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Principal Investigator: Jeffrey M Kidd
Organization: UNIVERSITY OF MICHIGAN AT ANN ARBOR
Fiscal Year: 2024
Award: $475,800
Funding agency: National Institute of General Medical Sciences
Abstract
Short INterspersed Elements (SINEs) are mobile genetic elements that are present in all mammalian
genomes. Most mammalian SINEs can be subdivided into two general categories: (1) those derived from 7SL
signal recognition particle RNA (e.g., human Alu elements); and (2) those derived from transfer RNAs (e.g.,
canine SINEC_Cf elements). Alu and SINEC_Cf elements have had a major impact on genome evolution and
comprise an astounding ~11% and ~15% of human and canine genomic DNA, respectively. The vast majority
of SINEs have been rendered immobile by mutational processes; however, some human-specific Alu elements
and canine SINEC_Cf elements can mobilize to new genomic locations by a “copy and paste” mechanism
termed retrotransposition. To date, greater than 76 independent germline Alu retrotransposition events have
been implicated as the cause of human diseases, including cancer. SINEC_Cf retrotransposition events are
responsible for various diseases and phenotypic differences in canines. SINEs do not encode proteins; thus,
they are classified as `non-autonomous' retrotransposons. Previous studies, including our preliminary data,
demonstrate that a protein encoded by an autonomous Long INterspersed Element-1 (LINE-1) retrotransposon
(LINE-1 ORF2p) is required for Alu and SINEC_Cf element retrotransposition. We hypothesize that the
structure of Alu RNA, and by extension SINEC_Cf RNA, and unidentified host factor(s) allow these RNAs to
localize to the ribosome, where they can compete with the LINE-1 poly(A) tail for LINE-1 ORF2p binding to
promote their retrotransposition. Here, we propose to use a combination of molecular biological, evolutionary
inference, genetic, genomic, and biochemical approaches to: (1) use established RNA secondary structure
models, Illumina-based SHAPE-MaP chemical probing, and established cultured cell assays to uncover cis-
acting RNA structures and sequences required for human-specific Alu and SINEC_Cf retrotransposition; and
(2) exploit differences between HeLa cell isolates that differ in their ability to support Alu and SINEC_Cf
retrotransposition to identify host factor(s) critical for SINE retrotransposition. This proposal builds on
successful collaborations between the Moran and Kidd laboratories at the University of Michigan and will
combine the Moran laboratory's expertise in transposable element and RNA biology with the Kidd laboratory's
expertise in computational and statistical genomics and evolutionary biology to elucidate SINE
retrotransposition mechanisms.
Terms: <7S RNA><7SL RNA><Alleles><Allelomorphs><Alu Elements><Alu Family><Alu Repetitive Sequences><Assay><Binding><Bioassay><Biochemical><Biological><Biological Assay><Biology><CRISPR><CRISPR/Cas system><Cancers><Candidate Disease Gene><Candidate Gene><Canine Species><Canis familiaris><Categories><Cell Body><Cell Isolation><Cell Line><Cell Segregation><Cell Separation><Cell Separation Technology><CellLine><Cells><Cellular Assay><Chemicals><Cis-Acting Locus><Cis-Acting Sequence><Classification><Clustered Regularly Interspaced Short Palindromic Repeats><Collaborations><Complement><Complement Proteins><Cultured Cells><DNA Transposable Elements><DNA seq><DNA sequencing><DNAseq><Data><Disease><Disorder><Dogs><Dogs Mammals><Elements><Event><Evolution><Exons><Functional RNA><Generations><Genetic><Genetic Alteration><Genetic Change><Genetic defect><Genome><Genomic DNA><Genomics><Germ Lines><Goals><HeLa><Hela Cells><Host Factor><Host Factor Protein><Human><Immobilization><Integration Host Factors><Intervening Sequences><Introns><Knock-out><Knockout><Laboratories><Long Interspersed Elements><Malignant Neoplasms><Malignant Tumor><Maps><Mediating><Mice><Mice Mammals><Michigan><Mobile Genetic Elements><Modeling><Modern Man><Molecular><Molecular Interaction><Murine><Mus><Mutation><Non-Coding><Non-Coding RNA><Non-Polyadenylated RNA><Non-translated RNA><Noncoding RNA><Nontranslated RNA><ORFs><Open Reading Frames><Paste substance><Pastes><Phenotype><Poly(A) Tail><Process><Protein Coding Region><Proteins><RNA><RNA Gene Products><RNA Seq><RNA Sequences><RNA sequencing><RNAseq><Retrotransposition><Retrotransposon><Ribonucleic Acid><Ribonucleoproteins><Ribosomes><SINEs><SRP><Short Interspersed DNA Sequence Elements><Short Interspersed Element><Short Interspersed Nucleotide Elements><Signal Recognition Particle><Strains Cell Lines><Structural Models><Structure><Systematics><Technology><Testing><Transfer RNA><Transposable Elements><Triplet Codon-Amino Acid Adaptor><Universities><Untranslated RNA><biologic><candidate identification><canine><causal allele><causal gene><causal mutation><causal variant><causative mutation><causative variant><cell assay><cell sorting><complementation><cultured cell line><differential expression><differentially expressed><domestic dog><entire genome><experiment><experimental research><experimental study><experiments><full genome><gDNA><gene locus><genetic element><genetic locus><genome mutation><genomic location><genomic locus><human disease><malignancy><mammalian genome><neoplasm/cancer><noncoding><orthopedic freezing><particle><permissiveness><signal recognition particle 7S RNA><signal recogniton particle 7S RNA><tRNA><transcriptional differences><transcriptome sequencing><transcriptomic sequencing><transfer Ribonucleic acids><whole genome>