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Article

Rising Roles of Small Noncoding RNAs in Cotranscriptional Regulation: In Silico Study of miRNA and piRNA Regulatory Network in Humans

by 1,*,†, 2,*,†, 3,‡ and 2,4,‡
1
U.O.C. Genetica Medica e di Laboratorio, Ospedale Antonio Cardarelli, 80131 Napoli, Italy
2
Dipartimento Scienze della Vita e Sanità Pubblica, Sezione di Biologia Applicata, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
3
UOC Lab. di Genetica Medica, Azienda Ospedaliero Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy
4
Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
*
Authors to whom correspondence should be addressed.
M.C. and L.D.P. contributed equally.
W.L. and N.B. share senior authorship.
Genes 2020, 11(5), 482; https://doi.org/10.3390/genes11050482
Received: 20 March 2020 / Revised: 9 April 2020 / Accepted: 27 April 2020 / Published: 29 April 2020
Gene expression regulation is achieved through an intricate network of molecular interactions, in which trans-acting transcription factors (TFs) and small noncoding RNAs (sncRNAs), including microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), play a key role. Recent observations allowed postulating an interplay between TFs and sncRNAs, in that they may possibly share DNA-binding sites. The aim of this study was to analyze the complete subset of miRNA and piRNA sequences stored in the main databases in order to identify the occurrence of conserved motifs and subsequently predict a possible innovative interplay with TFs at a transcriptional level. To this aim, we adopted an original in silico workflow to search motifs and predict interactions within genome-scale regulatory networks. Our results allowed categorizing miRNA and piRNA motifs, with corresponding TFs sharing complementary DNA-binding motifs. The biological interpretation of the gene ontologies of the TFs permitted observing a selective enrichment in developmental pathways, allowing the distribution of miRNA motifs along a topological and chronological frame. In addition, piRNA motifs were categorized for the first time and revealed specific functional implications in somatic tissues. These data might pose experimental hypotheses to be tested in biological models, towards clarifying novel in gene regulatory routes. View Full-Text
Keywords: gene expression regulation; miRNA; piRNA; transcriptional modulation; binding motifs; regulatory pathways; epigenetics; in silico gene expression regulation; miRNA; piRNA; transcriptional modulation; binding motifs; regulatory pathways; epigenetics; in silico
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MDPI and ACS Style

Chetta, M.; Di Pietro, L.; Bukvic, N.; Lattanzi, W. Rising Roles of Small Noncoding RNAs in Cotranscriptional Regulation: In Silico Study of miRNA and piRNA Regulatory Network in Humans. Genes 2020, 11, 482. https://doi.org/10.3390/genes11050482

AMA Style

Chetta M, Di Pietro L, Bukvic N, Lattanzi W. Rising Roles of Small Noncoding RNAs in Cotranscriptional Regulation: In Silico Study of miRNA and piRNA Regulatory Network in Humans. Genes. 2020; 11(5):482. https://doi.org/10.3390/genes11050482

Chicago/Turabian Style

Chetta, Massimiliano, Lorena Di Pietro, Nenad Bukvic, and Wanda Lattanzi. 2020. "Rising Roles of Small Noncoding RNAs in Cotranscriptional Regulation: In Silico Study of miRNA and piRNA Regulatory Network in Humans" Genes 11, no. 5: 482. https://doi.org/10.3390/genes11050482

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