title: The effects of ClrB internal mutant overexpression and creA deletion on the transcriptome of Penicillium oxalicum

status: Public on Jan 01 2019

city: Qingdao

first: Guodong

last: Liu

state: Shandong

address: Binhai Road 72

department: State Key Laboratory of Microbial Technology

institute: Shandong University

summary: The synthesis of cellulolytic enzymes by filamentous fungi are mainly regulated at the transcriptional level. The essential role of transcriptional activator ClrB/CLR-2 in the induction of cellulase genes has been reported in several fungal species. In this study, we identified the C-terminal region of ClrB in Penicillium oxalicum as a transcriptional activation domain using a yeast reporter gene system. Overexpression of a mutant ClrBID fusing the DNA-binding and transcriptional activation domains of ClrB together enabled cellulase production under cellulase non-inducing conditions. Strikingly, the ClrBID-overexpression strain produced cellulase in the presence of glucose at a level similar to that of reference strain on cellulose. Combination of ClrBID overexpression and deletion of carbon catabolite-repressor gene creA suggested an additive effect of the two manipulations on carbon catabolite de-repression. A similar modification of ClrB in Aspergillus niger also resulted in cellulase production on glucose. The results indicated that the post-transcriptional control of ClrB activity involves its central region, and provided a potential strategy for engineering Penicillium and Aspergillus strains for cellulase production on easy-to-use carbon sources.

overall_design: A total of 15 samples were analzyed, which include biological triplicates. The reference strain M12 was considered as a control.

first: Liwei

last: Gao


title: IDH3a KO effect on global DNA methylation

status: Public on Nov 30 2018

city: Chicago

first: Yanrong

last: Ji

state: IL

address: Arthur J. Rubloff Building, 750 North Lake Shore Drive, 11th Floor

department: Feinberg School of Medicine

country: USA

institute: Northwestern University

type: Methylation profiling by genome tiling array

summary: IDH3a KO in NHAs was demonstrated to exert global DNA methylation changes. These studies were followed by an Illumina EPIC methylation array to evaluate the location of differentially methylated CpGs

overall_design: 4 biological replicates for each condition (IDH3a wild-type vs. CRISPR/Cas9 KO) were used and gDNA was extracted. gDNA was then analyzed via an Illumina EPIC methylation array chip

first: Jasmine

middle: L

last: May

first: Alexander

middle: H

last: Stegh


title: Coupled single-cell epigenome editing and profiling reveals causal gene regulatory networks [Perturb-ATAC (GBC/sgRNA)]

status: Public on Dec 20 2018

city: Stanford

first: Paul

last: Khavari

state: CA

address: 269 Campus Drive, CCSR 2150

institute: Stanford University

summary: Here we present Perturb-ATAC, a method which combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells, based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by Assay of Transposase-accessible Chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in ~3,700 single cells, encompassing more than 75 unique genotype-phenotype relationships.

overall_design: Single-cell epigenome and perturbation identification in lymphoblastoid cells and epidermal keratinocytes.

first: Adam

middle: J

last: Rubin

first: Kevin

middle: R

last: Parker

first: Ansuman

middle: T

last: Satpathy

first: Howard

middle: Y

last: Chang

middle: A


title: The role of Gch1 and Nos2  in the macrophage response to BCG infection

city: Oxford

first: Eileen

last: McNeill

address: Wellcome Trust Centre for Human Genetics, Roosevelt Drive

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

summary:
Inducible nitric oxide synthase (iNOS) plays a crucial role in controlling growth of mycobacteria, presumed to be via nitric oxide (NO) mediated killing. However, NOS enzymes can also signal through NO-independent pathways, and production of NO by NOS requires the cofactor tetrahydrobiopterin (BH4).  We compared Nos2-/- mice to mice with macrophage BH4 deficiency (Gch1fl/flTie2cre), due to a leukocyte-specific deletion of Gch1, to uncover the specific contribution of NO-independent NOS functions to anti-mycobacterial immunity.
We used microarrays to detail the global programme of gene expression in uninfected and BCG infected macrophages that were either deficient in iNOS (Nos2-/- vs C57bl6/J) or BH4/Gch1 (GCHfl/flTie2cre vs GCHfl/fl)

overall_design: Bone Marrow Derived Macrophages (BMDM) were cultured form C57bl6/J (Nos2+/+), Nos2-/-, GCHfl/fl and GCHfl/flTie2cre bone marrow.  Differentiated macrophages from 4 animals per genotype were infected with BCG (Pasteur) in the presence of interferon gamma or left uninfected for 24 hours as control samples.

first: Elena

last: Stylianou

first: Helen

last: McShane

first: Keith

middle: M

last: Channon


title: Transcriptional profiling of M. tuberculosis treated with DG167 and INH

city: Newark

first: Pradeep

last: Kumar

state: NJ

address: 185 So Orange Avenue, MSB/A920A

department: Medicine

institute: Rutgers-New Jersey Medical SChool

type: Expression profiling by high throughput sequencing

summary: We report that combined treatment with both DG167 and INH activates a cellular response associated with loss of persistence and induction of cidality that is distinct from the cellular response induced by single drug treatment.

overall_design: Triplicate samples for each treatment

first: David

last: Alland


title: Centromeric DNA destabilizes H3 nucleosomes to promote CENP-A deposition during the cell cycle (part 3)

status: Public on Nov 29 2018

city: Edinburgh

first: Robin

last: Allshire

state: Midlothian

address: Max Born Cresent

institute: The University of Edinburgh

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Centromeres are the regions of eukaryotic chromosomes where kinetochores are assembled and direct the correct segregation of chromosomes.  Active centromeres are defined by presence of nucleosomes containing CENP-A, a histone H3 variant, which alone is sufficient to direct kinetochore assembly.  Once assembled at a location CENP-A chromatin and the kinetochore is maintained at that location though a positive feedback loop where kinetochore proteins recruited by CENP-A promote deposition of new CENP-A following replication.  Although CENP-A chromatin itself is a heritable entity, it is normally associated with specific sequences such as human alpha satellite arrays.  Such analyses suggest that properties of centromeric DNA itself may favour assembly of CENP-A rather than H3 nucleosomes.  To investigate the innate properties of centromeric DNA we have examined histone dynamics on this DNA assembled in CENP-A chromatin at endogenous centromeres and when assembled only in H3 chromatin at an ectopic location. We demonstrate that H3 occupancy on centromeric DNA is innately low while H3 turnover is high.  Moreover, even at an ectopic location centromeric DNA programs H3 deposition in S phase and its eviction during G2 when CENP-A is otherwise deposited.  G2 accumulation of RNAPII on centromeric DNA during G2 is consistent with transcription-coupled destabilisation of H3 nucleosomes to favour CENP-A deposition.

overall_design: ChIP-Nexus samples were preprared for histone H3 and H4 from wild type strain and strain bearing an ectopically inserted central core DNA.

first: Manu

last: Shukla

first: Pin

last: Tong


title: High-throughput transcriptome sequencing reveals extremely high doses of ionizing radiation-response genes in Caenorhabditis elegans

status: Public on Nov 28 2018

city: GuangZhou

first: Youqin

last: Xu

address: No.1023-1063, Shatai Road South, Baiyun District

country: China

institute: Southern Medical University

overall_design: This study sought novel ionizing radiation-response (IR-response) genes in Caenorhabditis elegans (C. elegans). C. elegans were divided into three groups and exposed to different high doses of IR: 0 gray (Gy), 200 Gy, and 400 Gy. Total RNA was extracted from each group and sequenced. When the transcriptomes were compared among these groups, many genes were shown to be differentially expressed, and these genes were significantly enriched in IR-related biological processes and pathways, including Gene Ontology (GO) terms related to cellular behaviours, cellular growth and purine metabolism and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to ATP binding, GTPase regulator activity, and RNA degradation. Quantitative reverse-transcription PCR (qRT-PCR) confirmed that these genes displayed differential expression across the treatments. Further gene network analysis showed a cluster of novel gene families, such as the guanylate cyclase (GCY), Sm-like protein (LSM), diacylglycerol kinase (DGK), skp1-related protein (SKR), and Glutathione S-Transferase (GST) gene families, which were upregulated. Thus, these genes likely play important roles in IR response. Meanwhile, some important genes that are well known to be involved in key signalling pathways, such as phosphoinositide-specific phospholipase C-3 (PLC-3), phosphatidylinositol 3-kinase age-1 (AGE-1), Raf homolog serine/threonine-protein kinase (LIN-45), and protein cbp-1 (CBP-1), also showed differential expression during IR response, suggesting that IR response might perturb these key signalling pathways. Our study revealed a series of novel IR-response genes in Caenorhabditis elegans that might act as  regulators of IR response and represent promising markers of IR exposure.

first: Chao

last: Zhang


title: Interleukin-27 is a potential marker for the onset of post-transplant malignancies

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

country: Italy

institute: University of Bari

summary:
Malignancies represent the third leading cause of post-transplant mortality worldwide. The main challenge for transplant physicians is a timely diagnosis of this condition. The aim of the study was to identify a soluble diagnostic marker for monitoring the development of post-transplant malignancies.
This is a multicentre, observational, perspective, case-control study. We enrolled 47 patients with post-transplant solid neoplasia. As a control group we employed 106 transplant recipients without a history of neoplasia and matched them with cases for the main demographic and clinical features. We investigated the transcriptomic profiles of peripheral blood mononuclear cells from kidney graft recipients with and without post-transplant malignancies enrolled in two of the participating centres, randomly selected from the whole study population. Microarray results were confirmed by quantitative polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) in the remaining patients from the same transplant centres and validated in a further independent group enrolled in two different transplant centres.
We identified 535 differentially expressed genes comparing patients with and without post-transplant malignancies (fold change ≥2.5; false discovery rate <5%). The cancer pathway was closely related to gene expression data, and one of the most down-regulated genes in this pathway was interleukin-27 (IL-27), a cytokine regulating anti-tumour immunity. Quantitative PCR and ELISA confirmed the microarray data. Interestingly, IL-27 plasma levels were able to discriminate patients with post-transplant neoplasia with a specificity of 80% and a sensitivity of 81%. This observation was confirmed in an independent set of patients from two different transplant centres.
Our data suggest that IL-27 may represent a potential immunological marker for the timely identification of post-transplant neoplasia.

overall_design: For microarray analysis, we studied 8 patients that presented a post-kidney Transplant malignancies, 8 kidney Transplanted patients without malignancies, 8 not-transplanted patients with malignancies and 8 healthy subjects.

first: Federica

last: Rascio

first: Gianluigi

last: Zaza

first: Matteo

last: Accetturo

first: Simona

last: Simone

first: Barbara

last: Infante

first: Lucrezia

last: Furian

first: Giuseppe

last: Castellano

first: Pasquale

last: Ditonno

first: Michele

last: Battaglia

first: Luigi

last: Cormio

last: Carrieri

first: Antonio

last: Lupo

first: Paolo

last: Rigotti

first: Loreto

last: Gesualdo

first: Giovanni

last: Stallone

last: Grandaliano


title: Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [BiSulfite-seq]

city: St. Louis

first: John

middle: R.

last: Edwards

state: MO

address: 660 S. Euclid Ave, Campus Box 8220

department: Center for Pharmacogenomics

institute: Washington University School of Medicine

type: Methylation profiling by high throughput sequencing

summary: The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF-gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5.

overall_design: For RNA-seq, gene expression was compared in whole two-week-old zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA-Seq analysis in three-week-old zebrafish larvae that were WT, mda5mk29/mk29 , zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS, DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.

first: Srivarsha

last: Rajshekar

first: Mary

middle: G

last: Goll


title: RNA-seq and microRNA-seq reveal RNAs and microRNAs under the regulation of miR-125b in NCCIT tumor cells

city: Beijing

first: Su-Ren

last: Chen

address: 1Beichen West Road, Chaoyang District

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Genes induced by senescence in soybean

status: Public on Nov 27 2018

city: Viçosa

first: Otavio Jose

middle: Bernardes

last: Brustolini

state: MG

address: Av. PHRolfs, S/N

department: Bioquimica e Biologia Molecular

country: Brazil

institute: Universidade Federal de Viçosa

summary: Comparison between two vegetative stages of the soybean cultivar BR16: 20 and 80 days after germination (DAG)

overall_design: Examination of 2 vegetative stages: 20 and 80 DAGs

first: Elizabeth

middle: P

last: Fontes

first: Dalton

middle: O

last: Ferreira

first: Jose

middle: F

last: Silva

first: Otávio


title: Interactive responses of Solanum dulcamara to drought and insect feeding are herbivore species specific

status: Public on Nov 26 2018

city: Nijmegen

first: Duy

last: Nguyen

address: Heyendaalseweg 135

department: Molecular Plant Physiology

country: Netherlands

institute: Radboud University

summary: In nature, plants are frequently subjected to multiple biotic and abiotic stresses, resulting in a convergence of adaptive responses. We hypothesized that hormonal signalling regulating defences to different herbivores may interact with drought response, causing distinct resistance phenotypes. To test this, we studied hormonal and transcriptomic responses of Solanum dulcamara subjected to drought and herbivory by the generalist Spodoptera exigua (BAW) or the specialist Leptinotarsa decemlineata (CPB). Bioassays showed that plants under drought became more resistant to BAW, but not to CPB. While drought did not alter BAW-induced hormonal responses, it enhanced CPB-induced accumulation of jasmonic acid and salicylic acid (SA) as well as supressed ethylene (ET) emission. Microarray analyses showed that under drought BAW herbivory enhanced several herbivore-induced responses, including cell-wall remodelling and metabolism of carbohydrates, lipids and secondary metabolites. In contrast, CPB herbivory enhanced several photosynthesis-related and pathogen responses in drought-stressed plants. This may divert resources away from the production of effective defences and increase tissue nutritive value. In conclusion, while BAW suffers from the drought-enhanced defences, CPB may benefit from effects of the enhanced SA and reduced ET signalling. This suggests that the fine-tuned interaction between the plant and its specialist herbivore is sustained under drought.

overall_design: 24 samples for 8 treatment groups (3 replicate each) were analysed. Leaves of plants under control watering regime (CON) or drought treatment (DRY) were either undamaged (NO) or fed upon by Spodoptera exigua (BAW2) or Leptinotarsa decemlineata (CPB2) for 48 h. Samples from plants under control watering regime that were fed by S. exigua (BAW1) and L. decemlineata (CPB1) for 24h were also included.

first: Yvonne

last: Poeschl

first: Tobias

last: Lortzing

first: Rick

last: Hoogveld

first: Andreas

last: Gogol-Döring

first: Simona

last: Cristescu

first: Anke

last: Steppuhn

first: Celestina

last: Mariani

first: Ivo

last: Rieu

first: Nicole

last: van Dam


title: Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome

first: John

last: Edwards


title: Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis

status: Public on Dec 11 2018

city: Pune

first: Payel

last: Ghosh

state: Maharashtra

address: Ganeshkhind

department: Bioinformatics Centre

country: India

institute: Savitribai Phule Pune University

summary: Fis and H-NS are two well-known NAPs in proteobacteria which play crucial role in both genome organization and gene regulation. However, the global effects of Fis and H-NS on gene expression remain unclear.  Here, to decipher transcriptional regulatory roles of Fis and H-NS we have performed RNA-sequencing to compare gene expression between the wild-type E. coli and its knockout mutants for fis and hns. We integrated our RNA-seq results with publically available ChIP-seq data to define direct and indirect regulation by Fis and H-NS. The regulatory networks thus provide a comprehensive view of coordinated regulatory roles for these important nucleoid-associated proteins.

overall_design: mRNA profiles of total six samples were generated using Illumina HiSeq 2500. Wild-type, fis mutant and hns mutant E. coli K-12 MG1655 strains were cultured in M9 minimal media at mid-exponential growth phase with biological duplicates.

first: Priyanka

last: Gawade

first: Gaurav

last: Gunjal

first: Anamika

last: Sharma


title: Expression data from IGRA positive and IGRA negative

status: Public on Nov 22 2018

city: Mexico

first: Martha

last: Torres

state: Mexico City

address: Calzada de Tlalpan 4502

department: Microbiology

country: Mexico

institute: Instituo Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

summary:
Treatment of latent tuberculosis infection (LTBI) in individuals at greatest risk for reactivation is an important component of TB control and elimination strategies. However, blood biomarkers for monitoring LTBI treatment have not been identified.
We performed a microarray analysis to identify the gene expression profile in whole blood from healthy individuals reactive to the tuberculin skin test (TST) with/without a positive in-house interferon-γ release assay (IGRA) before and after isoniazid (INH) prophylactic therapy.

overall_design: Volunteers who were in contact with TB cases and TST positive were recruited. Samples were classified into two main groups according to IGRA status: IGRA-positive and IGRA-negative. Three time measurements control (t0) plus isoniazid treatment after 1 month (t1) and after 6 months (t6) created six groups for differential expression analysis.

first: Claudia

last: Rangel

first: Eleane

last: de Oyarzabal


title: RNA sequencing data in AGS-BX1 cells treated with C7

status: Public on Nov 21 2018

city: Hong Kong

first: Kwai

middle: Fung

last: Hui

state: Hong Kong

address: L7-01, Laboratory Block, FMB, 21 Sassoon Road, Pokfulam

department: Paediatrics and Adolescent Medicine

country: Hong Kong

institute: HKU

summary: C7 is a novel lytic cycle inducer of Epstein-Barr virus (EBV) in EBV-positive epithelial cells. To analyze the potential signaling pathways that are activated by C7 for induction of EBV lytic cycle, we performed a RNA sequencing to analyze the RNA expression profiles in AGS-BX1 gastric carcinoma cells before and after treatment with C7.

overall_design: AGS-BX1 cells are either untreated or treated with C7 with 8 or 24h. RNA was extracted for RNA-sequencing.

first: K

last: HUI

first: S

last: Yiu

first: C

middle: K

last: Choi

first: A

last: Chiang


title: Portal Hypertension Induced Changes in Splenic microRNA Expression

city: Kumamoto

first: Junji

last: Saruwatari

state: Select One...

address: 5-1 Oe-honmachi, Chuo-ku

department: Department of Pharmacology and Therapeutics

country: Japan

institute: Kumamoto University

summary: Splenomegaly is caused by several pathological conditions, including portal hypertension, which is most frequently caused by chronic liver disease (e.g., liver cirrhosis).  The detailed mechanisms through which portal pressure induces splenomegaly and the precise pathophysiological conditions in portal hypertension-induced splenomegaly remain to be fully elucidated. We used microarrays to identify the differential microRNA expression underlying the portal hypertension-induced splenomegaly.

overall_design: Transcriptomic profile of microRNAs in whole spleen tissues from three male Sprague–Dawley rats with partial portal vein ligation (PPVL) as well as from the three sham rats without PPVL as controls.

first: Chao

last: Dong

first: Guilin

last: Wang

first: Yasuko

last: Iwakiri


title: Gene expression data from human endometrial cancer cells treated with siRNA targeting Efp

status: Public on Nov 20 2018

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

summary: To examine the role of Efp in endometrial cancer cells, Ishikawa and HEC-1A cells were treated with siRNA targeting Efp (siEfp) or control siRNA (siControl). Microarray analysis showed that Efp knockdown represses NF-κB-signaling pathway-associated genes.

overall_design: Total RNA was extracted from Ishikawa and HEC-1A cells treated with siEfp or siControl and then used for Affymetrix microarrays analysis.

first: Wataru

last: Sato

first: Kuniko

last: Horie-Inoue

first: Satoshi

last: Inoue


title: Bulk RNA-seq analysis of HUVEC cell cultures with Cerebral Cavernous Malformation (CCM) protein knockdown

status: Public on Nov 19 2018

city: Atlanta

first: Denis

last: Tsygankov

state: GA

address: North Ave NW

department: Biomedical Engineering

institute: Georgia Institute of Technology

summary: Gene expression profiles of WT (wild type) and CCM-1, -2, and -3 KD (knockdown of krit1, ccm2 and pdcd10 genes) cells under 2D (Matrigel-coated plastic) and 3D (Matrigel) conditions. Deep sequencing of RNA was performed for cells at the initial (2hrs) and later (6hrs) stages of EC tubule formation.

overall_design: Comparative analysis of gene expression of healthy and diseased cells in the tube formation assay

first: Olga

last: Chernaya

first: Anastasia

last: Zhurikhina

first: Siarhei

last: Hladyshau

first: William

last: Pilcher

first: Katherine

last: Young

first: Jillian

last: Ortner

first: Vaishnavi

last: Andra

first: Todd

last: Sulchek


title: Normal miRNA Expression Throughout Gestation in the Mare

city: Lexington

first: Shavahn

middle: C

last: Loux

state: KY

address: 1400 Nicholasville

department: Veterinary Science

institute: University of Kentucky

summary: To characterize miRNA expression throughout gestation, we utilized small RNA sequencing to evaluate matched chorioallantois and serum samples from mares at 4 m gestation (n = 3), 10 m gestation (n = 3) and postpartum (n = 3), as well as serum from diestrus mares (n = 6).

overall_design: Next-generation sequencing of chorioallantois and serum in mares throughout gestation, including diestrus serum.

first: Pouya

last: Dini

first: Kai

first: David

last: Baxter

first: Kirsten

middle: E

last: Scoggin

first: Arnold

last: Stromberg

first: Mats

last: Troedsson

first: Edward

last: Squires

first: Barry

last: Ball


title: Evaluation of mRNA expression in the equine chorioallantoic membrane

summary:
Purpose:The goal of this study was to evalute gene expression patterns of equine chorioallantoic membrane during different stages of the pregnancy
Method: mRNA profile of equine chorioallantoic membrane (CAM) from 45days, 4months, 6months and 10months  (4 samples for each time points) generated by RNA-sequencing,using a Illumina HiSeq 4000 ( HiSeq 4000 sequencing kit version 1). The sequence reads  were trimmed for adapters and quality using TrimGalore Version 0.4.4,and then mapped to EquCab2.0 using STAR-2.5.2b.  Final quantification at the gen level was performed by analyzing the BAM files in cufflinks using the Equus_caballus_ENSEMBL_88 gtf file as Guide.

overall_design: mRNA profile of equine chorioallantoic membrane (CAM) generated by RNA-sequencing, using a Illumina HiSeq 4000 (HiSeq 4000 sequencing kit version 1).

last: Wang

middle: H

middle: L


title: Multivalent H3K9me2 Reader ADCP1 Functions as a plant HP1 to Maintain Epigenetic Silencing

status: Public on Nov 15 2018

first: QIANWEN

last: SUN

address: Zhongguancun Street

department: School of life sciences

institute: Tsinghua University

summary: Heterochromatin formation is important for genome stability and transposon silencing. The evolutionally conserved Heterochromatin Protein 1 (HP1) recognizes H3K9me3 and maintains heterochromatin from fission yeast to mammalians. However, it is still questioned about the presence of HP1 protein in plants. Here, we discovered a multivalent H3K9me2 reader ADCP1 in Arabidopsis through biophysical and structural studies, and agenet domain in ADCP1 has the similar function of chromo domain in HP1. We further showed that ADCP1 was essential for heterochromatin maintenance through modulating H3K9me2 and DNA methylation levels. Similar to human HP1alpha and fly HP1a, ADCP1 was also able to mediate heterochromatin phase separation both in vitro and in vivo. Our results demonstrate the plant specific and evolution conserved ADCP1 functions as the HP1 equivalent protein in plant.

overall_design: ADCP1 ChIP performed with GFP antibody using ADCP1-GFP tagged transgenic plants, and Col-0 with no tag as control. H3K9me2 ChIP performed in Col-0 and adcp1-1 mutant and H3 ChIP as positive control. BS-seq perfomed with gDNA of Col-0 and adcp1-1. Total RNAs extracted from Col-0 and adcp1-1 for sequencing.

first: Lingling

last: Cheng

first: Qianwen

last: Sun


title: Transcriptomes and molecular pathway analysis of the liver in the red-eared slider turtle Trachemys scripta elegans under chronic salinity stress

status: Public on Nov 16 2018

city: HaiKou

last: Li

state: HaiNan

address: No. 99, longkun south road

department: Hainan normal university

institute: College of Life Science

summary: In order to understand the molecular mechanisms of salinity adaptation, high-throughput RNA-Seq was utilized to discover the gene expression profiles and pathways that responded to elevated salinity in the liver of T. s. elegans

overall_design: Three turtles from each group were divided into three groups exposed to 0, 5, or 15 psu (practical salinity units) for 30 days, and sampled following a 24 h fast and anesthetized by storing at -20℃ cryo-anesthesia for 0.5-1 h.

first: Meiling

last: Hong

first: Aiping

last: Jiang


title: Spatio-temporal m(i)RNA architecture and 3' UTR regulation in the C. elegans germline

city: Berlin

first: Nikolaus

last: Rajewsky

state: Berlin

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

summary: In animal germlines, regulation of cell proliferation and differentiation is particularly important but poorly understood. Here, using a cryo-cut approach, we mapped RNA expression along the Caenorhabditis elegans germline and, using mutants, dissected gene regulatory mechanisms that control spatio-temporal expression. We detected, at near single-cell resolution, > 10,000 mRNAs, > 300 miRNAs and numerous unannotated miRNAs. Most RNAs were organized in distinct spatial patterns. Germline-specific miRNAs and their targets were co-localized. Moreover, we observed differential 3’ UTR isoform usage for hundreds of mRNAs. In tumorous gld-2 gld-1 mutants, gene expression was strongly perturbed. In particular, differential 3’ UTR usage was significantly impaired. We propose that PIE-1, a transcriptional repressor, functions to maintain spatial gene expression. Our data also suggest that cpsf-4 and fipp-1 control differential 3’ UTR usage for hundreds of genes. Finally, we constructed a “virtual gonad” enabling “virtual in situ hybridizations” and access to all data (https://shiny.mdc-berlin.de/spacegerm/).

overall_design: Investigation of the spatio-temporal gene expression in the Caenorhabditis elegans germline using a cryo-based approach and single cell protocols.

first: Asija

last: Diag

first: Marcel

last: Schilling

first: Filippos

last: Klironomos

first: Salah

last: Ayoub


title: The SOG1 transcriptional activator and the MYB3R family of repressors control a complex gene network in response to DNA damage in Arabidopsis [RNA-seq t vs t0]

city: La Jolla

first: Julie

middle: Ann

last: Law

address: 10010 North Torrey Pines Rd

department: PLANT MOLECULAR AND CELLULAR BIOLOGY LABORATORY

institute: The Salk Institute for Biological Studies

summary: To combat DNA damage, organisms mount a DNA Damage Response (DDR) that results in cell cycle regulation, DNA repair, and, in severe cases, cell death. Underscoring the importance of gene regulation in this response, studies in Arabidopsis have demonstrated that all the aforementioned processes rely on SUPRESSOR OF GAMMA 1 (SOG1), a NAC transcription factor (TF). However, the expression networks connecting SOG1 to these processes remain largely unknown and, although the DDR spans from minutes to hours, most transcriptomic data corresponds to single time-point snapshots. Here, we generated transcriptional models of the DDR from gamma-irradiated ([gamma]-IR) wild-type and sog1 seedlings during a 24-hour timecourse using DREM, the Dynamic Regulatory Events Miner. In the wild-type model, the NAC and MYB3R TF families are implicated in the induction and repression of damage responsive genes, respectively, and the 2,400 differentially expressed genes form 11 subgroups with distinct expression profiles, biological functions, and cis-regulatory features. Within this network, SOG1 acts as a transcriptional activator, directly targeting 300 genes, including TFs, DNA repair factors, and cell cycle regulators, and, indirectly influencing the expression of most, but not all, of the remaining [gamma]-IR-responsive genes.  Among these indirect targets are many cell cycle genes that are repressed by the MYB3R TFs after DNA damage and group together within the DREM model, linking these TFs to specific expression subgroups. Together, this transcriptional roadmap of the DDR provides insight into many [gamma]-IR-responsive genes and reveals the first layer of interactions connecting SOG1 to the diverse processes coordinated in response to DNA damage.

overall_design: 36 mRNA-seq libraries were sequenced

first: Clara

last: Bourbousse


title: The SOG1 transcriptional activator and the MYB3R family of repressors control a complex gene network in response to DNA damage in Arabidopsis [RNA-seq myb3r135 vs wt]

overall_design: 8 mRNA-seq libraries were sequenced


title: The SOG1 transcriptional activator and the MYB3R family of repressors control a complex gene network in response to DNA damage in Arabidopsis [RNA-seq gIR vs mock wt]

overall_design: 16 mRNA-seq libraries were sequenced


title: The SOG1 transcriptional activator and the MYB3R family of repressors control a complex gene network in response to DNA damage in Arabidopsis [RNA-seq DREMmodel]

summary: To combat DNA damage, organisms mount a DNA Damage Response (DDR) that results in cell cycle regulation, DNA repair, and, in severe cases, cell death. Underscoring the importance of gene regulation in this response, studies in Arabidopsis have demonstrated that all the aforementioned processes rely on SUPRESSOR OF GAMMA 1 (SOG1), a NAC transcription factor (TF). However, the expression networks connecting SOG1 to these processes remain largely unknown and, although the DDR spans from minutes to hours, most transcriptomic data corresponds to single time-point snapshots. Here, we generated transcriptional models of the DDR from gamma-irradiated ([gamma]-IR) wild-type and sog1 seedlings during a 24-hour timecourse using DREM, the Dynamic Regulatory Events Miner. In the wild-type model, the NAC and MYB3R TF families are implicated in the induction and repression of damage responsive genes, respectively, and the 2,400 differentially expressed genes form 11 subgroups with distinct expression profiles, biological functions, and cis-regulatory features. Within this network, SOG1 acts as a transcriptional activator, directly targeting 300 genes, including TFs, DNA repair factors, and cell cycle regulators, and, indirectly influencing the expression of most, but not all, of the remaining[gamma]-IR-responsive genes.  Among these indirect targets are many cell cycle genes that are repressed by the MYB3R TFs after DNA damage and group together within the DREM model, linking these TFs to specific expression subgroups. Together, this transcriptional roadmap of the DDR provides insight into many[gamma]-IR-responsive genes and reveals the first layer of interactions connecting SOG1 to the diverse processes coordinated in response to DNA damage.

overall_design: 48 mRNA-seq libraries were sequenced


title: Mobile PEAR transcription factors integrate hormone and miRNA cues to prime cambial growth

status: Public on Nov 09 2018

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: In addition to apical growth, plants undergo radial growth to increase girth, a particularly prominent feature in trees. During both apical and radial growth the phytohormones auxin and cytokinins form symmetries that govern further growth patterns. But whereas the gene regulatory networks interpreting the hormonal fields during apical growth are well established, such networks are not known for the radial growth. We show here that the initiation of radial growth occurs around early protophloem sieve element (PSE) cell files of the root procambial tissue in Arabidopsis. In this domain cytokinin signalling promotes expression of a pair of novel mobile transcription factors, PHLOEM EARLY DOF (PEAR1, PEAR2) and their four homologs (OBP2, DOF6, TMO6 and HCA2), collectively called PEAR proteins. The PEAR proteins form a short-range concentration gradient peaking at PSE and activating gene expression that promotes radial growth. The expression and function of PEAR proteins are antagonized by well-established polarity transcription factors, HD-ZIP III, whose expression is concentrated in the more internal domain of radially non-dividing procambial cells by the function of auxin and mobile miR165/166. The PEAR proteins locally promote transcription of their inhibitory HD-ZIP III genes, thereby establishing a negative feedback loop that forms a sharp boundary demarking the zone of cell divisions. Taken together, we have established a network, in which the PEAR - HD-ZIP III module integrates the spatial information of the hormonal domains and miRNA gradients during root procambial development, to provide a pre-pattern with actively dividing and more quiescent zones, thus priming radial growth.

overall_design:
4-day-old plants grown on MS were treated with the indicated compounds for the indicated time, whereafter roots were harvested and total RNA was isolated.

PEAR1 = AT2G37590; PEAR2 = AT5G02460

first: Wouter

last: Smet

first: Mark

middle: V

last: Boekschoten

middle: J

first: Bert

last: De Rybel


title: Shift from androgen to estrogen action causes fibrosis, abdominal muscle atrophy, and inguinal herniation in males

status: Public on Nov 14 2018

city: Chicago

first: Hong

last: Zhao

address: 303 E. Superior St., Suite 4-121

department: OB/GYN

institute: Northwestern university

summary:
Local biosynthesis of estrogen in lower abdominal skeletal muscle tissue leads to estrogen receptor-α-mediated fibrosis, muscle atrophy, and inguinal hernia.
We used microarrays to detail the gene expression after aromatase expression in lower abdominal muscle tissue and identify distinct classes of up-regulated or down-regulated genes.

overall_design: Total RNA obtained from lower abdominal muscle tissues of humanized aromatase transgneic mice (AromhumL and AromhumH) compared to those of wild type (WT) mice.

first: Serdar

last: Bulun


title: The SOG1 transcriptional activator and the MyB3R family of repressors control a complex gene network in response to DNA damage in Arabidopsis [SOG1 ChIP-seq]

summary: To combat DNA damage, organisms mount a DNA Damage Response (DDR) that results in cell cycle regulation, DNA repair, and, in severe cases, cell death. Underscoring the importance of gene regulation in this response, studies in Arabidopsis have demonstrated that all the aforementioned processes rely on SUPRESSOR OF GAMMA 1 (SOG1), a NAC transcription factor (TF). However, the expression networks connecting SOG1 to these processes remain largely unknown and, although the DDR spans from minutes to hours, most transcriptomic data corresponds to single time-point snapshots. Here, we generated transcriptional models of the DDR from gamma-irradiated ([gamma]-IR) wild-type and sog1 seedlings during a 24-hour timecourse using DREM, the Dynamic Regulatory Events Miner. In the wild-type model, the NAC and MyB3R TF families are implicated in the induction and repression of damage responsive genes, respectively, and the 2,400 differentially expressed genes form 11 subgroups with distinct expression profiles, biological functions, and cis-regulatory features. Within this network, SOG1 acts as a transcriptional activator, directly targeting 300 genes, including TFs, DNA repair factors, and cell cycle regulators, and, indirectly influencing the expression of most, but not all, of the remaining [gamma]-IR-responsive genes.  Among these indirect targets are many cell cycle genes that are repressed by the MyB3R TFs after DNA damage and group together within the DREM model, linking these TFs to specific expression subgroups. Together, this transcriptional roadmap of the DDR provides insight into many [gamma]-IR-responsive genes and reveals the first layer of interactions connecting SOG1 to the diverse processes coordinated in response to DNA damage.

overall_design: 6 ChIP-seq libraries were sequenced


title: The non-canonical SMC protein SmcHD1 antagonises TAD formation on the inactive X chromosome (Repli-seq)

status: Public on Nov 07 2018

city: Oxford

first: Michal

last: Gdula

address: South Parks Road

institute: Oxford University

summary: In this study we investigate the role of the non-canonical SMC family protein, SmcHD1in the X inactivation.

overall_design: Allele-specific repli-seq experiments were done in wild-type and SmcHD1mut (SmcHD1 null MommeD1 mutant cells) interspecific MEFs

middle: R

first: Tatyana

middle: B

last: Nesterova

first: Greta

last: Pintacuda

first: Jonathan

last: Godwin

first: Michael

last: McClellan

first: Skirmantas

last: Kriaucionis

first: Felix

last: Krueger

first: Wolf

last: Reik

first: Ye

last: Zhan

first: Hakan

last: Ozadam

first: Job

last: Dekker

first: Catherine

last: Green

first: Daniela

last: Moralli

first: Edith

last: Heard

first: Neil

last: Brockdorff


title: Expression data from Notch intracellular domain overexpressing primary murine liver sinusoidal endothelial cells

status: Public on Nov 05 2018

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
Liver sinusoidal endothelial cells (LSEC) constitute discontinuous, permeable microvessels, with a characteristic programme of gene expression that differs significantly from continuous microvascular endothelial cells e.g. in the lung. Notch signalling plays a crucial role in a variety of processes in endothelial cells such as vascular morphogenesis, and vascular differentiation.
We used microarrays to analyse the programme of gene expression in murine liver endothelial cells with enhanced Notch signalling.

overall_design: Murine liver sinusoidal endothelial cells (mLSEC) from Notch intracellular domain hepatic endothelial cell specific overexpression mice (NICD-OE-HEC) and control mice were isolated for RNA extraction and hybridization on Affymetrix microarrays.

first: Manuel

last: Winkler


title: Transcriptional profiling of Pseudomonas aeruginosa and Staphylococcus aureus during in vitro co-culture

status: Public on Nov 01 2018

city: Geneva

first: Thilo

last: Kohler

address: 1, rue Michel Servet

department: Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva

summary: We analyzed the transcriptome of both S. aureus and P. aeruginosa after 3h of co-culture

sample_organism:
Pseudomonas aeruginosa
Staphylococcus aureus

overall_design: RNAseq was performed in 3 technical replicates for each condition: 1. RNA extracted from S. aureus monoculture (SM); 2. RNA extracted from P. aeruginosa monoculture (PM); 3. RNA extracted from S: aureus and P. aeruginosa co-culture (CC)

first: M

last: Tognon

first: T

last: Köhler


title: Comprehensive and comparative analysis of gene expression induced by LPA- and CP-609,550 in normal human epidermal keratinocytes (NHEKs)

city: Kyoto

first: Ratklao

last: Siriwach

address: Sakyo-ku, Shogoin Kawahara-cho

department: Department of Drug Discovery Medicine

institute: Kyoto University Graduate School of Medicine

summary: We screened highly expressed G-protein coupled receptors (GPCRs) in normal human epidermal keratinocytes  (NHEKs). We then tested the effect of ligands of selected GPCRs for their potency to induce the expression of FLG, a crucial skin barrier marker gene, in NHEKs. We used CP-609,550, a JAK inhibitor, as a positive control. As a result, we identified Oleoyl-L-α-lysophosphatidic acid (LPA) as a strong FLG inducer in NHEKs. In addition, we found that LPA induced NHEKs morphological changes characteristics of differentiated keratinocytes. Notably, although CP-609,550 also induced FLG expression in NHEKs, it didn't affect NHEKs cell morphology. We further conducted comprehensive and comparative microarray analysis of gene expression induced by LPA and CP-609,550 in NHEKs. We found that LPA treatment not only induced FLG expression but also expression of several genes related to keratinocytes differentiation, epidermis development and cornified envelope. This was not observed in the CP-609,550-treated cells.

overall_design: Gene expression induced by 10μM Oleoyl-L-α-lysophosphatidic acid or 1μM CP-609,550 in NHEKs were measured at 72h and compared to gene expression in the vehicle control-treated NHEKs. Three independent experiments were performed for each condition.

first: Akiko

last: Sumitomo


title: Expression data for eidididymal fat from high fat diet mice.

status: Public on Nov 06 2018

first: Vandana

last: Sharma

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

summary:
Using a C57BL6/J mouse model of diet-induced obesit,we observed that mannose supplementation of high fat diet (HFD)-fed mice prevents weight gain,lowers adiposity, reduces liver steatosis, and improves glucose tolerance and insulin sensitivity.
We used microarrays to determine the gene expression pattern in epididymal fat frommice weaned on Normal diet (ND), HFD and HFD with mannose (HFDM)

overall_design: Epididymal fat was collected from 3 mice each weaned on ND or HFD or HFDM for RNA isolation.

first: Hudson

last: Freeze


title: Molecular and functional heterogeneity of IL-10-producing CD4+ T cells [Mouse SMART-seq2]

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

institute: Universitätsklinikum Hamburg-Eppendorf

summary: IL-10 is a prototypical anti-inflammatory cytokine, which is fundamental to the maintenance of immune homeostasis, especially in the intestine. There is an assumption that cells producing IL-10 have an immunoregulatory function. However, here we report that IL-10-producing CD4+ T cells are phenotypically and functionally heterogeneous. By combining single cell transcriptome and functional analyses, we identified a subpopulation of IL-10-producing Foxp3Neg CD4+ T cells that displays regulatory activity unlike other IL-10-producing CD4+ T cells, which are unexpectedly pro-inflammatory. The combinatorial expression of co-inhibitory receptors is sufficient to discriminate IL-10-producing CD4+ T cells with regulatory function from others and to identify them across different tissues and disease models in mice and humans. These regulatory IL-10-producing Foxp3Neg CD4+ T cells have a unique transcriptional program, which goes beyond the regulation of IL-10 expression. Finally, we found that patients with Inflammatory Bowel Disease (IBD), demonstrate a deficiency in this specific regulatory T-cell subpopulation.

overall_design: We isolated T-cells from the spleen and small intestine of mice treated with anti-CD3. We sorted the IL-10+ CD4+ T-cells and sequenced them on a single cell level using the SMART-seq2 protocol.

first: Leonie

last: Brockmann

first: Shiwa

last: Soukou

first: Paulo

last: Czarnewski

first: Ergen

last: Can

first: Eduardo

last: Villablanca

first: Nicola

last: Gagliani

first: Samuel

last: Huber


title: Circulating miRNA panels for specific and early detection in bladder cancer

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

institute: Toray industries inc

summary: A serum miRNA combination could be a powerful classifier for the detection of patients with bladder cancer.

overall_design: Serum microRNA profiles of 972 samples, which consist of 392 bladder cancer, 100 non-cancer control, and 480 other types of cancer patients.

first: Wataru

last: Usuba

first: Fumihiko

last: Urabe

first: Yusuke

last: Yamamoto

first: Juntaro

last: Matsuzaki

first: Hideo

last: Sasaki

first: Makiko

last: Ichikawa

first: Yoshiaki

last: Aoki

first: Shumpei

last: Niida

first: Hiromi

last: Sakamoto

first: Ken

last: Kato

first: Shin

last: Egawa

first: Tatsuya

last: Chikaraishi

first: Hiroyuki

last: Fujimoto

first: Takahiro

last: Ochiya


title: Comparative global methylation profile in DMS114 cells before and after acquired resistance to PD173074

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

summary: The development of acquired resistance (AR) to tyrosine kinase inhibitors (TKIs) of FGFR1 activation is currently not well understood. To gain a deeper insight into this matter in lung cancer, we used the FGFR1-amplified DMS114 cell line and generated multiple clones with AR to an FGFR1-TKI. We molecularly scrutinized the resistant cells, using whole-exome sequencing, RNA sequencing and global DNA methylation analysis. Our results show a de novo activation of AKT and ERK, and a reactivation of mTOR. Furthermore, the resistant cells exhibited strong upregulation and activation of MET, indicating crosstalk between the FGFR1 and MET axes. The resistant cells also underwent a global decrease in promoter hypermethylation of the CpG islands. Finally, we observed clonal expansion of a pre-existing change in AKT1, leading to S266L substitution, within the kinase domain of AKT. Our results demonstrate that AR to FGFR1-TKI involves deep molecular changes that promote the activation of MET and AKT, coupled with common gene expression and DNA methylation profiles. The expansion of a substitution at AKT was the only shared genetic change, and this may have contributed to the AR.

overall_design: The lung cancer cell line DMS114, which carries genetic activation of FGFR1, was used as a cancer cell model to investigate acquired resistance to FGFR1 tyrosine kinase inhibitors. We obtained three clones from the DMS114 parental cells that had become refractory to the inhibitor, PD173074 (DMS114-PR1, DMS114-PR3, DMS114-PR4).

first: Pol

last: Gimenez-Xavier

first: Eva

last: Pros

first: Ana

last: Aza

first: Raul

last: Tonda

first: Anna

last: Esteve-Codina

first: Marc

last: Dabad

first: Montse

last: Sanchez-Cespedes


title: Mannose alters gut microbiome, prevents diet induced obesity and improves host metabolism

first: Vandana

last: Sharma

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

overall_design: Refer to individual Series


title: H3K27me3 and CTCF ChIP-seq in reciprocal wild-type and SmcHD1 MommeD1mut MEF cell lines

first: Michal

middle: R.

last: Gdula

overall_design: Set of allele-specific ChIP-seq experiments on female clonal inter-specific (M.m.domesticus FVB x M.m.Castaneus) MEF cell lines: wild-type MEFs, SmcHD1 MomeD1 mut MEFs (SmcHD1 null) and  SmcHD1 CRISPR KO MEFs (derived from wild-type MEFs after establishemnt of X inactivation). Each ChIP library was accompanied with respective input library and each experiment was done in biological replicates (2-4).

first: Tatyana

last: Nesterova

first: Greta

last: Pintacuda

first: Jonathan

last: Godwin

first: Michael

last: McClellan

first: Skirmantas

last: Kriaucionis

first: Felix

last: Krueger

first: Wolf

last: Reik

first: Ye

last: Zhan

first: Hakan

last: Ozadam

first: Job

last: Dekker

first: Catherine

middle: M

last: Green

first: Daniela

last: Moralli

first: Edith

last: Heard

first: Neil

last: Brockdorff


title: 237 HBOC Patients negative for BRCA1/2 mutations

status: Public on Oct 31 2018

city: Hannover

first: Doris

last: Steinemann

address: Carl-Neuberg-Straße 1

department: Human Genetics

institute: Medizinische Hochschule Hannover

summary: NGS-based multiple gene panel resequencing in combination with a high resolution CGH-array was used to identify genetic risk factors for hereditary breast and/or ovarian cancer in 237 high risk patients who were previously tested negative for pathogenic BRCA1/2 variants. All patients were screened for pathogenic variants in 94 different cancer predisposing genes. We identified 32 pathogenic variants in 14 different genes (ATM, BLM, BRCA1, CDH1, CHEK2, FANCG, FANCM, FH, HRAS, PALB2, PMS2, PTEN, RAD51C and NBN) in 30 patients (12.7%). Two pathogenic BRCA1 variants that were previously undetected due to less comprehensive and sensitive methods were found. Five pathogenic variants are novel, three of which occur in genes yet unrelated to hereditary breast and/or ovarian cancer (FANCG, FH and HRAS). In our cohort we discovered a remarkably high frequency of truncating variants in FANCM (2.1%), which has recently been suggested as a susceptibility gene for hereditary breast cancer. Two patients of our cohort carried two different pathogenic variants each and ten other patients in whom a pathogenic variant was confirmed also harbored a variant of unknown significance in a breast and ovarian cancer susceptibility gene. We were able to identify pathogenic variants predisposing for tumor formation in 12.3% of BRCA1/2 negative breast and/or ovarian cancer patients.

overall_design: 237 individual DNA samples (extracted from blood) from 237 different HBOC patients were analyzed

first: Jana

last: van Luttikhuizen


title: Insulin signaling and reduced glucocorticoid receptor activity attenuate post-prandial gene expression in liver

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: C57BL/6J mice were subjected to night restricted feeding (ZT12-ZT24) and livers were isolated immediate before (ZT10) and after feeding (ZT14). Combined RNA-seq, DNase-seq and H3K27Ac ChIP-seq identified hundreds of genes and enhancers regulated by acute feeding. Importantly, this feeding regulated transcriptional program follows similar rhythmic expression patterns as the intrinsic circadian transcriptional programs. ChIP-seq showed that feeding repressed enhancers were occupied by both GR and FOXO1 and occupancy of these factors were suppressed by feeding correlating with increased insulin levels and reduced corticosterone levels. Interestingly, despite considerable genome-wide overlap between GR and FOXO1, injection of dexamethasone (dex) or insulin receptor antagonist (S961) immediately before feeding, demonstrated that the glucocorticoid and insulin receptor pathways control distinct transcriptional programs. And strikingly, only combined dex and S961 treatment reversed feeding induced changes to most of the hepatic transcriptome. These corticosteroid and insulin regulated transcriptional programs are dysregulated in diet-induced obese animals.

overall_design: Hepatic mRNA expression, DNase accessibility and H3K27 acetylation profiles were obtained from mice fed during the night and fasted during the day. Livers were isolated at ZT10, ZT14-fed and ZT14-unfed. In addition, hepatic pre-prandial or post-prandial mRNA expression profiles were obtained from mice with liver specific disruption of Irs1 and Irs2 or mice with liver specific disruption of Nr3c1. Moreover, pre -and post-prandial hepatic mRNA expression, GR occupancy and H3K27 acetylation profiles were obtained from mice injected pre-prandial with dexamethasone and pre -and post-prandial mRNA expression profiles were obtained from mice injected pre-prandial with S961. Lastly, pre -and postprandial mRNA expression profiles were obtained from diet-induced obese mice and lean controls.

first: Adrija

last: Kalvisa

first: Majken

last: Siersbæk


title: DNA methylation profiling of acute chorioamnionitis-associated placentas and fetal membranes : insights into epigenetic variation in spontaneous preterm births

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

summary: Acute chorioamnionitis (aCA) is a commonly reported histologic lesion in at least 40% of spontaneous preterm deliveries. It is typically characterized by an infiltration of maternal neutrophils into the chorioamniotic membranes and is also associated with other placental inflammatory lesions such as acute intervillositis and acute villitis. DNA methylation (DNam) is an easily measurable epigenetic mark, which is more stable than mRNA. While DNAm may influence gene expression in specific cell types, it may also reflect altered cell composition. Studies have previously documented aCA-associated cellular changes primarily in the context of a polymicrobial invasion of the amniotic space. We, thus hypothesize that changes in DNAm associated with aCA will occur predominantly as a consequence of the response to infection, in particular due to alterations in the number of neutrophils and/or other alterations in cell populations inherent to the placenta.  Pooled chorionic villus samples (22 aCA cases, 22 non-aCA cases) and fetal membranes (amnion and chorion) (9 aCA cases, 7 non-aCA cases) were evaluated using the Illumina EPIC array, which quantifies DNAm at >850,000 sites in the genome. We identified 66 differentially methylated sites associated with aCA (FDR <0.15, methylation difference >0.05). At the same thresholds, ~20% chorionic villi sites were also differentially methylated in chorion, but none were observed in amnion. Using publicly available datasets, we identified 2069 neutrophil-specific CpGs by differential methylation analysis. Euclidean clustering of our chorionic villi DNAm data (n=44 samples) using 2069 neutrophil-specific CpG sites largely separated aCA cases from the non-aCA cases, suggesting activation of innate immune responses in aCA-associated placentas.

overall_design: Placental samples from 44 preterm placentas (chorionic villi), and matched chorion and amnion for 16 of these cases were were profiled using theInfinium HumanMethylation850 BeadChip. 4 chorionic villi samples were run in duplicates as technical replicates

first: Chaini

last: Konwar


title: Expression data from graft infiltrating macrophages treated with mTORi-HDL nanobiologics

city: New York

first: Jordi

last: Ochando

state: New York

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary:
Inducing graft acceptance without chronic immunosuppression remains an elusive goal in organ transplantation. Recent data demonstrate that non-self recognition by graft infiltrating macrophages initiates transplant rejection. Using an experimental transplantation mouse model, we isolated graft-infiltrating macrophages from two transplantation settings: untreated rejecting mice and treated with mTORi-HDL nanobiologics.
We used microarrays to detail the global programme of gene expression underlying macrophage dependent organ transplant rejection and identified distinct classes of up-regulated genes during this process, which are down-regulated following tolerogenic treatment with mTORi-HDL nanobiologics.

overall_design: BALB/c donor hearts were transplanted into fully allogeneic C57BL/6 mice. Transplant recipients were either left untreated (Control) and rejected their allografts or were treated with mTORi-HDL nanobiologics (Sample) on days 0, 2, and 5 post-transplantation. Donor heart allografts were isolated on day 6 post-transplantation and graft-infiltrating macrophages were isolated by fluorescence-activated cell sorting (FACS) for microarray analysis.

first: Manisha

last: Brahmachary


title: The Lysosomal Transcription Factor TFEB regulates myelination downstream of the Rag-Ragulator complex.

city: Stanford

first: Harini

last: Iyer

state: California

address: 279 Campus Drive, B300 Beckman Center

department: Developmental Biology

institute: Stanford University

summary: Purpose: To identify genes that are differentially expressed in oligodendrocytes between control and rraga mutant zebrafish, we performed RNA seq using the Illumina platform

overall_design: Oligodendrocytes were isolated from control and rraga mutant zebrafish at 5 days post fertilization using FACS sorting of Cldnk:GFP positive cells. RNA was extracted from these cells and sequenced using standard Illumina protocol.

first: Ana

last: Meireles

first: Kimberle

last: Shen

first: William

middle: S

last: Talbot

first: Lida

last: Zoupi

first: Anna

last: Williams

first: Ellen

last: Bouchard


title: Transcriptome analysis of pathways and drug transporters after hyperosmotic stress of renal MDCK I cells

city: Karise

first: Rune

middle: Nørgaard

last: Rasmussen

address: Vesterled 4

department: Drug transporters in ADME

institute: Southern University of Denmark

summary:
Purpose: To perform pathway analysis of MDCK I treated with hyperosmolality and to investigate how hyperosmolality affects the expression of membrane transporters.
Method: MDCK I cells were treated for 24 h with medium supplemented with 200 mOsm raffinose, NaCl or urea (total of 500 mOsm). The control was regular medium (300 mOsm). RNA was isolated from 12 replicates from each condition and a cDNA library was prepared using TruSeq RNA Library Preparation Kit v2 from Illumina following the manufacturer's protocol. The sequencing was done with a HiSeq with single read and a length of 51. The alignment was done with Hisat 2, the count with FeatureCount and the statistical analysis with DESeq2.
Results: The pathways the cell cycle, the cytokine-cytokine receptor interaction pathway, and the chemokine-signaling pathway were significantly activated in MDCK I cells after treatment of 200 mOsm raffinose or NaCl (total: 500 mOsm), and not 200 mOsm urea, for 24 hours. Several membrane transporters were regulated by hyperosmolality.
Conclusion: Hyperosmolality has an inflammatory-like response in MDCK I cells and it also affects the expression of several membrane transporters.

overall_design: Investigate the expression of membrane transporters in 200 mOsm raffinose, NaCl or urea (total: 500 mOsm) treated MDCK I cells compared to the control (300 mOsm). Performed with 12 replicates per condition.

middle: N

first: Kenneth

last: Christensen

first: René

last: Holm

first: Carsten

middle: U

last: Nielsen


title: The large fraction of heterochromatin in Drosophila neurons is simultaneously bound by B-type lamin and HP1a

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

summary: In most mammalian cell lines, chromatin located at the nuclear periphery is represented by condensed heterochromatin as observed by both microscopy observations and DamID mapping of lamina-associated domains (LADs), enriched in dimethylated Lys9 of histone H3 (H3K9me2). In Drosophila Kc167 cell culture, where LADs were only mapped to the moment, they are neither H3K9me2-enriched, nor overlap with the domains of Heterochromatin Protein 1a (HP1a). Here, using a cell type-specific DamID approach we mapped genome-wide LADs, HP1a and Pc domains from the central brain, Repo-positive glia, Elav-positive neurons and the fat body of Drosophila third instar larvae. Silent or weakly-expressed genes occupy LADs, HP1a and Pc domains, with genes residing in the HP1a-bound LADs expressed at the lowest level. However, a fraction of HP1a domains contain actively expressed genes. The inter-LAD regions that are shared by all cell types are populated by ubiquitously expressed genes, whereas the conserved LADs are less abundant than in mammals. Importantly, in the central brain and in neurons we found strong overlap of HP1a domains with LADs both in the chromosome arms and in pericentromeric regions. In the glia and fat bodies, this overlap was less frequent. Consistent with these results, centromeres appear to reside closer to nuclear lamina in neurons than in Kc167 cells. The discovery of Drosophila peripheral chromatin bound by both HP1a and B-type lamin implies that mechanisms of heterochromatin compaction and attachment to nuclear lamina may be similar in Drosophila and mammals.

overall_design: We determined DamID scores for Polycomb (Pc), Lamin Dm0 (Lam) and Heterochromatin Protein 1a (HP1a) normalized by Dam only control, for Drosophila larval central brain, Repo+ glial cells of larval central brain, Elav+ neurons of larval central brain and larval fat bodies. All samples were performed with 2 biological replicates. In case of Dam only control for larval central brain, each biological replicate was performed with 3 technical replicates.

first: Alexey

last: Pindyurin

first: Artem

middle: A

last: Ilyin

first: Anton

last: Ivankin

first: Mikhail

last: Tselebrovsky

first: Valentina

last: Nenasheva

first: Elena

last: Mikhaleva

first: Ludo

last: Pagie

first: Yuri

middle: Y

last: Shevelyov


title: Infection of RoNi cells with Sendai Cantell virus, MARV371bat virus, and VP35 mutant MARV371bat-R301A virus at MOI of 1.0

city: Frederick

first: Catherine

last: Arnold

state: MD

address: 1425 Porter St

department: Diagnostic Systems Division

institute: US Army Medical Research Institute of Infectious Diseases

summary: Study was performed in order to determine the scope of antiviral response of Rousettus aegyptiacus-derived fibroblasts to Sendai and Marburg virus infection.  This study aids in understanding the function of the expanded immune repertoire of Rosettus aegyptiacus.

overall_design: 3 timepoints, three replicates.  Mock, SeV, MARV, and MARV VP35mut infected samples.  36  total samples.

first: Jonathan

middle: C

last: Guito


title: VEGF related gene expression signatures of breast cancer cells

first: Marina

last: Kiso

address: Sakyoku

institute: Kyoto university

summary: To further development of our gene expression approach, we have employed whole genome microarray expression profiling to identify genes related to VEGF in MDA-MB-231 breast cancer cell line.

overall_design:
Total RNA of MDA-MB-231, VEGF-knocked out MDA-MB-231, recombinant VEGF(rhVEGF) treated VEGF-knocked out MDA-MB-231, soluble NRP1 overexpressed MDA-MB-231 cells were used. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agileng Technologies, Santa Clara, CA).
VEGF was knocked out using CRISPR/Cas9 system. Soluble NRP1 works as VEGF-TRAP. Cell were cultured for 48 hours before RNA extraction. rhVEGF treatment was done for 48 hours.

first: Fumiaki

last: Sato


title: Genome-wide maps of ParBF (SopB) binding on plasmid F or E.coli chromosome carrying parSF

status: Public on Oct 30 2018

city: Toulouse

first: Delphine

last: Labourdette

address: Hall Gilbert Durand - Bio5 - 135 Avenue de Rangueil

department: LISBP

country: France

institute: INSA

summary: We report the genome-wide analysis from chromatin immunoprecipitated DNA (ChIP-sequencing) at very high resolution of the DNA binding pattern of ParBF (SopB) either on the full length plasmid F or on E. coli chromosome carrying the parSF centromere sequence. We also varied the intracellular ParBF concentration to discriminate between the several proposed mechanism of partition complexes assembly.

overall_design: Differencial examination of ParBF binding by comparing input and IP (affinity-purified anti-ParBF antibody) samples

first: Roxanne

middle: E

last: Diaz

first: Jean-Yves

last: Bouet


title: Pancreatic adenocarcinoma cell lines were treated with Agaricus blazei Murrill hot water extract (AbE).

city: Sendai

first: Toru

last: Furukawa

address: 2-1 Seiryomachi, Aobaku

department: Department of Investigative Pathology

institute: Tohoku University Graduate School of Medicine

summary: Pancreatic cancer is one of the most aggressive human malignancies with 7.1% five-year survival rate due to late-stage diagnosis and lack of effective treatment. A novel active compound to be useful for treating pancreatic cancer is absolutely demanded. Agaricus blazei (A. blazei) Murrill has been shown to have an anti-cancer activity, however, its specific efficacy and underlying mechanism is poorly understood. Here, we demonstrated that A. blazei hot water extract (AbE) showed significant growth inhibition of cultured pancreatic cancer cells with less suppressive effect on the normal human pancreatic duct epithelial cells. The pancreatic cancer cells committed G0/G1 cell cycle arrest and caspase-dependent apoptosis. Moreover, we uncovered significant alterations of global gene expression in the pancreatic cancer cells by AbE treatment. Signature of alteration of gene expression indicated that AbE induced repression of genes associated with kinetochore function, spindle formation, centromere maintenance, and cyclins and cyclin dependent kinases, which were essential for cell cycle progression. The gene expression analysis also showed upregulation of proapoptotic genes. These results indicate that AbE could be useful for treatment of pancreatic cancer and a good candidate to isolate potent active compound for development of novel drug for pancreatic cancer.

overall_design: Cells of a human pancreatic adenocarcinoma cell line were seeded at 250,000 cells/10 cm dish with an appropriate growth medium. After 24 hours of the seeding, the growth medium was replaced with the growth medium with 0.045 % Agaricus blazei Murrill hot water extract (AbE) as treated or the growth medium with water in the same volume of AbE as control (mock). Adherent cells were collected after 48 hours of the treatment. Total RNAs were extracted from both control and treated cells using RNeasy midi kit (QIAGEN, Hilden, Germany) according to the supplier’s instructions. cRNAs labelled with Cyanin 3 were synthesized by means of the T7-linear amplification method from 500 ng of the total RNAs employing Low RNA Input Linear Amplification Kit (Agilent Technologies, Palo Alto, CA, U.S.A.) and purified using RNeasy mini kit (QIAGEN). For each hybridization, 1.65 µg cRNAs were fragmented at 60 ºC for 30 minutes using Gene Expression Hybridization Kit (Agilent Technologies) and hybridized at 65 ºC for 17 hours to an 4×44K Whole Human Genome Microarray slide (Agilent Technologies) in accordance with the manufacture’s instructions. Miroarrays were scanned, and signals in the scanned image were converted to intensity values that were subsequently normalized by Hokkaido System Science Co., Ltd. (Sapporo, Japan). Cell lines employed for this study were three human pancreatic cancer cell lines, MIA PaCa-2, PCI-35, and PK-8. The experiment was performed using the three cell lines and independently triplicated in each cell line. Correlation coefficients were referred for quality control, and one of AbE treated PK-8 was excluded because its correlation coefficient to the other replicates was below 0.01.

first: Yoshihisa

last: Matsushita

first: Yoshiyuki

last: Furutani

first: Rumiko

last: Matsuoka


title: Nicotinamide promotes cell survival and differentiation as kinase inhibitor in human pluripotent stem cells

status: Public on Oct 29 2018

city: Macau

first: Ren

last: Zhili

address: Avenida da Universidade

institute: University of Macau

summary: We examined the effect of nicotinamide on cell survival and differentiation in human pluripotent stem cells. Nicotinamide inhibited the phosphorylation of myosin light chain, suppressed actomyosin contraction, and led to improved cell survival after individualization. Then we analyzed the global gene expression profile after 24 hours of nicotinamide and ROCK inhibitor treatment, and found that the gene expression profile of human embryonic stem cell (hESC) treated with nicotinamide was much different from that of ROCK inhibitor treatment. Further analysis demonstrates that nicotinamide is an inhibitor of multiple kinases, including ROCK and CK1. We demonstrated that nicotinamide affected human embryonic stem cell (hESC) pluripotency and differentiation as a selective kinase inhibitor.

overall_design: Total RNA obtained from human embryonic stem cell (hESC) culture in E8 medium (E8 24 hrs), E8 medium with nicotinamide 10 mM treatment  (Nam 24 hrs), or E8 medium with 10 μM ROCK inhibitor Y27632 treatment (ROCKi 24 hrs) for 24 hours. HESCs were treated with BMP4 for 6 days as mesoderm differentiation control (Mesoderm).

first: Guokai

last: Chen


title: A variably imprinted epiallele impacts seed development

city: Cambridge

first: Mary

last: Gehring

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The contribution of epigenetic variation to phenotypic variation is unclear. Imprinted genes, because of their strong association with epigenetic modifications, represent an opportunity for the discovery of such phenomena. In mammals and flowering plants, a subset of genes are expressed from only one parental allele in a process called gene imprinting. Imprinting is associated with differential DNA methylation and chromatin modifications between parental alleles. In flowering plants imprinting occurs in endosperm seed tissue. Proper endosperm development is essential for the production of viable seeds.  We previously showed that in Arabidopsis thaliana intraspecific imprinting variation is correlated with naturally occurring DNA methylation polymorphisms. Here, we investigated the mechanisms and function of allele-specific imprinting of the class IV homeodomain-Leucine zipper (HD-ZIP) transcription factor HDG3. In imprinted strains, HDG3 is expressed primarily from the methylated paternally inherited allele. We manipulated the methylation state of endogenous HDG3 in a non-imprinted strain and demonstrated that methylation of a proximal transposable element is sufficient to promote HDG3 expression and imprinting. Gain of HDG3 imprinting was associated with earlier endosperm cellularization. These results indicate that epigenetic variation alone is sufficient to explain imprinting variation and show that epialleles can underlie variation in seed development phenotypes.

overall_design: Examination of gene expression by mRNA-Seq in Col-0, Col-0 x Cvi and hdg3-1 Col-0 mutant endosperm

first: PRV

last: Satyaki


title: Systematic detection of host pathways universally inhibited by Plasmodium yoelii parasites for immune intervention

city: Bethesda

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

summary: Malaria is a disease with diverse symptoms depending on host immune status and pathogenicity of Plasmodium parasites. The continuous parasite growth within a host suggests mechanisms of immune evasion and/or inhibition. To identify pathways commonly inhibited by malaria infection, we infected C67BL/6 mice with four Plasmodium yoelii strains causing different disease phenotypes and 24 progeny of a genetic cross. mRNAs from mouse spleens day 1 and/or day 4 post infection (p.i.) were hybridized to a mouse microarray to identify activated or inhibited pathways, upstream regulators, and linkages to parasite genetic loci. Strong interferon responses were observed after infection with N67 strain, whereas initial inhibition and later activation of hematopoiesis pathways were found after infection with 17XNL parasite. Inhibition of pathways such as Th1 activation, dendritic cell (DC) maturation, and NFAT immune regulation were observed in mice infected with all the parasite strains day 4 p.i., suggesting universally inhibited immune pathways. Treatment of infected mice with antibodies against T cell receptors OX40 or CD28 to activate malaria-inhibited pathways enhanced host survival. Controlled activation of these pathways may provide important strategies for better disease management and for developing an effective vaccine.

overall_design: Whole spleen RNA from mice infected with malaria parental strains N67, 17XNL, and 24 individual progeny strains from the cross, harvested 24 hrs post infection. Naive mice received uninfected RBCs. RNA was isolated from three independent replicate infections per strain (different mice). In addition, three to four technical replicates (repeat amplification/label/hybridization) were performed on RNA from parental strain infections.

first: Lu

last: Xia

first: Jian

last: Wu

first: Sittiporn

last: Pattaradilokrat

first: Keyla

last: Tumas

first: Xiao

last: He

first: Ruili

last: Huang

first: Carole

last: Long

first: Rongfu

last: Wang

first: Xin-zhuan

last: Su


title: Analysis of gene expression changes induced in adipose tissue by an extract of Artemisia scoparia in high-fat diet-induced obese male mice

city: Baton Rouge

first: Jacqueline

last: Stephens

state: LA

address: 6400 Perkins Road

department: Adipocyte Biology

institute: LSU

summary: Analysis of effects of A scoparia on gene expression in adipose tissue. Current study was designed to examine the whole-body and tissue-specific effects of A scoparia on metabolic parameters in the context of high-fat diet-induced obesity and insulin resistance.

overall_design: Total RNA extracted from adipose tissue of male mice after 4 weeks of feeding with high-fat diet or HFD supplemented with 1% w/w of an A scoparia extract.

first: Anik

last: Boudreau

first: Allison

last: Richard

first: Ruth

last: Dunn

first: Jasmine

last: Burrell

first: Jean-Marc

last: Schwarz

first: David

last: Ribnicky

first: Jennifer

last: Rood

first: Michael

last: Salbaum


title: Transcriptome analysis of total RNA in human osteosarcoma cell line U2OS before and after inhibition of zinc finger protein ZNF768

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

summary: Inhibition of ZNF768 function was achieved by conditional over expression expression of the C-terminal zinc finger of ZNF768 for 12h. For preparation of total RNA cells were resuspended in TRIzol reagent (Life Technologies) at 0.9Mio/ml and snap-frozen.  After thawing RNA was extracted from 0.4ml of TriZol lysate using the direct-zol RNA Miniprep (Zymo Research, Irvine CA, USA) as described in the manufacturer’s protocol. RNA was assessed for purity by UV-vis spectrometry (Nanodrop) and for integrity by Bioanalyzer (Agilent Bioanalyzer 2100, Agilent, Santa Clara USA)). RNA was of high purity (abs. 260/280 >1.9, abs 269/239>2.1) and integrity (Bioanalyzer RIN>9 ) and thus used for further processing. For production of RNA-seq libraries total RNA was DNAse treated (dsDNAse, Fermentas) and 100 ng of this RNA was processed with a strand-specific protocol (RNA-seq complete kit, NuGEN, San Carlos, USA). In brief the RNA was reverse transcribed to cDNA with a reduced set of hexamer primers, avoiding excessive representation of rRNA in the cDNA. Second strand cDNA synthesis was done in presence of dUTP. After ultrasonic fragmentation of the cDNA and end repair, Illumina-compatible adapter were ligated. Adapters contained uracil in one strand, allowing complete digestion of the second-strand derived DNA. After strand selection the libraries were amplified, assessed for correct insert size on the Agilent Bioanalyser and diluted to 10nM. Barcoded libraries were mixed in equimolar amounts and sequenced on an Illumina HiSeq1500 in single-read mode with a read length of 100 b.

first: Michaela

last: Rohrmoser

last: Kluge

first: Yousra

last: Yahia

first: Anita

last: Eber-Gruber

first: Stefan

last: Krebs

first: Helmut

last: Blum

first: Ann

middle: K

last: Greifenberg

first: Matthias

last: Geyer

first: Nicolas

last: Descostes

first: Ahmad

last: Maqbool

first: Jean-Christophe

last: Andrau

first: Dirk

last: Eick


title: Intrinsic dynamics of an endogenous human gene reveal the basis of expression heterogeneity

first: Daniel

last: Larson

state: Maryland

address: 41 Medlars Dr

institute: National Institutes of Health

summary: Transcriptional regulation in metazoans occurs through long range genomic contacts between enhancers and promoters, and most genes are transcribed in episodic ‘bursts’ of RNA synthesis. The relationship between these two phenomena and the dynamic regulation of genes in response to upstream signals is unknown. Here, we describe the use of live-cell RNA imaging coupled with Hi-C measurements to dissect the regulation of the estrogen-responsive TFF1 gene under endogenous regulation. Although this gene is highly induced, we observe short active periods and variable inactive periods ranging from minutes to days. The heterogeneity in inactive times gives rise to the widely-observed ‘noise’ in human gene expression and explains the distribution of protein levels in human tissue. We derive a mathematical model of regulation that relates transcription, chromosome structure, and the cell’s ability to ‘sense’ changes in estrogen and predicts that hypervariability is largely dynamic and does not reflect a stable biological state.

overall_design: We used 3e HiC to look at the estradiol induced entropy changes for ER bound enhancers.

first: Joseph

last: Rodriguez

first: Gang

last: Ren

first: Christopher

last: Day

first: Keji

last: Zhao

first: Carson

last: Chow


title: Hippocampal methylome of rats exposed to lead at different developmental stages

city: Philadelphia

first: Jay

last: Schneider

state: PA

address: 1020 Locust St

department: Anatomy,Pathology and Cell biology

institute: Thomas Jefferson University

summary:
Developmental lead (Pb) exposure results in persistent cognitive/behavioral impairments as well as an elevated risk for developing a variety of diseases in later life. Environmental exposures during development can result in a variety of epigenetic changes, including alterations in DNA methylation, that can influence gene expression patterns and affect the function and development of the nervous system. The present promoter-based methylation microarray profiling study explored the extent to which developmental Pb exposure may modify the methylome of a brain region, hippocampus, known to be sensitive to the effects of Pb exposure. Male and female Long Evans rats were exposed to 0 ppm, 150 ppm, 375 ppm, or 750 ppm Pb through perinatal exposures (gestation through lactation), early postnatal exposures (birth through weaning), or long-term postnatal exposures (birth through postnatal day 55). Results showed a significant contribution of sex to the hippocampal methylome and effects of Pb exposure level, with non-linear dose response effects on methylation. Surprisingly, the developmental period of exposure contributed only a small amount of variance to the overall data and gene ontology (GO) analysis revealed the largest number of overrepresented GO terms in the groups with the lowest level of exposure. The highest number of significant differentially methylated regions was found in females exposed to Pb at the lowest exposure level. Our data reinforce the significant effect that low level Pb exposure may have on gene-specific DNA methylation patterns in brain and that this occurs in a sex-dependent manner.

NimbleGen Rat CpG Island plus RefSeq Promoter 720k array

overall_design: Male and female Long-Evans rats were used for different Pb exposure paradigms: perinatal (PERI), early postnatal (EPN), and long-term postnatal (LPN) exposures. Controls (no lead exposure) were also included and all the comparisons were made to control group.


title: Transcriptome analysis of total RNA in the Raji B cell line

first: Caroline

last: Friedel

summary: RNA-seq was performed for total RNA in the Raji B cell line

overall_design: Four biological replicates of total RNA in the Raji B cells were subjected to RNA-seq

first: Michaela

last: Rohrmoser

first: Michael

last: Kluge

first: Yousra

last: Yahia


title: Four SWI2/SNF2 chromatin remodeling proteins play roles as “double agents” in the tug of war between RNA-directed DNA methylation and active DNA demethylation in Arabidopsis [small RNA]

city: Nanjing

first: Dong-Lei

last: Yang

state: Jiangsu Province

address: Weigang 1

department: Agriculture College

institute: Nanjing Agricultural University

summary: Here we report that CLSY4 and its three paralogous SWI2/SNF2-type chromatin remodeling proteins function in both RdDM and active DNA demethylation for dynamic regulation of DNA methylation in Arabidopsis. We identified CLSY4 initially in a genetic screen for DNA demethylation factors and subsequently demonstrated that it also plays an important role in RdDM. Comprehensive genetic analyses using single and high order mutants of CLSY family proteins revealed their roles as double agents in the tug of war between methylation and demethylation reactions. The four CLSY proteins collectively are necessary for the canonical RdDM pathway; meanwhile, each CLSY also mediates active DNA demethylation at specific loci where DNA methylation is dependent on one or more of the other three CLSY proteins. Our results revealed dual functions of the four chromatin remodeling proteins in regulating genomic DNA methylation status, and thus provide new insights into the mechanisms underlying the dynamic regulation of DNA methylation in Arabidopsis.

overall_design: small RNA sequencing data of clsy1234 and WT

first: Jian-Kang

last: Zhu


title: Four SWI2/SNF2 chromatin remodeling proteins play roles as “double agents” in the tug of war between RNA-directed DNA methylation and active DNA demethylation in Arabidopsis [Bisulfite-seq]

overall_design: whole genome wide DNA methylation data by bisulphite sequencing


title: miRNA profiles of exosomes secreted by head and neck cancer-associated fibroblasts and the paired normal fibroblasts

status: Public on Oct 27 2018

city: Shanghai

first: xing

last: qin

state: Shanghai

address: Zhizaoju load 639

institute: Shanghai Jiaotong University

summary:
Exosomal miRNAs secreted by cancer-associated fibroblasts (CAFs) play a critical role in facilitating head and neck cancer (HNC) progression. A few studies in other cancers have confirmed some CAF-specific miRNAs could be delivered to tumor cells via exosome, thus contributing to chemoresistance.
To identify the specific miRNAs responsible for the capability of CAF-derived exosomes to promote cisplatin resistance in recipient HNC cells, a miRNA array was conducted to identify miRNAs involved in exosomes derived from CAFs and the paired normal fibroblasts (NFs).

overall_design: NFs (n=3) or CAFs (n=3) were incubated with serum-free DMEM for 48 h and the conditioned medium (CM) was collected and put together. The CM was filtered through a 0.22 μm PVDF filter and exosomes were isolated from NF- or CAF-CM by ultracentrifugation. Then, the NF- and CAF-derived exosomes were sent for miRNA array analysis.

first: Jianjun

last: Zhang

first: Wantao

last: Chen

first: Xing

last: Qin

first: Ming

last: Yan


title: Trisomy-TAC-seq II

city: Tartu

first: Hindrek

last: Teder

address: Tiigi 61b

country: Estonia

institute: The Competence Centre on Health Technologies

summary: TAC-seq experiment to detect in vitro fetal trisomy at different range of fetal fraction. Fetal fraction ranges are 0%, 10%,  20% and 100%.

overall_design: 12 samples, 4 sample types, 3 replicas per sample type.

first: Kaarel

last: Krjutskov

first: Tatjana

last: Jatsenko

first: Kadri

last: Rekker


title: Single-cell transcriptome profiling of the Ciona larval brain

status: Public on Oct 26 2018

city: Atlanta

first: Alberto

last: Stolfi

state: Georgia

address: 950 Atlantic Dr

department: School of Biological Sciences

country: USA

institute: Georgia Institute of Technology

summary: The tadpole-type larva of Ciona has emerged as an intriguing model system for the study of neurodevelopment. The Ciona intestinalis connectome has been recently mapped, revealing the smallest central nervous system (CNS) known in any chordate, with only 177 neurons. This minimal CNS is highly reminiscent of larger CNS of vertebrates, sharing many conserved developmental processes, anatomical compartments, neuron subtypes, and even specific neural circuits. Thus, the Ciona tadpole offers a unique opportunity to understand the development and wiring of a chordate CNS at single-cell resolution. Here we report the use of single-cell RNAseq to profile the transcriptomes of single cells isolated by fluorescence-activated cell sorting (FACS) from the whole brain of Ciona robusta (formerly intestinalis Type A) larvae. We have also compared these profiles to bulk RNAseq data from specific subsets of brain cells isolated by FACS using cell type-specific reporter plasmid expression. Taken together, these datasets have begun to reveal the compartment- and cell-specific gene expression patterns that define the organization of the Ciona larval brain.

overall_design: Single-cell RNAseq to profile the transcriptomes of single cells isolated by fluorescence-activated cell sorting (FACS) from the whole brain of Ciona robusta (formerly intestinalis Type A) larvae. Bulk RNAseq data from specific subsets of brain cells isolated by FACS using cell type-specific reporter plasmid expression.

first: Sarthak

last: Sharma

first: Wei

last: Wang


title: Four SWI2/SNF2 chromatin remodeling proteins play roles as "double agents" in the tug of war between RNA-directed DNA methylation and active DNA demethylation in Arabidopsis

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

overall_design: Refer to individual Series


title: Analysis if IGF1-mediated cardioprotection after acute myocardial infarction in C57BL6/J mice

city: Düsseldorf

first: Axel

last: Gödecke

address: Moorenstrasse 5

department: Cardiovascular Physiology

institute: Heinrich-Heine-Universität - UKD

summary: In order to identify potential mechanisms involved in cardioprotection by IGF1 we performed microarray analysis of the infarcted areas on day1, day2, and day7 after acute myocardial infarction.

overall_design: Myocardial infarction was induced in C57BL6/J mice by 45 min occlusion of the left anterior descending coronary artery followed by reperfusion for 24, 48,  and 168 h, respectively. Animals of the IGF1 groups received 40 ng/g mature recombinant IGF1 subcutaneously as bolus at the begin of reperfusion. In addition, IGF1 was administered continuously for the first three days of reperfusion (1 µg/g/d) using micro-osmotic pumps (Alzet, 1003D) that were implanted subcutaneously. Control mice were sham-operated and received osmotic minipumps containing only vehicle.

first: Andre

last: Heinen

first: Rianne

last: Nederlof

last: Spychala

first: Patrick

last: Petzsch

first: Karl

last: Köhrer


title: FAM210B is an erythropoietin target and regulates erythroid heme synthesis by controlling mitochondrial iron import and ferrochelatase activity

city: Kowloon Tong

first: Jiahai

last: Shi

state: Kowloon

address: Department of Biomedical Sciences, 1F, Block 1, To, 1F, Block 1, To Yu, 1F, Block 1, To Yuen Building

institute: City University of Hong Kong

summary: To understand the downstream  pathways of the Epo signaling, we have emplyed microarray gene expression profiling to discover the gene expression changes in 32D cells upon the Epo stimulation.

overall_design: 32D-EpoR cells are cultured in the presence and absence of Epo. Two independent experiments were performed using cells from different passages.


title: Hippocampus of SAMR1 and SAMP8 mice [mRNA]

city: Barcelona

first: Christian

middle: Griñán

last: Ferré

address: Joan XIII, s/n

department: Pharmacology, Toxicology and Therapeutic Chemistry

institute: University of Barcelona

summary:
A growing body of research shows that epigenetic mechanisms are critically involved in normal and pathological aging. The Senescence-Accelerated Mouse Prone 8 (SAMP8) can be considered an useful tool to better understand the dynamics of the global epigenetic landscape during the aging process since its phenotype is not fully explained by genetic factors.
Here we investigated dysfunctional age-related transcriptional profiles and epigenetic programming enzymes in the hippocampus of 2- and 9-month-old SAMP8 female mice using the Senescent-Accelerated Resistant 1 (SAMR1) mouse strain as control.
SAMP8 mice presented 1,062 genes dysregulated at 2 months of age, and 1,033 genes at 9 months, with 92 genes concurrently dysregulated at both ages in reference to age mated SAMR1. SAMP8 mice showed a significant decrease in global DNA methylation (5-mC) at 2 months while hydroxymethylation (5-hmC) levels were increased in SAMP8 mice at 2 and 9 months of age compared to SAMR1. These changes were accompanied by changes in the expression of several enzymes that regulate 5-mC and methylcytosine oxidation. Acetylated H3 and H4 histone levels were significantly diminished in SAMP8 mice at 2-month-old compared to SAMR1 and altered Histone DeACetylase (HDACs) profiles were detected in both young and old SAMP8 mice. We analyzed 84 different mouse miRNAs known to be altered in neurological diseases or involved in neuronal development. Compared with SAMR1, SAMP8 mice showed 28 and 17 miRNAs differentially expressed at 2 and 9 months of age, respectively, 6 of these miRNAs overlapped at both ages. We used several bioinformatic approaches to integrate our data in mRNA:miRNA regulatory networks and functional predictions for young and aged animals.
In sum, our study reveals interplay between epigenetic mechanisms and gene networks that seems to be relevant for the progression towards a pathological aging and provides several potential markers and therapeutic candidates for Alzheimer’s Disease (AD) and age-related cognitive impairment.

overall_design: mRNA expression profiling of SAMR1 vs SAMP8 hippocampus samples at 2 and 9 months of age

first: Celia

last: González-Castillo

first: Daniel

last: Ortuño-Sahagún


title: LncRNA and mRNA expression patterns in bladder cancer patients with lymph nodes metastasis.

status: Public on Oct 25 2018

city: Changsha

first: Jinbo

last: Chen

state: Hunan

address: No.87 Xiangya Rd

department: Urology

institute: Xiangya Hospital

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

summary: Bladder cancer (BCa) is one of the most common cancers in urinary system worldwide.  And lymphatic metastasis is one of the most common route and its status associates with prognosis for BCa patients. However, the precise molecular mechanisms of BCa metastasis and progression remain poorly understood. Recent studies have shown that long non-coding (lncRNA) plays critical roles in a myriad of biological processes and human diseases. The roles of lncRNA in BCa lymph nodes metastasis remain unknown. In the current study, we revealed thousands of differentially expressed lncRNAs in BCa primary tumor tissues vs. metastatic lymph nodes. We may provide novel insight into the molecular mechanism underlying the disease and potential novel diagnostic or therapeutic targets for BCa.

overall_design: Microarray expression profiling of mRNAs and lncRNAs were conducted using RNA extracted from 3 bladder cancer metastatic lymph node samples and 3 primary tumor samples.

first: Yewen

last: Zhu

first: Yu

last: Cui

first: Chao

last: Li

first: Peihua

last: Liu

first: Huihuang

first: Xiongbing

last: Zu


title: Whole-transcriptome profiling of neovascularized corneas reveal miR-204 as a potent biotherapy deliverable by rAAVs [nCounter - microRNAs]

city: Worcester

first: Guangping

last: Gao

state: Massachusetts

address: Albert Sherman Center (AS6-2011)

department: Gene Therapy Center

institute: University of Massachusetts, Medial School

summary: Current drugs that directly target pro-angiogenic factors to inhibit or reverse corneal neovascularization, the major sight-threatening pathology caused by angiogenic stimuli, require multiple rounds of administration and have limited efficacies. Here we report the profiling of anti-angiogenic corneal microRNAs (miRNAs), and a framework that employs discovered miRNAs as biotherapies deliverable by recombinant adeno-associated viruses (rAAVs). By querying differentially expressed miRNAs in neovascularized mouse corneas induced by alkali-burn, we have revealed 39 miRNAs that are predicted to target more than 5,500 differentially expressed corneal mRNAs. Among these corneal miRNAs, we selected miR-204 and assessed its efficacy as a therapeutic miRNA in injured corneas. Our results show that delivery of miR-204 by rAAV is efficacious and safe for mitigating corneal NV. Overall, our work demonstrates the discovery of therapeutic miRNAs in corneal disorders and their translation into viable clinical vectors.

overall_design: Profiling of microRNAs in normal mouse corneas and corneas injured by alkali burn treatment.

first: Yi

last: Lu

first: Phillip

middle: W

last: Tai

first: Jianzhong

last: Ai

first: Dominic

last: Gessler

first: Qin

last: Su

first: Qiang

last: Zheng

middle: D

last: Zamore

first: Xun

last: Xu


title: Temporal integrative analysis of mRNA and microRNAs expression profiles and epigenetic alterations in female SAMP8, a model of age-related cognitive decline

first: Christian

last: Ferré

type:
Expression profiling by array
Expression profiling by RT-PCR


title: IL-12 and IL-23 dependent gene induction in purified CD19+, CD8+, CD4+, gdTCR+ and CD56+ cells

city: New York

first: Yelena

last: Nemirovskaya

address: 1230 York Avenue

institute: Rockefeller University

summary: The aim of this experiment was to study IL-12 and IL-23 dependent gene induction in different immune cell types in order to assess where these two pathways converge and diverge

overall_design: CD19+, CD8+, CD4+, gdTCR+ and CD56+ cells were purified by MACS or sorting and stimulated with IL-12 (20ng/ml) or IL-23 (100ng/ml)

first: Jean-Laurent

last: Casanova

first: Ruben

last: Martinez-Barricarte

first: Janet

last: Markle


title: Methylation profile of ewing sarcoma cell lines

status: Public on Oct 24 2018

city: Seville

first: Ana

middle: Monteiro

last: Amaral

address: avenida manuel siurot s/n

department: Molecular pathology of sarcomas

institute: Institute of Biomedicine of Seville

summary: Study of promoter methylation of ewing sarcoma cell lines and mesenchymal stem cell from ewing sarcoma patients and healthy donors

overall_design: Genomic DNAs were extracted from 24 2D cultures, after bisulfite treatment, genomic DNAs were hybridized in Illumina Human Methylation 27 bead chip

first: Enrique

last: de Álava


title: A mechanistic classification of clinical phenotypes in neuroblastoma (telomere maintenance cohort)

city: Cologne

first: Matthias

last: Fischer

address: Kerpener Str. 62

department: Department of Experimental Pediatric Oncology

institute: University Children’s Hospital of Cologne

summary: Our study proposes a precise mechanistic classification of clinical neuroblastoma phenotypes that is based on telomere maintenance mechanisms and RAS or p53 pathway mutations. A crucial factor in telomere maintenance is overexpression of TERT. We therefore determined a TERT expression threshold to identify MYCN-WT TERT-WT tumors whose TERT mRNA levels are comparable to those of tumors bearing MYCN or TERT alterations.

overall_design: Single-color gene expression profiles from 208 neuroblastoma tumors were generated using 44K oligonucleotide microarrays. Stages were classified according to the International Neuroblastoma Staging System.

first: Christoph

last: Bartenhagen


title: A mechanistic classification of clinical phenotypes in neuroblastoma