Mechanisms of miRNA-Mediated Gene Regulation from Common Downregulation to mRNA-Specific Upregulation by Ayla Valinezhad Orang, Reza Safaralizadeh, Mina Kazemzadeh-Bavili

“…Discovered in 1993, micoRNAs (miRNAs) are now recognized as one of the major regulatory gene families in eukaryotes. To date, 24521 microRNAs have been discovered and there are certainly more to come. …”
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Comparative genomics of Aspergillus nidulans and section Nidulantes by Sebastian Theobald, Tammi Vesth, Jane L. Nybo, Jens C. Frisvad, Inge Kjærbølling, Stephen Mondo, Kurt LaButti, Sajeet Haridas, Robert Riley, Alan A. Kuo, Asaf A. Salamov, Jasmyn Pangilinan, Anna Lipzen, Maxim Koriabine, Mi Yan, Kerrie Barry, Alicia Clum, Ellen K. Lyhne, Elodie Drula, Ad Wiebenga, Astrid Müller, Ronnie J.M. Lubbers, Roland S. Kun, Ana Carolina dos Santos Gomes, Miia R. Mäkelä, Bernard Henrissat, Blake A. Simmons, Jon K. Magnuson, Jakob B. Hoof, Uffe H. Mortensen, Paul S. Dyer, Michelle Momany, Thomas O. Larsen, Igor V Grigoriev, Scott E. Baker, Ronald P. de Vries, Mikael R. Andersen

“…Aspergillus nidulans is an important model organism for eukaryotic biology and the reference for the section Nidulantes in comparative studies. …”
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The history of Drosophila studies: steps in the development of genetics by N. N. Yurchenko, A. V. Ivannikov, I. K. Zakharov

“…Owing to Drosophila’s biologic features, it became a universal eukaryotic model for genetic, embryological, morphological, physiological, molecular, and cellular studies. …”
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eEF-2K Deficiency Boosts the Virus-Specific Effector CD8⁺ T Cell Responses During Viral Infection by Liqing Wang, Benny Shone Song, Rayansh Poojary, Xiaofang Xiong, Xingcong Ren, Jin-Ming Yang, Jianxun Song

“…In this study, we revealed a critical role of eukaryotic elongation factor-2 kinase (eEF-2K), a negative regulator of protein synthesis, in regulating T cells during vaccinia virus (VACV) infection. …”
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eIF3 engages with 3’-UTR termini of highly translated mRNAs by Santi Mestre-Fos, Lucas Ferguson, Marena I Trinidad, Nicholas T Ingolia, Jamie HD Cate

“…Here, we investigate the role of eukaryotic initiation factor 3 (eIF3) in early differentiation of human pluripotent stem cell (hPSC)-derived neural progenitor cells (NPCs). …”
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Lawsonia intracellularis T3SS effector LI0758, an Rce1 ortholog, activates MAPK and NF-κB signaling in mammalian cells by Yuanxiu Zhong, Yiyun Duan, Fenju Lai, Jinhua Zhang, Yimin Dai

“…Bioinformatics analyses indicate that LI0758 is an ortholog of Rce1, a eukaryotic CAAX protein endoprotease, sharing a similar subcellular localization on the endoplasmic reticulum (ER). …”
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Periodic Distribution of a Putative Nucleosome Positioning Motif in Human, Nonhuman Primates, and Archaea: Mutual Information Analysis by Daniela Sosa, Pedro Miramontes, Wentian Li, Víctor Mireles, Juan R. Bobadilla, Marco V. José

“…Alu repetitive elements contribute to the most fundamental structure of nucleosome positioning in higher Eukaryotes. In some regions of primate chromosomes, the distribution of the decamer shows symmetrical patterns including inverted repeats.…”
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Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy by Carmina Lichauco, Eric J Foss, Tonibelle Gatbonton-Schwager, Nelson F Athow, Brandon Lofts, Robin Acob, Erin Taylor, James J Marquez, Uyen Lao, Shawna Miles, Antonio Bedalov

“…The association between late replication timing and low transcription rates in eukaryotic heterochromatin is well known, yet the specific mechanisms underlying this link remain uncertain. …”
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Comprehensive Analysis of the Proteome of <i>S. cerevisiae</i> Wild-Type and <i>pdr</i>5Δ Cells in Response to Bisphenol A (BPA) Exposure by Valentina Rossio, Joao A. Paulo

“…To investigate the impact of BPA on eukaryotic cells, we analyzed the proteome changes of wild-type and <i>PDR5</i>-deleted <i>S. cerevisiae</i> strains exposed to different doses of BPA using sample multiplexing-based proteomics. …”
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CysQ of , a Protozoa, May Have Been Acquired from Bacteria by Horizontal Gene Transfer by Ji Young Lee, Sangsoo Kim

“…According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, the sulfate assimilation pathway, where CysQ plays an important role, is well conserved in most eukaryotes as well as prokaryotes. However, the Apicomplexa, including C. parvum, largely lack orthologous genes of the pathway, suggesting its loss in those protozoan lineages. …”
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Specialized contact sites regulate the fusion of chlamydial inclusion membranes by Christine Linton, Jordan Wesolowski, Anna Lobley, Toshiyuki Yamaji, Kentaro Hanada, Fabienne Paumet

“…This regulatory mechanism contrasts with eukaryotic or viral fusion systems that are either composed of multiple proteins or use a change in pH to initiate membrane fusion. …”
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Multi-tissue characterization of the constitutive heterochromatin proteome in Drosophila identifies a link between satellite DNA organization and transposon repression. by Ankita Chavan, Lena Skrutl, Federico Uliana, Melanie Pfister, Franziska Brändle, Laszlo Tirian, Delora Baptista, Dominik Handler, David Burke, Anna Sintsova, Pedro Beltrao, Julius Brennecke, Madhav Jagannathan

“…Noncoding satellite DNA repeats are abundant at the pericentromeric heterochromatin of eukaryotic chromosomes. During interphase, sequence-specific DNA-binding proteins cluster these repeats from multiple chromosomes into nuclear foci known as chromocenters. …”
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Protein multiplicity: exemplifying an overwhelmingly likely pattern of molecular evolution? by Les Hatton, Greg Warr

“…We show that the predictions of the CoHSI theory are borne out to a high degree of statistical robustness for the multiplicious proteins of eukaryotes, bacteria, archaea, and viruses whether considered separately or in totality. …”
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Unidirectional MCM translocation away from ORC drives origin licensing by Agata Butryn, Julia F. Greiwe, Alessandro Costa

“…Abstract The MCM motor of the eukaryotic replicative helicase is loaded as a double hexamer onto DNA by the Origin Recognition Complex (ORC), Cdc6, and Cdt1. …”
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The systemic evolutionary theory of the origin of cancer (SETOC): an update by Antonio Mazzocca, Giovanni Ferraro, Giovanni Misciagna

“…Abstract The Systemic Evolutionary Theory of the Origin of Cancer (SETOC) is a recently proposed theory founded on two primary principles: the cooperative and endosymbiotic process of cell evolution as described by Lynn Margulis, and the integration of complex systems operating in eukaryotic cells, which is a core concept in systems biology. …”
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Functional Characterization of the Canine Heme-Regulated eIF2α Kinase: Regulation of Protein Synthesis by Kimon C. Kanelakis, Jayashree Pyati, Pamela C. Wagaman, Jui Chang Chuang, Young Yang, Nigel P. Shankley

“…The heme-regulated inhibitor (HRI) negatively regulates protein synthesis by phosphorylating eukaryotic initiation factor-2α (eIF2α) thereby inhibiting protein translation. …”
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Genome-wide identification and analysis of the NF-Y transcription factor family reveal its potential roles in tobacco (Nicotiana tabacum L.) by Zhen Tian, Luyao Xue, Jincun Fu, Wenting Song, Baojian Wang, Jinhao Sun, Xiujiang Yue, Fanrui Cheng, Jingjing Mao, Jiangtao Chao, Dawei Wang, Shaopeng Li

“…Nuclear Factor Y (NF-Y) represents a group of transcription factors commonly present in higher eukaryotes, typically consisting of three subunits: NF-YA, NF-YB, and NF-YC. …”
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Alternative Splicing of Cdh23 Exon 68 Is Regulated by RBM24, RBM38, and PTBP1 by Nana Li, Haibo Du, Rui Ren, Yanfei Wang, Zhigang Xu

“…Alternative splicing plays a pivotal role in modulating the function of eukaryotic proteins. In the inner ear, many genes undergo alternative splicing, and errors in this process lead to hearing loss. …”
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ALKBH5 suppresses gastric cancer tumorigenesis and metastasis by inhibiting the translation of uncapped WRAP53 RNA isoforms in an m6A-dependent manner by Ziqi Zheng, Feizhi Lin, Baiwei Zhao, Guoming Chen, Chengzhi Wei, Xiaojiang Chen, Runcong Nie, Ruopeng Zhang, Zhoukai Zhao, Zhiwei Zhou, Yuanfang Li, Weigang Dai, Yijia Lin, Yongming Chen

“…Abstract The N6-methyladenosine (m6A) modification serves as an essential epigenetic regulator in eukaryotic cells, playing a significant role in tumorigenesis and cancer progression. …”
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EFFECT OF FLANKING SEQUENCES ON THE ACCURACY OF THE RECOGNITION OF TRANSCRIPTION FACTOR BINDING SITES by T. M. Khlebodarova, D. Yu. Oshchepkov, V. G. Levitsky, O. A. Podkolodnaya, E. V. Ignatieva, E. A. Ananko, I. L. Stepanenko, N. A. Kolchanov

“…The development of in vitro methods produced new experimental information on protein binding to DNA, which is accumulated in databases and used in studies of mechanisms regulating gene expression and in the development of computer-assisted methods of binding site recognition in pro- and eukaryotic genomes. However, it is still questionable to what extent sequences selected in vitro reflect the actual structures of natural transcription factor (TF) binding sites. …”
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