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https://www.readbyqxmd.com/read/29143279/arabidopsis-noncoding-rna-modulates-seedling-greening-during-deetiolation
#1
Yuqiu Wang, Jian Li, Xing-Wang Deng, Danmeng Zhu
Seedling greening is essential for the survival of plants emerging from the soil. The abundance of chlorophyll precursors, including protochlorophyllide (Pchlide), is precisely controlled during the dark-to-light transition, as over-accumulation of Pchlide can lead to cellular photooxidative damage. Previous studies have identified and characterized multiple regulators controlling this important process. HID1 (hidden treasure 1) is the first noncoding RNA (ncRNA) found in photomorphogenesis. Under continuous red light, HID1 has been shown to inhibit hypocotyl elongation by repressing the transcription of PIF3 (phytochrome interacting factor 3)...
October 13, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/29143182/noncoding-rnas-in-the-regulation-of-pluripotency-and-reprogramming
#2
REVIEW
Vladimir V Sherstyuk, Sergey P Medvedev, Suren M Zakian
Pluripotent stem cells have great potential for developmental biology and regenerative medicine. Embryonic stem cells, which are obtained from blastocysts, and induced pluripotent stem cells, which are generated by the reprogramming of somatic cells, are two main types of pluripotent cells. It is important to understand the regulatory network that controls the pluripotency state and reprogramming process. Various types of noncoding RNAs (ncRNAs) have emerged as substantial components of regulatory networks...
November 15, 2017: Stem Cell Reviews
https://www.readbyqxmd.com/read/29141604/genome-wide-identification-of-mirnas-and-lncrnas-in-cajanus-cajan
#3
Chandran Nithin, Amal Thomas, Jolly Basak, Ranjit Prasad Bahadur
BACKGROUND: Non-coding RNAs (ncRNAs) are important players in the post transcriptional regulation of gene expression (PTGR). On one hand, microRNAs (miRNAs) are an abundant class of small ncRNAs (~22nt long) that negatively regulate gene expression at the levels of messenger RNAs stability and translation inhibition, on the other hand, long ncRNAs (lncRNAs) are a large and diverse class of transcribed non-protein coding RNA molecules (> 200nt) that play both up-regulatory as well as down-regulatory roles at the transcriptional level...
November 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29140524/noncodev5-a-comprehensive-annotation-database-for-long-non-coding-rnas
#4
ShuangSang Fang, LiLi Zhang, JinCheng Guo, YiWei Niu, Yang Wu, Hui Li, LianHe Zhao, XiYuan Li, XueYi Teng, XianHui Sun, Liang Sun, Michael Q Zhang, RunSheng Chen, Yi Zhao
NONCODE (http://www.bioinfo.org/noncode/) is a systematic database that is dedicated to presenting the most complete collection and annotation of non-coding RNAs (ncRNAs), especially long non-coding RNAs (lncRNAs). Since NONCODE 2016 was released two years ago, the amount of novel identified ncRNAs has been enlarged by the reduced cost of next-generation sequencing, which has produced an explosion of newly identified data. The third-generation sequencing revolution has also offered longer and more accurate annotations...
November 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29138457/functional-annotation-of-structural-ncrnas-within-enhancer-rnas-in-the-human-genome-implications-for-human-disease
#5
Chao Ren, Feng Liu, Zhangyi Ouyang, Gaole An, Chenghui Zhao, Jun Shuai, Shuhong Cai, Xiaochen Bo, Wenjie Shu
Enhancer RNAs (eRNAs) are a novel class of non-coding RNA (ncRNA) molecules transcribed from the DNA sequences of enhancer regions. Despite extensive efforts devoted to revealing the potential functions and underlying mechanisms of eRNAs, it remains an open question whether eRNAs are mere transcriptional noise or relevant biologically functional species. Here, we identified a catalogue of eRNAs in a broad range of human cell/tissue types and extended our understanding of eRNAs by demonstrating their multi-omic signatures...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29134599/phage-genome-annotation-using-the-rast-pipeline
#6
Katelyn McNair, Ramy Karam Aziz, Gordon D Pusch, Ross Overbeek, Bas E Dutilh, Robert Edwards
Phages are complex biomolecular machineries that have to survive in a bacterial world. Phage genomes show many adaptations to their lifestyle such as shorter genes, reduced capacity for redundant DNA sequences, and the inclusion of tRNAs in their genomes. In addition, phages are not free-living, they require a host for replication and survival. These unique adaptations provide challenges for the bioinformatics analysis of phage genomes. In particular, ORF calling, genome annotation, noncoding RNA (ncRNA) identification, and the identification of transposons and insertions are all complicated in phage genome analysis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29119346/structure-target-specificity-and-expression-of-pn_lnc_n13-a-long-non-coding-rna-differentially-expressed-in-apomictic-and-sexual-paspalum-notatum
#7
Ana Ochogavía, Giulio Galla, José Guillermo Seijo, Ana María González, Michele Bellucci, Fulvio Pupilli, Gianni Barcaccia, Emidio Albertini, Silvina Pessino
KEY MESSAGE: ncRNA PN_LNC_N13 shows contrasting expression in reproductive organs of sexual and apomictic Paspalum notatum genotypes. Apomictic plants set genetically maternal seeds whose embryos derive by parthenogenesis from unreduced egg cells, giving rise to clonal offspring. Several Paspalum notatum apomixis related genes were identified in prior work by comparative transcriptome analyses. Here, one of these candidates (namely N13) was characterized. N13 belongs to a Paspalum gene family including 30-60 members, of which at least eight are expressed at moderate levels in florets...
November 8, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29118556/long-non-coding-rna-in-pancreatic-adenocarcinoma-and-pancreatic-neuroendocrine-tumors
#8
REVIEW
Dimitrios Moschovis, Maria Gazouli, Maria Tzouvala, Antonios Vezakis, George Karamanolis
Interest in non-coding regions of DNA has been increasing since the mapping of the human genome revealed that human DNA contains far fewer genes encoding proteins than previously expected. However, analysis of the derivatives of DNA transcription (transcriptomics) revealed that the majority of the genetic material is transcribed into non-coding RNA (ncRNA), indicating that these molecules probably provide the functional diversity and complexity of the physiology of the human body that cannot be attributed to the proteins...
2017: Annals of Gastroenterology: Quarterly Publication of the Hellenic Society of Gastroenterology
https://www.readbyqxmd.com/read/29108237/the-circrna-interactome-innovative-hallmarks-of-the-intra-and-extracellular-radiation-response
#9
Valerie Bríd O'Leary, Jan Smida, Martina Matjanovski, Corinna Brockhaus, Klaudia Winkler, Simone Moertl, Saak Victor Ovsepian, Michael John Atkinson
Generated by Quaking (QKI), circular RNAs (circRNAs) are newly recognised non-coding RNA (ncRNA) members characterised by tissue specificity, increased stability and enrichment within exosomes. Studies have shown that ionizing radiation (IR) can influence ncRNA transcription. However, it is unknown whether circRNAs or indeed QKI are regulated by IR. Microarray circRNA profiling and next generation sequencing revealed that circRNA expression was altered by low and medium dose exposure sourced predominantly from genes influencing the p53 pathway...
October 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/29107014/circular-rna-profiling-reveals-chi_circ_0008219-function-as-microrna-sponges-in-pre-ovulatory-ovarian-follicles-of-goats-capra-hircus
#10
Hu Tao, Qi Xiong, Feng Zhang, Nian Zhang, Yang Liu, Xiaojun Suo, Xiaofeng Li, Qianping Yang, Mingxin Chen
Circular RNAs (circRNAs) are a new class of non-coding RNAs in animals and are a novel target of non-coding RNA (ncRNA) regulation. The mechanism and function of circRNAs have been reported in some species and tissues. However, there is little available information on the functions of circRNAs in the goat reproductive system. In the present study, we deeply sequenced and analyzed circRNAs through bioinformatics to reveal the expression profiles, and predicted 13,950 circRNAs in the pre-ovulatory ovarian follicles of goats for the first time...
October 26, 2017: Genomics
https://www.readbyqxmd.com/read/29106639/mndr-v2-0-an-updated-resource-of-ncrna-disease-associations-in-mammals
#11
Tianyu Cui, Lin Zhang, Yan Huang, Ying Yi, Puwen Tan, Yue Zhao, Yongfei Hu, Liyan Xu, Enmin Li, Dong Wang
Accumulating evidence suggests that diverse non-coding RNAs (ncRNAs) are involved in the progression of a wide variety of diseases. In recent years, abundant ncRNA-disease associations have been found and predicted according to experiments and prediction algorithms. Diverse ncRNA-disease associations are scattered over many resources and mammals, whereas a global view of diverse ncRNA-disease associations is not available for any mammals. Hence, we have updated the MNDR v2.0 database (www.rna-society.org/mndr/) by integrating experimental and prediction associations from manual literature curation and other resources under one common framework...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29093215/salt-stress-and-ctd-phosphatase-like-4-mediate-the-switch-between-production-of-small-nuclear-rnas-and-mrnas
#12
Akihito Fukudome, Di Sun, Xiuren Zhang, Hisashi Koiwa
Phosphorylation of the RNA polymerase II (Pol II) C-terminal domain (CTD) regulates transcription of protein-coding mRNAs and non-coding RNAs (ncRNAs). CTD function in transcription of protein-coding RNAs has been studied extensively, but its role in plant ncRNA transcription remains obscure. Here, using Arabidopsis thaliana CTD PHOSPHATASE-LIKE 4 knock-down lines (CPL4RNAi), we showed that CPL4 functions in genome-wide, conditional production of 3'-extensions of small nuclear RNAs (snRNAs) and biogenesis of novel transcripts from protein-coding genes downstream of the snRNAs (snRNA-Downstream Protein-coding Genes, snR-DPGs)...
November 1, 2017: Plant Cell
https://www.readbyqxmd.com/read/29079534/epigenetic-reprogramming-in-liver-fibrosis-and-cancer
#13
Caroline L Wilson, Derek A Mann, Lee A Borthwick
Novel insights into the epigenetic control of chronic liver diseases are now emerging. Recent advances in our understanding of the critical roles of DNA methylation, histone modifications and ncRNA may now be exploited to improve management of fibrosis/cirrhosis and cancer. Furthermore, improved technologies for the detection of epigenetic markers from patients' blood and tissues will vastly improve diagnosis, treatment options and prognostic tracking. The aim of this review is to present recent findings from the field of liver epigenetics and to explore their potential for translation into therapeutics to prevent disease promoting epigenome reprogramming and reverse epigenetic changes...
October 25, 2017: Advanced Drug Delivery Reviews
https://www.readbyqxmd.com/read/29073095/broad-role-for-ybx1-in-defining-the-small-noncoding-rna-composition-of-exosomes
#14
Matthew J Shurtleff, Jun Yao, Yidan Qin, Ryan M Nottingham, Morayma M Temoche-Diaz, Randy Schekman, Alan M Lambowitz
RNA is secreted from cells enclosed within extracellular vesicles (EVs). Defining the RNA composition of EVs is challenging due to their coisolation with contaminants, lack of knowledge of the mechanisms of RNA sorting into EVs, and limitations of conventional RNA-sequencing methods. Here we present our observations using thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) to characterize the RNA extracted from HEK293T cell EVs isolated by flotation gradient ultracentrifugation and from exosomes containing the tetraspanin CD63 further purified from the gradient fractions by immunoisolation...
October 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29062204/repertoire-of-noncoding-rnas-in-corpus-luteum-of-early-pregnancy-in-buffalo-bubalus-bubalis
#15
A Jerome, S M K Thirumaran, S N Kala
AIM: The present study was designed to identify other noncoding RNAs (ncRNAs) in the corpus luteum (CL) during early pregnancy in buffalo. MATERIALS AND METHODS: For this study, CL (n=2) from two buffalo gravid uteri, obtained from the slaughter house, was transported to laboratory after snap freezing in liquid nitrogen (-196°C). The stage of pregnancy was determined by measuring the crown-rump region of the fetus. This was followed by isolation of RNA and deep sequencing...
September 2017: Veterinary World
https://www.readbyqxmd.com/read/29049011/-omics-of-food-borne-gastroenteritis-global-proteomic-and-mutagenic-analysis-of-salmonella-enterica-serovar-enteritidis
#16
Aryashree Arunima, Soujanya D Yelamanchi, Chandrashekhar Padhi, Sangeeta Jaiswal, Daniel Ryan, Bhawna Gupta, Gajanan Sathe, Jayshree Advani, Harsha Gowda, T S Keshava Prasad, Mrutyunjay Suar
Salmonella Enteritidis causes food-borne gastroenteritis by the two type three secretion systems (TTSS). TTSS-1 mediates invasion through intestinal lining, and TTSS-2 facilitates phagocytic survival. The pathogens' ability to infect effectively under TTSS-1-deficient background in host's phagocytes is poorly understood. Therefore, pathobiological understanding of TTSS-1-defective nontyphoidal Salmonellosis is highly important. We performed a comparative global proteomic analysis of the isogenic TTSS-1 mutant of Salmonella Enteritidis (M1511) and its wild-type isolate P125109...
October 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29037607/dynamic-organization-of-lncrna-and-circular-rna-regulators-collectively-controlled-cardiac-differentiation-in-humans
#17
Yongsheng Li, Jinwen Zhang, Caiqin Huo, Na Ding, Junyi Li, Jun Xiao, Xiaoyu Lin, Benzhi Cai, Yunpeng Zhang, Juan Xu
Advances in developmental cardiology have increased our understanding of the early aspects of heart differentiation. However, understanding noncoding RNA (ncRNA) transcription and regulation during this process remains elusive. Here, we constructed transcriptomes for both long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) in four important developmental stages ranging from early embryonic to cardiomyocyte based on high-throughput sequencing datasets, which indicate the high stage-specific expression patterns of two ncRNA types...
October 2017: EBioMedicine
https://www.readbyqxmd.com/read/29036693/icg-a-wiki-driven-knowledgebase-of-internal-control-genes-for-rt-qpcr-normalization
#18
Jian Sang, Zhennan Wang, Man Li, Jiabao Cao, Guangyi Niu, Lin Xia, Dong Zou, Fan Wang, Xingjian Xu, Xiaojiao Han, Jinqi Fan, Ye Yang, Wanzhu Zuo, Yang Zhang, Wenming Zhao, Yiming Bao, Jingfa Xiao, Songnian Hu, Lili Hao, Zhang Zhang
Real-time quantitative PCR (RT-qPCR) has become a widely used method for accurate expression profiling of targeted mRNA and ncRNA. Selection of appropriate internal control genes for RT-qPCR normalization is an elementary prerequisite for reliable expression measurement. Here, we present ICG (http://icg.big.ac.cn), a wiki-driven knowledgebase for community curation of experimentally validated internal control genes as well as their associated experimental conditions. Unlike extant related databases that focus on qPCR primers in model organisms (mainly human and mouse), ICG features harnessing collective intelligence in community integration of internal control genes for a variety of species...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29031633/translation-of-noncoding-rnas-focus-on-lncrnas-pri-mirnas-and-circrnas
#19
REVIEW
Lian-Ju Li, Rui-Xue Leng, Yin-Guang Fan, Hai-Feng Pan, Dong-Qing Ye
Mammalian genome is pervasively transcribed, producing large number of noncoding RNAs (ncRNAs), including long noncoding RNAs (lncRNAs), primary miRNAs (pri-miRNA), and circular RNAs (circRNAs). The translation of these ncRNAs has long been overlooked. Increasing studies, however, based on ribosome profiling in various organisms provide important clues to unanticipated translation potential of lncRNAs. Moreover, a few functional peptides encoded by lncRNAs and pri-miRNAs underline the significance of their translation...
October 12, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/29029611/identification-of-15-candidate-structured-noncoding-rna-motifs-in-fungi-by-comparative-genomics
#20
Sanshu Li, Ronald R Breaker
BACKGROUND: With the development of rapid and inexpensive DNA sequencing, the genome sequences of more than 100 fungal species have been made available. This dataset provides an excellent resource for comparative genomics analyses, which can be used to discover genetic elements, including noncoding RNAs (ncRNAs). Bioinformatics tools similar to those used to uncover novel ncRNAs in bacteria, likewise, should be useful for searching fungal genomic sequences, and the relative ease of genetic experiments with some model fungal species could facilitate experimental validation studies...
October 13, 2017: BMC Genomics
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