Chromatin remodeling as a guide to transcriptional regulatory networks in mammals
- PMID: 12577302
- DOI: 10.1002/jcb.10397
Chromatin remodeling as a guide to transcriptional regulatory networks in mammals
Abstract
An important challenge of genome biology is a dissection of transcriptional regulatory networks that operate inside the nucleus during ontogeny and disease (Wyrick and Young [2002] Curr. Opin. Genet. Dev. 12:130). Limitations of existing experimental tools greatly complicate such analysis in the human genome: for example, genome-wide expression profiling of cells responding to a stimulus fails to reveal a majority of the genes involved in the functional network of responding to that stimulus [Giaver et al., 2002; Birrell et al., 2002]. This article discusses recent advances in analyzing mammalian transcriptional regulatory circuits [Nikiforov et al., 2002; Weinmann et al., 2002; Ren et al., 2000]. As evidenced by these and other data, paucity of information about the location of regulatory DNA elements in the human genome presents an obstacle to comprehensive transcription network analysis. It has been known since the late 1970s that chromatin over active regulatory DNA stretches is stably remodeled into "nuclease hypersensitive sites" [Elgin, 1988; Gross and Garrard 1988]. Massively parallel analysis of such remodeling in cell nuclei identifies regulatory DNA that is difficult to map comprehensively using other approaches, reveals genes poised for rapid activation, and offers a novel perspective on the "epigenome"--the regulatory program being executed by the genome in a given cell type.
Copyright 2003 Wiley-Liss, Inc.
Similar articles
-
Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data.BMC Bioinformatics. 2006 Jul 4;7:330. doi: 10.1186/1471-2105-7-330. BMC Bioinformatics. 2006. PMID: 16817975 Free PMC article.
-
Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors.Methods Enzymol. 2004;376:304-15. doi: 10.1016/S0076-6879(03)76020-0. Methods Enzymol. 2004. PMID: 14975314 Review. No abstract available.
-
The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding.Curr Opin Cell Biol. 2006 Jun;18(3):291-8. doi: 10.1016/j.ceb.2006.04.002. Epub 2006 May 2. Curr Opin Cell Biol. 2006. PMID: 16647254 Review.
-
Generation of p53 target database via integration of microarray and global p53 DNA-binding site analysis.Methods Mol Biol. 2004;281:33-54. doi: 10.1385/1-59259-811-0:033. Methods Mol Biol. 2004. PMID: 15220520
-
Mapping of genetic and epigenetic regulatory networks using microarrays.Nat Genet. 2005 Jun;37 Suppl:S18-24. doi: 10.1038/ng1559. Nat Genet. 2005. PMID: 15920525 Review.
Cited by
-
A capsid-modified helper-dependent adenovirus vector containing the beta-globin locus control region displays a nonrandom integration pattern and allows stable, erythroid-specific gene expression.J Virol. 2005 Sep;79(17):10999-1013. doi: 10.1128/JVI.79.17.10999-11013.2005. J Virol. 2005. PMID: 16103151 Free PMC article.
-
The emerging role of fibroblast-like synoviocytes-mediated synovitis in osteoarthritis: An update.J Cell Mol Med. 2020 Sep;24(17):9518-9532. doi: 10.1111/jcmm.15669. Epub 2020 Jul 19. J Cell Mol Med. 2020. PMID: 32686306 Free PMC article. Review.
-
Comparative analysis of the myoglobin gene in whales and humans reveals evolutionary changes in regulatory elements and expression levels.PLoS One. 2023 Aug 29;18(8):e0284834. doi: 10.1371/journal.pone.0284834. eCollection 2023. PLoS One. 2023. PMID: 37643191 Free PMC article.
-
An integrated encyclopedia of DNA elements in the human genome.Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247. Nature. 2012. PMID: 22955616 Free PMC article.
-
Long-range DNase I hypersensitivity mapping reveals the imprinted Igf2r and Air promoters share cis-regulatory elements.Genome Res. 2005 Oct;15(10):1379-87. doi: 10.1101/gr.3783805. Genome Res. 2005. PMID: 16204191 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Research Materials
