The main goal of our research is to uncover evolutionary-conserved mechanisms contributing to organismal development, cell identity and differentiation. We are mainly interested in how chromatin factors regulate developmental programs and in deciphering the role of histone methylation in embryonic and postembryonic development. To achieve our aim, we use genetic and phenotypic analyses combined with biochemical approaches.
OUR MODEL SYSTEM: C.elegans
C. elegans is our favorite model system for several reasons. First, C. elegans is a multicellular organism and therefore provides an opportunity to study tissue- or organ-specific proteins without the complexity of higher eukaryotes. Second, it is a well-established system for genetic studies. Third, the C. elegans genome has been completely sequenced and additional information, such as the phenotypes associated to reduction (by RNAi) or loss of genes, is publicly available. Finally, in C. elegans gene families are often represented by single genes, allowing biological analyses in absence of functional redundancy.
We are mainly interested in neuronal development, germline development and its integrity after stresses. We identified several Histone Lysine demethylases and methyltransferases relevant for these processes.
Histone Lysine demethylases and Histone Lysine methyltransferases
Histone Lysine demethylases (KDMs) are enzymes removing methyl marks from the histone tails and they often contain a JmjC domain. In the past few years, we have uncovered the functions of a subset of histone demethylases. We are exploring the functions of these demethylases using genetic and biochemical approaches, including chromatin immunoprecipitation followed by deep sequencing and transcriptome analysis, with the aim to identify direct target genes. Similar projects regarding Histone Lysine methyltransferases (KMTs), enzymes that add a methyl group to the histone tails, have been more recently initiated.
C. elegans is an excellent system to study many aspects of neuronal development, including axon pathfinding and neuronal cell body migration.
In human aberrant histone lysine methylation has been linked to neurodevelopment diseases and several genes involved specifically in H3K4 methylation regulation are mutated in intellectual disorders. Our recent results indicate that KDM5/RBR-2 and KDM7/JMJD-1.2, involved in H3K4 regulation and recognition, respectively, controls axon migration by regulating actin remodeling and Hedgehog pathway.
We are currently analyzing other Histone Lysine regulators for axon pathfinding and we are testing the relevance of chromatin factors in neuronal cell body migration.
Figure 1. Axon pathfinding of PVQ neurons in wild-type animals and in a demethylase mutant. Aberrant migration of axon is observed in about 22% of mutant animals. From Mariani et al, 2016
Germline integrity after stress
With the aim to identify modulators of histone lysine methylation that play relevant roles in germline integrity, screens have been performed using a variety of stressors, including IR, UV and agents interfering with DNA replication. We recently discover a role for KDM8/JMJD-5, a regulator of H3K36me2, in germline protection after irradiation. Similarly, KDM7/JMJD-1.2, a regulator for H3K9/23/27me2, protects the embryo after DNA replication stress.
We are currently analyzing the role of Histone Lysine regulators in Germ cell fate and germline maintenance.
A) Loss of jmjd-5 increases the sensitivity to IR. B) Increased level of H3K36me2 in jmjd-5 mutant. C) Increased and persistent RAD-51 staining in jmjd-5 germ cells. From Amendola et al, 2017
Selected publications (Link to ORCID: 0000-0001-5828-2512)
JMJD-1.2 controls multiple histone post-translational modifications in germ cells and protects the genome from replication stress. Myers TR, Amendola PG, Lussi YC, Salcini AE. Sci Rep. 2018 Feb 28;8(1):3765. doi: 10.1038/s41598-018-21914-9. PMID:29491442
Proteomic Characterization of Caenorhabditis elegans Larval Development. Xia T, Horton ER, Salcini AE, Pocock R, Cox TR, Erler JT. Proteomics. 2018 Jan;18(2). doi:10.1002/pmic.201700238. Epub 2017 Dec 27. PMID:29178193
JMJD-5/KDM8 regulates H3K36me2 and is required for late steps of homologous recombination and genome integrity. Amendola PG, Zaghet N, Ramalho JJ, Vilstrup Johansen J, Boxem M, Salcini AE. PLoS Genet. 2017 Feb 16;13(2):e1006632. doi: 10.1371/journal.pgen.1006632. eCollection 2017 Feb. PMID:28207814
JMJD-1.2/PHF8 controls axon guidance by regulating Hedgehog-like signaling. Riveiro AR, Mariani L, Malmberg E, Amendola PG, Peltonen J, Wong G, Salcini AE. Development. 2017 Mar 1;144(5):856-865. doi: 10.1242/dev.142695. Epub 2017 Jan 26. PMID:28126843
Impaired removal of H3K4 methylation affects cell fate determination and gene transcription. Lussi YC, Mariani L, Friis C, Peltonen J, Myers TR, Krag C, Wong G, Salcini AE. Development. 2016 Aug 30. pii: dev.139139. PMID: 27578789
The H3K4me3/2 histone demethylase RBR-2 controls axon guidance by repressing the actin-remodeling gene wsp-1. Mariani L, Lussi YC, Vandamme J, Riveiro A, Salcini AE.
Development. 2016 Mar 1;143(5):851-63. doi: 10.1242/dev.132985. PMID: 26811384
Dynamic changes of histone H3 marks during Caenorhabditis elegans lifecycle revealed by middle-down proteomics. Sidoli S, Vandamme J, Salcini AE, Jensen ON. Proteomics. 2015 Oct 28. [Epub ahead of print]
H3K23me2 is a new heterochromatic mark in Caenorhabditis elegans. Vandamme J, Sidoli S, Mariani L, Friis C, Christensen J, Helin K, Jensen ON, Salcini AE. Nucleic Acids Res. 2015 Nov 16;43(20):9694-710. Epub 2015 Oct 17.
The C. elegans H3K27 Demethylase UTX-1 Is Essential for Normal Development, Independent of Its Enzymatic Activity. Vandamme J, Lettier G, Sidoli S, Di Schiavi E, Nørregaard Jensen O, Salcini AE (2012). PLoS Genet 8(5): e1002647.
A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation. Kleine-Kohlbrecher D, Christensen J, Vandamme J, Abarrategui I, Bak M, Tommerup N, Shi X, Gozani O, Rappsilber J, Salcini AE, Helin K. Mol Cell. 2010 Apr 23;38(2):165-78. Epub 2010 Mar 25.
C.elegans intersectin: a synaptic protein regulating neurotransmission. Rose S, Malabarba MG, Krag C., Schultz A, Tsushima H, Di Fiore PP, Salcini AE. (2007). Mol Biol Cell 18(12):5091-9.
UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Agger K, Cloos PA, Christensen J, Pasini D, Rose S, Rappsilber J, Issaeva I, Canaani E, Salcini AE, Helin K. (2007). Nature. 449(7163):731-4.
RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3. Christensen J, Agger K, Cloos PA, Pasini D, Rose S, Sennels L, Rappsilber J, Hansen KH, Salcini AE, Helin K. (2007). Cell. 128(6):1063-76.
TTP specifically regulates the internalization of the transferrin receptor. Tosoni D, Puri C, Confalonieri S, Salcini AE, De Camilli P, Tacchetti C, Di Fiore PP. (2005). Cell 123:875-88.
The Eps15 C. elegans homologue EHS-1 is implicated in synaptic vesicle recycling. 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).Nat Cell Biol 3:755-60.
Binding specificity and in vivo targets of the EH domain, a novel protein-protein interaction module. Salcini AE, Confalonieri S, Doria M, Santolini E, Tassi E, Minenkova O, Cesareni G, Pelicci PG, Di Fiore PP. (1997). Genes Dev 11:2239-49.