Enhancer adoption by an LTR retrotransposon generates viral-like particles causing developmental limb phenotypes [ChIP-seq]

Mammalian genomes are scattered with transposable elements (TEs). Silencing of TEs prevents harmful effects caused by either global activation leading to genome instability or insertional mutation disturbing gene transcription. However, whether the activation of a TE can be pathological without directly affecting gene expression is largely unknown. Here, we show that a TE insertion can adopt nearby regulatory activity, producing cell-type-specific viral-like particles (VLPs) in the embryo and affecting organ formation. Failure to silence an LTR retrotransposon inserted upstream of the Fgf8 gene results in their co-expression during development. VLPs assembly in the Fgf8-expressing cells of the developing limb triggers apoptotic cell death, resulting in a limb malformation resembling human ectrodactyly. We rescued this phenotype with mutations in the retrotransposon coding sequence, preventing its full endogenous retroviral cycle. Our findings illustrate how TE insertion is incorporated into the local genomic regulatory landscape and show that VLP production in post-implantation embryos can be pathological. We study how the insertion of an endogenous retrovitrus lead to a developmental malformation. Using the Dactylaplasia mouse model which carry a MusD ERV insertion at the Fgf8 locus, we carried out capture-HiC, CTCF Chip-seq, 4C-seq, single-cell RNA-sequencing and bulk RNA-seq to identify change in the 3D genome and expression of the MusD mRNA. We further confirm that the MusD retroviral proteins and particles are produced and lead to cell death, causing a string limb phenotype.

哺乳动物基因组中广泛散布着转座因子（transposable elements, TEs）。对TEs的沉默可规避全局性激活引发基因组不稳定，或插入突变干扰基因转录所导致的有害效应。然而，TE激活在未直接影响基因表达的情况下是否具有致病性，目前尚不清楚。本研究发现，一段TE插入序列可获得邻近的调控活性，在胚胎中产生细胞类型特异性的病毒样颗粒（viral-like particles, VLPs），并影响器官发生。若无法沉默插入至Fgf8基因上游的长末端重复序列（LTR）逆转录转座子，则会使其在发育过程中与Fgf8发生共表达。在表达Fgf8的发育肢芽细胞内组装VLPs，会触发细胞凋亡，进而导致类似人类缺指（趾）症的肢体畸形。我们通过对该逆转录转座子的编码区引入突变，阻断其完整的内源性逆转录病毒周期，从而挽救了该表型。本研究阐明了TE插入序列如何被整合到局部基因组调控图谱中，并证明着床后胚胎中的VLPs产生可具有致病性。本研究探究了内源性逆转录病毒的插入如何导致发育畸形：利用携带Fgf8位点MusD内源性逆转录病毒（MusD ERV）插入的指（趾）发育不全小鼠模型，我们开展了捕获Hi-C、CCCTC结合因子染色质免疫共沉淀测序（CTCF ChIP-seq）、4C测序（4C-seq）、单细胞RNA测序及批量RNA测序，以解析三维基因组的变化及MusD mRNA的表达情况。我们进一步证实，MusD逆转录病毒蛋白及颗粒的产生会引发细胞死亡，最终导致条索状肢体表型。