Article
Biochemistry & Molecular Biology
Nicola Zilio, Helle D. Ulrich
Summary: Mapping the genome-wide distribution of single-strand breaks is crucial for understanding damage signaling and DNA repair. This article reviews classical and newly developed high-resolution methods for mapping single-strand breaks, highlighting the valuable insights they provide into the impact of this type of damage on the genome.
Article
Chemistry, Multidisciplinary
Gil Nifker, Assaf Grunwald, Sapir Margalit, Zuzana Tulpova, Yael Michaeli, Hagai Har-Gil, Noy Maimon, Elad Roichman, Leonie Schuetz, Elmar Weinhold, Yuval Ebenstein
Summary: Proteins and enzymes in the cell nucleus require physical access to their DNA target sites in order to perform genomic tasks such as gene activation and transcription. Chromatin accessibility is a central regulator of gene expression and holds essential information on the cell type and state. By utilizing a combination of E. coli Dam methyltransferase and a fluorescent cofactor analogue, we were able to generate fluorescent tags in accessible DNA regions within the cell nucleus, and then detect these accessible portions using single-molecule optical genome mapping in nanochannel arrays. This method allows for the characterization of long-range structural variations and their associated chromatin structure, resulting in the creation of whole-genome, allele-specific chromatin accessibility maps composed of long DNA molecules extended in silicon nanochannels.
Article
Agriculture, Dairy & Animal Science
Jiankui Wang, Guoying Hua, Ganxian Cai, Yuhao Ma, Xue Yang, Letian Zhang, Rui Li, Jianbin Liu, Qing Ma, Keliang Wu, Yaofeng Zhao, Xuemei Deng
Summary: Through genome-wide resequencing and transcriptome sequencing, it was found that the fine wool sheep bred by multiple-ovulation and embryo transfer technique had coarse wool similar to their ancestors. A significantly associated methylation locus on chromosome 4 and the hypermethylation of SOSTDC1 gene in coarse wool lambs were identified. The overexpression of SOSTDC1 gene was specifically found in the nucleus of the dermal papilla of primary wool follicles in coarse wool lamb skin. This study contributes to the understanding of domestication and breeding of fine wool sheep.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2023)
Article
Microbiology
Rui Guo, Meixia He, Xiaoqing Zhang, Xiuling Ji, Yunlin Wei, Qi-Lin Zhang, Qi Zhang
Summary: In this study, the cold-adapted oleaginous yeast strain Rhodosporidium kratochvilovae strain YM25235 genome was assembled using the Nanopore Platform, and transcriptomic data from low and normal temperature conditions were analyzed using RNA-seq. A total of 1,300 differentially expressed genes were identified, with enriched pathways related to metabolic processes and signaling pathways. Validation of RNA-seq results was conducted using qPCR.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Veterinary Sciences
Adelaida Hernaiz, Arianne Sanz, Sara Sentre, Beatriz Ranera, Oscar Lopez-Perez, Pilar Zaragoza, Juan J. Badiola, Hicham Filali, Rosa Bolea, Janne M. Toivonen, Inmaculada Martin-Burriel
Summary: This study found DNA methylation alterations in the thalamus of sheep infected with scrapie, a form of transmissible spongiform encephalopathy. Hypomethylated regions were associated with genes involved in transmembrane transport and cell adhesion, while hypermethylated regions were related to genes involved in intracellular signal transduction. Furthermore, differentially expressed genes and genes highly expressed in specific types of CNS cells contained differentially methylated regions.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Environmental Sciences
Min Zhang, Jun Shi, Huiping Deng
Summary: This study found that microplastics caused inflammatory damage and histological changes in the heart tissue of mice. It also discovered the role of m6A modification in gene expression in microplastic-induced cardiotoxicity, providing new insights into the chronic toxicity of microplastic exposure on the heart.
Article
Cell Biology
Estelle Colin, Yannis Duffourd, Martin Chevarin, Emilie Tisserant, Simon Verdez, Julien Paccaud, Ange-Line Bruel, Frederic Tran Mau-Them, Anne-Sophie Denomme-Pichon, Julien Thevenon, Hana Safraou, Thomas Besnard, Alice Goldenberg, Benjamin Cogne, Bertrand Isidor, Julian Delanne, Arthur Sorlin, Sebastien Moutton, Melanie Fradin, Christele Dubourg, Magali Gorce, Dominique Bonneau, Salima El Chehadeh, Francois-Guillaume Debray, Martine Doco-Fenzy, Kevin Uguen, Nicolas Chatron, Bernard Aral, Nathalie Marle, Paul Kuentz, Anne Boland, Robert Olaso, Jean-Francois Deleuze, Damien Sanlaville, Patrick Callier, Christophe Philippe, Christel Thauvin-Robinet, Laurence Faivre, Antonio Vitobello
Summary: Multi-omics technologies provide valuable and increasingly accessible tools for diagnostic laboratories to help patients with unresolved rare diseases, especially those clinically diagnosed with rare OMIM diseases. However, there is currently no consensus on the optimal diagnostic care pathway to follow after negative results with standard approaches.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Xingping Chen, Junyi Luo, Jie Liu, Ting Chen, Jiajie Sun, Yongliang Zhang, Qianyun Xi
Summary: MiR-143 plays a crucial role in inhibiting hepatoma cell proliferation in hepatocellular carcinoma and liver fibrosis. DNA methyltransferase 3 alpha (DNMT3a) is a target of miR-143, regulating primary organic solid tumors through DNA methylation mechanisms. Our study found changes in DNA methylation levels in the liver through Whole-Genome Bisulfite Sequencing (WGBS) analysis, and identified differentially methylated regions (DMRs) and related genes enriched in pathways such as metabolism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Jian Zhang, Ziai Peng, Qiling Liu, Guili Yang, Libin Zhou, Wenjian Li, Hui Wang, Zhiqiang Chen, Tao Guo
Summary: In this study, the dynamic changes caused by carbon ion beam (CIB) irradiation on rice seeds were comprehensively characterized using whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) techniques. The analysis revealed that the highest number of differentially expressed genes (DEGs) was observed at 48 hours post-irradiation, with the replication and repair pathway being enriched at this time point. These results suggest that DNA damage response (DDR) and DNA repair mechanisms are quickly activated within the initial stage (48 hours) after irradiation.
Article
Obstetrics & Gynecology
Min Yang, Xin Tao, Katherine Scott, Yiping Zhan, Richard T. Scott, Emre Seli
Summary: The study revealed that embryos with different developmental potentials exhibit different DNA methylation profiles at the blastocyst stage, indicating a potential negative correlation between genome-wide methylation level and embryo quality.
HUMAN REPRODUCTION
(2021)
Article
Biochemical Research Methods
Alexander Y. Trick, Hoan Thanh Ngo, Anju H. Nambiar, Marisa M. Morakis, Fan-En Chen, Liben Chen, Kuangwen Hsieh, Tza-Huei Wang
Summary: In this study, a streamlined workflow for extraction of plasma from whole blood, HIV RNA extraction, and quantitative polymerase chain reaction (qPCR) in a portable magnetofluidic cartridge platform for use at the point-of-care was outlined. The viral particles were isolated from blood using a 3D-printed filter module and then automated nucleic acid capture and purification were performed using magnetic beads, followed by qPCR using compact instrumentation. The study demonstrated rapid detection of HIV viral particles from whole blood in a short period of time.
Article
Multidisciplinary Sciences
Rongjie Fu, Wei He, Jinzhuang Dou, Oscar D. Villarreal, Ella Bedford, Helen Wang, Connie Hou, Liang Zhang, Yalong Wang, Dacheng Ma, Yiwen Chen, Xue Gao, Martin Depken, Han Xu
Summary: The authors developed a high-throughput dual-target synthetic system to explore the sequence determinants of CRISPR/Cas9 specificity. They revealed sequence rules and developed a prediction model and a strategy for Cas9-based allele-specific editing. The study provides insights into the off-target effects of CRISPR/Cas9 and expands the application of allele-specific genome editing.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Itaru Yanagi, Rena Akahori, Ken-ichi Takeda
Summary: The study investigated the ionic current blockades when poly-(dT)(60) or dNTPs passed through SiN nanopores in an aqueous solution containing (NH4)(2)SO4. The dwell time of poly-(dT)(60) and dCTP in the nanopores was significantly longer in the aqueous solution containing (NH4)(2)SO4 compared to the solution without it. The prolonged dwell time effect was also observed when the nanopores were fabricated via dielectric breakdown in the aqueous solution containing (NH4)(2)SO4 and remained even after replacing the solution with one without (NH4)(2)SO4. Furthermore, the four types of dNTPs could be statistically identified based on their current blockade values when passed through the same nanopore.
Article
Plant Sciences
Alessia Russo, Baptiste Mayjonade, Daniel Frei, Giacomo Potente, Roman T. Kellenberger, Lea Frachon, Dario Copetti, Bruno Studer, Juerg E. Frey, Ueli Grossniklaus, Philipp M. Schluter
Summary: This article describes a method for extracting high molecular weight (HMW) DNA from low input plant material, which is easy to follow and quick. It successfully enables HMW DNA extraction from different plant species and is suitable for long-read sequencing on the Oxford Nanopore Technologies PromethION(R) platform.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Jinsoo Ahn, In-Sul Hwang, Mi-Ryung Park, Seongsoo Hwang, Kichoon Lee
Summary: The study aimed to investigate the DNA methylation and expression patterns associated with the DIRAS3 gene in pigs. The findings revealed high expression of DIRAS3 in the hypothalamus of adult pigs and monoallelic expression of the gene across all tested tissues. It suggested a potential relationship between DNA methylation and unique gene expression patterns in pig development.
Article
Chemistry, Multidisciplinary
Qing Wang, Kaiyue Tan, Hong Wang, Jinhua Shang, Yeqing Wan, Xiaoqing Liu, Xiaocheng Weng, Fuan Wang
Summary: The study introduces an epigenetically responsive DNAzyme system that can be specifically activated by FTO demethylation for precise intracellular imaging-directed gene regulation, offering a versatile toolbox for programmable gene regulation in synthetic biology.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Yafen Wang, Xiong Zhang, Shaoqing Han, Wei Yang, Zonggui Chen, Fan Wu, Jizhou Liu, Xiaocheng Weng, Xiang Zhou
Summary: The study introduces Al-seq as a method to profile uracil at single-nucleotide resolution and show its centromeric enrichment, revealing the biological significance of uracil as an epigenetic modification derived from cytosine deamination.
ACS CENTRAL SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Yafen Wang, Zonggui Chen, Xiong Zhang, Xiaocheng Weng, Jikai Deng, Wei Yang, Fan Wu, Shaoqing Han, Chao Xia, Yu Zhou, Yu Chen, Xiang Zhou
Summary: This study presents a method for detecting f(5)C modifications in RNA and a transcriptome-wide f(5)C mapping technique called f(5)C-seq. Over 1000 f(5)C sites were identified in Saccharomyces cerevisiae using f(5)C-seq, and it was found that f(5)C has a preference for wobble sites in mRNA, suggesting its potential role in translation regulation.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xuguo Zhu, Lijun Xiong, Ruitu Lyu, Yinghui Shen, Lu Liu, Shuangqi Li, Christian Argueta, Li Tan
Summary: Estrogen signaling has been found to regulate the expression of TET2 gene and the level of 5hmC, playing a role in the epigenetic regulation of breast cancer cells.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Ruitu Lyu, Xuguo Zhu, Yinghui Shen, Lijun Xiong, Lu Liu, Hang Liu, Feizhen Wu, Christian Argueta, Li Tan
Summary: Aberrant DNA methylation is a key feature of malignant tumors, and the TET2 gene may play a role in enhancing survival rates for ER alpha-positive breast cancer patients. Loss of TET2 leads to abnormal DNA methylation, impacting enhancer regions and impeding estrogen-induced gene transcription. This study sheds light on the epigenetic mechanisms involved in breast cancer progression.
Article
Chemistry, Multidisciplinary
Shengjie Xie, Zisong Cong, Weihua Wang, Shanshan Qin, Xiaocheng Weng, Heng Song, Xiang Zhou
Summary: A new dual-cationic amphiphilic AIEgen, TPhBT-PyP, was designed with near-infrared emission and efficient O-1(2) generation. The amphiphilicity of TPhBT-PyP was achieved by the dual-positive charges of pyridinium and TPP groups, enabling it to efficiently target mitochondria and distinguish Gram-positive bacteria. TPhBT-PyP demonstrated excellent performance in photodynamic therapy, inducing cancer cell apoptosis and killing S. aureus bacteria.
CHEMICAL COMMUNICATIONS
(2023)
Review
Chemistry, Multidisciplinary
Jing Mo, Xiaocheng Weng, Xiang Zhou
Summary: With increasing research interest, more than 170 types of chemical modifications of RNA have been characterized. These modifications do not alter the primary sequence of RNA but modulate gene activity. Developing innovative labeling and detection methodologies is crucial for understanding the biological significance and clinical prospects of RNA modifications.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Qi Wei, Shaoqing Han, Kexin Yuan, Zhiyong He, Yuqi Chen, Xin Xi, Jingyu Han, Shen Yan, Yingying Chen, Bifeng Yuan, Xiaocheng Weng, Xiang Zhou
Summary: A new method was developed to enrich inosine-containing RNA and accurately identify editing sites using Endonuclease V and sodium periodate. The method was validated in the human brain and revealed that A-to-I editing primarily occurs in the 3'UTR of RNA. Comparison between human and mouse brain editing sites showed higher conservation in exons. Application of the method in mouse brain diseases revealed decreased editing in neuronal activity genes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Ruiqi Zhao, Xin Fang, Zhibiao Mai, Xi Chen, Jing Mo, Yingying Lin, Rui Xiao, Xichen Bao, Xiaocheng Weng, Xiang Zhou
Summary: RNA-protein interactions are regulated by RNA secondary structures. The KASRIC strategy was developed to identify single-stranded RNA binding proteins (ssRBPs). Using KASRIC, 3180 candidate RBPs and 244 candidate ssRBPs were identified, including both previously reported and novel ssRBPs. Functional analysis of the candidate ssRBPs showed enrichment in RNA splicing and degradation processes. The KASRIC strategy facilitates the investigation of RNA-protein interactions.
Article
Chemistry, Multidisciplinary
Yalun Xie, Shaoqing Han, Qiming Li, Zhentian Fang, Wei Yang, Qi Wei, Yafen Wang, Yu Zhou, Xiaocheng Weng, Xiang Zhou
Summary: This study presents a chemical method (m(6)A-ORL-Seq) for high-throughput detection of m(6)A modifications in the transcriptome, and successfully identifies around four thousand high-confidence m(6)A sites in the human transcriptome. Unlike traditional antibody or enzyme-based methods, this new approach provides a novel perspective for single-base m(6)A detection at the transcriptome level.
Article
Chemistry, Multidisciplinary
Chen Hong, Qing Wang, Yingying Chen, Yuhui Gao, Jinhua Shang, Xiaocheng Weng, Xiaoqing Liu, Fuan Wang
Summary: The article introduces a novel method for accurate intracellular imaging of metal ions by utilizing an epigenetic demethylation-regulating DNAzyme system, which repairs and activates DNAzyme to achieve accurate imaging of metal ions.
Article
Chemistry, Analytical
Wei Li, Hongmei Yang, Yafen Wang, Xiaocheng Weng, Fang Wang
Summary: This method demonstrates the selective recognition of 6mA through DNA ligase's selective ligation reaction towards A-C mismatch and 6mA-C mismatch, further combined with RCA amplification to achieve highly sensitive identification of 6mA in dsDNA at single-base resolution.
Article
Biochemistry & Molecular Biology
Bingyao Wang, Xiong Zhang, Yafen Wang, Kun Chen, Fang Wang, Xiaocheng Weng, Xiang Zhou
Summary: A one-pot fluorescence-based assay was developed to quantitatively detect A3A activity by combining cytosine deamination and uracil excision. The fluorescent turn-on effect at 520 nm can be used to evaluate A3A activity and screen inhibitors.
RSC CHEMICAL BIOLOGY
(2021)