Chromatin remodeling and expression dynamics reveal conserved and species-specific regulation during mouse and chicken limb development [RNA-seq]

Understanding the origin of morphological diversity across vertebrates is central to evolutionary developmental biology. cis-regulatory elements (CRE) such as enhancers and promoters interpret precise spatiotemporal cues to control and coordinate gene expression. To get insights into both conserved and species-specific variations during early limb patterning and outgrowth, we leverage genome-wide comprehensive assessment of chromatin accessibility and transcriptional changes during mouse forelimb and chicken wing bud development. Our analysis reveals temporal modulation of chromatin accessibility and expression as well as their temporal relationship during the progression of mouse forelimb and chicken wing bud development. Transcription factor binding site enrichment analysis and putative TF occupancy as inferred by integrating TF binding motifs and chromatin accessibility information reveal temporal TF-DNA interactions during forelimb/wing bud patterning. Finally, the integration of accessibility, expression, and TF binding site information allowed to identify candidate gene targets of HAND2 and GLI3 that include conserved as well as species-specific transcriptional regulator-gene interactions. RNA-seq analysis of developing mouse forelimb and chicken wing buds

解析脊椎动物形态多样性的起源，是进化发育生物学（evolutionary developmental biology）的核心研究议题。顺式调控元件（cis-regulatory elements, CRE）如增强子与启动子，可精准解读时空信号以调控并协调基因表达。为探究早期肢体模式形成与向外生长过程中物种保守与物种特异性的变异规律，本研究针对小鼠前肢与鸡翅芽发育过程中的染色质可及性与转录组变化开展全基因组范围的综合评估。分析结果显示，在小鼠前肢与鸡翅芽发育进程中，染色质可及性与基因表达呈现时序性调控特征，且二者存在时序关联。通过整合转录因子（transcription factor, TF）结合基序与染色质可及性信息所推断的转录因子结合位点（transcription factor binding site）富集分析与推定转录因子占用情况，揭示了肢体/鸡翅芽模式形成过程中时序性的转录因子-DNA互作关系。最后，通过整合染色质可及性信息、基因表达数据与转录因子结合位点信息，本研究鉴定出HAND2与GLI3的候选靶基因，其中既包含物种保守的转录调控因子-基因互作关系，也涵盖物种特异性的互作模式。针对发育中小鼠前肢与鸡翅芽的RNA测序（RNA-seq）分析