Transposition Xuhua Xia [email protected] http://dambe.bio.uottawa.ca Causes of genomic

Transposition Xuhua Xia xxia@uottawa.ca http://dambe.bio.uottawa.ca Causes of genomic

Transposition Xuhua Xia [email protected] http://dambe.bio.uottawa.ca Causes of genomic evolution Variation in genome size and gene content sequence duplication (genome, segmental, gene) horizontal gene transfer transposition (Barbara McClintock) Genomic mutation replication fidelity DNA repair strand bias DNA modification functional constraints Slide 2 Barbara McClintock and the jumping genes Background knowledge: 1. Double fertilization 2. Genetics of two loci Aleurone: the outermost layer of

endosperm. If male is AA and female aa, then endosperm genotype is Aaa Double fertilization in plants Aleurone: the outermost layer of endosperm. If male is AA and female aa, then endosperm genotype is Aaa Mendel's garden pea Vegetative tube cell and generative cell which divide to form two sperm cells Efficient DNA repair in the generative cells but not in Prayvegetative and Zhaurova 2008 tube Nature Education cell. 1:169 Genetics of two loci B B a a F1 A

a B b A B A A 4 types of gametes a b A b a B b b AB ab Ab aB AB

AABB AaBb AABb AaBB ab AaBb aabb Aabb aaBb Ab AABb Aabb AAbb AaBb aB AaBB aaBb AaBb aaBB Ab LR LW LW LR aB LR SR LR SR Dominant:

AA,Aa: Long aa: Short BB,Bb: Red bb: white Parental type: nonrecombinant Recombinant AB ab Ab aB AB LR LR LR LR ab LR SW LW SR If not linked: LR:LW:SR:SW = 9:3:3:1 Alfred Henry Sturtevant: the "proportion of crossovers could be used as an index of the distance between any two factors" (Sturtevant, 1913) Barbara McClintock's frustration: This is not true for some genes. The proportion of crossovers change dramatically Some genes change their locations. Genetics of two loci B

B a a F1 A a B b A B a b A b a B A A 4 types of gametes b b

AB ab Ab aB ab AaBb aabb Aabb aaBb Ab AABb Aabb AAbb AaBb aB AaBB aaBb AaBb aaBB Ab LP MW LW MP aB MR SP MP SR Codominant:

AA: Long Aa: Medium aa: Short BB: Red Bb: pink bb: white Parental type: nonrecombinant Recombinant What is your hypothesis for a dramatically changing proportion of crossovers? AB AABB AaBb AABb AaBB AB ab Ab aB AB LR MP LP MR ab MP SW

MW SP Table 1: Maize Genes Studied by Barbara McClintock Gene Description C' Dominant allele on the short arm of Chr9 that prevents color from being expressed in the aleurone layer of the maize kernel, causing a so-called "colorless" phenotype (which is actually white or yellow in color). This is also known as the inhibitor allele. C Recessive allele on the short arm of Chr9 that leads to color development. Bz Dominant allele on the short arm of Chr9 that leads to a purple phenotype. bz Recessive allele on the short arm of Chr9 that leads to a dark brown phenotype. Ds "Dissociation gene": Genetic location on the short arm of chromosome 9 at which chromosomal breakage occurs. Ac Activator gene: A factor of unknown location (at least when McClintock was conducting her research) that impacts the expression of Ds. Inferences: 1. C'??Ds genotype has colors: C' is disabled by Ds 2. CCCBzbzbzDs is dark brown instead of purple: Bz disabled by Ds, allowing bz to express 3. The genotype regains purple: Ds has moved away from original Ds 4. Ds effect depends on Ac, both defying mapping: they are jumping genes, and Ds needs As to jump

Pray and Zhaurova 2008 Nature Education 1:169 CCbzbz-- C'C'BzBzDsDs C'CCBzbzbzDs-- Mostly colorless, but some have dark brown or purple spots Further observations: 1. CCCBzbzbzDs-- may be dark brown instead of purple 2. The genotype above may regain the purple color 3. Ds effect depends on Ac, both defying mapping Activator (Ac) and Dissociation (Ds) gene structure The 4.6-kb autonomous Ac element makes a single 3.8-kb transcript encoding an 807-AA transposase Du et al. 2011 BMC Genomics. 12: 588. Transposase (TR) and transposon Donor DNA with transposon Transposase binding to transposon Transposon is freed from donor DNA which is then repaired Freed transposon ready to insert TIR TIR TIR

TIR TIR TIR TIR TIR TIR TIR Target DNA Transposon inserted into arget DNA Transpose genes Donor DNA TIR TIR TIR TIR gene gene TIR

TIR TIR TIR Target DNA TIR TIR gene TIR TIR In plants: The ups and downs of genome size evolution due to transposable elements, DNA segment duplications Haploid genome size (Mbp) Arabidopsis ~ 135 rice ~420 wheat ~ 1700 rye ~ 7900 North side ~ 8000 BARE-1 copies

% repetitive elements ~ 15% ~ 35% ~ 80% ~ 90% South side (hot & dry) ~ 22,000 copies BARE-1 (TE) in barley Within grasses, > 30-fold range in genome size Evolution canyon, Israel Kellogg & Bennetzen Am J Bot 91:1709, 2004 Environmental stress conditions (hot & dry) trigger retrotransposon copy number increase in barley Kalendar PNAS 97: 6603 (2000) Contribution of repetitive sequences to genome expansion Composition of human genome Repeated sequences comprise about half the human genome !! Transposable elements selfish DNA Microsatellites This categorization is not correct because transposable elements often contain proteincoding genes. Protein-coding

sequences Unique likely also includes very degenerate (unrecognizable) transposable elements De Koning PLoS Genet 7:e1002384, 2011 NB: Gene = exons + introns Long introns & short exons in human genes Gregory Nature Rev. Genet. 6:699, 2005 & textbooks Classification of transposons DNA transposons cut-and-paste DNA transposons (e.g., Ac) rolling-circle DNA transposons (Helitrons) self-synthesizing DNA transposons (Polintons) Retrotransposons long terminal repeat (LTR) retrotransposons: Ty1-copia, Ty3-gypsy, BEL-Pao-like and DIRS; ERV1, ERV2 and ERV3 (of endogenous retroviruses) non-LTR retrotransposons: LINEs (Long INterspersed Elements): with genes encoding all functions for transposition (autonomous retroelements) SINEs (Short INterspersed Elements): Wicker et al. 2007. Nature Reviews Genetics 8:973982 nonautonomous retroelements Kapitonov & Jurka 2008. Nature Reviews Genetics 9:411412 (used here)

DNA-mediated transposition element encodes transposase enzyme enabling integration into host genome Conservative Replicative element flanked by direct repeats increase in copy number Most DNA transposons are conservative Fig. 7.1 Some "conservative" transposition may not be conservative Species 1 Missing link Species 2 G1 G2 G3 G1 G2

G3 G1 G2 G3 Generation of direct repeat GAC CTG GAC CTG GAC GAC CTG CTG Transposon DNA Slide 17 RNA-mediated transposition - mobile retroelement encodes reverse transcriptase Fig. 7.1 RNA intermediate Retrotransposons are always replicative. LINE transposition http://porpax.bio.miami.edu/~cmallery/150/gene/sf16x7.jpg

SINES (include Alu), LINES: (Short & Long INterspersed Elements) SINEs use the machinery of LINES for their propagation and can have impact on human gene structure/expression - eg. can be recruited as exons (Aluexonization) - in human genome, Alu repeats (~282 nt) have > 1,000,000 copies dispersed in genome. It is derived from 7SL RNA gene which is ancient (present in invertebrate and even bacterial lineages), but Alu is primate-specific. - tRNA-derived Mammalian-wide interspersed repeat (MIR), ~260 nt, ~400,000 copies in human genome http://biol.lf1.cuni.cz/ucebnice/en/repetitive_dna.htm TSD: short tandem site duplication Figure 3. Presentation of the 5' end of the putative MIR transcript in a tRNA secondary structure. Imperfect stem symmetries are also predicted in other tRNA-derived SINE transcripts (4-6). The only inconsistency with a tRNA structure is the presence of six instead of seven residues in the anticodon loop. A3 H2 B3 G2 C3 F2 D3

E2 E3 D2 F3 C2 G3 A2 H3 B2 A2 H3 B2 G3 C2 F3 D2 E3 E2

D3 F2 C3 G2 A3 H2 B3 A1 H1 B1 G1 C1 F1 D1 E1 E1 D1 F1

C1 G1 A1 H1 B1 A Quantify the degree of tree symmetry B C Colless's I: A bifurcating tree with n species has n-1 internal nodes. Each internal node j has two descending clades with mj1 and mj2 species: D E F Tree1 G H H G Sum path length (SPL) is the sum of path lengths from root to tip. For n species:

F E D C Tree2 A B 24 Colless, D. H. 1982. Review of Phylogenetics: The Theory and Practise of phylogenetic systematics. Syst. Zool. 31:100-104 Agapow P. M., and A. Purvis. 2002. Power of eight tree shape statistics to detect non-random diversification: A comparison by simulation of two models of cladogenesis. Syst. Biol. 51:866-872. S14 S13 S12 S11 S10 S9 S8 S7 S6 S5 S4 S3 S2 S1 24 23 (A)

20 S14 S13 S12 S11 S10 S9 S8 S7 S6 S5 S4 S3 S2 S1 (B) S14 S13 S12 S11 S10 S9 S8 S7 S6 S5 S4 S3 S2 S1 (C)

21 14 22 Number of lineages 12 10 8 N_A N_B N_C 6 4 2 0 -25 -20 -15 -10 Time from present -5 0

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