WDR12, a Member of Nucleolar Pebow-Complex, Is Up-Regulated in Failing Hearts and Causes Deterioration of Cardiac Function
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Dynamic Control of Enhancer Activity Drives Stage-Specific Gene
ARTICLE https://doi.org/10.1038/s41467-019-09513-2 OPEN Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis Wenhao Yan 1,7, Dijun Chen 1,2,7, Julia Schumacher 1,2, Diego Durantini2,5, Julia Engelhorn3,6, Ming Chen4, Cristel C. Carles 3 & Kerstin Kaufmann 1 fi 1234567890():,; Enhancers are critical for developmental stage-speci c gene expression, but their dynamic regulation in plants remains poorly understood. Here we compare genome-wide localization of H3K27ac, chromatin accessibility and transcriptomic changes during flower development in Arabidopsis. H3K27ac prevalently marks promoter-proximal regions, suggesting that H3K27ac is not a hallmark for enhancers in Arabidopsis. We provide computational and experimental evidence to confirm that distal DNase І hypersensitive sites are predictive of enhancers. The predicted enhancers are highly stage-specific across flower development, significantly associated with SNPs for flowering-related phenotypes, and conserved across crucifer species. Through the integration of genome-wide transcription factor (TF) binding datasets, we find that floral master regulators and stage-specific TFs are largely enriched at developmentally dynamic enhancers. Finally, we show that enhancer clusters and intronic enhancers significantly associate with stage-specific gene regulation by floral master TFs. Our study provides insights into the functional flexibility of enhancers during plant devel- opment, as well as hints to annotate plant enhancers. 1 Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany. 2 Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany. 3 Université Grenoble Alpes (UGA), CNRS, CEA, INRA, IRIG-LPCV, 38000 Grenoble, France, 38000 Grenoble, France. -
A Genome-Wide Association Study of a Coronary Artery Disease Risk Variant
Journal of Human Genetics (2013) 58, 120–126 & 2013 The Japan Society of Human Genetics All rights reserved 1434-5161/13 www.nature.com/jhg ORIGINAL ARTICLE A genome-wide association study of a coronary artery diseaseriskvariant Ji-Young Lee1,16, Bok-Soo Lee2,16, Dong-Jik Shin3,16, Kyung Woo Park4,16, Young-Ah Shin1, Kwang Joong Kim1, Lyong Heo1, Ji Young Lee1, Yun Kyoung Kim1, Young Jin Kim1, Chang Bum Hong1, Sang-Hak Lee3, Dankyu Yoon5, Hyo Jung Ku2, Il-Young Oh4, Bong-Jo Kim1, Juyoung Lee1, Seon-Joo Park1, Jimin Kim1, Hye-kyung Kawk1, Jong-Eun Lee6, Hye-kyung Park1, Jae-Eun Lee1, Hye-young Nam1, Hyun-young Park7, Chol Shin8, Mitsuhiro Yokota9, Hiroyuki Asano10, Masahiro Nakatochi11, Tatsuaki Matsubara12, Hidetoshi Kitajima13, Ken Yamamoto13, Hyung-Lae Kim14, Bok-Ghee Han1, Myeong-Chan Cho15, Yangsoo Jang3,17, Hyo-Soo Kim4,17, Jeong Euy Park2,17 and Jong-Young Lee1,17 Although over 30 common genetic susceptibility loci have been identified to be independently associated with coronary artery disease (CAD) risk through genome-wide association studies (GWAS), genetic risk variants reported to date explain only a small fraction of heritability. To identify novel susceptibility variants for CAD and confirm those previously identified in European population, GWAS and a replication study were performed in the Koreans and Japanese. In the discovery stage, we genotyped 2123 cases and 3591 controls with 521 786 SNPs using the Affymetrix SNP Array 6.0 chips in Korean. In the replication, direct genotyping was performed using 3052 cases and 4976 controls from the KItaNagoya Genome study of Japan with 14 selected SNPs. -
An in Vivo Screen Identifies PYGO2 As a Driver for Metastatic Prostate Cancer
Published OnlineFirst May 16, 2018; DOI: 10.1158/0008-5472.CAN-17-3564 Cancer Molecular Cell Biology Research An In Vivo Screen Identifies PYGO2 as a Driver for Metastatic Prostate Cancer Xin Lu1,2,3, Xiaolu Pan1, Chang-Jiun Wu4, Di Zhao1, Shan Feng2, Yong Zang5, Rumi Lee1, Sunada Khadka1, Samirkumar B. Amin4, Eun-Jung Jin6, Xiaoying Shang1, Pingna Deng1,Yanting Luo2,William R. Morgenlander2, Jacqueline Weinrich2, Xuemin Lu2, Shan Jiang7, Qing Chang7, Nora M. Navone8, Patricia Troncoso9, Ronald A. DePinho1, and Y. Alan Wang1 Abstract Advanced prostate cancer displays conspicuous chromosomal inhibits prostate cancer cell invasion in vitro and progression of instability and rampant copy number aberrations, yet the identity primary tumor and metastasis in vivo. In clinical samples, PYGO2 of functional drivers resident in many amplicons remain elusive. upregulation associated with higher Gleason score and metastasis Here, we implemented a functional genomics approach to identify to lymph nodes and bone. Silencing PYGO2 expression in patient- new oncogenes involved in prostate cancer progression. Through derived xenograft models impairs tumor progression. Finally, integrated analyses of focal amplicons in large prostate cancer PYGO2 is necessary to enhance the transcriptional activation in genomic and transcriptomic datasets as well as genes upregulated response to ligand-induced Wnt/b-catenin signaling. Together, our in metastasis, 276 putative oncogenes were enlisted into an in vivo results indicate that PYGO2 functions as a driver oncogene in the gain-of-function tumorigenesis screen. Among the top positive 1q21.3 amplicon and may serve as a potential prognostic bio- hits, we conducted an in-depth functional analysis on Pygopus marker and therapeutic target for metastatic prostate cancer. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
GIGANTUS1 (GTS1), a Member of Transducin/WD40 Protein
Gachomo et al. BMC Plant Biology 2014, 14:37 http://www.biomedcentral.com/1471-2229/14/37 RESEARCH ARTICLE Open Access GIGANTUS1 (GTS1), a member of Transducin/WD40 protein superfamily, controls seed germination, growth and biomass accumulation through ribosome-biogenesis protein interactions in Arabidopsis thaliana Emma W Gachomo1,2†, Jose C Jimenez-Lopez3,4†, Lyla Jno Baptiste1 and Simeon O Kotchoni1,2* Abstract Background: WD40 domains have been found in a plethora of eukaryotic proteins, acting as scaffolding molecules assisting proper activity of other proteins, and are involved in multi-cellular processes. They comprise several stretches of 44-60 amino acid residues often terminating with a WD di-peptide. They act as a site of protein-protein interactions or multi-interacting platforms, driving the assembly of protein complexes or as mediators of transient interplay among other proteins. In Arabidopsis, members of WD40 protein superfamily are known as key regulators of plant-specific events, biologically playing important roles in development and also during stress signaling. Results: Using reverse genetic and protein modeling approaches, we characterize GIGANTUS1 (GTS1), a new member of WD40 repeat protein in Arabidopsis thaliana and provide evidence of its role in controlling plant growth development. GTS1 is highly expressed during embryo development and negatively regulates seed germination, biomass yield and growth improvement in plants. Structural modeling analysis suggests that GTS1 folds into a β-propeller with seven pseudo symmetrically arranged blades around a central axis. Molecular docking analysis shows that GTS1 physically interacts with two ribosomal protein partners, a component of ribosome Nop16, and a ribosome-biogenesis factor L19e through β-propeller blade 4 to regulate cell growth development. -
BOP1 (A-18): Sc-87884
SAN TA C RUZ BI OTEC HNOL OG Y, INC . BOP1 (A-18): sc-87884 BACKGROUND CHROMOSOMAL LOCATION Predominantly localized to the nucleolus, BOP1 (Block of proliferation 1 pro - Genetic locus: BOP1 (human) mapping to 8q24.3; Bop1 (mouse) mapping to tein) is a 746 amino acid highly conserved non-ribosomal protein that is in- 15 D3. volved in ribosome biogenesis. Truncation of the amino terminus of BOP1 leads to cell growth arrest in the G 1 phase and specific inhibition of 28S and SOURCE 5.8S rRNA synthesis, as well as a deficit in the cytosolic 60S ribosomal sub - BOP1 (A-18) is an affinity purified rabbit polyclonal antibody raised against a unit. This suggests that BOP1 is involved in the formation of mature rRNAs peptide mapping within an internal region of BOP1 of human origin. and in the biogenesis of the 60S ribosomal subunit. BOP1 physically inter acts with pescadillo (a protein involved in cell proliferation) and enables efficient PRODUCT incorporation of pescadillo into the nucleolar preribosomal complexes, there - by affecting rRNA maturation and the cell cycle. The BOP1-pescadillo com - Each vial contains 100 µg IgG in 1.0 ml of PBS with < 0.1% sodium azide plex is also necessary for biogenesis of 60S ribosomal subunits. Deregulation and 0.1% gelatin. of BOP1 may lead to colorectal tumorigenesis. Blocking peptide available for competition studies, sc-87884 P, (100 µg peptide in 0.5 ml PBS containing < 0.1% sodium azide and 0.2% BSA). REFERENCES 1. Strezoska, Z., Pestov, D.G. and Lau, L.F. 2000. -
The Tumor Suppressor Notch Inhibits Head and Neck Squamous Cell
The Texas Medical Center Library DigitalCommons@TMC The University of Texas MD Anderson Cancer Center UTHealth Graduate School of The University of Texas MD Anderson Cancer Biomedical Sciences Dissertations and Theses Center UTHealth Graduate School of (Open Access) Biomedical Sciences 12-2015 THE TUMOR SUPPRESSOR NOTCH INHIBITS HEAD AND NECK SQUAMOUS CELL CARCINOMA (HNSCC) TUMOR GROWTH AND PROGRESSION BY MODULATING PROTO-ONCOGENES AXL AND CTNNAL1 (α-CATULIN) Shhyam Moorthy Shhyam Moorthy Follow this and additional works at: https://digitalcommons.library.tmc.edu/utgsbs_dissertations Part of the Biochemistry, Biophysics, and Structural Biology Commons, Cancer Biology Commons, Cell Biology Commons, and the Medicine and Health Sciences Commons Recommended Citation Moorthy, Shhyam and Moorthy, Shhyam, "THE TUMOR SUPPRESSOR NOTCH INHIBITS HEAD AND NECK SQUAMOUS CELL CARCINOMA (HNSCC) TUMOR GROWTH AND PROGRESSION BY MODULATING PROTO-ONCOGENES AXL AND CTNNAL1 (α-CATULIN)" (2015). The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access). 638. https://digitalcommons.library.tmc.edu/utgsbs_dissertations/638 This Dissertation (PhD) is brought to you for free and open access by the The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at DigitalCommons@TMC. It has been accepted for inclusion in The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access) by an authorized administrator of DigitalCommons@TMC. For more information, please contact [email protected]. THE TUMOR SUPPRESSOR NOTCH INHIBITS HEAD AND NECK SQUAMOUS CELL CARCINOMA (HNSCC) TUMOR GROWTH AND PROGRESSION BY MODULATING PROTO-ONCOGENES AXL AND CTNNAL1 (α-CATULIN) by Shhyam Moorthy, B.S. -
The Temporal Mutational and Immune Tumour Microenvironment
www.nature.com/npjbcancer ARTICLE OPEN The temporal mutational and immune tumour microenvironment remodelling of HER2-negative primary breast cancers ✉ Leticia De Mattos-Arruda 1,2,3 , Javier Cortes 4,5,6,7,8, Juan Blanco-Heredia1,2, Daniel G. Tiezzi 3,9, Guillermo Villacampa10, Samuel Gonçalves-Ribeiro 10, Laia Paré11,12,13, Carla Anjos Souza1,2, Vanesa Ortega7, Stephen-John Sammut3,14, Pol Cusco10, Roberta Fasani10, Suet-Feung Chin 3, Jose Perez-Garcia4,5,6, Rodrigo Dienstmann10, Paolo Nuciforo10, Patricia Villagrasa12, Isabel T. Rubio10, Aleix Prat 11,12,13 and Carlos Caldas 3,14 The biology of breast cancer response to neoadjuvant therapy is underrepresented in the literature and provides a window-of- opportunity to explore the genomic and microenvironment modulation of tumours exposed to therapy. Here, we characterised the mutational, gene expression, pathway enrichment and tumour-infiltrating lymphocytes (TILs) dynamics across different timepoints of 35 HER2-negative primary breast cancer patients receiving neoadjuvant eribulin therapy (SOLTI-1007 NEOERIBULIN- NCT01669252). Whole-exome data (N = 88 samples) generated mutational profiles and candidate neoantigens and were analysed along with RNA-Nanostring 545-gene expression (N = 96 samples) and stromal TILs (N = 105 samples). Tumour mutation burden varied across patients at baseline but not across the sampling timepoints for each patient. Mutational signatures were not always conserved across tumours. There was a trend towards higher odds of response and less hazard to relapse when the percentage of 1234567890():,; subclonal mutations was low, suggesting that more homogenous tumours might have better responses to neoadjuvant therapy. Few driver mutations (5.1%) generated putative neoantigens. -
Genome-Wide Association Studies of Retinal Vessel Tortuosity Identify 173
medRxiv preprint doi: https://doi.org/10.1101/2020.06.25.20139725; this version posted March 24, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license . Genome-Wide Association Studies of retinal vessel tortuosity identify 173 novel loci, capturing genes and pathways associated with disease and vascular tissue pathomechanics Mattia Tomasoni1,2, Michael Johannes Beyeler1,2, Ninon Mounier2,3, Eleonora Porcu2,3,4, Sofia Ortin Vela1,2, Alexander Luke Button1,2, Tanguy Corre1,2,3, Hana Abouzeid5,6, Murielle Bochud3, Daniel Krefl1,2, Sven Bergmann1,2,7 1 Dept. of Computational Biology, University of Lausanne, Lausanne, Switzerland 2 Swiss Institute of Bioinformatics, Lausanne, Switzerland 3 Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland 4 Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland 5 Division of Ophthalmology, Geneva University Hospitals, Switzerland 6 Clinical Eye Research Center Memorial Adolphe de Rothschild, Geneva, Switzerland 7 Dept. of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa Corresponding authors: [email protected] [email protected] Abstract Fundus images of the eye allow for non-invasive inspection of the microvasculature system of the retina, which is informative of systemic cardiovascular health. We set up a fully automated image processing pipeline enabling the massively parallelised annotation of such images in terms of vessel type (i.e., artery or vein) and quantitative morphological properties, such as tortuosity (“bendiness”). -
Fanconi Anemia Protein FANCI Functions in Ribosome Biogenesis
Fanconi anemia protein FANCI functions in ribosome biogenesis Samuel B. Sondallea, Simonne Longerichb,1, Lisa M. Ogawab, Patrick Sungb,c, and Susan J. Basergaa,b,c,2 aDepartment of Genetics, Yale School of Medicine, New Haven, CT 06520; bDepartment of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06520; and cDepartment of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520 Edited by Joseph G. Gall, Carnegie Institution of Washington, Baltimore, MD, and approved December 28, 2018 (received for review July 8, 2018) Fanconi anemia (FA) is a disease of DNA repair characterized by bone responsible for the transcription of pre-ribosomal RNA (pre- marrow failure and a reduced ability to remove DNA interstrand rRNA) (33). The clear phenotypic overlap between FA and cross-links. Here, we provide evidence that the FA protein FANCI also bone marrow failure ribosomopathies and the connection between functions in ribosome biogenesis, the process of making ribosomes BRCA1 (FANCS) and RNAPI suggest a possible connection be- that initiates in the nucleolus. We show that FANCI localizes to the tween FA and defects in ribosome biogenesis. nucleolus and is functionally and physically tied to the transcription The process of making ribosomes in eukaryotes, termed ri- of pre-ribosomal RNA (pre-rRNA) and to large ribosomal subunit bosome biogenesis, initiates in the large nonmembrane-bound (LSU) pre-rRNA processing independent of FANCD2. While FANCI is nuclear organelle, the nucleolus (NO) (34, 35). In the NO, tan- known to be monoubiquitinated when activated for DNA repair, we dem repeats of ribosomal DNA (rDNA) (36) are transcribed by find that it is predominantly in the deubiquitinated state in the RNAPI, which generates a long pre-rRNA (37). -
Sumoylation of PES1 Upregulates Its Stability and Function Via Inhibiting Its Ubiquitination
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 7, No. 31 Research Paper SUMOylation of PES1 upregulates its stability and function via inhibiting its ubiquitination Shujing Li1, Miao Wang1, Xinjian Qu2, Zhaowei Xu1, Yangyang Yang1, Qiming Su2, Huijian Wu1,2 1School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China 2School of Life Science and Medicine, Dalian University of Technology, Panjin, China Correspondence to: Huijian Wu, email: [email protected] Keywords: PES1, SUMOylation, breast cancer, ubiquitination Received: July 21, 2015 Accepted: June 15, 2016 Published: July 08, 2016 ABSTRACT PES1 is a component of the PeBoW complex, which is required for the maturation of 28S and 5.8S ribosomal RNAs, as well as for the formation of the 60S ribosome. Deregulation of ribosomal biogenesis can contribute to carcinogenesis. In this study, we showed that PES1 could be modified by the small ubiquitin-like modifier (SUMO) SUMO-1, SUMO-2 and SUMO-3, and SUMOylation of PES1 was stimulated by estrogen (E2). One major SUMOylation site (K517) was identified in the C-terminal Glu-rich domain of PES1. Substitution of K517 with arginine abolished the SUMOylation of PES1. SUMOylation also stabilized PES1 through inhibiting its ubiquitination. In addition, PES1 SUMOylation positively regulated the estrogen signaling pathway. SUMOylation enhanced the ability of PES1 to promote estrogen receptor α (ERα)- mediated transcription by increasing the stability of ERα, both in the presence and absence of E2. Moreover, SUMOylation of PES1 also increased the proportion of S-phase cells in the cell cycle and promoted the proliferation of breast cancer cells both in vitro and in vivo. -
Overexpressed HSF1 Cancer Signature Genes Cluster in Human Chromosome 8Q Christopher Q
Zhang et al. Human Genomics (2017) 11:35 DOI 10.1186/s40246-017-0131-5 PRIMARY RESEARCH Open Access Overexpressed HSF1 cancer signature genes cluster in human chromosome 8q Christopher Q. Zhang1,4, Heinric Williams3,4, Thomas L. Prince3,4† and Eric S. Ho1,2*† Abstract Background: HSF1 (heat shock factor 1) is a transcription factor that is found to facilitate malignant cancer development and proliferation. In cancer cells, HSF1 mediates a set of genes distinct from heat shock that contributes to malignancy. This set of genes is known as the HSF1 Cancer Signature genes or simply HSF1-CanSig genes. HSF1-CanSig genes function and operate differently than typical cancer-causing genes, yet it is involved in fundamental oncogenic processes. Results: By utilizing expression data from 9241 cancer patients, we identified that human chromosome 8q21-24 is a location hotspot for the most frequently overexpressed HSF1-CanSig genes. Intriguingly, the strength of the HSF1 cancer program correlates with the number of overexpressed HSF1-CanSig genes in 8q, illuminating the essential role of HSF1 in mediating gene expression in different cancers. Chromosome 8q21-24 is found under selective pressure in preserving gene order as it exhibits strong synteny among human, mouse, rat, and bovine, although the biological significance remains unknown. Statistical modeling, hierarchical clustering, and gene ontology-based pathway analyses indicate crosstalk between HSF1-mediated responses and pre-mRNA 3′ processing in cancers. Conclusions: Our results confirm the unique role of chromosome 8q mediated by the master regulator HSF1 in cancer cases. Additionally, this study highlights the connection between cellular processes triggered by HSF1 and pre-mRNA 3′ processing in cancers.