TY - JOUR
T1 - Principles of mRNA control by human PUM proteins elucidated from multimodal experiments and integrative data analysis
AU - WOLFE, MICHAEL B.
AU - SCHAGAT, TRISTA L.
AU - PAULSEN, MICHELLE T.
AU - MAGNUSON, BRIAN
AU - LJUNGMAN, MATS
AU - PARK, DAEYOON
AU - ZHANG, CHI
AU - CAMPBELL, ZACHARY T.
AU - GOLDSTROHM, AARON C.
AU - FREDDOLINO, PETER L.
N1 - Publisher Copyright:
© 2020 Wolfe et al.
PY - 2020/11
Y1 - 2020/11
N2 - The human PUF-family proteins, PUM1 and PUM2, posttranscriptionally regulate gene expression by binding to a PUM recognition element (PRE) in the 3'-UTR of target mRNAs. Hundreds of PUM1/2 targets have been identified from changes in steady-state RNA levels; however, prior studies could not differentiate between the contributions of changes in transcription and RNA decay rates. We applied metabolic labeling to measure changes in RNA turnover in response to depletion of PUM1/2, showing that human PUM proteins regulate expression almost exclusively by changing RNA stability. We also applied an in vitro selection workflow to precisely identify the binding preferences of PUM1 and PUM2. By integrating our results with prior knowledge, we developed a "rulebook"of key contextual features that differentiate functional versus nonfunctional PREs, allowing us to train machine learning models that accurately predict the functional regulation of RNA targets by the human PUM proteins.
AB - The human PUF-family proteins, PUM1 and PUM2, posttranscriptionally regulate gene expression by binding to a PUM recognition element (PRE) in the 3'-UTR of target mRNAs. Hundreds of PUM1/2 targets have been identified from changes in steady-state RNA levels; however, prior studies could not differentiate between the contributions of changes in transcription and RNA decay rates. We applied metabolic labeling to measure changes in RNA turnover in response to depletion of PUM1/2, showing that human PUM proteins regulate expression almost exclusively by changing RNA stability. We also applied an in vitro selection workflow to precisely identify the binding preferences of PUM1 and PUM2. By integrating our results with prior knowledge, we developed a "rulebook"of key contextual features that differentiate functional versus nonfunctional PREs, allowing us to train machine learning models that accurately predict the functional regulation of RNA targets by the human PUM proteins.
KW - Machine learning
KW - Pumilio
KW - RNA decay
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U2 - 10.1261/rna.077362.120
DO - 10.1261/rna.077362.120
M3 - Article
C2 - 32753408
AN - SCOPUS:85093529241
SN - 1355-8382
VL - 26
SP - 1680
EP - 1703
JO - RNA
JF - RNA
IS - 11
ER -