c Illustration of a putative model for binding of the NEIL1 RNA to the ADAR1. The ADAR1 deaminase domain (silver) are modeled from ADAR2 by Phyre2. The dsRNA-binding domains (pink) are modeled in one possible conformation as described in the “Methods”. The editing site mismatch (also...
rerio and human orthologous RBPs of the core mRNA interactome and for non-RNA-binding orthologous proteins (non-RNA binders). (e) Examples of orthologous RBPs with increased copy number of motifs from c. Protein sequences are not drawn to scale; the relative position of domains and motifs ...
Predicting protein binding sites on arbitrary RNA or DNA sequences is along-standingand unsolved task of computa- tional biology research. While initial methods were predominantly mechanistic programs, often operating via scanning of sequences for a suitable binding site using a position-weight-matrix ...
respectively. Horizontal bars show the relative locations of RNA-binding regions (RBRs). (B) The left panel depicts the general topology of membrane-anchored p33 and p92, while the right panel shows an cross-section enlargement of them interacting to form the interior protein shell of a VRC sp...
Similar to previous experiments (Hentze et al., 2018), we found that the hESC interactome is strongly over-represented for known RNA-binding functions and RNA-binding domains associated with RNA metabolism (Figures S1D and S1E; Data S2A). Moreover, only 63% of the RNA-interacting proteins...
AGO protein contains two functional domains that may interact with miRNA: N-PAZ domain that usually plays the 3′-nucleotide-binding on miRNAs (around 3 bp long) [46] and MID-PIWI domain that interact with 11th or 15th nucleotide on miRNAs [63]. The evidences showed that the functional ...
The development of a safe, effective, reversible, non-hormonal contraceptive method for men has been an ongoing effort for the past few decades. However, despite significant progress on elucidating the function of key proteins involved in reproduction, u
RNA-binding proteins (RBPs) are an essential group of proteins that interact with RNA by recognizing specific RNA-binding domains, and are involved in post-transcriptional regulation of RNA splicing, translocation, sequence editing, intracellular localization, and translational control1,2,3. Accurately...
Many DNA-binding proteins were also enriched in PTex and 2C, in particular proteins containing Helix-Turn-Helix (HTH) DNA-binding domains (Fig.2g). This was unexpected since we included DNase treatment steps in the 2C and PTex protocols (see ‘Methods’). On the other hand, theS. aureus...
At the same time, HRAS over-expression resulted in selection of a shorter 3' UTR, which removes known miRNA binding sites present in the ALong UTR and likely increased translation of EGFR mRNAs [41]. Widespread 3'UTR shortening to escape miRNA regulation has been observed previously in ...