How does noncoding transcription regulate Hox genes?

BioEssays

Volumn 30, Issue 2, 2008, Pages 110-121

  Lempradl, Adelheid ^a   Ringrose, Leonie ^a  

^a INSTITUTE OF MOLECULAR BIOTECHNOLOGY   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

HOX PROTEIN;

CHROMATIN; LARVA; MODEL; NONHUMAN; REVIEW; VERTEBRATE;

ANIMALS; DROSOPHILA; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HOMEODOMAIN PROTEINS; MODELS, GENETIC; RNA, UNTRANSLATED; TRANSCRIPTION, GENETIC;

EID: 38849209297     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/bies.20704     Document Type: Review

References (71)

1. Sanchez-Elsner T, Gou D, Kremmer E, Sauer F. 2006. Noncoding RNAs of Trithorax Response Elements Recruit Drosophila Ash1 to Ultrabiothorax. Science 311:1118-1123.
2. Petruk S, Sedkov Y, Riley KM, Hodgson J, Schweisguth F, et al. 2006. Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in cis by transcriptional interference. Cell 127:1209-1221.
3. Petruk S, Sedkov Y, Brock HW, Mazo A. 2007. A model for initiation of mosaic HOX gene expression patterns by non-coding RNAs in early embryos. RNA Biol 4:1-6.
4. Manak JR, Dike S, Sementchenko V, Kapranov P, Biemar F, et al. 2006. Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nat Genet 38:1151-1158.
5. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, et al. 2005. The transcriptional landscape of the mammalian genome. Science 309:1559-1563.
6. ENCODE. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816.
7. Kapranov P, Willingham AT, Gingeras TR. 2007. Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 8:413-423.
8. Taft RJ, Pheasant M, Mattick JS. 2007. The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 29:288-299.
9. Costa FF. 2007. Non-coding RNAs: lost in translation? Gene 386:1-10.
10. Hogness DS, Lipshitz HD, Beachy PA, Peattie DA, Saint RB, et al. 1985. Regulation and products of the Ubx domain of the bithorax complex. Cold Spring Harb Symp Quant Biol 50:181-194.
11. Lipshitz HD, Peattie DA, Hogness DS. 1987. Novel transcripts from the Ultrabithorax domain of the bithorax complex. Genes Dev 1:307-322.
12. Sanchez-Herrero E, Akam M. 1989. Spatially ordered transcription of regulatory DNA in the bithorax complex of Drosophila. Development 107:321-329.
13. Cumberledge S, Zaratzian A, Sakonju S. 1990. Characterization of two RNAs transcribed from the cis-regulatory region of the abd-A domain within the Drosophila bithorax complex. Proc Natl Acad Sci USA 87:3259-3263.
14. Zhou J, Ashe H, Burks C, Levine M. 1999. Characterization of the transvection mediating region of the abdominal-B locus in Drosophila. Development 126:3057-3065.
15. Bae E, Calhoun VC, Levine M, Lewis EB, Drewell RA. 2002. Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex. Proc Natl Acad Sci USA 99:16847-16852.
16. Hogga I, Karch F. 2002. Transcription through the iab-7 cis-regulatory domain of the bithorax complex interferes with maintenance of Polycomb-mediated silencing. Development 129:4915-4922.
17. Rank G, Prestel M, Paro R. 2002. Transcription through intergenic chromosomal memory elements of the Drosophila bithorax complex correlates with an epigenetic switch. Mol Cell Biol 22:8026-8034.
18. Schmitt S, Prestel M, Paro R. 2005. Intergenic transcription through a polycomb group response element counteracts silencing. Genes Dev 19:697-708.
19. Prince V. 2002. The Hox Paradox: More complex(es) than imagined. Dev Biol 249:1-15.
20. Duboule D. 2007. The rise and fall of Hox gene clusters. Development 134:2549-2560.
21. Lewis EB1978. A gene complex controlling segmentation in Drosophila. Nature 276:565-570.
22. Karch F, Weiffenbach B, Peifer M, Bender W, Duncan I, et al. 1985. The abdominal region of the bithorax complex. Cell 43:81-96.
23. Lewis EB, Pfeiffer BD, Mathog DR, Celniker SE. 2003. Evolution of the homeobox complex in the Diptera. Curr Biol 13:R587-588.
24. Maeda RK, Karch F. 2006. The ABC of the BX-C: the bithorax complex explained. Development 133:1413-1422.
25. Martin CH, Mayeda CA, Davis CA, Ericsson CL, Knafels JD, et al. 1995. Complete sequence of the bithorax complex of Drosophila. Proc Natl Acad Sci USA 92:8398-8402.
26. Duboule D. 1998. Vertebrate Hox gene regulation: clustering and/or colinearity? Curr Opin Genet Dev 8:514-518.
27. Kmita M, Duboule D. 2003. Organizing axes in time and space; 25 years of colinear tinkering. Science 301:331-333.
28. Hoch M, Jackle H. 1993. Transcriptional regulation and spatial patterning in Drosophila. Curr Opin Genet Dev 3:566-573.
29. Busturia A, Morata G. 1988. Ectopic expression of homeotic genes caused by the elimination of the Polycomb gene in Drosophila imaginal epidermis. Development 104:713-720.
30. Muller J, Bienz M. 1991. Long range repression conferring boundaries of Ultrabithorax expression in the Drosophila embryo. Embo J 10:3147-3155.
31. Beuchle D, Struhl G, Muller J. 2001. Polycomb group proteins and heritable silencing of Drosophila Hox genes. Development 128:993-1004.
32. Simon J, Pfeifer M, Bender W, O'COnnor M. 1990. Regulatory elements of the bithorax complex that control expression along the anterior-posterior axis. EMBO J 9:3945-3956.
33. Chan CS, Rastelli L, Pirrotta V. 1994. A Polycomb response element in the Ubx gene that determines an epigenetically inherited state of repression. Embo J 13:2553-2564.
34. Chiang A, O'Connor MB, Paro R, Simon J, Bender W. 1995. Discrete Polycomb-binding sites in each parasegmental domain of the bithorax complex. Development 121:1681-1689.
35. Ringrose L, Paro R. 2007. Polycomb/Trithorax response elements and epigenetic memory of cell identity. Development 134:223-232.
36. Klymenko T, Muller J. 2004. The histone methyltransferases Trithorax and Ash1 prevent transcriptional silencing by Polycomb group proteins. EMBO Rep 5:373-377.
37. Orlando V, Jane EP, Chinwalla V, Harte PJ, Paro R. 1998. Binding of trithorax and Polycomb proteins to the bithorax complex: dynamic changes during early Drosophila embryogenesis. Embo J 17:5141-5150.
38. Ringrose L, Paro R. 2004. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu Rev Genet 38:413-443.
39. Busturia A, Bienz M. 1993. Silencers in abdominal-B, a homeotic Drosophila gene. Embo J 12:1415-1425.
40. Pirrotta V, Chan CS, McCabe D, Qian S. 1995. Distinct parasegmental and imaginal enhancers and the establishment of the expression pattern of the Ubx gene. Genetics 141:1439-1450.
41. Petruk S, Sedkov Y, Smith S, Tillib S, Kraevski V, et al. 2001. Trithorax and dC BP acting in a complex to maintain expression of a homeotic gene. Science 294:1331-1334.
42. Ronshaugen M, Biemar F, Piel J, Levine M, Lai EC. 2005. The Drosophila microRNA iab-4 causes a dominant homeotic transformation of halteres to wings. Genes Dev 19:2947-2952.
43. Gonzalez-Reyes A, Morata G. 1990. The developmental effect of overexpressing a Ubx product in Drosophila embryos is dependent on its interactions with other homeotic products. Cell 61:515-522.
44. Cleard F, Moshkin Y, Karch F, Maeda RK. 2006. Probing long-distance regulatory interactions in the Drosophila melanogaster bithorax complex using Dam identification. Nat Genet 38:931-935.
45. Ringrose L, Chabanis S, Angrand PO, Woodroofe C, Stewart AF. 1999. Quantitative comparison of DNA looping in vitro and in vivo: chromatin increases effective DNA flexibility at short distances. Embo J 18:6630-6641.
46. Irvine KD, Helfand SL, Hogness DS. 1991. The large upstream control region of the Drosophila homeotic gene Uitrabithorax. Development 111:407-424.
47. Bender W, Fitzgerald DP. 2002. Transcription activates repressed domains in the Drosophila bithorax complex. Development 129:4923-4930.
48. Bowman AB, Patel-King RS, Benashski SE, McCaffery JM, Goldstein LS, et al. 1999. Drosophila roadblock and Chlamydomonas L C7:a conserved family of dynein-associated proteins involved in axonal transport, flagellar motility, and mitosis. J Cell Biol 146:165-180.
49. Papp B, Muller J. 2006. Histone trimethylation and the maintenance of transcriptional ON and OFF states by trxG and PcG proteins. Genes Dev 20:2041-2054.
50. Sipos L, Kozma G, Molnar E, Bender W. 2007. In situ dissection of a Polycomb response element in Drosophila melanogaster. Proc Natl Acad Sci USA 104:12416-12421.
51. Duncan IW. 2002. Transvection effects in Drosophila. Annu Rev Genet 36:521-556.
52. Kennison JA, Southworth JW. 2002. Transvection in Drosophila. Adv Genet 46:399-420.
53. Castelli-Gair JE, Micol JL, Garcia-Bellido A. 1990. Transvection in the Drosophila Uitrabithorax gene: a Cbx1 mutant allele induces ectopic expression of a normal allele in trans. Genetics 126:177-184.
54. Hopmann R, Duncan D, Duncan I. 1995. Transvection in the iab-5,6,7 region of the bithorax complex of Drosophila: homology independent interactions in trans. Genetics 139:815-833.
55. Jijakli H, Ghysen A. 1992. Segmental determination in Drosophila central nervous system: analysis of the abdominal-A region of the bithorax complex. Int J Dev Biol 36:93-99.
56. Sipos L, Mihaly J, Karch F, Schedl P, Gausz J, et al. 1998. Transvection in the Drosophila Abd-B domain: extensive upstream sequences are involved in anchoring distant cis-regulatory regions to the promoter. Genetics 149:1031-1050.
57. Gemkow MJ, Verveer PJ, Arndt-Jovin DJ. 1998. Homologous association of the Bithorax-Complex during embryogenesis: consequences for transvection in Drosophila melanogaster. Development 125:4541-4552.
58. Pirrotta V. 1999. Transvection and chromosomal trans-interaction effects. Biochim Biophys Acta 1424:M1-8.
59. Castelli-Gair JE, Capdevila MP, Micol JL, Garcia-Bellido A. 1992. Positive and negative cis-regulatory elements in the bithoraxoid region of the Drosophila Uitrabithorax gene. Mol Gen Genet 234:177-184.
60. Muller M, Hagstrom K, Gyurkovics H, Pirrotta V, Schedl P. 1999. The mcp element from the Drosophila melanogaster bithorax complex mediates long-distance regulatory interactions. Genetics 153:1333-1356.
61. Sessa L, Breiling A, Lavorgna G, Silvestri L, Casari G, et al. 2007. Noncoding RNA synthesis and loss of Polycomb group repression accompanies the colinear activation of the human HOXA cluster. Rna 13:223-239.
62. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, et al. 2007. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129:1311-1323.
63. Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, et al. 2005. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120:169-181.
64. Chang HY, Chi JT, Dudoit S, Bondre C, van de Rijn M, et al. 2002. Diversity, topographic differentiation, and positional memory in human fibroblasts. Proc Natl Acad Sci USA 99:12877-12882.
65. Rinn JL, Bondre C, Gladstone HB, Brown PO, Chang HY. 2006. Anatomic demarcation by positional variation in fibroblast gene expression programs. PLoS Genet 2:e119.
66. Lin Q, Chen Q, Lin L, Smith S, Zhou J. 2007. Promoter targeting sequence mediates enhancer interference in the Drosophila embryo. Proc Natl Acad Sci USA 104:3237-3242.
67. Lin Q, Chen Q, Lin L, Zhou J. 2004. The Promoter Targeting Sequence mediates epigenetieally heritable transcription memory. Genes Dev 18:2639-2651.
68. Lin Q, Wu D, Zhou J. 2003. The promoter targeting sequence facilitates and restricts a distant enhancer to a single promoter in the Drosophila embryo. Development 130:519-526.
69. Cavalli G, Paro R. 1998. The Drosophila Fab-7 chromosomal element conveys epigenetic inheritance during mitosis and meiosis. Cell 93:505-518.
70. Ficz G, Heintzmann R, Arndt-Jovin DJ. 2005. Polycomb group protein complexes exchange rapidly in living Drosophila. Development 132:3963-3976.
71. Ringrose L, Rehmsmeier M, Dura JM, Paro R. 2003. Genome-wide prediction of Polycomb/Trithorax response elements in Drosophila melanogaster. Dev Cell 5:759-771.