eLife最新文献

Cells must adopt flexible regulatory strategies to make decisions regarding their fate, including differentiation, apoptosis, or survival in the face of various external stimuli. One key cellular strategy that enables these functions is stochastic gene expression programs. However, understanding how transcriptional bursting, and consequently, cell fate, responds to DNA damage on a genome-wide scale poses a challenge. In this study, we propose an interpretable and scalable inference framework, DeepTX, that leverages deep learning methods to connect mechanistic models and single-cell RNA sequencing (scRNA-seq) data, thereby revealing genome-wide transcriptional burst kinetics. This framework enables rapid and accurate solutions to transcription models and the inference of transcriptional burst kinetics from scRNA-seq data. Applying this framework to several scRNA-seq datasets of DNA-damaging drug treatments, we observed that fluctuations in transcriptional bursting induced by different drugs were associated with distinct fate decisions: 5'-iodo-2'-deoxyuridine treatment was associated with differentiation in mouse embryonic stem cells by increasing the burst size of gene expression, while low- and high-dose 5-fluorouracil treatments in human colon cancer cells were associated with changes in burst frequency that corresponded to apoptosis- and survival-related fate, respectively. Together, these results show that DeepTX enables genome-wide inference of transcriptional bursting from single-cell transcriptomics data and can generate hypotheses about how bursting dynamics relate to cell fate decisions.

Acetylation of lysine residues in the tail domain of histone H3 is well characterised, but lysine residues in the histone globular domain are also acetylated. Histone modifications in the globular domain have regulatory potential because of their impact on nucleosome stability but remain poorly characterised. In this study, we report the genome-wide distribution of acetylated H3 lysine 115 (H3K115ac), a residue on the lateral surface at the nucleosome dyad, using chromatin immunoprecipitation. In mouse embryonic stem cells, we find that detectable H3K115ac is enriched at the transcription start site of active CpG island promoters, but also at polycomb-repressed promoters prior to their subsequent activation during differentiation. By contrast, at enhancers, H3K115ac enrichment is dynamic, changing in line with gene activation and chromatin accessibility during differentiation. Most strikingly, we show that H3K115ac is detected as enriched on 'fragile' nucleosomes within nucleosome-depleted regions at promoters and active enhancers, where it coincides with transcription factor binding, and at CTCF-bound sites. These unique features suggest that H3K115ac correlates with, and could contribute to, nucleosome destabilisation and that it might be a valuable marker for identifying functionally important regulatory elements in mammalian genomes.

Experiments on Drosophila show that an evolutionarily conserved photoreceptor that senses light outside of the retina can regulate responses to direct visual cues.

Distal renal tubular acidosis (dRTA) is a disorder characterized by the inability of the collecting duct system to secrete acids during metabolic acidosis. The pathophysiology of dominant or recessive SLC4A1 variant-related dRTA has been linked with the mis-trafficking defect of mutant kAE1 protein. However, in vivo studies in kAE1 R607H dRTA mice and humans have revealed a complex pathophysiology implicating a loss of kAE1-expressing intercalated cells and intracellular relocation of the H⁺-ATPase in the remaining type-A intercalated cells. These cells also displayed accumulation of ubiquitin and p62 autophagy markers. The highly active transport properties of collecting duct cells require the maintenance of cellular energy and homeostasis, a process dependent on intracellular pH. Therefore, we hypothesized that the expression of dRTA variants affects intracellular pH and autophagy pathways. In this study, we report the characterization of newly identified dRTA variants and provide evidence of abnormal autophagy and degradative pathways in mouse inner medullary collecting duct cells and kidneys from mice expressing kAE1 R607H dRTA mutant protein. We show that reduced transport activity of the kAE1 variants correlated with increased cytosolic pH, reduced ATP synthesis, attenuated downstream autophagic pathways pertaining to the fusion of autophagosomes and lysosomes and/or lysosomal degradative activity. Our study elucidated a close relationship between the expression of defective kAE1 proteins, reduced mitochondrial activity, and decreased autophagy and protein degradative flux.

DNA aptamers are short, single-stranded DNA molecules that bind specifically to a range of targets such as proteins, cells, and small molecules. Typically, they are utilized in the development of therapeutic agents, diagnostics, drug delivery systems, and biosensors. Although aptamers perform well in controlled extracellular environments, their intracellular use has been less explored due to challenges of expressing them in vivo. In this study, we employed the bacterial retron system Eco2 to express a DNA light-up aptamer in Escherichia coli. Our data confirms that structure-guided insertion of the aptamer domain into the non-coding region of the retron enables reverse transcription and biosynthesis of functional aptamer constructs in bacteria. The purified DNA aptamer synthesized under intracellular conditions shows comparable activity to a chemically synthesized control. Our findings demonstrate that retrons can be used to express short DNA aptamers within living cells, potentially broadening and optimizing their application in intracellular settings.

The macaque genus includes 25 species with diverse social systems, ranging from low to high social tolerance grades. Such interspecific behavioral variability provides a unique model to tackle the evolutionary foundation of primate social brain. Yet, the neuroanatomical correlates of these social tolerance grades remain unknown. To address this question, we expressed social tolerance grades within a novel cognitive framework and analyzed post-mortem structural scans from 12 macaque species. Our results show that amygdala volume is a subcortical predictor of macaques' social tolerance, with high tolerance species exhibiting larger amygdala than low tolerance ones. We further investigated the developmental trajectory of amygdala across social grades and found that intolerant species showed a gradual increase in relative amygdala volume across the lifespan. Unexpectedly, tolerant species exhibited a decrease in relative amygdala volume across the lifespan, contrasting with the age-related increase observed in intolerant species-a developmental pattern previously undescribed in primates. Taken together, these findings provide valuable insights into the cognitive, neuroanatomical, and evolutionary basis of primates' social behaviors.

Oligo-astheno-teratozoospermia (OAT), a recurrent cause of male infertility, is the most frequent disorder of spermatogenesis with a predominantly genetic origin. Patients and mice bearing mutations in the ARMC2 gene exhibit reduced sperm concentration, multiple morphological defects, and impaired motility, defining a canonical OAT phenotype. Intracytoplasmic sperm injection (ICSI) is required to treat this condition; however, it is associated with a slightly increased risk of birth defects compared with natural conception, highlighting the need for novel targeted therapies. Here, in vivo testicular injection followed by electroporation of capped, polyadenylated naked messenger RNA (mRNA) was evaluated as a strategy to treat ARMC2-related infertility in mice. mRNAs encoding reporter proteins were used to assess expression efficiency and kinetics using in vivo and in vitro 2D and 3D imaging. Reporter proteins were detected in germ cells for up to three weeks, demonstrating the feasibility of mRNA-based approaches. These results were compared with a non-integrative plasmid Enhanced Episomal Vector, which induced weak and transient expression in spermatogenic cells. Delivery of Armc2 mRNA restored morphologically normal and motile sperm in deficient males, capable of producing embryos via in vitro fertilization and ICSI. These findings provide proof-of-concept that mRNA electroporation can restore sperm motility and fertilizing potential, offering a novel strategy to correct monogenic male infertility.

The brain is thought to optimise behaviour by generating predictions based on learned statistical regularities. Predictive processing seemingly explains expectation suppression (ES), the attenuation of neural activity in response to expected stimuli. However, the mechanisms behind ES are unclear, with conflicting evidence for alternative models. Sharpening models propose that expectations suppress neurons away from the expected stimulus, increasing the signal-to-noise ratio and boosting decoding for expected stimuli. In contrast, dampening models posit that expectations suppress neurons that are tuned to the expected stimuli, reducing overall response magnitude and decoding accuracy. The opposing process theory (OPT) suggests that both processes occur at different time points, namely that initial sharpening is followed by later dampening of the neural representations of the expected stimulus. Here we test this theory and shed light on the dynamics of expectation effects, both at single-trial level and over time. Thirty-one participants completed a statistical learning task in which a 'leading' image from one category predicted a 'trailing' image from a different category. Multivariate EEG analyses decoded stimulus information related to the trailing category. Within-trial, expectation increased decoding accuracy at early latencies and decreased it at later latencies, in line with OPT. However, across trials, stimulus expectation decreased decoding accuracy in initial trials and increased it in later trials. We theorise that these dissociable dynamics of expectation effects within and across trials support hierarchical learning mechanisms. While within-trial results support the OPT, across-trial results suggest that sharpening and dampening effects emerge at distinct stages of associative learning.

Automated detection of complex animal behavior remains a challenge in neuroscience. Developments in computer vision have greatly advanced automated behavior detection and allow high-throughput preclinical and mechanistic studies. An integrated hardware and software solution is necessary to facilitate the adoption of these advances in the field of behavioral neurogenetics, particularly for non-computational laboratories. We have published a series of papers using an open field arena to annotate complex behaviors such as grooming, posture, and gait as well as higher-level constructs such as biological age and pain. Here, we present our integrated rodent phenotyping platform, JAX Animal Behavior System (JABS), to the community for data acquisition, machine learning-based behavior annotation and classification, classifier sharing, and genetic analysis. The JABS Data Acquisition Module (JABS-DA) enables uniform data collection with its combination of 3D hardware designs and software for real-time monitoring and video data collection. JABS-Active Learning Module (JABS-AL) allows behavior annotation, classifier training, and validation. We introduce a novel graph-based framework (ethograph) that enables efficient boutwise comparison of JABS-AL classifiers. JABS-Analysis and Integration Module (JABS-AI), a web application, facilitates users to deploy and share any classifier that has been trained on JABS, reducing the effort required for behavior annotation. It supports the inference and sharing of the trained JABS classifiers and downstream genetic analyses (heritability and genetic correlation) on three curated datasets spanning 168 mouse strains that we are publicly releasing alongside this study. This enables the use of genetics as a guide to proper behavior classifier selection. This open-source tool is an ecosystem that allows the neuroscience and genetics community to share advanced behavior analysis and reduces the barrier to entry into this new field.