GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development

Abstract

Spermatogenic failure is a major cause of male infertility, which affects millions of couples worldwide. Recent discovery of long non-coding RNAs (lncRNAs) as critical regulators in normal and disease development provides new clues for delineating the molecular regulation in male germ cell development. However, few functional lncRNAs have been characterized to date. A major limitation in studying lncRNA in male germ cell development is the absence of germ cell-specific lncRNA annotation. Current lncRNA annotations are assembled by transcriptome data from heterogeneous tissue sources; specific germ cell transcript information of various developmental stages is therefore under-represented, which may lead to biased prediction or fail to identity important germ cell-specific lncRNAs. GermlncRNA provides the first comprehensive web-based and open-access lncRNA catalogue for three key male germ cell stages, including type A spermatogonia, pachytene spermatocytes and round spermatids. This information has been developed by integrating male germ transcriptome resources derived from RNA-Seq, tiling microarray and GermSAGE. Characterizations on lncRNA-associated regulatory features, potential coding gene and microRNA targets are also provided. Search results from GermlncRNA can be exported to Galaxy for downstream analysis or downloaded locally. Taken together, GermlncRNA offers a new avenue to better understand the role of lncRNAs and associated targets during spermatogenesis.Database URL: http://germlncrna.cbiit.cuhk.edu.hk/

The ReproGenomics Viewer: a multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community

“…While several databases devoted to reproductive biology were A c c e p t e d m a n u s c r i t p t TA. Darde et al developed to provide access to relevant microarray-based transcriptomics data (Lee et al, 2010;Hsueh and Rauch, 2012;Luk et al, 2015;Hua et al, 2015;Lardenois et al, 2010;Schuster et al, 2016;Lee et al, 2009;Zhang et al, 2013), until recently no resources were able to manage ultra-high-throughput sequencing data. To deal with these data, in 2015 we introduced the ReproGenomics Viewer (RGV) (Darde et al, 2015), a web-based genomic resource for researchers of the reproductive science community.…”

New transcriptomic tools to understand testis development and functions

“…As described earlier in this review, lncRNAs are expressed in a highly tissue-specific manner and especially in male GCs. GermlncRNA constitutes a dedicated catalogue of known and novel lncRNAs (Luk et al, 2015), by integrating several published transcriptomic studies covering three GC populations, i.e. type A Spg, pachytene Spc and round Spt (Gan et al, 2013;Lee et al, 2012Lee et al, , 2009Soumillon et al, 2013;Sun et al, 2013).…”

Factores nutricionales y no nutricionales pueden afectar la fertilidad masculina mediante mecanismos epigenéticos

“…Hoy día se conoce la implicación de los ARN no codificantes de cadena larga (lncRNA) en la espermatogénesis (p. ej. Tsx, HongrES2, Mrhl y Spga-lncRNA) (38), aunque Luk y cols. (38) concluyen que los lncRNA están infrarepresentados en las bases de datos de anotación actuales, resultando en una predicción errónea de los lncRNA y su funcionalidad en las células especializadas durante el desarrollo germinal de los hombres.…”

“…Tsx, HongrES2, Mrhl y Spga-lncRNA) (38), aunque Luk y cols. (38) concluyen que los lncRNA están infrarepresentados en las bases de datos de anotación actuales, resultando en una predicción errónea de los lncRNA y su funcionalidad en las células especializadas durante el desarrollo germinal de los hombres. Recientemente, se ha sugerido que el concepto de herencia transgeneracional no solamente está ligado a los patrones de metilación sino también a los sncARN.…”