Identification of Rhythmically Expressed LncRNAs in the Zebrafish Pineal Gland and Testis.

Shital Kumar Mishra,Han Wang,Taole Liu

doi:10.3390/ijms22157810

Shital Kumar Mishra, Han Wang + Show 1 more

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https://doi.org/10.3390/ijms22157810

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Abstract

Noncoding RNAs have been known to contribute to a variety of fundamental life processes, such as development, metabolism, and circadian rhythms. However, much remains unrevealed in the huge noncoding RNA datasets, which require further bioinformatic analysis and experimental investigation—and in particular, the coding potential of lncRNAs and the functions of lncRNA-encoded peptides have not been comprehensively studied to date. Through integrating the time-course experimentation with state-of-the-art computational techniques, we studied tens of thousands of zebrafish lncRNAs from our own experiments and from a published study including time-series transcriptome analyses of the testis and the pineal gland. Rhythmicity analysis of these data revealed approximately 700 rhythmically expressed lncRNAs from the pineal gland and the testis, and their GO, COG, and KEGG pathway functions were analyzed. Comparative and conservative analyses determined 14 rhythmically expressed lncRNAs shared between both the pineal gland and the testis, and 15 pineal gland lncRNAs as well as 3 testis lncRNAs conserved among zebrafish, mice, and humans. Further, we computationally analyzed the conserved lncRNA-encoded peptides, and revealed three pineal gland and one testis lncRNA-encoded peptides conserved among these three species, which were further investigated for their three-dimensional (3D) structures and potential functions. Our computational findings provided novel annotations and regulatory mechanisms for hundreds of rhythmically expressed pineal gland and testis lncRNAs in zebrafish, and set the stage for their experimental studies in the near future.

Highlights

Long noncoding RNAs, lacking protein coding abilities as their names imply, are a special class of the transcribed RNAs with a length longer than 200 nucleotide base pairs [1]
Expressed LncRNAs in the Zebrafish Pineal Gland, and Their Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Different circadian clock genes or circadian-clock-controlled genes are expressed in a time-of-day-specific manner, and peak at the specific time of day [32,33,34]
D-box, and the 123 night Long noncoding RNAs (lncRNAs) by RORE (Supplementary Tables S7–S11). These results indicate that most of these rhythmically expressed pineal gland lncRNAs are likely regulated by the circadian clock, and in particular, circadian regulation of morning lncRNAs is likely mediated by E-box, circadian regulation of evening lncRNAs is likely mediated by D-box, and circadian regulation of night lncRNAs is likely mediated by RORE, even though further experimental verification is needed

Summary

Introduction

Long noncoding RNAs (lncRNAs), lacking protein coding abilities as their names imply, are a special class of the transcribed RNAs with a length longer than 200 nucleotide base pairs [1]. LncRNAs do not encode functional proteins, they regulate a diverse set of biological processes such as genomic transcription [5], gene regulation [6], cell fate determination [7], development of the nervous system, muscle performance [8], and human diseases [9]. Several lncRNAs have recently been confirmed [10] to encode micropeptides ( known as microproteins), which are the polypeptides containing < 100 amino acids [11], distinguishable from the canonical proteins made of about 400 or more amino acids [12]. Another study identified a 60-amino=acid polypeptide ASRPS encoded by the lncRNA LINC00908, which contained sORFs [14,15]. A recent study identified the lncRNA MIR155HG, which encoded miPEP155—a 17-amino-acid micropeptide involved in antigen trafficking [10]. A recent study identified several lncRNA-encoded micropeptides implicated in tumorigenesis [16]

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