Poly-dA:dT Tracts Form an In Vivo Nucleosomal Turnstile

Boer, Carl G. de; Hughes, Timothy R.

doi:10.1371/journal.pone.0110479

Cited by 16 publications

(30 citation statements)

References 12 publications

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“…Related to this observation, we also show that nucleosome displacement is asymmetric with respect to the motifs, with a stronger effect observed on the 5' side of polyA motifs, recapitulating a recent observation made by studies of an in vitro nucleosome assembly system using purified components, including RSC and various PTFs (Krietenstein et al, 2016). Our findings may explain the earlier observation of an asymmetric arrangement of nucleosomes around polyA tracts in vivo (de Boer and Hughes, 2014;Wu and Li, 2010).…”

Section: The Role Of Dna Sequence In Shaping Promoter Nucleosome Archsupporting

confidence: 90%

Sequence-directed action of RSC remodeler and pioneer factors positions +1 nucleosome to facilitate transcription

Kubik¹,

O’Duibhir

et al. 2018

Preprint

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Accessible chromatin is important for RNA polymerase II recruitment and transcription initiation at eukaryotic promoters. We investigated the mechanistic links between promoter DNA sequence, nucleosome positioning and transcription. Our results indicate that precise positioning of the transcription start site-associated +1 nucleosome in yeast is critical for efficient TBP binding, and is driven by two key factors, the essential chromatin remodeler RSC and a small set of ubiquitous pioneer transcription factors. We find no evidence for recruitment of RSC by pioneer factors, but show instead that the strength and directionality of RSC action on nucleosomes depends upon the arrangement of two specific DNA motifs that promote its binding and nucleosome displacement activity at promoters. Thus, despite their widespread co-localization, RSC and pioneer factors predominantly act independently to generate accessible chromatin. Our results provide insight into how promoter DNA sequence instructs trans-acting factors to control nucleosome architecture and stimulate transcription initiation.(149 words)

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Section: The Role Of Dna Sequence In Shaping Promoter Nucleosome Archsupporting

confidence: 90%

Sequence-directed action of RSC remodeler and pioneer factors positions +1 nucleosome to facilitate transcription

Kubik¹,

O’Duibhir

et al. 2018

Preprint

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“…This suggests a mechanism whereby RSC, but not other remodelers, translates poly(dA:dT) orientation into directional displacement of nucleosomes (Figure 2D). Consequently, the canonical or average location of poly(dT) would be ~30 bp upstream of poly(dA) when genes are aligned at their +1 nucleosomes (Figure 2A, graph 2, and Figure S3C), as has been observed in vivo but has not been previously linked to directional action of RSC (de Boer and Hughes, 2014; Wu and Li, 2010). …”

Section: Resultsmentioning

confidence: 80%

Genomic Nucleosome Organization Reconstituted with Pure Proteins

Krietenstein

Wal

Watanabe

et al. 2016

Cell

255

396

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Summary Chromatin remodelers regulate genes by organizing nucleosomes around promoters, but their individual contributions are obfuscated by the complex in vivo milieu of factor redundancy and indirect effects. Genome-wide reconstitution of promoter nucleosome organization with purified proteins resolves this problem and is therefore a critical goal. Here we reconstitute four stages of nucleosome architecture using purified components: Yeast genomic DNA, histones, sequence-specific Abf1/Reb1, and remodelers RSC, ISW2, INO80, and ISW1a. We identify direct, specific and sufficient contributions that in vivo observations validate. First, RSC clears promoters by translating poly(dA:dT) into directional nucleosome removal. Second, partial redundancy is recapitulated where INO80 alone, or ISW2 at Abf1/Reb1sites, positions +1 nucleosomes. Third, INO80 and ISW2 each align downstream nucleosomal arrays. Fourth, ISW1a tightens the spacing to canonical repeat lengths. Such a minimal set of rules and proteins establishes core mechanisms by which promoter chromatin architecture arises through a blend of redundancy and specialization.

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“…This motif is similar to motifs reported in earlier studies 5 , 8 and associated with nucleosome boundaries. 38 Besides the poly-T/poly-A motif, a 15bp TATA-repeat was discovered. Both the TATA-repeat and poly-T/poly-A motif were reported for the first time and further studies are required to establish the functional correlation.…”

Section: Resultsmentioning

confidence: 99%

Low-coverage resequencing detects meiotic recombination pattern and features in tomato RILs

et al. 2017

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Traditional plant breeding relies on meiotic recombination for mixing of parental alleles to create novel allele combinations. Detailed analysis of recombination patterns in model organisms shows that recombination is tightly regulated within the genome, but frequencies vary extensively along chromosomes. Despite being a model organism for fruit developmental studies, high-resolution recombination patterns are lacking in tomato. In this study, we developed a novel methodology to use low-coverage resequencing to identify genome-wide recombination patterns and applied this methodology on 60 tomato Recombinant Inbred Lines (RILs). Our methodology identifies polymorphic markers from the low-coverage resequencing population data and utilizes the same data to locate the recombination breakpoints in individuals by using a variable sliding window. We identified 1,445 recombination sites comprising 112 recombination prone regions enriched for AT-rich DNA motifs. Furthermore, the recombination prone regions in tomato preferably occurred in gene promoters over intergenic regions, an observation consistent with Arabidopsis thaliana, Zea mays and Mimulus guttatus. Overall, our cost effective method and findings enhance the understanding of meiotic recombination in tomato and suggest evolutionarily conserved recombination associated genomic features.

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Poly-dA:dT Tracts Form an In Vivo Nucleosomal Turnstile

Cited by 16 publications

References 12 publications

Sequence-directed action of RSC remodeler and pioneer factors positions +1 nucleosome to facilitate transcription

Sequence-directed action of RSC remodeler and pioneer factors positions +1 nucleosome to facilitate transcription

Genomic Nucleosome Organization Reconstituted with Pure Proteins

Low-coverage resequencing detects meiotic recombination pattern and features in tomato RILs

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