Biology subjects

Elleder, D.

Publications and source records attributed to Elleder, D..

8 recordsLinked to original sources

bioRxiv2025

Decoding the avian missing gene mystery: dot chromosomes unmask extensive gene loss and novel genetic instability

The apparent absence of numerous conserved vertebrate genes from avian genomes has puzzled researchers for over a decade. In recent years, a subset of these genes has been identified; however, their sequences are unusually problematic, often evading detection by standard sequencing technologies. This limitation has hindered detailed investigation of the phenomenon--until recent progress in long read technologies, which are more robust against sequencing biases. This enabled us to classify real gene losses extensively, which strikingly revealed that a large number of the genes residing on so-called dot chromosomes were indeed lost during avian evolution. We demonstrate that dot microchromosomes--small, repeat-dense avian chromosomes--harbor widespread gene attrition, with 29% of ohnologs (duplicates from ancestral genome doublings) eliminated, far exceeding rates on other chromosomes. Moreover, we reveal that genes retained on these dot chromosomes exhibit a previously undescribed form of dynamic genetic instability. This instability, which we term sequence stuttering, is characterized by a massive expansion of short sequences within intronic regions. Intriguingly, in some cases, the expanding sequences appear to originate from neighboring exons. As a result, intron lengths vary extensively among individual chickens, suggesting that these events are evolutionarily recent. Since this phenomenon has not been reported in any other vertebrate species, our findings lay the groundwork for future research into its underlying mechanisms, evolutionary implications, and potential identification of similar loci across vertebrate genomes. SIGNIFICANCEThis study reveals extensive gene loss and a novel genetic instability, termed "sequence stuttering," on avian dot microchromosomes, providing new insights into avian genomic evolution. Approximately 29% of ohnologs on dot chromosomes are absent compared to other vertebrate chromosomes, possibly due to elevated GC content and recombination rates in euchromatin regions. This significant gene loss highlights dot chromosomes as hotspots for genomic reduction, potentially shaping avian-specific traits. Additionally, sequence stuttering--characterized by extensive intronic repeat expansions, sometimes incorporating exonic sequences--introduces marked length polymorphism within chicken populations, suggesting ongoing evolutionary dynamics. These findings underscore the unique role of dot chromosomes in avian genome evolution, emphasizing their contribution to genetic diversity and adaptation. This work lays the foundation for further investigation into the molecular mechanisms driving these phenomena and their broader implications for vertebrate genomic evolution.

genomics↗

bioRxiv2024

Regulation of B cell migration to the Bursa of Fabricius by CCR7 and cell adhesion molecules in chicken embryonic development

The development of functional B lymphocytes during chicken embryogenesis relies on a series of tightly regulated processes. Precursor B cells migrate from the spleen via the blood to the bursa of Fabricius, where they colonize the bursal follicles to undergo further maturation and differentiation. To better understand the molecular mechanisms underlying early B cell migration in the chicken embryo, transcriptome analysis of B cells isolated from the spleen, blood, and bursa at embryonic days (ED) 12, ED14, and ED16 was performed. These findings suggest that sphingosine-1-phosphate (S1P) and its receptors regulate B cell presence in the bloodstream, while CCR7 and CXCR4 guide B cells to the bursa. Additionally, integrins and cell adhesion molecules, such as PECAM1, appear to facilitate transendothelial migration into the bursal mesenchyme. This study highlights a coordinated interplay between chemokines, integrins and cell adhesion molecules involved in B cell recruitment and colonization of the bursa microenvironment. These findings enhance our understanding of early B cell migration and shed light on the mechanisms governing B cell trafficking during chicken embryonic development.

immunology↗

bioRxiv2024

Avian interferon regulatory factor (IRF) family reunion: IRF3 and IRF9 found

Interferon regulatory factors (IRFs) are a family of transcription factors in jawed vertebrates with important functions in immunity and many other key cellular processes. The genomes of most vertebrates encode ten IRF genes (IRF1 to IRF10). IRF3 and IRF9 have key roles in the interferon (IFN) induction and signaling. Most of our knowledge about the IFN pathways originates from the study of the mammalian IFN system, and the description of the corresponding avian components is not as complete. Both IRF3 and IRF9 were considered missing from the chicken genome and also from the genomes of all other avian species. Here we describe multiple avian IRF3 and IRF9 genes, all with difficult GC-rich sequence context which prevented their earlier characterization. IRF3 orthologs are more narrowly distributed and are present in the avian infraclass Palaeognathae residing in a syntenic genomic locus shared with other vertebrates. In contrast, IRF9 orthologs were found in most avian species with the notable exception of the order Galliformes. In about half of the avian orders analyzed, IRF9 was located in noncanonical chromosomal positions indicating past evolutionary translocations. Importantly, phylogenetic analysis confirmed the correct orthology of all newly described avian IRFs. We performed a series of experiments using duck (Anas platyrhynchos) IRF9, confirming its key role in the IFN signaling pathway. Knockout of IRF9 in duck embryonal fibroblasts decreases the induction of IFN-stimulated genes (ISGs). Full induction of ISGs in duck cells requires both intact IRF9 and canonical IFN-stimulated response element (ISRE). Lastly, intact IRF9 is needed for IFN-mediated protection of duck cells against vesicular stomatitis virus (VSV)-induced cytopathic effect. The identification of avian IRFs fills an important gap in our understanding of avian immunology and brings new questions related to the evolution of the IRF family.

immunology↗

bioRxiv2024

Generation and initial characterization of in vivo knockout of tetherin/BST2 in chicken

Tetherin/BST2 is an antiviral restriction factor initially described in mammals. It is active against multiple enveloped viruses at the budding phase, where it is able to physically link the budding virions to the virus-producing cell. We and others have previously identified tetherin orthologs in birds, and characterized the antiviral activity and interferon-inducibility of chicken tetherin. In this work, we have generated an in vivo model of tetherin absence in chicken by CRISPR/Cas9 modification of chicken primordial germ cells (PGC). The modified PGCs were transplanted into roosters with suppressed endogenous spermatogenesis, and transgenic (tetherin knockout) progeny was obtained by further crosses. The viability and phenotype of tetherin knockout animals did not differ from wild type chicken. In more detailed investigation, flow cytometry based differential white blood cell count revealed an increased number of heterophils in tetherin knockouts. Upon challenge with avian sarcoma and leukosis virus (ASLV), a prototypic avian retrovirus, we detected increase in viremia at days 6 and 13 post infection in tetherin knockout animals. The increased virus susceptibility is consistent with absence of antiviral tetherin. In summary, we introduce a new in vivo knockout model of chicken antiviral gene tetherin. These animals can be used in further characterizations of avian antiviral defenses and also to define thus far unknown physiological effects of tetherin in birds.

molecular biology↗

bioRxiv2023

Reinstatement of RIG-I in chickens via genetic modification reveals new insights into the dynamic evolution of avian immune sensors

Retinoic acid-inducible gene I (RIG-I) activates mitochondrial antiviral signaling proteins, initiating the antiviral response. RIG-I and RNF135, a ubiquitin ligase regulator, are missing in domestic chickens but conserved in mallard ducks. The chickens RIG-I loss was long believed to be linked to increased avian influenza susceptibility. We reinstated both genes in chickens and examined their susceptibility to infection with an H7N1 avian influenza virus. Uninfected RIG-I-expressing chickens exhibited shifts in T and B cells. At the same time, the H7N1 infection led to severe disease, persistent weight loss, and increased viral replication compared to wild-type chickens. The simultaneous expression of RIG-I and RNF135 potentiated the RIG-I activity and was associated with exacerbated inflammatory response and increased mortality without influencing virus replication. Additional animal infection experiments with two other avian influenza viruses validated these findings. They confirmed that the harmful effects triggered by RIG-I or RIG-I-RNF135-expression require a minimum degree of viral virulence. Our data indicate that the loss of RIG-I in chickens has likely evolved to counteract deleterious inflammation caused by viral infection and highlight an outcome of restoring evolutionary lost genes in birds. Significance StatementThe evolutionary loss of a crucial innate immune sensor like RIG-I in domestic chickens and its presence in closely related avian species such as ducks has long puzzled researchers. We genetically reinstated RIG-I in chickens, alongside its ubiquitination factor, RNF135, to uncover their roles in responding to influenza virus interactions in chickens. Our findings suggest that the loss of RIG-I in chickens may have occurred as an adaptive strategy to mitigate harmful inflammation associated with influenza infection. We shed light on an outcome of reinstating evolutionarily lost genes in birds and open new avenues for understanding immune responses in vertebrates.

immunology↗

bioRxiv2022

Unraveling the Palindromic and Non-Palindromic Motifsof Retroviral Integration Site Sequences by Statistical Mixture Models

A weak palindromic nucleotide motif is the hallmark of retroviral integration site alignments. Previously, the motifs were explained by an overlap of the non-palindromic motif being present on one of the half-site of targeted sequences. Here, we applied multicomponent mixture models to integration site sequences of diverse retroviruses. We demonstrate that the weak palindromic motifs result from a combination of independent sub-motifs restricted to only a few positions proximal to the site of integration. The sub-motifs are formed by either palindrome-forming nucleotide preference or nucleotide exclusion. Using the mixture models, we also identified HIV-1-favored palindromic sequences in Alu repeats serving as hotspots for integration. Our work presents a novel statistical approach to the analysis of retroviral integration site sequences, which can form a valuable tool in the analysis of DNA motifs. The presented results shed new light on the selection of target site sequences for retroviral integration.

microbiology↗

bioRxiv2022

Revealing genomic changes responsible for cannabinoid receptor loss in parrots: mechanism and functional effects

In vertebrates, an ancient duplication in the genes for cannabinoid receptors (CNRs) allowed the evolution of specialised endocannabinoid receptors expressed in the brain (CNR1) and the periphery (CNR2). While dominantly conserved throughout vertebrate phylogeny, our comparative genomic analysis suggests that certain taxa may have lost either the CNR1 regulator of neural processes or, more frequently, the CNR2 involved in immune regulation. Focussing on conspicuous CNR2 pseudogenization in parrots (Psittaciformes), a diversified crown lineage of cognitively-advanced birds, we highlight possible functional effects of such a loss. Parrots appear to have lost the CNR2 gene at at least two separate occasions due to chromosomal rearrangement. Using gene expression data from the brain and periphery of birds with experimentally-induced sterile inflammation, we compare CNR and inflammatory marker (interleukin 1 beta, IL1B) expression patterns in CNR2-deficient parrots (represented by the budgerigar, Melopsittacus undulatus and five other parrot species) with CNR2-intact passerines (represented by the zebra finch, Taeniopygia guttata). Though no significant changes in CNR expression were observed in either parrots or passerines during inflammation of the brain or periphery, we detected a significant up-regulation of IL1B expression in the brain after stimulation with lipopolysaccharide (LPS) only in parrots. As our analysis failed to show evidence for selection on altered CNR1 functionality in parrots, compared to other birds, CNR1 is unlikely to be involved in compensation for CNR2 loss in modulation of the neuroimmune interaction. Thus, our results provide evidence for the functional importance of CNR2 pseudogenization for regulation of neuroinflammation.

genomics↗

bioRxiv2021

The evolutionary history of a gammaretrovirus currently colonizing the mule deer genome is marked by extensive recombination

All vertebrate genomes have been colonized by retroviruses along their evolutionary trajectory. While endogenous retroviruses (ERVs) can contribute important physiological functions to contemporary hosts, such benefits are attributed to long-term co-evolution of ERV and host because germline infections are rare and expansion is slow, because the host effectively silences them. The genomes of several outbred species including mule deer (Odocoileus hemionus) are currently being colonized by ERVs, which provides an opportunity to study ERV dynamics at a time when few are fixed. Because we have locus-specific data on the distribution of cervid endogenous retrovirus (CrERV) in populations of mule deer, in this study we determine the molecular evolutionary processes acting on CrERV at each locus in the context of phylogenetic origin, genome location, and population prevalence. A mule deer genome was de novo assembled from short and long insert mate pair reads and CrERV sequence generated at each locus. CrERV composition and diversity have recently measurably increased by horizontal acquisition of a new retrovirus lineage. This new lineage has further expanded CrERV burden and CrERV genomic diversity by activating and recombining with existing CrERV. Resulting inter-lineage recombinants endogenized and subsequently retrotransposed. CrERV loci are significantly closer to genes than expected if integration were random and gene proximity might explain the recent expansion by retrotransposition of one recombinant CrERV lineage. Thus, in mule deer, retroviral colonization is a dynamic period in the molecular evolution of CrERV that also provides a burst of genomic diversity to the host population.

genomics↗