Gene Structure, cDNA Sequence, and mRNA Distribution

The rat HNF-3 (hepatocyte nuclear factor 3) gene family encodes three transcription factors known to be important in the regulation of gene expression in liver and lung. We have cloned and characterized the mouse genes and cDNAs for HNF-3α, β, and γ and analyzed their expression patterns in various adult tissues and mouse embryonic stages. The HNF-3 proteins are highly conserved between mouse and rat, with the exception of the amino terminus of HNF-3γ, which in mouse is more similar to those of HNF-3α and β than to the amino termini of the rat HNF-3γ protein. The mouse HNF-3 genes are small and contain only two or three (HNF-3β) exons with conserved intron-exon boundaries. The proximal promoter of the mouse HNF3β gene is remarkably similar to that of the previously cloned rat HNF-3β gene, but is different from the promoters of the HNF-3α and γ genes. The mRNA distribution of the mouse HNF-3 genes was analyzed by quantitative RNase protection with gene-specific probes. While HNF-3α and β are restricted mainly to endoderm-derived tissues (lung, liver, stomach, and small intestine), HNF-3γ is more extensively expressed, being present additionally in ovary, testis, heart, and adipose tissue, but missing from lung. Transcripts for HNF-3β and α are detected most abundantly in midgestation embryos (Day 9.5), while HNF-3γ expression peaks around Day 15.5 of gestation

The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia

<p>Abstract</p> <p>Background</p> <p>The different physiological repertoire of CA3 and CA1 neurons in the hippocampus, as well as their differing behaviour after noxious stimuli are ultimately based upon differences in the expressed genome. We have compared CA3 and CA1 gene expression in the uninjured brain, and after cerebral ischemia using laser microdissection (LMD), RNA amplification, and array hybridization.</p> <p>Results</p> <p>Profiling in CA1 vs. CA3 under normoxic conditions detected more than 1000 differentially expressed genes that belong to different, physiologically relevant gene ontology groups in both cell types. The comparison of each region under normoxic and ischemic conditions revealed more than 5000 ischemia-regulated genes for each individual cell type. Surprisingly, there was a high co-regulation in both regions. In the ischemic state, only about 100 genes were found to be differentially expressed in CA3 and CA1. The majority of these genes were also different in the native state. A minority of interesting genes (e.g. inhibinbetaA) displayed divergent expression preference under native and ischemic conditions with partially opposing directions of regulation in both cell types.</p> <p>Conclusion</p> <p>The differences found in two morphologically very similar cell types situated next to each other in the CNS are large providing a rational basis for physiological differences. Unexpectedly, the genomic response to ischemia is highly similar in these two neuron types, leading to a substantial attenuation of functional genomic differences in these two cell types. Also, the majority of changes that exist in the ischemic state are not generated de novo by the ischemic stimulus, but are preexistant from the genomic repertoire in the native situation. This unexpected influence of a strong noxious stimulus on cell-specific gene expression differences can be explained by the activation of a cell-type independent conserved gene-expression program. Our data generate both novel insights into the relation of the quiescent and stimulus-induced transcriptome in different cells, and provide a large dataset to the research community, both for mapping purposes, as well as for physiological and pathophysiological research.</p

Machine learning on large scale perturbation screens for SARS-CoV-2 host factors identifies β-catenin/CBP inhibitor PRI-724 as a potent antiviral

Expanding antiviral treatment options against SARS-CoV-2 remains crucial as the virus evolves under selection pressure which already led to the emergence of several drug resistant strains. Broad spectrum host-directed antivirals (HDA) are promising therapeutic options, however the robust identification of relevant host factors by CRISPR/Cas9 or RNA interference screens remains challenging due to low consistency in the resulting hits. To address this issue, we employed machine learning, based on experimental data from several knockout screens and a drug screen. We trained classifiers using genes essential for virus life cycle obtained from the knockout screens. The machines based their predictions on features describing cellular localization, protein domains, annotated gene sets from Gene Ontology, gene and protein sequences, and experimental data from proteomics, phospho-proteomics, protein interaction and transcriptomic profiles of SARS-CoV-2 infected cells. The models reached a remarkable performance suggesting patterns of intrinsic data consistency. The predicted HDF were enriched in sets of genes particularly encoding development, morphogenesis, and neural processes. Focusing on development and morphogenesis-associated gene sets, we found β-catenin to be central and selected PRI-724, a canonical β-catenin/CBP disruptor, as a potential HDA. PRI-724 limited infection with SARS-CoV-2 variants, SARS-CoV-1, MERS-CoV and IAV in different cell line models. We detected a concentration-dependent reduction in cytopathic effects, viral RNA replication, and infectious virus production in SARS-CoV-2 and SARS-CoV-1-infected cells. Independent of virus infection, PRI-724 treatment caused cell cycle deregulation which substantiates its potential as a broad spectrum antiviral. Our proposed machine learning concept supports focusing and accelerating the discovery of host dependency factors and identification of potential host-directed antivirals

The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia-0

<p><b>Copyright information:</b></p><p>Taken from "The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia"</p><p>http://www.biomedcentral.com/1471-2164/8/370</p><p>BMC Genomics 2007;8():370-370.</p><p>Published online 15 Oct 2007</p><p>PMCID:PMC2194787.</p><p></p>ull hemispheric infarcts. A, TTC-stained coronal section 24 h after induction of ischemia/hypoxia demonstrate a full hemispheric infarct which fully covers the hippocampal region. B, The cutting outlines used for Laser microdissection from coronal cryosections are demonstrated on a section stained with an antibody against NeuN and a secondary Cy3-coupled antibody. Actual Laser microdissections in the experiments were performed on Thionin-stained sections. C, Scheme showing the strategy used for detection of differentially regulated genes from amplified RNA. Samples from CA3 and CA1 regions were hybridized on two-color oligonucleotide arrays (Agilent). Direct competitive hybridizations were performed for all combinations: CA3 sham vs, CA1 sham, CA3 ischemia vs CA1 ischemia, CA3 ischemia vs CA3 sham, and CA1 ischemia vs CA1 sham. All experiments were also dye-swapped, and means of the two corresponding values used for further analyses. Arrays were statistically analyzed using linear modelling (limma, R)

The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia-4

<p><b>Copyright information:</b></p><p>Taken from "The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia"</p><p>http://www.biomedcentral.com/1471-2164/8/370</p><p>BMC Genomics 2007;8():370-370.</p><p>Published online 15 Oct 2007</p><p>PMCID:PMC2194787.</p><p></p>ischemic animals and the non-ischemic controls (means of n = 4 experiments for each region). In each of the hippocampal subregions more than 5000 genes could be identified exhibiting differential expression upon ischemia. A. 5243 differentially expressed genes were detected in the CA3 region. B. 5511 differentially expressed genes were detected in the CA1 region. Red: significantly regulated genes (p< 0.05; differentially regulated genes in blue). C, A total of 97 genes is significantly different between ischemic CA3 and ischemic CA1 regions (scatterplot; blue are significantly regulated genes p< 0.05). D, Bar graph showing the 5 most different genes with preference for CA3 or CA1 with their relative enrichment factors (prdma, pr-domain containing protein 8; Inhba, Inhibin beta A; Bok, Bcl-2 related ovarian killer; Sytl4, synaptotagmin-like 4; rbp 4, retinol binding protein 4; mpped1, metallophosphoesterase domain containing 1; mrg1, myeloid ecotropic viral integration site-related gene 1, alternative names: meis2, stra10)

The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia-2

<p><b>Copyright information:</b></p><p>Taken from "The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia"</p><p>http://www.biomedcentral.com/1471-2164/8/370</p><p>BMC Genomics 2007;8():370-370.</p><p>Published online 15 Oct 2007</p><p>PMCID:PMC2194787.</p><p></p>r CA1. The upper part of the graph shows the GO category "Biological process", the lower part "Molecular function". GO analysis were performed using the web-based L2L tool [29]. For "Biological process" there is a strong emphasis on terms related to neuron differentiation, synaptic function, and energy metabolism in CA3, and to GABA-signaling in CA1. For "Molecular function" we find enrichment of groups like ephrin receptors, serin-type protease inhibitors, and carbohydrate moiety transfer activities. In contrast in CA1 we observe an enrichment in deglycosylating activity, ligand-gated ion channels, and sulfotransferase activity. Black, expected matches; red, observed matches

The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia-5

<p><b>Copyright information:</b></p><p>Taken from "The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia"</p><p>http://www.biomedcentral.com/1471-2164/8/370</p><p>BMC Genomics 2007;8():370-370.</p><p>Published online 15 Oct 2007</p><p>PMCID:PMC2194787.</p><p></p>tting CA3/CA1 ratios in ischemia vs. sham reveals deviation from the diagonal. Difference ratios are attenuated by ischemia regardless of preferential CA3 or CA1 expression (red: p< 0.05). C, Inhibin beta A displays the highest change in preference between the native and ischemic state. The gene expression preference actually reverses from higher expression in CA1 in the native brain to higher expression in CA3 in the ischemic state. Verification with quantitative PCR shows comparable values to the array-derived ratios