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https://www.readbyqxmd.com/read/29340599/a-benchmark-study-of-scoring-methods-for-non-coding-mutations
#1
Damien Drubay, Daniel Gautheret, Stefan Michiels
Motivation: Detailed knowledge of coding sequences has led to different candidate models for pathogenic variant prioritization. Several deleteriousness scores have been proposed for the non-coding part of the genome, but no large-scale comparison has been realized to date to assess their performance. Results: We compared the leading scoring tools (CADD, FATHMM-MKL, Funseq2 and GWAVA) and some recent competitors (DANN, SNP and SOM scores) for their ability to discriminate assumed pathogenic variants from assumed benign variants (using the ClinVar, COSMIC and 1000 genomes project databases)...
January 11, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29324704/dissection-of-myogenic-differentiation-signatures-in-chickens-by-rna-seq-analysis
#2
Tingting Li, Genxi Zhang, Pengfei Wu, Lian Duan, Guohui Li, Qiuhong Liu, Jinyu Wang
A series of elaborately regulated and orchestrated changes in gene expression profiles leads to muscle growth and development. In this study, RNA sequencing was used to profile embryonic chicken myoblasts and fused myotube transcriptomes, long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs) at four stages of myoblast differentiation. Of a total of 2484 lncRNA transcripts, 2288 were long intergenic non-coding RNAs (lincRNAs) and 198 were antisense lncRNAs. Additionally, 1530 lncRNAs were neighboring 2041 protein-coding genes (<10 kb upstream and downstream) and functionally enriched in several pathways related to skeletal muscle development that have been extensively studied, indicating that these genes may be in cis-regulatory relationships...
January 11, 2018: Genes
https://www.readbyqxmd.com/read/29308735/targeting-lncrnas-for-cardiovascular-therapeutics-in-coronary-artery-disease
#3
Dongsheng Yu, Chuanfeng Tang, Peiyu Liu, Weichun Qian, Liang Sheng
Long non-coding RNAs (lncRNAs) could regulate gene expression at posttranscriptional state, and might be a new therapeutic option in human disease. Mounting studies in the past few years have documented important functions for lncRNAs in coronary artery diseases (CAD). Among these lncRNAs, H19, MIAT, ANRIL, lincRNA-p21, AC100865.1, OTTHUMT00000387022, NONHSAT112178, Novlnc6, MALAT1, LIPCAR and SRA have been proposed to be novel regulators and/or biomarkers of CAD, and involved in the initiation and progression of the pathology...
January 8, 2018: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/29297358/stable-solution-to-l-2-1-based-robust-inductive-matrix-completion-and-its-application-in-linking-long-noncoding-rnas-to-human-diseases
#4
Ashis Kumer Biswas, Dongchul Kim, Mingon Kang, Chris Ding, Jean X Gao
BACKGROUNDS: A large number of long intergenic non-coding RNAs (lincRNAs) are linked to a broad spectrum of human diseases. The disease association with many other lincRNAs still remain as puzzle. Validation of such links between the two entities through biological experiments are expensive. However, a plethora lincRNA-data are available now, thanks to the High Throughput Sequencing (HTS) platforms, Genome Wide Association Studies (GWAS), etc, which opens the opportunity for cutting-edge machine learning and data mining approaches to extract meaningful relationships among lincRNAs and diseases...
December 28, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29284742/the-long-intergenic-non-coding-rna-lincrna-landscape-of-the-soybean-genome
#5
Agnieszka Golicz, Mohan B Singh, Prem L Bhalla
Long intergenic non-coding RNAs (lincRNAs) are emerging as important regulators of diverse biological processes. However, our understanding of lincRNA abundance and function remains very limited especially for agriculturally important plants. Soybean is a major legume crop plant providing over a half of global oilseed production. Moreover, soybean can form symbiotic relationships with Rhizobium bacteria to fix atmospheric nitrogen. Soybean has a complex paleopolyploid genome and exhibits many vegetative and floral development complexities...
December 28, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29280973/transcriptome-wide-identification-and-characterization-of-potato-circular-rnas-in-response-to-pectobacterium-carotovorum-subspecies-brasiliense-infection
#6
Ran Zhou, Yongxing Zhu, Jiao Zhao, Zhengwu Fang, Shuping Wang, Junliang Yin, Zhaohui Chu, Dongfang Ma
Little information about the roles of circular RNAs (circRNAs) during potato-Pectobacterium carotovorum subsp. brasiliense (Pcb) interaction is currently available. In this study, we conducted the systematic identification of circRNAs from time series samples of potato cultivars Valor (susceptible) and BP1 (disease tolerant) infected by Pcb. A total of 2098 circRNAs were detected and about half (931, 44.38%) were intergenic circRNAs. And differential expression analysis detected 429 significantly regulated circRNAs...
December 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29276809/new-advances-in-human-x-chromosome-status-from-a-developmental-and-stem-cell-biology
#7
Benjamin Patterson, Yoshiaki Tanaka, In-Hyun Park
Recent advances in stem cell biology have dramatically increased the understanding of molecular and cellular mechanism of pluripotency and cell fate determination. Additionally, pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), arose as essential resources for disease modeling and cellular therapeutics. Despite these advancements, the epigenetic dysregulation in pluripotency such as the imprinting status, and X chromosome dosage compensation, and its consequences on future utility of PSCs yet remain unresolved...
December 2017: Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/29258423/the-coding-and-noncoding-transcriptome-of-neurospora-crassa
#8
Ibrahim Avi Cemel, Nati Ha, Geza Schermann, Shusuke Yonekawa, Michael Brunner
BACKGROUND: Long non protein coding RNAs (lncRNAs) have been identified in many different organisms and cell types. Emerging examples emphasize the biological importance of these RNA species but their regulation and functions remain poorly understood. In the filamentous fungus Neurospora crassa, the annotation and characterization of lncRNAs is incomplete. RESULTS: We have performed a comprehensive transcriptome analysis of Neurospora crassa by using ChIP-seq, RNA-seq and polysome fractionation datasets...
December 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29244011/a-deep-learning-method-for-lincrna-detection-using-auto-encoder-algorithm
#9
Ning Yu, Zeng Yu, Yi Pan
BACKGROUND: RNA sequencing technique (RNA-seq) enables scientists to develop novel data-driven methods for discovering more unidentified lincRNAs. Meantime, knowledge-based technologies are experiencing a potential revolution ignited by the new deep learning methods. By scanning the newly found data set from RNA-seq, scientists have found that: (1) the expression of lincRNAs appears to be regulated, that is, the relevance exists along the DNA sequences; (2) lincRNAs contain some conversed patterns/motifs tethered together by non-conserved regions...
December 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29229759/jmjd6-induces-hotair-an-oncogenic-lincrna-by-physically-interacting-with-its-proximal-promoter
#10
Antara Biswas, Abhijith Shettar, Geetashree Mukherjee, Paturu Kondaiah, Kartiki V Desai
<span style="color: black;">Using microarray analysis we found that HOX transcript antisense intergenic RNA (HOTAIR) is upregulated by Jumonji domain containing-6 (JMJD6), a bifunctional lysyl hydroxylase and arginine demethylase. In breast cancer, JMJD6 and HOTAIR RNAs increase tumor growth and associate with poor prognosis but no molecular relationship between them is known. We show that overexpression of JMJD6 increased HOTAIR expression and JMJD6 siRNAs suppressed it in ER+ MCF-7, triple negative MDA-MB-231 and non-breast cancer HEK 293 cells...
December 11, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29218910/pan-cancer-analysis-of-expressed-somatic-nucleotide-variants-in-long-intergenic-non-coding-rna
#11
Travers Ching, Lana X Garmire
Long intergenic non-coding RNAs have been shown to play important roles in cancer. However, because lincRNAs are a relatively new class of RNAs compared to protein-coding mRNAs, the mutational landscape of lincRNAs has not been as extensively studied. Here we characterize expressed somatic nucleotide variants within lincRNAs using 12 cancer RNA-Seq datasets in TCGA. We build machine-learning models to discriminate somatic variants from germline variants within lincRNA regions (AUC 0.987). We build another model to differentiate lincRNA somatic mutations from background regions (AUC 0...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29216625/missing-links-in-epithelial-mesenchymal-transition-long-non-coding-rnas-enter-the-arena
#12
Lei Wang, Fan Yang, Lin-Tao Jia, An-Gang Yang
Cancer metastasis occurs through a series of sequential steps, which involves dissemination of tumor cells from a primary site and colonization in distant tissues. To promote the invasion-metastasis cascade, carcinoma cells usually initiate a cell-biological program called epithelial-mesenchymal transition (EMT), which is orchestrated by a set of master regulators, including TGF-β, Snail, ZEB and Twist families. The biological activities of these molecules are tightly regulated by a variety of cell-intrinsic pathways as well as extracellular cues...
December 6, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29209947/copy-number-variation-arising-from-gene-conversion-on-the-human-y-chromosome
#13
Wentao Shi, Andrea Massaia, Sandra Louzada, Ruby Banerjee, Pille Hallast, Yuan Chen, Anders Bergström, Yong Gu, Steven Leonard, Michael A Quail, Qasim Ayub, Fengtang Yang, Chris Tyler-Smith, Yali Xue
We describe the variation in copy number of a ~ 10 kb region overlapping the long intergenic noncoding RNA (lincRNA) gene, TTTY22, within the IR3 inverted repeat on the short arm of the human Y chromosome, leading to individuals with 0-3 copies of this region in the general population. Variation of this CNV is common, with 266 individuals having 0 copies, 943 (including the reference sequence) having 1, 23 having 2 copies, and two having 3 copies, and was validated by breakpoint PCR, fibre-FISH, and 10× Genomics Chromium linked-read sequencing in subsets of 1234 individuals from the 1000 Genomes Project...
December 5, 2017: Human Genetics
https://www.readbyqxmd.com/read/29209086/long-noncoding-rnas-that-respond-to-fusarium-oxysporum-infection-in-cavendish-banana-musa-acuminata
#14
Wenbin Li, Chunqiang Li, Shuxia Li, Ming Peng
Long noncoding RNAs (lncRNAs) are a class of genes that influence a variety of biological functions through acting as signal, decoy, guide, and scaffold molecules. In banana (Musa spp.), an important economic fruit crop, particularly in Southeast Asia, the wilt disease caused by Fusarium oxysporum f. sp. cubense (Foc), especially strain Foc TR4, is disastrous. In banana, how the biogenesis of these lncRNAs is regulated in response to pathogen infection is still largely unknown. In this study, strand-specific paired-end RNA sequencing of banana samples was performed on susceptible and resistant cultivars inoculated with Foc, with three biological replicates and at two different times after infection...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29207671/ginkgo-biloba-extract-egb-761-induced-upregulation-of-lincrna-p21-inhibits-colorectal-cancer-metastasis-by-associating-with-ezh2
#15
Tingting Liu, Junzhong Zhang, Zhongqiu Chai, Gang Wang, Naiqiang Cui, Bing Zhou
EGb 761, the standard ginkgo biloba extract, is frequently prescribed in traditional Chinese medicine. Currently, there is no research focusing on its role in human colorectal cancer progression. In our study, we determined the anti-metastatic effect of EGb 761 on colorectal cancer cells and further explored the potential underlying regulatory mechanism. The cell migration and invasion assay indicated that EGb 761 treatment of colorectal cancer cells induced inhibition of cell migration and invasion ability in a concentration-dependent manner...
October 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/29207090/long-intergenic-non%C3%A2-coding-rna%C3%A2-p21-mediates-cardiac-senescence-via-the-wnt-%C3%AE-%C3%A2-catenin-signaling-pathway-in-doxorubicin-induced-cardiotoxicity
#16
Zhongdong Xie, Wenzheng Xia, Meng Hou
Doxorubicin (Dox)-induced cardiotoxicity has been a well‑known phenomenon to clinicians and scientists for decades. It has been confirmed that Dox‑dependent cardiotoxicity is accompanied by cardiac cellular senescence. However, the molecular mechanisms underlying Dox cardiotoxicity remains to be fully elucidated. Long non‑coding (lnc) RNAs regulate gene transcription and the fate of post‑transcriptional mRNA, which affects a broad range of age‑associated physiological and pathological conditions, including cardiovascular disease and cellular senescence...
November 28, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29167551/a-novel-snp-in-promoter-region-of-rp11-3n2-1-is-associated-with-reduced-risk-of-colorectal-cancer
#17
Ding Ye, Yunqing Hu, Fangyuan Jing, Yingjun Li, Simeng Gu, Xiyi Jiang, Yingying Mao, Qilong Li, Mingjuan Jin, Kun Chen
Single-nucleotide polymorphisms (SNPs) in the promoter region of long intergenic non-coding RNAs (lincRNAs) could play a regulatory role in its expression level and then get involved in colorectal cancer (CRC). Thus, we conducted a two-stage case-control study to investigate the associations of Tag SNPs within the promoter region of selected lincRNAs from microarray data with risk of CRC. A total of 320 cases and 319 controls were recruited in the test set to explore the associations between 16 SNPs with no deviations from Hardy-Weinberg equilibrium (HWE) and risk of CRC...
October 5, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/29156779/selecting-lncrnas-in-gastric-cancer-cells-for-directed-therapy-with-bioactive-peptides-and-chemotherapy-drugs
#18
Wenyan Han, Rui Xiao, Chuanling Zhang, Qimuge Suyila, Xian Li, Xiulan Su
Selecting lncRNAs for directed therapy with bioactive peptides and chemotherapy drugs may be an effective approach to treating gastric cancer (GC). We show genome-scale identification and characterization of differentially expressed lncRNAs in GC cells treated with a novel anti-cancer bioactive peptide (ACBP) and the chemotherapy drug oxaliplatin (ASLB). A total of 17,897 lncRNAs were identified through pairwise comparison, including 2,074 novel lncRNAs. Of those, 1,386 lncRNAs were differentially expressed (over 1...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29138516/the-functions-and-unique-features-of-long-intergenic-non-coding-rna
#19
REVIEW
Julia D Ransohoff, Yuning Wei, Paul A Khavari
Long intergenic non-coding RNA (lincRNA) genes have diverse features that distinguish them from mRNA-encoding genes and exercise functions such as remodelling chromatin and genome architecture, RNA stabilization and transcription regulation, including enhancer-associated activity. Some genes currently annotated as encoding lincRNAs include small open reading frames (smORFs) and encode functional peptides and thus may be more properly classified as coding RNAs. lincRNAs may broadly serve to fine-tune the expression of neighbouring genes with remarkable tissue specificity through a diversity of mechanisms, highlighting our rapidly evolving understanding of the non-coding genome...
November 15, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/29137272/immunological-cytokine-profiling-identifies-tnf-%C3%AE-as-a-key-molecule-dysregulated-in-autistic-children
#20
Jiang Xie, Li Huang, Xiaohong Li, Hua Li, Yongmei Zhou, Hua Zhu, Tianying Pan, Keith M Kendrick, Wenming Xu
Recent studies have suggested that the etiology of autism spectrum disorder (ASD) may be caused by immunological factors, particularly abnormalities in the innate immune system. However, it is still unclear which specific cytokines may be of most importance. The current study therefore investigated which cytokines showed altered concentrations in blood in ASD compared with healthy control children and which were also correlated with symptom severity. Our study sample included 32 children diagnosed with ASD and 28 age and sex-matched typically developing children...
October 10, 2017: Oncotarget
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