A5049740611- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Gene Regulatory Network Analysis
- Chromosomal and Genetic Variations
- Advanced Fluorescence Microscopy Techniques
- DNA Repair Mechanisms
- Particle Dynamics in Fluid Flows
- Plant Molecular Biology Research
- Immunotherapy and Immune Responses
- DNA and Nucleic Acid Chemistry
- Single-cell and spatial transcriptomics
- CRISPR and Genetic Engineering
- Statistical Methods and Bayesian Inference
- Cell Image Analysis Techniques
- T-cell and B-cell Immunology
- Developmental Biology and Gene Regulation
- Integrated Circuits and Semiconductor Failure Analysis
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- PARP inhibition in cancer therapy
- Immune Cell Function and Interaction
- Wnt/β-catenin signaling in development and cancer
Broad Institute
2021-2025
Massachusetts Institute of Technology
2019-2025
Allen Institute
2022-2025
Foundation Center
2025
Novo Nordisk (United States)
2024-2025
University of California, Berkeley
2016-2021
California Institute for Regenerative Medicine
2016-2020
Howard Hughes Medical Institute
2013-2020
Consorzio Italiano per la Ricerca in Medicina
2019
Berkeley College
2018
Folding of mammalian genomes into spatial domains is critical for gene regulation. The insulator protein CTCF and cohesin control domain location by folding loop structures, which are widely thought to be stable. Combining genomic biochemical approaches we show that co-occupy the same sites physically interact as a biochemically stable complex. However, using single-molecule imaging find binds chromatin much more dynamically than (~1–2 min vs. ~22 residence time). Moreover, after unbinding,...
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
Single-particle tracking (SPT) has become an important method to bridge biochemistry and cell biology since it allows direct observation of protein binding diffusion dynamics in live cells. However, accurately inferring information from SPT studies is challenging due biases both data analysis experimental design. To address bias, we introduce 'Spot-On', intuitive web-interface. Spot-On implements a kinetic modeling framework that accounts for known biases, including molecules moving...
During mitosis, transcription is shut off, chromatin condenses, and most factors (TFs) are reported to be excluded from chromosomes. How do daughter cells re-establish the original program? Recent discoveries that a select set of TFs remain bound on mitotic chromosomes suggest potential mechanism for maintaining transcriptional programs through cell cycle termed bookmarking. Here we report instead many associated with in mouse embryonic stem cells, exclusion previously described largely...
RNA Polymerase II (Pol II) and transcription factors form concentrated hubs in cells via multivalent protein-protein interactions, often mediated by proteins with intrinsically disordered regions. During Herpes Simplex Virus infection, viral replication compartments (RCs) efficiently enrich host Pol into membraneless domains, reminiscent of liquid-liquid phase separation. Despite sharing several properties phase-separated condensates, we show that RCs operate a distinct mechanism wherein...
It remains unclear why acute depletion of CTCF (CCCTC-binding factor) and cohesin only marginally affects expression most genes despite substantially perturbing three-dimensional (3D) genome folding at the level domains structural loops. To address this conundrum, we used high-resolution Micro-C nascent transcript profiling in mouse embryonic stem cells. We find that enhancer-promoter (E-P) interactions are largely insensitive to (3-h) CTCF, or WAPL. YY1 has been proposed as a regulator E-P...
Numerous transcription factors (TFs) encode information about upstream signals in the dynamics of their activation, but how downstream genes decode these remains poorly understood. Using microfluidics to control nucleocytoplasmic translocation budding yeast TF Msn2, we elucidate principles that govern different promoters convert dynamical Msn2 input into gene expression output single cells. Combining modeling and experiments, classify according signal-processing behavior reveal multiple,...
CCCTC-binding factor (CTCF) plays a key role in the formation of topologically associating domains (TADs) and loops interphase. During mitosis TADs are absent, but how TAD is dynamically controlled during cell cycle not known. Several contradicting observations have been made regarding CTCF binding to mitotic chromatin using both genomics- microscopy-based techniques. Here, we used four different assays address this debate. First, 5C, confirmed that readily detected interphase, absent...
Signaling pathways often transmit multiple signals through a single shared transcription factor (TF) and encode signal information by differentially regulating TF dynamics. However, will be lost unless it can reliably decoded downstream genes. To understand the limits on dynamic transduction, we apply theory to quantify how much gene expression yeast Msn2 transduce target genes in amplitude or frequency of its activation We find that although amount transmitted is limited, transduction...
Enhancer-gene communication is dependent on topologically associating domains (TADs) and boundaries enforced by the CCCTC-binding factor (CTCF) insulator, but underlying structures mechanisms remain controversial. Here, we investigate a boundary that typically insulates fibroblast growth (FGF) oncogenes disrupted DNA hypermethylation in gastrointestinal stromal tumors (GISTs). The contains an array of CTCF sites enforce adjacent TADs, one containing FGF genes other ANO1 its putative...
3D genomics methods such as Hi-C and Micro-C have uncovered chromatin loops across the genome linked these to gene regulation. However, only measure interaction probabilities on a relative scale. Here, we overcome this limitation by using live imaging data calibrate in mouse embryonic stem cells, thus obtaining absolute looping for 36,804 genome. We find that looped state is generally rare, with mean probability of 2.3% maximum 26% quantified loops. On average, CTCF-CTCF are stronger than...