Mammalian NET-seq reveals genome-wide nascent transcription coupled to RNA processing

T Nojima, T Gomes, ARF Grosso, H Kimura, MJ Dye… - Cell, 2015 - cell.com
Transcription is a highly dynamic process. Consequently, we have developed native
elongating transcript sequencing technology for mammalian chromatin (mNET-seq), which …

Mammalian NET-seq analysis defines nascent RNA profiles and associated RNA processing genome-wide

T Nojima, T Gomes, M Carmo-Fonseca… - Nature protocols, 2016 - nature.com
The transcription cycle of RNA polymerase II (Pol II) correlates with changes to the
phosphorylation state of its large subunit C-terminal domain (CTD). We recently developed …

Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution

A Mayer, J Di Iulio, S Maleri, U Eser, J Vierstra… - Cell, 2015 - cell.com
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 …

Genome-wide profiling of RNA polymerase transcription at nucleotide resolution in human cells with native elongating transcript sequencing

A Mayer, LS Churchman - Nature protocols, 2016 - nature.com
Many features of how gene transcription occurs in human cells remain unclear, mainly
because of a lack of quantitative approaches to follow genome transcription with nucleotide …

RNA-seq: from technology to biology

S Marguerat, J Bähler - Cellular and molecular life sciences, 2010 - Springer
Next-generation sequencing technologies are now being exploited not only to analyse static
genomes, but also dynamic transcriptomes in an approach termed RNA-seq. Although these …

POINT technology illuminates the processing of polymerase-associated intact nascent transcripts

R Sousa-Luis, G Dujardin, I Zukher, H Kimura… - Molecular cell, 2021 - cell.com
Mammalian chromatin is the site of both RNA polymerase II (Pol II) transcription and coupled
RNA processing. However, molecular details of such co-transcriptional mechanisms remain …

Predicting long non-coding RNAs using RNA sequencing

NE Ilott, CP Ponting - Methods, 2013 - Elsevier
The advent of next-generation sequencing, and in particular RNA-sequencing (RNA-seq),
technologies has expanded our knowledge of the transcriptional capacity of human and …

Nascent transcript sequencing visualizes transcription at nucleotide resolution

LS Churchman, JS Weissman - Nature, 2011 - nature.com
Recent studies of transcription have revealed a level of complexity not previously
appreciated even a few years ago, both in the intricate use of post-initiation control and the …

Global run-on sequencing (GRO-Seq)

A Gardini - Enhancer RNAs: Methods and Protocols, 2017 - Springer
Transcription occurring at gene loci results in accumulation of mature RNA molecules (ie,
mRNAs) that can be easily assayed by RT-PCR or RNA sequencing. However, the steady …

Finding the active genes in deep RNA-seq gene expression studies

T Hart, HK Komori, S LaMere, K Podshivalova… - BMC genomics, 2013 - Springer
Background Early application of second-generation sequencing technologies to transcript
quantitation (RNA-seq) has hinted at a vast mammalian transcriptome, including transcripts …