Laboratory for Structure and Function of Heterochromatin

Laboratory for Structure and Function of Heterochromatin

Our research is focused on satellite DNAs and other repetitive DNA sequences with the goal to understand their structure, evolutionary mechanisms, functionality and impact on genome dynamics and plasticity.

left right

Research interests

  1. Studies of sequence traits and evolution of satellite DNAs in closely related species of three distant invertebrate groups with different modes of reproduction and different centromeric organization
  2. Mapping and analyses of satellite DNA arrays at monocentric and holocentric chromosomes
  3. Study of organizational and mutational properties of satellite repeats at array borders and characterization of junction regions between families of repetitive sequences
  4. Satellite DNA-protein interactions in heterochromatin. Analysis of possible phasing of satellite monomers on nucleosomes as well as analysis of DNA-protein associations in centromere-specific nucleosomes
  5. Cytogenetics on monocentric/holocentric chromosomes

Objective

The main objective of the lab’s research is to understand origins and consequences of diversity of satellite DNAs, features, constraints imposed on and functional interactions in which satellite DNAs may contribute. Our interest is focused on satellite repeats in general, and in particular, on the structure and organization of repeats in centromeric as well as in telomeric areas.

Model organisms

In our research we use species from three distant groups of invertebrates. Selected model organisms have different modes of reproduction (sexual and parthenogenetic) and different organization of centromeres: the widespread satellite-rich regional centromeres (Insecta, Tenebrionidae), holocentric centromeres (Nematoda, Meloidogyne) and satellite-poor centromeres (Mollusca).

img164
Meloidogyne_incognita
donax trunculus

Goals

The approach based on comparative studies of satellite DNA/nucleosomal structure in species with different modes of reproduction and different centromeric organization offers information necessary to conclude about general principles of satellite DNA evolution and putative functional interactions in centromeres and in surrounding heterochromatin in general. Obtaining a more complete picture of heterochromatin serves as a crucial platform for unraveling organizational principles, function and evolution of eukaryotic genomes.

Selected papers

  • 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 shellSpisula 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

Brankica Mravinac
PhD

Research Associate
+385 1 457 1273
1603

Eva Šatović
dr.sc.

Postdoctoral Research Assistant
+385 1 457 1322
1828

Martina Pavlek

Doctoral student, assistant
1828

Miroslav Plohl
Professor dr. sc.

Senior Researcher
+385 1 456 1083
1613

Nevenka Meštrović Radan
dr. sc.

Associated Researcher
+385 1 457 1273
1603 1445

Invertebrate centromere genomics (CENGEN)

Glavni istraživač / voditelj: Miroslav Plohl

The main goal of this project is to identify CenH3 and CenH3-associated DNA sequences as well as their non-functional counterparts in order to explore genomics of differently organized centromeres: satellite DNA-rich, satellite DNA-poor and dispersed on holocentric chromosomes.

more »