Peter Jeppesen

Heterochromatin, HP1 and methylation at lysine 9 of histone H3 in animals

Abstract. We show that methylated lysine 9 of histone H3 (Me9H3) is a marker of heterochromatin in divergent animal species. It localises to both constitutive and facultative heterochromatin and replicates late in S-phase of the cell cycle. Significantly, Me9H3 is enriched in the inactive mammalian X chromosome (Xi) in female cells, as well as in the XY body during meiosis in the male, and forms a G-band pattern along the arms of the autosomes. Me9H3 is a constituent of imprinted chromosomes that are repressed. The paternal and maternal pronuclei in one-cell mouse embryos show a striking non-equivalence in Me9H3: the paternal pronucleus contains no immunocytologically detectable Me9H3. The levels of Me9H3 on the parental chromosomes only become equivalent after the two-cell stage. Finally, we provide evidence that Me9H3 is neither necessary nor sufficient for localisation of heterochromatin protein 1 (HP1) to chromosomal DNA.

Antibodies to defined histone epitopes reveal variations in chromatin conformation and underacetylation of centric heterochromatin in human metaphase chromosomes

Unfixed metaphase chromosome preparations from human lymphocyte cultures were immunofluorescently labelled using antibodies to defined histone epitopes. Both mouse monoclonal antibody HBC-7, raised against the N-terminal region of H2B, and rabbit serum R5/12, which recognizes H4 acetylated at Lys-12, gave non-uniform labelling patterns, whereas control antibodies against total histone fractions H4 and H1 produced homogeneous fluorescence. HBC-7 bound approximately uniformly to the bulk of the chromosomes, but the major heterochromatic domains of chromosomes 1, 9, 15, 16 and the Y showed significantly brighter fluorescence. Serum R5/12 indicated an overall reduction in acetylation of H4 in metaphase chromosomes compared with interphase nuclei, although some specific chromosomal locations had considerably elevated acetylation levels. Acetylation levels in the major heterochromatic domains appeared extremely low. To investigate further the differences noted in heterochromatin labelling, metaphases from cultures grown in the presence of various agents known to induce undercondensation of the major heterochromatic domains were similarly immunolabelled. Decondensed heterochromatin no longer exhibited higher than normal immunofluorescence levels with HBC-7. The higher resolution afforded by “stretching” the centromeric heterochromatin of chromosomes 1, 9 and 16 confirmed the low level of H4 acetylation in these domains. We consider the implications of these observations in relation to chromatin conformation and activity.

Transcriptional repression by methylation of CpG

Summary Methylated DNA in mammals is associated with transcriptional repression and nuclease resistant chromatin. In this review we discuss how these effects may be mediated by proteins that bind to methylated DNA.

Chinese hamster metaphase chromosomes isolated under physiological conditions. A partial characterization of associated non-histone proteins and protein cores.

In a previous report [2] we have described a non-histone protein core which could be isolated from Chinese hamster metaphase chromosomes. This core structure maintained the overall morphology of the metaphase chromosome even after removal of all of the histones, together with many of the non-histone proteins and the bulk of the DNA. As part of our work on the characterization of these core structures, we have developed a novel procedure for the isolation of metaphase chromosomes which avoids the use of high pH buffers and hexylene glycol, as well as eliminating the numerous centrifugation and resuspension steps previously employed. Chromosome cores prepared by 2 M NaCl extraction and DNase I digestion from metaphase chromosomes isolated under these more gentle, quasi-physiological conditions, are shown to contain a relatively simple subset of non-histone proteins. One-dimensional SDS-polyacrylamide gel electrophoresis shows two major groups of polypeptides having molecular weights 48 000-52 000 and 65 000-72 000 D respectively, with similarities in mobilities to the nuclear pore complex-lamina polypeptides and tubulins. However, more detailed analysis by two-dimensional gel electrophoresis and peptide mapping has failed to detect these proteins. A 52 000 D polypeptide component of the core is tentatively identified as the intermediate filament protein vimentin. The in vivo significance of chromosome cores is discussed.

Human autoimmune sera recognize a conserved 26 kD protein associated with mammalian heterochromatin that is homologous to heterochromatin protein 1 ofDrosophila

Immunofluorescence indicated that autoimmune sera from certain scleroderma/CREST patients, in addition to binding to the primary constrictions or centromeres, also labelled pericentromeric heterochromatin in mouse and human metaphase chromosomes. Immunoblotting has revealed that two conserved nuclear antigens are recognized by this CREST subgroup, one of mol. wt 26 kD (p26), and the other of mol. wt 23 kD (p23).In situ immunolabelling with affinity purified antibodies demonstrated that p26, but not p23, is concentrated in pericentromeric heterochromatin. Further studies have shown that both p26 and p23 are immunologically related to theDrosophila heterochromatin-associated protein HP1, and to other chromodomain proteins.

The organisation of repetitive DNA sequences on human chromosomes with respect to the kinetochore analysed using a combination of oligonucleotide primers and CREST anticentromere serum

The spatial relationship between the families of repetitive DNAs present at the centromeres of human chromosomes and the position of the kinetochore was examined by combining immunocytochemistry with the PRINS oligonucleotide primer extension technique. Heterochromatic domains were decondensed with 5′-azacytidine to facilitate this study. Using this approach our results clearly show that the alphoid DNA sequences are closely associated with the kinetochore of human chromosomes. Simple-sequence satellite DNAs occupy separate, non-overlapping domains within the centromere. These two major families are separated by a third, relatively low-copy repetitive DNA family, SAU-3A. Pulse-field gel electrophoresis was employed to analyse the centromeric domain of human chromosome no. 9 in more detail and the results although preliminary support the conclusions drawn from the immunocytochemistry/PRINS approach.

Analysis of centromere structure in the fly Megaselia scalaris (Phoridae, Diptera) using CREST sera, anti-histone antibodies, and a repetitive DNA probe

We have used CREST anti‐centromere sera, rabbit anti‐histone antibodies, and repetitive DNA analysis to study centromere structure in the fly Megaselia scalaris (Phoridae). In a panel of eight CREST sera, four were positive in immunofluorescence experiments for prekinetochores, ie centromeres in interphase nuclei. The access of the antibodies to CREST antigens may be compromised in the condensed state, since centromeres of prometaphase and metaphase chromosomes remained unstained. When Western blots of embryonic nuclei were probed with these four CREST sera, three of them showed a 17 kDa band. Human CENP‐A, likewise recognized by the CREST sera, is a 17 kDa protein. The remaining sera were negative for centromeres although some detected centrosomes and non‐histone chromosomal proteins not confined to the centromeres. The use of antibodies generated against histone H4 acetylated at four different sites of the N‐terminal domain revealed that heterochromatic regions of M scalaris mitotic chromosomes, ie pericentric and NOR‐associated segments, are hyperacetylated. This is at variance with a variety of other systems, where transcriptionally active chromatin is hyperacetylated. Finally, a repetitive 165 base pair fragment was isolated from genomic DNA of the fly and sequenced. An oligonucleotide from this sequence mapped to the centromere region of interphase nuclei and the pericentric regions of condensed chromosomes.

Immunofluorescence in cytogenetic analysis: method and applications

Control of the genetic information encoded by DNA in mammalian chromosomes is mediated by proteins, some of which are only transiently attached, although others are intrinsically associated with nucleic acid in the complex mixture known as chromatin. Chromatin-associated proteins range from the ubiquitous and abundant histones down to the most specific and rare of transcription factors. Although many chromatin proteins are probably excluded from highly condensed mitotic chromosomes, a number are retained throughout the cell cycle and can be detected on chromosomes in metaphase spreads. Comparing the distribution of a chromosomal protein with known cytogenetic markers on metaphase chromosomes can provide an important and potentially highly informative first source of data on the function of the protein under consideration. The aim of the present study is to summarize some of the principles involved in obtaining suitable chromosome preparations for subsequent immunolocalization of protein antigens. Some applications of the method will be included to illustrate how this approach has increased our understanding of chromosome structure and genetic regulation.

Allele-specific underacetylation of histone H4 downstream from promoters is associated with X-inactivation in human cells

We have used a novel approach to investigate the histone H4 acetylation status at X-inactivated genes compared with their active counterparts. Immunoprecipitation with a sheep antibody that preferentially binds multiply-acetylated H4 isoforms was used to select hyperacetylated chromatin from a human female lymphoblastoid cell line exhibiting non-random X-inactivation as a result of an X/autosome translocation. The distribution of active and inactive gene sequences between the immunoprecipitated and bulk chromatin was compared at four X-linked loci containing intragenic polymorphic microsatellite repeats to allow identification of individual alleles by polymerase chain reaction. We find that DNA sequences corresponding to transcriptionally silent alleles are consistently under-represented in the hyperacetylated fraction. As the microsatellite repeat sequences used to identify alleles range in distance from 6.5 kb to 25 kb downstream of promoters, we conclude that differential H4 acetylation of active and silent chromatin is not confined to regions involved in the initiation of transcription, contrary to previous reports.

Characterization of a polypeptide associated with coated vesicles and the cytoskeleton which is recognized by a CREST serum

Serum from an individual with the CREST syndrome (calcinosis, Raynauds phenomenon, esophageal dismotility, sclerodactyly, telangiectasia) reacts not only with kinetochores, but also with a cytoplasmic, phosphorylatable polypeptide, which is shown by immunofluorescence in whole cells and immunoelectronmicroscopy in sections to be associated with actin stress fibres in cultured mammalian cells. The antigen shows some variation in molecular weight between species, estimated by immunoblotting to range from 68 to 76 kD between mouse, Chinese hamster, sheep and human cells. Much of the polypeptide copurifies with coated vesicles, of which approx. 5% bound antibody from the serum, as detected by immunogold electronmicroscopy.