Journal article
Alternative polyadenylation drives genome-to-phenome information detours in the AMPKα1 and AMPKα2 knockout mice
Scientific reports, Vol.8(1), pp.6462-10
12/01/2018
Handle:
https://hdl.handle.net/2376/105551
PMCID: PMC5915415
PMID: 29691479
Abstract
Currently available mouse knockout (KO) lines remain largely uncharacterized for genome-to-phenome (G2P) information flows. Here we test our hypothesis that altered myogenesis seen in AMPKα1- and AMPKα2-KO mice is caused by use of alternative polyadenylation sites (APSs). AMPKα1 and AMPKα2 are two α subunits of adenosine monophosphate-activated protein kinase (AMPK), which serves as a cellular sensor in regulation of many biological events. A total of 56,483 APSs were derived from gastrocnemius muscles. The differentially expressed APSs (DE-APSs) that were down-regulated tended to be distal. The DE-APSs that were related to reduced and increased muscle mass were down-regulated in AMPKα1-KO mice, but up-regulated in AMPKα2-KO mice, respectively. Five genes:
Car3
(carbonic anhydrase 3),
Mylk4
(myosin light chain kinase family, member 4),
Neb
(nebulin),
Obscn
(obscurin) and
Pfkm
(phosphofructokinase, muscle) utilized different APSs with potentially antagonistic effects on muscle function. Overall, gene knockout triggers genome plasticity via use of APSs, completing the G2P processes. However, gene-based analysis failed to reach such a resolution. Therefore, we propose that alternative transcripts are minimal functional units in genomes and the traditional central dogma concept should be now examined under a systems biology approach.
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Details
- Title
- Alternative polyadenylation drives genome-to-phenome information detours in the AMPKα1 and AMPKα2 knockout mice
- Creators
- Shuwen Zhang - Pullman, WA USAYangzi Zhang - Pullman, WA USAXiang Zhou - Pullman, WA USAXing Fu - Pullman, WA USAJennifer J Michal - Pullman, WA USAGuoli Ji - Xiamen, ChinaMin Du - Pullman, WA USAJon F Davis - Pullman, WA USAZhihua Jiang - Pullman, WA USA
- Publication Details
- Scientific reports, Vol.8(1), pp.6462-10
- Academic Unit
- Animal Sciences, Department of; Integrative Physiology and Neuroscience, Department of
- Publisher
- Nature Publishing Group UK; London
- Identifiers
- 99900546839001842
- Language
- English
- Resource Type
- Journal article