1. EPIGENOMICS: DECIPHERING THE OTHER GENETIC CODE Sonia Guara Ciurana

2. Index  Introduction  DNA methylation  Chromatin modifications  ncRNAs

3. Introduction  Epigenome: record of the chemical changes in the DNA and histones of cells of an organism.  Epigenetics:  Mechanism that regulate the gene expression by introducing heritable changes without altering DNA sequence  Main mechanisms DNA methylation Chromatin (histone) modification ncRNAs

4. DNA methylation Is the covalent addition of a CH3 group in C followed by G (CpG dinucleotides) CpG islands In the promoter region of 50% of the genes Hypomethylated Hypermethylated

5. DNA methylation  There are many techniques to detect DNA methylation:  Bisulfite sequencing  Methylation-specific PCR (MSP) http://www.dnavision.com/pyrosequencing.php Zhang et al., Lab Chip, 2009

6. Chromatin modifications  Modifications that can suffer the histone tails:  Acetylation  Methylation  Phosphorylation  Ubiquitination Hamilton JP. Dig Dis. 2011

7. Chromatin modifications  The methods used to detect these modifications are:  Mass spectrometry  Chromatin ImmunoPrecipitation (ChIP) http://antibody.me/abcom/index2.html Nikolov et al., Moll Cell Proteomics. 2011

8. ncRNA  macroRNAs: regulate the expression of 1 or more genes on the same chromosome  Xist and Tsix  inactivation of X chromosome  shortRNAs: regulate the expression of 1 or more genes on different chromosomes or regulate mature RNAs

9. ncRNA  Methods to detect them:  RNA-seq Obtain total RNA Purify/enrich small RNASize selection Hybridize and ligate RNA adaptors Reverse transcriptionObtain cDNA Amplify the cDNA Sequence

10. Conlusion  The study of the epigenome is needed to better understand:  The expression of the genes  Some processes that occur in cells (differentation, signaling pathways…)  Complex diseases  It is needed better techniques to measure these modifications

11. References  Hamilton JP (2011). Epigenetics: principles and practicals. Dig Dis. 29: 130-135.  Nelissen ECM, van Montfoort APA, Dumoulin JCM & Evers JLH (2011). Epigenetics an the placenta. Human Reproduction. 17 (3): 397-417  Nikolov M. Stützer A, Mosch K, Krasauskas A, Soeroes S, Stark H, Urlaub H & Fischle W (2011). Chromatin affinity purification and quantitative mass spectrometry defining the interactome of histone modification patterns. Mol Cell Proteomics. 10 (11): M110.005371. DOI: 10.1074/mcp.M110.005371.  Zhang Y, Bailey V, Puleo CM, Easwaran H, Griffiths E, Herman JG, Baylin SB & Wang TH (2009). DNA methylation analysis on a droplet- in-oil PCR array. Lab Chip. 9: 1059-1064.  http://antibody.me/abcom/index2.html http://antibody.me/abcom/index2.html  http://www.dnavision.com/pyrosequencing.php http://www.dnavision.com/pyrosequencing.php

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