Biology subjects

Ravasi, T.

Publications and source records attributed to Ravasi, T..

At least 19 recordsLinked to original sources

bioRxiv2026

MicroRNA-mediated transgenerational plasticity reveals pathways for ocean warming resilience

With anthropogenic climate change driving unprecedented ocean warming and posing a major threat to marine organisms, phenotypic plasticity mediated by epigenetic mechanisms may enable acclimation and persistence across generations. MicroRNAs (miRNAs) are epigenetic regulators that have long been associated with maladaptive stress responses across generations, yet their role in facilitating transgenerational acclimation remains unexplored. To examine miRNAs role in transgenerational thermal plasticity, we conducted a fully factorial split-clutch design experiment in the coral reef fish Acanthochromis polyacanthus. Parents and offspring were exposed throughout development to control (+0{degrees}C) or elevated (+1.5{degrees}C) temperatures, and offspring hepatic miRNA and mRNA were profiled. We identified 678 miRNAs in A. polyacanthus, including 226 conserved and 452 novel sequences. Direct (developmental) and parental (transgenerational) warming caused similar numbers of miRNAs to alter expression, while mRNA expression was more strongly influenced by parental effects. The two parents had distinct effects on offspring miRNA-mRNA networks, with paternal warming mainly altering offspring metabolism and stress responses, while maternal exposure predominantly influencing immunity and tissue organization. Overall, mismatched parental temperatures created trade-offs in offspring, whereas congruent (biparental) warming led to a unique, non-additive, response with fewer miRNA changes and lack of stress pathway activation. Our findings reveal that miRNAs mediate both developmental and transgenerational plasticity, highlighting the capacity of transgenerational effects to influence climate resilience, while also emphasizing the necessity of accounting for both maternal and paternal contributions when predicting species adaptability to ocean warming.

evolutionary biology↗

bioRxiv2024

Shifts in Coral Reef Holobiont Communities in the High-CO2 Marine Environment of Iotorishima Island

Ocean acidification (OA), driven by rising atmospheric CO2, presents a serious threat to marine biodiversity, especially within coral reef ecosystems. Natural analogue sites, such as the high-pCO2 seep at I[o]torishima Island in Japan, offer insights into future conditions. This study investigated the holobiont communities of Symbiodiniaceae and bacteria in the zoantharian Palythoa tuberculosa at I[o]torishima and compared them to specimens from control sites in Okinawa and Hawaii. Using amplicon sequencing of the dinoflagellate internal transcribed spacer 2 (ITS2) region of ribosomal DNA and microbial 16S rRNA gene, we detected significant shifts in both Symbiodiniaceae and bacterial communities under high-pCO2 conditions at I[o]torishima. Specifically, P. tuberculosa at the seep site had reduced Symbiodiniaceae diversity, predominatly featuring Cladocopium C1 and C3 types. Additionally, its bacterial communities showed lower richness with distinct taxonomic profiles, including increased levels of Mollicutes and Vibrio spp. These results highlight the potentially adverse effects of OA on hexacoral holobionts and emphasize the need for detailed, high-resolution studies across various holobiont species and geographic locations. The shifts observed specifically in Symbiodiniaceae and bacterial communities at the I[o]torishima Seep suggest that holobionts may exhibit plasticity in response to environmental stress, which has implications for resilience and adaptation of zoantharians and other reef organisms amid climate change. This research provides crucial baseline data for predicting future coral reef compositions in an OA-affected world.

microbiology↗

bioRxiv2024

Neural Mechanisms of Mutualistic Fish Cleaning Behaviour: a Study in the Wild

One crucial interaction for the health of fish communities in coral reefs is performed by the cleaner fish by removing ectoparasites and other particles from the body of other fish, so called clients. Studying the underlying mechanisms of this behaviour is essential to understanding how species react to social stimuli and defining the drivers of mutualism. Here, we pinpoint the neural molecular mechanisms in the cleaning behaviour of Labroides dimidiatus in the wild through an in-situ interaction experiment at a coral reef in New Caledonia. Five cleaners and clients (Abudefduf saxatilis) were placed into underwater aquaria to interact, while five were not presented with a client. The brain transcriptomes revealed 291 differentially expressed genes in cleaners that were interacting with a client. Among these genes, grin2d, npy, slc6a3 and immediate early genes (fosb; fosl1; nr4a1) were related to learning and memory, glutamate and dopamine pathways, which confirm molecular pathways observed in laboratory studies. However, a new potential mechanism was found with npy (Neuropeptide Y) as a driver of feeding behaviour. These results show that in-situ experiments are essential for corroborating interpretations inferred from experiments in captivity and identify drivers of interspecific interactions.

animal behavior and cognition↗

bioRxiv2023

Cross-talk between tissues is critical for intergenerational acclimation to environmental change

An organisms reaction to environmental changes is mediated by coordinated responses of multiple tissues. Additionally, parental priming may increase offsprings acclimation potential to changing environmental conditions. As the effects of human-induced climate change, such as ocean acidification (OA), continue to intensify it is critical to assess the acclimation potential of species at the whole organismal scale. For this we need to understand the cross-talk between tissues in regulating and responding to pH changes. Here by using a multi-tissue approach we determine the influence of 1) variation in parental behavioural tolerance and 2) parental environment, on molecular responses of their offspring in a coral reef fish. The gills and liver showed the highest transcriptional response to OA conditions in juvenile fish regardless of the parental environment, while the brain and liver showed the greatest signal of intergenerational acclimation. Key functional pathways that were altered in the brain upon within-generational CO2 exposure were restored to control levels when parents were exposed to OA conditions. Furthermore, the expression of a new complement of genes involved in key functions was altered in the offspring only when parents were previously exposed to OA conditions. Therefore, previous parental conditioning to OA can reprogram tissue transcriptomic profiles of the offspring enabling them to better cope in an environment with elevated CO2 levels. Overall, our results reveal tissue-specific transcriptional changes underlying intergenerational plastic responses to elevated CO2 exposure and highlight the integration of these changes in promoting organismal acclimation to OA.

ecology↗

bioRxiv2023

Matching maternal and paternal experiences underpin molecular thermal acclimation

The environment experienced by one generation has the potential to affect the subsequent one through non-genetic inheritance of parental effects. Since both mothers and fathers can influence their offspring, questions arise regarding how the maternal, paternal and offspring experiences integrate into the resulting phenotype. We aimed to disentangle the maternal and paternal contributions to transgenerational thermal acclimation in a reef fish, Acanthochromis polyacanthus, by exposing two generations to elevated temperature (+1.5{degrees}C) in a full factorial design and analyzing the F2 hepatic gene expression. Paternal and maternal effects showed common but also parent-specific components, with the father having the largest influence in shaping the offspring transcriptomic profile. Fathers contributed to transgenerational response to warming through transfer of epigenetically controlled stress-response mechanisms while mothers influenced increased lipid metabolism regulation. However, the key to acclimation potential was matching thermal experiences of the parents. When both parents were exposed to the same condition, offspring showed increased structural RNA production and transcriptional regulation, whereas environmental mismatch in parents resulted in maladaptive parental condition-transfer, revealed by translation suppression and endoplasmic reticulum stress. Interestingly, the offsprings own environmental experience had the smallest influence on their hepatic transcription profiles. Taken together, our results show the complex nature of the interplay between paternal, maternal and offspring cue integration, and reveal that acclimation potential to ocean warming depends not only on maternal and paternal contributions, but importantly on congruent parental thermal experiences.

evolutionary biology↗

bioRxiv2023

Timing specific parental effects of ocean warming in a coral reef fish

Population and species persistence in a rapidly warming world will be determined by an organisms ability to acclimate to warmer conditions, especially across generations. There is potential for transgenerational acclimation, but the importance of ontogenetic timing in the transmission of environmentally induced parental effects remains mostly unknown. We aimed to disentangle the contributions of two critical ontogenetic stages (juvenile development and adult reproduction) to transgenerational plasticity, by exposing the coral reef fish Acanthochromis polyacanthus to simulated ocean warming with natural diel thermal fluctuations across two generations. By using hepatic transcriptomics, we discovered that the developmental environment of the offspring themselves had little effect on their acclimation potential at 2.5 months of life. Instead, the developmental experience of parents increased regulatory RNA production and protein synthesis, which could improve the offsprings response to warming. Conversely, reproduction in warmer water elicited stress response mechanisms, with suppression of translation and mitochondrial respiration. Mismatches between temperatures in the parental ontogenetic thermal experience deeply affected offspring gene expression profiles, and detrimental effects were also evident when warming occurred both during parents development and reproduction. This study reveals that the previous generations developmental temperature contributes substantially to thermal acclimation potential during early life, however prolonged heat stress will likely have adverse effects on the species persistence.

evolutionary biology↗

bioRxiv2023

Neuromolecular responses in disrupted mutualistic cleaning interactions under future environmental conditions

Mutualistic interactions, which constitute some of the most advantageous interactions among fish species, are highly vulnerable to environmental changes. A key mutualistic interaction is the cleaning service rendered by the cleaner wrasse, Labroides dimidiatus, which involves intricate processes of social behaviour to remove ectoparasites from client fish and can be altered in near-future environmental conditions. Here, we evaluated the neuromolecular mechanisms behind the behavioural disruption of cleaning interactions in response to future environments. We subjected cleaner wrasses and surgeonfish (Acanthurus leucosternon, serving as clients) to elevated temperature (Warming, 32{degrees}C), increased levels of CO2 (High CO2, 1000 ppm), and a combined condition of elevated CO2 and temperature (Warming & High CO2, 32{degrees}C & 1000 ppm) for 28 days. Each of these conditions resulted in behavioural disruptions concerning the motivation to interact and the quality of interaction (High CO2 -80.7%, Warming - 92.6%, Warming & High CO2 -79.5%, p<0.001). Using transcriptomic of the fore-, mid-, and hindbrain, we discovered that most transcriptional reprogramming in both species under warming conditions occurred primarily in the hind- and forebrain. The associated functions under warming were linked to stress, heat shock proteins, hypoxia, and behaviour. In contrast, elevated CO2 exposure affected a range of functions associated with GABA, behaviour, visual perception, and circadian rhythm. Interestingly, in the combined Warming & High CO2 condition, we did not observe any expression changes of behaviour. However, we did find signs of endoplasmic reticulum stress and apoptosis, suggesting not only an additive effect of the environmental conditions but also a trade-off between physiological performance and behaviour in the cleaner wrasse. We suggest that impending environmental shifts can affect the behaviour and molecular processes that sustain mutualistic interactions between L. dimidiatus and its clients, which could have a cascading effect on their adaptation potential and possibly cause large-scale impacts on coral reef ecosystems.

animal behavior and cognition↗

bioRxiv2022

Genetic architecture of behavioural resilience to ocean acidification

Genetic variation is essential for adaptation to rapid environmental changes. Identifying genetic variation associated with climate-change related phenotypes is therefore the necessary first step towards predictive models of genomic vulnerability. Here we used a whole-genome scan to identify candidate genetic variants associated with differences in behavioural resilience to ocean acidification in a coral reef fish. We identified three genomic regions that differ between individuals that are behaviourally tolerant compared with behaviourally sensitive to elevated CO2. These include a dopamine receptor (drd4rs), cadherin related family member 5-like (cdhr5l), Synapse-associated protein 1 (syap1), and GRB2 Associated Regulator of MAPK1 Subtype 2 (garem2), which have previously been found to modify behaviour related to boldness, novelty seeking, and learning in other species, and differ between behaviourally tolerant and sensitive individuals. Consequently, the identified genes are promising candidates in the search of the genetic underpinnings and adaptive potential of behavioural resilience to ocean acidification in fishes.

ecology↗

bioRxiv2022

Gobies inhabiting natural CO2 seeps reveal acclimation strategies to long-term acidification

Ocean acidification (OA) is known to affect the physiology, survival, behaviour, and fitness of various fish species with repercussions at the population, community, and ecosystem levels. Some fish species, however, seem to acclimate rapidly to OA conditions and even thrive in acidified environments. The molecular mechanisms that enable species to successfully inhabit high CO2 environments has not been fully elucidated especially in wild fish populations. Here, we used the natural CO2 seep in Vulcano Island, Italy to study the effects of elevated CO2 exposure on the brain transcriptome of the anemone goby, a species with high population density in the CO2 seep and investigate their potential for acclimation. When compared to fish from environments with ambient CO2, gobies living in the CO2 seep showed differences in expression of transcripts involved in ion transport and pH homeostasis, cellular stress, immune response, circadian rhythm, and metabolism. We also found evidence of potential adaptive mechanisms to restore the functioning of GABAergic pathways, whose activity can be affected by exposure to elevated CO2 levels. Our findings indicate that gobies living in the CO2 seep may be capable of mitigating CO2 induced oxidative stress and maintaining physiological pH while meeting the consequent increased energetic costs. The conspicuous difference in expression of core circadian rhythm transcripts could provide an adaptive advantage by increasing flexibility of physiological processes in elevated CO2 conditions thereby facilitating acclimation. Our results show potential molecular processes of acclimation to elevated CO2 in gobies enabling them to thrive in the acidified waters of Vulcano Island.

evolutionary biology↗

bioRxiv2022

The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into melanic pigmentation of anemonefish

Anemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfish Amphiprion clarkii possesses species-specific characteristics such as inter-species co-habitation, high intra-species color variation, no anemone specificity, and a broad geographic distribution, that can increase our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. Despite its position as an emerging model species, the genome of A. clarkii is yet to be published. Using PacBio long-read sequencing and Hi-C chromatin capture technology, we generated a high-quality chromosome-scale genome assembly initially comprised of 1,840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and annotated with 25,050 protein-coding genes encompassing 97.0 % of conserved actinopterygian genes, making the quality and completeness of this genome the highest amongst all published anemonefish genomes to date. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further analyses revealed higher copy numbers of erbb3b (a gene involved in melanophore development) in A. clarkii compared to other anemonefish, thus suggesting a possible link between erbb3b and the natural melanism polymorphism observed in A. clarkii. The publication of this high-quality genome, along with A. clarkiis many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.

genomics↗

bioRxiv2022

A chromosome-scale genome assembly of the false clownfish, Amphiprion ocellaris

BackgroundThe false clownfish Amphiprion ocellaris is a popular fish species and an emerging model organism for studying the ecology, evolution, adaptation, and developmental biology of reef fishes. Despite this, high-quality genomic resources for this species are scarce, hindering advanced genomic analyses. Leveraging the power of PacBio long-read sequencing and Hi-C chromosome conformation capture techniques, we constructed a high-quality chromosome-scale genome assembly for the clownfish A. ocellaris. ResultsThe initial genome assembly comprised of 1,551 contigs of 861.42 Mb, with an N50 of 863.85 kb. Hi-C scaffolding of the genome resulted in 24 chromosomes containing 856.61 Mb. The genome was annotated with 26,797 protein-coding genes and had 96.62 % completeness of conserved actinopterygian genes, making this genome the most complete and high quality among published anemonefish genomes. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further, comparative genomic analysis revealed 91 genome elements conserved only in A. ocellaris and its sister species Amphiprion percula, and not in other anemonefish species. These elements are close to genes that are involved in various nervous system functions and exhibited distinct expression patterns in brain tissue, potentially highlighting the genetic toolkits involved in lineage-specific divergence and behaviors of the clownfish branch. ConclusionsOverall, our study provides the highest quality A. ocellaris genome assembly and annotation to date, whilst also providing a valuable resource for understanding the ecology and evolution of reef fishes.

genomics↗

bioRxiv2021

Neuro-molecular characterization of fish cleaning interactions

Coral reef fish exhibit a large variety of behaviours crucial for fitness and survival. The cleaner wrasse Labroides dimidiatus displays cognitive abilities during interspecific interactions by providing services of ectoparasite cleaning, thus serving as a good example to understand the processes of complex social behaviour. However, little is known about the molecular underpinnings of cooperative behaviour between L. dimidiatus and a potential client fish (Acanthurus leucosternon). Therefore, we investigated the molecular mechanisms in three regions of the brain (fore-, mid-, and hindbrain) during the interaction of these fishes. Here we show, using transcriptomics, that most of the transcriptional response in both species was regulated in the hindbrain and forebrain regions and that the interacting behaviour responses of L. dimidiatus involved immediate early gene alteration, dopaminergic and glutamatergic pathways, the expression of neurohormones (such as isotocin) and steroids (e.g. progesterone and estrogen). In contrast, in the client, fewer molecular alterations were found, mostly involving pituitary hormone responses. The particular pathways found suggested learning and memory processes in the cleaner wrasse, while the client indicated stress relief.

animal behavior and cognition↗

bioRxiv2021

Diel CO2 fluctuations alter the molecular response of coral reef fishes to ocean acidification conditions

Environmental CO2 variation can modify the responses of marine organisms to ocean acidification, yet the underlying mechanisms for this effect remain unclear. On coral reefs, environmental CO2 fluctuates on a regular day-night cycle. Effects of future ocean acidification on coral reef fishes might therefore depend on their response to this diel cycle of CO2. To evaluate the effects on the brain molecular response, we exposed two common reef fishes (Acanthochromis polyacanthus and Amphiprion percula) to two projected future CO2 levels (750 and 1,000 atm) under both stable and diel fluctuating conditions. We found a common signature to stable elevated pCO2 for both species, which included the downregulation of immediate early genes, indicating lower brain activity. The transcriptional program was more strongly affected by higher average CO2 in a stable treatment than for fluctuating treatments, however, the largest difference in molecular response was between stable and fluctuating CO2 treatments. This indicates that a response to a change in environmental CO2 conditions is different for organisms living in a fluctuating than in stable environments. The differential regulation was related to steroid hormones and circadian rhythm (CR). Both species exhibited a marked difference in the expression of CR genes among CO2 treatments, possibly accommodating a more flexible adaptive approach to acid-base control, which could explain reduced impairment. Our results suggest that environmental CO2 fluctuations might enable reef fishes to phase shift their clocks and anticipate CO2 changes, thereby avoiding impairments and more successfully adjust to ocean acidification conditions.

ecology↗

bioRxiv2021

The time course of molecular acclimation to seawater in a euryhaline fish

The Arabian pupfish, Aphanius dispar, is a euryhaline fish inhabiting both inland nearly-freshwater desert ponds and highly saline Red Sea coastal lagoons of the Arabian Peninsula. Red Sea populations have been found to receive migrants from desert ponds that are flushed out to sea during flash floods, requiring rapid acclimation to a greater than 40 ppt change in salinity. To investigate the molecular pathways of salinity acclimation during such colonization events, a Red Sea coastal lagoon and a desert pond population were sampled, with the latter exposed to a rapid increase in water salinity. Changes in branchial gene expression were investigated via genome-wide transcriptome measurements over time from 6 hours to 21 days. The two natural populations displayed basal differences in genes related to ion transport, osmoregulation and immune system functions. These mechanisms were also differentially regulated in seawater transferred fish, revealing their crucial role in long-term adaptation. Other processes were only transiently activated shortly after the salinity exposure, including cellular stress response mechanisms, such as molecular chaperone synthesis and apoptosis. Tissue remodeling processes were also identified as transient, but took place later in the timeline, suggesting their importance to long-term acclimation as they likely equip the fish with lasting adaptations to their new environment. The alterations in branchial functional pathways displayed by Arabian pupfish in response to salinity increases are diverse. These reveal a large toolkit of molecular processes important for adaptation to hyperosmolarity that allow for successful colonization to a wide variety of different habitats.

genomics↗

bioRxiv2021

Desert fish populations tolerate extreme salinity change to overcome hydrological constraints

The unstable nature of freshwater ponds in arid landscapes represent a sizable challenge for strictly aquatic organisms, such as fishes. Yet the Arabian Desert, bordering the coastline of the Red Sea, plays host to a species very well adapted to such extreme environments: the Arabian pupfish, Aphanius dispar. In this study, we estimated patterns of hydrological connectivity; population structure and stable isotope for samples of A. dispar living in small, isolated ponds of nearly-freshwater in the Arabian desert and highly saline coastal lagoons along the Red Sea. The genomic and hydrological analyses indicate that populations are largely separated by drainage origin, as fish from desert ponds appear to be transported to coastal lagoons of the Red Sea along ephemeral river systems arising from flash flood events. Further, our study indicates there is an ecological change when being washed from pond environments to coastal waters, due to a significant shift in muscle stable isotopes ratios between both groups. Considering that the genetic breaks are mostly observed between drainage origin, this study suggests that A. dispar can survive large changes in salinity and ecological regimes over small time-scales.

evolutionary biology↗

bioRxiv2020

Proteomic responses to ocean acidification in the brain of juvenile coral reef fish

Elevated CO2 levels predicted to occur by the end of the century can affect the physiology and behaviour of marine fishes. For one important survival mechanism, the response to chemical alarm cues from conspecifics, substantial among-individual variation in the extent of behavioural impairment when exposed to elevated CO2 has been observed in previous studies. Whole brain transcriptomic data has further emphasized the importance of parental phenotypic variation in the response of juvenile fish to elevated CO2. In this study, we investigate the genome-wide proteomic responses of this variation in the brain of 5-week old spiny damselfish, Acanthochromis polyacanthus. We compared the expression of proteins in the brains of juvenile A. polyacanthus from two different parental behavioural phenotypes (sensitive and tolerant) that had been experimentally exposed to short-term, long-term and inter-generational elevated CO2. Our results show differential expression of key proteins related to stress response and epigenetic markers with elevated CO2 exposure. Proteins related to neurological development were also differentially expressed particularly in the long-term developmental treatment, which might be critical for juvenile development. By contrast, exposure to elevated CO2 in the parental generation resulted in only three differentially expressed proteins in the offspring, revealing potential for inter-generational acclimation. Lastly, we found a distinct proteomic pattern in juveniles due to the behavioural sensitivity of parents to elevated CO2, even though the behaviour of the juvenile fish was impaired regardless of parental phenotype. Our data shows that developing juveniles are affected in their brain protein expression by elevated CO2, but the effect varies with the length of exposure as well as due to variation of parental phenotypes in the population.

ecology↗

bioRxiv2020

Probing SWATH-MS as a tool for proteome level quantification in a non-model fish

Quantitative proteomics via mass spectrometry can provide valuable insight into molecular and phenotypic characteristics of a living system. Recent mass spectrometry developments include data-independent acquisition (SWATH/DIA-MS), an accurate, sensitive, and reproducible method for analyzing the whole proteome. The main requirement for this method is the creation of a comprehensive spectral library. New technologies have emerged producing larger and more accurate species-specific libraries leading to a progressive collection of proteome references for multiple molecular model species. Here, for the first time, we set out to compare different spectral library constructions using multiple tissues from a coral reef fish to demonstrate its value and feasibility for non-model organisms. We created a large spectral library composed of 12,553 protein groups from liver and brain tissues. Via identification of differentially expressed proteins (DEPs) under fish exposure to environmental stressors we validated the application and usefulness of these different spectral libraries. Successful identification of significant DEPs from different environmental exposures occurred using the library with a combination of DIA+DDA data as well as both tissue types. Further analysis revealed expected patterns of significantly upregulated heat shock proteins in a dual condition of ocean warming and acidification indicating the biological accuracy and relevance of the method. This study provides the first reference spectral library for a coral reef fish and for a non-model organism. It represents a useful guide for the future building of accurate spectral library references in non-model organisms allowing the discovery of ecologically relevant changes in the proteome.

molecular biology↗

bioRxiv2019

AGO1 in association with NEAT1 lncRNA contributes to nuclear and 3D chromatin architecture in human cells

Aside from their roles in the cytoplasm, RNA-interference components have been reported to localize also in the nucleus of human cells. In particular, AGO1 associates with active chromatin and appears to influence global gene expression. However, the mechanistic aspects remain elusive. Here, we identify AGO1 as a paraspeckle component that in combination with the NEAT1 lncRNA maintains 3D genome architecture. We demonstrate that AGO1 interacts with NEAT1 lncRNA and its depletion affects NEAT1 expression and the formation of paraspeckles. By Hi-C analysis in AGO1 knockdown cells, we observed global changes in chromatin organization, including TADs configuration, and A/B compartment mixing. Consistently, distinct groups of genes located within the differential interacting loci showed altered expression upon AGO1 depletion. NEAT1 knockout cells displayed similar changes in TADs and higher-order A/B compartmentalization. We propose that AGO1 in association with NEAT1 lncRNA can act as a scaffold that bridges chromatin and nuclear bodies to regulate genome organization and gene expression in human cells.

genomics↗