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mRNA processing

Nadin Haase, Wolf Holtkamp, Reinhard Lipowsky, Marina Rodnina, Sophia Rudorf
During protein synthesis, the nascent peptide chain traverses the peptide exit tunnel of the ribosome. We monitor the co-translational movement of the nascent peptide using a fluorescent probe attached to the N-terminus of the nascent chain. Due to fluorophore quenching, the time-dependent fluorescence signal emitted by an individual peptide is determined by co-translational events, such as secondary structure formation and peptide-tunnel interactions. To obtain information on these individual events, the measured ensemble fluorescence signal has to be decomposed into position-dependent intensities...
August 10, 2018: Nucleic Acids Research
Qiu Xiao, Jiawei Luo, Cheng Liang, Guanghui Li, Jie Cai, Pingjian Ding, Ying Liu
Long non-coding RNAs (lncRNAs) have been shown to be involved in multiple biological processes and play critical roles in tumorigenesis. Numerous lncRNAs have been discovered in diverse species, but the functions of most lncRNAs still remain unclear. Meanwhile, their expression patterns and regulation mechanisms are also far from being fully understood. With the advances of high-throughput technologies, the increasing availability of genomic data creates opportunities for deciphering the molecular mechanism and underlying pathogenesis of human diseases...
August 7, 2018: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Eirini Vasarmidi, Stella Sarantoulaki, Athina Trachalaki, George Margaritopoulos, Eleni Bibaki, Demetrios A Spandidos, Nikolaos Tzanakis, Katerina Antoniou
Idiopathic pulmonary fibrosis (IPF) is a chronic and irreversible interstitial lung disease with a poor prognosis and limited therapeutic options. Over the past decade, research efforts have focused on the pathogenetic mechanisms involved in this enigmatic lung disease. Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease often complicated by the development of interstitial lung disease (ILD), leading to high mortality and morbidity. Autophagy is a process regulating the turnover of subcellular components and organelles, and represents a major cellular homeostatic mechanism...
August 6, 2018: Molecular Medicine Reports
Dorota Pastuszak-Lewandoska, Daria Domańska-Senderowska, Adam Antczak, Jacek Kordiak, Paweł Górski, Karolina H Czarnecka, Monika Migdalska-Sęk, Ewa Nawrot, Justyna M Kiszałkiewicz, Ewa Brzeziańska-Lasota
BACKGROUND: The interleukin (IL)-4/IL-13/signal transducer and activator of transcription (STAT) 6 signaling pathway and the SOCS3 gene, one of its main regulators, constitute an important link between the inflammation process in the epithelial cells and inflammatory-related tumorigenesis. The present study is the first to evaluate IL-4, IL-13, STAT6, and SOCS3 mRNA expression in non-small cell lung carcinoma (NSCLC) histopathological subtypes. METHODS: Gene expression levels were assessed using TaqMan® probes by quantitative reverse transcription PCR (qRT-PCR) in lung tumor samples and unchanged lung tissue samples...
August 13, 2018: Molecular Diagnosis & Therapy
Yan Guo, Liwan Xing, Chaodong Qian, Zhishan Ding, Bo Jin
Atherosclerosis is the commonest cause of death in the world and one of the most important processes that occurs with increasing age because it is accompanied by progressive endothelial dysfunction. Recent studies demonstrated that Sirtuin 1 (SIRT1) might potentially affect cell senescence. However, the effect of SIRT1 on the regulation of human umbilical vein endothelial cell (HUVEC) senescence with total flavonoids (TFs) has not been addressed previously. This study investigated how SIRT1 functions in the process of HUVEC senescence when TFs are present and identified the potential molecular mechanisms involved...
2018: Evidence-based Complementary and Alternative Medicine: ECAM
Wentao Cai, Cong Li, Shuli Liu, Chenghao Zhou, Hongwei Yin, Jiuzhou Song, Qin Zhang, Shengli Zhang
Long non-coding RNAs (lncRNAs) have emerged as a novel class of regulatory molecules involved in various biological processes. However, their role in milk performance is unknown. Here, whole transcriptome RNA sequencing was used to generate the lncRNA transcriptome profiles in mammary tissue samples from 6 Chinese Holstein cows with 3 extremely high and 3 low milk protein percentage phenotypes. In this study, 6,450 lncRNA transcripts were identified through 5 stringent steps and filtration by coding potential...
2018: Frontiers in Genetics
Zhangyi Ouyang, Chao Ren, Feng Liu, Gaole An, Xiaochen Bo, Wenjie Shu
A-to-I editing, as a post-transcriptional modification process mediated by ADAR, plays a crucial role in many biological processes in metazoans. However, how and to what extent A-to-I editing diversifies and shapes population diversity at the RNA level are largely unknown. Here, we used 462 mRNA-sequencing samples from five populations of the Geuvadis Project and identified 16,518 A-to-I editing sites, with false detection rate of 1.03%. These sites form the landscape of the RNA editome of the human genome...
August 13, 2018: Scientific Reports
Hongyan Ren, Chiara Fabbri, Rudolf Uher, Marcella Rietschel, Ole Mors, Neven Henigsberg, Joanna Hauser, Astrid Zobel, Wolfgang Maier, Mojca Z Dernovsek, Daniel Souery, Annamaria Cattaneo, Gerome Breen, Ian W Craig, Anne E Farmer, Peter McGuffin, Cathryn M Lewis, Katherine J Aitchison
A key feature of major depressive disorder (MDD) is anhedonia, which is a predictor of response to antidepressant treatment. In order to shed light on its genetic underpinnings, we conducted a genome-wide association study (GWAS) followed by investigation of biological pathway enrichment using an anhedonia dimension for 759 patients with MDD in the GENDEP study. The GWAS identified 18 SNPs associated at genome-wide significance with the top one being an intronic SNP (rs9392549) in PRPF4B (pre-mRNA processing factor 4B) located on chromosome 6 (P = 2...
August 13, 2018: Translational Psychiatry
Rik G H Lindeboom, Arne H Smits, Matteo Perino, Gert Jan C Veenstra, Michiel Vermeulen
Early Xenopus development is characterized by a poor correlation between global mRNA and protein abundances due to maternal mRNA and protein loading. Therefore, proteome profiling is necessary to study gene expression dynamics during early Xenopus development. In contrast to mammals, single Xenopus eggs and embryos contain enough protein to allow identification and quantification of thousands of proteins using mass spectrometry-based proteomics. In addition to investigating developmental processes, single egg or blastomere proteomes can be used to study cell-to-cell variability at an unprecedented depth...
August 13, 2018: Cold Spring Harbor Protocols
Goldie Y L Lui, Carla Grandori, Christopher J Kemp
Cyclin-dependent kinase 12 (CDK12) belongs to the cyclin-dependent kinase (CDK) family of serine/threonine protein kinases that regulate transcriptional and post-transcriptional processes, thereby modulating multiple cellular functions. Early studies characterised CDK12 as a transcriptional CDK that complexes with cyclin K to mediate gene transcription by phosphorylating RNA polymerase II. CDK12 has been demonstrated to specifically upregulate the expression of genes involved in response to DNA damage, stress and heat shock...
August 13, 2018: Journal of Clinical Pathology
Lihua Wang, Hui Luo, Wangcheng Hu, Yuekun Yang, Ni Hong, Guoping Wang, Aiming Wang, Liping Wang
BACKGROUND: Pear ring rot, caused by Botryosphaeria species, is responsible for substantial economic losses by causing severe recession of pear tree growth in China. Mycovirus-mediated hypovirulence in plant pathogenic fungi is a crucial biological method to control fungal diseases. METHODS: We conducted a large-scale and comprehensive transcriptome analysis to identify mRNA in B. dothidea in response to mycovirus. De novo sequencing technology from four constructed libraries of LW-C (Botryosphaeria dothidea chrysovirus 1, BdCV1), LW-P (Botryosphaeria dothidea partitivirus 1, BdPV1), LW-CP (LW-1 strain infection with BdCV1 and BdPV1), and Mock (free virus) was used to investigate and compare gene expression changes in B...
August 13, 2018: Virology Journal
Bo Wang, Dongping Li, Rocio Rodriguez-Juarez, Allison Farfus, Quinn Storozynsky, Megan Malach, Emily Carpenter, Jody Filkowski, Anne E Lykkesfeldt, Olga Kovalchuk
BACKGROUND: Breast cancer is the most common malignancy in women worldwide. Although the endocrine therapy that targets estrogen receptor α (ERα) signaling has been well established as an effective adjuvant treatment for patients with ERα-positive breast cancers, long-term exposure may eventually lead to the development of acquired resistance to the anti-estrogen drugs, such as fulvestrant and tamoxifen. A better understanding of the mechanisms underlying antiestrogen resistance and identification of the key molecules involved may help in overcoming antiestrogen resistance in breast cancer...
August 13, 2018: BMC Cancer
Guang Xu, Ting Li, Jiayi Chen, Changyan Li, Haixin Zhao, Chengcheng Yao, Hua Dong, Kaiqing Wen, Kai Wang, Jie Zhao, Qing Xia, Tao Zhou, Huafeng Zhang, Ping Gao, Ailing Li, Xin Pan
Aged and damaged mitochondria can be selectively degraded by specific autophagic elimination, termed mitophagy. Defects in mitophagy have been increasingly linked to several diseases including neurodegenerative diseases, metabolic diseases and other aging-related diseases. However, the molecular mechanisms of mitophagy are not fully understood. Here, we identify PRPF8 (pre-mRNA processing factor 8), a core component of the spliceosome, as an essential mediator in hypoxia-induced mitophagy from an RNAi screen based on a fluorescent mitophagy reporter, mt-Keima...
August 13, 2018: Autophagy
Chang You, Bertha J Vandegrift, Huaibo Zhang, Amy W Lasek, Subhash C Pandey, Mark S Brodie
BACKGROUND: The ventral tegmental area (VTA) is important for alcohol-related reward and reinforcement. Mouse VTA neurons are hyposensitive to γ-aminobutyric acid (GABA) during ethanol withdrawal, and GABA responsiveness is normalized by in vitro treatment with histone deacetylase inhibitors (HDACi). The present study examined the effect of a systemically-administered HDACi, suberanilohydroxamic acid (SAHA) on GABA sensitivity and related molecular changes in VTA neurons during withdrawal after chronic ethanol intake in rats...
August 13, 2018: Alcoholism, Clinical and Experimental Research
Lei Zhang, Yufeng Wang, Liang Wang, Guozhi Yin, Weimin Li, Yao Xian, Wei Yang, Qingguang Liu
MicroRNAs (miRNAs) regulate a variety of development and physiologic processes, and play prominent roles in the initiation and progression of human cancers including hepatocellular carcinoma (HCC). MiR-23c is recently emerging as a cancer-associated miRNA, while its expression status and functional role in HCC are unrevealed yet. Here, we found that miR-23c underexpression was associated with the tumorigenesis of HCC based on TCGA data. qRT-PCR analysis revealed that miR-23c expression was reduced in HCC tissues and cell lines...
August 10, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Mohammad Askandar Iqbal, Shweta Arora, Gopinath Prakasam, George A Calin, Mansoor Ali Syed
Lung cancer is the cardinal cause of cancer-related deaths with restricted recourse of therapy throughout the world. Clinical success of therapies is not very promising due to - late diagnosis, limited therapeutic tools, relapse and the development of drug resistance. Recently, small ∼20-24 nucleotides molecules called microRNAs (miRNAs) have come into the limelight as they play outstanding role in the process of tumorigenesis by regulating cell cycle, metastasis, angiogenesis, metabolism and apoptosis. miRNAs essentially regulate gene expression via post-transcriptional regulation of mRNA...
August 10, 2018: Molecular Aspects of Medicine
Anna Stachurska, Tadeusz Sarna
Melanopsin is a G protein-coupled receptor with a peak sensitivity in the blue part of the spectrum, which plays a key role in non-visual light-mediated signalling. Recently its importance in forming visual pathway as well as its role in blood vessels photorelaxation was also revealed. Melanopsin was discovered in 1998 in Xenopus leavis. Since then the melanopsin presence was demonstrated across the species. The existence of two melanopsin genes (opn4m and opn4x) as well as melanopsin isoforms resulting from alternative splicing contribute to the variety in melanopsin-regulated processes...
August 13, 2018: Photochemistry and Photobiology
David S Fischer, Fabian J Theis, Nir Yosef
Temporal changes to the concentration of molecular species such as mRNA, which take place in response to various environmental cues, can often be modeled as simple continuous functions such as a single pulse (impulse) model. The simplicity of such functional representations can provide an improved performance on fundamental tasks such as noise reduction, imputation and differential expression analysis. However, temporal gene expression profiles are often studied with models that treat time as a categorical variable, neglecting the dependence between time points...
August 8, 2018: Nucleic Acids Research
Jorge Cruz-Reyes, Blaine H M Mooers, Pawan K Doharey, Joshua Meehan, Shelly Gulati
RNA editing causes massive remodeling of the mitochondrial mRNA transcriptome in trypanosomes and related kinetoplastid protozoa. This type of editing involves the specific insertion or deletion of uridylates (U) directed by small noncoding guide RNAs (gRNAs). Because U-insertion exceeds U-deletion by a factor of 10, editing increases the nascent mRNA size by up to 55%. In Trypanosoma brucei, the editing apparatus uses ~40 proteins and >1,200 gRNAs to create the functional open reading frame in 12 mRNAs...
August 12, 2018: Wiley Interdisciplinary Reviews. RNA
Qixin Leng, Jen-Hui Tsou, Min Zhan, Feng Jiang
PURPOSE: Fucosyltransferases (FUTs) catalyze fucosylation, which plays a central role in biological processes. Aberrant fucosylation is associated with malignant transformation. Here we investigated whether transcriptional levels of genes coding the FUTs in plasma could provide cell-free circulating biomarkers for lung cancer. METHODS: mRNA expression of all 13 Futs (Fut1-11, Pofut1, and Pofut2) was evaluated by PCR assay in 48 lung tumor tissues and the 48 matched noncancerous lung tissues, and plasma of 64 lung cancer patients and 32 cancer-free individuals to develop plasma Fut biomarkers...
August 12, 2018: Journal of Cancer Research and Clinical Oncology
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