Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq.
Cluster Analysis
Computational Biology
/ methods
Gene Expression Profiling
/ methods
Gene Ontology
High-Throughput Nucleotide Sequencing
/ methods
Humans
Promoter Regions, Genetic
Sequence Analysis, RNA
/ methods
Transcription Initiation Site
Transcription Initiation, Genetic
Transcriptome
Yeasts
/ genetics
Journal
Genome research
ISSN: 1549-5469
Titre abrégé: Genome Res
Pays: United States
ID NLM: 9518021
Informations de publication
Date de publication:
06 2020
06 2020
Historique:
received:
22
01
2020
accepted:
18
06
2020
pubmed:
15
7
2020
medline:
21
7
2021
entrez:
15
7
2020
Statut:
ppublish
Résumé
Accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation. However, current protocols for genome-wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5' ends from as little as 50 ng total RNA. Including depletion of uncapped RNA and reaction cleanups, a STRIPE-seq library can be constructed in about 5 h. We show application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for quantification of transcript levels and analysis of differential gene expression. In conjunction with our ready-to-use computational workflows, STRIPE-seq is a straightforward, efficient means by which to probe the landscape of transcriptional initiation.
Identifiants
pubmed: 32660958
pii: gr.261545.120
doi: 10.1101/gr.261545.120
pmc: PMC7370879
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
910-923Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM122566
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM128631
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR001108
Pays : United States
Informations de copyright
© 2020 Policastro et al.; Published by Cold Spring Harbor Laboratory Press.
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