Epigenetics - basic mechanisms and disease - Karl Ekwall

We are studying epigenetic modification mechanisms in fission yeast and human cell lines as model systems. In our basic research we focus on how these mechanisms contribute to cell cycle, cell differentiation and cellular quiescence. We also carry out applied collaborative clinical epigenetic projects especially in the areas of cancer and obesity. We have extensive expertise in chromatin analysis by genome-wide methods using our cellular model systems and samples from the clinic.

Illustration of a chromosome structure with a DNA spiral
Chromosome structure in eukaryotic cells. The DNA helix (yellow/blue) is wrapped approximately two turns around each nucleosome (grey spheres). Each nucleosome consists of eight histone proteins that can be epigenetically modified. Illustration: Karl Ekwall

Epigenetics is a rapidly expanding research field ranging from basic research to clinical applications. The term epigenetics comes from developmental biology and is a theory developed by Conrad Waddington in the 1940s to explain how genes are used during the process of morphogenesis and development of a multicellular organism (the process of epigenesis).  Since all somatic cells of an organism, with very few exceptions, contain exactly the same DNA sequence, epigenetics can possibly explain how the same DNA sequence can be used to express different genes in different cell types and tissues. A more modern definition of epigenetics is ‘nuclear inheritance’ which is not based on differences in the DNA sequence. With this we now consider all modifications of the chromatin template that together establish and propagate different stable patterns of gene expression.

Photo of the team members

Epigenetic modifications: Covalent chemical modifications to the DNA and to histones, histone variants, nucleosome positions, non-coding RNAs and the level of chromatin compaction all contribute to chromosomal structure and to the activity or silencing of genes. These chromatin-level alterations are defined as epigenetic when they are heritable from mother to daughter cell. Histone acetylation and methylation are the most common modifications and they occur at specific lysines mainly in the NTER region of histones H3 and H4. The modifications lead to functional changes in gene promoters and enhancers because they confer altered accessibility to transcriptional regulatory complexes, thus impacting on gene expression. Nucleosome remodelling activity of SNF2 enzymes results in nucleosome sliding, modulation of histone turnover, spacing of nucleosomes, histone eviction and histone exchange. These activities are central in epigenetic regulation and control accessibility to the DNA for a large number of factors involved in processes involving recognition of the DNA sequence i.e. RNA transcription, DNA replication, repair and recombination.

The powerful molecular genetic analysis in fission yeast (Schizosaccharomyces pombe) is important for dissecting the detailed molecular function of several epigenetic mechanisms including histone acetylation, histone methylation and SNF2 chromatin remodelling. Our work in human cell lines allows for identification of conserved epigenetic mechanisms and the clinical epigenetics projects show a relevance of epigenetic mechanisms in disease.

Group members

Karl Ekwall

Group leader

Lina Cordeddu

Senior lab manager

Selected Publications

Regulating retrotransposon activity through the use of alternative transcription start sites
Persson J, Steglich B, Smialowska A, Boyd M, Bornholdt J, Andersson R, Schurra C, Arcangioli B, Sandelin A, Nielsen O and Ekwall K. EMBO reports 2016 May;17(5):753-68. doi: 10.15252/embr.201541866.

Genetic Analysis of Schizosaccharomyces pombe.
Ekwall, K. and G. Thon. Cold Spring Harb Protoc 2017(8): pdb top079772.

Leo1 is essential for the dynamic regulation of heterochromatin and gene expression during cellular quiescence.
Oya E, Durand-Dubief M, Cohen A, Maksimov V, Schurra C, Nakayama JI, Weisman R, Arcangioli B, Ekwall K. Epigenetics Chromatin. 2019 Jul 17;12(1):45. doi: 10.1186/s13072-019-0292-7.

Chromatin remodeler Fft3 plays a dual role at blocked DNA replication forks.
Ait-Saada A, Khorosjutina O, Chen J, Kramarz K, Maksimov V, Svensson JP, Lambert S, Ekwall K. Life Sci Alliance. 2019 Oct 1;2(5):e201900433. doi: 10.26508/lsa.201900433. eCollection 2019 Oct.

Research Networks

  • Principal investigator for the KAW financed project ‘Clinical epigenetics of acute leukemia’ involving three research groups at KI (S Lehmann, R Ohlsson and K Ekwall; 2012-2017)


  • Appointed as visiting Professor at Nagoya City University (NCU) in Japan 2016-2017 (Karl Ekwall)

Research Project for a Master Student

We have a laboratory project on Functional studies of the Paf1C complex.

Please contact us if you are interested and have a relevant background.

Look under Project Directory/Campus Huddinge/Dept of Biosciences and Nutrition/Functional studies of the Paf1C complex

Content reviewer:
Sara Bruce