Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik

Permanent URI for this collectionhttps://hdl.handle.net/11147/9

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Subject: search.filters.subject.Gene expression regulation

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  • Article
    Citation - WoS: 37
    Citation - Scopus: 45
    On the Performance of Pre-Microrna Detection Algorithms
    (Nature Publishing Group, 2017) Saçar Demirci, Müşerref Duygu; Baumbach, Jan; Allmer, Jens
    MicroRNAs are crucial for post-transcriptional gene regulation, and their dysregulation has been associated with diseases like cancer and, therefore, their analysis has become popular. The experimental discovery of miRNAs is cumbersome and, thus, many computational tools have been proposed. Here we assess 13 ab initio pre-miRNA detection approaches using all relevant, published, and novel data sets while judging algorithm performance based on ten intrinsic performance measures. We present an extensible framework, izMiR, which allows for the unbiased comparison of existing algorithms, adding new ones, and combining multiple approaches into ensemble methods. In an exhaustive attempt, we condense the results of millions of computations and show that no method is clearly superior; however, we provide a guideline for biomedical researchers to select a tool. Finally, we demonstrate that combining all of the methods into one ensemble approach, for the first time, allows reliable purely computational pre-miRNA detection in large eukaryotic genomes.
  • Article
    Citation - WoS: 19
    Citation - Scopus: 29
    One Step Forward, Two Steps Back; Xeno-Micrornas Reported in Breast Milk Are Artifacts
    (Public Library of Science, 2016) Bağcı, Caner; Allmer, Jens
    Background: MicroRNAs (miRNAs) are short RNA sequences that guide post-transcriptional regulation of gene expression via complementarity to their target mRNAs. Discovered only recently, miRNAs have drawn a lot of attention. Multiple protein complexes interact to first cleave a hairpin from nascent RNA, export it into the cytosol, trim its loop, and incorporate it into the RISC complex which is important for binding its target mRNA. This process works within one cell, but circulating miRNAs have been described suggesting a role in cell-cell communication. Motivation: Viruses and intracellular parasites like Toxoplasma gondii use miRNAs to manipulate host gene expression from within the cellular environment. However, recent research has claimed that a rice miRNA may regulate human gene expression. Despite ongoing debates about these findings and general reluctance to accept them, a recent report claimed that foodborne plant miRNAs pass through the digestive tract, travel through blood to be incorporated by alveolar cells excreting milk. The miRNAs are then said to have some immunerelated function in the newborn. Principal Findings: We acquired the data that supports their claim and performed further analyses. In addition to the reported miRNAs, we were able to detect almost complete mRNAs and found that the foreign RNA expression profiles among samples are exceedingly similar. Inspecting the source of the data helped understand how RNAs could contaminate the samples. Conclusion: Viewing these findings in context with the difficulties foreign RNAs face on their route into breast milk and the fact that many identified foodborne miRNAs are not from actual food sources, we can conclude beyond reasonable doubt that the original claims and evidence presented may be due to artifacts. We report that the study claiming their existence is more likely to have detected RNA contamination than miRNAs.
  • Article
    Citation - WoS: 4
    Citation - Scopus: 7
    Master Regulators of Posttranscriptional Gene Expression Are Subject To Regulation
    (Humana Press, 2014) Hamid, Syed Muhammad; Akgül, Bünyamin
    MicroRNAs (miRNAs) are small noncoding RNAs of 17-25 nt in length that control gene expression posttranscriptionally. As master regulators of posttranscriptional gene expression, miRNAs themselves are subject to tight regulation at multiple steps. The most common mechanisms include miRNA transcription, processing, and localization. Additionally, intricate feedback loops between miRNAs and transcription factors result in unidirectional, reciprocal, or self-directed elegant control mechanisms. In this chapter, we focus on the posttranscriptional regulatory mechanisms that generate miRNAs whose sequence might be slightly different from the miRNA-coding sequences. Hopefully, this information will be helpful in the discovery of novel miRNAs as well as in the analysis of deep-sequencing data and ab initio prediction of miRNAs. © Springer Science+Business Media New York 2014.