Introduction Basic Genetic Mechanisms Eukaryotic Gene Regulation The Human Genome Projects Test 1

1. Molecular Genetics The Human Genome: Biology and Medicine • Introduction • Basic Genetic Mechanisms • Eukaryotic Gene Regulation • The Human Genome Projects • Test 1 • Genome I - Genes • Genome II – Repetitive DNA • Genome III - Variation • Test 2 • Monogenic and Complex Diseases • Finding ‘Disease’ Genes • Pharmacogenomics • Test 3 • Your Presentations • Your Presentations • Happy New Year!  http://priede.bf.lu.lv/ Studiju materiāli / MolekularasBioloģijas / MolGen / EN

2. Two ways of genome regulation Genomes, 3rd Edition

3. Chromatin and gene activity

4. 1. Euchromatin • the ‘usual ‘ form • contains (potentially) active genes 2. Heterochromatin • more condensed form • additional proteins (HP1) • constitutive • no genes • feature of all cells • e.g., centromeric, telomeric DNA • facultative • in some cells some of the time • inactive genes Molecular Biology of the Cell, 5th Edition The types of interphase chromatin The Positional effect – variability in gene expression that occurs after a new gene has been inserted into eukaryotic chromosome

5. Two ways in which chromatin structure can influence gene expression 1 heterochromatin – genes unaccessible euchromatin - genes accessible Gene OFF Gene ON 2 Genomes, 3rd Edition , modified

6. Types of alterations in euchromatin structure • 2. Nucleosome remodeling • remodeling (here) • histone replacement • histone removal • 1. Modifications of histones • activating (here) • repressing

7. The major types of histone modifications Recombinant DNA, 3rd Edition

8. Modifications of histones convey a specific meaning to chromatin (‘Histone code’)

9. Gene activity is substantially affected by DNA methylation CG sequences; leads tosilencing; CpG islands - usually in promoters

10. A model for the link between DNA methylation and gene silencing methyl-CpG-binding protein (MeCP) components of a histone deacetylase complex (HDAC) MeCP2 protein Genomes, 3rd Edition (modificēts)

11. Regulatory sequences and gene activity

12. Eukaryotes, like you, have many regulatory elements Molecular Biology of the Gene, 5th Edition Regulatory sequence – DNA sequence to which a gene regulatory protein binds

13. 2010, 11, 439-446 Major types of regulatory DNA elements in eukaryotes • Promoters – recognition sequences for binding of RNA polymerase • Enhancers – increase transcription of a related gene • Silencers – decrease transcription of a related gene • Insulators or boundary elements – block undesirable influences on genes: • 1. enhancer blockers – prevent ‘communication’ between enhancers and unrelated promoters • 2. barrier sequences – prevent spread of heterochromatin • 3. combined • LCR – locus control regions – activate some gene clusters TF – transkrition factor heterochromatin S – silencer P – promoter I – insulator E – enhancer

14. Composition of regulatory DNAelements is modular • RNA polymerase II promoter modules (Genomes, 3rd Ed.) • The core promoter modules • in all promoters • BRE, TATA, Inr, DPE • recognised by general transcription factors • Basal promoter modules • present in many RNA polymerase II promoters • set the basal level of transcription initiation, without responding to any tissue-specific signals • the CAAT box (recognised by the activators NF1 and NFY), the GC box (SP1)… • Response modules • found upstream of various genes • enable response to general signals from outside of the cell • CRE (the cyclic AMP response element) recognised by the CREB activator; SRE (serume response element), recognised by serume response factor… • Cell-specific modules • are located in the promoters of genes that are expressed in just 1 type of tissue • the erythroid module, which is binding site for the GATA-1 activator; the myoblast module, recognised by MyoD… • Modules for developmental regulators • mediate expression of genes that are active at specific developmental stages Genomes, 3rd Edition

15. This ensures efficient combinatorial control of gene expression Levine M & Tjian R (2003) Nature, 424, 147

16. A model for the control region of the human b-globin gene

17. What type of promoter recognition is characteristic to you? Genomes, 3rd Edition

18. Transcription initiation in eukaryotes requires General Transcription Factors (TF)

19. Some genes have alternative promoters, eg, dystrophin gene Alternative promoters C, cortical tissues; M, muscle; Ce, cerebellum; R, retinal tissue (and also brain and cardiac tissue); CNS, central nervous system(and also kidney); S, Schwann cells; G, general (most tissues other than muscle). Genomes, 3rd Edition Cilvēka distrofīna gēns

21. Eukaryotic transcription initiation also needs activator proteins Genomes, 3rd Edition

22. Activators aid the assembly of the transcription initiation complex Multi-subunit cofactors (mediators) Chromatin remodelling or modifying complexes Activator Levine M & Tjian R (2003) Nature, 424, 147

23. Activators may act from a large distance Two models: (i) direct-contact model (here); (ii) tracking model

24. Writing and reading the histone code during transcription initiation

25. INSULATORS divide genome into functional domains gene A enhancer gene B insulator (enhancer blocker) insulator (barrier sequence)

26. Insulators prevent inappropriate activation from enhancers thus maintaining the independence of a functional domain Molecular Biology of the Gene, 5th Edition

27. Models for enhancer-blocking activity E – enhancer EB - enhancer-blocker proteins

28. A model for establishment of silencing and barrier activity S – silencer, B – barrier elements, TF – transcription factor, CR – chromatin remodellers, HM – histone-modifying enzymes, R – repressor proteins 2010, 11, 439-446

29. Activity of some gene clusters requires LCRs

30. Composition of chicken b-globin LCR Vol. 7, 703-713

31. RNA interference • Phenomenon when very short RNAs (21-22 nts) repress – or silence – expression of genes with homology to those RNAs miRNA (micro RNA) • Regulation of gene expression – at least 30% of human genes • Precursor (pre-miRNA) – single-stranded RNA • Origin – transcripts of cell siRNA (small interfering RNA) • Defense against viruses and expansion of transposons • Precursor – double-stranded RNA • Origin - various

32. Mechanism of RNA interference RISC = RNA-induced silencing complex dsRNA = double-stranded RNA Molecular Biology of the Gene, 6th Edition (modified)

33. miRNA processing and mechanism of action

34. miRNAs are coded in both coding and noncoding sequences Molecular Biology of the Gene, 6th Edition (modified)

35. EPIGENETICS Waddington, 1942: “[T]he branchof biology which studies the causalinteractions between genes andtheirproducts, whichbring the phenotypeinto being” (epi[genesis] +genetics). Literally:epi(Greek: επί- on, over) genetics – something working above DNA.

36. EPIGENETIC INHERITANCE Any heritable difference in the phenotype of a cell that does not result from changes in the nucleotide sequence of DNA Specific epigenetic phenomena: 1. dosage compensation: a) X-chromosome inactivation; b) mono-allelic expression; 2. imprinting (parent-of-origin specific differences in gene activity)

37. Inheritance of DNA methylation DNMT1 (DNA methyltransferase 1)

38. Inheritance of histone modifications

39. Imprinting

40. Mechanism of imprinting in the mammalian Igf2 locus Molecular Biology of the Gene, 5th Edition

41. X chromosome inactivation

42. Mechanism of mammalian Xchromosome inactivation XIC : X-inactivation centerXIST: X-inactivation specific transcript

43. Molecular Biology of the Gene, 6th Edition

44. Identical twins are not identical

45. Phenotype = Genotype + Epigenotype + Environment