title: Solar simulated ultraviolet radiation induces histone 3 methylation changes in the gene promoters of matrix metalloproteinases 1 and 3 in primary human dermal fibroblasts [II]

status: Public on Aug 27 2014

city: Tuxedo

first: Lisa

last: Passantino

state: New York

address: 57 Old Forge Road

department: School of Medicine

institute: New York University

summary: Skin damage from solar ultraviolet radiation (UVR) accumulates in the dermal extracellular matrix (ECM) and contributes to photoaging. Following UVR exposure, matrix metalloproteinases (MMPs) are secreted by dermal fibroblasts to repair and remodel the ECM. Molecular signaling pathways delineating the induction of MMPs are currently well-defined; however, the effects of UV exposure on epigenetic mechanisms of MMP induction are not as well understood. An epigenetic mechanism would further describe how MMP genes are regulated in response to UV. In this study, we examined solar simulated UVR (ssUVR)-induced gene expression changes and alterations to histone methylation in the promoters of MMP1 and MMP3 in primary human dermal fibroblasts (HDF). This set of gene expression data was generated to identify photoaging related genes (including MMP) that were impacted by ssUVR exposure in our system.

overall_design: Primary neonatal human dermal fibroblasts (HDF) were irradiated a single time with 12 J/cm2 ssUVR. The sham treatments are negative controls (0 J/cm2 ssUVR). The cells were collected for gene expression analysis 1 day after exposure, and then 5 days after exposure. Affymetrix GeneChip Human Exon 1.0 ST arrays were used to characterize gene expression pattern alterations in response to ssUVR.

last: Gesumaria

first: Mary

last: Matsui

first: Thomas

last: Kluz

first: Max

last: Costa


title: Solar simulated ultraviolet radiation induces histone 3 methylation changes in the gene promoters of matrix metalloproteinases 1 and 3 in primary human dermal fibroblasts [I]

country: USA

overall_design: Primary neonatal human dermal fibroblasts (HDF) were irradiated a single time with 0, 4, or 12 J/cm2 ssUVR. The sham treatments are negative controls (0 J/cm2 ssUVR). The cells were collected for gene expression analysis 24 hours after exposure. Affymetrix GeneChip Human Exon 1.0 ST arrays were used to characterize gene expression pattern alterations in response to ssUVR.


title: Solar simulated ultraviolet radiation induces histone 3 methylation changes in the gene promoters of matrix metalloproteinases 1 and 3 in primary human dermal fibroblasts

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcriptional landscape of Rag2 -/- thymocytes [ChIP-Seq]

status: Public on Apr 01 2014

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed ChIP-Seq for hallmark TFs (Ets1, Runx1), histone modification marks (H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3), total RNA Pol II, short RNA-Seq as well as nucleosome mapping mainly in murine Rag2 -/- thymocytes. We also performed ChIP-Seq for E47 as well as nucleosome mapping, gene expression microarray analysis in CD4+ CD8+ DP thymocytes. Overall, we find a key role for the transcription factor Ets1, contributing towards alpha beta T cell lineage commitment via differential transactivation of stage-specific genes orchestrated by dynamic, co-association -mediated chromatin remodeling, as well as transcription dependent generation of a specialized chromatin structure at the TCR beta locus.

overall_design:
Genome-wide analysis via ChIP-Seq for Ets1, Runx1, total RNA Pol II binding,  H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3, short RNA-Seq, Mnase-Seq in murine Rag2 -/- thymocytes, ChIP-Seq for E47, Mnase-Seq and gene expression microarray analysis in DP thymocytes

This Series represents ChIP-Seq data.

first: Joaquin

last: Zacarias-Cabeza

first: Laurent

last: Vanhille

first: Frederic

last: Koch

first: Romain

last: Fenouil

first: Angelica

last: Santana

first: Aleksandra

last: Pekowska

first: Ahmad

last: Maqbool

first: Hélène

last: Holota

first: Aurélien

last: Griffon

first: Jean

last: Imbert

last: Ferrier

first: Salvatore

last: Spicuglia

first: Jean-Christophe

last: Andrau


title: Gene Expression Changes in the Development of the Soybean Seed-Globular Stage

status: Public on May 07 2014

city: Davis

first: John

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California

type: Expression profiling by high throughput sequencing

summary: We investigated soybean seed development because (1) soybean seeds are a major source of food and fuel, (2) soybean seeds have been an excellent system for studying the basic processes controlling seed development for over three decades, and (3) new soybean genomic resources, including the sequence of the soybean genome and the gene expression profiles for all seed compartments, tissues, and cell types, can be used to gain new insights into the regulatory processes required for seed differentiation. We sequenced messenger RNA populations of specific soybean seed compartments, which will provide new insights into gene expression that are important for “making a soybean seed.”

overall_design: Eight compartments of the globular stage of the soybean seeds were analyzed. Three or four biological replicates were collected for each compartment.

middle: J

first: Robert

middle: B

last: Goldberg

first: Ryan

last: Kirkbride

first: Julie

last: Pelletier

first: Tina

middle: Y

last: Wang

first: Ssu-Wei

last: Hsu

first: Shu-Heng

last: Chang

first: Russell

middle: W

last: Baden

first: Rie

last: Uzawa

first: Alexander

last: Olson

first: Lourenz

last: Balayan

first: Erik

last: Garber

first: Meryl

last: Hashimoto

first: Uranus

last: Chau


title: IpsA, a novel transcriptional regulator required for inositol derived lipid formation in Corynebacteria and Mycobacteria

status: Public on Jan 13 2014

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

summary: The development of new drugs against tuberculosis and diphtheria is focused on disrupting the biogenesis of the cell wall, the unique architecture of which confers resistance against current therapies. The enzymatic pathways involved in the synthesis of the cell wall by these pathogens are well understood but the underlying regulatory mechanisms are largely unknown. Here, we characterize IpsA, a LacI-type transcriptional regulator conserved among Mycobacteria and Corynebacteria that plays a role in the regulation of cell wall biogenesis. IpsA triggers myo-inositol formation by activating ino1, which encodes inositol phosphate synthase. An IpsA deletion mutant of Corynebacterium glutamicum  cultured on glucose displayed significantly impaired growth and presented an elongated cell morphology. Analysis of the polar lipid fraction of the cell wall revealed the absence of inositol-derived lipids. The phenotype of the C. glutamicum ΔipsA mutant was complemented by homologues from Corynebacterium diphtheriae (dip1969) and Mycobacterium tuberculosis (rv3575), indicating the conserved function of IpsA in the pathogenic species. Additional targets of IpsA with putative functions in cell wall biogenesis were identified and IpsA was shown to bind to a conserved palindromic motif within the corresponding promoter regions. myo-inositol was identified as an effector of IpsA, causing the dissociation of the IpsA-DNA complex in vitro.  This characterization of IpsA function and of its regulon sheds light on the complex transcriptional control of cell wall biogenesis in the mycolata taxon and generates novel targets for drug development.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: To identify genes which were regulated by IpsA (Cg2910), we performed DNA microarray analyses of ATCC 13032 ΔipsA against wild type. For this purpose RNA was isolated from cells cultivated in CGXII minimal medium with 2% glucose (w v-1) and harvested in the exponential growth phase at an OD600 of 1. Three biological replicates were performed.

first: Meike

last: Baumgart

first: Kerstin

last: Luder

first: Shipra

last: Grover

first: Cornelia

last: Gätgens

first: Gurdyal

middle: S

last: Besra

first: Julia

last: Frunzke


title: Transcriptional landscape of Rag2 -/- thymocytes

first: Pierre

last: Cauchy

type: Non-coding RNA profiling by high throughput sequencing


title: Transcriptional landscape of Rag2 -/- thymocytes [ShortRNA-Seq]

overall_design:
Genome-wide analysis via ChIP-Seq for Ets1, Runx1, total RNA Pol II binding,  H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3, short RNA-Seq, Mnase-Seq in murine Rag2 -/- thymocytes, ChIP-Seq for E47, Mnase-Seq and gene expression microarray analysis in DP thymocytes

This Series represents ShortRNA-Seq data.

first: Joaquin

last: Zacarias-Cabeza

first: Laurent

last: Vanhille

first: Frederic

last: Koch

first: Romain

last: Fenouil

first: Angelica

last: Santana

first: Aleksandra

last: Pekowska

first: Ahmad

last: Maqbool

first: Hélène

last: Holota

first: Aurélien

last: Griffon

first: Jean

last: Imbert

last: Ferrier

first: Salvatore

last: Spicuglia

first: Jean-Christophe

last: Andrau


title: C1 metabolism in Corynebacterium glutamicum: an endogenous pathway for oxidation of methanol to carbon dioxide

status: Public on Sep 27 2013

first: Tino

last: Polen

summary: Methanol is considered as an interesting carbon source in biobased microbial production processes. As Corynebacterium glutamicum is an important host in industrial biotechnology, in particular for amino acid production, we performed studies on the response of this organism to methanol. C. glutamicum wild type was able to convert 13C-labeled methanol to 13CO2. Analysis of global gene expression in the presence of methanol revealed several genes of ethanol catabolism to be up-regulated, indicating that some of the corresponding enzymes are involved in methanol oxidation. Indeed, a mutant lacking the alcohol dehydrogenase gene adhA showed a 62% reduced methanol consumption rate, indicating that AdhA is mainly responsible for methanol oxidation to formaldehyde. Further studies revealed that oxidation of formaldehyde to formate is catalyzed predominantly by two enzymes, the acetaldehyde dehydrogenase Ald and the mycothiol-dependent formaldehyde dehydrogenase AdhE. The deletion mutants aldadhE and aldmshC were severely impaired in their ability to oxidize formaldehyde, but residual methanol oxidation to CO2 was still possible. The oxidation of formate to CO2 is catalyzed by the formate dehydrogenase FdhF recently identified by us. Similar to ethanol, methanol catabolism is subject to carbon catabolite repression in the presence of glucose and is dependent on the transcriptional regulator RamA, which was previously shown to be essential for expression of adhA and ald. In conclusion, we were able to show that C. glutamicum possesses an endogeneous pathway for methanol oxidation to CO2 and to identify the enzymes and a transcriptional regulator involved in this pathway.

overall_design: Whole-genome DNA microarray analyses were performed to monitor changes in the global gene expression of C. glutamicum wild type in response to the presence of methanol.

first: Sabrina

last: Witthoff

first: Alice

last: Mühlroth

first: Jan

last: Marienhagen

first: Michael

last: Bott


title: Listeria monocytogenes Sigma B, but not PrfA, shows strain specific contributions to growth under salt stress, and prolongated lag phase of a sigB null mutant across strains

status: Public on Jul 20 2013

city: Sao Paulo

first: Vinicius

middle: Buccelli

last: Ribeiro

state: Sao Paulo

address: 580 Lineu Prestes Ave

country: Brazil

institute: University of Sao Paulo

summary: Listeria monocytogenes is well known to have the ability to survive and grow under a variety of stress conditions. The ability to survive and grow under osmotic stress conditions in particular appears to be important for both growth in certain foods and food associated environments as well as for host infection. To characterize the contributions of transcriptional regulators important for stress response and virulence (i.e., Sigma B - σB and PrfA), we initially analyzed three L. monocytogenes parent strains and isogenic mutants ( delta sigB, delta prfA, and delta sigB delta prfA), representing different serotypes and lineages, for their ability to grow in BHI with 11% NaCl (1.9M) at 25°C. No significant differences were observed in terms of growth between the parent strains and their respective mutants lacking prfA (i.e. delta prfA, and delta sigB delta prfA mutant strains). While for all strains, the delta sigB mutant showed a prolonged lag phase as compared to the parent strains, maximum growth rates were only reduced for the delta sigB mutant of lineage I and IV strains. Interestingly, for the serotype 1/2b strain, the delta sigB mutant reached a higher maximum cell density than the parent strain or the delta prfA mutant. Caco-2 intestinal epithelial cells invasion assays and hemolytic activity assays showed a significant role for σB in the former and for PrfA in the latter. To initially explore the mechanism that may contribute to the extended lag phase in the delta sigB mutant, microarray was performed to compare transcript levels between the lineage I, serotype 1/2b, parent strain and its isogenic delta sigB mutant in lag phase at 25°C in the presence of 11% NaCl. Microarray data showed significant lower and higher transcript levels for 135 and 173 genes, respectively, in the parent strain as compared to the delta sigB strains. Overall, 51 of the 173 σB up-regulated genes had previously been found among the 249 σB-dependent genes identified in a microarray study conducted in stationary phase cells, indicating that up to 122 genes may be transcribed in a σB-dependent manner during lag phase under salt stress. Notable genes that showed higher transcript levels in the parent strain include inlD (encoding an internalin protein that may be involved in virulence), sigH (encoding an alternative σ factor), glpK (encoding a glycerol kinase) and resD (encoding a two-component response regulator ResD); while, genes that showed lower transcript levels in the parent strain include dnaK (encoding a dihydroxyacetone kinase), groES (encoding a class I heat-shock protein GroES), grpE (encoding a co-chaperone GrpE) and fri (encoding a non-heme iron-binding ferritin). These data showed that although PrfA does not contribute to growth under osmotic stress at 25°C, σB does contribute to survival of L. monocytogenes under high salt conditions. Moreover, the σB-dependent transcriptome of L. monocytogenes lag phase cells under salt stress was characterized and includes previously identified as well as novel σB-dependent genes, including a number of stress response and virulence-associated genes.

overall_design: Independent RNA isolations were performed for one wildtype (lineage I) and ΔsigB strains from cells grown to lag phase. Three biological replicates were used in competitive whole-genome microarray experiments. For each set of hybridizations, RNA from a L. monocytogenes wildtype strain was hybridized with RNA from its isogenic ΔsigB null mutant.

last: RIBEIRO

first: Sana

last: MUJAHID

first: Renato

middle: H

last: ORSI

first: Teresa

last: BERGHOLZ

first: Martin

last: WIEDMANN

first: Kathryn

last: BOOR

first: Maria

middle: T

last: DESTRO


title: The two-component system ChrSA is crucial for heme tolerance and interferes with HrrSA in heme-dependent gene regulation in Corynebacterium glutamicum

status: Public on Oct 31 2012

summary: We recently showed that the two-component system (TCS) HrrSA plays a central role in the control of heme homeostasis in the Gram-positive soil bacterium Corynebacterium glutamicum. Here, we characterized the function of another TCS of this organism, ChrSA, which exhibits significant sequence similarity to HrrSA, and provide evidence for cross-regulation of the two systems. In this study ChrSA was shown to be crucial for heme resistance of C. glutamicum by activation of the putative heme-detoxifying ABC-transporter HrtBA in the presence of heme. Deletion of either hrtBA or chrSA resulted in a strongly increased sensitivity towards heme. DNA microarray analysis and gel retardation assays with the purified response regulator ChrA provided evidence for ChrA being a repressor of the heme biosynthesis operon hemAC and hemH and an activator of the ctaE-qcrCAB operon, encoding subunits of the cytochrome bc1-aa3 supercomplex of the respiratory chain. The heme oxygenase gene, hmuO, showed a strongly decreased mRNA level in the ΔchrSA mutant, but no significant binding of ChrA was observed in vitro. Promoter fusion studies of PchrSA with eyfp indicated positive autoregulation of the chrSA operon in the presence of heme. Interestingly, ChrA was also shown to bind to the hrrA promoter and to repress transcription of the paralog response regulator, suggesting a close link between HrrSA and ChrSA. Mutational analysis and in silico prediction resulted in the deduction of a 16-bp weakly conserved inverted repeat as consensus DNA-binding motif of ChrA. Altogether, the present study emphasizes ChrSA as a second TCS, besides HrrSA, involved in heme-dependent gene regulation in C. glutamicum.

overall_design: To identify the influence of ChrSA on global gene expression , DNA microarray analyses were performed with the ΔchrSA mutant compared to C. glutamicum wild type. For this purpose RNA was isolated from exponentially growing cells cultivated in CgXII minimal medium with 4% glucose and either 2.5 µM FeSO4 or 2.5 µM hemin as iron source. Three biological replicates were performed.

first: Antonia

last: Heyer

first: Cornelia

last: Gätgens

first: Jörn

last: Kalinowski

first: Julia

last: Frunzke


title: Homeostatic tissue responses in skin biopsies from NOMID patients with constitutive overproduction of IL-1b.

status: Public on Apr 30 2012

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: The autoinflammatory disorder, Neonatal-onset Multisystem Inflammatory Disease (NOMID) is the most severe phenotype of disorders caused by mutations in the CIAS1 gene that result in increased production and secretion of active IL-1≤. NOMID patients present with systemic and organ-specific inflammation of the skin, central nervous system and bony growth plates, and respond dramatically to treatment with IL-1 blocking agents. We compared the cellular infiltrates and transcriptome of skin biopsies from patients with NOMID (n=14) before treatment [lesional (LS) and non-lesional (pre-NL) skin] and after treatment (post-NL) with the IL-1 blocker anakinra (recombinant IL-1 receptor antagonist, Kineret®), to normal skin (n=5). Abundant neutrophils distinguish LS skin from pre-NL and post-NL skin. CD11c+ dermal dendritic cells and CD163+ macrophages expressed activated caspase-1 and are the likely sources of cutaneous IL-1 production. Treatment with anakinra led to the disappearance of neutrophils, but CD3+ T cells and HLA-DR+ cells remained elevated. Among the upregulated genes IL-6, IL-8, TNF, IL-17A, CCL20, and the neutrophil defensins DEFA1 and DEFA3 were differentially regulated in LS tissues (compared to normal skin). Important significantly downregulated pathways included IL-1R/TLR signaling, type I and II cytokine receptor signaling, mitochondrial dysfunction, and antigen presentation. Differential expression and regulation of microRNAs and pathways involved in post-transcriptional modification are indicative of epigenetic modification in the various tissue states. Overall, the dysregulated genes and pathways suggest extensive “adaptive” mechanisms to control inflammation, and maintain tissue homeostasis in the skin of patients with NOMID.

overall_design:
To determine the transcsriptome of skin samples in Neonatal-onset Multisystem Inflammatory Disease (NOMID), using pre-treatment non-lesional (pre-NL, n=4); lesional (LS, n=6); post-treatment non-lesional (post-NL, n=8), and normal skin (n=5).
Comparison of mean gene expression of each group at baseline, and considering treatment effect

first: Raphaela

last: Goldbach-Mansky

first: Michelle

middle: A

last: Lowes


title: Complex regulation of the PEP carboxykinase gene pck and characterization of its GntR-type regulator IolR as a repressor of myo-inositol utilization genes in Corynebacterium glutamicum

status: Public on Jul 29 2013

first: Tino

last: Polen

summary: DNA affinity chromatography with the promoter region of the Corynebacterium glutamicum pck gene, encoding phosphoenolpyruvate carboxykinase (PEPCk), led to the isolation of four transcriptional regulators, i.e.,  RamA, GntR1, GntR2 and IolR. Determination of the PEPCk activity of the deletion mutants ΔramA, ΔgntR1ΔgntR2, and ΔiolR indicated that RamA represses pck during growth on glucose about twofold, whereas GntR1, GntR2, and IolR activate pck expression about twofold, irrespective whether glucose or acetate served as carbon source. The DNA binding sites of the four regulators in the pck promoter region were identified and their positions correlated with the predicted functions as repressor or activators. The iolR gene is located upstream and in divergent orientation to a iol gene cluster, encoding proteins involved in myo-inositol uptake and degradation. Comparative DNA microarray analysis of the ΔiolR mutant and the parental wild-type revealed strongly elevated (>100-fold)  mRNA levels of the iol genes in the mutant, indicating that the primary function of IolR is the repression of the iol genes. IolR binding sites were identified in the promoter regions of iolC, iolT and iolR itself, which presumably is subject to negative autoregulation. A consensus DNA-binding motif was identified (5’-KGWCHTRACA-3’) which corresponds well to those of other GntR-type regulators of the HutC family. Taken together, our results disclose a complex regulation of the pck gene in C. glutamicum and identify IolR as an efficient repressor of genes involved in myo-inositol catabolism of this organism.

overall_design: To identify genes that are potentially regulated by IolR, the transcriptome profile of the iolR deletion strain was compared to that of the WT using DNA microarray analysis. The strains were grown in CGXII minimal medium with 4% (wt/vol) glucose as sole carbon source and RNA was isolated from cells harvested in the early exponential growth phase (OD600 of about 5). The transcriptome comparison was performed in triplicate starting from independent cultures. The second replicate included a dye-swap.

first: Simon

last: Klaffl

first: Melanie

last: Brocker

first: Bernhard

last: Eikmanns


title: The Two-component Signal Transduction System CopRS of Corynebacterium glutamicum is Required for Adaptation   to Copper-excess Stress

status: Public on Sep 05 2011

summary: Copper is an essential cofactor for many enzymes but at high concentrations it is toxic for the cell. Copper ion concentrations ≥50 µM inhibited growth of Corynebacterium glutamicum. The transcriptional response to 20 µM Cu2+ was studied using DNA microarrays and revealed 26 genes that showed a ≥3-fold increased mRNA level, including cg3280-cg3289. Several genes in this genomic region code for proteins presumably involved in the adaption to copper-induced stress, e. g. a multicopper oxidase and a copper-transport ATPase. In addition, this region includes the copRS genes (previously named cgtRS9) which encode a two-component signal transduction system composed of the histidine kinase CopS and the response regulator CopR. Deletion of the copRS genes increased the sensitivity of C. glutamicum towards copper ions, but not to other heavy metal ions. Using comparative transcriptome analysis of the ΔcopRS mutant and the wild type in combination with electrophoretic mobility shift assays and reporter gene studies the CopR regulon and the DNA-binding motif of CopR were identified. Evidence was obtained that CopR binds only to the intergenic region between cg3285 and cg3286 in the genome of C. glutamicum and activates expression of the divergently oriented gene clusters cg3285-cg3280 and cg3286-cg3289. Altogether, our data suggest that CopRS is the key regulatory system in C. glutamicum for the extracytoplasmic sensing of elevated copper ion concentrations and for induction of a set of genes capable of diminishing copper stress.

overall_design: Four or five biological replicates of each experiment were performed. Experiment 1: Transcriptome comparison of wild type grown with 1.25 µM or with 21.25 µM CuSO4; Exp. 2: WT vs. copRS deletion mutant grown with 21.25 µM CuSO4; For analysis via DNA microarrays, the RNA was isolated from exponentially growing cells cultivated in CgXII medium containing glucose as carbon source and either 1.25 uM CuSO4 or 21.25 uM CuSO4.

first: Stephanie

last: Schelder

first: Daniela

last: Zaade

first: Boris

last: Litsanov

first: Michael

last: Bott


title: Aberrantly microRNA profiling in cancerous hepatocytes versus normal primary hepatocytes

status: Public on Dec 30 2010

city: Wuhan

first: Xing-Xing

last: He

state: Hubei

address: 1095# Jie-Fang Avenue

department: Institute of Liver and Gastrointestinal Diseases

country: China

institute: Tongji Hospital

summary: MicroRNAs is a rapidly expanding area expected to change the way in which diseases will be diagnosed, treated and monitored in the future. Hepatocellular carcinoma (HCC) shows a rising incidence with high mortality but lack of effective targeted therapies. We identified the aberrantly expressed miRNAs involved in HCC through the comparison of miRNA expression profiling in cancerous hepatocytes with that in normal primary human hepatocytes and found 37 dysregulated miRNAs in HCC. There were 9 up-regulated miRNAs and 28 down-regulated miRNAs in HCC, of which, miR-221 and miR-99b were the most overexpressed miRNAs, while miR-375, miR-192, miR-146b-5p, miR-885-5p, miR-122* and miR-122 were noted for their greatest changes of decreased expression.  These aberrantly expressed miRNAs may provide insights into pathogenesis of HCC and thus may be used for diagnosis and therapy.

overall_design: Over the past few years, though several studies have uncovered aberrant miRNA expression profiles in HCC compared with matched nonmalignant tissues, the overlap of deregulated miRNAs from different platforms is limited. To solve this problem, we recommend a method that using primary cancer cells or cancer cell lines and nonmalignant primary cells to identify the specific aberrantly miRNA expression profiles in HCC and even in other types of cancer. Here, we identified the aberrantly expressed miRNAs involved in hepatoma through the comparison of miRNA expression profiling in cancerous hepatocytes with that in normal primary human hepatocytes and 37 dysregulated miRNAs were screened out by 2-fold change with a significant difference (P<0.05). Clustering analysis based on 13 miRNAs whose fold changes were over 15-fold change exhibited significantly differential expression pattern between the cancerous and normal hepatocytes.

first: Ying

last: Chang

first: Ju-sheng

last: Lin


title: Control of heme homeostasis in Corynebacterium glutamicum by the two-component system HrrSA

status: Public on Dec 17 2010

summary: The response regulator HrrA belonging to the HrrSA two-component system (previously named CgtSR11) is known to be repressed by the global iron-dependent regulator DtxR in Corynebacterium glutamicum. Sequence analysis indicated an involvement of the HrrSA system in heme-dependent gene expression. Growth experiments revealed that the non-pathogenic soil bacterium C. glutamicum is able to use hemin or hemoglobin as sole iron source. In DNA microarray analyses a putative operon encoding the hemin-binding protein HtaA and the putative hemin ABC transporter HmuTUV showed a strong upregulation in heme-grown cells. Deletion of the hmu operon clearly affects heme utilization, but does not completely abolish growth on heme or hemoglobin. As a central part of this study, we investigated the regulon of the response regulator HrrA via comparative transcriptome analysis of a hrrA deletion mutant and C. glutamicum wild type in combination with DNA-protein interaction studies with purified HrrA protein. Our data provide evidence for a heme-dependent transcriptional activation of heme oxygenase (hmuO), an enzyme involved in the utilization of heme as iron source. Besides hmuO, HrrA was shown to activate the expression of heme-containing components of the respiratory chain, namely ctaD and the ctaE-qcrCAB operon encoding subunits I and III of cytochrome aa3 oxidase and three subunits of the cytochrome bc1 complex. Furthermore, HrrA represses almost all genes involved in heme biosynthesis, including glutamyl-tRNA reductase (hemA), uroporphyrinogen decarboxylase (hemE), and ferrochelatase (hemH). Thus, our data clearly emphasize a central role of the HrrSA system in the control of heme homeostasis in C. glutamicum.

overall_design: Three biological replicates of each experiment were performed. Experiment 1: Transcriptome comparison of wild type grown und FeSO4 or heme as iron source; Exp. 2: WT vs. hrrA deletion mutant grown on FeSO4; Exp. 3: WT vs. hrrA mutant grown on heme. For analysis via DNA microarraysose RNA was isolated from exponentially growing cells cultivated in CgXII medium containing glucose as carbon source and either 2.5 uM FeSO4 or 2.5 uM heme as iron source.

first: Cornelia

last: Gätgens


title: Human retinal and photoreceptor gene expression profile

status: Public on Oct 05 2010

city: Seattle

first: Thomas

last: Reh

state: WA

address: 815 Mercer St

department: Biological Structure

institute: University of Washington

summary:
Comparison of gene expression profile between an 96 day human retina and photoreceptors present around the same time.
We used the Affymetrix Human Gene 1.0 ST array to compare their expression profiles.

overall_design: Retina from 96 and 90 day human retina was isolated and either directly used for RNA extraction or cultured with IRBP-GFP lentivirus and then the GFP expressing cells were FACS out and used for RNA extraction.

first: Deepak

last: Lamba


title: Expression data in the developing human retina at 19-20 weeks' gestation

status: Public on Dec 30 2008

city: Canberra

first: Peter

last: Kozulin

state: ACT

address: Building 46, Sullivan's Creek Road

department: Research School of Biological Sciences

country: Australia

institute: ANU

summary:
The retinas of simian primates include a specialized, cone-rich, macula which regards the central visual field and mediates high acuity and colour vision. A prominent feature of the macula is the fovea centralis - a 1 mm-wide, avascular depression in the inner retinal surface that corresponds with a local absence of rods and a peak spatial density of cones in the outer photoreceptor layer. The arrangement of macular photoreceptors, and their specialized ‘midget’ circuits, are the neural substrate for high resolution vision in primates. Macular-specific photoreceptor loss and abnormal blood vessel growth within the macula are the major causes of untreatable vision loss worldwide. However, the genes that regulate specialization of the macula, and the causes of its vulnerability to degeneration, remain obscure. Microarrays were used to compare gene expression between macula and non-macular regions during a critical phase of human retinal vascular development.

Keywords: Comparison of developing anatomical regions

overall_design: A 5 mm circular retinal biopsy was taken from the posterior pole (‘macula’ sample) from four human foetuses at 19-20 weeks gestation and another from the corresponding region immediately nasal to the optic disc (‘nasal’ sample). The remaining retina comprised the third sample region (‘surround’ sample). RNA was extracted from the three retinal biopsies from each specimen and hybridised onto individual Affymetrix arrays (total 12 arrays). Gene expression in the ‘macula’ region was compared with the ‘nasal’ and ‘surround’ regions, which served as baselines.

first: Riccardo

last: Natoli

first: Keely

middle: M

last: Bumsted O'Brien

first: Michele

middle: C

last: Madigan

first: Jan

last: Provis


title: Expression of PRAME in retinoblastoma primary tumors

status: Public on Oct 14 2010

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Transcriptome analysis of partially degraded and fragmented RNA samples from retinoblastoma primary tumors. Global gene expression profiling has shown great promise in high-throughput biomarker discovery for early disease detection in Retinoblastoma tumors.  In this analysis we have used 3 retinoblastoma primary tumors in triplicates which was normalised against human healthy Retina. Here, we have used nanogram scale of retinoblastoma RNA, processed in  HUMAN GENE 1.0 ST ARRAYS.

overall_design: We have analysed the gene expression in 2 normal healthy adult retina collected from cadaveric eyes and 3 retinoblastoma primary tumors

first: S

last: Krishnakumar

first: Nalini

last: Venkatesan

first: Srilatha

last: jasty

first: Lingam

last: Gopal

first: Vikas

last: Khetan


title: L-Glutamine metabolism and its regulation in C. glutamicum

first: Tino

last: Polen

summary: Corynebacterium glutamicum, a gram-positive soil bacterium used for the industrial production of amino acids such as L-glutamate and L-lysine, is able to use a number of different nitrogen sources, such as ammonium, urea, or creatinine. In this communication, we show that L-glutamine serves as an excellent nitrogen source for C. glutamicum and allows similar growth rates in glucose minimal medium as ammonium. A transcriptome comparison revealed a strong induction of the nitrogen starvation response when glutamine was used as nitrogen source. Subsequent growth experiments with a variety of mutants defective in nitrogen metabolism showed that glutamate synthase is crucial for glutamine utilization, while a putative glutaminase is dispensable under the experimental conditions used. The fact that the glutamate synthase encoding gltBD operon is under strict nitrogen control explains the necessity for induction of the nitrogen starvation response. The paradox situation that the nitrogen starvation response is induced although intracellular L-glutamine levels are high has implications on nitrogen sensing. In contrast to other gram-positive and gram-negative bacteria such as Bacillus subtilis, Salmonella typhimurium, and Klebsiella pneumoniae, a drop in glutamine concentration obviously does not serve as a nitrogen starvation signal in C. glutamicum.

overall_design: Three biological replicates were performed. To analyse how L-glutamine influences global gene expression when used as sole nitrogen source instead of ammonium, DNA microarray analyses were performed. For this purpose RNA was isolated from exponentially growing cells cultivated in CgXII medium containing glucose as carbon source and either L-glutamine or ammonium sulphate as nitrogen source.

first: Nadine

last: Rehm

first: Tobias

last: Georgi

first: Eva

last: Hiery

first: Ursula

last: Degner

first: Alfred

last: Schmiedl

first: Andreas

last: Burkovski

first: Michael

last: Bott


title: PIWI-associated piRNA in Drosophila melanogaster ovary

status: Public on Oct 25 2007

city: New Haven

first: Hang

last: Yin

state: CT

address: 10 Amistead Street, Room 220

department: Department of Cell Biology

institute: Yale University Stem Cell Center

summary:
Heterochromatin, representing the silenced state of transcription, largely consists of transposon-enriched and highly repetitive sequences. Implicated in heterochromatin formation and transcriptional silencing in Drosophila are PIWI and repeat-associated small interfering RNAs (rasiRNAs). Despite this, the role of PIWI in rasiRNA expression and heterochromatic silencing remains unknown. Here we report the identification and characterization of 12,903 PIWI-interacting RNAs (piRNAs) in Drosophila, demonstrating that rasiRNAs represent a subset of piRNAs.
Keywords: PIWI, piRNA, epigenetic regulation, heterochromatin

overall_design: PIWI-associated small RNA cDNA library was sequenced for one time by high-throughput 454 pyrosequencing.  Putative small RNA sequences were extracted and BLAST against the Drosophila melanogaster genome release 5. Presented here is a list of non-redundant PIWI-associated small RNAs, which have at least one genome match determined by BLASTn.

first: Haifan

last: Lin


title: Macrophage samples from the HMDP

status: Public on Oct 26 2012

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: Identify genes involved in regulation of inflammatory responses and gene-environemnt interactions, in macrophages from a set of mouse inbred strains termed the HMDP.  The HMDP is a genetically diverse mapping panel comprised of classical inbred and recombinant inbred wild type mice. The RMA values of genes were used for genome wide association as described in Bennett et al Genome Research 2010.

overall_design: GWAS for expression in primary macrophages of mouse inbred strains. Macrophages were exposed to bacterial lipopolysaccharide (LPS), oxidized lipids (OxPAPC) or control treatment conditions.

first: Luz

middle: D

last: Orozco

first: Brian

last: Bennett

first: Aldons

last: Lusis