RT Journal Article
SR Electronic
T1 A Multi-Parameter Analysis of Cellular Coordination of Multiple Transcriptome Regulation Mechanisms
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 104901
DO 10.1101/104901
A1 Wen Jiang
A1 Zhanyong Guo
A1 Nuno Lages
A1 W. Jim Zheng
A1 Denis Feliers
A1 Fangyuan Zhang
A1 Degeng Wang
YR 2017
UL http://biorxiv.org/content/early/2017/01/31/104901.abstract
AB To understand cellular coordination of multiple transcriptome regulation mechanisms, we simultaneously measured three parameters – transcription rate (TR), mRNA abundance (RA) and translation activity (TA) – and assessed mRNA stability with the RA to TR ratio. This revealed multiple quantitative insights. First, the dataset enabled an assessment of the contribution of the stabilization-by-translation regulatory mechanism. We observed an overall positive correlation between mRNA stability and translation activity. However, the correlation is moderate. Many genes deviate from the overall trend in a pathway/function specific manner. Second, the moderateness of this correlation can be explained by variation in individual mRNAs’ proportions occupied by un-translated regions (UTR), as the UTR proportion exhibits a negative relationship with the level of correlation between the two factors. High-UTR-proportion mRNAs largely defy the stabilization-by-translation regulatory mechanism, in that they stay out of the polysome complex but remain relatively stable; mRNAs with little UTRs, on the contrary, follow this regulation much better. Third, the genomic profiles of the three parameters are systematically different in terms of key statistical features. Sequentially more genes exhibit extreme low or high expression values from TR to RA, and then to TA. In other words, as a consequence of the cellular activities in coordinating these regulatory mechanisms, sequentially higher levels of selectivity are imposed on the gene expression process as genetic information flow from the genome to the proteome. In summary, we presented a quantitative delineation of the relationship among multiple transcriptome regulation parameters, i.e., how the cells coordinate corresponding regulatory mechanisms.