Spatial configuration of the chicken α-globin gene domain: Immature and active chromatin hubs

Nucleic Acids Research

Volumn 36, Issue 14, 2008, Pages 4629-4640

  Gavrilov, Alexey A ^a   Razin, Sergey V ^a  

^a INSTITUTE OF GENE BIOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA GLOBIN; DEOXYRIBONUCLEASE I; DNA;

ALPHA CHAIN; ANIMAL CELL; ANIMAL CELL CULTURE; ARTICLE; CELL PROLIFERATION; CHICKEN; CHROMATIN; CONTROLLED STUDY; CPG ISLAND; DNA CONFORMATION; DNA CROSS LINKING; EMBRYO; ERYTHROBLAST; GENE EXPRESSION; GENE INTERACTION; GENE PROBE; GENE STRUCTURE; GENETIC TRANSCRIPTION; LYMPHOID CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; REAL TIME POLYMERASE CHAIN REACTION; REGULATORY SEQUENCE; RESTRICTION FRAGMENT;

ANIMALS; BACTERIAL PROTEINS; CELL DIFFERENTIATION; CELL LINE; CELL LINE, TRANSFORMED; CHICK EMBRYO; CHICKENS; CHROMATIN; CPG ISLANDS; DEOXYRIBONUCLEASE BAMHI; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; ENHANCER ELEMENTS (GENETICS); ERYTHROBLASTS; ERYTHROCYTES; GLOBINS; LOCUS CONTROL REGION; LYMPHOCYTES; MODELS, GENETIC; POLYMERASE CHAIN REACTION; PROMOTER REGIONS (GENETICS); REGULATORY ELEMENTS, TRANSCRIPTIONAL; RESTRICTION MAPPING; TRANSCRIPTION, GENETIC;

EID: 49249099730     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn429     Document Type: Article

References (43)

1. Higgs,D.R., Vernimmen,D., De Gobbi,M., Anguita,E., Hughes,J., Buckle,V., Iborra,F., Garrick,D. and Wood,W.G. (2006) How transcriptional and epigenetic programmes are played out on an individual mammalian gene cluster during lineage commitment and differentiation. Biochem. Soc. Symp., 73, 11-22.
2. Recillas-Targa,F. and Razin,S.V. (2001) Chromatin domains and regulation of gene expression: Familiar and enigmatic clusters of chicken globin genes. Crit. Rev. Eukaryot. Gene Expr., 11, 227-242.
3. Razin,S.V. and Ioudinkova,E.S. (2007) Mechanisms controlling activation of the alpha-globin gene domain in chicken erythroid cells. Biochemistry (Mosc), 72, 467-470.
4. Flint,J., Tufarelli,C., Peden,J., Clark,K., Daniels,R.J., Hardison,R., Miller,W., Philipsen,S., Tan-Un,K.C., McMorrow,T. et al. (2001) Comparative genome analysis delimits a chromosomal domain and identifies key regulatory elements in the alpha globin cluster. Hum. Mol. Genet. 10, 371-382.
5. Razin,S.V., Ioudinkova,E.S. and Scherrer,K. (2000) Extensive methylation of a part of the CpG island located 3.0-4.5 Kbp upstream to the chicken alpha-globin gene cluster may contribute to silencing the globin genes in non-erythroid cells. J. Mol. Biol., 209, 845-852.
6. Razin,S.V., Shen,K., Ioudinkova,E. and Scherrer,K. (1999) Functional analysis of DNA sequences located within a cluster of DNase I hypersensitive sites colocalising with MAR element at the upstream border of the chicken a-globin gene domain. J. Cell Biochem., 74, 38-49.
7. Vyas,P., Vickers,M.A., Picketts,D.J. and Higgs,D.R. (1995) Conservation of position and sequence of a novel, widely expressed gene containing the major human alpha-globin regulatory element. Genomics, 29 679-689.
8. Knezetic,J. and Felsenfeld,G. (1980) Identification and characterization of a chicken α-globin enhancer. Mol. Cell Biol., 9, 893-901.
9. Tolhuis,B., Palstra,R.J., Splinter,E., Grosveld,F. and de Laat,W. (2002) Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol. Cell, 10, 1453-1465.
10. Vakoc,C.R., Letting,D.L., Gheldof,N., Sawado,T., Bender,M.A., Groudine,M., Weiss,M.J., Dekker,J. and Blobel,G.A. (2005) Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Mol. Cell, 17, 453-462.
11. Gribnau,J., de Boer,E., Trimborn,T., Wijgerde,M., Milot,E., Grosveld,F. and Fraser,P. (1998) Chromatin interaction mechanism of transcriptional control in vivo. EMBO J., 17, 6020-6027.
12. Wijgerde,M., Grosveld,F. and Fraser,P., (1995) Transcription complex stability and chromatin dynamics in vivo. Nature, 377, 209-213.
13. de Laat,W. and Grosveld,F. (2003) Spatial organization of gene expression: The active chromatin hub. Chromosome Res., 11, 447-459.
14. Kooren,J., Palstra,R.J., Klous,P., Splinter,E., von Lindern,M., Grosveld,F. and de Laat,W. (2007) Beta-globin active chromatin Hub formation in differentiating erythroid cells and in p45 NF-E2 knock-out mice. J. Biol. Chem., 282, 16544-16552.
15. Patrinos,G.P., de Krom,M., de Boer,E., Langeveld,A., Imam,A.M., Strouboulis,J., de Laat,W. and Grosveld,F.G. (2004) Multiple interactions between regulatory regions are required to stabilize an active chromatin hub. Genes Dev., 18, 1495-1509.
16. Zhou,G.L., Xin,L., Song,W., Di,L.J., Liu,G., Wu,X.S., Liu,D.P. and Liang,C.C. (2006) Active chromatin hub of the mouse alpha-globin locus forms in a transcription factory of clustered housekeeping genes. Mol. Cell Biol., 26, 5096-5105.
17. Klochkov,D., Rincon-Arano,H., Ioudinkova,E.S., Valadez-Graham,V., Gavrilov,A., Recillas-Targa,F. and Razin,S.V. (2006) A CTCF-dependent silencer located in the differentially methylated area may regulate expression of a housekeeping gene overlapping a tissue-specific gene domain. Mol. Cell Biol., 26, 1589-1597.
18. De Moura Gallo,C.V., Vassetzky,Y.S., Huesca,M. and Scherrer,K. (1992) A transcription-dependent DNase I-hypersensitive site in a far upstream segment of the chicken α-globin gene domain coincides with a matrix attachment region. Biochem. Biophys. Res. Commun., 184, 1181-1189.
19. Razin.S.V., De Moura Gallo,C.V. and Scherrer,K. (1994) Characterization ofthe chromatin structure in the upstream area of the chicken α-globin gene domain. Mol. Gen. Genet., 242. 649-652.
20. Valadez-Graham,V., Razin,S.V. and Recillas-Targa,F. (2004) CTCF-dependent enhancer blockers at the upstream region of the chicken alpha-globin gene domain. Nucleic Acids Res., 32. 1354-1362.
21. Dekker.J., Rippe,K., Dekker.M. and Kleckner.N. (2002) Capturing chromosome conformation. Science. 295, 1306-1311.
22. Liu,Z. and Garrard,W.T. (2005) Long-range interactions between three transcriptional enhancers, active Vkappa gene promoters, and a 3' boundary sequence spanning 46 kilobases. Mol. Cell Biol., 25 3220-3231.
23. Beug,H., Doederlein.G., Freudenstrein,C. and Graf,T. (1979) Erythroblast cell lines transformed by a temperature sensitive mutant of avian crythroblastosis virus. A model system to study erythroid differentiation in vitro. J. Cell Physiol., 1, 195-207.
24. Beug,H., Von Kirchbach,A., Doderlin,J., Conscience,J.F. and Graf,T. (1979) Chicken hematopoietic cells transformed by seven strains of defective avian leukemia viruses display three distinct phenotypes of differentiation. Cell, 18, 375-390.
25. Nicolas,R.H., Partington,G., Major,G.N., Smith,B., Carne,A.F., Huskissom,N. and Goodwin,G. (1991) Induction of differentiation of avian crythroblastosis virus-transformed crythroblasts by the protein kinase inhibitor H7: Analysis of the transcription factor EF1. Cell Growth Differ., 2, 129-135.
26. Rowley,P.T., Ohlsson-Wilhelm,B.M. and Farley,B.A. (1985) K562 human crythroleukemia cells demonstrate commitment. Blood, 65, 862-868.
27. Splinter,E., Grosveld,F. and de Laat,W. (2004) 3C technology: Analyzing the spatial organization of genomic loci in vivo. Methods Enzymol. 375, 493-507.
28. Razin,S.V., Rynditch,A., Borunova,V., Ioudinkova,E., Smalko,V. and Scherrer,K. (2004) The 33kb transcript of the chicken alpha-globin gene domain is part of the nuclear matrix. J. Cell Biochem., 92, 445-457.
29. Weintraub,H., Larsen,A. and Groudine,M. (1981) Alpha-Globin-gene switching during the development of chicken embryos: Expression and chromosome structure. Cell, 24, 333-344.
30. Bruns,G.A. and Ingram,V.M. (1973) Erythropoiesis in the developing chick embryo. Dev. Biol., 30, 455-459.
31. Singal,R., van Wert,J.M. and Ferdinand,L. Jr (2002) Methylation of alpha-type embryonic globin gene alpha pi represses transcription in primary erythroid cells. Blood, 100, 4217-4222.
32. Vernimmen,D., De Gobbi,M., Sloane-Stanley,J.A., Wood,W.G. and Higgs,D.R. (2007) Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. EMBO J., 26, 2041-2051.
33. Splinter E., Heath,H., Kooren,J., Palstra,R.J., Klous,P., Grosveld,F., Galjart,N. and de Laat,W. (2006) CTCF mediates long-range chromatin looping and local historic modification in the beta-globin locus. Genes Dev., 20, 2349-2354.
34. Hagege,H., Klous,P.. Braem,C., Splinter,E., Dekker,J., Cathala,G., de Laat,W. and Forne,T. (2007) Quantitative analysis of chromosome conformation capture assays (3C-qFCR). Nat. Protoc. 2, 1722-1733.
35. Wurtele,H. and Chartrand,P. (2006) Genome-wide scanning of 'HoxBl-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology. Chromosome Res., 14, 477-495.
36. Razin,S.V., Kekelidze,M.G., Lukanidin,E.M.. Scherrer,K. and Georhiev,G.P. (1996) Replication origin are attached to the nuclear skeleton. Nucleic Acids Res., 14, 8189-8207.
37. Verbovaia,L. and Razin,S.V. (1995) Analysis of the replication direction through the domain of a-globin-encoding genes. Gene, 166, 255-259.
38. Tufarelli,C., Hardison,R., Miller,W., Hughes,J., Clark,K., Ventress,N., Frischauf,A.M. and Higgs,D.R. (2004) Comparative analysis of the alpha-like globin clusters in mouse, rat, and human chromosomes indicates a mechanism underlying breaks in conserved synteny. Genome Res., 14, 623-630.
39. Hughes,J.R., Cheng,J.F., Ventress,N., Prabhakar,S., Clark,K., Anguita,E., De Gobbi,M., de Jong,P., Rubin,E. and Higgs,D.R. (2005) Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences. Proc. Natl Acad. Sci. USA, 102, 9830-9835.
40. Brown,J.L. and Ingram,V.M. (1974) Structural studies on chick embryonic hemoglobins. J. Biol. Chem., 249, 3960-3972.
41. Palstra,R.J., Tolhuis,B., Splinter,E., Nijmeijer,R., Grosveld,F. and de Laat,W. (2003) The beta-globin nuclear compartment, in development and erythroid differentiation. Nat. Genet., 35, 190-194.
42. Dodgson,J.B. and Engel,J.D. (1983) The nucleotide sequence of the adult chicken α-globin genes. J. Biol. Chem., 258, 4623-4629.
43. D globin region. Nucleic Acids Res., 19, 5321-5329.