factor. Swi5 recruits the Swi/Snf chromatin-remodeling complex, which then facilitates recruitment of the SAGA histone acetylase, which in turn permits the binding of the SBF transcription factor. We show here that SBF then recruits the SRB/mediator complex and that this process occurs in the absence of Cdk1 activity. The second wave is triggered by reactivation of Cdk1, which leads to recruitment of PolII, TFIIB, and TFIIH. RNA polymerase is, therefore, recruited to HO in two steps and not as a holoenzyme. A similar sequence of events occurs at other SBF-regulated promoters, such as CLN1, CLN2, and PCL1.

ARID1A is a member of the SWI/SNF family, whose members have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodelling complex SWI/SNF, which is required for transcriptional activation of genes normally repressed by chromatin. It possesses at least two conserved domains that could be important for its function. First, it has an ARID domain, which is a DNA-binding domain that can specifically bind an AT-rich DNA sequence known to be recognized by a SWI/SNF complex at the beta-globin locus. Second, the C-terminus of the protein can stimulate glucocorticoid receptor-dependent transcriptional activation. It is thought that the protein encoded by this gene confers specificity to the SWI/SNF complex and may recruit the complex to its targets through either protein-DNA or protein-protein interactions. Two transcript variants encoding ...

Abstract: Gene-gene interactions shape complex phenotypes and modify the effects of mutations during development and disease. The effects of statistical gene-gene interactions on phenotypes have been used to assign genes to functional modules. However, directional, epistatic interactions, which reflect regulatory relationships between genes, have been challenging to map at large-scale. Here, we used combinatorial RNA interference and automated single-cell phenotyping to generate a large genetic interaction map for 21 phenotypic features of Drosophila cells. We devised a method that combines genetic interactions on multiple phenotypes to reveal directional relationships. This network reconstructed the sequence of protein activities in mitosis. Moreover, it revealed that the Ras pathway interacts with the SWI/SNF chromatin-remodelling complex, an interaction that we show is conserved in human cancer cells. Our study presents a powerful approach for reconstructing directional regulatory networks ...

TY - JOUR. T1 - Loss of SMARCA4 (BRG1) protein expression as determined by immunohistochemistry in small-cell carcinoma of the ovary, hypercalcaemic type distinguishes these tumours from their mimics. AU - Clarke, B.A.. AU - Witkowski, L.. AU - Ton Nu, T.N.. AU - Shaw, P.A.. AU - Gilks, C.B.. AU - Huntsman, D.. AU - Karnezis, A.N.. AU - Sebire, N.. AU - Lamovec, J.. AU - Roth, L.M.. AU - Stewart, Colin. AU - Hasselblatt, M.. AU - Foulkes, W.D.. AU - Mccluggage, W.G.. PY - 2016. Y1 - 2016. N2 - © 2016 John Wiley & Sons LtdAims: Molecular investigation of small-cell carcinoma of the ovary, hypercalcaemic type (SCCOHT) has revealed that it is a monogenetic tumour characterized by alteration of SMARCA4 (BRG1), encoding a member of the switch/sucrose non-fermentable (SWI/SNF) chromatin remodelling complex. A large majority of cases show loss of expression of the corresponding SMARCA4/BRG1 protein. Furthermore, three cases of SCCOHT with retained SMARCA4 protein expression showed loss of SMARCB1/INI1 ...

PubMed journal article: Brahma-related gene 1 ameliorates the neuronal apoptosis and oxidative stress induced by oxygen-glucose deprivation/reoxygenation through activation of Nrf2/HO-1 signaling. Download Prime PubMed App to iPhone, iPad, or Android

Due to advances in molecular biology techniques, chromatin structure and function has re-emerged as a key research area in the investigation of gene regulation and expression. This indispensable new book provides the busy researcher with an overview of all the latest research in this important area. Topicality and breadth of coverage is assured by the contributions of an international group of over 30 leading scientists in this field. Contents list: Elements of chromatin structure: histones, nucleosomes, fibers; DNA structure: implications for chromatin structure and function; Replication and assembly; Promoter potentiation and activation: chromatin structure and transcriptional induction of heat shock genes; Initiation of expression: remodelling genes; Transcription on chromatin templates; Chromatin structure and epigenetic regulation in yeast; Epigenetic regulation in Drosophilia: a conspiracy of silence; Boundaries and domains; Epigenetic regulation in mammalian cells.Elgin, Sarah C. is the ...

FISH studies on several strongly transcribed chromosomal regions have shown a disposition for looping out from their respective chromosome territories (Mahy et al., 2002b; Volpi et al., 2000; Williams et al., 2002), suggesting a large-scale chromatin decondensation reminiscent of results obtained by targeting transcription factors to transgene arrays. In the first of these targeting studies chromatin decondensation was induced by the viral transcriptional VP16 acidic activation domain. Targeting was achieved within the context of large transgene arrays containing multiple-copy plasmid integrations; each plasmid carried direct repeats of 256 (Tumbar et al., 1999) or 96 (Tsukamoto et al., 2000) operator binding sites for fusion proteins between the lac or tet repressor and VP16. Despite the large opening activity observed, the biological relevance of these observations hinges on the actual physiological relevance of the experimental system. In particular, there are three obvious concerns.. First, ...

The Klose lab is interested in understanding how chromatin based and epigenetic processes contribute to regulation of gene expression.. To achieve this we use cutting edge biochemical, molecular, genetic, and genomic approaches in model stem cell and developmental systems.. Ultimately, our motivation is to understand how chromatin impinges on gene expression in normal cell biology as a way of informing therapeutic approaches to counteract its perturbation in cancer and other human diseases.. ...

TY - JOUR. T1 - Chromatin remodeling complex interacts with ADD1/SREBP1c to mediate insulin-dependent regulation of gene expression. AU - Lee, Yun Sok. AU - Sohn, Dong Hyun. AU - Han, Daehee. AU - Lee, Han Woong. AU - Seong, Rho Hyun. AU - Kim, Jae Bum. PY - 2007/1/1. Y1 - 2007/1/1. N2 - Insulin plays a critical role in whole-body energy homeostasis by regulating lipid and glucose metabolism. In fat and liver tissues, ADD1/SREBP1c is a key transcription factor to mediate insulin-dependent regulation of gene expression. Although transcriptional and proteolytic activation of ADD1/SREBP1c has been studied intensively, the mechanism by which insulin regulates expression of its target genes with ADD1/SREBP1c at the chromatin level is unclear. Here, we reveal that SWI/SNF chromatin remodeling factors interact with the ADD1/SREBP1c and actively regulate insulin-dependent gene expression. Insulin enhanced recruitment of SWI/SNF chromatin remodeling factors to its target gene promoters with concomitant ...

Transcriptional regulation of inflammatory gene expression has been at the forefront of studies of innate immunity and is coordinately regulated by transcription factors, including NF-κB, and chromatin modifiers. The growing evidence for involvement of chromatin in the regulation of gene expression in innate immune cells, has uncovered an evolutionarily conserved role of microbial sensing and chromatin remodeling. Toll-like receptors and RIG-I-like receptors trigger these signaling pathways leading to transcriptional expression of a set of genes involved in inflammation. Tightly regulated control of this gene expression is a paramount, and often foremost, goal of most biological endeavors. In this review, we will discuss the recent progress about the molecular mechanisms governing control of pro-inflammatory gene expression by an evolutionarily conserved novel nuclear protein Akirin2 in macrophages and its emergence as an essential link between NF-κB and chromatin remodelers for transcriptional

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Pay Per Article - You may access this article (from the computer you are currently using) for 1 day for US$35.00. Regain Access - You can regain access to a recent Pay per Article purchase if your access period has not yet expired.. ...

Enter the text here that is the new abstract information for your application. The organization of the nucleus and the regulated folding of the genome plays ess...

Chromatin is a complex polymer molecule in eukaryotic cells, primarily consisting of DNA and histones. Many works have shown that the 3D folding of chromatin structure plays an important role in DNA expression. The recently proposed Chro- mosome Conformation Capture technologies, especially the Hi-C assays, provide us an opportunity to study how the 3D structures of the chromatin are organized. Based on the data from Hi-C experiments, many chromatin 3D structure modeling methods have been proposed. However, there is limited ground truth to validate these methods and no robust chromatin structure alignment algorithms to evaluate the performance of these methods. In our work, we first made a thorough literature review of 25 publicly available population Hi-C-based chromatin 3D structure modeling methods. Furthermore, to evaluate and to compare the performance of these methods, we proposed a novel data simulation method, which combined the population Hi-C data and single-cell Hi-C data without ad ...

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This protocol describes the chromatin preparation from fresh or frozen tissues. The isolated chromatin can be used for chromatin immunoprecipitation assays using Diagenode&rsquo...

Single-cell chromatin accessibility sequencing from 13 mouse tissue types provides novel insights into regulatory dynamics and human disease states.

Chromatin remodelers can either organize or disrupt nucleosomal arrays, yet the mechanisms specifying these opposing actions are not clear. Here, we show that the outcome of nucleosome sliding by Chd1 changes dramatically ...

Dynamic organization of the human genome into chromatin regulates transcription initiation and elongation. Defects in chromatin modifications, assembly, disasse...

A number of years ago, inspired by the work of Dr. Bob Simpson [1], we developed a model system in yeast to study the events that occur when a gene is activated for transcription [2, 3]. This involves the purification from yeast cells of native plasmid ch

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We recommend using an alternative version SMARCA4 Polyclonal Antibody Background SNF2beta;/BRG1 is a member of the SWI/SNF family of proteins and is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which...

K. Balasubramanyam, R. A. Varier, M. Altaf, V. Swaminathan, N. B. Siddappa, U. Ranga and Kundu T.K., Curcumin, a novel p300/CBP specific inhibitor of acetyltransferase, represses the acetylation of histones/nonhistone proteins and HAT dependent chromatin transcription, J Biol Chem 279, 51163 - 51171 (2004 ...

c‐MYC and the SWI/SNF chromatin remodeling complex act as master regulators of transcription, and play a key role in human cancer. Although they are known to interact, the molecular details of their interaction are lacking. We have determined the structure of the RPT1 region of the INI1/hSNF5/BAF47/SMARCB1 subunit of the SWI/SNF complex that acts as a c‐MYC‐binding domain, and have localized the i ...

Recent years have seen major advances in elucidating the complexity of chromatin and its role as an epigenetic regulator of gene expression in eukaryotes. We now have a basic understanding of chromatin control and the enzymatic modifications that impart diverse regulatory cues to the functional activity of the genome. Most importantly, although research into chromatin has uncovered fascinating insights into the control of gene expression, it has also generated a large body of information that is being harnessed to develop new therapeutic modalities for treating cancer. Here, we discuss recent advances that support the contention that future generations of chromatin-modulating drugs will provide a significant group of new, mechanism-based therapeutics for cancer. ©2006 Elsevier Ltd. All rights reserved.

Foster SL, Hargreaves DC, Medzhitov R. Gene-specific control of inflammation by TLR-induced chromatin modifications. Nature. 2007;447,972-8. Learn More ...

Learn more about the Chromatin Modification Pathway from related diseases, pathways, genes and PTMs with the Novus Bioinformatics Tool.

Chromatin immunoprecipitation, next-gen sequencing, and other approaches allow researchers to study chromatin structure and DNA-binding interactions to determine how they regulate gene expression.

With great resolution comes great sequencing requirements, and those trying some chromatin conformation should catch T2C: Targeted Chromatin Capture.

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BRG1 is an essential component of the SWI/SNF chromatin remodeling complex and implicated in multiple functions through its interaction with different proteins, including the tumor suppressor protein pRb, serine-threonine kinase LKB1, and other transcrip

what is chromatin when it condesnses into chromosomes Chromatin is the same thing in metaphase than anyother point in the cell cycle, its DNA wrapp...

NEW TOOL: A new tool has been added to the Reports section on the side tool bar. This tool, Protein Group Counts, allows users to see the number of genes within all protein groups for any organism, or combination of organisms in the database.. UPDATE: The featured Chromatin Researcher Spotlight has been changed. Our new researcher is Professor Richard Amasino. His research statement is shown below. We have activated the archive section for the Chromatin Researcher Spotlight. Research statements for previous researchers can be accessed via the Archive link on the side tool bar ...

Chromatin UI - Icon Pack v1.4Requirements: 4.0+Overview: Chromatin UI is a new Material Design icon pack inspired by the grain effects from Google illustration. This icon pack is based on Nucleo UI but with three big difference : no long shadow, a grain effect end a vivid color.

Download|| Chromatin UI - Icon Pack v3.0 Apk | 40 MB | Resumable Links | Requires :Android 4.0.3 and up | Chromatin UI is a new Material Design icon

Posttranslational modifications play a key role in recruiting chromatin remodeling and modifying enzymes to specific regions of chromosomes to modulate chromatin structure. Alc1 (amplified in liver cancer 1), a member of the SNF2 ATPase superfamily with a carboxy-terminal macrodomain, is encoded by an oncogene implicated in the pathogenesis of hepatocellular carcinoma. Here we show that Alc1 interacts transiently with chromatin-associated proteins, including histones and the poly(ADP-ribose) polymerase Parp1. Alc1 ATPase and chromatin remodeling activities are strongly activated by Parp1 and its substrate NAD and require an intact macrodomain capable of binding poly(ADP-ribose). Alc1 is rapidly recruited to nucleosomes in vitro and to chromatin in cells when Parp1 catalyzes PAR synthesis. We propose that poly(ADP-ribosyl)ation of chromatin-associated Parp1 serves as a mechanism for targeting a SNF2 family remodeler to chromatin. ...

Chromatin compacts DNA to an extreme extend and allows eukaryotic genome fit the size of the nucleus. On the other hand, however, it must process the ability to untighten DNA and to permit the cellular machinery access to genome. Chromatin consists of nucleosomes in which a protein core is constituted by four canonical histones H2A, H2B, H3, H4 and wrapped around by 147 bp of DNA. Histone variants, and the chromatin remodelling machinery, can reorganize the compaction of chromatin and thus be important for epigenetic regulation of gene expression.. Histone variant H2A.Z is a universal mark of dynamic nucleosomes. H2A.Z is essential for growth, development and viability of a number of species including mammals. H2A.Z plays critical roles in multiple biological processes including gene transcription and replication, DNA repair, and genome integrity. The chromatin incorporation of H2A.Z is catalysed by SRCAP, an ATP-dependent, multi-component chromatin remodelling complex. The YL1 subunit of SRCAP ...

TY - JOUR. T1 - CAME. T2 - Identification of chromatin accessibility from nucleosome occupancy and methylome sequencing. AU - Piao, Yongjun. AU - Lee, Seong Keon. AU - Lee, Eun Joon. AU - Robertson, Keith D. AU - Shi, Huidong. AU - Ryu, Keun Ho. AU - Choi, Jeong Hyeon. PY - 2017/4/15. Y1 - 2017/4/15. N2 - Motivation: Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, Methyltransferase Accessibility Protocol for individual templates-Bisulfite Genome Sequencing (MAPit-BGS) and nucleosome occupancy and methylome sequencing (NOMe-seq) have been developed for simultaneously profiling chromatin accessibility and DNA methylation on single molecules. Therefore, there is a great demand in developing computational methods to identify chromatin ...

This organism was chosen because it has epigenetically defined regional centromeres whose chromatin and protein compositions are similar to those of their human counterparts, to identify factors responsible for the replacement of histone H3 with CENP-A at centromeres.. In this report, the KAIST research group systematically analyzed the roles of the ATP-dependent chromatin-remodelers in the centromeric chromatin assembly of fission yeast as they serve as strong candidates for such factors ...

Figure 3. NoRC regulates telomeric heterochromatin. (A) TIP5 localizes at telomeres. Left: Z‐projection of a deconvolved image of a representative U2OS cell stained with α‐TIP5 antibody (red) followed by Q‐FISH with a telomere‐specific PNA probe (green). The same nucleus depicting colocalization of TIP5 with telomeres (white spots) is shown below. Middle: a representative U2OS cell immunostained with α‐TIP5 (red) and α‐TRF2 (green) antibodies is shown. Colocalization of TIP5 and TRF2 is depicted in yellow. Right: quantification of telomeres colocalizing with TIP5 in a representative experiment (N=4), each dot on the plot represents one cell (unpaired t‐test, P‐value ***,0.001, n=45). Red bars indicate mean values. Scale bars, 5 μm. (B) TIP5 is associated with telomeres. ChIPs in U2OS cells monitoring TIP5, TRF2 and Pol I at telomeres. Telomere DNA was assayed by dot hybridization with a telomere‐specific riboprobe. Data are normalized to input values. Error bars represent ...

The Drosophila kismet gene was identified in a screen for dominant suppressors of Polycomb, a repressor of homeotic genes. Here we show that kismet mutations suppress the Polycomb mutant phenotype by blocking the ectopic transcription of homeotic genes. Loss of zygotic kismet function causes homeotic transformations similar to those associated with loss-of-function mutations in the homeotic genes Sex combs reduced and Abdominal-B. kismet is also required for proper larval body segmentation. Loss of maternal kismet function causes segmentation defects similar to those caused by mutations in the pair-rule gene even-skipped. The kismet gene encodes several large nuclear proteins that are ubiquitously expressed along the anterior-posterior axis. The Kismet proteins contain a domain conserved in the trithorax group protein Brahma and related chromatin-remodeling factors, providing further evidence that alterations in chromatin structure are required to maintain the spatially restricted patterns of ...

We have shown for the first time that the function of CAF-1 is important for viability following double-strand DNA repair. Furthermore, CAF-1 functions genetically in both homologous recombination and NHEJ, and its function during double-strand DNA repair is dependent on the interaction between CAF-1 and PCNA. Given the biochemical role of CAF-1 in DNA synthesis-coupled chromatin assembly, we propose that CAF-1 mediates chromatin assembly during double-strand DNA repair in vivo.. We have observed sensitivity of CAF-1 mutants to a variety of double-strand DNA-damaging agents. A systematic analysis of the yeast deletion collection also isolated the cac2Δ as a mutant sensitive to MMS (Chang et al. 2002). Similarly, mutants of the genes encoding Arabidopsis CAF-1, fas1, and fas2 are sensitive to MMS (Takeda et al. 2004). Given the role of CAF-1 in chromatin assembly during NER of single-strand lesions and the sensitivity of CAF-1 mutants to UV irradiation (Gaillard et al. 1996; Kaufman et al. 1997; ...

TY - JOUR. T1 - Poly-ADP-Ribose (PAR) as an epigenetic flag. AU - Corona, Davide. PY - 2009. Y1 - 2009. N2 - Epigenetics is the study of hereditable chromatin modifications, such as DNA methylation, histone modifications, and nucleosome-remodelling, which occur without alterations to the DNA sequence. The establishment of different epigenetic states in eukaryotes depends on regulatory mechanisms that induce structural changes in chromatin in response to environmental and cellular cues. Two classes of enzymes modulate chromatin accessibility: chromatin-covalent modifiers and ATP-dependent chromatin remodelling complexes. The first class of enzymes catalyzes covalent modifications of DNA as well as the amino- and carboxy-terminal tails of histones, while the second uses the energy of ATP hydrolysis to reposition nucleosomes along the chromatin fibers or to incorporate histone variants. Thus, epigenetic modifications are reversible nuclear reactions. In the last decade, many studies have strongly ...

INI1 (Integrase interactor 1), also known as SMARCB1, is the most studied subunit of chromatin remodelling complexes. Its role in colorectal tumorigenesis is not known. We examined SMARCB1/INI1 protein expression in 134 cases of colorectal cancer (CRC) and 60 matched normal mucosa by using tissue microarrays and western blot and categorized the results according to mismatch repair status (MMR), CpG island methylator phenotype, biomarkers of tumor differentiation CDX2, CK20, vimentin and p53. We validated results in two independent data sets and in cultured CRC cell lines. Herein, we show that negative SMARCB1/INI1 expression (11% of CRCs) associates with loss of CDX2, poor differentiation, liver metastasis and shorter patients survival regardless of the MMR status or tumor stage. Unexpectedly, even CRCs displaying diffuse nuclear INI1 staining (33%) show an adverse prognosis and vimentin over-expression, in comparison with the low expressing group (56%). The negative association of SMARCB1/INI1-lack of

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Oligodendrocyte precursor cells (OPCs) constitute the main proliferative cells in the adult brain, and deregulation of OPC proliferation-differentiation balance results in either glioma formation or defective adaptive (re)myelination. OPC differentiation requires significant genetic reprogramming implicating chromatin remodeling. Mounting evidence indicates that chromatin remodelers play important roles during normal development and their mutations are associated with neurodevelopmental defects, with CHD7 haploinsuficiency being the cause of CHARGE syndrome and CHD8 being one of the strongest Autism Spectrum Disorder (ASD) high-risk associated genes. Here, we report on uncharacterized functions of the chromatin remodelers Chd7 and Chd8 in OPCs. Their OPC-chromatin-binding profile combined with transcriptome and chromatin accessibility analyses of Chd7-deleted OPCs, demonstrates that Chd7 protects non-proliferative OPCs from apoptosis by chromatin-closing and transcriptional repression of p53.

Packaging of DNA into chromatin is essential for the regulation of genome function in eukaryotes. Nucleosomes, the basic units of chromatin, are composed of ∼147 bp of DNA that is wrapped around an octomer built by four types of histones. Covalent modifications of histones, along with other factors, such as DNA methylation, chromatin-remodeling proteins, and small RNAs, contribute to the regulation of gene expression (Berger, 2007; Kouzarides, 2007; Berr et al., 2011). Heterochromatin is often used to refer to the parts of the genome that contain chromatin modifications associated with repression of gene expression. Constitutive heterochromatin describes regions of the genome that are stably maintained as heterochromatin throughout development and is often associated with 5-methylcytosine and H3K9me2 in plants (Bernatavichute et al., 2008). By contrast, facultative heterochromatin describes regions of the genome that exist as heterochromatin in some cell types and as euchromatin in other ...

The ability to maintain genomic integrity prevents unrestricted cell proliferation and the progression of cancer. DNA repair pathways such as the DNA double-strand break (DSB) response are essential in maintaining this integrity. This system requires activation of the serine/threonine kinase ataxia telangiectasia mutated (ATM) through acetylation by TIP60, a histone acetyl transferase, and subsequent ATM autophosphorylation. During DNA repair, activated ATM phosphorylates the histone variant H2AX several kilobases either side of the break site. This phosphorylation acts a signal for additional repair proteins and chromatin remodeling complexes which repairs DNA. In a previous study, H2AX phosphorylation was induced through the over expression of TIP60 or the SWI3-ADA2-N-CoR-TFIIIB (SANT) domain of p400. It was hypothesised that over expressed TIP60 or SANT domain was able to sequester a putative negative regulator from the ATM-TIP60 complex and artificially induce activation. This study aimed to ...

A primary challenge in the H3K27M field has been to resolve the contradictory observations indicating that PRC2 has a high affinity for H3K27M peptides, yet PRC2 and H3K27M are often mutually excluded from chromatin in H3K27M DIPG (4, 6, 9, 10). Our studies revealed that interaction of H3K27M with PRC2 is a dynamic process that cannot be captured by static, steady-state approaches. Namely, there is an initial phase after H3K27M is expressed and incorporated into chromatin, followed by PRC2 recruitment to H3K27M-containing chromatin, presumably due to its higher affinity toward H3K27M (Fig. 2C). However, in the next phase, PRC2 is released from H3K27M, as they do not colocalize at steady-state conditions in both isogenic 293 T-REx systems (e.g., this study, Figs. 2 and 3) and the H3K27M DIPG themselves (6). This dynamic model therefore accommodates both the finding of high H3K27M and PRC2 affinity in select assays and their failure to be stably colocalized on chromatin in cells. In line with the ...

Subunits of mammalian SWI/SNF (mSWI/SNF or BAF) complexes have recently been implicated as tumor suppressors in human malignancies. To understand the full extent of their involvement, we conducted a proteomic analysis of endogenous mSWI/SNF complexes, which identified several new dedicated, stable s …

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Eukaryotic organisms package DNA into chromatin for compact storage in the cell nucleus, but this packaging process results in transcriptional repression of genes. Chromatin remodeling complexes have evolved to overcome the transcriptional repression caused by chromatin packaging of DNA into nucleosomes by histones. One example of a chromatin remodeling complex is the SWI/SNF complex in yeast which uses ATP to drive the chromatin apart and make DNA accessible to transcription factors. The yeast SWI2 protein was discovered as the catalytic subunit of the yeast SWI/SNF chromatin remodeling complex and is required for the complex to counteract the repressive nature of chromatin. BRG1 and BRM, SWI2 homologs, are part of human chromatin remodeling complexes and have been shown to play a redundant role in the regulation of certain cell cycle and cellular adhesion genes, as well as cellular pathways. Recent studies showing loss of BRG1 in human tumor cell lines and primary tissue samples, BRG1 ...

Signaling cascades are essential in instructing cell proliferation and differentiation during animal development and are often manifested by turning on or shutting off the expression of a group of genes. The specificity of different signaling pathways is usually determined by activating specific transcription factors that bind to the enhancers of their target genes. However, in eukaryotic cells the full transcription of a particular target gene is also dependent on the recruitment of chromatin remodelers and histone modifiers, in addition to transcription factors, in order to ensure a local chromatin environment that is permissive for the access of a complete set of regulatory proteins. Although CAF-1 was initially identified as a histone chaperone for DNA synthesis-coupled chromatin assembly (Smith and Stillman, 1989; Das et al., 2009), it is becoming increasingly evident that CAF-1 has functions in the regulation of other cellular and developmental processes, such as heterochromatin formation ...

The Polycomb group (PcG) proteins are transcriptional repressors that regulate lineage choices during development and differentiation. Recent studies have advanced our understanding of how the PcG proteins regulate cell fate decisions and how their deregulation potentially contributes to cancer. In this Review we discuss the emerging roles of long non-coding RNAs (ncRNAs) and a subset of transcription factors, which we call cell fate transcription factors, in the regulation of PcG association with target genes. We also speculate about how their deregulation contributes to tumorigenesis. ...

Metazoans regulate biological functions in a number of ways, including via gene expression. Epigenetics is the term for regulation of gene expression, other than via changes in the DNA sequence. Modification of DNA or histones by methylation, acetylation, phosphorylation, and ubiquitination affects gene expression and function. Enzymes that chemically modify genomic DNA and histones, as well as epigenetic chromatin remodeling factors, regulate chromatin accessibility and therefore gene expression. Some chromatin remodeling factors contain a chromatin organization modifier domain, or chromodomain, responsible for ATP hydrolysis-dependent chromatin reorganization. Other protein families regulating chromatin structure include bromodomain proteins, plant homeodomain proteins, and the inhibitor of growth family. During the process of stem cell differentiation into terminally differentiated cells, altered expression of chromatin modification enzyme and chromatin remodeling factor genes changes histone ...

Principal Investigator: Oliver Bell. In metazoans, packaging of genomic DNA into the nucleosomal protein scaffold of chromatin provides an opportunity to tightly regulate accessibility and readout of the genetic information. In particular, chemical modifications of nucleosomes and DNA have emerged as important determinants of genome accessibility. However, the dynamic regulation of chromatin state and its contribution to epigenetic inheritance of gene expression has remained enigmatic and a key challenge in the field of chromatin biology.. We have developed a novel technology that allows for rapid addition and removal of chromatin regulatory activities to a gene locus in any murine cell type. The Chromatin in vivo Assay (CiA) employs small molecules, which simultaneously bind two distinct peptide domains to induce dimerization between a chromatin modifier and a DNA binding protein. The CiA approach provides high temporal control allowing us to study the kinetics and epigenetic memory of histone ...

Meeting Description: The workshop will discuss the structural and dynamic aspects of chromatin and how they are regulated by other factors such as histone chaperones, chromatin factors, and chromatin remodelers. The talks will cover topics including nucleosome structure, nucleosome remodeling, covalent modification of histones, histone exchange, and histone variants. The workshop will also discuss various biophysical tools used to study chromatin including X-ray crystallography, NMR, single molecule, and computation. ...

SWI/SNF-type chromatin remodelers, such as BRAHMA (BRM), and H3K27 demethylases both have active roles in regulating gene expression at the chromatin level1-5, but how they are recruited to specific genomic sites remains largely unknown. Here we show that RELATIVE OF EARLY FLOWERING 6 (REF6), a plant-unique H3K27 demethylase6, targets genomic loci containing a CTCTGYTY motif via its zinc-finger (ZnF) domains and facilitates the recruitment of BRM. Genome-wide analyses showed that REF6 colocalizes with BRM at many genomic sites with the CTCTGYTY motif. Loss of REF6 results in decreased BRM occupancy at BRM-REF6 co-targets. Furthermore, REF6 directly binds to the CTCTGYTY motif in vitro, and deletion of the motif from a target gene renders it inaccessible to REF6 in vivo. Finally, we show that, when its ZnF domains are deleted, REF6 loses its genomic targeting ability. Thus, our work identifies a new genomic targeting mechanism for an H3K27 demethylase and demonstrates its key role in recruiting ...

Cancer is principally considered a genetic disease, and numerous mutations are thought essential to drive its growth. However, the existence of genomically stable cancers and the emergence of mutations in genes that encode chromatin remodelers raise the possibility that perturbation of chromatin structure and epigenetic regulation are capable of driving cancer formation. Here we sequenced the exomes of 35 rhabdoid tumors, highly aggressive cancers of early childhood characterized by biallelic loss of SMARCB1, a subunit of the SWI/SNF chromatin remodeling complex. We identified an extremely low rate of mutation, with loss of SMARCB1 being essentially the sole recurrent event. Indeed, in 2 of the cancers there were no other identified mutations. Our results demonstrate that high mutation rates are dispensable for the genesis of cancers driven by mutation of a chromatin remodeling complex. Consequently, cancer can be a remarkably genetically simple disease. ...

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SWI/SNF (switch/sucrose nonfermenting) complexes regulate transcription through chromatin remodeling and opposing gene silencing by Polycomb group (PcG) proteins. Genes encoding SWI/SNF components are critical for normal development and frequently mutated in human cancer. We characterized the in vivo contributions of SWI/SNF and PcG complexes to proliferation-differentiation decisions, making use of the reproducible development of the nematode Caenorhabditis elegans. RNA interference, lineage-specific gene knockout, and targeted degradation of SWI/SNF BAF components induced either overproliferation or acute proliferation arrest of precursor cells, depending on residual protein levels. Our data show that a high SWI/SNF BAF dosage is needed to arrest cell division during differentiation and to oppose PcG-mediated repression. In contrast, a low SWI/SNF protein level is necessary to sustain cell proliferation and hyperplasia, even when PcG repression is blocked. These observations show that ...

Abstract: Chromatin loop extrusion by Structural Maintenance of Chromosome (SMC) complexes is thought to underlie intermediate-scale chromatin organization inside cells. Motivated by a number of experiments suggesting that nucleosomes may block loop extrusion by SMCs, such as cohesin and condensin complexes, we introduce and characterize theoretically a composite loop extrusion factor (composite LEF) model. In addition to an SMC complex that creates a chromatin loop by encircling two threads of DNA, this model includes a remodeling complex that relocates or removes nucleosomes as it progresses along the chromatin, and nucleosomes that block SMC translocation along the DNA. Loop extrusion is enabled by SMC motion along nucleosome-free DNA, created in the wake of the remodeling complex, while nucleosome re-binding behind the SMC acts as a ratchet, holding the SMC close to the remodeling complex. We show that, for a wide range of parameter values, this collection of factors constitutes a composite ...

The compact structure of the eukaryotic genome dictates the accessibility to genes, and therefore adds an additional layer of regulation for gene expression. A specialized class of proteins called chromatin remodelers facilitates this process in the cell. The imitation switch (ISWI) subfamily of chromatin remodelers is a well studied class of proteins affecting gene expression. Its member ISW2 was recently shown to behave differently from other chromatin remodeling proteins. For instance, the ISW2 complex has been shown to be stimulated by ~5-6 fold in its ATPase activity when bound to a nucleosome rather than to a DNA molecule. Nucleosome remodeling by ISW2 has even been shown to depend on the N-terminal tail of histone H4 and therefore, the octamer of a nucleosome might be playing a significant role in nucleosome remodeling by the ISW2 complex. The aim in this investigation was to delineate the protein-protein interactions that the ISW2 complex establishes with the octamer upon binding to a

Ovarian cancer is the fifth leading cause of cancer-related deaths in women. There are about 20,000 new cases per year and only 46% of those women survive five years. Despite aggressive treatments of surgical resection followed by highly toxic chemotherapies and radiation, ovarian cancer outcomes have remained dismal due to lack of early detection and lack of availability of targeted treatments. Recent research has revealed that ovarian cancer subtypes have diverse genetic backgrounds and suggest a need to develop specialized therapeutic strategies for specific subtypes. Several ovarian cancer subtypes have high mutation frequencies in SWI/SNF (switch/sucrose non-fermentable) complex members. The SWI/SNF complex was first discovered in yeast for its involvement in mating type switching and sugar metabolism. The SWI/SNF complex is a chromatin remodeler whose job is to properly space and place nucleosomes, the protein spools for DNA, throughout the genome. Proper placement of these nucleosome ...

Single-cell chromatin accessibility sequencing has become a powerful technology for understanding epigenetic heterogeneity of complex tissues. However, there is a lack of open-source software for comprehensive processing, analysis, and visualization of such data generated using all existing experimental protocols. Here, we present scATAC-pro for quality assessment, analysis, and visualization of single-cell chromatin accessibility sequencing data. scATAC-pro computes a range of quality control metrics for several key steps of experimental protocols, with a flexible choice of methods. It generates summary reports for both quality assessment and downstream analysis. scATAC-pro is available at https://github.com/tanlabcode/scATAC-pro.

How is SWI/SNF Related, Matrix-Associated, Actin-Dependent, Regulator of Chromatin abbreviated? SMARC stands for SWI/SNF Related, Matrix-Associated, Actin-Dependent, Regulator of Chromatin. SMARC is defined as SWI/SNF Related, Matrix-Associated, Actin-Dependent, Regulator of Chromatin somewhat frequently.

If you have a question about this talk, please contact Zoubin Ghahramani.. Chromatin state segmentation-the division of a genome into regions of similar combinatorial patterns of DNA or histone modifications, as measured through high-throughput sequencing-is a common problem in genomics research. Recent large-scale projects have generated enormous amounts of chromatin state information, without corresponding advances in techniques for analyzing with these large, complex datasets.. In this talk, I will first outline the problem of chromatin state segmentation and discuss current approaches. I will then review the non-parametric Bayesian sticky HDP -HMM model for time-series segmentation, and introduce a variational mean-field algorithm for inference in the sticky HDP -HMM with an application to chromatin state segmentation.. This talk is part of the Machine Learning @ CUED series.. ...

Chromatin describes the complex of DNA and proteins that packs DNA into condensed structures. But this is not its only function: by packing the DNA it prevents possible transcription and therefore is a powerful mechanism for control of gene expression. Especially since the chromatin state can be passed on to progenies allowing for a fixed gene expression over multiple proliferations. Experiments in Drosophila could show that dependent on the position of gene on the chromosome and therefore its chromatin packing state different reproducible cell proliferation patterns emerged. The resulting different eye patterns lead to the hypothesis that the chromatin packaging state of a gene can govern the pattern phenotype of the corresponding tissue. Therefore chromatin engineering yields the possibility to further understand and manipulate cell patterns in mammalian cells. The basis for this project is a mammalian cell line that switches between two possible states reported by fluorescent proteins by ...

Chromatin describes the complex of DNA and proteins that packs DNA into condensed structures. But this is not its only function: by packing the DNA it prevents possible transcription and therefore is a powerful mechanism for control of gene expression. Especially since the chromatin state can be passed on to progenies allowing for a fixed gene expression over multiple proliferations. Experiments in Drosophila could show that dependent on the position of gene on the chromosome and therefore its chromatin packing state different reproducible cell proliferation patterns emerged. The resulting different eye patterns lead to the hypothesis that the chromatin packaging state of a gene can govern the pattern phenotype of the corresponding tissue. Therefore chromatin engineering yields the possibility to further understand and manipulate cell patterns in mammalian cells. The basis for this project is a mammalian cell line that switches between two possible states reported by fluorescent proteins by ...

A major focus of the current study was to use more natural arrays to investigate chromatin decondensation upon transcription induction. It is widely believed that chromatin is extensively compacted within nuclei, but that transcriptionally active regions decondense to the level of DNA wrapped around nucleosomes, namely a 10-nm fiber. To investigate chromatin organization in a transcriptionally active region, the authors constructed their arrays from bacterial artificial chromosomes (BACs) that contained known inducible mammalian genes. Consistent with several previous studies (Tumbar et al., 1999; Müller et al., 2001, 2004; Janicki et al., 2004), induction of transcription in these arrays caused them to decondense into a series of colinear spots (Fig. 1 B). By measuring the distance between these spots, the authors discovered that the degree of decondensation is not large: on average, the array decondenses to a level that is ∼96-fold more compacted than a 10-nm fiber.. A distinguishing ...

The mechanisms underlying the neurodevelopmental deficits associated with CHARGE syndrome, which include cerebellar hypoplasia, developmental delay, coordination problems, and autistic features, have not been identified. CHARGE syndrome has been associated with mutations in the gene encoding the ATP-dependent chromatin remodeler CHD7. CHD7 is expressed in neural stem and progenitor cells, but its role in neurogenesis during brain development remains unknown. Here we have shown that deletion of ...

The interplay of active and repressive histone modifications is assumed to have a key role in the regulation of gene expression. In contrast to this generally accepted view, we show that the transcription of genes temporally regulated during fly and worm development occurs in the absence of canonically active histone modifications. Conversely, strong chromatin marking is related to transcriptional and post-transcriptional stability, an association that we also observe in mammals. Our results support a model in which chromatin marking is associated with the stable production of RNA, whereas unmarked chromatin would permit rapid gene activation and deactivation during development. In the latter case, regulation by transcription factors would have a comparatively more important regulatory role than chromatin marks.. ...

Chromatin remodeling can be an essential component of transcription initiation. ATP-dependent chromatin redecorating complexes negligibly impacts reporter promoters combinatorial inactivation of SNF2 and ISW1 includes a synergistic impact by diminishing histone reduction during high temperature induction and getting rid of Pol II recruitment. Significantly in addition it eliminates preloading of HSF on and promoters before high temperature surprise and diminishes HSF binding during high temperature surprise. These observations claim that prior actions of chromatin redecorating complexes is essential for the activator binding. BAY 57-9352 Launch Chromatin redecorating at gene promoters has a critical function in activation of transcription. Its been confirmed these chromatin adjustments may range between post-translational adjustments of specific histones to the entire disassembly and removal of nucleosomes. The need for chromatin redecorating is certainly underscored with the demo that at least ...

How does chromatin structure determine the fate of transcripts? How do transcripts direct changes in chromatin? Our lab is investigating the role of chromatin and RNA in controlling transcriptional and post-transcriptional gene regulatory processes. We are focusing on gaining mechanistic insights into how small non-coding RNAs induce changes in chromatin and transcription in animals. We are also aiming to identify the role of chromatin on post-transcriptional gene regulatory processes. We use an interdisciplinary approach combining biochemistry, genetics, cell, molecular and computational biology and functional genomics as key tools to tackle these exciting questions.. ...

Chromosome conformation capture (3C) has revolutionized the ways in which the conformation of chromatin and its relationship to other molecular functions can be studied. 3C-based techniques are used to determine the spatial arrangement of chromosomes in organisms ranging from bacteria to humans. In particular, they can be applied to the study of chromosome folding and organization in model organisms with small genomes and for which powerful genetic tools exist, such as budding yeast. Studies in yeast allow the mechanisms that establish or maintain chromatin structure to be analyzed at very high resolution with relatively low cost, and further our understanding of these fundamental processes in higher eukaryotes as well. Here we provide an overview of chromatin structure and introduce methods for performing 3C, with a focus on studies in budding yeast. Variations of the basic 3C approach (e.g., 3C-PCR, 5C, and Hi-C) can be used according to the scope and goals of a given experiment.

Our appreciation of the critical role of the genomes 3D organization in gene regulation is steadily increasing. Recent 3C-based deep sequencing techniques elucidated a hierarchy of structures that underlie the spatial organization of the genome in the nucleus. At the top of this hierarchical organization are chromosomal territories and the megabase-scale A/B compartments that correlate with transcriptional activity within cells. Below them are the relatively cell-type-invariant topologically associated domains (TADs), characterized by high frequency of physical contacts between loci within the same TAD, and are assumed to function as regulatory units. Within TADs, chromatin loops bring enhancers and target promoters to close spatial proximity. Yet, we still have only rudimentary understanding how differences in chromatin organization between different cell types affect cell-type-specific gene expression programs that are executed under basal and challenged conditions. Here, we carried out a large-scale

Taken together, these studies will reveal how the transcriptional machinery competes with chromatin assembly to regulate transcription, not only during genome activation but potentially also during differentiation and reprogramming.. 2. The role of chromatin structure and nuclear architecture in genome activation. Chromatin regulates the accessibility of the genome for DNA binding proteins. Changes in chromatin structure and nuclear organization are thus critical to understanding how regions of the genome become transcriptionally competent. We have previously shown that dramatic changes in chromatin structure accompany the onset of zygotic gene expression (Vastenhouw et al., Nature 2010 PMID: 20336069; Zhang et al., GR 2014 PMID: 24285721). Thus, the onset of transcription during genome activation provides a powerful system to study the relationship between chromatin structure and transcriptional activity.. We have recently found that transcriptional activity and accumulation of the produced RNA ...

Thaete and colleagues (14) showed association of both SS18 and SS18-SSX with the DNA-dependent ATPase BRM, the catalytic subunit of SWI/SNF chromatin remodeling complexes. Subsequently, Kato and colleagues (15) showed that SS18 is a stable and integral component of SWI/SNF complexes using coimmunoprecipitation and mass spectroscopy in nuclear extracts of HeLa cells.. Middeljans and colleagues (16) extended these results by showing that the fusion oncoprotein is similarly incorporated into stable SWI/SNF complexes. All commonly observed subunits were recovered in reciprocal purifications between tandem affinity purification-tagged SS18-SSX1 and other subunits, indicating minimal perturbation of the core complex when the fusion oncogene is stably expressed in HEK293 cells. Kadoch and Crabtree (17) observed high-affinity binding of both SS18 and SS18-SSX to the core subunits of SWI/SNF, and immunodepletion of nuclear extracts showed undetectable levels outside of this association. In contrast with ...

DNA calls for the return of the nuclear envelope (NE) after mitosis, according to Ulbert et al. (page 469). The abundance of DNA may thus be one reason why the NE reforms so quickly.. NE reformation occurs so quickly that breaking down the process in vivo has so far been impossible. Many scientists instead use in vitro reconstitution assays, which indicate that chromatin decondensation (as occurs at the end of mitosis) initiates the recruitment of vesicle populations to chromatin. In the new work, the authors aimed to identify membrane and chromatin components that mediate this recruitment and thus NE assembly.. The main component of chromatin is, of course, DNA. The group found that excess naked DNA prevented in vitro NE reformation by titrating vesicles away from chromatin at early stages. DNA alone was a more potent inhibitor than chromatin, although chromatin proteins might also contribute, particularly later on as the envelope matures.. DNA does not bind pure liposomes, so the authors next ...

Duke University, Department of Pharmacology and Cancer Biology. David MacAlpine uses genomic approaches to study how the start sites of DNA replication are selected and regulated in the context of the local chromatin environment to maintain genomic stability and to ensure the accurate inheritance of genetic and epigenetic information. In the past two years he has published papers in Cell, Nature, PNAS, Genome Res (2X), EMBO J, Genes Dev (2X), MCB (2X) and NAR.. ...

Wysocka J, Swigut T, Xiao H, Milne TA, Kwon SY, Landry J, Kauer M, Tackett AJ, Chait BT, Badenhorst P, Wu C, Allis CD. A PHD finger of NURF couples histone H3 l

SCHLAP1 (SWI/SNF complex antagonist associated with prostate cancer 1 (non-protein coding)), Authors: Dessen P. Published in: Atlas Genet Cytogenet Oncol Haematol.

A full understanding of how the BAF complex exactly influences the fate of neuronal stem cells has been hindered by the absence of mutant models completely lacking BAF complexes. Here the scientists have been able to create knockout mutants lacking the entire BAF complex.. The result: The subunits BAF150 und BAF170 are central key factors, acting as scaffolding proteins for the interaction with the up to 15 subunits of the functional complex. These subunits serve as regulators of stability and functionality of the BAF complex, as indicated by a massive impairment of the murine forebrain development in BAF155/BAF170 deletion mutants.. Together with a dramatic reduction in active euchromatin, the loss of functional BAF-complexes resulted in a comprehensive decrease of gene expression events. Simultaneously, the scientists observed a global increase in repressive heterochromatin marks. The authors conclude: BAF complexes rather influence repression mechanism in neuronal cells indirectly than ...

Chromatin structures are regulated by various mechanisms including histone modification and chromatin remodeling, which involve the binding of transcription factors. By using tools such as chromatin immunoprecipitation , it...

James mammoth study (Prendergast et al, 2012) of human chromatin variation is published; it involved remapping 1.3 billion sequencing reads. He shows that it is possible to find variable sites in the human genome (SNPs) where the different variants (alleles) present carry different chromatin structures. These sites seem to be surprisingly rare in embryonic stem…