Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin

Scruggs, Benjamin S.; Gilchrist, Daniel A.; Nechaev, Sergei; Muse, Ginger W.; Burkholder, Adam; Fargo, David C.; Adelman, Karen

doi:10.1016/j.molcel.2015.04.006

Cited by 217 publications

(327 citation statements)

References 42 publications

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“…S7D, S14D,F). This result is in contrast to the offset in sense and antisense activities that is predicted by a model in which sense and antisense initiation events require distinct core promoters separated by ∼180 bp (Duttke et al 2015;Scruggs et al 2015); it suggests instead that bidirectional initiation may occur at the flanks of activator-bound sequences with little requirement for specific core promoter elements.…”

Section: Resultscontrasting

confidence: 93%

“…This decoupling of enhancer and promoter activity suggests that enhancers can activate promoters without initiating transcription. Our work builds on recent findings that distal enhancers and gene promoters have remarkably similar genomic architectures, each with divergent transcription from nucleosome-depleted cores Duttke et al 2015;Scruggs et al 2015). At gene promoters, the presence of a 5 ′ splicing signal protects against premature termination (Kaida et al 2010;Almada et al 2013;Ntini et al 2013).…”

Section: Discussionmentioning

confidence: 80%

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High-throughput functional comparison of promoter and enhancer activities

et al. 2016

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Promoters initiate RNA synthesis, and enhancers stimulate promoter activity. Whether promoter and enhancer activities are encoded distinctly in DNA sequences is unknown. We measured the enhancer and promoter activities of thousands of DNA fragments transduced into mouse neurons. We focused on genomic loci bound by the neuronal activity-regulated coactivator CREBBP, and we measured enhancer and promoter activities both before and after neuronal activation. We find that the same sequences typically encode both enhancer and promoter activities. However, gene promoters generate more promoter activity than distal enhancers, despite generating similar enhancer activity. Surprisingly, the greater promoter activity of gene promoters is not due to conventional core promoter elements or splicing signals. Instead, we find that particular transcription factor binding motifs are intrinsically biased toward the generation of promoter activity, whereas others are not. Although the specific biases we observe may be dependent on experimental or cellular context, our results suggest that gene promoters are distinguished from distal enhancers by specific complements of transcriptional activators.

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Section: Resultscontrasting

confidence: 93%

Section: Discussionmentioning

confidence: 80%

High-throughput functional comparison of promoter and enhancer activities

et al. 2016

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“…Our approach for calling transcription start sites with PRO-cap data is modeled after a similar analysis used for Start-seq data in mouse (Scruggs et al 2015). Using the starting lists of TSS annotations, we developed an algorithm to search for the position within ±250 bases of each annotation possessing the highest PRO-cap read count on the corresponding strand.…”

Section: Observed Tss Identificationmentioning

confidence: 99%

Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast

Booth¹,

Wang²,

Cheung³

et al. 2016

Genome Res.

146

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Complex regulation of gene expression in mammals has evolved from simpler eukaryotic systems, yet the mechanistic features of this evolution remain elusive. Here, we compared the transcriptional landscapes of the distantly related budding and fission yeast. We adapted the Precision Run-On sequencing (PRO-seq) approach to map the positions of RNA polymerase active sites genome-wide in Schizosaccharomyces pombe and Saccharomyces cerevisiae. Additionally, we mapped preferred sites of transcription initiation in each organism using PRO-cap. Unexpectedly, we identify a pause in early elongation, specific to S. pombe, that requires the conserved elongation factor subunit Spt4 and resembles promoter-proximal pausing in metazoans. PRO-seq profiles in strains lacking Spt4 reveal globally elevated levels of transcribing RNA Polymerase II (Pol II) within genes in both species. Messenger RNA abundance, however, does not reflect the increases in Pol II density, indicating a global reduction in elongation rate. Together, our results provide the first base-pair resolution map of transcription elongation in S. pombe and identify divergent roles for Spt4 in controlling elongation in budding and fission yeast.

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“…The finding is reminiscent of a mechanism called divergent transcription (39)(40)(41)(42) that is related to transcription initiation in opposite directions from the same promoter. The rather short transcripts initiated at nonuniform start sites that have been described for the upstream direction in divergent transcription are in line with the heterogeneous population of AAV2 minus strand transcripts that we identified both by 5'RACE and by RNase protection.…”

Section: Discussionmentioning

confidence: 99%

A Comprehensive RNA Sequencing Analysis of the Adeno-Associated Virus (AAV) Type 2 Transcriptome Reveals Novel AAV Transcripts, Splice Variants, and Derived Proteins

Stutika

Gogol-Döring

Botschen

et al. 2016

J Virol

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Adeno-associated virus (AAV) is recognized for its bipartite life cycle with productive replication dependent on coinfection with adenovirus (Ad) and AAV latency being established in the absence of a helper virus. The shift from latent to Ad-dependent AAV replication is mostly regulated at the transcriptional level. The current AAV transcription map displays highly expressed transcripts as found upon coinfection with Ad. So far, AAV transcripts have only been characterized on the plus strand of the AAV single-stranded DNA genome. The AAV minus strand is assumed not to be transcribed. Here, we apply Illumina-based RNA sequencing (RNA-Seq) to characterize the entire AAV2 transcriptome in the absence or presence of Ad. We find known and identify novel AAV transcripts, including additional splice variants, the most abundant of which leads to expression of a novel 18-kDa Rep/VP fusion protein. Furthermore, we identify for the first time transcription on the AAV minus strand with clustered reads upstream of the p5 promoter, confirmed by 5' rapid amplification of cDNA ends and RNase protection assays. The p5 promoter displays considerable activity in both directions, a finding indicative of divergent transcription. Upon infection with AAV alone, low-level transcription of both AAV strands is detectable and is strongly stimulated upon coinfection with Ad. A deno-associated viruses (AAV) are helper-dependent members of the parvovirus group that require coinfection with an unrelated helper virus, particularly adenovirus (Ad) for productive replication (1). Despite of several identified AAV serotypes most research has been done with prototype AAV type 2. The AAV2 genome consists of a linear, single-stranded DNA of 4.7 kb. Both ends carry identical inverted terminal repeats (ITR) of 145 bp (2), which flank the two major open reading frames (ORF), called rep and cap. The rep ORF codes for four nonstructural proteins, Rep78 and a C-terminally spliced variant, Rep68. In addition, N-terminally truncated versions thereof are expressed, called Rep52 and Rep40, respectively. The Rep proteins are required as regulators for various steps of the AAV life cycle. AAV cap harbors the ORF for the capsid proteins (VP1 to -3) and a separate ORF for the assembly-activating protein (AAP) (3).The current knowledge of AAV transcription dates back to early research in the 1980s when the three AAV2 promoters, p5, p19, or p40 and major transcripts derived thereof were characterized (4, 5). All AAV transcripts identified since then map to only one DNA plus strand (6), which led to the assumption that the complementary AAV minus strand was not transcribed. Furthermore, spliced AAV transcripts were identified displaying a single, shared intron located in the center of the AAV2 genome (4, 7). Initially, a single splice donor site at AAV nucleotide 1906 and a single splice acceptor site located at nucleotide (nt) 2228 were described. Later, an alternative splice acceptor site at nt 2201 was detected (8), allowing the expression of VP1 protein ...

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Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin

Cited by 217 publications

References 42 publications

High-throughput functional comparison of promoter and enhancer activities

High-throughput functional comparison of promoter and enhancer activities

Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast

A Comprehensive RNA Sequencing Analysis of the Adeno-Associated Virus (AAV) Type 2 Transcriptome Reveals Novel AAV Transcripts, Splice Variants, and Derived Proteins

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