Regulation of Antisense Transcription by NuA4 Histone Acetyltransferase and Other Chromatin Regulatory Factors

Uprety, Bhawana; Kaja, Amala; Ferdoush, Jannatul; Sen, Rwik; Bhaumik, Sukesh R.

doi:10.1128/mcb.00808-15

Cited by 11 publications

(23 citation statements)

References 67 publications

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“…Reverse transcription-PCR (RT-PCR) analysis was performed as done previously (22)(23)(24) and as briefly described in the supplemental material. The primer pairs used for PCR analysis of cDNAs are also described in the supplemental material.…”

Section: Wce Preparation and Western Blot Analysismentioning

confidence: 99%

Fine-Tuning of FACT by the Ubiquitin Proteasome System in Regulation of Transcriptional Elongation

Sen

Ferdoush

Kaja

et al. 2016

Molecular and Cellular Biology

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FACT (facilitates chromatin transcription), an evolutionarily conserved histone chaperone involved in transcription and other DNA transactions, is upregulated in cancers, and its downregulation is associated with cellular death. However, it is not clearly understood how FACT is fine-tuned for normal cellular functions. Here, we show that the FACT subunit Spt16 is ubiquitylated by San1 (an E3 ubiquitin ligase) and degraded by the 26S proteasome. Enhanced abundance of Spt16 in the absence of San1 impairs transcriptional elongation. Likewise, decreased abundance of Spt16 also reduces transcription. Thus, an optimal level of Spt16 is required for efficient transcriptional elongation, which is maintained by San1 via ubiquitylation and proteasomal degradation. Consistently, San1 associates with the coding sequences of active genes to regulate Spt16's abundance. Further, we found that enhanced abundance of Spt16 in the absence of San1 impairs chromatin reassembly at the coding sequence, similarly to the results seen following inactivation of Spt16. Efficient chromatin reassembly enhances the fidelity of transcriptional elongation. Taken together, our results demonstrate for the first time a fine-tuning of FACT by a ubiquitin proteasome system in promoting chromatin reassembly in the wake of elongating RNA polymerase II and transcriptional elongation, thus revealing novel regulatory mechanisms of gene expression. In eukaryotes, DNA is packaged into nucleosomes to form chromatin. Each nucleosome within chromatin consists of ϳ147 bp of DNA wrapped around a histone octamer containing one histone H3-H4 tetramer and two histone H2A-H2B dimers (1). Thus, chromatin structure plays crucial functions in regulation of DNA transactions such as transcription, replication, and DNA repair (2-4). A variety of factors are involved in altering chromatin structure and, hence, DNA transactions. These factors are generally classified as ATP-independent histone modifying enzymes, ATP-dependent chromatin remodelers, and histone chaperones. Histone modifying enzymes function through addition or removal of specific chemical groups (e.g., acetyl, methyl, ubiquitin, phospho, and SUMO), while ATP-dependent chromatin remodelers alter DNA-histone interactions or the composition of the nucleosome in an ATP-dependent manner. On the other hand, histone chaperones function by binding with nucleosomes or histones to facilitate assembly and/or disassembly of nucleosomes in an ATP-independent fashion. The histone chaperone that was first found to alter chromatin structure during transcription is FACT (facilitates chromatin transcription), which is evolutionarily conserved among eukaryotes (5, 6). In budding yeast (Saccharomyces cerevisiae), FACT is composed of Spt16 (suppressor of Ty) and Pob3 and physically interacts with nucleosomes with the assistance of the HMG (high mobility group) protein Nhp6. Likewise, FACT is also a heterodimer of Spt16 and SSRP1 (structurespecific recognition protein 1) in humans. SSRP1 contains HMG domain, while HMG domain is p...

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Section: Wce Preparation and Western Blot Analysismentioning

confidence: 99%

Fine-Tuning of FACT by the Ubiquitin Proteasome System in Regulation of Transcriptional Elongation

Sen

Ferdoush

Kaja

et al. 2016

Molecular and Cellular Biology

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“…The ChIP assay was performed as described previously (Bhaumik and Green 2003;Malik et al 2013;Sen et al 2014;Uprety et al 2016). Briefly, yeast cells were treated with 1% formaldehyde, collected, and resuspended in lysis buffer.…”

Section: Chip Assaymentioning

confidence: 99%

Two Distinct Regulatory Mechanisms of Transcriptional Initiation in Response to Nutrient Signaling

Ferdoush

Sen

Kaja³

et al. 2018

Genetics

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SAGA (Spt-Ada-Gcn5-Acetyltransferase) and TFIID (transcription factor IID) have been previously shown to facilitate the formation of the PIC (pre-initiation complex) at the promoters of two distinct sets of genes. Here, we demonstrate that TFIID and SAGA differentially participate in the stimulation of PIC formation (and hence transcriptional initiation) at the promoter of , a gene for the high-affinity inorganic phosphate (P) transporter for crucial cellular functions, in response to nutrient signaling. We show that transcriptional initiation of occurs predominantly in a TFIID-dependent manner in the absence of P in the growth medium. Such TFIID dependency is mediated via the NuA4 (nucleosome acetyltransferase of H4) histone acetyltransferase (HAT). Intriguingly, transcriptional initiation of also occurs in the presence of P in the growth medium, predominantly via the SAGA complex, but independently of NuA4 HAT. Thus, P in the growth medium switches transcriptional initiation of from NuA4-TFIID to SAGA dependency. Further, we find that both NuA4-TFIID- and SAGA-dependent transcriptional initiations of are facilitated by the 19S proteasome subcomplex or regulatory particle (RP) via enhanced recruitment of the coactivators SAGA and NuA4 HAT, which promote TFIID-independent and -dependent PIC formation for transcriptional initiation, respectively. NuA4 HAT does not regulate activator binding to , but rather facilitates PIC formation for transcriptional initiation in the absence of Pi in the growth medium. On the other hand, SAGA promotes activator recruitment to for transcriptional initiation in the growth medium containing Pi. Collectively, our results demonstrate two distinct stimulatory pathways for PIC formation (and hence transcriptional initiation) at by TFIID, SAGA, NuA4, and 19S RP in the presence and absence of an essential nutrient, P, in the growth media, thus providing new regulatory mechanisms of transcriptional initiation in response to nutrient signaling.

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“…In Saccharomyces cerevisiae, ncRNAs typically originate from nucleosome-depleted regions (NDRs), which are frequently associated with bidirectional promoters of protein-coding genes ( Neil et al., 2009 , Xu et al., 2009 ). However, such pervasive transcription from NDRs is limited by a combination of transcriptome surveillance mechanisms such as transcription attenuation mediated by the Nrd1-Nab3-Sen1 (NNS) termination complex ( Arigo et al., 2006 , Schulz et al., 2013 ), suppression of divergent transcription via histone marks ( Churchman and Weissman, 2011 , Marquardt et al., 2014 , Uprety et al., 2016 ), or rapid degradation of the resulting transcripts by the exosome ( Davis and Ares, 2006 , van Dijk et al., 2011 , Wyers et al., 2005 ).…”

Section: Introductionmentioning

confidence: 99%

Protein Abundance Control by Non-coding Antisense Transcription

et al. 2016

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SummaryStable unannotated transcripts (SUTs), some of which overlap protein-coding genes in antisense direction, are a class of non-coding RNAs. While case studies have reported important regulatory roles for several of such RNAs, their general impact on protein abundance regulation of the overlapping gene is not known. To test this, we employed seamless gene manipulation to repress antisense SUTs of 162 yeast genes by using a unidirectional transcriptional terminator and a GFP tag. We found that the mere presence of antisense SUTs was not sufficient to influence protein abundance, that observed effects of antisense SUTs correlated with sense transcript start site overlap, and that the effects were generally weak and led to reduced protein levels. Antisense regulated genes showed increased H3K4 di- and trimethylation and had slightly lower than expected noise levels. Our results suggest that the functionality of antisense RNAs has gene and condition-specific components.

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Regulation of Antisense Transcription by NuA4 Histone Acetyltransferase and Other Chromatin Regulatory Factors

Cited by 11 publications

References 67 publications

Fine-Tuning of FACT by the Ubiquitin Proteasome System in Regulation of Transcriptional Elongation

Fine-Tuning of FACT by the Ubiquitin Proteasome System in Regulation of Transcriptional Elongation

Two Distinct Regulatory Mechanisms of Transcriptional Initiation in Response to Nutrient Signaling

Protein Abundance Control by Non-coding Antisense Transcription

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