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Repetitive DNA

Repetitive DNA. Repetitive DNA. Larger genomes are not generated by increasing the number of copies of the same sequences present in smaller genomes. It is due to the presence of more repetitive DNA. Six major types of noncoding human DNA have been described. Noncoding DNA in Eukaryotes.

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Repetitive DNA

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  1. Repetitive DNA

  2. Repetitive DNA • Larger genomes are not generated by increasing the number of copies of the same sequences present in smaller genomes. • It is due to the presence of more repetitive DNA

  3. Six major types of noncoding human DNA have been described

  4. Noncoding DNA in Eukaryotes

  5. Noncoding DNA in Eukaryotes I. Noncoding DNA within genes -Protein-encoding exons are embedded within much larger noncoding introns II. Structural DNA -Called constitutive heterochromatin -Localized to centromeres and telomeres III. Simple sequence repeats (SSRs) -One- to six-nucleotide sequences repeated thousands of times

  6. Noncoding DNA in Eukaryotes IV. Segmental duplications -Consist of 10,000 to 300,000 bp that have duplicated and moved V. Pseudogenes -Inactive genes Transposable elements (transposons) -Mobile genetic elements -Four types: -Long interspersed elements (LINEs) -Short interspersed elements (SINEs) -Long terminal repeats (LTRs) -Dead transposons

  7. I. Introns in genes

  8. Introns and Exons • Introns--Untranslated intervening sequences in mRNA • Exons– Translated sequences • Process-RNA splicing • Heterogeneous nuclear RNA (hnRNA)-Transcript before splicing is complete

  9. From DNA to Protein(Why is this eukaryotic?)

  10. Splice Site Recognition • Introns contain invariant 5’-GU and 3’-AG sequences at their borders (GU-AG Rule) • Recognized by small nuclear ribonucleoprotein particles (snRNPs) that catalyze the cutting and splicing reactions. • Internal intron sequences are highly variable even between closely related homologous genes.

  11. Distribution of Uninterrupted and Interrupted Genes in Various Eukaryotes While majority of the genes in yeast are uninterrupted, most of genes in flies are interrupted by one or two introns and most genes in mammals are interrupted by many introns

  12. Sizes of Exons and Introns Exons Introns Exons coding for proteins usually are short, but introns usually range from very short to very long

  13. II. Structural DNA

  14. Prokaryotic Prokaryotic genes that are turned on and off together are often clustered into operons which are transcribed into one mRNA molecule and translated together Eukaryotic Eukaryotic genes coding for enzymes of a metabolic pathway are often scattered over different chromosomes and are individually transcribed  Compare the arrangement of coordinately controlled genes in prokaryotes and eukaryotes. • There is an increasing complexity of regulatory sequences from a simple bacterial gene controlled by a repressor to a human gene controlled by multiple activators and repressors.

  15. Major types of regulatory DNA elements in eukaryotes 2010, 11, 439-446 TF – transcrition factor • 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 heterochromatin S – silencer P – promoter I – insulator E – enhancer

  16. Noncoding DNA in Eukaryotes Each cell in our bodies has about 6 feet of DNA stuffed into it -However, less than one inch is devoted to genes! Complex genomes have roughly 10x to 30x more DNA than is required to encode all the RNAs or proteins in the organism or have any apparent regulatory function

  17. Non-Protein Coding Genes Encode functional RNAs • There are non-protein genes in the genome that encode functional RNAs. • These RNAs are important in regulating the expression of genes • Assigned Reading: The functional genomics of noncoding RNA. Mattick et al. (2005), Science 309: 1527-1528.

  18. III. Simple sequence repeats (SSRs)

  19. Simple sequence repeats (SSRs) • By fluorescence in situ hybridization (FISH),the simple-sequence DNAs are localized near the centromers and telomeres of mouse chromosome

  20. Types of repiteddnaTwo typesTandemly repetitiveInterspersed repetitive

  21. 1- Satellite DNAs

  22. Satellite DNAs • When eukaryotic DNA is centrifuged, fragmented and centrifuged to equilibrium in a Cesium chloride (CsCl) density gradient (CsCl gradient), two components are observed: • Main band: most of the genomic DNA • Satellite band: one or multiple miner bands; they could be heavier or lighter than the main band • The main band DNA has density of 1.701 g/cmwith a G-C content of 42%, and minor band DNA has the buoyant density of 1.690 g/cmwith a G-C content of 30%

  23. Describe where satellite DNA is found and what role it may play in the cell. • Satellite DNA  highly repetitive DNA consisting of short unusual nucleotide sequences that are tandemly repeated 1000’s of times • It is found at the tips of chromosomes and the centromere • Its function is not known, perhaps it plays a structural role during chromosome replication and separation.

  24. Most Simple-Sequence DNAs are Concentrated in Specific Chromosomal Locations.Satellite DNAs Lie in Heterochromatin • Highly repetitive DNA (simple sequence DNA): Satellite DNA is characterized by rapid rate of hybridization, consists of very short sequences repeated many times in tandem in large clusters. • In addition, multi-cellular eukaryotes have complex satellites with longer repeat units mainly in heterochromatic region (Centromeric heterchromatin---necessary for separation of chromosome to daughter cells • Satellite DNA Simple-sequence DNA (6% of the human genome), size 14 to 500 bp • Microsatellite, (also called as transposable elements) 1-13 bp. Interspersed repetitive DNA dispersed throughout the genome

  25. 2- Telomeres

  26. Describe the role of telomeres in solving the end-replication problem with the lagging DNA strand. • Telomere is a series of short tandem repeats at the ends of eukaryotic chromosomes; prevents chromosomes from shortening with each replication cycle

  27. Telomere Repeat Sequences Until recently, little was known about molecular structure of telomeres. However, during the last few years, telomeres have been isolated and characterized from several sp.

  28. Eukaryotic telomerase • Eukaryotic chromosomes are linear, not circular like prokaryotic chromosomes. Most eukaryotic chromosomes have short, species-specific sequences tandemly repeated at their telomeres • Blackburn and Greider • have shown that chromosome lengths are maintained by telomerase, which adds telomere repeats without using the cell’s regular replication machinery. • The ends of eukaryotic chromosomes are formed by an enzyme called telomerase .Telomerase an enzyme adds repeats of 3´ ends of eukaryotic chromosomes • In the ciliate Tetrahymena, the telomere repeat sequence is 5` TTGGGG-3`

  29. Tetrahymena- protozoa organism. • The telomeres of this organism end in the sequence 5'-TTGGGG-3'. • The telomerase adds a series of 5'-TTGGGG-3' repeats to the ends of the lagging strand. • A hairpin occurs when unusual base pairs between guanine residues in the repeat form. • Finally, the hairpin is removed at the 5'-TTGGGG-3' repeat. Thus the end of the chromosome is faithfully replicated. RNA Primer  -  Short stretches of ribonucleotides (RNA substrates) found on the lagging strand during DNA replication. Helps initiate lagging strand replication

  30. Interspersed repetitive ~1/2 of the human genome consists of interspersed repetitive sequences.

  31. 5- Transposable elements (transposons)

  32. Describe the effects of transposons and retrotransposons. • Transposons  jump and interrupt the normal functioning may increase or decrease production of one or more proteins • can carry a gene that can be activated when inserted downstream from an active promoter and vice versa • Retrotransposons  transposable elements that move within a genome by means of an RNA intermediate, a transcript of the retrotransposon DNA to insert it must be converted back to DNA by reverse transcriptase 

  33. Noncoding DNA in Eukaryotes 5- Transposable elements (transposons) -Mobile genetic elements -Four types: -Long interspersed elements (LINEs) -Short interspersed elements (SINEs) -Long terminal repeats (LTRs) -Dead transposons

  34. LINEs & SINEs Current definitions: LINEs = Active or degenerate descendants of transposable elements. SINEs = Non-autonomous transposable elements (lacking the ability to mediate their own transposition) and their degenerate descendents.

  35. Original definitions: interspersed repeats

  36. The reverse transcriptase has LINE specificity, i.e., a reverse transcriptase from one LINE will only recognize the 3’ end of that LINE, and will be less efficient at recognizing and reverse transcribing other LINEs.

  37. Ex: LINE in Human • 6 Kb in length • Has a poly A tail • Flanked by short repeats • 5% of genome • 95% of the sequence are truncated at • the 5’ end • Contains two reading frames • - OPR I ( 375 codons) • - OPR II ( 1,300 codons) • Does not posses long terminal repeats

  38. SINEs are retrosequences that range in length from 75 to 500 bp. SINEs do not possess any reading frame. Thus, their retropositionmust be aided by other genetic elements.

  39. Primate Alu + Rodent B1 All others SINE 7SL-RNAderived tRNA-derived

  40. Alu elements • Length = ~300 bp • Repetitive: > 1,000,000 times in the human genome • Constitute >10% of the human genome • Found mostly in intergenic regions and introns • Propagate in the genome through retroposition (RNA intermediates).

  41. Alu elements are found only in primates.  All the millions of Alu elements have accumulated in a mere ~65 million years.

  42. Alu elements can be sorted into distinct families according to shared patterns of variation.  At any given point in time, only one or several Alu “master copies” are capable of transposing. Early in primate evolution, Alu transposition rate was approximately one new jump in every live birth. Today, it is about one new jump in every 200 live births.

  43. Evolution of Alu elements & Rodent BI DNA

  44. GENETIC AND EVOLUTIONARY EFFECTS OF TRANSPOSITION 1. Duplicative transposition increases genome size. Lily Edible frog Sunflower

  45. 2. Bacterial transposons often carry genes that confer antibiotic or other forms of resistance. Plasmids can carry such transposons from cell to cell, so that resistance can spread throughout a population or an ecosystem.

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