A5085202358- Genomics and Chromatin Dynamics
- Chromosomal and Genetic Variations
- DNA and Nucleic Acid Chemistry
- Bacterial Genetics and Biotechnology
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Bacteriophages and microbial interactions
- Advanced Fluorescence Microscopy Techniques
- DNA Repair Mechanisms
- Epigenetics and DNA Methylation
- Genomics and Phylogenetic Studies
- Plant Molecular Biology Research
- Nanopore and Nanochannel Transport Studies
- Vector-borne infectious diseases
- Photoacoustic and Ultrasonic Imaging
- Advanced biosensing and bioanalysis techniques
- Genomic variations and chromosomal abnormalities
- Gene expression and cancer classification
- Protein Structure and Dynamics
- Plant Virus Research Studies
- Advanced Biosensing Techniques and Applications
- Viral Infections and Immunology Research
- Single-cell and spatial transcriptomics
- Powder Metallurgy Techniques and Materials
- Toxin Mechanisms and Immunotoxins
Illumina (United States)
2023-2025
Harvard University
2016-2023
Massachusetts Institute of Technology
2020-2023
Broad Institute
2021-2023
Allen Institute
2022
Harvard University Press
2017-2021
ORCID
2021
McGill University
2011-2020
Fertilization triggers assembly of higher-order chromatin structure from a condensed maternal and naïve paternal genome to generate totipotent embryo. Chromatin loops domains have been detected in mouse zygotes by single-nucleus Hi-C (snHi-C), but not bulk Hi-C. It is therefore unclear when how embryonic conformations are assembled. Here, we investigated whether mechanism cohesin-dependent loop extrusion generates structures within the one-cell Using snHi-C knockout embryos, demonstrate that...
Animal genomes are folded into loops and topologically associating domains (TADs) by CTCF loop-extruding cohesins, but the live dynamics of loop formation stability remain unknown. Here, we directly visualized chromatin looping at
Tethering DNA for packing purposes Condensin protein complexes are critical chromosome segregation and compaction. They form ring-shaped structures that encircle topologically constrain strands. Wang et al. show Bacillus subtilis condensin hold the two arms of circular together (see Perspective by Sherratt). The seem to do this encircling individual duplexes then tethering “handcuffing.” actively travel along function enlarge loops processively, leading Science , issue p. 524 ; see also 460
Cohesin folds mammalian interphase chromosomes by extruding the chromatin fiber into numerous loops. "Loop extrusion" can be impeded chromatin-bound factors, such as CTCF, which generates characteristic and functional organization patterns. It has been proposed that transcription relocalizes or interferes with cohesin active promoters are loading sites. However, effects of on have not reconciled observations extrusion cohesin. To determine how modulates extrusion, we studied mouse cells in...
Abstract Eukaryotic genomes are compacted into loops and topologically associating domains (TADs) 1–3 , which contribute to transcription, recombination genomic stability 4,5 . Cohesin extrudes DNA that thought lengthen until CTCF boundaries encountered 6–12 Little is known about whether loop extrusion impeded by DNA-bound machines. Here we show the minichromosome maintenance (MCM) complex a barrier restricts in G1 phase. Single-nucleus Hi-C (high-resolution chromosome conformation capture)...
To separate replicated sister chromatids during mitosis, eukaryotes and prokaryotes have structural maintenance of chromosome (SMC) condensin complexes that were recently shown to organize chromosomes by a process known as DNA loop extrusion. In rapidly dividing bacterial cells, the separating occurs concomitantly with ongoing transcription. How transcription interferes loop-extrusion is largely unexplored, but recent experiments sites high may directionally affect We quantitatively...
SMC complexes, such as condensin or cohesin, organize chromatin throughout the cell cycle by a process known loop extrusion. complexes reel in DNA, extruding and progressively growing DNA loops. Modeling assuming two-sided extrusion reproduces key features of organization across different organisms. In vitro single-molecule experiments confirmed that yeast condensins extrude loops, however, they remain anchored to their loading sites loops 'one-sided' manner. We therefore simulate one-sided...
Abstract Cohesin folds mammalian interphase chromosomes by extruding the chromatin fiber into numerous loops. “Loop extrusion” can be impeded chromatin-bound factors, such as CTCF, which generates characteristic and functional organization patterns. It has been proposed that transcription relocalizes or interferes with cohesin, active promoters are cohesin loading sites. However, effects of on have not reconciled observations extrusion cohesin. To determine how modulates extrusion, we...
Abstract DNA double-strand breaks (DSBs) occur every cell cycle and must be efficiently repaired. Non-homologous end joining (NHEJ) is the dominant pathway for DSB repair in G1-phase. The first step of NHEJ to bring two ends back into proximity (synapsis). Although synapsis generally assumed through passive diffusion, we show that diffusion unlikely produce speed observed cells. Instead, hypothesize loop extrusion facilitates synapsis. By combining experimentally constrained simulations...
Chromosomes are exceedingly long topologically-constrained polymers compacted in a cell nucleus. We recently suggested that chromosomes organized into loops by an active process of loop extrusion. Yet remain elusive to direct observations living cells; detection and characterization myriads such is major challenge. The lack tractable physical model polymer folded limits our ability interpret experimental data detect loops. Here, we introduce new – sequence loops, solve it analytically. Our...
Abstract Structural maintenance of chromosomes (SMC) complexes organize genomes by extruding DNA loops, while replisomes duplicate entire chromosomes. These essential molecular machines must collide frequently in every cell cycle, yet how such collisions are resolved vivo remains poorly understood. Taking advantage the ability to load SMC at defined sites Bacillus subtilis genome, we engineered head-on and head-to-tail between replisome. Replisome progression was monitored marker frequency...
Cell polarity arises through the spatial segregation of regulators. PAR proteins are regulators that localize asymmetrically to two opposing cortical domains. However, it is unclear how spatially segregated interact maintain their mutually exclusive partitioning. Here, single-molecule detection analysis in Caenorhabditis elegans embryos reveals PAR-2 diffuses only short distances, and, as a result, most molecules associate and dissociate from cortex without crossing into domain. Our results...
Super-resolution fluorescence imaging based on localization microscopy requires tuning the photoblinking properties of fluorescent dyes employed. Missing is a rapid way to analyze blinking rates fluorophore probes. Herein we present an ensemble autocorrelation technique for rapidly and simultaneously measuring bleaching rate constants from image time series probes that significantly faster than individual single-molecule trajectory analysis approaches. Our method accurate probe densities...
Abstract Eukaryotic genomes are compacted into loops and topologically associating domains (TADs), which contribute to transcription, recombination genomic stability. Cohesin extrudes DNA that thought lengthen until CTCF boundaries encountered. Little is known about whether loop extrusion impeded by DNA-bound macromolecular machines. We demonstrate the replicative helicase MCM a barrier restricts in G1 phase. Single-nucleus Hi-C of one-cell embryos revealed loading reduces CTCF-anchored...
Animal genomes are folded into loops and topologically associating domains (TADs) by CTCF cohesin, but whether these stable or dynamic is unknown. Here, we directly visualize chromatin looping at the Fbn2 TAD in mouse embryonic stem cells using super-resolution live-cell imaging quantify dynamics Bayesian inference. Our results consistent with cohesin-mediated loop extrusion cells, both stopping stabilizing cohesin. Surprisingly, rare dynamic, a looped fraction of ~3-6.5% median lifetime...
SUMMARY Fertilization triggers assembly of higher-order chromatin structure from a naïve genome to generate totipotent embryo. Chromatin loops and domains are detected in mouse zygotes by single-nucleus Hi-C (snHi-C) but not bulk Hi-C. We resolve this discrepancy investigating whether mechanism cohesin-dependent loop extrusion generates zygotic conformations. Using snHi-C knockout embryos, we demonstrate that the folds into depend on Scc1-cohesin regulated size Wapl. Remarkably, discovered...
We examine the diffusive behavior of single polymers under spatially varying entropic confinement. A nanofluidic slit embedded with a lattice pits was used to constrain DNA molecules discrete conformational states. Diffusion characterized by dwelling in specific conformations followed transitions neighboring In contrast studies involving simple 2D (nanoslit) and 1D (nanochannel) geometries, diffusivity showed nonmonotonic dependence respect parameters particular, nanopit array allows us...