H3K4me3 is an epigenetic modification to the DNA packaging protein Histone H3 that indicates tri-methylation at the 4th lysine residue of the histone H3 protein and is often involved in the regulation of gene expression.[1] The name denotes the addition of three methyl groups (trimethylation) to the lysine 4 on the histone H3 protein.

H3 is used to package DNA in eukaryotic cells (including human cells), and modifications to the histone alter the accessibility of genes for transcription. H3K4me3 is commonly associated with the activation of transcription of nearby genes. H3K4 trimethylation regulates gene expression through chromatin remodeling by the NURF complex.[2] This makes the DNA in the chromatin more accessible for transcription factors, allowing the genes to be transcribed and expressed in the cell. More specifically, H3K4me3 is found to positively regulate transcription by bringing histone acetylases and nucleosome remodelling enzymes (NURF).[3] H3K4me3 also plays an important role in the genetic regulation of stem cell potency and lineage.[4] This is because this histone modification is found more in areas of the DNA that are associated with development and establishing cell identity.[5]

Nomenclature

H3K4me3 indicates trimethylation of lysine 4 on histone H3 protein subunit:

Abbr. Meaning
H3 H3 family of histones
K standard abbreviation for lysine
4 position of amino acid residue

(counting from N-terminus)

me methyl group
3 number of methyl groups added

Lysine methylation

Methylation-lysine

This diagram shows the progressive methylation of a lysine residue. The tri-methylation denotes the methylation present in H3K4me3.

The H3K4me3 modification is created by a lysine-specific histone methyltransferase (HMT) transferring three methyl groups to histone H3.[6] H3K4me3 is methylated by methyltransferase complexes containing a protein WDR5, which contains the WD40 repeat protein motif.[7] WDR5 associates specifically with dimethylated H3K4 and allows further methylation by methyltransferases, allowing for the creation and readout of the H3K4me3 modification.[8] WDR5 activity has been shown to be required for developmental genes, like the Hox genes, that are regulated by histone methylation.[7]

Epigenetic marker

H3K4me3 is a commonly used histone modification. H3K4me3 is one of the least abundant histone modifications; however, it is highly enriched at active promoters near transcription start sites (TSS) [9] and positively correlated with transcription. H3K4me3 is used as a histone code or histone mark in epigenetic studies (usually identified through chromatin immunoprecipitation) to identify active gene promoters.

H3K4me3 promotes gene activation through the action of the NURF complex, a protein complex that acts through the PHD finger protein motif to remodel chromatin.[2] This makes the DNA in the chromatin accessible for transcription factors, allowing the genes to be transcribed and expressed in the cell.

Understanding histone modifications

The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as histones. The complexes formed by the looping of the DNA are known as chromatin. The basic structural unit of chromatin is the nucleosome: this consists of the core octamer of histones (H2A, H2B, H3 and H4) as well as a linker histone and about 180 base pairs of DNA. These core histones are rich in lysine and arginine residues. The carboxyl (C) terminal end of these histones contribute to histone-histone interactions, as well as histone-DNA interactions. The amino (N) terminal charged tails are the site of the post-translational modifications, such as the one seen in H3K4me1.[10][11]

Role in stem cells and embryogenesis

Regulation of gene expression through H3K4me3 plays a significant role in stem cell fate determination and early embryo development. Pluripotent cells have distinctive patterns of methylation that can be identified through ChIP-seq. This is important in the development of induced pluripotent stem cells. A way of finding indicators of successful pluripotent induction is through comparing the epigenetic pattern to that of embryonic stem cells.[12]

In bivalent chromatin, H3K4me3 is co-localized with the repressive modification H3K27me3 to control gene regulation.[13] H3K4me3 in embryonic cells is part of a bivalent chromatin system, in which regions of DNA are simultaneously marked with activating and repressing histone methylations.[13] This is believed to allow for a flexible system of gene expression, in which genes are primarily repressed, but may be expressed quickly due to H3K4me3 as the cell progresses through development.[4] These regions tend to coincide with transcription factor genes expressed at low levels.[4] Some of these factors, such as the Hox genes, are essential for control development and cellular differentiation during embryogenesis.[2][4]

DNA repair

H3K4me3 is present at sites of DNA double-strand breaks where it promotes repair by the non-homologous end joining pathway.[14] It has been implicated that the binding of H3K4me3 is necessary for the function of genes such as inhibitor of growth protein 1 (ING1), which act as a tumor suppressors and enact DNA repair mechanisms.[15]

When DNA damage occurs, DNA damage signalling and repair begins as a result of the modification of histones within the chromatin. Mechanistically, the demethylation of H3K4me3 is used required for specific protein binding and recruitment to DNA damage[16]

Epigenetic implications

The post-translational modification of histone tails by either histone modifying complexes or chromatin remodelling complexes are interpreted by the cell and lead to complex, combinatorial transcriptional output. It is thought that a Histone code dictates the expression of genes by a complex interaction between the histones in a particular region.[17] The current understanding and interpretation of histones comes from two large scale projects: ENCODE and the Epigenomic roadmap.[18] The purpose of the epigenomic study was to investigate epigenetic changes across the entire genome. This led to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone modifications together. Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of ChIP-sequencing revealed regions in the genome characterised by different banding.[19] Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance.[20] A look in to the data obtained led to the definition of chromatin states based on histone modifications.[21] Certain modifications were mapped and enrichment was seen to localize in certain genomic regions. Five core histone modifications were found with each respective one being linked to various cell functions.

The human genome was annotated with chromatin states. These annotated states can be used as new ways to annotate a genome independently of the underlying genome sequence. This independence from the DNA sequence enforces the epigenetic nature of histone modifications. Chromatin states are also useful in identifying regulatory elements that have no defined sequence, such as enhancers. This additional level of annotation allows for a deeper understanding of cell specific gene regulation.[22]

Methods

The histone mark H3K4me3 can be detected in a variety of ways:

1. Chromatin immunoprecipitation sequencing (ChIP-sequencing) measures the amount of DNA enrichment once bound to a targeted protein and immunoprecipitated. It results in good optimization and is used in vivo to reveal DNA-protein binding occurring in cells. ChIP-Seq can be used to identify and quantify various DNA fragments for different histone modifications along a genomic region.[23]

2. Micrococcal nuclease sequencing (MNase-seq) is used to investigate regions that are bound by well positioned nucleosomes. Use of the micrococcal nuclease enzyme is employed to identify nucleosome positioning. Well positioned nucleosomes are seen to have enrichment of sequences.[24]

3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin). It uses hyperactive Tn5 transposon to highlight nucleosome localisation.[25][26][27]

See also

References

  1. ^ Sims RJ, Nishioka K, Reinberg D (November 2003). "Histone lysine methylation: a signature for chromatin function". Trends in Genetics. 19 (11): 629–39. doi:10.1016/j.tig.2003.09.007. PMID 14585615.
  2. ^ a b c Wysocka J, Swigut T, Xiao H, Milne TA, Kwon SY, Landry J, et al. (July 2006). "A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling". Nature. 442 (7098): 86–90. Bibcode:2006Natur.442...86W. doi:10.1038/nature04815. PMID 16728976. S2CID 4389087.
  3. ^ Santos-Rosa H, Schneider R, Bernstein BE, Karabetsou N, Morillon A, Weise C, et al. (November 2003). "Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin". Molecular Cell. 12 (5): 1325–32. doi:10.1016/s1097-2765(03)00438-6. PMID 14636589.
  4. ^ a b c d Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, et al. (April 2006). "A bivalent chromatin structure marks key developmental genes in embryonic stem cells". Cell. 125 (2): 315–26. CiteSeerX 10.1.1.328.9641. doi:10.1016/j.cell.2006.02.041. PMID 16630819. S2CID 9993008.
  5. ^ Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, et al. (April 2006). "A bivalent chromatin structure marks key developmental genes in embryonic stem cells". Cell. 125 (2): 315–26. doi:10.1016/j.cell.2006.02.041. PMID 16630819.
  6. ^ Rice JC, Briggs SD, Ueberheide B, Barber CM, Shabanowitz J, Hunt DF, et al. (December 2003). "Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains". Molecular Cell. 12 (6): 1591–8. doi:10.1016/s1097-2765(03)00479-9. PMID 14690610.
  7. ^ a b Wysocka J, Swigut T, Milne TA, Dou Y, Zhang X, Burlingame AL, et al. (June 2005). "WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development". Cell. 121 (6): 859–72. doi:10.1016/j.cell.2005.03.036. PMID 15960974.
  8. ^ Ruthenburg AJ, Wang W, Graybosch DM, Li H, Allis CD, Patel DJ, Verdine GL (August 2006). "Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex". Nature Structural & Molecular Biology. 13 (8): 704–12. doi:10.1038/nsmb1119. PMC 4698793. PMID 16829959.
  9. ^ Liang G, Lin JC, Wei V, Yoo C, Cheng JC, Nguyen CT, et al. (May 2004). "Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome". Proceedings of the National Academy of Sciences of the United States of America. 101 (19): 7357–62. Bibcode:2004PNAS..101.7357L. doi:10.1073/pnas.0401866101. PMC 409923. PMID 15123803.
  10. ^ Ruthenburg AJ, Li H, Patel DJ, Allis CD (December 2007). "Multivalent engagement of chromatin modifications by linked binding modules". Nature Reviews. Molecular Cell Biology. 8 (12): 983–94. doi:10.1038/nrm2298. PMC 4690530. PMID 18037899.
  11. ^ Kouzarides T (February 2007). "Chromatin modifications and their function". Cell. 128 (4): 693–705. doi:10.1016/j.cell.2007.02.005. PMID 17320507.
  12. ^ Tesar PJ, Chenoweth JG, Brook FA, Davies TJ, Evans EP, Mack DL, et al. (July 2007). "New cell lines from mouse epiblast share defining features with human embryonic stem cells". Nature. 448 (7150): 196–9. Bibcode:2007Natur.448..196T. doi:10.1038/nature05972. PMID 17597760. S2CID 4430584.
  13. ^ a b Vastenhouw NL, Schier AF (June 2012). "Bivalent histone modifications in early embryogenesis". Current Opinion in Cell Biology. 24 (3): 374–86. doi:10.1016/j.ceb.2012.03.009. PMC 3372573. PMID 22513113.
  14. ^ Wei S, Li C, Yin Z, Wen J, Meng H, Xue L, Wang J (2018). "Histone methylation in DNA repair and clinical practice: new findings during the past 5-years". Journal of Cancer. 9 (12): 2072–2081. doi:10.7150/jca.23427. PMC 6010677. PMID 29937925.
  15. ^ Peña PV, Hom RA, Hung T, Lin H, Kuo AJ, Wong RP, et al. (July 2008). "Histone H3K4me3 binding is required for the DNA repair and apoptotic activities of ING1 tumor suppressor". Journal of Molecular Biology. 380 (2): 303–12. doi:10.1016/j.jmb.2008.04.061. PMC 2576750. PMID 18533182.
  16. ^ Gong F, Clouaire T, Aguirrebengoa M, Legube G, Miller KM (July 2017). "Histone demethylase KDM5A regulates the ZMYND8-NuRD chromatin remodeler to promote DNA repair". The Journal of Cell Biology. 216 (7): 1959–1974. doi:10.1083/jcb.201611135. PMC 5496618. PMID 28572115.
  17. ^ Jenuwein T, Allis CD (August 2001). "Translating the histone code". Science. 293 (5532): 1074–80. CiteSeerX 10.1.1.453.900. doi:10.1126/science.1063127. PMID 11498575. S2CID 1883924.
  18. ^ Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, et al. (The ENCODE Project Consortium) (June 2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature. 447 (7146): 799–816. Bibcode:2007Natur.447..799B. doi:10.1038/nature05874. PMC 2212820. PMID 17571346.
  19. ^ Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, Ward LD, et al. (October 2010). "Systematic protein location mapping reveals five principal chromatin types in Drosophila cells". Cell. 143 (2): 212–24. doi:10.1016/j.cell.2010.09.009. PMC 3119929. PMID 20888037.
  20. ^ Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, et al. (modENCODE Consortium) (December 2010). "Identification of functional elements and regulatory circuits by Drosophila modENCODE". Science. 330 (6012): 1787–97. Bibcode:2010Sci...330.1787R. doi:10.1126/science.1198374. PMC 3192495. PMID 21177974.
  21. ^ Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, et al. (March 2011). "Comprehensive analysis of the chromatin landscape in Drosophila melanogaster". Nature. 471 (7339): 480–5. Bibcode:2011Natur.471..480K. doi:10.1038/nature09725. PMC 3109908. PMID 21179089.
  22. ^ Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, et al. (Roadmap Epigenomics Consortium) (February 2015). "Integrative analysis of 111 reference human epigenomes". Nature. 518 (7539): 317–30. Bibcode:2015Natur.518..317.. doi:10.1038/nature14248. PMC 4530010. PMID 25693563.
  23. ^ "Whole-Genome Chromatin IP Sequencing (ChIP-Seq)" (PDF). Illumina. Retrieved 23 October 2019.
  24. ^ "MAINE-Seq/Mnase-Seq". illumina. Retrieved 23 October 2019.
  25. ^ Buenrostro JD, Wu B, Chang HY, Greenleaf WJ (January 2015). "ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide". Current Protocols in Molecular Biology. 109: 21.29.1–21.29.9. doi:10.1002/0471142727.mb2129s109. ISBN 9780471142720. PMC 4374986. PMID 25559105.
  26. ^ Schep AN, Buenrostro JD, Denny SK, Schwartz K, Sherlock G, Greenleaf WJ (November 2015). "Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions". Genome Research. 25 (11): 1757–70. doi:10.1101/gr.192294.115. PMC 4617971. PMID 26314830.
  27. ^ Song L, Crawford GE (February 2010). "DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells". Cold Spring Harbor Protocols. 2010 (2): pdb.prot5384. doi:10.1101/pdb.prot5384. PMC 3627383. PMID 20150147.
Categories