Lo AW, Magliano DJ, Sibson MC, Kalitsis P, Craig JM, and Choo KH
The Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia 3052.
The estrogen receptor alpha (ERalpha) regulates gene expression by either direct binding to estrogen response elements or indirect tethering to other transcription factors on promoter targets. To identify these promoter sequences, we conducted a genome-wide screening with a novel microarray technique called ChIP-on-chip.
See the abstract here
Wednesday, May 11, 2005
Tuesday, April 26, 2005
Sir2 and the acetyltransferase, Pat, regulate the archael chromatin protein, Alba.
Marsh VL, Peak-Chew SY, and Bell SD
Medical Research Council Cancer Cell Unit, Cambridge CB2 2XZ.
The DNA binding affinity of Alba, a chromatin protein of the archaeon Sulfolobus solfataricus P2, is regulated by acetylation of lysine 16. Here we identify an acetyl transferase that specifically acetylates Alba on this residue. The effect of acetylation is to lower the affinity of Alba for DNA. Remarkably, the acetyl transferase is conserved not only in archaea but also in bacteria, where it appears to play a role in metabolic regulation. Our data suggest therefore that S. solfataricus has co-opted this bacterial regulatory system to generate a rudimentary form of chromatin regulation. (added 2005/4/12)
See the full text:
http://www.jbc.org/cgi/reprint/M501280200v1
Medical Research Council Cancer Cell Unit, Cambridge CB2 2XZ.
The DNA binding affinity of Alba, a chromatin protein of the archaeon Sulfolobus solfataricus P2, is regulated by acetylation of lysine 16. Here we identify an acetyl transferase that specifically acetylates Alba on this residue. The effect of acetylation is to lower the affinity of Alba for DNA. Remarkably, the acetyl transferase is conserved not only in archaea but also in bacteria, where it appears to play a role in metabolic regulation. Our data suggest therefore that S. solfataricus has co-opted this bacterial regulatory system to generate a rudimentary form of chromatin regulation. (added 2005/4/12)
See the full text:
http://www.jbc.org/cgi/reprint/M501280200v1
Regulated chromatin domain comprising cluster of co-expressed genes in Drosophila melanogaster.
Kalmykova AI, Nurminsky DI, Ryzhov DV, and Shevelyov YY
Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences Moscow 123182, Russia.
Recently, the phenomenon of clustering of co-expressed genes on chromosomes was discovered in eukaryotes. To explore the hypothesis that genes within clusters occupy shared chromatin domains, we performed a detailed analysis of transcription pattern and chromatin structure of a cluster of co-expressed genes. We found that five non-homologous genes (Crtp, Yu, CK2betates, Pros28.1B and CG13581) are expressed exclusively in Drosophila melanogaster male germ-line and form a non-interrupted cluster in the 15 kb region of chromosome 2. The cluster is surrounded by genes with broader transcription patterns. Analysis of DNase I sensitivity revealed 'open' chromatin conformation in the cluster and adjacent regions in the male germ-line cells, where all studied genes are transcribed. In contrast, in somatic tissues where the cluster genes are silent, the domain of repressed chromatin encompassed four out of five cluster genes and an adjacent non-cluster gene CG13589 that is also silent in analyzed somatic tissues. The fifth cluster gene (CG13581) appears to be excluded from the chromatin domain occupied by the other four genes. Our results suggest that extensive clustering of co-expressed genes in eukaryotic genomes does in general reflect the domain organization of chromatin, although domain borders may not exactly correspond to the margins of gene clusters. (added 2005/03/09)
See full text here:
http://nar.oupjournals.org/cgi/content/full/33/5/1435
Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences Moscow 123182, Russia.
Recently, the phenomenon of clustering of co-expressed genes on chromosomes was discovered in eukaryotes. To explore the hypothesis that genes within clusters occupy shared chromatin domains, we performed a detailed analysis of transcription pattern and chromatin structure of a cluster of co-expressed genes. We found that five non-homologous genes (Crtp, Yu, CK2betates, Pros28.1B and CG13581) are expressed exclusively in Drosophila melanogaster male germ-line and form a non-interrupted cluster in the 15 kb region of chromosome 2. The cluster is surrounded by genes with broader transcription patterns. Analysis of DNase I sensitivity revealed 'open' chromatin conformation in the cluster and adjacent regions in the male germ-line cells, where all studied genes are transcribed. In contrast, in somatic tissues where the cluster genes are silent, the domain of repressed chromatin encompassed four out of five cluster genes and an adjacent non-cluster gene CG13589 that is also silent in analyzed somatic tissues. The fifth cluster gene (CG13581) appears to be excluded from the chromatin domain occupied by the other four genes. Our results suggest that extensive clustering of co-expressed genes in eukaryotic genomes does in general reflect the domain organization of chromatin, although domain borders may not exactly correspond to the margins of gene clusters. (added 2005/03/09)
See full text here:
http://nar.oupjournals.org/cgi/content/full/33/5/1435
Tuesday, February 01, 2005
Chd1 protein links histone methylation and acetylation
New paper in Nature identifies a new function for yeast chromodomain protein Chd1p, namely recognition and binding of histones methylated at lysine 4. Chd1 was identified as a component of the SAGA andSLIK complexes, recruiting SAGA and SLIK to chromatin containing methyl Lys4 H3. Using biotinylated peptides corresp. to the N-term tail of H3, they were able to pull down Chd1.
http://www.eurekalert.org/pub_releases/2005-01/uovh-inp011205.php
Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation
MARILYN G. PRAY-GRANT, JEREMY A. DANIEL, DAVID SCHIELTZ, JOHN R. YATES III & PATRICK A. GRANT
LINK TO PAPER IN NATURE
The specific post-translational modifications to histones influence many nuclear processes including gene regulation, DNA repair and replication. Recent studies have identified effector proteins that recognize patterns of histone modification and transduce their function in downstream processes. For example, histone acetyltransferases (HATs) have been shown to participate in many essential cellular processes, particularly those associated with activation of transcription. Yeast SAGA (Spt-Ada-Gcn5 acetyltransferase) and SLIK (SAGA-like) are two highly homologous and conserved multi-subunit HAT complexes, which preferentially acetylate histones H3 and H2B and deubiquitinate histone H2B. Here we identify the chromatin remodelling protein Chd1 (chromo-ATPase/helicase-DNA binding domain 1) as a component of SAGA and SLIK. Our findings indicate that one of the two chromodomains of Chd1 specifically interacts with the methylated lysine 4 mark on histone H3 that is associated with transcriptional activity. Furthermore, the SLIK complex shows enhanced acetylation of a methylated substrate and this activity is dependent upon a functional methyl-binding chromodomain, both in vitro and in vivo. Our study identifies the first chromodomain that recognizes methylated histone H3 (Lys 4) and possibly identifies a larger subfamily of chromodomain proteins with similar recognition properties.
http://www.eurekalert.org/pub_releases/2005-01/uovh-inp011205.php
Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation
MARILYN G. PRAY-GRANT, JEREMY A. DANIEL, DAVID SCHIELTZ, JOHN R. YATES III & PATRICK A. GRANT
LINK TO PAPER IN NATURE
The specific post-translational modifications to histones influence many nuclear processes including gene regulation, DNA repair and replication. Recent studies have identified effector proteins that recognize patterns of histone modification and transduce their function in downstream processes. For example, histone acetyltransferases (HATs) have been shown to participate in many essential cellular processes, particularly those associated with activation of transcription. Yeast SAGA (Spt-Ada-Gcn5 acetyltransferase) and SLIK (SAGA-like) are two highly homologous and conserved multi-subunit HAT complexes, which preferentially acetylate histones H3 and H2B and deubiquitinate histone H2B. Here we identify the chromatin remodelling protein Chd1 (chromo-ATPase/helicase-DNA binding domain 1) as a component of SAGA and SLIK. Our findings indicate that one of the two chromodomains of Chd1 specifically interacts with the methylated lysine 4 mark on histone H3 that is associated with transcriptional activity. Furthermore, the SLIK complex shows enhanced acetylation of a methylated substrate and this activity is dependent upon a functional methyl-binding chromodomain, both in vitro and in vivo. Our study identifies the first chromodomain that recognizes methylated histone H3 (Lys 4) and possibly identifies a larger subfamily of chromodomain proteins with similar recognition properties.
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