+ All Categories
Home > Documents > All-Trans Retinoic Acid Induces Chromatin Remodeling at the Promoter of the Mouse Liver, Bone, and...

All-Trans Retinoic Acid Induces Chromatin Remodeling at the Promoter of the Mouse Liver, Bone, and...

Date post: 25-Aug-2016
Category:
Upload: an
View: 214 times
Download: 1 times
Share this document with a friend
13
All-Trans Retinoic Acid Induces Chromatin Remodeling at the Promoter of the Mouse Liver, Bone, and Kidney Alkaline Phosphatase Gene in C3H10T 1/2 Cells Yang Wan Songhai Yang Fenyong Sun Jiayi Wang Qiongyu Chen An Hong Received: 9 January 2011 / Accepted: 31 May 2011 / Published online: 22 January 2012 Ó Springer Science+Business Media, LLC 2012 Abstract The alkaline phosphatase (ALP) gene is an important marker of osteo- blast differentiation and bone formation. Although the molecular mechanisms of increased ALP expression in response to all-trans retinoic acid (ATRA) have been reported, the role of ATRA in chromatin structure changes remains unknown. Our results show that the expression of mouse liver, bone, and kidney ALP (mL/B/K- ALP) induced by ATRA in C3H10T 1/2 cells was related to the retinoic acid nuclear receptors, RARa and RARb, which are not involved in the MAPK pathway. DNase I hypersensitivity analysis revealed an inducible hypersensitive site in the mL/B/K- ALP promoter at *520 bp upstream of the transcription start site. Chromatin immunoprecipitation experiments showed a cascade of transcription cofactor recruitment events during ATRA-induced upregulation of mL/B/K-ALP. Together, our results provide a link between ATRA-induced mL/B/K-ALP gene transcription and chromatin remodeling. Keywords Osteoblast differentiation Bone formation Gene regulation Histone modifications MAPK pathway Yang Wan and Songhai Yang have contributed equally to this study. Y. Wan F. Sun Q. Chen A. Hong (&) Institute of Genetic Engineering, Key Lab for Genetic Medicine of Guangdong Province, National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou 510632, Guangdong, China e-mail: [email protected] S. Yang Shaoguan Tielu Hospital, Shaoguan 512023, Guangdong, China J. Wang Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China 123 Biochem Genet (2012) 50:495–507 DOI 10.1007/s10528-011-9494-9
Transcript

All-Trans Retinoic Acid Induces ChromatinRemodeling at the Promoter of the Mouse Liver,Bone, and Kidney Alkaline Phosphatase Genein C3H10T 1/2 Cells

Yang Wan • Songhai Yang • Fenyong Sun •

Jiayi Wang • Qiongyu Chen • An Hong

Received: 9 January 2011 / Accepted: 31 May 2011 / Published online: 22 January 2012

� Springer Science+Business Media, LLC 2012

Abstract The alkaline phosphatase (ALP) gene is an important marker of osteo-

blast differentiation and bone formation. Although the molecular mechanisms of

increased ALP expression in response to all-trans retinoic acid (ATRA) have been

reported, the role of ATRA in chromatin structure changes remains unknown. Our

results show that the expression of mouse liver, bone, and kidney ALP (mL/B/K-

ALP) induced by ATRA in C3H10T 1/2 cells was related to the retinoic acid nuclear

receptors, RARa and RARb, which are not involved in the MAPK pathway. DNase

I hypersensitivity analysis revealed an inducible hypersensitive site in the mL/B/K-

ALP promoter at *520 bp upstream of the transcription start site. Chromatin

immunoprecipitation experiments showed a cascade of transcription cofactor

recruitment events during ATRA-induced upregulation of mL/B/K-ALP. Together,

our results provide a link between ATRA-induced mL/B/K-ALP gene transcription

and chromatin remodeling.

Keywords Osteoblast differentiation � Bone formation � Gene regulation �Histone modifications � MAPK pathway

Yang Wan and Songhai Yang have contributed equally to this study.

Y. Wan � F. Sun � Q. Chen � A. Hong (&)

Institute of Genetic Engineering, Key Lab for Genetic Medicine of Guangdong Province,

National Engineering Research Center of Genetic Medicine, Jinan University,

Guangzhou 510632, Guangdong, China

e-mail: [email protected]

S. Yang

Shaoguan Tielu Hospital, Shaoguan 512023, Guangdong, China

J. Wang

Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School

of Medicine, Shanghai 200025, China

123

Biochem Genet (2012) 50:495–507

DOI 10.1007/s10528-011-9494-9

Introduction

Alkaline phosphatases (ALP) are ubiquitous membrane-anchored enzymes that

catalyze the hydrolysis of monophosphate esters (Garen and Levinthal 1960).

Human and mouse ALP genes are different. According to the selected tissues in

which the ALP gene is expressed, there are four types of ALP isozymes in

mammals, each encoded by at least one gene alone (Yan et al. 2009). In humans,

the ALP genes are the tissue-nonspecific (liver/bone/kidney, L/B/K), placental,

intestinal, and germ-cell forms; in mice they are tissue-nonspecific (L/B/K-ALP,

predominantly expressed in liver, bone, kidney, and placenta), intestinal 1, intestinal

2 (restricted to the intestine), and embryonic (expressed in the early embryo at

various stages of development) (Harris 1990; Trowsdale et al. 1990; Terao et al.

1990). The mouse liver, bone, and kidney ALP gene (mL/B/K-ALP) plays an

important role in osteoblast differentiation and bone mineralization (Kim et al.

2004) and is considered to be a marker of differentiating osteoblasts both in vivo

and in vitro.

All-trans retinoic acid (ATRA), a physiological metabolite of vitamin A, plays a

role in the regulation of osteoblast proliferation, differentiation, and function

(Orimo and Shimada 2005). After being transferred into the nucleus by cellular

retinoic acid binding protein II (CRABPII), ATRA combines with retinoic acid

receptors (RARs) to regulate transcription (Budhu and Noy 2002). C3H10T 1/2

cells are mouse fibroblast cells with self-renewal and multipotent differentiation

potentials. They are similar to adult stem cells, in that they can differentiate into

osteoblasts and chondroblasts under different induction conditions. The MAPK

signal pathway plays an important role in regulating the differentiation of C3H10T

1/2 cells into osteoblasts. In eukaryotic cells, genomic DNA is wrapped into

chromosomes; thus, gene transcription requires dynamic changes of the chromo-

some configuration to facilitate the formation of transcription complexes. Although

studies examining the molecular mechanisms of ATRA-induced ALP regulation

have been reported extensively, few studies have investigated ATRA-mediated

chromosome structure changes. To elucidate the mechanisms underlying the

upregulation of ATRA-treated mL/B/K-ALP, we examined ATRA receptors and

signal pathways, characterized the chromatin remodeling, and identified the specific

spatial arrangement of the cotranscription factors during this process.

Materials and Methods

Materials and Cell Culture

Antibodies against RNA polymerase II (sc-9001), p300 (sc-584), GCN5 (sc-20698),

Brg 1 (sc-10768), Brm (sc-28710), HDAC1 (sc-7872), HDAC2 (sc-7899), HDAC3

(sc-11417), and HDAC4 (sc-11418) were purchased from Santa Cruz Biotechnol-

ogy (Santa Cruz, CA, USA). Antibodies to diacetyl-H3 (07-593) and tetra-acetyl-H4

(06-866) were obtained from Upstate (Charlottesville, VA, USA). The RAR

agonists Ch55, RARa (AM580), RARb2 (AC55649), and RARc (CD1530) were

496 Biochem Genet (2012) 50:495–507

123

purchased from Tocris Bioscience (Bristol, UK). Cycloheximide (CHX) and ATRA

were purchased from Sigma-Aldrich (St. Louis, MO, USA). The MAPK signaling

pathway inhibitors SB600125 (JNK inhibitor), SB203580 (p38 inhibitor), and

PD98059 (ERK inhibitor) were purchased from Calbiochem (San Diego, CA, USA).

C3H10T 1/2 cell lines were purchased from American Type Culture Collection

(Manassas, VA, USA) and cultured in Dulbecco’s modified Eagle’s medium

containing 10% fetal bovine serum, supplemented with L-glutamine (2 mM),

penicillin (100 U/ml), and streptomycin (100 mg/ml).

RNA Isolation and Quantitative Reverse Transcription PCR Analysis

Total RNA was isolated from cell cultures using Trizol reagent (Invitrogen,

Carlsbad, CA, USA). Total RNA (1 lg) was used for reverse transcription with the

MMLV reverse transcriptase (Toyobo Co., Osaka, Japan). PCR reactions were

performed in triplicate with primers for mL/B/K-ALP (F, 50 CTGACTGACCCTTC

GC TCTC 30, and R, 50 TGCTTGGCCTTACCCTCAT 30) and 18S RNA (F, 50

CCTGGATACCGCAGCTAGGA 30, and R, 50 GCGGCGCAATACGAATGCCCC

30) in separate wells, and monitored using Rotor-Gene 6000 (Corbett Life Science,

Sydney, Australia). Then quantitative reverse transcription PCR (qRT-PCR) was

performed to detect the mRNA expression level of the mL/B/K-ALP gene at

different time points as indicated. Results are presented as the amount of mL/B/K-

ALP mRNA present relative to that in untreated cells, and normalized to the level of

18S RNA.

DNase I Hypersensitivity Analysis

Cells were collected by trypsin digestion and lysed with buffers. Genomic DNA was

purified by phenol/chloroform and subsequent ethanol precipitation. The nuclei and

genomic DNA were digested with increasing concentrations of DNase I (0, 1, 3,

5 U/ml) (Takara Co., Tokyo, Japan) for 10 min at 37�C. Approximately 15 lg

DNase I-treated DNA was digested with Eco47III (Takara) and subjected to

electrophoresis on a 0.8% agarose gel using 19 TBE buffer. The DNA was

transferred to a nylon membrane. Southern blot assay probes were generated by

PCR using these primers: forward, 50 CACCCACCTCTACCTCATTG 30, and

reverse, 50 GGCTGTCCTGGAACTCACTC 30 (?2093 to ?2958). The genomic

DNA of the C3H10T 1/2 cells was used as template; PCR products were purified

and labeled using 32P.

Chromatin Immunoprecipitation Assays

Assays were performed according to the manufacturer’s instructions. A total of

2 9 106 cells was fixed with 1% formaldehyde, washed with cold phosphate-

buffered saline, and lysed in buffer. Nuclei were sonicated to shear DNA

(100–1,000 bp), and the lysates were pelleted and precleared. After immunopre-

cipitation with 3 lg antibody overnight, the protein–DNA-antibody complexes were

incubated with protein A beads (Invitrogen) and then washed with buffers. The

Biochem Genet (2012) 50:495–507 497

123

protein–DNA complexes were eluted in 1% SDS ? 0.1 M NaHCO3, and

crosslinking was reversed at 65�C. After protein digestion at 42�C, DNA was

purified using a DNA purification kit (Tiangen Biotech, Beijing, China). An equal

volume of ChIP DNA was subjected to real-time PCR using the primers F-50

GTAGGCAGAAAGACGCACAG 30 and R-50 TTCAGGGTGCAGCTGGCTTG 30,targeting the promoter region of -529 to -377, relative to the transcription start site

(TSS). Results are presented as the amount of antibody immunoprecipitation

relative to the untreated cells and normalized to the level of no antibody.

Results

ATRA Upregulation of mL/B/K-ALP Gene Expression

The upregulating effects of ATRA on the mL/B/K-ALP gene have been confirmed in

different cell lines by other studies (Heath et al. 1992). To detect ATRA-induced

mL/B/K-ALP gene expression in C3H10T 1/2 cells, we treated cells with 1 lM

ATRA for 0, 0.5, 1, 3, 6, 12, 24, 48, and 72 h, then RNA was extracted and qRT-

PCR was performed. The results show that the mL/B/K-ALP mRNA expression

level was upregulated in a time-dependent manner, which is similar to a previous

study by Orimo and Shimada (2005). Specifically, the changes in mL/B/K-ALPmRNA expression level were more obvious during 0–12 h than at other time points

(Fig. 1). At 1 h after ATRA treatment, mL/B/K-ALP gene expression was

approximately double that in untreated cells. The expression level continued to

increase, to 16 times that in untreated cells at 6 h and to 32 times the untreated level

at 12 h. When the cells were treated with 10 lg/ml CHX for 1 h before the

induction (Fig. 1), CHX did not affect the upregulating effects of ATRA. This result

suggests that ATRA-mediated mL/B/K-ALP gene expression does not require de

novo protein synthesis, and that the promoter is likely to be the direct target of

ATRA.

The major signaling pathway of retinoic acids is through the classic genomic

pathway of nuclear receptors (RARs). Moreover, ATRA does not bind the retinoic

acid X receptor (RXR) (Chambon 1996; Leid et al. 1992). Thus, we treated C3H10T

1/2 cells with 1 lM ATRA and 50 lM Ch55, a general agonist of RAR, to elucidate

the mechanism of ATRA-mediated mL/B/K-ALP upregulation. Transcription of mL/B/K-ALP was upregulated significantly in the presence of the RAR agonist (Fig. 1).

Moreover, treatment with ATRA together with inhibitors of the MAPK pathway

(JNK inhibitor-SB600125, p38 inhibitor-SB203580, ERK inhibitor-PD98059;

10 lM) did not affect mL/B/K-ALP upregulation (Fig. 1). These results suggest

that mL/B/K-ALP upregulation by ATRA is mediated directly by RARs and does

not involve the MAPK rapid phosphorylation pathway.

Next, C3H10T 1/2 cells were treated with 1 lM ATRA and 50 lM of the

agonists to RARa (AM580), RARb (AC55649), or RARc (CD1530) for 12 h, then

qRT-PCR was performed. RARa and RARb agonists upregulated the inducing

effects of ATRA on mL/B/K-ALP expression. The RARc agonist, however, did not

increase the ATRA-induced mL/B/K-ALP mRNA expression (Fig. 1).

498 Biochem Genet (2012) 50:495–507

123

Together, these results indicate that ATRA upregulates mL/B/K-ALP expression

directly through RARa and RARb, and that this process does not require de novo

protein synthesis and is not related to the MAPK rapid phosphorylation pathway.

ATRA-Sensitive Site Around the TSS of mL/B/K-ALP

The genomes of eukaryotic organisms are packaged into chromatin, the basic unit of

which is a nucleosome containing *147 bp of double-stranded DNA wrapped

Fig. 1 Quantitative reverse transcription PCR (qRT-PCR) analysis of the mL/B/K-ALP gene in treatedC3H10T 1/2 cells. a C3H10T 1/2 cells were treated with 1 lM ATRA for 1, 6, and 12 h. Untreated cellswere used as control. PCR was performed after RNA extraction. b Cells were treated with 10 lg/ml CHXfor 1 h before induction with ATRA for 6 h, untreated cells and cells treated with CHX only were used ascontrol. c C3H10T 1/2 cells were treated with ATRA and Ch55, or ATRA along with MAPK signalingpathway antagonists. RT-PCR products were separated by 1% agarose gel electrophoresis. d The mL/B/K-ALP expression in C3H10T 1/2 cells was investigated with the treatment of ATRA alone or thecombination of ATRA and RAR agonists. e The relative expression level of mL/B/K-ALP mRNA wasanalyzed by scanning the band intensity of samples in c and normalized to those of 18S RNA. *P \ 0.05,**P \ 0.01 versus the untreated control (a, b, and d), open triangle P \ 0.05, RAR agonists plus ATRAtreated versus the ATRA treated alone (d)

Biochem Genet (2012) 50:495–507 499

123

around an octamer of histone proteins (Khorasanizadeh 2004). It is generally

accepted that local chromatin structure affects gene transcription. We used DNase I

hypersensitivity assays to reveal regions of open chromatin around the mL/B/K-ALPgene in C3H10T 1/2 cells. The genomic fragments between -18,763 and

?4,178 bp (relative to the TSS) were analyzed. The probe was located in the

vicinity of the downstream restriction site (?2,093 and ?2,958 bp). Two bands

were obtained in ATRA-treated C3H10T 1/2 cells on Southern blots (Fig. 2). The

band of 22.9 kb represents the original Eco47III–Eco47III restriction fragment of

mL/B/K-ALP, the signal of which weakened with the increase in DNase I enzyme.

The lower band showed an increase in signal with the increase in concentration of

DNase I. It represents a single DNase hypersensitive site that was estimated to be

*4.7 kb upstream of the Eco47III site at ?4,178 bp, adjacent to the TSS of the mL/B/K-ALP promoter located at -520 bp (Fig. 2). In control experiments, increasing

DNase I concentrations did not produce any specific bands at 4.7 kb, suggesting that

Fig. 2 DNase I hypersensitive site analysis of the mL/B/K-ALP promoter region. a C3H10T 1/2 cellswere treated with or without 1 lM ATRA for 12 h. The arrowhead shows bands (about 4.7 kb) produceddue to DNase I cleavage. As a control, purified genomic DNA from C3H10T 1/2 cells was digested invitro with increasing concentrations of DNase I. b Schematic representation of the probe used to map theDNase hypersensitive sites within the mL/B/K-ALP promoter by indirect end-labeling techniques

500 Biochem Genet (2012) 50:495–507

123

the 520 bp hypersensitive site is a result of chromatin remodeling rather than DNase

I recognition.

Together, these results indicate that a new DNase I hypersensitive site was

produced in C3H10T 1/2 cells after ATRA induction, and the appearance of this site

may be related to the mL/B/K-ALP gene transcription after induction. ATRA

induction may have caused a change in the conformation of the chromatin near the

TSS, thereby exposing the previously embedded DNase I hypersensitive site.

Changes in Transcriptional Activity of mL/B/K-ALP Promoter Related

to Chromatin Remodeling and Histone Modifications

Studies have shown that transcription activation or inhibition requires not only the

binding of transcription factors at specific sites in the promoter but also the

recruitment of other protein complexes for chromosome remodeling and modifi-

cations. Chromatin can be modified in ways that affect DNA function through the

action of two main types of multiprotein complexes. The first is the adjustment of

specific histone–DNA contacts by ATP-dependent nucleosome remodeling enzymes

(Lusser and Kadonaga 2003). The second is the post-translational covalent

modification of histones through the addition or removal of phosphoryl, methyl,

or acetyl groups, among other covalent modifications (Lo et al. 2004). To

understand ATRA-induced chromatin remodeling and histone modifications, we

examined the interactions between the mL/B/K-ALP promoter and 11 factors using

chromatin immunoprecipitation in noninduced cells and in cells induced with

ATRA for 1, 6, or 12 h. For this, we chose primers around the ATRA-sensitive site

(Fig. 3).

We first examined the binding of RNA polymerase II, the core component of the

gene transcription complex, onto the mL/B/K-ALP promoter. A large amount of

RNA polymerase II was recruited to the transcription region of the promoter at 1 h

after ATRA treatment (Fig. 3). Thereafter, the degree of enrichment gradually

declined with the increase of induction time.

In the transcription complex, histone acetylation and promoter transcription

activity are closely associated. Typically, histone acetylation is associated with

transcriptional activation, and histone deacetylation is associated with a decrease in

transcriptional activity (Sterner and Berger 2000; Fischle et al. 2003). The levels of

histone acetylation are regulated by histone acetyltransferases (HATs) and histone

deacetylases (HDACs). Gene transcription can be affected not only by modifications

in the composition of the nucleosome octamer but also by the methylation,

acetylation, and phosphorylation of specific amino acids in H3 and H4 histones.

Therefore, we examined the changes in H3 and H4 acetylation levels during

induction. The H3 acetylation level in induced cells was 10 times that of noninduced

cells at 1 h, 12 times at 6 h, and 7.8 times at 12 h after ATRA induction (Fig. 3). H4

acetylation was 3 times that of control cells at 1 h after ATRA induction, rose to a

maximum of 12 times the control at 6 h, and returned to the 1-h level at 12 h after

induction.

We then examined the recruitment and enrichment of the acetyltransferases, p300

and GCN5, in the transcriptional complex (Fig. 3). Similar to the changes observed

Biochem Genet (2012) 50:495–507 501

123

Fig. 3 Quantitative RT-PCR results using various antibodies with ChIP. a ChIP production location onthe mL/B/K-ALP promoter. b–i C3H10T 1/2 cells were treated with ATRA for 0, 1, 6, or 12 h, followedby ChIP using different antibodies: RNA polymerase II (b), histones H3 (c) and H4 (d), acetyltransferasesp300 (e) and GCN5 (f), histone deacetylases (g), and the ATP-dependent chromosome remodeling factorsBrg1 (h) and Brm (i). All results are means of three independent experiments ± standard deviation.*P \ 0.05, **P \ 0.01 versus the untreated control

502 Biochem Genet (2012) 50:495–507

123

in H3 and H4 acetylation levels, a substantial amount of p300 was recruited to the

vicinity of the TSS at 6 h after ATRA induction. At 12 h, the p300 level decreased

to the level observed at 1 h after induction. GCN5 levels were twice that in

noninduced cells at 6 h after induction. GCN5 levels increased dramatically, by 131

times, at 12 h post-induction. These results demonstrated that histone acetylation

and recruitment of acetylases increased near the TSS of the mL/B/K-ALP promoter

after ATRA treatment.

We examined the recruitment of HDAC1, 2, 3, and 4 into the chromosome during

induction, with effects the opposite of those of p300 and GCN5 (Fig. 3). HDAC1, 2,

and 3 recruitment was similar, with their levels increasing significantly at 1 h after

induction, followed by a decrease after 6 h. HDAC4 was not recruited until 6 h after

induction, and its level subsequently decreased.

Using the DNase I hypersensitive assay, we showed that a new open site was

produced near the TSS after ATRA induction; thus, chromatin remodeling exposed

a previously embedded DNase I hypersensitive site. We examined the expression of

the ATP-dependent chromosome remodeling factors, Brg1 and Brm of the SWI2/

SNF2 family, during the induction (Fig. 3). The greatest degree of enrichment of

both Brg1 and Brm was observed at 6 h after induction, with Brg1 and Brm levels at

3 and 9 times that in control cells. At 12 h after induction, Brg1 and Brm levels had

decreased to 1.5 and 4.4 times the control levels.

Discussion

Retinoic acid regulates multiple biological processes, including cell proliferation

and differentiation, by virtue of its ability to modulate the rate of transcription of

numerous target genes. Retinoic acid induces the expression of the L/B/K-ALP gene

in rat fibroblast cell lines (Gianni et al. 1993). Even though the molecular

mechanism of this activation has been extensively studied (Orimo and Shimada

2005), the relationship between chromatin structure and transcriptional activity

remains unclear.

The transcriptional activities of retinoic acid are mediated by two members of the

nuclear hormone receptor superfamily: the RXR, which is activated by the 9-cis

isomer of retinoic acid, and the RAR, which responds to both 9-cis and ATRA.

These retinoid receptors bind to specific response elements in the promoter regions

(retinoic acid response elements, RAREs) of target genes and function as ligand-

inducible transcription factors (Chambon 1996; Leid et al. 1992; Mangelsdorf et al.

1994). RXR can bind to DNA and activate transcription as a homodimer. In

contrast, tight binding to DNA and transcriptional activation by RAR usually occurs

through heterodimerization with RXR (Durand et al. 1992; Hallenbeck et al. 1992;

Leid et al. 1992; Yu et al. 1991). Upon ligand binding, RAR–RXR heterodimers

recruit multicomponent coactivator complexes that in turn remodel chromatin and

bridge to the general transcription machinery to modulate gene expression (Glass

and Rosenfeld 2000; Xu et al. 1999). Both of these receptors are composed of three

subtypes: a, b, and c (Durand et al. 1992). Because RARs are the initial response

receptor of the activation by ATRA, we treated cells with RARa, b, and c agonist.

Biochem Genet (2012) 50:495–507 503

123

The results revealed that ATRA regulated mL/B/K-ALP expression through RARaand RARb (Fig. 1).

Retinoic acid can also activate gene transcription through nongenetic mecha-

nisms, by activating signal pathways that lead to the phosphorylation of

transcription factors (Canon et al. 2004). Because ATRA rapidly upregulates mL/B/K-ALP gene expression, we speculated that this process involved the MAPK rapid

phosphorylation pathway. When ATRA-induced C3H10T 1/2 cells were treated

with JNK, ERK, or P38 antagonists, upregulation of the mL/B/K-ALP gene

expression was unaffected. Moreover, treatment of cells with a general RAR agonist

only resulted in the induction of mL/B/K-ALP gene expression.

These results show that the ATRA-mediated upregulation of mL/B/K-ALP

involves RAR and is not related to the MAPK rapid phosphorylation pathway.

Using the luciferase activity assay and EMSA to examine fragments of different

lengths within 4.5 kb of the hL/B/K-ALP promoter in SaOS-2 osteosarcoma cell

lines, Orimo and Shimada (2005) identified a RARE located between -1,012 and

-999 bp upstream of the TSS of hL/B/K-ALP. In our study, we conducted a large-

scale screening of 22.9 kb (-18,763 to ?4,178 bp) fragments around the TSS using

DNase I hypersensitivity analysis and found a new DNase I-sensitive site at

*520 bp upstream of the TSS of the mL/B/K-ALP promoter in ATRA-induced

C3H10T 1/2 cells. Chromosomal structure is an obstacle for the binding of

transcription factors and the formation of the preinitiation complex (Adelman and

Lis 2002). Thus, the activation of gene transcription may be accompanied by

chromosome remodeling, which results in the appearance of new DNase I-sensitive

sites due to the increase in the accessibility of the local chromatin (Hebbes et al.

1994). Therefore, we inferred that ATRA mediates the upregulation of mL/B/K-ALPexpression by regulating its promoter accessibility, and that this site contains a

RARE. We found that in the mL/B/K-ALP gene, the potential RARE is located at

approximately -520 bp, but in the human gene the RARE is located at

approximately -630 bp (Orimo and Shimada 2005). Accordingly, the putative

RARE is consistent with the previous report of the murine RARE by Escalante et al.

(1996). As the DR5 sequence is a/g g g/t tcannnnn a/g g g/t tca (Leblanc and

Stunnenberg 1995), we detected a sequence, ggttca cagacgcgca gggtca (-324 to

-302), similar to the DR5 sequence around our RARE. Although the free bases are 10

instead of 5, our results can provide a better understanding of the mL/B/K-ALP gene.

Gene expression is under strict control. A series of transcription factors,

transcriptional cofactors, and chromosome-modifying enzymes act within the

genome to activate or inhibit gene expression (Reid et al. 2009). Histone-modifying

enzymes, as well as ATP-dependent remodeling enzymes, play an important role in

the regulation of the open state of chromatin. The regulation of histone or

nonhistone acetylation levels by HATS and HDACs has an important impact on the

open state of the gene. HATS and HDACs do not have specific binding sites and

need to be guided by specific transcription factors to act at the specific position of

the target gene. Histone acetylation increases its affinity for the SWI/SNF complex

(Han et al. 2006). The combined actions of histone acetylation and remodeling

enzymes allow the transcription spacer of the promoter to open further and allow the

binding of the transcription factor, thereby providing a binding site for other

504 Biochem Genet (2012) 50:495–507

123

transcriptional coactivators. In addition, this modification may increase the stability

of transcription complexes (Zhao and Benveniste 2008).

In this study, we used chromatin immunoprecipitation to examine the enrichment

of various factors in the specific promoter region of the mL/B/K-ALP gene during

ATRA induction. For purposes of discussion, we propose a model for the induction

of mL/B/K-ALP gene expression in C3H10T 1/2 cells that summarizes some of the

findings described here (Fig. 4). In the untreated condition, mL/B/K-ALP is

expressed at a low basal level. The chromosome is closed, and the TSS is wrapped

within the nucleosomes and unable to bind to the transcription complex. When the

cells are treated with ATRA, ATRA interacts with RARs, and the ATRA–RAR

complex binds to the RARE located in the promoter of the mL/B/K-ALP gene. H3

and H4 become acetylated under the action of acetylases, such as p300, GCN5,

HDAC 1, 2, 3, and 4; also, Brg1 and Brm are recruited to the vicinity of the TSS,

and the regulatory region of the gene is opened, allowing the recruitment of RNA

polymerase II. The transcription complex begins to form, and mL/B/K-ALPtranscription is initiated.

It is noteworthy that the levels of RNA polymerase II are contrary to the levels of

mL/B/K-ALP gene expression (Figs. 1, 3). In general, HATs are involved in

transcriptional activation, and HDACs play an important role in transcription

inhibition. We found, however, that the levels of HATs and HDACs during ATRA

induction were similar (Fig. 3). These results suggest that there may be other

transcription factors involved in the inducing progress of ATRA on mL/B/K-ALP.

In summary, our study demonstrates that in C3H10T 1/2 cells, ATRA

upregulates mL/B/K-ALP expression through RARa and RARb, unrelated to the

MAPK pathway. ATRA induces mL/B/K-ALP expression by promoting changes in

the structure of chromatin through the sequential and combined action of HATs,

HDACs, Brg1, and Brm.

Acknowledgments This study was supported by the National Natural Science Foundation of China

(Nos. 30600328 and 30740030).

Fig. 4 Schematic representation of the possible mechanism underlying ATRA treatment at the mL/B/K-ALP promoter in C3H10T 1/2 cells

Biochem Genet (2012) 50:495–507 505

123

References

Adelman K, Lis JT (2002) How does Pol II overcome the nucleosome barrier? Mol Cell 9:451–452

Budhu AS, Noy N (2002) Direct channeling of retinoic acid between cellular retinoic acid-binding protein

ii and retinoic acid receptor sensitizes mammary carcinoma cells to retinoic acid-induced growth

arrest. Mol Cell Biol 22:2632–2641

Canon E, Cosgaya JM, Scsucova S, Aranda A (2004) Rapid effects of retinoic acid on CREB and ERK

phosphorylation in neuronal cells. Mol Biol Cell 15:5583–5592

Chambon P (1996) A decade of molecular biology of retinoic acid receptors. FASEB J 10:940–954

Durand B, Saunders M, Leroy P, Leid M, Chambon P (1992) All-trans and 9-cis retinoic acid induction of

CRABPII transcription is mediated by RAR–RXR heterodimers bound to DR1 and DR2 repeated

motifs. Cell 71:73–85

Escalante AD, Recillas TF, Hernandez GD, Castro OS, Terao M, Garattini E, Covarrubias L (1996)

Retinoic acid and methylation cis-regulatory elements control the mouse tissue non-specific alkaline

phosphatase gene expression. Mech Dev 57:21–32

Fischle W, Wang Y, Allis CD (2003) Binary switches and modification cassettes in histone biology and

beyond. Nature 425:475–479

Garen A, Levinthal C (1960) A fine-structure genetic and chemical study of the enzyme alkaline

phosphatase of E. coli, I: purification and characterization of alkaline phosphatase. Biochim Biophys

Acta 38:470–483

Gianni M, Terao M, Sozzani S, Garattini E (1993) Retinoic acid and cyclic AMP synergistically induce

the expression of liver/bone/kidney-type alkaline phosphatase gene in L929 fibroblastic cells.

Biochem J 296:67–77

Glass CK, Rosenfeld MG (2000) The coregulator exchange in transcriptional functions of nuclear

receptors. Genes Dev 14:121–141

Hallenbeck PL, Marks MS, Lippoldt RE, Ozato K, Nikodem VM (1992) Heterodimerization of thyroid

hormone (TH) receptor with H-2RIIBP (RXR beta) enhances DNA binding and TH-dependent

transcriptional activation. Proc Natl Acad Sci USA 89:5572–5576

Han S, Lu J, Zhang Y, Cheng C, Han L, Wang X, Li L, Liu C, Huang B (2006) Recruitment of histone

deacetylase 4 by transcription factors represses interleukin-5 transcription. Biochem J 400:439–448

Harris H (1990) The human alkaline phosphatases: what we know and what we don’t know. Clin Chim

Acta 186:133–150

Heath JK, Suva LJ, Yoon K, Kiledjian M, Martin TJ, Rodan GA (1992) Retinoic acid stimulates

transcriptional activity from the alkaline phosphatase promoter in the immortalized rat calvarial cell

line, RCT-1. Mol Endocrinol 6:636–646

Hebbes TR, Clayton AL, Thorne AW, Crane-Robinson C (1994) Core histone hyperacetylation co-maps

with generalized DNase I sensitivity in the chicken beta-globin chromosomal domain. EMBO J

13:1823–1830

Khorasanizadeh S (2004) The nucleosome: from genomic organization to genomic regulation. Cell

116:259–272

Kim YJ, Lee MH, Wozney JM, Cho JY, Ryoo HM (2004) Bone morphogenetic protein-2-induced

alkaline phosphatase expression is stimulated by Dlx5 and repressed by Msx2. J Biol Chem

279:50773–50780

Leblanc BP, Stunnenberg HG (1995) 9-Cis retinoic acid signaling: changing partners causes some

excitement. Genes Dev 9:1811–1816

Leid M, Kastner P, Chambon P (1992) Multiplicity generates diversity in the retinoic acid signalling

pathways. Trends Biochem Sci 17:427–433

Lo WS, Henry KW, Schwartz MF, Berger SL (2004) Histone modification patterns during gene

activation. Methods Enzymol 377:130–153

Lusser A, Kadonaga JT (2003) Chromatin remodeling by ATP-dependent molecular machines. Bioessays

25:1192–1200

Mangelsdorf D, Umesono K, Evans RM (1994) The retinoid receptors. In: Sporn MB, Roberts AB,

Goodman DS (eds) The retinoids: biology, chemistry, and medicine, 2nd edn. Raven Press, New

York, pp 319–350

Orimo H, Shimada T (2005) Regulation of the human tissue-nonspecific alkaline phosphatase gene

expression by all-trans-retinoic acid in SaOS-2 osteosarcoma cell line. Bone 36:866–876

506 Biochem Genet (2012) 50:495–507

123

Reid G, Gallais R, Metivier R (2009) Marking time: the dynamic role of chromatin and covalent

modification in transcription. Int J Biochem Cell Biol 41:155–163

Sterner DE, Berger SL (2000) Acetylation of histones and transcription-related factors. Microbiol Mol

Biol Rev 64:435–459

Terao M, Studer M, Giannı M, Garattini E (1990) Isolation and characterization of the mouse liver/bone/

kidney-type alkaline phosphatase gene. Biochem J 268:641–648

Trowsdale J, Martin D, Bicknell D, Campbell I (1990) Alkaline phosphatases. Biochem Soc Trans

18:178–180

Xu L, Glass CK, Rosenfeld MG (1999) Coactivator and corepressor complexes in nuclear receptor

function. Curr Opin Genet Dev 9:140–147

Yan Y, Peng L, Liu WX, Wan FH (2009) Research progress in insect alkaline phosphatases. Acta

Entomol Sin 52:95–105

Yu VC, Delsert C, Andersen B, Holloway JM, Devary OV, Naar AM, Kim SY, Boutin JM, Glass CK,

Rosenfeld MG (1991) RXR beta: a coregulator that enhances binding of retinoic acid, thyroid

hormone, and vitamin D receptors to their cognate response elements. Cell 67:1251–1266

Zhao X, Benveniste EN (2008) Transcriptional activation of human matrix metalloproteinase-9 gene

expression by multiple co-activators. J Mol Biol 383:945–956

Biochem Genet (2012) 50:495–507 507

123


Recommended