Long-range bidirectional transcription is a general feature of developmental gene promoters in mammals (RNA-Seq 2)

Recent studies have revealed a myriad of non-coding transcripts in different organisms. For instances, the presence of short bidirectional transcripts is a hallmark of active promoters in mammals, while upstream non-coding transcripts can be detected at most expressed genes in conditions where the RNA degradation machinery is inhibited. Here, we used RNA-seq with very high sequencing depth to characterize strand specific transcripts from primary mouse tissues. We found that a substantial fraction of gene promoters sustain expression of long non-coding antisense transcripts. These transcripts have an average size of 6 kb, have features of mature transcripts, but remain associated with the chromatin. We named this new class of non-coding RNAs Long Upstream Antisense Transcripts (LUAT). Strikingly, the LUAT and coding gene pairs are usually co-regulated, with the associated genes often/generally coding for transcriptional regulators functioning during development and cell differentiation. Indeed, these bidirectional promoters share several characteristic of developmental gene promoters, including large CpG islands and high degree of conservation, and display symetrical GC skews. Finally, we found that bidirectional promoters have enlarged platforms of Pol II initiation, associated with an intensified rate of early transcriptional elongation. We concluded that promoters of developmental regulators are characterized by a specialized mechanism of Pol II transcription, whereby Pol II poising is directly coupled to relaxed bidirectional transcription. Expression of noncoding RNA transcripts in CD4-,CD8- double negative thymocytes from Rag2-/- mice was studied by strand-specific, ribosomal-depleted RNA-seq experiment, using Illumina sequencer近年来的研究已在多种生物中发现了大量非编码转录本（non-coding transcript）。例如，短双向转录本的存在是哺乳动物活性启动子的标志性特征；而在RNA降解机制被抑制的条件下，大多数表达基因的上游均可检测到非编码转录本。本研究采用超高测序深度的RNA测序（RNA-seq）技术，对原代小鼠组织的链特异性转录本进行了系统表征。研究发现，有相当比例的基因启动子可驱动长链反义非编码转录本的表达。此类转录本平均长度约6 kb，具备成熟转录本的典型特征，但仍与染色质紧密结合。我们将这类新型非编码RNA命名为长上游反义转录本（Long Upstream Antisense Transcripts，LUAT）。值得注意的是，LUAT与编码基因的配对通常存在共调控关系，且关联基因大多编码发育与细胞分化过程中发挥功能的转录调控因子。事实上，这类双向启动子具备发育相关基因启动子的多项特征，包括大型CpG岛、高度保守性，并呈现对称的GC偏斜（GC skew）。最终，本研究发现双向启动子拥有扩大的RNA聚合酶II（Pol II）起始平台，并伴随早期转录延伸速率的增强。据此我们得出结论：发育调控因子的启动子具备特殊的Pol II转录机制，即Pol II的停滞状态直接与松弛的双向转录相耦联。此外，本研究采用Illumina测序平台，通过链特异性、核糖体去除的RNA-seq实验，分析了Rag2基因敲除（Rag2-/-）小鼠的CD4⁻CD8⁻双阴性胸腺细胞中的非编码RNA转录本表达情况。