title: RNA-seq of RNase R treated and ribo- RNAs from leg muscle of Xinghua Chickens

city: Guangzhou

first: OuYang

last: Hongjia

state: Guangdong

address: Wushan street 483

department: College of Animal Science

institute: South China Agricultural University

summary: We have used RNA-seq to examine circular RNAs from RNase R treated and ribo- RNAs in  chicken leg muscle of three different development stages (11 embryo age, 16 embryo age, and 1 days post hatch). Our study reveals the prevalence of circRNAs in chicken, and has identified circRNAs differentially abundant in different stage of embryonic skeletal muscle, suggesting its important functions during poultry muscle development.

overall_design: To assess circRNA expression during chicken skeletal muscle development, we sequenced and analyzed leg musle at 11 embryo age, 16 embryo age, and 1 days post hatch.

first: Hongjia

last: Ouyang

first: Qinghua

last: Nie


title: Macrophages redirect phagocytosis by non-professional phagocytes and influence inflammation

status: Public on Nov 01 2016

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

country: USA

institute: Signature Science, LLC

type: Expression profiling by high throughput sequencing

summary: Professional phagocytes (such as macrophages) and non-professional phagocytes (such as epithelial cells) clear billions of apoptotic cells and particles on a daily basis. Since these phagocytes reside in proximity in most tissues, whether cross-communication exists between them during cell clearance, and how this might impact inflammation are not known. Here, we show that macrophages, via the release of a soluble growth factor and microvesicles, redirect the type of particles engulfed by non-professional phagocytes and influence their inflammatory response. During apoptotic cell engulfment or in response to inflammation-associated cytokines, macrophages released insulin-like growth factor 1 (IGF-1). The binding of IGF-1 to its receptor on non-professional phagocytes redirected their phagocytosis, such that uptake of larger apoptotic cells was dampened while engulfment of microvesicles was enhanced. Macrophages were refractory to this IGF-1 mediated engulfment modulation. Macrophages also released microvesicles, whose uptake by epithelial cells, enhanced by IGF-1, led to decreased inflammatory responses by epithelial cells. Consistent with these observations, deletion of IGF-1 receptor in airway epithelial cells led to exacerbated lung inflammation after allergen exposure. These genetic and functional studies reveal a novel IGF-1 and microvesicle-dependent communication between macrophages and epithelial cells that can critically influence the magnitude of tissue inflammation in vivo.

overall_design: 4 groups (N (control), H (HDM-treated), M (microvesicle treated), MH (HDM and microvesicle)), n=4 each, n=16 total

first: Claudia

last: Han

first: Ignacio

last: Juncadella

first: Jason

last: Kinchen

first: Monica

last: Buckley

first: Alexander

last: Klibanov

first: Kelly

last: Dryden

first: Suna

last: Onengut-Gumuscu

first: Uga

last: Erdbrugger

first: Yun

last: Shim

first: Kenneth

last: Tung

first: Kodi

last: Ravichandran


title: Transcriptomic profiles of intestinal stem cells cultured in natural and synthetic three-dimensional matrices

city: Lausanne

first: Nikolce

last: Gjorevski

address: Station 15 AI 1106

department: SV-IBI

country: Switzerland

institute: EPFL

summary: We used RNA-seq to define the gene expression profiles of intestinal stem cells (ISCs) expanded in Matrigel, degradable poly(ethylene) glycol (PEG) and non-degradable PEG matrices. Comparison of mRNA profiles between ISCs grown in Matrigel and non-degradable PEG show no major differences in expression of gene related to stemness, proliferation and signaling via the Wnt and Notch pathways. These results also show that ISC cultured in degradable PEG matrices upregulate stress- and inflammation-related genes compared with cells expanded in non-degradable PEG matrices.

overall_design: mRNA profiles of ISCs cultured in the three types of matrices for 4 days were generated in triplicate

first: Matthias

middle: P

last: Lutolf


title: Transcriptome comparison of PAX6 ablated mouse beta cells to WT beta cells, ChIP-seq analysis of PAX6 bound sites both in mouse and human beta cell lines (Min6 and EndoC), and ChIP-seq analysis fo histone mark H3K9ac on mouse pancreatic beta cells.

city: Jerusalem

first: Yuval

last: Dor

address: Ein Kerem

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Here, we report a key role for the transcription factor Pax6 in the maintenance of adult beta-cell identity and function. Pax6 is down regulated in beta-cells of diabetic db/db mice and in wild type mice treated with an insulin receptor antagonist, revealing metabolic control of expression. Deletion of Pax6 in beta-cells of adult mice leads to lethal hyperglycemia and ketosis, due to loss of beta-cell function and expansion of alpha-cells. Lineage tracing, transcriptome, and chromatin analyses show that Pax6 is a direct activator of beta-cell genes, maintaining mature beta-cell function and identity. In parallel, Pax6 binds promoters and enhancers to repress alternative islet cell genes including ghrelin, glucagon, and somatostatin. Chromatin analysis and shRNA-mediated gene suppression experiments indicate a similar function of PAX6 in human beta-cells. Reduced expression of Pax6 in metabolically stressed beta-cells may contribute to beta-cell failure and alpha-cell dysfunction in diabetes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA profiles of pancreatic  beta cells from 6-8 weeks old βPAX6 transgenic mice (MIP-CreER; Pax6lox/lox; Rosa26-LSL-YFP) and from their control littermates  (Rosa26-LSL-YFP) were generated byRNAseq. Whole genome map of PAX6 bound sites were generated by ChIP-seq on Min6 and EnodC cells (n=3) whole genome map of histones enriched for H3K9ac modification was generated by ChIP-seq on pancreatic beta cells from 16 months old Bl6 mice .

first: Avial

last: Swisa

first: Dana

last: Avrahami

first: Noa

last: Eden

first: Jia

last: Zhang

first: Eseye

last: Feleke

first: Yamit

last: Cohen-Tayar

first: Miri

last: Stolovich-Rain

first: Klaus

middle: H

last: Kaestner

first: Benjamin

last: Glaser

first: Ruth

last: Ashery-Padan


title: American alligator tooth dental lamina RNA-seq

city: Los Angeles

first: Ping

last: Wu

state: CA

address: 2011 Zonal Ave HMR313A

department: Pathology

institute: University of Southern California

summary: Comparison of RNA profiles at different stages of tooth regeneration

overall_design: Alligator tooth dental laminae were collected at different stages of tooth cycle. RNA-seq was performed to study changes of RNA expression through the cycle. There are 3-5 replicates in each of 4 stages.


title: MicroRNAs upregulated in cancer associated fibroblasts following gemctiabine treatment

city: South Bend

first: Reginald

last: Hill

state: Indiana

address: 1234 North Notre Dame Ave.

department: Biological Sciences

institute: University of Notre Dame

type: Non-coding RNA profiling by high throughput sequencing

summary: Cancer associated fibroblasts (CAFs) comprise the majority of the tumor bulk of pancreatic adenocarcinomas (PDACs).  Current efforts to eradicate these tumors focus predominantly on targeting the proliferation of rapidly growing cancer epithelial cells.  We know that this is largely ineffective with resistance arising in most tumors following exposure to chemotherapy.  Despite the long-standing recognition of the prominence of CAFs in PDAC, the effect of chemotherapy on CAFs and how they may contribute to drug resistance in neighboring cancer cells is not well characterized.  Here we show that CAFs exposed to chemotherapy play an active role in regulating the survival and proliferation of cancer cells.  We found that CAFs are intrinsically resistant to gemcitabine, the chemotherapeutic standard of care for PDAC.  Further, CAFs exposed to gemcitabine significantly increase the release of extracellular vesicles called exosomes. These exosomes increased chemoresistance-inducing factor, Snail, in recipient epithelial cells and promote proliferation and drug resistance.  Finally, treatment of gemcitabine-exposed CAFs with an inhibitor of exosome release, GW4869, significantly reduces survival in co-cultured epithelial cells, signifying an important role of CAF exosomes in chemotherapeutic drug resistance.  Collectively, these findings show the potential for exosome inhibitors as treatment options alongside chemotherapy for overcoming PDAC chemoresistance.

overall_design: Examination of miRNAs in gemcitabine treated versus untreated cancer associated fibroblasts.

first: Katherine

middle: E

last: Richards

first: Ann

last: Zeleniak

first: Melissa

middle: L

last: Fishel

first: Junmin

first: Laurie

last: Littlepage


title: Loss of Uhrf1 in neural stem cells leads to activation of retroviral elements and delayed neurodegeneration [RRBS]

city: Planegg-Martinsried

first: Gunnar

last: Schotta

address: Grosshaderner Strasse 9

department: Biomedical Center

country: Germany

institute: LMU Munich

type: Methylation profiling by high throughput sequencing

summary: In order to understand if early epigenetic mechanisms instruct the long-term behaviour of neural stem cells (NSCs) and their progeny, we examined the protein Uhrf1 as it is highly expressed in NSCs of the developing brain and rapidly downregulated upon differentiation. Conditional deletion of Uhrf1 in the developing cerebral cortex resulted in rather normal proliferation and neurogenesis but severe postnatal neurodegeneration. During development, deletion of Uhrf1 resulted in global DNA hypomethylation with a strong activation of the IAP family of endogenous retroviral elements, accompanied by an increase in hydroxy methyl cytosine. Downregulation of Tet enzymes rescued the IAP activation in Uhrf1 cKO cells, suggesting an antagonistic interplay between Uhrf1 and Tet on IAP regulation. As IAP upregulation persists into postnatal stages in the conditional Uhrf1 KO mice, our data show the lack of means to repress IAPs in differentiating neurons that normally never express Uhrf1. The high load of viral proteins and other transcriptional dysregulation ultimately lead to extensive postnatal neurodegeneration. Taken together, these data show that early developmental NSC factors can have long-term effects in neuronal differentiation and survival. Moreover, it highlights how specific the consequences of widespread changes in DNA methylation are for certain classes of retroviral elements.

overall_design: Two-condition experiment: cortices of heterozygous mice as control versus Uhrf1 conditional knockout mice

first: Markus

last: Schulze

first: Vidya

last: Ramesh

first: Magdalena

last: Götz


title: Loss of Uhrf1 in neural stem cells leads to activation of retroviral elements and delayed neurodegeneration [P5]

overall_design: Transcriptome analysis in control vs. Uhrf1-deficient brain


title: Loss of Uhrf1 in neural stem cells leads to activation of retroviral elements and delayed neurodegeneration

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

overall_design: Refer to individual Series


title: Loss of Uhrf1 in neural stem cells leads to activation of retroviral elements and delayed neurodegeneration [E16]


title: Loss of Uhrf1 in neural stem cells leads to activation of retroviral elements and delayed neurodegeneration [5hmC]

overall_design: 5hmC analysis in control vs. Uhrf1-deficient brain


title: Genome-wide analysis of gene expression in infarcted and non-infarcted left ventricle from NEIL3-deficient mice subjected to myocardial infarction

city: Oslo

first: Gunn

middle: Annette

last: Hildrestrand

state: Oslo

address: Sognsvannsveien 20

department: Microbiology

country: Norway

institute: Oslo University Hospital and University of Oslo

summary: Myocardial infarction (MI) triggers a reparative response involving fibroblast proliferation and differentiation driving extracellular matrix modulation necessary to form a stabilizing scar. Recently, it was shown that a genetic variant of the base excision repair enzyme endonuclease VIII-like 3 (NEIL3) was associated with increased risk of MI in humans. Here, we report elevated myocardial NEIL3 expression in heart failure patients and marked myocardial upregulation of Neil3 following MI in mice, especially in a fibroblast-enriched cell fraction. Neil3-/- mice showed increased mortality after MI compared to WT, caused by myocardial rupture. Neil3-/- hearts displayed enrichment of mutations in genes involved in mitogenesis of fibroblasts and transcriptome analysis revealed dysregulated fibrosis. Correspondingly, proliferation of vimentin+ and aSMA+ (myo)fibroblasts was increased in Neil3-/- hearts following MI. We propose that NEIL3 operates in genomic regions crucial for regulation of cardiac fibroblast proliferation and thereby controls extracellular matrix modulation after MI.

overall_design: RNA from infarcted and non-infarcted LV of WT and Neil3-/- C57BL/6 mice obtained three days after induced myocardial infarction were subjected to RNA sequencing using Illumina Hiseq 2000

first: Maria

middle: B

last: Olsen

middle: A

first: Katja

last: Scheffler

first: Leif

last: Vinge

first: Katrine

last: Alfsnes

first: Vuk

last: Palibrk

first: Christine

middle: G

last: Neurauter

first: Luisa

last: Luna

first: Jostein

last: Johansen

first: Jonas

last: Øgaard

first: Ingrid

middle: K

last: Ohm

first: Geir

last: Slupphaug

first: Anna

last: Kuśnierczyk

first: Arnt

last: Fiane

first: Sverre

last: Brorson

first: Lili

last: Zhang

first: Lars

last: Gullestad

first: William

last: Louch

first: Per

middle: O

last: Iversen

first: Ingunn

last: Østli

first: Arne

last: Klungland

last: Christensen

first: Ivar

last: Sjaastad

first: Pål

last: Sætrom

last: Yndestad

last: Aukrust

first: Magnar

last: Bjørås

first: Alexandra

middle: V

last: Finsen


title: The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University


title: Whole genome bisulfite sequencing of nrpd1 mutant in C24 background [methyl-seq]

summary: Arabidopsis ROS1 is the first genetically characterized DNA demethylase in eukaryotes.  Dysfunction of ROS1 leads to increase in DNA methylation level at thousands of  genomic loci. However, the features of ROS1 targets are not well understood. In this  study, we identified and characterized ROS1 target loci in Arabidopsis Col-0 and C24 ecotypes. Most ROS1 targets are transposable elements (TEs) and intergenic regions. Compared to other TEs, ROS1-targeted TEs are closer to protein coding genes, suggesting a role for ROS1 in preventing the spreading of DNA methylation from highly methylated TEs to nearby genes. Interestingly, we found that unlike general TEs, ROS1  targets are associated with an enrichment of H3K18ac and H3K27me3, and depletion of H3K27me and H3K9me2. We investigated the antagonism between ROS1 and RNA-directed DNA methylation (RdDM) by identifying and characterizing thousands of genomic regions regulated by both ROS1 and RdDM. Unexpectedly, we uncovered thousands of previously unidentified RdDM targets by analyzing the DNA methylome of ros1/nrpd1 double mutant plants. In addition, we show that ROS1 also antagonizes RdDM-independent DNA methylation at more than a thousand genomic loci. Our results provide significant insights into the genome-wide effects of both ROS1-mediated active DNA demethylation and RNA-directed DNA methylation as well as their interaction in plants.

overall_design: Using whole genome bisulfite sequencing to provide single-base resolution of DNA methylation status in nrpd1 mutant (C24 background)

first: Kai

last: Tang

first: Zhaobo

last: Lang


title: An RNA structure-mediated post-transcriptional model of α-1-antitrypsin deficiency

city: Chapel Hill

first: Alain

last: Laederach

state: NC

address: Coker Hall

department: Biology

institute: University of North Carolina Chapel Hill

summary: Six transcripts of the gene SERPINA1 (serpin family A member 1) were sequenced via SHAPE-MaP to obtain their secondary structure profiles. For each transcript, SHAPE-MaP includes a sample treated with 1M7 reagent ('p'), a minus reagent negative control ('m'), and a denatured control ('d'). The 1M7 reagent preferentially reacts with unpaired bases in RNA and subsequently induces mutations during the reverse transcription step of library preparation. After sequencing and alignment, the 'mutational profiles' of the 'p', 'd' and 'm' samples are used to calculate the SHAPE reactivity of each base in the transcript. SHAPE reactivity correlates to the tendency of a base to be paired as part of a secondary structure.

overall_design: Transcript-specific SHAPE-MaP on six SERPINA1 transcripts.

first: Meredith

last: Corley

first: Amanda

last: Solem

first: Gabriela

last: Phillips

first: Lela

last: Lackey

first: Benjamin

last: Ziehr

first: Nathaniel

last: Moorman


title: Liz transcription is required for evicting H3K27me3 marks at the Gpr1/Zdbf2 locus through the deposition of DNA methylation marks.

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

summary: To study the role of the Liz transcript on local chromatin features during early development, we used a culture-based system.  Mouse embryonic stem cells (ESCs) with a hypomethylated genome were obtained through their culture in 2i medium supplemented with vitamin C. To recapitulate de novo DNA methylation, these cells were directed towards an epiblast-like cell fate (EpiLC)  during seven days of culture in Activin A and Fgf2. The effect of Liz transcription on the maintenance of H3K27me3 marks at the Gpr1/Zdbf2 locus was inferred by the comparative ChIP-seq analysis of H3K27me3 enrichment in WT (E14) cells versus ∆Liz cells- which carry a TALEN-engineered 1.7kb homozygous deletion of the Liz Transcription Start Size (TSS)- at Day 0 (D0), D4 and D7 of EpiLC differentiation.

overall_design: H3K27me3 profiles were generated at three time points during differentiation in wild-type and mutant cells lacking the Liz RNA

first: Maxim

middle: C

last: Greenberg

first: Deborah

last: Bourc'his


title: HLH-30/TFEB-mediated autophagy functions in a cell-autonomous manner for epithelium intrinsic cellular defense against bacterial pore-forming toxin in C. elegans

city: Tainan

first: Huan-Da

last: Chen

address: No.1, University Road

country: Taiwan

institute: National Cheng Kung University

summary: Autophagy is an evolutionarily conserved intracellular system that maintains cellular homeostasis by degrading and recycling damaged cellular components. The transcription factor HLH-30/TFEB-mediated autophagy has been reported to regulate tolerance to bacterial infection, but less is known about the bona fide bacterial effector that activates HLH-30 and autophagy. Here, we unveil that bacterial membrane pore-forming toxin (PFT) induces autophagy through an HLH-30-dependent manner in Caenorhabditis elegans. Moreover, autophagy controls the susceptibility of animals to PFT toxicity through xenophagic degradation of PFT and repair of membrane-pore cell-autonomously in the PFT-targeted intestinal cells in C. elegans. These results demonstrate that autophagic pathways and autophagy are induced partly at the transcriptional level through HLH-30 activation and are required to protect metazoan upon PFT intoxication. Together, our data show a new and powerful connection between HLH-30-mediated autophagy and epithelium intrinsic cellular defense against the single most common mode of bacterial attack in vivo.

overall_design: Examination the genes expression pattern between wild type and hlh-30 mutant in response to Pore-forming toxin Cry5B.

first: Chang-Shi


title: Loss of Macf1 abolishes ciliogenesis and disrupts apicobasal polarity establishment in the retina

city: Bethesda

first: Koray Dogan

last: Kaya

state: MD

address: 6 CENTER DR

department: NEI

institute: NIH

summary: Microtubule actin crosslinking factor 1 (Macf1) plays a role in coordinated actions of actin and microtubules in multiple cellular processes. Here we show that Macf1 is also critical for ciliogenesis in multiple cell types. Ablation of Macf1 in the developing retina abolishes ciliogenesis and basal bodies fail to dock to ciliary vesicles or migrate apically. Photoreceptor polarity is randomized while inner retinal cells laminate correctly, suggesting that photoreceptor maturation is guided by polarity cues provided by cilia. Deletion of Macf1 in adult photoreceptors caused reversal of basal body docking and loss of outer segments, reflecting a continuous requirement for Macf1 function. Macf1 was also shown to interact with ciliary proteins Mkks and Talpid3. We propose that a disruption of trafficking across microtubles to actin filaments underlies the ciliogenesis defect in cells lacking Macf1, and that Mkks and Talpid3 are involved in the coordination of microtubule and actin interactions.

overall_design: RNA was isolated from confluent mouse embryonic fibroblasts (3 clones per genotype). MEFs where generated from Macf1flox/flox and Macf1flox/+ mice, and immortalized via transfection with the SV40 large T antigen. Cells were grown to 75% confluency and treated with AAV8-CMV-Cre (1.2x10e13vg/ml) overnight. Single cell colonies were generated and recombination for the Macf1 knockout allele (Macf1-/-) and heterozygous control (Macf1-/+) was confirmed by sequencing. Loss of protein expression was confirmed by western blot. Cells were grown to confluency and serum starved on gelatin coated glass coverslips prior to fixing and immunostaining as described for the retina.

first: Helen

last: May-Simera

first: Jessica

last: Gumerson

first: Chun

last: Gao

first: Maria

last: Campos

first: Stephanie

middle: M

last: Cologna

first: Tina

last: Beyer

first: Karsten

last: Boldt

first: Koray

middle: D

first: Nisha

last: Patel

first: Friedrich

last: Kretschmer

first: Matthew

middle: W

last: Kelley

first: Ronald

middle: S

last: Petralia

first: Megan

last: Davey

first: Tiansen

last: Li


title: Translational profiling of retinal ganglion cell optic nerve regeneration in Xenopus laevis

city: Lexington

first: Gregg

middle: Brooks

last: Whitworth

address: 204 West Washington St

institute: Washington and Lee Unversity

summary: Unlike adult mammals, adult frogs regrow and regenerate their optic nerve following a crush injury. Using Translational Ribosome Affinity Purification (TRAP), a method to isolate mRNAs actively undergoing translation in a target cell population, we have generated a transcriptional profile by RNA-Seq for retinal ganglion cells (RGC) during the period of recovery following an optic nerve injury.  Based on bioinformatics analysis using the JGI 9.1 Xenopus laevis gene models, our results reveal a profound shift in the composition of actively translating mRNAs during the early stages of RGC regeneration: as factors involved in cell signaling are rapidly downregulated, and those involved in core metabolism are upregulated.  We identified one highly upregulated gene in response to injury, uchl1, which coupled to downregulation of the synucleins (snca, scng), was previously implicated in neurodegenerative diseases.  Our injury-screen in Xenopus identified a previously unknown gene, gng8, as being associated with the regenerative process.  Our generated online database provides the Xenopus community a valuable resource for the identification of genes involved in the regeneration process to target for future functional studies.

overall_design: To investigate the changes in gene expression that occur as retinal ganglion cells (RGCs) recover and regrow following injury, we have used the TRAP method.  With TRAP we are able to isolate the actively translating pool of mRNAs from a specific cell type, in this case RGCs.  To do this, we created lines of transgenic frogs which express an eGFP-tagged variant of the large ribosomal protein rpl10a under the control of an RGC-specific promoter from the islet2b locus.  In our experimental framework, we quantify gene expression changes in RGCs recovering from optic nerve crush by comparing mRNA levels in samples collected from the eye undergoing a surgical crush (right) to the contralateral eye (left).  At discrete time points following optic nerve crush in the left eye, both eyes are rapidly dissected and the ribosome-associated RNAs purified from tissue extracts using eGFP antibodies conjugated to magnetic beads.  To control for the effects of surgery on RGCs, gene expression was also quantified in animals that underwent sham surgeries with no optic nerve crush ("sham" samples).  To control for the systemic effects of the surgical procedure per se, gene expression was also quantified in animals that did not undergo any surgery ("naive" sample).  These mRNA pools were used to construct libraries for RNA-Seq using poly(A) selection and 2x multiplexing.

first: Bayan

last: Misaghi

first: Andrew

last: Watson

first: David

last: Heinen

first: Nicholas

last: Marsh-Armstrong

first: Fiona


title: Whole genome bisulfite sequencing of ros1-1 mutant and C24 wild-type (WT)

first: Jian-Kang

last: Zhu

summary: Using whole genome bisulfite sequencing to provide single-base resolution of DNA methylation status in ros1-1 mutant and C24 WT

overall_design: 2 samples examined: C24 wild type with RD29A-LUC transgene, ros1-1 mutant (in C24 background with RD29A-LUC transgene)

first: Kai

last: Tang

first: Zhaobo

last: Lang


title: GR accelerates, but is largely dispensable for, adipogenesis

last: Ge

address: 50 South Dr Rm 4154

department: NIDDK

summary: Dexamethasone (DEX), a synthetic ligand for glucocorticoid receptor (GR), is routinely used to stimulate adipogenesis in culture. GR-depleted preadipocytes show adipogenesis defects one week after induction of differentiation. However, it has remained unclear whether GR is required for adipogenesis in vivo. By deleting GR in precursors of brown adipocytes, we found unexpectedly that GR is dispensable for brown adipose tissue development in mice. In culture, GR-deficient primary or immortalized white and brown preadipocytes showed severely delayed adipogenesis one week after induction of differentiation. However, when differentiation was extended to 3 weeks, GR-deficient preadipocytes showed similar levels of adipogenesis marker expression and lipid accumulation as the wild type cells, indicating that DEX-bound GR accelerates, but is dispensable for, adipogenesis. Consistently, DEX accelerates, but is dispensable for, adipogenesis in culture. We show that DEX-bound GR accelerates adipogenesis by directly promoting the expression of adipogenic transcription factors C/EBPb, C/EBPd, C/EBPa, KLF5, KLF9 and PPARg in the early phase of differentiation. Mechanistically, DEX-bound GR recruits histone H3K27 acetyltransferase CBP to promote activation of C/EBPb-primed enhancers of adipogenic genes. These results clarify the role of GR in adipogenesis in vivo and demonstrate that DEX-mediated activation of GR accelerates, but is dispensable for, adipogenesis.

overall_design: Expression profiling by RNA-seq at four time points (D0, 4h, D2, D7). Profiling of transcription factors (GR, C/EBPβ, p-CREB) binding, co-factors (CBP) binding and histone modifications (H3K4me1, H3K27ac) by ChIP-seq at two time points (0h, 4h) during adipogenesis of GRf/f brown preadipocytes in culture.

first: Young-Kwon

last: Park


title: robust statistical modeling improves sensitivity of high-throughput rnA structure probing experiments

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

summary: Structure probing coupled with high-throughput sequencing holds the potential to revolutionize our understanding of the role of RNA structure in regulation of gene expression. Despite major technological advances, intrinsic noise and high coverage requirements greatly limit the applicability of these techniques. Here we describe a probabilistic modeling pipeline which accounts for biological variability and biases in the data, yielding statistically interpretable scores for the probability of nucleotide modification transcriptome-wide. We demonstrate on two yeast data sets that our method has greatly increased sensitivity, enabling the identification of modified regions on many more transcripts compared with existing pipelines. It also provides confident predictions at much lower coverage levels than previously reported. Our results show that statistical modeling greatly extends the scope and potential of transcriptome-wide structure probing experiments.

overall_design: Two datasets of yeast transcriptome ChemModSeq data. Two samples probed with NAI and two negative control samples


title: Altered microRNAs expression and gene expression in allicin-treated ileal tissues revealed their potential roles in regulating host responses to antimicrobials

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

summary: Allicin is a natural extract from garlic that has been used as an antibiotic alternative in livestock production. Limited knowledge is known about the effects of allicin on gut microbiota and tissue. The aim of this study was to investigate the effects of allicin on the expression of ileal miRNAs and the tissue-associated total bacterial density in pre-weaned calves. Different doses of allicin (0 mg, 0.5 mg, 5 mg, 50 mg and 500 mg) were used to treat in vivo ileal loop tissues in pre-weaned calves for different periods (1 day, 3 days and 12 days). A total of 15 miRNAs showed allicin dose-dependent differential expression patterns. Four miRNAs (miR-132, miR-423-5p, miR-429 and miR-6529a) were upregulated in 50 mg or 500 mg treated gut tissues, while 11 miRNAs (miR-190a, miR-193a-3p, miR-196a, miR-196b, miR-2285aa, miR-2285o, miR-2887, miR-2904, miR-409a, miR-6523a and miR-96) were downregulated in 50 mg or 500 mg treated gut tissues. Functional analysis of differentially expressed mRNAs showed that the upregulated mRNAs regulate functions that may be involved in “disrupted microtubule function”, and the downregulated miRNAs may be associated with the “inhibited leukocyte transendothelial migration” and “promoted cell phagocytosis”.


title: CsoR is essential for maintaining copper homeostasis in Mycobacterium tuberculosis

city: Madison

first: Adel

last: Talaat

state: WI

address: 1656 Linden Dr.

department: Pathobiological Sciences

institute: UW-Madison

summary:
Purpose: CsoR, a copper responsive negative regulator of Mycobacterium tuberculosis has been shown to respond to copper and bind to its own regulon in in vitro experiments.  Here we examine the role of CsoR in vivo by examining the impact of  deletion of csoR on the host transcriptome.
Methods:  csoR was knocked out of M. tuberculosis H37Rv using the specialized transduction method developed by Bardarov et al (2002), followed by removal of the hygromycin marker with plasmid pYUB870.  Both wild type and confirmed csoR knockout were grown in copper free Sauton's media to late log phase before harvesting for transcriptomic studies.  RNA was extracted using a modified Trizol method prior to DNAse treatment and rRNA depletion.  Sequencing was done on an Illumina HiSeq 2000, filtered for quality using the FASTX-Toolkit, and mapped using Bowtie, and counts per locus generated with BedTools in the Galaxy platform.   Differential expression analysis was carried out in edgeR with significantly differentially expressed genes being identified as those with  ≥|2| fold differential expression between ΔcsoR and wild type strains, and  an FDR < 0.05.
Results: We found that 223 genes were differentially expressed between the ΔcsoR and wild type strains, 52  induced and 71  repressed. Differential expression of 10 of these genes, 6 induced and 4 repressed, was confirmed by qRT-PCR using SYBR green methodology.  The only copper responsive genes identified were those within the csoR operon: csoR, Rv0968, ctpV, Rv0970, suggesting that csoR may only regulate its own operon in response to copper.  Genes in the RicR regulon, another copper responsive transcriptional regulator, were not significantly differentially expressed, but some of these copper inducible genes were slightly down regulated suggesting that copper levels may be lower in the mutant strain as compared to wild type.  Notably, 44 of the 48 members of the dosR regulon, responsive to hypoxic and NO stress, were induced in the mutant vs wild type suggesting that csoR is necessary for maintaining homeostasis, likely through copper regulation, within the cell.
Conclusions: We have shown that CsoR is likely only directly regulating its own operon in response to copper, however it is required to maintain homeostasis, preventing a hypoxia-type stress response in the absense of copper.

overall_design: The transcriptional profile of M. tuberculosis ΔcsoR was compared to the wild type H37Rv parent strain.

first: Sarah

last: Marcus


title: RNA sequencing of Formalin-Fixed, Paraffin-Embedded Specimens for Gene Expression Quantification and Data Mining

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

summary: We compared the RNAseq data consistency between Ribo-Zero and RNase H kits

overall_design: RNA libraries were prepared using both Ribo-Zero and RNase H kits on breast cancer FFPE specimens. We sequenced these libraries and compared their data consistencies.

first: Xiao-Ou

last: Shu

first: Qiuyin

last: Cai


title: MethlyC-Seq of Col-0 (wild type, WT), nrpd1-3, nrpe1-11, ros1-4 single mutants and ros1-4nrpd1-3 double mutant

summary: Using MethylC-Seq to provide single-base resolution of DNA methylation status in WT,  nrpd1-3, nrpe1-11, ros1-4 single mutants and ros1-4nrpd1-3 double mutant

overall_design: MethylC-Seq: 1 WT and 4 mutants examined (nrpd1-3, nrpe1-11, ros1-4 single mutants and ros1-4nrpd1-3 double mutant)


title: Loss of Uhrf1 in neural stem cells leads to activation of retroviral elements and delayed neurodegeneration [E16VZ]

first: Gunnar

last: Schotta

first: Vidya

last: Ramesh

first: Magdalena

last: Götz


title: Widespread chromatin accessibility at repetitive elements links embryonic stem cells with human cancer

city: New York

last: Gomez

state: NY

address: 1230 York Ave

institute: Rockefeller University

summary: Examination of chromatin accessibility in three human embryonic stem cell lines unexpectedly identified a stem cell signature consisting of widespread enrichment of repetitive elements (RE).  Integrating genomic and biochemical approaches we found that RE in accessible chromatin are flanked by well positioned nucleosomes and distinct histone modifications, similar to that of other regulatory elements. Chromatin remodeling at repetitive elements during differentiation was associated with differential gene expression and developmental pathways.  Remarkably, we found that the chromatin environment of a mesenchymally-derived cancer, Ewing Sarcoma, mimics that of bone-marrow-derived multipotent stromal cells creating a permissive environment for the central oncogene responsible for this cancer.  Our data demonstrate that chromatin in stem cells is characterized by a unique signature consisting of an enrichment of repetitive elements that are associated with both differentiation and disease.

overall_design:
Examination of FAIRE-seq, DNase-seq, MNase-seq, RNA-seq in human stem cells and differentiated cells.
-----------------------------------
*Incomplete: No raw data provided for all bone marrow samples

first: Ian

last: Davis


title: Transcriptome of cancer associated fibroblasts before and after triptolide treatment in pancreatic cancer

city: Minneapolis

first: Xianda

last: Zhao

state: Minnesota

address: 515 Delaware St SE

department: Surgery

institute: University of Minnesota

summary: Pancreatic cancer is characterized by heavy desmoplasia. Triptolide and its water-soluble pro-drug Minnelide are extremely efficient against pancreatic cancer in animal models.  However, the effects of triptolide on pancreatic cancer stromal cells are largely unknown. The aim of this project is to indentify potential cellular functions that are affected by triptolide in pancreatic cancer associated fibroblasts.

overall_design: Cancer associated fibroblasts were isolated from pancreatic tumor of KPC mouse model. Cells were either untreated or treated with 100nM triptolide for 6h or 24h before RNA isolation. The RNA was quality tested using a Bioanalyzer 2100 (Agilent Technologies, CA, USA). cDNA was created by reverse transcription of oligo-dT purified polyadenylated RNA and fragmented, blunt-ended, and then ligated to barcoded adaptors. Then, the library was size selected, and the selection process was validated and quantified by capillary electrophoresis and qPCR, respectively. Samples were load on the HiSeq 2500 (Illumina Inc., CA, USA) to generate around 25 million paired-end 50bp reads for each sample.

first: Zhao

last: Xianda

first: Dudeja

last: Vikas

first: Banerjee

last: Sulagna

first: Saluja

last: Ashok


title: CHIP-SEQ of FOXA1 in parental MCF7 cells and tamoxifen resistant MCF7 cells

city: Houston

first: Xiaoyong

last: Fu

state: Tx

address: 1 Baylor Plaza

department: Breast Center

institute: Baylor College of Medicine

summary: ChIP sequencing of FOXA1 in MCF7 cells and tamoxifen resistant MCF7 cells

overall_design: ChIP sequencing for FOXA1 in MCF7 cells and tamoxifen resistant derivatives

first: Jeselsohn

last: Rinath

first: Brown

last: Myles

first: Schiff

last: Rachel

first: Fu

last: Xiaoyong


title: Natural variation of H3K27me3 modification between two Arabidopsis accessions and its inheritance in hybrid

city: Beijing

first: Mei

last: Yang

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: PKU

summary: Mechanism, inheritance patterns and biological significance remain unclear. Here, we generated genome-wide integrated maps of H3K27me3 modification and transcriptome for Col, C24 and their F1 hybrid, and their clf mutants. We found that H3K27me3 modification profiles were divergent between Col and C24, and were inherited mainly additively in hybrid. By comparing H3K27me3 modification ratio between parents to allelic H3K27me3 modification ratio in hybrid, we identified cis- and trans-regulatory divergence for H3K27me3 modification variation between Col and C24, and found that cis-regulatory divergence was the predominant contributor to H3K27me3 variation. The majority of genes with both cis- and trans-regulatory divergence displayed "cis-trans" interaction, whereas "cis+trans" interaction resulted in higher magnitude of H3K27me3 variation. H3K27me3 modification variation was negatively correlated with gene expression variation between Col and C24, both of which might rise from the same cis-regulatory divergence.  Moreover, cis-regulatory divergence could lead to the concurrent allelic H3K27me3 modification bias and allelic gene expression bias for auxin metabolic genes and stimulus responsive genes in Col×C24 hybrid. Natural variation of H3K27me3 modification and gene expression were changed upon CLF mutation, and heterosis, especially best-parent hetereosis, was largely compromised in clf hybrid. Together, our study provided a comprehensive analysis of regulatory divergence for natural variation of histone modification and its association with differential gene expression between Arabidopsis accessions and growth vigor in hybrid.

overall_design: Genome-wide integrated maps and allelic expression of mRNA and  histone modifications (H3K27me3) in the shoots of 14 day old seedlings of two Arabidopsis(Col and C24) and their hybrids (Col x C24).

first: Xuncheng

last: Wang

first: Guangming

last: He

first: Xingwang

last: Deng


title: Transcriptional profiles of virus-specific CD8+ T cells from control or anti-PD-L1-treated LCMV-Clone 13 infected mice one day or 18-29 weeks after treatment

status: Public on Oct 31 2016

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary: RNA-Seq analysis was used to study the profile of exhausted Tcells and how anti-PD-L1 treatment changed the properties of these cells short term & long term after treatment

first: KRISTEN

last: PAUKEN

middle: J

last: Wherry


title: Integrated transcriptomic and proteomic analysis of the molecular cargo of extracellular vesicles derived from porcine adipose tissue-derived mesenchymal stromal/stem cells

city: Rochester

first: Sneha

last: Nishtala

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

summary: Background: Mesenchymal stromal/stem cell (MSC) transplantation is a promising therapy for tissue regeneration. Extracellular vesicles (EVs) released by MSCs act as their paracrine effectors by delivering proteins and genetic material to recipient cells. To assess how their cargo mediates biological processes that drive their therapeutic effects, we integrated miRNA, mRNA, and protein expression data of EVs from porcine adipose tissue-derived MSCs. Methods: Simultaneous expression profiles of miRNAs, mRNAs, and proteins were obtained by high-throughput sequencing and LC-MS/MS proteomic analysis in porcine MSCs and their daughter EVs (n=3 each). TargetScan and ComiR were used to predict miRNA target genes. Functional annotation analysis was performed using DAVID 6.7 database to rank primary gene ontology categories for the enriched mRNAs, miRNA target genes, and proteins. STRING was used to predict associations between mRNA and miRNA target genes. Results: Differential expression analysis revealed 4 miRNAs, 255 mRNAs, and 277 proteins enriched in EVs versus MSCs (fold change >2, p<0.05). EV-enriched miRNAs target transcription factors (TFs) and EV-enriched mRNAs encode TFs, but TF proteins are not enriched in EVs. Rather, EVs are enriched for proteins that support extracellular matrix remodeling, blood coagulation, inflammation, and angiogenesis. Conclusions: Porcine MSC-derived EVs contain a genetic cargo of miRNAs and mRNAs that collectively control TF activity in EVs and recipient cells, as well as proteins capable of modulating cellular pathways linked to tissue repair. These properties provide the fundamental basis for considering therapeutic use of EVs in tissue regeneration.

overall_design:
Primary MSCs were isolated from abdominal fat (5-10g) of 3 female domestic pigs.  Simultaneous expression profiles of miRNAs, mRNAs, and proteins were obtained by high-throughput sequencing and LC-MS/MS proteomic analysis.
For this Series, primary MSCs were isolated from abdominal fat (5-10g) of 3 female domestic pigs.  Simultaneous expression profiles of miRNAs and mRNAs were obtained by high-throughput sequencing.

first: Alfonso

last: Eirin

first: Xiang-Yang

last: Zhu

first: Amrutesh

last: Puranik

first: John

middle: R

last: Woollard

first: Hui

last: Tang

first: Surendra

last: Dasari

first: Amir

last: Lerman

first: Andre

last: van Wijnen

first: Lilach


title: FOXA1 overexpression mediates endocrine resistance by increasing IL-8 in oestrogen receptor-positive breast cancer

first: Xiaoyong

last: Fu

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

relation:
SuperSeries of: GSE75201
SuperSeries of: GSE75329
SuperSeries of: GSE75369

overall_design: Refer to individual Series


title: A commonly inactivated tumor suppressor silences endogenous retroelements in somatic cells [ChIP-Seq]

city: London

first: Fred

last: Dick

state: ON

address: Cancer Research Labs 790 Commissioners Road East

institute: Western University

summary: Upon G1-S transition, cyclin-dependent kinases (CDKs) phosphorylate the retinoblastoma tumor suppressor protein (pRB) to release E2F transcription factors, which activate transcriptional programs, required for S-phase entry. Beyond the G1-S transition, pRB activity remains poorly understood. Our lab has discovered that pRB retains exclusive binding to E2F1 through an alternate E2F1-‘specific’ binding site at the pRB c-terminus independent of CDK phosphorylation. We have developed a gene-targeted mouse model that is defective for the E2F1-‘specific’ interaction. We are exploring the function of this complex through genome-wide binding and expression profiling. Overall, this work suggests an alternate pRB-E2F1 complex persists independent of CDK phosphorylation to establish regions of constitutive heterochromatin.

overall_design: Chromatin was isolated from passage 4 MEFs cross-linked with ethylene glycol bissuccinimidylsuccinate (EGS) and formaldehyde, and then sonicated to ≤ 400 bp. DNA fragments were immunoprecipitated using different antibodies, washed, then purified. DNA was prepared for sequencing according to the Illumina TruSeq protocol. Each protein immunoprecipitated includes one wild-type replicate as reference, and one replicate per mutant genotype assayed.

first: Frederick

first: Charles

last: Ishak

first: Aren

middle: E

last: Marshall


title: B2 SINE expression during MHV68 infecton

first: Yan

last: Guo

summary: Short interspersed nuclear elements (SINEs) are retrotransposons evolutionarily derived from endogenous RNA Polymerase III RNAs. Though SINE elements have undergone exaptation into gene regulatory elements, how transcribed SINE RNA impacts transcriptional and post-transcriptional regulation is largely unknown. This is partly due to a lack of information regarding which of the loci have transcriptional potential. Here, we present an approach (short interspersed nuclear element sequencing, SINE-seq), which selectively profiles RNA Polymerase III-derived SINE RNA, thereby identifying transcriptionally active SINE loci. Applying SINE-seq to monitor murine B2 SINE expression during a gammaherpesvirus infection revealed transcription from 28,270 SINE loci, with ~50% of active SINE elements residing within annotated RNA Polymerase II loci. Furthermore, B2 RNA can form intermolecular RNA-RNA interactions with complementary mRNAs, leading to nuclear retention of the targeted mRNA via a mechanism involving p54nrb. These findings illuminate a pathway for the selective regulation of mRNA export during stress via retrotransposon activation.

overall_design: NIH 3T3 murine fibroblasts were infected with MHV68 for 24 hours. Total RNA from two biological replicates was primer extended for B2 SINE RNA. Primer extenstion products were converted in to sequencing libraries and ran on a MiSeq at the UC Berkeley QB3 Vncent J. Coates Genomics Sequencing Laboratory.  Reads were aligned to he mouse mm10 reference genome using bwa. Reads mapping to known B2 SINEs (present in the repeatmasker tract of UCSC) were counted and normalizied RPKM values were computed using the BamUtil tool.

last: Karijolich

first: Britt

last: Glaunsinger


title: A commonly inactivated tumor suppressor silences endogenous retroelements in somatic cells


title: Assessing characteristics of RNA amplification methods for single cell RNA sequencing

first: Junhyong

last: Kim

address: 433 S University Avenue

summary: We conducted a large-scale control experiment to assess the transfer function of three scRNA-seq methods and factors modulating the function. Our approach was to dilute bulk total RNA (from a single source) to levels bracketing single-cell levels of total RNA (10 pg and 100 pg) in replicates and amplifying the RNA to levels sufficient for RNA sequencing.

overall_design:
We performed replicate transcriptome amplifications of Universal Human Reference RNA (UHR) and Human Brain Reference RNA (HBR) that were diluted to single-cell and ten-cell abundances (10 and 100 picograms (pg.) total RNA or ~200,000 and 2 million mRNA molecules, respectively) and were amplified using three single-cell RNA amplification methods. Methods included the antisense RNA IVT protocol (aRNA), a custom C1 SMARTer protocol (SmartSeq Plus) performed on a Fluidigm C1 96-well chip, and a modified NuGen Ovation RNA sequencing protocol (NuGen). Bulk ribo-depleted UHR and HBR RNA were sequenced and served as a reference. The general experimental scheme was consistent for all dilution replicates; however, there were differences across experimental groups in the specifics of experimental protocols, necessitated by particular methodologies. Because of these experimental differences, head-to-head comparison of methods is not appropriate and our goal is to provide quantitative analyses of factors affecting individual methods. Current results should be used in experimental planning, data analysis, and method optimization rather than as a performance test of any particular method.
Detailed experimental design:
Each collaborating center obtained reference RNA with the same lot number for Universal Human Reference (UHR) RNA (Agilent 740000, Lot 0006141415) and Human Brain Reference (HBR) (Ambion AM6050, Lot-105P055201A) and performed replicate amplification using a single amplification method, detailed below.
SmartSeq Plus: Reference RNA was diluted to an intermediate stock solution by serial dilution. A final 1000-fold dilution occurred on the C1 chip, such that individual wells in a given batch contained 9.99 pg. sampled from a common intermediate dilution. ERCC spike-in RNA mix 1 (Ambion 4456740) was also added for a final mass of approximately 7 femtograms (fg.) per sample, a 4,000,000x dilution from stock. Samples for each source RNA were prepared in single batches. After amplification, cDNA from the entire C1 96-well plate was quantified using picogreen. C1 chips with an average yield of less than 3 nanograms were discarded. The top 15 reactor wells by cDNA concentration were selected as representative 10 pg. samples for sequencing library preparation. Another 50 wells were selected by the same criteria. These were pooled in sets of 10, generating 5 100 pg. samples for each HBR and UHR. All samples for a given source were prepared in a single sequencing library preparation batch using Nextera XT C1 protocol.
NuGen: HBR samples were prepared in a single batch using amplification protocol 1, generating 4 10 pg. and 4 100 pg. amplified replicates. UHR samples were prepared in two batches, using either amplification protocol 1 or 2, generating 15 10 pg. and 11 100 pg. samples. A single sequencing library preparation was performed for each batch of samples using either Lucigen NxSeq or NuGen Ovation Rapid protocol.
aRNA: Amplification was performed as previously described (Morris J, Singh JM, Eberwine JH. Transcriptome analysis of single cells. J. Vis. Exp. [Internet]. 2011; Available from: http://www.jove.com/video/2634/transcriptome-analysis-of-single-cells). HBR samples were prepared in 4 batches from separate dilutions of reference RNA, generating 19 10 pg. and 3 100 pg. amplified replicates. ERCC spike-ins were added to 5 of the 10 pg. replicates before amplification at a dilution of 4,000,000x from stock. UHR samples were diluted and amplified in 2 batches from separate dilutions of reference RNA, generating 12 10 pg. and 7 100 pg. amplified replicates. A single sequencing library preparation was performed using Illumina TruSeq Stranded mRNA protocol modified to begin with amplified aRNA. A small numbers of reads were assigned to ERCC transcripts in replicates from the batch where ERCCs had been added that did not have spike-ins added (average of 0.5% of the number of reads assigned in spiked samples). 18 additional HBR 10 pg. replicates were amplified using aRNA for protocol optimization experiments. These samples were treated separately and were excluded from primary analysis.
Bulk UHR and HBR: For each reference RNA, three sequencing libraries were generated from bulk material at the same laboratory as the SmartSeq Plus replicates. Cytoplasmic and mitochondrial ribosomal RNA (rRNA) were depleted using Ribo-Zero Gold as part of Illumina TruSeq Stranded Total RNA protocol. Samples were sequenced on Illumina HiSeq 2000.
Because of differences in experimental design, direct comparison across methods of precision and the effect of input RNA abundance is difficult. For example, input RNA amount as a factor have different meanings for the different amplification methods: for SmartSeq Plus, because 100pg samples were constructed by pooling 10 pg. samples after cDNA amplification, any resulting effects involve library construction, while for aRNA and NuGen resulting effects reflect both cDNA amplification steps and library steps.

first: Hannah

last: Dueck

first: Rizi

last: Ai

first: Adrian

last: Camarena

first: Bo

last: Ding

first: Reymundo

last: Dominguez

first: Oleg

last: Evgrafov

first: Jian-Bing

last: Fan

first: Stephen

last: Fisher

first: Jennifer

last: Herstein

first: Tae

first: Jae

first: Ming-Yi

last: Lin

first: Rui

last: Liu

first: William

last: Mack

first: Sean

last: McGroty

first: Joseph

last: Nguyen

first: Neeraj

last: Salathia

first: Jamie

last: Shallcross

first: Tade

last: Souaiaia

last: Spaethling

first: Christopher

middle: P

last: Walker

first: Jinhui

last: Wang

first: Kai

first: Wei

last: Wildberg

first: Lina

last: Zheng

first: Robert

middle: H

last: Chow

first: James

last: Eberwine

last: Knowles

first: Kun

last: Zhang

first: Junhyoung


title: H3K4me3 and H3K27me3 ChIP-seq profiling in MCF7 cell lines under hypoxia and reoxygenation

city: Maastricht

first: Michiel

last: Adriaens

address: Universiteitssingel 60

department: Maastricht Centre for Systems Biology - MaCSBio

country: Netherlands

institute: Maastricht University

summary:
Purpose: Study hypoxia and reoxygenation induced changes in genome-wide H3K4me3 and H3K27me3 occupancy
Methods: Using the MCF7 breast epithelial adenocarcinoma cell line as a model, we studied epigenomic reprogramming as a function of fluctuating oxygen tension. To this end, we combined chromatin-immunoprecipitation and deep-sequencing analysis to identify H3K4me3-marks and H3K27me3-marks in MCF7 cells subjected to changes in oxygenation (i.e. acute hypoxia, chronic hypoxia, reoxygenation).
Results: H3K4me3 and H3K27me3-marks showed a rapid global increase at specific sites throughout the genome under hypoxia, both genic and inter-genic, that was partly restored upon reoxygenation.
Conclusions: Our data show that oxygen availability dynamically regulates the epigenetic state of the genome.

overall_design: Genome-wide H3K4me3-mark and H3K27me3-mark profiles were generated by combining ChIP analysis with deep sequencing using Illumina GAIIx.

first: Peggy

last: Prickaerts

first: Willem

last: Voncken

first: Brad

last: Wouters

first: Twan

last: Van Den Beucken


title: small RNA profiling of  WT, ros1-4, nrpd1 single mutants and  ros1-4/nrpd1doubble mutant [small RNA-seq]

city: West Lafayette

first: Jian-Kang

last: Zhu

address: 625 Agriculture Mall Dr.

institute: Purdue University

summary:
Arabidopsis ROS1 is the first genetically characterized DNA demethylase in eukaryotes.  Dysfunction of ROS1 leads to increase in DNA methylation level at thousands of  genomic loci. However, the features of ROS1 targets are not well understood. In this  study, we identified and characterized ROS1 target loci in Arabidopsis Col-0 and C24 ecotypes. Most ROS1 targets are transposable elements (TEs) and intergenic regions. Compared to other TEs, ROS1-targeted TEs are closer to protein coding genes, suggesting a role for ROS1 in preventing the spreading of DNA methylation from highly methylated TEs to nearby genes. Interestingly, we found that unlike general TEs, ROS1  targets are associated with an enrichment of H3K18ac and H3K27me3, and depletion of H3K27me and H3K9me2. We investigated the antagonism between ROS1 and RNA-directed DNA methylation (RdDM) by identifying and characterizing thousands of genomic regions regulated by both ROS1 and RdDM. Unexpectedly, we uncovered thousands of previously unidentified RdDM targets by analyzing the DNA methylome of ros1/nrpd1 double mutant plants. In addition, we show that ROS1 also antagonizes RdDM-independent DNA methylation at more than a thousand genomic loci. Our results provide significant insights into the genome-wide effects of both ROS1-mediated active DNA demethylation and RNA-directed DNA methylation as well as their interaction in plants.
Using small RNA-Seq(sRNA-Seq) to get small RNA profiling of  WT, ros1-4, nrpd1 single mutants and  ros1-4/nrpd1doubble mutant

overall_design: 4 samples examined: WT, ros1-4 single mutant, nrpd1-3 single mutatn, and ros1-4/nrpd1-3 double mutant. Each sample has two replicates.

last: Tang

first: Zhaobo

last: Lang


title: Phosphorylation of CBP20 links microRNA to root growth in the ethylene response

city: Austin

first: FAN

last: ZHANG

address: 2506 speedway, NMS5.324

institute: The University of Texas at Austin


title: Ethylene induced phosphorylation of CBP20 is involved in root growth [small RNA-seq]

summary:
We report that CBP20 phosphorylation can regulate root growth in ethylene. We examined the small RNA expression in roots and shoots of wild type (Col) and cbp20 mutant (in Col background).
Ethylene is one of the most essential hormones for plant developmental processes and stress responses. EIN2 is a key factor in ethylene signaling pathway and its function is regulated by phosphorylation. However, the phosphorylation regulation in the ethylene signaling pathway is largely unknown. Here we report the phosphorylation of CBP20 is regulated by ethylene, and the phosphorylation is involved in root elongation. The constitutive phosphorylation format of CBP20 rescues the cbp20 root ethylene hyposensitive phenotype, while the constitutive de-phosphorylation format of CBP20 is unable to rescue the root phenotype of cbp20 in response to ethylene. Genome wide study on ethylene regulated gene expression and microRNA expression in the roots and shoots of both Col and cbp20, together with the result of genetics validation suggest that ethylene induced phosphorylation of CBP20 is involved in root growth and one pathway is through the regulation of  microRNAs and their target genes in roots.

overall_design: Root and shoot small RNA profiles of 3-day old wild type (Col) and cbp20 mutant (in Col background) were generated by sequencing, in 2 replications, using Illumina HiSeq 4000

first: Hong

last: Qiao

first: Fan

first: Likai


title: Ethylene induced phosphorylation of CBP20 is involved in root growth [RNA-seq]

summary:
We report that CBP20 phosphorylation can regulate root growth in ethylene. We examined the gene expression in roots and shoots of wild type (Col) and cbp20 mutant (in Col background).
Ethylene is one of the most essential hormones for plant developmental processes and stress responses. EIN2 is a key factor in ethylene signaling pathway and its function is regulated by phosphorylation. However, the phosphorylation regulation in the ethylene signaling pathway is largely unknown. Here we report the phosphorylation of CBP20 is regulated by ethylene, and the phosphorylation is involved in root elongation. The constitutive phosphorylation format of CBP20 rescues the cbp20 root ethylene hyposensitive phenotype, while the constitutive de-phosphorylation format of CBP20 is unable to rescue the root phenotype of cbp20 in response to ethylene. Genome wide study on ethylene regulated gene expression and microRNA expression in the roots and shoots of both Col and cbp20, together with the result of genetics validation suggest that ethylene induced phosphorylation of CBP20 is involved in root growth and one pathway is through the regulation of  microRNAs and their target genes in roots.

overall_design: Root and shoot mRNA profiles of 3-day old wild type (Col) and cbp20 mutant (in Col background) were generated by sequencing, in 2 replications, using Illumina HiSeq 4000

last: Wang


title: DUAL RNASeq ANALYSIS REVEALS AN INCREASE OF FUNGAL PATHOGENICITY FUNCTIONS AND A ROLE OF PLANT GLUTAMINE SYNTHETASE IN NITROGEN-INDUCED SUSCEPTIBILITY TO THE RICE BLAST FUNGUS

city: Montpellier cedex 5

first: Elsa

last: Ballini

address: UMR BGPI – TA A-54/K – Equipe ICAP campus International de Baillarguet

department: Biology and ecology

institute: SupAgro Montpellier

summary: In order to understand the mechanisms of Nitrogen induced susceptibility (NIS) we’ve conducted a dual RNAseq experiment on rice infected tissues by Magnaporthe oryzae. At 0 day post inoculation and 2 days post inoculation tissues have been collected on mock inoculated and M. oryzae inoculated plants. Rice were conducted under two type of nitrogen fertilization: 0N all fertilization but nitrogen, 1N all fertilization and NH4NO3. The fertilization was applied one day before inoculation. RNAseq was conducted both on rice and fungal RNA.

sample_organism:
Oryza sativa
Pyricularia oryzae

platform_organism:
Oryza sativa
Pyricularia oryzae

overall_design: shoot tissus mRNA 28-day old rice plant were generated by deep sequencing. Three samples per conditions, Four conditions: 0N Mock, 0N Inoc, 1N Mock, 1N Inoc. 0N = plant fertilized one day before inoculation without nitrogen. 1N = plant fertilized one day before inoculation with NH4NO3. Mock = Plant inoculated with control solution (gelatin 0,5%). Inoc = Plant inoculated with Magnaporthe oryzae isolate Guy11 with gelatin 0,5%.

last: BALLINI

first: Huichuan

last: HUANG

first: Xiahong

last: HE

first: Jean-Benoit

last: MOREL


title: A study of Mediator subunit enhancer-promoter binding

city: Boston

first: Natalia

last: Petrenko

state: MA

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

summary: Mediator is a transcriptional co-activator recruited to enhancers by DNA-binding activators, and it also interacts with RNA polymerase (Pol) II as part of the preinitiation complex (PIC).  We demonstrate that a single Mediator complex associates with the enhancer and core promoter in vivo, indicating that it can physically bridge these transcriptional elements.  However, the Mediator kinase module associates strongly with the enhancer, but not with the core promoter, and it dissociates from the enhancer upon depletion of the TFIIH kinase.  Severing the kinase module from Mediator by removing the connecting subunit Med13 does not affect Mediator association at the core promoter, but increases occupancy at enhancers.  Thus, Mediator undergoes a compositional change in which the kinase module, recruited via Mediator to the enhancer, dissociates from Mediator to permit association with Pol II and the PIC.  As such, Mediator acts as a dynamic bridge between the enhancer and core promoter.

overall_design: 8 Mediator subunits' genome-wide binding is tested by Chip-seq before and after Kin28 anchor-away.

first: Yi

last: Jin

first: Koon

last: Wong

first: Kevin

last: Struhl


title: Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3

first: Michiel

last: Adriaens


title: Single-Cell Analysis Uncovers Clonal Acinar Cell Heterogeneity in the Adult Pancreas

city: Heidelberg

first: Ana

last: Martin-Villalba

state: Deutschland

address: Im Neuenheimer Feld 280

department: Molekulare Neurobiologie (A290)

institute: German Cancer Research Center (DKFZ)

summary: Acinar cells make up the majority of all cells in the pancreas, yet the source of new acinar cells during homeostasis remains unknown. Using multicolor lineage-tracing and organoid-formation assays, we identified the presence of a progenitor-like acinar cell subpopulation. These cells have long-term self-renewal capacity, albeit in a unipotent fashion. We further demonstrate that binuclear acinar cells are terminally differentiated acinar cells. Transcriptome analysis of single acinar cells revealed the existence of a minor population of cells expressing progenitor markers. Interestingly, a gain of the identified markers accompanied by a transient gain of proliferation was observed following chemically induced pancreatitis. Altogether, our study identifies a functionally and molecularly distinct acinar subpopulation and thus transforms our understanding of the acinar cell compartment as a pool of equipotent secretory cells.

overall_design:
The single-cell RNA-seq library preparation protocol was based on the SMART seq2 protocol (Picelli et al., 2014) with following modifications.
Acinar cells were isolated as described in the section Acinar Cell Isolation and Culture and resuspended in DPBS without Ca2+ and Mg2+ (PAN-Biotech). Cells were collected in a volume of 0.5 μL and transferred to a reaction tube containing 4 μL of 6 M guanidine-HCl (Sigma-Aldrich), 0.1% (v/v) Triton X-100 (Sigma-Aldrich) and 1% (v/v) 2-mercaptoethanol (Sigma-Aldrich). The tube was immediately transferred into liquid nitrogen and kept there for the duration of cell collection. Next, 2.2× RNA SPRI beads (Beckman Coulter) were added directly to the lysis buffer and incubated for 5 min at room temperature. The beads were washed twice with 70% ethanol. Air-dried beads were resuspended in a solution containing 2 μL of H20, 1 μL of oligo(dT) primer, and 1 μL of dNTP Mix (primer and nucleotides used as in Picelli et al., 2014). Twenty-four cells contained ERCC Spike-In RNAs (1:10,000; Mix2, Ambion) Mix in addition to primer and nucleotides. Beads were incubated for 3 min at 72°C, and reverse transcription and PCR (19 cycles) were performed as described by Picelli et al. (2014). PCR product was cleaned up using 0.8× DNA SPRI beads (Beckman Coulter), and air-dried beads were resuspended in 15 μL of H2O. The quality of cDNA library was assessed for each cell on a high-sensitivity DNA Bioanalyzer chip. Subsequent steps (tagmentation, amplification, multiplexing) were done as previously described (Llorens-Bobadilla et al., 2015). The DKFZ Genomics and Proteomics Core Facility conducted sequencing on an Illumina HiSeq2000 sequencer (paired-end 100 bp).

first: Damian

last: Wollny

first: Sheng

last: Zhao


title: Metabolic inhibition of Clostridium thermocellum M1570 by pentose sugars.

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

summary: Differential RNA-Seq analyses to investigate the basis for metabolic inhibition of Clostridium thermocellum M1570 by xylose.   The M1570 strain was developed in the C. thermocellum DSM 1313 Δhpt background strain. Lactate dehydrogenase (Ldh) and phosphotransacetylase (Pta) genes are deleted (Argyros DA, Tripathi SA, Barrett TF, Rogers SR, Feinberg LF, Olson DG, Foden JM, Miller BB, Lynd LR, Hogsett DA, Caiazza NC: High ethanol titers from cellulose by using metabolically engineered thermophilic, anaerobic microbes. Appl Environ Microbiol 2010, 77:8288-8294 )

overall_design: Differential RNA-Seq analyses was used to investigate the basis for metabolic inhibition of Clostridium thermocellum M1570 by xylose. Cultures were grown in serum bottles containing 40 mL of MTC medium with or without 15 g/L xylose and were harvested at mid-exponential phase. Quadruplicate cultures were used for each experimental condition tested.

first: Tobin

last: Verbeke

first: James

last: Elkins

first: Steven

last: Brown


title: Remission for loss of odontogenic potential in a new micromilieu in vitro

first: Yunfei

last: Zheng

state: Beijing

address: 22 Zhongguancun Avenue South, Haidian District

department: Oral and Maxillofacial Surgery

institute: Peking University School and Hospital of Stomatology

summary: During embryonic organogenesis, the odontogenic potential resides in dental mesenchyme from the bud stage until birth. Mouse dental mesenchymal cells (mDMCs) isolated from the inductive dental mesenchyme of developing molars are frequently used in the context of tooth development and regeneration. cultured mDMCs could retain the odontogenic potential for 24 h with a ratio of 60% for tooth formation, but mDMCs were incapable of supporting tooth formation after more than 24 h in culture. To reveal the underlying mechanism of the impairment of odontogenic potential, we generated gene expression profiles from mDMCs in culture using RNA-seq.

overall_design: To determine the transcriptional regulation following in vitro culture, dMCs from developing molar germs in embryonic day 14.5 (E14.5) mouse embryos were isolated. The cells cultured for 12h, 24h, 36h, and 48h were isolated and RNA of these cells was extracted. Illumina-based high-throughput sequencing (Illumina, San Diego, CA, USA) was used to obtain the transcriptome profiles of D0, D0.5, D1, D1.5 and D2 cells


title: Genomic Targets and Features of BarA-UvrY (-SirA) Signal Transduction Systems

city: Gainesville

first: Anastasia

middle: Haley

last: Potts

state: FL

address: 1355 Museum Drive, Bldg. 981

department: Department of Microbiology and Cell Science

institute: University of Florida

summary: Using ChIP-exo, we have identified at single nucleotide resolution genomic binding sites for UvrY in E. coli and its homolog SirA in S. Typhimurium.

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

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: Two samples: (1) Genomic binding sites of UvrY (E. coli) (2) genomic binding sites of SirA (S. Typhimurium) were analyzed

first: Tesfalem

last: Zere

first: Christopher

middle: A

last: Vakulskas

first: Yuanyuan

last: Leng

first: Archana

last: Pannuri

first: Raquel

last: Dias

first: Dongjie

last: Tang

first: Bryan

last: Kolaczkowski

first: Dimitris

last: Georgellis

first: Brian

last: Ahmer

first: Tony

last: Romeo


title: Next Generation Sequencing of small non-coding RNAs in the tissue of patients with renal cell carcinoma

city: Bonnn

first: Jörg

last: Ellinger

state: NRW

address: Sigmund-Freud-Straße 25

department: Urologie

institute: Universitätsklinikum Bonn

summary: Non-coding RNAs play an important role in the pathogenesis of human malignancies. So far, microRNAs have been investigated in detail in clear cell renal cell carcinoma, but the knowledge about other small non-coding RNAs like snoRNA, tRNA and piRNA remains small. There is increasing evidence that these non-coding RNAs are also involved in  regulation of gene expression, and we therefore performed small RNA sequencing in a cohort of 18 corresponding normal and malignant tissue samples from patients with clear cell renal cell carcinoma. We observed differential expression of microRNAs, but also some dysregulated tRNA and snoRNA in clear cell renal cell carcinoma tissue

overall_design:
small RNA expression profiling in clear cell renal cell carcinoma and corresponding normal renal tissues samples
Please note that each 'ccRCC' sample is followed by the corresponding normal renal tissue sample. For example, the '2014_001_002' is the corresponding normal tissue for '2014_001_001' ccRCC sample, except the last two samples 2014_001_028 and 2014_001_029 are listed in an inverse order.

first: J

first: M

last: Nientiedt

first: D

last: Schmidt

last: Deng


title: Rb1+/+ versus Rb1ΔS/ΔS RNA Seq

first: Fred

last: Dick

summary: Upon G1-S transition, cyclin-dependent kinases (CDKs) phosphorylate  the retinoblastoma tumor suppressor protein (pRB) to release E2F transcription factors, which activate transcriptional programs, required for S-phase entry. Beyond the G1-S transition, pRB activity remains poorly understood. Our lab has discovered that hyperphosphorylated pRB (ppRB), found beyond G1, retains exclusive binding to E2F1 through an alternate E2F1-‘specific’ binding site at the pRB c-terminus. We have developed a gene-targeted mouse model that is defective for the E2F1-‘specific’ interaction. We are exploring the function of this complex through genome-wide expression profiling. Overall, this work suggests an alternate pRB-E2F1 complex persists beyond the G1-S transition to establish regions of constitutive heterochromatin.

overall_design:
1.     Total RNA from passage 4 quiescent MEFs isolated using TRIzol RNA extraction protocol
2.     rRNA was depleted from total RNA using the RiboMinus Euk System V2 protocol according to manufacturer’s procotol
3.     rRNA-depleted RNA samples were submitted for picoanalyzer analysis to determine concentration, purity, and rRNA content
4.     Three wild-type and three mutant RNA samples with <10% rRNA remaining were submitted for library construction
5.     Library was used for Illumina HiSeq 2500 paired end sequencing.

first: Frederick

first: Charles

last: Ishak

first: Aren

last: Marshall

first: Sara

last: Ferwati


title: CXCR4 regulates extra-medullary myeloma through epithelial-mesenchymal transition-like transcriptional activation

first: Aldo

last: Roccaro

address: 450 Brookline Av

institute: Dana-Farber Cancer Institute

summary: We have developed EMD- and BM-prone and defined the presence of an EMT-like mRNA signature in both EMD- and BM-prone clones.

overall_design: Evaluation of RNA sequencing of EMD- and BM-prone clones as compared to the parental cells the two clones were originated from.

first: Yuji

last: Mishima

first: Irene

last: Ghobrial


title: MicroRNA expression profiles of bovine milk exosomes in response to Staphylococcus aureus infection

city: beltsvill

first: jiajie

last: sun

address: 10300 BALTIMORE AVENUE

department: Agriculture research sevice

institute: U.S. department of agriculture

summary: Milk is an essential source of nutrients to all mammalian offspring, and is rich in a wide variety of immunological components. Recently reported miRNAs that are present in breast milk and are selectively packaged into the exosomes, a type of membrane vesicles, secreted by most cell types. These exosomal miRNAs could be actively delivered into recipient cells, and play a key role in the regulation of innate and adaptive immunity. In the present study we analyzed the lactation-related miRNA expression profiles in bovine milk exosomes at 2 days post-infection with Staphylococcus aureus (S. aureus) using a deep sequencing. Analyzing over 76.44 million sequencing reads, a total of 720 miRNAs including 303 high-confident miRNA candidates were identified by two different approaches. The top 10 highly expressed miRNAs accounted for approximately 80% of all aligned reads, with the remaining miRNAs showing much lower expression. Bta-miR-101, -142-5p, -183, -2285g-3p, -223 and -99a-5p were significantly differentially regulated in S. aureus infected milk compared to their uninfected controls. Target prediction of the differently expressed miRNAs revealed 219 potential target candidates, and 22 unique target genes identified by David Gene Ontology analysis were significantly related to host immune processes and inflammation. This new knowledge of milk miRNA expression in response to S. aureus infection significantly provides new and comprehensive information on milk miRNA composition in general as well as changes occurring during an infection.

overall_design: Four exosomal small RNA libraries were constructed from S. aureus infected bovine breast milk at 2 days post-infection (dpi), and correspondingly four libraries from bovine milk prior to infection were used as controls. They were named control (1, 2, 3 and 4) and infection (1, 2, 3 and 4), respectively.

first: Tad

last: Sonstegard

first: JIAJIE

last: SUN


title: Signaling to histone H3 for augmented transcription in the inflammatory response

city: New York

first: Steven

middle: Zvi

last: Josefowicz

address: 1300 York Ave, Box 69

department: Laboratory of Epigenetics and Immunity

institute: Weill Cornell Medicine

summary: The inflammatory response depends upon selective, rapid transcription initiation and high-level generation of gene products for defense against pathogens and environmental insult1,2. Kinase cascades are broadly employed for rapid transmission of extracellular information, thereby regulating the cell’s environmental response. These pathways play a prominent role in the inflammatory process. Several kinases directly phosphorylate histone proteins in chromatin, representing a mechanism for the rapid modification of chromatin with the potential to regulate selective transcription responses to environmental cues3-10. However, the molecular functions of specific histone phosphorylation events in transcription are poorly understood. Here, we demonstrate a direct effect of histone H3 phosphorylation at serine 28 (H3S28p) on transcription activation and describe a prominent role for H3S28p in the amplification of inflammatory gene transcription following stimulation of mouse macrophages with bacterial lipopolysaccharide (LPS). We identify MSK kinases as the non-redundant kinases that mediate the rapid, stimulation-dependent deposition of H3S28p on chromatin. Pharmacological approaches, including the use of a novel chemical agent, reveal that MSK inhibition abolishes stimulation-dependent accumulation of H3S28p at LPS-induced genes and reduces production of inflammatory gene products. Mechanistically, H3S28p directly increases transcriptional output by augmenting recruitment of the transcription co-activator and histone acetyltransferase (HAT) p300, and increasing its HAT activity. Our results reveal a delegated role for H3S28p in selective augmentation of transcription during the rapid cellular response to environmental cues.

overall_design: Primary mouse bone marrow derived macrophages (BMDM) were used for NGS experiments. Briefly, BMDM were used unstimulated or following stimulation with S. typhosa LPS (100ng/mL) for the indicated period of time. Included in this submission are RNA-seq data for control DMSO treated BMDM (60' and 120' LPS stimulation), RMM-64 (5 uM) treated (60’ and 120’), SB747651A (5 uM) treated (60’ and 120’), and C646 (37.5 uM) teated (60’ and 120’). Further, ChIP-seq data for H3S28p time-course in BMDM stimulated with LPS includes one file each for 0’, 30’, 60’, 120’, 180’, 240’, and one file each at 0’ and 30’ for control DMSO treated, RMM-64 treated, SB747651A treated, and C646 treated BMDM. Also provided is an H3K27ac ChIP-seq time course in LPS stimulated BMDM: 0’, 30’, 120’, 180’, 240’.

middle: Z


title: XH lncRNA tend to participate in transcriptional or development regulations as their coding neighbors

first: jinlong

last: lu

address: 213 Hutchinson Hall

institute: University of Rochester

summary: We report that head to head long noncoding RNAs contribute to transcription and developmental process. Thousands of lncRNAs have been identified in the whole genome, and classified to several subgroups based on the genome position with their coding neighbors. XH, the head to head subgroup is associated with transcription and development in GO analysis. Here, we knockdown serveral XH lncRNA by shRNA in embryonic stem cells and induce nondirectional differentiation by removing LIF or neural differentiation by RA. Knockdown of XH lncRNAs led to uniform downregulation of nearby coding genes, and form regulatory circuits with its nearby coding genes to fine-tune embryonic lineage development. We propose that XH lncRNA may function primarily as 'cis-regulators' of the expression of nearby protein-coding genes, and tend to participate in transcriptional or development regulations as their coding neighbors.

overall_design: All RNA-seq(s) were designed to reveal the differentially expressed genes between wild-type or XH lncRNA knockdown ESCs during differentiation.

first: Sai

last: Luo

first: Jinlong

last: Lu

first: Xiaohua

last: Shen


title: Global loss of epigenetic and transcriptional fidility defines a subclass of cancer with immunotherapy resistance

status: Public on Oct 30 2016

city: Cincinnati

first: Kakajan

last: Komurov

state: Ohio

address: 3333 Burnet Ave

department: Experimental Hematology and Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: We report that some cancers have extensive loss of epigenetic and transcriptional fidelity, characterized widespread spurious transcription and mRNA processing defects (Loss of transcriptional fidelity: LTF+). LTF impairs transcriptional elongation and imposes a highly specific molecular phenotype where pathways regulated by long genes, such as those involved in inflammatory response are consistently impaired in LTF+ tumors. Accordingly LTF blunts inflammatory response and confers resistance to immune mediated anti-tumor attack, and correlates with poor response to immunotherapeutic drugs in renal cell carcinoma and melanoma patients. We show that genetic or chemical perturbation of gene body histone methylation or of transcriptional elongation can recapitulate LTF-like phenotype, imposing resistance to immune-mediated anti-tumor mechanisms in-vitro and in-vivo.

overall_design: Using single end RNAseq we examine the gene expression profile of 6 cell lines

first: Navneet

last: Singh

first: Vishnu

last: Modur

first: Vakul

last: Mohanty

first: Kwangmin

last: Choi

first: Yunzhu

last: Dong

first: Xiaoting

last: Chen

first: Kashish

last: Chetal

first: Nancy

last: Ratner

first: Nathan

last: Salomonis

first: Matthew

middle: T

last: Weirauch

first: Susan

last: Waltz

first: Edith

last: Janssen

first: Gang

last: Huang

first: Lisa

last: Privette-Vinnedge


title: The gene expression kinetics reveals a key role of jasmonic acid in rice disease resistance to Magnaporthe

first: Mengdi

last: Liu

address: No.38 Xueqing Road, Haidian District

institute: Novogene institute

summary: In rice, a number of resistance (R) genes that counter the blast fungus, Magnaporthe oryzae, have been cloned, but the mechanism by which they trigger disease resistance remains elusive. This is in part due to a lack of comprehensive transcriptome analyses during the resistance or disease progression. Here, we monitored the gene expression profiling in rice during its interactions with Magnaporthe by time-series transcriptome analyses. Distinct from previous studies, we focused on early infection stages within 24 hours post-inoculation. A comparison of those expression changes revealed a general difference in gene expression kinetics between compatible and incompatible interactions, and pointed to that the time when the pathogen just establishes its penetration into rice cells is a key point for the expressional changes. Such conclusions originated from the R gene Pid3-mediated immune responses were validated in the R gene Pi9-mediated responses, suggesting common molecular processes are shared by different R-mediated blast immunity. Our data highlighted the role of jasmonic acid (JA)-triggered signaling pathway (JA pathway) in the hormone signaling network for rice blast resistance. We confirmed that both exogenous and endogenous JA can induce the expression of many defense-related components revealed in above transcriptomic analyses and proved that the knock-down of OsCOI1 which encodes a JA receptor may deprive rice of the blast resistance mediated by R genes. Therefore, it is concluded that JA pathway plays an essential role in the establishment of blast resistance by modulating the expression of other defense-related components.

overall_design: We focused on early infection stages within 24 hours post-inoculation, the time when the pathogen just establishes its penetration into rice cells is a key point for the expressional changes. A comparison of kinetics gene expression changes between compatible and incompatible interactions.

first: L

last: Zhu

first: Z

middle: Q

last: Pang


title: Global analysis of selenoprotein expression reveals differential roles for Secisbp2 in UGA redefinition and mRNA stabilization

city: Salt Lake City

first: Michael

last: Howard

state: UT

department: Human Genetics

institute: University of Utah

summary: We describe the effects of knocking out the Secisbp2 and Trsp genes on selenoprotein expression and translation in mouse liver

overall_design: Livers from wild type mice and mice that were deleted for the Secisbp2 or Sec-tRNA (Trsp) genes (conditional deletion in hepatocytes) were harvested and processed for RNA-Seq and ribosome profiling. RNA-Seq was used to monitor mRNA abundance and ribosome profiling was used to monitor translation initiation and UGA-Sec redefinition efficiency.


title: RNA-binding profiles of Drosophila CPEB proteins Orb and Orb2

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

summary: Localized protein translation is critical in many biological contexts, particularly in highly polarized cells, such as neurons, to regulate gene expression in a spatiotemporal manner. The cytoplasmic polyadenylation element-binding (CPEB) family of RNA-binding proteins has emerged as a key regulator of mRNA transport and local translation required for early embryonic development, synaptic plasticity, and long-term memory (LTM). Drosophila Orb and Orb2 are single members of the CPEB1 and CPEB2 subfamilies of the CPEB proteins, respectively. At present, the identity of the mRNA targets they regulate is not fully known, and the binding specificity of the CPEB2 subfamily is a matter of debate. Using transcriptome-wide UV cross-linking and immunoprecipitation, we define the mRNA-binding sites and targets of Drosophila CPEBs. Both Orb and Orb2 bind linear cytoplasmic polyadenylation element-like sequences in the 3′ UTRs of largely overlapping target mRNAs, with Orb2 potentially having a broader specificity. Both proteins use their RNA-recognition motifs but not the Zinc-finger region for RNA binding. A subset of Orb2 targets is translationally regulated in cultured S2 cells and fly head extracts. Moreover, pan-neuronal RNAi knockdown of these targets suggests that a number of these targets are involved in LTM. Our results provide a comprehensive list of mRNA targets of the two CPEB proteins in Drosophila, thus providing insights into local protein synthesis involved in various biological processes, including LTM.

overall_design: PAR/iCLIP was performed in Orb or Orb2 transfected S2 cells with high-throughput sequencing in 4 to 7 replicates, two replicates of background mRNAseq of untransfected and Orb2-transfected S2 cells were done. B-isoxasole precipitation and RNA-Seq from both pellet and supernatant fractions were made.

first: Barbara

middle: K

last: Stepien

first: Cornelia

last: Oppitz

first: Ugur

last: Dag

first: Maria

last: Novatchkovaa

first: Sebastian

last: Krüttner

first: Alexander

last: Stark

first: Krystyna

last: Keleman


title: RNAseq and ChIPseq profiling of Foxn4 and Foxj1 in multiciliated cells

status: Public on Oct 29 2016

city: La Jolla

first: Ian

last: Quigley

state: CA

address: 10010 North Torrey Pines Road

department: Molecular Neurobiology Lab

institute: Salk Institute

summary: Foxn4 and Foxj1 are expressed in multiciliated cells. Here, we dissect their role with knockdowns using two different technologies (morpholinos and CRISPR) and examine Foxn4 genomic binding sites in wild-type tissue and tissue converted entirely into multiciliated cells.

overall_design: To examine Foxn4 and Foxj1's effect on multiciliated cells, we knocked them down in tissue where we also overexpressed an inducible form of multicilin (also known as mcidas; Stubbs et al., 2012). After injecting, we isolated ectoderm surgically and, when injected with multicilin, induced at mid-stage 11. We then harvested RNA or chromatin at 9 hours after induction, roughly corresponding to stage 18 and performed poly-a+  RNAseq (Illumina Truseq v2) or ChIPseq. We then aligned reads to X. laevis gene models (Mayball version, Chung and Kwon et al. 2014) or the genome (v7.1) and determined differential expression or binding targets. To determine differential expression, we compared RNAseq reads from ectoderm isolated from embryos injected with multicilin alone, as reported in Ma et al. 2014 (PMID: 24934224, NCBI GEO:GSE59309) with samples here injected with multicilin and Foxn4 or Foxj1 perturbations.

first: Chris

last: Kintner


title: Transcriptional profiling of post-positive selection thymocytes from HOIL- and SHARPIN-deficient mice

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Mice lacking components of the linear ubiquitin chain assembly complex (LUBAC) exhibit defects in thymocyte differentiation. To determine how two LUBAC components, HOIL and SHARPIN, mediate their effects, we purified thymocytes from CD4Cre Hoil-fl/fl or Sharpin-cpdm mice and compared their transcriptional profile to WT controls. We focused on the CD69+ MHCI low and CD69+ MHCI high subsets that follow positive selection.

overall_design: Thymocytes were prepared from 3 wildtype mice, 3 Cd4Cre Hoil-floxed mice and 3 Sharpin-cpdm mutant mice. CD69+ MHC I high and CD69+ MHC I low cells from each mouse were FACS purified on a MoFlo cell sorter.

last: Gray

first: Yifang

last: Hu


title: Transcriptional response of small-intestinal lamina propria CD4+ T cells to bacterial colonization

status: Public on Oct 28 2016

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

summary: We analyzed the transcriptional profile of small-intestinal lamina propria (SI-LP) CD4+ T cells isolated from germ-free and mice monocolonized with Bifidobacterium adolescentis, SFB, and Nexabiotic (a 23-strain, Th17-inducing, probiotic mix).

overall_design: CD4+ T cells were double-sorted from mice directly into lysis buffer.

first: Tze

middle: G

last: Tan

first: Naama

last: Geva-Zatorsky

first: Esen

last: Sefik

first: Lindsay

last: Kua

first: Debdut

last: Naskar

first: Fei

last: Teng

first: Lesley

last: Pasman

first: Adriana

last: Ortiz-Lopez

first: Ray

last: Jupp

first: Hsin-Jung

last: Wu

first: Dennis

middle: L

last: Kasper

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: RNA-seq analysis of a Streptococcus pyogenes mutant lacking the eukaryote-type ser/thr phosphatase (SP-STP)

city: Columbus

first: Vijay

last: Pancholi

state: OH

address: 420W 12th Ave, TMRF-288

department: Pathology

institute: Ohio State University

summary: We report the mRNA expression profile of Streptococcus pyogenes Type M1 strain M1T15448-derived mutant lacking Serine threonine phosphatase.

overall_design: Measuring transcriptome profiling in M1T1DSTP mutants vs M1T1-WT  5448 strain


title: The Epigenetic Landscape of T Cell Exhaustion

first: James

middle: John

last: Kaminski

address: 1 Blackfan Circle

department: Hematology / Oncology

institute: Boston Children's Hospital

summary: We used ATAC-Seq to define the accessible chromatin landscape in exhausted CD8+ T cells, showed that it is distinct from functional memory CD8+ T cells, and identified an exhaustion-specific enhancer of PD-1. In addition to the murine T cell data, we will provide the ATAC-Seq data used from human T cells in the paper.

overall_design: 10 ATAC-Seq samples from mouse CD8+ cells, two replicates for each of the following conditions [Naive, 8 days after acute LCMV infection, 27 days after acute LCMV infection, 8 days after chronic LCMV infection, 27 days after chronic LCMV infection]. 2 ATAC-Seq samples from EL4 cell line. 19 ATAC-Seq samples of T cells from human patients will be made available in an appropriate NCBI database.

first: Debattama

last: Sen


title: A commonly inactivated tumor suppressor silences endogenous retroelements in somatic cells [ChIP-Seq]

city: London

first: Fred

last: Dick

address: Cancer Research Labs 790 Commissioners Road East

institute: Western University

summary: Upon G1-S transition, cyclin-dependent kinases (CDKs) phosphorylate the retinoblastoma tumor suppressor protein (pRB) to release E2F transcription factors, which activate transcriptional programs, required for S-phase entry. Beyond the G1-S transition, pRB activity remains poorly understood. Our lab has discovered that hyperphosphorylated pRB (ppRB), found beyond G1, retains exclusive binding to E2F1 through an alternate E2F1-‘specific’ binding site at the pRB c-terminus. We have developed a gene-targeted mouse model that is defective for the E2F1-‘specific’ interaction. We are exploring the function of this complex through genome-wide expression profiling. Overall, this work suggests an alternate pRB-E2F1 complex persists beyond the G1-S transition to establish regions of constitutive heterochromatin

overall_design: Chromatin was isolated from passage 4 MEFs cross-linked with ethylene glycol bissuccinimidylsuccinate (EGS) and formaldehyde, and then sonicated to ≤ 400 bp. DNA fragments were immunoprecipitated using different antibodies, washed, then purified. DNA was prepared for sequencing according to the Illumina TruSeq protocol. Each protein immunoprecipitated includes one wild-type replicate as reference, and one replicate per mutant genotype assayed.

first: Frederick

first: Charles

last: Ishak

first: Aren

last: Marshall


title: Modulation of immunomodulatory peptide activity by 2-deoxy-d-glucose

city: Vancouver

first: Erin

last: Gill

state: British Columbia

address: 2259 Lower Mall

institute: University of British Columbia

summary: The goal of this study was to identify the role of glycolysis in the activity of immunomodulatory peptides with respect to macrophage function using the glycolytic inhibitor 2-deoxy-d-glucose

overall_design: Primary human monocyte derived macrophages were treated with 2-deoxy-d-glucose, the immunomodulatory peptide IDR-1018 or a combination of the two for 4 hours. Control samples of untreated macrophages were included. The study was completed in tripiclate (three independent, healthy donors).

first: Nicole

last: Afacan

first: Reza

last: Falsafi

first: Robert

last: Hancock


title: Network dynamics mediate circadian clock plasticity

city: Zurich

first: Steven

last: Brown

state: Switzerland

address: Winterthurerstrasse 190

department: Institute of Pharmacology and Toxicology

institute: University of Zurich

summary:
Purpose: Alteration in light dark cycle leads to changes in daily behavior in mammals. We have previously demonstrated that different light:dark cycle lengths result in dynamic changes in DNA methylation within the suprachiasmatic nuclei (SCN) that globally alter transcription of both clock genes and non-clock genes. The goal of this study was to re-examine DNA methylation in the SCN separately for dorsal and ventral regions.
Method: Six-week-old wild-type mice (C57BL/6Cr1) were entrained to light:dark cycles either 22, 24, or 26 hours in length (T22, T24, or T26) for six weeks. After 6 weeks, we recorded wheel-running behavior in constant darkness. After 3 days in DD, we used Clocklab software to predict time of activity onset for each mouse. Brains were isolated at the circadian time CT4 and then sliced immediately using vibratome, one coronal SCN slice of ~250μM was collected from the middle part of the SCN. Using ophthalmic knife vSCN and dSCN sub-regions were separated.  To get enough DNA, a pool of vSCN and dSCN was prepared twice from 5 mice from each T-cycle.
Genomic DNA was extracted from SCN slices by overnight Proteinase K digestion, followed by phenol-chloroform and ethanol precipitation. After RNase treatment, genomic DNA was sonicated to generate small fragments (average of 300bp), using a Covaris sonicator (BioRuptor). DNA immunoprecipitation was performed using Epiquik™ MeDIP Ultra Kit (EPIGENTEK™), following manufacturer's instructions. The methylated enriched DNA was then used for library preparation using Accel-NGS™ DNA Library Kits (Swift Biosciences), following manufacturer's instructions. Quality check, library preparation and sequencing were performed by Fasteris (CH).
Results: 13-21 x 10^6 reads were obtained from each meDIP library. Quality control was performed on the fasta raw sequence data using FastQC.MeDIP-seq data were aligned to the mm9 mouse genome build using the Burrows-Wheeler Alignment tool (BWA) (Li and Durbin, 2009). Mapped reads were than analyzed using the MEDIPS package (Lienhard et al., 2014). Methylation score was calculated for each region of 500bp across the genome.  CpG density-dependent normalization was incorporated.  Pairwise correlation analysis of the genome wide coverage profile between MEDIP replicate samples was performed using the MEDIPS.correlation function. Pearson correlation coefficient r varied between 0.85 and 0.92, indicating good reproducibility of MEDIP-seq signal. Differential methylation analysis was performed using MEDIPS in 500bp widows excluding regions with less than 8 unique mapped reads. DMR were than identified by filtering for a widows associated with a p ≤0.001. DMR were than mapped using the web based chip-seq tool “ChIPseek”  (Chen et al., 2014). Different sets of genes showed methylation changes in dorsal vs. ventral regions. Interestingly, far greater changes were observed in vSCN than in dSCN.

overall_design: MEDIP-seq profile of the suprachiasmatic nuclei (SCN) isolated from mice entrained to different light-dark cycle. Samples were generated by deep sequencing, in duplicates, using Illumina HiSeq 2500.

first: Abdelhalim

last: Azzi

first: Jennifer

last: Evans

first: Tanya

last: Leise

first: Jihwan

last: Myung

first: Toru

last: Takumi

first: Alec

last: Davidson


title: Effect of Aire deficiency on peripheral Tgd17 gene expression

first: CBDM

last: Lab

institute: Harvard Medical School

summary: We examine the transcriptional profile of lung Tgd17 cells from mice that are deficient for Aire compared to wild-type mice.

overall_design: Duplicate samples of 500 sorted lung resident CD27- Vg1,2,4,5- gd T cells from

first: Alexander

middle: O

last: Mann

first: Christophe

last: Benoist

first: Diane

last: Mathis