Limits...
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.

Show MeSH
Brm knockdown alters nucleosome organizations. (A) Nucleosome occupancy changes throughout each chromosome. The genome is scanned with a 200-bp window. The ratio of normalized nucleosome occupancy after over before Brm knockdown within each window is presented by a color. Red indicates the regions where occupancy increases by two or more folds after knockdown. Green indicates the regions where occupancy decreases by two or more folds after knockdown. Yellow indicates the regions with unchanged occupancy, i.e. the ratio is <2-fold. (B) The enrichment of nucleosome occupancy change in different genomic regions. The enrichment of nucleosome occupancy increase/decrease in promoters equals to the number of red/green windows in (A) locating in promoters normalized by the length of promoters. The enrichment of nucleosome occupancy change in genic and intergenic regions are calculated in the same way. (C) Left schematic diagram illustrates nucleosome position shift. The curve plot shows the cumulative frequency of position shift after knockdown. (D) The enrichment of the shifted nucleosomes in the different genomic regions. (E) Left schematic diagram illustrates nucleosome gain and loss. The bar plot shows the enrichment of the nucleosome gain and loss in the different genomic regions. (F) Left schematic diagram illustrates nucleosome fuzziness change. The bar plot shows the enrichment of the nucleosomes whose fuzziness is changed in the different genomic regions. The nucleosome enrichment in (D, E, F) equals to the number of each category of nucleosomes in a given genomic region normalized by the length of corresponding genomic regions (see ‘Materials and Methods’ section for details). KD, knockdown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4150808&req=5

Figure 2: Brm knockdown alters nucleosome organizations. (A) Nucleosome occupancy changes throughout each chromosome. The genome is scanned with a 200-bp window. The ratio of normalized nucleosome occupancy after over before Brm knockdown within each window is presented by a color. Red indicates the regions where occupancy increases by two or more folds after knockdown. Green indicates the regions where occupancy decreases by two or more folds after knockdown. Yellow indicates the regions with unchanged occupancy, i.e. the ratio is <2-fold. (B) The enrichment of nucleosome occupancy change in different genomic regions. The enrichment of nucleosome occupancy increase/decrease in promoters equals to the number of red/green windows in (A) locating in promoters normalized by the length of promoters. The enrichment of nucleosome occupancy change in genic and intergenic regions are calculated in the same way. (C) Left schematic diagram illustrates nucleosome position shift. The curve plot shows the cumulative frequency of position shift after knockdown. (D) The enrichment of the shifted nucleosomes in the different genomic regions. (E) Left schematic diagram illustrates nucleosome gain and loss. The bar plot shows the enrichment of the nucleosome gain and loss in the different genomic regions. (F) Left schematic diagram illustrates nucleosome fuzziness change. The bar plot shows the enrichment of the nucleosomes whose fuzziness is changed in the different genomic regions. The nucleosome enrichment in (D, E, F) equals to the number of each category of nucleosomes in a given genomic region normalized by the length of corresponding genomic regions (see ‘Materials and Methods’ section for details). KD, knockdown.

Mentions: We aligned the nucleosomal reads from MNase-seq against Drosophila genome. The read count in a given region indicates its nucleosome occupancy. We compared the genome-wide nucleosome occupancy before and after Brm knockdown. The results showed that nucleosome occupancy changes spread out the entire genome after Brm knockdown (Figure 2A and Supplementary Figure S3). To examine whether there is a bias in the distribution of nucleosome occupancy change in different genomic regions, we calculated the enrichment of nucleosome occupancy change in promoter, genic and intergenic regions. Our results showed a similar level of nucleosome occupancy increase in the all three genomic regions. In contrast, promoter and intergenic regions had higher enrichment of nucleosome occupancy decrease than genic regions. Moreover, nucleosome occupancy decrease was sufficiently higher than occupancy increase in either of the genomic regions (Figure 2B). This was partially attributed to the fact that Brahma-containing remodeling complexes (P)BAP promoted formation of nucleosome at their target sequences (30).


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)

Brm knockdown alters nucleosome organizations. (A) Nucleosome occupancy changes throughout each chromosome. The genome is scanned with a 200-bp window. The ratio of normalized nucleosome occupancy after over before Brm knockdown within each window is presented by a color. Red indicates the regions where occupancy increases by two or more folds after knockdown. Green indicates the regions where occupancy decreases by two or more folds after knockdown. Yellow indicates the regions with unchanged occupancy, i.e. the ratio is <2-fold. (B) The enrichment of nucleosome occupancy change in different genomic regions. The enrichment of nucleosome occupancy increase/decrease in promoters equals to the number of red/green windows in (A) locating in promoters normalized by the length of promoters. The enrichment of nucleosome occupancy change in genic and intergenic regions are calculated in the same way. (C) Left schematic diagram illustrates nucleosome position shift. The curve plot shows the cumulative frequency of position shift after knockdown. (D) The enrichment of the shifted nucleosomes in the different genomic regions. (E) Left schematic diagram illustrates nucleosome gain and loss. The bar plot shows the enrichment of the nucleosome gain and loss in the different genomic regions. (F) Left schematic diagram illustrates nucleosome fuzziness change. The bar plot shows the enrichment of the nucleosomes whose fuzziness is changed in the different genomic regions. The nucleosome enrichment in (D, E, F) equals to the number of each category of nucleosomes in a given genomic region normalized by the length of corresponding genomic regions (see ‘Materials and Methods’ section for details). KD, knockdown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Brm knockdown alters nucleosome organizations. (A) Nucleosome occupancy changes throughout each chromosome. The genome is scanned with a 200-bp window. The ratio of normalized nucleosome occupancy after over before Brm knockdown within each window is presented by a color. Red indicates the regions where occupancy increases by two or more folds after knockdown. Green indicates the regions where occupancy decreases by two or more folds after knockdown. Yellow indicates the regions with unchanged occupancy, i.e. the ratio is <2-fold. (B) The enrichment of nucleosome occupancy change in different genomic regions. The enrichment of nucleosome occupancy increase/decrease in promoters equals to the number of red/green windows in (A) locating in promoters normalized by the length of promoters. The enrichment of nucleosome occupancy change in genic and intergenic regions are calculated in the same way. (C) Left schematic diagram illustrates nucleosome position shift. The curve plot shows the cumulative frequency of position shift after knockdown. (D) The enrichment of the shifted nucleosomes in the different genomic regions. (E) Left schematic diagram illustrates nucleosome gain and loss. The bar plot shows the enrichment of the nucleosome gain and loss in the different genomic regions. (F) Left schematic diagram illustrates nucleosome fuzziness change. The bar plot shows the enrichment of the nucleosomes whose fuzziness is changed in the different genomic regions. The nucleosome enrichment in (D, E, F) equals to the number of each category of nucleosomes in a given genomic region normalized by the length of corresponding genomic regions (see ‘Materials and Methods’ section for details). KD, knockdown.
Mentions: We aligned the nucleosomal reads from MNase-seq against Drosophila genome. The read count in a given region indicates its nucleosome occupancy. We compared the genome-wide nucleosome occupancy before and after Brm knockdown. The results showed that nucleosome occupancy changes spread out the entire genome after Brm knockdown (Figure 2A and Supplementary Figure S3). To examine whether there is a bias in the distribution of nucleosome occupancy change in different genomic regions, we calculated the enrichment of nucleosome occupancy change in promoter, genic and intergenic regions. Our results showed a similar level of nucleosome occupancy increase in the all three genomic regions. In contrast, promoter and intergenic regions had higher enrichment of nucleosome occupancy decrease than genic regions. Moreover, nucleosome occupancy decrease was sufficiently higher than occupancy increase in either of the genomic regions (Figure 2B). This was partially attributed to the fact that Brahma-containing remodeling complexes (P)BAP promoted formation of nucleosome at their target sequences (30).

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