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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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NME2 binding sites before or after inducing NME2. (A) A Circos plot showing ChIP-seq peak distribution of NME2 on all chromosomes (1–22, and X and Y); peaks in red represent NME2 binding sites before induction; peaks in blue represent NME2 binding sites after induction (replicates are shown in both cases). Two projections from chromosomes 9 and 15 are shown. (B) Twelve-mer consensus NME2 binding motif identified using Gibbs sampler (upper panel)—distribution of the 12-mer motif within NME2 peaks constructed from read counts is shown in the lower panel.
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Figure 1: NME2 binding sites before or after inducing NME2. (A) A Circos plot showing ChIP-seq peak distribution of NME2 on all chromosomes (1–22, and X and Y); peaks in red represent NME2 binding sites before induction; peaks in blue represent NME2 binding sites after induction (replicates are shown in both cases). Two projections from chromosomes 9 and 15 are shown. (B) Twelve-mer consensus NME2 binding motif identified using Gibbs sampler (upper panel)—distribution of the 12-mer motif within NME2 peaks constructed from read counts is shown in the lower panel.

Mentions: ChIP followed by massively parallel sequencing (ChIP-seq) was performed in replicate for both conditions, before and after inducing NME2 (Figure 1A). Out of roughly 7 million sequence reads, >80% uniquely aligned to the reference human genome in each case (Supplementary Figure S2a). Using ChIP-seq reads enriched in NME2 relative to IgG, we found 2005 and 11 017 peaks before and after inducing NME2 in A549 cells, respectively. Although, number of NME2 binding sites increased after induction, a close inspection of peaks (sites of NME2 binding to DNA) showed that their chromosome-wise distribution was largely similar in both cases (Figure 1A: Circos plot, and Supplementary Figures S2b and c). The replicates were also similar (Figure 1A: Circos plot, and Supplementary Figure S2d). The frequency of TFBSs was also largely similar before and after induction of NME2 (Supplementary Figure S2e). A 12-mer consensus motif identified using Gibbs sampler (30) was present in >70% of the ChIP-seq peaks (Figure 1B upper panel). We noted that the motif found from ChIP-seq was similar to the one reported earlier from analysis of a single promoter (31) and unpublished data of Thakur et al. (submitted for publication) As expected, in more than 50% cases the NME2 motif occurred within 50 bp of the center of peak (Figure 1B lower panel). We next performed transcriptome profiling of A549 cells before and after NME2 induction. Comparative analysis of the expression profiles revealed 1679 genes as differentially expressed (781 genes were up and 898 genes down regulated (P < 0.05)) in NME2-induced cells; out of these we found at least one NME2 binding site (in the induced condition) within 10 kb of the TSS in as many as 1235 genes.


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)

NME2 binding sites before or after inducing NME2. (A) A Circos plot showing ChIP-seq peak distribution of NME2 on all chromosomes (1–22, and X and Y); peaks in red represent NME2 binding sites before induction; peaks in blue represent NME2 binding sites after induction (replicates are shown in both cases). Two projections from chromosomes 9 and 15 are shown. (B) Twelve-mer consensus NME2 binding motif identified using Gibbs sampler (upper panel)—distribution of the 12-mer motif within NME2 peaks constructed from read counts is shown in the lower panel.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: NME2 binding sites before or after inducing NME2. (A) A Circos plot showing ChIP-seq peak distribution of NME2 on all chromosomes (1–22, and X and Y); peaks in red represent NME2 binding sites before induction; peaks in blue represent NME2 binding sites after induction (replicates are shown in both cases). Two projections from chromosomes 9 and 15 are shown. (B) Twelve-mer consensus NME2 binding motif identified using Gibbs sampler (upper panel)—distribution of the 12-mer motif within NME2 peaks constructed from read counts is shown in the lower panel.
Mentions: ChIP followed by massively parallel sequencing (ChIP-seq) was performed in replicate for both conditions, before and after inducing NME2 (Figure 1A). Out of roughly 7 million sequence reads, >80% uniquely aligned to the reference human genome in each case (Supplementary Figure S2a). Using ChIP-seq reads enriched in NME2 relative to IgG, we found 2005 and 11 017 peaks before and after inducing NME2 in A549 cells, respectively. Although, number of NME2 binding sites increased after induction, a close inspection of peaks (sites of NME2 binding to DNA) showed that their chromosome-wise distribution was largely similar in both cases (Figure 1A: Circos plot, and Supplementary Figures S2b and c). The replicates were also similar (Figure 1A: Circos plot, and Supplementary Figure S2d). The frequency of TFBSs was also largely similar before and after induction of NME2 (Supplementary Figure S2e). A 12-mer consensus motif identified using Gibbs sampler (30) was present in >70% of the ChIP-seq peaks (Figure 1B upper panel). We noted that the motif found from ChIP-seq was similar to the one reported earlier from analysis of a single promoter (31) and unpublished data of Thakur et al. (submitted for publication) As expected, in more than 50% cases the NME2 motif occurred within 50 bp of the center of peak (Figure 1B lower panel). We next performed transcriptome profiling of A549 cells before and after NME2 induction. Comparative analysis of the expression profiles revealed 1679 genes as differentially expressed (781 genes were up and 898 genes down regulated (P < 0.05)) in NME2-induced cells; out of these we found at least one NME2 binding site (in the induced condition) within 10 kb of the TSS in as many as 1235 genes.

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