Salcini Group – University of Copenhagen

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Salcini Group

The aim of our research is to understand how chromatin factors regulate developmental programs. We are mainly interested to decipher how histone methylation control transcription during embryonic and postembryonic development.

OUR MODEL SYSTEM: C.ELEGANS
C.elegans is our favorite model system for several reasons. First, the organism has the advantage of a multicellular organism without the complexity of higher eukaryotes. The fact that C.elegans is a multicellular organism provides an opportunity to study tissue- or organ-specific proteins. Second, it is an appropriate system for genetic studies. Third, the C.elegans genome has been completely sequenced and other additional information such as the phenotypes of RNA interference (RNAi) of each gene (even with some limitation of the analysis) or that of some mutants is publicly available. Finally, in C. elegans gene families existing in higher eukaryotes are often represented by single genes, allowing a more suitable study in absence of functional redundancy.

 

Figure: C. Elegans 

CHROMATIN REMODELLING FACTORS IN C.ELEGANS DEVELOPMENT
In the nuclei of all eukaryotic cells, genomic DNA is tightly wrapped around histone complexes into a compacted structure called chromatin. Each histone complex is an octamer consisting of two copies of each of the histone core proteins H2A, H2B, H3 and H4. The N-terminal tails of these histones protrude from the octameric structure and are subject to a vast variety of post-translational modifications. These modifications remodel the structure of chromatin and represent a combinatorial "histone code" specifying the function of genomic regions in terms of chromosome segregation, DNA repair and transcriptional activity. 

Figure: Defects in gonad migration (top) and gonad development (bottom) in JMJD3 mutant, lacking a H3K27me3 demethylase activity 

Methylation of lysines (K) on histone tails
Trimethylated K4, K36 and K79 on histone H3 generally mark actively transcribed regions, whereas trimethylated K9 and K27 on histone H3 and K20 on histone H4 mark regions of transcriptionally silenced gene. To date, more than 20 Histone Methyl Transferases (HMTs) have been characterised and shown to play key roles in the regulation of development, differentiation, cell fates and in cancer. HOX genes, whose expression is established during body formation by early signalling events, represent a good example of this regulation.

Until recently, methylation was considered to constitute a permanent and irreversible histone modification. However, the recent discovery of histone demethylases has challenged this view. The largest group of histone demethylases contains a Jumonji (Jmj)C-domain, which catalyzes demethylation of specific methyl-lysine residues on histone H3.

Since methylation state of histone is an important clue during development, C.elegans is a suitable model system to study the in vivo roles of these demethylases, largely conserved in nematode. Characterization of mutant alleles carrying mutations in demethylases genes and microarray analysis identifying target genes will provide important contribution in understanding the roles of histone demethylases in a variety of processes such as embryonic and larval development, cell-fate decisions and organogenesis.

The levels of lysine methylation are modulated by the action of histone demethylases and histone methyltransferases. 

Histone Lysine demethylases:
They are enzymes removing methyl marks from the histone tails and they often contain a JmjC domain. We are investigating the role of several histone demethylases using C.elegans as model system. In the past few years, we have uncover the functions of a subset of histone demethylases (Christensen et al 2007, Agger et al, 2007, Vandamme et al, 2012, Kleine-Kohbrecher et al, 2010).  We are further exploring the functions of these demethylases using classical genetic approaches and biochemical approaches, including chromatin immunprecipitation followed by deep sequencing with the aim to identify direct target genes. We are additionally expanding our analysis to other uncharacterized demethylases.

Histone methyl transferases:
A new project regarding histone methylatransferases, enzymes that add a methyl group to the histone tails, has been recently initiated in collaboration with the groups of Kristian Helin, Anja Groth, Klaus Hansen and Ole Nørregaard Jensen and supported by the Danish National Research Foundation. In this project we aim to uncover the role of histone methyltransferases during postembryonic development and stress responses.

Selected recent publications

Vandamme J, Salcini AE. (2012) Catalytic-independent roles of UTX-1 in C. elegans development. Worm 2:2, 1-5; April/May/June 2013.

Vandamme J, Lettier G, Sidoli S, Di Schiavi E, Nørregaard Jensen O, Salcini AE. (2012) The C. elegans H3K27 Demethylase UTX-1 Is Essential for Normal Development, Independent of Its Enzymatic Activity. PLoS Genet 8(5): e1002647.

Krag C, Malmberg EK, Salcini AE. PI3KC2{alpha}, a class II PI3K, is required
for dynamin-independent internalization pathways. J Cell Sci. 2010 Nov 16. [Epub
ahead of print]

Kleine-Kohlbrecher D, Christensen J, Vandamme J, Abarrategui I, Bak M,
Tommerup N, Shi X, Gozani O, Rappsilber J, Salcini AE, Helin K. A functional link
between the histone demethylase PHF8 and the transcription factor ZNF711 in
X-linked mental retardation. Mol Cell. 2010 Apr 23;38(2):165-78. Epub 2010 Mar
25.

Rose S., Malabarba MG., Krag C., Schultz A., Tsushima H., Di Fiore PP., Salcini AE. (2007). C.elegans intersectin: a synaptic protein regulating neurotransmission. Mol Biol Cell 18(12):5091-9

Agger K, Cloos PA, Christensen J, Pasini D, Rose S, Rappsilber J, Issaeva I, Canaani E, Salcini AE, Helin K. (2007). UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature. 449(7163):731-4.

Christensen J, Agger K, Cloos PA, Pasini D, Rose S, Sennels L, Rappsilber J, Hansen KH, Salcini AE, Helin K. (2007). RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3. Cell. 128(6):1063-76. 

Tosoni D, Puri C, Confalonieri S, Salcini AE, De Camilli P, Tacchetti C, Di Fiore PP. (2005). TTP specifically regulates the internalization of the transferrin receptor. Cell 123:875-88.

Polo S, Confalonieri S, Salcini AE, Di Fiore PP. (2003). EH and UIM: endocytosis and more. Sci STKE 2003(213):re17.

Salcini AE, Hilliard MA, Croce A, Arbucci S, Luzzi P, Tacchetti C, Daniell L, De Camilli P, Pelicci PG, Di Fiore PP, Bazzicalupo P. (2001). The Eps15 C. elegans homologue EHS-1 is implicated in synaptic vesicle recycling. Nat Cell Biol 3:755-60.

Salcini AE, Confalonieri S, Doria M, Santolini E, Tassi E, Minenkova O, Cesareni G, Pelicci PG, Di Fiore PP. (1997). Binding specificity and in vivo targets of the EH domain, a novel protein-protein interaction module. Genes Dev 11:2239-49.

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