Reaction of human heterochromatin and euchromatin to spermine

The number of cell nuclei with X and Y chromatin and the number of nuclei with a diffuse and a coarse chromatin network were determined in diploid fibroblast cultures from persons with karyotypes of 47,XXY and 47,XYY after treatment with spermine. Spermine did not affect the number of nuclei with X and Y chromatin but led to a marked increase in the number of cells with a coarse chromatin pattern of their nucleus. After the action of spermin on peripheral blood lymphocyte cultures the number of metaphases with delayed chromosomal condensation caused by preliminary treatment with 5-bromodeoxyuridine was increased considerably, and the degree of this delay also was increased. The results indicate sensitivity of the euchromatin to the condensing action of spermine and inertia of the heterochromatin.Presented by Academician of the Academy of Medical Sciences of the USSR A. P. Avtsyn.Translated from Byulleten' Éksperimental'noi Biologii i Meditsiny, Vol. 79, No. 6, pp. 98–101, June, 1975.     

Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions

Human chromosomal regions enriched in segmental duplications are subject to extensive genomic reorganization. Such regions are particularly informative for illuminating the evolutionary history of a given chromosome. We have analyzed 866 kb of Y-chromosomal non-palindromic segmental duplications delineating four euchromatin/heterochromatin transition regions (Yp11.2/Yp11.1, Yq11.1/Yq11.21, Yq11.23/Yq12, and Yq12/PAR2). Several computational methods were applied to decipher the segmental duplication architecture and identify the ancestral origin of the 41 different duplicons. Combining computational and comparative FISH analysis, we reconstruct the evolutionary history of these regions. Our analysis indicates a continuous process of transposition of duplicated sequences onto the evolving higher primate Y chromosome, providing unique insights into the development of species-specific Y-chromosomal and autosomal duplicons. Phylogenetic sequence comparisons show that duplicons of the human Yp11.2/Yp11.1 region were already present in the macaque-human ancestor as multiple paralogs located predominantly in subtelomeric regions. In contrast, duplicons from the Yq11.1/Yq11.21, Yq11.23/Yq12, and Yq12/PAR2 regions show no evidence of duplication in rhesus macaque, but map to the pericentromeric regions in chimpanzee and human. This suggests an evolutionary shift in the direction of duplicative transposition events from subtelomeric in Old World monkeys to pericentromeric in the human/ape lineage. Extensive chromosomal relocation of autosomal-duplicated sequences from euchromatin/heterochromatin transition regions to interstitial regions as demonstrated on the pygmy chimpanzee Y chromosome support a model in which substantial reorganization and amplification of duplicated sequences may contribute to speciation.     

Su(var) genes regulate the balance between euchromatin and heterochromatin in Drosophila

Histone lysine methylation is an epigenetic mark to index chromosomal subdomains. In Drosophila, H3-K9 di- and trimethylation is mainly controlled by the heterochromatic SU(VAR)3-9 HMTase, a major regulator of position-effect variegation (PEV). In contrast, H3-K27 methylation states are independently mediated by the Pc-group enzyme E(Z). Isolation of 19 point mutants demonstrates that the silencing potential of Su(var)3-9 increases with its associated HMTase activity. A hyperactive Su(var)3-9 mutant, pitkin(D), displays extensive H3-K9 di- and trimethylation within but also outside pericentric heterochromatin. Notably, mutations in a novel Su(var) gene, Su(var)3-1, severely restrict Su(var)3-9-mediated gene silencing. Su(var)3-1 was identified as "antimorphic" mutants of the euchromatic H3-S10 kinase JIL-1. JIL-1(Su(var)3-1) mutants maintain kinase activity and do not detectably impair repressive histone lysine methylation marks. However, analyses with seven different PEV rearrangements demonstrate a general role of JIL-1(Su(var)3-1) in controlling heterochromatin compaction and expansion. Our data provide evidence for a dynamic balance between heterochromatin and euchromatin, and define two distinct mechanisms for Su(var) gene function. Whereas the majority of Su(var)s encode inherent components of heterochromatin that can establish repressive chromatin structures [intrinsic Su(var)s], Su(var)3-1 reflects gain-of-function mutants of a euchromatic component that antagonize the expansion of heterochromatic subdomains [acquired Su(var)s].     

Secondary uses and the governance of de-identified data: Lessons from the human genome diversity panel

Background

The Albanian medical system and Albanian health legislation have adopted a paternalistic position with regard to individual decision making. This reflects the practices of a not-so-remote past when state-run facilities and a totalitarian philosophy of medical care were politically imposed. Because of this history, advance directives concerning treatment refusal and do-not-resuscitate decisions are still extremely uncommon in Albania. Medical teams cannot abstain from intervening even when the patient explicitly and repeatedly solicits therapeutic abstinence. The Albanian law on health care has no provisions regarding limits or withdrawal of treatment. This restricts the individual's healthcare choices.

Discussion

The question of 'medically futile' interventions and pointless life-prolonging treatment has been discussed by several authors. Dutch physicians call such interventions 'medisch zinloos' (senseless), and the Netherlands, as one of the first states to legislate on end-of-life situations, actually regulates such issues through appropriate laws. In contrast, leaving an 'advance directive' is not a viable option for Albanian ailing individuals of advanced age. Verbal requests are provided during periods of mental competence, but unfortunately such instructions are rarely taken seriously, and none of them has ever been upheld in a legal or other official forum.

Summary

End-of-life decisions, treatment refusal and do-not-resuscitate policies are hazardous options in Albania, from the legal point of view. Complying with them involves significant risk on the part of the physician. Culturally, the application of such instructions is influenced from a mixture of religious beliefs, death coping-behaviors and an immense confusion concerning the role of proxies as decision-makers. Nevertheless, Albanian tradition is familiar with the notion of 'amanet', a sort of living will that mainly deals the property and inheritance issues. Such living wills, verbally transmitted, may in certain cases include advance directives regarding end-of-life decisions of the patient including refusal or termination of futile medical treatments. Since these living wills are never formally and legally validated, their application is impossible and treatment refusal remains still non practicable. Tricks to avoid institutional treatment under desperate conditions are used, aiming to provide legal coverage for medical teams and relatives that in extreme situations comply with the advice of withholding senseless treatment.     

Detection of the heteromorphic spectrum of heterochromatin in the human genome by in situ digestion using restriction endonuclease AluI.

A battery of selective banding techniques has been utilized to identify the heteromorphic markers in the human genome. The recent addition of the AluI/Giemsa (G)-technique has helped not only in identifying the variable sites, but in characterizing their heteromorphic spectra. In the present investigation, we classified the pericentromeric heterochromatin by the AluI/G-technique by its size and position using 50 normal individuals and suggested the potential uses of this banding technique over earlier methods.     

Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons

The sequencing of the chimpanzee genome and the comparison with its human counterpart have begun to reveal the spectrum of genetic changes that has accompanied human evolution. In addition to gross karyotypic rearrangements such as the fusion that formed human chromosome 2 and the human-specific pericentric inversions of chromosomes 1 and 18, there is considerable submicroscopic structural variation involving deletions, duplications, and inversions. Lineage-specific segmental duplications, detected by array comparative genomic hybridization and direct sequence comparison, have made a very significant contribution to this structural divergence, which is at least three-fold greater than that due to nucleotide substitutions. Since structural genomic changes may have given rise to irreversible functional differences between the diverging species, their detailed analysis could help to identify the biological processes that have accompanied speciation. To this end, interspecies comparisons have revealed numerous human-specific gains and losses of genes as well as changes in gene expression. The very considerable structural diversity (polymorphism) evident within both lineages has, however, hampered the analysis of the structural divergence between the human and chimpanzee genomes. The concomitant evaluation of genetic divergence and diversity at the nucleotide level has nevertheless served to identify many genes that have evolved under positive selection and may thus have been involved in the development of human lineage-specific traits. Genes that display signs of weak negative selection have also been identified and could represent candidate loci for complex genomic disorders. Here, we review recent progress in comparing the human and chimpanzee genomes and discuss how the differences detected have improved our understanding of the evolution of the human genome.     

Detection of the heteromorphic spectrum of heterochromatin in the human genome by in situ digestion using restriction endonuclease Alui

A battery of selective banding techniques has been utilized to identify the heteromorphic markers in the human genome. The recent addition of the AluI/Giemsa (G)-technique has helped not only in identifying the variable sites, but in characterizing their heteromorphic spectra. In the present investigation, we classified the pericentromeric heterochromatin by the AluI/G-technique by its size and position using 50 normal individuals and suggested the potential uses of this banding technique over earlier methods. © 1992 Wiley-Liss, Inc.     

GeneLynx: a gene-centric portal to the human genome.

GeneLynx is a meta-database providing an extensive collection of hyperlinks to human gene-specific information in diverse databases available on the Internet. The GeneLynx project is based on the simple notion that given any gene-specific identifier (accession number, gene name, text, or sequence), scientists should be able to access a single location that provides a set of links to all the publicly available information pertinent to the specified human gene. GeneLynx was implemented as an extensible relational database with an intuitive and user-friendly Web interface. The data are automatically extracted from more than 40 external resources, using appropriate approaches to maximize coverage of the available data. Construction and curation of the system is mediated by a custom set of software tools. An indexing utility is provided to facilitate the establishment of hyperlinks in external databases. A unique feature of the GeneLynx system is a communal curation system for user-aided annotation. GeneLynx can be accessed freely at http://www.genelynx.org.     

Genetic signature for human risk assessment: Lessons from trichloroethylene

Trichloroethylene (TCE), an organic solvent commonly used for metal degreasing and as a chemical additive, is a significant environmental contaminant that poses health concerns in humans. The US Environmental Protection Agency (EPA) is currently revising the 2001 TCE human risk assessment draft. The next draft is expected to be ready in 2008. TCE metabolites are detectable in humans and carry varying potencies for induction of cancers in animals. Genomic mechanisms have been explored in animals and humans to link TCE to carcinogenesis. DNA analysis provides an opportunity for detection of unique genetic alterations representing a signature of TCE exposure. These alterations can arise from genotoxic and nongenotoxic pathways at multiple points throughout tumorigenesis. Although fixation of alterations may require several stages of selection and modification, the spectra can be specific to TCE. Only a fraction of these alterations eventually lead to tumor formation and some contribute to tumor progression. Genetic events in two major TCE target organs are reviewed, including the VHL gene in kidney, and the Ras gene and genome‐wide hypomethylation in liver. Attempts to identify a genetic signature of TCE exposure are challenged by inconsistent findings, lack of evidence of promutagenic lesions, biological relevance of specific genomic changes, and likelihood of coexposures. For human risk assessment, genome‐wide screening is useful and is possible with the development of new DNA‐sequencing technologies. Genetic screening for preneoplastic and tumor tissues from high‐risk population is proposed to exclude the noise of passenger mutations and genetic polymorphisms. Environ. Mol. Mutagen., 2009. Published 2008 Wiley‐Liss, Inc.     

Decoding and rejuvenating human ageing genomes: Lessons from mosaic chromosomal alterations

One of the most curious findings emerged from genome-wide studies over the last decade was that genetic mosaicism is a dominant feature of human ageing genomes. The clonal dominance of genetic mosaicism occurs preceding the physiological and physical ageing and associates with propensity for diseases including cancer, Alzheimer’s disease, cardiovascular disease and diabetes. These findings are revolutionizing the ways biologists thinking about health and disease pathogenesis. Among all mosaic mutations in ageing genomes, mosaic chromosomal alterations (mCAs) have the most significant functional consequences because they can produce intercellular genomic variations simultaneously involving dozens to hundreds or even thousands genes, and therefore have most profound effects in human ageing and disease etiology. Here, we provide a comprehensive picture of the landscapes, causes, consequences and rejuvenation of mCAs at multiple scales, from cell to human population, by reviewing data from cytogenetic, genetic and genomic studies in cells, animal models (fly and mouse) and, more frequently, large-cohort populations. A detailed decoding of ageing genomes with a focus on mCAs may yield important insights into the genomic architecture of human ageing, accelerate the risk stratification of age-related diseases (particularly cancers) and development of novel targets and strategies for delaying or rejuvenating human (genome) ageing.