Features of endogenous cardiomyocyte chromatin revealed by super-resolution STED microscopy

Journal of Molecular and Cellular Cardiology

Volumn 53, Issue 4, 2012, Pages 552-558

  Mitchell Jordan, Scherise ^a   Chen, Haodong ^a   Franklin, Sarah ^a   Stefani, Enrico ^a   Bentolila, Laurent A ^b   Vondriska, Thomas M ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Cardiac hypertrophy; Chromatin; Super resolution microscopy

Indexed keywords

HISTONE H3;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ANTIBODY LABELING; ARTICLE; CELL STIMULATION; CHROMATIN; CHROMATIN STRUCTURE; CONFOCAL MICROSCOPY; CONTROLLED STUDY; GENE REARRANGEMENT; GENOME; HEART HYPERTROPHY; HEART MUSCLE CELL; IMAGE DISPLAY; IMAGE QUALITY; MAMMAL CELL; MICROSCOPY; NEWBORN; NONHUMAN; PRIORITY JOURNAL; RAT; STRUCTURE ANALYSIS; SUPER RESOLUTION STIMULATED EMISSION DEPLETION MICROSCOPY;

ANIMALS; CELL NUCLEUS; CELLS, CULTURED; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; GENE EXPRESSION; HISTONES; IMMUNOHISTOCHEMISTRY; MICROSCOPY; MYOCYTES, CARDIAC; PROTEIN STRUCTURE, TERTIARY; RATS;

EUKARYOTA; MAMMALIA;

EID: 84865568483     PISSN: 00222828     EISSN: 10958584     Source Type: Journal    
DOI: 10.1016/j.yjmcc.2012.07.009     Document Type: Article

References (30)

1. Alexander R.P., Fang G., Rozowsky J., Snyder M., Gerstein M.B. Annotating non-coding regions of the genome. Nat Rev Genet 2010, 11:559-571.
2. Raney B.J., Cline M.S., Rosenbloom K.R., Dreszer T.R., Learned K., Barber G.P., et al. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res 2011, 39:D871-D875.
3. Wang Z., Gerstein M., Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63.
4. Lieberman-Aiden E., van Berkum N.L., Williams L., Imakaev M., Ragoczy T., Telling A., et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009, 326:289-293.
5. van Steensel B., Dekker J. Genomics tools for unraveling chromosome architecture. Nat Biotechnol 2010, 28:1089-1095.
6. Bannister A.J., Zegerman P., Partridge J.F., Miska E.A., Thomas J.O., Allshire R.C., et al. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 2001, 410:120-124.
7. Lachner M., O'Carroll D., Rea S., Mechtler K., Jenuwein T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 2001, 410:116-120.
8. Nishioka K., Chuikov S., Sarma K., Erdjument-Bromage H., Allis C.D., Tempst P., et al. Set9, a novel histone H3 methyltransferase that facilitates transcription by precluding histone tail modifications required for heterochromatin formation. Genes Dev 2002, 16:479-489.
9. Strahl B.D., Ohba R., Cook R.G., Allis C.D. Methylation of histone H3 at lysine 4 is highly conserved and correlates with transcriptionally active nuclei in Tetrahymena. Proc Natl Acad Sci U S A 1999, 96:14967-14972.
10. Hell S.W. Far-field optical nanoscopy. Science 2007, 316:1153-1158.
11. Willig K.I., Kellner R.R., Medda R., Hein B., Jakobs S., Hell S.W. Nanoscale resolution in GFP-based microscopy. Nat Methods 2006, 3:721-723.
12. Rittweger E., Han K., Irvine S., Eggeling C., Hell S.W. STED microscopy reveals crystal colour centres with nanometric resolution. Nat Photonics 2009, 3:144-147.
13. Willig K.I., Rizzoli S.O., Westphal V., Jahn R., Hell S.W. STED microscopy reveals that synaptotagmin remains clustered after synaptic vesicle exocytosis. Nature 2006, 440:935-939.
14. Singh H, Lu R, Rodriguez PF, Wu Y, Bopassa JC, Stefani E, et al. Visualization and quantification of cardiac mitochondrial protein clusters with STED microscopy. Mitochondrion. 2011.
15. Engel F.B., Schebesta M., Duong M.T., Lu G., Ren S., Madwed J.B., et al. p38 MAP kinase inhibition enables proliferation of adult mammalian cardiomyocytes. Genes Dev 2005, 19:1175-1187.
16. MacLellan W.R., Garcia A., Oh H., Frenkel P., Jordan M.C., Roos K.P., et al. Overlapping roles of pocket proteins in the myocardium are unmasked by germ line deletion of p130 plus heart-specific deletion of Rb. Mol Cell Biol 2005, 25:2486-2497.
17. Franklin S, Chen H, Mitchell-Jordan SA, Ren S, Wang Y, Vondriska TM. Quantitative analysis of chromatin proteome reveals remodeling principles and identifies HMGB2 as a regulator of hypertrophic growth. Mol Cell Proteomics. 2012.
18. Iaccarino G., Dolber P.C., Lefkowitz R.J., Koch W.J. Bbeta-adrenergic receptor kinase-1 levels in catecholamine-induced myocardial hypertrophy: regulation by beta- but not alpha1-adrenergic stimulation. Hypertension 1999, 33:396-401.
19. Franklin S., Zhang M.J., Chen H., Paulsson A.K., Mitchell-Jordan S.A., Li Y., et al. Specialized compartments of cardiac nuclei exhibit distinct proteomic anatomy. Mol Cell Proteomics 2011, 10:703.
20. Wombacher R., Heidbreder M., van de Linde S., Sheetz M.P., Heilemann M., Cornish V.W., et al. Live-cell super-resolution imaging with trimethoprim conjugates. Nat Methods 2010, 7:717-719.
21. Wang W., Li G.W., Chen C., Xie X.S., Zhuang X. Chromosome organization by a nucleoid-associated protein in live bacteria. Science 2011, 333:1445-1449.
22. Bystricky K., Heun P., Gehlen L., Langowski J., Gasser S.M. Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques. Proc Natl Acad Sci U S A 2004, 101:16495-16500.
23. Horowitz-Scherer R.A., Woodcock C.L. Organization of interphase chromatin. Chromosoma 2006, 115:1-14.
24. Solovei I., Kreysing M., Lanctot C., Kosem S., Peichl L., Cremer T., et al. Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution. Cell 2009, 137:356-368.
25. McKinsey TA, Olson EN. Dual roles of histone deacetylases in the control of cardiac growth. Novartis Found Symp. 2004;259:132-41; discussion 41-5, 63-9.
26. Kaneda R., Takada S., Yamashita Y., Choi Y.L., Nonaka-Sarukawa M., Soda M., et al. Genome-wide histone methylation profile for heart failure. Genes Cells 2009, 14:69-77.
27. Mandelkern M., Elias J.G., Eden D., Crothers D.M. The dimensions of DNA in solution. J Mol Biol 1981, 152:153-161.
28. Wong H., Victor J.M., Mozziconacci J. An all-atom model of the chromatin fiber containing linker histones reveals a versatile structure tuned by the nucleosomal repeat length. PLoS One 2007, 2:e877.
29. Tremethick D.J. Higher-order structures of chromatin: the elusive 30nm fiber. Cell 2007, 128:651-654.
30. Farahani J.N., Schibler M.J., Bentolila L.A. Stimulated emission depletion (STED) microscopy: from theory to practice. Microscopy science, technology, applications and education 2010, vol. II:1539-1547. Formatex Research Center Publishing, No 4. Badajoz, Spain. A. Mendez-Vilas, J. Diaz (Eds.).