Patterns of sequence conservation in presynaptic neural genes

BACKGROUND: The neuronal synapse is a fundamental functional unit in the central nervous system of animals. Because synaptic function is evolutionarily conserved, we reasoned that functional sequences of genes and related genomic elements known to play important roles in neurotransmitter release would also be conserved. RESULTS: Evolutionary rate analysis revealed that presynaptic proteins evolve slowly, although some members of large gene families exhibit accelerated evolutionary rates relative to other family members. Comparative sequence analysis of 46 megabases spanning 150 presynaptic genes identified more than 26,000 elements that are highly conserved in eight vertebrate species, as well as a small subset of sequences (6%) that are shared among unrelated presynaptic genes. Analysis of large gene families revealed that upstream and intronic regions of closely related family members are extremely divergent. We also identified 504 exceptionally long conserved elements (≥360 base pairs, ≥80% pair-wise identity between human and other mammals) in intergenic and intronic regions of presynaptic genes. Many of these elements form a highly stable stem-loop RNA structure and consequently are candidates for novel regulatory elements, whereas some conserved noncoding elements are shown to correlate with specific gene expression profiles. The SynapseDB online database integrates these findings and other functional genomic resources for synaptic genes. CONCLUSION: Highly conserved elements in nonprotein coding regions of 150 presynaptic genes represent sequences that may be involved in the transcriptional or post-transcriptional regulation of these genes. Furthermore, comparative sequence analysis will facilitate selection of genes and noncoding sequences for future functional studies and analysis of variation studies in neurodevelopmental and psychiatric disorders

Rijedak tip Usherova sindroma

A case is presented of a very rare type of Usher’s syndrome detected in a 30-year-old woman in her 28th week of pregnancy. She reported left eye visual impairment with a one-month history. She underwent standard ophthalmologic examination with additional procedures scheduled after childbirth, including fluorescein angiography, visual field (Goldman and Octopus) and electroretinography. Fundus examination revealed pallor of the optic disk, diffuse retinal blood vessel narrowing, no retinal pigmentation, left macular edema, vitreous liquefaction, and posterior vitreous detachment. Goldman perimetry showed narrowing of all isopters to 10o, and Octopus perimetry showed peripheral decrease of retinal sensitivity. Electroretinography confirmed the diagnosis of retinitis pigmentosa sine pigmento. Upon collecting case history records, hearing disorders originating from childhood were discovered. To our knowledge, this type of retinitis in Usher’s syndrome has been reported only once in the available literature.Prikazan je vrlo rijedak oblik Usherova sindroma u tridesetogodišnje, 28 tjedana trudne bolesnice. Žalila se na gubitak vidne oštrine na lijevom oku, koja je trajala mjesec dana. Proveden je kompletan oftalmološki pregled, a nakon porođaja fluoresceinska angiografija, vidno polje (Goldmann i Octopus) i elektroretinograija. Na fundusu je nađen blijedi očni živac, difuzno suženje krvnih žila, dok pigmentacije na mrežnici nisu nađene, te edem lijeve žute pjege, likvefakcija staklovine i ablacija stražnje staklovine. Perimetrija po Goldmannu je pokazala suženje svih izoptera na 10o, a Octopus perimetrija smanjenje osjetljivosti perifernih dijelova mrežnice. Elektroretinografija je potvrdila dijagnozu pigmentoznog retinitisa bez pigmenta. Anamnestički se naknadno saznalo da je oštećenje sluha prisutno od djetinjstva. Prema našim spoznajama u literaturi je dosad opisan samo jedan slučaj ovakvog oblika retinitisa u Usherovu sindromu

Diagnostic Interview for Genetic Studies: validity and reliability of the Croatian version

OBJECTIVE: To test the validity and reliability of the Diagnostic Interview for Genetic Studies (DIGS) in patients with mental illness in Croatia. MATERIALS AND METHODS: Following translation, back-translation, and pilot testing, the Croatian version of DIGS (CRO-DIGS) was administered to a total of 150 inpatients and outpatients diagnosed at the Clinical Hospital in Split with bipolar and major depressive disorder (n=56), schizophrenia and schizoaffective disorder (n=62), and alcohol dependence or use disorders (n=32). Initial testing was performed independently by one interviewer and one observer blinded to the diagnosis, and a retest was performed after 8 weeks by a third examiner. RESULTS: The validity of CRO-DIGS was high (κ=0.916), with an excellent inter-rater (κ=0.824) reliability, especially for bipolar disorder (κ=0.956). Following an 8 week test-retest interval, the reliability for all diagnoses was found to be excellent (κ=0.843). CONCLUSION: Our study has shown excellent validity and reliability of the Croatian version of DIGS, making it a promising instrument to assess mental illness of patients. The development of a valid and reliable diagnostic tool such as the CRO-DIGS will considerably advance the scientific communities' ability to carry out genetic studies of psychiatric illness in the region

A Sequence-Ready BAC Contig of the GABA(A) Receptor Gene Cluster Gabrg1–Gabra2–Gabrb1 on Mouse Chromosome 5

The type-A receptors for the neurotransmitter GABA (γ-aminobutyric acid) are ligand-gated chloride channels that mediate postsynaptic inhibition. The functional diversity of these receptors comes from the use of a large repertoire of subunits encoded by separate genes, as well as from differences in subunit composition of individual receptors. In mammals, a majority of GABA(A) receptor subunit genes are located in gene clusters that may be important for their regulated expression and function. We have established a high-resolution physical map of the cluster of genes encoding GABA(A) receptor subunits α2 (Gabra2), β1 (Gabrb1), and γ(1) (Gabrg1) on mouse chromosome 5. Rat cDNA probes and specific sequence probes for all three GABA(A) receptor subunit genes have been used to initiate the construction of a sequence-ready contig of bacterial artificial chromosomes (BACs) encompassing this cluster. In the process of contig construction clones from 129/Sv and C57BL/6J BAC libraries were isolated. The assembled 1.3-Mb contig, consisting of 45 BACs, gives five- to sixfold coverage over the gene cluster and provides an average resolution of one marker every 32 kb. A number of BAC insert ends were sequenced, generating 30 new sequence tag sites (STS) in addition to 6 Gabr gene-based and 3 expressed sequence tag (EST)-based markers. STSs from, and surrounding, the Gabrg1–Gabra2–Gabrb1 gene cluster were mapped in the T31 mouse radiation hybrid panel. The integration of the BAC contig with a map of loci ordered by radiation hybrid mapping suggested the most likely genomic orientation of this cluster on mouse chromosome 5: cen–D5Mit151–Gabrg1–Gabra2–Gabrb1–D5Mit58–tel. This established contig will serve as a template for genomic sequencing and for functional analysis of the GABA(A) gene cluster on mouse chromosome 5 and the corresponding region on human chromosome 4. The sequence data described in this paper have been submitted to the GenBank/GSS data libraries under accession nos. AF156490 and AQ589406–AQ589436

From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes

<div><p></p><p>Understanding the core set of genes that are necessary for basic developmental functions is one of the central goals in biology. Studies in model organisms identified a significant fraction of essential genes through the analysis of null-mutations that lead to lethality. Recent large-scale next-generation sequencing efforts have provided unprecedented data on genetic variation in human. However, evolutionary and genomic characteristics of human essential genes have never been directly studied on a genome-wide scale. Here we use detailed phenotypic resources available for the mouse and deep genomics sequencing data from human populations to characterize patterns of genetic variation and mutational burden in a set of 2,472 human orthologs of known essential genes in the mouse. Consistent with the action of strong, purifying selection, these genes exhibit comparatively reduced levels of sequence variation, skew in allele frequency towards more rare, and exhibit increased conservation across the primate and rodent lineages relative to the remainder of genes in the genome. In individual genomes we observed ∼12 rare mutations within essential genes predicted to be damaging. Consistent with the hypothesis that mutations in essential genes are risk factors for neurodevelopmental disease, we show that <i>de novo</i> variants in patients with Autism Spectrum Disorder are more likely to occur in this collection of genes. While incomplete, our set of human orthologs shows characteristics fully consistent with essential function in human and thus provides a resource to inform and facilitate interpretation of sequence data in studies of human disease.</p></div

Population genetics properties of essential genes.

<p>A) Average numbers of exonic missense variants in EG, NLG and ALL. The plotted Z-score is normalized relative to the genome average. The plotted range is truncated to visualize differences between gene sets, with a full log-transformed plot available in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003484#pgen.1003484.s007" target="_blank">Figure S7</a>. B) Differences in the allele frequency distributions in four continental populations of the 1000G data for EG, NLG and ALL. A data point above the zero line corresponds to a relative excess of variants of a given allele frequency. It can be seen that the essential genes contain significantly more rare variants than either NLG or ALL. The reported p-values are with respect to all 1000 Genome samples combined.</p

Functional and evolutionary characteristics of essential genes.

<p>A) Distribution of the 2472 essential genes (EG) across the genome (obtained from <a href="http://www.ensembl.org" target="_blank">www.ensembl.org</a>). B) Essential genes are significantly enriched in HGMD disease genes (<i>P</i> = 1.73×10⁻¹⁴), haploinsufficient genes <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003484#pgen.1003484-Dang1" target="_blank">[21]</a> (<i>P</i> = 1.75×10⁻³³) and ubiquitously expressed genes (<i>P</i> = 9.23×10⁻²¹) when compared to NLG. C) Comparison of non-synonymous to synonymous substitution rates between human and rhesus, chimp, mouse and rat in EG, NLG and ALL. Plotted substitution rates are normalized to Z-scores relative to the genome average.</p

Analysis of individual mutational load in essential genes.

<p>The boxes span the lower and upper quartile with the median indicated by a red bar; whiskers extend to data points less than 1.5 times the interquartile range. Values are transformed to Z-scores relative to the genome average of all protein coding genes. The P-values given are for the comparison of EG versus NLG (top) and EG versus ALL (bottom). A) Ratio of non-synonymous to synonymous exonic variants. B) Gene-length corrected average number of exonic missense variants. C) Fraction of loss-of-function variants among all exonic missense variants. D) Estimates of mutational load in essential genes in each human genome at different allele frequencies. The plots show all exonic missense variants (blue), putative damaging exonic variants (orange) and loss-of-function variants (red). Error bars depict the standard deviation.</p