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D J Mathis

Publications and source records attributed to D J Mathis.

15 recordsLinked to original sources
PubMed1991

NF-X, a transcription factor implicated in MHC class II gene regulation.

The X box has been shown in several assay systems to be a critical element of MHC class II gene promoters. Several X box-binding activities have been discovered in nuclear extracts from a variety of cell lines. The critical question is: which of these are responsible for mediating X box function? This report provides a further characterization of NF-X, a highly specific X box-binding activity we described previously. The cell-type distribution, structural features, and binding site characteristics of NF-X are analyzed in detail, to facilitate comparison with other reported activities. Most importantly, the functional relevance of NF-X is assessed by scanning mutagenesis, and the results indicate that this complex is indeed involved in regulating MHC class II gene expression. With these data in mind, the relationship between NF-X and RF-X, an X box-binding activity reported to be absent in patients with severe combined immunodeficiency, is discussed.

Animals↗
PubMed1985

Inbred and wild mice carry identical deletions in their E alpha MHC genes.

Several inbred strains and a certain percentage of wild mice bear a deletion in the E alpha gene of the mouse major histocompatibility complex (H-2). This mutation prevents transcription of the E alpha gene and hence functional expression of the E alpha E beta dimer on the cell surface. Two strains were selected for a more precise localization of this deletion. BALB.B is a congenic line carrying the H-2b haplotype on the BALB/c background. CRO435 is an outbred stock derived from a wild mouse captured near Cairo, Egypt; it carries the H-2w37 haplotype including a null Ew28 alpha allele, as well as semi-lethal mutations in the H-2 linked t complex (tTuw7). From these two strains, we have isolated genomic clones that contain fragments spanning the E alpha deletion, and have sequenced the breakpoint region. The deletions in the two strains are identical, spanning 627 bp which include the promoter region and the signal peptide exon of the E alpha gene. Limited sequence comparison suggests that the Eb alpha allele of BALB.B is more closely related to the Ew28 alpha allele of CRO435 than both of these are to an E alpha-expressor allele, Ed alpha. It is therefore likely that the Eo deletions in the various inbred strains and wild mice are of the same origin, and we propose that they have been disseminated throughout the mouse population because of linkage to the t complex.

Animals↗
PubMed1984

Structure, regulatory polymorphisms, and allelic hypervariability regions in murine I-A alpha.

Class II major histocompatibility complex (MHC) molecules, the Ia antigens, are intimately involved in regulating the intensity and specificity of the cellular and humoral responses to T cell-dependent antigens. One approach to understanding the mechanism of this regulation is to analyze the structure and allelic polymorphism of Ia molecules. In addition there are regulatory polymorphisms in the expression of the I-E alpha and I-E beta class II MHC polypeptide chains. Analysis of the cDNA sequence indicates that I-A and I-E alpha chains are similar with short stretches of homology and other regions of nonhomology. Analysis of Northern blots of mRNA indicates that at least three separate types of regulatory polymorphisms result in failure of expression of I-E alpha. Comparison of allelic sequences of six alleles of the I-A alpha chain shows that almost all of the allelic polymorphism is in the first domain and that within the first domain it is clustered in three allelic hypervariable regions within the first domain of I-A alpha. The structural and functional implications of these findings are discussed.

Alleles↗
PubMed1983

The murine E alpha immune response gene.

We have isolated and sequenced cDNA and genomic clones of the murine E alpha gene, one of the immune response genes of the major histocompatibility complex. Comparison of our data with those recently reported for the human homolog DR alpha shows an identical intron-exon structure, and a good conservation of the protein-coding sequences, including the amino acids potentially involved in organizing the second external protein domain into an immunoglobulin-like fold. Noncoding sequences are less conserved, with the exception of the promoter region. Finally, we show that differential expression of the gene in various cell types appears to be transcriptionally regulated, and that genomic rearrangements do not seem necessary for expression.

Amino Acid Sequence↗
PubMed1983

Regions of allelic hypervariability in the murine A alpha immune response gene.

The murine Ia antigens, a group of cell surface glycoproteins, are involved in the control of the immune response. The structure of one of these class II major histocompatibility complex molecules, A alpha, was recently deduced from sequence analysis of a cDNA clone produced from k haplotype mice. We have now isolated and sequenced A alpha cDNA clones from five other mouse haplotypes: d, b, f, u, and q. Sequence comparison revealed a surprisingly high degree of allelic polymorphism. Interestingly, amino acid substitutions were clustered within the first external domain of this polypeptide chain, particularly at a few highly variable positions. Functional implications of A alpha polymorphism and possible mechanisms for its generation are discussed.

Alleles↗
PubMed1983

Several mechanisms can account for defective E alpha gene expression in different mouse haplotypes.

The murine Ia antigens, encoded by the I region of the major histocompatibility complex, are cell-surface glyco-proteins (consisting of alpha and beta polypeptides) thought to be involved in the control of immune responsiveness. Mice of haplotypes b, s, q, and f fail to express one of the Ia antigen complexes, the E complex, on the cell surface. We have attempted to determine at the molecular level how such a defect (or defects) might be generated. By using I-region E alpha and A alpha gene probes for analyses of RNA and DNA structure, it was possible to conclude that at least three mechanisms can operate. Mice of haplotypes b and s bear a deletion in the E alpha gene, f haplotype mice synthesize predominantly an E alpha mRNA of aberrant size, and mice of the q haplotype seem to have a defect in RNA processing or a problem with mRNA stability, or both.

Animals↗
PubMed1983

The murine Ia alpha chains, E alpha and A alpha, show a surprising degree of sequence homology.

The I region of the murine major histocompatibility complex codes for a group of glycoproteins, the Ia antigens, thought to be involved in the control of immune responsiveness. Each Ia antigen complex contains a "heavy chain," a "light chain," and the "invariant chain." We describe here the isolation and characterization of genomic and cDNA clones for one of the heavy chains, Ak alpha. The complete nucleotide sequence of the cDNA clone is presented, and the predicted amino acid sequence is compared with that of another alpha chain, Ek alpha. About 50% of the amino acids are identical, a finding somewhat unexpected on the basis of preliminary protein sequence data.

Amino Acid Sequence↗
PubMed1981

Specific in vitro initiation of transcription on the adenovirus type 2 early and late EII transcription units.

Three transcription units are present in the adenovirus type 2 region EII. Transcription units EIIaE and EIIaL encode the mRNA for the 72,000-dalton DNA binding protein, early and late in the lytic cycle, respectively, and transcription unit EIIb encodes the mRNA for the protein that binds to the 5' termini of adenovirus DNA. By using a cell-free transcription system in the presence of purified RNA polymerase B (or II), we have obtained specific initiation of transcription from both the EIIaE promoter, which does not contain a T-A-T-A box, and the EIIaL promoter, which does. In addition, we have identified a new EII T-A-T-A box promoter that is located close to the early non-T-A-T-A box promoter and is used both in vivo and in vitro.

Adenoviruses, Human↗
PubMed1980

HMG proteins (1 + 2) form beaded structures when complexed with closed circular DNA.

Structures bearing a resemblance to nucleosomes can be assembled by incubating calf thymus High Mobility Group proteins (1 + 2) with closed circular DNA. These HMG proteins are capable of forming beads and inducing superhelicity when bound to DNA. However, they do not protect from nuclease digestion the discrete DNA fragments characteristic of nucleosomes. The relationship between HMGs (1 + 2) and the "primitive" histone-like DNA-packaging proteins from prokaryotes and mitochondria is discussed.

Animals↗
PubMed1978

Effect of histone acetylation on structure and in vitro transcription of chromatin.

n-Butyrate treatment of growing Hela cells produces a dramatic increase in the levels of histone acetylation. We have exploited this system to study the effect of histone acetylation on chromatin structure. Chromatin containing highly acetylated histones is more rapidly digested to acid-soluble material by DNase I, but not by micrococcal nuclease. The same pattern of nuclease sensitivity was exhibited by in vitro-assembled chromatin consisting of SV40 DNA Form I and the 2 M salt-extracted core histones from butyrate-treated cells. Using this very defined system, it was possible to demonstrate that acetylated nucleosomes do not have a greatly diminished stability. Stability was measured in terms of exhange of histone cores onto competing naked DNA or sliding of histone cores along ligated naked DNA. Finally, it was shown that acetylated nucleosomes are efficient inhibitors of in vitro RNA synthesis by the E. coli holoenzyme as well as by the mammalian polymerases A and B.

Acetylation↗
PubMed1976

Subunit structure of rDNA-containing chromatin.

Recent studies indicate that chromatin has a repeating subunit structure. In an attempt to relate this organization to chromatin's role in selective gene transcription we have begun to examine the subunit structure of a specific gene. Tetrahymena pyriformis preferentially replicates the genes coding for rRNA (rDNA) during refeeding after prolonged starvation. By prelabeling cultures during exponential growth with [14C]thymidine and pulse-labeling during refeeding with [3H]thymidine, we have been able to differentially label bulk chromatin and rDNA-containing chromatin. Nuclei which contained at least 78% of their 3H label in rDNA were digested with staphylococcal nuclease, and the DNA digestion products analyzed on agarose gels. Both the kinetics of digestion and the digestion products were similar for 14C- and 3H-labeled chromatin. In order to monitor protein exchange, digestions were also performed on partially purified rDNA-containing chromatin or free rDNA in the presence of nuclei. While the chromatin had a digestion pattern like nuclei, the rDNA was afforded no protection from digestion. Our conclusion is that the chromatin containing rDNA (a repeated, extrachromosomal gene in Tetrahymena) exhibits a particulate structure very similar to that of bulk chromatin. This organization does not exist in free rDNA and is not the result of protein exchange during the nuclease digestion.

Animals↗
PubMedDate not supplied

Induction of altered chromatin structures by simian virus 40 enhancer and promoter elements.

Two simian virus 40 transcriptional promoter elements, the 72-base pair (bp) repeat and the 21-bp repeat region, induce chromatin structures of increased DNase I sensitivity when transposed elsewhere in the viral genome. The induction of a sufficiently long stretch of DNase I-sensitive chromatin leads to the appearance of a visible nucleosome-free region.

Chromatin↗