1. Trinucleotide repeats (TNRs) Dr. Derakhshandeh, PhD

2. INTRODUCTION Trinucleotide repeats (TNRs) are microsatellite sequences Disease-causing repeat instability is an important and unique form of mutation linked to more than 40 neurological, neurodegenerative and neuromuscular disorders. I.g. Huntington's disease, myotonic dystrophy and fragile X syndrome

3. Trinucleotide repeats TNRs undergo high frequency mutagenesis To understand better the molecular mechanisms of TNR instability in cultured cells

4. A new genetic assay was created using a shuttle vector The shuttle vector contains a promoter-TNR- reporter gene construct whose expression is dependent on TNR length.

5. The vector harbors the SV40 ori (CAGCTG)25–33

6. The shuttle vector is propagated in cultured cells It recovered and analyzed in yeast using selection for reporter gene expression. It recovered and analyzed in yeast using selection for reporter gene expression. Richard Pelletier, Nucleic Acids Research 2005 33(17):5667-5676

7. Disorders caused by trinucleotide repeat First: the mutant repeats show both somatic and germline instability Secondly: an earlier age of onset an earlier age of onset and increasing severity of phenotype in subsequent generations (anticipation) and increasing severity of phenotype in subsequent generations (anticipation) Finally, the parental origin of the disease allele can often influence anticipation Finally, the parental origin of the disease allele can often influence anticipation with paternal transmissions carrying a greater risk of expansion for many of these disorders.

8. Category of the trinucleotide repeat (based on the relative location) first subclass: –Repeats in non-coding sequences: For six diseases second subclass: –Exonic (CAG)n repeats code for polyglutamine tracts

9. Repeats in non-coding sequences

10. NON-CODING TRINUCLEOTIDE REPEAT DISORDERS Large and variable repeat expansions that result in multiple tissue: – dysfunction – degeneration Phenotypic manifestations within a disease are variable –Degree of somatic heterogeneity

11. Pre-mutations The larger mutations often are transmitted from a small pool of clinically silent intermediate size expansions CGG, GCC, GAA, CTG and CAG CGG, GCC, GAA, CTG and CAG particular trinucleotide sequence + its location with respect to a gene its location with respect to a gene –Important defining factors in dictating the unique mechanism of pathogenesis for each disease

12. Fragile X syndrome

13. Fragile X Syndrome

14. Fragile X syndrome Fragile X syndrome (FRAXA) Fragile XE MR (FRAXE) 1 in 2000 boys 1 in 4000 girls are estimated to be affected

15. Fragile X Syndrome most common inherited form of familial mental retardation (CGG)n trinucleotide expansion in the FMR1 gene leading to the typical Martin-Bell phenotype Clinical features vary depending on age Expansion of a (CCG)n repeat in the FMR2 gene corresponds to the FRAXE fragile site It lies distal to FRAXA It’s associated with mental retardation, but it is less frequent and lacks a consistent phenotype

16. The transcription of the FMR1 gene of normal and premutation alleles. Both alleles are translated into FMRP, which is demonstrated by Western blotting (lane N and P). The full mutation allele is hypermethylatedthereforetranscribed, which resultabsence of FMRP (lane F)

17. Repeats in non-coding sequences

18. Sequence of the 5'-UTR region of the FMR1 gene

19. Fragile X syndrome (FRAXA) Mental retardation Macroorchidism Some dysmorphic features Hyperactivity

20. Fragile X Syndrome

21. Fragile X syndrome (FRAXA) expansion of a polymorphic (CGG)n repeat in the 5'-untranslated region (UTR) > 230 trinucleotides > 230 trinucleotides hypermethylation together with a CpG island within the FMR1 promoter region transcriptional silencing of the FMR1 gene reduced FMR1 transcription and loss of gene product (FMRP)

22. Fragile XE MR (FRAXE) mild mental retardation variable behavior abnormalities expansion of a polymorphic (GCC)n repeat in the promoter region of the FMR2 gene the expanded repeats are hypermethylated leading to transcriptional silencing of FMR2 subsequent loss of gene product (FMR2)

23. Friedreich ataxia (FRDA)

25. autosomal recessive the only triplet repeat disorder that does not show anticipation Ataxia ( loss of voluntary muscular coordination) Diminished reflexes Cardiomyopathy ( heart enlargement) Diabetes Degeneration in the spinal cord

27. Friedreich ataxia FRDA is caused by a large intronic GAA repeat expansion located on chromosome 9 (Gene:X25/Potein: frataxin) which leads to reduced gene expression The expanded AT-rich sequence most probably causes self-association of the GAA/TTC tract, which stabilizes the DNA in a triplex structure

28. Repeats in non-coding sequences

29. FRDA & triplex structure A novel DNA structure sticky DNA lengths of (GAA.TTC)n in intron 1 of the frataxin gene of Friedreich's ataxia patients Sticky DNA is formed by the association of two purine.purine.pyrimidine (R.R.Y) triplexes in negatively supercoiled plasmids at neutral pH

30. Models of structures that may mediate mRNA synthesis and DNA replication inhibition by GAA·TTC repeats

31. in FRDA patients (GAA.TTC) (> 59 repeats) –the lengths of (GAA.TTC) (> 59 repeats) –inhibit transcription in vivo and in vitro –adopt the sticky conformation (GAAGGA.TCCTTC)65 –found in intron 1 –does not form sticky DNA –does not inhibit transcription –or associate with the disease Sakamoto,et al. MMol Cell. 1999 Apr;3(4):465-75.

32. frataxin is found in the mitochondria of humans we do not yet know its function there is a very similar protein in yeast, YFH1, there is a very similar protein in yeast, YFH1, YFH1 is involved in controlling: – iron levels – and respiratory function Frataxin and YFH1 are so similar, studying YFH1 may help us understand the role of frataxin in FRDA

34. Reduced X25 mRNA decreases frataxin levels a partial loss of frataxin function Disruption of the yeast X25 homolog (YFH1): Disruption of the yeast X25 homolog (YFH1): –abnormal accumulation of mitochondrial iron –loss of mtDNA –multiple iron–sulfur-dependent enzyme deficiencies –increased sensitivity to oxidative stress Frataxin : –hypersensitivity to iron and H2O2 stress

35. Frataxin insufficiency frataxin insufficiency may result in abnormal iron–sulfur homeostasis mitochondrial dysfunction free radical production oxidative stress cellular degeneration Wong, A, et al. Hum. Mol. Genet., 8, 425–430 (1999)

37. Myotonic dystrophy (DM)

38. multisystem disorder highly variable phenotypes AnticipationMyotonia muscle weakness Developmental abnormalities mental handicap Hypotonia respiratory distress are often evident in the more severe congenital myo­tonic dystrophy (CDM).

40. DM CTG trinucleotide repeat in the 3'-UTR of the protein kinase gene, DMPK The CTG repeat is located within the promoter of a upstream homeobox gene Loss of function of either or both of these proteins could contribute to some of the features in DM Korade-Mirnics, Z. et al. (1998) Nucleic Acids Res., 26, 1363–1368

41. Repeats in non-coding sequences

42. Spinocerebellar ataxia type 8 (SCBA8)

43. progressive ataxia with cerebellar atrophy decreased brisk reflexes SCA8 is expressed primarily in the brain is caused by an expanded CTG repeat in its 3'-terminal exon (~110–250 repeats)

45. Repeats in non-coding sequences

46. Parkinsonism(PD)

47. SCA-2 and SCA-3 repeats in Parkinsonism expansion of triplet repeats encoding polyglutamine (polyQ) tracts expansion of triplet repeats encoding polyglutamine (polyQ) tracts

48. POLYGLUTAMINE DISEASES

49. have repeat expansions that are much smaller in size and variation characterized by progressive neuronal dysfunction begins in mid-life and results in severe neurodegeneration

50. POLYGLUTAMINE DISEASES different polyglutamine diseases have little in common: –the length of the expansion > 35–40 –the greater the number of glutamine repeats in a protein the earlier the onset of disease and the more severe the symptoms

51. Expansion disorders Many major neurodegenerative diseases: Alzheimer's disease Parkinson's disease Huntington Disease

52. Alzheimer's disease

53. various types of familial Alzheimer's disease (AD) genes mutants of amyloid precursor protein (APP) polyglutamine repeat Q79

54. Huntington's disease

55. inherited as a autosomal dominant a polymorphic CAG repeat tract in exon 1, which is 35 units in length

56. Huntingtin in mitochondrial energy metabolism HD CAG size determines [ATP/ADP] in lymphoblastoid cells HD CAG repeat implicates a dominant property of huntingtin in mitochondrial energy metabolism Ihn Sik Seong, et al.Human Molecular Genetics 2005 14(19):2871-2880 Ihn Sik Seong, et al.Human Molecular Genetics 2005 14(19):2871-2880

57. HD CAG size determines [ATP/ADP] in lymphoblastoid cells

58. A Polymorphic Trinucleotide Repeat at DXS8170 in the Critical Region of X-Linked Retinitis Pigmentosa Locus RP3 at Xp21.1

59. possible mechanism of cell death the abnormally long sequence of glutamines acquires a shape that prevents the host protein from folding into its proper shape. if, the length of polyglutamine repeats is longer than the critical value found in disease, it acquires a specific shape called a β-helix.

60. Q37 chain under conditi ons in which it adopts β- strand topolo gies

61. Summary Since the identification in 1991 of repeat instability as a disease-causing mutation, gene- specific repeat instability is now known to be the mutational cause of at least 40 neurological, neurodegenerative and neuromuscular diseases. Both germline (parent-to-offspring) and tissue- specific somatic instability occurs. There are unique and common effectors for the instability of different repeat sequences, although each disease or locus is unique.