Biology subjects

Navratilova, P.

Publications and source records attributed to Navratilova, P..

8 recordsLinked to original sources

bioRxiv2026

Comparative epigenomics across the barley pangenome links structural variation to regulatory genome function

Structural variants (SVs) are abundant in plant genomes and influence agronomic traits, yet their regulatory interpretation remains challenging. Here, we combine pangenome-wide profiling of DNA methylation and chromatin accessibility across 20 barley genotypes, complemented by histone modification and chromatin interaction data in a subset of 10 genotypes. Comparative analysis of genotype-specific epigenomes reveals a globally conserved DNA methylation landscape across the barley pangenome alongside extensive regulatory variability at orthologous genes. We show that SVs do not broadly remodel global chromatin landscapes but instead act through context-dependent rewiring of local regulatory interactions. Despite this epigenomic stability, SVs may contribute to gene expression changes via chromatin contacts. Tissue-specific chromatin accessibility demonstrates that SV effects depend on developmental context. Integrating chromatin state variation with SVs at key vernalization genes explains epigenetic contributions to growth habit diversity. Together, these results provide a framework for interpreting the regulatory consequences of structural variation in crop genomes.

plant biology↗

bioRxiv2025

Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome

Regulation of transcription initiation is the ground level of modulating gene expression during plant development. This process relies on interactions between transcription factors and cis- regulatory elements (CREs), which become promising targets for crop bioengineering. To annotate CREs in the barley genome and understand mechanisms of distal regulation, we profiled several epigenetic features across three stages of barley embryo and leaves, and performed HiChIP to identify activating and repressive genomic interactions. Using machine learning, we integrated the data into seven chromatin states, predicting [~]77,000 CRE candidates, collectively representing 1.43% of the barley genome. Identified genomic interactions, often spanning multiple genes, linked thousands of CREs with their targets and revealed notably frequent promoter-promoter contacts. Using the LEA gene family as an example, we discuss possible roles of these interactions in transcription regulation. On the Vrn3 gene, we demonstrate the potential of our datasets to predict CREs for other developmental stages.

genomics↗

bioRxiv2024

Centromeric repeat diversity underlies non-Mendelian segregation pattern in hop (Humulus lupulus)

Aberrant meiosis in plants often leads to aneuploidy, genetic instability, and sterility. This can occur due to several factors, including chromosome misalignment, defective synapsis or environmental factors that may result in unusual genetic combinations in the offsprings. Unusual chromosome behavior during male meiosis in Humulus lupulus is linked to irregular chromosome segregation and genome instability. However, the origin of meiotic instability remains unclear. We analyzed the centromeric landscape of H. lupulus to determine its role in aberrant chromosomal segregation during cell division. Using a combination of bioinformatic, molecular and cytogenetic approaches, we identified new centromeric repeats and revealed two types of centromeric organizations. Cytogenetic localization on metaphase chromosomes confirmed the genomic distribution of major repeat arrays and revealed unique features that contribute to aberrant segregation. Two centromeric types are composed of the major repeats SaazCEN and SaazCRM1 which are further accompanied by chromosome-specific centromeric satellites, Saaz40, Saaz293, Saaz85, and HuluTR120. Chromosome 2 displays unbalanced segregation during the cell division, implicating an important role for its centromere structure in segregation patterns. Moreover, Saaz293 is a new marker for studying aneuploidy in hop. Our findings provide new insights on chromosome segregation in hop and highlight the diversity and complexity of the centromere organization in H. lupulus.

plant biology↗

bioRxiv2023

Extreme genome scrambling in cryptic Oikopleura dioica species

Genes are not randomly distributed throughout chromosomes. How gene order evolves and how selective constraints act to preserve or vary gene order, both at the macrosyntenic level of whole chromosomes or microsyntenic level of gene blocks, are central questions of evolutionary biology and genomics that remain largely unsolved. Here, after sequencing several genomes of the appendicularian tunicate Oikopleura dioica from different locations around the globe, we show an unprecedented amount of genome scrambling in animals with no obvious morphological differences, consistent with cryptic speciation. Our assemblies suggest that all members of this clade possess a common 3-chromosome karyotype, and that different species largely preserve gene content, despite the presence of thousands of rearrangements in gene order. The movements of genes are largely restricted to chromosome arms and sex-specific regions, which appear to be the primary unit of macrosynteny conservation, and examples of these within-arm movements can be seen in the Hox and Fgf gene families. Our approach employing whole-genome alignments demonstrates that segments containing protein-coding elements tend to be preserved at the microsyntenic scale, consistent with strong purifying selection, with appreciably less preservation of non-coding elements. Unexpectedly, scrambling did not preserve operon structure across species, suggesting an absence of selective pressure to maintain operon structure. As well, genome scrambling does not occur uniformly across all chromosomes, as short chromosome arms possess shorter genes, smaller operons, more breakpoints, and elevated dN/dS values compared to long chromosome arms. Estimation of divergence times among the cryptic O. dioica lineages yielded an estimated breakpoint accumulation rate of 6 to 25 breakpoints per megabase per million years, which is an order of magnitude higher than the rates for other ascidian tunicates or Drosophila species. Therefore, O. dioica appears to be an attractive animal system to unravel the mechanisms that underlie gene order and synteny conservation, as well as exploring the limits of genome scrambling without an apparent impact on phenotypic evolution.

genomics↗

bioRxiv2021

Prospects of telomere-to-telomere assembly in barley: analysis of sequence gaps in the MorexV3 reference genome

The first gapless, telomere-to-telomere (T2T) sequence assemblies of plant chromosomes were reported recently. However, sequence assemblies of most plant genomes remain fragmented. Only recent breakthroughs in accurate long-read sequencing have made it possible to achieve highly contiguous sequence assemblies with a few tens of contigs per chromosome, i.e. a number small enough to allow for a systematic inquiry into the causes of the remaining sequence gaps and the approaches and resources needed to close them. Here, we analyze sequence gaps in the current reference genome sequence of barley cv. Morex (MorexV3). Optical map and sequence raw data, complemented by ChIP-seq data for centromeric histone variant CENH3, were used to estimate the abundance of centromeric, ribosomal DNA and subtelomeric repeats in the barley genome. These estimates were compared with copy numbers in the MorexV3 pseudomolecule sequence. We found that almost all centromeric sequences and 45S ribosomal DNA repeat arrays were absent from the MorexV3 pseudomolecules and that the majority of sequence gaps can be attributed to assembly breakdown in long stretches of satellite repeats. However, missing sequences cannot fully account for the difference between assembly size and flow cytometric genome size estimates. We discuss the prospects of gap closure with ultra-long sequence reads.

genomics↗

bioRxiv2020

Anatomy and transcription dynamics of wheat ribosomal RNA loci revealed by optical mapping and RNA sequencing

Background and AimsThree out of four RNA components of ribosomes are encoded by 45S rDNA loci, whose transcripts are processed into 18S, 5.8S and 26S ribosomal RNAs. The loci are organized as long head-to-tail tandem arrays of nearly identical units spanning over several megabases of sequence. Due to this peculiar structure, the number of rRNA genes, their sequence composition and expression status remain unclear, especially in complex polyploid genomes harbouring multiple loci. Here we conducted a complex study to decipher structure and activity of both major and minor rRNA loci in hexaploid bread wheat (Triticum aestivum). MethodsWe employed an original, multi-omics approach, combining chromosome flow sorting and optical mapping with transcriptome and methylome sequencing. Key ResultsThe former two techniques enabled unbiased quantification of rDNA units in particular loci of the wheat genome. Total number of rRNA genes organized in tandem arrays was 4388, with 64.1, 31.4, 3.9 and 0.7% located in short arms of chromosomes 6B, 1B, 5D and 1A, respectively. At the expression level, only 1B and 6B loci contributed to transcription at roughly 2:1 ratio. The 1B:6B ratio varied among five analysed tissues (embryo, coleoptile, root tip, primary leaf, mature leaf), being the highest (2.64:1) in mature leaf and lowest (1.72:1) in coleoptile. Cytosine methylation was considerably higher in CHG contexts in the silenced 5D locus compared to the active 1B and 6B loci. ConclusionsA fine genomic organization and tissue-specific expression of rRNA loci were deciphered, for the first time, in a complex polyploid species. We documented various mechanisms of rRNA dosage control, including gene elimination and stable inactivation related to nucleolar subdominance of A and D-genome loci, and a subtle, developmentally regulated silencing of one of the major loci. The results are discussed in the context of wheat evolution and transcription regulation.

genomics↗

bioRxiv2018

Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR

In phylogenetically diverse organisms, the 5 ends of a subset of mRNAs are trans-spliced with a spliced leader (SL) RNA. The functions of SL trans-splicing, however, remain largely enigmatic. Here, we quantified translation genome-wide in the marine chordate, Oikopleura dioica, under inhibition of mTOR, a central growth regulator. Translation of trans-spliced TOP mRNAs was suppressed, showing that the SL sequence permits nutrient-dependent translational control of growth-related mRNAs. Under crowded, nutrient-limiting conditions, O. dioica continues to filter-feed, but arrests growth until favorable conditions return. Upon release from such conditions, initial recovery was independent of nutrient-responsive, trans-spliced genes, suggesting animal density sensing as a first trigger for resumption of development. Our results demonstrate a role for trans-splicing in the coordinated translational down-regulation of nutrient-responsive genes under limiting conditions.

genomics↗

bioRxiv2017

Distinct Core Promoter Codes Drive Transcription Initiation At Key Developmental Transitions In A Marine Chordate

Development is largely driven by transitions between transcriptional programs. The initiation of transcription at appropriate sites in the genome is a key component of this and yet few rules governing selection are known. Here, we used cap analysis of gene expression (CAGE) to generate bp-resolution maps of transcription start sites (TSSs) across the genome of Oikopleura dioica, a member of the closest living relatives to vertebrates. Our TSS maps revealed promoter features in common with vertebrates, as well as striking differences, and uncovered key roles for core promoter elements in the regulation of development. During spermatogenesis there is a genome-wide shift in mode of transcription initiation characterized by a novel core promoter element. This element was associated with > 70% of transcription in the testis, including the male-specific use of cryptic internal promoters within operons. In many cases this led to the exclusion of trans-splice sites, revealing a novel mechanism for regulating which mRNAs receive the spliced leader. During oogenesis the cell cycle regulator, E2F1, has been co-opted in regulating maternal transcription in endocycling nurse nuclei. In addition, maternal promoters lack the TATA-like element found in vertebrates and have broad, rather than sharp, architectures with ordered nucleosomes. Promoters of ribosomal protein genes lack the highly conserved TCT initiator. We also report an association between DNA methylation on transcribed gene bodies and the TATA-box, which indicates that this ancient promoter motif may play a role in selecting DNA for transcription-associated methylation in invertebrate genomes.

genomics↗