A5022062707- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- Plant Diversity and Evolution
- Cancer-related gene regulation
- Protein Degradation and Inhibitors
- Genomics and Phylogenetic Studies
- Plant biochemistry and biosynthesis
- DNA Repair Mechanisms
- Epigenetics and DNA Methylation
- Photosynthetic Processes and Mechanisms
- PARP inhibition in cancer therapy
- Peptidase Inhibition and Analysis
- Endoplasmic Reticulum Stress and Disease
- Fungal and yeast genetics research
- Chromosomal and Genetic Variations
- Genetics and Neurodevelopmental Disorders
- Signaling Pathways in Disease
- Natural Compounds in Disease Treatment
- Ubiquitin and proteasome pathways
- Mycorrhizal Fungi and Plant Interactions
- Plant and animal studies
- Banana Cultivation and Research
Minhang District Central Hospital
2025
Fudan University
2025
Fudan University Shanghai Cancer Center
2021-2025
State Key Laboratory of Genetic Engineering
2025
Shanghai Medical College of Fudan University
2021-2023
Fujian Agriculture and Forestry University
2019-2020
Abstract Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form so-called ANA-grade of angiosperms, which are extant representatives lineages that diverged earliest from lineage leading mesangiosperms 1–3 . Here we report 409-megabase genome sequence blue-petal water lily ( Nymphaea colorata ). Our phylogenomic analyses support Amborellales as successive sister all other angiosperms. The N. 19 transcriptomes reveal a Nymphaealean...
Abstract The proper regulation of transcription is essential for maintaining genome integrity and executing other downstream cellular functions 1,2 . Here we identify a stable association between the genome-stability regulator sensor single-stranded DNA (SOSS) 3 Integrator-PP2A (INTAC) 4–6 Through SSB1-mediated recognition DNA, SOSS–INTAC stimulates promoter-proximal termination attenuates R-loops associated with paused RNA polymerase II to prevent R-loop-induced instability....
Gene expression in metazoans is controlled by promoter-proximal pausing of RNA polymerase II, which can undergo productive elongation or termination. Integrator-PP2A (INTAC) plays a crucial role determining the fate paused polymerases, but underlying mechanisms remain unclear. Here, we establish rapid degradation system to dissect functions INTAC endonuclease and phosphatase modules. We find that both catalytic modules function at most if not all active promoters enhancers, yet...
Abstract The spliceosome, a highly dynamic macromolecular assembly, catalyzes the precise removal of introns from pre-mRNAs. Recent studies have provided comprehensive structural insights into step-wise catalytic splicing and final disassembly spliceosome. However, molecular details how spliceosome recognizes rejects suboptimal substrates remained unclear. Here, we show cryo-electron microscopy structures spliceosomal quality control complexes thermophilic eukaryote, Chaetomium thermophilum...
Transcription progression is governed by multitasking regulators including SPT5, an evolutionarily conserved factor implicated in virtually all transcriptional steps from enhancer activation to termination. Here we utilize a rapid degradation system and reveal crucial functions of SPT5 maintaining cellular chromatin RNA polymerase II (Pol II) levels. Rapid depletion causes pronounced reduction paused Pol at promoters enhancers, distinct negative elongation (NELF) resulting short-distance...
Rapeseed (Brassica napus L.) is a recent allotetraploid crop, which well known for its high oil production. Here, we report high-quality genome assembly of typical semi-winter rapeseed cultivar, 'Zhongshuang11' (hereafter 'ZS11'), using combination single-molecule sequencing and chromosome conformation capture (Hi-C) techniques. Most the high-confidence sequences (93.1%) were anchored to individual chromosomes with total 19 centromeres identified, matching exact count B. napus. The repeat in...
Pleiotropic transcription regulator RNA polymerase II (Pol II)–associated factor 1 (PAF1) governs multiple transcriptional steps and the deposition of several epigenetic marks. However, it remains unclear how ultimate outcome is determined by PAF1 whether relates to PAF1-controlled We use rapid degradation systems reveal direct functions in governing pausing partially recruiting Integrator-PP2A (INTAC), addition ensuring elongation. Following acute degradation, most destabilized undergoes...
Cells tightly regulate ribosome homeostasis to adapt changing environments. Ribosomes are degraded during stress, but the mechanisms responsible remain unclear. Here, we show that starvation induces selective depletion of 40S ribosomes following their ubiquitylation by E3 ligase RNF10. The atypical kinase RIOK3 specifically recognizes these ubiquitylated through a unique ubiquitin-interacting motif, visualized cryoelectron microscopy (cryo-EM). binding and ubiquitin recognition essential for...
Abstract Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung rich in eleostearic acid. Here, we report a high-quality chromosome-scale genome sequence of tree. The was assembled by combining Illumina short reads, Pacific Biosciences single-molecule real-time long and Hi-C sequencing data. size 1.12 Gb, with 28,422 predicted genes over 73% repeat sequences. V. fordii underwent ancient triplication event shared core eudicots but no further whole-genome...
Genome-wide human genetic studies have identified inherited cis-regulatory loci variants that predispose to cancers. However, the mechanisms by which these germline influence cancer progression, particularly through gene expression and proteostasis control, remain unclear. By analyzing genomic data from a gastric (GC) case-control study (2,117 individuals), focusing on ubiquitin-specific protease (USP) family, we identify single nucleotide polymorphism (SNP) rs72856331 (G>A) in promoter...
RNA polymerase II (Pol II)-mediated transcription in metazoans requires precise regulation. Pol II-associated protein 2 (RPAP2) was previously identified to transport from cytoplasm nucleus and dephosphorylates C-terminal domain (CTD). Here, we show that RPAP2 binds hypo-/hyper-phosphorylated with undetectable phosphatase activity. The structure of RPAP2-Pol shows mutually exclusive assembly pre-initiation complex (PIC) due three steric clashes. prevents disrupts II-TFIIF interaction impairs...
Fusarium wilt of banana is caused by the soilborne fungal pathogen oxysporum f. sp. cubense. We generated two chromosome-level assemblies F. cubense race 1 and tropical 4 strains using single-molecule real-time sequencing. The had 35 29 contigs with contig N50 lengths 2.08 4.28 Mb, respectively. These new references genomes represent a greater than 100-fold improvement over statistics previous short-read-based assemblies. high-quality reported here will be valuable resource for comparative...
SUMMARY Chromatin and transcription regulators are critical to defining cell identity through shaping epigenetic transcriptional landscapes, with their misregulation being closely linked oncogenesis. Pharmacologically targeting these regulators, particularly the activating BET proteins, has emerged as a promising approach in cancer therapy, yet intrinsic or acquired resistance frequently occurs poorly understood mechanisms. Using genome-wide CRISPR screens, we find that inhibitor efficacy...
Phalaenopsis equestris is an obligate crassulacean acid metabolism (CAM) plant with high ornamental and economic value. CAM photosynthesis associated drought tolerance efficient water utilization, which enhances the survival rate of plants in arid environments. The identification analysis CAM-related genes will be helpful to improve our understanding regulatory mechanisms metabolism. In this study, we analyzed RNA-Seq data identify differentially expressed (DEGs) between circadian day night...
Abstract Integrator-PP2A (INTAC) is a highly modular complex orchestrating the transition of paused RNA polymerase II into productive elongation or promoter-proximal premature termination, with its loss resulting in transcription dysregulation and genome instability. Here, we identify human DSS1—a flexible 70-residue protein found multiple functionally diverse complexes including 26S proteasome—as an integral subunit INTAC backbone. Structural analysis DSS1–INTAC, both alone association...
Abstract Tung tree ( Vernicia fordii ) is an economically important woody oil plant that produces tung containing a high proportion of eleostearic acid (∼80%). Here we report high-quality, chromosome-scale genome sequence 1.12 Gb with 28,422 predicted genes and over 73% repeat sequences. was assembled by combining Illumina short reads, PacBio single-molecule real-time long reads Hi-C sequencing data. Insertion time analysis revealed the repeat-driven expansion might be due to standing...
SUMMARY Modifications of histones are intricately linked with the regulation gene expression, demonstrated roles in various physiological processes and disease pathogenesis. Methylation histone H3 lysine 4 (H3K4), implemented by COMPASS family, is enriched at promoters associated cis-regulatory elements, H3K4 trimethylation (H3K4me3) considered a hallmark active promoters. However, relative deposition removal methylation, as well extent to which these events contribute transcriptional have...
Abstract RNA polymerase II (Pol II)-mediated transcription in metazoan requires precise regulation. II-associated protein 2 (RPAP2) was previously identified to transport Pol from cytoplasm nucleus and dephosphorylates C-terminal domain (CTD). We found that RPAP2 binds hypo/hyper-phosphorylated with undetectable phosphatase activity. Structure of RPAP2-Pol shows mutually exclusive assembly pre-initiation complex (PIC) due three steric clashes. prevents/disrupts II-TFIIF interaction impairs...