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Database (Oxford). 2015 May 17;2015:bav044. doi: 10.1093/database/bav044. Print 2015.

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

Author information

1
Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
2
Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
3
Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong-Shandong University (CUHK-SDU) Joint Laboratory on Reproductive Genetics and CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Shatin, Hong Kong, China, GigaScience, Beijing Genomics Institute-Hong Kong (BGI-HK) Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong, China, Beijing Genomics Institute-Shenzhen (BGI-SZ), Beishan Industrial Zone, Yantian District, Shenzhen, China and T

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/.

PMID:
25982314
PMCID:
PMC4433719
DOI:
10.1093/database/bav044
[Indexed for MEDLINE]
Free PMC Article

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