Invertebrate centromere genomics (CENGEN)

Datum početka projekta
01.10.2015.
Datum kraja projekta
30.09.2019.
Status
Aktivan
Kategorija projekta
Projekti Hrvatske zaklade za znanost
Ugovoreni iznos financiranja
997000 HRK

Project summary
Centromere is a domain essential for chromosomal segregation in cell divisions. Understanding its structure and function is of the highest importance in biology, and also crucial from biomedical point of view. Centromere identity involves both genomic and epigenetic mechanisms, favoring rapid co-evolution and species specificity of CenH3 and associated DNA sequences without impairing the function. Despite diversity in DNA sequences and sequence types, the most common centromeric DNA components in many animal and plant species are repetitive sequences such as satellite DNAs and transposable elements.

Complexity and variations make perception of centromere genomics still fragmental and worked out only in a few most common plant and animal model systems. The main goal of this research is to identify CenH3 and associated DNA sequences in order to explore genomics of differently organized centromeres: satellite DNA-rich, satellite DNA-poor and dispersed on holocentric chromosomes.

HRZZ14 Fig1

Model organisms
The research is focused on the three invertebrate model organisms:
1) the beetle Tribolium castaneum, having centromeres deeply embedded into the satDNA arrays of pericentromeric heterochromatin

Tribolium-Castaneum za upload

2) the root-knot nematode Meloidogyne incognita, possessing holocentric chromosomes

nematode za upload

3) the mollusk Crassostrea gigas, lacking abundant and uniformly distributed satDNAs (and/or heterochromatin) in centromeric regions.

david-nunuk-pacific-oyster

Methods

The research strategy combines CenH3 identification, chromatin immunoprecipitation (ChIP)-based assays using anti-CenH3 antibodies, fluorescence in situ hybridization (FISH), immunofluorescence in situ localization (IF) and the bioinformatics pipeline.

Fig 2

Equipment obtained during project implementation

Cytocentrifuge Shandon Cytospin4

Picture3

Selected publications

García-Souto D, Mravinac B, Šatović E, Plohl M, Moran P, Pasantes JJ (2017) Methylation profile of a satellite DNA constituting the intercalary G+C-rich heterochromatin of the cut trough shell Spisula subtruncata (Bivalvia, Mactridae). Scientific Reports 6930; 1-12 DOI:10.1038/s41598-017-07231-7

Šatović E, Vojvoda Zeljko T, Luchetti A, Mantovani B, Plohl M (2016) Adjacent sequences disclose potential for intra-genomic dispersal of satellite DNA repeats and suggest a complex network with transposable elements. BMC Genomics 17:997 DOI 10.1186/s12864-016-3347-1

Luchetti A, Šatović E, Mantovani B, Plohl M (2016) RUDI, a short interspersed element of the V-SINE superfamily widespread in molluscan genomes. Mol Genet Genomics 291:1419–1429. DOI 10.1007/s00438-016-1194-z

Pavlek M, Gelfand Y, Plohl M, Meštrović N (2015) Genome-wide analysis of tandem repeats in Tribolium castaneum genome reveals abundant and highly dynamic tandem repeat families with satellite DNA features in euchromatic chromosomal arms. DNA Research. 22:387–401. DOI: 10.1093/dnares/dsv021

Meštrović N, Mravinac B, Pavlek M, Vojvoda-Zeljko T, Šatović E, Plohl M (2015) Structural and functional liaisons between transposable elements and satellite DNAs. Chromosome Res. 23:583-596. DOI: 10.1007/s10577-015-9483-7.

Plohl M, Meštrović N, Mravinac B (2014) Centromere identity from the DNA point of view. Chromosoma, 123:313-325. DOI: 10.1007/s00412-014-0462-0

Šatović E, Plohl M (2013) Tandem repeat-containing MITEs in the clam Donax trunculus. Genome Biol Evol 5 (12): 2549-2559. DOI: 10.1093/gbe/evt202.

Meštrović N, Pavlek M, Car A, Castagnone-Sereno P, Abad P, Plohl M (2013) Conserved DNA motifs, including the CENP B box-like, are possible promoters of satellite DNA array rearrangements in nematodes. PLoS ONE 8(6): e67328.

Mravinac B, Meštrović N, Čavrak V, Plohl M (2011) TCAGG, an alternative telomeric sequence in insects. Chromosoma, 120:367-376.

Mravinac B, Plohl M. (2010) Parallelism in evolution of highly repetitive DNAs in sibling species. Mol Biol Evol, 27:1857-1867. DOI: 10.1093/molbev/msq068

Plohl M, Petrović V, Luchetti A, Ricci A, Šatović E, Passamonti M, Mantovani B. (2010) Long-term conservation vs. high sequence divergence: the case of an extraordinarily old satellite DNA in bivalve mollusks. Heredity 104:543-551. DOI:10.1038/hdy.2009.141

Meštrović, N., Plohl, M., Castagnone-Sereno, P. (2009) Relevance of satellite DNA genomic distribution in phylogenetic analysis: a case study with root-knot nematodes of the genusMeloidogyne. Mol. Phyl. Evol. 50, 204-208. DOI: 10.1016/j.ympev.2008.10.013

Plohl, M., Luchetti, A., Meštrović, N., Mantovani, B. (2008) Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric heterochromatin. Gene 409, 72-82

Meštrović N, Castagnone-Sereno P, Plohl M. (2006) Interplay of selective pressure and stochastic events directs evolution of the MEL 172 satellite DNA library in root-knot nematodes. Mol Biol Evol 23:2316-2325.

Meštrović, N., Plohl, M., Mravinac, B. and Ugarković, Đ. (1998) Evolution of satellite DNAs from the genus Palorus- experimental evidence for the "library" hypothesis. Mol. Biol. Evol. 15, 1062-1068

Positions available

PhD position open

 To find out more about opportunities in LSFH contact:  plohl@irb.hr

Funding
The project is funded by Croatian Science foundation http://www.hrzz.hr/default.aspx?id=47

logo-engleski za upload
Glavni istraživač / voditelj
Miroslav Plohl

Miroslav Plohl, prof. dr. sc.

znanstveni savjetnik Instituta "Ruđer Bošković"; naslovni redovni profesor Sveučilišta J. J. Strossmayer u Osijeku +385 1 456 1083

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