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Source: BMC Genomics

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Total 18 results found since Jan 2013.

Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus
Somatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour...
Source: BMC Genomics - September 20, 2021 Category: Genetics & Stem Cells Authors: Darrell Lizamore, Ross Bicknell and Chris Winefield Tags: Research article Source Type: research

Non-coding RNAs in the interaction between rice and Meloidogyne graminicola
Root knot nematodes (RKN) are plant parasitic nematodes causing major yield losses of widely consumed food crops such as rice (Oryza sativa). Because non-coding RNAs, including small interfering RNAs (siRNA), mic...
Source: BMC Genomics - July 20, 2021 Category: Genetics & Stem Cells Authors: Bruno Verstraeten, Mohammad Reza Atighi, Virginia Ruiz-Ferrer, Carolina Escobar, Tim De Meyer and Tina Kyndt Tags: Research Source Type: research

The RNAi machinery controls distinct responses to environmental signals in the basal fungus Mucor circinelloides
Conclusion: This work shows that the RNAi pathways play a relevant role in the regulation of a significant number of endogenous genes in M. circinelloides during exponential and stationary growth phases and opens up an important avenue for in-depth study of genes involved in the regulation of physiological and developmental processes in this fungal model.
Source: BMC Genomics - March 25, 2015 Category: Genetics & Stem Cells Authors: Francisco NicolásAna VilaSimon MoxonMaría CascalesSantiago Torres-MartínezRosa Ruiz-VázquezVictoriano Garre Source Type: research

Small RNAs derived from tRNAs and rRNAs are highly enriched in exosomes from both old and new world Leishmania providing evidence for conserved exosomal RNA Packaging
Conclusions: These results show that leishmania exosomes are selectively and specifically enriched in small RNAs derived almost exclusively from non-coding RNAs. These exosomes are competent to deliver their cargo of novel, potential small regulatory RNAs to macrophages where they may influence parasite-host cell interactions. The remarkably high degree of congruence in exosomal RNA content between L. donovani and L. braziliensis, argues for the presence of a conserved mechanism for exosomal RNA packaging in leishmania. These findings open up a new avenue of research on non-canonical, small RNA pathways in this trypanosoma...
Source: BMC Genomics - March 5, 2015 Category: Genetics & Stem Cells Authors: Ulrike LambertzMariana Oviedo OvandoElton VasconcelosPeter UnrauPeter MylerNeil Reiner Source Type: research

Integrative analysis of high-throughput RNAi screen data identifies the FER and CRKL tyrosine kinases as new regulators of the mitogenic ERK-dependent pathways in transformed cells
Conclusion: Based on a combined approach of large kinome-wide siRNA screens and ontology annotations, our study identifies for the first time two kinase groups differentially implicated in the control of cell proliferation. We further demonstrate that integrative analysis of the kinase interactome provides key information which can be used to facilitate or optimize target design for new therapeutic strategies. The complete list of protein-protein interactions from the two functional kinase groups will provide a useful database for future investigations.
Source: BMC Genomics - December 23, 2014 Category: Genetics & Stem Cells Authors: Philippe NizardFrédéric EzanDominique BonnierNolwenn Le MeurSophie LangouëtGeorges BaffetYannick Arlot-BonnemainsNathalie Théret Source Type: research

Simultaneous analysis of large-scale RNAi screens for pathogen entry
Conclusions: Our results show parallel RNAi screening can improve the results of individual screens. This is currently particularly interesting when large-scale parallel datasets are becoming more and more publicly available. Our comprehensive siRNA dataset provides a public, freely available resource for further statistical and biological analyses in the high-content, high-throughput siRNA screening field.
Source: BMC Genomics - December 22, 2014 Category: Genetics & Stem Cells Authors: Pauli RämöAnna DrewekCécile ArrieumerlouNiko BeerenwinkelHouchaima Ben-TekayaBettina CardelAlain CasanovaRaquel Conde-AlvarezPascale CossartGábor CsúcsSimone EicherMario EmmenlauerUrs GreberWolf-Dietrich HardtAri HeleniusChristoph KasperAndreas Kaufm Source Type: research

Complex coding of endogenous siRNA, transcriptional silencing and H3K9 methylation on native targets of germline nuclear RNAi in C. elegans
Conclusion: Germline nuclear RNAi in C. elegans is required to silence retrotransposons but not DNA transposon. Transcriptional silencing and H3K9me can occur independently of each other on the native targets of nuclear RNAi in C. elegans. Our results rule out a simple model in which nuclear Argonaute protein-associated-small RNAs are sufficient to trigger germline nuclear RNAi responses. In addition, the piRNA pathway and germline nuclear RNAi are specialized to target different types of foreign genetic elements for genome surveillance in C. elegans.
Source: BMC Genomics - December 22, 2014 Category: Genetics & Stem Cells Authors: Julie NiEsteban ChenSam Gu Source Type: research

Small RNA profiling reveals regulation of Arabidopsis miR168 and heterochromatic siRNA415 in response to fungal elicitors
Conclusion: Results here presented support a transcriptional regulatory mechanism underlying MIR168 expression. This finding highlights the importance of miRNA functioning in adaptive processes of Arabidopsis plants to fungal infection. The results of this study also lay a foundation for the involvement of RdDM processes through the activity of siRNA415 and miR823 in mediating regulation of immune responses in Arabidopsis plants.
Source: BMC Genomics - December 10, 2014 Category: Genetics & Stem Cells Authors: Patricia BaldrichKlementina KakarChristelle SiréAna Beatriz MorenoAngélique BergerMeritxell García-ChapaJuan José López-MoyaJosé Luis RiechmannBlanca San Segundo Source Type: research

Genome wide screening of RNAi factors of Sf21 cells reveal several novel pathway associated proteins
Conclusion: The database of RNAi-factors generated by whole genome association survey offers comprehensive outlook about conservation as well as specific differences of the proteins of RNAi machinery. Understanding the interior involved in different phases of gene silencing also offers impending tool for RNAi-based applications.
Source: BMC Genomics - Latest articles - September 9, 2014 Category: Genetics & Stem Cells Authors: Subhanita GhoshPavan KakumaniAjit KumarPawan MalhotraSunil MukherjeeRaj Bhatnagar Source Type: research

Genome-wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize
Conclusion: Our results show that maize has RNA-based silencing mechanisms that can trigger specific responses when plants interact with beneficial endophytic diazotrophic bacteria. Our findings suggest important roles for sRNA regulation in maize, and probably in other plants, during association with diazotrophic bacteria, emphasizing the up-regulation of Cu-miRNA.
Source: BMC Genomics - Latest articles - September 6, 2014 Category: Genetics & Stem Cells Authors: Flávia ThiebautCristian RojasClícia GrativolMariana MottaTauan VieiraMichael RegulskiRobert MartienssenLaurent FarinelliAdriana HemerlyPaulo Ferreira Source Type: research

Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava
Conclusion: Systematic and computational analysis of microRNAome and experimental validation collectively showed that miRNAs, ta-siRNAs, and possibly nat-siRNAs play important roles in chilling response and chilling acclimation in Cassava by regulating stress-related pathways, e.g. Auxin signal transduction. The conservation of these sncRNA might shed lights on the role of sncRNA-mediated pathways affected by chilling stress and stress acclimation in Euphorbiaceous plants.
Source: BMC Genomics - Latest articles - July 29, 2014 Category: Genetics & Stem Cells Authors: Jing XiaChangying ZengZheng ChenKevin ZhangXin ChenYufei ZhouShun SongCheng LuRuiju YangZi YangJunfei ZhouHai PengWenquan WangMing PengWeixiong Zhang Source Type: research

High-throughput sequencing reveals small RNAs involved in ASGV infection
Conclusions: This study is the first report on the apple sRNA-response to virus infection. The results revealed the vsiRNAs profile of an ASGV variant, as well as the alteration of the tRNA-derived sRNA profile in response to latent virus infection. It also highlights the importance of library preparation in the interpretation of high-throughput sequencing data.
Source: BMC Genomics - Latest articles - July 7, 2014 Category: Genetics & Stem Cells Authors: Marike VisserHans MareeD ReesJohan Burger Source Type: research

Dynamic imbalance between cancer cell subpopulations induced by Transforming Growth Factor Beta (TGF-beta) is associated with a DNA methylome switch
Conclusions: Our study reveals a self-perpetuating crosstalk between TGF-beta signaling and the DNA methylation machinery, which can be relevant in the establishment of cellular phenotypes. This is the first indication of the ability of TGF-beta to induce genome-wide changes in DNA methylation, resulting in a stable change in the proportion of liver cancer cell subpopulations.
Source: BMC Genomics - Latest articles - June 5, 2014 Category: Genetics & Stem Cells Authors: Marion MartinPierre-Benoit AnceyMarie-Pierre CrosGeoffroy DurandFlorence Le Calvez-KelmHector Hernandez-VargasZdenko Herceg Source Type: research

Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines
Conclusion: These results suggest that genetic variation might contribute to drug response via either cis- or trans- regulation of gene expression. GWAS analysis followed by functional pharmacogenomics studies might help identify novel biomarkers contributing to variation in response to these two drugs and enhance our understanding of underlying mechanisms of drug action.
Source: BMC Genomics - Latest articles - February 1, 2014 Category: Genetics & Stem Cells Authors: Liang LiBrooke FridleyKrishna KalariNifang NiuGregory JenkinsAnthony BatzlerRyan AboDaniel SchaidLiewei Wang Source Type: research

Comprehensive analysis of beta-catenin target genes in colorectal carcinoma cell lines with deregulated Wnt/beta-catenin signaling
Conclusions: Based on the large number of potential beta-catenin target genes found to be similarly regulated in DLD1, SW480 and LS174T cells as well as the large overlap with confirmed beta-catenin target genes, we conclude that DLD1 and SW480 colon carcinoma cell lines are suitable model systems to study Wnt/beta-catenin signaling and associated colorectal carcinogenesis. Furthermore, the confirmed and the newly identified potential beta-catenin target genes are useful starting points for further studies.
Source: BMC Genomics - Latest articles - January 28, 2014 Category: Genetics & Stem Cells Authors: Andreas HerbstVindi JurinovicStefan KrebsSusanne ThiemeHelmut BlumBurkhard GökeFrank Kolligs Source Type: research