Phan Mai H Q, Zehnder Tobias, Puntieri Fiona, Magg Andreas, Majchrzycka Blanka, Antonović Milan, Wieler Hannah, Lo Bai-Wei, Baranasic Damir, Lenhard Boris, Müller Ferenc, Vingron Martin, Ibrahim Daniel M
Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center for Regenerative Therapies, Berlin, Germany.
Max Planck Institute for Molecular Genetics, Berlin, Germany.
Nat Genet. 2025 May 27. doi: 10.1038/s41588-025-02202-5.
Developmental gene expression is a remarkably conserved process, yet most cis-regulatory elements (CREs) lack sequence conservation, especially at larger evolutionary distances. Some evidence suggests that CREs at the same genomic position remain functionally conserved independent of sequence conservation. However, the extent of such positional conservation remains unclear. Here, we profiled the regulatory genome in mouse and chicken embryonic hearts at equivalent developmental stages and found that most CREs lack sequence conservation. To identify positionally conserved CREs, we introduced the synteny-based algorithm interspecies point projection, which identifies up to fivefold more orthologs than alignment-based approaches. We termed positionally conserved orthologs 'indirectly conserved' and showed that they exhibited chromatin signatures and sequence composition similar to sequence-conserved CREs but greater shuffling of transcription factor binding sites between orthologs. Finally, we validated indirectly conserved chicken enhancers using in vivo reporter assays in mouse. By overcoming alignment-based limitations, we revealed widespread functional conservation of sequence-divergent CREs.
发育基因表达是一个高度保守的过程，然而大多数顺式调控元件（CREs）缺乏序列保守性，尤其是在较大的进化距离上。一些证据表明，位于相同基因组位置的CREs在功能上保持保守，与序列保守性无关。然而，这种位置保守性的程度仍不清楚。在这里，我们在小鼠和鸡胚胎心脏的等效发育阶段对调控基因组进行了分析，发现大多数CREs缺乏序列保守性。为了识别位置保守的CREs，我们引入了基于共线性的算法——种间点投影，该算法识别的直系同源物比基于比对的方法多五倍。我们将位置保守的直系同源物称为“间接保守”，并表明它们表现出与序列保守的CREs相似的染色质特征和序列组成，但直系同源物之间转录因子结合位点的洗牌更为频繁。最后，我们在小鼠体内使用报告基因检测法验证了间接保守的鸡增强子。通过克服基于比对的局限性，我们揭示了序列不同的CREs广泛的功能保守性。
