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Zhu M, Tong X, Qiu Q, Pan J, Wei S, Ding Y, Feng Y, Hu X, Gong C. Identification and characterization of extrachromosomal circular DNA in the silk gland of Bombyx mori. Insect Sci 2023; 30:1565-1578. [PMID: 36826848 DOI: 10.1111/1744-7917.13191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/30/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The silk gland cells of silkworm are special cells which only replicate DNA in the nucleus without cell division throughout the larval stage. The extrachromosomal circular DNAs (eccDNAs) have not yet been reported in the silk gland of silkworms. Herein, we have explored the characterization of eccDNAs in the posterior silk gland of silkworms. A total of 35 346 eccDNAs were identified with sizes ranging from 30 to 13 569 549 bp. Motif analysis revealed that dual direct repeats are flanking the 5' and 3' breaking points of eccDNA. The sequences exceeding 1 kb length in eccDNAs present palindromic sequence characteristics flanking the 5' and 3' breaking points of the eccDNA. These motifs might support possible models for eccDNA generation. Genomic annotation of the eccDNA population revealed that most eccDNAs (58.6%) were derived from intergenic regions, whereas full or partial genes were carried by 41.4% of eccDNAs. It was found that silk protein genes fib-H, fib-L, and P25, as well as the transcription factors SGF and sage, which play an important regulatory role in silk protein synthesis, could be carried by eccDNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses showed that the genes carried by eccDNAs were mainly associated with the development and metabolism-related signaling pathways. Moreover, it was found that eccDNAfib-L could promote the transcription of fib-L gene. Overall, the results of the present study not only provide a novel perspective on the mechanism of silk gland development and silk protein synthesis but also complement previously reported genome-scale eccDNA data supporting that eccDNAs are common in eukaryotes.
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Affiliation(s)
- Min Zhu
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
| | - Xinyu Tong
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
| | - Qunnan Qiu
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
| | - Jun Pan
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
| | - Shulin Wei
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
| | - Yuming Ding
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
| | - Yongjie Feng
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
| | - Xiaolong Hu
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
- Institute of Agricultural Biotechnology and Ecological Research, Soochow University, Suzhou, China
| | - Chengliang Gong
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
- Institute of Agricultural Biotechnology and Ecological Research, Soochow University, Suzhou, China
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