Establishing a GRU-GCN coordination-based prediction model for miRNA-disease associations by Kai-Cheng Chuang, Ping-Sung Cheng, Yu-Hung Tsai, Meng-Hsiun Tsai

“…Abstract Background miRNAs (microRNAs) are endogenous RNAs with lengths of 18 to 24 nucleotides and play critical roles in gene regulation and disease progression. Although traditional wet-lab experiments provide direct evidence for miRNA-disease associations, they are often time-consuming and complicated to analyze by current bioinformatics tools. …”
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RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models by Muhammad Nabeel Asim, Muhammad Ali Ibrahim, Tayyaba Asif, Andreas Dengel

“…Deciphering information of RNA sequences reveals their diverse roles in living organisms, including gene regulation and protein synthesis. Aberrations in RNA sequence such as dysregulation and mutations can drive a diverse spectrum of diseases including cancers, genetic disorders, and neurodegenerative conditions. …”
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Structure and Expression Analyses of SVA Elements in Relation to Functional Genes by Yun-Jeong Kwon, Yuri Choi, Jungwoo Eo, Yu-Na Noh, Jeong-An Gim, Yi-Deun Jung, Ja-Rang Lee, Heui-Soo Kim

“…Taken together, these data suggest that SVA elements cause transcript isoforms that contribute to modulation of gene regulation in various human tissues.…”
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Characterization of the Cannabis sativa glandular trichome epigenome by Lee J. Conneely, Bhavna Hurgobin, Sophia Ng, Muluneh Tamiru-Oli, Mathew G. Lewsey

“…Abstract Background The relationship between epigenomics and plant specialised metabolism remains largely unexplored despite the fundamental importance of epigenomics in gene regulation and, potentially, yield of products of plant specialised metabolic pathways. …”
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Tyrosine hydroxylase of the brain and it’s regulation by glucocorticoids by E. V. Sukhareva, T. S. Kalinina, V. V. Bulygina, N. N. Dygalo

“…Ontogenetic variation in the expression of Fos and Jun family proteins, which affects their ratio, can be one of the reasons for the TH gene regulation by glucocorticoids at near-term fetuses and neonates. …”
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DHX37 Impacts Prognosis of Hepatocellular Carcinoma and Lung Adenocarcinoma through Immune Infiltration by Yanni Xu, Qiongchao Jiang, Hejun Liu, Xiaoyun Xiao, Dinghong Yang, Phei Er Saw, Baoming Luo

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Lymphatic-derived oxysterols promote anti-tumor immunity and response to immunotherapy in melanoma by Mengzhu Sun, Laure Garnier, Romane Chevalier, Martin Roumain, Chen Wang, Julien Angelillo, Julien Montorfani, Robert Pick, Dale Brighouse, Nadine Fournier, David Tarussio, Stéphanie Tissot, Jean-Marc Lobaccaro, Tatiana V. Petrova, Camilla Jandus, Daniel E. Speiser, Manfred Kopf, Caroline Pot, Christoph Scheiermann, Krisztian Homicsko, Giulio G. Muccioli, Abhishek D. Garg, Stéphanie Hugues

“…We show in a lymphangiogenic murine melanoma that lymphatic endothelial cells (LECs) upregulate the enzyme Ch25h, which catalyzes the formation of 25-hydroxycholesterol (25-HC) from cholesterol and plays important roles in lipid metabolism, gene regulation, and immune activation. We identify a role for LECs as a source of extracellular 25-HC in tumors inhibiting PPAR-γ in intra-tumoral macrophages and monocytes, preventing their immunosuppressive function and instead promoting their conversion into proinflammatory myeloid cells that support effector T cell functions. …”
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A hammerhead ribozyme selects mechanically stable conformations for catalysis against viral RNA by Man Lu, Zhiqiang Cao, Luoan Xiong, Hongying Deng, Kangkang Ma, Ning Liu, Yanding Qin, Shen-Bo Chen, Jun-Hu Chen, Yao Li, Yijin Liu, Zhongbo Yu

“…Abstract Ribozymes, widely found in prokaryotes and eukaryotes, target nucleic acids and can be engineered as biotechnical tools or for gene regulation or immune therapy. Among them, hammerhead is the smallest and best characterized ribozyme. …”
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Borrelia burgdorferi tolerates alteration to P66 porin function in a murine infectivity model by Christa H. Fierros, Marie-Line Faucillion, Beth L. Hahn, Phillip Anderson, Mari Bonde, Julie R. Kessler, Matthew C. Surdel, Kyler S. Crawford, Yan Gao, Jieqing Zhu, Jieqing Zhu, Sven Bergström, Jenifer Coburn, Jenifer Coburn

“…Borrelia burgdorferi exists in a complex enzootic life cycle requiring differential gene regulation. P66, a porin and adhesin, is upregulated and essential during mammalian infection, but is not produced or required within the tick vector. …”
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Inhibition of inflammatory cell infiltration by antagonistic peptides that specifically bind to CCR5 via regulation of the NF-kB signaling pathway in rats with colitis by Yang-Da Song, Yi-Hang Song, Si-Xue Liu, Hua-Rong Huang, Ying-Qiang Zhong

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The study of miRNA-211 affects melanogenesis progress in Cashmere goats via suppressing <i>AP1S2</i> by B. Zhang, R. Liu, T. Ma, X. Li, Y. Zhao, H. Su, J. Li, Y. Li, H. Jiang, Q. Zhang

“…<p>Chromaticity is a key indicator of measuring economic worth of Cashmere goats, and gene regulation plays a major role in Cashmere goat color. …”
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Mono-allelic epigenetic regulation of polycistronic transcription initiation by RNA polymerase II in Trypanosoma brucei by Rudo Kieft, Laura Cliffe, Haidong Yan, Robert J. Schmitz, Stephen L. Hajduk, Robert Sabatini

“…With protein-coding genes organized as polycistronic transcription and apparent absence of promoter-mediated regulation of transcription initiation, it is believed that developmental gene regulation in trypanosomes is essentially post-transcriptional. …”
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ATF3 Knockdown Exacerbates Astrocyte Activation by Inhibiting Phosphorylation of Drp1 in Ischemic Stroke by Huang R, Huang X, Yang H, Wu H, Liu F, Saw PE, Cao M

“…Rong Huang,1 Xiaoyan Huang,1 Hongmei Yang,1 Haixuan Wu,1 Fan Liu,1 Phei Er Saw,2,3 Minghui Cao1,4 1Department of Anesthesiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, People’s Republic of China; 2Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, People’s Republic of China; 3Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, People’s Republic of China; 4Department of Anesthesiology, Shenshan Medical Center, Sun Yat-Sen Memorial Hospital, Sun Yat-sen University, Shanwei, 516600, People’s Republic of ChinaCorrespondence: Phei Er Saw; Minghui Cao, Email caipeie@mail.sysu.edu.cn; caomh@mail.sysu.edu.cnIntroduction: ATF3, a stress-induced transcription factor, has been implicated in the injury processes of various cell types, including neurons. …”
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The synergistic role of gut microbiota and RNA in metabolic diseases: mechanisms and therapeutic insights by Zhuo Huang, Zhuo Huang, Qinyan Yao, Qinyan Yao, Shuang Ma, Shuang Ma, Jinjie Zhou, Jinjie Zhou, Xiaoxuan Wang, Xiaoxuan Wang, Qingguo Meng, Qingguo Meng, Yaxin Liu, Yaxin Liu, Zihan Yu, Zihan Yu, Xin Chen, Xin Chen

“…Additionally, microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) serve as critical regulators in these processes, with emerging evidence showing that gut-derived metabolites affect post-transcriptional gene regulation. This review synthesizes the current understanding of the gut microbiota-RNA axis and its role in metabolic diseases. …”
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YPEL2 regulates the efficacy of BRD4-EZH2 dual targeting in EZH2Y641mut germinal center-derived lymphoma by Aránzazu Chamorro-Jorganes, Núria Profitós-Pelejà, Clara Recasens-Zorzo, Juan G Valero, Diana Reyes-Garau, Laura Magnano, Ray Butler, Antonio Postigo, Patricia Pérez-Galán, Marcelo Lima Ribeiro, Gaël Roué

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Conjugation of LasR Quorum-Sensing Inhibitors with Ciprofloxacin Decreases the Antibiotic Tolerance of P. aeruginosa Clinical Strains by Daria Bortolotti, Claudio Trapella, Alessandra Bragonzi, Paolo Marchetti, Vinicio Zanirato, Andrea Alogna, Valentina Gentili, Carlo Cervellati, Giuseppe Valacchi, Mariangela Sicolo, Giulia Turrin, Anna Fantinati, Dario Di Luca, Roberta Rizzo

“…During infection, P. aeruginosa produces a well-organized bacterial structure, called biofilm, activating the quorum-sensing (QS) signaling, a mechanism of gene regulation. In this work, we synthesized already known QS inhibitors (QSi) designed on the scaffold of the N-(3-oxododecanoyl) homoserine lactone (3O-C12-HSL) QS molecule and conjugated them with ciprofloxacin to inhibit P. aeruginosa biofilm formation and increase the antibiotic susceptibility of clinical strains. …”
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Analysis of Argonaute Complex Bound mRNAs in DU145 Prostate Carcinoma Cells Reveals New miRNA Target Genes by Jaroslaw Szczyrba, Volker Jung, Michaela Beitzinger, Elke Nolte, Sven Wach, Martin Hart, Sandra Sapich, Marc Wiesehöfer, Helge Taubert, Gunther Wennemuth, Norbert Eichner, Thomas Stempfl, Bernd Wullich, Gunter Meister, Friedrich A. Grässer

“…Posttranscriptional gene regulation by microRNAs (miRNAs) contributes to the induction and maintenance of prostate carcinoma (PCa). …”
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The hypolipidemic effect of MI-883, the combined CAR agonist/ PXR antagonist, in diet-induced hypercholesterolemia model by Jan Dusek, Ivana Mejdrová, Klára Dohnalová, Tomas Smutny, Karel Chalupsky, Maria Krutakova, Josef Skoda, Azam Rashidian, Ivona Pavkova, Kryštof Škach, Jana Hricová, Michaela Chocholouskova, Lucie Smutna, Rajamanikkam Kamaraj, Miloš Hroch, Martin Leníček, Stanislav Mičuda, Dirk Pijnenburg, Rinie van Beuningen, Michal Holčapek, Libor Vítek, Magnus Ingelman-Sundberg, Oliver Burk, Thales Kronenberger, Radim Nencka, Petr Pavek

“…Here we show a human CAR agonist/PXR antagonist, MI-883, which effectively regulates genes related to xenobiotic metabolism and cholesterol/bile acid homeostasis by leveraging CAR and PXR interactions in gene regulation. Through comprehensive analyses utilizing lipidomics, bile acid metabolomics, and transcriptomics in humanized PXR-CAR-CYP3A4/3A7 mice fed high-fat and high-cholesterol diets, we demonstrate that MI-883 significantly reduces plasma cholesterol levels and enhances fecal bile acid excretion. …”
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Development, opportunities, and challenges of siRNA nucleic acid drugs by Bowen Xiao, Shaopeng Wang, Yu Pan, Wenjun Zhi, Chensheng Gu, Tao Guo, Jiaqi Zhai, Chenxu Li, Yong Q. Chen, Rong Wang

“…The US Food and Drug Administration has approved six siRNA drugs in recent years: patisiran, givosiran, lumasiran, vutrisiran, inclisiran, and nedosiran. siRNA drugs are based on the post-transcriptional gene regulation mechanism of RNA interference. These drugs have gained widespread attention for their effectiveness, low dosage, and low frequency of administration. …”
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A dual role of Cohesin in DNA DSB repair by Michael Fedkenheuer, Yafang Shang, Seolkyoung Jung, Kevin Fedkenheuer, Solji Park, Davide Mazza, Robin Sebastian, Hiroyuki Nagashima, Dali Zong, Hua Tan, Sushil Kumar Jaiswal, Haiqing Fu, Anthony Cruz, Supriya V. Vartak, Jan Wisniewski, Vittorio Sartorelli, John J. O’Shea, Laura Elnitski, Andre Nussenzweig, Mirit I. Aladjem, Fei-Long Meng, Rafael Casellas

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