BB30055: Genes and genomes

1. BB30055: Genes and genomes Genomes - Dr. MV Hejmadi (bssmvh@bath.ac.uk) Lecture 2 – Repeat elements

2. Lecture 2 Repeat elements • What are repeat elements? • How did they originate? • Why are they important?

4. Repetitive DNA • Main classes based on origin • Tandem repeats • Interspersed repeats • Segmental duplications

5. 1) Tandem repeats/ clustered repeats Blocks of tandem repeats at • subtelomeres • pericentromeres • Short arms of acrocentric chromosomes • Ribosomal gene clusters

6. Tandem / clustered repeats Broadly divided into 3 types based on size and location Which of the classes of tandem repeats are likely to be found in a mRNA and which are unlikely? HMG3 – Chap 9 pp 265-270

7. Coutesy: Evani Viegas-Pequignot Satellites Large arrays of repeats Some examples Satellite 1,2 & 3 Sat a (Alphoid DNA) - found in all chromosomes Sat b satellite ICF syndrome (Immunodeficiency- Centromeric instability-Facial anomalies syndrome) Caused by hypomethylation of Sata in chromosomes 1,9,16

8. Minisatellites Moderate sized arrays of repeats Some examples Hypervariable minisatellite DNA - core of GGGCAGGAXG - found in telomeric regions - used in original DNA fingerprinting technique by Alec Jeffreys

9. Microsatellites VNTRs - Variable Number of Tandem Repeats, SSR - Simple Sequence Repeats /STR – short tandem repeats 1-13 bp repeats e.g. (A)n ; (AC)n • 2% of genome (dinucleotides - 0.5%) • Used as genetic markers (especially for disease mapping)

10. Microsatellite genotyping design PCR primers unique to one locus in the genome a single pair of PCR primers will produce different sized products for each of the different length microsatellites .

11. Genotype test in a large family using (CA)/(TG) marker D17S800 1 (3,6) 2 (1,5) 3 (3,5) 4 (2,5) 5 (3,6) etc Alleles Samples What is the genotype of sample 10, 13, 16 ? Why do you get the shadow bands? Suggested to be due to replication slippage

12. How are tandem repeats generated in the genome? strand slippage during replication Fig 11.5 HMG3 by Strachan and Read pp 330

13. strand slippage during replication

14. 2) Interspersed repeats A.k.a. Transposon-derived repeats ~ 45% of genome Arise mainly as a result of transposition either through DNA or RNA retrotransposons (retroposons) ‘copy and paste’ DNA transposons (‘cut & paste’) See lecture 3 for transposition

15. Classes of transposable elements Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632

16. Interspersed repeats (transposon-derived) major types * Updated from HGP publications HMG3 by Strachan & Read pp268-272

17. Repeat elements in the human genome

18. 3) Segmental duplications • Closely related sequence blocks (1-200kb) at different genomic loci • Segmental duplications can occur on homologous chromosomes (intrachromosomal) or non homologous chromosomes (interchromosomal) • Not always tandemly arranged • Relatively recent

19. Segmental duplications Segmental duplications in chromosome22

20. Repeat elements How did they originate? Tandem repeats – replication slippage etc Interspersed repeats – transposition events Segmental duplications – strand exchange, recombination events

21. Repeat elements • Evolutionary ‘signposts’ • Passive markers for mutation assays • Actively reorganise gene organisation by creating, shuffling or modifying existing genes • Provides information on chromosome structure and dynamics • Provides tools for medical, forensic, genetic analysis Why are they important?

22. Pathogenic potential of Short Tandem Repeats (STR) 1) Unstable expansion of short tandem repeats Characterised by anticipation Reduction or expansion of STR can be pathogenic HMG 3 Chapter 11 pp 337 - 344

23. 2) Unstable deletions of STRs STRs tend to be deletion hotspots

24. External opthalmoplegia Ptosis Ataxia Cataract Common 4977bp deletion in mt DNA Interspersed repeats are susceptible to deletions/duplications E.g. Kearns-Sayre syndrome- encephalomyopathy

25. Pathogenic potential of segmental duplications Nature Reviews Genetics 2, 791-800 (2001)

26. STRs are…  A) microsatellite sequences. B) generally highly polymorphic. C) Useful markers along the chromosome. D) a and b • b and c • a and c

27. Which of the following is not one of the four classes of transposon-derived repeat sequences?  A. LINES B. SINES C. DNA transposons D. Long terminal repeat transposons E. pseudogenes

28. When repeats of a region lie adjacent to each other they are called ___________ duplications ________________ gene transfer is the direct transfer of genes from one species in the germ line of another species.

29. True or False All Repetitive DNA elements in the human genome arose through a common mechanism

30. Recombination events Replication slippage Transposition events Tandem repeats Interspersed repeats Segmental duplications Match the columns

31. Reading Chapter 9: HMG 3 by Strachan & Read Repeat elements and disease Nature Reviews Genetics 2, 791-800 (2001)

32. C T CpG islands CpG TpG Methyl CpG Significance of CpG islands • Non-methylated CpG islands associated with the 5’ ends of genes • Usually overlap the promoter region • Aberrant methylation of CpG islands linked to pathologies like cancer or epigenetic diseases like Rhett’s syndrome Deamination methylated at C CpG islands show no methylation http://www.sanger.ac.uk/HGP/cgi.shtml

33. Inheritance of CpG methylation