Transcript E:Med - uni-freiburg.de

E:Med
Martin Vingron’s group
Jose M Muino
Martin Vingron’s group
• Sequence alignment
• Microarray gene analysis
• Gene regulation and evolution:
– (combinatorial) TF DNA binding prediction
– Histone modification  gene expression
– Factors affecting mutation rates
My projects:
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(RSE1):
– Regulation of recombination initiation by
epigenetic factors in response to stress
• Environment => Epigenetics => DNA breaks
• CancerEpisys:
– Epigenetics in Chronic Lymphocytic Leukemia
TFs => DNA methylation
Motifs overrepresented in
hypomethylated regions:
[…]
Clustering of overrepresented motifs
Hypomethylated regions
Cis-regulatory module
(ZNF423 + EBF1)
Predicted affinity of EBF1 correlates
with change in DNA methylation
Objective:
*To obtain pairs of TF and target regions that
influence epigenetic status
*Why the miss-regulation?:
Miss-regulation TF complex
Mutations
Needed:
*DNA met. & gene expression & SNPs
*Experimental validation
DNA methylation => TF binding
• Objective:
– To find pairs of TF  target genes which
coexpression is dependent of DNA methylation
• Needed:
– DNA met. & gene expression in same individuals
Epigenetics=> genetic mut.
• Objective:
– Does epigenetics affect genetic mut.?
– What happen first?
– Environment=>epigenetics=>mut.(?)
Hypo-methylated
• Needed:
– DNA met & mutations same individuals
– Experimental validation
Hyper-methylated
Web-tool for ChIP-seq analysis
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User-friendly
All public plant ChIP-seq (-chip) data available
Compatible with Integrated Genome Browser
Compatible with Galaxy