Functional Analysis of H2B-Lys-123 Ubiquitination in Regulation of H3-Lys-4 Methylation and Recruitment of RNA Polymerase II at the Coding Sequences of Several Active Genes in Vivo

Shukla, Abhijit; Stanojevic, Nadia; Duan, Zengqiang; Shadle, Thomas; Bhaumik, Sukesh R.

doi:10.1074/jbc.m513533200

Cited by 40 publications

(44 citation statements)

References 62 publications

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“…Notably, Set1 dimethylates and trimethylates H3K4 in the middle of the PHO84 ORF (Shukla et al 2006), raising the question of whether Set1 may also participate in PHO84 cosuppression. To address this possibility, an empty vector and plasmid N°1 were transformed into the Dset1 strain.…”

Section: Set1 Influences the Silencing In Trans By Promoting Productimentioning

confidence: 99%

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae

Camblong¹,

Beyrouthy²,

Guffanti³

et al. 2009

Genes Dev.

143

138

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Homology-dependent gene silencing, a phenomenon described as cosuppression in plants, depends on siRNAs. We provide evidence that in Saccharomyces cerevisiae, which is missing the RNAi machinery, protein coding gene cosuppression exists. Indeed, introduction of an additional copy of PHO84 on a plasmid or within the genome results in the cosilencing of both the transgene and the endogenous gene. This repression is transcriptional and position-independent and requires trans-acting antisense RNAs. Antisense RNAs induce transcriptional gene silencing both in cis and in trans, and the two pathways differ by the implication of the Hda1/2/3 complex. We also show that trans-silencing is influenced by the Set1 histone methyltransferase, which promotes antisense RNA production. Finally we show that although antisense-mediated cis-silencing occurs in other genes, transsilencing so far depends on features specific to PHO84. All together our data highlight the importance of noncoding RNAs in mediating RNAi-independent transcriptional gene silencing.[Keywords: Antisense RNA; cis and trans transcriptional gene silencing; PHO84; cosuppression; RNAi-independent TGS; noncoding RNA; S. cerevisiae] Supplemental material is available at http://www.genesdev.org.

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Section: Set1 Influences the Silencing In Trans By Promoting Productimentioning

confidence: 99%

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae

Camblong¹,

Beyrouthy²,

Guffanti³

et al. 2009

Genes Dev.

143

138

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“…BRE1 mediates specifically the transcription activation functions of Rad6 (Wood et al, 2003;Kao et al, 2004). Monoubiquitination of H2B by BRE1 and Rad6 has been shown to be required for trimethylation of histone H3 at Lys-4 (H3K4met3) at coding sequences of transcriptionally active genes in yeast and humans (Wood et al, 2005;Xiao et al, 2005;Zhu et al, 2005;Shukla et al, 2006). This H3 modification is indispensable for RNA polymerase II recruitment to the coding sequences of transcribed genes.…”

Section: Hub1 Affects G2-to-m Transition and Mitosismentioning

confidence: 99%

TheArabidopsis thalianaHomolog of YeastBRE1Has a Function in Cell Cycle Regulation during Early Leaf and Root Growth

et al. 2007

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Chromatin modification and transcriptional activation are novel roles for E3 ubiquitin ligase proteins that have been mainly associated with ubiquitin-dependent proteolysis. We identified HISTONE MONOUBIQUITINATION1 (HUB1) (and its homolog HUB2) in Arabidopsis thaliana as RING E3 ligase proteins with a function in organ growth. We show that HUB1 is a functional homolog of the human and yeast BRE1 proteins because it monoubiquitinated histone H2B in an in vitro assay. Hub knockdown mutants had pale leaf coloration, modified leaf shape, reduced rosette biomass, and inhibited primary root growth. One of the alleles had been designated previously as ang4-1. Kinematic analysis of leaf and root growth together with flow cytometry revealed defects in cell cycle activities. The hub1-1 (ang4-1) mutation increased cell cycle duration in young leaves and caused an early entry into the endocycles. Transcript profiling of shoot apical tissues of hub1-1 (ang4-1) indicated that key regulators of the G2-to-M transition were misexpressed. Based on the mutant characterization, we postulate that HUB1 mediates gene activation and cell cycle regulation probably through chromatin modifications.

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“…For analysis of global levels of Spt20p and actin in the ⌬eaf1 strain bearing SPT20 under the GAL1 promoter, yeast cells were grown in YPG medium to an OD 600 of 0.5 and then switched to YPD medium for 2 or 4 h. The harvested cells were lysed and sonicated to prepare the whole-cell extract with solubilized chromatin, following the protocol described previously for the ChIP assay (17,(52)(53)(54)(55)(56)(57)(58)(59)(60)(61). The whole-cell extract was run on an SDS-polyacrylamide gel and then analyzed by Western blotting.…”

Section: Plasmidsmentioning

confidence: 99%

“…The ChIP assay for TBP, TAF1p, TAF12p, and histone H4 acetylation was performed as described previously (17,(52)(53)(54)(55)(56)(57)(58)(59)(60)(61). For ChIP analysis of Myc-tagged Esa1p, Swc4p, Epl1p, Yng2p, Eaf1p, Eaf5p, and Spt20p, the ChIP protocol was modified as described previously (17,52,54,58,60).…”

Section: Plasmidsmentioning

confidence: 99%

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Eaf1p Is Required for Recruitment of NuA4 in Targeting TFIID to the Promoters of the Ribosomal Protein Genes for Transcriptional Initiation In Vivo

Uprety

Sen

Bhaumik

2015

Molecular and Cellular Biology

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NuA4 (nucleosome acetyltransferase of H4) promotes transcriptional initiation of TFIID (a complex of TBP and TBP-associated factors [TAFs])-dependent ribosomal protein genes involved in ribosome biogenesis. However, it is not clearly understood how NuA4 regulates the transcription of ribosomal protein genes. Here, we show that NuA4 is recruited to the promoters of ribosomal protein genes, such as RPS5, RPL2B, and RPS11B, for TFIID recruitment to initiate transcription, and the recruitment of NuA4 to these promoters is impaired in the absence of its Eaf1p component. Intriguingly, impaired NuA4 recruitment in a ⌬eaf1 strain depletes recruitment of TFIID (a TAF-dependent form of TBP) but not the TAF-independent form of TBP to the promoters of ribosomal protein genes. However, in the absence of NuA4, SAGA (Spt-Ada-Gcn5-acetyltransferase) is involved in targeting the TAF-independent form of TBP to the promoters of ribosomal protein genes for transcriptional initiation. Thus, NuA4 plays an important role in targeting TFIID to the promoters of ribosomal protein genes for transcriptional initiation in vivo. Such a function is mediated via its targeted histone acetyltransferase activity. In the absence of NuA4, ribosomal protein genes lose TFIID dependency and become SAGA dependent for transcriptional initiation. Collectively, these results provide significant insights into the regulation of ribosomal protein gene expression and, hence, ribosome biogenesis and functions.H istone H4 acetylation plays important roles in the regulation of eukaryotic transcription and other biological processes (1-3). In Saccharomyces cerevisiae, NuA4 (nucleosome acetyltransferase of H4) acetylates histone H4. In addition, NuA4 is involved in acetylation of histones H2A and H2A.Z (4-7). NuA4 is a multisubunit protein complex and is conserved from yeast to humans (Tip60 is the human homologue of yeast NuA4) (8). Like other histone lysine (K) acetyltransferases (KATs), NuA4 is involved in various cellular events, such as transcription, DNA repair, and cell cycle progression (9-27). In addition, NuA4 is proposed to regulate cellular aging and autophagy via acetylation of nonhistone proteins (28-30). Likewise, Tip60 has numerous nonhistone targets involved in various cellular activities (31, 32). In addition, Tip60 has been found to be involved in performing critical functions in DNA repair and stem cell regulation (33-36). Therefore, NuA4 and its human homologue are multifunctional in maintaining normal cellular functions.Esa1p is the catalytic subunit of NuA4 with KAT activity (37, 38). In addition, NuA4 has 12 other subunits (39, 40). These subunits include Tra1p (ATM-related factor), Epl1p (enhancer of polycomb homologue), Arp4p (actin-related protein), Yaf9p (leukemogenic factor ENL/AF9 homologue), Act1p, and 7 Esa1p-associated factors, Eaf1p to Eaf7p. Eaf2p and Eaf4p are also known as Swc4p and Yng2p, respectively. Although Esa1p is the catalytic subunit of NuA4, it cannot acetylate nucleosomal histones on its own but can acetylate naked/f...

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Functional Analysis of H2B-Lys-123 Ubiquitination in Regulation of H3-Lys-4 Methylation and Recruitment of RNA Polymerase II at the Coding Sequences of Several Active Genes in Vivo

Cited by 40 publications

References 62 publications

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae

TheArabidopsis thalianaHomolog of YeastBRE1Has a Function in Cell Cycle Regulation during Early Leaf and Root Growth

Eaf1p Is Required for Recruitment of NuA4 in Targeting TFIID to the Promoters of the Ribosomal Protein Genes for Transcriptional Initiation In Vivo

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