Identification of Factors Critical for SINE Retrotransposition

确定 SINE 逆转位的关键因素

• 批准号: 10095880
• 负责人: Jeffrey M Kidd
• 金额: $ 47.58万
• 依托单位: UNIVERSITY OF MICHIGAN AT ANN ARBOR
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-12-02 至 2024-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10095880
• 关键词: 7SL RNA; Alleles; Alu Elements; Binding; Biochemical; Biological; Biological Assay; Biology; CRISPR/Cas technology; Candidate Disease Gene; Canis familiaris; Categories; Cell Line; Cells; Cellular Assay; Chemicals; Cis-Acting Sequence; Collaborations; Complement; Cultured Cells; DNA Transposable Elements; DNA sequencing; Data; Elements; Event; Evolution; Exons; Generations; Genetic; Genome; Genomic DNA; Genomics; Goals; Hela Cells; Human; Integration Host Factors; Introns; Knock-out; Laboratories; Lead; Location; Long Interspersed Elements; Malignant Neoplasms; Maps; Mediating; Michigan; Mobile Genetic Elements; Modeling; Molecular; Mus; Mutation; Open Reading Frames; Paste substance; Poly(A) Tail; Process; Proteins; RNA; RNA Sequences; Retrotransposition; Retrotransposon; Ribonucleoproteins; Ribosomes; Short Interspersed Nucleotide Elements; Signal Recognition Particle; Structural Models; Structure; Technology; Testing; Transfer RNA; Universities; Untranslated RNA; base; causal variant; differential expression; disease phenotype; experimental study; human disease; mammalian genome; particle; transcriptome sequencing; whole genome

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.

摘要