R-loops at microRNA encoding loci promote co-transcriptional processing of pri-miRNAs in plants DOI Creative Commons
Lucía Gonzalo, Ileana Tossolini, Tomasz Gulanicz

et al.

Nature Plants, Journal Year: 2022, Volume and Issue: 8(4), P. 402 - 418

Published: April 21, 2022

In most organisms, the maturation of nascent RNAs is coupled to transcription. Unlike in animals, RNA polymerase II (RNAPII) transcribes microRNA genes (MIRNAs) as long and structurally variable pri-miRNAs plants. Current evidence suggests that miRNA biogenesis complex assembly initiates early during transcription However, it unknown whether processing occurs co-transcriptionally. Here, we used native elongating transcript sequencing data imaging techniques demonstrate plant We found entire co-transcriptionally for processed from loop hairpin but requires a second nucleoplasmic step those base. Furthermore, co- post-transcriptional mechanisms co-exist miRNAs dynamic balance. Notably, discovered R-loops, formed near start site region MIRNAs, promote co-transcriptional pri-miRNA processing. our results suggest neofunctionalization miRNAs, boosting countless regulatory scenarios.

Language: Английский

Gene regulation by long non-coding RNAs and its biological functions DOI Open Access
Luisa Statello, Chunjie Guo, Ling‐Ling Chen

et al.

Nature Reviews Molecular Cell Biology, Journal Year: 2020, Volume and Issue: 22(2), P. 96 - 118

Published: Dec. 22, 2020

Language: Английский

Citations

3669
Long non-coding RNAs: definitions, functions, challenges and recommendations DOI Open Access
John S. Mattick, Paulo Amaral, Piero Carninci

et al.

Nature Reviews Molecular Cell Biology, Journal Year: 2023, Volume and Issue: 24(6), P. 430 - 447

Published: Jan. 3, 2023

Language: Английский

Citations

1253
Sources, resolution and physiological relevance of R-loops and RNA–DNA hybrids DOI
Eva Petermann, Li Lan, Lee Zou

et al.

Nature Reviews Molecular Cell Biology, Journal Year: 2022, Volume and Issue: 23(8), P. 521 - 540

Published: April 22, 2022

Language: Английский

Citations

243
Biological roles of adenine methylation in RNA DOI
Konstantinos Boulias, Eric Lieberman Greer

Nature Reviews Genetics, Journal Year: 2022, Volume and Issue: 24(3), P. 143 - 160

Published: Oct. 19, 2022

Language: Английский

Citations

217
DNA damage and repair in age-related inflammation DOI
Yang Zhao, Matthew Simon, Andrei Seluanov

et al.

Nature reviews. Immunology, Journal Year: 2022, Volume and Issue: 23(2), P. 75 - 89

Published: July 13, 2022

Language: Английский

Citations

201
Cellular functions of the protein kinase ATM and their relevance to human disease DOI
Ji‐Hoon Lee, Tanya T. Paull

Nature Reviews Molecular Cell Biology, Journal Year: 2021, Volume and Issue: 22(12), P. 796 - 814

Published: Aug. 24, 2021

Language: Английский

Citations

196
Walking a tightrope: The complex balancing act of R-loops in genome stability DOI Creative Commons
Joshua R. Brickner, Jada L. Garzon, Karlene A. Cimprich

et al.

Molecular Cell, Journal Year: 2022, Volume and Issue: 82(12), P. 2267 - 2297

Published: May 3, 2022

Language: Английский

Citations

158
R-loops as Janus-faced modulators of DNA repair DOI
Aline Marnef, Gaëlle Legube

Nature Cell Biology, Journal Year: 2021, Volume and Issue: 23(4), P. 305 - 313

Published: April 1, 2021

Language: Английский

Citations

135
R-loop proximity proteomics identifies a role of DDX41 in transcription-associated genomic instability DOI Creative Commons
Thorsten Mosler, Francesca Conte, Gabriel M. C. Longo

et al.

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Dec. 16, 2021

Transcription poses a threat to genomic stability through the formation of R-loops that can obstruct progression replication forks. are three-stranded nucleic acid structures formed by an RNA-DNA hybrid with displaced non-template DNA strand. We developed Proximity Proteomics map R-loop proximal proteome human cells using quantitative mass spectrometry. implicate different cellular proteins in regulation and identify role tumor suppressor DDX41 opposing double strand break accumulation promoters. is enriched promoter regions vivo, unwind hybrids vitro. upon loss accompanied stress, increase breaks transcriptome changes associated inflammatory response. Germline loss-of-function mutations lead predisposition acute myeloid leukemia adulthood. propose instability-associated response may contribute development familial AML mutated DDX41.

Language: Английский

Citations

118
Proximity labeling identifies a repertoire of site-specific R-loop modulators DOI Creative Commons
Qingqing Yan, Phillip Wulfridge, J. Kenneth Doherty

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Jan. 10, 2022

Abstract R-loops are three-stranded nucleic acid structures that accumulate on chromatin in neurological diseases and cancers contribute to genome instability. Using a proximity-dependent labeling system, we identified distinct classes of proteins regulate vivo through different mechanisms. We show ATRX suppresses by interacting with RNAs preventing R-loop formation. Our proteomics screen also discovered an unexpected enrichment for containing zinc fingers homeodomains. One the most consistently enriched was activity-dependent neuroprotective protein (ADNP), which is frequently mutated ASD causal ADNP syndrome. find resolves vitro it necessary suppress at its genomic targets. Furthermore, deletion homeodomain severely diminishes resolution activity vitro, results accumulation targets, compromises neuronal differentiation. Notably, patient-derived human induced pluripotent stem cells contain syndrome-causing mutation exhibit CTCF findings point specific role ADNP-mediated physiological pathological function and, more broadly, finger regulation, important implications developmental disorders cancers.

Language: Английский

Citations

78