Immunofluorescent analysis of chromatin structure in relation to gene activity: a speculative essay

Targeting to transcriptionally active loci by the hydrophilic N-terminal domain of Drosophila DNA topoisomerase I

DNA topoisomerase I (topo I) from Drosophila melanogaster contains a nonconserved, hydrophilic N-terminal domain of about 430 residues upstream of the conserved core domains. Deletion of this N terminus did not affect the catalytic activity of topo I, while further removal of sequences into the conserved regions inactivated its enzymatic activity. We have investigated the cellular function of the Drosophila topo I N-terminal domain with top1-lacZ transgenes. There was at least one putative nuclear localization signal within the first 315 residues of the N-terminal domain that allows efficient import of the large chimeric proteins into Drosophila nuclei. The top1-lacZ fusion proteins colocalized with RNA polymerase II (pol II) at developmental puffs on the polytene chromosomes. Either topo I or the top1-lacZ fusion protein was colocalized with RNA pol II in some but not all of the nonpuff, interband loci. However, the fusion proteins as well as RNA pol II were recruited to heat shock puffs during heat treatment, and they returned to the developmental puffs after recovery from heat shock. By immunoprecipitation, we showed that two of the largest subunits of RNA pol II coprecipitated with the N-terminal 315-residue fusion protein by using antibodies against beta-galactosidase. These data suggest that the topo I fusion protein can be localized to the transcriptional complex on chromatin and that the N-terminal 315 residues were sufficient to respond to cellular processes, especially during the reprogramming of gene expression.

Monoclonal antibodies to nonhistone proteins associated with human colon cancer nuclear matrix

Hybridoma technology was applied in an effort to create highly specific probes for nonhistone proteins associated with human colon cancer nuclear matrix. Three stable monoclonal antibodies producing cloned cells No. 39, 54 and 58 are described here. All these antibodies showed high reactivity with human colon tumor nuclear matrix. Both antibodies No. 39 and 58 showed an extensive cross reactivity at high concentration of normal colon nuclear matrix. The antigens were determined to be a heterogeneous group of proteins with a major antigen of molecular weight of 140,000 for antibody No. 54 subclone 54-c-5-6 and two major antigens of molecular weight for 105,000 and 116,000 for antibody No. 39 subclone 39-d-11-12. Immunohistochemical localization of the antigens by the horseradish peroxidase bridge method demonstrated their presence in the nuclei.

Molecular and functional diversity of non-histone protein fraction NHCP1 from hamster Kirkman-Robbins hepatoma and liver

Non-histone protein fraction NHCP1 of micrococcal nuclease-sensitive and nuclease-resistant chromatin from Kirkman-Robbins hepatoma and hamster liver was studied by two-dimensional electrophoresis followed by Coomassie and silver staining and by microcomplement fixation technique in the presence of antibodies elicited against NHCP1 of both tissues. Apart from many common spots several tissue specific components associated with either nuclease-sensitive or nuclease-resistant chromatin were found. The presence of tissue specific components among NHCP1 from hepatoma and liver was confirmed by immunological analysis. It was stated that these components are exclusively localized in nuclease-resistant part of chromatin from neoplastic and normal tissues thus suggesting their structural function.

Antibodies directed against guanylic acid and guanosine are nucleolus specific probes

Purified antibodies against guanylic acid and guanosine binding to RNA at guanosine residues were used to probe human lymphocyte preparations by indirect immunofluorescence. Neither antibody gave any banding pattern with metaphase chromosomes but both showed binding to specific sites in the interphase nuclei. Evidence presented indicates that these sites are guanosine residues on rDNA transcripts at the nucleolar organizer regions.

Specificity of Kirkman-Robbins hepatoma non-histone chromatin proteins: electrophoretic and immunological analyses

The specificity of Kirkman-Robbins hepatoma and hamster liver non-histone chromatin proteins has been studied by comparing polypeptide patterns in polyacrylamide gel electrophoresis and by their immunological activity in the complement fixation test. Non-histone proteins were separated from DNA with a polyethylene glycol-dextran mixture and fractionated by hydroxylapatite chromatography into three classes named NHCP1, NHCP2, and NHCP3. Electrophoretic analysis indicated that among the non-histone proteins of Kirkman-Robbins hepatoma and hamster liver differences mainly of a quantitative nature can be observed. However, the polypeptides with molecular weight 25 000, 31 000, 36 000, 73 000 in NHCP1; 20 000, 40 000 in NHCP2 and 20 000, 23 000, 32 000, 38 000, 44 000, 75 000, 80 000 in NHCP3 were found to be specific for hepatoma chromatin. Application of antibodies against NHCP1, NHCP2 and dehistonized chromatin of Kirkman-Robbins hepatoma revealed that the highest specificity of NHCP2 eluted from hydroxylapatite with 100 mM phosphate buffer at pH 6.8. The NHCP1 of hepatoma shares some common antigenic determinants with analogous proteins of liver. On the other hand non-histone proteins specific for hepatoma dehistonized chromatin can be localized in the NHCP3 and partially in the NHCP1 fractions.

Hepatoma-associated nonhistone chromosomal proteins

In order to compare nonhistone proteins in normal and neoplastic hepatocytes, we elicited antisera to Morris hepatoma 7777 dehistonized chromatin. By the enzyme-linked immunosorbent assay, the antisera demonstrated specificity for Morris hepatoma 7777 and little reactivity to normal rat liver chromatin. Morris hepatomas 7288c, 7800 and 5123tc shared some antigenic hepatoma nonhistone proteins. Neoplasia induced in rats fed 3'-methyl-4-dimethylaminoazobenzene changed the immunospecificity of the liver chromatin to a new type that was antigenically similar to Morris hepatoma 7777. Fetal rat liver chromatin and regenerating rat liver chromatin did not bind antibody. To further characterize the antigenic nonhistone proteins, we analyzed Morris hepatoma 7777 chromatin and normal rat liver chromatin by the immunoblot technique. Nonhistone proteins that demonstrated immunoreactivity were predominantly high molecular weight proteins.

Monoclonal antibodies against a specific nonhistone chromosomal protein of Drosophila associated with active genes

Hybridomas secreting monoclonal antibodies have been produced by fusion of NS-1 mouse myeloma cells with the spleen cells of mice inoculated with a 60-65,000-mol wt fraction of proteins released from Drosophila embryo nuclei treated with DNase I. The antibodies secreted by the hybridomas were examined with polytene chromosomes of formaldehyde-fixed salivary gland squashes by an immunofluorescence assay. Most of the clonal antibodies obtained resulted in specific staining of the chromosomes relative to the cytoplasmic debris. In the case of clone 28, the antibodies showed a preferential association with sites of gene activity, both puffs and loci identified as puffing at some time during the third instar and prepupal period. In larvae that were heat shocked (exposed to 35 degrees C for 15 min before removal and fixation of the glands), the antibodies of clone 28 stained preferentially the induced heat-shock loci while continuing to stain most of the normal set of loci. The antigen for clone 28 was identified as a single protein of approximately 62,000 mol wt by using the antibodies followed by 125I-rabbit anti-mouse Ig to stain nitrocellulose replicas of SDS polyacrylamide gels of total chromosomal proteins. This study demonstrates that monoclonal antibodies can be used successfully in immunofluorescence staining of formaldehyde-fixed polytene chromosomes. The results verify the hypothesis that a specific nonhistone chromosomal protein is preferentially associated with the set of loci that includes both active sites and those scheduled to be active at some time in this developmental program. Such proteins may play a general role in the mechanisms of cell determination and gene activation.