Comprehensive comparative analysis of 5′-end RNA-sequencing methods

Xian Adiconis; Adam L. Haber; Sean K. Simmons; Ami Levy Moonshine; Zhe Ji; Michele A. Busby; Xi Shi; Justin Jacques; Madeline A. Lancaster; Jen Q. Pan; Aviv Regev; Joshua Z. Levin

doi:10.1038/s41592-018-0014-2

Comprehensive comparative analysis of 5′-end RNA-sequencing methods

Xian Adiconis, Adam L. Haber, Sean K. Simmons, Ami Levy Moonshine, Zhe Ji, Michele A. Busby, Xi Shi, Justin Jacques, Madeline A. Lancaster, Jen Q. Pan, Aviv Regev, Joshua Z. Levin^*

^*Corresponding author for this work

Pharmacology

Research output: Contribution to journal › Article › peer-review

69 Scopus citations

Abstract

Specialized RNA-seq methods are required to identify the 5′ ends of transcripts, which are critical for studies of gene regulation, but these methods have not been systematically benchmarked. We directly compared six such methods, including the performance of five methods on a single human cellular RNA sample and a new spike-in RNA assay that helps circumvent challenges resulting from uncertainties in annotation and RNA processing. We found that the 'cap analysis of gene expression' (CAGE) method performed best for mRNA and that most of its unannotated peaks were supported by evidence from other genomic methods. We applied CAGE to eight brain-related samples and determined sample-specific transcription start site (TSS) usage, as well as a transcriptome-wide shift in TSS usage between fetal and adult brain.

Original language	English (US)
Pages (from-to)	505-511
Number of pages	7
Journal	Nature Methods
Volume	15
Issue number	7
DOIs	https://doi.org/10.1038/s41592-018-0014-2
State	Published - Jul 1 2018

Funding

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/s41592-018-0014-2

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abstract = "Specialized RNA-seq methods are required to identify the 5′ ends of transcripts, which are critical for studies of gene regulation, but these methods have not been systematically benchmarked. We directly compared six such methods, including the performance of five methods on a single human cellular RNA sample and a new spike-in RNA assay that helps circumvent challenges resulting from uncertainties in annotation and RNA processing. We found that the 'cap analysis of gene expression' (CAGE) method performed best for mRNA and that most of its unannotated peaks were supported by evidence from other genomic methods. We applied CAGE to eight brain-related samples and determined sample-specific transcription start site (TSS) usage, as well as a transcriptome-wide shift in TSS usage between fetal and adult brain.",

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AU - Haber, Adam L.

AU - Simmons, Sean K.

AU - Levy Moonshine, Ami

AU - Ji, Zhe

AU - Busby, Michele A.

AU - Shi, Xi

AU - Jacques, Justin

AU - Lancaster, Madeline A.

AU - Pan, Jen Q.

AU - Regev, Aviv

AU - Levin, Joshua Z.

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AB - Specialized RNA-seq methods are required to identify the 5′ ends of transcripts, which are critical for studies of gene regulation, but these methods have not been systematically benchmarked. We directly compared six such methods, including the performance of five methods on a single human cellular RNA sample and a new spike-in RNA assay that helps circumvent challenges resulting from uncertainties in annotation and RNA processing. We found that the 'cap analysis of gene expression' (CAGE) method performed best for mRNA and that most of its unannotated peaks were supported by evidence from other genomic methods. We applied CAGE to eight brain-related samples and determined sample-specific transcription start site (TSS) usage, as well as a transcriptome-wide shift in TSS usage between fetal and adult brain.

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Comprehensive comparative analysis of 5′-end RNA-sequencing methods

Abstract

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ASJC Scopus subject areas

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