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https://www.readbyqxmd.com/read/28749988/switching-of-dominant-retrotransposon-silencing-strategies-from-posttranscriptional-to-transcriptional-mechanisms-during-male-germ-cell-development-in-mice
#1
Kota Inoue, Kenji Ichiyanagi, Kei Fukuda, Michael Glinka, Hiroyuki Sasaki
Mammalian genomes harbor millions of retrotransposon copies, some of which are transpositionally active. In mouse prospermatogonia, PIWI-interacting small RNAs (piRNAs) combat retrotransposon activity to maintain the genomic integrity. The piRNA system destroys retrotransposon-derived RNAs and guides de novo DNA methylation at some retrotransposon promoters. However, it remains unclear whether DNA methylation contributes to retrotransposon silencing in prospermatogonia. We have performed comprehensive studies of DNA methylation and polyA(+) RNAs (transcriptome) in developing male germ cells from Pld6/Mitopld and Dnmt3l knockout mice, which are defective in piRNA biogenesis and de novo DNA methylation, respectively...
July 27, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28749585/mir3954-is-a-trigger-of-phasirnas-that-affects-flowering-time-in-citrus
#2
Yuanlong Liu, Lili Ke, Guizhi Wu, Yuantao Xu, Xiaomeng Wu, Rui Xia, Xiuxin Deng, Qiang Xu
In plant, a few 22 nt miRNAs direct cleavages of their targets and trigger the biogenesis of phased small interfering RNAs (phasiRNAs) in plant. In this study, we characterized a miRNA triggering phasiRNAs generation, miR3954, and explored its downstream target genes and potential function. Our results demonstrated that miR3954 showed specific expression in the flowers of citrus species and it targeted a NAC transcription factor (Cs7g22460) and two non-coding RNA transcripts (lncRNAs, Cs1g09600 and Cs1g09635)...
July 27, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28748214/functionally-pathogenic-ears2-variants-in-vitro-may-not-manifest-a-phenotype-in-vivo
#3
Nathan McNeill, Alessia Nasca, Aurelio Reyes, Benjamin Lemoine, Brandi Cantarel, Adeline Vanderver, Raphael Schiffmann, Daniele Ghezzi
OBJECTIVE: To investigate the genetic etiology of a patient diagnosed with leukoencephalopathy, brain calcifications, and cysts (LCC). METHODS: Whole-exome sequencing was performed on a patient with LCC and his unaffected family members. The variants were subject to in silico and in vitro functional testing to determine pathogenicity. RESULTS: Whole-exome sequencing uncovered compound heterozygous mutations in EARS2, c.328G>A (p.G110S), and c...
August 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28743023/principles-of-transgenerational-small-rna-inheritance-in-caenorhabditis-elegans
#4
REVIEW
Oded Rechavi, Itamar Lev
Examples of transgenerational inheritance of environmental responses are rapidly accumulating. In Caenorhabditis elegans nematodes, such heritable information transmits across generations in the form of RNA-dependent RNA polymerase-amplified small RNAs. Regulatory small RNAs enable sequence-specific gene regulation, and unlike chromatin modifications, can move between tissues, and escape from immediate germline reprogramming. In this review, we discuss the path that small RNAs take from the soma to the germline, and elaborate on the mechanisms that maintain or erase parental small RNA responses after a specific number of generations...
July 24, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28742088/genome-wide-identification-of-hami-melon-mirnas-with-putative-roles-during-fruit-development
#5
Hong Zhang, Lan Yin, Huaisong Wang, Guangzhi Wang, Xinli Ma, Meihua Li, Haibo Wu, Qiushi Fu, Yi Zhang, Hongping Yi
MicroRNAs represent a family of small endogenous, non-coding RNAs that play critical regulatory roles in plant growth, development, and environmental stress responses. Hami melon is famous for its attractive flavor and excellent nutritional value, however, the mechanisms underlying the fruit development and ripening remains largely unknown. Here, we performed small RNA sequencing to investigate the roles of miRNAs during Hami melon fruit development. Two batches of flesh samples were collected at four fruit development stages...
2017: PloS One
https://www.readbyqxmd.com/read/28741097/distribution-and-phylogenetic-analysis-of-blastocystis-sp-subtypes-isolated-from-ibd-patients-and-healthy-individuals-in-iran
#6
H Mirjalali, M R Abbasi, N Naderi, Z Hasani, E S Mirsamadi, C R Stensvold, H Balaii, H Asadzadeh Aghdaei, M R Zali
Blastocystis is a single-celled intestinal parasite commonly found in humans and a broad range of animals all over the world. In humans, its role in health and disease remains unsettled. The aim of our study was to investigate the distribution of Blastocystis and Blastocystis subtypes (ST) in patients with inflammatory bowel disease (IBD) and control subjects. A total of 71 stool samples were collected from IBD patients, 69 and 2 of whom had ulcerative colitis (UC) and Crohn's Disease (CD), respectively. Moreover, 166 stool samples from healthy subjects were included as control samples...
July 25, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28738012/evaluation-of-protein-kinase-ck2-as-a-therapeutic-target-for-squamous-cell-carcinoma-of-cats
#7
Claire M Cannon, Janeen H Trembley, Betsy T Kren, Gretchen M Unger, M Gerard O'Sullivan, Ingrid Cornax, Jaime F Modiano, Khalil Ahmed
OBJECTIVE To investigate protein kinase CK2 (CK2) expression in squamous cell carcinoma (SCC) of cats and to examine effects of CK2 downregulation on in vitro apoptosis and viability in SCC. SAMPLE Biopsy specimens of oral mucosa and testis and blood samples from clinically normal cats, biopsy specimens of oral SCC from cats, and feline SCC (SCCF1) and mammary gland carcinoma (K12) cell lines. PROCEDURES Immunohistochemical labeling for CK2α was performed on biopsy specimens. Sequences of the CK2α subunit gene and CK2α' subunit gene in feline blood and feline cancer cell lines were determined by use of PCR and reverse-transcription PCR assays followed by direct Sanger sequencing...
August 2017: American Journal of Veterinary Research
https://www.readbyqxmd.com/read/28737826/comparison-of-isolation-methods-of-exosomes-and-exosomal-rna-from-cell-culture-medium-and-serum
#8
Yue-Ting Tang, Yi-Yao Huang, Lei Zheng, Si-Hua Qin, Xu-Ping Xu, Tai-Xue An, Yong Xu, Ying-Song Wu, Xiu-Mei Hu, Bao-Hong Ping, Qian Wang
Exosomes are cell-derived vesicles and are abundant in biological fluids; they contain RNA molecules which may serve as potential diagnostic biomarkers in 'precision medicine'. To promote the clinical application of exosomal RNA (exoRNA), many isolation methods must be compared and validated. Exosomes in cell culture medium (CCM) and serum may be isolated using ultracentrifugation (UC), ExoQuick or Total Exosome Isolation Reagent (TEI), and exoRNA may be extracted using TRIzol-LS, SeraMir, Total Exosome RNA Isolation (TER), HiPure Liquid RNA/miRNA kit (HLR), miRNeasy or exoRNeasy...
July 24, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28737113/micrornas-roles-in-regulating-neuroinflammation
#9
Andrew D Gaudet, Laura K Fonken, Linda R Watkins, Randy J Nelson, Phillip G Popovich
MicroRNAs (miRNAs) are small noncoding RNAs that broadly affect cellular and physiological function in all multicellular organisms. Here, the role of miRNAs in neuroinflammation is considered. miRNAs are 21- to 23-oligonucleotide RNAs that regulate translation of specific RNAs by binding to complementary regulatory RNA sequences, thereby causing mRNA degradation or sequestration. More than 5000 miRNAs likely exist in humans, and each miRNA binds an average of 200 RNAs. Specific immunomodulatory miRNAs can regulate a set of RNAs in a coordinated manner, suggesting that effective miRNA-based therapeutic manipulations for neuroinflammatory conditions may be revealed...
July 1, 2017: Neuroscientist: a Review Journal Bringing Neurobiology, Neurology and Psychiatry
https://www.readbyqxmd.com/read/28736753/combination-of-rt-pcr-and-proteomics-for-the-identification-of-crimean-congo-hemorrhagic-fever-virus-in-ticks
#10
Isabel G Fernández de Mera, Ilias Chaligiannis, Angélica Hernández-Jarguín, Margarita Villar, Lourdes Mateos-Hernández, Anna Papa, Smaragda Sotiraki, Francisco Ruiz-Fons, Alejandro Cabezas-Cruz, Christian Gortázar, José de la Fuente
Crimean-Congo hemorrhagic fever (CCHF) is an emerging tick-borne zoonotic disease caused by the CCHF virus (CCHFV). In this study, an experimental approach combining RT-PCR and proteomics was used for the identification and characterization of CCHFV in 106 ticks from 7 species that were collected from small ruminants in Greece. The methodological approach included an initial screening for CCHFV by RT-PCR followed by proteomics analysis of positive and control negative tick samples. This novel approach allowed the identification of CCHFV-positive ticks and provided additional information to corroborate the RT-PCR findings using a different approach...
July 2017: Heliyon
https://www.readbyqxmd.com/read/28736700/profiling-and-characterization-of-a-longissimus-dorsi-muscle-microrna-dataset-from-an-f2-duroc%C3%A2-%C3%A3-%C3%A2-pietrain-pig-resource-population
#11
Kaitlyn R Daza, Juan P Steibel, Deborah Velez-Irizarry, Nancy E Raney, Ronald O Bates, Catherine W Ernst
To elucidate the effects of microRNA (miRNA) regulation in skeletal muscle of adult pigs, miRNA expression profiling was performed with RNA extracted from longissimus dorsi (LD) muscle samples from 174 F2 pigs (~ 5.5 months of age) from a Duroc × Pietrain resource population. Total RNA was extracted from LD samples, and libraries were sequenced on an Illumina HiSeq 2500 platform in 1 × 50 bp format. After processing, 232,826,977 total reads were aligned to the Sus scrofa reference genome (v10.2.79), with 74...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28736361/-effect-of-nucleolin-silencing-on-differentiation-of-rat-neural-stem-cells-in-vitro-and-the-molecular-mechanism
#12
Chong-Feng Chen, Huai-Cai Yang, Guo-Sheng Liu
OBJECTIVE: To investigate the effect of nucleolin silencing on the differentiation of rat neural stem cells (NSCs) and the role of Wnt signaling pathway in mediating such effect. METHODS: Adenovirus vectors expressing small interfering RNA (siRNA) against nucleolin were constructed, verified, and packaged in HEK293A cells. The adenovirus was then transfected into NSCs isolated from neonatal SD rats and the differentiation of the NSCs was examined by detecting the expressions of neuron specific encloase (NSE) and glial fibrillary acidic protein (GFAP) using immunocytochemistry...
July 20, 2017: Nan Fang Yi Ke da Xue Xue Bao, Journal of Southern Medical University
https://www.readbyqxmd.com/read/28733144/the-spliceosome-a-protein-directed-metalloribozyme
#13
REVIEW
Yigong Shi
Pre-mRNA splicing is executed by the ribonucleoprotein machinery spliceosome. Nearly forty years after the discovery of pre-mRNA splicing, the atomic structure of the spliceosome has finally come to light. Four distinct conformational states of the yeast spliceosome have been captured at atomic or near-atomic resolutions. Two catalytic metal ions at the active site are specifically coordinated by the U6 small nuclear RNA (snRNA) and catalyze both the branching reaction and the exon ligation. Of the three snRNAs in the fully-assembled spliceosome, U5 and U6, along with 30 contiguous nucleotides of U2 at its 5'-end, remain structurally rigid throughout the splicing reaction...
July 18, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28732463/common-and-phylogenetically-widespread-coding-for-peptides-by-bacterial-small-rnas
#14
Robin C Friedman, Stefan Kalkhof, Olivia Doppelt-Azeroual, Stephan A Mueller, Martina Chovancová, Martin von Bergen, Benno Schwikowski
BACKGROUND: While eukaryotic noncoding RNAs have recently received intense scrutiny, it is becoming clear that bacterial transcription is at least as pervasive. Bacterial small RNAs and antisense RNAs (sRNAs) are often assumed to be noncoding, due to their lack of long open reading frames (ORFs). However, there are numerous examples of sRNAs encoding for small proteins, whether or not they also have a regulatory role at the RNA level. METHODS: Here, we apply flexible machine learning techniques based on sequence features and comparative genomics to quantify the prevalence of sRNA ORFs under natural selection to maintain protein-coding function in 14 phylogenetically diverse bacteria...
July 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28728593/high-throughput-sequencing-of-small-rnas-reveals-dynamic-micrornas-expression-of-lipid-metabolism-during-camellia-oleifera-and-c-meiocarpa-seed-natural-drying
#15
Jin-Ling Feng, Zhi-Jian Yang, Shi-Pin Chen, Yousry A El-Kassaby, Hui Chen
BACKGROUND: Camellia species are ancient oilseed plants with a history of cultivation over two thousand years. Prior to oil extraction, natural seed drying is often practiced, a process affecting fatty acid quality and quantity. MicroRNAs (miRNA) of lipid metabolism associated with camellia seed natural drying are unexplored. To obtain insight into the function of miRNAs in lipid metabolism during natural drying, Illumina sequencing of C. oleifera and C. meiocarpa small-RNA was conducted...
July 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28727769/small-subunit-ribosomal-metabarcoding-reveals-extraordinary-trypanosomatid-diversity-in-brazilian-bats
#16
Maria Augusta Dario, Ricardo Moratelli Mendonça da Rocha, Philipp Schwabl, Ana Maria Jansen, Martin S Llewellyn
BACKGROUND: Bats are a highly successful, globally dispersed order of mammals that occupy a wide array of ecological niches. They are also intensely parasitized and implicated in multiple viral, bacterial and parasitic zoonosis. Trypanosomes are thought to be especially abundant and diverse in bats. In this study, we used 18S ribosomal RNA metabarcoding to probe bat trypanosome diversity in unprecedented detail. METHODOLOGY/PRINCIPAL FINDINGS: Total DNA was extracted from the blood of 90 bat individuals (17 species) captured along Atlantic Forest fragments of Espírito Santo state, southeast Brazil...
July 20, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28727754/dysregulation-of-endothelial-colony-forming-cell-function-by-a-negative-feedback-loop-of-circulating-mir-146a-and-146b-in-cardiovascular-disease-patients
#17
Ting-Yu Chang, Wei-Chi Tsai, Tse-Shun Huang, Shu-Han Su, Chih-Young Chang, Hsiu-Yen Ma, Chun-Hsien Wu, Chih-Yung Yang, Chi-Hung Lin, Po-Hsun Huang, Cheng-Chung Cheng, Shu-Meng Cheng, Hsei-Wei Wang
Functional impairment of endothelial colony-forming cells (ECFCs), a specific cell lineage of endothelial progenitor cells (EPCs) is highly associated with the severity of coronary artery disease (CAD), the most common type of cardiovascular disease (CVD). Emerging evidence show that circulating microRNAs (miRNAs) in CAD patients' body fluid hold a great potential as biomarkers. However, our knowledge of the role of circulating miRNA in regulating the function of ECFCs and the progression of CAD is still in its infancy...
2017: PloS One
https://www.readbyqxmd.com/read/28727728/an-integrative-genomics-approach-identifies-novel-pathways-that-influence-candidaemia-susceptibility
#18
Vasiliki Matzaraki, Mark S Gresnigt, Martin Jaeger, Isis Ricaño-Ponce, Melissa D Johnson, Marije Oosting, Lude Franke, Sebo Withoff, John R Perfect, Leo A B Joosten, Bart Jan Kullberg, Frank L van de Veerdonk, Iris Jonkers, Yang Li, Cisca Wijmenga, Mihai G Netea, Vinod Kumar
Candidaemia is a bloodstream infection caused by Candida species that primarily affects specific groups of at-risk patients. Because only small candidaemia patient cohorts are available, classical genome wide association cannot be used to identify Candida susceptibility genes. Therefore, we have applied an integrative genomics approach to identify novel susceptibility genes and pathways for candidaemia. Candida-induced transcriptome changes in human primary leukocytes were assessed by RNA sequencing. Genetic susceptibility to candidaemia was assessed using the Illumina immunochip platform for genotyping of a cohort of 217 patients...
2017: PloS One
https://www.readbyqxmd.com/read/28727543/non-small-cell-lung-cancer-radiogenomics-map-identifies-relationships-between-molecular-and-imaging-phenotypes-with-prognostic-implications
#19
Mu Zhou, Ann Leung, Sebastian Echegaray, Andrew Gentles, Joseph B Shrager, Kristin C Jensen, Gerald J Berry, Sylvia K Plevritis, Daniel L Rubin, Sandy Napel, Olivier Gevaert
Purpose To create a radiogenomic map linking computed tomographic (CT) image features and gene expression profiles generated by RNA sequencing for patients with non-small cell lung cancer (NSCLC). Materials and Methods A cohort of 113 patients with NSCLC diagnosed between April 2008 and September 2014 who had preoperative CT data and tumor tissue available was studied. For each tumor, a thoracic radiologist recorded 87 semantic image features, selected to reflect radiologic characteristics of nodule shape, margin, texture, tumor environment, and overall lung characteristics...
July 20, 2017: Radiology
https://www.readbyqxmd.com/read/28724941/novel-small-rna-spike-in-oligonucleotides-enable-absolute-normalization-of-small-rna-seq-data
#20
Stefan Lutzmayer, Balaji Enugutti, Michael D Nodine
Normalization of high-throughput small RNA sequencing (sRNA-Seq) data is required to compare sRNA levels across different samples. Commonly used relative normalization approaches can cause erroneous conclusions due to fluctuating small RNA populations between tissues. We developed a set of sRNA spike-in oligonucleotides (sRNA spike-ins) that enable absolute normalization of sRNA-Seq data across independent experiments, as well as the genome-wide estimation of sRNA:mRNA stoichiometries when used together with mRNA spike-in oligonucleotides...
July 19, 2017: Scientific Reports
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