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Supplement-Molecular Sys Biology Supplementary Material for: Iwona Stelniec-Klotz, Stefan Legewie, Oleg Tchernitsa, Franziska Witzel, Bertram Klinger, Christine Sers, Hanspeter Herzel, Nils Blüthgen and Reinhold Schäfer: Reverse-engineering a hierarchical regulatory network downstream of oncogenic KRAS Content (9 Figures, 3 Tables, 1 Text, 1 List of References) Supplementary Figures S1: Nuclear protein levels of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA after silencing in KRAS-transformed RAS-ROSE cells. S2: Impact of transcription factor knock-down on the KRAS pathway-mediated mRNA expression profile S3: RNA expression of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA after silencing in KRAS- transformed RAS-ROSE cells S4: Effects of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA knock-down in RAS-ROSE cells on the activity of cytoplasmic signaling downstream of RAS S5: Effect of Fosl1 overepxression and Otx1 knockdown on Fosl1mRNA and phospho-Erk. S6: Effects on growth characteristics of RAS-ROSE cells after silencing Fosl1, Hmga2, Klf6, JunB S7: Effects on growth characteristics of RAS-ROSE cells after silencing Otx1, Gfi1, RelA S8: Effects on distribution of cell cycle phases in KRAS-transformed RAS-ROSE cells after silencing of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA S9: Effect of perturbation strength and noise on algorithm performance. Supplementary Tables S1: Rules for finding transcription factor-related patterns in genome-wide expression data (related to Fig. 3B and C). S2: Known interaction (related to Fig. 4) S3: Quantification of the network. Supplementary Texts Generation of artificial data sets Supplementary References Supplementary Fig. 1 Nuclear protein levels of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA after silencing in KRAS-transformed RAS-ROSE cells. Western Blot analysis of nuclear protein levels of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1 and RelA in RAS-ROSE cells 48 h after transfections with scrambled siRNAduplex (Sc), transfection reagents only (Mock) and two independent transcription factor specific siRNAs (1, 2). ß-tubulin control (*). 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  • Downloaded from UCSC Genome Browser Was Performed Using Rna-Star/2.4.2A (Dobin Et Al., 2013)
    Neuromesodermal progenitor origin of trunk neural crest in vivo Martyna Lukoseviciute1,2, Sarah Mayes1, Tatjana Sauka-Spengler1,∗ Abstract Neural crest (NC) is a vertebrate-specific population of multipotent embryonic cells predisposed to diverse derivatives along the anteroposterior (A-P) axis. Only cranial NC progenitors give rise to ectomesenchymal cell types, whereas trunk NC is biased for neuronal cell fates. By integrating multimodal single-cell analysis, we provide evidence for divergent embryonic origins of cranial vs. trunk NC that explain this dichotomy. We show that the NC regulator foxd3 is heterogeneously expressed across the A-P axis and identify its specific cranial and trunk autoregulatory enhancers. Whereas cranial-specific enhancer is active in the bona fide NC, the trunk foxd3 autoregulatory element surprisingly marked bipotent tailbud neuromesodermal progenitors (NMps). We integrated NMp single cell epigemomics and trasncriptomics data and for the first time reconstructed anamniote NMp gene regulatory network. Moreover, using pseudotime and developmental trajectory analyses of NMps and NC during normal development and in foxd3 mutants, we demonstrate an active role for foxd3 in balancing non-cranial NC and NMp fates during early embryonic devel- opment. Strikingly, we show that a portion of posterior NC in the developing zebrafish embryo is derived from the pro-neural NMps. This suggests a common embryonic origin of trunk NC and NM progenitors that is distinct from cranial NC anlage, and elucidates pro-neural bias of trunk NC. Keywords: neural crest, neuromesodermal progenitors, gene regulatory network, axial progenitors, embryo patterning Introduction The neural crest (NC) is a unique multipotent cell population that gives rise to an extraordinary diversity of tissues in vertebrate embryos, including chondrocytes and osteocytes of the craniofacial skeleton, neurons and glia of the peripheral nervous system, and all skin pigment cells in the body.
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  • The Viral Oncoproteins Tax and HBZ Reprogram the Cellular Mrna Splicing Landscape
    bioRxiv preprint doi: https://doi.org/10.1101/2021.01.18.427104; this version posted January 18, 2021. 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. The viral oncoproteins Tax and HBZ reprogram the cellular mRNA splicing landscape Charlotte Vandermeulen1,2,3, Tina O’Grady3, Bartimee Galvan3, Majid Cherkaoui1, Alice Desbuleux1,2,4,5, Georges Coppin1,2,4,5, Julien Olivet1,2,4,5, Lamya Ben Ameur6, Keisuke Kataoka7, Seishi Ogawa7, Marc Thiry8, Franck Mortreux6, Michael A. Calderwood2,4,5, David E. Hill2,4,5, Johan Van Weyenbergh9, Benoit Charloteaux2,4,5,10, Marc Vidal2,4*, Franck Dequiedt3*, and Jean-Claude Twizere1,2,11* 1Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium.2Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.3Laboratory of Gene Expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium.4Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA. 5Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.6Laboratory of Biology and Modeling of the Cell, CNRS UMR 5239, INSERM U1210, University of Lyon, Lyon, France.7Department of Pathology and Tumor Biology, Kyoto University, Japan.8Unit of Cell and Tissue Biology, GIGA Institute, University of Liege, Liege, Belgium.9Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Catholic University of Leuven, Leuven, Belgium.10Department of Human Genetics, CHU of Liege, University of Liege, Liege, Belgium.11Lead Contact. *Correspondence: [email protected]; [email protected]; [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.01.18.427104; this version posted January 18, 2021.
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    RBPJ-DEPENDENT AND -INDEPENDENT NOTCH2 SIGNALING REGULATES CILIARY BODY DEVELOPMENT IN THE MOUSE EYE By Yi Zhou B.S., Tsinghua University, 2010 Submitted to the graduate degree program in Anatomy and Cell Biology and the Graduate Faculty of the University of Kansas in partial fulfillment of the requirements for the degree of Doctor of Philosophy. ________________________________ Ting Xie, Ph.D., Co-Chair ________________________________ William Kinsey, Ph.D., Co-Chair ________________________________ Dale Abrahamson, Ph.D. ________________________________ Peter Smith, Ph.D. ________________________________ Jerry Workman, Ph.D. Date Defended: Jan 6th, 2016 The Dissertation Committee for Yi Zhou certifies that this is the approved version of the following dissertation: RBPJ-DEPENDENT AND -INDEPENDENT NOTCH2 SIGNALING REGULATES CILIARY BODY DEVELOPMENT IN THE MOUSE EYE ________________________________ Ting Xie, Ph.D., Co-Chair ________________________________ William Kinsey, Ph.D., Co-Chair Date Approved: Jan 15th, 2016 ii ABSTRACT The ciliary body (CB) is a two-layered structure in the anterior eye, which is composed of the pigmented outer ciliary epithelium (OCE) and the non-pigmented inner ciliary epithelium (ICE). It is responsible for aqueous humor secretion and lens accommodation. Despite the important roles in maintaining normal eye functions, its development still remains poorly understood. The Notch signaling pathway is an evolutionarily conserved pathway that has diverse functions during tissue development and homeostasis. Canonical Notch signaling is mediated through the recombination signal binding protein for immunoglobulin kappa J region (RBPJ)-dependent transcription activation and repression. In this study, I have demonstrated that Notch2 and RBPJ are important regulators of CB development by conditionally deleting them in the developing CB.
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    Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press A MASSIVELY PARALLEL REPORTER ASSAY REVEALS CONTEXT-DEPENDENT ACTIVITY OF HOMEODOMAIN BINDING SITES IN VIVO Andrew E. O. Hughes1, Connie A. Myers1, and Joseph C. Corbo1* 1Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA *To whom correspondence should be addressed. Tel: +1 314 362 6254; Fax: +1 314 362 4096; Email: [email protected] Running title: Context-dependent activity of CRX binding sites Key words: homeodomain, cis-regulatory element, massively parallel reporter assay, transcription factor binding site, retina 1 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press ABSTRACT Cone-rod homeobox (CRX) is a paired-like homeodomain transcription factor (TF) and a master regulator of photoreceptor development in vertebrates. The in vitro DNA binding preferences of CRX have been described in detail, but the degree to which in vitro binding affinity is correlated with in vivo enhancer activity is not known. In addition, paired-class homeodomain TFs can bind DNA cooperatively as both homodimers and heterodimers at inverted TAAT half-sites separated by two or three nucleotides. This dimeric configuration is thought to mediate target specificity, but whether monomeric and dimeric sites encode distinct levels of activity is not known. Here, we used a massively parallel reporter assay to determine how local sequence context shapes the regulatory activity of CRX binding sites in mouse photoreceptors. We assayed inactivating mutations in >1,700 TF binding sites and found that dimeric CRX binding sites act as stronger enhancers than monomeric CRX binding sites.
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    USING THE MOUSE RETINA TO MODEL THE ROLE OF SOX2 IN NEURAL INDUCTION Whitney E. Heavner A dissertation submitted to the faculty of the University of North Carolina at Chapel Hill in partial fulfillment of the requirements for a degree of Doctor of Philosophy in the Program in Genetics and Molecular Biology Chapel Hill 2013 Approved by Robert Duronio, Ph.D. Stephen Crews, Ph.D. Norman Sharpless, M.D. Ellen Weiss, Ph.D. Mark Zylka, Ph.D. © 2013 Whitney E. Heavner ALL RIGHTS RESERVED ii ABSTRACT WHITNEY E. HEAVNER: Using the Mouse Retina to Model the Role of SOX2 in Neural Induction (Under the direction of Dr. Larysa Pevny) Neural competence is the ability of a progenitor cell to generate a neuron. The eye is one of the few tissues derived from the neural ectoderm that contains both neurogenic and non-neurogenic cells, all of which arise from a common progenitor pool. Therefore, the eye is a particularly useful model to study the molecular mechanisms that confer neural competence. Moreover, this cell fate dichotomy is highly reminiscent of the earlier process of neural induction, or the decision of an ectoderm precursor cell to become neural plate or epidermis. The HMG-box transcription factor SOX2 is crucial for both of these processes. Little is known about the role of SOX2 in neural induction, and what is known has been worked out primarily in lower vertebrates. Humans and mice with mutations in SOX2 exhibit a range of neural defects; therefore, from the perspective of human health, it is important to understand SOX2’s function in mammalian neuroepithelium.
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