LPS Resistance of SPRET/Ei Mice Is Mediated by Gilz, Encoded by the Tsc22d3 Gene on the X Chromosome
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A Steroid Receptor Coactivator Stimulator (MCB-613) Attenuates Adverse Remodeling After Myocardial Infarction
A steroid receptor coactivator stimulator (MCB-613) attenuates adverse remodeling after myocardial infarction Lisa K. Mullanya,1, Aarti D. Rohiraa,1, John P. Leachb,2, Jong H. Kimc,d,2, Tanner O. Monroec, Andrea R. Ortiza, Brittany Storka, M. Waleed Gabere, Poonam Sarkare, Andrew G. Sikoraf, Todd K. Rosengartg, Brian Yorka, Yongcheng Songh, Clifford C. Dacsoa, David M. Lonarda, James F. Martinc,d,3, and Bert W. O’Malleya,3 aDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030; bPenn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; cDepartment of Molecular Physiology and Biophysics, Baylor College of Medicine, TX 77030; dCardiomyocyte Renewal Lab, Texas Heart Institute, Houston, TX 77030; eDepartment of Pediatrics, Baylor College of Medicine, Houston, TX 77030; fDepartment of Otolaryngology-Head & Neck Surgery, Baylor College of Medicine, Houston, TX 77030; gDepartment of Surgery, Baylor College of Medicine, Houston, TX 77030; and hDepartment of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030 Contributed by Bert W. O’Malley, September 16, 2020 (sent for review June 23, 2020; reviewed by Chris Glass and Philip W. Shaul) Progressive remodeling of the heart, resulting in cardiomyocyte maintenance of metabolic regulation in diverse organ systems (CM) loss and increased inflammation, fibrosis, and a progressive including the heart (16). Specifically in the heart, recent findings decrease in cardiac function, are hallmarks of myocardial infarction indicate that SRC family members regulate cardiomyocyte func- (MI)-induced heart failure. We show that MCB-613, a potent small tion during early cardiac development (17) and in response to molecule stimulator of steroid receptor coactivators (SRCs) atten- cardiac metabolic stress (18). -
Discovery of Osmotic Sensitive Transcription Factors in Fish Intestine Via a Transcriptomic Approach
Wong et al. BMC Genomics 2014, 15:1134 http://www.biomedcentral.com/1471-2164/15/1134 RESEARCH ARTICLE Open Access Discovery of osmotic sensitive transcription factors in fish intestine via a transcriptomic approach Marty Kwok-Shing Wong1*, Haruka Ozaki2, Yutaka Suzuki2, Wataru Iwasaki1,2,3 and Yoshio Takei1 Abstract Background: Teleost intestine is crucial for seawater acclimation by sensing osmolality of imbibed seawater and regulating drinking and water/ion absorption. Regulatory genes for transforming intestinal function have not been identified. A transcriptomic approach was used to search for such genes in the intestine of euryhaline medaka. Results: Quantitative RNA-seq by Illumina Hi-Seq Sequencing method was performed to analyze intestinal gene expression 0 h, 1 h, 3 h, 1 d, and 7 d after seawater transfer. Gene ontology (GO) enrichment results showed that cell adhesion, signal transduction, and protein phosphorylation gene categories were augmented soon after transfer, indicating a rapid reorganization of cellular components and functions. Among >50 transiently up-regulated transcription factors selected via co-expression correlation and GO selection, five transcription factors, including CEBPB and CEBPD, were confirmed by quantitative PCR to be specific to hyperosmotic stress, while others were also up-regulated after freshwater control transfer, including some well-known osmotic-stress transcription factors such as SGK1 and TSC22D3/ Ostf1. Protein interaction networks suggest a high degree of overlapping among the signaling of transcription factors that respond to osmotic and general stresses, which sheds light on the interpretation of their roles during hyperosmotic stress and emergency. Conclusions: Since cortisol is an important hormone for seawater acclimation as well as for general stress in teleosts, emergency and osmotic challenges could have been evolved in parallel and resulted in the overlapped signaling networks. -
S41467-020-18249-3.Pdf
ARTICLE https://doi.org/10.1038/s41467-020-18249-3 OPEN Pharmacologically reversible zonation-dependent endothelial cell transcriptomic changes with neurodegenerative disease associations in the aged brain Lei Zhao1,2,17, Zhongqi Li 1,2,17, Joaquim S. L. Vong2,3,17, Xinyi Chen1,2, Hei-Ming Lai1,2,4,5,6, Leo Y. C. Yan1,2, Junzhe Huang1,2, Samuel K. H. Sy1,2,7, Xiaoyu Tian 8, Yu Huang 8, Ho Yin Edwin Chan5,9, Hon-Cheong So6,8, ✉ ✉ Wai-Lung Ng 10, Yamei Tang11, Wei-Jye Lin12,13, Vincent C. T. Mok1,5,6,14,15 &HoKo 1,2,4,5,6,8,14,16 1234567890():,; The molecular signatures of cells in the brain have been revealed in unprecedented detail, yet the ageing-associated genome-wide expression changes that may contribute to neurovas- cular dysfunction in neurodegenerative diseases remain elusive. Here, we report zonation- dependent transcriptomic changes in aged mouse brain endothelial cells (ECs), which pro- minently implicate altered immune/cytokine signaling in ECs of all vascular segments, and functional changes impacting the blood–brain barrier (BBB) and glucose/energy metabolism especially in capillary ECs (capECs). An overrepresentation of Alzheimer disease (AD) GWAS genes is evident among the human orthologs of the differentially expressed genes of aged capECs, while comparative analysis revealed a subset of concordantly downregulated, functionally important genes in human AD brains. Treatment with exenatide, a glucagon-like peptide-1 receptor agonist, strongly reverses aged mouse brain EC transcriptomic changes and BBB leakage, with associated attenuation of microglial priming. We thus revealed tran- scriptomic alterations underlying brain EC ageing that are complex yet pharmacologically reversible. -
Mouse Mid2 Conditional Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Mid2 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Mid2 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Mid2 gene (NCBI Reference Sequence: NM_011845 ; Ensembl: ENSMUSG00000000266 ) is located on Mouse chromosome X. 9 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 9 (Transcript: ENSMUST00000112993). Exon 5 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Mid2 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-340F6 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 5 starts from about 49.34% of the coding region. The knockout of Exon 5 will result in frameshift of the gene. The size of intron 4 for 5'-loxP site insertion: 11103 bp, and the size of intron 5 for 3'-loxP site insertion: 1122 bp. The size of effective cKO region: ~628 bp. The cKO region does not have any other known gene. Page 1 of 7 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele gRNA region 5' gRNA region 3' 1 5 6 9 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Mid2 Homology arm cKO region loxP site Page 2 of 7 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats. -
Efficient Analysis of Mouse Genome Sequences Reveal Many Nonsense Variants
Efficient analysis of mouse genome sequences reveal many nonsense variants Sophie Steelanda,b,1, Steven Timmermansa,b,1, Sara Van Ryckeghema,b, Paco Hulpiaua,b, Yvan Saeysa,c, Marc Van Montagud,e,f,2, Roosmarijn E. Vandenbrouckea,b,3, and Claude Liberta,b,2,3 aInflammation Research Center, Flanders Institute for Biotechnology (VIB), 9052 Ghent, Belgium; bDepartment of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium; cDepartment of Internal Medicine, Ghent University, 9052 Ghent, Belgium; dDepartment of Plant Systems Biology, VIB, 9052 Ghent, Belgium; eDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; and fInternational Plant Biotechnology Outreach, VIB, Ghent, Belgium Contributed by Marc Van Montagu, March 30, 2016 (sent for review December 31, 2015; reviewed by Bruce Beutler, Stefano Bruscoli, Stefan Rose-John, and Klaus Schulze-Osthoff) Genetic polymorphisms in coding genes play an important role alive, archiving them, and distributing mutant strains to in- when using mouse inbred strains as research models. They have terested users (4). been shown to influence research results, explain phenotypical Since Clarence Little showed in the early 20th century that the differences between inbred strains, and increase the amount of principle of inbreeding also applies to mice, several hundred interesting gene variants present in the many available inbred inbred mouse strains have been generated (5). Some of these lines. SPRET/Ei is an inbred strain derived from Mus spretus that strains display specific phenotypes that are the result of a mutant has ∼1% sequence difference with the C57BL/6J reference ge- gene, and in several cases have formed the basis for identifying nome. -
SUPPLEMENTARY NOTE Co-Activation of GR and NFKB
SUPPLEMENTARY NOTE Co-activation of GR and NFKB alters the repertoire of their binding sites and target genes. Nagesha A.S. Rao1*, Melysia T. McCalman1,*, Panagiotis Moulos2,4, Kees-Jan Francoijs1, 2 2 3 3,5 Aristotelis Chatziioannou , Fragiskos N. Kolisis , Michael N. Alexis , Dimitra J. Mitsiou and 1,5 Hendrik G. Stunnenberg 1Department of Molecular Biology, Radboud University Nijmegen, the Netherlands 2Metabolic Engineering and Bioinformatics Group, Institute of Biological Research and Biotechnology, National Hellenic Research Foundation, Athens, Greece 3Molecular Endocrinology Programme, Institute of Biological Research and Biotechnology, National Hellenic Research Foundation, Greece 4These authors contributed equally to this work 5 Corresponding authors E-MAIL: [email protected] ; TEL: +31-24-3610524; FAX: +31-24-3610520 E-MAIL: [email protected] ; TEL: +30-210-7273741; FAX: +30-210-7273677 Running title: Global GR and NFKB crosstalk Keywords: GR, p65, genome-wide, binding sites, crosstalk SUPPLEMENTARY FIGURES/FIGURE LEGENDS AND SUPPLEMENTARY TABLES 1 Rao118042_Supplementary Fig. 1 A Primary transcript Mature mRNA TNF/DMSO TNF/DMSO 8 12 r=0.74, p< 0.001 r=0.61, p< 0.001 ) 2 ) 10 2 6 8 4 6 4 2 2 0 Fold change (mRNA) (log Fold change (primRNA) (log 0 −2 −2 −2 0 2 4 −2 0 2 4 Fold change (RNAPII) (log2) Fold change (RNAPII) (log2) B chr5: chrX: 56 _ 104 _ DMSO DMSO 1 _ 1 _ 56 _ 104 _ TA TA 1 _ 1 _ 56 _ 104 _ TNF TNF Cluster 1 1 _ Cluster 2 1 _ 56 _ 104 _ TA+TNF TA+TNF 1 _ 1 _ CCNB1 TSC22D3 chr20: chr17: 25 _ 33 _ DMSO DMSO 1 _ 1 _ 25 _ 33 _ TA TA 1 _ 1 _ 25 _ 33 _ TNF TNF Cluster 3 1 _ Cluster 4 1 _ 25 _ 33 _ TA+TNF TA+TNF 1 _ 1 _ GPCPD1 CCL2 chr6: chr22: 77 _ 35 _ DMSO DMSO 1 _ 77 _ 1 _ 35 _ TA TA 1 _ 1 _ 77 _ 35 _ TNF Cluster 5 Cluster 6 TNF 1 _ 1 _ 77 _ 35 _ TA+TNF TA+TNF 1 _ 1 _ TNFAIP3 DGCR6 2 Supplementary Figure 1. -
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The Journal of Immunology Enhancer Turnover Is Associated with a Divergent Transcriptional Response to Glucocorticoid in Mouse and Human Macrophages Alasdair W. Jubb,*,†,1 Robert S. Young,*,1 David A. Hume,† and Wendy A. Bickmore* Phenotypic differences between individuals and species are controlled in part through differences in expression of a relatively con- served set of genes. Genes expressed in the immune system are subject to especially powerful selection. We have investigated the evolution of both gene expression and candidate enhancers in human and mouse macrophages exposed to glucocorticoid (GC), a regulator of innate immunity and an important therapeutic agent. Our analyses revealed a very limited overlap in the repertoire of genes responsive to GC in human and mouse macrophages. Peaks of inducible binding of the GC receptor (GR) detected by chro- matin immunoprecipitation-Seq correlated with induction, but not repression, of target genes in both species, occurred at distal regulatory sites not promoters, and were strongly enriched for the consensus GR-binding motif. Turnover of GR binding between mice and humans was associated with gain and loss of the motif. There was no detectable signal of positive selection at species- specific GR binding sites, but clear evidence of purifying selection at the small number of conserved sites. We conclude that enhancer divergence underlies the difference in transcriptional activation after GC treatment between mouse and human macrophages. Only the shared inducible loci show evidence of selection, and therefore these loci may be important for the subset of responses to GC that is shared between species. The Journal of Immunology, 2016, 196: 813–822. -
Insights Into Functional Connectivity in Mammalian Signal Transduction Pathways by Pairwise
bioRxiv preprint doi: https://doi.org/10.1101/2019.12.30.891200; this version posted December 30, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Insights into Functional Connectivity in Mammalian Signal Transduction Pathways by Pairwise Comparison of Protein Interaction Partners of Critical Signaling Hubs Chilakamarti V. Ramana * Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03766, USA *Correspondence should be addressed: Chilakamarti V .Ramana, Telephone. (603)-738-2507, E-mail: [email protected] ORCID ID: /0000-0002-5153-8252 1 bioRxiv preprint doi: https://doi.org/10.1101/2019.12.30.891200; this version posted December 30, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract Growth factors and cytokines activate signal transduction pathways and regulate gene expression in eukaryotes. Intracellular domains of activated receptors recruit several protein kinases as well as transcription factors that serve as platforms or hubs for the assembly of multi-protein complexes. The signaling hubs involved in a related biologic function often share common interaction proteins and target genes. This functional connectivity suggests that a pairwise comparison of protein interaction partners of signaling hubs and network analysis of common partners and their expression analysis might lead to the identification of critical nodes in cellular signaling. -
Mai Muudatuntuu Ti on Man Mini
MAIMUUDATUNTUU US009809854B2 TI ON MAN MINI (12 ) United States Patent ( 10 ) Patent No. : US 9 ,809 ,854 B2 Crow et al. (45 ) Date of Patent : Nov . 7 , 2017 Whitehead et al. (2005 ) Variation in tissue - specific gene expression ( 54 ) BIOMARKERS FOR DISEASE ACTIVITY among natural populations. Genome Biology, 6 :R13 . * AND CLINICAL MANIFESTATIONS Villanueva et al. ( 2011 ) Netting Neutrophils Induce Endothelial SYSTEMIC LUPUS ERYTHEMATOSUS Damage , Infiltrate Tissues, and Expose Immunostimulatory Mol ecules in Systemic Lupus Erythematosus . The Journal of Immunol @(71 ) Applicant: NEW YORK SOCIETY FOR THE ogy , 187 : 538 - 552 . * RUPTURED AND CRIPPLED Bijl et al. (2001 ) Fas expression on peripheral blood lymphocytes in MAINTAINING THE HOSPITAL , systemic lupus erythematosus ( SLE ) : relation to lymphocyte acti vation and disease activity . Lupus, 10 :866 - 872 . * New York , NY (US ) Crow et al . (2003 ) Microarray analysis of gene expression in lupus. Arthritis Research and Therapy , 5 :279 - 287 . * @(72 ) Inventors : Mary K . Crow , New York , NY (US ) ; Baechler et al . ( 2003 ) Interferon - inducible gene expression signa Mikhail Olferiev , Mount Kisco , NY ture in peripheral blood cells of patients with severe lupus . PNAS , (US ) 100 ( 5 ) : 2610 - 2615. * GeneCards database entry for IFIT3 ( obtained from < http : / /www . ( 73 ) Assignee : NEW YORK SOCIETY FOR THE genecards. org /cgi - bin / carddisp .pl ? gene = IFIT3 > on May 26 , 2016 , RUPTURED AND CRIPPLED 15 pages ) . * Navarra et al. (2011 ) Efficacy and safety of belimumab in patients MAINTAINING THE HOSPITAL with active systemic lupus erythematosus : a randomised , placebo FOR SPECIAL SURGERY , New controlled , phase 3 trial . The Lancet , 377 :721 - 731. * York , NY (US ) Abramson et al . ( 1983 ) Arthritis Rheum . -
E-Mutpath: Computational Modelling Reveals the Functional Landscape of Genetic Mutations Rewiring Interactome Networks
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.22.262386; this version posted August 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. e-MutPath: Computational modelling reveals the functional landscape of genetic mutations rewiring interactome networks Yongsheng Li1, Daniel J. McGrail1, Brandon Burgman2,3, S. Stephen Yi2,3,4,5 and Nidhi Sahni1,6,7,8,* 1Department oF Systems Biology, The University oF Texas MD Anderson Cancer Center, Houston, TX 77030, USA 2Department oF Oncology, Livestrong Cancer Institutes, Dell Medical School, The University oF Texas at Austin, Austin, TX 78712, USA 3Institute For Cellular and Molecular Biology (ICMB), The University oF Texas at Austin, Austin, TX 78712, USA 4Institute For Computational Engineering and Sciences (ICES), The University oF Texas at Austin, Austin, TX 78712, USA 5Department oF Biomedical Engineering, Cockrell School of Engineering, The University oF Texas at Austin, Austin, TX 78712, USA 6Department oF Epigenetics and Molecular Carcinogenesis, The University oF Texas MD Anderson Science Park, Smithville, TX 78957, USA 7Department oF BioinFormatics and Computational Biology, The University oF Texas MD Anderson Cancer Center, Houston, TX 77030, USA 8Program in Quantitative and Computational Biosciences (QCB), Baylor College oF Medicine, Houston, TX 77030, USA *To whom correspondence should be addressed. Nidhi Sahni. Tel: +1 512 2379506; Email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.22.262386; this version posted August 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
Glucocorticoid Receptor and Klf4 Co-Regulate Anti-Inflammatory Genes in Keratinocytes
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital.CSIC Glucocorticoid receptor and Klf4 co-regulate anti-inflammatory genes in keratinocytes Lisa M. Sevilla1, Víctor Latorre1,2, Elena Carceller1, Julia Boix1, Daniel Vodák3, Ian Geoffrey Mills4, 5, 6, and Paloma Pérez1 1 Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas (IBV- CSIC), Jaime Roig 11, E-46010 Valencia, Spain. 2 Faculty of Human and Medical Sciences, The University of Manchester, Manchester UK 3 Bioinformatics Core Facility, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Norway 4 Prostate Cancer Research Group, Centre for Molecular Medicine (Norway), University of Oslo and Oslo University Hospitals, Oslo, Norway 5 Department of Cancer Prevention, Oslo University Hospitals, Oslo, Norway. 6 Department of Urology, Oslo University Hospitals, Oslo, Norway. Corresponding autor and person to whom reprint requests should be addressed: Paloma Pérez, PhD Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas (IBV- CSIC) Jaime Roig 11, E-46010, Valencia, Spain Phone: +34-96-339-1766 Fax: +34-96-369-0800 e-mail: [email protected] Grants and fellowships supporting the writing of paper: SAF2011-28115 of the Ministerio de Economía y Competitividad from the Spanish government. EC and JB are recipients of FPU and FPI fellowships of the Spanish Ministery, respectively Disclosure Statement: The authors have nothing to disclose. Abstract The glucocorticoid (GC) receptor (GR) and Kruppel-like factor Klf4 are transcription factors that play major roles in the skin homeostasis by regulating the expression of overlapping gene subsets. -
GILZ-Dependent Modulation of Mtorc1 Regulates Spermatogonial Maintenance Hue M
© 2018. Published by The Company of Biologists Ltd | Development (2018) 145, dev165324. doi:10.1242/dev.165324 STEM CELLS AND REGENERATION RESEARCH ARTICLE GILZ-dependent modulation of mTORC1 regulates spermatogonial maintenance Hue M. La1,2,*, Ai-Leen Chan1,2,*, Julien M. D. Legrand1,2, Fernando J. Rossello1,2, Christina G. Gangemi1,2, Antonella Papa3, Qiang Cheng4, Eric F. Morand4 and Robin M. Hobbs1,2,‡ ABSTRACT prospermatogonia) upon migration to the basement membrane of Male fertility is dependent on spermatogonial stem cells (SSCs) that the seminiferous cords. The undifferentiated population contains self-renew and produce differentiating germ cells. Growth factors isolated spermatogonia (A-single or As) plus chains of cells produced within the testis are essential for SSC maintenance interconnected by cytoplasmic bridges. Two-cell chains are but intrinsic factors that dictate the SSC response to these stimuli known as A-paired (Apr) whereas chains of four or more cells are poorly characterised. Here, we have studied the role of GILZ, are known as A-aligned (Aal). Lineage-tracing studies demonstrate α a TSC22D family protein and spermatogenesis regulator, in that SSCs are marked by GFR 1 and typically As and Apr,whereas spermatogonial function and signalling. Although broadly expressed most undifferentiated cells, particularly Aal, are committed in the germline, GILZ was prominent in undifferentiated spermatogonia progenitors and marked by NGN3 (Hara et al., 2014; Nakagawa + and Gilz deletion in adults resulted in exhaustion of the GFRα1+ et al., 2010). NGN3 Aal may revert to SSCs through chain SSC-containing population and germline degeneration. GILZ loss fragmentation, particularly upon tissue damage (Nakagawa et al., γ was associated with mTORC1 activation, suggesting enhanced 2010).