Module 13 - Epigenetics Flashcards
Imprinted genes exists in ______; each having its own _______.
clusters, ICR/DMD
Where does DNA methylation occur and how does it help silence gene expression?
- CpG islands - usually unmethylated, but if methylated synonymous with silencing (not vice versa)
- Intergenic regions - usually methylated - genomic integrity
- Repetitive elements - usually methylated - genomic integrity
Methylatio can interfere with transcription factor binding or it could also bind with proteins which recuit other factors that alter chromatin state.
What are long noncoding RNAs?
- >200 nucekotides in length
- sliced, capped, and polyadenylated
- constrained in nucleus, not translated
- expressed in developmentally controlled manner
- Exp. Xist
Explain disorders that may arise from the inappropriate expression of the imprinted gene controlled by the Kcnq1 locus in either paternal or maternal allele.
ICR/DMD is the start site of the Kcnq1ot1 lnRNA. Methylation of the ICR on maternal allele means Kncq1ot1 lncRNA is inactive. This lcRNA recruits G9a and PRC2 that perform that H3K9me and H3K27me, which silenced genes (including Cdkn1c).
If ICR is unmethylated in maternal gene, functional genes will be silenced, including the Cdkn1c (Beckwith-Weideman). If ICR is methylated in paternal gene, this will lead to an overdosage of gene product from the expressed genes (Silver-Russell)
Define epigenetics.
Epigenetics is the study of changes in gene expression that occur without changes in DNA sequence. These changes are mitotically heritable.
What is XCI (X Chromosome Inactivation)?
X Inactivation is an epigenetic dosage compensation mechanism in mammals, so that males and females have the same does of genes in X chromosome.
How do histone tail modification correlate with different chromatin states? Explain this in regards to chromodomain proteins.
HTMs are “read” by other chromatin proteins and interactions that may:
- alter chromatin packaging
- bring about other histone modifications
It doesn not alter gene expression directly, but rather mark chromatin to be altered by other factors. Examples of this factors:
- H3K4me -> CDH1 - ATP-dependent chromatin remodeller
- H3K9me -> HP1 - essential heterochromatin protein, can recuit DNMT1 ->bind to HDAC-> histone deacetylation, KMT (lysine MT) to spread H3K9me mark
- H3K27me -> CBX2 - part of polycomb repressive complex that lays down H2AK119ub
Descibe how Angelman and Prader-Willi Syndrome arise in regards to inappropriate expression of the imprinted gene
Both syndromes are associated with the imprinted cluster of genes on chromosome 15q11-13, with maternally imprinted ICR. There are split imprinting centre: AS-IC and PWS-IC, where AS cause a methylation in the PWS in oocytes.
PWS-IC acts as a start site for Snurf/Snrpn lncRNA, which makes snoRNAs and Ube3a-as, stopping Ube3a transcription in the paternal copy.
Angelman Syndrome arises due to the failure to express Ube3a, which may be caused by deletion of AS-IC, deletion of maternal copy of Ube3a, or mutation on the Ube3a sequence (only through maternal transmission). Prader-Willi Syndrome arises from deletion or inappropriate silencing of paternal copy, leading to non-expression of functional gene. Only occurs through paternal transmission.
Describe the process of DNA methylation and how it is restored through DNA replication.
DNA methylation involves the methylation of 5’ group of cytosines within CpG dinucleotides (5’—C—phosphate—G—3’ ). The process is laid down by de novo methyltransferases, DNMT3A and DNMT3B in mammals. Due to the conservative nature of DNA replication, each of the daughter DNA are hemi-methylated. This recognised by DNMT1 and the other strand is methylated, restoring symmetric methylation.
Describe how parental imprinting occurs, in regards to epigenetic reprogramming and imprint control regions.
Parental imprinting refers to an allele specific expression, based on parent-of-origin of the allele. Expression of these imprinted genes is controlled by imprint control regions (ICR) and associated with DNA methylation at the ICR/DMD. ICR methylation is established in primordial germ cells and then maintained in the embryo. Epigenetic marks must be reset between generations to restore totipotency and this occurs durings gametogenesis.
Mention types of histone tail modifications and their functions.
Most modifications occur on the N-terminal tails that protrude from the nucleosome, accesible to chromatin proteins.
- Histone Acetylation:
- correlated with gene activity, partly due to reduced positive charge of histones (weaker bond to DNA)
- not mitotically heritable, not strictly epigenetic
- Histone Methylation
- correlated to either transcriptional activity or inactivity
- H3K4me - active locus, around promoter
- H3K9me - inactive locus, constitutive heterochromatin
- H3K27me - inactive locus, facultative heterochromatin
Mention molecular hallmarks of X inactivation.
Inactive X chromosome has:
- Xist long noncoding RNA
- low levels of histone acetylation
- Accumulation of H3K27me and H3K9me
- DNA methylation of inactivated CpG islands
Mention diseases associated with disrupted epigenetic silencing.
ICF Syndrome:
- autosomal recessive disorder
- mutation in DNMT3B
- hypomethylation of CpG islands of inactive X and Y chromsomes
- hypomethylation at centromeres
Rett Syndrome:
- mutation in a methyl binding domain (MBD) protein - MeCP2
- X-linked neurodevelopmental syndrome
Angelman and Prader Willi Syndrome
Beckwith-Weideman and Silver-Russell Syndrome
How does Xist influence epigenetic silencing?
XIST is expressed from the chromosome that will be the inactive X. lncRNA Xist will then coat the inactive X. Xist RNA binds Hnrnpk, which then recruits polycomb recessive complex 1, which impart H2AK119ub. H2AK119 recruits PRC2, which imparts H3K27me. It also binds with HDAC3 which allows hisotne deacetylation.
Explain how disruptions to epigenetic control occur in cancer and how they may influence treatment.
Cancer arises by inactivation of tumour suppressor genes and activation of oncogenes. Distruptions can be achieved genetically or epigenetically. In regards to epigenetic, cancer cells are associated with a tumour suppressor hypermethylation in the CpG islands (silencing) and a genome wide hypomethylation (loss of genomic integrity and inappropriate activation of genes).
These epimutations are reversible and cancer drugs are developed to reverse some these epigenetic deviations.
Describe the process of DNA demethylation and when do they occur.
DNA demethylation shown to occur in early development, in primordial germ cell development and at later specific stages of differentiation.
It can happen by:
- Passive demethylation - lack of DNMT and DNA replication
- Active demethylation - involves multiple steps in TET proteins
Explain the influence of the environment on epigenetic makeup.
For example, dietary and nutrition intake may influence on epigentoype (and phenotype) in mice. Sensitive periods during embryogenesis/gametogenesis are susceptible to epigenetic changes/marks as they are being established rather than maintained.
