Steroidogenic Factor-1 (SF-1) is a nuclear receptor that has a pivotal role in the development of adrenal glands and gonads and in the control of steroid hormone production, being also implicated in the pathogenesis of adrenocortical tumors. We have analyzed the mechanisms how SF-1 controls gene expression in adrenocortical cells and showed that it regulates different categories of genes according to its dosage. Significant correlations exist between the localization of SF-1-binding sites in chr ...[more]
Project description:The goal of this study was to identify genomic binding sites of the NRSF/REST transcription factor under conditions of basal and increased SF-1 dosage in the H295R human adrenocortical tumor cell line. 4 samples: input DNA (2 replicates) - NRSF/REST ChIP basal SF-1 dosage - NRSF/REST ChIP increased SF-1 dosage
Project description:The goal of this study was to identify chromatin regulatory sites by FAIRE-seq under conditions of basal and increased dosage of transcription factor SF-1 in the H295R human adrenocortical tumor cell line. 4 samples: input DNA in basal SF-1 expression conditions - FAIRE-seq in basal SF-1 expression conditions - input DNA in SF-1 overexpression conditions - FAIRE-seq in SF-1 overexpression conditions
Project description:SF-1 is a nuclear receptor transcription factor playing a key role in adrenogonadal development and in adrenocortical tumorigenesis when overexpressed. We studied gene expression profiles using Affymetrix microarrays in the H295R/TR SF-1 adrenocortical cancer cell line, where SF-1 expression can be increased in a doxycycline-dependent manner (Mol. Endocrinol. 21: 2968–2987, 2007) H295R/TR SF-1 cells were cultured either in basal conditions or with doxycycline (Dox) added to the culture medium for 72 hours. RNA was extracted and hybridized to HG-U133 Plus 2.0 Affymetrix microarrays.
Project description:SF-1 is a nuclear receptor transcription factor playing a key role in adrenogonadal development and in adrenocortical tumorigenesis when overexpressed. NRSF/REST is a transcriptional repressor that represses expression of neuronal genes in non-neural tissues. Some data suggest that SF-1 and NRSF/REST can functionally interact in adrenocortical cancer cells. We studied gene expression profiles using Affymetrix microarrays in the H295R/TR SF-1 adrenocortical cancer cell line. In this cell line, SF-1 expression can be increased in a doxycycline-dependent manner (Mol. Endocrinol. 21: 2968–2987, 2007). The effects of a control siRNA and sRNAs specific for SF-1 and for NRSF/REST (in basal or increased SF-1 expression conditions) on gene expression were measured. In H295R/TR SF-1 cells SF-1 and NRSF/REST (in conditions of basal and increased SF-1 dosage) expression were knocked down by Amaxa nucleofection. RNA was extracted and hybridized to Human Gene 1.0 ST Affymetrix microarrays.
Project description:In plants, maintenance-methylation mediated by METHYLTRANSFERASE-1 (MET1), siRNA-directed de-novo methylation, and chromatin remodeling by DECREASE IN DNA METHYLATION -1 (DDM1) promote transcriptional gene-silencing of transposable elements (TEs). This process is mostly investigated at steady states reflecting how long-established silent conditions are maintained, faithfully re-iterated or temporarily modified during growth, stress and over generations. How invasive TEs are detected and silenced de novo, however, remains largely unknown. Using inbred lineages of hybrid Arabidopsis epigenomes combining wild-type and met1 or ddm1 chromosomes, we have deciphered the timing, spatial distribution and mechanisms underpinning the proliferation and eventual demise of the endogenous retrotransposon évadé (EVD). Both developmental and molecular features of EVD biology, including a remarkable ability to evade RNA interference, ultimately contribute to its silencing over multiple generations. The underlying processes are accompanied by widespread diversification of the Arabidopsis genome and de-novo epiallelism creating an extensive reservoir of selectable and potentially adaptive traits. Differential expression of EVADE small RNAs between three generations of one specific Col0 met1 derived EpiRIL.
Project description:Virus resistance relies in some plant-viral interactions on the RNA-DEPENDANT RNA POLYMERASE 6 (RDR6), a major actor of RNA silencing that acts at the post-transcriptional level. Here, we demonstrate that RDR6 also plays a role in basal defense and race-specific resistance. RDR6 and the microRNA miR472, which target the mRNAs of disease resistance genes of coiled-coil nucleotide-binding leucine-rich-repeats family (e.g. RPS5), act in cooperation to control post-transcriptionally these immune receptors. Induction of these resistance genes is primed in rdr6- and miR472-elicited mutants and this effect is associated with an enhanced basal and race-specific immunity in these backgrounds. Comparison of Col0 WT sRNA with miR472 over-expressor mutant.
Project description:Plants and invertebrates protect themselves from viruses through RNA interference (RNAi), yet it remains unknown whether this defense mechanism exists in mammals. Antiviral RNAi involves the processing of viral long double-stranded (ds) RNA molecules into small interfering RNAs (siRNAs) by the ribonuclease (RNAse) III Dicer. These siRNAs are incorporated into effector complex(es) containing members of the Argonaute (Ago) protein family and guide silencing of complementary target viral RNAs. Here, we detect the accumulation of phased Dicer-dependent virus-derived siRNA (viRNAs) and demonstrate their loading into Ago2 after infection of mouse embryonic stem (ES) cells with Encephalomyocarditis virus (EMCV). We further show that the production of these viRNAs is drastically reduced, yet not completely abolished, if ES cells are first induced to differentiate before infection. Finally, we reveal that the mammalian virus Nodamura virus (NoV) encodes for a protein that counteracts such antiviral RNAi in ES cells supporting the existence of an effective RNAi-based immunity in mammals. Infection of wild-type or mutant mouse ES cells and analysis of small RNAs from total extracts or immunoprecipitated components of the RNAi pathway
Project description:We generated 38-bp Illumina reads from single messenger RNA libraries from three diverse developmental stages of the two-spotted spider mite to capture small RNA diversity across development. Adult, nymphal+larvae and embryonic stages were separated using sieves of various pore sizes, and mites of various developmental stages were carefully selected for small RNA library preparation. Samples were a mix of males and females to capture male and female patterns of small RNA composition and were reared on beans (Phaseolus vulgaris cv California Red Kidney). Small RNA reads were used for miRNA prediction, piRNA discovery, and for quantitation of small RNA-generating loci (i.e. expression across development). Examination of small RNA from spider mites of adult, embryonic and pooled larval/nymphal developmental stages.