Advances in Extrachromosomal Circular DNA and Their Application in Domestic Animal Breeding

doi:10.13560/j.cnki.biotech.bull.1985.2021-0217

Abstract

Abstract:

Extrachromosomal circular DNA（eccDNA）,exiting as double-stranded circular DNA,arise from and are outside of chromosome. They are common in eukaryote,but have strong heterogeneity in count,length,origin,which lead to functional diversity,including telomere prolonging,rDNA copy number maintenance,aging,drug resistance,tumorigenesis. The associations between eccDNA and domestic animal phenotypes have been reported as well. Here,we review the current knowledge related to eccDNA classification,biogenesis,functions,and identification,and discuss some possible future directions of eccDNA applications in animal breeding.

Key words: eccDNA, ecDNA, high-throughput sequencing, molecular marker, animal breeding

CAO Xiu-kai, WANG Shan, GE Ling, ZHANG Wei-bo, SUN Wei. Advances in Extrachromosomal Circular DNA and Their Application in Domestic Animal Breeding[J]. Biotechnology Bulletin, 2022, 38(1): 247-257.

Figures/Tables 5

Fig.1 eccDNA classification eccDNA in narrow sense are < 100 kb,including t-circle,ERC and microDNA according to their origins. Notably,spcDNA is a concept in the early stage of studying eccDNA,it emphasizes their sizes rather than their sequence features. eccDNA with size ranging from several hundred kilobases to several megabases are common in tumor and termed as ecDNA

Fig.2 Possible mechanisms of forming eccDNA A：Formed by HR. B：Formed by NHEJ. C：Formed by DNA replication. D：Formed by transcription mediated by R-loop. There are 11 kinds of potential mechanisms for eccDNA formation and their detail information can be found in references listed in Table 1

Table 1 Corresponding references of 11 kinds of potential mechanisms for eccDNA formation

机制编号 Mechanism No.	eccDNA类型eccDNA type	时间/类型 Year/Type	参考文献 Reference
1	ERC	2019,Review	[59]
	ERC	2019,Article	[60]
	t-circle	2004,Review	[61]
	t-circle	2019,Article	[60]
	microDNA	2015,Article	[54]
	microDNA	2019,Article	[60]
2	ERC	1999,Article	[62]
	ecDNA	2010,Article	[63]
	microDNA	2018,Review	[64]
3	ERC	2019,Article	[53]
	t-circle	2004,Review	[61]
	t-circle	2019,Article	[53]
4	t-circle	2004,Review	[61]
	ecDNA	2020,Review	[65]
	ecDNA	2020,Review	[66]
5	ecDNA	2020,Review	[65]
		2020,Review	[66]
		2020,Review	[67]
6	DM	2020,Review	[65]
		2020,Review	[66]
		2020,Review	[67]
7	microDNA	2015,Article	[54]
7	microDNA	2018,Review	[64]
8	microDNA	2015,Article	[54]
8	microDNA	2018,Review	[64]
9	microDNA	2015,Article	[54]
9	microDNA	2018,Review	[64]
10	ERC	2018,Article	[68]
	DM	2004,Article	[30]
	DM	2020,Review	[69]
11	microDNA	2018,Review	[64]
11	microDNA	2020,Review	[70]

Fig.3 An overview of current understanding of eccDNA functions

Fig.4 Methods for eccDNA identification Microscope and 2D electrophoresis are used for eccDNA identification in total DNA or after enrichment of low molecular weight（LMW）DNA[10,35,88]. High-throughput sequencing library is constructed by：eccDNA of expected sizes are enriched by CsCl-EB or plasmid extraction kit,and then high-throughput sequencing is conducted after rolling circle amplification（RCA）or Tn5 treatment. Split and discordant read pairs are used for eccDNA identification. Genome WGS and ATAC-seq data are also for eccDNA identification

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