My long term goal is to understand the functions of interspersed repeats in human DNA. Studies proposed here define the properties of a family of repeated sequences called THE-1, which consists of 10,000 genomic copies and has hallmarks of transposable elements. The structure of the 2 kb THE-1 repeats resembles copia-like/proviral elements. THE-1 repeats hybridize to both discrete length poly A plus RNA and a number of discrete length extrachromosomal circular DNAs. The following experiments will describe the structure, transcription and transposition of THE-1 repeats. Structure: Sequence studies of the ends of THE-1 repeats will test preliminary findings that THE-1 elements insert into specific sequences. Other transporon-like families which are related to THE-1 will be identified by several alternative screening procedures. Transcription: Although most polymorphic THE-1 repeats are pseudogenes, one or more members probably code for an mRNA. The relationship of discrete length RNAs to THE-1 will be mapped and significant open reading frames will be identified by sequencing cDNA clones. The in vivo translation of THE-1 RNA will be tested. The nearly single copy THE-1 sequences present in prosimian will be isolated as probable examples of an authentic THE-1 gene structure. The prosimian gene in turn would be employed to isolate the human THE-1 gene. Transposition: Restriction fragment length polymorphism in human and non human primates of single copy sequences flanking THE-1 repeats will be determined to measure the mobility of THE-1 sequences. Since the discrete length extrachromosomal circular DNAs are far larger than the 2 kb THE-1 sequence to which they hybridize, recombinant DNAs will be isolated from these circular DNAs for: 1) structural analysis to decide their relationship to THE-1 and whether they are transpositional intermediates and 2) as a source of hybridization probes to isolate the transpositionally active sequences.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM021346-14
Application #
3270423
Study Section
Molecular Biology Study Section (MBY)
Project Start
1977-09-01
Project End
1991-08-31
Budget Start
1987-09-01
Budget End
1988-08-31
Support Year
14
Fiscal Year
1987
Total Cost
Indirect Cost
Name
University of California Davis
Department
Type
Schools of Arts and Sciences
DUNS #
094878337
City
Davis
State
CA
Country
United States
Zip Code
95618
Li, Tzu Huey; Schmid, Carl W (2004) Alu's dimeric consensus sequence destabilizes its transcripts. Gene 324:191-200
Rubin, Carol M; Kimura, Richard H; Schmid, Carl W (2002) Selective stimulation of translational expression by Alu RNA. Nucleic Acids Res 30:3253-61
Li, T H; Schmid, C W (2001) Differential stress induction of individual Alu loci: implications for transcription and retrotransposition. Gene 276:135-41
Kim, C; Rubin, C M; Schmid, C W (2001) Genome-wide chromatin remodeling modulates the Alu heat shock response. Gene 276:127-33
Schmid, C; Heng, H H; Rubin, C et al. (2001) Sperm nuclear matrix association of the PRM1-->PRM2-->TNP2 domain is independent of Alu methylation. Mol Hum Reprod 7:903-11
Kimura, R H; Choudary, P V; Stone, K K et al. (2001) Stress induction of Bm1 RNA in silkworm larvae: SINEs, an unusual class of stress genes. Cell Stress Chaperones 6:263-72
Li, T H; Kim, C; Rubin, C M et al. (2000) K562 cells implicate increased chromatin accessibility in Alu transcriptional activation. Nucleic Acids Res 28:3031-9
Li, T; Spearow, J; Rubin, C M et al. (1999) Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo. Gene 239:367-72
Kimura, R H; Choudary, P V; Schmid, C W (1999) Silk worm Bm1 SINE RNA increases following cellular insults. Nucleic Acids Res 27:3380-7
Schmid, C W (1998) Does SINE evolution preclude Alu function? Nucleic Acids Res 26:4541-50

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