Molecular Data, Functional Studies of the SH3 Recognition Motif and Correlation Between Wild-Type MED25 and PMP22 RNA Levels in CMT1A Animal Models
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Analysis of Trans Esnps Infers Regulatory Network Architecture
Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Anat Kreimer All rights reserved ABSTRACT Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer eSNPs are genetic variants associated with transcript expression levels. The characteristics of such variants highlight their importance and present a unique opportunity for studying gene regulation. eSNPs affect most genes and their cell type specificity can shed light on different processes that are activated in each cell. They can identify functional variants by connecting SNPs that are implicated in disease to a molecular mechanism. Examining eSNPs that are associated with distal genes can provide insights regarding the inference of regulatory networks but also presents challenges due to the high statistical burden of multiple testing. Such association studies allow: simultaneous investigation of many gene expression phenotypes without assuming any prior knowledge and identification of unknown regulators of gene expression while uncovering directionality. This thesis will focus on such distal eSNPs to map regulatory interactions between different loci and expose the architecture of the regulatory network defined by such interactions. We develop novel computational approaches and apply them to genetics-genomics data in human. We go beyond pairwise interactions to define network motifs, including regulatory modules and bi-fan structures, showing them to be prevalent in real data and exposing distinct attributes of such arrangements. We project eSNP associations onto a protein-protein interaction network to expose topological properties of eSNPs and their targets and highlight different modes of distal regulation. -
Discovery of Genes by Phylocsf Supplemental
Supplemental Materials for Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci Supplemental Methods ....................................................................................................................... 2 Supplemental annotation methods ........................................................................................................... 2 Manual annotation overview ...................................................................................................................................... 2 Summary diagram for the workflow used in this study ................................................................................. 3 Transcriptomics analysis ............................................................................................................................................. 3 Comparative annotation ............................................................................................................................................... 4 Overlap of novel annotations with transposon sequences ........................................................................... 6 Assessing the novelty of annotations ...................................................................................................................... 7 Additional considerations for the annotation of PCCRs in other species ............................................... 7 PhyloCSF and browser tracks .................................................................................................................... -
FBXL19 Recruits CDK-Mediator to Cpg Islands of Developmental Genes Priming Them for Activation During Lineage Commitment
RESEARCH ARTICLE FBXL19 recruits CDK-Mediator to CpG islands of developmental genes priming them for activation during lineage commitment Emilia Dimitrova1, Takashi Kondo2†, Angelika Feldmann1†, Manabu Nakayama3, Yoko Koseki2, Rebecca Konietzny4‡, Benedikt M Kessler4, Haruhiko Koseki2,5, Robert J Klose1* 1Department of Biochemistry, University of Oxford, Oxford, United Kingdom; 2Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; 3Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan; 4Nuffield Department of Medicine, TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; 5CREST, Japan Science and Technology Agency, Kawaguchi, Japan Abstract CpG islands are gene regulatory elements associated with the majority of mammalian promoters, yet how they regulate gene expression remains poorly understood. Here, we identify *For correspondence: FBXL19 as a CpG island-binding protein in mouse embryonic stem (ES) cells and show that it [email protected] associates with the CDK-Mediator complex. We discover that FBXL19 recruits CDK-Mediator to †These authors contributed CpG island-associated promoters of non-transcribed developmental genes to prime these genes equally to this work for activation during cell lineage commitment. We further show that recognition of CpG islands by Present address: ‡Agilent FBXL19 is essential for mouse development. Together this reveals a new CpG island-centric Technologies, Waldbronn, mechanism for CDK-Mediator recruitment to developmental gene promoters in ES cells and a Germany requirement for CDK-Mediator in priming these developmental genes for activation during cell lineage commitment. Competing interests: The DOI: https://doi.org/10.7554/eLife.37084.001 authors declare that no competing interests exist. -
Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications
Stem Cell Rev and Rep DOI 10.1007/s12015-016-9662-8 Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications Behnam Ahmadian Baghbaderani 1 & Adhikarla Syama2 & Renuka Sivapatham3 & Ying Pei4 & Odity Mukherjee2 & Thomas Fellner1 & Xianmin Zeng3,4 & Mahendra S. Rao5,6 # The Author(s) 2016. This article is published with open access at Springerlink.com Abstract We have recently described manufacturing of hu- help determine which set of tests will be most useful in mon- man induced pluripotent stem cells (iPSC) master cell banks itoring the cells and establishing criteria for discarding a line. (MCB) generated by a clinically compliant process using cord blood as a starting material (Baghbaderani et al. in Stem Cell Keywords Induced pluripotent stem cells . Embryonic stem Reports, 5(4), 647–659, 2015). In this manuscript, we de- cells . Manufacturing . cGMP . Consent . Markers scribe the detailed characterization of the two iPSC clones generated using this process, including whole genome se- quencing (WGS), microarray, and comparative genomic hy- Introduction bridization (aCGH) single nucleotide polymorphism (SNP) analysis. We compare their profiles with a proposed calibra- Induced pluripotent stem cells (iPSCs) are akin to embryonic tion material and with a reporter subclone and lines made by a stem cells (ESC) [2] in their developmental potential, but dif- similar process from different donors. We believe that iPSCs fer from ESC in the starting cell used and the requirement of a are likely to be used to make multiple clinical products. We set of proteins to induce pluripotency [3]. Although function- further believe that the lines used as input material will be used ally identical, iPSCs may differ from ESC in subtle ways, at different sites and, given their immortal status, will be used including in their epigenetic profile, exposure to the environ- for many years or even decades. -
Tumour-Stroma Signalling in Cancer Cell Motility and Metastasis
Tumour-Stroma Signalling in Cancer Cell Motility and Metastasis by Valbona Luga A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy, Department of Molecular Genetics, University of Toronto © Copyright by Valbona Luga, 2013 Tumour-Stroma Signalling in Cancer Cell Motility and Metastasis Valbona Luga Doctor of Philosophy Department of Molecular Genetics University of Toronto 2013 Abstract The tumour-associated stroma, consisting of fibroblasts, inflammatory cells, vasculature and extracellular matrix proteins, plays a critical role in tumour growth, but how it regulates cancer cell migration and metastasis is poorly understood. The Wnt-planar cell polarity (PCP) pathway regulates convergent extension movements in vertebrate development. However, it is unclear whether this pathway also functions in cancer cell migration. In addition, the factors that mobilize long-range signalling of Wnt morphogens, which are tightly associated with the plasma membrane, have yet to be completely characterized. Here, I show that fibroblasts secrete membrane microvesicles of endocytic origin, termed exosomes, which promote tumour cell protrusive activity, motility and metastasis via the exosome component Cd81. In addition, I demonstrate that fibroblast exosomes activate autocrine Wnt-PCP signalling in breast cancer cells as detected by the association of Wnt with Fzd receptors and the asymmetric distribution of Fzd-Dvl and Vangl-Pk complexes in exosome-stimulated cancer cell protrusive structures. Moreover, I show that Pk expression in breast cancer cells is essential for fibroblast-stimulated cancer cell metastasis. Lastly, I reveal that trafficking in cancer cells promotes tethering of autocrine Wnt11 to fibroblast exosomes. These studies further our understanding of the role of ii the tumour-associated stroma in cancer metastasis and bring us closer to a more targeted approach for the treatment of cancer spread. -
Downloaded from Ftp://Ftp.Uniprot.Org/ on July 3, 2019) Using Maxquant (V1.6.10.43) Search Algorithm
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.385096; this version posted November 17, 2020. 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-ND 4.0 International license. The proteomic landscape of resting and activated CD4+ T cells reveal insights into cell differentiation and function Yashwanth Subbannayya1, Markus Haug1, Sneha M. Pinto1, Varshasnata Mohanty2, Hany Zakaria Meås1, Trude Helen Flo1, T.S. Keshava Prasad2 and Richard K. Kandasamy1,* 1Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491 Trondheim, Norway 2Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India *Correspondence to: Professor Richard Kumaran Kandasamy Norwegian University of Science and Technology (NTNU) Centre of Molecular Inflammation Research (CEMIR) PO Box 8905 MTFS Trondheim 7491 Norway E-mail: [email protected] (Kandasamy R K) Tel.: +47-7282-4511 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.385096; this version posted November 17, 2020. 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-ND 4.0 International license. Abstract CD4+ T cells (T helper cells) are cytokine-producing adaptive immune cells that activate or regulate the responses of various immune cells. -
Algorithms to Integrate Omics Data for Personalized Medicine
ALGORITHMS TO INTEGRATE OMICS DATA FOR PERSONALIZED MEDICINE by MARZIEH AYATI Submitted in partial fulfillment of the requirements For the degree of Doctor of Philosophy Thesis Adviser: Mehmet Koyut¨urk Department of Electrical Engineering and Computer Science CASE WESTERN RESERVE UNIVERSITY August, 2018 Algorithms to Integrate Omics Data for Personalized Medicine Case Western Reserve University Case School of Graduate Studies We hereby approve the thesis1 of MARZIEH AYATI for the degree of Doctor of Philosophy Mehmet Koyut¨urk 03/27/2018 Committee Chair, Adviser Date Department of Electrical Engineering and Computer Science Mark R. Chance 03/27/2018 Committee Member Date Center of Proteomics Soumya Ray 03/27/2018 Committee Member Date Department of Electrical Engineering and Computer Science Vincenzo Liberatore 03/27/2018 Committee Member Date Department of Electrical Engineering and Computer Science 1We certify that written approval has been obtained for any proprietary material contained therein. To the greatest family who I owe my life to Table of Contents List of Tables vi List of Figures viii Acknowledgements xxi Abstract xxiii Abstract xxiii Chapter 1. Introduction1 Chapter 2. Preliminaries6 Complex Diseases6 Protein-Protein Interaction Network6 Genome-Wide Association Studies7 Phosphorylation 10 Biweight midcorrelation 10 Chapter 3. Identification of Disease-Associated Protein Subnetworks 12 Introduction and Background 12 Methods 15 Results and Discussion 27 Conclusion 40 Chapter 4. Population Covering Locus Sets for Risk Assessment in Complex Diseases 43 Introduction and Background 43 iv Methods 47 Results and Discussion 59 Conclusion 75 Chapter 5. Application of Phosphorylation in Precision Medicine 80 Introduction and Background 80 Methods 83 Results 89 Conclusion 107 Chapter 6. -
Biomolecules
biomolecules Article Multivalent and Bidirectional Binding of Transcriptional Transactivation Domains to the MED25 Coactivator Heather M. Jeffery 1,2 and Robert O. J. Weinzierl 1,* 1 Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; heather.jeff[email protected] 2 Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK * Correspondence: [email protected] Received: 31 July 2020; Accepted: 17 August 2020; Published: 19 August 2020 Abstract: The human mediator subunit MED25 acts as a coactivator that binds the transcriptional activation domains (TADs) present in various cellular and viral gene-specific transcription factors. Previous studies, including on NMR measurements and site-directed mutagenesis, have only yielded low-resolution models that are difficult to refine further by experimental means. Here, we apply computational molecular dynamics simulations to study the interactions of two different TADs from the human transcription factor ETV5 (ERM) and herpes virus VP16-H1 with MED25. Like other well-studied coactivator-TAD complexes, the interactions of these intrinsically disordered domains with the coactivator surface are temporary and highly dynamic (‘fuzzy’). Due to the fact that the MED25 TAD-binding region is organized as an elongated cleft, we specifically asked whether these TADs are capable of binding in either orientation and how this could be achieved structurally and energetically. The binding of both the ETV5 and VP16-TADs in either orientation appears to be possible but occurs in a conformationally distinct manner and utilizes different sets of hydrophobic residues present in the TADs to drive the interactions. We propose that MED25 and at least a subset of human TADs specifically evolved a redundant set of molecular interaction patterns to allow binding to particular coactivators without major prior spatial constraints. -
Structure of the Mammalian Mediator
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.05.326918; this version posted October 6, 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. Structure of the Mammalian Mediator Haiyan Zhao1.#, Natalie Young1,#, Jens Kalchschmidt2,#, Jenna Lieberman2, Laila El Khattabi3, Rafael Casellas2,4 and Francisco J. Asturias1,* 1Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora CO 80045, USA 2Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA 3Institut Cochin Laboratoire de Cytogénétique Constitutionnelle Pré et Post Natale, 75014 Paris France 4Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA #,*These authors contributed equally to this work *Correspondence should be addressed to F.J.A. ([email protected]) 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.05.326918; this version posted October 6, 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. The Mediator complex plays an essential and multi-faceted role in regulation of RNA polymerase II transcription in all eukaryotes. Structural analysis of yeast Mediator has provided an understanding of the conserved core of the complex and its interaction with RNA polymerase II but failed to reveal the structure of the Tail module that contains most subunits targeted by activators and repressors. Here we present a molecular model of mammalian (Mus musculus) Mediator, derived from a 4.0 Å resolution cryo-EM map of the complex. -
Structure of Mammalian Mediator Complex Reveals Tail Module Architecture and Interaction with a Conserved Core
ARTICLE https://doi.org/10.1038/s41467-021-21601-w OPEN Structure of mammalian Mediator complex reveals Tail module architecture and interaction with a conserved core Haiyan Zhao 1,5, Natalie Young1,5, Jens Kalchschmidt2,5, Jenna Lieberman2, Laila El Khattabi3, ✉ Rafael Casellas2,4 & Francisco J. Asturias1 1234567890():,; The Mediator complex plays an essential and multi-faceted role in regulation of RNA poly- merase II transcription in all eukaryotes. Structural analysis of yeast Mediator has provided an understanding of the conserved core of the complex and its interaction with RNA polymerase II but failed to reveal the structure of the Tail module that contains most subunits targeted by activators and repressors. Here we present a molecular model of mammalian (Mus musculus) Mediator, derived from a 4.0 Å resolution cryo-EM map of the complex. The mammalian Mediator structure reveals that the previously unresolved Tail module, which includes a number of metazoan specific subunits, interacts extensively with core Mediator and has the potential to influence its conformation and interactions. 1 Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO, USA. 2 Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD, USA. 3 Institut Cochin Laboratoire de Cytogénétique Constitutionnelle Pré et Post Natale, Paris, France. 4 Center for Cancer ✉ Research, NCI, NIH, Bethesda, MD, USA. 5These authors contributed equally: Haiyan Zhao, Natalie Young, Jens Kalchschmidt. email: Francisco. [email protected] -
Surfactant Expression Defines an Inflamed Subtype of Lung Adenocarcinoma Brain Metastases That Correlates with Prolonged Survival
Published OnlineFirst January 17, 2020; DOI: 10.1158/1078-0432.CCR-19-2184 CLINICAL CANCER RESEARCH | TRANSLATIONAL CANCER MECHANISMS AND THERAPY Surfactant Expression Defines an Inflamed Subtype of Lung Adenocarcinoma Brain Metastases that Correlates with Prolonged Survival Kolja Pocha1, Andreas Mock1,2,3,4, Carmen Rapp1, Steffen Dettling1, Rolf Warta1,4, Christoph Geisenberger1, Christine Jungk1, Leila R. Martins5, Niels Grabe6, David Reuss7,8, Juergen Debus4,9, Andreas von Deimling4,7,8, Amir Abdollahi4,9, Andreas Unterberg1, and Christel C. Herold-Mende1,4 ABSTRACT ◥ Purpose: To provide a better understanding of the interplay of three surfactant metabolism-related genes (SFTPA1, SFTPB, between the immune system and brain metastases to advance and NAPSA) was closely associated with TIL numbers. Their therapeutic options for this life-threatening disease. expression was not only prognostic in brain metastasis but also Experimental Design: Tumor-infiltrating lymphocytes (TIL) in primary lung adenocarcinoma. Correlation with scRNA-seq were quantified by semiautomated whole-slide analysis in data revealed that brain metastases with high expression of brain metastases from 81 lung adenocarcinomas. Multi-color surfactant genes might originate from tumor cells resembling staining enabled phenotyping of TILs (CD3, CD8, and FOXP3) alveolar type 2 cells. Methylome-based estimation of immune cell on a single-cell resolution. Molecular determinants of the fractions in primary lung adenocarcinoma confirmed a positive extent of TILs in brain metastases were analyzed by transcrip- association between lymphocyte infiltration and surfactant tomics in a subset of 63 patients. Findings in lung adenocarci- expression. Tumors with a high surfactant expression displayed noma brain metastases were related to published multi-omic atranscriptomicprofile of an inflammatory microenvironment. -
Investigating the Role of the Mediator Complex in Plant Defence
Investigating the role of the Mediator complex in plant defence Thorya A Fallath Master of Biotechnology Bachelor of biology A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2016 School of Agriculture & Food Sciences Abstract The Mediator complex is an evolutionarily conserved protein complex involved in transcriptional regulation. In plants, the Mediator complex plays an important role in regulating development as well as the response to abiotic and biotic stress. In this thesis, I investigated three subunits of the Arabidopsis thaliana Mediator complex MEDIATOR25, MEDIATOR18 and MEDIATOR20 (MED25, MED18 and MED20) in plant defence. MED25 has been shown to interact with several transcription factors (TFs) to control jasmonate (JA)-associated transcription. Here, I investigated these interactions further and characterized the minimum protein domains of the TFs needed for interaction and identified new proteins that interact with MED25. The results showed that the protein sequence corresponding to amino acids 138-218 of ETHYLENE RESPONSE FACTOR1 (ERF1) appears to be the minimum protein length for interaction with MED25 and contains the conserved motif (CMIX). Although the protein motif has been found in different proteins in A. thaliana that belong to a variety of families, only members from the IXc AP2/ERF family were found to interact with the MED25 ACID domain. Apart from MED25, I found that the MED18 and MED20 subunits interact within the Mediator complex and infection of the corresponding mutants with Fusarium oxysporum revealed that they display a high level of resistance. RNAseq analysis of F. oxysporum infected med18 and med20 roots showed that salicylic acid (SA)-associated PATHOGENESIS RELATED genes and (ROS) reactive oxygen producing genes were up-regulated while some JA-regulated genes were repressed.