SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA

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Title: SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA
Authors: Cvetesic, N
Leitch, HG
Borkowska, M
Mueller, F
Carninci, P
Hajkova, P
Lenhard, B
Item 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.
Issue Date: Dec-2018
Date of Acceptance: 25-Oct-2018
URI: http://hdl.handle.net/10044/1/66444
DOI: https://doi.org/10.1101/gr.235937.118
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/Funder: Wellcome Trust
Commission of the European Communities
Funder's Grant Number: 106954/Z/15/Z
648879
Keywords: 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
Animals
Gene Library
High-Throughput Nucleotide Sequencing
Mice
Promoter Regions, Genetic
RNA, Messenger
Sequence Analysis, RNA
Transcription Initiation Site
Animals
Mice
RNA, Messenger
Sequence Analysis, RNA
Gene Library
Transcription Initiation Site
Promoter Regions, Genetic
High-Throughput Nucleotide Sequencing
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
Bioinformatics
06 Biological Sciences
11 Medical and Health Sciences
Publication Status: Published
Open Access location: https://genome.cshlp.org/content/early/2018/11/07/gr.235937.118.full.pdf+html
Online Publication Date: 2018-11-07
Appears in Collections:Clinical Sciences
Molecular Sciences
Faculty of Medicine



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