Transcript Epigenomics
EPIGENOMICS: DECIPHERING THE OTHER GENETIC CODE Sonia Guara Ciurana Index Introduction DNA methylation Chromatin modifications ncRNAs 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 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 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 Chromatin modifications Modifications that can suffer the histone tails: Acetylation Methylation Phosphorylation Ubiquitination Hamilton JP. Dig Dis. 2011 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 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 ncRNA Methods to detect them: RNA-seq Obtain total RNA Purify/enrich small RNA Size selection Hybridize and ligate RNA adaptors Obtain cDNA Amplify the cDNA Sequence Reverse transcription 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 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 dropletin-oil PCR array. Lab Chip. 9: 1059-1064. http://antibody.me/abcom/index2.html http://www.dnavision.com/pyrosequencing.php THANK YOU FOR YOUR ATTENTION