Nature Search

In situ structure and assembly of the multidrug efflux pump AcrAB-TolC

Multidrug efflux pumps actively expel a wide range of toxic substrates from bacteria and play a major role in drug resistance. Here authors show the in situ structure of the efflux pump AcrAB-TolC obtained by electron cryo-tomography and subtomogram averaging.

Xiaodong Shi
Muyuan Chen
Zhao Wang
ResearchOpen Access14 Jun 2019
Nature Communications

Volume: 10, P: 1-6
The HTPmod Shiny application enables modeling and visualization of large-scale biological data

Dijun Chen et al. present HTPmod, a Shiny web application for modeling and visualization of large-scale genomic and phenomic datasets. The authors show that HTPmod can quickly reproduce analyses of high-throughput biological datasets and produce publication-quality figures.

Dijun Chen
Liang-Yu Fu
Kerstin Kaufmann
ResearchOpen Access05 Jul 2018
Communications Biology

Volume: 1, P: 1-8
Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana

Homeotic transcription factors and miRNAs promote floral organ specification. Here Chen et al. reconstruct gene regulatory networks in Arabidopsis flowers and find evidence for feed forward loops between transcription factors, miRNAs and their targets that determine organ-specific gene expression.

Dijun Chen
Wenhao Yan
Kerstin Kaufmann
ResearchOpen Access31 Oct 2018
Nature Communications

Volume: 9, P: 1-13
Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis

Enhancer elements can control spatial and temporal patterns of gene expression. Here the authors profile chromatin accessibility, histone modifications and gene expression during Arabidopsis flower development providing evidence for sets of distal enhancers acting in a highly stage-specific manner.

Wenhao Yan
Dijun Chen
Kerstin Kaufmann
ResearchOpen Access12 Apr 2019
Nature Communications

Volume: 10, P: 1-16
ChIP-Hub provides an integrative platform for exploring plant regulome

A comprehensive data portal to explore plant regulomes is still unavailable. Here, the authors develop a web-based platform ChIP-Hub in the ENCODE standards and demonstrate its applications in the identification of hierarchical regulatory network, tissue-specific chromatin dynamics, putative enhancers and chromatin states.

Liang-Yu Fu
Tao Zhu
Dijun Chen
ResearchOpen Access14 Jun 2022
Nature Communications

Volume: 13, P: 1-15
Capture of regulatory factors via CRISPR–dCas9 for mechanistic analysis of fine-tuned SERRATE expression in Arabidopsis

This study demonstrates an efficient method for capturing key regulators of target genes named CASPA–dCas9. With this method, the authors uncover the precise regulatory mechanism and key factors controlling SERRATE expression in Arabidopsis.

Wei Chen
Jingyi Wang
Bo Sun
Research02 Jan 2024
Nature Plants

Volume: 10, P: 86-99
Lipid-accumulated reactive astrocytes promote disease progression in epilepsy

Chen et al. describe a new subtype of reactive astrocyte formed by APOE-mediated lipid accumulation in individuals with epilepsy and mouse models. These reactive astrocytes aggravate seizure symptoms and could serve as new therapeutic targets for epilepsy.

Zhang-Peng Chen
Suji Wang
Chao Yan
Research20 Mar 2023
Nature Neuroscience

Volume: 26, P: 542-554
Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits

The authors present a comprehensive regulome atlas for rice by mapping chromatin accessibility across 23 tissues from three rice varieties. By integrating matched RNA-seq data, they accurately predict numerous associations between non-coding regulatory elements and target genes. This study provides a foundational resource for gene editing and breeding strategies targeting non-coding regions in rice, potentially advancing crop improvement efforts.

Tao Zhu
Chunjiao Xia
Weibo Xie
ResearchOpen Access03 Aug 2024
Nature Communications

Volume: 15, P: 1-17
Structure of the MacAB–TolC ABC-type tripartite multidrug efflux pump

Cryo-electron microscopy of the tripartite MacA–MacB–TolC multidrug transporter.

Anthony W. P. Fitzpatrick
Salomé Llabrés
Dijun Du
Research15 May 2017
Nature Microbiology

Volume: 2, P: 1-8
The draft genome of sweet orange (Citrus sinensis)

Yijun Ruan and colleagues report the draft genome of the sweet orange, Citrus sinensis. Their data suggests sweet orange originated from a cross between pummelo and mandarin.

Qiang Xu
Ling-Ling Chen
Yijun Ruan
ResearchOpen Access25 Nov 2012
Nature Genetics

Volume: 45, P: 59-66
Single cell transcriptomic analyses implicate an immunosuppressive tumor microenvironment in pancreatic cancer liver metastasis

The metastatic tumour microenvironment in pancreatic ductal adenocarcinoma (PDAC) remains to be explored. Here, the authors perform single cell RNA sequencing analysis for synchronously resected PDAC primary tumours and matched liver metastases and find differences in cellular composition.

Shu Zhang
Wen Fang
Ying Lv
ResearchOpen Access23 Aug 2023
Nature Communications

Volume: 14, P: 1-19
A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys

Non-human primates are attractive laboratory animal models that can accurately reflect some developmental and pathological features of humans. Here the authors chart a reference cell map of cynomolgus monkeys using both scATAC-seq and scRNA-seq data across multiple organs, providing insights into the molecular dynamics and cellular heterogeneity of this organism.

Jiao Qu
Fa Yang
Dijun Chen
ResearchOpen Access13 Jul 2022
Nature Communications

Volume: 13, P: 1-19
Tumor vascular endothelial cells promote immune escape by upregulating PD-L1 expression via crosstalk between NF-κB and STAT3 signaling pathways in nasopharyngeal carcinoma

Yan Wang
Yuanyuan Chen
Desheng Weng
ResearchOpen Access25 Feb 2025
Cell Death & Disease

Volume: 16, P: 1-13
Ultra-low noise optical injection locking amplifier with AOM-based coherent detection scheme

Zitong Feng
Fei Yang
Haiwen Cai
ResearchOpen Access03 Sept 2018
Scientific Reports

Volume: 8, P: 1-7
Dynamic and spatial restriction of Polycomb activity by plant histone demethylases

REF6 is a histone demethylase that antagonizes the effect of the Polycomb gene-silencing complex. Genome-wide approaches on a novel triple mutant show that REF6 and its paralogues dynamically and spatially restrict Polycomb activity during development.

Wenhao Yan
Dijun Chen
Kerstin Kaufmann
Research13 Aug 2018
Nature Plants

Volume: 4, P: 681-689
Epstein-Barr virus causes vascular abnormalities in epithelial malignancies through upregulating ANXA3-HIF-1α-VEGF pathway

Yuanyuan Chen
Muping Di
Jianchuan Xia
Research22 May 2024
Oncogene

Volume: 43, P: 2143-2159
Insights into the increasing virulence of the swine-origin pandemic H1N1/2009 influenza virus

Wei Zou
Dijun Chen
Meilin Jin
ResearchOpen Access03 Apr 2013
Scientific Reports

Volume: 3, P: 1-9
The SMARCA4^R1157W mutation facilitates chromatin remodeling and confers PRMT1/SMARCA4 inhibitors sensitivity in colorectal cancer

Xiangwei Zeng
Bing Yao
Quan Zhao
ResearchOpen Access15 Mar 2023
npj Precision Oncology

Volume: 7, P: 1-14
Manipulation and prediction of spike morphology traits for the improvement of grain yield in wheat

Zifeng Guo
Yusheng Zhao
Thorsten Schnurbusch
ResearchOpen Access26 Sept 2018
Scientific Reports

Volume: 8, P: 1-10

Search

In situ structure and assembly of the multidrug efflux pump AcrAB-TolC

The HTPmod Shiny application enables modeling and visualization of large-scale biological data

Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana

Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis

ChIP-Hub provides an integrative platform for exploring plant regulome

Capture of regulatory factors via CRISPR–dCas9 for mechanistic analysis of fine-tuned SERRATE expression in Arabidopsis

Lipid-accumulated reactive astrocytes promote disease progression in epilepsy

Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits

Structure of the MacAB–TolC ABC-type tripartite multidrug efflux pump

The draft genome of sweet orange (Citrus sinensis)

Single cell transcriptomic analyses implicate an immunosuppressive tumor microenvironment in pancreatic cancer liver metastasis

A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys

Tumor vascular endothelial cells promote immune escape by upregulating PD-L1 expression via crosstalk between NF-κB and STAT3 signaling pathways in nasopharyngeal carcinoma

Ultra-low noise optical injection locking amplifier with AOM-based coherent detection scheme

Dynamic and spatial restriction of Polycomb activity by plant histone demethylases

Epstein-Barr virus causes vascular abnormalities in epithelial malignancies through upregulating ANXA3-HIF-1α-VEGF pathway

Insights into the increasing virulence of the swine-origin pandemic H1N1/2009 influenza virus

The SMARCA4^R1157W mutation facilitates chromatin remodeling and confers PRMT1/SMARCA4 inhibitors sensitivity in colorectal cancer

Manipulation and prediction of spike morphology traits for the improvement of grain yield in wheat

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