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.
Highlights
Information flow from the genome to phenome is dependent on genesis of new RNAs that serve as key as intermediates in this process[1]
These findings suggest that differentially expressed alternative polyadenylation sites (APSs) (DE-APSs) executed function in neuron
Using 16 reads per site as a cutoff, we identified a total of 56,483 APSs expressed in murine gastrocnemius muscles (Supplementary Table S1)
Summary
Information flow from the genome to phenome is dependent on genesis of new RNAs that serve as key as intermediates in this process[1]. Alternative polyadenylation that results in more than one 3′UTR (untranslated region) end per gene is a critical RNA processing mechanism that affects transcriptome diversity and gene expression dynamics[2]. We used WTTS-seq to understand transcriptome changes that alter information flows from genome to the obese phenotype[7]. Results from this effort indicate that DIO stimulated hypothalamic APSs on protein coding genes enriched for cell (neuron) projection morphogenesis, synaptic transmission, dendrite development, synapse organization, regulation of ion transport, learning, neurotransmitter transport, and regulation of vesicle-mediated transport as top ten summary pathways revealed by the Metascape program[8]. Our data clearly demonstrated that alternative transcripts serve as sensitive and powerful biomarkers that can be used to link genes to their functions via detailed biological processes
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