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https://www.readbyqxmd.com/read/28548969/transcriptome-profiling-in-preadipocytes-identifies-long-noncoding-rnas-as-sam68-targets
#1
Naomi Li, Steven Hébert, Jingwen Song, Claudia L Kleinman, Stéphane Richard
The KH-type RNA binding protein Sam68 is required for adipogenesis. We have previously shown that Sam68-deficient mice have a lean phenotype and are protected against dietary-induced obesity due to defects in mTOR and S6K1 alternative splicing. Herein we profiled the transcriptome of Sam68 wild type and deficient 3T3-L1 mouse preadipocytes. We identified 652 protein-coding genes and 9 ncRNAs that were significantly altered with the loss of Sam68. As expected, downregulated genes were significantly associated with GO terms linked to cell migration, motility, and fat cell differentiation, while upregulated genes were mostly associated with GO terms linked to neurogenesis...
May 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28546511/the-nanci-nkx2-1-gene-duplex-buffers-nkx2-1-expression-to-maintain-lung-development-and-homeostasis
#2
Michael J Herriges, David J Tischfield, Zheng Cui, Michael P Morley, Yumiao Han, Apoorva Babu, Su Li, MinMin Lu, Isis Cendan, Benjamin A Garcia, Stewart A Anderson, Edward E Morrisey
A subset of long noncoding RNAs (lncRNAs) is spatially correlated with transcription factors (TFs) across the genome, but how these lncRNA-TF gene duplexes regulate tissue development and homeostasis is unclear. We identified a feedback loop within the NANCI (Nkx2.1-associated noncoding intergenic RNA)-Nkx2.1 gene duplex that is essential for buffering Nkx2.1 expression, lung epithelial cell identity, and tissue homeostasis. Within this locus, Nkx2.1 directly inhibits NANCI, while NANCI acts in cis to promote Nkx2...
May 25, 2017: Genes & Development
https://www.readbyqxmd.com/read/28546230/tincr-expression-is-associated-with-unfavorable-prognosis-in-patients-with-hepatocellular-carcinoma
#3
Feng Tian, Jian Xu, Fangxi Xue, Encui Guan, Xiaoguang Xu
Emerging evidences are accumulating that long noncoding RNAs (lncRNAs) have recently been identified to participate in various cellular processes. Terminal differentiation-induced ncRNA (TINCR) is a newly identified lncRNA with its functional roles not fully elucidated in human malignancy. The current study aims to identify the clinical significance of TINCR in prognosis and malignant progression of hepatocellular carcinoma (HCC). TINCR expression in HCC specimens with various stages of tumorigenesis were measured by qRT-PCR...
May 25, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28546213/tudor-sn-mediated-endonucleolytic-decay-of-human-cell-micrornas-promotes-g1-s-phase-transition
#4
Reyad A Elbarbary, Keita Miyoshi, Jason R Myers, Peicheng Du, John M Ashton, Bin Tian, Lynne E Maquat
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression. The pathways that mediate mature miRNA decay are less well understood than those that mediate miRNA biogenesis. We found that functional miRNAs are degraded in human cells by the endonuclease Tudor-SN (TSN). In vitro, recombinant TSN initiated the decay of both protein-free and Argonaute 2-loaded miRNAs via endonucleolytic cleavage at CA and UA dinucleotides, preferentially at scissile bonds located more than five nucleotides away from miRNA ends...
May 26, 2017: Science
https://www.readbyqxmd.com/read/28545146/transcriptomics-technologies
#5
Rohan Lowe, Neil Shirley, Mark Bleackley, Stephen Dolan, Thomas Shafee
Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst noncoding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. The first attempts to study the whole transcriptome began in the early 1990s, and technological advances since the late 1990s have made transcriptomics a widespread discipline...
May 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28544609/global-circular-rna-expression-profile-of-human-gastric-cancer-and-its-clinical-significance
#6
Yongfu Shao, Jinyun Li, Rongdan Lu, Tianwen Li, Yunben Yang, Bingxiu Xiao, Junming Guo
Circular RNAs (circRNAs) are a new class of noncoding RNAs. However, the expression profile and clinical significance of circRNAs in human gastric cancer is unclear. The global circRNA expression profile in human gastric cancer was measured by circRNA microarray. Hsa_circ_0014717, one of the most downregulated circRNAs in microarray, was selected as a targeted circRNA to explore its levels in gastric tissues and gastric juice. Freeze-thaw experiment and incubation experiment confirmed the stability of gastric juice circRNAs...
May 23, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28544557/lncrna-tcons_00026907-is-involved-in-the-progression-and-prognosis-of-cervical-cancer-through-inhibiting-mir-143-5p
#7
Xuejing Jin, Xiangjian Chen, Yan Hu, Furong Ying, Ruanmin Zou, Feng Lin, Zhengzheng Shi, Xuejie Zhu, Xiaojian Yan, Shi Li, Hua Zhu
Our previous long noncoding RNA (lncRNA) microarray revealed that lncRNA-TCONS_00026907 is aberrantly expressed between cervical cancer tissues and adjacent tissues. This study aims to explore the potential role of TCONS_00026907 in the development of cervical cancer. The expression levels of TCONS_00026907 in cervical cancer tissues and adjacent tissues from 83 patients of cervical cancer were detected by quantitative real-time polymerase chain reaction and the survival rate was analyzed. In vitro, HeLa and SiHa cells were transfected with small hairpin RNA (shRNA)-TCONS_00026907, then cell proliferation, cycle distribution, apoptosis, migration and invasion were measured...
May 23, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28541478/genome-size-in-north-american-fireflies-substantial-variation-likely-driven-by-neutral-processes
#8
Sarah Sander Lower, J Spencer Johnston, Kathrin Stanger-Hall, Carl E Hjelmen, Shawn J Hanrahan, Katharine Korunes, David Hall
Eukaryotic genomes show tremendous size variation across taxa. Proximate explanations for genome size variation include differences in ploidy and amounts of noncoding DNA, especially repetitive DNA. Ultimate explanations include selection on physiological correlates of genome size such as cell size, which in turn influence body size, resulting in the often-observed correlation between body size and genome size. In this study, we examined body size and repetitive DNA elements in relationship to the evolution of genome size in North American representatives of a single beetle family, the Lampyridae (fireflies)...
May 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28541302/the-long-noncoding-rna-lnc-egfr-stimulates-t-regulatory-cells-differentiation-thus-promoting-hepatocellular-carcinoma-immune-evasion
#9
Runqiu Jiang, Junwei Tang, Yun Chen, Lei Deng, Jie Ji, Yu Xie, Ke Wang, Wei Jia, Wen-Ming Chu, Beicheng Sun
Long noncoding RNAs play a pivotal role in T-helper cell development but little is known about their roles in Treg differentiation and functions during the progression of hepatocellular carcinoma (HCC). Here, we show that lnc-epidermal growth factor receptor (EGFR) upregulation in Tregs correlates positively with the tumour size and expression of EGFR/Foxp3, but negatively with IFN-γ expression in patients and xenografted mouse models. Lnc-EGFR stimulates Treg differentiation, suppresses CTL activity and promotes HCC growth in an EGFR-dependent manner...
May 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28541271/protein-altering-and-regulatory-genetic-variants-near-gata4-implicated-in-bicuspid-aortic-valve
#10
Bo Yang, Wei Zhou, Jiao Jiao, Jonas B Nielsen, Michael R Mathis, Mahyar Heydarpour, Guillaume Lettre, Lasse Folkersen, Siddharth Prakash, Claudia Schurmann, Lars Fritsche, Gregory A Farnum, Maoxuan Lin, Mohammad Othman, Whitney Hornsby, Anisa Driscoll, Alexandra Levasseur, Marc Thomas, Linda Farhat, Marie-Pierre Dubé, Eric M Isselbacher, Anders Franco-Cereceda, Dong-Chuan Guo, Erwin P Bottinger, G Michael Deeb, Anna Booher, Sachin Kheterpal, Y Eugene Chen, Hyun Min Kang, Jacob Kitzman, Heather J Cordell, Bernard D Keavney, Judith A Goodship, Santhi K Ganesh, Gonçalo Abecasis, Kim A Eagle, Alan P Boyle, Ruth J F Loos, Per Eriksson, Jean-Claude Tardif, Chad M Brummett, Dianna M Milewicz, Simon C Body, Cristen J Willer
Bicuspid aortic valve (BAV) is a heritable congenital heart defect and an important risk factor for valvulopathy and aortopathy. Here we report a genome-wide association scan of 466 BAV cases and 4,660 age, sex and ethnicity-matched controls with replication in up to 1,326 cases and 8,103 controls. We identify association with a noncoding variant 151 kb from the gene encoding the cardiac-specific transcription factor, GATA4, and near-significance for p.Ser377Gly in GATA4. GATA4 was interrupted by CRISPR-Cas9 in induced pluripotent stem cells from healthy donors...
May 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28540679/genome-wide-analysis-of-microrna-regulated-transcripts
#11
David Chevalier, Glen M Borchert
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression by either degrading transcripts or repressing translation . Over the past decade the significance of miRNAs has been unraveled by the characterization of their involvement in crucial cellular functions and the development of disease. However, continued progress in understanding the endogenous importance of miRNAs, as well as their potential uses as therapeutic tools, has been hindered by the difficulty of positively identifying miRNA targets...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540676/micrornas-biomarkers-diagnostics-and-therapeutics
#12
Weili Huang
MicroRNAs (miRNAs) are small noncoding RNAs (21-23 nucleotides in length) that regulate gene expression at translational or posttranslational levels. The major regulatory mechanisms include translational repression or mRNA degradation (Filipowicz et al., Curr Opin Struct Biol 15:331-341, 2005).Aberrant expression of miRNAs has been found to be associated with a variety of human diseases such as cancers/tumors, diabetes, viral infections, cardiovascular diseases, neurodegenerative diseases, and other diseases (Wang et al...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540675/viral-micrornas-host-micrornas-regulating-viruses-and-bacterial-microrna-like-rnas
#13
Sara-Elizabeth Cardin, Glen M Borchert
As masters of genome-wide regulation, miRNAs represent a key component in the complex architecture of cellular processes. Over the last decade, it has become increasingly apparent that miRNAs have many important roles in the development of disease and cancer. Recently, however, their role in viral and bacterial gene regulation as well as host gene regulation during disease progression has become a field of interest. Due to their small size, miRNAs are the ideal mechanism for bacteria and viruses that have limited room in their genomes, as a single miRNA can target up to ~30 genes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540673/micrornas-long-noncoding-rnas-and-their-functions-in-human-disease
#14
Min Xue, Ying Zhuo, Bin Shan
Majority of the human genome is transcribed into RNAs with absent or limited protein-coding potential. microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are two major families of the non-protein-coding transcripts. miRNAs and lncRNAs can regulate fundamental cellular processes via diverse mechanisms. The expression and function of miRNAs and lncRNAs are tightly regulated in development and physiological homeostasis. Dysregulation of miRNAs and lncRNAs is critical to pathogenesis of human disease. Moreover, recent evidence indicates a cross talk between miRNAs and lncRNAs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28538188/identification-and-characterization-of-a-class-of-malat1-like-genomic-loci
#15
Bin Zhang, Yuntao S Mao, Sarah D Diermeier, Irina V Novikova, Eric P Nawrocki, Tom A Jones, Zsolt Lazar, Chang-Shung Tung, Weijun Luo, Sean R Eddy, Karissa Y Sanbonmatsu, David L Spector
The MALAT1 (Metastasis-Associated Lung Adenocarcinoma Transcript 1) gene encodes a noncoding RNA that is processed into a long nuclear retained transcript (MALAT1) and a small cytoplasmic tRNA-like transcript (mascRNA). Using an RNA sequence- and structure-based covariance model, we identified more than 130 genomic loci in vertebrate genomes containing the MALAT1 3' end triple-helix structure and its immediate downstream tRNA-like structure, including 44 in the green lizard Anolis carolinensis. Structural and computational analyses revealed a co-occurrence of components of the 3' end module...
May 23, 2017: Cell Reports
https://www.readbyqxmd.com/read/28537886/adam9-enhances-cdcp1-by-inhibiting-mir-1-through-egfr-signaling-activation-in-lung-cancer-metastasis
#16
Kuo-Liang Chiu, Yu-Sen Lin, Ting-Ting Kuo, Chia-Chien Lo, Yu-Kai Huang, Hsien-Fang Chang, Eric Y Chuang, Ching-Chan Lin, Wei-Chung Cheng, Yen-Nien Liu, Liang-Chuan Lai, Yuh-Pyng Sher
MicroRNAs (miRNAs), which are endogenous short noncoding RNAs, can regulate genes involved in important biological and pathological functions. Therefore, dysregulation of miRNAs plays a critical role in cancer progression. However, whether the aberrant expression of miRNAs is regulated by oncogenes remains unclear. We previously demonstrated that a disintegrin and metalloprotease domain 9 (ADAM9) promotes lung metastasis by enhancing the expression of a pro-migratory protein, CUB domain containing protein 1 (CDCP1)...
May 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28537233/-canonical-and-noncanonical-rna-polyadenylation
#17
I G Ustyantsev, J S Golubchikova, O R Borodulina, D A Kramerov
Polyadenylation is the non-template addition of adenosine nucleotides at the 3'-end of RNA, which occurs after transcription and generates a poly(A) tail up to 250-300 nucleotides long. In the first section of our review, we consider the classical process of mRNA 3'-terminus formation, which involves the cleavage of the transcript synthesized by RNA polymerase II and the associated poly(A) tail synthesis by canonical polyadenylate polymerase. Nucleotide sequences needed for mRNA cleavage and poly(A) tail synthesis, in particular the AAUAAA polyadenylation signal, as well as numerous proteins and their complexes involved in mRNA cleavage and polyadenylation, is described in detail...
March 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28536698/the-critical-role-of-long-noncoding-rna-in-osteogenic-differentiation-of-human-bone-marrow-mesenchymal-stem-cells
#18
Xiaoling Qiu, Bo Jia, Xiang Sun, Weitao Hu, Hongxing Chu, Shuaimei Xu, JianJiang Zhao
Objective. Long noncoding RNAs (lncRNAs) have been demonstrated to regulate many biological processes including differentiation. However, their role in osteogenic differentiation was poorly known. Materials and Methods. In this study, we first globally profiled the differentially expressed lncRNAs and mRNAs during osteogenic differentiation of human bone marrow mesenchymal stem cells (hBMMSCs). Bioinformatics analysis was performed to further analyze these significantly changed molecules. Then the role of lncRNA ENST00000502125...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28536328/-microrna-in-various-aspects-of-cancer-development
#19
Sho Nambara, Koshi Mimori
MicroRNAs(miRNAs)are small(18-25 nucleotides)noncoding RNA molecules that bind to partially complementary mRNA sequences, resulting in target degradation or translation inhibition. A single miRNA can influence the expression of hundreds of target genes, and miRNAs have been implicated as key molecules in various diseases, including cancer. Many studies have shown that the miRNAs play an important role in cancer cells and tumor microenvironment and may be biomarkers for early detection and therapeutic targets for various cancers...
May 2017: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/28535931/the-dimensions-dynamics-and-relevance-of-the-mammalian-noncoding-transcriptome
#20
REVIEW
Ira W Deveson, Simon A Hardwick, Tim R Mercer, John S Mattick
The combination of pervasive transcription and prolific alternative splicing produces a mammalian transcriptome of great breadth and diversity. The majority of transcribed genomic bases are intronic, antisense, or intergenic to protein-coding genes, yielding a plethora of short and long non-protein-coding regulatory RNAs. Long noncoding RNAs (lncRNAs) share most aspects of their biogenesis, processing, and regulation with mRNAs. However, lncRNAs are typically expressed in more restricted patterns, frequently from enhancers, and exhibit almost universal alternative splicing...
May 20, 2017: Trends in Genetics: TIG
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