Chromatin architectures at fission yeast transcriptional promoters and replication origins

Robert M. Givens; William K.M. Lai; Jason M. Rizzo; Jonathan E. Bard; Piotr A. Mieczkowski; Janet Leatherwood; Joel A. Huberman; Michael J. Buck

doi:10.1093/nar/gks351

Chromatin architectures at fission yeast transcriptional promoters and replication origins

Robert M. Givens, William K.M. Lai, Jason M. Rizzo, Jonathan E. Bard, Piotr A. Mieczkowski, Janet Leatherwood, Joel A. Huberman, Michael J. Buck

Biochemistry & Molecular Biology

Research output: Contribution to journal › Article › peer-review

29 Scopus citations

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 nucleosomedepleted regions (NDRs), ordered nucleosome arrays downstream and less regularly spaced upstreamnucleosomes. 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.

Original language	English (US)
Pages (from-to)	7176-7189
Number of pages	14
Journal	Nucleic acids research
Volume	40
Issue number	15
DOIs	https://doi.org/10.1093/nar/gks351
State	Published - Aug 2012

All Science Journal Classification (ASJC) codes

Genetics

Access to Document

10.1093/nar/gks351

Fingerprint Dive into the research topics of 'Chromatin architectures at fission yeast transcriptional promoters and replication origins'. Together they form a unique fingerprint.

Cite this

@article{8c6b046e2aed45f3826cae72dd9a6989,

title = "Chromatin architectures at fission yeast transcriptional promoters and replication origins",

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 nucleosomedepleted regions (NDRs), ordered nucleosome arrays downstream and less regularly spaced upstreamnucleosomes. 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.",

author = "Givens, {Robert M.} and Lai, {William K.M.} and Rizzo, {Jason M.} and Bard, {Jonathan E.} and Mieczkowski, {Piotr A.} and Janet Leatherwood and Huberman, {Joel A.} and Buck, {Michael J.}",

note = "Funding Information: National Institutes of Health [GM70566 to J.A.H.]; the National Science Foundation [IIS1016929 to M.J.B.]; a PhRMA predoctoral fellowship in Informatics (to J.M.R.). Funding for open access charge: Department of Biochemistry, SUNY at Buffalo. Funding Information: R.M.G. is grateful for the support of Lt. Col. and Mrs C. M. Givens, R. Tafari, and the NY State Department of Labor during data analysis and article preparation. Copyright: Copyright 2012 Elsevier B.V., All rights reserved.",

year = "2012",

month = aug,

doi = "10.1093/nar/gks351",

language = "English (US)",

volume = "40",

pages = "7176--7189",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "15",

}

Chromatin architectures at fission yeast transcriptional promoters and replication origins. / Givens, Robert M.; Lai, William K.M.; Rizzo, Jason M.; Bard, Jonathan E.; Mieczkowski, Piotr A.; Leatherwood, Janet; Huberman, Joel A.; Buck, Michael J.

In: Nucleic acids research, Vol. 40, No. 15, 08.2012, p. 7176-7189.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Chromatin architectures at fission yeast transcriptional promoters and replication origins

AU - Givens, Robert M.

AU - Lai, William K.M.

AU - Rizzo, Jason M.

AU - Bard, Jonathan E.

AU - Mieczkowski, Piotr A.

AU - Leatherwood, Janet

AU - Huberman, Joel A.

AU - Buck, Michael J.

N1 - Funding Information: National Institutes of Health [GM70566 to J.A.H.]; the National Science Foundation [IIS1016929 to M.J.B.]; a PhRMA predoctoral fellowship in Informatics (to J.M.R.). Funding for open access charge: Department of Biochemistry, SUNY at Buffalo. Funding Information: R.M.G. is grateful for the support of Lt. Col. and Mrs C. M. Givens, R. Tafari, and the NY State Department of Labor during data analysis and article preparation. Copyright: Copyright 2012 Elsevier B.V., All rights reserved.

PY - 2012/8

Y1 - 2012/8

N2 - 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 nucleosomedepleted regions (NDRs), ordered nucleosome arrays downstream and less regularly spaced upstreamnucleosomes. 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.

AB - 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 nucleosomedepleted regions (NDRs), ordered nucleosome arrays downstream and less regularly spaced upstreamnucleosomes. 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.

UR - http://www.scopus.com/inward/record.url?scp=84867298738&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84867298738&partnerID=8YFLogxK

U2 - 10.1093/nar/gks351

DO - 10.1093/nar/gks351

M3 - Article

C2 - 22573177

AN - SCOPUS:84867298738

VL - 40

SP - 7176

EP - 7189

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 15

ER -

Chromatin architectures at fission yeast transcriptional promoters and replication origins

Abstract

All Science Journal Classification (ASJC) codes

Access to Document

Other files and links

Cite this