PDF(Pubmed)
Abstract：
Long noncoding RNAs (lncRNAs) are functional bridges connecting the genome with phenotypes by interacting with DNA, mRNA, and proteins. Using publically available acute heat stress (AHS)-related RNA-seq data, we discovered novel lncRNAs and tested their association with AHS along with ~ 8800 known lncRNAs and ~ 28,000 mRNA transcripts. Our pipeline discovered a total of 145 potentially novel-lncRNAs. One of them (Fishcomb_p-value = 0.06) along with another novel transcript (annotated as protein-coding; Fishcomb_p-value = 0.03) were identified as significantly associated with AHS. We found five known-lncRNAs and 134 mRNAs transcripts that were significantly associated with AHS. Four novel lncRNAs interact cis-regulated with 12 mRNA transcripts and are targeted by 11 miRNAs. Also six meta-lncRNAs associate with 134 meta-mRNAs through trans-acting co-expression, each targeted by 15 and 216 miRNAs, respectively. Three of the known-lncRNAs significantly co-expressed with almost 97 of the significant mRNAs (Pearson correlation p-value < 0.05). We report the mentioned three known-lncRNAs (ENSGALT00000099876, ENSGALT00000107573, and ENSGALT00000106323) as the most, significantly regulatory elements of AHS in chicken. It can be concluded that in order to alleviate the adverse effects of AHS on chicken, the manipulation of the three regulatory lncRNAs could lead to a more desirable result than the manipulation of the most significant mRNAs.
摘要：
长链非编码RNA（lncRNA）是通过与DNA相互作用连接基因组与表型的功能性桥梁，mRNA和蛋白质。使用公开可用的急性热应激(AHS)相关RNA-seq数据，我们发现了新的lncRNAs，并测试了它们与AHS的关联，以及~8800个已知的lncRNAs和~28,000个mRNA转录本。我们的管道总共发现了145个潜在的新lncRNAs。其中一个（Fishcomb_p值=0.06）以及另一个新的转录本（注释为蛋白质编码；Fishcomb_p值=0.03）被鉴定为与AHS显着相关。我们发现了与AHS显著相关的5种已知的lncRNAs和134种mRNAs转录物。四种新的lncRNAs与12种mRNA转录物顺式调节相互作用，并被11种miRNA靶向。此外，6个meta-lncRNAs通过反式作用共表达与134个meta-mRNAs相关，每个靶向15和216个miRNA，分别。三个已知的lncRNA与几乎97个显著的mRNA显著共表达(Pearson相关p值<0.05)。我们报告提到的三个已知的lncRNAs（ENSGALT00000099876，ENSGALT00000107573和ENSGALT00000106323）是最，鸡AHS的显著调控元件。可以得出结论，为了减轻AHS对鸡肉的不利影响，3种调节lncRNAs的操作可以导致比最显著的mRNAs的操作更理想的结果。
