title: The use of Microarray Technology to screen for tumor related genes regulated in myeloid leukosis of chicken, during infection with avian leucosis virus subgroup J.

status: Public on Jul 11 2013

first: yuhao

last: li

address: 483 Wushan Road, Tianhe District,

department: College of Veterinary Medicine

institute: South China Agricultural University

summary: To survey avian leukosis virus subgroup J (ALV-J) integration in myeloid leukosis (ML) of chicken, we developed an ALV-J insertional identification platform based on hybrid-capture target enrichment and next-generation sequencing (NGS). In addition, we used gene expression profiling and bioinformatics to associate integration sites to transcriptional activity and to genetic features of the tumor cell genome.

overall_design: We selected six cases of ALV-J positive and diagnosed as ML for integration sites identify from commercial broiler breeder flocks in Guangdong Province of China between November 2011 and March 2012. All tumors were diagnosed on the basis of characteristic gross and microscopic lesions. Furthermore, PCR tests on the genomic DNA of tissues and virus isolation assay only showed ALV-J-specific positive results in previously study. We randomly chose 4 independent myeloid leukosis samples from the six cases for gene expression profile analysis. And 3 ALV-negative tissue samples from specific-pathogen-free (SPF) chickens at the same age were use as negative controls. Thus a total of 7 samples were hybridized, three representing control.

first: Yuhao

last: Li

first: Ming

last: Liao


title: Whole genome profile of SWNCT and MWCNT vs. asbestos subchronic exposures to human small airway epithelial cells

status: Public on Jul 22 2013

city: Morgantown

first: Todd

middle: A

last: Stueckle

state: WV

address: 1095 Willowdale Road

department: Health Effects Laboratory Division

country: USA

institute: National Institute for Occupational Safety and Health

summary: Recent in vivo studies reported that inhaled carbon nanotube distribute in the alveolar region resulting in an acute inflammation, progressive fibrotic response and particle accumulation at the bronchoalveolar junction with low clearance.  With similar biopersistence and shape as asbestos, a known lung carcinogen, growing concern has arisen for elevated risk of carbon nanotube-induced lung carcinogenesis; however few studies have evaluated long-term human health risks associated with chronic pulmonary carbon nanotube exposures compared to asbestos. To address this knowledge gap, we conducted subchronic in vitro exposures of dispersed single walled carbon nanotube, multi-walled carbon nanotube and crocidolite asbestos to human small airway epithelial cells to assess their neoplastic transformation potential. Subchronic single-, multi-walled carbon nanotube and asbestos exposures caused human lung cell neoplastic transformation exhibited by increased proliferation, anchorage-independent growth, invasion and angiogenesis.  Whole genome profiling and protein expression analyses showed that carbon nanotube-induced transformation mechanism(s) was largely different from asbestos-related inflammatory signaling, suggesting specific carbon nanotube-induced carcinogenic potential. This study provides novel carbon nanotube and asbestos toxicogenomic information for risk assessment and an in vitro model to evaluate transformation potential of carbon nanotubes and other nanoparticles.

overall_design: Whole genome expression profiling was conducted on human immortalized small airway epithelial cells (SAEC-hTERT) following 6 month in vitro chronic exposure to six separate treatments to assess differences in carbon nanotube (CNT) vs. asbestos potential tumorigenesis signaling.  Dispersed single wall CNT (D-SWCNT), multi-wall CNT (D-MWCNT), ultrafine carbon black (D-UFCB), crocidolite asbestos (ASB) and saline (SAL) exposed cells were compared to Survanta® dispersant (DISP) passage control cells.  Each treatment possessed 3 biological cDNA replicates.  One technical replicate was performed per biological sample.

first: Liying

middle: W

last: Rojanasakul


title: Expression analysis of African Green Monkeys after treatment with a miR-33a/b-targeting LNA-antimiR

status: Public on Aug 23 2013

city: Charlestown

first: Veerle

last: Rottiers

state: MA

address: 149, 13th Street

department: Cancer Center

institute: Massachusetts General Hospital

summary:
Investigation of whole genome gene expression level changes in African Green Monkeys treated with antimiR-33a/b, compared to the animal treated with vehicle
The treatment of the monkeys is further described in Rottiers V, Obad S, McGarrah R, Black JC, Lindholm M, Goody R, Lawrence M, Whetstine JR, Gerszten RE, Kauppinen S, Näär AM. (2013). Pharmacological inhibition of a microRNA family in non-human primates by a seed-targeting 8-mer antimiR oligonucleotide. Accepted for publication at Science Translational Medicine.
MicroRNAs (miRNAs) regulate many aspects of human biology. They target mRNAs for translational repression or degradation through base-pairing with 3’ UTRs, primarily via seed sequences (nucleotides 2-8 in the mature miRNA sequence). A number of individual miRNAs and miRNA families share seed sequences and targets, but differ in the sequences outside of the seed. miRNAs have been implicated in the etiology of a wide variety of human diseases and therefore represent promising therapeutic targets. However, potential redundancy and compensatory action of different miRNAs sharing the same seed sequence, and the challenge of simultaneously targeting miRNAs that differ significantly in non-seed sequences complicates therapeutic targeting approaches. We recently demonstrated effective inhibition of entire miRNA families using seed-targeting 8-mer locked nucleic acid (LNA)-modified antimiRs in short-term experiments in mammalian cells and in mice. However, the long-term efficacy and safety of this approach in higher organisms, such as humans and non-human primates, has not been determined. Here, we show that pharmacological inhibition of the miR-33 family, key regulators of cholesterol/lipid homeostasis, by a subcutaneously delivered 8-mer LNA-modified antimiR in obese and insulin-resistant non-human primates results in de-repression of miR-33 targets, such as ABCA1, increases circulating high-density lipoprotein-cholesterol (HDL-C), and is well tolerated over 108 days of treatment. These findings demonstrate the efficacy and safety of an 8-mer LNA-antimiR against a miRNA family in a non-human primate metabolic disease model, suggesting that this could be a feasible approach for therapeutic targeting of miRNA families sharing the same seed sequence in human diseases.

overall_design: Expression analysis study in obese Non Human Primates (African Green Monkeys). Five animals treated with antimiR-33a/b were compared to five animals treated with vehicle.

first: Susanna

last: Obad

first: Andreas

last: Petri

first: Robert

last: McGarrah

first: Marie

last: Lindholm

first: Joshua

middle: C

last: Black

first: Sumita

last: Sihna

first: Robin

middle: J

last: Goody

first: Matthew

middle: S

last: Lawrence

first: Andrew

last: deLemos

first: Henrik

middle: F

last: Hansen

first: Steve

last: Whittaker

last: Henry

first: Rohn

last: Brookes

first: S

middle: H

last: Najafi-Shoushtari

first: Raymond

middle: T

last: Chung

first: Johnathan

middle: R

last: Whetstine

middle: E

last: Gerszten

first: Sakari

last: Kauppinen

first: Anders

middle: M

last: Näär


title: In vivo determination of candidate direct targets of the nonsense mediated decay pathway in intact Drosophila

status: Public on Jul 01 2013

city: Houston

first: Hao

last: Hu

state: Texas

address: 1155 Pressler Blvd, Unit 1340

department: Epidemiology

institute: MD Anderson Cancer Center

summary: Regulation of mRNA stability is a critical step in the control of gene expression. The nonsense mediated mRNA decay (NMD) pathway is one important mRNA stability pathway and has been shown to function in regulating a significant portion of the transcriptome. Perhaps the most significant outstanding question surrounding NMD regulation of endogenous gene expression is the identification of transcripts directly targeted by the NMD pathway versus secondary response genes, whose expression levels are dependent on the activity of direct targets. Here, we present for the first time in an intact animal, the experimental identification of direct targets of NMD. We find that most genes (74%) that are upregulated in NMD mutants appear not to be direct targets of NMD. More surprisingly, we find that the vast majority (97%) of candidate direct targets are not found to be increased in expression in a NMD mutant background. These results imply negative feedback renormalizes the levels of most direct targets of NMD, suggesting they would have been missed in previous analyses. We find that our candidate direct target genes have disproportionately long 3’ UTRs compared to non-targeted control genes. Long 3’ UTRs have been shown to target mRNAs for NMD in experimental systems, and our results imply this is the case in vivo. Our results will allow for the understanding of the function of the NMD pathway in endogenous gene regulation, during normal development, as well as in pathological states.

overall_design: Starting with a Nonsense Mediated Decay(NMD) mutant, in which expression levels of both primary and secondary NMD targets should be increased, we introduce a wild-type copy of the mutated factor and evaluated the transcriptome profile change overtime. Following reintroduction, expression levels of transcripts that are direct targets of NMD should decrease rapidly. Conversely, the levels of indirect targets will remain high until direct targets return to wild-type levels, which will occur later in the timecourse. This allows us to identify direct NMD targets.


title: Expression analysis of human aortic valve interstitial cells (hAVICs), mitral valve interstitial cells(hMVICs) and dermal firbroblasts (hDFs)

status: Public on Jun 30 2013

city: Nanjing

first: xiangqing

last: kong

address: No.300 Guangzhou Road

country: China

institute: The First Affiliated Hospital of Nanjing Medical University

summary: Investigation of whole genome gene expression level changes in hAVICs and hMVICs, compared to human dermal fibroblasts.

overall_design: A three chip assay using total RNA obtained from primary cultured normal valve interstital cells and human dermal fibroblasts was performed. Each chip measures the expression level of 45,033 genes from normal AVICs,MVICs and DFs.

first: Wei

last: Sun

first: Xiangqing

last: Kong


title: Characterization of the molecular interplay between Moraxella catarrhalis and human respiratory tract epithelial cells: Expression response of human phanryngeal epithelial Detroit 562 cells to adherent Moraxella catarrhalis strain BBH18

status: Public on Jun 27 2013

city: Nijmegen

first: Hester

last: Bootsma

address: Kapittelweg 29

department: Pediatrics

country: Netherlands

institute: Radboud University Medical Centre

summary: During the course of infection, respiratory pathogens like Moraxella catarrhalis needs to adhere to epithelial cells of different host niches such as the nasopharynx and lungs. Consequently, efficient adhesion to epithelial cells is considered an important virulence trait of M. catarrhalis.  We examined the interaction between human pharyngeal epithelial Detroit 562 cells and M. catarrhalis BBH18 during adherence using a combination of Tn-seq, a genome-wide negative selection screenings technology, and expression profiling of both host and pathogen. The results described in this study are further discussed in Stefan P.W. de Vries, Marc J. Eleveld, Peter W.M. Hermans, Hester J. Bootsma: Characterization of the molecular interplay between Moraxella catarrhalis and human respiratory tract epithelial cells, submitted.

overall_design: RNA was isolated from Detroit cells exposed to culture medium alone (n=6; control), and Detroits cells exposed to adherent M. catarrhalis BBH18 (n=6) using RNeasy columns. Total RNA was labeled according to standard Nimblegen gene expression array protocols and hybridized to a 12x135 Nimblegen human expression array for read-out.

first: Stefan

middle: P

last: de Vries

first: Marc

last: Eleveld

first: Peter

last: Hermans


title: Development of microRNA expression signatures in laryngeal tumors

status: Public on Jun 04 2013

city: Hachioji

first: Kaho

last: Minoura

state: Tokyo

country: Japan

institute: Agilent Technologies Japan Ltd

summary:
Background: MicroRNA (miRNA) is an emerging subclass of small non-coding RNAs that regulates gene expression and has a pivotal role for many physiological processes including cancer development. Recent reports revealed the role of miRNAs as ideal biomarkers and therapeutic targets due to their tissue- or disease-specific nature. Head and neck cancer (HNC) is a major cause of cancer-related mortality and morbidity, and laryngeal cancer has the highest incidence in it. However, the molecular mechanisms involved in laryngeal cancer development remain to be known and highly sensitive biomarkers and novel promising therapy is necessary.

Methodology/Principal Findings: To explore laryngeal cancer-specific miRNAs, RNA from 5 laryngeal surgical specimens including cancer and non-cancer tissues were hybridized to microarray carrying 723 human miRNAs. The resultant differentially expressed miRNAs were further tested by using quantitative real time PCR (qRT-PCR) on 43 laryngeal tissue samples including cancers, noncancerous counterparts, benign diseases and precancerous dysplasias. Significant expressional differences between matched pairs were reproduced in miR-133b, miR-455-5p, and miR-196a, among which miR-196a being the most promising cancer biomarker as validated by qRT-PCR analyses on additional 84 tissue samples. Deep sequencing analysis revealed both quantitative and qualitative deviation of miR-196a isomiR expression in laryngeal cancer. In situ hybridization confirmed laryngeal cancer-specific expression of miR-196a in both cancer and cancer stroma cells. Finally, inhibition of miR-196a counteracted cancer cell proliferation in both laryngeal cancer-derived cells and mouse xenograft model.

Conclusions/Significance: Our study provided the possibilities that miR-196a might be very useful in diagnosing and treating laryngeal cancer.

overall_design:
To explore laryngeal cancer-specific miRNAs, RNA from 5 laryngeal surgical specimens including cancer and non-cancer tissues were hybridized to microarray carrying 723 human miRNAs.
Total RNA including low molecular weight RNA from tissue samples was isolated using the mirVanaTM miRNA Isolation Kit (Ambion) according to the manufacturer's instructions. The quality of the RNA samples was assessed using an Agilent 2100 Bioanalyzer, and only the samples meeting the criteria of 28S/18S > 1 and RNA Integrity Number (RIN) ≥ 7.5 were used for all analyses. For microarray analysis, we used the Human miRNA Microarray Kit V2 (Agilent Technologies, Santa Clara, CA), which contains 20-40 features targeting each of 723 human miRNAs (Agilent design ID 019118) as annotated in the Sanger miRBase, release 10.1. Labeling and hybridization of total RNA samples were performed according to the manufacturer's protocol. One hundred ng of total RNA was used as an input into the labeling reaction, and the entire reaction was hybridized to each array for 20 hours at 55°C. The results were analyzed using Agilent GeneSpring GX7.3. Normal controls and cancer samples were compared using Welch's t-test (p<0.05) and differentially expressed miRNAs with at least a 2-fold change in expression were considered to be potential biomarkers.

first: Koichiro

last: Saito


title: Gene expression profiles of canine mammary carcinomas of various grades of malignancy

status: Public on May 31 2013

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

summary: The objective of the present study was to assess the gene expression profiles of canine mammary carcinoma (in unsupervised manner) classified by pathologists as the 1st, the 2nd and the 3rd grade of malignancy and compare their molecular and pathological classifications. Our analysis showed that some pathologically distinct tumours may have similar gene expression and vice-versa. Probably that is why the patients with the same pathological type of cancer often have various outcomes and respond in a heterogenous manner to anticancer agents. The molecular classification, contrary to the pathological methods, reflects the biological processes and pathways within the tumour cell, not only the morphological features. It is also helpful in the better understanding of cancer biology (genes responsible for tumourigenesis, molecular interactions within the tumour or genes involved in specific pathways which could be a target for future therapy).

overall_design: 18 canine mammary tumours (6 of the 1st grade of malignancy, 6 of the 2nd grade of malignancy and 6 of the 3rd grade of malignancy) were subjected to the analysis. RNA was isolated, reverse transcribed and hybridized on cDNA microarrays. Pooled RNA from all of the tumours was used as a reference, and dye-swaps were performed. Then, the unsupervised hierarchical analysis was performed.

first: K

last: Pawłowski

first: H

last: Maciejewski

first: I

last: Dolka

first: J

last: Mol

first: T

last: Motyl

first: M


title: Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types (exon expression)

city: Stanford

first: Craig

middle: Patrick

last: Giacomini

state: CA

address: 269 Campus Drive (CCSR 3245A)

department: Pathology

institute: Stanford University

summary: Custom Agilent 8 x 15K microarray interrogating exon level expression of a set of genes previously known to be involved in oncogenic rearrangements.  The goal of this study was to discover novel gene fusions by screening for exonic expression transitions within individual genes.

overall_design: Sixteen cancer samples and cell lines, including eight positive controls with known gene fusions and eight sarcoma specimens, where gene fusions have yet to be discovered, were hybridized against a common reference mRNA control (pooled from 11 diverse cell lines)

first: Jonathan

last: Pollack


title: Transcriptome analysis of inhibitor-treated schistosome female

status: Public on May 30 2013

city: São Paulo

first: Katia

middle: Cristina Pereira

last: Oliveira

state: O

address: Av Prof lineu prestes 748

department: Centro de Parasitologia e Micologia

country: Brazil

institute: Instituto Adolfo Lutz

summary: Transcriptional profiling of  S. mansoni adult females treated with Herbimycin A (4.5 µM ) or TGF beta receptor type I kinase inhibitor (TRIKI, 300 nM) or a combined treatment with both inhibitors (Herbimycin A 4.5µM and TRIKI 300nM)   vs. Non-treated S.mansoni adult females (DMSO during 48h)

overall_design: Two conditions (treated vs. Non-treated) with three biological samples of treated worms (Herbimycin, TRIKI or Herb+TRIKI) and in parallel other three biological samples of non-treated worms (DMSO) for each treatment condition. For each sample (three treated and three non-treated for each inhibitor combination) were performed two technical replicas.

first: Christin

last: Buro

first: Svenja

last: Beckmann

first: Silke

last: Leutner

first: Zhigang

last: Lu

first: Colette

last: Dissous

last: Cailliau

first: Sergio

last: Verjovski-Almeida

first: Christoph

middle: G

last: Grevelding


title: Expression analysis of neural progenitor cells derived from iPS cells generated from skin fibroblasts and umbilical cord mesenchymal cells

status: Public on May 06 2013

city: Guangzhou

first: Pengfei

last: Liu

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences

summary:
Investigation of whole genome gene expression level changes in neural progenitor cells derived from iPS cells generated from umbilical cord mesenchymal cells, compared to neural progenitor cells derived from iPS cells generated fromskin fibroblasts. Analyze the difference between neural progenitor cells derived from iPS cells generated from different origins.
The method to induce reprogramming of somatic cells and human iPS cells for neural differentiation is described in Cai J, Li W, Su H, Qin D, Yang J, et al. (2010) Generation of human induced pluripotent stem cells from umbilical cord matrix and amniotic membrane mesenchymal cells. J Biol Chem 285: 11227-11234. and Kim DS, Lee JS, Leem JW, Huh YJ, Kim JY, et al. (2010) Robust enhancement of neural differentiation from human ES and iPS cells regardless of their innate difference in differentiation propensity. Stem Cell Rev 6: 270-281.

overall_design: A two-chip study using total RNA recovered from one neural progenitor cell line derived from iPS cells generated from skin fibroblasts (GZF1C7NSCP3) and one neural progenitor cell line derived from iPS cells generated from umbilical cord mesenchymal cells (VMC2C7NSCP3). No replicates were made. Each chip measures the expression level of 45,033 genes from the two samples with fourteen 60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

last: Liiu


title: Adipose tissue nutrigenomic study in Iberian pigs with dietary intervention of oleic acid supplementation

status: Public on Jun 14 2013

city: Madrid

first: Cristina

last: Ovilo

address: Ctra Coruña km 7.5

country: Spain

institute: INIA-CSIC

summary:
We studied the influence of the oleic acid content of the diet on adipose tissue transcriptome.
Iberian pigs were fed a standard (C) or a high oleic sunflower oil enriched (HO) diet. Transcriptome analyses were performed in adipose tissue samples (inner layer) obtained at slaughter (110 kg live weight) employing the Affymetrix porcine GeneChip. Normalized and filtered microarray expression data (background corrected and base-2 logarithmic-transformed) were analyzed through Bayesian inference using the GEAMM v.1.6 program. Statistically significant expression differences (FDR<0.10) between C and HO groups were observed for a total of ten probes corresponding to nine different known genes. Six genes were overexpressed in the HO group and three were overexpressed in the C group. Expression differences between groups ranged from 1.38 to 2.75-fold. The two most significantly DE genes were related with immune defense (TCRB and GPR183) and others were related with nutrient metabolism as glicerolipid metabolism (GK), phospholipid and sphingolipid metabolism (PPM1L), carbohydrate metabolism (FBP2) aminoacid metabolism and energy homeostasis (PRSS35 and CKB) and gene expression regulation and adipogenesis (RXRG).

overall_design: 15 Iberian castrated male pigs were adscribed to one of two experimental groups at 28 kg live weight (7 animals in Control group and 8 animals in High Oleic group). Nutritional treatment was maintained until sacrifice of the animals at 110 kg of live weight. At the sacrifice, backfat adipose tissue was sampled from each animal at the level of the last rib.


title: Experiment comparing transcriptomes of red and purple tissue sections on Del/Ros1 Moneymaker fruit

city: Norwich

first: Andreas

last: Magusin

address: Norwich Research Park

department: Crop Genetics

country: United Kingdom

institute: John Innes Centre

summary:
Microarray analysis was used to compare the gene expression profiles of red and purple sectors of VIGS (Virus-induced gene silencing)-treated Del/Ros1 fruit in the MoneyMaker background.
Fruit were silenced at the mature green stage and harvested at differing number of days after breaker.

overall_design: Custom two-colour microarray (TOM2); where one channel was employed as a common reference.

first: Yang

last: Zhang

first: Eugenio

last: Butelli

first: Rosalba

last: De Stefano

first: Henk-Jan

last: Schoonbeek

first: Chiara

last: Pagliarani

first: Nikolaus

last: Wellner

first: Lionel

last: Hill

first: Diego

last: Orzaez

first: Antonio

last: Granell

middle: D

last: Jones

first: Cathie

last: Martin


title: Underexpression of miR-224 in methotrexate resistant human colon cancer cells

status: Public on May 29 2013

city: Barcelona

first: Carlos

last: Ciudad

state: Barcelona

address: Av. Juan XXIII-27

department: Biochemistry and Molecular Biology

institute: University of Barcelona

summary:
A summary of the work associated to these microarrays is the following:

MicroRNAs (miRNAs) are small non-coding RNAs involved in RNA silencing that play a role in many biological processes. They are involved in the development of many diseases, including cancer. Extensive experimental data show that they play a role in the pathogenesis of cancer as well as the development of drug resistance during treatment. MiRNA microarrays of sensitive and MTX-resistant HT29 colon cancer cells were performed. The results were analyzed using the GeneSpring GX11.5 software. Differentially expressed microRNAs in resistant cells were identified and miR-224, which was greatly underexpressed and displayed robust raw signal values, was selected for further studies. Putative targets were predicted using TargetScan 5.1 software and intersected with the data from expression microarrays previously performed. This approach allowed us to identify miR-224 targets that were differentially expressed more than 2-fold in resistant cells. Among them, ARL3, CDS2, DCP2, HSPC159, MYST3 and SLC4A4 were validated at the mRNA level by qRT-PCR. Functional assays using an anti-miR against miR-224 desensitized the cells toward MTX, mimicking the resistant phenotype. On the other hand, siRNA treatment against SLC4A4 or incubation of Poly Purine Reverse Hoogsteen (PPRH) hairpins against CDS2 or HSPC159 increased sensitivity to MTX. These results revealed a role for miR-224 and its targets in MTX resistance in HT29 colon cancer cells.
KEYWORDS
Methotrexate, miRNAs, drug resistance, DHFR

overall_design: Two cell lines are compared in the study, which are HT29 colon cancer cells sensitive to methotrexate and HT29 cells resistant to 10e-5M MTX. Six samples are provided which correspond to 3 samples for the control condition and 3 samples for the resistant condition. Data files from miRNA and mRNA (previously submitted to GEO as GSE11440) microarrays were analyzed with GeneSpring GX11.5 software (Agilent Technologies) to find differentially expressed miRNAs and their cellular target genes in the resistant cell lines compared to their sensitive counterparts.

first: Nuria

last: Mencia

first: Elisabet

last: Selga

first: Veronique

last: Noe


title: ChIP-chip of Geobacter sulfurreducens PCA with antibody against various sigma factors under various conditions

status: Public on May 01 2013

city: La Jolla

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

type: Expression profiling by genome tiling array

summary: We applied a ChIP-chip approach to elucidate the binding profiles of sigma factors (RpH, RpoN and RpoS) experimentally under different growth conditions. This technique localizes DNA fragments within DNA-protein complexes enriched by chromatin immunoprecipitation using high-density oligonucleotide tilling arrays.

overall_design: A 10 ChIP-chip study using immunoprecipitated DNA (IP-DNA)  from three culture condtions against three alternative sigma factors .  The high-density oligonucleotide tiling arrays used were consisted of 381,174 oligonucleotide probes spaced 20 bp apart (30-bp overlap between two probes) across the G.sulfurreducens genome (NimbleGen). Experiments were conducted as three bioliogical replicates (different cultures).


title: Expression analysis of Saccharomyces cerevisiae wild-type and rph1Δ two and 24 hours following menadione treatment

status: Public on Mar 22 2013

city: New Haven

first: Elizabeth

middle: Anne

last: Schroeder

state: CT

address: 310 Cedar St. BML 369

department: Genetics

institute: Yale University

summary:
Investigation of whole genome gene expression changes at short (2 hours) and extended (24 hours) timepoints in wild-type Saccharomyces cerevisiae treated with 50 μM menadione during exponential growth compared to an rph1Δ strain
Transient treatment with 50 μM menadione elevates mitochondrial ROS and extends chronological lifespan in yeast. Deletion of RPH1, a H3K36me3 histone demethylase, block chronological lifespan extension. This study aimed to identify Rph1p-dependent gene expression changes induced by menadione treatment that may support chronological lifespan extension.
Reference: Bonawitz, N.D., Chatenay-Lapointe, M., Wearn, C.M., and Shadel, G.S. (2008). Expression of the rDNA-encoded mitochondrial protein Tar1p is stringently controlled and responds differentially to mitochondrial respiratory demand and dysfunction. Curr Genet 54, 83-94.

overall_design: A 24 chip study using total RNA recovered from two separate cultures each of Saccharomyces cerevisiae wild-type DBY2006 and rph1Δ. Each chip measures expression levels of 5,777 transcripts from NCBI build June 2008 with 8 probes per transcript and 3 replicate probe sets.

first: Nuno

last: Raimundo

first: Gerald

last: Shadel


title: Multicolor miRNA fluorescence in situ hybridization for tumor differential diagnosis

status: Public on Mar 14 2013

city: Kingston

first: Harriet

last: Feilotter

state: Ontario

address: 88 Stuart St

department: Pathology and molecular department

country: Canada

institute: Queen's University

summary: miRNAs are excellent tumor biomarkers because of their cell-type specificity and abundance. However, many miRNA detection methods, such as real-time (RT)-PCR, obliterate valuable visuospatial information in tissue samples. To enable miRNA visualization in formalin-fixed paraffin-embedded (FFPE) tissues, we developed multicolor miRNA fluorescence in situ hybridization (FISH). For proof-of-concept, we differentiated two skin tumors, namely Basal cell carcinoma (BCC) and Merkel cell carcinoma (MCC), with overlapping histologic features but distinct cellular origins. Using sequencing-based miRNA profiling and discriminant analysis, we identified tumor-specific miRNAs (miR-205 and miR-375) in BCC and MCC respectively. We addressed three major shortcomings in miRNA FISH, identifying optimal conditions for miRNA fixation and rRNA retention using model compounds and HPLC analyses, enhancing signal amplification and detection by increasing probe-hapten linker lengths, and improving probe specificity using shortened probes with minimal rRNA sequence complementarity. We validated our method on 4 BCC and 12 MCC tumors. Amplified miR-205 and miR-375 signals were normalized against directly detectable reference rRNA signals. Tumors were classified using pre-defined cut-off values; all were correctly identified in blinded analysis. We established a reliable miRNA FISH technique for parallel visualization of differentially expressed miRNAs in FFPE tumor tissues

overall_design: 6 MCC samples 2 normal skin samples were profiled with Agilent miRNA array platform

first: Neil

last: Renwick

first: Pavol

last: Cekan


title: Transcriptome of short RNA fraction in Rickettsia conorii

status: Public on Mar 02 2013

city: Marseille

first: Aurélie

last: Renvoisé

address: 27 bd Jean Moulin

country: France

institute: Urmite

type: Non-coding RNA profiling by high throughput sequencing

summary: We constructed a small RNA cDNA library, using small RNA fraction with a length of 19-29 bases, and we performed deep sequencing of the cDNA library.

overall_design: R. conorii subsp. conorii strain Malish 7 was cultivated on XTC cells for 3 days at 28°C. RNA enriched with small RNA fractions was further extracted and cDNA was synthesized.

first: Svetlana

last: Shabalina

first: Khalid

last: Karkouri

first: Gregory

last: Gimenez

first: Quentin

last: Leroy

first: Eugene

last: Koonin

first: Didier

last: Raoult


title: Histone H3 lysine9 acetylation, rather than lysine4 trimethylation, marks meiotic recombination hotspots and promotes recombination initiation in fission yeast

status: Public on Mar 07 2013

city: Meguro-ku

first: Shintaro

last: YAMADA

address: 3-8-1 Komaba

institute: University of Tokyo

type: Genome binding/occupancy profiling by genome tiling array

summary: Histone modifications are associated with meiotic recombination hotspots, discrete sites with  augmented recombination frequency. For example, trimethylation of histone H3 lysine4 (H3K4me3)  marks most hotspots in budding yeast and mouse. Modified histones are known to regulate meiotic  recombination partly by promoting DNA double strand break (DSB) formation, but the role and precise  landscape of histone modifications at hotspots remain unclear. Here, we studied hotspot-associated  modifications in fission yeast and found general features: acetylation of H3 lysine9 (H3K9ac) is  strikingly elevated, and H3K4me3 is not significantly enriched. Remarkably, elimination of H3K9ac  reduced binding of the DSB-inducing enzyme Rec12 and DSB at hotspots. We also found that the H3K4  metyltransferase Set1 promotes DSB formation at some loci, but it restricts Rec12 binding to hotspots.  These results suggest that H3K9ac rather than H3K4me3 is a hotspot-associated mark involved in  meiotic DSB formation in fission yeast.

overall_design: S.pombe cells in a pat1-114 background were induced to enter meiosis by the haploid meiosis system, and harvested one hour after the induction. ChIP were performed using anti-H3Cter, H3K9ac, -H3K14ac and -H3K4me3 antibodies.   pat1-114 rad50S rec12+-FLAG cells in a wild type, H3K9A or set1+ deletion background were induced to enter meiosis by the haploid meiosis system, and harvested five hours after the induction. ChIP were performed using anti-FLAG antibodies.

last: Yamada

first: Kunihiro

last: Ohta

first: Takatomi


title: DNA topoisomerase III localizes to centromeres and affects centromeric CENP-A levels in fission yeast

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

summary: Centromeres are specialized chromatin regions marked by the presence of nucleosomes containing the centromere-specific histone H3 variant CENP-A, which is essential for chromosome segregation. Assembly and disassembly of nucleosomes is intimately linked to DNA topology and DNA topoisomerases have previously been implicated in the dynamics of canonical H3 nucleosomes. Here we show that Schizosaccharomyces pombe Top3 and its partner Rqh1 are involved in controlling the levels of CENP-ACnp1 at centromeres. Both top3 and rqh1 mutants display defects in chromosome segregation. Using chromatin immunoprecipitation and tiling microarrays we show that Top3 unlike Top1 and Top2 is highly enriched at centromeric central domains, demonstrating that Top3 is the major topoisomerase in this region. Moreover, centromeric Top3 occupancy positively correlates with CENP-ACnp1 occupancy.  Intriguingly, both top3 and rqh1 mutants display increased relative enrichment of CENP-ACnp1 at centromeric central domains. Thus, Top3 and Rqh1 normally limit the levels of CENP-ACnp1 in this region. This new role is independent of the established function of Top3 and Rqh1 in homologous recombination downstream of Rad51. Therefore, we hypothesize that the Top3-Rqh1 complex has an important role in controlling centromere DNA topology which in turn affects the dynamics of CENP-ACnp1 nucleosomes.

overall_design:
For transcription: Total RNA from top3-105 mutant and WT control cells after 8 hours at 36C in biological duplicates.
For Top3-myc chromatin immunoprecipitation: DNA immunoprecipitated with mouse anti-Myc using chromatin extracts from cells expressing Top3-Myc from the endogenous locus at 30C in biological duplicates normalized to input DNA from wild type cells at 30C in biological duplicates.
For CENP-A/Cnp1 chromatin immunoprecipitation: DNA immunoprecipitated with anti-Cnp1 serum using chromatin extracts from top3-105 mutant and wild type control cells after 8 hours at 36C in in biological duplicates normalized to input DNA from each strain.

first: Ulrika

last: Norman-Axelsson

first: Mickaël

last: Durand-Dubief

first: Punit

last: Prasad


title: Changes in gene expression in fruitfly ovaries in mutants affecting components of rasiRNA system

status: Public on Mar 11 2013

city: Moscow

first: Sergey

middle: A

last: Lavrov

address: Kurchatov sq. 2

department: DMBC

country: Russia

institute: IMG

summary:
rasiRNA (rasiRNAs, repeat-associated short interfering RNAs) system is a mechanism of silencing of mobile element transpositions in germline of a number of species including Drosophila melanogaster. rasiRNA itself is a short  RNAs which participate in transposon transcription repression and mRNA degradation. Defects in rasiRNA system lead to increased transposition rate and developmental abnormalities due to accumulation of double-strand DNA breaks in fruitfly testes and ovaries.
A number of proteins participate in rasiRNA-mediated repression including SPN-E (homeless), PIWI and ARMI. Mutations in the genes of these proteins lead to significant mobile element mRNA accumulation.
We performed microarray-based study of effects of spn-E mutation on expression in fruitfly ovaries - one of the organs where rasiRNA system work. Our goal was the identification of other (besides mobile elements) targets of rasiRNA system regulation

overall_design:
Total RNA samples were extracted from ovaries of
1) spn-E1/spn-Ehls03987 trans-heterozygotes and mix of heterozygotes spn-E1/TM3 and spn-Ehls03987/TM3 (spn-E/+ hereafter).
2) Piwi2/PiwiNT trans-heterozygotes and mix of heterozygotes PiwiNT/CyO and Piwi2/CyO (Piwi/+ hereafter).
Samples were reverse transcribed, IVT-amplified and labeled with Cy3 or Cy5. Mix of differently labeled aRNAs was hybridized to Oligo14Kv2 microarray slides (CDMC), washed, scanned and treated in GenePix 6 (Molecular Devices) and subsequently in FlexArray 1.6.2 (McGill University and Génome Québec Innovation Centre).
Three biological replica (one sample dye-swapped) were produced and analyzed.

first: Alina

last: Korbut


title: Real-time quantitative PCR analysis of human astrocytomas

status: Public on Feb 12 2013

city: México.

first: Ruth

last: Ruiz-Esparza

address: Centro Médico Nacional Siglo XXI, IMSS, México,

department: Pediatría

country: Mexico

institute: Instituto Mexicano del Seguro Social

summary: Pediatric astrocytomas, a leading cause of death associated with cancer, are the most common primary central nervous system tumors found in children. Most studies of these tumors focus on adults, not children. We examined the global protein and microRNAs expression pattern by 2D SDS-PAGE, mass spectrometry (MALDI-TOF) and RT2 miRNA PCR Array System. MicroRNAs analysis revealed for the first time novel microRNAs involved in astrocytomas biology. Interestingly, miR-138 and miR-145 down-regulation appear to be associated with protein over-expression of vimentin and Bax, respectively. In conclusion, our results show that novel proteins and microRNAs altered on pediatric astrocytoma could serve as biomarkers to distinguish between astrocytoma grades. Astrocytoma samples were colected from patients and total RNA isolation (30 mg of tissue) was performed using the TRIzol® protocol (Invitrogen, USA) according to the manufacturer′s instructions. Samples were analyzed using SA Biosciences RT2 miRNA PCRArray System  to determied the miRNA expression between control samples and tumors

overall_design: RT2 miRNA PCR Array. Eigth tumor samples and two control tissue (including two control tissue replicates) were used as indicated in the sumary. A total of 3ug of RNA from each tumr samples and control tissue were placed in the PCR Array

first: Diego

last: Arenas

last: Ruiz Espaza


title: Reference Genes for MiRNAome Analysis of Urothelial Carcinomas

status: Public on Feb 26 2013

city: Berlin

first: Hellmuth-A

last: Meyer

address: Charitéplatz 1

department: Department of Urology

country: Germany

institute: Charite

summary:
Background/Objective: Quantitative real-time PCR (RT-qPCR) is widely used in miRNA expression studies on cancer. To compensate for the analytical variability produced by the multiple steps of the method, relative quantification of the measured miRNAs is required, which is based on normalization to endogenous reference genes. A literature search in PubMed revealed that no study has been performed so far on reference miRNAs for normalization of miRNA expression in urothelial carcinoma. The aim of this study was to identify suitable reference genes for miRNA expression studies by RT-qPCR in urothelial carcinoma.
Methods: Candidate reference miRNAs were selected from 24 papillary urothelial carcinoma and normal bladder tissue samples by miRNA microarrays. The usefulness of these candidate reference miRNAs together with the commonly for normalization purposes used small nuclear RNAs RNU6B, RNU48, and Z30 were thereafter validated by RT-qPCR in 58 tissue samples and analyzed by the algorithms geNorm, NormFinder, and BestKeeper.
Principal Findings: Based on the miRNA microarray data, a total of 16 miRNAs were identified as putative reference genes. After validation by RT-qPCR, miR-101, miR-125a-5p, miR-148b, miR-151-3p, miR-151-5p, miR-181a, miR-181b miR-29c, miR-324-3p, miR-424, miR-874, RNU6B, RNU48, and Z30 were used for geNorm, NormFinder, and BestKeeper analyses that gave different combinations of recommended reference genes for normalization.
Conclusions: The present study provided the first systematic analysis for identifying suitable reference miRNAs for miRNA expression studies of urothelial carcinoma by RT-qPCR. Different combinations of reference genes resulted in reliable expression data for both strongly and less strongly altered miRNAs. Notably, RNU6B, which is the most frequently used reference gene for miRNA studies, gave inaccurate normalization. The combination of four (miR-125a-5p, miR-148b, miR-151-3p, and miR-151-5p) or three (miR-148b, miR-874, miR-181b) miRNA reference genes is recommended for normalization.

overall_design: Candidate reference miRNAs (for RT-qPCR analysis) were selected from 24 papillary urothelial carcinoma and normal bladder tissue samples by miRNA microarrays.

first: N

last: Ratert

first: H

first: M

last: Jung

last: Mollenkopf

first: I

last: Wagner

first: K

last: Miller

first: E

last: Kilic

first: A

last: Erbersdobler

first: S

last: Weikert


title: microRNA expression signature of monocyte-derived dendritic cells (DCs) from peripheral blood mononuclear cells (PBMCs)

status: Public on Jan 28 2013

city: kunming

last: Zhao

address: Eastern Jiaochang road,32#

institute: Kunming institute of zoology.CAS

summary: In order to detect the microRNA expression profile of in vitro generated dendritic cells , purified monocytes from PBMCs were used as dendritic cell (DCs) precursors and were cultured in medium with cocktail for differentiation and maturation to immature dendritic cells (iDCs) and mature dendritic cells (mDCs). microRNA samples were isolated from precursor, iDCs and mDCs and used for microarray-based microRNAs expression profiles.

overall_design: To generate enough amount of immature DC (iDCs) and mature DCs (mDCs), monocytes were differentiated with GM-CSF and rhIL-4 for 2 days and maturated in the presence of TNF-α, IL-1β, IL-6 and PGE2 for another 2 days. With the anticipation to insight developmental-stage-specific microRNAs with potential functions related to monocyte derived DCs, global microRNAs expression profiling was set using microarray technology.microRNA expression profiles were performed in triplicate independent experiments starting for 3 groups of precursor, iDC and mDC generated from different blood donors.

first: Fengchao

last: Lang

first: Yan

last: Guo

first: Huatang

last: Zhang


title: MicroRNA expression data in Idiopathic Pulmonary Fibrosis

status: Public on Jan 04 2013

city: Pittsburgh

first: Kusum

middle: Vijay

last: Pandit

state: PA

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

institute: University of Pittsburgh

summary: Idiopathic pulmonary fibrosis (IPF) is an untreatable fibrotic lung disease characterized by fibroblast proliferation and epithelial mesenchymal transition. Using miRNA expression microarrays we identified 96 differentially expressed miRNA in IPF lungs which included let-7d, miR-30 family, miR-29 family and miR-154 family.

overall_design: Lung tissue samples for microarray analysis were obtained through the University of Pittsburgh Health Sciences Tissue Bank. 13 samples were obtained from surgical remnants of biopsies or lungs explanted from patients with IPF who underwent pulmonary transplant, and 12 control normal lung tissues obtained from the disease free margins with normal histology of lung cancer resection specimens. The morphologic diagnosis of IPF was based on typical microscopic findings consistent with usual interstitial pneumonia. Total RNA was labeled with Cy3 and hybridized on Agilent 8X15K microRNA array (Agilent Technologies, Santa Clara, CA). After 20 hours hybridization, arrays were washed and scanned according to the manufacturer’s protocol.

middle: V

first: Naftali

last: Kaminski


title: Effect of Curcumin on expression profile of Schistosoma mansoni adult worms

status: Public on Dec 30 2012

first: Katia

last: Oliveira

summary: Transcriptional profiling of Curcumin treated S. mansoni adult worms (15uM of Curcumin in DMSO during 24h) vs. Non-treated S.mansoni adult worms (DMSO during 24h)

overall_design: Two conditions (treated vs. Non-treated) with four biological samples of treated worms (Curcumin 1, 2, 3 and 4) and four biological samples of non-treated worms (Control 1, 2, 3 and 4). For each sample (four treated and four non-treated) were performed two technical replicas.

first: Enyara

last: Morais

middle: C

first: Érika

middle: B

last: Moreira

first: Lizandra

last: Magalhães

first: Sergio

last: Verjovski-Almeida

first: Vanderlei

last: Rodrigues


title: Genome-wide Analysis of the Pho Regulon in a pstCA mutant of Citrobacter rodentium

status: Public on Dec 25 2012

city: Parkville

first: Matthew

middle: J

last: Wakefield

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute

summary: to investigate global gene expression of C. rodentium strain ICC169 and its isogenic pstCA and phoB mutants when grown in phosphate-rich and phosphate-low medium

overall_design: Genotype: 3 levels (wt, pstCA, phoB)  phosphate: 2 levels (low, high)

first: Catherine

last: Cheng

first: Ji

last: Yang

first: Marija

last: Tauschek

first: Roy

last: Robins-Browne


title: ChIP-chip of Hmt1-9myc from S. cerevisiae

city: AMHERST

first: Eric

last: Milliman

state: NY

address: 109 COOKE HALL

department: Biology

institute: SUNY AT BUFFALO

summary: A comprehensive genome-wide binding profile for Hmt1 was obtained through the method of ChIP-chip using NimbleGen high-resolution tiling microarrays.  Of the approximately 1000 Hmt1-binding sites found, the majority fall within or proximal to an ORF.  However, Hmt1 occupancy is found at a number of other genomic features such as tRNA and snoRNA genes, thereby implicating a regulatory role in the biogenesis of these non-coding RNAs.  RNA hybridization analysis shows that Hmt1 loss-of-function mutants display higher steady-state tRNA abundance relative to the wild-type.  Co-immunoprecipitation studies show that Hmt1 interacts with the TFIIIB component Bdp1, suggesting a role for Hmt1 in modulating RNA pol III transcription to regulate tRNA production.

overall_design: ChIP-chip of Hmt1-9myc using Nimblegen high-resoluion tiling arrays

first: Michael

last: Yu


title: Comparative analysis of Gallus gallus cecal epithelia following Eimeria tenella infection

status: Public on Dec 10 2012

city: Lanzhou

first: Aijiang

last: Guo

state: Gansu

address: 1 Xujiaping Yanchangbu Chengguan District

institute: Lanzhou veterinary research institute, CAAS

summary:
Relative expression levels of mRNAs in chicken cecal epithelia experimentally infected with Eimeria tenella were measured at 4.5 days post-infection. Two weeks old chickens were uninfected (negative control) or were orally inoculated with sporulated oocysts of Eimeria tenella. Cecal epithelia samples were collected from >12 birds in infected or uninfected group at 4.5 d following infections, in which samples from 4 birds were pooled together to form a total 3 biological replicates in each group. Parasite merozoites were also collected from four infected chickens at 5 d after infections. Uninfected control samples, merozoites and infection group samples were selected for RNA extraction and hybridization on Affymetrix microarrays.
We used Affymetrix GeneChip chicken genome arrays to detail the chicken cecal epithelia gene expression in the control and E. tenella-infected birds.

sample_organism:
Eimeria tenella
Gallus gallus

overall_design: Infected, uninfected chicken cecal epithelia and merozoites were selected for RNA extraction and hybridization with Affymetrix microarrays. Our goal was to analyze global transcriptome changes in chicken cecal mucous membranes in response to E. tenella infection in vivo. We used infected (T1,T2,T3; three biological replicates) and uninfected (Neg1, Neg2, Neg3; three biological replicates) samples to identify genes that were differentially expressed. Meanwhile, RNA and probes were also prepared from parasite merozoites (Mzt) from infected samples (Mzt) and used as an additional control in microarray hybridization.

first: Guan

last: Zhu

first: Xue

last: Cai

first: Ai

first: Hong

last: Yan

middle: N

last: Luo

first: Wei

last: Gong

first: Jian

first: Guang

middle: F

last: Tian


title: TGFB signaling effect on cultured NHLF cells

first: Jadranka

last: Milosevic

state: PA - Pennsylvania

address: 2330 Tilbury Avenue

summary: TGFβ activates a signal transduction cascade that results in the microRNAs and genes transcription. The objective of this study is to identify miRNAs which are regulated through TGFB signaling pathway

overall_design: Cultured NHLF cells at 30-50% confluence were treated with 5 ng/mL TGFB1 or DMSO.

first: Marcus

last: Marister

first: Naftali

last: Kaminski


title: MiRNAs expression data from GM0637 treated with and without ATM inhibitor after DNA damage

status: Public on Nov 14 2012

city: Houston

first: Guohui

last: Wan

state: TX

address: 7777 Knight Road

department: Cancer Biology

institute: The University of Texas M.D. Anderson Cancer Center

summary: GM0637 cell were pretreated with ATM inhibitor before adding DNA damaging agent neocarzinostatin (NCS), and cells were harvested after 4 hours for the microarray analyses of whole-genome miRNAs.

overall_design: To examine how miRNAs are regulated in the DNA damage response, we assessed the genome-wide mature miRNA expression in GM0637 cells treated with or without ATM inhibitor (ATM-IN)


title: Transcriptome analysis of mediator Med20 mutant and dcr1 mutant in S.pombe

status: Public on Nov 06 2012

city: Gothenburg

first: Claes

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

institute: Gothenburg University

summary:
At Schizosaccharomyces pombe centromeres, non-coding RNAs are transcribed by RNA polymerase II and processed by the RNAi machinery to direct heterochromatin formation. Mediator is a regulator of RNA polymerase II transcription and we here demonstrated that it also controls the levels of centromeric transcripts. Loss of the Mediator subunit Med20 increases transcription of non-coding RNAs and disrupts the centromeric heterochromatin structure.
We have used tilling arrays to study the gene expression changes in Med20 deletionVs WT  and Med20 dcr1 double mutant Vs Dcr1 mutant in exponentially growing fission yeast cells to detect how the Med20 gene affect centromeric expression.

overall_design: RNA samples were taken from exponentially growing fission yeast cells and reverse transcribed  cDNA from the RNA are hybridized to affymetrix pombe tilling arrays: wild type,med20 mutant, Dcr1 mutants and med20,dcr1 double mutant.

first: Jonas

last: Carlsten

first: Xuefeng


title: CHD1 remodelers space nucleosomes in vitro and link regular arrays to 5’ ends of genes in S. Pombe

status: Public on Oct 11 2012

first: Karl

last: Ekwall

summary: Nucleosome positioning governs access to eukaryotic genomes. Many genes show a stereotypic organisation at their 5’ end: a nucleosome free region just upstream of the transcription start site (TSS) followed by a regular nucleosomal array over the coding region. The determinants for this pervasive pattern are unclear, but nucleosome remodeling ATPases likely are critical. Now we employ deletion mutants to study the role of nucleosome remodeling ATPases in global nucleosome positioning in S. pombe and the corresponding changes in expression patterns. We find a striking evolutionary shift in remodeling enzyme usage between budding and fission yeast. The S. pombe RSC remodeling complex seems not involved in nucleosome positioning, despite its prominent role in S. cerevisiae. While lacking ISWI-type remodelers, S. pombe has two CHD1-type ATPases, Hrp1 and Hrp3. We demonstrate nucleosome spacing activity for both in vitro, and together they are essential for linking regular genic arrays to most TSSs in vivo. Impaired chromatin may but need not lead to changes in transcription. The absence of both causes changed expression for about 20% and increased antisense transcription for 15% of all annotated elements.

overall_design:
For RNA expression: total RNA from hrp1D, hrp3D, hrp1Dhrp3D and wt (with actinomycin D) and total RNA from snf21ts at 25C and 34C, snf21ts swr1D at 25C and 34C, pht1D swr1D (without actinomycin D).
For nucleosome mapping: Nucleosomal DNA in pht1Δ swr1Δ mutant, snf21- ts mutant, snf21- ts swr1Δ mutant, mit1Δ mutant, hrp1Δ mutant, hrp3Δ mutant and hrp1Δ hrp3Δ mutant S.pombe vs. Genomic Input DNA in wildtype and mit1Δ mutant S.pombe.

first: Julia

last: Jakubsche

first: Jenna

last: Persson

first: Punit

last: Prasad

first: Ulrika

last: Norman

first: Annelie

last: Strålfors

first: Olga

last: Khorosjutina

first: Nils

last: Krietenstein

first: Peter

last: Svensson

first: Philipp

last: Korber


title: miRNA transcript levels in ccRCC-derived cell lines and proximal tubular epithelial cell samples

status: Public on Nov 01 2012

city: Groningen

first: Klaas

last: Kok

institute: UMCG

summary: Despite numerous studies reporting deregulated microRNA (miRNA) and gene expression patterns in clear cell renal cell carcinoma (ccRCC), no direct comparisons have been made to its presumed normal counterpart; the renal proximal epithelial tubular cells (PTEC). The aim of this study  was to determine the miRNA expression profiles of ten clear cell renal cell carcinoma-derived cell lines and short-term cultures of PTEC, and to correlate these with their gene expression, and copy-number profiles. Using microarray-based methods, a significantly altered expression level in ccRCC cell lines was observed for 23 miRNAs and 1630 genes. The set of miRNAs with significantly decreased expression levels include all members of the miR-200 family known to be involved in the epithelial to mesenchymal transition (EMT) process. Expression levels of 13 of the 47 validated target genes for the downregulated miRNAs were increased more than two-fold.  Our data reinforce the importance of the EMT process in the development of ccRCC. For mRNA expression data of these cell lines see GEO Series accession number GSE20491.

overall_design: MicroRNA profiling was performed on two proximal tubular epithelial cell samples (both cell samples were hybridized twice (biological duplicates)) and ten clear cell renal cell carcinoma- derived cell lines (one of which; RCC-JF in duplicate)

first: Gerben

last: Duns

first: Inge

last: Van Duivenbode


title: Gene expression profile of the developing human retinal pigment epithelium

status: Public on Jan 01 2013

city: Harbin

first: Shaomin

last: Peng

address: 246 XueFu Road

institute: The Second Hospital of Harbin Medical University

summary:
The microarray technique was used to investigate gene expression level changes in human retinal pigment epithelium (RPE) microdissected from fetal eyes (13 and 16 weeks of gestation) and adult eyes (40-60 years old). The gene expression analysis of human fetal RPE during development were performed and compared to human native RPE.
Of the 45,033 probe sets on the microarray, 30,736 were detected. 3498 differentially expressed genes could be clustered into 8 patterns of expression that were statistically significant. Analyzing expression pattern of genes coding for key functions (pigment synthesis, visual cycle, phagocytosis, adherens and tight junction, transcellular transport) indicates human RPE achieved a high degree of maturity at early pregnancy. Compare to 154 signature genes of RPE, 148 candidate genes were identified in this studies including 53 down-regulated genes and 5 up-regulated genes. qRT2-PCR results showed similar expression trends with the microarray at three time points.These ﬁndings indicate human RPE has different expression pattern compared to other animals.

overall_design: A three chip study using total RNA pooled equally from three 13-week fetal eyes, two 16-week fetal eyes and two adult eyes for three time points (13, 16 week gestation and mature adult eye). Experiment was repeated in another group samples. This is a six chip study totally.

first: Zhongyu

last: Zhang

first: Yan


title: miR-10b*, a master inhibitor of the cell cycle, is downregulated in human breast tumors

status: Public on Oct 30 2012

city: Rehovot

first: Noa

last: Bossel Ben-Moshe

address: Hertzl Street

country: Israel

institute: Weizmann

summary: Deciphering the molecular mechanisms involved in breast tumorigenesis has been the subject of extensive research in the last years; yet unpredictable response and development of resistance to adjuvant therapies remain major questions in the management of breast cancer patients. The power of miR expression signatures has emerged recently from several studies. Normal and breast tumor tissues can be discriminated by a miR signature as reported by Iorio et al (Iorio et al, 2005). Recent findings have also linked deregulated miR expression to breast cancer metastasis (Adorno et al, 2009; Huang et al, 2008; Tavazoie et al, 2008). Moreover, microRNAs are considering as a powerful tool in diagnosis and prognosis of breast cancer. In our study, we measured microRNA expression profiles from 64 primary breast cancer patients, comprising 56 matched tumor and adjacent peritumoral breast tissues, 5 tumor and 3 peritumor unmatched tissues. Our aim was to identify new microRNAs involved in the process of neoplastic transformation. The microarray data analysis identified, in every subgroup of breast cancers analyzed, a specific subset of microRNAs that were differentially expressed in tumor compared to peritumoral tissues. Among these miRs, we identified two (miR-10b* and miR-139-5p) that were down-regulated and three (miR-425, miR-454 and miR-301a) that were up-regulated for all three subtypes. We further show that microRNA-10b* is a master regulator of breast cancer cell proliferation. Two canonical CpG islands (5kb) upstream from the precursor sequence are hypermethylated in breast cancer tissues analyzed. Ectopic delivery of synthetic microRNA-10b* in breast cancer cell lines or into xenograft mouse breast tumors inhibits cell proliferation and impairs tumor growth in vivo, respectively. We identified and validated in vitro and in vivo three novel target mRNAs of miR-10b*, BUB1, PLK1 and CCNA2 genes, which play a remarkable role in cell cycle regulation and whose high expression in breast cancer patients reduced disease free survival, relapse free survival and metastasis free survival when compared to low expressors. This also suggests that restoration of microRNA-10b* expression might bear therapeutic promise.

overall_design: In exploring the potential involvement of miRs in breast tumorigenesis, we profiled the miRs expression of 64 primary breast cancer patients, comprising 56 matched tumor and adjacent peritumoral breast tissues, 5 tumor and 3 peritumor unmatched tissues, using the Agilent microarray platform. For 14 samples technical replicate were also performed.

first: Francesca

last: Biagioni

first: Giulia

last: Fontemaggi

first: Valeria

last: Canu

first: Federica

last: Mori

first: Barbara

last: Antoniani

first: Anna

last: Di Benedetto

first: Raffaela

last: Santoro

first: Sabrina

last: Germoni

first: Fernanda

last: De Angelis

last: Cambria

first: Roi

last: Avraham

first: Giuseppe

last: Grasso

last: Strano

first: Paola

last: Muti

first: Marcella

last: Mottolese

first: Yosef

last: Yarden

first: Eytan

last: Domany

first: Giovanni

last: Blandino


title: Genome-wide binding site of Rec10 and Rec15 during meiosis

status: Public on Jul 28 2012

city: Kisarazu

first: Kazuto

last: Kugou

state: Chiba

address: 2-6-7 KazusaKamatatri

department: Department of Frontier Research

institute: Kazusa DNA Research Institute

summary: Higher-order chromosome structure is assumed to control various DNA-templated reactions in eukaryotes. Meiotic chromosomes implement developed structures called “axes” and “loops”; both are suggested to tether each other, activating Spo11 to catalyze meiotic DNA double-strand breaks (DSBs) at recombination hotspots. We found that the Schizosaccharomyces pombe Spo11 homolog Rec12 and its partners form two distinct subcomplexes, DSBC (Rec6-Rec12-Rec14) and SFT (Rec7-Rec15-Rec24). Additionally, Mde2, whose expression is strictly regulated by the replication checkpoint, interacts with a component of each subcomplex. The SFT subcomplex binds to both axes via direct interaction of Rec15 with Rec10 in axes and DSB sites, hence axial Rec10 can partially tether DSB sites located in loops. Importantly, this multiprotein-based tethered axis-loop complex is destabilized in the absence of Mde2. We therefore propose a novel mechanism by which Mde2 functions as a recombination initiation mediator to tether axes and loops, in liaison with the meiotic replication checkpoint.

overall_design: ChIP-chip analyses of Rec10 (in wild type), Mde2 (in wild type and rec15∆), and Rec15 (in wild type, rec10∆, rec24∆ and mde2∆) at meiosis 4 hours.

first: Tomoichiro

last: Miyoshi

first: Masaru

last: Ito

first: Shintaro

last: Yamada

first: Masaki

last: Furuichi

first: Arisa

last: Oda

first: Takatomi

first: Kouji

last: Hirota

first: Hisao

last: Masai

first: Kunihiro

last: Ohta


title: Expression profiling of mmi1 delta cells, using tiling microarray in S. pombe

status: Public on Aug 31 2012

city: La Tronche

first: andre

last: VERDEL

address: Rond point de la chantourne

department: Department of Cell Differentiation and Transformation

institute: INSERM/UJF U823

summary: We used tiling microarrays to identify up-regulated genes in mmi1 delta cells. Because these cells grow very poorly due to misexpression of mei4 gene, we combined mmi1 delta mutation to a partial deletion of mei4. Cells carrying only mei4 partial deletion were also analyzed in our transcriptomics to verify that variations observed in mmi1 delta cells are not due mei4 mutation.

overall_design: RNA levels from S. pombe cells with only mei4 partial deletion (SPV481) or with mei4 partial deletion in combination with mmi1 delta deletion (SPV903) were compared to wild type cells (SPV8), using Affymetrix S. pombe Tiling 1.0FR microarrays. Two biological replicates were analyzed for each experiment.

first: Aurélia

last: Vavasseur

first: Edwige

last: Hiriart

first: Leila

last: Touat-Todeschini

first: Benoit

last: Gilquin

first: Daniel

last: Perazza

first: Joel

last: Lachuer

first: Séverine

last: Croze

first: Nicolas

last: Nazaret

first: André

last: Verdel

first: Emeline

last: Lambert


title: Expression analysis of Plasmodium falciparum 3D7 delta-PfPuf2 mutant

status: Public on Jul 06 2012

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

summary:
Investigation of whole genome gene expression level changes in Plasmodium falciparum 3D7 delta-PfPuf2 mutant, compared to the wild-type strain 3D7.  The mutation engineered into this strain render tanslational control.
The mutants analyzed in this study are further described in Miao J, Li J, Fan Q, Li X, Li X, Cui L.2010. The Puf-family RNA-binding protein PfPuf2 regulates sexual development and sex differentiation in the malaria parasite Plasmodium falciparum. J Cell Sci. 123(7):1039-49 (PMID 20197405).

overall_design: A 12 chip study using total RNA recovered from six separate wild-type cultures of Plasmodium falciparum 3D7 at gametocyte stage III (three cultures) and stage V (three cultures) and six separate cultures of dalta PfPuf2 mutant at  gametocyte stage III (three cultures) and stage V (three cultures).  Each chip measures the expression level of 5,367 genes from Plasmodium falciparum 3D7 with 45-60 mer probes with two replicates on final array of 71618 probes.

first: Miao

last: Jun

first: Cui

last: Liwang


title: microRNA and cancer progression in breast tumors

status: Public on Dec 16 2012

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

summary:
miRNAs are small non-coding RNAs frequently altered in human malignancies. They regulate protein-coding gene expression by mediating mRNA degradation and/or repressing translation via the association with the 3’ untranslated region (3’ UTR) of the mRNAs. Aberrant miRNA expression can influence several gene networks and pathways implicated in tumorigenesis and metastasis formation.
To reveal miRNAs involved in breast cancer progression we investigated miRNA expression in 77 ductal breast carcinoma biopsies and 17 mammoplasties by microarray analysis. 16 differentially expressed miRNAs were identified comparing patients with or without disease relapse within 72 months from surgery.

overall_design:
We have performed a microarray miRNA expression analysis on 77 ductal breast carcinoma biopsies and 17 normal tissues from mammoplastic reductions using the Human Agilent platform (V2).
77 frozen tumor specimens were selected from the Tumor Bank of the Department of Obstetrics and Gynecology, University of Turin. They were obtained from patients who underwent primary surgical treatment between 1988 and 2001 at a median age of 54 years (25-82). Eligibility criteria were the following: diagnosis of invasive breast cancer, all T and N stages, no distant metastasis at diagnosis (M0), complete clinical-pathological data and updated follow up. All patients were treated with radical modified mastectomy or quadrantectomy and axillary dissection plus breast irradiation. As normal breast controls 17 frozen mammoplastic reductions (EPFL, Lausanne) were included in the screening. Appropriate ethical approval was obtained for this study.

first: Daniela

last: Cimino

first: Cristiano

last: De Pittà

first: Matteo

last: Zampini

first: Silvia

last: Casara

first: Francesca

last: Orso

first: Eva

last: Pinatel

first: Chiara

last: Romuladi

first: Riccardo

last: Ponzone

first: Cathrin

last: Brisken

first: Paolo

last: Provero

first: Michele

last: De Bortoli

first: Piero

last: Sismondi

last: Taverna


title: Deep sequencing analysis of human red blood cells

status: Public on Jul 01 2012

city: Zurich

first: imane

last: azzouzi

address: Steinwiesstrasse 75

department: Haematology division

country: Switzerland

institute: Children's Hospital Zurich

summary: Small RNAs isolated from RBCs were size fractionated by gel electrophoresis and used for the creation of 6 libraries. For the library from healthy children (library 1), RNA from 4 individuals was pooled. Libraries were multiplexed and analyzed on a 454 sequencing platform 26 yielding 569,621 sequence reads after demultiplexing into the 6 libraries

overall_design: Analysis of 6 small RNA libraries from human red blood cells

first: Imane

last: Azzouzi

first: Hansjoerg

last: Moest

first: Bernd

last: Wollscheid

first: Markus

last: Schmugge

first: Oliver

last: Speer


title: Transcriptional profile of Pseudomonas syringae pv phaseolicola at low temperature

status: Public on Dec 31 2012

city: Irapuato

first: Jose Luis

last: Hernandez-Flores

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León

department: Ingeniería Genética

institute: Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional

summary: In order to obtain a global view about the strategies used by phytopathogenic bacteria, in response to physiologically relevant temperature changes. We used the DNA microarray technology to compare gene expression profile in the model bacterial pathogen P. syringae pv. phaseolicola NPS3121 grown at 18 ºC and 28ºC.

overall_design: To carry out this study, we used this DNA microarray of P. syringae pv. phaseolicola NPS3121. Each microarray experiment was repeated six times; two technical replicates with the same RNA samples and three biological replicates using RNA isolated from a different culture.


title: DamID for Cid14 in wild-type and swi6∆

status: Public on Jun 12 2012

city: Basel

first: Katrina

last: Woolcock

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

summary: HP1 proteins are major components of heterochromatin, which is generally perceived to be an inert and transcriptionally inactive chromatin structure. Yet, HP1 binding to chromatin is highly dynamic and robust silencing of heterochromatic genes can involve RNA processing. Here we demonstrate by a combination of in vivo and in vitro experiments that the fission yeast HP1Swi6 protein guarantees tight repression of heterochromatic genes through RNA sequestration and degradation. Stimulated by positively charged residues in the hinge region, RNA competes with methylated histone H3K9 for binding to the chromodomain of HP1Swi6. Hence, HP1Swi6 binding to RNA is incompatible with stable heterochromatin association. We propose a model in which an ensemble of HP1Swi6 proteins functions as a heterochromatin-specific checkpoint capturing and priming heterochromatic RNAs for the RNA degradation machinery. Sustaining a functional checkpoint requires continuous exchange of HP1Swi6 within heterochromatin, which explains the dynamic localization of HP1 proteins on heterochromatin.

overall_design: Methylation levels in strains expressing Dam-Cid14 fusions were compared to those in a Dam only expressing strain. 2 biological replicates for each strain.

first: Claudia

last: Keller

first: Marc

last: Bühler


title: miRNA profiling of CD4+ T cells in chronically infected HIV-1 patients, LTNPs and healthy controls

status: Public on May 22 2012

city: Darlinghurst

first: Sanjay

last: Swaminathan

state: New South Wales

address: 405 Liverpool St

institute: St Vincent's Centre for Applied Medical Centre

summary: We extracted total RNA from CD4+ T cells from 3 patient groups: chronic HIV-1 patients (CHI), long term non-progressors (LTNPs) and healthy controls (HC).  Array results show that a large number of miRNAs are altered in HIV-1 infected patients compared to HC.  Most of the differentially expressed miRNAs are down-regulated but there are some up-regulated miRNAs.  A particular family of miRNAs which appear to be downregulated in HIV-1 infected patients is the let-7 family of miRNAs.

overall_design: In this study, we have included 8 healthy controls, 7 LTNPs and 7 CHI patients.  We extracted RNA from magnetically separated CD4+ T cells (separated from peripheral blood mononuclear cells) and ran them on an Agilent miRNA array.

first: Kazuo

last: Suzuki


title: VGF-derived peptide attenuates development of type 2 diabetes via enhancement of islet beta cell survival and function  survival and function

status: Public on May 10 2012

city: Chapel Hill

first: Jonathan

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

country: USA

institute: The University of North Carolina at Chapel Hill

type:
Expression profiling by array
Third-party reanalysis

summary: Deterioration of functional islet β-cell mass is the final step in progression to Type 2 diabetes. We previously reported that overexpression of Nkx6.1 in rat islets has the dual effects of enhancing glucose-stimulated insulin secretion (GSIS) and increasing β-cell replication. Here we show that Nkx6.1 strongly upregulates the prohormone VGF in rat islets and that VGF is both necessary and sufficient for Nkx6.1-mediated enhancement of GSIS. Moreover, the VGF-derived peptide TLQP-21 potentiates GSIS in rat and human islets and improves glucose tolerance in vivo. Chronic injection of TLQP-21 in pre-diabetic ZDF rats preserves islet mass and slows diabetes onset. TLQP-21 prevents islet cell apoptosis by a pathway similar to that used by GLP-1, but independent of the GLP-1, GIP, or VIP receptors. Unlike GLP-1, TLQP-21 does not inhibit gastric emptying or increase heart rate. We conclude that a TLQP-21 is a novel agent for enhancing islet β-cell survival and function.

overall_design: We utilized a “sample x reference” experimental design strategy in which RNA extracted from rat pancreatic islets was hybridized to the microarray slide in the presence of labeled rat reference RNA (RRR, Stratagene, LaJolla, CA). Cultures were treated with adenoviruses expressing either the hamster form of Nkx6.1, the mouse form of Pdx1, or the beta-galactosidase enzyme. 3-5 biological replicates each representing independent islet isolations were used for microarray analysis. Briefly, five hundred nanograms of total RNA were used for gene expression profiling following reverse transcription and T-7 polymerase-mediated amplification/labeling with Cyanine-5. Labeled subject cRNA was co-hybridized to Operon rat 27K oligonucleotide arrays with equimolar amounts of Cyanine-3 labeled RRR. Slides were hybridized, washed, and scanned on a Gene Pix 5000 microarray scanner.

first: Samuel

last: Stephens

first: Hans

last: Hohmeier

first: Jie

last: An

first: Albert

middle: Y

last: Sun

first: Geoffrey

middle: S

last: Pitt

first: Christopher

last: Newgard


title: TGF-beta treated Schistosoma mansoni

status: Public on Feb 20 2012

city: São Paulo

first: Katia

last: Oliveira

address: Av Prof lineu prestes 748

department: Centro de Parasitologia e Micologia

institute: Instituto Adolfo Lutz

summary: Transcriptional profiling of TGF-beta treated Schistosoma mansoni adult worms  vs. Non-treated Schistosoma mansoni adult worms

overall_design: Two conditions (treated vs. Non-treated) with three biological samples of treated worms (TGF1, 4 and 5) and two biological samples of non-treated worms that were pooled into a single sample (pool). For each sample (three treated or polled non-treated) were performed four technical replicas

first: Sergio

last: Verjovski-Almeida

first: Phillip

last: LoVerde


title: RNA interference keeps Atf1-bound stress response genes in check at nuclear pores

status: Public on Mar 19 2012

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

overall_design: Refer to individual Series


title: MicroRNA profile of differentiated vs. dedifferentiated human fetal retinal pigment epithelial (hfRPE) cells

status: Public on Feb 29 2012

city: Philadelphia

first: Jeffrey

last: Adijanto

address: 1020 Locust Street

department: Anatomy, Pathology, and Cell Biology

institute: Thomas Jefferson University

summary: We performed microRNA microarray analysis to determine microRNAs that are differentially expressed between the differentiated hfRPE monolayer (pigmented, hexagonally packed) and dedifferentiated hfRPE cells (non-pigmented, fibroblast-like). Experiment was performed using the Agilent-019118 Human miRNA Microarray 2.0 G4470B.

overall_design: 2 -condition experiment: differentiated and dedifferentiated hfRPE cells. 3 biological replicates for each condition.  Also includes a sample that has characteristics of both cell types (representing a transitional state).

first: Zi

middle: X

last: Wang


title: DamID for Swi6, Rdp1, Dcr1, Ago1, Arb1, Cid14, Rrp6, Nup85 and Amo1 in Schizosaccharomyces pombe

first: Katrina

last: Woolcock

summary: RNA interference (RNAi) pathways are prevalent throughout the eukaryotic kingdom and well known to regulate gene expression on a post-transcriptional level in the cytoplasm. Less is known about possible functions of RNAi in the nucleus. In the fission yeast Schizosaccharomyces pombe, RNAi is crucial to establish and maintain centromeric heterochromatin and functions to repress genome activity by a chromatin silencing mechanism referred to as co-transcriptional gene silencing (CTGS). Mechanistic details and the physiological relevance of CTGS are unknown. Here we show that RNAi components interact with chromatin at nuclear pores to keep stress response genes in check. We demonstrate that RNAi-mediated CTGS represses stress inducible genes by degrading mRNAs under non-induced conditions. Under chronic heat stress conditions, a Dicer thermoswitch deports Dicer to the cytoplasm, thereby disrupting CTGS and enabling expression of genes implicated in the acquisition of thermotolerance. Taken together, our work highlights a role for nuclear pores and the stress response transcription factor Atf1 in coordinating the interplay between the RNAi machinery and the S. pombe genome and uncovers a novel mode of RNAi regulation in response to an environmental cue.

overall_design: Methylation levels in strains expressing Dam fusions were compared to those in a Dam only expressing strain.

first: Dimos

last: Gaidatzis

first: Hans-Rudolf

last: Hotz


title: RNA expression for dcr1D, rdp1D, ago1D and swi6D

overall_design: Total RNA extracted from wild-type and mutant strains to compare global expression. At least 2 biological replicates for each sample were performed.

first: Marc

last: Bühler


title: DamID of Ima1 and Man1 in Schizosaccharomyces pombe

status: Public on Jan 18 2012

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

institute: Universitätsklinikum Hamburg-Eppendorf

summary: The metazoan nuclear periphery is involved in transcriptional regulation and chromatin organisation. To test whether this is also the case in the fission yeast Schizosaccharomyces pombe, we performed DamID experiments with two inner nuclear membrane (INM) proteins, Ima1 and Man1. The resulting map showed that about a third of the genome is associated with the nuclear periphery. We find that both INM proteins preferentially associate with lowly expressed genes, and are depleted from highly expressed genes. Further, intergenic regions of divergent gene pairs are more frequently associated with the periphery than convergent pairs, indicating that transcription points away from the periphery rather than toward it

overall_design: We recorded methylation levels for both Ima1- and Man1-Dam fusion proteins and compared them to Dam-only control samples. Three biological replicates for each experiment were done, except for Ima1, where just 2 arrays could be used.

first: Guillaume

last: Filion

first: Bas

last: van Steensel

first: Karl

last: Ekwall


title: Nucleosomal organization of replication origins and meiotic recombination hotspots in fission yeast

status: Public on Dec 31 2011

city: Salamanca

first: Luis

last: Quintales

address: Calle Zacarías González, 2

department: Universidad de Salamanca / CSIC

institute: Instituto de Biología Funcional y Genómica (IBFG)

summary: In Schizosaccharomyces pombe, DNA replication origins (ORIs) and meiotic recombination hotspots lack consensus sequences and show a bias towards mapping at large intergenic regions (IGRs). To explore whether this preference depended on underlying chromatin features, we have generated genome-wide nucleosome profiles during mitosis and meiosis. We have found that meiotic double-strand break sites (DSB) colocalize strictly with nucleosome-depleted regions (NDRs) and that large IGRs include clusters of NDRs that overlap with almost half of all DSBs. By contrast, ORIs do not colocalize with NDRs and they are regulated independently of DSBs. Physical relocation of NDRs at ectopic loci or modification of their genomic distribution during meiosis was paralleled by the generation of new DSB sites. Over 80% of all meiotic DSBs colocalize with NDRs that are also present during mitosis, indicating that the recombination pattern is largely dependent on constitutive properties of the genome and, to a lesser extent, on the transcriptional profile during meiosis. The organization of ORIs and of DSBs regions in S. pombe reveals similarities and differences relative to Saccharomyces cerevisiae.

overall_design: Ten different samples including a total of 14 independent microarray experiments were analyzed. Two samples of immunoprecipitated DNA (including 2 biological replicates of each) for ORC mapping. Four samples of mononucleosomal DNA (including 2 biological replicates of one of them) for nucleosome mapping. Four samples of total RNA for genome-wide transcription mapping (including 2 biological replicates of one of them). Affymetrix GeneChip 1.0FR tiling microarrays (GPL7715) were used for all the experiments.

first: Elisa

last: de Castro

first: Ignacio

last: Soriano

first: Laura

last: Marín

first: Rebeca

last: Serrano

first: Francisco

last: Antequera


title: Development of gene expression profile for a seasonal variation study in a natural population of Riba-Roja, in the Ebro River, Spain

status: Public on Jan 27 2012

city: Barcelona

first: Anna

last: Navarro Cuenca

address: C/Jordi Girona 18-26

department: Environmental Toxicology

institute: IDAEA-CSIC

summary: To analyze the impact of seasonal and environmental variations on the physiology and metabolism of zebramussel, we use a custom microarray developed in our laboratory, using 4057 publicly availabe DNA sequences from Dreissena and other realted genera. Transcriptome profiles were analyszed using half-body samples captured in  Riba Roja (low Ebro River), a location considered relatively free of chemical pollution, at three different stages of the vital cycle. The results showed a clear separation on transcriptome profiles between samples collected in February and June (pre- and spawning, respectively) and samples collected during gonad resorption (September). A total of 753 transcripts changed significantly their mRNA levels during these three months (ANOVA p<0.01, fc ±1.5). These changes could be considered as response to variations of temperature, reproductive stages, as well as food availability. Genes involved in oxidative stress were overrepresented in September, whereas genes related to reproductive functions were overrrepresented in the spawning and pre-spawning period.

overall_design: For each season (February: pre-spawning; June: Spawning; September: gonad resorption) it was used 2 biological replicates using the half body as a target tissue to analyze .

last: Navarro

first: Bruno

last: Campos


title: Rif1 is a global regulator of timing of replication origin firing in fission yeast

status: Public on Dec 13 2011

city: Tokyo

first: Yutaka

last: Kanoh

address: 2-1-6 Kamikitazawa, Setagaya-ku

department: Genome Medicine

institute: Tokyo Metropolitan Institute of Medical Science

summary:
One of the long-standing questions in eukaryotic DNA replication is the mechanisms that determine where and when a particular segment of the genome is replicated. Cdc7/Hsk1 is a conserved kinase required for initiation of DNA replication, and may affect the site selection and timing of origin firing. We identified rif1∆, a null mutant of rif1+, a conserved telomere binding factor, as an efficient bypass mutant of fission yeast hsk1. Extensive deregulation of dormant origins over a wide range of the chromosomes occurs in rif1∆ in the presence or absence of HU. At the same time, many early-firing, efficient origins are suppressed or delayed in firing timing in rif1∆. Rif1 binds not only to telomeres but also to many specific locations on the arm segments that only partially overlap with the pre-Replicative Complex assembly sites, although Rif1 tends to bind in the vicinity of the late/ dormant origins activated in rif1∆. The binding to the arm segments occurs through M to G1 phase in a manner independent of Taz1 and appears to be essential for the replication timing program during normal cell cycle. Our data demonstrate that Rif1 is a critical determinant of origin activation program on the fission yeast chromosomes.
BrdU incorporation profiles at early S-phase in Wild vs rif1∆. Cdc45 binding profiles at early S-phase in Wild vs rif1∆. Rif1 binidng sites aroud G1/S boudary and at M-phase. Mcm4 binding sites in wild, hsk1-89 temperature mutant and rif1∆.

overall_design: Each BrdUIP or ChIP sample vs. Input at Metaphase sample

first: Motoshi

last: Hayano

first: Seiji

last: Matsumoto

first: Claire

last: Renard-Guillet

first: Katsuhiko

last: Shirahige

first: Hisao

last: Masai


title: miRNA expression profiling of NKTCL (Natural Killer/T-Cell Lymphoma) samples

status: Public on Nov 23 2011

city: Singapore

first: Chong-Lei

last: Bi

address: #12-02, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive

country: Singapore

institute: Cancer Science Institute Singapore

summary: We performed a comprehensive genome-wide miRNA expression profiling (MEP) of extranodal nasal-type Natural Killer/T-cell lymphoma (NKTL) using formalin fixed paraffin-embedded tissue (FFPE) (n=30) and NK cell lines (n=6) in comparison with normal NK cells, with the objective of understanding the pathogenetic role of miRNA deregulation in NKTL.

overall_design: Total RNA, including miRNA, were extracted using Ambion Recoverall Kit and profiled using Agilent human miRNA V2.

first: Siok-Bian

last: Ng

first: Viknesvaran

last: Selvarajan

first: Junli

last: Yan

first: Gaofeng

last: Huang

first: Baohong

last: Lin

first: Wee-Joo

last: Chng


title: miRNA expression profiles of erythroid cells following hydroxyurea treatment for sickle cell anemia

status: Public on Nov 21 2011

city: Memphis

first: Aisha

last: Walker

state: TN

address: 262  Danny Thomas Place; MS 313

institute: St Jude Children's Research Hospital

summary: We hypothesized that miRNA regulation may be invloved in hydroxyurea-mediated fetal hemoglobin induction. Microarray analysis was utilized as an initial screening tool to determine differential miRNA expression in CD71+ erythroid cells comparing cells from control individuals without sickle cell anemia to patients with sickle cell anemia prior to treatment with hydroxyurea and patients receiving the maximum tolerated dose (MTD) of hydroxurea.

overall_design: CD71+ cells were isolated from whole blood of control individuals (n=2), pediatric patients without hydroxyurea treatment (n=3) and pediatric patients at hydroxyurea MTD (n=3). All 8 samples were analyzed for miRNA expression.

middle: L

first: Yong-Dong

last: Wang


title: Identification of miRNAs involved in cell response to ionising radiation and modeled microgravity

status: Public on Apr 09 2012

first: Gerolamo

last: Lanfranchi

summary:
BACKGROUND:
Ionizing radiation (IR) can be extremely harmful for human cells since an improper DNA-damage response (DDR) to IR can contribute to carcinogenesis initiation. Perturbations in DDR pathway can originate from alteration in the functionality of the microRNA-mediated gene regulation, being microRNAs (miRNAs) small noncoding RNA that act as post-transcriptional regulators of gene expression. In this study we gained insight into the role of miRNAs in the regulation of DDR to IR under microgravity, a condition of weightlessness experienced by astronauts during space missions, which could have a synergistic action on cells, increasing the risk of radiation exposure.
METHODOLOGY/PRINCIPAL FINDINGS:
We analyzed miRNA expression profile of human peripheral blood lymphocytes (PBL) incubated for 4 and 24 h in normal gravity (1 g) and in modeled microgravity (MMG) during the repair time after irradiation with 0.2 and 2Gy of γ-rays. Our results show that MMG alters miRNA expression signature of irradiated PBL by decreasing the number of radio-responsive miRNAs. Moreover, let-7i*, miR-7, miR-7-1*, miR-27a, miR-144, miR-200a, miR-598, miR-650 are deregulated by the combined action of radiation and MMG. Integrated analyses of miRNA and mRNA expression profiles, carried out on PBL of the same donors, identified significant miRNA-mRNA anti-correlations of DDR pathway. Gene Ontology analysis reports that the biological category of "Response to DNA damage" is enriched when PBL are incubated in 1 g but not in MMG. Moreover, some anti-correlated genes of p53-pathway show a different expression level between 1 g and MMG. Functional validation assays using luciferase reporter constructs confirmed miRNA-mRNA interactions derived from target prediction analyses.
CONCLUSIONS/SIGNIFICANCE:
On the whole, by integrating the transcriptome and microRNome, we provide evidence that modeled microgravity can affects the DNA-damage response to IR in human PBL.

overall_design: miRNA expression profiling was analysed in human peripheral blood lymphocytes (PBL) irradiated with gamma-rays (0.2 and 2.0 Gy) and incubated in modeled microgravity (mmg) and in parallel ground conditions (1g) for 4h and 24h. Six independent experiments were performed for each donor to address wich miRNAs were regulated on IR stress. The level of each miRNA was represented as Log2.

first: Cristina

last: Girardi

first: Cristiano

last: De Pitta

first: Silvia

last: Casara

first: Gabriele

last: Sales

first: Lucia

last: Celotti

first: Maddalena

last: Mognato


title: Single-base resolution DNA methylomes of rice and functional roles of DNA methylation

status: Public on Nov 04 2011

city: Kunming

first: xin

last: li

address: 32 Jiaochang Road

country: China

institute: Kunming Insititute of Zoology, Chinese Academy of Sciences,P.R.China

type: Expression profiling by high throughput sequencing

summary: To examine the rice genome methylation landscape and assess its functional significance, we generated the first single-base resolution genome methylation maps for Oryza sativa ssp. japonica, indica and their wild relatives, Oryza rufipogon and Oryza nivara. The methylation level of rice genomes is four times higher than that of Arabidopsis. Methylation in the promoter and gene body regions have similar patterns and effects on gene expression as those in Arabidopsis but different from a previous study on rice chromosomes 4 and 10. Most interestingly, we discovered for the first time that methylation in gene transcriptional termination regions can significantly repress gene expression, and the effect is even stronger than promoter methylation, which opens a new direction in the study of epigenetic regulation of gene expressions. Through integrated analysis of genetic, methylome and expression variation between cultivated and wild rice, we found that the genetic factor reflected by DNA variations may be the major determinant for methylation patterns at the whole-genome level and that methylation variation can only account for limited expression variation of genes between cultivated and wild rice.

sample_organism:
Oryza rufipogon
Oryza sativa
Oryza nivara

overall_design:
A single young panicle from each of the cultivated rice subspecies and the two wild rice species was ground in liquid nitrogen to fine powder using mortar and pestle. Total RNAs were isolated using the RNeasy Plant Mini Kit (Qiagen). DGE-tag libraries were constructed using the DGE-Tag Profiling NlaIII Sample Prep Kit (Illumina) according to the manufacturer's instructions.

This submission represents the gene expression component of the study.

first: Xin

last: Li

first: et

last: al


title: Whole transcriptome profiling of successful immune response to Vibrio infections in the oyster Crassostrea gigas by digital gene expression analysis

status: Public on Nov 01 2011

city: Montpellier

first: piquemal

last: david

address: 134 rue du Curat

institute: Skuld Tech

summary: The cultivated Pacific oyster Crassostrea gigas has suffered for decades large scale summer mortality phenomenon resulting from the interaction between the environment parameters, the oyster physiological and/or genetic status and the presence of pathogenic microorganisms including Vibrio species. To obtain a general picture of the molecular mechanisms implicated in C. gigas immune responsiveness to circumvent Vibrio infections, we have developed the first deep sequencing study of the transcriptome of hemocytes, the immunocompetent cells. Using Digital Gene Expression (DGE), we generated a transcript catalog of up-regulated genes from oysters surviving infection with virulent Vibrio strains (Vibrio splendidus LGP32 and V. aestuarianus LPi 02/41) compared to an avirulent one, V. tasmaniensis LMG 20012(T). For that an original experimental infection protocol was developed in which only animals that were able to survive infections were considered for the DGE approach. We report the identification of cellular and immune functions that characterize the oyster capability to survive pathogenic Vibrio infections. Functional annotations highlight genes related to signal transduction of immune response, cell adhesion and communication as well as cellular processes and defence mechanisms of phagocytosis, actin cytosqueleton reorganization, cell trafficking and autophagy, but also antioxidant and anti-apoptotic reactions. In addition, quantitative PCR analysis reveals the first identification of pathogen-specific signatures in oyster gene regulation, which opens the way for in depth molecular studies of oyster-pathogen interaction and pathogenesis. This work is a prerequisite for the identification of those physiological traits controlling oyster capacity to survive a Vibrio infection and, subsequently, for a better understanding of the phenomenon of summer mortality.

overall_design: 4 Samples.

first: David

last: Piquemal


title: MicroRNA Expression Profiling of Carcinoma In Situ (CIS) Cells of the Testis.

city: Copenhagen

first: Henrik

last: Leffers

address: Universitetsparken 13

department: August Krogh Building

country: Denmark

institute: Dept. of Biology, Copenhagen University

summary: Testicular germ cell tumours (TGCTs) of young adult men, seminoma (SEM) and nonseminoma (NSEM), develop from a precursor cell, carcinoma in situ (CIS), which resembles foetal gonocytes and retains embryonic pluripotency. We used microarrays to analyse microRNA (miRNA) expression in 12 human testis samples with CIS cells and compared it to the miRNA expression profiles of normal adult testis, testis with Sertoli-cell-only (SCO) that lack germ cells, testis tumours (SEM and embryonal carcinoma, EC; an undifferentiated component of NSEM) and foetal male and female gonads. Principal component analysis revealed distinct miRNA expression profiles characteristic for each of the different tissue types. We identified several miRNAs that were unique to testis with CIS cells, foetal gonads, and testis tumours. These included miRNAs from the hsa-miR-371~373 and -302~367 clusters that have previously been reported in germ cell tumours and three miRNAs (hsa-miR-96, -141 and -200c) that were also expressed in human epididymis. We found several miRNAs that were upregulated in testis tumours: hsa-miR-9, -105 and the hsa-miR-182~183~96 cluster were highly expressed in SEM, while the hsa-miR-515~526 cluster was high in EC. We conclude that miRNA expression profile changes during testis development and that the miRNA profile of adult testis with CIS cells shares characteristic similarities with the expression in foetal gonocytes.

overall_design: We used Agilent microarrays to determine the expression of microRNAs in samples from testis. We first used Agilent-016436 Human miRNA Microarray 1.0 G4472A (GPL9081; miRNA ID version) on 4 samples: normal testis, testis with 30% carcinoma in situ (CIS) tubules, testis with 50% CIS tubules and testis with 99-100% CIS tubules. This allowed us to determine the correlation between miRNA expressiona and the content of CIS cells in the samples. This is the file with data from those four arrays. Next, we used Agilent-019118 Human miRNA Microarray 2.0 G4470B (GPL8936; Probe Name version) on 24 samples that included normal testis, testis with the precursor for testis cancer carcinoma in situ (CIS), Sertoli-cell-only testis (contains the somatic testis cells but no germ cells), seminom and non-seminom tumours, and foetal gonads. This constitute the main part of the experiment and the publication, but the data was submitted to GEO in an independent file.

first: Guy

middle: W

last: Novotny

first: Kirstine

last: Belling

first: Jesper

last: Bramsen

first: John

middle: E

last: Nielsen

first: Jette

last: Bork-Jensen

first: Kristian

last: Almstrup

first: Si

last: Sonne

first: Jørgen

last: Kjems

first: Ewa

last: Rajpert-De Meyts