Functional Effects of Retrotransposons

Johns Hopkins Pathology

R Graphics Output

Figure 1: GWAS cancer signals and overlapping retrotransposon insertions

Functional effects of polymorphic Alu insertions

Lead investigator: Lindsay Horvath, Ph.D.

Polymorphic retrotransposons are a major source of structural variation in the genome with the most prevalent form being Alu elements.  Our hypothesis is that a subset of these Alu elements have a functional consequence; specifically, we are interested in those Alu elements whose effects may explain phenotypic differences.  To this end, I have focused my research efforts on polymorphic Alu elements that map to regions identified in genome-wide association studies (GWAS) as being linked to a phenotype risk.  My projects seek to address two important components of this hypothesis.  First, we are creating a catalog of polymorphic Alu elements that could be the functional variant detected in previous GWAS reports.  We are using genetics approaches to evaluate which of these candidate elements, if functional, have a strong enough relationship with the trait-associated SNP to have been detected in the original GWAS reports (Figure 1).  For the best candidates we are interested in examining the distribution of the Alu in the patient population.  The second major aim of my projects is to evaluate the functional consequence of polymorphic Alu elements using reporter systems to identify mechanism(s) and loci at which the Alu appears to have an effect.  Genome editing at the endogenous site will confirm these finds and allow further dissection of the mechanism.


In vivo models of Alu insertion effects

Lead investigator: Chunhong Liu, Ph.D.

Insertions of mobile elements are major sources of structural variation in our genome, and we have found these occur frequently in linkage disequilibrium with trait associated SNPs identified by GWAS. Our overarching hypothesis is that a subset of Alu insertions has phenotypic consequence. My projects are to model the effects of two polymorphic Alu insertions in allelogenic transgenic mouse models. We first modify human gene in Bacterial Artificial Chromosomes (BACs) by replacing the regions immediately surrounding the Alu insertion with a synthesized DNA fragment, comprising LoxP, the allele with Alu insertion, FRT, LoxP, the allele without Alu insertion, FRT using BAC Red/ET recombination and rpsL-neo counter-selection system in E. coli (Figure 2). We next generate the allelogenic transgenic mice carrying these BACs. These mice are great models to isolate and measure the effects of common, naturally-occurring Alu insertion polymorphisms in vivo.

Figure 2: Modification of BACs














Retrotransposon Biology and Mapping          ♦          Epigenetics and Expression