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Title: Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity
Authors: Yadav, Vinod Kumar
Thakur, Ram Krishna
Eckloff, Bruce
Baral, Aradhita
Singh, Ankita
Halder, Rashi
Kumar, Akinchan
Alam, Mohammad Parwez
Kundu, Tapas Kumar
Pandita, Raj
Pandita, Tej K.
Wieben, Eric D.
Chowdhury, Shantanu
Keywords: Biochemistry & Molecular Biology
Nm23/Nucleoside Diphosphate Kinase
Histone Modifications
Cancer Metastasis
Cell Invasion
Human Genome
Issue Date: 2014
Publisher: Oxford University Press
Citation: Yadav, VK; Thakur, RK; Eckloff, B; Baral, A; Singh, A; Halder, R; Kumar, A; Alam, MP; Kundu, TK; Pandita, R; Pandita, TK; Wieben, ED; Chowdhury, S, Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity. Nucleic Acids Research 2014, 42 (15) 9602-9611,
Nucleic Acids Research
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.
Description: Open Access
ISSN: 0305-1048
Appears in Collections:Research Papers (Tapas K. Kundu)

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