enChIP

enChIP (engineered DNA-binding molecule-mediated ChIP) is the technology to isolate specific DNA regions for identification of their associated molecules using engineered DNA-binding molecules recognizing the target DNA regions. Engineered DNA-binding molecules include the CRISPR complexes consisting of a catalytically inactive form of Cas9 protein (dCas9) and guide RNA (gRNA), transcription-activator-like effector (TAL or TALE), and others. The technology is covered by our patents (JP 5954808, EP 2963113, US 11466306).
(in cell or in vitro, engineered DNA-binding molecule, tag, target molecules, downstream application)

2013

• Fujita T, Fujii H: Efficient isolation of specific genomic regions and identification of associated proteins by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR. Biochem. Biophys. Res. Commun. (2013) 439, 132-136.
  (in cell, CRISPR, 3xFLAG, protein, mass spetrometry (MS))
  Biochem. Biophys. Res. Commun.
• Fujita T, Asano Y, Ohtsuka J, Takada Y, Saito K, Ohki R, Fujii H: Identification of telomere-associated molecules by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP). Sci. Rep. (2013) 3, 3171.
  (in cell, TAL, 3xFLAG, protein / RNA, MS / RT-PCR)
  Sci. Rep.
• Byrum SD, Taverna SD, Tackett A: Purification of a specific native genomic locus for proteomic analysis. Nucleic Acds Res. (2013) 41, e195.
  (in cell, TAL, Protein A, protein, MS)
  PubMed

2014

• Fujita T, Fujii H: Identification of proteins associated with an IFNγ-responsive promoter by a retroviral expression system for enChIP using CRISPR. PLoS One (2014) 9, e103084.
  (in cell, CRISPR, 3xFLAG, protein, MS (stable isotope labeling using amino acids in cell culture (SILAC))
  PLoS One
• Waldrip ZJ, Byrum SD, Storey AJ, Gao J-X, Byrd AK, Mackintosh SG, Wahls W, Taverna SD, Raney KD, Tackett AJ: A CRISPR-based approach for proteomic analysis of a single genomic locus. Epigenetics (2014) 9, 1207-1211.
  (in cell, CRISPR, Protein A, protein, MS)
  PubMed
• Fujita T, Fujii H: Efficient isolation of specific genomic regions retaining molecular interactions by the iChIP system using recombinant exogenous DNA-binding proteins. BMC Mol. Biol. (2014) 15, 26.
  (in vitro, TAL, 3xFLAG)
  BMC Mol. Biol.

2015

• Fujita T, Yuno M, Okuzaki D, Ohki R, Fujii H: Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing. PLoS One (2015) 10, e0123387.
  (in cell, TAL, 3xFLAG, RNA, RNA-Seq)
  PLoS One

2016

• Fujita T, Yuno M, Fujii H: Efficient sequence-specific isolation of DNA fragments and chromatin by in vitro enChIP technology using recombinant CRISPR ribonucleoproteins. Genes Cells (2016) 21, 370-377.
  (in vitro, CRISPR, 3xFLAG / biotin)
  Genes Cells
• Fujita T, Yuno M, Fujii H: Allele-specific locus binding and genome editing by CRISPR at the p16INK4a locus. Sci. Rep. (2016) 6, 30485.
  (in cell and in vitro, CRISPR, 3xFLAG)
  Sci. Rep.

2017

• Fujita T, Yuno M, Suzuki Y, Sugano S, Fujii H: Identification of physical interactions between genomic regions by enChIP-Seq. Genes Cells (2017) 22, 506-520.
  (in cell, CRISPR, 3xFLAG, DNA, next generation sequencing (NGS))
  Genes Cells
• Fujita T, Kitaura F, Yuno M, Suzuki Y, Sugano S, Fujii H: Locus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with the Pax5 promoter in a chicken B cell line. DNA Res. (2017) 24, 537-548.
  (in vitro, CRISPR, 3xFLAG, DNA, NGS)
  DNA Res.
• Zhang Y, Hu J-F, Wang H, Cui J, Gao S, Hoffman AR, Li W: CRISPR Cas9-guided chromatin immunoprecipitation identifies miR483 as an epigenetic modulator of IGF2 imprinting in tumors. Oncotarget (2017) 8, 34177-34192.
  (in cell, CRISPR, anti-Cas9 Ab, RNA, RNA-Seq)
  PubMed
• Liu X, Zhang Y, Chen Y, Li M, Zhou F, Li K, Cao H, Ni M, Liu Y, Gu Z, Dickerson KE, Xie S, Hon GC, Xuan Z, Zhang MQ, Shao Z, Xu J: In situ capture of chromatin interactions by biotinylated dCas9. Cell (2017) 170, 1028-1043.
  (in cell, CRISPR, biotin, protein / DNA, MS / chromosome conformation capture (3C))
  PubMed

2018

• Han B, Zhou B, Qu Y, Gao B, Xu Y, Chung S, Tanaka H, Yang W, Giuliano AE, Cui X: FOXC1-induced non-canonical WNT5A-MMP7 signaling regulates invasiveness in triple-negative breast cancer. Oncogene (2018) 37, 1399-1408.
  (in cell, CRISPR, FLAG, protein, MS)
  PubMed
• Fujita T, Kitaura F, Oji A, Tanigawa N, Yuno M, Ikawa M, Taniuchi I, Fujii H: Transgenic mouse lines expressing the 3xFLAG-dCas9 protein for enChIP analysis. Genes Cells (2018) 23, 318-325.
  (in cell, CRISPR, 3xFLAG)
  Genes Cells
• Fujita T, Yuno M, Fujii H: enChIP systems using different CRISPR orthologues and epitope tags. BMC Res. Notes (2018) 11, 154.
  (in cell, CRISPR (Sa and Sp), 3xFLAG / 2xAM)
  BMC Res. Notes
• Campbell AE, Shadle SC, Jagannathan S, Lim JW, Resnick R, Tawil R, van der Maarel SM, Tapscott SJ: NuRD and CAF-1-mediated silencing of the D4Z4 array is modulated by DUX4-induced MBD3L proteins. eLife (2018) 7, e31023.
  (in cell, CRISPR, 3xFLAG, protein, MS)
  eLife
• Tsui C, Inouye C, Levy M, Lu A, Florens L, Washburn MP, Tjian R: dCas9-targeted locus-specific protein isolation method identifies histone gene regulators. Proc. Natl. Acad. Sci. USA (2018) 115, E2734-E2741.
  (in vitro, CRISPR, 3xFLAG, protein, MS)
  PubMed
• Hamidian A, Vaapil M, von Stedingk K, Fujita T, Persson CU, Eriksson P, Veerla S, De Preter K, Speleman F, Fujii H, Påhlman S, Mohlin S: Promoter-associated proteins of EPAS1 identified by enChIP-MS - A putative role of HDX as a negative regulator. Biochem. Biophys. Res. Commun. (2018) 499, 291-298.
  (in cell, CRISPR, 3xFLAG, protein, MS (SILAC))
  PubMed
• Fujita T, Yuno M, Fujii H: An enChIP system for the analysis of bacterial genome functions. BMC Res. Notes (2018) 11, 387.
  (in cell, CRISPR, 3xFLAG)
  BMC Res. Notes
• Lee J, Lim H, Jang H, Hwang B, Lee JH, Cho J, Lee JH, Bang D.: CRISPR-Cap: multiplexed double-stranded DNA enrichment based on the CRISPR system. Nucleic Acids Res. (2018) 47, e1.
  (in vitro, CRISPR, biotin)
  PubMed
• Mochizuki Y, Chiba T, Kataoka K, Yamashita S, Sato T, Kato T, Takahashi K, Miyamoto T, Kitazawa M, Hatta T, Natsume T, Takai S, Asahara H: Combinatorial CRISPR/Cas9 approach to elucidate a far-upstream enhancer complex for tissue-specific Sox9 expression. Dev. Cell (2018) 46(6):794-806.e6.
  (in cell, CRISPR, HA, protein / DNA, MS / NGS)
  PubMed
• Fang F, Xia N, Angulo B, Carey J, Cady Z, Durruthy-Durruthy J, Bennett T, Sebastiano V, Reijo Pera RA: A distinct isoform of ZNF207 controls self-renewal and pluripotency of human embryonic stem cells. Nat Commun. (2018) 9(1):4384.
  (in cell, TAL, 3xFLAG, protein, MS)
  PubMed
• Chen N, Zhao G, Yan X, Lv Z, Yin H, Zhang S, Song W, Li X, Li L, Du Z, Jia L, Zhou L, Li W, Hoffman AR, Hu JF, Cui J: A novel FLI1 exonic circular RNA promotes metastasis in breast cancer by coordinately regulating TET1 and DNMT1. Genome Biol. (2018) 19(1):218.
  (in cell, CRISPR, anti-Cas9 Ab, RNA, RNA-Seq)
  PubMed

2019

• Kuscu C, Mammadov R, Czikora A, Unlu H, Tufan T, Fischer NL, Arslan S, Bekiranov S, Kanemaki M, Adli M: Temporal and spatial epigenome editing allows precise gene regulation in mammalian cells. J. Mol. Biol. (2019) 431, 111-121.
  (in cell, CRISPR, HA, DNA, PCR)
  PubMed
• Slesarev A, Viswanathan L, Tang Y, Borgschulte T, Achtien K, Razafsky D, Onions D, Chang A, Cote C: CRISPR/CAS9 targeted CAPTURE of mammalian genomic regions for characterization by NGS. Sci. Rep. (2019) 5, 3587.
  (in vitro, CRISPR, biotin, DNA, NGS)
  PubMed
• Baumgarten S, Bryant JM, Sinha A, Reyser T, Preiser PR, Dedon PC, Scherf A: Transcriptome-wide dynamics of extensive m6A mRNA methylation during Plasmodium falciparum blood-stage development. Nat Microbiol. (2019) 4, 2246-2259.
  (in cell, CRISPR, HA, DNA, NGS)
  PubMed

2020

• Carpenter MD, Hu Q, Bond AM, Lombroso SI, Czarnecki KS, Lim CJ, Song H, Wimmer ME, Pierce RC, Heller EA: Nr4a1 suppresses cocaine-induced behavior via epigenetic regulation of homeostatic target genes. Nat. Commun. (2020) 11, 504.
  (in cell, CRISPR, AM, DNA, PCR)
  PubMed
• González-Rico FJ, Vicente-García C, Fernández A, Muñoz-Santos D, Montoliu L, Morales-Hernández A, Merino JM, Román A-C, Fernández-Salguero PM: Alu retrotransposons modulate Nanog expression through dynamic changes in regional chromatin conformation via aryl hydrocarbon receptor. Epigenetics & Chromatin (2020) 13, 15.
  (in cell, CRISPR, 3xFLAG, protein, MS)
  PubMed
• Shamsi F, Xue R, Huang TL, Lundh M, Liu Y, Leiria LO, Lynes MD, Kempf E, Wang C-H, Sugimoto S, Nigro P, Landgraf K, Schulz T, Li Y, Emanuelli B, Kothakota S, WIlliams ST, Jessen N, Pedersen SB, Böttcher Y, Blüher M, Körner A, Goodyear LJ, Mohammadi M, Kahn CR, Tseng Y-H: FGF6 and FGF9 regulate UCP1 expression independent of brown adipogenesis. Nat. Commun. (2020) 11, 1421.
  (in cell, CRISPR, 3xFLAG, protein, MS)
  PubMed
• Seo W, Shimizu K, Kojo S, Okeke A, Kohwi-Shigematsu T, Fujii S-i, Taniuchi I: Runx-mediated regulation of CCL5 via antagonizing two enhancers influences immune cell function and anti-tumor immunity. Nat. Commun. (2020) 11, 1562.
  (in cell, CRISPR, 3xFLAG, DNA, NGS)
  PubMed
• Huang Y, Xiang Y, Xie Z, Cai Y, Yang Q, Huang H, Chen Z, Xiao Z, He Q: Mass spectrometry-based proteomic capture of proteins bound to the MACC1 promoter in colon cancer. Clin Exp Metastasis (2020) 37, 477-487.
  (in cell, CRISPR, 3xFLAG, protein, MS)
  PubMed
• Nguyen T, Sun YBY, Holmes ML, Tripathi P, Pflueger J, Rossello FJ, Schröder J, Davidson KC, Nefzger CM, Das PP, Haigh JJ, Lister R, Schittenhelm RB, Polo JM: TINC- A method to dissect regulatory complexes at single-Locus resolution- reveals an extensive protein complex at the Nanog promoter. Stem Cell Reports (2020) 15, 1246-1259.
  (in cell, TALE, 3xHA, protein, MS)
  PubMed

2021

• Yuno M, Nagata S, Fujita T, Fujii H: MSCV-based retroviral plasmids expressing 3xFLAG-Sp-dCas9 for enChIP analysis. Biol. Methods Protoc. (2021) 6, bpab013.
  (in cell, CRISPR, 3xFLAG)
  Biol. Methods Protoc.
• Takeda T, Yokoyama Y, Takahashi H, Okuzaki D, Asai K, Itakura H, Miyoshi N, Kobayashi S, Uemura M, Fujita T, Ueno H, Mori M, Doki Y, Fujii H, Eguchi H, Yamamoto H: A stem cell marker KLF5 regulates CCAT1 via three-dimensional genome structure in colorectal cancer cells. Br. J. Cancer (2021) 126, 109-119.
  (in vitro, CRISPR, 3xFLAG, DNA, NGS)
  Br. J. Cancer

2022

• Okada H, Saga Y: Repurposing of the enhancer-promoter communication underlies the compensation of Mesp2 by Mesp1. PLoS Genet. (2022) 18, e1010000.
  (in cell, CRISPR, 3xFLAG, DNA, qPCR)
  PubMed
• Fujii H, Fujita T: An enChIP system for the analysis of genome functions in budding yeast. Biol. Methods Protoc. (2022) 7, bpac025.
  (in cell, CRISPR, 3xFLAG)
  Biol. Methods Protoc.
• Burramsetty AK, Nishimura K, Kishimoto T, Hamzah M, Kuno A, Fukuda A, Hisatake K: Locus-specific isolation of the Nanog chromatin identifies regulators relevant to pluripotency of mouse embryonic stem cells and reprogramming of somatic cells. Int. J. Mol. Sci. (2022) 23, 15242.
  (in cell, CRISPR, biotin, protein, MS)
  PubMed