Pseudogenes contribute to the evolution of topological domains across species via forming three-dimensional genome [ChIP-seq]

The human genome harbors 15,000 pseudogenes, except very few can transcribe non-coding RNAs or encode truncated proteins, a large number of which without transcriptional capacity are functional unknown. Here, we found that DNA sequence of pseudogenes can form chromatin contacts, acting as anchors of chromatin loops and boundaries of topological associated domains (TADs), many of them are proved to be structural important and essential for human embryonic stem cells (hESCs) survival. Incorporating genetic data, we defined a hominoidea-specific pseudogene, TUBBP2, which acted as a TAD boundary by enriching CTCF, to maintain the 3D genome and self-renewal of hESCs. Evolutionally, TUBBP2 was generated in 18.8 million years ago through retroposition and inherited the CTCF binding motif from its parent gene-TUBB, thus enhance the strength of TADs at the insertion site in great apes genome. More amazing, by inheritance from parent genes or sequence variation, a part of pseudogenes can introduce additional CTCF binding sequence at their insertion sites to generate species-specific topological domains, which may contribute to species evolution. Overall, we not only demonstrate the essentiality of pseudogenes in the formation and maintenance of 3D chromatin structure, but provide insights on their functions of driving species evolution. We performed Hi-C, ChIP-seq for CTCF in WT/TUBBP2 KO human embryonic stem cells (hESC),each with two replicates. To find out how pseudogenes influence gene expression in hESC, we also performed RNA-seq in WT/KRT18P37 KO hESC, and in WT/TUBBP2 KO/ALOX KO hESC, each with two replicates.