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Abstract：
The long noncoding RNAs (lncRNAs) are involved in numerous fundamental biological processes, including circadian regulation. Although recent studies have revealed insights into the functions of lncRNAs, how the lncRNAs regulate circadian rhythms still requires a deeper investigation. In this study, we generate two datasets of RNA-seq profiles of the mouse (Mus musculus) testis under light-dark (LD) cycle. The first dataset included 18,613 unannotated transcripts measured at 12 time points, each with duplicate samples, under LD conditions; while the second dataset included 21,414 unannotated transcripts measured at six time points, each with three replicates, under desynchronized and control conditions. We identified 5964 testicular lncRNAs in each dataset by BLASTing these transcripts against the known mouse lncRNAs from the NONCODE database. MetaCycle analyses were performed to identify 519, 475, and 494 rhythmically expressed mouse testicular lncRNAs in the 12-time-point dataset, the six-time-point control dataset, and the six-time-point desynchronized dataset, respectively. A comparison of the expression profiles of the lncRNAs under desynchronized and control conditions revealed that 427 rhythmically expressed lncRNAs from the control condition became arrhythmic under the desynchronized condition, suggesting a possible loss of rhythmicity. In contrast, 446 arrhythmic lncRNAs from the control condition became rhythmic under the desynchronized condition, suggesting a possible gain of rhythmicity. Interestingly, 48 lncRNAs were rhythmically expressed under both desynchronized and control conditions. These oscillating lncRNAs were divided into morning lncRNAs, evening lncRNAs, and night lncRNAs based on their time-course expression patterns. We interrogated the promoter regions of these rhythmically expressed mouse testicular lncRNAs to predict their possible regulation by the E-box, D-box, or RORE promoter motifs. GO and KEGG analyses were performed to identify the possible biological functions of these rhythmically expressed mouse testicular lncRNAs. Further, we conducted conservation analyses of the rhythmically expressed mouse testicular lncRNAs with lncRNAs from humans, rats, and zebrafish, and uncovered three mouse testicular lncRNAs conserved across these four species. Finally, we computationally predicted the conserved lncRNA-encoded peptides and their 3D structures from each of the four species. Taken together, our study revealed thousands of rhythmically expressed lncRNAs in the mouse testis, setting the stage for further computational and experimental validations.
摘要：
长链非编码RNA（lncRNAs）参与许多基本的生物过程，包括昼夜节律调节。尽管最近的研究揭示了lncRNAs的功能，lncRNAs如何调节昼夜节律仍需要更深入的研究。在这项研究中,我们在明暗（LD）周期下生成小鼠（Musmusculus）睾丸的RNA-seq谱的两个数据集。第一个数据集包括在12个时间点测量的18,613个未注释的转录本，每个都有重复的样本，在LD条件下；而第二个数据集包括在六个时间点测量的21,414个未注释的转录本，每个都有三个重复，在非同步和控制条件下。我们通过对来自NONCODE数据库的已知小鼠lncRNA的这些转录物进行BLASTN来鉴定每个数据集中的5964个睾丸lncRNA。进行MetaCycle分析以鉴定12个时间点数据集中的519、475和494个有节奏表达的小鼠睾丸lncRNAs，六个时间点控制数据集，和六个时间点去同步的数据集，分别。在去同步和对照条件下lncRNAs的表达谱的比较显示，在去同步条件下，来自对照条件的427个有节奏表达的lncRNAs变得心律失常，暗示可能失去节律性。相比之下,来自对照条件的446个心律失常lncRNAs在去同步条件下变得有节律，暗示可能获得节律性。有趣的是,48个lncRNA在去同步和对照条件下有节奏地表达。这些振荡的lncRNAs被分成早晨的lncRNAs，晚上lncRNAs，和基于其时程表达模式的夜间lncRNAs。我们研究了这些有节奏表达的小鼠睾丸lncRNAs的启动子区域，以预测它们可能被E-box调节。D-box,或RORE启动子基序。进行GO和KEGG分析以鉴定这些节律表达的小鼠睾丸lncRNA的可能生物学功能。Further,我们对有节奏表达的小鼠睾丸lncRNAs和来自人类的lncRNAs进行了保守性分析，老鼠,和斑马鱼,并发现了在这四个物种中保守的三个小鼠睾丸lncRNAs。最后,我们计算预测了保守的lncRNA编码的肽和它们的3D结构从四个物种。一起来看,我们的研究揭示了小鼠睾丸中有数千个有节奏表达的lncRNAs，为进一步的计算和实验验证奠定了基础。
