Limits...
Recruitment of the ATP-dependent chromatin remodeler dMi-2 to the transcribed region of active heat shock genes.

Mathieu EL, Finkernagel F, Murawska M, Scharfe M, Jarek M, Brehm A - Nucleic Acids Res. (2012)

Bottom Line: Interestingly, dMi-2 binding extends several hundred base pairs beyond the polyadenylation site into the region where transcriptional termination occurs.We find that dMi-2 does not associate with the entire nucleosome-depleted hsp70 locus 87A.Rather, dMi-2 binding is restricted to transcribed regions.

View Article: PubMed Central - PubMed

Affiliation: Institute for Molecular Biology and Tumor Research, Philipps-University, Emil-Mannkopff-Strasse 2, 35037 Marburg, Germany.

ABSTRACT
The ATP-dependent chromatin remodeler dMi-2 can play both positive and negative roles in gene transcription. Recently, we have shown that dMi-2 is recruited to the hsp70 gene in a heat shock-dependent manner, and is required to achieve high transcript levels. Here, we use chromatin immunoprecipitation sequencing (ChIP-Seq) to identify other chromatin regions displaying increased dMi-2 binding upon heat shock and to characterize the distribution of dMi-2 over heat shock genes. We show that dMi-2 is recruited to the body of at least seven heat shock genes. Interestingly, dMi-2 binding extends several hundred base pairs beyond the polyadenylation site into the region where transcriptional termination occurs. We find that dMi-2 does not associate with the entire nucleosome-depleted hsp70 locus 87A. Rather, dMi-2 binding is restricted to transcribed regions. Our results suggest that dMi-2 distribution over active heat shock genes are determined by transcriptional activity.

Show MeSH

Related in: MedlinePlus

Seven chromosomal regions display increased dMi-2 binding after heat shock. (A) ChIP-Seq identified seven regions which displayed increased dMi-2 binding after heat shock. Chromosomal locations, lengths and fold-enrichment (HS/NHS) are given in the table. Genome browser images of dMi-2 ChIP-Seq tracks from control (NHS) and heat-shocked (HS) cells are shown. Reads are displayed as coverage per base pair (Y axis). (B) All seven regions are close to or overlap with known heat shock genes. Genome browser images of dMi-2 (red) and IgG (green) ChIP-Seq tracks from control (NHS) and heat-shocked (HS) cells are shown. Reads are displayed as coverage per base pair (Y axis). (C) Validation of ChIP-Seq data by ChIP-qPCR. Regions of hsp70, hsp26 and CG3884 that were analysed by dMi-2 and IgG ChIP-qPCR are indicated below the ChIP-Seq profile which is reproduced for comparison. Error bars denote standard deviations from three (hsp70) or two (hsp26, CG3884) biological replicates.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3367206&req=5

gks178-F2: Seven chromosomal regions display increased dMi-2 binding after heat shock. (A) ChIP-Seq identified seven regions which displayed increased dMi-2 binding after heat shock. Chromosomal locations, lengths and fold-enrichment (HS/NHS) are given in the table. Genome browser images of dMi-2 ChIP-Seq tracks from control (NHS) and heat-shocked (HS) cells are shown. Reads are displayed as coverage per base pair (Y axis). (B) All seven regions are close to or overlap with known heat shock genes. Genome browser images of dMi-2 (red) and IgG (green) ChIP-Seq tracks from control (NHS) and heat-shocked (HS) cells are shown. Reads are displayed as coverage per base pair (Y axis). (C) Validation of ChIP-Seq data by ChIP-qPCR. Regions of hsp70, hsp26 and CG3884 that were analysed by dMi-2 and IgG ChIP-qPCR are indicated below the ChIP-Seq profile which is reproduced for comparison. Error bars denote standard deviations from three (hsp70) or two (hsp26, CG3884) biological replicates.

Mentions: Next, we sought to identify chromatin regions displaying a significant HS-dependent increase in dMi-2 binding. We found seven regions, ranging in length from 1 to 9 kb that exhibited a 3.3- to 10.6-fold increase in dMi-2 binding in HS-treated cells (Figure 2A).Figure 2.


Recruitment of the ATP-dependent chromatin remodeler dMi-2 to the transcribed region of active heat shock genes.

Mathieu EL, Finkernagel F, Murawska M, Scharfe M, Jarek M, Brehm A - Nucleic Acids Res. (2012)

Seven chromosomal regions display increased dMi-2 binding after heat shock. (A) ChIP-Seq identified seven regions which displayed increased dMi-2 binding after heat shock. Chromosomal locations, lengths and fold-enrichment (HS/NHS) are given in the table. Genome browser images of dMi-2 ChIP-Seq tracks from control (NHS) and heat-shocked (HS) cells are shown. Reads are displayed as coverage per base pair (Y axis). (B) All seven regions are close to or overlap with known heat shock genes. Genome browser images of dMi-2 (red) and IgG (green) ChIP-Seq tracks from control (NHS) and heat-shocked (HS) cells are shown. Reads are displayed as coverage per base pair (Y axis). (C) Validation of ChIP-Seq data by ChIP-qPCR. Regions of hsp70, hsp26 and CG3884 that were analysed by dMi-2 and IgG ChIP-qPCR are indicated below the ChIP-Seq profile which is reproduced for comparison. Error bars denote standard deviations from three (hsp70) or two (hsp26, CG3884) biological replicates.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3367206&req=5

gks178-F2: Seven chromosomal regions display increased dMi-2 binding after heat shock. (A) ChIP-Seq identified seven regions which displayed increased dMi-2 binding after heat shock. Chromosomal locations, lengths and fold-enrichment (HS/NHS) are given in the table. Genome browser images of dMi-2 ChIP-Seq tracks from control (NHS) and heat-shocked (HS) cells are shown. Reads are displayed as coverage per base pair (Y axis). (B) All seven regions are close to or overlap with known heat shock genes. Genome browser images of dMi-2 (red) and IgG (green) ChIP-Seq tracks from control (NHS) and heat-shocked (HS) cells are shown. Reads are displayed as coverage per base pair (Y axis). (C) Validation of ChIP-Seq data by ChIP-qPCR. Regions of hsp70, hsp26 and CG3884 that were analysed by dMi-2 and IgG ChIP-qPCR are indicated below the ChIP-Seq profile which is reproduced for comparison. Error bars denote standard deviations from three (hsp70) or two (hsp26, CG3884) biological replicates.
Mentions: Next, we sought to identify chromatin regions displaying a significant HS-dependent increase in dMi-2 binding. We found seven regions, ranging in length from 1 to 9 kb that exhibited a 3.3- to 10.6-fold increase in dMi-2 binding in HS-treated cells (Figure 2A).Figure 2.

Bottom Line: Interestingly, dMi-2 binding extends several hundred base pairs beyond the polyadenylation site into the region where transcriptional termination occurs.We find that dMi-2 does not associate with the entire nucleosome-depleted hsp70 locus 87A.Rather, dMi-2 binding is restricted to transcribed regions.

View Article: PubMed Central - PubMed

Affiliation: Institute for Molecular Biology and Tumor Research, Philipps-University, Emil-Mannkopff-Strasse 2, 35037 Marburg, Germany.

ABSTRACT
The ATP-dependent chromatin remodeler dMi-2 can play both positive and negative roles in gene transcription. Recently, we have shown that dMi-2 is recruited to the hsp70 gene in a heat shock-dependent manner, and is required to achieve high transcript levels. Here, we use chromatin immunoprecipitation sequencing (ChIP-Seq) to identify other chromatin regions displaying increased dMi-2 binding upon heat shock and to characterize the distribution of dMi-2 over heat shock genes. We show that dMi-2 is recruited to the body of at least seven heat shock genes. Interestingly, dMi-2 binding extends several hundred base pairs beyond the polyadenylation site into the region where transcriptional termination occurs. We find that dMi-2 does not associate with the entire nucleosome-depleted hsp70 locus 87A. Rather, dMi-2 binding is restricted to transcribed regions. Our results suggest that dMi-2 distribution over active heat shock genes are determined by transcriptional activity.

Show MeSH
Related in: MedlinePlus