Topologically-associating domains: gene warehouses adapted to serve transcriptional regulation

Razin, Sergey V.; Гаврилов, А. В.; Vassetzky, Yegor S.; Ulianov, Sergey V.

doi:10.1080/21541264.2016.1181489

Cited by 19 publications

(17 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Gradual fixation of chromosome fusions may be linked to various selective pressures or to genetic drift [34,68,69]. It is also conceivable that the degree to which centric fusions are tolerated by the species' genome might be determined by specific properties linked to chromatin functional arrangement within the interphase nucleus, such as, e.g., elevated plasticity in the organization of chromosome territories, compartments, and topologically-associating domains [70][71][72][73][74][75][76]. It has been shown, for instance, that properly separated chromosome territories prevent the formation of inter-chromosomal fusions [77] and that changes in the architecture of the interphase genome may lead to severe consequences in gene expression [76].…”

Section: Discussionmentioning

confidence: 99%

Centric Fusions behind the Karyotype Evolution of Neotropical Nannostomus Pencilfishes (Characiforme, Lebiasinidae): First Insights from a Molecular Cytogenetic Perspective

Sember

Oliveira

Ráb

et al. 2020

Genes

View full text Add to dashboard Cite

Lebiasinidae is a Neotropical freshwater family widely distributed throughout South and Central America. Due to their often very small body size, Lebiasinidae species are cytogenetically challenging and hence largely underexplored. However, the available but limited karyotype data already suggested a high interspecific variability in the diploid chromosome number (2n), which is pronounced in the speciose genus Nannostomus, a popular taxon in ornamental fish trade due to its remarkable body coloration. Aiming to more deeply examine the karyotype diversification in Nannostomus, we combined conventional cytogenetics (Giemsa-staining and C-banding) with the chromosomal mapping of tandemly repeated 5S and 18S rDNA clusters and with interspecific comparative genomic hybridization (CGH) to investigate genomes of four representative Nannostomus species: N. beckfordi, N. eques, N. marginatus, and N. unifasciatus. Our data showed a remarkable variability in 2n, ranging from 2n = 22 in N. unifasciatus (karyotype composed exclusively of metacentrics/submetacentrics) to 2n = 44 in N. beckfordi (karyotype composed entirely of acrocentrics). On the other hand, patterns of 18S and 5S rDNA distribution in the analyzed karyotypes remained rather conservative, with only two 18S and two to four 5S rDNA sites. In view of the mostly unchanged number of chromosome arms (FN = 44) in all but one species (N. eques; FN = 36), and with respect to the current phylogenetic hypothesis, we propose Robertsonian translocations to be a significant contributor to the karyotype differentiation in (at least herein studied) Nannostomus species. Interspecific comparative genome hybridization (CGH) using whole genomic DNAs mapped against the chromosome background of N. beckfordi found a moderate divergence in the repetitive DNA content among the species’ genomes. Collectively, our data suggest that the karyotype differentiation in Nannostomus has been largely driven by major structural rearrangements, accompanied by only low to moderate dynamics of repetitive DNA at the sub-chromosomal level. Possible mechanisms and factors behind the elevated tolerance to such a rate of karyotype change in Nannostomus are discussed.

show abstract

Section: Discussionmentioning

confidence: 99%

Centric Fusions behind the Karyotype Evolution of Neotropical Nannostomus Pencilfishes (Characiforme, Lebiasinidae): First Insights from a Molecular Cytogenetic Perspective

Sember

Oliveira

Ráb

et al. 2020

Genes

View full text Add to dashboard Cite

show abstract

“…2), which are involved in genome compartmentalization and support the tissue-specific transcriptional regulation in all metazoa. 40,41 In the yeast, Saccharomyces cerevisiae, some chromosomal regions replicate at different times, 42,43 as well as in mammals and other eukaryotes. 37 In this perspective, it is possible to suggest that the B chromosome of A. scabripinnis studied, herein, exhibits chromatin accessible for transcription, particularly in the light bands corresponding with early replication.…”

Section: Discussionmentioning

confidence: 99%

Dynamics of Replication and Nuclear Localization of the B Chromosome in Kidney Tissue Cells in Astyanax scabripinnis (Teleostei: Characidae)

et al. 2020

View full text Add to dashboard Cite

B chromosomes are extra genomic compounds found in different taxonomic groups, including plants and animals. Obtaining patterns of resolutive chromosomal bands is necessary to understand the nuclear organization, variability and nature of B chromosome chromatin and possible transcriptional regions. In this study, we analyzed 35 Astyanax scabripinnis specimens sampled from Fazenda Lavrinha, a stream in the Paraíba do Sul river basin, Brazil. Through the incorporation of the thymidine analog 5¢-bromo-2¢-deoxyuridine (5-BrdU) in vivo, it was possible to recognize the replicating regions of the B chromosome at the beginning of the S phase, differentially characterized in relationship to the regions of late replication. In this perspective, it is possible to suggest that the B chromosome of this species possesses a territory and the chromatin accessible for transcription, especially in the light (i.e., early replicating) bands (p1.1; p1.3; and p2.1 and q1.1, q1.3, q2.1, and q2.2). The latereplicating regions are corresponding to the blocks of constitutive heterochromatin. They show a preferential accumulation of satellite DNA As51. By the use of the fluorochrome chromomycin A3 (CMA3), it was possible to identify GC-rich chromosomal regions, corresponding to late-replicating parts of genome, confirming the revealed data by the replication banding and C-banding. In addition, the analysis by confocal microscopy in kidney cells indicates the location of a peripheral anchorage of this chromosome in the nuclear lamina, reinforcing the idea of downregulation of the associated regions.

show abstract

“…Within this probabilistic model we observed a stark decline in phasing information within 10 Mb distance from the source SNV. This decline is likely due to the formation of highly interacting genomic regions and corresponding organisational chromatin structures such as self-interacting TADs (Mb scale) and higher order metaTADs which form depending on the transcriptional activity of the genomic region (Razin et al 2016;Fraser et al 2015;Ulianov et al 2016). Our proximity scaling model improves the haplotype reconstruction accuracy by not only assigning importance to variant relations based on the frequency of their observation, but also by taking genomic distances between variants into account.…”

Section: Discussionmentioning

confidence: 99%

GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data

Markowski

Kempfer

Kukalev

et al. 2020

Preprint

View full text Add to dashboard Cite

MotivationUnderstanding haplotype-specific regulatory mechanisms becomes increasingly important in genomics and medical research. Investigating differences in allele-specific gene expression, epigenetic changes and their causal variants greatly benefits from haplotype reconstruction or phasing of genetic variants, but direct evidence for the haplotype structure is difficult to obtain from standard short-read sequencing data. Chromatin conformation data obtained from 3C experiments allows inference of haplotypes because inter-chromosomal contacts are more frequent than homologous intra-chromosomal contacts, but these data suffer from technical biases owing to the digestion and ligation process of the 3C technique. Genome Architecture Mapping (GAM) is a novel digestion-and ligation-free method for the inference of chromatin conformation from nuclear cryosections. Due to its high resolution and independence of enzymatic digestion it is well-suited for haplotype reconstruction and for detecting haplotype-specific chromatin contacts. ResultsHere, we present GAMIBHEAR, a tool for accurate haplotype reconstruction from GAM data. GAMIBHEAR aggregates allelic co-observation frequencies across multiple nuclear slices and employs a GAM-specific probabilistic model of haplotype capture to optimise phasing accuracy. Using a hybrid mouse embryonic stem cell line with known haplotype structure as a benchmark dataset, we assess correctness and completeness of the reconstructed haplotypes, and demonstrate the power of GAM data and the accuracy of GAMIBHEAR to infer genome-wide haplotypes. Availability GAMIBHEAR is available as an R package under the open source GPL-2 license at https://bitbucket.org/schwarzlab/gamibhear Maintainer: julia.markowski@mdc-berlin.de

show abstract

Topologically-associating domains: gene warehouses adapted to serve transcriptional regulation

Abstract: Structural-functional domains have long been hypothesized to occur in eukaryotic chromosomes, but their existence still remains controversial. Here, we discuss the current state of studies of 3D genome folding and the relation of this folding to the functional organization of the genome.

Cited by 19 publications

References 38 publications

Centric Fusions behind the Karyotype Evolution of Neotropical Nannostomus Pencilfishes (Characiforme, Lebiasinidae): First Insights from a Molecular Cytogenetic Perspective

Centric Fusions behind the Karyotype Evolution of Neotropical Nannostomus Pencilfishes (Characiforme, Lebiasinidae): First Insights from a Molecular Cytogenetic Perspective

Dynamics of Replication and Nuclear Localization of the B Chromosome in Kidney Tissue Cells in Astyanax scabripinnis (Teleostei: Characidae)

GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data

Contact Info

Product

Resources

About