Human-zebrafish non-coding conserved elements act in vivo to regulate transcription

Nucleic Acids Research

Volumn 33, Issue 17, 2005, Pages 5437-5445

  Shin, Jordan T ^d   Priest, James R ^a,b,e   Ovcharenko, Ivan ^c   Ronco, Amy ^d   Moore, Rachel K ^d   Burns, C Geoffrey ^d   MacRae, Calum A ^d  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b DOE JOINT GENOME INSTITUTE   (United States)

^c LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^d MASSACHUSETTS GENERAL HOSPITAL   (United States)

^e STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; GREEN FLUORESCENT PROTEIN; LUCIFERASE; FIREFLY LUCIFERASE; LUMINESCENT AGENT; RENILLA LUCIFERIN 2 MONOOXYGENASE;

ARTICLE; CONSERVATION GENETICS; CORE GENE; FISH GENETICS; GENE EXPRESSION; GENE IDENTIFICATION; HUMAN; HUMAN GENOME; IN VIVO STUDY; MOLECULAR EVOLUTION; NON CODING SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; QUANTITATIVE ASSAY; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION; TRANSGENE; ZEBRA FISH; ANIMAL; ANIMAL EMBRYO; COMPARATIVE STUDY; DNA RESPONSIVE ELEMENT; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GENOME; GENOMICS; METABOLISM; PRENATAL DEVELOPMENT; TRANSGENIC ANIMAL;

DANIO RERIO; TAKIFUGU; VERTEBRATA;

ANIMALS; ANIMALS, GENETICALLY MODIFIED; BASE SEQUENCE; CONSERVED SEQUENCE; EMBRYO, NONMAMMALIAN; GENE EXPRESSION REGULATION; GENOME, HUMAN; GENOMICS; HUMANS; LUCIFERASES, FIREFLY; LUCIFERASES, RENILLA; LUMINESCENT AGENTS; RESPONSE ELEMENTS; TRANSCRIPTION, GENETIC; ZEBRAFISH;

EID: 27144526227     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki853     Document Type: Article

References (35)

1. Waterston,R.H., Lindblad-Toh,K., Birney,E., Rogers,J., Abril,J.F., Agarwal,P., Agarwala,R., Ainscough,R., Alexandersson,M., An,P. et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562.
2. Ovcharenko,I., Stubbs,L. and Loots,G.G. (2004) Interpreting mammalian evolution using Fugu genome comparisons. Genomics, 84, 890-895.
3. Barton,L.M., Gottgens,B., Gering,M., Gilbert,J.G., Grafham,D., Rogers,J., Bentley,D., Patient,R. and Green,A.R. (2001) Regulation of the stem cell leukemia (SCL) gene: A tale of two fishes. Proc. Natl Acad. Sci. USA, 98, 6747-6752.
4. Loots,G.G., Locksley,R.M., Blankespoor,C.M., Wang,Z.E., Miller,W., Rubin,E.M. and Frazer,K.A. (2000) Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science, 288, 136-140.
5. Pennacchio,L.A., Olivier,M., Hubacek,J.A., Cohen,J.C., Cox,D.R., Fruchart,J.C., Krauss,R.M. and Rubin,E.M. (2001) An apolipoprotein influencing triglycerides in humans and mice revealed by comparative sequencing. Science, 294, 169-173.
6. Frazer,K.A., Sheehan,J.B., Stokowski,R.P., Chen,X., Hosseini,R., Cheng,J.F., Fodor,S.P., Cox,D.R. and Patil,N. (2001) Evolutionarily conserved sequences on human chromosome 21. Genome Res., 11, 1651-1659.
7. DeSilva,U., Elnitski,L., Idol,J.R., Doyle,J.L., Gan,W., Thomas,J.W., Schwartz,S., Dietrich,N.L., Beckstrom-Sternberg,S.M., McDowell,J.C. et al. (2002) Generation and comparative analysis of approximately 3,3 Mb of mouse genomic sequence orthologous to the region of human chromosome 7q11.23 implicated in Williams syndrome. Genome Res., 12, 3-15.
8. Dermitzakis,E.T., Reymond,A., Lyle,R., Scamuffa,N., Ucla,C., Deutsch,S., Stevenson,B.J., Flegel,V., Bucher,P., Jongeneel,C.V. et al. (2002) Numerous potentially functional but non-genic-conserved sequences on human chromosome 21. Nature, 420, 578-582.
9. Dermitzakis,E.T., Reymond,A., Scamuffa,N., Ucla,C., Kirkness,E., Rossier,C. and Antonarakis,S.E. (2003) Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs). Science, 302, 1033-1035.
10. Bejerano,G., Pheasant,M., Makunin,I., Stephen,S., Kent,W.J., Mattick,J.S. and Haussler,D. (2004) Uitraconserved elements in the human genome. Science, 304, 1321-1325.
11. Spitz,F., Gonzalez,F. and Duboule,D. (2003) A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell, 113, 405-417.
12. Nobrega,M.A., Ovcharenko,I., Afzal,V. and Rubin,E.M. (2003) Scanning human gene deserts for long-range enhancers. Science, 302, 413.
13. Woolfe,A., Goodson,M., Goode,D.K., Snell,P., McEwen,G.K., Vavouri,T., Smith,S.F., North,P., Callaway,H., Kelly,K. et al. (2005) Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol., 3, e7.
14. Ward,A.C., McPhee,D.O., Condron,M.M., Varma,S., Cody,S.H., Onnebo,S.M., Paw,B.H., Zon,L.I. and Lieschke,G.J. (2003) The zebrafish spi1 promoter drives myeloid-specific expression in stable transgenic fish. Blood, 102, 3238-3240.
15. Xu,C., Wu,G., Zohar,Y. and Du,S.J. (2003) Analysis of myostatin gene structure, expression and function in zebrafish. J. Exp. Biol., 206, 4067-4079.
16. Shentu,H., Wen,H.J., Her,G.M., Huang,C.J., Wu,J.L. and Hwang,S.P. (2003) Proximal upstream region of zebrafish bone morphogenetic protein 4 promoter directs heart expression of green fluorescent protein. Genesis, 37, 103-112.
17. Kimura-Yoshida,C., Kitajima,K., Oda-Ishii,I., Tian,E., Suzuki,M., Yamamoto,M., Suzuki,T., Kobayashi,M., Aizawa,S. and Matsuo,I. (2004) Characterization of the pufferfish Otx2 cis-regulators reveals evolutionarily conserved genetic mechanisms for vertebrate head specification. Development, 131, 57-71.
18. Son,O.L., Kim,H.T., Ji,M.H., Yoo,K.W., Rhee,M. and Kim,C.H. (2003) Cloning and expression analysis of a Parkinson's disease gene, uch-L1, and its promoter in zebrafish. Biochem. Biophys, Res. Commun., 312, 601-607.
19. Luo,W., Williams,J., Smallwood,P.M., Touchman,J.W., Roman,L.M. and Nathans,J. (2004) Proximal and distal sequences control UV cone pigment gene expression in transgenic zebrafish. J. Biol. Chem., 279, 19286-19293.
20. Her,G.M., Yeh,Y.H. and Wu,J.L. (2004) Functional conserved elements mediate intestinal-type fatty acid binding protein (I-FABP) expression in the gut epithelia of zebrafish larvae. Dev. Dyn., 230, 734-742.
21. Lin,C.Y., Chen,Y.H., Lee,H.C. and Tsai,H.J. (2004) Novel cis-element in intron 1 represses somite expression of zebrafish myf-5. Gene, 334, 63-72.
22. Wang,T.M., Chen,Y.H., Liu,C.F. and Tsai,H.J. (2002) Functional analysis of the proximal promoter regions of fish rhodopsin and myf-5 genes using transgenesis. Mar. Biotechnol. (NY), 4, 247-255.
23. Tidyman,W.E., Sehnert,A.J., Huq,A., Agard,J., Deegan,F., Stainier,D.Y. and Ordahl,C.P. (2003) In vivo regulation of the chicken cardiac troponin T gene promoter in zebrafish embryos. Dev. Dyn., 227, 484-496.
24. Huang,C.J., Tu,C.T., Hsiao,C.D., Hsieh,F.J. and Tsai,H.J. (2003) Germ-line transmission of a myocardium-specific GFP transgene reveals critical regulatory elements in the cardiac myosin light chain 2 promoter of zebrafish. Dev. Dyn., 228, 30-40.
25. Ovcharenko,I., Nobrega,M.A., Loots,G.G. and Stubbs,L. (2004) ECR Browser: A tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Res., 32, W280-W286.
26. Karolchik,D., Baertsch,R., Diekhaus,M., Furey,T.S., Hinrichs,A., Lu,Y.T., Roskin,K.M.; Schwartz,M., Sugnet,C.W., Thomas,D.J. et al. (2003) The UCSC Genome Browser Database. Nucleic Acids Res., 31, 51-54.
27. Harris,M.A., Clark,J., Ireland,A., Lomax,J., Ashburner,M., Foulger,R., Eilbeck,K., Lewis,S., Marshall,B., Mungall,C. et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res., 32, D258-261.
28. Rozen,S. and Skaletsky,H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol., 132, 365-386.
29. Rottbauer,W., Saurin,A.J., Lickert,H., Shen,X., Burns,C.G., Wo,Z.G., Kemler,R., Kingston,R., Wu,C. and Fishman,M. (2002) Reptin and pontin antagonistically regulate heart growth in zebrafish embryos. Cell, 111, 661-672.
30. Boffelli,D., Nobrega,M.A. and Rubin,E.M. (2004) Comparative genomics at the vertebrate extremes. Nat. Rev. Genet, 5, 456-465.
31. Kim,J., Bergmann,A., Lucas,S., Stone,R. and Stubbs,L. (2004) Lineage-specific imprinting and evolution of the zinc-finger gene ZIM2. Genomics, 84, 47-58.
32. Ovcharenko,I., Loots,G.G., Nobrega,M.A., Hardison,R.C., Miller,W. and Stubbs,L. (2005) Evolution and functional classification of vertebrate gene deserts. Genome Res., 15, 137-145.
33. Stuart,G.W., McMurray,J.V. and Westerfield,M. (1988) Replication, integration and stable germ-line transmission of foreign sequences injected into early zebrafish embryos. Development, 103, 403-412.
34. Stuart,G.W., Vielkind,J.R., McMurray,J.V. and Westerfield,M. (1990) Stable lines of transgenic zebrafish exhibit reproducible patterns of transgene expression. Development, 109, 577-584.
35. Gilmour,D.T., Jessen,J.R. and Lin,S. (2002) In Nusslein-Volhard,C. and Dahm,R. (eds), Manipulating gene expression in the zebrafish. Zebrafish: A Practical Approach. Oxford University Press, Oxford, Vol. 261, pp. 121-143.