From glacier to sauna: RNAseq of the human pathogen Exophiala dermatitidis
ABSTRACT: We report the transcriptome response of Exophiala dermatitidis submitted to different temperature conditions 2 Temperature conditions (45C, 1C), 2 exposition length (1 hour, 1 week) compared to optimal condition (37C)
Project description:PR-SET7-mediated histone-4 lysine-20 methylation has been implicated in mitotic condensation, DNA damage response and replication licencing. Here we show that PR-SET7 function in the liver is pivotal for maintaining genome integrity. Hepatocyte-specific deletion of PR-SET7 in mouse embryos resulted in G2 arrest followed by massive cell death and defect in liver organogenesis. Inactivation at postnatal stages caused cell duplication-dependent hepatocyte necrosis with unusual features of autophagy, termed "endonucleosis". Necrotic death was accompanied by inflammation, fibrosis and compensatory growth induction of neighboring hepatocytes and resident ductal progenitor cells. Prolonged necrotic-regenerative cycles coupled with oncogenic STAT3 activation replaced pre-existing hepatocytes with hepatocellular carcinoma derived entirely from ductal progenitor cells. Hepatocellular carcinoma in these mice displays a cancer stem cell gene signature specified by the co-expression of ductal progenitor markers and oncofetal genes. Mice carrying hepatocyte specific inactivation of PR-SET7 were generated in order to investigate the function of PR-SET7 histone methyl transferase in liver organogenesis, hepatocyte proliferation and liver regeneration. P15 WT mice were injected intra-peritoneally (ip) with 25ml per kg DEN (diethyl nitrosamine). Mice were examined for RNA expression at 8 months old.
Project description:Smyd3 is a histone methyltransferase implicated in tumorigenesis. Here we show that Smyd3 expression in mice is required but not sufficient for chemically induced liver and colon cancer formation. In these organs Smyd3 is functioning in the nucleus as a direct transcriptional activator of several key genes involved in cell proliferation, epithelial-mesenchymal transition, JAK/Stat3 oncogenic pathways, as well as of the c-myc and b-catenin oncogenes. Smyd3 specifically interacts with H3K4Me3-modified histone tails and is recruited to the core promoter regions of many but not all active genes. Smyd3 binding density on target genes positively correlates with increased RNA Pol-II density and transcriptional outputs. The results suggest that Smyd3 is an essential transcriptional potentiator of a multitude of cancer-related genes. Standard Smyd3-deficient (Smyd3-KO) mice were generated using gene-trap ES cell clones (AS0527 from International Gene Trap Consortium), in which a selection cassette, containing the splice acceptor site from mouse EN2 exon 2 followed by the beta-galactosidase and neomycin resistance gene fusion gene and the SV40 polyadenylation sequence was inserted into the 5th intron of the Smyd3 gene. The resulting mice were devoid of Smyd3 mRNA and protein in all tissues, including liver and colon. For the generation of Smyd3-Tg mice the open reading frame of the mouse Smyd3 cDNA, which contained 3 Flag epitopes at the 3’ end was inserted into the StuI site of the pTTR1-ExV3 plasmid (Yan et al, 1990). The 6.8 kb HindIII fragment containing the mouse transthyretin enhancer/promoter, intron 1, Smyd3 cDNA, three Flag epitopes and SV40 poly-A site was used to microinject C57Bl/6 fertilized oocytes. Founder animals were identified by Southern blotting and crossed with F1 mice to generate lines. Specific overexpression in the liver was tested by RT-PCR analysis in different tissues.
Project description:miRNAs has an important role in the diagnosis and treatment of amyotrophic lateral sclerosis. we aimed to profile dysregulation of miRNAs in ALS blood and neuromuscular junction as well as healthy blood control by Next Generation Sequencing (NGS). The expression of three up-regulated miRNAs, as miR-338-3p, miR-223-3p and miR-326, in the ALS samples compared to healthy controls, has been validated by qRT-PCR in a cohort of 45 samples collected previously. Bioinformatics tools were used to perform ALS microRNAs target analysis and to predict novel miRNAs secondary structure. The analysis of the NGS data identified 696 and 44 novel miRNAs which were differentially expressed in ALS tissues.
Project description:Sma- and Mad-related protein 4 (SMAD4) is closely associated with the development of ovarian follicular. However, current knowledge of the genome-wide view on the role of SMAD4 gene in mammalian follicular granulosa cells (GCs) is still largely unknown. In the present study, RNA-Seq was performed to investigate the effects of SMAD4 knockdown by RNA interference (SMAD4-siRNA) in porcine follicular GCs. A total of 1025 differentially expressed genes (DEGs), including 530 upregulated genes and 495 downregulated genes, were identified in SMAD4-siRNA treated GCs compared with that treated with NC-siRNA. Furthermore, functional enrichment analysis indicated that upregulated DEGs in SMAD4-siRNA treated cells were mainly enriched in cell-cycle related processes, interferon signaling pathway, and immune system process, while downregulated DEGs were mainly involved in extracellular matrix organization/disassembly, pathogenesis, and cell adhesion. In particular, cell cycle and TGF-β signaling pathway were discovered as the canonical pathways changed under the SMAD4 silencing. Taken together, our data reveals SMAD4 knockdown alters the expression of numerous genes involved in key biological processes of the development of follicular GCs and provides a novel global clue of the role of SMAD4 gene in porcine follicular GCs. mRNA profiles of NC-siRNA treated and SMAD4-siRNA treated porcine GCs were generated by RNA sequencing using Ion Torren Proton
Project description:p-Hydroxycinnamates, such as p-coumarate and ferulate, are components of plant cell walls and have a number of commercial applications. Previously, we had shown that the soil Actinobacterium Rhodococcus jostii RHA1 (RHA1) grows on ferulate, catabolizing it via vanillate and the β-ketoadipate pathway. We used transcriptomics to identify genes in RHA1 that were specifically up-regulated during growth on ferulate. These include three operons predicted to encode the uptake and β-oxidative deacetylation of ferulate and p-coumarate: couHLT, couMNO and couR. A couL mutant did not grow on p-coumarate, ferulate or their dihydro derivatives, but grew on vanillate. Purified CouL catalyzed the thioesterification of several p-hydroxycinnamates. Among the tested substrates, the best were p-coumarate and caffeate (kcat/KM ~400 mM-1s-1), and sinapate was not transformed. Of these, p-coumarate was also RHA1’s preferred growth substrate. Although the data indicate that p-hydroxycinnamates are catabolized via β-oxidation, the pathway lacks a typical β-ketothiolase. The data further suggest the involvement of two formaldehyde detoxification pathways in vanillate catabolism. This study augments our understanding of the bacterial catabolism of biomass and facilitates the production of aromatics from renewable feedstocks. Transcriptomes of R. jostii RHA1 from ferulate and benzoate cultures were analysed using Ion PGMTM system.
Project description:We describe a case of severe neonatal anemia with kernicterus due to compound heterozygosity for null mutations in KLF1, each inherited from asymptomatic parents. One of the mutations is novel. This is the first described case of a KLF1 null human. The phenotype of severe DAT-negative non-spherocytic hemolytic anaemia (NSHA), jaundice, hepato-splenomegaly, and marked erythroblastosis is more severe than that present in CDA type IV due to dominant mutations in the second zinc-finger of KLF1. There was a very high level of HbF expression into childhood (>70%), consistent with a key role for KLF1 in human hemoglobin switching. We performed RNA-seq on circulating erythroblasts and found human KLF1 acts like mouse Klf1 to coordinate expression of many genes required to build a red cell including those encoding globins, cytoskeletal components, AHSP, heme synthesis enzymes, cell cycle regulators, and blood group antigens. We identify novel KLF1 target genes including KIF23 and KIF11 which are required for proper cytokinesis. We also identify new roles for KLF1 in autophagy, global transcriptional control and RNA splicing. We suggest loss of KLF1 should be considered in otherwise unexplained cases of severe neonatal NSHA or hydrops fetalis. mRNA sequencing on peripheral blood from a family trio (mother, father and proband) where parents were asymptomatic and proband had severe neonatal anemia.
Project description:Marek's disease virus (MDV) belongs to the alphaherpesviruses and is the causative agent of fatal T cell lymphomas in chickens. Aftermaths of MDV infections lead to substantial losses in poultry industry and there is evidence that MDV constantly evolves towards higher virulence. This study takes a detailed look at the very first step of the viral life cycle in the host: the infection of B cells. Recently, it has become possible to culture and infect primary chicken B cells ex vivo, enabling us to apply those cells to RNAseq analysis. Here, we provide novel insights into MDV gene expression profiles and post-transcriptional modifications of this important poultry pathogen in its primary target cells for lytic replication. Remarkably enough, we could detect a novel hypothetical MDV gene, identify multicistronic transcripts and previously unannotated splice forms. These findings lay the foundation for future research on MDV replication and pathogenesis and the developed bioinformatics pipeline can be easily transferred to other herpesviruses or large DNA viruses to identify unknown transcript isoforms and associated motifs.
Project description:Multiple system atrophy (MSA) is a fatal rapidly progressive Ia-synucleinopathy, characterized by prominent Ia-synuclein accumulation in oligodendrocytes. In this study we investigated miRNA expression in the substantia nigra and striatum of MSA transgenic mice (Tg(Plp1-SNCA)1Haa) and wild type controls. This forms part of a larger study in which we investigated miRNA-mRNA regulatory network in substantia nigra and striatum of MSA transgenic mice in pre-motor stage of neurodegenration.
Project description:We previously found that the SF3A mRNA splicing complex was required for a robust innate immune response; SF3A acts in part by inhibiting the production of a negatively acting splice form of the TLR signaling adaptor MyD88. Here we inhibit SF3A1 using RNAi and subsequently perform an RNAseq study to identify the full complement of genes and splicing events regulated by SF3A in murine macrophages. Surprisingly, SF3A has substantial specificity for mRNA splicing events in innate immune signaling pathways compared to other pathways, affecting the splicing of many genes in the TLR signaling pathway to modulate the innate immune response. RNAseq was used to monitor the effects of SF3A1 siRNA-mediated knockdown in murine macrophages. Three biological replicates were used for each of the four treatment combinations (with/without siRNA, with/without LPS). The first replicates for each combination were each sequenced in two runs, which were combined in the analysis.
Project description:The pathogen and host factors that contribute to the establishment of foot-and-mouth disease virus (FMDV) persistence are currently not understood. Using primary bovine soft palate multilayers in combination with RNA sequencing, we analyzed the transcriptional responses during acute and persistent FMDV infection.