title: A CpG island methylator phenotype in acute myeloid leukemia independent of IDH mutations and associated with a favorable outcome

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

summary: Acute myeloid leukemia (AML) causes the most leukemia-related deaths in the United States. Although genetic changes are assessed in the clinic for risk stratification, current classifications are imperfect and epigenetic determinants of AML curability remain poorly understood. To address this gap in knowledge we performed genome-wide DNA methylation analysis using the next-generation sequencing-based Digital Restriction Enzyme Analysis of Methylation (DREAM) assay on 96 clinical AML samples, and 35 normal peripheral blood controls. We identified patterns of aberrant DNA hypermethylation in distinct subsets of cases, and these patterns were associated with unique clinical, and genetic features. Validation an extension of these findings was performed using 194 samples from The Cancer Genome Atlas (TCGA).

overall_design: Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the methylation profile of human genomic DNA from the bone marrow of 96 patients with acute myeloid leukemia (AML) and peripheral blood from 35 healthy controls. Briefly, genomic DNA was sequentially digested by SmaI and XmaI, which both recognize the sequence CCCGGG. SmaI is methylation sensitive, where XmaI is methylation insensitive. Distinct signatures, 5’-GGG at unmethylated sites or 5’-CCGGG at methylated sites were created by enzyme digestion and ultimately high througput sequencing was used to map these sites to the genome. Methylation ratios for each individual CCCGGG site were calculated as a proportion of methylated counts to the sum of unmethylated and methylated counts, and subsequently adjusted for differences in restriction enzyme efficiency using values obtained from spiked in standards.

first: Andrew

last: Kelly

first: Heike

last: Kroeger

first: Jumpei

last: Yamazaki

first: Rodolphe

last: Taby

first: Frank

last: Neumann

first: Sijia

last: Yu

first: Justin

middle: T

last: Lee

first: Bela

last: Patel

first: Rong

last: He

first: Shoudan

last: Liang

first: Yue

last: Lu

first: Matteo

last: Cesaroni

first: Sherry

last: Pierce

first: Steven

last: Kornblau

first: Carlos

last: Bueso-Ramos

first: Farhad

last: Ravandi

first: Hagop

last: Kantarjain

first: Jean-Pierre

last: Issa


title: Satb1 Orchestrates the Expression of Lineage-Specifying Genes in Post-Selection Thymocytes

status: Public on Jan 19 2017

city: San Francisco

first: Hunter

last: Richards

state: CA

address: 513 Parnassus Ave., HSW 863

department: Orofacial Sciences

country: USA

institute: UCSF

type: Genome binding/occupancy profiling by high throughput sequencing

summary: T-cell receptor (TCR) signaling by MHC class-I and -II induces thymocytes to acquire cytotoxic and helper fates via induction of Runx3 or ThPOK transcription factors, respectively. The mechanisms by which TCR signaling is translated into transcriptional programs for each cell fate remain elusive. We show that a genome organizer, Satb1, activates genes for lineage-specifying factors, including ThPOK and Runx3, in post-selection thymocytes. Indeed, Satb1-deficient thymocytes are partially redirected to inappropriate T lineages after MHC selection. Although Satb1 is dispensable for maintaining ThPOK in CD4+ T cells, it is necessary for restraining expression of the Treg factor FoxP3. Collectively, our findings demonstrate that Satb1 shapes the primary T-cell pool by initially directing lineage-specific transcriptional programs and subsequently balancing effector versus regulatory subsets via FoxP3 repression.

overall_design: sequencing of Satb1-ChIP and input control from 6 wk old thymus

middle: W

first: Ichiro

last: Taniuchi


title: RNA-seq of major tissues and xylem cell types of Populus trichocarpa

city: Raleigh

first: Vincent

middle: L

last: Chiang

state: NC

address: 840 Main Campus Drive

department: Forestry and Environmental Resources

institute: North Carolina State University

type: Expression profiling by high throughput sequencing

summary: We used the stem cross-sections of P. trichocarpa and our recently developed laser capture microdissection (LCM) to collect fibers, vessels, and a combination of 3 cell types (fibers + vessels + rays). Total RNA from the three samples was isolated, amplified, and analyzed by full-transcriptome RNA-sequencing. The sequencing reads were mapped to the P. trichocarpa genome.

overall_design: Different major tissues (shoot tip, leaf, phloem, primary root, stem differentiating xylem) and xylem tissue cell types (fiber, vessel, ray cells) were analyzed by RNA-seq.

first: V


title: Profiling in vivo Bone Lesion and ex vivo Bone-In-Culture Array Samples by Next-Generation Sequencing

status: Public on Jan 20 2017

city: Buffalo

first: Hai

last: Wang

state: NY

address: Elm and Carlton Streets, MRC 328

department: Molecular and Cellular Biology

institute: Roswell Park Cancer Institute

summary: Based on RNA-seq, we performed transcriptomic profiling to examine the similarities or differences between BICA (bone-in-culture array) and IVBL (in vivo bone lesion). CIBERSORT analysis reveals that the major local cellular components are comparable between BICA and IVBL, but differ dramatically in orthotopic tumors. Principle component analysis of human RNAs indicated that the transcriptomic profiles of cancer cells in BICA are more closely mimicking IVBL, as compared to cancer cells in 2D and in orthotopic tumors. These results provide transcriptome-wide evidence supporting BICA as a platform to mimic bone microenvironment.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 2D culture cells, orthotopic tumors, BICA samples and bone lesions, all developed by MCF-7, are subject to NGS and then analyzed.

first: Xiang

last: Zhang

first: Lin

last: Tian


title: Differentially expressed genes in longissimus dorsi by RNA-Sequencing in goats at different postnatal stages

city: Chengdu

first: Jiangjiang

last: Zhu

state: Sichuan

address: #16, South Section, 1st Ring Road

department: Institute of Qinghai-Tibetan Plateau

country: China

institute: Southwest Uniersity for Nationalities

summary: Intramuscular fat (IMF) and its fatty acid composition in longissimus dorsi muscle (LM) are changed along with the growth of age, which partly determines the flavor and nutritional value of goat meat. However, unlike cattle, there is few data available on the transcriptome-wide changes at different postnatal stages in small ruminants specially for goats. In this study, the transcriptome by RNA sequencing of goat LM tissues collected from kid, youth and adult period were mapped to goat genome. Out of a total of 24689 unigenes, 20435 unigenes were annotated. Based on FPKM a total of 111 annotated differentially expressed genes (DEG) were identified among different postnatal stages, which was then classified to 16 possible expression patterns by series-cluster analysis. Functional classification through GO was used for selecting the top expressed genes related to lipid metabolism. Using co-expression analysis, we identified the node genes for lipid metabolism regulation. In conclusion, these data may provide candidate genes with high probability of having functional roles in regulating goat IMF deposition during the various growth stages.

overall_design:
Examination of the differentially expressed genes in longissimus dorsi by RNA-Sequencing in goats at different postnatal stages
Muscle transcriptome of goat three stages_SRP068688

first: Yaqiu

last: Lin


title: Jmjd2c/Kdm4c facilitates the assembly of essential enhancer-protein complexes at the onset of embryonic stem cell differentiation

status: Public on Jan 18 2017

city: London

first: Rute

middle: A.

last: Tomaz

state: London

address: IRDB, Imperial College, Hammersmith Campus, Du Cane Road

country: United Kingdom

institute: Imperial College London

summary:
Jmjd2/Kdm4 H3K9-demethylases cooperate in promoting mouse embryonic stem cell (ESC) identity. However, little is known about their importance at the exit of ESC pluripotency. Here, we uncover that Jmjd2c facilitates this process by stabilizing the assembly of Mediator-Cohesin complexes at lineage-specific enhancers.
Functionally, we show that Jmjd2c is required in ESCs to initiate appropriate gene expression programs upon somatic multi-lineage differentiation. In the absence of Jmjd2c, differentiation is stalled at an early post-implantation epiblast-like stage, while Jmjd2c-knockout ESCs remain capable of forming extra-embryonic endoderm derivatives.
Dissection of the underlying molecular basis revealed that Jmjd2c is re-distributed to lineage-specific enhancers during ESC priming for differentiation. Interestingly, Jmjd2c-bound enhancers are co-occupied by the H3K9-methyltransferase G9a/Ehmt2, independently of its H3K9-modifying activity.
Loss of Jmjd2c abrogates G9a recruitment and furthermore destabilizes loading of the Mediator and Cohesin components Med1 and Smc1a at newly activated and poised enhancers in ESC-derived epiblast-like cells. These findings unveil Jmjd2c-G9a as novel enhancer-associated factors, and implicate Jmjd2c as a molecular scaffold for the assembly of essential enhancer-protein complexes with impact on timely gene activation.

overall_design: Flag ChIP was performed for identification of Flag-Jmjd2c binding sites in mouse ES cells cultured in either naïve (2i/LIF) or primed (serum/LIF) conditions.

middle: A

first: Jennifer

last: Harman

first: Donja

last: Karimlou

first: Lauren

last: Weavers

first: Lauriane

last: Fritsch

first: Tony

last: Bou-Kheir

first: Emma

last: Bell

first: Ignacio

last: del Valle Torres

first: Kathy

middle: K

last: Niakan

first: Cynthia

last: Fisher

first: Onkar

last: Joshi

first: Hendrik

middle: G

last: Stunnenberg

first: Edward

last: Curry

first: Slimane

last: Ait-Si-Ali

first: Helle

middle: F

last: Jørgensen

first: Véronique

last: Azuara


title: The mammalian LINC complex controls mechanosensing at a genome-wide level: miRNA-sequencing

city: Gainesville

first: Tanmay

last: Lele

state: FL

address: Bldg 723, Room 329

department: Chemical Engineering

institute: University of Florida

type: Non-coding RNA profiling by high throughput sequencing

summary: Mechanical cues influence the shape, growth, and function of tissues and organs and are necessary for the development of engineered tissues. Yet, how cells sense mechanical cues and transduce them into changes in gene expression is not well understood. It is known that mechanical forces transmitted to the nucleus induce chromatin remodeling, promote DNA repair, contribute to the motion of intranuclear organelles and cause direct dissociation of protein complexes inside nuclei. Yet, the extent to which such signals impact gene expression is not understood. Because mechanical forces from the cytoskeleton to the nucleus interior are transmitted by the LINC (linker of nucleoskeleton-to-cytoskeleton) complex, we disrupted the LINC complex and performed genome wide expression studies using RNA sequencing. LINC disruption altered the expression of hundreds of genes at a genome-wide scale. We asked how LINC disruption affected the mechanosensitivity of individual genes by quantifying fold changes in gene expression on soft and stiff substrates. Remarkably, LINC disruption tended to preserve gene mechanosensitivity, but to reverse its direction. LINC disruption did not cause changes in nuclear shape, nor eliminated nuclear shape sensitivity to substrate rigidity. Our results show for the first time that the LINC complex regulates mechano-sensing at a genome-wide level, and argue for a distinct mechanism that does not require changes in nuclear morphology.

overall_design: MicroRNA profiles of NIH 3T3 TetON cells that were induced to express either SS-GFP-KDEL (control) or SS-HA-Sun1L-KDEL by the addition of doxycycline. Two (2) substrate stiffnesses were used (1 kPa and 308 kPa), Y27632 or blebbistatin was used for certain samples to inhibit myosin II activity. A total of 6x3 reps= 18 samples were analyzed.

first: Samer

last: Alam

first: Qiao

last: Zhang

first: Nripesh

last: Prasad

first: Yuan

last: Li

first: Srikar

last: Chamala

first: Ram

last: Kuchibhotla

first: K

last: Cbirendra

first: Shawn

last: Levy

first: Jeffrey

last: Nickerson

first: Kyle

last: Roux


title: Pooled CRISPR screening with single-cell transcriptome read-out

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

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

summary: We combined CRISPR genome editing with single-cell RNA sequencing to assess complex phenotypes in pooled cellular screens. Our method for CRISPR droplet sequencing (CROP-seq) comprises four key components: a gRNA vector that makes individual gRNAs detectable in single-cell transcriptomes, a high-throughput assay for single-cell RNA-seq, a computational pipeline for assigning single-cell transcriptomes to gRNAs, and a bioinformatic method for analyzing and interpreting gRNA-induced transcriptional profiles. CROP-seq allowed us to link gRNA expression to the associated transcriptome responses in thousands of single cells using a straightforward and broadly applicable screening workflow. Additional information are available from the CROP-seq website http://crop-seq.computational-epigenetics.org

overall_design:
Drop-seq species mixing experiment was performed with human HEK293T and mouse 3T3 cells in a 1:1 proportion as described by Macosko et al.

For CROP-seq, Jurkat cells were transduced with a gRNA library targeting high-level regulators of T cell receptor signaling and a set of transcription factors. After 10 days of antibiotic selection and expansion, cells were stimulated with anti-CD3 and anti-CD28 antibodies or left untreated. Both conditions were analyzed using CROP-seq, measuring TCR activation for each gene knockout. Our dataset comprises 5,905 high-quality single-cell transcriptomes with uniquely assigned gRNAs.

All CROP-seq raw data files are multiplexed with single-cell reads. Each read 1 contains the cell barcode (12 bp) and a molecule barcode (8 bp) and read 2 contains the transcriptome read. The libraries are pooled by nature but also intrinsically labelled. The file CROP-seq_Jurkat_TCR.digital_expression.csv.gz contains gene level expression quantifications of each gene for each cell which corresponds to the cell barcode in read1.

For the Drop-seq_HEK293T-3T3 sample (Drop-seq species mixing), reads aligning to two genomes were used to quantify for each cell barcode the amount of reads coming from each genome. In a similar way, in the CROP-seq_HEK293T sample (CROP-seq gRNA mixing), the number of gRNA molecules detected per cell barcode (which is possible due to the polyadenylation of these gRNA-containing transcripts when expressed from a Pol2 promoter as engineered) were counted.

first: Paul

last: Datlinger

first: André

last: Rendeiro

first: Christian

last: Schmidl

first: Thomas

last: Krausgruber

first: Peter

last: Traxler

first: Johanna

last: Klughammer

first: Linda

middle: C

last: Schuster

first: Amelie

last: Kuchler

first: Donat

last: Alpar


title: Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex (ChIP-seq)

city: Chapel Hill

first: Gary

last: Johnson

address: 4009 Genetic Medicine Building, 120 Mason Farm Road

department: Pharmacology

institute: University of North Carolina School of Medicine

summary: Targeting the dysregulated BRaf-MEK-ERK pathway in cancer has increasingly emerged in clinical trial design. Despite clinical responses in specific cancers using inhibitors targeting BRaf and MEK, resistance develops often involving non-genomic adaptive bypass mechanisms.   Inhibition of MEK1/2 by trametinib in triple negative breast cancer (TNBC) patients induced dramatic transcriptional responses, including upregulation of receptor tyrosine kinases (RTKs) comparing tumor samples before and after one week of treatment.  In preclinical models MEK inhibition induced genome-wide enhancer formation involving the seeding of BRD4, MED1, H3K27 acetylation and p300 that drives transcriptional adaptation.  Inhibition of P-TEFb associated proteins BRD4 and CBP/p300 arrested enhancer seeding and RTK upregulation. BRD4 bromodomain inhibitors overcame trametinib resistance, producing sustained growth inhibition in cells, xenografts and syngeneic mouse TNBC models.  Pharmacological targeting of P-TEFb members in conjunction with MEK inhibition by trametinib is an effective strategy to durably inhibit epigenomic remodeling required for adaptive resistance.

overall_design: 44 experimental samples analyzed, one chromatin input control sample for each cell line

first: Jon

middle: S

last: Zawistowski


title: The genome-wide transcriptional response to varying RpoS levels in Escherichia coli.

city: Claremont

first: Daniel

last: Stoebel

address: 301 Platt Blvd

department: Biology

institute: Harvey Mudd College

summary: We varied RpoS levels using a mutation or an arabinose-inducible RpoS construct during stationary phase in rich media. We then sequenced cDNA from three separate RpoS levels, corresponding to 0%, 26% and 100% of wild-type levels.

overall_design: Two replicates at each of the three RpoS levels.

middle: M


title: Syntrophic interactions within the multi-species exoelectrogenic biofilm community in bio-electrochemical systems

city: Karlsruhe

first: Andreas

last: Doetsch

address: Haid-und-Neu-Str. 9

department: Physiology and Biochemistry of Nutrition

country: Germany

institute: Max Rubner-Institute

summary: Anode-associated multi-species exoelectrogenic biofilms are essential to the function of bioelectrochemical systems (BESs). The investigation of electrode-associated biofilms is critical to advance understanding of the function of individual members within communities that thrive using an electrode as the terminal electron acceptor. This study focusses on the analysis of a model biofilm community consisting of Shewanella oneidensis, Geobacter sulfurreducens and Geobacter metallireducens. The conducted experiments revealed that the organisms can build a stable biofilm on an electrode surface that is rather resilient to changes in the redox potential of the anode surface. The community operated at maximum electron transfer rates with electrode potentials of 0.04 V versus normal hydrogen electrode. Current densities decreased gradually with lower potentials and reached half-maximal values at -0.08 V. A positive interaction of the individual strains could be observed in our experiments. At least S. oneidensis and G. sulfurreducens show an upregulation of their central metabolism as a response to cultivation under mixed-species conditions. Interestingly, G. sulfurreducens was detected in the planktonic phase of the bioelectrochemical reactors only in mixed-culture experiments but not when it was grown in the absence of the other two organisms. It is possible that G. sulfurreducens cells used flavins which were released by S. oneidensis cells as electron shuttles. This would allow the organism to broaden its environmental niche. To the best of our knowledge, this is the first study describing the dynamics of biofilm formation of a model exoelectrogenic community, the resilience of the biofilm, and the molecular responses towards mixed-species conditions.

sample_organism:
Geobacter metallireducens
Geobacter sulfurreducens
Shewanella oneidensis

overall_design: RNA-seq of three species growing as biofilms on electrodes. Triplicate samples were analyzed for each species in pure culture and a mixed culture of all three species. Samples were taken from the biofilms and the plantonic phase, independently.

first: Anna

last: Prokhorova

last: Dötsch

first: Johannes

last: Gescher


title: Chromatin remodelling factor SMARCD2 (BAF60B) regulates transcriptional networks controlling early and late differentiation of neutrophil granulocytes

city: Martinsried

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

institute: Ludwig-Maximilians University Munich

summary: Differentiation of haematopoietic stem cells followsa hierarchical program of transcription-factor regulated events. Early myeloid cell differentiation is dependent on PU.1 and CEBPA (CCAAT/enhancer binding protein alpha), late myeloid differentiation is orchestrated by CEBPE (CCAAT/enhancer binding protein epsilon). The influence of SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodelling factors as novel master regulators of haematopoietic differentiation is only beginning to be explored. Here, we identified three homozygous loss-of-function mutations in SMARCD2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2), a member of the SWI/SNF complex, in three unrelated pedigrees. We find that SMARCD2-deficient hematopoiesis results in dysfunctional neutrophil granulocytes, characterized by specific granule deficiency, myelodysplasia, and an excess of blast cells.  We can show that SMARCD2 controls early steps in the differentiation of myeloid-erythroid progenitor cells in mice and zebra fish. In vitro SMARCD2 interacts with the transcription factor CEBPE. Furthermore, we find that SMARCD2 controls expression of neutrophil proteins stored in specific granules and leads to transcriptional and chromatin changes in AML cells. Hence, we identify SMARCD2 as a key factor controlling myelopoiesis and as a potential tumour suppressor in leukemia.

overall_design:
We analyzed CD45.2+ Lin- Mac+/low Sca1+ cKit+ (LSK) cells from Smarcd2 wild-type, heterozygous and mutant foetal livers in at least 5 replicates
Additionally, we analysed three different progenitor populations from Smarcd2 wild-type and homozygous knock-out foetal livers:
CD45+Lin-Sca-1-CD177+CD34lowCD16/32 (FCGR)low(MEP)
CD45+Lin-Sca-1-CD177+CD34+CD16/32(FCGR)int  (CMP)
CD45+Lin-Sca-1-CD177+CD34+CD16/32(FCGR)high (GMP)

first: Maximilian

last: Witzel


title: Transcriptome Analysis using customized AZ microarray on Flower pedicel Abscission and non abscission zones in Tomato (Solanum lycopersicum c.v New Yorker) Plants.

city: Bet-Dagan

first: Srivignesh

last: Sundaresan

state: Israel

address: P.O.Box 6, Bet- Dagan

department: Post Harvest Technology

country: Israel

institute: Agricultural Research Organisation, The volcani center, Israel

summary: To extend our previous knowledge from our gene expression studies on Flower pedicel Abscission zone using Affymetrix microarray chip we have employed whole transcriptome analysis by NGS as a discovery platform to identify and add the transcripts to pre-existing database. We designed the Customized AZ Microarray chip with the transcripts obtained from NGS (includes novel transcripts), pre existing Agilent probes, and some additional transcripts from previous databases. The flower pedicel AZ tissue and non abscission(NAZ) pedicel tissues was sampled at six time points (0, 4, 8, 12, 16 and 20 h), following flower removal, and analyzed for their gene expression profiles using the customized AZ microarray.

overall_design: Solanum lycopersicum Custom Microarray 4x180K Array designed by Genotypic Technology Private  Limited. (AMADID:043310)

first: Shimon

last: Meir

first: Sonia

last: Philosoph-Hadas


title: Pervasive translational regulation of the cell Q1 signalling circuitry underlies mammalian development

city: Stanford

first: Zhen

last: Shi

state: California

address: 279 Campus Drive

institute: Stanford

summary: The degree and dynamics of translational control during mammalian development remain poorly understood. Here we monitored translation of the mammalian genome as cells become specified and organize into tissues in vivo. This identified unexpected and pervasive translational regulation of most of the core signalling circuitry including Shh,Wnt, Hippo, PI3K and MAPK pathways. We further identify and functionally characterize a complex landscape of upstream open reading frames (uORFs) across 5'-untranslated regions (UTRs) of key signalling components. Focusing on the Shh pathway, we demonstrate the importance of uORFs within the major SHH receptor, Ptch1, in control of cell signalling and neuronal differentiation. Finally, we show that the expression of hundreds of mRNAs underlying critical tissue-specific developmental processes is largely regulated at the translation but not transcript levels. Altogether, this work reveals a new layer of translational control to major signalling components and gene regulatory networks that diversifies gene expression spatially across developing tissues.

overall_design: Here, we monitored translation of the mammalian genome as cells become specified and organize into tissues in-vivo.

first: Kotaro

last: Fujii

first: Olena

last: Zhulyn

first: Nicolas

last: Denans

first: Maria

last: Barna


title: Analysis of the role for the transcription factor TgAP2IV-4 (TGGT1_318470) in regulating gene expression in Toxoplasma development

city: St. Louis

first: Joshua

middle: B

last: Radke

state: Missouri

address: 660 Euclid Ave, CB8230

department: Molecular Microbiology

institute: Washington University School of Medicine

summary:
Differential gene expression analysis of TgAP2IV-4 knockout parasites in type I RH diCRE (RHCre) and type II Prudku80 (PruQ) genetic background
The gene regulatory role for TgAP2IV-4 was evaluated, in vitro, as tachyzoites (pH 7.0) in 8 strains: RHCre-AP2IV-4 floxed; RHCre-delta_ap2IV-4 clones 27 and 30, PSMB794 cosmid complemented RHCre-dAP2IV-4 populations;  PruQ-AP2IV-4 floxed; PruQ-delta_ap2IV-4 clones 10 and 34.

overall_design: 16 total samples.  Each condition presented as 2 biological replicates

first: Dong-Pyo

last: Hong

first: Michael

last: White


title: The mammalian LINC complex controls mechanosensing at a genome-wide level: RNA-Seq

first: Tanmay

last: Lele

overall_design: mRNA profiles of NIH 3T3 TetON cells that were induced to express either SS-GFP-KDEL (control) or SS-HA-Sun1L-KDEL by the addition of doxycycline. Two (2) substrate stiffnesses were used (1 kPa and 308 kPa), Y27632 or blebbistatin was used for certain samples to inhibit myosin II activity. A total of 6x3 reps= 18 samples were analyzed.

first: Samer

last: Alam

first: Qiao

last: Zhang

first: Nripesh

last: Prasad

first: Yuan

last: Li

first: Srikar

last: Chamala

first: Ram

last: Kuchibhotla

first: Birendra

last: KC

first: Shawn

last: Levy

first: Jeffrey

last: Nickerson

first: Kyle

last: Roux


title: iPSCs Reveal Protective Modifiers of the BMPR2 mutation in Pulmonary Arterial Hypertension

first: Marlene

last: Rabinovitch

address: 269 Campus Drive

institute: Stanford University School of Medicine

summary: The goal of this study is to compare transcriptome profiling (RNA-seq) in controls, unaffected BMPR2 mutation carriers and affected familial pulmonary arterial hypertension patients, to elucidate a protective feature in iPS derived endothelial cells from the mutation carriers.

overall_design: mRNA profiles of iPSC-ECs from unrelated control (n=3), unaffected BMPR2 mutation carriers (n=3) and FPAH patients with BMPR2 mutation (n=5).

first: MingXia

last: Gu

first: Ning-Yi

last: Shao

first: Joseph

last: Wu

last: Rabinovich


title: Store operated Ca2+ entry (SOCE) controls ameloblast cell function and enamel development

status: Public on Jan 17 2017

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

country: United Arab Emirates

institute: NYUAD

summary: Abstarct:Mutations in the endoplasmic reticulum (ER) Ca2+ sensor stromal interaction molecule 1 (STIM1) result is a number of disease states including abnormal enamel formation. However, these defects in enamel have remained unclear given a lack of animal models available. We generated Stim1/2K14Cre mice to ablate the activity of STIM1 and its homologue STIM2 in enamel cells. These mice showed impaired Ca2+ entry in enamel cells and although enamel formed, it was severely hypomineralized and mechanically weak. RNA-sequencing of enamel cells provided a global overview of loss of Ca2+ sensor activity. ER stress markers associated with unfolded protein response (UPR) were increased. Cell morphology was altered showing loss of the typical ruffled-border and mislocalized mitochondria. We also identified decreased glutathione system and potentially associated with this, increased ROS and abnormal mitochondria. The Ca2+ extrusion system and enamel gene expression were also altered. These data might represent the first in vivo study linking Stim1/2 ablation with increased UPR function, decreased glutathione metabolism, increased ROS and abnormal mitochondria. Loss of ER Ca2+ sensors Stim1/2 in enamel cells has substantial detrimental effects at the cell and mineral phase level.

overall_design: Total RNA from enamel organ was isolated for 3 wild type (WT) and 3 Knock out (DKO) for, mus musculus were generated by deep sequencing using Illumina HiSeq 4000.

first: M

last: Eckstein

last: Vaeth

first: C

last: Fornai

first: T

last: Bromage

last: Vinu

last: Nurbaeva

first: J

last: Sorge

first: P

last: Coelho

first: Y

first: S

last: Feske

first: R

last: Lacruz


title: In vitro transcription start sites (TSSs) determined by 5'-RACE

first: Shigeki

last: Nagai

address: 299 Campus Dr

department: Structural Biology

institute: Stanford University

summary: We report the TSSs of transcripts derived from in vitro chromatin transcription

overall_design: Examination of in vitro TSSs from chromatin or naked DNA templates

middle: P

last: Eagen

first: Roger

middle: D

last: Kornberg


title: Epigenetic regulation of Plasmodium falciparum adaptive plasticity in the mosquito

city: Armilla

first: Elena

last: Gómez-Díaz

state: Granada

address: Avda. del Conocimiento, 17

department: Institute of Parasitology and Biomedicine Lopez-Neyra (IPBLN)

country: Spain

institute: Spanish National Research Council (CSIC)

summary: P. falciparum undergoes antigenic variation during its life cycle in the human host. To accomplish this, the malaria parasite has developed mechanisms that ensure the expression of a single member of the var gene family to produce one of the PfEMP1 variant proteins. Here we carry out RNA-seq and ChIP-seq analyses of histone modifications to explore transcriptional and epigenomic changes taking place between the transmissible stages of the parasite i.e. gametocytes present in human blood and sporozoites present in the mosquito salivary glands. We find that most var genes are expressed at low levels in gametocytes but a single var gene is selected during the oocyst stage in the mosquito. Clonal expression of a specific var gene is accompanied by the establishment of specific histone modification patterns in the active and inactive genes. These modifications are epigenetically transmitted from the oocyst to the infective sporozoite stage, where expression of the active var gene is amplified by the transcription of an antisense lncRNA. The findings suggest a critical role for the mosquito immune system in determining the choice of var gene activation prior to transmission to the human host.

overall_design: ChIP-seq and RNA-seq were performed on adult female A. gambiae midguts and salivary glands infected with P.falciparum using membrane feeding.

first: Rakiswendé

last: Yerbanga

first: Thierry

last: Lefevre

first: Anna

last: Cohuet

first: Jean

last: Ouédraogo

first: Victor

last: Corces


title: Modulation of microRNA-mRNA Target Pairs by Human Papillomavirus 16 Oncoproteins

city: Huntsville

first: Nripesh

last: Prasad

state: Alabama

address: 601 Genome way

institute: Hudson Alpha Institute for Biotechnology

summary: The E6 and E7 proteins are the major oncogenic drivers encoded by high-risk human papillomaviruses (HPVs). While many aspects of the transforming activities of these proteins have been extensively studied, there are fewer studies that have investigated how HPV E6/E7 expression affects expression of cellular noncoding RNAs.  The goal of our study was to investigate HPV16 E6/E7 modulation of cellular microRNA (miR) levels and to determine the potential consequences on cellular gene expression.  We performed deep sequencing of small and large cellular RNAs in primary, undifferentiated cultures of human foreskin keratinocytes (HFKs) with stable expression of HPV16 E6/E7 or a control vector.  After integration of the two data sets we identified 51 differentially expressed cellular miRs associated with modulation of 1,456 potential target mRNAs in HPV16 E6/E7 expressing HFKs.  We discovered that the degree of differential miR expression in HFKs expressing HPV16 E6/E7 was not necessarily predictive of the number of corresponding mRNA targets or the potential impact on gene expression.  Additional analyses of the identified miR-mRNA pairs suggest modulation of specific biological activities and biochemical pathways.  Overall, our study supports the model that perturbation of cellular miR expression by HPV16 E6/E7 importantly contributes to the rewiring of cellular regulatory circuits by the high-risk HPV E6 and E7 proteins that contribute to oncogenic transformation.

overall_design: A total of 8 samples were analyzed, including two replicates of donor and passage matched human foreskin keratinocyte populations transduced with a control LXSN vector, a vector expressing HPV16 E6 alone, HPV16 E7 alone or both HPV16E6 and E7. Large and smal RNA was harvested from each of these samples.  RNAseq was performed using large RNA from two populations expressing a control vector and two populations expressing HPV16 E6 and E7 together only (a total of 4 samples).  All 8 samples were subjected to small RNAseq (miRNAseq).

first: Mallory

middle: E

last: Harden

first: Anthony

last: Griffiths

first: Karl

last: Munger


title: A Molecular Roadmap for Induced Multi-lineage Trans-differentiation of Fibroblasts by Chemical Combinations

city: Hangzhou

first: Guoji

last: Guo

state: Zhejiang

address: Yuhangtang Road 866

department: School of Medicine

institute: Zhejiang University

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

overall_design: Refer to individual Series


title: RNA sequencing of ID4-GFP Bright and ID4-GFP Dim spermatogonia from postnatal day 8 transgenic Id4-Gfp (LT11) mouse pups and ID4-GFP+ spermatogonia from ID4 overexpression mouse model and control

city: Pullman

first: Jon

last: Oatley

state: WA

address: 1770 NE Stadium Way

institute: Washington State University

summary: Mice that constitutively overexpress ID4 in germ cells have impaired spermatogenic lineage development.  The transcriptome of ID4-GFP+ spermatogonia from testes of ID4 overexpression animals was compared to the ID4-GFP+ population from controls

overall_design: Comparison of transcriptomes of ID4-GFP+ spermatogonia from animals constitutively overexpressing ID4 and control animals

first: Aileen

middle: R

last: Helsel


title: XBP1 coregulates unfolded protein response, acute phase response and DNA damage response during mouse liver regeneration

city: Pamplona

first: Tomas

last: Aragon

address: Avda Pio XII 55

department: Gene Therapy and Regulation of Expression

institute: CIMA - University of Navarra

summary: Partial hepatectomy (PH) imposes increased protein synthesis demands on remaining hepatocytes. Activation of IRE1α, a key sensor of endoplasmic reticulum (ER) stress, elicits XBP1 mRNA splicing and production of XBP1 protein, a main trigger of the unfolded protein response (UPR). Using genome-wide ChIPseq analysis we have explored the role of XBP1 during liver regeneration.  XBP1 was induced in liver at 6h after PH in an IL-6 dependent manner. After PH, XBP1 silencing caused persistent ER stress, defective acute phase response (APR), increased hepatocellular damage and regenerative delay. At 6h post-PH, XBP1 bound an increased number of genes implicated in proteostasis, APR, metabolism, antioxidant defense and DNA damage response (DDR). ). XBP1 was linked to regulatory sequences containing canonical UPR motifs as well as motifs characteristic of other nuclear factors suggesting molecular interactions during liver regeneration. Upon PH, XBP1 bound the promoter of STAT3, a molecule downregulated in XBP1-silenced livers. XBP1 was indispensable for ser727-STAT3 phosphorylation, a post-translational modification implicated in cell proliferation and DNA damage repair. During active DNA replication XBP1 deficient livers showed high levels of the DNA double-strand break marker γ-H2AX, in association with defective upregulation of Eme1 and Fen1, two main executors of DDR. In conclusion, XBP1 is induced after PH and co-regulates UPR, APR and DDR during liver regeneration.

overall_design: Peak calls from XBP1 ChIPseq data from 8 samples, including Liver from C57 mice

first: Josepmaria

last: Argemí

first: Theresia

last: Kress

first: Bruno

last: Amati

first: Jesus

last: Prieto

first: Tomás


title: A Molecular Roadmap for Induced Multi-lineage Trans-differentiation of Fibroblasts by Chemical Combinations [ChIP-seq]

summary: Recent advances highlight the power of small molecules for promoting cellular reprogramming. Yet, the full potential of such chemicals in cell fate manipulation and the underlying mechanisms needs further characterization. Through functional screening assays, we found that mouse embryonic fibroblast can be induced to trans-differentiate into a wide range of somatic lineages simultaneously by treatment with a combination of four chemicals. Genomic analysis of the process indicates activation of multi-lineage modules and relaxation of epigenetic silencing programs. In addition, we identify Sox2 as an important regulator within the induced network. Single cell analysis uncovers a priming state that enables transition from fibroblast cells to diverse somatic lineages. Finally, we demonstrate that modification of the culture system enables directional trans-differentiation towards cardiac, neuronal or adipocytic lineages. Our study describes a cell fate control system that may be harnessed for regenerative medicine.

overall_design: Examination of 2 different histone modifications in 6TCF treated MEFs and control MEFs.

first: Daosheng

last: Huang

first: Xiaoping

last: Han


title: An Argonaute phosphorylation cycle promotes microRNA-mediated silencing [GeCKO screen]

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: MicroRNAs (miRNAs) perform critical functions in normal physiology and disease by associating with Argonaute proteins and downregulating partially complementary messenger RNAs (mRNAs).  To identify new regulators of the miRNA pathway, we employed CRISPR-Cas9 genome-wide loss-of-function screening coupled with a fluorescent reporter of miRNA activity.  Iterative rounds of screening revealed a novel mechanism whereby target engagement by Argonaute 2 (AGO2) triggers its hierarchical, multi-site phosphorylation by CSNK1A1 on a set of highly conserved residues (S824-S834), followed by rapid dephosphorylation by the ANKRD52-PPP6C phosphatase complex.  Although genetic and biochemical studies demonstrated that AGO2 phosphorylation on these residues inhibits target mRNA binding, inactivation of this phosphorylation cycle globally impairs miRNA-mediated silencing.  Analysis of the transcriptome-wide binding profile of non-phosphorylatable AGO2 revealed a dramatic expansion of the target repertoire bound at steady-state, effectively reducing the active pool of AGO2 on a per target basis.  These findings support a model in which an AGO2 phosphorylation cycle stimulated by target engagement regulates miRNA:target interactions to maintain the global efficiency of miRNA-mediated silencing.

overall_design: Multiple genome-scale CRISPR-Cas9 screens were performed in HCT116 cells expressing one of two reporters.

first: Ryan

middle: J

last: Golden


title: An Argonaute phosphorylation cycle promotes microRNA-mediated silencing [eCLIP-seq]

overall_design: Used eCLIP to elucidate RNA sequences bound to either WT FH-AGO2 or 5xA FH-AGO2.  AGO2 knockout cells were included as a control.

middle: T


title: An Argonaute phosphorylation cycle promotes microRNA-mediated silencing [polyA RNA-seq]

overall_design: RNA-seq analysis was performed to identify differentially expressed transcripts in parental cells and cells deficient in either ANKRD52, AGO2, or ANKRD52; CSNK1A1.


title: Single-cell indexed RNA-Seq of human hematopoietic stem and progenitors

city: Barcelona

first: Lars

last: Velten

address: C. Dr. Aiguader 88, P05

department: Bioinformatics and Genomics

institute: CRG

summary: To characterize early human hematopoiesis on a single-cell level we developed an approach termed index-omics, which combines flow-cytometric, single-cell transcriptomic and single-cell lineage fate data. Healthy human bone marrow was labeled with a panel of up to 11 FACS surface markers commonly used to identify human hematopoietic stem and progenitor cells (HSPCs). Lin-CD34+38+ progenitors and Lin-CD34+CD38- stem cell enriched HSPCs were individually sorted, their surface marker fluorescence intensities recorded, and subjected to single-cell RNAseq or single-cell ex vivo cultures.

overall_design: For transcriptomics, human bone marrow was stained with antibodies against Lineage markers (CD4, CD8, CD11b, CD14, CD19, CD20, CD56 and CD235a), CD7, CD10, CD34, CD38, CD45RA, CD49f, CD90 and CD135. For individual 1, 8 96-well plates of Lin-cd34+cd38+ and 6 96 well plates of Lin-cd34+cd38- cells were sorted into lysis buffer and subjected to a modified smart-seq2 protocol. For individual 2, 4 96-well plates of Lin-cd34+cd38+, 7 plates of Lin-cd34+cd38- and 1 plate of Lin-cd34+cd38-cd45RA-cd90+ were sorted into lysis buffer and subjected to QUARTZ Seq (Sasagawa et al 2013). For single-cell culture, human bone marrow from a third individual was stained with antibodies against CD2, CD34, CD38, CD45RA, CD71, CD90, CD130, CD135, FCER1A, KEL and a Lineage cocktail as above, plus CD10. Lineage output was then determined by automated FACS following prolonged ex-vivo cultivation. The files transcriptomics_raw_filtered_I1.csv and transcriptomics_raw_filtered_I2.csv contain the raw read counts for the cells that passed quality control. transcriptomics_normalized_filtered_I1.csv and transcriptomics_raw_filtered_I2.csv contain the readcounts normalized by posterior odds ratio (POR) as described in our manuscript. The files transcriptomics_facs_indeces_filtered_I1.csv and transcriptomics_facs_indeces_filtered_I2.csv contain the FACS surface marker expression for the cells that passed filter. Additionally, FACS surface marker expression is given as a characteristic of each sample. The file culture_data.csv contains the FACS surface marker expression, quantification of cell types in the mature colony, and scoring of colony type of the cells that were subjected to ex-vivo culture.

first: Simon

last: Haas

last: Raffel

first: Sandra

last: Blaskiewicz

first: Saiful

last: Islam

first: Bianca

last: Hennig

first: Christoph

last: Hirche

last: Lutz

first: Eike

last: Buss

first: Daniel

last: Nowak

first: Tobias

last: Boch

first: Wolf-Karsten

last: Hofmann

last: Ho

first: Wolfgang

last: Huber

first: Andreas

last: Trumpp

first: Marieke

last: Essers

last: Steinmetz


title: Spatiotemporal analysis of shade-induced transcriptional reprogramming in Arabidopsis reveals patterns underlying organ-specific growth

city: Lausanne

first: Markus

middle: Volker

last: Kohnen

state: Vaud

address: Genopode Building

department: Center for Integrative Genomics (CIG)

country: Switzerland

institute: Université de Lausanne

summary: In response to neighbor proximity plants increase growth of specific organs (e.g. hypocotyl) to enhance access to sunlight. Shade enhances the activity of Phytochrome Interacting Factors (PIFs) by releasing those bHLH transcription factors from phytochrome B-mediated inhibition. PIFs promote elongation by inducing auxin production in cotyledons. In order to elucidate spatiotemporal aspects of the neighbor proximity response, we analyzed changes in transcript abundance at different time points during a shade treatment in dissected cotyledons and hypocotyls. We concentrated our analysis on these two organs because the former is considered as the primary shade-sensing organ while elongation is rapidly triggered in the hypocotyl. We conclude that PIFs initiate transcriptional reprogramming in both organs within 15 minutes comprising regulated expression of several early auxin response genes. This suggests that hypocotyl growth is elicited by both local and distal auxin signals. With time the transcriptional response diverges increasingly between organs. We identify genes whose differential expression may underlie organ-specific elongation. Finally, we uncover a growth promotion gene expression signature shared between responses to different environments and organs.

overall_design: Arabidopsis thaliana Col-0 was grown for 5 days in a 16 h : 8 h, light : dark photoperiod at 21°C on one horizontal plate of c. 140 mm in diameter per sample. Each plate contained 25 ml ½ MS medium covered with a nylon mesh. On day 6 at ZT2, seedlings were either kept in high R/FR or transferred to low R/FR. After 0, 15, 45, 90 or 180 min after the onset of low R/FR samples of both light qualities were imbibed within 75 sec in ice-cold 100 % (v/v) acetone and two times subjected to about 600 mbar below atmospheric pressure for 5 min while remaining on ice. The dissection of acetone-fixed seedlings was carried out in 70 % (v/v) 4°C-cold ethanol under a binocular lens. Cotyledon and hypocotyl material of 50 seedlings per sample were collected in 100 % (v/v) ethanol. For each time point and light condition duplicates were prepared. Plant materials were manually ground using pestles and total RNA was extracted using the RNeasy Kit (QIAGen) with on-column DNA digestion, according to the manufacturer’s instructions. Finally RNA samples were precipitated using 3M NAOH (pH 5.2) and 100 % (v/v) ethanol. The precipitate was visualize with glycogen and washed with 80 % (v/v) ice-cold ethanol. Stranded libraries were prepared using 400 ng high quality RNA using the TruSeq protocol according to th manufacturer’s instructions (Illumina). This included RNA purification steps using AMPure XP beads and cDNA preparation using a mix of random and polyA primer. RNA-seq libraries were subsequently sequenced with a HISEQ 2500 (Illumina) in the Genome Technology Facility (GTF).

middle: V

first: Emanuel

last: Schmid-Siegert

first: Martine

last: Trevisan

first: Laure

last: Allenbach-Petrolati

first: Fabien

last: Sénéchal

first: Patricia

last: Müller-Moulé

first: Julin

middle: N

last: Maloof

first: Ioannis

last: Xenarios

first: Christian

last: Fankhauser


title: High Throughput Analysis Reveals Novel Maternal Germline RNAs Critical for PGC Preservation and Proper Migration

city: Miami

first: Mary

middle: Lou

last: King

state: Fl

address: 1600 nw 10th ave

department: Cell Biology

institute: University of Miami: Miller school of Medicine

summary: During oogenesis hundreds of RNAs are selectively localized to either the animal or vegetal cortical region. These maternal RNAs include determinants of both somatic and germline fates. Although microarray analysis has contributed to identifying localized determinants, it is not comprehensive and is limited to known transcripts. Here, we utilized high throughput RNA-sequencing analysis to comprehensively interrogate both animal and vegetal pole RNAs in the fully-grown Xenopus laevis oocyte. We identified 411 enriched RNAs at the vegetal pole, 198 of them annotated transcripts, and 27 RNAs enriched at the animal pole, 15 annotated. Of these, 90 were novel RNAs over 4-fold enriched at the vegetal pole and 6 over 10-fold at the animal pole. Unlike mRNAs, we found that microRNAs were not asymmetrically distributed. Whole mount in situ hybridization revealed all 17 selected RNAs were localized, confirming our data set. Biological function and network analysis of vegetally enriched transcripts identified protein-modifying enzymes, receptors, ligands, RNA binding proteins and 10 transcription factors or co-factors with 5 defining hubs linking 47 genes in a network. Initial functional studies of maternal vegetally-localized RNAs show, for the first time, that sox7 plays an important role in primordial germ cell (PGC) development and efnb1(ephrinB1), known to play important roles in migration/adhesion in the nervous system, is required for proper PGC migration. Based on our findings, we propose potential pathways operating at the vegetal pole that highlight where future investigations might be most fruitful.

overall_design: Examination of animal and vegetal pole samples of stg. VI X. laevis oocyte to determine vegetally enriched genes that may contribute to germ plasm and PGCs.

first: Dawn

middle: A

last: Owens

first: Amanda

last: Butler

middle: L


title: Mammalian sperm exhibit epigenetic priming of embryonic and adult regulatory landscapes (ATAC-Seq)

city: Atlanta

first: Yoonhee

last: Jung

state: Georgia

address: 615 Michael Street

department: Human Genetics

institute: Emory university

summary: The mammalian sperm genome is generally thought to be condensed and transcriptionally inert. Here we show that most promoters in mouse sperm contain elongating RNA polymerase II and are flanked by several positioned nucleosomes marked by a variety of active histone modifications. The sperm genome is bound by several transcription factors, including Nanog, Oct4, Mediator, condensin, and the pioneer factor FoxA1. These proteins are found at promoters, enhancers, and super-enhancers, many of which are active in mESCs or adult tissues. CTCF and cohesin are also present in sperm DNA, where they mediate interactions that organize the sperm genome into domains and compartments that overlap extensively with those found in mESCs. These results indicate that the sperm genome is rich in epigenetic information and   primed for its expression during embryonic and adult life, and suggest mechanisms by which environmental effects on the paternal germline can be transmitted trans-generationally.

overall_design: Analysis of the distribution of histone modifications and chromatin proteins in mouse sperm

first: Yoon-Hee

first: Michael

last: Sauria

first: Xiaowen

last: Lyu

first: James

last: Taylor

first: Victor

last: Corces


title: Mammalian sperm exhibit epigenetic priming of embryonic and adult regulatory landscapes (ChIP-Seq)


title: Next Generation Sequencing Analysis of control and SRSF2-/- Huh7 cells Transcriptomes

city: Shanghai

first: Chunling

last: Luo

address: yueyang road,number 320

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: We generated the SRSF2-/- Huh7 cells,and collected the cells at 2 days after transfected with siRNA. Then, we extracted RNAs and performed next generation sequencing. By comparing sequencing data from control and SRSF2 -/- samples, we profiled the alternative splicing events and gene expression regulated by SRSF2 in HCC.

overall_design: Huh7 cells mRNA profiles of  control and SRSF2-/- were generated by deep sequencing, using Illumina HiSeq2000.


title: Mammalian sperm exhibit epigenetic priming of embryonic and adult regulatory landscapes (BS-Seq)

type: Methylation profiling by high throughput sequencing


title: Fibrin Hydrogels Induce Mixed Dorsal/Ventral Spinal Neuron Identities During Differentiation of Human Induced Pluripotent Stem Cells

city: Victoria

first: Stephanie

middle: M.

last: Willerth

state: BC

address: 3800 Finnerty Rd.

department: Department of Mechanical Engineering/Division of Medical Science

country: Canada

institute: University of Victoria

summary:
We hypothesized that generating spinal motor neurons (sMNs) from human induced pluripotent stem cell (hiPSC)-derived neural aggregates (NAs) using a chemically-defined differentiation protocol would be more effective inside of 3D fibrin hydrogels compared to 2D poly-L-ornithine(PLO)/laminin-coated tissue culture plastic surfaces. We performed targeted RNA-Seq using next generation sequencing to determine the substrate-specific differences in gene expression that regulate cell phenotype. Cells cultured on both substrates expressed sMN genes CHAT and MNX1, though persistent WNT signaling contributed to a higher expression of genes associated with interneurons in NAs cultured in 3D fibrin scaffolds. Cells in fibrin also expressed lower levels of astrocyte progenitor genes and higher levels of the neuronal-specific gene TUBB3, suggesting a purer population of neurons compared to 2D cultures.

STATEMENT OF SIGNIFICANCE:
Fibrin scaffolds can support the neuronal differentiation of pluripotent stem cells. This study provides insight into how fibrin hydrogels affect neuronal induction by analyzing of the signaling pathways activated during the differentiation process. These insights can then be used to tailor the properties of these hydrogels to optimize the generation of sMNs for regenerative medicine applications.

overall_design: 45 samples and 6 sample groups. Minimum of 6 replicates per sample group. Sample groups can be differentiated by day and substrate

first: John

last: Edgar

first: Meghan

last: Robinson


title: Tethered Oligonucleotide-Primed sequencing (TOP-seq): a high resolution economical approach for DNA epigenome profiling

status: Public on Jan 16 2017

city: Vilnius

first: Saulius

last: Klimašauskas

address: Sauletekio al. 7

department: Department of Biological DNA Modification, Institute of Biotechnology

country: Lithuania

institute: Vilnius University

summary: We describe the development and thorough validation of a new approach for epigenome analysis (named TOP-seq) that is based on a novel concept – combination of selective covalent tagging and targeted genomic sequencing of the genome. The technique reports the modification status of each genomic CpG site by priming the DNA polymerase action from a tethered oligonucleotide probe that is selectively attached to the unmodified CpG sites.

overall_design:
DNA methylation analysis of 4 human tissues/cell lines (Prefrontal brain cortex - 4 replicates; IMR90 - 9 replicates; Neuroblastoma specific LA1-55n - 3 replicates; Non-neuronal progenitor LA1-5s - 3 replicates)

Please note that processed files created by merging data from multiple samples are linked as Series supplementary file and are indicated in the corresponding Sample description field.

first: Zdislav

last: Staševskij

first: Povilas

last: Gibas

first: Juozas

last: Gordevičius

first: Edita

last: Kriukienė


title: Dirofilaria immitis exhibits sex- and stage-specific differences in excretory/secretory miRNA profiles in vitro

city: Sainte-Anne-de-Bellevue

first: Lucienne

last: Tritten

state: QC

address: 21111 Lakeshore Road

department: Institute of Parasitology

institute: McGill University

summary: We report analyses of the types, amounts and stage-dependence of microRNAsfound in D. immitis culture media recovered after incubating 800,000 microfilariae for 6 days, 500 third-stage larvae (L3) and 500 fourth-stage larvae (L4) for 7 days, as well as 40 adult females and 40 adult males for 48 hours, all separately.

overall_design: Examination of excretory/secretory miRNAs in 5 different stages of Dirofilaria immitis released in culture media.

first: Timothy

middle: G

last: Geary


title: Fine-mapping of DNA modifications in the lactase gene region of mice

city: Toronto

first: Edward

middle: Saehong

last: Oh

state: Ontario

address: 250 College st

department: Krembil Family Epigenetics Laboratory

institute: Centre for Addiction and Mental Health

summary: Transcriptional variation between cells of the same type is a widespread phenomenon which allows for tissues to exhibit regional differences in biological function and disease vulnerability. We analyzed an in vivo transcriptional gradient occurring in enterocytes along the proximal-to-distal axis of the mouse small intestine via bisulfite padlock probe technique. DNA modifications at the lactase gene were investigated in infant and adult mice as well as following lactose-treatment.

overall_design: DNA modifications were investigated in mouse enterocytes isolated from  mice small intestine dissected into nine equal parts (three sections of  duodenum, jejunum and ileum). Analysis was performed on infant (postnatal day  6; n=10, 3-4 per segment) and adult (P60; n=71, 5-6 per segment) mice, or on  mice treated with lactose (n=35; 7-9 per segment) or lactose-free milk (n=32;  5-9 per segment).

first: Art

last: Petronis

first: Viviane

last: Labrie

first: Richie

last: Jeremian

first: Gabriel

first: Daniel

last: Groot


title: An Argonaute phosphorylation cycle promotes microRNA-mediated silencing

first: Joshua

last: Mendell


title: An Argonaute phosphorylation cycle promotes microRNA-mediated silencing [whole transcriptome RNA-seq]

overall_design: Whole-transcriptome RNA-seq analysis was performed to identify differentially expressed transcripts in cells reconstituted with either wild-type FH-AGO2 or 5xA FH-AGO2.  Parental cells and AGO2 knockout cells were used as controls.

first: Ryan

last: Golden


title: PRC2 preserves cellular plasticity and restricts intestinal secretory lineage commitment

city: Milan

first: Sri Ganesh

last: Jammula

address: Via Adamello 16

country: Italy

institute: IFOM-IEO

overall_design: Refer to individual Series


title: Deep sequencing of wheat sRNA transcriptome reveals distinct temporal expression pattern of miRNAs in response to heat, light and UV

city: Ottawa

first: Sylvie

last: Cloutier

address: 960 Carling Avenue

institute: Agriculture and Agri-Food Canada

summary: Understanding of plant adaptation to abiotic stresses has implications in plant breeding, especially in the context of climate change. MicroRNAs (miRNAs) and short interfering RNAs play a crucial role in gene regulation. Here, wheat plants were exposed to one of the following stresses: continuous light, heat or ultraviolet radiations over five consecutive days and, leaf tissues from three biological replicates were harvested at 0, 1, 2, 3, 7 and 10 days after treatment (DAT). A total of 72 small RNA libraries were sequenced on the Illumina platform generating ~524 million reads corresponding to ~129 million distinct tags from which 232 conserved miRNAs were identified. The expression levels of 1, 2 and 79 miRNAs were affected by ultraviolet radiations, continuous light and heat, respectively. Approximately 55% of the differentially expressed miRNAs were downregulated at 0 and 1 DAT including miR398, miR528 and miR156 that control mRNAs involved in activation of signal transduction pathways and flowering. Other putative targets included histone variants and methyltransferases. These results suggest a temporal miRNA-guided post-transcriptional regulation that enables wheat to respond to abiotic stresses, particularly heat. Designing novel wheat breeding strategies such as regulatory gene-based marker assisted selection depends on accurate identification of stress induced miRNAs.

overall_design: Wheat plants were exposed to one of the following stresses: continuous light, heat or ultraviolet radiations over five consecutive days and, leaf tissues from three biological replicates were harvested at 0, 1, 2, 3, 7 and 10 days after treatment (DAT). A total of 72 small RNA libraries were sequenced on the Illumina platform

first: Raja

last: Ragupathy

first: Sridhar

last: Ravichandran

first: Safiur

last: Mahdi

first: Douglas

last: Huang

first: Elsa

last: Reimer

first: Michael

last: Domaratzki


title: PRC2 preserves cellular plasticity and restricts intestinal secretory lineage commitment (RNA-seq)

summary: These data include RNA Seq data generated from wild type and Eed Ko intestinal crypts from AhCre and AhCreEedf/f mice.

overall_design: Total RNA extracted from wild type and Eed Ko intestinal crypts.

first: Fulvio

last: Chiacchiera

first: S

first: Diego

last: Pasini


title: PRC2 preserves cellular plasticity and restricts intestinal secretory lineage commitment (ChIP-seq)

summary: These data include the genome wide occupancy of histone modifications and target protein by ChIP sequencing in mouse crypt cells.

overall_design: Immuno-precipitation of formaldehyde cross-linked chromatin prepared from wild type crypt cells using specific antibody against different target protein/modification.

first: Alessandra

last: Rossi


title: Mammalian sperm exhibit epigenetic priming of embryonic and adult regulatory landscapes (HiC-Seq)

first: Yoonhee

last: Jung

first: Yoon-Hee

last: Sauria

first: Xiaowen

last: Lyu

first: James

last: Taylor

first: Victor

last: Corces


title: CPEB4 prevents hepatic steatosis

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

institute: IRB Barcelona

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


title: Mammalian sperm exhibit epigenetic priming of embryonic and adult regulatory landscapes


title: Dissecting cell-type-specific roles of androgen receptor in prostate homeostasis and regeneration through lineage tracing

city: Santa Cruz

first: Zhu

middle: A.

last: Wang

state: CA

address: 1156 High Street

department: MCD Biology

institute: University of California Santa Cruz

summary: We used RNA-seq to compare the gene expression profiles of adult mouse prostate luminal cells and luminal cells that have the androgen receptor (AR) gene deleted. Our analyses show that AR-null luminal cells have altered expression levels of genes involved in cell-matrix adhesion, cytoskeleton regulation, and MAPK and TGF-beta signaling pathways. These results are consistent with our finding that AR-null luminal cells have abnormal cell morphology and loss of cell polarity.

overall_design: Lineage marked wild-type luminal cells and AR-deleted luminal cells were flow-sorted based on YFP fluorescence respectively, and their expression profiles were analyzed by RNA-seq.

first: Qing

last: Xie

first: Tao

last: Cai


title: RNA-seq of Nothobranchius furzeri (Nfu) brain after miR29 knock-down

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

summary:
Comparing gene expression level by Illumina sequencing of brain Nfu tissue w/ and w/o knock-down of miR29

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 8 samples, 4 samples per group, 2 groups: 1) miR29 knock-down 2) control group w/o miR29 knock-down (MZM04/10p)

first: Roberto

last: Ripa

first: Luca

last: Dolfi

first: Marco

last: Terrigno

last: Pandolfini

first: Valeria

last: Arcucci

last: Groth

first: Mario

last: Baumgart

first: Matthias

last: Platzer

first: Alessandro

last: Cellerino


title: Gene expression profiling of cell subpopulations from different regions of the mouse brain

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: As a starting point for dissecting the cellular heterogeneity of astrocytes in the adult brain, we focused our initial studies on the olfactory bulb (OB) and combined an Aldh1l1-GFP reporter mouse with candidate cell surface markers to isolate astrocyte sub-populations using FACS analysis.  To this end, we screened a panel of cell surface antigens for their ability to divide the Aldh1l1-GFP astrocyte population within the OB into distinct sub-populations. Candidate cell surface markers were selected based on previously published gene expression profiling data from our lab and others and antibody availability. Different subpopulations from different brain regions were profiled for gene expression.

overall_design: Gene expression profiles (by RNA-seq) were taken of mouse cell lines in 6 populations and 3 brain regions.

first: Fengju

last: Chen

first: Benjamin

last: Deneen


title: DNA methylation patterns in twins discordant for ALS reveal concordant signatures of disease [RRBS]

status: Public on Jan 15 2017

city: Darlinghurst

first: Paul

last: Young

state: NSW

address: 405 Liverpool Street

country: Australia

institute: Victor Chang Cardiac Research Institute

summary: Our data suggest twin pair specific methylation differences exist in blood that reside in genes that are enriched for neuronal pathways.

overall_design: methylation profiling by RRBS, of 5 monozygotic twin pairs discordant for ALS

first: Michael

last: Buckland

first: Roger

last: Pamphlett

first: Catherine

last: Suter


title: Molecular response of Sargassum vulgare to acidified waters in natural CO2 vents – Insights from de novo transcriptomic analysis

city: Ischia

first: Amit

last: Kumar

address: Villa Dohrn

department: Department of Integrative Ecology

institute: Stazione Zoologica Anton Dohrn

summary: Sargassum is one of the most diverse brown algal genus with more than 150 known species, mostly benthic and few pelagic species.  They contribute significantly to global primary production and serve as important habitat for wide range of marine organisms. Sargassum vulgare is one of the dominant habitat forming species along Mediterranean coast. Despite their huge ecological importance, it is relatively unknown how they will respond under future global climate change scenario. This work used de novo transcriptome sequencing approach to understand the molecular response of S. vulgare to chronic acidification at the shallow underwater volcanic CO2 vents off Ischia Island, Italy. Keywords: brown algae, Sargassum, de novo transcriptome, ocean acidification, CO2 vents.

overall_design: In total six cDNA libraries (obtained each from pool of three S. vulgare thalli growing under the acidified conditions, and three cDNA libraries, obtained each from pool of three thalli growing in the normal conditions) were multiplexed and sequenced in a single lane of Illumina 1000 flow cell.

first: Kumar

last: Amit

first: Castellano

last: Immacolata

first: Patti

last: Francesco

first: Delledonne

last: Massimo

first: Palumbo

last: Anna

first: Buia

middle: M

last: Cristina


title: Single-cell Gene Expression Analysis Reveals Transcriptional Diversity among Human Spermatogonia

city: Münster

first: Nina

last: Neuhaus

address: Albert-Schweitzer-Campus 1, D11

department: Centre of Reproductive Medicine and Andrology

institute: University Hospital of Münster

summary: Two individual human OCT4-positive spermatogonia were selected for global transcriptional capture using shallow RNA-seq. Successful cDNA synthesis and amplification was confirmed as reads mapped primarily to exons. It has to be noted though, that a comparision of cell to cell data is not possible as coverage of the whole transcriptome was too low, approximately <1.0x coverage. Nonetheless, RNA-seq data provided first information of highly abundant transcripts in individual human spermatogonia. Spermatogonia-specific expression of selected candidate genes with high RPKM values including DDX5, EEF1A1 and TSPY1 was confirmed by immunohistochemistry.

overall_design: Human testicular biopsies with qualitatively normal spermatogenesis were used to establish human germ cell cultures. Spermatogonia were selected based on morphological characteristics via micromanipulation.

first: Juyong

last: Yoon

first: Nicole

last: Terwort

first: Sabine

last: Kliesch

first: Jochen

last: Seggewiss

first: Andreas

last: Huge

first: Reinhard

last: Voss

first: Stefan

last: Schlatt

first: Rashel

last: Grindberg

first: Hans

last: Schöler


title: DNA methylation patterns in twins discordant for ALS reveal concordant signatures of disease

first: Paul

last: Young


title: Molecular consequences of Csf1R (M-CSF receptor) inhibition by PLX3397 in the pilocarpine-induced chronic epileptic mouse hippocampus

city: Braine-l'Alleud

first: Jonathan

last: van Eyll

address: UCB Pharma - Building S2C

department: NewMedicines

country: Belgium

institute: UCB Pharma

summary: Efficacy of Csf1R inhibition by PLX3397 compound in a mouse model of chronic epilepsy has been assessed by daily administration of either vehicle, 3 mg/kg or 30 mg/kg during 2 weeks monitoring. At the end of the study, RNA was extracted from study animals hippocampi to assess treatment consequences at the gene expression level in view of the in vivo efficacy results and the previously identified consequences of epilepsy in hyppocampus. Naive healthy mice were added separately to determine baseline expression.

overall_design: RNA was extracted from chronic epilepsy mouse hippocampi after 2 weeks daily exposure to vehicle, PLX3397 3mg/kg or 30 mg/kg. Healthy, non-epileptic mice, were added separately to determine baseline expression.

first: Catherine

last: Vandenplas

first: Bénédicte

last: Danis

first: Karine

last: Leclercq

first: Patrik

last: Foerch

first: Rafal

last: Kaminski


title: Adaptation of Porphyromonas gingivalis to Streptococcus gordonii observed using time-coursed RNA-Seq

city: Seattle

first: David

middle: A. C.

last: Beck

address: Benjamin Hall IRB, Rm 440, UW Box 355014

department: ChemE & eScience Institute

institute: University of Washington

summary: Periodontal diseases are one of the most common human maladies and appear to be caused by the interaction of proximal pathogens such as Porphyromonas gingivalis but only as part of the polymicrobial community known as dental plaque. Streptococcus gordonii is an early colonizing oral organism that binds to oral surfaces and provides adherence for organisms such as P. gingivalis. Together P. gingivalis and S. gordonii form one of the simplest models of potentially pathogenic dental plaque. We used RNA sequencing to monitor the transcriptome of P. gingivalis over time in a biofilm model both in the presence and absence of S. gordonii. Samples were taken at 5, 30, 120, 240, and 360 minutes after shifing from planktonic to sessile conditions and growth media to PBS. When compared to planktonic cells increased transcripts were found for stress, amino acid catabolism, and comeptence and decreased transcripts for DNA replication. The presence of S. gordonii resulted in fewer changes from planktonic cells implying physiological support to Pl gingivalis making the transition from planktonic to sessile easier.

overall_design: Samples included model biofilms from 5, 30, 120, 240, and 360 minutes after transitioning from planktonic to sessile.  Samples were taken for both P. gingivalis alone and equal cell counts of P. gingivalis and S. gordonii mixed and transitioned to a sessile state. Two or three biological replicates were taken for each time point. Planktonic P. gingivalis cells were measured as a time zero control. The results were compared to the time zero control and P. gingivalis plus S. gordonii samples were compared to P. gingivalis alone samples at each time point.

first: Erik

last: Hendrickson

first: Tiansong

last: Wang

first: Daniel

middle: P

last: Miller

first: Qian

first: Marvin

last: Whitely

first: Richard

last: Lamont

first: Murray

last: Hackett


title: Comparative DNA Methylation analysis reveals genes regulating adipogenesis in Laiwu pigs over two developmental stages

status: Public on Jan 13 2017

city: Taian

first: Yuding

address: No. 61, Daizong Street

institute: Shandong Agricultural University

summary: We performed DNA methylation analysis of the longissimus dorsi (LD) muscle between two development stages (120 and 240 days after birth) in Laiwu pigs, an indigenous fatty pig breed in North China. This study provides a reference for exploring methylation regulation mechanisms affecting fat deposition in obese pigs.

overall_design: Examination of DNA Methylation variation of different development stages in Laiwu pig.

first: Cai

last: Ma

first: Yi

last: Sun

first: Li

last: Kang

first: Yunliang

last: Jiang


title: CPEB4 prevents hepatic steatosis [RIP-Seq]

city: Barcelona

first: Oscar

last: Reina Garcia

summary:
The Cytoplasmic Polyadenylation Element Binding (CPEB)-family of RNA-binding proteins regulates pre-mRNA processing and translation of CPE-containing mRNAs in early embryonic development and synaptic activity. However, the specific functions of each CPEB in the adult organism are poorly understood. Here we show that CPEB4 is required to suppress high fat diet- and aging-induced endoplasmic reticulum (ER) stress, and its subsequent hepatic steatosis. Stress-activated expression of CPEB4 in the liver is controlled through a double layer of regulation. First, Cpeb4 is transcriptionally regulated by the circadian clock and then, its mRNA translation is regulated by the Unfolded Protein Response (UPR) through the upstream Open Reading Frames (uORFs) present in its 5’ UTR. Thus, CPEB4 is synthesized only upon ER-stress but the amplitude of the induction is circadian. In turn, CPEB4 activates a second wave of UPR-translation required to maintain ER and mitochondrial homeostasis. Our results suggest that combined transcriptional and translational regulation of CPEB4 generates a “circadian mediator”, which
coordinates the hepatic UPR activity with periods of high ER protein-folding demand preventing non-alcoholic fatty liver disease (NAFLD).

overall_design: RNA-immunoprecipitation sequencing of CPEB4-associated mRNAs in WT and CPEB4-KO primary hepatocytes.

first: Carlos

last: Maillo

first: Raul

last: Mendez


title: Beauveria bassiana MBF 1 (BbMBF1) regulating genes involved in fungal resistance to oxidative stress

city: Hangzhou

first: Shenghua

last: Ying

address: Yu-hang-tang Road 688

institute: Zhejiang University

summary: Gene BbMBF1 playes an essential role in fungal response to oxidative stress, a determinant to the biocontrol  potential of entomopathogenic fungi.  The genome-wide exprssion analysis involved in stress response was analyzed by using high throughput sequencing (RNA-Seq). Our transcriptional profiles revealed that numerous differentially expressed genes (DEGs), of which involved in metabolism, cell transport and cell rescue, were significantly controlled by BbMBF1 during response to oxidative stress.

overall_design: Total RNA obtained from BbMBF1 disruption mutant were compared to that of wild type strain (WT) grown in SDB mediua (Glucose 4%, Peptone 1%, and Yeast extract 1%).

first: Sheng-Hua

first: Ming-Guang

last: Feng


title: CPEB4 prevents hepatic steatosis [RNA-Seq]

overall_design: mRNA profiles of total liver RNA and liver ER-associated RNA from WT and CPEB4-KO mice


title: RNA-Seq of Bacillus subtilis and its phage AR9 during the infection

status: Public on Jan 14 2017

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: Time course of after infection (5 min, 20 min and 40 min) of Bacillus subtilis by phage AR9

sample_organism:
Bacillus subtilis
Bacillus phage AR9

platform_organism:
Bacillus subtilis
Bacillus phage AR9

overall_design: Examination of changes of gene expression at early (5 min), middle (20 min) and late (40 min) stages of infection of Bacillus subtilis by phage AR9. Mapping of transcription start sites of phage AR9.

first: Daria

last: Lavysh

first: Konstantin

last: Severinov


title: Differential expression analysis of a Vibrio parahaemolyticus ∆luxO mutant compared to wild-type in mouse intestinal mucus

city: Newark

first: E Fidelma

last: Boyd

state: DE

address: 118 Wolf Hall

institute: University of Delaware

summary: Vibrio parahaemolyticus is the leading bacterial cause for seafood-related gastroenteritis worldwide. As an intestinal pathogen, V. parahaemolyticus competes with other commensal bacteria for the same pool of nutrients. The major source of nutrition for intestinal bacteria is intestinal mucus. We wanted to determine the expression profile of wild-type V. parahaemolyticus in mouse intestinal mucus and then perform a differential expression analysis in a ∆luxO deletion mutant, in which the high cell density quorum sensing regulator OpaR is constitutively expressed and low cell density regulator AphA is repressed.

overall_design: RNA-Seq analysis was performed on RNA isolated from two biological replicates of wild-type Vibrio parahaemolyticus strain RIMD2210633 and three biological replicates the  ∆luxO mutant strain, grown in M9 minimal media supplemented with mouse intestinal mucus.

first: Sai

middle: S

last: Kalburge

first: Ethna

middle: F


title: Comparative expression profile of microRNAs in Anopheles anthropophagus midgut after blood feeding and Plasmodium infection

city: Wenzhou

first: liyang

last: huang

institute: Wenzhou Medical College

summary: High-throughput sequencing was performed to identify miRNAs profiles of Anopheles anthropophagus midguts after blood feeding and Plasmodium infection. The expression patterns of miRNA in different midgut libraries were compared basing on transcripts per million reads (TPM). This study provides novel regulated miRNAs information of An. anthropophagus during blood feeding and parasite infection

overall_design: Experiment was divided into three groups.Midguts dissection of female adults was performed 48 h post-blood feeding on P. berghei–infected or uninfected ICR mice . Total RNAs were extracted from dissected tissue. The small RNA samples were collected and subsequently sequenced by illumina Hiseq2000 . Raw reads generated post high-throughput sequencing was processed. Clean reads derived from deep sequencing were trimmed and filtered with BOWTIE software to fetch sequences having an appropriate length (15-32 nt). Mature and pre-miRNA sequences of available mosquito species namely Anopheles gambiae, Aedes aegypti were used as a reference miRNAs database from the mirbase v.21. Data derived from three midguts libraries generated after sequencing were analyzed separately. The identification of novel miRNA were performed by using RNA fold and miRDeep2 .

first: Wenquan

last: Liu

first: Zhenhua

last: Hao

first: Liyang

last: Huang

first: Lingzi

last: Chen

first: Qimei

last: Wei

first: Liya

last: Cai

first: Shaohui

last: Liang


title: Genome-wide analysis of simian virus 40 infected cells

city: Kunming

first: Jiandong

last: Shi

state: Yunnan

address: 935# Jiaoling Road

department: Department of Vaccine Research

institute: Institute of Medical Biology

summary:
The goal of this study was to compare the whole transcriptional profile (RNA-seq) of simian virus 40 infection and mock infected Vero cells at 72 hours post infection.
Circular RNAs (circRNAs), identified as a class of widely expressed endogenous regulatory RNAs, are involved in diverse physiological and pathological processes. However, their role in viral pathogenesis and cellular antiviral response remains unexplored. In this study, a potent DNA tumor virus, simian virus 40 (SV40), was used as a model to investigate the viral influences on cellular circRNA transcriptome.
Using RNA-seq, 15,241 putative circRNAs were identified de novo from 5,057 parental genes in monkey kidney–derived Vero cells. The expression of selected circRNAs was confirmed by reverse transcription-polymerase chain reaction and Sanger sequencing. Further analysis showed that most circRNAs comprised multiple exons, and most parental genes produced multiple circRNA isoforms. A total of 134 significantly dysregulated circRNAs, including 103 upregulated and 31 downregulated circRNAs, were found after SV40 infection. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that various cancer-related pathways, including p53 and Wnt pathway, could be affected by SV40 infection via the alteration of the circRNA hosting genes. Moreover, diverse cellular immune pathways, including Toll-like receptor pathway and Janus kinase–signal transducer and activator of transcription pathway, could also be affected by SV40 infection. An integrated circRNA-miRNA-gene analysis suggested the putative function of circRNAs as cellular and viral miRNA decoys to indirectly regulate the gene expression during SV40 infection. This study presented the first comprehensive expression and functional profile of circRNAs in response to SV40 infection, thus providing new insights into the mechanisms of viral pathogenesis and cellular immune response.

overall_design: Whole transcriptome profiles of  simian virus 40 infection and mock infected Vero cells at 72 hours post infection were generated by deep sequencing, in triplicate, using Illumina Hiseq 4000 platform.

first: Yunzhang

last: Hu


title: The Nature and Nurture of Cell Heterogeneity: Accounting for Macrophage Gene-environment Interactions with Single-cell RNA-Seq

city: Oxford

first: Eshita

last: Sharma

state: Oxfordshire

address: Roosevelt Drive, Headington

department: Bioinformatics

institute: Wellcome Trust Centre for Human Genetics

summary:
Background: Single-cell RNA-Seq can be a valuable and unbiased tool to dissect cellular heterogeneity, despite the transcriptome’s limitations in describing higher functional phenotypes and protein events. Perhaps the most important shortfall with transcriptomic ‘snapshots’ of cell populations is that they risk being descriptive, only cataloging heterogeneity at one point in time, and without microenvironmental context. Studying the genetic (‘nature’) and environmental (‘nurture’) modifiers of heterogeneity, and how cell population dynamics unfold over time in response to these modifiers is key when studying highly plastic cells such as macrophages.
Results: We introduce the programmable PolarisTM microfluidic lab-on-chip for single-cell sequencing, which performs live-cell imaging while controlling for the culture microenvironment of each cell. Using gene-edited macrophages we demonstrate how previously unappreciated knockout effects of SAMHD1, such as an altered oxidative stress response, have a large paracrine signaling component. Furthermore, we demonstrate single-cell pathway enrichments for cell cycle arrest and APOBEC3G degradation, both associated with the oxidative stress response and altered proteostasis. Interestingly, SAMHD1 and APOBEC3 are both HIV-1 inhibitors (‘restriction factors’), with no previously known co-regulation.
Conclusion: As single-cell methods continue to mature, so will the ability to move beyond simple ‘snapshots’ of cell populations towards studying the determinants of population dynamics. By combining single-cell culture, live-cell imaging, and single-cell sequencing, we have demonstrated the ability to study cell phenotypes and microenvironmental influences. It’s these microenvironmental components - ignored by standard single-cell workflows - that likely determine how macrophages, for example, react to inflammation and form treatment resistant HIV reservoirs.

overall_design: Stem cell derived macrophages (wildtype and SAMHD1 knockout) were single-cell cultured for 1h or 8h under for different media conditions (with/without lipopolysaccharide, with/without conditioned media to account for inter-macrophage signalling)

first: Quin

last: Wills


title: mRNA Expression Profiles of Macronuclear Development in Oxytricha trifallax Implicate Scores of Functionally and Evolutionarily Diverse DNA and RNA Binding Proteins in the Program

first: Alan

last: Zahler

address: Sinsheimer Labs

institute: UC Santa Cruz

summary: As part of sexual reproduction, the stichotrichous ciliate Oxytricha trifallax orchestrates a remarkable transformation of one of the newly formed germline micronuclear genomes, in which hundreds of thousands of gene pieces are stitched together, excised from chromosomes, and amplified dozens of times, to yield a functional somatic macronuclear genome composed of ~16,000 distinct DNA molecules that typically encode a single gene. Little is known about the proteins that carry out this process. We profiled mRNA expression as a functional of macronuclear development and identified hundreds of mRNAs preferentially expressed at specific times during the program. We find that a disproportionate number of these mRNAs encode proteins that are involved in DNA and RNA functions. Many mRNAs preferentially expressed during macronuclear development have paralogs that are not differentially expressed during development or are expressed at different times, including many components of RNA polymerase II and homologous recombination complexes, suggesting that gene duplication and functional specialization were a key source of evolutionary innovation. While many mRNAs preferentially expressed during macronuclear development encode proteins with no recognizable homolog, hundreds encode proteins that are well-conserved, including a disproportionate number with links to germline function or development in multicellular lineages. These analyses have thus identified scores of factors that may have ancient roles in sexual propagation, germline specialization and differentiation, in addition to dozens of novel factors with striking expression patterns, some of which likely evolved to carry out these extraordinary DNA manipulations.

overall_design: Examination of gene expression changes during macronuclear development in the ciliated protozoan Oxytricha trifallax

first: Zachary

middle: T

last: Neeb

first: Daniel

middle: J

last: Hogan

first: Sol

last: Katzman


title: A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7]

city: Dallas

first: Stephen

last: Li

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

summary: Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration.

overall_design: Gene expression profile was generated by comparing sorted Twist2+ and Pax7+ cells from skeletal muscle after brief culture in growth medium

first: Ning

first: Eric

last: Olson


title: A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7 fresh sort]

overall_design: Gene expression profile was generated by comparing freshly sorted Twist2+ and Pax7+ cells from skeletal muscle

last: Liu


title: A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle

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

overall_design: Refer to individual Series


title: RNA Sequencing Reveals Regulation of Marginal Zone B-Cell Differentiation by MicroRNA-146a

city: los angeles

first: matteo

last: pellegrini

address: 610 charles young drive east

institute: UCLA

summary: Splenocytes were FACS-sorted from Wild-type and Mir146a-/- mice to isolate specific B-cell developmental stages. Utilizing high-throughput sequencing, we comparatively analyzed developmental stage-specific splenic B cell transcriptomes, including Transitional-1 (T1), Transitional-2 (T2), Marginal zone (MZ) and Follicular (FO) in both Wild-type and Mir146a-/- B cells. Two replicates of each developmental stage were submitted for high-throughput sequencing.

overall_design: Transcriptomic profiles of primary B cell developmental subsets (T1, T2 MZ, FO) from Wild-type and Mir146a-/- mice in duplicate.

first: Dinesh

last: Rao

first: Jennifer

last: King


title: A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 overexpression]

overall_design: Gene expression profile was generated by comparing Twist2- or GFP-overexpressing Tw2 myoblasts before and after differentiation.


title: Epigenetic alterations affecting transcription factors and signaling pathways in stromal cells of endometriosis: Expression data (RNA-seq)

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

summary: Endometriosis is characterized by growth of endometrial-like tissue outside the uterine cavity. Since its pathogenesis may involve epigenetic changes, we used Illumina 450K Methylation Beadchips to profile CpG methylation in endometriosis stromal cells compared to stromal cells from normal endometrium. We validated and extended the Beadchip data using bisulfite sequencing (bis-seq), and analyzed differential methylation (DM) at the CpG-level and by an element-level classification for groups of CpGs in chromatin domains. Genes found to have DM included examples encoding transporters (SLC22A23), signaling components (BDNF, DAPK1, ROR1, and WNT5A) and transcription factors (GATA family, HAND2, HOXA cluster, NR5A1, OSR2, TBX3). Intriguingly, among the TF genes with DM we also found JAZF1, a proto-oncogene affected by chromosomal translocations in endometrial stromal tumors. Using RNA-Seq we identified a subset of the DM genes showing differential expression (DE), with the likelihood of DE increasing with the extent of the DM and its location in enhancer elements. Supporting functional relevance, treatment of stromal cells with the hypomethylating drug 5aza-dC led to activation of DAPK1 and SLC22A23 and repression of HAND2, JAZF1, OSR2, and ROR1 mRNA expression. We found that global 5hmC is decreased in endometriotic versus normal stroma, and for JAZF1 and BDNF examined by oxidative bis-seq, found that when 5hmC is detected, patterns of 5hmC paralleled those of 5mC. Together with prior studies, these results define a consistent epigenetic signature in endometriosis stromal cells and nominate specific transcriptional and signaling pathways as therapeutic targets.

overall_design: Total RNA from 9 primary cell cultures of endometriosis stromal cells from ovarian ectopic sites (OESC) and control endometrial stromal cells (CESC)  were examined using RNA-Seq.

first: Iveta

last: Yotova

first: Emily

last: Hsu

first: Catherine

last: Do

first: Aulona

last: Gaba

first: Matthias

last: Sczabolcs

first: Sabine

last: Dekan

first: Lukas

last: Kenner

first: Rene

last: Wenzl


title: Vitamin D/Vitamin D Receptor (VDR) Axis Regulates LMNA gene expression

city: St Louis

first: Susana

last: Gonzalo

state: MO

address: 1100 S Grand Blvd

department: Biochemistry and Molecular Biology

institute: Saint Louis University


title: Vitamin D/Vitamin D Receptor (VDR) Axis Regulates LMNA gene expression [ChIP-Seq]

summary: ChIP with VDR antibody followed by DNA sequencing to determine if VDR binds the LMNA gene locus

overall_design: BJ fibroblasts were treated with 10-7 M 1,25D or FBS (vehicle) for 24 h, and cells crosslinked, sonicated, and chromatin isolated to perform ChIP analyses as described in Gonzalez-Suarez et al. EMBO Journal 2009. Chromatin was immunoprecipitated using anti-VDR antibody (10 mg) or IgG (10 mg) as control.

first: Dale

last: Dorsett

first: Ray

last: Kreienkamp


title: Lurbinectedin specifically triggers the degradation of phosphorylated RNA Polymerase II and the formation of DNA breaks in cancer cells

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

summary: We have defined the mechanism of action of lurbinectedin, a marine-derived drug exhibiting a potent anti-tumorigenic activity across several cancer cell lines and tumor xenografts. This drug currently undergoing clinical evaluation in ovarian, breast and small-cell lung cancer patients inhibits the transcription process through (1) its binding to CG rich sequences, mainly located around the promoter of protein coding genes; (2) the irreversible stalling of elongating RNA polymerase II (Pol II) on the DNA template and its specific degradation by the ubiquitin/proteasome machinery and (3) the generation of DNA breaks. The finding that inhibition of Pol II phosphorylation prevents its degradation and the formation of DNA breaks after drug treatment underscores the connection between transcription elongation and DNA repair. Our results not only help to better understand the high specificity of this drug in cancer therapy but also improve our understanding of an important transcription regulation mechanism.

overall_design: To identify genomic binding sites of lurbinectedin in A549 lung cancer cells, we performed a chemical affinity capture (Chem-Seq) with magnetic streptavidin beads to isolate the biotin-linked lurbinectedin DNA fragments followed by massively parallel DNA sequencing.

first: Gema

last: Santamaria

first: Carlos

last: Genes

first: Emmanuel

last: Compe

last: Ye

first: Jean

last: Egly

last: Galmarini


title: On the Relationships in Rhesus Macaques between Chronic Ethanol Consumption and the Brain Transcriptome (Central Nucleus of the Amigdala - CeA)

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

summary: This is the first description of the effects of chronic ethanol consumption on the brain transcriptome in a non-human primate (rhesus macaque).  Thirty male animals self-administered ethanol on a daily basis for over 12 months. Gene expression was measured with RNA-Seq in the central nucleus of the amygdala (CeA). Genes negatively correlated with consumption were enriched in functional annotations associated with translation and included clusters of ribosomal and mitochondrial ribosomal proteins. Genes positively correlated with consumption were enriched in membrane annotations including neuron and synapse part. Genes in the latter category included Ctnna2, Shank1, Vamp2, and Syn1. Gene-level expression data were clustered using the Weighted Gene Coexpression Network Analysis (WGCNA) algorithm to identify hub nodes affected by excessive consumption. Key hubs included Nf1, Nkain2, Tmem108 and Penk. The data were also analyzed for alternative exon usage (Iancu et al., 2015). Additional translation and membrane related genes affected by excessive consumption were detected. These included Grm2, Dpysl2 and Kcnc4. Overall, the data illustrate that the effects of excessive ethanol consumption are broad, consistent with the observation that ethanol affects the expression of numerous hub genes.

overall_design: 28 samples of Rhesus Macaques that were experimentally naïve at the onset of alcohol induction (Macaca mulatta, n = 28, 4-11 years, 6-8 kg), were first induced to drink 4% (w/v) ethanol and then allowed to self-administer ethanol for over 12 months under open access conditions (22h/d, 7d/wk) with concurrent meals and continuous access to water.

first: Ovidiu

middle: D

last: Iancu

first: Alexander

last: Colville

first: Nicole

last: Walter

first: Denesa

last: Oberbeck

first: James

middle: B

last: Daunais

first: Christina

last: Zheng

first: Robert

last: Searles

first: Shannon

last: McWeeney

first: Kathleen

last: Grant

last: Hitzemann


title: Integrated genomic analyses of de novo pathways underlying atypical meningiomas [miRNA-seq]

status: Public on Jan 12 2017

city: New Haven

first: Akdes

last: Serin Harmanci

state: Connecticut

address: 300 Cedar Street TAC S330

department: Departments of Neurosurgery and Genetics

institute: Yale University

summary: Meningiomas are mostly benign brain tumors, with a potential for becoming atypical or malignant. Based on comprehensive genomic, transcriptomic and epigenomic analyses of meningiomas, we compared benign tumors to atypical ones. We show that the vast majority of primary (de novo atypical meningiomas display loss of NF2, which co-occurs either with genomic instability or recurrent mutations in SMARCB1. These tumors harbor increased H3K27me3 repressive signal and a hypermethylated phenotype, mainly occupying the polycomb repressive complex 2 (PRC2 binding sites in human embryonic stem cells (hESCs, thereby phenocopying a more primitive cellular state. Consistent with this observation, and based on differential gene expression analysis as well as correlation of mRNA:miRNA regulatory networks, atypical meningiomas exhibit up-regulation of EZH2, the catalytic subunit of the PRC2 complex, well as the E2F2 and FOXM1 transcriptional networks that promote proliferation through activation of the cell cycle pathways. In addition, based on H3K27ac ChIP-seq analysis, we show atypical tumors to display an activated super-enhancer near the meningeal identity transcription factor ZIC1, leading to its transcriptional upregulation. Importantly, these primary atypical meningiomas do not harbor activating TERT promoter mutations, which have been reported in atypical tumors that progressed from benign ones. Our results establish the genomic landscape of primary atypical meningiomas, differentiating their profile from benign and progressed tumors and establishing novel therapeutic targets.

overall_design: Analysis of meningioma miRNA data for each mutation subtype.

first: Mark

last: Youngblood

first: Murat

last: Gunel