Comparative Analysis of Expression of Histone H2a Genes in Mouse

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2005 Aug 16

PMID 16098230

Citations 11

Authors

Hiromi Nishida

Takahiro Suzuki

Hiroki Ookawa

Yasuhiro Tomaru

Yoshihide Hayashizaki

Affiliations

Soon will be listed here.

Abstract

Background: At least 18 replication-dependent histone H2a genes are distributed in 3 Hist gene clusters on different chromosomes of the mouse genome. In this analysis we designed specific PCR primers for each histone H2a transcript and studied the expression levels and patterns using quantitative RT-PCR (qRT-PCR). In addition, we compared histone H3 K9 acetylation levels in the promoter regions of H2a genes by ChIP (chromatin immunoprecipitation)--quantitative PCR (qPCR) analysis.

Results: RT-PCR analysis indicated that all 20 histone H2a genes assessed in this study are expressed. The replication-dependent histone H2a genes have different expression levels but similar expression patterns. Among the 20 histone H2a genes, the expression-level of H2afz, a replication-independent gene, was highest, and that of Hist1h2aa, a replication-dependent gene, was lowest. Among 18 replication-dependent H2a genes, the expression level of Hist3h2a was highest. The ChIP-qPCR analysis showed that histone H3 K9 acetylation levels in promoter regions of both H2afz and Hist3h2a are clearly higher than that in the promoter region of Hist1h2aa. The H3 K9 acetylation level in the promoter of Hist1h2aa is similar to that in the gamma-satellite region.

Conclusion: These results strongly suggest that histone H3 K9 acetylation plays a role in the expression of histone genes.

Citing Articles

Histone variants: The bricks that fit differently.

Hegazy Y, Dhahri H, El Osmani N, George S, Chandler D, Fondufe-Mittendorf Y J Biol Chem. 2024; 301(1):108048.

PMID: 39638247 PMC: 11742582. DOI: 10.1016/j.jbc.2024.108048.

Transcriptional inhibition after irradiation occurs preferentially at highly expressed genes in a manner dependent on cell cycle progression.

Chen Z, Wang X, Gao X, Arslanovic N, Chen K, Tyler J Elife. 2024; 13.

PMID: 39392398 PMC: 11469672. DOI: 10.7554/eLife.94001.

Transcriptional inhibition after irradiation occurs preferentially at highly expressed genes in a manner dependent on cell cycle progression.

Chen Z, Wang X, Gao X, Arslanovic N, Chen K, Tyler J bioRxiv. 2023; .

PMID: 38045243 PMC: 10690177. DOI: 10.1101/2023.11.20.567799.

Human L1 Transposition Dynamics Unraveled with Functional Data Analysis.

Chen D, Cremona M, Qi Z, Mitra R, Chiaromonte F, Makova K Mol Biol Evol. 2020; 37(12):3576-3600.

PMID: 32722770 PMC: 7743743. DOI: 10.1093/molbev/msaa194.

Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities.

Sanson K, Hanna R, Hegde M, Donovan K, Strand C, Sullender M Nat Commun. 2018; 9(1):5416.

PMID: 30575746 PMC: 6303322. DOI: 10.1038/s41467-018-07901-8.

References

Rice J, Allis C . Histone methylation versus histone acetylation: new insights into epigenetic regulation. Curr Opin Cell Biol. 2001; 13(3):263-73. DOI: 10.1016/s0955-0674(00)00208-8. View

Nishida H, Tomaru Y, Oho Y, Hayashizaki Y . Naturally occurring antisense RNA of histone H2a in mouse cultured cell lines. BMC Genet. 2005; 6:23. PMC: 1156883. DOI: 10.1186/1471-2156-6-23. View

Marzluff W, Gongidi P, Woods K, Jin J, Maltais L . The human and mouse replication-dependent histone genes. Genomics. 2002; 80(5):487-98. View

Marzluff W, Duronio R . Histone mRNA expression: multiple levels of cell cycle regulation and important developmental consequences. Curr Opin Cell Biol. 2002; 14(6):692-9. DOI: 10.1016/s0955-0674(02)00387-3. View

Meneghini M, Wu M, Madhani H . Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell. 2003; 112(5):725-36. DOI: 10.1016/s0092-8674(03)00123-5. View

Czechowski T, Bari R, Stitt M, Scheible W, Udvardi M . Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J. 2004; 38(2):366-79. DOI: 10.1111/j.1365-313X.2004.02051.x. View

Sims 3rd R, Mandal S, Reinberg D . Recent highlights of RNA-polymerase-II-mediated transcription. Curr Opin Cell Biol. 2004; 16(3):263-71. DOI: 10.1016/j.ceb.2004.04.004. View

Ehrenhofer-Murray A . Chromatin dynamics at DNA replication, transcription and repair. Eur J Biochem. 2004; 271(12):2335-49. DOI: 10.1111/j.1432-1033.2004.04162.x. View

Shestakova E, Mansuroglu Z, Mokrani H, Ghinea N, Bonnefoy E . Transcription factor YY1 associates with pericentromeric gamma-satellite DNA in cycling but not in quiescent (G0) cells. Nucleic Acids Res. 2004; 32(14):4390-9. PMC: 514366. DOI: 10.1093/nar/gkh737. View

10.

Mannironi C, Bonner W, Hatch C . H2A.X. a histone isoprotein with a conserved C-terminal sequence, is encoded by a novel mRNA with both DNA replication type and polyA 3' processing signals. Nucleic Acids Res. 1989; 17(22):9113-26. PMC: 335118. DOI: 10.1093/nar/17.22.9113. View

11.

Hatch C, Bonner W . The human histone H2A.Z gene. Sequence and regulation. J Biol Chem. 1990; 265(25):15211-8. View

12.

Harris M, Bohni R, Schneiderman M, Ramamurthy L, Schumperli D, Marzluff W . Regulation of histone mRNA in the unperturbed cell cycle: evidence suggesting control at two posttranscriptional steps. Mol Cell Biol. 1991; 11(5):2416-24. PMC: 359999. DOI: 10.1128/mcb.11.5.2416-2424.1991. View

13.

Osley M . The regulation of histone synthesis in the cell cycle. Annu Rev Biochem. 1991; 60:827-61. DOI: 10.1146/annurev.bi.60.070191.004143. View

14.

Oswald F, Dobner T, Lipp M . The E2F transcription factor activates a replication-dependent human H2A gene in early S phase of the cell cycle. Mol Cell Biol. 1996; 16(5):1889-95. PMC: 231176. DOI: 10.1128/MCB.16.5.1889. View

15.

Luger K, Mader A, Richmond R, Sargent D, Richmond T . Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature. 1997; 389(6648):251-60. DOI: 10.1038/38444. View

16.

Roh T, Cuddapah S, Zhao K . Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev. 2005; 19(5):542-52. PMC: 551575. DOI: 10.1101/gad.1272505. View

17.

Nishida H, Suzuki T, Tomaru Y, Hayashizaki Y . A novel replication-independent histone H2a gene in mouse. BMC Genet. 2005; 6:10. PMC: 554098. DOI: 10.1186/1471-2156-6-10. View

18.

Livak K, Schmittgen T . Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2002; 25(4):402-8. DOI: 10.1006/meth.2001.1262. View