Dataset Information

BLM helicase protein negatively regulates stress granule formation through unwinding RNA G-quadruplex structures

ABSTRACT: Bloom’s syndrome (BLM) protein is a known nuclear helicase that is able to unwind DNA secondary structures such as G-quadruplexes. However, its role in the regulation of cytoplasmic processes that involve RNA G-quadruplexes (rG4s) has not been previously studied. Here, we demonstrate that BLM is recruited to stress granules (SGs), which are cytoplasmic biomolecular condensates composed of RNA-binding proteins and RNAs. BLM is enriched in SGs upon different stress conditions and in an rG4-dependent manner. We show that BLM unwinds rG4s efficiently, thus acting as a negative regulator of SG formation, potentially via its unwinding function. Altogether, our data expand the cellular activity of BLM and shed light on the function that helicases play in the dynamics of biomolecular condensates.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Alon Savidor

LAB HEAD: Prof. Eran Hornstein

PROVIDER: PXD039534 | Pride | 2023-10-24

REPOSITORIES: Pride

ACCESS DATA

Publications

BLM helicase protein negatively regulates stress granule formation through unwinding RNA G-quadruplex structures.

Danino Yehuda M YM Molitor Lena L Rosenbaum-Cohen Tamar T Kaiser Sebastian S Cohen Yahel Y Porat Ziv Z Marmor-Kollet Hagai H Katina Corine C Savidor Alon A Rotkopf Ron R Ben-Isaac Eyal E Golani Ofra O Levin Yishai Y Monchaud David D Hickson Ian D ID Hornstein Eran E

Nucleic acids research 20230901 17

Bloom's syndrome (BLM) protein is a known nuclear helicase that is able to unwind DNA secondary structures such as G-quadruplexes (G4s). However, its role in the regulation of cytoplasmic processes that involve RNA G-quadruplexes (rG4s) has not been previously studied. Here, we demonstrate that BLM is recruited to stress granules (SGs), which are cytoplasmic biomolecular condensates composed of RNAs and RNA-binding proteins. BLM is enriched in SGs upon different stress conditions and in an rG4-d ...[more]

PMID: 37503837

Similar Datasets

Project description:RNA structures are of crucial importance for biological function and gene regulation. Guanine (G)-rich sequences in RNA can assemble to form RNA G-quadruplex (rG4) structures; specific rG4s have been shown to regulate gene expression, and are associated with human diseases. However, no transcriptome-wide method has been reported to map rG4s, limiting our understanding of the rG4 structure and its relationship with function and regulation. Here we introduce a transcriptome-wide rG4 profiling method, rG4-Seq, in which the rG4-mediated reverse transcriptase stalling is read out by next-generation sequencing at nucleotide resolution. We apply this method to human RNA and report the first global map of rG4 structures for any organism. Our analysis identifies over 3,000 rG4s, and increases to over 11,000 upon addition of a rG4 stabilizing ligand Pyridostatin (PDS). Notably, we discover that besides canonical rG4s, many rG4s are non-canonical with novel structural features such as long-loops, bulges, and 2-quartet. We also find that rG4 formation is associated with its stability, Cytosine (C)-content, and the stability of alternative RNA structures. Our data reveals that rG4s can be found in messenger RNAs (mRNAs) and long intergenic noncoding RNAs (lincRNAs). In mRNAs, rG4s are enriched in untranslated regions, and are significantly correlated with microRNA target sites and polyadenylation signals. Remarkably, we found that majority of our in vitro identified rG4s can change the in silico predicted RNA structure to uncover alternative RNA conformation.. Futhermore, the rG4s that have analogues in many ortholog genes across different species show a preferential association with RNA processing and stability. rG4-seq is a broadly applicable method that enables the RNA G4 structurome and its biological roles to be interrogated and can be readily applied in other organisms on a transcriptome-wide scale. 12 samples, 150 bp single-ended RNA-Seq libraries from cell extracts after performing RTS reaction in different buffers (Li, K and K+PDS rich buffer). Each of the 3 conditions has 4 libraries from independent biological replicates.

Dataset Information

BLM helicase protein negatively regulates stress granule formation through unwinding RNA G-quadruplex structures

Publications

BLM helicase protein negatively regulates stress granule formation through unwinding RNA G-quadruplex structures.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure