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https://www.readbyqxmd.com/read/29475067/transcriptional-profiling-of-male-cd-1-mouse-lungs-and-harderian-glands-supports-the-involvement-of-calcium-signaling-in-acrylamide-induced-tumors
#1
Nikolai L Chepelev, Rémi Gagné, Timothy Maynor, Byron Kuo, Cheryl A Hobbs, Leslie Recio, Carole L Yauk
Acrylamide (AA) exposure causes increased incidence of forestomach, lung, and Harderian gland tumors in male mice. One hypothesized mode of action (MOA) for AA-carcinogenicity includes genotoxicity/mutagenicity as a key event, possibly resulting from AA metabolism to the direct genotoxic metabolite glycidamide. Alternatively, altered calcium signaling (CS) has been proposed as a central key event in the MOA. To examine the plausibility of these proposed MOAs, RNA-sequencing was performed on tumor target tissues: Harderian glands (the most sensitive tumor target tissue in the rodent 2-year cancer bioassay) and lungs of AA-exposed male CD-1 mice...
February 20, 2018: Regulatory Toxicology and Pharmacology: RTP
https://www.readbyqxmd.com/read/29474932/profiling-g-protein-coupled-receptors-of-fasciola-hepatica-identifies-orphan-rhodopsins-unique-to-phylum-platyhelminthes
#2
Paul McVeigh, Erin McCammick, Paul McCusker, Duncan Wells, Jane Hodgkinson, Steve Paterson, Angela Mousley, Nikki J Marks, Aaron G Maule
G protein-coupled receptors (GPCRs) are established drug targets. Despite their considerable appeal as targets for next-generation anthelmintics, poor understanding of their diversity and function in parasitic helminths has thwarted progress towards GPCR-targeted anti-parasite drugs. This study facilitates GPCR research in the liver fluke, Fasciola hepatica, by generating the first profile of GPCRs from the F. hepatica genome. Our dataset describes 147 high confidence GPCRs, representing the largest cohort of GPCRs, and the largest set of in silico ligand-receptor predictions, yet reported in any parasitic helminth...
February 5, 2018: International Journal for Parasitology, Drugs and Drug Resistance
https://www.readbyqxmd.com/read/29474929/multi-posttranscriptional-regulations-lessen-the-repressive-effect-of-srpk1-on-brown-adipogenesis
#3
Jung-Chun Lin
Alternative splicing has been widely demonstrated to function as pivotal regulation in specifying cellular fates and biological functions. The relative expression or cellular localization of a splicing factor constitutes an important mechanism in spatiotemporal programming of cell- and stage-specific splicing profiles. In this study, results of deep RNA-sequencing (RNA-Seq) analyses first revealed the reprogrammed splicing profile and reduced expression of serine/arginine-rich splicing factor protein kinase 1 (SRPK1) throughout the development of brown adipose tissue (BAT)...
February 20, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29474909/mapping-the-mouse-cell-atlas-by-microwell-seq
#4
Xiaoping Han, Renying Wang, Yincong Zhou, Lijiang Fei, Huiyu Sun, Shujing Lai, Assieh Saadatpour, Zimin Zhou, Haide Chen, Fang Ye, Daosheng Huang, Yang Xu, Wentao Huang, Mengmeng Jiang, Xinyi Jiang, Jie Mao, Yao Chen, Chenyu Lu, Jin Xie, Qun Fang, Yibin Wang, Rui Yue, Tiefeng Li, He Huang, Stuart H Orkin, Guo-Cheng Yuan, Ming Chen, Guoji Guo
Single-cell RNA sequencing (scRNA-seq) technologies are poised to reshape the current cell-type classification system. However, a transcriptome-based single-cell atlas has not been achieved for complex mammalian systems. Here, we developed Microwell-seq, a high-throughput and low-cost scRNA-seq platform using simple, inexpensive devices. Using Microwell-seq, we analyzed more than 400,000 single cells covering all of the major mouse organs and constructed a basic scheme for a mouse cell atlas (MCA). We reveal a single-cell hierarchy for many tissues that have not been well characterized previously...
February 22, 2018: Cell
https://www.readbyqxmd.com/read/29474815/complete-mitochondrial-genome-of-the-tea-looper-caterpillar-ectropis-obliqua-lepidoptera-geometridae-with-a-phylogenetic-analysis-of-geometridae
#5
Li Qian, Wang Xiaoxi, Chen Xuexin, Han Baoyu
The complete mitochondrial genome (mitogenome) of the Ectropis obliqua (Lepidoptera: Geometridae) was sequenced and compared with other species of Geometridae. The mitochondrial genome of E. obliqua is 15,475 bp long and contains 37 genes including 13 protein coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and an A + T-rich region. Gene cluster trnI-trnQ-trnM rearranged to trnM-trnI-trnQ comparing with the ancestral mitogenome of insects. All tRNA genes have typical cloverleaf secondary structure except for trnS (AGN)...
February 20, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29474693/the-use-of-rna-sequencing-and-correlation-network-analysis-to-study-potential-regulators-of-leaf-color-transformation
#6
Tuo Yang, Keting Li, Suxiao Hao, Jie Zhang, Tingting Song, Ji Tian, Yuncong Yao
Anthocyanins are plant pigments that contribute to the color of leaves, flowers and fruits, and that beneficial to human health in the form of dietary antioxidants. The study of a transformable crabapple cultivar, 'India magic', which has red buds and green mature leaves, using mRNA profiling of four leaf developmental stages, allowed us to characterize molecular mechanisms regulating red color formation in early leaf development and the subsequent rapid down-regulation of anthocyanin biosynthesis. This analysis of differential gene expression during leaf development, revealed that ethylene signaling responsive genes are upregulated during leaf pigmentation...
February 20, 2018: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29474673/genetic-instability-associated-with-loop-or-stem-loop-structures-within-transcription-units-can-be-independent-of-nucleotide-excision-repair
#7
John A Burns, Moinuddin A Chowdhury, Laura Cartularo, Christian Berens, David A Scicchitano
Simple sequence repeats (SSRs) are found throughout the genome, and under some conditions can change in length over time. Germline and somatic expansions of trinucleotide repeats are associated with a series of severely disabling illnesses, including Huntington's disease. The underlying mechanisms that effect SSR expansions and contractions have been experimentally elusive, but models suggesting a role for DNA repair have been proposed, in particular the involvement of transcription-coupled nucleotide excision repair (TCNER) that removes transcription-blocking DNA damage from the transcribed strand of actively expressed genes...
February 21, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29474580/recently-evolved-tumor-suppressor-transcript-tp73-as1-functions-as-sponge-of-human-specific-mir-941
#8
Haiyang Hu, Jian-Mei Liu, Zhenyu Hu, Xi Jiang, Xiaode Yang, Jiangxia Li, Yao Zhang, Haijing Yu, Philipp Khaitovich
MicroRNA (miRNA) sponges are vital components of posttranscriptional gene regulation. Yet, only a limited number of miRNA sponges have been identified. Here, we show that the recently evolved non-coding tumor suppressor transcript, antisense RNA to TP73 gene (TP73-AS1), functions as a natural sponge of human-specific miRNA miR-941. We find unusually nine high-affinity miR-941 binding sites clustering within 1kb region on TP73-AS1, which forms miR-941 sponge region. This sponge region displays increased sequence constraint only in humans, and its formation can be traced to the tandem expansion of a 71-nt-long sequence containing a single miR-941 binding site in old world monkeys...
February 20, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29474579/direct-observation-of-nucleic-acid-binding-dynamics-by-the-telomerase-essential-n-terminal-domain
#9
Shankar Shastry, Olga Steinberg-Neifach, Neal Lue, Michael D Stone
Telomerase is a specialized enzyme that maintains telomere length by adding DNA repeats to chromosome ends. The catalytic protein subunit of telomerase utilizes the integral telomerase RNA to direct telomere DNA synthesis. The telomerase essential N-terminal (TEN) domain is required for enzyme function; however, the precise mechanism of the TEN domain during catalysis is not known. We report a single-molecule study of dynamic TEN-induced conformational changes in its nucleic acid substrates. The TEN domain from the yeast Candida parapsilosis (Cp) exhibits a strong binding preference for double-stranded nucleic acids, with particularly high affinity for an RNA-DNA hybrid mimicking the template-product complex...
February 21, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29474559/genomic-alterations-and-complex-subclonal-architecture-in-sporadic-gh-secreting-pituitary-adenomas
#10
Mirella Hage, Say Viengchareun, Erika Brunet, Chiara Villa, Dominique Pineau, Jérôme Bouligand, Jean Paul Teglas, Clovis Adam, Fabrice Parker, Marc Lombès, Gérard Tachdjian, Stéphane Gaillard, Philippe Chanson, Lucie Tosca, Peter Kamenický
Purpose: The molecular pathogenesis of growth hormone (GH)-secreting pituitary adenomas is not fully understood. Cytogenetic alterations might serve as alternative driver events in GNAS mutation-negative somatotroph tumors. Experimental Design: We performed cytogenetic profiling of pituitary adenomas obtained from 39 acromegalic patients and 4 patients with sporadic gigantism by using array comparative genomic hybridization (array-CGH) analysis. We explored intratumor DNA copy-number heterogeneity in two tumor samples by using DNA fluorescence in situ hybridization (FISH)...
February 21, 2018: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29474557/penndiff-detecting-differential-alternative-splicing-and-transcription-by-rna-sequencing
#11
Yu Hu, Jennie Lin, Jian Hu, Gang Hu, Kui Wang, Hanrui Zhang, Muredach P Reilly, Mingyao Li
Motivation: Alternative splicing and alternative transcription are a major mechanism for generating transcriptome diversity. Differential alternative splicing and transcription (DAST), which describe different usage of transcript isoforms across different conditions, can complement differential expression in characterizing gene regulation. However, the analysis of DAST is challenging because only a small fraction of RNA-seq reads is informative for isoforms. Several methods have been developed to detect exon-based and gene-based DAST, but they suffer from power loss for genes with many isoforms...
February 20, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29474419/transcriptome-analysis-in-different-developmental-stages-of-batocera-horsfieldi-coleoptera-cerambycidae-and-comparison-of-candidate-olfactory-genes
#12
Hua Yang, Yan Cai, Zhihang Zhuo, Wei Yang, Chunping Yang, Jin Zhang, Yang Yang, Baoxin Wang, Fengrong Guan
The white-striped longhorn beetle Batocera horsfieldi (Coleoptera: Cerambycidae) is a polyphagous wood-boring pest that causes substantial damage to the lumber industry. Moreover olfactory proteins are crucial components to function in related processes, but the B. horsfieldi genome is not readily available for olfactory proteins analysis. In the present study, developmental transcriptomes of larvae from the first instar to the prepupal stage, pupae, and adults (females and males) from emergence to mating were built by RNA sequencing to establish a genetic background that may help understand olfactory genes...
2018: PloS One
https://www.readbyqxmd.com/read/29474379/small-rna-populations-revealed-by-blocking-rrna-fragments-in-drosophila-melanogaster-reproductive-tissues
#13
Emily K Fowler, Irina Mohorianu, Damian T Smith, Tamas Dalmay, Tracey Chapman
RNA interference (RNAi) is a complex and highly conserved regulatory mechanism mediated via small RNAs (sRNAs). Recent technical advances in high throughput sequencing have enabled an increasingly detailed analysis of sRNA abundances and profiles in specific body parts and tissues. This enables investigations of the localized roles of microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, variation in the proportions of non-coding RNAs in the samples being compared can hinder these analyses. Specific tissues may vary significantly in the proportions of fragments of longer non-coding RNAs (such as ribosomal RNA or transfer RNA) present, potentially reflecting tissue-specific differences in biological functions...
2018: PloS One
https://www.readbyqxmd.com/read/29473964/waking-the-neighbours-disruption-of-h-ns-repression-by-overlapping-transcription
#14
Joseph T Wade, David C Grainger
The histone-like nucleoid structuring (H-NS) protein and its analogues bind large stretches of horizontally acquired AT-rich DNA in a broad range of bacterial species. Binding by H-NS silences the promoters within such DNA that would otherwise deplete the cellular pool of RNA polymerase. Selective de-repression can occur when sequence-specific DNA-binding proteins locally disrupt H-NS function; this mechanism is important for the regulation of many virulence genes. In this issue of Molecular Microbiology, Rangarajan and Schnetz show that when transcription from a neighbouring region invades an H-NS-bound locus, it can disrupt local H-NS repression...
February 23, 2018: Molecular Microbiology
https://www.readbyqxmd.com/read/29473878/alternative-mrna-splicing-in-the-pathogenesis-of-obesity
#15
REVIEW
Chi-Ming Wong, Lu Xu, Mabel Yin-Chun Yau
Alternative mRNA splicing is an important mechanism in expansion of proteome diversity by production of multiple protein isoforms. However, emerging evidence indicates that only a limited number of annotated protein isoforms by alternative splicing are detected, and the coding sequence of alternative splice variants usually is only slightly different from that of the canonical sequence. Nevertheless, mis-splicing is associated with a large array of human diseases. Previous reviews mainly focused on hereditary and somatic mutations in cis-acting RNA sequence elements and trans-acting splicing factors...
February 23, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29473818/transcriptomic-sequencing-reveals-diverse-adaptive-gene-expression-responses-of-human-vascular-smooth-muscle-cells-to-nitro-conjugated-linoleic-acid
#16
Shengdi Li, Ziyi Chang, Tianqing Zhu, Yixue Li, Bruce A Freeman, Y Eugene Chen, Jifeng Zhang
Nitro-conjugated linoleic acid (NO2 -CLA) is formed by metabolic and inflammatory reactions of nitric oxide and nitrite, and represents the most abundant nitro-fatty acid species in humans. These electrophilic fatty acid nitroalkene derivatives mediate pleiotropic cell signaling responses. Here, we report a systematic approach to investigate the effect of NO2 -CLA on human coronary artery smooth muscle cells (hCASMC), based on the RNA-seq and bioinformatics analysis. There were extensive differentially expressed genes in NO2 -CLA vs...
February 23, 2018: Physiological Genomics
https://www.readbyqxmd.com/read/29473733/%C3%AE-l-threose-nucleic-acids-as-biocompatible-antisense-oligonucleotides-for-suppressing-gene-expression-in-living-cells
#17
Ling Sum Liu, Hoi Man Leung, Dick Yan Tam, Tsz Wan Lo, Sze Wing Wong, Pik Kwan Lo
Due to the chemical simplicity of α- L-Threose nucleic acid (TNA) and its ability to exchange genetic information between itself and RNA, it has been raised significant interests in TNA as RNA ancestor. We herein explore the biological properties and evaluate the potency of sequence-designed TNA polymers to suppress gene expression in living environments. We found that sequence-specific TNA macromolecules exhibit strong affinity and specificity towards the complementary RNA targets, are highly biocompatible and non-toxic in living cell system, and readily enter a number of cell lines without using transfecting agents...
February 23, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29473500/crispr-cas-system-as-a-genome-engineering-platform-applications-in-biomedicine-and-biotechnology
#18
Atieh Hashemi
Genome editing mediated by clustered regularly interspaced palindromic repeats (CRISPR) and its associated proteins (Cas) has recently been considered to be used as efficient, rapid and site-specific tools in the modification of endogenous genes in biomedically important cell types and whole organisms. It has become a predictable and precise method of choice for genome engineering by specifying a 20-nt targeting sequence within its guide RNA. First, this review aims to describe the biology of CRISPR system...
February 20, 2018: Current Gene Therapy
https://www.readbyqxmd.com/read/29473487/new-design-development-and-optimization-of-an-in-house-quantitative-taqman-real-time-pcr-assay-for-hiv-1-viral-load-measurement
#19
Hassan Noorbazargan, Seyed Alireza Nadji, Siamak Mirab Samiee, Mahdi Paryan, Samira Mohammadi-Yeganeh
Background Viral load measurement is commonly applicable to monitor HIV infection in patients to determine the number of HIV-RNA in serum samples of individuals. The aim of the present study was to set up a highly specific, sensitive, and reproducible home-brewed Real-time PCR assay based on TaqMan chemistry to quantify HIV-1 RNA genome. Methods In this study, three sets of primer pairs and a TaqMan probe were designed for HIV subtypes conserved sequences. An internal control was included in this assay to evaluate the presence of inhibition...
February 23, 2018: HIV Clinical Trials
https://www.readbyqxmd.com/read/29473240/loss-of-ppm1f-expression-predicts-tumour-recurrence-and-is-negatively-regulated-by-mir-590-3p-in-gastric-cancer
#20
Jing Zhang, Ming Jin, Xiaoyu Chen, Rui Zhang, Yanxia Huang, Hui Liu, Jinshui Zhu
OBJECTIVES: MicroRNAs (miRNAs) as small non-coding RNA molecules act by negatively regulating their target genes. Recent studies have shown that protein phosphatase Mg2+/Mn2+-dependent 1F (PPM1F) plays a critical role in cancer metastasis. But, the regulation mechanisms of PPM1F by miRNAs in gastric cancer (GC) remain undefined. METHODS: The correlation of PPM1F or miR-590-3p (miR-590) expression with clinicopathological features and prognosis of the patients with GC was analysed by TCGA RNA-sequencing data...
February 22, 2018: Cell Proliferation
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