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small RNA sequencing

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https://www.readbyqxmd.com/read/28210624/rna-sequencing-analysis-reveals-interactions-between-breast-cancer-or-melanoma-cells-and-the-tissue-microenvironment-during-brain-metastasis
#1
Ryo Sato, Teppei Nakano, Mari Hosonaga, Oltea Sampetrean, Ritsuko Harigai, Takashi Sasaki, Ikuko Koya, Hideyuki Okano, Jun Kudoh, Hideyuki Saya, Yoshimi Arima
Metastasis is the main cause of treatment failure and death in cancer patients. Metastasis of tumor cells to the brain occurs frequently in individuals with breast cancer, non-small cell lung cancer, or melanoma. Despite recent advances in our understanding of the causes and in the treatment of primary tumors, the biological and molecular mechanisms underlying the metastasis of cancer cells to the brain have remained unclear. Metastasizing cancer cells interact with their microenvironment in the brain to establish metastases...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28209810/genome-sequence-of-southern-tomato-virus-in-asymptomatic-tomato-sweet-hearts
#2
Ricardo I Alcalá-Briseño, Sevgi Coşkan, Maria A Londoño, Jane E Polston
The genome sequence of Southern tomato virus in asymptomatic Solanum lycopersicum 'Sweet Hearts' (STV-Florida) in Florida was assembled from small RNAs sequenced by Illumina RNA-seq. The STV-Florida genome shared 99.0 to 99.9% similarity with full genome sequences from Bangladesh, China, Mexico, and the United States (Mississippi and North Carolina).
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28209552/detection-of-giardia-duodenalis-assemblage-e-infections-at-the-tibetan-plateau-area-yaks-are-suitable-hosts
#3
Wang Guang-Hua, Wang Ge-Ping, Li Xiu-Ping, Ma Li-Qing, Gabriele Karanis, Eleni Christodoulou-Vafeiadou, Panagiotis Karanis
The prevalence of Giardia duodenalis (G. duodenalis) assemblages in yaks is poorly known. The present study examined 297 fecal samples from weaned yak, 4 to 7 months of age, from 3 different farms, in Tibetan Plateau Area (TPA) of the Qinghai Province in Western China. The prevalence of infection was determined by light and immunofluorescence microscopy, and nested-PCR. PCR was performed for the small subunit ribosomal RNA (SSU) amplified 16 positive for G. duodenalis products. The prevalence of Giardia species was 5...
February 13, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28209125/the-mitochondrial-genome-sequences-of-the-round-goby-and-the-sand-goby-reveal-patterns-of-recent-evolution-in-gobiid-fish
#4
Irene Adrian-Kalchhauser, Ola Svensson, Verena E Kutschera, Magnus Alm Rosenblad, Martin Pippel, Sylke Winkler, Siegfried Schloissnig, Anders Blomberg, Patricia Burkhardt-Holm
BACKGROUND: Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic sequences. Usually, vertebrate mitochondrial genomes measure between 16.5 and 17 kilobases (kb). RESULTS: During genome sequencing projects for two novel vertebrate models, the invasive round goby and the sand goby, we found that the sand goby genome is exceptionally small (16...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28207896/rna-seq-analysis-of-chikungunya-virus-infection-and-identification-of-granzyme-a-as-a-major-promoter-of-arthritic-inflammation
#5
Jane A C Wilson, Natalie A Prow, Wayne A Schroder, Jonathan J Ellis, Helen E Cumming, Linden J Gearing, Yee Suan Poo, Adam Taylor, Paul J Hertzog, Francesca Di Giallonardo, Linda Hueston, Roger Le Grand, Bing Tang, Thuy T Le, Joy Gardner, Suresh Mahalingam, Pierre Roques, Phillip I Bird, Andreas Suhrbier
: Chikungunya virus (CHIKV) is an arthritogenic alphavirus causing epidemics of acute and chronic arthritic disease. Herein we describe a comprehensive RNA-Seq analysis of feet and lymph nodes at peak viraemia (day 2 post infection), acute arthritis (day 7) and chronic disease (day 30) in the CHIKV adult wild-type mouse model. Genes previously shown to be up-regulated in CHIKV patients were also up-regulated in the mouse model. CHIKV sequence information was also obtained with up to ≈8% of the reads mapping to the viral genome; however, no adaptive viral genome changes were apparent...
February 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28207848/resolving-host-pathogen-interactions-by-dual-rna-seq
#6
REVIEW
Alexander J Westermann, Lars Barquist, Jörg Vogel
The transcriptome is a powerful proxy for the physiological state of a cell, healthy or diseased. As a result, transcriptome analysis has become a key tool in understanding the molecular changes that accompany bacterial infections of eukaryotic cells. Until recently, such transcriptomic studies have been technically limited to analyzing mRNA expression changes in either the bacterial pathogen or the infected eukaryotic host cell. However, the increasing sensitivity of high-throughput RNA sequencing now enables "dual RNA-seq" studies, simultaneously capturing all classes of coding and noncoding transcripts in both the pathogen and the host...
February 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28207000/spatial-transcriptomic-analysis-of-cryosectioned-tissue-samples-with-geo-seq
#7
Jun Chen, Shengbao Suo, Patrick Pl Tam, Jing-Dong J Han, Guangdun Peng, Naihe Jing
Conventional gene expression studies analyze multiple cells simultaneously or single cells, for which the exact in vivo or in situ position is unknown. Although cellular heterogeneity can be discerned when analyzing single cells, any spatially defined attributes that underpin the heterogeneous nature of the cells cannot be identified. Here, we describe how to use Geo-seq, a method that combines laser capture microdissection (LCM) and single-cell RNA-seq technology. The combination of these two methods enables the elucidation of cellular heterogeneity and spatial variance simultaneously...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28203245/small-rnas-derived-from-the-t-dna-of-agrobacterium-rhizogenes-in-hairy-roots-of-phaseolus-vulgaris
#8
Pablo Peláez, Alejandrina Hernández-López, Georgina Estrada-Navarrete, Federico Sanchez
Agrobacterium rhizogenes is a pathogenic bacteria that causes hairy root disease by transferring bacterial DNA into the plant genome. It is an essential tool for industry and research due to its capacity to produce genetically modified roots and whole organisms. Here, we identified and characterized small RNAs generated from the transfer DNA (T-DNA) of A. rhizogenes in hairy roots of common bean (Phaseolus vulgaris). Distinct abundant A. rhizogenes T-DNA-derived small RNAs (ArT-sRNAs) belonging to several oncogenes were detected in hairy roots using high-throughput sequencing...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28203233/exo-mirexplorer-a-comprehensive-resource-for-exploring-and-comparatively-analyzing-exogenous-micrornas
#9
Ling-Ling Zheng, Kai-Wen Deng, An-Cheng Deng, Jie Wu, Jian-Hua Yang, Zhao-Rong Lun, Liang-Hu Qu
MicroRNAs (miRNAs) are small regulatory RNAs that play important roles in animals, plants, and viruses. Deep-sequencing technology has been widely adopted in miRNA investigations. However, it is still a big mysterious why nearly all sequencing data contain miRNA sequences from exogenous species, called exo-miRNAs. In this study, we developed a novel platform, exo-miRExplorer, for mining and identifying exo-miRNAs from high-throughput small RNA sequencing experiments which originated from tissues and cell lines of multiple organisms...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28202522/histone-acetyltransferase-activity-of-mof-is-required-for-mll-af9-leukemogenesis
#10
Daria G Valerio, Haiming Xu, Chun-Wei Chen, Takayuki Hoshii, Meghan E Eisold, Christopher Delaney, Monica Cusan, Aniruddha J Deshpande, Chun-Hao Huang, Amaia Lujambio, Y George G Zheng, Johannes Zuber, Tej K Pandita, Scott W Lowe, Scott A Armstrong
Chromatin-based mechanisms offer therapeutic targets in acute myeloid leukemia (AML) that are of great current interest. In this study, we conducted an RNAi-based screen to identify druggable chromatin regulator-based targets in leukemias marked by oncogenic rearrangements of the MLL gene. In this manner, we discovered the H4K16 histone acetyltransferase (HAT) MOF to be a potent suppressor of leukemia cell growth. Conditional deletion of Mof in a mouse model of MLL-AF9-driven leukemogenesis reduced tumor burden and prolonged host survival...
February 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28202045/identification-of-micrornas-and-their-response-to-the-stress-of-plant-allelochemicals-in-aphis-gossypii-hemiptera-aphididae
#11
Kang-Sheng Ma, Fen Li, Ying Liu, Ping-Zhuo Liang, Xue-Wei Chen, Xi-Wu Gao
BACKGROUND: MicroRNAs (miRNAs) are a group of short non-coding RNAs involved in the inhibition of protein translation or in mRNA degradation. Although the regulatory roles of miRNAs in various biological processes have been investigated, there is as yet an absence of studies about the regulatory roles of miRNAs involved in the metabolism of plant allelochemicals in insects. RESULTS: We constructed five small RNA libraries from apterous Aphis gossypii adults that had fed on an artificial diet containing various allelochemicals...
February 16, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28201982/transcriptome-profile-of-rat-genes-in-injured-spinal-cord-at-different-stages-by-rna-sequencing
#12
Ling-Ling Shi, Nan Zhang, Xiu-Mei Xie, Yue-Juan Chen, Rui Wang, Lin Shen, Jian-Sheng Zhou, Jian-Guo Hu, He-Zuo Lü
BACKGROUND: Spinal cord injury (SCI) results in fatal damage and currently has no effective treatment. The pathological mechanisms of SCI remain unclear. In this study, genome-wide transcriptional profiling of spinal cord samples from injured rats at different time points after SCI was performed by RNA-Sequencing (RNA-Seq). The transcriptomes were systematically characterized to identify the critical genes and pathways that are involved in SCI pathology. RESULTS: RNA-Seq results were obtained from total RNA harvested from the spinal cords of sham control rats and rats in the acute, subacute, and chronic phases of SCI (1 day, 6 days and 28 days after injury, respectively; n = 3 in every group)...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28199486/gsg1-trnp1-and-tmem215-mark-subpopulations-of-bipolar-interneurons-in-the-mouse-retina
#13
Ko Uoon Park, Grace Randazzo, Kenneth L Jones, Joseph A Brzezinski
Purpose: How retinal bipolar cell interneurons are specified and assigned to specialized subtypes is only partially understood. In part, this is due to a lack of early pan- and subtype-specific bipolar cell markers. To discover these factors, we identified genes that were upregulated in Blimp1 (Prdm1) mutant retinas, which exhibit precocious bipolar cell development. Methods: Postnatal day (P)2 retinas from Blimp1 conditional knock-out (CKO) mice and controls were processed for RNA sequencing...
February 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28197372/fam13a-is-associated-with-non-small-cell-lung-cancer-nsclc-progression-and-controls-tumor-cell-proliferation-and-survival
#14
Felix Eisenhut, Lisanne Heim, Sonja Trump, Susanne Mittler, Nina Sopel, Katerina Andreev, Fulvia Ferrazzi, Arif B Ekici, Ralf Rieker, Rebekka Springel, Vera L Assmann, Matthias Lechmann, Sonja Koch, Marina Engelhardt, Christina Warnecke, Denis I Trufa, Horia Sirbu, Arndt Hartmann, Susetta Finotto
Genome-wide association studies (GWAS) associated Family with sequence similarity 13, member A (FAM13A) with non-small cell lung cancer (NSCLC) occurrence. Here, we found increased numbers of FAM13A protein expressing cells in the tumoral region of lung tissues from a cohort of patients with NSCLC. Moreover, FAM13A inversely correlated with CTLA4 but directly correlated with HIF1α levels in the control region of these patients. Consistently, FAM13A RhoGAP was found to be associated with T cell effector molecules like HIF1α and Tbet and was downregulated in immunosuppressive CD4(+)CD25(+)Foxp3(+)CTLA4(+) T cells...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28196981/rna-based-recognition-and-targeting-sowing-the-seeds-of-specificity
#15
REVIEW
Stanislaw A Gorski, Jörg Vogel, Jennifer A Doudna
RNA is involved in the regulation of multiple cellular processes, often by forming sequence-specific base pairs with cellular RNA or DNA targets that must be identified among the large number of nucleic acids in a cell. Several RNA-based regulatory systems in eukaryotes, bacteria and archaea, including microRNAs (miRNAs), small interfering RNAs (siRNAs), CRISPR RNAs (crRNAs) and small RNAs (sRNAs) that are dependent on the RNA chaperone protein Hfq, achieve specificity using similar strategies. Central to their function is the presentation of short 'seed sequences' within a ribonucleoprotein complex to facilitate the search for and recognition of targets...
February 15, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/28195208/a-pupal-transcriptomic-screen-identifies-ral-as-a-target-of-store-operated-calcium-entry-in-drosophila-neurons
#16
Shlesha Richhariya, Siddharth Jayakumar, Katharine Abruzzi, Michael Rosbash, Gaiti Hasan
Transcriptional regulation by Store-operated Calcium Entry (SOCE) is well studied in non-excitable cells. However, the role of SOCE has been poorly documented in neuronal cells with more complicated calcium dynamics. Previous reports demonstrated a requirement for SOCE in neurons that regulate Drosophila flight bouts. We refine this requirement temporally to the early pupal stage and use RNA-sequencing to identify SOCE mediated gene expression changes in the developing Drosophila pupal nervous system. Down regulation of dStim, the endoplasmic reticular calcium sensor and a principal component of SOCE in the nervous system, altered the expression of 131 genes including Ral, a small GTPase...
February 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28194691/rnai-mediated-simultaneous-resistance-against-three-rna-viruses-in-potato
#17
Amir Hameed, Muhammad Nouman Tahir, Shaheen Asad, Rakhshanda Bilal, Joyce Van Eck, Georg Jander, Shahid Mansoor
RNA interference (RNAi) technology has been successfully applied in stacking resistance against viruses in numerous crop plants. During RNAi, the production of small interfering RNAs (siRNAs) from template double-standard RNA (dsRNA) derived from expression constructs provides an on-switch for triggering homology-based targeting of cognate viral transcripts, hence generating a pre-programmed immunity in transgenic plants prior to virus infection. In the current study, transgenic potato lines (Solanum tuberosum cv...
February 13, 2017: Molecular Biotechnology
https://www.readbyqxmd.com/read/28194372/mir-34b-5p-suppresses-melanoma-differentiation-associated-gene-5-mda5-signaling-pathway-to-promote-avian-leukosis-virus-subgroup-j-alv-j-infected-cells-proliferaction-and-alv-j-replication
#18
Zhenhui Li, Qingbin Luo, Haiping Xu, Ming Zheng, Bahareldin Ali Abdalla, Min Feng, Bolin Cai, Xiaocui Zhang, Qinghua Nie, Xiquan Zhang
Avian leukosis virus subgroup J (ALV-J) is an oncogenic retrovirus that has a similar replication cycle to multiple viruses and therefore can be used as a model system for viral entry into host cells. However, there are few reports on the genes or microRNAs (miRNAs) that are responsible for the replication of ALV-J. Our previous miRNA and RNA sequencing data showed that the expression of miR-34b-5p was significantly upregulated in ALV-J-infected chicken spleens compared to non-infected chicken spleens, but melanoma differentiation-associated gene 5 (MDA5) had the opposite expression pattern...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28192788/metabolic-gatekeeper-function-of-b-lymphoid-transcription-factors
#19
Lai N Chan, Zhengshan Chen, Daniel Braas, Jae-Woong Lee, Gang Xiao, Huimin Geng, Kadriye Nehir Cosgun, Christian Hurtz, Seyedmehdi Shojaee, Valeria Cazzaniga, Hilde Schjerven, Thomas Ernst, Andreas Hochhaus, Steven M Kornblau, Marina Konopleva, Miles A Pufall, Giovanni Cazzaniga, Grace J Liu, Thomas A Milne, H Phillip Koeffler, Theodora S Ross, Isidro Sánchez-García, Arndt Borkhardt, Keith R Yamamoto, Ross A Dickins, Thomas G Graeber, Markus Müschen
B-lymphoid transcription factors, such as PAX5 and IKZF1, are critical for early B-cell development, yet lesions of the genes encoding these transcription factors occur in over 80% of cases of pre-B-cell acute lymphoblastic leukaemia (ALL). The importance of these lesions in ALL has, until now, remained unclear. Here, by combining studies using chromatin immunoprecipitation with sequencing and RNA sequencing, we identify a novel B-lymphoid program for transcriptional repression of glucose and energy supply...
February 13, 2017: Nature
https://www.readbyqxmd.com/read/28190401/rapid-transcriptional-plasticity-of-duplicated-gene-clusters-enables-a-clonally-reproducing-aphid-to-colonise-diverse-plant-species
#20
Thomas C Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T Mugford, Patrice Baa-Puyoulet, Anthony Bretaudeau, Bernardo Clavijo, Stefano Colella, Olivier Collin, Tamas Dalmay, Thomas Derrien, Honglin Feng, Toni Gabaldón, Anna Jordan, Irene Julca, Graeme J Kettles, Krissana Kowitwanich, Dominique Lavenier, Paolo Lenzi, Sara Lopez-Gomollon, Damian Loska, Daniel Mapleson, Florian Maumus, Simon Moxon, Daniel R G Price, Akiko Sugio, Manuella van Munster, Marilyne Uzest, Darren Waite, Georg Jander, Denis Tagu, Alex C C Wilson, Cock van Oosterhout, David Swarbreck, Saskia A Hogenhout
BACKGROUND: The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants. This remarkable ability makes M. persicae a highly destructive pest of many important crop species...
February 13, 2017: Genome Biology
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