#eccDNA
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genomebiolevol.bsky.social
Our recent Perspective on extrachromosomal circular DNA is the focus of December's GBE Highlight.

Highlight: Running Circles Around Genome Architecture
🔗 doi.org/10.1093/gbe/evaf232

#genome #evolution #eccDNA
GBE | Highlight: Running Circles Around Genome Architecture
December 17, 2025 at 12:03 PM
plosbiology.org
Previous studies of extrachromosomal circular DNA #eccDNA in #plants are based on short-read seq. @vanderschuren-lab.bsky.social uses long-read seq to obtain a map of full-length eccDNAs from #Arabidopsis, identifying their genomic origins & epigenetic regulation @plosbiology.org 🧪 plos.io/44Mq3RI
Dynamics and distribution of eccDNA in Arabidopsis. Left: Schematic representation of eccDNA amplification and sequencing via CIDER-Seq pipeline. Top right: EccDNA size distribution in Arabidopsis Col-0 leaf tissues (n = 4,158). The x-axis shows eccDNA size in kb and the y-axis shows the percentage of eccDNAs belonging to each window. Middle right: Size ranges of eccDNAs with marked median and quantiles (n = 4,190). Bottom right: Percentages of eccDNA reads mapping to TAIR CDS, TE, or intergenic databases (values represent the average of three replicates).
July 18, 2025 at 7:52 AM
fusionconf.bsky.social
Studying or interested in #eccDNA, #ecDNA? Join our Extrachromosomal Circular DNA conference, 31 Oct–03 Nov 2025.

Send in an abstract & explore this dynamic & rapidly evolving field with leaders in ecDNA research➡️ bit.ly/3YmCmBY

💸Grants available for ALL career levels
📆Talk submission: 04 Sep 2025
August 26, 2025 at 4:07 PM
dbaquero.bsky.social
In our study, we show that EVs from Methanobrevibacter smithii — the predominant archaeon in the human gut — harbor proviral DNA and circular extrachromosomal DNA (eccDNA) that encodes key enzymes for methanogenesis, suggesting a potential impact on methane production in the gut.
Characterization of M. smithii EVs
June 3, 2025 at 3:57 PM
fusionconf.bsky.social
🧬🌟We're excited to add an Extrachromosomal Circular DNA conference to our 2025 calendar!🧬🌟
Chairs Birgitte Regenberg (Univ. of Copenhagen) & Zhao Zhang (Duke Univ.) are bringing a fantastic line up of speakers together in Mexico this year. More details➡️https://bit.ly/4az0PbV #ecDNA25 #eccDNA #ecDNA
January 23, 2025 at 4:39 PM
hirotok.bsky.social
「染色体外環状DNA」（eccDNA）というのがパワーワード！
北大の黒岩さんの研究室発ですね。
トゲネズミおもしろいなあ。Y染色体を失わなかった方のオキナワトゲネズミでは、Y遺伝子の大々的な重複が起きているというのも、一筋縄ではない性決定の進化を感じさせてやまないですね

オス化遺伝子、「環状DNA」に載りX染色体へ移動か Y染色体ないトゲネズミ 東京科学大など | Science Portal - 科学技術の最新情報サイト「サイエンスポータル」 scienceportal.jst.go.jp/newsflash/20...
オス化遺伝子、「環状DNA」に載りX染色体へ移動か Y染色体ないトゲネズミ 東京科学大など | Science Portal - 科学技術の最新情報サイト「サイエンスポータル」
南西諸島には、生物の性別を決定する「性染色体」が珍しい特徴を持つトゲネズミがいる。これらの3種のゲノム（全遺伝情報）配列を、東京科学大学などの研究グループが詳しく解読し、性染色体の進化過程の仮説を
scienceportal.jst.go.jp
August 13, 2025 at 1:09 AM
miki--tan.bsky.social
アマミトゲネズミとトクノシマトゲネズミの共通祖先では、染色体外環状DNA（eccDNA）[用語1]がX染色体に入り込むことによりY遺伝子がX染色体に移動し、最終的にY染色体が消失したことが示唆されました。

mammalでこんなんあるって知っちゃうと染色体検査に縋ってアスリートを男だ女だケチつけたところで本当に意味あんだかなと思っちゃうね
www.isct.ac.jp/ja/news/be94...
Y染色体はどこへ？—ユニークな進化の軌跡 | Science Tokyo - 東京科学大学
www.isct.ac.jp
June 5, 2025 at 4:51 AM
cpricejones.bsky.social
eccDNA perhaps?
March 20, 2025 at 2:16 PM
biorxivpreprint.bsky.social
Comparative analysis of eccDNA and circRNA tools shows increased accuracy of tool combination https://www.biorxiv.org/content/10.1101/2025.07.14.664708v1
July 18, 2025 at 10:47 PM
genesndiseases.bsky.social
Reviewing the #Biogenesis, characteristics, and functions of #eccDNA, and its role in regulating #Tumorigenesis & cancer treatment, with insights into its potential for inspiring precision medicine and identifying #PrognosticBiomarkers.

#OpenAccess: doi.org/10.1016/j.ge...
January 28, 2026 at 4:50 PM
zhaozheng0503.bsky.social
1/5: ☺️☺️ Recently, we have published a database paper in the MBE journal @molbioevol.bsky.social titled "eccDNABase: A Comprehensive and High-Quality Database for Extrachromosomal Circular DNA". #eccDNA #disease #multi_species

academic.oup.com/mbe/article/...
eccDNABase: A Comprehensive and High-Quality Database for Extrachromosomal Circular DNA
Abstract. Extrachromosomal circular DNA (eccDNA) refers to small, circular DNA molecules that originate from chromosomal sequences and are prevalent across
academic.oup.com
October 9, 2025 at 3:23 AM
rikenekorin.bsky.social
chloroquest.com/06/08/2025/1...

eccDNAっていう、環状DNAが存在しているらしいです。植物内に。
ほとんどはゴミで（笑）、たまたま遺伝子全長が入ったときに、遺伝子発現をサポートすると。
トランスポゾン近傍は、コンスタントにeccDNA化する場合もあるみたい。それが優位に働く場合もあると。
生物の制御は複雑ですねぇ。
これぞ基礎研究って感じですか。
”ほぼゴミ、まれに宝”の設計（DNA）切れ端――植物のeccDNAを読み解く最新研究
eccDNAは多くが副産物だが、稀にコピー数ブーストや再統合のタネになる。“全長”で読み解いた最新研究から、TE・エピゲノム・細胞状態との関係を解説。
chloroquest.com
August 6, 2025 at 2:39 PM
ibb-uab.bsky.social
📄Nou article del Grup de Recerca en Integritat i Inestabilitat del Genoma:

“EccDNA atlas in male mice reveals features protecting genes against transcription-induced eccDNA formation”

🔗https://www.uab.cat/ca/ibb/noticies/20250313/pub-iig

#IBBpaper
@aruizherrera.bsky.social
March 13, 2025 at 1:09 PM
theplantcell.bsky.social
IN BRIEF: Palmer amaranth’s arsenal: Rearrangement of eccDNA provides dual herbicide resistance in Amaranthus palmeri (Yu-Hung Hung) doi.org/10.1093/plce... #PlantScience
doi.org
May 19, 2025 at 6:13 PM
toheitka.bsky.social
The preprint provides a map through the test cases, including repeats, eccDNA and even linked and separated rDNA. Even more info and the corresponding code, you will find at Ludwig's github:

github.com/crimBubble/r...
October 31, 2023 at 10:53 AM
biorxivpreprint.bsky.social
Technical and biological variations in the purification of extrachromosomal circular DNA (eccDNA) and the finding of more eccDNA in the plasma of lung adenocarcinoma patients compared with healthy donors https://www.biorxiv.org/content/10.1101/2024.03.05.583481v1
Technical and biological variations in the purification of extrachromosomal circular DNA (eccDNA) and the finding of more eccDNA in the plasma of lung adenocarcinoma patients compared with healthy donors https://www.biorxiv.org/content/10.1101/2024.03.05.583481v1
Abstract: Human plasma DNA originates from all tissues and organs, holding the potential as a versat
www.biorxiv.org
March 8, 2024 at 3:22 AM
genesndiseases.bsky.social
This review provides an overview of the biogenesis, distinguishing features, and functions of #ExtrachromosomalCircularDNA (eccDNA), its role and mechanisms during cancer treatment, and highlights its potential for precision #CancerTherapy. #medsky

#OpenAccess: www.sciencedirect.com/science/arti...
Extrachromosomal circular DNA and their roles in cancer progression
March 21, 2025 at 2:00 PM
grahamerwin.bsky.social
They find both eccDNA and ecDNA present in these neuroblastoma tumors. I'll focus mostly on their ecDNA results here. The ecDNAs are large and carry full genes.
November 18, 2024 at 9:11 PM
biorxivpreprint.bsky.social
ECCFP: a consecutive full pass based bioinformatic analysis for eccDNA identification using Nanopore sequencing data https://www.biorxiv.org/content/10.1101/2025.05.13.653627v1
May 16, 2025 at 10:48 AM
chmoei.bsky.social
🔍 Their study (Baquero et al., Nat Comms) shows EVs from Methanobrevibacter smithii carry eccDNA and methanogenesis-related enzymes - hinting at EV roles in horizontal gene transfer and methane production.
June 3, 2025 at 2:13 PM
somssich.bsky.social
📜 Palmer amaranth’s arsenal: Rearrangement of eccDNA provides dual herbicide resistance in Amaranthus palmeri

🧑‍🔬 Yu-Hung Hung

📔 @theplantcell.bsky.social

🔗 academic.oup.com/plcell/advan...

#️⃣ #PlantScience #Glyphosate #HerbicideResistance #Herbicides #PlantGMOs #PlantPhysiology #InvasiveWeeds
Palmer amaranth’s arsenal: Rearrangement of eccDNA provides dual herbicide resistance in Amaranthus palmeri
Yu-Hung Hung; Palmer amaranth’s arsenal: Rearrangement of eccDNA provides dual herbicide resistance in Amaranthus palmeri, The Plant Cell, , koaf077, https
academic.oup.com
April 9, 2025 at 7:20 AM
zhaozheng0503.bsky.social
5/5: Given its extensive and curated datasets, eccDNABase serves as a valuable resource for both basic and translational research, offering deeper insights into the role of eccDNA in health and disease. The database is publicly accessible at cgga.org.cn/eccDNABase/.
ecDNABase database
cgga.org.cn
October 9, 2025 at 3:23 AM
biorxiv-bioinfo.bsky.social
scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse https://www.biorxiv.org/content/10.1101/2024.07.18.604058v1
scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse https://www.biorxiv.org/content/10.1101/2024.07.18.604058v1
Extrachromosomal circular DNA (eccDNA), an extrachromosomal circular structured DNA, is extensively
www.biorxiv.org
July 22, 2024 at 8:46 PM
biorxivpreprint.bsky.social
scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse https://www.biorxiv.org/content/10.1101/2024.07.18.604058v1
scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse https://www.biorxiv.org/content/10.1101/2024.07.18.604058v1
Extrachromosomal circular DNA (eccDNA), an extrachromosomal circular structured DNA, is extensively
www.biorxiv.org
July 22, 2024 at 8:46 PM
biorxiv-molbio.bsky.social
Technical and biological variations in the purification of extrachromosomal circular DNA (eccDNA) and the finding of more eccDNA in the plasma of lung adenocarcinoma patients compared with healthy donors https://www.biorxiv.org/content/10.1101/2024.03.05.583481v1
Technical and biological variations in the purification of extrachromosomal circular DNA (eccDNA) and the finding of more eccDNA in the plasma of lung adenocarcinoma patients compared with healthy donors https://www.biorxiv.org/content/10.1101/2024.03.05.583481v1
Abstract: Human plasma DNA originates from all tissues and organs, holding the potential as a versat
www.biorxiv.org
March 8, 2024 at 3:22 AM