Abstract
Emerging evidence indicated that many long non-coding (lnc)RNAs function in multiple biological processes and dysregulation of their expression can cause diseases. Most regulatory lncRNAs interact with biological macromolecules such as DNA, RNA, and protein. LncRNAs regulate gene expression through epigenetic modification, transcription, and posttranscription, through DNA methylation, histone modification, and chromatin remodeling. Interestingly, differential lncRNA expression profiles in human oocytes and cumulus cells was recently assessed, however, lncRNAs in human follicle development has not previously been described. In this study, transcriptome dynamics in human primordial, primary and small antral follicles were interrogated and revealed information of lncRNA genes. It is known that some lncRNAs form a complex with paraspeckle proteins and therefore, we extended our transcriptional analysis to include genes encoding paraspeckle proteins. Primordial, primary follicles and small antral follicles was isolated using laser capture micro-dissection from ovarian tissue donated by three women having ovarian tissue cryopreserved before chemotherapy. After RN sequencing, a bioinformatic class comparison was performed and primordial, primary and small antral follicles were found to express several lncRNA and genes encoding paraspeckle proteins. Of particular interest, we detected the lncRNAs XIST, NEAT1, NEAT2 (MALAT1), and GAS5. Moreover, we noted a high expression of FUS, TAF15, and EWS components of the paraspeckles, proteins that belong to the FET (previously TET) family of RNA-binding proteins and are implicated in central cellular processes such as regulation of gene expression, maintenance of genomic integrity, and mRNA/microRNA processing. We also interrogated the intra-ovarian localization of the FUS, TAF15, and EWS proteins using immunofluorescence. The presence and the dynamics of genes that encode lncRNA and paraspeckle proteins may suggest that these may mediate functions in the cyclic recruitment and differentiation of human follicles and could participate in biological processes known to be associated with lncRNAs and paraspeckle proteins, such as gene expression control, scaffold formation and epigenetic control through human follicle development. This comprehensive transcriptome analysis of lncRNAs and genes encoding paraspeckle proteins expressed in human follicles could potentially provide biomarkers of oocyte quality for the development of non-invasive tests to identify embryos with high developmental potential.
Highlights
The nuclei of mammalian cells are highly organized and composed of distinct subnuclear structures termed nuclear bodies (Naganuma and Hirose, 2013; Yamazaki and Hirose, 2015)
Primordial follicles were defined as an oocyte surrounded by one layer of flattened granulosa cells (Figure 1) and primary follicles were defined as an oocyte surrounded by a single layer of cubic granulosa cells (Figure 1)
We identified the presence of long non-coding RNAs’ (lncRNAs) as well as the genes encoding the paraspeckle proteins, offering insights into how their transcripts are expressed during human follicle development
Summary
The nuclei of mammalian cells are highly organized and composed of distinct subnuclear structures termed nuclear bodies (Naganuma and Hirose, 2013; Yamazaki and Hirose, 2015). Paraspeckles are mammalian-specific sub-nuclear bodies built on long, non-protein-coding RNA (lncRNA), NEAT1 (nuclear-enriched abundant transcript 1), which assembles various protein components, including RNA-binding proteins of the DBHS (Drosophila behavior and human splicing) family. Paraspeckle formation proceeds in conjunction with NEAT1 lncRNA biogenesis and involves the cooperation of multiple paraspeckle-localized RNA-binding proteins (Naganuma and Hirose, 2013; Yamazaki and Hirose, 2015). Paraspeckle proteins include DBHS (Drosophila melanogaster behavior, human splicing) proteins, PSPC1 (paraspeckle component 1), NONO (non-POU domain-containing octamer-binding), and SFPQ [splicing factor, proline- and glutamine-rich ( known as PSF (PTB-associated splicing factor)], RNA binding motif (RBM) 14, and CPSF6 (cleavage and polyadenylation specific factor 6) [Reviewed in (Yamazaki and Hirose, 2015)]. The paraspeckle proteins NONO, SFPQ, RBM14, EWS, FUS, TAF15, and TDP-43 are RNA binding proteins that mediate transcription and RNA processing (Auboeuf et al, 2005)
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