The Three-Dimensional Structure of Human Interphase Chromosomes Is Related to the Transcriptome Map

ABSTRACT The three-dimensional (3D) organization of the chromosomal fiber in the human interphase nucleus is an important but poorly understood aspect of gene regulation. Here we quantitatively analyze and compare the 3D structures of two types of genomic domains as defined by the human transcriptome map. While ridges are gene dense and show high expression levels, antiridges, on the other hand, are gene poor and carry genes that are expressed at low levels. We show that ridges are in general less condensed, more irregularly shaped, and located more closely to the nuclear center than antiridges. Six human cell lines that display different gene expression patterns and karyotypes share these structural parameters of chromatin. This shows that the chromatin structures of these two types of genomic domains are largely independent of tissue-specific variations in gene expression and differentiation state. Moreover, we show that there is remarkably little intermingling of chromatin from different parts of the same chromosome in a chromosome territory, neither from adjacent nor from distant parts. This suggests that the chromosomal fiber has a compact structure that sterically suppresses intermingling. Together, our results reveal novel general aspects of 3D chromosome architecture that are related to genome structure and function.

[1]  Anne E Carpenter,et al.  In Vivo HP1 Targeting Causes Large-Scale Chromatin Condensation and Enhanced Histone Lysine Methylation , 2005, Molecular and Cellular Biology.

[2]  R Berezney,et al.  Segregation of transcription and replication sites into higher order domains. , 1998, Science.

[3]  Nick Gilbert,et al.  Chromatin Architecture of the Human Genome Gene-Rich Domains Are Enriched in Open Chromatin Fibers , 2004, Cell.

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

[5]  Jordi Garcia-Fernàndez,et al.  The genesis and evolution of homeobox gene clusters , 2005, Nature Reviews Genetics.

[6]  Cameron S. Osborne,et al.  Replication and transcription: Shaping the landscape of the genome , 2005, Nature Reviews Genetics.

[7]  A. Pombo,et al.  Intermingling of Chromosome Territories in Interphase Suggests Role in Translocations and Transcription-Dependent Associations , 2006, PLoS biology.

[8]  S. Gasser,et al.  Sir-Mediated Repression Can Occur Independently of Chromosomal and Subnuclear Contexts , 2004, Cell.

[9]  Juliet A. Ellis,et al.  The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. , 2001, Human molecular genetics.

[10]  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.

[11]  Charles Kooperberg,et al.  Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing , 2002, Nature Genetics.

[12]  David Haussler,et al.  Integration of the cytogenetic map with the draft human genome sequence. , 2003, Human molecular genetics.

[13]  Ernst H. K. Stelzer,et al.  Structure and dynamics of human interphase chromosome territories in vivo , 1998, Human Genetics.

[14]  Keji Zhao,et al.  Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. , 2005, Genes & development.

[15]  B. Trask,et al.  Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus , 1995, The Journal of cell biology.

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

[17]  Angus I. Lamond,et al.  Spatial Organization of Large-Scale Chromatin Domains in the Nucleus: A Magnified View of Single Chromosome Territories , 1997, The Journal of cell biology.

[18]  W. Bickmore,et al.  Considering Nuclear Compartmentalization in the Light of Nuclear Dynamics , 2003, Cell.

[19]  Alan Tunnacliffe,et al.  Cytogenetic analysis by chromosome painting using dop‐pcr amplified flow‐sorted chromosomes , 1992, Genes, chromosomes & cancer.

[20]  Owen T McCann,et al.  Replication timing of the human genome. , 2004, Human molecular genetics.

[21]  Wendy A Bickmore,et al.  Nuclear re-organisation of the Hoxb complex during mouse embryonic development , 2005, Development.

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

[23]  J A Aten,et al.  Chromosomes as well as chromosomal subdomains constitute distinct units in interphase nuclei. , 1999, Journal of cell science.

[24]  Giorgio Bernardi,et al.  Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds. , 2002, Gene.

[25]  Matthias Merkenschlager,et al.  Association of Transcriptionally Silent Genes with Ikaros Complexes at Centromeric Heterochromatin , 1997, Cell.

[26]  M. Levi,et al.  Replicon clusters may form structurally stable complexes of chromatin and chromosomes. , 1994, Journal of cell science.

[27]  T. Elston,et al.  Stochasticity in gene expression: from theories to phenotypes , 2005, Nature Reviews Genetics.

[28]  T. Chen,et al.  Modal karyotype of human leukemia cell line, K562 (ATCC CCL 243). , 1985, Cancer genetics and cytogenetics.

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

[30]  L. Trakhtenbrot,et al.  Clonal expansion and not cell interconversion is the basis for the neuroblast and nonneuronal types of the SK-N-SH neuroblastoma cell line. , 2003, Cancer genetics and cytogenetics.

[31]  Sue Povey,et al.  Gene map of the extended human MHC , 2004, Nature Reviews Genetics.

[32]  Thomas Ried,et al.  From Silencing to Gene Expression Real-Time Analysis in Single Cells , 2004, Cell.

[33]  Joseph Rosenecker,et al.  Transcription-dependent spatial arrangements of CFTR and adjacent genes in human cell nuclei , 2004, The Journal of cell biology.

[34]  P. Dimitri,et al.  The paradox of functional heterochromatin , 2005, BioEssays : news and reviews in molecular, cellular and developmental biology.

[35]  Zlatko Trajanoski,et al.  Generic Features of Tertiary Chromatin Structure as Detected in Natural Chromosomes , 2004, Molecular and Cellular Biology.

[36]  Thomas Cremer,et al.  Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells , 2004, Chromosome Research.

[37]  N. Carter,et al.  DNA microarrays for comparative genomic hybridization based on DOP‐PCR amplification of BAC and PAC clones , 2003, Genes, chromosomes & cancer.

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

[39]  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.

[40]  Roland Eils,et al.  Topology of genes and nontranscribed sequences in human interphase nuclei. , 2004, Experimental cell research.

[41]  B. Trask,et al.  Regional differences in the compaction of chromatin in human G0/G1 interphase nuclei , 1997, Chromosome Research.

[42]  W. Bickmore,et al.  Re-modelling of nuclear architecture in quiescent and senescent human fibroblasts , 2000, Current Biology.

[43]  A. Belmont,et al.  Differential large-scale chromatin compaction and intranuclear positioning of transcribed versus non-transcribed transgene arrays containing β-globin regulatory sequences , 2004, Journal of Cell Science.

[44]  Thomas Cremer,et al.  Nuclear Organization of Mammalian Genomes , 1999, The Journal of cell biology.

[45]  D. Geerts,et al.  Domain-wide regulation of gene expression in the human genome. , 2007, Genome research.

[46]  Pamela A. Silver,et al.  Genome-Wide Localization of the Nuclear Transport Machinery Couples Transcriptional Status and Nuclear Organization , 2004, Cell.

[47]  E. Schröck,et al.  Comprehensive and definitive molecular cytogenetic characterization of HeLa cells by spectral karyotyping. , 1999, Cancer research.

[48]  D. Tranchina,et al.  Stochastic mRNA Synthesis in Mammalian Cells , 2006, PLoS biology.

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

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

[51]  M. Schwab,et al.  Conditional expression of N-myc in human neuroblastoma cells increases expression of alpha-prothymosin and ornithine decarboxylase and accelerates progression into S-phase early after mitogenic stimulation of quiescent cells. , 1996, Oncogene.

[52]  R Eils,et al.  Three-dimensional reconstruction of painted human interphase chromosomes: active and inactive X chromosome territories have similar volumes but differ in shape and surface structure , 1996, The Journal of cell biology.

[53]  Nick Gilbert,et al.  The role of chromatin structure in regulating the expression of clustered genes , 2005, Nature Reviews Genetics.

[54]  H. Bussemaker,et al.  The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. , 2003, Genome research.

[55]  N. Archidiacono,et al.  Comparative mapping of human alphoid sequences in great apes using fluorescence in situ hybridization. , 1995, Genomics.

[56]  R Eils,et al.  Compartmentalization of interphase chromosomes observed in simulation and experiment. , 1999, Journal of molecular biology.

[57]  C Roskelley,et al.  A biomarker that identifies senescent human cells in culture and in aging skin in vivo. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[58]  R. Armstrong,et al.  Nuclear organization in differentiating oligodendrocytes , 2002, Journal of Cell Science.

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

[60]  C Cremer,et al.  Organization of early and late replicating DNA in human chromosome territories. , 1999, Experimental cell research.

[61]  Carol J. Bult,et al.  Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence , 2006, The Journal of cell biology.

[62]  J. Ragoussis,et al.  Subchromosomal positioning of the epidermal differentiation complex (EDC) in keratinocyte and lymphoblast interphase nuclei. , 2002, Experimental cell research.

[63]  Roland Eils,et al.  Separate and variably shaped chromosome arm domains are disclosed by chromosome arm painting in human cell nuclei , 1998, Chromosome Research.

[64]  Thomas Cremer,et al.  Spatial preservation of nuclear chromatin architecture during three-dimensional fluorescence in situ hybridization (3D-FISH). , 2002, Experimental cell research.

[65]  A. Pardee.  G1 events and regulation of cell proliferation. , 1989, Science.

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