Microfluidics-Based Chromosome Conformation Capture (3C) Technology for Examining Chromatin Organization with a Low Quantity of Cells

Analytical Chemistry
Chen Sun, Chang Lu

Abstract

Detecting three-dimensional (3D) genome organization in the form of physical interactions between various genomic loci is of great importance for understanding transcriptional regulations and cellular fate. Chromosome Conformation Capture (3C) method is the gold standard for examining chromatin organization, but usually requires a large number of cells (>107). This hinders studies of scarce tissue samples from animals and patients using the method. Here we developed a microfluidics-based approach for examining chromosome conformation by 3C technology. Critical 3C steps, such as digestion and religation of BAC DNA and cross-linked chromatin, were implemented on a microfluidic chip using a low quantity of cells (<104). Using this technology, we analyzed the chromatin looping interactions in the human β-globin. We envision that our method will provide a powerful tool for low-input analysis of chromosome conformation and epigenetic regulations.

References

Oct 17, 1998·Science·M A BurnsD T Burke
Jan 15, 2000·The Journal of Biological Chemistry·G L LukacsA S Verkman
Feb 16, 2002·Science·Job DekkerNancy Kleckner
Nov 12, 2002·Nature Genetics·David CarterPeter Fraser
Feb 5, 2003·Current Opinion in Biotechnology·Brian M PaegelRichard A Mathies
Jun 27, 2003·Trends in Biochemical Sciences·Job Dekker
Sep 16, 2003·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Wouter de Laat, Frank Grosveld
Feb 12, 2004·Methods in Enzymology·Erik SplinterWouter de Laat
Mar 17, 2004·Nature Biotechnology·Jong Wook HongStephen R Quake
May 18, 2004·Current Opinion in Cell Biology·Séverine Chambeyron, Wendy A Bickmore
May 25, 2004·Nucleic Acids Research·Emil P Kartalov, Stephen R Quake
Jun 17, 2004·Genes & Development·George P PatrinosFrank G Grosveld
Sep 14, 2004·Nature Genetics·Cameron S OsbornePeter Fraser
Sep 21, 2004·Nature Immunology·Charalampos G Spilianakis, Richard A Flavell
Nov 19, 2004·American Journal of Human Genetics·Dirk A Kleinjan, Veronica van Heyningen
Apr 6, 2005·Human Molecular Genetics·Adam G West, Peter Fraser
May 1, 2007·Angewandte Chemie·Nitin AgrawalVictor M Ugaz
May 25, 2007·Nature·Peter Fraser, Wendy Bickmore
Jul 21, 2007·Nature Protocols·Hélène HagègeThierry Forné
Feb 12, 2008·Current Protocols in Molecular Biology·Adriana MieleJob Dekker
May 7, 2009·Lab on a Chip·Angela R WuStephen R Quake
Feb 27, 2010·Analytical Chemistry·Benjamin R CiprianyPaul D Soloway
Jun 29, 2010·Journal of Bacteriology·Anja NenningerConrad W Mullineaux
Oct 15, 2010·Nature Biotechnology·Bas van Steensel, Job Dekker
Jan 5, 2012·Genes & Development·Elzo de Wit, Wouter de Laat
Jun 2, 2012·Methods : a Companion to Methods in Enzymology·Jon-Matthew BeltonJob Dekker
Dec 4, 2012·Methods : a Companion to Methods in Enzymology·Wouter de Laat, Job Dekker
May 2, 2014·Proceedings of the National Academy of Sciences of the United States of America·Aaron M StreetsYanyi Huang
Jun 13, 2014·Lab on a Chip·Sai MaChang Lu
Apr 19, 2015·Trends in Genetics : TIG·Viviana I Risca, William J Greenleaf
Jul 28, 2015·Nature Methods·Zhenning CaoChang Lu
Sep 26, 2015·Lab on a Chip·Manjima DharDino Di Carlo
Oct 13, 2015·Nature Biotechnology·Assaf RotemBradley E Bernstein

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Citations

Jul 25, 2019·Lab on a Chip·Chengyu DengChang Lu
Mar 1, 2019·Biotechnology for Biofuels·Pierre BodénèsChun-Yen Wang
Jun 3, 2021·International Journal of Molecular Sciences·Mengsheng ZhaZheng Wang

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