Editorial: Bioinformatics of Non-Coding RNAs with Applications to Biomedicine: Recent Advances and Open Challenges

  • Laganà A
  • Ferro A
  • Croce C
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Abstract

The recent advances in the functional characterization of non-protein-coding RNAs (ncRNAs) have represented a major breakthrough in the life sciences. Large-scale projects, such as ENCODE, have shown that the human genome is pervasively transcribed and that a large proportion of the mammalian transcriptome consists of ncRNA transcripts. ncRNA genes can be roughly classified into short ncRNAs (<200 nt) and long ncRNAs (>200 nt). The first class includes well characterized, infrastructural molecules, such as rRNA, tRNA, and snoRNA, which have a housekeeping role in essential processes like splicing and translation, and regulatory ncRNA such as miRNA and piRNA, which are involved in post-transcriptional regulation of gene expression and in the silencing of transposable elements during germ line development, respectively. The second class of ncRNA consists of longer transcripts that are still poorly characterized mostly due to their heterogeneity in size, structure, and biogenesis. LncRNA genes outnumber short ncRNAs and are probably more abundant than protein coding genes. Such RNAs exhibit various degrees of conservation and are often polyadenylated and tissue-specific. Accumulating evidence indicates that they likely have a broad range of functions, including chromatin remodeling, gene regulation, and protein transport and trafficking. Genetic and epigenetic aberrations affecting ncRNA gene sequences and their expression have been linked to a variety of pathological conditions, including cancer, cardiovascular, and neurolog-ical diseases. Recently, high-throughput sequencing techniques have enabled the study of entire transcriptomes at single nucleotide resolution, providing unprecedented details of their organization, expression, modifications, and structure. Bioinformatics tools constitute an essential resource for ncRNA research, providing a powerful means to organize, integrate, and analyze the huge amount of data generated by such technologies. The aim of this Research Topic is to review current knowledge, introduce novel methods, and discuss open challenges of this exciting and innovative field in connection with the most important biomedical applications. We have collected five original research and methods articles and four reviews, spanning the full scope of the Research Topic. Two excellent reviews focus on the discovery of ncRNA from NGS data. Kang and Friedländer (2015) surveyed computational tools to predict animal miRNAs from short RNA sequencing data (RNAseq). The authors covered the basics of miRNA prediction, reviewed several methods, described the algorithms, and discussed their strengths. They also described algorithms for specific cases, such as prediction from massively pooled data or in species without reference genomes, and discussed challenges and future directions of the field. Veneziano et al. (2015), instead, provided Frontiers in Bioengineering and Biotechnology | www.frontiersin.org October 2015 | Volume 3 | Article 156 1

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Laganà, A., Ferro, A., & Croce, C. M. (2015). Editorial: Bioinformatics of Non-Coding RNAs with Applications to Biomedicine: Recent Advances and Open Challenges. Frontiers in Bioengineering and Biotechnology, 3. https://doi.org/10.3389/fbioe.2015.00156

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