Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility
Diana A. Stavreva,David A. Garcia,Grégory Fettweis,Prabhakar R. Gudla,George Zaki,Vikas Soni,Andrew McGowan,Geneva Williams,Anh Huynh,Murali Palangat,R. Louis Schiltz,Thomas A. Johnson,Diego M. Presman,Matthew L. Ferguson,Gianluca Pegoraro,Arpita Upadhyaya,Gordon L. Hager +16 more
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TLDR
It is demonstrated that transcription factor (TF) nuclear mobility determines burst duration, whereas its bound fraction determines burst frequency, and a striking co-bursting pattern between TSs located at proximal and distal positions in the nucleus is uncovered.About:
This article is published in Molecular Cell.The article was published on 2019-09-19 and is currently open access. It has received 79 citations till now. The article focuses on the topics: Transcriptional bursting & Bursting.read more
Citations
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Journal ArticleDOI
Pioneer Transcription Factors Initiating Gene Network Changes
TL;DR: The current understanding of the mechanisms by which pioneer factors initiate gene network changes and will ultimately contribute to the ability to control cell fates at will are focused on.
Journal ArticleDOI
Structure and mechanism of the RNA polymerase II transcription machinery.
TL;DR: A wealth of structural and functional data that have enabled a deeper understanding of Pol II transcription mechanisms are summarized and mechanistic questions that remain unanswered or controversial are highlighted.
Journal ArticleDOI
What Is a Transcriptional Burst
TL;DR: This review tries to reconcile the different views of the transcriptional process emerging from studies of bursting, and how this work contextualizes the relative importance of different regulatory inputs to normal dynamic ranges of gene activity.
Journal ArticleDOI
An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors.
David A. Garcia,David A. Garcia,Thomas A. Johnson,Diego M. Presman,Grégory Fettweis,Kaustubh Wagh,Kaustubh Wagh,Lorenzo Rinaldi,Diana A. Stavreva,Ville Paakinaho,Rikke A.M. Jensen,Rikke A.M. Jensen,Susanne Mandrup,Arpita Upadhyaya,Gordon L. Hager +14 more
TL;DR: In this article, the authors used single-molecule tracking and machine-learning-based classification to directly measure the nuclear mobility of the glucocorticoid receptor (GR) in live cells.
Journal ArticleDOI
Mechanical Regulation of Transcription: Recent Advances.
Kaustubh Wagh,Kaustubh Wagh,Momoko Ishikawa,David A. Garcia,David A. Garcia,Diana A. Stavreva,Arpita Upadhyaya,Gordon L. Hager +7 more
TL;DR: In this paper, the authors highlight the importance of mechanotransduction as one of the governing principles of cancer progression and emphasize the need to conduct further studies of the molecular mechanisms involved in sensing mechanical cues and coordinating transcriptional responses.
References
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Journal ArticleDOI
Random Forests
TL;DR: Internal estimates monitor error, strength, and correlation and these are used to show the response to increasing the number of features used in the forest, and are also applicable to regression.
Book ChapterDOI
Nonparametric Estimation from Incomplete Observations
Edward L. Kaplan,Paul Meier +1 more
TL;DR: In this article, the product-limit (PL) estimator was proposed to estimate the proportion of items in the population whose lifetimes would exceed t (in the absence of such losses), without making any assumption about the form of the function P(t).
Journal ArticleDOI
Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
Sven Heinz,Christopher Benner,Nathanael J. Spann,Eric Bertolino,Yin C. Lin,Peter Laslo,Jason X. Cheng,Cornelis Murre,Harinder Singh,Harinder Singh,Christopher K. Glass +10 more
TL;DR: It is demonstrated in macrophages and B cells that collaborative interactions of the common factor PU.1 with small sets of macrophage- or B cell lineage-determining transcription factors establish cell-specific binding sites that are associated with the majority of promoter-distal H3K4me1-marked genomic regions.
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