Transcript LINEs
‘mobile’ DNA: transposable elements Transposable elements Discrete sequences in the genome that have the ability to translocate or copy itself across to other parts of the genome without any requirement for sequence homology by using a self-encoded recombinase called transposase Transposable elements move from place to place in the genome 1930s Marcus Rhoades and 1950s Barbara McClintock – transposable elements in corn 1983 McClintock received Nobel Prize Found in all organisms Most 50 – 10,000 bp May be present hundreds of times in a genome TEs can generate mutations in adjacent genes TEs in Maize Fig 15.19 Genes VII by B. Lewin Common mechanism of transposition Transposons encode transposases that catalyse transposition events Regulation of transposase expression essential Fig13.24a: Hartwell Common mechanism of transposition Common mechanism of transposition 2 sequential steps Site specific cleavage of DNA at the end of TE Complex of transposasetranspososome element ends (transpososome) brought to DNA target where strand transfer is carried out by covalent joining of 3’end of TE to target DNA Common mechanism of transposition transposase (blue) binds and assembles a paired end complex (PEC) by dimerization, a process that might involve divalent metal ions (Me2+). PEC is then active for the cleavage reactions that remove flanking donor DNA (thin black lines) and transfer of the transposon ends into target DNA (black dotted line). Trends in Microbiology 2005 Vol13(11) pp 543-549 Catalytic domain of transposase involved in a transphosphorylation reaction that initiates DNA cleavage & strand transfer Fig 15.14 Fig 15.10 GenesVII Lewin Transposition can occur via RNA intermediates Class I TEs – Use a ‘copy & paste’ mechanism DNA intermediates Class II TEs Use a ‘cut and paste’ mechanism Generally short sequences See interspersed repeats from the repetitive elements lecture How transposons move Classes of transposable elements Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632 Interspersed repeats (transposon-derived) major types class size Copy % number genome* LINE L1 (Kpn family) L2 ~6.4kb 0.5x106 0.3 x 106 16.9 3.2 SINE Alu ~0.3kb 1.1x106 10.6 LTR e.g.HERV ~1.3kb 0.3x106 8.3 mariner ~0.25kb 1-2x104 2.8 DNA transposon family * Updated from HGP publications HMG3 by Strachan & Read pp268-272 LINEs (long interspersed elements) Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632 LINEs Most ancient of eukaryotic genomes Autonomous transposition (reverse trancriptase) ~6-8kb long, located mainly in euchromatin Internal polymerase II promoter and 2 ORFs 3 related LINE families in humans – LINE-1, LINE-2, LINE-3. LINE-1 still active (~17% of human genme) Believed to be responsible for retrotransposition of SINEs and creation of processed pseudogenes LINEs (long interspersed elements) HMG3 by Strachan & Read pp268-272 SINEs (short interspersed elements) Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632 SINEs Non-autonomous (successful freeloaders! ‘borrow’ RT from other sources such as LINEs) ~100-300bp long Internal polymerase III promoter No proteins Share 3’ ends with LINEs 3 related SINE families in humans – active Alu, inactive MIR and Ther2/MIR3. 100-300bp 1,500,000 13% LINES and SINEs have preferred insertion sites In this example, yellow represents the distribution of mys (a type of LINE) over a mouse genome where chromosomes are orange. There are more mys inserted in the sex (X) chromosomes. Try the link below to do an online experiment which shows how an Alu insertion polymorphism has been used as a tool to reconstruct the human lineage http://www.geneticorigins.org/geneticorigins/p v92/intro.html Long Terminal Repeats (LTR) Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632 Long Terminal Repeats (LTR) Repeats on the same orientation on both sides of element e.g. ATATATnnnnnnnnnnnnnnATATAT • contain sequences that serve as transcription promoters as well as terminators. • These sequences allow the element to code for an mRNA molecule that is processed and polyadenylated. • At least two genes coded within the element to supply essential activities for retrotransposition. • RNA contains a specific primer binding site (PBS) for initiating reverse transcription. • small direct repeats formed at the site of integration. Long Terminal Repeats (LTR) Autonomous or non-autonomous Autonomous LTR encode retroviral genes gag, pol genes e.g HERV Non-autonomous elements lack the pol and sometimes the gag genes e.g. MaLR Ancestral repeats (AR) ‘transpositional fossils’ Comprise ~ 25% of the genome ~780 classes Largely nonfunctional Sporadic cases where AR have acquired anew function after insertion MER121 is highly conserved among mammals!! DNA transposons Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632 DNA intermediate Class II TEs IS elements and transposons bounded by inverted terminal repeats (ITR) e.g. ATGCNNNNNNNNNNNCGTA Class II TEs DNA intermediate Prokaryotic IS elements (e.g. IS10, Ac/Ds, mariner) encode only transposase sequences eukaryotic transposons encode additional genes such as antibiotic resistance genes Some types of rearrangements mediated by DNA transposons Gene (2005)345 pp91-100 Transposons move in different ways Classified into 5 families on the basis of their transposition pathways 1) 2) 3) 4) 5) DDE-transposases RT/En transposases (reverse transcriptase/endonuclease) Tyrosine (Y) transposases Serine (S) transposases Rolling circle (RC) or Y2 transposases Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77) Transposons can be used to transfer DNA between bacterial cells Transposons (pink) integrate into new sites on the chromosome or plasmids by non-homologous recombination. Integrons (dark green) use similar mechanisms to exchange single gene cassettes (brown). Nature Reviews Microbiology 3, 722-732 (2005) Some transposons can encode integrons Integrons are assembly platforms — DNA elements that acquire open reading frames embedded in exogenous gene cassettes and convert them to functional genes by ensuring their correct expression. e.g. bacterial Tn7 also encodes an integron — a DNA segment containing several cassettes of antibiotic-resistance genes. These cassettes can undergo rearrangements in hosts that express a related recombinase, leading to alternative combinations of antibiotic-resistance genes. Integrons Mobile Integrons Superintegrons Mazel Nature Reviews Microbiology 4, 608–620 (August 2006) Reading 1) Chapter 9 pp 265-268 HMG 3 by Strachan and Read 2) Chapter 10: pp 339-348 Genetics from genes to genomes by Hartwell et al (2/e)