Journal of Genetics and Genomics

The tunicate Ciona robusta offers a tractable non-vertebrate chordate model for probing gene function via tissue-specific, CRISPR/Cas9-mediated mutagenesis in F0. Building on Arcadia Sciences Zoogle platform, which identifies and ranks orthologs of human genes from various non-traditional model organisms, we carried out a pilot project to probe the developmental roles of three notochord- and endoderm-expressed candidate orthologs of human disease genes (Fcho, Pgm3, and Nckap1) alongside a fourth gene (Plastin) implicated in papilla cell elongation. This preprint compiles and updates a series of research project milestones previously posted episodically on Zenodo. Here we summarize the full results and our conclusion about this pilot project. Using CRISPR/Cas9, we found that tissue-specific knockout of Pgm3 and, to a lesser extent, Fcho caused significant defects in larval tail elongation. Separately, CRISPR knockout of Plastin, an actin-bundling gene expressed throughout the sensory-adhesive papillae of the larva, caused a subtle reduction in papilla cell elongation when combined as a duoble knockout with another actin-bundling protein-encoding gene, Villin. These results identify Pgm3 as the most promising candidate for further development as a Ciona-based model of human disease and demonstrate the utility of tissue-specific CRISPR screening for prioritizing candidate disease gene orthologs identified through comparative genomics platforms like Zoogle.

Bi-allelic variants of RNU4ATAC, transcribed into the minor spliceosome component U4atac snRNA, are associated to variable severity of microcephaly, growth retardation, skeletal dysplasia and immunodeficiency as main features. Previous studies highlighted the dramatic effect of U4atac deficiency on splicing of U12-type introns, which represent less than 1% of all introns in the human genome. More recently, our team evidenced a link between U4atac and the primary cilium/centrosome complex through the identification of patients carrying RNU4ATAC bi-allelic variants and exhibiting an atypical Joubert syndrome, a well-known ciliopathy. Yet, the underlying mechanisms remain elusive. Here, we further explored the link of RNU4ATAC to primary cilium and aimed at identifying ciliary U12-type intron containing genes that contribute to the brain abnormalities seen in patients. For that, we performed a transcriptomic analysis of heads of our morpholino oligonucleotide (MO)-mediated u4atac zebrafish model. Through the combined analysis of the generated dataset with those obtained from RNU4ATAC patient cells, we identified two candidate genes: TMEM107, coding for a structural protein of the cilium transition zone, and RFX7, encoding a transcription factor involved in primary cilium formation. By conducting complementary genetic approaches in zebrafish model, we showed that both gene orthologues, tmem107l and rfx7b, functionally interact with u4atac and are required for correct brain development. Altogether, our findings establish TMEM107 and RFX7 as key components of the molecular pathway linking U4atac dysfunction to ciliary defects and impaired brain development, providing new physiopathological insights and therapeutic perspectives for RNU4ATAC-related disorders.

Protein-protein interactions (PPIs) play a crucial role in enabling proteins to carry out their functions within various biological processes (Hui et al., 2003). Since the introduction of the yeast two-hybrid (Y2H) method for PPI detection in 1989 (Fields and Song, 1989), the identification of PPIs has become a significant focus in modern biological research. PPI goes beyond examining individual proteins, allowing researchers to establish a comprehensive network that regulates biological processes. Rice, as a key model organism in plant biological studies, has been at the forefront of PPI research. In 2008, prominent rice scientists in China called for concerted efforts to define a comprehensive protein-protein interaction network experimentally, which aimed to facilitate the prediction of the functional mechanisms operating throughout a plants lifecycle (Zhang et al., 2008). With efforts for 2 decades, the experimentally identified rice PPIs have reached over ten thousand. Several public databases have been established to systematically collate and store PPIs, including STRING (Szklarczyk et al., 2019), BioGRID (Oughtred et al., 2020), IntAct (del Toro et al., 2022), PRIN (Gu et al., 2011), RicePPINet (Liu et al., 2017) and RiceNet v2 (Lee et al., 2015). However, most PPI datasets in rice stem from computational predictions, while experiment-based rice PPI datasets are fragmented due to the lack of systematic profiling at the rice PPIome level, which largely hinders information sharing in the rice research community. To bridge this gap, we constructed the Port of Protein-Protein Interactomes (POPPIN; https://riceome.hzau.edu.cn/poppin/), an integrated database dedicated to sharing experimentally verified PPIs and functional clues in rice. Empowered by high-throughput PPIome profiling technologies and text mining assisted by a large language model (Huang et al., 2025; Liu et al., 2025), POPPIN currently has deposited over 150,451 pieces of rice PPI-related information. Additionally, POPPIN provides detailed protein information, including GO annotations, subcellular localizations, domains, trait ontology (TO) information, and hyperlinks to external biological databases. Through offering a user-friendly web interface for search and dynamic network visualization, POPPIN serves as the first large-scale, experiment-based database for searchable PPIs in rice, and has the potential to be extended to other species under this structural framework.

PAX9 is an evolutionarily conserved paired-box transcription factor that is critical for embryonic development and human diseases. The mouse model has been predominantly used to investigate Pax9 functions. Zebrafish has emerged as a complementary vertebrate model for various human diseases, including cancers. Until recently, the functions of the zebrafish pax9 gene in jaw and hematopoiesis have started to be uncovered. However, detailed pax9 spatiotemporal expression, molecular mechanisms, and potential functions in other zebrafish organs remain largely unknown. With the technical advances in CRISPR-Cas9, non-homologous end joining (NHEJ) has made knockin and knockout a convenient way to examine endogenous gene expression in vivo and to generate a loss-of-function allele simultaneously. Here, we first generated pax9 knockin fish lines by inserting fluorescent proteins at the start of the endogenous pax9 coding region. Then, we examined pax9 expression in real time from early embryonic stages through adulthood. Except for previously reported expression domains, we were able to identify pax9 expression in high resolution in the paired and median fins, where pax9 marks anterior fin rays. Moreover, our knockin and knockout mutants showed increased fin ray number in median fins, but no evident effect on paired fins in pax9 null mutants. Thus, PAX9 is critical for median fin patterning in zebrafish.

Desertification exerts dramatic selection pressures on the evolution of plants. Despite the key role of ecological adaptation by natural selection to arid grasslands and subsequent intraspecific divergence, specific mechanisms driving this process remain poorly understood. Psammochloa villosa, a perennial forage grass endemic to the arid grasslands in Northwest China, where it thrives in shifting and semi-fixed sand land due to its exceptional drought tolerance, provides an ideal system to study adaptive evolution to aridity. In our study, we assembled a high-quality, chromosome-scale genome and conducted genomic resequencing of 42 populations across its major distribution. The genome assembly, which is approximately 1.55 Gb in size, has a super-scaffold N50 of 66.79 Mb, with 75.84% of the sequences identified as transposable elements. Coalescent phylogeny and genomic collinearity analyses strongly supported that P. villosa and Neotrinia splendens, as the closest taxa, shared a recent whole-genome duplication (WGD) event occurring approximately 18-20 Mya and followed by their divergence around ~11.2 Mya. Based on ancestral grass karyotype (AGK) reconstruction from synteny analysis, our results suggest that, relative to the AGK after the {rho}-WGD event, P. villosa and N. splendens underwent similar chromosomal restructuring and lineage-specific retention of numerous copies, providing a genomic basis for potential ecological adaptation and intraspecific diversification. The expanded XTH family, which encodes enzymes mediating xyloglucan endotransglucosylation and hydrolysis and thereby regulating xyloglucan remodeling, showed strong transcriptional responses under PEG-6000 treatment, suggesting that retained copies may be associated with xerophytic adaptation in P. villosa. Together, these findings suggest that WGD-derived gene retention created a delayed reservoir of genetic diversity that was later shaped by desertification and Qinghai-Xizang Plateau environmental changes, contributing to climate-associated genomic islands and intraspecific differentiation.

Current studies in human genomics typically rely on the standard genome reference GRCh38 which is known to be biased toward populations of European ancestry and therefore has limitations when applied to other populations. Although various graph-based pangenome references were constructed for several populations to deal with this bias, their usage in practice is currently still limited compared to linear genome references. Here we present a framework for constructing a population-specific genome reference using GRCh38 as backbone with alternate-contig awareness to enhance genomic data analysis in the target population. We demonstrated the advantages of our framework using both public and in-house Vietnamese whole-genome sequencing (WGS) datasets. Genomic variants derived from high-coverage WGS data of the 1000 Vietnamese Genomes Project (VN1K) were imported into our framework to build a Vietnamese-specific Genome Reference (VGR). VGR was then compared to GRCh38 in read alignment and variant calling using high-coverage WGS data of 99 Vietnamese individuals (KHV) from the 1000 Genomes Project (1kGP). Using Omni array genotyping data from 99 KHV samples as an independent benchmark, we found that VGR improved variant-calling precision and reduced false-positive calls compared to GRCh38. Our framework could be easily used for other populations as long as they have a variant database similar to VN1K. Our code is publicly available at github.com/VinGenome/VGR

The specificity protein 7 (SP7), also known as Osterix (OSX), is a zinc-finger transcription factor essential for osteoblast differentiation and skeletal development. Hereafter, the protein is referred to as OSX/SP7 throughout the manuscript. Although OSX/SP7 has been extensively studied in mammals and teleost fish, its developmental expression pattern in chicken (Gallus gallus) has not been described. Using an experimentally isolated chicken OSX/SP7 sequence, we examined OSX/SP7 mRNA expression during embryogenesis by in situ hybridization. As expected, OSX/SP7 expression was detected in developing skeletal elements undergoing ossification. Unexpectedly, transcripts were also observed in the neuroepithelium, retina, central nervous system, embryonic muscles and integument. Notably, OSX/SP7 expression was present in the neural tube from Hamburger and Hamilton stage 9 and persisted in the developing central nervous system until at least HH40, suggesting that OSX/SP7 functions during avian development may extend beyond osteogenesis. In addition, we reconstructed the chicken OSX/SP7 coding sequence and inferred its associated untranslated regions. The reconstructed ORF was independently supported by maternal and paternal haplotype-resolved chicken genome assemblies and retained the characteristic domain architecture of vertebrate OSX/SP7 proteins despite substantial divergence outside the DNA-binding domain. Taken together, these findings broaden the developmental landscape of OSX/SP7 expression in birds and provide new molecular resources for future studies of OSX/SP7 regulation and function during vertebrate development.

Genome editing has revolutionized biomedical sciences and is now an essential tool to define molecular pathways through genetic interaction and loss-of-function studies. Through its diverse variations, it allows for the generation of specific knockout cell lines or organisms, as well as the creation of endogenously edited gene regions. While high-throughput methodologies exist to map CRISPR/Cas9 genetic modifications, the validation of guide efficiencies in cell populations is often performed through analysis of the targeted gene product by western blotting or by deconvolution of Sanger sequencing chromatograms using TIDE or ICE assays. Here, we highlight a rapid nanopore sequencing pipeline, which we have named NanoCutSight, to quantify the percentage of indels at a specific genomic locus and to identify the types of modifications generated. We also benchmarked the methodology on various guide RNAs and in both cultured cell and organoid models. We believe that NanoCutSight will simplify the analysis of complex sample editing and enable the rapid screening of edited samples.

A protein whose removal or deletion causes significant disruption or collapse of a protein-protein interaction (PPI) network is referred to as a vulnerable protein. Such proteins may serve as valuable therapeutic or diagnostic targets in disease-associated networks. In this study, two PPI networks were constructed, one for HPV-positive and the other for HPV-negative head and neck squamous cell carcinoma (HNSCC), and the vulnerable proteins of these networks were identified by the node deletion approach. After analyzing the networks, 27 unique vulnerable proteins in HPV-positive and 72 unique vulnerable proteins in HPV-negative HNSCC were identified. Among them, one HPV-positive and seven HPV-negative HNSCC vulnerable proteins were further chosen by integrating multi-omics data. To exploit the vulnerabilities of these proteins, candidate synthetic lethal (SL) partners were predicted whose inhibition may selectively impair tumor survival. Subsequently, drug-gene interaction analysis was performed to identify inhibitors targeting the SL partners of these vulnerable proteins. Notably, in HPV-positive HNSCC, TOP2A, CHEK1, and CHEK2 genes were identified as SL partners of TTN, and their inhibitors were already clinically approved. While in HPV-negative HNSCC, ADA and MMP19 were identified as an SL partner of LMO7; TMEM45B, CDH3, and ELF3 genes were identified as an SL partner of CGN; and ZNF433 was identified as an SL partner of FLNC. However, MMP19, ZNF433, and TMEM45B inhibitors were not reported. Thus, these vulnerable proteins, including their SL partners, provide novel avenues to explore and develop more efficient and precise therapeutic and diagnostic strategies.

Despite significant advancements in microsurgical techniques in recent years, the treatment and prognosis of craniopharyngiomas remain unsatisfactory. As a central nervous system tumor located adjacent to important brain structures such as the hypothalamus-pituitary axis and accompanied by a highly inflammatory microenvironment, the tumor heterogeneity and tumor microenvironment characteristics of papillary craniopharyngiomas (PCPs) remain unclear. In this study, we integrated multimodal single-cell and spatial profiling from PCP tissue and peripheral blood mononuclear cells (PBMCs) to elucidate the tumor heterogeneity and microenvironment characteristics of PCP. Our single-cell and spatial analyses defined four specific tumor cell states in PCP, representing specific transcriptional regulatory programs and spatial heterogeneity characteristics during tumor progression. By constructing a spatial niche composed of tumor, immune, and stromal cells, we analyzed the cellular and spatial ecosystem of PCP at multiple levels to further assess the communication relationships between different tumor cell states and microenvironment cells. This study established a multidimensional molecular atlas of PCP from the perspectives of cell state, spatial structure, and microenvironment interactions, providing a foundation for understanding its biological behavior and exploring new intervention strategies.

Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, yet the molecular mechanisms driving tumor initiation and progression are incompletely understood. Here, we integrate single-cell long-read sequencing, proteomics, and DNA methylation data to identify tumor-specific targets from unannotated isoforms in CRC. Analysis of 29,429 isoforms across 3,262 single cells revealed 3,338 novel isoforms, comprising 2,779 Novel In Catalog (NIC) and 559 Novel Not in Catalog (NNC). Cross-referencing with 68 normal tissues from GTEx identified 3 tumor-specific candidates absent from normal colon. Among these, CAST (Calpastatin) emerged as a tumor-specific suppressor, with a 63.1-fold higher expression in tumor (2.62) versus normal colon (0.03). CAST protein was confirmed in 100 tumor samples by mass spectrometry (mean expression: 0.22). Mutational analysis of 100 CRC samples revealed 8 deleterious mutations, including 2 nonsense, 2 splice-site, 2 missense, 1 frameshift, and 1 in-frame variant, consistent with a tumor-suppressor role. Promoter methylation analysis of 393 tumor samples showed that 89.3% (351/393) were hypomethylated ({beta} < 0.1), whereas only 1.5% (6/393) were hypermethylated ({beta} > 0.3), indicating demethylation-mediated reactivation. Furthermore, CAST expression was negatively correlated with promoter methylation and regulated by the miR-200 family (miR-200c: 13.48, miR-141: 10.13, miR-429: 8.09). Our findings establish CAST as a tumor-specific suppressor in CRC and provide a generalizable framework for discovering therapeutic targets from unannotated isoforms.

The neural crest and neurogenic placodes, which arise from the neural plate border, give rise to morphological characteristics that distinguish vertebrates from invertebrates (Gans & Northcutt, 1983). Recent studies have suggested that embryos of ascidians, a group of tunicates that are the closest invertebrate relatives of vertebrates, possess cells that share an evolutionary origin with vertebrate neural crest cells (Abitua et al., 2012; Fatieieva et al., 2025; Ishida & Satou, 2024; Stolfi et al., 2015; Todorov et al., 2024; Waki et al., 2015) and neurogenic placode cells (Abitua et al., 2015; Ikeda et al., 2013; Liu et al., 2023; Liu & Satou, 2019; Manni et al., 2004; Mazet et al., 2005; Papadogiannis et al., 2022; Wagner & Levine, 2012). To dissect the neural plate border of ascidian embryos at the molecular level, and to gain deeper insights into evolutionary origins of the neural crest and neurogenic placodes, we comprehensively analyzed expression patterns of transcription factor genes at single-cell resolution. We demonstrated that the ascidian neural plate border consists of three domains with distinct gene expression profiles: the anterior, inner lateral, and outer lateral domains. A cross-species comparison of transcriptomes from ascidians and zebrafish suggests that the anterior domain is homologous to zebrafish neurogenic placodes, the inner lateral domain to the neural crest and tail bud and the outer lateral domain to the median fin fold ectoderm. We propose that a tripartite neural plate border was present in the last common ancestor of vertebrates and tunicates, providing a blueprint for evolutionary emergence of vertebrate morphological novelties.

The teleost whole-genome duplication (TGD) contributed to functional diversification of opsins. Some TGD paralogs, including those of parapinopsin (PP), Vertebrate Ancient (VA) opsin, and long wavelength-sensitive (LWS) opsin, show different absorption spectra and/or expression patterns. However, our knowledge of detailed evolutionary processes and mechanisms by which TGD contributed to opsin diversification is still limited. Here, we report that TGD paralogs of parietopsin (PT1 and PT2) are retained in extant species. While most species, including the zebrafish, have only PT1, several characins, including the red piranha (Pygocentrus nattereri), retain both PT1 and PT2. The Mexican tetra (Astyanax mexicanus) and catfishes have only PT2. To assess the degree of functional diversification between PT1 and PT2, we characterized spectral properties and expression patterns. Maximum absorption spectra differ slightly among PTs. Those of red piranha PT1, PT2, Mexican tetra PT2, and Japanese catfish (Silurus asotus) PT2 were located at 517 nm, 528 nm, 517 nm, and ~535 nm, respectively. Fluorescence in situ hybridization showed that (1) piranha PT1 and PT2 are expressed in the same pineal cells, and (2) they are also co-expressed with PP1. Based on these findings, functional diversification of opsins after gene duplication is discussed.

RNA sequencing (RNA-seq) is widely used to investigate transcriptional programs in plant biology, yet the need to combine multiple specialized tools and bioinformatics expertise to convert raw sequencing reads into biologically interpretable results remains a major technical barrier for many plant biologists. Here, we present VizR (VIsualiZation of Rna seq), a web- based platform that integrates end-to-end RNA-seq analysis and visualization within a single integrated environment. VizR automates upstream processing, including quality control, adapter trimming, genome alignment, and transcript quantification, and connects the resulting expression data to downstream exploratory analyses. Its interface is designed to make expression patterns immediately searchable and interpretable: users can query genes through an equalizer-style expression-pattern interface, inspect expression profiles using inline heatmaps embedded in gene tables, and perform context-integrated gene ontology analysis throughout the workflow. VizR also supports comparative analysis through interactive Venn diagram module, allowing users to transfer gene sets directly from result tables. As a Docker- based application, VizR can be deployed locally and accessed through a standard web browser. By unifying automated RNA-seq processing, interactive visualization, and functional interpretation, VizR lowers the technical barrier to transcriptome analysis and provides a practical platform for plant biology research.

The long-standing challenge of seasonal influenza vaccines providing poor protection is attributed to the rapid and continuous evolution of the virus. In theory, the recommendation of vaccine strain is to predict the dominant strain with best fitness in the upcoming season. Here, we develop FutureFlu, a biologically-grounded framework that quantifies the fitness score of influenza variants in upcoming seasons, by integrating metrics on three levels: molecular genetic divergence, individual immune escape, and population-scale transmission dynamics. The fitness scores of influenza variants present strong positive correlation with their actual observed frequencies in the next seasons. Validation across 24 seasons of three influenza subtypes shows FutureFlu recommends antigenically matched vaccine strains more frequently than annual recommendations, particularly for challenging subtypes: 83.3% versus 45.8% seasons for A/H3N2, and 75.0% versus 33.3% seasons for B/Victoria. Furthermore, FutureFlu significantly outperforms the currently used methods in vaccine strain selection whether or not there is available antigenic data from hemagglutination inhibition (HI) assay, which provides a valuable supplement for WHO vaccine recommendation. To support global public health implementation, an open online platform (futureflu.com.cn) has been established to offer real-time viral fitness predictions and vaccine recommendations.

Local ancestry inference (LAI) reveals population compositions of an individuals chromo-somes, which empowers population genetics and genetic association studies of diverse populations. The recent availability of large genomic datasets from biobanks offers unprecedented opportunities for LAI. However, such datasets are typically only accessible from cloud-based platforms, and the lack of efficient and cost-effective tooling makes LAI prohibitive for resource-constrained researchers. Here, we develop Recomb-Mix Cloud, a cloud-ready pipeline for LAI based on Recomb-Mix, a recently introduced efficient LAI method. Recomb-Mix focuses on individual variants while maintaining a lower computational burden than other LAI methods focusing on genomic windows. Recomb-Mix Cloud offers a cloud-friendly complete pipeline from panel sample selection, marker alignment, compact reference panel construction, Recomb-Mix threading, and generating LAI calls in common data formats. Recomb-Mix Cloud also offers a set of pre-computed compact population reference panels constructed based on data from the Human Genome Diversity Project and the 1000 Genomes Project. Our results showed Recomb-Mix is about one and two orders of magnitude cheaper and faster than FLARE and RFMix, two popular LAI methods, while offering largely consistent LAI calls on the All of Us Researcher Workbench. The estimated overall compute cost per All of Us sample for whole-genome LAI analysis using Recomb-Mix Cloud with a pre-computed reference panel is just $0.01, compared with $0.43 for FLARE and $4.58 for RFMix. Therefore, Recomb-Mix Cloud is well-positioned to democratize local ancestry-based genetics research on modern biobank-sized data. The Recomb-Mix Cloud pipeline and the compact reference panels are available at https://github.com/ucfcbb/Recomb-Mix.

Aldehyde dehydrogenase 1a3 (Aldh1a3) is an enzyme involved in retinoic acid synthesis with dynamic expression patterns during development, including in the urogenital system. Here, we generated a bicistronic Aldh1a3-P2A-TagBFP knock-in mouse using CRISPR/Cas9 genome editing, inserting TagBFP immediately upstream of the endogenous Aldh1a3 stop codon. Correct targeting was confirmed by Oxford Nanopore long-read sequencing, and heterozygous and homozygous mice were viable and fertile without overt morphological abnormalities. TagBFP fluorescence faithfully overlapped with endogenous Aldh1a3 immunoreactivity and reproduced established expression domains in the developing craniofacial region, intestine, kidney, and broader urogenital system. Extensive characterization of the urogenital system revealed dynamic, spatially restricted BFP reporter activity in Aldh1a3-expressing domains across several key structures, including the ureteric bud and collecting duct lineage, seminal vesicles, caput epididymis, and developing uterine horns. The Aldh1a3-P2A-TagBFP mouse provides a fluorescent resource for visualizing Aldh1a3 expression across development and in adult tissues, including for the characterization of Aldh1a3-expressing domains in the urogenital system. The relatively low fluorescence intensity of TagBFP should be considered when assessing low-level reporter expression.

Archaea are promising chassis organisms in biotechnology, and the accurate annotation of their chromosomal replication origins (oriCs) is the key to unlocking their full potential. However, the existing Ori-Finder 2 web server suffers from low accuracy, slow speed, and limited scalability. In this study, we present Ori-Finder-Arch, an updated web server for high-performance oriC prediction in archaea. This pipeline integrates HMMER-based replication initiation protein (RIP) annotation, refined consensus motif recognition, and GC profile-based DNA unwinding element (DUE) detection. On a benchmark set of experimentally validated oriCs, Ori-Finder-Arch achieved a recall of 95.6% and a precision of 86.0%, substantially outperforming Ori-Finder 2 (62.2% and 63.6%, respectively), while running 4.75 times faster and supporting diverse assembly levels. When applied to the available archaeal assemblies, it successfully annotated 17,472 oriCs. Meanwhile, the web server provides interactive visualizations at different levels. In conclusion, Ori-Finder-Arch offers an efficient, accurate, and user-friendly platform for advanced studies of archaeal DNA replication initiation and synthetic biology applications, and is freely available at https://tubic.org/Ori-Finder-Arch/ and https://tubic.tju.edu.cn/Ori-Finder-Arch/.

Retinal development has been extensively studied and key transcriptional regulators that drive fate decisions have been identified for major cell classes. These findings were confirmed and deepened in recent years with the advance of single cell RNA sequencing (Scrase). However, many processes that guide progenitor to postmitotic cell differentiation remain elusive, especially since some genes seem to yield different cell populations without apparent correlation with expression level or timing. Here, differential transcript isoform usage might play a role in diversifying the function of developmental genes. In short-read based scRNAseq, isoforms can only be identified if a read maps to a unique sequence or exon junction. However, due to the sparsity and very short reads, these events are extremely rare. We combined a commercial scRNAseq kit, that produces barcoded, full-length cDNA with Oxford Nanopore Technologies based long-read sequencing to generate the first single cell long-read sequencing dataset of fetal human retina. It can help elucidate the role of alternative splicing in retinal development and guide the design of transcript-specific gene therapies for retinal regeneration.

Chromosome was "self-assembled" into a complex three-dimensional topology in the nucleus, which provided the structural basis for important biological processes such as gene expression regulation and cell differentiation. The current understanding of the three-dimensional organization of the genome is based on high-throughput sequencing and imaging technologies to visualize the conformation of chromatin in its native environment. This study proposes a new research perspective and technical means to use fusion genes to determine the interaction information and three-dimensional structure of chromosomes. This three-dimensional information provided by the fusion gene spectrum not only shows the universality of the spatial layout of chromosomes, but also increases the interpretability of the occurrence of fusion genes. The chromatin conformation capture data of multiple tissues and periods is significantly correlated with the strength of fusion genes. For example, the frequency of trans-interaction between chromosomes 11 and 17 was the highest, and the frequency of fusion gene occurrence corresponding to KMT2A on chromosome 11 was the highest. Therefore, we infer that this structural universality is a common feature of the human genome, which provides a theoretical basis and data for predicting chromosome fusion events.