Full Text Journal Articles by
Author John Arne Dahl

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LSD1 represses a neonatal/reparative gene program in adult intestinal epithelium.

Rosalie T Zwiggelaar, Håvard T Lindholm, Madeleine Fosslie, Marianne Terndrup Pedersen, Yuki Ohta, Alberto Díez-Sánchez, Mara Martín-Alonso, Jenny Ostrop, Mami Matano, Naveen Parmar, Emilie Kvaløy, Roos R Spanjers, Kamran Nazmi, Morten Rye, Finn Drabløs, Cheryl Arrowsmith, John Arne Dahl, Kim B Jensen, Toshiro Sato, Menno J Oudhoff,

Intestinal epithelial homeostasis is maintained by adult intestinal stem cells, which, alongside Paneth cells, appear after birth in the neonatal period. We aimed to identify regulators of neonatal intestinal epithelial development by testing a small library of epigenetic modifier inhibitors in Paneth cell-skewed organoid cultures. We found that lysine-specific demethylase ... Read more >>

Sci Adv (Science advances)
[2020, 6(37):]

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Intestinal-epithelial LSD1 controls cytoskeletal-mediated cell identity including goblet cell effector responses required for gut inflammatory and infectious diseases

Naveen Parmar, Kyle Burrows, Håvard Lindholm, Rosalie Zwiggelaar, Mara Martín-Alonso, Madeleine Fosslie, Bruce Vallance, John Arne Dahl, Colby Zaph, Menno Oudhoff,

ABSTRACT Infectious and inflammatory diseases in the intestine remain a serious threat for patients world-wide. Reprogramming of the intestinal epithelium towards a protective effector state is important to manage inflammation and immunity. The role of epigenetic regulatory enzymes within these processes is not yet defined. Here, we use a mouse ... Read more >>

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LSD1 represses a neonatal/reparative gene program in adult intestinal epithelium

Rosalie Zwiggelaar, Håvard Lindholm, Madeleine Fosslie, Marianne Pedersen, Yuki Ohta, Alberto Díez-Sánchez, Mara Martín-Alonso, Jenny Ostrop, Mami Matano, Naveen Parmar, Emilie Kvaløy, Roos Spanjers, Kamran Nazmi, Morten Rye, Finn Drabløs, Cheryl Arrowsmith, John Arne Dahl, Kim Jensen, Toshiro Sato, Menno Oudhoff,

ABSTRACT Intestinal epithelial homeostasis is maintained by adult intestinal stem cells, which, alongside Paneth cells, appear after birth in the neonatal period. We aimed to identify new regulators of neonatal intestinal epithelial development by testing a small library of epigenetic modifier inhibitors in Paneth cell-skewed organoid cultures. We found that ... Read more >>

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KDM4A regulates the maternal-to-zygotic transition by protecting broad H3K4me3 domains from H3K9me3 invasion in oocytes.

Aditya Sankar, Mads Lerdrup, Adeel Manaf, Jens Vilstrup Johansen, Javier Martin Gonzalez, Rehannah Borup, Robert Blanshard, Arne Klungland, Klaus Hansen, Claus Yding Andersen, John Arne Dahl, Kristian Helin, Eva R Hoffmann,

The importance of germline-inherited post-translational histone modifications on priming early mammalian development is just emerging1-4. Histone H3 lysine 9 (H3K9) trimethylation is associated with heterochromatin and gene repression during cell-fate change5, whereas histone H3 lysine 4 (H3K4) trimethylation marks active gene promoters6. Mature oocytes are transcriptionally quiescent and possess remarkably ... Read more >>

Nat Cell Biol (Nature cell biology)
[2020, 22(4):380-388]

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Going low to reach high: Small-scale ChIP-seq maps new terrain.

Madeleine Fosslie, Adeel Manaf, Mads Lerdrup, Klaus Hansen, Gregor D Gilfillan, John Arne Dahl,

Chromatin immunoprecipitation (ChIP) enables mapping of specific histone modifications or chromatin-associated factors in the genome and represents a powerful tool in the study of chromatin and genome regulation. Importantly, recent technological advances that couple ChIP with whole-genome high-throughput sequencing (ChIP-seq) now allow the mapping of chromatin factors throughout the genome. ... Read more >>

Wiley Interdiscip Rev Syst Biol Med (Wiley interdisciplinary reviews. Systems biology and medicine)
[2020, 12(1):e1465]

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5-hydroxymethylcytosine Marks Mammalian Origins Acting as a Barrier to Replication.

Terezia Prikrylova, Julia Robertson, Francesca Ferrucci, Dorota Konorska, Håvard Aanes, Adeel Manaf, Beibei Zhang, Cathrine Broberg Vågbø, Anna Kuśnierczyk, Karin M Gilljam, Caroline Løvkvam-Køster, Marit Otterlei, John Arne Dahl, Jorrit Enserink, Arne Klungland, Adam B Robertson,

In most mammalian cells, DNA replication occurs once, and only once between cell divisions. Replication initiation is a highly regulated process with redundant mechanisms that prevent errant initiation events. In lower eukaryotes, replication is initiated from a defined consensus sequence, whereas a consensus sequence delineating mammalian origin of replication has ... Read more >>

Sci Rep (Scientific reports)
[2019, 9(1):11065]

Cited: 1 time

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Histone Methylations Define Neural Stem/Progenitor Cell Subtypes in the Mouse Subventricular Zone.

Zhichao Zhang, Adeel Manaf, Yanjiao Li, Sonia Peña Perez, Rajikala Suganthan, John Arne Dahl, Magnar Bjørås, Arne Klungland,

Neural stem/progenitor cells (NSPCs) persist in the mammalian brain throughout life and can be activated in response to the physiological and pathophysiological stimuli. Epigenetic reprogramming of NPSC represents a novel strategy for enhancing the intrinsic potential of the brain to regenerate after brain injury. Therefore, defining the epigenetic features of ... Read more >>

Mol Neurobiol (Molecular neurobiology)
[2020, 57(2):997-1008]

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Epigenetic age is a cell-intrinsic property in transplanted human hematopoietic cells.

Arne Søraas, Mieko Matsuyama, Marcos de Lima, David Wald, Jochen Buechner, Tobias Gedde-Dahl, Camilla Lund Søraas, Brian Chen, Luigi Ferrucci, John Arne Dahl, Steve Horvath, Shigemi Matsuyama,

The age of tissues and cells can be accurately estimated by DNA methylation analysis. The multitissue DNA methylation (DNAm) age predictor combines the DNAm levels of 353 CpG dinucleotides to arrive at an age estimate referred to as DNAm age. Recent studies based on short-term observations showed that the DNAm ... Read more >>

Aging Cell (Aging cell)
[2019, 18(2):e12897]

Cited: 5 times

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Positioning Europe for the EPITRANSCRIPTOMICS challenge.

Michael F Jantsch, Alessandro Quattrone, Mary O'Connell, Mark Helm, Michaela Frye, Manuel Macias-Gonzales, Marie Ohman, Stefan Ameres, Luc Willems, Francois Fuks, Anastasis Oulas, Stepanka Vanacova, Henrik Nielsen, Cecile Bousquet-Antonelli, Yuri Motorin, Jean-Yves Roignant, Nikolaos Balatsos, Andras Dinnyes, Pavel Baranov, Vincent Kelly, Ayelet Lamm, Gideon Rechavi, Mattia Pelizzola, Janis Liepins, Irina Holodnuka Kholodnyuk, Vanessa Zammit, Duncan Ayers, Finn Drablos, John Arne Dahl, Janusz Bujnicki, Carmen Jeronimo, Raquel Almeida, Monica Neagu, Marieta Costache, Jasna Bankovic, Bojana Banovic, Jan Kyselovic, Luis Miguel Valor, Stefan Selbert, Pinar Pir, Turan Demircan, Victoria Cowling, Matthias Schäfer, Walter Rossmanith, Denis Lafontaine, Alexandre David, Clement Carre, Frank Lyko, Raffael Schaffrath, Schraga Schwartz, Andre Verdel, Arne Klungland, Elzbieta Purta, Gordana Timotijevic, Fernando Cardona, Alberto Davalos, Ester Ballana, Donal O Carroll, Jernej Ule, Rupert Fray,

The genetic alphabet consists of the four letters: C, A, G, and T in DNA and C,A,G, and U in RNA. Triplets of these four letters jointly encode 20 different amino acids out of which proteins of all organisms are built. This system is universal and is found in all ... Read more >>

RNA Biol (RNA biology)
[2018, 15(6):829-831]

Cited: 10 times

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How low can you go? Pushing the limits of low-input ChIP-seq.

John Arne Dahl, Gregor D Gilfillan,

In the past decade, chromatin immunoprecipitation sequencing (ChIP-seq) has emerged as the dominant technique for those wishing to perform genome-wide protein:DNA profiling. Owing to the tissue- and cell-type-specific nature of epigenetic marks, the field has been driven towards obtaining data from ever-lower cell numbers. In this review, we focus on ... Read more >>

Brief Funct Genomics (Briefings in functional genomics)
[2018, 17(2):89-95]

Cited: 6 times

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Parental micronutrient deficiency distorts liver DNA methylation and expression of lipid genes associated with a fatty-liver-like phenotype in offspring.

Kaja H Skjærven, Lars Martin Jakt, Jorge M O Fernandes, John Arne Dahl, Anne-Catrin Adam, Johanna Klughammer, Christoph Bock, Marit Espe,

Micronutrient status of parents can affect long term health of their progeny. Around 2 billion humans are affected by chronic micronutrient deficiency. In this study we use zebrafish as a model system to examine morphological, molecular and epigenetic changes in mature offspring of parents that experienced a one-carbon (1-C) micronutrient ... Read more >>

Sci Rep (Scientific reports)
[2018, 8(1):3055]

Cited: 7 times

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Genome-wide profiling of DNA 5-hydroxymethylcytosine during rat Sertoli cell maturation.

Miriam Landfors, Jostein Johansen, Jan Magnus Aronsen, Cathrine Broberg Vågbø, Louis C Doré, Chuan He, Ivar Sjaastad, Pål Sætrom, Péter Fedorcsák, John Arne Dahl, Håvard Aanes, Markus Fußer, Arne Klungland,

Sertoli cells have dual roles during the cells' lifetime. In the juvenile mammal, Sertoli cells proliferate and create the structure of the testis, and during puberty they cease to proliferate and take on the adult role of supporting germ cells through spermatogenesis. Accordingly, many genes expressed in Sertoli cells during ... Read more >>

Cell Discov (Cell discovery)
[2017, 3:17013]

Cited: 1 time

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Reversible RNA modifications in meiosis and pluripotency.

Arne Klungland, John Arne Dahl, Gareth Greggains, Peter Fedorcsak, Adam Filipczyk,

Post-transcriptional RNA modifications were discovered several decades ago, but the reversible nature of RNA modifications has only recently been discovered. Owing to technological advances, knowledge of epitranscriptomic marks and their writers, readers and erasers has recently advanced tremendously. Here we focus on the roles of the dynamic methylation and demethylation ... Read more >>

Nat Methods (Nature methods)
[2016, 14(1):18-22]

Cited: 7 times

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Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition.

John Arne Dahl, Inkyung Jung, Håvard Aanes, Gareth D Greggains, Adeel Manaf, Mads Lerdrup, Guoqiang Li, Samantha Kuan, Bin Li, Ah Young Lee, Sebastian Preissl, Ingunn Jermstad, Mads Haugland Haugen, Rajikala Suganthan, Magnar Bjørås, Klaus Hansen, Knut Tomas Dalen, Peter Fedorcsak, Bing Ren, Arne Klungland,

Maternal-to-zygotic transition (MZT) is essential for the formation of a new individual, but is still poorly understood despite recent progress in analysis of gene expression and DNA methylation in early embryogenesis. Dynamic histone modifications may have important roles in MZT, but direct measurements of chromatin states have been hindered by ... Read more >>

Nature (Nature)
[2016, 537(7621):548-552]

Cited: 124 times

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Sequencing of FTO and ALKBH5 in men undergoing infertility work-up identifies an infertility-associated variant and two missense mutations.

Miriam Landfors, Sigve Nakken, Markus Fusser, John-Arne Dahl, Arne Klungland, Peter Fedorcsak,

To assess whether men with reduced semen quality exhibit genetic variants in the genes coding for the messenger RNA methylation erasers FTO and ALKBH5.DNA of men undergoing infertility work-up was extracted and the FTO and ALKBH5 genes were sequenced. Statistical analysis was used to study the correlation between the identified ... Read more >>

Fertil. Steril. (Fertility and sterility)
[2016, 105(5):1170-1179.e5]

Cited: 7 times

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DNA base modifications in honey bee and fruit fly genomes suggest an active demethylation machinery with species- and tissue-specific turnover rates.

Erik M K Rasmussen, Cathrine B Vågbø, Daniel Münch, Hans E Krokan, Arne Klungland, Gro V Amdam, John Arne Dahl,

Well-known epigenetic DNA modifications in mammals include the addition of a methyl group and a hydroxyl group to cytosine, resulting in 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) respectively. In contrast, the abundance and the functional implications of these modifications in invertebrate model organisms such as the honey bee (Apis mellifera) and ... Read more >>

(Biochemistry and biophysics reports)
[2016, 6:9-15]

Cited: 3 times

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Dynamic RNA modifications in disease.

Arne Klungland, John Arne Dahl,

While the presence of 6-methyladenosine (m6A) modifications in mRNA was noted several decades ago, the first enzyme reversing this modification was identified very recently. Today we know of two methyltransferases introducing m6A in mRNA--METTL3 and METTL14--and two demethylases that remove it have been identified-FTO (ALKBH9) and ALKBH5. The conserved role ... Read more >>

Curr Opin Genet Dev (Current opinion in genetics & development)
[2014, 26:47-52]

Cited: 37 times

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Micro chromatin immunoprecipitation (μChIP) from early mammalian embryos.

John Arne Dahl, Arne Klungland,

Chromatin immunoprecipitation (ChIP) is a powerful method for mapping protein-DNA interactions in vivo. Genomic localization of histone modifications, transcription factors, and other regulatory proteins can be revealed by ChIP. However, conventional ChIP protocols require the use of large numbers of cells, which prevents the application of ChIP to rare cell ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2015, 1222:227-245]

Cited: 4 times

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DNA metabolism: bases of DNA repair and regulation.

Adam B Robertson, John Arne Dahl, Arne Klungland,

Nat. Chem. Biol. (Nature chemical biology)
[2014, 10(7):487-488]

Cited: 3 times

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

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

More than 100 structurally distinct RNA modifications have been identified in all kingdoms of life. These post-transcriptional modifications are widely present in various RNAs, including ribosomal RNA (rRNA), transfer RNA (tRNA), messenger RNA (mRNA), long non-coding RNA (lncRNA), etc. We have shown that the methylation of N(6)-methyladenine (m(6)A) can be ... Read more >>

RNA Biol (RNA biology)
[2013, 10(6):915-918]

Cited: 31 times

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

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

N(6)-methyladenosine (m(6)A) is the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Here we report ALKBH5 as another mammalian demethylase that oxidatively reverses m(6)A in mRNA in vitro and in vivo. This demethylation activity of ALKBH5 significantly affects mRNA export and RNA metabolism as well as the ... Read more >>

Mol Cell (Molecular cell)
[2013, 49(1):18-29]

Cited: 646 times

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Histone modifications and mRNA expression in the inner cell mass and trophectoderm of bovine blastocysts.

Doris Herrmann, John Arne Dahl, Andrea Lucas-Hahn, Philippe Collas, Heiner Niemann,

Normal development depends on the precise sequence of changes in the configuration of chromatin; these are primarily related to specific biochemical modifications such as acetylation or methylation of histones and DNA methylation. While the role of DNA methylation during preimplantation development has been studied extensively, little is known about histone ... Read more >>

Epigenetics (Epigenetics)
[2013, 8(3):281-289]

Cited: 11 times

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Histone H3 lysine 27 methylation asymmetry on developmentally-regulated promoters distinguish the first two lineages in mouse preimplantation embryos.

John Arne Dahl, Andrew H Reiner, Arne Klungland, Teruhiko Wakayama, Philippe Collas,

First lineage specification in the mammalian embryo leads to formation of the inner cell mass (ICM) and trophectoderm (TE), which respectively give rise to embryonic and extraembryonic tissues. We show here that this first differentiation event is accompanied by asymmetric distribution of trimethylated histone H3 lysine 27 (H3K27me3) on promoters ... Read more >>

PLoS One (PloS one)
[2010, 5(2):e9150]

Cited: 51 times

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Fast genomic muChIP-chip from 1,000 cells.

John Arne Dahl, Andrew H Reiner, Philippe Collas,

Genome-wide location analysis of histone modifications and transcription factor binding relies on chromatin immunoprecipitation (ChIP) assays. These assays are, however, time-consuming and require large numbers of cells, hindering their application to the analysis of many interesting cell types. We report here a fast microChIP (muChIP) assay for 1,000 cells in ... Read more >>

Genome Biol (Genome biology)
[2009, 10(2):R13]

Cited: 25 times

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Sensitive on-chip quantitative real-time PCR performed on an adaptable and robust platform.

Torsten Lund-Olesen, Martin Dufva, John Arne Dahl, Philippe Collas, Mikkel Fougt Hansen,

A robust, flexible and efficient system for performing high sensitivity quantitative on-chip real-time PCR for research purposes is presented. The chips used consist of microchannels etched in silicon. The surface in the channels is a thermally grown silicon dioxide and the channel is sealed by a glass lid. The chips ... Read more >>

Biomed Microdevices (Biomedical microdevices)
[2008, 10(6):769-776]

Cited: 4 times

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