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Developing a pipeline for identification,characterization and molecular editing of cis-regulatory elements:a case study in potato

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aBIOTECH 2025年第1期6卷 91-96页

作者： Min Wan Handan Xie Hongwei Guo Shenglin Jing Deying Zeng Bing Li Bo Zhu Zixian Zeng Department of Biological Science College of Life SciencesSichuan Normal UniversityChengdu 610101China Plant Functional Genomics and Bioinformatics Research Center Sichuan Normal UniversityChengdu 610101China Crop Research Institute Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan ProvinceSichuan Academy of Agricultural SciencesChengdu 610066China

Crop breeding requires a balance of tradeoffs among key agronomic traits caused by gene *** molecular manipulation of genes can effectively improve target traits,but this may not reduce gene pleiotropy,potentially leading to undesirable traits or even lethal ***,molecular editing of cis-regulatory elements(CREs)of target genes may facilitate the dissection of gene pleiotropy to fine-tune gene *** this study,we developed a pipeline,in potato,which employs open chromatin to predict candidate CREs,along with both transient and genetic assays to validate the function of CREs and CRISPR/Cas9 to edit candidate *** used StCDF1 as an example,a key gene for potato tuberization and identified a 288 bp-core promoter region,which showed photoperiodic inducibility.A homozygous CRISPR/Cas9-editing line was established,with two deletions in the core promoter,which displayed a reduced expression level,resulting in late tuberization under both longday and short-day *** pipeline provides an alternative pathway to improve a specific trait with limited downside on other phenotypes.

关键词： Cis-regulatory element Potato CRISPR Genome-editing

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ConsensuSV-ONT – A modern method for accurate structural variant calling

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Scientific Reports 2025年第1期15卷 1-9页

作者： Pietryga, Antoni Chiliński, Mateusz Gadakh, Sachin Plewczynski, Dariusz Laboratory of Bioinformatics and Computational Genomics Faculty of Mathematics and Information Science Warsaw University of Technology Warsaw Poland Faculty of Electrical Engineering Warsaw University of Technology Warsaw Poland Laboratory of Functional and Structural Genomics Centre of New Technologies University of Warsaw Warsaw Poland Section for Computational and RNA Biology Department of Biology University of Copenhagen Copenhagen Denmark

Improvements in sequencing technology make the development of new tools for detection of structural variance more and more common. However, since the tools available for the long-read Oxford Nanopore sequencing are limited, and the selection of the optimal tool presents a challenge, there is a need to create a tool based on Consensus that combines existing work to identify a set of high-quality, reliable structural variants that can be used for further downstream analysis. The field has also been subject to revolution in machine learning techniques, especially deep learning. To address the aforementioned need and developments, we propose a novel, fully automated ConsensuSV-ONT algorithm. The method uses six independent, state-of-the-art structural variant callers for long-read sequencing along with a convolutional neural network for filtering high-quality variants. We provide a runtime environment in the form of a docker image, wrapping a nextflow pipeline for efficient processing using parallel computing. The solution is complete in its form and is ready to use not only by computer scientists but accessible and easy to use for everyone working with Oxford Nanopore long-read sequencing data. © The Author(s) 2025.

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Characterizing somatic mutations in ovarian cancer germline risk regions

Communications Biology

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Communications Biology 2025年第1期8卷 1-9页

作者： Lai, Ping-Hung Tyrer, Jonathan P. Pharoah, Paul Gayther, Simon A. Jones, Michelle R. Peng, Pei-Chen Department of Computational Biomedicine Cedars-Sinai Medical Center West Hollywood CA United States CR-UK Department of Oncology University of Cambridge Strangeways Research Laboratory Cambridge United Kingdom Center for Inherited Oncogenesis Department of Medicine UT Health San Antonio San Antonio TX United States Center for Bioinformatics and Functional Genomics Department of Biomedical Sciences Cedars-Sinai Medical Center Los Angeles CA United States

Epithelial ovarian cancer (EOC) genetics research has been focused on germline or somatic mutations independently. Emerging evidence suggests that the somatic mutational landscape can be shaped by the germline genetic background. In this study, we aim to unravel the role of somatic alterations within EOC germline susceptibility regions by incorporating functional annotations. We investigate somatic events, including mutational signatures, point mutations, copy number alterations, and transcription factor binding disruptions, within 33 EOC germline susceptibility regions. Our analysis identifies significant associations between candidate germline susceptibility genes and somatic mutational signatures known to be key risk factors for EOC, such as mismatch repair deficiency, age-related mutagenesis, and homologous recombination deficiency. In addition, we find somatic point mutations and copy number alterations are significantly enriched in histotype-specific active enhancers and promoters within EOC risk loci. Furthermore, we examine the impact of germline variants and somatic mutations on transcription factor binding sites, identifying cancer developmental transcription factor motifs frequently affected by both types of mutations. Overall, our study highlights the importance of integrating germline and somatic mutations with regulatory and epigenomic data to gain insights into the genetic basis of EOC. © The Author(s) 2025.

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Non-coding Transcripts from Enhancers:New Insights into Enhancer Activity and Gene Expression Regulation

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genomics, Proteomics & bioinformatics 2017年第3期15卷 201-207页

作者： Hongjun Chen Guangshi Du Xu Song Ling Li Center for Functional Genomics and Bioinformatics Key Laboratory of Bio-Resources and Eco-Environment of Ministry of EducationCollege of Life ScienceSichuan University State Key Laboratory of Biotherapy West China HospitalSichuan University

Long non-coding RNAs （lncRNAs） have gained widespread interest in the past decade owing to their enormous amount and surprising functions implicated in a variety of biological pro- cesses. Some lncRNAs exert function as enhancers, i.e., activating gene transcription by serving as the cis-regulatory molecules. Furthermore, recent studies have demonstrated that many enhancer elements can be transcribed and produce RNA molecules, which are termed as enhancer RNAs （eRNAs）. The eRNAs are not merely the by-product of the enhancer transcription. In fact, many of them directly exert or regulate enhancer activity in gene activation through diverse mechanisms. Here, we provide an overview of enhancer activity, transcription of enhancer itself, characteristics of eRNAs, as well as their roles in regulating enhancer activity and gene expression.

关键词： LncRNA Enhancer transcriptioneRNA Enhancer activity Gene expression

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Long non-coding RNA-guided regulation in organisms

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Science China(Life Sciences) 2013年第10期56卷 891-896页

作者： QI WenChuan SONG Xu LI Ling Center for Functional Genomics and Bioinformatics Key Laboratory of Bio-Resources and Eco-Environment of Ministry of EducationCollege of Life ScienceSichuan University State Key Laboratory of Biotherapy West China HospitalSichuan University

It is clear that RNA is more than just a messenger between gene and *** mammalian genome is pervasively transcribed,giving rise to tens of thousands of non-coding *** all of these transcripts are functional remains to be elucidated,but it is evident that there are many functional long non-coding RNAs(lncRNAs).Recent studies have set out to decode the regulatory role and functional diversity of *** we organize these studies to highlight the significant involvements of lncRNAs in regulation of gene expression and human physiological and pathological processes,which are achieved by their interaction with DNA,RNA or protein.

关键词： lncRNAs gene expression physiological and pathological processes interaction

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Dormancy heterogeneity among Arabidopsis thaliana seeds is linked to individual seed size

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Plant Communications 2024年第2期5卷 215-227页

作者： Michal Krzyszton Sebastian P.Sacharowski Veena Halale Manjunath Katarzyna Muter Grzegorz Bokota Ce Wang Dariusz Plewczynski Tereza Dobisova Szymon Swiezewski Laboratory of Seeds Molecular Biology Institute of Biochemistry and BiophysicsPAS02-106 WarsawPoland Laboratory of Functional and Structural Genomics Centre of New TechnologiesUniversity of WarsawWarsawPoland Laboratory of Bioinformatics and Computational Genomics Faculty of Mathematics and Information ScienceWarsaw University of TechnologyWarsawPoland Labdeers Ltd. 680-01 BoskoviceCzech Republic

Production of morphologically and physiologically variable seeds is an important strategy that helps plants to survive in unpredictable natural ***,the model plant Arabidopsis thaliana and most agronomically essential crops produce visually homogenous *** automated phenotype analysis,we observed that small seeds in Arabidopsis tend to have higher primary and secondary dormancy levels than large *** analysis revealed distinct gene expression profiles between large and small *** seeds have higher expression of translation-related genes implicated in germination *** contrast,small seeds have elevated expression of many positive regulators of dormancy,including a key regulator of this process,the DOG1 *** in DOG1 expression are associated with differential production of its alternative cleavage and polyadenylation isoforms;in small seeds,the proximal poly(A)site is selected,resulting in a short mRNA ***,single-seed RNA sequencing analysis demonstrated that large seeds resemble DOG1 knockout mutant ***,on the single-seed level,expression of genes affected by seed size is correlated with expression of genes that position seeds on the path toward *** results demonstrate an unexpected link between seed size and dormancy phenotypes in a species that produces highly homogenous seed pools,suggesting that the correlation between seed morphology and physiology is more widespread than initially assumed.

关键词： seed size dormancy DOG1 Arabidopsis

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The Non-Coding RNA Llme23 Drives the Malignant Property of Human Melanoma Cells

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Journal of Genetics and genomics 2013年第4期40卷 179-188页

作者： Chuan-Fang Wu Guang-Hong Tan Cheng-Chuan Ma Ling Li Center for Functional Genomics and Bioinformatics Ministry of EducationKey Laboratory for Bio-Resource and Eco-EnvironmentCollege of Life ScienceSichuan University Hainan Provincial Key Laboratory of Tropical Medicine Hainan Medical College Center for Functional Genomics and Bioinformatics Ministry of EducationKey Laboratory for Bio-Resource and Eco-EnvironmemCollege of Life ScienceSichuan University

Several lines of evidence support the notion that increased RNA-binding ability of polypyrimidine tract-binding（PTB） proteinassociated splicing factor（PSF） and aberrant expression of long non-coding RNAs（IncRNAs） are associated with mouse and human *** identify the PSF-binding IncRNA involved in human oncogenesis,we screened a nuclear RNA repertoire of human melanoma cell line,YUSAC,through RNA-SELEX affinity chromatography.A previously unreported IncRNA,termed as Llme23,was found to bind immobilized PSF *** specific binding of Llme23 to both recombinant and native PSF protein was confirmed in vitro and in vivo. The expression of PSF-binding Llme23 is exclusively detected in human melanoma *** down Llme23 remarkably suppressed the malignant property of YUSAC cells,accompanied by the repressed expression of proto-oncogene *** results may indicate that Llme23 can function as an oncogenic RNA and directly associate the PSF-binding IncRNA with human melanoma.

关键词： LncRNA Llme23 PSF Melanoma Rab23

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Design and in vitro evaluation of novel tetrazole derivatives of dianisidine as anticancer agents targeting Bcl-2 apoptosis regulator

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Scientific Reports 2025年第1期15卷 1-16页

作者： Wioletta Olejarz Karol Sadowski Piotr Roszkowski Anna Bielenica Marta Struga Daniel Szulczyk Maciej Wiśniewski Department of Biochemistry and Pharmacogenomics Faculty of Pharmacy Medical University of Warsaw 02-097 Warsaw Poland Centre for Preclinical Research Medical University of Warsaw 02-097 Warsaw Poland Faculty of Chemistry University of Warsaw Pasteura 1 02-093 Warszawa Poland Department of Biochemistry Medical University of Warsaw 02-097 Warsaw Poland Laboratory of Bioinformatics and Computational Genomics Faculty of Mathematics and Information Science Warsaw University of Technology Warsaw Poland Laboratory of Functional and Structural Genomics Centre of New Technologies University of Warsaw Warsaw Poland

This study examines the synthesis and biological evaluation of novel tetrazole derivatives of 3,3′-dimethoxybenzidine as potential anticancer agents, focusing on their cytotoxic, apoptotic, and anti-inflammatory properties. Ten derivatives were synthesized using thioureas as precursors, characterized through spectroscopic methods, and assessed for their in silico toxicological profiles using the ADMET-AI and ProTox 3.0 platforms. In vitro cytotoxic activity was evaluated against four human cancer cell lines (HTB-140, A549, HeLa, SW620) and one normal cell line (HaCaT) using MTT and LDH assays. Mechanistic studies included apoptosis assessment via flow cytometry and interleukin-6 (IL-6) analysis using ELISA. The synthesized tetrazole derivatives demonstrated significant anticancer potential, exhibiting selective cytotoxicity against cancer cell lines, robust induction of apoptosis, and a notable reduction in IL-6 levels. Their favorable toxicity profiles, as observed in both in silico and in vitro evaluations, support their potential as promising candidates for further development. The tested compounds showed strong inhibitory activity against the apoptosis regulator Bcl-2, with binding affinities comparable to those of native ligands. Western blot analysis revealed a dramatic loss of Bcl-2 protein expression in selected cancer cells during exposure to compound5. Additionally, this research highlights the innovative use of hazardous substrates in drug discovery, aligning with the principles of green chemistry. Future efforts should focus on optimizing the most active derivatives and conducting in vivo studies to confirm their therapeutic potential and safety.

关键词： Anticancer Apoptosis Cytotoxicity Tetrazoles Toxicology

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Coagulation factors Ⅶ, Ⅸ and Ⅹ are effective antibacterial proteins against drug-resistant Gram-negative bacteria

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细胞研究（英文版） 2019年第9期29卷 711-724页

作者： Jinwu Chen Xiaojie Li Ling Li Ting Zhang Qing Zhang Fangming Wu Diyue Wang Hongze Hu Changlin Tian Dongsheng Liao Liang Zhao Danxia Song Yongyun Zhao Chuanfang Wu Xu Song Center for Functional Genomics and Bioinformatics Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu 610064 Sichuan China Center for Functional Genomics and Bioinformatics Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu 610064 Sichuan China State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu 610041 Sichuan China High Magnetic Field Laboratory Chinese Academy of Sciences Hefei 230031 Anhui China CAS key Laboratory of Soft Matter Chemistry Department of Chemistry University of Science and Technology of China Hefei 230026 Anhui China High Magnetic Field Laboratory Chinese Academy of Sciences Hefei 230031 Anhui China Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences University of Science and Technology of China Hefei 230026 Anhui China

Infections caused by drug-resistant "superbugs" pose an urgent public health threat due to the lack of effective drugs;however,certain mammalian proteins with intrinsic antibacterial activity might be ***,we reveal an antibacterial property against Gram-negative bacteria for factors Ⅶ,Ⅸ and Ⅹ,three proteins with well-established roles in initiation of the coagulation *** factors exert antibacterial function via their light chains (LCs).Unlike many antibacterial agents that target cell metabolism or the cytoplasmic membrane,the LCs act by hydrolyzing the major components of bacterial outer membrane,lipopolysaccharides,which are crucial for the survival of Gram-negative *** LC of factor Ⅶ exhibits in vitro efficacy towards all Gram-negative bacteria tested,including extensively drug-resistant (XDR) pathogens,at nanomolar *** is also highly effective in combating XDR Pseudomonas aeruginosa and Acinetobacter baumannii infections in *** decoding a unique mechanism whereby factors Ⅶ,Ⅸ and Ⅹ behave as antimicrobial proteins,this study advances our understanding of the coagulation system in host defense,and suggests that these factors may participate in the pathogenesis of coagulation disorder-related diseases such as sepsis via their dual functions in blood coagulation and resistance to ***,this study may offer new strategies for combating Gram-negative "superbugs".

关键词： Immunology Mechanisms of disease

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Aptamer blocking S-TLR4 interaction selectively inhibits SARS-CoV-2 induced inflammation

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Signal Transduction and Targeted Therapy 2022年第5期7卷 1383-1385页

作者： Gang Yang Shengnan Zhang Yuchun Wang Ling Li Yu Li Deyu Yuan Fatao Luo Jincun Zhao Xu Song Yongyun Zhao Center for Functional Genomics and Bioinformatics College of Life ScienceSichuan UniversityChengduSichuan 610064P.R.China State Key Laboratory of Respiratory Disease Guangzhou Institute of Respiratory DiseaseThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdong 510182China

Excessive inflammatory responses lead to increased mortality from the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).Nearly all deceased patients infected with SARS-CoV-2 are found to have cytokine storm syndrome and viral *** are prone to superinfections exacerbating the course of disease.1 Therefore,preventing hyperinflammation is critical for avoiding this cytokine storm ***,specific immunomodulators are under clinical research or application,including targeting inflammatory cytokines(sarilumab,anakinra,tocilizumab,infliximab,adalimumab)and inflammatory pathway(baricitinib,ruxolitinib).

关键词： inflammation mortality acute

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