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

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SLIC-CAGE : high-resolution transcription start site mapping using nanogram-levels of total RNA. / Cvetesic, Nevena; Leitch, Harry G; Borkowska, Malgorzata; Müller, Ferenc; Carninci, Piero; Hajkova, Petra; Lenhard, Boris.

In: Genome Research, Vol. 28, No. 12, 12.2018, p. 1943-1956.

Research output: Contribution to journalArticlepeer-review

Harvard

Cvetesic, N, Leitch, HG, Borkowska, M, Müller, F, Carninci, P, Hajkova, P & Lenhard, B 2018, 'SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA', Genome Research, vol. 28, no. 12, pp. 1943-1956. https://doi.org/10.1101/gr.235937.118

APA

Cvetesic, N., Leitch, H. G., Borkowska, M., Müller, F., Carninci, P., Hajkova, P., & Lenhard, B. (2018). SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA. Genome Research, 28(12), 1943-1956. https://doi.org/10.1101/gr.235937.118

Vancouver

Author

Cvetesic, Nevena ; Leitch, Harry G ; Borkowska, Malgorzata ; Müller, Ferenc ; Carninci, Piero ; Hajkova, Petra ; Lenhard, Boris. / SLIC-CAGE : high-resolution transcription start site mapping using nanogram-levels of total RNA. In: Genome Research. 2018 ; Vol. 28, No. 12. pp. 1943-1956.

Bibtex

@article{251164e89a9840fb9707be246e6ac04b,
title = "SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA",
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 the 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 µg), 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. This 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 11.5 primordial germ cells.",
author = "Nevena Cvetesic and Leitch, {Harry G} and Malgorzata Borkowska and Ferenc M{\"u}ller and Piero Carninci and Petra Hajkova and Boris Lenhard",
year = "2018",
month = dec,
doi = "10.1101/gr.235937.118",
language = "English",
volume = "28",
pages = "1943--1956",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",
number = "12",

}

RIS

TY - JOUR

T1 - SLIC-CAGE

T2 - high-resolution transcription start site mapping using nanogram-levels of total RNA

AU - Cvetesic, Nevena

AU - Leitch, Harry G

AU - Borkowska, Malgorzata

AU - Müller, Ferenc

AU - Carninci, Piero

AU - Hajkova, Petra

AU - Lenhard, Boris

PY - 2018/12

Y1 - 2018/12

N2 - 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 the 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 µg), 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. This 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 11.5 primordial germ cells.

AB - 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 the 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 µg), 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. This 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 11.5 primordial germ cells.

U2 - 10.1101/gr.235937.118

DO - 10.1101/gr.235937.118

M3 - Article

C2 - 30404778

VL - 28

SP - 1943

EP - 1956

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 12

ER -