epigenomics: deciphering the other genetic code sonia guara ciurana
TRANSCRIPT
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 methylationIs 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.phpZhang 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-seqObtain total
RNA
Purify/enrich small RNA
Size selection
Hybridize and ligate RNA adaptors
Reverse transcription
Obtain cDNA
Amplify the cDNA
Sequence
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 droplet-in-oil PCR array. Lab Chip. 9: 1059-1064.
http://antibody.me/abcom/index2.html http://www.dnavision.com/pyrosequencing.php
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