Table_9_Transcriptome Analysis Reveals the Profile of Long Non-coding RNAs During Chicken Muscle Development.XLSX

The developmental complexity of muscle arises from elaborate gene regulation. Long non-coding RNAs (lncRNAs) play critical roles in muscle development through the regulation of transcription and post-transcriptional gene expression. In chickens, previous studies have focused on the lncRNA profile during the embryonic periods, but there are no studies that explore the profile from the embryonic to post-hatching period. Here, we reconstructed 14,793 lncRNA transcripts and identified 2,858 differentially expressed lncRNA transcripts and 4,282 mRNAs from 12-day embryos (E12), 17-day embryos (E17), 1-day post-hatch chicks (D1), 14-day post-hatch chicks (D14), 56-day post-hatch chicks (D56), and 98-day post-hatch chicks (D98), based on our published RNA-seq datasets. We performed co-expression analysis for the differentially expressed lncRNAs and mRNAs, using STEM, and identified two profiles with opposite expression trends: profile 4 with a downregulated pattern and profile 21 with an upregulated pattern. The cis- and trans-regulatory interactions between the lncRNAs and mRNAs were predicted within each profile. Functional analysis of the lncRNA targets showed that lncRNAs in profile 4 contributed to the cell proliferation process, while lncRNAs in profile 21 were mainly involved in metabolism. Our work highlights the lncRNA profiles involved in the development of chicken breast muscle and provides a foundation for further experiments on the role of lncRNAs in the regulation of muscle development.

肌肉发育的复杂性源于精细的基因调控机制。长非编码RNA（lncRNA）通过调控转录及转录后基因表达，在肌肉发育过程中发挥着至关重要的作用。在鸡类研究中，既往研究主要集中于胚胎期的lncRNA图谱，然而，尚无研究探讨从胚胎期至孵化后的完整图谱。本研究基于我们已发表的RNA测序数据集，重建了14,793个lncRNA转录本，并从12天胚胎（E12）、17天胚胎（E17）、1日龄孵化后雏鸡（D1）、14日龄孵化后雏鸡（D14）、56日龄孵化后雏鸡（D56）以及98日龄孵化后雏鸡（D98）中鉴定出2,858个差异表达的lncRNA转录本和4,282个mRNA。通过STEM方法对差异表达的lncRNA和mRNA进行共表达分析，识别出两个表达趋势相反的图谱：图谱4呈现下调模式，而图谱21呈现上调模式。在每个图谱中，预测了lncRNA与mRNA之间的顺式和反式调控相互作用。对lncRNA靶点的功能分析表明，图谱4中的lncRNA有助于细胞增殖过程，而图谱21中的lncRNA主要参与代谢过程。本研究突出了参与鸡胸肌发育的lncRNA图谱，并为进一步探讨lncRNA在肌肉发育调控中的角色提供了实验基础。