title: Transcriptome assembly and gene expression profiling of Olympia oysters (Ostrea lurida) during low salinity exposure

status: Public on Apr 28 2018

city: Hayward

first: Tyler

last: Evans

state: California

address: 25800 Carlos Bee Blvd

department: Biological Sciences

institute: California State University East Bay

summary: Illumina RNA sequencing to assmeble a transcriptome for the oyster Ostrea lurida and identify genes signficantly differentially expressed among three populations of oysters that differ in their tolerance of low salinity. Our new transcripmotme provides an important genomic resource for future work in this species of conservation concern. Genes differentially expressed between oyster populations provide insight into mechanisms underlying different low salinity tolerances.

overall_design: Oysters from three populations (each with six repliicates) were exposed to control (34 parts per thousand) and low salinity (5 part per thousand) treatment (total n=36). A cDNA library was created for each sample and sequenced using the Illumina HiSeq 4000 platform. Twelve individual samples were multiplexed into one paired-end 150bp lane


title: RNA-Seq analysis of prostate cancer cell line C4-2 treated with siRNA control (siCont), siEAF2, sip53 or concurrent siEAF2 and sip53

status: Public on Apr 25 2018

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

country: USA

institute: University of Pittsburgh

type: Expression profiling by high throughput sequencing

summary: The tumor suppressor genes EAF2 and p53 are frequently dysregulated in prostate cancers. Recently, we reported that concurrent p53 nuclear staining and EAF2 downregulation were associated with high Gleason score. Combined loss of EAF2 and p53 in a murine model induced prostate tumors, and concurrent knockdown of EAF2 and p53 in prostate cancer cells enhanced proliferation and migration, further suggesting that EAF2 and p53 could functionally interact in the suppression of prostate tumorigenesis. Here, RNA-seq analyses identified differentially regulated genes in response to concurrent knockdown of p53 and EAF2. Several of these genes were associated with the STAT3 signaling pathway, and this was verified by significantly increased p-STAT3 immunostaining in the Eaf2-/-p53-/- mouse prostate. STAT3 knockdown abrogated the stimulation of C4-2 cell proliferation by concurrent knockdown of EAF2 and p53. Furthermore, immunostaining of p-STAT3 was increased in human prostate cancer specimens with EAF2 downregulation and/or p53 nuclear staining. Our findings suggest that simultaneous inactivation of EAF2 and p53 can act to activate STAT3 and drive prostate tumorigenesis.

overall_design: C4-2 prostate cancer cells treated with siEAF2 and/or sip53 mRNA profiles were generated by deep sequencing, using Illumina HiSeq 2000.

middle: R

first: Anish

middle: B

last: Chakka

first: Sri

last: Chaparala

first: Laura

middle: E

last: Pascal


title: RNA editing in nascent RNA affects pre-mRNA splicing

city: Los Angeles

first: Xinshu

last: Xiao

address: 610 Charles E. Young Drive S, Terasaki Life Sciences Building, Room 2000B

institute: University of California Los Angeles

summary: In eukaryotes, nascent RNA transcripts undergo an intricate series of RNA processing steps to achieve mRNA maturation. RNA editing and alternative splicing are two major RNA processing steps that can introduce significant modifications to the final gene products. By tackling these processes in isolation, recent studies have enabled substantial progress in understanding their global RNA targets and regulatory pathways. However, the interplay between individual steps of RNA processing, an essential aspect of gene regulation, remains poorly understood. By sequencing the RNA of different subcellular fractions, we examined the timing of adenosine-to-inosine (A-to-I) RNA editing and its impact on alternative splicing. We observed that > 90% A-to-I RNA editing events occurred in the chromatin-associated RNA prior to polyadenylation. We report about 500 editing sites in the 3’ acceptor sequences that can alter splicing of the associated exons. Interestingly, these exons are highly conserved during evolution and reside in genes with important cellular function. Furthermore, we identified a second class of exons whose splicing is likely modulated by RNA secondary structures that are recognized by the RNA editing machinery. The genome-wide analyses, supported by experimental validations, revealed remarkable interplay between RNA editing and splicing and expanded the repertoire of functional RNA editing sites.

overall_design: Subcellular fractionation RNA sequencing libraries were generated in triplicates from U87MG cells.

first: Yun-Hua

last: Hsiao


title: Metabolic and Transcriptional Alterations in the Early Stages of Cardiac Fuel Switch Hint at Novel mTOR-mediated Regulation of Hypertrophy

status: Public on Apr 27 2018

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

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

overall_design: Refer to individual Series

first: Cam

last: Patterson

first: Rosalind

middle: A

last: Coleman


title: Topological demarcation by HMGB2 is disrupted early upon senescence entry and induces CTCF clustering across cell types [HiChIP]

city: Koeln

first: Milos

last: Nikolic

state: Nordrhein-Westfalen

address: Robert Koch Str. 21

country: Germany

institute: Center for Molecular Medicine Cologne

summary: We hypothesized that entry into senescence of different primary human cells can be triggered by one early molecular event affecting the spatial organization of chromosomes. To test this, we combined whole-genome chromosome conformation capture, population and single-cell transcriptomics, super-resolution imaging, and functional analyses applied on proliferating and replicatively-senescent populations from three distinct human cell types. We found a number of genes involved in DNA conformation maintenance being suppressed upon senescence across cell types. Of these, the abundant high mobility group (HMG) B1 and B2 nuclear factors are quantitatively removed from cell nuclei before typical senescence markers appear, and mark a subset of topologically-associating domain (TAD) boundaries. Their loss coincides with obvious reorganization of chromatin interactions via the dramatic spatial clustering of CTCF foci. HMGB2 knock-down recapitulates this senescence-induced CTCF clustering, while also affecting insulation at TAD boundaries.

overall_design: HiChIP was generated in IMR90 and HUVEC using HindIII restriction digestion.

first: Papantonis

last: Argyris

first: Nikolic

last: Milos

first: Zirkel

last: Anne


title: Fosl1 transdifferentiate embryonic stem cells to differentiated trophoblast stem cells

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway NMS 4.246

department: Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology

institute: University of Texas at Austin

type: Genome binding/occupancy profiling by high throughput sequencing


title: Topological demarcation by HMGB2 is disrupted early upon senescence entry and induces CTCF clustering across cell types [DROP-seq]

summary: Ageing-relevant processes, like cellular senescence, are characterized by complex, often stochastic, effects giving rise to heterogeneous cell populations. We hypothesized that entry into senescence by different primary human cells can be triggered by one early molecular event affecting the spatial organization of chromosomes. To test this, we combined whole-genome chromosome conformation capture, population and single-cell transcriptomics, super-resolution imaging, and functional analyses applied on proliferating and replicatively-senescent populations from three distinct human cell types. We found a number of genes involved in DNA conformation maintenance being suppressed upon senescence across cell types. Of these, the abundant HMGB1 and HMGB2 nuclear factors are quantitatively removed from cell nuclei before typical senescence markers appear, and mark a subset of topologically-associating domain (TAD) boundaries. Their loss coincides with obvious reorganization of chromatin interactions via the dramatic spatial clustering of CTCF foci. HMGB2 knock-down recapitulates this senescence-induced CTCF clustering, while also affecting insulation at TAD boundaries. We accordingly propose that HMGB-mediated deregulation of chromosome conformation constitutes a primer for the ensuing senescent program across cell types.

overall_design: HUVEC cells at passage 4 and passage 16 were subjected to single-cell RNA DROP-seq.

first: Anne

last: Zirkel

first: Konstantinos

last: Sofiadis

first: Jan-Philipp

last: Mallm

first: Christian

last: Becker

first: Janine

last: Altmüller

first: Julia

last: Franzen

first: Mirjam

last: Kokker

first: Eduardo

middle: G

last: Gusmao

first: Ivan

last: Costa

first: Roland

first: Wolfgang

last: Wagner

first: Peter

last: Nürnberg

first: Karsten

last: Rippe

first: Argyris

last: Papantonis


title: Viral challenge as a potential driver of histone loss in dinoflagellates

city: Vancouver

first: Nicholas

last: Irwin

state: British Columbia

address: 2350 Health Sciences Mall

department: Biochemistry

country: Canada

institute: University of British Columbia

summary: Within canonical eukaryotic nuclei, DNA is bound to highly conserved histone protein octamers, together termed nucleosomes, which facilitate DNA condensation and contribute to genomic regulation. The dinoflagellates, a group of unicellular algae, are a striking exception to this otherwise universal feature and have abandoned histones as their primary DNA packaging proteins. Phylogenetic analyses suggest that histone loss coincides with genome enlargement and the emergence of liquid crystalline chromosomes, the predominant constituent of which appears to be apparently viral-derived proteins termed dinoflagellate-viral-nucleoproteins (DVNPs) . However, the evolutionary mechanisms that drove dinoflagellate chromatin divergence, especially histone depletion, remain unknown.  Here, using Saccharomyces cerevisiae as a heterologous model, we show that DVNP antagonizes eukaryotic chromatin and has a toxicity that can be attenuated through histone depletion. Using a combination of ChIP-seq and MNase-seq we demonstrate that DVNP localizes specifically to histone binding sites, displaces histones, and coincides with global transcriptional disruption.

overall_design: Sonication based DVNP ChIP seq in wildtype yeast expressing DVNP-3HA-NLS in triplicate (both ChIPs and inputs). Sonication based Rpb3 (RNAP II) ChIP-seq and Mnase-seq in control and DVNP-3HA-NLS expressing cells done in duplicate.

first: Benjamin

last: Martin

first: LeAnn

middle: J

last: Howe


title: Fosl1 transdifferentiate embryonic stem cells to differentiated trophoblast stem cells. (ChIP-seq)

first: Jonghwan

last: Kim

summary: During mammalian embryonic development, the first lineage commitment event gives rise to two distinct cell populations: the trophectoderm (TE) and the inner cell mass (ICM). The TE consists of outer cells of the blastocyst and ultimately forms the placenta while the ICM gives rise to all the embryonic tissues. Numerous transcription factors (TFs) guiding ICM differentiation into different embryonic tissues have been characterized. However, only a few TFs that are required for TE specification and differentiation have been identified, and much less is understood as to how these TFs interact with other TFs or with their chromosomal targets in order to drive cell fate towards TE lineage. Understanding trophectoderm development is crucial because cells in this lineage are required for proper embryo implantation in the uterus. Defects in this lineage can cause early failure of pregnancy as well as other pregnancy related disorders such as preeclampsia and intrauterine growth restriction (IUGR). Here, we characterize the function of one of TE-specific TF, Fosl1, which was previously suggested as having some role in placental development. We utilized mouse embryonic stem (ES) cells (derived from ICM) and showed that ectopic expression of Fosl1 can transdifferentiate ES cells to differentiated TS cells (trophoblast giant-like cells). We show that Fosl1 does so by directly binding and activating TE specific genes and genes associated with epithelial-mesenchymal transition (EMT). Using mouse trophoblast stem (TS) cells, we also establish that Fosl1 is required for specification of TS cells to trophoblast giant cells (TGCs) subtype. Therefore, we postulate that Fosl1 is a key regulator of TS cell differentiation.

overall_design: ChIP assays were performed using BirA-expressing ES cell lines- expressing BirA only or BirA and biotin-tagged Fosl1 as previously described (Kim et al. 2009) using streptavidin magnetic particles.

first: Kim

last: Jonghwan


title: Topological demarcation by HMGB2 is disrupted early upon senescence entry and induces CTCF clustering across cell types [ChIP-Seq]

first: Milos

last: Nikolic

overall_design: Genome-wide binding profiles for the non-histone DNA-binding proteins HMGB1 and HMGB2 were investigated in HUVEC and IMR90

first: Anne

last: Zirkel


title: Loss of Dnmt3a Immortalizes Hematopoietic Stem Cells in vivo

city: Houston

first: Hyun Jung

last: Park

address: One Baylor Plaza

department: Dan L. Duncan Cancer Center

institute: Baylor College of Medicine

type: Methylation profiling by high throughput sequencing


title: Loss of Dnmt3a Immortalizes Hematopoietic Stem Cells in vivo [WGBS]

summary: Recent epidemiological studies have shown that cancer-associated DNMT3A mutations can be detected in the blood of a large proportion of asymptotic elderly individuals. It is important to understand how these mutations provide a competitive advantage to HSCs and allow them to establish clonal dominance. Here we demonstrate that the stress of serial HSC transplantation immortalizes Dnmt3a-null HSCs.

overall_design: Dnmt3a-null system cells transplanted multiple times in mice were sequenced for RNA-Seq, ChIP-Seq, and methylation using Illumina Nextseq

first: Hyun

first: Mira

last: Jeong

first: Margaret

last: Goodell

first: Grant

last: Challen


title: Loss of Dnmt3a Immortalizes Hematopoietic Stem Cells in vivo [RNA-Seq]

overall_design: Dnmt3a-null system cells transplanted multiple times in mice were sequenced for RNA-Seq, ChIP-Seq, and methylation using Illumina Hiseq 2000


title: RNA-seq profiling of the Tg(myo6b:GFP-2A-rpl10a-3xHA) zebrafish hair cell IP vs. whole fish IN

status: Public on Apr 24 2018

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

summary: We have developed and tested the efficiency of the Tg(myo6b:GFP-2A-rpl10a-3xHA) zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells (IP) compared to the whole fish transcriptome (IN).  We show through RNA-seq that HA-tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts.

overall_design: Tg(myo6b:GFP-2A-rpl10a-3xHA) were homogenized at 5dpf and the hair cell translatome was enriched for by HA-tagged ribosome immunoprecipitation, followed by RNA extraction. IP samples were compared to input RNA controls (IN) in independent biological triplicates.

first: Maggie

last: Matern

first: Katie

middle: S

last: Kindt

first: Ronna

last: Hertzano


title: Topological demarcation by HMGB2 is disrupted early upon senescence entry and induces CTCF clustering across cell types


title: NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence [ATAC-Seq]

city: London

first: Shamith

last: Samarajiwa

address: ICTEM Building, Hammersmith Campus, Du Cane Road,

department: Genetics and Genomics Section  Department of Metabolism, Digestion and Reproduction

country: United Kingdom

institute: Imperial College London

summary: We describe the accessible chormatin landscape in RAS-induced (RIS) and NOTCH induced senescence (NIS) using ATAC-seq. By expressing active NOTCH (N1ICD) in the context of RIS, we find that N1ICD antagonizes the formation of accessible regions in RIS. By performing co-cultures, we demonstrate that cells expressing a NOTCH1 ligand, JAGGED1, can antagonize the formation of RIS specific accessible regions.

overall_design: Interrogation of accessible regions in RIS and NIS cells using ATAC-seq in IMR90 cells expressing ER:HRAS(G12V) and infected with a control (pWZL) vector or pWZL FLAG-N1ICD, and treated with 100nM 4OHT for 6 days or untreated.  In co-culture experiments, IMR90 cells expressing ER:HRAS(G12V) and mRFP1 are cultured at a ratio of 1:1 with tumour cell lines for 6 days with 4OHT before isolating red (IMR90 cells) using flow cytometry to perform ATAC-seq. To determine the effect of HMGA1 depletion on the distribution of nucleosome free regions in RIS cells, IMR90 cells expressing ER:HRAS(G12V) were retrovirally infected with a short hairpin targetting HMGA1 (shHMGA1) and treated for 6 days with 4OHT before ATAC-seq.

first: Aled

last: Parry

first: Dóra

last: Bihary

first: Masashi

last: Narita


title: Loss of Dnmt3a Immortalizes Hematopoietic Stem Cells in vivo [ChIP-Seq]


title: NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence [ChIP-Seq]

summary: We describe the accessible chormatin landscape in RAS-induced (RIS) and NOTCH induced senescence (NIS) using ATAC-seq. By expressing active NOTCH (N1ICD) in the context of RIS, we find that N1ICD antagonizes the formation of accessible regions in RIS. By performing co-cultures, we demonstrate that cells expressing a NOTCH1 ligand, JAGGED1, can antagonize the formation of RIS specific accessible regions. Many of these accessible regions form at enhancers, characterised using ChIP-seq against H3K4me1 and H3K27Ac

overall_design: Mapping of H3K4me1 and H3K27Ac using ChIP-Seq in IMR90 ER:HRAS(G12V) cells treated with 4OHT for 6 days or untreated


title: Differential expression of genes in Fezf2KO mouse retina and control retina

city: Minato-ku, Tokyo

first: Sumiko

last: Watanabe

address: 4-6-1 Shirokane-dai

department: Institute of Medical Science

country: Japan

institute: University of Tokyo

summary: To analyze roles of transcription factor Fezf2 in retinal development, knockout mouse of Fezf2 was generated, and gene expression pattern of Fezf2-KO retina and control retina was examined by RNA-seq.

first: Haruna

last: Suzuki-Kerr


title: NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence


title: Metabolic and Transcriptional Alterations in the Early Stages of Cardiac Fuel Switch Hint at Novel mTOR-mediated Regulation of Hypertrophy [Agilent Expression]

first: Jonathan

last: Schisler

summary:
1. Background- Long-chain acyl-CoA synthetases (ACSL) catalyze the conversion of long-chain fatty acids (FA) to fatty acyl-CoAs.  Cardiac-specific ACSL1 knockout results in a shift towards glycolysis that promotes mTORC1-mediated ventricular hypertrophy.  We used unbiased metabolomics and gene expression analyses to examine the early effects of genetic inactivation of FA oxidation on cardiac metabolism and function.
2. Methods and Results- Compared to WT hearts, global cardiac transcriptional analysis revealed differential expression of 245 genes in Acsl1H-/- hearts 2 weeks after Acsl1 ablation.  Comparison of the 2- and 10-week transcriptional responses uncovered 139 genes whose expression was uniquely changed upon short-term cardiac inactivation of ACSL1.  In particular, partial ACSL1 ablation led to the distinct upregulation of fibrosis genes, a phenomenon not observed after complete ACSL1 knockout.  Metabolomic analysis identified 65 metabolites altered in hearts displaying partially reduced ACSL activity, whereas rapamycin treatment normalized the cardiac metabolomic fingerprint.  Chronic mTOR inhibition via rapamycin treatment revealed novel mTORC1 targets involved in fibrosis, amino acid catabolism, and mitochondrial transport and metabolism.
3. Conclusions- Short-term cardiac-specific ACSL1 inactivation (Acsl1H-/-) resulted in metabolic and transcriptional derangements distinct from those observed upon complete ACSL1 knockout, leading to the identification of novel mTORC1 targets that regulate cardiac hypertrophy development, and suggesting heart-specific mTOR signaling that occurs during the early stages of substrate switching.  Moreover, the rate of increased glucose use correlated negatively with hypertrophy development, strongly suggesting that hearts do not become hypertrophied if they can compensate or switch faster from FA to glucose use.

overall_design: Two-condition experiment, cadiac gene expression of Acsl1H-/- vs Acsl1flox/flox mice 2 weeks or 10 weeks after tamoxifen treatment. Biological replicates: 3-4 per condition.

first: Cam

last: Patterson

first: Rosalind

last: Coleman


title: Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance.

first: Elana

middle: Judith

last: Fertig

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore


title: Histone H3.1K27 methylation promotes NHEJ by antagonizing FANCD2 on Chromatin

city: shanghai

first: Jin

last: Sun

department: life science and technology

country: China

institute: Tongji University

summary: The goals of this project are to study the transcriptome profiling (RNA-seq) of human fribroblast cells undergoing H3K27me3 decrease by histone mutants incorporation (H3.1K27A/M vs H3.1wt) or shRNA-mediated knockdown of specific histone H3K27me3 methyl-transferase EZH2 (shEZH2 vs shNC)

overall_design: mRNA profiles of human primary fibroblast stable cell lines with overexpression of H3.1WT, H3.1K27A or H3.1K27M or shRNA-mediated knock-down of EZH2 or negative control (NC) were generated by deep sequencing, in triplicate, using Illumina next-generation sequencing.

first: FangLin

first: Ye

last: Zhang

first: Jianfeng

last: Chang


title: TFAP2C regulates transcription in human naive pluripotency by opening enhancers

city: Montreal

first: William

middle: Abraham

last: Pastor

state: QC

address: 3655 Promenade Sir William Osler

institute: McGill University

summary: Naive and primed pluripotent human embryonic stem cells bear transcriptional similarity to pre- and post-implantation epiblast and thus constitute a developmental model for understanding the pluripotent stages in human embryo development. To identify new transcription factors that differentially regulate the unique pluripotent stages, we mapped open chromatin using ATAC-seq and found enrichment of the activator protein-2 (AP2) transcription factor binding motif at naive-specific open chromatin. We determined that the AP2 family member TFAP2C is upregulated during primed to naive reversion and becomes widespread at naive-specific enhancers. TFAP2C functions to maintain pluripotency and repress neuroectodermal differentiation during the transition from primed to naive by facilitating the opening of enhancers proximal to pluripotency factors. Additionally, we identify a previously undiscovered naive-specific POU5F1 (OCT4) enhancer enriched for TFAP2C binding. Taken together, TFAP2C establishes and maintains naive human pluripotency and regulates OCT4 expression by mechanisms that are distinct from mouse.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: This dataset includes 52 RNA-seq, 37 ATAC-seq and 20 ChIP-seq samples.

first: Wanlu

last: Liu


title: eCLIP in immortalized human mammary epithelial cells

city: Philadelphia

first: Peter

last: Choi

address: 3501 Civic Center Blvd, CTRB 4400

department: Pathology and Laboratory Medicine

institute: The Children's Hospital of Philadelphia

summary: The epithelial-to-mesenchymal transition (EMT) contributes to tumor heterogeneity and has been implicated in tumor initiation and metastasis. To systematically identify genes involved in EMT, we performed a genome-scale expression screen in human mammary epithelial cells and found a striking enrichment in RNA splicing factors. In particular, the RNA-binding proteins QKI and RBFOX1 were necessary and sufficient to promote EMT and stem-like states. Among the transcripts cooperatively regulated by both factors, we found that alternative splicing of the actin-binding protein FLNB plays an essential role in the regulation of EMT. The skipping of FLNB exon 30 and the elevated expression of QKI were strongly associated with EMT gene signatures in both basal B subtype breast cancer cell lines and basal-like breast cancer patient samples. These observations demonstrate that alternative splicing regulated by QKI and RBFOX1 plays an active role in promoting EMT in basal-like breast cancers.

overall_design: Immortalized human mammary epithelial cells stably overexpressing V5-tagged QKI or RBFOX1 were treated by UV crosslinking at 254nm with 400mJ/cm^2. Cells were processed as described in Van Nostrand et al (PMID: 27018577), with some slight modifications, as described in Li et al, 2017 (submitted).Immunoprecipitation was done using anti-V5 antibody (Life Technologies R96025) and for each protein, libraries were prepared from two replicates plus one size-matched input control for sequencing on the NextSeq 500 (single-end, 75bp).

first: Ji

last: Li

last: Hahn


title: Exosome-mediated direct conversion of human fibroblasts into neural progenitor-like cells [WTS]

city: Incheon Metropolitan City

first: Yong Seung

last: Lee

address: SimGokro 100gil 25

department: College of Medicine

country: South Korea

institute: Catholic Kwandong University

summary: Exosome, a kind of extracellular vesicles, has been introduced as a vehicle for horizontal transferring of genetic material. We induced autologous exosome containing a cocktail of reprogramming factors (‘reprosome’) to convert fibroblasts into neural progenitor cells (NPC). The fibroblasts were sonicated and subsequently cultured in NSC media for 1 day to induce release of reprosomes composed of reprogramming factors associated to chromatin remodeling and neural lineage-specific factors. After treated with reprosomes, fibroblasts were converted into NPCs (rNPC) with great efficiency via activation of chromatin remodeling, as fast as it required only five days for formation of 1,500 spheroids showing NPC-like phenotype. The rNPCs maintained self-renewal and proliferative properties for several weeks and successfully differentiated into neuron, astrocyte, and oligodendrocyte, in vitro and in vivo. Reprosome-mediated cellular reprogramming is simple, safe, and efficient, thus providing a new paradigm for clinical application that requires autologous stem cells.

overall_design: mRNA and miRNA profiles of exosome releasd from HDF cell by RNA-Seq analysis

first: Yong

first: Woon

middle: Y

last: Jung

first: Hyejung

last: Heo

first: Min

last: Park

first: Seung-Hun

last: Oh

first: Soonhag

last: Kim


title: Exosome-mediated direct conversion of human fibroblasts into neural progenitor-like cells [RNA-Seq]

overall_design: DNA methlylation profiles of exosome (reprosome) treated cells (rNPC) and, control cells were HDF cells and hNSC cells


title: Alternative splicing regulated by QKI and RBFOX1 promotes the mesenchymal cell state in breast cancer

overall_design: Refer to individual Series


title: Exosome-mediated direct conversion of human fibroblasts into neural progenitor-like cells [MBD-seq]


title: The fungus Aspergillus niger consumes sugars in a sequential manner that is not mediated by the carbon catabolite repressor CreA

status: Public on Apr 23 2018

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

summary: Aspergillus niger is a filamentous ascomycete fungus that is commonly found in most biotopes around the globe. In nature, A. niger degrades the plant biomass polysaccharides to monomeric sugars, transports them into the cells, and uses a variety of catabolic pathways to convert them into biochemical building blocks and energy. We show that when grown in liquid cultures, A. niger takes up plant-biomass derived monomeric sugars (and maltose) in a highly sequential manner, rather than simultaneously. Interestingly, this sequential uptake was not mediated by the fungal general carbon catabolite repressor protein CreA, which has been shown to mediate the use of preferential carbon sources over non-preferential carbon sources. Furthermore, transcriptome analysis strongly indicated that the preferential use of the monomeric sugars is arranged at the level of transport, but it is not reflected in transcriptional regulation of sugar catabolism. Therefore, the results indicate that the regulation of sugar transport and catabolism are separate physiological processes in A. niger.

overall_design: We aim to understand the response of A. niger while growing on a mixture of monomeric sugars as carbon source. Biological duplicates were grown and sampled at different time points (12, 18, 24, 33 hours), Affimetrix microarray experiments were performed on these samples.

first: Miia

last: Mäkelä

first: María

last: Aguilar-Pontes

first: Diana

last: van Rossen-Uffink

first: Mao

last: Peng

middle: P


title: Exosome-mediated direct conversion of human fibroblasts into neural progenitor-like cells

type: Non-coding RNA profiling by high throughput sequencing


title: The cohesin ring uses its hinge to organize DNA using non-topological as well as topological mechanisms

city: Oxford

first: Kim

last: Nasmyth

address: South Parks Road

institute: University of Oxford

summary: As predicted by the notion that sister chromatid cohesion is mediated by entrapment of sister DNAs inside cohesin rings, there is a perfect correlation between co-entrapment of circular minichromosomes and sister chromatid cohesion. In most cells where cohesin loads onto chromosomes but fails to form cohesion, loading is accompanied by entrapment of individual DNAs. However, cohesin with a hinge whose positively charged lumen has been neutralized not only loads onto and translocates along chromatin but also organizes it into chromatid-like threads, despite largely failing to entrap DNAs inside its ring. Thus, cohesin engages chromatin in both a non-topological and a topological manner. Further, mutation of three highly conserved lysines within the Smc1 hinge abolishes all loading without affecting cohesin’s initial recruitment to centromers or its ability to hydrolyze ATP. We suggest that loading and translocation are mediated by conformational changes in cohesin’s hinge driven by cycles of ATP hydrolysis.

overall_design: Effect of hinge mutations of S. cerevisiae cohesin complexes on loading onto chromosomes, assessed by calibrated ChIP-seq on an Ion Torrent Proton (Life Technologies)

first: Naomi

last: Petela


title: The miRNA profile of P. xylostella in response to chlorantraniliprole exposure

status: Public on Apr 22 2018

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

country: Australia

institute: The University of Queensland

summary: miRNAs play important roles in various biological processes through post-transcriptional regulation of gene expression. We previously identified 203 mature miRNAs in Diamondback moth, Plutella xylostella. This species has developed extremely high levels of resistance to chlorantraniliprole and other class of insecticides in the field. In this study, we examined the miRNA profile of P. xylostella in response to chlorantraniliprole exposure. The smRNA-seq data analyses showed that insecticide treatment caused significant changes in the abundance of some miRNAs. Increasing exposure time (6h to 24h) and insecticide concentration (0.01 to 0.1 ppm) induced more dysregulated miRNAs in DBM larvae.

overall_design: To determine P. xylostella miRNA responses to a xenobiotic stress, we exposed the susceptible DBM larvae to two doses of Chlorantraniliprole (0.01 and 0.1 ppm). Total RNA samples were collected from surviving larvae 6 and 24 h post-treatment. This included 16 samples (three replicates for each time and dose of treatment plus two replicates of control larvae at both times).

first: Sassan

last: Asgari


title: Glucocorticoid Regulated Transcriptome in Wild-type and GR-C3 Knockin Mouse Embryonic Fibroblasts

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Glucocorticoids are primary stress hormones and their synthetic derivatives are widely used clinically. The therapeutic efficacy of these steroids is limited by severe side effects and glucocorticoid resistance. Multiple glucocorticoid receptor (GR) isoforms are produced by alternative translation initiation; however, the role individual isoforms play in controlling tissue-specific responses to glucocorticoids in vivo is unknown. We have generated knockin mice that exclusively express the most active receptor isoform, GR-C3. The GR-C3 knockin mice die at birth due to respiratory distress but can be completely rescued by antenatal glucocorticoid administration. To evaluate the GR-C3 transcriptome, we prepared mouse embryonic fibroblasts (MEFs) from E12.5 wild-type (WT) and GR-C3 knockin embryos and treated the cells with vehicle or the synthetic glucocorticoid Dexamethasone (Dex) for 6 hours.  The GR-C3 isoform was found to have a markedly different gene-regulatory profile than GR in WT MEFs.

overall_design: GR-C3 knockin mice were generated by standard gene targeting procedures.  In brief, ES cells were generated in which exon 2 of the NR3C1 gene was replaced by a neomycin cassette. An exchange vector was generated containing a hygromycin cassette and a mutant NR3C1 exon 2 in which the ATG start codon for GR-C3 was left intact but mutated to ATC for each of the other seven translational isoforms. The exchange vector and Cre-recombinase were transfected into the targeted ES cells by electroporation, and positive ES cells were selected using G418 (sensitive) and hygromycin (resistant). A GR-C3 positive ES cell clone was injected into C57Bl/6 blastocysts to create chimeric mice. Chimeric males were bred with C57Bl/6 females for germline transmission, and the hygromycin cassette was deleted using Flp-deleter mice. The resulting mice were maintained on a C57Bl/6 background and intercrossed to produce WT, heterozygous GR-C3 knockin, and homozygous GR-C3 knockin mice. WT and homozygous GR-C3 knockin MEFs were generated from E12.5 embryos. WT and homozygous GR-C3 knockin MEFs cells were stimulated with either vehicle (control) or 100nM Dex for 6 hours.  Total RNA was harvested for microarray analysis using the RNeasy Mini Kit (Qiagen) and RNase-Free DNase Kit (Qiagen) from 3 biological replicates of vehicle-treated WT MEFs, Dex-treated WT MEFs, vehicle-treated GR-C3 knockin MEFs, and Dex-treated GR-C3 knockin MEFs.

first: Sivapriya

last: Ramamoorthy

first: Robert

middle: H

last: Oakley

first: John

last: Cidlowski


title: Epigenetic regulation by BAF (mSWI/SNF) complexes limits neural stem cell proliferation by suppressing Wnt signaling in late cortical neurogenesis

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

summary: We have analyzed changes in gene expression, histone 3 lysine 4 dimethyl (H3K4me2) and histone 3 lysine 37 trimethyl (H3K27me3) levels in the embryonic cortex at E17.5 resulting from conditional deletion of BAF complex - i.e., double knockout of BAF155 and BAF170, in late cortical progenitors utilizing Cre expression under human GFAP (hGFAP) promoter (dcKO_hGFAP-Cre). Moreover, we also analyzed gene expression in WT E17.5 cortex treated with vehicle and Wnt inhibitor together with that of in dcKO_hGFAP-Cre cortex treated with Wnt inhibitor. Gene expression studies were conducted by RNA-Seq and histone marks were analyzed by ChIP-Seq.

overall_design: Examination of H3K4me2 and H3K27me3 levels, and gene expression in murine E17.5 cortex of WT and BAF dcKO_hGFAP-Cre.

first: Cemil

last: Kerimoglu

first: Andre

last: Fischer


title: Exosome-mediated direct conversion of human fibroblasts into neural progenitor-like cells [ncRNA-Seq]

first: Yong Seung

last: Lee

overall_design: mRNA and miRNA profiles of exosome releasd from UHDF (HDF cells were cultured in NSC medium after ultrasound stimulus) cell by RNA-Seq analysis

first: Yong

first: Woon

last: Jung

first: Hyejung

last: Heo

first: Min

last: Park

first: Seung-Hun

last: Oh

first: Soonhag

last: Kim


title: Pseudouridylation of tRNA-derived fragments steers translation control in stem cells

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

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


title: Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance. (Methylation)

first: Elana

last: Fertig

summary: BACKGROUND: Targeted therapies specifically act by blocking the activity of proteins that are encoded by genes critical for tumorigenesis. However, most cancers acquire resistance and long-term disease remission is rarely observed. Understanding the time course of molecular changes responsible for the development of acquired resistance could enable optimization of patients treatment options. Clinically, acquired therapeutic resistance can only be studied at a single time point in resistant tumors. To determine the dynamics of these molecular changes, we obtained high throughput omics data weekly during the development of cetuximab resistance in a head and neck cancer in vitro model. RESULTS: An unsupervised algorithm, CoGAPS, was used to quantify the evolving transcriptional and epigenetic changes. Applying a PatternMarker statistic to the results from CoGAPS enabled novel heatmap-based visualization of the dynamics in these time course omics data. We demonstrate that transcriptional changes result from immediate therapeutic response or resistance, whereas epigenetic alterations only occur with resistance. Integrated analysis demonstrates delayed onset of changes in DNA methylation relative to transcription, suggesting that resistance is stabilized epigenetically. CONCLUSIONS: Genes with epigenetic alterations associated with resistance that have concordant expression changes are hypothesized to stabilize resistance. These genes include FGFR1, which was associated with EGFR inhibitor resistance previously. Thus, integrated omics analysis distinguishes the timing of molecular drivers of resistance. Our findings provide a relevant towards better understanding of the time course progression of changes resulting in acquired resistance to targeted therapies. This is an important contribution to the development of alternative treatment strategies that would introduce new drugs before the resistant phenotype develops.

overall_design: DNA methylation profiling was performed for 23 samples including 2 replicates of parental SCC25 cetuximab sensitive cell line, generations of SCC25 cell lines treated with either cetuximab or PBS over weeks (each week of treatment labeled C1 to C11), and a set of 11 stable cetuximab resistant clones derived from SCC25. Sequencing was performed at the Johns Hopkins Medical Institutions (JHMI) Deep Sequencing & Microarray Core Facility. Total RNA was isolated from a total of 1x106 cells using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) following manufacturer’s instructions. The RNA concentration was determined by the spectrophotometer Nanodrop (Thermo Fisher Scientific, Waltham, MA) and quality was assessed using the 2100 Bioanalyzer (Agilent, Santa Clara, CA) system. An RNA Integrity Number (RIN) of 7.0 was considered as the minimum to be used in the subsequent steps for RNAseq. Library preparation was performed using the TrueSeq Stranded Total RNAseq Poly A1 Gold Kit (Illumina, San Diego, CA), according to manufacturer’s recommendations, followed by mRNA enrichment using poly(A) enrichment for ribosomal RNA (rRNA) removal. Sequencing was performed using the HiSeq platform (Illumina) for 2X100bp sequencing. Reads were aligned to hg19 with MapSplice16 and gene expression counts were quantified with RSEM17. Gene counts were upper-quartile normalized and log transformed for analysis following the RSEM v2 pipeline used to normalize TCGA RNA-seq data.

first: Christine

last: Chung


title: A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation

status: Public on Apr 21 2018

city: San Francisco

first: Yan

last: Zhang

state: CA

address: 600 16th Street

department: Microbiology and Immunology

institute: UC San Francisco

summary: Temperature influences the structural and functional properties of cellular components, necessitating stress responses to restore homeostasis following temperature shift. The heat shock circuitry is well understood, but that controlling the E. coli cold-shock adaptation program is not.  We found that during the growth arrest phase (acclimation) that follows shift to low temperature, protein synthesis increases and ORF-wide mRNA secondary structure decreases. We identified two components of an mRNA surveillance system that enable recovery of translation during acclimation: RNase R assures appropriate mRNA degradation and the Csps dynamically adjust mRNA secondary structure to globally modulate protein expression level. Csps also remodel their own mRNAs to tune their expression to cellular need. Thus, appropriate translation is dynamically adjusted with Csp control. The universality of Csps in bacteria suggests broad utilization of this control mechanism.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design:
Ribosome profiling, total RNA/mRNA-seq and DMS-seq data at 37°C and following cold shock in E. coli

Please note that the samples with _1 and _2 (in the sample titles) represent biological replicates of the same experiments.

first: David

last: Burkhardt

first: Silvi

last: Rouskin

first: Gene-Wei

last: Li

first: Jonathan

last: Weissman

first: Carol

last: Gross


title: Pseudouridylation of tRNA-derived fragments steers translation control in stem cells [iCLIP]

summary: Pseudouridylation (Ψ) is the most abundant and widespread type of RNA epigenetic modification in living organisms; however, the biological role of Ψ remains poorly understood. Here, we show that a Ψ-driven posttranscriptional program steers translation control to impact stem cell commitment during early embryogenesis. Mechanistically, the Ψ ‘writer’ PUS7 modifies and activates a network of tRNA-derived fragments (tRFs) targeting the translation initiation complex. PUS7 inactivation in embryonic stem cells impairs tRF-mediated translational regulation leading to high protein biosynthesis and abnormal germ layer specification. Dysregulation of PUS7 and tRFs in myeloid malignancies associates with altered translation rates, suggesting a role of Ψ in tumorigenesis. Our findings unveil a critical function of Ψ in directing translational control in stem cells with promisingly broad implications for human disease.

overall_design: Small RNA (<200nt) sequencing of WT and PUS7KO human embryonic stem cell (hESC). 4 replicates per condition.

first: Nicola

last: Guzzi

first: Maciej

last: Cièsla

first: Stefan

last: Lang

first: Sonali

last: Arora

first: Marios

last: Dimitriou

first: Roberto

last: Munita

first: Michal

last: Lubas

first: Kazuki

last: Okuyama

first: Anders

last: Lund

first: Göran

last: Jonsson

first: Mikael

last: Sigvardsson

first: Eva

last: Hellström-Lindberg

first: Andrew

last: Hsieh

first: Cristian

last: Bellodi


title: Pseudouridylation of tRNA-derived fragments steers translation control in stem cells [small RNA-seq]

first: Shamit

last: Soneji


title: HI-C 2.0: AN OPTIMIZED HI-C PROCEDURE FOR HIGH-RESOLUTION GENOME-WIDE MAPPING OF CHROMOSOME CONFORMATION

city: Worcester

first: Job

last: Dekker

state: Massachusetts

address: 368 Plantation Street

department: Program in Systems Biology

institute: UMass Medical School

summary: Chromosome conformation capture-based methods such as Hi-C have become mainstream techniques for the study of the 3D organization of genomes. These methods convert chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions).  Here, we describe an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (Kb) resolution. It also includes steps to reduce random ligation and the generation of uninformative molecules, such as unligated ends, to improve the amount of valid intra-chromosomal read pairs. This protocol allows for obtaining information on conformational structures such as compartment and topologically associating domains, as well as high-resolution conformational features such as DNA loops.

first: Houda

last: Belaghzal

first: Johan

last: Gibcus


title: Expression data of human dermal papilla cell with or without beta-estradiol

city: Edogawa-ku

first: Yujiro

last: Endo

state: Tokyo

address: 7-2-1 Hirai

department: Research & Development Headquarters

institute: Lion Corporation

summary: The dermal papilla plays a key role in the regulation of the hair biology. Accordingly, human dermal papilla cells (hDPCs) may be functionally impaired in female pattern hair loss. A previous observation that beta-estradiol (E2) increased hair density in ovariectomized mice suggested that E2 might modulate the biological properties of hDPCs. Therefore, to further explore the effect of E2 on hDPCs, a global gene expression analysis was conducted.

overall_design: Analysis were performed using DPCs (n = 3) as a control group and DPCs_estradiol (n = 3) as a test group.


title: Identification and characterization of miRNAs expressed in the corpora allata of Aedes aegypti

status: Public on Apr 19 2018

first: Kayvan

last: Etebari

summary: We used our deep sequence data and bioinformatics to analyzed the miRNA repertoires expressed in the CA of pupae, sugar-fed and blood-fed female Aedes aegypti mosquitoes. In total, 156 mature miRNAs were detected in the CA, with 84 displaying significant differences in expression among the three CA developmental stages. Notably, the changes in the miRNA repertoire in the CA in the pupa-adult transition have completely different characteristics compared with the changes from sugar-fed to blood-fed mosquitoes.

overall_design: Corpora allata-corpora cardiaca complexes (CA) were dissected from three different developmental stages of Aedes aegypti females (pupae, sugar-fed and blood-fed). Total RNA was extracted from 50 CAs from each developmental stage in triplicate using Norgen Biotek’s total RNA purification kit. The small RNA libraries were generated using the Illumina Truseq™ Small RNA Preparation kit according to Illumina’s TruSeq™ Small RNA Sample Preparation Guide at LC Sciences facility (Texas, USA). The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. Raw sequencing reads (40 nts) were obtained using Illumina’s Sequencing Control Studio software.

first: Marcela

last: Nouzova

first: Sassan

last: Asgari

first: Fernando

last: Noriega


title: SiO2 Nanoparticles Modulate The Electrical Activity Of Neuroendocrine Cells Without Exerting Genomic Effects

status: Public on Apr 20 2018

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

institute: University of Groningen

summary: Different electrophysiological approaches are combined with a genomic screening in order to analyze, in GT1-7 neuroendocrine cells, the impact of SiO2 nanoparticles (NPs; 503nm in diameter) on electrical activity and gene expression. It is found that 20 µg mL-1 NPs induce depolarization of the membrane potential, with a modulation of the firing of action potentials. Recordings of electrical activity with Multielectrode Arrays provide further evidence that the NPs evoke a temporary increase in firing frequency, without affecting the functional behaviour on a longer time scale (hours). Finally, NPs incubation up to 24 h does not induce any change in gene expression

overall_design: Transcriptome profiling by high-throughput sequencing of NP-treated cells at various timepoints

first: C

last: Distasi

first: FA

last: Ruffinatti

first: M

last: Dionisi

first: S

last: Antoniotti

first: A

last: Gilardino

first: G

last: Croci

last: Alberto

first: E

last: Castrofiorio

first: D

last: Morandi

last: Martra

last: Oliviero

first: L

last: Munaron

last: Lovisolo


title: Iron response of HepG2 cells

city: Dunedin

first: Christopher

middle: Michael

last: Brown

address: 710 Cumberland Street

country: New Zealand

institute: University of Otago

summary: RNA-seq of HepG2 cells in response to iron

overall_design: RNA-seq experiment conducted in two biological replicates. Total RNA samples were submitted to the Otago Genomics and Bioinformatics Facility at the University of Otago (Dunedin, New Zealand) under contract to the New Zealand Genomics Limited for library construction and sequencing. The libraries were prepared using TruSeq stranded mRNA sample preparation kit according to the manufacturer’s protocol (Illumina) and pair-end sequenced on one lane of HiSeq 2000 (Illumina), generating 100-bp reads.

first: Chun Shen

last: Lim

first: Torsten

last: Kleffmann

first: Samuel

last: Wardell

first: Chris

middle: M


title: Non-cell autonomous Otx2 homeoprotein regulates visual cortex plasticity through Gadd45b

city: paris

first: Jessica

last: Apulei

address: 11 place marcelin berthelot

country: France

institute: Collège de France

summary: A better understanding of how Otx2 regulates plasticity in the visual cortex requires that its non-cell autonomous transcription targets be identified. We dissected layer IV of the visual cortex and used RNA-sequencing to analyze gene expression at postnatal day 30 (P30) and P100 in wild-type (WT) and Otx2+/GFP heterozygotes mice. The rationale is that CP plasticity is opened at P30 in WT but not in Otx2+/GFP mice, given that genetic deletion delays CP opening (Sugiyama et al., 2008), and that the CP is closed at P100 in WT mice and not yet in Otx2+/GFP mice. Thus, genes with similar expression at P30 in Otx2+/GFP and at P100 in WT mice but with a different level of expression during the critical period (P30 in WT or P100 Otx2+/GFP mice) were considered as potential genes involved in plasticity.

overall_design: Examination of genes expression at P30 and P100 in wild-type and Otx2 (+/GFP) mice. 4 mice were pooled per condition and experiment was done in duplicate.

first: Clémence

last: Bernard

first: Namsuk

last: Kim

first: Corinne

last: Blugeon

first: Laurent

last: Jourdren

first: Ariel

last: Di Nardo

first: Alain

last: Prochiantz


title: Gene expression profiling after a chronic exposure to benzo[a]pyrene (B[a]P) and/or ethanol in steatotic or non-steatotic HepaRG cells.

status: Public on Apr 18 2018

city: Rennes

first: Simon

last: Bucher

address: 2 Avenue du Pr. L. Bernard

institute: INSERM U1241

summary: The aim of this study was to determine in the human HepaRG cell line whether lipid overload (steatosis) could favor the cytotoxicity of benzo[a]pyrene (B[a]P) alone or in association with ethanol.

overall_design: Differentiated HepaRG cells (Aninat et al., Drug Metab Dispos 2006) were treated during 16 days with or without a mixture of fatty acids (150 µM stearic acid and 150 µM oleic acid). After 2 days from the start of the experiments, steatotic and non-steatotic cells were also treated with 1 or 2.5 µM B[a]P, associated or not with 25 mM ethanol. Independent cultures were performed in triplicate. In total, 36 samples were analyzed in this study.

first: Cédric

last: Coulouarn

first: Bernard

last: Fromenty


title: Transcriptome analysis of wild-type and VaAQUILO overexpressing Arabidopsis

city: Wuhan

first: Xiaoming

last: Sun

state: Hubei

address: Lumo road, No. 1

institute: Wuhan Botanical Garden, Chinese Academy of Sciences

summary: To gain the possible direct or indirect targets of VaAQUILO, RNA-Seq was carried out on three biological replicates of wild-type and 3 transgenic Arabidopsis lines mixture (#1, #2 and #3) under normal and cold treatment conditions (Based on the distribution of samples in a first PCA plot, the two most similar replicates per condition were considered for further statistical analyses) .

overall_design: Examination of gene expression changes after overexpression of VaAQUILO in Arabidopsis and identification of VaAQUILO downstream genes.

first: José

middle: T

last: Matus

first: Shaohua

last: Li

first: Zhenchang

last: Liang

first: Haiping

last: Xin


title: The catalytic activity of ceramide synthase 2 regulates transcription of genes involved in lipid metabolism and cell division

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: The replacement of two consecutive histidine residues by alanine residues in the catalytic center of ceramide synthase 2 in new transgenic mouse mutants (CerS2 H/A) leads to inactivation of catalytic activity and reduces protein level to 60% of the WT level. We show here by qRT-PCR and transcriptome analyses that several transcripts of genes involved in lipid metabolism and cell division are differentially regulated in livers of CerS2 H/A mice. Thus very long chain ceramides produced by CerS2 are required for transcriptional regulation of target genes. The previously described formation of hepatocarcinomas in CerS2 KO mice occurred already in 6‑week-old animals and also originated in the loss of CerS2 catalytic activity. The additional loss of the CerS2 homeodomain in newly generated CerS2 Del mice that almost completely lack CerS2 protein expression mostly corroborated the transcriptional effects of the CerS2 catalytic domain (nevertheless, it appears to have independent effects such as induction of cholangiocarcinomas.

overall_design: Whole genome transcript levels were measured in liver total RNA preparations from 16 mice of four different genotypes (four 6-week-old mice per genotype)

first: Andreas

last: Bickert

first: Martina

last: van Uelft

first: Paul

last: Kern

first: Stefanie

last: Herresthal

first: Thomas

last: Ulas

first: Katharina

last: Gutbrod

last: Degen

middle: L

first: Peter

last: Dörmann

first: Dieter

last: Hartmann

first: Reinhard

last: Bauer

first: Klaus

last: Willecke


title: Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

city: Copenhagen

first: Mireya

last: Plass

address: Robert-Rössle Str. 10

institute: MDC-Berlin

summary: Flatworms of the species Schmidtea mediterranea are immortal –adult animals contain a large pool of pluripotent stem cells that continuously differentiate to all adult cell types. Therefore, single-cell transcriptome profiling of adult animals should reveal mature and progenitor cells. Here, by combining perturbation experiments, gene expression analysis, a computational method that predicts future cell states from the transcriptional changes, and a novel lineage reconstruction method, we placed all major cell types onto a single lineage tree that connects all cells to a single stem cell compartment. We characterize gene expression changes during differentiation and discover cell types important for regeneration. Our results demonstrate the importance of single-cell transcriptome analysis for mapping and reconstructing fundamental processes of developmental and regenerative biology at unprecedented resolution.

overall_design: Single cell sequencing by drop-seq of Schmidtea mediterranea whole cells including 2 bulk population wild type samples fixed in methanol, 1 bulk population wild type sample cryopreserved, 2 bulk population wild type alive sample and 2 bulk population after control and Smed-h2b RNAi samples fixed in methanol and 3 wt samples at 3 different regeneration time points (day 0, day 2, day 4) fixed in methanol.

first: Jordi

last: Solana

first: F. Alexander

last: Wolf

first: Salah

last: Ayoub

first: Aristotelis

last: Misios

first: Petar

last: Glažar

first: Benedikt

last: Obermayer

first: Fabian

last: Theis

first: Christine

last: Kocks

first: Nikolaus

last: Rajewsky


title: MYCN drives glutaminolysis in neuroblastoma and confers sensitivity to ROS augmenting agents

city: Memphis

first: JUN

last: YANG

state: TN

address: 262 Danny Thomas Place

department: Surgery

institute: St Jude Children's Research Hospital

summary: Through a small scale metabolic-modulator screening, we have identified dimethyl fumarate (DMF), a FDA approved drug for multiple sclerosis, which suppresses neuroblastoma cell growth in vitro and in vivo. Mechanistically, DMF suppresses neuroblastoma cell growth through inducing ROS and subsequently suppressing MYCN expression.

overall_design: Biological duplicate samples were treated with 100uM of DMF for 6 and 12 hours.

first: Jun

last: Yang

first: Ruoning

last: Wang


title: The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity

first: Irina

last: Chelysheva

address: Roosevelt Dr

department: NDM

summary: Ribosome biogenesis is a complex and intricate process involving multiple factors. A plethora of auxiliary proteins assist the correct assembly of rRNA and ribosomal proteins into mature ribosomes. Defects in this process cause dysfunctional ribosomes which may alter protein synthesis and impair cell fitness. Despite its importance, yet we are lacking mechanistic details of ribosome biogenesis. Here we show that the widely-conserved RNA chaperone Hfq, which is an important post-transcriptional regulator in sRNA-mRNA basepairing in Escherichia coli, plays a critical role in rRNA processing and consequently ribosome assembly. Hfq binds the 17S rRNA precursor and facilitates its correct processing and folding to mature 16S rRNA. Strikingly, Hfq depletion decreases the pool of mature 70S ribosomes. Mutations in residues located in the distal face of Hfq render reduced ribosome levels in contrast to mutations in the proximal and rim surfaces which govern interactions with the sRNAs. Our results indicate that the described Hfq-dependent regulation of ribosomes is independent of its function as sRNA-regulator. Furthermore, we observed that inactivation of Hfq compromises translation efficiency and fidelity, both features of aberrantly assembled ribosomes. Our work expands the functions of Hfq beyond its function in small RNA-mediated regulation and unveil a novel role of Hfq as crucial auxiliary factor in ribosome biogenesis and translation.

overall_design: Ribosome Profiling and RNA-seq of E. coli WT and ∆hfq mutant

first: José

last: Andrade

first: Ricardo

middle: F

last: Dos Santos

first: Zoya

last: Ignatova

first: Cecília

last: Arraiano


title: Gene Expression in the BAT and WAT of ob/ob and ob/ob/Cidea-/-/Cidec-/- mice

city: Beijing

first: Linkang

last: Zhou

state: Beijing

address: Haidian District

institute: Tsinghua Unversity

summary:
ob/ob mice is an obese mice. CIDE family proteins including Cidea, Cideb and Cidec play important role in lipid metabolism. Cidea is mainly expressed in the brown adipose tissue (BAT). Cidec is mainly expressed in the BAT and white adipose tissue (WAT). We generated ob/ob/Cidea-/-/Cidec-/- mice to investigate the phenotype of fat tissue. ob/ob/Cidea-/-/Cidec-/- mice are lean when compared with ob/ob mice. The tissue weight and TAG content of BAT and WAT was extreamly decreased in ob/ob/Cidea-/-/Cidec-/- mice compared with that in ob/ob mice.
We next extract the total RNA from the BAT and WAT of ob/ob and ob/ob/Cidea-/-/Cidec-/- mice, to perform microarray analysis using Mouse Gene 1.0 ST array system, Affymetrix. We then analysised the up-regulated and down regulated pathways.

overall_design: We extract the RNA of BAT and WAT from 4 month old mice and hybridization on Affymetrix microarrays. We then analysis the data.

first: Xiayu

last: Xia

first: Yangnan

last: Gu


title: Early arthritis B cell gene expression profiling

city: Newcastle upon Tyne

first: Arthur

last: Pratt

address: Framlington Place

department: Faculty of Medical Sciences

institute: Newcastle University

summary: 242 patients recruited from an early arthritis clinic donated RNA and DNA from freshly isolated and purified peripheral blood CD19+ B cells. Global gene expression measurement was carried out using Illumina BeadChip HT12v4 microarrays. Objectives included the identification of B cell transcripts differentially expressed between disease phenotypes, where all patients were naive to immunomodulatory therapy. In addition an eQTL analysis was carried out with reference to known genotype data for this cohort of patients

overall_design: Cross sectional; diagnoses confirmed at >2 years' follow-up.

first: Nishanthi

last: Thalayasingam

first: Jonathan

last: Massey

first: Andrew

last: Skelton

first: Nisha

last: Nair

first: Amy

last: Anderson

first: Alexander

last: Clark

first: Julie

last: Diboll

first: Dennis

middle: W

last: Lendrem

first: Louise

middle: N

last: Reynard

first: Heather

last: Cordell

first: Steve

last: Eyre

first: John

middle: D

last: Isaacs

first: Anne

last: Barton


title: Transcriptome analysis of Col, ore3 and ore12 during dark-induced leaf senescence

city: Jeju-si

first: Jeongsik

last: Kim

state: Jeju

address: 102 Jejudaehakroe

department: Faculty of Science Education

institute: Jeju National University

summary: Comparative analysis of genes affected in ore3 and ore12 during dark-induced leaf senescence

overall_design: Col, ore3 and ore12 at 0,1,2,3 days during dark-induced leaf senescence, duplicated samples

first: Hye Ryun

last: Woo

first: Pyung Ok

last: Lim


title: Analysis of differentially expressed genes between human Bone Marrow Stromal cells (hBMSC) and relative fully differentiated adipocytes from two healthy donor

status: Public on Apr 17 2018

city: Verona

first: Carmine

last: Carbone

state: Select a State or Province

address: p.zza L.A. Scuro 10

country: Italy

institute: Policlinico Universitario GB Rossi

summary: We compared gene expression profiles in human bone Marrow Stromal Cells (hBMSC) from two healthy donor versus fully differentiated adipocytes by microarray analysis in order to identify groups of genes associated with a specific adipocytes secreted molecules.

overall_design: Total RNA was obtained from subconfluent cells using Trizol reagent

first: Federica

last: di Nicolantonio


title: Ribosome maturation by YbeY stabilises Type III secretion system transcripts in enterohaemorrhagic E. coli

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

institute: University of New South Wales

summary: Enterohaemorrhagic E. coli is a significant human pathogen that utilises a type 3 secretion system (T3S) to colonise the reservoir host, cattle, and humans. Transposon mutagenesis showed the ybeZYX-Int operon to be required for normal T3S levels. Deletion analyses identified the endoribonuclease ybeY, which was previously linked to 16S ribosomal RNA maturation and small RNA (sRNA) function. Loss of ybeY in EHEC had additional pleiotropic effects, including temperature sensitivity and reduced growth. UV-crosslinking revealed specific binding of ybeY to the “neck” and “beak” regions of 16S ribosomal RNA, but identified no significant sRNA association. Sub-inhibitory concentrations of the translation initiation inhibitor kasugamycin provoked degradation of a polycistronic T3S mRNA. We conclude that T3S is particularly sensitive to depletion of initiating ribosomes, explaining the inhibition of T3S in the ∆ybeY strain. Accessory virulence transcripts may be preferentially degraded in cells with reduced translational capacity, potentially reflecting the priorities for protein production.

overall_design: UV-crosslinking analysis of RNA-protein interactions was performed as previously described (Tree et al. 2014) in biological duplicate with a control (untagged) sample. PCR amplified cDNA libraries were sequenced using an Illumina MiSeq platform. Data analysis were performed using the pyCRAC software package (Webb et al., 2014) as described in Sy et al. (2017). To identify statistically significant YbeY binding sites pyCalculateFDR was used on mapped reads with settings: 100nt flanking sequence for features (-r 100), p-value threshold of 0.05 (-m 0.05), minimum coverage of 10 reads (--min=10), and 500 iterations (--iterations=500). YbeY binding sites with FDR<0.05, recovered in both HTF tagged replicates, and absent from the untagged control for retained for further analysis.


title: Transcriptomic Profiling of Mice with Klf5 Deletion in Context of Oncogenic Kras Expression

city: Stony Brook

first: Agnieszka

middle: B.

last: Bialkowska

state: New York

address: HSC-T17 Room 090

department: Dept. of Medicine

institute: Stony Brook University

summary: This study used Illumina RNA-sequencing to examine transcriptomic profile of mice with Klf5 knockout in context of oncogenic Kras expression. The study analyzed total RNA extracted from pancreas of mice 2 days after cerulein-induce pancreatitis. In addition, this study include 2 biological replicate of mice with each of the following genotypes: Ptf1aCreERTM, Ptf1aCreERTM;Klf5fl/fl, Ptf1aCerERTM;LSL-KrasG12D, and Ptf1aCreERTM;LSL-KrasG12D;Klf5fl/fl.

overall_design: Transcriptomic profiling of pancreata from 2 Ptf1aCreERTM mice, 2 Ptf1aCreERTM;Klf5fl/fl mice, 2 Ptf1aCerERTM;LSL-KrasG12D mice, and 2 Ptf1aCreERTM;LSL-KrasG12D;Klf5fl/fl mice 2 days after cerulein-induced pancreatitis.

first: Ping

last: He

middle: B


title: Role of XRN2 ribonucleolytic activity in RNA metabolism

city: Warszawa

first: Tomasz

middle: M.

last: Kuliński

state: Mazowieckie

address: ul. Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

summary: We analysed the effect of depriving the human cell of the catalytic activity of the nuclear 5’ to 3’ exoribonuclease XRN2. Catalytic amino acids in this protein had been defined previously, so it was possible to design a mutated catalytically inactive form of the protein (XRN2D233A-D235A) (PMID: 19194460). We created 293 Flp-In T-REx stable cell lines that induciby silence endogenous XRN2, and concomitantly express wild-type or inactive XRN2 in fusion with EGFP at the C-terminus. Thus, complementation of silencing of endogenous XRN2 with the expression of mutant version of the protein allows to directly link potential phenotypes with the lack of XRN2 enzymatic activity. To this end we isolated total RNA from tetracycline-treated cells, depleted it from rRNA and conducted strand-specific deep sequencing.

overall_design: 6 samples were analysed. 3 replicates of control cells (endogenous copy of XRN2 gene is silenced and catalytically active exogenous XRN2-EGFP is expressed) and 3 replicates of cells deprived of XRN2 ribonucleolytic activity (endogenous copy of XRN2 gene is silenced and catalytically inactive exogenous XRN2(D233AD235A)-EGFP is expressed)

last: Kulinski

first: Roman

middle: J

last: Szczesny

first: Andrzej

last: Dziembowski


title: Genome-wide binding of GATA2 in 3T3-L1 und C3H10T1/2 cells and expression profile of primary mesenchymal cells with ectopic GATA2 expression

city: Berlin

first: Cornelius

last: Fischer

state: Berlin

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine (MDC)

summary: The transcription factor GATA2 is required for the expansion and differentiation of hematopoietic stem cells. GATA2 is also expressed in mesenchymal cells and was implicated in the regulation of adipocyte differentiation. Here we investigated genome-wide binding of endogenous GATA2 in mesenchymal cell lines and investigated the transcriptional responses of GATA2 overexpression in primary mesenchymal stem cells.

overall_design: Genomic occupancy profiled by high throughput sequencing (ChIP-seq) in 3T3-L1 cells and C3H10T1/2 cells for GATA2.

first: Alexander

last: Tolkachov

first: Thomas

last: Ambrosi

first: Chung

last: Han

first: Matthias

last: Münzner

first: Susanne

last: Mathia

first: Marjo

last: Salminen

first: Georg

last: Seifert

first: Mario

last: Thiele

last: Duda

first: Sascha

last: Sauer

first: Tim

last: Schulz

first: Michael

last: Schupp


title: Intestinal IKKa is required for tumor initiation in APC mutant mice

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

summary: We have generated a mouse model for tumor initiation carrying a mutation in APC and lacking IKKα in intestinal epithelial cells. IKKα-deficient intestinal cells primarily failed to generate adenomas, and the few adenomas arising in this background displayed a significant reduction in cell proliferation. Using an in vitro model for intestinal tumoroids (derived from adenoma initiating cells), we have performed RNA sequencing of wild type and IKKα-deficient intestinal tumoroids. This has demonstrated that epithelial IKKα controls transcription of stem cell-related genes and genes associated with proliferation and apoptosis.

overall_design: RNA sequencing of IKKa WT and KO tumoroids, done in triplicates

first: Carlota

last: Colomer

first: Anna

last: Vert

first: Lluís


title: Genome-wide bisulphite sequencing of Arabidopsis thaliana embryo and endosperm

city: Berkeley

first: Jennifer

last: Frost

address: 231 Koshland Hall

department: Plant and Microbial Biology

institute: University of California, Berkeley

summary: The DEMETER (DME) DNA glycosylase mediates genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-demethylation are small, AT-rich transposons and boundaries of large heterochromatic transposons, but how DME interacts with chromatin is unclear. To investigate the interaction between DME and chromatin, we analyzed DNA methylation in Arabidopsis seeds and pollen deficient in the chromatin remodeler FAcilitates Chromatin Transactions (FACT) complex. We find that FACT co-localizes with nuclear DME, and is required for DME activity in chromatin domains with high nucleosome occupancy and histone modifications associated with heterochromatin, which comprise over half of DME target loci. We also demonstrate that heterochromatin-associated linker histone H1 mediates the requirement for FACT at a subset of DME-target loci. However, FACT is not required for DME demethylation of targets in euchromatic regions.  Thus, chromatin structure determines the degree to which FACT facilitates access of DME to its targets.

overall_design: DNA methylation was measured in pools of 50-100 hand-microdissected embryos and endosperm from Arabidopsis mutants and controls; FACS sorted Arabidpsis sperm and vegetative cell nuclei: mutants were ssrp1-3 plus sibling wild-type (two bioreplicates), spt16-3 plus sibling wild-type, h1.1 h1.2 ssrp1 triple mutants plus h1.1 h1.2 sibling controls

first: Robert


title: JMJD6 licenses estrogen receptor alpha-dependent enhancer RNA and coding gene activation by modulating CARM1/MED12 co-activator complex in breast cancer [Gro-Seq]

status: Public on Apr 16 2018

city: Ganzhou

first: Wenjuan

last: Zhang

state: Jiangxi

address: No. 23, Qingnian Road

department: First Affiliated Hospital

institute: Gannan Medical University

summary: Enhancers are genomic regulatory elements shown to play key roles in controlling cell type-specific gene expression, regulated by signal-dependent transcription factors and co-factors. Distinct classes of enhancers can specify distinct gene expression profiles and biological outcomes. Recent studies suggested that bidirectional non-coding RNAs (ncRNAs), referred as enhancer RNA (eRNAs), are transcribed on enhancers, which are tightly associated with enhancer activity. However, the protein factors which govern the activation of enhancers remain poorly characterized. Here we reported that a Jumonji C (JmjC) domain-containing protein demethylase, JMJD6, is a determinant for estrogen/estrogen receptor (ER)-induced enhancer activation, coding gene transcription, breast cancer cell growth and tumorigenesis. Mechanistically, JMJD6 was found to be specifically recruited onto ER-bound active enhancers in response to estrogen stimulation, which was required for RNA Pol II recruitment and eRNA production of enhancers, leading to transcriptional activation of cognate estrogen target genes. Furthermore, JMJD6 was found to be physically and functionally associated with MED12 in the mediator complex to regulate estrogen-induced transcriptional activation, with JMJD6 was required for MED12 recruitment onto active enhancers. Specifically, JMJD6 was essential for MED12 to interact with CARM1, an arginine methyltransferase well known to be implicated in estrogen-induced transcriptional activation, which methylated MED12 at its c-terminus at multiple arginine methylation sites and was required for MED12 binding with chromatin. Collectively, our data uncovered a critical regulator of estrogen/estrogen receptor-induced enhancer activation and coding gene transcription, providing a potential drug candidate for developing novel strategies targeting ER-positive breast cancers.

overall_design: Gro-seq performed in this study was designed to understand the molecular mechanisms underlying JMJD6 regulation of breast cancer

first: Wen

last: Liu

first: Wen-juan


title: Analysis of experience-regulated transcriptome and imprintome during critical periods of mouse visual system development

city: Taipei

first: Hsien-Sung

last: Huang

address: Rm: 1547, 15th Floor, No.1, Sec.1, Ren-ai Rd.

country: Taiwan

institute: National Taiwan University

summary: Visual system development is light-experience dependent, which strongly implicates epigenetic mechanisms in light-regulated maturation. Among many epigenetic processes, genomic imprinting is an epigenetic mechanism through which monoallelic gene expression occurs in a parent-of-origin-specific manner. It is unknown if genomic imprinting contributes to visual system development. We profiled the transcriptome and imprintome during critical periods of mouse visual system development under normal- and dark-rearing conditions using B6/CAST F1 hybrid mice. We identified experience-regulated, isoform-specific, and brain region-specific imprinted genes. We also found imprinted microRNAs were predominantly clustered into the Dlk1-Dio3 imprinted locus with light experience affecting some imprinted miRNA expression. Our findings provide the first comprehensive analysis of light-experience regulation of the transcriptome and imprintome during critical periods of visual system development. Our results may contribute to therapeutic strategies for visual impairments and circadian rhythm disorders resulting from a dysfunctional imprintome.

overall_design: We performed RNA-Seq on retina, motor cortex, SCN and visual cortex from normal- and dark-reard mouse and DNA-Seq on one mouse tail. The strain of mouse is a hybrid of B6 and CAST. F1i is the offspring from the mating of female CAST and male B6 mice. The F1r is the offspring from the mating of female B6 and male CAST mice.


title: Prerequisite Barcoding of Cell-Type-Restricted Enhancers by ESC Transcription Factors in ESCs Licenses Their Robust Developmental Activation

city: La jolla

first: Hong

last: Kim

address: 9500 Gilman Dr.

institute: University of California, Sand diego

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

overall_design: Refer to individual Series


title: JMJD6 licenses estrogen receptor alpha-dependent enhancer RNA and coding gene activation by modulating CARM1/MED12 co-activator complex in breast cancer [ChIP-Seq]

overall_design: ChIP-seq performed in this study was designed to understand the molecular mechanisms underlying JMJD6 regulation of breast cancer


title: Prerequisite Barcoding of Cell-Type-Restricted Enhancers by ESC Transcription Factors in ESCs Licenses Their Robust Developmental Activation [ChIP-Seq]

summary: While cell-type-restricted enhancers are initially detected following cooperative binding of positionally-determined DNA binding transcription factors during determination/differentiation, it remains unknown whether there are preceding events in embryonic stem cells (ESCs) that are functionally important to activate cell-type-restricted enhancer networks. Here, using murine macrophages as a model, we report that, while largely devoid of characteristic enhancer marks (H3K4me1, H3K4me2, H3K27Ac, H3K27me3 and p300) in ESCs, macrophage enhancers are activated as transcription units mainly by the binding of a single, at most two, ESC transcription factors. This provides “premarking” of these enhancers, as is also observed for other cell types. In contrast, ESC-active enhancers are cooperatively bound by multiple ESC transcription factors, including Esrrb, Nanog, Oct4 and Sox2 (ENOS). Interestingly, the strength of this signature in ESCs is functionally important for subsequent robust cell-restricted enhancer activation during macrophage differentiation events, as independently demonstrated by analysis of multiple ENOS motif–deleted macrophage-restricted enhancers. The ENOS-determined location of hydroxymethylation of the enhancers in ESCs could serve as a potential molecular memory for subsequent enhancer activation in the mature macrophage. These findings suggest that the massive repertoire of cell-type-restricted enhancers are essentially hierarchically and obligatorily “barcoded” by binding of a single ESC transcription factor in ESCs, with the strength of their binding dictating enhancer activation in mature cells.

overall_design: All ChIP-Seq experiments were designed to understand [1] the unique signature and function of ESC factors in cell type specific enhancers [2] the chromatin signature in macrophage enhancers in 2i or serum cultured ESCs.


title: Idiopathic pulmonary fibrosis bronchoalveolar lavage cells RNA-seq indicates macrophage expression of pro-inflammatory M1/M2 activation concomitant with radical species metabolism inhibition

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

institute: European Brain Research Institute

summary: Current concepts of idiopathic pulmonary fibrosis (IPF) are that microscopic injury drives alveolar epithelial cell dysregulated activation and epithelial mesenchymal transition, ensuing fibrocyte recruitment,  fibroblast proliferation and ECM deposition. With the background that IPF is also characterized by chronic accumulation of activated alveolar macrophages (aMAC) in the lower respiratory tract, we assessed IPFaMAC gene expression to identify patterns of activation, by RNA-seq using Illumina platform. To this we evaluated a population of 7 normal smoking controls and 16  IPF smoking patients. All IPFs had abnormal lung function and bronchoalveolar lavage (BAL) showing  >80% macrophage counts and augmented spontaneous O2 radical release. RNA was extracted from whole BAL cells. Reads were mapped onto the UCSC mRNA database (GRCh37/hg19 version), and transcripts were aggregated by gene symbol, obtaining a final 19,723 unique protein-coding gene ID list, used for further analysis.

overall_design: RNA-seq transcriptomics of idiopathic pulmonary fibrosis (IPF) patients vs controls: RNA samples were extracted from macrophages obtained from bronchoalveolar lavage (BAL)

first: Jungnam

last: Lee

first: Ermanno

last: Puxeddu

first: Lazarus

middle: K

last: Mramba

first: Massimo

last: Amicosante

first: Carmen

last: Swaisgood

first: Marco

last: Pallante

first: Mark

last: Brantly

first: Cesare

last: Saltini


title: Di- and trimeric biological switches made of nanobody-cytokine receptor fusion proteins simulate  IL-23 signaling

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

summary: Cytokine-induced signal transduction is executed by natural biological switches, which among many others control immune related processes. To construct a biological device, that simulates cytokine signaling, we utilized nanobodies to generate synthetic cytokine receptors (SyCyR). High affinity GFP- and mCherry-nanobodies were selected and extracellularly fused to trans-membrane and intracellular domains of IL-23 cytokine receptors. Soluble homo- and heterodimeric GFP:mCherry fusion proteins served as SyCyR ligands. Heterodimeric GFP-mCherry and homodimeric GFP fusion proteins efficiently phenocopied IL-23 signal transduction, respectively, as demonstrated by STAT3-, ERK- and Akt-activation, SOCS3 expression and transcriptome profiling. Interestingly, the homodimeric GFP fusion protein induced IL-23 receptor homo-dimerization and activation of IL-23-like signal transduction

overall_design: We used microarrays to detail the the overall influence of the constructs to confirm background free stimulation of cytokine signalling to elucidate receptor combinations with trans-phosphorylation capacity.

first: Erika

last: Engelowski

first: Christian

last: Binsch

first: Hadi

last: Al-Hasani

first: Jürgen

last: Scheller


title: JMJD6 licenses estrogen receptor alpha-dependent enhancer RNA and coding gene activation by modulating CARM1/MED12 co-activator complex in breast cancer

first: Wenjuan

last: Zhang


title: Locus-specific control of the de novo DNA methylation pathway [ChIP-seq]

status: Public on Apr 14 2018

city: San Diego

first: Julie

last: Law

state: CALIFORNIA

address: 10010 N Torrey Pines Rd, La Jolla

institute: Salk Institute for Biological Studies

summary: Abstract: Cytosine DNA methylation plays crucial roles in gene regulation, transposon silencing, and diverse developmental processes. While methylation patterns are known to differ between cell-types, tissues, and disease states, how these differences arise remains poorly understood. In plants, DNA methylation is established via the RNA-directed DNA methylation pathway (RdDM), wherein 24-nucleotide small interfering RNAs (siRNAs) guide methylation at cognate genomic loci1. RNA POLYMERASE-IV (Pol-IV), a plant-specific polymerase, initiates the biogenesis of these methylation-targeting RNAs, thus understanding how Pol-IV is regulated is critical in determining how specific patterns of DNA methylation are generated. Here we show roles for four Pol-IV-associated factors, CLASSY (CLSY) 1-42,3, in both locus-specific and global regulation of Pol-IV function. Individually, each CLSY protein controls siRNA production and Pol-IV chromatin association at unique set of loci. This translates into locus-specific DNA methylation losses and the release of silencing. In addition to locus-specific effects, several layers of redundancy were identified: The clsy1,2 and clsy3,4 mutants act synergistically, regulating thousands more siRNA loci than the single mutants. Furthermore, the clsy1,2- and clsy3,4-dependent loci are mutually exclusive and geographically distinct, revealing a striking division of labor amongst the CLSY family. Finally, the clsy quadruple mutant causes global siRNA losses, demonstrating that Pol-IV is completely dependent on the CLSY family. Investigation into the mechanisms underlying the CLSY specificity revealed connections between clsy1,2- and clsy3,4-dependent loci and either SAWADEE HOMEODOMAIN HOMOLOG 1 or DNA METHYLTRANSFERASE 1, demonstrating a reliance on different chromatin modifications, H3K9 or CG DNA methylation, respectively4,5. Together, these findings not only shed light on Pol-IV function, but also reveal an additional layer of complexity to the RdDM pathway that enables the locus-specific control of DNA methylation patterns. Given the parallels between methylation systems in plants and mammals1, these findings will be informative for analogous processes in a broad range of organisms.

overall_design: 14 ChIP-seq libraries were sequenced

first: Ming

last: Zhou


title: Analysis of microarray data reliability and pathway networks using experimental formalin-fixed paraffin-embedded tissue

status: Public on Apr 13 2018

city: Vienna

first: Isabella

last: Wimmer

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

summary: We assessed the usability of microarrays, which base on formalin-fixed paraffin-embedded (FFPE) tissue.

overall_design: We used CX3CR1-CreERT2+/–/iDTR+/– mice, which were injected with tamoxifen and diphtheria toxin to induce the depletion of microglia cells. Tissue was harvested 10 days post injection. We included 4 depleted mice as well as 4 control mice that received tamoxifen injections only. From each mouse brain, the motor cortex and the somatosensory cortex were microdissected.

first: F

last: Brunner

first: I


title: Systematic evaluation of RNA quality and microarray data reliability in human formalin-fixed paraffin-embedded and fresh frozen tissue samples

summary: We assessed the feasibility and reliability of microarray studies using formalin-fixed paraffin-embedded (FFPE) tissue-derived RNA compared with transcriptome data from paired fresh-frozen (FF) material. We established a robust workflow to generate highly reproducible microarray datasets from only 2 ng RNA input. For prior quality assessment, inspection of Agilent Bioanalyzer electropherograms, calculation of RNA fragment size distribution (DV200) and routine qPCR for selected references genes were done.

overall_design: The study bases on tissue samples (hippocampus of right hemisphere) from three epileptic patients suffering from Rasmussen encephalitis. After surgical resection, the tissue was coronally cut into two parts. One part was immediately snap-frozen and stored at -80 °C (FF samples). The second half was fixed in 4% PFA and embedded in paraffin (FFPE samples).

first: A

middle: R

last: Tröscher


title: Systematic evaluation of RNA quality and microarray data reliability in rat formalin-fixed paraffin-embedded and fresh frozen tissue samples

overall_design: The study bases on microdissected striatal areas from rat brain tissue. We included 3 samples derived from FF tissue and 3 samples derived from FFPE blocks.


title: The miRNA-targeted transcriptome of porcine alveolar macrophages upon infection with Porcine Reproductive and Respiratory Syndrome Virus

city: Jouy-en-Josas

last: Moroldo

address: Domaine de Vilvert

department: Animal Genetics

institute: INRA


title: GATA2 in mesenchymal stem cells controls bone trabecularization and hematopoiesis

first: Cornelius

last: Fischer


title: Gene expression analysis on renal tubule epithelial cells, mIMCD3, with or without FGF23 stimulation.

city: Wakayama

first: Mitsuru

last: Yashiro

state: Wakayama Prefecture

address: 811-1, Kimiidera

department: Nephrology

institute: Wakayama Medical University

summary: FGF23 has been known to play an important role of calcium-phosphorus (Ca-P) metabolism. Recently, biological roles of FGF23 other than Ca-P metabolism were reported, such as commitment to myocardium enlargement and immunological roles in spleen. Thus, it was thought FGF23 might have roles other than Ca-P metabolism in renal tubule epithelial cells. So, we tried to identify new biological roles of FGF23 in those cells using DNA microarray analysis in mouse renal tubule epithelial cell line, mIMCD3, with FGF23 stimulation. As the results, expressions of 8 genes were upregulated and those of 18 genes were downregulated in mIMCD3 with FGF23 stimulation compared to those in mIMCD3 without FGF23 stimulation. Three out of 8 upregulated genes were protein coding genes and remaining 5 genes were non protein coding genes. Fifteen out of 18 downregulated genes were protein coding genes and remaining 3 genes were non protein coding genes.

overall_design: To identify new biological roles of FGF23 in renal tubule epithelial cells other than Ca-P metabolism, the gene expression analysis using DNA microarray was performed using total RNA from mouse renal tubule epithelial cell line, mIMCD3 stimulated with 10ng/mL of FGF23 for 4hours. We use total RNA from mIMCD3 without FGF23 stimulation as a control. The gene expressions were directly compared between with and without FGF23 stimulation on mIMCD3.

first: Masaki

last: Ohya

first: Toru

last: Mima

first: Yumi

last: Ueda

first: Yuri

last: Nakashima

first: Kazuki

last: Kawakami

first: Yohei

last: Ishizawa

first: Shuto

last: Yamamoto

first: Sou

last: Kobayashi

first: Takurou

last: Yano

first: Yusuke

last: Tanaka

first: Kouji

last: Okuda

first: Tomohiro

last: Sonou

last: Syoshihara

first: Yuko

last: Iwashita

first: Yu

first: Kouichi

last: Tatsuta

first: Ryo

last: Matoba

first: Shigeo

last: Nagi

first: Takashi

last: Shigematsu


title: Systematic evaluation of RNA quality and microarray data reliability in formalin-fixed paraffin-embedded and fresh frozen tissue samples

first: Isabella

last: Wimmer

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus


title: Single-cell RNA-seq of murine small intestine crypts

city: Utrecht

first: Jean-Charles

last: Boisset

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: We here systematically studied the interaction network of small intestine crypt cells.We first created a reference of cell types based on single-cell mRNA sequencing, which we used to create virtual doublets and triplets. These virtual combinations were then used to train a machine learning algorithm (random forests) in order to infer the cell types present in the actual picked doublets or triplets. We then counted the number of interactions in between defferent cell types, and compared it to label permution simulation to identify interactions that happens more or less than expected by chance.

overall_design: After dissociation of the small intestine crypts, we sorted single-cells for mRNA sequencing. In addition, after mild dissociation of the small intestine crypts, we picked small interacting structures (cell doublets, triplets), and sequenced their mRNAs.

first: Mauro

last: Muraro

first: Anna

last: Lyubimova

first: Alexander

last: van Oudenaarden


title: Downregulated d-limonene transgenic orange trees with increased linalool content showed resistance to Phyllosticta citricarpa

city: Valencia

first: Ana

last: Rodríguez

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: Biotecnología de cítricos

institute: Instituto de Biología Molecular y Celular de Plantas (IBMCP)

summary: Terpene volatiles play an important role in the interactions among specialized pathogens and fruits. Citrus Black Spot (CBS), caused by the fungus Phyllosticta citricarpa, is associated with losses in different citrus-growing areas worldwide. The pathogen may infect the fruit for 20-24 weeks after petal fall but the typical hard spot symptoms appear when the fruit become almost mature, as consequence of fungal colonization and induction of cell lyses around essential oil cavities. D-limonene represents about 95% of total oil gland content in mature orange fruit. We have used here d-limonene synthase downregulated orange fruit generated via an antisense (AS) approach to investigate whether d-limonene decrease content in peel oil glands may affect fruit interaction with P. citricarpa compared to that of empty-vector (EV) controls. AS fruit showed enhanced resistance to the fungus compared to EV ones. Because of d-limonene decreased content, an over-accumulation of linalool and other monoterpene alcohols was found in AS compared to EV fruit. A global gene expression analysis at 2h and 8d after inoculation with P. citricarpa revealed activation of defence responses in AS fruit, via the upregulation of different PR genes, likely due to the enhanced constitutive accumulation of linalool and other alcohols. When assayed in vitro and in vivo, the main altered terpene volatile compounds including linalool at concentrations emulating those present in AS fruit, showed strong antifungal activity. We show here that terpene engineering in fruit peels could be a promising method for developing new strategies to obtain resistance to fruit diseases.

overall_design: Microarray assays were performed with the flavedo of two independent antisense (AS1 and AS7) and empty-vector (EV) control transgenic ‘Navelina’ mature orange fruit. AS and EV samples were compared randomly on the same slide with three biological replicates for each genotype (AS1, AS7 and EV) at two time-points (2 hours and 8 days after inoculation with the fungus Phyllosticta citricarpa)

first: Vanessa

last: Kava

first: Lorena

last: Latorre-García

first: Geraldo

last: da Silva Jr

first: Rosana

middle: G

last: Pereira

first: Chirlei

last: Glienke

first: Lisandra

middle: S

last: Ferreira-Maba

first: Antonio

last: Vicent

first: Takehiko

last: Shimada

first: Leandro

last: Peña


title: The miRNA-targeted transcriptome of porcine alveolar macrophages upon infection with Porcine Reproductive and Respiratory Syndrome Virus (RISC bound RNA)

first: Marco

last: Moroldo

summary: Porcine alveolar macrophages were challenged in vitro with a low virulent strain of the Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) to identify and characterize the population of host genes subjected to miRNA post-transcriptional regulation durign early viral infection.  We employed a high-throughput biochemical assay, i.e. the immunoprecipitation of RISCs followed by microarray analysis of the RISC-bound miRNA targets (RIP-Chip). qPCR analyses were carried out to validate the resolution of the microarray and to determine levels of expression of a panel of eight miRNAs (ssc-miR-142-3p, ssc-miR-142-5p, ssc-let-7f, miR-146a-5p, miR-155-5p, ssc-miR-181a, ssc-miR-21 and ssc-miR-335).

overall_design: Lung alveolar macrophages were obtained by lung lavage from 4 animals. Cells were infected in vitro with the strain Finistère at multiplicity of infection of 2, or mock infected.  Infected cells were harvested at 7 and 10 hours post-infection; control (mock infected) cells were collected at the same times. Total RNAs were extracted from total cell contents and from RISC (RNA-induced Silencing Complex) immunoprecipitates. RNAs were hybridized on microarrays and transcripts analyzed for relative enrichment in RISC (RIP-Chip technology).

first: Sophie

last: Dhorne-Pollet

first: Nuria

last: Mach

first: Patricia

last: Renson

first: Florence

last: Jaffrézic

first: Guillemette

last: Marot

first: Tatiana

last: Maroilley

first: Jérôme

last: Lecardonnel

first: Olivier

last: Bourry

first: Elisabetta

last: Giuffra


title: DNA methylation signatures of pulmonary arterial smooth muscle cells in chronic thromboembolic pulmonary hypertension

city: Beijing

first: Ying

last: Wang

address: 8 Gongren Tiyuchang Nanlu, Chaoyang District

institute: Beijing Chao-Yang Hospital

type: Methylation profiling by genome tiling array

overall_design:
Genome wide DNA methylation profiling of normal  pulmonary arterial smooth muscle cell lines (PASMCs) and PASMCs of chronic thromboembolic pulmonary hypertension (CTEPH) patients. The Illumina Infinium 450k Human DNA methylation Beadchip  was used to obtain DNA methylation profiles across approximately 485,000 CpGs. Samples included 3 normal commercially human cell lines and  cultured PASMCs from the patient endarterectomy tissues of five patients with CTEPH.
Bisulphite converted DNA from the 8 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip