Structural and cellular transcriptome foundations of human brain disease
Yashar ZeighamiTrygve E. BakkenThomas Nickl‐JockschatZeru PetersonAnil G. JeggaJeremy A. MillerAlan C. EvansEd S. LeinMichael Hawrylycz
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Abstract Genes associated with risk for brain disease exhibit characteristic expression patterns that reflect both anatomical and cell type relationships. Brain-wide transcriptomic patterns of disease risk genes provide a molecular based signature for identifying disease association, often differing from common phenotypic classification. Analysis of adult brain-wide transcriptomic patterns associated with 40 human brain diseases identified five major transcriptional patterns, represented by tumor-related, neurodegenerative, psychiatric and substance abuse, and two mixed groups of diseases. Brain disease risk genes exhibit unique anatomic transcriptomic signatures, based on differential co-expression, that often uniquely identify the disease. For cortical expressing diseases, single nucleus data in the middle temporal gyrus reveals cell type expression gradients separating neurodegenerative, psychiatric, and substance abuse diseases. By homology mapping of cell types across mouse and human, transcriptomic disease signatures are found largely conserved, but with psychiatric and substance abuse related diseases showing important specific species differences. These results describe the structural and cellular transcriptomic landscape of disease in the adult brain, highlighting significant homology with the mouse yet indicating where human data is needed to further refine our understanding of disease-associated genes.Keywords:
Human brain
Homology
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Vestibular dysfunction is a frequent clinical problem, leading to dizziness and imbalance. Genes play an important role in its etiology, but the genetics are complex and poorly understood. In this study we have analyzed the complex inheritance pattern in the Epistatic circler mouse, which shows circling behavior indicative of vestibular dysfunction in the mouse. This phenotype exists in a proportion of the F2-generation from an intercross between C57L/J and SWR/J mouse strains. Genetic investigation indicates that the circling behavior is caused by a major recessively inherited gene derived from the SWR/J strain (the Ecs -gene) in combination with at least three different modifier genes derived from C57L/J (the Ecl -genes). Genetic mapping made it possible to localize the Ecs -gene to chromosome 14 and the Ecl -genes to chromosome 3, 4, and 13. This study illustrates the feasibility of identifying genes for multifactorial traits in mice.
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ABSTRACT We have analyzed 31 mutations that have dominant effects on the behavior or morphology of the nematode Caenorhabditis elegans. These mutations appear to define 15 genes. We have studied ten of these genes in some detail and have been led to two notable conclusions. First, loss of gene function for four of these ten genes results in a wild-type phenotype; if these genes represent a random sample from the genome, then we would estimate that null mutations in about half of the genes in C. elegans would result in a nonmutant phenotype. Second, the dominant effects of mutations in nine of these ten genes are caused by novel gene functions, and in all nine cases the novel function is antagonized by the wild-type function.
Caenorhabditis
Loss function
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Leucine-rich repeat
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Analysis of the DNA sequences of new members of the Saccharomyces cerevisiae MEL1-MEL10 gene family showed high homology between the members. The MEL gene family, alpha-galactosidase-coding sequences, have diverged into two groups; one consisting of MEL1 and MEL2 and the other of MEL3-MEL10. In two S. cerevisiae strains containing five or seven MEL genes each, all the genes are nearly identical, suggesting very rapid distribution of the gene to separate chromosomes. The sequence homology and the abrupt change to sequence heterogeneity at the centromere-proximal 3' end of the MEL genes suggest that the distribution of the genes to new chromosomal locations has occurred partly by reciprocal recombination at solo delta sequences. We identified a new open reading frame sufficient to code for a 554 amino acid long protein of unknown function. The new open reading frame (Accession number Z37509) is located in the 3' non-coding region of MEL3-MEL10 genes in opposite orientation to the MEL genes (Accession numbers Z37508, Z37510, Z37511). Northern analysis of total RNA showed no hybridization to a homologous probe, suggesting that the gene is not expressed efficiently if at all.
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Summary Leaf trichome density in M imulus guttatus can be altered by the parental environment. In this study, we compared global gene expression patterns in progeny of damaged and control plants. Significant differences in gene expression probably explain the observed trichome response, and identify additional responsive pathways. Using whole transcriptome RNA sequencing, we estimated differential gene expression between isogenic seedlings whose parents had, or had not, been subject to leaf damage. We identified over 900 genes that were differentially expressed in response to parental wounding. These genes clustered into groups involved in cell wall and cell membrane development, stress response pathways, and secondary metabolism. Gene expression is modified as a consequence of the parental environment in a targeted way that probably alters multiple developmental pathways, and may increase progeny fitness if they experience environments similar to that of their parents.
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Significance Human genes homozygous for apparent loss of function (LoF) variants are increasingly reported in a sizeable proportion of individuals without overt clinical phenotypes. Here, we found 166 genes with 179 predicted LoF variants for which the frequency of homozygous individuals exceeds 1% in at least one of the populations present in databases ExAC and gnomAD. These putatively dispensable genes showed relaxation of selective constraints, suggesting that a considerable proportion of these genes may be undergoing pseudogenization. Eight of these LoF variants displayed robust signals of positive selection, including two variants in genes involved in resistance to infectious diseases. The identification of dispensable genes will facilitate the identification of functions that are now redundant, or possibly even advantageous, for human survival.
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ABSTRACT Eighty-eight mutants of C. elegans that display a roller phenotype (a helically twisted body) have been isolated and characterized genetically and phenotypically. The mutations are located in 14 different genes. Most genes contain a number of alleles. Their distribution among the chromosomes appears nonrandom, with seven of the genes being located on linkage group 11, some very closely linked. The phenotypes of the mutants suggest that there are five different classes of genes, each class representing a set of similar phenotypic effects: Left Roller (four genes), Right Roller (one gene), Left Squat (one gene), Right Squat (two genes) and Left Dumpy Roller (six genes). The classes of mutants differ with respect to a number of characteristics that include the developmental stages affected and the types of aberrations observed in cuticle structure. A variety of gene interactions were found, arguing that these genes are involved in a common developmental process. The presence of alterations in cuticle morphology strongly suggests that these genes are active in the formation of the nematode cuticle.
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Caenorhabditis
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