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mRNA processing

Jaijam Suwanwela, Kanokporn Hansamuit, Jeeranan Manokawinchoke, Noppadol Sa-Ard-Iam, Rangsini Mahanonda, Prasit Pavasant, Thanaphum Osathanon
OBJECTIVE: Jagged1 regulates several biological functions in human periodontal ligament cells (hPDLs). The present study aimed to evaluate mRNA expression profiling of Jagged1 treated hPDLs using microarray technique. METHODS: Notch ligands, Jagged1, were indirectly immobilized on tissue culture surface. Subsequently, hPDLs were seeded on Jagged1 immobilized surface and maintained in growth medium for 48 h. Total RNA was collected and processed. Gene expression profiling was examined using microarray technique...
February 18, 2019: Oral Diseases
Mirjana Babić Leko, Vera Župunski, Jason Kirincich, Dinko Smilović, Tibor Hortobágyi, Patrick R Hof, Goran Šimić
Two clinically distinct diseases, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), have recently been classified as two extremes of the FTD/ALS spectrum. The neuropathological correlate of FTD is frontotemporal lobar degeneration (FTLD), characterized by tau-, TDP-43-, and FUS-immunoreactive neuronal inclusions. An earlier discovery that a hexanucleotide repeat expansion mutation in chromosome 9 open reading frame 72 ( C9orf72 ) gene causes ALS and FTD established a special subtype of ALS and FTLD with TDP-43 pathology (C9FTD/ALS)...
2019: Behavioural Neurology
Hui He, Xiufang Li, Yuling He
Background: Given that the therapeutic effect of hyperbaric oxygen (HBO) therapy on traumatic brain injury (TBI) has been debated for a long time, it is necessary to clarify the mechanism underlying the effect of HBO on acute TBI. Methods: This study investigated the effect of HBO therapy on neuronal apoptosis induced by acute TBI using the mouse model of TBI. The number of apoptotic cells and expression of apoptosis-associated factors (including caspase 3, pAkt/Akt, pGSK3β/GSK3β, and β-catenin) in pericontusional cortices of mice exposed to sham, TBI, and TBI + HBO treatment were measured and analyzed using TUNEL assay, quantitative reverse-transcription PCR, and Western blot...
2019: Neuropsychiatric Disease and Treatment
Jingxin Wang, John Hammond, Kristen A Johnson
In the process of drug development of RNA-targeting small molecules, elucidating the structural changes upon their interactions with target RNA sequences is desired. We herein provide a detailed in vitro and in-cell selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) protocol to study the RNA structural change in the presence of an experimental drug for spinal muscular atrophy (SMA), survival of motor neuron (SMN)-C2, and in exon 7 of the pre-mRNA of the SMN2 gene. In in vitro SHAPE, an RNA sequence of 140 nucleotides containing SMN2 exon 7 is transcribed by T7 RNA polymerase, folded in the presence of SMN-C2, and subsequently modified by a mild 2'-OH acylation reagent, 2-methylnicotinic acid imidazolide (NAI)...
January 30, 2019: Journal of Visualized Experiments: JoVE
Hazuki Takahashi, Harshita Sharma, Piero Carninci
Targeted-protein enhancement is of importance not only for the study of biological processes but also for therapeutic and biotechnological applications. Here, we present a method to selectively up-regulate protein expression of desired genes in cultured cells by means of synthetic antisense non-coding RNAs known as SINEUPs. This positive control of gene expression is at the post-transcriptional level and exerted by an inverted short interspersed nuclear element (SINE) repeat at the 3' end of SINEUPs that comprises its effector domain (ED)...
February 1, 2019: Journal of Visualized Experiments: JoVE
Patricia P Coltri, Maria G P Dos Santos, Guilherme H G da Silva
Cancer arises from alterations in several metabolic processes affecting proliferation, growth, replication and death of cells. A fundamental challenge in the study of cancer biology is to uncover molecular mechanisms that lead to malignant cellular transformation. Recent genomic analyses revealed that many molecular alterations observed in cancers come from modifications in the splicing process, including mutations in pre-mRNA regulatory sequences, mutations in spliceosome components, and altered ratio of specific splicing regulators...
February 17, 2019: Wiley Interdisciplinary Reviews. RNA
Hongjun Bian, Yi Zhou, Dawei Zhou, Yongsheng Zhang, Deya Shang, Jianni Qi
Non-coding RNAs (ncRNAs) have been emerging players in cell development, differentiation, proliferation and apoptosis. Based on their differences in length and structure, they are subdivided into several categories including long non-coding RNAs (lncRNAs >200nt), stable non-coding RNAs (60-300nt), microRNAs (miRs or miRNAs, 18-24nt), circular RNAs, piwi-interacting RNAs (26-31nt) and small interfering RNAs (about 21nt). Therein, miRNAs not only directly regulate gene expression through pairing of nucleotide bases between the miRNA sequence and a specific mRNA that leads to the translational repression or degradation of the target mRNA, but also indirectly affect the function of downstream genes through interactions with lncRNAs and circRNAs...
February 17, 2019: Journal of Cellular and Molecular Medicine
Ram Pratap Singh, Enrique Escobar, David Wildt, Seema Patel, Guilherme M J Costa, Budhan Pukazhenthi
Complete spermatogenesis has been achieved in vitro in mouse testicular explants with resulting sperm used to produce pups after Intra Cytoplasm Sperm Injection and Embryo Transfer. In the present study, we evaluated the influence of sphingosine-1-phosphate (S1P) on spermatogenesis of frozen-thawed lamb testis explants in vitro. Thawed testicular pieces were cultured for 12 d on agarose blocks in serum-free growth medium containing 0, 2, 5 or 10 μM S1P. At the end of D6 and D12, some pieces were fixed and processed for histology...
January 31, 2019: Theriogenology
Gustavo Núñez-Acuña, Cristian Gallardo-Escárate
The salmon louse Lepeophtheirus salmonis is a marine ectoparasite that has a detrimental impact on salmon farms. Genomic knowledge of adult stages is critical to understand the reproductive success and lifecycle completion of this species. Here, we report a comprehensive characterization of the L. salmonis miRNome with emphasis on the sex-differences of the parasite. Small-RNA sequencing was conducted on males and females, and mRNA-sequencing was also conducted to identify miRNA-targets at these stages. Based on bioinformatics analyses, 3101 putative miRNAs were found in L...
February 13, 2019: Marine Genomics
Huijuan Li, Hong Chang, Xueqin Song, Weipeng Liu, Lingyi Li, Lu Wang, Yongfeng Yang, Luwen Zhang, Wenqiang Li, Yan Zhang, Dong-Sheng Zhou, Xingxing Li, Chen Zhang, Yiru Fang, Yan Sun, Jia-Pei Dai, Xiong-Jian Luo, Yong-Gang Yao, Xiao Xiao, Luxian Lv, Ming Li
Recent European genome-wide association studies (GWAS) have revealed strong statistical correlations between MDD and numerous zero-to-high linked variants in the genomic region containing major histocompatibility complex (MHC) genes (MHC region), but the underlying molecular mechanisms are still unclear. To better understand the roles of this genomic region in the neurobiology of MDD, we applied a convergent functional genomics approach to integrate GWAS data of MDD relevant biological phenotypes, gene-expression analyses results obtained from brain samples, and genetic analyses of independent Chinese MDD samples...
February 16, 2019: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
Emilie Noe, Nicolas Bonneau, Marie-Line Fournier, Stéphanie Caillé, Martine Cador, Catherine Le Moine
Opiate withdrawal induces an early aversive state which can be associated to contexts and/or cues, and re-exposure to either these contexts or cues may participate in craving and relapse. Nucleus accumbens (NAC), hippocampus (HPC) and basolateral amygdala (BLA) are crucial substrates for acute opiate withdrawal, and for withdrawal memory retrieval. Also HPC and BLA interacting with the NAC are suggested to respectively mediate the processing of context and cue representations of drug-related memories. Here we used a paradigm of conditioned suppression of operant food seeking, allowing to differentiate context and cue related responses, to study the influence of withdrawal memories on operant behavior and the underlying neural substrates...
February 13, 2019: Neurobiology of Learning and Memory
Fei Ma, Xu Liu, Shibo Zhou, Wenjie Li, Chunxiao Liu, Michelle Chadwick, Cheng Qian
LncRNAs have been proven to play crucial roles in various processes of breast cancer. LncRNA FGF13-AS1 has been identified as one of the 25 downregulated lncRNAs in breast cancer through analyzing data from two cohorts and TCGA by another group of our lab. In this study, we report that FGF13-AS1 expression is decreased in breast cancer tissue compared with corresponding normal tissue, and the downregulation of FGF13-AS1 is associated with poor prognosis. Functional studies show that FGF13-AS1 inhibits breast cancer cells proliferation, migration, and invasion by impairing glycolysis and stemness properties...
February 13, 2019: Cancer Letters
Patrycja Przygodzka, Izabela Papiewska-Pająk, Helena Bogusz-Koziarska, Ewelina Sochacka, Joanna Boncela, M Anna Kowalska
Epithelial-to-mesenchymal transition (EMT) in cancer cells, represents early stages of metastasis and is a promising target in colorectal cancer (CRC) therapy. There have been many attempts to identify markers and key pathways induced throughout EMT but the process is complex and depends on the cancer type and tumour microenvironment. Here we used the colon cancer cell line HT29, which stably overexpressed Snail, the key transcription factor in early EMT, as a model for colorectal adenocarcinoma cells with a pro-metastatic phenotype...
February 15, 2019: Scientific Reports
Swetlana Rot, Tom Kaune, Helge Taubert, Thomas Greither, Johanna Kotrba, Antje Güttler, Henri Wichmann, Udo Bilkenroth, Andreas Wienke, Bilal Al-Nawas, Matthias Bache, Dirk Vordermark, Claudia Wickenhauser, Daniel Bethmann, Alexander W Eckert, Matthias Kappler
BACKGROUND: The human leucine-rich, repeat-containing G protein-coupled receptor 5 (LGR5) is a stem cell marker in numerous adult tissues and is overexpressed in a large number of human carcinoma including colon cancer, breast cancer and oral squamous cell carcinomas (OSCC). The role of the full length transcript (LGR5FL) in progression and prognosis of several cancers was reported. However, the biological function of three splice variants of LGR5 (LGR5Δ5, LGR5Δ8 and LGR5Δ5-8) has yet to be thoroughly investigated...
February 15, 2019: BMC Cancer
Charles Nelson, Victor Ambros
let-7 is a microRNA whose sequence and roles in developmental progression are conserved Generally, transcription of let-7 primary transcript ( pri-let- 7) occurs early in development, whilst processing of the mature let-7 microRNA arises during cellular differentiation. In C. elegans and other animals, the RNA binding protein LIN-28 post-transcriptionally inhibits let-7 biogenesis at early developmental stages, but the mechanisms by which LIN-28 does this are not fully understood. Nor is it understood how the developmental regulation of let-7 might influence the expression or activities of other microRNAs of the same seed family...
February 15, 2019: Development
Cinthia Amiñoso, María Gordillo-Marañón, Jaime Hernández, Jesús Solera
Glycogen storage disease type II, or Pompe disease, is an autosomal recessive disorder caused by deficiency of lysosomal acid alpha-glucosidase (GAA). We performed genetic analysis to confirm the diagnosis of Pompe disease in a 61-year-old patient with progressive weakness in extremities, severe Sleep Apnea-Hypopnea Syndrome, a significant reduction of alpha-glucosidase in liquid sample of peripheral blood and muscular biopsy diagnosis. GAA gene sequencing showed the patient is homozygous for the splice-site mutation c...
December 15, 2018: Neuromuscular Disorders: NMD
Manchi Rajesh, Biju Sam Kamalam, Alexander Ciji, Md Shabaz Akhtar, Nityanand Pandey, Subodh Gupta, Debajit Sarma, Narrotam Prasad Sahu, Atul Kumar Singh
In vertebrates, myogenic regulatory factors (MRFs) play an important role in muscle growth through the processes of cell determination and differentiation. Herein, we report the molecular characterisation of two MRFs, myogenin (myog) and myogenic factor 6 (myf6) in Indian snow trout Schizothorax richardsonii. The full length mRNA sequence of Srmyog and Srmyf6 was 1437 and 1296 bp, with an ORF of 762 and 720 bp, encoding a putative protein of 253 and 239 amino acids, respectively. In silico analysis and predicted tertiary protein structure revealed that both these nuclear localized MRFs contained the highly conserved basic helix loop helix motif, to potentially aid in dimerization with functional partners and DNA binding...
February 12, 2019: Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology
Mike Hook, Fuyi Xu, Elena Terenina, Wenyuan Zhao, Athena Starlard-Davenport, Pierre Mormede, Byron C Jones, Megan K Mulligan, Lu Lu
Tac2 is expressed in a number of areas throughout the brain, including the hippocampus. However, knowledge about its function has been only well explored in the hypothalamus in the context of reproductive health. In this study, we identified and validated increased hippocampal Tac2 mRNA expression in response to chronic mild stress in mice. Expression quantitative trait locus (eQTL) analysis showed Tac2 is cis-regulated in the hippocampus. Using a systems genetics approach, we constructed a Tac2 co-expression network to better understand the relationship between Tac2 and the hippocampal stress response...
February 12, 2019: Gene
Ruili Han, Xiangnan Wang, Xinlei Wang, Yaping Guo, Donghua Li, Guoxi Li, Yanbin Wang, Xiangtao Kang, Zhuanjian Li
Zinc finger proteins are a class of transcription factors with finger-like domains and have diverse uses in biological processes, including development, differentiation, and metabolism. In this study, we identified the absence of the 24 bp sequence in the third exon of the zinc finger protein 764-like (ZNF764L) gene that lead to the production of two new transcripts, ZNF764L-SV1 and ZNF764L-SV2, and the sum of the expression levels of the two transcripts is approximately equal the total RNA expression level...
February 12, 2019: Gene
Raymond D Socha, John Chen, Nobuhiko Tokuriki
Genetic variation among orthologous genes has been largely formed through neutral genetic drift while maintaining their functional role. Yet, because the evolution of gene occurs within each organismal host, their sequence changes are also associated with adaptation to specific environment. Thus, genetic variation can create critical phenotypic variation, particularly when genes are transferred to a new host by horizontal gene transfer (HGT). Unveiling "hidden phenotypic variation" is particularly important for genes that confer resistance to antibiotics...
February 12, 2019: Journal of Molecular Biology
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