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1.
Mol Cell Endocrinol ; 499: 110612, 2020 01 01.
Article in English | MEDLINE | ID: mdl-31604124

ABSTRACT

Studies in vivo have suggested the involvement of CREB-regulated transcription coactivator (CRTC)2 on ACTH-induced transcription of the key steroidogenic protein, Steroidogenic Acute Regulatory (StAR). The present study uses two ACTH-responsive adrenocortical cell lines, to examine the role of CRTC on Star transcription. Here we show that ACTH-induced Star primary transcript, or heteronuclear RNA (hnRNA), parallels rapid increases in nuclear levels of the 3 isoforms of CRTC; CRTC1, CRTC2 and CRTC3. Furthermore, ACTH promotes recruitment of CRTC2 and CRTC3 by the Star promoter and siRNA knockdown of either CRTC3 or CRTC2 attenuates the increases in ACTH-induced Star hnRNA. Using pharmacological inhibitors of PKA, MAP kinase and calcineurin, we show that the effects of ACTH on Star transcription and CRTC nuclear translocation depend predominantly on the PKA pathway. The data provides evidence that CRTC2 and CRTC3, contribute to activation of Star transcription by ACTH, and that PKA/CRTC-dependent pathways are part of the multifactorial mechanisms regulating Star transcription.


Subject(s)
Adrenocorticotropic Hormone/pharmacology , Hormones/pharmacology , Phosphoproteins/genetics , Transcription Factors/metabolism , Animals , Cell Line , Cell Nucleus/metabolism , Female , Mice , Promoter Regions, Genetic , Protein Transport/drug effects , RNA, Heterogeneous Nuclear/genetics , Rats , Signal Transduction/drug effects , Transcriptional Activation/drug effects
2.
Am J Physiol Cell Physiol ; 311(1): C129-35, 2016 07 01.
Article in English | MEDLINE | ID: mdl-27122159

ABSTRACT

Vitamin C (ascorbic acid, AA) is indispensable for normal metabolism of all mammalian cells including pancreatic acinar cells (PACs). PACs obtain AA from their surroundings via transport across the cell membrane. Chronic alcohol exposure negatively affects body AA homeostasis; it also inhibits uptake of other micronutrients into PACs, but its effect on AA uptake is not clear. We examined this issue using both in vitro (266-6 cells) and in vivo (mice) models of chronic alcohol exposure. First, we determined the relative expression of the AA transporters 1 and 2 [i.e., sodium-dependent vitamin C transporter-1 (SVCT-1) and SVCT-2] in mouse and human PACs and found SVCT-2 to be the predominant transporter. Chronic exposure of 266-6 cells to alcohol significantly inhibited AA uptake and caused a marked reduction in SVCT-2 expression at the protein, mRNA, and heterogeneous nuclear RNA (hnRNA) levels. Similarly, chronic alcohol feeding of mice significantly inhibited AA uptake and caused a marked reduction in level of expression of the SVCT-2 protein, mRNA, and hnRNA. These findings suggest possible involvement of transcriptional mechanism(s) in mediating chronic alcohol effect on AA uptake by PACs. We also observed significant epigenetic changes (histone modifications) in the Slc23a2 gene (reduction in H3K4me3 level and an increase in H3K27me3 level) in the alcohol-exposed 266-6 cells. These findings show that chronic alcohol exposure inhibits PAC AA uptake and that the effect is mediated, in part, at the level of transcription of the Slc23a2 gene and may involve epigenetic mechanism(s).


Subject(s)
Alcohol Drinking/adverse effects , Ascorbic Acid/metabolism , Ethanol/toxicity , Pancreas, Exocrine/drug effects , Sodium-Coupled Vitamin C Transporters/metabolism , Alcohol Drinking/metabolism , Animals , Biological Transport , Cell Line, Tumor , Down-Regulation , Epigenesis, Genetic , Humans , Mice , Models, Animal , Pancreas, Exocrine/metabolism , Pancreas, Exocrine/pathology , RNA, Heterogeneous Nuclear/genetics , RNA, Heterogeneous Nuclear/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , Sodium-Coupled Vitamin C Transporters/genetics , Transcription, Genetic
4.
J Neuroendocrinol ; 26(3): 195-204, 2014 Mar.
Article in English | MEDLINE | ID: mdl-24428719

ABSTRACT

The regulation of transcription of the growth hormone (GH) gene by glucocorticoids was studied in MtT/S cells, a cell line derived from an oestrogen-induced mammotrophic tumour in the rat, and in the primary culture of the anterior pituitary gland of adult mice. The levels of the GH heteronuclear RNA (GH hnRNA), which are mainly determined by the transcription rate, increased by 25-fold during 24 h in response to dexamethasone (DEX; 1 µM) in MtT/S cells that were cultured in the medium containing charcoal-stripped serum for 7 days. The stimulatory effect of DEX on the GH hnRNA levels was detectable as early as 30 min. This rapid effect of DEX did not require on-going protein synthesis, whereas it was considered that DEX requires the presence of unknown cellular proteins produced independently of DEX stimulation. By contrast, on-going protein synthesis was required for DEX action when incubated for 6 h, as has been observed in the previous studies. The specific inhibitor of glucocorticoid receptor, RU486, inhibited both rapid (30 min) and delayed (6 h) the effects of glucocorticoids on GH hnRNA levels. Membrane impermeable glucocorticoid, corticosterone-bovine serum albumin conjugate (CSBSA), was found to have effects similar to those of DEX and free corticosterone (CS), suggesting that glucocorticoids regulate GH gene transcription at least in part through the membrane bound receptors. From pharmacological studies, it was suggested that phosphatidylinositol 3-kinase (PI3K) activation is involved in the rapid effects but not in the delayed effects of glucocorticoids. This also suggests that the delayed effects of glucocorticoids depend on mechanisms other than the activation of PI3-kinase. Finally, both rapid and delayed effects of CS and CSBSA were observed not only in MtT/S cells, but also in the mouse pituitary cells in primary culture. Therefore, it is possible that the membrane initiated action of glucocorticoids is involved in the regulation of GH transcription in normal pituitary cells, as well as in pituitary tumour cells.


Subject(s)
Dexamethasone/pharmacology , Growth Hormone/genetics , Transcription, Genetic/drug effects , Animals , Base Sequence , Cell Line , DNA Primers , Mice , RNA, Heterogeneous Nuclear/genetics , Real-Time Polymerase Chain Reaction
5.
Mol Cell ; 51(3): 338-48, 2013 Aug 08.
Article in English | MEDLINE | ID: mdl-23891561

ABSTRACT

During meiosis in yeast, global splicing efficiency increases and then decreases. Here we provide evidence that splicing improves due to reduced competition for the splicing machinery. The timing of this regulation corresponds to repression and reactivation of ribosomal protein genes (RPGs) during meiosis. In vegetative cells, RPG repression by rapamycin treatment also increases splicing efficiency. Downregulation of the RPG-dedicated transcription factor gene IFH1 genetically suppresses two spliceosome mutations, prp11-1 and prp4-1, and globally restores splicing efficiency in prp4-1 cells. We conclude that the splicing apparatus is limiting and that pre-messenger RNAs compete. Splicing efficiency of a pre-mRNA therefore depends not just on its own concentration and affinity for limiting splicing factor(s), but also on those of competing pre-mRNAs. Competition between RNAs for limiting processing factors appears to be a general condition in eukaryotes for a variety of posttranscriptional control mechanisms including microRNA (miRNA) repression, polyadenylation, and splicing.


Subject(s)
Meiosis/genetics , RNA Precursors/genetics , RNA Precursors/metabolism , RNA Splicing , Saccharomyces cerevisiae/genetics , Base Sequence , Down-Regulation , Protein Serine-Threonine Kinases/genetics , RNA Splicing Factors , RNA, Fungal/genetics , RNA, Fungal/metabolism , RNA, Heterogeneous Nuclear/genetics , RNA, Heterogeneous Nuclear/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA-Binding Proteins/genetics , Ribonucleoprotein, U4-U6 Small Nuclear/genetics , Ribosomal Proteins/biosynthesis , Ribosomal Proteins/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/biosynthesis , Saccharomyces cerevisiae Proteins/genetics , Sequence Analysis, RNA , Sirolimus/pharmacology , Spliceosomes/genetics , Trans-Activators/biosynthesis , Transcription, Genetic
6.
Invest Ophthalmol Vis Sci ; 54(1): 697-707, 2013 Jan 23.
Article in English | MEDLINE | ID: mdl-23299472

ABSTRACT

PURPOSE: We investigated the impact of PININ (PNN) and epithelial splicing regulatory protein 1 (ESRP1) on alternative pre-mRNA splicing in the corneal epithelial context. METHODS: Isoform-specific RT-PCR assays were performed on wild-type and Pnn knockout mouse cornea. Protein interactions were examined by deconvolution microscopy and co-immunoprecipitation. For genome-wide alternative splicing study, immortalized human corneal epithelial cells (HCET) harboring doxycycline-inducible shRNA against PNN or ESRP1 were created. Total RNA was isolated from four biological replicates of control and knockdown HCET cells, and subjected to hGlue3_0 transcriptome array analysis. RESULTS: Pnn depletion in developing mouse corneal epithelium led to disrupted alternative splicing of multiple ESRP-regulated epithelial-type exons. In HCET cells, ESRP1 and PNN displayed close localization in and around nuclear speckles, and their physical association in protein complexes was identified. Whole transcriptome array analysis on ESRP1 or PNN knockdown HCET cells revealed clear alterations in transcript profiles and splicing patterns of specific subsets of genes. Separate RT-PCR validation assays confirmed successfully specific changes in exon usage of several representative splice variants, including PAX6(5a), FOXJ3, ARHGEF11, and SLC37A2. Gene ontologic analyses on ESRP1- or PNN-regulated alternative exons suggested their roles in epithelial phenotypes, such as cell morphology and movement. CONCLUSIONS: Our data suggested that ESRP1 and PNN modulate alternative splicing of a specific subset of target genes, but not general splicing events, in HCET cells to maintain or enhance epithelial characteristics.


Subject(s)
Alternative Splicing , Cell Adhesion Molecules/genetics , Epithelium, Corneal/metabolism , Gene Expression Regulation , Nuclear Proteins/genetics , RNA Precursors/genetics , RNA, Heterogeneous Nuclear/genetics , RNA-Binding Proteins/genetics , Animals , Cell Adhesion Molecules/metabolism , Cells, Cultured , Epithelium, Corneal/cytology , Exons , Gene Expression Profiling , Humans , Immunoblotting , Mice , Mice, Knockout , Microscopy, Fluorescence , Mutation , Nuclear Proteins/metabolism , RNA Precursors/metabolism , RNA, Heterogeneous Nuclear/metabolism , RNA-Binding Proteins/metabolism , Reverse Transcriptase Polymerase Chain Reaction
7.
Hum Mol Genet ; 21(R1): R90-6, 2012 Oct 15.
Article in English | MEDLINE | ID: mdl-22936691

ABSTRACT

New data are revealing a complex landscape of gene regulation shaped by chromatin states that extend into the bodies of transcribed genes and associate with distinct RNA elements such as exons, introns and polyadenylation sites. Exons are characterized by increased levels of nucleosome positioning, DNA methylation and certain histone modifications. As pre-mRNA splicing occurs co-transcriptionally, changes in the transcription elongation rate or epigenetic marks can influence exon splicing. These new discoveries broaden our understanding of the epigenetic code and ascribe a novel role for chromatin in controlling pre-mRNA processing. In this review, we summarize the recently discovered interplay between the modulation of chromatin states and pre-mRNA processing with the particular focus on how these processes communicate with one another to control gene expression.


Subject(s)
Chromatin/genetics , Epigenesis, Genetic , RNA Precursors/genetics , RNA Splicing , RNA, Messenger/genetics , Chromatin Assembly and Disassembly , DNA Methylation , Exons/genetics , Gene Expression Regulation , Histones/metabolism , Humans , RNA Precursors/metabolism , RNA, Heterogeneous Nuclear/genetics , RNA, Heterogeneous Nuclear/metabolism , RNA, Messenger/metabolism , Transcription, Genetic
8.
BMC Evol Biol ; 12: 112, 2012 Jul 09.
Article in English | MEDLINE | ID: mdl-22776158

ABSTRACT

BACKGROUND: Force, Lynch and Conery proposed the duplication-degeneration-complementation (DDC) model in which partitioning of ancestral functions (subfunctionalization) and acquisition of novel functions (neofunctionalization) were the two primary mechanisms for the retention of duplicated genes. The DDC model was tested by analyzing the transcriptional induction of the duplicated fatty acid-binding protein (fabp) genes by clofibrate in zebrafish. Clofibrate is a specific ligand of the peroxisome proliferator-activated receptor (PPAR); it activates PPAR which then binds to a peroxisome proliferator response element (PPRE) to induce the transcriptional initiation of genes primarily involved in lipid homeostasis. Zebrafish was chosen as our model organism as it has many duplicated genes owing to a whole genome duplication (WGD) event that occurred ~230-400 million years ago in the teleost fish lineage. We assayed the steady-state levels of fabp mRNA and heterogeneous nuclear RNA (hnRNA) transcripts in liver, intestine, muscle, brain and heart for four sets of duplicated fabp genes, fabp1a/fabp1b.1/fabp1b.2, fabp7a/fabp7b, fabp10a/fabp10b and fabp11a/fabp11b in zebrafish fed different concentrations of clofibrate. RESULT: Electron microscopy showed an increase in the number of peroxisomes and mitochondria in liver and heart, respectively, in zebrafish fed clofibrate. Clofibrate also increased the steady-state level of acox1 mRNA and hnRNA transcripts in different tissues, a gene with a functional PPRE. These results demonstrate that zebrafish is responsive to clofibrate, unlike some other fishes. The levels of fabp mRNA and hnRNA transcripts for the four sets of duplicated fabp genes was determined by reverse transcription, quantitative polymerase chain reaction (RT-qPCR). The level of hnRNA coded by a gene is an indirect estimate of the rate of transcriptional initiation of that gene. Clofibrate increased the steady-state level of fabp mRNAs and hnRNAs for both the duplicated copies of fabp1a/fabp1b.1, and fabp7a/fabp7b, but in different tissues. Clofibrate also increased the steady-state level of fabp10a and fabp11a mRNAs and hnRNAs in liver, but not for fabp10b and fabp11b. CONCLUSION: Some duplicated fabp genes have, most likely, retained PPREs, but induction by clofibrate is over-ridden by an, as yet, unknown tissue-specific mechanism(s). Regardless of the tissue-specific mechanism(s), transcriptional control of duplicated zebrafish fabp genes by clofibrate has markedly diverged since the WGD event.


Subject(s)
Clofibrate/pharmacology , Fatty Acid-Binding Proteins/genetics , Gene Expression Regulation, Developmental/drug effects , Peroxisome Proliferators/pharmacology , Zebrafish/genetics , Animals , Genes, Duplicate , Mitochondria, Heart/drug effects , Mitochondria, Liver/drug effects , Organ Specificity , RNA, Heterogeneous Nuclear/genetics , RNA, Messenger/genetics , Response Elements , Transcription Initiation, Genetic , Up-Regulation , Zebrafish/metabolism
9.
Methods Mol Biol ; 789: 89-110, 2011.
Article in English | MEDLINE | ID: mdl-21922402

ABSTRACT

Measurements of changes in pre-mRNA levels by intron-specific probes are generally accepted as more closely reflecting changes in gene transcription rates than are measurements of mRNA levels by exonic probes. This is, in part, because the pre-mRNAs, which include the primary transcript and various splicing intermediates located in the nucleus (also referred to as heteronuclear RNAs, or hnRNAs), are processed rapidly (with half-lives <60 min) as compared to neuropeptide mRNAs, which are then transferred to the cytoplasm and which have much longer half-lives (often over days). In this chapter, we describe the use of exon-and intron-specific probes to evaluate oxytocin (OT) and vasopressin (VP) neuropeptide gene expression by analyses of their mRNAs and hnRNAs by quantitative in situ hybridization (qISH) and also by using specific PCR primers in quantitative, real-time PCR (qPCR) procedures.


Subject(s)
Introns/genetics , Neuropeptides/genetics , Animals , Humans , In Situ Hybridization , Oxytocin/genetics , RNA Precursors/genetics , RNA, Heterogeneous Nuclear/genetics , Real-Time Polymerase Chain Reaction/methods , Vasopressins/genetics
10.
RNA ; 17(6): 1132-47, 2011 Jun.
Article in English | MEDLINE | ID: mdl-21525146

ABSTRACT

Metazoan replication-dependent histone mRNAs are the only nonpolyadenylated cellular mRNAs. Formation of the histone mRNA 3' end requires the U7 snRNP, which contains Lsm10 and Lsm11, and FLASH, a processing factor that binds Lsm11. Here, we identify sequences in Drosophila FLASH (dFLASH) that bind Drosophila Lsm11 (dLsm11), allow localization of dFLASH to the nucleus and histone locus body (HLB), and participate in histone pre-mRNA processing in vivo. Amino acids 105-154 of dFLASH bind to amino acids 1-78 of dLsm11. A two-amino acid mutation of dLsm11 that prevents dFLASH binding but does not affect localization of U7 snRNP to the HLB cannot rescue the lethality or histone pre-mRNA processing defects resulting from an Lsm11 null mutation. The last 45 amino acids of FLASH are required for efficient localization to the HLB in Drosophila cultured cells. Removing the first 64 amino acids of FLASH has no effect on processing in vivo. Removal of 13 additional amino acids of dFLASH results in a dominant negative protein that binds Lsm11 but inhibits processing of histone pre-mRNA in vivo. Inhibition requires the Lsm11 binding site, suggesting that the mutant dFLASH protein sequesters the U7 snRNP in an inactive complex and that residues between 64 and 77 of dFLASH interact with a factor required for processing. Together, these studies demonstrate that direct interaction between dFLASH and dLsm11 is essential for histone pre-mRNA processing in vivo and for proper development and viability in flies.


Subject(s)
Carrier Proteins/chemistry , Carrier Proteins/metabolism , Drosophila Proteins/chemistry , Drosophila Proteins/metabolism , Drosophila/genetics , Histones/genetics , RNA Precursors/metabolism , RNA, Messenger/metabolism , Ribonucleoproteins, Small Nuclear/chemistry , Ribonucleoproteins, Small Nuclear/metabolism , Animals , Binding Sites , Carrier Proteins/genetics , Cells, Cultured , Drosophila/metabolism , Drosophila Proteins/genetics , Histones/metabolism , RNA Processing, Post-Transcriptional , RNA, Heterogeneous Nuclear/genetics , RNA, Heterogeneous Nuclear/metabolism , Ribonucleoprotein, U7 Small Nuclear/genetics , Ribonucleoprotein, U7 Small Nuclear/metabolism , Ribonucleoproteins, Small Nuclear/genetics
11.
Am J Physiol Regul Integr Comp Physiol ; 298(4): R1098-110, 2010 Apr.
Article in English | MEDLINE | ID: mdl-20106992

ABSTRACT

The mechanism and route whereby glucagon-like peptide 1 (GLP-1) receptor agonists, such as GLP-1 and exendin-4 (Ex-4), access the central nervous system (CNS) to exert their metabolic effects have yet to be clarified. The primary objective of the present study was to investigate the potential role of two circumventricular organs (CVOs), the area postrema (AP) and the subfornical organ (SFO), in mediating the metabolic and CNS-stimulating effects of Ex-4. We demonstrated that electrolytic ablation of the AP, SFO, or AP + SFO does not acutely prevent the anorectic effects of Ex-4. AP + SFO lesion chronically decreased food intake and body weight and also modulated the effect of Ex-4 on the neuronal activation of brain structures involved in the hypothalamic-pituitary-adrenal axis and glucose metabolism. The results of the study also showed that CVO lesions blunted Ex-4-induced expression of c-fos mRNA (a widely used neuronal activity marker) in 1) limbic structures (bed nucleus of the stria terminalis and central amygdala), 2) hypothalamus (paraventricular hypothalamic nucleus, supraoptic nucleus, and arcuate nucleus), and 3) hindbrain (lateral and lateral-external parabrachial nucleus, medial nucleus of the solitary tract, and ventrolateral medulla). In conclusion, although the present results do not support a role for the CVOs in the anorectic effect induced by a single injection of Ex-4, they suggest that the CVOs play important roles in mediating the actions of Ex-4 in the activation of CNS structures involved in homeostatic control.


Subject(s)
Area Postrema/physiopathology , Hypoglycemic Agents/pharmacology , Peptides/pharmacology , Subfornical Organ/physiopathology , Venoms/pharmacology , Animals , Body Composition/drug effects , Body Weight/drug effects , Brain/enzymology , Brain/physiopathology , Deglutition Disorders/chemically induced , Deglutition Disorders/physiopathology , Energy Intake/drug effects , Energy Metabolism/drug effects , Exenatide , Genes, fos , Glucokinase/genetics , Male , Organ Size , RNA, Heterogeneous Nuclear/genetics , RNA, Messenger/drug effects , RNA, Messenger/genetics , Rats , Rats, Wistar
12.
Endocrinology ; 151(2): 793-801, 2010 Feb.
Article in English | MEDLINE | ID: mdl-20032051

ABSTRACT

The expression of the TRH gene in the paraventricular nucleus (PVH) of the hypothalamus is required for the normal production of thyroid hormone (TH) in rodents and humans. In addition, the regulation of TRH mRNA expression by TH, specifically in the PVH, ensures tight control of the set point of the hypothalamic-pituitary-thyroid axis. Although many studies have assumed that the regulation of TRH expression by TH is at the level of transcription, there is little data available to demonstrate this. We used two in vivo model systems to show this. In the first model system, we developed an in situ hybridization (ISH) assay directed against TRH heteronuclear RNA to measure TRH transcription directly in vivo. We show that in the euthyroid state, TRH transcription is present both in the PVH and anterior/lateral hypothalamus. In the hypothyroid state, transcription is activated in the PVH only and can be shut off within 5 h by TH. In the second model system, we employed transgenic mice that express the Cre recombinase under the control of the genomic region containing the TRH gene. Remarkably, TH regulates Cre expression in these mice in the PVH only. Taken together, these data affirm that TH regulates TRH at the level of transcription in the PVH only and that genomic elements surrounding the TRH gene mediate its regulation by T(3). Thus, it should be possible to identify the elements within the TRH locus that mediate its regulation by T(3) using in vivo approaches.


Subject(s)
Gene Expression Regulation/physiology , Thyrotropin-Releasing Hormone/genetics , Transcription, Genetic , Animals , Genes, Reporter , Green Fluorescent Proteins/genetics , Immunohistochemistry , Integrases/genetics , Mice , Mice, Inbred C57BL , Propylthiouracil/pharmacology , RNA, Heterogeneous Nuclear/genetics , RNA, Messenger/genetics , Thyrotropin-Releasing Hormone/metabolism , Transcription, Genetic/drug effects
13.
Pharmacogenet Genomics ; 19(11): 852-63, 2009 Nov.
Article in English | MEDLINE | ID: mdl-20431511

ABSTRACT

OBJECTIVE: To identify the mechanisms underlying the decreased allelic expression of a common CYP2A13 allele (7520C>G) in the human lung; CYP2A13 is expressed selectively in the respiratory tract, and is highly efficient in the metabolic activation of several chemical carcinogens. METHODS: The 7520C/G alleles were compared for mRNA stability in cells and relative heterogeneous nuclear RNA (hnRNA) levels in human lungs. Promoter region single nucleotide polymorphisms (SNPs) were identified and analyzed through in-vitro reporter gene assays and gel-shift assays, to uncover the causative SNPs responsible for the decreased allelic expression. RESULTS: (i) The 7520C>G SNP does not influence CYP2A13 mRNA stability in CYP2A13-transfected human lung or nasal epithelial cells; (ii) levels of the 7520G hnRNA were consistently lower (<10%) than the levels of the 7520C hnRNA in lung samples from nine heterozygous individuals; (iii) three SNPs (-1479T>C, -3101T>G, and -7756G>A) in linkage disequilibrium with the 7520C>G variation were found to cause altered interaction with DNA-binding proteins and decreases in promoter activity; (iv) the suppressive effects of the -1479T>C, -3101T>G, and -7756G>A SNPs on the CYP2A13 promoter were additive, whereas the negative effects of the -1479T>C SNP were enhanced by methylation of -1479C. CONCLUSION: The decrease in the expression of 7520G allele was because of the cumulative suppressive effects of multiple SNPs, with each by itself having a relatively small effect on CYP2A13 transcription.


Subject(s)
Alleles , Aryl Hydrocarbon Hydroxylases/genetics , Gene Expression Regulation, Enzymologic , Lung/enzymology , Polymorphism, Single Nucleotide/genetics , Promoter Regions, Genetic/genetics , RNA, Heterogeneous Nuclear/genetics , Aryl Hydrocarbon Hydroxylases/metabolism , Base Sequence , Cell Line, Tumor , Child , Child, Preschool , DNA Methylation/genetics , Electrophoretic Mobility Shift Assay , Female , Genes, Reporter/genetics , Humans , Infant , Male , Molecular Sequence Data , Pregnancy , Protein Binding , RNA Stability , RNA, Messenger/genetics , RNA, Messenger/metabolism , Transcription, Genetic
14.
Anal Bioanal Chem ; 392(6): 1109-22, 2008 Nov.
Article in English | MEDLINE | ID: mdl-18762920

ABSTRACT

The scattered and limited data on hnRNAs (pre-mRNAs) of cytochromes P450 (CYP) are compiled and discussed for the first time. The methods for determination and quantification of hnRNAs are compared. In most cases, CYP hnRNA levels were determined as a parameter of transcriptional activity. It is known, however, that some CYPs, in particular CYP2E1, are in addition specifically and extensively regulated by post-transcriptional processes. Obviously, these processes also influence the processing of CYP hnRNAs so that their levels cannot be considered a mere result of transcription. The underlying mechanisms of post-transcriptional CYP hnRNA and mRNA regulation are not well understood. It is our aim therefore to bring together available data on CYP hnRNA and to discuss them in the light of recent advances in knowledge concerning pre-mRNA processing and interactions between RNA and low molecular weight interfering RNAs. By doing this, we hope to drive research in a direction which appears promising in providing some long-awaited answers with respect to mechanisms of post-transcriptional CYP regulation.


Subject(s)
Cytochrome P-450 Enzyme System/metabolism , RNA Precursors/metabolism , RNA Processing, Post-Transcriptional/physiology , RNA, Heterogeneous Nuclear/metabolism , RNA, Messenger/metabolism , Transcription, Genetic/physiology , Animals , Cytochrome P-450 Enzyme System/genetics , Humans , Organ Specificity , Polymerase Chain Reaction , RNA Precursors/genetics , RNA Processing, Post-Transcriptional/genetics , RNA, Heterogeneous Nuclear/genetics , RNA, Messenger/genetics , Transcription, Genetic/genetics
15.
Prog Brain Res ; 170: 43-51, 2008.
Article in English | MEDLINE | ID: mdl-18655870

ABSTRACT

Intron-specific probes measure heteronuclear RNA (hnRNA) levels and thus approximate the transcription rates of genes, in part because of the rapid turnover of this intermediate form of RNA in the cell nucleus. Previously, we used oxytocin (Oxt)- and vasopressin (Avp)- intron-specific riboprobes to measure changes in Oxt and Avp hnRNA levels in the supraoptic nucleus (SON) by quantitative in situ hybridization (ISH) after various classical physiological perturbations, including acute and chronic salt loading, and lactation. In the present experiments, we used a novel experimental model to study the neurotransmitter regulation of Oxt and Avp gene expression in the rat SON in vivo. Bilateral cannulae connected via tubing to Alzet osmotic mini-pumps were positioned over the SON. In every experiment, one SON was infused with PBS and served as the control SON in each animal, and the contralateral SON received infusions of various neurotransmitter agonists and antagonists. Using this approach, we found that Avp but not Oxt gene expression increased after acute (2-5h) combined excitatory amino acid agonist and GABA antagonist treatment, similar to what we found after an acute hyperosmotic stimulus. Since both OXT and AVP are known to be comparably and robustly secreted in response to acute osmotic stimuli in vivo and glutamate agonists in vitro, our results indicate a dissociation between OXT secretion and Oxt gene transcription in vivo.


Subject(s)
Central Nervous System/physiology , Oxytocin/genetics , Supraoptic Nucleus/physiology , Vasopressins/genetics , Animals , DNA Primers , In Situ Hybridization , Introns , Male , Oxytocin/metabolism , Polymerase Chain Reaction , RNA, Heterogeneous Nuclear/genetics , Rats , Rats, Sprague-Dawley , Transcription, Genetic , Vasopressins/metabolism
16.
Stem Cells Dev ; 16(6): 905-19, 2007 Dec.
Article in English | MEDLINE | ID: mdl-17999636

ABSTRACT

During the past decade, regenerative medicine has been the subject of intense interest due, in large part, to our growing knowledge of embryonic stem (ES) cell biology. ES cells give rise to cell lineages from the three primordial germ layers--endoderm, mesoderm, and ectoderm. This process needs to be channeled if these cells are to be differentiated efficiently and used subsequently for therapeutic purposes. Indeed, an important area of investigation involves directed differentiation to influence the lineage commitment of these pluripotent cells in vitro. Various strategies involving timely growth factor supplementation, cell co-cultures, and gene transfection are used to drive lineage specific emergence. The underlying goal is to control directly the center of gene expression and cellular programming--the nucleus. Gene expression is enabled, managed, and sustained by the collective actions and interactions of proteins found in the nucleus--the nuclear proteome--in response to extracellular signaling. Nuclear proteomics can inventory these nuclear proteins in differentiating cells and decipher their dynamics during cellular phenotypic commitment. This review details what is currently known about nuclear effectors of stem cell differentiation and describes emerging techniques in the discovery of nuclear proteomics that will illuminate new transcription factors and modulators of gene expression.


Subject(s)
Embryonic Stem Cells/cytology , Embryonic Stem Cells/physiology , Nuclear Proteins/genetics , Proteomics , Animals , Cell Differentiation , Cell Nucleus/physiology , Ectoderm/cytology , Endoderm/cytology , Humans , Mesoderm/cytology , RNA, Heterogeneous Nuclear/genetics
17.
Genetica ; 128(1-3): 261-72, 2006.
Article in English | MEDLINE | ID: mdl-17028956

ABSTRACT

LINE-1 (L1) retrotransposons comprise about 17% of the human genome and include a recently transposed set of Ta-L1 elements that are polymorphic in humans. Although it is widely believed that L1s play an essential role in shaping and functioning of mammalian genomes, the understanding of the impact of L1 insertions on gene expression is far from being comprehensive. Here we compared hnRNA contents for allele pairs of genes heterozygous for Ta-L1 insertions in their introns in human cell lines of various origin. We demonstrated that some Ta-L1 insertions correlated with decreased content of the corresponding hnRNAs. This effect was characteristic of only nearly full-sized L1s and seemed to be tissue specific.


Subject(s)
Genome, Human , Introns , Long Interspersed Nucleotide Elements , Alleles , Base Sequence , Cell Line , DNA Primers/genetics , Evolution, Molecular , HeLa Cells , Heterozygote , Humans , Jurkat Cells , RNA, Heterogeneous Nuclear/genetics , RNA, Heterogeneous Nuclear/metabolism , Reverse Transcriptase Polymerase Chain Reaction , Transcription, Genetic
18.
Int J Parasitol ; 36(12): 1295-304, 2006 Oct.
Article in English | MEDLINE | ID: mdl-16860325

ABSTRACT

Mitochondrial gene expression in kinetoplastids is controlled after transcription, potentially at the levels of RNA maturation, stability and translation. Among these processes, RNA editing by U-insertion/deletion catalysed by multi-subunit editing complexes is best characterised at the molecular level. Nevertheless, mitochondrial RNA metabolism overall remains poorly understood, including the potential regulatory factors that may interact with the relevant catalytic molecular machines and/or RNA substrates. Here we report on a approximately 25kDa polypeptide in mitochondrial extracts that exhibits a preferential "zero-distance" photo-crosslinking interaction with an A6 pre-mRNA model substrate for RNA editing containing a single [(32)P] at the first editing site. The approximately 25kDa polypeptide purified away from editosomes upon ion-exchange chromatography and glycerol gradient sedimentation. Competition assays with homologous and heterologous transcripts suggest that the preferential recognition of the A6 substrate is based on relatively low-specificity RNA-protein contacts. Our mapping and substrate truncation analyses suggest that the crosslinking activity primarily targeted a predicted stem-loop region containing the first editing sites. Consistent with the notion that pre-mRNA folding may be required, pre-annealing with guide RNA abolished crosslinking. Interestingly, this preferential protein interaction with the A6 substrate seemed to require adenosine 5'-triphosphate but not hydrolysis. As in other biological systems, fine regulation in vivo may be brought about by transient networks of relatively low-specificity interactions in which multiple auxiliary factors bind to mRNAs and/or editing complexes in unique higher-order assemblies.


Subject(s)
Protozoan Proteins/genetics , RNA Editing/genetics , RNA Precursors/genetics , RNA, Protozoan/genetics , Trypanosoma brucei brucei/genetics , Adenosine Triphosphate/genetics , Animals , Base Sequence , Cross-Linking Reagents , Gene Expression Regulation/genetics , Mitochondria/genetics , Mitochondrial Proteins/genetics , Molecular Weight , Nucleic Acid Conformation , RNA/genetics , RNA, Guide, Kinetoplastida/genetics , RNA, Heterogeneous Nuclear/genetics , RNA, Messenger/genetics , RNA, Mitochondrial
19.
J Cell Sci ; 118(Pt 14): 3173-83, 2005 Jul 15.
Article in English | MEDLINE | ID: mdl-16014382

ABSTRACT

Overexpression of heterogeneous nuclear ribonucleoproteins (hnRNPs) A2 and B1 has been observed in a variety of tumour types, however, it is unknown whether this dysregulation is a consequence of, or a driving force for, unregulated cell proliferation. We have shown that the levels of hnRNPs A1, A2 and B1, but not A3, are modulated during the cell cycle of Colo16 squamous carcinoma cells and HaCaT immortalized keratinocytes, suggesting that A1, A2 and B1 are needed at particular cell cycle stages. However, the levels of hnRNP A1, A2 and B1 mRNAs were constant, indicating that regulation of protein levels was controlled at the level of translation. RNAi suppression of hnRNP A1 or A3 alone did not affect the proliferation of Colo16 cells but the proliferation rate was significantly reduced when both were suppressed simultaneously, or when either was suppressed together with hnRNP A2. Reducing hnRNP A2 expression in Colo16 and HaCaT cells by RNAi led to a non-apoptotic-related decrease in cell proliferation, reinforcing the view that this protein is required for cell proliferation. Suppression of hnRNP A2 in Colo16 cells was associated with increased p21 levels but p53 levels remained unchanged. In addition, expression of BRCA1 was downregulated, at both mRNA and protein levels. The observed effects of hnRNP A2 and its isoforms on cell proliferation and their correlation with BRCA1 and p21 expression suggest that these hnRNP proteins play a role in cell proliferation.


Subject(s)
Heterogeneous-Nuclear Ribonucleoprotein Group A-B/physiology , Ribonucleoproteins/biosynthesis , Blotting, Northern , Blotting, Western , Cell Cycle/physiology , Cell Growth Processes/physiology , Cell Line, Tumor , Genes, BRCA1/physiology , HeLa Cells , Heterogeneous-Nuclear Ribonucleoprotein Group A-B/biosynthesis , Heterogeneous-Nuclear Ribonucleoprotein Group A-B/genetics , Humans , Immunohistochemistry , In Situ Nick-End Labeling , RNA, Heterogeneous Nuclear/genetics , RNA, Messenger/biosynthesis , RNA, Messenger/genetics , Reverse Transcriptase Polymerase Chain Reaction , Ribonucleoproteins/analysis , Ribonucleoproteins/genetics , Transfection
20.
Am J Cardiol ; 95(6): 787-9, 2005 Mar 15.
Article in English | MEDLINE | ID: mdl-15757614

ABSTRACT

We tested the hypothesis that triiodothyronine (T3) supplementation alters gene transcription in the left ventricular myocardium of infants undergoing cardiopulmonary bypass for ventricular septal defect repair. To our knowledge, a novel heteronuclear assay demonstrated for the first time in human heart that rapid change in T3 levels altered the adenine nucleotide translocase-1 transcription rate during cardiopulmonary bypass.


Subject(s)
Cardiopulmonary Bypass , Heart Septal Defects, Ventricular/surgery , Myocardium/pathology , Transcription, Genetic/genetics , Triiodothyronine/physiology , Adenine Nucleotide Translocator 1/genetics , Biopsy, Needle , Female , Heart Septal Defects, Ventricular/genetics , Humans , Infant , Male , Polymerase Chain Reaction , RNA, Heterogeneous Nuclear/genetics , Sodium-Calcium Exchanger/genetics , Tetralogy of Fallot , Transcription, Genetic/drug effects , Triiodothyronine/administration & dosage , Ventricular Myosins/genetics
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