Rhythmic Behavior Is Controlled by the SRm160 Splicing Factor in Drosophila melanogaster [Developmental and Behavioral Genetics]
Circadian clocks organize the metabolism, physiology, and behavior of organisms throughout the day–night cycle by controlling daily rhythms in gene expression at the transcriptional and post-transcriptional levels. While many transcription factors underlying circadian oscillations are known, the splicing factors that modulate these rhythms remain largely unexplored. A genome-wide assessment of the alterations of gene expression in a null mutant of the alternative splicing regulator SR-related matrix protein of 160 kDa (SRm160) revealed the extent to which alternative splicing impacts on behavior-related genes. We sho...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Beckwith, E. J., Hernando, C. E., Polcownuk, S., Bertolin, A. P., Mancini, E., Ceriani, M. F., Yanovsky, M. J. Tags: Developmental and Behavioral Genetics Source Type: research
Insights into the Evolution and Function of Auxin Signaling F-Box Proteins in Arabidopsis thaliana Through Synthetic Analysis of Natural Variants [Developmental and Behavioral Genetics]
The evolution of complex body plans in land plants has been paralleled by gene duplication and divergence within nuclear auxin-signaling networks. A deep mechanistic understanding of auxin signaling proteins therefore may allow rational engineering of novel plant architectures. Toward that end, we analyzed natural variation in the auxin receptor F-box family of wild accessions of the reference plant Arabidopsis thaliana and used this information to populate a structure/function map. We employed a synthetic assay to identify natural hypermorphic F-box variants and then assayed auxin-associated phenotypes in accessions expre...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Wright, R. C., Zahler, M. L., Gerben, S. R., Nemhauser, J. L. Tags: Developmental and Behavioral Genetics Source Type: research
Stress-Induced Sleep After Exposure to Ultraviolet Light Is Promoted by p53 in Caenorhabditis elegans [Developmental and Behavioral Genetics]
Stress-induced sleep (SIS) in Caenorhabditis elegans is important for restoration of cellular homeostasis and is a useful model to study the function and regulation of sleep. SIS is triggered when epidermal growth factor (EGF) activates the ALA neuron, which then releases neuropeptides to promote sleep. To further understand this behavior, we established a new model of SIS using irradiation by ultraviolet C (UVC) light. While UVC irradiation requires ALA signaling and leads to a sleep state similar to that induced by heat and other stressors, it does not induce the proteostatic stress seen with heat exposure. Based on the ...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: DeBardeleben, H. K., Lopes, L. E., Nessel, M. P., Raizen, D. M. Tags: Developmental and Behavioral Genetics Source Type: research
Kinetochore Components Required for Centromeric Chromatin Assembly Are Impacted by Msc1 in Schizosaccharomyces pombe [Cellular Genetics]
Eukaryotic chromosome segregation requires a protein complex known as the kinetochore that mediates attachment between mitotic spindle microtubules and centromere-specific nucleosomes composed of the widely conserved histone variant CENP-A. Mutations in kinetochore proteins of the fission yeast Schizosaccharomyces pombe lead to chromosome missegregation such that daughter cells emerge from mitosis with unequal DNA content. We find that multiple copies of Msc1—a fission yeast homolog of the KDM5 family of proteins—suppresses the temperature-sensitive growth defect of several kinetochore mutants, including mis16 ...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Gao, C., Langbein, L., Kamal, F., George, A. A., Walworth, N. C. Tags: Cellular Genetics Source Type: research
SID-1 Functions in Multiple Roles To Support Parental RNAi in Caenorhabditis elegans [Cellular Genetics]
Systemic RNA interference (RNAi) in Caenorhbaditis elegans requires sid-1, sid-3, and sid-5. Injected, expressed, or ingested double-stranded RNA (dsRNA) is transported between cells, enabling RNAi in most tissues, including the germline and progeny (parental RNAi). A recent report claims that parental RNAi also requires the yolk receptor rme-2. Here, we characterize the role of the sid genes and rme-2 in parental RNAi. We identify multiple independent paths for maternal dsRNA to reach embryos and initiate RNAi. We showed previously that maternal and embryonic sid-1 contribute independently to parental RNAi. Here we demons...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Wang, E., Hunter, C. P. Tags: Cellular Genetics Source Type: research
Silencing of Repetitive DNA Is Controlled by a Member of an Unusual Caenorhabditis elegans Gene Family [Gene Expression]
We describe here a novel locus, pals-22 (for protein containing ALS2CR12 signature), required to prevent silencing of repetitive transgenes in neurons and other somatic tissue types. pals-22 deficiency also severely impacts animal vigor and confers phenotypes reminiscent of accelerated aging. We find that pals-22 is a member of a large family of divergent genes (39 members), defined by homology to the ALS2CR12 protein family. While gene family members are highly divergent, they show striking patterns of chromosomal clustering. The family expansion appears C. elegans-specific and has not occurred to the same extent in other...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Leyva-Diaz, E., Stefanakis, N., Carrera, I., Glenwinkel, L., Wang, G., Driscoll, M., Hobert, O. Tags: Gene Expression Source Type: research
The Yeast Heterochromatin Protein Sir3 Experienced Functional Changes in the AAA+ Domain After Gene Duplication and Subfunctionalization [Gene Expression]
In this study, we investigated whether Sir3 evolved new or optimized properties after subfunctionalization . This possibility is supported by our observation that nonduplicated Orc1/Sir3 proteins from three species were unable to complement a sir3 mutation in Saccharomyces cerevisiae. To identify regions of Sir3 that may have evolved new properties, we created chimeric proteins of ScSir3 and nonduplicated Orc1 from Kluyveromyces lactis. We identified the AAA+ base subdomain of KlOrc1 as insufficient for heterochromatin formation in S. cerevisiae. In Orc1, this subdomain is intimately associated with other ORC subunits, ena...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Hanner, A. S., Rusche, L. N. Tags: Gene Expression Source Type: research
Multi-population Genomic Relationships for Estimating Current Genetic Variances Within and Genetic Correlations Between Populations [Genomic Selection]
In this study, we present a genomic relationship matrix which directly estimates current genetic variances as well as genetic correlations between populations. (Source: Genetics)
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Wientjes, Y. C. J., Bijma, P., Vandenplas, J., Calus, M. P. L. Tags: Genomic Selection Source Type: research
Incorporating Gene Annotation into Genomic Prediction of Complex Phenotypes [Genomic Selection]
In this study, we propose a novel strategy to incorporate gene annotation into GP of complex phenotypes by defining haploblocks according to gene positions. Haplotype effects are then modeled as categorical or as numerical allele dosage variables. The underlying concept of this approach is to build the statistical model on variables representing the biologically functional units. We evaluate the new methods with data from a heterogeneous stock mouse population, the Drosophila Genetic Reference Panel (DGRP), and a rice breeding population from the Rice Diversity Panel. Our results show that using gene annotation to define h...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Gao, N., Martini, J. W. R., Zhang, Z., Yuan, X., Zhang, H., Simianer, H., Li, J. Tags: Genomic Selection Source Type: research
Dissecting Causal Pathways Using Mendelian Randomization with Summarized Genetic Data: Application to Age at Menarche and Risk of Breast Cancer [Methods, Technology, and Resources]
In conclusion, multivariable Mendelian randomization using summarized genetic data provides a rapid and accessible analytic strategy that can be undertaken using publicly available data to better understand causal mechanisms. (Source: Genetics)
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Burgess, S., Thompson, D. J., Rees, J. M. B., Day, F. R., Perry, J. R., Ong, K. K. Tags: Methods, Technology, and Resources Source Type: research
Evolutionarily Conserved Alternative Splicing Across Monocots [Methods, Technology, and Resources]
One difficulty when identifying alternative splicing (AS) events in plants is distinguishing functional AS from splicing noise. One way to add confidence to the validity of a splice isoform is to observe that it is conserved across evolutionarily related species. We use a high throughput method to identify junction-based conserved AS events from RNA-Seq data across nine plant species, including five grass monocots (maize, sorghum, rice, Brachpodium, and foxtail millet), plus two nongrass monocots (banana and African oil palm), the eudicot Arabidopsis, and the basal angiosperm Amborella. In total, 9804 AS events were found ...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Mei, W., Boatwright, L., Feng, G., Schnable, J. C., Barbazuk, W. B. Tags: Methods, Technology, and Resources Source Type: research
MIP-MAP: High-Throughput Mapping of Caenorhabditis elegans Temperature-Sensitive Mutants via Molecular Inversion Probes [Methods, Technology, and Resources]
Mutants remain a powerful means for dissecting gene function in model organisms such as Caenorhabditis elegans. Massively parallel sequencing has simplified the detection of variants after mutagenesis but determining precisely which change is responsible for phenotypic perturbation remains a key step. Genetic mapping paradigms in C. elegans rely on bulk segregant populations produced by crosses with the problematic Hawaiian wild isolate and an excess of redundant information from whole-genome sequencing (WGS). To increase the repertoire of available mutants and to simplify identification of the causal change, we performed ...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Mok, C. A., Au, V., Thompson, O. A., Edgley, M. L., Gevirtzman, L., Yochem, J., Lowry, J., Memar, N., Wallenfang, M. R., Rasoloson, D., Bowerman, B., Schnabel, R., Seydoux, G., Moerman, D. G., Waterston, R. H. Tags: Methods, Technology, and Resources Source Type: research
Lipid and Carbohydrate Metabolism in Caenorhabditis elegans [Metabolism, Physiology, and Aging]
Lipid and carbohydrate metabolism are highly conserved processes that affect nearly all aspects of organismal biology. Caenorhabditis elegans eat bacteria, which consist of lipids, carbohydrates, and proteins that are broken down during digestion into fatty acids, simple sugars, and amino acid precursors. With these nutrients, C. elegans synthesizes a wide range of metabolites that are required for development and behavior. In this review, we outline lipid and carbohydrate structures as well as biosynthesis and breakdown pathways that have been characterized in C. elegans. We bring attention to functional studies using mut...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Watts, J. L., Ristow, M. Tags: Metabolism, Physiology, and Aging Source Type: research
Gene Tagging Strategies To Assess Protein Expression, Localization, and Function in Drosophila [Methods]
Analysis of gene function in complex organisms relies extensively on tools to detect the cellular and subcellular localization of gene products, especially proteins. Typically, immunostaining with antibodies provides these data. However, due to cost, time, and labor limitations, generating specific antibodies against all proteins of a complex organism is not feasible. Furthermore, antibodies do not enable live imaging studies of protein dynamics. Hence, tagging genes with standardized immunoepitopes or fluorescent tags that permit live imaging has become popular. Importantly, tagging genes present in large genomic clones o...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Kanca, O., Bellen, H. J., Schnorrer, F. Tags: Methods Source Type: research
Do Gametes Woo? Evidence for Their Nonrandom Union at Fertilization [Review]
A fundamental tenet of inheritance in sexually reproducing organisms such as humans and laboratory mice is that gametes combine randomly at fertilization, thereby ensuring a balanced and statistically predictable representation of inherited variants in each generation. This principle is encapsulated in Mendel’s First Law. But exceptions are known. With transmission ratio distortion, particular alleles are preferentially transmitted to offspring. Preferential transmission usually occurs in one sex but not both, and is not known to require interactions between gametes at fertilization. A reanalysis of our published wor...
Source: Genetics - October 4, 2017 Category: Genetics & Stem Cells Authors: Nadeau, J. H. Tags: Reviews Source Type: research
