Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity

Vinod K umar Yadav, Ram K rishna Thakur, Bruce Eckloff, Aradhita Baral, Ankita Singh, Rashi Halder, Akinchan Kumar, Mohammad P arwez Alam, Tapas K. Kundu, Raj Pandita, Tej K. Pandita, Eric D Wieben, Shantanu Chowdhury

Research output: Contribution to journalArticle

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Abstract

Previous studies have analyzed patterns of transcription, transcription factor (TF) binding or mapped nucleosome occupancy across the genome. These suggest that the three aspects are genetically connected but the cause and effect relationships are still unknown. For example, physiologic TF binding studies involve many TFs, consequently, it is difficult to assign nucleosome reorganization to the binding site occupancy of any particular TF. Therefore, several aspects remain unclear: does TF binding influence nucleosome (re)organizations locally or impact the chromatin landscape at a more global level; are all or only a fraction of TF binding a result of reorganization in nucleosome occupancy and do all TF binding and associated changes in nucleosome occupancy result in altered gene expression? With these in mind, following characterization of two states (before and after induction of a single TF of choice) we determined: (i) genomic binding sites of the TF, (ii) promoter nucleosome occupancy and (iii) transcriptome profiles. Results demonstrated that promoter-proximal TF binding influenced expression of the target gene when it was coupled to nucleosome repositioning at or close to its binding site in most cases. In contrast, only in few cases change in target gene expression was found when TF binding occurred without local nucleosome reorganization.

Original languageEnglish (US)
Pages (from-to)9602-9611
Number of pages10
JournalNucleic Acids Research
Volume42
Issue number15
DOIs
StatePublished - Sep 1 2014

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Nucleosomes
Transcription Factors
Binding Sites
Gene Expression
Transcriptome
Chromatin
Genome

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Yadav, V. K. U., Thakur, R. K. R., Eckloff, B., Baral, A., Singh, A., Halder, R., ... Chowdhury, S. (2014). Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity. Nucleic Acids Research, 42(15), 9602-9611. https://doi.org/10.1093/nar/gku596

Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity. / Yadav, Vinod K umar; Thakur, Ram K rishna; Eckloff, Bruce; Baral, Aradhita; Singh, Ankita; Halder, Rashi; Kumar, Akinchan; Alam, Mohammad P arwez; Kundu, Tapas K.; Pandita, Raj; Pandita, Tej K.; Wieben, Eric D; Chowdhury, Shantanu.

In: Nucleic Acids Research, Vol. 42, No. 15, 01.09.2014, p. 9602-9611.

Research output: Contribution to journalArticle

Yadav, VKU, Thakur, RKR, Eckloff, B, Baral, A, Singh, A, Halder, R, Kumar, A, Alam, MPA, Kundu, TK, Pandita, R, Pandita, TK, Wieben, ED & Chowdhury, S 2014, 'Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity', Nucleic Acids Research, vol. 42, no. 15, pp. 9602-9611. https://doi.org/10.1093/nar/gku596
Yadav, Vinod K umar ; Thakur, Ram K rishna ; Eckloff, Bruce ; Baral, Aradhita ; Singh, Ankita ; Halder, Rashi ; Kumar, Akinchan ; Alam, Mohammad P arwez ; Kundu, Tapas K. ; Pandita, Raj ; Pandita, Tej K. ; Wieben, Eric D ; Chowdhury, Shantanu. / Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity. In: Nucleic Acids Research. 2014 ; Vol. 42, No. 15. pp. 9602-9611.
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