madsben

• Falnes, Pål; Malecki, Jedrzej Mieczyslaw; Gonzalez-Molina, Maria del Carmen Herrera; Bengtsen, Mads & Davydova, Erna (2023). Human seven-β-strand (METTL) methyltransferases - conquering the universe of protein lysine methylation. Journal of Biological Chemistry. ISSN 0021-9258. 299(6), p. 1–15. doi: 10.1016/j.jbc.2023.104661. Full text in Research Archive Show summary

  Lysine methylation is an abundant posttranslational modification, which has been most intensively studied in the context of histone proteins, where it represents an important epigenetic mark. Lysine methylation of histone proteins is primarily catalyzed by SET-domain methyltransferases (MTases). However, it has recently become evident that also another MTase family, the so-called seven-β-strand (7BS) MTases, often denoted METTLs (methyltransferase-like), contains several lysine (K)-specific MTases (KMTs). These enzymes catalyze the attachment of up to three methyl groups to lysine residues in specific substrate proteins, using S-adenosylmethionine (AdoMet) as methyl donor. About a decade ago, only a single human 7BS KMT was known, namely the histone-specific DOT1L, but 15 additional 7BS KMTs have now been discovered and characterized. These KMTs typically target a single nonhistone substrate that, in most cases, belongs to one of the following three protein groups: components of the cellular protein synthesis machinery, mitochondrial proteins, and molecular chaperones. This article provides an extensive overview and discussion of the human 7BS KMTs and their biochemical and biological roles.

• Bengtsen, Mads; Winje, Ivan Myhre; Eftestøl, Einar; Landskron, Johannes; Sun, Chengyi & Nygård, Kamilla Børve [Show all 10 contributors for this article] (2021). Comparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle. PLoS Genetics. ISSN 1553-7390. 17:e1009907(11). doi: 10.1371/journal.pgen.1009907. Full text in Research Archive Show summary

  Muscle cells have different phenotypes adapted to different usage, and can be grossly divided into fast/glycolytic and slow/oxidative types. While most muscles contain a mixture of such fiber types, we aimed at providing a genome-wide analysis of the epigenetic landscape by ChIP-Seq in two muscle extremes, the fast/glycolytic extensor digitorum longus (EDL) and slow/oxidative soleus muscles. Muscle is a heterogeneous tissue where up to 60% of the nuclei can be of a different origin. Since cellular homogeneity is critical in epigenome-wide association studies we developed a new method for purifying skeletal muscle nuclei from whole tissue, based on the nuclear envelope protein Pericentriolar material 1 (PCM1) being a specific marker for myonuclei. Using antibody labelling and a magnetic-assisted sorting approach, we were able to sort out myonuclei with 95% purity in muscles from mice, rats and humans. The sorting eliminated influence from the other cell types in the tissue and improved the myo-specific signal. A genome-wide comparison of the epigenetic landscape in EDL and soleus reflected the differences in the functional properties of the two muscles, and revealed distinct regulatory programs involving distal enhancers, including a glycolytic super-enhancer in the EDL. The two muscles were also regulated by different sets of transcription factors; e.g. in soleus, binding sites for MEF2C, NFATC2 and PPARA were enriched, while in EDL MYOD1 and SIX1 binding sites were found to be overrepresented. In addition, more novel transcription factors for muscle regulation such as members of the MAF family, ZFX and ZBTB14 were identified.

• Castañeda, Fernando Rodriguez-; Lemma, Roza Berhanu; Torre, Ignacio Cuervo; Bengtsen, Mads; Moen, Lisa Marie & Ledsaak, Marit [Show all 8 contributors for this article] (2018). The SUMO protease SENP1 and the chromatin remodeller CHD3 interact and jointly affect chromatin accessibility and gene expression. Journal of Biological Chemistry. ISSN 0021-9258. 293(40), p. 15439–15454. doi: 10.1074/jbc.RA118.002844. Full text in Research Archive Show summary

  The small ubiquitin-like modifier (SUMO) post-translationally modifies lysine residues of transcription factors and co-regulators and thereby contributes to an important layer of control of the activities of these transcriptional regulators. Likewise, deSUMOylation of these factors by the sentrin-specific proteases (SENPs) also plays a role in gene regulation, but whether SENPs functionally interact with other regulatory factors that control gene expression is unclear. In the present work, we focused on SENP1, specifically, on its role in activation of gene expression investigated through analysis of the SENP1 interactome, which revealed that SENP1 physically interacts with the chromatin remodeler chromodomain helicase DNA-binding protein 3 (CHD3). Using several additional methods, including GST pull-down and co-immunoprecipitation assays, we validated and mapped this interaction, and using CRISPR-Cas9–generated CHD3- and SENP1-KO cells (in the haploid HAP1 cell line), we investigated whether these two proteins are functionally linked in regulating chromatin remodeling and gene expression. Genome-wide ATAC-Seq analysis of the CHD3- and SENP1-KO cells revealed a large degree of overlap in differential chromatin openness between these two mutant cell lines. Moreover, motif analysis and comparison with ChIP-Seq profiles in K562 cells pointed to an association of CHD3 and SENP1 with CCCTC-binding factor (CTCF) and SUMOylated chromatin–associated factors. Lastly, genome-wide RNA-Seq also indicated that these two proteins co-regulate the expression of several genes. We propose that the functional link between chromatin remodeling by CHD3 and deSUMOylation by SENP1 uncovered here provides another level of control of gene expression.

• Gundersen, Kristian; Bruusgaard, Jo C.; Egner, Ingrid Marie; Eftestøl, Einar & Bengtsen, Mads (2018). Muscle memory: virtues of your youth? Journal of Physiology. ISSN 0022-3751. 596(18), p. 4289–4290. doi: 10.1113/JP276354. Full text in Research Archive
• Winje, Ivan; Bengtsen, Mads; Eftestøl, Einar; Juvkam, Inga; Bruusgaard, Jo C. & Gundersen, Kristian (2018). Specific labelling of myonuclei by an antibody against pericentriolar material 1 on skeletal muscle tissue sections. Acta Physiologica. ISSN 1748-1708. 223(4), p. 1–9. doi: 10.1111/apha.13034. Full text in Research Archive Show summary

  Aim: Skeletal muscle is a heterogeneous tissue containing several different cell types, and only about 40%‐50% of the cell nuclei within the tissue belong to myofibres. Existing technology, attempting to distinguish myonuclei from other nuclei at the light microscopy level, has led to controversies in our understanding of the basic cell biology of muscle plasticity. This study aims at demonstrating that an antibody against the protein pericentriolar material 1 (PCM1) can be used to reliably identify myonuclei on histological cross sections from humans, mice and rats. Methods: Cryosections were labelled with a polyclonal antibody against PCM1. The specificity of the labelling for myonuclei was verified using 3D reconstructions of confocal z‐stacks triple‐labelled for DNA, dystrophin and PCM1, and by co‐localization with nuclear mCherry driven by the muscle‐specific Alpha‐Actin‐1 promoter after viral transduction. Results: The PCM1 antibody specifically labelled all myonuclei, and myonuclei only, in cryosections of muscles from rats, mice and men. Nuclei in other cell types including satellite cells were not labelled. Both normal muscles and hypertrophic muscles after synergist ablation were investigated. Conclusion: Pericentriolar material 1 can be used as a specific histological marker for myonuclei in skeletal muscle tissue without relying on counterstaining of other structures or cumbersome and subjective analysis of nuclear positioning.

• Simovski, Boris; Vodak, Daniel; Gundersen, Sveinung; Domanska, Diana Ewa; Azab, Abdulrahman & Holden, Lars [Show all 25 contributors for this article] (2017). GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome. GigaScience. 6(7), p. 1–12. doi: 10.1093/gigascience/gix032. Full text in Research Archive Show summary

  Background: Recent large-scale undertakings such as ENCODE and Roadmap Epigenomics have generated experimental data mapped to the human reference genome (as genomic tracks) representing a variety of functional elements across a large number of cell types. Despite the high potential value of these publicly available data for a broad variety of investigations, little attention has been given to the analytical methodology necessary for their widespread utilisation. Findings: We here present a first principled treatment of the analysis of collections of genomic tracks. We have developed novel computational and statistical methodology to permit comparative and confirmatory analyses across multiple and disparate data sources. We delineate a set of generic questions that are useful across a broad range of investigations and discuss the implications of choosing different statistical measures and null models. Examples include contrasting analyses across different tissues or diseases. The methodology has been implemented in a comprehensive open-source software system, the GSuite HyperBrowser. To make the functionality accessible to biologists, and to facilitate reproducible analysis, we have also developed a web-based interface providing an expertly guided and customizable way of utilizing the methodology. With this system, many novel biological questions can flexibly be posed and rapidly answered. Conclusions: Through a combination of streamlined data acquisition, interoperable representation of dataset collections and customizable statistical analysis with guided setup and interpretation, the GSuite HyperBrowser represents a first comprehensive solution for integrative analysis of track collections across the genome and epigenome. The software is available at: https://hyperbrowser.uio.no

• Bengtsen, Mads; Sørensen, Linda Therese; Aabel, Linn Ingeborg; Ledsaak, Marit; Matre, Vilborg & Gabrielsen, Odd Stokke (2017). The adaptor protein ARA55 and the nuclear kinase HIPK1 assist c-Myb in recruiting p300 to chromatin. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. ISSN 1874-9399. 1860(7), p. 751–760. doi: 10.1016/j.bbagrm.2017.05.001. Full text in Research Archive Show summary

  LIM-domain proteins, containing multiple cysteine-rich zinc finger-like motifs, have been shown to play diverse roles in several cellular processes. A common theme is that they mediate important protein-protein interactions that are key to their function. Androgen receptor-associated protein 55 (ARA55) belongs to this family of bridging proteins containing four C-terminal LIM domains. It has a dual role with functions both at focal adhesions and in the nucleus, apparently shuttling between the two compartments. In the present work, we have expanded our understanding of its nuclear functions by showing that it interacts with three nuclear regulators not previously linked to ARA55. We first identified ARA55 as a novel interaction partner of the nuclear kinase HIPK1 and found that ARA55, like HIPK1, also interacts with the transcription factor c-Myb. In search of a function for these associations, we observed that the coactivator p300 not only binds to c-Myb, but to ARA55 as well. When combined, c-Myb, p300, HIPK1 and ARA55 caused strong synergistic activation of a chromatinized reporter gene. In parallel, all partners, including p300, were efficiently recruited to chromatin at the c-Myb-bound promoter. Consistent with this cooperation, we found that c-Myb and ARA55 share a common set of target genes in an osteosarcoma cellular context. We propose that ARA55 and HIPK1 assist c-Myb in recruiting the coactivator and acetyltransferase p300 to chromatin.

• Ledsaak, Marit; Bengtsen, Mads; Molværsmyr, Ann-Kristin; Fuglerud, Bettina Maria; Matre, Vilborg & Eskeland, Ragnhild [Show all 7 contributors for this article] (2016). PIAS1 binds p300 and behaves as a coactivator or corepressor of the transcription factor c-Myb dependent on SUMO-status. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. ISSN 1874-9399. 1859(5), p. 705–718. doi: 10.1016/j.bbagrm.2016.03.011. Full text in Research Archive
• Bengtsen, Mads; Klepper, Kjetil; Gundersen, Sveinung; Torre, Ignacio Cuervo; Drabløs, Finn & Hovig, Johannes Eivind [Show all 9 contributors for this article] (2015). c-Myb Binding Sites in Haematopoietic Chromatin Landscapes. PLOS ONE. 10(7). doi: 10.1371/journal.pone.0133280. Full text in Research Archive Show summary

  Strict control of tissue-specific gene expression plays a pivotal role during lineage commit- ment. The transcription factor c-Myb has an essential role in adult haematopoiesis and func- tions as an oncogene when rearranged in human cancers. Here we have exploited digital genomic footprinting analysis to obtain a global picture of c-Myb occupancy in the genome of six different haematopoietic cell-types. We have biologically validated several c-Myb foot- prints using c-Myb knockdown data, reporter assays and DamID analysis. We show that our predicted conserved c-Myb footprints are highly dependent on the haematopoietic cell type, but that there is a group of gene targets common to all cell-types analysed. Further- more, we find that c-Myb footprints co-localise with active histone mark H3K4me3 and are significantly enriched at exons. We analysed co-localisation of c-Myb footprints with 104 chromatin regulatory factors in K562 cells, and identified nine proteins that are enriched together with c-Myb footprints on genes positively regulated by c-Myb and one protein enriched on negatively regulated genes. Our data suggest that c-Myb is a transcription fac- tor with multifaceted target regulation depending on cell type.

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• Bengtsen, Mads (2022). Epigenetiske endringer ved bruk av anabole steroider. Full text in Research Archive
• Bengtsen, Mads (2022). How does testosterone induced hypertrophy affects the muscle epigenome. Full text in Research Archive
• Aders, Eirin; Nygård, Kamilla Børve; Bengtsen, Mads & Gundersen, Kristian (2021). Uncovering epigenetic mechanisms behind muscle memory. Full text in Research Archive
• Dyhre, Benjamin; Bengtsen, Mads; Nygård, Kamilla Børve; Millay, Douglas P. & Eftestøl, Einar (2021). How does a reduced myonuclear number affect epigenetic regulation of muscle function? Full text in Research Archive
• Bengtsen, Mads (2021). Anabolic steroid-induced alterations in the muscle epigenome. Full text in Research Archive
• Bengtsen, Mads; Winje, Ivan; Eftestøl, Einar; Domanska, Diana Ewa; Landskron, Johannes & Gundersen, Kristian (2019). The Epigenetic landscape of two phenotypic extreme skeletal muscles - soleus and EDL. Acta Physiologica. ISSN 1748-1708. doi: 10.1111/apha.13414. Full text in Research Archive
• Nygård, Kamilla; Juvkam, Inga; Bengtsen, Mads & Gundersen, Kristian (2019). NFATs regulatory potential and role in skeletal muscle during voluntary exercise. Acta Physiologica. ISSN 1748-1708. doi: 10.1111/apha.13414. Full text in Research Archive
• Bengtsen, Mads; Winje, Ivan; Landskron, Johannes; Meza-Zepeda, Leonardo A. & Gundersen, Kristian (2019). The Epigenetic landscape of two phenotypic extreme skeletal muscles. Full text in Research Archive
• Bengtsen, Mads; Winje, Ivan; Landskron, Johannes; Meza-Zepeda, Leonardi A & Gundersen, Kristian (2019). The Epigenetic landscape of two phenotypic extreme skeletal muscles. Full text in Research Archive
• Bengtsen, Mads; Winje, Ivan; Landskron, Johannes; Meza-Zepeda, Leonardo A. & Gundersen, Kristian (2018). The Epigenetic landscape of two phenotypic extreme skeletal muscles. Full text in Research Archive
• Bengtsen, Mads (2017). A model for studying epigenetics in muscles. Full text in Research Archive
• Sæther, Thomas; Bengtsen, Mads; Molværsmyr, Ann-Kristin; Pattabiraman, D.R.; Alm-Kristiansen, Anne Hege & Ledsaak, Marit [Show all 8 contributors for this article] (2012). Regulating the regulator: SUMO functions as a master switch for the transcription factor c-Myb. Full text in Research Archive Show summary

  The oncoprotein c-Myb is an essential hematopoietic transcription factor that controls proliferation and differentiation of progenitors during blood cell development. This transcriptional activator plays a direct role in lineage fate selection, cell cycle progression, and differentiation of myeloid as well as B- and T-lymphoid progenitors. Recent studies have shown that c-Myb accomplishes this by controlling the expression of several important hematopoietic transcriptions factors, and in that way acts as a master regulator. c-Myb is modified by SUMO on two lysines in its C-terminal regulatory domain (CRD), and is able to bind SUMO via a SUMO-interacting motif (SIM) in the central transactivation domain. Both these SUMO-contacts are important in regulating the transactivation activity of c-Myb, and breaking these contacts makes c-Myb super active. We have found that the ability of c-Myb to synergize with other transcription factors on compound promoters is restricted by synergy control, linked to the SUMOylation of CRD. De-SUMOylation of c-Myb leads to a dramatic change in synergy behavior, which correlates with a SUMO-dependent differential recruitment of p300 and a corresponding local change in histone H3 and H4 acetylation. Using cell-based transformation assays, we have addressed the abilities of c-Myb SUMO binding and conjugation mutants to transform hematopoietic cells. Interestingly, only loss of SUMO binding, and not SUMO conjugation, enhances the myeloid transformational potential of c-Myb. c-Myb with the SIM mutated confers a high proliferative ability and causes an effective differentiation block. This establishes SUMO binding as a mechanism responsible for keeping the transforming potential of the oncoprotein in check. Taken together this implies that SUMO functions as a master regulatory switch for c-Myb. Given that the SUMO-system may be perturbed in different cancers, c-Myb may be particularly vulnerable to such changes and thus mediate dramatic downstream effects.

• Bengtsen, Mads (2016). The Transcription Factor c-Myb - Investigation of its Genome-wide Occupancy and Activation Mechanisms. University of Oslo. Full text in Research Archive

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