Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 Mar;30(2):e70011.
doi: 10.1111/gtc.70011.

Potential Role of Trap Clone Accumulation Areas (TCAAs) in Sustaining Pluripotency in Mouse Embryonic Stem Cells

Masatake Araki  1 , Luna Ikeda  1 , Takumi Yonemori  1 , Kumiko Yoshinobu  1 , Mariko Yamane  2   3   4 , Takumi Ichikawa  2   3   4 , Kimi Araki  1
Affiliations
Free article

Potential Role of Trap Clone Accumulation Areas (TCAAs) in Sustaining Pluripotency in Mouse Embryonic Stem Cells

Masatake Araki et al. Genes Cells. 2025 Mar.
Free article

Abstract

Analysis of gene trap clones (TCs) revealed the existence of regions where TCs accumulate in the absence of genes. These regions were designated as trap clone accumulation areas (TCAAs). To ascertain the physiological function of TCAAs, negative control regions devoid of genes and TCs (NC1 and NC11), two randomly selected known gene sets (G1 and G11), and a set of genes presumed to be involved in maintaining pluripotency in embryonic stem (ES) cells (GP) were generated and compared with TCAAs. The assay for transposase-accessible chromatin with sequencing (ATAC-Seq) results indicated that TCAAs exhibited characteristics comparable to G1, G11, and GP, suggesting an open chromatin structure. Oct4-chromatin immunoprecipitation-sequencing (ChIP-seq) demonstrated that TCAAs had markedly elevated signals compared to G1 and 11, and a comparable level to that of GP. With regard to H3K4me1 and H3K27ac, which are associated with enhancer activity, TCAAs were observed to exhibit significantly higher levels than G1 and 11 and a comparable level to that of GP. Furthermore, approximately half of the super-enhancers overlapped with TCAAs in an ES cell-specific manner. These findings suggest that TCAAs are involved in maintaining the pluripotency of mouse ES cells.

Keywords: gene trap; non‐coding sequence; pluripotency; super‐enhancer.

PubMed Disclaimer

References

    1. Araki, K., T. Imaizumi, T. Sekimoto, et al. 1999. “Exchangeable Gene Trap Using the Cre/Mutated Lox System.” Cellular and Molecular Biology 45, no. 5: 737–750.
    1. Araki, M., K. Araki, and K.‐I. Yamamura. 2009. “International Gene Trap Project: Towards Gene‐Driven Saturation Mutagenesis in Mice.” Current Pharmaceutical Biotechnology 10, no. 2: 221–229. https://doi.org/10.2174/138920109787315006.
    1. Araki, M., M. Nakahara, M. Muta, et al. 2014. “Database for Exchangeable Gene Trap Clones: Pathway and Gene Ontology Analysis of Exchangeable Gene Trap Clone Mouse Lines.” Development, Growth & Differentiation 56, no. 2: 161–174. https://doi.org/10.1111/dgd.12116.
    1. Henninger, J. E., O. Oksuz, K. Shrinivas, et al. 2021. “RNA‐Mediated Feedback Control of Transcriptional Condensates.” Cell 184, no. 1: 207–225. https://doi.org/10.1016/j.cell.2020.11.030.
    1. Jiang, Y., F. Qian, X. Bai, et al. 2019. “SEdb: A Comprehensive Human Super‐Enhancer Database.” Nucleic Acids Research 47, no. D1: D235–D243. https://doi.org/10.1093/nar/gky1025.

MeSH terms

LinkOut - more resources