Real-time observation of the initiation of RNA polymerase II transcription

Nature
Furqan M FazalSteven M Block

Abstract

Biochemical and structural studies have shown that the initiation of RNA polymerase II transcription proceeds in the following stages: assembly of the polymerase with general transcription factors and promoter DNA in a 'closed' preinitiation complex (PIC); unwinding of about 15 base pairs of the promoter DNA to form an 'open' complex; scanning downstream to a transcription start site; synthesis of a short transcript, thought to be about 10 nucleotides long; and promoter escape. Here we have assembled a 32-protein, 1.5-megadalton PIC derived from Saccharomyces cerevisiae, and observe subsequent initiation processes in real time with optical tweezers. Contrary to expectation, scanning driven by the transcription factor IIH involved the rapid opening of an extended transcription bubble, averaging 85 base pairs, accompanied by the synthesis of a transcript up to the entire length of the extended bubble, followed by promoter escape. PICs that failed to achieve promoter escape nevertheless formed open complexes and extended bubbles, which collapsed back to closed or open complexes, resulting in repeated futile scanning.

References

Nov 1, 1992·Genes & Development·C GiardinaJ T Lis
May 1, 1995·Molecular and Cellular Biology·C Giardina, J T Lis
Aug 6, 1993·Science·C Giardina, J T Lis
Jan 1, 1993·Annual Review of Biochemistry·R C Conaway, J W Conaway
Sep 6, 1996·The Journal of Biological Chemistry·N L HenryR D Kornberg
Aug 19, 1997·Proceedings of the National Academy of Sciences of the United States of America·A DvirJ W Conaway
Feb 21, 1998·The EMBO Journal·F C HolstegeH T Timmers
Apr 16, 1998·Proceedings of the National Academy of Sciences of the United States of America·S MalikR G Roeder
May 2, 2001·Proceedings of the National Academy of Sciences of the United States of America·L SpanglerA Dvir
Jul 5, 2006·Nature Structural & Molecular Biology·Gail Miller, Steven Hahn
Nov 18, 2006·Science·Achillefs N KapanidisRichard H Ebright
May 9, 2007·Nature Reviews. Genetics·Albin SandelinDavid A Hume
Aug 3, 2007·Proceedings of the National Academy of Sciences of the United States of America·Roger D Kornberg
Nov 8, 2011·Molecular Cell·Timothy W SikorskiStephen Buratowski
Dec 7, 2011·Nature Photonics·Furqan M Fazal, Steven M Block
Mar 14, 2012·Proceedings of the National Academy of Sciences of the United States of America·Kenji MurakamiRoger D Kornberg
Apr 12, 2012·Proceedings of the National Academy of Sciences of the United States of America·Matthew H LarsonSteven M Block
Jul 4, 2012·Nature Structural & Molecular Biology·Sebastian GrünbergSteven Hahn
Aug 14, 2012·Journal of Molecular Biology·Daniel J KosloverSteven M Block
Jan 11, 2013·The Journal of Biological Chemistry·Kenji MurakamiRoger D Kornberg
Sep 28, 2013·Science·Kenji MurakamiRoger D Kornberg
Apr 16, 2014·Proceedings of the National Academy of Sciences of the United States of America·Volker SchweikhardSteven M Block
Jun 16, 2015·Molecular Cell·Kenji MurakamiRoger D Kornberg

❮ Previous
Next ❯

Citations

Oct 21, 2015·Proceedings of the National Academy of Sciences of the United States of America·Kenji MurakamiRoger D Kornberg
Feb 6, 2016·Histochemistry and Cell Biology·Klara Weipoltshammer, Christian Schöfer
Sep 9, 2016·Optics Express·Amr A E SalehJennifer A Dionne
Oct 12, 2016·ACS Central Science·Andrew J Spakowitz
Oct 30, 2016·Proceedings of the National Academy of Sciences of the United States of America·Eitan LernerShimon Weiss
Apr 4, 2017·Protein Science : a Publication of the Protein Society·Yazan AlhadidShimon Weiss
Jan 30, 2018·Acta Biochimica Et Biophysica Sinica·Deyu ZhaoYing Gao
Oct 16, 2015·BioTechniques·Jeffrey Perkel
Nov 7, 2017·Nature Structural & Molecular Biology·Eric J TomkoEric A Galburt
Nov 29, 2017·Proceedings of the National Academy of Sciences of the United States of America·Nivedita DamodarenKenji Murakami
Nov 24, 2017·ELife·Libing YuRichard H Ebright
Apr 18, 2018·Protein Science : a Publication of the Protein Society·Jenna K Rimel, Dylan J Taatjes
May 28, 2019·Genes & Development·Leighton Core, Karen Adelman
Oct 20, 2019·Proceedings of the National Academy of Sciences of the United States of America·Donal S Luse
Feb 22, 2017·Biomolecular Concepts·Ana Lisica, Stephan W Grill
May 20, 2016·Nature·Steven Hahn, Stephen Buratowski
Sep 8, 2016·Genes & Development·Huimin Chen, Daniel R Larson
May 5, 2017·Protein Science : a Publication of the Protein Society·M MarchettiG J L Wuite
Oct 9, 2019·Proceedings of the National Academy of Sciences of the United States of America·Rina FujiwaraKenji Murakami
Jun 27, 2018·International Journal of Molecular Sciences·Alf MånssonDilson E Rassier
Dec 10, 2020·Proceedings of the National Academy of Sciences of the United States of America·Grace A RosenJeff Gelles
Nov 11, 2020·The Journal of Biological Chemistry·Ruth Q JacobsDavid A Schneider
Jan 17, 2021·Journal of Molecular Biology·Eric J TomkoEric A Galburt
Feb 9, 2021·Frontiers in Bioengineering and Biotechnology·Pisrut PhummiratDaryl Preece
Oct 29, 2020·Genome Génome / Conseil National De Recherches Canada·Rachel M PriceSheila S Teves
Jan 8, 2021·The Journal of Biological Chemistry·Ruth Q JacobsDavid A Schneider
Jun 9, 2021·Nature Communications·Trevor van EeuwenKenji Murakami
Aug 18, 2021·The Journal of Biological Chemistry·Chun-Ying Lee, Sua Myong
Oct 30, 2019·Chemical Reviews·Sonisilpa MohapatraTaekjip Ha
Jan 9, 2020·Accounts of Chemical Research·Michelle L SolomonJennifer A Dionne

❮ Previous
Next ❯

Methods Mentioned

BETA
footprinting
PCR
electrophoresis

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.