Fixing the Model for Transcription: the DNA Moves, Not the Polymerase

Overview

Journal Transcription

Specialty Molecular Biology

Date 2011 Feb 18

PMID 21326910

Citations 22

Authors

Argyris Papantonis

Peter R Cook

Affiliations

Soon will be listed here.

Abstract

The traditional model for transcription sees active polymerases tracking along their templates. An alternative (controversial) model has active enzymes immobilized in "factories." Recent evidence supports the idea that the DNA moves, not the polymerase, and points to alternative explanations of how regulatory motifs like enhancers and silencers work.

Citing Articles

A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model.

Golov A, Gavrilov A, Kaplan N, Razin S Elife. 2024; 12.

PMID: 39688903 PMC: 11651654. DOI: 10.7554/eLife.91596.

An emerging paradigm in epigenetic marking: coordination of transcription and replication.

Fenstermaker T, Petruk S, Mazo A Transcription. 2024; 15(1-2):22-37.

PMID: 38378467 PMC: 11093037. DOI: 10.1080/21541264.2024.2316965.

Enhancer-promoter contact formation requires RNAPII and antagonizes loop extrusion.

Zhang S, Ubelmesser N, Barbieri M, Papantonis A Nat Genet. 2023; 55(5):832-840.

PMID: 37012454 DOI: 10.1038/s41588-023-01364-4.

Episomes and Transposases-Utilities to Maintain Transgene Expression from Nonviral Vectors.

Kreppel F, Hagedorn C Genes (Basel). 2022; 13(10).

PMID: 36292757 PMC: 9601623. DOI: 10.3390/genes13101872.

RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis.

Zhang S, Ubelmesser N, Josipovic N, Forte G, Slotman J, Chiang M Sci Adv. 2021; 7(43):eabg8205.

PMID: 34678064 PMC: 8535795. DOI: 10.1126/sciadv.abg8205.

References

Jackson D, McCready S, Cook P . RNA is synthesized at the nuclear cage. Nature. 1981; 292(5823):552-5. DOI: 10.1038/292552a0. View

Schoenfelder S, Sexton T, Chakalova L, Cope N, Horton A, Andrews S . Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet. 2009; 42(1):53-61. PMC: 3237402. DOI: 10.1038/ng.496. View

Andersen J, Lyon C, Fox A, Leung A, Lam Y, Steen H . Directed proteomic analysis of the human nucleolus. Curr Biol. 2002; 12(1):1-11. DOI: 10.1016/s0960-9822(01)00650-9. View

Sutherland H, Bickmore W . Transcription factories: gene expression in unions?. Nat Rev Genet. 2009; 10(7):457-66. DOI: 10.1038/nrg2592. View

Tan-Wong S, French J, Proudfoot N, Brown M . Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene. Proc Natl Acad Sci U S A. 2008; 105(13):5160-5. PMC: 2278189. DOI: 10.1073/pnas.0801048105. View

Raab J, Kamakaka R . Insulators and promoters: closer than we think. Nat Rev Genet. 2010; 11(6):439-46. PMC: 3477808. DOI: 10.1038/nrg2765. View

Papantonis A, Larkin J, Wada Y, Ohta Y, Ihara S, Kodama T . Active RNA polymerases: mobile or immobile molecular machines?. PLoS Biol. 2010; 8(7):e1000419. PMC: 2903595. DOI: 10.1371/journal.pbio.1000419. View

Ferrai C, Xie S, Luraghi P, Munari D, Ramirez F, Branco M . Poised transcription factories prime silent uPA gene prior to activation. PLoS Biol. 2010; 8(1):e1000270. PMC: 2797137. DOI: 10.1371/journal.pbio.1000270. View

De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi B . A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol. 2010; 8(5):e1000384. PMC: 2867938. DOI: 10.1371/journal.pbio.1000384. View

10.

Misteli T . Higher-order genome organization in human disease. Cold Spring Harb Perspect Biol. 2010; 2(8):a000794. PMC: 2908770. DOI: 10.1101/cshperspect.a000794. View

11.

Eskiw C, Rapp A, Carter D, Cook P . RNA polymerase II activity is located on the surface of protein-rich transcription factories. J Cell Sci. 2008; 121(Pt 12):1999-2007. DOI: 10.1242/jcs.027250. View

12.

Herbert K, Greenleaf W, Block S . Single-molecule studies of RNA polymerase: motoring along. Annu Rev Biochem. 2008; 77:149-76. PMC: 2854675. DOI: 10.1146/annurev.biochem.77.073106.100741. View

13.

Fullwood M, Liu M, Pan Y, Liu J, Xu H, Mohamed Y . An oestrogen-receptor-alpha-bound human chromatin interactome. Nature. 2009; 462(7269):58-64. PMC: 2774924. DOI: 10.1038/nature08497. View

14.

Wachsmuth M, Caudron-Herger M, Rippe K . Genome organization: balancing stability and plasticity. Biochim Biophys Acta. 2008; 1783(11):2061-79. DOI: 10.1016/j.bbamcr.2008.07.022. View

15.

Gingeras T . Implications of chimaeric non-co-linear transcripts. Nature. 2009; 461(7261):206-11. PMC: 4020519. DOI: 10.1038/nature08452. View

16.

Price D . Poised polymerases: on your mark...get set...go!. Mol Cell. 2008; 30(1):7-10. DOI: 10.1016/j.molcel.2008.03.001. View

17.

Papantonis A, Cook P . Genome architecture and the role of transcription. Curr Opin Cell Biol. 2010; 22(3):271-6. PMC: 2884177. DOI: 10.1016/j.ceb.2010.03.004. View

18.

Gillespie P, Blow J . Clusters, factories and domains: The complex structure of S-phase comes into focus. Cell Cycle. 2010; 9(16):3218-26. PMC: 3041163. DOI: 10.4161/cc.9.16.12644. View

19.

Xu M, Cook P . Similar active genes cluster in specialized transcription factories. J Cell Biol. 2008; 181(4):615-23. PMC: 2386102. DOI: 10.1083/jcb.200710053. View

20.

Miele A, Gheldof N, Tabuchi T, Dostie J, Dekker J . Mapping chromatin interactions by chromosome conformation capture. Curr Protoc Mol Biol. 2008; Chapter 21:Unit 21.11. DOI: 10.1002/0471142727.mb2111s74. View