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Chromatin Modifications by Methylation and Ubiquitination: Implications in the Regulation of Gene Expression

Saint Louis University School of Medicine and the Saint Louis University Cancer Center, St. Louis, Missouri 63104, USA.
Annual Review of Biochemistry (Impact Factor: 26.53). 02/2006; 75(1):243-69. DOI: 10.1146/annurev.biochem.75.103004.142422
Source: PubMed

ABSTRACT It is more evident now than ever that nucleosomes can transmit epigenetic information from one cell generation to the next. It has been demonstrated during the past decade that the posttranslational modifications of histone proteins within the chromosome impact chromatin structure, gene transcription, and epigenetic information. Multiple modifications decorate each histone tail within the nucleosome, including some amino acids that can be modified in several different ways. Covalent modifications of histone tails known thus far include acetylation, phosphorylation, sumoylation, ubiquitination, and methylation. A large body of experimental evidence compiled during the past several years has demonstrated the impact of histone acetylation on transcriptional control. Although histone modification by methylation and ubiquitination was discovered long ago, it was only recently that functional roles for these modifications in transcriptional regulation began to surface. Highlighted in this review are the recent biochemical, molecular, cellular, and physiological functions of histone methylation and ubiquitination involved in the regulation of gene expression as determined by a combination of enzymological, structural, and genetic methodologies.

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    • "H2Bub1 can modulate chromatin structure and DNA accessibility to regulate diverse DNA-dependent processes such as gene transcription (Zhang, 2003; Shilatifard, 2006; Pinder et al., 2013). RNA interference against human RNF20/RNF40 leads to reduced H2Bub1 and subsequent repression of HOX gene expression (Zhu et al., 2005). "
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    ABSTRACT: Histone H2B monoubiquitination (H2Bub1) is an important regulatory mechanism in eukaryotic gene transcription and is essential for normal plant development. However, the function of H2Bub1 in reproductive development remains elusive. Here, we report OsHUB1 (Oryza sativa HISTONE MONO-UBIQUITINATION1) and OsHUB2, the homologues of Arabidopsis HUB1 and HUB2 proteins which function as E3 ligases in H2Bub1, are involved in late anther development in rice. oshub mutants exhibit abnormal tapetum development and aborted pollen in postmeiotic anthers. Knock-out of OsHUB1 or OsHUB2 results in the loss of H2Bub1, and a reduction in the levels of dimethylated lysine 4 on histone 3 (H3K4me2). Anther transcriptome analysis revealed that several key tapetum degradation-related genes including OsC4, OsCP1 and UDT1 were down-regulated in the mutants. Further, chromatin immunoprecipitation assays demonstrate that H2Bub1 directly targets OsC4, OsCP1 and UDT1 genes and enrichment of H2Bub1 and H3K4me2 in the targets is consistent to some degree. Our studies suggest that histone H2B monoubiquitination, mediated by OsHUB1 and OsHUB2, is an important epigenetic modification that in concert with H3K4me2 modulates transcriptional regulation of anther development in rice. Copyright © 2015, American Society of Plant Biologists.
    Plant physiology 07/2015; DOI:10.1104/pp.114.256578 · 7.39 Impact Factor
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    • "Comparing H3K36me3 ChIP-seq and mRNA-seq results revealed an absence of H3K36me3 on undetectably and weakly expressed genes (log 10 FPKM <0) (Supplemental Fig. S1E), consistent with previous findings that H3K36me3 marks actively transcribed genes (Shilatifard 2006; Kouzarides 2007). For genes that are actively expressed at moderate levels (log 10 FPKM between 0 and 1), their mRNA levels positively correlated with their gene body H3K36me3 marking (Spearman's correlation , ρ = 0.17, 0.13, and 0.14; P-value < 0.001) (Supplemental Fig. S1E). "
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    Genes & development 04/2015; 29(7):718-31. DOI:10.1101/gad.254144.114 · 12.64 Impact Factor
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    • "Euchromatin in the yeast Saccharomyces cerevisiae is characterized by Dot1-mediated H3K79 trimethylation (H3K79me3) (Briggs et al. 2002; van Leeuwen et al. 2002; Henry et al. 2003; Wood et al. 2003; Kao et al. 2004; Xiao et al. 2005; Pavri et al. 2006; Shilatifard 2006). H3K79me3, a mark closely associated with active transcription , is typically present in the coding regions of genes but absent from intergenic regions as well as subtelomeric heterochromatin (Ng et al. 2003; Pokholok et al. 2005), both of which are transcriptionally silent. "
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