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

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 - Nucleic Acids Res. (2014)

Bottom Line: 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?

View Article: PubMed Central - PubMed

Affiliation: GNR Center for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi, India.

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TF binding and nucleosome repositioning models analyzed in this study. Nucleosome shift in the vicinity of TF binding results in repositioning of the −1 nucleosome (upper panel), whereas co-occupancy (center panel) or target site binding that has no associated nucleosome repositioning in close vicinity either before or after induction of the TF (lower panel) shows no significant change in −1 or +1 nucleosome positions. Percentage of nucleosomes is based on genome-wide total for respective cases; to avoid arbitrary assignment genes were considered in more than one category where applicable.
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Figure 5: TF binding and nucleosome repositioning models analyzed in this study. Nucleosome shift in the vicinity of TF binding results in repositioning of the −1 nucleosome (upper panel), whereas co-occupancy (center panel) or target site binding that has no associated nucleosome repositioning in close vicinity either before or after induction of the TF (lower panel) shows no significant change in −1 or +1 nucleosome positions. Percentage of nucleosomes is based on genome-wide total for respective cases; to avoid arbitrary assignment genes were considered in more than one category where applicable.

Mentions: A549 cells depleted for NME2 were generated using commercially available short hairpin RNAs (from Origene Inc., USA; catalog no. TR311160) and stable cell clones were selected in presence of puromycin. For analysis of nucleosome repositioning, we considered a distance of 300 bp (+/− 150 bases), in other words, a nucleosome was denoted as repositioned in the NME2-induced condition when detected beyond 300 bp of a nucleosome found in the cells before NME2 induction. In order to avoid arbitrary assignments, in cases where a gene belonged to more than one category (while assigning NME2 nucleosome associations during repositioning analysis (Figure 5)) it was considered in all the respective cases.


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

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 - Nucleic Acids Res. (2014)

TF binding and nucleosome repositioning models analyzed in this study. Nucleosome shift in the vicinity of TF binding results in repositioning of the −1 nucleosome (upper panel), whereas co-occupancy (center panel) or target site binding that has no associated nucleosome repositioning in close vicinity either before or after induction of the TF (lower panel) shows no significant change in −1 or +1 nucleosome positions. Percentage of nucleosomes is based on genome-wide total for respective cases; to avoid arbitrary assignment genes were considered in more than one category where applicable.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150765&req=5

Figure 5: TF binding and nucleosome repositioning models analyzed in this study. Nucleosome shift in the vicinity of TF binding results in repositioning of the −1 nucleosome (upper panel), whereas co-occupancy (center panel) or target site binding that has no associated nucleosome repositioning in close vicinity either before or after induction of the TF (lower panel) shows no significant change in −1 or +1 nucleosome positions. Percentage of nucleosomes is based on genome-wide total for respective cases; to avoid arbitrary assignment genes were considered in more than one category where applicable.
Mentions: A549 cells depleted for NME2 were generated using commercially available short hairpin RNAs (from Origene Inc., USA; catalog no. TR311160) and stable cell clones were selected in presence of puromycin. For analysis of nucleosome repositioning, we considered a distance of 300 bp (+/− 150 bases), in other words, a nucleosome was denoted as repositioned in the NME2-induced condition when detected beyond 300 bp of a nucleosome found in the cells before NME2 induction. In order to avoid arbitrary assignments, in cases where a gene belonged to more than one category (while assigning NME2 nucleosome associations during repositioning analysis (Figure 5)) it was considered in all the respective cases.

Bottom Line: 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?

View Article: PubMed Central - PubMed

Affiliation: GNR Center for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi, India.

Show MeSH