DOCSLIB.ORG

Methylome-Wide Change Associated with Response to Electroconvulsive Therapy in Depressed Patients Lea Sirignano 1,Joseffrank 1, Laura Kranaster 2, Stephanie H

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Methylome-Wide Change Associated with Response to Electroconvulsive Therapy in Depressed Patients Lea Sirignano 1,Joseffrank 1, Laura Kranaster 2, Stephanie H Sirignano et al. Translational Psychiatry (2021) 11:347 https://doi.org/10.1038/s41398-021-01474-9 Translational Psychiatry ARTICLE Open Access Methylome-wide change associated with response to electroconvulsive therapy in depressed patients Lea Sirignano 1,JosefFrank 1, Laura Kranaster 2, Stephanie H. Witt 1,FabianStreit 1, Lea Zillich1, Alexander Sartorius2, Marcella Rietschel 1 and Jerome C. Foo 1 Abstract Electroconvulsive therapy (ECT) is a quick-acting and powerful antidepressant treatment considered to be effective in treating severe and pharmacotherapy-resistant forms of depression. Recent studies have suggested that epigenetic mechanisms can mediate treatment response and investigations about the relationship between the effects of ECT and DNA methylation have so far largely taken candidate approaches. In the present study, we examined the effects of ECT on the methylome associated with response in depressed patients (n = 34), testing for differentially methylated CpG sites before the first and after the last ECT treatment. We identified one differentially methylated CpG site associated with the effect of ECT response (defined as >50% decrease in Hamilton Depression Rating Scale score, HDRS), TNKS (q < 0.05; p = 7.15 × 10−8). When defining response continuously (ΔHDRS), the top suggestive differentially methylated CpG site was in FKBP5 (p = 3.94 × 10−7). Regional analyses identified two differentially methylated regions on chromosomes 8 (Šídák’s p = 0.0031) and 20 (Šídák’s p = 4.2 × 10−5) associated with ΔHDRS. Functional pathway analysis did not identify any significant pathways. A confirmatory look at candidates previously proposed to be involved in ECT mechanisms found CpG sites associated with response only at the nominally significant level (p < 0.05). Despite the limited sample size, the present study was able to identify epigenetic change associated with ECT response suggesting that this approach, especially when involving larger 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; samples, has the potential to inform the study of mechanisms involved in ECT and severe and treatment-resistant depression. Introduction ECT in such a subgroup of severely depressed patients is a Depression is a major contributor to global burden of promising approach to gain insights into the underlying disease and despite worldwide research efforts, the het- mechanisms of depression and treatment response. erogeneous nature of the disorder makes it difficult to DNA methylation is thought to be involved in disease definitively unravel its underlying etiology and the factors pathology through its influence on gene expression and influencing treatment response1,2. Electroconvulsive cellular function5,6. There is evidence that pre-treatment therapy (ECT) is an intervention with rapid and striking methylation profiles may predict likelihood of achieving antidepressant effects and is the treatment of choice for remission7 and the literature on DNA methylation in patients with severe and treatment-resistant depression3,4. depression has pointed to several possible genes of interest Studying biological changes associated with response to (e.g., BDNF, SLC6A4, NR3C1, FKBP5, etc. for reviews, – see7 10) as being related to antidepressant response. Investigating change of methylation levels during treat- Correspondence: Jerome C. Foo ([email protected]) 1Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental ment may inform the biological processes underlying both Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, depression and antidepressant response. Examining these Germany changes in ECT patients offers an optimal research setting 2Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, as: (1) treatment effects are substantial and occur soon Germany © The Author(s) 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a linktotheCreativeCommons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Sirignano et al. Translational Psychiatry (2021) 11:347 Page 2 of 9 after the intervention, and (2) ECT patients represent a Materials and methods subgroup of patients with the most severe form of This study was approved by the Ethics Committee (II), depression. It is likely that this subgroup is not only Medical Faculty Mannheim, University of Heidelberg. All clinically but also genetically more homogenous, especially patients provided written consent after a detailed expla- as these patients tend to show a higher genetic burden for nation of the content of the study. All experimental major depression than those with less severe forms11. procedures were performed in accordance with the The few studies exploring differences in methylation Declaration of Helsinki. related to ECT are only beginning to give insight into the factors involved. A translational study observed that the Participants response to electroconvulsive stimulation (ECS) in rats Patients (n = 34) diagnosed with a major unipolar was predicted by higher p11 promoter methylation and depressive episode (based on International Classification found this also to be the case in two human samples (n = of Diseases version 10, ICD-10), older than 18 years, 11; n = 65) in response to ECT12. Another candidate and assigned to ECT treatment were recruited at the gene is brain-derived neurotrophic factor (BDNF)which Department of Psychiatry and Psychotherapy at the is involved in neuroplastic changes associated with stress Central Institute of Mental Health (CIMH) in Mannheim, and depression13,14. Methylation differences of the pro- Germany, between 2014 and 2016. Criteria for assignment moter region of BDNF have been observed in many to ECT were treatment-resistant depression (i.e., failure of psychiatric disorders15, and also after use of anti- two adequate dose-duration antidepressants from differ- depressant medication16. Studies in animals and humans ent classes, or psychotherapy in the current episode), also propose an involvement of BDNF in response to positive experience of ECT from a previous episode, or ECT: after ECS/ECT, alterations of BDNF levels have severe depression with (a) psychotic symptoms, (b) severe been found in rats17, and in humans, differences in suicidality, or (c) the refusal of food or fluid intake. expression of BDNF have been described18,19. Further- Patients were excluded if they had any substance-use- more, associations between pre-treatment BDNF levels related disorders (other than tobacco and alcohol use and ECT outcome have been described, but whether disorders) or a lifetime diagnosis of schizophrenia. All BDNF levels are indicative of response remains to be participants were of Caucasian descent. The patients kept determined20,21. the same medication regimens throughout ECT treat- Research on ECT-related changes in methylation levels ment. This sample is a subset of a sample reported in a has largely focused on candidate genes. However, as ECT previous genetic study in ECT patients11. Descriptive and is a non-specific treatment with widespread, yet uncertain clinical characteristics of the participants are described effects on biological processes, the selection of predefined in Table 1. candidates, relying on prior knowledge may not give the full picture. As such, an approach investigating the whole Depression and DNA methylation assessment methylome is expected to yield new and relevant insights. The 21-item version of the Hamilton Depression Rating Few studies have made use of these technologies in ECT Scale (HDRS) was administered and blood was collected samples to date. Moschny et al.22 examined longitudinal from patients prior to the first (T1) and after the last DNA methylation before and after ECT in a small group (T2) session of ECT (average sessions: 10.82, range: of patients (8 responders and 4 non-responders). They did 5–25 sessions). T2 was between 1 and 7 days after the last not find any significant differences in global DNA ECT session. Time of collection was kept constant methylation, but identified eight genes potentially impli- between 8:30 and 9:30 a.m. at both timepoints to keep it cated in either ECT response or its mechanism through close to the clinical interview conducted around the same analysis of single probe variance, and two genes whose time, as well as preclude any potential confounding methylation changed during treatment course. effects arising from ward routines and circadian fluctua- In the present study, we aimed to identify changes in tions23,24. Standard procedures for extraction and pro- methylation levels associated with the effects of ECT and cessing were followed. DNA extraction was performed to find potential biomarkers for antidepressant response. using the Chemagic Magnetic Separation
Load more

Recommended publications
  • Analyses of Allele-Specific Gene Expression in Highly Divergent
    ARTICLES Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance James J Crowley1,10, Vasyl Zhabotynsky1,10, Wei Sun1,2,10, Shunping Huang3, Isa Kemal Pakatci3, Yunjung Kim1, Jeremy R Wang3, Andrew P Morgan1,4,5, John D Calaway1,4,5, David L Aylor1,9, Zaining Yun1, Timothy A Bell1,4,5, Ryan J Buus1,4,5, Mark E Calaway1,4,5, John P Didion1,4,5, Terry J Gooch1,4,5, Stephanie D Hansen1,4,5, Nashiya N Robinson1,4,5, Ginger D Shaw1,4,5, Jason S Spence1, Corey R Quackenbush1, Cordelia J Barrick1, Randal J Nonneman1, Kyungsu Kim2, James Xenakis2, Yuying Xie1, William Valdar1,4, Alan B Lenarcic1, Wei Wang3,9, Catherine E Welsh3, Chen-Ping Fu3, Zhaojun Zhang3, James Holt3, Zhishan Guo3, David W Threadgill6, Lisa M Tarantino7, Darla R Miller1,4,5, Fei Zou2,11, Leonard McMillan3,11, Patrick F Sullivan1,5,7,8,11 & Fernando Pardo-Manuel de Villena1,4,5,11 Complex human traits are influenced by variation in regulatory DNA through mechanisms that are not fully understood. Because regulatory elements are conserved between humans and mice, a thorough annotation of cis regulatory variants in mice could aid in further characterizing these mechanisms. Here we provide a detailed portrait of mouse gene expression across multiple tissues in a three-way diallel. Greater than 80% of mouse genes have cis regulatory variation. Effects from these variants influence complex traits and usually extend to the human ortholog. Further, we estimate that at least one in every thousand SNPs creates a cis regulatory effect.
    [Show full text]
  • 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.
    [Show full text]
  • BIOINFORMATICS Pages 1–7
    Vol. 00 no. 00 2010 BIOINFORMATICS Pages 1–7 Integrative classification and analysis of multiple arrayCGH datasets with probe alignment Ze Tian and Rui Kuang∗ Department of Computer Science and Engineering, University of Minnesota Twin Cities, Minneapolis, USA Received on XXXXX; revised on XXXXX; accepted on XXXXX Associate Editor: XXXXXXX ABSTRACT 2009). Chromosome copy number variations can be measured by Motivation: Array comparative genomic hybridization (ArrayCGH) comparative genomic hybridization (CGH), which compares the is widely used to measure DNA copy numbers in cancer research. copy number of a differentially labeled case sample with a reference ArrayCGH data report log-ratio intensities of thousands of probes DNA from a normal individual. ArrayCGH technology based on sampled along the chromosomes. Typically, the choices of the DNA microarray can currently allow genome-wide identification locations and the lengths of the probes vary in different experiments. of regions with copy number variations at different resolutions This discrepancy in choosing probes poses a challenge in integrated (Carter, 2007). The arrayCGH data was used to discriminate healthy classification or analysis across multiple arrayCGH datasets. We patients from cancer patients and classify patients of different cancer propose an alignment based framework to integrate arrayCGH subtypes. Thus, arrayCGH data is considered as a new source of samples generated from different probe sets. The alignment biomarkers that provide important information of candidate cancer framework seeks an optimal alignment between the probe series loci for the classification of patients and discovery of molecular of one arrayCGH sample and the probe series of another sample, mechanisms of cancers (Sykes et al., 2009).
    [Show full text]
  • Progress in Understanding 2-Hydroxyglutaric Acidurias
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Springer - Publisher Connector J Inherit Metab Dis (2012) 35:571–587 DOI 10.1007/s10545-012-9462-5 METABOLIC DISSERTATION Progress in understanding 2-hydroxyglutaric acidurias Martijn Kranendijk & Eduard A. Struys & Gajja S. Salomons & Marjo S. Van der Knaap & Cornelis Jakobs Martijn Kranendijk Received: 13 December 2011 /Revised: 25 January 2012 /Accepted: 30 January 2012 /Published online: 6 March 2012 # The Author(s) 2012. This article is published with open access at Springerlink.com Abstract The organic acidurias D-2-hydroxyglutaric acidu- D2HGDH gene encoding D-2-hydroxyglutarate ria (D-2-HGA), L-2-hydroxyglutaric aciduria (L-2-HGA), dehydrogenase and combined D,L-2-hydroxyglutaric aciduria (D,L- L-2-HG L-2-hydroxyglutaric acid 2-HGA) cause neurological impairment at young age. L-2-HGA L-2-hydroxyglutaric aciduria Accumulation of D-2-hydroxyglutarate (D-2-HG) and/or L- L-2-HGDH L-2-hydroxyglutarate dehydrogenase 2-hydroxyglutarate (L-2-HG) in body fluids are the bio- enzyme chemical hallmarks of these disorders. The current review L2HGDH gene encoding L-2-hydroxyglutarate describes the knowledge gathered on 2-hydroxyglutaric dehydrogenase acidurias (2-HGA), since the description of the first patients D,L-2-HGA combined D,L-2-hydroxyglutaric aciduria in 1980. We report on the clinical, genetic, enzymatic and IDH2 gene encoding isocitrate dehydrogenase 2 metabolic characterization of D-2-HGA type I, D-2-HGA 2-KG 2-ketoglutaric acid type II, L-2-HGA and D,L-2-HGA, whereas for D-2-HGA HOT hydroxyacid-oxoacid transhydrogenase type I and type II novel clinical information is presented enzyme which was derived from questionnaires.
    [Show full text]
  • 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.
    [Show full text]
  • Epigenetics Page 1
    Epigenetics esiRNA ID Gene Name Gene Description Ensembl ID HU-13237-1 ACTL6A actin-like 6A ENSG00000136518 HU-13925-1 ACTL6B actin-like 6B ENSG00000077080 HU-14457-1 ACTR1A ARP1 actin-related protein 1 homolog A, centractin alpha (yeast) ENSG00000138107 HU-10579-1 ACTR2 ARP2 actin-related protein 2 homolog (yeast) ENSG00000138071 HU-10837-1 ACTR3 ARP3 actin-related protein 3 homolog (yeast) ENSG00000115091 HU-09776-1 ACTR5 ARP5 actin-related protein 5 homolog (yeast) ENSG00000101442 HU-00773-1 ACTR6 ARP6 actin-related protein 6 homolog (yeast) ENSG00000075089 HU-07176-1 ACTR8 ARP8 actin-related protein 8 homolog (yeast) ENSG00000113812 HU-09411-1 AHCTF1 AT hook containing transcription factor 1 ENSG00000153207 HU-15150-1 AIRE autoimmune regulator ENSG00000160224 HU-12332-1 AKAP1 A kinase (PRKA) anchor protein 1 ENSG00000121057 HU-04065-1 ALG13 asparagine-linked glycosylation 13 homolog (S. cerevisiae) ENSG00000101901 HU-13552-1 ALKBH1 alkB, alkylation repair homolog 1 (E. coli) ENSG00000100601 HU-06662-1 ARID1A AT rich interactive domain 1A (SWI-like) ENSG00000117713 HU-12790-1 ARID1B AT rich interactive domain 1B (SWI1-like) ENSG00000049618 HU-09415-1 ARID2 AT rich interactive domain 2 (ARID, RFX-like) ENSG00000189079 HU-03890-1 ARID3A AT rich interactive domain 3A (BRIGHT-like) ENSG00000116017 HU-14677-1 ARID3B AT rich interactive domain 3B (BRIGHT-like) ENSG00000179361 HU-14203-1 ARID3C AT rich interactive domain 3C (BRIGHT-like) ENSG00000205143 HU-09104-1 ARID4A AT rich interactive domain 4A (RBP1-like) ENSG00000032219 HU-12512-1 ARID4B AT rich interactive domain 4B (RBP1-like) ENSG00000054267 HU-12520-1 ARID5A AT rich interactive domain 5A (MRF1-like) ENSG00000196843 HU-06595-1 ARID5B AT rich interactive domain 5B (MRF1-like) ENSG00000150347 HU-00556-1 ASF1A ASF1 anti-silencing function 1 homolog A (S.
    [Show full text]
  • Teleological Role of L-2-Hydroxyglutarate
    © 2020. Published by The Company of Biologists Ltd | Disease Models & Mechanisms (2020) 13, dmm045898. doi:10.1242/dmm.045898 RESEARCH ARTICLE Teleological role of L-2-hydroxyglutarate dehydrogenase in the kidney Garrett Brinkley1, Hyeyoung Nam1, Eunhee Shim1,*, Richard Kirkman1, Anirban Kundu1, Suman Karki1, Yasaman Heidarian2, Jason M. Tennessen2, Juan Liu3, Jason W. Locasale3, Tao Guo4, Shi Wei4, Jennifer Gordetsky5, Teresa L. Johnson-Pais6, Devin Absher7, Dinesh Rakheja8, Anil K. Challa9 and Sunil Sudarshan1,10,‡ ABSTRACT insight into the physiological role of L2HGDH as well as mechanisms L-2-hydroxyglutarate (L-2HG) is an oncometabolite found elevated in that promote L-2HG accumulation in disease states. renal tumors. However, this molecule might have physiological roles that extend beyond its association with cancer, as L-2HG levels are KEY WORDS: L-2-hydroxyglutarate, L-2-hydroxyglutarate dehydrogenase, TCA cycle, PPARGC1A elevated in response to hypoxia and during Drosophila larval development. L-2HG is known to be metabolized by L-2HG dehydrogenase (L2HGDH), and loss of L2HGDH leads to elevated INTRODUCTION L-2HG levels. Despite L2HGDH being highly expressed in the kidney, Oncometabolites are small molecules that have been found elevated its role in renal metabolism has not been explored. Here, we report our in various malignancies. To date, these molecules include the findings utilizing a novel CRISPR/Cas9 murine knockout model, with tricarboxylic acid (TCA) cycle intermediates succinate and fumarate a specific focus on the role of L2HGDH in the kidney. Histologically, as well as both enantiomers of 2-hydroxyglutarate (D-2HG and L2hgdh knockout kidneys have no demonstrable histologic L-2HG) (Tomlinson et al., 2002; Baysal et al., 2000; Niemann and abnormalities.
    [Show full text]
  • Moyamoya Disease Susceptibility Gene RNF213 Links Inflammatory
    www.nature.com/scientificreports OPEN Moyamoya disease susceptibility gene RNF213 links inflammatory and angiogenic signals in Received: 19 March 2015 Accepted: 03 July 2015 endothelial cells Published: 17 August 2015 Kazuhiro Ohkubo1,*, Yasunari Sakai1,*, Hirosuke Inoue1, Satoshi Akamine1, Yoshito Ishizaki1, Yuki Matsushita1, Masafumi Sanefuji1, Hiroyuki Torisu1,3, Kenji Ihara1,2, Marco Sardiello4 & Toshiro Hara1 Moyamoya disease (MMD) is a cerebrovascular disorder characterized by occlusive lesions of the circle of Willis. To date, both environmental and genetic factors have been implicated for pathogenesis of MMD. Allelic variations in RNF213 are known to confer the risk of MMD; however, functional roles of RNF213 remain to be largely elusive. We herein report that pro-inflammatory cytokines, IFNG and TNFA, synergistically activated transcription of RNF213 both in vitro and in vivo. Using various chemical inhibitors, we found that AKT and PKR pathways contributed to the transcriptional activation of RNF213. Transcriptome-wide analysis and subsequent validation with quantitative PCR supported that endogenous expression of cell cycle-promoting genes were significantly decreased with knockdown of RNF213 in cultured endothelial cells. Consistently, these cells showed less proliferative and less angiogenic profiles. Chemical inhibitors for AKT (LY294002) and PKR (C16) disrupted their angiogenic potentials, suggesting that RNF213 and its upstream pathways cooperatively organize the process of angiogenesis. Furthermore, RNF213 down-regulated expressions of matrix metalloproteases in endothelial cells, but not in fibroblasts or other cell types. Altogether, our data illustrate that RNF213 plays unique roles in endothelial cells for proper gene expressions in response to inflammatory signals from environments. Moyamoya disease (MMD) represents a specific intracranial vascular disorder characterized by progres- sive, occlusive lesions of internal carotid arteries and branches in the circle of Willis1,2.
    [Show full text]
  • 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 ....................................................................................................................
    [Show full text]
  • Genome-Wide Profiling of RNA Editing Sites in Sheep Yuanyuan Zhang1,2, Deping Han1, Xianggui Dong1, Jiankui Wang1, Jianfei Chen1, Yanzhu Yao1, Hesham Y
    Zhang et al. Journal of Animal Science and Biotechnology (2019) 10:31 https://doi.org/10.1186/s40104-019-0331-z RESEARCH Open Access Genome-wide profiling of RNA editing sites in sheep Yuanyuan Zhang1,2, Deping Han1, Xianggui Dong1, Jiankui Wang1, Jianfei Chen1, Yanzhu Yao1, Hesham Y. A. Darwish1,3, Wansheng Liu2* and Xuemei Deng1* Abstract Background: The widely observed RNA-DNA differences (RDDs) have been found to be due to nucleotide alteration by RNA editing. Canonical RNA editing (i.e., A-to-I and C-to-U editing) mediated by the adenosine deaminases acting on RNA (ADAR) family and apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) family during the transcriptional process is considered common and essential for the development of an individual. To date, an increasing number of RNA editing sites have been reported in human, rodents, and some farm animals; however, genome-wide detection of RNA editing events in sheep has not been reported. The aim of this study was to identify RNA editing events in sheep by comparing the RNA-seq and DNA-seq data from three biological replicates of the kidney and spleen tissues. Results: A total of 607 and 994 common edited sites within the three biological replicates were identified in the ovine kidney and spleen, respectively. Many of the RDDs were specific to an individual. The RNA editing-related genes identified in the present study might be evolved for specific biological functions in sheep, such as structural constituent of the cytoskeleton and microtubule-based processes. Furthermore, the edited sites found in the ovine BLCAP and NEIL1 genes are in line with those in previous reports on the porcine and human homologs, suggesting the existence of evolutionarily conserved RNA editing sites and they may play an important role in the structure and function of genes.
    [Show full text]
  • Small RAB Gtpases Regulate Multiple Steps of Mitosis
    CORE Metadata, citation and similar papers at core.ac.uk Provided by CONICET Digital REVIEW published: 17 February 2016 doi: 10.3389/fcell.2016.00002 Small RAB GTPases Regulate Multiple Steps of Mitosis Stéphanie Miserey-Lenkei 1* and María I. Colombo 2 1 Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport Group, CNRS UMR 144, Paris, France, 2 Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología-CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina GTPases of the RAB family are key regulators of multiple steps of membrane trafficking. Several members of the RAB GTPase family have been implicated in mitotic progression. In this review, we will first focus on the function of endosome-associated RAB GTPases reported in early steps of mitosis, spindle pole maturation, and during cytokinesis. Second, we will discuss the role of Golgi-associated RAB GTPases at the metaphase/anaphase transition and during cytokinesis. Keywords: RABs GTPases, mitosis, endosomes, golgi complex, trafficking INTRODUCTION Edited by: In mammalian cells, GTPases of the RAB family are key regulators of multiple steps of membrane Letizia Lanzetti, traffic. RAB GTPases play a central role in the formation of transport carriers from a donor University of Turin, Italy membrane, movement of these carriers along cytoskeletal tracks and finally anchoring/fusion Reviewed by: to the correct acceptor membrane (Stenmark, 2009). RAB GTPases represent a large family Andrew Alexander Peden, of small guanosine triphosphate (GTP)-binding proteins that comprise more than 60 known University of Sheffield, UK Anna Akhmanova, members. RAB GTPases are localized on distinct membrane-bound compartments and cycle Utrecht University, Netherlands between an active GTP-bound form and an inactive guanosine diphosphate (GDP)-bound *Correspondence: form.
    [Show full text]
  • Temporal Proteomic Analysis of HIV Infection Reveals Remodelling of The
    1 1 Temporal proteomic analysis of HIV infection reveals 2 remodelling of the host phosphoproteome 3 by lentiviral Vif variants 4 5 Edward JD Greenwood 1,2,*, Nicholas J Matheson1,2,*, Kim Wals1, Dick JH van den Boomen1, 6 Robin Antrobus1, James C Williamson1, Paul J Lehner1,* 7 1. Cambridge Institute for Medical Research, Department of Medicine, University of 8 Cambridge, Cambridge, CB2 0XY, UK. 9 2. These authors contributed equally to this work. 10 *Correspondence: [email protected]; [email protected]; [email protected] 11 12 Abstract 13 Viruses manipulate host factors to enhance their replication and evade cellular restriction. 14 We used multiplex tandem mass tag (TMT)-based whole cell proteomics to perform a 15 comprehensive time course analysis of >6,500 viral and cellular proteins during HIV 16 infection. To enable specific functional predictions, we categorized cellular proteins regulated 17 by HIV according to their patterns of temporal expression. We focussed on proteins depleted 18 with similar kinetics to APOBEC3C, and found the viral accessory protein Vif to be 19 necessary and sufficient for CUL5-dependent proteasomal degradation of all members of the 20 B56 family of regulatory subunits of the key cellular phosphatase PP2A (PPP2R5A-E). 21 Quantitative phosphoproteomic analysis of HIV-infected cells confirmed Vif-dependent 22 hyperphosphorylation of >200 cellular proteins, particularly substrates of the aurora kinases. 23 The ability of Vif to target PPP2R5 subunits is found in primate and non-primate lentiviral 2 24 lineages, and remodeling of the cellular phosphoproteome is therefore a second ancient and 25 conserved Vif function.
    [Show full text]