Long human mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome

Genome Research

Volumn 7, Issue 10, 1997, Pages 959-966

  Hardison, Ross C ^a   Oeltjen, John ^b   Miller, Webb ^a,c  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

^c Pennsylvania State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA GLOBIN; MYOSIN HEAVY CHAIN; PROTEIN TYROSINE KINASE;

ANIMAL CELL; GENE; GENE CLUSTER; GENE LOCUS; GENE SEQUENCE; GENETIC PROCEDURES; GENOME; HUMAN; HUMAN CELL; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REGULATOR GENE; SEQUENCE HOMOLOGY; SEQUENCE TAGGED SITE; SHORT SURVEY;

ANIMALIA;

EID: 0030722935     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.7.10.959     Document Type: Short Survey

References (43)

1. Adams, M.D., J.M. Kelley, J.D. Gocayne, M. Dubnick, M.J. Polymeropoulos, H. Xiao, C.R. Merril, A. Wu, R. Olde, R.F. Moreno et al. 1991. Complementary DNA sequencing: Expressed sequence tags and human genome project. Science 252: 1651-1656.
2. Boguski, M.S. 1995. The turning point in genome research. Trends Biochem. Sci. 20: 295-296.
3. Boguski, M.S., D.R. Cox, and R.M. Myers. 1996. Genomes and evolution: Editorial overview. Curr. Opin. Genet. Dev. 6: 683-685.
4. Burset, M.R. and R. Guigó. 1996. Evaluation of gene structure prediction programs. Genomics 34: 353-367.
5. Caterina, J.J., T.M. Ryan, K.M. Pawlik, R.D. Palmiter, R.L. Brinster, R.R. Behringer, and T.M. Townes. 1991. Human β-globin locus control region: Analysis of the 5′ DNaseI hypersensitive site HS2 in transgenic mice. Proc. Natl. Acad. Sci. 88: 1626-1630.
6. Charnay, P., R. Treisman, P. Mellon, M. Chao, R. Axel, and T. Maniatis. 1984. Differences in human α-and β-globin gene expression in mouse erythroleukemia cells: The role of intragenic sequences. Cell 38: 251-263.
7. Craddock, C.F., P. Vyas, J.A. Sharpe, H. Ayyub, W.G. Wood, and D.R. Higgs. 1995. Contrasting effects of alpha and beta globin regulatory elements on chromatin structure may be related to their different chromosomal environments. EMBO J. 14: 1718-1726.
8. Dembo, A., S. Karlin, and O. Zeitouni. 1994. Limit distribution of maximal non-aligned two-sequence segmental score. Ann. Probabil. 22: 2022-2039.
9. Elnitski, L., W. Miller, and R. Hardison. 1997. Conserved E boxes function as part of the enhancer in hypersensitive site 2 of the β-globin locus control region: Role of basic helix-loop-helix proteins. J. Biol. Chem. 272: 369-378.
10. Fischel-Ghodsian, N., R.D. Nicholls, and D.R. Higgs. 1987. Unusual features of CpG-rich (HTF) islands in the human α-globin complex: Association with nonfunctional pseudogenes and presence within the 3′ portion of the ζ genes. Nucleic Acids Res. 15: 9215-9225.
11. Flint, J., K. Thomas, G. Micklem, H. Raynham, K. Clark, N.A. Doggett, A. King, and D.R. Higgs. 1997. The relationship between chromosome structure and function at a human telomeric region. Nature Genet. 15: 252-257.
12. Forrester, W.C., C. Thompson, J.T. Elder, and M. Groudine. 1986. A developmentally stable chromatin structure in the human β-globin gene cluster. Proc. Natl. Acad. Sci. 83: 1359-1363.
13. Grosveld, F., M. Antoniou, M. Berry, E. de Boer, N. Dillon, J. Ellis, P. Fraser, O. Hanscombe, J. Hurst, A. Imam, M. Lindenbaum, S. Philipsen, S. Pruzina, J. Strouboulis, S. Raguz-Bolognesi, and D. Talbot. 1993. The regulation of human globin gene switching. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 339: 183-191.
14. Groudine, J., T. Kohwi-Shigematsu, R. Gelinas, G. Stamatoyannopoylos, and T. Papyannopoulou. 1983. Human fetal to adult hemoglobin switching: Changes in chromatin structure of the β-globin gene locus. Proc. Natl. Acad. Sci. 80: 7551-7555.
15. Gumucio, D., D. Shelton, W. Zhu, D. Millinoff, T. Gray, J. Bock, J. Slightom, and M. Goodman. 1996. Evolutionary strategies for the elucidation of cis and trans factors that regulate the developmental switching programs of the β-like globin genes. Mol. Phylog. Evol. 5: 18-32.
16. Hardison, R., D. Krane, D. Vandenbergh, J.-F. Cheng, J. Mansberger, J. Taddie, S. Schwartz, X. Huang, and W. Miller. 1991. Sequence and comparative analysis of the rabbit α-like globin gene cluster reveals a rapid mode of evolution in a G+C rich region of mammalian genomes. J. Mol. Biol. 222: 233-249.
17. Himmelman, A., C. Thevenin, K Harrison, and J.H. Kehrl. 1996. Analysis of Bruton's tyrosine kinase gene promoter reveals critical PU.1 and SP1 sites. Blood 87: 1036-1044.
18. Huang, X., R. Hardison, and W. Miller. 1990. A space-efficient algorithm for local similarities. Comput. Appl. Biosci. 6: 373-381.
19. Jackson, J.D., W. Miller, and R.C. Hardison. 1996a. Sequences within and flanking hypersensitive sites 3 and 2 of the βglobin locus control region required for synergistic versus additive interaction with the ζ-globin gene promoter. Nucleic Acids Res. 24: 4327-4335.
20. Jackson, J.D., H. Petrykowska, S. Philipsen, W. Miller, and R. Hardison. 1996b. Role of DNA sequences outside the cores of DNase hypersensitive sites (HSs) in functions of the β-globin locus control region: Domain opening and synergism between HS2 and HS3. J. Biol. Chem. 271: 11871-11878.
21. James-Pederson, M., S. Yost, B. Shewchuk, T. Zeigler, R. Miller, and R. Hardison. 1995. Flanking and intragenic sequences regulating the expression of the rabbit α-globin gene. J. Biol. Chem. 270: 3965-3973.
22. Koop, B.F. 1995. Human and rodent sequence comparisons: A mosaic model of genomic evolution. Trends Genet. 11: 367-371.
23. Koop, B.F. and L. Hood. 1994. Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA. Nature Genet. 7: 48-53.
24. Koop, B.F., L. Rowen, K. Wang, C.L. Kuo, D. Seto, J.A. Lenstra, S. Howard, W. Shan, P. Deshpande, and L. Hood. 1994. The human T-cell receptor TCRAC/TCRDC (Ca/Cd) region: Organization, sequence and evolution of 97.6 kb of DNA. Genomics 19: 478-493.
25. Lam, L. and E.H. Bresnick. 1996. A novel DNA binding protein, HS2NF5, interacts with a functionally important sequence of the human β-globin locus control region. J. Biol. Chem. 13: 32421-32429.
26. Lamerdin, J.E., M.A. Montgomery, S.A. Stilwagen, L.K. Scheidecker, R.S. Tebbs, K.W. Brookman, L.H. Thompson, and A.V. Carrano. 1995. Genomic sequence comparison of the human and mouse XRCC1 DNA repair gene regions. Genomics 25: 547-554.
27. Lamerdin, J.E., S.A. Stilwagen, M.H. Ramirez, L. Stubbs, and A.V. Carrano. 1996. Sequence analysis of the ERCC2 gene regions of human, mouse, and hamster reveals three linked genes. Genomics 34: 399-409.
28. Li, W.-H., M. Gouy, P. Sharp, C. O'hUigin, and Y.-W. Yang 1990. Molecular phylogeny of rodentia, lagomorpha, primates, artiodactyla and carnivora and molecular clocks. Proc. Natl. Acad. Sci. 87: 6703-6707.
29. Makalowski, W., J. Zhang, and M.S. Boguski. 1996. Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences. Genome Res. 6: 8456-857.
30. Margot, J.B., G.W. Demers, and R.C. Hardison. 1989. Complete nucleotide sequence of the rabbit β-like globin gene cluster: Analysis of intergenic sequences and comparison with the human β-like globin gene cluster. J. Mol. Biol. 205: 15-40.
31. Mitchell, P. and R. Tjian. 1989. Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science 245: 371-378.
32. Muller, S., P. Sideras, C.I.E. Smith, and K.G. Xanthopoulos. 1996. Cell specific expression of human Bruton's agammaglobulinemia tyrosine kinase gene (Btk) is regulated by Sp1-and Spi-1/PU.1-family members. Oncogene 13: 1955-1964.
33. Oeltjen, J.C., T.M. Malley, D.M. Muzny, W. Miller, R.A. Gibbs, and J.W. Belmont. 1997. Large scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains. Genome Res. 7: 315-329.
34. Robbins, J. 1996. Regulation of cardiac gene expression during development. Cardiovascul. Res. 31: E2-E16.
35. Schuler, G.D., M.S. Boguski, E.A. Stewart, L.D. Stein, G. Gyapay, K. Rice, R.E. White, P. Rodriguez-Tome, E. Aggarwal, E. Bajorek et al. 1996. A gene map of the human genome. Science 274: 540-546.
36. Shewchuk, B.M. 1997. "Effect of CpG islands from the α-globin gene cluster on gene expression: Evidence for a chromatin-dependent activity.α Ph.D. Thesis. The Pennsylvania State University, University Park, PA.
37. Shewchuk, B.M. and R.C. Hardison. 1997. CpG islands from the α-globin gene cluster increase gene expression in an integration-dependent manner. Mol. Cell. Biol. 17: 5856-5866.
38. Sideras, P., S. Muller, H. Shiels, H. Jin, W.N. Khan, L. Nilsson, E. Parkinson, J.D. Thomas, L. Branden, I. Larsson, W.E. Paul, F.S. Rosen, F.W. Alt, D. Vetrie, C.I.E. Smith, and K.G. Xanthopoulos. 1994. Genomic organization of mouse and human's Bruton's tyrosine agammaglobulinemia tyrosine kinase (Btk) loci. J. Immunol. 153: 5607-5617.
39. Smit, A.F.A. 1996. The origin of interspersed repeats in the human genome. Curr. Opin. Genet. Dev. 6: 743-748.
40. Stamatoyannopoulos, G. and A.W. Nienhuis. 1994. Hemoglobin switching. In The molecular basis of blood diseases (ed. G. Stamatoyannopoulos, A.W. Nienhuis, P.W. Majerus, and H. Varmus), pp. 107-155. W.B. Saunders, Philadelphia, PA.
41. Tuan, D., W. Solomon, Q. Li, and I.M. London. 1985. The β-like globin gene domain in human erythroid cells. Proc. Natl. Acad. Sci. 82: 6384-6388.
42. Velculescu V., L. Zhang, W. Zhou, J. Vogelstein, M. Basrai, D. Bassett, Jr, P. Hieter, B. Vogelstein, and K. Kinzler. 1997. Characterization of the yeast transcriptome. Cell 88: 243-251.
43. Yost, S.E., B. Shewchuk, and R. Hardison. 1993. Nuclear protein binding sites in a transcriptional control region of the rabbit α-globin gene. Mol. Cell. Biol. 13: 5439-5449.