Johnstone, S. | bioRxiv Science

bioRxiv2023

High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion dynamics

DNA looping is vital for establishing many enhancer-promoter interactions. While CTCF is known to anchor many cohesin-mediated loops, the looped chromatin fiber appears to predominantly exist in a poorly characterized actively extruding state. To better characterize extruding chromatin loop structures, we used CTCF MNase HiChIP data to determine both CTCF binding at high resolution and 3D contact information. Here we present FactorFinder, a tool that identifies CTCF binding sites at near base-pair resolution. We leverage this substantial advance in resolution to determine that the fully extruded (CTCF-CTCF) state is rare genome-wide with locus-specific variation from ~1-10%. We further investigate the impact of chromatin state on loop extrusion dynamics, and find that active enhancers and RNA Pol II impede cohesin extrusion, facilitating an enrichment of enhancer-promoter contacts in the partially extruded loop state. We propose a model of topological regulation whereby the transient, partially extruded states play active roles in transcription.

genomics↗

bioRxiv2023

Pharmacological PINK1 activation ameliorates Pathology in Parkinson's Disease models

PINK1 loss-of-function mutations and exposure to mitochondrial toxins are causative for Parkinsons disease (PD) and Parkinsonism, respectively. We demonstrate that pathological -synuclein deposition, the hallmark pathology of idiopathic PD, induces mitochondrial dysfunction and impairs mitophagy, driving accumulation of the PINK1 substrate pS65-Ubiquitin (pUb) in primary neurons and in vivo. We synthesized MTK458, a brain penetrant small molecule that binds to PINK1 and stabilizes an active heterocomplex, thereby increasing mitophagy. MTK458 mediates clearance of -synuclein pathology in PFF seeding models in vitro and in vivo and reduces pUb. We developed an ultrasensitive assay to quantify pUb levels in plasma and observed an increase in pUb in PD subjects that correlates with disease progression, paralleling our observations in PD models. Our combined findings from preclinical PD models and patient biofluids suggest that pharmacological activation of PINK1 is worthy of further study as a therapeutic strategy for disease modification in PD. HighlightsO_LIDiscovery of a plasma Parkinsons Disease biomarker candidate, pS65-Ubiquitin (pUb) C_LIO_LIPlasma pUb levels correlate with disease status and progression in PD patients. C_LIO_LIIdentification of a potent, brain penetrant PINK1 activator, MTK458 C_LIO_LIMTK458 selectively activates PINK1 by stimulating dimerization and stabilization of the PINK1/TOM complex C_LIO_LIMTK458 drives clearance of -synuclein pathology and normalizes pUb in in vivo Parkinsons models C_LI

neuroscience↗