Yu Feng

ORCID: 0000-0003-4239-8320
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About
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Research Areas
  • RNA and protein synthesis mechanisms
  • Bacterial Genetics and Biotechnology
  • Bacteriophages and microbial interactions
  • RNA modifications and cancer
  • Antibiotic Resistance in Bacteria
  • Genetic diversity and population structure
  • ATP Synthase and ATPases Research
  • Genomics and Phylogenetic Studies
  • Plant Diversity and Evolution
  • Mitochondrial Function and Pathology
  • Cancer-related molecular mechanisms research
  • Photosynthetic Processes and Mechanisms
  • Plant and Fungal Species Descriptions
  • Tuberculosis Research and Epidemiology
  • RNA Research and Splicing
  • CRISPR and Genetic Engineering
  • Enzyme Structure and Function
  • Epigenetics and DNA Methylation
  • Plant and animal studies
  • Mycobacterium research and diagnosis
  • Natural product bioactivities and synthesis
  • Bacterial biofilms and quorum sensing
  • Chromosomal and Genetic Variations
  • Vibrio bacteria research studies
  • Genetic Mapping and Diversity in Plants and Animals

Zhejiang University
2012-2025

Sir Run Run Shaw Hospital
2019-2025

Shanghai University of Traditional Chinese Medicine
2025

Chinese Academy of Sciences
2014-2024

Chengdu Institute of Biology
2022-2024

Nanjing University
2024

Central Hospital of Zibo
2024

Pudong New Area People's Hospital
2024

China Institute of Veterinary Drug Control
2023-2024

Blood Center of Zhejiang Province
2024

During transcription initiation, RNA polymerase (RNAP) binds and unwinds promoter DNA to form an RNAP-promoter open complex. We have determined crystal structures at 2.9 3.0 Å resolution of functional initiation complexes comprising Thermus thermophilus polymerase, σ(A), a fragment corresponding the bubble downstream double-stranded The show that σ recognizes -10 element discriminator through interactions include unstacking insertion into pockets three bases RNAP -4/+2 region pocket +2 base....

10.1126/science.1227786 article EN Science 2012-10-20
Catherine Doust Pierre Fontanillas Else Eising Scott D. Gordon Zhengjun Wang and 95 more Gökberk Alagöz Barbara Molz Stella Aslibekyan Adam Auton Elizabeth Babalola Robert K. Bell Jessica Bielenberg Katarzyna Bryc Emily Bullis Daniella Coker Gabriel Cuéllar-Partida Devika Dhamija Sayantan Das Sarah L. Elson Teresa Filshtein Kipper Fletez‐Brant Will Freyman Pooja Gandhi Karl Heilbron Barry Hicks David A. Hinds Ethan M. Jewett Yunxuan Jiang Katelyn Kukar Keng‐Han Lin Maya Lowe Jey C. McCreight Matthew H. McIntyre Steven J. Micheletti Meghan E. Moreno Joanna L. Mountain Priyanka Nandakumar Elizabeth S. Noblin Jared O’Connell Aaron A. Petrakovitz G. David Poznik Morgan Schumacher Anjali J. Shastri Janie F. Shelton Jingchunzi Shi Suyash Shringarpure Vinh Tran Joyce Y. Tung Xin Wang Wei Wang Catherine H. Weldon Peter Wilton Alejandro Hernandez Corinna Wong Christophe Toukam Tchakouté Filippo Abbondanza Andrea G. Allegrini Till F. M. Andlauer Cathy L. Barr Manon Bernard Kirsten Blokland Milene Bonte Dorret I. Boomsma Thomas Bourgeron Daniel Brandeis Manuel Carreiras Fabiola Ceroni Valéria Csépe Philip S. Dale Peter F. de Jong Jean‐François Démonet Eveline L. de Zeeuw Yu Feng Marie-Christine Franken Margot Gerritse Alessandro Gialluisi Sharon Guger Marianna E. Hayiou‐Thomas Juan Hernández Jouke‐Jan Hottenga Charles Hulme Philip R. Jansen Juha Kere Elizabeth N. Kerr Tanner Koomar Karin Landerl Gabriel Leonard Zhijie Liao Maureen W. Lovett Heikki Lyytinen Angela Martinelli Urs Maurer Jacob J. Michaelson Nazanin Mirza‐Schreiber Kristina Moll Angela Morgan Bertram Müller‐Myhsok Dianne F. Newbury Markus M. Nöthen Tomáš Paus

Abstract Reading and writing are crucial life skills but roughly one in ten children affected by dyslexia, which can persist into adulthood. Family studies of dyslexia suggest heritability up to 70%, yet few convincing genetic markers have been found. Here we performed a genome-wide association study 51,800 adults self-reporting diagnosis 1,087,070 controls identified 42 independent significant loci: 15 genes linked cognitive ability/educational attainment, 27 new potentially more specific...

10.1038/s41588-022-01192-y article EN cc-by Nature Genetics 2022-10-20

Class II transcription activators function by binding to a DNA site overlapping core promoter and stimulating isomerization of an initial RNA polymerase (RNAP)-promoter closed complex into catalytically competent RNAP-promoter open complex. Here, we report 4.4 angstrom crystal structure intact bacterial class activation The comprises Thermus thermophilus activator protein TTHB099 (TAP) [homolog Escherichia coli catabolite (CAP)], T. RNAP σ(A) holoenzyme, TAP-dependent promoter,...

10.1126/science.aaf4417 article EN Science 2016-06-09

Abstract Purpose: PI3K and STAT3 are frequently activated in cancer progression. However, little is known about the underlying mechanisms by which regulate head neck squamous cell (HNSCC) growth. The lncRNA HOX transcript antisense RNA (HOTAIR) was found to modulate progression of HNSCC. In this study, we attempted establish correlation PI3K/STAT3/HOTAIR signaling with HNSCC its sensitivity toward platinum-based targeted anti-EGFR combination therapy. Experimental Design: We first analyzed...

10.1158/1078-0432.ccr-16-2248 article EN Clinical Cancer Research 2018-03-14

Abstract As one of the great survivors plant kingdom, barnyard grasses ( Echinochloa spp.) are most noxious and common weeds in paddy ecosystems. Meanwhile, at least two species have been domesticated cultivated as millets. In order to better understand genomic forces driving evolution toward weed crop characteristics, we assemble genomes three (allohexaploid E. crus-galli colona , allotetraploid oryzicola ) re-sequence 737 accessions millets from 16 rice-producing countries. Phylogenomic...

10.1038/s41467-022-28359-9 article EN cc-by Nature Communications 2022-02-03

In response to DNA damage, bacterial RecA protein forms filaments with the assistance of DinI protein. The stimulate autocleavage LexA, repressor more than 50 SOS genes, and activate response. During late phase response, UmuD λ CI, leading mutagenic repair lytic cycle, respectively. Here, we determined cryo-electron microscopy structures Escherichia coli in complex DinI, UmuD, λCI by helical reconstruction. reveal that LexA dimers bind filament groove cleave an intramolecular intermolecular...

10.1073/pnas.2217493120 article EN cc-by-nc-nd Proceedings of the National Academy of Sciences 2023-01-04

We have previously demonstrated that the V0 domain of coated vesicle V-ATPase, a 250-kDa integral complex, does not form functional proton channel (Zhang, J., Myers, M., and Forgac, M. (1992) J. Biol. Chem. 267, 9773-9778). In present study we describe dissociation complex separation subunits by gel filtration. Dicyclohexylcarbodiimide-inhibitable passive conductance reconstituted vesicles containing reassembled was measured in response to K+/valinomycin-generated membrane potential....

10.1016/s0021-9258(17)31546-6 article EN cc-by Journal of Biological Chemistry 1994-09-01

We have previously demonstrated that the coated vesicle vacuolar H(+)-ATPase (V-ATPase) can be inactivated by formation of intramolecular disulfide bonds (Feng, Y., and Forgac, M. (1992) J. Biol. Chem. 267, 19769-19772). The bond responsible for inactivation distinguished from other form fact inactivating is blocked ATP or high ionic strength. By taking advantage these properties, we selectively labeled ATPase at relevant cysteine residues with fluorescein maleimide. After analyzing...

10.1016/s0021-9258(17)36822-9 article EN cc-by Journal of Biological Chemistry 1994-05-01

Previous studies have shown an anticancer effect of vitamin D, but the mechanisms underlying this action not been fully explored. Here we show that 1,25-dihydroxyvitamin D3 (VD3, active form D) significantly promoted apoptosis in undifferentiated gastric cancer cell line HGC-27, and was accompanied by a concurrent increase phosphatase tensin homolog deleted on chromosome 10 (PTEN) expression VD3 treatment. In contrast, knockdown PTEN stable transfection small interfering RNA greatly...

10.1111/j.1742-4658.2009.07542.x article EN FEBS Journal 2010-01-18

We report that bacterial RNA polymerase (RNAP) is the functional cellular target of depsipeptide antibiotic salinamide A (Sal), and we Sal inhibits RNAP through a novel binding site mechanism. show synthesis in cells mutations confer Sal-resistance map to genes. interacts with active-center ‘bridge-helix cap’ comprising N-terminal hinge’, ‘F-loop’, ‘link region’. nucleotide addition transcription initiation elongation. present crystal structure defines interactions between effects on...

10.7554/elife.02451 article EN cc-by eLife 2014-04-30

Using a combination of genetic, biochemical, and structural approaches, we show that the cyclic-peptide antibiotic GE23077 (GE) binds directly to bacterial RNA polymerase (RNAP) active-center ‘i’ ‘i+1’ nucleotide binding sites, preventing initiating nucleotides, thereby transcription initiation. The target-based resistance spectrum for GE is unusually small, reflecting fact site on RNAP includes residues active center cannot be substituted without loss activity. different from rifamycin...

10.7554/elife.02450 article EN cc-by eLife 2014-04-22

Abstract Background Common walnut ( Juglans regia L.) is one of the top four most consumed nuts in world due to its health benefits and pleasant taste. Despite economic importance, evolutionary history genetic control adaptation agronomic traits remain largely unexplored. Results We report a comprehensive genomic variation map based on whole-genome resequencing 815 accessions. Evolutionary analyses suggest that Chinese J. diverged from sigillata with extensive hybridizations after split two...

10.1186/s13059-021-02517-6 article EN cc-by Genome biology 2021-10-27

Abstract LIN28 is an RNA binding protein with important roles in early embryo development, stem cell differentiation/reprogramming, tumorigenesis and metabolism. Previous studies have focused mainly on its role the cytosol where it interacts Let-7 microRNA precursors or mRNAs, few addressed LIN28’s within nucleus. Here, we show that displays dynamic temporal spatial expression during murine development. Maternal drops upon exit from 2-cell stage, zygotic induced at forming nucleolus 4-cell...

10.1007/s13238-021-00864-5 article EN cc-by Protein & Cell 2021-07-31

We have recently demonstrated that Cys-254 of the 73-kDa A subunit clathrin-coated vesicle (H+)-ATPase is responsible for sensitivity enzyme to sulfhydryl reagents (Feng, Y., and Forgac, M. (1992) J. Biol. Chem. 267, 5817-5822). In present study we observe purified enzyme, disulfide bond formation causes inactivation proton transport which reversed by dithiothreitol (DTT). DTT also restores activity oxidized following treatment with N-ethylmaleimide (NEM). These results indicate between...

10.1016/s0021-9258(19)88619-2 article EN cc-by Journal of Biological Chemistry 1992-10-01

Abstract Bacteriophage Q protein engages σ-dependent paused RNA polymerase (RNAP) by binding to a DNA site embedded in late gene promoter and renders RNAP resistant termination signals. Here, we report single-particle cryo-electron microscopy (cryo-EM) structure of an intact Q-engaged arrested complex. The reveals key interactions responsible for pause, engagement, Q-mediated transcription antitermination. shows that two protomers (Q I II ) bind direct-repeat contact distinct elements the...

10.1038/s41467-019-10958-8 article EN cc-by Nature Communications 2019-07-02

DNA methylation affects gene expression and maintains genome integrity. The DNA-dependent RNA polymerase IV (Pol IV), together with the RNA-dependent RDR2, produces double-stranded small interfering precursors essential for establishing maintaining in plants. We determined cryo–electron microscopy structures of Pol IV–RDR2 holoenzyme backtracked transcription elongation complex. These reveal that RDR2 form a complex their active sites connected by an interpolymerase channel, through which...

10.1126/science.abj9184 article EN Science 2021-12-23
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