eRapport

Novel and known DNA modifications - role in disease

Prosjekt
Prosjektnummer
2012082
Ansvarlig person
Arne Klungland
Institusjon
Oslo universitetssykehus HF
Prosjektkategori
Helse Sør-Øst forskningsgruppe 4
Helsekategori
Disputed aetiology and other
Forskningsaktivitet
1. Underpinning
Rapporter
2015
Prosjektet fokuserer på å utvikle metoder for karakterisering av kjemiske modifikasjoner på RNA. Disse modifikasjonene er reversible og kan være essensielle for at cellen skal kunne dele seg. Dersom gener som medvirker til at disse kjemiske modifikasjonene dannes eller fjernes blir mutert vil cellen, og hele individer, utvikle sykdomstrekk.Det har lenge vært kjent at kjemiske modifikasjoner på protein og DNA regulerer gen-uttrykk og er viktige for sykdom, spesielt kreft da de er viktige for korrekt gen-uttrykk og korrekt celledeling. Mange av disse modifikasjonene er reversible og bidrar blant annet til omprogrammering av gener ved befruktning og under embryoutvikling. For noen år siden oppdaget vi og andre at modifikasjoner på RNA også kan være reversible og at de er viktige for blant annet meiose og fertilitet i mus. Siste år har vi publisert arbeider hvor nye metoder for identifikasjon av en spesiell type modifikasjon (6-metyladenin). Vi har også studert gener som regulerer 6-metyladenin i prøver fra pasienter med nedsatt fertilitet. I vårt hovedarbeid har vi sammen med forskere ved Rockefeller Universitetet utviklet en metode for enkeltbaseoppløsning sekvensering av 6-metyladenine. Metoden går ut på at RNA først degraderes til passende størrelse (ca 100 nukleotider). Antistoff bindes til 6-metyladenin og kryssbindes ved UV-lys. Deretter benyttes protease for å fjerne antistoffet. Da det alltid vil være en rest av antistoffet (noen aminosyrer) igjen på RNAet blir det ofte introdusert en mutasjon når RNA-et benyttes som templat for cDNA syntese. Ved hjelp av mutasjoner som introduseres kan vi identifisere den metylerte bases. Denne teknikken vil nå muliggjøre mutasjonsanalyser hvor metylerte adenin erstattes med f.eks guanin og vil være viktig for å identifisere hvilke gen og modifikasjoner som forårsaker sykdomsutvikling.
2014
Dynamic chemical modifications in proteins, DNA and RNA are fundamental for disease related processes. Such modifications can be heritable in humans. We focus our research on an exciting family of hydroxylases that targets various macromolecules and have unique roles in disease. - Due to exciting finding on reversible modifications in RNA, this project continues with a focus on m6A modifications in RNA.Despite massive research after the human sequencing project we do not know the causes of many human diseases. Many diseases have a high heritability, yet, large whole-genome studies have identified only a limited number of disease causing gene variants. It is now evident that dynamic chemical modifications in proteins, DNA and RNA are fundamental for disease related processes. Such modifications can be heritable in humans The role of histone modifications and methylation of DNA is widely studied and has recently been designated unique roles in numerous diseases, including cancer. In recent years, we have focused our research on a fascinating family of hydroxylases with homology to E. coli AlkB¸ ALKBH1-8 and the less conserved member FTO/AlKBH9. AlkB from E. coli directly reverses DNA base damage while the 9 mammalian AlkB homologs have remarkable different substrates including histone H2A and actin (Stem Cells 2012, Nat Commun 2013), DNA and various RNA species (EMBO J 2006, Canc Res 2008, Mol Cell Biol 2010, Nature Commun 2011). We are particularly intrigued by the recent observations that the most frequent internal mRNA modification, 6-methyladenine (6mA), can be reversed (Mol Cell 2013). Thus, it is likely that improper reversal of 6mA is a major cause of key human diseases, including obesity and obesity associated diseases such as type II diabetes. We have also identified other modifications in RNA that can be reversed (not published yet). The inproper regulation of this modification is absolutely required for cellular homeostasis and mutations in genes reversing this modification lead to developmental defects.
2013
Dynamic chemical modifications in proteins, DNA and RNA are fundamental for disease related processes. Such modifications can be heritable in humans. We focus our research on an exciting family of hydroxylases that targets various macromolecules and have unique roles in disease.Despite massive research after the human sequencing project we do not know the causes of many human diseases. Many diseases have a high heritability, yet, large whole-genome studies have identified only a limited number of disease causing gene variants. It is now evident that dynamic chemical modifications in proteins, DNA and RNA are fundamental for disease related processes. Such modifications can be heritable in humans The role of histone modifications and methylation of DNA is widely studied and has recently been designated unique roles in numerous diseases, including cancer. In recent years, we have focused our research on a fascinating family of hydroxylases with homology to E. coli AlkB¸ ALKBH1-8 and the less conserved member FTO/AlKBH9. AlkB from E. coli directly reverses DNA base damage while the 9 mammalian AlkB homologs have remarkable different substrates including histone H2A and actin (Stem Cells 2012, Nat Commun 2013), DNA and various RNA species (EMBO J 2006, Canc Res 2008, Mol Cell Biol 2010, Nature Commun 2011). We are particularly intrigued by the recent observations that the most frequent internal mRNA modification, 6-methyladenine (6mA), can be reversed (Mol Cell 2013). Thus, it is likely that improper reversal of 6mA is a major cause of key human diseases, including obesity and obesity associated diseases such as type II diabetes. We have also initiated some studies for innovation and during the last two years several patents have been obtained in the area of modified bases in DNA and we have received one innovation prize (at UiO/OUH, 2012) and three grants for further improving these products. Several products have been patented and three products have been licensed and produced for the research marked.
2012
Reversible modifications on DNA, RNA and proteins are crucial for correct biological functions. This project currently focuses on the identification of novel reversible marks on DNA and RNA.Reversible modifications on DNA, RNA and proteins are crucial for correct biological functions. We have focused our research on identifying novel gene functions related to the introduction and removal of modifications, erroneous and regulatory, on DNA. Recently, our work has expanded to also include reversible modifications on mRNA. Part of this research relates to the AlkB homologs. The conservation of most of the human AlkB homologues across the animal kingdom clearly suggests fundamental and important functions. Very few macromolecular demethylases have been identified, and the Alkbh proteins likely represent completely novel and highly interesting functions. We believe that gene-targeting in mice is required for illuminating their precise molecular role. Such analysis might also be very relevant for studying regulation during embryo development and stem cell differentiation. Our in vivo experiments will profit considerably if we, or others, are able to reveal the exact biochemical activities of these AlkB homologs. However, biochemical properties clarified by in vitro assays must be verified in a genetic model to establish its biological relevance. Due to fruitful collaborations, nationally and internationally, we have contributed to the identification of novel enzymatic reaction introducing and removing modifications on DNA and tRNA (2007-2011). More recently we have identified, in collaboration with Chuan He (Chicago) and Yungui Yang (Beijing), reversible modifications on mRNA (Edotors choice in Science January 2013). The regulation of modifications in mRNA might contribute substantially to human pathologies including obesity, diabetes II and sterility. We have also identified other reversible marks on RNA 8which will hopefully be published by end of 2013).
Vitenskapelige artikler
Klungland A, Yang YG

Endogenous DNA Damage and Repair Enzymes: -A short summary of the scientific achievements of Tomas Lindahl, Nobel Laureate in Chemistry 2015.

Genomics Proteomics Bioinformatics 2016 Jun;14(3):122-5. Epub 2015 des 12

PMID: 26689322

Fusser M, Kernstock S, Aileni VK, Egge-Jacobsen W, Falnes PØ, Klungland A

Lysine Methylation of the Valosin-Containing Protein (VCP) Is Dispensable for Development and Survival of Mice.

PLoS One 2015;10(11):e0141472. Epub 2015 nov 6

PMID: 26544960

Ke S, Alemu EA, Mertens C, Gantman EC, Fak JJ, Mele A, Haripal B, Zucker-Scharff I, Moore MJ, Park CY, Vågbø CB, Kussnierczyk A, Klungland A, Darnell JE, Darnell RB

A majority of m6A residues are in the last exons, allowing the potential for 3' UTR regulation.

Genes Dev 2015 Oct 1;29(19):2037-53. Epub 2015 sep 24

PMID: 26404942

Chymkowitch P, Nguéa AP, Aanes H, Koehler CJ, Thiede B, Lorenz S, Meza-Zepeda LA, Klungland A, Enserink JM

Sumoylation of Rap1 mediates the recruitment of TFIID to promote transcription of ribosomal protein genes.

Genome Res 2015 Jun;25(6):897-906. Epub 2015 mar 23

PMID: 25800674

Bjørge MD, Hildrestrand GA, Scheffler K, Suganthan R, Rolseth V, Kusnierczyk A, Rowe AD, Vågbø CB, Vetlesen S, Eide L, Slupphaug G, Nakabeppu Y, Bredy TW, Klungland A, Bjørås M

Synergistic Actions of Ogg1 and Mutyh DNA Glycosylases Modulate Anxiety-like Behavior in Mice.

Cell Rep 2015 Dec 29;13(12):2671-8. Epub 2015 des 17

PMID: 26711335

Robertson Adam B, Robertson Julia, Fusser Markus, Klungland Arne

Endonuclease G preferentially cleaves 5-hydroxymethylcytosine-modified DNA creating a substrate for recombination.

Nucleic Acids Res 2014 Dec 1;42(21):13280-93. Epub 2014 okt 29

PMID: 25355512

Klungland Arne, Dahl John Arne

Dynamic RNA modifications in disease.

Curr Opin Genet Dev 2014 Jun;26():47-52. Epub 2014 jul 5

PMID: 25005745

Zdzalik Daria, Vågbø Cathrine B, Kirpekar Finn, Davydova Erna, Puscian Alicja, Maciejewska Agnieszka M, Krokan Hans E, Klungland Arne, Tudek Barbara, van den Born Erwin, Falnes Pål Ø

Protozoan ALKBH8 oxygenases display both DNA repair and tRNA modification activities.

PLoS One 2014;9(6):e98729. Epub 2014 jun 10

PMID: 24914785

Jonson Ida, Ougland Rune, Klungland Arne, Larsen Elisabeth

Oxidative stress causes DNA triplet expansion in Huntington's disease mouse embryonic stem cells.

Stem Cell Res 2013 Nov;11(3):1264-71. Epub 2013 aug 27

PMID: 24041806

Li Ming-Ming, Nilsen Anja, Shi Yue, Fusser Markus, Ding Yue-He, Fu Ye, Liu Bo, Niu Yamei, Wu Yong-Sheng, Huang Chun-Min, Olofsson Maria, Jin Kang-Xuan, Lv Ying, Xu Xing-Zhi, He Chuan, Dong Meng-Qiu, Rendtlew Danielsen Jannie M, Klungland Arne, Yang Yun-Gui

ALKBH4-dependent demethylation of actin regulates actomyosin dynamics.

Nat Commun 2013;4():1832.

PMID: 23673617

Furu Kari, Klungland Arne

Tzfp represses the androgen receptor in mouse testis.

PLoS One 2013;8(4):e62314. Epub 2013 apr 25

PMID: 23634227

Zheng Guanqun, Dahl John Arne, Niu Yamei, Fu Ye, Klungland Arne, Yang Yun-Gui, He Chuan

Sprouts of RNA epigenetics: the discovery of mammalian RNA demethylases.

RNA Biol 2013 Jun;10(6):915-8. Epub 2013 apr 17

PMID: 23619745

Solberg Anja, Robertson Adam B, Aronsen Jan Magnus, Rognmo Øivind, Sjaastad Ivar, Wisløff Ulrik, Klungland Arne

Deletion of mouse Alkbh7 leads to obesity.

J Mol Cell Biol 2013 Jun;5(3):194-203. Epub 2013 apr 8

PMID: 23572141

Zheng Guanqun, Dahl John Arne, Niu Yamei, Fedorcsak Peter, Huang Chun-Min, Li Charles J, Vågbø Cathrine B, Shi Yue, Wang Wen-Ling, Song Shu-Hui, Lu Zhike, Bosmans Ralph P G, Dai Qing, Hao Ya-Juan, Yang Xin, Zhao Wen-Ming, Tong Wei-Min, Wang Xiu-Jie, Bogdan Florian, Furu Kari, Fu Ye, Jia Guifang, Zhao Xu, Liu Jun, Krokan Hans E, Klungland Arne, Yang Yun-Gui, He Chuan

ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility.

Mol Cell 2013 Jan 10;49(1):18-29. Epub 2012 nov 21

PMID: 23177736

Nordstrand Line M, Furu Kari, Paulsen Jonas, Rognes Torbjørn, Klungland Arne

Alkbh1 and Tzfp repress a non-repeat piRNA cluster in pachytene spermatocytes.

Nucleic Acids Res 2012 Nov;40(21):10950-63. Epub 2012 sep 10

PMID: 22965116

Ougland Rune, Lando David, Jonson Ida, Dahl John A, Moen Marivi Nabong, Nordstrand Line M, Rognes Torbjørn, Lee Jeannie T, Klungland Arne, Kouzarides Tony, Larsen Elisabeth

ALKBH1 is a histone H2A dioxygenase involved in neural differentiation.

Stem Cells 2012 Dec;30(12):2672-82.

PMID: 22961808

Møllersen Linda, Rowe Alexander D, Illuzzi Jennifer L, Hildrestrand Gunn A, Gerhold Katharina J, Tveterås Linda, Bjølgerud Anja, Wilson David M, Bjørås Magnar, Klungland Arne

Neil1 is a genetic modifier of somatic and germline CAG trinucleotide repeat instability in R6/1 mice.

Hum Mol Genet 2012 Nov;21(22):4939-47. Epub 2012 aug 21

PMID: 22914735

Kleppa Liv, Mari Pierre-Olivier, Larsen Elisabeth, Lien Guro Flor, Godon Camille, Theil Arjan F, Nesse Gaute J, Wiksen Hege, Vermeulen Wim, Giglia-Mari Giuseppina, Klungland Arne

Kinetics of endogenous mouse FEN1 in base excision repair.

Nucleic Acids Res 2012 Oct;40(18):9044-59. Epub 2012 jul 18

PMID: 22810208

Calvo Jennifer A, Meira Lisiane B, Lee Chun-Yue I, Moroski-Erkul Catherine A, Abolhassani Nona, Taghizadeh Koli, Eichinger Lindsey W, Muthupalani Sureshkumar, Nordstrand Line M, Klungland Arne, Samson Leona D

DNA repair is indispensable for survival after acute inflammation.

J Clin Invest 2012 Jul;122(7):2680-9. Epub 2012 jun 11

PMID: 22684101

Meza Trine J, Moen Marivi N, Vågbø Cathrine B, Krokan Hans E, Klungland Arne, Grini Paul E, Falnes Pål Ø

The DNA dioxygenase ALKBH2 protects Arabidopsis thaliana against methylation damage.

Nucleic Acids Res 2012 Aug;40(14):6620-31. Epub 2012 apr 24

PMID: 22532610

Robertson Adam B, Dahl John Arne, Ougland Rune, Klungland Arne

Pull-down of 5-hydroxymethylcytosine DNA using JBP1-coated magnetic beads.

Nat Protoc 2012 Feb;7(2):340-50. Epub 2012 jan 26

PMID: 22281869

Doktorgrader
Anja Solberg

Physiological Roles of Mouse Alkbh7: Implications in Obesity and Running Endurance.

Disputert:
august 2013
Hovedveileder:
Arne Klungland
Deltagere
  • Miriam Landfors Doktorgradsstipendiat
  • Dominique Ober Doktorgradsstipendiat
  • John Arne Dahl Forsker (annen finansiering)
  • Håvard Aanes Postdoktorstipendiat
  • Xu Zhao Postdoktorstipendiat
  • Endalkachew Ashenafi Alemu Postdoktorstipendiat
  • Miaomiao Li Doktorgradsstipendiat
  • Ida Jonson Doktorgradsstipendiat
  • Arne Klungland Prosjektleder

eRapport er utarbeidet av Sølvi Lerfald og Reidar Thorstensen, Regionalt kompetansesenter for klinisk forskning, Helse Vest RHF, og videreutvikles av de fire RHF-ene i fellesskap, med støtte fra Helse Vest IKT

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