Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation DOI Creative Commons
Nadiya Khyzha, Steven Henikoff, Kami Ahmad

et al.

Nature Methods, Journal Year: 2022, Volume and Issue: 19(11), P. 1383 - 1392

Published: Oct. 3, 2022

Abstract Whereas techniques to map chromatin-bound proteins are well developed, mapping chromatin-associated RNAs remains a challenge. Here, we describe Reverse Transcribe and Tagment (RT&Tag), in which associated with chromatin epitope targeted by an antibody followed protein A-Tn5 transposome. Localized reverse transcription generates RNA/cDNA hybrids that subsequently tagmented Tn5 transposases for downstream sequencing. We demonstrate the utility of RT&Tag Drosophila cells capturing noncoding RNA roX2 dosage compensation complex maturing transcripts silencing histone modifications. also show can detect N6-methyladenosine-modified mRNAs, genes producing methylated characterized extensive promoter pausing polymerase II. The high efficiency situ tethering tagmentation makes especially suitable rapid low-cost profiling RNAs.

Language: Английский

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
RNA polymerase II speed: a key player in controlling and adapting transcriptome composition DOI Creative Commons
Lisa Muniz, Estelle Nicolas, Didier Trouche

et al.

The EMBO Journal, Journal Year: 2021, Volume and Issue: 40(15)

Published: July 13, 2021

RNA polymerase II (RNA Pol II) speed or elongation rate, i.e., the number of nucleotides synthesized per unit time, is a major determinant transcriptome composition. It controls co-transcriptional processes such as splicing, polyadenylation, and transcription termination, thus regulating production alternative splice variants, circular RNAs, alternatively polyadenylated transcripts, read-through transcripts. itself regulated in response to intra- extra-cellular stimuli can turn affect composition these stimuli. Evidence points potentially important role modification through regulation for adaptation cells changing environment, pointing function cellular physiology. Analyzing dynamics may therefore be central fully understand physiological processes, development multicellular organisms. Recent findings also raise possibility that deregulation detrimental participate disease progression. Here, we review initial current approaches measure speed, well providing an overview factors controlling which are affected. Finally, discuss cell

Language: Английский

Citations

140
Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT DOI Open Access
Haruhiko Ehara, Tomoya Kujirai, Mikako Shirouzu

et al.

Science, Journal Year: 2022, Volume and Issue: 377(6611)

Published: Aug. 18, 2022

During gene transcription, RNA polymerase II (RNAPII) traverses nucleosomes in chromatin, but the mechanism has remained elusive. Using cryo–electron microscopy, we obtained structures of RNAPII elongation complex (EC) passing through a nucleosome presence transcription factors Spt6, Spn1, Elf1, Spt4/5, and Paf1C histone chaperone FACT (facilitates chromatin transcription). The show snapshots EC progression on DNA mediating downstream disassembly, followed by its reassembly upstream EC, which is facilitated FACT. dynamically adapts to successively occurring subnucleosome intermediates, forming an interface with EC. form “cradle” at DNA-exit site support reassembly. These explain while maintaining structure epigenetic information.

Language: Английский

Citations

114
U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes DOI Creative Commons
Claudia A. Mimoso, Karen Adelman

Molecular Cell, Journal Year: 2023, Volume and Issue: 83(8), P. 1264 - 1279.e10

Published: March 24, 2023

Language: Английский

Citations

59
Alternative splicing in EMT and TGF-β signaling during cancer progression DOI
Ying E. Zhang, Christina H. Stuelten

Seminars in Cancer Biology, Journal Year: 2024, Volume and Issue: 101, P. 1 - 11

Published: April 15, 2024

Language: Английский

Citations

19
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

Citations

70
Supercoiling-mediated feedback rapidly couples and tunes transcription DOI Creative Commons
Christopher P. Johnstone, Kate E. Galloway

Cell Reports, Journal Year: 2022, Volume and Issue: 41(3), P. 111492 - 111492

Published: Oct. 1, 2022

Transcription induces a wave of DNA supercoiling, altering the binding affinity RNA polymerases and reshaping biochemical landscape gene regulation. As supercoiling rapidly diffuses, transcription dynamically reshapes regulation proximal genes, forming complex feedback loop. However, theoretical framework is needed to integrate biophysical with transcriptional To investigate role supercoiling-mediated within multi-gene systems, we model under influence polymerase dynamics, allowing us identify patterns expression that result from physical inter-gene coupling. We find syntax—the relative ordering orientation genes—defines profiles, variance, burst correlation two-gene systems. Furthermore, can enhance or weaken Our results suggest couples behavior between neighboring providing regulatory mechanism tunes variance in engineered networks explains co-localized native circuits.

Language: Английский

Citations

62
Secondary structures in RNA synthesis, splicing and translation DOI Creative Commons
Ilias Georgakopoulos-Soares, Guillermo E. Parada, Martin Hemberg

et al.

Computational and Structural Biotechnology Journal, Journal Year: 2022, Volume and Issue: 20, P. 2871 - 2884

Published: Jan. 1, 2022

Even though the functional role of mRNA molecules is primarily decided by nucleotide sequence, several properties are determined secondary structure conformations. Examples structures include long range interactions, hairpins, R-loops and G-quadruplexes they formed through interactions non-adjacent nucleotides. Here, we discuss advances in our understanding how can impact RNA synthesis, splicing, translation half-life. During determine polymerase II (RNAPII) speed, thereby influencing splicing. Splicing also binding proteins their rates modulated structures. For initiation translation, control choice start site. highlight mechanisms which modulate these processes, technologies to detect study them systematically, consider roles disease.

Language: Английский

Citations

45
Chloroplast gene expression: Recent advances and perspectives DOI Creative Commons
Yi Zhang, Lin Tian, Congming Lu

et al.

Plant Communications, Journal Year: 2023, Volume and Issue: 4(5), P. 100611 - 100611

Published: May 4, 2023

Chloroplasts evolved from an ancient cyanobacterial endosymbiont more than 1.5 billion years ago. During subsequent coevolution with the nuclear genome, chloroplast genome has remained independent, albeit strongly reduced, its own transcriptional machinery and distinct features, such as chloroplast-specific innovations to gene expression complicated post-transcriptional processing. Light activates of genes via mechanisms that optimize photosynthesis, minimize photodamage, prioritize energy investments. Over past few years, studies have moved stage describing phases explore underlying mechanisms. In this review, we focus on recent advances emerging principles govern in land plants. We discuss PPR protein engineering biotechnological impacts RNA research, new techniques for elucidating molecular expression, some important aspects improving crop yield stress tolerance. also remaining biological mechanistic questions be answered future.

Language: Английский

Citations

43
Pre-mRNA splicing and its cotranscriptional connections DOI Creative Commons
Hossein Shenasa, David L. Bentley

Trends in Genetics, Journal Year: 2023, Volume and Issue: 39(9), P. 672 - 685

Published: May 24, 2023

Language: Английский

Citations

34