title: Spo11-oligo mapping in Saccharomyces species (S. paradoxus, S. mikatae, S. kudriavzevii) and wild-derived S. cerevisiae strains (YPS128, UWOPS03-461.4)

city: New York

first: Isabel

last: Lam

state: New York

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: The nonrandom distribution of meiotic recombination shapes heredity and genetic diversification. A widely held view is that individual hotspots - favored sites of recombination initiation - are always ephemeral because they evolve rapidly toward extinction. An alternative view, often ignored or dismissed as implausible, predicts conservation of the positions of hotspots if they are chromosomal features under selective constraint, such as gene promoters. Here we empirically test opposite predictions of these theories by comparing genome-wide maps of meiotic recombination initiation from widely divergent species in the Saccharomyces clade. We find that the frequent overlap of hotspots with promoters is true of the species tested and, consequently, hotspot positions are well conserved. Remarkably, however, the relative strength of individual hotspots is also highly conserved, as are larger-scale features of the distribution of recombination initiation. This stability, not predicted by prior models, suggests that the particular shape of the yeast recombination landscape is adaptive, and helps in understanding evolutionary dynamics of recombination in other species.

sample_organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus
Saccharomyces kudriavzevii
Saccharomyces mikatae

overall_design: Ten samples total: two biological replicate Spo11-oligo maps of each of the following: wild-derived S. cerevisiae strain YPS128, wild-derived S. cerevisiae UWOPS03-461.4, S. paradoxus YPS138, S. mikatae IFO1815, S. kudriavzevii ZP591

last: Keeney


title: Gene expression during biting behavior in zombie ants reflects the complexity of fungal pathogenic manipulation of ants

status: Public on Aug 18 2015

city: Munich

first: Charissa

last: de Bekker

state: Bayern

address: Goethestrasse 31

department: Institute for Medical Psychology

country: Germany

institute: Ludwig Maximilian University

type: Expression profiling by high throughput sequencing

summary: The biting behavior observed in Carpenter ants infected by the specialized fungus Ophiocordyceps unilateralis s.l. is an example of a complex host behavioral manipulation by parasite. Though parasitic manipulation of host behavior is generally assumed to be due to the parasite’s gene expression, few studies have set out to test this. We experimentally infected Carpenter ants to collect tissue from both parasite and host during the time period when manipulated biting behavior is experienced. Upon observation of synchronized biting, samples were collected and subjected to RNA-Seq analyses. We also sequenced and annotated the O. unilateralis s.l. genome as a reference for the fungal reads. Our mixed transcriptomics approach, together with a comparative genomics study, shows that the majority of the fungal genes that are up-regulated during manipulated biting behavior are unique to the O. unilateralis s.l. genome. This study furthermore reveals that the fungal parasite might be regulating immune- and neuronal stress responses in the host during manipulated biting, as well as impairing its chemosensory communication and causing apoptosis. Moreover, we found genes up-regulated during manipulation that putatively encode for proteins with reported effects on behavioral outputs, proteins involved in various neuropathologies, and proteins involved in the biosynthesis of secondary metabolites such as alkaloids.

sample_organism:
Camponotus castaneus
Ophiocordyceps unilateralis

overall_design: Analysis of mixed transcriptomes during host-parasite interactions. In triplicates, we examinated the gene expression of ant host (Camponotus castaneus) and fungal parasite (Ophiocordyceps unilateralis s.l.) in infected ant heads during and after manipulated biting behavior. As controls, we used healthy ants and fungal cultures grown in shaking flasks with Grace's insect medium supplemented with 10% FBS.

first: Robim

middle: A

last: Ohm

first: Raquel

middle: G

last: Loreto

first: Aswathy

last: Sebastian

first: Istvan

middle: U

last: Albert

first: Martha

last: Merrow

first: Andreas

last: Brachmann

first: David

middle: P

last: Hughes


title: Single-Cell mRNA Sequencing Reveals Rare Intestinal Cell Types

status: Public on Aug 19 2015

city: Freiburg

first: Dominic

last: Grün

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Understanding the development and function of an organ requires the characterization of all of its cell types. Traditional methods for visualizing and isolating sub-populations of cells are based on mRNA or protein expression of only few known marker genes. The unequivocal identification of a specific marker gene, however, poses a major challenge, particularly if this cell type is rare. Identifying rare cell types, such as stem cells, short-lived progenitors, cancer stem cells, or circulating tumor cells is crucial to acquire a better understanding of normal or diseased tissue biology. To address this challenge we sequenced the transcriptome of hundreds of randomly selected cells from mouse intestinal organoids, cultured self-organizing epithelial structures that contain all cell lineages of the mammalian intestine. Organoid buds, like intestinal crypts, harbor stem cells that continuously differentiate into a variety of cell types, occurring at widely different abundances. Since available computational methods can only resolve more abundant cell types, we developed RaceID, an algorithm for rare cell type identification in complex populations of single cells. We demonstrate that this algorithm can resolve cell types represented by only a single cell in a population of randomly sampled organoid cells. We use this algorithm to identify Reg4 as a novel marker for enteroendocrine cells, a rare population of hormone producing intestinal cells. Next, we use Reg4 expression to enrich for these rare cells and investigate the heterogeneity within this population. Reassuringly, RaceID confirmed the existence of known enteroendocrine lineages, and moreover, discovered novel subtypes, which we subsequently validated in vivo. Having validated RaceID by this proof-of-principle experiment we then apply the algorithm to ex vivo isolated LGR5 positive cells and their direct progeny and demonstrate homogeneity of the stem cell pool. We envision broad applicability of our method for discovering rare cell types and the corresponding marker genes in healthy and diseased organs.

overall_design: Small intestinal crypts were isolated from a single wild-type C57BL/6 mouse, a Reg4-dsRed-knock-in mouse and an Lgr5-GFP-DTR mouse. The crypts were propagated and expanded in culture as organoids. For each experiment, multiple organoids were harvested and dissociated into single cells. Each experiment was done twice, using different passage of the same organoid culture. We also included a pool-and-split control for 96 Reg4-dsRed positive intetsinal cells and a control library with 5 mouse embryonic stem cells (wells 1-5), 5 mouse embryonic fibroblasts (wells 6-10), 75 random organoid cells (wells 11-85), 5 wells without primer and without template (wells 86 and 93-96), and five wells with primer and without template (wells 87-92). We also sequenced two 96 well plates of Lgr5-EGFP positive single cells isolated ex vivo, and Lgr5 progeny collected after five days of lineage tracing. Label induction was performed using an Lgr5-Cre reporter mouse expressing YFP from Rosa26 promoter with a loxP flanked transcriptional road block in between. Five 96 well plates of YFP positive were sequenced. Sample number four also contains also unrelated samples (single cell barcode 49-96), which should be discarded.

first: Anna

last: Lyubimova

first: Lennart

last: Kester

first: Kay

last: Wiebrands

first: Onur

last: Basak

first: Nobuo

last: Sasaki

first: Hans

last: Clevers

first: Alexander

last: van Oudenaarden


title: Non-paradoxical evolutionary stability of the recombination initiation landscape in Saccharomycetes

status: Public on Aug 17 2015

first: Isabel

last: Lam

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

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

platform_organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus
Saccharomyces kudriavzevii
Saccharomyces mikatae

overall_design: Refer to individual Series


title: Transcriptome analysis of CD4+ T cells reveals imprint of BACH2 and IFNγ regulation

city: Dublin

first: Emma

middle: Marie

last: Quinn

state: Leinster

address: Institute of Molecular Medicine, St James's hospital Campus

department: Clinical Medicine

country: Ireland

institute: Trinity College Dublin

summary:
We used RNA sequencing to profile over 70 transcriptomes of CD4+ T cells, a cell type crucial for Coeliac Disease CD pathogenesis, in both stimulated and resting samples from individuals with CD and unaffected controls
The data gave us the opportunity to (i) compare gene expression between cases and controls; (ii) specifically assess whether genes that have been genetically associated with the disease were being DE; (iii) and also look for known and novel aspects of pathogenesis in the transcriptome of this specific cellular compartment.

overall_design: RNA sequencing was performed on mRNA  extracted from the CD4+ T cells of 15 Coeliac patients and 11 Controls that had been stimulated with anti-CD3/anti-CD28, PMA and left unstimulated. In total we sequenced 74 transcriptome samples using 50bp reads on an Illumina HiSeq™ 2000.

middle: M

first: Ciara

last: Coleman

first: Ben

last: Molloy

first: Valerie

last: Trimble

first: Nasir

last: Muhmud

first: Ross

last: McManus


title: Whole-genome nucleosome mapping in meiotic diploid Saccharomyces species (S. paradoxus, S. mikatae, S. kudriavzevii) and wild-derived S. cerevisiae strains (YPS128, UWOPS03-461.4)

summary: We determined nucleosome positions genome-wide in diploid Saccharomyces species undergoing early stages of synchronous meiosis. This study sought to assess if meiotic DNA double-strand break formation occurred preferentially in promoter nucleosome-depleted regions in other Saccharomyces species, as it does in S. cerevisiae SK1 (Pan et al. 2011 Cell 144:719-731).

overall_design: Twelve samples were sequenced: three samples of S. cerevisiae YPS128 (two biological replicates, and a technical replicate digested with different amount of MNase), two biological replicates of S. cerevisiae UWOPS03-461.4, three samples of S. paradoxus (two biological replicates, and a technical replicate digested with different amount of Mnase), two biological replicates of S. mikatae, two biological replicates of S. kudriavzevii.

first: Scott

last: Keeney


title: An Interaction between RRP6 and SU(VAR)3-9 Targets RRP6 to Heterochromatin and Contributes to Heterochromatin Maintenance in Drosophila melanogaster [RNA-seq]

status: Public on Aug 20 2015

city: Stockholm

first: Neus

last: Visa

address: Svante Arrhenius väg 20c

department: Molecular Biosciences, The Wenner-Gren Institute (MBW)

country: Sweden

institute: Stockholm University

summary: We have investigated the effect of RRP6 depletion on the transcriptome of S2 cells using Illumina deep RNA sequencing. We have also carried out Illumina ChIP-seq analysis of RRP6 genome occupancy in control S2 cells (GFP-KD) and in cells depleted of SU(VAR)3-9.

overall_design: 8 samples total; 4 RNA-Seq samples (1 RRP6-KD and 1 GFP-KD, 2 biological replicates each); and 4 ChIP-Seq samples (RRP6 IP in GFP-KD and in Su(var)3-9-KD conditions; plus their respective Input samples).

first: Andrea

middle: B

last: Eberle

first: Antoni

last: Gañez-Zapater

first: Antonio

last: Jordán-Pla

first: Viktoria

last: Hessle

first: Gilad

last: Silberberg

first: Anne

last: von-Euler

first: Rebecca

last: Silverstein


title: Human DIS3 shapes the RNA polymerase II transcriptome degrading variety of unwanted transcripts.

city: Warszawa

first: Andrzej

last: Dziembowski

address: Pawinskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

summary: Human DIS3 is a nuclear, catalytic subunit of the exosome complex containing exonucleolytic and endonucleolytic active domains. To identify DIS3 targets genome-wide we conducted comprehensive transcriptomic analysis of HEK293 cells producing mutated DIS3 versions and Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) experiments. Pervasive transcription products like Promoter Upstream Transcripts (PROMPTs) accumulated robustly in catalytic DIS3 mutants, representing ~8% of PAR-CLIP reads. Importantly, RNAs originating from unannotated genomic regions increased ~2.5 times in double DIS3 mutants, covering ~70% of genome and allowing for discovery of thousands of  novel transcripts. The first intron of many pre-mRNAs accumulated in DIS3 mutants indicating a widespread premature RNA polymerase II termination. The short form of NEAT1 lincRNA was overexpressed in DIS3 mutants, leading to increased number of paraspeckles. Moreover, there was a global deregulation of mRNAs in DIS3 double mutant. Finally, snoRNA precursors accumulated, which correlated with a strong PAR-CLIP signal indicating that DIS3 but not RRP6 is a main snoRNA processing enzyme. In aggregate, we demonstrate that DIS3 is a major nucleoplasmic activity responsible for shaping the human transcriptome.

overall_design: RNA-seq experiments were performed in triplicates for DIS3 wild type (control), DIS3 PIN, DIS3 RNB domain mutants and DIS3 PIN RNB double mutant. RNA-seq samples from DIS3 wild type and DIS3 double mutant were additionally sequenced in deeper resolution, also in triplicates. DIS3 PAR-CLIP experiment was performed in duplicate. Pol II ChIP-seq experiment in WT and DIS3 PIN RNB double-mutants cells was performed in triplicates.

first: Teresa

last: Szczepińska

first: Katarzyna

last: Kalisiak

first: Rafal

last: Tomecki

first: Anna

last: Labno

first: Lukasz

middle: S

last: Borowski

first: Tomasz

last: Kulinski

first: Dorota

last: Adamska


title: An ensemble-guided approach identifies ClpP as a major regulator of transcript levels in nitric oxide-stressed Escherichia coli

city: Princeton

first: Mark

last: Brynildsen

state: NJ

address: 25 William Street

department: Chemical and Biological Engineering

institute: Princeton University

summary: In this study, we discovered that elimination of ClpP in E. coli largely impaired its ability to detoxify nitric oxide (NO•). Using a quantitative model of NO• stress, we employed an ensemble approach to identify the underlying mechanism. The ensemble of models consisted of 127 plausible mechanisms through which ΔclpP could impact the NO• response network, and in silico analyses identified conditions enabling discrimination between mechanisms. The corresponding experiments were conducted and used to reject inconsistent mechanisms until the attenuated NO• detoxification of ΔclpP was attributed to deficient transcript levels of hmp, which encodes NO• dioxygenase. Further analysis (including RNA sequencing) revealed that ΔclpP imparted widespread perturbations to the expression of NO•-responsive genes. This work identified a target for anti-infective therapies based on disabling NO• defenses, and demonstrated the utility of model-based approaches for exploring the complex, systems-level stress exerted by NO•.

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

overall_design: Using RNA sequencing via Illumina HiSeq 2500, mRNA profiles of aerobic exponential-phase E. coli WT MG1655 and a ΔclpP mutant, untreated and treated with 250 μM DPTA (an NO•-releasing compound) for 10 min. Samples were obtained in biological triplicate, multiplexed, and barcoded for identification.

first: Jonathan

middle: L

last: Robinson


title: Ribosome profiling reveals an important role for translational control in circadian gene expression

city: Philadelphia

first: Nicholas

last: Lahens

state: PA

address: Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421

department: ITMAT

institute: University of Pennsylvania

summary: Physiological and behavioral circadian rhythms are driven by a conserved transcriptional/translational negative feedback loop in mammals. Although most core clock factors are transcription factors, post-transcriptional control introduces delays that are critical for circadian oscillations. Little work has been done on circadian regulation of translation, so to address this deficit we conducted ribosome profiling experiments in a human cell model for an autonomous clock. We found that most rhythmic gene expression occurs with little delay between transcription and translation, suggesting that the lag in the accumulation of some clock proteins relative to their mRNAs does not arise from regulated translation. Nevertheless, we found that translation occurs in a circadian fashion for many genes, sometimes imposing an additional level of control on rhythmically expressed mRNAs and, in other cases, conferring rhythms on non-cycling mRNAs.  Most cyclically transcribed RNAs are translated at one of two major times in a 24h day, while rhythmic translation of most non-cyclic RNAs is phased to a single time of day. Unexpectedly, we found that the clock also regulates the formation of cytoplasmic processing (P) bodies, which control the fate of mRNAs, suggesting circadian coordination of mRNA metabolism and translation.

overall_design: U2-OS cell time course over one day of 12 wildtype total RNA-seq samples, 12 wildtype ribosome profiling samples, 12 Bmal1 knockdown total RNA-seq samples and 12 Bmal1 knockdown ribosome profiling samples. All samples have duplicates.

first: Christopher

last: Jang

middle: F

first: John

last: Hogenesch

first: Amita

last: Sehgal


title: Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

country: China

institute: shenzhen university

type: Non-coding RNA profiling by high throughput sequencing

summary: 3’ uridylation is increasingly recognized as a conserved RNA modification process associated with RNA turnover in eukaryotes. 2’-O-methylation on the 3’ terminal ribose protects micro(mi)RNAs from 3’ truncation and 3’ uridylation in Arabidopsis. Previously, we identified HESO1 as the nucleotidyl transferase that uridylates most unmethylated miRNAs in vivo, but substantial 3’ tailing of miRNAs still remains in heso1 loss-of-function mutants. In this study, we found that among nine HESO1 paralogs, UTP:RNA URIDYLYLTRANSFERASE 1 (URT1) is the single most predominant nucleotidyl transferase that tails miRNAs. URT1 and HESO1 prefer substrates with different 3’ end nucleotides in vitro and act cooperatively to tail different forms of the same miRNAs in vivo. Moreover, both HESO1 and URT1 exhibit nucleotidyl transferase activity on AGO1-bound miRNAs. Although these enzymes are able to add long tails to AGO1-bound miRNAs, the tailed miRNAs remain associated with AGO1. In fact, we show that a tailed miRNA acquires the ability to trigger the production of secondary siRNAs. Therefore, 3’ uridylation could endow new properties to miRNAs in addition to its known effects in miRNA degradation.

overall_design: 12 small RNA libraries were sequenced

first: Bin

last: Tu

first: Xuemei

last: Chen


title: A high-resolution map of inner kinetochore proteins in fission yeast regional centromeres

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: We use high-resolution chemical cleavage mapping and both native and cross-linked chromatin immunoprecipitation with paired-end sequencing to elucidate the profile of nuceleosomes containing the centromere-specific variant of H3 (cenH3), known as CENP-A or Cnp1 in fission yeast. We find that in the central domain of fission yeast centromeres H3 nucleosomes are nearly absent and CENP-A nucleosomes are more widely spaced that nucleosomes elsewere. CENP-A (Cnp1), CENP-C (Cnp3), CENP-T (Cnp20) and CENP-I (Mis6) are highly enriched at every position in the central domain except at tRNA genes, with weak enrichment in the flanking heterochromatin where these proteins show no evidence of the positioning that has been seen in point centromeres and in the satellite-rich centromeres of plants and animals. Our findings suggest that classical regional centromeres are distinguished from other centromere classes by the absence of cenH3 nucleosome positioning.

overall_design: We have analyzed the chromatin landscape of the Schizosaccharomyces pombe genome using paired-end ChIP-seq and MNase-seq (chemical cleavage)

first: Paul

last: Talbert

first: Jitendra

last: Thakur

first: Steven


title: Aubergine iCLIP reveals direct regulation of mRNAs involved in germ cell development by piRNAs in the early embryo

city: MONTPELLIER

first: Simonelig

last: Martine

address: 141, rue de la Cardonille

department: Genetics and Development

country: France

institute: Institut de Genetique Humaine - CNRS

summary: The Piwi-interacting RNA (piRNA) pathway plays an essential role in the repression of transposons in the germline. Other functions of piRNAs such as post-transcriptional regulation of mRNAs are now emerging. Here, we perform iCLIP with the PIWI protein Aubergine (Aub) and identify hundreds of maternal mRNAs interacting with Aub in the early Drosophila embryo. Gene expression profiling reveals that a proportion of these mRNAs undergoes Aub-dependent destabilization during the maternal-to-zygotic transition. Strikingly, Aub-dependent unstable mRNAs encode germ cell determinants. iCLIP with an Aub mutant that is unable to bind piRNAs confirms that binding of Aub to mRNAs is piRNA dependent. Base-pairing between piRNAs and mRNAs can induce mRNA cleavage and decay that are essential for embryonic development. These results reveal a general regulation of maternal mRNAs by Aub and piRNAs, which plays a key developmental role in the embryo, by mediating decay and localization of mRNAs encoding germ cell determinants.

overall_design: We used Aub iCLIP (individual-nucleotide resolution UV cross-linking and immunoprecipitation) to identify RNAs interacting with Aub in 0-2h-Drosophila embryo

first: Bridlin

last: Barckmann

first: Stéphanie

last: Pierson

first: Jérémy

last: Dufourt

first: Catherine

last: Papin

first: Claudia

last: Armenise

first: Thomas

last: Gretzinger

first: Séverine

last: Chambeyron

first: Grégory

last: Baronian

first: Jean-Pierre

last: Desvignes

first: Philipp

last: Port

first: Simon

last: bullock

first: Tomaz

last: Curk

first: Martine

last: Simonelig


title: ChIPmentation: fast, cheap, low-input ChIP-seq for histones and transcription factors

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) is widely used to map histone marks and transcription factor binding throughout the genome. Here we present ChIPmentation, a method that combines ChIP with sequencing library preparation by Tn5 transposase (“tagmentation”). ChIPmentation introduces sequencing-compatible adapters in a single-step reaction directly on bead-bound chromatin, which reduces time, cost, and input requirements, making ChIPmentation a convenient and high-throughput alternative to existing ChIP-seq protocols.

overall_design: This submission includes sequencing data for 87 samples: 52 ChIPmentation and 24 ChIP-seq for 10 different antibodies with at least two biological replicates each and matched immunoglobulin controls in the majority of cases;  2 ATAC-seq samples were sequenced for comparison; Additionally, 9 samples of a experimental protocol which we called “ChIP-tagmentation” were produced without replication.

first: Christian

last: Schmidl

first: Andre

last: Rendeiro

first: Nathan

middle: C

last: Sheffield


title: RNA Deep Sequencing Reveals Expression Patterns of Long Non-coding RNAs during Swine Ovary Development

city: Guang zhou

first: Liu

last: Jing

address: Wushan street 483#

institute: south china agricultural university

summary: In this study, we obtained the expression profiles of lncRNAs during the development of swine ovaries with RNA-seq technology. The results showed 103,233 and 94,251 lncRNAs were identified from the libraries of ovaries from 30-day-old and 90-day-old swine, respectively, and 37,323 were significantly differentially expressed between the two libraries. The target genes of 903 lncRNAs were acquired through prediction, and KEGG pathway analysis showed the differential lncRNAs were involved in 268 pathways, including ovarian follicular development processes and pathways, such as the GnRH signaling pathway and estrogen signaling pathway. As swine is an ideal biological model for human genetics, the work will help further understand human reproduction.

overall_design: Examination of lncRNA profiles  in  two ovary samples of 30 and 90 days.

first: J

last: Liu

last: Li


title: Hybrid Mimics and Hybrid Vigor in Arabidopsis

city: Canberra

first: Li

last: Wang

state: ACT

address: North-Science Road, Acton ACT 2601

country: Australia

institute: CSIRO


title: Hnf-1β ChIP-Seq

status: Public on Aug 15 2015

city: Dallas

first: Min Soo

last: Kim

state: Texas

address: 5323 Harry Hines Blvd.

department: Department of Clinical Sciences

institute: University of Texas Southwestern

summary:
Genome Wide mapping of Hnf-1β in kidney cells.
Tissue-specific transcription factor that is expressed in the kidney and other epithelial organs. Humans with mutations in HNF1? develop kidney cysts, and HNF-1β regulates the transcription of several cystic disease genes. However, the complete spectrum of HNF-1β-regulated genes and pathways is not known. Here, we used ChIP-seq and DNA microarray analysis to identify 1,545 protein-coding genes that are directly regulated by HNF-1β in kidney epithelial cells. Pathway analysis predicted that HNF-1β regulates cholesterol metabolism. The expression of genes that are essential for cholesterol synthesis, including Srebf2 and Hmgcr, was reduced by expression of dominant-negative mutant HNF-1β or kidney-specific inactivation of HNF-1β. The levels of cholesterol biosynthetic intermediates and the rate of cholesterol synthesis were decreased in HNF-1β mutant cells. In addition, HNF-1β directly regulated the renal epithelial expression of PCSK9, a key regulator of cholesterol uptake, and depletion of cholesterol in the culture medium mitigated the inhibitory effects of mutant HNF-1β on SREBP-2 and HMGCR. These findings reveal a novel role of HNF-1β in regulating multiple steps in renal cholesterol metabolism.

overall_design:
Hnf-1β binding in 2 different samples.
Immunoprecipitation of chromatin bound to HNF-1β in mIMCD3 cells was carried for two control (anti-IgG) and two experimental (anti-HNF-1β) samples.

first: Karam

last: Aboudehen

first: Peter

last: Igarashi


title: Hybrid Mimics and Hybrid Vigor in Arabidopsis (F6 data)

summary: F1 hybrids can outperform their parents in yield and vegetative biomass, features of hybrid vigor which form the basis of the hybrid seed industry.  The yield advantage of the F1 is lost in the F2 and subsequent generations.  In Arabidopsis, from F2 plants which have a F1 –like phenotype, we have by recurrent selection produced pure breeding F5/F6 lines “Hybrid Mimics”, in which the characteristics of the F1 Hybrid are stabilized.  These Hybrid Mimic lines, like the F1 Hybrid, have larger leaves than the parent plant, the leaves having increased photosynthetic cell numbers, and in some lines increased size of cells, suggesting an increased supply of photosynthate.  A comparison of the differentially expressed genes in the F1 Hybrid with those of eight Hybrid Mimic lines has identified metabolic pathways altered in both; these pathways include down regulation of defense response pathways and altered abiotic response pathways.  F6 Hybrid Mimic lines are mostly homozygous at each locus in the genome yet retain the large F1-like phenotype.  Many alleles in the F6 plants, when they are homozygous, have expression levels different to the level in the parent.  We consider this altered expression to be a consequence of trans-regulation of genes from one parent by genes from the other parent.  Transregulation could also arise from epigenetic modifications in the F1.  The pure breeding Hybrid Mimics have been valuable in probing the mechanisms of hybrid vigor and may also prove to be useful hybrid vigor equivalents in agriculture.

overall_design:
Plant Materials: Seeds were sterilized and sown onto plates containing MSN medium (MS salts supplemented with 1% (w/v) sucrose, pH7 with KOH, 0.6% wt/vol Noble agar).  After 2 days at 4°C, the plates were transferred to a growth room with conditions of 22 °C/18 °C (day/night) and 16h light/8h dark cycle under Philips Cool Daylight TLD 58W/840 fluorescent tubes providing a photosynthetic photon flux density of 130 - 150μmol photons m-2·s-1 as measured using a quantum meter (Model MQ-200 calibrated for electric light source, Apogee).  At 18 days after sowing (DAS), the plants were transferred to soil and grown to the reproductive stage in a growth room with controlled light conditions (OSRAM L 36W/865 LumLux Daylight, 130 - 150μmol photons m-2·s-1).  To minimize the edge effects, the positioning of both plates and trays on the shelves was rotated every two days.  All the plants were grown under the condition described above unless specified.
Plant sample preparation and RNA extraction:  For the transcriptomes of 15 DAS plants, the aerial tissues of 15 day seedlings were sampled.  For the transcriptomes of plants at 28 DAS, the four largest leaves of 28 day plants from the parental lines (C24, Ler), the reciprocal Hybrids and eight F4 Hybrid Mimic lines were harvested.  Each sample comprised a pool of five plants.  Two biological replicates of each sample were sequenced.  Total RNA was isolated using QIAGEN RNeasy MiniKitTM following the product instructions.  To eliminate variation in experimental conditions in different positions in the growth room, nine F4 plant lines were divided into two batches to ensure plants were grown on the same shelves in each experiment.   Parental lines C24 and Ler and the F1 Hybrid from which the F4 lines derived from were grown under the same conditions in each experiment as controls.  The first batch including samples C24 (RepA and RepB), Ler (RepA and RepB), C24 x Ler F1, F4-L1-1, F4-L1-2, F4-L2-1, F4-L2-2 and F4-S-1 were grown under the condition describe above, we also sampled the five smallest C24 seedlings and five smallest Ler seedlings among the population (n = 50); the mRNA sequencing was performed by the Australian Genome Research Facility (AGRF).  The second batch including C24 (RepC and RepD), Ler (RepC and RepD), Ler x C24 F1 Hybrid, F4-L3-1, F4-L3-2, F4-L4-1 and F4-L4-2 were grown in the same light intensity as above but under different light tubes (SYLVANIA PREMIUM extra FL36W/865 Super Daylight deluxe light tube).
For the transcriptome of the two F6 Hybrid Mimic lines at 15 DAS, C24, Ler, Ler x C24 F1 Hybrids and three siblings from each F6 line (L3-1-1-2 and L4-2-1-2) were grown on MS medium (MS salts supplemented with 1% (w/v) sucrose, pH 5.7 with KOH, add 0.6% wt/vol agar) with controlled light conditions (SYLVANIA PREMIUM extra FL36W/865 Super Daylight deluxe, 130 - 150μmol photons m-2·s-1).  The mRNA sequencing service was provided by AGRF on the Illumina platform, 100bp paired ends.

first: Ian

middle: K

last: Greaves

first: Michael

last: Groszmann

first: Li Min

last: Wu

first: Elizabeth

last: Dennis

first: W

middle: J

last: Peacock


title: Hybrid Mimics and Hybrid Vigor in Arabidopsis (F4 data)


title: small RNA-Seq of the CA1 hippocampal subregion from 3 month and 20 month old animals treated orally with vehicle or SAHA

city: Goettingen

first: Eva

last: Benito Garagorri

state: Niedersachsen

address: Von Siebold Strasse 3A

department: Epigenetics of Aging

institute: DZNE Goettingen

summary: Aging and increased amyloid burden are major risk factors for cognitive diseases such as Alzheimer's Disease (AD). An effective therapy does not yet exist. Here we use mouse models for age-associated memory impairment and amyloid deposition to study transcriptome and cell type-specific epigenome plasticity at the systems level in the brain and in peripheral organs. We show that at the level of epigenetic gene-expression aging and amyloid pathology are associated with inflammation and impaired synaptic function in the hippocampal CA1 region. While inflammation is associated with increased gene-expression that is linked to a subset of transcription factors, de-regulation of plasticity genes is mediated via different mechanisms in the amyloid and the aging model. Amyloid pathology impairs histone-acetylation and decreases expression of plasticity genes while aging affects differential splicing that is linked to altered H4K12 acetylation at the intron-exon junction in neurons but not in non-neuronal cells. We furthermore show that oral administration of the clinically approved histone deacetylase inhibitor Vorinostat not only restores spatial memory, but also exhibits an anti-inflammatory action and reinstates epigenetic balance and transcriptional homeostasis at the level of gene expression and exon usage.  This is the first systems-level investigation of transcriptome plasticity in the hippocampal CA1 region in aging and AD models and of the effects of an orally dosed histone deacetylase inhibitor. Our data has important implications for the development of minimally invasive and cost-effective therapeutic strategies against age-associated cognitive decline. In fact, our data strongly suggest to test Vorinostat in patients suffering from AD.

overall_design: small RNA profile from aged animals (hippocampal CA1 region) treated with oral vehicle or SAHA for 4 weeks

last: Benito-Garagorri

last: Fischer


title: mRNA-Seq of the CA1 hippocampal subregion and liver from 3 month and 20 month old animals treated orally with vehicle or SAHA and mRNA-Seq of CA1 of 10 month old WT or APP/PS1-21 transgenic animals treated orally with vehicle or SAHA

overall_design: mRNA profile from aged (CA1 and liver) and APP/PS1 (CA1) animals treated with oral vehicle or SAHA for 4 weeks


title: Genome-wide analysis of H4K12 acetylation in neuronal and non-neuronal nuclei in young animals treated with vehicle, WT littermates of APP/PS1-21 animals treated with vehicle and aged and APP/PS1-21 animals treated with oral vehicle or SAHA for 4 weeks

overall_design: Examination of H4K12 acetylation in neuronal and non-neuronal nuclei of young/old animals and WT/APP/PS1-21 animals. Inputs are also provided.


title: The Host Response to a Clinical MDR Mycobacterial Strain Cultured in a Detergent-Free Environment: A Global Transcriptomics Approach

status: Public on Aug 13 2015

city: Bellville

first: Abhilasha

last: Madhvi

state: Western Cape

address: Francie van Zijl Drive. Tygerberg

country: South Africa

institute: Stellenbosch University

summary: We infect bone marrow derived macrophages (BMDMs) with Mycobacterium cultured with and without Tween 80 and asses the host response to these bacteria through RNAseq

overall_design: Uninfected BMDMs served as controls, BMDMs infected with detergent-free M.tb (designated RNT), BMDMs infected with Tween cultured m.tb (designated RT). 3 groups with 3 biological replicates, each analysed in triplicate.

first: G

middle: R

last: Leisching

first: B

last: Baker


title: The DNA-binding inhibitor Id3 regulates IL-9 production in CD4+ T cells

status: Public on Aug 14 2015

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

summary: The molecular mechanisms by which signaling via transforming growth factor-β (TGF-β) and interleukin 4 (IL-4) control the differentiation of IL-9-producing CD4+ helper T cells (TH9 cells) remain incompletely understood. We found here that the DNA-binding inhibitor Id3 regulated TH9 cell differentiation, as deletion of Id3 increased IL-9 production from CD4+ T cells. Mechanistically, TGF-β1 and IL-4 downregulated Id3 expression, and this process required the kinase TAK1. A reduction in Id3 expression enhanced binding of the transcription factors E2A and GATA-3 to the Il9 promoter region, which promoted Il9 transcription. Notably, Id3’s control of TH9 differentiation regulated anti-tumor immunity in an experimental melanoma-bearing model in vivo and also in human CD4+ T cells in vitro. Thus, our study reveals a previously unrecognized TAK1–Id3–E2A–GATA-3 pathway that regulates TH9 differentiation.

overall_design: Comapring of GATA3 binding after the TGF-β1 and IL-4 stimulations

first: Hiroko

last: Nakatsukasa

first: Dunfang

last: Zhang

first: Takashi

last: Maruyama

first: WanJun

last: Chen


title: Reinstating transcriptome plasticity and memory function in mouse models for cognitive decline

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

overall_design: Refer to individual Series


title: Identification of Lhx5 binding sites and Gene expression data from Lhx5 mutant mouse embryos

city: Heidelberg

first: Gonzalo

last: Alvarez-Bolado

address: Im Neuenheimer Feld 307

institute: Institute for Anatomy and Cell Biology


title: Mitotic stress is an integral part of the oncogene-induced senescence program that promotes multinucleation and cell cycle arrest

city: Glasgow

last: Adams

address: Switchback Rd, Bearsden

country: United Kingdom

institute: University of Glasgow, Beatson Institute for Cancer Research

summary: Oncogene-induced senescence (OIS) is a tumor suppression mechanism that blocks cell proliferation in response to oncogenic signalling. OIS is frequently accompanied by multinucleation; however, the origin of this is unknown. Here we show that multinucleate OIS cells originated mostly from failed mitosis. Prior to senescence, mutant RasV12 activation in primary human fibroblasts compromised mitosis, associated with abnormal expression of mitotic genes that enter M-phase.  Simultaneously, RasV12 activation enhanced survival of damaged mitoses, culminating in extended mitotic arrest and aberrant exit from mitosis via mitotic slippage. ERK-dependent transcriptional up-regulation of Mcl1 was responsible for enhanced slippage of cells with mitotic defects and subsequent cell survival. Importantly, mitotic slippage and oncogene signalling synergistically induced senescence and key senescence regulators p21 and p16. We propose that activated Ras induces transcriptional changes that predispose cells undergoing OIS to mitotic stress and multinucleation.

overall_design: We used RNA-seq of IMR90 cells with inducible expression of oncogenic RasV12 that were synchronised in mitosis, to characterise the nature of mitotic defects that lead to multinucleation of oncogene-induced senescent cells

first: Dina

last: Dikovskaya

first: John

last: Cole

middle: D


title: Identification of Lhx5 binding sites

summary: Lhx5 mutant mouse embryos show loss of a neuronal nucleus of the brain, called the mammillary body and essential for memory. We found out that this is caused by a loss of appropriate specification of mammillary neurons and we identified in a microarray study downstream targets responsible for the observed phenotype. Here we wanted to find out which of our identified targets are under direct control of Lhx5.

overall_design: In order to identify the direct targets of Lhx5 we decided to use a ChIP-Seq approach. For this approach we generated a stably transfected Neuro2a cell line that expresses a FLAG-tagged version of Lhx5 under the control of the Tet-ON system. As a control we transfected Neuro2a cells with a construct that only expresses the FLAG-tag.

last: Heide


title: Mus musculus Stra8-deficient fetal ovary transcriptome

city: Cambridge

first: Ying Qi Shirleen

last: Soh

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

summary: Identification of the mouse embryonic germ cell Stra8-/- transcriptome

first: Ying

middle: Q

first: David

last: Page


title: Mus musculus Dazl-deficient fetal ovary transcriptome

summary: Identification of the mouse embryonic germ cell Dazl-/- transcriptome


title: Mus musculus embryonic germ cell transcriptome

summary: Identification of the mouse embryonic germ cell transcriptome

first: Mark

middle: E

last: Gill

first: Jacob

last: Mueller


title: Genome-wide maps of H3K27me3 modification sites in sk-hep-1,sk-hep-1-shEZH2 and LO2 cells.

city: guangzhou

first: Li

last: Changpeng

address: kai yuan road

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

summary: We report the application of chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) for high-throughput profiling of H3K27me3 modifications in sk-hep-1(sk), sk-hep-1-shEZH2 (sks) and LO2 cells. Following standard ChIP procedure, 10 ng of each DNA sample was used for Illumina sequencing. Statistically significant ChIP-enriched regions (peaks) were identified by sk vs sks (p-value threshold of 10-2) or sk vs LO2 (p-value threshold of 10-3). Enriched peaks were annotated by the nearest gene using the newest UCSC RefSeq database. We identify genes modified by EZH2-mediated H3K27me3. This study provides insights into these down stream genes modified by EZH2 regulated H3K27me3 in HCC cell lines.

overall_design: Examination of H3K27me3 in 3 HCC cell lines.

first: Xie

last: Dan

first: Cai

last: MY


title: Mus musculus anterior and posterior ovary transcriptome at E12.5 and E13.5

summary: Identification of genes expressed in the anterior and posterior thirds of mouse fetal ovary


title: Maternal piRNAs are essential for germline development following de-novo establishment of endo-siRNAs in Caenorhabditis elegans

city: Mainz

first: Rene

last: Ketting

address: Ackermannweg 4

institute: IMB

summary: The Piwi-piRNA pathway represents a germline specific transposon-defense system. C. elegans Piwi, prg-1, is a non-essential gene and triggers a secondary RNAi response that depends on so-called mutator genes, endo-siRNAs (22G-RNAs) and at least one 22G-RNA-binding Argonaute protein, HRDE-1. Interestingly, through a poorly understood mechanism, silencing of PRG-1 targets can become PRG-1 independent. This state, also known as RNAe, is heritable and depends on mutator genes and HRDE-1. We studied how the transgenerational memory of RNAe and the piRNA pathway interact. We find that maternally provided PRG-1 is required for the de-novo establishment of 22G-RNA populations, especially those targeting transposons. Strikingly, attempts to re-establish 22G-RNAs in absence of both PRG-1 and RNAe memory result in severe germline proliferation defects. This is accompanied by a disturbed balance between gene-activating and -repressing 22G-RNA pathways. We propose a model in which CSR-1 prevents the loading of HRDE-1 and that both PRG-1 and HRDE-1 help to keep mutator activity focused on the proper targets.

overall_design: Small RNA sequencing of C. elegans L1 and L2 larvae from wild-type and mutants with impaired endo-siRNA pathway. There are 29 samples that include wild-type controls and mutants with at least 2 biological replicates for each genetic background. Small RNA sequencing of input and HRDE-1 immunoprecipitates from wild-type and cde-1(tm1021) mutants.

first: Bruno

last: de Albuquerque

first: Maria

last: Placentino

first: René


title: PAF1, a molecular regulator of promoter-proximal pausing   by RNA Polymerase II

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: The control of promoter-proximal pausing and the release of RNA polymerase II (RNA Pol II) is a widely used mechanism for regulating gene expression in metazoans, especially for genes that respond to environmental and developmental cues. Here, we identify Pol II associated Factor 1 (PAF1) as a major regulator of promoter-proximal pausing. Knockdown of PAF1 leads to increased release of paused Pol II into gene bodies at thousands of genes. Genes with the highest levels of paused Pol II exhibit the largest redistribution of Pol II from the promoter-proximal region into the gene body in the absence of PAF1. PAF1 depletion results in increased nascent transcription and increased levels of phosphorylation of Pol II’s c-terminal domain on serine 2 (Ser2P). These changes can be explained by the recruitment of the Ser2P kinase Super Elongation Complex (SEC) effecting increased release of paused Pol II into productive elongation, thus establishing a novel function for PAF1 as a major regulator of pausing in metazoans.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: ChIP-seq of Pol II of different forms, SEC subunits, PAFc subunits and H2Bub in human cell lines targeted by PAF1 or scramble shRNA. ChIP-seq of total Pol II in HCT116 cells targeted by BRE1A or scramble shRNA. ChIP-seq of total Pol II in S2 cells targeted by Paf1 or LacZ RNAi. Total RNA-seq, nascent RNA-seq and GRO-seq in HCT116 cells targeted by PAF1 or scramble shRNA.

first: Fei Xavier

first: Ashley

last: Woodfin


title: Aberrant haematopoiesis in Dnmt2 mutant mice [HTS 2]

city: Mannheim

first: Francesca

last: Tuorto

address: Ludolf-Krehl-Str. 13-17

department: Division of Biochemistry  Mannheim Institute for Innate Immunoscience (MI3)

institute: Deutsches Krebsforschungszentrum

summary: Bone marrow primary cells from Dnmt2-/- and wildtype mice were used to identify difference in mRNA translation

overall_design: Ribosome-protected mRNA fragments from RNAase I cleavage was sequenced in wildtype and Dnmt2-/- primary bone marrow cells. Small RNA libraries were performed according to the protocol using NEB NEXT Small RNA library Prep Set for Illumina (Multiplex Compatible) E7330, and size-selected (150 base pairs) before sequencing.

first: Nader

last: Alerasool

first: Sebastian

last: Bender


title: Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

summary: Oxidative stress that originates from reactive oxygen species (ROS) is an inevitable consequence of aerobic respiration in bacteria. Three transcription factors (TFs), OxyR, SoxR, and SoxS play a critical role in transcriptional regulation of the defense system. However, the full genome-wide regulatory potential of them remains elusive. Here, we comprehensively reconstruct genome-wide OxyR, SoxR, and SoxS transcriptional regulatory networks in Escherichia coli under oxidative stress. Integrative data analysis reveals that OxyR, SoxR, and SoxS regulons are comprised of 38 genes in 28 transcription units (TUs), 11 genes in 10 TUs, and 34 genes in 25 TUs, respectively, significantly expanding the current knowledge of their regulatory networks. Comparison of them to other stress-response regulatory networks highlights minimal overlap between their regulons, indicating that E. coli has a series of relatively distinct stress responses covering the range of different stresses. We also demonstrate that these intricate networks coordinate detoxification process with DNA and protein damage repair, cell wall synthesis, divalent metal ion homeostasis, as well as metabolic robustness to produce overall response of E. coli to oxidative stress.

overall_design: A total of eight samples were analyzed. WT, ΔoxyR, ΔsoxR, and ΔsoxS  mutant cells were cultured in M9 minimal media with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.

first: Sang

middle: W

last: Seo


title: CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

city: Shanghai

first: Qiang

last: Wu

address: 800 Dongchuan Road

department: Institute of Systems Biomedicine

institute: Shanghai Jiao Tong University

summary: CTCF/cohesin play a central role in insulator function and higher-order chromatin organization of mammalian genomes. Recent studies identified a correlation between the orientation of CTCF-binding sites (CBSs) and chromatin loops. To test the functional significance of this observation, we combined CRISPR/Cas9-based genomic-DNA-fragment editing with chromosome-conformation-capture experiments to show that the location and relative orientations of CBSs determine the specificity of long-range chromatin looping in mammalian genomes, using protocadherin (Pcdh) and β-globin as model genes. Inversion of CBS elements within the Pcdh enhancer reconfigures the topology of chromatin loops between the distal enhancer and target promoters, and alters gene-expression patterns. Thus, although enhancers can function in an orientation-independent manner in reporter assays, in the native chromosome context the orientation of at least some enhancers carrying CBSs can determine both the architecture of topological chromatin domains and enhancer/promoter specificity. The findings reveal how 3D chromosome architecture can be encoded by genome sequence.

overall_design: HEC-1B mRNA profiles of HS5-1 Inversion

first: Ya

last: Guo

first: Quan

last: Xu

first: Daniele

last: Canzio

first: Jia

last: Shou

first: Jinhuan

last: Li

first: David

last: Gorkin

first: Inkyung

last: Jung

first: Haiyang

first: Yanan

last: Zhai

first: Yuanxiao

last: Tang

first: Yichao

last: Lu

first: Yonghu

first: Zhilian

last: Jia

first: Wei

first: Michael

last: Zhang

first: Bing

last: Ren

first: Adrian

last: Krainer

first: Tom

last: Maniatis


title: The maize death acids, 10-oxo-11-phytoenoic acid and derivatives, are rapidly induced phytoalexins with multiple biological activities

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: Plant cellular damage promotes the interaction of lipoxygenases (LOX) with free fatty acids to yield 9- and 13-hydroperoxides which are further metabolized into diverse oxylipins. The enzymatic action of 13-LOX on linolenic acid enables production of 12-oxo-phytodienoic acid (12-OPDA) and its downstream products, jointly known as jasmonates. As signals, jasmonates have related yet distinct roles in the regulation of plant resistance against insect and pathogen attack. An additional and conceptually parallel pathway involving 9-LOX activity on linoleic acid leads to the production of 10-oxo-11-phytoenoic acid (10-OPEA). Despite structural similarity to jasmonates, physiological roles for 10-OPEA have remained unclear. Both 12-OPDA and 10-OPEA equally promote the transcription of numerous defense genes encoding glutathione S-transferases, cytochrome P450s, and pathogenesis-related proteins; however, 10-OPEA activity diverges in the context of reduced protease inhibitor transcript accumulation. To identify additional differential responses, we subsequently performed whole transcriptome analyses using RNAseq. These comparisons provide a platform for further examination of plant response specificity to the cyclopentenone 10-OPEA.

overall_design: A total of 12 samples were analyzed, comprised of two treatments (10-OPEA and 12-OPDA) and a DMSO carrier control (5%DMSO/0.1%Tween 20 in H20), all in replicates of four.


title: Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress

first: Donghyuk

last: Kim


title: Gene expression analyses and distribution of H3K4me3 modification during eosinophil development (GMP to EoP to Eosinophil)

city: Cincinnati

first: Patricia

middle: C.

last: Fulkerson

state: OH

address: 3333 Burnet Ave, ML 7028

institute: Cincinnati Children's Hospital Medical Center

summary: To identify regulators of homeostatic eosinophilopoiesis in mice, we took a global approach to identify genome-wide transcriptome and epigenome changes that occur during homeostasis at critical developmental stages, including eosinophil-lineage commitment (eosinophil progenitor [EoP] compared to granulocyte-monocyte progenitor [GMP]) and lineage maturation (eosinophil compared to EoP). Our analyses revealed markedly greater transcriptome alterations associated with eosinophil maturation (1199 genes) compared to eosinophil-lineage commitment (490 genes), highlighting the greater transcriptional investment necessary for differentiation. Our analyses also delineated a 976 gene eosinophil-lineage transcriptome that included a repertoire of 56 transcription factors, many of which have never previously been associated with eosinophils. Epigenomic studies revealed that genes that were specifically induced with eosinophil-lineage commitment in EoPs were “poised” with active chromatin marks in GMPs, despite not being expressed in GMPs. In contrast, a majority of the genes that were highly and specifically induced with maturation in eosinophils was not associated with poised chromatin, suggesting distinct epigenetic regulation between genes induced with lineage commitment compared to genes induced with cell maturation during eosinophil development.

overall_design: RNA Seq and H3K4me3 distribution of GMPs, EoPs and eosinophils sorted from Balb/c bone marrow. RNA Seq libraries were prepared from 2 independent sorts of each cell type (GMP, EoPs, Eosinophils [Eos]). ChIP Seq was performed with chromatin from one sort of each cell type.


title: Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [ChIP-seq]

overall_design: A total of six samples were analyzed. oxyR-8myc, soxR-8myc, and soxS-8myc tagged cells were cultured in M9 minimal media with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.

first: Sang

last: Seo


title: Comparison of Hi-C results using in-solution versus in-nucleus ligation

status: Public on Aug 12 2015

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

summary: Chromosome conformation capture (3C) and derivative (4C, 5C and Hi-C) methods employ ligation of diluted cross-linked chromatin complexes, intended to favor proximity-dependent, intra-complex ligation. We previously described an alternative Hi-C protocol with ligation in preserved nuclei rather than in solution. Here we directly compare Hi-C methods employing "in-nucleus ligation" and the standard "in-solution ligation". The results show that in-nucleus ligation captures chromatin interactions more consistently over a wider range of distances, and significantly reduces both experimental noise and bias. Thus in-nucleus ligation not only simplifies the experimental procedures, but also produces higher quality data with benefits for the entire range of 3C applications.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We created Hi-C libraries by two different methods, in-solution ligation and in-nucleus ligation, from two biological replicates each of mouse foetal liver cells (mouse-1 and mouse-2) and human ES cells (human-1 and human-2) or the mixture of these two species. We also sequenced a random ligation library prepared by reversal of the cross-links and purification of the DNA prior to ligation.

first: Takashi

last: Nagano

first: Csilla

last: Várnai

first: Stefan

last: Schoenfelder

first: Biola-Maria

last: Javierre

first: Peter

last: Fraser


title: Genome-wide study of nuclear poly(A) binding protein Nab2p depletion

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

institute: ScilifeLab - Karolinska Institutet

summary: Polyadenylation of mRNA is a key step in eu- karyotic gene expression. However, despite the ma- jor impact of poly(A) tails on mRNA metabolism, the precise roles of poly(A)-binding proteins (PABPs) in nuclear mRNA biogenesis remain elusive. Here, we demonstrate that rapid nuclear depletion of the S. cerevisiae PABP Nab2p leads to a global loss of cellular mRNA, but not of RNA lacking poly(A) tails. Disappearance of mRNA is a nuclear event, but not due to decreased transcription. Instead, the absence of Nab2p results in robust nuclear mRNA decay by the ribonucleolytic RNA exosome in a polyadenylation-dependent process. We con- clude that Nab2p is required to protect early mRNA and therefore constitutes a crucial nuclear mRNA biogenesis factor.

overall_design: For RNAseq experiments, 2 independent biological replicates of Nab2-AA cells (Y3284) without rapamycin, or treated for 15’ or 30’, as well as control cells (Y2615) treated with rapamycin for 30’ were used.  S. Pombe spike-in were used to normalize across samples.

first: Manfred

last: Schmid

first: Pawel

last: Olszewski

first: Ishaan

last: Gupta

first: Lars

last: Steinmetz

first: Torben

last: Heick Jensen


title: Aberrant haematopoiesis in Dnmt2 mutant mice

first: Francesca

last: Tuorto

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


title: Research resource: global identification of estrogen receptor β target genes in triple negative breast cancer cells

city: Chapel Hill

first: Erin

last: Shanle

state: NC

address: 3010 Genetic Medicine, 120 Mason Farm Road

department: Biochemistry and Biophysics

institute: University of North Carolina at Chapel Hill

summary: The goal of this work was to identify all estrogen receptor beta target genes using RNA sequencing in MDA-MB-468 triple negative breast cancer cells engineered with inducible expression of full length estrogen receptor beta.

overall_design: MDA-MB-468 breast cancer cells with inducible ERb expression (MDA-468-ERb cells) were treated in triplicate with vehicle (control, no ERb) or doxycycline (plus ERb) for 48 hr prior to treatment with 0.1% DMSO vehicle or 10 nM 17b-estradiol for 4 hr.

first: E

first: W

last: Xu


title: A Gene Regulatory Program for Meiotic Prophase in the Fetal Ovary

first: Ying Qi Shirleen

last: Soh


title: Aberrant hematopoiesis in Dnmt2 mutant mice [HTS 1]

summary: Bone marrow samples from Dnmt2-/- and wildtype mice were used to identify differentially tRNA fragment expression

overall_design: Total RNA was extracted using Trizol reagents (Invitrogen) and treated with DNase I (Ambion). RNA were end-repaired with T4 PNK. Small RNA libraries were performed according to the protocol using NEB NEXT Small RNA library Prep Set for Illumina (Multiplex Compatible) E7330, and size-selected (120-170 base pairs) before sequencing.

first: Sebatian

last: Bender


title: microRNA-196 regulates vertebral number and identity across species

city: South San Francisco

first: Vikram

last: Agarwal

state: CA

address: 1130 Veterans Blvd

institute: Calico Life Sciences

summary:
Purpose: In this study, we identify global transcriptome alterations following removal of individual or multiple miR-196 family members in mouse. Next generation sequencing-derived transcriptome profiling (RNA-seq) was performed.
Methods: A GFP reporter cassette was engineered to replace the mature miR-196a1 and miR-196a2 miRNA genomic loci in mouse (creating a knockout). GFP positive cells from an extensive knock-out allellic series of the three individual miR-196 genes, as detailed below, were isolated from E9.5 mouse embryos by FACS. miR-196b knockout cells were not marked with a fluorescent reporter and an assumption of co-expression with miR-196a2 was made. mRNA profiles were generated by deep sequencing in a minimum of four biological replicates per genotype, using an Illumina HiSeq 2000 instrument. Read information was mapped to the mouse genome and processed as described.
Conclusions: Our study represents the first detailed analysis of embryonic transcriptomes following loss of single and multiple miR-196 family members. We identify complex dysregulation of many Hox genes, in addition to key developmental signalling pathways involved in somitogenesis.

overall_design: mRNA profiles of E9.5 mouse embryos with miR-196 loss-of-function were generated by deep sequencing, in a minimum of four biological replicates, using Illumina HiSeq 2000.

first: Edwina

last: McGlinn

first: David

middle: P

last: Bartel

first: Clifford

last: Tabin


title: Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

summary: SMC condensin complexes play a central role in compacting and resolving replicated chromosomes in virtually all organisms yet how they accomplish this remains elusive. In Bacillus subtilis, condensin is loaded at centromeric parS sites, where it encircles DNA and individualizes newly replicated origins. Using chromosome conformation capture and cytological assays, we show that condensin recruitment to origin-proximal parS sites is required for the juxtaposition of the two chromosome arms. Recruitment to ectopic parS sites promotes alignment of large tracks of DNA flanking these sites. Importantly, insertion of parS sites on opposing arms indicates that these ?zip-up? interactions only occur between adjacent DNA segments. Collectively, our data suggest that condensin resolves replicated origins by promoting the juxtaposition of DNA flanking parS sites drawing sister origins in on themselves and away from each other. These results are consistent with a model in which condensin encircles the DNA flanking its loading site and then slides down, tethering the two arms together. Lengthwise condensation via loop-extrusion could provide a generalizable mechanism by which condensin acts dynamically to individualize origins in B. subtilis and, when loaded along eukaryotic chromosomes, to resolve them during mitosis.

overall_design: Hi-C experiments were performed on wild type and mutant cells of Bacillus subtilis PY79 growing in rich or poor media. ChIP-seq experiments were performed on two strains of Bacillus subtilis PY79 growing in the same condition as in Hi-C experiments.

first: X

first: D

middle: Z

last: Rudner


title: Myogeneic differentiation in Rb1 or Kdm5a/Jarid1a/Rbp2 deficient mouse embryonic fibroblasts.

first: Elizaveta

middle: V

last: Benevolenskaya

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

summary: Cells lacking Rb1 are deficient in differentiation. Loss of Kdm5a rescues myogenic differentiation, as judged by appearance of morphologically normal myotubes that display expression of late markers of differentiation. In order to better understand how Kdm5a loss rescues differentiation, we induced mouse embryonic fibroblasts (MEFs) of different genotypes to undergo myogenic differentiation and analyzed gene expression changes in wild-type, Kdm5a-/-, Rb1-/- and Kdm5a-/-; Rb1-/- cells. Rb1-/- cells stained single nucleated, did not exhibit morphological changes and increased expression of the myogenic marker MYHC. Except for Rb1-/- cells, all other cells were undergoing successful convertion into aligned multinucleated myotubes and were MYHC-positive. We obtained purified populations of myotubes for the wild-type and Kdm5a-/-; Rb1-/- cells.

overall_design: RNA-seq analysis of gene expression in Rb1 or Kdm5a deficient MEFs that were induced for myogenic differentiation.

first: Abul

last: Islam


title: Interaction between TBP and condensing drives the organization and faithful segregation of mitotic chromosomes

city: Eugene

first: Hideki

last: Tanizawa

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

summary: Genome/chromosome organization is highly ordered and controls nuclear events. Here, we show that the TATA box-binding protein (TBP) interacts with the Cnd2 kleisin subunit of condensin to mediate interphase and mitotic chromosome organization in fission yeast. TBP recruits condensin onto RNA polymerase III-transcribed (Pol III) genes and highly transcribed Pol II genes; condensin in turn associates these genes with centromeres. Inhibition of the Cnd2-TBP interaction disrupts condensin localization across the genome and the proper assembly of mitotic chromosomes, leading to severe defects in chromosome segregation and eventually causing cellular lethality. We propose that the Cnd2-TBP interaction coordinates transcription with chromosomal architecture by linking dispersed gene loci with centromeres. This chromosome arrangement can contribute to the efficient transmission of physical force at the kinetochore to chromosomal arms, thereby supporting the fidelity of chromosome segregation.

overall_design: Genome-wide distributions of condensin and Pol III factors in fission yeast.

first: Iwasaki

last: Osamu

first: Tanizawa

last: Hideki

first: Noma

last: Ken-ichi


title: Global transcriptional analysis of mouse fibroblasts, chemically-induced neurons (neuron-like cells) from mouse fibroblasts and mouse primary cortical neurons by RNA-seq

city: Beijing

first: Yan-Tao

last: Ma

address: No. 5 Yiheyuan Road

institute: Peking University

summary: Recently, direct reprogramming between divergent lineages has been achieved by introducing cell-fate-determining transcription factors. This progress may provide alternative cell resources for drug discovery and regenerative medicine. However, the genetic manipulation may limit the future application of these approaches. In this study, we identified a novel small-molecule cocktail that directly converted fibroblasts into neuronal cell fate with a high yield up after 16-days of induction. After a further maturation stage, these chemically-induced neurons (CiNs) possessed neuron-specific expression patterns, generated action potentials and formed functional synapses. Gene expression profiling revealed the activation of neuronal specific genes in the early stage of small molecule treatment. Overall, our findings prove the principle of chemically-induced direct reprogramming of somatic cell fates across germ layers without genetic manipulation, and show that cell fate can be manipulated through disrupting initial cell program and activating target cell master genes with pure chemicals.

overall_design: Total of 15 samples were analyzed, including mouse fibroblasts, mouse cortical primary neurons and chemically-induced neurons by different duration of chemical induction (Day0, Day4, Day8, Day19) and different small-molecule cocktail (FICB, FICB-1)

first: Xiang

last: Li

first: Xiaohan

last: Zuo

first: Junzhan

last: Jing

first: Yantao

first: Yang

last: Zhao

first: Hongkui

last: Deng


title: KANADI1-regulated genes in shade

status: Public on Aug 11 2015

city: Frederiksberg C

first: Daniel

last: Straub

address: Thorvaldsensvej 40

department: Plant and Environmental Sciences

country: Denmark

institute: University of Copenhagen

summary: RNA-Seq of Arabidopsis thaliana Col-0 and 35S::FLAG-GR-KAN1 plants grown in ambient light or shade.

overall_design: 8 samples (Col-0 wildtype, 35S::FLAG-GR-KAN1 each in shade or ambient light, each with mock or Dexamethasone treatment) with two technical replicates were sequenced.

first: Yakun

last: Xie

first: Ronny

last: Brandt

first: Mark

last: Stahl

first: Stephan

last: Wenkel


title: Comparative genomics provides insight into the diversity of the attaching and effacing Escherichia coli (AEEC) virulence plasmids

city: Baltimore

first: Sean

last: Daugherty

state: Maryland

address: 801 W. Baltimore St.

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

summary: Global transcriptional analysis of the EPEC prototype strain E2348/69 and its plasmid mutants containing a deletion of perABC, or missing the entire EAF plasmid (strain JPN15).

overall_design: RNA sequencing was performed on the EPEC prototype strain E2348/69 and its plasmid mutants, strain ΔperABC and strain JPN15, during growth in laboratory media and conditions that have been previously demonstrated to induce expression of EPEC virulence factors.

first: Tracy

last: Hazen

first: James

last: Kaper

last: Nataro

first: David

last: Rasko


title: Changes in H3K4 methylation in KDM5A/JARID1A/RBP2 knockout cells.

first: Elizaveta

last: Benevolenskaya

summary: We sought to determine H3K4me3 distribution in mouse embryonic stem (ES) cells deficient for RBP2 compared with wild-type cells. RBP2 modifies methylated lysine residues on histone tails. As a result of this analysis, we identified genomic regions with changed H3K4me3 status and described these in gene ontology (GO) categories.

overall_design: Examination of histone methylation in the absence of histone demethylase RBP2

first: Abul

last: Islam


title: Quantitative Genomic Analysis of RecA Protein Binding During DNA Double-Strand Break Repair Reveals RecBCD Action in vivo

city: Edinburgh

first: Charlotte

middle: Anne

last: Cockram

address: Mayfield Road

department: ICB

institute: University of Edinburgh

summary: Here we have developed a method that combines chromatin immunoprecipitation with next-generation sequencing (ChIP-Seq) and mathematical modeling to quantify RecA protein binding during the active repair of a single DSB in the chromosome of Escherichia coli.

overall_design: Examination of RecA binding during double-strand break repair in Escherichia coli

first: Milana

last: Filatenkova

first: Vincent

last: Danos

first: Meriem

last: El Karoui

last: Leach


title: Transcriptome analyses of cortical projection neurons and interneurons via Tbr2(Eomes)-mediated transgenic lineage tracing

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: In the cerebral cortex, projection neurons and interneurons work coordinately to establish functional neural networks and to control the balance between excitatory versus inhibitory synaptic activities for normal cortical functions. While the specific mechanisms that control productions of projection neurons and interneurons are beginning to be revealed, a global characterization of the molecular differences between these two groups of neurons is in need for a more comprehensive understanding of their developmental specifications as well as their cortical functions. Previous studies have shown that the majority of cortical projection neurons are produced by radial glial cells (RGCs) through intermediate progenitor cells (IPCs) which can be marked by the expression of transcription factor Tbr2(Eomes). In this study, taking advantage of lineage tracing power of combining Tbr2(Eomes)-GFP and DCX-mRFP transgenic reporter mice, we prospectively separated IPC-derived neurons (IPNs) from non-IPC-derived neurons (non-IPNs) of the embryonic cortex. Molecular characterizations revealed that IPNs and non-IPNs were enriched with projection neurons and interneurons, respectively. Transcriptome analyses documented distinct groups of genes differentially expressed between these two groups of neurons. These data present a useful resource for further investigation of the molecular regulations and functions of projection neurons and interneurons.

overall_design: Transcriptome of two cortical neuron groups were analyzed

first: Jiancheng

last: Liu

first: Qiang

last: Lu


title: Decoding breast cancer tissue-stroma interactions using species-specific sequencing

city: Stockholm

first: Daniel

last: Ramsköld

address: Nobels väg 3

institute: Karolinska Institutet

summary: Decoding genome-wide effects of experimental tissue-tissue or cell-cell interactions is important, for example, to better understand tumor-stroma interactions after transplantation (xenografting). Transcriptome analysis of intermixed human and mouse cells has frequently relied on the need to separate the two cell populations prior to transcriptome analysis, which introduces confounding effects on gene expression. To circumvent this problem, we perform a bioinformatics-based genome-wide transcriptome analysis technique separating the mouse and human transcriptome part of a dataset, which allows a mixed mouse and human cell population to be sequenced without prior cell sorting. We use the new technology – which we call S3 (“S-cube” for Species-specific sequencing) technology – to provide new insights into the Notch downstream response following Notch ligand-stimulation and to explore transcriptional changes following transplantation of luminal (MCF7) and basal-type (MDA-MB-231) human breast cancer cells into mammary fat pad tissue in mice.

overall_design: Analysis of Notch response to ligand in three settings: co-culture, immobilized ligand and xenografted tumors

first: Indira

last: Chivukula

first: Urban

last: Lendahl


title: CXCL12/CXCR4 signaling mediates niche occupancy and tumor maintenance in T-cell leukemia

city: New York

first: Thomas

last: Trimarchi

state: NY

address: 550 First Ave Smilow 1307

department: Pathology

institute: NYU School of Medicine

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy characterized by infiltration of the bone marrow and other sites with transformed T cell progenitors. The role of tissue microenvironments in the pathogenesis of T-ALL or any other type of acute leukemia is little understood. In delineating interactions between T-ALL cells and their environment, we initially found that T-ALL cells express high surface levels of the chemokine receptor CXCR4. Intravital imaging of an intact tibia revealed T-ALL cells in direct contact with bone marrow stromal cells producing the CXCR4 ligand, CXCL12. Genetic targeting of CXCR4 on T-ALL cells resulted in a marked reduction of leukemia burden and prolonged disease remission, and disruption of the CXCL12/CXCR4 axis using small molecule inhibitors prevented T-ALL progression in a primary xenograft model. Finally, we were able to show that CXCR4 inhibition significantly decreased expression of Myc and its target genes. Myc expression is a key regulator of T-ALL leukemia initiating cell (LIC) activity, suggesting that CXCR4 inhibition can suppress LIC activity by silencing the Myc response in T-ALL cells. Our data suggest that targeting of CXCL12/CXCR4 signaling could be a powerful new tool for combating T-ALL, a disease with no current targeted therapies.

overall_design: Mouse T-ALL cells were treated ex vivo with Cxcr4 inhibitor AMD3100 or vehicle control. Additionally, mouse T-ALL primary tumors were isolated from control (Cxcr4+/+) or knockout (Cxcr4-/-) animals. Total RNA was extracted from samples using the RNeasy Plus Mini Kit (Qiagen). Samples were then subject to PolyA selection using oligo-dT beads (Life Technologies, Carlsbad, CA) according to the manufacturer's instructions. The resulting RNA samples were then used as input for library construction using the dUTP method as described by Parkhomchuck et al., 2009. RNA libraries were then sequenced on the Illumina HiSeq 2500 using 50bp single-end reads.


title: Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

institute: UNIST

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

overall_design: Refer to individual Series


title: T cell help controls the speed of the cell cycle in germinal center B cells.

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

summary: The germinal center (GC) is a microanatomical compartment wherein high-affinity antibody-producing B cells are selectively expanded. B cells proliferate and mutate their antibody genes in the dark zone (DZ) of the GC and are then selected by T cells in the light zone (LZ) on the basis of affinity. Here, we show that T cell help regulates the speed of cell cycle phase transitions and DNA replication of GC B cells. Genome sequencing and single-molecule analyses revealed that T cell help shortens S phase by regulating replication fork progression while preserving the relative order of replication origin activation. Thus, high-affinity GC B cells are selected by a mechanism that involves prolonged dwell time in the DZ where selected cells undergo accelerated cell cycles.

overall_design: To determine whether GC B cells receiving high levels of T cell help show a specific change in gene expression, we compared DZ cells in the G1 phase of the cell cycle from αDEC-OVA and control αDEC-CS treated GCs using a fluorescent ubiquitination-based cell cycle indicator (Fucci-tg). RNA sequencing revealed that T cell-mediated selection produced an increase in gene expression programs associated with the cell cycle, metabolism, including the metabolism of nucleotides, and genes downstream of c-Myc and the E2F transcription factors.

first: Alexander

last: Gitlin

first: Christian

middle: T

last: Mayer

first: Ziv

last: Shulman

first: Mathew

last: Jones

first: Amnon

last: Koren

first: Michel

last: Nussenzweig


title: Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [ChIP-seq]

city: Ulsan

summary: The response to acid stress is a fundamental process in bacteria. Three transcription factors, GadE, GadW, and GadX (GadEWX) are known to play a critical role in the transcriptional regulation of glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the regulatory role of GadEWX in coordinating interacting cellular functions is still unknown. Here, we comprehensively reconstruct genome-wide GadEWX transcriptional regulatory network in E. coli K-12 MG1655 under acidic stress. Integrative data analysis reveals that GadEWX regulons are comprised of 45 genes in 31 transcription units (TUs), significantly expanding the current knowledge of the GadEWX regulatory network. We demonstrate that GadEWX directly and coherently regulate several proton efflux/influx and generating/consuming enzymes with pairs of negative-feedback loops to maintain pH homeostasis by controlling proton flow. In addition, GadEWX regulate genes with assorted functions including molecular chaperones, acid resistance, stress response, and other regulatory activities. These results present a comprehensive understating on how GadEWX simultaneously coordinates many other cellular processes to produce the overall response of E. coli to acid stress.

overall_design: A total of six samples were analyzed. GadE-8-myc, GadW-8 -myc, and GadX-8-myc tagged cells were cultured in M9 glucose minimal media at pH 5.5 with biological duplicates.

first: Sang

last: Seo


title: Comparative transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus)

city: Shanghai

first: Renyi

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

summary: Cucumber (Cucumis sativus L.) fruit is a type of fleshy fruit that is harvested immaturely. Early fruit development directly determines the final fruit length and diameter, and consequently the fruit yield and quality.  Different cucumber varieties display huge variations of fruit length, but how fruit length is determined at the molecular level  remains poorly understood. To understand the genes and gene networks that regulate fruit length in cucumber, high throughout RNA-seq data were used to compare the transcriptomes of early fruit from two near isogenic lines with different fruit lengths. 3955 genes were found to be differentially expressed, among which 2368 genes were significantly up-regulated and 1587 down-regulated in the line with long fruit. Microtubule and cell cycle related genes were dramatically activated in the long fruit, and transcription factors were implicated in the fruit length regulation in cucumber. Thus, our results built a foundation to dissect the molecular mechanism of fruit length control in cucumber, a key agricultural trait of significant economic importance.

overall_design: Comparative analysis of fruit from two near-isogenic lines, 408 (long fruit) and 409 (short fruit),  was employed to discover  genes and networks that regulate the fruit length. Two biological replicates were used from each line.

first: Jiang

last: Li

first: Yan

last: Shuangshuang

first: Ren

last: Huazhong

first: Li

last: Yanqiang

first: Xia

last: Mengxue

first: Yang

last: Wencai

last: Liying

first: Liu

last: Renyi

first: Zhang

last: Xiaolan


title: Transcripyome analysis of Brucella melitensis 16M and otpR mutant using Solexa/Illumina platform

first: Qingmin

last: Wu

address: No. 2 Yuanming west Road

institute: China Agricultural University

summary: We sequenced the mRNA of Brucella melitensis 16M and otpR mutant under acid stress to identify genes that were regulated by regulator OtpR.

overall_design: Examination of mRNA levels in individual sample under acid stress.


title: Wnt addiction of genetically defined cancers reversed by PORCN inhibition

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

institute: Cardiff University

summary: Enhanced sensitivity to Wnts is an emerging hallmark of a subset of cancers, defined in part by mutations regulating the abundance of their receptors. Inhibition of Wnt secretion by blocking an essential post-translational modification, palmitoleation, provides a useful therapeutic intervention. Inhibition of PORCN in RSPO3-translocated cancers via treatment with ETC-159 causes a marked remodeling of the transcriptome, with loss of cell cycle, stem cell, and proliferation genes and an increase in differentiation markers. Inhibition of Wnt signaling by PORCN inhibition holds promise as differentiation therapy in genetically defined human cancers.

overall_design: RNA-seq of colorectal PDXs with confirmed R-spondin fusion genes. RNA-seq was performed in 2 conditions (Vehicle and treatment with ETC-159 (an inhibitor of PORCN) with 4 replicates per condition.

first: Nathan

last: Harmston

first: Babita

last: Madam

first: Enrico

last: Petretto

first: David

middle: M

last: Virshup


title: MacroH2A1 ChIP-seq from H-RasV12 expressing senescent IMR90 human primary lung fibroblasts

city: Bronx

first: Matthew

middle: Jon

last: Gamble

address: 1300 Morris Park Ave / Golding 203

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: Oncogene induced senescence (OIS) is a tumor suppressive mechanism typified by stable proliferative arrest, a persistent DNA damage response and the senescent-associated secretory phenotype (SASP). MacroH2A1, a tumor suppressive histone variant, is upregulated during OIS. Using ChIP-seq, we found that macroH2A1 undergoes dramatic relocalization during OIS. SASP genes are enriched in macroH2A1-containing chromatin and macroH2A1 is a critical component of the positive feedback loop that maintains SASP expression. Endoplasmic reticulum (ER) stress, a feature of OIS that requires macroH2A1, leads to ATM activation. ER stress triggers a negative feedback loop reducing SASP expression by causing the ATM-dependent removal of macroH2A1 from SASP genes. MacroH2A1 represents a critical control point in the regulation of SASP expression during OIS by We demonstrate that SASP gene expression is regulated by the combined actions of a positive feedback loop that requires macroH2A1 and a negative feedback loop where ER stress leads to ATM activation critical for the removal of macroH2A1 from SASP genes and consequently their repression.

overall_design: macroH2A1 ChIP and corresponding input samples from H-RasV12 OIS IMR90 cells were sequenced

first: Hongshan

last: Chen


title: In vivo transcriptional activation using CRISPR-Cas9 in Drosophila

status: Public on Aug 10 2015

city: Boston

first: Norbert

last: Perrimon

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: Identifying putative transcription factor target genes by combining CRISPR/Cas9-based transcriptional activation with RNAseq in Drosophila S2R+ cells. This study focuses on the transcription factors Twist and Snail, singly and together.

overall_design: RNA from Drosophila cells following CRISPR/Cas9-based activation of Twist, Snail, or Twist and Snail together, compared with non-targeting sgRNA. Two biological replicates for each experiment

first: Nobert

first: Xiaochun

last: Ni


title: Function and regulation of Cph2 in Candida albicans [RNA-Seq]

city: Irvine

first: Haoping

last: Liu

address: Med. Sci. I, Rm D234

department: Dept. of Biological Chemistry

institute: University of California

summary: Candida albicans is associated with humans as both a harmless commensal organism and a pathogen. Cph2 is a transcription factor whose DNA binding domain is similar to mammalian sterol response element binding proteins (SREBPs). SREBPs are master regulators of cellular cholesterol levels, and are highly conserved from fungi to mammals. However, ergosterol biosynthesis is regulated by the zinc finger transcription factor Upc2 in C. albicans and several other yeasts. Cph2 is not necessary for ergosterol biosynthesis, but important for colonization in the murine gastrointestinal tract. Here we demonstrate that Cph2 is a membrane-associated transcription factor that is processed to release the N-terminal DNA binding domain like SREBPs; but its cleavage is not regulated by cellular levels of ergosterol or oxygen. ChIP-Seq shows that Cph2 binds to the promoters of HMS1 and other components of the regulatory circuit for GI tract colonization. In addition, 50% of Cph2 targets are also bound by Hms1 and other factors of the regulatory circuit. Several common targets function at the head of the glycolysis pathway. Thus, Cph2 is an integral part of the regulatory circuit for GI colonization that regulates glycolytic flux. RNA-seq shows a significant overlap in genes differentially regulated by Cph2 and hypoxia, and Cph2 is important for optimal expression of some hypoxia-responsive genes in glycolysis and the citric acid cycle. We suggest that Cph2 and Upc2 regulate hypoxia-responsive expression in different pathways, consistent with a synthetic lethal defect of the cph2 upc2 double mutant in hypoxia.

overall_design: Expression profiling by high throughput sequencing. RNA sequencing was performed on wild type and cph2 deletion strains. 2 biological replicates were sequenced for each strain.

first: Shelley

last: Lane

first: Pietro

last: Di Lena

first: Pierre

last: Baldi


title: Function and regulation of Cph2 in Candida albicans

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


title: Omega-3 fatty acids partially revert the metabolic gene expression profile induced by long-term calorie restriction

city: Guelph

first: Angela

last: Cánovas

state: ON

address: 50 Stone Road East

department: Animal Biosciences

country: Canada

institute: University of Guelph

summary: Calorie restriction (CR) consistently extends longevity and delays age-related diseases across several animal models. We have previously shown that different dietary fat sources can modulate life span and mitochondrial ultrastructure, function and membrane fatty acid composition in mice maintained on a 40% CR. In particular, animals consuming lard as the main fat source (CR-Lard) lived longer than CR mice consuming diets with soybean oil (CR-Soy) or fish oil (CR-Fish) as the predominant lipid source.  In the present work, a transcriptomic analysis in liver and skeletal muscle was performed in order to elucidate possible mechanisms underlying the changes in energy metabolism and longevity induced by dietary fat in CR mice. After 8 months of CR, transcription downstream of several mediators of inflammation was inhibited in liver. In contrast, proinflammatory signaling was increased in the CR-Fish versus other CR groups. Dietary fish oil induced a gene expression pattern consistent with increased transcriptional regulation by several cytokines (TNF, GM-CSF, TGF-b) and sex hormones when compared to the other CR groups. The CR-Fish  also had lower expression of genes involved in fatty acid biosynthesis and increased expression of mitochondrial and peroxisomal fatty acid b-oxidation genes than the other CR diet groups. Our data suggest that a diet high in n-3 PUFA, partially reverts CR-related changes in gene expression of key processes, such as inflammation and steroid hormone signaling, and this may mitigate life span extension with CR in mice consuming diets high in fish oil.

overall_design: Sixteen male C57BL/6 mice were purchased at 14 weeks of age from the Jackson Laboratory (Sacramento, CA) and fed a commercial rodent chow diet (Harlan Teklad #7012). The mice were allowed ad libitum access to food and their food intake was monitored for two weeks. At 4 months of age, the animals were randomly assigned to four groups. The Control group received 95% of the daily ad libitum caloric intake (13.6 kcal/day) to avoid excessive weight gain and obesity, and the other three groups received 60% of the ad libitum consumption (8.6 kcal/day). A total of 31 mice samples (eight control, eight fish, eight lard and seven soy distributed in liver (n=16) and muscle (n=15) tissues) were analyzed by RNA-Sequencing.  However, 2 samples (1071 control liver [JFM42H], 1125 fish muscle [JFM45D]) were discarded for further analysis after performing cluster analysis (they were clustering in a different groups). Also their RIN values were not as high as those of the other samples, indicating lower quality of the RNA.

first: José

middle: A

last: López-Domínguez

first: Juan

middle: F

last: Medrano

first: Alma

last: Islas-Trejo

first: Kyoungmi

last: Kim

first: Sandra

middle: L

last: Taylor

last: Villalba

first: Guillermo

last: López-Lluch

first: Plácido

last: Navas

first: Jon

last: Ramsey


title: Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]

first: Donghyuk

department: Department of Chemical Engineering

overall_design: A total of eight samples were analyzed. WT and gadEWX mutant cells were cultured in M9 glucose minimal media at pH 5.5 with biological duplicates.

first: Sang

last: Seo


title: Reduced Glucose Sensation Can Increase the Fitness of Saccharomyces cerevisiae Lacking Mitochondrial DNA

status: Public on Aug 07 2015

city: Sariyer

first: Cory

middle: David

last: Dunn

state: Istanbul

address: Rumelifeneri Yolu

department: Molecular Biology and Genetics

country: Turkey

institute: Koç University

summary:
Damage to the mitochondrial genome (mtDNA) can lead to diseases for which there are no clearly effective treatments. Since mitochondrial function and biogenesis are controlled by the nutrient environment of the cell, it is possible that perturbation of conserved, nutrient-sensing pathways may successfully treat mitochondrial disease. We found that restricting glucose or otherwise reducing the activity of the protein kinase A (PKA) pathway can lead to improved proliferation of Saccharomyces cerevisiae cells lacking mtDNA and that the transcriptional response to mtDNA loss is reduced in cells with diminished PKA activity. We have excluded many pathways and proteins from being individually responsible for the benefits provided to cells lacking mtDNA by PKA inhibition, and we found that robust import of mitochondrial polytopic membrane proteins may be required in order for cells without mtDNA to receive the full benefits of PKA reduction. Finally, we have discovered that the transcription of genes involved
in arginine biosynthesis and aromatic amino acid catabolism is altered after mtDNA damage. Our results highlight the potential importance of nutrient detection and availability on the outcome of mitochondrial dysfunction.

overall_design: Four experimental conditions were used:  BY4743 (WT) cells containing empty pRS426 vector and containing mtDNA because EtBr was not used, BY4743 (WT) cells containing empty pRS426 vector and lacking mtDNA after 24 hours of treatment with 25 µg/ml ethidium bromide, BY4743 (WT) cells overexpressing TIP41 from plasmid pRS426 and lacking mtDNA after 24 hours of treatment with 25 µg/ml ethidium bromide, and BY4743 (WT) cells overexpressing PDE2 from plasmid pRS426 and lacking mtDNA after 24 hours of treatment with 25 µg/ml ethidium bromide.  Two replicates were performed for each sample type.

first: Emel

last: Akdoğan

first: Mehmet

last: Tardu

first: Gülkız

last: Baytek

first: Görkem

last: Garipler

first: Halil

last: Kavaklı

middle: D


title: A transcriptome atlas of embryonic skin

first: Michael

last: Rendl

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

summary: We co-isolated hair follicle placode and dermal condensate cells along with other specific cell types from E14.5 embryonic mouse skin. With next-generation RNA-sequencing we defined gene expression patterns in the context of the entire embryonic skin.

overall_design: FACS was used to isolate specific cell types from E14.5 embryonic mouse skin.

first: Rachel

last: Sennett

first: Zichen

last: Wang


title: RNA-Seq dependent transcriptional analysis unveils adaptive mechanisms in the intestine of sea cucumber Apostichopus japonicus during aestivation

status: Public on Aug 08 2015

city: Yantai

first: Ye

last: Zhao

state: Shandong Province

address: Qingquan Road No.30

institute: Yantai University

summary: Sea cucumbers (Holothuroidea; Echinodermata), cycle annually between aestivation when water temperature is above about 25°C in the summer and active life when temperature is below about 18°C. We used RNA-Seq to determine gene expression profiles of intestine tissue of A.japonicus during non-aestivation (NA), deep-aestivation (DA), and arousal from aestivation (AA).

overall_design: At least 15 individuals per stage, intestines at NA, DA and AA stages were used for our experiments.

first: Muyan

last: Chen


title: Inhibition of miR-29 has a significant lipid-lowering benefit through suppression of lipogenic programs in liver

city: Chapel Hill

first: Praveen

last: Sethupathy

address: 120 Mason Farm Rd

department: Genetics

institute: UNC Chapel Hill

summary: MicroRNAs (miRNAs) are important regulators and potential therapeutic targets of metabolic disease. In this study we show by in vivo administration of locked nucleic acid (LNA) inhibitors that suppression of endogenous miR-29 lowers plasma cholesterol levels by ~40%, commensurate with the effect of statins, and reduces fatty acid content in the liver by ~20%. Whole transcriptome sequencing of the liver reveals 883 genes dysregulated (612 down, 271 up) by inhibition of miR-29. The set of 612 down-regulated genes are most significantly over-represented in lipid synthesis pathways. Among the up-regulated genes are the anti-lipogenic deacetylase sirtuin 1 (Sirt1) and the anti-lipogenic transcription factor aryl hydrocarbon receptor (Ahr), the latter of which we demonstrate is a direct target of miR-29. In vitro radiolabeled acetate incorporation assays confirm that pharmacologic inhibition of miR-29 significantly reduces de novo cholesterol and fatty acid synthesis. Our findings indicate that miR-29 controls hepatic lipogenic programs, likely in part through regulation of Ahr and Sirt1, and therefore may represent a candidate therapeutic target for metabolic disorders such as dyslipidemia.

overall_design: Hepatic mRNA profiles of C57BL/6J female mice treated with LNA against miR-29a, miR-29b and miR-29c versus saline.

first: C

last: Kurtz

first: Emily

middle: E

last: Fannin

first: Cynthia

last: Toth

first: Daniel

middle: S

last: Pearson

first: Kasey

middle: C

last: Vickers


title: Mapping of dsRNA in yeast using reconstituted RNAi pathway

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

institute: Institut Curie

summary: Small RNA produced by Dicer (Dcr1) are used to map dsRNA in wild-type strain and a xrn1-delta mutant of S. cerevisiae, inactivated for the cytoplasmic 5'-3' RNA decay pathway.

overall_design: Small RNA sequencing in wild-type and xrn1-delta strains of S. cerevisiae, with or without reconstituted RNAi pathway.

first: Marc

last: Descrimes

first: Antonin

last: Morillon