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exosome and RNA sequence

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https://www.readbyqxmd.com/read/28096131/nutrition-micrornas-and-human-health
#1
REVIEW
Juan Cui, Beiyan Zhou, Sharon A Ross, Janos Zempleni
MicroRNAs (miRs) hybridize with complementary sequences in mRNA and silence genes by destabilizing mRNA or preventing translation of mRNA. Over 60% of human protein-coding genes are regulated by miRs, and 1881 high-confidence miRs are encoded in the human genome. Evidence suggests that miRs not only are synthesized endogenously, but also might be obtained from dietary sources, and that food compounds alter the expression of endogenous miR genes. The main food matrices for studies of biological activity of dietary miRs include plant foods and cow milk...
January 2017: Advances in Nutrition
https://www.readbyqxmd.com/read/28069372/rna-exosome-and-non-coding-rna-coupled-mechanisms-in-aid-mediated-genomic-alterations
#2
REVIEW
Brice Laffleur, Uttiya Basu, Junghyun Lim
The eukaryotic RNA exosome is a well-conserved protein complex with ribonuclease activity implicated in RNA metabolism. Various families of non-coding RNAs have been identified as substrates of the complex, underscoring its role as a non-coding RNA processing/degradation unit. However, the role of RNA exosome and its RNA processing activity on DNA mutagenesis/alteration events have not been investigated until recently. B lymphocytes use two DNA alteration mechanisms, class switch recombination (CSR) and somatic hypermutation (SHM), to re-engineer their antibody gene expressing loci until a tailored antibody gene for a specific antigen is satisfactorily generated...
January 7, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28051166/identification-of-small-rnas-in-extracellular-vesicles-from-the-commensal-yeast-malassezia-sympodialis
#3
Simon Rayner, Sören Bruhn, Helen Vallhov, Anna Andersson, R Blake Billmyre, Annika Scheynius
Malassezia is the dominant fungus in the human skin mycobiome and is associated with common skin disorders including atopic eczema (AE)/dermatitis. Recently, it was found that Malassezia sympodialis secretes nanosized exosome-like vesicles, designated MalaEx, that carry allergens and can induce inflammatory cytokine responses. Extracellular vesicles from different cell-types including fungi have been found to deliver functional RNAs to recipient cells. In this study we assessed the presence of small RNAs in MalaEx and addressed if the levels of these RNAs differ when M...
January 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28043542/the-analysis-of-exosomal-micro-rnas-in-peripheral-blood-mononuclear-cell-derived-macrophages-after-infection-with-bacillus-calmette-gu%C3%A3-rin-by-rna-sequencing
#4
Esmaeil Mortaz, Shamila D Alipoor, Payam Tabarsi, Ian M Adcock, Johan Garssen, Ali Akbar Velayati
OBJECTIVE/BACKGROUND: Tuberculosis (TB) is a major global threat to human health, especially in low-income countries. The diagnosis of TB is challenging because of the limitations of specificity and sensitivity with the current diagnostics. Novel, selective biomarkers for TB would be of great practical value. Exosomes are bioactive vesicles with 30-100nm in diameter, which are secreted from almost all cell types and are found in virtually every human body fluid. Exosomes transport micro-RNAs (miRNAs), which are post-transcriptional regulators of gene expression, around the body and allow miRNAs to modulate biological pathways in target cells...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28017589/distinctive-patterns-of-transcription-and-rna-processing-for-human-lincrnas
#5
Margarita Schlackow, Takayuki Nojima, Tomas Gomes, Ashish Dhir, Maria Carmo-Fonseca, Nick J Proudfoot
Numerous long intervening noncoding RNAs (lincRNAs) are generated from the mammalian genome by RNA polymerase II (Pol II) transcription. Although multiple functions have been ascribed to lincRNAs, their synthesis and turnover remain poorly characterized. Here, we define systematic differences in transcription and RNA processing between protein-coding and lincRNA genes in human HeLa cells. This is based on a range of nascent transcriptomic approaches applied to different nuclear fractions, including mammalian native elongating transcript sequencing (mNET-seq)...
January 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28005467/defining-the-purity-of-exosomes-required-for-diagnostic-profiling-of-small-rna-suitable-for-biomarker-discovery
#6
Camelia Quek, Shayne A Bellingham, Chol-Hee Jung, Benjamin J Scicluna, Mitch C Shambrook, Robyn A Sharples, Lesley Cheng, Andrew F Hill
Small non-coding RNAs (ncRNA), including microRNAs (miRNA), enclosed in exosomes are being utilised for biomarker discovery in disease. Two common exosome isolation methods involve differential ultracentrifugation or differential ultracentrifugation coupled with Optiprep gradient fractionation. Generally, the incorporation of an Optiprep gradient provides better separation and increased purity of exosomes. The question of whether increased purity of exosomes is required for small ncRNA profiling, particularly in diagnostic and biomarker purposes, has not been addressed and highly debated...
December 22, 2016: RNA Biology
https://www.readbyqxmd.com/read/28000095/exosomes-from-ipscs-delivering-sirna-attenuate-intracellular-adhesion-molecule-1-expression-and-neutrophils-adhesion-in-pulmonary-microvascular-endothelial-cells
#7
Zhihai Ju, Jinhui Ma, Chen Wang, Jie Yu, Yeru Qiao, Feilong Hei
The pro-inflammatory activation of pulmonary microvascular endothelial cells resulting in continuous expression of cellular adhesion molecules, and subsequently recruiting primed neutrophils to form a firm neutrophils-endothelium (PMN-EC) adhesion, has been examined and found to play a vital role in acute lung injury (ALI). RNA interference (RNAi) is a cellular process through harnessing a natural pathway silencing target gene based on recognition and subsequent degradation of specific mRNA sequences. It opens a promising approach for precision medicine...
December 21, 2016: Inflammation
https://www.readbyqxmd.com/read/27943208/small-rna-library-construction-for-exosomal-rna-from-biological-samples-for-the-ion-torrent-pgm%C3%A2-and-ion-s5%C3%A2-system
#8
Lesley Cheng, Andrew F Hill
Next-generation deep sequencing (NGS) technology represents a powerful and innovative approach to profile small RNA. Currently, there are a number of large-scale and benchtop sequencing platforms available on the market. Although each platform is relatively straightforward to operate, constructing cDNA libraries can be the most difficult part of the NGS workflow. Constructing quality libraries is essential to obtaining a successful sequencing run of high-quality reads and coverage. The quality and yield of RNA affect hybridization and ligation of sequencing adapters...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27917920/transcriptome-and-long-noncoding-rna-sequencing-of-three-extracellular-vesicle-subtypes-released-from-the-human-colon-cancer-lim1863-cell-line
#9
Maoshan Chen, Rong Xu, Hong Ji, David W Greening, Alin Rai, Keiichi Izumikawa, Hideaki Ishikawa, Nobuhiro Takahashi, Richard J Simpson
Previously we reported that LIM1863 colorectal cancer (CRC) cells secrete three distinct extracellular vesicle subtypes - two subpopulations of exosomes (apical EpCAM-Exos and basolateral A33-Exos) and shed microvesicles (sMVs) - with distinct protein and miRNA signatures. Here, we extend our omics approach to understand the fundamental role of LIM1863-derived EVs by performing a comprehensive analysis of their mRNAs and long non-coding RNAs (lncRNAs) using RNA-Seq. We show that 2,389 mRNAs, 317 pseudogene transcripts, 1,028 lncRNAs and 206 short non-coding RNAs selectively distributed to (i...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27872161/identification-of-urinary-exosomal-noncoding-rnas-as-novel-biomarkers-in-chronic-kidney-disease
#10
Rimpi Khurana, Glory Ranches, Simon Schafferer, Melanie Lukasser, Michael Rudnicki, Gert Mayer, Alexander Hüttenhofer
In chronic kidney disease (CKD), the decline in the glomerular filtration rate is associated with increased morbidity and mortality and thus poses a major challenge for healthcare systems. While the contribution of tissue-derived miRNAs and mRNAs to CKD progression has been extensively studied, little is known about the role of urinary exosomes and their association with CKD. Exosomes are small, membrane-derived endocytic vesicles that contribute to cell-to-cell communication and are present in various body fluids, such as blood or urine...
February 2017: RNA
https://www.readbyqxmd.com/read/27858503/high-throughput-sequencing-of-two-populations-of-extracellular-vesicles-provides-an-mrna-signature-that-can-be-detected-in-the-circulation-of-breast-cancer-patients
#11
Andrew Conley, Valentina R Minciacchi, Dhong Hyun Lee, Beatrice S Knudsen, Beth Y Karlan, Luigi Citrigno, Giuseppe Viglietto, Muneesh Tewari, Michael R Freeman, Francesca Demichelis, Dolores Di Vizio
Extracellular vesicles (EVs) contain a wide range of RNA types with a reported prevalence of non-coding RNA. To date a comprehensive characterization of the protein coding transcripts in EVs is still lacking. We performed RNA-Sequencing (RNA-Seq) of two EV populations and identified a small fraction of transcripts that were expressed at significantly different levels in large oncosomes and exosomes, suggesting they may mediate specialized functions. However, these two EV populations exhibited a common mRNA signature that, in comparison to their donor cells, was significantly enriched in mRNAs encoding E2F transcriptional targets and histone proteins...
November 18, 2016: RNA Biology
https://www.readbyqxmd.com/read/27799337/small-rna-sequencing-in-cells-and-exosomes-identifies-eqtls-and-14q32-as-a-region-of-active-export
#12
Emily K Tsang, Nathan S Abell, Xin Li, Vanessa Anaya, Konrad J Karczewski, David A Knowles, Raymond G Sierra, Kevin S Smith, Stephen B Montgomery
Exosomes are small extracellular vesicles that carry heterogeneous cargo, including RNA, between cells. Increasing evidence suggests that exosomes are important mediators of intercellular communication and biomarkers of disease. Despite this, the variability of exosomal RNA between individuals has not been well quantified. To assess this variability, we sequenced the small RNA of cells and exosomes from a 17-member family. Across individuals, we show that selective export of miRNAs occurs not only at the level of specific transcripts, but that a cluster of 74 mature miRNAs on chromosome 14q32 is massively exported in exosomes while mostly absent from cells...
January 5, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27791479/two-distinct-extracellular-rna-signatures-released-by-a-single-cell-type-identified-by-microarray-and-next-generation-sequencing
#13
Cecilia Lässer, Ganesh Vilas Shelke, Ashish Yeri, Dae-Kyum Kim, Rossella Crescitelli, Stefania Raimondo, Margareta Sjöstrand, Yong Song Gho, Kendall Van Keuren Jensen, Jan Lötvall
Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated 2 distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not...
January 2, 2017: RNA Biology
https://www.readbyqxmd.com/read/27788488/serum-exosomal-mir-4772-3p-is-a-predictor-of-tumor-recurrence-in-stage-ii-and-iii-colon-cancer
#14
Chang Liu, Cathy Eng, Jianjun Shen, Yue Lu, Yoko Takata, Amir Mehdizadeh, George J Chang, Miguel A Rodriguez-Bigas, Yanan Li, Ping Chang, Yixiang Mao, Manal M Hassan, Fangyu Wang, Donghui Li
PURPOSE: The study was aimed to evaluate the prognostic or predictive value of serum exosomal microRNAs (miRNAs) for tumor recurrence and response to adjuvant therapy in stage II and stage III colon cancer. RESULTS: 145 differentially expressed mature miRNAs were identified (P<0.05) and 10 top hits were carried forward in validation test. MiR-4772-3p was significantly under-expressed in 27 patients with recurrence compared to in 57 patients without recurrence (P=0...
24, 2016: Oncotarget
https://www.readbyqxmd.com/read/27780738/next-generation-sequencing-based-small-rna-profiling-of-cerebrospinal-fluid-exosomes
#15
Yohsuke Yagi, Takuya Ohkubo, Hideya Kawaji, Akira Machida, Haruka Miyata, Saori Goda, Sugata Roy, Yoshihide Hayashizaki, Harukazu Suzuki, Takanori Yokota
MicroRNAs (miRNAs), particularly those found in human body fluids, have been suggested as potential biomarkers. Among various body fluids, the cerebrospinal fluid (CSF) shows promise as a profiling target for diagnosis and monitoring of neurological diseases. However, relevant genome-scale studies are limited and no studies have profiled exosomal miRNAs in CSF. Therefore, we conducted a next-generation sequencing-based genome-wide survey of small RNAs in the exosomal and non-exosomal (supernatant) fractions of healthy human CSF as well as serum in each donor...
January 1, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/27760749/circulating-mirnas-as-potential-alternative-cell-signaling-associated-with-maternal-recognition-of-pregnancy-in-the-mare
#16
Kristin M Klohonatz, Ashely D Cameron, Joanna R Hergenreder, Juliano C da Silveira, Aeriel D Belk, D N R Veeramachaneni, Gerrit J Bouma, Jason E Bruemmer
During early pregnancy, the conceptus and mare communicate to establish pregnancy. Cell-secreted vesicles (e.g., exosomes) have been reported in serum. Exosomes contain bioactive materials, such as miRNA, that can mediate cell responses. We hypothesized that a) exosomes are present in mare circulation and quantity varies with pregnancy status, b) exosomes contain miRNAs unique to pregnancy status, and c) miRNAs target pathways in endometrium based upon pregnancy status of the mare. First, serum samples were obtained from mares in a crossover design, with each mare providing samples from a pregnant and nonmated control cycle (n = 3/sample day) on Days 12, 14, 16, and 18 postovulation...
December 2016: Biology of Reproduction
https://www.readbyqxmd.com/read/27758893/genome-wide-mapping-of-uncapped-and-cleaved-transcripts-reveals-a-role-for-the-nuclear-mrna-cap-binding-complex-in-cotranslational-rna-decay-in-arabidopsis
#17
Xiang Yu, Matthew R Willmann, Stephen J Anderson, Brian D Gregory
RNA turnover is necessary for controlling proper mRNA levels posttranscriptionally. In general, RNA degradation is via exoribonucleases that degrade RNA either from the 5' end to the 3' end, such as XRN4, or in the opposite direction by the multisubunit exosome complex. Here, we use genome-wide mapping of uncapped and cleaved transcripts to reveal the global landscape of cotranslational mRNA decay in the Arabidopsis thaliana transcriptome. We found that this process leaves a clear three nucleotide periodicity in open reading frames...
October 2016: Plant Cell
https://www.readbyqxmd.com/read/27732855/the-rna-binding-protein-syncrip-is-a-component-of-the-hepatocyte-exosomal-machinery-controlling-microrna-sorting
#18
Laura Santangelo, Giorgio Giurato, Carla Cicchini, Claudia Montaldo, Carmine Mancone, Roberta Tarallo, Cecilia Battistelli, Tonino Alonzi, Alessandro Weisz, Marco Tripodi
Despite clear evidence that exosomal microRNAs (miRNAs) are able to modulate the cellular microenvironment and that exosomal RNA cargo selection is deregulated in pathological conditions, the mechanisms controlling specific RNA sorting into extracellular vesicles are still poorly understood. Here, we identified the RNA binding protein SYNCRIP (synaptotagmin-binding cytoplasmic RNA-interacting protein; also known as hnRNP-Q or NSAP1) as a component of the hepatocyte exosomal miRNA sorting machinery. SYNCRIP knockdown impairs sorting of miRNAs in exosomes...
October 11, 2016: Cell Reports
https://www.readbyqxmd.com/read/27711183/xrn1-is-a-species-specific-virus-restriction-factor-in-yeasts
#19
Paul A Rowley, Brandon Ho, Sarah Bushong, Arlen Johnson, Sara L Sawyer
In eukaryotes, the degradation of cellular mRNAs is accomplished by Xrn1 and the cytoplasmic exosome. Because viral RNAs often lack canonical caps or poly-A tails, they can also be vulnerable to degradation by these host exonucleases. Yeast lack sophisticated mechanisms of innate and adaptive immunity, but do use RNA degradation as an antiviral defense mechanism. One model is that the RNA of yeast viruses is subject to degradation simply as a side effect of the intrinsic exonuclease activity of proteins involved in RNA metabolism...
October 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27608715/plasma-exosome-micrornas-are-indicative-of-breast-cancer
#20
Bethany N Hannafon, Yvonne D Trigoso, Cameron L Calloway, Y Daniel Zhao, David H Lum, Alana L Welm, Zhizhuang J Zhao, Kenneth E Blick, William C Dooley, W Q Ding
BACKGROUND: microRNAs are promising candidate breast cancer biomarkers due to their cancer-specific expression profiles. However, efforts to develop circulating breast cancer biomarkers are challenged by the heterogeneity of microRNAs in the blood. To overcome this challenge, we aimed to develop a molecular profile of microRNAs specifically secreted from breast cancer cells. Our first step towards this direction relates to capturing and analyzing the contents of exosomes, which are small secretory vesicles that selectively encapsulate microRNAs indicative of their cell of origin...
2016: Breast Cancer Research: BCR
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