SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA
File(s)
Published version
Author(s)
Type
Journal Article
Abstract
Cap analysis of gene expression (CAGE) is a methodology for genome-wide quantitative mapping of mRNA 5′ ends to precisely capture transcription start sites at a single nucleotide resolution. In combination with high-throughput sequencing, CAGE has revolutionized our understanding of rules of transcription initiation, led to discovery of new core promoter sequence features and discovered transcription initiation at enhancers genome-wide. The biggest limitation of CAGE is that even the most recently improved version (nAnT-iCAGE) still requires large amounts of total cellular RNA (5 micrograms), preventing its application to scarce biological samples such as those from early embryonic development or rare cell types. Here, we present SLIC-CAGE, a Super-Low Input Carrier-CAGE approach to capture 5′ ends of RNA polymerase II transcripts from as little as 5-10 ng of total RNA. The dramatic increase in sensitivity is achieved by specially designed, selectively degradable carrier RNA. We demonstrate the ability of SLIC-CAGE to generate data for genome-wide promoterome with 1000-fold less material than required by existing CAGE methods by generating a complex, high quality library from mouse embryonic day (E) 11.5 primordial germ cells.
Date Issued
2018-12
Date Acceptance
2018-10-25
Citation
Genome Research, 2018, 28 (12), pp.1943-1956
ISSN
1088-9051
Publisher
Cold Spring Harbor Laboratory Press
Start Page
1943
End Page
1956
Journal / Book Title
Genome Research
Volume
28
Issue
12
Copyright Statement
This manuscript is Open Access. This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International license), as described at http://creativecommons.org/licenses/by/4.0/.
Sponsor
Wellcome Trust
Commission of the European Communities
Identifier
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000451913800015&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
Grant Number
106954/Z/15/Z
648879
Subjects
Science & Technology
Life Sciences & Biomedicine
Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Genetics & Heredity
ANALYSIS GENE-EXPRESSION
CAP-ANALYSIS
PROMOTER ELEMENT
GERM-CELL
RECOGNITION
DROSOPHILA
NANOCAGE
DPE
Publication Status
Published
Date Publish Online
2018-11-07