Highlighting chromosome loops in DNA-picked chromatin (DPC)

Growing evidence supports the concept that dynamic intra- and inter-chromosomal links between specific loci contribute to the creation of cell-type specific gene expression profiles. Therefore, analysis of the establishment of peculiar functional correlations between sites, also distant on linear DNA, that govern the transcriptional process appears to be of fundamental relevance. We propose here an experimental approach showing that 17β-estradiol-induced transcription associates to formation of loops between the promoter and termination regions of hormone-responsive genes. This strategy reveals as a tool to be also suitably used, in conjunction with automated techniques, for an extensive analysis of sites shared by multiple genes for induced expression.

[1]  Yu Liang,et al.  Inhibition of the histone demethylase LSD1 blocks α-herpesvirus lytic replication and reactivation from latency , 2009, Nature Medicine.

[2]  Raymond K. Auerbach,et al.  Mapping accessible chromatin regions using Sono-Seq , 2009, Proceedings of the National Academy of Sciences.

[3]  Robert E. Kingston,et al.  Purification of Proteins Associated with Specific Genomic Loci , 2009, Cell.

[4]  Xiang-Dong Fu,et al.  Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules , 2008, Proceedings of the National Academy of Sciences.

[5]  J. French,et al.  Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene , 2008, Proceedings of the National Academy of Sciences.

[6]  E. Avvedimento,et al.  DNA Oxidation as Triggered by H3K9me2 Demethylation Drives Estrogen-Induced Gene Expression , 2008, Science.

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

[8]  P. Fraser Transcriptional control thrown for a loop. , 2006, Current opinion in genetics & development.

[9]  Thomas Cremer,et al.  Chromosome territories--a functional nuclear landscape. , 2006, Current opinion in cell biology.

[10]  P. Percipalle,et al.  Molecular functions of nuclear actin in transcription , 2006, The Journal of cell biology.

[11]  Michael Hampsey,et al.  A role for the CPF 3'-end processing machinery in RNAP II-dependent gene looping. , 2005, Genes & development.

[12]  G. Puca,et al.  Modulation of RIZ gene expression is associated to estradiol control of MCF-7 breast cancer cell proliferation. , 2005, Experimental cell research.

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

[14]  D. Bentley,et al.  Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors. , 2005, Current opinion in cell biology.

[15]  Tom Misteli,et al.  Concepts in nuclear architecture , 2005, BioEssays : news and reviews in molecular, cellular and developmental biology.

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

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

[18]  Antonin Morillon,et al.  Gene loops juxtapose promoters and terminators in yeast , 2004, Nature Genetics.

[19]  Heike Brand,et al.  Estrogen Receptor-α Directs Ordered, Cyclical, and Combinatorial Recruitment of Cofactors on a Natural Target Promoter , 2003, Cell.

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

[21]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.

[22]  C. Allis,et al.  Translating the Histone Code , 2001, Science.

[23]  Myles Brown,et al.  Cofactor Dynamics and Sufficiency in Estrogen Receptor–Regulated Transcription , 2000, Cell.

[24]  P. Cook The organization of replication and transcription. , 1999, Science.

[25]  Y. Hayashizaki,et al.  Identification of the Syrian hamster cardiomyopathy gene. , 1997, Human molecular genetics.

[26]  D. Jackson,et al.  Active RNA polymerases are localized within discrete transcription "factories' in human nuclei. , 1996, Journal of cell science.

[27]  B. O’Malley,et al.  FRAP reveals that mobility of oestrogen receptor-α is ligand- and proteasome-dependent , 2000, Nature Cell Biology.

[28]  C. Vincenz,et al.  The nucleoprotein hybridization method for isolating active and inactive genes as chromatin. , 1991, Methods in cell biology.