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Drosophila Brahma complex remodels nucleosome organizations in multiple aspects.

Shi J, Zheng M, Ye Y, Li M, Chen X, Hu X, Sun J, Zhang X, Jiang C - Nucleic Acids Res. (2014)

Bottom Line: The results show that Brm knockdown leads to nucleosome occupancy changes throughout the entire genome with a bias in occupancy decrease.Nucleosome arrays around the 5' ends of genes are reorganized in five patterns as a result of Brm knockdown.Further analyses reveal abundance of AT-rich motifs for transcription factors in the remodeling regions.

View Article: PubMed Central - PubMed

Affiliation: Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.

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Distribution of Brahma-dependent remodeling regions (RRs) regulating gene transcription. (A) RRs are enriched in promoter regions. (B) Distribution of RRs around TSS. (C) Scatter plot compares the transcription level of the genes whose TSS located within 1 kb of these RRs before and after Brm knockdown, and highlights the differentially expressed ones in red and green (2-fold, P < 0.01, t-test). (D) GO term analysis for the differentially expressed genes in (C). (E) Sequence composition of the top 10 motifs identified in RRs. W = AT, Y = CT, R = AG, K = GT.
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Figure 4: Distribution of Brahma-dependent remodeling regions (RRs) regulating gene transcription. (A) RRs are enriched in promoter regions. (B) Distribution of RRs around TSS. (C) Scatter plot compares the transcription level of the genes whose TSS located within 1 kb of these RRs before and after Brm knockdown, and highlights the differentially expressed ones in red and green (2-fold, P < 0.01, t-test). (D) GO term analysis for the differentially expressed genes in (C). (E) Sequence composition of the top 10 motifs identified in RRs. W = AT, Y = CT, R = AG, K = GT.

Mentions: To systematically identify Brahma-dependent chromatin remodeling regions, we developed a comparative approach to detect difference in nucleosome occupancy before and after Brm knockdown. The analysis identified 3758 remodeling regions that were enriched in the promoter regions. Particularly, there was abundance of the remodeling regions adjacently upstream of TSS (Figure 4A and B). We further collected 1301 genes whose TSS located within 1 kb of these remodeling regions. Only 14.3% of these genes were differentially expressed. Seventy genes were up-regulated and 116 genes were down-regulated after Brm knockdown (Figure 4C). Intriguingly, changes of these gene expression affected embryonic development and morphogenesis (Figure 4D).


Drosophila Brahma complex remodels nucleosome organizations in multiple aspects.

Shi J, Zheng M, Ye Y, Li M, Chen X, Hu X, Sun J, Zhang X, Jiang C - Nucleic Acids Res. (2014)

Distribution of Brahma-dependent remodeling regions (RRs) regulating gene transcription. (A) RRs are enriched in promoter regions. (B) Distribution of RRs around TSS. (C) Scatter plot compares the transcription level of the genes whose TSS located within 1 kb of these RRs before and after Brm knockdown, and highlights the differentially expressed ones in red and green (2-fold, P < 0.01, t-test). (D) GO term analysis for the differentially expressed genes in (C). (E) Sequence composition of the top 10 motifs identified in RRs. W = AT, Y = CT, R = AG, K = GT.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150808&req=5

Figure 4: Distribution of Brahma-dependent remodeling regions (RRs) regulating gene transcription. (A) RRs are enriched in promoter regions. (B) Distribution of RRs around TSS. (C) Scatter plot compares the transcription level of the genes whose TSS located within 1 kb of these RRs before and after Brm knockdown, and highlights the differentially expressed ones in red and green (2-fold, P < 0.01, t-test). (D) GO term analysis for the differentially expressed genes in (C). (E) Sequence composition of the top 10 motifs identified in RRs. W = AT, Y = CT, R = AG, K = GT.
Mentions: To systematically identify Brahma-dependent chromatin remodeling regions, we developed a comparative approach to detect difference in nucleosome occupancy before and after Brm knockdown. The analysis identified 3758 remodeling regions that were enriched in the promoter regions. Particularly, there was abundance of the remodeling regions adjacently upstream of TSS (Figure 4A and B). We further collected 1301 genes whose TSS located within 1 kb of these remodeling regions. Only 14.3% of these genes were differentially expressed. Seventy genes were up-regulated and 116 genes were down-regulated after Brm knockdown (Figure 4C). Intriguingly, changes of these gene expression affected embryonic development and morphogenesis (Figure 4D).

Bottom Line: The results show that Brm knockdown leads to nucleosome occupancy changes throughout the entire genome with a bias in occupancy decrease.Nucleosome arrays around the 5' ends of genes are reorganized in five patterns as a result of Brm knockdown.Further analyses reveal abundance of AT-rich motifs for transcription factors in the remodeling regions.

View Article: PubMed Central - PubMed

Affiliation: Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.

Show MeSH