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Comprehensive comparative analysis of 5'-end RNA-sequencing methods.

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.

SUBMITTER: Adiconis X

PROVIDER: S-EPMC6075671 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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Comprehensive comparative analysis of 5'-end RNA-sequencing methods.

Adiconis Xian X Haber Adam L AL Simmons Sean K SK Levy Moonshine Ami A Ji Zhe Z Busby Michele A MA Shi Xi X Jacques Justin J Lancaster Madeline A MA Pan Jen Q JQ Regev Aviv A Levin Joshua Z JZ

Nature methods 20180604 7

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) metho ...[more]

PMID: 29867192

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