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https://www.readbyqxmd.com/read/29040964/polymorphisms-in-adrenergic-receptor-genes-in-qinchuan-cattle-show-associations-with-selected-carcass-traits
#1
Chu-Gang Mei, Lin-Sheng Gui, Hong-Cheng Wang, Wan-Qiang Tian, Yao-Kun Li, Lin-Sen Zan
The beta-adrenergic receptors coded by the ADRB1, ADRB2 and ADRB3 genes play important roles in mediating metabolic effects, especially lipolysis, insulin resistance and energy balance. This study investigated the expression levels of these three genes in different tissues of Qinchuan cattle by real-time polymerase chain reaction (RT-PCR). Expressed levels of RNA from the ADRB2 gene were generally much higher than for ADRB1 and ADRB3. ADRB1 and ADRB2 expression levels were highest in subcutaneous fat and lower in muscle, whereas ADRB3 expression was higher in muscle tissue...
October 12, 2017: Meat Science
https://www.readbyqxmd.com/read/29040713/human-argonaute3-has-slicer-activity
#2
Mi Seul Park, Hong-Duc Phan, Florian Busch, Samantha H Hinckley, James A Brackbill, Vicki H Wysocki, Kotaro Nakanishi
Of the four human Argonaute (AGO) paralogs, only AGO2 has been shown to have slicer activity. The others (AGO1, AGO3 and AGO4) have been thought to assemble with microRNAs to form slicer-independent effector complexes that bind target mRNAs and silence gene expression through translational repression and deadenylation but not cleavage. Here, we report that recombinant AGO3 loaded with miR-20a cleaves complementary target RNAs, whereas AGO3 loaded with let-7a, miR-19b or miR-16 does not, indicating that AGO3 has slicer activity but that this activity depends on the guide RNA...
October 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040704/in-planta-processing-of-the-spcas9-grna-complex
#3
Masafumi Mikami, Seiichi Toki, Masaki Endo
In CRISPR/Cas9-mediated genome editing in plants, Streptococcus pyogenes Cas9 (SpCas9) protein and the required guide RNA (gRNA) are, in most cases, expressed from a stably integrated transgene. Generally, SpCas9 protein is expressed from an RNA polymerase (pol) II promoter, while gRNA is expressed from a pol III promoter. However, pol III promoters have not been much characterized other than in model plants, making it difficult to select appropriate promoters for specific applications, while pol II transcripts have to be processed to generate functional gRNAs...
October 12, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29040692/rmbase-v2-0-deciphering-the-map-of-rna-modifications-from-epitranscriptome-sequencing-data
#4
Jia-Jia Xuan, Wen-Ju Sun, Peng-Hui Lin, Ke-Ren Zhou, Shun Liu, Ling-Ling Zheng, Liang-Hu Qu, Jian-Hua Yang
More than 100 distinct chemical modifications to RNA have been characterized so far. However, the prevalence, mechanisms and functions of various RNA modifications remain largely unknown. To provide transcriptome-wide landscapes of RNA modifications, we developed the RMBase v2.0 (http://rna.sysu.edu.cn/rmbase/), which is a comprehensive database that integrates epitranscriptome sequencing data for the exploration of post-transcriptional modifications of RNAs and their relationships with miRNA binding events, disease-related single-nucleotide polymorphisms (SNPs) and RNA-binding proteins (RBPs)...
October 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040648/molecular-basis-for-asymmetry-sensing-of-sirnas-by-the-drosophila-loqs-pd-dcr-2-complex-in-rna-interference
#5
Jan-Niklas Tants, Stephanie Fesser, Thomas Kern, Ralf Stehle, Arie Geerlof, Christoph Wunderlich, Michael Juen, Christoph Hartlmüller, Romy Böttcher, Stefan Kunzelmann, Oliver Lange, Christoph Kreutz, Klaus Förstemann, Michael Sattler
RNA interference defends against RNA viruses and retro-elements within an organism's genome. It is triggered by duplex siRNAs, of which one strand is selected to confer sequence-specificity to the RNA induced silencing complex (RISC). In Drosophila, Dicer-2 (Dcr-2) and the double-stranded RNA binding domain (dsRBD) protein R2D2 form the RISC loading complex (RLC) and select one strand of exogenous siRNAs according to the relative thermodynamic stability of base-pairing at either end. Through genome editing we demonstrate that Loqs-PD, the Drosophila homolog of human TAR RNA binding protein (TRBP) and a paralog of R2D2, forms an alternative RLC with Dcr-2 that is required for strand choice of endogenous siRNAs in S2 cells...
October 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040625/rise-a-database-of-rna-interactome-from-sequencing-experiments
#6
Jing Gong, Di Shao, Kui Xu, Zhipeng Lu, Zhi John Lu, Yucheng T Yang, Qiangfeng Cliff Zhang
We present RISE (http://rise.zhanglab.net), a database of RNA Interactome from Sequencing Experiments. RNA-RNA interactions (RRIs) are essential for RNA regulation and function. RISE provides a comprehensive collection of RRIs that mainly come from recent transcriptome-wide sequencing-based experiments like PARIS, SPLASH, LIGR-seq, and MARIO, as well as targeted studies like RIA-seq, RAP-RNA and CLASH. It also includes interactions aggregated from other primary databases and publications. The RISE database currently contains 328,811 RNA-RNA interactions mainly in human, mouse and yeast...
October 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040360/elucidating-the-editome-bioinformatics-approaches-for-rna-editing-detection
#7
Maria Angela Diroma, Loredana Ciaccia, Graziano Pesole, Ernesto Picardi
RNA editing is a widespread co/posttranscriptional mechanism affecting primary RNAs by specific nucleotide modifications, which plays relevant roles in molecular processes including regulation of gene expression and/or the processing of noncoding RNAs. In recent years, the detection of editing sites has been improved through the availability of high-throughput RNA sequencing (RNA-Seq) technologies. Accurate bioinformatics pipelines are essential for the analysis of next-generation sequencing (NGS) data to ensure the correct identification of edited sites...
October 11, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29040311/putative-endogenous-filovirus-vp35-like-protein-potentially-functions-as-an-ifn-antagonist-but-not-a-polymerase-cofactor
#8
Tatsunari Kondoh, Rashid Manzoor, Naganori Nao, Junki Maruyama, Wakako Furuyama, Hiroko Miyamoto, Asako Shigeno, Makoto Kuroda, Keita Matsuno, Daisuke Fujikura, Masahiro Kajihara, Reiko Yoshida, Manabu Igarashi, Ayato Takada
It has been proposed that some non-retroviral RNA virus genes are integrated into vertebrate genomes. Endogenous filovirus-like elements (EFLs) have been discovered in some mammalian genomes. However, their potential roles in ebolavirus infection are unclear. A filovirus VP35-like element (mlEFL35) is found in the little brown bat (Myotis lucifugus) genome. Putative mlEFL35-derived protein (mlEFL35p) contains nearly full-length amino acid sequences corresponding to ebolavirus VP35. Ebola virus VP35 has been shown to bind double-stranded RNA, leading to inhibition of type I interferon (IFN) production, and is also known as a viral polymerase cofactor that is essential for viral RNA transcription/replication...
2017: PloS One
https://www.readbyqxmd.com/read/29039971/genome-wide-analysis-of-the-transcription-start-sites-and-promoter-motifs-of-phytoplasmas
#9
Takamichi Nijo, Yutaro Neriya, Hiroaki Koinuma, Nozomu Iwabuchi, Yugo Kitazawa, Kazuyuki Tanno, Yukari Okano, Kensaku Maejima, Yasuyuki Yamaji, Kenro Oshima, Shigetou Namba
Phytoplasmas are obligate intracellular parasitic bacteria that infect both plants and insects. We previously identified the sigma factor RpoD-dependent consensus promoter sequence of phytoplasma. However, the genome-wide landscape of RNA transcripts, including non-coding RNAs (ncRNAs) and RpoD-independent promoter elements, was still unknown. In this study, we performed an improved RNA sequencing analysis for genome-wide identification of the transcription start sites (TSSs) and the consensus promoter sequences...
October 17, 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/29036980/-cd137-induces-vascular-muscle-cells-phenotype-transformation-through-activating-nuclear-factor-of-activated-t-cells-1-signaling
#10
W Zhong, B Li, J Liu, Y Xu, R Chen, C Shao, Z Q Wang, J C Yan
Objective: To investigate whether CD137 induces primary vascular muscle cells (VSMCs) phenotype transformation through activating nuclear factor of activated T-cells 1(NFATc1) signaling. Methods: VSMCs were obtained from aorta of C57BL/6J mice (8 weeks, male) through tissue-piece inoculating. Cells were divided into control group, CD137 agonist group (treated with CD137L recombinant protein) and anti-CD137 group (treated with anti-CD137 antibody). In si-RNA transfection assay, cells were divided into si-control group and si-NFATc1 group which were transfected with control or si-NFATc1 sequence respectively...
September 24, 2017: Zhonghua Xin Xue Guan Bing za Zhi
https://www.readbyqxmd.com/read/29036714/accounting-for-technical-noise-in-differential-expression-analysis-of-single-cell-rna-sequencing-data
#11
Cheng Jia, Yu Hu, Derek Kelly, Junhyong Kim, Mingyao Li, Nancy R Zhang
Recent technological breakthroughs have made it possible to measure RNA expression at the single-cell level, thus paving the way for exploring expression heterogeneity among individual cells. Current single-cell RNA sequencing (scRNA-seq) protocols are complex and introduce technical biases that vary across cells, which can bias downstream analysis without proper adjustment. To account for cell-to-cell technical differences, we propose a statistical framework, TASC (Toolkit for Analysis of Single Cell RNA-seq), an empirical Bayes approach to reliably model the cell-specific dropout rates and amplification bias by use of external RNA spike-ins...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036671/crispr-cas9-mediated-gene-knockout-is-insensitive-to-target-copy-number-but-is-dependent-on-guide-rna-potency-and-cas9-sgrna-threshold-expression-level
#12
Garmen Yuen, Fehad J Khan, Shaojian Gao, Jayne M Stommel, Eric Batchelor, Xiaolin Wu, Ji Luo
CRISPR/Cas9 is a powerful gene editing tool for gene knockout studies and functional genomic screens. Successful implementation of CRISPR often requires Cas9 to elicit efficient target knockout in a population of cells. In this study, we investigated the role of several key factors, including variation in target copy number, inherent potency of sgRNA guides, and expression level of Cas9 and sgRNA, in determining CRISPR knockout efficiency. Using isogenic, clonal cell lines with variable copy numbers of an EGFP transgene, we discovered that CRISPR knockout is relatively insensitive to target copy number, but is highly dependent on the potency of the sgRNA guide sequence...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036654/detection-of-expanded-rna-repeats-using-thermostable-group-ii-intron-reverse-transcriptase
#13
Samuel T Carrell, Zhenzhi Tang, Sabine Mohr, Alan M Lambowitz, Charles A Thornton
Cellular accumulation of repetitive RNA occurs in several dominantly-inherited genetic disorders. Expanded CUG, CCUG or GGGGCC repeats are expressed in myotonic dystrophy type 1 (DM1), myotonic dystrophy type 2 (DM2), or familial amyotrophic lateral sclerosis, respectively. Expanded repeat RNAs (ER-RNAs) exert a toxic gain-of-function and are prime therapeutic targets in these diseases. However, efforts to quantify ER-RNA levels or monitor knockdown are confounded by stable structure and heterogeneity of the ER-RNA tract and background signal from non-expanded repeats...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036649/the-smad3-transcription-factor-binds-complex-rna-structures-with-high-affinity
#14
Thayne H Dickey, Anna M Pyle
Several members of the SMAD family of transcription factors have been reported to bind RNA in addition to their canonical double-stranded DNA (dsDNA) ligand. RNA binding by SMAD has the potential to affect numerous cellular functions that involve RNA. However, the affinity and specificity of this RNA binding activity has not been well characterized, which limits the ability to validate and extrapolate functional implications of this activity. Here we perform quantitative binding experiments in vitro to determine the ligand requirements for RNA binding by SMAD3...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036644/roles-of-female-and-male-genotype-in-post-mating-responses-in-drosophila-melanogaster-roles-of-female-and-male-genotype-in-female-drosophila-melanogaster-transcriptional-physiological-and-behavioral-responses-to-mating
#15
Sofie Y N Delbare, Clement Y Chow, Mariana F Wolfner, Andrew G Clark
Mating induces a multitude of changes in female behavior, physiology and gene expression. Interactions between female and male genotype lead to variation in post-mating phenotypes and reproductive success. So far, few female molecules responsible for these interactions have been identified. Here, we used Drosophila melanogaster from five geographically dispersed populations to investigate such female x male genotypic interactions at the female transcriptomic and phenotypic levels. Females from each line were singly-mated to males from the same five lines, for a total of 25 combinations...
October 4, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29036633/rna-sequencing-of-brassica-napus-reveals-cellular-redox-control-of-sclerotinia-infection
#16
Ian J Girard, Chaobo Tong, Michael G Becker, Xingyu Mao, Junyan Huang, Teresa de Kievit, W G Dilantha Fernando, Shengyi Liu, Mark F Belmonte
Brassica napus is one of the world's most valuable oilseeds and is under constant pressure by the necrotrophic fungal pathogen, Sclerotinia sclerotiorum, the causal agent of white stem rot. Despite our growing understanding of host pathogen interactions at the molecular level, we have yet to fully understand the biological processes and underlying gene regulatory networks responsible for determining disease outcomes. Using global RNA sequencing, we profiled gene activity at the first point of infection on the leaf surface 24 hours after pathogen exposure in susceptible (B...
September 27, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29036602/n6-adenine-dna-methylation-is-associated-with-the-linker-dna-of-h2a-z-containing-well-positioned-nucleosomes-in-pol-ii-transcribed-genes-in-tetrahymena
#17
Yuanyuan Wang, Xiao Chen, Yalan Sheng, Yifan Liu, Shan Gao
DNA N6-methyladenine (6mA) is newly rediscovered as a potential epigenetic mark across a more diverse range of eukaryotes than previously realized. As a unicellular model organism, Tetrahymena thermophila is among the first eukaryotes reported to contain 6mA modification. However, lack of comprehensive information about 6mA distribution hinders further investigations into its function and regulatory mechanism. In this study, we provide the first genome-wide, base pair-resolution map of 6mA in Tetrahymena by applying single-molecule real-time (SMRT) sequencing...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036598/global-dna-methylation-analysis-reveals-mir-214-3p-contributes-to-cisplatin-resistance-in-pediatric-intracranial-nongerminomatous-malignant-germ-cell-tumors
#18
Tsung-Han Hsieh, Yun-Ru Liu, Ting-Yu Chang, Muh-Lii Liang, Hsin-Hung Chen, Hsei-Wei Wang, Yun Yen, Tai-Tong Wong
Background: Pediatric central nervous system germ cell tumors (CNSGCTs) are rare and heterogeneous neoplasms, and they can be divided into germinomas and nongerminomatous GCTs (NGGCTs). NGGCTs are further subdivided into mature teratomas and nongerminomatous malignant GCTs (NGMGCTs). Clinical outcomes suggest that NGMGCTs have poor prognosis and survival, and that they require more extensive radiotherapy and adjuvant chemotherapy. However, the mechanisms underlying this difference are still unclear...
October 3, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/29036566/the-role-of-alternative-splicing-and-differential-gene-expression-in-cichlid-adaptive-radiation
#19
Pooja Singh, Christine Börger, Heather More, Christian Sturmbauer
Species diverge eco-morphologically through the continuous action of natural selection on functionally important structures, producing alternative adaptive morphologies. In cichlid fishes, the oral and pharyngeal jaws are such key structures. Adaptive variation in jaw morphology contributes to trophic specialisation, which is hypothesised to fuel their rapid speciation in the East African Great Lakes. Much is known about the genes involved in cichlid jaw and craniofacial development. However, it is still unclear what salient sources of variation gave rise to trophic-niche specialisation, facilitating adaptive radiation...
September 27, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29036542/database-resources-of-the-big-data-center-in-2018
#20
(no author information available yet)
The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations)...
October 3, 2017: Nucleic Acids Research
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