title: Genome-Wide expression under osmotic stress conditions in Saccharomyces cerevisiae

status: Public on Jan 03 2013

city: Burjassot

first: Paula

last: Alepuz

state: Valencia

address: Doctor Moliner, 50

department: Biochemistry and molecular biology

institute: University of Valencia

type: Expression profiling by genome tiling array

summary:
Changes in RNA levels during osmotic stress were investigated. Total RNA was extracted from a wild-type yeast strain before and after treatment with 0.4 M NaCl and the corresponding cDNAs were hybridazed on Tiling arrays. In particular, for all the intron-containing genes, the changes in the levels of intron signal in stressed cells related to the intron signal in the non-stressed cells, and the changes in the levels of exon signal in stresses cells related to the exon signal in non-stressed cells were investigated.
The supplementary bar file contains the ratios between stress signals respect to non-stress signals, using the average of the 3 biological replicas.

overall_design: For the tiling array experiments, total RNA was extracted from exponentially YPD growing W303-1A cells before and after treatment for 15 min with 0.4M NaCl. The hybridization of tiling array Affymetrix (GeneChip® S. cerevisiae Tiling 1.0R Array) with cDNA produced from total RNA, was carried out according to the Affymetrix protocol and using GeneChip® Hybridization, Wash and Stain Kit (P/N 900720). The final data were obtained from the results of three independent biological experiments.    High-density tiling arrays images were normalised and analysed using the Affymetrix Tiling Analysis Software; and were visualized by the Integrated Genome Browser (Affymetrix).

first: Jose

middle: E

last: Perez-Ortin

last: Romero-Santacreu


title: AGO6 functions in RNA-mediated transcriptional gene silencing in shoot and root meristems in Arabidopsis thaliana

status: Public on Dec 01 2011

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

country: USA

institute: Donald Danforth Plant Science Center

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA-directed DNA methylation (RdDM) is a small interfering RNA (siRNA)-mediated epigenetic modification that contributes to transposon silencing in plants. RdDM requires a complex transcriptional machinery that includes specialized RNA polymerases, named Pol IV and Pol V, as well as chromatin remodelling proteins, transcription factors, RNA binding proteins, and other plant-specific proteins whose functions are not yet clarified. In Arabidopsis thaliana, DICER-LIKE3 and members of the ARGONAUTE4 group of AROGONAUTE (AGO) proteins are involved, respectively, in generating and using 24-nt siRNAs that trigger methylation and transcriptional gene silencing (TGS) of homologous promoter sequences. AGO proteins act in silencing effector complexes by anchoring the 3â and 5â ends of the guide siRNAs at their N-terminal PAZ domain and MID domain, respectively. In addition, many AGO proteins cleave complementary target RNAs through an endonuclease (âslicerâ) activity in their C-terminal PIWI domain. AGO4 is the main AGO protein implicated in the RdDM pathway. Here we report the identification of the related AGO6 in a forward genetic screen for mutants defective in RdDM and TGS in shoot and root apical meristems in Arabidopsis thaliana. The identification of AGO6, and not AGO4, in our screen is consistent with the primary expression of AGO6 in shoot and root growing points and the preferential association of Pol V with AGO6.

overall_design: Examination of siRNA abundance in the trasngenic wild type plant (contains trigger and silencer transgenes) and the ago6-4 mutant.

first: Lucia

last: Daxinger

first: Marjori

last: Matzke

first: Stacey

middle: A

last: Simon

middle: C


title: Cohesin association to replication sites depends on Rad50 and promotes fork restart

status: Public on Oct 01 2012

city: Montpellier

first: Philippe

last: Pasero

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics - CNRS

type: Genome binding/occupancy profiling by genome tiling array

summary: The cohesin complex holds together newly-replicated chromatids and is involved in diverse pathways that preserve genome integrity. We show that in budding yeast, cohesin is transiently recruited to active replication origins and it spreads along DNA as forks progress. When DNA synthesis is impeded, cohesin accumulates at replication sites and is critical for the recovery of stalled forks. Cohesin enrichment at replication forks does not depend on H2A(X) formation, which differs from its loading requirements at DNA double-strand breaks (DSBs). However, cohesin localization is largely reduced in rad50delta mutants and cells lacking both Mec1 and Tel1 checkpoint kinases. Interestingly, cohesin loading at replication sites depends on the structural features of Rad50 that are important for bridging sister chromatids, including the CXXC hook domain and the length of the coiled-coil extensions. Together, these data reveal a novel function for cohesin in the maintenance of genome integrity during S phase.

overall_design: Scc1 ChIP, Rad50 ChIP and BrdU IP in wild type and mutants at different stages of the cell cycle.

first: Mireille

last: Tittel-Elmer

first: Armelle

last: Lengronne

first: Marta

middle: B

last: Davidson

first: Julien

last: Bacal

last: François

first: Marcel

last: Hohl

first: John

middle: H

last: Petrini

first: Jennifer

last: Cobb


title: Genome-wide analysis of SAS-I-mediated H4 K16 acetylation

status: Public on Jan 18 2012

city: Berlin

first: Ho-Ryun

last: Chung

address: Ihnestr. 75

department: Computational Molecular Biology

country: Germany

institute: Max-Planck-Institut for molecular Genetics

summary: The MYST HAT Sas2 is part of the SAS-I complex. The target for acetylation by Sas2 is Lys16 of histone H4 (H4 K16Ac). This acetylation site marks euchromatic regions and opposes the spreading of heterochromatin at telomere-proximal regions. Changes of SAS-I-mediated H4 K16Ac on a genome-wide scale comparing wt and sas2∆ cells were investigated in this study. We found a pronounced, genome-wide loss of H4 K16 acetylation in the body of transcribed genes in the absence of Sas2. Furthermore, the influence of Sas2 on gene expression was investigated in RNA expression arrays.

overall_design: H4 K16Ac and H4 in wt and sas2∆ was ChIPed. ChIP experiments were performed three times with independent chromatin preparations.

first: Franziska

last: Heise

first: Ludger

last: Klein-Hitpass


title: Budding yeast Wapl controls sister chromatid cohesion maintenance and the chromosome condensation status [PK-ChIP]

status: Public on Nov 22 2012

city: London

first: Rahul

last: Thadani

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Cancer Research UK

summary: Cohesin acetylation by Eco1 during DNA replication establishes sister chromatid cohesion. We show that acetylation makes cohesin resistant to Wapl activity from S-phase until mitosis. Wapl turns out to be a key regulator of cohesin dynamics on chromosomes by controling cohesin maintenance following its establishment in S-phase and its role in chromosome condensation.

overall_design: The Affymetrix Saccharomyces cerevisiae Chip Tiling 1.0R Arrays were used to analyze the binding pattern of Scc1 along the genome of Saccharomyces cerevisiae in late G1 and metaphase arrested cells.

first: Lidia

last: Lopez-Serra

first: Vanessa

last: Borges

first: Gavin

last: Kelly

first: Frank

last: Uhlmann


title: Gene expression profiles in human oral squamous cell carcinoma tissues and cell lines

status: Public on Sep 30 2012

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

country: Japan

institute: Ehime University Graduate School of Medicine

summary: Common overexpressing genes were identified in all human oral squamous cell carcinoma tissues and/or cultured cells.

overall_design: Ten oral squamous cell carcinoma tissues and 10 human oral squamous cell carcinoma cell lines were analyzed. Three normal oral mucosa tissues and a human non-neoplastic keratinocyte cell lines were used as control samples.


title: Spo11-accessory proteins link DNA double-strand break sites to the chromosome axis in early meiotic recombination

status: Public on Aug 28 2011

city: Vienna

first: Franz

last: Klein

address: Dr. Bohrg. 9

department: Chromosome Biology

country: Austria

institute: University of Vienna, MFPL

summary: Meiotic recombination between homologous chromosomes initiates via programmed DNA double-strand breaks (DSBs), generated by complexes comprising Spo11 transesterase plus accessory proteins. DSBs arise concomitantly with the development of axial chromosome structures, where the coalescence of axis sites produces linear arrays of chromatin loops. Recombining DNA sequences map to loops, but are ultimately tethered to the underlying axis. How and when such tethering occurs is currently unclear. Using ChIPchip in yeast, we show that Spo11-accessory proteins Rec114, Mer2 and Mei4 stably interact with chromosome axis sequences, upon phosphorylation of Mer2 by S-phase Cdk. This axis tethering requires meiotic axis components (Red1/Hop1) and is modulated in a domain-specific fashion by cohesin. Loss of Rec114, Mer2 and Mei4 binding correlates with loss of DSBs. Our results strongly suggest that hotspot sequences become tethered to axis sites by the DSB machinery prior to DSB formation.

overall_design: 34 ChIPs

first: Silvia

last: Panizza

first: Marco

last: Mendoza

first: Marc

last: Berlinger

first: Lingzhi

last: Huang

first: Alain

last: Nicolas

first: Katsuhiko

last: Shirahige


title: Androgen receptor splice variants mediate enzalutamide resistance in castration-resistant prostate cancer cell lines

status: Public on Oct 23 2012

city: Minneapolis

first: Scott

last: Dehm

address: Mayo Mail Code 806, 420 Delaware St SE

institute: Masonic Cancer Center, University of Minnesota

summary: The goal of this experiment was to compare the gene expression programs mediated by androgen/AR vs. constitutively active, truncated AR variants in castration-resistant CWR-R1 prostate cancer cells.  Because constitutive activity of truncated AR variants can mask androgen/AR target genes, the androgen/AR transcriptional program was assessed by silencing the trucnated AR 1/2/3/CE3 variant with siRNA targeting AR exon CE3 and treating cells with vehicle (ethanol) or 1nM DHT.  Similarly, because full-length AR activity can mask truncated AR variant target genes, the AR variant transcriptional program was assessed under castrate conditions by selectively silencing full-length AR with siRNA targeting AR exon 7, and comparing this profile with CWR-R1 cells transfected wtih siRNA targeting AR exon 1, which silences all AR expression (full-length and truncated AR variants).

overall_design: CWR-R1 cells were maintained under castrate conditions in long term culture in order to enrich for the population of cells harboring a 48kb intragenic deletion in AR intron 1.  These late-passage CWR-R1 cells were electroporated with siRNAs targeting AR exon 1, AR exon 7, or AR exon CE3.  Electroporated cells were seeded in RPMI 1640 medium containing antibiotics and 5% charcoal-stripped, steroid-depleted medium and allowed to recover for 48h.  After this 48h recovery, electroporated cells were switched to serum-free RPMI 1640 with 1nM DHT or 0.1% ethanol (vehicle control) for an additional 24h prior to extraction of total RNA.  Three independent biological replicates were performed.

middle: M


title: The replication checkpoint protects fork stability by releasing transcribed genes from nuclear pores.

status: Public on Jul 22 2011

city: Milano

first: Andrea

last: Cocito

state: MI

address: Via Adamello 16

department: Molecular Medicine Program

country: Italy

institute: IFOM Institute FIRC  of Molecular Oncology

summary: Transcription hinders replication fork progression and stability, and the Mec1/ATR checkpoint protects fork integrity. Examining checkpoint-dependent mechanisms controlling fork stability, we find that fork reversal or dormant origin firing owing to checkpoint defects are rescued in checkpoint mutants lacking THO, TREX-2 or inner basket nucleoporins.  Gene gating tethers transcribed genes to the nuclear periphery and is counteracted by checkpoint kinases through phosphorylation of nucleoporins such as Mlp1. Checkpoint mutants fail to detach transcribed genes from nuclear pores, thus generating topological impediments for incoming forks. Releasing this topological complexity by introducing a double-strand break between a fork and a transcribed unit prevents fork collapse. Mlp1 mutants mimicking constitutive checkpoint-dependent phosphorylation also alleviate checkpoint defects. We propose that the checkpoint assists fork progression and stability at transcribed genes by phosphorylating key nucleoporins and counteracting gene gating, thus neutralizing the topological tension generated at nuclear pore gated genes.

overall_design:
S.cerevisiae oligonucleotide microarrays were provided by Affymetrix (S.cerevisiae Tiling 1.0R, P/N 900645).
BrdU and proteins ChIP-chip analyses were carried out as described (Bermejo et al., Cell, 2009).

first: Rodrigo

last: Bermejo

first: Thelma

last: Capra

first: Rachel

last: Jossen

first: Arianna

last: Colosio

first: Camilla

last: Frattini

first: Walter

last: Carotenuto

first: Ylli

last: Doksani

first: Hannah

first: Belen

last: Gonzalez-Gomez

first: Andres

last: Aguilera

first: Yuki

last: Katou

last: Foiani


title: dNTP pools determine fork progression and origin usage under replication stress

status: Public on Jan 01 2012

first: Philippe

last: Pasero

summary: Intracellular levels of deoxyribonucleoside triphosphate (dNTP) must be tightly regulated to preserve genome integrity. Indeed, alterations in dNTP pools have recently been associated with increased mutagenesis, genomic instability and tumorigenesis. However, the mechanisms by which low or imbalanced dNTP pools affect DNA replication remain poorly understood. Here, we have modulated the activity of ribonucleotide reductase (RNR), a key enzyme catalyzing a rate-limiting step of dNTP production, to monitor the effect of altered dNTP levels on replication dynamics in budding yeast. We show that dNTP pools are limiting for normal DNA synthesis as upregulation of RNR activity increases replication fork speed. In contrast, inhibition of RNR activity with hydroxyurea (HU) induces a sharp transition from a regular- to a slow-replication mode within minutes after S-phase entry. Interestingly, we found that upregulation of RNR activity delays this transition and that dNTP levels modulate both fork speed and origin usage under replication stress. Moreover, we report that chromosomal instability (CIN) mutants show increased dNTP pools and enhanced DNA synthesis in the presence of HU. Since upregulation of RNR allows forks to progress faster in the presence of DNA lesions, we propose that CIN mutants adapt to chronic replication stress by upregulating dNTP pools.

overall_design: BrdU-IP from wild-type cells (30°C) and 12 mutant yeast cells. See Series GSE21014 for wild-type at 25°C and mutants already published in Crabbé et al. NSMB 2010

first: Jérôme

last: Poli

first: Olga

last: Tsaponina

first: Laure

last: Crabbé

last: Keszthelyi

first: Véronique

last: Pantesco

first: Andrei

last: Chabes

first: Armelle

last: Lengronne


title: Two tobacco transgenic lines over-expressing grapevine polygalacturonase-inhibiting protein (Vvpgip1)  vs. WT tobacco under normal growth conditions

status: Public on Dec 08 2011

city: Stellenbosch

first: Erik

last: Alexandersson

address: Victoria Street

country: South Africa

institute: IWBT, Stellenbosch University

summary: Polygalacturonase-inhibiting proteins (PGIPs) in plant cell walls inhibit fungal endopolygalacturonases (ePGs). Their action directly limits the effective ingress of the pathogen and is thought to lead to an up-regulated defense response. We previously showed that, PGIP activity, ePG inhibition and decreased Botrytis cinerea susceptibility were correlated in tobacco plants over-expressing grapevine (Vitis vinifera) Vvpgip1. In order to evaluate the base-line impact of PGIP over-expression, the transcriptome and hormone profiles of two transgenic lines with characterized resistance phenotypes were investigated in the absence of pathogen infection.

overall_design: Three microarray slides in total were hybridized: two slides using Vvpgip1 line 37 and WT, with a dye swap included to account for dye bias; and one slide using Vvpgip1 line 45 as test and WT as reference.

first: Melané

last: Vivier


title: Genome-wide binding of THO and Sub2 in Saccharomyces cerevisiae

status: Public on Jun 29 2011

city: Seville

first: Andrés

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

summary:
THO/TREX is a conserved nuclear complex that functions in mRNP biogenesis and prevents transcription-associated recombination. Whether or not it has a ubiquitous role in the genome is an open question. ChIP-chip studies reveal that the Hpr1 component of THO and the Sub2 RNA-dependent ATPase have genome wide-distributions at active ORFs in yeast. In contrast to RNAPII, evenly distributed from promoter to termination regions, THO and Sub2 are absent at promoters and distributed in a sharp 5’→3’ gradient.
Importantly, ChIP-chips reveal an over-recruitment of Rrm3 in active genes in THO mutants that is reduced by overexpression of RNase H1. Our work establishes a genome-wide function for THO-Sub2 in transcription elongation and mRNP biogenesis that function to prevent the accumulation of transcription-mediated replication obstacles, including R-loops.

overall_design: ChIP-chip studies were perfomed with tagged forms of the Hpr1 component of THO (Hpr1-FLAG), the Sub2 RNA-dependent ATPase of TREX (Sub2-FLAG), the Rpb3 subunit of RNA polymerase II (Rpb3-PK) and the Rrm3 protein (Rrm3-FLAG) in the yeast S. cerevisiae.

first: Belén

last: Gómez-González

first: María

last: García-Rubio

first: Rodrigo

last: Bermejo

first: Katsuhiko

last: Shirahige

first: Antonio

last: Marín

first: Marco


title: microRNA expression in Barrett's esophagus and esophageal adenocarcinoma

status: Public on Mar 15 2012

city: Utrecht

first: Jantine

middle: Wilhelmina Paula Maria

last: van Baal

address: Heidelberglaan 100

department: Gastroenterology and Hepatology

country: Netherlands

institute: University Medical Center Utrecht

summary: Barrett's esophagus is a metaplastic condition of the distal esophagus, characterized by the replacement of normal squamous epithelium by columnar epithelium. Patients with BE have an increased risk of developing esophageal adenocarcinoma. MicroRNAs have been implicated to be disease and tissue specific, however limited data of microRNA expression in the esophagus is available. Therefore we evaluated microRNA expression profiles of esophageal adenocarcinoma and compared these with Barrett's esophagus and normal squamous esophagus.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: In total 12 samples were analyzed. 4 esophageal adenocarcinoma, 4 Barrett's esophagus and 4 normal squamous esophagus

middle: W

last: vanBaal

first: Peter

middle: D

last: Siersema


title: Differential expression of miRNA in stretched rat alveolar epithelial cells

status: Public on Mar 06 2012

city: Philadelphia

first: Nadir

last: Yehya

state: PA

address: 390 Towne Bldg, U Penn

department: Bioengineering

institute: University of Pennsylvania

summary: Cyclic stretch of alveoli is characteristic of mechanical ventilation, and is postulated to be partly responsible for the lung injury and inflammation in ventilator induced lung injury. We propose that miRNAs may regulate some of the stretch response and, therefore, hypothesized that miRNAs would be differentially expressed between stretched and unstretched rat alveolar epithelial cells (RAECs).

overall_design: RAECs were isolated and cultured to express type I epithelial characteristics, after which they were equibiaxially stretched to 25% change in surface area at 15 cycles/minute for 1 or 6 hrs, or served as unstretched controls, and miRNA were extracted (n = 4 for all groups).

first: Adi

last: Yerrapureddy

first: John

last: Tobias

first: Susan

middle: S

last: Margulies


title: Differential microRNA profile in frontal cortex of suicide completers compared to control

status: Public on Jun 02 2012

city: PARIS

first: Gilles

last: Maussion

address: 16 rue Henri Huchard

institute: INSERM U675

summary:
Background:
TrkB-T1 is a BDNF receptor lacking a tyrosine kinase domain that is highly expressed in astrocytes and regulates BDNF-evoked calcium transients. Previous studies indicate that downregulation of TrkB-T1 in frontal cortex may be involved in neurobiological processes underlying suicide.

Methods:
	In a microarray screening study (N=8), we interrogated all known microRNA in the frontal cortex of suicide completers with low expression of TrkB-T1 and normal controls. These findings were validated and followed up in a larger sample of cases and controls (N=55) Functional analyses included microRNA silencing, microRNA overexpression and luciferase assays to investigate specificity and to validate interactions between differentially expressed microRNA and TrkB-T1

Results:
	microRNAs Hsa-miR-185* and Hsa-miR-491-3p were upregulated in suicide completers with low expression of TrkB.T1 (Pnominal: 9.10-5 and 1.8.10-4 respectively; FDR-corrected p=0.031). Bioinformatic analyses revealed five putative binding sites for the DiGeorge syndrome linked microRNA Hsa-miR-185*in the 3’UTR of TrkB-T1, but none for Hsa-miR-491-3P. The increase of Hsa-miR-185* in frontal cortex of suicide completers was validated then confirmed in a larger, randomly selected group of suicide completers, where an inverse correlation between Hsa-miR-185* and TrkB-T1 expression was observed ( R=-0.404; p=0.002). Silencing and overexpression studies performed in human cell lines confirmed the inverse relationship between hsa-mir-185* and trkB-T1 expression. Luciferase assays demonstrated that Hsa-miR-185* binds to sequences in the 3’UTR of TrkB-T1.

Conclusion:
These results suggest that an increase of Hsa-miR-185* expression levels regulates, at least in part, the TrkB-T1 decrease observed in the frontal cortex of suicide completers and further implicate the 3MB 22q11 region in psychopathology.

overall_design:
The microarray analysis consists in to compare the microRNA profile of four suicide completers with low TrkB-T1 expression level and four controls.
Each RNA extract was labeled with Hy3 and hybridyzed with a reference sample labeled with Hy5. The reference sample was a pool of the eight RNA samples

first: Jennie

last: Yang

first: Volodymyr

last: Yerko

first: Philip

last: Barker

first: Naguib

last: Mechawar

first: Carl

last: Ernst

first: Gustavo

last: Turecki


title: microRNA (miRNA) expression profiling of PBMCs of Parkinson's disease (PD) patients and controls

status: Public on Sep 30 2011

city: Lisbon

first: Sofia

last: Oliveira

state: Portugal

address: Av. Prof Egas Moniz

department: Edificio Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

summary: To investigate the role of miRNAs in the etiology of idiopathic PD, we conducted global miRNA expression profiling in peripheral blood mononuclear cells (PBMCs) of PD patients and controls.

overall_design: Total RNA was extracted from the PBMCs of 19 PD patients and 13 controls, labeled and hybridized to Exiqon microarrays spotted with probes for 733 human miRNAs.

first: Joaquim

middle: J

last: Ferreira

first: Madalena

last: Martins

first: Alexandra

last: Rosa


title: MEDIATOR subunit med8 binding in Saccharomyces cerevisiae

status: Public on Nov 22 2011

city: Gothenburg

first: Claes

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

country: Sweden

institute: Gothenburg University

type: Methylation profiling by genome tiling array

summary: The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild type Mediator forms stable complexes with the tails of Histone H3 and H4.  These binding assays also showed Mediator – histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing.  Finally, these findings were validated by tiling array analysis, that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization.

overall_design: Med8-TAP strain ChIPed with IgG beads  vs. Input in Saccharomyces cerevisiae

first: Xuefeng

last: Zhu


title: Topoisomerase II binds nucleosome-free DNA and acts redundantly with Topoisomerase I to enhance recruitment of RNA Pol II in budding yeast

status: Public on Aug 01 2011

city: Los Angeles

first: Adam

last: Sperling

state: CA

address: 611 Charles E. Young Dr. East

department: Biological Chemistry

institute: University of California Los Angeles

summary: DNA topoisomerases are known to promote transcription in prokaryotes by removing excessive DNA supercoils produced during elongation. However, it is unclear how topoisomerases in eukaryotes are recruited and function in the transcription pathway in the context of nucleosomes. To address this problem we present high-resolution genome wide maps of one of the major eukaryotic topoisomerases, Topoisomerase II (Top2) and nucleosomes in the budding yeast, Saccharomyces cerevisiae. Our data indicate that at promoters Top2 binds primarily to DNA that is nucleosome free. However, while nucleosome loss enables Top2 occupancy the opposite is not the case and the loss of Top2 has little effect on nucleosome density. We also find that Top2 is involved in transcription. Not only is Top2 enriched at highly transcribed genes but Top2 is required redundantly with Top1 for optimal recruitment of RNA polymerase II at their promoters. These findings and the examination of candidate activated genes suggest that nucleosome loss induced by nucleosome remodeling factors during gene activation enable Top2 binding which in turn acts redundantly with Top1 to enhance recruitment of RNA polymerase II.

overall_design:
For Agilent Data: Top2, Pol2 and H3 were ChIP'd from yeast strains and normalized to input or to each other.

For Affymetrix Data: Top2 and H3 were ChIP'd from yeast strains and normalized to input.

first: Kyeong

last: Jeong

first: Tasuku

last: Kitada

first: Michael

last: Grunstein


title: Small RNA sequencing in nine-day old nutrient-replete and N or P-limited wild type Arabidopsis seedlings

status: Public on Apr 21 2011

city: Esch-Belval

first: Patrick

last: May

state: Luxembourg

address: 7, avenue des Hauts-Fourneaux

department: Luxembourg Centre for Systems Biomedicine

country: Luxembourg

institute: University of Luxembourg

summary: Identification of nutrient-specific microRNA expressed in Arabidopsis seedlings

overall_design: Small RNA sequencing of Arabidopsis wild type ecotype Columbia (Col-0) seedling under different nutrient limitation conditions

first: Wolf-RÃ¼diger

last: Scheible

first: Przemyslaw

last: Nuc

first: Bikram

last: Pant


title: Integrated miRNA-mRNA-analysis of human monocyte derived macrophages upon Mycobacterium avium subsp. hominissuis infection

status: Public on Apr 22 2011

first: Soroush

last: Sharbati

address: Oertzenweg 19b

department: Institute of Veterinary Biochemistry

institute: Freie Universitaet Berlin

type:
Non-coding RNA profiling by array
Expression profiling by array

summary: The host response to mycobacterial infections was studied after infection of macrophages derived from primary human monocytes. mRNA and miRNA expression studies were performed to identify key regulators of immune defence and their targets.

overall_design: Experimental samples were taken 6h, 24h and 48h after infection of monocyte derived macrophages with two mycobacterial strains (MAH10091 and MAH104)

first: Jutta

first: Astrid

last: Lewin

first: Barbara

last: Kutz-Lohroff

first: Elisabeth

last: Kamal

first: Ralf

last: Einspanier


title: Global placental gene expression profiling in the first and third  trimesters of normal human pregnancy

status: Public on Apr 13 2011

city: Tromsø

first: Chris

last: Fenton

address: Thor Knutsen vg 6

department: Microarray

country: Norway

institute: UITO

summary: The human placenta is a rapidly developing organ with a relatively short life span that performs multiple functions until birth. Investigations into molecular mechanisms that control placental plasticity during its maturation might be useful in understanding patho-physiology of pregnancy-specific disorders. We hypothesized that molecular rearrangements and phenotypic adaptations that are necessary for normal placental development and maturation are reflected in its genotype. Our objective was to investigate global gene expression profile in the first and third trimester normal human placentas.

overall_design: 21 women were recruited with uncomplicated pregnancies that were delivered at term and 16 healthy women undergoing surgical abortion at 9-12 weeks gestation. We compared global placental gene expression profile by Human Genome Survey Microarray v.2.0 (Applied Biosystems). A total of 37 hybridisations were performed applying direct comparison design.

first: Ruth

last: Paulssen

first: Christopher

first: Vasilis

last: Sitras

first: Ase

last: Vårtun

first: Ganesh

last: Acharya


title: Genome wide analysis of Saccharomyces nascent RNA

status: Public on Nov 26 2010

city: Dresden

first: Fernando

last: Carrillo Oesterreich

address: Pfotenhauerstr. 108

institute: MPI-CBG

summary: To address co-transcriptional pre-mRNA processing events, Saccharomyces nascent RNA was isolated by chromatin fractionation and analyzed on a genome-wide high density tiling microarray. Co-transcriptional splicing efficiencies were derived by determination of intronic relative to exonic sequence concentrations.

overall_design: Nascent RNA, mRNA and genomic DNA were isolated from wild-type Saccharomyces cells and analyzed on a genome-wide high-density tiling microarry (Saccharomyces Tiling 1.0R Array, Affymetrix). At least 3 independent biological replicates were analyzed (nascent RNA (nRNA): 3 replicates, mRNA: 3 replicates, genomic DNA (gDNA): 4 replicates).

first: Julia

last: Jarrells

first: Karla

last: Neugebauer


title: Human auxiliary liver and combined kidney transplantation

status: Public on Mar 02 2011

first: Madeleine

last: Ingelsten

address: Bruna Straket 16

department: Renal Center

institute: Gothenburg university

summary:
10 biopsies from one patient undergoing a auxiliary liver and combined kidney transplantation, where one liver lobe is replaced by an auxiliary liver lobe. Thereafter the kidney is transplanted.
Keywords: Time course study

overall_design: 10 samples, no replicates.


title: Whole-genome microarray of adipose derived mesenchymal stem cells from differentially-aged mice

status: Public on Nov 30 2010

city: Verona

first: Mirco

last: Galiè

address: via Le Grazie, 8

department: Neuroscience, Biomedicine and Movement Sciences

institute: University of Verona

summary: whole-genome microarray profiling of mesenchymal stem cells isolated from the inguinal fat pad of mice of different age.

overall_design: Whole genome transcriptional profile of mesenchymal stem cells isolated from FVB mice of 1 (n=3) or 12 (n=3) months of age.

first: Daniele

last: Peroni


title: MCF7 tet-off cells treated or not with 80 ng/ml doxycycline for 12d

status: Public on May 20 2011

city: Zurich

first: Leah

middle: N

last: Cueni

address: Wolfgang Pauli-Str. 10

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich

summary: Tet-on and tet-off systems are among the most popular vector systems for inducible transgene expression in mammalian cells. In tet-regulated systems the expression of the transgene depends on the presence or absence of the antibiotic tetracycline or its derivative doxycycline, which are added to the cell culture medium in concentrations considered to be far below cytotoxic levels. Therefore, potential effects on the treated cells, which are exerted by the antibiotic itself and unrelated to transgene expression, are often ignored. We examined the influence of low dose doxycycline on the transcriptional profile of two independent clones of MCF7 human breast carcinoma cells, transfected with tet-off regulator and response plasmids but not harboring any transgene. Treatment with 80 ng/ml doxycycline for 12 days markedly altered gene expression in these cells. Many genes associated with interferon-signaling were up-regulated while cell cycle-associated genes were down-regulated, which was also accompanied by a reduction of cell growth. These results highlight the importance of appropriate controls when working with tet-regulated gene expression systems, to allow distinction between the effects of transgene expression and potential “side effects” of the antibiotic used for its regulation.

overall_design: MCF7 human breast carcinoma cells were stably transfected with the pTet-Off-regulator plasmid and the pTRE2hyg response plasmid, not comprising any transgene. Two independent cell clones were grown in their normal growth medium for 12 days in the presence or absence of 80ng/ml doxycycline. The medium was renewed every second day. After 12 days, total RNA was extracted using the Trizol reagent.

first: Michael

last: Detmar


title: The neural crest-enriched microRNA miR-452 regulates epithelial-mesenchymal signaling in the first pharyngeal arch

status: Public on Nov 10 2010

city: San Francisco

first: Deepak

last: Srivastava

address: 1650 Owens St.

department: Gladstone Institute of Cardiovascular Disease

institute: J. David Gladstone Institutes

summary:
S23 experiment:
We sought to identify the microRNAs (miRNAs) enriched in the neural crest cell (NCC) population from E11.5 mouse embryos.  To accomplish this, we utilized a transgenic mouse line harboring Cre-recombinase under the control of the Wnt1 NCC-specific promoter and also carrying the R26R-YFP allele.  We sorted YFP+ (NCCs) and YFP- (non-NCCs) from E11.5 Wnt1Cre-R26R mouse embryos via FACS and compared the relative enrichment of miRNAs in the YFP+ population by miRNA microarray.

220 experiment:
We sought to identify the microRNAs (miRNAs) enriched in the neural crest cell (NCC) population from E10.5 mouse embryos.  To accomplish this, we utilized a transgenic mouse line harboring Cre-recombinase under the control of the Wnt1 NCC-specific promoter and also carrying the R26R-YFP allele.  We sorted YFP+ (NCCs) and YFP- (non-NCCs) from E10.5 Wnt1Cre-R26R mouse embryos via FACS and compared the relative enrichment of miRNAs in the YFP+ population by miRNA microarray.

221 experiment:
Our research has shown that heterozygous deletion of the miRNA processing enzyme Dicer leads to developmental delay of the thymus in mouse embryos.  We sought to identify the microRNAs (miRNAs) affected by the loss of a single copy of Dicer in the neural crest cell (NCC) population from E10.5 mouse embryos.  To accomplish this, we utilized a transgenic mouse line harboring a floxed allele of Dicer, Cre-recombinase under the control of the Wnt1 NCC-specific promoter, and also carrying the R26R-YFP allele.  We sorted YFP+ (NCCs) cells from E10.5 Dicerfl/+,Wnt1Cre,R26R and Dicer+/+,Wnt1Cre,R26R mouse embryos via FACS and compared the relative expression of miRNAs in the Dicer-heterozygotes compared to Dicer-wildtypes by miRNA microarray.

overall_design:
S23 experiment:
RNA from YFP+ (NCCs) and YFP- (non-NCCs) cells sorted by FACS from E11.5 Wnt1Cre-R26R mouse embryos was isolated and hybridized to Exiqon miRNA microarrays v10.  Cells from five E11.5 embryos were sorted into YFP+ and YFP- populations and pooled.

220 experiment:
RNA from YFP+ (NCCs) and YFP- (non-NCCs) cells sorted by FACS from E10.5 Wnt1Cre-R26R mouse embryos was isolated and hybridized to Exiqon miRNA microarrays v10.  Cells from ten E10.5 embryos were sorted into YFP+ and YFP- populations and pooled.

221 experiment:
RNA from YFP+ (NCCs) cells sorted by FACS from E10.5 Dicerfl/+,Wnt1Cre,R26R and Dicer+/+,Wnt1Cre,R26R mouse embryos was isolated and hybridized to Exiqon miRNA microarrays v10.  Cells from ten embryos were sorted into YFP+ populations and pooled for each genotype.


title: Nucleosome depletion in Saccharomyces cerevisiae terminator

status: Public on Sep 21 2010

city: Boston

first: Xiaochun

last: Fan

state: MA

address: 220 Longwood Ave.

department: Biological Chemistry & Molecular Pharmacology

institute: Harvard Medical School

summary:
H3 ChIP and input DNA were hybridized to Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array

Genome-wide mapping of nucleosomes generated by micrococcal nuclease (MNase) suggests that yeast promoter and terminator regions are very depleted of nucleosomes, predominantly because their DNA sequences intrinsically disfavor nucleosome formation. However, MNase has strong DNA sequence specificity that favors cleavage at promoters and terminators and accounts for some of the correlation between
occupancy patterns of nucleosomes assembled in vivo and in vitro. Using an improved method for measuring nucleosome occupancy in vivo that does not involve MNase, we confirm that promoter regions are strongly depleted of nucleosomes, but find that terminator regions are much less depleted than expected. Unlike at promoter regions,
nucleosome occupancy at terminators is strongly correlated with the orientation of and distance to adjacent genes. In addition, nucleosome occupancy at terminators is strongly affected by growth conditions, indicating that it is not primarily determined by intrinsic histone-DNA interactions. Rapid removal of RNA polymerase II (Pol II) causes increased nucleosome occupancy at terminators, strongly suggesting a
transcription-based mechanism of nucleosome depletion. However, the distinct behavior of terminator regions and their corresponding coding regions suggests that nucleosome depletion at terminators is not simply associated with passage of Pol II, but rather involves a distinct mechanism linked to 3’ end formation.

overall_design: Yeast chromatin from cells grown in YPD or YP; normal cells or Pol II depleted cells was ChIPed with anti-H3 antibody from Abcam, vs input DNA

first: Zarmik

last: Moqtaderi

first: Yi

last: Jin

first: Yong

last: Zhang

first: Shirley

middle: X

last: Liu

first: Kevin

last: Struhl


title: Chromatin-dependent binding of the S. cerevisiae HMGB protein Nhp6A affects nucleosome dynamics and transcription

status: Public on Sep 15 2010

first: Noah

middle: L.

last: Dowell

address: 615 Charles E. Young Drive South, BSRB 357

institute: UCLA

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

overall_design: Refer to individual Series


title: Progerin Expression in Endothelial Cells Induces Endothelial Dysfunction

status: Public on Dec 02 2010

first: Belinda

last: Yap

address: 77 Avenue Louis Pasteur, NRB 752

department: Pathology

institute: Brigham and Women's Hospital, Harvard Medical School

summary: Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare, genetic premature aging disorder associated with severe atherosclerosis, often resulting in fatal heart attacks and strokes.  Progerin, the mutant protein in HGPS, also is expressed in healthy individuals and may play a role in the development of atherosclerosis during physiologic aging.  Here, we provide evidence for a primary involvement of vascular endothelium in the pathogenesis of accelerated atherosclerosis in HGPS. Expression of progerin in cultured human endothelial cells induces a dysfunctional phenotype, manifested by activation of multiple pro-inflammatory, pro-atherogenic genes.  In particular, our data implicate endothelial-derived interleukin-1 (IL-1) as a key mediator of a pro-inflammatory vascular phenotype.  Endothelial activation also is detectable in a mouse model of HGPS, and appears to be conveyed to neighboring vascular cells via autocrine and paracrine signaling. These new mechanistic insights into the vascular pathobiology of HGPS may have therapeutic implications for this disease.

overall_design: Genome-wide transcriptional profiling was carried out to assess functional phenotypic changes in endothelial cells (EC) as a result of progerin expression.  Cultured EC were infected with an adenovirus expressing progerin (Ad-Progerin), and as a control, an adenovirus that did not express any construct (Ad-Null).  Experiments were preformed with three different EC cultures.

first: Jeanne-Marie

last: Kiely

first: George

last: Stravrakis

first: Yuzhi

first: Guillermo

last: Garcia-Cardena

last: Gimbrone Jr


title: Chromatin-dependent binding of the S. cerevisiae HMGB protein Nhp6A affects nucleosome dynamics and transcription [Affymetrix]

summary: The Saccharomyces cerevisiae protein Nhp6A is a model for the abundant and multifunctional HMGB family of chromatin-associated proteins.  Nhp6A binds DNA in vitro without sequence-specificity and bends DNA sharply, but its role in chromosome biology is poorly understood.  We show by whole genome ChIP-chip that Nhp6A is localized to specific regions of chromosomes that include about 23% of RNA polymerase II promoters.  Nhp6A binding functions to stabilize positioned nucleosomes within promoter and 5' coding regions of these genes.  Both genomic binding and transcript expression studies point to functionally-related groups of genes that are specifically bound by Nhp6A and whose transcription is altered by the absence of Nhp6.  Genomic analyses of Nhp6A mutants specifically defective in DNA bending reveals a critical role of DNA bending for co-regulation of transcription but not for targeted binding by Nhp6A.

overall_design: Nhp6A (WT and point mutants) were ChIPed using a polyclonal antibody.  Histone H3 was ChIPed using a commercially available antibody.  IP experiments were compared to two sonicated, crosslinked chromatin samples (Input).

first: Reid

last: Johnson


title: Gene expression profiling of MCF7 breast cancer xenografts overexpressing podoplanin

status: Public on May 25 2010

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Replication termination is mediated by Top2 and occurs at genomic loci containing pausing elements

status: Public on Aug 28 2010

first: Andrea

last: Cocito

address: Via Adamello 16

institute: IFOM Institute FIRC  of Molecular Oncology

summary:
[original title] Chromosome replication initiates at multiple replicons and terminates when forks converge.

In Escherichia coli, the Tus-TER complex mediates polar fork converging at the terminator region and aberrant termination events challenge chromosome integrity and segregation. Since in eukaryotes termination is less characterized, we used budding yeast to identify the factors assisting fork fusion at replicating chromosomes.
Using genomic and mechanistic studies we have identified and characterized 71 chromosomal termination regions (TERs). TERs contain fork pausing elements that influence fork progression and merging. The Rrm3 DNA helicase assists fork progression across TERs counteracting the accumulation of X-shaped structures. The Top2 DNA topoisomerase associates at TERs in S-phase and G2/M facilitates fork fusion and prevents DNA breaks and genome rearrangements at TERs.
We propose that in eukaryotes replication fork barriers, Rrm3 and Top2 coordinate replication fork progression and fusion at termination regions thus counteracting abnormal genomic transitions.

Signal tracks in BED format suitable for visualization on the UCSC genome browser can be found at http://bio.ifom-ieo-campus.it/supplementary/Fachinetti_et_al_MOLCELL_2010

overall_design:
S.cerevisiae oligonucleotide microarrays were provided by Affymetrix (S.cerevisiae Tiling 1.0R, P/N 900645).
BrdU and proteins ChIP-chip analyses were carried out as described (Bermejo et al., Cell, 2009).

first: Daniele

last: Fachinetti

first: Rodrigo

last: Bermejo

first: Simone

last: Minardi

first: Yuki

last: Katou

first: Yutaka

last: Kanoh

first: Katsuhiko

last: Shirahige

first: Anna

last: Azvolinsky

first: Virginia

last: Zakian

first: Marco

last: Foiani


title: Role of Gcn5 in KCl stress adaptation in S. cerevisiae and S. pombe: transcriptional and genomic analyses

status: Public on Mar 01 2010

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

institute: Karolinska Institute

sample_organism: Saccharomyces cerevisiae/Schizosaccharomyces pombe fusant

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae


title: Bulk Segregant Analysis Reveals a Novel Xylose Utilization Gene from Saccharomyces cerevisiae

status: Public on Apr 09 2010

city: Stanford

first: Gavin

last: Sherlock

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

type: Genome variation profiling by genome tiling array

summary: To determine the genomic location of a gene that permits xylose utilization we conducted bulk segregant analysis (BSA) using Affymetrix yeast tiling arrays.  BSA works by taking advantage of DNA sequence polymorphisms between different strains and the fact that it is relatively easy to pool large numbers of meiotic spore products (segregants) in yeast.  Pooling segregants based on their phenotype allows the region of the genome responsible for the phenotype to be detected.  This is because DNA polymorphisms in regions unlinked to the locus causing the phenotype will segregate randomly and be “evened” out, while around the genomic region of interest, sequences or polymorphisms responsible for the trait will be present in all positive segregants, and absent in all negative segregants.  In our case, a Simi White wine strain (S. cerevisiae) carrying the locus responsible for xylose utilization was crossed to a laboratory strain of Saccharomyces cerevisiae; this strain was estimated to carry DNA polymorphisms relative to the laboratory strain at a level of approximately .5%.  Spores from the Simi White / S288c diploid were screened for the xylose utilization phenotype and 39 positive spores were combined into one pool and 39 negative spores into another pool, and genomic DNA (gDNA) was isolated from each pool.  We then hybridized the positive and negative gDNA pools to tiling microarrays that were based on the S288c reference genome with the expectation that regions of the genome derived from Simi White will hybridize less robustly to the array because of the DNA polymorphisms between Simi White and S288c.  Log2 ratios of probe intensities were calculated (negative/positive), and a peak appeared in the chromosome XV right subtelomeric region that corresponds to less robust hybridization to the microarray of the positive pool gDNA coming from this region of the genome

overall_design: gDNA isolated from 39 pooled "xylose positive" S. cerevisiae segregants from ("Simi White" x S288c) compared to gDNA isolated from 39 pooled "xylose negative" segregants from the same cross

first: Jared

last: Wenger

first: Katja

last: Schwartz


title: RNA Synthesis Precision is Regulated by Preinitiation Complex Turnover

status: Public on Sep 08 2010

city: Charlottesville

first: Kunal

last: Poorey

state: VA

address: 1340 Jefferson Park Avenue

department: Biomedical Sciences: Biochemistry, Molecular Biology & Genetics

institute: University of Virginia Health System

summary: TATA-binding protein (TBP) nucleates the assembly of the transcription preinitiation complex (PIC), and although TBP can bind promoters with high stability in vitro, recent results establish that virtually the entire TBP population is highly dynamic in yeast nuclei in vivo.  This dynamic behavior is surprising in light of models which posit that a stable TBP-containing scaffold facilitates transcription reinitiation at active promoters.  The dynamic behavior of TBP is a consequence of the enzymatic activity of the essential Snf2/Swi2 ATPase Mot1, suggesting that ensuring a highly mobile TBP population is critical for transcriptional regulation on a global scale.  Here high-resolution tiling arrays were used to define how perturbed TBP dynamics impact the precision of RNA synthesis in Saccharomyces cerevisiae.  We find that Mot1 plays a broad role in establishing the precision and efficiency of RNA synthesis: in mot1-42 cells, RNA length changes were observed for 713 genes, about twice the number observed in set2∆ cells, which display a previously reported propensity for spurious initiation within open reading frames.  Loss of Mot1 led to both aberrant transcription initiation and termination, with prematurely terminated transcripts representing the largest class of events. Genetic and genomic analyses support the conclusion that these effects on RNA length are mechanistically tied to dynamic TBP occupancies at certain types of promoters.  These results suggest a new model whereby dynamic disassembly of the PIC can influence productive RNA synthesis.

overall_design: High resolutionng arrays were used to define the locations of TBP, to identify TBP binding sites susceptible to Mot1 action, and to define how perturbed TBP dynamics impact the precision of RNA synthesis in Saccharomyces cerevisiae.

first: Rebekka

middle: O

last: Sprouse

first: Melissa

last: Wells

first: Ramya

last: Viswanathan

first: Stefan

last: Bekiranov

first: David

middle: T

last: Auble


title: Xylose Utilization Gene in Saccharomyces cerevisiae


title: miR-31 inhibits lymphatic lineage-specific differentiation in vitro and lymphatic vessel development in vivo

status: Public on Jun 04 2010

first: Jay

middle: Woo

last: Shin

state: Zurich

address: Wolfgang-Paulistrasse 10; HCI H394

summary: The lymphatic vascular system maintains tissue fluid homeostasis, helps mediate afferent immune responses and promotes cancer metastasis. MicroRNAs (miRNAs) have recently emerged as key and potent regulators of the genome that control virtually all aspects of cell and organism biology. Surprisingly, the physiological importance and functional activities of miRNAs in the lymphatic vascular system have not been explored. To address this, we first defined the in vitro miRNA expression profiles of primary human lymphatic endothelial cells (LECs) and blood vascular endothelial cells (BVECs). Comparative analysis of these profiles identified 4 BVEC-signature and 2 LEC-signature miRNAs. Further expression analysis by quantitative real-time PCR analysis and by in situ hybridization (ISH) studies confirmed these vascular lineage-specific expression patterns in vivo.  Functional characterization of the BVEC-signature miRNA, miR-31, identified a novel BVEC-specific post-transcriptional regulatory mechanism that inhibits lymphatic-specific transcription programs in vitro and lymphatic vascular development during Xenopus embryogenesis. These effects are, in part, mediated via direct post-transcriptional repression of PROX1, a master regulator of lymphatic lineage-specific differentiation. Together, these findings indicate that miR-31, and miRNAs in general, are potent regulators of vascular lineage-specific differentiation and development.

overall_design: 500,000 LECs were transfected with 2 µM Pre-miR-31 or Pre-miR-Neg molecules in biological duplicate and total RNA isolated using the mirVana isolation kit 48 hours post-transfection. The transcriptome profiles of these cells were defined using the Applied Biosystems Human Genome Survey Microarray v2.0 as described. Briefly, dioxigenin-UTP-labeled cRNA was generated from 1.5 µg of total RNA using the NanoAmp RT-IVT Labeling Kit (Applied Biosystems). 20 µg cRNA were fragmented and hybridized to the microarrays using the Applied Biosystems Chemiluminescence Detection Kit. Signal detection, image acquisition and initial analyses were performed using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer. Raw data were normalized using Quantile normalization available from R/Bioconductor. Present calls were defined based on average signal-to-noise ratios (S/N ratio) >3 and quality (error) values <5,00025. Feature signal intensities were converted to log2 values. miR-31-repressed genes were identified based on present calls in both Pre-miR-Neg arrays, log2(Pre31/PreNeg) ≤-0.59 and p-values <0.05, while miR-31-induced genes were present in both Pre-miR-31 arrays, had log2(Pre31/PreNeg) ≥0.59 and p-values <0.05. P-values were calculated using empirical Bayes statistics for differential expression.

first: Deena

last: Pedrioli

first: Vasilios

last: Dabouras

first: Terhi

last: Karpanen

first: Giorgia

last: Jurisic

first: Daniela

last: Marino

first: Roland

middle: E

last: Kalin

first: Sebastian

last: Leidel

first: Paolo

last: Cinelli

last: Schulte-Merker

first: André

last: Brändli

first: Michael

last: Detmar


title: H3 Lysine 4 Is Acetylated at Active Gene Promoters and Is Regulated by H3 Lysine 4 Methylation

status: Public on Feb 15 2011

city: Montréal

first: Benoit

last: Guillemette

state: Qc

address: 2950, chemin de Polytechnique

department: IRIC

country: Canada

institute: Université de Montréal

summary:
Methylation of histone H3 lysine 4 (H3K4me) is an evolutionarily conserved modification whose role in the regulation of gene expression has been extensively studied. In contrast, the function of H3K4 acetylation (H3K4ac) has received little attention because of a lack of tools to separate its function from that of H3K4me. Here we show that, in addition to being methylated, H3K4 is also acetylated in budding yeast. Genetic studies reveal that the histone acetyltransferases (HATs) Gcn5 and Rtt109 contribute to H3K4 acetylation in vivo. Whilst removal of H3K4ac from euchromatin mainly requires the histone deacetylase (HDAC) Hst1, Sir2 is needed for H3K4 deacetylation in heterochomatin.
Using genome-wide chromatin immunoprecipitation (ChIP), we show that H3K4ac is enriched at promoters of actively transcribed genes and located just upstream of H3K4 tri-methylation (H3K4me3), a pattern that has been conserved in human cells. We find that the Set1-containing complex (COMPASS), which promotes H3K4me2 and -me3, also serves to limit the abundance of H3K4ac at gene promoters. In addition, we identify a group of genes that have high levels of H3K4ac in their promoters and are inadequately expressed in H3-K4R, but not in set1  mutant strains suggesting that H3K4ac plays a positive role in transcription. Our results reveal a novel regulatory feature of promoter-proximal chromatin, involving mutually exclusive histone modifications of the same histone residue (H3K4ac and H3K4me).

overall_design: Yeast cells were grown in YPD to mid-log phase and harvested for genome-wide ChIP studies of histone modifications H3K4ac and H3K4me3 (normalised to non-modified H3 ChIP). Complete datasets from two separate experiments are uploaded: 1. Comparing H3K4ac/H3 vs H3K4me3/H3 in a WT (BY4741) strain. 2. Comparing H3K4ac/H3 in a WT (BY4741) vs a set1 deletion strain (set1D). Each ChIP experiment was done in biological triplicates (_01-_02-_03).

first: Richard

last: Festenstein

first: Alain

last: Verreault


title: γH2A is a component of yeast heterochromatin required for telomere elongation

status: Public on Jan 05 2011

first: Tasuku

last: Kitada

address: 611 Charles E Young Dr East

institute: University of California, Los Angeles

summary: Histones of heterochromatin are deacetylated in yeast and methylated in more complex eukaryotes to regulate heterochromatin structure and gene silencing. Here, we report that histone H2A phosphorylated at serine 129 (γH2A) in Saccharomyces cerevisiae is a conceptually new type of heterochromatin modification that functions downstream of silent chromatin assembly. We show that γH2A is enriched throughout yeast telomeric and silent mating locus (HM) heterochromatin where γH2A results from the action of kinases Tel1 and Mec1. Interestingly, mutation of γH2A has no apparent effect on the binding of Sir (silent information regulator) complex or on gene silencing. In contrast, deletion of SIR3 abolishes the formation of γH2A at heterochromatin. To address the function of γH2A, we used a ∆rif1 mutant strain in which telomeres are excessively elongated to show that γH2A is required for the optimal recruitment of Cdc13, a regulator of telomere elongation, and for telomere elongation itself. Thus, a histone modification that parallels Sir3 protein binding is shown here to be dispensable for the formation of a silent structure but is important for a crucial heterochromatin-specific downstream function in telomere homeostasis.

overall_design: gamma-H2A and RNA polymerase II ChIP vs. INPUT in YDS2.

first: Thomas

last: Schleker

first: Adam

last: Sperling

first: Wei

last: Xie

first: Susan

last: Gasser

last: Grunstein


title: SRF Overexpression Leads to Altered Expression of MicroRNAs and Contributes to Cardiac Hypertrophy

status: Public on Feb 16 2011

city: Little Rock

first: Scott

middle: Allen

last: Helms

state: AR

address: 4301 W. Markham

department: Reynolds Center on Aging

institute: University of Arkansas for Medical Sciences

summary: The role of SRF in the regulation of microRNA expression and microRNA biogenesis in cardiac hypertrophy has not been well established. In this report, we employed a distinct transgenic mouse model to study the impact of SRF on cardiac microRNA expression and microRNA biogenesis. Cardiac-specific overexpression of SRF (SRF-Tg) led to altered expression of a number of microRNAs.

overall_design: To study the effect of SRF level on cardiac gene expression and function in the mouse heart, we employed the cardiac-specific transgenic approach to increase the SRF protein level in one mouse model. The ventricular tissue samples used for the microRNA array analysis were obtained from 6-month-old wild-type mice and age-matched SRF-Tg mice. The RNA sample isolation and microRNA array were performed in triplets for both wild-type and transgenic mice.

first: Xiaomin

last: Zhang

first: Gohar

last: Azhar

middle: A

first: Jeanne

middle: Y

last: Wei


title: Gene expression profiling of peripheral blood cells for early detection of breast cancer

status: Public on Jan 15 2010

city: Oslo

first: Jørgen

middle: Mømb

last: Aarøe

address: Montebello

institute: The Norwegian Radium Hospital

summary: Purpose: Early detection of breast cancer is key to successful treatment and patient survival. We have previously reported the potential use of gene expression profiling of peripheral blood cells for early detection of breast cancer. The aim of the present study was to validate these findings using a larger sample size and a commercially available microarray platform.

overall_design: Experimental Design: Blood samples were collected from 121 females referred for diagnostic mammography following an initial suspicious screening mammogram. Diagnostic work-up revealed that 67 of these women had breast cancer while 54 had no malignant disease. Additionally, 9 samples from 6 healthy female controls (three pregnant women, one breast-feeding woman and two healthy controls at different timepoints in their menstrual cycle) were included. Gene expression analyses were conducted using high-density oligonucleotide microarrays. Partial Least Square Regression was used for model building and predictors were identified using a Jackknifing approach. Prediction performance was determined by a 20-fold double cross validation approach

first: J

first: T

last: Lindahl

first: V

last: Dumeaux

first: S

last: Sæbø

first: N

last: Hagen

first: D

last: Tobin

first: P

last: Skaane

first: A

last: Lönneborg

last: Sharma

first: A-L

last: Børresen-Dale


title: In Silico ascription of gene expression differences to tumor and stromal cells in a model to study impact on breast cancer outcome

status: Public on Sep 14 2010

first: Simen

last: Myhre

department: Dept of Genetics

institute: Oslo University Hospital

summary: We present a method for identifying and ascribing differentially expressed genes to tumor epithelial and/or stromal cells, by utilizing pathologic information and weighted t-statistics

overall_design:
Sets of differentially expressed gene-probes were identified in tumors from patients who developed distant metastasis compared with those who did not, by weighing the contribution from each tumor with the relative content of stromal and tumor epithelial cells in their individual tumor specimen. The analyses were performed under various assumptions of mRNA transcription level from tumor epithelial cells compared with stromal cells.

Supplementary files:
Human_AB1700_Annotations_09_06.txt: This file includes  control probes and obsolete probes not listed in GPL2986.
Raw_data.txt: This file includes control probes not listed in GPL2986.

first: Hayat

last: Mohammed

first: Trine

last: Tramm

first: Jan

last: Alsner

first: Jens

last: Overgaard

first: Anne-Lise

first: Arnoldo

last: Frigessi

first: Therese

last: Sørlie


title: Genomic analysis of replication profiles identifies RFCCtf18 as a key mediator of the replication stress response

status: Public on Oct 26 2010

city: Montpellier

first: Philippe

last: Pasero

address: 141 rue de la Cardonille

institute: Institute of Human Genetics - CNRS

summary: Maintenance of genome stability during DNA replication depends on surveillance mechanisms that prevent fork collapse and regulate replication timing. To dissect the checkpoint pathways signalling paused forks, we have screened a collection of S. cerevisiae mutants for their ability to activate Rad53, using the repression of late origins as readout for checkpoint efficiency. These genomic data redefine the role of key checkpoint factors. Indeed, they show that DNA damage sensors such as the 9-1-1 clamp and its loader RFCRad24 are unexpectedly dispensable to signal paused forks. In contrast, we found that the alternative clamp loader RFCCtf18 is essential for the Mrc1-dependent activation of Rad53. Moreover, we report that forks collapse in ctf18delta mutants and activate a secondary checkpoint pathway that represses very late origins in a Rad9-dependent manner. We propose a novel and integrated view of the replication checkpoint in which different pathways cooperate to fine tune the cellular response to arrested forks.

overall_design: BrdU-IP from wild-type and 20 mutant yeast cells. Cdc45p IP from 2 yeast strains.  Controls (Input DNA) and replicates are included and used to obtain the results files.

first: Laure

last: Crabbé

first: Aubin

last: Thomas

first: Véronique

last: Pantesco

first: John

last: De Vos

first: Armelle

last: Lengronne


status: Public on Sep 02 2010

city: wenzhou

first: wu

middle: zhe

last: bao

address: west road of xueyuan

department: Department of Neurosurgery

country: China

institute: First Affiliated Hospital of Wenzhou Medical College

summary: Little is known about the function of microRNA in prolactinomas treated with bromocriptine. The aim of the study was to explore the microRNAs associated with bromocriptine-treated prolactinomas.

overall_design: Six samples are analyzed, no replicates are included.A common reference consisted of a mix of the products that was spotted on the array.

first: Zhe

middle: B

last: Wu

first: Wei

middle: M

last: Zheng

first: Nader

last: Sanai

first: Yun

last: Chen

first: Xiang

last: Xue

first: Qi

middle: C

last: Zhuge

first: Zhi

middle: P

last: Su

first: Cheng

last: Wang

first: Li

last: Lu

first: Jin


title: Genome-wide localization of Gcn5 under normal and stress conditions in S. cerevisiae and S. pombe

first: Anthony

last: Wright

summary: Here we studied genome-wide localization  of Gcn5  under normal and KCl stress conditions in both yeast species. We found that in Saccharomyces cerevisiae, the enrichment of Gcn5 on genes changes from a relatively even distribution between coding region and intergenic region in the absence of stress, to a predominant localization in gene coding regions under stress conditions. This altered pattern changes are at global level indicates an important role of Gcn5 in modifying chromatin structure for stress adaptation in S. cerevisiae. The altered pattern changes are not observed in Saccharomyces pombe suggesting the different regulatory mechinery between two yeast speices. The related data series is GSE5218, where we have compared the gene regulation of Gcn5 at expression level in S. cerevisiae and S. pombe.

overall_design: Genome-localization of Gcn5-myc tagged strains are compared with wild type controls under normal condtions or KCl stress condtions in S. cerevisiae and S. pombe. Two biological replicates for control and experiemnt groups are used.

first: Yongtao

last: Xue-Franzén

first: Anna

last: Johnsson


title: Gene Expression Kinetics

status: Public on Mar 06 2010

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

summary: We have taken five different time points of a Yeast culture in exponential grow in rich medium, each one elapsed ten minutes from de previous one (from OD600 0.36 to 0.47). Then, for each time point we have measured the transcription rates (TR) and mRNA amounts (RA) for all the genes using the Genomic run-on (GRO) technique .

overall_design: For each time point we have measured the transcription rates (GRO) with 3 replicates (except for the t2 that only has 2 replicates due to technical problems) and mRNA amounts (cDNA RP) with 3 replicates for all the genes. The data were normalized using a gDNA hybridization for each filter.

first: Vicent

last: Pelechano


title: Gene expression profiling of MCF7 breast cancer xenografts overexpressing podoplanin (human array)

first: Leah

middle: N

last: Cueni

address: Wolfgang Pauli-Str. 10

institute: ETH Zurich

summary:
Expression of the membrane glycoprotein podoplanin is upregulated in several human cancers and might be associated with their malignant progression. The exact biological function and molecular targets of cancer cell-expressed podoplanin have remained unclear, however. Here, we ectopically overexpressed podoplanin in a human breast carcinoma xenograft model to study its role in cancer progression. To identify molecular mediators of podoplanin-induced effects we compared transcriptional profiles of podoplanin-overexpressing and control tumors.

Keywords: comparative transcriptional profiling

overall_design: MCF7 human breast carcinoma cells were stably transfected with the pTet-Off-regulator plasmid and the pTRE2hyg response plasmid, comprising or not full-length cDNA of human podoplanin (transcript variant 1, GenBank Accession number NM_006474). Three podoplanin-overexpressing and three control clones were isolated and each of them was injected bilaterally into the mammary fat pads of five female nude mice. Tumors were harvested after 24 days of growth and RNA was extracted from each of them. RNA of the 10 tumors derived from the same cell clone was pooled to give a total of six samples for microarray analysis (3x podoplanin-overexpressing, 3x control).

first: Michael

last: Detmar


title: Effect of LIN28 on miRNA profile at day 5 of neurogliogenesis in vitro

status: Public on Feb 25 2010

city: Stratford

first: Eric

last: Moss

state: NJ

address: 2 Medical Center Dr.

department: Molecular Biology

country: USA

institute: UMDNJ

summary:
Comparison of mouse P19 and P19+Lin28 cells at day 5 of retinoic acid-induced differentiation
The cell lines differ in that one constitutively expresses Lin28 from a heterologous promoter.

overall_design: Two biological replicates of two cell lines, one of which is stably transfected, harvested at a single day of differentiation in vitro.

first: Erica

last: Balzer

middle: G


title: Systems epidemiology of blood transcriptome variability in a representative sample of postmenopausal women

city: Tromsoe

first: Vanessa

last: Dumeaux

address: University of Tromsoe

institute: "The Norwegian Women and Cancer project"

summary: Using a large representative sample of postmenopausal women in the Norwegian Women and Cancer (NOWAC) postgenome study, we investigated blood gene expression changes due to intra-technical variability, normal inter-individuality (age, body mass index, fasting status), and exposure variables (smoking, hormone therapy and medication use) at proportion and level of real life situation revealing mechanistic insights of these effects mirrored in blood.

overall_design:
We used a representative sample of postmenopausal women (N=286) in the NOWAC postgenome study. We investigated blood gene expression changes due to intra-technical variability, normal inter-individuality (age, body mass index, fasting status), and exposure variables (smoking, hormone therapy and medication use). A total of 304 arrays, including 18 technical replicates, were analyzed. We filtered out samples which had less than 40% probes with a signal to noise ratio (S/N) greater than or equal to 3. When a technical replicate was conducted, the array with the least number of probes with S/N greater than or equal to 3 was excluded. After samples filtration, a total of 286 arrays were analyzed.

The following samples were filtered out; they were not used in the normalization processing, and none of the study conclusions are based on these samples.
NWbAB_ 1
NWbAB_ 2
NWbAB_ 3
NWbAB_ 4
NWbAB_ 5
NWbAB_ 7
NWbAB_ 8
NWbAB_ 61
NWbAB_ 63
NWbAB_ 116
NWbAB_ 120
NWbAB_ 121
NWbAB_ 180
NWbAB_ 183
NWbAB_ 214
NWbAB_ 249
NWbAB_ 254
NWbAB_ 299

Sample records (GSMxxxx) are not provided for the filtered-out samples. However, the metadata for the filtered-out samples is included in the Series supplementary file GSE15289_filtered_metadata.txt. The raw data for both the filtered-out samples and non-filtered-out samples (GSM381832-GSM382117) are included in the Series supplementary file GSE15289_raw.txt.


title: Arabidopsis Argonaute4, Argonaute6 and Argonaute9 associated small RNAs

status: Public on Feb 21 2010

city: Cambridge

first: Krys

last: Kelly

address: Downing Street

department: Plant Sciences

institute: University of Cambridge

summary:
We sequenced the small RNA bound to AGO4, AGO6 and AGO9 and compared these sRNAs to other libraries isolated such as total sRNAs, ago4 mutant, drd3-1 mutant, an AGO4 D660A slicer mutant and AGO6 and AGO9 under the AGO4 promoter.

Keywords: Epigenetics

overall_design:
Illumina samples: There are 17 unique samples representing 2 biological replicates of AGO6IP, 2 biological replicates of AGO9 IP, 3 biological replicates of total floral small RNAs, 1 technical replicate of total floral small RNA.
454 samples: These samples comprise 3 biological replicates of FLAG AGO4 IP.

first: Ericka

middle: R

last: Havecker

first: Laura

last: Wallbridge

first: Thomas

middle: J

last: Hardcastle

first: Maxwell

middle: S

last: Bush

first: Krystyna

first: Ruth

last: Dunn

first: Frank

last: Schwach

first: David

last: Studholme

first: John

middle: H

last: Doonan

last: Baulcombe


title: Aggressive Potato virus YNTN (PVYNTN) and mild PVYN isolates trigger different specific responses in susceptible potato

status: Public on Oct 01 2009

city: Ljubljana

first: Polona

last: Kogovsek

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary: Potato virus YNTN (PVYNTN) is one of the most devastating potato virus causing great losses in the potato production industry. PVYNTN induces severe symptoms on inoculated leaves and a disease known as potato tuber necrosis ringspot disease (PTNRD) develops on tubers. Closely related PVYN isolate induces only mild symptoms on inoculated potato leaves and no symptoms on tubers. The early response of sensitive potato cvs. Igor and Nadine to inoculation with PVYNTN and PVYN was analysed allowing identification of genes involved in severe symptoms induction. Microarray and quantitative-PCR analysis was carried out to identify differentially expressed genes after inoculation with both virus isolates. Two distinct groups of genes were shown to have a role in severe symptoms development – one group of genes related to energy production and a second group of genes connected with virus spread. Earlier accumulation of sugars and decrease in photosynthesis was observed in leaves inoculated with aggressive PVYNTN isolate than in leaves inoculated with milder PVYN isolate. PVYNTN isolate was shown not to activate differential expression of antioxidant metabolism and pectinmethylesterase inhibitor (PMEI) leading to a delay in plant response and on the other hand it limited callose deposition enabling faster virus spread through the plant.

overall_design: Each microarray was hybridized with PVYNTN inoculated sample and PVYN inoculated sample from the same biological replicate. Three biological replicates were analyzed.

first: Kogovsek

last: Polona

first: Blejec

last: Andrej


title: GRO analysis of rap1-sil, tpk1 & tpk2.

status: Public on Aug 24 2009

first: Jose

last: Perez-Ortin

summary:
GRO (Genomic run-on) experiments with different mutants that affect to the accumulation of non active RNA pol II along the yeast genome.

Keywords: Genomic run-on GRO

overall_design: There are 4 different strains: rap1-sil (without the silencing domain), RAP1(both from Graham I.R. et al 1999) and tpk1 & tpk2 mutants (Euroscarf). For each experiment there are GRO data (Transcription Rate) and gDNA data used for normalizing the GRO signals. The last number of the GRO filters correspond to the number of gDNA filters.There are 3 independent biological replicates of Rap1 and rap1-sil experiments and 2 for the tpk1 & tpk2 experiments.

first: Vicent

last: Pelechano

middle: E


title: Unphosphorylated SR-like Protein Npl3 Stimulates RNA Polymerase II Elongation

status: Public on Sep 06 2008

first: Miriam

last: Bucheli

address: 240 Longwood Ave.,

department: BCMP

institute: Harvard Medical School

summary:
The production of a functional mRNA is regulated at every step of transcription. An area not well-understood is the transition of RNA polymerase II from elongation to termination. The S. cerevisiae SR-like protein Npl3 functions to negatively regulate transcription termination by antagonizing the binding of polyA/termination proteins to the mRNA. In this study, Npl3 is shown to interact with the CTD and have a direct stimulatory effect on the elongation activity of the polymerase. The interaction is inhibited by phosphorylation of Npl3. In addition, Casein Kinase 2 was found to specifically phosphorylate Npl3 and affect its ability to compete against Rna15 (Cleavage Factor I) for binding to polyA signals. Our results suggest that phosphorylation of Npl3 promotes its dissociation from the mRNA/RNAP II, and contributes to the association of the polyA/termination factor Rna15. This work defines a novel role for Npl3 in elongation and its regulation by phosphorylation.

Keywords: Gene expression on a tiling array

overall_design: RNA for NPL3, npl3-120, npl3-S411A, and rna15-2 was extracted. Sense RNA was synthesized using whole transcript sense target labeling assay (Affymetrix, HMS Biopolymers Facility). Two biological replicates of each strain were hybridized to S. cerevisiae Tiling 1.0R Arrays, for a total of 8 microarrays.  Intensities were analyzed using the Tiling Analysis Software (TAS) from Affymetrix.

first: Jessica

middle: L

last: Dermody

first: Jonathan

last: Dreyfuss

first: Judit

last: Villén

first: Babatunde

last: Ogundipe

first: Steven

last: Gygi

first: Peter

last: Park

first: Alfred

last: Ponticelli

first: Claire

last: Moore

first: Stephen

last: Buratowski


title: RPCC analysis of rap1-sil, tpk1 & tpk2.

type: Genome binding/occupancy profiling by array

summary:
RPCC (RNA pol II ChIP-on-chip) experiments with different mutants that affect to the accumulation of non active RNA pol II along the yeast genome.

Keywords: ChIP-chip

overall_design: There are 4 different strains: rap1-sil (without the silencing domain), RAP1 (both from Graham I.R. et al 1999) and tpk1 & tpk2 mutants (Euroscarf). The IP was done using an Ab against the RNApol II CTD (8WG16 Covance).There are 3 independent biological replicates of Rap1 and rap1-sil experiments and 2 for the tpk1 & tpk2 experiments.


title: Transcriptomic analysis of src1 mutant

status: Public on Aug 27 2008

summary:
Gene expression analysis of a src1 yeast strain mutant and wt yeast strain  growing in exponential phase in YPD
Keywords: genetic modification

overall_design: Transcriptomic analysis of three independent replicates of wt and src1 yeast strain growing in exponential phase

first: Oreto

last: Antúnez

first: José

last: Pérez-Ortín


title: mRNA amount analysis of W303 hog1 mutant strain subjected to osmotic stress

status: Public on Apr 23 2009

summary:
mRNA amount (RA) analysis of W303 hog1 mutant yeast strain growing in exponential phase in YPD subjected to osmotic stress

Keywords: Time course

overall_design: Transcriptomic analysis of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F18-F24).


title: Gene expression profiling indicates inflammatory pathways involved in IUGR due to placental insufficiency

status: Public on Aug 01 2008

city: Tromsø

first: Ruth

middle: Hracky

last: Paulssen

address: MH-Bygget Breivika

department: Institute of Clinical Medicine

institute: Universitetet i Tromsø

summary: Intrauterine growth restriction (IUGR) represents a major obstetric challenge with perinatal  complications and a risk factor of developing disease in adult life. Placental insufficiency is   one of the common features accompanying IUGR. The aim of this study was to evaluate   global placental gene expression profile in IUGR compared to normal pregnancies. Placental   samples were collected by eight IUGR pregnancies with placental insufficiency ascertained   by Doppler and eight healthy controls. A 30K Human Genome Survey Microarray v.2.0   (Applied Biosystems) was used to evaluate global gene expression profile.  Principal   component analysis showed good separation in terms of gene expression patterns between the   groups. Pathway analysis with Bonferroni correction for multiple testing showed significant   (p<0.05) up-regulation of inflammation mediated by chemokine and cytokine signalling   pathway in the IUGR placentas. Genes involved in metabolism of glucocorticoids (HSD11B1   and DHRS2) were found differentially expressed. We found no imprinted genes to be   differentially expressed and only one gene involved in epigenetic modifications (MBD3) to be   down-regulated in the IUGR placentas, indicating that IUGR due to placental insufficiency is   not associated to placental imprinting. Subgroup analysis between pure IUGR and IUGR with   preeclampsia placentas showed only 27 differentially expressed genes suggesting common   pathophysiology.

overall_design: Eight placental samples from normal human placenta compared to eight human placental samples from patients with intrauterine growth restrictions due to placental insufficiency

first: Vasilis

last: Sitras

first: Ganesh

last: Acharya

first: Jørn

last: Leirvik

first: A

last: Vårtun


title: Transcription rate analysis of W303 hog1 mutant strain subjected to osmotic stress

first: Jose

last: Perez-Ortin

summary:
Transcription rate (TR) analysis of W303 hog1 mutant yeast strain growing in exponential phase in YPD subjected to osmotic stress

Keywords: Time course

overall_design: Transcription rate analysis by means of GRO of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F18-F24).


title: Hydroxyurea stimulates production of pro-inflammatory cytokines in endothelial cells: Relevance to sickle cell disease.

status: Public on Apr 09 2009

city: Bures-sur-Yvette

first: Arndt

last: Benecke

address: 35 route des Chartres

department: Integrative Biology

country: France

institute: Institut des Hautes Etudes Scientifiques & I.R.I.-CNRS

summary:
In sickle cell disease (SCD) hemoglobin S (HbS) polymerization renders red blood cells (RBC) both fragile and rigid and accounts for anemia and vasoocclusive crises (VOC). Abnormal RBC adhesion to vascular endothelial cells (VEC), in a context of chronic inflammation, cell activation and vascular tone abnormalities, is a major event in triggering VOC. Hydroxyurea (HU) is the only drug with a proven efficiency at decreasing VOC occurrence. HU decreases HbS polymerization and RBC adhesion. We studied HU effect on the other cellular partner of adhesion, i.e.VEC. HU-induced TrHBMEC transcriptome variations were analyzed by micro-arrays both in basal and pro-inflammatory conditions after 24h and 48h of treatment. Among the endothelial HU target genes we focused on those related to adhesion and inflammation phenomena. HU had no impact on adhesion genes as a whole, still expression of VCAM-1, a key adhesion receptor, was decreased. In contrast, HU had a significant effect on the inflammation gene cluster. It stimulates pro-inflammatory genes such as IL-1A, IL-1B, IL-6, IL-8, CCL2, CCL5 and CCL8 both at the mRNA and protein levels and also in HPMEC and HUVEC primary cells. This may suggest that HU increases inflammation in SCD patients to a threshold engaging an anti-inflammatory response.
Keywords: Treated TrHBME cell line

overall_design: Biological and technical relicates, 4 conditions: TrHBME cells non-treated, treated with cytokine, hydroxyurea or both and observed after 24 or 48H

first: Sandrine

last: Laurance

first: Omer

last: Dossou-Yovo

first: François-Xavier

last: Pellay

first: Michelle

last: Hauchecorne

first: Emmanuelle

last: Verger

first: Claudine

last: Lapoumeroulie

first: Jacques

last: Elion


title: Genome wide gene expression profiling of visceral adipose tissue among Asian Indian diabetics

status: Public on Jun 03 2009

city: Jaipur

first: Sandeep

middle: Kumar

last: Mathur

state: Rajasthan

address: JLN Marg

department: Endocrinology

country: India

institute: S.M.S.Medical College

summary: Genes showing differential expression in visceral adipose tissue obtained from Asia Indian obese women suffering from type-2 diabetes mellitus as compared to age and BMI matched normal glucose tolerant women were identified by genome wide transcriptomic profiling in 5 diabetic and 5 control subjects respectively.

overall_design:
In this study, omental biopsies were obtained from 5 diabetic and 5 control women undergoing cholecystectomy. All the subjects age > 55 years, BMI > 30, free from infection and malignancy. Expression profiling of 32878 probes for 29,098 genes was done in all participants.
A matrix file containing both processed and raw data is linked below as a supplementary file.

middle: K

first: Dinesh

last: Jindal

first: Atima

last: Agarwal


title: Placental gene expression in severe preeclampsia.

status: Public on Jun 20 2008

first: Ruth

last: Paulssen

summary:
The series is composed of thirty hybridizations for analysis of differentially expressed genes in normal placenta tissues from patients with normal labor and placenta tissues from patients with severe preeclampsia. Patients tissues samples were obtained from (Vasilis. Total RNA extraction was performed by using the MagNa Pure Compact RNA Isolation Kit (Roche Applied Science).
Keywords: Gene expression study, Disease state

overall_design: Twenty-six out of 50 normal placentas were randomly selected to match with 17 preeclamptic placentas, accounting for parity. Microarrays were performed applying a direct comparison design.

first: Halvor

last: Grønaas

first: Aase

last: Ancharya


title: Early response of potato plants to virus (PVY-NTN) inoculation

status: Public on Mar 21 2008

first: Spela

last: Baebler

summary:
Potato virus YNTN (PVYNTN), causing potato tuber ring necrosis disease, dramatically lowers the quantity and the quality of the potato yield all over the world. The cultivar Igor is one of the most susceptible cultivars, developing severe disease symptoms on plants as well as on tubers. Finding genes differentially expressed in the early response to infection, when the host response is more defense- than infection- related, could improve our understanding of the potato - PVYNTN  interaction. Differential gene expression in early response of potato cv. Igor plants to PVYNTN infection was studied using potato TIGR cDNA-microarrays. Expression was compared between mock inoculated and virus infected plants 12 hours after inoculation, in four biological replicates.
Keywords: direct comparison

overall_design: Each microarray was hybridized with a virus inoculated sample and mock inoculated sample from the same biological replicate. Four biological replicates were analyzed.

first: Ana

last: Rotter


title: DNA interactions with the ribosomal enhancer

status: Public on Apr 08 2009

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

summary:
DNA-DNA interactions are important for the control of gene expression. However, DNA interactions that occur in trans are difficult to identify. We used 4Cs to identify DNA regions that interact with the yeast ribosomal DNA enhancer.
We used 4Cs to identify DNA regions that physically interact with the yeast ribosomal enhancer.
Keywords: 4C

overall_design:
Yeast cells were grown to exponential stage and cross linked, digested with Msp1, diluted and ligated. Fragments that interact with the ribosomal enhancer were amplified by nested PCR> Cut samples were used as a negative control. One set of samples were treated with phenanthroline prior to cross-linking.
8 samples, 4 sets of 2 biological replicates
Background controls: J0001.CEL, J0003.CEL, J0005.CEL, J0007.CEL
Cut-ligated: J0002.CEL, J0004.CEL, J0006.CEL, J0008.CEL

first: Dharani

last: Sontam

first: Rebecca

last: Grierson

first: Beatrix

last: Jones


title: Comparison of globin RNA processing methods for genome-wide transcriptome analysis from whole-blood

status: Public on Feb 12 2008

first: Vanessa

last: Dumeaux

summary:
Whole blood rather than purified peripheral blood mononuclear cells is likely to become the prime tissue using expression microarrays for disease predication or prognosis however excess of globin mRNA may reduce probe detection sensitivity. In our study, we assessed whether whole-blood or globin-reduced RNA gives the most robust and sensitive results to detect small gene expression changes in response to hormone replacement therapy exposure. Each sample (N = 12) were hybridized according to 3 different protocols: no globin reduction (controls), globin reduction using peptid nucleic acids (PNA) and using magnetic beads in the GlobinClear kit from Ambion. Finally, 7 and 4 technical replicates were conducted in no globin reduction and PNA groups, respectively. Both globin reduction approaches were mostly efficient at reducing globin RNA from cRNA. Samples processed by GlobinClear kit gave a very distinct gene expression profiles from the controls while samples processed with PNA gave an intermediary profile closest to the non globin reduction group with a slight increased sensitivity of transcript detection but a loss of reproducibility. Overall, no sign of higher sensitivity in detection of gene expression changes followed by hormone exposure was observed after globin reduction which was therefore judged not beneficial.
Keywords: Groups comparaison

overall_design:
To assess effect of globin reduction protocols on gene expression from whole-blood, we selected 12 postmenopausal women (6 HRT users and 6 non-HRT users) who were not using other medication than HRT at the time of blood sampling and in order to cover a wide body mass index (BMI) range in both HRT and non HRT users. The samples were also selected to contain the highest concentration of total extracted RNA. Each sample was hybridized according to 3 different protocols: no globin reduction (controls), globin reduction using PNAs, globin reduction using magnetic beads in the GlobinClear™ kit from Ambion.
The reproducibility of the globin reduction method compared to the non globin reduction approach was investigated for the PNA method only since this method was the most effective and specific. We planned to conduct 7 technical replicates in each group (i.e. no globin reduction and PNA groups). During amplification process with PNA, 4 samples failed to reverse transcript long fragment of mRNA certainly due to inhibitory contamination and these arrays were therefore excluded from our analyses. One sample (sample 34) was amplified with PNA twice the same day to study technical reproducibility without amplification date effect. Finally, a total of 47 arrays were conducted including 7 and 4 technical replicates in no globin reduction and PNA group, respectively.


title: PVY-NTN elicits diverse gene expression response in different potato genotypes in the first 12 hours after inoculation

status: Public on Jul 09 2008

summary: Potato virus YNTN (PVYNTN), causing potato tuber ring necrosis disease, dramatically lowers the quantity and the quality of the potato yield all over the world. While cultivar Igor is one of the most susceptible cultivars, developing severe disease symptoms on plants as well as on tubers, cv. Sante is resistant and thus not affected by the virus. Finding genes differentially expressed in the early response to infection, when the host response is more defense- than infection- related, could improve our understanding of the potato - PVYNTN  interaction. Moreover, the differences in the response of the sensitive and resistant cultivar can pinpoint the genes involved in differential sensitivity of the cultivars. Differential gene expression in the early response of potato cvs. Igor and Sante to PVYNTN infection was studied using potato TIGR cDNA-microarrays. Expression was compared between mock inoculated and virus infected plants 0.5 and 12 hours after inoculation.

overall_design: Each microarray was hybridized with a virus inoculated sample and mock inoculated sample from the same biological replicate. At least three biological replicates were analyzed.


title: Salt stress in 7 Solanaceae species, replicate 1 and 2

status: Public on Feb 13 2008

city: Rockville

first: Jia

last: Liu

state: MD

address: 9712 Medical Center Drive

institute: Plant Genomics

summary:
Seven different Solanaceae species, Potato (Solanum tubersosum), Tomato (Solanum lycopersicum), Eggplant (Solanum melangena), Pepper (Capsicum annuum), Tobacco (Nicotiana tabaccum), Petunia and Nicotiana benthiamana were subjected to salt stress. The stress applied was 150mM NaCl and control plants were watered without the additional salt. Samples were collected at 0, 6, 12, 24, 48 and 96 hours after the first application of the salt. RNA was isolated using Qiagen RNeasy.
Keywords: Direct comparison

sample_organism:
Capsicum annuum
Solanum lycopersicum
Nicotiana tabacum
Nicotiana benthamiana
Petunia x hybrida
Solanum tuberosum
Solanum virginianum

overall_design: 76 hybs total

first: Buell

last: Robin


title: Tomato expression profiles in response to tomato psyllid infestation

status: Public on Feb 21 2008

summary:
Lycopersicon esculentum cv. Moneymaker tomato plants were grown for 4 weeks in greenhouse conditions (16h/8h light/darkness, 27 °C).  L. esculentum was randomly sorted into two groups of 16 plants each and a third reference group of 6 plants.  All plants were contained individually in mesh bags.  One group of 16 plants was infested with 25 female adult tomato psyllids that were 2-3 days old per plant.   The other two groups of 16 and 6 plants were not infested (healthy control, and reference pool).  After 3 days, the adults were removed from the infested plants to allow for egg eclosion and eventually nymphal development.  In this study, leaves infested and healthy plants were harvested for RNA extraction at 0, 3, 11, and 17 days after infestation with tomato psyllids. The reference pool was harvested on day 0.   Tissue (all-leaflets) from at least three plants per group was collected, flash frozen in liquid nitrogen and pooled for each time point (0, 3, 11 and 17 days after infestation) to represent treatments for before feeding (0 d), adult feeding and egg deposition (3 d), 1st and 2nd instar feeding (11 d) and 3rd to 5th instar feeding (17 d ), respectively.  The whole experiment was repeated three times (three biological replicates).   Plant tissues were ground using a cold mortar and pestle.  Total tomato leaf RNA was extracted using the hot-phenol protocol.  The RNA was precipitated, pooled, cleaned with a kit and stored at –80C. Two populations of single-stranded cDNAs will be generated from the aliquots and labeled with the cyanine Cy3 and Cy5 fluorophores.  RNA isolated from the reference pool (0 d) will be pooled from each replicate and will be labeled with Cy5; this is the reference sample for each hybridization.  RNA isolated from leaves infested with tomato psyllids and healthy uninfested plants from each time point will be query samples labeled with Cy3.    The two samples of labeled cDNA will be simultaneously hybridized to the same microarray.
Keywords: Reference design

overall_design: 22 hybs total

first: Timothy

last: Paine


title: A Top2 and Hmo1-mediated genome architectural pathway preventing chromosome fragility.

status: Public on Sep 05 2009

city: Milano

first: Andrea

last: Cocito

address: Via Adamello 16

department: Molecular Medicine Program

institute: IFOM Institute FIRC  of Molecular Oncology

summary:
Specialized topoisomerases solve the topological constraints arising when replication forks encounter transcription. We have investigated Top2 contribution in S phase transcription.  Specifically in S phase, Top2 binds intergenic regions close to transcribed genes without influencing their transcription. The Top2-bound loci exhibit low nucleosome density and accumulate yH2A when Top2 is defective. These intergenic loci associate with the HMG-protein Hmo1 throughout the cell cycle and are refractory to the histone variant Htz1. In top2 mutants, Hmo1 is deleterious and accumulates at pericentromeric regions in G2/M. Our data indicate that Top2 is dispensable for transcription and that Hmo1 and Top2 bind in the proximity of genes transcribed in S phase suppressing chromosome fragility at the M-G1 transition. We propose that an Hmo1-dependent epigenetic signature together with Top2 mediate a S-phasen architectural pathway controlling replicon dynamics when forks encounter transcriptionto preserve genome integrity.
Signal tracks in BED format suitable for visualization on the UCSC genome browser can be found at http://bio.ifom-ieo-campus.it/supplementary/Bermejo_et_al_CELL_2009

overall_design: The Chip on chip analysis was carried out as described (Bermejo et al., 2007; Katou et al., 2006; Katou et al., 2003), employing anti-Flag monoclonal antibody M2 (Sigma-Aldrich) anti-PK SV5-Pk1 antibody (AbD Serotec) and anti-γH2A antibodies (a gift from Alain Verreault). Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays and processed with TAS software Rev 1.1.

first: Rodrigo

last: Bermejo

first: Thelma

last: Capra

first: Victor

last: Gonzalez-Huici

first: Daniele

last: Fachinetti

first: Gioacchino

last: Natoli

first: Yuki

last: Katou

first: Hiroshi

last: Mori

first: Ken

last: Kurokawa

first: Katsuhiko

last: Shirahige

first: Marco

last: Foiani