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

Authors
  • Prudêncio, Pedro1
  • Rebelo, Kenny2
  • Grosso, Ana Rita3
  • Martinho, Rui Gonçalo4
  • Carmo-Fonseca, Maria2
  • 1 Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal; Center for Biomedical Research, Universidade do Algarve, Faro, Portugal. Electronic address: [email protected] , (Portugal)
  • 2 Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal. , (Portugal)
  • 3 Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal; UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal. , (Portugal)
  • 4 Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal; Center for Biomedical Research, Universidade do Algarve, Faro, Portugal; iBiMED, Departamento de Ciências Médicas, Universidade de Aveiro, Aveiro, Portugal. , (Portugal)
Type
Published Article
Journal
Methods
Publisher
Elsevier
Publication Date
Jun 01, 2020
Volume
178
Pages
89–95
Identifiers
DOI: 10.1016/j.ymeth.2019.09.003
PMID: 31493517
Source
Medline
Keywords
Language
English
License
Unknown

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. Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.

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