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J B Dodgson

Publications and source records attributed to J B Dodgson.

At least 55 records · Page 3Linked to original sources
PubMed1987

Structure and expression of the chicken ferritin H-subunit gene.

Although the genomes of many species contain multiple copies of ferritin heavy (H)- and light (L)-chain sequences, the chicken genome contains only a single copy of the H-subunit gene. The primary transcription unit of this gene is 4.6 kilobase pairs and contains four exons which are posttranscriptionally spliced to generate a mature transcript of 869 nucleotides. Chicken and human ferritin H-subunit genomic loci are organized with similar exon-intron boundaries. They exhibit approximately 85% nucleotide identity in coding regions, which yield proteins 93% identical in amino acid sequence. We have identified a sequence of 22 highly conserved nucleotides in the 5' untranslated sequences of chicken, human, and tadpole ferritin H-subunit genes and propose that this conserved sequence may regulate iron-modulated translation of ferritin H-subunit mRNAs.

Amino Acid Sequence↗
PubMed1985

Isolation of recombinant cDNAs encoding chicken erythroid delta-aminolevulinate synthase.

We report the isolation of cDNA clones encoding delta-aminolevulinate synthase (ALA synthase; EC 2.3.1.37), the first enzyme in the heme biosynthetic pathway in animal cells. The gene was isolated from a chicken erythroid cDNA library prepared in the bacteriophage lambda fusion/expression vector gt11, using rabbit antibody raised against the relatively abundant chicken liver enzyme. The chicken liver and red cell ALA synthase isozymes share substantial crossreactivity to the antibody, thereby allowing isolation of the erythroid-specific gene by using the heterologous antibody in immune screening of the red cell cDNA library. Preliminary analysis documenting the tissue specificity of transcription indicates that the enzyme is encoded by a highly homologous set of messages, which appear to differ in size in various avian tissues. From analysis using strand-specific RNA probes, it appears that the different ALA synthase mRNAs detected may be transcribed from a family of genes that are closely related in nucleotide sequence and are each regulated in a developmentally specific manner.

5-Aminolevulinate Synthetase↗
PubMed1985

Replacement variant histone genes contain intervening sequences.

The nucleotide sequences of two chicken histone genes encoding replacement variant H3.3 polypeptides are described. Unlike the replication variant genes of chickens (and almost all other organisms), these genes contain intervening sequences; introns are present in both genes in the 5' noncoding and coding sequences. Furthermore, the replacement variant histone mRNAs are post-transcriptionally polyadenylated. The locations, but not the sizes, of the two introns within the coding segments of the two genes have been exactly conserved, whereas the intron positions in their respective 5' flanking regions differ. Although both H3.3 genes predict the identical histone polypeptide sequence, they are as different from one another as each of them is from a more common replication variant H3.2 gene in silent base substitutions within the coding sequences. Thus, the H3.3 polypeptide sequence has been precisely maintained over a great evolutionary period, suggesting that this class of histones performs a strongly selected biological function. Although replacement variant histones can account for more than 50% of the total H3 protein in the nuclei of specific chicken tissues, the steady-state level of H3.3 mRNA is nearly the same (and is quite low) in all tissues and ages of animals examined. These properties suggest novel mechanisms for the control of the basal histone biosynthesis which takes place outside of the S phase of the cell cycle.

Age Factors↗
PubMed1984

An unusual 5' splice sequence is efficiently utilized in vivo.

The minor adult chicken alpha-globin gene (alpha D) has an intron splicing sequence at the 5' end of the second intron that begins with the dinucleotide G-C rather than the usual G-T. To understand what role this splice sequence plays in the processing and maturation of nuclear RNA to cytoplasmic RNA, we have analyzed the intron processing of the alpha D-globin transcript in both heterologous (monkey) and homologous (chicken) cells using simian virus 40 and retrovirus vectors, respectively. In both cell types, both introns of the alpha D-globin gene are efficiently and precisely removed.

Animals↗
PubMed1984

Isolation and characterization of six different chicken actin genes.

Genes representing six different actin isoforms were isolated from a chicken genomic library. Cloned actin cDNAs as well as tissue-specific mRNAs enriched in different actin species were used as hybridization probes to group individual actin genomic clones by their relative thermal stability. Restriction maps showed that these actin genes were derived from separate and nonoverlapping regions of genomic DNA. Of the six isolated genes, five included sequences from both the 5' and 3' ends of the actin-coding area. Amino acid sequence analysis from both the NH2- and COOH-terminal regions provided for the unequivocal identification of these genes. The striated isoforms were represented by the isolated alpha-skeletal, alpha-cardiac, and alpha-smooth muscle actin genes. The nonmuscle isoforms included the beta-cytoplasmic actin gene and an actin gene fragment which lacked the 5' coding and flanking sequence; presumably, this region of DNA was removed from this gene during construction of the genomic library. Unexpectedly, a third nonmuscle chicken actin gene was found which resembled the amphibian type 5 actin isoform (J. Vandekerckhove, W. W. Franke, and K. Weber, J. Mol. Biol., 152:413-426). This nonmuscle actin type has not been previously detected in warm-blooded vertebrates. We showed that interspersed, repeated DNA sequences closely flanked the alpha-skeletal, alpha-cardiac, beta-, and type 5-like actin genes. The repeated DNA sequences which surround the alpha-skeletal actin-coding regions were not related to repetitious DNA located on the other actin genes. Analysis of genomic DNA blots showed that the chicken actin multigene family was represented by 8 to 10 separate coding loci. The six isolated actin genes corresponded to 7 of 11 genomic EcoRI fragments. Only the alpha-smooth muscle actin gene was shown to be split by an EcoRI site. Thus, in the chicken genome each actin isoform appeared to be encoded by a single gene.

Actins↗
PubMed1983

The nucleotide sequence of the embryonic chicken beta-type globin genes.

The complete nucleotide sequence is reported for both of the embryonic chicken beta-type globin genes, rho and epsilon. These two genes lie at the 5' end and 3' end, respectively, of the four closely linked chicken beta-type globin genes relative to the direction of transcription. Both genes have structures that are typical of functional beta-type globin genes in that they contain two intervening sequences with the 5'-most intron being relatively small (108 base pairs in both) and the 3' intron being large (541 base pairs in rho and 973 base pairs in epsilon). Both embryonic genes contain consensus flanking sequences which are similar to those previously found in the adult chicken beta-globin gene and in a variety of other genes transcribed by RNA polymerase II. The rho- and epsilon-globin gene sequences are very similar from approximately nucleotide -130 (with the mRNA initiation site as +1) to the end of exon II. Noncoding sequences outside this region (e.g. intron II and DNA 5' to -130) are highly divergent. This may indicate that the DNA sequence elements which specifically activate embryonic beta-type globin gene expression in primitive red cells are contained within the -130 to +468 region. Comparison of the overall sequences of rho and epsilon to that of beta strongly supports the hypothesis that the embryonic avian beta-type globin genes diverged from the adult beta-gene by a process separate from that which was responsible for the generation of nonadult mammalian beta-type globin genes.

Amino Acid Sequence↗
PubMed1983

Genomic organization, DNA sequence, and expression of chicken embryonic histone genes.

We have isolated and characterized in detail 15 lambda Charon 4A recombinant bacteriophage containing histone genes from a chicken genomic library. Restriction enzyme-mapping analysis and Southern hybridization to sequenced, homologous histone probes indicate that these genes are not tandemly reiterated within the chicken genome; they usually reside in clusters even though there is no unique array of genes that appears to constitute a typical cluster. Chicken H4 and H1 genes were identified within the genomic recombinants and subsequently sequenced. Extensive regions of homology exist in the 5'- and 3'-flanking regions of the chicken H4 gene when compared to H4 genes from other organisms. In addition to the well documented histone-specific domains, two previously unreported regions of homology lie 5' to this gene: an octanucleotide and a pentanucleotide sequence lying 59 and 116 nucleotides upstream from the H4 gene CAP site, respectively. The H1 gene sequence predicts that the H1 polypeptide is 217 amino acids in length. The 5'-flanking domain of this gene contains, in addition to the transcriptional initiation site and the ATA box, two unusual sequences: one is a nonamer which resides 29 nucleotides upstream from the "ATA" box and is conserved in both the chicken and sea urchin H1 genes, while the other is a GC-rich repetitive sequence element. The majority of the chicken histone genes among the 15 unique lambda recombinant clones are expressed almost exclusively during in ovo development (i.e. from at least 4 days postfertilization up to hatching, about 20-21 days postfertilization) and appear not to be associated with any particular tissue type.

Amino Acid Sequence↗
PubMed1983

The nucleotide sequence of the adult chicken alpha-globin genes.

The complete nucleotide sequence is reported of the two adult chicken alpha-globin genes, alpha A and alpha D. These two genes, expressed in a 3:1 ratio, respectively, in adult red cells, are widely divergent, suggesting that they have evolved separately for several hundred million years. Although the genes are closely linked in the chicken chromosome, the nucleotide sequences determined clearly rule out any recent gene conversion events. As expected, both genes contain two relatively short intervening sequences. The 3' intron of the alpha D gene begins with the dinucleotide GC rather than the typical GT. Extensive flanking sequences are reported for both genes. The chromosomal sequences of the two genes are compared to each other and to sequenced mammalian alpha-globin genes.

Amino Acid Sequence↗
PubMed1983

Analysis of the adult chicken beta-globin gene. Nucleotide sequence of the locus, microheterogeneity at the 5'-end of beta-globin mRNA, and aberrant nuclear RNA species.

We have determined the nucleotide sequence of the adult chicken beta-globin gene locus. The structure of the adult chicken beta-globin gene is, for the most part, analogous to that of mammalian beta-globin genes thus far examined. The gene occupies 1525 nucleotides (nt) from the major cap site to the poly(A) addition site. Introns of 92 and 810 nt interrupt the coding sequence at positions corresponding to amino acid codons 30/31 and 104/105. The regions of most significant homology outside of the transcribed sequence occur within the 5'-untranslated region where the CCAAT and ATA boxes are found -74 and -30 nucleotides from the major chicken beta-globin mRNA CAP site. Using both primer-extension and mung bean nuclease mapping to localize the 5' terminus of the adult beta-globin mRNA within the transcription unit of this gene it was found that 5'-untranslated region is heterogeneous in length with termini 80 and 83 nucleotides from the translational initiation codon. In examining the transcription unit of this gene and the processing of its RNA species during maturation to mRNA, three distinct classes of beta-globin complementary nuclear RNAs are observed. One class of RNA consists of species whose size ranges from 1750 to 900 nt. These RNAs contain all or portions of the introns and are polyadenylated. Although the introns appear to be removed in a multistep fashion, a single kinetic processing pathway is not obvious. An additional processing pathway which leads to the accumulation of stable aberrant RNAs is also observed. This second class of RNA species contains first intron sequences, but lacks portions of the beta-globin coding sequence and thus is too small to become processed to functional mRNA. The third class of beta-globin complementary RNAs appear to migrate during gel electrophoresis at positions equivalent in size to RNAs of greater than gene length (2400-4500 nt), but are probably also never processed into mature mRNA.

Amino Acid Sequence↗
PubMed1983

Unusual structure of the chicken embryonic alpha-globin gene, pi'.

We report the DNA sequence of the globin locus encoding the chicken embryonic alpha-globin, pi'. The structure differs significantly from that of the two chicken adult alpha-globin genes, alpha A and alpha D, as well as from that of previously studied adult alpha-globin genes in that the introns of the pi' gene are substantially larger than those in adult alpha-globin loci. In contrast, the pi' introns are structurally similar to the only other expressed embryonic alpha-globin gene reported to date, the human zeta gene. While completing the sequence of the pi' gene, we determined that only one chromosomal locus within the chicken genome hybridizes to a pi' central exon probe. These data lead to the conclusion that if the equimolar chicken embryonic alpha-globin polypeptides, called pi and pi', are indeed independently transcribed, then that transcription occurs from alleles of the same gene; however, we favor the possibility that the pi gene does not actually exist. This conclusion is drawn from the observation that the two chromosomal alleles of embryonic alpha-globins (represented by recombinant bacteriophage lambda CaG5 and lambda CaG7) both encode pi'.

Alleles↗
PubMed1982

Complete nucleotide sequence of a chicken H2b histone gene.

The complete nucleotide sequence of a chicken H2b histone gene has been determined along with extensive flanking sequence both 5' and 3' from the gene. This H2b gene was isolated on a lambda Charon 4A-chicken DNA recombinant in which it is closely linked to two H3 histone genes. The H2b histone gene predicts a chicken H2b histone protein sequence differing in 5 of 125 amino acids from the sequence of a calf thymus H2b histone. The gene is uninterrupted and is flanked by several consensus sequences seen in many other eucaryotic genes. In particular, unlike many other histone genes it contains a 3'-AATAAA sequence usually associated with genes coding for polyadenylated mRNA.

Amino Acid Sequence↗
PubMed1981

Chromosomal arrangement of the chicken beta-type globin genes.

We have isolated the chicken beta-type globin genes from a library of chicken DNA--lambda Charon 4A recombinant bacteriophage. There are four beta-type genes within this segment of the genome; we believe this represents all of the beta-type genes of the chicken. The recombinant lambda C beta G1 contains the embryonic epsilon- and adult beta-globin genes. The hatching beta H- and embryonic rho-globin genes are found in the recombinant lambda C beta G2. Although lambda C beta G1 and lambda C beta G2 do not physically overlap, we present evidence that all four genes are closely linked and transcribed from the same DNA strand. These experiments demonstrate that the chromosomal regions represented by lambda C beta G1 and lambda C beta G2 lie approximately 1.6 kb apart in the chicken genome. A third recombinant lambda C beta G3 extends the genomic locus studied in the vicinity of the beta-type globin genes to approximately 39 kb. The physical order of the chicken beta-type globin genes within this segment of the chromosome is 5' ... rho--beta H--beta--epsilon ... 3'. This arrangement is unique among the vertebrate beta-type globin gene clusters thus far examined, in that embryonic genes are located at the 5' and 3' ends of the cluster while the hatching and adult genes occupy central positions.

Animals↗
PubMed1981

Adult chicken alpha-globin genes alpha A and alpha D: no anemic shock alpha-globin exists in domestic chickens.

Three alpha-type globin genes have been identified in the alpha-globin linkage group of chickens. No other alpha-type genes hae been directly shown to be within 10 kilobase pairs of any of these three closely linked genes. These three genes have been conclusively identified by DNA sequence analysis. The gene at the 5' end of the linkage group is an embryonic alpha-type globin gene, pi or pi', and the central gene corresponds to the minor adult alpha- globin, alpha D. The 3'-terminal gene sequence corresponds to the sequence of cDNA clones previously described as "alpha S", presumed anemic shock-induced alpha-globin gene [Salser, W. A., Cummings, I., Liu, A., Strommer, J., Padayatty, J. & Clarke, P. (1979) in Cellular and Molecular Regulation of Hemoglobin Switching, eds. Stamatoyannopoulos, G. & Nienheis, A. (Grune and Stratton, New York), pp. 621-643; Richards, R. I. & Wells, J. R. E. (1980) J. Biol. Chem. 255, 9306-9311]. Several groups of workers have isolated alpha S-type cDNA clones but no one has identified a cDNA clone corresponding to the published amino acid sequence of the major chicken alpha-globin, alpha A. We have identified the alpha S-type sequence as the only abundant alpha-like globin sequence in cDNA clones made from reticulocyte mRNA isolated from nonanemic chickens. Therefore, we suggest that the alpha S-type sequence corresponds to the true alpha A-globin species.

Amino Acid Sequence↗
PubMed1981

Histone genes are clustered but not tandemly repeated in the chicken genome.

The recombinant chicken DNA library was screened for histone genes by using pSp17, a recombinant sea urchin DNA probe containing the H2a and H3 genes of Strongylocentrotus purpuratus. Three of the isolated lambda recombinants have been analyzed by restriction enzyme mapping and Southern blotting; one histone H3 gene-encoding recombinant was further analyzed by DNA sequence determination. These studies reveal that the chicken histone genes are not tandemly reiterated, but that, at the least, several histone genes are physically closely linked in a nonrepetitive arrangement within the chicken genome. The evolutionary implications of this arrangement versus that seen in Drosophila and sea urchins is discussed.

Amino Acid Sequence↗
PubMed1980

Analysis of the closely linked adult chicken alpha-globin genes in recombinant DNAs.

Recombinant bacteriophage (from a library of chicken chromosomal DNA fragments inserted into lambda Charon 4A) have been isolated which contain the coding information for both of the adult chicken alpha-globin genes, alpha A and alpha D. One of these recombinant phage also contains an as yet unidentified embryonic alpha-like globin gene sequence. The two adult genes are encoded on the same DNA strand and are separated by approximately 2.4 kilobase pairs, with the arrangement of the genes relative to the direction of transcription being 5'-alpha D-alpha A-3'. Electron microscopic R-loop visualization experiments demonstrate that both alpha-globin genes contain two intervening sequences of similar size in a manner analogous to the structure observed in the mouse alpha-globin gene. The linkage of the two highly divergent chicken adult alpha-globin genes further underscores the principle that chromosomal clustering of families of developmentally related genes may be a general phenomenon in higher eukaryotic gene sequence arrangement.

Animals↗