Abstract
A severe bottleneck in the size of the PV Alu subfamily in the common ancestor of human and gorilla has been used to isolate an Alu source gene. The human PV Alu subfamily consists of about one thousand members which are absent in gorilla and chimpanzee DNA. Exhaustive library screening shows that there are as few as two PV Alus in the gorilla genome. One is gorilla-specific, i.e., absent in the orthologous loci in both human and chimpanzee, suggesting the independent retrotranspositional activity of the PV subfamily in the gorilla lineage. The second of these two gorilla PV Alus is present in both human and chimpanzee DNAs and is the single PV Alu known to precede the radiation of these three species. The orthologous Alu in gibbon DNA resembles the next older Alu subfamily. Thus, this Alu locus is originally templated by a non-PV source gene and acquired characteristic PV sequence variants by mutational drift in situ, consequently becoming the first member and presumptive founder of this PV subfamily.
Similar content being viewed by others
References
Bailey AD, Stanhope M, Slightom JL, Goodman M, Shen CC, Shen C-KJ (1992) Tandemly duplicated a globin genes of gibbon. J Biol Chem 267:18398–18406
Batzer MA, Kilroy GE, Richard PE, Shaikh TH, Desselle TD, Hoppers CL, Deininger PL (1990) Structure and variability of recently inserted Alu family members. Nucleic Acids Res 18:6793–6798
Batzer MA, Deininger PL (1991) A human-specific subfamily of Alu sequences. Genomics 9:481–487
Batzer MA, Schmid CW, Deininger PL (1993) Evolutionary analysis of repetitive DNA sequences. Methods Enzymol 224
Britten RJ, Kohne DE (1968) Repeated sequences in DNA. Science 161:529–540
Britten RJ, Baron WF, Stout DB, Davidson EH (1988) Sources and evolution of human Alu repeated sequences. Proc Natl Acad Sci USA 85:4770–4774
Dombroski BA, Mathias SL, Nanthakumar E, Scott AF, Kazazian HH, Jr (1991) Isolation of an active human transposable element. Science 254:1805–1808
Jagadeeswaran P, Forget BG, Weissman SM (1981) Short interspersed repetitive DNA elements in eukaryotes: transposable DNA elements generated by reverse transcription of RNA Pol III transcripts? Cell 26:141–142
Jurka J, Smith T (1988) A fundamental division in the Alu family of repeated sequences. Proc Natl Acad Sci USA 85:4775–4778
Jurka J, Milosavljevic (1991) Reconstruction of human Alu genes. J Mol Evol 32:105–121
Leeflang EP, Liu W, Hashimoto C, Choudary PV, Schmid CW (1992) Phylogenetic evidence for multiple Alu source genes. J Mol Evol 35:7–16
Leeflang EP, Chenokov IN, Schmid CW (1993) Mobility of short interspersed repeats within the chimpanzee lineage. J Mol Evol 37:566–572
Lobo SM, Hernandez N (1989) A 76 by mutation converts a human RNA Polymerase II snRNA promoter into an RNA Polymerase III promoter. Cell 58:55–57
Matera AG, Hellmann U, Schmid CW (1990a) A transpositionally and transcriptionally competent Alu subfamily. Mol Cell Biol 10:5424–5432
Matera AG, Hellmann U, Hintz MF, Schmid CW (1990b) Recently transposed Alu repeats result from multiple source genes. Nucleic Acids Res 18:6019–6023
Mitchell P, Tjian R (1989) Transcriptional regulation in mammalian cells by sequence specific DNA binding proteins. Science 245:371–378
Murphy S, Di Liegro C, Melli M (1987) The in vitro transcription of the 7SK RNA gene by RNA polymerase III is dependent only on the presence of an upstream promoter. Cell 51:81–87
Quentin Y (1988) The Alu family developed through successive waves of fixation closely connected with primate lineage history. J Mol Evol 27:194–202
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning, Vol III, Appendix B: 1–28, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
Schmid CW, Jelinek WR (1982) The Alu family of dispersed repetitive sequences. Science 216:1065–1070
Schmid CW, Maraia R (1992) Transcriptional and transpositional selection of active SINE sequences. Curr Opin Genet Dev 2:874–882
Shen MR, Batzer MA, Deininger PL (1991) Evolution of the master Alu gene(s). J Mol Evol 33:311–320
Slagel V, Flemington E, Traina-Droge V, Bradshaw H Jr, Deininger PL (1987) Clustering and sub-family relationships of the Alu family in the human genome. Mol Biol Evol 4:19–29
Ullu E, Weiner AM (1985) Upstream sequences modulate the internal promoter of the human 7SL RNA gene. Nature 318:371–374
Van Arsdell SW, Denison RA, Bernstein LB, Weiner AM (1981) Direct repeats flank three small nuclear RNA pseudogenes in the human genome. Cell 26:11–17
Willard C, Nguyen HT, Schmid CW (1987) Existence of at least three distinct Alu subfamilies. J Mol Evol 26:180–186
Author information
Authors and Affiliations
Additional information
Correspondence to: C.W. Schmid
Rights and permissions
About this article
Cite this article
Leeflang, E.P., Liu, WM., Chesnokov, I.N. et al. Phylogenetic isolation of a human alu flounder gene: Drift to new subfamily identity. J Mol Evol 37, 559–565 (1993). https://doi.org/10.1007/BF00182741
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00182741