1887
banner image
No data available.
Please log in to see this content.
You have no subscription access to this content.
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
f
Chromatin modification mapping in nanochannels
Rent:
Rent this article for
Access full text Article
/content/aip/journal/bmf/7/6/10.1063/1.4833257
1.
1. G. Felsenfeld and M. Groudine, “ Controlling the double helix,” Nature 421(6921), 448453 (2003).
http://dx.doi.org/10.1038/nature01411
2.
2. K. Luger, A. W. Mäder, R. K. Richmond, D. F. Sargent, and T. J. Richmond, “ Crystal structure of the nucleosome core particle at 2.8 A resolution,” Nature 389(6648), 251260 (1997).
http://dx.doi.org/10.1038/38444
3.
3. T. Kouzarides, “ Chromatin modifications and their function,” Cell 128(4), 693705 (2007).
http://dx.doi.org/10.1016/j.cell.2007.02.005
4.
4. J. D. McGhee and G. Felsenfeld, “ Nucleosome structure,” Annu Rev Biochem. 49, 11151156 (1980).
http://dx.doi.org/10.1146/annurev.bi.49.070180.005343
5.
5. A. P. Wolffe, Chromatin: Structure and Function, 3rd ed. (Academic Press, Waltham, MA, 1999).
6.
6. B. D. Strahl and C. D. Allis, “ The language of covalent histone modifications,” Nature 403(6765), 4145 (2000).
http://dx.doi.org/10.1038/47412
7.
7. P. Collas, “ The current state of chromatin immunoprecipitation,” Mol Biotechnol. 45(1), 87100 (2010).
http://dx.doi.org/10.1007/s12033-009-9239-8
8.
8. B. R. Cipriany, R. Zhao, P. J. Murphy, S. L. Levy, C. P. Tan, H. G. Craighead, and P. D. Soloway, “ Single molecule epigenetic analysis in a nanofluidic channel,” Anal. Chem. 82(6), 24802487 (2010).
http://dx.doi.org/10.1021/ac9028642
9.
9. P. J. Murphy, B. R. Cipriany, C. B. Wallin, C. Y. Ju, K. Szeto, J. A. Hagarman, J. J. Benitez, H. G. Craighead, and P. D. Soloway, “ Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells,” Proc. Natl. Acad. Sci. U. S. A. 110(19), 77727777 (2013).
http://dx.doi.org/10.1073/pnas.1218495110
10.
10. P. Lichter, C. J. Tang, K. Call, G. Hermanson, G. A. Evans, D. Housman, and D. C. Ward, “ High-resolution mapping of human chromosome 11 by in situ hybridization with cosmid clones,” Science 247(4938), 6469 (1990).
http://dx.doi.org/10.1126/science.2294592
11.
11. H. H. Q. Heng, J. Squire, and L. C. Tsui, “ High-resolution mapping of mammalian genes by in situ hybridization to free chromatin,” Proc. Natl. Acad. Sci. U. S. A. 89(20), 95099513 (1992).
http://dx.doi.org/10.1073/pnas.89.20.9509
12.
12. M. D. Blower, B. A. Sullivan, and G. H. Karpen, “ Conserved organization of centromeric chromatin in flies and humans,” Dev. Cell 2(3), 319330 (2002).
http://dx.doi.org/10.1016/S1534-5807(02)00135-1
13.
13. S. M. Cohen, P. D. Chastain, M. Cordeiro-Stone, and D. G. Kaufman, “ DNA replication and the GINS complex: Localization on extended chromatin fibers,” Epigenetics Chromatin 2(1), 6 (2009).
http://dx.doi.org/10.1186/1756-8935-2-6
14.
14. J. O. Tegenfeldt, C. Prinz, H. Cao, S. Chou, W. W. Reisner, R. Riehn, Y. M. Wang, E. C. Cox, J. C. Sturm, P. Silberzan, and R. H. Austin, “ The dynamics of genomic-length DNA molecules in 100-nm channels,” Proc. Natl. Acad. Sci. U.S.A. 101(30), 1097910983 (2004).
http://dx.doi.org/10.1073/pnas.0403849101
15.
15. W. Reisner, K. J. Morton, R. Riehn, Y. M. Wang, Z. N. Yu, M. Rosen, J. C. Sturm, S. Y. Chou, E. Frey, and R. H. Austin, “ Statics and dynamics of single DNA molecules confined in nanochannels,” Phys. Rev. Lett. 94(19), 196101 (2005).
http://dx.doi.org/10.1103/PhysRevLett.94.196101
16.
16. J. H. Carpenter, A. Karpusenko, J. Pan, S. F. Lim, and R. Riehn, “ Density fluctuations dispersion relationship for a polymer confined to a nanotube,” Appl. Phys. Lett. 98(25), 253704 (2011).
http://dx.doi.org/10.1063/1.3602922
17.
17. A. Karpusenko, J. H. Carpenter, C. Zhou, S. F. Lim, J. Pan, and R. Riehn, “ Fluctuation modes of nanoconfined DNA,” J. Appl. Phys.111(2), 24701247018 (2012).
http://dx.doi.org/10.1063/1.3675207
18.
18. D. E. Streng, S. F. Lim, J. H. Pan, A. Karpusenka, and R. Riehn, “ Stretching chromatin through confinement,” Lab Chip 9(19), 27722774 (2009).
http://dx.doi.org/10.1039/b909217j
19.
19. Y. M. Wang, J. O. Tegenfeldt, W. Reisner, R. Riehn, X. J. Guan, L. Guo, I. Golding, E. C. Cox, J. Sturm, and R. H. Austin, “ Single-molecule studies of repressor-DNA interactions show long-range interactions,” Proc. Natl. Acad. Sci. U.S.A. 102(28), 97969801 (2005).
http://dx.doi.org/10.1073/pnas.0502917102
20.
20. S. F. Lim, A. Karpusenko, J. J. Sakon, J. A. Hook, T. A. Lamar, and R. Riehn, “ DNA methylation profiling in nanochannels,” Biomicrofluidics 5(3), 034106 (2011).
http://dx.doi.org/10.1063/1.3613671
21.
21. T. Matsuoka, B. C. Kim, J. Huang, N. J. Douville, M. D. Thouless, and S. Takayama, “ Nanoscale squeezing in elastomeric nanochannels for single chromatin linearization,” Nano Lett. 12(12), 64806484 (2012).
http://dx.doi.org/10.1021/nl304063f
22.
22. R. Riehn, W. Reisner, J. O. Tegenfeldt, Y. M. Wang, C.-K. Tung, S. F. Lim, E. C. Cox, J. Sturm, and R. H. Austin, “ Nanochannels for genomic DNA analysis: The long and short of it,” in Integrated Biochips for DNA Analysis, 1st ed., edited by R. H. Liu and A. P. Lee (Landes Bioscience, Austin, Texas, 2007), pp. 151186.
23.
23. W. Reisner, N. B. Larsen, A. Silahtaroglu, A. Kristensen, N. Tommerup, J. O. Tegenfeldt, and H. Flyvbjerg, “ Single-molecule denaturation mapping of DNA in nanofluidic channels,” Proc. Natl. Acad. Sci. 107(30), 1329413299 (2010).
http://dx.doi.org/10.1073/pnas.1007081107
24.
24. P. G. De Gennes, Scaling Concepts in Polymer Physics (Cornell University Press, Ithaca, NY, 1979).
25.
25. N. T. Crump, C. A. Hazzalin, E. M. Bowers, R. M. Alani, P. A. Cole, and L. C. Mahadevan, “ Dynamic acetylation of all lysine-4 trimethylated histone H3 is evolutionarily conserved and mediated by p300/CBP,” Proc. Natl. Acad. Sci. U.S.A. 108(19), 78147819 (2011).
http://dx.doi.org/10.1073/pnas.1100099108
http://aip.metastore.ingenta.com/content/aip/journal/bmf/7/6/10.1063/1.4833257
Loading
/content/aip/journal/bmf/7/6/10.1063/1.4833257
Loading

Data & Media loading...

Loading

Article metrics loading...

/content/aip/journal/bmf/7/6/10.1063/1.4833257
2013-11-21
2014-08-22

Abstract

We report the simultaneous mapping of multiple histone tail modifications on chromatin that has been confined to nanofluidic channels. In these channels, chromatin is elongated, and histone modification can be detected using fluorescently tagged monoclonal antibodies. Using reconstituted chromatin with three distinct histone sources and two histone tail modification probes (H3K4me3 and H3K9ac), we were able to distinguish chromatin from the different sources. Determined ratios of the two modifications were consistent with the bulk composition of histone mixtures. We determined that the major difficulty in transitioning the mapping method to site-specific profiling within single genomic molecules is the interference of naturally aggregating, off-the shelf antibodies with the internal structure of chromatin.

Loading

Full text loading...

/deliver/fulltext/aip/journal/bmf/7/6/1.4833257.html;jsessionid=3t0rl7gt2rxgb.x-aip-live-06?itemId=/content/aip/journal/bmf/7/6/10.1063/1.4833257&mimeType=html&fmt=ahah&containerItemId=content/aip/journal/bmf

Most read this month

Article
content/aip/journal/bmf
Journal
5
3
Loading

Most cited this month

true
true
This is a required field
Please enter a valid email address
This feature is disabled while Scitation upgrades its access control system.
This feature is disabled while Scitation upgrades its access control system.
752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Chromatin modification mapping in nanochannels
http://aip.metastore.ingenta.com/content/aip/journal/bmf/7/6/10.1063/1.4833257
10.1063/1.4833257
SEARCH_EXPAND_ITEM