1: Biochem Pharmacol. 2005 Aug 15;70(4):606-17. Cloning and functional characterization of the rat alpha2B-adrenergic receptor gene promoter region: Evidence for binding sites for erythropoiesis-related transcription factors GATA1 and NF-E2. Schaak S, Cussac D, Labialle S, Mignotte V, Paris H. INSERM Unit 388, Institut Louis Bugnard, CHU Rangueil, Batiment L3, BP 84225, 31432 Toulouse Cedex 4, France. In the rat, the alpha2B-adrenergic receptor (alpha2B-AR) is encoded by the rat non-glycosylated (RNG) gene and is primarily expressed in the kidney, brain and liver of adult animals. High levels of alpha2B-AR are also found during fetal life in the placenta, liver and blood, where it is borne by cells of the erythropoietic lineage. As a first step to define the mechanisms responsible for the spatio-temporal pattern of alpha2B-AR expression, a genomic fragment containing 2.8 kb of the 5'-flanking region, the ORF and approximately 20 kb of the 3'-flanking region of the RNG gene was isolated. RNase protection assays performed on RNA from placenta or kidney using a series of riboprobes permitted to locate the transcription start site 372 bases upstream from the start codon. Transient transfection of various cells, including rat proximal tubule in primary culture, with constructs containing luciferase as a reporter gene demonstrated that: (i) the 5'-flanking region exhibited a strong and sense-dependent transcriptional activity and (ii) the 332 bp fragment (-732/-401 relative to the start codon), which lacks a TATA box but contains Sp1 sites, is sufficient to drive expression. Analysis of chromatin susceptibility to DNaseI digestion identified two hypersensitive sites (HS1 and HS2) located 1.7 and 1.0 kb, respectively, upstream from ATG and containing recognition sequences for erythroid transcription factors. EMSA showed specific binding of GATA1 and NF-E2 to these elements. Taken together, the results suggest that the chromatin environment in the vicinity of these boxes plays a critical role for alpha2B-AR expression during fetal life. PMID: 15993847 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 2: Biochem Biophys Res Commun. 2004 Jul 16;320(1):108-15. Induction of CRMP-2 by GDNF and analysis of the CRMP-2 promoter region. Kodama Y, Murakumo Y, Ichihara M, Kawai K, Shimono Y, Takahashi M. Department of Pathology, Nagoya University Graduate School of Medicine, Japan. Collapsin response mediator protein-2 (CRMP-2) is a mammalian homologue of UNC-33 of Caenorhabditis elegans. Mutations of CRMP-2 result in abnormal axon termination. Recently, it was demonstrated that CRMP-2 binds to tubulin heterodimers to promote microtubule assembly that is critical for axonal differentiation and growth during development. Here we show that glial cell line-derived neurotrophic factor (GDNF) enhances CRMP-2 expression in TGW human neuroblastoma cells via activation of RET receptor tyrosine kinase. GDNF-mediated CRMP-2 expression was regulated mainly by the extracellular regulated kinase (ERK) pathway, but was independent of activation of phosphatidylinositol 3-kinase and Src family kinases. Analysis of the promoter region of the CRMP-2 gene revealed that the region 214-48 bp upstream of the transcriptional start site is important for CRMP-2 expression. The SP1, E2F, and GATA1/2 binding sites appeared to play some roles in regulation of CRMP-2 expression. As expected, the CRMP-2 protein accumulated in extended neurites of TGW cells treated with GDNF. However, neuritogenesis of TGW cells was mostly dependent on Src family kinase activity and not ERK activity, indicating that the increased expression of CRMP-2 alone was not sufficient for neuritogenesis. PMID: 15207709 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 3: Gene. 2003 Feb 13;305(1):113-20. Genomic structure and promoter analysis of human NeuAc alpha2,3Gal beta1,3GalNAc alpha2,6-sialyltransferase (hST6GalNAc IV) gene. Kim SW, Kang NY, Lee SH, Kim KW, Kim KS, Lee JH, Kim CH, Lee YC. Division of Biotechnology, Faculty of Natural Resources and Life Science, Dong-A University, Busan 604-714, South Korea. We have cloned the genomic DNA encoding the human NeuAc alpha2,3Gal beta1,3GalNAc alpha2,6-sialyltransferase (hST6GalNAc IV) and analysed its structure. The hST6GalNAc IV gene was found to span about 9 kb and to be composed of six exons. The 5'-RACE (rapid amplification of cDNA ends) results indicated that mRNA isoform of the hST6GalNAc IV was generated by alternative splicing in the 5'-untranslated region. The expression of this gene was highly restricted in human fetal tissues. The potential transcriptional start site was determined by CapSite hunting. Sequence analysis of the 5'-flanking region of this gene lacked canonical TATA and CAAT boxes, but contained several putative binding sites for transcription factors SP1, MZF1, GATA1, LMO2COM, NFAT, HFH8 and USF, etc. Functional analysis of the 5'-flanking region by transient expression method revealed a high transcriptional activity in both HepG2 cells and Molt4 cells in a cell type-dependent manner, but not in SK-N-MC cells. These results suggest cell type-specific regulation of the basal hST6GalNAc IV promoter activity. PMID: 12594047 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 4: Zhongguo Shi Yan Xue Ye Xue Za Zhi. 2002 Apr;10(2):100-3. Sequence analysis of 5'-flanking region of human pax-5 gene exon 1B. Liu ML, Rahman M, Hirabayashi Y, Sasaki T. Department of Nephrology and Rheumatology, The Third Affiliated Hospital, Jiangxi Medical College, Nanchang 330008, China. Pax-5 gene is important transcription factor in B-lymphopoiesis and B-cell development. To understand the regulatory mechanism of pax-5 expression, the immediate 5'-flanking region (6 671 bp) of human pax-gene exon 1B was isolated and characterized. Analysis of the total sequence showed that the proximal promoter includes 3 CAT boxes, 1 SP1 and 1 E box. However, there was no consensus sequence for a TATA box in the 5'-flanking region. Putative regulatory sites of further upstream in the sequence revealed 6 LMO(2)COM, 5 NFAT, 2 LPOLYA-B, 3 GATA1, 2 AP4, 10 MZF1, 1 ETS1-B, 1 GATA3, 1 NKX25, 2 RORA1, 1 LYF1, 2 Ikaros2, 2 TCF11, 1 GATA-C and 1 FREAC7. Therefore, the 5'-flanking region of human pax-5 exon 1B could be involved in regulating the expression of human pax-5 and B-cell differentiation and development. PMID: 12513807 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 5: J Biol Chem. 2003 Jan 24;278(4):2571-80. Epub 2002 Nov 8. Regulation of expression of the phospholipid hydroperoxide/sperm nucleus glutathione peroxidase gene. Tissue-specific expression pattern and identification of functional cis- and trans-regulatory elements. Borchert A, Savaskan NE, Kuhn H. Institute of Biochemistry, Humboldt University Medical School Charite, Monbijoustrasse 2, 10117 Berlin, Germany. A sperm nucleus glutathione peroxidase (snGPx), which is closely related to the phospholipid hydroperoxide glutathione peroxidase (phGPx), was recently discovered in late spermatids. Both GPx isoforms originate from a joint ph/snGPx gene, but their N-terminal peptides are encoded by alternative first exons. The expression of the two enzymes is differentially regulated in various cells, but little is known about the regulatory mechanisms. To explore the tissue-specific regulation of expression of the two isoenzymes, we first investigated their tissue distribution. Whereas phGPx is expressed at low levels in many organs, snGPx was only detected in testis, kidney, and in the human embryonic kidney cell line HEK293. Subcellular fractionation studies and immunoelectron microscopy revealed a cytosolic localization. To explore the mechanistic reasons for the differential expression pattern, we first tested the activity of the putative phGPx and snGPx promoters. The 5'-flanking region of the joint ph/snGPx gene exhibits strong promoter activity. In contrast, the putative snGPx promoter, which comprises 334 bp of intronic sequences, lacks major promoter activity. However, it strongly suppresses the activity of the ph/snGPx promoter. These data suggest negative regulatory elements in the first intron of the ph/snGPx gene, and DNase protection assays revealed the existence of several protein-binding sites. The corresponding trans-regulatory proteins (SP1, ERG1, GATA1, SREBP1, USF1, and CREBP1) were identified, and in vivo binding of EGR1 and SREBP1 was shown by chromatin immunoprecipitation. These data indicate for the first time somatic expression of the snGPx and provide evidence for the existence of intronic negative cis-regulatory elements in the ph/snGPx gene. Our failure to detect an alternative snGPx promoter suggests that transcription of the ph/snGPx gene may be regulated by a joint basic promoter. The decision, which GPx isoform is expressed in a given cell, appears to be made by alternative splicing of a joint primary transcript. PMID: 12427732 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 6: Gene. 2000 Dec 30;260(1-2):103-12. Genomic organization, 5'flanking region and tissue-specific expression of mouse phosphofructokinase C gene. Gunasekera D, Kemp RG. Department of Biochemistry and Molecular Biology, Chicago Medical School, 3333 Green Bay Road, North Chicago, IL 60064, USA. Using a combination of mouse bacterial artificial chromosome (BAC) genomic library screening, long-range polymerase chain reaction (PCR) amplification, genomic walking and DNA sequencing, we have characterized the intron/exon boundaries, the sizes of each intron and 5' flanking region of the mouse PFK-C gene. The gene spans approximately 55 kb and comprises 22 exons separated by 21 introns. All intron/exon splice junctions conform to the GT/AG rule. The mouse PFK-C gene organization is similar to that of the human and rabbit PFK-A and human and mouse PFK-B genes. However, PFK-C has much larger intronic sequences throughout the gene. Anchored PCR was performed to amplify about 1.0 kb of genomic DNA upstream of the translational start site. Sequence analysis of the PFK-C 5' flanking region revealed that it is devoid of TATA and CAAT boxes at the usual positions, but it contained several putative binding sites for transcription factors AP1, GATA1, NKX2.5 and STAT. The 5' flanking region was not enriched in GC dinucleotides and lacked CpG islands and putative binding sites for SP1. Four transcription initiation sites have been identified by full-length RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) between -61 and -32 bp from the translation initiation codon.Reverse transcription-PCR analysis revealed that PFK-A, PFK-B and PFK-C genes were expressed, in all mouse tissues tested, at varying levels. PFK-A mRNA was more abundantly expressed in all tissues than were the PFK-B and PFK-C genes. Based on the mouse PFK-C signal normalized to 18S rRNA, the PFK-C mRNA was expressed at the highest levels in the brain, heart, thymus and testicles, whereas low levels were observed in the kidney, liver, muscle, and lung. PMID: 11137296 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 7: Genomics. 2000 Dec 1;70(2):223-31. Human uroporphyrinogen-III synthase: genomic organization, alternative promoters, and erythroid-specific expression. Aizencang G, Solis C, Bishop DF, Warner C, Desnick RJ. Department of Human Genetics, Mount Sinai School of Medicine, New York, New York 10029, USA. Uroporphyrinogen-III (URO) synthase is the heme biosynthetic enzyme defective in congenital erythropoietic porphyria. The approximately 34-kb human URO-synthase gene (UROS) was isolated, and its organization and tissue-specific expression were determined. The gene had two promoters that generated housekeeping and erythroid-specific transcripts with unique 5'-untranslated sequences (exons 1 and 2A) followed by nine common coding exons (2B to 10). Expression arrays revealed that the housekeeping transcript was present in all tissues, while the erythroid transcript was only in erythropoietic tissues. The housekeeping promoter lacked TATA and SP1 sites, consistent with the observed low level expression in most cells, whereas the erythroid promoter contained GATA1 and NF-E2 sites for erythroid specificity. Luciferase reporter assays demonstrated that the housekeeping promoter was active in both erythroid K562 and HeLa cells, while the erythroid promoter was active only in erythroid cells and its activity was increased during hemin-induced erythroid differentiation. Thus, human URO-synthase expression is regulated during erythropoiesis by an erythroid-specific alternative promoter. PMID: 11112350 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 8: J Biol Chem. 2000 Jan 28;275(4):2295-304. Uroporphyrinogen III synthase. An alternative promoter controls erythroid-specific expression in the murine gene. Aizencang GI, Bishop DF, Forrest D, Astrin KH, Desnick RJ. Department of Human Genetics, Mount Sinai School of Medicine, New York, New York 10029, USA. Uroporphyrinogen III synthase (URO-synthase, EC 4.2.1.75) is the fourth enzyme of the heme biosynthetic pathway and is the defective enzyme in congenital erythropoietic porphyria. To investigate the erythroid-specific expression of murine URO-synthase, the cDNA and approximately 24-kilobase genomic sequences were isolated and characterized. Three alternative transcripts were identified containing different 5'-untranslated regions (5'-UTRs), but identical coding exons 2B through 10. Transcripts with 5'-UTR exon 1A alone or fused to exon 1B were ubiquitously expressed (housekeeping), whereas transcripts with 5'-UTR exon 2A were only present in erythroid cells (erythroid-specific). Analysis of the TATA-less housekeeping promoter upstream of exon 1A revealed binding sites for ubiquitously expressed transcription factors Sp1, NF1, AP1, Oct1, and NRF2. The TATA-less erythroid-specific promoter upstream of exon 2A had nine putative GATA1 erythroid enhancer binding sites. Luciferase promoter/reporter constructs transfected into NIH 3T3 and mouse erythroleukemia cells indicated that the housekeeping promoter was active in both cell lines, while the erythroid promoter was active only in erythroid cells. Site-specific mutagenesis of the first GATA1 binding site markedly reduced luciferase activity in K562 cells (<5% of wild type). Thus, housekeeping and erythroid-specific transcripts are expressed from alternative promoters of a single mouse URO-synthase gene. PMID: 10644678 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 9: Blood. 1996 Mar 1;87(5):1793-801. Functional interaction of GATA1 with erythroid Kruppel-like factor and Sp1 at defined erythroid promoters. Gregory RC, Taxman DJ, Seshasayee D, Kensinger MH, Bieker JJ, Wojchowski DM. Department of Veterinary Science, The Pennsylvania State University, University Park, USA. GATA and CACC elements commonly are codistributed within the regulatory domains of a variety of erythroid genes. Using Drosophila S2 cells, the actions of GATA1, Sp1, and erythroid Kruppel-like factor (EKLF) at these elements within model erythroid promoters have been assessed. For each promoter studied (erythroid pyruvate kinase, glycophorin B, and a murine betamaj globin-derived construct, GCT) Sp1 and EKLF each activated transcription despite differences in CACC element sequence, orientation, and positioning. However, GATA1 acted in apparent cooperativity with Sp1 at the pyruvate kinase promoter; with EKLF at the betamaj globin-derived GCT promoter; and with either Sp1 or EKLF at the glycophorin B promoter. Thus, GATA1 may functionally interact with each of these Kruppel-like factors depending on promoter context; and at the GCT promoter, transcriptional activation by GATA1 and EKLF was > or = 10-fold higher than levels attributable to additive effects. The possibility that interactions between these activators may be direct was supported by the specific binding of baculoviral-expressed EKLF to GATA1. This report underlines the likelihood that discrete roles exist for Sp1 and EKLF in erythroid gene activation, and supports a mechanism of direct cooperativity for EKLF and GATA1 as coregulators. PMID: 8634425 [PubMed - indexed for MEDLINE] --------------------------------------------------------------- 10: Nucleic Acids Res. 1991 Apr 11;19(7):1413-9. Hypersensitive site 4 of the human beta globin locus control region. Pruzina S, Hanscombe O, Whyatt D, Grosveld F, Philipsen S. National Institute for Medical Research, Mill Hill, London, UK. The Locus Control Region (LCR) of the human beta globin gene domain is defined by four erythroid-specific DNasel hypersensitive sites (HSS) located upstream of this multigene cluster. The LCR confers copy number dependent high levels of erythroid specific expression to a linked transgene, independent of the site of integration. To assess the role of the individual hypersensitive sites of the LCR, we have localized HSS4 to a 280bp fragment that is functional both in murine erythroleukaemia (MEL) cells and in transgenic mice. This fragment coincides with the major area of hypersensitivity 'in vivo' and contains a number of DNasel footprints. Bandshift analysis shows that these footprints correspond to binding sites for the erythroid specific proteins GATA1 and NF-E2 and a number of ubiquitous proteins, including jun/fos, Sp1 and TEF2. PMID: 2027748 [PubMed - indexed for MEDLINE] ---------------------------------------------------------------