Nucleic Acids Research, 2003, Vol. 31, No. 12 3257-3266
© 2003 Oxford University Press
Nuclear matrix association of the human ß-globin locus utilizing a novel approach to quantitative real-time PCR
1 Department of Obstetrics and Gynecology, 2 Center for Molecular Medicine and Genetics, 3 Department of Computer Sciences and 4 Center for Scientific Computing, Wayne State University, Detroit, MI, USA and 5 Department of Molecular and Medical Genetics, University of Toronto and Developmental Biology Program, Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada
*To whom correspondence should be addressed at 253 C.S. Mott Center, 275 East Hancock, Detroit, MI 48201, USA. Tel: +1 313 577 0765; Fax: +1 313 577 8554; Email: steve{at}compbio.med.wayne.edu
The human ß-globin locus is home to five genes that are regulated in a tissue-specific and developmental stage-specific manner. While the exact mode of expression remains somewhat enigmatic, a significant effort has been focused at the locus control region (LCR). The LCR is marked by five DNase I-hypersensitive sites (HS) 
15 kb upstream of the 
-globin gene. Nuclear matrix-associated regions (MARs) organize chromatin into functional domains and at least one of the HS appears bound to the nuclear matrix. We have employed an in vivo based PCR MAR assay to investigate the role of MAR-mediated regulation of the ß-globin locus. This was facilitated with a novel reaction efficiency based quantitative real-time PCR analysis software tool, Target Analysis Quantification. Using a log-linear regression strategy, discordances were eliminated. This allowed us to reliably estimate the relative amount of initial template associated with the nuclear matrix at 15 unique regions spanning the ß-globin locus in both non-expressing and expressing cell lines. A dynamic association dependent on expression status was revealed both at the LCR/5'HS region and within the second intron of the ß-globin gene. These results provide the first evidence that nuclear matrix association dynamically mediates the looping of the ß-globin locus to achieve transcriptional control.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. K. Linnemann and S. A. Krawetz Silencing by nuclear matrix attachment distinguishes cell-type specificity: association with increased proliferation capacity Nucleic Acids Res., May 1, 2009; 37(9): 2779 - 2788. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. K. Linnemann, A. E. Platts, and S. A. Krawetz Differential nuclear scaffold/matrix attachment marks expressed genes Hum. Mol. Genet., February 15, 2009; 18(4): 645 - 654. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. P. Martins and S. A. Krawetz Decondensing the protamine domain for transcription PNAS, May 15, 2007; 104(20): 8340 - 8345. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. A. Swinburne, C. A. Meyer, X. S. Liu, P. A. Silver, and A. S. Brodsky Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription Genome Res., July 1, 2006; 16(7): 912 - 921. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Wen, S. Huang, H. Rogers, L. A. Dickinson, T. Kohwi-Shigematsu, and C. T. Noguchi SATB1 family protein expressed during early erythroid differentiation modifies globin gene expression Blood, April 15, 2005; 105(8): 3330 - 3339. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Sayegh, S. Jhunjhunwala, R. Riblet, and C. Murre Visualization of looping involving the immunoglobulin heavy-chain locus in developing B cells Genes & Dev., February 1, 2005; 19(3): 322 - 327. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. P. Martins, G. C. Ostermeier, and S. A. Krawetz Nuclear Matrix Interactions at the Human Protamine Domain: A WORKING MODEL OF POTENTIATION J. Biol. Chem., December 10, 2004; 279(50): 51862 - 51868. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. J. Namciu and R. E. K. Fournier Human Matrix Attachment Regions Are Necessary for the Establishment but Not the Maintenance of Transgene Insulation in Drosophila melanogaster Mol. Cell. Biol., December 1, 2004; 24(23): 10236 - 10245. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. H. Q. Heng, S. Goetze, C. J. Ye, G. Liu, J. B. Stevens, S. W. Bremer, S. M. Wykes, J. Bode, and S. A. Krawetz Chromatin loops are selectively anchored using scaffold/matrix-attachment regions J. Cell Sci., March 1, 2004; 117(7): 999 - 1008. [Abstract] [Full Text] [PDF]
|
|