The Organization of Histone H 3 Modifications as Revealed by a Panel of Specific Monoclonal Antibodies

Histone modifications play critical roles in the epigenetic regulation of gene expression and in the maintenance of genome integrity. Acetylation and methylation of histone H3 are particularly important in gene activation and silencing. We generated and characterized a panel of mouse monoclonal antibodies that specifically recognize different modifications on K4, K9, and K27 residues on histone H3. By using these antibodies for chromatin immunoprecipitation and immunoblotting, we analyzed the relationship between different modifications in nearby nucleosomes in human cells. Within a few nucleosome neighbors, trimethyl-K4 was associated with acetyl-K27, rather than with dimethyl-K4 and acetyl-K9, consistent with their co-localization on active promoters. Furthermore, simultaneous immunofluorescence using directly-labeled antibodies revealed that diand tri-methylation on K4 was diminished during replicative senescence. These highly-reliable and fully-characterized monoclonal antibodies may facilitate future epigenomic studies on healthy and diseased cells.

[1]  T. Mikkelsen,et al.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.

[2]  R. Young,et al.  A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells , 2007, Cell.

[3]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[4]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

[5]  Nathaniel D. Heintzman,et al.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.

[6]  E. Lander,et al.  The Mammalian Epigenome , 2007, Cell.

[7]  Peter A. Jones,et al.  The Epigenomics of Cancer , 2007, Cell.

[8]  T. Kouzarides.  Chromatin Modifications and Their Function , 2007, Cell.

[9]  F. Ishikawa,et al.  Loss of linker histone H1 in cellular senescence , 2006, The Journal of cell biology.

[10]  A. Krainer,et al.  Jcb: Article Introduction , 2022 .

[11]  L. Mahadevan,et al.  Enhanced histone acetylation and transcription: a dynamic perspective. , 2006, Molecular cell.

[12]  Christoph Plass,et al.  ChIP-chip comes of age for genome-wide functional analysis. , 2006, Cancer research.

[13]  J. Rice,et al.  A Trans-tail Histone Code Defined by Monomethylated H4 Lys-20 and H3 Lys-9 Demarcates Distinct Regions of Silent Chromatin* , 2006, Journal of Biological Chemistry.

[14]  James A. Cuff,et al.  A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells , 2006, Cell.

[15]  Karl P Nightingale,et al.  Histone modifications: signalling receptors and potential elements of a heritable epigenetic code. , 2006, Current opinion in genetics & development.

[16]  Chintamani,et al.  Qualitative and quantitative dermatoglyphic traits in patients with breast cancer: a prospective clinical study , 2007, BMC Cancer.

[17]  Megan F. Cole,et al.  Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast , 2005, Cell.

[18]  S. Horvath,et al.  Global histone modification patterns predict risk of prostate cancer recurrence , 2005, Nature.

[19]  Eric S. Lander,et al.  Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse , 2005, Cell.

[20]  I. Talianidis,et al.  Histone modifications defining active genes persist after transcriptional and mitotic inactivation , 2005, The EMBO journal.

[21]  J. Martens,et al.  Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. , 2003, Molecular cell.

[22]  H. Willard,et al.  Chromatin of the Barr body: histone and non-histone proteins associated with or excluded from the inactive X chromosome. , 2003, Human molecular genetics.

[23]  S. Lowe,et al.  Rb-Mediated Heterochromatin Formation and Silencing of E2F Target Genes during Cellular Senescence , 2003, Cell.

[24]  A. C. Chinault,et al.  Differentially methylated forms of histone H3 show unique association patterns with inactive human X chromosomes , 2002, Nature Genetics.

[25]  C. Allis,et al.  Translating the Histone Code , 2001, Science.

[26]  T. Kanda,et al.  Histone–GFP fusion protein enables sensitive analysis of chromosome dynamics in living mammalian cells , 1998, Current Biology.

[27]  B. Turner,et al.  Histone H4 acetylation distinguishes coding regions of the human genome from heterochromatin in a differentiation‐dependent but transcription‐independent manner. , 1995, The EMBO journal.

[28]  K. Kimura,et al.  Identification of the nature of modification that causes the shift of DNA topoisomerase II beta to apparent higher molecular weight forms in the M phase. , 1994, The Journal of biological chemistry.

[29]  B. Turner,et al.  Histone H4 isoforms acetylated at specific lysine residues define individual chromosomes and chromatin domains in Drosophila polytene nuclei , 1992, Cell.