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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

Intron-containing genes show a marked shift in the occupancy of RNAPII Ser 5-P in the absence of Chd1. The top 500 genes with the highest transcription rate (TR) as measured by RNAPII Ser-5 P occupancy[35] were defined as the high TR genes. Upper and lower panels show average profiles of RNAPII Ser 5-P and Ser 2-P occupancies, respectively. The left panels show the high TR gene set without any intron-containing genes (n =382), whereas the right panels show only the intron-containing genes from among the high TR genes (n =118). The shaded bands represent the 95% confidence interval of the data.
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Fig4: Intron-containing genes show a marked shift in the occupancy of RNAPII Ser 5-P in the absence of Chd1. The top 500 genes with the highest transcription rate (TR) as measured by RNAPII Ser-5 P occupancy[35] were defined as the high TR genes. Upper and lower panels show average profiles of RNAPII Ser 5-P and Ser 2-P occupancies, respectively. The left panels show the high TR gene set without any intron-containing genes (n =382), whereas the right panels show only the intron-containing genes from among the high TR genes (n =118). The shaded bands represent the 95% confidence interval of the data.

Mentions: Since we had observed strong Chd1 binding on the genes with high transcription rate (TR), we examined the effect of CHD1 deletion on the peak shapes of RNAPII Ser 5-P at the subset of high TR genes. Interestingly, the average peak shapes of RNAPII Ser 5-P were shifted toward the 5′ end of the high TR genes in chd1Δ relative to WT cells (see Additional file1: Figure S4A). In S. cerevisiae, high TR genes include a considerable number of intron-containing genes. In order to identify the primary determinant of Chd1 sensitivity, we separated the high TR intron-less and intron-containing genes. Strikingly, intron-containing genes showed substantial changes in RNAPII Ser 5-P occupancy, whereas the high TR genes excluding intron-containing genes had little alteration in the chd1Δ mutant (Figure 4). When the RNAPII Ser 5-P occupancy for the high TR intron-containing genes was aligned by exon-intron junctions, the shift to the upstream direction in chd1Δ was more evident at 3′ end of introns (Figure 5A). Recent studies have shown that introns result in pausing of RNAPII[31–33], and independently, that Chd1 relieves RNAPII stalling at promoters in mammalian cells[34]. Our data suggest that Chd1 could additionally relieve the stalling of the early elongating form of RNAPII at introns.Figure 4


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)

Intron-containing genes show a marked shift in the occupancy of RNAPII Ser 5-P in the absence of Chd1. The top 500 genes with the highest transcription rate (TR) as measured by RNAPII Ser-5 P occupancy[35] were defined as the high TR genes. Upper and lower panels show average profiles of RNAPII Ser 5-P and Ser 2-P occupancies, respectively. The left panels show the high TR gene set without any intron-containing genes (n =382), whereas the right panels show only the intron-containing genes from among the high TR genes (n =118). The shaded bands represent the 95% confidence interval of the data.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Intron-containing genes show a marked shift in the occupancy of RNAPII Ser 5-P in the absence of Chd1. The top 500 genes with the highest transcription rate (TR) as measured by RNAPII Ser-5 P occupancy[35] were defined as the high TR genes. Upper and lower panels show average profiles of RNAPII Ser 5-P and Ser 2-P occupancies, respectively. The left panels show the high TR gene set without any intron-containing genes (n =382), whereas the right panels show only the intron-containing genes from among the high TR genes (n =118). The shaded bands represent the 95% confidence interval of the data.
Mentions: Since we had observed strong Chd1 binding on the genes with high transcription rate (TR), we examined the effect of CHD1 deletion on the peak shapes of RNAPII Ser 5-P at the subset of high TR genes. Interestingly, the average peak shapes of RNAPII Ser 5-P were shifted toward the 5′ end of the high TR genes in chd1Δ relative to WT cells (see Additional file1: Figure S4A). In S. cerevisiae, high TR genes include a considerable number of intron-containing genes. In order to identify the primary determinant of Chd1 sensitivity, we separated the high TR intron-less and intron-containing genes. Strikingly, intron-containing genes showed substantial changes in RNAPII Ser 5-P occupancy, whereas the high TR genes excluding intron-containing genes had little alteration in the chd1Δ mutant (Figure 4). When the RNAPII Ser 5-P occupancy for the high TR intron-containing genes was aligned by exon-intron junctions, the shift to the upstream direction in chd1Δ was more evident at 3′ end of introns (Figure 5A). Recent studies have shown that introns result in pausing of RNAPII[31–33], and independently, that Chd1 relieves RNAPII stalling at promoters in mammalian cells[34]. Our data suggest that Chd1 could additionally relieve the stalling of the early elongating form of RNAPII at introns.Figure 4

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