Stem loop binding protein promotes SARS-CoV-2 replication via -1 programmed ribosomal frameshifting by Tanxiu Chen, Ruimin Zhu, Tingfu Du, Hao Yang, Xintian Zhang, Zhixing Wang, Yong Zhang, Wenqi Quan, Bin Yin, Yunpeng Liu, Shuaiyao Lu, Xiaozhong Peng

“…Using RNA pull-down assays combined with mass spectrometry screening, we discovered five host proteins interacting with -1 PRF RNA, including Stem Loop Binding Protein (SLBP). Our findings revealed that SLBP overexpression enhanced frameshifting and promoted viral replication. …”
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Subgenic Pol II interactomes identify region‐specific transcription elongation regulators by Kevin M Harlen, L Stirling Churchman

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Characteristics of the integration sites and module structures of the Tn916 and its family by Lei Song, Jingxiu Duan, Tianren Liu, Jiaojiao Sun, Zhiling Hao

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Demonstration of the presence of the "deleted" MIR122 gene in HepG2 cells. by Ibrahim A Y Hamad, Yue Fei, Anastasia Z Kalea, Dan Yin, Andrew J P Smith, Jutta Palmen, Steve E Humphries, Philippa J Talmud, Ann P Walker

“…Several groups reported that the widely-used hepatocytic cell line HepG2 had deficient expression of miR-122, previously ascribed to deletion of the pre-mir-122 stem-loop region. We aimed to characterise this deletion by direct sequencing of 6078 bp containing the pri-mir-122 promoter and pre-mir-122 stem-loop region in HepG2 and Huh-7, a control hepatocytic cell line reported to express miR-122, supported by sequence analysis of cloned genomic DNA. …”
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RETRACTED: IAV Antagonizes Host Innate Immunity by Weakening the LncRNA-LRIR2-Mediated Antiviral Functions by Na Chen, Baoge Zhang

“…In addition, the antiviral function of LRIR2 is mainly dependent on the stem-loop structures of 1–118 nt and 575–683 nt. Taken together, IAV could antagonize host innate immunity by weakening the LncRNA-LRIR2-mediated antiviral functions. …”
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Structures and mechanisms of U6 snRNA m6A modification by METTL16 by Jue Ju, Kozo Tomita

“…The structures reveal that U6 snRNA is recruited to METTL16 through specific interactions between the C-terminal kinase-associated 1 (KA-1) domain of METTL16 and the internal stem-loop (ISL) of U6 snRNA. Upon SAM binding to the catalytic pocket within the N-terminal methyltransferase domain (MTD), U6 snRNA undergoes a structural rearrangement that positions the target adenine-containing motif at the catalytic site. …”
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High-throughput sequencing of small RNAs from pollen and silk and characterization of miRNAs as candidate factors involved in pollen-silk interactions in maize. by Xiao Ming Li, Ya Lin Sang, Xiang Yu Zhao, Xian Sheng Zhang

“…As candidates for factors associated with pollen-silk (pistil) interactions, expression patterns of the two sets of differentially expressed miRNAs were confirmed by stem-loop real-time RT-PCR. Transcript levels of 22 predicted target genes were also validated using real-time RT-PCR; most of these exhibited expression patterns contrasting with those of their corresponding miRNAs. …”
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The environmental adaptation of acidophilic archaea: promotion of horizontal gene transfer by genomic islands by Jingxuan Qiu, Huiling Tao, Hongyu Li, Xinyi Liu, Rui Liu, Muhammed Naveed Nawaz, Xingjie Wang, Liyuan Ma

“…In the majority of GIs, the GC content was lower than the average GC content of the strain genome, suggesting that GIs were typically looped out of the genomes with poor stability and transferred into those with higher stability. tRNAs with classical stem-loop secondary structures have been found at the ends of several GIs, suggesting that GIs frequently integrate near tRNAs. …”
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Evolution of mitochondrial RNA editing sites and stop codon-lacking transcripts in angiosperms by Runxian Yu, Lumei Liu, Matthias Jost, Ran Zhao, Stefan Wanke, Yuannian Jiao

“…Besides the known t-element previously identified in A. thaliana, we revealed another distinct motif that may contribute to the post-transcriptional processing of nad6 transcripts. Novel stem-loop motifs that may mediate the formation of stop codon-lacking transcripts of ccmC, sdh3 and sdh4 genes were also identified. …”
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Virus versus host plant microRNAs: who determines the outcome of the interaction? by Fatemeh Maghuly, Rose C Ramkat, Margit Laimer

“…In the current study, computational and stem-loop Reverse Transcription - Polymerase Chain Reaction (RT-PCR) approaches were employed to a) predict and validate virus encoded mature miRNAs (miRs) in 39 DNA-A sequences of the bipartite genomes of African cassava mosaic virus (ACMV) and East African cassava mosaic virus-Uganda (EACMV-UG) isolates, b) determine whether virus encoded miRs/miRs* generated from the 5'/3' harpin arms have the capacity to bind to genomic sequences of the host plants Jatropha or cassava and c) investigate whether plant encoded miR/miR* sequences have the potential to bind to the viral genomes. …”
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A Downmodulated MicroRNA Profiling in Patients with Gastric Cancer by Tao Zhang, Chang Liu, Shi Huang, Yuanping Ma, Jiansong Fang, Yuanneng Chen

“…A high-throughput miR sequencing method was applied to detect the aberrantly expressed miRs in a subset of 6 paired samples. The stem-loop quantitative real-time polymerase chain reaction (qRT-PCR) assay was subsequently performed to confirm the sequencing results in the remaining 6 paired samples. …”
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Inhibition of HIV Replication by Cyclic and Hairpin PNAs Targeting the HIV-1 TAR RNA Loop by Gregory Upert, Audrey Di Giorgio, Alok Upadhyay, Dinesh Manvar, Nootan Pandey, Virendra N. Pandey, Nadia Patino

“…In particular, we showed that the TPP conjugate of a linear 16-mer PNA targeting the apical stem-loop region of TAR impedes Tat-mediated transactivation of the HIV-1 LTR in vitro and also in cell culture systems. …”
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A cohort of mRNAs undergo high-stoichiometry NSUN6-mediated site-specific m5C modification by Yuan-Yuan Zhang, Cai-Tao Li, You-Jia Zhou, Hao Li, Jing Li, Qing-Ping Xiong, Wei Zhou, Wenze Huang, Qiangfeng Cliff Zhang, Yangfei Xiang, En-Duo Wang, Beisi Xu, Ru-Juan Liu

“…Here, we biochemically validate that NSUN6, a tRNA structure-dependent methyltransferase, independently catalyzes 5-methylcytidine (m5C) formation with robust activity on mRNA by recognizing the CUCCA motif in a certain stem-loop structure. NSUN6 employs different strategies to recognize tRNA and mRNA substrates. …”
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MICRORNA IN MONITORING OF THE EVOLUTION OF GLIAL CEREBRAL TUMORS by R. Yu. Seliverstov, M. I. Zaraiskiy, R. V. Tyurin, A. G. Naryshkin, V. G. Valerko, V. V. Semiglazov, Ch. Takahachi

“…The study of miRNA-21, -128, and -342 expressions was carried out according to the semiquantitative StemLoopRealTime protocol, using small U6 RNA as a reference gene. …”
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Feasibility of predicting the evolution of cerebral gliomas based on study of microRNA expression levels in blood plasma and saliva by R. Yu. Seliverstov, M. I. Zaraiskii, A. F. Gurchin, G. V. Kataeva, R. V. Tyurin, A. G. Naryshkin, V. G. Valerko

“…MicroRNA expression was studied in plasma and saliva according to the StemLoop-RealTime protocol, using fluorescently labeled samples with small miRNA U6 as a reference gene. …”
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An intranasal ASO therapeutic targeting SARS-CoV-2 by Chi Zhu, Justin Y. Lee, Jia Z. Woo, Lei Xu, Xammy Huu Wrynla, Livia H. Yamashiro, Fei Ji, Scott B. Biering, Erik Van Dis, Federico Gonzalez, Douglas Fox, Eddie Wehri, Arjun Rustagi, Benjamin A. Pinsky, Julia Schaletzky, Catherine A. Blish, Charles Chiu, Eva Harris, Ruslan I. Sadreyev, Sarah Stanley, Sakari Kauppinen, Silvi Rouskin, Anders M. Näär

“…We identify an LNA ASO binding to the 5′ leader sequence of SARS-CoV-2 that disrupts a highly conserved stem-loop structure with nanomolar efficacy in preventing viral replication in human cells. …”
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Analysis of miRNAs miR-125a-5p, -27a-5p, -193a-5p, -135b-5p, -451a, -495-3p and -136-5p in parental ovarian cancer cells and secreted extracellular vesicles by G. O. Skryabin, A. A. Beliaeva, A. D. Enikeev, D. V. Bagrov, A. M. Keremet, А. V. Komelkov, D. S. Elkin, D. M. Sylantieva, E. M. Tchevkina

“…Cultivation of ovarian cancer cell lines: OVCAR-3, OVCAR-4, OVCAR-8 and SKOV3; EVs isolation from conditioned medium by ultracentrifugation; EVs validation by nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), western blot analysis of exosomal markers; isolation of miRNAs from cells and EVs; analysis of miRNAs by Stem-Loop – reverse transcription-quantitative polymerase chain reaction.Results. …”
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Noncanonical Poly(A) Polymerase TENT4 Drives Expression of Subgenomic Hepatitis A Virus RNAs in Infected Cells by You Li, Ankit Gupta, Brian N. Papas, David Aponte-Diaz, Jayden M. Harris, Ichiro Misumi, Jason K. Whitmire, Craig E. Cameron, Marcos Morgan, Stanley M. Lemon

“…Surprisingly, nanopore sequencing revealed a low abundance of HAV subgenomic RNAs (hsRNAs) that extend from the 5′ end of the genome to a site within the 5′ untranslated RNA (5′UTR) immediately downstream of a stem-loop to which the ZCCHC14-TENT4 complex is recruited. …”
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Circular dichroism as a means to follow DNA gymnastics: on the shoulders of giants by M. Mills, C. Lin, M. Chauhan, H.H. Klump

“…This is the first report of DNA stem-loops self-assembled by 'foot-loop' interactions into either two-dimensional strings or three-dimensional spirals, distinguished by circular dichroism spectroscopy. …”
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