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High-Confidence Coding and Noncoding Transcriptome Maps

Title
High-Confidence Coding and Noncoding Transcriptome Maps
Author
남진우
Keywords
RNA-SEQ READS; INTEGRATIVE ANALYSIS; SPLICE JUNCTIONS; HUMAN GENOME; LANDSCAPE; RECONSTRUCTION; ANNOTATION; EXPRESSION; REVEALS; QUANTIFICATION
Issue Date
2017-04
Publisher
COLD SPRING HARBOR LAB PRESS
Citation
GENOME RESEARCH, v. 27, no. 6, page. 1050-1062
Abstract
The advent of high-throughput RNA sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic genomes. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed based on RNA-seq reads that lack their orientations (known as unstranded reads) and certain boundary information. Methods to expand the usability of unstranded RNA-seq data by predetermining the orientation of the reads and precisely determining the boundaries of assembled transcripts could significantly benefit the quality of the resulting transcriptome maps. Here, we present a high-performing transcriptome assembly pipeline, called CAFE, that significantly improves the original assemblies, respectively assembled with stranded and/or unstranded RNA-seq data, by orienting unstranded reads using the maximum likelihood estimation and by integrating information about transcription start sites and cleavage and polyadenylation sites. Applying large-scale transcriptomic data comprising 230 billion RNA-seq reads from the ENCODE, Human BodyMap 2.0, The Cancer Genome Atlas, and GTEx projects, CAFE enabled us to predict the directions of about 220 billion unstranded reads, which led to the construction of more accurate transcriptome maps, comparable to the manually curated map, and a comprehensive lncRNA catalog that includes thousands of novel lncRNAs. Our pipeline should not only help to build comprehensive, precise transcriptome maps from complex genomes but also to expand the universe of noncoding genomes.
URI
https://genome.cshlp.org/content/27/6/1050http://repository.hanyang.ac.kr/handle/20.500.11754/113735
ISSN
1088-9051; 1549-5469
DOI
10.1101/gr.214288.116
Appears in Collections:
COLLEGE OF NATURAL SCIENCES[S](자연과학대학) > LIFE SCIENCE(생명과학과) > Articles
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