Cis-regulatory modes of Ultrabithorax inactivation in butterfly forewings
Cis-regulatory modes of Ultrabithorax inactivation in butterfly forewings
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DOI：
10.1101/2023.08.18.553910
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发表时间：
2023-10
期刊：
影响因子：
7.7
通讯作者：
A. Tendolkar;Anyi Mazo-Vargas;L. Livraghi;Joseph J. Hanly;Kelsey C. Van Horne;L. Gilbert;Arnaud Martin-Arna
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文献类型：
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作者：
A. Tendolkar;Anyi Mazo-Vargas;L. Livraghi;Joseph J. Hanly;Kelsey C. Van Horne;L. Gilbert;Arnaud Martin-Arna
Hox基因簇编码在动物发育过程中驱动区域专门化的转录因子：例如，Hox因子Ubx在昆虫的后胸椎（T3）翼附件中表达，并将其与中胸椎T2翼附件区分开来。Hox转录调控需要沉默活性，以防止错误组织中的虚假激活和调控串扰，但除了果蝇之外，很少在昆虫中进行研究，这表明衍生的Hox错位为两个基因组簇，即分离的Antennapedia （Antp）和Ultrabithorax （Ubx）。在这里，我们研究了Ubx如何局限于蝴蝶的后翅，在一个连续的Hox集群中。通过分析蝴蝶Junonia coenia的Hi-C和ATAC-seq数据，我们发现拓扑相关结构域（TAD）维持了Ubx周围染色质开口的后向富集剖面。这个TAD由一个边界元（BE）隔开，边界元将它与Antp位点周围的连接翼活性区域分开。这种BE的CRISPR突变扰动在前翼释放异位Ubx表达，诱导具有后翼特性的同型克隆。进一步对Ubx TAD内的两个非编码RNA编码区和一个假定的顺式调控模块进行突变诘问，导致罕见的两个方向的同质转化，表明存在激活和抑制染色质特征。我们还描述了在蝴蝶中获得的一系列自发的前翅同型表型，并讨论了它们可能的突变基础。通过利用在蝴蝶中发现的广泛的翅膀专业化，我们对Ubx调控的初步探索表明，沉默和绝缘序列的存在可以防止其在前翼中的虚假表达。
Hox gene clusters encode transcription factors that drive regional specialization during animal development: e.g. the Hox factor Ubx is expressed in the insect metathoracic (T3) wing appendages and differentiates them from T2 mesothoracic identities. Hox transcriptional regulation requires silencing activities that prevent spurious activation and regulatory crosstalks in the wrong tissues, but this has seldom been studied in insects other than Drosophila, which shows a derived Hox dislocation into two genomic clusters that disjoined Antennapedia (Antp) and Ultrabithorax (Ubx). Here we investigated how Ubx is restricted to the hindwing in butterflies, amidst a contiguous Hox cluster. By analysing Hi-C and ATAC-seq data in the butterfly Junonia coenia, we show that a Topologically Associated Domain (TAD) maintains a hindwing-enriched profile of chromatin opening around Ubx. This TAD is bordered by a Boundary Element (BE) that separates it from a region of joined wing activity around the Antp locus. CRISPR mutational perturbation of this BE releases ectopic Ubx expression in forewings, inducing homeotic clones with hindwing identities. Further mutational interrogation of two non-coding RNA encoding regions and one putative cis-regulatory module within the Ubx TAD cause rare homeotic transformations in both directions, indicating the presence of both activating and repressing chromatin features. We also describe a series of spontaneous forewing homeotic phenotypes obtained in Heliconius butterflies, and discuss their possible mutational basis. By leveraging the extensive wing specialization found in butterflies, our initial exploration of Ubx regulation demonstrates the existence of silencing and insulating sequences that prevent its spurious expression in forewings.