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ultraconserved regions

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https://www.readbyqxmd.com/read/27914101/tuc-338-promotes-invasion-and-metastasis-in-colorectal-cancer
#1
Chenghai Wang, Zheng Wang, Jie Zhou, Shuang Liu, Cong Wu, Caihong Huang, Yongling Ding
Ultraconserved regions (UCRs) are non-protein coding gene sequences that are strictly conserved across among different species. Emerging evidence demonstrates that transcribed ultraconserved regions (TUCRs) encoding noncoding RNAs serve as regulators of gene expression. In recent decades, increasing evidence implicates the involvement of UCRs in carcinogenesis. The role of TUC.338 in cervical cancers was an oncogene in previous studies. Until now, the role of TUC.338 in colorectal cancers remains undefined...
December 3, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27862524/sequence-capture-and-next-generation-sequencing-of-ultraconserved-elements-in-a-large-genome-salamander
#2
Catherine E Newman, Christopher C Austin
Amidst the rapid advancement in next-generation sequencing (NGS) technology over the last few years, salamanders have been left behind. Salamanders have enormous genomes - up to 40 times the size of the human genome - and this poses challenges to generating NGS data sets of quality and quantity similar to those of other vertebrates. However, optimization of laboratory protocols is time-consuming and often cost prohibitive, and continued omission of salamanders from novel phylogeographic research is detrimental to species facing decline...
November 14, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27846191/noncoding-transcribed-ultraconserved-region-t-ucr-uc-261-participates-in-intestinal-mucosa-barrier-damage-in-crohn-s-disease
#3
Xiao Xian Qian, Jiang Chen Peng, An Tao Xu, Di Zhao, Yu Qi Qiao, Tian Rong Wang, Jun Shen, Zhi Hua Ran
BACKGROUND: To date, 481 ultraconserved regions (UCRs) have been discovered in human genome. We aimed to investigate the transcribed UCR (T-UCR) characteristics in Crohn's disease (CD ) and determine whether T-UCR uc.261 participated in intestinal mucosa barrier damage. METHODS: T-UCRs were screened in active CD mucosa using the Arraystar Human T-UCR Microarray and validated with quantitative real-time reverse transcription PCR, together with tight junction proteins (TJPs) including junctional adhesion molecule-A, occludin, claudin-1, and zonula occluden-1...
December 2016: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/27768256/high-phylogenetic-utility-of-an-ultraconserved-element-probe-set-designed-for-arachnida
#4
James Starrett, Shahan Derkarabetian, Marshal Hedin, Robert W Bryson, John E McCormack, Brant C Faircloth
Arachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress...
October 21, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27692237/an-ultraconserved-brain-specific-enhancer-within-adgrl3-lphn3-underpins-attention-deficit-hyperactivity-disorder-susceptibility
#5
Ariel F Martinez, Yu Abe, Sungkook Hong, Kevin Molyneux, David Yarnell, Heiko Löhr, Wolfgang Driever, Maria T Acosta, Mauricio Arcos-Burgos, Maximilian Muenke
BACKGROUND: Genetic factors predispose individuals to attention-deficit/hyperactivity disorder (ADHD). Previous studies have reported linkage and association to ADHD of gene variants within ADGRL3. In this study, we functionally analyzed noncoding variants in this gene as likely pathological contributors. METHODS: In silico, in vitro, and in vivo approaches were used to identify and characterize evolutionary conserved elements within the ADGRL3 linkage region (~207 Kb)...
December 15, 2016: Biological Psychiatry
https://www.readbyqxmd.com/read/27618837/wnt-signalling-modulates-transcribed-ultraconserved-regions-in-hepatobiliary-cancers
#6
Pietro Carotenuto, Matteo Fassan, Rosantony Pandolfo, Andrea Lampis, Caterina Vicentini, Luciano Cascione, Viola Paulus-Hock, Luke Boulter, Rachel Guest, Luca Quagliata, Jens Claus Hahne, Rachel Ridgway, Tam Jamieson, Dimitris Athineos, Angelo Veronese, Rosa Visone, Claudio Murgia, Giulia Ferrari, Vincenza Guzzardo, Thomas Ronald Jeffry Evans, Martin MacLeod, Gui Ji Feng, Trevor Dale, Massimo Negrini, Stuart J Forbes, Luigi Terracciano, Aldo Scarpa, Tushar Patel, Nicola Valeri, Paul Workman, Owen Sansom, Chiara Braconi
OBJECTIVE: Transcribed-ultraconserved regions (T-UCR) are long non-coding RNAs which are conserved across species and are involved in carcinogenesis. We studied T-UCRs downstream of the Wnt/β-catenin pathway in liver cancer. DESIGN: Hypomorphic Apc mice (Apcfl/fl) and thiocetamide (TAA)-treated rats developed Wnt/β-catenin dependent hepatocarcinoma (HCC) and cholangiocarcinoma (CCA), respectively. T-UCR expression was assessed by microarray, real-time PCR and in situ hybridisation...
September 12, 2016: Gut
https://www.readbyqxmd.com/read/27543758/hidden-histories-of-gene-flow-in-highland-birds-revealed-with-genomic-markers
#7
Eugenia Zarza, Brant C Faircloth, Whitney L E Tsai, Robert W Bryson, John Klicka, John E McCormack
Genomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species-rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well-studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial DNA (mtDNA) largely conformed to the standard model of allopatric divergence, although there was also evidence for more obscure histories of gene flow in a small sample of nuclear markers...
October 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27500182/altered-t-ucrs-expression-profile-in-the-spinal-cord-of-mice-with-neuropathic-pain
#8
Bao-Chun Jiang, Tian Yang, Li-Na He, Yuan-Xiang Tao, Yong-Jing Gao
Spinal cord plays an important role in the transmission and modulation of nociceptive information. Global changes in gene expression in the spinal cord contribute to the induction and maintenance of neuropathic pain. Transcribed Ultraconserved Regions (T-UCRs), a novel class of long noncoding RNAs, can regulate gene expression at both transcriptional and post-transcriptional levels and are related to many human diseases such as cancer, Alzheimer's disease, and heart diseases. In this study, we screened abnormal T-UCRs expression in the spinal cord under spinal nerve ligation (SNL)-induced neuropathic pain condition...
2016: Translational Perioperative and Pain Medicine
https://www.readbyqxmd.com/read/27447964/ultraconserved-long-non-coding-rna-uc-63-in-breast-cancer
#9
Alberto Marini, Anna Maria Lena, Emanuele Panatta, Cristina Ivan, Leng Han, Han Liang, Margherita Annicchiarico-Petruzzelli, Nicola Di Daniele, George A Calin, Eleonora Candi, Gerry Melino
Transcribed-ultraconserved regions (T-UCRs) are long non-coding RNAs (lncRNA) encoded by a subset of long ultraconserved stretches in the human genome. Recent studies revealed that the expression of several T-UCRs is altered in cancer and growing evidences underline the importance of T-UCRs in oncogenesis, offering also potential new strategies for diagnosis and prognosis. We found that overexpression of one specific T-UCRs named uc.63 is associated with bad outcome in luminal A subtype of breast cancer patients...
July 13, 2016: Oncotarget
https://www.readbyqxmd.com/read/27427784/high-throughput-snp-genotyping-of-historical-and-modern-samples-of-five-bird-species-via-sequence-capture-of-ultraconserved-elements
#10
Haw Chuan Lim, Michael J Braun
Sample availability limits population genetics research on many species, especially taxa from regions with high diversity. However, many such species are well represented in museum collections assembled before the molecular era. Development of techniques to recover genetic data from these invaluable specimens will benefit biodiversity science. Using a mixture of freshly preserved and historical tissue samples, and a sequence capture probe set targeting >5000 loci, we produced high-confidence genotype calls on thousands of single nucleotide polymorphisms (SNPs) in each of five South-East Asian bird species and their close relatives (N = 27-43)...
September 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27363020/globally-increased-ultraconserved-noncoding-rna-expression-in-pancreatic-adenocarcinoma
#11
Jinmai Jiang, Ana Clara P Azevedo-Pouly, Roxana S Redis, Eun Joo Lee, Yuriy Gusev, David Allard, Dhruvitkumar S Sutaria, Mohamed Badawi, Ola A Elgamal, Megan R Lerner, Daniel J Brackett, George A Calin, Thomas D Schmittgen
Transcribed ultraconserved regions (T-UCRs) are a class of non-coding RNAs with 100% sequence conservation among human, rat and mouse genomes. T-UCRs are differentially expressed in several cancers, however their expression in pancreatic adenocarcinoma (PDAC) has not been studied. We used a qPCR array to profile all 481 T-UCRs in pancreatic cancer specimens, pancreatic cancer cell lines, during experimental pancreatic desmoplasia and in the pancreases of P48Cre/wt; KrasLSL-G12D/wt mice. Fourteen, 57 and 29% of the detectable T-UCRs were differentially expressed in the cell lines, human tumors and transgenic mouse pancreases, respectively...
June 23, 2016: Oncotarget
https://www.readbyqxmd.com/read/27247329/combinatorial-gene-regulatory-functions-underlie-ultraconserved-elements-in-drosophila
#12
Maria Warnefors, Britta Hartmann, Stefan Thomsen, Claudio R Alonso
Ultraconserved elements (UCEs) are discrete genomic elements conserved across large evolutionary distances. Although UCEs have been linked to multiple facets of mammalian gene regulation their extreme evolutionary conservation remains largely unexplained. Here, we apply a computational approach to investigate this question in Drosophila, exploring the molecular functions of more than 1,500 UCEs shared across the genomes of 12 Drosophila species. Our data indicate that Drosophila UCEs are hubs for gene regulatory functions and suggest that UCE sequence invariance originates from their combinatorial roles in gene control...
September 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27154519/long-noncoding-rna-uc-338-promotes-cell-proliferation-through-association-with-bmi1-in-hepatocellular-carcinoma
#13
Changwen Bo, Na Li, Xiuli Li, Xianwei Liang, Yonghui An
Hepatocellular carcinoma (HCC) is one of the most common human cancers all over the world. Increasing evidences have demonstrated that long noncoding RNAs (lncRNAs) play important roles in malignant transformation, tumor growth and metastasis in HCC. Among lncRNAs, ultraconserved RNAs (ucRNAs) containing an ultraconserved region have been report to contribute to human cancers. lncRNA ultraconserved element 338 (uc.338) was first found to be upregulated in HCC and promote cell growth. However, the exact mechanism by which uc...
October 2016: Human Cell
https://www.readbyqxmd.com/read/27043659/ultraconserved-region-containing-transformer-2%C3%AE-4-controls-senescence-of-colon-cancer-cells
#14
K Kajita, Y Kuwano, Y Satake, S Kano, K Kurokawa, Y Akaike, K Masuda, K Nishida, K Rokutan
Ultraconserved regions (UCRs) are >200 bp genomic segments with perfect human-to-rodent sequence identity. Transcribed UCRs constitute a new category of noncoding RNAs whose functions remain poorly understood. The human transformer 2β (TRA2B) gene contains a 419-bp UCR spanning the 276-bp exon 2 and its neighboring introns. TRA2B exon 2 has premature stop codons, whereas an exon 2-containing splice variant (TRA2β4) was expressed preferentially in the nuclei of human colon cancer cells. TRA2β4 knockdown p53-independently stimulated CDKN1A transcription and increased p21, resulting in the appearance of senescent cells...
2016: Oncogenesis
https://www.readbyqxmd.com/read/26943042/long-non-coding-rna-containing-ultraconserved-genomic-region-8-promotes-bladder-cancer-tumorigenesis
#15
Michele Olivieri, Matteo Ferro, Sara Terreri, Montano Durso, Alessandra Romanelli, Concetta Avitabile, Ottavio De Cobelli, Anna Messere, Dario Bruzzese, Ivan Vannini, Luciana Marinelli, Ettore Novellino, Wei Zhang, Mariarosaria Incoronato, Gennaro Ilardi, Stefania Staibano, Laura Marra, Renato Franco, Sisto Perdonà, Daniela Terracciano, Bogdan Czerniak, Giovanna L Liguori, Vincenza Colonna, Muller Fabbri, Ferdinando Febbraio, George A Calin, Amelia Cimmino
Ultraconserved regions (UCRs) have been shown to originate non-coding RNA transcripts (T-UCRs) that have different expression profiles and play functional roles in the pathophysiology of multiple cancers. The relevance of these functions to the pathogenesis of bladder cancer (BlCa) is speculative. To elucidate this relevance, we first used genome-wide profiling to evaluate the expression of T-UCRs in BlCa tissues. Analysis of two datasets comprising normal bladder tissues and BlCa specimens with a custom T-UCR microarray identified ultraconserved RNA (uc...
April 12, 2016: Oncotarget
https://www.readbyqxmd.com/read/26925787/uc-206-regulates-cell-proliferation-and-apoptosis-by-targeting-p53-in-cervical-cancer-cells
#16
Q Li, X Li, C Wang
Ultraconserved regions (UCRs) are non-protein coding gene sequences with strict conserved across among different species. Emerging evidence demonstrates that UCRs encoding noncoding RNAs (ncRNAs) serve as regulators of gene expression. In recent decades, increasing evidence implicates the involvement of UCRs in carcinogenesis. Previous studies showed RNA expression of uc.206 was increased in colorectal cancer. Until now, the role of uc.206 in cervical cancers remains undefined. This study revealed that uc.206 is significantly up-regulated in cervical cancer (CC) tissue and negatively correlates with the expression of the pro-apoptotic gene P53 in RNA level...
2016: Neoplasma
https://www.readbyqxmd.com/read/26902966/genetic-variants-in-ultraconserved-regions-associate-with-prostate-cancer-recurrence-and-survival
#17
Bo-Ying Bao, Victor C Lin, Chia-Cheng Yu, Hsin-Ling Yin, Ta-Yuan Chang, Te-Ling Lu, Hong-Zin Lee, Jiunn-Bey Pao, Chao-Yuan Huang, Shu-Pin Huang
Ultraconserved regions (UCRs) are DNA segments of longer than 200 bp in length that are completely conserved between human, rat, and mouse genomes. Recent studies have shown that UCRs are frequently located at fragile sites involved in cancers, and their levels of transcription can be altered during human tumorigenesis. We systematically evaluated 14 common single-nucleotide polymorphisms (SNPs) within UCRs in three cohorts of prostate cancer patients, to test the hypothesis that these UCR SNPs might influence clinical outcomes...
2016: Scientific Reports
https://www.readbyqxmd.com/read/26865273/analysis-of-a-rapid-evolutionary-radiation-using-ultraconserved-elements-evidence-for-a-bias-in-some-multispecies-coalescent-methods
#18
Kelly A Meiklejohn, Brant C Faircloth, Travis C Glenn, Rebecca T Kimball, Edward L Braun
Rapid evolutionary radiations are expected to require large amounts of sequence data to resolve. To resolve these types of relationships many systematists believe that it will be necessary to collect data by next-generation sequencing (NGS) and use multispecies coalescent ("species tree") methods. Ultraconserved element (UCE) sequence capture is becoming a popular method to leverage the high throughput of NGS to address problems in vertebrate phylogenetics. Here we examine the performance of UCE data for gallopheasants (true pheasants and allies), a clade that underwent a rapid radiation 10-15 Ma...
July 2016: Systematic Biology
https://www.readbyqxmd.com/read/26821912/comparison-of-target-capture-and-restriction-site-associated-dna-sequencing-for-phylogenomics-a-test-in-cardinalid-tanagers-aves-genus-piranga
#19
Joseph D Manthey, Luke C Campillo, Kevin J Burns, Robert G Moyle
Restriction-site associated DNA sequencing (RAD-seq) and target capture of specific genomic regions, such as ultraconserved elements (UCEs), are emerging as two of the most popular methods for phylogenomics using reduced-representation genomic data sets. These two methods were designed to target different evolutionary timescales: RAD-seq was designed for population-genomic level questions and UCEs for deeper phylogenetics. The utility of both data sets to infer phylogenies across a variety of taxonomic levels has not been adequately compared within the same taxonomic system...
July 2016: Systematic Biology
https://www.readbyqxmd.com/read/26683706/a-transcribed-ultraconserved-noncoding-rna-uc-173-is-a-key-molecule-for-the-inhibition-of-lead-induced-neuronal-apoptosis
#20
Aruo Nan, Xinke Zhou, Lijian Chen, Meiling Liu, Nan Zhang, Li Zhang, Yuanwei Luo, Zhenzhong Liu, Lijun Dai, Yiguo Jiang
As a common toxic metal, lead has significant neurotoxicity to brain development. Long non-coding RNAs (lncRNAs) function in multiple biological processes. However, whether lncRNAs are involved in lead-induced neurotoxicity remains unclear. Uc.173 is a lncRNA from a transcribed ultra-conservative region (T-UCR) of human, mouse and rat genomes. We established a lead-induced nerve injury mouse model. It showed the levels of Uc.173 decreased significantly in hippocampus tissue and serum of the model. We further tested the expression of Uc...
January 5, 2016: Oncotarget
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