TALE Factors Poise Promoters for Activation by Hox Proteins

Developmental Cell

Volumn 28, Issue 2, 2014, Pages 203-211

  Choe, Seong Kyu ^a,b   Ladam, Franck ^a   Sagerström, Charles G ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^b Wonkwang University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

HOX PROTEIN; RNA POLYMERASE II; SERINE; TALE PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; BLASTULA; CHROMATIN; CONTROLLED STUDY; DEVELOPMENTAL STAGE; EMBRYO; EMBRYO DEVELOPMENT; GASTRULA; HISTONE MODIFICATION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN PHOSPHORYLATION; TRANSCRIPTION REGULATION; ZEBRA FISH;

ANIMALS; BLASTULA; GASTRULA; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HOMEODOMAIN PROTEINS; PHOSPHORYLATION; POSITIVE TRANSCRIPTIONAL ELONGATION FACTOR B; PROMOTER REGIONS, GENETIC; RNA POLYMERASE II; TRANSCRIPTIONAL ACTIVATION; ZEBRAFISH; ZEBRAFISH PROTEINS;

EID: 84892972684     PISSN: 15345807     EISSN: 18781551     Source Type: Journal    
DOI: 10.1016/j.devcel.2013.12.011     Document Type: Article

References (40)

1. Adelman K., Lis J.T. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat. Rev. Genet. 2012, 13:720-731.
2. Barrow J.R., Capecchi M.R. Targeted disruption of the Hoxb-2 locus in mice interferes with expression of Hoxb-1 and Hoxb-4. Development 1996, 122:3817-3828.
3. Carpenter E.M., Goddard J.M., Chisaka O., Manley N.R., Capecchi M.R. Loss of Hox-A1 (Hox-1.6) function results in the reorganization of the murine hindbrain. Development 1993, 118:1063-1075.
4. Chambeyron S., Bickmore W.A. Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev. 2004, 18:1119-1130.
5. Chambeyron S., Da Silva N.R., Lawson K.A., Bickmore W.A. Nuclear re-organisation of the Hoxb complex during mouse embryonic development. Development 2005, 132:2215-2223.
6. Chao S.H., Price D.H. Flavopiridol inactivates P-TEFb and blocks most RNA polymerase II transcription invivo. J.Biol. Chem. 2001, 276:31793-31799.
7. Choe S.K., Vlachakis N., Sagerström C.G. Meis family proteins are required for hindbrain development in the zebrafish. Development 2002, 129:585-595.
8. Choe S.K., Lu P., Nakamura M., Lee J., Sagerström C.G. Meis cofactors control HDAC and CBP accessibility at Hox-regulated promoters during zebrafish embryogenesis. Dev. Cell 2009, 17:561-567.
9. Dollé P., Lufkin T., Krumlauf R., Mark M., Duboule D., Chambon P. Local alterations of Krox-20 and Hox gene expression in the hindbrain suggest lack of rhombomeres 4 and 5 in homozygote null Hoxa-1 (Hox-1.6) mutant embryos. Proc. Natl. Acad. Sci. USA 1993, 90:7666-7670.
10. Erickson T., Scholpp S., Brand M., Moens C.B., Waskiewicz A.J. Pbx proteins cooperate with Engrailed to pattern the midbrain-hindbrain and diencephalic-mesencephalic boundaries. Dev. Biol. 2007, 301:504-517.
11. Ferretti E., Marshall H., Pöpperl H., Maconochie M., Krumlauf R., Blasi F. Segmental expression of Hoxb2 in r4 requires two separate sites that integrate cooperative interactions between Prep1, Pbx and Hox proteins. Development 2000, 127:155-166.
12. Ferretti E., Cambronero F., Tümpel S., Longobardi E., Wiedemann L.M., Blasi F., Krumlauf R. Hoxb1 enhancer and control of rhombomere 4 expression: complex interplay between PREP1-PBX1-HOXB1 binding sites. Mol. Cell. Biol. 2005, 25:8541-8552.
13. Goddard J.M., Rossel M., Manley N.R., Capecchi M.R. Mice with targeted disruption of Hoxb-1 fail to form the motor nucleus of the VIIth nerve. Development 1996, 122:3217-3228.
14. Ho R.K., Kimmel C.B. Commitment of cell fate in the early zebrafish embryo. Science 1993, 261:109-111.
15. Huang H., Rastegar M., Bodner C., Goh S.L., Rambaldi I., Featherstone M. MEIS C termini harbor transcriptional activation domains that respond to cell signaling. J.Biol. Chem. 2005, 280:10119-10127.
16. Jacobs Y., Schnabel C.A., Cleary M.L. Trimeric association of Hox and TALE homeodomain proteins mediates Hoxb2 hindbrain enhancer activity. Mol. Cell. Biol. 1999, 19:5134-5142.
17. Ji X., Zhou Y., Pandit S., Huang J., Li H., Lin C.Y., Xiao R., Burge C.B., Fu X.D. SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase. Cell 2013, 153:855-868.
18. Lindeman L.C., Andersen I.S., Reiner A.H., Li N., Aanes H., Østrup O., Winata C., Mathavan S., Müller F., Aleström P., Collas P. Prepatterning of developmental gene expression by modified histones before zygotic genome activation. Dev. Cell 2011, 21:993-1004.
19. Mann R.S., Lelli K.M., Joshi R. Hox specificity unique roles for cofactors and collaborators. Curr. Top. Dev. Biol. 2009, 88:63-101.
20. Mark M., Lufkin T., Vonesch J.L., Ruberte E., Olivo J.C., Dollé P., Gorry P., Lumsden A., Chambon P. Two rhombomeres are altered in Hoxa-1 mutant mice. Development 1993, 119:319-338.
21. McClintock J.M., Kheirbek M.A., Prince V.E. Knockdown of duplicated zebrafish hoxb1 genes reveals distinct roles in hindbrain patterning and a novel mechanism of duplicate gene retention. Development 2002, 129:2339-2354.
22. Moens C.B., Selleri L. Hox cofactors in vertebrate development. Dev. Biol. 2006, 291:193-206.
23. Nguyen V.T., Kiss T., Michels A.A., Bensaude O. 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes. Nature 2001, 414:322-325.
24. Peterlin B.M., Price D.H. Controlling the elongation phase of transcription with P-TEFb. Mol. Cell 2006, 23:297-305.
25. Saleh M., Rambaldi I., Yang X.J., Featherstone M.S. Cell signaling switches HOX-PBX complexes from repressors to activators of transcription mediated by histone deacetylases and histone acetyltransferases. Mol. Cell. Biol. 2000, 20:8623-8633.
26. Slattery M., Riley T., Liu P., Abe N., Gomez-Alcala P., Dror I., Zhou T., Rohs R., Honig B., Bussemaker H.J., Mann R.S. Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell 2011, 147:1270-1282.
27. Soshnikova N., Duboule D. Epigenetic temporal control of mouse Hox genes invivo. Science 2009, 324:1320-1323.
28. Studer M., Lumsden A., Ariza-McNaughton L., Bradley A., Krumlauf R. Altered segmental identity and abnormal migration of motor neurons in mice lacking Hoxb-1. Nature 1996, 384:630-634.
29. Tie F., Banerjee R., Stratton C.A., Prasad-Sinha J., Stepanik V., Zlobin A., Diaz M.O., Scacheri P.C., Harte P.J. CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing. Development 2009, 136:3131-3141.
30. Tischfield M.A., Bosley T.M., Salih M.A., Alorainy I.A., Sener E.C., Nester M.J., Oystreck D.T., Chan W.M., Andrews C., Erickson R.P., Engle E.C. Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development. Nat. Genet. 2005, 37:1035-1037.
31. Vastenhouw N.L., Zhang Y., Woods I.G., Imam F., Regev A., Liu X.S., Rinn J., Schier A.F. Chromatin signature of embryonic pluripotency is established during genome activation. Nature 2010, 464:922-926.
32. Vlachakis N., Choe S.K., Sagerström C.G. Meis3 synergizes with Pbx4 and Hoxb1b in promoting hindbrain fates in the zebrafish. Development 2001, 128:1299-1312.
33. Wang Z., Iwasaki M., Ficara F., Lin C., Matheny C., Wong S.H., Smith K.S., Cleary M.L. GSK-3 promotes conditional association of CREB and its coactivators with MEIS1 to facilitate HOX-mediated transcription and oncogenesis. Cancer Cell 2010, 17:597-608.
34. Waskiewicz A.J., Rikhof H.A., Hernandez R.E., Moens C.B. Zebrafish Meis functions to stabilize Pbx proteins and regulate hindbrain patterning. Development 2001, 128:4139-4151.
35. Waskiewicz A.J., Rikhof H.A., Moens C.B. Eliminating zebrafish pbx proteins reveals a hindbrain ground state. Dev. Cell 2002, 3:723-733.
36. Weicksel S.E., Xu J., Sagerström C.G. Dynamic nucleosome organization at hox promoters during zebrafish embryogenesis. PLoS ONE 2013, 8:e63175.
37. Wu S.F., Zhang H., Cairns B.R. Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm. Genome Res. 2011, 21:578-589.
38. Würtele H., Chartrand P. Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology. Chromosome Res. 2006, 14:477-495.
39. Yang Z., Zhu Q., Luo K., Zhou Q. The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription. Nature 2001, 414:317-322.
40. Yang Z., Yik J.H., Chen R., He N., Jang M.K., Ozato K., Zhou Q. Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4. Mol. Cell 2005, 19:535-545.