Coordinate Regulation Of Genes Research Articles

Coordinate gene regulation during hematopoiesis is related to genomic organization.

Gene loci are found in nuclear subcompartments that are related to their expression status. For instance, silent genes are often localized to heterochromatin and the nuclear periphery, whereas active genes tend to be found in the nuclear center. Evidence also suggests that chromosomes may be specifically positioned within the nucleus; however, the nature of this organization and how it is achieved are not yet fully understood. To examine whether gene regulation is related to a discernible pattern of genomic organization, we analyzed the linear arrangement of co-regulated genes along chromosomes and determined the organization of chromosomes during the differentiation of a hematopoietic progenitor to erythroid and neutrophil cell types. Our analysis reveals that there is a significant tendency for co-regulated genes to be proximal, which is related to the association of homologous chromosomes and the spatial juxtaposition of lineage-specific gene domains. We suggest that proximity in the form of chromosomal gene distribution and homolog association may be the basis for organizing the genome for coordinate gene regulation during cellular differentiation.

Abstract 668: Inhibition of DNA Methyltransferase Inhibits the Ang II-Induced Increase in Blood Pressure, Vascular Remodeling and Target Organ Damage

Growth signals stimulate DNA methyltransferase (DNMT) expression through extracellular signal-regulated kinases 1/2 (ERK1/2) pathway and that inhibition of ERK1/2 signaling results in repression of DNMT expression and activation of expression of some DNMT-repressed genes. Angiotensin II (Ang II) has been shown to stimulate ERK1/2 signaling in resistance arteries. We hypothesized that Ang II stimulates DNMT expression resulting in methylation and repression of antihypertensive genes such as 11β-hydroxysteroid dehydrogenase 2 (11β-HSD2) and that blocking DNMT activity may inhibit Ang II-induced hypertension, vascular remodeling, and target organ damage. C57BL/6J (C57) mice were treated with the specific DNMT inhibitor 5′-aza-2′-deoxycytidine (aza-CdR, 1 mg/kg/day) intraperitoneally for 3 consecutive days before subcutaneous Ang II infusion for 28d at a pressure dose of 0.7 mg/kg/day using Alzet osmotic minipumps. Systolic blood pressure was monitored during this period and tissues were harvested to determine vascular wall thickness, cardiac hypertrophy, and expression and methylation of 11β-HSD2 in arteries and the kidneys. Ang II infusion induced a more than 2-fold increase in DNMT1 expression (n=6, p≤ 0.05). Moreover, blocking DNMT1 activity significantly inhibited the Ang II-induced increase in systolic and diastolic blood pressure (from 102 ± 3 to138 ± 7 for saline-treated vs. 101 ± 4 to 105 ± 6 mm Hg for aza-CdR-treated mice, n=8, p≤ 0.01 for saline vs.aza-CdR in the presence of Ang II treatment). In addition, expression of 11β-HSD2 was inhibited by Ang II treatment. However, expression of 11β-HSD2 was found to be above the background observed in absence of Ang II when Ang II treatment was associated with DNMT activity blockade. Methylation-specific PCR indicated that 11β-HSD2 was methylated in the arteries and kidneys but its Ang II-dependency is still to be determined. Finally when DNMT activity was inhibited, the Ang II-induced increase cardiac hypertrophy (heart/body weight) and wall/lumen ratio in the carotid arteries were significantly inhibited (n= 8, p≤ 0.05). These results suggest that DNA methylation plays a critical role in the coordinate regulation of genes involved in the pathogenesis of hypertension and vascular remodeling.

Genetic and transcriptomic analysis of transcription factor genes in the model halophilic Archaeon: coordinate action of TbpD and TfbA

BackgroundArchaea are prokaryotic organisms with simplified versions of eukaryotic transcription systems. Genes coding for the general transcription factors TBP and TFB are present in multiple copies in several Archaea, including Halobacterium sp. NRC-1. Multiple TBP and TFBs have been proposed to participate in transcription of genes via recognition and recruitment of RNA polymerase to different classes of promoters.ResultsWe attempted to knock out all six TBP and seven TFB genes in Halobacterium sp. NRC-1 using the ura3-based gene deletion system. Knockouts were obtained for six out of thirteen genes, tbpCDF and tfbACG, indicating that they are not essential for cell viability under standard conditions. Screening of a population of 1,000 candidate mutants showed that genes which did not yield mutants contained less that 0.1% knockouts, strongly suggesting that they are essential. The transcriptomes of two mutants, ΔtbpD and ΔtfbA, were compared to the parental strain and showed coordinate down regulation of many genes. Over 500 out of 2,677 total genes were regulated in the ΔtbpD and ΔtfbA mutants with 363 regulated in both, indicating that over 10% of genes in both strains require the action of both TbpD and TfbA for normal transcription. Culturing studies on the ΔtbpD and ΔtfbA mutant strains showed them to grow more slowly than the wild-type at an elevated temperature, 49°C, and they showed reduced viability at 56°C, suggesting TbpD and TfbA are involved in the heat shock response. Alignment of TBP and TFB protein sequences suggested the expansion of the TBP gene family, especially in Halobacterium sp. NRC-1, and TFB gene family in representatives of five different genera of haloarchaea in which genome sequences are available.ConclusionSix of thirteen TBP and TFB genes of Halobacterium sp. NRC-1 are non-essential under standard growth conditions. TbpD and TfbA coordinate the expression of over 10% of the genes in the NRC-1 genome. The ΔtbpD and ΔtfbA mutant strains are temperature sensitive, possibly as a result of down regulation of heat shock genes. Sequence alignments suggest the existence of several families of TBP and TFB transcription factors in Halobacterium which may function in transcription of different classes of genes.

Quorum sensing inSerratia

Many bacteria use cell-cell communication to monitor their population density, synchronize their behaviour and socially interact. This communication results in a coordinated gene regulation and is generally called quorum sensing. In gram-negative bacteria, the most common quorum signal molecules are acylated homoserine lactones (AHLs), although other low-molecular-mass signalling molecules have been described such as Autoinducer-2 (AI-2). The phenotypes that are regulated in Serratia species by means of AHLs are remarkably diverse and of profound biological and ecological significance, and often interconnected with other global regulators. Furthermore, AHL- and AI-2-mediated systems (less profoundly studied) are continuously being discovered and explored in Serratia spp., many having interesting twists on the basic theme. Therefore, this review will highlight the current known quorum sensing systems in Serratia spp., including the important nosocomial pathogen Serratia marcescens.

Inhibition of Quorum Sensing–Regulated Behaviors by Scorzonera sandrasica

Many Gram-negative bacteria use N-acyl homoserine lactone signal molecules to monitor their own population density and coordinate gene regulation in a process called quorum sensing (QS). Increasing evidence implies that certain eukaryotes produce QS-inhibitory compounds. In this work, we tested 46 terrestrial plants materials for their ability to inhibit QS-regulated behaviors in different bacterial species. Plant materials were dried and extracted using different solvents. The chloroform-soluble compounds extracted from Scorzonera sandrasica were found to inhibit violacein production, a QS-regulated behavior in Chromobacterium violaceum. In addition, the chloroform extract was also able to inhibit QS-regulated carbapenem antibiotic production in Erwinia carotovora. Because the regulation of many bacterial processes is controlled by QS systems, the finding of natural compounds acting as QS inhibitors suggests an attractive tool to control and handle detrimental infections caused by human, animal, and plant pathogens.

Oxidative Phenotype Protects Myofibers from Pathological Insults Induced by Chronic Heart Failure in Mice

The fiber specificity of skeletal muscle abnormalities in chronic heart failure (CHF) has not been defined. We show here that transgenic mice (8 weeks old) with cardiac-specific overexpression of calsequestrin developed CHF (50.9% decrease in fractional shortening and 56.4% increase in lung weight, P<0.001), cachexia (37.8% decrease in body weight, P<0.001), and exercise intolerance (69.3% decrease in running distance to exhaustion, P<0.001) without a significant change in muscle fiber-type composition. Slow oxidative soleus muscle maintained muscle mass, whereas fast glycolytic tibialis anterior and plantaris muscles underwent atrophy (11.6 and 13.3%, respectively; P<0.05). In plantaris muscle, glycolytic type IId/x and IIb, but not oxidative type I and IIa, fibers displayed significant decreases in cross-sectional area (20.3%, P<0.05). Fast glycolytic white vastus lateralis muscle showed sarcomere degeneration and decreased cytochrome c oxidase IV (39.5%, P<0.01) and peroxisome proliferator-activated receptor gamma co-activator 1alpha protein expression (30.3%, P<0.01) along with a dramatic induction of the MAFbx/Atrogin-1 mRNA. These findings suggest that exercise intolerance can occur in CHF without fiber type switching in skeletal muscle and that oxidative phenotype renders myofibers resistant to pathological insults induced by CHF.

In silico comparative genomic analysis of GABAA receptor transcriptional regulation

BackgroundSubtypes of the GABAA receptor subunit exhibit diverse temporal and spatial expression patterns. In silico comparative analysis was used to predict transcriptional regulatory features in individual mammalian GABAA receptor subunit genes, and to identify potential transcriptional regulatory components involved in the coordinate regulation of the GABAA receptor gene clusters.ResultsPreviously unreported putative promoters were identified for the β2, γ1, γ3, ε, θ and π subunit genes. Putative core elements and proximal transcriptional factors were identified within these predicted promoters, and within the experimentally determined promoters of other subunit genes. Conserved intergenic regions of sequence in the mammalian GABAA receptor gene cluster comprising the α1, β2, γ2 and α6 subunits were identified as potential long range transcriptional regulatory components involved in the coordinate regulation of these genes. A region of predicted DNase I hypersensitive sites within the cluster may contain transcriptional regulatory features coordinating gene expression. A novel model is proposed for the coordinate control of the gene cluster and parallel expression of the α1 and β2 subunits, based upon the selective action of putative Scaffold/Matrix Attachment Regions (S/MARs).ConclusionThe putative regulatory features identified by genomic analysis of GABAA receptor genes were substantiated by cross-species comparative analysis and now require experimental verification. The proposed model for the coordinate regulation of genes in the cluster accounts for the head-to-head orientation and parallel expression of the α1 and β2 subunit genes, and for the disruption of transcription caused by insertion of a neomycin gene in the close vicinity of the α6 gene, which is proximal to a putative critical S/MAR.

?Cradle?to?grave? regulation of mRNA fate

Microarray studies in Saccharomyces cerevisiae have set the benchmark for genome-wide analyses, available data-sets covering practically every stage of gene expression from DNA-binding by transcription factors to mRNA export, sub-cellular localisation, translation and decay. A theme to emerge from such data has been the prevalence of coordinate gene regulation. Thus, gene modules or ?regulons? are well recognised at the level of gene transcription and the activity of transcription factors provides an obvious molecular explanation for such coordination. More surprising was the organisation of mRNAs into co-regulated ?post-transcriptional operons?. RNA-binding proteins (RBPs), but also ribonucleoprotein (RNP) complexes involving noncoding RNA, have been proposed as the conceptual equivalent of transcription factors at this level.

Direct and Coordinate Regulation of Multidrug Resistance Genes by the c-Myc Oncoprotein.

The deregulation of ATP-binding cassette (ABC) transporters responsible for the efflux of anticancer agents may be achieved either by mutations or single nucleotide polymorphisms (SNPs) affecting the biophysical and biochemical properties of the transporters or by an increase in their expression level. Consequently, chemoresistance will develop. In this study we have investigated regulatory mechanisms involved in the activation of ABC transporters. We have first examined how ABC genes are regulated at the transcriptional level and which transcription factors concur to such a control. The expression level of all 48 human ABC drug transporters was determined as a function of c-Myc expression in a p493 lymphoblastoid cell line harboring c-Myc driven by a tetracycline-responsive promoter. Our results demonstrated that c-Myc affected the transcription of several ABC genes, such as ABCA2, ABCB1, ABCB9, ABCC1, ABCC4, ABCE1, ABCF1, ABCF2, ABCF3, a majority of which, has been found implicated in chemoresistance. To evaluate whether c-Myc affects the transcription of those ABC genes directly, chromatin immunoprecipitation (ChIP) was performed in p493 cells. The results have shown a direct binding of c-Myc to the promoters of the ABC genes tested, with the only exception of ABCB1. To further confirm a direct role of c-Myc on ABC gene transcription, ABC gene promoters were cloned into a luciferase reporter assay and their activity was tested in various lymphoblastoid cell line variants, expressing different levels of c-Myc. Results proved a dose-dependent transcription activation of ABC reporters induced by c-Myc, which suggested that the c-Myc oncoprotein could regulate the level of expression of a large number of ABC genes in lymphocytes. Furthermore, we have investigated the expression of c-Myc and ABC genes in chronic myeloid leukemia (CML) in order to verify whether high expression levels of c-Myc may affect transcription of ABC drug transporters also in CML cells. In fact, recent studies reported that Bcr-Abl may positively regulate c-Myc expression. Our results showed that c-Myc is highly expressed in CD34+ cells from newly diagnosed chronic phase (CP)-CML patients, and that it can significantly upregulate the expression of several ABC genes, particularly that of the ABCC1 and ABCC4. We have demonstrated that c-Myc was physically associated with the promoter of tested ABC genes and their direct regulator as assessed by ChIP in the Kasumi-4 cell line, which has been derived from a Ph+ CML patient and expresses the CD34 antigen. Taken together, our findings support the model of a direct and coordinate regulation of a large set of ABC genes by the c-Myc transcription factor. Our study suggests that c-myc deregulation of ABC genes could be an important molecular mechanism altering imatinib transport. Thus, we concluded that c-Myc could be involved in the development of chemoresistance in CML, as well as resistance to targeted drugs, such as imatinib. Currently, we are further assessing transcriptional deregulation of specific ABC genes, and SNPs affecting the functional properties of ABC transporters, by comparing CP-CML patients responsive to imatinib, which have been shown to represent over 90% of treated individuals, and patients who developed resistance.

A new paradigm for the regulation of the mammalian ribosomal RNA genes

Ribosome assembly occurs co-transcriptionally on the rRNA genes. This process requires the co-ordinated expression and assembly of many hundreds of proteins and is finely tuned to cell and organism growth. Co-ordinate regulation of the rRNA genes and the ribosomal protein genes is therefore essential for high-fidelity ribosome assembly. Recent work shows that rRNA gene transcription is regulated at the level of elongation via the mitogen-activated protein kinase pathway. We argue that this may provide an explanation for the high fidelity of ribosome assembly.

Diminished Hepatic Gluconeogenesis via Defects in Tricarboxylic Acid Cycle Flux in Peroxisome Proliferator-activated Receptor γ Coactivator-1α (PGC-1α)-deficient Mice

The peroxisome proliferator-activated receptor gamma (PPARgamma) coactivator 1alpha (PGC-1alpha) is a highly inducible transcriptional coactivator implicated in the coordinate regulation of genes encoding enzymes involved in hepatic fatty acid oxidation, oxidative phosphorylation, and gluconeogenesis. The present study sought to assess the effects of chronic PGC-1alpha deficiency on metabolic flux through the hepatic gluconeogenic, fatty acid oxidation, and tricarboxylic acid cycle pathways. To this end, hepatic metabolism was assessed in wild-type (WT) and PGC-1alpha(-/-) mice using isotopomer-based NMR with complementary gene expression analyses. Hepatic glucose production was diminished in PGC-1alpha(-/-) livers coincident with reduced gluconeogenic flux from phosphoenolpyruvate. Surprisingly, the expression of PGC-1alpha target genes involved in gluconeogenesis was unaltered in PGC-1alpha(-/-) compared with WT mice under fed and fasted conditions. Flux through tricarboxylic acid cycle and mitochondrial fatty acid beta-oxidation pathways was also diminished in PGC-1alpha(-/-) livers. The expression of multiple genes encoding tricarboxylic acid cycle and oxidative phosphorylation enzymes was significantly depressed in PGC-1alpha(-/-) mice and was activated by PGC-1alpha overexpression in the livers of WT mice. Collectively, these findings suggest that chronic whole-animal PGC-1alpha deficiency results in defects in hepatic glucose production that are secondary to diminished fatty acid beta-oxidation and tricarboxylic acid cycle flux rather than abnormalities in gluconeogenic enzyme gene expression per se.

GLYCOSYLTRANSFERASES OF LIPOPHILIC SMALL MOLECULES

Glycosyltransferases of small molecules transfer sugars to a wide range of acceptors, from hormones and secondary metabolites to biotic and abiotic chemicals and toxins in the environment. The enzymes are encoded by large multigene families and can be identified by a signature motif in their primary sequence, which classifies them as a subset of Family 1 glycosyltransferases. The transfer of a sugar onto a lipophilic acceptor changes its chemical properties, alters its bioactivity, and enables access to membrane transporter systems. In vitro studies have shown that a single gene product can glycosylate multiple substrates of diverse origins; multiple enzymes can also glycosylate the same substrate. These features suggest that in a cellular context, substrate availability is a determining factor in enzyme function, and redundancy depends on the extent of coordinate gene regulation. This review discusses the role of these glycosyltransferases in underpinning developmental and metabolic plasticity during adaptive responses.

Isolation, endocrine regulation and mRNA distribution of the 3‐hydroxy‐3‐methylglutaryl coenzyme A synthase (HMG‐S) gene from the pine engraver, Ips pini (Coleoptera: Scolytidae)

We isolated a full-length cDNA encoding 3-hydroxy-3-methylglutaryl coenzyme A synthase (HMG-S) from the pine engraver beetle, Ips pini (Say), and examined its genomic structure. The intron-less gene has a predicted 460 amino acid cytosolic protein product with 73% identity to HMG-S from Dendroctonus jeffreyi, and high identity (58-64%) with other insect HMG-Ss. Topically applied juvenile hormone (JH) III induced HMG-S mRNA levels up to 6.5-fold in both sexes, mostly in the anterior midgut, though there were differences between males and females in the timing, sensitivity to JH III dose and tissue distribution of HMG-S mRNA. These data further validate the coordinate regulation of mevalonate pathway genes for de novo isoprenoid pheromone production in bark beetles.

Regulation of quorum sensing inPseudomonas

Bacteria use small signal molecules in order to monitor their population density and coordinate gene regulation in a process called quorum sensing. In Gram-negative bacteria, the most common signal molecules are acylated homoserine lactones. Several Pseudomonas species produce acylated homoserine lactones that control important functions including pathogenicity and plant growth promotion. Many reports indicate that the quorum sensing systems of Pseudomonas are significantly regulated and interconnected with regulons of other global regulators. The integration of quorum sensing into additional regulatory circuits increases the range of environmental and metabolic signals beyond that of cell density, as well as further tuning the timing of the response. This review will focus on the regulation of quorum sensing in Pseudomonas, highlighting a complex response that might serve a given species to adapt in its particular environment.

Johannes Reinke (1839–1931) and his “Dominanten” theory – An early concept of gene regulation and morphogenesis

Johannes Reinke (1839–1931) was one of the most eminent and influential botanists, politician, philosopher and “anti-Haeckelist” of the 19th century. Educated in the mid 19th century he had faced revolutionary changes in the scientific understanding of the origin and evolution of life. Working mainly at the phenotypic level, Reinke was interested in the basic mechanisms and the guiding idea behind all processes which coordinated gene regulation and morphogenesis. What drove Reinke in his search of regulatory mechanisms for evolutionary patterns and processes was his religious belief. For the origin of the very first life, Reinke believed in creation but once life was established, evolution followed natural laws. This led to his early concept of “Dominanten” entities, which regulate gene transcription and morphogenesis, anticipating the ideas of Goldschmidt and v. Uexküll.

The inflammatory transcriptome of reactive murine astrocytes and implications for their innate immune function

Upon injury, astrocytes assume an activated state associated with the release of inflammatory mediators. To model this, we stimulated murine primary astrocytes with a complete inflammatory cytokine mix consisting of TNF-alpha, IL-1beta and IFN-gamma. We analysed the transcriptional response of 480 genes at 4 and 16 h after stimulation on a chip designed to give a representative overview over the inflammation-relevant part of the transcriptome of macrophage-like cells. The list of the 182 genes found to be significantly regulated in astrocytes revealed an intriguing co-ordinate regulation of genes linked to the biological processes of antiviral/antimicrobial defence, antigen presentation and facilitation of leucocyte invasion. The latter group was characterized by very high up-regulations of chemokine genes. We also identified regulations of a thymidylate kinase and an interferon-regulated protein with a tetratricopeptide motive, both up to now only known from macrophages. The transcriptional regulations were confirmed on the protein level by a proteomic analysis. These findings taken together suggest that activated astrocytes in brain behave similarly in many respects to inflamed macrophages in the periphery.

Transcript analysis of early nodulation events in Medicago truncatula.

Within the first 72 h of the interaction between rhizobia and their host plants, nodule primordium induction and infection occur. We predicted that transcription profiling of early stages of the symbiosis between Medicago truncatula roots and Sinorhizobium meliloti would identify regulated plant genes that likely condition key events in nodule initiation. Therefore, using a microarray with about 6,000 cDNAs, we compared transcripts from inoculated and uninoculated roots corresponding to defined stages between 1 and 72 h post inoculation (hpi). Hundreds of genes of both known and unknown function were significantly regulated at these time points. Four stages of the interaction were recognized based on gene expression profiles, and potential marker genes for these stages were identified. Some genes that were regulated differentially during stages I (1 hpi) and II (6-12 hpi) of the interaction belong to families encoding proteins involved in calcium transport and binding, reactive oxygen metabolism, and cytoskeleton and cell wall functions. Genes involved in cell proliferation were found to be up-regulated during stages III (24-48 hpi) and IV (72 hpi). Many genes that are homologs of defense response genes were up-regulated during stage I but down-regulated later, likely facilitating infection thread progression into the root cortex. Additionally, genes putatively involved in signal transduction and transcriptional regulation were found to be differentially regulated in the inoculated roots at each time point. The findings shed light on the complexity of coordinated gene regulation and will be useful for continued dissection of the early steps in symbiosis.

Transcriptome Analysis of Human Hematopoietic Progenitor Cells during In Vitro Erythroid Differentiation.

The hematopoietic progenitor cell (HPC) has the potential to differentiate into multiple cell types. Deciphering transcriptional regulatory networks necessary for HPCs to undergo lineage commitment is critical. Toward this goal, we established a serum-free in vitro differentiation system for human HPCs using CD34−positive cells isolated from peripheral blood of normal donors. Cells were cultured in the presence of Epo, SCF and IL-3 for two-weeks, and assessed for total hemoglobin and percent fetal hemoglobin. Adult-derived HPCs express large amounts of Hb A after approximately one week of culture with little expression of Hb F. Transcriptome analysis, using Affymetrix Human Genome U133 Plus 2.0 Arrays on RNA from days 1, 3, 5, 7, 9, 11 and 13 of culture shows more than 1500 differentially-expressed (DE)(> 2-fold up or down) genes, a subset of which were validated independently by real-time RT-PCR. Up-regulated erythroid-specific genes included those for blood group antigens (Kell, Duffy, Rhesus), membrane proteins (ankryin 1, α- and β-spectrin, Band 4.1, Band 4.2, Band 4.9, glycophorin A), receptors (transferrin and erythropoietin receptors), heme biosynthesis enzymes (ALAS, ALAD, UROS, UROD, CPOX, PPOX, FECH), and transcription factors important in globin-gene expression (EKLF, BKLF, NFE2, GATA1) as well as α-, β- and γ-globin mRNAs. Down-regulated genes included those expressed in hematopoietic stem cells (GATA2, CD34) and non-erythroid hematopoietic lineages (MHC class I and II genes, CD33, CD53). The DE genes were clustered into a limited number of expression patterns, suggesting coordinate regulation of genes within each cluster. The DE gene set was examined in silico for co-regulation using transcriptional regulatory network analysis employing PAINT v3.2 software (Vadigepalli R et al., OMICS. 2003; 7(3):235–52). GATA binding sites were represented on 149 of the DE gene promoters. Several transcriptional regulatory elements (TRE) were statistically significantly enriched in the DE gene set when compared to the array gene set. These include TRE for AP-1, CREB, GATA-1 and Oct-1. Co-regulation of genes in the different gene clusters will be analyzed by PAINT and findings validated by examination of TRE:transcription factor interactions. These studies should help define timing of transcription factor occupancy in relation to epigenetic changes occurring prior to transcriptome alteration during differentiation of human erythroid cells.

“Promoter Array” Studies Identify Cohorts of Genes Directly Regulated by Methylation, Copy Number Change, or Transcription Factor Binding in Human Cancer Cells

DNA microarrays of promoter sequences have been developed in order to identify the profile of genes bound and activated by DNA regulatory proteins such as the transcription factors c-Jun and ATF2 as well as DNA-modifying methylases. The arrays contain 3083 unique human promoter sequences from +500 to -1000 nts from the transcription start site. Cisplatin-induced DNA damage rapidly leads to specific activation of the Jun kinase pathway leading to increased phosphorylation of c-Jun and ATF2-DNA complexes at hundreds of sites within 3 hours. Using three statistical criteria, approximately 269 most commonly phosphorylated c-Jun/ATF2-DNA complexes were identified and representative cases were verified by qPCR measurement of ChIP-captured DNA. Expression was correlated at the mRNA and protein levels. The largest functional cohort was 24 genes of known DNA repair function, most of which exhibited increased protein expression indicated coordinate gene regulation. In addition, cell lines of prostate cancer exhibit stable methylation or copy number changes that reflect the alterations of the corresponding primary tumors. 504 (18.5%) promoters showed differential hybridization between immortalized control prostate epithelial and cancer cell lines. Among candidate hypermethylated genes in cancer-derived lines, eight had previously been observed in prostate cancer, and 13 were previously determined methylation targets in other cancers. The vast majority of genes that appear to be both differentially methylated and differentially regulated between prostate epithelial and cancer cell lines are novel methylation targets, including PAK6, RAD50, TLX3, PIR51, MAP2K5, INSR, FBN1, GG2-1, representing a rich new source of candidate genes to study the role of DNA methylation in prostate tumors. Earlier studies using prototype promoter arrays examine approximately 7% of the proximal regulatory sequences while the current gene regulatory events surveyed here occur on a large scale and may rapidly effect the coordinated expression of a large number of genes.

Arabidopsis TCP20 links regulation of growth and cell division control pathways

During postembryonic plant development, cell division is coupled to cell growth. There is a stringent requirement to couple these processes in shoot and root meristems. As cells pass through meristems, they transit through zones with high rates of cell growth and proliferation during organogenesis. This transition implies a need for coordinate regulation of genes underpinning these two fundamental cell functions. Here, we report a mechanism for coregulation of cell division control genes and cell growth effectors. We identified a GCCCR motif necessary and sufficient for high-level cyclin CYCB1;1 expression at G2/M. This motif is overrepresented in many ribosomal protein gene promoters and is required for high-level expression of the S27 and L24 ribosomal subunit genes we examined. p33(TCP20), encoded by the Arabidopsis TCP20 gene, binds to the GCCCR element in the promoters of cyclin CYCB1;1 and ribosomal protein genes in vitro and in vivo. We propose a model in which organ growth rates, and possibly shape in aerial organs, are regulated by the balance of positively and negatively acting teosinte-branched, cycloidea, PCNA factor (TCP) genes in the distal meristem boundary zone where cells become mitotically quiescent before expansion and differentiation.