Analysis of Mammalian Native Elongating Transcript sequencing (mNET-seq) high-throughput data

Pedro Prudêncio, Kenny Rebelo, Ana Rita Grosso, Rui Gonçalo Martinho, Maria Carmo-Fonseca

Research output: Contribution to journalArticle

Abstract

Mammalian Native Elongating Transcript sequencing (mNET-seq) is a recently developed technique that generates genome-wide profiles of nascent transcripts associated with RNA polymerase II (Pol II) elongation complexes. The ternary transcription complexes formed by Pol II, DNA template and nascent RNA are first isolated, without crosslinking, by immunoprecipitation with antibodies that specifically recognize the different phosphorylation states of the polymerase large subunit C-terminal domain (CTD). The coordinate of the 3′ end of the RNA in the complexes is then identified by high-throughput sequencing. The main advantage of mNET-seq is that it provides global, bidirectional maps of Pol II CTD phosphorylation-specific nascent transcripts and coupled RNA processing at single nucleotide resolution. Here we describe the general pipeline to prepare and analyse high-throughput data from mNET-seq experiments.

Original languageEnglish
JournalMethods
DOIs
Publication statusPublished - 1 Jan 2019

Fingerprint

Phosphorylation
Throughput
RNA
DNA Polymerase II
RNA Polymerase II
Transcription
Immunoprecipitation
Crosslinking
Elongation
Nucleotides
Pipelines
Genes
Genome
Antibodies
Processing
Experiments

Keywords

  • Co-transcriptional splicing
  • mNET-seq
  • Nascent RNA
  • RNA polymerase II

Cite this

Prudêncio, Pedro ; Rebelo, Kenny ; Grosso, Ana Rita ; Martinho, Rui Gonçalo ; Carmo-Fonseca, Maria. / Analysis of Mammalian Native Elongating Transcript sequencing (mNET-seq) high-throughput data. In: Methods. 2019.
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Analysis of Mammalian Native Elongating Transcript sequencing (mNET-seq) high-throughput data. / Prudêncio, Pedro; Rebelo, Kenny; Grosso, Ana Rita; Martinho, Rui Gonçalo; Carmo-Fonseca, Maria.

In: Methods, 01.01.2019.

Research output: Contribution to journalArticle

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