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. 2017 Sep 8;7:10968. doi: 10.1038/s41598-017-11368-w

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© The Author(s) 2017

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Functional annotation of eccDNA. (A) Genes (exons, 5′UTRs, 3′UTRs), regulatory elements (CpG Islands, DNase Clusters, H3K4Me1, H3K4Me3, H3K27Ac) and repetitive sequences (RepeatMasker) were intersected with eccDNAs (sized less than 1000 bp) in samples 1, 2 and 4. Random regions with matched chromosomes and lengths with eccDNAs were generated as random controls. The fold change stands for the ratio between elements counts in eccDNAs and the controls. Higher frequency of 3′UTRs, exons, DNase Clusters, H3K4Me1 and H3K27Ac are observed in eccDNA regions in all samples. Sample 4 also has higher enrichment of 5′UTRs and CpG island sequences. (B) Representative eccDNAs associated with genes and regulatory elements. Upper: Representative eccDNA with overall sequence coverage and split reads. Lower: Gene transcripts and epigenomic marks for regulatory DNA elements in the eccDNA region. The region covers two exons of MYH15 gene. Histone marks of H3K4Me1, H3K4Me3, H3K27Ac, and DNase I hypersensitivity tracks from ENCODE are also shown.