Identification and functional characterization of the RPP13 gene family in potato (Solanum tuberosum L.) for disease resistance by Baoqi Yuan, Chuang Li, Qingfeng Wang, Qi Yao, Xiaowei Guo, Yuhang Zhang, Zhongwei Wang

“…Phylogenetic analysis grouped these genes into four evolutionary clades, indicating a high level of conservation. Cis-regulatory element analysis identified that the promoter region of StRPP13-26 is enriched with pathogen-responsive elements such as the WUN-motif and MYC, suggesting its potential role in disease defense. …”
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Evolutionary analysis of DELLA proteins in sweet potato and related species reveals their roles in development and stress responses by Zhidan Zuo, Haoqiang Zhao, Yue Fan, Yixuan Zhu, Wenpeng Song, Hong Zhai, Shaozhen He, Huan Zhang, Ning Zhao, Qingchang Liu, Shaopei Gao

“…A multitude of shared cis-regulatory elements related to stress responses were identified in the DELLA gene promoters. …”
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Regulation and Function of the Peg3 Imprinted Domain by Hongzhi He, Joomyeong Kim

“…This Peg3 domain shares several features with the other imprinted domains, including an evolutionarily conserved domain structure, along with transcriptional co-regulation through shared cis regulatory elements, as well as functional roles in controlling fetal growth rates and maternal-caring behaviors. …”
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Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells by John D. Blair, Austin Hartman, Fides Zenk, Philipp Wahle, Giovanna Brancati, Carol Dalgarno, Barbara Treutlein, Rahul Satija

“…Here we present Phospho-seq, an integrated approach that aims to quantify cytoplasmic and nuclear proteins, including those with post-translational modifications, and to connect their activity with cis-regulatory elements and transcriptional targets. We utilize a simplified benchtop antibody conjugation method to create large custom neuro-focused antibody panels for simultaneous protein and scATAC-seq profiling on whole cells, alongside both experimental and computational strategies to incorporate transcriptomic measurements. …”
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A mechanism-informed deep neural network enables prioritization of regulators that drive cell state transitions by Xi Xi, Jiaqi Li, Jinmeng Jia, Qiuchen Meng, Chen Li, Xiaowo Wang, Lei Wei, Xuegong Zhang

“…Applied to single-cell multi-omics data on type 2 diabetes and hair follicle development, regX reliably prioritizes key transcription factors and candidate cis-regulatory elements that drive cell state transitions. …”
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Omics based technology application in poultry meat research by Huaijun Zhou, Austin Quach, Mahesh Nair, Behnam Abasht, Byungwhi Kong, Brian Bowker

“…This Poultry Science Association symposium paper includes 5 sections that cover: 1) functional annotation of cis-regulatory elements in the genome informs genetic control of complex traits in poultry, 2) mass spectrometry for proteomics, metabolomics, and lipidomics, 3) proteomic approaches to investigate meat quality, 4) spatial transcriptomics and metabolomics studies of wooden breast disease, and 5) multiomics analyses on chicken meat quality and spaghetti meat. …”
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Characterization of lysine acetyltransferase and deacetylase genes and their roles in anthocyanin biosynthesis in grape by Wen Tang, Feiyue Li, Danni Yang, Mengyu Xu, Jinggui Fang, Suwen Lu

“…Promoter region analysis revealed numerous cis-regulatory elements linked to light, hormone, and stress responsiveness. …”
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New insights into the salt-responsive regulation in eelgrass at transcriptional and post-transcriptional levels by Huan Zhao, Huan Zhao, Xu Dong, Xu Dong, Dazuo Yang, Dazuo Yang, Qingchao Ge, Qingchao Ge, Peng Lu, Peng Lu, Chang Liu, Chang Liu

“…Eelgrass (Zostera marina), a representative marine angiosperm, serves as an ideal model for investigating the mechanisms underlying salt tolerance.MethodsThis study integrated mRNA, sRNA, and degradome sequencing data to identify key genes associated with salt tolerance in eelgrass.ResultsThe results indicate that a series of genes involved in biological processes such as “in response to water deprivation” and “biosynthesis of secondary metabolites” respond to salt stress. Analysis of cis-regulatory elements and expression similarities suggests that the ABA synthase 9-cis-epoxycarotenoid dioxygenase (NCED) may be regulated by ERF members, while phenylalanine ammonia-lyase (PAL) may be regulated by MYB members. …”
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Genome wide identification of MATE and ALMT gene family in lentil (Lens culinaris Medikus) and expression profiling under Al stress condition by Ankita Tripathi, Dharmendra Singh, Jyotika Bhati, Deepti Singh, Jyoti Taunk, Jawaher Alkahtani, Abdulrahman Al-Hashimi, Madan Pal Singh

“…The MATE promoter regions harboured many stress responsive as well as Al resistance transcription factor 1 related cis-regulatory elements. Predicted 3D (three-dimensional) structure and molecular docking revealed that 5 LcMATE proteins could bind citrate and contain amino acids related to its secretion via citrate exuding motif and other neighbouring sites. …”
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Polymorphism of the LCT gene regulatory region in Turkicspeaking populations of the Altay-Sayan region (southern Siberia) by I. V. Pilipenko, M. S. Pristyazhnyuk, V. F. Kobzev, M. I. Voevoda, A. S. Pilipenko

“…At a molecular-genetic level, lactase persistence is determined by the presence of specific alleles of polymorphic sites in cis-regulatory elements of the LCT gene located on chromosome 2q21. …”
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Genome-Wide Identification and In Silico Expression Analysis of <i>CCO</i> Gene Family in <i>Citrus clementina</i> (Citrus) in Response to Abiotic Stress by Sadaf Sarwar, Adnan Sami, Muhammad Zeshan Haider, Layba Tasawar, Jannat Akram, Arsalan Ahmad, Muhammad Shafiq, Haitham E. M. Zaki, Gabrijel Ondrasek, Muhammad Shafiq Shahid

“…Promoter sequencing analysis indicated the presence of different cis-regulatory elements that likely interacted with phytohormones, such as auxin and abscisic acid among others. …”
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Identification and expression analysis of P-type ATPase IIIA subfamily in Puccinia Striiformis f. sp. tritici by Yingjie Sun, Hong Tao, Hong Han, Yiping Zou, Yingyu Xue, Shiwen Chen, Fei Tao

“…Thirty-six major cis-regulatory elements were detected within the PMA gene family members. …”
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Comparative analysis of NR and NiR gene families reveals nitrite formation mechanisms in two Toona species by Yi Wei, Jianhua Dai, Yanru Fan, Hengfu Yin, Jun Liu, Xiaojiao Han

“…All the seven NR and NiR genes in both T. sinensis and T. ciliata harbor various cis-regulatory elements within their promoter sequences, which are associated with development, stress response, and hormonal regulation. …”
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THE BIOSYNTHESIS REGULATION OF POTATO STEROIDAL GLYCOALKALOIDS by K. A. Ivanova, S. V. Gerasimova, E. K. Khlestkina

“…As a promising target for reducing SGA levels in tubers, the genes encoding PGA enzymes (belonging to the CYP72 subfamily cytochrome-P450-dependent monooxygenases catalyzing the conversion of hydrocholesterol to trihydrocholesterol) and SGT (SGA glycosyltransferases that catalyze the conversion of solanidine to its toxic glycosylated derivatives α-solanine and α-chaconine) are considered. Cis-regulatory elements in the promoter regions of some glycoalkaloid biosynthesis genes, including elements responsible for tissue-specific expression, are described. …”
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Genome-wide identification of MGT gene family in soybean (Glycine max) and their expression analyses under magnesium stress conditions by Ammar Anwar, Junaid Akhtar, Saba Aleem, Maida Aleem, Muhammad Khuram Razzaq, Saud Alamri, Qasim Raza, Iram Sharif, Arooj Iftikhar, Shehreen Naseer, Zaheer Ahmed, Iqrar Ahmed Rana, Waheed Arshad, Muhammad Imran Khan, Javaid Akhter Bhat, Muqadas Aleem, Abdel-Rhman Z. Gaafar, Mohamed S. Hodhod

“…GmMGTs showed diverse tissue-specific and stress-response expression patterns due to the presence of stress-related cis-regulatory elements in their promoter regions. Under Mg-deficiency and surplus stress conditions, a decrease in root length, shoot length, and root and shoot fresh as well dry weight in susceptible genotypes showed the variegated expression of MGTs in soybean genotypes. …”
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