title: Genome-wide mapping of the binding sites of transcription factor Cst6p in Saccharomyces cerevisiae

city: Mölndal

first: David

last: Bergenholm

state: SWEDEN

address: Axgatan 139

institute: Chalmers tekniska högskola

summary: The transcription factor Cst6p in Saccharomyces cerevisiae has been reported to play important roles in several biological processes. However, the genome-wide targets of Cst6p and the mechanisms for its physiological functions remain unknown. Here, we mapped the genome-wide binding sites of Cst6p with ChIP-exo at high resolution. Cst6p binds to the promoter regions of 59 genes with various biological functions when cells are grown on ethanol, but hardly binds to the genome on glucose. The growth deficiency of CST6 deletion mutant on ethanol is attributed to the markedly decreased expression of carbonic anhydrase gene NCE103, which is a direct target of Cst6p. The target genes of Cst6p have a large overlap with those of stress-responsive transcription factors, such as Sko1p and Skn7p. In addition, the CST6 deletion mutant growing on ethanol shows hypersensitivity to oxidative stress and ethanol stress, assigning Cst6p as a new member of the stress-responsive transcriptional regulatory network. These results show that genome-wide binding site mapping is able to provide new insights into the function of transcription factors, and highlight the highly connected and condition-dependent nature of the transcriptional regulatory network in S. cerevisiae.

overall_design: The binding sites of Cst6p when cells were grown in glucose or ethanol were measured in biological duplicates, so there are four samples in total.

first: Guodong

first: Jens

last: Nielsen


title: Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations [ChIP-seq]

status: Public on Apr 04 2016

city: Adelaide

first: Joanna

last: Achinger-Kawecka

state: SA

address: AHMS Building, North Terrace

country: Australia

institute: South Australian Immunogenomics Cancer Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: A three-dimensional chromatin state underpins the structural and functional basis of the genome by bringing regulatory elements and genes into close spatial proximity to ensure proper, cell-type specific gene expression profiles. Here, we perform HiC chromosome conformation, ChIP-seq and RNA-seq to investigate how the three-dimensional organization of the cancer genome is disrupted in the context of epigenetic remodelling and atypical gene expression programs.

overall_design: Hi-C, ChIP-seq and RNA-seq were conducted in three human prostate cell lines: normal prostate epithelial cells (PrEC) and prostate cancer cells (PC3 and LNCaP).

first: P

last: Taberlay

first: J


title: Determination of a comprehensive alternative splicing regulatory network and the combinatorial regulation by key factors during Epithelial-to-Mesenchymal Transition [EMT.time course]

status: Public on Apr 05 2016

city: Los Angeles

first: Yi

last: Xing

state: CA

address: 650 Charles E. Young Dr. South

department: Department of Microbiology, Immunology, & Molecular Genetics

country: USA

institute: UCLA

type: Expression profiling by high throughput sequencing

summary: The epithelial to mesenchymal transition (EMT) is an essential biological process during embryonic development and has also been implicated in cancer metastasis. Previous studies have characterized transcriptional regulation and key transcription factors that impact EMT. However, the role of alternative splicing (AS) regulation in EMT has only recently emerged and remains relatively uncharacterized. Here we used a robust in vitro EMT model to dynamically and comprehensively characterize splicing switches during EMT in a temporal manner.

overall_design: We generated a H358 clone stably expressing a doxycycline (Dox)-inducible cDNA encoding a Zeb1-mCherry fusion protein. Over a 7-day time course following Dox treatment, cells have undergone EMT. We harvested total RNA and protein at each day of the EMT time course and a no Dox-treated control in biological triplicates. We made cDNA libraries for each replicate and subjected them to RNA-seq.

first: Russ

last: Carstens


title: Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations [RNA-seq]

first: C

middle: M

last: Gould

first: K

middle: A

last: Giles

middle: C


title: Distinct myeloid progenitor differentiation pathways uncovered through single cell RNA sequencing

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

summary: Haematopoietic stem cells can differentiate into all blood cell types. In this process, cells become progressively restricted to a single cell type. The order in which differentiating cells loose lineage potential, and the prospective isolation of cells with a defined potential remains a long-standing question.    We performed gene expression analysis of haematopoietic cells from Gata1-EGFP reporter mice, leading to a model for hematopoiesis where the initial lineage decision consists of a seperation of erythroid/megakaryocyte/mast cell/eosinophil potential from lymphopoietic/monocyte/neutrophil potential

overall_design: Find unbiased heterogeneity in the preGM hematopoietic progenitor population

first: Roy

last: Drissen

first: Alice

last: Giustacchini

first: Supat

last: Thongjuea

first: Sten

middle: E

last: Jacobsen


title: Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations

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

overall_design: Refer to individual Series


title: Nuclear Transfer nTreg model reveals fate-determining TCRbeta and peripheral nTreg precursors

city: Freiburg

first: Manching

last: Ku

address: Mathildenstrasse 1

department: Hematology and Oncology

country: Germany

institute: Medical Center - University of Freiburg

summary: To study the development and function of “natural-arising” T regulatory (nTreg) cells, we developed a novel nTreg model on pure nonobese diabetic background using epigenetic reprogramming via somatic cell nuclear transfer. On RAG1-deficient background, we found that monoclonal FoxP3+ CD4+ Treg cells developed in the thymus in the absence of other T cells. Adoptive transfer experiments revealed that the thymic niche is not a limiting factor in nTreg development. In addition, we showed that the T-cell receptor (TCR) β-chain of our nTreg model was not only sufficient to bias T-cell development toward the CD4 lineage, but we also demonstrated that this TCR β-chain was able to provide stronger TCR signals. This TCR-β–driven mechanism would thus unify former per se contradicting hypotheses of TCR-dependent and -independent nTreg development. Strikingly, peripheral FoxP3− CD4+ T cells expressing the same TCR as this somatic cell nuclear transfer nTreg model had a reduced capability to differentiate into Th1 cells but were poised to differentiate better into induced nTreg cells, both in vitro and in vivo, representing a novel peripheral precursor subset of nTreg cells to which we refer to as pre-nTreg cells.

overall_design: We performed RNA-Seq analysis to determine the transcriptional differences between monoclonal FoxP3GFP-positive and -negative CD4+ T cells from NOD.TCRab.FoxP3GFP.Rag-/- and compared it with polyclonal FoxP3GFP-positive and -negative CD4+ T cells from NOD.FoxP3GFP mice

first: Oktay

last: Kirak

first: Eugene

last: Ke


title: Transcriptome and Micronome analysis of OPLL

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

country: China

institute: The Second Military Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Ossification of the posterior longitudinal ligament (OPLL) is formed by heterogeneous ossification of posterior longitudinal ligament. The patho-mechanism of OPLL is still largely unknown. MicroRNAs are small nucleatides that function as regulators of gene expression in almost any biological process. However, few microRNAs are reported to have a role in the pathological process of OPLL. Therefore, we performed high-throughput microRNA sequencing and transcriptome sequencing of primary OPLL and PLL cells in order to decipher the interacting network of microRNAs in OPLL.

overall_design: MRNA and microRNA profiles were done using primary culture cells of human ossification of the posterior longitudinal ligament (OPLL) tissue and normal posterior longitudinal ligament (PLL) tissue.

first: Yang

last: Liu


title: Refining mouse annotations via targeted RNA sequencing

city: Paris

first: Giovanni

last: Bussotti

address: 25-28 Rue du Dr Roux

country: France

institute: Institute Pasteur

summary: In this work we aim to improve the understanding of the mouse transcriptome complexity, investigate the expressed fraction of the genome and ameliorate the available mouse annotations. We utilized CatureSeq, a recently described strategy meant to enhance the sequencing coverage of low abundant genes. In our experimental design we generated oligonucleotide probes to select annotated and putative long-noncoding RNA and splice junctions. This allowed us to improve dramatically the sequencing throughput of the targeted regions. As a consequence our approach permitted the simultaneous identification of thousands of exons and the expansion of the already known ones

overall_design: The mouse gene assembly is anlaysed by targeted RNA sequencing of lncRNA and splice junctions. 8 mouse tissues and 16 samples are considered in the analysis. Each sample was added with external RNA controls. The controls are polyadenylated transcripts of known concentration designed to be added to an RNA analysis experiment after sample isolation.

first: Tomasso

last: Leonardi

first: Michael

last: Clark

first: Tim

last: Mercer


title: Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations [Hi-C]

first: Joanna

last: Achinger-Kawecka

summary: A three-dimensional chromatin state underpins the structural and functional basis of the genome by bringing regulatory elements and genes into close spatial proximity to ensure proper, cell-type specific gene expression profiles. Here, we perform Hi-C chromosome conformation to investigate how the three-dimensional organization of the cancer genome is disrupted in the context of epigenetic remodelling and atypical gene expression programs.

first: P

last: Taberlay

first: J


title: Chromosomal deletions linked to p53 loss of heterozygosity promote cancer through p53-independent mechanisms

city: Chengdu

first: Yu

address: 6 Wangjiang Road

institute: Sichuan University

summary: The purpose of current study is to identify the differentiated gene expression associated with mouse 11B3 deletion, syntenic to human chromosome 17p13.1. We compared four different mouse acute myeloid leukemia cells, freshly isolated from mouse bone marrows with either 11B3fl/p53fl;shNf1;shMll3;Vav1-Cre or p53fl/fl;shNf1;shMll3;Vav1-Cre. The RNA-seq results indicate that genes located on chromosome 11B3 mostly reduce gene expression level in 11B3 deleted leukemia cells.

overall_design: Examination RNA expression level in 11B3-deleted vs p53-loss only samples.

first: Scott

middle: W

last: Lowe


title: Long-range chromosome interactions mediated by cohesin shape circadian gene expression

city: New York

first: Yichi

state: NY

address: 1275 York Avenue

institute: MSKCC


title: Long-range chromosome interactions mediated by cohesin shape circadian gene expression [RNA-Seq]

summary: Mammalian circadian rhythm is established by the negative feedback loops consisting of a set of clock genes, which lead to the circadian expression of thousands of downstream genes. As genome-wide transcription is organized under the high-order chromosome structure, it is unclear how circadian gene expression is influenced by chromosome structure. In this study, we focus on the function of chromatin structure proteins cohesin as well as CTCF (CCCTC-binding factor) in circadian rhythm. We analyzed the interactome of a Bmal1-bound enhancer upstream of a clock gene, Nr1d1, by 4C-seq and observed that cohesin binding sites are enriched in the interactome. Integrating circadian transcriptome data and cistrome data, we found that cohesin-CTCF co-binding sites tend to insulate the phases of circadian oscillating genes while cohesin-non-CTCF sites facilitate the interaction between circadian enhancer and promoter. A coarse-grained model integrating the long-range effect of cohesin and CTCF markedly improved our mechanistic understanding of circadian gene expression. This model is subsequently supported by our RNA-seq data from cohesin knockout cells. Cohesin is required at least in part for driving the circadian gene expression by facilitating the enhancer-promoter looping. Taken together, our study provided a novel insight into the relationship between circadian transcriptome and the high-order chromosome structure.

overall_design: RNA-Seq in WT and Smc3-/- mouse embryonic fibroblast cells

first: Weimin

last: Guo

first: Ping

last: Li

first: Yan

last: Zhang

first: Zenghua

last: Fan

first: Zhihu

last: Zhao

first: Jun

last: Yan


title: Transcriptome analysis of estradiol-inducible overexpression of transcription factor WRKY75 in Arabidopsis thaliana

status: Public on Apr 03 2016

city: Helsinki

first: Mikael

last: Brosché

address: Viikinkaari 1

department: Department of Biosciences

country: Finland

institute: University of Helsinki

summary: Sequence-specific transcription factor WRKY75 is highly responsive to reactive oxygen species on transcriptional level in the rosettes of Arabidopsis thaliana. In addition, it acts in developmental responses, acquisition of nutrients, and in stress responses. In the root, WRKY75 is a repressor of root hair formation, it regulates the phosphate starvation response, and the response to certain pathogens. In order to find the target genes of WRKY75, the effects of estradiol-inducible overexpression of WRKY75 on transcriptome was studied using RNA-seq.

overall_design: Two independent inducible WRKY75 overexpressor lines (N2102362 and N2102363) were treated with estradiol for 3 hours and four biological replicates, five plant per replicate, were used for RNA-seq. As a control, wild type Col-0 was treated with estradiol or water for 3 hours and three biological replicates, five plant per replicate, were used for RNA-seq.

first: Lauri

last: Vaahtera

first: Katariina

last: Vuorinen


title: Transcriptional Regulationand Chromatin Dynamics inHuman Epithelial Cell Differentiation (RNA-seq)

city: Segrate

first: Luca

last: Petiti

state: Milan

address: Via Fratelli Cervi, 93

country: Italy

institute: ITB-CNR

summary: Transcriptional profiling of KP and DK through RNA-seq

overall_design: RNA-sequencing of KP and DK

first: Alessia

last: Cavazza

first: Annarita

last: Miccio

first: Oriana

last: Romano

first: Guidantonio

last: Tagliazucchi

first: Clelia

last: Peano

first: Marco

last: Severgnini

first: Ermanno

last: Rizzi

first: Gianluca

last: De Bellis

first: Silvio

last: Bicciato

first: Fulvio

last: Mavilio


title: Transcriptome analysis of apoplastic reactive oxygen species (ROS) signaling and dissection of the roles of WRKY25, WRKY33 and WRKY75 in the transcriptional reprogramming triggered by apoplastic ROS

summary: In order to dissect the roles of sequence-specific transcription factors WRKY25, WRKY33 and WRKY75 in apoplastic ROS signaling, a transcriptome profiling of ozone response was done using two arabidopsis mutants: a double mutant wrky25 wrky33 and a single mutant wrky75. The single mutant lines used for transcriptomic analyses were obtained from NASC: wrky25 (SAIL_529_B11) and wrky33 (SALK_006603) were crossed to generate double mutant wrky25 wrky33. T-DNA insertion mutant wrky75-25 (N121525) was obtained from NASC.

overall_design: Three biological replicates, five plants per replicate, treated with 350 ppb ozone for 2 hours, were used for RNA-seq analysis. For each genotype, also non-ozone-treated samples were collected. For the Col-0 control line, an additional fourth replicate with/without ozone was done.


title: Long-range chromosome interactions mediated by cohesin shape circadian gene expression [4C]

first: Yichi

last: Xu

overall_design: 4C-seq of a Bmal1 enhancer in mouse liver

first: Weimin

last: Guo

first: Ping

last: Li

first: Yan

last: Zhang

first: Zenghua

last: Fan


title: Transcriptional Regulationand Chromatin Dynamics inHuman Epithelial Cell Differentiation


title: Gene body methylation patterns in Daphnia are associated with gene family size

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

country: Belgium

institute: Ghent University

type: Methylation profiling by high throughput sequencing

summary: We report the characterized gene body methylation patterns in two Daphnia species.

sample_organism:
Daphnia pulex
Daphnia magna

platform_organism:
Daphnia pulex
Daphnia magna

overall_design: Examination of cytosine methylation in DNA samples of 2 Daphnia species following bi-sulfite treatment.

first: Dieter

middle: I

last: De Coninck

first: Michael

last: Pfrender

first: Karel

last: De Schamphelaere


title: Transcriptional Regulationand Chromatin Dynamics inHuman Epithelial Cell Differentiation (CAGE)

first: Luca

last: Petiti

summary: Investigation of promoters usage in KP cells

overall_design: KP cells promoter usage profiling by CAGE-seq

first: Alessia

last: Cavazza

first: Annarita

last: Miccio

first: Oriana

last: Romano


title: Colon cancer shperes are sensitive to Fenretinide

first: Jiansheng

last: Liu

state: Shanghai

address: No.845 LingShan Road, PuDong District

department: Renji Hospital

institute: Shanghai Jiao Tong University,School of Medicine.

summary: Fenretinide has shown its antitumor activity in many tumor types with low cytotoxicity to normal cells. Recently, we have shown that fenretinide could eradicate chronic myeloid leukemia stem/progenitor cells and spheres from ovarian cancer. In this study, we investigate whether fenretinide could selectively target sphere cells of colon cancer. Using high-throughtput microarray system, we identified GO terms and pathway signatures enriched in fenretinide treated HT29 cells and HT29 derived sphere cells.

overall_design: Colon cancer cells HT29 were cultured in sphere formation conditions, HT29 cells and HT29 derived sphere cells were treated with fenretinide, and total RNA from those spheres and corresponding adhered cell was hybridized on Affymetrix U133 plus 2.0 genechip.

first: Lanlan

first: Yanzhi

last: Du


title: Propogation of anxiety-traits through the maternal line via parallel and segregated gametic and non-gametic epigenetic mechanisms

first: Shifra

middle: Liba

last: Klein

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell

summary: Maternal stress, anxiety, and depression increase the risk of psychiatric disorders in the progeny. These maternal effects can extend beyond the first generation and affect the grandchildren. In contrast to paternal, maternal effects can impact the offspring not only during gametogenesis, but also through fetal and early-postnatal life, increasing phenotypic complexity and the overall impact. To better understand its non-genetic structure, we dissected a complex maternally-transmitted phenotype to elementary behaviors and their corresponding transmission mechanisms. Chronic stress and depression are associated with reduced serotonin1A receptor (5-HT1AR) levels, and we reported that 5-HT1AR+/- dams transmit anxiety/stress-reactivity traits to their wild-type offspring. Here we show that the maternal effect is propagated to multiple generations, and that the behavioral traits are not transmitted in unison, but rather via parallel and segregated mechanisms, each with generation-dependent penetrance and gender specificity. The “risk-avoidance” and “hypoactivity” traits of anxiety were transmitted, via a neuro-immune pathway, consecutively from mother to the wild-type F1, F2, and occasionally F3 generation by iterative non-gametic-programming, while the “increased stress-reactivity” trait was transmitted to the F2 generation by gametic-programming. Iterative non-gametic-programming of anxiety was linked, via gene expression changes and clustered DNA hypo/hypermethylation at intragenic enhancers, to sphingolipid metabolism and GPCRs in the F1/F2 hippocampus, suggesting dysregulated lipid raft functioning/transmembrane signaling. Conversely, gametic-programming of behavior was predominantly associated with hypomethylation at different promoter-enhancing sequences within a set of genes with diverse neuronal functions. Since differential methylation appeared only postnatally in F2 neurons and was absent in F3 neurons, it is secondary to earlier F2 gametic changes that survive reprogramming in the early embryo, but are erased in F3 germ-cells. Our data introduce parallel and segregated non-genetic transmission of traits as a mechanism that may explain the propagation and pleiotropy of complex behavioral and psychiatric disease phenotypes across generations.

overall_design: Compared three generations of male offspring from wild-type and 5HT1A-R-/+ Swiss Webster mothers with two replicates per sample. Included as well is F2 embryo transfer from wild-type and het parents in wild-type surogates

first: Emma

last: Mitchell

middle: L

first: Ali

last: Sharma

first: Judith

middle: G

last: Toth

first: Kimon

last: Argyropoulos

first: Luendro

last: Barboza

first: Charlotte

last: Bavley

first: Analia

last: Bortolozzi

first: Francesco

last: Artigas

first: Ji-eun

last: Oh

first: Niraj

last: Lodhi

first: Jarrod

last: Dudakov

first: Miklos


title: Profiling miRNAs of high, low and non-producing CHO cells during biphasic Fed-Batch cultivations reveal interesting targets for cell line engineering

city: Biberach

first: Fabian

last: Stiefel

address: Hubertus-Liebrecht-Strasse 35

institute: University of Applied Sciences Biberach

summary: Fed-batch cultivation of recombinant Chinese hamster ovary (CHO) cell lines is one of the most widely used production mode for commercial manufacturing of recombinant protein therapeutics. Furthermore, fed-batch cultivations are often conducted as biphasic processes where culture temperature is decreased to maximize volumetric product yields. However, it still remains to be elucidated which intracellular regulatory elements actually control the observed pro-productive phenotypes. Recently, several studies have revealed microRNAs (miRNAs) to be important molecular switches of cell phenotypes since single miRNAs are capable of regulating entire physiological pathways. In this study, we analyzed miRNA profiles of two different recombinant CHO cell lines (high and low producer), and compared them to a non-producing CHO DG44 host cell line during fed-batch cultivation at 37 versus 30 °C culture temperature. Taking advantage of next-generation sequencing combined with cluster, correlation and differential expression analyses, we could identify 89 different miRNAs, which might be interesting for CHO cell engineering. Functional validation experiments using 19 validated target miRNAs confirmed that these miRNAs indeed induced changes in process relevant phenotypes such as recombinant protein production, apoptosis, necrosis and proliferation. Furthermore, computational miRNA target prediction combined with functional clustering identified putative target genes and cellular pathways, which might be regulated by these miRNAs. Taken together, our study systematically identified novel target miRNAs during different phases and conditions of a biphasic fed-batch process and functionally evaluated their potential for host cell engineering.

overall_design: 36 miRNA libraries from three different CHO cell lines and two process condition. In the control run temperature was maintained at 30°C, while temperature was reduced to 30°C after reaching mid exponential phase

first: Friedemann

last: Hesse


title: A molecular shift in limb identity underlies the convergent evolution and development of feathered feet

city: Orem

first: Eric

last: Domyan

state: UT

address: 800 W University Parkway

department: Department of Biology

institute: Utah Valley University

summary: The genetic and developmental mechanisms that control the decision between scale and feather growth – two profoundly different epidermal appendages, and an important developmental shift in the evolution of birds from their dinosaurian ancestors – remain poorly understood. Domestic pigeons display dramatic variation in foot epidermal appendages within a single species, and classical studies suggest that a small number of genes control much of this variation; thus pigeons provide a tractable model to understand skin appendage specification and variation. Here we show that feathered feet in pigeons are the consequence of a partial transformation of limb-type identity mediated by cis-regulatory changes in the hindlimb-specific transcription factor Pitx1 and forelimb-specific transcription factor Tbx5. We also demonstrate that ectopic hindlimb expression of Tbx5 is associated with the development of foot feathers in domestic chickens, suggesting that similar developmental mechanisms underlie phenotypic convergence in avian lineages that diverged over 100 MYA. These results show how qualitative and quantitative changes in expression of regional patterning genes can generate localized changes in organ fate and morphology, and provide a viable molecular mechanism for the evolution of hindlimb scale and feather distribution in dromaeosaurs.

overall_design: Examination of H3K27ac status in embryonic limb buds from two domestic pigeon breeds, racing homer and Indian fantail

middle: T

first: Michael

middle: D

last: Shapiro

first: Carlos

middle: R

last: Infante

first: Douglas

middle: B

last: Menke


title: Differential regulation of meristem size, morphology and organization by the ERECTA, CLAVATA and class III HD-ZIP pathways

status: Public on Apr 02 2016

city: Elche

first: Héctor

last: Candela

address: Edificio Vinalopó, Avenida de la Universidad s/n

department: Instituto de Bioingeniería

country: Spain

institute: Universidad Miguel Hernández de Elche

summary: The shoot apical meristem (SAM) of angiosperm plants is a highly organized minute structure that gives rise to all above-ground organs. The SAM is divided into three different functional domains. The central zone (CZ) at the SAM tip harbors the self-renewing pluripotent stem cells and the organizing center, providing daughter cells that are continuously displaced into the interior rib zone (RZ) or to the surrounding peripheral zone (PZ), from which organ primordia are initiated. Despite the constant flow of cells from the CZ into the RZ or PZ, and cell recruitment for primordium formation, a stable balance is maintained between the distinct cell populations in the SAM. Here we combined an in depth phenotypic analysis with a comparative RNA-Seq approach to characterize meristems from selected combinations of clavata3 (clv3), jabba-1D (jba1D) and erecta (er) mutants. We demonstrate that CLV3 restricts meristem expansion along the apical basal axis, while class III HD-ZIP and ER pathways restrict meristem expansion laterally, but in distinct and possibly perpendicular orientations. Our k-means analysis reveals that clv3, jba-1D/+ and er lead to meristem enlargement by affecting different aspects of meristem function, e.g., that clv3 displays increase in stem cell population, whereas jba-1D/+ er exhibits increase in mitotic activity and in meristematic cell population. We demonstrate that thecombination of genetic and mRNA-Seq comparative approach provides a precise and sensitive method to identify cell type specific transcriptomes in a small structure such as the SAM.

overall_design: Ten samples enriched in shoot apical meristem tissue were analyzed, corresponding to 5 different genotypes (Col-0, clv3-2, jba-1D/+, jba-1D/+ er-20, and jba-1D/+ er-20 clv3-2) at two different developmental stages (8-day-old seedlings and 15-day-old seedlings).

first: Tali

last: Mandel

first: Udi

last: Landau

first: Lior

last: Asis

first: Einat

last: Zilinger

first: Cristel

last: Carles

first: Leor

last: Williams


title: Mapping of variable DNA methylation across multiple cell types defines a dynamic regulatory landscape of the human genome

status: Public on Apr 06 2016

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

summary: DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Many studies have mapped DNA methylation changes associated with embryogenesis, cell differentiation and cancer at a genome-wide scale. Our understanding of genome-wide DNA methylation changes in a developmental or disease-related context has been steadily growing. However, the investigation of which CpGs are variably methylated in different normal cell or tissue types is still limited. Here we present an in-depth analysis of 54 single-CpG-resolution DNA methylomes of normal human cell types by integrating high-throughput sequencing-based methylation data. We find that the percentage of unmethylated CpGs is relatively fixed regardless of cell type. However, which CpGs are unmethylated is cell-type specific. We categorize the 26 million human autosomal CpGs based on their methylation levels across multiple cell types to identify variably methylated CpGs. Among all the autosomal CpGs, 22.6% exhibit variable DNA methylation across cell types included in our study. These variably methylated CpGs form 66 thousand variably methylated regions (VMRs), encompassing 11% of the genome. By integrating a multitude of genomic data, we found that VMRs enrich for histone modifications indicative of enhancers, suggesting their role as regulatory elements marking cell type specificity. VMRs enrich for transcription factor binding sites in a tissue-dependent manner. Importantly, they enrich for GWAS variants, suggesting VMRs could potentially be implicated in disease and complex traits. Taken together, our results highlight the link among CpG methylation variation, genetic variation and disease risk in a tissue-specific manner for many human cell types.

overall_design: Processed data includes new Samples and 75 Samples from  GSE16368 and 2 Samples from  GSE51565.

first: Junchen

last: Gu

last: Stevens

first: Ting

last: Wang

first: Xiaoyun

last: Xing

first: James

last: Jarvis

first: Jacqueline

last: Payton

first: Theodore

last: Cicero


title: Localization of RNAPII and 3’ end formation factor CstF subunits on C. elegans genes and operons [RNA-seq]

city: Boulder

first: Alfonso

last: Garrido-Lecca

address: 347 UCB

institute: CU Boulder

summary: Transcription termination is mechanistically coupled to pre-mRNA 3’ end formation to prevent transcription much beyond the gene 3’ end. C. elegans, however, engages in polycistronic transcription of operons in which 3’ end formation between genes is not accompanied by termination. We have performed RNA polymerase II (RNAPII) and CstF ChIP-seq experiments to investigate at a genome-wide level how RNAPII can transcribe through multiple poly-A signals without causing termination. Our data shows that transcription proceeds in some ways as if operons were composed of multiple adjacent single genes. Total RNAPII shows a small peak at the promoter of the gene cluster and a much larger peak at 3’ ends. These 3’ peaks coincide with maximal phosphorylation of Ser2 within the C-terminal domain (CTD) of RNAPII and maximal localization of the 3’ end formation factor CstF. This pattern occurs at all 3’ ends including those at internal sites in operons where termination does not occur. Thus the normal mechanism of 3’ end formation does not always result in transcription termination. Furthermore, reduction of CstF50 by RNAi did not substantially alter the pattern of CstF64, total RNAPII, or Ser2 phosphorylation at either internal or terminal 3’ ends. However, CstF50 RNAi did result in a subtle reduction of CstF64 binding upstream of the site of 3’ cleavage, suggesting that the CstF50/CTD interaction may facilitate bringing the 3’ end machinery to the transcription complex.

overall_design: RNA-seq analysis of wild type (empty vector) and RNAi CstF50 mRNA (polyA-selected) and rRNA-depleted RNA (total RNA).

first: Thomas

last: Blumenthal

first: Tassa

last: Saldi


title: Analysis of glucocorticoid receptor (NR3C1), NFkb (p65 subunit), and RNA polymerase 2 (RNAP2) binding in Beas-2B airway epithelial cells

status: Public on Apr 01 2016

city: Aurora

first: Tzu Lip

last: Phang

state: CO

address: 12700 East 19th Avenue

department: Medicine

institute: University of Colorado, Denver

summary: The objective of this study was to determine binding patterns for GR, 65 and RNAP2 in Beas-2B airway epithelial cells after treatment with dexamethasone (100 nm), TNF (20 ng/ml) or both for one hour.

overall_design: This study utilized duplicate samples for each treatment condition and immunoprecipitation except for p65 immunoprcipitation of TNF treated samples, which was analyzed as a single sample.  Input from vehicle treated cells was used a control. Experimental comparisons were made between the following samples/ treatment conditions.  Duplicate samples of Beas-2B cells treated with ethanol (vehicle) were used for ChIP of GR, p65, and RNAP2 (2 samples each antibody). Duplicate samples of Beas-2B cells treated with dexamethasone were used for ChIP of GR and RNAP2 (2 samples each antibody).  Duplicate samples of Beas-2B cells treated with TNF were used for ChIP of p65 and RNAP2 (1 sample p65, 2 samples RNAP2). Duplicate samples of Beas-2B cells treated with dexamethasone + TNF were used for ChIP of GR, p65 and RNAP2 (2 samples each antibody).

first: Vineela

last: Kadiyala

first: Sarah

middle: K

last: Sasse

first: Tzu

first: Anthony

middle: N

last: Gerber


title: SIRT6 suppresses pancreatic cancer through control of Lin28b

city: Boston

first: Kenneth

last: Ross

state: MA

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Localization of RNAPII and 3’ end formation factor CstF subunits on C. elegans genes and operons [ChIP-seq]

overall_design: ChIP-seq examination of RNAPII and CstF subunits using C. elegans in duplicates.


title: SIRT6 suppresses pancreatic cancer through control of Lin28b [miRNA-seq]

summary: Chromatin remodeling proteins are frequently dysregulated in human cancer, yet little is known about how they control tumorigenesis. Here, we uncover an epigenetic program mediated by the NAD+-dependent histone deacetylase Sirtuin 6 (SIRT6) that is critical for suppression of pancreatic ductal adenocarcinoma (PDAC), one of the most lethal malignancies. SIRT6 inactivation accelerates PDAC progression and metastasis via upregulation of Lin28b, a negative regulator of the let-7 microRNA. SIRT6 loss results in histone hyperacetylation at the Lin28b promoter, Myc recruitment, and pronounced induction of Lin28b and downstream let-7 target genes, HMGA2, IGF2BP1 and IGF2BP3. This epigenetic program defines a distinct subset representing 30-40% of human PDAC, characterized by poor prognosis and an exquisite dependence on Lin28b for tumor growth. Thus, we identify SIRT6 as an important PDAC tumor suppressor, and uncover the Lin28b pathway as a potential therapeutic target in a molecularlydefined PDAC subset.

overall_design: Small RNA-Seq experiments for PLKO and shLIN28B (three replicates each) in human Panc3.27 PDAC cells to identify miRNAs modulateed by LIN28B knockdown.

first: Sita

last: Kugel

first: Raul

last: Mostoslavsky

first: Esha

last: Jain


title: Transcriptional Regulationand Chromatin Dynamics in Human Epithelial Cell Differentiation (ChIP-seq)

first: Luca

last: Petiti

summary: Genome-wide mapping of H3K4me1, H3K4me3 and H3K27ac in KP and DK

overall_design:
ChIP-seq for H3K4me1, H3K4me3 and H3K27ac in KP and DK
p63 profiling of DK through ChIP-seq

first: Alessia

last: Cavazza

first: Annarita

last: Miccio

first: Oriana

last: Romano

first: Guidantonio

last: Tagliazucchi

first: Clelia

last: Peano

first: Marco

last: Severgnini

first: Ermanno

last: Rizzi

first: Gianluca

last: De Bellis

first: Silvio

last: Bicciato

first: Fulvio

last: Mavilio


title: SIRT6 suppresses pancreatic cancer through control of Lin28b [ChIP-seq]

overall_design: ChIP-Seq experiments to examine H3K56ac histone modifications in murine PDAC cells that are Sirt6 wild type (WT), Sirt6 knock-out (KO), and Sirt6 KO cells engineered to express Sirt6 WT (Sirt6 KO + Sirt6 WT Restored).

first: Alon

last: Goren


title: Differential gene expression in intestinal mouse crypts after loss of KLF5

city: Houston

first: Noah

middle: F

last: Shroyer

state: Texas

address: 1 Baylor Plaza

department: Medicine - Gastroenterology

institute: Baylor College of Medicine

summary: To determine potential targets of KLF5 we performed RNA-sequencing on jejunal crypts isolated from Klf5-deficient and wildtype mice, using three biological replicates per genotype.  We identified 1,480 genes that showed significant differential expression with at least a 2-fold difference between Klf5-deficient and wildtype (q-value ≤ 0.05) (Figure 5A; Supplementary Table 1).  Klf5 expression was significantly downregulated 2.7-fold.

overall_design: Comparison of gene expression after loss of KLF5 in the intestine.  Isolated jejunal crypts from 3 wildtype and 3 knockout animals were compared.

first: Kristin

last: Bell


title: Leveraging natural variation in the Saccharomyces cerevisiae stress response to understand lignocellulosic hydrolysate toxicity

city: Madison

first: Maria

middle: Isabel

last: Sardi

state: Wisconsin

address: 425 Henry Mall

department: Microbiology

institute: University of Wisconsin-Madison

summary: Here, we explored natural variation in stress tolerance and in transcriptomic responses to synthetic hydrolysate, mimicking chemically pretreated plant material, to dissect the physiological effects hydrolysate components.  Using six different Saccharomyces cerevisiae strains that together maximized phenotypic and genetic diversity, we explored transcriptomic differences between resistant and sensitive strains.  We identified both common and strain-specific responses.  Comparing responses of resistant and sensitive strains provided insights about primary cellular targets of hydrolysate toxins, implicating cell wall structure, protein and DNA stability, energy stores and redox balance.  Importantly, we uncovered lower expression of thiamine genes while in the presence of toxins, which we argue are most likely an indirect effect that increases sensitivity.    We also demonstrate synergistic interactions between the nutrient composition, osmolarity, pH, and classes of hydrolysate toxins.  Together, this work provides a platform for further dissecting hydrolysate toxins and strain responses.

overall_design: RNA-seq and transcriptome analysis of six S. cerevisiae natural isolates having different resistant to lignocellulosic hydrolysate. Two biological replicate cell samples (collected on different days) were harvested for RNAseq analysis.    Strains were grown in YPD, synthetic hydrolysate without toxins (SynH -HTs), and synthetic hydrolysate with toxins (SynH).  Cells were grown for at least three generations to log phase (OD600 ~0.5) and collected by centrifugation.

first: Audrey

last: Gasch


title: The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome

city: Brisbane

first: Amin

middle: Roushdy

last: Mohamed

state: Queensland

address: 306 Carmody Rd, University of Queensland

department: Agriculture and Food

institute: CSIRO

summary: Despite the ecological significance of the relationship between reef-building corals and intracellular photosynthetic dinoflagellates of the genus Symbiodinium, very little is known about the molecular mechanisms involved in the establishment of the relationship. Indeed, microarray-based analyses point to the conclusion that host gene expression is largely or completely unresponsive during the establishment of symbiosis with a competent strain of Symbiodinium. In the present study, the use of Illumina RNAseq technology allowed detection of a transient period of differential expression involving a small number of genes (1073 transcripts; <3% of the transcriptome) 4h after the exposure of Acropora digitifera planulae to a competent strain of Symbiodinium (a clade B strain). This phenomenon has not previously been detected as a consequence of both the lower sensitivity of the microarray approaches used and the sampling times used. The results imply that complex changes occur, including transient suppression of mitochondrial metabolism and protein synthesis, but are also consistent with the hypothesis that the symbiosome is a phagosome that has undergone early arrest, raising the possibility of common mechanisms in the symbiotic interactions of corals and symbiotic sea anemones with their endosymbionts.

overall_design: There were 2 conditions (Symbiodinium-infected and control). Samples were taken at 3 time points, there were 3 replicates per condition. 16 samples were analysed comparing the Symbiodinium-infected samples to the control ones

first: Vivian

last: Cumbo

first: Saki

last: Harii

first: Chuya

last: Shinzato

first: Cheong

middle: X

last: Chan

first: Mark

last: Ragan

first: David

last: Bourne

first: Bette

last: Willis

first: Eldon

last: Ball

first: Nori

last: Satoh

middle: J

last: Miller


title: Genomic distribution of 5-hydroxymethylcytosine in mouse kidney and its relationship with gene expression

city: Shanghai

first: Hao

last: Wang

address: 180 Fenglin Road

institute: Fudan University

summary: Ten-Elven Translocation (TET) proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytonsie (5hmC). Our recent work found a decline in global 5hmC level in mouse kidney insulted by ischemia reperfusion (IR). However, the genomic distribution of 5hmC in mouse kidney and its relationship with gene expression remain elusive. Here, we profiled the DNA hydroxymethylome of mouse kidney by hMeDIP-seq and revealed that 5hmC is enriched in genic regions but depleted from intergenic regions. Correlation analyses showed that 5hmC enrichment in gene body is positively associated with gene expression level in mouse kidney. Moreover, IR injury-associated genes (both up- and down-regulated genes during renal IR injury) in mouse kidney exhibit significantly higher 5hmC enrichment in their gene body regions when compared to those un-changed genes. Collectively, our study not only provides the first DNA hydroxmethylome of kidney tissues but also suggests that DNA hyper-hydroxymethylation in gene body may be a novel epigenetic mark of IR injury-associated genes.

overall_design: Eamination of the genome-wide distribution of 5-hydroxymethylcytosine in mouse kidney tissues

first: Li

last: Tan


title: Localization of RNAPII and 3 end formation factor CstF subunits on C. elegans genes and operons

first: Alfonso

last: Garrido-Lecca


title: RNA-seq transcriptome analysis of Panax japonicus, and its comparison with other Panax species to identify potential genes involved in the saponins biosynthesis

city: Chiba

first: Mami

last: Yamazaki

address: Inohana 1-8-1, Chuo-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Chiba University

summary: In this study, we have performed Illumina based RNA sequencing to characterize the transcriptome and expression profiles of genes expressed in 5 tissues of P. japonicus. RNA sequencing and de novo transcriptome assembly for P. japonicus resulted in a total of 135,235 unigenes with 78,794 (58.24%) unigenes being annotated using NCBI-nr database. Transcriptome profile and GO enrichment analysis for 5 tissues of P. japonicus showed that although each tissue was characterized by several unique unigenes with leaf showing the most unique unigenes among all, overall processes were evenly conserved across all tissues.

overall_design: Examination of 5 tissues of Panax japonicus

first: Kazuki

last: Saito

first: Amit

last: Rai


title: Genome-wide analysis of E.coli response to mitomycin (MMC) treatment in wild type and recN mutant

city: Paris

first: Olivier

last: Espeli

address: 11 place Marcelin Berthelot

department: CIRB

institute: College de France

summary: We report the role of recN in the induction of the sos response

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

overall_design: Examination of gene profiling at two time points after addition of mitomycin (MMC) at 10µg/ml

first: Elise

last: Vickridge


title: Histone H3 Lysine 27 methylation Regulates Skeletal Growth by Suppressing Wnt and TGF-β Signaling

first: Tatsuya

last: Kobayashi

address: 50 Blossom Street, Thier 1101

department: Endocrine Unit

institute: Massachusetts General Hospital

summary: Polycomb repressive complex 2 (PRC2) controls maintenance and lineage determination of stem cells by suppressing genes that regulate cellular differentiation and tissue development.  However, the role of PRC2 in lineage-committed somatic cells is largely unknown.  In this study, we ablated Eed, an essential component of PRC2, in growth plate chondrocytes to study the role of PRC2 in skeletal development. In this study, we profiled genes assocaited with H3K27me3 histone 3 modification in primary rib chondrocytes.

overall_design: Mouse primary chodnrocytes were subjected to ChIP analysis using H3K27me3 antibody.  ChIP'ed DNA and Input DNA were sequenced by Otogenetics (Necros, GA)

first: G

last: Papaioannou

first: F

last: Mirzamohammadi

first: T


title: RNA-Seq of single cells from regenerating Arabidopsis root

city: Rehovot

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

country: Israel

institute: Hebrew University

summary: Plant roots can regenerate after complete excision of their tip, including the stem cell niche, but it is not clear what developmental program mediates such repair. Here, we use a combination of lineage tracing, single-cell RNA-seq, and marker analysis to test different models of tissue reassembly. We show that rapid cell-identity transitions lead to the formation of a new stem cell niche from multiple remnant tissues. The transcriptome of regenerating cells prior to stem cell activation resembled that of the embryonic root progenitor, and regeneration defects were more severe in embryonic versus adult root mutants. Furthermore, the signaling domains of the hormones auxin and cytokinin mirrored their embryonic dynamics, and manipulation of both hormones altered the position of new tissues and stem cell niche markers. Our findings suggest that plant organ regeneration resembles the developmental stages of embryonic patterning and is guided by spatial information laid down by complementary hormone domains.

overall_design: 215 single cells isolated from marked stele tissue (either using WOL or AHP6 promoters), before, at 3h, 16h and 46h post root tip decapitation

first: Alison

last: Mello

first: Tal

last: Nawy

first: Pui-Leng

last: Ip

first: Nicholas

last: DelRose

first: Ashley

last: Powers

first: Rahul

last: Satija

first: Kenneth

last: Birnbaum


title: Analysis of Early-scnRNAs of Tetrahymena

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

institute: Institute of Human Genetics, CNRS

summary: scnRNAs co-IPed with Twi1p from wild-type cells @3 hpm

overall_design: Small RNAs co-precipitated with the Argonaute protein Twi1p were analyzed by high-throughput sequencing

first: Tomoko

last: Noto


title: Regulation of androgen receptor signaling by Oct1 recruitment in prostate cancer

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

summary: Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. To investigate the AR signaling, we performed ChIP sequence analysis in AR-positive prostate cancer cell lines, LNCaP and VCaP. In addition, we also examined the effect of PI polyamide specificly inhibit Oct1 binding to AR occupied-regions.

overall_design: ChIP sequence analysis of AR binding sites and epigenetic condition in two prostate cancer cells

first: Satoshi

last: Inoue


title: Determination of the Sp5 regulated transcriptome in differentiating ES cells

city: Frederick

first: Mark

last: Kennedy

state: MD

address: 1050 Boyles St., Bldg 539, Rm 205

department: Cancer and Developmental Biology

institute: NIH/NCI

summary: Sp5 is a target and critical transducer of the Wnt/beta-catenin signaling pathway and is essential for mesoderm differentiation in vertebrate embryos. We established a doxycycline inducible ES cell line to over-express Flag epitope-tagged Sp5 protein in differentiating ES cells which have the capacity to form mesoderm cells in vitro. The goal of this study was to identify the genes/gene networks regulated by Sp5 to understand how it regulates mesoderm differentiation by identifying important target genes which may mediate its activity.

overall_design: Total RNA was extracted from ES cells after 3 days of differentiating following F-Sp5 over-expression from day 2 to 3. We compared the transcriptome of differentially expressed genes between untreated (minus) and doxycycline treated (plus) ES cells to identify Sp5 regulated genes.

first: Terry

middle: P

last: Yamaguchi


title: Determination of the Lef1 regulated tanscriptome in differentiating ES cells

middle: W

summary: Lef1 is a critical transducer of the Wnt/beta-catenin signaling pathway that is essential for mesoderm differentiation in vertebrate embryos. We established a doxycycline inducible ES cell line to over-express Flag-tagged Lef1 in differentiating ES cells which have the capacity to form mesoderm cells in vitro. The goal of this study was to identify the genes/gene networks regulated by Lef1 to understand how it regulates mesoderm differentiation and to establish the Lef1-regulated, Wnt/beta-catenin transcriptome.

overall_design: Total RNA was extracted from ES cells after 3 days of differentiating following Lef1 over-expression from day 2 to 3. We compared the transcriptome of differentially expressed genes in untreated and doxycycline treated ES cells to identify Lef1 regulated genes.


title: Dissecting stages of human kidney development and Tumorigenesis with surface markers affords simple prospective Purification of nephron stem cells

city: Ramat-Gan

first: Tomer

last: Kalisky

address: Faculty of Engineering

department: Bioengineering

institute: Bar-Ilan University

summary: When assembling a nephron during development a multipotent stem cell pool becomes restricted as differentiation ensues. A faulty differentiation arrest in this process leads to transformation and initiation of a Wilms' tumor. Mapping these transitions with respective surface markers affords accessibility to specific cell subpopulations. NCAM1 and CD133 have been previously suggested to mark human renal progenitor populations. Herein, using cell sorting, RNA sequencing, in vitro studies with serum-free media and in vivo xenotransplantation we demonstrate a sequential map that links human kidney development and tumorigenesis; In nephrogenesis, NCAM1+CD133- marks SIX2+ multipotent renal stem cells transiting to NCAM1+CD133+ differentiating segment-specific SIX2- epithelial progenitors and NCAM1-CD133+ differentiated nephron cells. In tumorigenesis, NCAM1+CD133- marks SIX2+ blastema that includes the ALDH1+ WT cancer stem/initiating cells, while NCAM1+CD133+ and NCAM1-CD133+ specifying early and late epithelial differentiation, are severely restricted in tumor initiation capacity and tumor self-renewal. Thus, negative selection for CD133 is required for defining NCAM1+ nephron stem cells in normal and malignant nephrogenesis.

overall_design: Human fetal kidney mRNA profiles of 3 cell populations (NCAM1+/CD133-, NCAM+/CD133+, NCAM-/CD133+) were generated by deep sequencing using Illumina HiSeq.

first: Naomi

last: Shakked

first: Benjamin

last: Dekel


title: TRX-1 Regulates SKN-1 Nuclear Localization Cell Non-Autonomously in Caenorhabditis elegans

first: Katie

last: McCallum

state: TX

address: 6431 Fannin St

institute: UT Health Science Center

summary: The Caenorhabditis elegans oxidative stress response transcription factor, SKN-1, is essential for the maintenance of redox homeostasis and is a functional ortholog of the Nrf family of transcription factors. The numerous levels of regulation that govern these transcription factors underscore their importance. Here, we add a thioredoxin, encoded by trx-1, to the expansive list of SKN-1 regulators. We report that loss of trx-1 promotes nuclear localization of intestinal SKN-1 in a redox-independent, cell non-autonomous fashion from the ASJ neurons. Furthermore, this regulation is not general to the thioredoxin family, as two other C. elegans thioredoxins TRX-2 and TRX-3 do not play a role in this process. Moreover, TRX-1-dependent regulation requires signaling from the p38 MAPK signaling pathway. However, while TRX-1 regulates SKN-1 nuclear localization, SKN-1 transcriptional activity remains largely unaffected. Interestingly, RNA-Seq revealed that loss of trx-1 elicits a general, organism-wide down-regulation of several classes of genes; those encoding for collagens and lipid transport and localization being most prevalent. However, one prominent lipase-related gene, lips-6, is highly up regulated upon loss of trx-1 in a skn-1-dependent manner. Together, these results uncover a novel role for a thioredoxin in regulating intestinal SKN-1 nuclear localization in a cell non-autonomous manner, thereby contributing to the understanding of the processes involved in maintaining redox homeostasis throughout an organism.

overall_design: Four samples were analyzed: Two nematode strains were analyzed, each under non-stressed and stressed (10mM NaAs) conditions

middle: C

first: Swathi

last: Arur

first: Bin

last: Liu

first: Danielle

middle: A

last: Garsin


title: Comprehensive RNA profiling of susceptible and resistant (LepR1) Brassica napus to L. Maculans

city: Winnipeg

first: Michael

middle: G.

last: Becker

state: Manitoba

address: 66 Chancellors Circle

department: Biological Sciences

country: Canada

institute: University of Manitoba

summary: The hemibiotrophic fungal pathogen Leptosphaeria maculans is the causal agent of blackleg disease in Brassica napus (canola, oilseed rape) and causes significant losses in crop yields worldwide. While genetic resistance has been used to mitigate the disease, little information about the genes and gene regulatory networks underlying blackleg resistance is currently available. High-throughput RNA sequencing and rigorous bioinformatics approaches revealed dynamic changes in the host transcriptome and identified plant defense pathways specific to the host-pathogen incompatible LepR1-AvrLepR1 interaction.

sample_organism:
Brassica napus
Plenodomus lingam

platform_organism:
Brassica napus
Plenodomus lingam

overall_design: In total, 36 samples were sequenced – 18 from the resistant (LepR1) genotype and 18 from the susceptible genotype (Westar). Samples were collected 0, 3, 7, and 11 days post inoculation in triplicate. Mock inoculated controls were collected at 3, 7, and 11 days post inoculation in duplicate. Samples were sequenced on the Illumina HiSeq2500 at the UC Davis Genome Core, 50 bp SR.

first: Xuehua

last: Zhang

first: W

last: Fernando

last: Belmonte


title: The PIN domain endonuclease Utp24 cleaves pre-ribosomal RNA at two coupled sites in yeast and humans

city: Newcastle upon Tyne

first: Claudia

last: Schneider

address: Framlington Place

institute: Newcastle University

summary:
Purpose: Pre-ribosomal RNA is cleaved at defined sites, but many endonucleases involved in 18S rRNA release are not known. We apply an in vivo cross-linking technique coupled with deep sequencing (CRAC) that captures transcriptome-wide interactions between a yeast candidate pre-rRNA endonuclease (Utp24) and its targets in a living cell.
Methods: We apply CRAC to an HTP-tagged Utp24 protein (HTP: His6 - TEV cleavage site - two copies of the z-domain of Protein A).  At least two independent experiments were performed and analyzed separately.
Results: We found that yeast Utp24 UV-crosslinked in vivo to the U3 snoRNA and all (pre-)rRNA elements that form the central pseudoknot in the 18S rRNA. The pseudoknot is an evolutionarily highly conserved structure that is required to ensure pre-rRNA processing at three cleavage sites (A0, A1 and A2) and still present in the mature rRNA. According to our crosslinking data, the endonuclease Utp24 is placed in close proximity to site A1 at the 5'-end of the 18S rRNA.
Conclusion: Our study strongly supports the hypothesis that Utp24 cleaves pre-rRNA at sites A1 and A2.

overall_design: Examination of targets for pre-rRNA endonucleases in yeast cells.

first: Graeme

last: Wells

first: Franziska

last: Weichmann

first: David

last: Colvin

first: Katherine

middle: E

last: Sloan

first: Grzegorz

last: Kudla

last: Tollervey

first: Nicholas

last: Watkins


title: Targeting Oct1 genomic function inhibits androgen receptor signaling and castration-resistant prostate cancer growth

first: Ken-ichi

last: Takayama

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

overall_design: Refer to individual Series


title: Genome-wide binding profiles of Sp5 in differentiation mouse embryonic stem cells

first: Mark

last: Kennedy

summary: We have determined the genome-wide binding profile of the transcription factor Sp5. Flag-tagged Sp5 was targeted to the HPRT locus in A2Lox.cre ES cells to allow for Doxycycline inducible expression. ES cells were cultured as embryoid bodies for 2 days to prime them for germ layer differentiation. Cells were then treated with Doxycycline for 24 hrs. We found that Flag-Sp5 prefentially bound to promoters associatd with several growth factor signalling pathways, but most prominently with the Wnt/beta-catenin pathway to selectively promote mesoderm differentiation over neural. These data implicate Sp5 as new regulator of Wnt/beta-catenin target expression to promotes ES cell differentation into the mesoderm lineage.

overall_design: Examination of Sp5 transcription factor binding in differentiating embryonic stem cells.

first: Terry

last: Yamaguchi


title: Unique cell-type specific patterns of DNA methylation in the root meristem

status: Public on Mar 31 2016

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute


title: Cdk1 activity levels drive periodic transcription independently of cell cycle progression

city: Gothenburg

first: Zsolt

last: Szilagyi

address: Medicinaregatan 9A

country: Sweden

institute: University of Gothenburg

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae


title: Transcriptomes of Two Esca Relevant Fungi, Phaeoacremonium aleophilum and Phaeomoniella chlamydospora, Respond Very Differently to Co-cultured Vitis callus Culture

city: Tulln

first: Harald

last: Berger

state: NOE

address: Konrad-Lorenzstraße 43

department: DAGZ

country: Austria

institute: Universität f. Bodenkultur Wien

summary: In order to understand how P.al and P.ch respond to the environment set by V. vinifera we analyzed the transcriptomes of two fungi in axenic or mixed cultures with V. vinifera plant cells (callus culture). We could observe that these fungi respond with different strategies to the plant cell challange where P.ch induces de-toxification and translation machinery genes and P.al alters primary metabolism and induces heat shock related genes.

sample_organism:
Phaeomoniella chlamydospora
Phaeoacremonium minimum

overall_design: Two fungal strains where co-inoculated with V. vinivera callus, each experiment was repeated

first: Jochen

last: Fischer

first: Eckhard

last: Thines

first: Stephane

last: Compant


title: Characterization of pro- and anti-inflammatory activation states in embryonic stem cell derived microglia

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

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

summary: Embryonic stem cell derived microglia (ESdM) were treated with different inflammatory stimulants to analyze their ability to adopt different activation states. These were characterized using ELISA, flow cytometry, quantitative real time PCR, and RNA-sequencing.

overall_design: Analysis of cytokine secretion, cell surface marker, gene expression, and RNA-seq expression data of differentially activated ESdM

first: Eva

last: Beins

first: Svenja

last: Ternes

first: Thomas

last: Ulas

last: Neumann

middle: L

first: Andreas

last: Zimmer


title: Identification of chemicals that mimic transcriptional changes associated with autism, brain aging and neurodegeneration

city: Chapel Hill

last: Zylka

state: NC

address: 5109D Neuroscience Research Building

institute: University of North Carolina - Chapel Hill

summary: Environmental factors, including pesticides, have been linked to autism and neurodegeneration risk using retrospective epidemiological studies.  Here, we sought to prospectively identify chemicals that share transcriptomic signatures with neurological disorders by exposing mouse cortical neuron-enriched cultures to hundreds of chemicals commonly found in the environment and on food.  We find that rotenone, a pesticide associated with Parkinson’s disease risk, and certain fungicides, including pyraclostrobin, trifloxystrobin, famoxadone, and fenamidone, produce transcriptional changes in vitro that are similar to those seen in brain samples from humans with autism, advanced age and neurodegeneration (Alzheimer’s disease, Huntington’s disease).  These chemicals stimulate free radical production and disrupt microtubules in neurons, effects that can be reduced by pretreating with a microtubule stabilizer, an antioxidant, or with sulforaphane.  Our study provides an approach to prospectively identify environmental chemicals that transcriptionally mimic autism and other brain disorders.

overall_design: 405 total samples, consisting of 297 unique chemicals and vehicle controls.

first: Jeremy

middle: M

last: Simon

first: Brandon

last: Pearson


title: RNAseq measurments of gene expression during simultanous replication and mitosis using the S. Pombe minimal cell cycle strain

summary: Cell cycle arrested G1 cells were exposed to high Cdk1 activity, so undergo replication and mitosis at the same time.

overall_design: Samples were collected at the indicated time points (0, 20, 40) from released (R) vs. Arrested (A) cells.

first: Gabor

last: Banyai

first: Damien

last: Coudrouse


title: Unique cell-type specific patterns of DNA methylation in the root meristem (RNA-seq)

middle: R

last: Ecker

state: CA

summary: DNA methylation is an epigenetic modification that differs between plant organs and tissues, but the extent of variation between cell types is not known. Here, we report single-base resolution whole genome DNA methylomes, mRNA transcriptomes, and small RNA transcriptomes for six cell populations covering the major cell types of the Arabidopsis root meristem. We identify widespread cell type specific patterns of DNA methylation, especially in the CHH sequence context. The genome of the columella root cap is the most highly methylated Arabidopsis cell characterized to date. It is hypermethylated within transposable elements, accompanied by increased abundance of transcripts encoding RNA-directed DNA methylation (RdDM) pathway components and 24 nt small RNAs. Absence of the nucleosome remodeler DECREASED DNA METHYLATION 1, required for maintenance of DNA methylation, and low abundance of histone transcripts involved in heterochromatin formation suggests a loss of heterochromatin may occur in the columella, thus allowing access of RdDM factors to the whole genome, and producing excess 24 nt small RNAs in this tissue. Together, these maps provide new insights into the epigenomic diversity that exists between distinct plant somatic cell types.

overall_design: RNA-seq from six cell populations covering the major cell types of the Arabidopsis root meristem.

first: Taiji

last: Kawakatsu

first: Ryan

last: Lister


title: SNHG5 siRNA  knock down in HCT116 cells

city: Aarhus

first: Morten

middle: Muhlig

last: Nielsen

address: Palle Juul-Jensens Bouleward 99

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

summary: SnoRNA host gene 5 was knocked down with two different siRNAs and profiled for gene expression.

overall_design: three replicates of two different siRNAs against SNHG5 and a control siRNA

first: Nkero

middle: D

last: Damas

first: Jakob

middle: S

last: Pedersen

first: Anders

middle: H

last: Lund


title: Unique cell-type specific patterns of DNA methylation in the root meristem (MethylC-seq)

first: Joseph

overall_design: MethylC-seq from six cell populations covering the major cell types of the Arabidopsis root meristem.


title: Sp5 and Sp8 recruit b-catenin to the Tcf1-Lef1 enhanceosome to activate Wnt target gene transcription

first: Mark

last: Kennedy


title: RNA-seq of mouse P19 half-life samples upon loss of UPF3A

first: Miles

last: Wilkinson

state: California

address: 2880 Torrey Pines Scenic Drive, Rm 4811

department: Department of Reproductive Medicine

institute: University of California, San Diego

summary: Gene duplication is a major evolutionary force driving adaptation and speciation, as it allows for the acquisition of new functions and can augment or diversify existing functions. Here, we report a gene duplication event that yielded another outcome – the generation of antagonistic functions. One product of this duplication event – UPF3B – is critical for the nonsense-mediated RNA decay (NMD) pathway, while its autosomal counterpart – UPF3A – encodes an enigmatic protein previously shown to have trace NMD activity. Using loss-of-function approaches in vitro and in vivo, we discovered that UPF3A acts primarily as a potent NMD inhibitor that stabilizes hundreds of transcripts. Evidence suggests that UPF3A acquired repressor activity through simple impairment of a critical domain, a rapid mechanism that may have been widely used in evolution. Mice conditionally lacking UPF3A exhibit “hyper” NMD and display defects in embryogenesis and gametogenesis, consistent with UPF3A serving as a molecular rheostat that directs developmental events.

overall_design: Examination of transcript stability with loss of UPF3A in mouse P19 cells.

first: Samantha

last: Jones

first: Jennifer

last: Dumdie

first: Eleen

middle: Y

last: Shum


title: Identification of small RNA loci that are synthesized by RNA-dependent RNA polymerases1/2/6

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

institute: RIKEN

summary: To identify RDR1/2/6 dependent small RNA loci of transcribed regions under 2hr drought stress- and untreated conditions, expression profiles of small RNA between rdr1/2/6 and wild-type using hi-seq 2000.

overall_design: rdr1/2/6 and wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on MS medium for 2weeks. Then, their plants were transfered to dry plastic dish for 2 hours. small RNA fraction was s extracted from the sample using Ambion mirVana miRNA Isolation Kit. small RNA labrary was constructed using TruSeq Small RNA Library Preparation Kits and applied to hi-seq 2000.

first: Kayoko

last: Mizunashi

first: Maho

last: Tanaka

first: Kei

last: Iida

first: Ri-ichiroh

last: Manabe

first: Motoaki

last: Seki


title: Transcriptomic characterization of the impact of 2'-fucosyllactose supplementation on intestinal adaptation following ileocecal resection.

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
Purpose: To identify the impact of 2'-FL supplementation on adaptive response following extensive intestinal resection.
Methods: Transcriptomic profiles were obtained from mice undergoing ileocecal recection (8-10 week old male mice) and again at 8 weeks post-surgery.    At the time of resection and again at 8 weeks post-op, small bowel samples were obtained from treatment and control animals and submitted for mRNA profiling.  During these 8 weeks treatment animals (n=3) received 2'-FL supplementationion while controls (n=3) received only standard diet.
Results: We observe enrichment in genes and pathways related to anti-microbial peptides, metabolism, and energy processing.  Supplementation of 2'-FL increases energy availability and enhances the adaptive response.

overall_design: Male C57BL/6 mice at 8 to 10 weeks of age were submitted to ileocecal recection.  Following resection, half were supplemented with 2'-FL for 8 weeks; small bowels were obtained and submitted for mRNA profiling,

first: Ethan

last: Mezoff

first: Michael

last: Helmrath


title: SRiD- A facile DNA barcode generation and management system for high throughput screening

city: Grenoble

first: sandeep

middle: kumar

last: Nadendla

state: Isere

address: 17 Rue des martyrs

department: iRTSV/Biomics

institute: CEA

summary: 20 random DNA barcodes were designed in silico and transfected into PC3 cells. Barcodes were sequenced using Illumina-Miseq technology to find the sequence and their respective copy numbers. Current file contains the raw data of these DNA barcodes in fastq format

overall_design: Validating an algorithm called SRiD that generates random DNA barcodes that do not match a genome of interest, in this case human genome. 20 DNA barcodes were used for this validation.

first: Sandeep

middle: K

first: Xavier

last: Gidrol


title: Usv101 is a key regulator of cryptococcal virulence  and determinant of host response

city: Saint Louis

first: Ezekiel

last: Maier

state: MO

address: 4515 McKinley Ave

department: Computer Science

institute: Washington University in Saint Louis

summary: Cryptococcus neoformans is a fungal pathogen responsible for hundreds of thousands of deaths per year. Its critical virulence factor is a polysacharride capsule which grows large upon entry into a mammalian host. We previously identified USV101 as a transcription factor whose deletion results in enlarged capsules. Here, we characterize strains lacking or overexpressing USV101 in terms of their virulence-related phenotypes, the altered course of infection by them and immune response to them in a mouse model, the relationship of Usv101 to other transcription factors involved in capsule regulation, and the changes in Usv101 activity during capsule induction.

overall_design: To study the function of Usv101, a key C. neoformans regulator of virulence, and its interactions with downstream capsule-regulating TFs GAT201 and SP1, expression profiles were generated by RNA-seq of a usv101 deletion mutant, a USV101 overexpression mutant, strains expressing GAT201 under various promoters, various double mutants, and wildtype cells grown in a capsule non-inducing condition, a capsule inducing condition for 90 minutes, or a capsule inducing condition for 24 hours.

first: Stacey

last: Gish

middle: J

first: Brian

last: Haynes

first: Felipe

last: Santiago

first: Deepa

last: Srikanta

first: Cynthia

middle: Z

last: Ma

first: Lucy

middle: X

last: Li

first: Matt

last: Williams

first: Erika

last: Crouch

first: Shabaana

last: Khader

last: Brent

first: Tamara

last: Doering


title: Genome-wide analysis of Musashi-2 targets reveals novel functions in governing epithelial cell migration

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary:
The Musashi-2 (Msi2) RNA-binding protein maintains stem cell self-renewal and promotes oncogenesis by enhancing cell proliferation in hematopoietic and gastrointestinal tissues. However, it is unclear how Msi2 recognizes and regulates mRNA targets in vivo and whether Msi2 primarily controls cell growth in all cell types. Here we identified Msi2 targets with HITSCLIP and revealed that Msi2 primarily recognizes mRNA 3UTRs at sites enriched in multiple copies of UAG motifs in epithelial progenitor cells. RNA-seq and ribosome profiling demonstrated that Msi2 promotes targeted mRNA decay without affecting translation efficiency. Unexpectedly, the most prominent Msi2 targets identified are key regulators that govern cell motility with a high enrichment in focal adhesion and extracellular matrix-receptor interaction, in addition to regulators of cell growth and survival. Loss
of Msi2 stimulates epithelial cellmigration, increases the number of focal adhesion and also compromises cell growth. These findings provide new insights into the molecular mechanisms of Msi2’s recognition and repression of targets and uncover a key function of Msi2 in restricting epithelial cell migration.

overall_design: Identification of direct Musashi-2 targets in keratinocytes through the use of RNA-Seq, Ribosome-Profiling, and Msi2-HITS-CLIP

first: C

last: Bennett

first: K

first: R

last: Yi


title: Modulation of splicing catalysis for therapeutic targeting of leukemia with mutations in genes encoding spliceosomal proteins

city: Madison

first: Heidi

last: Dvinge

state: WI

address: 440 Henry Mall

department: Biomolecular Chemistry

institute: UW-Madison

summary: Mutations in genes encoding splicing factors (which we refer to as spliceosomal genes) are commonly found in patients with myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). These mutations recurrently affect specific amino acid residues, leading to perturbed normal splice site and exon recognition. Spliceosomal gene mutations are always heterozygous and rarely occur together with one another, suggesting that cells may tolerate only a partial deviation from normal splicing activity. To test this hypothesis, we engineered mice to express a mutated allele of serine/arginine-rich splicing factor 2 (Srsf2P95H) - which commonly occurs in individuals with MDS and AML - in an inducible, hemizygous manner in hematopoietic cells. These mice rapidly succumbed to fatal bone marrow failure, demonstrating that Srsf2-mutated cells depend on the wild-type Srsf2 allele for survival. In the context of leukemia, treatment with the spliceosome inhibitor E7107 resulted in substantial reductions in leukemic burden, specifically in isogenic mouse leukemias and patient-derived xenograft AMLs carrying spliceosomal mutations. Whereas E7107 treatment of mice resulted in widespread intron retention and cassette exon-skipping in leukemic cells regardless of Srsf2 genotype, the magnitude of splicing inhibition following E7107 treatment was greater in Srsf2-mutated than in Srsf2-wild-type leukemia, consistent with the differential effect of E7107 on survival. Collectively, these data provide genetic and pharmacologic evidence that leukemias with spliceosomal gene mutations are preferentially susceptible to additional splicing perturbations in vivo as compared to leukemias without such mutations. Modulation of spliceosome function may thus provide a new therapeutic avenue in genetically defined subsets of individuals with MDS or AML.

overall_design: We created an isogenic murine leukemia model by retroviral overexpression of the MLL-AF9 fusion oncogene in Vav-Cre Srsf2+/+ or Vav-Cre Srsf2P95H/+ BM cells followed by transplantation into lethally irradiated recipient mice. In order to determine the mechanistic origins of the Srsf2 mutant-selective effects of E7107, we analyzed transcriptional changes after five consecutive days of E7107 or vehicle treatment in vivo. GFP+ Cd11b+ cells were purified from the BM of recipient mice exactly three hours after the last dose of E7107 and were subjected to paired-end 2x50bp RNA-seq. For the knock-in/knock-out experiments, we generated inducible, hemizygous Srsf2P95H mice to study the effects of wildtype Srsf2 deletion with concomitant activation of the Srsf2P95H allele. Mx1-cre Srsf2fl/+ mice were crossed to Srsf2P95H/+ mice to generate Srsf2 wildtype (Mx1-cre Srsf2+/+), Srsf2 heterozygous knockout (Mx1-Cre Srsf2+/-), Srsf2 heterozygous P95H mutant (Mx1-Cre Srsf2P95H/+), and Srsf2 hemizygous P95H mutant (Mx1-Cre Srsf2P95H/-) mice, which were subjected to single-end 101bp RNA-seq.

last: Bradley

first: Omar

last: Abdel-Wahab

first: H

first: S

last: Lee


title: Transposon mutagenesis reveals fludarabine-resistance mechanisms in chronic lymphocytic leukemia

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

summary:
Purpose:To identify resistance mechanisms for the chemotherapeutic drug fludarabine in chronic lymphocytic leukemia (CLL), as innate and acquired resistance to fludarabine-based chemotherapy represents a major challenge for long-term disease control.
Methods: We employed piggyBac transposon-mediated mutagenesis, combined with next-generation sequencing, to identify genes that confer resistance to fludarabine in a human CLL cell line.
Results: RNA-seq profiling of fludarabine-resistant cells suggested deregulated MAPK signaling as involved in mediating drug resistance in CLL.

overall_design: To address if the fludarabine-resistant HG3 cells were transcriptionally different at a global level compared to their parental cells, we performed RNA-sequencing of three pairs of HG3 pools

first: Mats

last: Hellström


title: Transcriptome profiles in compatible and incompatible interactions between soybean and Fusarium oxysporum

city: Ames

first: Alessandra

last: Lanubile

state: Iowa

address: Seed Science Building

department: Plant Pathology

institute: Iowa State University

summary: Fusarium oxysporum is one of the most common species causing soybean root rot and seedling blight in the U.S. In a recent study, significant variation in aggressiveness was observed among isolates of F. oxysporum collected from roots in Iowa, ranging from highly pathogenic to weakly or non-pathogenic isolates. In the present work, a RNA-seq-based analysis was used for the first time to investigate the molecular aspect of the interaction of a partially resistant soybean genotype with non-pathogenic/pathogenic isolates of F. oxysporum at 72 and 96 hours post inoculation (hpi). Markedly different gene expression profiles were observed in compatible and incompatible host-pathogen combinations. A peak of differentially expressed genes (DEGs) was observed at 72 hpi in soybean roots in response to both isolates, although the number of DEGs was about eight times higher for the pathogenic isolate compared to the non-pathogenic one (1,659 vs. 203 DEGs, respectively). Furthermore, not only the number of genes, but also the magnitude of induction was much greater in response to the pathogenic isolate. This response included a stronger activation of many well-known defense-related genes, and several genes involved in ethylene biosynthesis and signalling, transcription factors, secondary and sugar metabolism. In addition, 1130 fungal genes were differentially expressed between the F. oxysporum isolates in planta during the infection process. Interestingly, 10% of these genes encode plant cell-wall degrading enzymes, reactive oxygen species-related enzymes and fungal proteins involved in primary metabolic pathways. Such information may be useful in the development of new methods of broadening resistance of soybean to F. oxysporum, including the silencing of important fungal genes, and also to understand the molecular basis of soybean-F. oxysporum interactions.

overall_design: Soybean seedlings mRNA profiles inoculated with a non-pathogenic and pathogenic isolates of F. oxysporum and collected at 72 and 96 hpi, were generated using Illumina HiSeq 2500. Control seedlings were also included for each time of inoculation. Three biological replicates were considered for each condition, 18 samples in total.

first: Usha

last: Muppirala

first: Andrew

last: Severin

first: Adriano

last: Marocco

first: Gary

middle: P

last: Munkvold


title: Contrasting invertebrate immune defense behaviors caused by a single gene, the Caenorhabditis elegans neuropeptide receptor gene npr-1

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 1-9

department: Evolutionary Ecology and Genetics, Zoological Institute

summary:
The nematode Caenorhabditis elegans feeds on microbes in its natural environment. Some of these microbes are pathogenic and thus harmful to C. elegans. To minimize resulting fitness reductions, C. elegans has evolved various defence mechanisms including behavioural responses (e.g. avoidance behaviour) that reduce contact with the infectious microbes. In this study, we characterized the genetic architecture of natural variation in C. elegans avoidance behaviour against the infectious stages of the Gram-positive bacterium Bacillus thuringiensis. We performed an analysis of quantitative trait loci (QTLs) using recombinant inbred lines (RILs) and introgression lines (ILs) generated from a cross of two genetically as well as phenotypically distinct natural isolates N2 and CB4856. The analysis identified several QTLs that underlie variation in the behavioural response to pathogenic and/or non-pathogenic bacteria. One of the candidates is the npr-1 gene. This gene encodes a homolog of the mammalian neuropeptide receptor. Npr-1 was previously indicated to fully contribute to behavioural defence against the Gram-negative bacterium Pseudomonas aeruginosa and food patch-leaving behaviour on Escherichia coli. Interestingly, in our study, npr-1 is not the only gene mediating avoidance behaviour toward Bacillus thuringiensis. Moreover, our functional analyses show that npr-1 alleles appear to influence survival and avoidance behaviour toward Bacillus thuringiensis in exactly the opposite way than toward Pseudomonas aeruginosa. Our findings highlight the role of npr-1 in fine-tuning nematode behaviour in an ecological context depending on the microbe to which C. elegans is exposed.
These opposite phenotypes reflect the diversity in innate immunity to pathogens. To understand the mechanism involved in these opposite phenotypes, we carried out a whole-genome transcriptomics study by RNA-Sequencing. This study includes two pathogens: Pseudomonas aeruginosa PA14 and Bacillus thuringiensis B-18247 (BT247), two strains: N2 and npr-1 (ur89), two time points (12 and 24h) and standard lab food E. coli OP50 as control.

overall_design: mRNA profiles of wild type (WT) and npr-1 (ur89) C.elegans exposed to either Bacillus thuringiensis B-18247, Pseudomonas aeruginosa PA14 or standard lab food E. coli OP50 at 12h or 24h were generated by deep sequencing, in double or triplicate, using Illumina HiSeq2000.

first: Rania

last: Nakad

first: Katja

last: Dierking


title: Wiskott-Aldrich Syndrome-causative mutations disrupt alternative splicing and promote gene networks predisposed to hematologic malignancies

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

summary: Wiskott-Aldrich syndrome (WAS) is characterized by X-linked thrombocytopenia, eczema, immunodeficiency, recurrent infections and increased risk of autoimmunity and malignancies. WAS is caused by mutations in the WAS gene, which encodes the exclusively hematopoietic WAS protein (WASp) that is classically characterized as aν actin nucleator. However, disruption of F-actin polymerization by WAS mutations can not account for many aspects of WAS pathogenesis. Ignorance of other functions of WASP precludes in-depth understanding of the pathogenic effects of mutant WASP, and therefore hampers development of effective therapy. Here we generated induced pluripotent stem cells (iPSCs) from WAS patients (WAS-iPSC) bearing different mutations and corresponding isogenic iPSCs in which the pathogenic mutations had been corrected by targeted genome editing. Hematopoietic cells differentiated from WAS-iPSCs not only recapitulated known disease phenotypes, but also revealed novel defects of WASP deficient cells. WASP co-localized with nuclear pores, nucleoli, nuclear speckles and PML bodies by immunocytochemistry and/or serial block face scanning microscopy (SBF-SEM). MudPIT (multi-dimensional protein identification technology) analysis revealed that WASP physically interacted with nuclear body components, nuclear structural proteins, chromatin modifying complexes, and many RNA-binding proteins including major components of the spliceosome. Next-generation sequencing captured a dramatic global change of alternative splicing in WAS patient cells. WAS mutation impacted splicing of multiple genes frequently mutated in myelodysplastic syndrome and other cancers. RNA sequencing showed that WAS-iPSC derived immune cells misregulated many cell cycle regulators, tumor suppressors, immune function genes and splicing factors, and activated gene networks that drive cancer development and inflammatory diseases. Together these data uncovered previously unappreciated functions of the WASP and provided a mechanistic understanding of the pathogenesis of malignancy and autoimmunity in the most severe form of WAS. These new knowledge could help develop targeted therapy for WAS in the future.

sample_organism:
Homo sapiens
unidentified plasmid

platform_organism:
Homo sapiens
unidentified plasmid

overall_design: Human WAS-iPSCs (p.Phe35*) and gene corrected WAS-iPSCs (cWAS-iPSC) were differentiated into macrophages. WAS patient derived B-lymphocyte line ID00003 (p.Glu133Lys) and a wile-type B-lymphocyte line GM11518 were cultured using standard protocol. Total RNAs were extracted and been analyzed by RASL-seq.

first: Mo

last: Li

first: Jinsong

last: Qiu

first: Yu

last: Zhou

first: Juan

last: Belmonte


title: Next generation sequencing for understading the  role of nitrate reductase in remodeling intermediate metabolism in Phaeodactylum tricornutum

city: New Brunswick

first: Orly

last: Levitan

state: NJ

address: 71 Dudley Road

institute: Rutgers university

summary: We have done next generation sequencing of optically thin, exponentialy growing WT Phaeodactylum tricornutum and our ~50% nitrate reductase knock-down cultures. Culture were grown with and without nitrogen source to improve our undestanding of the pathways regulation under conditions that promote lipid accumulation (N-starvation).

overall_design: 3 biologically independent exponentially growing culture of the WT and the NR21 knock-down were pelleted and washed several times with N-free media. Each culture was devided to 2 replicates with initial cell concentration of 2.5X105 cells/mL, one with NaNO3 as nitrogen source and the other without any nitrogen source. The cuture were bubbled for 48 hours and sampled for transcriptome together with other physiological parameters and lipid analysis after reachign exponential growth.

first: Jorge

last: Dinamarca

first: Ehud

last: Zelzion

first: Paul

middle: G

last: Falkowski


title: HEK293 Heat-shock experiment

status: Public on Mar 30 2016

city: Sydney

first: Jon

last: Burdach

state: NSW

address: UNSW

department: BABS

institute: University of New South Wales

summary: HEK293 cells were heatshocked and differentially expressed transcripts were identified

overall_design: Transcriptomes of heatshocked HEK293 cells were compared to control cells. Heatshock and control samples were treated and sequenced in triplicate.

first: Laura

last: Trakman

first: Chris

last: Hewson

first: Kevin

middle: V

last: Morris


title: Dissection of the F. graminearum transcriptome in response to an active or passive host identifies new pathogen-specific genes.

first: Harald

last: Berger

summary: Comparing RNA Seq- Data of all three sample types- pathogenic growth, saprophytic growth on same plant substrate, axenic growth under starvation after consumption of the mycotoxin inducing nitrogen source L-ornithine- allows to distinguish between genes whose transcription is affected by nutrient starvation or plant matrix effects from those that respond to defense mechanisms deriving from the active, living plant and thus may allow new insights into pathogenicity of the fungus.

overall_design: Three different growth conditions with two to three replicates

first: Stefan

last: Boedi

first: Christian

last: Sieber

first: Martin

last: Münsterkötter

first: Imer

last: Maloku

first: Michael

last: Sulyok

first: Viktoria

last: Preiser

first: Kurt

last: Brunner

first: Hermann

last: Bürstmayr

first: Rudulf

last: Krska

first: Marc

last: Lemmens

first: Ulrich

last: Güldener

first: Joseph

last: Strauss


title: Genomic distribution of linker histone varinat H1T

city: Imabari-shi

first: Koji

last: Hayakawa

state: Ehime

address: 1-3 Ikoino-oka

department: Department of Toxicology, Faculty of Veterinary Medicine

institute: Okayama University of Science

summary: We report genome-wide distribution of germ cell-specific linker histone variant H1T in cancer cell line AGS, MDA-MB-231, and mouse embryonic stem cells (mESCs). We found that H1T expressed not only testis but also non-germ cells such as cancer cells and pluripotent stem cells and showed the biased distribution at rDNA repeat unit. Moreover, on the rDNA region, H1T regulated the chromatin structure and pre-rRNA expression. This study using ChIP-seq analysis provides genomic distribution of H1T in non-germinal cells.

overall_design: ChIP-seq analysis of linker histone H1T in AGS, MDA-MB-231 and mESCs

first: Ruiko

last: Tani


title: ChIP-seq analysis of E2f4, H3K4me2 and H3K27ac in the mouse livers

city: shanghai

first: Xuxu

last: Sun

address: 227 south chongqing road

department: school of medicine

institute: shanghai jiao tong university

summary: Arid1a is the subunit of SWI/SNF complex, which was reported to guide SWI/SNF to DNA. Here, we found that loss of Arid1a in the liver  results in improved liver regeneration after partial hepatectomy.Genome-wide analysis showed that after hepatectomy,loss of Arid1a reduces the recruitment and activity of E2F4 on target promoters, resulting in expression programs that favor regeneration during injury. Correspondingly, these promoters showed increased H3k4me2 and H3k27ac marks, indicating de-repression of these E2f target genes.

overall_design: The post partial hepatectomy mice liver cells were fixed and isolated, analysis of genomic occupancy of E2f4,H3K4me2,H3K27ac in  hepatocytes from Arid1a WT and Arid1a liver specific KO mice by ChIP-seq.

first: Chao

last: Xing

first: Mohammed

last: Kanchwala

first: Hao

last: Zhu


title: RNA-seq transcriptonal profiling in partial hepatectomy liver tissues in Arid1a WT and liver specific KO mice.

summary: Arid1a is the subunit of SWI/SNF complex, which was reported to guide SWI/SNF to DNA. Here, we found that loss of Arid1a in the liver  results in improved liver regeneration after partial hepatectomy.Genome-wide analysis showed that after hepatectomy,loss of Arid1a reduces the recruitment and activity of E2F4 on target promoters, resulting in expression programs that favor regeneration during injury.RNAseq shows transcriptional profiling in WT and Arid1a LKO livers pre- and post-hepatectomy, which confirmed the E2F4 target genes and cell cycle genes were upregulated after hepatectomy.

overall_design: After partial hepatectomy, liver transcriptional profiling in WT and Arid1a liver specific KO mice were generated by RNA-seq analysis.

first: Hanquan

last: Liang


title: MeDIP in mouse ESC

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

summary:
It has widely accepted that 5-methylcytosine is the only form of DNA methylation in mammalian genomes, whereas the other forms, such as N6-methyladenine, primarily exist in prokaryotes and only a few eukaryotes.  Herein, we demonstrated the surprising presence of N6-methyladenine in mammalian genomes, especially, mouse embryonic stem cells. This modification is enriched at histone variant H2A.X-deposited genomic regions in wild type embryonic stem cells.  Our work also showed that a previously unknown DNA demethylase, Alkbh1, is the major demethylase for N6-methyladenine in embryonic stem cells.  Increase of N6-methyladenine levels in Alkbh1 deficient cells leads to silencing of genes that regulate embryonic development. Surprisingly, genes located on the X-chromosome, but not the Y-chromosome or autosomes are preferentially silenced by N6-methyladenine. Strikingly, N6-methyladenine in Alkbh1 deficient cells are specifically deposition at young, full-length subfamilies of LINE1 transposons that are strongly enriched on the X chromosome. Furthermore, N6-methyladenine deposition on LINE1s pattern is inversely correlated with their evolutionary age.   The deposition of N6-methyladenine results in epigenetic silencing of such L1s, which are otherwise actively transcribed in wild type embryonic stem cells, and the neighboring enhancers and genes.  Furthermore, N6-methyladenine induced-silencing resists gene activation signals during embryonic stem cell differentiation. Thus, N6-methyladenine adopts a new function in epigenetic silencing in evolution, distinct from its role in gene activation in other organisms. In summary, our results demonstrate that N6-methyladenine unexpectedly constitutes a crucial component of the epigenetic regulation repertoire in mammalian genomes.
First, we used N6mA or 5mC antibody to enrich for DNA molecules with DNA modification in mouse ESCs as previously described methods. Then, co-purified DNA molecules from WT or KO ESCs were subject to HiSeq2000 sequencing and data analysis for DNA modification sites.

overall_design: DNA IP coupling with HiSeq sequencing

first: Tao

last: Wu

first: Kaixuan

last: Lin


title: In vivo analysis of astrocyte ribosome-associated mRNA after traumatic spinal cord injury

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

summary:
Analysis of gene expression by astrocytes or non-astrocyte cells in spinal cord injury (SCI) lesions may lead to the identification of molecules that impact on axon regrowth. We conducted genome-wide RNA sequencing of (i) immunoprecipitated astrocyte-specific ribosome-associated RNA (ramRNA) from WT or STAT3-CKO astrocytes, and (ii) the non-precipitated (flow-through) RNA deriving from non-astrocyte cells in the same tissue samples 14 days following SCI.
DOI: 10.1038/nature17623

overall_design: Young adult female mGFAP-Cre-RiboTag or mGFAP-Cre-RiboTag-STAT3-LoxP mice underwent severe crush SCI at thoracic level 10. 14 days following SCI, the central 3mm of the SCI lesion was extracted, homogenized and (i) astrocyte-specific ribosome-associated RNA (ramRNA) precipitated via a hemagglutinin (HA) tag targeted to either WT (n=4) or STAT3-CKO (n=3) astrocytes, and (ii) the non-precipitated (flow-through) RNA deriving from non-astrocyte cells in the same tissue samples. Sex and age-matched mGFAP-Cre-RiboTag mice served as uninjured controls (n=4).

first: Joshua

middle: E

last: Burda

first: Mark

middle: A

last: Anderson

first: Yilong

last: Ren

first: Timothy

middle: M

last: O'Shea

first: Giovanni

last: Coppola

first: Baljit

last: Khakh

last: Deming

first: Michael

last: Sofroniew


title: Identification of small non-coding RNAs in zebrafish

city: Aveiro

first: Ana

last: Soares

address: Campus de Santiago

country: Portugal

institute: University of Aveiro

summary: MicroRNAs (miRNAs) are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes, namely developmental timing, cell differentiation, cell proliferation, immune response and infection. For this reason, their identification is essential to understand eukaryotic biology. Their small size, low abundance and high instability complicated early identification; however, cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish (Danio rerio). For this, a series of cDNA libraries were prepared from small non-coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted.

overall_design: Small RNA libraries were prepared from different zebrafish developmental stages, namely, 24 hours post-fertilization (hpf), 72 hpf, 96 hpf, 5 days post-fertilization (dpf), 45 dpf, young adult and from adult brain, eyes, gills, heart, skin and fins.

middle: R

first: Patrícia

last: Pereira

first: Bruno

last: Santos

first: Conceição

last: Egas

middle: C

last: Gomes

first: Joel

last: Arrais

first: José

middle: L

last: Oliveira

first: Gabriela

last: Moura

first: Manuel