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1.
J Cell Biol ; 219(9)2020 09 07.
Article in English | MEDLINE | ID: mdl-32673398

ABSTRACT

In mammals, argonaute (AGO) proteins have been characterized for their roles in small RNA-mediated posttranscriptional and also in transcriptional gene silencing. Here, we report a different role for AGO1 in estradiol-triggered transcriptional activation in human cells. We show that in MCF-7 mammary gland cells, AGO1 associates with transcriptional enhancers of estrogen receptor α (ERα) and that this association is up-regulated by treating the cells with estrogen (E2), displaying a positive correlation with the activation of these enhancers. Moreover, we show that AGO1 interacts with ERα and that this interaction is also increased by E2 treatment, but occurs in the absence of RNA. We show that AGO1 acts positively as a coactivator in estradiol-triggered transcription regulation by promoting ERα binding to its enhancers. Consistently, AGO1 depletion decreases long-range contacts between ERα enhancers and their target promoters. Our results point to a role of AGO1 in transcriptional regulation in human cells that is independent from small RNA binding.


Subject(s)
Argonaute Proteins/genetics , Estrogens/genetics , Eukaryotic Initiation Factors/genetics , Transcription Factors/genetics , Transcription, Genetic/genetics , Transcriptional Activation/genetics , Cell Line , Cell Line, Tumor , Enhancer Elements, Genetic/genetics , Estradiol/genetics , Gene Expression Regulation, Neoplastic/genetics , HEK293 Cells , Humans , MCF-7 Cells , Promoter Regions, Genetic/genetics , Protein Binding/genetics
2.
Cancer Cell ; 34(6): 982-995.e7, 2018 12 10.
Article in English | MEDLINE | ID: mdl-30503705

ABSTRACT

Enhancer profiling is a powerful approach for discovering cis-regulatory elements that define the core transcriptional regulatory circuits of normal and malignant cells. Gene control through enhancer activity is often dominated by a subset of lineage-specific transcription factors. By integrating measures of chromatin accessibility and enrichment for H3K27 acetylation, we have generated regulatory landscapes of chronic lymphocytic leukemia (CLL) samples and representative cell lines. With super enhancer-based modeling of regulatory circuits and assessments of transcription factor dependencies, we discover that the essential super enhancer factor PAX5 dominates CLL regulatory nodes and is essential for CLL cell survival. Targeting enhancer signaling via BET bromodomain inhibition disrupts super enhancer-dependent gene expression with selective effects on CLL core regulatory circuitry, conferring potent anti-tumor activity.


Subject(s)
Chromatin/genetics , Enhancer Elements, Genetic/genetics , Gene Expression Regulation, Leukemic/genetics , Leukemia, Lymphocytic, Chronic, B-Cell/genetics , Acetylation , Animals , Azepines/pharmacology , Cell Line, Tumor , Chromatin/drug effects , Chromatin/metabolism , Gene Expression Regulation, Leukemic/drug effects , Histones/metabolism , Humans , Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy , Leukemia, Lymphocytic, Chronic, B-Cell/metabolism , Mice, Knockout , PAX5 Transcription Factor/genetics , PAX5 Transcription Factor/metabolism , Protein Binding , Proteins/antagonists & inhibitors , Proteins/genetics , Proteins/metabolism , Triazoles/pharmacology , Xenograft Model Antitumor Assays/methods
3.
Genesis ; 56(8): e23222, 2018 08.
Article in English | MEDLINE | ID: mdl-30096221

ABSTRACT

In a previous bioinformatics analysis we identified 10 conserved Drosophila melanogaster sequences that reside upstream from protein coding genes (CGs). Here we characterize one of these genomic regions, which constitutes a Drosophila melanogaster cis-regulatory module (CRM) that we denominate TT-CRM. The TT-CRM is 646 bp long and is located in one of the introns of CG32239 and resides about 3,500 bp upstream of CG13711 and about 620 bp upstream of CG12493. Analysis of 646 bp-lacZ lines revealed that TT-CRM drives gene expression not only to the larval, prepupal, and pupal tracheal system but also to the adult dorsal longitudinal muscles. The patterns of mRNA expression of the transgene and of the CGs that lie in the vicinity of TT-CRM were investigated both in dissected trachea and in adult thoraces. Through RT-qPCR we observed that in the tracheal system the pattern of expression of 646 bp-lacZ is similar to the pattern of expression of CG32239 and CG13711, whereas in the thoracic muscles 646 bp-lacZ expression accompanies the expression of CG12493. Together, these results suggest new functions for two previously characterized D. melanogaster genes and also contribute to the initial characterization of a novel CRM that drives a dynamic pattern of expression throughout development.


Subject(s)
Enhancer Elements, Genetic/genetics , Gene Expression Regulation, Developmental/genetics , Trachea/embryology , Animals , Base Sequence , Drosophila Proteins/genetics , Drosophila melanogaster/genetics , Gene Expression/genetics , Introns/genetics , Larva/metabolism , Muscle, Skeletal/growth & development , Muscle, Skeletal/metabolism , Promoter Regions, Genetic/genetics , Trachea/metabolism
4.
Trends Biochem Sci ; 43(6): 452-468, 2018 06.
Article in English | MEDLINE | ID: mdl-29673772

ABSTRACT

Gene expression in higher eukaryotes is precisely regulated in time and space through the interplay between promoters and gene-distal regulatory regions, known as enhancers. The original definition of enhancers implies the ability to activate gene expression remotely, while promoters entail the capability to locally induce gene expression. Despite the conventional distinction between them, promoters and enhancers share many genomic and epigenomic features. One intriguing finding in the gene regulation field comes from the observation that many core promoter regions display enhancer activity. Recent high-throughput reporter assays along with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-related approaches have indicated that this phenomenon is common and might have a strong impact on our global understanding of genome organisation and gene expression regulation.


Subject(s)
Enhancer Elements, Genetic/genetics , Promoter Regions, Genetic/genetics , Animals , Gene Expression Regulation/genetics , High-Throughput Screening Assays , Humans
5.
Mol Cell Endocrinol ; 439: 407-418, 2017 01 05.
Article in English | MEDLINE | ID: mdl-27697584

ABSTRACT

With the aim to analyze whether bisphenol A (BPA) modifies ß-Casein (ß-Cas) synthesis and transcriptional regulation in perinatally exposed animals, here, pregnant F0 rats were orally exposed to 0, 0.6 or 52 µg BPA/kg/day from gestation day 9 until weaning. Then, F1 females were bred and mammary glands were obtained on lactation day 2. Perinatal BPA exposure decreased ß-Cas expression without modifying the activation of prolactin receptor. It also decreased the expression of glucocorticoid receptor in BPA52-exposed dams and ß1 and α6 integrins as well as dystroglycan in both BPA groups. In addition, BPA exposure altered the expression of histone-modifying enzymes and induced histone modifications and DNA methylation in the promoter, enhancer and exon VII of the ß-Cas gene. An impaired crosstalk between the extracellular matrix and lactogenic hormone signaling pathways and epigenetic modifications of the ß-Cas gene could be the molecular mechanisms by which BPA decreased ß-Cas expression.


Subject(s)
Benzhydryl Compounds/toxicity , Caseins/genetics , Gene Expression Regulation, Developmental/drug effects , Mammary Glands, Animal/metabolism , Phenols/toxicity , Prenatal Exposure Delayed Effects/genetics , Transcription, Genetic/drug effects , Animals , Caseins/metabolism , Cell Communication/drug effects , DNA Methylation/genetics , Enhancer Elements, Genetic/genetics , Exons/genetics , Female , Histones/metabolism , Lactation/genetics , Laminin/metabolism , Pregnancy , Prenatal Exposure Delayed Effects/pathology , Promoter Regions, Genetic , Protein Processing, Post-Translational/drug effects , Rats, Wistar , Receptors, Glucocorticoid/metabolism , Receptors, Laminin/metabolism , Receptors, Prolactin/metabolism , Signal Transduction/drug effects , Signal Transduction/genetics
6.
Gene ; 591(1): 191-200, 2016 Oct 10.
Article in English | MEDLINE | ID: mdl-27397649

ABSTRACT

In the early Drosophila melanogaster embryo, the gene regulatory network controlled by Dpp signaling is involved in the subdivision of dorsal ectoderm into the presumptive dorsal epidermis and amnioserosa. In this work, we aimed to identify new Dpp downstream targets involved in dorsal ectoderm patterning. We used oligonucleotide D. melanogaster microarrays to identify the set of genes that are differential expressed between wild type embryos and embryos that overexpress Dpp (nos-Gal4>UAS-dpp) during early stages of embryo development. By using this approach, we identified 358 genes whose relative abundance significantly increased in response to Dpp overexpression. Among them, we found the entire set of known Dpp target genes that function in dorsal ectoderm patterning (zen, doc, hnt, pnr, ush, tup, and others) in addition to several up-regulated genes of unknown functions. Spatial expression pattern of up-regulated genes in response to Dpp overexpression as well as their opposing transcriptional responses to Dpp loss- and gain-of-function indicated that they are new candidate target genes of Dpp signaling pathway. We further analyse one of the candidate genes, CG13653, which is expressed at the dorsal-most cells of the embryo during a restricted period of time. CG13653 orthologs were not detected in basal lineages of Dipterans, which unlike D. melanogaster develop two extra-embryonic membranes, amnion and serosa. We characterized the enhancer region of CG13653 and revealed that CG13653 is directly regulated by Dpp signaling pathway.


Subject(s)
Drosophila Proteins/genetics , Drosophila melanogaster/embryology , Drosophila melanogaster/genetics , Embryo, Nonmammalian/metabolism , Gene Expression Profiling , Gene Expression Regulation, Developmental , Signal Transduction/genetics , Animals , Base Pairing/genetics , Base Sequence , Drosophila Proteins/metabolism , Embryonic Development/genetics , Enhancer Elements, Genetic/genetics , Genes, Insect , Mutation/genetics , Oligonucleotide Array Sequence Analysis , Reproducibility of Results
7.
Mol Biol Cell ; 27(12): 1921-7, 2016 06 15.
Article in English | MEDLINE | ID: mdl-27099369

ABSTRACT

One of the earliest manifestations of neural induction is onset of expression of the neural marker Sox2, mediated by the activation of the enhancers N1 and N2. By using loss and gain of function, we find that Sox2 expression requires the activity of JmjD2A and the Msk1 kinase, which can respectively demethylate the repressive H3K9me3 mark and phosphorylate the activating H3S10 (H3S10ph) mark. Bimolecular fluorescence complementation reveals that the adaptor protein 14-3-3, known to bind to H3S10ph, interacts with JMJD2A and may be involved in its recruitment to regulatory regions of the Sox2 gene. Chromatin immunoprecipitation reveals dynamic binding of JMJD2A to the Sox2 promoter and N-1 enhancer at the time of neural plate induction. Finally, we show a clear temporal antagonism on the occupancy of H3K9me3 and H3S10ph modifications at the promoter of the Sox2 locus before and after the neural plate induction. Taken together, our results propose a series of epigenetic events necessary for the early activation of the Sox2 gene in neural progenitor cells.


Subject(s)
Jumonji Domain-Containing Histone Demethylases/metabolism , SOXB1 Transcription Factors/genetics , SOXB1 Transcription Factors/metabolism , 14-3-3 Proteins/metabolism , Animals , Chick Embryo , Embryonic Development/genetics , Enhancer Elements, Genetic/genetics , Epigenomics , Gene Expression Regulation, Developmental/genetics , Neural Plate/metabolism , Neural Stem Cells/metabolism , Phosphorylation , Promoter Regions, Genetic , Ribosomal Protein S6 Kinases, 90-kDa/metabolism , Transcription Factors/metabolism
8.
Genet Mol Res ; 13(4): 9899-909, 2014 Nov 27.
Article in English | MEDLINE | ID: mdl-25501200

ABSTRACT

Phospholipase C zeta 1 (PLCζ1), which transcribes a key protein, has an important function in oocyte activation and embryo development because PLCζ1 can trigger a series of intracellular Ca2+ oscillations in mammals. In this study, a novel splice variant in the testis tissues of adult and fetal Chinese Holstein bulls was characterized by reverse transcription-polymerase chain reaction (RT-PCR) and sequencing analysis. The novel splice variant PLCζ1-sv1 was derived from the PLCζ1 complete transcript (PLCζ1-complete) by alternative splicing; the alternative splicing pattern exhibited alternative 5'-splice sites. The full-length transcript, PLCζ1-complete, is the main transcript found in fetal and adult cow testis tissue. Quantitative real-time PCR (qPCR) analysis demonstrated that the expression levels of the PLCζ1-complete transcript were significantly higher than those of the PLCζ1-sv1 splice variant in bovine testis tissues. PLCζ1 protein sequencing analysis showed that the amino acids at positions 453 to 457 were deleted in PLCζ1-sv1, thereby terminating transcription prematurely. In summary, this study provided information to elucidate the structure and function of the bovine PLCζ1 gene.


Subject(s)
Alternative Splicing/genetics , Phospholipase C gamma/genetics , Testis/enzymology , Amino Acid Sequence , Animals , Base Sequence , Cattle , China , Enhancer Elements, Genetic/genetics , Exons/genetics , Male , Molecular Sequence Data , Nucleotide Motifs/genetics , Phospholipase C gamma/chemistry , Protein Structure, Tertiary , RNA, Messenger/genetics , RNA, Messenger/metabolism , Transcription, Genetic
9.
Philos Trans R Soc Lond B Biol Sci ; 368(1632): 20130017, 2013 Dec 19.
Article in English | MEDLINE | ID: mdl-24218630

ABSTRACT

Deciphering the genetic bases that drive animal diversity is one of the major challenges of modern biology. Although four decades ago it was proposed that animal evolution was mainly driven by changes in cis-regulatory DNA elements controlling gene expression rather than in protein-coding sequences, only now are powerful bioinformatics and experimental approaches available to accelerate studies into how the evolution of transcriptional enhancers contributes to novel forms and functions. In the introduction to this Theme Issue, we start by defining the general properties of transcriptional enhancers, such as modularity and the coexistence of tight sequence conservation with transcription factor-binding site shuffling as different mechanisms that maintain the enhancer grammar over evolutionary time. We discuss past and current methods used to identify cell-type-specific enhancers and provide examples of how enhancers originate de novo, change and are lost in particular lineages. We then focus in the central part of this Theme Issue on analysing examples of how the molecular evolution of enhancers may change form and function. Throughout this introduction, we present the main findings of the articles, reviews and perspectives contributed to this Theme Issue that together illustrate some of the great advances and current frontiers in the field.


Subject(s)
Biodiversity , Computational Biology/methods , Enhancer Elements, Genetic/genetics , Evolution, Molecular , Animals , Binding Sites/genetics , Computational Biology/trends , Conserved Sequence/genetics , Humans
10.
Philos Trans R Soc Lond B Biol Sci ; 368(1632): 20130019, 2013 Dec 19.
Article in English | MEDLINE | ID: mdl-24218632

ABSTRACT

The developmental brain gene NPAS3 stands out as a hot spot in human evolution because it contains the largest number of human-specific, fast-evolving, conserved, non-coding elements. In this paper we studied 2xHAR142, one of these elements that is located in the fifth intron of NPAS3. Using transgenic mice, we show that the mouse and chimp 2xHAR142 orthologues behave as transcriptional enhancers driving expression of the reporter gene lacZ to a similar NPAS3 expression subdomain in the mouse central nervous system. Interestingly, the human 2xHAR142 orthologue drives lacZ expression to an extended expression pattern in the nervous system. Thus, molecular evolution of 2xHAR142 provides the first documented example of human-specific heterotopy in the forebrain promoted by a transcriptional enhancer and suggests that it may have contributed to assemble the unique properties of the human brain.


Subject(s)
Enhancer Elements, Genetic/genetics , Evolution, Molecular , Gene Expression Regulation/genetics , Nerve Tissue Proteins/genetics , Prosencephalon/metabolism , Transcription Factors/genetics , Animals , Basic Helix-Loop-Helix Transcription Factors , Computational Biology , Conserved Sequence/genetics , DNA Primers/genetics , Galactosides , Humans , Immunohistochemistry , In Situ Hybridization , Indoles , Lac Operon/genetics , Mice , Mice, Transgenic , Nerve Tissue Proteins/metabolism , Pan troglodytes/genetics , Short Interspersed Nucleotide Elements/genetics , Species Specificity , Transcription Factors/metabolism
11.
Philos Trans R Soc Lond B Biol Sci ; 368(1632): 20130027, 2013 Dec 19.
Article in English | MEDLINE | ID: mdl-24218639

ABSTRACT

Mutations in regulatory regions including enhancers are an important source of variation and innovation during evolution. Enhancers can evolve by changes in the sequence, arrangement and repertoire of transcription factor binding sites, but whole enhancers can also be lost or gained in certain lineages in a process of turnover. The proopiomelanocortin gene (Pomc), which encodes a prohormone, is expressed in the pituitary and hypothalamus of all jawed vertebrates. We have previously described that hypothalamic Pomc expression in mammals is controlled by two enhancers-nPE1 and nPE2-that are derived from transposable elements and that presumably replaced the ancestral neuronal Pomc regulatory regions. Here, we show that nPE1 and nPE2, even though they are mammalian novelties with no homologous counterpart in other vertebrates, nevertheless can drive gene expression specifically to POMC neurons in the hypothalamus of larval and adult transgenic zebrafish. This indicates that when neuronal Pomc enhancers originated de novo during early mammalian evolution, the newly created cis- and trans-codes were similar to the ancestral ones. We also identify the neuronal regulatory region of zebrafish pomca and confirm that it is not homologous to the mammalian enhancers. Our work sheds light on the process of gene regulatory evolution by showing how a locus can undergo enhancer turnover and nevertheless maintain the ancestral transcriptional output.


Subject(s)
Enhancer Elements, Genetic/genetics , Evolution, Molecular , Gene Expression Regulation/genetics , Pro-Opiomelanocortin/genetics , Vertebrates/genetics , Zebrafish Proteins/genetics , Animals , Animals, Genetically Modified , Computational Biology , Conserved Sequence/genetics , Immunohistochemistry , In Situ Hybridization , Mutation/genetics , Neurons/metabolism , Zebrafish
12.
Spine (Phila Pa 1976) ; 38(24): 2079-84, 2013 Nov 15.
Article in English | MEDLINE | ID: mdl-24026150

ABSTRACT

STUDY DESIGN: To inhibit ß-catenin specifically signaling in chondrocytes Col2-ICAT transgenic mice were generated. Anomalies in caudal vertebrae were detected during embryonic and postnatal stages of Col2-ICAT transgenic mice. OBJECTIVE: To determine the role of canonical ß-catenin signaling in caudal vertebral development. SUMMARY OF BACKGROUND DATA: ß-catenin signaling plays a critical role in skeletal development. Col2-ICAT transgenic mice were generated to selectively block ß-catenin signaling by overexpression of the ICAT gene in chondrocytes. METHODS: Tails of E16.5 transgenic embryos and adult Col2-ICAT transgenic mice and their wild-type littermates were collected and analyzed. Skeletal preparation, 3-dimensional micro-computed tomographic and histological analyses were performed to evaluate changes in the structure of caudal vertebrae. Bromodeoxyuridine labeling was performed to evaluate changes in chondrocyte proliferation in caudal vertebrae. RESULTS: Skeletal preparation and 3-dimensional micro-computed tomographic analyses revealed bone deformation and angulated deformities in tail tissue in Col2-ICAT transgenic mice. Histological studies revealed abnormal bone development and dysplastic caudal vertebrae in Col2-ICAT transgenic mice. Inhibition of ß-catenin signaling in cartilage resulted in vertebral dysplasia leading to aberrant resegmenting process. Thus, 2 poorly developed sclerotomes failed to fuse to form a complete vertebrae. BrdU labeling revealed a decreased chondrocyte proliferation in both cartilageous templates of transgenic embryos and the growth plate of adult Col2-ICAT transgenic mice. CONCLUSION: Wnt/ß-catenin signaling plays an important role in vertebral development. Inhibition of ß-catenin signaling in chondrocytes results in caudal vertebra deformity in mice, which may occur as early as in the stage of sclerotome formation. LEVEL OF EVIDENCE: N/A.


Subject(s)
Chondrocytes/metabolism , Signal Transduction , Spine/metabolism , beta Catenin/metabolism , Adaptor Proteins, Signal Transducing , Animals , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Cell Proliferation , Chondrocytes/cytology , Collagen Type II/genetics , Embryo, Mammalian/abnormalities , Embryo, Mammalian/metabolism , Enhancer Elements, Genetic/genetics , Immunohistochemistry , Mice , Mice, Inbred C57BL , Mice, Transgenic , Promoter Regions, Genetic/genetics , Repressor Proteins , Spine/abnormalities , Spine/diagnostic imaging , Tail/abnormalities , Tail/diagnostic imaging , Tail/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , X-Ray Microtomography , beta Catenin/genetics
13.
PLoS One ; 8(3): e58540, 2013.
Article in English | MEDLINE | ID: mdl-23520519

ABSTRACT

The tumor suppressor Adenomatous Polyposis coli (APC) gene is mutated or lost in most colon cancers. Alterations in Protein kinase C (PKC) isozyme expression and aberrant regulation also comprise early events in intestinal carcinomas. Here we show that PKCδ expression levels are decreased in colon tumor cell lines with respect to non-malignant cells. Reciprocal co-immunoprecipitation and immunofluorescence studies revealed that PKCδ interacts specifically with both full-length (from non-malignant cells) and truncated APC protein (from cancerous cells) at the cytoplasm and at the cell nucleus. Selective inhibition of PKCδ in cancer SW480 cells, which do not possess a functional ß-catenin destruction complex, did not affect ß-catenin-mediated transcriptional activity. However, in human colon carcinoma RKO cells, which have a normal ß-catenin destruction complex, negatively affected ß-catenin-mediated transcriptional activity, cell proliferation, and the expression of Wnt target genes C-MYC and CYCLIN D1. These negative effects were confirmed by siRNA-mediated knockdown of PKCδ and by the expression of a dominant negative form of PKCδ in RKO cells. Remarkably, the PKCδ stably depleted cells exhibited augmented tumorigenic activity in grafted mice. We show that PKCδ functions in a mechanism that involves regulation of ß-catenin degradation, because PKCδ inhibition induces ß-catenin stabilization at the cytoplasm and its nuclear presence at the C-MYC enhancer even without Wnt3a stimulation. In addition, expression of a dominant form of PKCδ diminished APC phosphorylation in intact cells, suggesting that PKCδ may modulate canonical Wnt activation negatively through APC phosphorylation.


Subject(s)
Adenomatous Polyposis Coli Protein/metabolism , Cell Proliferation , Colonic Neoplasms/metabolism , Protein Kinase C-delta/metabolism , Wnt Signaling Pathway , Wnt3A Protein/metabolism , Adenomatous Polyposis Coli Protein/genetics , Animals , Cell Line, Tumor , Cell Nucleus/genetics , Cell Nucleus/metabolism , Cell Nucleus/pathology , Colonic Neoplasms/pathology , Cyclin D1/genetics , Cyclin D1/metabolism , Cytoplasm/genetics , Cytoplasm/metabolism , Enhancer Elements, Genetic/genetics , Humans , Mice , Mice, Nude , Phosphorylation/genetics , Protein Kinase C-delta/genetics , Protein Stability , Proteolysis , Proto-Oncogene Proteins c-myc/genetics , Proto-Oncogene Proteins c-myc/metabolism , Wnt3A Protein/genetics , beta Catenin/genetics , beta Catenin/metabolism
14.
J Exp Bot ; 63(5): 2189-202, 2012 Mar.
Article in English | MEDLINE | ID: mdl-22210906

ABSTRACT

Plants have evolved a plethora of responses to cope with phosphate (Pi) deficiency, including the transcriptional activation of a large set of genes. Among Pi-responsive genes, the expression of the Arabidopsis phospholipase DZ2 (PLDZ2) is activated to participate in the degradation of phospholipids in roots in order to release Pi to support other cellular activities. A deletion analysis was performed to identify the regions determining the strength, tissue-specific expression, and Pi responsiveness of this regulatory region. This study also reports the identification and characterization of a transcriptional enhancer element that is present in the PLDZ2 promoter and able to confer Pi responsiveness to a minimal, inactive 35S promoter. This enhancer also shares the cytokinin and sucrose responsive properties observed for the intact PLDZ2 promoter. The EZ2 element contains two P1BS motifs, each of which is the DNA binding site of transcription factor PHR1. Mutation analysis showed that the P1BS motifs present in EZ2 are necessary but not sufficient for the enhancer function, revealing the importance of adjacent sequences. The structural organization of EZ2 is conserved in the orthologous genes of at least eight families of rosids, suggesting that architectural features such as the distance between the two P1BS motifs are also important for the regulatory properties of this enhancer element.


Subject(s)
Arabidopsis Proteins/genetics , Arabidopsis/genetics , Enhancer Elements, Genetic/genetics , Gene Expression Regulation, Plant/genetics , Phosphates/deficiency , Phospholipase D/genetics , Amino Acid Motifs , Amino Acid Sequence , Arabidopsis/cytology , Arabidopsis/enzymology , Arabidopsis/physiology , Arabidopsis Proteins/metabolism , DNA Mutational Analysis , Molecular Sequence Data , Organ Specificity , Phospholipase D/metabolism , Phospholipids/metabolism , Phylogeny , Plant Roots/cytology , Plant Roots/enzymology , Plant Roots/genetics , Plant Roots/physiology , Plants, Genetically Modified , Promoter Regions, Genetic/genetics , Sequence Alignment , Sequence Deletion
15.
DNA Cell Biol ; 31(1): 57-66, 2012 Jan.
Article in English | MEDLINE | ID: mdl-21848426

ABSTRACT

Two important polymorphisms of folate cycle enzymes, methylenetetrahydrofolate reductase (MTHFR) C677T and thymidylate synthase (TS) enhancer region (TSER) 28-bp tandem repeat, are related to risk of various types of cancer, including brain tumors, although there are few studies on this subject. A case-control study of these two polymorphisms in astrocytomas of different grades was carried out using polymerase chain reaction-restriction fragment length polymorphism, also determining the immunohistochemical expression of TS. The MTHFR 677 TT genotype was less associated with astrocytic tumors (odds ratio [OR]=0.00; p=0.0238), but the TSER polymorphism did not show any significant association. Combined genotype TT-double repeats/triple repeats (2R/3R) had a protective effect against astrocytomas (OR=0.00; p=0.0388). Expression of TS protein was observed in the majority of cases, with grade IV tumors being the exception. Moreover, the median H-score for the pilocytic astrocytomas was significantly higher when compared with that for diffuse tumors. There was an inverse correlation between the 2R/2R genotype and the highest TS-expressing tumors, and 3R/3R was relatively more frequent among the tumors grouped in the third and fourth quartiles. Our results provide support for the role of MTHFR and TS polymorphism in gliomagenesis, possibly because of the alteration of DNA methylation and repair status. Moreover, high levels of TS expression were detected in these tumors.


Subject(s)
Astrocytoma/genetics , Methylenetetrahydrofolate Reductase (NADPH2)/genetics , Polymorphism, Genetic , Thymidylate Synthase/genetics , Astrocytoma/enzymology , Case-Control Studies , Enhancer Elements, Genetic/genetics , Female , Gene Frequency , Genotype , Humans , Immunohistochemistry , Male , Odds Ratio , Polymerase Chain Reaction , Polymorphism, Restriction Fragment Length , Thymidylate Synthase/metabolism
16.
Proc Natl Acad Sci U S A ; 108(37): 15270-5, 2011 Sep 13.
Article in English | MEDLINE | ID: mdl-21876128

ABSTRACT

The proopiomelanocortin gene (POMC) is expressed in a group of neurons present in the arcuate nucleus of the hypothalamus. Neuron-specific POMC expression in mammals is conveyed by two distal enhancers, named nPE1 and nPE2. Previous transgenic mouse studies showed that nPE1 and nPE2 independently drive reporter gene expression to POMC neurons. Here, we investigated the evolutionary mechanisms that shaped not one but two neuron-specific POMC enhancers and tested whether nPE1 and nPE2 drive identical or complementary spatiotemporal expression patterns. Sequence comparison among representative genomes of most vertebrate classes and mammalian orders showed that nPE1 is a placental novelty. Using in silico paleogenomics we found that nPE1 originated from the exaptation of a mammalian-apparent LTR retrotransposon sometime between the metatherian/eutherian split (147 Mya) and the placental mammal radiation (≈ 90 Mya). Thus, the evolutionary origin of nPE1 differs, in kind and time, from that previously demonstrated for nPE2, which was exapted from a CORE-short interspersed nucleotide element (SINE) retroposon before the origin of prototherians, 166 Mya. Transgenic mice expressing the fluorescent markers tomato and EGFP driven by nPE1 or nPE2, respectively, demonstrated coexpression of both reporter genes along the entire arcuate nucleus. The onset of reporter gene expression guided by nPE1 and nPE2 was also identical and coincidental with the onset of Pomc expression in the presumptive mouse diencephalon. Thus, the independent exaptation of two unrelated retroposons into functional analogs regulating neuronal POMC expression constitutes an authentic example of convergent molecular evolution of cell-specific enhancers.


Subject(s)
Enhancer Elements, Genetic/genetics , Evolution, Molecular , Mammals/genetics , Neurons/metabolism , Retroelements/genetics , Animals , Base Sequence , Female , Gene Expression Regulation, Developmental , Genes, Reporter/genetics , Humans , Mice , Mice, Transgenic , Molecular Sequence Data , Neurons/cytology , Phylogeny , Placenta/metabolism , Pregnancy , Pro-Opiomelanocortin/genetics , Time Factors
17.
Eur J Pharmacol ; 660(1): 181-7, 2011 Jun 11.
Article in English | MEDLINE | ID: mdl-21211522

ABSTRACT

The gene encoding the prohormone proopiomelanocortin (POMC) is mainly expressed in two regions in vertebrates, namely corticotrophs and melanotrophs in the pituitary and a small population of neurons in the arcuate nucleus of the hypothalamus. In this latter region, POMC-derived peptides participate in the control of energy balance and sensitivity to pain. Neuronal expression of POMC is conferred by two enhancers, nPE1 and nPE2, which are conserved in most mammals, but no transcription factors are yet known to bind to these enhancers. In this work, by means of a one-hybrid screening, we identify that nPE2 possesses an element recognized by transcription factors of the nuclear receptor superfamily. This element, named NRBE, is conserved in all known nPE2 enhancers and is necessary to confer full enhancer strength to nPE2-driven reporter gene expression in transgenic mice assays, indicating that the phylogenetic conservation of the element is indicative of its functional importance. In a search for candidate nuclear receptors that might control POMC we observed that estrogen receptor alpha (ESR1) - a known regulator of energy balance at the hypothalamic level - can bind to the NRBE element in vitro. In addition we observed by immunofluorescence that ESR1 is coexpressed with POMC in around 25-30% of hypothalamic neurons of males and females during late embryonic stages and adulthood. Thus, our results indicate that hypothalamic expression of POMC is controlled by nuclear receptors and establish ESR1 as a candidate regulator of POMC.


Subject(s)
Conserved Sequence , Enhancer Elements, Genetic/genetics , Estrogen Receptor alpha/metabolism , Hypothalamus/cytology , Neurons/metabolism , Pro-Opiomelanocortin/genetics , Pro-Opiomelanocortin/metabolism , Animals , Base Sequence , Female , Gene Expression Regulation, Developmental , Humans , Male , Mice , Molecular Sequence Data , Protein Binding , Protein Transport
18.
Mol Endocrinol ; 24(9): 1846-62, 2010 Sep.
Article in English | MEDLINE | ID: mdl-20667985

ABSTRACT

The Gram-negative bacterial endotoxin lipopolysaccharide (LPS) elicits a variety of biological responses. Na(+)/I(-) symporter (NIS)-mediated iodide uptake is the main rate-limiting step in thyroid hormonogenesis. We have recently reported that LPS stimulates TSH-induced iodide uptake. Here, we further analyzed the molecular mechanism involved in the LPS-induced NIS expression in Fisher rat thyroid cell line 5 (FRTL-5) thyroid cells. We observed an increase in TSH-induced NIS mRNA expression in a dose-dependent manner upon LPS treatment. LPS enhanced the TSH-stimulated NIS promoter activity denoting the NIS-upstream enhancer region (NUE) as responsible for the stimulatory effects. We characterized a novel putative conserved kappaB site for the transcription factor nuclear factor-kappaB (NF-kappaB) within the NUE region. NUE contains two binding sites for the transcription factor paired box 8 (Pax8), main regulator of NIS transcription. A physical interaction was observed between the NF-kappaB p65 subunit and paired box 8 (Pax8), which appears to be responsible for the synergic effect displayed by these transcription factors on NIS gene transcription. Moreover, functional blockage of NF-kappaB signaling and site-directed mutagenesis of the kappaB cis-acting element abrogated LPS stimulation. Silencing expression of p65 confirmed its participation as an effector of LPS-induced NIS stimulation. Furthermore, chromatin immunoprecipitation corroborated that NIS is a novel target gene for p65 transactivation in response to LPS. Moreover, we were able to corroborate the LPS-stimulatory effect on thyroid cells in vivo in LPS-treated rats, supporting that thyrocytes are capable of responding to systemic infections. In conclusion, our results reveal a new mechanism involving p65 in the LPS-induced NIS expression, denoting a novel aspect in thyroid cell differentiation.


Subject(s)
Gene Expression Regulation/drug effects , Lipopolysaccharides/pharmacology , Paired Box Transcription Factors/metabolism , Symporters/genetics , Transcription Factor RelA/metabolism , Animals , Base Sequence , Binding Sites , Enhancer Elements, Genetic/genetics , Gene Silencing/drug effects , Humans , Molecular Sequence Data , PAX8 Transcription Factor , Protein Binding/drug effects , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA, Small Interfering/metabolism , Rats , Symporters/metabolism , Thyroid Gland/cytology , Thyroid Gland/drug effects , Thyroid Gland/metabolism , Thyrotropin/pharmacology , Transcription, Genetic/drug effects , Transcriptional Activation/drug effects , Up-Regulation/drug effects
19.
Genet Mol Res ; 9(2): 639-50, 2010 Apr 13.
Article in English | MEDLINE | ID: mdl-20449796

ABSTRACT

Transposable elements contribute to the size, structure, variation, and diversity of the genome and have major effects on gene function. Sequencing projects have revealed the diversity of transposable elements in many organisms and have shown that they constitute a high percentage of the genome. PCR-based techniques using degenerate primers designed from conserved enzyme domains of transposable elements can provide quick and extensive surveys, making study of diversity and abundance and their applications possible in species where full genome sequence data are not yet available. We studied cassava (Manihot esculenta) En/Spm-like transposons (Meens) with regard to genomic distribution, sequence diversity and methylation status. Cassava transposase fragments characteristic of En/Spm-like transposons were isolated, cloned and characterized. Sequence analysis showed that cassava En/Spm-like elements are highly conserved, with overall identity in the range of 68-98%. Southern hybridization supports the presence of multiple copies of En/Spm-like transposons integrated in the genome of all cassava cultivars that we tested. Hybridization patterns of HpaII- and MspI-digested cassava genomic DNA revealed highly methylated sequences. There were no clear differences in hybridization pattern between the cultivars. We did not detect RNA transcripts of Meens by Northern procedures. We examined the possibility of recent transposition activities of the cassava En/Spm-like elements.


Subject(s)
DNA Transposable Elements/genetics , Enhancer Elements, Genetic/genetics , Manihot/genetics , Suppression, Genetic/genetics , Transcription, Genetic , Amino Acid Sequence , Base Sequence , Blotting, Southern , Cloning, Molecular , DNA Methylation/genetics , Genetic Variation , Genome, Plant/genetics , Molecular Sequence Data , Phylogeny , Polymerase Chain Reaction , Sequence Alignment , Sequence Analysis, DNA , Transposases/chemistry , Transposases/genetics , Zea mays/genetics
20.
J Cell Physiol ; 221(3): 658-67, 2009 Dec.
Article in English | MEDLINE | ID: mdl-19711354

ABSTRACT

Calcium/calmodulin-dependent protein kinase IV (CaMKIV) plays a key role in the regulation of calcium-dependent gene expression. The expression of CaMKIV and the activation of CREB regulated genes are involved in memory and neuronal survival. We report here that: (a) a bioinformatic analysis of 15,476 promoters of the human genome predicted several Wnt target genes, being CaMKIV a very interesting candidate; (b) CaMKIV promoter contains TCF/LEF transcription motifs similar to those present in Wnt target genes; (c) biochemical studies indicate that lithium and the canonical ligand Wnt-3a induce CaMKIV mRNA and protein expression levels in rat hippocampal neurons as well as CaMKIV promoter activity; (d) treatment of hippocampal neurons with Wnt-3a increases the binding of beta-catenin to the CaMKIV promoter: (e) In vivo activation of the Wnt signaling improve spatial memory impairment and restores the expression of CaMKIV in a mice double transgenic model for Alzheimer's disease which shows decreased levels of the kinase. We conclude that CaMKIV is regulated by the Wnt signaling pathway and that its expression could play a role in the neuroprotective function of the Wnt signaling against the Alzheimer's amyloid peptide.


Subject(s)
Calcium-Calmodulin-Dependent Protein Kinase Type 4/metabolism , Signal Transduction/physiology , Wnt Proteins/metabolism , beta Catenin/metabolism , Alzheimer Disease/drug therapy , Alzheimer Disease/metabolism , Alzheimer Disease/pathology , Animals , Behavior, Animal/drug effects , Calcium-Calmodulin-Dependent Protein Kinase Type 4/genetics , Cell Line , Computational Biology , Disease Models, Animal , Enhancer Elements, Genetic/genetics , Gene Expression/drug effects , Gene Expression/genetics , Hippocampus/cytology , Hippocampus/drug effects , Hippocampus/pathology , Humans , Lithium Chloride/pharmacology , Lithium Chloride/therapeutic use , Mice , Mice, Inbred Strains , Mice, Transgenic , Neurons/drug effects , Neurons/metabolism , Neuropsychological Tests , Promoter Regions, Genetic/genetics , Protein Binding/genetics , Rats , Rats, Inbred Strains , TCF Transcription Factors/metabolism , Transfection , Wnt Proteins/pharmacology , Wnt3 Protein , Wnt3A Protein , beta Catenin/genetics
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