Promoter and upstream regulatory activities of the mouse cellular retinoic acid-binding protein-I gene

4D label-free quantitative proteomic analysis identifies CRABP1 as a novel candidate gene for litter size in rabbits†

In commercial rabbit breeding, litter size is a crucial reproductive trait. This trait directly determines the reproductive ability of female rabbits and is crucial for evaluating the production efficiency. We here compared differentially expressed proteins of in the ovary tissue from New Zealand female rabbits with high (H) and low (L) litter sizes by using 4D label-free quantitative proteomic technology and identified 92 differential proteins. The biological functions of these proteins were revealed through gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Most distributions of GO and KEGG were related to reproduction, growth development, and metabolism. Furthermore, a novel candidate gene cellular retinoic acid binding protein-1 (CRABP1), which was highly expressed in the L group, was selected for further biological function verification. The Cell Counting Kit-8 (CCK-8) assay and flow cytometry analysis revealed that CRABP1 can promote granulosa cell (GC) apoptosis and inhibit GC proliferation. Furthermore, qRT-PCR and western blotting analysis revealed that CRABP1 regulates the genes (HSD17B1, Wnt-10b, FSHR, TAF4B, BMP15, and BMP6) and protein (Wnt-10b) associated with steroid hormone synthesis and follicle development. The PCR product direct sequencing method revealed single nucleotide polymorphisms in the core promoter region of CRABP1. Luciferase activity assays revealed that the transcriptional activity of the GG genotype was significantly higher than that of the TT or TG genotype. Different genotypes are accompanied by changes in transcription factors, which indicates that T-359G polymorphism can regulate CRABP1 expression. In general, we identified litter size-related genes and revealed the mechanism underlying the effect of CRABP1 on litter size. CRABP1 serves as a key factor in the reproductive capacity of rabbits and can act as a molecular biomarker for the breeding of New Zealand rabbits.

Sonic Hedgehog-Gli1 Signaling and Cellular Retinoic Acid Binding Protein 1 Gene Regulation in Motor Neuron Differentiation and Diseases

Cellular retinoic acid-binding protein 1 (CRABP1) is highly expressed in motor neurons. Degenerated motor neuron-like MN1 cells are engineered by introducing SOD^G93A or AR-65Q to model degenerated amyotrophic lateral sclerosis (ALS) or spinal bulbar muscular atrophy neurons. Retinoic acid (RA)/sonic hedgehog (Shh)-induced embryonic stem cells differentiation into motor neurons are employed to study up-regulation of Crabp1 by Shh. In SOD^G93A or AR-65Q MN1 neurons, CRABP1 level is reduced, revealing a correlation of motor neuron degeneration with Crabp1 down-regulation. Up-regulation of Crabp1 by Shh is mediated by glioma-associated oncogene homolog 1 (Gli1) that binds the Gli target sequence in Crabp1′s neuron-specific regulatory region upstream of minimal promoter. Gli1 binding triggers chromatin juxtaposition with minimal promoter, activating transcription. Motor neuron differentiation and Crabp1 up-regulation are both inhibited by blunting Shh with Gli inhibitor GANT61. Expression data mining of ALS and spinal muscular atrophy (SMA) motor neurons shows reduced CRABP1, coincided with reduction in Shh-Gli1 signaling components. This study reports motor neuron degeneration correlated with down-regulation in Crabp1 and Shh-Gli signaling. Shh-Gli up-regulation of Crabp1 involves specific chromatin remodeling. The physiological and pathological implication of this regulatory pathway in motor neuron degeneration is supported by gene expression data of ALS and SMA patients.

Cellular Retinoic Acid Binding Proteins: Genomic and Non-genomic Functions and their Regulation

Cellular retinoic acid binding proteins (CRABPs) are high-affinity retinoic acid (RA) binding proteins that mainly reside in the cytoplasm. In mammals, this family has two members, CRABPI and II, both highly conserved during evolution. The two proteins share a very similar structure that is characteristic of a "β-clam" motif built up from10-strands. The proteins are encoded by two different genes that share a very similar genomic structure. CRABPI is widely distributed and CRABPII has restricted expression in only certain tissues. The CrabpI gene is driven by a housekeeping promoter, but can be regulated by numerous factors, including thyroid hormones and RA, which engage a specific chromatin-remodeling complex containing either TRAP220 or RIP140 as coactivator and corepressor, respectively. The chromatin-remodeling complex binds the DR4 element in the CrabpI gene promoter to activate or repress this gene in different cellular backgrounds. The CrabpII gene promoter contains a TATA-box and is rapidly activated by RA through an RA response element. Biochemical and cell culture studies carried out in vitro show the two proteins have distinct biological functions. CRABPII mainly functions to deliver RA to the nuclear RA receptors for gene regulation, although recent studies suggest that CRABPII may also be involved in other cellular events, such as RNA stability. In contrast, biochemical and cell culture studies suggest that CRABPI functions mainly in the cytoplasm to modulate intracellular RA availability/concentration and to engage other signaling components such as ERK activity. However, these functional studies remain inconclusive because knocking out one or both genes in mice does not produce definitive phenotypes. Further studies are needed to unambiguously decipher the exact physiological activities of these two proteins.

Chromatin remodeling and epigenetic regulation of the CrabpI gene in adipocyte differentiation

Retinoic acid (RA) acts by binding to nuclear RA receptors (RARs) to regulate a broad spectrum of downstream target genes in most cell types examined. In cytoplasm, RA binds specifically to cellular retinoic acid binding proteins I (CRABPI), and II. Although the function of CRABPI in animals remains the subject of debate, it is believed that CRABPI binding facilitates RA metabolism, thereby modulating the concentration of RA and the type of RA metabolites in cells. The basal promoter of the CrabpI gene is a housekeeping promoter that can be regulated by thyroid hormones (T3), DNA methylation, sphinganine, and ethanol acting on its upstream regulatory region. T3 regulation of CrabpI is mediated by the binding of thyroid hormone receptor (TR) to a TR response element (TRE) approximately 1 kb upstream of the basal promoter. Specifically, in the adipocyte differentiation process, T3 regulation is bimodal and closely associated with the cellular differentiation status: T3 activates CrabpI in predifferentiated cells (e.g., mesenchymal precursors or fibroblasts), but suppresses this gene once cells are committed to adipocyte differentiation. These disparate effects are functions of T3-triggered differential recruitment of coregulatory complexes in conjunction with chromatin looping/folding that alters the configuration of this genomic locus along adipocyte differentiation. Subsequent sliding, disassembly and reassembly of nucleosomes occur, resulting in specific changes in the conformation of the basal promoter chromatin at different stages of differentiation. This chapter summarizes studies illustrating the epigenetic regulation of CrabpI expression during adipocyte differentiation. Understanding the pathways regulating CrabpI in this specific context might help to illuminate the physiological role of CRABPI in vivo. This article is part of a special issue entitled: Retinoid and Lipid Metabolism.

RIP140 in thyroid hormone-repression and chromatin remodeling of Crabp1 gene during adipocyte differentiation

Cellular retinoic acid binding protein 1 (Crabp1) gene is biphasically (proliferation versus differentiation) regulated by thyroid hormone (T3) in 3T3-L1 cells. This study examines T3-repression of Crabp1 gene during adipocyte differentiation. T3 repression of Crabp1 requires receptor interacting protein 140 (RIP140). During differentiation, the juxtaposed chromatin configuration of Crabp1 promoter with its upstream region is maintained, but the 6-nucleosomes spanning thyroid hormone response element to transcription initiation site slide bi-directionally, with the third nucleosome remaining at the same position throughout differentiation. On the basal promoter, RIP140 replaces coactivators GRIP1 and PCAF and forms a repressive complex with CtBP1, HDAC3 and G9a. Initially active chromatin marks on this promoter, histone modifications H3-Ac and H3K4-me3, are weakened whereas repressive chromatin marks, H3K9-me3 and H3K27-me3 modification and recruitment of G9a, HP1α, HP1γ and H1, are intensified. This is the first study to examine chromatin remodeling, during the phase of hormone repression, of a bi-directionally regulated hormone target gene, and provides evidence for a functional role of RIP140 in chromatin remodeling to repress hormone target gene expression.

Expression of cellular retinoic acid-binding protein I is specific to neurons in adult transgenic mouse brain

Cellular retinoic acid binding protein I (CRABP-I) plays a role in retinoic acid (RA) metabolism or transport. This report shows specific neuronal expression of CRABP-I in adult transgenic mouse brain using CRABP-I promotor-driven lac-Z and neuron- and astrocyte-markers. Double staining indicates that CRABP-I is expressed in neurons and large cells (>12 microm) but to much lesser degree the astrocytes. CRABP-I-lac-Z(+) neurons were distributed throughout the brain, but in a very discreet pattern in each brain region. CRABP-I expression in specific populations of brain neurons suggests that RA is extensively metabolized in mature brains, mostly in neurons. Additionally, the genetic basis of its specific expression in these brain areas is located in the 5' regulatory region of this gene.

Frequent methylation-associated silencing of a candidate tumor-suppressor, CRABP1, in esophageal squamous-cell carcinoma

Epigenetic alterations and the resulting inactivation of tumor suppressor genes often contribute to the development of various cancers. To identify novel candidates that may be silenced by aberrant methylation in esophageal squamous-cell carcinoma (ESCC), we analysed ESCC cell lines by a recently developed method known as bacterial artificial chromosome array-based methylated CpG island amplification (BAMCA), and selected candidates through BAMCA-assisted strategy. In the course of this program, we identified frequent CpG methylation-dependent silencing of the gene encoding cellular retinoic acid binding protein 1 (CRABP1) in our panel of ESCC cell lines. Expression of CRABP1 mRNA was restored in gene-silenced ESCC cells after treatment with 5-aza 2'-deoxycytidine. The DNA methylation status of the CRABP1 CpG island with clear promoter activity correlated inversely with expression of this gene. CpG methylation of CRABP1 was frequently observed in primary ESCC tissues as well. Restoration of CRABP1 expression in ESCC cells lacking the protein reduced cell growth by inducing arrest at G(0)-G(1), whereas knockdown of the gene in cells expressing CRABP1 promoted cell growth. Among 113 primary ESCC tumors, the absence of immunoreactive CRABP1 was significantly associated with de-differentiation of cancer cells and with distant lymph-node metastases in the patients. These results indicate that CRABP1 appears to have a tumor-suppressor function in esophageal epithelium, and its epigenetic silencing may play a pivotal role during esophageal carcinogenesis. Its expression status in biopsies or resected tumors might serve as an index for identifying ESCC patients for whom combined therapeutic modalities would be recommended.

Thyroid hormone-induced juxtaposition of regulatory elements/factors and chromatin remodeling of Crabp1 dependent on MED1/TRAP220

The cellular retinoic acid binding protein I gene is induced by thyroid hormone (T3) through a T3 response element (TRE) approximately 1 kb upstream of the basal promoter. The upstream region is organized into a positioned nucleosomal array with the N1 nucleosome spanning the GC box region. T3 induces apparent interactions between chromatin segments containing the TRE and the GC box regions and the sliding of upstream nucleosomes toward N1 with concomitant N1 remodeling. Concurrently, the chromatin-remodeling factor BRM is replaced by BRG1 and histones are hyperacetylated. All these events are abolished in Med1/Trap220 null cells, indicating a key role for TRAP/Mediator in these processes. A MED1/TRAP220-containing Mediator complex constitutively occupies the GC box region but not the TRE, serving as a nexus for distal and proximal factors. This indicates new TRAP/Mediator functions in facilitating ultimate recruitment and function of RNA polymerase II and the general transcription machinery.

Receptor interacting protein 140 as a thyroid hormone-dependent, negative co-regulator for the induction of cellular retinoic acid binding protein I gene

Over-expression of receptor interacting protein 140 (RIP140) suppressed thyroid hormone (T3) induction of cellular retinoic acid binding I protein (CRABPI) gene in P19 embryonal carcinoma cells. CRABPI induction by T3 is mediated by a direct-repeat four-element bound by T3 receptor (T3R) and retinoid receptor X (RXR). Three receptor-interacting domains (RIDs) in RIP140 mediate its interaction with T3R: one constitutive RID within the amino terminus, and two T3-dependent RIDs in the central portion and the carboxyl terminus. In co-immunoprecipitation and chromatin immunoprecipitation assays, RIP140 formed complexes with T3R/RXR in solution and on the endogenous target, the CRABPI promoter. T3 treatment resulted in elevated histone acetylation of the endogenous CRABPI gene promoter, but simultaneous expression of RIP140 resulted in significantly reduced histone acetylation of this promoter, primarily through the recruitment of HDAC4. This study presents the first evidence that over-expressed RIP140 acts as a T3-dependent negative co-regulator for T3 induction of the endogenous CRABPI gene in P19 cells.

Upregulation of cellular retinoic acid-binding protein I expression by ethanol

Acute and chronic ethanol ingestion cause embryopathy similar to that of hyper- or hypovitaminosis A. Experimental data have suggested interaction between vitamin A and alcohol signaling pathways at the level of metabolic interference, which ultimately affects the concentration of retinoic acid (RA) in animals. The present study was set up to examine the possible effects of alcohol on cellular RA binding protein I (CRABP-I) expression during embryonic development by using transgenic mouse embryos and P19 embryonal carcinoma cells as experimental models. It was found that expression of the mouse CRABP-I gene was elevated in developing embryos at mid-gestation stages as a result of ethanol consumption by the mothers. Specific elevation of this gene was detected in the limb bud and the gut. In the P19 model, the CRABP-I gene was directly upregulated by ethanol, which was not blocked by a protein synthesis inhibitor. Furthermore, the regulation of the CRABP-I gene by ethanol was mediated by the 5' upstream regulatory region of the CRABP-I gene promoter. A potential interaction of vitamin A and ethanol at the level of CRABP-I gene expression is discussed.

Regulation of mouse kappa opioid receptor gene expression by retinoids

The effect of retinoids on the expression of kappa opioid receptor (KOR) gene was examined in normal and transgenic animals. KOR-lacZ transgene expression was specifically elevated in KOR-positive areas of the developing CNS by depleting vitamin A from animal diets. The endogenous KOR mRNA species, including all three isoforms, were also upregulated by depleting vitamin A in developing animals. Change in the expression of isoforms a and b is similar in prenatal stages but differs during postnatal development. Interestingly, upregulation of isoform c is most significant postnatally. The regulation of KOR gene by vitamin A was substantiated in a mouse embryonal carcinoma P19 culture system in which retinoic acid (RA), the most potent ingredient of vitamin A, was able to suppress the expression of all the three KOR isoforms and KOR protein. The RA-mediated suppression was blocked by an RA receptor antagonist and a histone deacetylase (HDAC) inhibitor. By using a reporter transfection assay in P19 cells, the potential genetic element responsible for RA-mediated suppression of KOR gene expression was located to intron 1 of the mouse KOR gene, which could also be blocked by HDAC inhibitor. Furthermore, suppression of KOR gene expression by RA in P19 cells appeared to be an indirect event and required protein synthesis. A role of RA in KOR gene regulation during developmental stages was discussed.

Promoter activity of mouse kappa opioid receptor gene in transgenic mouse

The biological activity of mouse kappa opioid receptor (KOR) gene promoter was examined in transgenic mice using a beta-galactosidase (lacZ) reporter strategy for the first time. A lacZ cDNA was inserted at the 5th amino acid in the coding region of a mouse KOR genomic segment containing 3 kb of the 5' regulatory region, to generate a Kor-lacZ fusion gene which was then used to generate transgenic mice. The expression of transgene was demonstrated at the RNA level by reverse transcription-polymerase chain reaction (RT-PCR), and at the protein level by in situ lacZ enzyme assay. From studying three independent transgenic mouse lines that express this transgene, it is concluded that Kor-lacZ expression begins at embryonic day 9.5 (E9.5) and increases in several brain areas and neural tube as embryos develop. At E12.5 and E13.5, Kor-lacZ expression is found primarily in the mantle layer of midbrain, hindbrain and medulla oblongata, cranial ganglion and vagus nerve. At E15.5 and E17.5, the transgene is expressed in eye, ear, neopallial cortex, caudate putamen, lateral ventricle, thalamus, hypothalamus and pons. Therefore, the 3 kb 5' regulatory sequence of the mouse KOR gene is functional in transgenic animals and directs a specific expression pattern recapitulating that of the endogenous KOR gene expression during developmental stages. However, in adult animals, this transgene is only expressed in the brain, indicating that the regulatory information for peripheral expression in the adult is not encoded within this 3 kb upstream sequence.

A novel nuclear receptor heterodimerization pathway mediated by orphan receptors TR2 and TR4

A unique heterodimerization pathway involving orphan receptors TR2 and TR4 is demonstrated. TR2 and TR4 preferentially form heterodimers in solution as well as on DNA elements containing a direct repeat-5 (DR5). The in vitro interaction between TR2 and TR4 is demonstrated by the yeast and the mammalian two-hybrid interaction assays, the pull-down assay, and the gel mobility shift assay. The in vivo interaction is demonstrated by following the intracellular localization of fusion receptors tagged with a green fluorescent protein. The dimerization is mediated by the ligand binding domains, and the three leucine residues on helix 10 of TR2 are critical for this interaction. In addition, coexpression of these two receptors exerts a much stronger repressive activity on a DR5-containing reporter than expressing either receptor alone. In the developing testis, TR2 and TR4 are coexpressed in the same testicular cell populations and exhibit a parallel pattern of expression along development. The preferential heterodimerization between TR2 and TR4 and their coexistence in specific germ cell populations suggest a physiological role of TR2/TR4 heterodimers in germ cell development.

Regulation of the CRABP-I gene during mouse embryogenesis

The cellular retinoic acid binding protein type I (CRABP-I) shows a highly specific expression pattern during mouse embryonic development. The tissues that express CRABP-I, i.e. the central nervous system (CNS), neural crest, branchial arches, limb bud and frontonasal mass, coincide with those that are most sensitive to unphysiological retinoic acid (RA) concentrations. We have investigated the transcriptional elements that are responsible for the spatiotemporal regulation of CRABP-I expression in the mouse embryo. We show here that a 16 kb fragment harbours all the elements needed for the correct spatiotemporal expression pattern. Upon further dissection of this fragment we have found that expression in the CNS is driven by elements in the upstream region of the gene, while expression in mesenchymal and neural crest tissue is regulated via element(s) located downstream of exon II of the gene. Two distinct fragments in the upstream region are required for expression in the CNS, as neither of these fragments alone is able to drive correct expression of a reporter gene in transgenic mice. DNAseI footprinting analysis of the two upstream fragments revealed the presence of a number of protected elements. One of these regulatory elements has the hallmarks of an RA response element, suggesting that CRABP-I expression in neural tissue can be directly modulated by RA via the RARs/RXRs.

Studies of dual promoters of mouse kappa-opioid receptor gene

Dual promoters were identified in the mouse kappa-opioid receptor (KOR) gene. The distal promoter was located in the 5'-upstream region of exon 1 and the proximal promoter was located in the first intron of this gene. The transcription initiation site of the proximal promoter was mapped to the -93rd nucleotide position from the ATG codon in a primer extension experiment. The expression of KOR mRNAs transcribed from these two promoters in mouse central nervous system and an embryonal carcinoma cell line P19 was confirmed in a ribonuclease protection assay. In non-neuronal tissues, only the transcripts initiated from the distal promoter were detected. The biological activities of these two promoters were determined in transient transfection of P19 cells with a series of reporters, each truncated at various 5'-upstream regions. It was concluded that the distal promoter was located between nucleotide positions -990 and -570, and the proximal promoter was located between nucleotide positions -330 and -93, relative to the translation initiation codon. The presence of dual promoters in the KOR gene suggested potential regulation of KOR expression by using different promoters.

The CRABP I gene contains two separable, redundant regulatory regions active in neural tissues in transgenic mouse embryos

The CRABP I gene is expressed in a spatiotemporal pattern in neural and mesenchymal tissues at the onset of organogenesis. The neural pattern of CRABP I expression includes specific rhombomeres of the hindbrain, neural crest cells and their derivatives the optic stalk, and the central area of the neural retina. We have created transgenic mouse lines with CRABP I 5' and transcribed regions fused to the lacZ structural gene that recapitulate much of this neural pattern of expression. Sequences 5' of the transcription initiation site between -7.8 and -3.2 kb confer beta-galactosidase expression to specific rhombomeres, migrating neural crest cells, trigeminal ganglion, the optic stalk, and the neural retina. We have also defined a region located between exon 1 and exon 8 that confers a portion of this expression pattern, including the mesencephalic projections of the trigeminal ganglion, the inner layer of the neural retina, and the peripheral layer of the posterior hindbrain. CRABP I expression in mesenchyme appears to require sequences in addition to or outside of those examined here.

Characterization of a negative response DNA element in the upstream region of the cellular retinoic acid-binding protein-I gene of the mouse

A negative, regulatory DNA element from the mouse cellular retinoic acid-binding protein I gene promoter was identified. This DNA element, located approximately 1 kilobase upstream from the transcription initiation site of this gene, contained a pair of direct repeats (DRs) separated by 4 base pairs (DR4, TGACCTTTGGGGACCT). By examining a series of reporters deleted or mutated within this DR4 region, it was concluded that the core sequence of this DR4, including both repeats and the spacer, was required for suppressive activity in the mouse embryonal carcinoma cell line P19. From gel retardation experiments, it was concluded that both repeated sequences were essential for specific protein binding, but the spacer sequence was not as critical. Specific residues required for protein binding to this DR4 were identified. In P19 cells, retinoic acid induced the binding of nuclear factors to DR4 and suppressed the activities of the reporters containing this DR4. Co-expression of retinoic acid receptor beta or thyroid hormone receptor beta1 (T3Rbeta1) significantly inhibited the expression of this reporter in P19 cells. Gel retardation with in vitro-synthesized nuclear receptors demonstrated specific binding of this DR4 by T3Rbeta1 monomers, homodimers, or heterodimers of T3Rbeta1/retinoid receptor X beta. A biological function of DR4 in crabp-I gene regulation in P19 cells was suggested.

Transgenic animals as new approaches in pharmacological studies

Transgenic animals are becoming useful tools for pharmacological studies. The use of transgenic technology raises two types of questions, "How are transgenic animals made?" and "What types of pharmacological questions can be answered using transgenic technologies?" Answers to these questions are discussed in this review. The production of animals with specific genetic alteration can be achieved by two strategies. The first involves the simple addition of DNA sequences to the chromosomes. The second strategy is to select particular genetic loci for site-specific changes. There are two well-established procedures for simple introduction of DNA into an animal genome, pronuclear DNA injection and transduction using a retrovirus. In contrast, methods for targeting specific DNA sequences to definite sites in the chromosomes are evolving rapidly. Some of these procedures can be used in combination to make a different variety of gene alterations in animals. Pharmacological studies where transgenic technology has been extensively used are discussed, including studies in the cardiovascular system, the nervous system, the endocrine system, cancer, and toxicology.