Literature DB >> 31399713

Nascent RNA analyses: tracking transcription and its regulation.

Erin M Wissink1, Anniina Vihervaara1, Nathaniel D Tippens1,2, John T Lis3.   

Abstract

The programmes that direct an organism's development and maintenance are encoded in its genome. Decoding of this information begins with regulated transcription of genomic DNA into RNA. Although transcription and its control can be tracked indirectly by measuring stable RNAs, it is only by directly measuring nascent RNAs that the immediate regulatory changes in response to developmental, environmental, disease and metabolic signals are revealed. Multiple complementary methods have been developed to quantitatively track nascent transcription genome-wide at nucleotide resolution, all of which have contributed novel insights into the mechanisms of gene regulation and transcription-coupled RNA processing. Here we critically evaluate the array of strategies used for investigating nascent transcription and discuss the recent conceptual advances they have provided.

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Year:  2019        PMID: 31399713      PMCID: PMC6858503          DOI: 10.1038/s41576-019-0159-6

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  211 in total

1.  RNA exosome depletion reveals transcription upstream of active human promoters.

Authors:  Pascal Preker; Jesper Nielsen; Susanne Kammler; Søren Lykke-Andersen; Marianne S Christensen; Christophe K Mapendano; Mikkel H Schierup; Torben Heick Jensen
Journal:  Science       Date:  2008-12-04       Impact factor: 47.728

2.  Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality.

Authors:  Evgenia Ntini; Aino I Järvelin; Jette Bornholdt; Yun Chen; Mette Boyd; Mette Jørgensen; Robin Andersson; Ilka Hoof; Aleks Schein; Peter R Andersen; Pia K Andersen; Pascal Preker; Eivind Valen; Xiaobei Zhao; Vicent Pelechano; Lars M Steinmetz; Albin Sandelin; Torben Heick Jensen
Journal:  Nat Struct Mol Biol       Date:  2013-07-14       Impact factor: 15.369

Review 3.  On the Dependency of Cellular Protein Levels on mRNA Abundance.

Authors:  Yansheng Liu; Andreas Beyer; Ruedi Aebersold
Journal:  Cell       Date:  2016-04-21       Impact factor: 41.582

Review 4.  Enhancers as non-coding RNA transcription units: recent insights and future perspectives.

Authors:  Wenbo Li; Dimple Notani; Michael G Rosenfeld
Journal:  Nat Rev Genet       Date:  2016-03-07       Impact factor: 53.242

Review 5.  The pol II CTD: new twists in the tail.

Authors:  Justyna Zaborowska; Sylvain Egloff; Shona Murphy
Journal:  Nat Struct Mol Biol       Date:  2016-09-06       Impact factor: 15.369

Review 6.  Born to run: control of transcription elongation by RNA polymerase II.

Authors:  Fei Xavier Chen; Edwin R Smith; Ali Shilatifard
Journal:  Nat Rev Mol Cell Biol       Date:  2018-07       Impact factor: 94.444

7.  Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.

Authors:  Leighton J Core; André L Martins; Charles G Danko; Colin T Waters; Adam Siepel; John T Lis
Journal:  Nat Genet       Date:  2014-11-10       Impact factor: 38.330

8.  Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin.

Authors:  Benjamin S Scruggs; Daniel A Gilchrist; Sergei Nechaev; Ginger W Muse; Adam Burkholder; David C Fargo; Karen Adelman
Journal:  Mol Cell       Date:  2015-05-28       Impact factor: 17.970

Review 9.  Regulatory Enhancer-Core-Promoter Communication via Transcription Factors and Cofactors.

Authors:  Muhammad A Zabidi; Alexander Stark
Journal:  Trends Genet       Date:  2016-11-02       Impact factor: 11.639

Review 10.  Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution.

Authors:  Hannah K Long; Sara L Prescott; Joanna Wysocka
Journal:  Cell       Date:  2016-11-17       Impact factor: 41.582

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  47 in total

Review 1.  FLEP-seq: simultaneous detection of RNA polymerase II position, splicing status, polyadenylation site and poly(A) tail length at genome-wide scale by single-molecule nascent RNA sequencing.

Authors:  Yanping Long; Jinbu Jia; Weipeng Mo; Xianhao Jin; Jixian Zhai
Journal:  Nat Protoc       Date:  2021-07-30       Impact factor: 13.491

Review 2.  Causes and consequences of RNA polymerase II stalling during transcript elongation.

Authors:  Melvin Noe Gonzalez; Daniel Blears; Jesper Q Svejstrup
Journal:  Nat Rev Mol Cell Biol       Date:  2020-11-18       Impact factor: 94.444

3.  Unique and contrasting effects of light and temperature cues on plant transcriptional programs.

Authors:  Mai Jarad; Rea Antoniou-Kourounioti; Jo Hepworth; Julia I Qüesta
Journal:  Transcription       Date:  2020-10-04

4.  Lessons from eRNAs: understanding transcriptional regulation through the lens of nascent RNAs.

Authors:  Joseph F Cardiello; Gilson J Sanchez; Mary A Allen; Robin D Dowell
Journal:  Transcription       Date:  2019-12-19

5.  Definition of a small core transcriptional circuit regulated by AML1-ETO.

Authors:  Kristy R Stengel; Jacob D Ellis; Clare L Spielman; Monica L Bomber; Scott W Hiebert
Journal:  Mol Cell       Date:  2020-12-30       Impact factor: 17.970

6.  DMP-1 promoter-associated antisense strand non-coding RNA, panRNA-DMP-1, physically associates with EGFR to repress EGF-induced squamous cell carcinoma migration.

Authors:  Shigeki Suzuki; Hang Yuan; Shizu Hirata-Tsuchiya; Kazuma Yoshida; Akiko Sato; Eiji Nemoto; Hideki Shiba; Satoru Yamada
Journal:  Mol Cell Biochem       Date:  2021-01-09       Impact factor: 3.396

7.  Dynamics of transcriptional and post-transcriptional regulation.

Authors:  Mattia Furlan; Stefano de Pretis; Mattia Pelizzola
Journal:  Brief Bioinform       Date:  2021-07-20       Impact factor: 11.622

8.  The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5' and 3' gene regions.

Authors:  Jonathan Fischer; Yun S Song; Nir Yosef; Julia di Iulio; L Stirling Churchman; Mordechai Choder
Journal:  J Biol Chem       Date:  2020-06-09       Impact factor: 5.157

9.  Stress-induced transcriptional memory accelerates promoter-proximal pause release and decelerates termination over mitotic divisions.

Authors:  Anniina Vihervaara; Dig Bijay Mahat; Samu V Himanen; Malin A H Blom; John T Lis; Lea Sistonen
Journal:  Mol Cell       Date:  2021-03-29       Impact factor: 17.970

10.  The Herpes Simplex Virus 1 Protein ICP4 Acts as both an Activator and a Repressor of Host Genome Transcription during Infection.

Authors:  Thomas Rivas; James A Goodrich; Jennifer F Kugel
Journal:  Mol Cell Biol       Date:  2021-07-12       Impact factor: 4.272

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