1 / 27

BB30055: Genes and genomes

BB30055: Genes and genomes. Genomes - Dr. MV Hejmadi (bssmvh@bath.ac.uk). Lecture 2 – Repeat elements. Lecture 2 – Repeat elements. What are repeat elements? How did they originate? Why are they important?. Repetitive elements. Main classes based on origin Tandem repeats

heenan
Download Presentation

BB30055: Genes and genomes

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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?

  3. Repetitive elements • Main classes based on origin • Tandem repeats • Interspersed repeats • Segmental duplications

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

  5. Tandem / clustered repeats Broadly divided into 4 types based on size HMG3 by Strachan and Read pp 265-268

  6. Satellites Large arrays of repeats Some examples Satellite 1,2 & 3 a (Alphoid DNA) - found in all chromosomes b satellite HMG3 by Strachan and Read pp 265-268

  7. 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 HMG3 by Strachan and Read pp 265-268

  8. 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) Individual genotype HMG3 by Strachan and Read pp 265-268

  9. 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 .

  10. 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

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

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

  13. 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

  14. Segmental duplications Intrachromosomal duplications occur within a chromosome / arm Prone to translocations Interchromosomal segments duplicated among non homologous chromosomes Prone to deletions/ duplications Nature Reviews Genetics2, 791-800 (2001);

  15. Chromosome rearrangements originate from double strand break repair or homologous recombination between repeat sequences

  16. Segmental duplications Segmental duplications in chromosome22

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

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

  19. strand slippage during replication Fig 11.5 HMG3 by Strachan and Read pp 330

  20. Alu repeats (type of SINE) evolved from processed copies of the 7SL RNA gene

  21. Repeat elements Evolutionary ‘signposts’ • Passive markers for mutation assays • Actively reorganise gene organisation by creating, shuffling or modifying existing genes Chromosome structure and dynamics Provide 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

  23. 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. References • Chapters 9 and 11 HMG 3 by Strachan and Read • Chapter 10: pp 339-348 Genetics from genes to genomes by Hartwell et al (2/e) • Nature (2001) 409: pp 879-891

More Related