Mohammad Mahdi Karimi

The paper investigates how spatial and transcriptional dynamics at Cd4 and Cd8 loci influence T cell lineage choice in the thymus, revealing locus-specific chromatin environments that drive differentiation.

This study shows that the FACT complex regulates cohesin dynamics on chromatin, facilitating loop extrusion and preventing cohesin accumulation in transcribed regions.

The paper identifies a DNA-bound intermediate during MCM2-7 helicase activation and shows how DNA unwinding is coupled to helicase complex disassembly and DNA exit.

The paper investigates the role of Dux and MERVL in ZGA, totipotency, and cell toxicity using CRISPRa and a 2C-GFP reporter system, finding that MERVL activation contributes to expanded fate potential but not all totipotency features, while Dux-induced toxicity is independent of MERVL and involves Noxa.

This study benchmarks TE detection tools on long-read data, showing significant variation in performance and highlighting tool-specific strengths and limitations.

The paper examines RTE expression and methylation in human blood, finding correlations with biological aging but not chronological age, and identifies potential mechanisms and cell types involved.

The paper integrates inflammation, cell-type composition, and immune signatures in MDS to identify prognostic subgroups using MOFA, finding that high inflammation correlates with better prognosis while SRSF2 mutations are linked to poor outcomes.

The paper identifies mitochondrial defects in eliminated cells during early mouse development and shows that cell competition removes cells with mitochondrial DNA mutations and sequence changes.

The paper identifies a conserved serine in UBE2D3 that, when phosphorylated by Aurora B, reduces UBE2D3 levels and affects early embryonic development in mice.

This study shows that FACT is required for cohesin stability on chromatin and the formation of cohesin-dependent TAD-like structures, but not sister chromatid cohesion.

LIONS detects and quantifies TE-initiated transcripts from RNA-seq data by addressing computational limitations in TE transcription analysis.

The paper examines H3K9me3 marking of transposable elements in human and chimpanzee induced pluripotent stem cells, finding limited species-specificity and no strong link to gene expression divergence.