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https://www.readbyqxmd.com/read/29777057/glycogen-synthase-kinase-3-gsk-3-activity-regulates-mrna-methylation-in-mouse-embryonic-stem-cells
#1
Kelsie J Faulds, Jennifer N Egelston, Laura J Sedivy, Matthew K Mitchell, Sanjana Garimella, Hanna Kozlowski, Angelo D'Alessandro, Kirk C Hansen, Jeremy L Balsbaugh, Christopher J Phiel
Glycogen synthase kinase-3 (Gsk-3) activity regulates multiple signal transduction pathways, and is also a key component of the network responsible for maintaining stem cell pluripotency. Genetic deletion of Gsk-3α and Gsk-3β or inhibition of Gsk-3 activity via small molecules promotes stem cell pluripotency, yet the mechanism underlying the role for Gsk-3 in this process remains ambiguous. Another cellular process that has been shown to affect stem cell pluripotency is mRNA methylation (m6 A). Here, we describe an intersection between these components - the regulation of m6 A by Gsk-3...
May 18, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29775757/molecular-characterization-of-physis-tissue-by-rna-sequencing
#2
Christopher R Paradise, Catalina Galeano-Garces, Daniela Galeano-Garces, Amel Dudakovic, Todd A Milbrandt, Daniel B F Saris, Aaron J Krych, Marcel Karperien, Gabriel B Ferguson, Denis Evseenko, Scott M Riester, Andre J van Wijnen, A Noelle Larson
The physis is a well-established and anatomically distinct cartilaginous structure that is crucial for normal long-bone development and growth. Abnormalities in physis function are linked to growth plate disorders and other pediatric musculoskeletal diseases. Understanding the molecular pathways operative in the physis may permit development of regenerative therapies to complement surgically-based procedures that are the current standard of care for growth plate disorders. Here, we performed next generation RNA sequencing on mRNA isolated from human physis and other skeletal tissues (e...
May 15, 2018: Gene
https://www.readbyqxmd.com/read/29774201/investigation-of-experimental-factors-that-underlie-brca1-2-mrna-isoform-expression-variation-recommendations-for-utilizing-targeted-rna-sequencing-to-evaluate-potential-spliceogenic-variants
#3
Vanessa L Lattimore, John F Pearson, Margaret J Currie, Amanda B Spurdle, Bridget A Robinson, Logan C Walker
PCR-based RNA splicing assays are commonly used in diagnostic and research settings to assess the potential effects of variants of uncertain clinical significance in BRCA1 and BRCA2 . The Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium completed a multicentre investigation to evaluate differences in assay design and the integrity of published data, raising a number of methodological questions associated with cell culture conditions and PCR-based protocols. We utilized targeted RNA-seq to re-assess BRCA1 and BRCA2 mRNA isoform expression patterns in lymphoblastoid cell lines (LCLs) previously used in the multicentre ENIGMA study...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/29774045/transposon-derived-non-coding-rnas-and-their-function-in-plants
#4
REVIEW
Jungnam Cho
Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans -acting regulatory roles of TE-derived RNAs have been rarely studied...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29774021/mitotic-spindle-organizing-protein-mzta-mediates-septation-signaling-by-suppressing-the-regulatory-subunit-of-protein-phosphatase-2a-para-in-aspergillus-nidulans
#5
Ping Jiang, Shujun Zheng, Ling Lu
The proper timing and positioning of cytokinesis/septation is crucial for hyphal growth and conidiation in Aspergillus nidulans . The septation initiation network (SIN) components are a conserved spindle pole body (SPB) localized signaling cascade and the terminal kinase complex SidB-MobA, which must localize on the SPB in this pathway to trigger septation/cytokinesis. The regulatory subunit of phosphatase PP2A-ParA has been identified to be a negative regulator capable of inactivating the SIN. However, little is known about how ParA regulates the SIN pathway and whether ParA regulates the septum formation process through affecting the SPB-localized SIN proteins...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29773173/gene-expression-in-adverse-reaction-to-metal-debris-around-metal-on-metal-arthroplasty-an-rna-seq-based-study
#6
Antti Pemmari, Tiina Leppänen, Erja-Leena Paukkeri, Antti Eskelinen, Teemu Moilanen, Eeva Moilanen
Joint replacement surgery is a standard treatment of advanced osteoarthritis (OA). Since 2000, cobalt-chromium (CoCr) metal-on-metal (MoM) implants were widely used in hip arthroplasties. Some patients developed "adverse reaction to metal debris" (ARMD) around the prosthesis, resulting in a need for revision surgery. In the present study, we addressed the pathogenesis of ARMD by genome-wide expression analysis. Pseudosynovial ARMD tissue was obtained from revision surgery of Articular Surface Replacement (ASR, DePuy, Warsaw, IN, USA) hip arthroplasties...
July 2018: Journal of Trace Elements in Medicine and Biology
https://www.readbyqxmd.com/read/29772548/epigenetic-regulation-of-genes-involved-in-the-reverse-cholesterol-transport-through-interaction-with-mirnas
#7
Mohamed Zaiou, Bertrand Henri Rihn, Ahmed Bakillah
microRNAs (miRNAs) are a group of small non-coding RNA molecules known to regulate target genes at the post-transcriptional level. miRNAs are implicated in the regulation of multiple pathophysiological processes including dyslipidemia, a major risk factor for atherosclerosis. Emerging evidence suggests that miRNAs act as a novel class of epigenetic regulators of high-density lipoproteins cholesterol (HDL-C) from synthesis to clearance contributing remarkably to the pathogenesis of atherosclerosis. Accumulating studies have revealed that miRNAs such as miR-33, miR-27, miR-144, miR-758 and miR-20 are involved in the post-transcriptional control of ABCA1, ABCG1 and SCARB1 genes regulatory network of the reverse cholesterol transport (RCT)...
June 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/29772238/tgf-%C3%AE-1-induced-fascin1-expression-facilitates-the-migration-and-invasion-of-kidney-carcinoma-cells-through-erk-and-jnk-signaling-pathways
#8
Jianyu Yang, Naiwen Zhang, Ruxu Gao, Yuyan Zhu, Zhe Zhang, Xiaolong Xu, Jianfeng Wang, Zeliang Li, Xiankui Liu, Zhenhua Li, Jun Li, Jianbin Bi, Chuize Kong
Transforming growth factor-β1 (TGF-β1) plays a crucial role in the signaling network that controls cellular invasion and motility capability during tumor development. To investigate whether fascin1 plays a crucial role in TGF-β1-facilitated invasion and migration of kidney cancer cells (KCC), real-time PCR and western blotting were used to test the fascin1 expression after TGF-β1 treatment (10 ng/ml) in 769-P and OSRC cells. Fascin1 was silenced using the small interfering RNA (siRNA) technique. Cytoskeleton staining was used to test the change of Cytoskeleton...
May 14, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29769607/facs-seq-analysis-of-pax3-derived-cells-identifies-non-myogenic-lineages-in-the-embryonic-forelimb
#9
Arun J Singh, Chih-Ning Chang, Hsiao-Yen Ma, Stephen A Ramsey, Theresa M Filtz, Chrissa Kioussi
Skeletal muscle in the forelimb develops during embryonic and fetal development and perinatally. While much is known regarding the molecules involved in forelimb myogenesis, little is known about the specific mechanisms and interactions. Migrating skeletal muscle precursor cells express Pax3 as they migrate into the forelimb from the dermomyotome. To compare gene expression profiles of the same cell population over time, we isolated lineage-traced Pax3+ cells (Pax3 EGFP ) from forelimbs at different embryonic days...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769539/integrated-analysis-of-hepatic-mrna-and-mirna-profiles-identified-molecular-networks-and-potential-biomarkers-of-nafld
#10
Mingzhe Zhu, Qianlei Wang, Wenjun Zhou, Tao Liu, Lili Yang, Peiyong Zheng, Li Zhang, Guang Ji
To enhance our understanding of molecular mechanisms and mine novel biomarkers of non-alcoholic fatty liver disease (NAFLD), RNA sequencing was performed to gain hepatic expression profiles of mRNAs and miRNAs in NAFLD and normal rats. Using DESeq with thresholds of a two-fold change and a false discovery rate (FDR) less than 0.05, 336 mRNAs and 21 miRNAs were identified as differentially expressed. Among those, 17 miRNAs (e.g., miR-144-3p, miR-99a-3p, miR-200b-3p, miR-200b-5p, miR-200c-3p, etc.) might serve as novel biomarkers of NAFLD...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769325/the-ancient-phosphatidylinositol-3-kinase-signaling-system-is-a-master-regulator-of-energy-and-carbon-metabolism-in-algae
#11
Rishiram Ramanan, Quynh-Giao Tran, Dae-Hyun Cho, Jae-Eun Jeong, Byung-Hyuk Kim, Sang-Yoon Shin, Sae-Hae Choi, Kwang-Hyeon Liu, Dae-Soo Kim, Seon-Jin Lee, Jose L Crespo, Hee-Gu Lee, Hee-Mock Oh, Hee-Sik Kim
Algae undergo a complete metabolic transformation under stress by arresting cell growth, inducing autophagy, and hyper-accumulating biofuel precursors such as triacylglycerols and starch. However, the regulatory mechanisms behind this stress-induced transformation are still unclear. Here, we use biochemical, mutational, and 'omics' approaches to demonstrate that phosphatidylinositol 3-kinase (PI3K) signaling mediates the homeostasis of energy molecules and influences carbon metabolism in algae. In Chlamydomonas reinhardtii, the inhibition and knockdown (KD) of algal class III PI3K led to significantly decreased cell growth, altered cell morphology, and higher lipid and starch contents...
May 16, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29769220/retinoic-acid-induced-expression-of-hnf1%C3%AE-and-fzd4-is-required-for-pancreas-development-in-xenopus-laevis
#12
Maja B Gere, Claudia Pommerenke, Thomas Lingner, Tomas Pieler
Retinoic acid (RA) is required for pancreas specification in Xenopus and other vertebrates. However, the gene network that is directly induced by RA-signalling in this context remains to be defined. We identified the transcription factor Hnf1β and the Wnt-receptor Fzd4/Fzd4s as direct RA-target genes through RNA-sequencing of in vitro generated pancreatic explants. Functional analyses of Hnf1β and Fzd4/Fzd4s in programmed pancreatic explants and whole embryos revealed their requirement for pancreatic progenitor formation and differentiation...
May 16, 2018: Development
https://www.readbyqxmd.com/read/29767548/disruption-of-chloroplast-function-through-downregulation-of-phytoene-desaturase-enhances-the-systemic-accumulation-of-an-aphid-borne-phloem-restricted-virus
#13
Stacy L DeBlasio, Ana Rita Rebelo, Katherine Parks, Stewart Gray, Michelle Cilia
Chloroplasts play a central role in pathogen defense in plants. However, the majority of studies explaining the relationship between pathogens and chloroplasts have focused on pathogens that infect mesophyll cells. In contrast, the family Luteoviridae comprises RNA viruses that replicate and traffic exclusively in the phloem. Recently, our lab has shown that Potato leafroll virus (PLRV), the type species in the genus Polerovirus, forms an extensive interaction network with chloroplast-localized proteins, which is partially dependent on the PLRV capsid readthrough domain (RTD)...
May 16, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29767370/network-analysis-of-gene-expression
#14
Roby Joehanes
Studies have pointed out that the expression of genes are highly regulated, which result in a cascade of distinct patterns of coexpression forming a network. Identifying and understanding such patterns is crucial in deciphering molecular mechanisms that underlie the pathophysiology of diseases. With the advance of high throughput assay of messenger RNA (mRNA) and high performance computing, reconstructing such network from molecular data such as gene expression is now possible. This chapter discusses an overview of methods of constructing such networks, practical considerations, and an example...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29767230/competing-endogenous-rna-regulatory-network-in-papillary-thyroid-carcinoma
#15
Shouhua Chen, Xiaobin Fan, He Gu, Lili Zhang, Wenhua Zhao
The present study aimed to screen all types of RNAs involved in the development of papillary thyroid carcinoma (PTC). RNA‑sequencing data of PTC and normal samples were used for screening differentially expressed (DE) microRNAs (DE‑miRNAs), long non‑coding RNAs (DE‑lncRNAs) and genes (DEGs). Subsequently, lncRNA‑miRNA, miRNA‑gene (that is, miRNA‑mRNA) and gene‑gene interaction pairs were extracted and used to construct regulatory networks. Feature genes in the miRNA‑mRNA network were identified by topological analysis and recursive feature elimination analysis...
May 11, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29765976/differential-expression-profiling-of-long-noncoding-rna-and-mrna-during-osteoblast-differentiation-in-mouse
#16
Minjung Kim, Youngseok Yu, Ji-Hoi Moon, InSong Koh, Jae-Hyung Lee
Long noncoding RNAs (lncRNAs) are emerging as an important controller affecting metabolic tissue development, signaling, and function. However, little is known about the function and profile of lncRNAs in osteoblastic differentiation in mice. Here, we analyzed the RNA-sequencing (RNA-Seq) datasets obtained for 18 days in two-day intervals from neonatal mouse calvarial pre-osteoblast-like cells. Over the course of osteoblast differentiation, 4058 mRNAs and 3948 lncRNAs were differentially expressed, and they were grouped into 12 clusters according to the expression pattern by fuzzy c-means clustering...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29765519/long-noncoding-rnas-are-associated-with-metabolic-and-cellular-processes-in-the-jejunum-mucosa-of-pre-weaning-calves-in-response-to-different-diets
#17
Rosemarie Weikard, Frieder Hadlich, Harald M Hammon, Doerte Frieten, Caroline Gerbert, Christian Koch, Georg Dusel, Christa Kuehn
Long noncoding RNAs (lncRNAs) emerged as important regulatory component of mechanisms involved in gene expression, chromatin modification and epigenetic processes, but they are rarely annotated in the bovine genome. Our study monitored the jejunum transcriptome of German Holstein calves fed two different milk diets using transcriptome sequencing (RNA-seq). To identify potential lncRNAs within the pool of unknown transcripts, four bioinformatic lncRNA prediction tools were applied. The intersection of the alignment-free lncRNA prediction tools (CNCI, PLEK and FEELnc) predicted 1,812 lncRNA transcripts concordantly comprising a catalogue of 1,042 putative lncRNA loci expressed in the calves' intestinal mucosa...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29764999/targetable-bet-proteins-and-e2f1-dependent-transcriptional-program-maintains-the-malignancy-of-glioblastoma
#18
Liang Xu, Ye Chen, Anand Mayakonda, Lynnette Koh, Yuk Kien Chong, Dennis L Buckley, Edwin Sandanaraj, See Wee Lim, Ruby Yu-Tong Lin, Xin-Yu Ke, Mo-Li Huang, Jianxiang Chen, Wendi Sun, Ling-Zhi Wang, Boon Cher Goh, Huy Q Dinh, Dennis Kappei, Georg E Winter, Ling-Wen Ding, Beng Ti Ang, Benjamin P Berman, James E Bradner, Carol Tang, H Phillip Koeffler
Competitive BET bromodomain inhibitors (BBIs) targeting BET proteins (BRD2, BRD3, BRD4, and BRDT) show promising preclinical activities against brain cancers. However, the BET protein-dependent glioblastoma (GBM)-promoting transcriptional network remains elusive. Here, with mechanistic exploration of a next-generation chemical degrader of BET proteins (dBET6), we reveal a profound and consistent impact of BET proteins on E2F1- dependent transcriptional program in both differentiated GBM cells and brain tumor-initiating cells...
May 15, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29764394/comprehensive-analysis-of-coding-lncrna-gene-co-expression-network-uncovers-conserved-functional-lncrnas-in-zebrafish
#19
Wen Chen, Xuan Zhang, Jing Li, Shulan Huang, Shuanglin Xiang, Xiang Hu, Changning Liu
BACKGROUND: Zebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefore, how to take advantage of the mature zebrafish system to deeply investigate the lncRNAs' function and conservation is really intriguing. RESULTS: We systematically collected and analyzed a series of zebrafish RNA-seq data, then combined them with resources from known database and literatures...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29764377/transcriptome-display-during-tilapia-sex-determination-and-differentiation-as-revealed-by-rna-seq-analysis
#20
Wenjing Tao, Jinlin Chen, Dejie Tan, Jing Yang, Lina Sun, Jing Wei, Matthew A Conte, Thomas D Kocher, Deshou Wang
BACKGROUND: The factors determining sex in teleosts are diverse. Great efforts have been made to characterize the underlying genetic network in various species. However, only seven master sex-determining genes have been identified in teleosts. While the function of a few genes involved in sex determination and differentiation has been studied, we are far from fully understanding how genes interact to coordinate in this process. RESULTS: To enable systematic insights into fish sexual differentiation, we generated a dynamic co-expression network from tilapia gonadal transcriptomes at 5, 20, 30, 40, 90, and 180 dah (days after hatching), plus 45 and 90 dat (days after treatment) and linked gene expression profiles to both development and sexual differentiation...
May 15, 2018: BMC Genomics
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