Deciphering the regulatory logic for cell type-specific transcription based on intranuclear dynamics of transcription factors and cis-regulatory DNAs

为了在简单的脊索动物模型玻璃海鞘中获得基因组范围的转录活性景观，我们使用Illumina基因组分析仪通过大规模平行测序对其mRNA的5'端进行了大规模测序。然后将获得的5 '末端序列用于在基因组上定位转录起始位点（TSS）。这些数据还用于绘制反式剪接转录物的5 '端。这些数据已被用于确定一个反式剪接基因的TSS和C.非营利组织的发起人。基于这些数据，我们进一步分析了细胞类型特异性的基因调控机制，在体内通过检查转录因子，顺式调节DNA的功能，和染色质水平的相互作用。使用青鳉作为脊椎动物模型，我们已经发现，两个相邻基因的上游顺式调控区之间的物理相互作用是一个广泛保守的机制，在胚胎发育过程中的空间调控转录。

To obtain a genome wide landscape of transcriptional activity in the simple chordate model Ciona intestinalis, we have conducted a large scale sequencing of 5' ends of their mRNAs by massively parallel sequencing using the Illumina Genome Analyzer. The obtained 5'-end sequences were then used to map transcription start sites (TSSs) on the genome. The data were also used to map 5'-ends of trans-spliced transcripts. These data have been used to determine the TSS of a trans-spliced gene and for genome-wide profiling of C. intestinalis promoters. Based on these data, we further analyzed cell type-specific gene regulatory mechanisms in vivo by examining function of transcription factors, cis-regulatory DNAs, and chromatin level interactions. Using medaka as a vertebrate model, we have revealed that physical interactions between upstream cis-regulatory regions of two adjacent genes are a widely conserved mechanism for spatially regulated transcription during embryogenesis.