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MNET sequencing facilitates identification of native elongating transcripts in control and Carm1 KO melanoma cells

ABSTRACT: mNET sequencing facilitates identification of native elongating transcripts in control and Carm1 KO melanoma cells

PROVIDER: PRJNA626449 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11569182_1.fastq.gz	Fastqsanger.gz
	SRR11569182_2.fastq.gz	Fastqsanger.gz
	SRR11569183_1.fastq.gz	Fastqsanger.gz
	SRR11569183_2.fastq.gz	Fastqsanger.gz
	SRR11569184_1.fastq.gz	Fastqsanger.gz

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mNET sequencing facilitates identification of native elongating transcripts in control and Carm1 KO melanoma cells

Project description:We investigated whether RNA Pol II mediated transcription was altered in Carm1 KO compared to control KO tumor cells. We examined p-Ser2 CTD Pol II relative to total CTD Pol II using mammalian native elongating transcript sequencing (mNET-Seq) (Nojima et al., 2016). Inactivation of the Carm1 gene substantially increased the normalized read density of p-Ser2 CTD Pol II tags relative total Pol II tags. These data provide evidence for altered transcriptional regulation in Carm1 deficient cells.

2022-01-31 | GSE148905 | GEO

mNET-seq on INTS11-degron cells

Project description:We measured the the dwell time of existed paused RNAPII at the promoter by mammalian native elongating transcript sequencing (mNET-seq).

2023-04-23 | GSE230126 | GEO

mNET-seq on COMPASS-degron cells

Project description:We measured the the dwell time of existed paused RNAPII at the promoter by mammalian native elongating transcript sequencing (mNET-seq). We found a median RNAPII half-life of 5.3 min at protein-coding genes in DMSO pre-treated control mESCs, whereas the RNAPII half-life at these genes significantly slowdown to 8.96 min when pre-treated with Auxin in the DPY30-mAID degron cell. The data suggested that loss H3K4me3 directly slows down the release of paused RNAPII throughout genes.

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Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

Project description:Major features of transcription by human RNA polymerase II (Pol II) remain poorly defined due to a lack of quantitative approaches for visualizing Pol II progress at nucleotide resolution. We developed a simple and powerful approach for performing native elongating transcript sequencing (NET-seq) in human cells that globally maps strand-specific Pol II density at nucleotide resolution. NET-seq exposes a mode of antisense transcription that originates downstream and converges on transcription from the canonical promoter. Convergent transcription is associated with a distinctive chromatin configuration and is characteristic of lower-expressed genes. Integration of NET-seq with genomic footprinting data reveals stereotypic Pol II pausing coincident with transcription factor occupancy. Finally, exons retained in mature transcripts display Pol II pausing signatures that differ markedly from skipped exons, indicating an intrinsic capacity for Pol II to recognize exons with different processing fates.

2015-04-23 | GSE61332 | GEO

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

The arginine methyltransferase CARM1 represses p300•ACT•CREMt axis and is required for spermiogenesis

Project description:DEGs in the round and elongating spermatids between the WT and Carm1-null testis.

2018-05-30 | GSE107984 | GEO

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

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Project description:Antisense transcription can regulate sense gene expression. However, previous annotations of antisense transcription units have been based on detection of mature antisense long non-coding (aslnc)RNAs by RNA-Seq and/or micro-arrays, only giving a partial view of the antisense transcription landscape and incomplete molecular bases for antisense-mediated regulation. Here, we used Native Elongating Transcript sequencing to map genome-wide nascent antisense transcription in fission yeast. Strikingly, antisense transcription was detected for most protein-coding genes, correlating with low sense transcription, especially when overlapping the mRNA start site. RNA profiling revealed that the resulting aslncRNAs mainly correspond to cryptic Xrn1/Exo2-sensitive transcripts (XUTs). ChIP-Seq analyses showed that antisense (as)XUTs expression is associated with specific histone modifications patterns. Finally, we showed that asXUTs are controlled by the histone chaperone Spt6 and respond to meiosis induction, in both cases anti-correlating with levels of the paired-sense mRNAs, supporting physiological significance to antisense-mediated gene attenuation. Our work highlights that antisense transcription is much more extended than anticipated and might constitute an additional non-promoter determinant of gene regulation complexity.

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CARM1 substrate identification

Project description:The goal of the project was global identification of CARM1 substrates. Arginine methylation landscapes were profiled and compared in wild type and CARM1 knockout cells to determine in vivo substrates of CARM1.

2017-07-03 | PXD005871 | Pride

Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts [mNET]

Project description:Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts [mNET]

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