"PhD Course Fall 2017"

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1 Prof. Fahd M. Nasr Faculty of Sciences Lebanese University Beirut, Lebanon Winding your way through the genome, transcriptome, proteome to human diseases "PhD Course Fall 2017" Lecture 3 1

2 Genome structure, organization, function and evolution: Part II Lecture 3 Minisatellites and microsatellites 2 other types of tandemly repeated DNA Minisatellites clusters up to 20kb repeats up to 25bp Telomeric DNA hundreds of copies of the motif 5 -TTAGGG-3 Microsatellites shorter cluster (~150bp) repeats 13bp Dinucleotide repeats 140,000 (half are CA) Single nucleotide repeats 120,000 (AAAAA) 2

3 The use of microsatellite analysis in genetic profiling Transposable elements TEs have played a significant role in the history of biological research TEs had a major influence on the structure of genomes during evolution Cause mutations Their study the concept "selfish DNA" Manipulated as useful gene transfer vectors 3

4 Transposable elements The majority of genomic DNA has no obvious biological role Dominated by repetitive DNA elements the remnants of transposable elements (TE) or their activity Some TEs have become inactive during evolution Some TEs are dependent upon enzymes encoded in trans by other TEs Some TEs remain active "Targets" for mutation by transposable genetic elements 4

5 Transposable Elements Also called transposons or jumping genes First observed in Maize for more than 60 yrs ago by Barbara McClintock Idea slow to find acceptance Confirmed in E. coli during 70 s McClintock received Nobel Prize in 1983 Transposons are ubiquitous and make up large portions of many genomes (~50% for humans) Up to hundreds of thousands of copies 5

6 TEs come in two general types The "copy and paste" retrotransposons RNA copy RT to DNA integrated in the genome The "cut and paste" TEs direct excision from DNA insertion elsewhere in the genome 6

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8 RNA transposons Retroelements eukaryotic genomes LTR retroelements Ty sequence in yeast 5.9kb copies/genome copies of 330bp LTR of Ty (solo delta) ERVs (Endogenous Retrovirus) in human 240,000 copies/genome (4.7%) Non LTR retroelements 8

9 The Ty transposable element of yeast Ty Elements in Yeast Similarities with retroviruses Transpose RNA copy DNA using reverse transcriptase Evidence Intron in the Ty element was monitored through transposition the intron was removed, indicating an RNA intermediate Ty elements encode a reverse transcriptase Virus-like particles transposition-competent structures Ty elements are referred to as retrotransposons 9

10 RNA transposons that lack LTRs Non LTR retroelements or retroposons LINEs (Long Interspersed Nuclear Elements) 10 6 copies/human genome (20%) LINE-1 6.1kb (and LINE-2, LINE-3) SINEs (Short Interspersed Nuclear Elements) 1.7x10 6 copies/genome (14%) bp no genes Alu (commonest SINE) 1.2x10 6 c/genome Transposable elements in the human genome 10

11 Human retrosposons LINEs repeated sequences >5kb Autonomous elements with functional transposition genes Nonautonomous derivatives with internal deletions SINEs bp repeats LINEs 20% of the human genome L1 is the best studied type L1 elements are about 5% of the human genome Full-length element (6.5kb) not abundant most are deleted versions Full-length L1 a large ORF reverse transcriptases L1 transpose via RNA use a different mechanism for transposition Clinically, cases of hemophilia result from newly transposed L1 Insertions into the gene for factor VIII a child has L1 in the factor VIII gene, but neither parent does 11

12 The structure of an Alu element DNA transposons DNA-to-DNA transposition Less common than retrotransposons Ac/Ds elements of maize DNA transposons in prokaryotes IS (insertion sequence) minimum transposable element gene transposase Composite transposons Tn3-type transposons Transposable phages 12

13 IS Elements Insertion sequences Minimum transposable element Less than 2 kb in size IS1, IS2, IS10R, etc. Encode a transposase gene for transposition Have inverted terminal repeat sequences of about bp on average Recognition sites for transposase action The insertion sequence (IS) transposable element, IS1 13

14 Schematic of the integration of an IS element into chromosomal DNA 14

15 Composite and non-composite transposons Ac-Ds System in Maize Activator (Ac) and Dissociation (Ds) mutations in maize (McClintock) The Ac locus could move and also cause Ds to move Turn off genes when they became associated with them 15

16 Barbara McClintock discovered jumping genes in the 1940 s and called them activator (Ac) and dissociation (Ds) elements Ds element disrupts the purple pigment 16

17 Ac/Ds transposon family of maize Ac is 4.2kb functional transposase gene Transposase recognizes the 11bp inverted repeats (IRs) at either end of the Ac sequence and catalyzes its transposition Ds has an internal deletion no transposase Ds has the IR sequences Ds element is also able to transpose Ten different types of Ds elements in maize genome 194bp to several kilobases 17

18 Structure of Ac and Ds deletion derivatives 18

19 Kernel color in corn and transposon effects Kernels on an ear of corn 19

20 Phenotypes produced by transposable elements in corn kernels The Ac transposition mechanism 20

21 Gene Type of TE Disease/genetic disorder APC Alu Colon cancer BRCA1 Alu Breast cancer/ovarian cancer BRCA2 Alu Breast cancer/ovarian cancer M LVI2 Alu Leukemia NF1 Alu Neurofibromatosis type I APC Alu Cancer of the colon BAAT LTR Hypercholanemia M SLN LTR Cancer ADH1C LTR Role in alcoholism HSD17B1 LTR Breast cancer FKTN L1 Fukuyama-type congenital muscular dystrophy DM D L1 Duchenne muscular dystrophy CYBB L1 Chronic granulomatous disease RP2 L1 X-linked retinitis pigmentosa F8 Alu Hemophilia A CYBB L1 Chronic granulomatous disease U2AF65 Alu Loss of hnrnp C binding, leading to aberrant exonization OAT Alu OAT deficiency COL4A3 Alu Alport syndrome GUSB Alu Sly syndrome PDHX L1 Pyruvate dehydrogenase complex deficiency RPS6KA3 L1 Coffin-Lowry syndrome 21

22 Human diseases linked to TE 22

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