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Saccharomyces cerevisiae

ABSTRACT: Native Elongating Transcript sequencing (NET-seq) in wild-type and three members of the CAF-I complex

PROVIDER: PRJNA241515 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1197980.fastq.gz	Fastqsanger.gz
	SRR1197973.fastq.gz	Fastqsanger.gz
	SRR1197974.fastq.gz	Fastqsanger.gz
	SRR1197975.fastq.gz	Fastqsanger.gz
	SRR1197976.fastq.gz	Fastqsanger.gz

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Native elongating transcript sequencing (NET-seq) of wild type Saccharomyces cerevisiae and of DST1, RCO1, SET1, SET2, EAF3 deletion strains

Project description:We present an approach (native elongating transcript sequencing, NET-seq), based on deep sequencing of 3M-bM-^@M-^Y ends of nascent transcripts associated with RNA polymerase, to monitor transcription at nucleotide resolution. Application of NET-seq in Saccharomyces cerevisiae reveals that while promoters are generally capable of divergent transcription, the Rpd3S deacetylation complex enforces strong directionality to most promoters by suppressing antisense transcript initiation. Our studies also reveal pervasive polymerase pausing and backtracking throughout the body of transcripts. Average pause density shows prominent peaks at each of the first four nucleosomes, with the peak location occurring in good agreement with in vitro biophysical measurements. Thus nucleosome-induced pausing represents a major barrier to transcriptional elongation in vivo. Examination of nascent transcripts in yeast and mutant strains

2011-01-19 | E-GEOD-25107 | biostudies-arrayexpress

Native elongating transcript sequencing (NET-seq) of wild type Saccharomyces cerevisiae and of DST1, RCO1, SET1, SET2, EAF3 deletion strains

Project description:We present an approach (native elongating transcript sequencing, NET-seq), based on deep sequencing of 3’ ends of nascent transcripts associated with RNA polymerase, to monitor transcription at nucleotide resolution. Application of NET-seq in Saccharomyces cerevisiae reveals that while promoters are generally capable of divergent transcription, the Rpd3S deacetylation complex enforces strong directionality to most promoters by suppressing antisense transcript initiation. Our studies also reveal pervasive polymerase pausing and backtracking throughout the body of transcripts. Average pause density shows prominent peaks at each of the first four nucleosomes, with the peak location occurring in good agreement with in vitro biophysical measurements. Thus nucleosome-induced pausing represents a major barrier to transcriptional elongation in vivo.

2011-01-19 | GSE25107 | GEO

Saccharomyces cerevisiae

Project description:Native elongating transcript sequencing (NET-seq) of wild type Saccharomyces cerevisiae and of DST1, RCO1, SET1, SET2, EAF3 deletion strains

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TEF-seq/NET-seq applied to factors Rpb3, Paf1, Spt6, Spt16, Cet1, Pcf11, Ssu72, Set2

Project description:Here we adapt native elongating transcript sequencing (NET-seq) to develop transcription elongation factor associated nascent elongating transcript sequencing (TEF-seq). In this the RNA polymerase II (Pol2) transcription elongation complex (TEC) is immunoprecipitated via associated transcription elongation factors (TEFs). Sequencing from the 3' end of the Pol2-associated nascent transcript shows the position of the final incorporated nucleotide giving strand-specific, single nucleotide resolution maps of the level of TEF association with Pol2 during transcription.

2021-01-18 | E-MTAB-4568 | biostudies-arrayexpress

Native Elongating Transcript sequencing (NET-seq) in wild-type and three members of the CAF-I complex.

Project description:We performed a fluorescent reporter based screen to identify factors determining transcriptional directionality from bidirectional promoters that give rise to a coding and a non-coding transcript. Promoters like these are most frequent in many organisms and non-coding transcription from this origin represents a large fraction of total long non-coding transcripts. We applied NET-seq to compare nascent transcription in yeast wild-type and mutations in the three members of the CAF-I complex. This technique avoids the technical issue of co-transcriptional RNA degradation and is a powerful approach to address questions concerning non-coding transcription. We find divergent non-coding transcription to be elevated in CAF-I mutants. One condition, yeast grown in YPD media to mid-log phase. 8 NET-seq libraries are deposited, 2 biological repeats of the wild-type and two biological repeast each of the CAF-I complex member mutants (CAC1, CAC2, CAC3).

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Project description:We characterized the transcribed active enhancers of a human neuronal cell line derived from fetal mesencephalon (LUHMES) during differentiation by native elongating transcript-cap analysis of gene expression (NET-CAGE). Raw data files starting from 'Total' are conventional CAGE method outputs, and those starting from 'Nascent' are NET-CAGE method outputs.

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Schizosaccharomyces pombe

Project description:Native Elongating Transcript Sequencing (NET-Seq) in wild-type fission yeast cells

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Native Elongating Transcript sequencing (NET-seq) in wild-type and three members of the CAF-I complex

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Project description:Native elongating transcript sequencing (NET-seq), nascnet RNA-seq, and total RNA-seq of wild type and RNA polymerase II C-terminal domain mutants and ChIP-nexus of RNA polymerase II C-terminal domains phosphoisoforms and splicing factors in S. cerevisiae

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Project description:The purpose of this study was to investigate the role of the yeast protein, high mobility group protein (Hmo1), in rRNA synthesis. For over twenty years, Hmo1 has been proposed to be an activator of transcription by Pol I, but its regulatory mechanism remains largely undefined. Therefore, we used native elongating transcript sequencing (NET-seq) to explore the role of this factor in transcription by Pol I. Our NET-seq results demonstrated that in cells lacking Hmo1 (hmo1D), Pol I occupancy was significantly increased across the rDNA template, indicating an increased pause propensity in these cells. These data suggest that Hmo1 is an important transcription elongation factor for Pol I.

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