H2B ubiquitylation promotes RNA Pol II processivity via PAF1 and pTEFb

Abstract

Histone H2B ubiquitination plays an important role in transcription regulation. It has been shown that H2B ubiquitination is regulated by multiple upstream events associated with elongating RNA polymerase. Here we demonstrate that H2B K34 ubiquitylation by the MOF-MSL complex is part of the protein networks involved in early steps of transcription elongation. Knocking down MSL2 in the MOF-MSL complex affects not only global H2BK34ub, but also multiple cotranscriptionally regulated histone modifications. More importantly, we show that the MSL, PAF1, and RNF20/40 complexes are recruited and stabilized at active gene promoters by direct binary interactions. The stabilized complexes serve to regulate chromatin association of pTEFb through a positive feedback loop and facilitate Pol II transition during early transcription elongation. Results from our biochemical studies are underscored by genome-wide analyses that show high RNA Pol II processivity and transcription activity at MSL target genes.

Figure 1. Confirmation of MSL2 mediated H2BK34ub in vitro and in vivo using a newly development anti-H2BK34ub antibody

A. Dot-blot for unmodified H2B or branched H2BK34ub peptides using antibodies as indicated on right. Quantities of H2B or H2BK34ub peptides were indicated on top. B. Immunoblot for the chemically synthesized H2BK120ub protein using antibodies indicated on left. C. In vitro ubiquitylation assay using either MSL1/2 or RNF20/40 as the E3 ubiquitin ligase as indicated on top. Recombinant nucleosomes were used as the substrates. Ubiquitylated H2B was detected by anti-HA, anti-H2BK120ub or anti-H2BK34ub antibodies as indicated on left. Immunoblot using anti-H4 antibody was used as the loading control. D. Immunoblot for total H2BK34ub, H4K16ac and H4 from HeLa cells treated with or without MSL2 or MOF siRNAs as indicated on top. See also Figure S1.

Figure 2. Mutual dependence of chromatin binding by MSL, RNF20/40 and PAF1C

A. Immunoblot for histones isolated from HeLa cells after control or RNF20 and RNF40 siRNA treatments. B. Immunoblot for histones isolated from HeLa cells after RNF20/40 or MSL1/2 knockdown. C. Immunoblot for histones isolated from HeLa cells after control or PAF1C siRNA treatment. D. Immunoblot for proteins in soluble and chromatin fractions after control and PAF1 knockdown. For A–D, antibodies were shown on left. Immunoblot for H4 GAPDH were used as controls to indicate good separation of soluble and chromatin fractions in B and D. See also Figure S2.

Figure 3. MSL1 directly interacts with RNF20

A. Flag-tagged MSL1, MSL2, MSL3 or MOF was individually incubated with the His-tagged RNF20/40 complex and subject to M2-agarose purification. The immune-precipitated (IP) proteins were blotted with antibodies indicated on left. Input controls for RNF20 and RNF40 were at bottom. B. Flag-tagged RNF40 or RNF20 was individually incubated with His-MSL1 and subject to M2-agarose purification. Immunoblot for the IPed proteins were performed using antibodies on left. C. Left, schematics for MSL1 truncation mutants used in the pull down assays. Right, immunoblots using antibodies indicated on right.

Figure 4. The MSL1/2 complex directly interacts with PAF1

A. Flag-tagged PAF1, CTR9, LEO1, CDC73, RTF1 or Ski8 was individually incubated with the recombinant MSL1/2 complex and subject to M2 purification. Immunoblots for IP and inputs were shown using antibodies indicated on left. B. Flag-tagged MSL1, MSL2, MSL3 or MOF was incubated with the PAF1 protein and subject to M2 purification. Immunoblot using antibodies indicated on left was shown. C,D. Left, schematics for MSL1 (C) and MSL2 (D) truncation mutants used in the IP experiments. Right, immunoblot for IPed proteins using truncated proteins and recombinant PAF1 proteins as indicated on top.

Figure 5. Binary interactions of PAF1C, RNF20/40 and MSL complexes stabilize their interactions and regulate pTEFb chromatin recruitment

A. Flag-tagged PAF1 was incubated with His-tagged RNF20/40 or MSL1/2 as indicated on top. Immunoblot was performed for IP and input proteins using antibodies indicated on left. B. Flag-tagged MSL1/MSL2 heterodimer (Flag-MSL1) was incubated with His-tagged RNF20/40 or PAF1 as indicated on top. Immunoblot was performed for IP and input proteins. C. Immunoblot for histones isolated from HeLa cells treated with control or CDK9 siRNAs. Antibodies were indicated on left. D. Immunoblot for proteins distributed in soluble vs. chromatin fractions in cells treated with control or CDK9 siRNAs. E. Immunoblot for proteins distributed in soluble vs. chromatin fractions in cells treated with control, PAF1, RNF20/40, MSL1/2 siRNAs as indicated on top. F. Immunoblot for proteins distribution after MSL2 knockdown followed by overexpression of Myc-tagged RNAi resistant MSL2 or MSL2 ^H64Y mutant as indicated on top. For A–F, antibodies were indicated on left. See also Figure S3.

Figure 6. Interplays of the MSL complex with transcription elongation factors at Hoxa9 and Meis1 loci in cells

HeLa cells were treated with control, PAF1, RNF20/40 or CDK9 siRNAs and subject to CHIP analyses for MSL2 (A), RNF20 (B), PAF1 (C), CDK9 (D), Pol II Ser2p (E) and Pol II Ser5p (F). Primer sets for HOXA9 (A9), MEIS1 (M1) and Oct4 (O4) used in ChIP assays were indicated on bottom. Signals for each experiment were normalized to 5% input. Means and standard deviations (as error bars) from at least three independent experiments were presented.

Figure 7. Genome-wide analyses of Msl2 target genes

A. Genome-wide distribution of Msl2 relative to gene structure. Relative ratio of Msl2 peaks at each defined genomic region versus total peaks was indicated as %. B. Genome average of Mof/Msl2 (blue) and Pol II Ser2p (black) binding on scaled genes. Y-axis, count enrichment after normalization against gene length and read counts. C. Bar plot showing distribution of the Msl complex, as defined by the joint peaks for Mof and Msl2, and Pol II Ser2phos relative to nearest TSS. Each bin (X-axis) represents a 500bp region. D. Heat map representation of ChIP-seq peaks for Pol II, Pol II Ser2, Msl2 and Mof at genes bound by the Msl complex within ±3.5kb of TSS. The rank was ordered from highest Msl2 to lowest Msl2 binding. Red means enrichment, white means no enrichment. Total enrichment within ±3.5kb of TSS was calculated. E. Distribution of traveling ratio for all genes with TR values. Traveling ratio for genes was calculated as described previously (Rahl et al., 2010). Cumulative distribution function (CDF) of traveling ratio for genes bound by the Mof/Msl2 complex (red), Mof alone (black) and non-Mof targets (blue) were plotted. p-values (Wilcoxon Signed-rank test) for TR difference were 4.023e-13 (red-black), 4.391e-13 (red-blue). See also Figure S4–6.