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Title: SATB1 regulates SPARC expression in K562 cell line through binding to a specific sequence in the third intron

Abstract

Special AT-rich binding protein 1 (SATB1), a cell type-specific nuclear matrix attachment region (MAR) DNA-binding protein, tethers to a specific DNA sequence and regulates gene expression through chromatin remodeling and HDAC (histone deacetylase complex) recruitment. In this study, a SATB1 eukaryotic expression plasmid was transfected into the human erythroleukemia K562 cell line and individual clones that stably over-expressed the SATB1 protein were isolated. Microarray analysis revealed that hundreds of genes were either up- or down-regulated in the SATB1 over-expressing K562 cell lines. One of these was the extra-cellular matrix glycoprotein, SPARC (human secreted protein acidic and rich in cysteine). siRNA knock-down of SATB1 also reduced SPARC expression, which was consistent with elevated SPARC levels in the SATB1 over-expressing cell line. Bioinformatics software Mat-inspector showed that a 17 bp DNA sequence in the third intron of SPARC possessed a high potential for SATB1 binding; a finding confirmed by Chromatin immunoprecipitation (ChIP) with anti-SATB1 antibody. Our results show for the first time that forced-expression of SATB1 in K562 cells triggers SPARC up-regulation by binding to a 17 bp DNA sequence in the third intron.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2]
  1. Department of Biochemistry and Molecular Biology, Medical School of Shanghai Jiao Tong University, 280 Chongqing Road(S), Shanghai 200025 (China)
  2. Department of Biochemistry and Molecular Biology, Medical School of Shanghai Jiao Tong University, 280 Chongqing Road(S), Shanghai 200025 (China). E-mail: jianlu@shsmu.edu.cn
Publication Date:
OSTI Identifier:
20991311
Resource Type:
Journal Article
Resource Relation:
Journal Name: Biochemical and Biophysical Research Communications; Journal Volume: 356; Journal Issue: 1; Other Information: DOI: 10.1016/j.bbrc.2007.01.201; PII: S0006-291X(07)00017-4; Copyright (c) 2007 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; ANTIBODIES; CHROMATIN; COMPLEXES; COMPUTER CODES; CYSTEINE; DNA; DNA SEQUENCING; GENE REGULATION; GLYCOPROTEINS; NUCLEAR MATRIX

Citation Formats

Li, K., Cai, R., Dai, B.B., Zhang, X.Q., Wang, H.J., Ge, S.F., Xu, W.R., and Lu, J. SATB1 regulates SPARC expression in K562 cell line through binding to a specific sequence in the third intron. United States: N. p., 2007. Web. doi:10.1016/j.bbrc.2007.01.201.
Li, K., Cai, R., Dai, B.B., Zhang, X.Q., Wang, H.J., Ge, S.F., Xu, W.R., & Lu, J. SATB1 regulates SPARC expression in K562 cell line through binding to a specific sequence in the third intron. United States. doi:10.1016/j.bbrc.2007.01.201.
Li, K., Cai, R., Dai, B.B., Zhang, X.Q., Wang, H.J., Ge, S.F., Xu, W.R., and Lu, J. Fri . "SATB1 regulates SPARC expression in K562 cell line through binding to a specific sequence in the third intron". United States. doi:10.1016/j.bbrc.2007.01.201.
@article{osti_20991311,
title = {SATB1 regulates SPARC expression in K562 cell line through binding to a specific sequence in the third intron},
author = {Li, K. and Cai, R. and Dai, B.B. and Zhang, X.Q. and Wang, H.J. and Ge, S.F. and Xu, W.R. and Lu, J.},
abstractNote = {Special AT-rich binding protein 1 (SATB1), a cell type-specific nuclear matrix attachment region (MAR) DNA-binding protein, tethers to a specific DNA sequence and regulates gene expression through chromatin remodeling and HDAC (histone deacetylase complex) recruitment. In this study, a SATB1 eukaryotic expression plasmid was transfected into the human erythroleukemia K562 cell line and individual clones that stably over-expressed the SATB1 protein were isolated. Microarray analysis revealed that hundreds of genes were either up- or down-regulated in the SATB1 over-expressing K562 cell lines. One of these was the extra-cellular matrix glycoprotein, SPARC (human secreted protein acidic and rich in cysteine). siRNA knock-down of SATB1 also reduced SPARC expression, which was consistent with elevated SPARC levels in the SATB1 over-expressing cell line. Bioinformatics software Mat-inspector showed that a 17 bp DNA sequence in the third intron of SPARC possessed a high potential for SATB1 binding; a finding confirmed by Chromatin immunoprecipitation (ChIP) with anti-SATB1 antibody. Our results show for the first time that forced-expression of SATB1 in K562 cells triggers SPARC up-regulation by binding to a 17 bp DNA sequence in the third intron.},
doi = {10.1016/j.bbrc.2007.01.201},
journal = {Biochemical and Biophysical Research Communications},
number = 1,
volume = 356,
place = {United States},
year = {Fri Apr 27 00:00:00 EDT 2007},
month = {Fri Apr 27 00:00:00 EDT 2007}
}
  • The control of expression of the Drosophila melanogaster tropomyosin I (TmI) gene has been investigated by P-element transformation and rescue of the flightless TmI mutant strain, Ifm(3)3. To localize cis-acting DNA sequences that control TmI gene expression, Ifm(3)3 flies were transformed with P-element plasmids containing various deletions and rearrangements of the TmI gene. The effects of these mutations on TmI gene expression were studied by analyzing both the extent of rescue of the Ifm(3)3 mutant phenotypes and determining TmI RNA levels in the transformed flies by primer extension analysis. The results of this analysis indicate that a region located withinmore » intron 1 of the gene is necessary and sufficient for directing muscle-specific TmI expression in the adult fly. This intron region has characteristics of a muscle regulatory enhancer element that can function in conjunction with the heterologous nonmuscle hsp70 promoter to promote rescue of the mutant phenotypes and to direct expression of an hsp70-Escherichia coli lacZ reporter gene in adult muscle. The enhancer can be subdivided further into two domains of activity based on primer extension analysis of TmI mRNA levels and on the rescue of mutant phenotypes.« less
  • SATB1 is expressed primarily in thymocytes and can act as a transcriptional repressor. SATB1 binds in vivo to the matrix attachment regions (MARs) of DNA, which are implicated in the loop domain organization of chromatin. The role of MAR-binding proteins in specific cell lineages is unknown. We generated SATB1-null mice to determine how SATB1 functions in the T-cell lineage. SATB1-null mice are small in size, have disproportionately small thymi and spleens, and die at 3 weeks of age. At the cellular level, multiple defects in T-cell development were observed. Immature CD3-CD4-CD8 triple negative (TN) thymocytes were greatly reduced in number,more » and thymocyte development was blocked mainly at the DP stage. The few peripheral CD4{sup +} single positive (SP) cells underwent apoptosis and failed to proliferate in response to activating stimuli. At the molecular level, among 589 genes examined, at least 2% of genes including a proto-oncogene, cytokine receptor genes, and apoptosis-related genes were derepressed at inappropriate stages of T-cell development in SATB1-null mice. For example, IL-2R{alpha} and IL-7R{alpha} genes were ectopically transcribed in CD4{sup 4+}-CD{sup 8+} double positive (DP) thymocytes. SATB1 appears to orchestrate the temporal and spatial expression of genes during T-cell development, thereby ensuring the proper development of this lineage. Our data provide the first evidence that MAR-binding proteins can act as global regulators of cell function in specific cell lineages.« less
  • Mitogen-activated protein kinases (MAPKs) have been implicated as regulators of cellular differentiation. The biological effect of MAPK signaling in the nucleus is achieved by signal-responsive transcription factors. Here, we have investigated the connection of MAPKs, transcription factor AP-1, and {alpha}{sub 2}{beta}{sub 1} integrin expression in K562 cells undergoing differentiation along the megakaryocytic pathway. We report that three distinct MAPKs, ERK, JNK, and p38, are activated during the TPA-induced megakaryocytic differentiation. Activation of MAPK pathways is followed by acquisition of the AP-1 DNA-binding and transactivation capacities. AP-1 DNA-binding activity consists primarily of JunD, c-Fos, and Fra-1, and is accompanied with themore » increased expression and phosphorylation of these subunits. While inhibition of JNK mainly prevents expression and phosphorylation of JunD and c-Jun, inhibition of the ERK pathway suppresses both phosphorylation and expression of Jun proteins, and expression of c-Fos and Fra-1. Furthermore, only the activity of the ERK pathway is essential for the differentiation response, as determined by expression of {alpha}{sub 2}{beta}{sub 1} (CD49b) integrin. The importance of AP-1 as a mediator ERK signaling during differentiation is demonstrated by the findings that expression of c-fos siRNA and dominant negative AP-1/c-Jun{sup bZIP} downregulate the TPA- and ERK-induced expression of {alpha}{sub 2}{beta}{sub 1} integrin mRNAs and proteins. Conversely, coexpression of JunD or c-Jun and c-Fos can induce {alpha}{sub 2}{beta}{sub 1} integrin expression independently of upstream signals. Taken together, the results show that AP-1 is a nuclear target of the ERK-pathway and mediates {alpha}{sub 2}{beta}{sub 1} integrin expression during megakaryocytic differentiation of K562 cells.« less
  • The nuclear location and relocation of genes play crucial regulatory roles in gene expression. SATB1, a MAR-binding protein, has been found to regulate {beta}-like globin genes through chromatin remodeling. In this study, we generated K562 cells over-expressing wild-type or nuclear matrix targeting sequences (NMTS)-deficient SATB1 and found that like wild-type SATB1, NMTS-deficient SATB1 induces out loop of {beta}-globin cluster from its chromosome territory (CT), while it is unable to associate the cluster with the nuclear matrix as wild-type SATB1 does and had no regulatory functions to the {beta}-globin cluster. Besides, our data showed that the transacting factor occupancies and chromatinmore » modifications at {beta}-globin cluster were differentially affected by wild-type and NMTS-deficient SATB1. These results indicate that SATB1 regulates {beta}-like globin genes at the nuclear level interlaced with chromatin and DNA level, and emphasize the nuclear matrix binding activity of SATB1 to its regulatory function.« less
  • Differentiating erythroblasts execute a dynamic alternative splicing program shown here to include extensive and diverse intron retention (IR) events. Cluster analysis revealed hundreds of developmentallydynamic introns that exhibit increased IR in mature erythroblasts, and are enriched in functions related to RNA processing such as SF3B1 spliceosomal factor. Distinct, developmentally-stable IR clusters are enriched in metal-ion binding functions and include mitoferrin genes SLC25A37 and SLC25A28 that are critical for iron homeostasis. Some IR transcripts are abundant, e.g. comprising ~50% of highly-expressed SLC25A37 and SF3B1 transcripts in late erythroblasts, and thereby limiting functional mRNA levels. IR transcripts tested were predominantly nuclearlocalized. Splicemore » site strength correlated with IR among stable but not dynamic intron clusters, indicating distinct regulation of dynamically-increased IR in late erythroblasts. Retained introns were preferentially associated with alternative exons with premature termination codons (PTCs). High IR was observed in disease-causing genes including SF3B1 and the RNA binding protein FUS. Comparative studies demonstrated that the intron retention program in erythroblasts shares features with other tissues but ultimately is unique to erythropoiesis. Finally, we conclude that IR is a multi-dimensional set of processes that post-transcriptionally regulate diverse gene groups during normal erythropoiesis, misregulation of which could be responsible for human disease.« less