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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

Loss of Chd1 leads to changes in local occupancy of RNAPII Ser 5-P. (A) Wide view shows no large-scale occupancy changes of either form of elongating RNAPII between wild-type (WT) and chd1Δ. (B) Close-up of highly transcribed genes showing that RNAPII Ser 5-P shifts upstream in chd1Δ, but RNAPII Ser 2-P peaks appear very similar between WT and chd1Δ. (C) shapeDiff quantification of the peak shape similarity of RNAPII Ser 5-P and RNAPII Ser 2-P between WT and chd1Δ. The effect of CHD1 deletion on changes in peak shape is much stronger for RNAPII Ser 5-P than for RNAPII Ser-2 P.
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Fig3: Loss of Chd1 leads to changes in local occupancy of RNAPII Ser 5-P. (A) Wide view shows no large-scale occupancy changes of either form of elongating RNAPII between wild-type (WT) and chd1Δ. (B) Close-up of highly transcribed genes showing that RNAPII Ser 5-P shifts upstream in chd1Δ, but RNAPII Ser 2-P peaks appear very similar between WT and chd1Δ. (C) shapeDiff quantification of the peak shape similarity of RNAPII Ser 5-P and RNAPII Ser 2-P between WT and chd1Δ. The effect of CHD1 deletion on changes in peak shape is much stronger for RNAPII Ser 5-P than for RNAPII Ser-2 P.

Mentions: It is known that overall gene expression levels are only slightly altered by the loss of Chd1[27, 28], but cryptic and antisense transcription is notably increased[12, 13, 23, 29, 30]. Based on these observations and our results above, we hypothesized that while the loss of Chd1 does not lead to partial or complete loss of elongating RNAPII, its local positioning is affected. To test this hypothesis, we measured the occupancies of RNAPII Ser 5-P and RNAPII Ser 2-P separately in a chd1Δ strain. In the broad genomic view, we did not observe dramatic changes in the occupancy of either form of elongating RNAPII (Figure 3A). When we examined individual genes, however, the binding peak shapes of RNAPII Ser 5-P were disrupted at some highly transcribed genes, especially RP genes (Figure 3B). In order to quantitate the peak shape similarities of elongating RNAPII between WT and chd1Δ strains on a genome-wide scale, we again used shapeDiff to generate correlations for each gene. Interestingly, RNAPII Ser 2-P was relatively unaffected by the loss of Chd1 (median correlation =0.69), but RNAPII Ser 5-P peak shapes were clearly affected by the deletion of CHD1 (median correlation =0.38) (Figure 3C).Figure 3


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)

Loss of Chd1 leads to changes in local occupancy of RNAPII Ser 5-P. (A) Wide view shows no large-scale occupancy changes of either form of elongating RNAPII between wild-type (WT) and chd1Δ. (B) Close-up of highly transcribed genes showing that RNAPII Ser 5-P shifts upstream in chd1Δ, but RNAPII Ser 2-P peaks appear very similar between WT and chd1Δ. (C) shapeDiff quantification of the peak shape similarity of RNAPII Ser 5-P and RNAPII Ser 2-P between WT and chd1Δ. The effect of CHD1 deletion on changes in peak shape is much stronger for RNAPII Ser 5-P than for RNAPII Ser-2 P.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Loss of Chd1 leads to changes in local occupancy of RNAPII Ser 5-P. (A) Wide view shows no large-scale occupancy changes of either form of elongating RNAPII between wild-type (WT) and chd1Δ. (B) Close-up of highly transcribed genes showing that RNAPII Ser 5-P shifts upstream in chd1Δ, but RNAPII Ser 2-P peaks appear very similar between WT and chd1Δ. (C) shapeDiff quantification of the peak shape similarity of RNAPII Ser 5-P and RNAPII Ser 2-P between WT and chd1Δ. The effect of CHD1 deletion on changes in peak shape is much stronger for RNAPII Ser 5-P than for RNAPII Ser-2 P.
Mentions: It is known that overall gene expression levels are only slightly altered by the loss of Chd1[27, 28], but cryptic and antisense transcription is notably increased[12, 13, 23, 29, 30]. Based on these observations and our results above, we hypothesized that while the loss of Chd1 does not lead to partial or complete loss of elongating RNAPII, its local positioning is affected. To test this hypothesis, we measured the occupancies of RNAPII Ser 5-P and RNAPII Ser 2-P separately in a chd1Δ strain. In the broad genomic view, we did not observe dramatic changes in the occupancy of either form of elongating RNAPII (Figure 3A). When we examined individual genes, however, the binding peak shapes of RNAPII Ser 5-P were disrupted at some highly transcribed genes, especially RP genes (Figure 3B). In order to quantitate the peak shape similarities of elongating RNAPII between WT and chd1Δ strains on a genome-wide scale, we again used shapeDiff to generate correlations for each gene. Interestingly, RNAPII Ser 2-P was relatively unaffected by the loss of Chd1 (median correlation =0.69), but RNAPII Ser 5-P peak shapes were clearly affected by the deletion of CHD1 (median correlation =0.38) (Figure 3C).Figure 3

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