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PubMed2026

3D epigenome of glial cell types in developing human cortex.

The human cortex is complex and heterogeneous, undergoing extensive expansion during development1,2. Our prior study of neurogenesis, including radial glia (RG), intermediate progenitor cells, excitatory neurons and interneurons demonstrated that chromatin looping underlies transcriptional regulation for lineage-specific genes, shedding light on how non-coding genetic variants contribute to neuropsychiatric disorders by means of cell-type-specific gene regulation3. RG have a crucial role in generating cellular diversity through both neurogenesis and gliogenesis and can be further classified into ventricular RG (vRG) and outer RG (oRG)4,5. Given their significance in cortical development, we conducted a comprehensive three-dimensional (3D) epigenomic analysis of four main glial populations, including vRG, oRG, oligodendrocyte precursor cells and microglia, from the mid-gestational human neocortex. By integrating gene expression, chromatin accessibility, DNA methylation and 3D chromatin interactions, we identified cell-type-specific candidate cis-regulatory elements (cCREs) and validated their regulatory function using transgenic mouse embryos. Using machine learning, we prioritized 112 schizophrenia risk variants within glia cCREs and further confirmed the predicted vRG enhancer disruption by the rs4449074 risk allele in vivo. Finally, oRG cCREs are enriched for human accelerated regions compared with other cCREs and a subset of human accelerated regions show activity differences from their chimpanzee orthologues that interact with genes involved in neuronal development. Our findings advance the understanding of human-specific gene regulation during corticogenesis.

Journal Article↗
PubMed2006

RNAi: a potential therapy for the dominantly inherited nucleotide repeat diseases.

Genetic diseases that are accompanied by central nervous system involvement are often fatal. Among these are the autosomal dominant neurogenetic diseases caused by nucleotide repeat expansion. For example, Huntington's disease (HD) and spinal cerebellar ataxia are caused by expansion of a tract of CAGs encoding glutamine. In HD and the other CAG-repeat expansion diseases, the expansion is in the coding region. Myotonic dystrophy is caused by repeat expansions of CUG or CCTG in noncoding regions, and the mutant RNA is disease causing. Treatments for these disorders are limited to symptomatic intervention. RNA interference (RNAi), which is a method for inhibiting target gene expression, provides a unique tool for therapy by attacking the fundamental problem directly. In this review, we describe briefly several representative disorders and their respective molecular targets, and methods to accomplish therapeutic RNAi. Finally, we summarize studies performed to date.

Animals↗
PubMed2002

Human demographic history: refining the recent African origin model.

Recent studies of large portions of the human genome support a recent origin of modern humans from an African stock after a bottleneck of moderate size followed by a range expansion out of Africa. Under this simple scenario, patterns of molecular diversity suggest that balancing selection could be more prevalent than positive selection in coding regions.

Africa↗
PubMed2004

Detecting the footprint of positive selection in a european population of Drosophila melanogaster: multilocus pattern of variation and distance to coding regions.

The effects on nucleotide variation of adaptations to temperate habitats and of the possible bottleneck associated with the origin of European populations of Drosophila melanogaster should be detectable in DNA sequences given the short time elapsed relative to the species population size. We surveyed nucleotide variation in 109 fragments distributed across the X chromosome in a European population of D. melanogaster to detect the footprint of positive selection. Fragments were located primarily in large noncoding regions. Multilocus tests based on Tajima's D statistic revealed a significant departure from neutral expectations in a stationary panmictic population, with an important contribution from both positive and negative D values. A positive relationship between Tajima's D values and distance to coding region was detected, with a comparative excess of significantly negative D values in the subset of fragments closer to coding regions. Also, there was a significant heterogeneity in the polymorphism to divergence ratio, with 12 fragments contributing 42% to the test statistic. Moreover, these fragments were comparatively closer to coding regions. These findings would imply positive selection events, and thus selective sweeps, during the species expansion to Europe.

Animals↗
PubMed1983

Two-dimensional gel comparisons of murine H-2D region-associated antigens of different H-2 haplotypes.

The heterogeneity of histocompatibility antigens encoded within the H-2D region of murine chromosome 17 was investigated in several mouse strains using monoclonal antibodies. Sequential immunoprecipitation and two dimensional gel electrophoresis (2D) were used to determine the number and structural relatedness of antigenically distinct products of the same H-2D region. Strikingly different, haplotype-specific patterns were observed. The three antigenically distinct molecules, Dd, Ld and Rd, all encoded within the Dd region, each showed a unique constellation of spots by 2D analysis, although the Ld and Rd molecules showed more structural similarity to each other than either molecule showed to the Dd molecule. Comparisons of the Ld and Rd molecules using sequential precipitations and a cloned Ld gene suggested that they are not conformation or glycosylation variants of the same polypeptide, implying they have different primary amino acid sequences. Using an anti-Ld antibody, the Ldml molecule was isolated from cells of the Dd region mutant mouse strain B10.D2-H-2dml and was found to have a 2D gel profile clearly distinguishable from the profile of either Ld or Dd molecules isolated from the wild-type strain B10.D2. Of the three antigenically-distinct molecules determined by the Dq region, the 2D gel profile of the Rq molecule was different from that of the Dq and Lq, the latter two molecules being indistinguishable. In contrast to these findings, analysis of the gene products of the Db region failed to resolve either antigenic or molecular heterogeneity and the multiple, antigenically distinct gene products of the Dw16 region were indistinguishable by 2D comparisons. These haplotype specific variations in the structural relatedness and number of antigenically distinct molecules determined by D region genes support the hypothesis that class I MHC genes are in a dynamic evolutionary state of gene expansion and contraction.

Animals↗
PubMed2005

Economy, speed and size matter: evolutionary forces driving nuclear genome miniaturization and expansion.

BACKGROUND: Nuclear genome size varies 300 000-fold, whereas transcriptome size varies merely 17-fold. In the largest genomes nearly all DNA is non-genic secondary DNA, mostly intergenic but also within introns. There is now compelling evidence that secondary DNA is functional, i.e. positively selected by organismal selection, not the purely neutral or 'selfish' outcome of mutation pressure. The skeletal DNA theory argued that nuclear volumes are genetically determined primarily by nuclear DNA amounts, modulated somewhat by genes affecting the degree of DNA packing or unfolding; the huge spread of nuclear genome sizes is the necessary consequence of the origin of the nuclear envelope and the nucleation of its assembly by DNA, plus the adaptively significant 300 000-fold range of cell volumes and selection for balanced growth by optimizing karyoplasmic volume ratios (essentially invariant with cell volume in growing/multiplying cells). This simple explanation of the C-value paradox is refined here in the light of new insights into the nature of heterochromatin and the nuclear lamina, the genetic control of cell volume, and large-scale eukaryote phylogeny, placing special emphasis on protist test cases of the basic principles of nuclear genome size evolution. GENOME MINIATURIZATION: and Expansion Intracellular parasites (e.g. Plasmodium, microsporidia) dwarfed their genomes by gene loss and eliminating virtually all secondary DNA. The primary driving forces for genome reduction are metabolic and spatial economy and cell multiplication speed. Most extreme nuclear shrinkage yielded genomes as tiny as 0.38 Mb (making the nuclear genome size range effectively 1.8 million-fold!) in some minute enslaved nuclei (nucleomorphs) of cryptomonads and chlorarachneans, chimaeric cells that also retain a separate normal large nucleus. The latter shows typical correlation between genome size and cell volume, but nucleomorphs do not despite co-existing in the same cell for >500 My. Thus mutation pressure does not inexorably increase genome size; selection can eliminate essentially all non-coding DNA if need be. Nucleomorphs and microsporidia even reduced gene size. Expansion of secondary DNA in the main nucleus, and in large-celled eukaryotes generally, must be positively selected for function. Ciliate nuclear dimorphism provides a key test that refutes the selfish DNA and strongly supports the skeletal DNA/karyoplasmic ratio interpretation of genome size evolution. GENETIC CONTROL OF CELL VOLUME IS MULTIGENIC: The quantitatively proportional correlation between genome size and cell size cannot be explained by purely mutational theories, as eukaryote cell volumes are causally determined by cell cycle control genes, not by DNA amounts.

Animals↗
PubMed1997

The expansion of the CAG repeat in ataxin-2 is a frequent cause of autosomal dominant spinocerebellar ataxia.

The autosomal dominant spinocerebellar ataxias (ADSCAs) are a heterogeneous group of late-onset neurodegenerative disorders with overlapping clinical features. Genetic linkage studies have identified at least seven distinct loci for the ADSCAs, allowing the genetic classification of these disorders. The spinocerebellar ataxia type 2 (SCA2) locus was mapped to chromosome 12, and a gene responsible for this disorder was recently isolated. The mutation causing SCA2 is an expansion of a trinucleotide CAG repeat contained within the coding region of a novel gene. We describe the results of genotypic analysis for the SCA2 repeat in individuals with ADSCA who were previously found negative for CAG repeat expansions in the SCA1, SCA3, or SCA6 genes. The expanded CAG repeat has been identified in 15 independent families. Repeat instability and anticipation were observed in two large kindreds. The SCA2 mutation was found in 18% of our ADSCA kindreds, confirming the high proportion of SCA2 among this group of disorders.

Adolescent↗
PubMed2001

Vehicles for genetic vaccines against human immunodeficiency virus: induction of T cell-mediated immune responses.

Success of a candidate vaccine against human immunodeficiency virus (HIV) depends on the type, site, strength, longevity and specificity of the immune responses it induces. The specificity of a vaccine is determined by the HIV-derived immunogens it employs in its formulation. Central to the other features is a correct and efficient delivery of the immunogens to the relevant cells of the immune system, which leads to orchestrated actions of millions of cells of several types and functions at multiple sites in the body. Thus, for elicitation of cytotoxic T lymphocyte responses, immunogens have to be delivered to the so called 'professional' antigen-presenting cells in a way that leads to a specific activation and expansion of naïve or precursor T cells, subsequent maturation of effector functions and, importantly, generation of a potent immunological memory. Many aspects of theseprocesses are currently unknown. However, it is very likely that the immunogenicities of genetic vaccines, i.e. vaccines delivering genes coding for immunogens rather than purified possibly adjuvanted proteins or peptides themselves, are in great part determined by the choice of vaccine vehicles and route of administration. In addition, vaccine immunogenicities can be augmented semi-rationally by immunogen engineering and co-delivering immunomodulatory molecules, and empirically by combining different vehicles expressing the same immunogen in heterologous prime-boost protocols. In any case, a successful vaccination strategy against HIV as well as other chronic viral infections has to elicit better immune responses than the natural infections do.

AIDS Vaccines↗
PubMed1995

Molecular cloning of a full-length cDNA for dentatorubral-pallidoluysian atrophy and regional expressions of the expanded alleles in the CNS.

Dentatorubral-pallidoluysian atrophy (DRPLA) is an autosomal dominant neurodegenerative disorder characterized by genetic anticipation and variable combinations of symptoms including myoclonus, epilepsy, cerebellar ataxia, choreoathetosis, and dementia. Recently, we discovered that DRPLA is caused by unstable expansion of a CAG repeat of a gene on the short arm of chromosome 12. We determined the consensus DRPLA cDNA sequence containing the complete coding region for 1,185 amino acids. The CAG repeat, which is expanded in DRPLA, is located 1,462 bp downstream from the putative methionine initiation codon and encodes a poly-glutamine tract. Although poly-serine and proline tracts exist near the CAG repeats, these polyserine or proline tracts did not show any polymorphisms, which is in strong contrast to the high heterogeneity in the length of the CAG repeat. Northern blot analysis revealed a 4.7-kb transcript that is widely expressed in various tissues including heart, lung, kidney, placenta, skeletal muscle, and brain. Reverse transcription-PCR analysis revealed that the expanded alleles are transcribed to levels comparable to those of normal alleles. These results indicate that there is no difference in transcriptional efficiency between expanded and normal alleles. Furthermore, mRNA from cerebellar hemispheres of DRPLA patients showed smaller sizes of CAG repeats compared with other regions of the brain, which reflects somatic mosaicism of the expanded alleles of the DRPLA gene.

Alleles↗
PubMed2003

Trinucleotide expansions leading to an extended poly-L-alanine segment in the poly (A) binding protein PABPN1 cause fibril formation.

The nuclear poly(A) binding protein (PABPN1) stimulates poly(A) polymerase and controls the lengths of poly(A) tails during pre-mRNA processing. The wild-type protein possesses 10 consecutive Ala residues immediately after the start methionine. Trinucleotide expansions in the coding sequence result in an extension of the Ala stretch to maximal 17 Ala residues in total. Individuals carrying the trinucleotide expansions suffer from oculopharyngeal muscular dystrophy (OPMD). Intranuclear inclusions consisting predominantly of PABPN1 have been recognized as a pathological hallmark of the genetic disorder. To elucidate the molecular events that lead to disease, recombinant PABPN1, and N-terminal fragments of the protein with varying poly-L-alanine stretches were analyzed. As the full-length protein displayed a strong tendency to aggregate into amorphous deposits, soluble N-terminal fragments were also studied. Expansion of the poly-L-alanine sequence to the maximal length observed in OPMD patients led to an increase of alpha-helical structure. Upon prolonged incubation the protein was found in fibrils that showed all characteristics of amyloid-like fibers. The lag-phase of fibril formation could be reduced by seeding. Structural analysis of the fibrils indicated antiparallel beta-sheets.

Amino Acid Sequence↗
PubMed2005

Biological, cellular, and molecular characteristics of an inducible transgenic skin tumor model: a review.

The genetically initiated Tg.AC transgenic mouse carries a transgene consisting of an oncogenic v-Ha-ras coding region flanked 5' by a mouse zeta-globin promoter and 3' by an SV-40 polyadenylation sequence. Located on chromosome 11, the transgene is transcriptionally silent until activated by chemical carcinogens, UV light, or full-thickness wounding. Expression of the transgene is an early event that drives cellular proliferation resulting in clonal expansion and tumor formation, the unique characteristics now associated with the Tg.AC mouse. This ras-dependent phenotype has resulted in the widespread interest and use of the Tg.AC mouse in experimental skin carcinogenesis and as an alternative carcinogenesis assay. This review examines the general biology of the tumorigenic responses observed in Tg.AC mice, the genetic interactions of the ras transgene, and explores the cellular and molecular regulation of zeta-globin promoted transgene expression. As a prototype alternative model to the current long-term rodent bioassays, the Tg.AC has generated a healthy discussion on the future of transgenic bioassays, and opened the doors for subsequent models for toxicity testing. The further exploration and elucidation of the molecular controls of transgene expression will enhance the usefulness of this mouse and enable a better understanding of the Tg.AC's discriminate response to chemical carcinogens.

Animals↗
PubMed2002

Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum.

The Malaria's Eve hypothesis, proposing a severe recent population bottleneck (about 3,000-5,000 years ago) of the human malaria parasite Plasmodium falciparum, has prompted a debate about the origin and evolution of the parasite. The hypothesis implies that the parasite population is relatively homogeneous, favouring malaria control measures. Other studies, however, suggested an ancient origin and large effective population size. To test the hypothesis, we analysed single nucleotide polymorphisms (SNPs) from 204 genes on chromosome 3 of P. falciparum. We have identified 403 polymorphic sites, including 238 SNPs and 165 microsatellites, from five parasite clones, establishing chromosome-wide haplotypes and a dense map with one polymorphic marker per approximately 2.3 kilobases. On the basis of synonymous SNPs and non-coding SNPs, we estimate the time to the most recent common ancestor to be approximately 100,000-180,000 years, significantly older than the proposed bottleneck. Our estimated divergence time coincides approximately with the start of human population expansion, and is consistent with a genetically complex organism able to evade host immunity and other antimalarial efforts.

Animals↗
PubMed1975

Normal and altered phenotypic expression of immunoglobulin genes.

Genetically controlled intraspecific differences between immunoglobulins (allotypes) provide valuable markers for the study of the quantitative expression of allelic and nonallelic alternative forms of immunoglobulins (Igs) during the normal development of rabbits. Heterozygous rabbits are mosaics of cells expressing different Ig-genes since fully differentiated productive cells generally secrete only one of alternative forms of Ig. The proportions of cells that differentiate to produce allelic forms of immunoglobulins during normal development depend on the particular heterozygous genotype. The normal proportions of some markers can be drastically altered if the differentiation of lymphoid cells in the young rabbit occurs in the milieu of antibody specific for one form (allotype suppression). An initiating step in the establishment of persistent allotype suppression is probably the interaction of antiallotype antibody with allotype-bearing receptors on lymphoid cell surfaces, but the mechanism for the maintenance of a state of chronic suppression may well be more complex. Allotype suppression can be viewed as one example of numerous immunological phenomena that reflect specific and finely tuned regulatory mechanisms governing the differentiation and clonal expansion of lymphoid cells destined to secrete immunoglobulins.

Alleles↗
PubMed1999

Transcribed dinucleotide microsatellites and their associated genes from channel catfish Ictalurus punctatus.

The presence of trinucleotide microsatellites within genes is a well-known cause for a number of genetic diseases. However, the precise distribution of dinucleotide microsatellites within genes is less well documented. Here we report 15 unique cDNAs containing dinucleotide repeats from the channel catfish Ictalurus punctatus. Gene identities of nine of the 15 cDNAs were determined, of which three encode structural genes, and six encode regulatory proteins. Five cDNAs harbored dinucleotide repeats in the 5' untranslated region (5'-NTR), nine in the 3'-NTR, and one in the coding region. The presence of these transcribed dinucleotide repeats and their potential expansion in size within coding regions could lead to disruption of the original protein and/or formation of new genes by frame shift. The low number of dinucleotide repeats within coding regions suggests that they were strongly selected against. All the transcribed microsatellite loci examined were polymorphic making them useful for gene mapping in catfish.

Animals↗
PubMed2003

Triplet repeats in human genome: distribution and their association with genes and other genomic regions.

MOTIVATION: Simple sequence repeats (SSRs) or microsatellite repeats are found abundantly in many prokaryotic and eukaryotic genomes. Among SSRs, triplet repeats are of special significance because some of them have been linked to various genetic disorders. The objective of the study is to analyze the triplet repeats of complete human genome and to identify the genes that contain the triplet repeats in their coding region. The analysis will help us to identify the candidate genes that have potential for repeat expansion. RESULTS: We have analyzed triplet repeats in the complete human genome from the publicly available sequences. Our analysis revealed that AGC and CCG repeat were predominantly present in the coding regions of the genome while UTRs and the upstream sequences contained CCG repeats in relative abundance. Analysis of density of triplet repeats (bp/Mb) revealed that AAT and AAC were the abundant repeats whereas ACT and ACG were the rare repeats found in human genome. We could identify about 2135 known or predicted genes that were associated with at least one of the triplet repeat types. A large proportion of putative transcripts that were identified by gene finding programs were found to be associated with triplet repeats. These transcripts will be the candidate genes for analysis of triplet repeat expansion and a possible association with disease phenotypes. Identification of 171 genes which contain a minimum of ten repeat units will be of particular interest in future in correlating their association with any disease phenotype due to the expansion potential of repeats present in them. The list of genes and other details of analysis are given in the online supplementary data (http://www.ingenovis.com/tripletrepeats).

Databases, Nucleic Acid↗
PubMed2003

Spinocerebellar ataxia type 6 and episodic ataxia type 2: differences and similarities between two allelic disorders.

Spinocerebellar ataxia type 6 (SCA6) is one of three allelic disorders caused by mutations of CACNA1A gene, coding for the pore-forming subunit of calcium channel type P/Q. SCA6 is associated with small expansions of a CAG repeat at the 3' end of the gene, while point mutations are responsible for its two allelic disorders (Episodic Ataxia type 2 and Familial Hemiplegic Migraine). Genetic, clinical, pathological and pathophysiological data of SCA6 patients are reviewed and compared to those of other SCAs with expanded CAG repeats as well as to those of its allelic channelopathies, with particular reference to Episodic Ataxia type 2. Overall SCA6 appears to share features with both types of disorders, and the question as to whether it belongs to polyglutamine disorders or to channelopathies remains unanswered at present.

Alleles↗
PubMed1996

Mutations in American families with spinocerebellar ataxia (SCA) type 3: SCA3 is allelic to Machado-Joseph disease.

We identified an expansion of the CAG trinucleotide repeat in the coding region of the Machado-Joseph disease gene in 7 of 24 American families diagnosed with autosomal dominant ataxia. All affected individuals were heterozygous for an expanded allele that ranged from 67 to more than 200 CAG repeats, whereas the normal allele had 14 to 33 repeats. In contrast to the Azorean-Portuguese origins of Machado-Joseph disease, the two largest American families were of German and Dutch-African descent. Clinical, pathologic, and genetic evaluations suggest that American families with spinocerebellar ataxia type 3 differ from those with Machado-Joseph disease by their ethnic origins, predominant spinopontine atrophy, lack of dystonic features, and larger CAG repeat expansion.

Adult↗