Leung, J. | Search bioRxiv

bioRxiv2018

Sae2/CtIP prevents R-loop accumulation in eukaryotic cells

The Sae2/CtIP protein is required for efficient processing of DNA double-strand breaks that initiate homologous recombination in eukaryotic cells. Sae2/CtIP is also important for survival of single-stranded Top1-induced lesions and CtIP is known to associate directly with transcription-associated complexes in mammalian cells. Here we investigate the role of Sae2/CtIP at single-strand lesions in budding yeast and in human cells and find that depletion of Sae2/CtIP promotes the accumulation of stalled RNA polymerase and RNA-DNA hybrids at sites of highly expressed genes. Overexpression of the RNA-DNA helicase Senataxin suppresses DNA damage sensitivity and R-loop accumulation in Sae2/CtIP-deficient cells, and a catalytic mutant of CtIP fails to complement this sensitivity, indicating a role for CtIP nuclease activity in the repair process. Based on this evidence, we propose that R-loop processing by 5 flap endonucleases is a necessary step in the stabilization and removal of nascent R-loop initiating structures in eukaryotic cells.

molecular biology↗

bioRxiv2017

Dependence of Intravoxel Incoherent Motion MR threshold b-value selection for separating perfusion and diffusion compartment and liver fibrosis diagnostic performance.

PurposeTo explore how the selection of threshold b-value impacts Intravoxel Incoherent Motion (IVIM) diffusion parameters of PF (f), Dslow (D),and Dfast (D*) values and their performance for liver fibrosis detection.\n\nMaterials and MethodsFifteen healthy volunteers and 33 hepatitis-b patients were included. With a 1.5 T MR scanner and respiration gating, IVIM data was acquired with 10 b-values of 10,20,40,60,80,100,150, 200, 400, and 800 s/mm2. Signal measurement was performed on right liver. Segmented-unconstrained analysis was used to compute IVIM parameters, and six threshold b-values between 40 and 200 s/mm2 were compared. PF, Dslow, and Dfast values were placed along the x-axis, y-axis, and z-axis, and a plane was defined to separate volunteers from patients.\n\nResultsHigher threshold b-values were associated with higher PF measurement; while lower threshold b-values led to higher Dslow and Dfast measurements. The dependence of PF, Dslow, and Dfast on threshold b-value differed between healthy livers and fibrotic livers; with the healthy livers showing a higher dependence. Threshold b-value=60 s/mm2 showed the largest mean distance between healthy liver datapoints vs. fibrotic liver datapoints in 3-dimensional space.\n\nConclusionFor segmented-unconstrained analysis, the selection of threshold b-value=60 s/mm2 improves IVIM diffusion differentiation between healthy livers and fibrotic livers.

biophysics↗