Positive and negative regulatory elements of the rabbit embryonic eglobin gene revealed by an improved multiple alignment program and functional analysis

The ϵ-globin genes of mammals are expressed in early embryos, but are silenced during fetal and adult erythropoiesis. As a guide to defining the regulatory elements involved in this developmental switch, we have searched the sequences of ϵ-globin genes from different mammals for highly conserved segments. The search was facilitated by the development of a new program, called yama, to generate a multiple alignment of very long sequences using an improved scoring scheme. This allowed us to generate a multiple alignment of sequences from a more divergent group than previously analyzed, as demonstrated here for representatives of four mammalian orders. In parallel experiments, we constructed a series of deletion mutations in the 5′ flank of the rabbit ϵ-globin gene and tested their effect on an ϵ-globin-luciferase hybrid reporter gene. These results show that 121 bp of 5′ flank, containing CACC, CCAAT and ATA motifs, is sufficient for expression in erythroid K562 cells. Both positive and negative cis-acting c...

[1]  S. G. Shapiro,et al.  A 5' control region of the human epsilon-globin gene is sufficient for embryonic specificity in transgenic mice. , 1993, The Journal of biological chemistry.

[2]  R. Hardison,et al.  Nuclear protein-binding sites in a transcriptional control region of the rabbit alpha-globin gene , 1993, Molecular and cellular biology.

[3]  M. Goodman,et al.  The beta globin gene cluster of the prosimian primate Galago crassicaudatus: nucleotide sequence determination of the 41-kb cluster and comparative sequence analyses. , 1992, Genomics.

[4]  G. Kollias,et al.  Position-independent, high-level expression of the human β-globin gene in transgenic mice , 1987, Cell.

[5]  M. Dyer,et al.  Developmental regulation of the human embryonic beta-like globin gene is mediated by synergistic interactions among multiple tissue- and stage-specific elements , 1993, Molecular and cellular biology.

[6]  W. Miller,et al.  Use of long sequence alignments to study the evolution and regulation of mammalian globin gene clusters. , 1993, Molecular biology and evolution.

[7]  M. Gouy,et al.  Molecular phylogeny of Rodentia, Lagomorpha, Primates, Artiodactyla, and Carnivora and molecular clocks. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[8]  R. Raghow,et al.  In vitro methylation of the promoter and enhancer of Pro alpha 1(I) collagen gene leads to its transcriptional inactivation. , 1991, The Journal of biological chemistry.

[9]  A. Bailey,et al.  CACC box and enhancer response of the human embryonic ε globin promoter , 1993 .

[10]  S. Altschul.  Gap costs for multiple sequence alignment. , 1989, Journal of theoretical biology.

[11]  M. Goodman,et al.  Rejection of the "flying primate" hypothesis by phylogenetic evidence from the epsilon-globin gene. , 1992, Science.

[12]  P. Vyas,et al.  Regulation of human embryonic globin genes zeta 2 and epsilon in stably transformed mouse erythroleukemia cells. , 1992, Blood.

[13]  P. Romeo,et al.  GATA and Ets cis-acting sequences mediate megakaryocyte-specific expression , 1993, Molecular and cellular biology.

[14]  Bjoern Peters,et al.  The epsilon-globin gene silencer. Characterization by in vitro transcription. , 1992, The Journal of biological chemistry.

[15]  M. Atchison,et al.  Isolation of a candidate repressor/activator, NF-E1 (YY-1, delta), that binds to the immunoglobulin kappa 3' enhancer and the immunoglobulin heavy-chain mu E1 site. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[16]  R. Perry,et al.  Delta, a transcription factor that binds to downstream elements in several polymerase II promoters, is a functionally versatile zinc finger protein. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[17]  G. Lanyon,et al.  Multiple origins of transcription in the 4.5 Kb upstream of the ϵ-globin gene , 1983, Cell.

[18]  Webb Miller,et al.  A space-efficient algorithm for local similarities , 1990, Comput. Appl. Biosci..

[19]  P. Powers,et al.  Nucleotide sequence of 16-kilobase pairs of DNA 5' to the human epsilon-globin gene. , 1985, The Journal of biological chemistry.

[20]  G. Stamatoyannopoulos,et al.  Demonstration of a human epsilon-globin gene silencer with studies in transgenic mice. , 1992, Blood.

[21]  M. Goodman,et al.  Embryonic ε and γ globin genes of a prosimian primate (Galago crassicaudatus): Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints , 1988 .

[22]  C. Hutchison,et al.  Nucleotide sequence of the BALB/c mouse β-globin complex , 1989 .

[23]  J. Rine,et al.  Two DNA-binding factors recognize specific sequences at silencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae , 1988, Molecular and cellular biology.

[24]  P. Bushel,et al.  Negative regulation of the human epsilon-globin gene by transcriptional interference: role of an Alu repetitive element , 1990, Molecular and cellular biology.

[25]  D. Tuan,et al.  The "beta-like-globin" gene domain in human erythroid cells. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Yang Shi,et al.  Transcriptional repression by YY1, a human GLI-Krüippel-related protein, and relief of repression by adenovirus E1A protein , 1991, Cell.

[27]  A. Schechter,et al.  Activation of the human ε- and β-globin promoters by SV40 T antigen , 1989 .

[28]  N. Proudfoot,et al.  Distinct negative regulation of the human embryonic globin genes zeta and epsilon. , 1993, Gene expression.

[29]  R. Hardison.  Comparison of the beta-like globin gene families of rabbits and humans indicates that the gene cluster 5'-epsilon-gamma-delta-beta-3' predates the mammalian radiation. , 1984, Molecular biology and evolution.

[30]  T. Ley,et al.  Structure and function of the murine β-globin locus control region 5′ HS-3 , 1992 .

[31]  C. Y. Yu,et al.  The CACC box upstream of human embryonic epsilon globin gene binds Sp1 and is a functional promoter element in vitro and in vivo. , 1991, The Journal of biological chemistry.

[32]  R. Hardison,et al.  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 , 1989 .

[33]  M. Goodman,et al.  Phylogenetic footprinting reveals unexpected complexity in trans factor binding upstream from the epsilon-globin gene. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[34]  A. Schechter,et al.  Binding of erythroid and non-erythroid nuclear proteins to the silencer of the human ε-globin-encoding gene , 1992 .

[35]  Webb Miller,et al.  Comparative analysis of the locus control region of the rabbit β-like globin gene cluster: HS3 increases transient expression of an embryonic ε-globin gene , 1993 .

[36]  E. Schon,et al.  Sequence and linkage of the goat εI and εII β-globin genes* , 1983 .

[37]  A. Schechter,et al.  Identification of a transcriptional silencer in the 5'-flanking region of the human epsilon-globin gene. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[38]  A. Dean,et al.  Transcriptional role of a conserved GATA-1 site in the human epsilon-globin gene promoter , 1991, Molecular and cellular biology.

[39]  J. Diffley,et al.  Protein-DNA interactions in the epsilon-globin gene silencer. , 1993, The Journal of biological chemistry.

[40]  A. Dean,et al.  Enhancer-dependent transcription of the epsilon-globin promoter requires promoter-bound GATA-1 and enhancer-bound AP-1/NF-E2 , 1993, Molecular and cellular biology.

[41]  T A Gray,et al.  Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes , 1992, Molecular and cellular biology.

[42]  C. Shoulders,et al.  The primary structure of the human ϵ-globin gene , 1980, Cell.

[43]  R. Hardison.  The nucleotide sequence of the rabbit embryonic globin gene beta 4. , 1983, The Journal of biological chemistry.