Mailand Group – University of Copenhagen

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CPR > Research > Protein Signaling > Mailand Group

Mailand group (Ubiquitin Signaling)

The Mailand group was established at CPR in 2009 and is headed by professor and group leader Niels Mailand.

In the Mailand group at CPR we aim to understand the cellular signaling processes that underpin and regulate the DNA damage response (DDR), a sophisticated network of pathways that protect the integrity of the genome after genotoxic insults, and which plays a central role in safeguarding cell and organism fitness. Although it is clear that the organization of the DDR is supremely complex and involves intricate, multi-layered regulatory mechanisms, we still have only a partial understanding of these processes, their wiring and coordination, as well as their biological ramifications. Hence, there is a need for new innovative approaches capable of systematically defining the scope and functions of the cellular processes that respond to DNA damage. Our principal strategy to meet these challenges is to take advantage of in-house expertise and facilities in proteomics and advanced cell imaging, through dedicated collaborations. Using these powerful technologies together with our long-standing experience in characterizing cellular signaling processes, we are well placed to identify and functionally dissect new factors and mechanisms that operate in cells to protect genome stability. We have also begun to analyze the biological functions of new DDR factors by means of approaches such as mouse knockout models and structural biology studies.

The ongoing projects in the lab fit broadly into the following research themes:

Systematic discovery and characterization of new factors in the DNA damage response  

We are applying innovative proteomics-driven strategies to comprehensively identify the factors recruited to different types of DNA lesions and the surrounding chromatin areas. Most recently, in collaboration with Prof. Matthias Mann (Max Planck Institute of Biochemistry, Munich, Germany) we developed and used a powerful new proteomics-based method termed CHROMASS, which allows for the first time systematic mapping of the dynamic protein landscape at sites of DNA damage. Using this method, we were able to comprehensively define the inventory of cellular proteins that function at DNA interstrand crosslinks (Raschle et al., Science 2015). We are thus able to obtain detailed systems-level views of how cells respond to various types of DNA damage, thereby allowing unique new insights into the nature and dynamics of the factors acting directly in the context of genotoxic insults. These surveys are revealing a range of new factors with important functions in the DNA damage response. For instance, we identified two new proteins, SLF1 and SLF2, which physically bridge RAD18 and the SMC5/6 complex, thereby promoting recruitment of the latter complex to DNA damage sites (Raschle et al., Science 2015). We are currently studying a range of additional new components identified in CHROMASS experiments, and which have important functions in cellular responses to DNA damage and replication stress. We are also applying CHROMASS to survey the composition of chromatin after other types of DNA lesions.

Figure 1: CHROMASS enables comprehensive identification of the proteins undergoing enrichment at chromatin in response to DNA damage or replication stress. This reveals new genome stability maintenance factors, such as SLF1 and SLF2, which physically link RAD18 and the SMC5/6 complex, thereby promoting SMC5/6 recruitment to damaged DNA (Raschle et al., Science 2015).

 

Exploration of ubiquitin-dependent signaling processes in the DNA damage response
Ubiquitin-dependent protein modification has been implicated as a key regulatory mechanism in many critical DNA damage signaling and repair pathways. However, systematic exploration of the scope and extent of this involvement has been lacking. We are studying global protein ubiquitylation dynamics on a site-specific level in response to different types of DNA damage. We published the first global survey of UV-regulated ubiquitylation changes in human cells (Povlsen et al., Nature Cell Biology 2012). This study, together with a range of related screens performed in the lab, has provided new and unprecedented insights into the proteome-wide dynamics of DNA damage-regulated ubiquitylation, revealing that genotoxic insults affect the ubiquitylation of a far broader range of proteins than had been previously appreciated. We are currently interrogating the functional roles of a series of other factors modified by DNA damage-regulated ubiquitylation that were identified in these screens.

We are particularly interested in ubiquitin-dependent responses to DNA double-strand breaks (DSBs), one of the most cytotoxic DNA lesions. We pioneered the discovery and characterization of the RNF8 and RNF168 E3 ubiquitin ligases, whose sequential actions promote recruitment of many DNA repair factors to DSB-surrounding chromatin areas (Mailand et al., Cell 2007; Doil et al., Cell 2009). We have also identified a number of factors that accumulate at DSB sites in an RNF8/RNF168-dependent manner (Bekker-Jensen et al., Nature Cell Biol 2010; Poulsen et al., J Cell Biol 2012; Raschle et al., Science 2015). Most recently, we discovered that histone H1 is a central target of RNF8, whose K63-linked polyubiquitylation after DNA damage generates a direct recruitment platform for RNF168, which subsequently amplifies DSB-induced chromatin ubiquitylation leading to recruitment of downstream repair factors (Thorslund et al., Nature 2015). These findings implicate, for the first time, post-translational modifications of H1 in the ‘histone code’ for DNA repair, the role of which we are now investigating in more detail.

  

Figure 2: RNF8 promotes UBC13-dependent K63-linked polyubiquitylation of H1-type linker histones, generating a recruitment platform for RNF168, which subsequently amplifies DSB-induced chromatin ubiquitylation leading to recruitment of downstream repair factors (Thorslund et al., Nature 2015).

Roles of ubiquitin-like modifier proteins in genome stability maintenance
In addition to ubiquitin, we are also interested in regulatory functions of ubiquitin-like modifier proteins (UBLs) in the DNA damage response and beyond. We have devoted considerable efforts to studying mechanisms of how SUMO-dependent signaling facilitates the DNA damage response, using approaches similar to those described above. For instance, we identified a new SUMO-targeted ubiquitin ligase (STUbL), RNF111, which functions in the DNA damage response (Poulsen et al., J Cell Biol 2013), and we have discovered an important regulatory role of SUMO-dependent signaling in the Fanconi anemia DNA repair pathway (Gibbs-Seymour et al., Mol Cell 2015). We have also characterized in detail how an atypical UBL, UBL5, promotes pre-mRNA splicing, cell proliferation, and the DNA damage response (Oka et al., EMBO Reports 2014; Oka et al., EMBO J 2015). Current efforts are aimed at further exploring the involvement of SUMO, as well as less well characterized UBLs, in regulation of genome maintenance pathways, using both systems-wide and focused studies as described above.

 

 

Figure 3: SUMO-dependent modification of the FANCI-FANCD2 complex promotes its turnover from DNA damage sites via the SUMO-targeted ubiquitin ligase RNF4 and the DVC1/p97 complex.

Research in the Mailand lab is funded by The Novo Nordisk Foundation, European Research Council (ERC), EMBO, Danish Council for Independent Research, The Danish Cancer Society, and The Lundbeck Foundation.

Available positions in the Mailand Group
For inquiries about available positions in the lab, please contact Prof. Niels Mailand (email: niels.mailand@cpr.ku.dk).

Selected recent publications:

Hoffmann S, Smedegaard S, Nakamura K, Mortuza GB, Raschle M, Ibanez de Opakua A, Oka Y, Feng Y, Blanco FJ, Mann M, Montoya G, Groth A, Bekker-Jensen S, Mailand N. (2016). TRAIP is a PCNA-binding ubiquitin ligase that protects genome stability after replication stress. J Cell Biol 212, 63-75.

Bekker-Jensen S, Mailand N. (2015). RNF138 joins the HR team. Nature Cell Biol 17, 1375-1377.

Thorslund T, Ripplinger A, Hoffmann S, Wild T, Uckelmann M, Villumsen B, Narita T, Sixma TK, Choudhary C, Bekker-Jensen S, Mailand N. (2015). Histone H1 couples initiation and amplification of ubiquitin signaling after DNA damage. Nature, 527, 389-393.

Tollenaere M, Villumsen B, Blasius M, Wagner SA, Borisova M, Bartek J, Choudhary C, Beli P, Mailand N, Bekker-Jensen S. (2015). p38-, MK2- and 14-3-3-dependent sequestration of CEP131/AZI1 promotes stress-induced remodeling of centriolar satellites. Nature Commun 6, 10075.

Raschle M, Smeenk G, Hansen RK, Temu T, Oka Y, Hein MY, Nagaraj N, Long DT, Walter JC, Hofmann K, Storchova Z, Bekker-Jensen S, Mailand N, Mann M. (2015). Proteomics reveals dynamic assembly of repair complexes during bypass of DNA crosslinks. Science 384, 1253671.

Oka Y, Bekker-Jensen S, Mailand N. (2015). Ubiquitin-like protein UBL5 is required for the functional integrity of the Fanconi anemia DNA repair pathway. EMBO J 34, 1385-1398.

Gibbs-Seymour I, Mailand N. (2015). SLX4: Not SIMply a nuclease scaffold? Mol Cell 57, 3-5.

Gibbs-Seymour I, Oka Y, Rajendra E, Weinert BT, Passmore LA, Patel KJ, Olsen JV, Choudhary C, Bekker-Jensen S, Mailand N. (2014). Ubiquitin-SUMO circuitry controls activated Fanconi Anemia ID complex dosage in response to DNA damage. Mol Cell 57, 150-164.

Oka Y, Varmark H, Vitting-Seerup K, Beli P, Waage J, Hakobyan A, Mistrik M, Choudhary C, Rohde M, Bekker-Jensen S, Mailand N. (2014). UBL5 is essential for pre-mRNA splicing and sister chromatid cohesion in human cells. EMBO Rep 15, 956-964.

Villumsen BH, Povlsen LK, Danielsen JR, Sylvestersen KB, Merdes A, Beli P, Yang Y, Choudhary C, Nielsen ML, Mailand N, Bekker-Jensen S. (2013). A new cell stress response that triggers centriolar satellite reorganization and ciliogenesis. EMBO J 32, 3029-3040.

Toledo L, Altmeyer M, Rask MB, Lukas C, Larsen DH, Povlsen LK, Bekker-Jensen S, Mailand N, , Bartek J, Lukas J. (2013). ATR prohibits replication catastrophe by preventing global exhaustion of RPA. Cell 155, 1088-1103.

Poulsen SL, Hansen RK, Wagner SA, Choudhary C, Bekker-Jensen S, Mailand N. (2013). RNF111/Arkadia is a SUMO-targeted ubiquitin ligase that facilitates the DNA damage response. J Cell Biol 201, 797-807.

Mosbech A, Lukas C, Bekker-Jensen S, Mailand N. (2013). USP44 counteracts the RNF8/RNF168-mediated response to DNA double-strand breaks. J Biol Chem 288, 16579-16587.

Mailand N, Gibbs-Seymour I, Bekker-Jensen S. (2013). Regulation of PCNA-protein interactions during replication of damaged DNA. Nature Rev Mol Cell Biol 14, 269-282.

Mosbech A, Gibbs-Seymour I, Kagias K, Thorslund T, Beli P, Povlsen LK, Nielsen SV, Smedegaard S, Sedgwick G, Lukas C, Petersen RH, Lukas J, Choudhary C, Pocock R, Bekker-Jensen S, Mailand N. (2012). DVC1 (C1orf124) is a DNA damage-targeting p97 adaptor that promotes ubiquitin-dependent responses to replication blocks. Nature Struct Mol Biol 19, 1084-1092.

Povlsen, LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C. (2012). Systems-wide analysis of ubiquitylation dynamics reveals a key role of PAF15 ubiquitylation in DNA damage bypass. Nature Cell Biol 14, 1089-1098.

 

Poulsen M, Lukas C, Lukas J, Bekker-Jensen S, Mailand N. (2012). Human RNF169 is a negative regulator of the ubiquitin-dependent response to DNA double-strand breaks. J Cell Biol 197, 189-199.

 

Danielsen JR, Povlsen LK, Villumsen BH, Streicher W, Nilsson J, Wikström M, Bekker-Jensen S, Mailand N. (2012). DNA damage-inducible SUMOylation of HERC2 promotes RNF8 binding via a novel SUMO-binding Zinc finger. J Cell Biol 197, 179-187.