DNA methylation

Long-range regulatory sequence models reveal a phylogenetic boundary in vertebrate genome evolution

The paper uses sequence-to-function models to show that long-range regulatory information in vertebrate genomes stops being shared before local sequence information, with a phylogenetic boundary around 320-435 Mya.

CPDD: Adapting an autoregressive DNA language model for bidirectional phage genome modeling

CPDD adapts an autoregressive DNA language model for bidirectional phage genome modeling, achieving higher random-mask restoration accuracy and supporting fitness prediction and classification.

Nucleobase-Specific Recognition of DNA by Protamine

This study shows that protamines, despite being intrinsically disordered, bind DNA with nucleobase-specific preferences, favoring GC over AT in the major groove and vice versa in the minor groove.

A global post-transcriptional regulator directs Acinetobacter baumannii carbon preference and gut colonization

This study identifies CsrA as a global regulator of carbon preference and gut colonization in Acinetobacter baumannii, revealing its role in repressing arginine/ornithine catabolism and enhancing competitive fitness.

Maternal separation remodels Purkinje cell circuits and impairs cerebellar synaptic plasticity

This study shows that maternal separation alters cerebellar circuitry and synaptic plasticity, leading to behavioral and neurobiological deficits in mice.

Age-associated repression of HNF4α is a driver and potential therapeutic target in liver metabolic dysfunction

This study identifies age-associated repression of HNF4α as a driver of liver metabolic dysfunction and shows that restoring HNF4α can reverse some age-related liver defects.

Tfcp2l1 recruits Thrap3 to sustain ESC self-renewal via Jmjd1c exon-5 splicing and DNA repair choice

This study identifies Tfcp2l1 and Thrap3 as regulators of ESC self-renewal through exon-5 splicing of Jmjd1c and DNA repair pathway choice.

Population dynamics in extreme environments: shared histories of strong selection lead to predictable patterns across separate high-elevation populations of small mammals

The paper examines genetic and phenotypic variation in deer mice across elevation gradients, finding predictable patterns in extreme environments that could inform species vulnerability to environmental change.

SAMP1/TMEM201 protects alveolar type 2 cells from DNA damage-associated senescence and restrains pulmonary fibrosis

This study identifies SAMP1 as a protector of alveolar type 2 cells against DNA damage-induced senescence and shows its role in limiting pulmonary fibrosis in a mouse model.

TideCluster: clustering and classification of tandem repeats for comparative and pangenomic analysis

TideCluster is a pipeline for clustering and classifying tandem repeats across genomes, demonstrated on Arabidopsis and Solanum species.

The tiger shark, Galeocerdo cuvier (Peron & Lesueur, 1822), genome reveals genomic and epigenomic signatures of shark evolution and demographic history

The paper generates the first chromosome-scale genome and methylome for the tiger shark, revealing genomic and epigenomic features of shark evolution and population decline.

Thermosensory pathway makes a U-turn to respond to heat

The paper shows that heat stress reverses the growth-promoting thermomorphogenesis pathway in Arabidopsis by suppressing auxin and PIF4 in cotyledons, revealing an active molecular mechanism.

PP271, a novel bacteriophage primase-polymerase, enables Primer-Free DNA Amplification

This paper characterizes PP271, a novel bacteriophage PrimPol enzyme, showing it can synthesize DNA primers that are efficiently extended by Phi29 DNA polymerase for primer-free amplification.

The MarR-family regulator TilR links biosynthesis of enterotoxin tilimycin with physiologic adaptation in Klebsiella oxytoca

This study identifies TilR, a MarR-family regulator in Klebsiella oxytoca, as a repressor of tilimycin biosynthesis and links it to metabolic and virulence-related gene expression.

The biochemical composition of coronavirus Nucleocapsid proteins drives the bicistronic properties of their sub-genomic mRNAs

The paper identifies conserved overlapping accessory ORFs in coronavirus N genes and shows that nucleotide and codon biases drive their formation.

SARDINE unlocks EWAS summary statistics for large-scale epigenetic biomarker analysis

SARDINE uses EWAS summary statistics to estimate epigenetic clock-phenotype associations without individual-level data, revealing heterogeneity in biomarker associations with aging and diseases.

Temporal changes in genetic variation during the invasion of Lygodium japonicum in North America

This study uses herbarium specimens to analyze genetic variation in Lygodium japonicum during its invasion of North America, identifying Asia as the source and finding evidence of rapid adaptation and reduced non-coding diversity.

Epigenome-informed Polymer Modeling Reveals Chromosome Folding Landscapes across Distinct Genetic and Epigenetic Contexts

This study uses epigenome-informed polymer modeling to generate chromosomal conformational ensembles from epigenomic data, revealing how genetic and epigenetic contexts shape chromosome folding landscapes.

Asymmetric division and polar growth define a non-canonical cell cycle in Bradyrhizobium.

This study describes the asymmetric cell division and polar growth in Bradyrhizobium, revealing a unique cell cycle program with distinct nucleoid dynamics and chromosome organization.

Evolutionary dynamics of the pan-centromere architecture in oaks

The paper analyzes centromere evolution in oaks, showing lineage-specific expansion of QuCEN146 satellite drives turnover, while LTR-rich centromeres show low polymorphism due to suppressed recombination.

Quantum Entanglement as a Physical Determinant of Genomic Instability in TP53

The paper explores whether quantum entanglement, measured via von Neumann Entropy, influences TP53 mutation patterns, finding elevated entropy at known mutational hotspots but cautioning about limited validation.

Hybrid RY-mers increase aDNA alignment sensitivity

This paper introduces hybrid RY-mers to improve aDNA alignment sensitivity and efficiency, showing higher accuracy and reduced runtime compared to existing methods.

Long-read DNA sequencing reveals global hypomethylation and focal hypermethylation in SDHx-deficient pheochromocytoma and paraganglioma

The paper uses long-read sequencing to analyze DNA methylation patterns in SDHx-deficient PPGLs and finds global hypomethylation with focal hypermethylation at specific CpG islands.

A three-factor model can explain symmetry breaking and the n-1 rule during X-chromosome inactivation

This paper introduces a three-factor mathematical model to explain symmetry breaking and the n-1 rule in X-chromosome inactivation by integrating Xist, an X-linked activator, and SPEN.

Learning Strand-Equivariant Tokenizations of DNA with MirrorDNA

This paper introduces MirrorDNA, a DNA language model with a strand-equivariant tokenizer that improves prediction consistency across DNA strands.

2'-O-Methylated ncRNA condensates form a recombination center for IgH synapsis

This study shows that FBL-mediated 2'-O-methylation of GLTs forms condensates that drive IgH synapsis and CSR in B cells.

Genomic and Epigenomic Relationships Capture Different Patterns of Genotype-by-Environment Interaction in Grapevine Clones

This study compares how genomic and epigenomic relationships contribute to genotype-by-environment interaction in grapevine clones, finding that epigenomic factors capture more GEI variance than genomic factors.

Widespread Saccharomyces hybridization in agave fermentations arises repeatedly from asymmetric parental diversity

The paper identifies widespread Saccharomyces hybridization in agave fermentations, showing multiple independent origins and asymmetric parental genetic diversity.

Rates of molecular and morphological evolution are uncoupled across the eukaryote Tree of Life

The paper investigates correlations between molecular and morphological evolutionary rates across eukaryotes and finds little evidence of a link, suggesting differing evolutionary dynamics at genomic and phenotypic levels.

The long noncoding RNA FOSIL shapes the dynamics of FOS induction

This study shows that the lncRNA FOSIL regulates the timing and resolution of FOS induction by modulating chromatin structure and nuclear speckle dynamics.