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https://www.readbyqxmd.com/read/28304380/comprehensive-analysis-of-the-cancer-genome-atlas-reveals-a-unique-gene-and-non-coding-rna-signature-of-fibrolamellar-carcinoma
#1
Timothy A Dinh, Eva C M Vitucci, Eliane Wauthier, Rondell P Graham, Wendy A Pitman, Tsunekazu Oikawa, Mengjie Chen, Grace O Silva, Kevin G Greene, Michael S Torbenson, Lola M Reid, Praveen Sethupathy
Fibrolamellar carcinoma (FLC) is a unique liver cancer primarily affecting young adults and characterized by a fusion event between DNAJB1 and PRKACA. By analyzing RNA-sequencing data from The Cancer Genome Atlas (TCGA) for >9,100 tumors across ~30 cancer types, we show that the DNAJB1-PRKACA fusion is specific to FLCs. We demonstrate that FLC tumors (n = 6) exhibit distinct messenger RNA (mRNA) and long intergenic non-coding RNA (lincRNA) profiles compared to hepatocellular carcinoma (n = 263) and cholangiocarcinoma (n = 36), the two most common liver cancers...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28251479/changes-in-lncrnas-and-related-genes-in-%C3%AE-thalassemia-minor-and-%C3%AE-thalassemia-major
#2
Jing Ma, Fei Liu, Xin Du, Duan Ma, Likuan Xiong
β-thalassemia is caused by β-globin gene mutations. However, heterogeneous phenotypes were found in individuals with same genotype, and still undescribed mechanism underlies such variation. We collected blood samples from 30 β-thalassemia major, 30 β-thalassemia minor patients, and 30 matched normal controls. Human lncRNA Array v2.0 (8 × 60 K, Arraystar) was used to detect changes in long non-coding RNAs (lncRNAs) and mRNAs in three samples each from β-thalassemia major, β-thalassemia minor, and control groups...
March 2, 2017: Frontiers of Medicine
https://www.readbyqxmd.com/read/28249171/cis-acting-complex-trait-associated-lincrna-expression-correlates-with-modulation-of-chromosomal-architecture
#3
Jennifer Yihong Tan, Adam Alexander Thil Smith, Maria Ferreira da Silva, Cyril Matthey-Doret, Rico Rueedi, Reyhan Sönmez, David Ding, Zoltán Kutalik, Sven Bergmann, Ana Claudia Marques
Intergenic long noncoding RNAs (lincRNAs) are the largest class of transcripts in the human genome. Although many have recently been linked to complex human traits, the underlying mechanisms for most of these transcripts remain undetermined. We investigated the regulatory roles of a high-confidence and reproducible set of 69 trait-relevant lincRNAs (TR-lincRNAs) in human lymphoblastoid cells whose biological relevance is supported by their evolutionary conservation during recent human history and genetic interactions with other trait-associated loci...
February 28, 2017: Cell Reports
https://www.readbyqxmd.com/read/28247361/bioinformatics-for-novel-long-intergenic-noncoding-rna-lincrna-identification-in-skeletal-muscle-cells
#4
Xianlu Peng, Kun Sun, Jiajian Zhou, Hao Sun, Huating Wang
Long intergenic noncoding RNAs (lincRNAs) have emerged as critical participators in gene regulation in myriads of cell types. The development of the whole transcriptome sequencing technology, or RNA-seq , has enabled novel lincRNA detection, but the bioinformatics analysis toward distinguishing reliable ones remains a challenge. Here, we describe the bioinformatics workflow developed for identifying novel lincRNAs step by step, including read alignment, transcriptome assembly and transcript filtering.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28187707/transcriptome-analysis-of-coding-and-long-non-coding-rnas-highlights-the-regulatory-network-of-cascade-initiation-of-permanent-molars-in-miniature-pigs
#5
Fu Wang, Yang Li, Xiaoshan Wu, Min Yang, Wei Cong, Zhipeng Fan, Jinsong Wang, Chunmei Zhang, Jie Du, Songlin Wang
BACKGROUND: In diphyodont mammals, the additional molars (permanent molars) bud off from the posterior-free end of the primary dental lamina compared with successional teeth (replacement teeth) budding off from the secondary dental lamina. The diphyodont miniature pig has proved to be a valuable model for studying human molar morphogenesis. The additional molars show a sequential initiation pattern related to the specific tooth development stage of additional molars in miniature pigs during the morphogenesis of additional molars...
February 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28183149/long-non-coding-rna-analysis-of-muscular-responses-to-testosterone-deficiency-in-huainan-male-pigs
#6
Baosong Xing, Xianxiao Bai, Hongxia Guo, Junfeng Chen, Liushuai Hua, Jiaqing Zhang, Qiang Ma, Qiaoling Ren, Huashuai Wang, Jing Wang
Long non-coding RNAs (lncRNAs) participated in growth and development of skeletal muscle; however, little is known about their response to testosterone deficiency in porcine skeletal muscle. We compared lean mass related carcass traits and lncRNAs expression files in Longissimus dorsi (LD) muscle between intact and castrated Huainan male pigs. The results showed that castration significantly reduced eye muscle area and lean meat percentage (P < 0.05), but increased the fat mass weight (P < 0.05). Meanwhile, 8946 lncRNAs, including 6743 intergenic lncRNAs (lincRNAs), 498 anti-sense lncRNAs, and 1705 intronic lncRNAs, were identified in porcine LD, among which, 385 lncRNAs were considered as the differentially expressed candidates between intact groups and castrated groups (q-value < 0...
February 9, 2017: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/28151474/lincrna-gm4419-knockdown-ameliorates-nf-%C3%AE%C2%BAb-nlrp3-inflammasome-mediated-inflammation-in-diabetic-nephropathy
#7
Hong Yi, Rui Peng, Lu-Yu Zhang, Yan Sun, Hui-Min Peng, Han-Deng Liu, Li-Juan Yu, Ai-Ling Li, Ya-Juan Zhang, Wen-Hao Jiang, Zheng Zhang
Diabetic nephropathy (DN) as the primary cause of end-stage kidney disease is a common complication of diabetes. Recent researches have shown the activation of nuclear factor kappa light-chain enhancer of activated B cells (NF-κB) and NACHT, LRR and PYD domain-containing protein 3 (NLRP3) inflammasome are associated with inflammation in the progression of DN, but the exact mechanism is unclear. Long noncoding RNAs (lncRNAs) have roles in the development of many diseases including DN. However, the relationship between lncRNAs and inflammation in DN remains largely unknown...
February 2, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28143393/identification-and-evolutionary-analysis-of-long-non-coding-rnas-in-zebra-finch
#8
Chih-Kuan Chen, Chun-Ping Yu, Sung-Chou Li, Siao-Man Wu, Mei-Yeh Jade Lu, Yi-Hua Chen, Di-Rong Chen, Chen Siang Ng, Chau-Ti Ting, Wen-Hsiung Li
BACKGROUND: Long non-coding RNAs (lncRNAs) are important in various biological processes, but very few studies on lncRNA have been conducted in birds. To identify IncRNAs expressed during feather development, we analyzed single-stranded RNA-seq (ssRNA-seq) data from the anterior and posterior dorsal regions during zebra finch (Taeniopygia guttata) embryonic development. Using published transcriptomic data, we further analyzed the evolutionary conservation of IncRNAs in birds and amniotes...
January 31, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28129115/hotair-epigenetically-modulates-pten-expression-via-microrna-29b-a-novel-mechanism-in-regulation-of-liver-fibrosis
#9
Fujun Yu, Bicheng Chen, Peihong Dong, Jianjian Zheng
Homeobox transcript antisense RNA (HOTAIR), as a long intergenic non-coding RNA (lincRNA), is upregulated in various cancers and involved in diverse cellular functions. However, its role in liver fibrosis is unclear. In this study, HOTAIR expression was upregulated in hepatic stellate cells (HSCs) in vivo and in vitro during liver fibrosis. HOTAIR knockdown suppressed HSC activation including α-smooth muscle actin (α-SMA) and typeIcollagen in vitro and in vivo. Both HSC proliferation and cell cycle were inhibited by HOTAIR knockdown...
January 4, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28108491/transcriptome-analysis-identifies-multifaceted-regulatory-mechanisms-dictating-a-genetic-switch-from-neuronal-network-establishment-to-maintenance-during-postnatal-prefrontal-cortex-development
#10
Yvet Kroeze, Martin Oti, Ellen van Beusekom, Roel H M Cooijmans, Hans van Bokhoven, Sharon M Kolk, Judith R Homberg, Huiqing Zhou
The prefrontal cortex (PFC) is one of the latest brain regions to mature, which allows the acquisition of complex cognitive abilities through experience. To unravel the underlying gene expression changes during postnatal development, we performed RNA-sequencing (RNA-seq) in the rat medial PFC (mPFC) at five developmental time points from infancy to adulthood, and analyzed the differential expression of protein-coding genes, long intergenic noncoding RNAs (lincRNAs), and alternative exons. We showed that most expression changes occur in infancy, and that the number of differentially expressed genes reduces toward adulthood...
January 19, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28107589/serum-lincrna-p21-as-a-potential-biomarker-of-liver-fibrosis-in-chronic-hepatitis-b-patients
#11
Fujun Yu, Guangyao Zhou, Kate Huang, XuFei Fan, Guojun Li, Bicheng Chen, Peihong Dong, Jianjian Zheng
Serum long non-coding RNAs (lncRNAs) are emerging as promising biomarkers for various human diseases. The aim of this study was to investigate the feasibility of using serum long intergenic non-coding RNA-p21 (lincRNA-p21) as a biomarker for chronic hepatitis B patients. Serum lincRNA-p21 levels were quantified using real-time PCR in 417 CHB patients and 363 healthy controls. The promoter methylation level of lincRNA-p21 was detected using bisulphite-sequencing analysis in primary hepatic stellate cells (HSCs)...
January 20, 2017: Journal of Viral Hepatitis
https://www.readbyqxmd.com/read/28106309/transposable-elements-tes-contribute-to-stress-related-long-intergenic-noncoding-rnas-in-plants
#12
Dong Wang, Zhipeng Qu, Lan Yang, Qingzhu Zhang, Zhi-Hong Liu, Trung Do, David L Adelson, Zhen-Yu Wang, Iain Searle, Jian-Kang Zhu
Noncoding RNAs have been extensively described in plant and animal transcriptomes by using high-throughput sequencing technology. Of these non-coding RNAs, a growing number of long intergenic noncoding RNAs (lincRNAs) have been described in multicellular organisms, however the origins and functions of many lincRNAs remain to be explored. In many eukaryotic genomes, transposable elements (TEs) are widely distributed and often account for large fractions of plant and animal genomes yet the contribution of TEs to lincRNAs is largely unknown...
January 20, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28040802/dysregulated-long-intergenic-non-coding-rna-modules-contribute-to-heart-failure
#13
Lin Pang, Jing Hu, Guanxiong Zhang, Xiang Li, Xinxin Zhang, Fulong Yu, Yujia Lan, Jinyuan Xu, Bo Pang, Dong Han, Yun Xiao, Xia Li
Long intergenic non-coding RNAs (lincRNAs) are emerging as important regulatory molecules involved in diseases including heart failure. However, little is known about how the lincRNAs work together with protein-coding genes (PCGs) contributing to the pathogenesis of heart failure. In this study, we constructed a comprehensive transcriptome profile of lincRNAs, PCGs and miRNAs using RNA-seq and miRNA-seq data of 16 heart failure patients (HFs) and 8 non-failing individuals (NFs). Through integrating lincRNA and PCG expression profiles, we identified HF-associated lincRNA modules...
September 13, 2016: Oncotarget
https://www.readbyqxmd.com/read/28033318/a-point-mutation-in-a-lincrna-upstream-of-gdnf-is-associated-to-a-canine-insensitivity-to-pain-a-spontaneous-model-for-human-sensory-neuropathies
#14
Jocelyn Plassais, Laetitia Lagoutte, Solenne Correard, Manon Paradis, Eric Guaguère, Benoit Hédan, Alix Pommier, Nadine Botherel, Marie-Christine Cadiergues, Philippe Pilorge, David Silversides, Maud Bizot, Mark Samuels, Carme Arnan, Rory Johnson, Christophe Hitte, Gilles Salbert, Agnès Méreau, Pascale Quignon, Thomas Derrien, Catherine André
Human Hereditary Sensory Autonomic Neuropathies (HSANs) are characterized by insensitivity to pain, sometimes combined with self-mutilation. Strikingly, several sporting dog breeds are particularly affected by such neuropathies. Clinical signs appear in young puppies and consist of acral analgesia, with or without sudden intense licking, biting and severe self-mutilation of the feet, whereas proprioception, motor abilities and spinal reflexes remain intact. Through a Genome Wide Association Study (GWAS) with 24 affected and 30 unaffected sporting dogs using the Canine HD 170K SNP array (Illumina), we identified a 1...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/28017589/distinctive-patterns-of-transcription-and-rna-processing-for-human-lincrnas
#15
Margarita Schlackow, Takayuki Nojima, Tomas Gomes, Ashish Dhir, Maria Carmo-Fonseca, Nick J Proudfoot
Numerous long intervening noncoding RNAs (lincRNAs) are generated from the mammalian genome by RNA polymerase II (Pol II) transcription. Although multiple functions have been ascribed to lincRNAs, their synthesis and turnover remain poorly characterized. Here, we define systematic differences in transcription and RNA processing between protein-coding and lincRNA genes in human HeLa cells. This is based on a range of nascent transcriptomic approaches applied to different nuclear fractions, including mammalian native elongating transcript sequencing (mNET-seq)...
January 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/27999969/functions-of-long-intergenic-non-coding-linc-rnas-in-plants
#16
Masashi Yamada
Whole transcriptome analyses in many organisms have revealed that most transcribed RNAs do not encode proteins. These non-coding RNAs likely contribute to the regulation of gene expression during the development of multicellular organisms. In eukaryotes, the roles of small RNAs, one class of non-coding RNAs, in transcriptional and post-transcriptional regulation have been well characterized. However, the functions of a second class of non-coding RNAs, long intergenic noncoding (linc) RNAs, are relatively unknown, especially in plants...
January 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/27988178/a-novel-protein-coding-potential-of-long-intergenic-non-coding-rnas-lincrnas-in-the-kinetoplastid-protozoan-parasite-leishmania-major
#17
Harsh Pawar, Kalpana Pai, Milind S Patole
Cutaneous leishmaniasis (CL) is caused by a kinetoplastid protozoan parasite Leishmania major, as a skin ulcer at the site of the sandfly bite. CL is curable and in most cases ulcers heal spontaneously within three to six months leaving a scar and disfiguration. Complete genome of L. major was reported in 2005 at the very initial phase of kinetoplastid parasite genome sequencing project. Presently, L. major genome is most studied and comprehensively annotated genome and therefore, it is being used as a reference genome for annotating recently sequenced Leishmanial genomes...
March 2017: Acta Tropica
https://www.readbyqxmd.com/read/27979905/a-long-noncoding-rna-lincrna-tnfaip3-acts-as-a-coregulator-of-nf-%C3%AE%C2%BAb-to-modulate-inflammatory-gene-transcription-in-mouse-macrophages
#18
Shibin Ma, Zhenping Ming, Ai-Yu Gong, Yang Wang, Xiqiang Chen, Guoku Hu, Rui Zhou, Annemarie Shibata, Patrick C Swanson, Xian-Ming Chen
Long intergenic noncoding RNAs (lincRNAs) are long noncoding transcripts (>200 nt) from the intergenic regions of annotated protein-coding genes. We report here that the lincRNA gene lincRNA-Tnfaip3, located at mouse chromosome 10 proximal to the tumor necrosis factor α-induced protein 3 (Tnfaip3) gene, is an early-primary response gene controlled by nuclear factor-κB (NF-κB) signaling in murine macrophages. Functionally, lincRNA- Tnfaip3 appears to mediate both the activation and repression of distinct classes of inflammatory genes in macrophages...
March 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/27976428/long-intragenic-non-coding-rna-lincrna-p21-suppresses-development-of-human-prostate-cancer
#19
Xiaohai Wang, Yuan Ruan, Xingjie Wang, Wei Zhao, Qi Jiang, Chenyi Jiang, Yuyang Zhao, Yongzhi Xu, Feng Sun, Yiping Zhu, Shujie Xia, Dongliang Xu
OBJECTIVES: Prostate cancer is one of the most frequent malignancies in men, worldwide, although its underlying mechanisms are not fully understood. Long non-coding RNAs participate in development of human cancers. In this invetsigation, we aimed to study the roles of lincRNA-p21 in development of human prostate cancer. MATERIALS AND METHODS: Expression of lincRNA-p21 was assessed by real-time PCR in cell lines and in human tissues. Lentivirus carrying sh-lincRNA-p21, lincRNA-p21 or control constructs were used to determine their effects on cell proliferation and apoptosis...
April 2017: Cell Proliferation
https://www.readbyqxmd.com/read/27927715/chromatin-environment-transcriptional-regulation-and-splicing-distinguish-lincrnas-and-mrnas
#20
Marta Melé, Kaia Mattioli, William Mallard, David M Shechner, Chiara Gerhardinger, John L Rinn
While long intergenic noncoding RNAs (lincRNAs) and mRNAs share similar biogenesis pathways, these transcript classes differ in many regards. LincRNAs are less evolutionarily conserved, less abundant, and more tissue-specific, suggesting that their pre- and post-transcriptional regulation is different from that of mRNAs. Here, we perform an in-depth characterization of the features that contribute to lincRNA regulation in multiple human cell lines. We find that lincRNA promoters are depleted of transcription factor (TF) binding sites, yet enriched for some specific factors such as GATA and FOS relative to mRNA promoters...
January 2017: Genome Research
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