Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation

Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation

Motivation: Pre-mRNA cleavage and polyadenylation are essential steps for 3′-end maturation and subsequent stability and degradation of mRNAs. This process is highly controlled by cis-regulatory elements surrounding the cleavage/polyadenylation sites (polyA sites), which are frequently constrained b...

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Main Authors: Hafez, Dina, Ni, Ting, Mukherjee, Sayan, Zhu, Jun, Ohler, Uwe
Format: Online
Language:English
Published: Oxford University Press 2013
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694680/
id pubmed-3694680
recordtype oai_dc
spelling pubmed-36946802013-06-27 Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation Hafez, Dina Ni, Ting Mukherjee, Sayan Zhu, Jun Ohler, Uwe Ismb/Eccb 2013 Proceedings Papers Committee July 21 to July 23, 2013, Berlin, Germany Motivation: Pre-mRNA cleavage and polyadenylation are essential steps for 3′-end maturation and subsequent stability and degradation of mRNAs. This process is highly controlled by cis-regulatory elements surrounding the cleavage/polyadenylation sites (polyA sites), which are frequently constrained by sequence content and position. More than 50% of human transcripts have multiple functional polyA sites, and the specific use of alternative polyA sites (APA) results in isoforms with variable 3′-untranslated regions, thus potentially affecting gene regulation. Elucidating the regulatory mechanisms underlying differential polyA preferences in multiple cell types has been hindered both by the lack of suitable data on the precise location of cleavage sites, as well as of appropriate tests for determining APAs with significant differences across multiple libraries. Oxford University Press 2013-07-01 2013-06-19 /pmc/articles/PMC3694680/ /pubmed/23812974 http://dx.doi.org/10.1093/bioinformatics/btt233 Text en © The Author 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Hafez, Dina
Ni, Ting
Mukherjee, Sayan
Zhu, Jun
Ohler, Uwe
spellingShingle Hafez, Dina
Ni, Ting
Mukherjee, Sayan
Zhu, Jun
Ohler, Uwe
Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation
author_facet Hafez, Dina
Ni, Ting
Mukherjee, Sayan
Zhu, Jun
Ohler, Uwe
author_sort Hafez, Dina
title Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation
title_short Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation
title_full Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation
title_fullStr Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation
title_full_unstemmed Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation
title_sort genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation
description Motivation: Pre-mRNA cleavage and polyadenylation are essential steps for 3′-end maturation and subsequent stability and degradation of mRNAs. This process is highly controlled by cis-regulatory elements surrounding the cleavage/polyadenylation sites (polyA sites), which are frequently constrained by sequence content and position. More than 50% of human transcripts have multiple functional polyA sites, and the specific use of alternative polyA sites (APA) results in isoforms with variable 3′-untranslated regions, thus potentially affecting gene regulation. Elucidating the regulatory mechanisms underlying differential polyA preferences in multiple cell types has been hindered both by the lack of suitable data on the precise location of cleavage sites, as well as of appropriate tests for determining APAs with significant differences across multiple libraries.
publisher Oxford University Press
publishDate 2013
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694680/
_version_ 1611990061910327296

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