DNA exposure and condensation in the X and 21 chromosomes

Effects of human sex chromosome dosage on spatial chromosome organization

Sex chromosome aneuploidies (SCAs) are common genetic syndromes characterized by the presence of an aberrant number of X and Y chromosomes due to meiotic defects. These conditions impact the structure and function of diverse tissues, but the proximal effects of SCAs on genome organization are unknown. Here, to determine the consequences of SCAs on global genome organization, we have analyzed multiple architectural features of chromosome organization in a comprehensive set of primary cells from SCA patients with various ratios of X and Y chromosomes by use of imaging-based high-throughput chromosome territory mapping (HiCTMap). We find that X chromosome supernumeracy does not affect the size, volume, or nuclear position of the Y chromosome or an autosomal chromosome. In contrast, the active X chromosome undergoes architectural changes as a function of increasing X copy number as measured by a decrease in size and an increase in circularity, which is indicative of chromatin compaction. In Y chromosome supernumeracy, Y chromosome size is reduced suggesting higher chromatin condensation. The radial positioning of chromosomes is unaffected in SCA karyotypes. Taken together, these observations document changes in genome architecture in response to alterations in sex chromosome numbers and point to trans-effects of dosage compensation on chromosome organization.

X chromosome inactivation: new players in the initiation of gene silencing

X chromosome inactivation (XCI) is a dosage compensation process that was adopted by female mammals to balance gene dosage between XX females and XY males. XCI starts with the upregulation of the non-coding RNA Xist, after which most X-linked genes are silenced and acquire a repressive chromatin state. Even though the chromatin marks of the inactive X have been fairly well described, the mechanisms responsible for the initiation of XCI remain largely unknown. In this review, we discuss recent developments that revealed unexpected factors playing a role in XCI and that might be of crucial importance to understand the mechanisms responsible for the very first steps of this chromosome-wide gene-silencing event.

X chromosome inactivation: silencing, topology and reactivation

To ensure X-linked gene dosage compensation between females (XX) and males (XY), one X chromosome undergoes X chromosome inactivation (XCI) in female cells. This process is tightly regulated throughout development by many different factors, with Xist as a key regulator, encoding a long non-coding RNA, involved in establishment of several layers of repressive epigenetic modifications. Several recent studies on XCI focusing on identification and characterization of Xist RNA-protein interactors, revealed new factors involved in gene silencing, genome topology and nuclear membrane attachment, amongst others. Also, new insights in higher order chromatin organization have been presented, revealing differences between the topological organization of active and inactive X chromosomes (Xa and Xi), with associated differences in gene expression. Finally, further evidence indicates that the inactive state of the Xi can be (partially) reversed, and that this X chromosome reactivation (XCR) might be associated with disease.

Bidirectional transcription of trinucleotide repeats: roles for excision repair

Genomic instability at repetitive DNA regions in cells of the nervous system leads to a number of neurodegenerative and neuromuscular diseases, including those with an expanded trinucleotide repeat (TNR) tract at or nearby an expressed gene. Expansion causes disease when a particular base sequence is repeated beyond the normal range, interfering with the expression or properties of a gene product. Disease severity and onset depend on the number of repeats. As the length of the repeat tract grows, so does the size of the successive expansions and the likelihood of another unstable event. In fragile X syndrome, for example, CGG repeat instability and pathogenesis are not typically observed below tracts of roughly 50 repeats, but occur frequently at or above 55 repeats, and are virtually certain above 100-300 repeats. Recent evidence points to bidirectional transcription as a new aspect of TNR instability and pathophysiology. Bidirectional transcription of TNR genes produces novel proteins and/or regulatory RNAs that influence both toxicity and epigenetic changes in TNR promoters. Bidirectional transcription of the TNR tract appears to influence aspects of its stability, gene processing, splicing, gene silencing, and chemical modification of DNAs. Paradoxically, however, some of the same effects are observed on both the expanded TNR gene and on its normal gene counterpart. In this review, we discuss the possible normal and abnormal effects of bidirectional transcription on trinucleotide repeat instability, the role of DNA repair in causing, preventing, or maintaining methylation, and chromatin environment of TNR genes.

Time-dependent segmentation of BrdU-signal leads to late detection problems in studies using BrdU as cell label or proliferation marker

Bromodeoxyuridine incorporates into DNA during mitosis. A long-term stability of the incorporated BrdU is important for the recovery of BrdU-labeled cells. For testing the stability of BrdU incorporation into DNA we pulse-labeled mesenchymal stem cells with BrdU and observed these cells in vitro over 4 weeks. During this time the BrdU-signal was permanently decreasing. Starting with cells containing evenly stained BrdU-nuclei, so-called filled cells, already 3 days after BrdU removal we detected cells containing so-called segmented and punctated BrdU-signals. The number of those labeled cells continuously increased over time. Interestingly, the loss of BrdU in the nucleus was accompanied by an increasing labeling of the cytosol. Further, we injected BrdU intraperitoneally into rats after ischemia and detected BrdU-positive cells in the hippocampus 3 and 23 days after the last BrdU injection. While after 3 days most of the BrdU-positive cells in the hippocampus displayed a filled BrdU-signal, 23 days after BrdU removal an increased number of segmented and punctated BrdU-positive nuclei was detected. The gradual degradation of the BrdU-signal was not caused by cell death. The consequence of this BrdU degradation would be an underestimation of cell proliferation and an overestimation of cell death of newly generated cells.

The facultative heterochromatin of the inactive X chromosome has a distinctive condensed ultrastructure

The mammalian inactive X chromosome (Xi) is a model for facultative heterochromatin. Increased DNA compaction for the Xi, and for facultative heterochromatin in general, has long been assumed based on recognition of a distinct Barr body using nucleic-acid staining. This conclusion has been challenged by a report revealing equal volumes occupied by the inactive and active X chromosomes. Here, we use light and electron microscopy to demonstrate in mouse and human fibroblasts a unique Xi ultrastructure, distinct from euchromatin and constitutive heterochromatin, containing tightly packed, heterochromatic fibers/domains with diameters in some cases approaching that of prophase chromatids. Significant space between these packed structures is observed even within condensed regions of the Xi. Serial-section analysis also reveals extensive contacts of the Xi with the nuclear envelope and/or nucleolus, with nuclear envelope association being observed in all cells. Implications of our results for models of Xi gene silencing and chromosome territory organization are discussed.

Gender-specific 5-HT1A receptor changes in BrdU nuclear labeling patterns in neonatal dentate gyrus

The actions of 5-HT1A receptors on cell proliferation in the rat neonatal dentate gyrus are unknown. We injected a 5-HT1A receptor agonist (ipsapirone) or antagonist (Way 100635) 1 h before injections of BrdU in neonates of both genders between days 2-4, a peak time of dentate gyrus granule cell proliferation. The BrdU immunoreactive (IR) nuclei in the granule cell layer and subgranular zone were examined after 2 weeks. The BrdU-IR nuclear staining patterns were classified as being either diffuse (homogenous dark BrdU-staining throughout the nucleus) or punctate (multiple distinct small stained spots within the nucleus). Most BrdU-labeled nuclei with a diffuse pattern were seen in the subgranular zone while the punctate pattern nuclei were seen within the granular cell layer of the dentate gyrus. 5-HT1A antagonist showed no overall change in absolute number or pattern of labeled nuclei compared to control animals. After a 5-HT1A agonist, there was also no differences in the total number of BrdU-IR nuclei (punctate and diffuse pattern). However, in both genders, the proportion of the BrdU-labeled nuclei showing a punctate compared to diffuse pattern increased: 33% in females and 18% in males. In females, the 5-HT1A receptor agonist increased the number of nuclei showing a punctate pattern by 41%, while in males the 5-HT1A receptor agonist decreased the number of nuclei showing a diffuse pattern by 29%. These results indicate gender-specific 5-HT1A receptor action on the state of nuclear DNA in the cells of the dentate gyrus, without increasing the total number of BrdU-labeled nuclei.

Cyclic AMP and the reverse transformation reaction

Traditional methods for cancer treatment have been aimed at killing the cancer cells. Unfortunately this approach all too often is accompanied by harmful killing of normal cells. The present paper describes an experimental program in our laboratory in which cancer cells are treated so as to revert to normal cell behavior. This process, which we have named reverse transformation, appears to offer considerable hope in the treatment of a large number of malignancies.

Long-term expression driven by herpes simplex virus type-1 amplicons may fail due to eventual degradation or extrusion of introduced transgenes

In gene therapy applications employing herpes simplex virus amplicon-based vectors, a prevailing problem is the down-regulation of transgene expression over time. We have applied a combined immunocytochemistry and fluorescent in situ hybridization method to determine whether down-regulation of transgene expression at the single-cell level correlates with loss of vector DNA from the host cell nucleus. Utilizing separate fluorescent labels (i.e., rhodamine, fluorescein, and 4',6'-diamidino-2-phenlindole), we were able to simultaneously detect transgenes, their products, and their locations relative to the nuclear compartment of a single cell. Detection of the reporter gene lacZ and its encoded protein beta-galactosidase (beta-gal) was accomplished in in vivo experiments of the dentate gyrus of rats. A time course study of the expression of the transgene post-stereotactic microinfusion up to 60 days was made. Expression reached maximal levels within 12-24 h after infection, and lacZ presence was reduced to less than 3% of its maximal levels within 36 h after infection. In comparing days 1 and 60 post-stereotactic microinfusion, only one-fifth of the original DNA was observed in the area of a 100-mm radius around the site of microinfusion at day 60. Moreover, by comparing the locations of the reporter gene in cells that expressed the encoded protein versus those that did not, we found that introduced transgenes were preferentially localized in the nuclear periphery of down-regulated host cells, compared to expressing host cells. These results suggest that nuclear compartmentalization may play a role in the down-regulation of our reporter gene by means of peripheralization, extrusion, and/or degradation.

Essay on the nucleoli survey by the alpha- and beta-satellite DNA probes of the acrocentric chromosomes in mitogen-stimulated human lymphocytes

The two constitutive heterochromatin (alpha- and beta-satellite DNA) probes of human acrocentric chromosomes were assayed separately to label the nucleoli in the phytohemagglutinin (PHA)-stimulated human lymphocytes. Fluorescent in situ hybridisation (FISH) results have shown that: a) whole (100%) signal-nucleoli overlapping was obtained with both heterochromatin probes in maximally activated nuclei (MANs); b) partial overlapping was observed in non-activated or slightly activated nuclei; c) random signal-nucleolus overlapping (background level) was found to be approximately 6% by the NOR-irrelevant euchromatic probe (D5S23); d) Yq-nucleolus association in the MANs was found to be approximately 97% without the subtraction of the background level. We concluded that: a) acrocentric alpha- or beta-satellite DNA probes may be used as nucleolar markers only in the MANs and not in slightly activated or non-activated nuclei; b) the distances between rDNA loci and alpha-/beta-satellite DNA on human acrocentrics are short enough to permit their observation on the same nucleolus.

Repositioning of human interphase chromosomes by nucleolar dynamics in the reverse transformation of HT1080 fibrosarcoma cells

An experimental system which should be valuable for studying the role of spatial positioning of the nuclear genome in human cell function has been developed. Reverse transformation of the malignant HT1080 fibrosarcoma cell line upon treatment with 8-chloro-cAMP results in growth inhibition, cytoskeletal reorganization, changes in nuclear shape and chromatin accessibility, and formation of prominent nucleoli. Fluorescent in situ hybridization was used to study DNA positioning during nuclear remodeling. Morphometric analysis of the hybridization sites for both repetitive sequences and "painting probes" for whole chromosomes indicated dispersal of acrocentric chromosomes in untreated cells and a highly organized central location of these ribosome gene-containing chromosomes in association with one or a few large nucleoli in nondividing treated cells. The results suggest that there was a directed movement of interphase chromosomes during a response which normalized a malignant cell line. These large-scale repositionings may serve two functions in restoring a normal transcriptional setup to the nucleus. First, ribosome genes are placed in the nucleolus, their transcriptional suborganelle. Second, nucleolar anchorings together with additional perinucleolar centromeric associations orient the domain shapes of entire chromosomes, installing gene-rich chromosomal regions into pockets of (accessible) DNAse I-sensitive chromatin populated by spliceosomes.

Gene identification and DNA sequence analysis in the GC-poor 20 megabase region of human chromosome 21

In contrast to the distal half of the long arm of chromosome 21, the proximal half of approximately 20 megabases of DNA, including 21q11-21 bands, is low in GC content, CpG islands, and identified genes. Despite intensive searches, very few genes and cDNAs have been found in this region. Since the 21q11-21 region is associated with certain Down syndrome pathologies like mental retardation, the identification of relevant genes in this region is important. We used a different approach by constructing microdissection libraries specifically for this region and isolating unique sequence microclones for detailed molecular analysis. We found that this region is enriched with middle and low-copy repetitive sequences, and is also heavily methylated. By sequencing and homology analysis, we identified a significant number of genes/cDNAs, most of which appear to belong to gene families. In addition, we used unique sequence microclones in direct screening of cDNA libraries and isolated 12 cDNAs for this region. Thus, although the 21q11-21 region is gene poor, it is not completely devoid of genes/cDNAs. The presence of high proportions of middle and low-copy repetitive sequences in this region may have evolutionary significance in the genome organization and function of this region. Since 21q11-21 is heavily methylated, the expression of genes in this region may be regulated by a delicate balance of methylation and demethylation, and the presence of an additional copy of chromosome 21 may seriously disturb this balance and cause specific Down syndrome anomalies including mental retardation.