A5086156105- Epigenetics and DNA Methylation
- Genomics and Chromatin Dynamics
- Single-cell and spatial transcriptomics
- RNA Research and Splicing
- Chromatin Remodeling and Cancer
- CRISPR and Genetic Engineering
- Genetics and Neurodevelopmental Disorders
- Histone Deacetylase Inhibitors Research
- Protein Degradation and Inhibitors
Fudan University
2020-2024
Zhongshan Hospital
2023-2024
State Key Laboratory of Genetic Engineering
2023-2024
Abstract Single-cell Hi-C (scHi-C) analysis has been increasingly used to map chromatin architecture in diverse tissue contexts, but computational tools define loops at high resolution from scHi-C data are still lacking. Here, we describe Single-Nucleus Analysis Pipeline for (SnapHiC), a method that can identify and accuracy data. Using 742 mouse embryonic stem cells, benchmark SnapHiC against number of developed mapping interactions bulk Hi-C. We further demonstrate its use by analyzing...
Abstract Transcriptional Mediator controls diverse gene programs for various developmental and pathological processes. The human MED23/R617Q mutation was reported in a familial intellectual disability (ID) disorder, although the underlying mechanisms remain poorly understood. Constructed by editing, Med23/R617Q knock-in mutant mice exhibited embryonic lethality due to largely reduced protein level, but R617Q HEK293T cells didn’t change its expression incorporation into Complex. RNA-seq...
Abstract While a rich set of putative cis -regulatory sequences involved in mouse fetal development have been annotated recently on the basis chromatin accessibility and histone modification patterns, delineating their role developmentally regulated gene expression continues to be challenging. To fill this gap, here we mapped contacts between promoters distal across genome seven tissues six developmental stages forebrain. We identified 248,620 long-range interactions centered at 14,138...
Abstract Single cell Hi-C (scHi-C) analysis has been increasingly used to map the chromatin architecture in diverse tissue contexts, but computational tools define contacts at high resolution from scHi-C data are still lacking. Here, we describe SnapHiC, a method that can identify loops and accuracy data. We benchmark SnapHiC against HiCCUPS, common tool for mapping bulk data, using 742 mouse embryonic stem cells. further demonstrate its utility by analyzing single-nucleus methyl-3C-seq...
Single-cell high-throughput chromatin conformation capture technologies (scHi-C) has been used to map spatial organization in complex tissues. However, computational tools detect differential contacts (DCCs) from scHi-C datasets development and through disease pathogenesis are still lacking. Here, we present SnapHiC-D, a pipeline identify DCCs between two datasets. Compared methods designed for bulk Hi-C data, SnapHiC-D detects with high sensitivity accuracy. We cell-type-specific at 10 Kb...
Abstract HDAC8, a member of class I HDACs, plays pivotal role in cell cycle regulation by deacetylating the cohesin subunit SMC3. While cyclins and CDKs are well-established regulators, our knowledge other regulators remains limited. Here we reveal acetylation K202 HDAC8 as key regulator responsive to stress. primarily catalyzed Tip60, restricts activity, leading increased SMC3 arrest. Furthermore, cells expressing mutant form mimicking display significant alterations gene expression,...
Abstract While a rich set of putative cis -regulatory sequences involved in mouse fetal development has been annotated recently based on chromatin accessibility and histone modification patterns, delineating their role developmentally regulated gene expression continues to be challenging. To fill this gap, we mapped contacts between promoters distal genome-wide seven tissues, for one them, across six developmental stages. We identified 248,620 long-range interactions centered at 14,138...