Evolutionarily distinct and sperm-specific supersized chromatin loops are marked by Helitron transposons in Xenopus tropicalis
Zhaoying Shi,
Jinsheng Xu,
Longjian Niu,
Wei Shen,
Shuting Yan,
Yongjun Tan,
Xuebo Quan,
Edwin Cheung,
Kai Huang,
Yonglong Chen,
Li Li,
Chunhui Hou
Affiliations
Zhaoying Shi
Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
Jinsheng Xu
Department of Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China
Longjian Niu
China State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen 518055, China; Shenzhen Key Laboratory of Cardiovascular Health and Precision Medicine, Southern University of Science and Technology, Shenzhen 518055, China
Wei Shen
Department of Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China
Shuting Yan
Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
Yongjun Tan
Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China; China State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
Xuebo Quan
Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
Edwin Cheung
Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China; Frontier Science Centre for Precision Oncology of Ministry of Education, University of Macau, Taipa, Macau 999078, China
Kai Huang
Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China; Corresponding author
Yonglong Chen
Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China; Corresponding author
Li Li
Department of Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; Corresponding author
Chunhui Hou
China State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Corresponding author
Summary: Transposable elements (TEs) are abundant in metazoan genomes and have multifaceted effects on host fitness. However, the mechanisms underlying the functions of TEs are still not fully understood. Here, we combine Hi-C, ATAC-seq, and ChIP-seq assays to report the existence of multimegabase supersized loop (SSL) clusters in the Xenopus tropicalis sperm. We show that SSL anchors are inaccessible and devoid of the architectural protein CTCF, RNA polymerase II, and modified histones. Nearly all SSL anchors are marked by Helitrons, a class II DNA transposon. Molecular dynamics simulations indicate that SSL clusters are likely formed via a molecular agent-mediated chromatin condensation process. However, only slightly more SSL anchor-associated genes are expressed at late embryo development stages, suggesting that SSL anchors might only function in sperm. Our work shows an evolutionarily distinct and sperm-specific genome structure marked by a subset of Helitrons, whose establishment and function remain to be explored.
