Understanding the transcriptome through RNA structure

Y Wan, M Kertesz, RC Spitale, E Segal… - Nature Reviews …, 2011 - nature.com
RNA structure is crucial for gene regulation and function. In the past, transcriptomes have
largely been parsed by primary sequences and expression levels, but it is now becoming …

The human RBPome: from genes and proteins to human disease

Y Neelamraju, S Hashemikhabir, SC Janga - Journal of proteomics, 2015 - Elsevier
RNA binding proteins (RBPs) play a central role in mediating post transcriptional regulation
of genes. However less is understood about them and their regulatory mechanisms. In this …

Extensive transcriptional heterogeneity revealed by isoform profiling

V Pelechano, W Wei, LM Steinmetz - Nature, 2013 - nature.com
Transcript function is determined by sequence elements arranged on an individual RNA
molecule. Variation in transcripts can affect messenger RNA stability, localization and …

[PDF][PDF] Stress-induced translation inhibition through rapid displacement of scanning initiation factors

S Bresson, V Shchepachev, C Spanos, TW Turowski… - Molecular cell, 2020 - cell.com
Cellular responses to environmental stress are frequently mediated by RNA-binding
proteins (RBPs). Here, we examined global RBP dynamics in Saccharomyces cerevisiae in …

[HTML][HTML] Dynamical control enables the formation of demixed biomolecular condensates

AZ Lin, KM Ruff, F Dar, A Jalihal, MR King… - Nature …, 2023 - nature.com
Cellular matter can be organized into compositionally distinct biomolecular condensates.
For example, in Ashbya gossypii, the RNA-binding protein Whi3 forms distinct condensates …

[PDF][PDF] Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition

C Baejen, P Torkler, S Gressel, K Essig, J Söding… - Molecular cell, 2014 - cell.com
Biogenesis of eukaryotic messenger ribonucleoprotein complexes (mRNPs) involves the
synthesis, splicing, and 3′ processing of pre-mRNA, and the assembly of mature mRNPs …

Computational analysis of conserved RNA secondary structure in transcriptomes and genomes

SR Eddy - Annual review of biophysics, 2014 - annualreviews.org
Transcriptomics experiments and computational predictions both enable systematic
discovery of new functional RNAs. However, many putative noncoding transcripts arise …

Finding the target sites of RNA‐binding proteins

X Li, H Kazan, HD Lipshitz… - Wiley Interdisciplinary …, 2014 - Wiley Online Library
RNA–protein interactions differ from DNA–protein interactions because of the central role of
RNA secondary structure. Some RNA‐binding domains (RBDs) recognize their target sites …

Alternative polyadenylation diversifies post‐transcriptional regulation by selective RNA–protein interactions

I Gupta, S Clauder‐Münster, B Klaus… - Molecular systems …, 2014 - embopress.org
Recent research has uncovered extensive variability in the boundaries of transcript isoforms,
yet the functional consequences of this variation remain largely unexplored. Here, we …

A conserved mechanism of TOR-dependent RCK-mediated mRNA degradation regulates autophagy

G Hu, T McQuiston, A Bernard, YD Park, J Qiu… - Nature cell …, 2015 - nature.com
Autophagy is an essential eukaryotic pathway requiring tight regulation to maintain
homeostasis and preclude disease. Using yeast and mammalian cells, we report a …