Differential Regulation of CENP-A and Histone H3 Phosphorylation in G2/M
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Cross-Talk Between Histone H3 Tails Produces Cooperative Nucleosome Acetylation
Cross-talk between histone H3 tails produces cooperative nucleosome acetylation Shanshan Li and Michael A. Shogren-Knaak1 Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011 Edited by Jerry L. Workman, Stowers Institute for Medical Research, Kansas City, MO, and accepted by the Editorial Board September 23, 2008 (received for review May 9, 2008) Acetylation of histone proteins by the yeast Spt-Ada-Gcn5-acetyl- nucleosomes, with an average distance between nucleosome cen- tansferase (SAGA) complex has served as a paradigm for under- ters of 212 bp (12). Although these nucleosomes are arrayed in a standing how posttranslational modifications of chromatin regu- linear fashion in genomic sequence, in many cases they adopt more late eukaryotic gene expression. Nonetheless, it has been unclear complex higher-order structures. Short-range interactions between to what extent the structural complexity of the chromatin sub- nucleosomes within a strand of chromatin allow chromatin to adopt strate modulates SAGA activity. By using chromatin model sys- a more compact 30-nm fiber structure (13, 14), and long-range tems, we have found that SAGA-mediated histone acetylation is interactions between distant nucleosomes provide a means for .(highly cooperative (cooperativity constant of 1.97 ؎ 0.15), employ- chromatin to potentially adopt 100- to 400-nm fiber structures (15 ing the binding of multiple noncontiguous nucleosomes to facili- Moreover, a number of recent studies suggest that different func- tate maximal acetylation activity. Studies with various chromatin tional forms of chromatin can adopt complex looping structures, substrates, including those containing novel asymmetric histone where regions of the genome that are separated by large distances octamers, indicate that this cooperativity occurs only when both in sequence can be brought together in space (16). -
Histones H3 and H4 Are Components of Upstream Activation Factor Required for the High-Level Transcription of Yeast Rdna by RNA Polymerase I
Proc. Natl. Acad. Sci. USA Vol. 94, pp. 13458–13462, December 1997 Biochemistry Histones H3 and H4 are components of upstream activation factor required for the high-level transcription of yeast rDNA by RNA polymerase I JOHN KEENER*, JONATHAN A. DODD*, DOMINIQUE LALO, AND MASAYASU NOMURA† Department of Biological Chemistry, University of California, Irvine, CA 92697-1700 Contributed by Masayasu Nomura, October 16, 1997 ABSTRACT RNA polymerase I (Pol I) transcription in consisting of Rrn6p, Rrn7p, and Rrn11p; refs. 3, 9, and 10), the yeast Saccharomyces cerevisiae is greatly stimulated in vivo Rrn3p (5), and Pol I are required. In addition to these factors, and in vitro by the multiprotein complex, upstream activation upstream activation factor (UAF) and TATA box-binding factor (UAF). UAF binds tightly to the upstream element of the protein, as well as the upstream element, are required for a rDNA promoter, such that once bound (in vitro), UAF does not high level of transcription from the yeast rDNA promoter (4, readily exchange onto a competing template. Of the polypep- 11). Purified UAF previously was shown to contain three tides previously identified in purified UAF, three are encoded genetically defined subunits, Rrn5p, Rrn9p, and Rrn10p, and by genes required for Pol I transcription in vivo: RRN5, RRN9, two uncharacterized subunits, p30 and p18 (4). and RRN10. Two others, p30 and p18, have remained unchar- DNA in the eukaryotic nucleus is organized as chromatin, acterized. We report here that the N-terminal amino acid consisting mostly of regularly repeating nucleosomes in which sequence, its mobility in gel electrophoresis, and the immu- DNA is wrapped around an octameric structure of core noreactivity of p18 shows that it is histone H3. -
Structure–Function Studies of Histone H3/H4 Tetramer Maintenance During Transcription by Chaperone Spt2
Downloaded from genesdev.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Structure–function studies of histone H3/H4 tetramer maintenance during transcription by chaperone Spt2 Shoudeng Chen,1,5 Anne Rufiange,2,5 Hongda Huang,1 Kanagalaghatta R. Rajashankar,3,4 Amine Nourani,2 and Dinshaw J. Patel1 1Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA; 2Groupe St-Patrick de Recherche en Oncologie Fondamentale, L’Hôtel-Dieu de Québec (Université Laval), Québec G1R 2J6, Canada; 3Northeastern Collaborative Access Team (NE-CAT), Advanced Photon Source, Argonne National Laboratory, Chicago, Illinois 60439, USA; 4Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA Cells use specific mechanisms such as histone chaperones to abrogate the inherent barrier that the nucleosome poses to transcribing polymerases. The current model postulates that nucleosomes can be transiently disrupted to accommodate passage of RNA polymerases and that histones H3 and H4 possess their own chaperones dedicated to the recovery of nucleosomes. Here, we determined the crystal structure of the conserved C terminus of human Suppressors of Ty insertions 2 (hSpt2C) chaperone bound to an H3/H4 tetramer. The structural studies demonstrate that hSpt2C is bound to the periphery of the H3/H4 tetramer, mimicking the trajectory of nucleosomal-bound DNA. These structural studies have been complemented with in vitro binding and in vivo functional studies on mutants that disrupt key intermolecular contacts involving two acidic patches and hydrophobic residues on Spt2C. We show that contacts between both human and yeast Spt2C with the H3/H4 tetramer are required for the suppression of H3/ H4 exchange as measured by H3K56ac and new H3 deposition. -
The Histone Variant H3.3 Marks Active Chromatin by Replication-Independent Nucleosome Assembly
Molecular Cell, Vol. 9, 1191–1200, June, 2002, Copyright 2002 by Cell Press The Histone Variant H3.3 Marks Active Chromatin by Replication-Independent Nucleosome Assembly Kami Ahmad and Steven Henikoff1 ment are not clear. A study in Tetrahymena concluded Fred Hutchinson Cancer Research Center that no protein difference between histone H3 variants 1100 Fairview Avenue North was required for replacement histone deposition and Seattle, Washington 98109 that expression of either variant outside of S phase ap- peared to be sufficient (Yu and Gorovsky, 1997). In con- trast, by examining the dynamics of histone proteins in Summary Drosophila nuclei we show that the major histone H3 and the replacement histone H3.3 proteins have distinct Two very similar H3 histones—differing at only four properties during in vivo chromatin assembly. Histone amino acid positions—are produced in Drosophila H3.3 participates in replication-independent (RI) nucleo- cells. Here we describe a mechanism of chromatin some assembly and is targeted to transcriptionally ac- regulation whereby the variant H3.3 is deposited at tive loci throughout the cell cycle. Transcription-coupled particular loci, including active rDNA arrays. While the deposition of H3.3-containing nucleosomes may be a major H3 is incorporated strictly during DNA replica- general mechanism for rapidly replacing permanently tion, amino acid changes toward H3.3 allow replica- modified nucleosomes and for heritably activating tion-independent (RI) deposition. In contrast to repli- genes. cation-coupled (RC) deposition, RI deposition does not require the N-terminal tail. H3.3 is the exclusive Results substrate for RI deposition, and its counterpart is the only substrate retained in yeast. -
Histone H3.3 and Its Proteolytically Processed Form Drive a Cellular Senescence Programme
ARTICLE Received 21 Mar 2014 | Accepted 9 Sep 2014 | Published 14 Nov 2014 DOI: 10.1038/ncomms6210 Histone H3.3 and its proteolytically processed form drive a cellular senescence programme Luis F. Duarte1,2,3, Andrew R.J. Young4, Zichen Wang3,5, Hsan-Au Wu1,3, Taniya Panda1,2, Yan Kou3,5, Avnish Kapoor1,2,w, Dan Hasson1,2, Nicholas R. Mills1,2, Avi Ma’ayan5, Masashi Narita4 & Emily Bernstein1,2 The process of cellular senescence generates a repressive chromatin environment, however, the role of histone variants and histone proteolytic cleavage in senescence remains unclear. Here, using models of oncogene-induced and replicative senescence, we report novel histone H3 tail cleavage events mediated by the protease Cathepsin L. We find that cleaved forms of H3 are nucleosomal and the histone variant H3.3 is the preferred cleaved form of H3. Ectopic expression of H3.3 and its cleavage product (H3.3cs1), which lacks the first 21 amino acids of the H3 tail, is sufficient to induce senescence. Further, H3.3cs1 chromatin incorporation is mediated by the HUCA histone chaperone complex. Genome-wide transcriptional profiling revealed that H3.3cs1 facilitates transcriptional silencing of cell cycle regulators including RB/E2F target genes, likely via the permanent removal of H3K4me3. Collectively, our study identifies histone H3.3 and its proteolytically processed forms as key regulators of cellular senescence. 1 Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York 10029, USA. 2 Department of Dermatology, Icahn School of Medicine at Mount Sinai, One Gustave L. -
Abo1 Is Required for the H3k9me2 to H3k9me3 Transition in Heterochromatin Wenbo Dong1, Eriko Oya1, Yasaman Zahedi1, Punit Prasad 1,2, J
www.nature.com/scientificreports OPEN Abo1 is required for the H3K9me2 to H3K9me3 transition in heterochromatin Wenbo Dong1, Eriko Oya1, Yasaman Zahedi1, Punit Prasad 1,2, J. Peter Svensson 1, Andreas Lennartsson1, Karl Ekwall1 & Mickaël Durand-Dubief 1* Heterochromatin regulation is critical for genomic stability. Diferent H3K9 methylation states have been discovered, with distinct roles in heterochromatin formation and silencing. However, how the transition from H3K9me2 to H3K9me3 is controlled is still unclear. Here, we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining global nucleosome organisation in fssion yeast. We identifed several key factors involved in heterochromatin silencing that interact genetically with Abo1: histone deacetylase Clr3, H3K9 methyltransferase Clr4, and HP1 homolog Swi6. Cells lacking Abo1 cultivated at 30 °C exhibit an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin has increased H3K9me2 but decreased H3K9me3 levels compared to wild-type. In contrast, facultative heterochromatin regions exhibit reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both the centromeres and subtelomeres, but not in a subset of heterochromatin islands in our condition. Thus, our work uncovers a role of Abo1 in stabilising directly or indirectly Clr4 recruitment to allow the H3K9me2 to H3K9me3 transition in heterochromatin. In eukaryotic cells, the regions of the chromatin that contain active genes are termed euchromatin, and these regions condense in mitosis to allow for chromosome segregation and decondense in interphase to allow for gene transcription1. Te chromatin regions that remain condensed throughout the cell cycle are defned as het- erochromatin regions and are transcriptionally repressed2,3. -
Posttranslational Modification of CENP-A Influences The
Posttranslational modification of CENP-A influences the conformation of centromeric chromatin Aaron O. Baileya,1, Tanya Panchenkob,1, Kizhakke M. Sathyanc, Janusz J. Petkowskid, Pei-Jing Paie, Dina L. Baif, David H. Russelle, Ian G. Macarad, Jeffrey Shabanowitzf, Donald F. Huntf,g, Ben E. Blackb,2, and Daniel R. Foltza,c,2 Departments of aCell Biology, cBiochemistry and Molecular Genetics, dMicrobiology, fChemistry, and gPathology, University of Virginia, Charlottesville, VA 22908; bDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059; and eDepartment of Chemistry, Texas A&M University, College Station, TX 77842-3012 Edited* by C. David Allis, The Rockefeller University, New York, NY, and approved June 13, 2013 (received for review January 7, 2013) Centromeres are chromosomal loci required for accurate segrega- of these proteins are highly divergent, sharing only 24% identity. tion of sister chromatids during mitosis. The location of the cen- Several lysine residues in the canonical H3 N terminus are highly tromere on the chromosome is not dependent on DNA sequence, conserved targets of acetylation and methylation that mediate but rather it is epigenetically specified by the histone H3 variant epigenetic regulation of local chromatin activity (12, 13). Post- centromere protein A (CENP-A). The N-terminal tail of CENP-A is translational modification (PTM) of histones is usually combi- highly divergent from other H3 variants. Canonical histone N natorial, and the net PTM status of these histones can negatively fl termini are hotspots of conserved posttranslational modification; or positively in uence transcription or direct global condensa- however, no broadly conserved modifications of the vertebrate tion of chromatin. -
Phosphorylation of Histone H3: a Balancing Act Between Chromosome Condensation and Transcriptional Activation
Review TRENDS in Genetics Vol.20 No.4 April 2004 Phosphorylation of histone H3: a balancing act between chromosome condensation and transcriptional activation Scott J. Nowak1,2 and Victor G. Corces1 1Department of Biology, The Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA 2Present address: Skirball Institute of Biomolecular Medicine, 540 First Avenue, New York, NY 10016, USA In recent years, the covalent modification of histone sufficiently malleable and modifiable to enable access to tails has emerged as a crucial step in controlling the genetic information. Such a structure is the composite transcription of eukaryotic genes. Phosphorylation of material termed chromatin, which contains the entire the serine 10 residue of the N-terminal tail of histone H3 genome and associated proteins [1]. Because DNA is is crucial for chromosome condensation and cell-cycle compacted into a highly condensed and ordered structure, progression during mitosis and meiosis. In addition, considerable interest has focused on how the transcrip- this modification is important during interphase tional machinery gains access to the genes contained because it enables the transcription of an increasing within chromatin and expresses them in an organized number of genes that are activated as a consequence of program, as is required in the processes of cellular a variety of cell-signaling events. The location of the differentiation and development. The alteration of chro- serine 10 residue in close proximity to other modifiable matin organization, via covalent modification and/or amino acids in the histone H3 tail enables the possibility remodeling of this structure, is thought to provide access of an interaction between phosphorylation of serine 10 to the genes for the transcription apparatus. -
1 Enhancer Regions Show High Histone H3.3 Turnover That Changes During 1 Differentiation 2 3 4 Aimee M. Deaton1,2, Mariluz
1 Enhancer regions show high histone H3.3 turnover that changes during 2 differentiation 3 4 5 Aimee M. Deaton1,2, Mariluz Gómez-Rodrı́guez3, Jakub Mieczkowski1, Michael Y. 6 Tolstorukov1, Sharmistha Kundu1, Ruslan Sadreyev1,4, Lars E.T. Jansen3*, Robert E. 7 Kingston1*. 8 9 1 Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics 10 Harvard Medical School, Boston, MA 02114. 11 2 Present address: Amgen Inc, 360 Binney St, Cambridge, MA 02142. 12 3 Instituto Gulbenkian de Ciencia, 2780-156, Oeiras, Portugal. 13 4 Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA. 14 15 * For correspondence: [email protected] (LETJ), [email protected] (REK) 16 17 18 Abstract 19 20 The organization of DNA into chromatin is dynamic; nucleosomes are frequently 21 displaced to facilitate the ability of regulatory proteins to access specific DNA 22 elements. To gain insight into nucleosome dynamics, and to follow how dynamics 23 change during differentiation, we used a technique called time-ChIP to 24 quantitatively assess histone H3.3 turnover genome-wide during differentiation of 25 mouse ESCs. We found that, without prior assumptions, high turnover could be used 26 to identify regions involved in gene regulation. High turnover was seen at 27 enhancers, as observed previously, with particularly high turnover at super- 28 enhancers. In contrast, regions associated with the repressive Polycomb-Group 29 showed low turnover in ESCs. Turnover correlated with DNA accessibility. Upon 30 differentiation, numerous changes in H3.3 turnover rates were observed, the 31 majority of which occurred at enhancers. -
Histone H4 and the Maintenance of Genome Integrity
Downloaded from genesdev.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Histone H4 and the maintenance of genome integrity Paul C. Megee, 1 Brian A. Morgan, 2 and M. Mitchell Smith 3 Department of Microbiology, University of Virginia School of Medicine Charlottesville, Virginia 22908 USA The normal progression of Saccharomyces cerevisiae through nuclear division requires the function of the amino-terminal domain of histone H4. Mutations that delete the domain, or alter 4 conserved lysine residues within the domain, cause a marked delay during the G2 +M phases of the cell cycle. Site-directed mutagenesis of single and multiple lysine residues failed to map this phenotype to any particular site; the defect was only observed when all four lysines were mutated. Starting with a quadruple lysine-to-glutamine substitution allele, the insertion of a tripeptide containing a single extra lysine residue suppressed the G2+M cell cycle defect. Thus, the amino-terminal domain of histone H4 has novel genetic functions that depend on the presence of lysine per se, and not a specific primary peptide sequence. To determine the nature of this function, we examined H4 mutants that were also defective for G2/M checkpoint pathways. Disruption of the mitotic spindle checkpoint pathway had no effect on the phenotype of the histone amino-terminal domain mutant. However, disruption of RADg, which is part of the pathway that monitors DNA integrity, caused precocious progression of the H4 mutant through nuclear division and increased cell death. These results indicate that the lysine-dependent function of histone H4 is required for the maintenance of genome integrity, and that DNA damage resulting from the loss of this function activates the RAD9-dependent G2/M checkpoint pathway. -
Eighteenth Edition Rams - March 2021
AATCGCCCAAGACAACATGGGGTTGCAGGTGTAAATCGATAAAAGAAG GGTAGGTATCGTTCACGGGGCACACTACTAGCGGGGCTTAGATAGCAA CTAGGGGTTCTTCACGCAEIGHTEENTHGCGCAAGA EDITIONCACATG -C MARCHGCTA T2021AAATGCTAGAT AACTGACATTATACTTATCAATGGGGAATAGGTCAGATAGATGGCACCA CATCGCACACTTATAGGCACGTCACCTGAGCCGACTCGAAATCCGCTTA TACTGCGACAAAATCATCCGCTCGGTTGATCTAGGATCGGGACTATATC CAGCGCRISPRCCCTAGCTCATTCTCAGAGGGAGCGACGAATGCTCAGC GAGGAGTTGTTCTGACCCGTGACGGAGTACTCTTTACTATCAAGTATAG CCAGTCTTGCCCCGATCGCTATACATTATTTGATGCCCCCCRISPRATAGC CGCAGTCATTCGACAGATTAGGCCCACCACCACCTCCCCTTGAGATTGG TATCRISPRCGCAACTGTAAGCAACATTACGGAAGGGCTACTCTAGATTG AACTCGCGTACAAGGTTTACCAAAGTGCATAAATCGACGGCCCCTCACG GCGGCCGTTAGCGCTCTAGAACCGAAACTAAGHACTACRISPRAACGCC GAAGACCCACGCCAATACAGTTCCGCGCCACGGAGGTAACTTACATGC CGCTCCCCGCRISPRGTTTACGGGTCATGCCTACCCCTCGGCATTCATGG GACTCAAACCTATCCCCGCAGCCGGAGCTTAAGAAAGAGCTAACACTTA GTTCGCATTCAAAATCGGTAAATTAATTAACATGCCGCAACGCGTCTATA AATGCCRISPRGTTCACCAACGTCCCGAGTTTTAACCTAGAAGCATATGTG CTGACCGTTAGCATGGAACTGCGTAACCTGACGGTCRISPRGTTCATCAC CTCGCGATCTCGTCAACTTGGCCATCGCCATCTGGTGGACCCCGGAATC AAAGCTGCTGACTAGAGGCGTTGAATCGCCCAAGACAACATGGCRISPR TTGCAGGTGTAAATCGATAAAAGAAGGGGTAGGTATCGTTCACGGGGC CATAGCCRISPRGGGGCTTAGATAGCAAACTAGGGGTTCTTCACGCAGC Interview: facing sex bias in biomedical research CAAGACACATGCGCTATAAATGCTAGATCAACTGACATTATACTTATCAA GGGGAZebrasATA ofG Medicine:GTCAG whenATA GthrombocytesATGGCA areCC scarceACCATCGCACACTTATAGGCAC TCACCOurTG futureAGC CwithGA CRISPR:CTCG a AbraveAAT newCC world?GCTTAGTACTGCGACAAAATCATCCG TCGGTCRISPR/Cas9TGATCTA geneGG editingATCG asG aG cancerACT therapyATATCGCAGCGCCCTAGCTCATTCTC -
Spreading and Epigenetic Inheritance of Heterochromatin Require a Critical Density of Histone H3 Lysine 9 Tri-Methylation
Spreading and epigenetic inheritance of heterochromatin require a critical density of histone H3 lysine 9 tri-methylation Amber R. Cutter DiPiazzaa, Nitika Tanejaa,1, Jothy Dhakshnamoorthya, David Wheelera, Sahana Hollaa, and Shiv I. S. Grewala,2 aLaboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892 Edited by Steven E. Jacobsen, University of California, Los Angeles, CA, and approved April 20, 2021 (received for review January 12, 2021) Heterochromatin assembly requires methylation of histone H3 domains coat pericentromeric, subtelomeric, and the silent mating- lysine 9 (H3K9me) and serves as a paradigm for understanding the type (mat) regions (9–12). Heterochromatin assembly is a multistep importance of histone modifications in epigenetic genome control. process that includes nucleation and spreading. The de novo nu- Heterochromatin is nucleated at specific genomic sites and spreads cleation of heterochromatin occurs at specific sites, such as repeat across extended chromosomal domains to promote gene silencing. elements within constitutive heterochromatin domains, from where Moreover, heterochromatic structures can be epigenetically inherited heterochromatin factors spread to surrounding sequences (13, 14). in a self-templating manner, which is critical for stable gene repres- RNAi machinery (13, 15), as well as factors involved in nuclear sion. The spreading and inheritance of heterochromatin are believed RNA processing and noncanonical RNA polymerase II termi- to be dependent on preexisting H3K9 tri-methylation (H3K9me3), nation (12, 16–19), nucleate heterochromatin by targeting the which is recognized by the histone methyltransferase Clr4/Suv39h multisubunit Clr4 methyltransferase complex (ClrC) (20) that is via its chromodomain, to promote further deposition of H3K9me. responsible for mono-, di-, and tri-methylation of histone H3K9 However, the process involving the coupling of the “read” and “write” (H3K9me1/2/3) (6, 21).