The Arp8 and Arp4 module acts as a DNA sensor controlling INO80 chromatin remodeling

Brahma, Sandipan; Ngubo, Mzwanele; Paul, Somnath; Udugama, Maheshi; Bartholomew, Blaine

doi:10.1038/s41467-018-05710-7

Cited by 69 publications

(72 citation statements)

References 37 publications

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“…To effect sliding, INO80 requires at least 40 -50 bp of free extranucleosomal DNA ahead of the nucleosome 19,20 . The region around 40 -50 bp ahead of the sliding nucleosome's edge is enganged by the Arp8 module of INO80 [21][22][23] , and disrupting the module's DNA binding via mutation abolishes sliding and reduces +1 positioning genome-wide 23 . Intriguingly, we found that the region of rigid DNA also starts ~43 bp upstream of the edge of the +1 nucleosome (Fig.…”

Section: Chromatin Remodelers Sense Dna Mechanicsmentioning

confidence: 99%

Measuring DNA mechanics on the genome scale

Basu

Bobrovnikov

Qureshi

et al. 2020

Preprint

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Mechanical deformations of DNA such as bending are ubiquitous and implicated in diverse cellular functions. However, the lack of high-throughput tools to directly measure the mechanical properties of DNA limits our understanding of whether and how DNA sequences modulate DNA mechanics and associated chromatin transactions genome-wide. We developed an assay called loop-seq to measure the intrinsic cyclizability of DNA, a proxy for DNA bendability, in high throughput. We measured the intrinsic cyclizabilities of 270,806 50 bp DNA fragments that span the entire length of S. cerevisiae chromosome V and other genomic regions, and also include random sequences. We discovered sequence-encoded regions of unusually low bendability upstream of Transcription Start Sites (TSSs). These regions disfavor the sharp DNA bending required for nucleosome formation and are co-centric with known Nucleosome Depleted Regions (NDRs). We show biochemically that low bendability of linker DNA located about 40 bp away from a nucleosome edge inhibits nucleosome sliding into the linker by the chromatin remodeler INO80. The observation explains how INO80 can create promoter-proximal nucleosomal arrays in the absence of any other factors by reading the DNA mechanical landscape. We show that chromosome wide, nucleosomes are characterized by high DNA bendability near dyads and low bendability near the linkers. This contrast increases for nucleosomes deeper into gene bodies, suggesting that DNA mechanics plays a previously unappreciated role in organizing nucleosomes far from the TSS, where nucleosome remodelers predominate. Importantly, random substitution of synonymous codons does not preserve this contrast, suggesting that the evolution of codon choice has been impacted by selective pressure to preserve sequence-encoded mechanical modulations along genes. We also provide evidence that transcription through the TSS-proximal nucleosomes is impacted by local DNA mechanics. Overall, this first genome-scale map of DNA mechanics hints at a mechanical code with broad functional implications.

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Section: Chromatin Remodelers Sense Dna Mechanicsmentioning

confidence: 99%

Measuring DNA mechanics on the genome scale

Basu

Bobrovnikov

Qureshi

et al. 2020

Preprint

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“…The affinity of the protein to DNA especially with the Hs.con sequences is low; however, we observed that compared to the cloned protein, the nuclear extracts showed higher affinity to DNA The structure and interaction of the sub-complexes of the canonical INO80 complex has been analysed; it was shown that Ino80 (via the HSA domain), Arp8 (via N-terminus) and Arp4 (via C-terminus) interact with the extranucleosomal DNA in yeast [39]. The HSA domain of Ino80 along with the spacer (protrusion region 2) was demonstrated to bind to specific nucleotides at entry DNA (nts -110/-111 and -124) [39]. In another report, the crystal structure of the Arp8 module of yeast INO80 established that the HSA domain provides a binding platform for extranucleosomal entry DNA for bringing about nucleosome sliding in yeast Ino80 [38].…”

Section: Discussionmentioning

confidence: 89%

The regulatory function of dIno80 correlates with its DNA binding activity

Jain

Maini

Narang

et al. 2019

Preprint

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Running title: DNA binding activity of dIno80 Abbreviations: dIno80, Drosophila Ino80; hIno80; human Ino80; Ino80, Inositol requiring mutant 80; ETP, Enhancer of Trithorax and Polycomb; FID, fluorescence intercalator displacement; DBINO, DNA binding domain of Ino80; EMSA, electrophoretic mobility shift assay. Highlights  dIno80 has a DNA binding domain through which it recognizes a consensus sequence and interacts with DNA.  dIno80 interacts with variants of the consensus sequence with variable affinity.  dIno80 can regulate the expression of downstream as well as upstream reporter gene.  dIno80 can complement the function of Pho and rescue Pho lethality. 2 ABSTRACTThe INO80 complex, including the Ino80 protein, forms a highly conserved canonical complex that remodels chromatin in the context of multiple cellular functions. The Drosophila homologue, dIno80, is involved in homeotic gene regulation during development as a canonical Pho-dIno80 complex. Previously, we found that dIno80 regulates homeotic genes by interacting with epigenetic regulators, such as polycomb and trithorax, suggesting the occurrence of non-canonical Ino80 complexes. Here using spectroscopic methods and gel retardation assays, we identified a set of consensus DNA sequences that DNA binding domain of dIno80 (DBINO)interacts with havingdifferential affinity and high specificity. Testing these sequences in reporters showed that this interaction can positively regulate transcription. We also demonstrated that over-expressing dIno80 can rescue the pupal lethality of pleiohomeotic (pho) deficient flies. These results suggest that, in addition to its known function as a chromatin remodeler, dIno80 has sequence preference for interaction with DNA to regulate transcription.

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“…Notably, the functional domains (ATP-and nucleotide-binding sites), which are the most crucial for ACTR8 function, are well preserved in TV2-TV6. According to a previous study, the N-terminal region of ACTR8 is critical for functional activity and N-terminal deletions have deleterious effects on the expressed protein, whereas deletions in the C-terminal region did not have such effects [29][30][31].…”

Section: Protein Structure Analysis Of Various Actr8 Gene Transcriptsmentioning

confidence: 94%

A single mutation in ACTR8 gene results in lineage-specific expression in primates

Choe

Park

Cho

et al. 2020

Preprint

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Background: Alternative splicing (AS) generate various transcripts from a single gene and thus plays a significant role in transcriptomic diversity and proteomic complexity. Alu elements are primate-specific transposable elements (TEs) and can provide a donor or acceptor site for AS. In a study on TE-mediated AS, we recently identified a novel Alu Sz6-exonized ACTR8 transcript of a crab-eating monkey ( Macaca fascicularis ). In the present study, we sought to analyse the molecular mechanism of Alu Sz6-derived exonization in ACTR8 gene.Results: We performed RT-PCR and genomic PCR using the tissue RNA and DNA samples from the crab-eating monkey and various other primates, including humans, to study Alu Sz6-derived exonization in ACTR8 gene and transcript variants expression. Alu Sz6 integration was estimated to have occurred before the divergence of simians and prosimians. The novel transcript was expressed only in Old world monkeys and apes, and humans. Lineage-specific expression of ACTR8 gene was due to a ‘G’ duplication in the Alu Sz6 sequences of Old world monkey and ape lineages. Six alternative transcripts (TV1-TV6) generated by various AS mechanisms were newly identified. Based on in-silico analysis, the alternative transcripts were transcribed into new isoforms with C-terminus deletion.Conclusion: ‘G’ duplication together with TE exonization and AS via various mechanisms resulted in a different fate of ACTR8 gene expression during primate evolution.

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The Arp8 and Arp4 module acts as a DNA sensor controlling INO80 chromatin remodeling

Cited by 69 publications

References 37 publications

Measuring DNA mechanics on the genome scale

Measuring DNA mechanics on the genome scale

The regulatory function of dIno80 correlates with its DNA binding activity

A single mutation in ACTR8 gene results in lineage-specific expression in primates

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