Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification

The mytilin gene cluster: Shedding light on the enigmatic origin of mussel dispensable genes

Mussels exhibit a sophisticated innate immune response characterized by many highly variable molecules responsible for recognizing and killing potential pathogenic microorganisms. The complexity of this molecular arsenal is marked by the occurrence of gene presence-absence (PAV), a phenomenon that targets numerous expanded lineage-specific gene families. This phenomenon enhances inter-individual sequence variability, further enriching the diversity of the repertoire of molecules involved in the immune response. Until now, the origin of mussel dispensable genes, which, unlike core genes, are not shared by all individuals, has remained elusive. In this study, by analyzing the resequenced genomes of more than 160 individuals in four distinct species of the Mytilus complex, we characterize the repertoire of mytilin genes encoding hemocyte-specific antimicrobial peptides (AMPs). We define a canonical gene architecture comprising four protein-coding genes and two pseudogenes in most haplotypes. However, the organization of the locus displays a marked intra-specific diversity due to the presence of variable alleles, the frequent pseudogenization of mytilin G1 and structural variants associated with additional dispensable mytilin genes, which often retain features that support functional preservation. Molecular phylogeny supports an ancient origin for dispensable mytilin genes, predating the radiation of modern Mytilus species. This suggests that most widespread extant haplotypes derive from a larger and more complex ancestral mytilin gene cluster and that dispensable mytilin genes are vestigial AMPs that have been retained only in a few populations where their presence may have contributed to fitness advantages and local adaptation.

The comprehensive transcriptomic atlas of porcine immune tissues and the peripheral blood mononuclear cell (PBMC) immune dynamics reveal core immune genes

BACKGROUND

Viral diseases have profoundly influenced the sustainable development of the swine farming industry. With the development of genomics technology, the combination of transcriptome, genetic variation, immune response, and QTL mapping data to illustrate the interactions between pathogen and host immune system, will be an effective tool for identification of disease resistance genes in pigs. The immune system of an organism is the source of disease resistance in livestock, consisting of various immune tissues, as well as the immune cells and cytokines they produced. However, comprehensive systematic studies on transcriptome of porcine immune tissues are still rare. Poly(I:C), as a viral mimic, is commonly used to study immune responses of the body during viral infections, and serves as a valuable tool for investigating immune mechanisms in swine.

RESULTS

WGCNA analysis identified core immune genes across six immune tissues (bone marrow, jejunum, lymph node, PBMC, spleen, thymus) in Landrace pigs, which are also crucial for the development of PBMCs. The examination of the changes in the proportion of immune cells during three developmental stages (1-month-old, 4-month-old, 7-month-old) shows a shift from innate immunity to humoral immunity. By integrating different epigenetic genomics datasets, we identified several core immune genes and their causal variants, including IFI44, IFIT5, EIF2AK2 and others, which are closely related to immune development and response. Functional validation studies reveal that the IFI44 gene acts as a negative regulator of the antiviral response; its inhibition effect significantly reduced Poly(I:C)-induced cell necrosis, while enhancing apoptosis to combat viral infections.

CONCLUSION

Our study elucidated the fundamental transcriptional program in porcine immune tissues and the immunodynamics underlying development of PBMCs, identifying many core immune genes, including IFI44, which plays a critical negative regulator role in the antiviral response, providing valuable insights for breeding programs aimed at enhancing pig disease resistance.

An updated Gallus gallus genome annotation through multi-tissue transcriptome analysis

This study presents an updated Gallus gallus genome annotation through a comprehensive multi-tissue transcriptome analysis aimed at enhancing the Functional Annotation of Animal Genomes (FAANG) efforts. Generating RNA sequencing data from 20 different chicken tissues and cell types allowed for the identification of 110,930 transcript isoforms, including approximately 37,000 unannotated transcripts. This expanded resource significantly enhances transcript diversity and functional annotation. We analyzed allele-specific expression (ASE) across tissues, revealing 11,530 unique ASE genes. Our findings elucidate the intricate landscape of gene expression patterns and allelic imbalances. Notably, tissue-specific isoforms and differentially expressed genes, particularly in reproductive and muscle tissues, showcase their relevance for traits like fertility and meat quality. The identification of novel lncRNAs and protein-coding genes underscores the necessity of continued genomic improvements. This work contributes valuable resources for breeding strategies focused on disease resistance and productivity enhancement, addressing global agricultural challenges and the evolving needs of poultry science.

New perspectives on Drosophila melanogaster de novo gene origination revealed by investigation of ancient African genetic variation

De novo genes can be defined as sequences producing evolutionarily derived transcripts that are not homologous to transcripts produced in an ancestor. While they appear to be taxonomically widespread, there is little agreement regarding their abundance, their persistence times in genomes, the population genetic processes responsible for their spread or loss, or their possible functions. In Drosophila melanogaster, 2 approaches have been used to discover these genes and investigate their properties. One uses traditional comparative approaches and existing genomic resources and annotations. A second approach uses raw transcriptome data to discover unannotated genes for which there is no evidence of presence in related species. Investigations using the second approach have focused on D. melanogaster genotypes from recently established cosmopolitan populations. However, most of the genetic variation in the species is found in African populations, suggesting the possibility that fuller understanding of genetic novelties in the species may follow from studies of these populations. Here, we investigate de novo gene candidates expressed in testis and accessory glands in a sample of flies from Zambia and compare them with candidate de novo genes expressed in North American populations. We report a large number of previously undiscovered de novo gene candidates, most of which are expressed polymorphically. Many are predicted to code for secreted proteins. In spite of much different levels of genomic variation in Zambian and North American populations, they express similar numbers of candidate de novo genes. We find evidence from genetic analysis of Raleigh inbred lines that a fraction of rarely expressed gene candidates in this population represent deleterious transcription promoted by inbreeding depression. Many de novo gene candidates are expressed in multiple tissues and both sexes, raising questions about how they may interact with natural selection. The relative importance of positive and negative selection, however, remains unclear.

Gene Duplication and Alternative Splicing as Evolutionary Drivers of Proteome Specialization

Animals comprise hundreds of cell types, each with specialized biological functions. However, many genes expressed in each cell type belong to widely conserved gene families with ancestrally ubiquitous expression. This raises a paradox: how have these genes evolved to shape cell type-specific traits without compromising their ancestral function in all other cells? This can be achieved through gene duplication and the origin of regulated, alternatively spliced exons, which generate new related proteins in the form of paralogous genes and alternative isoforms, respectively. Here, we explore how such new related proteins can contribute to the evolution of specific cell types while preserving broader ancestral roles. Specifically, we separately classify possible expression and functional fates for new related proteins and discuss their interplays and evolutionary likelihood. Our primary hypothesis is that expression specialization, mostly coupled with functional specialization, is the predominant fate for both paralogous genes and alternative isoforms throughout animal evolution.

Novel compound heterozygous mutations in LMAN2L cause early childhood refractory epilepsy

BACKGROUND

Autosomal recessive mental retardation-52(MRT52) is a subtype of mental retardation whose clinical features include global developmental delay, severe intellectual disability with poor speech, and mild seizures in early childhood. Mutations in the LMAN2L gene resulting in mental retardation and seizures have been previously reported in 3 families. Here we describe 2 children in 1 family who presented with severe intellectual disability and drug-refractory epilepsy( DRE) at 2 months of age.

METHODS

Two individuals from 1 family admitted to the pediatric department of Qilu Hospital were included in the study. Whole exome sequencing (WES) was used to detect LMAN2L gene variants. The clinical manifestations, electroencephalography, neuroimaging characteristics and treatment of epilepsy were retrospectively analyzed.

RESULT

We identified two new LMAN2L compound heterozygous variants, c.476A > G, p.D159G, c.1060_1061del, p.S354Pfs*29, which appeared in two children from the same family. Both cases showed severe postnatal psychomotor developmental lag and developed seizures at 2 months of age, which manifested themselves in a variety of ways and were not relieved by the administration of multiple antiepileptic drugs.

CONCLUSION

Complex heterozygous mutations at the newly identified locus of LMAN2L cause refractory epilepsy, with epileptic symptoms beginning at 2 months of age and manifesting as multiple seizure types and developmental delays. This is the first report to link LMAN2L to the phenotype of epileptic encephalopathy and refractory epilepsy, suggesting that the heterozygous p.D159G, p.S354Pfs*29 LMAN2L variants are likely pathogenic. These 2 newly identified pathogenic variants enrich the spectrum of pathogenic variants in the LMAN2L gene.

Molecular subtyping of hypertensive disorders of pregnancy

Hypertensive disorders of pregnancy (HDP), including preeclampsia, affect 1 in 6 pregnancies, are major contributors to maternal morbidity and mortality, yet lack precision medicine strategies. Analyzing transcriptomic data from a prospectively-collected diverse cohort (n = 9102), this study reveals distinct RNA subtypes in maternal blood, reclassifying clinical HDP phenotypes like early/late-onset preeclampsia. The placental gene PAPPA2 strongly predicts the most severe forms of preeclampsia in individuals without pre-existing high risk factors, months before symptoms, and its overexpression correlates with earlier delivery in a dose-dependent manner. Further, molecular subtypes characterized by immune genes are upregulated in less severe forms of HDP. These results reclassify HDP clinical phenotypes into two distinct molecular subtypes, placental-associated or immune-associated. Validation performance for placental-associated HDP yields an AUC of 0.88 in the advanced maternal age population without pre-existing high risk factors. Molecular subtypes create new opportunities to apply precision-based medicine in maternal health.

Uncovering critical transitions and molecule mechanisms in disease progressions using Gaussian graphical optimal transport

Understanding disease progression is crucial for detecting critical transitions and finding trigger molecules, facilitating early diagnosis interventions. However, the high dimensionality of data and the lack of aligned samples across disease stages have posed challenges in addressing these tasks. We present a computational framework, Gaussian Graphical Optimal Transport (GGOT), for analyzing disease progressions. The proposed GGOT uses Gaussian graphical models, incorporating protein interaction networks, to characterize the data distributions at different disease stages. Then we use population-level optimal transport to calculate the Wasserstein distances and transport between stages, enabling us to detect critical transitions. By analyzing the per-molecule transport distance, we quantify the importance of each molecule and identify trigger molecules. Moreover, GGOT predicts the occurrence of critical transitions in unseen samples and visualizes the disease progression process. We apply GGOT to the simulation dataset and six disease datasets with varying disease progression rates to substantiate its effectiveness. Compared to existing methods, our proposed GGOT exhibits superior performance in detecting critical transitions.

HuTAge: a comprehensive human tissue- and cell-specific ageing signature atlas

Summary

Ageing is a complex process that involves interorgan and intercellular interactions. To obtain a clear understanding of ageing, cross-tissue single-cell data resources are required. However, a complete resource for humans is not available. To bridge this gap, we developed HuTAge, a comprehensive resource that integrates cross-tissue age-related information from The Genotype-Tissue Expression project with cross-tissue single-cell information from Tabula Sapiens to provide human tissue- and cell-specific ageing molecular information.

Availability and implementation

HuTAge is implemented within an R Shiny application and can be freely accessed at https://igcore.cloud/GerOmics/HuTAge/home. The source code is available at https://github.com/matsui-lab/HuTAge.

Solanum pan-genetics reveals paralogues as contingencies in crop engineering

Pan-genomics and genome-editing technologies are revolutionizing breeding of global crops1,2. A transformative opportunity lies in exchanging genotype-to-phenotype knowledge between major crops (that is, those cultivated globally) and indigenous crops (that is, those locally cultivated within a circumscribed area)3-5 to enhance our food system. However, species-specific genetic variants and their interactions with desirable natural or engineered mutations pose barriers to achieving predictable phenotypic effects, even between related crops6,7. Here, by establishing a pan-genome of the crop-rich genus Solanum8 and integrating functional genomics and pan-genetics, we show that gene duplication and subsequent paralogue diversification are major obstacles to genotype-to-phenotype predictability. Despite broad conservation of gene macrosynteny among chromosome-scale references for 22 species, including 13 indigenous crops, thousands of gene duplications, particularly within key domestication gene families, exhibited dynamic trajectories in sequence, expression and function. By augmenting our pan-genome with African eggplant cultivars9 and applying quantitative genetics and genome editing, we dissected an intricate history of paralogue evolution affecting fruit size. The loss of a redundant paralogue of the classical fruit size regulator CLAVATA3 (CLV3)10,11 was compensated by a lineage-specific tandem duplication. Subsequent pseudogenization of the derived copy, followed by a large cultivar-specific deletion, created a single fused CLV3 allele that modulates fruit organ number alongside an enzymatic gene controlling the same trait. Our findings demonstrate that paralogue diversifications over short timescales are underexplored contingencies in trait evolvability. Exposing and navigating these contingencies is crucial for translating genotype-to-phenotype relationships across species.

Localized Tissue-Specific Gene Expression and Gene Duplications are Important Sources of Social Morph Differences in a Social Bumblebee

Understanding the expression of multiple behaviorally and morphologically distinct phenotypes from a single genome represents a fundamental topic in evolutionary biology. Central to the complication of expressing phenotypes, which may differ in their optima, is the sharing of largely the same genome, which is predicted to manifest in conflict at the genomic level. This is particularly true for social insects where molecular mechanisms, such as differential gene expression, contribute to observed phenotypic differences between reproductive and nonreproductive morphs. In comparison, other mechanisms, such as tissue-specific expression and gene duplications, have been posited as contributing to social morph differences yet formal investigations are limited. Here, using a combination of transcriptomics for multiple tissues and comparative genomics, we show that in a social bumblebee, the strongest differences in gene expression are found in reproductive tissues, such as the spermatheca, an organ previously believed as vestigial in workers but recently shown as functional. In comparison, we find modest expression differences in genes between queens and workers for the brain, fat body, and ovary, which are traditionally investigated in social evolution. Interestingly, morph-biased genes in these three tissues display higher tissue-specificity suggesting that while social morphs may express a shared core transcriptome, localized expression profiles may contribute to phenotypic differences. We also find evidence of differential usage of duplicated genes by queens and workers, highlighting structural variants as a contributing factor to morph differences. Collectively, our findings highlight how social insects can utilize tissue-specific gene regulation and structural variants to contribute to phenotypic differences.

Enhancing oxygen utilization and mitigating oxidative stress in Tibetan chickens for adaptation to high-altitude hypoxia

Tibetan chicken (TBC) is one of the native poultry species that is well adapted to the high-altitude environment of the Qinghai-Tibet Plateau. To elucidate the genetic mechanisms underlying adaptation, the transcriptomes of five tissues (heart (HE), lung (LU), liver (LI), ovary (OV), and abdominal fat (AB)) were compared between TBCs and Roman chickens (RMCs) inhabiting the plateau for one year. Moreover, weighted gene co-expression network analysis (WGCNA) was applied to detect tissue-associated modules and hub genes. A total of 1105, 239, 400, 483, and 275 differentially expressed genes (DEGs) were identified in the LI, HE, LU, AB, and OV tissues, respectively. Fifteen tissue-specific modules were identified in TBC and thirteen in RMC. Analysis of transcription factor (TF) binding sites revealed nineteen hub TFs in TBC and twenty in RMC across the pool of hub genes in these two breeds. Functional enrichment analyses demonstrated that TBC exhibited robust capacity for oxygen transport, heme binding, oxidative phosphorylation, and antioxidant responses in high-altitude regions. Further investigation of the function of hub TFs indicated the involvement of ATF4, CEBPA, TCF7L1, and GFI1B in improving oxygen transport in TBCs. These hub TFs were associated with angiogenesis or hematopoiesis and likely linked to various regulatory functions and facilitate communication across multiple tissues. In conclusion, TBCs have developed a systemic adaptive mechanism to cope with high altitudes, involving the coordinated transcriptional regulation in multi-tissues to enhance oxygen transport and utilization, along with amelioration of oxidative stress.

Survey of gene, lncRNA and transposon transcription patterns in four mouse organs highlights shared and organ-specific sex-biased regulation

BACKGROUND

Sex-biased gene regulation is the basis of sexual dimorphism in phenotypes and has been studied across different cell types and different developmental stages. However, sex-biased expression of transposable elements (TEs), which represent nearly half of the mammalian genome and have the potential of influencing genome integrity and regulation, remains underexplored.

RESULTS

We report a survey of gene, lncRNA, and TE expression in four organs from mice with different combinations of gonadal and genetic sex. The data show remarkable variability among organs with respect to the impact of gonadal sex on transcription with the strongest effects observed in the liver. In contrast, the X-chromosome dosage alone had a modest influence on sex-biased transcription across organs, albeit interaction between X-dosage and gonadal sex cannot be ruled out. The presence of the Y-chromosome influences TE, but not gene or lncRNA, expression in the liver. Notably, 90% of sex-biased TEs (sDETEs) reside in clusters. Moreover, 54% of these clusters overlap or reside less than 100 kb from sex-biased genes or lncRNAs, share the same sex bias, and also have higher expression levels than sDETE clusters that do not co-localize with other types of sex-biased transcripts. We test the heterochromatic sink hypothesis that predicts higher expression of TEs in XX individuals finding no evidence to support it.

CONCLUSIONS

Our data show that sex-biased expression of TEs varies among organs with the highest numbers of sDETEs found in the liver following trends observed for genes and lncRNAs. It is enhanced by proximity to other types of sex-biased transcripts.

Multi-omics analysis reveals critical cis-regulatory roles of transposable elements in livestock genomes

Transposable elements (TEs) are important sources of genetic and regulatory variation, yet their functional roles in domesticated animals remain insufficiently explored. To address this gap, we comprehensively annotated TE types, ages, and distributions in the genomes of pig (Sus scrofa), cattle (Bos taurus), and chicken (Gallus gallus). Our analysis revealed species-specific patterns in TE abundance, amplification, and activity in modern genomes. By integrating transcriptomic and epigenomic data, we explored the impact of specific TE types on cis-regulatory elements (CREs) and constructed a TE expression atlas across five tissues in all three species. Our findings underscored the critical roles of tissue-specific TE expression and chromatin accessibility in regulating tissue-specific biological processes. Most notably, we developed a computational framework to uncover TE-mediated gene regulatory networks (TE-GRNs). Our findings provide valuable insights into the regulatory functions of TEs in livestock and offer a robust approach for studying TE-GRNs in diverse biological contexts.

Long-read transcriptomics of a diverse human cohort reveals widespread ancestry bias in gene annotation

Accurate gene annotations are fundamental for interpreting genetic variation, cellular function, and disease mechanisms. However, current human gene annotations are largely derived from transcriptomic data of individuals with European ancestry, introducing potential biases that remain uncharacterized. Here, we generate over 800 million full-length reads with long-read RNA-seq in 43 lymphoblastoid cell line samples from eight genetically-diverse human populations and build a cross-ancestry gene annotation. We show that transcripts from non-European samples are underrepresented in reference gene annotations, leading to systematic biases in allele-specific transcript usage analyses. Furthermore, we show that personal genome assemblies enhance transcript discovery compared to the generic GRCh38 reference assembly, even though genomic regions unique to each individual are heavily depleted of genes. These findings underscore the urgent need for a more inclusive gene annotation framework that accurately represents global transcriptome diversity.

Machine learning-based prediction reveals kinase MAP4K4 regulates neutrophil differentiation through phosphorylating apoptosis-related proteins

Neutrophils, an essential innate immune cell type with a short lifespan, rely on continuous replenishment from bone marrow (BM) precursors. Although it is established that neutrophils are derived from the granulocyte-macrophage progenitor (GMP), the molecular regulators involved in the differentiation process remain poorly understood. Here we developed a random forest-based machine-learning pipeline, NeuRGI (Neutrophil Regulatory Gene Identifier), which utilized Positive-Unlabeled Learning (PU-learning) and neural network-based in silico gene knockout to identify neutrophil regulators. We interrogated features including gene expression dynamics, physiological characteristics, pathological relatedness, and gene conservation for the model training. Our identified pipeline leads to identifying Mitogen-Activated Protein Kinase-4 (MAP4K4) as a novel neutrophil differentiation regulator. The loss of MAP4K4 in hematopoietic stem cells and progenitors in mice induced neutropenia and impeded the differentiation of neutrophils in the bone marrow. By modulating the phosphorylation level of proteins involved in cell apoptosis, such as STAT5A, MAP4K4 delicately regulates cell apoptosis during the process of neutrophil differentiation. Our work presents a novel regulatory mechanism in neutrophil differentiation and provides a robust prediction model that can be applied to other cellular differentiation processes.

Dynamics of X chromosome hyper-expression and inactivation in male tissues during stick insect development

Differentiated sex chromosomes are frequently associated with major transcriptional changes: the evolution of dosage compensation (DC) to equalize gene expression between the sexes and the establishment of meiotic sex chromosome inactivation (MSCI). Our study investigates the mechanisms and developmental dynamics of dosage compensation and meiotic sex chromosome inactivation in the stick insect species T. poppense. Stick insects are characterized by XX/X0 sex determination, with an X chromosome that likely evolved prior to the diversification of insects over 450 Mya. We generated a chromosome-level genome assembly and analyzed gene expression from various tissues (brain, gut, antennae, leg, and reproductive tract) across developmental stages in both sexes. Our results show that complete dosage compensation is maintained in male somatic tissues throughout development, mediated by upregulation of the single X chromosome. Contrarily, in male reproductive tissues, dosage compensation is present only in the early nymphal stages. As males reach the 4th nymphal stage and adulthood, X-linked gene expression diminishes, coinciding with the onset of meiosis and MSCI, which involves classical silencing histone modifications. These findings reveal the dynamic regulation of X-linked gene expression in T. poppense, and suggest that reduced X-expression in insect testes is generally driven by MSCI rather than an absence of dosage compensation mechanisms. Our work provides critical insights into sex chromosome evolution and the complex interplay of dosage compensation and MSCI across tissues and developmental stages.

Network properties constrain natural selection on gene expression in Caenorhabditis elegans

Gene regulatory networks (GRNs) integrate genetic and environmental signals to coordinate complex phenotypes and evolve through a balance of selection and drift. Using publicly available datasets from Caenorhabditis elegans, we investigated the extent of natural selection on transcript abundance by linking population-scale variation in gene expression to fecundity, a key fitness component. While the expression of most genes covaried only weakly with fitness, which is typical for polygenic traits, we identified seven transcripts under significant directional selection. These included nhr-114 and feh-1, implicating variation in nutrient-sensing and metabolic pathways as impacting fitness. Stronger directional selection on tissue-specific and older genes highlighted the germline and nervous system as focal points of adaptive change. Network position further constrained selection on gene expression; high-connectivity genes faced stronger stabilizing and directional selection, highlighting GRN architecture as a key factor in microevolutionary dynamics. The activity of transcription factors such as zip-3, which regulates mitochondrial stress responses, emerged as targets of selection, revealing potential links between energy homeostasis and fitness. Our findings demonstrate how GRNs mediate the interplay between selection and drift, shaping microevolutionary trajectories of gene expression and phenotypic diversity.

Time-dependent RNA transcriptional profiling of abomasal mucosa in cattle infected with Ostertagia ostertagi

In this study, we infected Holstein calves with Ostertagia ostertagi stage 3 larvae (L3) and determined gene expression profiles of abomasal fundic and pyloric mucosa by RNA sequencing (RNA-seq) at 3-5, 7-9, 10, and 21 days post-infection (dpi), which represent late L3 and early L4 (between 3-5 dpi), mid to late L4 (between 7-9 and 10 dpi) and adult stages (21 dpi) of the parasitic stage. Bioinformatics analyses were performed to profile the transcriptomic changes over time as well as between cattle abomasal tissues. The results will help understand the gastric responses of the host, especially the immune responses, at different phases of early nematode infection. Such an undertaking is crucial for an in-depth comprehension of host responses, where immunologic reagents for cattle are highly limited. The RNA-seq datasets generated in this study provide a vital data resource, allowing for future comparative analyses to similar data resources or using more advanced analytical technologies in mechanisms of host-parasite interactions.

Gene expression atlas of the Colorado potato beetle (Leptinotarsa decemlineata)

The Colorado potato beetle (CPB) is a major pest of potato crops, known for its remarkable ability to develop resistance to more than 50 pesticides. For decades, CPB has served as a model species for studying insecticide resistance, insect physiology, diapause, reproduction, and evolution. However, research progress on CPB has been hindered by the lack of comprehensive genomic and transcriptomic resources. Here, leveraging a recently established chromosome-level genome assembly, we constructed a gene expression atlas of CPB using transcriptomic data from 61 samples representing major organs and developmental stages. By integrating short- and long-read sequencing technologies, we enhanced the genome annotation and identified 6,623 additional genes that were previously undetected. Furthermore, we developed a web portal to facilitate the search and visualization of the gene expression atlas, providing an accessible resource for the research community. The CPB gene expression atlas offers valuable tools and comprehensive data that will accelerate future research in pest control and insect biology.

Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits

There is growing evidence that a wide range of human diseases and physiological traits are influenced by genetic variation of cis-regulatory elements. We and others have shown that a subset of promoter elements, termed Epromoters, also function as enhancer regulators of distal genes. This opens a paradigm in the study of regulatory variants, as single nucleotide polymorphisms (SNPs) within Epromoters might influence the expression of several (distal) genes at the same time, which could disentangle the identification of disease-associated genes. Here, we built a comprehensive resource of human Epromoters using newly generated and publicly available high-throughput reporter assays. We showed that Epromoters display intrinsic and epigenetic features that distinguish them from typical promoters. By integrating Genome-Wide Association Studies (GWAS), expression Quantitative Trait Loci (eQTLs) and 3D chromatin interactions, we found that regulatory variants at Epromoters are concurrently associated with more disease and physiological traits, as compared with typical promoters. To dissect the regulatory impact of Epromoter variants, we evaluated their impact on regulatory activity by analyzing allelic-specific high-throughput reporter assays and provided reliable examples of pleiotropic Epromoters. In summary, our study represents a comprehensive resource of regulatory variants supporting the pleiotropic role of Epromoters.

A gene expression atlas of Nicotiana tabacum across various tissues at transcript resolution

Alternative splicing (AS) expands the transcriptome diversity by selectively splicing exons and introns from pre-mRNAs to generate different protein isoforms. This mechanism is widespread in eukaryotes and plays a crucial role in development, environmental adaptation, and stress resistance. In this study, we collected 599 tobacco RNA-seq datasets from 35 projects. 207,689 transcripts were identified in this study, of which 35,519 were annotated in the reference genome, while 172,170 transcripts were newly annotated. Additionally, tissue-specific analysis revealed 4,585 transcripts that were uniquely expressed in different tissues, highlighting the complexity and specialization of tobacco gene expression. The analysis of AS events (ASEs) across different tissues showed significant variability in the expression levels of ASE-derived transcripts, with some of these transcripts being associated with stress resistance, such as the geranyl diphosphate synthase (GGPPS). Moreover, we identified 21,763 splicing quantitative trait locus (sQTLs), which were enriched in genes involved in biological processes such as histone acetylation. Furthermore, sQTLs involved genes related to plant hormone signal transduction, terpenoid backbone biosynthesis, and other resistance pathways. These findings not only reveal the diversity of gene expression in tobacco but also provide new insights and strategies for improving tobacco quality and resistance.

Epigene functional diversity: isoform usage, disordered domain content, and variable binding partners

BACKGROUND

Epigenes are defined as proteins that perform post-translational modification of histones or DNA, reading of post-translational modifications, form complexes with epigenetic factors or changing the general structure of chromatin. This specialized group of proteins is responsible for controlling the organization of genomic DNA in a cell-type specific fashion, controlling normal development in a spatial and temporal fashion. Moreover, mutations in epigenes have been implicated as causal in germline pediatric disorders and as driver mutations in cancer. Despite their importance to human disease, to date, there has not been a systematic analysis of the sources of functional diversity for epigenes at large. Epigenes' unique functions that require the assembly of pools within the nucleus suggest that their structure and amino acid composition would have been enriched for features that enable efficient assembly of chromatin and DNA for transcription, splicing, and post-translational modifications.

RESULTS

In this study, we assess the functional diversity stemming from gene structure, isoforms, protein domains, and multiprotein complex formation that drive the functions of established epigenes. We found that there are specific structural features that enable epigenes to perform their variable roles depending on the cellular and environmental context. First, epigenes are significantly larger and have more exons compared with non-epigenes which contributes to increased isoform diversity. Second epigenes participate in more multimeric complexes than non-epigenes. Thirdly, given their proposed importance in membraneless organelles, we show epigenes are enriched for substantially larger intrinsically disordered regions (IDRs). Additionally, we assessed the specificity of their expression profiles and showed epigenes are more ubiquitously expressed consistent with their enrichment in pediatric syndromes with intellectual disability, multiorgan dysfunction, and developmental delay. Finally, in the L1000 dataset, we identify drugs that can potentially be used to modulate expression of these genes.

CONCLUSIONS

Here we identify significant differences in isoform usage, disordered domain content, and variable binding partners between human epigenes and non-epigenes using various functional genomics datasets from Ensembl, ENCODE, GTEx, HPO, LINCS L1000, and BrainSpan. Our results contribute new knowledge to the growing field focused on developing targeted therapies for diseases caused by epigene mutations, such as chromatinopathies and cancers.

Mitigating Metabolic Dysfunction-associated Steatotic Liver Disease (MASLD): The Role of Bioactive Phytoconstituents in Indian Culinary Spices

PURPOSE OF REVIEW

The term metabolic dysfunction-associated steatotic liver disease (MASLD) refers to a group of progressive steatotic liver conditions that include metabolic dysfunction-associated steatohepatitis (MASH), which has varying degrees of liver fibrosis and may advance to cirrhosis, and independent hepatic steatosis. MASLD has a complex underlying mechanism, with patients exhibiting diverse causes and phases of the disease. India has a pool prevalence of MASLD of 38.6% in adults. In 2023, the term NAFLD has been redefined and changed to MASLD. Currently, there are no drugs approved by the FDA for the treatment of MASLD. This study investigates the potential of bioactive phytoconstituents present in spices as a therapeutic approach for MASLD. Moreover, it offers comprehensive data on several pre-clinical studies of bioactive phytoconstituents derived from spices that primarily focus on treating obesity-associated MASLD.

RECENT FINDINGS

Spices include a high amount of bioactive chemicals and several research have indicated their diverse pharmacological activities. Bioactive phytoconstituents from common Indian spices like cinnamic acid, eugenol, curcumin, allicin, 6-gingerols, capsaicin, piperine, eucalyptol, trigonelline, and linalool have been reported to exhibit anti-MASLD effects both in-vivo and in-vitro. Bioactive phytoconstituents from different culinary species of India have shown promising potential against MASLD in pre-clinical status. Further clinical studies on a large scale would be beneficial for paving the path to the development of a new drug which is the need of time.

Testis- and ovary-expressed polo-like kinase transcripts and gene duplications affect male fertility when expressed in the Drosophila melanogaster germline

Polo-like kinases (Plks) are essential for spindle attachment to the kinetochore during prophase and the subsequent dissociation after anaphase in both mitosis and meiosis. There are structural differences in the spindle apparatus among mitosis, male meiosis, and female meiosis. It is therefore possible that alleles of Plk genes could improve kinetochore attachment or dissociation in spermatogenesis or oogenesis, but not both. These opposing effects could result in sexually antagonistic selection at Plk loci. In addition, Plk genes have been independently duplicated in many different evolutionary lineages within animals. This raises the possibility that Plk gene duplication may resolve sexual conflicts over mitotic and meiotic functions. We investigated this hypothesis by comparing the evolution, gene expression, and functional effects of the single Plk gene in Drosophila melanogaster (polo) and the duplicated Plks in D. pseudoobscura (Dpse-polo and Dpse-polo-dup1). Dpse-polo-dup1 is expressed primarily in testis, while other Drosophila Plk genes have broader expression profiles. We found that the protein-coding sequence of Dpse-polo-dup1 is evolving significantly faster than a canonical polo gene across all functional domains, yet the essential structure of the encoded protein has been retained. We present additional evidence that the faster evolution of Dpse-polo-dup1 is driven by the adaptive fixation of amino acid substitutions. We also found that over or ectopic expression of polo or Dpse-polo in the D. melanogaster male germline resulted in greater male infertility than expression of Dpse-polo-dup1. Last, expression of Dpse-polo or an ovary-derived transcript of polo in the male germline caused males to sire female-biased broods, suggesting that some Plk transcripts can affect the meiotic transmission of the sex chromosomes in the male germline. However, there was no sex bias in the progeny when Dpse-polo-dup1 was ectopically expressed, or a testis-derived transcript of polo was overexpressed in the D. melanogaster male germline. Our results therefore suggest that Dpse-polo-dup1 may have experienced positive selection to improve its regulation of the male meiotic spindle, resolving sexual conflict over meiotic Plk functions. Alternatively, Dpse-polo-dup1 may encode a hypomorphic Plk that has reduced deleterious effects when overexpressed in the male germline. Similarly, testis transcripts of D. melanogaster polo may be optimized for regulating the male meiotic spindle, and we provide evidence that the untranslated regions of the polo transcript may be involved in sex-specific germline functions.

Plasma protein-based organ-specific aging and mortality models unveil diseases as accelerated aging of organismal systems

Aging is a complex process manifesting at molecular, cellular, organ, and organismal levels. It leads to functional decline, disease, and ultimately death, but the relationship between these fundamental biomedical features remains elusive. By applying elastic net regularization to plasma proteome data of over 50,000 human subjects in the UK Biobank and other cohorts, we report interpretable organ-specific and conventional aging models trained on chronological age, mortality, and longitudinal proteome data. These models predict organ/system-specific disease and indicate that men age faster than women in most organs. Accelerated organ aging leads to diseases in these organs, and specific diets, lifestyles, professions, and medications influence organ aging rates. We then identify proteins driving these associations with organ-specific aging. Our analyses reveal that age-related chronic diseases epitomize accelerated organ- and system-specific aging, modifiable through environmental factors, advocating for both universal whole-organism and personalized organ/system-specific anti-aging interventions.

Chromosome-level echidna genome illuminates evolution of multiple sex chromosome system in monotremes

BACKGROUND

A thorough analysis of genome evolution is fundamental for biodiversity understanding. The iconic monotremes (platypus and echidna) feature extraordinary biology. However, they also exhibit rearrangements in several chromosomes, especially in the sex chromosome chain. Therefore, the lack of a chromosome-level echidna genome has limited insights into genome evolution in monotremes, in particular the multiple sex chromosomes complex.

RESULTS

Here, we present a new long reads-based chromosome-level short-beaked echidna (Tachyglossus aculeatus) genome, which allowed the inference of chromosomal rearrangements in the monotreme ancestor (2n = 64) and each extant species. Analysis of the more complete sex chromosomes uncovered homology between 1 Y chromosome and multiple X chromosomes, suggesting that it is the ancestral X that has undergone reciprocal translocation with ancestral autosomes to form the complex. We also identified dozens of ampliconic genes on the sex chromosomes, with several ancestral ones expressed during male meiosis, suggesting selective constraints in pairing the multiple sex chromosomes.

CONCLUSION

The new echidna genome provides an important basis for further study of the unique biology and conservation of this species.

Multiomics analysis provides insights into musk secretion in muskrat and musk deer

BACKGROUND

Musk, secreted by the musk gland of adult male musk-secreting mammals, holds significant pharmaceutical and cosmetic potential. However, understanding the molecular mechanisms of musk secretion remains limited, largely due to the lack of comprehensive multiomics analyses and available platforms for relevant species, such as muskrat (Ondatra zibethicus Linnaeus) and Chinese forest musk deer (Moschus berezovskii Flerov).

RESULTS

We generated chromosome-level genome assemblies for the 2 species of muskrat (Ondatra zibethicus Linnaeus) and musk deer (Moschus berezovskii Flerov), along with 168 transcriptomes from various muskrat tissues. Comparative analysis with 11 other vertebrate genomes revealed genes and amino acid sites with signs of adaptive convergent evolution, primarily linked to lipid metabolism, cell cycle regulation, protein binding, and immunity. Single-cell RNA sequencing in muskrat musk glands identified increased acinar/glandular epithelial cells during secretion, highlighting the role of lipometabolism in gland development and evolution. Additionally, we developed MuskDB (http://muskdb.cn/home/), a freely accessible multiomics database platform for musk-secreting mammals.

CONCLUSIONS

The study concludes that the evolution of musk secretion in muskrats and musk deer is likely driven by lipid metabolism and cell specialization. This underscores the complexity of the musk gland and calls for further investigation into musk secretion-specific genetic variants.

Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants

BACKGROUND

Three-dimensional (3D) chromatin organization is emerging as a key factor in gene regulation in eukaryotes. Recent studies using high-resolution Hi-C analysis have explored fine-scale local chromatin contact domains in plants, as exemplified by the basic contact domains established at accessible gene border regions in Arabidopsis (Arabidopsis thaliana). However, we lack effective tools to identify these contact domains and examine their structural dynamics.

RESULTS

We developed the Hi-C-based 3D Gene Domain analysis Tool (Hi-GDT) to identify fine-scale local chromatin contact domains in plants, with a particular focus on gene borders. Hi-GDT successfully identifies local contact domains, including single-gene and multigene domains, with high reproducibility. Hi-GDT can also be used to discover local contact domains that are differentially organized in association with differences in gene expression between tissue types, genotypes, or in response to environmental stimuli.

CONCLUSIONS

Hi-GDT is a valuable tool for identifying genes regulated by dynamic 3D conformational changes, expanding our understanding of the structural and functional relevance of local 3D chromatin organization in plants. Hi-GDT is publicly available at https://github.com/CDL-HongwooLee/Hi-GDT.

Positive Selection on Mammalian Immune Genes-Effects of Gene Function and Selective Constraint

Genome-wide analyses of various taxa have repeatedly shown that immune genes are important targets of positive selection. However, little is known about what factors determine which immune genes are under positive selection. To address this question, we here focus on the mammalian immune system and investigate the importance of gene function and other factors such as gene expression, protein-protein interactions, and overall selective constraint as determinants of positive selection. We compiled a list of >1,100 immune genes that were divided into six functional categories and analyzed using data from rodents. Genes encoding proteins that are in direct interactions with pathogens, such as pattern recognition receptors (PRRs), are often expected to be key targets of positive selection. We found that categories containing cytokines, cytokine receptors, and other cell surface proteins involved in, for example, cell-cell interactions were at least as important targets as PRRs, with three times higher rate of positive selection than nonimmune genes. The higher rate of positive selection on cytokines and cell surface proteins was partly an effect of these categories having lower selective constraint. Nonetheless, cytokines had a higher rate of positive selection than nonimmune genes even at a given level of selective constraint, indicating that gene function per se can also be a determinant of positive selection. These results have broad implications for understanding the causes of positive selection on immune genes, specifically the relative importance of host-pathogen coevolution versus other processes.

Multiomic analysis of genes related to oil traits in legumes provide insights into lipid metabolism and oil richness in soybean

Soybean (Glycine max) and common bean (Phaseolus vulgaris) diverged approximately 19 million years ago. While these species share a whole-genome duplication (WGD), the Glycine lineage experienced a second, independent WGD. Despite the significance of these WGDs, their impact on gene families related to oil-traits remains poorly understood. Here, we report an in-depth investigation of oil-related gene families in soybean, common bean, and twenty-eight other legume species. We adopted a systematic approach that included 605 RNAseq samples for transcriptome and co-expression analyses, identification of orthologous groups, gene duplication modes and evolutionary rates, and family expansions and contractions. We curated a list of oil candidate genes and found that 91.5% of the families containing these genes expanded in soybean in comparison to common bean. Notably, we observed an expansion of triacylglycerol (TAG) biosynthesis (∼3:1) and an erosion of TAG degradation (∼1.4:1) families in soybean in comparison to common bean. In addition, TAG degradation genes were two-fold more expressed in common bean than in soybean, suggesting that oil degradation is also important for the sharply contrasting seed oil contents in these species. We found 17 transcription factor hub genes that are likely regulators of lipid metabolism. Finally, we inferred expanded and contracted families and correlated these patterns with oil content found in different legume species. In summary, our results do not only shed light on the evolution of oil metabolism genes in soybean, but also present multifactorial evidence supporting the prioritization of promising candidate genes that, if experimentally validated, could accelerate the development of high-oil soybean varieties.

Integrated transcriptomic analysis reveals evolutionary and developmental characteristics of tendon ossification in teleost

BACKGROUND

Intermuscular bones (IBs) are segmental intramembranous ossifications located within myosepta. They share similarities with tendon ossification, a form of heterotopic ossification (HO). The mechanisms underlying IB formation remain incompletely understood.

RESULTS

In this study, we systematically analyzed transcriptome data across multiple tissues, species, time points, and resolutions in teleosts. First, we identified IB-specific expression genes using the tau index method. Through cross-species comparisons of the tendon development process, we discovered that candidate genes were primarily enriched in extracellular matrix organization, ossification, regulation of angiogenesis, and other related processes. We also revealed that some of these candidate genes are abnormally expressed in runx2b-/- zebrafish, which lack IBs. To clarify the trajectory of cell differentiation during IB formation, we demonstrated that myoseptal stem cells differentiate into osteoblasts, fibroblasts, and tenocytes in runx2b+/+ zebrafish. However, in runx2b-/- zebrafish, the differentiation of myoseptal stem cell into osteoblast was inhibited, while differentiation into clec3bb + tenocyte and fibroblast was enhanced. Additionally, runx2b deficiency led to the upregulation of clec3bb expression in the clec3bb + tenocyte cluster. Notably, a compensatory effect was observed in cell differentiation and gene expression in runx2b-/- zebrafish, suggesting that runx2b and the candidate genes, such as clec3bb, were involved in the gene network of IB development.

CONCLUSIONS

The results elucidate cell differentiation process during tendon ossification in teleosts and identify the key factor clec3bb involved in this process. These findings provide a foundation for understanding tendon ossification in teleosts and for further research on tendon ossification in mammals.

The genome of the sapphire damselfish Chrysiptera cyanea: a new resource to support further investigation of the evolution of Pomacentrids

The number of high-quality genomes is rapidly increasing across taxa. However, it remains limited for coral reef fish of the Pomacentrid family, with most research focused on anemonefish. Here, we present the first assembly for a Pomacentrid of the genus Chrysiptera. Using PacBio long-read sequencing with 94.5× coverage, the genome of the Sapphire Devil, Chrysiptera cyanea, was assembled and annotated. The final assembly comprises 896 Mb pairs across 91 contigs, with a BUSCO completeness of 97.6%, and 28,173 genes. Comparative analyses with chromosome-scale assemblies of related species identified contig-chromosome correspondences. This genome will be useful as a comparison to study specific adaptations linked to the symbiotic life of closely related anemonefish. Furthermore, C. cyanea is found in most tropical coastal areas of the Indo-West Pacific and could become a model for environmental monitoring. This work will expand coral reef research efforts, highlighting the power of long-read assemblies to retrieve high quality genomes.

A generative framework for enhanced cell-type specificity in rationally designed mRNAs

mRNA delivery offers new opportunities for disease treatment by directing cells to produce therapeutic proteins. However, designing highly stable mRNAs with programmable cell type-specificity remains a challenge. To address this, we measured the regulatory activity of 60,000 5' and 3' untranslated regions (UTRs) across six cell types and developed PARADE (Prediction And RAtional DEsign of mRNA UTRs), a generative AI framework to engineer untranslated RNA regions with tailored cell type-specific activity. We validated PARADE by testing 15,800 de novo-designed sequences across these cell lines and identified many sequences that demonstrated superior specificity and activity compared to existing RNA therapeutics. mRNAs with PARADE-engineered UTRs also exhibited robust tissue-specific activity in animal models, achieving selective expression in the liver and spleen. We also leveraged PARADE to enhance mRNA stability, significantly increasing protein output and therapeutic durability in vivo. These advancements translated to notable increases in therapeutic efficacy, as PARADE-designed UTRs in oncosuppressor mRNAs, namely PTEN and P16, effectively reduced tumor growth in patient-derived neuroglioma xenograft models and orthotopic mouse models. Collectively, these findings establish PARADE as a versatile platform for designing safer, more precise, and highly stable mRNA therapies.

Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton

Although epigenetic modification has long been recognized as a vital force influencing gene regulation in plants, the dynamics of chromatin structure implicated in the intertwined transcriptional regulation of duplicated genes in polyploids have yet to be understood. Here, we document the dynamic organization of chromatin structure in two subgenomes of allotetraploid cotton (Gossypium hirsutum) by generating 3D genomic, epigenomic and transcriptomic datasets from 12 major tissues/developmental stages covering the life cycle. We systematically identify a subset of genes that are closely associated with specific tissue functions. Interestingly, these genes exhibit not only higher tissue specificity but also a more pronounced homoeologous bias. We comprehensively elucidate the intricate process of subgenomic collaboration and divergence across various tissues. A comparison among subgenomes in the 12 tissues reveals widespread differences in the reorganization of 3D genome structures, with the Dt subgenome exhibiting a higher extent of dynamic chromatin status than the At subgenome. Moreover, we construct a comprehensive atlas of putative functional genome elements and discover that 37 cis-regulatory elements (CREs) have selection signals acquired during domestication and improvement. These data and analyses are publicly available to the research community through a web portal. In summary, this study provides abundant resources and depicts the regulatory architecture of the genome, which thereby facilitates the understanding of biological processes and guides cotton breeding.

Accelerated cell-type-specific regulatory evolution of the human brain

The molecular basis of human brain evolution is a key piece in understanding the evolution of human-specific cognitive and behavioral traits. Comparative studies have suggested that human brain evolution was accompanied by accelerated changes of gene expression (referred to as "regulatory evolution"), especially those leading to an increase of gene products involved in energy production and metabolism. However, the signals of accelerated regulatory evolution were not always consistent across studies. One confounding factor is the diversity of distinctive cell types in the human brain. Here, we leveraged single-cell human and nonhuman primate transcriptomic data to investigate regulatory evolution at cell-type resolution. We relied on six well-established major cell types: excitatory and inhibitory neurons, astrocytes, microglia, oligodendrocytes, and oligodendrocyte precursor cells. We found pervasive signatures of accelerated regulatory evolution in the human brains compared to the chimpanzee brains in the major six cell types, as well as across multiple neuronal subtypes. Moreover, regulatory evolution is highly cell type specific rather than shared between cell types and strongly associated with cellular-level epigenomic features. Evolutionarily differentially expressed genes (DEGs) exhibit greater cell-type specificity than other genes, suggesting their role in the functional specialization of individual cell types in the human brain. As we continue to unfold the cellular complexity of the brain, the actual scope of DEGs in the human brain appears to be much broader than previously estimated. Our study supports the acceleration of cell-type-specific functional programs as an important feature of human brain evolution.

Repeated global adaptation across plant species

Global adaptation occurs when all populations of a species undergo selection toward a common optimum. This can occur by a hard selective sweep with the emergence of a new globally advantageous allele that spreads throughout a species' natural range until reaching fixation. This evolutionary process leaves a temporary trace in the region affected, which is detectable using population genomic methods. While selective sweeps have been identified in many species, there have been few comparative and systematic studies of the genes involved in global adaptation. Building upon recent findings showing repeated genetic basis of local adaptation across independent populations and species, we asked whether certain genes play a more significant role in driving global adaptation across plant species. To address this question, we scanned the genomes of 17 plant species to identify signals of repeated global selective sweeps. Despite the substantial evolutionary distance between the species analyzed, we identified several gene families with strong evidence of repeated positive selection. These gene families tend to be enriched for reduced pleiotropy, consistent with predictions from Fisher's evolutionary model and the cost of complexity hypothesis. We also found that genes with repeated sweeps exhibit elevated levels of gene duplication. Our findings contrast with recent observations of increased pleiotropy in genes driving local adaptation, consistent with predictions based on the theory of migration-selection balance.

Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay

Nucleotide sequences along a gene provide instructions to transcriptional and cotranscriptional machinery allowing genome expansion into the transcriptome. Nucleotide sequence can often be shared between two genes and in some occurrences, a gene is located completely within a different gene; these are known as host/nested gene pairs. In these instances, if both genes are transcribed, overlap can result in a transcriptional crosstalk where genes regulate each other. Despite this, a comprehensive annotation of where such genes are located and their expression patterns is lacking. To address this, we provide an up-to-date catalog of host/nested gene pairs in mouse and human, showing that over a tenth of all genes contain a nested gene. We discovered that transcriptional co-occurrence is often tissue specific. This coexpression was especially prevalent within the transcriptionally permissive tissue, testis. We use this developmental system and scRNA-seq analysis to demonstrate that the coexpression of pairs can occur in single cells and transcription in the same place at the same time can enhance the transcript diversity of the host gene. In agreement, host genes are more transcript-diverse than the rest of the transcriptome. Host/nested gene configurations are common in both human and mouse, suggesting that interplay between gene pairs is a feature of the mammalian genome. This highlights the relevance of transcriptional crosstalk between genes which share nucleic acid sequence. The results and analysis are available on an Rshiny application (https://hngeneviewer.sites.er.kcl.ac.uk/hn_viewer/).

Gene expression profiles in specific skeletal muscles and meat quality characteristics of sheep and goats

Lamb meat is highly valued across various cultures and regions due to its unique flavor and nutritional benefits. As the primary component of edible meat, skeletal muscle holds significant economic value and research importance. However, previous studies have largely focused on a limited array of muscle groups, overlooking the differences between various types. Therefore, a comprehensive transcriptomic and meat quality analysis of the skeletal muscles of sheep and goats is essential to improve meat production traits. In this study, we performed RNA sequencing and assessed meat quality in 10 different skeletal muscles from 2-year-old Liangshan Black sheep and Meigu Black goats. We generated 803.16 Gb of high-quality bulk RNA sequencing data with six biological replicates for each muscle. This dataset provides a deeper understanding of the gene expression profiles and meat quality characteristics of different muscle tissues in sheep and goats, laying the foundation for broader comparative research.

Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation

Skeletal muscle, the largest human organ by weight, is relevant in several polygenic metabolic traits and diseases including type 2 diabetes (T2D). Identifying genetic mechanisms underlying these traits requires pinpointing cell types, regulatory elements, target genes, and causal variants. Here, we use genetic multiplexing to generate population-scale single nucleus (sn) chromatin accessibility (snATAC-seq) and transcriptome (snRNA-seq) maps across 287 frozen human skeletal muscle biopsies representing nearly half a million nuclei. We identify 13 cell types and integrate genetic variation to discover >7,000 expression quantitative trait loci (eQTL) and >100,000 chromatin accessibility QTLs (caQTL) across cell types. Learning patterns of e/caQTL sharing across cell types increased precision of effect estimates. We identify high-resolution cell-states and context-specific e/caQTL with significant genotype by context interaction. We identify nearly 2,000 eGenes colocalized with caQTL and construct causal directional maps for chromatin accessibility and gene expression. Almost 3,500 genome-wide association study (GWAS) signals across 38 relevant traits colocalize with sn-e/caQTL, most in a cell-specific manner. These signals typically colocalize with caQTL and not eQTL, highlighting the importance of population-scale chromatin profiling for GWAS functional studies. Finally, our GWAS-caQTL colocalization data reveal distinct cell-specific regulatory paradigms. Our results illuminate the genetic regulatory architecture of human skeletal muscle at high resolution epigenomic, transcriptomic, and cell-state scales and serve as a template for population-scale multi-omic mapping in complex tissues and traits.

Correlating gene expression levels with transcription factor binding sites facilitates identification of key transcription factors from transcriptome data

Identification of key transcription factors from transcriptome data by correlating gene expression levels with transcription factor binding sites is important for transcriptome data analysis. In a typical scenario, we always set a threshold to filter the top ranked differentially expressed genes and top ranked transcription factor binding sites. However, correlation analysis of filtered data can often result in spurious correlations. In this study, we tested four methods for creating the gene expression inputs (ranked gene list) in the correlation analysis: star coordinate map transformation (START), expression differential score (ED), preferential expression measure (PEM), and the specificity measure (SPM). Then, Kendall's tau correlation statistical algorithms implementing the standard (STD), LINEAR, MIX-LINEAR, DENSITY-CURVE, and MIXED-DENSITY-CURVE weighting methods were used to identify key transcription factors. ED was identified as the optimal method for creating a ranked gene list from filtered expression data, which can address the "unable to detect negative correlation" fallacy presented by other methods. The MIXED-DENSITY-CURVE was the most sensitive for identifying transcription factors from the gene set and list in which only the top proportion was correlated. Ultimately, 644 transcription factor candidates were identified from the transcriptome data of 1,206 cell lines, six of which were validated by wet lab experiments. The Jinzer and Flaver software implementing these methods can be obtained from http://www.thua45/cn/flaver under a free academic license.

The first chicken oocyte nucleus whole transcriptomic profile defines the spectrum of maternal mRNA and non-coding RNA genes transcribed by the lampbrush chromosomes

Lampbrush chromosomes, with their unusually high rate of nascent RNA synthesis, provide a valuable model for studying mechanisms of global transcriptome up-regulation. Here, we obtained a whole-genomic profile of transcription along the entire length of all lampbrush chromosomes in the chicken karyotype. With nuclear RNA-seq, we obtained information about a wider set of transcripts, including long non-coding RNAs retained in the nucleus and stable intronic sequence RNAs. For a number of protein-coding genes, we visualized their nascent transcripts on the lateral loops of lampbrush chromosomes by RNA-FISH. The set of genes transcribed on the lampbrush chromosomes is required for basic cellular processes and is characterized by a broad expression pattern. We also present the first high-throughput transcriptome characterization of miRNAs and piRNAs in chicken oocytes at the lampbrush chromosome stage. Major targets of predicted piRNAs include CR1 and long terminal repeat (LTR) containing retrotransposable elements. Transcription of tandem repeat arrays was demonstrated by alignment against the whole telomere-to-telomere chromosome assemblies. We show that transcription of telomere-derived RNAs is initiated at adjacent LTR elements. We conclude that hypertranscription on the lateral loops of giant lampbrush chromosomes is required for synthesizing large amounts of transferred to the embryo maternal RNA for thousands of genes.

Single-cell multi-omics sequencing uncovers region-specific plasticity of glioblastoma for complementary therapeutic targeting

Glioblastoma (GBM) cells are highly heterogeneous and invasive, leading to treatment resistance and relapse. However, the molecular regulation in and distal to tumors remains elusive. Here, we collected paired tissues from the tumor core (TC) and peritumoral brain (PTB) for integrated snRNA-seq and snATAC-seq analyses. Tumor cells infiltrating PTB from TC behave more like oligodendrocyte progenitor cells than astrocytes at the transcriptome level. Dual-omics analyses further suggest that the distal regulatory regions in the tumor genome and specific transcription factors are potential determinants of regional heterogeneity. Notably, while activator protein 1 (AP-1) is active in all GBM states, its activity declines from TC to PTB, with another transcription factor, BACH1, showing the opposite trend. Combined inhibition of AP-1 and BACH1 more efficiently attenuates the tumor progression in mice and prolongs survival than either single-target treatment. Together, our work reveals marked molecular alterations of infiltrated GBM cells and a synergy of combination therapy targeting intratumor heterogeneity in and distal to GBM.

Ancestry-specific gene expression in peripheral monocytes mediates risk of neurodegenerative disease

It is hypothesised that peripheral immune states responding to regional environmental triggers contribute to central neurodegeneration. Region-specific genetic selection pressures require this hypothesis to be assessed in an ancestry specific manner. Here we utilise genome-wide association studies and expression quantitative trait loci from African, East Asian and European ancestries to show that genes causing neurodegeneration are preferentially expressed in innate rather than adaptive immune cells, and that expression of these genes mediates the risk of neurodegenerative disease in monocytes in an ancestry-specific manner.

Regulation of cell-mediated immune responses in dairy bulls via long non-coding RNAs from submandibular lymph nodes, peripheral blood, and the spleen

Cell-mediated immune responses (CMIRs) are critical to building a robust immune system and reducing disease susceptibility in cattle. Long non-coding RNAs (lncRNAs) regulate various biological processes. However, to the best of our knowledge, the characterization and functions of lncRNAs and their regulations on the bovine CMIR have not been investigated comprehensively. In this study, experimental bulls were immunized with heat-killed preparation of Candida albicans (HKCA) to induce delayed-type hypersensitivity (DTH). Three bulls were classified as high- CMIR responders and three were low-CMIR responders, based on their classical DTH skin reactions. LncRNAs were identified in the submandibular lymph nodes, peripheral blood, and spleen of high- and low-CMIR animals using strand-specific RNA sequencing. A total of 21,003 putative lncRNAs were identified across tissues, and 420, 468, and 599 lncRNAs were differentially expressed between the two groups in the submandibular lymph node, peripheral blood, and spleen tissues, respectively. Functional analysis of the differentially expressed lncRNA (DElncRNA) target genes showed that a number of immune-related Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched, including immune response, cell adhesion, nucleosome, DNA packaging, antigen processing and presentation, and complement and coagulation cascades. Tissue specificity analysis indicated that lncRNA transcripts have stronger tissue specificity than mRNA. Furthermore, an interaction network was constructed based on DElncRNAs and DEGs, and 11, 14, and 11 promising lncRNAs were identified as potential candidate genes influencing immune response regulation in submandibular lymph nodes, peripheral blood, and spleen tissues, respectively. These results provide a foundation for further research into the biological functions of lncRNAs associated with bovine CMIR and identify candidate lncRNA markers for cell-mediated immune responses.

A transcriptomic hourglass in brown algae

Complex multicellularity has emerged independently across a few eukaryotic lineages and is often associated with the rise of elaborate, tightly coordinated developmental processes1,2. How multicellularity and development are interconnected in evolution is a major question in biology. The hourglass model of embryonic evolution depicts how developmental processes are conserved during evolution, and predicts morphological and molecular divergence in early and late embryogenesis, bridged by a conserved mid-embryonic (phylotypic) period linked to the formation of the basic body plan3,4. Initially found in animal embryos5-8, molecular hourglass patterns have recently been proposed for land plants and fungi9,10. However, whether the hourglass pattern is an intrinsic feature of all complex multicellular eukaryotes remains unknown. Here we tested the presence of a molecular hourglass in the brown algae, a eukaryotic lineage that has evolved multicellularity independently from animals, fungi and plants1,11,12. By exploring transcriptome evolution patterns of brown algae with distinct morphological complexities, we uncovered an hourglass pattern during embryogenesis in morphologically complex species. Filamentous algae without canonical embryogenesis display transcriptome conservation in multicellular stages of the life cycle, whereas unicellular stages are more rapidly evolving. Our findings suggest that transcriptome conservation in brown algae is associated with cell differentiation stages, but is not necessarily linked to embryogenesis. Together with previous work in animals, plants and fungi, we provide further evidence for the generality of a developmental hourglass pattern across complex multicellular eukaryotes.

DOR activation in mature oligodendrocytes regulates α-ketoglutarate metabolism leading to enhanced remyelination in aged mice

The decreased ability of mature oligodendrocytes to produce myelin negatively affects remyelination in demyelinating diseases and aging, but the underlying mechanisms are incompletely understood. In the present study, we identify a mature oligodendrocyte-enriched transcriptional coregulator diabetes- and obesity-related gene (DOR)/tumor protein p53-inducible nuclear protein 2 (TP53INP2), downregulated in demyelinated lesions of donors with multiple sclerosis and in aged oligodendrocyte-lineage cells. Dor ablation in mice of both sexes results in defective myelinogenesis and remyelination. Genomic occupancy in oligodendrocytes and transcriptome profiling of the optic nerves of wild-type and Dor conditional knockout mice reveal that DOR and SOX10 co-occupy enhancers of critical myelinogenesis-associated genes including Prr18, encoding an oligodendrocyte-enriched, proline-rich factor. We show that DOR targets regulatory elements of genes responsible for α-ketoglutarate biosynthesis in mature oligodendrocytes and is essential for α-ketoglutarate production and lipid biosynthesis. Supplementation with α-ketoglutarate restores oligodendrocyte-maturation defects in Dor-deficient adult mice and improves remyelination after lysolecithin-induced demyelination and cognitive function in 17-month-old wild-type mice. Our data suggest that activation of α-ketoglutarate metabolism in mature oligodendrocytes can promote myelin production during demyelination and aging.

Long noncoding RNA network for lncRNA-mRNA interactions throughout swine estrous cycle reveals developmental and hormonal regulations in reproductive tissues

The mechanism of estrous cycles of pigs should be explored because their reproductive traits are useful for manipulating productivity and solving problems such as infertility. These estrous cycles should be elucidated to understand the complex interactions between various reproductive tissues (including the ovary, oviduct, and endometrium) and the complex range of hormone secretions during estrous cycles. Long non-coding RNAs (lncRNAs) regulate target genes at transcriptional, post-transcriptional, and post-translational regulation levels in various species. However, unlike mRNAs, lncRNAs in pigs have not been sufficiently annotated, and understanding the protein level of coding genes has limitations in determining the mechanism of the reproductive traits of porcine. In this study, the lncRNAs of the porcine ovary, oviduct, and endometrium were investigated on days 0, 3, 6, 9, 12, 15, and 18 of the estrous cycle. In addition, the characteristics and functions of the identified lncRNAs were explored. 19,021 novel lncRNA transcripts were selected, and the comparison of the characteristics of the newly identified lncRNA and mRNA showed that similar to those of previous studies. Four lncRNA networks were chosen through network analysis. The cis-acting genes of lncRNAs included in each network were identified, and expression patterns were compared. The main lncRNAs (XLOC_021792, XLOC_017111, ENSSSCG00000050977, XLOC_000342, ENSSSCG00000050380, ENSSSCG00000045111, XLOC_008338, XLOC_004128, and ENSSSCG00000040267) were determined from the network by considering the cis-acting genes. Specific novel lncRNAs were discovered in the reproductive tissues during the swine estrous cycle, and their time-serial expression dynamics were confirmed. As the main lncRNAs are involved in the development of each reproductive tissue and hormone action, they can be utilized as potential biomarkers to help improve and develop the reproductive traits of pigs.

Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements in Barley (Hordeum vulgare)

Miniature inverted-repeat transposable elements (MITEs) constitute a class of class II transposable elements (TEs) that are abundant in plant genomes, playing a crucial role in their evolution and diversity. Barley (Hordeum vulgare), the fourth-most important cereal crop globally, is widely used for brewing, animal feed, and human consumption. However, despite their significance, the mechanisms underlying the insertion or amplification of MITEs and their contributions to barley genome evolution and diversity remain poorly understood. Through our comprehensive analysis, we identified 32,258 full-length MITEs belonging to 2,992 distinct families, accounting for approximately 0.17% of the barley genome. These MITE families can be grouped into four well-known superfamilies (Tc1/Mariner-like, PIF/Harbinger-like, hAT-like, and Mutator-like) and one unidentified superfamily. Notably, we observed two major expansion events in the barley MITE population, occurring approximately 12-13 million years ago (Mya) and 2-3 Mya. Our investigation revealed a strong preference of MITEs for gene-related regions, particularly in promoters, suggesting their potential involvement in regulating host gene expression. Additionally, we discovered that 7.73% miRNAs are derived from MITEs, thereby influencing the origin of certain miRNAs and potentially exerting a significant impact on post-transcriptional gene expression control. Evolutionary analysis demonstrated that MITEs exhibit lower conservation compared to genes, consistent with their dynamic mobility. We also identified a series of MITE insertions or deletions associated with domestication, highlighting these regions as promising targets for crop improvement strategies. These findings significantly advance our understanding of the fundamental characteristics and evolutionary patterns of MITEs in the barley genome. Moreover, they contribute to our knowledge of gene regulatory networks and provide valuable insights for crop improvement endeavors.

Dynamic Landscapes of Long Noncoding RNAs During Early Root Development and Differentiation in Glycine max and Glycine soja

Soybean (Glycine max) is an important crop for its nutritional value. Its wild relative, Glycine soja, provides a valuable genetic resource for improving soybean productivity. Root development and differentiation are essential for soybean plants to take up water and nutrients, store energy and anchor themselves. Long noncoding RNAs (lncRNAs) have been reported to play critical roles in various biological processes. However, the spatiotemporal landscape of lncRNAs during early root development and differentiation in soybeans is scarcely characterized. Using RNA sequencing and transcriptome assembly, we identified 1578 lncRNAs in G. max and 1454 in G. soja, spanning various root portions and time points. Differential expression analysis revealed 82 and 69 lncRNAs exhibiting spatiotemporally differential expression patterns in G. max and G. soja, respectively, indicating their involvement in the early stage of root architecture formation. By elucidating multiple competitive endogenous RNA (ceRNA) networks involving lncRNAs, microRNAs and protein-coding RNAs, we unveiled intricate regulatory mechanisms of lncRNA in early root development and differentiation. Our efforts significantly expand the transcriptome annotations of soybeans, unravel the dynamic landscapes of lncRNAs during early root development and differentiation, and provide valuable resources into the field of soybean root research.