Literature DB >> 29501816

Imaging transcriptional dynamics.

Bomyi Lim1.   

Abstract

Recent advances in imaging techniques have enabled visualizations of nascent transcripts or individual protein molecules at high spatiotemporal resolution, revealing the complex nature of transcriptional regulation. Here, we highlight recent studies that have provided comprehensive insights to transcriptional dynamics using such quantitative imaging techniques. Specifically, they demonstrated that transcriptional activity is stochastic, and such transcriptional bursting is modulated by multiple components like chromatin environments, concentration of transcription factors, and enhancer-promoter interactions. Moreover, recent studies suggested that regulation of transcriptional activity is more complex than previously thought, by showing that transcription factors and RNA polymerases also move within the cell with distinct kinetics and sometimes form dynamic clusters to mediate transcriptional initiation.
Copyright © 2018 Elsevier Ltd. All rights reserved.

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Year:  2018        PMID: 29501816      PMCID: PMC6082720          DOI: 10.1016/j.copbio.2018.02.008

Source DB:  PubMed          Journal:  Curr Opin Biotechnol        ISSN: 0958-1669            Impact factor:   9.740


  54 in total

1.  Post-replicative nonribosomal transcription units in D. melanogaster embryos.

Authors:  S L McKnight; O L Miller
Journal:  Cell       Date:  1979-07       Impact factor: 41.582

2.  Transcriptional Pre-patterning of Drosophila Gastrulation.

Authors:  Bomyi Lim; Yuji Yamazaki; Michael Levine
Journal:  Curr Biol       Date:  2017-01-12       Impact factor: 10.834

3.  Cohesin Loss Eliminates All Loop Domains.

Authors:  Suhas S P Rao; Su-Chen Huang; Brian Glenn St Hilaire; Jesse M Engreitz; Elizabeth M Perez; Kyong-Rim Kieffer-Kwon; Adrian L Sanborn; Sarah E Johnstone; Gavin D Bascom; Ivan D Bochkov; Xingfan Huang; Muhammad S Shamim; Jaeweon Shin; Douglass Turner; Ziyi Ye; Arina D Omer; James T Robinson; Tamar Schlick; Bradley E Bernstein; Rafael Casellas; Eric S Lander; Erez Lieberman Aiden
Journal:  Cell       Date:  2017-10-05       Impact factor: 41.582

4.  Precise developmental gene expression arises from globally stochastic transcriptional activity.

Authors:  Shawn C Little; Mikhail Tikhonov; Thomas Gregor
Journal:  Cell       Date:  2013-08-15       Impact factor: 41.582

5.  Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation.

Authors:  Tetsuya Muramoto; Danielle Cannon; Marek Gierlinski; Adam Corrigan; Geoffrey J Barton; Jonathan R Chubb
Journal:  Proc Natl Acad Sci U S A       Date:  2012-04-23       Impact factor: 11.205

6.  Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency.

Authors:  Elsa Abranches; Ana M V Guedes; Martin Moravec; Hedia Maamar; Petr Svoboda; Arjun Raj; Domingos Henrique
Journal:  Development       Date:  2014-07       Impact factor: 6.868

7.  Enhancer Control of Transcriptional Bursting.

Authors:  Takashi Fukaya; Bomyi Lim; Michael Levine
Journal:  Cell       Date:  2016-06-09       Impact factor: 41.582

8.  Single-RNA counting reveals alternative modes of gene expression in yeast.

Authors:  Daniel Zenklusen; Daniel R Larson; Robert H Singer
Journal:  Nat Struct Mol Biol       Date:  2008-11-16       Impact factor: 15.369

9.  Rapid dynamics of general transcription factor TFIIB binding during preinitiation complex assembly revealed by single-molecule analysis.

Authors:  Zhengjian Zhang; Brian P English; Jonathan B Grimm; Stephanie A Kazane; Wenxin Hu; Albert Tsai; Carla Inouye; Changjiang You; Jacob Piehler; Peter G Schultz; Luke D Lavis; Andrey Revyakin; Robert Tjian
Journal:  Genes Dev       Date:  2016-09-15       Impact factor: 11.361

10.  Bursty gene expression in the intact mammalian liver.

Authors:  Keren Bahar Halpern; Sivan Tanami; Shanie Landen; Michal Chapal; Liran Szlak; Anat Hutzler; Anna Nizhberg; Shalev Itzkovitz
Journal:  Mol Cell       Date:  2015-02-26       Impact factor: 17.970

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  9 in total

Review 1.  Phase Separation and Transcription Regulation: Are Super-Enhancers and Locus Control Regions Primary Sites of Transcription Complex Assembly?

Authors:  Aishwarya Gurumurthy; Yong Shen; Eliot M Gunn; Jörg Bungert
Journal:  Bioessays       Date:  2018-11-30       Impact factor: 4.345

2.  Epigenome editing and epigenetic gene regulation in disease phenotypes.

Authors:  Gaochen Jin; Bomyi Lim
Journal:  Korean J Chem Eng       Date:  2022-03-15       Impact factor: 3.146

Review 3.  Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics.

Authors:  Takayuki Nojima; Nick J Proudfoot
Journal:  Nat Rev Mol Cell Biol       Date:  2022-01-25       Impact factor: 113.915

Review 4.  Nascent RNA analyses: tracking transcription and its regulation.

Authors:  Erin M Wissink; Anniina Vihervaara; Nathaniel D Tippens; John T Lis
Journal:  Nat Rev Genet       Date:  2019-08-09       Impact factor: 53.242

5.  Epigenetic imprinting alterations as effective diagnostic biomarkers for early-stage lung cancer and small pulmonary nodules.

Authors:  Jian Zhou; Tong Cheng; Xing Li; Jie Hu; Encheng Li; Ming Ding; Rulong Shen; John P Pineda; Chun Li; Shaohua Lu; Hongyu Yu; Jiayuan Sun; Wenbin Huang; Xiaonan Wang; Han Si; Panying Shi; Jing Liu; Meijia Chang; Maosen Dou; Meng Shi; Xiaofeng Chen; Rex C Yung; Qi Wang; Ning Zhou; Chunxue Bai
Journal:  Clin Epigenetics       Date:  2021-12-14       Impact factor: 6.551

6.  Degree of Freedom of Gene Expression in Saccharomyces cerevisiae.

Authors:  Zhen Yang; Feng Xu; Aijuan Xue; Hong Lv; Yungang He
Journal:  Microbiol Spectr       Date:  2022-03-01

7.  Dynamics of Drosophila endoderm specification.

Authors:  Shannon E Keenan; Maria Avdeeva; Liu Yang; Daniel S Alber; Eric F Wieschaus; Stanislav Y Shvartsman
Journal:  Proc Natl Acad Sci U S A       Date:  2022-04-11       Impact factor: 12.779

Review 8.  Enhancer-Mediated Formation of Nuclear Transcription Initiation Domains.

Authors:  Matthew D Gibbons; Yu Fang; Austin P Spicola; Niko Linzer; Stephen M Jones; Breanna R Johnson; Lu Li; Mingyi Xie; Jörg Bungert
Journal:  Int J Mol Sci       Date:  2022-08-18       Impact factor: 6.208

Review 9.  RNA Structure and Cellular Applications of Fluorescent Light-Up Aptamers.

Authors:  Saskia Neubacher; Sven Hennig
Journal:  Angew Chem Int Ed Engl       Date:  2018-11-05       Impact factor: 15.336

  9 in total

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