Literature DB >> 36173569

STREAMING-Tag System: Technology to Enable Visualization of Transcriptional Activity and Subnuclear Localization of Specific Endogenous Genes.

Hiroaki Ohishi1, Hiroshi Ochiai2.   

Abstract

The Spliced TetO REpeAt, MS2 repeat, and INtein sandwiched reporter Gene tag (STREAMING-tag) system enables imaging of nuclear localization as well as the transcription activity of a specific endogenous gene at sub-100-nm resolution in living cells. The use of this system combined with imaging of epigenome states enables a detailed analysis of the impact of epigenome status on transcriptional dynamics. In this chapter, we describe a method for quantifying distances between Nanog gene and clusters of cofactor BRD4 using the STREAMING-tag system in mouse embryonic stem cells.
© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Gene regulation; ImageJ; Live imaging; Python; RNAPII; STREAMING-tag; Trackpy; Transcriptional bursting; Transcriptional regulatory factor

Mesh：

Substances：

Year:  2023        PMID： 36173569     DOI： 10.1007/978-1-0716-2724-2_8

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  23 in total

1.  Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH.

Authors:  Sheel Shah; Yodai Takei; Wen Zhou; Eric Lubeck; Jina Yun; Chee-Huat Linus Eng; Noushin Koulena; Christopher Cronin; Christoph Karp; Eric J Liaw; Mina Amin; Long Cai
Journal:  Cell       Date:  2018-06-07       Impact factor: 41.582

Review 2.  What shapes eukaryotic transcriptional bursting?

Authors:  Damien Nicolas; Nick E Phillips; Felix Naef
Journal:  Mol Biosyst       Date:  2017-06-27

Review 3.  Nuclear compartmentalization as a mechanism of quantitative control of gene expression.

Authors:  Prashant Bhat; Drew Honson; Mitchell Guttman
Journal:  Nat Rev Mol Cell Biol       Date:  2021-08-02       Impact factor: 94.444

Review 4.  Transcription in Living Cells: Molecular Mechanisms of Bursting.

Authors:  Joseph Rodriguez; Daniel R Larson
Journal:  Annu Rev Biochem       Date:  2020-03-24       Impact factor: 23.643

Review 5.  Determinants of enhancer and promoter activities of regulatory elements.

Authors:  Robin Andersson; Albin Sandelin
Journal:  Nat Rev Genet       Date:  2019-10-11       Impact factor: 53.242

6.  Transcriptional burst frequency and burst size are equally modulated across the human genome.

Authors:  Roy D Dar; Brandon S Razooky; Abhyudai Singh; Thomas V Trimeloni; James M McCollum; Chris D Cox; Michael L Simpson; Leor S Weinberger
Journal:  Proc Natl Acad Sci U S A       Date:  2012-10-11       Impact factor: 11.205

Review 7.  Organization and regulation of gene transcription.

Authors:  Patrick Cramer
Journal:  Nature       Date:  2019-08-28       Impact factor: 49.962

8.  General properties of transcriptional time series in Escherichia coli.

Authors:  Lok-Hang So; Anandamohan Ghosh; Chenghang Zong; Leonardo A Sepúlveda; Ronen Segev; Ido Golding
Journal:  Nat Genet       Date:  2011-05-01       Impact factor: 38.330

9.  Stochastic mRNA synthesis in mammalian cells.

Authors:  Arjun Raj; Charles S Peskin; Daniel Tranchina; Diana Y Vargas; Sanjay Tyagi
Journal:  PLoS Biol       Date:  2006-10       Impact factor: 8.029

10.  Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

Authors:  Hiroshi Ochiai; Tetsutaro Hayashi; Mana Umeda; Mika Yoshimura; Akihito Harada; Yukiko Shimizu; Kenta Nakano; Noriko Saitoh; Zhe Liu; Takashi Yamamoto; Tadashi Okamura; Yasuyuki Ohkawa; Hiroshi Kimura; Itoshi Nikaido
Journal:  Sci Adv       Date:  2020-06-17       Impact factor: 14.136
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