Novel non-transposable-element regulation patterns of KZFP family reveal new drivers of its rapid evolution

Pan Shen; Qijian Zheng; Aishi Xu; Junhua Liu; Yushan Hou; Chao Gao; Chunyan Tian; Fuchu He; Dong Yang

The disorder scores of proteins and domains 459 Structural disorder ration (SDR): The longest protein encoded by each gene was 460 selected as the representative protein for subsequent analyses. IUPred (Dosztanyi, 461 2018) was used to obtain the disorder score of each amino acid in a protein or domain. 462 The disorder rate of a protein is the ratio of the number of disordered amino acids (the 463 disorder score is greater than 0.5) to the total number of amino acids. According to 464 SDR values, proteins can be divided into four classes: completely structured (SDR = 465 . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.15.041848 doi: bioRxiv preprint 21 0), highly structured (0 < SDR ≤ 10 %), relatively disordered (10 % < SDR ≤ 30 %), 466 and highly disordered (30 % < SDR ≤ 100 %). 467 Consecutively disordered region number (CDRN): 1) for the domains or proteins 468 which are longer than 50 aa, a CDR consists of 20 or more consecutively disordered 469 amino acids; 2) for the domains which are shorter than 50 aa, a region containing 470 consecutively disordered residues exceeding 40% of all domain residues is considered 471 to be a CDR. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.15.041848 doi: bioRxiv preprint 22 retrieved from Ensembl release 83. The region from +2,000 bp to -500 bp of their 491 nearest TSS were annotated as promoters (Tsankov et al., 2015) . The genes whose 492 promoters were overlapped with KZFP peaks were considered to be potential KZFP 493 target genes. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.15.041848 doi: bioRxiv preprint 24 Cell culture and transfections 541 The HEK293T cells were maintained in DMEM supplemented with 10% fetal 542 bovine serum (Zhejiang Tianhang Biotechnology, Hangzhou, China). 543 The human ESC line H9 was cultured following the protocols as previously The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.15.041848 doi: bioRxiv preprint 25 experimental errors were calculated. All data were analyzed using the ABI PRISM 566 SDS 2.0 software (Perkin-Elmer). The expression of genes was normalized to the 567 GAPDH gene. The PCR primers were listed in supplementary file 1. 568 Chromatin immunoprecipitation (ChIP) assay. 569 ChIP was performed as previously described (Yuan et al., 2015) . The following 570 primers were used: Primers: STK38 (5'-CAGCAAGCAACTCACCAGAG-3',