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Combinations of Histone Modifications for Pattern Genes

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Abstract

Histone post-translational modifications play important roles in transcriptional regulation. It is known that multiple histone modifications can act in a combinatorial manner. In this study, we investigated the effects of multiple histone modifications on expression levels of five gene categories (four kinds of pattern genes and non-pattern genes) in coding regions. The combinatorial patterns of modifications for the five gene categories were also studied in the regions. Our results indicated that the differences in the expression levels between any two gene categories were significant. There were some corresponding differences in multiple histone modification levels among the five gene categories. Multiple histone modifications jointly impacted expression levels of every gene category. Four mutual combinations of histone modifications were found and analyzed.

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References

  • Bannister AJ, Kouzarides T (2005) Reversing histone methylation. Nature 436:1103–1106

    Article  Google Scholar 

  • Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Holko M, Ayanbule O, Yefanov A, Soboleva A (2011) NCBI GEO: archive for functional genomics data sets—10 years on. Nucleic Acids Res 39:D1005–D1010

    Article  Google Scholar 

  • Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K (2007) High-resolution profiling of histone methylations in the human. Cell 129:823–837

    Article  Google Scholar 

  • Butte AJ, Dzau VJ, Glueck SB (2001) Further defining housekeeping, or “maintenance,” genes focus on “a compendium of gene expression in normal human tissues”. Physiol Genomics 7:95–96

    Google Scholar 

  • Cheng C, Yan KK, Yip KY, Rozowsky J, Alexander R, Shou C, Gerstein M (2011) A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. Genome Biol 12:R15

    Article  Google Scholar 

  • Eisenberg E, Levanon EY (2003) Human housekeeping genes are compact. Trends Genet 19:362–365

    Article  Google Scholar 

  • Fischer JJ, Toedling J, Krueger T, Schueler M, Huber W, Sperling S (2008) Combinatorial effects of four histone modifications in transcription and differentiation. Genomics 91:41–51

    Article  Google Scholar 

  • Fuchs SM, Laribee RN, Strahl BD (2009) Protein modifications in transcription elongation. Biochim Biophys Acta 1789:26–36

    Article  Google Scholar 

  • Fuchs SM, Krajewski K, Baker RW, Miller VL, Strahl BD (2011) Influence of combinatorial histone modifications on antibody and effector protein recognition. Curr Biol 21:53–58

    Article  Google Scholar 

  • Greer S, Honeywell R, Geletu M, Arulanandam R, Raptis L (2010) Housekeeping genes; expression levels may change with density of cultured cells. J Immunol Methods 355:76–79

    Article  Google Scholar 

  • Guan X, Rastogi N, Parthun MR, Freitas MA (2013) Discovery of histone modification crosstalk networks by stable isotope labeling of amino acids in cell culture mass spectrometry (SILAC MS). Mol Cell Proteomics 12:2048–2059

    Article  Google Scholar 

  • Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130:77–88

    Article  Google Scholar 

  • Hayter AJ (1986) The maximum familywise error rate of Fisher’s least significant difference test. J Am Stat Assoc 81:1000–1004

    Article  Google Scholar 

  • Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B (2009) Histone modifications at human enhancers reflect global cell-typespecific gene expression. Nature 459:108–112

    Article  Google Scholar 

  • Jaschek R, Tanay A (2009) Spatial clustering of multivariate genomic and epigenomic information. In: Proceedings of the 13th annual international conference on research in computational molecular biology, Springer

  • Karlic R, Chung HR, Vlahovicek K, Vingron M (2010) Histone modification levels are predictive for gene expression. Proc Natl Acad Sci USA 107:2926–2931

    Article  Google Scholar 

  • Kornberg RD, Lorch Y (1999) Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98:285–294

    Article  Google Scholar 

  • Kurdistani SK, Tavazoie S, Grunstein M (2004) Mapping global Histone acetylation patterns to gene expression. Cell 117:721–733

    Article  Google Scholar 

  • Lee KK, Workman JL (2007) Histone acetyltransferase complexes: one size doesn’t fit all. Nat Rev Mol Cell Biol 8:284–295

    Article  Google Scholar 

  • Liang S, Li Y, Be X, Howes S, Liu W (2006) Detecting and profiling tissue-selective genes. Physiol Genomics 26:158–162

    Article  Google Scholar 

  • Liu X, Chen X, Yu X, Tao Y, Bode AM, Dong Z, Cao Y (2013) Regulation of microRNAs by epigenetics and their interplay involved in cancer. J Exp Clin Cancer Res 32:96

    Article  Google Scholar 

  • Lui JC, Chen W, Cheung CS, Baron J (2014) Broad shifts in gene expression during early postnatal life are associated with shifts in histone methylation patterns. PLoS one 28:e86957

    Article  Google Scholar 

  • Modena P, Lualdi E, Facchinetti F, Galli L, Teixeira MR, Pilotti S, Sozzi G (2005) SMARCB1/INI1 tumor suppressor gene is frequently inactivated in epithelioid sarcomas. Cancer Res 65:4012–4019

    Article  Google Scholar 

  • Ooga M, Inoue A, Kageyama S, Akiyama T, Nagata M, Aoki F (2008) Changes in H3K79 methylation during preimplantation development in mice. Biol Reprod 78:413–424

    Article  Google Scholar 

  • Pan JB, Hu SC, Wang H, Zou Q, Ji ZL (2012) PaGeFinder: quantitative identification of spatiotemporal pattern genes. Bioinformatics 28:1544–1545

    Article  Google Scholar 

  • Pan JB, Hu SC, Shi D, Cai MC, Li YB, Zou Q, Ji ZL (2013) PaGenBase: a pattern gene database for the global and dynamic understanding of gene function. PLoS one 8:e80747

    Article  Google Scholar 

  • Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A (2011) ArrayExpress update–an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res 39:D1002–D1004

    Article  Google Scholar 

  • Schones DE, Zhao K (2008) Genome-wide approaches to studying chromatin modifications. Nat Rev Genet 9:179–191

    Article  Google Scholar 

  • Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403:41–45

    Article  Google Scholar 

  • Teng S, Yang JY, Wang L (2013) Genome-wide prediction and analysis of human tissue-selective genes using microarray expression data. BMC Med Genomics 6:S10

    Article  Google Scholar 

  • Thorrez L, Laudadio I, Van Deun K, Quintens R, Hendrickx N, Granvik M, Lemaire K, Schraenen A, Van Lommel L, Lehnert S, Aguayo-Mazzucato C, Cheng-Xue R, Gilon P, Van Mechelen I, Bonner-Weir S, Lemaigre F, Schuit F (2011) Tissue-specific disallowance of housekeeping genes: the other face of cell differentiation. Genome Res 21:95–105

    Article  Google Scholar 

  • Ucar D, Hu Q, Tan K (2011) Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering. Nucleic Acids Res 39:1–13

    Article  Google Scholar 

  • Wang ZB, Zang CZ, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40:897–903

    Article  Google Scholar 

  • Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW 3rd, Su AI (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol 10:R130

    Article  Google Scholar 

  • Xiao SJ, Zhang C, Zou Q, Ji ZL (2010) TiSGeD: a database for tissue-specific genes. Bioinformatics 26:1273–1275

    Article  Google Scholar 

  • Yu H, Zhu S, Zhou B, Xue H, Han JD (2008) Inferring causal relationships among different histone modifications and gene expression. Genome Res 18:1314–1324

    Article  Google Scholar 

  • Zhang Y, Reinberg D (2001) Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails. Genes Dev 15:2343–2360

    Article  Google Scholar 

  • Zhang Y, Lv J, Liu H, Zhu J, Su J, Wu Q, Qi Y, Wang F, Li X (2010) HHMD: the human histone modification database. Nucleic Acids Res 38:D149–D154

    Article  Google Scholar 

  • Zippo A, Serafini R, Rocchigiani M, Pennacchini S, Krepelova A, Oliviero S (2009) Histone crosstalk between H3S10ph and H4K16ac generates a histone code that mediates transcription elongation. Cell 138:1122–1136

    Article  Google Scholar 

  • Zou Q, Li J, Hong Q, Lin Z, Wu Y, Shi H, Ju Y (2015) Prediction of microRNA-disease associations based on social network analysis methods. Biomed Res Int 2015:810514

    Google Scholar 

Download references

Acknowledgments

Thanks are due to Richard A. Rothery for grammatical correctness. This work was supported by the National Natural Science Foundation of China (Grant No. 31260274) and the Inner Mongolia Natural Science Foundation of China (Grant No. 2012MS0517).

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  1. School of Mathematics, Physics and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou, 014010, China

    Xiang-Jun Cui & Chen-Xia Shi

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  1. Xiang-Jun Cui
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  2. Chen-Xia Shi
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Correspondence to Xiang-Jun Cui.

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Cui, XJ., Shi, CX. Combinations of Histone Modifications for Pattern Genes. Acta Biotheor 64, 121–132 (2016). https://doi.org/10.1007/s10441-016-9276-1

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