Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF

Nucleosome assembly requires the coordinated deposition of histone complexes H3-H4 and H2A-H2B to form a histone octamer on DNA. In the current paradigm, specific histone chaperones guide the deposition of first H3-H4 and then H2A-H2B(1-5). Here, we show that the acidic domain of DNA repair factor APLF (APLFAD) can assemble the histone octamer in a single step, and deposit it on DNA to form nucleosomes. The crystal structure of the APLFAD-histone octamer complex shows that APLFAD tethers the histones in their nucleosomal conformation. Mutations of key aromatic anchor residues in APLFAD affect chaperone activity in vitro and in cells. Together, we propose that chaperoning of the histone octamer is a mechanism for histone chaperone function at sites where chromatin is temporarily disrupted.

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NAP1-Related Protein 1 (NRP1) has multiple interaction modes for chaperoning histones H2A-H2B

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2011089117 ◽

2020 ◽

Vol 117 (48) ◽

pp. 30391-30399

Author(s):

Qiang Luo ◽

Baihui Wang ◽

Zhen Wu ◽

Wen Jiang ◽

Yueyue Wang ◽

...

Keyword(s):

Interaction Mechanism ◽

Histone Chaperones ◽

Related Protein ◽

Nucleosome Assembly ◽

Nucleosome Assembly Protein ◽

Vitro Binding ◽

Multiple Interaction ◽

Α Helix

Nucleosome Assembly Protein 1 (NAP1) family proteins are evolutionarily conserved histone chaperones that play important roles in diverse biological processes. In this study, we determined the crystal structure ofArabidopsisNAP1-Related Protein 1 (NRP1) complexed with H2A-H2B and uncovered a previously unknown interaction mechanism in histone chaperoning. Both in vitro binding and in vivo plant rescue assays proved that interaction mediated by the N-terminal α-helix (αN) domain is essential for NRP1 function. In addition, the C-terminal acidic domain (CTAD) of NRP1 binds to H2A-H2B through a conserved mode similar to other histone chaperones. We further extended previous knowledge of the NAP1-conserved earmuff domain by mapping the amino acids of NRP1 involved in association with H2A-H2B. Finally, we showed that H2A-H2B interactions mediated by αN, earmuff, and CTAD domains are all required for the effective chaperone activity of NRP1. Collectively, our results reveal multiple interaction modes of a NAP1 family histone chaperone and shed light on how histone chaperones shield H2A-H2B from nonspecific interaction with DNA.

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Histone Chaperone Nap1 Is a Major Regulator of Histone H2A-H2B Dynamics at the InducibleGALLocus

Molecular and Cellular Biology ◽

10.1128/mcb.00835-15 ◽

2016 ◽

Vol 36 (8) ◽

pp. 1287-1296 ◽

Cited By ~ 12

Author(s):

Xu Chen ◽

Sheena D'Arcy ◽

Catherine A. Radebaugh ◽

Daniel D. Krzizike ◽

Holli A. Giebler ◽

...

Keyword(s):

Critical Role ◽

Histone Chaperones ◽

Histone H2a ◽

Nucleosome Assembly ◽

Content Type ◽

Nucleosome Assembly Protein ◽

Nucleosome Assembly Protein 1 ◽

Histone Exchange

Histone chaperones, like nucleosome assembly protein 1 (Nap1), play a critical role in the maintenance of chromatin architecture. Here, we use theGALlocus inSaccharomyces cerevisiaeto investigate the influence of Nap1 on chromatin structure and histone dynamics during distinct transcriptional states. When theGALlocus is not expressed, cells lacking Nap1 show an accumulation of histone H2A-H2B but not histone H3-H4 at this locus. Excess H2A-H2B interacts with the linker DNA between nucleosomes, and the interaction is independent of the inherent DNA-binding affinity of H2A-H2B for these particular sequences as measuredin vitro. When theGALlocus is transcribed, excess H2A-H2B is reversed, and levels of all chromatin-bound histones are depleted in cells lacking Nap1. We developed anin vivosystem to measure histone exchange at theGALlocus and observed considerable variability in the rate of exchange across the locus in wild-type cells. We recapitulate this variability within vitronucleosome reconstitutions, which suggests a contribution of DNA sequence to histone dynamics. We also find that Nap1 is required for transcription-dependent H2A-H2B exchange. Altogether, these results indicate that Nap1 is essential for maintaining proper chromatin composition and modulating the exchange of H2A-H2Bin vivo.

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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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Role for DNA repair factor XRCC4 in immunoglobulin class switch recombination

Journal of Experimental Medicine ◽

10.1084/jem.20070255 ◽

2007 ◽

Vol 204 (7) ◽

pp. 1717-1727 ◽

Cited By ~ 101

Author(s):

Pauline Soulas-Sprauel ◽

Gwenaël Le Guyader ◽

Paola Rivera-Munoz ◽

Vincent Abramowski ◽

Christelle Olivier-Martin ◽

...

Keyword(s):

Dna Repair ◽

B Lymphocyte ◽

Alternative Pathway ◽

Class Switch Recombination ◽

Immunoglobulin Class ◽

Class Switch ◽

Lentiviral Transgenesis ◽

Repair Factor

V(D)J recombination and immunoglobulin class switch recombination (CSR) are two somatic rearrangement mechanisms that proceed through the introduction of double-strand breaks (DSBs) in DNA. Although the DNA repair factor XRCC4 is essential for the resolution of DNA DSB during V(D)J recombination, its role in CSR has not been established. To bypass the embryonic lethality of XRCC4 deletion in mice, we developed a conditional XRCC4 knockout (KO) using LoxP-flanked XRCC4 cDNA lentiviral transgenesis. B lymphocyte restricted deletion of XRCC4 in these mice lead to an average two-fold reduction in CSR in vivo and in vitro. Our results connect XRCC4 and the nonhomologous end joining DNA repair pathway to CSR while reflecting the possible use of an alternative pathway in the repair of CSR DSB in the absence of XRCC4. In addition, this new conditional KO approach should be useful in studying other lethal mutations in mice.

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In Vivo Study of the Nucleosome Assembly Functions of ASF1 Histone Chaperones in Human Cells

Molecular and Cellular Biology ◽

10.1128/mcb.00510-07 ◽

2008 ◽

Vol 28 (11) ◽

pp. 3672-3685 ◽

Cited By ~ 28

Author(s):

Angélique Galvani ◽

Régis Courbeyrette ◽

Morgane Agez ◽

Françoise Ochsenbein ◽

Carl Mann ◽

...

Keyword(s):

Dna Synthesis ◽

Histone H3 ◽

Direct Determination ◽

Human Cells ◽

Chromatin Assembly ◽

Histone Chaperones ◽

Nucleosome Assembly ◽

Assembly Factor

ABSTRACT Histone chaperones have been implicated in nucleosome assembly and disassembly as well as histone modification. ASF1 is a highly conserved histone H3/H4 chaperone that synergizes in vitro with two other histone chaperones, chromatin assembly factor 1 (CAF-1) and histone repression A factor (HIRA), in DNA synthesis-coupled and DNA synthesis-independent nucleosome assembly. Here, we identify mutants of histones H3.1 and H3.3 that are unable to interact with human ASF1A and ASF1B isoforms but that are still competent to bind CAF-1 and HIRA, respectively. We show that these mutant histones are inefficiently deposited into chromatin in vivo. Furthermore, we found that both ASF1A and ASF1B participate in the DNA synthesis-independent deposition of H3.3 in HeLa cells, thus highlighting an unexpected role for ASF1B in this pathway. This pathway does not require interaction of ASF1 with HIRA. We provide the first direct determination that ASF1A and ASF1B play a role in the efficiency of nucleosome assembly in vivo in human cells.

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Structural basis of nucleosome assembly by the Abo1 AAA+ ATPase histone chaperone

Nature Communications ◽

10.1038/s41467-019-13743-9 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 7

Author(s):

Carol Cho ◽

Juwon Jang ◽

Yujin Kang ◽

Hiroki Watanabe ◽

Takayuki Uchihashi ◽

...

Keyword(s):

High Speed ◽

Atp Hydrolysis ◽

Structural Features ◽

Structural Basis ◽

Dependent Manner ◽

Histone Chaperones ◽

Nucleosome Assembly ◽

Chromatin Dynamics ◽

Aaa Atpase

AbstractThe fundamental unit of chromatin, the nucleosome, is an intricate structure that requires histone chaperones for assembly. ATAD2 AAA+ ATPases are a family of histone chaperones that regulate nucleosome density and chromatin dynamics. Here, we demonstrate that the fission yeast ATAD2 homolog, Abo1, deposits histone H3–H4 onto DNA in an ATP-hydrolysis-dependent manner by in vitro reconstitution and single-tethered DNA curtain assays. We present cryo-EM structures of an ATAD2 family ATPase to atomic resolution in three different nucleotide states, revealing unique structural features required for histone loading on DNA, and directly visualize the transitions of Abo1 from an asymmetric spiral (ATP-state) to a symmetric ring (ADP- and apo-states) using high-speed atomic force microscopy (HS-AFM). Furthermore, we find that the acidic pore of ATP-Abo1 binds a peptide substrate which is suggestive of a histone tail. Based on these results, we propose a model whereby Abo1 facilitates H3–H4 loading by utilizing ATP.

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