Chromatin Architectures at Fission Yeast Transcriptional Promoters and Replication Origins

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2012 May 11

PMID 22573177

Citations 24

Authors

Robert M Givens

William K M Lai

Jason M Rizzo

Jonathan E Bard

Piotr A Mieczkowski

Janet Leatherwood

Joel A Huberman

Michael J Buck

Affiliations

Soon will be listed here.

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.

Citing Articles

Transcriptional Regulation Technology for Gene Perturbation in Fission Yeast.

Ishikawa K, Saitoh S Biomolecules. 2023; 13(4).

PMID: 37189462 PMC: 10135669. DOI: 10.3390/biom13040716.

Opposing Roles of FACT for Euchromatin and Heterochromatin in Yeast.

Takahata S, Murakami Y Biomolecules. 2023; 13(2).

PMID: 36830746 PMC: 9953268. DOI: 10.3390/biom13020377.

Implementation of dCas9-mediated CRISPRi in the fission yeast Schizosaccharomyces pombe.

Ishikawa K, Soejima S, Masuda F, Saitoh S G3 (Bethesda). 2021; 11(4).

PMID: 33617628 PMC: 8137136. DOI: 10.1093/g3journal/jkab051.

Chromosome Structural Mechanics Dictates the Local Spreading of Epigenetic Marks.

Sandholtz S, Kannan D, Beltran B, Spakowitz A Biophys J. 2020; 119(8):1630-1639.

PMID: 33010237 PMC: 7642308. DOI: 10.1016/j.bpj.2020.08.039.

Absolute nucleosome occupancy map for the genome.

Oberbeckmann E, Wolff M, Krietenstein N, Heron M, Ellins J, Schmid A Genome Res. 2019; 29(12):1996-2009.

PMID: 31694866 PMC: 6886505. DOI: 10.1101/gr.253419.119.

References

Song J, Liu X, Liu X, He X . A high-resolution map of nucleosome positioning on a fission yeast centromere. Genome Res. 2008; 18(7):1064-72. PMC: 2493395. DOI: 10.1101/gr.075374.107. View

de Castro E, Soriano I, Marin L, Serrano R, Quintales L, Antequera F . Nucleosomal organization of replication origins and meiotic recombination hotspots in fission yeast. EMBO J. 2011; 31(1):124-37. PMC: 3252569. DOI: 10.1038/emboj.2011.350. View

Lantermann A, Stralfors A, Fagerstrom-Billai F, Korber P, Ekwall K . Genome-wide mapping of nucleosome positions in Schizosaccharomyces pombe. Methods. 2009; 48(3):218-25. DOI: 10.1016/j.ymeth.2009.02.004. View

Dubey D, Kim S, Todorov I, Huberman J . Large, complex modular structure of a fission yeast DNA replication origin. Curr Biol. 1996; 6(4):467-73. DOI: 10.1016/s0960-9822(02)00514-6. View

Okuno Y, Satoh H, Sekiguchi M, Masukata H . Clustered adenine/thymine stretches are essential for function of a fission yeast replication origin. Mol Cell Biol. 1999; 19(10):6699-709. PMC: 84658. DOI: 10.1128/MCB.19.10.6699. View

Chuang R, Kelly T . The fission yeast homologue of Orc4p binds to replication origin DNA via multiple AT-hooks. Proc Natl Acad Sci U S A. 1999; 96(6):2656-61. PMC: 15824. DOI: 10.1073/pnas.96.6.2656. View

Heichinger C, Penkett C, Bahler J, Nurse P . Genome-wide characterization of fission yeast DNA replication origins. EMBO J. 2006; 25(21):5171-9. PMC: 1630417. DOI: 10.1038/sj.emboj.7601390. View

Hayashi M, Katou Y, Itoh T, Tazumi A, Tazumi M, Yamada Y . Genome-wide localization of pre-RC sites and identification of replication origins in fission yeast. EMBO J. 2007; 26(5):1327-39. PMC: 1817633. DOI: 10.1038/sj.emboj.7601585. View

Mickle K, Ramanathan S, Rosebrock A, Oliva A, Chaudari A, Yompakdee C . Checkpoint independence of most DNA replication origins in fission yeast. BMC Mol Biol. 2007; 8:112. PMC: 2235891. DOI: 10.1186/1471-2199-8-112. View

10.

Moreno S, Klar A, Nurse P . Molecular genetic analysis of fission yeast Schizosaccharomyces pombe. Methods Enzymol. 1991; 194:795-823. DOI: 10.1016/0076-6879(91)94059-l. View

11.

Lantermann A, Straub T, Stralfors A, Yuan G, Ekwall K, Korber P . Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae. Nat Struct Mol Biol. 2010; 17(2):251-7. DOI: 10.1038/nsmb.1741. View

12.

de Hoon M, Imoto S, Nolan J, Miyano S . Open source clustering software. Bioinformatics. 2004; 20(9):1453-4. DOI: 10.1093/bioinformatics/bth078. View

13.

Woodcock C, Ghosh R . Chromatin higher-order structure and dynamics. Cold Spring Harb Perspect Biol. 2010; 2(5):a000596. PMC: 2857170. DOI: 10.1101/cshperspect.a000596. View

14.

Chuang R, Chretien L, Dai J, Kelly T . Purification and characterization of the Schizosaccharomyces pombe origin recognition complex: interaction with origin DNA and Cdc18 protein. J Biol Chem. 2002; 277(19):16920-7. DOI: 10.1074/jbc.M107710200. View

15.

Langmead B, Trapnell C, Pop M, Salzberg S . Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; 10(3):R25. PMC: 2690996. DOI: 10.1186/gb-2009-10-3-r25. View

16.

Campos E, Reinberg D . Histones: annotating chromatin. Annu Rev Genet. 2009; 43:559-99. DOI: 10.1146/annurev.genet.032608.103928. View

17.

Erard M, Barker D . Electron microscopic studies of condensed mitotic chromosomes in the fission yeast Schizosaccharomyces pombe. Biol Cell. 1985; 55(1-2):27-34. DOI: 10.1111/j.1768-322x.1985.tb00406.x. View

18.

Durand-Dubief M, Persson J, Norman U, Hartsuiker E, Ekwall K . Topoisomerase I regulates open chromatin and controls gene expression in vivo. EMBO J. 2010; 29(13):2126-34. PMC: 2905247. DOI: 10.1038/emboj.2010.109. View

19.

Godde J, Widom J . Chromatin structure of Schizosaccharomyces pombe. A nucleosome repeat length that is shorter than the chromatosomal DNA length. J Mol Biol. 1992; 226(4):1009-25. DOI: 10.1016/0022-2836(92)91049-u. View

20.

Clyne R, Kelly T . Genetic analysis of an ARS element from the fission yeast Schizosaccharomyces pombe. EMBO J. 1995; 14(24):6348-57. PMC: 394760. DOI: 10.1002/j.1460-2075.1995.tb00326.x. View