From computational models of the splicing code to regulatory mechanisms and therapeutic implications
C Capitanchik, OG Wilkins, N Wagner… - Nature Reviews …, 2024 - nature.com
Since the discovery of RNA splicing and its role in gene expression, researchers have
sought a set of rules, an algorithm or a computational model that could predict the splice …
sought a set of rules, an algorithm or a computational model that could predict the splice …
Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo
Summary Polycomb repressive complex 2 (PRC2) is reported to bind to many RNAs and
has become a central player in reports of how long non-coding RNAs (lncRNAs) regulate …
has become a central player in reports of how long non-coding RNAs (lncRNAs) regulate …
The regulatory landscape of interacting RNA and protein pools in cellular homeostasis and cancer
CJ Gallardo-Dodd, C Kutter - Human Genomics, 2024 - Springer
Biological systems encompass intricate networks governed by RNA-protein interactions that
play pivotal roles in cellular functions. RNA and proteins constituting 1.1% and 18% of the …
play pivotal roles in cellular functions. RNA and proteins constituting 1.1% and 18% of the …
Prediction of protein-RNA interactions from single-cell transcriptomic data
Proteins are crucial in regulating every aspect of RNA life, yet understanding their
interactions with coding and noncoding RNAs remains limited. Experimental studies are …
interactions with coding and noncoding RNAs remains limited. Experimental studies are …
LARP1 binds ribosomes and TOP mRNAs in repressed complexes
JA Saba, Z Huang, KL Schole, X Ye, SD Bhatt… - The EMBO …, 2024 - embopress.org
Terminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in
mammals and are regulated to tune ribosome synthesis to cell state. Previous studies have …
mammals and are regulated to tune ribosome synthesis to cell state. Previous studies have …
Interrogation of RNA-protein interaction dynamics in bacterial growth
Characterising RNA–protein interaction dynamics is fundamental to understand how
bacteria respond to their environment. In this study, we have analysed the dynamics of 91 …
bacteria respond to their environment. In this study, we have analysed the dynamics of 91 …
Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data
The uncovering of protein-RNA interactions enables a deeper understanding of RNA
processing. Recent multiplexed crosslinking and immunoprecipitation (CLIP) technologies …
processing. Recent multiplexed crosslinking and immunoprecipitation (CLIP) technologies …
Predicting conserved functional interactions for long noncoding RNAs via deep learning
MB Kratz, KN Smith - Frontiers in RNA Research, 2024 - frontiersin.org
Long noncoding RNA (lncRNA) genes outnumber protein coding genes in the human
genome and the majority remain uncharacterized. A major difficulty in generalizing …
genome and the majority remain uncharacterized. A major difficulty in generalizing …
[HTML][HTML] LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins
JA Saba, Z Huang, KL Schole, X Ye, SD Bhatt, Y Li… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Terminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in
mammals and are regulated to tune ribosome synthesis to cell state. Previous studies …
mammals and are regulated to tune ribosome synthesis to cell state. Previous studies …
[HTML][HTML] Phosphorylation of intrinsically disordered regions steers the protein-RNA binding profiles
Due to their capacity to mediate repetitive protein interactions, intrinsically disordered
regions (IDRs) are crucial for the formation of various types of protein-RNA complexes. The …
regions (IDRs) are crucial for the formation of various types of protein-RNA complexes. The …