Preparation and application of immunological probes for nucleosomes.
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Animals↗
Biomedical subjects
M Bustin
Publications and source records attributed to M Bustin.
Mouse non-histone chromosomal protein HMG-17 cDNA sequence.
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Amino Acid Sequence↗
Cloning of the chicken chromosomal protein HMG-14 cDNA reveals a unique protein with a conserved DNA binding domain.
The isolation and sequencing of a cDNA clone coding for the entire sequence of chicken chromosomal protein HMG-14 is described. The open reading frame constitutes only 25% of the transcript; the 5'-untranslated region is extremely rich in GC residues; and the 3'-untranslated region is highly enriched in AT residues. Comparison with other cDNAs coding for HMG-14 and HMG-17 reveals that the transcripts of genes coding for this family of chromosomal proteins have a characteristic structure. The deduced amino acid sequence is unique and different from all other known HMG-14 and -17 sequences. Analysis of amino acid position identity between the chicken HMG-14 and other HMG-14/-17 proteins revealed that the protein has 37% similarity to the HMG-17 group and 69% similarity to the HMG-14 group; therefore, the protein is classified as belonging to the HMG-14 group. Additional analysis leads to the conclusion that the chicken cDNA described here codes for the true homolog of calf and human HMG-14 protein. Comparison of all the known HMG-14 sequences reveals the DNA binding domain is conserved and contains the invariant dodecapeptide PKRRSARLSAKP. The HMG-14 proteins have a distinct charge distribution along the polypeptide chain: while the central region is positively charged the C-terminal domain is negatively charged.
Animals↗
Single copy gene for the chicken non-histone chromosomal protein HMG-17.
A chicken genomic library was screened with the human cDNA encoding the non-histone chromosomal protein HMG-17 and a 4565-base pair fragment containing the entire gene encoding this protein was isolated and characterized. Sequence analysis of the fragment revealed that from the start to end of transcription, the HMG-17 gene is 3293 base pairs long and is comprised of 6 exons ranging in size from 30 to 890 base pairs. Upstream of the putative cap site are both a CAAT box and a TATA box as well as several Sp1 binding sites. The gene has an extremely high content of G and C residues (75%) in a 1150-base pair fragment starting 500 base pairs from the putative cap site. This region satisfies the definition of an HpaII tiny fragment island. Southern analysis indicated that there is a single copy of this gene in chickens, whereas Northern analysis revealed that a single transcript is being synthesized from this gene. A comparison of the chicken and human cDNA and protein sequences and subsequent calculation of the evolutionary rates indicated that HMG-17 is a slowly evolving gene. The present article, which is the first study on the isolation and characterization of a complete gene coding for a high mobility group non-histone protein, indicates that the gene has features characteristic of housekeeping genes.
Amino Acid Sequence↗
Immunopurification of the suppressor tRNA dependent rabbit beta-globin readthrough protein.
In mammalian cells, the rabbit beta-globin readthrough protein is the only known example of a naturally occurring readthrough protein which does not involve a viral system. To provide an efficient means for its isolation, detection, and study, we elicited specific antibodies against this unique protein. The 22 amino acid peptide corresponding to the readthrough portion of this protein was synthesized, coupled to keyhole limpet hemocyanin, and injected into sheep. Specific antibodies to the peptide were produced as demonstrated by the enzyme-linked immunosorbent assay technique and by immunoblotting. The antibodies did not react with globin. The rabbit beta-globin readthrough protein was separated from globin and other reticulocyte proteins by polyacrylamide gel electrophoresis and visualized by silver staining or by labeling with [35S]methionine. Incorporation of [35S]methionine into the readthrough protein was significantly enhanced upon addition of an opal suppressor tRNA to reticulocyte lysates. Immunoblotting revealed that the readthrough protein also occurs in lysates without added suppressor tRNA. The antibodies were purified on an affi-gel column which had been coupled with the peptide antigen. The readthrough protein was then purified from reticulocytes by immunoaffinity chromatography and by high-performance liquid chromatography. The results provide conclusive evidence that the beta-globin readthrough protein is naturally occurring in rabbit reticulocytes.
Amino Acid Sequence↗
Retropseudogenes for human chromosomal protein HMG-17.
The human genome contains multiple copies of sequences homologous to the cDNA coding for non-histone chromosomal protein HMG-17. To study the mechanism of generation and dispersion of the HMG-17 multigene family a human genomic library was screened and 70 clones isolated and studied by Southern transfer and restriction site analysis. The results suggest that most of the clones contain unique sequences. Sequence analysis of two genomic clones indicates that they contain elements typical of processed retropseudogenes. Even though both sequences contained open reading frames the sequences lacked introns, were flanked by short, direct repeats and lacked elements associated with functional genes. The sequences of the two pseudogenes were 85% homologous to each other and each was 90% homologous to the human cDNA. Based on the sequence difference in the open reading frame between the pseudogenes and the cDNA it can be estimated that the sequences arose approximately ten million years ago from a common precursor. The present paper, which is the first study on genes coding for this nucleosomal binding protein, indicates that the HMG-17 multigene family is the largest known human retropseudogene family.
Base Sequence↗
Chicken non-histone chromosomal protein HMG-17 cDNA sequence.
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Amino Acid Sequence↗
Modulation of the cellular ratio of chromosomal high mobility group proteins 14 to 17 in transfected cells.
The cDNAs coding for human nonhistone chromosomal high mobility group (HMG) proteins 14 and 17 have been introduced into the eukaryotic expression vector pSVL under the transcriptional control of the SV40 late promoter and the constructs used to transfect COS cells. Transfection with plasmid pSVL14s, containing the HMG-14 cDNA in the sense orientation, increased the endogenous levels of HMG-14 mRNA 50-fold and the levels of HMG-14 protein 3-fold. Transfection with pSVL17s, which contains the HMG-17 mRNA in the sense orientation, resulted in a 19-fold increase in mRNA levels and a 3-fold increase in the protein level. Transfection with pSVL17as, containing the HMG-17 in the antisense orientation, resulted in a noticeable decrease in the protein levels. The overproduction of HMG mRNAs does not affect the level of other cellular mRNAs and the increase in the cellular level of either HMG-14 or -17 did not affect the level of the other HMG or that of any other cellular protein examined. The results suggest that COS cells can tolerate large excess of HMG mRNAs and protein, that the relative amounts of HMG-14 and HMG-17 and their mRNAs are not constant, and that neither the transcription nor the translation of the proteins is coordinately regulated.
Animals↗
Cell cycle regulated synthesis of an abundant transcript for human chromosomal protein HMG-17.
The abundance and cell cycle dependent expression of the mRNA for human nonhistone protein HMG-17 were studied in synchronized HeLa cells. Slot blot analysis indicates that the HMG-17 mRNA is a very abundant message, significantly more so than histone or actin mRNA. RNA prepared from tissue culture cells contains higher amounts of HMG-17 transcripts than RNA prepared from liver suggesting a correlation between the rate of cell division and HMG-17 mRNA levels. HMG-17 mRNA is present in the cells throughout the cell cycle however there is a significant increase in the mRNA levels late in S phase suggesting that the protein is deposited on chromatin after nucleosome assembly. Synthesis of the HMG-17 transcript is not coupled to DNA replication suggesting that the cell cycle related expression during late S phase is regulated in a different manner from that of the nucleosomal histones.
Cell Cycle↗
Immunochemical analysis of the structure and function of chromosomal proteins.
Immunochemical approaches are useful in studying the nuclear organization and cellular function of chromosomal components. Antibodies specific to histones and to defined nonhistone proteins have been used to study nucleosome heterogeneity, to visualize the presence of histone in transcriptionally active chromatin, and to isolate DNA sequences associated with specific chromosomal proteins.
Animals↗
Chromosomal protein HMG-14. Complete human cDNA sequence and evidence for a multigene family.
The isolation and sequencing of cDNA clone coding for the entire sequence of human nonhistone chromosomal protein HMG-14 is described. Sequence analysis reveals that the open reading frame constitutes only 25% of the transcript, that the 5'-untranslated region is extremely rich in GC residues (75%), and that the 3'-untranslated region is highly enriched in AT residues. The amino acid sequence, deduced from the reading frame, is 94% homologous to the calf thymus protein suggesting evolutionary constraints on the conformation of the protein. The human genome contains 60-90 HMG-14 gene copy equivalents which, as suggested by Southern analysis, are not tandemly arranged. Northern analysis of RNA isolated from several sources reveals that a single-sized mRNA codes for this protein. Southern analysis reveals that cross-hybridizing sequences are present in the genome of several different species indicating that the evolutionary origin of this gene was over 350 million years ago. The overall features of the human HMG-14 cDNA are very similar to those of the human HMG-17 cDNA, and the number of gene equivalents present in the human genome is similar for the two proteins. However, their nucleotide sequence is significantly different indicating that the multigene family coding for HMG-14 is distinct from that coding for HMG-17.
Base Sequence↗
Chromosomal proteins HMG-14 and HMG-17. Distinct multigene families coding for similar types of transcripts.
Human nonhistone chromosomal proteins HMG-14 and HMG-17 are encoded by genes which are part of multigene families. Southern analysis of human, mouse, and rat genomic restriction digests reveals that the two families are distinct. Although the cDNAs of HMG-14 and HMG-17 do not cross-hybridize, they have several similar structural features: the open reading frame comprises only 23% of the transcripts, the 5'-untranslated region is extremely GC rich whereas the 3'-untranslated region is unusually long and AT rich. The overall sequence homology between the two transcripts is highest (71%) in the 90 nucleotides coding for the DNA-binding domains of the proteins. The sequence of the human HMG-14 and HMG-17 proteins, deduced from the open reading frame, differs by more than 50%; the DNA-binding domains of the proteins show 74% sequence homology. However, even in this 30-residue long peptide there are significant differences between the proteins as the proline content of HMG-17 (8 residues) is twice that of HMG-14. The two proteins have different hydropathy index profiles and are serologically distinct. The multigene families may have evolved independently from similar genetic elements or from a shared ancestral gene in which the nucleotide sequence coding for the DNA-binding domain of the protein is the most conserved region. The structural differences between the molecules and the differences in their DNA-binding domains suggest that the proteins may be involved in distinguishable cellular functions.
Amino Acid Sequence↗
Chromatin structure of the cytochrome P-450c gene changes following induction.
The chromatin structure of cytochrome P-450c and P-450d genes, which in the liver are highly inducible by 3-methylcholanthrene, was studied in normal and carcinogen-treated rats by using a cDNA probe specific for P-450c and a genomic probe that recognizes both genes. Digestion with micrococcal nuclease revealed that the active genes are not present in the typical 200 base pair nucleosomal structure. Gene induction is associated with a rearrangement of the nuclear organization of the genes. By use of indirect end-label hybridization, three DNase I hypersensitive sites were mapped, one in the 5'-terminal region and two in the 3' region of the P-450c gene. Gene induction, by treatment with 3-methylcholanthrene, changes the location of the DNase I site present in the 5' region without affecting the sites present in the 3' region. Rat thymus chromatin does not contain these DNase I hypersensitive sites, suggesting that, in the liver, the chromatin structure is altered so as to allow tissue-specific expression of the P-450c gene. The chromatin structure of the highly inducible P-450c gene is compared to that of the P-450m gene, which is induced to a significantly smaller extent and is constitutively expressed.
Animals↗
Immunofractionation of chromatin regions associated with histone H1o.
Two monoclonal antibodies, which were elicited against histone H5, bind to purified rat liver chromatin and to rat liver H1o but not to rat liver H1. The monoclonal antibodies were immobilized on CNBr-Sepharose and the resulting immunoaffinity column was used to fractionate rat liver oligonucleosomes. Enzyme-linked immunoabsorbant assay (ELISA) and immunoblotting experiments indicate that the nucleosomes bound to the column were tenfold enriched in their content of H1o. Oligonucleosomes, prepared from the livers of either untreated or 3-methylcholanthrene-treated adult rats, were fractionated on the anti-H1o affinity column. The DNA purified from the unfractionated nucleosomes, from the unbound nucleosomes and from the nucleosomes which were bound to the column was examined with various 32P-labeled probes. A slight enrichment in H1o was detected in the coding region of the rat albumin gene. In contrast DNA which was bound to the column was significantly depleted in sequences hybridizing with total cellular RNA (which contains mostly ribosomal RNA) and with sequences hybridizing to the 3'-terminal region of a cytochrome P-450 gene, which is inducible by the chemical carcinogen 3-methylcholanthrene, regardless of whether isolated from control or from carcinogen-treated rat livers. Our experiments clearly demonstrate that chromatin can be efficiently immunofractionated. The results suggest that the H1o content of chromatin regions containing genes which are constitutively transcribed is not necessarily different from that of regions containing non-transcribed genes and that highly inducible genes may be segregated into chromatin regions which are depleted of H1o.
Animals↗
Chromosomal protein HMG-17. Complete human cDNA sequence and evidence for a multigene family.
Antibodies elicited against chromosomal protein HMG-17, purified from calf, were used to screen a human lambda gt11 cDNA expression library and isolate the full length cDNA coding for this protein. Sequence analysis reveals that the nucleotide distribution along this cDNA is highly asymmetric. The amino acid sequence, deduced from the reading frame, reveals that the human HMG-17 is, respectively, 96 and 92% homologous with the calf and chicken protein. The amino acid substitution are conservative suggesting evolutionary constraints on the conformation of the protein. The human genome contains 35-50 HMG-17 gene copies which, as revealed by Southern analysis, are distributed at several loci. Northern analysis of total RNA isolated from 3 human cell lines, indicates that each cell contains a single-size mRNA coding for this protein. Nucleotide sequences which cross-hybridize, under stringent conditions, with the human HMG-17 cDNA are present in the genome of rodents and absent from the genomes of sea urchin, Drosophila, and yeast. The availability of a probe for the HMG-17 gene may help elucidate the cellular role of this protein which may confer specific conformations to transcribable regions in the genome.
Amino Acid Sequence↗
Immunofractionation of DNA sequences associated with HMG-17 in chromatin.
Antibodies specific for chromosomal protein HMG-17 were immobilized on CNBr-Sepharose and the resulting immunoaffinity column was used to purify chromatin segments enriched in HMG-17. The DNA was purified from both the nucleosomal fraction which was bound to the column and from the fraction which was not bound, and examined with DNA probes representing repetitive DNA, non-transcribed genes, transcribed genes and inducible genes. The results suggest that HMG-17 is preferentially associated with DNA sequences coding for genes, regardless of whether they are transcribed, and therefore support the notion that HMG-17 confers specific structural characteristics on selected regions in the genome.
Animals↗
Exchange of proteins during immunofractionation of chromatin.
The migration and rearrangement of chromosomal proteins during immunofractionation of chromatin has been investigated. Oligonucleosomes from two different chromatins, chicken erythrocyte or rat liver, were mixed with oligonucleosomes from the other species which had been depleted of histones H1/H5 and high mobility group proteins (HMGs). The mixture was treated with buffers of various ionic strengths and immunofractionated on an anti-H1 degrees/H5 or anti-HMG-17 IgG-Sepharose column. The type of DNA, which was retained as the bound fraction on the column, was determined by slot blot analysis using nick-translated repetitive DNA probes from either chicken or rat. The results indicate that in low ionic strength buffers (i.e., below 40 mM NaCl), there is very little exchange of either histone H5 or HMG-17 among nucleosomes and therefore we suggest that it is possible to fractionate nucleosomes according to their antigenic content.
Animals↗
Adenocarcinoma of the lower esophagus. A disease primarily of white men with Barrett's esophagus.
Sex and racial predilection, social history, and histology were analyzed in a biopsy-proven adenocarcinoma of the lower esophagus/esophagogastric junction collected over a 5-year period in two teaching institutions with different patient populations. Adenocarcinoma occurred in 11% of patients with biopsy-proven esophageal cancer. The disease occurred only in males at one center, and in a 7:1 ratio of males to females at the other center. Clear racial predilection was seen, since 12 of 13 patients with adenocarcinoma of the esophagus were white, whereas less than 20% of patients with squamous carcinoma of the esophagus were white. The finding of Barrett's epithelium in eight of the 13 cases strongly supports the theory that in white males, Barrett's epithelium is a precursor lesion of adenocarcinoma of the esophagus/esophagogastric junction.
Adenocarcinoma↗