DNA methylation

Delocalized DNA holes imprint mutation position in mismatch-repair-deficient cancers

The paper identifies a specific mutation pattern in mismatch-repair-deficient cancers linked to DNA hole delocalization and oxidation, showing enrichment at 5' guanines and depletion at 3' guanines.

Epigenomic heterogeneity and spatial organization during human reprogramming

This study examines epigenomic and spatial changes during human reprogramming, finding distinct molecular and spatial patterns in productive versus unsuccessful trajectories.

A domesticated totivirus-like tandem array undergoes interspecific transfer and asymmetric evolution

The paper shows a domesticated totivirus-like gene array in yeasts evolves faster than its exogenous relatives and undergoes interspecific transfer and asymmetric evolution.

FBRSL1 couples ncPRC1.3 to CoREST to repress cell-cycle genes during human neuronal differentiation

This study shows FBRSL1 couples ncPRC1.3 to CoREST for transcriptional repression during neuronal differentiation, contrasting AUTS2's activating role.

A new epigenetic framework for DNA methylation, hydroxymethylation, and gene expression during brain aging.

The paper shows that cell identity and regulatory logic are preserved during brain aging, but cell-type-specific changes occur in DNA modifications and gene expression.

A novel clonal and axenic isolation pipeline for the human gut protist Blastocystis reveals within-subtype strain coexistence

This study develops a new cultivation method for Blastocystis, revealing that multiple strains can coexist within a single host.

CnidoSite: A Multi-Omics Database for Cnidarians

CnidoSite provides a centralized multi-omics database for cnidarians, integrating genomic, transcriptomic, proteomic, and phenotypic data to study thermal tolerance and environmental adaptation.

The relevance of GGCC methylation for cyanobacterial gene expression regulation

The paper investigates the impact of GGCC methylation on gene expression in Synechocystis 6803 and finds it affects over 300 genes, with context-specific effects on promoter regions.

Local population genetic structure of Andrena flavipes (Hymenoptera, Andrenidae), a nest-philopatric communal mining bee, reveals isolation-by-distance and high inbreeding

The paper assesses genetic structure and inbreeding in Andrena flavipes bees using SNPs, finding isolation-by-distance and high inbreeding despite high genetic variation.

Chirality-Driven Photonic PCR Enables Label-Free Genetic Amplification

This paper introduces a chirality-driven photonic PCR method that enables rapid, label-free genetic amplification by using chiral plasmonic nanoparticles to enhance photothermal conversion and DNA synthesis efficiency.

Cowpea Chlorotic Mottle Virus virus-like particles as DNA or RNA delivery vehicle to fish cells

This study evaluates CCMV VLPs as DNA/RNA delivery vehicles for fish cells and zebrafish, showing efficient in vivo DNA transfer to myocytes.

Decoding pseudoexon activation by deep intronic variants using a high-throughput minigene assay in the NF1 gene

The paper develops a high-throughput minigene assay to identify pseudoexon-activating variants in the NF1 gene and benchmarks splicing prediction tools.

Lowly polymorphic pathogen proteins may not be under evolutionary constraint

The paper argues that low diversity in pathogen proteins does not necessarily indicate evolutionary constraint and introduces a tool to explore diversity and divergence in Plasmodium falciparum proteins.

Predicting cell-state-specific gene regulation from DNA across species

Bolero predicts cell-state-specific gene regulation from DNA across species by integrating cell-state embeddings and biological variables.

NEIL2 regulates RNA polymerase II dynamics to suppress transcription replication conflicts in pancreatic cancer

This study identifies NEIL2 as a regulator of RNA polymerase II dynamics that suppresses transcription replication conflicts in pancreatic cancer cells.

DNA methylation alterations in MIR10B, MIR21, MIR100, MIR127 and MIR143 genes associated with advanced carotid artery atherosclerosis: a targeted bisulfite sequencing study of vascular tissues and peripheral blood

LongVerse: verified AI agents for Nanopore and PacBio DNA methylation analysis

LongVerse uses AI agents to generate haplotype-resolved DNA methylation calls from Nanopore and PacBio reads, achieving high agreement with bisulfite sequencing and reducing errors compared to existing methods.

Structural basis for aphidicolin inhibition of human processive DNA synthesis

This study reveals the structural mechanism of aphidicolin inhibition of human DNA polymerases Pol δ and Pol ε, showing how it blocks DNA synthesis by altering the polymerase conformation.

Molecular Data From Herbarium Specimens Reveal A Potential Extirpation of Azolla microphylla From California

The paper analyzes molecular data from historical herbarium specimens and modern samples to assess the status of Azolla species in California, finding potential extirpation of Azolla microphylla.

Phylogenomic Characterization of Two Alternaria Lineages Associated with Cotton Leaf Spot in Tennessee

The paper identifies two phylogenetically distinct Alternaria lineages associated with cotton leaf spot in Tennessee, confirming one as a causal agent.

What happens when Arctic sea-ice melts? Macroalgae as a summer refuge for sympagic nematode Theristus melnikovi

The paper investigates the summer habitat of the sympagic nematode Theristus melnikovi in Svalbard, finding that macroalgae-associated specimens represent phenotypic variation within the species rather than a separate morphotype.

Integrated Multiomics Reveals Intergenerational Brain Sensory System Remodeling Induced by Parental Intermittent Fasting

This study shows that parental intermittent fasting induces intergenerational molecular changes in the brain, affecting sensory pathways and sex-dependent gene expression in offspring.

PeakLocus: A transcript-aware toolkit for RNA-Centric Genomic Annotation

PeakLocus assigns RNA features to transcript intervals with high accuracy, outperforming existing tools in benchmark tests across multiple species.

RiboGRAM learns multi-scale non-coding RNA grammar for structural and regulatory inference

The paper introduces RiboGRAM, a model that learns non-coding RNA sequence grammar for structural and regulatory inference across multiple organisms.

Latent-Factor Stability Is Not Sufficient: Evaluating SABLE-MO in Simulated and Cancer Multi-Omics Data

The paper evaluates SABLE-MO's performance in identifying shared factors in multi-omics data, finding that stricter retention reduces errors but does not eliminate them.

Sequence-dependent conformational and mechanical landscapes of double-stranded nucleic acids

This study introduces cgNA+, a model predicting sequence-dependent mechanical properties of dsNAs with high accuracy, revealing hidden regulatory layers in nucleic acid mechanics.

Dynamic evolution of EZHIP, an inhibitor of the Polycomb Repressive Complex 2 in mammals

EZHIP, a PRC2 inhibitor, arose on the placental mammal X chromosome, evolves under positive selection in primates, and duplicated, including a testis-expressed primate paralog, EZHIP2, whose gorilla copy inhibits H3K27me3.

Genomic variation and ancestry of Helicobacter pylori in the admixed population of Cabo Verde reveal host adaptation, limited host-pathogen ancestry concordance, and signatures of trans-Atlantic slave trade migrations

Modulator Resolves Transcript-, Allele-, and Condition-associated RNA Modification Differences from Direct RNA Sequencing

Modulator processes nanopore direct-RNA sequencing data to differentiate transcript-, allele-, and condition-associated RNA modifications, improving the analysis of RNA modifications in single molecules.

Testing Thirty Years of Hypotheses: Ancient Trout-Salmon Introgression and Limited Pre-Colonial Gene Flow Between Rainbow and Cutthroat Trout Shaped Pacific Salmonid Evolution

This study tests hypotheses about ancient introgression and gene flow in Pacific salmonids, finding introgression between trout and salmon ancestors but not between trout lineages.