Our genomes are mostly made up of repetitive 'junk DNA'derived from insertions of mobile elements. Our group has developed methods to identify polymorphic insertions of these understudied sequences, demonstrated they are major sources of structural variation our genome, and found they occur frequently in linkage disequilibrium with trait associated SNPs identified by GWAS. Experiments by others and characterizations of the non-random distribution of mobile DNAs in genomes indicate they have significant potential to effect gene function. Our overarching hypothesis is that a subset of Alu insertions - the most prevalent and polymorphic mobile DNAs in humans - has phenotypic consequence. Our specific objectives are to isolate and characterize the effects of two polymorphic Alu insertions in allelogenic transgenic mouse models. The first insertion polymorphism to be studied is an intronic Alu 287bp in the angiotensin converting enzyme (ACE) gene locus. ACE encodes a key component of the renin-angiotensin-aldosterone blood pressure control system and is also involved in vascular homeostasis through degradation of bradykinin;the Alu is a well-studied marker of reduced ACE enzyme levels and presumed to be functional, although this has not been directly tested. The second polymorphism we propose to study is a 168bp intronic Alu insertion in the AT-rich interactive domain-containing protein 5B (ARID5B) locus. We recently associated this polymorphic Alu with risk for developing the most common childhood cancer, precursor B-cell acute lymphoblastic leukemia (ALL). The proposed studies will be the first to isolate and measure effects common, naturally-occurring TE insertion polymorphisms in vivo and to generate models to study mechanisms of these effects. More broadly, the work will provide a study design for mouse modeling in GWAS follow-up and begin work to make available an allelogenic YAC resource for studying functions of other Alu insertions.

Public Health Relevance

The purpose of the proposed studies is to test the hypothesis that inherited Alu insertion polymorphisms impact gene expression and result in human phenotypes. We will test this by developing two transgenic mouse models in which effects of an Alu insertion can be studied in isolation of effects of other genetic variants and position effects We will also conduct feasibility studies for development of an allelogenic yeast artificial chromosome (YAC) resource. This will support studies of polymorphic Alu insertions at other loci where these genetic variants are strong candidates for contributing to human disease.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Special Emphasis Panel (ZGM1-GDB-7 (CP))
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Krasnewich, Donna M
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Johns Hopkins University
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Kryatova, Maria S; Steranka, Jared P; Burns, Kathleen H et al. (2017) Insertion and deletion polymorphisms of the ancient AluS family in the human genome. Mob DNA 8:6
Payer, Lindsay M; Steranka, Jared P; Yang, Wan Rou et al. (2017) Structural variants caused by Alu insertions are associated with risks for many human diseases. Proc Natl Acad Sci U S A 114:E3984-E3992
Tang, Zuojian; Steranka, Jared P; Ma, Sisi et al. (2017) Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer. Proc Natl Acad Sci U S A 114:E733-E740
Ardeljan, Daniel; Taylor, Martin S; Ting, David T et al. (2017) The Human Long Interspersed Element-1 Retrotransposon: An Emerging Biomarker of Neoplasia. Clin Chem 63:816-822
Taylor, Martin S; LaCava, John; Dai, Lixin et al. (2016) Characterization of L1-Ribonucleoprotein Particles. Methods Mol Biol 1400:311-38
Achanta, Pragathi; Steranka, Jared P; Tang, Zuojian et al. (2016) Somatic retrotransposition is infrequent in glioblastomas. Mob DNA 7:22
Zampella, John G; Rodi?, Nemanja; Yang, Wan Rou et al. (2016) A map of mobile DNA insertions in the NCI-60 human cancer cell panel. Mob DNA 7:20
Rodi?, Nemanja; Steranka, Jared P; Makohon-Moore, Alvin et al. (2015) Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma. Nat Med 21:1060-4
Halper-Stromberg, Eitan; Steranka, Jared; Burns, Kathleen H et al. (2014) Visualization and probability-based scoring of structural variants within repetitive sequences. Bioinformatics 30:1514-21
Rodi?, Nemanja; Sharma, Reema; Sharma, Rajni et al. (2014) Long interspersed element-1 protein expression is a hallmark of many human cancers. Am J Pathol 184:1280-6

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