The L1 family of long interspersed repetitive DNA in rabbits: Sequence, copy number, conserved open reading frames, and similarity to keratin

G. William Demers, Michael J. Matunis, Ross Cameron Hardison

Research output: Contribution to journalArticle

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Abstract

The L1 family of long interspersed repetitive DNA in the rabbit genome (L1Oc) has been studied by determining the sequence of the five L1 repeats in the rabbit β-like globin gene cluster and by hybridization analysis of other L1 repeats in the genome. L1Oc repeats have a common 3′ end that terminates in a poly A addition signal and an A-rich tract, but individual repeats have different 5′ ends, indicating a polar truncation from the 5′ end during their synthesis or propagation. As a result of the polar truncations, the 5′ end of L1Oc is present in about 11,000 copies per haploid genome, whereas the 3′ end is present in at least 66,000 copies per haploid genome. One type of L1Oc repeat has internal direct repeats of 78 bp in the 3′ untranslated region, whereas other L1Oc repeats have only one copy of this sequence. The longest repeat sequenced, L1Oc5, is 6.5 kb long, and genomic blot-hybridization data using probes from the 5′ end of L1Oc5 indicate that a full length L1Oc repeat is about 7.5 kb long, extending about 1 kb 5′ to the sequenced region. The L1Oc5 sequence has long open reading frames (ORFs) that correspond to ORF-1 and ORF-2 described in the mouse L1 sequence. In contrast to the overlapping reading frames seen for mouse L1, ORF-1 and ORF-2 are in the same reading frame in rabbit and human L1s, resulting in a discistronic structure. The region between the likely stop codon for ORF-1 and the proposed start codon for ORF-2 is not conserved in interspecies comparisons, which is further evidence that this short region does not encode part of a protein. ORF-1 appears to be a hybrid of sequences, of which the 3′ half is unique to and conserved in mammalian L1 repeats. The 5′ half of ORF-1 is not conserved between mammalian L1 repeats, but this segment of L1Oc is related significantly to type II cytoskeletal keratin.

Original languageEnglish (US)
Pages (from-to)3-19
Number of pages17
JournalJournal Of Molecular Evolution
Volume29
Issue number1
DOIs
StatePublished - Jul 1 1989

Fingerprint

keratin
Keratins
Open Reading Frames
open reading frames
genome
rabbits
Rabbits
DNA
Genome
Reading Frames
Haploidy
haploidy
genomics
probe
Type II Keratin
hybridization
Nucleic Acid Hybridization
protein
family
gene

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

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title = "The L1 family of long interspersed repetitive DNA in rabbits: Sequence, copy number, conserved open reading frames, and similarity to keratin",
abstract = "The L1 family of long interspersed repetitive DNA in the rabbit genome (L1Oc) has been studied by determining the sequence of the five L1 repeats in the rabbit β-like globin gene cluster and by hybridization analysis of other L1 repeats in the genome. L1Oc repeats have a common 3′ end that terminates in a poly A addition signal and an A-rich tract, but individual repeats have different 5′ ends, indicating a polar truncation from the 5′ end during their synthesis or propagation. As a result of the polar truncations, the 5′ end of L1Oc is present in about 11,000 copies per haploid genome, whereas the 3′ end is present in at least 66,000 copies per haploid genome. One type of L1Oc repeat has internal direct repeats of 78 bp in the 3′ untranslated region, whereas other L1Oc repeats have only one copy of this sequence. The longest repeat sequenced, L1Oc5, is 6.5 kb long, and genomic blot-hybridization data using probes from the 5′ end of L1Oc5 indicate that a full length L1Oc repeat is about 7.5 kb long, extending about 1 kb 5′ to the sequenced region. The L1Oc5 sequence has long open reading frames (ORFs) that correspond to ORF-1 and ORF-2 described in the mouse L1 sequence. In contrast to the overlapping reading frames seen for mouse L1, ORF-1 and ORF-2 are in the same reading frame in rabbit and human L1s, resulting in a discistronic structure. The region between the likely stop codon for ORF-1 and the proposed start codon for ORF-2 is not conserved in interspecies comparisons, which is further evidence that this short region does not encode part of a protein. ORF-1 appears to be a hybrid of sequences, of which the 3′ half is unique to and conserved in mammalian L1 repeats. The 5′ half of ORF-1 is not conserved between mammalian L1 repeats, but this segment of L1Oc is related significantly to type II cytoskeletal keratin.",
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The L1 family of long interspersed repetitive DNA in rabbits : Sequence, copy number, conserved open reading frames, and similarity to keratin. / Demers, G. William; Matunis, Michael J.; Hardison, Ross Cameron.

In: Journal Of Molecular Evolution, Vol. 29, No. 1, 01.07.1989, p. 3-19.

Research output: Contribution to journalArticle

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