The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells

To fully understand genome function, the linear genome map must be integrated with a spatial map of chromosomes in the nucleus. Distinct nuclear addresses for a few human chromosomes have been described. Previously we have demonstrated that the gene-rich human chromosome 19 is located in a more central position in the nucleus than the similarly sized, but gene-poor, chromosome 18. To determine whether these two chromosomes are a paradigm for the organization of chromatin in the human nucleus, we have now analysed the nuclear organization of every human chromosome in diploid lymphoblasts and primary fibroblasts. We find that the most gene-rich chromosomes concentrate at the centre of the nucleus, whereas the more gene-poor chromosomes are located towards the nuclear periphery. In contrast, we find no significant relationship between chromosome size and position within the nucleus. Proteins of the nuclear membrane or lamina are candidates for molecules that might anchor regions of the genome at the nuclear periphery and it has been suggested that disruption of this organization may play a role in some disease pathologies. We show that the intranuclear organization of chromosomes is not altered in cells that lack the integral nuclear membrane protein emerin, from an individual with X-linked Emery--Dreifuss muscular dystrophy. This suggests that emerin is not necessary for localizing chromosomes at the nuclear periphery and that the muscular dystrophy phenotype in such individuals is not due to grossly altered nuclear organization of chromatin.

The human preprotachykinin-A gene promoter has been highly conserved and can drive human-like marker gene expression in the adult mouse CNS

Toward an understanding of the mechanisms controlling Preprotachykinin-A (PPTA) transcription, we introduced a 380-kb human yeast artificial chromosome containing the PPTA gene tagged with the beta-galactosidase gene into transgenic mice. This resulted in a pattern of LacZ expression in the central nervous system (CNS) remarkably similar to that reported for PPTA mRNA in the rat. However, the human gene drove expression in areas of the mouse CNS not associated with strong PPTA expression in rodents but which have been shown to express PPTA in the human. This study clearly demonstrates the high degree of conservation of the mechanisms involved in PPTA transcription that has occurred throughout 100 million of divergent human and rodent evolution. This study also defines the maximum linear extent of the human PPT-A promoter. We believe these findings constitute the removal of a significant obstacle in studying the transcriptional regulation of the human PPTA gene in vivo.

The long-term psychological effects of a disaster experienced in adolescence: I: The incidence and course of PTSD

Previous studies have shown that children and adolescents exposed to traumatic experience in a disaster can suffer from high levels of post-traumatic stress. The present paper is the first a series reporting on the long-term follow-up of a group of young adults who as teenagers had survived a shipping disaster-the sinking of the "Jupiter" in Greek waters-between 5 and 8 years previously. The general methodology of the follow-up study as a whole is described, and the incidence and long-term course of Post-Traumatic Stress Disorder (PTSD). It is the first study of its kind on a relatively large, representative sample of survivors, using a standardised diagnostic interview, and comparing survivors with a community control group. Survivors of the Jupiter disaster (N = 217), and 87 young people as controls, were interviewed using the Clinician Administered PTSD Scale (CAPS). Of the 217 survivors, 111 (51.7%) had developed PTSD at some time during the follow-up period, compared with an incidence in the control group of 3.4 % (N = 87). In the large majority of cases of PTSD in the survivors for whom time of onset was recorded, 90 % (N = 110), onset was not delayed, being within 6 months of the disaster. About a third of those survivors who developed PTSD (30%, N = 111) recovered within a year of onset, through another third (34 %, N = 111) were still suffering from the disorder at the time of follow-up, between 5 and 8 years after the disaster. Issues relating to the generalisability of these findings are discussed.

An evolutionarily conserved germ cell-specific hnRNP is encoded by a retrotransposed gene

The gene encoding heterogeneous ribonucleoprotein (hnRNP) G recently has been mapped to the X chromosome. All mammals have a Y chromosome-encoded homologue of HNRNP G called RBMY, which is implicated with a role in male fertility and is a candidate for the azoospermia factor gene. We have identified a new member of this gene family, HNRNP G-T, and have mapped it as a single-copy gene on chromosome 11. This gene contains an uninterrupted open reading frame and no introns, consistent with derivation from a retroposon. However, unlike many retroposon-derived genes, HNRNP G-T is not a pseudogene. An antiserum raised to the conceptual reading frame of HNRNP G-T showed that it encodes a protein that is highly expressed in germ cells and in particular in the nuclei of meiotic spermatocytes. Surprisingly, although this antiserum was raised against human hnRNP G-T protein, it can also detect a similar protein in the testis of several mammals. This suggests that the protein is highly conserved and that the retrotransposition event generating the HNRNP G-T gene pre-dated at least the common ancestor of mouse and man. The existence of an additional testis-specific hnRNP G family member provides evidence for the importance of these proteins in normal germ cell development.

Expression and genomic characterization of protein phosphatase inhibitor-1: a novel marker for mesothelium in the mouse

Protein phosphatase inhibitor-1 (inhibitor-1 or I-1) is involved in signal transduction and is an endogenous inhibitor of protein phosphatase-1. The mouse I-1 protein sequence has been deduced from cDNA and is strongly homologous to the published rat sequence. A mouse genomic library was screened, and the I-1 gene was characterized and localized by fluorescent in situ hybridization (FISH) to chromosome 15F. Protein expression in a range of embryonic and adult tissue was analysed using confocal microscopy. Inhibitor-1 is expressed by: the coelomic epithelium; the epithelial bounding layer of cells of the kidney, lung, liver, heart, intestine and gonad; and the surface ectoderm. The blast cells of the kidney do not express I-1. We conclude that I-1 is a marker for mesothelium.

A prospective study of dominance and coronary heart disease in the Normative Aging Study

The purpose of this study was to examine the prospective relation between dominance, as assessed by a Minnesota Multiphasic Personality Inventory (MMPI-2)-derived dominance scale, and incidence of coronary heart disease (CHD), independent of participants' anger level. The study was performed in the VA Normative Aging Study, an ongoing cohort of older (mean age 61 years) men. A total of 1,225 men who were free of CHD in 1986 completed the MMPI-2. A factor analysis of selected MMPI items provided the basis for the construction of a dominance scale and an anger scale. During an average of 8 years of follow-up, 158 cases of incident CHD occurred, including 29 cases of fatal CHD, 69 cases of nonfatal myocardial infarction (MI), and 60 cases of angina pectoris (AP). Compared with men reporting the lowest levels of dominance (lower tertile), the multivariate-adjusted relative risk among men reporting the highest levels of dominance (upper tertile) was 1.80 (95% confidence interval [CI] 1.21 to 3.24) for combined nonfatal MI and fatal CHD. Additional adjustment for anger scores did not significantly alter this relation. There was no significant relation between dominance and AP. Our data suggest that dominance is an independent risk factor for CHD in older men.

Re-modelling of nuclear architecture in quiescent and senescent human fibroblasts

Spatial organisation of the genome within the nucleus can play a role in maintaining the expressed or silent state of some genes [1]. There are distinct addresses for specific chromosomes, which have different functional characteristics, within the nuclei of dividing populations of human cells [2]. Here, we demonstrate that this level of nuclear architecture is altered in cells that have become either quiescent or senescent. Upon cell cycle exit, a gene-poor human chromosome moves from a location at the nuclear periphery to a more internal site in the nucleus, and changes its associations with nuclear substructures. The chromosome moves back toward the edge of the nucleus at a distinctive time after re-entry into the cell cycle. There is a 2-4 hour period at the beginning of G1 when the spatial organisation of these human chromosomes is established. Lastly, these experiments provide evidence that temporal control of DNA replication can be independent of spatial chromosome organisation. We conclude that the sub-nuclear organisation of chromosomes in quiescent or senescent mammalian somatic cells is fundamentally different from that in proliferating cells and that the spatial organisation of the genome is plastic.

Juxta-centromeric region of human chromosome 21 is enriched for pseudogenes and gene fragments

A physical map including four pseudogenes and 10 gene fragments and spanning 500 kb in the juxta-centromeric region of the long arm of human chromosome 21 is presented. cDNA fragments isolated from a selected cDNA library were characterized and mapped to the 831B6 YAC and to two BAC contigs that cover 250 kb of the region. An 85 kb genomic sequence located in the proximal region of the map was analyzed for putative exons. Four pseudogenes were found, including psiIGSF3, psiEIF3, psiGCT-rel whose functional copies map to chromosome 1p13, chromosome 2 and chromosome 22q11, respectively. The TTLL1 pseudogene corresponds to a new gene whose functional copy maps to chromosome 22q13. Ten gene fragments represent novel sequences that have related sequences on different human chromosomes and show 97-100% nucleotide identity to chromosome 21. These may correspond to pseudogenes on chromosome 21 and to functional genes in other chromosomes. The 85 kb genomic sequence was analyzed also for GC content, CpG islands, and repetitive sequence distribution. A GC-poor L isochore spanning 40 kb from satellite 1 was observed in the most centromeric region, next to a GC-rich H isochore that is a candidate region for the presence of functional genes. The pericentric duplication of a 7.8 kb region that is derived from the 22q13 chromosome band is described. We showed that the juxta-centromeric region of human chromosome 21 is enriched for retrotransposed pseudogenes and gene fragments transferred by interchromosome duplications, but we do not rule out the possibility that the region harbors functional genes also.

Differences in the localization and morphology of chromosomes in the human nucleus

Using fluorescence in situ hybridization we show striking differences in nuclear position, chromosome morphology, and interactions with nuclear substructure for human chromosomes 18 and 19. Human chromosome 19 is shown to adopt a more internal position in the nucleus than chromosome 18 and to be more extensively associated with the nuclear matrix. The more peripheral localization of chromosome 18 is established early in the cell cycle and is maintained thereafter. We show that the preferential localization of chromosomes 18 and 19 in the nucleus is reflected in the orientation of translocation chromosomes in the nucleus. Lastly, we show that the inhibition of transcription can have gross, but reversible, effects on chromosome architecture. Our data demonstrate that the distribution of genomic sequences between chromosomes has implications for nuclear structure and we discuss our findings in relation to a model of the human nucleus that is functionally compartmentalized.

Vaccination with live Escherichia coli expressing Brucella abortus Cu/Zn superoxide dismutase protects mice against virulent B. abortus

Vaccination of mice with Escherichia coli expressing Brucella Cu/Zn superoxide dismutase (SOD) [E. coli(pBSSOD)] induced a significant level of protection against virulent Brucella abortus challenge, although this level was not as high as the one reached with B. abortus vaccine strain RB51. In addition, vaccination with E. coli(pBSSOD) induced antibodies to Cu/Zn SOD and a strong proliferative response of splenocytes when stimulated in vitro with a thioredoxin-Cu/Zn SOD fusion protein.

A sequence-ready 3-Mb PAC contig covering 16 breakpoints of the Wilms tumor/anirida region of human chromosome 11p13

A large body of evidence that links alterations of chromosome 11p13 to tumor formation and various developmental disorders has been accumulated. To address the underlying genetic events it would be helpful to have a comprehensive gene map of the region, and this is most readily achieved by generating the complete genomic sequence. Building upon previous mapping and YAC contig analysis we have established a 3-Mb sequence-ready PAC contig. It was constructed by chromosome walking and independently verified by fingerprint analysis of individual clones. The contig starts from the catalase gene on the centromeric side and reaches beyond the PAX6 gene at the 11p13/p14.1 boundary. Additional smaller contigs on either side were identified, but still have to be linked up. The 3-Mb contig spans the central region of deletions encompassing 16 chromosomal breakpoints in patients with WAGR syndrome (Wilms tumor, aniridia, genitourinary malformation, mental retardation), and its construction is an important step in facilitating functional analysis of these genes.

Molecular cloning of a human cDNA IGSF3 encoding an immunoglobulin-like membrane protein: expression and mapping to chromosome band 1p13

We report the isolation and characterization of a novel cDNA IGSF3 that contains a 3648-bp open reading frame encoding an apparent immunoglobulin (Ig)-like membrane protein characterized by eight Ig domains. IGSF3 has an overall structural similarity and strong sequence similarity to V7, a human leukocyte surface protein. The IGSF3 mRNA is highly expressed in placenta, kidney, and lung, but is also present in a wide range of other human tissues. Although a small internal sequence of the IGSF3 cDNA hybridizes to a YAC derived from the centromeric region of chromosome 21, in situ hybridization experiments on human metaphase chromosomes show that the gene corresponding to the long cDNA that we cloned is located in chromosome band 1p13 and that related sequences are located on chromosomes 2 and 13. These data serve to emphasize the potential difficulties in transcriptional mapping in centromeric regions.

The Epstein-Barr virus nuclear protein SM is both a post-transcriptional inhibitor and activator of gene expression

The Epstein-Barr virus (EBV) nuclear protein BS-MLF1 (SM) is expressed early after entry of EBV into the lytic cycle. SM transactivates reporter gene constructs driven by a wide variety of promoters, but the mechanism of SM action is poorly understood. In this study, we demonstrate that the SM protein inhibits expression of intron-containing genes and activates expression of intron-less genes. We demonstrate that SM has the predicted inhibitory effect on expression of a spliced EBV gene but activates an unspliced early EBV gene. SM inhibited gene expression at the post-transcriptional level by preventing the accumulation of nuclear and cytoplasmic RNA transcripts. Conversely, SM led to increased accumulation of nuclear mRNA from intron-less genes without affecting the rate of transcription, indicating that SM enhances nuclear RNA stability. The ratio of cytoplasmic to nuclear polyadenylated mRNA was increased in the presence of SM, suggesting that SM also enhances nucleo-cytoplasmic mRNA transport. The degree of transactivation by SM was dependent on the sequence of the 3'-untranslated region of the target mRNA. Finally, we demonstrate that the amino-terminal portion of SM fused to glutathione-S-transferase binds radioactively labeled RNA in vitro, indicating that SM is a single-stranded RNA binding protein. Importantly, the latent and immediate-early genes of EBV contain introns whereas many early and late genes do not. Thus, SM may down-regulate synthesis of host cell proteins and latent EBV proteins while simultaneously enhancing expression of specific lytic EBV genes by binding to mRNA and modulating its stability and transport.

Waiting lists. The wrong target

The numbers now waiting for treatment in the NHS are more than double what they were in 1948 despite huge increases in activity. Increased activity has not reduced the time patients wait. Mean waiting times in the 1990s were 13-14 weeks, the same as in the 1960s and 1970s. An increase in activity to reduce the numbers waiting for treatment may, in fact, increase the number being put on the waiting list. Government targets should concentrate on how long individual patients have to wait, rather than reducing the numbers on the waiting list.

Scaffold attachments within the human genome

It is generally agreed that, above the level of the 30 nm fibre, eukaryotic chromatin is constrained into loops, but there is disagreement about the nature of the substructure that serves to anchor loops and the DNA sequences that act as the attachment sites. This problem may stem from the very different methods that all purport to separate loop and attached DNAs. We have tested ideas about how the genome is arranged into loops by analysing the average loop size over different cytologically resolvable regions of human chromosomes using fluorescence in situ hybridisation with loop and attached DNA fractions. Variations in average loop size, along and between chromosomes, measurable at this level of resolution were small but significant and were dependent on the extraction method. This emphasises the fundamental differences between the nuclear substructure probed by different protocols. DNA attached to the nuclear ‘scaffold’ or ‘matrix’ hybridises preferentially to gene-poor regions of the genome (G-bands). Conversely, fractions attached to the nuclear ‘skeleton’ hybridise preferentially to gene-rich R-bands and sites of high levels of transcription. The inactive X chromosome has a deficit of associations with the nuclear skeleton but not with the matrix or scaffold. A large excess of attached sequences is found at some sites of constitutive heterochromatin, but not at centromeres.

The reticulocalbin gene maps to the WAGR region in human and to the Small eye Harwell deletion in mouse

We describe the localization of the gene encoding reticulocalbin, a Ca2+-binding protein of the endoplasmic reticulum, on human chromosome 11p13 midway between the WT1 and the PAX6 genes and show that it is hemizygously deleted in WAGR individuals. The mouse reticulocalbin gene is also shown to map to the region of conserved synteny on mouse chromosome 2 and to be deleted in the Small eye Harwell (SeyH) mutation. Loss of the reticulocalbin gene could contribute to the early lethality of SeyH and SeyDey homozygotes.