Skirmantas Kriaučionis

How mutation rate evolves: Gene expression shapes genome-wide mutation rates in Drosophila melanogaster and Caenorhabditis elegans

The paper investigates how gene expression influences genome-wide mutation rates in Drosophila melanogaster and Caenorhabditis elegans, finding that highly expressed genes have lower mutation rates due to transcription-coupled repair.

Absolute quantitative and base-resolution sequencing reveals comprehensive landscape of pseudouridine across the human transcriptome

This paper introduces BACS, a method for single-base resolution pseudouridine quantification, and identifies {Psi} sites in human RNA and viral transcripts.

Introduction of cytosine-5 DNA methylation sensitizes cells to oxidative damage

This study shows that introducing 5mC into E. coli increases sensitivity to oxidative stress and alkylating agents due to reactive oxygen species and DNA damage.

Nucleosome wrapping energy in CpG islands and the role of epigenetic base modifications

The paper models how CpG island density and epigenetic modifications affect DNA nucleosome wrapping energy and probability.

UXS1 regulates UDP-GlcA levels to support growth of UGDH-high cancer cells

The paper identifies UXS1 as a selectively essential gene in UGDH-high cancer cells, showing it regulates UDP-GlcA levels to prevent toxicity and highlights it as a therapeutic target.

A critique of the hypothesis that CA repeats are primary targets of neuronal MeCP2

The paper investigates whether CA repeats are primary targets of MeCP2 and finds no evidence supporting this hypothesis, instead showing they contribute modestly to MeCP2-mediated gene expression.

Neuronal non-CG methylation is an essential target for MeCP2 function

This study shows that MeCP2's binding to non-CG methylation, specifically mCAC trinucleotides, is critical for normal brain function, as demonstrated by severe Rett syndrome-like phenotypes in mice with a modified MeCP2 domain.

Distinct Contribution of DNA Methylation and Histone Acetylation to the Genomic Occupancy of Transcription Factors

The paper investigates how DNA methylation and histone acetylation independently affect transcription factor binding and gene expression in mouse embryonic stem cells.

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads

This paper introduces a method to measure DNA replication dynamics on single molecules using nanopore sequencing and applies it to yeast to discover new replication origins.

The non-canonical SMC protein SmcHD1 antagonises TAD formation on the inactive X chromosome

This study shows that SmcHD1 prevents TAD formation on the inactive X chromosome by altering chromatin structure and epigenetic marks.