DNA methylation

The paper maps gene expression, chromatin accessibility, and DNA methylation in developing human brain cells to understand regulatory interactions and their role in disease.

This study examines transcriptional and DNA methylation changes in the hippocampus and prefrontal cortex of irradiated mice, identifying cell-type-specific gene expression and methylation patterns linked to cognitive deficits.

The paper tests the 'anvil effect' hypothesis by showing that surface-adherent bacteria are preferentially lysed during mechanical extraction, leading to DNA yield bias.

The paper uses ocean current models to predict genomic diversity patterns in coastal species, finding that lineage source regions (LSRs) better explain genetic structure than isolation-by-distance.

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.

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

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.

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

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.

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

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.

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.

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

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

The paper identifies new genetic code variants in ciliates, including an unprecedented codon reassignment in Licnophora and a previously unreported reassignment in Balantidium ctenopharyngodoni.

The paper characterizes a unique cluster of Shigella-like organisms in Bangladesh, identifying them as potentially a new serotype of S. boydii based on phenotypic, genotypic, and serological analyses.

HiSpoT is a PCR-based method for preparing NGS libraries for spoligotyping MTBC isolates, offering high-throughput, low-cost, and accurate strain typing with open-source tools for analysis.

The paper identifies promoter hypomethylation as a driver of transcriptomic plasticity and aberrant gene expression in colorectal cancer, linking it to distinct cell states and metastatic behavior.

The paper shows RNA polymerase backtracking promotes type III-A CRISPR DNA targeting by inhibiting GreA anti-backtracking factors, which suppress Cas10-Csm activity.

The paper identifies PICJIs as large mobile genetic elements in E. coli and Salmonella that spread antimicrobial resistance and defense systems via a specific bacteriophage.

UMR-seq reveals epigenetic variation in plant hypomethylomes, showing UMRs are enriched in regulatory loci and improve genomic prediction and trait association mapping in wheat.

This study investigates how PWO1 and PWO2 proteins interact with circadian and epigenetic signaling to regulate flowering time in Arabidopsis.

The paper identifies CD200R1 as a marker for an immature NK-cell precursor in tonsils, distinguishing between oligopotent and more restricted developmental stages.

The paper investigates the mcm4Chaos3 mutation in yeast, showing it causes genome instability by impairing specific centromere-proximal origins.

The paper shows that most hnRNP proteins are excluded from DNA double-strand breaks, with hnRNPH1's exclusion dependent on its GYR domain and independent of recruitment pathways.

This study shows FoxO1 and HNF1α work together to change nucleosome structure and stability to activate transcription.

The paper identifies tandem repeats in methanogenic archaea and their viruses, showing they contribute to genomic diversity and adaptation potential.

This study shows that proteolytic feedback regulates quorum sensing in Pseudomonas aeruginosa by controlling RhlR stability, affecting virulence and biofilm formation.

This study shows that Polycomb-marked promoter methylation gains in aging and cancer occur independently of replication and are driven by age-related epigenetic drift rather than oncogenic signaling.