Genomic analysis links the American mink Royal pastel coat phenotype to retroviral element type 1 insertion in the HPS3 gene.

To date, only 10 of the more than 30 fur colours that had been observed in American mink (Neogale vison) have been linked to specific genes. The Royal pastel fur colour is part of a large family of brownish colours that are quite similar to one another, making breeding and selecting processes more difficult. Here we carried out whole-genome sequencing of five American minks with Royal pastel (b/b) phenotypes originating from two distinct mink populations. We identified an insertion of endogenous retroviral element type 1 (ERV1) into the first intron of the gene encoding the HPS3 protein, which regulates the trafficking of tyrosinase-containing vesicles to maturing melanosomes. With Cas9-targeted nanopore sequencing, we reconstructed the full-length sequence of the 11.7 Kb ERV1 insertion and observed hypermethylation that spread to the HPS3 gene promoter region. These findings highlight the role of HPS3 in the formation of melanosomes and melanin, as well as the genetic process regulating the intensity and spectrum of hair colour. Moreover, in mink breeding projects, these data are also useful for tracking economically important fur qualities.

Peripheral Blood Gene Expression Profiling Reveals Molecular Pathways Associated with Cervical Artery Dissection.

Cervical artery dissection (CeAD) is the primary cause of ischemic stroke in young adults. Monogenic heritable connective tissue diseases account for fewer than 5% of cases of CeAD. The remaining sporadic cases have known risk factors. The clinical, radiological, and histological characteristics of systemic vasculopathy and undifferentiated connective tissue dysplasia are present in up to 70% of individuals with sporadic CeAD. Genome-wide association studies identified CeAD-associated genetic variants in the non-coding genomic regions that may impact the gene transcription and RNA processing. However, global gene expression profile analysis has not yet been carried out for CeAD patients. We conducted bulk RNA sequencing and differential gene expression analysis to investigate the expression profile of protein-coding genes in the peripheral blood of 19 CeAD patients and 18 healthy volunteers. This was followed by functional annotation, heatmap clustering, reports on gene-disease associations and protein-protein interactions, as well as gene set enrichment analysis. We found potential correlations between CeAD and the dysregulation of genes linked to nucleolar stress, senescence-associated secretory phenotype, mitochondrial malfunction, and epithelial-mesenchymal plasticity.

Neuronal Hyperactivation in EEG Data during Cognitive Tasks Is Related to the Apolipoprotein J/Clusterin Genotype in Nondemented Adults.

The clusterin (CLU) rs11136000 CC genotype is a probable risk factor for Alzheimer's disease (AD). CLU, also known as the apolipoprotein J gene, shares certain properties with the apolipoprotein E (APOE) gene with a well-established relationship with AD. This study aimed to determine whether the electrophysiological patterns of brain activation during the letter fluency task (LFT) depend on CLU genotypes in adults without dementia. Previous studies have shown that LFT performance involves activation of the frontal cortex. We examined EEG alpha1 and alpha2 band desynchronization in the frontal regions during the LFT in 94 nondemented individuals stratified by CLU (rs11136000) genotype. Starting at 30 years of age, CLU CC carriers exhibited more pronounced task-related alpha2 desynchronization than CLU CT&TT carriers in the absence of any differences in LFT performance. In CLU CC carriers, alpha2 desynchronization was significantly correlated with age. Increased task-related activation in individuals at genetic risk for AD may reflect greater "effort" to perform the task and/or neuronal hyperexcitability. The results show that the CLU genotype is associated with neuronal hyperactivation in the frontal cortex during cognitive tasks performances in nondemented individuals, suggesting systematic vulnerability of LFT related cognitive networks in people carrying unfavorable CLU alleles.

Genetic Variant in GRM1 Underlies Congenital Cerebellar Ataxia with No Obvious Intellectual Disability.

Metabotropic glutamate receptor 1 (mGluR1) plays a crucial role in slow excitatory postsynaptic conductance, synapse formation, synaptic plasticity, and motor control. The GRM1 gene is expressed mainly in the brain, with the highest expression in the cerebellum. Mutations in the GRM1 gene have previously been known to cause autosomal recessive and autosomal dominant spinocerebellar ataxias. In this study, whole-exome sequencing of a patient from a family of Azerbaijani origin with a diagnosis of congenital cerebellar ataxia was performed, and a new homozygous missense mutation in the GRM1 gene was identified. The mutation leads to the homozygous amino acid substitution of p.Thr824Arg in an evolutionarily highly conserved region encoding the transmembrane domain 7, which is critical for ligand binding and modulating of receptor activity. This is the first report in which a mutation has been identified in the last transmembrane domain of the mGluR1, causing a congenital autosomal recessive form of cerebellar ataxia with no obvious intellectual disability. Additionally, we summarized all known presumable pathogenic genetic variants in the GRM1 gene to date. We demonstrated that multiple rare variants in the GRM1 underlie a broad diversity of clinical neurological and behavioral phenotypes depending on the nature and protein topology of the mutation.

Genetic association of apolipoprotein E genotype with EEG alpha rhythm slowing and functional brain network alterations during normal aging.

The ε4 allele of the apolipoprotein E (APOE4+) genotype is a major genetic risk factor for Alzheimer's disease (AD), but the mechanisms underlying its influence remain incompletely understood. The study aimed to investigate the possible effect of the APOE genotype on spontaneous electroencephalogram (EEG) alpha characteristics, resting-state functional MRI (fMRI) connectivity (rsFC) in large brain networks and the interrelation of alpha rhythm and rsFC characteristics in non-demented adults during aging. We examined the EEG alpha subband's relative power, individual alpha peak frequency (IAPF), and fMRI rsFC in non-demented volunteers (age range 26-79 years) stratified by the APOE genotype. The presence of the APOE4+ genotype was associated with lower IAPF and lower relative power of the 11-13 Hz alpha subbands. The age related decrease in EEG IAPF was more pronounced in the APOE4+ carriers than in the APOE4+ non-carriers (APOE4-). The APOE4+ carriers had a stronger fMRI positive rsFC of the interhemispheric regions of the frontoparietal, lateral visual and salience networks than the APOE4- individuals. In contrast, the negative rsFC in the network between the left hippocampus and the right posterior parietal cortex was reduced in the APOE4+ carriers compared to the non-carriers. Alpha rhythm slowing was associated with the dysfunction of hippocampal networks. Our results show that in adults without dementia APOE4+ genotype is associated with alpha rhythm slowing and that this slowing is age-dependent. Our data suggest predominant alterations of inhibitory processes in large-scale brain network of non-demented APOE4+ carriers. Moreover, dysfunction of large-scale hippocampal network can influence APOE-related alpha rhythm vulnerability.

Genomic analysis of a novel Neanderthal from Mezmaiskaya Cave provides insights into the genetic relationships of Middle Palaeolithic populations.

The Mezmaiskaya cave is located on the North Caucasus near the border that divides Europe and Asia. Previously, fossil remains for two Neanderthals were reported from Mezmaiskaya Cave. A tooth from the third archaic hominin specimen (Mezmaiskaya 3) was retrieved from layer 3 in Mezmaiskaya Cave. We performed genome sequencing of Mezmaiskaya 3. Analysis of partial nuclear genome sequence revealed that it belongs to a Homo sapiens neanderthalensis female. Based on a high-coverage mitochondrial genome sequence, we demonstrated that the relationships of Mezmaiskaya 3 to Mezmaiskaya 1 and Stajnia S5000 individuals were closer than those to other Neanderthals. Our data demonstrate the close genetic connections between the early Middle Palaeolithic Neanderthals that were replaced by genetically distant later group in the same geographic areas. Based on mitochondrial DNA (mtDNA) data, we suggest that Mezmaiskaya 3 was the latest Neanderthal individual from the early Neanderthal's branches. We proposed a hierarchical nomenclature for the mtDNA haplogroups of Neanderthals. In addition, we retrieved ancestral mtDNA mutations in presumably functional sites fixed in the Neanderthal clades, and also provided the first data showing mtDNA heteroplasmy in Neanderthal specimen.

Identification of mutant gene for Black crystal coat and non-allelic gene interactions in Neogale vison.

Sable (Martes zibellina) and American mink (Neogale vison) are valuable species characterized by a variety of coat colour produced on fur farms. Black crystal fur phenotype is Mendelian codominant trait: heterozygous animals (Cr/ +) have white guard hairs scattered predominantly on the spine and the head, while homozygous (Cr/Cr) minks have coats resembling the Himalayan (ch/ch) or white Hedlund (h/h) types. It is one of the most recent of more than 35 currently known phenotypic traits of fur colour in American mink. Black crystal fur phenotype was first described in 1984 in the Russian population of mink, which had undergone selection for domestic defensive response to humans. Here, we performed whole-genome sequencing of American mink with Cr/Cr phenotype. We identified a missense mutation in the gene encoding the α-COP subunit of the COPI complex (COPA). The COPI complex mediates retrograde trafficking from the Golgi system to the endoplasmic reticulum and sorting of transmembrane proteins. We observed an interaction between a newly identified mutation in the COPA gene and a mutation in the microphthalmia-associated transcription factor (MITF), the latter mutation led to the formation of the white Hedlund (h/h) phenotype. Double heterozygotes for these mutations have an entirely white coat and a black-eyed phenotype similar to the phenotype of Cr/Cr or h/h minks. Our data could be useful for tracking economically valuable fur traits in mink breeding programs to contribute to global fur production.

Studying of Molecular Regulation of Developmental Processes of Lower Metazoans Exemplified by Cnidaria Using High-Throughput Sequencing.

A unique set of features and characteristics of species of the Cnidaria phylum is the one reason that makes them a model for a various studies. The plasticity of a life cycle and the processes of cell differentiation and development of an integral multicellular organism associated with it are of a specific scientific interest. A new stage of development of molecular genetic methods, including methods for high-throughput genome, transcriptome, and epigenome sequencing, both at the level of the whole organism and at the level of individual cells, makes it possible to obtain a detailed picture of the development of these animals. This review examines some modern approaches and advances in the reconstruction of the processes of ontogenesis of cnidarians by studying the regulatory signal transduction pathways and their interactions.

Genomics of Ancient Pathogens: First Advances and Prospects.

Paleogenomics is one of the urgent and promising areas of interdisciplinary research in the today's world science. New genomic methods of ancient DNA (aDNA) analysis, such as next generation sequencing (NGS) technologies, make it possible not only to obtain detailed genetic information about historical and prehistoric human populations, but also to study individual microbial and viral pathogens and microbiomes from different ancient and historical objects. Studies of aDNA of pathogens by reconstructing their genomes have so far yielded complete sequences of the ancient pathogens that played significant role in the history of the world: Yersinia pestis (plague), Variola virus (smallpox), Vibrio cholerae (cholera), HBV (hepatitis B virus), as well as the equally important endemic human infectious agents: Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy), and Treponema pallidum (syphilis). Genomic data from these pathogens complemented the information previously obtained by paleopathologists and allowed not only to identify pathogens from the past pandemics, but also to recognize the pathogen lineages that are now extinct, to refine chronology of the pathogen appearance in human populations, and to reconstruct evolutionary history of the pathogens that are still relevant to public health today. In this review, we describe state-of-the-art genomic research of the origins and evolution of many ancient pathogens and viruses and examine mechanisms of the emergence and spread of the ancient infections in the mankind history.

Shadow coat colour in American mink associated with a missense mutation in the KIT gene.

The classical genetic analysis describes more 35 mutations that are involved in the formation of the American mink (Neovison vison) fur colour phenotype. To date, only eight of these mutations have been linked to specific genes. Shadow is a member of the commercially valuable Black cross colour family. Here, we performed whole-genome sequencing of the American mink with a Shadow Silverblue (Sh /+ p/p) phenotype. We identified a missense mutation (c.2374 G>T) in the gene encoding the KIT proto-oncogene, receptor tyrosine kinase gene (KIT), which plays a critical role in melanogenesis as well as in the survival, growth and development of other cell types. The reported mutation results in amino acid substitution p.Asp792Tyr in a highly conserved catalytic loop of the KIT protein.

Complete genomic and epigenetic maps of human centromeres.

Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, and functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere human genome assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric and centromeric repeats, which constitute 6.2% of the genome (189.9 megabases). Detailed maps of these regions revealed multimegabase structural rearrangements, including in active centromeric repeat arrays. Analysis of centromere-associated sequences uncovered a strong relationship between the position of the centromere and the evolution of the surrounding DNA through layered repeat expansions. Furthermore, comparisons of chromosome X centromeres across a diverse panel of individuals illuminated high degrees of structural, epigenetic, and sequence variation in these complex and rapidly evolving regions.

Novel genes bearing mutations in rare cases of early-onset ataxia with cerebellar hypoplasia.

We propose an approach for the identification of mutant genes for rare diseases in single cases of unknown etiology. All genes with rare biologically significant variants sorted from individual exome data are tested further for profiling of their spatial-temporal and cell/tissue specific expression compared to that of their paralogs. We developed a simple bioinformatics tool ("Essential Paralogue by Expression" (EPbE)) for such analysis. Here, we present rare clinical forms of early ataxia with cerebellar hypoplasia. Using whole-exome sequencing and the EPbE tool, we identified two novel mutant genes previously not associated with congenital human diseases. In Family I, the unique missense mutation (p.Lys258Glu) was found in the LRCH2 gene inherited in an X-linked manner. p.Lys258Glu occurs in the evolutionarily invariant site of the leucine-rich repeat domain of LRCH2. In Family II and Family III, the identical genetic variant was found in the CSMD1 gene inherited as an autosomal-recessive trait. The variant leads to amino acid substitution p.Gly2979Ser in a highly conserved region of the complement-interacting domain of CSMD1. The LRCH2 gene for Family I patients (in which congenital cerebellar hypoplasia was associated with demyelinating polyneuropathy) is expressed in Schwann and precursor Schwann cells and predominantly over its paralogous genes in the developing cerebellar cortex. The CSMD1 gene is predominantly expressed over its paralogous genes in the cerebellum, specifically in the period of late childhood. Thus, the comparative spatial-temporal expression of the selected genes corresponds to the neurological manifestations of the disease.

The Interactive Effect of Genetic and Epigenetic Variations in FKBP5 and ApoE Genes on Anxiety and Brain EEG Parameters.

FKBP51 is a key stress-responsive regulator of the hypothalamic-pituitary-adrenal axis. To elucidate the contribution of rs1360780 FKBP5 C/T alleles to aging and longevity, we genotyped FKBP5 in a cohort of 800 non-demented and Alzheimer's disease (AD) subjects of different age, taking into account the allele state of ApoE ε4, the major risk factor for AD. Furthermore, we searched for the association of FKBP5 with subcohorts of non-demented subjects evaluated for anxiety and resting-state quantitative EEG characteristics, associated with cognitive, emotional, and functional brain activities. We observed that increased state anxiety scores depend on the combination of the FKBP5 and ApoE genotypes and on the DNA methylation state of the FKBP5 promoter and ApoE genotype. We also found a significant gender-dependent correlation between FKBP5 promoter methylation and alpha-, delta-, and theta-rhythms. Analysis of the FKBP5 expression in an independent cohort revealed a significant upregulation of FKBP5 in females versus males. Our data suggest a synergistic effect of the stress-associated (FKBP5) and neurodegeneration-associated (ApoE) gene alleles on anxiety and the gender-dependent effect of FKBP5 on neurophysiological brain activity.

Neurodevelopmental Syndrome with Intellectual Disability, Speech Impairment, and Quadrupedia Is Associated with Glutamate Receptor Delta 2 Gene Defect.

Bipedalism, speech, and intellect are the most prominent traits that emerged in the evolution of Homo sapiens. Here, we describe a novel genetic cause of an "involution" phenotype in four patients, who are characterized by quadrupedal locomotion, intellectual impairment, the absence of speech, small stature, and hirsutism, observed in a consanguineous Brazilian family. Using whole-genome sequencing analysis and homozygous genetic mapping, we identified genes bearing homozygous genetic variants and found a homozygous 36.2 kb deletion in the gene of glutamate receptor delta 2 (GRID2) in the patients, resulting in the lack of a coding region from the fifth to the seventh exons. The GRID2 gene is highly expressed in the cerebellum cortex from prenatal development to adulthood, specifically in Purkinje neurons. Deletion in this gene leads to the loss of the alpha chain in the extracellular amino-terminal protein domain (ATD), essential in protein folding and transport from the endoplasmic reticulum (ER) to the cell surface. Then, we studied the evolutionary trajectories of the GRID2 gene. There was no sign of strong selection of the highly conservative GRID2 gene in ancient hominids (Neanderthals and Denisovans) or modern humans; however, according to in silico tests using the Mfold tool, the GRID2 gene possibly gained human-specific mutations that increased the stability of GRID2 mRNA.

Genome Analysis of Sable Fur Color Links a Lightened Pigmentation Phenotype to a Frameshift Variant in the Tyrosinase-Related Protein 1 Gene.

Sable (Martes zibellina) is one of the most valuable species of fur animals. Wild-type sable fur color varies from sandy-yellow to black. Farm breeding and 90 years of directional selection have resulted in a generation of several sable breeds with a completely black coat color. In 2005, an unusually chocolate (pastel) puppy was born in the Puschkinsky State Fur Farm (Russia). We established that the pastel phenotype was inherited as a Mendelian autosomal recessive trait. We performed whole-genome sequencing of the sables with pastel fur color and identified a frameshift variant in the gene encoding membrane-bound tyrosinase-like enzyme (TYRP1). TYRP1 is involved in the stability of the tyrosinase enzyme and participates in the synthesis of eumelanin. These data represent the first reported variant linked to fur color in sables and reveal the molecular genetic basis for pastel color pigmentation. These data are also useful for tracking economically valuable fur traits in sable breeding programs.

Genome analysis of American minks reveals link of mutations in Ras-related protein-38 gene to Moyle brown coat phenotype.

Over 35 fur colours have been described in American mink (Neovison vison), only six of which have been previously linked to specific genes. Moyle fur colour belongs to a wide group of brownish colours that are highly similar to each other, which complicates selection and breeding procedures. We performed whole genome sequencing for two American minks with Moyle (m/m) and Violet (a/a m/m /p/p) phenotypes. We identified two frame-shift mutations in the gene encoding Ras-related protein-38 (RAB38), which regulates the trafficking of tyrosinase-containing vesicles to maturing melanosomes. The results highlight the role of RAB38 in the biogenesis of melanosomes and melanin and the genetic mechanism contributing to hair colour variety and intensity. These data are also useful for tracking economically valuable fur traits in mink breeding programmes.

Chromatin profiling of cortical neurons identifies individual epigenetic signatures in schizophrenia.

Both heritability and environment contribute to risk for schizophrenia. However, the molecular mechanisms of interactions between genetic and non-genetic factors remain unclear. Epigenetic regulation of neuronal genome may be a presumable mechanism in pathogenesis of schizophrenia. Here, we performed analysis of open chromatin landscape of gene promoters in prefrontal cortical (PFC) neurons from schizophrenic patients. We cataloged cell-type-based epigenetic signals of transcriptional start sites (TSS) marked by histone H3-K4 trimethylation (H3K4me3) across the genome in PFC from multiple schizophrenia subjects and age-matched control individuals. One of the top-ranked chromatin alterations was found in the major histocompatibility (MHC) locus on chromosome 6 highlighting the overlap between genetic and epigenetic risk factors in schizophrenia. The chromosome conformation capture (3C) analysis in human brain cells revealed the architecture of multipoint chromatin interactions between the schizophrenia-associated genetic and epigenetic polymorphic sites and distantly located HLA-DRB5 and BTNL2 genes. In addition, schizophrenia-specific chromatin modifications in neurons were particularly prominent for non-coding RNA genes, including an uncharacterized LINC01115 gene and recently identified BNRNA_052780. Notably, protein-coding genes with altered epigenetic state in schizophrenia are enriched for oxidative stress and cell motility pathways. Our results imply the rare individual epigenetic alterations in brain neurons are involved in the pathogenesis of schizophrenia.

Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons.

Human prefrontal cortex (PFC) is associated with broad individual variabilities in functions linked to personality, social behaviors, and cognitive functions. The phenotype variabilities associated with brain functions can be caused by genetic or epigenetic factors. The interactions between these factors in human subjects is, as of yet, poorly understood. The heterogeneity of cerebral tissue, consisting of neuronal and nonneuronal cells, complicates the comparative analysis of gene activities in brain specimens. To approach the underlying neurogenomic determinants, we performed a deep analysis of open chromatin-associated histone methylation in PFC neurons sorted from multiple human individuals in conjunction with whole-genome and transcriptome sequencing. Integrative analyses produced novel unannotated neuronal genes and revealed individual-specific chromatin "blueprints" of neurons that, in part, relate to genetic background. Surprisingly, we observed gender-dependent epigenetic signals, implying that gender may contribute to the chromatin variabilities in neurons. Finally, we found epigenetic, allele-specific activation of the testis-specific gene nucleoporin 210 like (NUP210L) in brain in some individuals, which we link to a genetic variant occurring in <3% of the human population. Recently, the NUP210L locus has been associated with intelligence and mathematics ability. Our findings highlight the significance of epigenetic-genetic footprinting for exploring neurologic function in a subject-specific manner.-Gusev, F. E., Reshetov, D. A., Mitchell, A. C., Andreeva, T. V., Dincer, A., Grigorenko, A. P., Fedonin, G., Halene, T., Aliseychik, M., Goltsov, A. Y., Solovyev, V., Brizgalov, L., Filippova, E., Weng, Z., Akbarian, S., Rogaev, E. I. Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons.

Genome analysis identifies the mutant genes for common industrial Silverblue and Hedlund white coat colours in American mink.

The fur colour of American mink (Neovison vison) involves over 35 traits, but only three of these have been linked to specific genes. Despite being the most popular, coat colours Silverblue and Hedlund white remain uncharacterized genetically. The former is the first genetic mutant of fur colour identified in minks, while the latter is a commercially valuable phenotype that can be dyed easily. Here, we performed the whole genome sequencing for two American mink breeds with Silverblue and Hedlund white coats. We identified mutations in splice donor sites of genes coding melanophilin (MLPH) and microphthalmia-associated transcription factor (MITF) that regulate melanosome transport and neural-crest-derived melanocyte development, respectively. Both mutations cause mRNA splicing impairments that lead to a shift in open reading frames of MLPH and MITF. We conclude that our data should be useful for tracking economically valuable fur traits in mink breeding programs to contribute to global fur production.

Haplotype analysis of APOE intragenic SNPs.

BACKGROUND: APOE Îµ4 allele is most common genetic risk factor for Alzheimer's disease (AD) and cognitive decline. However, it remains poorly understood why only some carriers of APOE Îµ4 develop AD and how ethnic variabilities in APOE locus contribute to AD risk. Here, to address the role of APOE haplotypes, we reassessed the diversity of APOE locus in major ethnic groups and in Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset on patients with AD, and subjects with mild cognitive impairment (MCI), and control non-demented individuals. RESULTS: We performed APOE gene haplotype analysis for a short block of five SNPs across the gene using the ADNI whole genome sequencing dataset. The compilation of ADNI data with 1000 Genomes identified the APOE ε4 linked haplotypes, which appeared to be distant for the Asian, African and European populations. The common European ε4-bearing haplotype is associated with AD but not with MCI, and the Africans lack this haplotype. Haplotypic inference revealed alleles that may confer protection against AD. By assessing the DNA methylation profile of the APOE haplotypes, we found that the AD-associated haplotype features elevated APOE CpG content, implying that this locus can also be regulated by genetic-epigenetic interactions. CONCLUSIONS: We showed that SNP frequency profiles within APOE locus are highly skewed to population-specific haplotypes, suggesting that the ancestral background within different sites at APOE gene may shape the disease phenotype. We propose that our results can be utilized for more specific risk assessment based on population descent of the individuals and on higher specificity of five site haplotypes associated with AD.