DOCSLIB.ORG

Differentially Expressed Genes and Gene Networks Involved in Pig

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Differentially expressed genes and gene networks involved in pig ovarian follicular atresia Elena Mormede, Stéphane Fabre, Agnes Bonnet, Danielle Monniaux, Christele Robert-Granie, Magali San Cristobal, Julien Sarry, Florence Vignoles, Florence Gondret, Philippe Monget, et al. To cite this version: Elena Mormede, Stéphane Fabre, Agnes Bonnet, Danielle Monniaux, Christele Robert-Granie, et al.. Differentially expressed genes and gene networks involved in pig ovarian follicular atresia. Phys- iological Genomics, American Physiological Society, 2017, 49 (2), pp.67-80. 10.1152/physiolge- nomics.00069.2016. hal-01529483 HAL Id: hal-01529483 https://hal.archives-ouvertes.fr/hal-01529483 Submitted on 27 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - NonCommercial| 4.0 International License Physiol Genomics 49: 67–80, 2017. First published December 9, 2016; doi:10.1152/physiolgenomics.00069.2016. RESEARCH ARTICLE Systems Biology and Polygenic Traits Differentially expressed genes and gene networks involved in pig ovarian follicular atresia Elena Terenina,1 Stephane Fabre,1 Agnès Bonnet,1 Danielle Monniaux,2 Christèle Robert-Granié,1 Magali SanCristobal,1 Julien Sarry,1 Florence Vignoles,1 Florence Gondret,3,4 Philippe Monget,2 and X Gwenola Tosser-Klopp1 1GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France; 2INRA UMR 0085, CNRS UMR 7247, Université Francois Rabelais de Tours, IFCE, Physiologie de la Reproduction et des Comportements, Nouzilly, France; 3INRA, UMR1348 Pegase, Saint᎑Gilles, France; and 4AgroCampus-Ouest, UMR1348 Pegase, Saint᎑Gilles, France Submitted 15 June 2016; accepted in final form 2 December 2016 Terenina E, Fabre S, Bonnet A, Monniaux D, Robert-Granié C, atresia. This process may be considered as physiologically SanCristobal M, Sarry J, Vignoles F, Gondret F, Monget P, normal, allowing the ovary to generate the ovulatory quota Tosser-Klopp G. Differentially expressed genes and gene networks characteristic of the species, at each sexual cycle. involved in pig ovarian follicular atresia. Physiol Genomics 49: A number of studies in antral growing follicles have indi- 67–80, 2017. First published December 9, 2016; doi:10.1152/physi- cated that follicular atresia is initiated and caused by apoptosis olgenomics.00069.2016.—Ovarian folliculogenesis corresponds to the development of follicles leading to either ovulation or degenera- (programmed cell death) of granulosa cells (53, 56, 71, 107). tion, this latter process being called atresia. Even if atresia involves Two general pathways have been suggested to be involved in apoptosis, its mechanism is not well understood. The objective of this the physiological induction of apoptosis: negative induction by study was to analyze global gene expression in pig granulosa cells of survival factor withdrawal and positive induction by the bind- ovarian follicles during atresia. The transcriptome analysis was per- ing of a specific ligand, such as tumor necrosis factor-alpha or formed on a 9,216 cDNA microarray to identify gene networks and Fas ligand, to its membrane receptor (41). In follicles, apopto- candidate genes involved in pig ovarian follicular atresia. We found sis is triggered when endocrine and/or intra-follicular concen- 1,684 significantly regulated genes to be differentially regulated trations of survival factors, particularly gonadotropins and between small healthy follicles and small atretic follicles. Among some growth factors, are inadequate (93). It is now recognized them, 287 genes had a fold-change higher than two between the two follicle groups. Eleven genes (DKK3, GADD45A, CAMTA2, that a diverse spectrum of pro- and antiapoptosis susceptibility CCDC80, DAPK2, ECSIT, MSMB, NUPR1, RUNX2, SAMD4A, and genes are thus expressed in germ cells and/or somatic cells of ZNF628) having a fold-change higher than five between groups could the ovary, including members of the BCL2 and caspase gene likely serve as markers of follicular atresia. Moreover, automatic families (108). Many of these genes are regulated by gonado- confrontation of deregulated genes with literature data highlighted 93 tropins and growth factors, and changes in the temporal pattern genes as regulatory candidates of pig granulosa cell atresia. Among of cell death gene expression suggest that an intimate associ- these genes known to be inhibitors of apoptosis, stimulators of ation exists between the products of these genes and the apoptosis, or tumor suppressors INHBB, HNF4, CLU, different inter- activation of apoptosis. leukins (IL5, IL24), TNF-associated receptor (TNFR1), and cyto- The biochemical characteristics of apoptosis have been in- chrome-c oxidase (COX) were suggested as playing an important role in porcine atresia. The present study also enlists key upstream regu- vestigated to discover causative factors and markers identify- lators in follicle atresia based on our results and on a literature review. ing follicles at the early stages of atresia. Results from studies The novel gene candidates and gene networks identified in the current of ovarian gene expression in vivo and in vitro have indicated study lead to a better understanding of the molecular regulation of that ovarian products, such as steroid hormones, transforming ovarian follicular atresia. growth factor family members, insulin-like growth factor (IGF) 1, IGF-binding proteins (IGFBPs), and inhibins could pig ovary; folliculogenesis; atresia; gene expression; cDNA microar- ray; biomarkers; upstream regulators; functional pathways play a role in atretic process (2, 42). However, most of this information has been acquired based on candidate-gene ap- proaches. OVARIAN FOLLICULOGENESIS REFERS to the development of folli- In the present study, we propose a high-throughput tran- cles leading to either ovulation or degeneration. This degener- scriptomic approach to get a better understanding of the mo- ation process is called atresia. In mammals, it has long been lecular actors, their regulatory genes, and physiological recognized that the majority of follicles present at birth become networks involved in pig follicle atresia. A specific microar- atretic, so that only Ͻ1% of follicles ovulate during ovarian ray has been developed to identify genes expressed in follicular growth and development (53, 107). Thus, the most granulosa cells along the terminal ovarian follicle growth in highly probable fate for a follicle is to degenerate by entering the pig (17). This represents a useful tool to study porcine ovarian follicular atresia. The aims of this study were 1)to analyze global gene expression changes in pig granulosa Address for reprint requests and other correspondence: E. Terenina; GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France (e-mail: cells of ovarian follicles during atresia and 2) to identify the [email protected]). gene networks and propose new candidates genes that can 1094-8341/17 Copyright © 2017 the American Physiological Society 67 Downloaded from www.physiology.org/journal/physiolgenomics by ${individualUser.givenNames} ${individualUser.surname} (194.167.077.053) on July 30, 2018. Copyright © 2017 American Physiological Society. All rights reserved. 68 TARGET GENES OF PIG OVARIAN FOLLICULAR ATRESIA further serve as targets to characterize and modulate atresia Microarray data analysis. Raw data and normalized data were in granulosa cells. submitted to the GEO database as GSM596969 (https://www.ncbi.nlm. nih.gov/geo/query/acc.cgi?accϭGSM596969). MATERIAL AND METHODS Data exploration and statistical analysis were performed using R software (http://www.r-project.org). The data coming from complex Collection of ovaries. Estrous cycles of 10 sows were synchronized probes hybridization were analyzed on a natural logarithmic scale. As by oral administration of 20 mg/day altrenogest (Regumate; Hoechst- a first step, negative spots with Ͼ7 intensity values were checked on Roussel, Paris, France) for 18 days. Ovaries were removed by lapa- images and replaced by the median of negative spots in case of rotomy 24 or 96 h after the last altrenogest feeding. All procedures obvious overshining effect or hybridization stain. Then, luciferase- were approved by the Agricultural and Scientific Research agencies positive controls were removed, and the correlations of the gene and conducted at an INRA experimental farm (animal experimenta- expressions from each membrane were examined within condition. tion authorization C37-175-2) in accordance with the guidelines for Hybridizations with a correlation coefficient Ͻ0.80 were discarded. Care and Use of Agricultural Animals in Agricultural Research and Spots with low signal value (below the average of empty spots ϩ 3 Teaching. standard deviations) were considered as unexpressed and were ex- Granulosa cell isolation and RNA extraction. Once ovaries were cluded from the analysis. Finally, the negative control spots were collected, all visible (Ͼ1 mm in diameter) antral follicles were
Recommended publications
  • 02-09-2017 06:01:33Pm Esmo.Org Type

    02-09-2017 06:01:33Pm Esmo.Org Type

    08-09-2017 10:00 - 11:30 Type: Special Session Palma Title: Medical oncology as a contributor to global policy: How to improve national cancer Auditorium plans Chair(s): G. Curigliano, IT; L. Stevens, US 10:00 - 10:05 Introduction L. Stevens, Rio De Janeiro, BR 10:05 - 10:20 Overview of NCCP, including forming the multi-disciplinary and multi-sectoral partnership A. Ilbawi, Geneva, CH 10:20 - 10:35 Example from Central Asia Leadership Forum D. Kaidarova, Almaty, KZ 10:35 - 10:50 Example from Central Europe J. Jassem, Gdańsk, PL 10:50 - 11:05 Example from Eastern Europe S. Krasny, Minsk, BY 11:05 - 11:30 Interactive Q&A G. Curigliano, Milan, IT Last update: 02-09-2017 06:01:33pm esmo.org 12:00 - 13:30 Type: Opening session Madrid Auditorium Title: Opening session and Award lectures Chair(s): F. Ciardiello, IT 12:00 - 12:10 ESMO Presidential Address F. Ciardiello, Naples, IT 12:10 - 12:15 EACR Presidential Address A. Berns, Amsterdam, NL 12:15 - 12:20 Welcome to Madrid M. Martin Jimenez, Madrid, ES 12:20 - 12:25 ESMO 2017 Scientific Address A. Sobrero, Genova, IT 12:25 - 12:30 EACR 2017 Scientific Address R. Marais, Manchester, GB 12:30 - 12:32 Presentation of the ESMO Award by C. Zielinski, Vienna, AT 12:32 - 12:47 ESMO Award lecture - Oncology: The importance of teamwork M. Martin Jimenez, Madrid, ES 12:47 - 12:49 Presentation of the ESMO Translational Research Award by C. Zielinski, Vienna, AT 12:49 - 13:04 ESMO Translational Research Award lecture: Monitoring and targeting colorectal cancer evolution A.
  • Ccdc80 and Ccdc80-L1: Identification and Functional Analysis of Two Novel Genes Involved in Zebrafish (Danio Rerio) Development

    Ccdc80 and Ccdc80-L1: Identification and Functional Analysis of Two Novel Genes Involved in Zebrafish (Danio Rerio) Development

    UNIVERSITÀ DEGLI STUDI DI MILANO SCUOLA DI DOTTORATO IN SCIENZE BIOLOGICHE E MOLECOLARI DIPARTIMENTO DI BIOLOGIA DOTTORATO DI RICERCA IN BIOLOGIA CELLULARE E MOLECOLARE XXIV CICLO ccdc80 and ccdc80-l1: Identification and Functional Analysis of Two Novel Genes Involved in Zebrafish (Danio rerio) Development settori scientifico/disciplinari: BIO/06; BIO/11 Tesi di dottorato di Chiara Brusegan R08215 TUTOR: prof. Franco Cotelli COORDINATORE DEL DOTTORATO: prof. Martino Bolognesi A.A. 2010/2011 Index Part I 1. Abstract 1 2. State of the art 2 2.1 Motility of the zebrafish embryo 2 2.2 Muscle formation 3 2.3 Neural differentiation 6 2.4 Identification of zebrafish ccdc80 genes 9 3. Aim of the project 13 4. Materials and Methods 14 4.1 Zebrafish lines and maintenance 14 4.2 Sequence analysis 14 4.3 RT-PCR 15 4.4 Synthesis of probes for whole mount in situ hybridization (WISH) 16 4.5 Whole-mount in situ hybridization 17 4.6 Immunohistochemistry 17 4.7 Histological sections 18 4.8 Injections 18 4.9 Cyclopamine treatment 19 4.10 Statistical analysis 19 5. Results 20 5.1 Identification of ccdc80 homologs in the genome of zebrafish 20 5.2.1 ccdc80 expression profiling 22 5.2.2 ccdc80-loss- and gain-of-function affects somitogenesis in vivo 23 5.2.3 ccdc80 is involved in somitogenesis, but not in the development of the notochord 25 5.2.4 ccdc80 is positively regulated by the Hedgehog pathway 26 5.3.1 ccdc80-l1 expression profiling 27 5.3.2 ccdc80-l1 knocked-down embryos displayed impaired motility 29 5.3.3 ccdc80-l1 loss of function does not affect somitogenesis nor muscle pioneers and adaxial cells formation 30 5.3.4 analysis of neurogenesis of primary motoneurons in ccdc80-l1 morphants 32 5.3.5 Also ccdc80-l1 expression is positively regulated by the Hedgehog pathway 35 5.4.1 ccdc80 expression is not regulated by ccdc80-l1, nor vice versa 37 6.
  • Proteomic Profile of Human Spermatozoa in Healthy And

    Proteomic Profile of Human Spermatozoa in Healthy And

    Cao et al. Reproductive Biology and Endocrinology (2018) 16:16 https://doi.org/10.1186/s12958-018-0334-1 REVIEW Open Access Proteomic profile of human spermatozoa in healthy and asthenozoospermic individuals Xiaodan Cao, Yun Cui, Xiaoxia Zhang, Jiangtao Lou, Jun Zhou, Huafeng Bei and Renxiong Wei* Abstract Asthenozoospermia is considered as a common cause of male infertility and characterized by reduced sperm motility. However, the molecular mechanism that impairs sperm motility remains unknown in most cases. In the present review, we briefly reviewed the proteome of spermatozoa and seminal plasma in asthenozoospermia and considered post-translational modifications in spermatozoa of asthenozoospermia. The reduction of sperm motility in asthenozoospermic patients had been attributed to factors, for instance, energy metabolism dysfunction or structural defects in the sperm-tail protein components and the differential proteins potentially involved in sperm motility such as COX6B, ODF, TUBB2B were described. Comparative proteomic analysis open a window to discover the potential pathogenic mechanisms of asthenozoospermia and the biomarkers with clinical significance. Keywords: Proteome, Spermatozoa, Sperm motility, Asthenozoospermia, Infertility Background fertilization failure [4] and it has become clear that iden- Infertility is defined as the lack of ability to achieve a tifying the precise proteins and the pathways involved in clinical pregnancy after one year or more of unprotected sperm motility is needed [5]. and well-timed intercourse with the same partner [1]. It is estimated that around 15% of couples of reproductive age present with infertility, and about half of the infertil- Application of proteomic techniques in male ity is associated with male partner [2, 3].
  • Copy Number Alterations of BCAS1 in Squamous Cell Carcinomas

    Copy Number Alterations of BCAS1 in Squamous Cell Carcinomas

    The Korean Journal of Pathology 2011; 45: 271-275 DOI: 10.4132/KoreanJPathol.2011.45.3.271 Copy Number Alterations of BCAS1 in Squamous Cell Carcinomas Yu Im Kim · Ahwon Lee1 Background: Breast carcinoma amplified sequence 1 BCAS1( ), located in 20q13, is amplified and Jennifer Kim · Bum Hee Lee overexpressed in breast cancers. Even though BCAS1 is expected to be an oncogene candidate, Sung Hak Lee · Suk Woo Nam its contribution to tumorigenesis and copy number status in other malignancies is not reported. To elucidate the role of BCAS1 in squamous cell carcinomas, we investigated the copy number Sug Hyung Lee · Won Sang Park status and expression level of BCAS1 in several squamous cell carcinoma cell lines, normal kera- Nam Jin Yoo · Jung Young Lee tinocytes and primary tumors. Methods: We quantitated BCAS1 gene by real-time polymerase Sang Ho Kim · Su Young Kim chain reaction (PCR). Expression level of BCAS1 was measured by real-time reverse transcrip- tion-PCR and immunoblot. Results: Seven (88%) of 8 squamous cell carcinoma cell lines showed Departments of Pathology and 1Hospital copy number gain of BCAS1 with various degrees. BCAS1 gene in primary tumors (73%) also Pathology, The Catholic University of Korea showed copy number gain. However, expression level did not show a linear correlation with copy College of Medicine, Seoul, Korea number changes. Conclusions: We identified copy number gain of BCAS1 in squamous cell car- cinomas. Due to lack of linear correlation between copy numbers of BCAS1 and its expression Received: March 10, 2010 level, we could not confirm that the overexpression of BCAS1 is a common finding in squamous Accepted: May 24, 2011 cell carcinoma cell lines.
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    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.
  • Views of the NIH

    Views of the NIH

    CLINICAL EPIDEMIOLOGY www.jasn.org Genetic Variants Associated with Circulating Fibroblast Growth Factor 23 Cassianne Robinson-Cohen ,1 Traci M. Bartz,2 Dongbing Lai,3 T. Alp Ikizler,1 Munro Peacock,4 Erik A. Imel,4 Erin D. Michos,5 Tatiana M. Foroud,3 Kristina Akesson,6,7 Kent D. Taylor,8 Linnea Malmgren,6,7 Kunihiro Matsushita,5,9,10 Maria Nethander,11 Joel Eriksson,12 Claes Ohlsson,12 Daniel Mellström,12 Myles Wolf,13 Osten Ljunggren,14 Fiona McGuigan,6,7 Jerome I. Rotter,8 Magnus Karlsson,6,7 Michael J. Econs,3,4 Joachim H. Ix,15,16 Pamela L. Lutsey,17 Bruce M. Psaty,18,19 Ian H. de Boer ,20 and Bryan R. Kestenbaum 20 Due to the number of contributing authors, the affiliations are listed at the end of this article. ABSTRACT Background Fibroblast growth factor 23 (FGF23), a bone-derived hormone that regulates phosphorus and vitamin D metabolism, contributes to the pathogenesis of mineral and bone disorders in CKD and is an emerging cardiovascular risk factor. Central elements of FGF23 regulation remain incompletely under- stood; genetic variation may help explain interindividual differences. Methods We performed a meta-analysis of genome-wide association studies of circulating FGF23 con- centrations among 16,624 participants of European ancestry from seven cohort studies, excluding par- ticipants with eGFR,30 ml/min per 1.73 m2 to focus on FGF23 under normal conditions. We evaluated the association of single-nucleotide polymorphisms (SNPs) with natural log–transformed FGF23 concentra- tion, adjusted for age, sex, study site, and principal components of ancestry.
  • Primate Specific Retrotransposons, Svas, in the Evolution of Networks That Alter Brain Function

    Primate Specific Retrotransposons, Svas, in the Evolution of Networks That Alter Brain Function

    Title: Primate specific retrotransposons, SVAs, in the evolution of networks that alter brain function. Olga Vasieva1*, Sultan Cetiner1, Abigail Savage2, Gerald G. Schumann3, Vivien J Bubb2, John P Quinn2*, 1 Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, U.K 2 Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK 3 Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, D-63225 Germany *. Corresponding author Olga Vasieva: Institute of Integrative Biology, Department of Comparative genomics, University of Liverpool, Liverpool, L69 7ZB, [email protected] ; Tel: (+44) 151 795 4456; FAX:(+44) 151 795 4406 John Quinn: Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK, [email protected]; Tel: (+44) 151 794 5498. Key words: SVA, trans-mobilisation, behaviour, brain, evolution, psychiatric disorders 1 Abstract The hominid-specific non-LTR retrotransposon termed SINE–VNTR–Alu (SVA) is the youngest of the transposable elements in the human genome. The propagation of the most ancient SVA type A took place about 13.5 Myrs ago, and the youngest SVA types appeared in the human genome after the chimpanzee divergence. Functional enrichment analysis of genes associated with SVA insertions demonstrated their strong link to multiple ontological categories attributed to brain function and the disorders. SVA types that expanded their presence in the human genome at different stages of hominoid life history were also associated with progressively evolving behavioural features that indicated a potential impact of SVA propagation on a cognitive ability of a modern human.
  • A Single-Cell Transcriptomic Landscape of Primate Arterial Aging

    A Single-Cell Transcriptomic Landscape of Primate Arterial Aging

    ARTICLE https://doi.org/10.1038/s41467-020-15997-0 OPEN A single-cell transcriptomic landscape of primate arterial aging Weiqi Zhang 1,2,3,4,5,13, Shu Zhang6,7,13, Pengze Yan3,8,13, Jie Ren7,9,13, Moshi Song3,5,8, Jingyi Li2,3,8, Jinghui Lei4, Huize Pan2,3, Si Wang3,5,8, Xibo Ma3,10, Shuai Ma2,3,8, Hongyu Li2,3, Fei Sun2,3, Haifeng Wan3,5,11, ✉ ✉ ✉ Wei Li 3,5,11, Piu Chan4, Qi Zhou3,5,11, Guang-Hui Liu 2,3,4,5,8 , Fuchou Tang 6,7,9,12 & Jing Qu 3,5,11 Our understanding of how aging affects the cellular and molecular components of the vas- 1234567890():,; culature and contributes to cardiovascular diseases is still limited. Here we report a single-cell transcriptomic survey of aortas and coronary arteries in young and old cynomolgus monkeys. Our data define the molecular signatures of specialized arteries and identify eight markers discriminating aortic and coronary vasculatures. Gene network analyses characterize tran- scriptional landmarks that regulate vascular senility and position FOXO3A, a longevity- associated transcription factor, as a master regulator gene that is downregulated in six subtypes of monkey vascular cells during aging. Targeted inactivation of FOXO3A in human vascular endothelial cells recapitulates the major phenotypic defects observed in aged monkey arteries, verifying FOXO3A loss as a key driver for arterial endothelial aging. Our study provides a critical resource for understanding the principles underlying primate arterial aging and contributes important clues to future treatment of age-associated vascular disorders. 1 CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  • Bif (SH3GLB1) Human Shrna Plasmid Kit (Locus ID 51100) Product Data

    Bif (SH3GLB1) Human Shrna Plasmid Kit (Locus ID 51100) Product Data

    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TR301721 Bif (SH3GLB1) Human shRNA Plasmid Kit (Locus ID 51100) Product data: Product Type: shRNA Plasmids Product Name: Bif (SH3GLB1) Human shRNA Plasmid Kit (Locus ID 51100) Locus ID: 51100 Synonyms: Bif-1; CGI-61; dJ612B15.2; PPP1R70 Vector: pRS (TR20003) Format: Retroviral plasmids Components: SH3GLB1 - Human, 4 unique 29mer shRNA constructs in retroviral untagged vector(Gene ID = 51100). 5µg purified plasmid DNA per construct Non-effective 29-mer scrambled shRNA cassette in pRS Vector, TR30012, included for free. RefSeq: NM_001206651, NM_001206652, NM_001206653, NM_016009, NM_016009.1, NM_016009.2, NM_016009.3, NM_016009.4, NM_001206653.1, NM_001206652.1, NM_001206651.1, BC007455, BC007455.2, NM_001206652.2, NM_016009.5 Summary: This gene encodes a SRC homology 3 domain-containing protein. The encoded protein interacts with the proapoptotic member of the Bcl-2 family, Bcl-2-associated X protein (Bax) and may be involved in regulating apoptotic signaling pathways. This protein may also be involved in maintaining mitochondrial morphology. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2011] shRNA Design: These shRNA constructs were designed against multiple splice variants at this gene locus. To be certain that your variant of interest is targeted, please contact [email protected]. If you need a special design or shRNA sequence, please utilize our custom shRNA service. This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 Bif (SH3GLB1) Human shRNA Plasmid Kit (Locus ID 51100) – TR301721 Performance OriGene guarantees that the sequences in the shRNA expression cassettes are verified to Guaranteed: correspond to the target gene with 100% identity.
  • Actin Binding LIM 1 (Ablim1) Negatively Controls Osteoclastogenesis by Regulating Cell Migration and Fusion

    Actin Binding LIM 1 (Ablim1) Negatively Controls Osteoclastogenesis by Regulating Cell Migration and Fusion

    Received: 14 September 2017 | Accepted: 16 March 2018 DOI: 10.1002/jcp.26605 ORIGINAL RESEARCH ARTICLE Actin binding LIM 1 (abLIM1) negatively controls osteoclastogenesis by regulating cell migration and fusion Haruna Narahara1,2 | Eiko Sakai1 | Yu Yamaguchi1 | Shun Narahara1 | Mayumi Iwatake1,* | Kuniaki Okamoto1,† | Noriaki Yoshida2 | Takayuki Tsukuba1 1 Department of Dental Pharmacology, Graduate School of Biomedical Sciences, Actin binding LIM 1 (abLIM1) is a cytoskeletal actin-binding protein that has been Nagasaki University, Nagasaki, Japan implicated in interactions between actin filaments and cytoplasmic targets. Previous 2 Department of Orthodontics and Dentofacial Orthopedics, Graduate School of Biomedical biochemical and cytochemical studies have shown that abLIM1 interacts and co- Sciences, Nagasaki University, Nagasaki, Japan localizes with F-actin in the retina and muscle. However, whether abLIM1 regulates Correspondence osteoclast differentiation has not yet been elucidated. In this study, we examined the Takayuki Tsukuba, Department of Dental role of abLIM1 in osteoclast differentiation and function. We found that abLIM1 Pharmacology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852- expression was upregulated during receptor activator of nuclear factor kappa-B ligand 8588, Japan. (RANKL)-induced osteoclast differentiation, and that a novel transcript of abLIM1 was Email: [email protected] exclusively expressed in osteoclasts. Overexpression of abLIM1 in the murine Funding information monocytic cell line, RAW-D suppressed osteoclast differentiation and decreased JSPS KAKENHI, Grant numbers: 15H05298, 16K15790, 17H04379 expression of several osteoclast-marker genes. By contrast, small interfering RNA-induced knockdown of abLIM1 enhanced the formation of multinucleated osteoclasts and markedly increased the expression of the osteoclast-marker genes. Mechanistically, abLIM1 regulated the localization of tubulin, migration, and fusion in osteoclasts.
  • High-Fidelity CRISPR/Cas9

    High-Fidelity CRISPR/Cas9

    ARTICLE DOI: 10.1038/s41467-018-05766-5 OPEN High-fidelity CRISPR/Cas9- based gene-specific hydroxymethylation rescues gene expression and attenuates renal fibrosis Xingbo Xu1,2, Xiaoying Tan2,3, Björn Tampe 3, Tim Wilhelmi1,2, Melanie S. Hulshoff1,2,4, Shoji Saito3, Tobias Moser 5, Raghu Kalluri6, Gerd Hasenfuss1,2, Elisabeth M. Zeisberg1,2 & Michael Zeisberg2,3 fi 1234567890():,; While suppression of speci c genes through aberrant promoter methylation contributes to different diseases including organ fibrosis, gene-specific reactivation technology is not yet available for therapy. TET enzymes catalyze hydroxymethylation of methylated DNA, reac- tivating gene expression. We here report generation of a high-fidelity CRISPR/Cas9-based gene-specific dioxygenase by fusing an endonuclease deactivated high-fidelity Cas9 (dHFCas9) to TET3 catalytic domain (TET3CD), targeted to specific genes by guiding RNAs (sgRNA). We demonstrate use of this technology in four different anti-fibrotic genes in different cell types in vitro, among them RASAL1 and Klotho, both hypermethylated in kidney fibrosis. Furthermore, in vivo lentiviral delivery of the Rasal1-targeted fusion protein to interstitial cells and of the Klotho-targeted fusion protein to tubular epithelial cells each results in specific gene reactivation and attenuation of fibrosis, providing gene-specific demethylating technology in a disease model. 1 Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany. 2 German Center for Cardiovascular Research (DZHK) Partner Site, Göttingen, Germany. 3 Department of Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany. 4 Department of Pathology and Medical Biology, University Medical Center Groningen, Hanzeplein 1, 9713 Groningen, GZ, Netherlands.
  • Supplemental Information

    Supplemental Information

    Supplemental information Dissection of the genomic structure of the miR-183/96/182 gene. Previously, we showed that the miR-183/96/182 cluster is an intergenic miRNA cluster, located in a ~60-kb interval between the genes encoding nuclear respiratory factor-1 (Nrf1) and ubiquitin-conjugating enzyme E2H (Ube2h) on mouse chr6qA3.3 (1). To start to uncover the genomic structure of the miR- 183/96/182 gene, we first studied genomic features around miR-183/96/182 in the UCSC genome browser (http://genome.UCSC.edu/), and identified two CpG islands 3.4-6.5 kb 5’ of pre-miR-183, the most 5’ miRNA of the cluster (Fig. 1A; Fig. S1 and Seq. S1). A cDNA clone, AK044220, located at 3.2-4.6 kb 5’ to pre-miR-183, encompasses the second CpG island (Fig. 1A; Fig. S1). We hypothesized that this cDNA clone was derived from 5’ exon(s) of the primary transcript of the miR-183/96/182 gene, as CpG islands are often associated with promoters (2). Supporting this hypothesis, multiple expressed sequences detected by gene-trap clones, including clone D016D06 (3, 4), were co-localized with the cDNA clone AK044220 (Fig. 1A; Fig. S1). Clone D016D06, deposited by the German GeneTrap Consortium (GGTC) (http://tikus.gsf.de) (3, 4), was derived from insertion of a retroviral construct, rFlpROSAβgeo in 129S2 ES cells (Fig. 1A and C). The rFlpROSAβgeo construct carries a promoterless reporter gene, the β−geo cassette - an in-frame fusion of the β-galactosidase and neomycin resistance (Neor) gene (5), with a splicing acceptor (SA) immediately upstream, and a polyA signal downstream of the β−geo cassette (Fig.