419
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Study on chromatin regulation patterns of expression vectors in the PhiC31 integration site

, , , , , & show all
Article: 2337085 | Received 15 Oct 2023, Accepted 26 Mar 2024, Published online: 09 Apr 2024

References

  • Fang-Yan X. Advances in the application of gene editing technology in gene therapy. Biol Chem Eng. 2019;5(1):162–16. doi: 10.3969/j.issn.2096-0387.2019.01.047
  • Lalonde ME, Durocher Y. (2017). Therapeutic glycoprotein production in mammalian cells. J Biotechnol, 251:128–140. doi: 10.1016/j.jbiotec.2017.04.028
  • Groth AC, Olivares EC, Thyagarajan B. A phage integrase directs efficient site-specific integration in human cells. Proc Natl Acad Sci USA. 2000;97(11):5995–6000. doi: 10.1073/pnas.090527097
  • Damavandi N, Raigani M, Joudaki A, et al. (2017). Rapid characterization of the CHO platform cell line and identification of pseudo attP sites for PhiC31 integrase. Protein Expr Purif, 140:60. doi: 10.1016/j.pep.2017.08.002
  • Chalberg TW, Portlock JL, Olivares EC, et al. Integration specificity of phage phiC31 integrase in the human genome. J Mol Biol. 2006;357(1):28–48. doi: 10.1016/j.jmb.2005.11.098
  • Ahmadi S, Nematpour F, Davami M, et al. PhiC31 integrase can improve the efficiency of different construct designs for monoclonal antibody expression in CHO cells. Protein Expr Purif. 2017;134:89–95. doi: 10.1016/j.pep.2017.04.005
  • Ahmadi M, Mahboudi F, Mohammad RAE, et al. Evaluating the efficiency of phiC31 integrase-mediated monoclonal antibody expression in CHO cells. Biotechnol Prog. 2016;32(6):1570–1576. doi: 10.1002/btpr.2362
  • Thyagarajan B, Calos MP. Site-specific integration for high-level protein production in mammalian cells. Methods Mol Biol. 2005;308(308):99–106. doi: 10.1385/1-59259-922-2:099
  • Nick G, Bernard R. The relationship between chromatin structure and transcriptional activity in mammalian genomes. Brief Funct Genomic Proteomic. 2005;4(2):129–142. doi: 10.1093/bfgp/4.2.129
  • Dahodwala H, Lee KH. (2019). The fickle CHO: a review of the causes, implications, and potential alleviation of the CHO cell line instability problem. Curr Opin Biotechnol, 60:128–137. doi: 10.1016/j.copbio.2019.01.011
  • Karow M, Calos MP. The therapeutic potential of phiC31 integrase as a gene therapy system. Expert Opin Biol Ther. 2011;11(10):1287. doi: 10.1517/14712598.2011.601293
  • Andrew P, Futreal L, Coin M, et al. A census of human cancer genes. Nat Rev Cancer. 2004. doi: 10.1038/nrc1299
  • Mitelman F, Johansson B, Mertens F. Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer. Nature Genet. 2004;36:4. doi: 10.1038/ng1335
  • Nakayama G, Kawaguchi Y, Koga K, et al. Site-specific gene integration in cultured silkworm cells mediated by φC31 integrase. Mol Biol Rep. 2006;2006(1):1–8. doi:10.1007/s00438-005-0026-3
  • Calos M. The φC31 integrase system for gene therapy. Curr Gene Ther. 2007;6(6):633–645. doi: 10.2174/156652306779010642
  • Nakanishi H, Higuchi Y, Yamashita F, et al. (2014). Targeted gene integration using the combination of a sequence-specific DNA-binding protein and phiC31 integrase. J Biotechnol, 186:139–147. doi: 10.1016/j.jbiotec.2014.07.012
  • Pourtabatabaei S, Ghanbari S, Damavandi N, et al. Targeted integration into pseudo attP sites of CHO cells using CRISPR/Cas9. J Biotechnol. 2021;337(1):1–7. doi: 10.1016/j.jbiotec.2021.06.018
  • Kheirandish MH, Rahmani B, Jaliani HZ, et al. Efficient site-specific integration in CHO-K1 cells using CRISPR/Cas9-modified donors. Mol Biol Rep. 2023;50(7):5889–5899. doi: 10.1007/s11033-023-08529-8
  • Macarthur CC, Xue H, Van Hoof D, et al. Chromatin insulator elements block transgene silencing in engineered human embryonic stem cell lines at a defined chromosome 13 locus. Stem Cells Devel. 2012;21(2):191. doi: 10.1089/scd.2011.0163
  • Susanne A, Frieder S, Birgit K-L, et al. Enhanced efficiency through nuclear localization signal fusion on phage PhiC31-integrase: activity comparison with Cre and FLPe recombinase in mammalian cells. Nucleic Acids Res. 2002;30(11):2299–2306.
  • Portoy V, Lin SHS, Li KH, et al. saRNA-guided Ago2 targets the RITA complex to promoters to stimulate transcription. Cell Res. 2016;26(3):320–335. doi: 10.1038/cr.2016.22
  • Lacoste A, Berenshteyn F, Brivanlou AH. An efficient and reversible transposable system for gene delivery and lineage-specific differentiation in human embryonic stem cells. Cell Stem Cell. 2009;5(3):332–342. doi: 10.1016/j.stem.2009.07.011
  • Tang D, Gunson J, Tran E, et al. Expressing antigen binding fragments with high titers in a targeted integration CHO host by optimizing expression vector gene copy numbers and position: a case study. Biotechnol Prog. 2022;38(6):e3290. doi: 10.1002/btpr.3290 Epub 20220816 PubMed PMID: 36537257.
  • Beal KM, Bandara KR, Ali SR, et al. The impact of expression vector position on transgene transcription allows for rational expression vector design in a targeted integration system. Biotechnology Journal. 2023;18(9):e2300038. doi: 10.1002/biot.202300038 Epub 20230605 PubMed PMID: 37272404.
  • Vaschetto LM. RNA activation: a diamond in the rough for genome engineers. J Cell Biochem. 2018;119(1):247–249. doi: 10.1002/jcb.26228 Epub 20170717 PubMed PMID: 28636278.
  • Wang B, Sun J, Shi J, et al. Small-activating RNA can change nucleosome positioning in human fibroblasts. J Biomol Screen. 2016;21(6):634–642. doi: 10.1177/1087057116637562 Epub 20160318 PubMed PMID: 26993320.
  • Williams S, Mustoe T, Mulcahy T, et al. CpG-island fragments from the HNRPA2B1/CBX3 genomic locus reduce silencing and enhance transgene expression from the hCMV promoter/enhancer in mammalian cells. BMC Biotechnol. 2005;5:17. doi: 10.1186/1472-6750-5-17 Epub 20050603 PubMed PMID: 15935093; PubMed Central PMCID: PMC1175082.
  • Lay FD, Kelly TK, Jones PA. Nucleosome occupancy and methylome sequencing (NOMe-seq). Methods Mol Biol. 2018;1708:267–284. doi: 10.1007/978-1-4939-7481-8_14 PubMed PMID: 29224149.
  • Xi Y, Li W. BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinf. 2009;10:232. doi: 10.1186/1471-2105-10-232 Epub 20090727 PubMed PMID: 19635165; PubMed Central PMCID: PMC2724425.
  • Requena F, Asenjo HG, Barturen G, et al. NOMePlot: analysis of DNA methylation and nucleosome occupancy at the single molecule. Sci Rep. 2019;9(1):8140. doi: 10.1038/s41598-019-44597-2 Epub 20190531 PubMed PMID: 31148571; PubMed Central PMCID: PMC6544651.
  • GQ WB, Liu L. Influence of the interaction between chromatin regulatory elements and different promoters on gene expression regulation. Chin J Biotechnol. 2021;37(9):3310–3322.
  • Hesson LB, Sloane MA, Wong JW, et al. Altered promoter nucleosome positioning is an early event in gene silencing. Epigenetics. 2014;9(10):1422–1430. doi: 10.4161/15592294.2014.970077 PubMed PMID: 25437056; PubMed Central PMCID: PMC4622968.
  • Li YJ, Fu XH, Liu DP, et al. Opening the chromatin for transcription. Int J Biochem Cell Biol. 2004;36(8):1411–1423. doi: 10.1016/j.biocel.2003.11.003 PubMed PMID: 15147721.
  • Wolffe AP, Guschin D. Review: chromatin structural features and targets that regulate transcription. J Struct Biol. 2000;129(2–3):102–122. doi: 10.1006/jsbi.2000.4217 PubMed PMID: 10806063.
  • Workman JL, Kingston RE. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu Rev Biochem. 1998;67:545–579. doi: 10.1146/annurev.biochem.67.1.545 PubMed PMID: 9759497.
  • Maunakea AK, Nagarajan RP, Bilenky M, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010;466(7303):253–257. doi: 10.1038/nature09165 PubMed PMID: 20613842; PubMed Central PMCID: PMC3998662.