Genomic features underlie the co-option of SVA transposons as cis-regulatory elements in human pluripotent stem cells.
Genomic features underlie the co-option of SVA transposons as cis-regulatory elements in human pluripotent stem cells.
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DOI：
10.1371/journal.pgen.1010225
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发表时间：
2022-06
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影响因子：
4.5
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中科院分区：
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将转座元件（TE）驯化为功能性顺式调节元件是一种普遍现象。然而，为什么一些 TE 被选为功能增强剂，而另一些 TE 却没有，其背后的机制却未被充分认识。 SINE-VNTR-Alus (SVA) 是人类基因组中最年轻的转座子群体，其中约 3,700 个拷贝被注释，其中近一半是人类特异性的。许多研究表明，SVA 是人类基因调控中最常见的增选 TE 之一，但此类过程背后的机制尚未得到彻底研究。在这里，我们利用 CRISPR 干扰 (CRISPRi)、计算和功能基因组学来阐明 SVA 驯化为人类干细胞基因调控的基因组特征。我们发现约 750 个 SVA 被选为人类诱导多能干细胞中的功能性顺式调节元件。这些 SVA 比非增选的 SVA 更接近基因，并且具有更多的转录因子结合位点。我们发现，由侧翼 YY1/2 和 OCT4 结合位点组成的长 DNA 基序在增选 SVA 中富集，并且这两个转录因子连续结合在 TE 序列上。我们使用 CRISPRi 从表观遗传学上抑制干细胞样 NCCIT 细胞中的活性 SVA。活性 SVA 的表观遗传扰动强烈减弱 YY1/OCT4 结合并影响邻近基因的表达。最终，SVA 抑制导致约 3,000 个差异表达基因，其中 131 个是与注释的 SVA 最接近的基因。总之，我们证明了 SVA 调节人类基因表达，并发现位置和序列组成有助于 SVA 驯化到基因调控网络中。 SINE-VNTR-Alus (SVA) 是人类基因组中最年轻的转座子群体，其中注释了约 3,700 个拷贝。人类基因组中注释的 SVA 中近一半是我们物种所独有的。许多研究表明，SVA 是人类基因调控中最常见的增选 TE 之一，但此类过程背后的机制尚未得到彻底研究。在这里，我们通过关注人类诱导多能干细胞（iPSC）和多能样细胞系（NCCIT）来填补这一知识空白。通过分析组蛋白标记、基因表达谱以及基因组编辑（CRISPR 干扰），我们鉴定了约 750 个在人类多能细胞中充当增强子和启动子的 SVA，并表征了涉及转录因子 OCT4 和 YY1 的 SVA 共选择机制。通过我们的 CRISPR 方法，我们证明抑制 750 个活性 SVA 会导致约 3,000 个基因的表达发生改变。
Domestication of transposable elements (TEs) into functional cis-regulatory elements is a widespread phenomenon. However, the mechanisms behind why some TEs are co-opted as functional enhancers while others are not are underappreciated. SINE-VNTR-Alus (SVAs) are the youngest group of transposons in the human genome, where ~3,700 copies are annotated, nearly half of which are human-specific. Many studies indicate that SVAs are among the most frequently co-opted TEs in human gene regulation, but the mechanisms underlying such processes have not yet been thoroughly investigated. Here, we leveraged CRISPR-interference (CRISPRi), computational and functional genomics to elucidate the genomic features that underlie SVA domestication into human stem-cell gene regulation. We found that ~750 SVAs are co-opted as functional cis-regulatory elements in human induced pluripotent stem cells. These SVAs are significantly closer to genes and harbor more transcription factor binding sites than non-co-opted SVAs. We show that a long DNA motif composed of flanking YY1/2 and OCT4 binding sites is enriched in the co-opted SVAs and that these two transcription factors bind consecutively on the TE sequence. We used CRISPRi to epigenetically repress active SVAs in stem cell-like NCCIT cells. Epigenetic perturbation of active SVAs strongly attenuated YY1/OCT4 binding and influenced neighboring gene expression. Ultimately, SVA repression resulted in ~3,000 differentially expressed genes, 131 of which were the nearest gene to an annotated SVA. In summary, we demonstrated that SVAs modulate human gene expression, and uncovered that location and sequence composition contribute to SVA domestication into gene regulatory networks. SINE-VNTR-Alus (SVAs) are the youngest group of transposons in the human genome, where ~3,700 copies are annotated. Nearly half of the SVAs annotated in the human genome are exclusive to our species. Many studies indicate that SVAs are among the most frequently co-opted TEs in human gene regulation, but the mechanisms underlying such processes have not yet been thoroughly investigated. Here, we filled this knowledge-gap by focusing on human induced pluripotent stem cells (iPSCs) and on a pluripotent-like cell line (NCCITs). Through the analysis of histone marks, gene expression profiles, and by means of genome editing (CRISPR-interference), we identified ~750 SVAs that work as enhancers and promoters in human pluripotent cells, and characterized a mechanism for SVA co-option involving the transcription factors OCT4 and YY1. With our CRISPR approach, we demonstrated that repressing the 750 active SVAs leads to alteration in the expression of ~3,000 genes.