EPIGENETICS

OUTLINES

• Introduction and Definition• Factor affecting epigenetics and Inheritance• Mechanism• Epigenetic phenomenon• Cancer and epigenetics• Diagnosis • Therapies targeting epigenetic modification• Future

Introduction • Genetics explains phenotypic trait in

organisms through presence or absence of specific nucleotide sequence of DNA.

• However, that does not adequately explain the expression or lack of expression of all genes.

• That indicates, there are other control mechanism; such as DNA methylation and chromatin modification

Definition • C.H. Waddington coined the term

epigenetics to mean above or in addition to genetics to explain differentiation

• Epigenetics refers to the study of changes in the regulation of gene activity and expression that are not dependent on gene DNA sequence.

• While epigenetics often refers to the study of single genes or sets of genes, epigenomics refers to more global analyses of epigenetic changes across the entire genome

• Disruption of such control mechanism is associated with a variety of disease

– With behavioral/neurological manifestation

– Disorder of tissue growth

– Endocrine disorder

– Neoplasia

Inheritance

• parent’s experiences are passed on to offspring through epigenetic tags

• When the zygote is formed many epigenetic tags are removed from the chromosomes of the parents, but some remain

• Identical twins– from same zygote– same genetic information

(including epigenetic tags)

• While infants – similar environments, – so little variation in

epigenome

• Difference in the twins’ epigenomes makes them become different when they are older

• One can develop a disease while the other is fine

Methylation of Agouti Genes in Mice

Environment can Influence Epigenetic Changes

Emma Whitelaw, Henry Stewart Talks

Factors during pregnancy affecting the transmission of epigenome

• nutrition of mother

• Stress, social interactions, physical activity as Stress hormones can travel from the mother to a fetus

• exposure to toxins

GRANDMOTHER’S CURSE!!!!!

Some of the effects ofsmoking may be passed from grandmother to

grandchild

Epigenetics Mechanisms

Gene Expression

RNA Interference

Histone Modifications DNA Methylation

• Epigenetic alteration are outside the primary sequence, but nonetheless affect the ability of gene to be expressed.

• DNA in most cells packaged with histone to form nucleosome in ‘beads on a string’ structure.

• Chromatin regulation involves high-order conformational changes– Relaxation or tightening of this thread of DNA-

histone complex

• Further regulation is by assembling promoter-enhancer complexes via long-range DNA looping– Can be blocked by specific DNA-sequence called

insulator

• The core histones are subject to diverse post-translational modifications, including methylation and acetylation– That project from tightly structured nucleosome core

DNA methylation

Histone

MethylatedDNA

Effect of methylation

Methylation turns off genes.

Acetylation turn genes on.

5-Methyl Cytosine is Found in Heterochromatic Regions

Natural Roles of DNA Methylation in Mammalian System

Imprinting

X chromosome inactivation

Heterochromatin maintenance

Developmental controls

Tissue specific expression controls

DNA Methylation and Other Human Diseases

• -- Imprinting Disorder:• Beckwith-Wiedemann syndrom (BWS)• Prader-Willi syndrome (PWS)• Transient neonatal diabetes mellitus (TNDM)

• -- Repeat-instability diseases• Fragile X syndrome (FRAXA)• Facioscapulohumeral muscular dystroph

• -- Defects of the methylation machinery• Systemic lupus erythemtosus (SLE)• Immunodeficiency, centromeric instability and facial

anomalies (ICF) syndrome

Histone Modifications

Histone modificationthe histone code

– Acetylation– Methylation– Phosphorylation– Ubiquitylation– sumoylation

• Enzymes catalyzing– Histone

acetyltransferase– Histone deacetylase– Histone

methyltransferase– Histone kinase

Histone Modification Status Correlates with Transcriptional Activity

• Gene activation correlated with H3-K9 acetylation • Gene silencing associated with H3-K9 methylation

Role of histone modification

• DNA transcription• DNA repair• DNA replication

Histone Modifications and Human Diseases

Coffin-Lowry syndrome is a rare genetic disorder characterized by mental retardation and abnormalities of the head and facial and other areas. It is caused by mutations in the RSK2 gene (histone phosphorylation) and is inherited as an X-linked dominant genetic trait. Males are usually more severely affected than females.

Rubinstein-Taybi syndrome is characterized by short stature, moderate to severe intellectual disability, distinctive facial features, and broad thumbs and first toes. It is caused by mutations in CREB-binding protein (histone acetylation)

RNA interference

siRNA Mediated Heterochromatin Maintenance

X-inactivation

• One X-chromosome in female cells is condensed and located on nuclear periphery

• Complete silencing of one entire chromosome is certainly one of the most dramatic epigenetic phenomenon

• Key-transcript, X-inactivation specific transport lack protein-coding function

• Production of Xist rapidly attract histone-modifying enzymes, followed in turn by DNA-methylation

• Inactive x-chromosome is evidently ‘locked in’ by chromatin modification-– Methylation of Histone H3 at lysine K27– Hypoacetylation of histone at H3 ande H4– Dense CpG methylation of CpG islands

Genomic imprinting

• Most autosomal genes in mammalian have biallelic expression

• But a small number of genes are expressed from only one parental allele – Imprinting –become essential for viability

• Maternally derived genes are growth-limiting• Paternally derived genes are growth-

enhancing

Androgenetic and gynogenetic tumor

• Benign overian teratoma (bimaternal origin)

• Hydatidiform mole (biparenatal origin)

• Usually benign

• Diagnosis: histopathology + immunostaining of protein product of imprinted gene– Neoplastic trophoblast of complete

hydatidiform mole fails to express imprinted gene (CDKN1C and PHLDA2)- those normally imprinted from maternal allele

Prader-willi and Angelman syndrome

• Chromosomal band 15q11-q13 is a megabase scale chromosomal domain including multiple imprinted gene

– One portion of gene is maternally expressed/paternally silenced

– Adjacent portion oppositely imprinted

– Deletion of paternal homologue – PWS – Deletion of maternal homologue - AS

• Whether these diseases are due to large deletion, microdeletion, epimutation majority can be diagnosed by simple Southern blot or PCR-based assays for DNA mutation

• Gain of methylation in PWS

• Loss of mutation kin AS

Cancer epigenetics

• A common paradigm of cancer epigenetics is hypermethylation of CpG island of tumor suppressor gene promoter

• Hypermethylated promoter DNA is associated with virtually every type of human tumor– With each type of tumor having own signature of

methylated genes

Cancer Methylated genes

Prostate GSTP1

Renal VHL

Colon and endometrial MLH1 (mismatch repair gene)

Esophageal APC

• Global hypomethylation: overall in 5-methylcytosine content in the genome– Found in premalignant and early stages of some

neoplasm– Important in tumor progression

• Gene-specific hypomethylation: – Often affect promoter region of proto-oncogene

and oncogene which are normally highly methylated

DNA Methylation and Cancer

Technologies for Studying Epigenetics/Epigenomics

DNA Methylation

Irizarry et. Al. (2008) Genome Research 18(5):780

Microarray or deep sequencing

Bisulfite Sequencing

5’3’

Expression array

Exon array

Splicing array

Promoter array

Tiling array

exon intron

Global Interrogation of DNA Methylation using Microarrays

promoter

• Earliest method, still the most direct and least subject to artifact is southern blotting of genomic DNA with methylation-sensitive restriction enzyme.

• Restriction enzymes ( e.g. HpaІІ, SmaІ, NotІ) with CpG as part of their recognition sequence do not cut that sequence when the C is methylated

Technologies for Interrogating Epigenetics/Epigenomics

http://www.nature.com/jid/journal/v125/n2/extref/5603467x1.jpg

ChIP-chip

Antibody specific to one type of histone modification

Histone Modifications

ChIP-seq

Deep sequencing

Demethylation in cancer therapy

HDAC inhibitors

Interchromosome regulation of genes

Scaffold proteinSATB1

• More higher structure than chromatin

• Play important role in T-cell development