MAAPER: model-based analysis of alternative polyadenylation using 3′ end-linked reads

Abstract Most eukaryotic genes express alternative polyadenylation (APA) isoforms. A growing number of RNA sequencing methods, especially those used for single-cell transcriptome analysis, generate reads close to the polyadenylation site (PAS), termed nearSite reads, hence inherently containing info...

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Main Authors:	Wei Vivian Li, Dinghai Zheng, Ruijia Wang, Bin Tian
Format:	Article
Language:	English
Published:	BMC 2021-08-01
Series:	Genome Biology
Subjects:	Alternative polyadenylation RNA sequencing Bioinformatic tool 3′ end reads Cellular stress Trophoblasts
Online Access:	https://doi.org/10.1186/s13059-021-02429-5

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record_format	Article
spelling	doaj-c936850cff8d4b479959056b2950b07e2021-08-15T11:45:47ZengBMCGenome Biology1474-760X2021-08-0122112110.1186/s13059-021-02429-5MAAPER: model-based analysis of alternative polyadenylation using 3′ end-linked readsWei Vivian Li0Dinghai Zheng1Ruijia Wang2Bin Tian3Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Rutgers, The State University of New JerseyDepartment of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical SchoolDepartment of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical SchoolDepartment of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical SchoolAbstract Most eukaryotic genes express alternative polyadenylation (APA) isoforms. A growing number of RNA sequencing methods, especially those used for single-cell transcriptome analysis, generate reads close to the polyadenylation site (PAS), termed nearSite reads, hence inherently containing information about APA isoform abundance. Here, we present a probabilistic model-based method named MAAPER to utilize nearSite reads for APA analysis. MAAPER predicts PASs with high accuracy and sensitivity and examines different types of APA events with robust statistics. We show MAAPER’s performance with both bulk and single-cell data and its applicability in unpaired or paired experimental designs.https://doi.org/10.1186/s13059-021-02429-5Alternative polyadenylationRNA sequencingBioinformatic tool3′ end readsCellular stressTrophoblasts
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Wei Vivian Li Dinghai Zheng Ruijia Wang Bin Tian
spellingShingle	Wei Vivian Li Dinghai Zheng Ruijia Wang Bin Tian MAAPER: model-based analysis of alternative polyadenylation using 3′ end-linked reads Genome Biology Alternative polyadenylation RNA sequencing Bioinformatic tool 3′ end reads Cellular stress Trophoblasts
author_facet	Wei Vivian Li Dinghai Zheng Ruijia Wang Bin Tian
author_sort	Wei Vivian Li
title	MAAPER: model-based analysis of alternative polyadenylation using 3′ end-linked reads
title_short	MAAPER: model-based analysis of alternative polyadenylation using 3′ end-linked reads
title_full	MAAPER: model-based analysis of alternative polyadenylation using 3′ end-linked reads
title_fullStr	MAAPER: model-based analysis of alternative polyadenylation using 3′ end-linked reads
title_full_unstemmed	MAAPER: model-based analysis of alternative polyadenylation using 3′ end-linked reads
title_sort	maaper: model-based analysis of alternative polyadenylation using 3′ end-linked reads
publisher	BMC
series	Genome Biology
issn	1474-760X
publishDate	2021-08-01
description	Abstract Most eukaryotic genes express alternative polyadenylation (APA) isoforms. A growing number of RNA sequencing methods, especially those used for single-cell transcriptome analysis, generate reads close to the polyadenylation site (PAS), termed nearSite reads, hence inherently containing information about APA isoform abundance. Here, we present a probabilistic model-based method named MAAPER to utilize nearSite reads for APA analysis. MAAPER predicts PASs with high accuracy and sensitivity and examines different types of APA events with robust statistics. We show MAAPER’s performance with both bulk and single-cell data and its applicability in unpaired or paired experimental designs.
topic	Alternative polyadenylation RNA sequencing Bioinformatic tool 3′ end reads Cellular stress Trophoblasts
url	https://doi.org/10.1186/s13059-021-02429-5
work_keys_str_mv	AT weivivianli maapermodelbasedanalysisofalternativepolyadenylationusing3endlinkedreads AT dinghaizheng maapermodelbasedanalysisofalternativepolyadenylationusing3endlinkedreads AT ruijiawang maapermodelbasedanalysisofalternativepolyadenylationusing3endlinkedreads AT bintian maapermodelbasedanalysisofalternativepolyadenylationusing3endlinkedreads
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MAAPER: model-based analysis of alternative polyadenylation using 3′ end-linked reads

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