Nucleosome binding by the pioneer transcription factor OCT4.

Scientific Reports
Kenta EchigoyaHitoshi Kurumizaka

Abstract

Transcription factor binding to genomic DNA is generally prevented by nucleosome formation, in which the DNA is tightly wrapped around the histone octamer. In contrast, pioneer transcription factors efficiently bind their target DNA sequences within the nucleosome. OCT4 has been identified as a pioneer transcription factor required for stem cell pluripotency. To study the nucleosome binding by OCT4, we prepared human OCT4 as a recombinant protein, and biochemically analyzed its interactions with the nucleosome containing a natural OCT4 target, the LIN28B distal enhancer DNA sequence, which contains three potential OCT4 target sequences. By a combination of chemical mapping and cryo-electron microscopy single-particle analysis, we mapped the positions of the three target sequences within the nucleosome. A mutational analysis revealed that OCT4 preferentially binds its target DNA sequence located near the entry/exit site of the nucleosome. Crosslinking mass spectrometry consistently showed that OCT4 binds the nucleosome in the proximity of the histone H3 N-terminal region, which is close to the entry/exit site of the nucleosome. We also found that the linker histone H1 competes with OCT4 for the nucleosome binding. These findings...Continue Reading

References

Mar 15, 1981·Journal of Molecular Biology·F Caron, J O Thomas
Feb 20, 1996·Proceedings of the National Academy of Sciences of the United States of America·A FlausT J Richmond
Dec 29, 2000·Nature·T MisteliD T Brown
Oct 27, 2001·Acta Crystallographica. Section D, Biological Crystallography·A ReményiM Wilmanns
Jul 21, 2004·Journal of Computational Chemistry·Eric F PettersenThomas E Ferrin
Dec 2, 2004·Acta Crystallographica. Section D, Biological Crystallography·Gerard J KleywegtT Alwyn Jones
Oct 26, 2005·Nucleic Acids Research·Alexander E F Smith, Kevin G Ford
Jan 10, 2006·Developmental Cell·Eran MeshorerTom Misteli
Nov 22, 2007·Science·Junying YuJames A Thomson
Dec 24, 2010·Nature Reviews. Molecular Cell Biology·Alexandre Gaspar-MaiaMiguel Ramalho-Santos
May 17, 2012·PLoS Genetics·Yunzhe ZhangYuhong Fan
Aug 30, 2012·Methods in Enzymology·Kristin R BrogaardJonathan Widom
Feb 5, 2013·Nature Cell Biology·Daniel EschHans R Schöler
Nov 12, 2013·Nature Methods·Alp KucukelbirHemant D Tagare
Nov 13, 2013·Proceedings of the National Academy of Sciences of the United States of America·Bing-Rui ZhouYawen Bai
Jan 28, 2014·Nature·Maria A ChristophorouTony Kouzarides
Dec 17, 2014·Genes & Development·Makiko Iwafuchi-Doi, Kenneth S Zaret
Jul 23, 2015·Development·Jennifer Tsialikas, Jennifer Romer-Seibert
Jul 28, 2015·Molecular Cell·Bing-Rui ZhouYawen Bai
Aug 19, 2015·Journal of Structural Biology·Alexis Rohou, Nikolaus Grigorieff
Jan 31, 2016·Current Opinion in Genetics & Development·Kenneth S Zaret, Susan E Mango
Aug 31, 2016·Methods in Enzymology·S H W Scheres
Dec 3, 2016·Nucleic Acids Research·Shujiro OkudaYasushi Ishihama
May 6, 2017·Molecular Cell·Jan BednarStefan Dimitrov
Aug 11, 2017·The Journal of Cell Biology·Annalisa IzzoRobert Schneider
Nov 22, 2017·Journal of Biochemistry·Masako Koyama, Hitoshi Kurumizaka
Feb 10, 2018·Cell·Samuel A LambertMatthew T Weirauch
Aug 4, 2018·Methods in Molecular Biology·Tomoya KujiraiHitoshi Kurumizaka

❮ Previous
Next ❯

Citations

Sep 5, 2020·Annual Review of Genetics·Kenneth S Zaret
Oct 17, 2020·Journal of Molecular Biology·Hitoshi KurumizakaYoshimasa Takizawa
Apr 1, 2021·BMC Bioinformatics·K C KishanFeng Cui
Apr 7, 2021·Current Opinion in Chemical Biology·Jinrong Min, Ke Liu
May 1, 2021·3 Biotech·Chandrima DeyRajkumar P Thummer
Jun 20, 2021·Cell·Alicia K Michael, Nicolas H Thomä
Aug 7, 2021·Nature Cell Biology·Gareth A RobertsAbdenour Soufi
Aug 21, 2021·Cellular and Molecular Life Sciences : CMLS·Helen Ray-Jones, Mikhail Spivakov

❮ Previous
Next ❯

Methods Mentioned

BETA
salt dialysis
electrophoretic mobility shift assay
electrophoresis
PCR
gel filtration

Software Mentioned

xProphet
xQuest
RELION
EPU

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.

Related Papers

BioRxiv : the Preprint Server for Biology
Caitlin M MacCarthyVlad Cojocaru
Proceedings of the National Academy of Sciences of the United States of America
Cheng Tan, Shoji Takada
Cell
R H Morse, R T Simpson
Scientific American
R D Kornberg, A Klug
Cell Research
Ryan T Wagner, Austin J Cooney
© 2021 Meta ULC. All rights reserved