Thomas Keane, WTSI 14 th May, 2011 Assessing the impact of transposable element variation on mouse phenotypes and traits Thomas Keane Vertebrate Resequencing Informatics Wellcome Trust Sanger Institute Cambridge, UK Christoffer Nellåker and Chris Ponting MRC Functional Genomics Unit University of Oxford Oxford, UK
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Assessing the impact of transposable element variation on mouse phenotypes and traits
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Thomas Keane, WTSI 14th May, 2011
Assessing the impact of transposable element variation on mouse phenotypes and traits
Thomas Keane Vertebrate Resequencing Informatics Wellcome Trust Sanger Institute Cambridge, UK
Christoffer Nellåker and Chris Ponting MRC Functional Genomics Unit University of Oxford Oxford, UK
Thomas Keane, WTSI 14th May, 2011
Transposable Elements (TEs)
Transposons are segments of DNA that can move within the genome A minimal ‘genome’ – ability to replicate and change location
Dominate landscape of mammalian genomes 38-45% of rodent and primate genomes Genome size proportional to number of TEs
Class 1 (RNA intermediate) and 2 (DNA intermediate) Potent genetic mutagens Disrupt expression of genes Genome reorganisation and evolution Transduction of flanking sequence
Transposable elements (TEs) active amongst laboratory mouse strains Mouse Genomes Project: Whole genome sequencing of 17 key laboratory mouse strains 13 classical laboratory strains and 4 wild derived inbred strains Average of ~25x illumina sequencing per strain
Thomas Keane, WTSI 14th May, 2011
Agouti Mouse Model
Dolinoy PNAS 2007;104:13056–13061
Thomas Keane, WTSI 14th May, 2011
Mouse TEs
3 main classes of TEs in mouse genome Long interspersed nuclear elements (LINE) Short interspersed nuclear elements (SINE) Endogenous retrovirus superfamily (ERV)
Etn, IAP, MuLV, IS2, MaLR, VL30, RLTR
Key questions What is the true extent and distribution of TEs in the germline of laboratory mouse
strains? What can we learn about the selective pressure acting on TEs maintained in the
germline? How much phenotypic variation and complex traits can we associate with TEs?
Thomas Keane, WTSI 14th May, 2011
TE Calling
Terminology B6+: Present in the reference genome B6-: Not present in reference TEV: Transposable element variant
Computational calling methods B6+
SVMerge* pipeline: Integrate calls from several read-pair based SV ‘deletion’ (!) callers (Kim Wong, WTSI)
B6-
RetroSeq** pipeline developed Identifies discordant mate pairs and compares to a library of known TE sequences
Size estimation Full length element (~5-8kb) vs. solo LTR (<1kb) 30-40x physical coverage long fragment (~3kb) end reads (15 strains) Test if insertion point spanned by 3kb fragment read pairs
*Wong K, Keane TM, Stalker J, Adams DJ (2010) SVMerge: Enhanced structural variant and breakpoint detection by integration of multiple detection methods and local assembly, Genome Biology, 11:R128
**RetroSeq available from https://github.com/tk2/RetroSeq
Thomas Keane, WTSI 14th May, 2011
B6+ TEV Example
C57B6/NJ strain has the ERV Absent in DBA/2J strain Flanking spanning read pairs denote
absence
DBA/2J
C57B6/NJ
Thomas Keane, WTSI 14th May, 2011
B6- TEV Example
NOD/ShiLtJ Full length (~8kb) IAP insertion Not spanned by 3kb fragment