Unknown

Dataset Information

0

MountainClimber Identifies Alternative Transcription Start and Polyadenylation Sites in RNA-Seq.

ABSTRACT: Alternative transcription start (ATS) and alternative polyadenylation (APA) create alternative RNA isoforms and modulate many aspects of RNA expression and protein production. However, ATS and APA remain difficult to detect in RNA sequencing (RNA-seq). Here, we developed mountainClimber, a de novo cumulative-sum-based approach to identify ATS and APA as change points. Unlike many existing methods, mountainClimber runs on a single sample and identifies multiple ATS or APA sites anywhere in the transcript. We analyzed 2,342 GTEx samples (36 tissues, 215 individuals) and found that tissue type is the predominant driver of transcript end variations. 75% and 65% of genes exhibited differential APA and ATS across tissues, respectively. In particular, testis displayed longer 5' untranslated regions (UTRs) and shorter 3' UTRs, often in genes related to testis-specific biology. Overall, we report the largest study of transcript ends across human tissues to our knowledge. mountainClimber is available at github.com/gxiaolab/mountainClimber.

SUBMITTER: Cass AA 

PROVIDER: S-EPMC6813887 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

Json Xml
altmetric image

Publications

mountainClimber Identifies Alternative Transcription Start and Polyadenylation Sites in RNA-Seq.

Cass Ashley A AA   Xiao Xinshu X  

Cell systems 20190918 4

Alternative transcription start (ATS) and alternative polyadenylation (APA) create alternative RNA isoforms and modulate many aspects of RNA expression and protein production. However, ATS and APA remain difficult to detect in RNA sequencing (RNA-seq). Here, we developed mountainClimber, a de novo cumulative-sum-based approach to identify ATS and APA as change points. Unlike many existing methods, mountainClimber runs on a single sample and identifies multiple ATS or APA sites anywhere in the tr  ...[more]

Similar Datasets

Unknown SEASTAR: systematic evaluation of alternative transcription start sites in RNA.
| S-EPMC5934623 | biostudies-literature
Transcriptomics Profiling of alternative transcription start sites and alternative polyadenylation sites in Xenopus tropicalis
2020-02-01 | GSE110063 | GEO
Unknown Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq.
| S-EPMC8744680 | biostudies-literature
Unknown Cloning and characterization of buffalo NANOG gene: alternative transcription start sites, splicing, and polyadenylation in embryonic stem cell-like cells.
| S-EPMC3358104 | biostudies-literature
Unknown CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data.
| S-EPMC10636040 | biostudies-literature
Genomics Profiling of alternative transcription start sites and alternative polyadenylation sites in Xenopus tropicalis
| PRJNA432702 | ENA
Unknown Identifying transcription start sites and active enhancer elements using BruUV-seq.
| S-EPMC4675984 | biostudies-literature
Unknown Regulating retrotransposon activity through the use of alternative transcription start sites.
| S-EPMC5341516 | biostudies-literature
Unknown Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq.
| S-EPMC3045608 | biostudies-literature
Unknown Pervasive isoform-specific translational regulation via alternative transcription start sites in mammals.
| S-EPMC4965872 | biostudies-literature