Mitochondrial Function and Maize Kernel Development Requires Dek2, a Pentatricopeptide Repeat Protein Involved in nad1 mRNA Splicing [Cellular Genetics]
This study indicated that Dek2 is a new PPR protein that affects the splicing of mitochondrial nad1 intron 1 and is required for mitochondrial function and kernel development. (Source: Genetics)
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Qi, W., Yang, Y., Feng, X., Zhang, M., Song, R. Tags: Cellular Genetics Source Type: research
Insight into the RNA Exosome Complex Through Modeling Pontocerebellar Hypoplasia Type 1b Disease Mutations in Yeast [Cellular Genetics]
Pontocerebellar hypoplasia type 1b (PCH1b) is an autosomal recessive disorder that causes cerebellar hypoplasia and spinal motor neuron degeneration, leading to mortality in early childhood. PCH1b is caused by mutations in the RNA exosome subunit gene, EXOSC3. The RNA exosome is an evolutionarily conserved complex, consisting of nine different core subunits, and one or two 3'-5' exoribonuclease subunits, that mediates several RNA degradation and processing steps. The goal of this study is to assess the functional consequences of the amino acid substitutions that have been identified in EXOSC3 in PCH1b patients. To ana...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Fasken, M. B., Losh, J. S., Leung, S. W., Brutus, S., Avin, B., Vaught, J. C., Potter-Birriel, J., Craig, T., Conn, G. L., Mills-Lujan, K., Corbett, A. H., van Hoof, A. Tags: Cellular Genetics Source Type: research
Rewiring of Signaling Networks Modulating Thermotolerance in the Human Pathogen Cryptococcus neoformans [Gene Expression]
This study provides insight into the thermotolerance of C. neoformans by elucidating the regulatory mechanisms of Sch9 and Hsf1 through the genome-scale identification of temperature-dependent genes. (Source: Genetics)
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Yang, D.-H., Jung, K.-W., Bang, S., Lee, J.-W., Song, M.-H., Floyd-Averette, A., Festa, R. A., Ianiri, G., Idnurm, A., Thiele, D. J., Heitman, J., Bahn, Y.-S. Tags: Gene Expression Source Type: research
Coordination of Cell Cycle Progression and Mitotic Spindle Assembly Involves Histone H3 Lysine 4 Methylation by Set1/COMPASS [Gene Expression]
Methylation of histone H3 lysine 4 (H3K4) by Set1 complex/COMPASS is a hallmark of eukaryotic chromatin, but it remains poorly understood how this post-translational modification contributes to the regulation of biological processes like the cell cycle. Here, we report a H3K4 methylation-dependent pathway in Saccharomyces cerevisiae that governs toxicity toward benomyl, a microtubule destabilizing drug. Benomyl-sensitive growth of wild-type cells required mono- and dimethylation of H3K4 and Pho23, a PHD-containing subunit of the Rpd3L complex. set1 and pho23 deletions suppressed defects associated with ipl1-2 aurora kinase...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Beilharz, T. H., Harrison, P. F., Miles, D. M., See, M. M., Le, U. M. M., Kalanon, M., Curtis, M. J., Hasan, Q., Saksouk, J., Margaritis, T., Holstege, F., Geli, V., Dichtl, B. Tags: Gene Expression Source Type: research
An Evolutionarily Conserved Transcriptional Activator-Repressor Module Controls Expression of Genes for D-Galacturonic Acid Utilization in Aspergillus niger [Gene Expression]
The expression of genes encoding extracellular polymer-degrading enzymes and the metabolic pathways required for carbon utilization in fungi are tightly controlled. The control is mediated by transcription factors that are activated by the presence of specific inducers, which are often monomers or monomeric derivatives of the polymers. A D-galacturonic acid-specific transcription factor named GaaR was recently identified and shown to be an activator for the expression of genes involved in galacturonic acid utilization in Botrytis cinerea and Aspergillus niger. Using a forward genetic screen, we isolated A. niger mutants th...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Niu, J., Alazi, E., Reid, I. D., Arentshorst, M., Punt, P. J., Visser, J., Tsang, A., Ram, A. F. J. Tags: Gene Expression Source Type: research
Variation and Evolution of the Meiotic Requirement for Crossing Over in Mammals [Genome Integrity and Transmission]
The segregation of homologous chromosomes at the first meiotic division is dependent on the presence of at least one well-positioned crossover per chromosome. In some mammalian species, however, the genomic distribution of crossovers is consistent with a more stringent baseline requirement of one crossover per chromosome arm. Given that the meiotic requirement for crossing over defines the minimum frequency of recombination necessary for the production of viable gametes, determining the chromosomal scale of this constraint is essential for defining crossover profiles predisposed to aneuploidy and understanding the paramete...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Dumont, B. L. Tags: Genome Integrity and Transmission Source Type: research
The Nucleotide Excision Repair Pathway Limits L1 Retrotransposition [Genome Integrity and Transmission]
Long interspersed elements 1 (L1) are active mobile elements that constitute almost 17% of the human genome. They amplify through a "copy-and-paste" mechanism termed retrotransposition, and de novo insertions related to these elements have been reported to cause 0.2% of genetic diseases. Our previous data demonstrated that the endonuclease complex ERCC1-XPF, which cleaves a 3' DNA flap structure, limits L1 retrotransposition. Although the ERCC1-XPF endonuclease participates in several different DNA repair pathways, such as single-strand annealing, or in telomere maintenance, its recruitment to DNA lesions is best character...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Servant, G., Streva, V. A., Derbes, R. S., Wijetunge, M. I., Neeland, M., White, T. B., Belancio, V. P., Roy-Engel, A. M., Deininger, P. L. Tags: Genome Integrity and Transmission Source Type: research
Maintenance of Heterochromatin by the Large Subunit of the CAF-1 Replication-Coupled Histone Chaperone Requires Its Interaction with HP1a Through a Conserved Motif [Genome Integrity and Transmission]
In eukaryotic cells, the organization of genomic DNA into chromatin regulates many biological processes, from the control of gene expression to the regulation of chromosome segregation. The proper maintenance of this structure upon cell division is therefore of prime importance during development for the maintenance of cell identity and genome stability. The chromatin assembly factor 1 (CAF-1) is involved in the assembly of H3-H4 histone dimers on newly synthesized DNA and in the maintenance of a higher order structure, the heterochromatin, through an interaction of its large subunit with the heterochromatin protein HP1a. ...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Roelens, B., Clemot, M., Leroux-Coyau, M., Klapholz, B., Dostatni, N. Tags: Genome Integrity and Transmission Source Type: research
Histone H4 Facilitates the Proteolysis of the Budding Yeast CENP-ACse4 Centromeric Histone Variant [Genome Integrity and Transmission]
The incorporation of histone variants into nucleosomes can alter chromatin-based processes. CENP-A is the histone H3 variant found exclusively at centromeres that serves as an epigenetic mark for centromere identity and is required for kinetochore assembly. CENP-A mislocalization to ectopic sites appears to contribute to genomic instability, transcriptional misregulation, and tumorigenesis, so mechanisms exist to ensure its exclusive localization to centromeres. One conserved process is proteolysis, which is mediated by the Psh1 E3 ubiquitin ligase in Saccharomyces cerevisiae (budding yeast). To determine whether there are...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Deyter, G. M. R., Hildebrand, E. M., Barber, A. D., Biggins, S. Tags: Genome Integrity and Transmission Source Type: research
A New Mechanism for Mendelian Dominance in Regulatory Genetic Pathways: Competitive Binding by Transcription Factors [Statistical Genetics and Genomics]
We report a new mechanism for allelic dominance in regulatory genetic interactions that we call binding dominance. We investigated a biophysical model of gene regulation, where the fractional occupancy of a transcription factor (TF) on the cis-regulated promoter site it binds to is determined by binding energy (–G) and TF dosage. Transcription and gene expression proceed when the TF is bound to the promoter. In diploids, individuals may be heterozygous at the cis-site, at the TF’s coding region, or at the TF’s own promoter, which determines allele-specific dosage. We find that when the TF’s coding r...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Porter, A. H., Johnson, N. A., Tulchinsky, A. Y. Tags: Statistical Genetics and Genomics Source Type: research
Pathway-Structured Predictive Model for Cancer Survival Prediction: A Two-Stage Approach [Statistical Genetics and Genomics]
Heterogeneity in terms of tumor characteristics, prognosis, and survival among cancer patients has been a persistent problem for many decades. Currently, prognosis and outcome predictions are made based on clinical factors and/or by incorporating molecular profiling data. However, inaccurate prognosis and prediction may result by using only clinical or molecular information directly. One of the main shortcomings of past studies is the failure to incorporate prior biological information into the predictive model, given strong evidence of the pathway-based genetic nature of cancer, i.e., the potential for oncogenes to be gro...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Zhang, X., Li, Y., Akinyemiju, T., Ojesina, A. I., Buckhaults, P., Liu, N., Xu, B., Yi, N. Tags: Statistical Genetics and Genomics Source Type: research
The Spike-and-Slab Lasso Generalized Linear Models for Prediction and Associated Genes Detection [Statistical Genetics and Genomics]
Large-scale "omics" data have been increasingly used as an important resource for prognostic prediction of diseases and detection of associated genes. However, there are considerable challenges in analyzing high-dimensional molecular data, including the large number of potential molecular predictors, limited number of samples, and small effect of each predictor. We propose new Bayesian hierarchical generalized linear models, called spike-and-slab lasso GLMs, for prognostic prediction and detection of associated genes using large-scale molecular data. The proposed model employs a spike-and-slab mixture double-exponential pr...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Tang, Z., Shen, Y., Zhang, X., Yi, N. Tags: Statistical Genetics and Genomics Source Type: research
Controlling the Rate of GWAS False Discoveries [Statistical Genetics and Genomics]
With the rise of both the number and the complexity of traits of interest, control of the false discovery rate (FDR) in genetic association studies has become an increasingly appealing and accepted target for multiple comparison adjustment. While a number of robust FDR-controlling strategies exist, the nature of this error rate is intimately tied to the precise way in which discoveries are counted, and the performance of FDR-controlling procedures is satisfactory only if there is a one-to-one correspondence between what scientists describe as unique discoveries and the number of rejected hypotheses. The presence of linkage...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Brzyski, D., Peterson, C. B., Sobczyk, P., Candes, E. J., Bogdan, M., Sabatti, C. Tags: Statistical Genetics and Genomics Source Type: research
Cell Biology of the Caenorhabditis elegans Nucleus [WormBook]
Studies on the Caenorhabditis elegans nucleus have provided fascinating insight to the organization and activities of eukaryotic cells. Being the organelle that holds the genetic blueprint of the cell, the nucleus is critical for basically every aspect of cell biology. The stereotypical development of C. elegans from a one cell-stage embryo to a fertile hermaphrodite with 959 somatic nuclei has allowed the identification of mutants with specific alterations in gene expression programs, nuclear morphology, or nuclear positioning. Moreover, the early C. elegans embryo is an excellent model to dissect the mitotic processes of...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Cohen-Fix, O., Askjaer, P. Tags: WormBook Source Type: research
Three-Dimensional Genome Organization and Function in Drosophila [Flybook]
Understanding how the metazoan genome is used during development and cell differentiation is one of the major challenges in the postgenomic era. Early studies in Drosophila suggested that three-dimensional (3D) chromosome organization plays important regulatory roles in this process and recent technological advances started to reveal connections at the molecular level. Here we will consider general features of the architectural organization of the Drosophila genome, providing historical perspective and insights from recent work. We will compare the linear and spatial segmentation of the fly genome and focus on the two key ...
Source: Genetics - January 2, 2017 Category: Genetics & Stem Cells Authors: Schwartz, Y. B., Cavalli, G. Tags: Flybook Source Type: research
