Integrated molecular mechanism directing nucleosome reorganization by human FACT

Tsunaka, Yasuo; Fujiwara, Yoshi; Oyama, Takuji; Hirose, Susumu; Morikawa, Kosuke

doi:10.1101/gad.274183.115

Cited by 138 publications

(220 citation statements)

References 63 publications

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“…Spt16 can bind H2A/H2B dimers in vivo and in vitro and H3/H4 tetramers in vitro but with higher specificity for H2A/H2B (30,(33)(34)(35)(36)(37). Recently it was demonstrated that the middle domain of human Spt16 interacts with the H3/H4 tetramer, and the AID domain interacts with H2B (38). The best studied transcriptional role for Spt16 involves the catalysis of nucleosomal reorganization during transcriptional elongation (25, 39 -41).…”

mentioning

confidence: 99%

The Modifier of Transcription 1 (Mot1) ATPase and Spt16 Histone Chaperone Co-regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization

True¹,

Muldoon²,

Carver

et al. 2016

Journal of Biological Chemistry

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Modifier of transcription 1 (Mot1) is a conserved and essential Swi2/Snf2 ATPase that can remove TATA-binding protein (TBP) from DNA using ATP hydrolysis and in so doing exerts global effects on transcription. Spt16 is also essential and functions globally in transcriptional regulation as a component of the facilitates chromatin transcription (FACT) histone chaperone complex. Here we demonstrate that Mot1 and Spt16 regulate a largely overlapping set of genes in Saccharomyces cerevisiae. As expected, Mot1 was found to control TBP levels at co-regulated promoters. In contrast, Spt16 did not affect TBP recruitment. On a global scale, Spt16 was required for Mot1 promoter localization, and Mot1 also affected Spt16 localization to genes. Interestingly, we found that Mot1 has an unanticipated role in establishing or maintaining the occupancy and positioning of nucleosomes at the 5 ends of genes. Spt16 has a broad role in regulating chromatin organization in gene bodies, including those nucleosomes affected by Mot1. These results suggest that the large scale overlap in Mot1 and Spt16 function arises from a combination of both their unique and shared functions in transcription complex assembly and chromatin structure regulation.

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mentioning

confidence: 99%

The Modifier of Transcription 1 (Mot1) ATPase and Spt16 Histone Chaperone Co-regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization

True¹,

Muldoon²,

Carver

et al. 2016

Journal of Biological Chemistry

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“…4A; Hondele et al 2013). Recent structural analyses of the S. cerevisiae Spt16-CTD:H2A-H2B complex has challenged the role of the Spt16-MD U-turn in targeting H2A-H2B and instead revealed that the primary H2A-H2B-binding site exists within the acidic Spt16-C and Pob3-C (SSRP1) domains (Kemble et al 2015), a conclusion independently validated by others (Tsunaka et al 2016). Interestingly, the minimal region of Spt16 that binds H2A-H2B (S965-E990 in S. cerevisiae) (Kemble et al 2015) corresponds to approximately the same region of human Spt16 (Spt16 956-960), which we identified to bind to CENP-T/-W.…”

Section: Spt16 Can Bind Either H2a-h2b or Cenp-t/-wmentioning

confidence: 94%

“…The region of Spt16 that is sufficient to bind CENP-T/-W (Spt16 amino acids 956-960) is within the minimum region of S. cerevisiae Spt16 (amino acids 958-999), determined to be sufficient to bind H2A-H2B (Kemble et al 2015). No H2A-H2B binding by the Spt16MD domain was detected with either yeast or human Spt16 (Kemble et al 2015;Tsunaka et al 2016), and, similarly, we did not find any binding between the human Spt16MD domain (amino acids 650-933) and CENP-T HFD /-W. The interaction between CENP-T/-W and FACT excludes the interaction between FACT and H2A-H2B and exhibits distinct properties.…”

Section: Fact Regulates In Vivo Dynamics Of Cenp-t/-wmentioning

confidence: 99%

The CENP-T/-W complex is a binding partner of the histone chaperone FACT

et al. 2016

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The CENP-T/-W histone fold complex, as an integral part of the inner kinetochore, is essential for building a proper kinetochore at the centromere in order to direct chromosome segregation during mitosis. Notably, CENP-T/-W is not inherited at centromeres, and new deposition is absolutely required at each cell cycle for kinetochore function. However, the mechanisms underlying this new deposition of CENP-T/-W at centromeres are unclear. Here, we found that CENP-T deposition at centromeres is uncoupled from DNA synthesis. We identified Spt16 and SSRP1, subunits of the H2A-H2B histone chaperone facilitates chromatin transcription (FACT), as CENP-W binding partners through a proteomic screen. We found that the C-terminal region of Spt16 binds specifically to the histone fold region of CENP-T/-W. Furthermore, depletion of Spt16 impairs CENP-T and CENP-W deposition at endogenous centromeres, and site-directed targeting of Spt16 alone is sufficient to ensure local de novo CENP-T accumulation. We propose a model in which the FACT chaperone stabilizes the soluble CENP-T/-W complex in the cell and promotes dynamics of exchange, enabling CENP-T/-W deposition at centromeres.

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“…More importantly, genomic analyses showed that FACT destabilizes the N/N+2 Micro-C interactions (tetranucleosomal motifs) to facilitate gene transcription in yeast. Distinct domains of FACT have been shown to interact with H2A/H2B or H3/H4 separately (Stuwe et al 2008;Zhang et al 2015;Tsunaka et al 2016), suggesting that these distinct domains of FACT might be responsible for their different activities in remodeling the nucleosome and/or the tetranucleosomal unit. It will be of great interest to generate a series of FACT mutants to resolve the distinctive activity in remodeling the nucleosome and/or the tetranucleosome using singlemolecule measurements.…”

Section: Epigenetic Regulation Of Chromatin Fibers By Chromatin Factorsmentioning

confidence: 99%

Structure and Epigenetic Regulation of Chromatin Fibers

Chen

2017

Cold Spring Harb Symp Quant Biol

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In eukaryotes, genomic DNA is hierarchically packaged by histones into chromatin on several levels to fit inside the nucleus. As a central-level structure between nucleosomal arrays and higher-order chromatin organizations, the 30-nm chromatin fiber and its dynamics play a crucial role in gene regulation. However, despite considerable efforts over the past three decades, the fundamental structure and its dynamic regulation of chromatin fibers still remain as a big challenge in molecular biology. Here, we mainly summarize the most recent progress in elucidating the structure of the 30-nm chromatin fiber in vitro and epigenetic regulation of chromatin fibers by chromatin factors, particularly histone variants. In addition, we also discuss recent studies in unraveling the three-dimensional organization of chromatin fibers in situ by genomic approaches and electron microscopy.In eukaryotic cells, the accessibility of DNA is dependent on the packing density of chromatin fibers. Genomic DNA firstly wraps around a histone octamer to form a nucleosome, which is connected by linker DNA to form the primary chromatin structure, the "beads-on-a-string" nucleosomal array. Nucleosomes in the array are further compacted by linker histone H1 to form a 30-nm chromatin fiber-typically regarded as the secondary structure of chromatin. Chromatin fibers are further organized into other higher-levels of chromatin structures, but so far details of these structural levels still remain obscure. The three-dimensional (3D) organization of genomic DNA plays a critical role in regulating DNA-related biological processes, such as gene transcription and DNA replication, repair, and recombination. Elucidating the structure and dynamics of chromatin fibers in molecular details is the key to understanding the epigenetic regulation of gene expression by different chromatin factors. HIGH-RESOLUTION STRUCTURE OF 30-NM CHROMATIN FIBERSIt is still a puzzle how genomic DNA is hierarchically organized in eukaryotic cells. From a structural point of view, the DNA double-helix structure discovered by Watson and Crick is surely the most important milestone in molecular biology (Watson and Crick 1953). After more than 40 years, the high-resolution structure of the nucleosome core particle (NCP) has been defined by crystal Xray studies (Luger et al. 1997), which undoubtedly reveals the structural details of histone-histone and histone-DNA interactions within nucleosomes (Fig. 1). Other high-resolution structures of NCPs containing core histones from different species or with a different DNA sequence, different histone variants, or different nucleosome-binding proteins/peptides have been resolved subsequently to investigate the regulation of nucleosome structure as reviewed previously (Cutter and Hayes 2015;McGinty and Tan 2015;Zhu and Li 2016).Afterward, the manner of how a "beads-on-a-string" nucleosomal array folds into a condensed 30-nm chromatin fiber remains to be determined. Two basic classes of structural models had been proposed previously based on ...

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Integrated molecular mechanism directing nucleosome reorganization by human FACT

Cited by 138 publications

References 63 publications

The Modifier of Transcription 1 (Mot1) ATPase and Spt16 Histone Chaperone Co-regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization

The Modifier of Transcription 1 (Mot1) ATPase and Spt16 Histone Chaperone Co-regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization

The CENP-T/-W complex is a binding partner of the histone chaperone FACT

Structure and Epigenetic Regulation of Chromatin Fibers

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