表觀遺傳-醫(yī)學分子生物學

1、Epigenetics,Classical Genetics: The Central Dogma,Introduction to Epigenetics,The Human Genome Project (HGP),Key findings:Approx. 24,000 genes in human beingAll human races are 99.99% alikeChallenges:24,000 genes vs.

2、 100,000 proteinsNon-coding (98%) vs. coding DNA (2%)Genotype vs. Phenotype,Introduction to Epigenetics,They may look the same, but are they?,Position effect variegation,Paramutation at the maize,Epigenetic biology,Int

3、roduction to Epigenetics,Epigenetic differences arise during the lifetime of monozygotic twins,PNAS, July 26,2005, Vol.102,Introduction to Epigenetics,Epigenetics,Definition: The study of any potentially stable and, idea

4、lly, heritable change in gene expression or cellular phenotype that occurs without changes in Watson-Crick base-pairing of DNA.One example: cellular differentiation/developmenttotipotent stem cells become the various

5、 pluripotent cell lines of the embryo which in turn become fully differentiated cells,Introduction to Epigenetics,Change: Genetics vs. Epigenetics,Introduction to Epigenetics,1938, Hermann Muller first described the Posi

6、tion-effect variegation 1942, Conrad Waddington defined epigenetics as “the branch of biology which studies the causal interactions between genes and their products, which bring the phenotype into being”1950s, R. Brink

7、 discovered Paramutation in maize1961, Mary Lyon proposed the random inactivation of one female X chromosome to explain the mottled phenotype of female mice heterozygous for coat color genes1983, discovered the DNA met

8、hylation……,Brief History of Epigenetics,Introduction to Epigenetics,Epigenetics Events,Paramutation, bookmarking, imprinting, gene silencing, X chromosome inactivation, position effect, reprogramming, transvection, ma

9、ternal effects, the progress of carcinogenesis, many effects of teratogens, regulation of histone modifications and heterochromatin, technical limitations affecting parthenogenesis & cloning……,Introduction to Epig

10、enetics,Epigenetic Research: techniques,ChIP; ChIP-on-chip; ChIP-seq fluorescent in situ hybridization methylation-sensitive restriction enzymes Hpa II and MSp I DNA adenine methyltransferase identification (Da

11、mID) Nat Protoc,2007, 2(6): 1467–78. bisulfite sequencing. computational epigenetics ……,Introduction to Epigenetics,Published papers in Epigenetics,,15472,PubMed search using “epigenetics” as the key word,Introduc

12、tion to Epigenetics,The Focuses of Epigenetic Reseach,Introduction to Epigenetics,Genomic LevelChromatin RemodelingDNA modificaitionHistone modificationother modificationsX-chromosome Inactivation: DNA methy

13、lation; ncRNA genomic imprinting: DNA methylation; ncRNA …… RNA levelncRNARNAi (RNA Interference)miRNA (microRNA)RNA-interacting protein……,The Levels of Epigenetic Reseach,Introduction to Epigenetics,DN

14、A modification Protein modification ncRNA regulation,Chromatin Remodeling,The nucleosome,The spacing and positioning of nucleosomes at critical cis-acting control regions (i.e., promoters) are tailored for the prope

15、r regulation of the locus.,Higher-Order Structuring of Chromatin,Chromatin Remodeling,The Structure of a Nucleosome,DNA methylation: is a type of chemical modification of DNA that can be inherited and subsequently remove

16、d without changing the original DNA sequence Histone Modifications: change the chromatin template by cis-effects that alter internucleosomal contacts and spacing, or the trans-effects caused by histone and non-histone p

17、rotein associations with the template.,Chromatin Remodeling,Chromatin-remodeling: Dynamic structural changes to the chromatin occurring throughout the cell division cycle. These changes range from the local changes neces

18、sary for transcriptional regulation to global changes necessary for chromosome segregation,Euchromatin vs. Heterochromatin,Chromatin Remodeling,Chromatin Remodeling,Chromatin Remodeling,Chromatin remodeling: Dynamic stru

19、ctural changes tothe chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.

20、,Chromatin Remodeling,Non-covalent mannerChromatin remodeling complexesHistone variantsCovalent mannerHistone modificationDNA methylationNon-coding RNA,Chromatin Remodeling: mechanism,I. Chromatin Remodeler,Non-cov

21、alent mannerChromatin remodeling complexesHistone variantsCovalent mannerHistone modificationDNA methylationNon-coding RNA,Fact: work coordinately,Chromatin Remodeling: mechanism,Chromatin remodeler: Non-covalent m

22、anner,are ATP-hydrolyzing machines Functions: fully package the genomerestructure, mobilize or eject nucleosomes specialize chromatin regions provide regulated DNA accessibility in packaged regions.,I. Chromat

23、in Remodeler,Chromatin remodeler Families,All contain a SWI2/SNF2-family ATPase subunit characterized by an ATPase domain that is split in two parts: DExx (red ) and HELICc (orange).,I. Chromatin Remodeler,Chromatin remo

24、deler: a complex,I. Chromatin Remodeler,The actions of remodelers on nucleosomes,I. Chromatin Remodeler,Histone Variants,I. Chromatin Remodeler,The actions of remodelers on nucleosomes,I. Chromatin Remodeler,Chromatin St

25、ructure remodeling Complexes: a work model,Mol. Cell, 2006, 21 (3): 417–25.,I. Chromatin Remodeler,Histone Modifications,II. Histone Modification,http://porpax.bio.miami.edu/~cmallery/150/gene/c7.19.4.histone.mod.jpg,Si

26、tes of Histone Modifications,http://www.nature.com/nsmb/journal/v14/n11/images/nsmb1337-F1.gif,II. Histone Modification,Coordinated recruitment of histone-modifying activities,II. Histone Modification,Histone Modificatio

27、ns 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 ph

28、osphorylation) 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

29、disability, distinctive facial features, and broad thumbs and first toes. It is caused by mutations in CREB-binding protein (histone acetylation),II. Histone Modification,DNA methylation,HypomethylationHypermethylation

30、,http://www.cellscience.com/reviews7/Taylor1.jpg,III. DNA methylation,Imprinting X chromosome inactivation Heterochromatin maintenance Developmental controls Tissue specific expression controls,The Roles of D

31、NA Methylation,III. DNA methylation,DNA methylation and demethylation,III. DNA methylation,Regulation of Gene Expression by DNA methylation,Interference with transcription factor binding,Attraction of Methyl-CpG-binding

32、proteins,III. DNA methylation,DNA Methylation and Cancer,Nature Reviews Genetics, 6: 597,III. DNA methylation,DNA Methylation and Other Human Diseases,-- Imprinting Disorder: Beckwith-Wiedemann syndrom (BWS) Prader-Wil

33、li syndrome (PWS) Transient neonatal diabetes mellitus (TNDM)-- Repeat-instability diseases Fragile X syndrome (FRAXA) Facioscapulohumeral muscular dystroph-- Defects of the methylation machinery Systemic lupus e

34、rythemtosus (SLE) Immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome,III. DNA methylation,Seven distinct mechanisms of chromatin remodeling,Chromatin Remodeling,Coordinated modification of ch

35、romatin,The transition of a naïve chromatin template to active euchromatin(left) or the establishment of repressive heterochromatin (right), involving a series of coordinated chromatin modification. In the case of t

36、ranscriptional activation, this is accompanied by the action of nucleosome-remodeling complexes and replacement of core histones with histone variants (yellow),Chromatin Remodeling,Epigenetic modifications leading to gen

37、e transcriptonal regulation,Chromatin Remodeling,Epigenetics and Human Disease,Disorder of genomic imprintingDisorder affecting chromatin structure in transDisorder affecting chromatin structure in cisEpigenetics-envi

38、ronment interations,Epigenetics-environment interations,Bird A. Perceptions of epigenetics. Nature, 2007, 447(7143): 396-8. 2. Feil R. Epigenetics: Ready for the marks. Nature, 2009, 461(7262): 359-60. 3. Mai

39、er VK, Chioda M, Becker PB. ATP-dependent chromatosome remodeling. Biol Chem, 2008, 389(4): 345-52. 4. Ko M, Sohn DH, Chung H, Seong RH. Chromatin remodeling, development and disease. Mutat Res, 2008,