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Unit-length line-1 transcripts in human teratocarcinoma cells.
J Skowronski1, T G Fanning, M F Singer
1Laboratory of Biochemistry, National Cancer Institute, Bethesda, Maryland 20892.
Molecular and Cellular Biology
|April 1, 1988
Summary
Human Line-1 (L1) RNA in teratocarcinoma cells reveals diverse transcripts, including potential functional genes and pseudogenes. This study characterizes L1 RNA, identifying conserved sequences and open reading frames, classifying them as class II retrotransposons.
Area of Science:
- Molecular Biology
- Genomics
- Retrotransposon Research
Background:
- Line-1 (L1) elements are abundant retrotransposons in the human genome.
- Cytoplasmic polyadenylated L1 RNA plays a role in gene expression and genome dynamics.
- Understanding L1 RNA transcription and function is crucial for studying genome evolution.
Purpose of the Study:
- To characterize the approximately 6.5-kilobase cytoplasmic poly(A)+ Line-1 (L1) RNA in human teratocarcinoma cells (NTera2D1).
- To analyze the sequences of cloned L1 cDNAs to understand the diversity and structure of L1 transcripts.
- To investigate the potential for functional L1 genes and pseudogenes based on sequence analysis.
Main Methods:
- Primer extension analysis of cytoplasmic poly(A)+ L1 RNA.
- Cloning and sequencing of complementary DNA (cDNA) derived from L1 RNA.
- Bioinformatic analysis of cDNA sequences to identify open reading frames (ORFs) and conserved regions.
Main Results:
- Characterized ~6.5 kb cytoplasmic poly(A)+ L1 RNA, with transcripts often initiating at the presumed 'unit' length 5' terminus.
- Sequencing of 19 cDNA clones revealed significant sequence variation, indicating transcription from multiple genomic L1 elements.
- Identified two conserved open reading frames (ORF1 and ORF2) and conserved 5' and 3' noncoding regions, with ORF2 frequently interrupted by stop codons in pseudogene transcripts.
Conclusions:
- Human L1 RNA transcripts originate from a diverse set of genomic L1 elements, including both potential functional genes and numerous pseudogenes.
- The presence of conserved ORFs and sequence elements suggests a conserved structure and potential function for some L1 elements.
- Mammalian L1 elements represent a class of class II retrotransposons, similar to invertebrate movable elements, with implications for genome evolution.