ncRNAimprint: A comprehensive database of mammalian imprinted noncoding RNAs

Abstract

Imprinted noncoding RNAs (ncRNAs) are expressed mono-allelically in a parent-of-origin-dependent manner, which is mainly evident in mammals. Lying at a crossroad between imprinted genes and ncRNAs, imprinted ncRNAs show distinct features. They are likely to function in nontraditional ways compared to non-imprinted ncRNAs, and are much more responsible for the mechanism of genomic imprinting compared to imprinted protein-coding genes. An increasing number of human diseases have been shown to be related to abnormalities in imprinted ncRNAs. Due to their functional importance, many studies focusing on imprinted ncRNAs have been published in recent years; however, there is no systematic collection or description of imprinted ncRNAs and the rapidly growing knowledge is scattered in various places. Here, we describe a new database, ncRNAimprint, which serves as a comprehensive resource center for mammalian imprinted ncRNAs. A catalog of imprinted ncRNAs, including snoRNAs, microRNAs, piRNAs, siRNAs, antisense ncRNAs, and mRNA-like ncRNAs, was annotated in detail using information extracted from relevant literature and databases. Comprehensive collections of imprinted ncRNA-related diseases, imprinting control regions (ICRs), and imprinted regions were manually compiled to provide resources for current research focusing on imprinted ncRNAs. Small RNA deep sequencing reads that fully matched within imprinted regions were also included to offer useful evidence in detecting novel imprinted ncRNAs and to aid in analyzing expression patterns of known imprinted ncRNAs. A search page including four effective search forms and two graphical browsers was created for rapid retrieval and visualization of these data. The imprinted ncRNA database is freely accessible at http://rnaqueen.sysu.edu.cn/ncRNAimprint.