Discrete human dihydrofolate reductase gene transcripts present in polysomal RNA map with their 5' ends several hundred nucleotides upstream of the main mRNA start site

Functional Mutations in the microRNA-155 Promoter Modulate its Transcription Efficiency and Expression

Limited research has been conducted on porcine miR-155 promoters, and previous study from our group have identified two haplotypes (TT and CC) in different pig breeds, each associated with five fully linked mutation sites within or near the miR-155 gene (Li et al. Dev Comp Immunol 39(1):110-116, 2013). In this study, the promoter region of porcine miR-155 was screened, and two important transcription factors, Foxp3 and RelA, were identified. The binding ability of Foxp3 protein was found to be affected by the first mutation site (A/C) using EMSA analysis. In vitro experiments revealed that the expression level of miR-155 was significantly higher in the C haplotype compared to the T haplotype. Additionally, northern blotting assays indicated that both the first mutation site (A/C) and the fourth mutation site (G/T) had a significant impact on miR-155 expression levels. These findings provide further insights into the transcriptional regulation of porcine miR-155 and identify crucial mutation sites that influence miR-155 expression. This knowledge can serve as a basis for identifying potential molecular markers associated with disease resistance in swine.

Molecular mechanisms of long noncoding RNAs and their role in disease pathogenesis

LncRNAs are long non-coding regulatory RNAs that are longer than 200 nucleotides. One of the major functions of lncRNAs is the regulation of specific gene expression at multiple steps including, recruitment and expression of basal transcription machinery, post-transcriptional modifications and epigenetics [1]. Emerging evidence suggests that lncRNAs also play a critical role in maintaining tissue homeostasis during physiological and pathological conditions, lipid homeostasis, as well as epithelial and smooth muscle cell homeostasis, a topic that has been elegantly reviewed [2-5]. While aberrant expression of lncRNAs has been implicated in several disease conditions, there is paucity of information about their contribution to the etiology of diseases [6]. Several studies have compared the expression of lncRNAs under normal and cancerous conditions and found differential expression of several lncRNAs, suggesting thereby an involvement of lncRNAs in disease processes [7, 8]. Furthermore, the ability of lncRNAs to influence epigenetic changes also underlies their role in disease pathogenesis since epigenetic regulation is known to play a critical role in many human diseases [1]. LncRNAs thus are not only involved in homeostatic functioning but also play a vital role in the progression of many diseases, thereby underscoring their potential as novel therapeutic targets for the alleviation of a variety of human disease conditions.

Non-Coding RNAs As Transcriptional Regulators In Eukaryotes

Non-coding RNAs up to 1,000 nucleotides in length are widespread in eukaryotes and fulfil various regulatory functions, in particular during chromatin remodeling and cell proliferation. These RNAs are not translated into proteins: thus, they are non-coding RNAs (ncRNAs). The present review describes the eukaryotic ncRNAs involved in transcription regulation, first and foremost, targeting RNA polymerase II (RNAP II) and/or its major proteinaceous transcription factors. The current state of knowledge concerning the regulatory functions of SRA and TAR RNA, 7SK and U1 snRNA, GAS5 and DHFR RNA is summarized herein. Special attention is given to murine B1 and B2 RNAs and human Alu RNA, due to their ability to bind the active site of RNAP II. Discovery of bacterial analogs of the eukaryotic small ncRNAs involved in transcription regulation, such as 6S RNAs, suggests that they possess a common evolutionary origin.

Transcription of ncDNA: Many roads lead to local gene regulation

Transcription of ncDNA occurs throughout eukaryotic genomes, generating a wide array of ncRNAs. One large class of ncRNAs includes those transcribed over the promoter regions of nearby protein coding genes. Recent studies, primarily focusing on individual genes have uncovered multiple mechanisms by which promoter-associated transcriptional activity locally alters gene expression.

Regulation of human dihydrofolate reductase activity and expression

Dihydrofolate reductase (DHFR) enzyme catalyzes tetrahydrofolate regeneration by reduction of dihydrofolate using NADPH as a cofactor. Tetrahydrofolate and its one carbon adducts are required for de novo synthesis of purines and thymidylate, as well as glycine, methionine and serine. DHFR inhibition causes disruption of purine and thymidylate biosynthesis and DNA replication, leading to cell death. Therefore, DHFR has been an attractive target for chemotherapy of many diseases including cancer. Over the following years, in order to develop better antifolates, a detailed understanding of DHFR at every level has been undertaken such as structure-functional analysis, mechanisms of action, transcriptional and translation regulation of DHFR using a wide range of technologies. Because of this wealth of information created, DHFR has been used extensively as a model system for enzyme catalysis, investigating the relations between structure in-silico structure-based drug design, transcription from TATA-less promoters, regulation of transcription through the cell cycle, and translational autoregulation. In this review, the current understanding of human DHFR in terms of structure, function and regulation is summarized.

Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript

Alternative promoters within the same gene are a general phenomenon in gene expression. Mechanisms of their selective regulation vary from one gene to another and are still poorly understood. Here we show that in quiescent cells the mechanism of transcriptional repression of the major promoter of the gene encoding dihydrofolate reductase depends on a non-coding transcript initiated from the upstream minor promoter and involves both the direct interaction of the RNA and promoter-specific interference. The specificity and efficiency of repression is ensured by the formation of a stable complex between non-coding RNA and the major promoter, direct interaction of the non-coding RNA with the general transcription factor IIB and dissociation of the preinitiation complex from the major promoter. By using in vivo and in vitro assays such as inducible and reconstituted transcription, RNA bandshifts, RNA interference, chromatin immunoprecipitation and RNA immunoprecipitation, we show that the regulatory transcript produced from the minor promoter has a critical function in an epigenetic mechanism of promoter-specific transcriptional repression.

The 5'-untranslated RNA of the human dhfr minor transcript alters transcription pre-initiation complex assembly at the major (core) promoter

The human dhfr minor transcript is distinguished from the predominant dhfr mRNA by an approximately 400 nucleotide extension of the 5'-untranslated region, which corresponds to the major (core) promoter DNA (its template). Based on its unusual sequence composition, we hypothesized that the minor transcript 5'-UTR might be capable of altering transcription pre-initiation complex assembly at the core promoter, through direct interactions of the RNA with specific regulatory polypeptides or the promoter DNA itself. We found that the minor transcript 5'-UTR selectively sequesters transcription factor Sp3, and to a lesser extent Sp1, preventing their binding to the dhfr core promoter. This allows a third putative transcriptional regulatory protein, which is relatively resistant to sequestration by the minor transcript RNA, the opportunity to bind the dhfr core promoter. The selective sequestration of Sp3 > Sp1 by the minor transcript 5'-UTR involves an altered conformation of the RNA, and a structural domain of the protein distinct from that required for binding to DNA. As a consequence, the minor transcript 5'-UTR inhibits transcription from the core promoter in vitro (in trans) in a concentration-dependent manner. These results suggest that the dhfr minor transcript may function in vivo (in cis) to regulate the transcriptional activity of the major (core) promoter.

Long-term exposure to methotrexate induces immunophenotypic changes, decreased methotrexate uptake and increased dihydrofolate gene copy number in Jurkat T cells

Methotrexate (MTX) treatment of rheumatoid arthritis may require increasing doses to maintain clinical efficacy. An overall plateau of clinical response is reached after only six months of treatment. To study the immunologic, biochemical and genetic effects of MTX on T cells, the Jurkat T cell line was made MTX-resistant by serial addition of methotrexate sodium into culture medium. Cells proliferated and divided successfully in MTX concentrations ranging to 15 microM. MTX resistance of Jurkat T cells in vitro was accompanied by significantly (P < 0.05) decreased expression of CD2, CD3, CD4, CD28, and CD69, IL-2 production, and MTX uptake assessed by cell association or disassociation of 3[H]-MTX or fluoresceinated MTX (FMTX), respectively. In addition, there was DHFR gene amplification and increased levels of DHFR in all resistant cell lines. Both permanent and transient phenotypic changes developed in resultant cell lines exposed to increasing concentrations of MTX in vitro. Expression of CD4 and CD25 and sensitivity to MTX returned to near-parental levels after removal of MTX from culture medium, whereas expression of CD26 and MTX uptake were significantly increased. Expression of CD2, CD3, CD69 and IL-2 production as well as the DHFR levels did not return to the parental phenotype after removal from MTX. We conclude that MTX-cultured cells express depressed levels of cell-surface markers vital for T cell function and activation. The return of enhancement of these cell-surface markers critical to T cell activation suggests a possible mechanism for the severe flares experienced by rheumatoid arthritis patients when drug treatment is discontinued.

Accumulation of E2F-4.DP-1 DNA binding complexes correlates with induction of dhfr gene expression during the G1 to S phase transition

Previously genomic DNase I footprinting showed changes in protein binding to two overlapping E2F sites correlates with activation of dhfr gene expression at the G1/S boundary of the Chinese hamster cell cycle (Wells, J., Held, P., Illenye, S., and Heintz, N. H. (1996) Mol. Cell. Biol. 16, 634-647). Here gel mobility and antibody supershift assays were used to relate changes in the components of E2F DNA binding complexes in cell extracts to repression and induction of dhfr gene expression. In extracts from log phase cells, E2F complexes contained predominantly E2F-4 and E2F-2 in association with DP-1, and DNA binding assays showed complexes containing E2F-2 preferentially interact with only one of the two overlapping E2F sites. In serum starvation-stimulation experiments, arrest in G1 by low serum was accompanied by decreased levels of dhfr mRNA and the appearance of an E2F-4.DP-1.p130 complex. After serum stimulation, induction of dhfr gene expression was preceded by loss of the p130 complex in mid G1 and coincided with marked increases in two free E2F.DP-1 complexes in late G1, one of which contained E2F-4 and a second which contained an unidentified E2F. We suggest activation of dhfr gene expression after serum stimulation requires at least two temporally distinct processes, relief of p130-mediated repression and subsequent activation of transcription by free E2F.

Molecular cloning of human cDNA with a sequence highly similar to that of the dihydrofolate reductase gene in brain libraries derived from Alzheimer's disease patients

A polyclonal antibody was raised against a serine protease purified from the extracellular fluid of familial Alzheimer's disease lymphoblastoid cells. Using this antibody, a cDNA library from familial Alzheimer's disease cells and two cDNA libraries from the brains of two Alzheimer's disease patients were screened independently. The familial Alzheimer's disease protein 1 (FADP1) cDNA clones isolated from these three libraries were subjected to DNA sequence analysis. The nucleotide sequence of FADP1 cDNA is highly similar to the 5' portion of the human dihydrofolate reductase (DHFR) gene, however, the sequence corresponding to exon 1 of the DHFR gene is completely disrupted and contains a 247-bp DNA insert with a sequence unique to FADP1. Moreover, FADP1 cDNA harbours a large open reading frame, including the unique insert, which has the potential to code an approximately 50-kDa protein. The deduced amino acid sequence of this protein contains 12 cysteine residues potentially involved in six disulfide bonds, a proline-rich segment and a hydrophobic segment. Northern-blot analysis with the unique insert DNA probe verified that FADP1 protein is expressed in both lymphoblastoid and brain cells derived from Alzheimer's disease patients.

Transcripts from a mosquito dihydrofolate reductase gene: evidence for heterogeneity at the 5' end

Heterogeneity among transcripts from the mosquito (Aedes albopictus) dihydrofolate reductase (DHFR) gene in wild-type C7-12 cells and in methotrexate-resistant Mtx-5011-128 cells has been analyzed by Northern blotting, RNAase mapping, and primer extension. In both sensitive and resistant cells, a major transcription initiation site mapped c. 11 nucleotides downstream of the TATAA box, near position -66 relative to the AUG codon. Two other major transcription initiation sites mapped approx. eight and 45 nucleotides, respectively, upstream of the TATAA box. In addition, at least six minor sites were detected, four of which mapped within TATA-like sequences. Within the AT-rich region flanking the 5'-end of the mosquito DHFR gene were four T-rich motifs and three "GTTTGTG" repeats. Additional "GTTTGTG" repeats occurred in the first exon and in the single 56 nucleotide intron of the mosquito DHFR gene. In contrast to the heterogeneity at the 5'-ends of mosquito DHFR transcripts, the 3'-end terminated at a single position, c. 22 nucleotides downstream of the polyadenylation signal.

Nucleotide sequence of the Drosophila glucose-6-phosphate dehydrogenase gene and comparison with the homologous human gene

Glucose-6-phosphate dehydrogenase (G6PD) has a major role in NADPH production and is found in almost all cell types. The structural gene for G6PD is X-linked in Drosophila melanogaster, as it is in most eukaryotic organisms, and due to its ubiquitous expression, it can be considered a typical 'housekeeping' gene. Here we present the complete nucleotide (nt) sequence of G6PD cDNAs as well as the genomic copy of the G6PD gene. The G6PD gene has three introns so that the protein-coding region is divided into four segments. The 5'-end of mature G6PD mRNA is located 289 +/- 1 nt upstream from the start codon. The sequence upstream from the transcription start point is G + T-rich and contains no commonly found transcription regulatory elements, such as a TATA box or GGGCGG sequence. D. melanogaster G6PD is 65% homologous with the human G6PD protein but has no homology with the human sequence for the first 42 amino acid residues. The G6PD gene was shown to be active when transduced to autosomal positions. For each transformant, G6PD activity in both male and female adults was not significantly different, indicating that the transduced gene, unlike the resident G6PD, is not dosage-compensated in males.

Nucleotide sequence and nuclease hypersensitivity of the Chinese hamster dihydrofolate reductase gene promoter region

We have sequenced the 1240 base pairs (bp) upstream from the translation start site of the hamster dihydrofolate reductase (DHFR) gene. The DNA in the 5' flanking region contains several elements that are homologous in both sequence and relative location to corresponding elements in the human and murine DHFR genes: an 11-bp element adjacent to the ATG codon, a 19-bp element that coincides with the major transcription start site, and two 29-bp upstream elements that are represented 4 times in the murine DHFR gene but only once in the human gene. Two clusters of short, G/C-rich elements conforming to the consensus binding sequence for the transcription factor Spl are located in the upstream region in all three genes. The symmetrical placement of the G/C boxes coincides with a symmetrical DNase I hypersensitive pattern in the chromatin, suggesting that the Spl protein may be involved in maintaining chromatin structure in this region.

Scrapie and cellular PrP isoforms are encoded by the same chromosomal gene

PrP 27-30 is the major protein in purified preparations of scrapie agent. An almost complete PrP cDNA was used to select PrP-related genomic clones from normal hamster DNA. The gene contains a noncoding exon of 56 to 82 bp and a 2 kb coding exon, separated by a 10 kb intron. Transcription initiates at the same multiple sites in vivo and in vitro. The promoter lacks a TATA box and contains three repeats of the sequence GCCCCGCCC, which resembles the Sp1 binding site found in "housekeeping" genes. The PrP coding sequence encodes a presumptive amino-terminal signal peptide. The primary structure of PrP encoded by the gene of a healthy animal does not differ from that encoded by a cDNA from a scrapie-infected animal, suggesting that the different properties of PrP from normal and scrapie-infected brains are due to post-translational events.

Estradiol-dependent transcription initiation upstream from the chicken apoVLDLII gene coding for the very-low-density apolipoprotein II

We have investigated RNAs originating from the 5'-flanking region of the chicken very-low-density apolipoprotein II (apoVLDLII) gene. S1 nuclease mapping and primer extension experiments revealed two minor upstream transcription start points located 1105 and 1530 nucleotides in front of the apoVLDLII gene. Transcription starting at these points is dependent upon estradiol as is transcription from the major start points. The transcripts are polyadenylated, but are not detectable in polysomes. Run-on assays indicated that the low concentration of the upstream initiated transcripts is due both to low transcription levels and to low transcript stability. The sequence around the upstream start points does not show strong homologies with consensus sequences of promoters for eukaryotic protein encoding genes. Nevertheless, the upstream sequences are transcribed in vivo by RNA polymerase II.