Bru-seq

Nascent RNA sequencing

Overview

Bru-seq refers to a family of related technologies for exploring the dynamics of transcription biology in mammalian cells. The methods are related by the selection and sequencing of only RNA molecules that were metabolically labelled during an exposure of the cells to bromouridine (Bru).

Dr. Wilson has worked for more than a decade with Bru-seq inventor and project leader, Dr. Mats Ljungman, to help develop the associated bioinformatics tools for data analysis. The pipeline and browser that developed by our team have served the needs of researchers worldwide, most recently in work done within the ENCODE Project (publications pending).

Learn more about Bru-Seq

https://rna.umich.edu/research/cores/bru-seq-lab/

Publications

Co-transcriptional splicing efficiencies differ within genes and between cell types

Bedi K, Magnuson BR, Narayanan I, Paulsen M, Wilson TE, Ljungman M

RNA 27(7):829-40 (2021)

PMID: 33975916 PMC8208053

Characterization of novel primary miRNA transcription units in human cells using Bru-seq nascent RNA sequencing

Bedi K, Paulsen MT, Wilson TE, Ljungman M

NAR Genom Bioinform 2(1):lqz014 (2020)

PMID: 31709421 PMC6824518

Transcriptional and post-transcriptional regulation of the ionizing radiation response by ATM and p53

Venkata Narayanan I, Paulsen MT, Bedi K, Berg N, Ljungman EA, Francia S, Veloso A, Magnuson B, di Fagagna FD, Wilson TE, Ljungman M

Sci Rep 7:43598 (2017)

PMID: 28256581 PMC5335570

Identifying transcription start sites and active enhancer elements using BruUV-seq

Magnuson B, Veloso A, Kirkconnell KS, de Andrade Lima LC, Paulsen MT, Ljungman EA, Bedi K, Prasad J, Wilson TE, Ljungman M

Sci Rep 5:17978 (2015)

PMID: 26656874 PMC4675984

Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications

Veloso A, Kirkconnell KS, Magnuson B, Biewen B, Paulsen MT, Wilson TE, Ljungman M

Genome Res 24(6):896-905 (2014)

PMID: 24714810 PMC4032854

Use of Bru-Seq and BruChase-Seq for genome-wide assessment of the synthesis and stability of RNA

Paulsen MT, Veloso A, Prasad J, Bedi K, Ljungman EA, Magnuson B, Wilson TE, Ljungman M

Methods 67(1):45-54 (2014)

PMID: 23973811 PMC4009065

Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response

Paulsen MT, Veloso A, Prasad J, Bedi K, Ljungman EA, Tsan YC, Chang CW, Tarrier B, Washburn JG, Lyons R, Robinson DR, Kumar-Sinha C, Wilson TE, Ljungman M

Proc Natl Acad Sci U S A 110(6):2240-5 (2013)

PMID: 23345452 PMC3568384

Genome-wide transcriptional effects of the anti-cancer agent camptothecin

Veloso A, Biewen B, Paulsen MT, Berg N, Carmo de Andrade Lima L, Prasad J, Bedi K, Magnuson B, Wilson TE, Ljungman M

PLoS One 8(10):e78190 (2013)

PMID: 24194914 PMC3806802