k./ Oxford University Press 1990
Nucleic Acids Research, Vol. 18, No. I
Novel short interspersed repeat in human DNA David J.Kaplan and Craig H.Duncan* Center for Molecular Biology, Wayne State University, Detroit, Ml, USA Submitted November 15, 1989 The sequences below represent four members of a novel interspersed repetitive sequence family in the human genome. The sequence marked Ano (EMBL DNA Databank Accession number # X16294) was found in our laboratory during a search for composite transposable elements in the human genome. The sequence marked FIX is from the first intron of the gene for human blood clotting factor IX (1). The sequence marked HMG is found 3' to the human gene for non-histone chromosomal protein HMG-14 (2). The sequence marked (32M is found in the third intron of the human 12 microglobulin gene (3). The double slash marks in the FIX sequence denote 10 bp of sequence which is not shown. The GenBank databank numbering systems were used for the FIX, HMG, and 32M sequences. A probe was prepared corresponding to the sequence marked Ano and used to estimate the distribution of this sequence in human DNA. In one experiment the probe was hybridized to a panel of restriction digested mammalian genomic DNAs. The resulting autoradiograph showed hybridization of this probe to disperse sets of restriction fragments from human, baboon, and macaque chromosomal DNAs, but no hybridization to mouse or
cow chromosomal DNAs. In the second experiment, the same radiolabelled probe hybridized, in situ, to a bacteriophage library containing human DNA inserts of average size 15 kb. In the resulting autoradiograph, 47 out of 25,000 bacteriophage plaques showed a hybridization signal. Given the statistical nature of this test, this result is compatible with an abundance of 500-1000 copies per haploid human genome. Footnote Note: After this manuscript was submitted we learned of the work of Dr. J.Jurka. He has independently discovered other classes of low frequency repeats by computer analysis of human DNA sequences in databanks.
REFERENCES 1. Yoshitake,S., Schach,B.G., Foster,D.C., Davie,E.W. and Kurachi,K. (1985)
Biochemistry 24, 3736-3750. 2. Landsman,D., McBride,O.W., Soares,N., Crippa,M.P., Srikantha,T. and Bustin,M. (1989) J. Biol. Chem. 264, 3421-3427. 3. Gussow,D., Rein,R., Ginjaar,I., Hochstenbach,F., Seemann,G., Kotman,A. and Ploegh,H.L. (1987) J. Immunol. 139, 3132-3138. ; 100 Ano
8102 FIX ,8095 HMS AAACCr-A i 1869 BN
200 Ano 8213 FIX 8200 HM _riT9TCA7CE 1974 5B /
t
t=_
CA_
256 8268 8248 2030
Ano
FIX HMS
Ra.
Figure 1. Sequences of four members of a novel interspersed repeat family in human DNA.
*
To whom correspondence should be addressed at Laboratory 12, 4th floor MCHT, 2727 2nd Avenue, Detroit, MI 48201, USA
192
Nucleic Acids Research, Vol. 18, No. I
Novel short interspersed repeat in human DNA David J.Kaplan and Craig H.Duncan* Center for Molecular Biology, Wayne State University, Detroit, Ml, USA Submitted November 15, 1989 The sequences below represent four members of a novel interspersed repetitive sequence family in the human genome. The sequence marked Ano (EMBL DNA Databank Accession number # X16294) was found in our laboratory during a search for composite transposable elements in the human genome. The sequence marked FIX is from the first intron of the gene for human blood clotting factor IX (1). The sequence marked HMG is found 3' to the human gene for non-histone chromosomal protein HMG-14 (2). The sequence marked (32M is found in the third intron of the human 12 microglobulin gene (3). The double slash marks in the FIX sequence denote 10 bp of sequence which is not shown. The GenBank databank numbering systems were used for the FIX, HMG, and 32M sequences. A probe was prepared corresponding to the sequence marked Ano and used to estimate the distribution of this sequence in human DNA. In one experiment the probe was hybridized to a panel of restriction digested mammalian genomic DNAs. The resulting autoradiograph showed hybridization of this probe to disperse sets of restriction fragments from human, baboon, and macaque chromosomal DNAs, but no hybridization to mouse or
cow chromosomal DNAs. In the second experiment, the same radiolabelled probe hybridized, in situ, to a bacteriophage library containing human DNA inserts of average size 15 kb. In the resulting autoradiograph, 47 out of 25,000 bacteriophage plaques showed a hybridization signal. Given the statistical nature of this test, this result is compatible with an abundance of 500-1000 copies per haploid human genome. Footnote Note: After this manuscript was submitted we learned of the work of Dr. J.Jurka. He has independently discovered other classes of low frequency repeats by computer analysis of human DNA sequences in databanks.
REFERENCES 1. Yoshitake,S., Schach,B.G., Foster,D.C., Davie,E.W. and Kurachi,K. (1985)
Biochemistry 24, 3736-3750. 2. Landsman,D., McBride,O.W., Soares,N., Crippa,M.P., Srikantha,T. and Bustin,M. (1989) J. Biol. Chem. 264, 3421-3427. 3. Gussow,D., Rein,R., Ginjaar,I., Hochstenbach,F., Seemann,G., Kotman,A. and Ploegh,H.L. (1987) J. Immunol. 139, 3132-3138. ; 100 Ano
8102 FIX ,8095 HMS AAACCr-A i 1869 BN
200 Ano 8213 FIX 8200 HM _riT9TCA7CE 1974 5B /
t
t=_
CA_
256 8268 8248 2030
Ano
FIX HMS
Ra.
Figure 1. Sequences of four members of a novel interspersed repeat family in human DNA.
*
To whom correspondence should be addressed at Laboratory 12, 4th floor MCHT, 2727 2nd Avenue, Detroit, MI 48201, USA
192
