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Chd1 co-localizes with early transcription elongation factors independently of H3K36 methylation and releases stalled RNA polymerase II at introns.

Park D, Shivram H, Iyer VR - Epigenetics Chromatin (2014)

Bottom Line: Using genome-wide approaches, we found that the loss of Chd1 significantly disrupted nucleosome arrays within the gene bodies of highly transcribed genes.We also found that Chd1 is physically recruited to gene bodies, and that its occupancy specifically corresponds to that of the early elongating form of RNA polymerase, RNAPII Ser 5-P.We also found that deletion of the histone methyltransferase for H3K36 (SET2) did not affect either Chd1 occupancy or nucleosome organization genome-wide.

View Article: PubMed Central - PubMed

Affiliation: Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas, 2500 Speedway, Austin, TX 78712 USA.

ABSTRACT

Background: Chromatin consists of ordered nucleosomal arrays that are controlled by highly conserved adenosine triphosphate (ATP)-dependent chromatin remodeling complexes. One such remodeler, chromodomain helicase DNA binding protein 1 (Chd1), is believed to play an integral role in nucleosomal organization, as the loss of Chd1 is known to disrupt chromatin. However, the specificity and basis for the functional and physical localization of Chd1 on chromatin remains largely unknown.

Results: Using genome-wide approaches, we found that the loss of Chd1 significantly disrupted nucleosome arrays within the gene bodies of highly transcribed genes. We also found that Chd1 is physically recruited to gene bodies, and that its occupancy specifically corresponds to that of the early elongating form of RNA polymerase, RNAPII Ser 5-P. Conversely, RNAPII Ser 5-P occupancy was affected by the loss of Chd1, suggesting that Chd1 is associated with early transcription elongation. Surprisingly, the occupancy of RNAPII Ser 5-P was affected by the loss of Chd1 specifically at intron-containing genes. Nucleosome turnover was also affected at these sites in the absence of Chd1. We also found that deletion of the histone methyltransferase for H3K36 (SET2) did not affect either Chd1 occupancy or nucleosome organization genome-wide.

Conclusions: Chd1 is specifically recruited onto the gene bodies of highly transcribed genes in an elongation-dependent but H3K36me3-independent manner. Chd1 co-localizes with the early elongating form of RNA polymerase, and affects the occupancy of RNAPII only at genes containing introns, suggesting a role in relieving splicing-related pausing of RNAPII.

No MeSH data available.


Related in: MedlinePlus

Chd1 co-localizes with early elongating RNAPII. (A) In a wide view, Chd1 occupancy appears similar to both RNAPII Ser 5-P and Ser 2-P occupancy. (B) Close-up views of highly expressed genes reveal that Chd1 occupancy appears similar to the occupancy profile of RNAPII Ser 5-P, but not Ser 2-P. (C) The peak shapes of Chd1 are quantitatively compared with those of either RNAPII Ser 5-P or Ser 2-P using shapeDiff. Histogram of correlation coefficients shows that RNAPII Ser 5-P has high correlation with Chd1 occupancy, whereas RNAPII Ser 2-P has little correlation with Chd1 on a genome wide scale.
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Fig2: Chd1 co-localizes with early elongating RNAPII. (A) In a wide view, Chd1 occupancy appears similar to both RNAPII Ser 5-P and Ser 2-P occupancy. (B) Close-up views of highly expressed genes reveal that Chd1 occupancy appears similar to the occupancy profile of RNAPII Ser 5-P, but not Ser 2-P. (C) The peak shapes of Chd1 are quantitatively compared with those of either RNAPII Ser 5-P or Ser 2-P using shapeDiff. Histogram of correlation coefficients shows that RNAPII Ser 5-P has high correlation with Chd1 occupancy, whereas RNAPII Ser 2-P has little correlation with Chd1 on a genome wide scale.

Mentions: Recent studies examining Chd1 occupancy using low-throughput and genomic approaches give conflicting data regarding its occupancy at promoters, gene bodies or both regions of genes[10, 13, 14, 16]. We performed ChIP-seq using a Myc-tagged Chd1 strain to determine its occupancy. Our data were consistent with the study of Gkikopoulos T et al. (see Additional file1: Figure S2)[10]. Given the effect of Chd1 on nucleosome occupancy at highly transcribed genes that we had observed earlier, we wanted to assess the relationship of Chd1 binding to markers of transcriptional activity. We, therefore, compared Chd1 binding to that of different forms of elongating RNA polymerase that we measured separately using ChIP-seq. At the chromosomal scale, Chd1 occupancy appeared similar to both RNAPII Ser 5-P and RNAPII Ser 2-P occupancy (Figure 2A). Moreover, Myc-tagged Chd1 could co-immunoprecipitate both RNAPII Ser 5-P and Ser 2-P from cell extracts, suggesting an in vivo association (see Additional file1: Figure S3). However at individual genes, the Chd1 binding pattern was strikingly similar to the pattern of RNAPII Ser 5-P occupancy but not to that of RNAPII Ser 2-P (Figure 2B). To quantify this similarity in binding patterns, we carried out shapeDiff analysis of Chd1 and RNAPII occupancy over genes. Chd1 binding peak shapes were more strongly correlated with RNAPII Ser 5-P (median =0.54) than with RNAPII Ser 2-P (median =0.04) (Figure 2C). The 2,056 genes had a correlation coefficient greater than 0.6 in the peak shape comparison between Chd1 and RNAPII Ser 5-P. The distribution of the peak shape correlations confirmed that Chd1 is co-localized with an early transcription elongation factor (RNAPII Ser 5-P) rather than a late transcription elongation factor (RNAPII Ser 2-P).Figure 2


Chd1 co-localizes with early transcription elongation factors independently of H3K36 methylation and releases stalled RNA polymerase II at introns.

Park D, Shivram H, Iyer VR - Epigenetics Chromatin (2014)

Chd1 co-localizes with early elongating RNAPII. (A) In a wide view, Chd1 occupancy appears similar to both RNAPII Ser 5-P and Ser 2-P occupancy. (B) Close-up views of highly expressed genes reveal that Chd1 occupancy appears similar to the occupancy profile of RNAPII Ser 5-P, but not Ser 2-P. (C) The peak shapes of Chd1 are quantitatively compared with those of either RNAPII Ser 5-P or Ser 2-P using shapeDiff. Histogram of correlation coefficients shows that RNAPII Ser 5-P has high correlation with Chd1 occupancy, whereas RNAPII Ser 2-P has little correlation with Chd1 on a genome wide scale.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4230344&req=5

Fig2: Chd1 co-localizes with early elongating RNAPII. (A) In a wide view, Chd1 occupancy appears similar to both RNAPII Ser 5-P and Ser 2-P occupancy. (B) Close-up views of highly expressed genes reveal that Chd1 occupancy appears similar to the occupancy profile of RNAPII Ser 5-P, but not Ser 2-P. (C) The peak shapes of Chd1 are quantitatively compared with those of either RNAPII Ser 5-P or Ser 2-P using shapeDiff. Histogram of correlation coefficients shows that RNAPII Ser 5-P has high correlation with Chd1 occupancy, whereas RNAPII Ser 2-P has little correlation with Chd1 on a genome wide scale.
Mentions: Recent studies examining Chd1 occupancy using low-throughput and genomic approaches give conflicting data regarding its occupancy at promoters, gene bodies or both regions of genes[10, 13, 14, 16]. We performed ChIP-seq using a Myc-tagged Chd1 strain to determine its occupancy. Our data were consistent with the study of Gkikopoulos T et al. (see Additional file1: Figure S2)[10]. Given the effect of Chd1 on nucleosome occupancy at highly transcribed genes that we had observed earlier, we wanted to assess the relationship of Chd1 binding to markers of transcriptional activity. We, therefore, compared Chd1 binding to that of different forms of elongating RNA polymerase that we measured separately using ChIP-seq. At the chromosomal scale, Chd1 occupancy appeared similar to both RNAPII Ser 5-P and RNAPII Ser 2-P occupancy (Figure 2A). Moreover, Myc-tagged Chd1 could co-immunoprecipitate both RNAPII Ser 5-P and Ser 2-P from cell extracts, suggesting an in vivo association (see Additional file1: Figure S3). However at individual genes, the Chd1 binding pattern was strikingly similar to the pattern of RNAPII Ser 5-P occupancy but not to that of RNAPII Ser 2-P (Figure 2B). To quantify this similarity in binding patterns, we carried out shapeDiff analysis of Chd1 and RNAPII occupancy over genes. Chd1 binding peak shapes were more strongly correlated with RNAPII Ser 5-P (median =0.54) than with RNAPII Ser 2-P (median =0.04) (Figure 2C). The 2,056 genes had a correlation coefficient greater than 0.6 in the peak shape comparison between Chd1 and RNAPII Ser 5-P. The distribution of the peak shape correlations confirmed that Chd1 is co-localized with an early transcription elongation factor (RNAPII Ser 5-P) rather than a late transcription elongation factor (RNAPII Ser 2-P).Figure 2

Bottom Line: Using genome-wide approaches, we found that the loss of Chd1 significantly disrupted nucleosome arrays within the gene bodies of highly transcribed genes.We also found that Chd1 is physically recruited to gene bodies, and that its occupancy specifically corresponds to that of the early elongating form of RNA polymerase, RNAPII Ser 5-P.We also found that deletion of the histone methyltransferase for H3K36 (SET2) did not affect either Chd1 occupancy or nucleosome organization genome-wide.

View Article: PubMed Central - PubMed

Affiliation: Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas, 2500 Speedway, Austin, TX 78712 USA.

ABSTRACT

Background: Chromatin consists of ordered nucleosomal arrays that are controlled by highly conserved adenosine triphosphate (ATP)-dependent chromatin remodeling complexes. One such remodeler, chromodomain helicase DNA binding protein 1 (Chd1), is believed to play an integral role in nucleosomal organization, as the loss of Chd1 is known to disrupt chromatin. However, the specificity and basis for the functional and physical localization of Chd1 on chromatin remains largely unknown.

Results: Using genome-wide approaches, we found that the loss of Chd1 significantly disrupted nucleosome arrays within the gene bodies of highly transcribed genes. We also found that Chd1 is physically recruited to gene bodies, and that its occupancy specifically corresponds to that of the early elongating form of RNA polymerase, RNAPII Ser 5-P. Conversely, RNAPII Ser 5-P occupancy was affected by the loss of Chd1, suggesting that Chd1 is associated with early transcription elongation. Surprisingly, the occupancy of RNAPII Ser 5-P was affected by the loss of Chd1 specifically at intron-containing genes. Nucleosome turnover was also affected at these sites in the absence of Chd1. We also found that deletion of the histone methyltransferase for H3K36 (SET2) did not affect either Chd1 occupancy or nucleosome organization genome-wide.

Conclusions: Chd1 is specifically recruited onto the gene bodies of highly transcribed genes in an elongation-dependent but H3K36me3-independent manner. Chd1 co-localizes with the early elongating form of RNA polymerase, and affects the occupancy of RNAPII only at genes containing introns, suggesting a role in relieving splicing-related pausing of RNAPII.

No MeSH data available.


Related in: MedlinePlus