A5101983080- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Chromosomal and Genetic Variations
- Plant Molecular Biology Research
- RNA and protein synthesis mechanisms
- Epigenetics and DNA Methylation
- DNA Repair Mechanisms
- Genetic Mapping and Diversity in Plants and Animals
- RNA modifications and cancer
- Plant Virus Research Studies
- Protein Structure and Dynamics
- Protein Degradation and Inhibitors
- Advanced biosensing and bioanalysis techniques
Howard Hughes Medical Institute
2018-2022
University of California, Berkeley
2018-2022
California Institute for Regenerative Medicine
2019-2022
Consorzio Italiano per la Ricerca in Medicina
2019-2021
University of Massachusetts Chan Medical School
2015-2019
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
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...
Covalent histone modifications are highly conserved and play multiple roles in eukaryotic transcription regulation. Here, we mapped 26 genome-wide exponentially growing yeast during a dramatic transcriptional reprogramming—the response to diamide stress. We extend prior studies showing that steady-state modification patterns reflect genomic processes, especially transcription, display limited combinatorial complexity. Interestingly, the stress document modest increase complexity of space,...
The organization of chromatin into higher order structures is essential for chromosome segregation, the repair DNA-damage, and regulation gene expression. Using Micro-C XL to detect chromosomal interactions, we observed pervasive presence cohesin-dependent loops with defined positions throughout genome budding yeast, as seen in mammalian cells. In early S phase, cohesin stably binds associated regions (CARs) genome-wide. Subsequently, positioned accumulate CARs at bases loops. Cohesin...
Abstract It remains unclear why acute depletion of CTCF and cohesin only marginally affects expression most genes despite substantially perturbing 3D genome folding at the level domains structural loops. To address this conundrum, we used high-resolution Micro-C nascent transcript profiling to find that enhancer-promoter (E-P) interactions are largely insensitive (3-hour) CTCF, cohesin, WAPL. YY1 has been proposed be a regulator E-P loops, but also had minimal effects on transcription,...
ABSTRACT Over the past decade, 3C-related methods, complemented by increasingly detailed microscopic views of nucleus, have provided unprecedented insights into chromosome folding in vivo. Here, to overcome resolution limits inherent majority genome-wide architecture mapping studies, we extend a recently-developed Hi-C variant, Micro-C, map at nucleosome human embryonic stem cells and fibroblasts. Micro-C maps robustly capture well-described features mammalian including A/B compartment...
ABSTRACT Chromatin folding below the scale of topologically associating domains (TADs) remains largely unexplored in mammals. Here, we used a high-resolution 3C-based method, Micro-C, to probe links between 3D-genome organization and transcriptional regulation mouse stem cells. Combinatorial binding transcription factors, cofactors, chromatin modifiers spatially segregate TAD regions into “microTADs” with distinct regulatory features. Enhancer-promoter promoter-promoter interactions...
Mammalian genomes are folded into Topologically Associating Domains (TADs), consisting of cell-type specific chromatin loops anchored by CTCF and cohesin. Since cohesin expressed ubiquitously, how CTCF-mediated formed poses a paradox. Here we show RNase-sensitive self-association in vitro that an RNA-binding region (RBR) mediates clustering vivo . Intriguingly, deleting the RBR abolishes or impairs almost half all mouse embryonic stem cells. Disrupted loop formation correlates with abrogated...
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...
The genome is packaged and organized in an ordered, nonrandom manner, specific chromatin segments contact nuclear substructures to mediate this organization. tRNA genes (tDNAs) are binding sites for transcription factors architectural proteins thought play important role the organization of genome. In study, we investigate roles tDNAs genomic chromosome function by editing a so that it lacked any tDNAs. Surprisingly our analyses tDNA-less show loss does not grossly affect architecture or...
ABSTRACT The organization of chromatin into higher-order structures is essential for chromosome segregation, the repair DNA-damage, and regulation gene expression. Using Micro-C XL to detect chromosomal interactions, we observed pervasive presence cohesin-dependent loops with defined positions throughout genome budding yeast, as seen in mammalian cells. In early S phase, cohesin stably binds associated regions (CARs) genome-wide. Subsequently, positioned accumulate CARs at bases loops....
ABSTRACT Structural analysis of chromosome folding in vivo has been revolutionized by Chromosome Conformation Capture (3C) and related methods, which use proximity ligation to identify chromosomal loci physical contact. We recently described a variant 3C technique, Micro-C, chromatin is fragmented mononucleosomes using micrococcal nuclease, enabling nucleosome-resolution maps the genome. Here, we describe an improved Micro-C protocol long crosslinkers, termed XL, exhibits greatly increased...
SUMMARY Quiescence is a stress-resistant state in which cells reversibly exit the mitotic cell cycle and suspend most cellular processes. essential for stem maintenance its misregulation implicated tumor formation. One of conserved hallmarks quiescent cells, from Saccharomyces cerevisiae to humans, highly condensed chromatin. Here, we use Micro-C XL map chromatin contacts at single-nucleosome resolution genome-wide elucidate mechanisms functions S. cells. We describe previously...
Abstract The genome is packaged and organized in an ordered, non-random manner specific chromatin segments contact nuclear substructures to mediate this organization. While transfer RNA genes (tDNAs) are essential for the generation of tRNAs, these loci also binding sites transcription factors architectural proteins thought play important role organization genome. In study, we investigate tDNAs genomic chromosome function by editing a so that it lacks any tDNAs. Surprisingly our analyses...