Article
Plant Sciences
Weizhi Ouyang, Xiwen Zhang, Yong Peng, Qing Zhang, Zhilin Cao, Guoliang Li, Xingwang Li
Summary: In this study, researchers developed a nucleus CUT&Tag (nCUT&Tag) protocol based on the live-cell CUT&Tag technology, which allows for histone modifications profiling in both monocot rice and dicot rapeseed using minimal starting materials and completing all steps in just 1 day. nCUT&Tag can identify active and repressive histone marks such as H3K4me3 and H3K9me2 efficiently, making it a promising alternative strategy for plant epigenomic studies.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
William M. Yashar, Garth Kong, Jake VanCampen, Brittany M. Smith, Daniel J. Coleman, Lucia Carbone, Galip Gurkan Yardimci, Julia E. Maxson, Theodore P. Braun
Summary: The study presents a new method GoPeaks for detecting histone modification peaks with improved sensitivity compared to traditional algorithms, which is of great significance for epigenetic research.
Article
Multidisciplinary Sciences
Yasuhiro Fujiwara, Yuji Tanno, Hiroki Sugishita, Yusuke Kishi, Yoshinori Makino, Yuki Okada
Summary: Epigenome research uses various methods to locate proteins like transcription factors and histone modifications. The CUT&Tag method, employing a Protein-A Tn5 transposase fusion protein, is important for chromatin accessibility. Dynabeads, particularly MyOne-T1, show improved suspendability and sensitivity for CUT&Tag assays.
Article
Anatomy & Morphology
Bagdeser Akdogan-Ozdilek, Katherine L. Duval, Fanju W. Meng, Patrick J. Murphy, Mary G. Goll
Summary: This study demonstrates the potential of defining emerging chromatin landscapes in vertebrate embryogenesis by combining improved chromatin profiling methods with the strengths of the zebrafish system.
DEVELOPMENTAL DYNAMICS
(2022)
Article
Biotechnology & Applied Microbiology
Xiao-Yuan Tao, Xue-Ying Guan, Gao-Jie Hong, Yu-Qing He, Su-Juan Li, Shou-Li Feng, Jian Wang, Guang Chen, Fei Xu, Jia-Wei Wang, Sheng-Chun Xu
Summary: In contrast to CUT & Tag approaches for profiling bulk histone modifications, current CUT & Tag methods for analysing specific transcription factor (TF)-DNA interactions remain technically challenging due to TFs having relatively low abundance. Moreover, an efficient CUT & Tag strategy for plant TFs is not yet available. Here, we first applied biotinylated Tn5 transposase-mediated CUT & Tag (B-CUT & Tag) to produce high-quality libraries for interrogating TF-DNA interactions.
Our study provides a convenient and highly efficient CUT & Tag strategy called B-CUT & Tag for profiling TF-chromatin interactions that is widely applicable to the annotation of cis-regulatory elements for crop improvement. Furthermore, we demonstrate the functions of AtSPL9 in modulating growth-defence trade-offs and successfully validated the binding of SPL9 in Arabidopsis and PHR2 in rice using the B-CUT & Tag-qPCR method.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Multidisciplinary Sciences
Hussein M. E. Hussein, Matteo Rinaldi, Marvin Onabajo, Cristian Cassella
Summary: This study introduces a new type of wireless sensor network that does not require batteries or chips, using lumped components on a printed substrate to achieve sensing and information transmission, breaking traditional paradigms in energy supply and collection. The network possesses exceptional sensitivity and dynamic range without the need for expensive manufacturing. The device operates in the ultra-high-frequency range, capable of passively and continuously detecting temperature changes remotely.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Weipeng Zhang, Bo Zhao, Qizhi Yang, Liming Zhou, Hanlu Jiang, Kang Niu, Jian Ding
Summary: This study developed an intelligent inspection and temperature and humidity monitoring system based on RFID cotton bale, which effectively improves working efficiency and storage security through the use of the PSO-ANN algorithm for data processing.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Xingpeng Di, Liyuan Xiang, Zhongyu Jian
Summary: The study reveals that YAP is an important transcriptional coactivator binding to transcriptional factors and plays a role in downstream gene transcription. Through RNA-seq and CUT&Tag analysis of human bladder smooth muscle cells with YAP knockout, 141 differentially expressed genes were identified, of which 36 genes were directly regulated by YAP. Furthermore, hub genes including CDCA5, CENPA, DTL, NCAPH, and NEIL3 were found to contribute to cell proliferation. The study suggests that YAP may be a crucial target for pBOO-associated bladder fibrosis in bladder smooth muscle cells.
FRONTIERS IN GENETICS
(2023)
Article
Plant Sciences
Aicen Zhang, Yangyang Wei, Yining Shi, Xiaojuan Deng, Jingjing Gao, Yilong Feng, Dongyang Zheng, Xuejiao Cheng, Zhaoguo Li, Tao Wang, Kunbo Wang, Fang Liu, Renhai Peng, Wenli Zhang
Summary: This study has provided insights into the roles of H3K4me3 and H3K27me3 in regulating gene expression in cotton. The results show that H3K4me3 and H3K27me3 have distinct regulatory roles between the A and D subgenomes, as well as differences in enrichment levels in homeologous genes. This indicates that H3K4me3 and H3K27me3 play important roles in cotton polyploidization and domestication.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Computer Science, Hardware & Architecture
Francesco Restuccia, Ryan Kastner
Summary: Modern FPGA system on chips utilize complex multimanager, multisubordinate on-chip communication networks which may lead to safety and security issues. Cut and forward presents a novel switching method designed to ensure safety and security in multicomponent communication architectures on FPGA systems on chips.
IEEE TRANSACTIONS ON COMPUTER-AIDED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS
(2022)
Article
Environmental Sciences
Jian Yang, Minhai Liu, Weiliang Shen, Tingting Zhou, Xiongfei Wu, Qi Li, Zhihua Lin
Summary: In this study, the function of H3K4me3 in gill tissues of large yellow croaker under low salinity stress was investigated using RNA-seq and CUT&Tag analyses. The results showed that H3K4me3 plays an important role in the epigenetic regulation of gene expression during low salinity stress, providing novel insights into the response mechanisms of aquatic animals to abiotic stress.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Yizhi Cui, Hongzhi Liu, Yutong Ming, Zheng Zhang, Li Liu, Ruijun Liu
Summary: G-quadruplex (G4) is a non-classical DNA structure that plays an important role in biological processes. Computational methods are necessary for predicting G4s due to their distribution in functional regions in a cell-type-specific manner. In this study, we developed a new prediction model based on machine learning and constructed a dataset using high-resolution sequencing data from G4 CUT & Tag. Our results demonstrate the influence of flanking sequences on G4 formation and the higher GC content of G4 flanking sequences. Furthermore, we identified G4 motifs for known transcription factors in the high-resolution dataset.
BRIEFINGS IN FUNCTIONAL GENOMICS
(2023)
Article
Biochemical Research Methods
Nityanand Kumawat, Soja Saghar Soman, Sanjairaj Vijayavenkataraman, Sunil Kumar
Summary: Microfluidic paper-based analytical devices (microPADs) are simple-to-use and low-cost point-of-care testing platforms. We propose a new method, called cut and heat (CH-microPADs), for producing hydrophilic channels and reservoirs on various porous media. Compared to existing methods, the devices fabricated with this technique have excellent mechanical strength and chemical resistance, making them suitable for clinical diagnostics, biological sensing, food processing, and the chemical industry.
Article
Chemistry, Analytical
Teng Sun, Jianan Hui, Lin Zhou, Bo Lin, Hebin Sun, Yanan Bai, Jianlong Zhao, Hongju Mao
Summary: In this study, a cut-and-paste (CAP) method is developed to fabricate microfluidic patches for real-time monitoring of glucose and lactate in sweat. The CAP method allows for the quick and automated production of the patches, which have low-cost, versatility, and mechanical flexibility. The results of this study indicate the potential of the CAP method in the development of wearable sweat microfluidic devices for individualized health monitoring.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Biochemistry & Molecular Biology
Leiming Wu, Zi Luo, Yanni Shi, Yizhe Jiang, Ruonan Li, Xinxin Miao, Fang Yang, Qing Li, Han Zhao, Jiquan Xue, Shutu Xu, Tifu Zhang, Lin Li
Summary: A transient and simplified tsCUT&Tag method was developed for high-throughput chromatin profiling in plants. This method provided higher data quality and signal resolution compared to traditional ChIP-seq, and when combined with machine learning, it has great potential for profiling the transcription factor binding landscape during plant development.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Article
Plant Sciences
Ting Zhao, Xiaoyuan Tao, Menglin Li, Mengtao Gao, Jiedan Chen, Na Zhou, Gaofu Mei, Lei Fang, Linyun Ding, Baoliang Zhou, Tianzhen Zhang, Xueying Guan
Article
Multidisciplinary Sciences
Ke Wan, Kening Lu, Mengtao Gao, Ting Zhao, Yuxin He, Dong-Lei Yang, Xiaoyuan Tao, Guosheng Xiong, Xueying Guan
Summary: The CLE gene family encodes important short peptide hormones involved in plant shoot apical meristem division and root and vascular bundle development regulation. Studies on the GhCLE gene family in cotton show functional conservation in apical shoot development regulation.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Ting Zhao, Huan Mei, Zeyi Cao, Luyao Wang, Xiaoyuan Tao, Shouli Feng, Lei Fang, Xueying Guan
Summary: The study found significant activation of lincRNAs in the absence of CG DNA methylation rather than non-CG. This research provides us with a working model of the contribution of DNA methylation to regulation of the dynamic activity of lincRNA transcription.
Article
Biotechnology & Applied Microbiology
Luyao Wang, Jin Han, Kening Lu, Menglin Li, Mengtao Gao, Zeyi Cao, Ting Zhao, Xue Chen, Xiaoyuan Tao, Quanjia Chen, Xueying Guan
Summary: An evolutionary model using diploid and allotetraploid cotton species found that 80% of non-coding transcripts in allotetraploid cotton are uniquely activated compared to its diploid ancestors. The function of activated lncRNAs in allotetraploid cotton is largely unknown. Transcriptome analysis revealed that lncRNA expression is preferentially associated with flanking PCGs, and a low-throughput functional screening identified lncRNAs related to plant height and stress tolerance. The study suggests that lncRNAs are more active under abiotic stresses, such as temperature stress, and may play a cis-regulatory role in response to environmental stimuli.
Article
Multidisciplinary Sciences
Xiaoyuan Tao, Mengtao Gao, Siyuan Wang, Xueying Guan
Summary: This article introduces a CUT&Tag method for epigenomic research in plants. By tethering a specific antibody and protein A-transposase, targeted chromatin can be cleaved in situ. Modifications for plant nuclei isolation are also provided.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Article
Plant Sciences
Rui Fan, Xiao-yuan Tao, Zhi-qiang Xia, Soonliang Sim, Li-song Hu, Bao-duo Wu, Qing-huang Wang, Chao-yun Hao
Summary: In this study, a comparative analysis of transcriptome and metabolome between P. flaviflorum and P. nigrum upon P. capsici infection was conducted. The resistant P. flaviflorum showed significant differences in gene expression profiles, enriched in plant-pathogen interaction, phytohormone signal transduction, and secondary metabolic pathways. Metabolome analysis revealed differences in ABA, SA, IAA, and JA-Ile levels between the two species. The study provides insights into the molecular mechanisms underlying the resistance of P. flaviflorum and its potential use in managing oomycete pathogens in black pepper production.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Xiaoyuan Tao, Shouli Feng, Sujuan Li, Guang Chen, Jian Wang, Lizhi Xu, Xujun Fu, Jing Yu, Shengchun Xu
Summary: The dU-Tn5 method is a user-friendly and comparable quality strand-specific RNA sequencing protocol, which can be used for the discovery of novel transcripts, genome annotation, and gene expression level profiling.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Bin Chen, Shouli Feng, Junfeng Hou, Ying Zhu, Fei Bao, Hailiang Han, Heping Tan, Guiyue Wang, Fucheng Zhao
Summary: This study identified key genes related to sugar metabolism in sweet corn kernels through gene expression analysis. The results revealed that both photosynthesis efficiency and sugar metabolism rate play a role in sugar accumulation in sweet corn. This provides new insights for breeding high-sugar cultivars and lays the foundation for studying the regulatory mechanisms of kernel sugar content in corn.
Article
Biotechnology & Applied Microbiology
Xiao-Yuan Tao, Xue-Ying Guan, Gao-Jie Hong, Yu-Qing He, Su-Juan Li, Shou-Li Feng, Jian Wang, Guang Chen, Fei Xu, Jia-Wei Wang, Sheng-Chun Xu
Summary: In contrast to CUT & Tag approaches for profiling bulk histone modifications, current CUT & Tag methods for analysing specific transcription factor (TF)-DNA interactions remain technically challenging due to TFs having relatively low abundance. Moreover, an efficient CUT & Tag strategy for plant TFs is not yet available. Here, we first applied biotinylated Tn5 transposase-mediated CUT & Tag (B-CUT & Tag) to produce high-quality libraries for interrogating TF-DNA interactions.
Our study provides a convenient and highly efficient CUT & Tag strategy called B-CUT & Tag for profiling TF-chromatin interactions that is widely applicable to the annotation of cis-regulatory elements for crop improvement. Furthermore, we demonstrate the functions of AtSPL9 in modulating growth-defence trade-offs and successfully validated the binding of SPL9 in Arabidopsis and PHR2 in rice using the B-CUT & Tag-qPCR method.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Fujie Liu, Sheng Cai, Zhifeng Ma, Haoran Yue, Liangshuai Xing, Yingying Wang, Shouli Feng, Liang Wang, Lingjun Dai, Hui Wan, Jianbo Gao, Mengfei Chen, Mehboob-ur- Mehboob-ur-Rahman, Baoliang Zhou
Summary: This study shows that the Myb-like transcription factor, RVE2, confers resistance to Verticillium wilt (VW) in cotton by regulating the jasmonic acid (JA) pathway. RVE2 is essential for the activation of JA-mediated disease-resistance response. RVE2 physically interacts with TPL/TPRs and disrupts JAZ proteins to recruit TPL and TPR1 in a NINJA-dependent manner, thereby regulating JA response.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Yayao Zhang, Yihao Zang, Jinwen Chen, Shouli Feng, Zhiyuan Zhang, Yan Hu, Tianzhen Zhang
Summary: The GhLYI gene in cotton encodes a truncated EIN3 protein that regulates senescence by activating senescence-associated genes, while also acting as an ethylene signal response factor and a positive regulator.
Article
Plant Sciences
Xiaoyuan Tao, Menglin Li, Ting Zhao, Shouli Feng, Hailin Zhang, Luyao Wang, Jin Han, Mengtao Gao, Kening Lu, Quanjia Chen, Baoliang Zhou, Xueying Guan
Summary: The study identified a lincRNA, DAN1, which was generated through hybridization and WGD events in cotton evolution. DAN1 is involved in drought response and enhances plant tolerance to drought stress by regulating genes in auxin-response pathways.
