Histone modifications defining active genes persist after transcriptional and mitotic inactivation

We examined various histone modifications across the promoter and the coding regions of constitutively active hepatic genes in G0/G1‐enriched, mitotically arrested and α‐amanitin‐blocked cells. Gene activation correlated with localized histone hyperacetylation, H3‐K4 tri‐ or dimethylation and H3‐K79 dimethylation and localized nucleosome remodeling at the promoter and the 5′ portion of the coding regions. Nucleosomes at more downstream locations were monomethylated at H3‐K4. CBP, PCAF, Brg‐1, SNF2H and FACT were recruited to the coding regions in a gene‐specific manner, in a similarly restricted promoter‐proximal pattern. Elongator, however, associated with the more downstream regions. While all factors were dissociated from the chromatin after transcriptional inactivation by α‐amanitin, the histone modifications remained stable. In mitotic cells, histone modifications on parental nucleosomes were preserved and were regenerated in a transcription‐dependent manner at the newly deposited nucleosomes, as the cells entered the next G1 phase. The findings suggest that histone modifications may function as molecular memory bookmarks for previously active locations of the genome, thus contributing to the maintenance of active chromatin states through cell division.

[1]  Philip R. Gafken,et al.  Histone H3.3 is enriched in covalent modifications associated with active chromatin. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[2]  B. Turner,et al.  Cellular Memory and the Histone Code , 2002, Cell.

[3]  I. Talianidis,et al.  Regulatory Mechanisms Controlling Human Hepatocyte Nuclear Factor 4α Gene Expression , 2001, Molecular and Cellular Biology.

[4]  S. Henikoff,et al.  The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. , 2002, Molecular cell.

[5]  R. Kingston,et al.  Localized recruitment of a chromatin-remodeling activity by an activator in vivo drives transcriptional elongation. , 2003, Genes & development.

[6]  Dimitris Thanos,et al.  Ordered Recruitment of Chromatin Modifying and General Transcription Factors to the IFN-β Promoter , 2000, Cell.

[7]  Tony Kouzarides,et al.  Histone H3 lysine 4 methylation patterns in higher eukaryotic genes , 2004, Nature Cell Biology.

[8]  Richard A Young,et al.  Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. , 2002, Molecular cell.

[9]  Kevin Struhl,et al.  Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. , 2003, Molecular cell.

[10]  Dimitris Thanos,et al.  Deciphering the Transcriptional Histone Acetylation Code for a Human Gene , 2002, Cell.

[11]  Andrew J. Bannister,et al.  Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain , 2001, Nature.

[12]  B. Cairns,et al.  Transcriptional inhibition of genes with severe histone h3 hypoacetylation in the coding region. , 2002, Molecular cell.

[13]  R. Kingston,et al.  Cooperation between Complexes that Regulate Chromatin Structure and Transcription , 2002, Cell.

[14]  Stuart L. Schreiber,et al.  Active genes are tri-methylated at K4 of histone H3 , 2002, Nature.

[15]  B M Turner,et al.  Histone acetylation and an epigenetic code. , 2000, BioEssays : news and reviews in molecular, cellular and developmental biology.

[16]  G. Orphanides,et al.  FACT Facilitates Transcription-Dependent Nucleosome Alteration , 2003, Science.

[17]  S. Berger,et al.  Histone modifications in transcriptional regulation. , 2002, Current opinion in genetics & development.

[18]  R. van Driel,et al.  Nuclear distribution of transcription factors in relation to sites of transcription and RNA polymerase II. , 1997, Journal of cell science.

[19]  Stuart L Schreiber,et al.  Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin. , 2003, Molecular cell.

[20]  D. Reinberg,et al.  Facts about FACT and transcript elongation through chromatin. , 2004, Current opinion in genetics & development.

[21]  B. Emerson.  Specificity of Gene Regulation , 2002, Cell.

[22]  T. Jenuwein.  Re-SET-ting heterochromatin by histone methyltransferases. , 2001, Trends in cell biology.

[23]  M. Yaniv,et al.  Components of the Human SWI/SNF Complex Are Enriched in Active Chromatin and Are Associated with the Nuclear Matrix , 1997, The Journal of cell biology.

[24]  T. Kouzarides.  Histone methylation in transcriptional control. , 2002, Current opinion in genetics & development.

[25]  D. Reinberg,et al.  Human Elongator facilitates RNA polymerase II transcription through chromatin , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[26]  A. Kristjuhan,et al.  Elongator interactions with nascent mRNA revealed by RNA immunoprecipitation. , 2004, Molecular cell.

[27]  R Ohba,et al.  A novel histone acetyltransferase is an integral subunit of elongating RNA polymerase II holoenzyme. , 1999, Molecular cell.

[28]  I. Talianidis,et al.  Modulation of hepatic gene expression by hepatocyte nuclear factor 1. , 1997, Science.

[29]  Karl Mechtler,et al.  Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins , 2001, Nature.

[30]  G. Almouzni,et al.  Histone H3.1 and H3.3 Complexes Mediate Nucleosome Assembly Pathways Dependent or Independent of DNA Synthesis , 2004, Cell.

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

[32]  I. Talianidis,et al.  Dynamics of enhancer-promoter communication during differentiation-induced gene activation. , 2002, Molecular cell.

[33]  I. Talianidis,et al.  Coordination of PIC Assembly and Chromatin Remodeling During Differentiation-Induced Gene Activation , 2002, Science.

[34]  M. Yaniv,et al.  The hbrm and BRG‐1 proteins, components of the human SNF/SWI complex, are phosphorylated and excluded from the condensed chromosomes during mitosis. , 1996, The EMBO journal.

[35]  M. Johnston,et al.  The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation. , 2003, Molecular cell.

[36]  I. Talianidis,et al.  Acetylation regulates transcription factor activity at multiple levels. , 2000, Molecular cell.

[37]  D. Reinberg,et al.  Tracking FACT and the RNA Polymerase II Elongation Complex Through Chromatin in Vivo , 2003, Science.

[38]  S. Grewal,et al.  Heterochromatin: new possibilities for the inheritance of structure. , 2002, Current opinion in genetics & development.

[39]  Paul Tempst,et al.  Elongator is a histone H3 and H4 acetyltransferase important for normal histone acetylation levels in vivo , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[40]  C. Allis,et al.  Histone and chromatin cross-talk. , 2003, Current opinion in cell biology.

[41]  T. Jenuwein,et al.  The many faces of histone lysine methylation. , 2002, Current opinion in cell biology.

[42]  M. Kirschner,et al.  Mitotic inactivation of a human SWI/SNF chromatin remodeling complex. , 1998, Genes & development.