Genome function and nuclear architecture: from gene expression to nanoscience.

Biophysical, chemical, and nanoscience approaches to the study of nuclear structure and activity have been developing recently and hold considerable promise. A selection of fundamental problems in genome organization and function are reviewed and discussed in the context of these new perspectives and approaches. Advancing these concepts will require coordinated networks of physicists, chemists, and materials scientists collaborating with cell, developmental, and genome biologists.

[1]  R. van Driel,et al.  Ultrastructural analysis of transcription and splicing in the cell nucleus after bromo-UTP microinjection. , 1999, Molecular biology of the cell.

[2]  Robert H Singer,et al.  Single-Cell Gene Expression Profiling , 2002, Science.

[3]  T. Misteli The concept of self-organization in cellular architecture , 2001, The Journal of cell biology.

[4]  G. Sudlow,et al.  Large-Scale Chromatin Unfolding and Remodeling Induced by VP16 Acidic Activation Domain , 1999, The Journal of cell biology.

[5]  D. Balding,et al.  HLA Sequence Polymorphism and the Origin of Humans , 2006 .

[6]  H. Willard Artificial Chromosomes Coming to Life , 2000, Science.

[7]  Steven P. Gygi,et al.  Comprehensive proteomic analysis of the human spliceosome , 2002, Nature.

[8]  Denis Hochstrasser,et al.  Functional proteomic analysis of human nucleolus. , 2002, Molecular biology of the cell.

[9]  P. Stankiewicz,et al.  Genome architecture, rearrangements and genomic disorders. , 2002, Trends in genetics : TIG.

[10]  T. Pederson,et al.  Fluorescent RNA cytochemistry: tracking gene transcripts in living cells. , 2001, Nucleic acids research.

[11]  Kathy Chen,et al.  Network dynamics and cell physiology , 2001, Nature Reviews Molecular Cell Biology.

[12]  D L Spector,et al.  Nuclear domains. , 2001, Journal of cell science.

[13]  S. Simon,et al.  Tracking single proteins within cells. , 2000, Biophysical journal.

[14]  L. Hood,et al.  A Genomic Regulatory Network for Development , 2002, Science.

[15]  A. Murray,et al.  Interphase chromosomes undergo constrained diffusional motion in living cells , 1997, Current Biology.

[16]  J M Anderson,et al.  Protein-mediated macrophage adhesion and activation on biomaterials: a model for modulating cell behavior , 1999, Journal of materials science. Materials in medicine.

[17]  E. Manders,et al.  Spatial Relationship between Transcription Sites and Chromosome Territories , 1999, The Journal of cell biology.

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

[19]  R. Hardison Conserved noncoding sequences are reliable guides to regulatory elements. , 2000, Trends in genetics : TIG.

[20]  D. Mccormick Sequence the Human Genome , 1986, Bio/Technology.

[21]  J. Kirz,et al.  Soft X-ray microscopes and their biological applications , 1995, Quarterly Reviews of Biophysics.

[22]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[23]  F. Pinaud,et al.  Ultrahigh-resolution multicolor colocalization of single fluorescent probes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[24]  T. Cremer,et al.  Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[25]  S. Weiss Fluorescence spectroscopy of single biomolecules. , 1999, Science.

[26]  Wendy A. Bickmore,et al.  Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH , 2002, The Journal of cell biology.

[27]  Nancy A. Jenkins,et al.  Recombineering: a powerful new tool for mouse functional genomics , 2001, Nature Reviews Genetics.

[28]  Hans Lehrach,et al.  Functional Annotation of Mouse Genome Sequences , 2001, Science.

[29]  A. Pombo,et al.  Genomics meets nanoscience: probing genes and the cell nucleus at 10-9 meters , 2002, Genome Biology.

[30]  T. Pederson Dynamics and genome-centricity of interchromatin domains in the nucleus , 2002, Nature Cell Biology.

[31]  E. Sackmann,et al.  Gold Plating and Biofunctionalization of Ferromagnetic Magnetic Tweezers: Application for Local Studies of Soft Surface-Grafted Polymer Films , 2001 .

[32]  T. Maniatis,et al.  An extensive network of coupling among gene expression machines , 2002, Nature.

[33]  F. Baas,et al.  The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains , 2001, Science.

[34]  J. Politz,et al.  Review: movement of mRNA from transcription site to nuclear pores. , 2000, Journal of structural biology.

[35]  E. Sackmann,et al.  Measurement of local viscoelasticity and forces in living cells by magnetic tweezers. , 1999, Biophysical journal.

[36]  S. Berger,et al.  Chromatin goes global. , 2001, Molecular cell.

[37]  Juri Rappsilber,et al.  Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex , 1998, Nature Genetics.

[38]  Colin N. Dewey,et al.  Initial sequencing and comparative analysis of the mouse genome. , 2002 .

[39]  J. Lucchesi,et al.  X-ray microscopic studies of the Drosophila dosage compensation complex. , 2000, Journal of structural biology.

[40]  B. Niemann,et al.  Zone-plate X-ray microscopy , 1980, Quarterly Reviews of Biophysics.

[41]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

[42]  M. Mann,et al.  Directed Proteomic Analysis of the Human Nucleolus , 2002, Current Biology.

[43]  Thomas Ried,et al.  Multicolour spectral karyotyping of mouse chromosomes , 1996, Nature Genetics.

[44]  B. Turner,et al.  Cellular Memory and the Histone Code , 2002, Cell.

[45]  A. Bradley,et al.  From mouse to man: generating megabase chromosome rearrangements. , 2001, Trends in genetics : TIG.

[46]  J. Onuchic,et al.  Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse , 2002, Proceedings of the National Academy of Sciences of the United States of America.

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

[48]  H. Kimura,et al.  Specialized transcription factories within mammalian nuclei. , 2000, Critical reviews in eukaryotic gene expression.

[49]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[50]  P. Wolynes,et al.  The middle way. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Cameron S. Osborne,et al.  Long-range chromatin regulatory interactions in vivo , 2002, Nature Genetics.

[52]  S. Hell,et al.  Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[53]  A. West,et al.  Insulators and boundaries: versatile regulatory elements in the eukaryotic genome. , 2001, Science.

[54]  Michael Levine,et al.  Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[55]  S. Gasser,et al.  Visualizing Chromatin Dynamics in Interphase Nuclei , 2002, Science.

[56]  T. Kues,et al.  Visualization and tracking of single protein molecules in the cell nucleus. , 2001, Biophysical journal.

[57]  B. Niemann,et al.  Computed tomography of cryogenic biological specimens based on X-ray microscopic images. , 2000, Ultramicroscopy.

[58]  Tatjana Singer,et al.  Genetic Networks , 2005, Plant Physiology.

[59]  T. Pederson,et al.  Protein Mobility within the Nucleus—What Are the Right Moves? , 2001, Cell.

[60]  M H Meisler Evolutionarily conserved noncoding DNA in the human genome: how much and what for? , 2001, Genome research.

[61]  John W. Sedat,et al.  Multiple regimes of constrained chromosome motion are regulated in the interphase Drosophila nucleus , 2001, Current Biology.

[62]  G. Schneider,et al.  Cryo X-ray microscopy with high spatial resolution in amplitude and phase contrast. , 1998, Ultramicroscopy.

[63]  Michael Litt,et al.  The insulation of genes from external enhancers and silencing chromatin , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[64]  S. Dimitrov,et al.  Higher-order structure of chromatin and chromosomes. , 2001, Current opinion in genetics & development.

[65]  Christoph Cremer,et al.  Spatially modulated illumination microscopy allows axial distance resolution in the nanometer range. , 2002, Applied optics.

[66]  Martin J. Lercher,et al.  Clustering of housekeeping genes provides a unified model of gene order in the human genome , 2002, Nature Genetics.

[67]  D. Spector,et al.  Visualization of gene activity in living cells , 2000, Nature Cell Biology.

[68]  T. Cremer,et al.  Chromosome territories, nuclear architecture and gene regulation in mammalian cells , 2001, Nature Reviews Genetics.

[69]  S. Schreiber,et al.  Signaling Network Model of Chromatin , 2002, Cell.

[70]  James G. McNally,et al.  Large-scale chromatin decondensation and recondensation regulated by transcription from a natural promoter , 2001, The Journal of cell biology.

[71]  Wendy A Bickmore,et al.  Chromatin Motion Is Constrained by Association with Nuclear Compartments in Human Cells , 2002, Current Biology.

[72]  C Cremer,et al.  Three‐dimensional spectral precision distance microscopy of chromatin nanostructures after triple‐colour DNA labelling: a study of the BCR region on chromosome 22 and the Philadelphia chromosome , 2000, Journal of microscopy.

[73]  U. Aebi,et al.  Actin in the nucleus: what form and what for? , 2002, Journal of structural biology.

[74]  L G Griffith,et al.  Cell adhesion and motility depend on nanoscale RGD clustering. , 2000, Journal of cell science.

[75]  W. Bickmore,et al.  Human acrocentric chromosomes with transcriptionally silent nucleolar organizer regions associate with nucleoli , 2001, The EMBO journal.

[76]  Tom Misteli,et al.  Chromosome positioning in the interphase nucleus. , 2002, Trends in cell biology.

[77]  T. Liesegang The human transcriptome map: Clustering of highly expressed genes in chromosomal domains. Caron H, ∗ van Schaik B, van der Mee M, et al. Science 2001;291:1289–1292. , 2001 .

[78]  Dirk Schübeler,et al.  Nuclear compartmentalization and gene activity , 2000, Nature Reviews Molecular Cell Biology.

[79]  Aviv Regev,et al.  Representation and Simulation of Biochemical Processes Using the pi-Calculus Process Algebra , 2000, Pacific Symposium on Biocomputing.

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

[81]  T Misteli,et al.  Functional architecture in the cell nucleus. , 2001, The Biochemical journal.

[82]  B. Nies,et al.  Selective RGD-Mediated Adhesion of Osteoblasts at Surfaces of Implants. , 1999, Angewandte Chemie.

[83]  Susan M. Gasser,et al.  Live Imaging of Telomeres yKu and Sir Proteins Define Redundant Telomere-Anchoring Pathways in Yeast , 2002, Current Biology.

[84]  Jason R. Swedlow,et al.  Cajal Body dynamics and association with chromatin are ATP-dependent , 2002, Nature Cell Biology.

[85]  J. Ragoussis,et al.  Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. , 2000, Journal of cell science.

[86]  G. Nucifora,et al.  Genetic lesions and perturbation of chromatin architecture: A road to cell transformation , 2001, Journal of cellular biochemistry.

[87]  Alexander Egner,et al.  Fast 100-nm resolution three-dimensional microscope reveals structural plasticity of mitochondria in live yeast , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[88]  H. Boyen,et al.  Ordered Deposition of Inorganic Clusters from Micellar Block Copolymer Films , 2000 .

[89]  Craig L. Peterson,et al.  Chromatin Higher Order Folding--Wrapping up Transcription , 2002, Science.

[90]  W. Fontana,et al.  Small Numbers of Big Molecules , 2002, Science.

[91]  C. S. Chen,et al.  Geometric control of cell life and death. , 1997, Science.

[92]  S. P. Fodor,et al.  Large-Scale Transcriptional Activity in Chromosomes 21 and 22 , 2002, Science.

[93]  J. Lewis,et al.  Like attracts like: getting RNA processing together in the nucleus. , 2000, Science.

[94]  Eric H Davidson,et al.  New computational approaches for analysis of cis-regulatory networks. , 2002, Developmental biology.