High-resolution 3D DNA fish using plasmid probes and computational correction of optical aberrations to study chromatin structure at the sub-megabase scale

Methods in Molecular Biology

Volumn 1262, Issue , 2015, Pages 37-53

  Giorgetti, Luca ^a   Piolot, Tristan ^a   Heard, Edith ^a  

^a NONE

Author keywords

Chromatic aberrations; Chromosome structure; Deconvolution; High resolution 3D DNA FISH; Topologically associating domains

Indexed keywords

DNA; GENOMIC DNA; CHROMATIN; DNA PROBE;

ANIMAL CELL; ANIMAL CELL CULTURE; ARTICLE; CHROMATIN STRUCTURE; DNA DETERMINATION; DNA NICK TRANSLATION; EMBRYONIC STEM CELL; FLUORESCENCE IN SITU HYBRIDIZATION; IMAGE ANALYSIS; MICROSCOPY; MOUSE; NONHUMAN; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; THREE DIMENSIONAL IMAGING; TISSUE CULTURE; CELL CULTURE; CHROMATIN; COMPUTER ASSISTED DIAGNOSIS; DNA PROBE; GENETICS; HUMAN; PROCEDURES;

CELLS, CULTURED; CHROMATIN; DNA PROBES; EMBRYONIC STEM CELLS; HUMANS; IMAGE INTERPRETATION, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; IN SITU HYBRIDIZATION, FLUORESCENCE; PLASMIDS;

EID: 84921766204     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-2253-6_3     Document Type: Article

References (12)

1. de Laat W, Duboule D (2013) Topology of mammalian developmental enhancers and their regulatory landscapes. Nature 502(7472): 499–506
2. Gibcus JH, Dekker J (2013) The hierarchy of the 3D genome. Mol Cell 49(5): 773–782
3. Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B (2012) A map of the cis-regulatory sequences in the mouse genome. Nature 488(7409):116–120
4. Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J, Sedat J, Gribnau J, Barillot E, Bluthgen N, Dekker J, Heard E (2012) Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485(7398): 381–385
5. Giorgetti L, Galupa R, Nora EP, Piolot T, Lam F, Dekker J, Tiana G, Heard E (2014) Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription. Cell 157(4):950–963
6. Beliveau BJ, Joyce EF, Apostolopoulos N, Yilmaz F, Fonseka CY, McCole RB, Chang Y, Li JB, Senaratne TN, Williams BR, Rouillard JM, Wu CT (2012) Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Proc Natl Acad Sci U S A 109(52):21301–21306
7. Boyle S, Rodesch MJ, Halvensleben HA, Jeddeloh JA, Bickmore WA (2011) Fluorescence in situ hybridization with highcomplexity repeat-free oligonucleotide probes generated by massively parallel synthesis. Chromosome Res 19(7):901–909
8. Bienko M, Crosetto N, Teytelman L, Klemm S, Itzkovitz S, van Oudenaarden A (2013) A versatile genome-scale PCR-based pipeline for high-definition DNA FISH. Nat Methods 10(2):122–124
9. Sorzano CO, Thevenaz P, Unser M (2005) Elastic registration of biological images using vector-spline regularization. IEEE Trans Biomed Eng 52(4):652–663
10. Bolte S, Cordelieres FP (2006) A guided tour into subcellular colocalization analysis in light microscopy. J Microsc 224(Pt 3):213–232
11. Sengupta P, Van Engelenburg S, Lippincott- Schwartz J (2012) Visualizing cell structure and function with point-localization superresolution imaging. Dev Cell 23(6):1092–1102
12. Mlynarczyk-Evans S, Royce-Tolland M, Alexander MK, Andersen AA, Kalantry S, Gribnau J, Panning B (2006) X chromosomes alternate between two states prior to random X-inactivation. PLoS Biol 4(6):e159