Biology subjects

Black, E.

Publications and source records attributed to Black, E..

3 recordsLinked to original sources

bioRxiv2022

ATR protects centromere identity by promoting DAXX association with PML nuclear bodies

Centromere protein A (CENP-A) defines centromere identity and nucleates kinetochore formation for mitotic chromosome segregation. Here, we show that Ataxia telangiectasia and Rad3-related (ATR) kinase, a master regulator of the DNA damage response, protects CENP-A occupancy at interphase centromeres in a DNA damage-independent manner. As ATR localizes to promyelocytic leukemia nuclear bodies (PML NBs) in unperturbed cells, we hypothesized that ATR protects CENP-A occupancy by regulating the localization of the histone H3.3 chaperone and PML NB component, DAXX. Indeed, we found that ATR inhibition reduces DAXX association with PML NBs, resulting in the DAXX-dependent loss of CENP-A from interphase centromeres. Lastly, we demonstrate that CENP-A occupancy is not restored until G1 of the following cell cycle, leading to increased mitotic chromosome segregation defects. These findings demonstrate a novel mechanism by which ATR protects centromere identity and genome stability.

cell biology↗

bioRxiv2022

Corruption of DNA End-Joining in Mammalian Chromosomes by Progerin Expression

Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare genetic condition characterized by features of accelerated aging and a life expectancy of about 14 years. HGPS is commonly caused by a point mutation in the LMNA gene which codes for lamin A, an essential component of the nuclear lamina. The HGPS mutation alters splicing of the LMNA transcript, leading to a truncated, farnesylated form of lamin A termed "progerin." HGPS is associated with accumulation of genomic DNA double-strand breaks (DSBs), suggesting altered DNA repair. DSB repair normally occurs by either homologous recombination (HR), an accurate, templated form of repair, or by non-homologous end joining (NHEJ), an error-prone non-templated rejoining of DNA ends. Some NHEJ events occur via high-fidelity joining of DNA ends and we refer to such events as precise ligation (PL). Previously, we reported that expression of progerin correlated with increased NHEJ relative to HR. We now report on progerins impact on the nature of DNA end-joining. We used a model system involving a DNA end-joining reporter substrate integrated into the genome of cultured thymidine kinase-deficient mouse fibroblasts. Some cells were engineered to express progerin. DSBs were induced in the substrate through expression of endonuclease I-SceI, and DSB repair events were recovered through selection for thymidine kinase function. Progerin expression correlated with a significant shift away from PL and toward error-prone NHEJ. Our work suggests that progerin suppresses interactions between complementary sequences at DNA termini, shifting DSB repair toward low-fidelity DNA end-joining and perhaps contributing to aging through compromised genome stability.

molecular biology↗

bioRxiv2021

ThruTracker: Open-Source Software for 2-D and 3-D Animal Video Tracking

O_LITracking animal movement patterns using videography is an important tool in many biological disciplines ranging from biomechanics to conservation. Reduced costs of technology such as thermal videography and unmanned aerial vehicles has made video-based animal tracking more accessible, however existing software for processing acquired video limits the application of these methods. C_LIO_LIHere, we present a novel software program for high-throughput 2-D and 3-D animal tracking. ThruTracker provides tools to allow video tracking under a variety of conditions with minimal technical expertise or coding background and without the need for paid licenses. Notable capabilities include calibrating the intrinsic properties of thermal cameras; tracking and counting hundreds of animals at a time; and the ability to make 3-D calibrations without dedicated calibration objects. Automated 2-D and 3-D workflows are integrated to allow for analysis of largescale datasets. C_LIO_LIWe tested ThruTracker with two case studies. The 2-D workflow is demonstrated by counting bats emerging from bridges and caves using thermal Videography. Tests show that ThruTracker has a similar accuracy compared to humans under a variety of conditions. The 3-D workflow is shown for making accurate calibrations for tracking bats and birds at wind turbines using only the wind turbine itself as a calibration object. C_LIO_LIThruTracker is a robust software program for tracking moving animals in 2-D and 3-D. Major applications include counting animals such as bats, birds, and fish that form large aggregations, and documenting movement trajectories over medium spatial scales ([~]100,000 m3). When combined with emerging technologies, we expect videographic techniques to continue to see widespread adoption for an increasing range of biological applications. C_LI

animal behavior and cognition↗