title: Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity.
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.
authors: GNR Center for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi, India.
authors: Vinod Kumar
authors: VK
authors: Yadav
authors: Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, Delhi, India.
authors: Ram Krishna
authors: RK
authors: Thakur
authors: Advanced Genomics Technology Center, Mayo Clinic, Rochester, MN, USA.
authors: Bruce
authors: B
authors: Eckloff
authors: Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, Delhi, India.
authors: Aradhita
authors: A
authors: Baral
authors: Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, Delhi, India.
authors: Ankita
authors: A
authors: Singh
authors: GNR Center for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi, India.
authors: Rashi
authors: R
authors: Halder
authors: Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, Delhi, India.
authors: Akinchan
authors: A
authors: Kumar
authors: Dr B.R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi 110 007, India.
authors: Mohammad Parwez
authors: MP
authors: Alam
authors: Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, India.
authors: Tapas K
authors: TK
authors: Kundu
authors: Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030, USA.
authors: Raj
authors: R
authors: Pandita
authors: Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030, USA.
authors: Tej K
authors: TK
authors: Pandita
authors: Advanced Genomics Technology Center, Mayo Clinic, Rochester, MN, USA.
authors: Eric D
authors: ED
authors: Wieben
authors: GNR Center for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi, India Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, Delhi, India shantanuc@igib.res.in.
authors: Shantanu
authors: S
authors: Chowdhury
mesh_terms: D001665:Binding Sites; D045744:Cell Line, Tumor; D015894:Genome, Human; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics; D054778:NM23 Nucleoside Diphosphate Kinases / Q000378:metabolism; D009707:Nucleosomes / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D054778:NM23 Nucleoside Diphosphate Kinases; D009707:Nucleosomes; D014157:Transcription Factors; C517940:NME2 protein, human