Software for computing and annotating genomic ranges

Analysis of somatic piRNAs in the malaria mosquito Anopheles coluzzii reveals atypical classes of genic small RNAs

Piwi-interacting small RNAs (piRNA) play a key role in controlling the activity of transposable elements (TEs) in the animal germline. In diverse arthropod species, including the pathogen vectors mosquitoes, the piRNA pathway is also active in nongonadal somatic tissues, where its targets and functions are less clear. Here, we studied the features of small RNA production in head and thorax tissues of an uninfected laboratory strain of Anopheles coluzzii focusing on the 24-32-nt-long RNAs. Small RNAs derived from repetitive elements constitute a minor fraction while most small RNAs process from long noncoding RNAs (lncRNAs) and protein-coding gene mRNAs. The majority of small RNAs derived from repetitive elements and lncRNAs exhibited typical piRNAs features. By contrast, majority of protein-coding gene-derived 24-32 nt small RNAs lack the hallmarks of piRNAs and have signatures of nontemplated 3' end tailing. Most of the atypical small RNAs exhibit female-biased expression and originate from mitochondrial and nuclear genes involved in energy metabolism. We also identified atypical genic small RNAs in Anopheles gambiae somatic tissues, which further validates the noncanonical mechanism of their production. We discuss a novel mechanism of small RNA production in mosquito somatic tissues and the possible functional significance of genic small RNAs.

Blood DNA Methylation Analysis Reveals a Distinctive Epigenetic Signature of Vasospasm in Aneurysmal Subarachnoid Hemorrhage

Vasospasm is a potentially preventable cause of poor prognosis in patients with aneurysmal subarachnoid hemorrhage (aSAH). Epigenetics might provide insight on its molecular mechanisms. We aimed to analyze the association between differential DNA methylation (DNAm) and development of vasospasm. We conducted an epigenome-wide association study in 282 patients with aSAH admitted to our hospital. DNAm was assessed with the EPIC Illumina chip (> 850 K CpG sites) in whole-blood samples collected at hospital admission. We identified differentially methylated positions (DMPs) at the CpG level using Cox regression models adjusted for potential confounders, and then we used the DMP results to find differentially methylated regions (DMRs) and enriched biological pathways. A total of 145 patients (51%) experienced vasospasm. In the DMP analysis, we identified 31 CpGs associated with vasospasm at p-value < 10-5. One of them (cg26189827) was significant at the genome-wide level (p-value < 10-8), being hypermethylated in patients with vasospasm and annotated to SUGCT gene, mainly expressed in arteries. Region analysis revealed 13 DMRs, some of them annotated to interesting genes such as POU5F1, HLA-DPA1, RUFY1, and CYP1A1. Functional enrichment analysis showed the involvement of biological processes related to immunity, inflammatory response, oxidative stress, endothelial nitric oxide, and apoptosis. Our findings show, for the first time, a distinctive epigenetic signature of vasospasm in aSAH, establishing novel links with essential biological pathways, including inflammation, immune responses, and oxidative stress. Although further validation is required, our results provide a foundation for future research into the complex pathophysiology of vasospasm.

Epigenome-wide association study of pregnancy exposure to green space and placental DNA methylation

Green space exposure during pregnancy has been associated with lower risk of adverse birth outcomes, but the biological mechanisms remain unclear. Epigenetic changes, such as DNA methylation (DNAm), may contribute to this association. The placenta, crucial for foetal development, has been understudied in relation to prenatal green space exposure and DNAm on a genome-wide scale. Here, we aimed to investigate the association between green space exposure during pregnancy and epigenome-wide placental DNAm in 550 mother-child pairs from the Barcelona Life Study Cohort (BiSC) in Spain. Green space exposure was assessed as (i) residential surrounding greenness (satellite-based Normalized Difference Vegetation Index (NDVI) in buffers of 100 m, 300 m and 500 m), (ii) residential distance to the nearest major green space (meters), (iii) use of green space (hours/week), and (iv) visual access to greenery through the home window (≥half of the view). Placental DNAm was measured with the EPIC array. Differentially methylated positions (DMPs) were identified using robust linear regression models adjusted for covariates, while differentially methylated regions (DMRs) were identified using the dmrff method. After Bonferroni correction, cg14852540, annotated to SLC25A10 gene, showed an inverse association with residential greenness within 500 m buffer. Additionally, 101 DMPs were suggestively significant (p-values <1 × 10-5) and annotated to genes involved in glucocorticoid-related pathways, inflammatory response, oxidative stress response, and oocyte maturation. No DMRs were identified. Overall, we identified an association between residential greenness and DNAm levels at one CpG in the SLC25A10 gene. Larger studies are needed to validate these findings and understand the biological pathways.

Evolution of tumor stress response during cytoreductive surgery for ovarian cancer

Upfront treatment for patients with advanced high-grade serous ovarian cancer (HGSOC) includes a multi-hour cytoreductive surgery. Although the procedure is necessary for maximal tumor cytoreduction, understanding of the biology of systemic and intratumoral responses induced by surgical cytoreduction is limited. Through analysis of matched tumor and normal tissues and peripheral blood collected at multiple time points during cytoreductive surgery in patients with HGSOC, we demonstrate that surgery leads to rapid induction of systemic inflammatory response and activation of inflammatory signaling in the tumor and normal tissue, with interleukin-6 emerging as a dominant inflammatory pathway. A parallel study in a syngeneic murine HGSOC model recapitulated these findings and demonstrated accelerated tumor growth in response to surgery. This study highlights the previously unappreciated impact of specimen collection timing on the tumor signaling networks and provides insights into stress pathways activated by surgery, generating rationale for perioperative therapeutic interventions to reduce protumorigenic effects.

Integrating Plasma Cell-Free DNA Fragment End Motif and Size with Genomic Features Enables Lung Cancer Detection

Early detection of lung cancer is important for improving patient survival rates. Liquid biopsy using whole-genome sequencing of cell-free DNA (cfDNA) offers a promising avenue for lung cancer screening, providing a potential alternative or complementary approach to current screening modalities. Here, we aimed to develop and validate an approach by integrating fragment and genomic features of cfDNA to enhance lung cancer detection accuracy across diverse populations. Deep learning-based classifiers were trained using comprehensive cfDNA fragmentomic features from participants in multi-institutional studies, including a Korean discovery dataset (218 patients with lung cancer and 2,559 controls), a Korean validation dataset (111 patients with lung cancer and 1,136 controls), and an independent Caucasian validation cohort (50 patients with lung cancer and 50 controls). In the discovery dataset, classifiers using fragment end motif by size, a feature that captures both fragment end motif and size profiles, outperformed standalone fragment end motif and fragment size classifiers, achieving an area under the curve (AUC) of 0.917. The ensemble classifier integrating fragment end motif by size and genomic coverage achieved an improved performance, with an AUC of 0.937. This performance extended to the Korean validation dataset and demonstrated ethnic generalizability in the Caucasian validation cohort. Overall, the development of a deep learning-based classifier integrating cfDNA fragmentomic and genomic features in this study highlights the potential for accurate lung cancer detection across diverse populations. Significance: Evaluating fragment-based features and genomic coverage in cell-free DNA offers an accurate lung cancer screening method, promising improvements in early cancer detection and addressing challenges associated with current screening methods.

Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements

Pangenome methods have the potential to uncover hitherto undiscovered sequences missing from established reference genomes, making them useful to study evolutionary and speciation processes in diverse organisms. The cichlid fishes of the East African Rift Lakes represent one of nature's most phenotypically diverse vertebrate radiations, but single-nucleotide polymorphism (SNP)-based studies have revealed little sequence difference, with 0.1%-0.25% pairwise divergence between Lake Malawi species. These were based on aligning short reads to a single linear reference genome and ignored the contribution of larger-scale structural variants (SVs). We constructed a pangenome graph that integrates six new and two existing long-read genome assemblies of Lake Malawi haplochromine cichlids. This graph intuitively represents complex and nested variation between the genomes and reveals that the SV landscape is dominated by large insertions, many exclusive to individual assemblies. The graph incorporates a substantial amount of extra sequence across seven species, the total size of which is 33.1% longer than that of a single cichlid genome. Approximately 4.73% to 9.86% of the assembly lengths are estimated as interspecies structural variation between cichlids, suggesting substantial genomic diversity underappreciated in SNP studies. Although coding regions remain highly conserved, our analysis uncovers a significant proportion of SV sequences as transposable element (TE) insertions, especially DNA, LINE, and LTR TEs. These findings underscore that the cichlid genome is shaped both by small-nucleotide mutations and large, TE-derived sequence alterations, both of which merit study to understand their interplay in cichlid evolution.

Interactions of erythromycin and an antibiotic mixture with the gut microbiome of juvenile rainbow trout

Erythromycin (ERY) is a commonly used antibiotic found in wastewater effluents and the environment globally. Due to the bioactivity by which they kill and prevent bacterial growth, ERY and other antibiotics may have significant unwanted impacts on the gut microbiome of fishes. The overall objective of this project was to assess effects on the gut microbiome in response to exposure to ERY alone or in a mixture with other common antibiotics, which was accomplished in two experiments. The objectives of experiment 1 as a pilot study were to understand uptake and depuration of ERY in juvenile rainbow trout (RBT) over a 7-d exposure to three concentrations of ERY followed by a 7-d depuration period. Furthermore, throughout the study changes in gut microbiome were assessed. In experiment 2, an identical experimental design was used to assess the effects of a mixture of antibiotics containing, in addition to ERY, 100 μg/g each of ampicillin, metronidazole, and ciprofloxacin. In that study, three matrices were analyzed, with gut collected for 16S rRNA metabarcoding, blood plasma for non-targeted metabolomics, and brain tissue for mRNA-seq analysis. ERY was relatively quickly depurated from fish and gut microbiome dysbiosis was observed at 7 d after exposure, with a slight recovery after the 7-d depuration period. A greater number of plasma metabolites was dysregulated at 14 d compared to 7 d revealing distinct temporal dynamics compared to gut microbiome dysbiosis. Furthermore, several transformation products of antibiotics and biomarker metabolites were observed in plasma due to antibiotic exposure. The transcriptome of the brain was only slightly altered due to antibiotic exposure. Results of these studies will help inform aquaculture practitioners and risk assessors when assessing the potential impacts of antibiotics present in fish feed and the environment, with implications for host health.

Ribo-seq guided design of enhanced protein secretion in Komagataella phaffii

The production of recombinant proteins requires the precise coordination of various biological processes, including protein synthesis, folding, trafficking, and secretion. The overproduction of a heterologous protein can impose various bottlenecks on these networks. Identifying and alleviating these bottlenecks can guide strain engineering efforts to enhance protein production. The methylotrophic yeast Komagataella phaffii is used for its high capacity to produce recombinant proteins. Here, we use ribosome profiling to identify bottlenecks in protein secretion during heterologous expression of human serum albumin (HSA). Validation of this analysis showed that the knockout of non-essential genes whose gene products target the ER, through co- and post-translational mechanisms, and have high ribosome utilization can increase production of a heterologous protein, HSA. A triple knockout in co-translationally translocated carbohydrate and acetate transporter Gal2p, cell wall maintenance protein Ydr134cp, and the post-translationally translocated cell wall protein Aoa65896.1 increased HSA production by 35%. This data-driven strain engineering approach uses cell-level information to identify gene targets for phenotype improvement. This specific case identifies hits and creates strains with improved HSA production, with Ribo-seq and bioinformatic analysis to identify non-essential ER targeted proteins that are high ribosome utilizers.

High expression of miR-7974 predicts poor prognosis and is associated with autophagy in estrogen receptor-positive breast cancer

Estrogen receptor-positive (ER+) breast cancers (BC) cause death despite well-established treatments. MicroRNAs (miRNAs) have potential as biomarkers specific to cancer subtypes and tissues, therefore miRNA-based biomarkers could help improve patient survival. In this study, we investigated a relatively unknown miRNA, miR-7974. We utilized small RNA data from 204 breast tissue samples to study miR-7974 association with clinicopathological features and outcomes for BC patients. Additionally, in vitro and in ovo methods were used to identify miR-7974 role at molecular and cellular level in MCF-7 cells. Findings were validated using MDA-MB-453 cells. MiR-7974 was upregulated in many clinicopathological features of BC (P<0.05). Furthermore, the highest expression of miR-7974 was associated with poor relapse-free survival in ER+ BC patients [hazard ratio (HR)=8.70; 95% confidence interval (CI)=3.28-23.06; P=1.37x10-05] and poor BC-specific survival in patients receiving only surgical treatment (HR=8.36; 95% CI=1.01-69.06; P=0.049). Our studies revealed that miR-7974 targets autophagy gene, MAP1LC3B, identified as direct miR-7974 target (P<0.05) in MCF-7 cells. In vitro analyses indicated overexpressing miR-7974 had anti-proliferative effect in MCF7 and MDA-MB-453 cells. Overall, our results demonstrate potential prognostic role of miR-7974 in ER+ BC.

Strigolactones optimise plant water usage by modulating vessel formation

Wood formation is crucial for plant growth, enabling water and nutrient transport through vessel elements, derived from cambium stem cells (CSCs). CSCs produce vascular cell types in a bidirectional manner, but their regulation and cell fate trajectories remain unclear. Here, using single-cell transcriptome analysis in Arabidopsis thaliana, we reveal that the strigolactone (SL) signalling pathway negatively regulates vessel element formation, impacting plant water usage. While SL signalling is generally active in differentiating vascular tissues, it is low in developing vessels and CSCs, where it modulates cell fate decisions and drought response. SL-dependent changes in vessel element formation directly affect transpiration rates via stomata, underscoring the importance of vascular tissue composition in water balance. Our findings demonstrate the role of structural alignment in water-transport tissues under unstable water conditions, offering insights for enhancing drought resistance in plants through long-term modulation of vascular development.

Rapid Neural DNA Methylation Responses to Predation Stress in Trinidadian Guppies

DNA methylation (DNAm) is a well-studied epigenetic mechanism implicated in environmentally induced phenotypes and phenotypic plasticity. However, few studies investigate the timescale of DNAm shifts. Thus, it is uncertain whether DNAm can change on timescales relevant for rapid phenotypic shifts, such as during the expression of short-term behavioural plasticity. DNAm could be especially reactive in the brain, potentially increasing its relevance for behavioural plasticity. Most research investigating neural changes in methylation has been conducted in mammalian systems, on isolated individuals, and using stressors that are less ecologically relevant, reducing their generalisability to other natural systems. We exposed pairs of male and female Trinidadian guppies (Poecilia reticulata) to alarm cue, conspecific skin extract that reliably induces anti-predator behaviour, or a control cue. Whole-genome bisulphite sequencing on whole brains at various time points following cue exposure (0.5, 1, 4, 24, and 72 h) allowed us to uncover the timescale of neural DNAm responses. Males and females both showed rapid shifts in DNAm in as little as 0.5 h. However, males and females differed in the time course of their responses: both sexes showed a peak in the number of loci showing significant responses at 4 h, but males showed an additional peak at 72 h. We suggest that this finding could be due to the differing longer-term plastic responses between the sexes. This study shows that DNAm can be rapidly induced by an ecologically relevant stressor in fish and suggests that DNAm could be involved in short-term behavioural plasticity.

Alternative splicing categorizes organ development by stage and reveals unique human splicing variants linked to neuromuscular disorders

Alternative splicing (AS) diversifies protein expression and contributes to species-specific differences in organ development. Here, we focused on stage-specific splicing variants and their correlation with disease in human compared to mouse during brain and heart development. Temporal transcriptomic analysis revealed that splicing factors (SFs) can accurately classify organ developmental stages, and 5 SFs were identified specifically upregulated in human during organogenesis. Additionally, inter-stage splicing variations were identified across analogous human and mouse developmental stages. Developmentally dynamic alternative splicing genes (devASGs) were enriched in various neurodevelopmental disorders in both species, with the most significant changes observed in human newborn brain and 16 weeks post-conception heart. Intriguingly, diseases specifically enriched in humans were primarily associated with neuro-muscular dysfunction, and human-specific neuromuscular devASGs were linked to mannose glycosylation and ciliary motility. These findings highlight the significance of SFs and AS events in organogenesis, and inform the selection of appropriate models for translational research.

Impact of DNA methylation on digestive and metabolic gene expression in red pandas (Ailurus fulgens) during the transition from milk to bamboo diet

BACKGROUND

DNA methylation plays a crucial role in species development and environmental adaptation. In mammals, there are significant dietary changes from infancy to adulthood. Notably, the red panda transitions from milk consumption as juveniles to a bamboo-based diet as adults, with significant alterations in food characteristics and nutritional content. However, the regulatory role of DNA methylation in this process remains unclear. In this study, we investigate the regulatory role of DNA methylation on the expression of digestive and metabolic genes in the liver and pancreas during the red panda's dietary transition from suckling stage to adulthood.

RESULTS

Our findings reveal significant differences in DNA methylation patterns before and after dietary transition, highlighting the specific alterations in the methylation profiles of genes involved in lipid, carbohydrate, and amino acid metabolism. We found that perilipin-4 (PLIN4) is hypomethylated and highly expressed in the liver of adult red pandas, facilitating lipid droplet formation and storage, crucial for adapting to the low-fat content in bamboo. In contrast, genes like lipoprotein lipase (LPL), crucial for lipid breakdown, exhibited hypermethylated with low-expression patterns, reflecting a reduced lipid metabolism capacity in adults. Carbohydrate metabolism-related genes like ADH4 and FAM3C are hypomethylated and highly expressed in adults, enhancing glycogen production and glucose utilization. Genes involved in protein metabolism like CTSZ and GLDC, exhibit hypomethylated with high-expression and hypermethylated with low-expression patterns in the pancreas of adults, respectively, contributing to protein metabolism balance post-weaning.

CONCLUSION

This study reveals the regulatory role of DNA methylation in the dietary transition of red pandas from milk to bamboo and provides methylation evidence for the molecular regulation of adaptive expression of digestive and metabolic genes in red pandas with specialized diets.

AlphaMissenseR: an integrated framework for investigating missense mutations in human protein-coding genes

Summary

AlphaMissense is an AI model from Google DeepMind that predicts the pathogenicity of every possible missense mutation in the human proteome. We present AlphaMissenseR, an R/Bioconductor package that facilitates performant and reproducible access to these predictions and that provides functionality for analysis, visualization, validation, and benchmarking. AlphaMissenseR integrates with Bioconductor facilities for genomic region analysis, and provides multi-level visualization and interactive exploration of variant pathogenicity in a genome browser and on 3D protein structures. In addition, AlphaMissenseR integrates with major clinical and experimental variant databases for contrasting predicted and clinically derived pathogenicity scores, and for systematic benchmarking of existing and new variant effect prediction methods across a large collection of deep mutational scanning assays.

Availability and implementation

AlphaMissense data resources are distributed under the CC-BY 4.0 license and the AlphaMissenseR package is available from Bioconductor (https://bioconductor.org/packages/AlphaMissenseR) under the Artistic 2.0 license.

Meis transcription factors regulate cardiac conduction system development and adult function

AIMS

The cardiac conduction system (CCS) is progressively specified during development by interactions among a discrete number of transcription factors (TFs) that ensure its proper patterning and the emergence of its functional properties. Meis genes encode homeodomain TFs with multiple roles in mammalian development. In humans, Meis genes associate with congenital cardiac malformations and alterations of cardiac electrical activity; however, the basis for these alterations has not been established. Here, we studied the role of Meis TFs in cardiomyocyte development and function during mouse development and adult life.

METHODS AND RESULTS

We studied Meis1 and Meis2 conditional deletion mouse models that allowed cardiomyocyte-specific elimination of Meis function during development and inducible elimination of Meis function in cardiomyocytes of the adult CCS. We studied cardiac anatomy, contractility, and conduction. We report that Meis factors are global regulators of cardiac conduction, with a predominant role in the CCS. While constitutive Meis deletion in cardiomyocytes led to congenital malformations of the arterial pole and atria, as well as defects in ventricular conduction, Meis elimination in cardiomyocytes of the adult CCS produced sinus node dysfunction and delayed atrio-ventricular conduction. Molecular analyses unravelled Meis-controlled molecular pathways associated with these defects. Finally, we studied in transgenic mice the activity of a Meis1 human enhancer related to an single-nucleotide polymorphism (SNP) associated by Genome-wide association studies (GWAS) to PR (P and R waves of the electrocardiogram) elongation and found that the transgene drives expression in components of the atrio-ventricular conduction system.

CONCLUSION

Our study identifies Meis TFs as essential regulators of the establishment of cardiac conduction function during development and its maintenance during adult life. In addition, we generated animal models and identified molecular alterations that will ease the study of Meis-associated conduction defects and congenital malformations in humans.

Mis-splicing-derived neoantigens and cognate TCRs in splicing factor mutant leukemias

Mutations in RNA splicing factors are prevalent across cancers and generate recurrently mis-spliced mRNA isoforms. Here, we identified a series of bona fide neoantigens translated from highly stereotyped splicing alterations promoted by neomorphic, leukemia-associated somatic splicing machinery mutations. We utilized feature-barcoded peptide-major histocompatibility complex (MHC) dextramers to isolate neoantigen-reactive T cell receptors (TCRs) from healthy donors, patients with active myeloid malignancy, and following curative allogeneic stem cell transplant. Neoantigen-reactive CD8+ T cells were present in the blood of patients with active cancer and had a distinct phenotype from virus-reactive T cells with evidence of impaired cytotoxic function. T cells engineered with TCRs recognizing SRSF2 mutant-induced neoantigens arising from mis-splicing events in CLK3 and RHOT2 resulted in specific recognition and cytotoxicity of SRSF2-mutant leukemia. These data identify recurrent RNA mis-splicing events as sources of actionable public neoantigens in myeloid leukemias and provide proof of concept for genetically redirecting T cells to recognize these targets.

MHCII reduction is insufficient to protect mice from alpha-synuclein-induced degeneration and the Parkinson's HLA locus exhibits epigenetic regulation

Major histocompatibility complex class II (MHCII) molecules are antigen presentation proteins and increased in post-mortem Parkinson's disease (PD) brain. Attempts to decrease MHCII expression have led to neuroprotection in PD mouse models. Our group reported that a single nucleotide polymorphism (SNP) at rs3129882 in the MHCII gene Human Leukocyte Antigen (HLA) DRA is associated with increased MHCII transcripts and surface protein and increased risk for late-onset idiopathic PD. We therefore hypothesized that decreased MHCII may mitigate dopaminergic degeneration. During an ongoing α-synuclein lesion, mice with MHCII reduction in systemic and brain innate immune cells (LysMCre + I-Abfl/fl or CRE+) displayed brain T cell repertoire shifts and greater preservation of the dopaminergic phenotype in nigrostriatal terminals. Next, we investigated a human cohort to characterize the immunophenotype of subjects with and without the high-risk GG genotype at the rs3129882 SNP. We confirmed that the high-risk GG genotype is associated with peripheral changes in MHCII inducibility, frequency of CD4 + T cells, and differentially accessible chromatin regions within the MHCII locus. Although our mouse studies indicate that myeloid MHCII reduction coinciding with an intact adaptive immune system is insufficient to fully protect dopamine neurons from α-synuclein-induced degeneration, our data are consistent with the overwhelming evidence implicating antigen presentation in PD pathophysiology.

The length of G1 phase is an essential determinant of H3K27me3 landscape across diverse cell types

Stem cells have lower facultative heterochromatin as defined by trimethylation of histone H3 lysine 27 (H3K27me3) compared to differentiated cells. However, the mechanisms underlying these differential H3K27me3 levels remain elusive. Because H3K27me3 levels are diluted 2-fold in every round of replication and then restored through the rest of the cell cycle, we reasoned that the cell cycle length could be a key regulator of total H3K27me3 levels. Here, we propose that a short G1 phase restricts H3K27me3 levels in stem cells. To test this model, we determined changes to H3K27me3 levels in mouse embryonic stem cells (mESCs) globally and at specific loci upon G1 phase lengthening - accomplished by thymidine block or growth in the absence of serum (with the "2i medium"). H3K27me3 levels in mESCs increase with G1 arrest when grown in serum and in 2i medium. Additionally, we observed via CUT&RUN and ChIP-seq that regions that gain H3K27me3 in G1 arrest and 2i media overlap, supporting our model of G1 length as a critical regulator of the stem cell epigenome. Furthermore, we demonstrate the inverse effect - that G1 shortening in differentiated human HEK293 cells results in a loss of H3K27me3 levels. Finally, in human tumor cells with extreme H3K27me3 loss, lengthening of the G1 phase leads to H3K27me3 recovery despite the presence of the dominant negative, sub-stoichiometric H3.K27M mutation. Our results indicate that G1 length is an essential determinant of H3K27me3 landscapes across diverse cell types.

Vesicular and non-vesicular extracellular small RNAs direct gene silencing in a plant-interacting bacterium

Extracellular plant small RNAs (sRNAs) and/or double-stranded RNA (dsRNA) precursors act as triggers of RNAi in interacting filamentous pathogens. However, whether any of these extracellular RNA species direct gene silencing in plant-interacting bacteria remains unknown. Here, we show that Arabidopsis transgenic plants expressing sRNAs directed against virulence factors of a Pseudomonas syringae strain, reduce its pathogenesis. This Antibacterial Gene Silencing (AGS) phenomenon is directed by Dicer-Like (DCL)-dependent antibacterial sRNAs, but not cognate dsRNA precursors. Three populations of active extracellular sRNAs were recovered in the apoplast of these transgenic plants. The first one is mainly non-vesicular and associated with proteins, whereas the second one is located inside Extracellular Vesicles (EVs). Intriguingly, the third population is unbound to proteins and in a dsRNA form, unraveling functional extracellular free sRNAs (efsRNAs). Both Arabidopsis transgene- and genome-derived efsRNAs were retrieved inside bacterial cells. Finally, we show that salicylic acid (SA) promotes AGS, and that a substantial set of endogenous efsRNAs exhibits predicted bacterial targets that are down-regulated by SA biogenesis and/or signaling during infection. This study thus unveils an unexpected AGS phenomenon, which may have wider implications in the understanding of how plants regulate microbial transcriptome, microbial community composition and genome evolution of associated bacteria.

Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids

Splicing is often dysregulated in cancer, leading to alterations in the expression of canonical and alternatively spliced isoforms. We used the multiplexed arrays sequencing (MAS-seq) protocol of PacBio to sequence full-length transcripts in patient-derived organoid (PDO) cells of clear cell renal cell carcinoma (ccRCC). The sequencing revealed a heterogeneous dysregulation of splicing across 2599 single ccRCC cells. The majority of novel transcripts could be removed with stringent filtering criteria. The remaining 31,531 transcripts (36.6% of the 86,182 detected transcripts on average) were previously uncharacterized. In contrast to known transcripts, many of the novel transcripts have cell-specific expression. Novel transcripts common to ccRCC cells belong to genes involved in ccRCC-related pathways, such as hypoxia and oxidative phosphorylation. A novel transcript of the ccRCC-related gene nicotinamide N-methyltransferase is validated using PCR. Moreover, >50% of novel transcripts possess a predicted complete protein-coding open reading frame. An analysis of the most dominant transcript-switching events between ccRCC and non-ccRCC cells shows many switching events that are cell- and sample-specific, underscoring the heterogeneity of alternative splicing events in ccRCC. Overall, our study elucidates the intricate transcriptomic architecture of ccRCC, underlying its aggressive phenotype and providing insights into its molecular complexity.

Efficient and easy gene expression and genetic variation data analysis and visualization using exvar

RNA sequencing data manipulation workflows are complex and require various skills and tools. This creates the need for user-friendly and integrated genomic data analysis and visualization tools. We developed a novel R package using multiple Cran and Bioconductor packages to perform gene expression analysis and genetic variant calling from RNA sequencing data. Multiple public datasets were analyzed using the developed package to validate the pipeline for all the supported species. The developed R package, named "exvar", includes multiple data analysis functions and three data visualization shiny apps integrated as functions. Also, it could be used to analyze several species' data. The exvar package is available in the project's GitHub repository ( https://github.com/omicscodeathon/exvar ).

DuplexDiscoverer: a computational method for the analysis of experimental duplex RNA-RNA interaction data

For a few years, it has been possible to experimentally probe the universe of cis and trans RNA-RNA interactions in a transcriptome-wide manner. These experiments give rise to so-called duplex data, i.e. short reads generated via high-throughput sequencing that each encode information on a cis or trans RNA-RNA interaction. These raw duplex data require complex, subsequent computational analyses in order to be interpreted as solid evidence for actual cis and trans RNA-RNA interactions. While several methods have already been proposed to tackle this challenge, almost all of them lack one or more desirable feature-computational efficiency, ability to readily alter the main processing steps and parameter values, p-value estimation for predictions, and interoperability with the common bioinformatics tools for transcriptomics. To overcome these challenges, we present DuplexDiscoverer-a computational method and R package that allows for the efficient, adjustable, and conceptually coherent analysis of duplex data. DuplexDiscoverer is readily adaptable to analysing data from different experimental protocols and its results seamlessly integrate with the most commonly used bioinformatics tools for transcriptomics in R. Most importantly, DuplexDiscoverer generates predictions that are of superior or comparable quality to those of the existing methods while significantly improving time and memory efficiency.

Protocol for assembling, prioritizing, and characterizing piRNA clusters using the piRNA Cluster Builder

PIWI-interacting RNAs (piRNAs) play a critical role in safeguarding genome integrity in germ cells, ensuring fertility. Here, we provide a protocol for processing piRNA sequencing data, identifying piRNA-rich genomic regions as piRNA clusters, and preparing these clusters for downstream analyses. We describe steps for assembling piRNA cluster regions using an R-based tool, the piRNA Cluster Builder (PICB), which integrates unique and multimapping piRNA reads stepwise. The protocol allows for parameter optimizations and generates normalized outputs for prioritization of piRNA clusters. For complete details on the use and execution of this protocol, please refer to Konstantinidou et al.1.

Essential genes encoded by the mating-type locus of the human fungal pathogen Cryptococcus neoformans

Fungal sexual reproduction is controlled by the mating-type (MAT) locus. In contrast to a majority of species in the phylum Basidiomycota that have tetrapolar mating-type systems, the opportunistic human pathogen Cryptococcus neoformans employs a bipolar mating-type system, with two mating types (a and α) determined by a single MAT locus that is unusually large (~120 kb) and contains more than 20 genes. While several MAT genes are associated with mating and sexual development, others control conserved cellular processes (e.g., cargo transport and protein synthesis), of which five (MYO2, PRT1, RPL22, RPL39, and RPO41) have been hypothesized to be essential. In this study, through genetic analysis involving sporulation of heterozygous diploid deletion mutants, as well as in some cases construction and analyses of conditional expression alleles of these genes, we confirmed that with the exception of MYO2, both alleles of the other four MAT genes are indeed essential for cell viability. We further showed that while MYO2 is not essential, its function is critical for infectious spore production, faithful cytokinesis, adaptation for growth at high temperature, and pathogenicity in vivo. Our results demonstrate the presence of essential genes in the MAT locus that are divergent between cells of opposite mating types. We discuss possible mechanisms to maintain functional alleles of these essential genes in a rapidly evolving genomic region in the context of fungal sexual reproduction and mating-type evolution.IMPORTANCESexual reproduction is essential for long-term evolutionary success. Fungal cell-type identity is governed by the MAT locus, which is typically rapidly evolving and highly divergent between different mating types. In this study, we show that the a and α alleles of four genes encoded in the MAT locus of the opportunistic human fungal pathogen C. neoformans are essential. We demonstrate that a fifth gene, MYO2, which had been predicted to be essential, is in fact dispensable for cell viability. However, a functional MYO2 allele is important for cytokinesis and fungal pathogenicity. Our study highlights the need for careful genetic analyses in determining essential genes, which is complementary to high-throughput approaches. Additionally, the presence of essential genes in the MAT locus of C. neoformans provides insights into the function, maintenance, and evolution of these fast-evolving genomic regions.

Long-read sequencing reveals novel structural variation markers for key agronomic and quality traits of food-grade soybean

Long read sequencing has been widely used to detect structure variations that are not captured by short read sequencing in plant genomic research. In this study, we described an analysis of whole genome re-sequencing of 29 soybean varieties using nanopore long-read sequencing. The compiled germplasm reflects diverse applications of food-grade soybeans, including soy milk and tofu production, as well as consumption of natto, sprout, and edamame (vegetable soybean). We have identified 365,497 structural variations in these newly re-sequenced genomes and found that the newly identified structural variations are associated with important agronomic traits. These traits include seed weight, flowering time, plant height, oleic acid content, methionine content, and Kunitz trypsin inhibitor content, all of which significantly impact soybean production, quality, and market value. Experimental validation supports the roles of predicted candidate genes and structural variants in these biological processes. Our research provides a new source for rapid marker discovery in soybean and other crop genomes using structural variation and whole genome sequencing.

Decoding RAP1 's Role in Yeast mRNA Splicing

Messenger RNA (mRNA) splicing is a fundamental and tightly regulated process in eukaryotes, where the spliceosome removes non-coding sequences from pre-mRNA to produce mature mRNA for protein translation. Alternative splicing enables the generation of multiple RNA isoforms and protein products from a single gene, regulating both isoform diversity and abundance. While splicing is widespread in eukaryotes, only ∼3% of genes in Saccharomyces cerevisiae undergo splicing, with most containing a single intron. However, intron-containing genes, primarily ribosomal protein genes, are highly expressed and constitute about one-third of the total mRNA pool. These genes are transcriptionally regulated by Repressor Activator Protein 1 ( RAP1 ), prompting us to investigate whether RAP1 influences mRNA splicing. Using RNA sequencing, we identified a novel role for RAP1 in alternative splicing, particularly in intron retention (IR) while minor effects were observed on alternative 3' and 5' splice site usage. Many IR-containing transcripts introduced premature termination codons, likely leading to degradation via nonsense-mediated decay (NMD). Consistent with previous literature, genes with predicted NMD in our study also had reduced overall expression levels suggesting that RAP1 plays an important role in this understudied mechanism of gene expression regulation.

Early transcriptional effects of inflammatory cytokines reveal highly redundant cytokine networks

Inflammatory cytokines are fundamental mediators of the organismal response to injury, infection, or other harmful stimuli. To elucidate the early and mostly direct transcriptional signatures of inflammatory cytokines, we profiled all immunologic cell types by RNAseq after systemic exposure to IL1β, IL6, and TNFα. Our results revealed a significant overlap in the responses, with broad divergence between myeloid and lymphoid cells, but with very few cell-type-specific responses. Pathway and motif analysis identified several main controllers (NF-κB, IRF8, and PU.1), but the largest portion of the response appears to be mediated by MYC, which was also implicated in the response to γc cytokines. Indeed, inflammatory and γc cytokines elicited surprisingly similar responses (∼50% overlap in NK cells). Significant overlap with interferon-induced responses was observed, paradoxically in lymphoid but not myeloid cell types. These results point to a highly redundant cytokine network, with intertwined effects between disparate cytokines and cell types.

Protocol to analyze deep-learning-predicted functional scores for noncoding de novo variants and their correlation with complex brain traits

Functional impact of noncoding variants can be predicted using computational approaches. Although predictive scores can be insightful, implementing the scores for a custom variant set and associating scores with complex traits require multiple phases of analysis. Here, we present a protocol for prioritizing variants by generating deep-learning-predicted functional scores and relating them with brain traits. We describe steps for score prediction, statistical comparison, phenotype correlation, and functional enrichment analysis. This protocol can be generalized to different models and phenotypes. For complete details on the use and execution of this protocol, please refer to Mondragon-Estrada et al.1.

Eosinophil innate immune memory after bacterial skin infection promotes allergic lung inflammation

Microbial exposure at barrier interfaces drives development and balance of the immune system, but the consequences of local infections for systemic immunity and secondary inflammation are unclear. Here, we show that skin exposure to the bacterium Staphylococcus aureus persistently shapes the immune system of mice with specific impact on progenitor and mature bone marrow neutrophil and eosinophil populations. The infection-imposed changes in eosinophils were long-lasting and associated with functional as well as imprinted epigenetic and metabolic changes. Bacterial exposure enhanced cutaneous allergic sensitization and resulted in exacerbated allergen-induced lung inflammation. Functional bone marrow eosinophil reprogramming and pulmonary allergen responses were driven by the alarmin interleukin-33 and the complement cleavage fragment C5a. Our study highlights the systemic impact of skin inflammation and reveals mechanisms of eosinophil innate immune memory and organ cross-talk that modulate systemic responses to allergens.

Predicting and comparing transcription start sites in single cell populations

The advent of 5' single-cell RNA sequencing (scRNA-seq) technologies offers unique opportunities to identify and analyze transcription start sites (TSSs) at a single-cell resolution. These technologies have the potential to uncover the complexities of transcription initiation and alternative TSS usage across different cell types and conditions. Despite the emergence of computational methods designed to analyze 5' RNA sequencing data, current methods often lack comparative evaluations in single-cell contexts and are predominantly tailored for paired-end data, neglecting the potential of single-end data. This study introduces scTSS, a computational pipeline developed to bridge this gap by accommodating both paired-end and single-end 5' scRNA-seq data. scTSS enables joint analysis of multiple single-cell samples, starting with TSS cluster prediction and quantification, followed by differential TSS usage analysis. It employs a Binomial generalized linear mixed model to accurately and efficiently detect differential TSS usage. We demonstrate the utility of scTSS through its application in analyzing transcriptional initiation from single-cell data of two distinct diseases. The results illustrate scTSS's ability to discern alternative TSS usage between different cell types or biological conditions and to identify cell subpopulations characterized by unique TSS-level expression profiles.

HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy

Clear cell renal cell carcinoma (ccRCC), despite having a low mutational burden, is considered immunogenic because it occasionally undergoes spontaneous regressions and often responds to immunotherapies. The signature lesion in ccRCC is inactivation of the VHL tumor suppressor gene and consequent upregulation of the HIF transcription factor. An earlier case report described a ccRCC patient who was cured by an allogeneic stem cell transplant and later found to have donor-derived T cells that recognized a ccRCC-specific peptide encoded by a HIF-responsive endogenous retrovirus (ERV), ERVE-4. We report that ERVE-4 is one of many ERVs that are induced by HIF, translated into HLA-bound peptides in ccRCCs, and capable of generating antigen-specific T cell responses. Moreover, ERV expression can be induced in non-ccRCC tumors with clinical-grade HIF stabilizers. These findings have implications for leveraging ERVs for cancer immunotherapy.

Profiling transcriptome composition and dynamics within nuclear compartments using SLAM-RT&Tag

Nuclear compartments are membrane-less regions enriched in functionally related molecules. RNA is a major component of many nuclear compartments, but the identity and dynamics of transcripts within nuclear compartments are poorly understood. Here, we applied reverse transcribe and tagment (RT&Tag) to human cell lines to identify the transcript populations of Polycomb domains and nuclear speckles. We also developed SLAM-RT&Tag, which combines RNA metabolic labeling with RT&Tag, to quantify transcript dynamics within nuclear compartments. We observed unique transcript populations with differing structures and dynamics within each compartment. Intriguingly, exceptionally long genes are transcribed adjacent to Polycomb domains and are transiently associated with chromatin. By contrast, nuclear speckles act as quality control checkpoints that transiently confine incompletely spliced polyadenylated transcripts and facilitate their post-transcriptional splicing. In summary, we demonstrate that transcripts at Polycomb domains and nuclear speckles undergo distinct RNA processing mechanisms, highlighting the pivotal role of compartmentalization in RNA maturation.

Tissue-specific methylomic responses to a lifestyle intervention in older adults associate with metabolic and physiological health improvements

Across the lifespan, diet and physical activity profiles substantially influence immunometabolic health. DNA methylation, as a tissue-specific marker sensitive to behavioral change, may mediate these effects through modulation of transcription factor binding and subsequent gene expression. Despite this, few human studies have profiled DNA methylation and gene expression simultaneously in multiple tissues or examined how molecular levels react and interact in response to lifestyle changes. The Growing Old Together (GOTO) study is a 13-week lifestyle intervention in older adults, which imparted health benefits to participants. Here, we characterize the DNA methylation response to this intervention at over 750 thousand CpGs in muscle, adipose, and blood. Differentially methylated sites are enriched for active chromatin states, located close to relevant transcription factor binding sites, and associated with changing expression of insulin sensitivity genes and health parameters. In addition, measures of biological age are consistently reduced, with decreases in grimAge associated with observed health improvements. Taken together, our results identify responsive molecular markers and demonstrate their potential to measure progression and finetune treatment of age-related risks and diseases.

Ubiquitous MEIS transcription factors actuate lineage-specific transcription to establish cell fate

Control of gene expression is commonly mediated by distinct combinations of transcription factors (TFs). This cooperative action allows the integration of multiple biological signals at regulatory elements, resulting in highly specific gene expression patterns. It is unclear whether combinatorial binding is also necessary to bring together TFs with distinct biochemical functions, which collaborate to effectively recruit and activate RNA polymerase II. Using a cardiac differentiation model, we find that the largely ubiquitous homeodomain proteins MEIS act as actuators, fully activating transcriptional programs selected by lineage-restricted TFs. Combinatorial binding of MEIS with lineage-enriched TFs, GATA, and HOX, provides selectivity, guiding MEIS to function at cardiac-specific enhancers. In turn, MEIS TFs promote the accumulation of the methyltransferase KMT2D to initiate lineage-specific enhancer commissioning. MEIS combinatorial binding dynamics, dictated by the changing dosage of its partners, drive cells into progressive stages of differentiation. Our results uncover tissue-specific transcriptional activation as the result of ubiquitous actuator TFs harnessing general transcriptional activator at tissue-specific enhancers, to which they are directed by binding with lineage- and domain-specific TFs.

The complexity of tobacco smoke-induced mutagenesis in head and neck cancer

Tobacco smoke, alone or combined with alcohol, is the predominant cause of head and neck cancer (HNC). We explore how tobacco exposure contributes to cancer development by mutational signature analysis of 265 whole-genome sequenced HNC samples from eight countries. Six tobacco-associated mutational signatures were detected, including some not previously reported. Differences in HNC incidence between countries corresponded with differences in mutation burdens of tobacco-associated signatures, consistent with the dominant role of tobacco in HNC causation. Differences were found in the burden of tobacco-associated signatures between anatomical subsites, suggesting that tissue-specific factors modulate mutagenesis. We identified an association between tobacco smoking and alcohol-related signatures, indicating a combined effect of these exposures. Tobacco smoking was associated with differences in the mutational spectra, repertoire of driver mutations in cancer genes and patterns of copy number change. Our results demonstrate the multiple pathways by which tobacco smoke can influence the evolution of cancer cell clones.

Learning and teaching biological data science in the Bioconductor community

Modern biological research is increasingly data-intensive, leading to a growing demand for effective training in biological data science. In this article, we provide an overview of key resources and best practices available within the Bioconductor project-an open-source software community focused on omics data analysis. This guide serves as a valuable reference for both learners and educators in the field.

Comparative characterization of human accelerated regions in neurons

Human accelerated regions (HARs) are conserved genomic loci that have experienced rapid nucleotide substitutions following the divergence from chimpanzees1,2. HARs are enriched in candidate regulatory regions near neurodevelopmental genes, suggesting their roles in gene regulation3. However, their target genes and functional contributions to human brain development remain largely uncharacterized. Here we elucidate the cis-regulatory functions of HARs in human and chimpanzee induced pluripotent stem (iPS) cell-induced excitatory neurons. Using genomic4 and chromatin looping information, we prioritized 20 HARs and their chimpanzee orthologues for functional characterization via single-cell CRISPR interference, and demonstrated their species-specific gene regulatory functions. Our findings reveal diverse functional outcomes of HAR-mediated cis-regulation in human neurons, including attenuated NPAS3 expression by altering the binding affinities of multiple transcription factors in HAR202 and maintaining iPS cell pluripotency and neuronal differentiation capacities through the upregulation of PUM2 by 2xHAR.319. Finally, we used prime editing to demonstrate differential enhancer activity caused by several HAR26;2xHAR.178 variants. In particular, we link one variant in HAR26;2xHAR.178 to elevated SOCS2 expression and increased neurite outgrowth in human neurons. Thus, our study sheds new light on the endogenous gene regulatory functions of HARs and their potential contribution to human brain evolution.

Heat inducible nuclear translocation of Kdm6bb drives temperature dependent sex reversal in Nile tilapia

Understanding the primary molecular events driving temperature-dependent sex reversal (TSR) has proven challenging, particularly in distinguishing these from secondary effects of sexual differentiation. The mechanisms translating temperature into a sex-determining signal in fish are still largely unknown. Through combined transcriptomic and genome-wide histone methylation analyses of gonads in Nile tilapia (Oreochromis niloticus) exposed to normal and elevated temperatures, we observed significant upregulation of male-promoting genes (amh, dmrt1, gsdf) and suppression of female-promoting genes (wt1a and foxl3) at high temperature. These changes were correlated with methylation changes in H3K27 and H3K4 in the promoter regions of these genes. Among the histone methylation enzymes induced by high temperature, we identified the H3K27 demethylase Kdm6bb to be a key factor. Gene deletion and biochemical studies confirmed that Kdm6bb significantly impacts the H3K27 methylation level, that influences sex determination. Crucially, we discovered that the TSR function of Kdm6bb is mediated by the alternative inclusion of a previously unrecognized intron, enabling nuclear translocation of the demethylase to perform its function. Our findings refute the previously proposed "translation deficiency" mechanism of kdm6bb, and highlight the critical role of mRNA alternative splicing and subcellular localization of the demethylase in temperature-induced sex reversal.

Scalable high-performance single cell data analysis with BPCells

The growth of single-cell datasets to multi-million cell atlases has uncovered major scalability problems for single-cell analysis software. Here, we present BPCells, a package for high-performance single-cell analysis of RNA-seq and ATAC-seq datasets. BPCells uses disk-backed streaming compute algorithms to reduce memory requirements by nearly 70-fold compared to in-memory workflows with little to no loss of execution speed. BPCells also introduces high-performance compressed formats based on bitpacking compression for ATAC-seq fragment files and single-cell sparse matrices. These novel compression algorithms help to accelerate disk-backed analysis by reducing data transfer from disk, while providing the lowest computational overhead of all compression algorithms tested. Using BPCells, we perform normalization and PCA of a 44 million cell dataset on a laptop, demonstrating that BPCells makes working with the largest contemporary single-cell datasets feasible on modest hardware, while leaving headroom on servers for future datasets an order of magnitude larger.

A multi-omics approach reveals impaired lipid metabolism and oxidative stress in a zebrafish model of Alexander disease

Alexander disease (AxD) is a rare leukodystrophy caused by heterozygous mutations in the GFAP gene. To date, several in vitro and in vivo models have been generated in an attempt to unravel the main mechanisms underlying this complex disease. However, none of these models is suitable for investigating the global dysregulation caused by AxD. To address this shortcoming, we have generated a stable transgenic zebrafish line (zAxD) carrying the human GFAP p.R239C mutation, which is associated with severe phenotypes of AxD type I patients. We then performed transcriptomics and proteomics analyses on the whole larvae of our zAxD model, confirming the involvement of several pathways such as the immune system response and inflammation, oxidative stress, extracellular matrix, lipoxidation and lipid metabolism, which were previously reported in more limited omic studies. Interestingly, new pathways emerged as well, including tyrosine and butanoate metabolic processes. Biochemical assays confirmed alterations in cell respiration and lipid metabolism as well as elevated oxidative stress. These findings confirm the reliability of the zAxD model to apply a whole-organism approach to investigate the molecular basis of the disease.

A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines

The human genome contains instructions to transcribe more than 200,000 RNAs. However, many RNA transcripts are generated from the same gene, resulting in alternative isoforms that are highly similar and that remain difficult to quantify. To evaluate the ability to study RNA transcript expression, we profiled seven human cell lines with five different RNA-sequencing protocols, including short-read cDNA, Nanopore long-read direct RNA, amplification-free direct cDNA and PCR-amplified cDNA sequencing, and PacBio IsoSeq, with multiple spike-in controls, and additional transcriptome-wide N6-methyladenosine profiling data. We describe differences in read length, coverage, throughput and transcript expression, reporting that long-read RNA sequencing more robustly identifies major isoforms. We illustrate the value of the SG-NEx data to identify alternative isoforms, novel transcripts, fusion transcripts and N6-methyladenosine RNA modifications. Together, the SG-NEx data provide a comprehensive resource enabling the development and benchmarking of computational methods for profiling complex transcriptional events at isoform-level resolution.

Linking CRISPR-Cas9 double-strand break profiles to gene editing precision with BreakTag

Cas9 can cleave DNA in both blunt and staggered configurations, resulting in distinct editing outcomes, but what dictates the type of Cas9 incisions is largely unknown. In this study, we developed BreakTag, a versatile method for profiling Cas9-induced DNA double-strand breaks (DSBs) and identifying the determinants of Cas9 incisions. Overall, we assessed cleavage by SpCas9 at more than 150,000 endogenous on-target and off-target sites targeted by approximately 3,500 single guide RNAs. We found that approximately 35% of SpCas9 DSBs are staggered, and the type of incision is influenced by DNA:gRNA complementarity and the use of engineered Cas9 variants. A machine learning model shows that Cas9 incision is dependent on the protospacer sequence and that human genetic variation impacts the configuration of Cas9 cuts and the DSB repair outcome. Matched datasets of Cas9 and engineered variant incisions with repair outcomes show that Cas9-mediated staggered breaks are linked with precise, templated and predictable single-nucleotide insertions, demonstrating that a scission-based gRNA design can be used to correct clinically relevant pathogenic single-nucleotide deletions.

Leveraging the MethMotif Toolkit to Characterize Context-Specific Features and Roles of Methylation Sensitive Transcription Factors

This article presents a comprehensive guide for using the MethMotif platform, which includes the MethMotif database, the TFregulomeR R package, and a new R library, Forked-TF, designed specifically for analyzing leucine-zipper transcription factors (TFs) that bind DNA as dimers. The MethMotif platform integrates transcription factor binding site (TFBS) motifs with DNA methylation profiles, providing an in-depth analysis of how methylation modulates TF binding across different cell types and conditions. The protocols are organized into three main workflows: (1) Exploration of transcription factor dimerization partners, (2) visualization of methylation-specific TF motifs using TFregulomeR, and (3) characterization of leucine-zipper TF binding patterns with a focus on dimerization. Using the platform's MethMotif database, users can retrieve ChIP-seq and DNA methylation data, intersect TFBS peak regions, and generate TFBS-methylation-informed motif logos. A case study of CEBPB in K562 cells is included to demonstrate the use of the platform, showing how to identify TF dimers, analyze their co-binding behavior, and visualize the impact of DNA methylation on binding specificity. The protocols also provide step-by-step instructions for software installation, data input formats, and interpretation of results, making it accessible to researchers with varying levels of computational expertise. Through these protocols, users can uncover how DNA methylation and TF dimerization influence gene regulatory networks, with a focus on leucine-zipper TFs in a cell-type-specific context. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Exploration of transcription factor dimerization partners Support Protocol 1: Software installation Support Protocol 2: Docker installation Support Protocol 3: Verifying installation Basic Protocol 2: Visualization of alternative cofactors Basic Protocol 3: Characterization of bZIP partners/cofactors Basic Protocol 4: Context-independent and context-dependent analysis.

Prenatal cannabis exposure is associated with alterations in offspring DNA methylation at genes involved in neurodevelopment, across the life course

Prenatal cannabis exposure (PCE) is of increasing concern globally, due to the potential impact on offspring neurodevelopment, and its association with childhood and adolescent brain development and cognitive function. However, there is currently a lack of research addressing the molecular impact of PCE, that may help to clarify the association between PCE and neurodevelopment. To address this knowledge gap, here we present epigenome-wide association study data across multiple time points, examining the effect of PCE and co-exposure with tobacco using two longitudinal studies, the Avon Longitudinal Study of Parents and Children (ALSPAC) and the Christchurch Health and Development Study (CHDS) at birth (0 y), 7 y and 15-17 y (ALSPAC), and ~27 y (CHDS). Our findings reveal genome-wide significant DNA methylation differences in offspring at 0 y, 7 y, 15-17 y, and 27 y associated with PCE alone, and co-exposure with tobacco. Importantly, we identified significantly differentially methylated CpG sites within the genes LZTS2, NPSR1, NT5E, CRIP2, DOCK8, COQ5, and LRP5 that are shared between different time points throughout development in offspring. Notably, functional pathway analysis showed enrichment for differential DNA methylation in neurodevelopment, neurotransmission, and neuronal structure pathways, and this was consistent across all timepoints in both cohorts. Given the increasing volume of epidemiological evidence that suggests a link between PCE and adverse neurodevelopmental outcomes in exposed offspring, this work highlights the need for further investigation into PCE, particularly in larger cohorts.

Methylseq, single-nuclei RNAseq, and discovery proteomics identify pathways associated with nephron-deficit CKD in the HSRA rat model

Low nephron numbers are associated with an increased risk of developing chronic kidney disease (CKD) and hypertension, which are significant global health problems. To investigate the impact of nephron deficiency, our laboratory developed a novel inbred rat model (HSRA rat). In this model, ∼75% of offspring are born with a single kidney (HSRA-S), compared with two-kidney littermates (HSRA-C). HSRA-S rats show impaired kidney development, resulting in ∼20% fewer nephrons. Our previous data and current findings demonstrate that nephron deficit (failure of one kidney to form and altered development in the remaining kidney) predisposes HSRA-S to CKD late in life (with increased proteinuria by 18 mo of age in HSRA-S = 51 ± 3.4 vs. HSRA-C = 8 ± 1.5 mg/24 h). To understand early molecular mechanisms contributing to the increased predisposition to CKD, Methylseq using reduced representation bisulfite sequencing, single-nuclei (sn)RNAseq, and discovery proteomics were performed in kidneys of 4-wk-old HSRA rats. Methylation analysis revealed a small number of differences, including five differentially methylated cytosines and six differentially methylated regions between groups. The snRNAseq analysis identified differentially expressed genes in most kidney cell types, with several hundred genes dysregulated depending on the analysis method (Seurat vs. DESeq2). Notably, many genes are involved in kidney development. Discovery proteomic analysis identified 366 differentially expressed proteins. A key finding was dysregulation of Deptor/DEPTOR and Amdhd2/AMDHD2 across omics layers, suggesting a potential role in compensatory mechanisms or the genetic basis of altered kidney development. Further understanding of these mechanisms may guide interventions to preserve nephron health and slow kidney disease progression.NEW & NOTEWORTHY The HSRA rat is a novel model of nephron deficiency and provides a unique opportunity to study the association between nephron number and chronic kidney disease (CKD). Previous work characterized the impact of age, hypertension, and diabetes on the development of CKD in HSRA animals. This study examined early changes in epigenetics, cell-type specific transcriptome, and proteomic changes in the kidney that likely predispose the model to CKD with age.

The Expansion and Diversification of Epigenetic Regulatory Networks Underpins Major Transitions in the Evolution of Land Plants

Epigenetic silencing is essential for regulating gene expression and cellular diversity in eukaryotes. While DNA and H3K9 methylation silence transposable elements (TEs), H3K27me3 marks deposited by the Polycomb repressive complex 2 (PRC2) silence varying proportions of TEs and genes across different lineages. Despite the major development role epigenetic silencing plays in multicellular eukaryotes, little is known about how epigenetic regulatory networks were shaped over evolutionary time. Here, we analyze epigenomes from diverse species across the green lineage to infer the chronological epigenetic recruitment of genes during land plant evolution. We first reveal the nature of plant heterochromatin in the unicellular chlorophyte microalga Chlorella sorokiniana and identify several genes marked with H3K27me3, highlighting the deep origin of PRC2-regulated genes in the green lineage. By incorporating genomic phylostratigraphy, we show how genes of differing evolutionary age occupy distinct epigenetic states in plants. While young genes tend to be silenced by H3K9 methylation, genes that emerged in land plants are preferentially marked with H3K27me3, some of which form part of a common network of PRC2-repressed genes across distantly related species. Finally, we analyze the potential recruitment of PRC2 to plant H3K27me3 domains and identify conserved DNA-binding sites of ancient transcription factor families known to interact with PRC2. Our findings shed light on the conservation and potential origin of epigenetic regulatory networks in the green lineage, while also providing insight into the evolutionary dynamics and molecular triggers that underlie the adaptation and elaboration of epigenetic regulation, laying the groundwork for its future consideration in other eukaryotic lineages.

Endogenous DNA damage at sites of terminated transcripts

DNA damage promotes mutations that fuel cancer, ageing and neurodegenerative diseases1-3, but surprisingly, the causes and types of damage remain largely unknown. There are three identified mechanisms that damage DNA during transcription: collision of RNA polymerase (RNAP) with the DNA-replication machinery head-on and co-directionally4-6, and R-loop-induced DNA breakage7-10. Here we identify novel DNA damage reaction intermediates11,12 and uncover a fourth transcription-related source of DNA damage: endogenous DNA damage at sites of terminated transcripts. We engineered proteins to capture single-stranded DNA (ssDNA) ends with 3' polarity in bacterial and human cells. In Escherichia coli, spontaneous 3'-ssDNA-end foci were unexpectedly frequent, at one or more per cell division, and arose via two identifiable pathways, both of which were dependent on DNA replication. A pathway associated with double-strand breaks was suppressed by overexpression of replicative DNA polymerase (pol) III, suggesting competition between pol III and DNA damage-promoting proteins. Mapping of recurrent 3'-ssDNA-ends identified distinct 3'-ssDNA-end-hotspots, mostly unrelated to double-strand breaks, next to the 5'-CCTTTTTT transcription-terminator-like sequence. These 3'-ssDNA-termini coincide with RNA 3'-termini identified by DirectRNA sequencing13 or simultaneous 5' and 3' end RNA sequencing (SEnd-seq)14 and were prevented by a mutant RNAP that reads through terminators. Our findings reveal that transcription termination or pausing can promote DNA damage and subsequent genomic instability.

Transient chemical-mediated epigenetic modulation confers unrestricted lineage potential on human primed pluripotent stem cells

Human primed pluripotent stem cells are capable of generating all the embryonic lineages. However, their extraembryonic trophectoderm potentials are limited. It remains unclear how to expand their developmental potential to trophectoderm lineages. Here we show that transient treatment with a cocktail of small molecule epigenetic modulators imparts trophectoderm lineage potentials to human primed pluripotent stem cells while preserving their embryonic potential. These chemically treated cells can generate trophectoderm-like cells and downstream trophoblast stem cells, diverging into syncytiotrophoblast and extravillous trophoblast lineages. Transcriptomic and CUT&Tag analyses reveal that these induced cells share transcriptional profiles with in vivo trophectoderm and cytotrophoblast, and exhibit reduced H3K27me3 modification at gene loci specific to trophoblast lineages compared with primed pluripotent cells. Mechanistic exploration highlighted the critical roles of epigenetic modulators HDAC2, EZH1/2, and KDM5s in the activation of trophoblast lineage potential. Our findings demonstrate that transient epigenetic resetting activates unrestricted lineage potential in human primed pluripotent stem cells, and offer new mechanistic insights into human trophoblast lineage specification and in vitro models for studying placental development and related disorders.

DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation

BACKGROUND

A critical area of recent cancer research is the emergence of transition states between normal and cancer that exhibit increased cell plasticity which underlies tumor cell heterogeneity. Pancreatic ductal adenocarcinoma (PDAC) can arise from the combination of a transition state termed acinar-to-ductal metaplasia (ADM) and a gain-of-function mutation in the proto-oncogene KRAS. During ADM, digestive enzyme-producing acinar cells acquire a transient ductal epithelium-like phenotype while maintaining their geographical acinar organization. One route of ADM initiation is the overexpression of the Krüppel-like factor 4 gene (KLF4) in the absence of oncogenic driver mutations. Here, we asked to what extent cells acquire and retain an epigenetic memory of the ADM transition state in the absence of oncogene mutation.

METHODS

We profiled the DNA methylome and transcriptome of KLF4-induced ADM in transgenic mice at various timepoints during and after recovery from ADM. We validated the identified DNA methylation and transcriptomic signatures in the widely used caerulein model of inducible pancreatitis.

RESULTS

We identified differential DNA methylation at Kras-downstream PI3K and Rho/Rac/Cdc42 GTPase pathway genes during ADM, as well as a corresponding gene expression increase in these pathways. Importantly, differential methylation persisted after gene expression returned to normal. Caerulein exposure, which induces widespread digestive system changes in addition to ADM, showed similar changes in DNA methylation in ADM cells. Regions of differential methylation were enriched for motifs of KLF and AP-1 family transcription factors, as were those of human pancreatic intraepithelial neoplasia (PanIN) samples, demonstrating the relevance of this epigenetic transition state memory in human carcinogenesis. Finally, single-cell spatial transcriptomics revealed that these ADM transition cells were enriched for PI3K pathway and AP1 family members.

CONCLUSIONS

Our comprehensive study of DNA methylation in the acinar-ductal metaplasia transition state links epigenetic memory to cancer-related cell plasticity even in the absence of oncogenic mutation.

Reelin marks cocaine-activated striatal neurons, promotes neuronal excitability, and regulates cocaine reward

Drugs of abuse activate defined neuronal populations in reward structures such as the nucleus accumbens (NAc), which promote the enduring synaptic, circuit, and behavioral consequences of drug exposure. While the molecular and cellular effects arising from experience with drugs like cocaine are increasingly well understood, mechanisms that dictate NAc neuronal recruitment remain unknown. Here, we leveraged unbiased single-nucleus transcriptional profiling and targeted in situ detection to identify Reln (encoding the secreted glycoprotein, Reelin) as a marker of cocaine-activated neuronal populations within the rat NAc. A CRISPR interference approach enabling selective Reln knockdown in the adult NAc altered expression of calcium signaling genes, promoted a transcriptional trajectory consistent with loss of cocaine sensitivity, and decreased MSN excitability. Behaviorally, Reln knockdown prevented cocaine locomotor sensitization, abolished cocaine place preference memory, and decreased cocaine self-administration behavior. These results identify Reelin as a critical mechanistic link between neuronal activation and cocaine-induced behavioral adaptations.