Elucidating chromatin and nuclear domain architecture with electron spectroscopic imaging

Electron microscopy has been the ‘gold standard’ of spatial resolution for studying the structure of the cell nucleus. Electron spectroscopic imaging (ESI) offers advantages over conventional transmission electron microscopy by eliminating the need for heavy-atom contrast agents. ESI also provides mass-dependent and element-specific information at high resolution, permitting the distinguishing of structures that are primarily composed of protein, DNA, or RNA. The technique can be applied to understand the structural consequences of epigenetic modifications, such as modified histones, on chromatin fiber morphology. ESI can also be applied to elucidate the multifunctional behavior of subnuclear ‘organelles’ such as the nucleolus and promyelocytic leukemia nuclear bodies.

[1]  G. Dellaire,et al.  Organization of chromatin in the interphase mammalian cell. , 2005, Micron.

[2]  G. Schroth,et al.  Protein and DNA requirements for the transcription factor IIIA-induced distortion of the 5 S rRNA gene promoter. , 1996, Journal of molecular biology.

[3]  François-Michel Boisvert,et al.  Promyelocytic Leukemia (Pml) Nuclear Bodies Are Protein Structures That Do Not Accumulate RNA , 2000, The Journal of cell biology.

[4]  G. Dellaire,et al.  Chromatin Contributes to Structural Integrity of Promyelocytic Leukemia Bodies through a SUMO-1-independent Mechanism* , 2004, Journal of Biological Chemistry.

[5]  T. Maniatis,et al.  Factor required for mammalian spliceosome assembly is localized to discrete regions in the nucleus , 1990, Nature.

[6]  Paul S. Freemont,et al.  Promyelocytic leukemia nuclear bodies associate with transcriptionally active genomic regions , 2004, The Journal of cell biology.

[7]  Joe S. Mymryk,et al.  Size, position and dynamic behavior of PML nuclear bodies following cell stress as a paradigm for supramolecular trafficking and assembly , 2003, Journal of Cell Science.

[8]  M. Thiry Differential location of nucleic acids within interchromatin granule clusters. , 1993, European journal of cell biology.

[9]  F. Boisvert,et al.  Direct visualization of a protein nuclear architecture. , 1999, Molecular biology of the cell.

[10]  D. Bazett-Jones,et al.  Short-range DNA looping by the Xenopus HMG-box transcription factor, xUBF. , 1994, Science.

[11]  D. Bazett-Jones,et al.  Organization of highly acetylated chromatin around sites of heterogeneous nuclear RNA accumulation. , 1998, Molecular biology of the cell.

[12]  J. Politz,et al.  The Nucleolus and the Four Ribonucleoproteins of Translation , 2000, The Journal of cell biology.

[13]  Graham Dellaire,et al.  PML nuclear bodies: dynamic sensors of DNA damage and cellular stress , 2004, BioEssays : news and reviews in molecular, cellular and developmental biology.

[14]  W. Bickmore,et al.  The spatial relationship of human chromosomes within the nuclei of normal and emerin-mutant cells , 2001 .

[15]  D. Bazett-Jones,et al.  DNA looping in the RNA polymerase I enhancesome is the result of non-cooperative in-phase bending by two UBF molecules. , 2001, Nucleic acids research.

[16]  J. Mcneil,et al.  Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains , 2003, The Journal of cell biology.

[17]  R. Eils,et al.  Three-Dimensional Maps of All Chromosomes in Human Male Fibroblast Nuclei and Prometaphase Rosettes , 2005, PLoS biology.

[18]  Angus I Lamond,et al.  The dynamics of the nucleolus. , 2003, Critical reviews in eukaryotic gene expression.

[19]  I. Koprowska,et al.  A cytopathologic study of tobacco tar-induced lesions of uterine cervix of mouse. , 1959, Journal of the National Cancer Institute.

[20]  Mark Groudine,et al.  Gene Order and Dynamic Domains , 2004, Science.

[21]  H. Leonhardt,et al.  Probing Intranuclear Environments at the Single-Molecule Level , 2007, Biophysical journal.

[22]  D. Bazett-Jones,et al.  Visualization and analysis of unfolded nucleosomes associated with transcribing chromatin. , 1996, Nucleic acids research.

[23]  G. Dellaire,et al.  Beyond Repair Foci: Subnuclear Domains and the Cellular Response to DNA Damage , 2007, Cell Cycle.

[24]  G. Dellaire,et al.  Correlative light and electron spectroscopic imaging of chromatin in situ. , 2004, Methods in enzymology.

[25]  Kojima Structure and function , 2005 .

[26]  D. Bazett-Jones,et al.  Stoichiometric analysis of protein- and nucleic acid-based structures in the cell nucleus. , 1999, Micron.

[27]  W. Bickmore,et al.  Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. , 2004, Genes & development.

[28]  D. Bazett-Jones,et al.  Electron spectroscopic imaging of chromatin. , 1999, Methods.

[29]  A. F. Neuwald,et al.  Purification and biochemical characterization of interchromatin granule clusters , 1999, The EMBO journal.

[30]  R. Bristow,et al.  Promyelocytic leukemia nuclear bodies behave as DNA damage sensors whose response to DNA double-strand breaks is regulated by NBS1 and the kinases ATM, Chk2, and ATR , 2006, The Journal of cell biology.

[31]  T Misteli,et al.  Protein dynamics: implications for nuclear architecture and gene expression. , 2001, Science.

[32]  Graham Dellaire,et al.  Application of Quantum Dots as Probes for Correlative Fluorescence, Conventional, and Energy-filtered Transmission Electron Microscopy , 2004, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[33]  A. Hollaender International symposium on the nucleolus--its structure and function. Introduction. , 1966, National Cancer Institute monograph.

[34]  K. Kimura,et al.  Efficient supercoiling of DNA by a single condensin complex as revealed by electron spectroscopic imaging. , 2002, Molecular cell.

[35]  J. Politz,et al.  A nonribosomal landscape in the nucleolus revealed by the stem cell protein nucleostemin. , 2005, Molecular biology of the cell.

[36]  Cameron S. Osborne,et al.  Active genes dynamically colocalize to shared sites of ongoing transcription , 2004, Nature Genetics.

[37]  D. Bazett-Jones,et al.  Same Serial Section Correlative Light and Energy-filtered Transmission Electron Microscopy , 2003, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.