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https://www.readbyqxmd.com/read/28637293/conserved-non-exonic-elements-a-novel-class-of-marker-for-phylogenomics
#1
Scott V Edwards, Alison Cloutier, Allan J Baker
Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved non-exonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species...
June 16, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28637169/novel-molecules-lncrnas-trfs-and-circrnas-deciphered-from-next-generation-sequencing-rna-sequencing-computational-databases-and-tools
#2
A Saleembhasha, Seema Mishra
Powerful next-generation sequencing (NGS) technologies, more specifically RNA sequencing (RNA-seq), have been pivotal toward the detection and analysis and hypotheses generation of novel biomolecules, long noncoding RNAs (lncRNAs), tRNA-derived fragments (tRFs) and circular RNAs (circRNAs). Experimental validation of the occurrence of these biomolecules inside the cell has been reported. Their differential expression and functionally important role in several cancers types as well as other diseases such as Alzheimer's and cardiovascular diseases have garnered interest toward further studies in this research arena...
June 20, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28636635/microrna-144-3p-inhibits-autophagy-activation-and-enhances-bacillus-calmette-gu%C3%A3-rin-infection-by-targeting-atg4a-in-raw264-7-macrophage-cells
#3
Le Guo, Linlin Zhou, Qian Gao, Aijun Zhang, Jun Wei, Dantong Hong, Yuankui Chu, Xiangguo Duan, Ying Zhang, Guangxian Xu
MicroRNAs (miRNAs) are small noncoding nucleotides that play major roles in the response of host immune cells. Autophagy plays a key role in activating the antimicrobial host defense against Mycobacterium tuberculosis (M. tuberculosis). Whether miRNAs specifically influence the activation of macrophage autophagy during M. tuberculosis infection is largely unknown. In the present study, we demonstrate that Mycobacterium bovis Bacillus Calmette-Guérin (BCG) infection of macrophages leads to increased expression of miR-144-3p, which targets autophagy-related gene 4a (ATG4a), to inhibit autophagy activation and antimicrobial responses to BCG...
2017: PloS One
https://www.readbyqxmd.com/read/28635400/the-long-noncoding-rna-foxcut-promotes-proliferation-and-migration-by-targeting-foxc1-in-nasopharyngeal-carcinoma
#4
Yu-Zhong Xu, Fang-Fang Chen, Yu Zhang, Qin-Fei Zhao, Xiao-Long Guan, Hai-Yong Wang, Ang Li, Xin Lv, Shu-Sheng Song, Ying Zhou, Xiao-Jun Li
Long noncoding RNAs play an important role in various biological processes, including tumorigenesis. FOXC1 (Forkhead box C1) is a member of the Forkhead box family of transcription factors and plays a crucial role in nasopharyngeal carcinoma. In this study, a novel long noncoding RNA (FOXCUT) located upstream of FOXC1 was investigated in 42 nasopharyngeal carcinoma patients. Our analysis revealed that the expression levels of FOXCUT and FOXC1 in nasopharyngeal carcinoma tissues were significantly higher than those observed in chronic nasopharyngitis tissues and that FOXCUT expression was positively correlated with FOXC1 expression...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28635106/long-noncoding-rna-and-its-contribution-to-autism-spectrum-disorders
#5
REVIEW
Jie Tang, Yizhen Yu, Wei Yang
Recent studies have indicated that long noncoding RNAs (lncRNAs) play important roles in multiple processes, such as epigenetic regulation, gene expression regulation, development, nutrition-related and other diseases, toxic response, and response to drugs. Although the functional roles and mechanisms of several lncRNAs have been discovered, a better understanding of the vast majority of lncRNAs remains elusive. To understand the functional roles and mechanisms of lncRNAs is critical because these transcripts represent the majority of the transcriptional output of the mammalian genome...
June 20, 2017: CNS Neuroscience & Therapeutics
https://www.readbyqxmd.com/read/28634418/long-noncoding-rnas-as-biomarkers-in-cancer
#6
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/28634073/long-noncoding-rna-meg3-mediated-angiogenesis-after-cerebral-infarction-through-regulating-p53-nox4-axis
#7
Renya Zhan, Kangli Xu, Jianwei Pan, Qingsheng Xu, Shengjie Xu, Jian Shen
OBJECTIVE: This study aimed to explore the mechanism of lncRNA MEG3 on angiogenesis after cerebral infarction (CI). METHODS: The rat brain microvascular endothelial cells (RBMVECs) isolated from rat was used to establish CI model, which were treated with oxygen-glucose deprivation/reoxygenation (OGD/R). The genes mRNA and protein expression levels in RBMVECs were determined by the quantitative real-time polymerase chain reaction (RT-qPCR) and western blot, respectively...
June 17, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28633494/silencing-effect-of-hominoid-highly-conserved-non-coding-sequences-on-embryonic-brain-development
#8
Morteza Mahmoudi Saber, Naruya Saitou
Superfamily Hominoidea, which consists of Hominidae (humans and great apes) and Hylobatidae (gibbons), is well-known for sharing human-like characteristics, however, the genomic origins of these shared unique phenotypes have mainly remained elusive. To decipher the underlying genomic basis of Hominoidea-restricted phenotypes, we identified and characterized Hominoidea-restricted highly conserved noncoding sequences (HCNSs) that are a class of potential regulatory elements which may be involved in evolution of lineage-specific phenotypes...
June 19, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28632999/long-noncoding-rna-lnc-sox5-modulates-crc-tumorigenesis-by-unbalancing-tumor-microenvironment
#9
Wu Kaiming, Zhenxian Zhao, Kuanzhi Liu, Jian Zhang, Guanghua Li, Liang Wang
Long non-coding RNAs (LncRNAs) have been recently regarded as systemic regulators in multiple biological processes including tumorigenesis. In this study, we observed the expression of lncRNA lnc-sox5 was significantly increased in colorectal cancer (CRC). Despite the CRC cell growth, cell cycle and cell apoptosis was not affected by lnc-sox5 knock-down, lnc-sox5 knock-down suppressed CRC cell migration and invasion. In addition, xenograft animal model suggested that lnc-sox5 knock-down significantly suppressed the CRC tumorigenesis...
June 20, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28630923/ribosome-rearrangements-at-the-onset-of-translational-bypassing
#10
Xabier Agirrezabala, Ekaterina Samatova, Mariia Klimova, Miguel Zamora, David Gil-Carton, Marina V Rodnina, Mikel Valle
Bypassing is a recoding event that leads to the translation of two distal open reading frames into a single polypeptide chain. We present the structure of a translating ribosome stalled at the bypassing take-off site of gene 60 of bacteriophage T4. The nascent peptide in the exit tunnel anchors the P-site peptidyl-tRNA(Gly) to the ribosome and locks an inactive conformation of the peptidyl transferase center (PTC). The mRNA forms a short dynamic hairpin in the decoding site. The ribosomal subunits adopt a rolling conformation in which the rotation of the small subunit around its long axis causes the opening of the A-site region...
June 2017: Science Advances
https://www.readbyqxmd.com/read/28630499/spatio-temporal-analysis-of-coding-and-long-noncoding-transcripts-during-maize-endosperm-development
#11
Eun-Deok Kim, Yuqing Xiong, Youngjae Pyo, Dong-Hwan Kim, Byung-Ho Kang, Sibum Sung
The maize endosperm consists of three major compartmentalized cell types: the starchy endosperm (SE), the basal endosperm transfer cell layer (BETL), and the aleurone cell layer (AL). Differential genetic programs are activated in each cell type to construct functionally and structurally distinct cells. To compare gene expression patterns involved in maize endosperm cell differentiation, we isolated transcripts from cryo-dissected endosperm specimens enriched with BETL, AL, or SE at 8, 12, and 16 days after pollination (DAP)...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28630232/long-noncoding-rna-h19-promotes-neuroinflammation-in-ischemic-stroke-by-driving-histone-deacetylase-1-dependent-m1-microglial-polarization
#12
Jue Wang, Haiping Zhao, Zhibin Fan, Guangwen Li, Qingfeng Ma, Zhen Tao, Rongliang Wang, Juan Feng, Yumin Luo
BACKGROUND AND PURPOSE: Long noncoding RNA H19 is repressed after birth, but can be induced by hypoxia. We aim to investigate the impact on and underlying mechanism of H19 induction after ischemic stroke. METHODS: Circulating H19 levels in stroke patients and mice subjected to middle cerebral artery occlusion were assessed using real-time polymerase chain reaction. H19 siRNA and histone deacetylase 1 (HDAC1) plasmid were used to knock down H19 and overexpress HDAC1, respectively...
June 19, 2017: Stroke; a Journal of Cerebral Circulation
https://www.readbyqxmd.com/read/28630177/integrated-genome-and-transcriptome-sequencing-identifies-a-noncoding-mutation-in-the-genome-replication-factor-donson-as-the-cause-of-microcephaly-micromelia-syndrome
#13
Gilad D Evrony, Dwight R Cordero, Jun Shen, Jennifer N Partlow, Timothy W Yu, Rachel E Rodin, R Sean Hill, Michael E Coulter, Anh-Thu N Lam, Divya Jayaraman, Dianne Gerrelli, Diana G Diaz, Chloe Santos, Victoria Morrison, Antonella Galli, Ulrich Tschulena, Stefan Wiemann, M Jocelyne Martel, Betty Spooner, Steven C Ryu, Princess C Elhosary, Jillian M Richardson, Danielle Tierney, Christopher A Robinson, Rajni Chibbar, Dana Diudea, Rebecca Folkerth, Sheldon Wiebe, A James Barkovich, Ganeshwaran H Mochida, James Irvine, Edmond G Lemire, Patricia Blakley, Christopher A Walsh
While next-generation sequencing has accelerated the discovery of human disease genes, progress has been largely limited to the "low hanging fruit" of mutations with obvious exonic coding or canonical splice site impact. In contrast, the lack of high-throughput, unbiased approaches for functional assessment of most noncoding variants has bottlenecked gene discovery. We report the integration of transcriptome sequencing (RNA-seq), which surveys all mRNAs to reveal functional impacts of variants at the transcription level, into the gene discovery framework for a unique human disease, microcephaly-micromelia syndrome (MMS)...
June 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28630135/inhibition-of-the-cardiac-fibroblast-enriched-lncrna-meg3-prevents-cardiac-fibrosis-and-diastolic-dysfunction
#14
Maria-Teresa Piccoli, Shashi Gupta, Janika Viereck, Ariana Foinquinos, Sabine Samolovac, Freya Kramer, Ankita Garg, Janet Remke, Karina Zimmer, Sandor Batkai, Thomas Thum
Rationale: Cardiac fibroblasts (CFs) drive extracellular matrix (ECM) remodeling following pressure overload, leading to fibrosis and diastolic dysfunction. Recent studies described the role of long noncoding RNAs (lncRNAs) in cardiac pathologies. Nevertheless, detailed reports on lncRNAs regulating CF biology and describing their implication in cardiac remodeling are still missing. Objective: Here, we aimed at characterizing lncRNA expression in murine CFs following chronic pressure overload, in order to identify CF-enriched lncRNAs and investigate their function and contribution to cardiac fibrosis and diastolic dysfunction...
June 19, 2017: Circulation Research
https://www.readbyqxmd.com/read/28629949/the-diversity-of-long-noncoding-rnas-and-their-generation
#15
REVIEW
Huang Wu, Li Yang, Ling-Ling Chen
Long noncoding RNAs (lncRNAs) are emerging as potential key regulators in gene expression networks and exhibit a surprising range of shapes and sizes. Several distinct classes of lncRNAs are transcribed from different DNA elements, including promoters, enhancers, and intergenic regions in eukaryotic genomes. Additionally, others are derived from long primary transcripts with noncanonical RNA processing pathways, generating new RNA species with unexpected formats. These lncRNAs can be processed by several mechanisms, including ribonuclease P (RNase P) cleavage to generate mature 3' ends, capping by small nucleolar RNA (snoRNA)-protein (snoRNP) complexes at their ends, or the formation of circular structures...
June 16, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28629368/identification-and-characterization-of-long-intergenic-noncoding-rnas-in-bovine-mammary-glands
#16
Chao Tong, Qiaoling Chen, Lili Zhao, Junfei Ma, Eveline M Ibeagha-Awemu, Xin Zhao
BACKGROUND: Mammary glands of dairy cattle produce milk for the newborn offspring and for human consumption. Long intergenic noncoding RNAs (lincRNAs) play various functions in eukaryotic cells. However, types and roles of lincRNAs in bovine mammary glands are still poorly understood. RESULTS: Using computational methods, 886 unknown intergenic transcripts (UITs) were identified from five RNA-seq datasets from bovine mammary glands. Their non-coding potentials were predicted by using the combination of four software programs (CPAT, CNCI, CPC and hmmscan), with 184 lincRNAs identified...
June 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28628227/microrna-mediated-drug-resistance-in-ovarian-cancer
#17
REVIEW
Aynaz Mihanfar, Amir Fattahi, Hamid Reza Nejabati
The development of intrinsic or acquired resistance to chemotherapeutic agents used in the treatment of various human cancers is a major obstacle for the successful abolishment of cancer. The accumulated efforts in the understanding the exact mechanisms of development of multidrug resistance (MDR) have led to the introduction of several unique and common mechanisms. Recent studies demonstrate the regulatory role of small noncoding RNA or miRNA in the several parts of cancer biology. Practically all aspects of cell physiology under normal and disease conditions are reported to be controlled by miRNAs...
June 19, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28628087/chromatin-enriched-lncrnas-can-act-as-cell-type-specific-activators-of-proximal-gene-transcription
#18
Michael S Werner, Matthew A Sullivan, Rohan N Shah, Rangarajan D Nadadur, Adrian T Grzybowski, Vasiliy Galat, Ivan P Moskowitz, Alexander J Ruthenburg
We recently described a new class of long noncoding RNAs (lncRNAs) that are distinguished by especially tight chromatin association and whose presence is strongly correlated to expression of nearby genes. Here, we examine the cis-enhancer mechanism of this class of chromatin-enriched RNA (cheRNA) across multiple human cell lines. cheRNAs are largely cell type specific and provide the most reliable chromatin signature to predict cis-gene transcription in every human cell type examined. Targeted depletion of three cheRNAs decreases expression of their neighboring genes, indicating potential co-activator function, and single-molecule fluorescence in situ hybridization (smFISH) of one cheRNA-distal target gene pair suggests a spatial overlap consistent with a role in chromosome looping...
June 19, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28627442/the-association-of-rs710886-in-lncrna-pcat1-with-bladder-cancer-risk-in-a-chinese-population
#19
Yadi Lin, Yuqiu Ge, Yunyan Wang, Gaoxiang Ma, Xiaowei Wang, Hanting Liu, Meilin Wang, Zhengdong Zhang, Haiyan Chu
OBJECTIVE: The long noncoding RNA PCAT1 is an important gene involved in urinary tumors. In this study, we aimed to explore the association between polymorphisms in PCAT1 and bladder cancer susceptibility. METHODS: A two-stage case-control study was conducted to assess the association between four tagging SNPs (i.e., rs4871771, rs1902432, rs16901904 and rs710886) and bladder cancer risk. Odds ratios (ORs) and their 95% confidence intervals (CIs) were calculated with unconditional univariate and multivariate logistic regression...
June 13, 2017: Gene
https://www.readbyqxmd.com/read/28626222/the-role-of-epigenetics-in-renal-ageing
#20
REVIEW
Paul G Shiels, Dagmara McGuinness, Maria Eriksson, Jeroen P Kooman, Peter Stenvinkel
An ability to separate natural ageing processes from processes specific to morbidities is required to understand the heterogeneity of age-related organ dysfunction. Mechanistic insight into how epigenetic factors regulate ageing throughout the life course, linked to a decline in renal function with ageing, is already proving to be of value in the analyses of clinical and epidemiological cohorts. Noncoding RNAs provide epigenetic regulatory circuits within the kidney, which reciprocally interact with DNA methylation processes, histone modification and chromatin...
June 19, 2017: Nature Reviews. Nephrology
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