Genome architecture and the role of transcription

During development or in response to environmental stimuli, eukaryotic genes change both their expression and position in 3D nuclear space. Then, is a gene transcribed because of its position, or is position determined by transcription? Are genes stochastically or deterministically engaged in transcription cycles? Recent results confirm that RNA polymerases and their transcription factors play central roles in genome organization, and that stochastic events can give rise to apparently deterministic expression. As is so often the case in biology, structure both determines function and is influenced by it.

[1]  Michael D. Wilson,et al.  Species-Specific Transcription in Mice Carrying Human Chromosome 21 , 2008, Science.

[2]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[3]  D. S. Broomhead,et al.  Pulsatile Stimulation Determines Timing and Specificity of NF-κB-Dependent Transcription , 2009, Science.

[4]  T. Mikkelsen,et al.  Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites , 2007, Proceedings of the National Academy of Sciences.

[5]  Leighton J. Core,et al.  Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters , 2008, Science.

[6]  Job Dekker,et al.  Yeast Silent Mating Type Loci Form Heterochromatic Clusters through Silencer Protein-Dependent Long-Range Interactions , 2009, PLoS genetics.

[7]  Alistair N Boettiger,et al.  Synchronous and Stochastic Patterns of Gene Activation in the Drosophila Embryo , 2009, Science.

[8]  Jessica Cande,et al.  Stalled Hox promoters as chromosomal boundaries. , 2009, Genes & development.

[9]  D. Thanos,et al.  Virus Infection Induces NF-κB-Dependent Interchromosomal Associations Mediating Monoallelic IFN-β Gene Expression , 2008, Cell.

[10]  Pamela A Silver,et al.  Intron length increases oscillatory periods of gene expression in animal cells. , 2008, Genes & development.

[11]  D. Larson,et al.  Single-RNA counting reveals alternative modes of gene expression in yeast , 2008, Nature Structural &Molecular Biology.

[12]  S. Q. Xie,et al.  Poised Transcription Factories Prime Silent uPA Gene Prior to Activation , 2010, PLoS biology.

[13]  P. Fraser,et al.  Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus , 2009, Nature.

[14]  Gene W. Yeo,et al.  Divergent Transcription from Active Promoters , 2008, Science.

[15]  Jennifer A. Mitchell,et al.  Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells , 2010, Nature Genetics.

[16]  B. Jones,et al.  Global identification of yeast chromosome interactions using Genome conformation capture. , 2009, Fungal genetics and biology : FG & B.

[17]  Wendy A. Bickmore,et al.  Transcription factories: gene expression in unions? , 2009, Nature Reviews Genetics.

[18]  R. Singer,et al.  Transcriptional Pulsing of a Developmental Gene , 2006, Current Biology.

[19]  Christoforos Nikolaou,et al.  Nucleosome positioning as a determinant of exon recognition , 2009, Nature Structural &Molecular Biology.

[20]  G. Blobel,et al.  Exchange of GATA factors mediates transitions in looped chromatin organization at a developmentally regulated gene locus. , 2008, Molecular cell.

[21]  Davide Marenduzzo,et al.  Entropic organization of interphase chromosomes , 2009, The Journal of cell biology.

[22]  Leping Li,et al.  NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly. , 2008, Genes & development.

[23]  Peter R Cook,et al.  A model for all genomes: the role of transcription factories. , 2010, Journal of molecular biology.

[24]  S. Raghunayakula,et al.  Gene Looping Is Conferred by Activator-dependent Interaction of Transcription Initiation and Termination Machineries* , 2009, The Journal of Biological Chemistry.

[25]  A. Pombo,et al.  Transcription and Chromatin Organization of a Housekeeping Gene Cluster Containing an Integrated β-Globin Locus Control Region , 2008, PLoS genetics.

[26]  E. Liu,et al.  An Oestrogen Receptor α-bound Human Chromatin Interactome , 2009, Nature.

[27]  三代 剛 Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster , 2009 .

[28]  P. Cook,et al.  RNA polymerase II activity is located on the surface of protein-rich transcription factories , 2008, Journal of Cell Science.

[29]  Noah Spies,et al.  Biased chromatin signatures around polyadenylation sites and exons. , 2009, Molecular cell.

[30]  Peter R. Cook,et al.  Similar active genes cluster in specialized transcription factories , 2008, The Journal of cell biology.

[31]  A. Hoffman,et al.  Glucocorticoid Receptor Activation of the Ciz1-Lcn2 Locus by Long Range Interactions* , 2009, Journal of Biological Chemistry.

[32]  Nora Engel,et al.  Three-dimensional conformation at the H19/Igf2 locus supports a model of enhancer tracking , 2008, Human molecular genetics.

[33]  D. Bentley,et al.  RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes , 2008, Nature Structural &Molecular Biology.

[34]  D. Komura,et al.  A wave of nascent transcription on activated human genes , 2009, Proceedings of the National Academy of Sciences.

[35]  Ville Paakinaho,et al.  Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers , 2009, Nucleic acids research.

[36]  D. Spector,et al.  A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence , 2008, The Journal of cell biology.

[37]  M. Hampsey,et al.  A transcription-independent role for TFIIB in gene looping. , 2007, Molecular cell.

[38]  Helen A. Foster,et al.  The spatial repositioning of adipogenesis genes is correlated with their expression status in a porcine mesenchymal stem cell adipogenesis model system , 2009, Chromosoma.

[39]  G. Ast,et al.  Chromatin organization marks exon-intron structure , 2009, Nature Structural &Molecular Biology.

[40]  N. Proudfoot,et al.  Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex. , 2009, Genes & development.

[41]  M. Elowitz,et al.  Frequency-modulated nuclear localization bursts coordinate gene regulation , 2008, Nature.

[42]  Dimitris Thanos,et al.  Transcription factors mediate long-range enhancer–promoter interactions , 2009, Proceedings of the National Academy of Sciences.

[43]  E. Bertolino,et al.  Transcriptional repression mediated by repositioning of genes to the nuclear lamina , 2008, Nature.

[44]  D. Longo,et al.  Dynamic bookmarking of primary response genes by p300 and RNA polymerase II complexes , 2009, Proceedings of the National Academy of Sciences.

[45]  M. Sung,et al.  Sustained Oscillations of NF-κB Produce Distinct Genome Scanning and Gene Expression Profiles , 2009, PloS one.

[46]  M. Wong-Riley,et al.  Chromosome Conformation Capture of All 13 Genomic Loci in the Transcriptional Regulation of the Multisubunit Bigenomic Cytochrome c Oxidase in Neurons* , 2009, The Journal of Biological Chemistry.

[47]  M. Fornerod,et al.  Characterization of the Drosophila melanogaster genome at the nuclear lamina , 2006, Nature Genetics.

[48]  Clifford S. Deutschman,et al.  Transcription , 2003, The Quran: Word List (Volume 3).

[49]  L. Wessels,et al.  Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions , 2008, Nature.

[50]  Thomas Cremer,et al.  Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution , 2009, Cell.

[51]  Tom Misteli,et al.  The Meaning of Gene Positioning , 2008, Cell.