p53-Dependent DNA damage response sensitive to editing-defective tRNA synthetase in zebrafish.

Brain and heart pathologies are caused by editing defects of transfer RNA (tRNA) synthetases, which preserve genetic code fidelity by removing incorrect amino acids misattached to tRNAs. To extend understanding of the broader impact of synthetase editing reactions on organismal homeostasis, and based on effects in bacteria ostensibly from small amounts of mistranslation of components of the replication apparatus, we investigated the sensitivity to editing of the vertebrate genome. We show here that in zebrafish embryos, transient overexpression of editing-defective valyl-tRNA synthetase (ValRS(ED)) activated DNA break-responsive H2AX and p53-responsive downstream proteins, such as cyclin-dependent kinase (CDK) inhibitor p21, which promotes cell-cycle arrest at DNA damage checkpoints, and Gadd45 and p53R2, with pivotal roles in DNA repair. In contrast, the response of these proteins to expression of ValRS(ED) was abolished in p53-deficient fish. The p53-activated downstream signaling events correlated with suppression of abnormal morphological changes caused by the editing defect and, in adults, reversed a shortened life span (followed for 2 y). Conversely, with normal editing activities, p53-deficient fish have a normal life span and few morphological changes. Whole-fish deep sequencing showed genomic mutations associated with the editing defect. We suggest that the sensitivity of p53 to expression of an editing-defective tRNA synthetase has a critical role in promoting genome integrity and organismal homeostasis.

Marine Natural Product Honaucin A Attenuates Inflammation by Activating the Nrf2-ARE Pathway.

The cyanobacterial marine natural product honaucin A inhibits mammalian innate inflammation in vitro and in vivo. To decipher its mechanism of action, RNA sequencing was used to evaluate differences in gene expression of cultured macrophages following honaucin A treatment. This analysis led to the hypothesis that honaucin A exerts its anti-inflammatory activity through activation of the cytoprotective nuclear erythroid 2-related factor 2 (Nrf2)-antioxidant response element/electrophile response element (ARE/EpRE) signaling pathway. Activation of this pathway by honaucin A in cultured human MCF7 cells was confirmed using an Nrf2 luciferase reporter assay. In vitro alkylation experiments with the natural product and N-acetyl-l-cysteine suggest that honaucin A activates this pathway through covalent interaction with the sulfhydryl residues of the cytosolic repressor protein Keap1. Honaucin A presents a potential therapeutic lead for diseases with an inflammatory component modulated by Nrf2-ARE.

Omics Pipe: a community-based framework for reproducible multi-omics data analysis.

MOTIVATION: Omics Pipe (http://sulab.scripps.edu/omicspipe) is a computational framework that automates multi-omics data analysis pipelines on high performance compute clusters and in the cloud. It supports best practice published pipelines for RNA-seq, miRNA-seq, Exome-seq, Whole-Genome sequencing, ChIP-seq analyses and automatic processing of data from The Cancer Genome Atlas (TCGA). Omics Pipe provides researchers with a tool for reproducible, open source and extensible next generation sequencing analysis. The goal of Omics Pipe is to democratize next-generation sequencing analysis by dramatically increasing the accessibility and reproducibility of best practice computational pipelines, which will enable researchers to generate biologically meaningful and interpretable results. RESULTS: Using Omics Pipe, we analyzed 100 TCGA breast invasive carcinoma paired tumor-normal datasets based on the latest UCSC hg19 RefSeq annotation. Omics Pipe automatically downloaded and processed the desired TCGA samples on a high throughput compute cluster to produce a results report for each sample. We aggregated the individual sample results and compared them to the analysis in the original publications. This comparison revealed high overlap between the analyses, as well as novel findings due to the use of updated annotations and methods. AVAILABILITY AND IMPLEMENTATION: Source code for Omics Pipe is freely available on the web (https://bitbucket.org/sulab/omics_pipe). Omics Pipe is distributed as a standalone Python package for installation (https://pypi.python.org/pypi/omics_pipe) and as an Amazon Machine Image in Amazon Web Services Elastic Compute Cloud that contains all necessary third-party software dependencies and databases (https://pythonhosted.org/omics_pipe/AWS_installation.html).

Group-based variant calling leveraging next-generation supercomputing for large-scale whole-genome sequencing studies.

MOTIVATION: Next-generation sequencing (NGS) technologies have become much more efficient, allowing whole human genomes to be sequenced faster and cheaper than ever before. However, processing the raw sequence reads associated with NGS technologies requires care and sophistication in order to draw compelling inferences about phenotypic consequences of variation in human genomes. It has been shown that different approaches to variant calling from NGS data can lead to different conclusions. Ensuring appropriate accuracy and quality in variant calling can come at a computational cost. RESULTS: We describe our experience implementing and evaluating a group-based approach to calling variants on large numbers of whole human genomes. We explore the influence of many factors that may impact the accuracy and efficiency of group-based variant calling, including group size, the biogeographical backgrounds of the individuals who have been sequenced, and the computing environment used. We make efficient use of the Gordon supercomputer cluster at the San Diego Supercomputer Center by incorporating job-packing and parallelization considerations into our workflow while calling variants on 437 whole human genomes generated as part of large association study. CONCLUSIONS: We ultimately find that our workflow resulted in high-quality variant calls in a computationally efficient manner. We argue that studies like ours should motivate further investigations combining hardware-oriented advances in computing systems with algorithmic developments to tackle emerging 'big data' problems in biomedical research brought on by the expansion of NGS technologies.

Differential expression and intrachromosomal evolution of the sghC1q genes in zebrafish (Danio rerio).

The secreted globular head C1q (sghC1q) genes can be characterized as a family of genetic loci encoding signal peptides followed by single complement component 1q globular (gC1q) motifs. Members of this family have been referred to as precerebellin-like (Cblnl), C1q-like or ovary specific C1q-like factors, and are transcribed in response to infection and/or during early development. This study was primarily undertaken to identify the zebrafish sghC1q (or DrsghC1q) genes that increase their transcription in response to infection and to examine their transcriptional patterns during early development. Twenty sghC1q genes were found in the zebrafish (Danio rerio) genome (Zv9). Two of the examined twenty genes showed significant up-regulation within 24h of infection with the fish pathogen Streptococcus iniae, and eleven of the examined twenty were expressed during early development. Due to the clustered nature of these genes on chromosomes two and seven, intrachromosomal duplication events are hypothesized and explored.

The C1q domain containing proteins: Where do they come from and what do they do?

The gene sequence encoding an N-terminal collagen stalk followed by a globular complement 1q domain (gC1q), an architecture that characterizes the C1q A, B and C chains of the first complement component (C1), did not become prevalent until the cephalochordates and urochordates. However, genes encoding only the globular complement 1q domain (ghC1q) are more ancient as they exist within many lower vertebrate and invertebrate genomes, and are even present in the prokaryotes. These genes can be divided into two groups, the first, which appears to be the more ancient form, encodes proteins that are not secreted (cghC1q). The second group encodes proteins in which the globular domain is preceded by a signal peptide indicating secretion (sghC1q). In this review we examine bioinformatic evidence for C1q domain containing (C1qDC) genes in many organisms and integrate these observations with research performed and published on the biochemistry and functions of this fascinating set of proteins.