Chromatin architectures at fission yeast transcriptional promoters and replication origins.

Nucleic Acids Research
Robert M GivensMichael J Buck

Abstract

We have used micrococcal nuclease (MNase) digestion followed by deep sequencing in order to obtain a higher resolution map than previously available of nucleosome positions in the fission yeast, Schizosaccharomyces pombe. Our data confirm an unusually short average nucleosome repeat length, ∼152 bp, in fission yeast and that transcriptional start sites (TSSs) are associated with nucleosome-depleted regions (NDRs), ordered nucleosome arrays downstream and less regularly spaced upstream nucleosomes. In addition, we found enrichments for associated function in four of eight groups of genes clustered according to chromatin configurations near TSSs. At replication origins, our data revealed asymmetric localization of pre-replication complex (pre-RC) proteins within large NDRs-a feature that is conserved in fission and budding yeast and is therefore likely to be conserved in other eukaryotic organisms.

References

Jan 1, 1977·Proceedings of the National Academy of Sciences of the United States of America·D LohrK E Van Holde
Nov 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·P T Lowary, J Widom
Apr 1, 1996·Current Biology : CB·D D DubeyJ A Huberman
Feb 1, 1997·Nucleic Acids Research·Y OkunoH Masukata
Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Mar 17, 1999·Proceedings of the National Academy of Sciences of the United States of America·R Y Chuang, T J Kelly
Oct 16, 1999·The EMBO Journal·M Gómez, F Antequera
Oct 31, 2001·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·T Takahashi, H Masukata
Feb 12, 2004·Bioinformatics·M J L de HoonS Miyano
Jun 8, 2004·Bioinformatics·Alok J Saldanha
Nov 17, 2004·Proceedings of the National Academy of Sciences of the United States of America·Kerstin BystrickySusan M Gasser
Mar 30, 2006·Proceedings of the National Academy of Sciences of the United States of America·Lior DavidLars M Steinmetz
Oct 21, 2006·The EMBO Journal·Christian HeichingerPaul Nurse
Sep 18, 2007·Nature Genetics·William LeeCorey Nislow
Dec 21, 2007·BMC Molecular Biology·Katie L MickleJoel A Huberman
Apr 16, 2008·Genome Research·Jun S SongXiangwei He
Nov 8, 2008·PLoS Computational Biology·Yair FieldEran Segal
Dec 19, 2008·Nature·Noam KaplanEran Segal
Feb 11, 2009·Nature Reviews. Genetics·Cizhong Jiang, B Franklin Pugh
Feb 24, 2009·Methods : a Companion to Methods in Enzymology·Alexandra LantermannKarl Ekwall
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Nov 6, 2009·Annual Review of Genetics·Eric I Campos, Danny Reinberg
Dec 10, 2009·Genome Research·Heather K MacAlpineDavid M MacAlpine
Mar 31, 2010·Genes & Development·Matthew L EatonDavid M MacAlpine
Apr 9, 2010·Annual Review of Biochemistry·Hisao MasaiMasako Oda
May 11, 2010·Cold Spring Harbor Perspectives in Biology·Christopher L Woodcock, Rajarshi P Ghosh
Jun 8, 2010·The EMBO Journal·Mickaël Durand-DubiefKarl Ekwall
Dec 25, 2010·Genome Biology·William K M Lai, Michael J Buck

❮ Previous
Next ❯

Citations

Nov 28, 2013·Proceedings of the National Academy of Sciences of the United States of America·Georgette Moyle-HeyrmanJi-Ping Wang
May 24, 2013·Genome Biology and Evolution·Luke M Noble, Alex Andrianopoulos
Jan 4, 2013·PLoS Computational Biology·Tobias WarneckeBen Lehner
Jan 21, 2015·Cell Cycle·Csenge GalSimon K Whitehall
Sep 29, 2015·Briefings in Bioinformatics·Vladimir B Teif
Apr 8, 2015·The Plant Journal : for Cell and Molecular Biology·Joana Sequeira-Mendes, Crisanto Gutierrez
Oct 8, 2013·Journal of Molecular Biology·Laura MojardínFrancisco Antequera
Jun 5, 2013·Biochimica Et Biophysica Acta·Purnima Bhargava
Dec 23, 2014·Chromosoma·Corinna LielegPhilipp Korber
May 23, 2015·Nature Reviews. Molecular Cell Biology·Michalis FragkosMarcel Méchali
Apr 15, 2014·Seminars in Cell & Developmental Biology·Claire Renard-GuilletHisao Masai
Jan 18, 2017·Critical Reviews in Biochemistry and Molecular Biology·Matthew W ParkerJames M Berger
Nov 10, 2018·Genome Research·Xinyang Yu, Michael J Buck
Dec 5, 2014·Epigenetics & Chromatin·Maria Tsompana, Michael J Buck
Sep 7, 2019·Nature Communications·Zhi-Xiong ZhouThomas A Kunkel
Nov 22, 2013·Biochemical Society Transactions·Punit Prasad, Karl Ekwall
Nov 7, 2019·Genome Research·Elisa OberbeckmannPhilipp Korber
Dec 7, 2019·Physical Review Letters·Bruno BeltranAndrew J Spakowitz
Feb 23, 2021·G3 : Genes - Genomes - Genetics·Ken IshikawaShigeaki Saitoh
Oct 4, 2020·Biophysical Journal·Sarah H SandholtzAndrew J Spakowitz

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE28071

Methods Mentioned

BETA
electrophoresis
MNase-Seq
ChIP-chip
MNase-sequencing
MNase-chip
immunoprecipitation

Software Mentioned

ArchAlign
TreeView
BowTie
ArchTEx
Cluster
Java

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.