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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