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Generation of pigs with a Belgian Blue mutation in MSTN using CRISPR/ Cpf1-assisted ssODN-mediated homologous recombination
ZOU Yun-long, LI Zhi-yuan, ZOU Yun-jing, HAO Hai-yang, HU Jia-xiang, LI Ning, LI Qiu-yan
2019, 18 (6): 1329-1336.   DOI: 10.1016/S2095-3119(19)62694-8
Abstract245)      PDF in ScienceDirect      
CRISPR/Cpf1 has emerged recently as an effective tool for genome editing in many organisms, but its use in pigs to generate precise genetic modifications has seldom been described.  Myostatin (MSTN) is a well-characterized negative regulator of muscle development, and natural mutations in this gene cause a double-muscled phenotype in many species.  However, to the best of our knowledge, no naturally occurring mutation in MSTN has been found in pigs.  In addition, no living pig models with sophisticated modifications orthologous to natural mutations in MSTN have yet been reported.  In this study, we exploited the CRISPR/Cpf1 system to introduce a predefined modification orthologous to the natural MSTN mutation found in Belgian Blue cattle (thus known as the Belgian Blue mutation).  Our research demonstrated that the cutting efficiency of CRISPR/Cpf1 was 12.3% in mixed porcine fetal fibroblasts in drug free medium, and 41.7% in clonal colonies obtained using G418 selection.  Then, the Cpf1-sgRNA vector, ssODN template, and a self-excision cassette were co-transfected into porcine fetal fibroblasts.  After G418 selection, 8 clonal colonies were examined and 5 with genetic modification were found.  Of these 5, 2 harbored the precise 11-bp deletion.  Using 1 heterozygous clonal colony, 2 cloned Duroc piglets were successfully generated, which was heterozygous for the Belgian Blue mutation.  In summary, our results demonstrate that CRISPR/Cpf1 system can be used efficiently to generate double-stranded breaks, and also to mediate homologous recombination to introduce precise genomic modifications in pigs.
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Comparative analysis of flower-meristem-identity gene APETALA2 (AP2) codon in different plant species
WU Yan-qing, LI Zhi-yuan, ZHAO Da-qiu, TAO Jun
2018, 17 (04): 867-877.   DOI: 10.1016/S2095-3119(17)61732-5
Abstract625)      PDF in ScienceDirect      
The flower-meristem-identity gene APETALA2 (AP2), one of class-A genes, is involved in the establishment of the floral meristem and the forming of sepals and petals.  Codon usage bias (CUB) identifies differences among species, meanwhile dynamic analysis of base composition can identify the molecular mechanisms and evolutionary relationships of a specific gene.  In this study, eight coding sequences (CDS) of AP2 gene were selected from different plant species using the GenBank database.  Their nucleotide composition (GC content), genetic index, relative synonymous codon usage (RSCU) and relative codon usage bias (RCUB) were calculated with R Software to compare codon bias and base composition dynamics of AP2 gene codon usage patterns in different plant species.  The results showed that the usage of AP2 gene codons from different plant species were influened by GC bias, especially GC3s.  Overall, base composition analysis indicated that the usage frequency of codon AT in the gene coding sequence was higher than GC among AP2 gene CDS from different plant species.  Furthermore, most AP2 gene CDSs ended with AT; AGA, GCU and UGU had relatively high RSCU values as the most dominant codon; the usage characteristic of the AP2 gene codon in Malus domestica was similar to that of Vitis vinifera; Paeonia lactiflora was similar to Paeonia suffruticosa and Solanum lycopersicum was similar to Petunia×hybrida.  There was a moderate preference in the usage of AP2 gene codon among different plant species from relatively low frequency of optimal codon (Fop) values and high effective number of codons (ENC) value.  This study has revealed the usage characteristics of the AP2 gene codon from the comparision of AP2 gene codon preference and base dynamics in different plant species and provide a platform for further study towards transgenic engineering and codon optimization.
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