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Exploring Epigenetics, Gene Regulation, and Mutation Rates in Cancer and Stress Response

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This project investigates the interplay between epigenetic factors, gene regulation, and mutation rates in response to environmental stressors. Key research focuses on regulatory mechanisms such as transcription factor (TF) and DNA binding predictions, as well as the impact of histone modifications on gene expression. Further studies aim to identify pairs of TFs and their target genes, assess the effects of DNA methylation on coexpression, and analyze epigenetic influences in Chronic Lymphocytic Leukemia. A user-friendly web tool for ChIP-seq analysis complements this research.

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Exploring Epigenetics, Gene Regulation, and Mutation Rates in Cancer and Stress Response

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  1. E:Med Martin Vingron’s group Jose M Muino

  2. 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

  3. My projects: • (RSE1): • Regulation of recombination initiation by epigenetic factors in response to stress • Environment => Epigenetics => DNA breaks • CancerEpisys: • Epigenetics in Chronic Lymphocytic Leukemia

  4. TFs => DNA methylation Motifs overrepresented in hypomethylated regions: Clustering of overrepresented motifs […] Cis-regulatory module (ZNF423 + EBF1) Hypomethylated regions 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

  5. 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

  6. Epigenetics=> genetic mut. • Objective: • Does epigenetics affect genetic mut.? • What happen first? • Environment=>epigenetics=>mut.(?) • Needed: • DNA met & mutations same individuals • Experimental validation Hypo-methylated Hyper-methylated

  7. Web-tool for ChIP-seq analysis • User-friendly • All public plant ChIP-seq (-chip) data available • Compatible with Integrated Genome Browser • Compatible with Galaxy

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