Role of the Conserved Sir3-BAH Domain in Nucleosome Binding and Silent Chromatin Assembly

Chromatin assembly factor-1 (CAF-1), a complex consisting of p150, p60, and p48 subunits, is highly conserved from yeast to humans and facilitates nucleosome assembly of newly replicated DNA in vitro. To investigate roles of CAF-1 in vertebrates, we generated two conditional DT40 mutants, respectively, devoid of CAF-1p150 and p60. Depletion of each of these CAF-1 subunits led to delayed S-phase progression concomitant with slow DNA synthesis, followed by accumulation in late S/G2 phase and aberrant mitosis associated with extra centrosomes, and then the final consequence was cell death. We demonstrated that CAF-1 is necessary for rapid nucleosome formation during DNA replication in vivo as well as in vitro. Loss of CAF-1 was not associated with the apparent induction of phosphorylations of S-checkpoint kinases Chk1 and Chk2. To elucidate the precise role of domain(s) in CAF-1p150, functional dissection analyses including rescue assays were preformed. Results showed that the binding abilities of CAF-1p150 with CAF-1p60 and DNA polymerase sliding clamp proliferating cell nuclear antigen (PCNA) but not with heterochromatin protein HP1-γ are required for cell viability. These observations highlighted the essential role of CAF-1–dependent nucleosome assembly in DNA replication and cell proliferation through its interaction with PCNA.

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HMGN dynamics and chromatin function

Biochemistry and Cell Biology ◽

10.1139/o03-040 ◽

2003 ◽

Vol 81 (3) ◽

pp. 113-122 ◽

Cited By ~ 21

Author(s):

Frédéric Catez ◽

Jae-Hwan Lim ◽

Robert Hock ◽

Yuri V Postnikov ◽

Michael Bustin

Keyword(s):

Binding Sites ◽

Protein Composition ◽

Nuclear Proteins ◽

Chromatin Interactions ◽

Binding Partners ◽

Nucleosomal Dna ◽

Transient Interactions ◽

And Function ◽

Nucleosome Binding

Recent studies indicate that most nuclear proteins, including histone H1 and HMG are highly mobile and their interaction with chromatin is transient. These findings suggest that the structure of chromatin is dynamic and the protein composition at any particular chromatin site is not fixed. Here we discuss how the dynamic behavior of the nucleosome binding HMGN proteins affects the structure and function of chromatin. The high intranuclear mobility of HMGN insures adequate supply of protein throughout the nucleus and serves to target these proteins to their binding sites. Transient interactions of the proteins with nucleosomes destabilize the higher order chromatin, enhance the access to nucleosomal DNA, and impart flexibility to the chromatin fiber. While roaming the nucleus, the HMGN proteins encounter binding partners and form metastable multiprotein complexes, which modulate their chromatin interactions. Studies with HMGN proteins underscore the important role of protein dynamics in chromatin function.Key words: HMG, nuclear proteins, chromatin, HMGN.

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ATRX in chromatin assembly and genome architecture during development and disease

Biochemistry and Cell Biology ◽

10.1139/o11-038 ◽

2011 ◽

Vol 89 (5) ◽

pp. 435-444 ◽

Cited By ~ 18

Author(s):

Nathalie G. Bérubé

Keyword(s):

Gene Regulation ◽

Chromatin Remodeling ◽

Chromatin Structure ◽

Higher Order ◽

Chromatin Assembly ◽

Genome Architecture ◽

Chromatin Conformation ◽

Mammalian Development ◽

Mitosis And Meiosis

The regulation of genome architecture is essential for a variety of fundamental cellular phenomena that underlie the complex orchestration of mammalian development. The ATP-dependent chromatin remodeling protein ATRX is emerging as a key regulatory component of nucleosomal dynamics and higher order chromatin conformation. Here we provide an overview of the role of ATRX at chromatin and during development, and discuss recent studies exposing a repertoire of ATRX functions at heterochromatin, in gene regulation, and during mitosis and meiosis. Exciting new progress on several fronts suggest that ATRX operates in histone variant deposition and in the modulation of higher order chromatin structure. Not surprisingly, dysfunction or absence of ATRX protein has devastating consequences on embryonic development and leads to human disease.

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A dual role of H4K16 acetylation in the establishment of yeast silent chromatin

The EMBO Journal ◽

10.1038/emboj.2011.170 ◽

2011 ◽

Vol 30 (13) ◽

pp. 2610-2621 ◽

Cited By ~ 64

Author(s):

Mariano Oppikofer ◽

Stephanie Kueng ◽

Fabrizio Martino ◽

Szabolcs Soeroes ◽

Susan M Hancock ◽

...

Keyword(s):

Dual Role ◽

Silent Chromatin ◽

H4k16 Acetylation

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The role of the chromatin assembly complex (CAF-1) and its p60 subunit (CHAF1b) in homeostasis and disease

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms ◽

10.1016/j.bbagrm.2015.05.009 ◽

2015 ◽

Vol 1849 (8) ◽

pp. 979-986 ◽

Cited By ~ 20

Author(s):

Andrew Volk ◽

John D. Crispino

Keyword(s):

Chromatin Assembly

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The role of aTp-dependent chromatin remodeling factors in chromatin assembly in vivo

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj19.476 ◽

2019 ◽

Vol 23 (2) ◽

pp. 160-167

Author(s):

Iu. A. Il’ina ◽

A. Yu. Konev

Keyword(s):

Dna Repair ◽

Chromatin Remodeling ◽

Molecular Motor ◽

Chromatin Assembly ◽

Histone Chaperones ◽

Nucleosome Assembly ◽

Male Pronucleus ◽

Histone Exchange

Chromatin assembly is a fundamental process essential for chromosome duplication subsequent to DNA replication. In addition, histone removal and incorporation take place constantly throughout the cell cycle in the course of DNA-utilizing processes, such as transcription, damage repair or recombination. In vitro studies have revealed that nucleosome assembly relies on the combined action of core histone chaperones and ATP-utilizing molecular motor proteins such as ACF or CHD1. Despite extensive biochemical characterization of ATP-dependent chromatin assembly and remodeling factors, it has remained unclear to what extent nucleosome assembly is an ATP-dependent process in vivo. Our original and published data about the functions of ATP-dependent chromatin assembly and remodeling factors clearly demonstrated that these proteins are important for nucleosome assembly and histone exchange in vivo. During male pronucleus reorganization after fertilization CHD1 has a critical role in the genomescale, replication-independent nucleosome assembly involving the histone variant H3.3. Thus, the molecular motor proteins, such as CHD1, function not only in the remodeling of existing nucleosomes but also in de novo nucleosome assembly from DNA and histones in vivo. ATP-dependent chromatin assembly and remodeling factors have been implicated in the process of histone exchange during transcription and DNA repair, in the maintenance of centromeric chromatin and in the loading and remodeling of nucleosomes behind a replication fork. Thus, chromatin remodeling factors are involved in the processes of both replication-dependent and replication-independent chromatin assembly. The role of these proteins is especially prominent in the processes of large-scale chromatin reorganization; for example, during male pronucleus formation or in DNA repair. Together, ATP-dependent chromatin assembly factors, histone chaperones and chromatin modifying enzymes form a “chromatin integrity network” to ensure proper maintenance and propagation of chromatin landscape.

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Yeast heterochromatin is a dynamic structure that requires silencers continuously

Genes & Development ◽

10.1101/gad.14.4.452 ◽

2000 ◽

Vol 14 (4) ◽

pp. 452-463 ◽

Cited By ~ 1

Author(s):

Tzu-Hao Cheng ◽

Marc R. Gartenberg

Keyword(s):

Chromatin Immunoprecipitation ◽

Transcriptional Silencing ◽

Dynamic Structure ◽

Regulatory Elements ◽

S Phase ◽

Silent Chromatin ◽

Site Specific ◽

Site Specific Recombination ◽

Silent State

Transcriptional silencing of the HM loci in yeast requirescis-acting elements, termed silencers, that function during S-phase passage to establish the silent state. To study the role of the regulatory elements in maintenance of repression, site-specific recombination was used to uncouple preassembled silent chromatin fragments from silencers. DNA rings excised from HMR were initially silent but ultimately reactivated, even in G1- or G2/M-arrested cells. In contrast, DNA rings bearing HML-derived sequence were stably repressed due to the presence of a protosilencing element. These data show that silencers (or protosilencers) are required continuously for maintenance of silent chromatin. Reactivation of unstably repressed rings was blocked by overexpression of silencing proteins Sir3p and Sir4p, and chromatin immunoprecipitation studies showed that overexpressed Sir3p was incorporated into silent chromatin. Importantly, the protein was incorporated even when expressed outside of S phase, during G1 arrest. That silencing factors can associate with and stabilize preassembled silent chromatin in non-S-phase cells demonstrates that heterochromatin in yeast is dynamic.

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The role of nucleoplasmin in chromatin assembly and disassembly

Molecular Chaperones ◽

10.1007/978-94-011-2108-8_2 ◽

1993 ◽

pp. 7-13

Author(s):

R. A. Laskey ◽

A. D. Mills ◽

A. Phillpott ◽

G. H. Leno ◽

S. M. Dillworth ◽

...

Keyword(s):

Chromatin Assembly ◽

Chromatin Assembly And Disassembly

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Sex-specific phenotypes of histone H4 point mutants establish dosage compensation as the critical function of H4K16 acetylation in Drosophila

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1817274115 ◽

2018 ◽

Vol 115 (52) ◽

pp. 13336-13341 ◽

Cited By ~ 11

Author(s):

Ömer Copur ◽

Andrey Gorchakov ◽

Katja Finkl ◽

Mitzi I. Kuroda ◽

Jürg Müller

Keyword(s):

Gene Transcription ◽

Dosage Compensation ◽

Causative Role ◽

Histone H4 ◽

Dosage Compensation Complex ◽

Critical Function ◽

Zygotic Gene ◽

H4k16 Acetylation ◽

Nucleosome Binding

Acetylation of histone H4 at lysine 16 (H4K16) modulates nucleosome–nucleosome interactions and directly affects nucleosome binding by certain proteins. In Drosophila, H4K16 acetylation by the dosage compensation complex subunit Mof is linked to increased transcription of genes on the single X chromosome in males. Here, we analyzed Drosophila containing different H4K16 mutations or lacking Mof protein. An H4K16A mutation causes embryonic lethality in both sexes, whereas an H4K16R mutation permits females to develop into adults but causes lethality in males. The acetyl-mimic mutation H4K16Q permits both females and males to develop into adults. Complementary analyses reveal that males lacking maternally deposited and zygotically expressed Mof protein arrest development during gastrulation, whereas females of the same genotype develop into adults. Together, this demonstrates the causative role of H4K16 acetylation by Mof for dosage compensation in Drosophila and uncovers a previously unrecognized requirement for this process already during the onset of zygotic gene transcription.

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