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https://www.readbyqxmd.com/read/29792948/comparative-transcriptome-analysis-reveals-significant-differences-in-gene-expression-between-appressoria-and-hyphae-in-colletotrichum-gloeosporioides
#1
Meiyu Wang, Zongshan Zhou, Jianyuan Wu, Zhirui Ji, Junxiang Zhang
Fruit rot caused mainly by Colletotrichum gloeosporioides is a major cause of pre- and/or post-harvest diseases, which seriously constrains production, marketing, and export of fruits. To infect the host, this fungus evolves a specialized infection structure called the appressorium. Extensive past studies have characterized many appressorium-related genes in C. gloeosporioides, separately. However, a comprehensive understanding of the genes contributing to appressorium formation is far from complete. Here, global changes in gene expression were analyzed between appressoria and hyphae using RNA-Seq...
May 21, 2018: Gene
https://www.readbyqxmd.com/read/29792846/adenosine-receptor-distribution-in-rhesus-monkey-ocular-tissue
#2
Krista M Beach, Li-Fang Hung, Baskar Arumugam, Earl L Smith, Lisa A Ostrin
Adenosine receptor (ADOR) antagonists, such as 7-methylxanthine (7-MX), have been shown to slow myopia progression in humans and animal models. Adenosine receptors are found throughout the body, and regulate the release of neurotransmitters such as dopamine and glutamate. However, the role of adenosine in eye growth is unclear. Evidence suggests that 7-MX increases scleral collagen fibril diameter, hence preventing axial elongation. This study used immunohistochemistry (IHC) and reverse-transcription quantitative polymerase chain reaction (RT-qPCR) to examine the distribution of the four ADORs in the normal monkey eye to help elucidate potential mechanisms of action...
May 21, 2018: Experimental Eye Research
https://www.readbyqxmd.com/read/29791798/non-natural-linker-configuration-in-2-6-dipeptidyl-anthraquinones-enhances-the-inhibition-of-tar-rna-binding-annealing-activities-by-hiv-1-nc-and-tat-proteins
#3
Alice Sosic, Irene Saccone, Caterina Carraro, Thomas Kenderdine, Elia Gamba, Giuseppe Caliendo, Angela Corvino, Ferdinando Fiorino, Paola DiVaio, Elisa Magli, Elisa Perissutti, Vincenzo Santagada, Beatrice Severino, Valentina Spada, Daniele Fabris, Francesco Frecentese, Barbara Gatto
The HIV-1 nucleocapsid (NC) protein represents an excellent molecular target for the development of antiretrovirals by virtue of its well-characterized chaperone activities, which play pivotal roles in essential steps of the viral life cycle. Our ongoing search for candidates able to impair NC binding/annealing activities led to the identification of peptidyl-anthraquinones as a promising class of nucleic acid ligands. Seeking to elucidate the inhibition determinants and increase the potency of this class of compounds, we have now explored the effects of chirality in the linker connecting the planar nucleus to the basic side chains...
May 23, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29791316/roles-of-the-exon-junction-complex-components-in-the-central-nervous-system-a-mini-review
#4
Katarzyna Bartkowska, Beata Tepper, Kris Turlejski, Ruzanna L Djavadian
The exon junction complex (EJC) consists of four core proteins: Magoh, RNA-binding motif 8A (Rbm8a, also known as Y14), eukaryotic initiation factor 4A3 (eIF4A3, also known as DDX48), and metastatic lymph node 51 (MLN51, also known as Casc3 or Barentsz), which are involved in the regulation of many processes occurring between gene transcription and protein translation. Its main role is to assemble into spliceosomes at the exon-exon junction of mRNA during splicing. It is, therefore, a range of functions concerning post-splicing events such as mRNA translocation, translation, and nonsense-mediated mRNA decay (NMD)...
May 23, 2018: Reviews in the Neurosciences
https://www.readbyqxmd.com/read/29791153/a-probabilistic-framework-for-constructing-temporal-relations-in-replica-exchange-molecular-trajectories
#5
Aditya Chattopadhyay, Min Zheng, Mark Paul Waller, U Deva Priyakumar
Knowledge of the structure and dynamics of biomolecules is essential for elucidating the underlying mechanisms of biological processes. Given the stochastic nature of many biological processes, like protein unfolding, it's almost impossible that two independent simulations will generate the exact same sequence of events, which makes direct analysis of simulations difficult. Statistical models like Markov Chains, transition networks etc. help in shedding some light on the mechanistic nature of such processes by predicting long-time dynamics of these systems from short simulations...
May 23, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29790943/mutalisk-a-web-based-somatic-mutation-analyis-toolkit-for-genomic-transcriptional-and-epigenomic-signatures
#6
Jongkeun Lee, Andy Jinseok Lee, June-Koo Lee, Jongkeun Park, Youngoh Kwon, Seongyeol Park, Hyonho Chun, Young Seok Ju, Dongwan Hong
Somatic genome mutations occur due to combinations of various intrinsic/extrinsic mutational processes and DNA repair mechanisms. Different molecular processes frequently generate different signatures of somatic mutations in their own favored contexts. As a result, the regional somatic mutation rate is dependent on the local DNA sequence, the DNA replication/RNA transcription dynamics and epigenomic chromatin organization landscape in the genome. Here, we propose an online computational framework, termed Mutalisk, which correlates somatic mutations with various genomic, transcriptional and epigenomic features in order to understand mutational processes that contribute to the generation of the mutations...
May 22, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29790665/long-noncoding-rna-ufc1-is-activated-by-e2f1-and-exerts-oncogenic-properties-by-functioning-as-a-cerna-of-foxp3
#7
Jie Xi, Jing Feng, Saitian Zeng, Ping Huang
Cervical cancer is one of the most common gynecologic cancers around the world. Long noncoding RNAs (lncRNAs) are considered to be important regulators of some biological processes. Recently, it has been reported that linc-UFC1 is a putative oncogene in some cancers. However, the functional roles of linc-UFC1 have not been investigated in cervical cancer. Here, it was demonstrated that linc-UFC1 expression was significantly increased in cervical cancer tissues, and its overexpression was associated with the poor survival of patients with cervical cancer...
May 23, 2018: Cancer Medicine
https://www.readbyqxmd.com/read/29790454/xpo5-genetic-polymorphisms-in-cancer-risk-and-prognosis
#8
Ana Sofia Patrão, Francisca Dias, Ana Luísa Teixeira, Joaquina Maurício, Rui Medeiros
miRNAs are small noncoding RNA molecules that have a very important role in gene expression regulation and, therefore, in cell homeostasis. SNPs in certain miRNA-related genes have been shown to influence cancer risk and prognosis. miRNA cellular processing is complex and involves multiple proteins. XPO5 is a key factor in this process as it is responsible for the nuclear export of the precursor pre-miRNA to the cytoplasm, where it will be further processed to its final miRNA conformation in order to be loaded to RNA inducing silencing complex to exert its regulatory effect...
May 23, 2018: Pharmacogenomics
https://www.readbyqxmd.com/read/29790275/suppressor-of-clathrin-deficiency-scd6-an-emerging-rgg-motif-translation-repressor
#9
REVIEW
Debadrita Roy, Purusharth I Rajyaguru
Translation control plays a key role in variety of cellular processes. Translation initiation factors augment translation, whereas translation repressor proteins inhibit translation. Different repressors act by distinct mechanisms to accomplish the repression process. Although messenger RNAs (mRNAs) can be repressed at various steps of translation, most repressors have been reported to target the initiation step. We focus on one such translation repressor, an Arginine-Glycine-Glycine (RGG)-motif containing protein Scd6...
May 22, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29790249/the-mechanisms-of-epigenetic-inheritance-how-diverse-are-they
#10
Oleg N Tikhodeyev
Although epigenetic inheritance (EI) is a rapidly growing field of modern biology, it still has no clear place in fundamental genetic concepts which are traditionally based on the hereditary role of DNA. Moreover, not all mechanisms of EI attract the same attention, with most studies focused on DNA methylation, histone modification, RNA interference and amyloid prionization, but relatively few considering other mechanisms such as stable inhibition of plastid translation. Herein, we discuss all known and some hypothetical mechanisms that can underlie the stable inheritance of phenotypically distinct hereditary factors that lack differences in DNA sequence...
May 22, 2018: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/29789863/intricate-relationships-between-naked-viruses-and-extracellular-vesicles-in-the-crosstalk-between-pathogen-and-host
#11
REVIEW
Susanne G van der Grein, Kyra A Y Defourny, Erik F J Slot, Esther N M Nolte-'t Hoen
It is a long-standing paradigm in the field of virology that naked viruses cause lysis of infected cells to release progeny virus. However, recent data indicate that naked virus types of the Picornaviridae and Hepeviridae families can also leave cells via an alternative route involving enclosure in fully host-derived lipid bilayers. The resulting particles resemble extracellular vesicles (EV), which are 50 nm-1 μm vesicles released by all cells. These EV contain lipids, proteins, and RNA, and generally serve as vehicles for intercellular communication in various (patho)physiological processes...
May 22, 2018: Seminars in Immunopathology
https://www.readbyqxmd.com/read/29789787/physiological-and-pathological-function-of-serine-arginine-rich-splicing-factor-4-and-related-diseases
#12
REVIEW
Wanyan Tan, Wei Wang, Qingfeng Ma
Serine/arginine-rich splicing factors (SRSFs) have one or two RNA recognition motifs in the N terminal and a serine/arginine-enriched domain in the C terminal. SRSFs are essential components of spliceosomes and are involved in alternative splicing, spliceosome assembly, mRNA export, and nonsense-mediated mRNA decay. The maintenance of cellular and tissue homeostasis relies on accurate alternative splicing, and various patterns of abnormal alternative splicing can cause different diseases. SRSF4 is associated with many physiological and pathological processes and has applications in the diagnosis and prognosis of specific diseases...
2018: BioMed Research International
https://www.readbyqxmd.com/read/29789713/upregulation-of-the-long-noncoding-rna-foxd2-as1-promotes-carcinogenesis-by-epigenetically-silencing-ephb3-through-ezh2-and-lsd1-and-predicts-poor-prognosis-in-gastric-cancer
#13
Tong-Peng Xu, Wen-Yu Wang, Pei Ma, You Shuai, Kun Zhao, Yan-Fen Wang, Wei Li, Rui Xia, Wen-Ming Chen, Er-Bao Zhang, Yong-Qian Shu
Accumulating data indicate that long noncoding RNAs (lncRNAs) serve as important modulators in biological processes and are dysregulated in diverse tumors. The function of FOXD2-AS1 in gastric cancer (GC) progression and related biological mechanisms remain undefined. A comprehensive analysis identified that FOXD2-AS1 enrichment was upregulated markedly in GC and positively correlated with a large tumor size, a later pathologic stage, and a poor prognosis. Gene-set enrichment analysis (GSEA) in GEO datasets uncovered that cell cycle and DNA replication associated genes were enriched in patients with high FOXD2-AS1 expression...
May 23, 2018: Oncogene
https://www.readbyqxmd.com/read/29789704/single-cell-rna-sequencing-for-the-study-of-development-physiology-and-disease
#14
REVIEW
S Steven Potter
An ongoing technological revolution is continually improving our ability to carry out very high-resolution studies of gene expression patterns. Current technology enables the global gene expression profiles of single cells to be defined, facilitating dissection of heterogeneity in cell populations that was previously hidden. In contrast to gene expression studies that use bulk RNA samples and provide only a virtual average of the diverse constituent cells, single-cell studies enable the molecular distinction of all cell types within a complex population mix, such as a tumour or developing organ...
May 22, 2018: Nature Reviews. Nephrology
https://www.readbyqxmd.com/read/29789581/intron-retention-and-nuclear-loss-of-sfpq-are-molecular-hallmarks-of-als
#15
Raphaelle Luisier, Giulia E Tyzack, Claire E Hall, Jamie S Mitchell, Helen Devine, Doaa M Taha, Bilal Malik, Ione Meyer, Linda Greensmith, Jia Newcombe, Jernej Ule, Nicholas M Luscombe, Rickie Patani
Mutations causing amyotrophic lateral sclerosis (ALS) strongly implicate ubiquitously expressed regulators of RNA processing. To understand the molecular impact of ALS-causing mutations on neuronal development and disease, we analysed transcriptomes during in vitro differentiation of motor neurons (MNs) from human control and patient-specific VCP mutant induced-pluripotent stem cells (iPSCs). We identify increased intron retention (IR) as a dominant feature of the splicing programme during early neural differentiation...
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29789577/long-non-coding-rna-gm2199-rescues-liver-injury-and-promotes-hepatocyte-proliferation-through-the-upregulation-of-erk1-2
#16
Qiang Gao, Yunyan Gu, Yanan Jiang, Li Fan, Zixiang Wei, Haobin Jin, Xirui Yang, Lijuan Wang, Xuguang Li, Sheng Tai, Baofeng Yang, Yan Liu
Long non-coding RNAs (lncRNAs) are a new class of regulators of various human diseases. This study was designed to explore the potential role of lncRNAs in experimental hepatic damage. In vivo hepatic damage in mice and in vitro hepatocyte damage in AML12 and NCTC1469 cells were induced by carbon tetrachloride (CCl4 ) treatments. Expression profiles of lncRNAs and mRNAs were analyzed by microarray. Bioinformatics analyses were conducted to predict the potential functions of differentially expressed lncRNAs with respect to hepatic damage...
May 22, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29789545/dynamic-transcriptomic-m-6-a-decoration-writers-erasers-readers-and-functions-in-rna-metabolism
#17
Ying Yang, Phillip J Hsu, Yu-Sheng Chen, Yun-Gui Yang
N6 -methyladenosine (m6 A) is a chemical modification present in multiple RNA species, being most abundant in mRNAs. Studies on enzymes or factors that catalyze, recognize, and remove m6 A have revealed its comprehensive roles in almost every aspect of mRNA metabolism, as well as in a variety of physiological processes. This review describes the current understanding of the m6 A modification, particularly the functions of its writers, erasers, readers in RNA metabolism, with an emphasis on its role in regulating the isoform dosage of mRNAs...
May 22, 2018: Cell Research
https://www.readbyqxmd.com/read/29788428/puf60-activated-exons-uncover-altered-3-splice-site-selection-by-germline-missense-mutations-in-a-single-rrm
#18
Jana Královicová, Ivana Ševcíková, Eva Stejskalová, Mina Obuca, Michael Hiller, David Stanek, Igor Vorechovský
PUF60 is a splicing factor that binds uridine (U)-rich tracts and facilitates association of the U2 small nuclear ribonucleoprotein with primary transcripts. PUF60 deficiency (PD) causes a developmental delay coupled with intellectual disability and spinal, cardiac, ocular and renal defects, but PD pathogenesis is not understood. Using RNA-Seq, we identify human PUF60-regulated exons and show that PUF60 preferentially acts as their activator. PUF60-activated internal exons are enriched for Us upstream of their 3' splice sites (3'ss), are preceded by longer AG dinucleotide exclusion zones and more distant branch sites, with a higher probability of unpaired interactions across a typical branch site location as compared to control exons...
May 18, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29787563/graph-complexity-analysis-identifies-an-etv5-tumor-specific-network-in-human-and-murine-low-grade-glioma
#19
Yuan Pan, Christina Duron, Erin C Bush, Yu Ma, Peter A Sims, David H Gutmann, Ami Radunskaya, Johanna Hardin
Conventional differential expression analyses have been successfully employed to identify genes whose levels change across experimental conditions. One limitation of this approach is the inability to discover central regulators that control gene expression networks. In addition, while methods for identifying central nodes in a network are widely implemented, the bioinformatics validation process and the theoretical error estimates that reflect the uncertainty in each step of the analysis are rarely considered...
2018: PloS One
https://www.readbyqxmd.com/read/29787292/signature-microrna-expression-profile-is-associated-with-spontaneous-hypertension-in-african-green-monkey
#20
Xiaojun Zhou, Jin Wang, Yunzhi Fa, Huahu Ye
Chlorocebus aethiops sabaeus, the African Green monkey (AGM), has been proved to exhibit renal vascular remodeling and spontaneous hypertension. However, little is known about the roles of microRNAs (miRNAs) in this process.Using small RNA deep sequencing, we compared the plasma miRNA expression patterns between hypertensive (HT) AGMs and normotensive (NT) AGMs. Expression of miRNAs (miR-122, miR-339, miR-296-5p) was validated independently in plasma samples from 10 HT AGMs and 10 NT AGMs (fold changes are 2...
May 22, 2018: Clinical and Experimental Hypertension: CHE
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