Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana

The 3D genome is characterized by a complex organization made of genomic and epigenomic layers with profound implications on gene regulation and cell function. However, the understanding of the fundamental mechanisms driving the crosstalk between nuclear architecture and (epi)genomic information is still lacking. The plant Arabidopsis thaliana is a powerful model organism to address these questions owing to its compact genome for which we have a rich collection of microscopy, chromosome conformation capture (Hi-C) and ChIP-seq experiments. Using polymer modelling, we investigate the roles of nucleolus formation and epigenomics-driven interactions in shaping the 3D genome of A. thaliana. By validation of several predictions with published data, we demonstrate that self-attracting nucleolar organizing regions and repulsive constitutive heterochromatin are major mechanisms to regulate the organization of chromosomes. Simulations also suggest that interphase chromosomes maintain a partial structural memory of the V-shapes, typical of (sub)metacentric chromosomes in anaphase. Additionally, self-attraction between facultative heterochromatin regions facilitates the formation of Polycomb bodies hosting H3K27me3-enriched gene-clusters. Since nucleolus and heterochromatin are highly-conserved in eukaryotic cells, our findings pave the way for a comprehensive characterization of the generic principles that are likely to shape and regulate the 3D genome in many species.

Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana

ABSTRACTThe 3D genome is characterized by a complex organization made of genomic and epigenomic layers with profound implications on gene regulation and cell function. However, the understanding of the fundamental mechanisms driving the crosstalk between nuclear architecture and (epi)genomic information is still lacking. The plant Arabidopsis thaliana is a powerful model organism to address these questions owing to its compact genome for which we have a rich collection of microscopy, Chromosome Conformation Capture (Hi-C), and ChIP-seq experiments. Using polymer modelling, we investigate the roles of nucleolus formation and epigenomics-driven interactions in shaping the 3D genome of A. thaliana. By validation of several predictions with published data, we demonstrate that self-attracting nucleolar organizing regions and repulsive constitutive heterochromatin are major mechanisms to regulate the organization of chromosomes. Simulations also suggest that interphase chromosomes maintain a partial structural memory of the V-shapes, typical of (sub)metacentric chromosomes in anaphase. Additionally, self-attraction between facultative heterochromatin regions facilitates the formation of Polycomb bodies hosting H3K27me3-enriched gene-clusters. Since nucleolus and heterochromatin are highly-conserved in eukaryotic cells, our findings pave the way for a comprehensive characterization of the generic principles that are likely to shape and regulate the 3D genome in many species.

Cytogenetic characterization of Ameivula ocellifera (Spix, 1825) (Squamata, Teiidae) from the brazilian northeast

Ameivula is as a new genus of Teiidae family that emerged after extensive revision of species that comprised the former complex of species called Cnemidophorus group. Its species has a wide distribution from the northeast of Brazil to northern Argentina. Cytogenetic studies in the Teiidae family have shown that karyotypical data are important tools in phylogenetic and systematic studies within this group allowing to determine the position of species in the family. Thus, this study aimed to describe the karyotype of Ameivula ocellifera (Spix, 1825) from Picos, Piauí state in the Brazilian Northeast. Specimens were collected from August 2014 to October 2015 using interception traps and pitfalls, mounted randomly along the Caatinga area. The animals were collected and transported to Federal Institute of Piauí, campus Picos, where was carried out all laboratory procedures. Individuals analyzed showed a diploid number of 2n = 50 for both sexes, with karyotype composed by 30 macrochromosomes and 20 microchromosomes of telocentric and subtelocentric types. There were no heteromorphic sex chromosomes in the studied specimens. C-band technique evidenced the heterochromatic blocks in pericentromeric and telomeric regions of chromosomes. The nucleolar organizing regions appeared as a simple unit located at the terminal portion of the long arm of chromosomal pair number 5. The chromosomal characteristics of A. ocellifera analyzed do not show divergences regarding individuals from other regions. However, the nucleolar organizing regions seems to be a good chromosomal marker that permits to distinguish the species already studied.

Cytogenetic markers as tools in delimiting species of the highly diverse Neotropical fish Bryconamericus (Characiformes: Characidae)

ABSTRACT Bryconamericus is a highly diverse group of characid fishes, being cytogenetic a valuable tool for the delimitation of species. Bryconamericus aff. iheringii (Upper Uruguay/Lower Paraná), B. coeruleus (Upper Paraná), B. cf. ecai e B. cf. eigenmanni (Upper Uruguay) were studied cytogenetically, and presented 2n=52 chromosomes, with interpopulational/interspecific variation of karyotype and fundamental number. Heterochromatin was evidenced in pericentromeric, telomeric and interstitial regions, and it was shown to be an important cytogenetic marker. Single nucleolar organizing regions (NORs) were found in B. cf. eigenmanni, B. cf. ecai and B. aff. iheringii (Lower Paraná), and multiple in B. aff. iheringii (Upper Uruguay) and B. coeruleus, with occurrence of two patterns for the first species, and three for the second. The 5S/18S rDNA-FISH confirmed the location of the NORs and showed single 5S rDNA cistrons only in B. aff. iheringii (Lower Paraná), evidencing the dispersion of both genes, often co-located, in the karyotype of the others species. The data of this work contribute for the delimitation of the species of the genus. Co-localization of ribosomal genes may represent a plesiomorphic condition for the group, and their dispersion suggest the occurrence of duplication, pseudogeneization and transposition events mediated by mobile genetic elements.

Cytogenetic and molecular studies in conservation breeding of Pulawska breed pigs

The paper presents the genetic characteristics of Pulawska breed pigs carried out on the basis of cytogenetic and molecular studies. Among chromosome markers, polymorphic variants of specific chromosome structures such as centromeric heterochromatin areas (C bands) and nucleolar organizing regions (NOR bands) were taken into account. The described breed-specific tendencies concerning size polymorphism of these structures are the source of chromosome markers that are useful for identifying the linkage with genes controlling important production traits. On the other hand, molecular studies presented in this work included DNA markers of the STR and SNP type (with particular consideration of the PRL, FST, MC4R, TNNT3, MTTP and DIO3 genes), which are useful in determining the genetic background of functional traits, as well as the characteristics of the breeds for terms of genetic variation, especially conservative breeds, where it is appropriate to maintain the existing genetic diversity and intra-breed variability.