Transcription levels of a long noncoding RNA shape a cell fate regulatory circuit (TSS-seq)

Long noncoding RNAs (lncRNA) play diverse roles in gene regulation controlling key cellular processes, most notably, cell-fate programming {Anderson, 2016 #20;Flynn, 2014 #16;Guttman, 2011 #35;Wang, 2011 #18}. Many long noncoding RNAs (lncRNAs) act in cis through transcription-coupled chromatin alterations that drive changes in local gene expression { Martens, 2004 #47; Kim, 2012 #74;van Werven, 2012 #57;Hainer, 2011 #73;Kim, 2016 #41;Ard, 2016 #21;Latos, 2012 #7}. How transcription of some lncRNAs leads to activation of gene expression, while others inhibit and repress gene expression remains poorly understood {Kornienko, 2013 #17}. Here we investigated in S. cerevisiae the function of the lncRNA IRT2, which is expressed upstream in the promoter of the master regulator for entry into meiosis, IME1. We report the surprising finding that distinct levels of IRT2 transcription regulates opposing chromatin and transcription states in order to ensure that only diploids, and not haploids, enter meiosis and form gametes. In haploid cells, IRT2 transcription at very low levels is required for the correct induction of the adjacent lncRNA IRT1, which in turn represses the IME1 promoter and prevents meiotic entry {van Werven, 2012 #57}. Low levels of IRT2 transcription stimulates histone exchange delivering acetylated histone H3 lysine 56 (H3K56ac) to chromatin, thereby facilitating chromatin disassembly and recruitment of the transcriptional activator of IRT1, Rme1. Inhibiting IRT2 transcription, or mutations that resulted in cells lacking H3K56ac impairs Rme1 recruitment and IRT1 induction, and consequently haploid cells induce IME1 and undergo a lethal meiosis. In contrast to its function at low levels, increasing IRT2 transcription enhances transcription-coupled chromatin assembly and interferes with IRT1 expression, promoting IME1 expression and meiotic entry in diploid cells {Moretto, 2018 #10}. Thus, transcription of lncRNAs, even at very low levels, can play an important role in regulating gene expression, and changes in lncRNA transcription levels can confer distinct regulatory and cell fate outcomes.长链非编码RNA（long noncoding RNAs，lncRNA）在调控基因表达、控制关键细胞进程中发挥着多样功能，其中尤以细胞命运编程最为突出{Anderson, 2016 #20;Flynn, 2014 #16;Guttman, 2011 #35;Wang, 2011 #18}。诸多长链非编码RNA可通过转录偶联染色质重塑发挥顺式调控作用，进而改变局部基因表达水平{ Martens, 2004 #47; Kim, 2012 #74;van Werven, 2012 #57;Hainer, 2011 #73;Kim, 2016 #41;Ard, 2016 #21;Latos, 2012 #7}。部分长链非编码RNA的转录可激活基因表达，而另一些则会抑制基因表达，其背后的调控机制仍有待阐明{Kornienko, 2013 #17}。 本研究以酿酒酵母（Saccharomyces cerevisiae）为模型，探究了长链非编码RNA IRT2的功能——IRT2的转录位点位于减数分裂进入主控调控因子IME1的启动子上游区域。本研究发现了一项意外结果：IRT2转录的不同水平可调控截然相反的染色质与转录状态，以此确保仅二倍体细胞而非单倍体细胞能够进入减数分裂并形成配子。 在单倍体细胞中，极低水平的IRT2转录是正确诱导相邻长链非编码RNA IRT1表达的必要条件；而IRT1会进一步抑制IME1的启动子活性，阻止细胞进入减数分裂{van Werven, 2012 #57}。低水平的IRT2转录可促进组蛋白交换，将乙酰化组蛋白H3赖氨酸56（H3K56ac）招募至染色质，进而推动染色质解离，并招募IRT1的转录激活因子Rme1。若抑制IRT2转录，或是通过突变使细胞丧失H3K56ac修饰，则会破坏Rme1的招募与IRT1的诱导，最终导致单倍体细胞异常激活IME1并发生致死性减数分裂。 与低水平IRT2转录的功能相反，提高IRT2的转录水平会增强转录偶联的染色质组装过程，抑制IRT1的表达，进而促进二倍体细胞中IME1的表达与减数分裂的进入{Moretto, 2018 #10}。综上，即使是极低水平的长链非编码RNA转录，也可在基因表达调控中发挥重要作用；而长链非编码RNA转录水平的变化，可带来截然不同的调控效果与细胞命运结局。