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https://www.readbyqxmd.com/read/29222702/molecular-insights-into-the-non-recombining-nature-of-the-spinach-male-determining-region
#1
Tomohiro Kudoh, Mitsuhiko Takahashi, Takayuki Osabe, Atsushi Toyoda, Hideki Hirakawa, Yutaka Suzuki, Nobuko Ohmido, Yasuyuki Onodera
Spinach (Spinacia oleracea L.) is a dioecious plant with male heterogametic sex determination and homomorphic sex chromosomes (XY). The dioecism is utilized for producing commercial hybrid seeds, and hence understanding the molecular-genetic basis of the species' sex determining locus is an important issue for spinach breeding. In this study, seven dominant DNA markers were shown to completely co-segregate with the male-determining gene in segregating spinach populations comprising > 1500 plants. In addition, these seven dominant DNA markers were completely associated with the male-determining gene in over 100 spinach germplasm accessions and cultivars...
December 8, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29222368/novel-lncrna-erbb4-ir-promotes-diabetic-kidney-injury-in-db-db-mice-by-targeting-mir-29b
#2
Si F Sun, Patrick Mk Tang, Min Feng, Xiao Jun, Xiao R Huang, Ping Li, Ronal Cw Ma, Hui Y Lan
TGF-β/Smad signaling plays an important role in diabetic nephropathy. The present study identified a novel Smad3-dependent long non-coding RNA (lncRNA) Erbb4-IR in the development of type-2 diabetic nephropathy (T2DN) in db/db mice. We found that Erbb4-IR was highly expressed in T2DN of db/db mice and was specifically induced by AGE via a Smad3-dependent mechanism. The functional role of Erbb4-IR in T2DN was revealed by kidney-specific silencing of Erbb4-IR to protect against the development of T2DN such as elevated microalbuminuria, serum creatinine and progressive renal fibrosis in db/db mice, and to block AGE-induced collagen I and IV expression in mouse mesangial cells (mMCs) and mouse tubular epithelial cells (mTECs)...
December 8, 2017: Diabetes
https://www.readbyqxmd.com/read/29220646/dissecting-cell-type-composition-and-activity-dependent-transcriptional-state-in-mammalian-brains-by-massively-parallel-single-nucleus-rna-seq
#3
Peng Hu, Emily Fabyanic, Deborah Y Kwon, Sheng Tang, Zhaolan Zhou, Hao Wu
Massively parallel single-cell RNA sequencing can precisely resolve cellular diversity in a high-throughput manner at low cost, but unbiased isolation of intact single cells from complex tissues such as adult mammalian brains is challenging. Here, we integrate sucrose-gradient-assisted purification of nuclei with droplet microfluidics to develop a highly scalable single-nucleus RNA-seq approach (sNucDrop-seq), which is free of enzymatic dissociation and nucleus sorting. By profiling ∼18,000 nuclei isolated from cortical tissues of adult mice, we demonstrate that sNucDrop-seq not only accurately reveals neuronal and non-neuronal subtype composition with high sensitivity but also enables in-depth analysis of transient transcriptional states driven by neuronal activity, at single-cell resolution, in vivo...
December 7, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29219968/programmable-self-assembly-of-three-dimensional-nanostructures-from-10-000-unique-components
#4
Luvena L Ong, Nikita Hanikel, Omar K Yaghi, Casey Grun, Maximilian T Strauss, Patrick Bron, Josephine Lai-Kee-Him, Florian Schueder, Bei Wang, Pengfei Wang, Jocelyn Y Kishi, Cameron Myhrvold, Allen Zhu, Ralf Jungmann, Gaetan Bellot, Yonggang Ke, Peng Yin
Nucleic acids (DNA and RNA) are widely used to construct nanometre-scale structures with ever increasing complexity, with possible application in fields such as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early kilodalton-scale examples containing typically tens of unique DNA strands. The introduction of DNA origami, which uses many staple strands to fold one long scaffold strand into a desired structure, has provided access to megadalton-scale nanostructures that contain hundreds of unique DNA strands...
December 6, 2017: Nature
https://www.readbyqxmd.com/read/29219730/a-comprehensive-profile-of-circulating-rnas-in-human-serum
#5
Sinan Uğur Umu, Hilde Langseth, Cecilie Bucher-Johannessen, Bastian Fromm, Andreas Keller, Eckart Meese, Marianne Lauritzen, Magnus Leithaug, Robert Lyle, Trine B Rounge
Non-coding RNA (ncRNA) molecules have fundamental roles in cells and many are also stable in body fluids as extracellular RNAs. In this study, we used RNA sequencing (RNA-seq) to investigate the profile of small non-coding RNA (sncRNA) in human serum. We analyzed 10 billion Illumina reads from 477 serum samples, included in the Norwegian population-based Janus Serum Bank (JSB). We found that the core serum RNA repertoire includes 258 micro RNAs (miRNA), 441 piwi-interacting RNAs (piRNA), 411 transfer RNAs (tRNA), 24 small nucleolar RNAs (snoRNA), 125 small nuclear RNAs (snRNA) and 123 miscellaneous RNAs (misc-RNA)...
December 8, 2017: RNA Biology
https://www.readbyqxmd.com/read/29214215/genomic-and-transcriptomic-heterogeneity-in-metaplastic-carcinomas-of-the-breast
#6
Salvatore Piscuoglio, Charlotte K Y Ng, Felipe C Geyer, Kathleen A Burke, Catherine F Cowell, Luciano G Martelotto, Rachael Natrajan, Tatiana Popova, Christopher A Maher, Raymond S Lim, Ino de Bruijn, Odette Mariani, Larry Norton, Anne Vincent-Salomon, Britta Weigelt, Jorge S Reis-Filho
Metaplastic breast cancer (MBC) is a rare special histologic type of triple-negative breast cancer, characterized by the presence of neoplastic cells showing differentiation towards squamous epithelium and/or mesenchymal elements. Here we sought to define whether histologically distinct subgroups of MBCs would be underpinned by distinct genomic and/or transcriptomic alterations. Microarray-based copy number profiling identified limited but significant differences between the distinct MBC subtypes studied here, despite the limited sample size (n = 17)...
2017: NPJ Breast Cancer
https://www.readbyqxmd.com/read/29212859/human-hair-follicle-transcriptome-profiling-a-minimally-invasive-tool-to-assess-molecular-adaptations-upon-low-volume-high-intensity-interval-training
#7
Jing Zhang, Sarah J Wallace, Maria Y Shiu, Ingrid Smith, Shawn G Rhind, Valerie S Langlois
High-intensity interval training (HIIT) has become a popular fitness training approach under both civilian and military settings. Consisting of brief and intense exercise intervals, HIIT requires less time commitment yet is able to produce the consistent targeted physical adaptations as conventional endurance training. To effectively characterize and monitor HIIT-induced cellular and molecular responses, a highly accessible yet comprehensive biomarker discovery source is desirable. Both gene differential expression (DE) and gene set (GS) analyses were conducted using hair follicle transcriptome established from pre and postexercise subjects upon a 10-day HIIT program by RNA-Seq, Comparing between pre and posttraining groups, differentially expressed protein coding genes were identified...
December 2017: Physiological Reports
https://www.readbyqxmd.com/read/29212819/transcriptional-and-translational-dynamics-during-maternal-to-zygotic-transition-in-early-chicken-development
#8
Young Sun Hwang, Minseok Seo, Sohyun Bang, Heebal Kim, Jae Yong Han
Maternal-to-zygotic transition (MZT) is the critical process for the establishment of embryonic identity across vertebrates. During this period, the massive transcriptional activation, called zygotic genome activation (ZGA), is mediated by maternally stored factors, and maternal mRNA clearance by conserved zygotic microRNAs (miRNAs) occurs; however, the important transition in avian species was identified by morphologic perspectives only. In this study, we performed transcriptome analysis to examine the molecular transitions of intrauterine development in chickens...
December 6, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29212818/the-histone-demethylase-kdm5a-is-required-for-the-repression-of-astrocytogenesis-and-regulated-by-the-translational-machinery-in-neural-progenitor-cells
#9
Sun-Young Kong, Woosuk Kim, Ha-Rim Lee, Hyun-Jung Kim
Histone demethylases are known to play important roles in the determination of the fate of stem cells and in cancer progression. In this study, we show that the lysine 4 of histone H3 (H3K4), lysine-specific demethylase 5A (KDM5A) is essential for the repression of astrocyte differentiation in neural progenitor cells (NPCs), and its expression is regulated by translational machinery. Knockdown of KDM5A in NPCs increased astrocytogenesis, and conversely, KDM5A overexpression reduced the transcriptional activity of the Gfap promoter...
December 6, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29209947/copy-number-variation-arising-from-gene-conversion-on-the-human-y-chromosome
#10
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/29208987/genome-wide-dna-methylation-changes-associated-with-olfactory-learning-and-memory-in-apis-mellifera
#11
You Li, Li-Zhen Zhang, Yao Yi, Wan-Wan Hu, Ya-Hui Guo, Zhi-Jiang Zeng, Zachary-Y Huang, Zi-Long Wang
The honeybee is a model organism for studying learning and memory formation and its underlying molecular mechanisms. While DNA methylation is well studied in caste differentiation, its role in learning and memory is not clear in honeybees. Here, we analyzed genome-wide DNA methylation changes during olfactory learning and memory process in A. mellifera using whole genome bisulfite sequencing (WGBS) method. A total of 853 significantly differentially methylated regions (DMRs) and 963 differentially methylated genes (DMGs) were identified...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29207917/functional-effects-of-snps-in-myh9-and-risks-of-nonsyndromic-orofacial-clefts
#12
Y Wang, D Li, Y Xu, L Ma, Y Lu, Z Wang, L Wang, W Zhang, Y Pan
Nonsyndromic orofacial clefts (NSOCs) are congenital newborn malformations. Myosin heavy chain 9 ( MYH9) is a candidate gene of NSOCs. To investigate the associations between single-nucleotide polymorphisms (SNPs) of MYH9 and NSOC susceptibility, a 2-stage case-control study was designed and 4 potentially functional SNPs of MYH9 (rs12107, rs2269529, rs9619601, rs5756130) were selected and genotyped by iPLEX Sequenom MassARRAY and TaqMan assay in the first stage (599 NSOC cases and 590 controls). The significant SNPs in the first stage were replicated in the second stage (676 NSOC cases and 705 controls) by TaqMan assay...
December 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/29206165/current-research-on-non-coding-ribonucleic-acid-rna
#13
REVIEW
Jing Wang, David C Samuels, Shilin Zhao, Yu Xiang, Ying-Yong Zhao, Yan Guo
Non-coding ribonucleic acid (RNA) has without a doubt captured the interest of biomedical researchers. The ability to screen the entire human genome with high-throughput sequencing technology has greatly enhanced the identification, annotation and prediction of the functionality of non-coding RNAs. In this review, we discuss the current landscape of non-coding RNA research and quantitative analysis. Non-coding RNA will be categorized into two major groups by size: long non-coding RNAs and small RNAs. In long non-coding RNA, we discuss regular long non-coding RNA, pseudogenes and circular RNA...
December 5, 2017: Genes
https://www.readbyqxmd.com/read/29203801/de-novo-design-of-rna-binding-proteins-with-a-prion-like-domain-related-to-als-ftd-proteinopathies
#14
Kana Mitsuhashi, Daisuke Ito, Kyoko Mashima, Munenori Oyama, Shinichi Takahashi, Norihiro Suzuki
Aberrant RNA-binding proteins form the core of the neurodegeneration cascade in spectrums of disease, such as amyotrophic lateral sclerosis (ALS)/frontotemporal dementia (FTD). Six ALS-related molecules, TDP-43, FUS, TAF15, EWSR1, heterogeneous nuclear (hn)RNPA1 and hnRNPA2 are RNA-binding proteins containing candidate mutations identified in ALS patients and those share several common features, including harboring an aggregation-prone prion-like domain (PrLD) containing a glycine/serine-tyrosine-glycine/serine (G/S-Y-G/S)-motif-enriched low-complexity sequence and rich in glutamine and/or asparagine...
December 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29202874/sensitive-detection-of-hiv-1-resistance-to-zidovudine-and-impact-on-treatment-outcomes-in-low-to-middle-income-countries
#15
Richard M Gibson, Gabrielle Nickel, Michael Crawford, Fred Kyeyune, Colin Venner, Immaculate Nankya, Eva Nabulime, Emmanuel Ndashimye, Art F Y Poon, Robert A Salata, Cissy Kityo, Peter Mugyenyi, Miguel E Quiñones-Mateu, Eric J Arts
BACKGROUND: Thymidine analogs, namely AZT (Zidovudine or Retrovir™) and d4T (Stavudine or Zerit™) are antiretroviral drugs still employed in over 75% of first line combination antiretroviral therapy (cART) in Kampala, Uganda despite aversion to prescribing these drugs for cART in high income countries due in part to adverse events. For this study, we explored how the continued use of these thymidine analogs in cART could impact emergence of drug resistance and impact on future treatment success in Uganda, a low-income country...
December 4, 2017: Infectious Diseases of Poverty
https://www.readbyqxmd.com/read/29202695/single-cell-rna-seq-analysis-reveals-dynamic-trajectories-during-mouse-liver-development
#16
Xianbin Su, Yi Shi, Xin Zou, Zhao-Ning Lu, Gangcai Xie, Jean Y H Yang, Chong-Chao Wu, Xiao-Fang Cui, Kun-Yan He, Qing Luo, Yu-Lan Qu, Na Wang, Lan Wang, Ze-Guang Han
BACKGROUND: The differentiation and maturation trajectories of fetal liver stem/progenitor cells (LSPCs) are not fully understood at single-cell resolution, and a priori knowledge of limited biomarkers could restrict trajectory tracking. RESULTS: We employed marker-free single-cell RNA-Seq to characterize comprehensive transcriptional profiles of 507 cells randomly selected from seven stages between embryonic day 11.5 and postnatal day 2.5 during mouse liver development, and also 52 Epcam-positive cholangiocytes from postnatal day 3...
December 4, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29198469/novel-small-molecule-inhibitors-of-protein-kinase%C3%A2-c-epsilon-reduce-ethanol-consumption-in%C3%A2-mice
#17
Angelo Blasio, Jingyi Wang, Dan Wang, Florence P Varodayan, Matthew B Pomrenze, Jacklyn Miller, Anna M Lee, Thomas McMahon, Sandeep Gyawali, Hua-Yu Wang, Marisa Roberto, Stanton McHardy, Michael A Pleiss, Robert O Messing
BACKGROUND: Despite the high cost and widespread prevalence of alcohol use disorders, treatment options are limited, underscoring the need for new, effective medications. Previous results using protein kinase C epsilon (PKCε) knockout mice, RNA interference against PKCε, and peptide inhibitors of PKCε predict that small-molecule inhibitors of PKCε should reduce alcohol consumption in humans. METHODS: We designed a new class of PKCε inhibitors based on the Rho-associated protein kinase (ROCK) inhibitor Y-27632...
December 1, 2017: Biological Psychiatry
https://www.readbyqxmd.com/read/29197719/functional-diversification-upon-leader-protease-domain-duplication-in-the-citrus-tristeza-virus-genome-role-of-rna-sequences-and-the-encoded-proteins
#18
Sung-Hwan Kang, Osama O Atallah, Yong-Duo Sun, Svetlana Y Folimonova
Viruses from the family Closteroviridae show an example of intra-genome duplications of more than one gene. In addition to the hallmark coat protein gene duplication, several members possess a tandem duplication of papain-like leader proteases. In this study, we demonstrate that domains encoding the L1 and L2 proteases in the Citrus tristeza virus genome underwent a significant functional divergence at the RNA and protein levels. We show that the L1 protease is crucial for viral accumulation and establishment of initial infection, whereas its coding region is vital for virus transport...
November 30, 2017: Virology
https://www.readbyqxmd.com/read/29196750/a-novel-y-specific-long-non-coding-rna-associated-with-cellular-lipid-accumulation-in-hepg2-cells-and-atherosclerosis-related-genes
#19
Elsa Molina, Guat S Chew, Stephen A Myers, Elyse M Clarence, James M Eales, Maciej Tomaszewski, Fadi J Charchar
There is an increasing appreciation for the role of the human Y chromosome in phenotypic differences between the sexes in health and disease. Previous studies have shown that genetic variation within the Y chromosome is associated with cholesterol levels, which is an established risk factor for atherosclerosis, the underlying cause of coronary artery disease (CAD), a major cause of morbidity and mortality worldwide. However, the exact mechanism and potential genes implicated are still unidentified. To date, Y chromosome-linked long non-coding RNAs (lncRNAs) are poorly characterized and the potential link between these new regulatory RNA molecules and hepatic function in men has not been investigated...
December 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29195078/a-next-generation-connectivity-map-l1000-platform-and-the-first-1-000-000-profiles
#20
Aravind Subramanian, Rajiv Narayan, Steven M Corsello, David D Peck, Ted E Natoli, Xiaodong Lu, Joshua Gould, John F Davis, Andrew A Tubelli, Jacob K Asiedu, David L Lahr, Jodi E Hirschman, Zihan Liu, Melanie Donahue, Bina Julian, Mariya Khan, David Wadden, Ian C Smith, Daniel Lam, Arthur Liberzon, Courtney Toder, Mukta Bagul, Marek Orzechowski, Oana M Enache, Federica Piccioni, Sarah A Johnson, Nicholas J Lyons, Alice H Berger, Alykhan F Shamji, Angela N Brooks, Anita Vrcic, Corey Flynn, Jacqueline Rosains, David Y Takeda, Roger Hu, Desiree Davison, Justin Lamb, Kristin Ardlie, Larson Hogstrom, Peyton Greenside, Nathanael S Gray, Paul A Clemons, Serena Silver, Xiaoyun Wu, Wen-Ning Zhao, Willis Read-Button, Xiaohua Wu, Stephen J Haggarty, Lucienne V Ronco, Jesse S Boehm, Stuart L Schreiber, John G Doench, Joshua A Bittker, David E Root, Bang Wong, Todd R Golub
We previously piloted the concept of a Connectivity Map (CMap), whereby genes, drugs, and disease states are connected by virtue of common gene-expression signatures. Here, we report more than a 1,000-fold scale-up of the CMap as part of the NIH LINCS Consortium, made possible by a new, low-cost, high-throughput reduced representation expression profiling method that we term L1000. We show that L1000 is highly reproducible, comparable to RNA sequencing, and suitable for computational inference of the expression levels of 81% of non-measured transcripts...
November 30, 2017: Cell
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