iChIP

iChIP (insertional ChIP) is the technology to isolate specific DNA regions for identification of their associated molecules by insertion of recognition sequences of an exogenous DNA-binding molecule into the target DNA regions followed by affinity purification with the exogenous DNA-binding molecule. The technology is covered by our patents (US 8415098, JP 5413924).
(in cell or in vitro, DNA-binding molecule, tag, target molecules, downstream application)

2009

• Hoshino A, Fujii H: Insertional chromatin immunoprecipitation: a method for isolating specific genomic regions. J. Biosci. Bioeng. (2009), 108, 446-449.
  (in cell, LexA, 1xFLAG / calmodulin-binding peptide, protein, ChIP)
  PubMed

2010

• McCullagh E, Seshan A, El-Samad H, Madhani HD: Coordinate control of gene expression noise and interchromosomal interactions in a MAP kinase pathway. Nat. Cell Biol., (2010) 12, 954-962.
  (in cell, LacI, mCherry, genomic DNA, microarray (chip))
  PubMed

2011

• Fujita T, Fujii H: Direct identification of insulator components by insertional chromatin immunoprecipitation. PLoS One (2011) 6, e26109.
  (in cell, LexA, 1xFLAG / calmodulin-binding peptide, protein / RNA, mass spectrometry (MS) / RT-PCR)
  PLoS One

2012

• Fujita T, Fujii H: Efficient isolation of specific genomic regions by insertional chromatin immunoprecipitation (iChIP) with a second-generation tagged LexA DNA-binding domain. Adv. Biosci. Biotechnol. (2012) 3, 626-629.
  (in cell, LexA, 3xFLAG)
  Adv. Biosci. Biotechnol.
• Agelopoulos M, McKay DJ, Mann RS: Developmental regulation of chromatin conformation by Hox proteins in Drosophila. Cell Rep. (2012) 1, 350-359.
  (in cell, lacI, 3xFLAG, protein, ChIP)
  PubMed
• Byrum SD, Raman A, Taverna SD, Tackett AJ: ChAP-MS: a method for identification of proteins and histone posttranslational modifications at a single genomic locus. Cell Rep. (2012) 2, 198-205.
  (in cell, LexA, Protein A, protein, MS (stable isotope labeling using amino acids in cell culture (SILAC))
  PubMed

2013

• Pourfarzad F, Aghajanirefah A, de Boer E, Ten Have S, Bryn van Dijk T, Kheradmandkia S, Stadhouders R, Thongjuea S, Soler E, Gillemans N, von Lindern M, Demmers J, Philipsen S, Grosveld F: Locus-specific proteomics by TChP: targeted chromatin purification. Cell Rep. (2013) 4, 589-600.
  (in cell, TetR, biotin / HA, protein, MS)
  PubMed

2014

• 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, LexA, 3xFLAG, RNA, RT-PCR)
  BMC Mol. Biol.

2015

• Fujita T, Kitaura F, Fujii H: A critical role of the Thy28-MYH9 axis in B cell-specific expression of the Pax5 gene in chicken B cells. PLoS One (2015) 10, e0116579.
  (in cell, LexA, 3xFLAG, protein, MS (SILAC))
  PLoS One

2017

• 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 cell, LexA, 3xFLAG, genomic DNA, next generation sequencing (NGS))
  DNA Res.

2019

• Bui PL, Nishimura K, Seminario Mondejar G, Kumar A, Aizawa S, Murano K, Nagata K, Hayashi Y, Fukuda A, Onuma Y, Ito Y, Nakanishi M, Hisatake K: Template activating factor-I α regulates retroviral silencing during reprogramming.
  Cell Rep. (2019) 29, 1909-1922.e5.
  (in cell, LexA, 3xFLAG, protein, MS)
  PubMed

2020

• Husain A, Xu J, Fujii H, Nakata M, Kobayashi M, Wang JY, Rehwinkel J, Honjo T, Begum NA: SAMHD1-mediated dNTP degradation is required for efficient DNA repair during antibody class switch recombination. EMBO J. (2020) 39, e102931.
  (in cell, LexA, 3xFLAG, protein, MS (SILAC))
  EMBO J.

2024

• Fujita T, Fujii H: iChIP-SILAC analysis identifies epigenetic regulators of CpG methylation of the p16INK4A gene. FEBS Lett. (2024) doi: 10.1002/1873-3468.14878.
  (in cell, LexA, 3xFLAG, protein, MS (SILAC))
  FEBS Lett.