Binding specificities of human RNA binding proteins towards structured and linear RNA sequences

Abstract

of RBPs for which we obtained a motif bound to short linear sequences, whereas 36 ~30% preferred structured motifs folding into stem-loops. We also found that 37 many RBPs can bind to multiple distinctly different motifs. Analysis of the matches 38 of the motifs on human genomic sequences suggested novel roles for many RBPs in 39 regulation of splicing, and revealed RBPs that are likely to control specific classes 40 of transcripts. Global analysis of the motifs also revealed an enrichment of G and U 41 nucleotides. Masking of G and U by proteins increases the specificity of RNA folding, 42 as both G and U can pair to two other RNA bases via canonical Watson-Crick or G-U 43 base pairs. The collection containing 145 high resolution binding specificity 44 models for 86 RBPs is the largest systematic resource for the analysis of human 45RBPs, and will greatly facilitate future analysis of the various biological roles of this 46 important class of proteins. 48All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/317909 doi: bioRxiv preprint first posted online May. 9, 2018; 2 INTRODUCTION 49 50The abundance of protein and RNA molecules in a cell depends both on their rates 51 of production and degradation. These rates are determined directly or indirectly by the 52 sequence of DNA. The transcription rate of RNA and the rate of degradation of proteins is 53 determined by DNA and protein sequences, respectively. However, most regulatory steps 54 that control gene expression are influenced by the sequence of the RNA itself. These 55 processes include RNA splicing, localization, stability, and translation. These processes 56 can be affected by RNA-binding proteins (RBPs) that specifically recognize short RNA 57 sequence elements (Glisovic et al., 2008). 58RBPs can recognize their target sites using two mechanisms: they can form direct 59 contacts to the RNA bases of an unfolded RNA chain, and/or recognise folded RNA-60 structures (Loughlin et al., 2009 256 oligonucleotides, and the desired RBP is then used to select its target sites followed 95 by detection of the bound sites using a second microarray. RNAcompete has been used to 96All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. given protein with 15 amino-acids of flanking sequence (see Table S1 for details). 127Constructs containing subsets of RBDs were also analyzed for some very large RBPs. 128Taken together our clone collection covered 942 distinct proteins. The RBPs were 129 expressed in E.coli as fusion proteins with thioredoxin, incorporating an N-terminal 13...

Subcellular mRNA Localization Regulates Ribosome Biogenesis in Migrating Cells

“…Other significantly enriched categories included transcripts involved in RNA processing, intracellular trafficking, cell migration, adhesion, and extracellular matrix (ECM), among others ( Figure 3J; Dataset S7). Such diversity in targets is in line with recent in vitro findings that have revealed LARP6 to possess a highly complex binding specificity, capable of interacting with multiple structural as well as short or gapped linear motifs (Jolma et al, 2020). Together, these results reveal that LARP6 binds to a plethora of transcripts, with RP-mRNAs constituting one of the major target groups.…”

Purine-responsive expression of the Leishmania donovani NT3 purine nucleobase transporter is mediated by a conserved RNA stem–loop

“…Several genes are differentially expressed in response to purine stress, but we were unable to identify the LdNT3 purine response element elsewhere in the L. donovani genome via bioinformatics analysis. 3 However, this does not preclude the possibility that LdNT3 is part of a purine-responsive regulon consisting of multiple genes under the control of a common RBP, as the ability of individual RBPs to interact with several disparate binding sites is well-documented (24,25). Indeed, our observation that the stem-loop is sufficient to confer purine responsiveness to a transcript that is over 90-fold more abundant than LdNT3 strongly suggests that its binding partner is present in substantial excess of what is required for LdNT3 regulation and may therefore play a role in regulating other genes within or outside of the purine stress response pathway.…”

Crystallization and biochemical studies of the NYN domain of human KHNYN

“…1a). The NYN domains of ZC3H12A, ZC3H12B and ZC3H12C share a negatively charged active site with four aspartic acid residues that coordinate one Mg 2+ ion (Jolma et al, 2020;Yokogawa et al, 2016;Xu et al, 2012;Garg et al, 2021). They share significant sequence identity (56-57%) with the NYN domain of human KHNYN (Fig.…”

“…KHNYN is an essential cofactor of ZAP with nuclease activity (Ficarelli et al, 2019), and the ZAP-KHNYN complex functions similarly to ZC3H12A, but with the zinc-finger RNA-binding domain and the NYN endonuclease domain in two different proteins (Jolma et al, 2020;Garg et al, 2021;Yokogawa et al, 2016;Xu et al, 2012;Ficarelli et al, 2021). Here, we report the production, crystallization and data collection of the NYN domain (residues 477-636) of human KHNYN in complex with a heptameric single-stranded RNA (UAUUUAU) from the 3 0 -UTR of interferon lambda 3 (IFNL3).…”