Frederic L. Chedin

Sequence and Structural Alignments Reveal Insights into ANKLE2 Evolution and Function

The paper uses sequence and structural alignments to study ANKLE2 evolution and function, revealing conserved domains and potential roles in DNA damage response.

The R-loop Grammar predicts R-loop formation under different topological constraints

The paper introduces an R-loop grammar to predict R-loop formation using sequence data and shows it outperforms previous methods across different DNA topologies.

RNase H1 levels dramatically affect mitochondrial genome maintenance with little impact on nuclear R-loops in murine B cells

This study shows that RNase H1 is critical for mitochondrial genome maintenance in B cells but has little effect on nuclear R-loops.

Protein-mediated stabilization and nicking of the non-template DNA strand dramatically affect R-loop formation in vitro

This study shows that DNA-binding proteins and nicks increase R-loop formation in vitro, revealing their roles in R-loop dynamics and initiation.

Exploration and analysis of R-loop mapping data with RLBase

The paper reprocesses R-loop mapping data, develops new quality methods, and introduces RLBase, a web server for exploring and analyzing R-loop datasets.

Quality-controlled R-loop meta-analysis reveals the characteristics of R-Loop consensus regions

The paper reprocesses R-loop mapping datasets to assess data quality and identifies consensus R-loop regions, revealing methodological differences and biological subtypes.

Genomic patterns of transcription-replication interactions in mouse primary B cells

The paper introduces TRIPn-Seq to identify transcription-replication interactions in mouse B cells, finding they correlate with replication stress and genomic instability.

Recognition of cellular RNAs by the S9.6 antibody creates pervasive artefacts when imaging RNA:DNA hybrids

This study shows that the S9.6 antibody binds RNA rather than RNA:DNA hybrids in fixed cells, leading to unreliable imaging data.

SF3B1-targeted Splicing Inhibition Triggers Transcriptional Stress Response and Global Alterations in R-Loop Landscape

This study shows that SF3B1 inhibition causes intron retention and R-loop changes, with R-loop gains linked to stress-response gene readthrough and not DNA damage.

High-Throughput Single-Molecule R-loop Footprinting Reveals Principles of R-loop Formation

The paper develops SMRF-seq to profile R-loops with high resolution and shows they form from unspliced transcripts at genic hotspots, influenced by DNA sequence and topology.

The sequence of the extruded non-template strand determines the architecture of R-loops.

This study shows that the sequence of the non-template strand determines the three-dimensional architecture of R-loops, which influences their impact on genome stability.

DNA Topoisomerase I differentially modulates R-loops across the human genome

This study shows DNA Topoisomerase I regulates R-loop formation by causing gains and losses at different genomic regions, affecting replication and cell cycle progression.

The affinity of the S9.6 antibody for double-stranded RNAs impacts the mapping of R-loops in fission yeast.

This study shows that dsRNAs interfere with R-loop detection using S9.6 antibody-based DRIPc-seq in fission yeast, revealing genuine R-loops and their transcriptomic impact.