High-resolution genome-wide mapping of histone modifications

Tae-young Roh*, Wing Chi Ngau+, Kairong Cui*, David Landsman+ &

Keji Zhao**Laboratory of Molecular immunology, National heart blood and lung institute NIH

+ Computational biology Branch, National Center for Biotechnology information, National Library of Medicine, NIH

CHiP on Chip

• Using chromatin immunoprecipitation combined with microarray chips you may find global positions in witch proteins will bind

• This method has several limitations.

Global positioning of transcriptional regulators

GMAT

• Combines ChiP and SAGE to identify sequences immunoprecipitated by a specific antibody

• Will be able to determine global transcription factors and effectors of transcriptional regulation.

GMAT

Chromatin structure

Ways machinery gets in

Nucleosome makeup

Nucleosomes are made up of histone H1, H2a H2b, H3 and H4

This makeup is duplicatedplanarly

Histones

Histones are conserved at N-terminus among all species

Gcn 5 works to help acetylate histones

Chromatin IP for to

test antibody

specificity

Acetylated Histone Plots

Inducible genes marked by histone acetylation in off state

No tags detected around silent mating loci

Figure 2 thumbnail

(a,b) Distribution of diacetylated K9/K14 histone H3 (a) and tetra-acetylated histone H4 (b) The normalized tag count represents the number of times that a particular tag was detected in the GMAT library divided by the number of hits of the tag sequence in the genome. The tags with normalized values 1 were mapped on to the chromosomes and plotted against the sequence coordinates of the chromosomes. The 'blow-up' panels show the detected tags in the first 50-kb region of the left end of chromosome III. The silent mating locus, HMLalpha, is indicated. The positions of ORFs on the Watson and Crick strand of template within this region are indicated below the panels.

QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.

3 major patterns of histone H4 acetylation

Hypoacetylation correlates with telomeric repression

H3 Acetylation in orf

Figure 3 thumbnail

The highest acetylation levels are detected in the 5' end of coding regions of yeast genes. The observed tag count fraction (y axis) was derived as described in the Methods section. X axis indicates the ORF coordinates from -500 bp to +3,000 bp relative to the translation start codon ATG. (a) The analysis for histone H3 for wild-type yeast. (b) The GCN5 deletion inhibited the specific H3 acetylation in the 5' end of coding regions. (c) The data in a (blue line) and b (red line) were overlaid.

H4 Acetylation in orf

H3 Acetylation in orf

Figure 3 thumbnail

The highest acetylation levels are detected in the 5' end of coding regions of yeast genes. The observed tag count fraction (y axis) was derived as described in the Methods section. X axis indicates the ORF coordinates from -500 bp to +3,000 bp relative to the translation start codon ATG. (a) The analysis for histone H3 for wild-type yeast. (b) The GCN5 deletion inhibited the specific H3 acetylation in the 5' end of coding regions. (c) The data in a (blue line) and b (red line) were overlaid.

Conclusion

• GMAThas many advantages for global positioning on proteins