I) Development: tissue differentiation and timing II) Whole Chromosome Regulation

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1 Epigenesis: Gene Regulation Epigenesis : Gene Regulation I) Development: tissue differentiation and timing II) Whole Chromosome Regulation (X chromosome inactivation or Lyonization) III) Regulation during Protein Synthesis III.A) Photocopy (Transcriptional) Regulation III.A.1) Methylation III.A.2) Histone Modification III.A.3) Transcription Factors III.B) Editing Regulation 3.B.1) Alternative RNA splicing III.C) Pre-translational Regulation 3.C.1) interfering RNA IV) Regulation after Protein Synthesis IV.A) Many mechanisms Transcription factors Transcription: from gene (DNA) to RNA Mechanisms: - Transcription factors - Epigenetics Transcription factors Epigenesis and Development Example: Mammalian Sexual Development 1) Typical Course = Female 2) Males = Masculinized Females 2.a) 7 th week: SRY gene (sex-determining region of the Y chromosome) turns on 2.b) SRY protein acts as a transcription factor, influencing the expression of many other genes 2.c) testes develop 2.d) testes produce large amounts of androgens à masculinization SRY: sex determining region Y The SRY gene is found on the Y chromosome. The sexdetermining region Y protein produced acts as a transcription factor. This protein starts processes that cause a fetus to develop male gonads (testes) and prevent the development of female reproductive structures (uterus and fallopian tubes). 1

2 Transcription factors - Steroids Homeobox Genes shortly Hox genes Products of Hox genes The Hox genes contain a 180 bp conservated region: the homeobox The homeobox encodes a 60 AA length homeodomain = a DNA-binding helix turn helix motif The homeodomain proteins are transcription factors The Hox genes are selector genes (regulate the expression of other so-called realisator genes) The expression of several Hox genes is region-specific in the embryo Hierarchy of genes in Drosophila development Maternal factor Gap genes Pair rule genes Development of the number of segments Hierarchy of genes in Drosophila development hunchback (gap gene) bicoid (maternal factor) giant (gap gene) Krüppel (gap gene) Selector genes (Hox genes) Development of the features of the segments Realisator genes 2

3 Organization of Drosophila Hox genes The pattern of Hox expression HOM-C complex 3 Antennapedia complex Bithorax complex Abdominal B Ultrabithorax Abdominal A Antennapedia Sex comb reduced proboscipedia deformed labial The pattern of Hox expression the first lab is expressed alone the second pb is expressed with lab, etc. the last Abd-B is expressed with all the others there aren t wings, or legs on the abdomen WHY?? The more posterior Hox gene supresses the affect of more anterior For example: Ubx, AbdA and AbdB supresses the development of the legs What are the animals? An animal is an organism that displays a particular spatial pattern of gene expression. This pattern is the zootype. Every animal use the same regulation method to the developing of very different structures otd ems lb pb Scr Ubx Dfd AbdB eve Homeobox & Hox Genes (Drosophila and Mus) Mammalian Hox genes In mice and human 4 Hox clusters have been found Homology has been found between the Drosophyla and human Hox genes 3

4 13/02/16 Drosophyla and human Hox genes 4 clusters: Hox A: Chr. 16 Hox B: Chr. 11 Hox C: Chr 15 Hox D: Chr. 2 Transcription: from gene (DNA) to RNA Mechanisms: 13 paralog groups - Transcription 38 Hox genes factors -Epigenetics Epigenetics The term epigenetic refers to all heritable changes in gene expression and chromatin organization that are independent of the DNA sequence itself. 4

5 13/02/16 Epigenetic diseases Monozygous twins share a common genotype and are genetically identical There is significant phenotypic discordance: ØMental disorders ØCancer 5

6 Histone Modifications Histone acetylation Histone acetylation 6

7 DNA Methylation DNA Methylation At promoter, DNA methylation suppresses transcription With deamination, DNA methylation induces Cà T mutation Hypomethylation Hypermethylation Natural Roles of DNA Methylation in Mammalian System Ø Imprinting Ø X chromosome inactivation Ø Heterochromatin maintenance Ø Developmental controls Ø Tissue specific expression controls DNA Methylation and Cancer Demethylation in cancer therapy Robertson, Nature Reviews Genetics, Vol6, 597 Nat Rev Drug Discov 2006;5:

8 13/02/16 DNA methylation inhibitor, nucleoside analogues and non-nucleoside analogues Nat Rev Cancer 2006;5;37-50 Transcriptionally active chromatin regions tend to be hyperacetylated and hypomethylated. CHROMATIN IN PLURIPOTENT STEM CELLS VERSUS DIFFERENTIATED CELLS If a region of DNA or a gene is destined for silencing, chromatin remodeling enzymes such as histone deacetylases and ATP-dependent chromatin remodelers likely begin the gene silencing process. One or more of these activities may recruit DNA methyltransferase resulting in DNA methylation, followed finally by recruitment of the methyl-cpg binding proteins. The region of DNA will then be heritably maintained in an inactive state. A. Gaspar Maia et al. JANUARY VOLUME 12 - NATURE REVIEWS 8

9 13/02/16 The nucleus and Epigenesis For example: DNA methylation The nucleus contains the instructions that drive epigenesis/development Chromatin is the instructional unit (DNA plus proteins). The state of the chromatin is set by epigenetic control mechanisms Covert epigenetic changes occur during the early cleavages of the fertilized egg into the blastomeres of the embryo Nature 2004;429: Age Dependent Epigenetic differences in Monozygotic (MZ) twins Both mice and people have a gene called agouti. When a mouse's agouti gene is completely unmethylated it has a yellow coat color, is obese and prone to diabetes and cancer. When the agouti gene is methylated (as it is in normal mice) the coat color is brown and the mouse has a low disease risk. Fat yellow mice and skinny brown are genetically identical. You can think of the fat yellow mice as looking different because they have an epigenetic "mutation When researchers fed pregnant yellow mice a methyl-rich diet, most of the resulting pups were brown and healthy and stayed that way for life. These results indicate that an individual's adult health is heavily influenced by early prenatal factors. In other words, our health is not only determined by what we eat, but also what our parents ate. 9

10 13/02/16 mitochondrial methylation SAM SAMC ATP THF Formyl-THF Purines ser ser Formyl-THF mshmt B6 gly gly ATP folate Formate Formate DHF cshmt B6 MBE MS B12 Folate Methenyl-THF Methylene-THF cycle MTHFR MBE dump TS MAT SAM Met THF 5-MTHF Methionine cycle MT SAH Hcy SAHH CBS B6 Methylene-THF dtmp cytosolic methylation cystathionine CTH Sarcosine dimethylglycine MITOCHONDRION cysteine Glutamate glycine Pyrimidines glutathione CYTOSOL 10

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