Identification of disease-related aberrantly spliced transcripts in myeloma and strategies to target these alterations by RNA-based therapeutics by Daisuke Ogiya, Zuzana Chyra, Sigitas J. Verselis, Morgan O’Keefe, Jacquelyn Cobb, Ivane Abiatari, Srikanth Talluri, Anjana Anilkumar Sithara, Teru Hideshima, Michael P. Chu, Roman Hájek, David M. Dorfman, Linda M. Pilarski, Kenneth C. Anderson, Sophia Adamia

“…Whole-genome transcriptome analyses in a large cohort of MM patients demonstrated that alterations in pre-mRNA splicing (AS) are frequent in MM. This manuscript describes approaches to identify disease-specific alterations in MM and proposes RNA-based therapeutic strategies to eradicate such alterations. …”
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Sonic hedgehog signaling: Alternative splicing and pathogenic role in medulloblastoma by Meiyu Qu, Qiangqiang He, Jiahao Luo, Tingyu Shen, Ruibo Gao, Yana Xu, Chengyun Xu, Muhammad Qasim Barkat, Ling-Hui Zeng, Ximei Wu

“…Alternative splicing (AS) produces the different mRNA splicing bodies, which are then translated into multiple protein isoforms and participate in various biological functions. …”
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Coactivator-associated arginine methyltransferase 1: A versatile player in cell differentiation and development by Zhongrui Ma, Xinxing Lyu, Ning Qin, Haoyu Liu, Mengrui Zhang, Yongchao Lai, Bo Dong, Peiyuan Lu

“…CARM1 has been found to play important roles in cell differentiation and development, cell cycle progression, autophagy, metabolism, pre-mRNA splicing and transportation, and DNA replication. …”
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Circular RNAs Acting as miRNAs’ Sponges and Their Roles in Stem Cells by Juan Xiao, Shija Joseph, Mengwei Xia, Feng Teng, Xuejiao Chen, Rufeng Huang, Lihong Zhai, Wenbin Deng

“…Moreover, the expression of circRNAs is usually not correlated with their parental gene expression, indicating that they are not only a steady-state by-product of mRNA splicing but a product of variable splicing under novel regulation. …”
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Analysis of the substrate recognition state of TDP-43 to single-stranded DNA using fluorescence correlation spectroscopy by Akira Kitamura, Ai Shibasaki, Kayo Takeda, Ryoji Suno, Masataka Kinjo

“…The binding of TDP-43 to single-stranded DNA (ssDNA) or RNA is involved in transcriptional repression, regulation of RNA splicing, and RNA stabilization. Equilibrium dissociation constants (Kd) of TDP-43 and ssDNA or RNA have been determined using various methods; however, methods that can measure Kd with high sensitivity in a short time using a small amount of TDP-43 in solution would be advantageous. …”
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Ozone and nitrogen dioxide regulate similar gene expression responses in Arabidopsis but natural variation in the extent of cell death is likely controlled by different genetic loc... by Johanna Leppälä, Frank Gaupels, Enjun Xu, Luis O. Morales, Jörg Durner, Mikael Brosché

“…Further characterization of the GWAS candidate loci identified new regulators of O3 and NO2 induced cell death including ABH1, a protein that functions in abscisic acid signaling, mRNA splicing and miRNA processing. The GWAS results will facilitate further characterization of the control of programmed cell death and differences between oxidative and nitrosative stress in plants.…”
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The RNA‐binding protein Snd1/Tudor‐SN regulates hypoxia‐responsive gene expression by Juha Saarikettu, Saara Lehmusvaara, Marko Pesu, Ilkka Junttila, Juha Partanen, Petra Sipilä, Matti Poutanen, Jie Yang, Teemu Haikarainen, Olli Silvennoinen

“…Abstract Snd1 is an evolutionarily conserved RNA‐binding protein implicated in several regulatory processes in gene expression including activation of transcription, mRNA splicing, and microRNA decay. Here, we have investigated the outcome of Snd1 gene deletion in the mouse. …”
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Decryption of the survival “black box”: gene family expansion promotes the encystment in ciliated protists by Didi Jin, Chao Li, Xiao Chen, Yurui Wang, Khaled A. S. Al-Rasheid, Naomi A. Stover, Chen Shao, Tengteng Zhang

“…Like other hypotrich MAC genomes, the P. cristata MAC genome is extremely fragmented with a single gene on most chromosomes, and encodes introns that are generally small and lack a conserved branch point for pre-mRNA splicing. Gene family expansion analyses indicate that multiple gene families involved in the encystment are expanded during the evolution of P. cristata. …”
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Identification and Characterization of the Masculinizing Function of the <i>Helicoverpa armigera Masc</i> Gene by Zhongyuan Deng, Yakun Zhang, Yalu Li, Kaiyuan Huang, Xuewei Chen, Min Zhang, Jinyong Huang, Xinzhi Ni, Xianchun Li

“…Transfection of a mixture of three siRNAs of <i>HaMasc</i> into a male embryonic cell line of <i>H. armigera</i> led to the appearance of female-specific mRNA splicing isoforms of <i>H. armigera</i><i>doublesex</i> (<i>Hadsx</i>), a downstream target gene of <i>HaMasc</i> in the <i>H. armigera</i> sex determination pathway. …”
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Effects of the total replacement of fish-based diet with plant-based diet on the hepatic transcriptome of two European sea bass (<it>Dicentrarchus labrax</it>) half-sibfamilies sho... by Geay Florian, Ferraresso Serena, Zambonino-Infante Jose L, Bargelloni Luca, Quentel Claire, Vandeputte Marc, Kaushik Sachi, Cahu Chantal L, Mazurais David

“…Biological processes related to protein catabolism, amino acid transaminations, RNA splicing and blood coagulation were also found to be regulated by diet, while the expression of genes involved in protein and ATP synthesis differed between the half-sibfamilies.…”
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Molecular Characterization of a Novel Splicing Mutation Underlying Mucopolysaccharidosis (MPS) Type VI—Indirect Proof of Principle on Its Pathogenicity by Maria Francisca Coutinho, Marisa Encarnação, Liliana Matos, Lisbeth Silva, Diogo Ribeiro, Juliana Inês Santos, Maria João Prata, Laura Vilarinho, Sandra Alves

“…Special attention will be given to the use of reporter minigene systems, which may be constructed/designed to dissect the effect of this sort of alterations, providing an insight into their consequences over the normal pre-mRNA splicing process of the affected gene.…”
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From Proteomics to Personalized Medicine: The Importance of Isoflavone Dose and Estrogen Receptor Status in Breast Cancer Cells by Maria Ilieș, Alina Uifălean, Sergiu Pașca, Vishnu Mukund Dhople, Michael Lalk, Cristina Adela Iuga, Elke Hammer

“…Proteome profiling of paramagnetic beads prepared peptides by nano-LC UDMS^E and pathway enrichment analysis revealed that isoflavones affected distinct molecular pathways in MCF-7 and MDA-MB-231 cells, such as tyrosine kinases signaling pathway, cytoskeleton organization, lipid and phospholipid catabolism, extracellular matrix degradation and mRNA splicing. Also, in MCF-7 cells, low and high isoflavone doses induced different changes of the proteome, including cell cycle alterations. …”
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Identification of lncRNA and mRNA regulatory networks associated with gastric cancer progression by Ke-kang Sun, Ke-kang Sun, Chao Zu, Xiao-yang Wu, Qing-hua Wang, Peng Hua, Yi-fang Zhang, Xiao-jun Shen, Yong-you Wu

“…GO and KEGG analyses revealed several pathways and processes that were dysregulated, including the RNA transport, ECM-receptor interaction, and mRNA splicing pathways. In co-expression networks, E2F1, E2F4, and STAT2 were identified as key transcriptional regulators of these processes. …”
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Gal-3 Protein Expression and Localization in Prostate Tumours by Tânia Lima, Catarina Macedo-Silva, Diana Felizardo, João Fraga, Isa Carneiro, Carmen Jerónimo, Rui Henrique, Margarida Fardilha, Rui Vitorino

“…Gal-3 plays an important role in cell survival, mRNA splicing, and cell–cell and cell–matrix interactions. …”
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A Patient with Berardinelli-Seip Syndrome, Novel AGPAT2 Splicesite Mutation and Concomitant Development of Non-diabetic Polyneuropathy by Joanna Oswiecimska, Mateusz Dawidziuk, Tomasz Gambin, Katarzyna Ziora, Marta Marek, Sylwia Rzonca, D. Lys Guilbride, Shalini N. Jhangiani, Anna Obuchowicz, Alicja Sikora, James R. Lupski, Wojciech Wiszniewski, Pawel Gawlinski

“…Functional studies using RNA isolated from patient peripheral blood leucocytes showed abnormal RNA splicing resulting in the loss of 25 amino acids from the patient AGPAT2 protein coding sequence. …”
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Protomer alignment modulates specificity of RNA substrate recognition by Ire1 by Weihan Li, Kelly Crotty, Diego Garrido Ruiz, Mark Voorhies, Carlos Rivera, Anita Sil, R Dyche Mullins, Matthew P Jacobson, Jirka Peschek, Peter Walter

“…In metazoan cells, the Ire1 branch of the UPR initiates two functional outputs—non-conventional mRNA splicing and selective mRNA decay (RIDD). By contrast, Ire1 orthologs from Saccharomyces cerevisiae and Schizosaccharomyces pombe are specialized for only splicing or RIDD, respectively. …”
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The broad use of the Pm8 resistance gene in wheat resulted in hypermutation of the AvrPm8 gene in the powdery mildew pathogen by Lukas Kunz, Alexandros G. Sotiropoulos, Johannes Graf, Mohammad Razavi, Beat Keller, Marion C. Müller

“…The second category consisted of numerous destructive mutations to the AvrPm8 open reading frame such as disruptions of the start codon, gene truncations, gene deletions, and interference with mRNA splicing. With the exception of a single, likely ancient, gain-of-virulence mutation found in mildew isolates around the world, all AvrPm8 virulence haplotypes were found in geographically restricted regions, indicating that they occurred recently as a consequence of the frequent Pm8 use. …”
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Whole Genome Sequence of an Edible Mushroom <i>Stropharia rugosoannulata</i> (Daqiugaigu) by Shuwen Li, Shuxue Zhao, Chunhui Hu, Chengzhi Mao, Lizhong Guo, Hailong Yu, Hao Yu

“…The proteins of the stipe associated with carbon metabolism, energy production, and stress-response-related biological processes had higher abundance, whereas proteins involved in fatty acid synthesis and mRNA splicing showed higher expression in the cap than in the stipe. …”
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N6-methyladenosine (m6A) in cancer therapeutic resistance: Potential mechanisms and clinical implications by Dong Wang, Yan Zhang, Qingbo Li, Ao Zhang, Jingxuan Xu, Yu Li, Wen Li, Lin Tang, Fan Yang, Jingyan Meng

“…N6-methyladenosine (m6A) has been identified as the most common, abundant, and conserved internal transcriptional alterations of RNA modifications, regulating RNA splicing, translation, stabilization, degradation, and gene expression, and is involved in the development and progression of a variety of diseases, including cancer. …”
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Identification of Key Modules and Candidate Genes for Powdery Mildew Resistance of Wheat-<i>Agropyron cristatum</i> Translocation Line WAT-2020-17-6 by WGCNA by Mingming Yao, Xinhua Wang, Jiaohui Long, Shuangyu Bai, Yuanyuan Cui, Zhaoyi Wang, Caixia Liu, Fenglou Liu, Zhangjun Wang, Qingfeng Li

“…Gene ontology (GO) enrichment analysis showed that the six interested modules related to powdery mildew resistance were significantly enriched in N-methyltransferase activity, autophagy, mRNA splicing via spliceosome, chloroplast envelope, and AMP binding. …”
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