Cut&tag: a powerful epigenetic tool for chromatin profiling by Zhijun Fu, Sanjie Jiang, Yiwen Sun, Shanqiao Zheng, Liang Zong, Peipei Li

“…Analysis of transcription factors and chromatin modifications at the genome-wide level provides insights into gene regulatory processes, such as transcription, cell differentiation and cellular response. Chromatin immunoprecipitation is the most popular and powerful approach for mapping chromatin, and other enzyme-tethering techniques have recently become available for living cells. …”
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Molecular characterization and expression profiles of cytochrome P450 reductase gene in Sogatella furcifera (Hemiptera: Delphacidae) by YU Hang, LIU Su, ZHU Qingzi, ZHOU Wenwu, LIANG Qingmei, SHI Xiaoxiao, ZHU Zijie, ZHU Zengrong

“…Since insect P450 system is one of the most important metabolic adaptive traits involved in the degradation of xenobiotics and regulation of endogenous substrates. …”
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Transcriptional search to identify and assess reference genes for expression analysis in Solanumlycopersicum under stress and hormone treatment conditions by Yao-ke DUAN, Rong HAN, Yan SU, Ai-ying WANG, Shuang LI, Hao SUN, Hai-jun GONG

“…Tomato (Solanumlycopersicum) is a model plant for research on fruit development and stress response, in which gene expression analysis is frequently conducted. …”
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Integrative genomics of gene and metabolic regulation by estrogen receptors α and β, and their coregulators by Zeynep Madak‐Erdogan, Tze‐Howe Charn, Yan Jiang, Edison T Liu, John A Katzenellenbogen, Benita S Katzenellenbogen

“…Our findings delineate distinct TF‐coregulator assemblies that function as control nodes, specifying precise patterns of gene regulation, proliferation, and metabolism, as exemplified by two of the most important nuclear hormone receptors in human breast cancer.…”
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Expression characteristics of CsESA1 in citrus and analysis of its interacting protein by Xiao He, Huiying Wang, Wei Wei, Ziyue Han, Jiaqi Zuo, Qing He

“…Based on comparative transcriptome data, two cellulose synthase (CESA) genes responsive to CaLas infection induction were screened, and one gene cloned with higher differential expression level was selected and named CsCESA1. we verified the interaction between CsCESA1 and citrus exopolysaccharide 2 (CsEPS2) proteins. …”
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Differentially expressed genes in mycorrhized and nodulated roots of common bean are associated with defense, cell wall architecture, N metabolism, and P metabolism. by Kalpana Nanjareddy, Manoj-Kumar Arthikala, Brenda-Mariana Gómez, Lourdes Blanco, Miguel Lara

“…Here, we used ion torrent next-generation sequencing to perform comparative transcriptomics of common bean (Phaseolus vulgaris) roots colonized by AM or rhizobia. …”
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Role of molecular breeding in understanding salinity tolerance in cotton: limitations and perspectives by Shicong WANG, Meiling HOU, Hadiqa HASSAN, Fatima M. ABBAS, Zehbah A. AL AHMAD, Sameer H. QARI, Nurul A.B. HANIFAH

“… Cotton is a significant fiber crop globally and has a considerable share in many countries’ gross domestic product (GDP). It is the most critical contributor to the textile industry and provides income to millions of farmers. …”
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Effect of Low Red‐to‐Far‐Red Light on Stem Elongation and Pith Cell Development in Dicots by Linge Li, Yorrit van deKaa, Lotte van derKrabben, Ronald Pierik, Kaisa Kajala

“…We observed changes to the pith traits, including increases in pith layer number, pith cell diameter, and longitudinal cell length. We profiled the transcriptome in the entire internodes and in the hand‐dissected pith in the central cylinder of the internode in response to low R:FR treatment and identified transcription factors (TFs) of interest that were upregulated in the central cylinder, mostly GATA, TCP, and bZIPs. …”
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Gene expression profiling identifies molecular pathways associated with collagen VI deficiency and provides novel therapeutic targets. by Sonia Paco, Susana G Kalko, Cristina Jou, María A Rodríguez, Joan Corbera, Francesco Muntoni, Lucy Feng, Eloy Rivas, Ferran Torner, Francesca Gualandi, Anna M Gomez-Foix, Anna Ferrer, Carlos Ortez, Andrés Nascimento, Jaume Colomer, Cecilia Jimenez-Mallebrera

“…To address this we have applied microarrays to analyse the transcriptome of UCMD muscle and compare it to healthy muscle and other muscular dystrophies. …”
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Novel regulators of PrPC biosynthesis revealed by genome-wide RNA interference. by Daniel Heinzer, Merve Avar, Daniel Patrick Pease, Ashutosh Dhingra, Jiang-An Yin, Elke Schaper, Berre Doğançay, Marc Emmenegger, Anna Spinelli, Kevin Maggi, Andra Chincisan, Simon Mead, Simone Hornemann, Peter Heutink, Adriano Aguzzi

“…Here we performed an arrayed whole-transcriptome RNA interference screen to identify modulators of PrPC expression. …”
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Intermittent Supplemental Irradiation With Blue Light Promotes Leafy Heads in Lettuce by Yanke Liu, Yiqun Chen, Rongcheng Lin, Ep Heuvelink, Yang Li

“…ABSTRACT Red and blue lights are the most effective spectral components absorbed by plants and are typically applied in a constant spectrum in plant factory agricultural practices. …”
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Prognosis and Novel Drug Targets for Key lncRNAs of Epigenetic Modification in Colorectal Cancer by Peng Zhang, Tingting Zhang, Denggang Chen, Li Gong, Min Sun

“…Colorectal cancer (CRC) has been the 3rd most commonly malignant tumor of the gastrointestinal tract in the world. 5-Methylcytosine (m5C) and long noncoding RNAs (lncRNAs) have an essential role in predicting the prognosis and immune response for CRC patients. …”
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Reversible downregulation of HLA class I in adenoid cystic carcinoma by Xin Gao, Jeffrey Raizer, William C Faquin, Jong Chul Park, Thomas Denize, Ross D Merkin, Annie Li, Bianca L Gonda, Atul K Bhan, Stefan T Kaluziak, Markus D Herrmann, Yu-Chung Huang, Elizabeth M Codd, Adam von Paternos, Dawn R Mitchell, Prinjali Kalyan, Samantha E Flynn, Thuc Q Dzu, Chengzhuo Gao, Edwin Zhang, Julia J Mendel, Julia C Thierauf, Peter M Sadow, Diane Yang, Florian J Fintelmann, Jo Anne Fordham, Daniel L Faden, Lori J Wirth, A. John Iafrate

“…Background Adenoid cystic carcinoma (ACC) is a rare, but lethal cancer with low response rates to systemic therapies, such as cytotoxic chemotherapy and immune-checkpoint inhibitors (ICIs). …”
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Genome-wide identification and expression analyses of CYP450 genes in Chrysanthemum indicum by Yuyuan Chen, Tongjun Zhou, Jian Zhong, Yuxian Xu, Peng Zhang, Xiaoyu Yue, Hua Zhang, Ming Sun, Xuehao Fu

“…Chrysanthemum, an ornamental genus with considerable medicinal value, is one of the most economically important floricultural crops in the world. …”
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Proteome and Metabolome Alterations in Radish (<i>Raphanus sativus</i> L.) Seedlings Induced by Inoculation with <i>Agrobacterium tumefaciens</i> by Nadezhda Frolova, Daria Gorbach, Christian Ihling, Tatiana Bilova, Anastasia Orlova, Elena Lukasheva, Ksenia Fedoseeva, Irina Dodueva, Lyudmila A. Lutova, Andrej Frolov

“…This might be a part of the plant’s adaptation response to tumor-induced hypoxic stress, which most likely involved activation of sugar signaling.…”
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Network pharmacological investigation and experimental verification of the peel of Zea mays L. regulating metabolic reprogramming in the treatment of diabetic nephropathy by Andong Wang, Yuru Yang, Yaonan He, Guangtong Chen, Bai Ling, Bai Ling, Xiaotian Cheng, Xiaotian Cheng

“…BackgroundZea mays L. is one of the most significant genes in the Gramineae family, and the peel of Zea mays L. …”
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An alteration in the expression of cell wall structural proteins increases cell surface exposure of adhesins to promote virulence in Candida glabrata by Yaling Zhang, Shengwei Gong, Kang Xiong, Xiangtai Yu, Xinreng Mo, Chang Su, Yang Lu

“…Here, we applied RNA sequencing and an in vivo invasive infection model to elucidate the prompt response of C. glabrata during infection. Fungal transcriptomes show a dramatic alteration in the expression of Srp1/Tip1-family cell wall structural proteins during systemic infection. …”
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Selection and Validation of Reference Genes for RT-qPCR in Protonemal Tissue of the Desiccation-Tolerant Moss <i>Pseudocrossidium replicatum</i> Under Multiple Abiotic Stress Condi... by Rosa María Nava-Nolazco, Selma Ríos-Melendez, Santiago Valentín Galván-Gordillo, Angélica C. Martínez-Navarro, Mishael Sánchez-Pérez, Rocio Alejandra Chavez-Santoscoy, Martha Bibbins-Martínez, Ignacio Eduardo Maldonado-Mendoza, Analilia Arroyo-Becerra, Miguel Angel Villalobos-López

“…Our group is interested in identifying and characterising differentially expressed genes in response to abiotic stress in this species. However, a collection of validated reference genes for RT-qPCR analysis is essential to normalise the expression of genes in response to the conditions of interest. …”
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Genome-Wide Identification and Expression Analysis of the <i>CLAVATA3/ESR</i>-Related Gene Family in Tiger Nut by Maria Gancheva, Nina Kon’kova, Alla Solovyeva, Lavrentii Danilov, Konstantin Gusev, Ludmila Lutova

“…In this study, we identified 34 <i>CLE</i> genes in the genomes, proteomes, and transcriptomes of <i>C. esculentus</i> (<i>CeCLE</i>). …”
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LINE-1 transposition into murine Thyroglobulin results in congenital thyroid dysplasia. by Wendy J Bailey, Bart M G Smits, Zoltan Erdos, John M Gaspar, Pamela Lane, Sabu Kuruvilla, Thomas W Rosahl, Douglas Thudium, Jingzhou Wang, Warren E Glaab, Melissa MacGowan, Heather Multari, Christine Cumo, Adam Navis, Thomas Forest

“…Analysis of the thyroid transcriptome suggested that the presence of the LINE-1 interferes with the Tg gene splicing, resulting in exclusion of exon 26 from most Tg transcripts in animals homozygous (HOM) for the insertion. …”
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