Biology subjects

Solovei, I.

Publications and source records attributed to Solovei, I..

8 recordsLinked to original sources

bioRxiv2025

Reconfiguration of genome-lamina interactions marks the commissioning of limb cell-fates

Diverse forms of heterochromatin block inappropriate transcription and safeguard differentiation and cell identity. Yet, how and when heterochromatin is reconfigured to facilitate changes in cell- fate remains a key open question. Here, we address this by mapping a prevalent heterochromatic feature - genome-lamina interactions - relative to transcription in single-cells during mouse embryogenesis. We find that genome-lamina interactions remain relatively uniform between germ layers following gastrulation but are extensively reconfigured in diverse tissues during later organogenesis. Focusing on limb development, we demonstrate that genome-lamina interactions are selectively released in early multipotent progenitors at key developmental genes and their surrounding regulatory domains. This "lamina-release" often precedes gene expression at later developmental stages, suggesting it primes regulatory domains for future potential activation. Conversely, lamina-release coincides with chromatin opening at sites of crucial limb transcription factor binding, and so is closely intertwined with the regulatory machinery driving limb formation. Finally, we show that the boundaries of topologically-associated domains (TADs) constrain the spread of lamina-release at a limb gene locus. This ensures independent lamina dynamics between neighbouring domains. Together, our data suggest a previously unrecognised process where genome-lamina interactions are selectively released at regulatory domains to transition loci toward more permissive chromatin states, thereby potentiating cell type specific activation. Our work thus reveals how systematic heterochromatin reorganization links to developmental multipotency, providing mechanistic insights into cell-fate decisions in vivo.

developmental biology↗

bioRxiv2025

Ab-trapping - a peripheral staining artifact in antibody-based microscopy and genomics

Antibodies (Ab) are essential for detecting specific epitopes in microscopy and genomics, but can produce artifacts leading to erroneous interpretations. Here, we characterize a novel artifact, Ab-trapping, in which antibodies bind at the periphery of a cellular structure and do not diffuse further into its interior. This causes anomalous peripheral staining for multiple critical targets, including endogenous or ectopically expressed nuclear proteins like nucleolar proteins, histone variants and their modifications like H3K9me2. Ab-trapping can affect any assay relying on Ab diffusion, including immunofluorescence microscopy and recent genomics approaches like CUT&Tag. Critically, computational modeling and experimental validation reveal that Ab-trapping is caused by high epitope abundance, high Ab affinity, and low diffusion rates. Consequently, its effects can be mitigated by using alternative Abs and optimizing incubation conditions. Ab-trapping is therefore a considerable artifact that should be considered when designing experiments and interpreting results.

cell biology↗

bioRxiv2024

Eye features and retinal photoreceptors of the nocturnal aardvark (Orycteropus afer, Tubulidentata)

The nocturnal aardvark Orycteropus afer is the only extant species in the mammalian order Tubulidentata. Previous studies have claimed that it has an all-rod retina. In the retina of one aardvark, we found rod densities ranging from 124,000/mm2 in peripheral retina to 214,000/mm2 in central retina; the retina of another aardvark had 182,000 - 245,000 rods/mm2. This is moderate in comparison to other nocturnal mammals. With opsin immunolabelling we found that the aardvark also has a small population of cone photoreceptors. Cone densities ranged from 300 to 1,300/mm2 in one animal, and from 1,100 to 1,600/mm2 in the other animal, with large local variations and no large central-peripheral density gradient. Overall, cones comprised 0.25-0.9% of the photoreceptors. Both typical mammalian cone opsins, longwave-sensitive (L) and shortwave-sensitive (S), were present. However, there was colocalization of the two opsins in many cones across the retina (35 - 96% dual pigment cones). Pure L cones and S cones formed smaller populations. This probably results in poor colour discrimination. Thyroid hormones, important regulators of cone opsin expression, showed normal blood serum levels. The relatively low rod density and hence a relatively thin retina may be related to the fact that the aardvark retina is avascular and its oxygen and nutrient supply have to come from the choriocapillaris by diffusion. In contrast to some previous studies, we found that the aardvark eye has a reflective tapetum lucidum with features of a choroidal tapetum fibrosum, in front of which the retinal pigment epithelium is unpigmented. The discussion considers these findings from a comparative perspective.

zoology↗

bioRxiv2024

Co-transcriptional splicing is delayed in highly expressed genes

Transcription of the majority of eukaryotic genes is accompanied by splicing, a process that depends on the assembly of the spliceosome on introns. The timing of spliceosome assembly varies significantly between introns, transcripts, genes and species. While quick co-transcriptional intron removal has been demonstrated for many mammalian genes, most splicing events do not occur immediately after intron synthesis. In this study, we utilized the highly expressed Tg gene, which forms exceptionally long transcription loops (Leidescher et al., 2022), providing a convenient model for studying splicing dynamics using advanced light microscopy. Our single-cell oligopainting-based analysis revealed a delay in splicing several tens of kilobases downstream of a transcribed intron, a finding further supported by standard cell population analyses. We speculate that this phenomenon is due to the abnormally high transcription rate of the Tg gene, which may lead to a localized deficiency in splicing factors and, consequently, delayed spliceosome assembly on thousands of nascent transcripts decorating the gene. Additionally, we found that, in contrast to short introns (<10 kb), long Tg intron (>50 kb) is spliced promptly, providing further support for the idea that intron length may modulate splicing speed.

cell biology↗

bioRxiv2023

The highly and perpetually upregulated thyroglobulin gene is a hallmark of functional thyrocytes

Abnormalities are indispensable for studying normal biological processes and mechanisms. In the present work, we draw attention to the remarkable phenomenon of a perpetually and robustly upregulated gene, the thyroglobulin gene (Tg). The gene is expressed in the thyroid gland and, as it has been recently demonstrated, forms so-called transcription loops, easily observable by light microscopy. Using this feature, we show that Tg is expressed at a high level from the moment a thyroid cell acquires its identity and both alleles remain highly active over the entire life of the cell, i.e. for months or years depending on the species. We demonstrate that this high upregulation is characteristic of thyroglobulin genes in all major vertebrate groups. We provide evidence that Tg is not influenced by the thyroid hormone status, does not oscillate round the clock and is expressed during both the exocrine and endocrine phases of thyrocyte activity. We conclude that the thyroglobulin gene represents a valuable model to study the maintenance of a high transcriptional upregulation. SUMMARY STATEMENTThe thyroglobulin gene is highly and permanently expressed in thyrocytes of all vertebrates, at any condition and round the clock, offering a unique model to study mechanisms of high upregulation maintenance and chromatin dynamics

cell biology↗

bioRxiv2020

SPATIAL ORGANIZATION OF TRANSCRIBED EUKARYOTIC GENES

Despite the well-established role of nuclear organization in gene expression regulation, little is known about the reverse: how transcription shapes the spatial organization of the genome. Owing to small sizes of most previously studied genes and the limited resolution of microscopy, the structure and spatial arrangement of a single transcribed gene are still poorly understood. Here, we make use of several long highly expressed genes and demonstrate that they form transcription loops with polymerases moving along the loops and carrying nascent RNAs. Transcription loops can span across microns resembling lampbrush loops and polytene puffs. Extension and shape of transcription loops suggest their intrinsic stiffness, which we attribute to decoration with multiple voluminous nascent RNPs. Our data contradict the model of transcription factories and indicate that although microscopically resolvable transcription loops are specific for long highly expressed genes, the mechanisms underlying their formation can represent a general aspect of eukaryotic transcription.

cell biology↗

bioRxiv2019

Rod nuclear architecture determines contrast transmission of the retina and behavioral sensitivity in mice

Rod photoreceptors of nocturnal mammals display a striking inversion of nuclear architecture, which has been proposed as an evolutionary adaptation to dark environments. However, the nature of visual benefits and underlying mechanisms remains unclear. It is widely assumed that improvements in nocturnal vision would depend on maximization of photon capture, at the expense of image detail. Here we show that retinal optical quality improves 2-fold during terminal development, which, confirmed by a mouse model, happens due to nuclear inversion. We further reveal that improved retinal contrast-transmission, rather than photon-budget or resolution, leads to enhanced contrast sensitivity under low light condition. Our findings therefore add functional significance to a prominent exception of nuclear organization and establish retinal contrast-transmission as a decisive determinant of mammalian visual perception. One Sentence SummaryOur study reveals that chromatin compaction in rod cells augments contrast sensitivity in mice.

biophysics↗

bioRxiv2018

Heterochromatin drives organization of conventional and inverted nuclei

The mammalian cell nucleus displays a remarkable spatial segregation of active euchromatic from inactive heterochromatic genomic regions. In conventional nuclei, euchromatin is localized in the nuclear interior and heterochromatin at the nuclear periphery. In contrast, rod photoreceptors in nocturnal mammals have inverted nuclei, with a dense heterochromatic core and a thin euchromatic outer shell. This inverted architecture likely converts rod nuclei into microlenses to facilitate nocturnal vision, and may relate to the absence of particular proteins that tether heterochromatin to the lamina. However, both the mechanism of inversion and the role of interactions between different types of chromatin and the lamina in nuclear organization remain unknown. To elucidate this mechanism we performed Hi-C and microscopy on cells with inverted nuclei and their conventional counterparts. Strikingly, despite the inversion evident in microscopy, both types of nuclei display similar Hi-C maps. To resolve this paradox we developed a polymer model of chromosomes and found a universal mechanism that reconciles Hi-C and microscopy for both inverted and conventional nuclei. Based solely on attraction between heterochromatic regions, this mechanism is sufficient to drive phase separation of euchromatin and heterochromatin and faithfully reproduces the 3D organization of inverted nuclei. When interactions between heterochromatin and the lamina are added, the same model recreates the conventional nuclear organization. To further test our models, we eliminated lamina interactions in models of conventional nuclei and found that this triggers a spontaneous process of inversion that qualitatively reproduces the pathway of morphological changes during nuclear inversion in vivo. Together, our experiments and modeling suggest that interactions among heterochromatic regions are central to phase separation of the active and inactive genome in inverted and conventional nuclei, while interactions with the lamina are essential for building the conventional architecture from these segregated phases. Ultimately our data suggest that an inverted organization constitutes the default state of nuclear architecture.

biophysics↗