Genomic Organization Research Articles

Genomes are compartmentalized in mosaics of fairly homogeneous stretches of DNA with distinct average GC levels. These regions, termed isochores, show differences in gene composition and expression patterns, DNA methylation abundance and overall chromatin structure, and were thereby proposed to provide an ancient level of genome organization. Sequencing of the Trypanosoma cruzi genome revealed two main isochoric regions: a GC-poor "core" compartment, displaying synteny with those of phylogenetically related organisms and a GC-rich "disruptive" compartment, comprising repetitive sequences and gene families involved in the parasite-host interplay. Despite their potential relevance, several limitations preclude the precise distinction of both compartments on the parasite genome, which is currently based on the presence/absence of diagnostic gene markers. Here we present GCanner, an interactive tool for genome-wide GC composition analysis. When applied to T. cruzi, it allowed for the accurate and unbiased identification of the "core" and "disruptive" compartments. Seamless integration of isochoric data with efficient genomic mapping and compartmental distribution of genes of interest provides novel insights into parasite genome organization and facilitates structural and functional genomic analyses.

Chromatin plays essential roles in all nuclear processes, and the dynamic regulation of its accessibility is critical for orchestrating gene expression programs. Chromosome conformation capture (Hi-C) combines chromosome conformation capture (3C) techniques with next-generation sequencing (NGS) to map physical interactions between distant chromatin regions, enabling genome-wide analysis of three-dimensional genome architecture. We previously conducted the first Hi-C analysis of Trypanosoma cruzi to explore its spatial genome organization and its potential role in gene expression regulation. This chapter describes the experimental procedures for preparing 3C and Hi-C libraries and computational tools for data analysis.

Hybridisation is a powerful evolutionary force that can lead to diverse reproductive outcomes, including the emergence of asexual lineages such as hybridogenesis. During hybridogenesis, found in water frog hybrids Pelophylax esculentus, one parental genome is eliminated during gametogenesis while the other is clonally propagated to the gametes. Although this reproductive mode allowed hybrids to spread across Europe, the ability to undergo hybridogenesis varies in hybrids throughout their range. To explain this gametogenic variability, we investigated the role of genomic introgression. Using cytogenetic analysis, we examined gametogenesis in diploid and triploid hybrid males from four eastern Ukrainian population systems, known for high hybrid abundance and diverse gametogenic pathways. Most hybrids from the studied localities showed canonical hybridogenetic reproduction, characterised by the expected hybrid genome composition and no detectable intergenomic rearrangements or introgressions. We also identified hybrids with disrupted or absent genome elimination, which were incapable of hybridogenetic reproduction and exhibited reduced fertility and aneuploid gamete formation. These individuals exhibited intergenomic rearrangements, with chromosomal regions showing interchanges of parental chromosomes. Additionally, some chromosomal fragments did not match either parental genome, suggesting introgression from an unidentified lineage. Notably, half of the triploid hybrids had rearranged chromosomes, likely originating from diploid hybrids that failed parental genome elimination and transmitted diploid gametes. Our study reveals that hybridogenesis in P.esculentus is not a conserved mechanism but rather significantly relies on the genomic background. These findings highlight the role of genomic introgression in shaping reproductive diversity and influencing the evolution and persistence of asexual vertebrates.

Bibio Geoffroy, 1762 is a species-rich genus within the family Bibionidae. In this study, we present the complete mitochondrial genome of Bibio hordeiphagus Yang and Luo 1988 for the first time. Complete mitochondrial genome of B. hordeiphagus is 15,496 bp in length, comprising 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. The nucleotide composition of mitochondrial genome of B. hordeiphagus was 40.55% of A, 39.02% of T, 8.37% of G, and 12.05% of C. Based on the sequencing and annotating results, we conducted a preliminary phylogenetic analysis of Bibionomorpha. Our findings support the monophyly of both family Bibionidae and genus Bibio, with the family Bibionidae identified as the sister group to Sciaridae and Mycetophilidae. This study encompasses all reliable annotated mitochondrial genome data for Bibionidae and analyzed the higher-level phylogenetic relationships within the Bibionomorpha from the perspective of mitochondrial genome data.

Hybridization and polyploidization are key evolutionary forces shaping fish biodiversity. But their interaction with environmental factors, such as temperature, remains poorly understood. This study examined how maternal genome composition and incubation water temperature influence the hatching success, ploidy structure, morphology and early growth of polyploid Cobitis larvae. Crosses were performed using triploid Cobitis females with three genomic compositions (EEN, EET and ETN), representing combinations of genomes from C. elongatoides (E), C. taenia (T) and C. tanaitica (N), and diploid C. taenia males as sperm donors. Fertilized eggs were incubated at 18 °C, 22 °C and 28 °C. Triploid and tetraploid offspring occurred in comparable proportions on average across all groups, but developmental abnormalities were significantly more observed in tetraploid larvae. Females with EET and ETN genomes achieved higher hatching success than those with the EEN genome. Temperature had a pronounced effect on developmental timing and success: hatching occurred earliest at 28 °C, but survival decreased and abnormalities were most frequent. These results highlight genome- and temperature-dependent trade-offs in early development of Cobitis hybrids, providing new insight into reproductive dynamics and the potential resilience of polyploid systems under climate warming.

Background/Objectives: Satellite DNAs (satDNAs) are tandemly repeated sequences that play essential roles in chromosome structure, genome organization, and evolution. Despite their importance, the satellitome (the complete collection of satDNAs) of most avian lineages remains unexplored. We sought to describe the repeatome of three trogonid species, Trogon surrucura, T. melanurus, and Apaloderma vittatum with a focus on the satellitome to evaluate the general features of this lineage. Methods: Herein, we provide the first comparative characterization of the repeatome, with a particular focus on the comparative characterization of satDNAs in three trogonid species: T. surrucura, T. melanurus, and A. vittatum. Using a combination of bioinformatic pipelines and cytogenetic approaches. Results: We identified 16 satDNA families in T. surrucura, 15 in T. melanurus, and only 3 in A. vittatum. Sequence comparisons revealed that five families are shared between the two Trogon species, consistent with the library hypothesis, whereas no satDNAs were shared with A. vittatum. While both Trogon species exhibited a predominance of GC-rich repeats, A. vittatum represents the first bird described with a satellitome dominated by AT-rich satDNAs. In situ mapping in T. surrucura revealed chromosome-specific satDNAs restricted to pairs 1 and 2 and a Z-specific repeat that was strongly accumulated on its long arms, an atypical feature among birds. Conversely, the W chromosome showed a surprisingly low number of satDNAs, limited to centromeric signals. Conclusions: Our results reveal highly divergent satellitome landscapes among trogonids, characterized by lineage-specific differences in repeat composition, abundance, and chromosomal distribution. These findings support the view that satDNAs are dynamic genomic elements, whose amplification, loss, and chromosomal redistribution can influence genome architecture and play a role in avian speciation.

Evolutionary insights from the pangenome and pigment profiles of Parasynechococcus.

Unveiling the regulatory potential of the non-coding genome: Insights from the human genome project to precision medicine.

Human coronaviruses (HCoVs), composed of the viruses causing severe acute respiratory illness described as the syndromes resulting from infection with respiratory coronaviruses (e.g., human immunodeficiency viruses (HIVs), whose incubation period averages 7 to 15 days and 1 to 6 months, respectively) and the newly emerged ones (e.g., human respiratory herpesvirus 6). The spread of new variants over a short period of time requires urgent and effective therapeutic strategies..This review discusses the potential of nano-chitosan biopolymeric nanoparticles as a promising therapy for combating SARS-CoV-2 and related viruses. The study examined the structural features, genome organization, and pathogenesis of the viral strains causing the current pandemic-SARS-CoV, MERS-CoV, and most recently, the viruses responsible for the current "coronavirus" syndication, namely, the newly discovered coronavirus - known as the "SAR-corona subgroup, viral genome organization, pathogenesis, and host/virus away within the SAR Coronavirus family. The role of nano-chitosan as an anti-viral agent and as a drug delivery enhancer for improved-drug bioavailability and targeted therapy is also reviewed in the context. Nano-chitosan shows a strong antiviral effect on HCoVs via enhancing drug solubility and bioavailability. Its capacity as a carrier able to transport antiviral agents, and in vaccine delivery, diagnostics, as well as in the field of therapeutic applications, is an important advance in nanomedicine. Nano-chitosan is a potential candidate for the future pandemic of coronavirus. The incorporation of nano-chitosan into therapeutic approaches may improve existing therapies as well as contribute to more effective control of viral outbreaks. Future

This article provides a comprehensive analysis of Virus-Induced Gene Silencing (VIGS), which is an effective tool for studying the functional genomics of organisms that are poorly amenable to genomic editing. The VIGS method is grounded in the plant’s post-transcriptional gene silencing (PTGS) machinery and utilizes recombinant viral vectors to trigger systemic suppression of endogenous plant gene expression, leading to visible phenotypic changes that enable gene function characterization. This article details the application of VIGS in model organisms (Arabidopsis thaliana, Nicotiana benthamiana) and a wide range of crops, with a special focus on the Solanaceae family, particularly pepper (Capsicum annuum L.). This review analyzes the design and structural elements of viral vectors used for VIGS, such as Tobacco Rattle Virus (TRV), Broad Bean Wilt Virus 2 (BBWV2), Cucumber Mosaic Virus (CMV), geminiviruses (CLCrV, ACMV), and satellite virus-based systems. It also critically examines the key factors that determine silencing efficiency. These factors encompass insert design, agroinfiltration methodology, plant developmental stage, agroinoculum concentration, plant genotype, and environmental factors (temperature, humidity, photoperiod). Particular attention is given to optimization strategies, such as the use of viral suppressors of RNA silencing (VSRs). This article concludes with the achievements in using VIGS to identify pepper genes governing fruit quality (color, biochemical composition, pungency), resistance to biotic (bacteria, oomycetes, insects) and abiotic (temperature, salt, osmotic stress) factors, as well as genes regulating plant architecture and development. The results obtained demonstrate the advantages and limitations of VIGS, alongside future perspectives for its integration with multi-omics technologies to accelerate breeding and advance functional genomics studies in pepper.

The human genome attains an amazing spatial organization in the packaging of 2 m of DNA into a 10-μm nucleus. Such structural organization is achieved by the folding of chromatin and the regulation exerted by architectural proteins such as insulators. Chromatin insulators are boundary elements of the genome that, through enhancing blocking activities, demarcation of chromatin domains, and chromatin looping, regulate transcription. The review focuses on the identification and characterization of insulators in various species, discussing mainly the functions of the CCCTC-binding factor (CTCF) in mammals and functionally equivalent insulator proteins in Drosophila melanogaster. We review here the mechanisms of enhancer blocking, barrier activity, and loop extrusion, emphasizing their effects on topologically associating domains and chromatin architecture. Furthermore, we discuss new concepts that have come into prominence: tethering elements and redundancy among the insulator proteins, which contribute to chromatin organization. Advances in methodology, including chromosome conformation capture and high-resolution imaging techniques, have transformed our view of the dynamic interplay between the architecture of chromatin and transcription regulation. This review discusses the importance of insulators for genome organization and describes future directions in investigating their roles in both gene regulation and three-dimensional genomic architecture.

Cells rapidly and extensively remodel their transcriptome in response to stress to restore homeostasis, but the underlying mechanisms are not fully understood. Here, we characterize the dynamic changes in transcriptome, epigenetics, and 3D genome organization during the integrated stress response (ISR). ISR induction triggers widespread transcriptional changes within 6 h, coinciding with increased binding of ATF4, a key transcriptional effector. Notably, ATF4 binds to hundreds of genes even under non-stress conditions, priming them for stronger activation upon stress. The transcriptional changes at ATF4-bound sites during ISR do not rely on increased H3K27 acetylation, chromatin accessibility, or rewired enhancer-promoter looping. Instead, ATF4-mediated gene activation is linked to the redistribution of CEBPγ from non-ATF4 sites to a subset of ATF4-bound regions, likely by forming an ATF4/CEBPγ heterodimer. CEBPγ preferentially targets the sites pre-occupied by ATF4, as well as genomic regions exhibiting a unique higher-order chromatin structure signature. Thus, the transcriptional responses during ISR are largely pre-wired by intrinsic chromatin properties. These findings provide critical insights into transcriptional remodeling during ISR with broader implications for other stress responses.

The genus Aegilops L. is the closest wild relative of wheat ( Triticum L.), which contributed two of the three genomes to cultivated wheat. The genus Aegilops comprises 23 species differing in ploidy level and genome composition; diploid species possess the C, D, M, N, S, and U genome types, whereas various genome combinations are identified in tetraploid and hexaploid forms. The U genome is present in diploid Ae. umbellulata and eight polyploid species [ Ae. triuncialis , Ae. biuncialis , Ae. geniculata , Ae. peregrina , Ae. kotschyi , Ae. columnaris , Ae. neglecta (4× and 6×), and Ae. juvenalis ]. Some of these species have a wide distribution range, resulting in high adaptive capacity to various environmental conditions, and can serve as a valuable source of genetic diversity and useful genes for wheat breeding. The U genome is substantially rearranged relative to the genomes of common wheat, which hampers the direct transfer of useful traits from Aegilops to wheat. However, many genes conferring resistance to leaf rust ( Lr9 , Lr76 , Lr57 , Lr54 , Lr59 , Lr58 ), stripe rust ( Yr70 , Yr40 , Yr37 , Yr42 ), stem rust ( Sr53 ), nematodes ( CreX , CreY , Cre7 ), and various abiotic stresses have been successfully introgressed from Aegilops into the wheat genome. In this review, we describe the status of the contribution of Aegilops species carrying the U genome to wheat improvement, the methods used by different scientific teams to transfer genetic material, and the future prospective of exploitation of their useful traits in practical breeding.

BackgroundIn several contexts involving large collections of sets of biological sequences, a relevant problem is that of selecting significant groups of k-mers that characterize one set with regards to the others in the same collection.ResultsHere a software framework is proposed implementing a novel methodology for the extraction of k-mer dictionaries, from multiple sets of biological sequences. It has been implemented according to the most recent technologies for Big Data analytics, with the perspective of allowing its usage with a variety of input datasets of any size. In particular, two different packages are provided. The first is BioFt, enabling the extraction of recurrent patterns based on k-mers frequency and the computation of other metrics from information retrieval, here specialized for biological sequences. The second package BioSet2Vec, instead, extends the functionality of BioFt by allowing the creation of dictionaries according to different criteria.ConclusionsThe framework has been validated on three different case studies: (1) the characterization of different chromatin states; (2) the study of association between different diseases and related genes; (3) the analysis of genomes of different organisms. All tests performed on the considered datasets have shown the potentialities of the proposed approach.

Mammalian genomes are organized into distinct chromatin structures, which include small-scale nucleosome arrays and large-scale topologically associating domains (TADs). The mechanistic interplay between chromatin structures across scales is poorly understood. Here, we investigate how changes in nucleosome organization impact TAD structure by studying the role of the histone chaperone facilitates chromatin transcription (FACT) in 3D genome organization. We show that FACT depletion perturbs TADs, causing decreased insulation and weaker CTCF loops. These changes in TAD structure cannot be attributed to changes in chromatin occupancy of CTCF or cohesin and occur specifically in transcribed regions of the genome, where we observe perturbed nucleosome organization in the absence of FACT. FACT depletion therefore allows us to separate the role of nucleosome organization and CTCF binding and to demonstrate that the organization of nucleosomes at TAD boundaries contributes to TAD formation.

Introduction Equine abortus salmonellosis, caused by Salmonella abortus equi ( S. abortus equi ), is a contagious disease primarily characterized by abortion in pregnant equine animals. Due to its high pathogenicity and increasing incidence, this disease has attracted significant scientific attention. While the causes of abortion in mares are multifactorial and may involve numerous pathogenic factors, the specific impact of S. abortus equi on the vaginal microecological environment and its pivotal role as the primary causative agent of abortion remain poorly understood. Results Further analysis led to the successful isolation and identification of S. abortus equi from vaginal samples of aborted mares. A highly pathogenic isolate, designated as XJ2032, was selected for further analysis. To gain a more profound understanding of the functional genomic composition and genetic traits of this strain, whole-genome sequencing was conducted, and sophisticated bioinformatics techniques were employed to predict and annotate its gene sequences. Furthermore, animal model experiments, and PCR-based molecular biological detection methods were utilized to assess the virulence and drug resistance genes of the isolated strain XJ2032, further confirming its pathogenic potential. Conclusion Whole-genome sequencing analysis confirmed that strain XJ2032 is indeed S. abortus equi . Although its genome structure is largely conserved, some rearrangements and inversions were identified. The strain harbors multiple virulence genes and drug resistance genes, including horizontally transferable genes and mobile genetic elements. These findings suggest that genomic islands and bacteriophages play a vital role in the pathogenicity and genetic diversity of S. abortus equi .

Genome organization is reproducible and linked to gene expression, but the forces shaping it remain poorly understood. This hypothesis proposes that chromatin positioning is directed by a weak radial electric field generated by the nuclear membrane potential. Although classical models predict rapid charge screening, the confined and viscous nuclear interior, regulated by ion pumps, limits this process and allows a residual field to persist. This field biases the movement of charged macromolecules within the gel-like nucleoplasm, similar to electrophoresis. DNA is uniformly negative, but chromatin charge varies. GC-rich regions bind more nucleosomes and are less negative, drawing them inward with positively charged nuclear speckles, hubs of gene expression. Epigenetic modifications further modulate chromatin charge, producinga self-organized, dynamic radial architecture that regulates transcription. This framework connects the noncoding genome to expression and helps explain variable disease penetrance. Its testable predictions open new avenues for deciphering the logic of genome regulation.

Diseases caused by Begomovirus are a severe obstacle for dicotyledonous plants worldwide. In Bihar, a northern Indian state, we have been seeing indicators of stunting and chlorosis in lentil plants, with an incidence of 2.90%. Based on the series of tests between 2021 and 2024, the suspected organism was determined to be Begomovirus. After restriction digestion, HindIII and BglI, the RCA of three DNA samples revealed a linearized DNA of about ~ 2.7kb. With a genomic organization consisting of two ORFs in virion-sense and five ORFs in complementary sense separated by IR region, the associated virus was discovered to have 2746 nucleotide for DNA-A. When compared to the isolates of Mungbean yellow mosaic India virus (MYMIV), the genome sequences of DNA-A and DNA-B exhibited the highest nucleotide identity (98%). A single recombination event has been detected in DNA-A, with the major and minor parent classified as MYMIV isolates from Bangladesh and Paskistan, respectively. Two overlapping primers were designed using nucleotide sequence of MYMIV-Lentil isolate in order to amplify the virus's genome. DNA-A and DNA-B showed PCR-mediated amplification rates of 70.8 and 69.6%, respectively, when both primer sets were used. In order to ensure linked virus, whitefly-mediated transmission was tried in a controlled environment. In five examined lentil types, a meagre transmission rate (6.1-7.8%) was observed. The present evidence that a virus infects lentil crop rather than other microbe that cause stunting offers valuable insight for developing effective management measures.

Lamin A/C (LMNA), a key component of the nuclear envelope, is essential for maintaining nuclear integrity and genome organization [W. Xie et al., Curr. Biol. 26, 2651-2658 (2016)]. While LMNA dysregulation has been implicated in genomic instability across cancer and aging, the underlying mechanisms remain poorly understood [S. Graziano et al., Nucleus 9, 258-275 (2018)]. Here, we define a mechanistic role for LMNA in preserving genome stability in small-cell lung cancer (SCLC), a malignancy marked by extreme genomic instability [N. Takahashi et al., Cancer Res. Commun. 2, 503-517 (2022)]. LMNA depletion promotes R-loop accumulation, transcription-replication conflicts, replication stress, DNA breaks, and micronuclei formation. Mechanistically, LMNA deficiency disrupts nuclear pore complex organization, specifically reducing phenylalanine-glycine (FG)-nucleoporin incorporation, resulting in impaired RNA export and nuclear retention of RNA. LMNA expression is repressed by EZH2 and reexpressed during SCLC differentiation from neuroendocrine (NE) to non-NE states, and low LMNA levels correlate with poor clinical outcomes. These findings establish LMNA as a key regulator of nuclear transport and genome integrity, linking nuclear architecture to SCLC progression and therapeutic vulnerability.

The regulation of cell-type-specific transcription relies on complex 3D interactions between promoters and distal regulatory elements. Although Hi-C has advanced our understanding of genome architecture, its high sequencing demand limits use in large-scale or time course experiments. We introduce Micro-C-ChIP, a strategy combining Micro-C with chromatin immunoprecipitation to map 3D genome organization at nucleosome resolution for defined histone modifications. We profile H3K4me3 and H3K27me3-specific 3D genome architecture in mouse embryonic stem cells (mESC), hTERT-immortalized human retinal pigment epithelial (hTERT-RPE1) cells, and HCT-116 RAD21-mAID-mClover (HCT-116 RAD21-mAC) cells. We validate that Micro-C-ChIP reveals genuine 3D genome features that are not driven by ChIP-enrichment bias. We identify extensive promoter-promoter contact networks in mESCs and hTERT-RPE1, and resolve the distinct 3D architecture of bivalent promoters in mESCs. Together, our results demonstrate that Micro-C-ChIP is a high-resolution, cost-efficient approach to study histone-modification-specific chromatin folding.