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https://www.readbyqxmd.com/read/28640894/characterization-and-analysis-of-long-non-coding-rna-lncrna-in-in-vitro-and-ex-vivo-derived-cardiac-progenitor-cells
#1
Baron Arnone, Jake Y Chen, Gangjian Qin
Recent advancements in cell-based therapies for the treatment of cardiovascular disease (CVD) show continuing promise for the use of transplanted stem and cardiac progenitor cells (CPCs) to promote cardiac restitution. However, a detailed understanding of the molecular mechanisms that control the development of these cells remains incomplete and is critical for optimizing their use in such therapy. Long non-coding (lnc) RNA has recently emerged as a crucial class of regulatory molecules involved in directing a variety of critical biological processes including development, homeostasis and disease...
2017: PloS One
https://www.readbyqxmd.com/read/28640868/functional-metabolomics-as-a-tool-to-analyze-mediator-function-and-structure-in-plants
#2
Celine Davoine, Ilka N Abreu, Khalil Khajeh, Jeanette Blomberg, Brendan N Kidd, Kemal Kazan, Peer M Schenk, Lorenz Gerber, Ove Nilsson, Thomas Moritz, Stefan Björklund
Mediator is a multiprotein transcriptional co-regulator complex composed of four modules; Head, Middle, Tail, and Kinase. It conveys signals from promoter-bound transcriptional regulators to RNA polymerase II and thus plays an essential role in eukaryotic gene regulation. We describe subunit localization and activities of Mediator in Arabidopsis through metabolome and transcriptome analyses from a set of Mediator mutants. Functional metabolomic analysis based on the metabolite profiles of Mediator mutants using multivariate statistical analysis and heat-map visualization shows that different subunit mutants display distinct metabolite profiles, which cluster according to the reported localization of the corresponding subunits in yeast...
2017: PloS One
https://www.readbyqxmd.com/read/28637286/structure-seq2-sensitive-and-accurate-genome-wide-profiling-of-rna-structure-in-vivo
#3
Laura E Ritchey, Zhao Su, Yin Tang, David C Tack, Sarah M Assmann, Philip C Bevilacqua
RNA serves many functions in biology such as splicing, temperature sensing, and innate immunity. These functions are often determined by the structure of RNA. There is thus a pressing need to understand RNA structure and how it changes during diverse biological processes both in vivo and genome-wide. Here, we present Structure-seq2, which provides nucleotide-resolution RNA structural information in vivo and genome-wide. This optimized version of our original Structure-seq method increases sensitivity by at least 4-fold and improves data quality by minimizing formation of a deleterious by-product, reducing ligation bias, and improving read coverage...
June 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28637236/the-ribosome-assembly-gene-network-is-controlled-by-the-feedback-regulation-of-transcription-elongation
#4
Fernando Gómez-Herreros, Thanasis Margaritis, Olga Rodríguez-Galán, Vicent Pelechano, Victoria Begley, Gonzalo Millán-Zambrano, Macarena Morillo-Huesca, Mari Cruz Muñoz-Centeno, José E Pérez-Ortín, Jesús de la Cruz, Frank C P Holstege, Sebastián Chávez
Ribosome assembly requires the concerted expression of hundreds of genes, which are transcribed by all three nuclear RNA polymerases. Transcription elongation involves dynamic interactions between RNA polymerases and chromatin. We performed a synthetic lethal screening in Saccharomyces cerevisiae with a conditional allele of SPT6, which encodes one of the factors that facilitates this process. Some of these synthetic mutants corresponded to factors that facilitate pre-rRNA processing and ribosome biogenesis...
June 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28635594/translation-repression-via-modulation-of-the-cytoplasmic-poly-a-binding-protein-in-the-inflammatory-response
#5
Xu Zhang, Xiaoli Chen, Qiuying Liu, Shaojie Zhang, Wenqian Hu
Gene expression is precisely regulated during the inflammatory response to control infection and limit the detrimental effects of inflammation. Here, we profiled global mRNA translation dynamics in the mouse primary macrophage-mediated inflammatory response and identified hundreds of differentially translated mRNAs. These mRNAs' 3'UTRs have enriched binding motifs for several RNA-binding proteins, which implies extensive translational regulatory networks. We characterized one such protein, Zfp36, as a translation repressor...
June 21, 2017: ELife
https://www.readbyqxmd.com/read/28635587/ictv-virus-taxonomy-profile-ophioviridae
#6
María Laura García, Elena Dal Bó, John V da Graça, Selma Gago-Zachert, John Hammond, Pedro Moreno, Tomohide Natsuaki, Vicente Pallás, Jose A Navarro, Carina A Reyes, Gabriel Robles Luna, Takahide Sasaya, Ioannis E Tzanetakis, Anna María Vaira, Martin Verbeek, Ictv Report Consortium
The Ophioviridae is a family of filamentous plant viruses, with single-stranded negative, and possibly ambisense, RNA genomes of 11.3-12.5 kb divided into 3-4 segments, each encapsidated separately. Virions are naked filamentous nucleocapsids, forming kinked circles of at least two different contour lengths. The sole genus, Ophiovirus, includes seven species. Four ophioviruses are soil-transmitted and their natural hosts include trees, shrubs, vegetables and bulbous or corm-forming ornamentals, both monocots and dicots...
June 21, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28634911/novel-insights-into-a-reputably-irreversible-process-combined-mrna-and-mirna-profiling-of-tissue-from-vesicourethral-anastomotic-stenosis-after-radical-prostatectomy
#7
T S Worst, K Daskalova, A Steidler, K Berner-Leischner, R Röth, B Niesler, C-A Weis, M C Kriegmair, P Erben, D Pfalzgraf
PURPOSE: Until recently, tissue fibrosis-ultimately leading to permanent scaring-has been considered an irreversible process. However, recent findings indicate that it may be reversible after all. Vesicourethral anastomotic stenosis (VUAS) as fibrous narrowing is a frequent complication after radical prostatectomy with high recurrence rates and requires invasive treatment. The pathophysiology is poorly understood. Therefore, a combined mRNA and miRNA transcription profiling in tissue from VUAS was performed using nCounter technology...
June 20, 2017: World Journal of Urology
https://www.readbyqxmd.com/read/28634418/long-noncoding-rnas-as-biomarkers-in-cancer
#8
REVIEW
Luka Bolha, Metka Ravnik-Glavač, Damjan Glavač
Long noncoding RNAs (lncRNAs) are a relatively well-characterized class of noncoding RNA (ncRNA) molecules, involved in the regulation of various cell processes, including transcription, intracellular trafficking, and chromosome remodeling. Their deregulation has been associated with the development and progression of various cancer types, the fact which makes them suitable as biomarkers for cancer diagnosis and prognosis. In recent years, detection of cancer-associated lncRNAs in body fluids of cancer patients has proven itself as an especially valuable method to effectively diagnose cancer...
2017: Disease Markers
https://www.readbyqxmd.com/read/28634372/dna-methylation-changes-in-endometrium-and-correlation-with-gene-expression-during-the-transition-from-pre-receptive-to-receptive-phase
#9
Viktorija Kukushkina, Vijayachitra Modhukur, Marina Suhorutšenko, Maire Peters, Reedik Mägi, Nilufer Rahmioglu, Agne Velthut-Meikas, Signe Altmäe, Francisco J Esteban, Jaak Vilo, Krina Zondervan, Andres Salumets, Triin Laisk-Podar
The inner uterine lining (endometrium) is a unique tissue going through remarkable changes each menstrual cycle. Endometrium has its characteristic DNA methylation profile, although not much is known about the endometrial methylome changes throughout the menstrual cycle. The impact of methylome changes on gene expression and thereby on the function of the tissue, including establishing receptivity to implanting embryo, is also unclear. Therefore, this study used genome-wide technologies to characterize the methylome and the correlation between DNA methylation and gene expression in endometrial biopsies collected from 17 healthy fertile-aged women from pre-receptive and receptive phase within one menstrual cycle...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634160/high-throughput-characterization-of-cascade-type-i-e-crispr-guide-efficacy-reveals-unexpected-pam-diversity-and-target-sequence-preferences
#10
Becky Xu Hua Fu, Michael Wainberg, Anshul Kundaje, Andrew Z Fire
Interactions between Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNAs and CRISPR-associated (Cas) proteins form an RNA-guided adaptive immune system in prokaryotes. The adaptive immune system utilizes segments of the genetic material of invasive foreign elements in the CRISPR locus. The loci are transcribed and processed to produce small CRISPR RNAs (crRNAs), with degradation of invading genetic material directed by a combination of complementarity between RNA and DNA and in some cases recognition of adjacent motifs called PAMs (Protospacer Adjacent Motifs)...
June 20, 2017: Genetics
https://www.readbyqxmd.com/read/28633549/an-update-on-zika-vaccine-developments
#11
Anna Durbin, Annelies Wilder-Smith
The devastating consequences of congenital Zika virus (ZIKV) infection led to a global response directed toward a better understanding of the epidemiology and pathogenesis of ZIKV and to efforts at vaccine development. As a result, there are currently 45 ZIKV vaccine candidates in development. Areas covered: Both traditional (purified inactivated, live attenuated, viral-vectored, recombinant sub-unit) and novel (DNA, self-replicating RNA, mRNA) vaccine platforms are being utilized. For emergency use, vaccines that are appropriate for women of child-bearing age (including pregnant women) are being developed...
June 21, 2017: Expert Review of Vaccines
https://www.readbyqxmd.com/read/28632173/gene-expression-profiling-reveals-potential-players-of-left-right-asymmetry-in-female-chicken-gonads
#12
Zhiyi Wan, Yanan Lu, Lei Rui, Xiaoxue Yu, Fang Yang, Chengfang Tu, Zandong Li
Most female birds develop only a left ovary, whereas males develop bilateral testes. The mechanism underlying this process is still not completely understood. Here, we provide a comprehensive transcriptional analysis of female chicken gonads and identify novel candidate side-biased genes. RNA-Seq analysis was carried out on total RNA harvested from the left and right gonads on embryonic day 6 (E6), E12, and post-hatching day 1 (D1). By comparing the gene expression profiles between the left and right gonads, 347 differentially expressed genes (DEGs) were obtained on E6, 3730 were obtained on E12, and 2787 were obtained on D1...
June 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28630433/gut-microbiota-of-liver-transplantation-recipients
#13
Li-Ying Sun, Yun-Sheng Yang, Wei Qu, Zhi-Jun Zhu, Lin Wei, Zhi-Sheng Ye, Jian-Rui Zhang, Xiao-Ye Sun, Zhi-Gui Zeng
The characteristics of intestinal microbial communities may be affected by changes in the pathophysiology of patients with end-stage liver disease. Here, we focused on the characteristics of intestinal fecal microbial communities in post-liver transplantation (LT) patients in comparison with those in the same individuals pre-LT and in healthy individuals. The fecal microbial communities were analyzed via MiSeq-PE250 sequencing of the V4 region of 16S ribosomal RNA and were then compared between groups. We found that the gut microbiota of patients with severe liver disease who were awaiting LT was significantly different from that of healthy controls, as represented by the first principal component (p = 0...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28630425/reconstructing-cell-cycle-pseudo-time-series-via-single-cell-transcriptome-data
#14
Zehua Liu, Huazhe Lou, Kaikun Xie, Hao Wang, Ning Chen, Oscar M Aparicio, Michael Q Zhang, Rui Jiang, Ting Chen
Single-cell mRNA sequencing, which permits whole transcriptional profiling of individual cells, has been widely applied to study growth and development of tissues and tumors. Resolving cell cycle for such groups of cells is significant, but may not be adequately achieved by commonly used approaches. Here we develop a traveling salesman problem and hidden Markov model-based computational method named reCAT, to recover cell cycle along time for unsynchronized single-cell transcriptome data. We independently test reCAT for accuracy and reliability using several data sets...
June 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28630098/comparative-micrornaome-analysis-of-the-testis-and-ovary-of-the-chinese-giant-salamander
#15
Rui Chen, Jian Du, Lin Ma, Li-Qing Wang, Sheng-Song Xie, Chang-Ming Yang, Xian-Yong Lan, Chuan-Ying Pan, Wu-Zi Dong
MicroRNAs (miRNAs) are 18-24 nucleotides non-coding RNAs that regulate gene expression by post-transcriptional suppression of mRNA. The Chinese giant salamander (CGS, Andrias davidianus), which is an endangered species, has become one of important models of animal evolution; however, no miRNA studies on this species have been conducted. In this study, two small RNA libraries of CGS ovary and testis were constructed using deep sequencing technology. A bioinformatics pipeline was developed to distinguish miRNA sequences from other classes of small RNAs represented in the sequencing data...
June 19, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28630090/t-cell-transcriptomes-from-paroxysmal-nocturnal-hemoglobinuria-patients-reveal-novel-signaling-pathways
#16
Kohei Hosokawa, Sachiko Kajigaya, Keyvan Keyvanfar, Wangmin Qiao, Yanling Xie, Danielle M Townsley, Xingmin Feng, Neal S Young
Paroxysmal nocturnal hemoglobinuria (PNH) is a rare acquired disorder originating from hematopoietic stem cells and is a life-threating disease characterized by intravascular hemolysis, bone marrow (BM) failure, and venous thrombosis. The etiology of PNH is a somatic mutation in the phosphatidylinositol glycan class A gene (PIG-A) on the X chromosome, which blocks synthesis of the glycolipid moiety and causes deficiency in GPI-anchored proteins. PNH is closely related to aplastic anemia, in which T cells mediate destruction of BM...
June 19, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28630030/alzheimer-s-brains-show-inter-related-changes-in-rna-and-lipid-metabolism
#17
Shahar Barbash, Benjamin P Garfinkel, Rotem Maoz, Alon Simchovitz, Bettina Nadorp, Alessandro Guffanti, Estelle R Bennett, Courtney Nadeau, Andreas Türk, Lukas Paul, Torsten Reda, Yan Li, Aron S Buchman, David S Greenberg, Alexander Seitz, David A Bennett, Patrick Giavalisco, Hermona Soreq
Alzheimer's disease (AD) involves changes in both lipid and RNA metabolism, but it remained unknown if these differences associate with AD's cognition and/or post-mortem neuropathology indices. Here, we report RNA-sequencing evidence of inter-related associations between lipid processing, cognition level, and AD neuropathology. In two unrelated cohorts, we identified pathway-enriched facilitation of lipid processing and alternative splicing genes, including the neuronal-enriched NOVA1 and hnRNPA1. Specifically, this association emerged in temporal lobe tissue samples from donors where postmortem evidence demonstrated AD neuropathology, but who presented normal cognition proximate to death...
June 16, 2017: Neurobiology of Disease
https://www.readbyqxmd.com/read/28629365/evaluation-and-improvement-of-the-regulatory-inference-for-large-co-expression-networks-with-limited-sample-size
#18
Wenbin Guo, Cristiane P G Calixto, Nikoleta Tzioutziou, Ping Lin, Robbie Waugh, John W S Brown, Runxuan Zhang
BACKGROUND: Co-expression has been widely used to identify novel regulatory relationships using high throughput measurements, such as microarray and RNA-seq data. Evaluation studies on co-expression network analysis methods mostly focus on networks of small or medium size of up to a few hundred nodes. For large networks, simulated expression data usually consist of hundreds or thousands of profiles with different perturbations or knock-outs, which is uncommon in real experiments due to their cost and the amount of work required...
June 19, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28628975/highly-expressed-long-non-coding-rna-nnt-as1-promotes-cell-proliferation-and-invasion-through-wnt-%C3%AE-catenin-signaling-pathway-in-cervical-cancer
#19
Fangfang Hua, Shanshan Liu, Lihong Zhu, Ning Ma, Shan Jiang, Jun Yang
BACKGROUND: Cervical cancer is the most common gynecological malignancies in women worldwide. The previous study showed that lncRNA NNT-AS1 could play an important role in tumor development and metastasis of colorectal cancer. However, little is known about the function of NNT-AS1 in cervical cancer. The aim of this study was to investigate the expression profile of NNT-AS1 in cervical cancer and assess its possible molecular mechanism. METHODS: Relative expression levels of NNT-AS1 in cervical cancer tissues were determined by qRT-PCR...
June 13, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28628896/cholinergic-neuron-gene-expression-differences-captured-by-translational-profiling-in-a-mouse-model-of-alzheimer-s-disease
#20
Paul M McKeever, TaeHyung Kim, Andrew R Hesketh, Laura MacNair, Denise Miletic, Giorgio Favrin, Stephen G Oliver, Zhaolei Zhang, Peter St George-Hyslop, Janice Robertson
Cholinergic neurotransmission is impaired in Alzheimer's disease (AD), and loss of basal forebrain cholinergic neurons is a key component of disease pathogenicity and symptomatology. To explore the molecular basis of this cholinergic dysfunction, we paired translating ribosome affinity purification (TRAP) with RNA sequencing (TRAP-Seq) to identify the actively translating mRNAs in anterior forebrain cholinergic neurons in the TgCRND8 mouse model of AD. Bioinformatic analyses revealed the downregulation of 67 of 71 known cholinergic-related transcripts, consistent with cholinergic neuron dysfunction in TgCRND8 mice, as well as transcripts related to oxidative phosphorylation, neurotrophins, and ribosomal processing...
May 25, 2017: Neurobiology of Aging
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