Interactome Analysis Illustrates Diverse Gene Regulatory Processes Associated with LIN28A in Human iPS Cell-Derived Neural Progenitor Cells

Abstract

A single protein can be multifaceted, playing different roles depending on the cellular contexts and interacting molecules. LIN28A is a multi-functional RNA-binding protein that governs developmental timing, cell fate determination, stem cell pluripotency, cellular growth, and metabolism. LIN28A is best known as a post-transcriptional regulator of let-7 microRNA biogenesis, but its other roles have been increasingly recognized and studied. Although LIN28A-binding RNAs have been extensively analyzed, protein complexes associated with LIN28A have not been comprehensively studied. To more thoroughly understand the molecular roles of LIN28A, we profiled the endogenous LIN28A-interacting proteins using immunoprecipitation and liquid chromatography-tandem mass spectrometry. In order to enlighten its roles during neural development, we used neural progenitor cells differentiated from human induced pluripotent stem cells. We identified more than 400 LIN28A-interacting proteins, including 149 RNA-independent interactors. These interactors include proteins involved in RNA splicing and translation, as well as endoplasmic reticulum- or stress granule-localizing proteins, SWI/SNF chromatin remodeling complex. In addition, interaction with CARM1 methyltransferase led us to discover an arginine methylation of LIN28A. Overall, our analysis opens a new avenue for studying LIN28A’s gene regulatory roles including those in epigenetic regulation.