A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis.
During microRNA (miRNA) biogenesis, two endonucleolytic reactions convert stem-loop-structured precursors into mature miRNAs. These processing steps can be posttranscriptionally regulated by RNA-binding proteins (RBPs). Here, we have used a proteomics-based pull-down approach to map and characterize the interactome of a multitude of pre-miRNAs. We identify ∼180 RBPs that interact specifically with distinct ... pre-miRNAs. For functional validation, we combined RNAi and CRISPR/Cas-mediated knockout experiments to analyze RBP-dependent changes in miRNA levels. Indeed, a large number of the investigated candidates, including splicing factors and other mRNA processing proteins, have effects on miRNA processing. As an example, we show that TRIM71/LIN41 is a potent regulator of miR-29a processing and its inactivation directly affects miR-29a targets. We provide an extended database of RBPs that interact with pre-miRNAs in extracts of different cell types, highlighting a widespread layer of co- and posttranscriptional regulation of miRNA biogenesis.
Mesh Terms:
A549 Cells, Binding Sites, CRISPR-Cas Systems, DEAD-box RNA Helicases, Databases, Genetic, Gene Expression Regulation, Genomics, HEK293 Cells, HeLa Cells, Hep G2 Cells, High-Throughput Nucleotide Sequencing, Humans, Jurkat Cells, MCF-7 Cells, MicroRNAs, Nucleic Acid Conformation, Protein Binding, Proteomics, RNA Interference, RNA Precursors, RNA Processing, Post-Transcriptional, RNA, Messenger, RNA-Binding Proteins, Ribonuclease III, Sequence Analysis, RNA, Structure-Activity Relationship, Transcription, Genetic, Transfection, Tripartite Motif Proteins, Ubiquitin-Protein Ligases
A549 Cells, Binding Sites, CRISPR-Cas Systems, DEAD-box RNA Helicases, Databases, Genetic, Gene Expression Regulation, Genomics, HEK293 Cells, HeLa Cells, Hep G2 Cells, High-Throughput Nucleotide Sequencing, Humans, Jurkat Cells, MCF-7 Cells, MicroRNAs, Nucleic Acid Conformation, Protein Binding, Proteomics, RNA Interference, RNA Precursors, RNA Processing, Post-Transcriptional, RNA, Messenger, RNA-Binding Proteins, Ribonuclease III, Sequence Analysis, RNA, Structure-Activity Relationship, Transcription, Genetic, Transfection, Tripartite Motif Proteins, Ubiquitin-Protein Ligases
Mol. Cell
Date: Apr. 20, 2017
PubMed ID: 28431233
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