The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer–promoter communication

How distal cis -regulatory elements (e.g., enhancers) communicate with promoters remains an unresolved question of fundamental importance. Although transcription factors and cofactors are known to mediate this communication, the mechanism by which diffusible molecules relay regulatory information fr...

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Published inGenes & development Vol. 36; no. 1-2; pp. 7 - 16
Main Authors Karr, Jonathan P., Ferrie, John J., Tjian, Robert, Darzacq, Xavier
Format Journal Article
LanguageEnglish
Published United States Cold Spring Harbor Laboratory Press 01.01.2022
Subjects
Enhancer Elements, Genetic - genetics
Gene Expression Regulation
Promoter Regions, Genetic - genetics
Transcription Factors - genetics
Transcription Factors - metabolism
Transcription, Genetic
p300
3D genome
enhancer
transcription
gene regulation
coactivator
Online AccessGet full text
ISSN0890-9369
1549-5477
1549-5477
DOI10.1101/gad.349160.121

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Abstract How distal cis -regulatory elements (e.g., enhancers) communicate with promoters remains an unresolved question of fundamental importance. Although transcription factors and cofactors are known to mediate this communication, the mechanism by which diffusible molecules relay regulatory information from one position to another along the chromosome is a biophysical puzzle—one that needs to be revisited in light of recent data that cannot easily fit into previous solutions. Here we propose a new model that diverges from the textbook enhancer–promoter looping paradigm and offer a synthesis of the literature to make a case for its plausibility, focusing on the coactivator p300.
AbstractList How distal cis-regulatory elements (e.g., enhancers) communicate with promoters remains an unresolved question of fundamental importance. Although transcription factors and cofactors are known to mediate this communication, the mechanism by which diffusible molecules relay regulatory information from one position to another along the chromosome is a biophysical puzzle-one that needs to be revisited in light of recent data that cannot easily fit into previous solutions. Here we propose a new model that diverges from the textbook enhancer-promoter looping paradigm and offer a synthesis of the literature to make a case for its plausibility, focusing on the coactivator p300.How distal cis-regulatory elements (e.g., enhancers) communicate with promoters remains an unresolved question of fundamental importance. Although transcription factors and cofactors are known to mediate this communication, the mechanism by which diffusible molecules relay regulatory information from one position to another along the chromosome is a biophysical puzzle-one that needs to be revisited in light of recent data that cannot easily fit into previous solutions. Here we propose a new model that diverges from the textbook enhancer-promoter looping paradigm and offer a synthesis of the literature to make a case for its plausibility, focusing on the coactivator p300.
How distal -regulatory elements (e.g., enhancers) communicate with promoters remains an unresolved question of fundamental importance. Although transcription factors and cofactors are known to mediate this communication, the mechanism by which diffusible molecules relay regulatory information from one position to another along the chromosome is a biophysical puzzle-one that needs to be revisited in light of recent data that cannot easily fit into previous solutions. Here we propose a new model that diverges from the textbook enhancer-promoter looping paradigm and offer a synthesis of the literature to make a case for its plausibility, focusing on the coactivator p300.
How distal cis -regulatory elements (e.g., enhancers) communicate with promoters remains an unresolved question of fundamental importance. Although transcription factors and cofactors are known to mediate this communication, the mechanism by which diffusible molecules relay regulatory information from one position to another along the chromosome is a biophysical puzzle—one that needs to be revisited in light of recent data that cannot easily fit into previous solutions. Here we propose a new model that diverges from the textbook enhancer–promoter looping paradigm and offer a synthesis of the literature to make a case for its plausibility, focusing on the coactivator p300.
In this Perspective, Karr et al. propose a new model that diverges from the textbook enhancer–promoter looping paradigm and offer a synthesis of the literature to make a case for its plausibility, focusing on the coactivator p300. How distal cis -regulatory elements (e.g., enhancers) communicate with promoters remains an unresolved question of fundamental importance. Although transcription factors and cofactors are known to mediate this communication, the mechanism by which diffusible molecules relay regulatory information from one position to another along the chromosome is a biophysical puzzle—one that needs to be revisited in light of recent data that cannot easily fit into previous solutions. Here we propose a new model that diverges from the textbook enhancer–promoter looping paradigm and offer a synthesis of the literature to make a case for its plausibility, focusing on the coactivator p300.
Author Ferrie, John J.
Darzacq, Xavier
Karr, Jonathan P.
Tjian, Robert
AuthorAffiliation 1 University of California at Berkeley, Berkeley, California 94720, USA
2 Howard Hughes Medical Institute, Berkeley, California 94720, USA
AuthorAffiliation_xml – name: 2 Howard Hughes Medical Institute, Berkeley, California 94720, USA
– name: 1 University of California at Berkeley, Berkeley, California 94720, USA
Author_xml – sequence: 1
  givenname: Jonathan P.
  surname: Karr
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  orcidid: 0000-0003-0539-8217
  surname: Tjian
  fullname: Tjian, Robert
– sequence: 4
  givenname: Xavier
  orcidid: 0000-0003-2537-8395
  surname: Darzacq
  fullname: Darzacq, Xavier
BackLink https://www.ncbi.nlm.nih.gov/pubmed/34969825$$D View this record in MEDLINE/PubMed
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Issue 1-2
Keywords p300
3D genome
enhancer
transcription
gene regulation
coactivator
Language English
License 2022 Karr et al.; Published by Cold Spring Harbor Laboratory Press.
This article, published in Genes & Development, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
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Snippet How distal cis -regulatory elements (e.g., enhancers) communicate with promoters remains an unresolved question of fundamental importance. Although...
How distal -regulatory elements (e.g., enhancers) communicate with promoters remains an unresolved question of fundamental importance. Although transcription...
How distal cis-regulatory elements (e.g., enhancers) communicate with promoters remains an unresolved question of fundamental importance. Although...
In this Perspective, Karr et al. propose a new model that diverges from the textbook enhancer–promoter looping paradigm and offer a synthesis of the literature...
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StartPage 7
SubjectTerms Enhancer Elements, Genetic - genetics
Gene Expression Regulation
Promoter Regions, Genetic - genetics
Transcription Factors - genetics
Transcription Factors - metabolism
Transcription, Genetic
Title The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer–promoter communication
URI https://www.ncbi.nlm.nih.gov/pubmed/34969825
https://www.proquest.com/docview/2615916289
https://pubmed.ncbi.nlm.nih.gov/PMC8763055
Volume 36
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