DNA methylation

Transcription factor interactions promote binding to non-cognate DNA sites

This study shows how transcription factor interactions enable binding to non-cognate DNA sites by bridging across nucleosomal DNA gyres.

scPRIME-seq uncovers synchronized multimodal molecular collapse facilitated by pre-neoplastic epigenetic burden in prostate cancer

The paper introduces scPRIME-seq, a multimodal single-cell platform, and finds pre-neoplastic epigenetic changes drive tumor progression in prostate cancer.

Ethanol stress induces siRNA-mediated epimutations and phenotypic variability in fission yeast

This study shows ethanol stress increases siRNA-mediated epimutations in fission yeast, leading to transposon expression changes and phenotypic variability.

Probing Genomic Foundation Models with Splice-Variant Perturbations

This paper evaluates genomic foundation models using splice-variant perturbations, finding they match task-specific networks and generalize across mutation types.

DNA 6mA marks transcriptionally active chromatin in malaria parasites

The paper identifies 6mA methylation in Plasmodium falciparum, showing it is associated with active chromatin and transcription, and identifies a methyltransferase involved in this modification.

Structured biological evidence enables general-purpose language models to predict bacteriophage-host interactions

The paper introduces a structured-evidence framework for predicting bacteriophage-host interactions using a large language model, achieving high accuracy and enabling interpretable inference.

MacroH2A1 and H3K27me3 target cGAS to facultative heterochromatin to restrain innate immune activation

This study shows that macroH2A1 and H3K27me3 bind cGAS to sequester it in heterochromatin, preventing innate immune activation.

Cerberus: bidirectional state space blocks improve accuracy and efficiency of regulatory sequence models

The paper introduces Cerberus, an improved regulatory sequence model using bidirectional state space blocks, achieving higher accuracy and efficiency than existing models like Borzoi.

Multi-omic long-read sequencing reveals nucleosome control of transcriptional fidelity at the isoform level

The paper uses long-read sequencing to study how nucleosome positioning affects isoform expression by analyzing chromatin and RNA in yeast.

Mitochondrial dynamics can resolve stoichiometric challenges in plant mtDNA repair

This study models how mitochondrial dynamics in plants enhance DNA repair efficiency by improving stoichiometry through targeted import, fusion, and metabolon exchange.

Mosaic selection and gene flow at the onset of grain beetle domestication

The paper investigates gene flow and selection during the domestication of yellow mealworms, finding that adaptive gene flow contributes to adaptation to captivity rather than directly shaping production traits.

Is epigenetics Lamarck's revenge? The evolutionary and ecological impacts of DNA methylation in a California oak

The study investigates DNA methylation's role in Lamarckian inheritance in California oaks, finding environmental induction and gene expression associations but not stable transmission across generations.

Centromeric islands constrain CENP-A domain size and position

The paper shows that centromeric islands like Giglio constrain CENP-A domain size and position but are not required for centromere identity.

Empirical Bayes Estimation of Sample-Specific Correlation Networks for Cross-Sectional and Longitudinal Omics Data

PRISM estimates sample-specific correlation networks for cross-sectional and longitudinal omics data, improving accuracy and uncertainty quantification over existing methods.

Genomic signatures of coevolving phage-bacteria interaction networks

This study investigates how coevolution between phages and bacteria affects interaction networks by analyzing genetic changes in both hosts and phages.

Unexpected excess heterozygosity in a threatened, mycoheterotrophic, self-pollinating orchid

The paper investigates excess heterozygosity in the self-pollinating orchid Corallorhiza bentleyi, finding overdominance likely explains the phenomenon despite selfing and small population size.

Artificial Intelligence Applied to Epigenomic Data in Leukemia: A Systematic Review of Diagnostic, Prognostic and Monitoring Models

This paper reviews AI models using epigenomic data for leukemia diagnosis, prognosis, and monitoring, finding high accuracy in classification but limited external validation and prospective testing.

Active maintenance of accessible chromatin at poised meiotic promoters by the NFYA-NURF axis is required for meiotic entry in mice

The paper identifies the NFYA-NURF axis as essential for maintaining accessible chromatin at poised meiotic promoters, which is required for meiotic entry in mice.

Can carcasses cause environmental nucleic acid pollution? Implications for interpreting environmental RNA/DNA survey results

The paper investigates whether carcasses contribute to environmental RNA/DNA contamination and its implications for interpreting survey results.

High-throughput in vivo DNA data encoding by multiplexed conjugationand orthogonal base editing

The paper introduces a system for high-throughput in vivo DNA data encoding using bacterial conjugation and base editing, successfully encoding and retrieving binary data with high accuracy.

Characterization of two Martinezella spp. species: M. legmii sp. nov. and M. ivanii sp. nov., from tropical legume trees in Costa Rica

This paper describes the characterization and classification of two new Martinezella species isolated from tropical legume trees in Costa Rica using genomic and phenotypic analyses.

Taking a BREATH (Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories) to simultaneously infer phylogenetic and transmission trees for partially sampled outbreaks

BREATH simultaneously infers phylogenetic and transmission trees for outbreaks using sequence data, improving resolution and origin timing estimates in a tuberculosis outbreak.

CBFA2T3-GLIS2 establishes transcriptionally permissive enhancer hypermethylation associated with venetoclax response in pediatric AML

The paper identifies enhancer hypermethylation as a feature of C/G AML linked to venetoclax response and shows DNMT3B inhibition enhances treatment efficacy.

Maize genetic diversity is largely unstructured by human ethnolinguistic diversity in its center of origin

The paper quantifies anthropogenic effects on maize genetic diversity in the Americas using genotyping, human genomic data, and linguistic maps, finding weak genome-wide effects but localized language-associated loci.

Ancient Mitogenomes from Belize Provide Insights into the Mobility and Migration of Ancient Communities in Mesoamerica and the Caribbean.

The paper analyzes ancient mitogenomes from Belize to study maternal genetic continuity and mobility patterns among ancient Maya populations and their relation to present-day communities.

ATRX Deficiency Drives Aberrant Type I Interferon Signalling Through cGAS-Dependent Transcriptional Dysregulation

This study identifies ATRX deficiency as a driver of aberrant type I interferon signaling via cGAS-dependent transcriptional dysregulation in patients with cerebral white matter disease.

gRely: Relyability for genome trained sequence-to-expression models

gRely provides reliability scores for sequence-to-expression models, improving prediction filtering beyond magnitude thresholds in low-magnitude regimes.

8-Oxoguanine transcriptional miscoding can transiently reproduce PAH-associated premature-stop transcripts

The paper shows that 8-oxoguanine can create premature-stop transcripts in PAH genes, mimicking pathogenic variants without DNA mutation.

Durable and reversible epigenetic programming of human hematopoietic stem cells as a platform for modulation of platelet function

This study uses DNA methylation-based epigenome editing to durably and reversibly silence genes in human hematopoietic stem cells, demonstrating its application in modulating platelet function.

DNA polymerase kappa supports repair-associated DNA synthesis and genome maintenance in postmitotic neurons

This study identifies DNA polymerase kappa (POLK) as essential for DNA repair and genome maintenance in postmitotic neurons, showing its role in preventing neurodegeneration and aging-related stress.