title: Identification of PTBPs RNA binding sites in mouse brain

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

summary: PTBP1 and PTBP2 are RNA-binding proteins that control RNA processings, including alternative pre-mRNA splicing. The sequential down-regulation of the two proteins is necessary for neuronal maturation. However, their binding substrates in neural tissues have not been examined.

overall_design: Use modified version of iCLIP-seq protocols to identify RNA elements crosslinked to either flag-PTBP1 or PTBP2 in vivo in the mouse cerebral cortex.

first: Sika

last: Zheng

first: Chia


title: Transcriptome of the mouse neocortices

status: Public on Dec 07 2016

city: Riverside

first: Sikaz

state: CA

address: 201 School of Medicine Research Building, 900 University Avenue

department: Biomedical Sciences

country: USA

institute: University of California Riverside

type: Expression profiling by high throughput sequencing

summary: Derive  alternative splicing regulatory networks of PTBP1 and PTBP2

overall_design: transcriptome profiling at various ages and genotypes

first: Douglas

last: Black


title: A multi-step transcriptional and chromatin cascade underlies motor neuron programming (RNA-Seq)

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

summary: Direct programming via the overexpression of transcription factors (TFs) aims to control cell fate at a precision that will be instrumental for clinical applications. However, direct programming of terminal fates remains an obscure process. Taking advantage of the rapid and uniquely efficient programming of spinal motor neurons by overexpression of Ngn2, Isl1 and Lhx3, we have characterized gene expression, chromatin and transcription factor binding time-course dynamics during complete motor neuron programming. Our studies point to a surprisingly dynamic programming process. Promoter chromatin and expression analysis reveals at least three distinct phases of gene activation, while programming factor binding shifts from one set of targets to another, controlling regulatory region activity and gene expression. Furthermore, our evidence suggest that the enhancers and genes activated in the final stage of motor neuron processing are dependent on the combined activities of Isl1 and Lhx3 factors with Ebf and Onecut TFs that are themselves activated midway through the programming process. Our results suggest an unexpected multi-stage model of motor neuron programming in which the programming TFs require activation of a set of intermediate regulators before they complete the programming process.

overall_design: For bulk cell RNA-seq analysis, cells were collected at different time points after NIL induction and RNA isolated using TRIzol LS (Life Technologies) followed by purification using Qiagen RNAeasy kit

first: Silvia

last: Velasco

first: Mahmoud

middle: M

last: Ibrahim

first: Akshay

last: Kakumanu

first: Görkem

last: Garipler

first: Mohamed

middle: A

last: Al-Sayegh

first: Antje

last: Hirsekorn

first: Rahul

last: Satija

first: Uwe

last: Ohler

first: Esteban

middle: O

last: Mazzoni


title: A multi-step transcriptional and chromatin cascade underlies motor neuron programming (ATAC-Seq)

overall_design: 50,000 cells were harvested and washed in ice-cold PBS buffer. After centrifugation the supernatant was aspirated and the cell pellet was resuspended in a master mix of 22.5 µl RNase-free water, 25 µl TD buffer and 2.5 µl TDE1 (transposase enzyme, both Illumina Nextera DNA Library Prep kit), followed by incubation for 60 minutes at 37oC. The reaction was then cleaned using the DNA Clean and Concentrator-5 kit (Zymo Research). The optimal number of PCR cycles was determined to be Ct+4. qPCR reactions were performed using 10% of a master mix of sample, forward and reverse (barcode) primers, 1X SYBR Green I (Biozym) and 1X NEBNext PCR MasterMix (New England Biolabs). Following PCR amplification, the library was cleaned using the DNA Clean and Concentrator-5 kit and eluted in 15 µl 10 mM Tris-Cl pH 8.0. Sample was quantified using Qubit (Life Technologies) measurement and the fragment length distribution was determined using the Bioanalyzer DNA High Sensitivity assay (Agilent). Sequencing was performed on an Illumina NextSeq 500 using V2 chemistry for 150 cycles (paired-end 75nt).


title: Heterotypic mouse models of canine osteosarcoma recapitulate tumor heterogeneity and biological behavior

city: Minneapolis

first: Milcah

last: Scott

state: MN

address: 2101 6th Street Se

department: Department of Microbiology and Immunology

institute: University of Minnesota

summary:
Purpose: The goals of this study were to establish in vivo models that recapitulated the heterogeneous behavior of osteosarcoma and to develop an approach to distinguish genes expressed from tumor cells apart from those expressed from host cells in next generation sequencing (NGS) data from xenograft tumors.

Methods: We used cell lines derived from two spontaneous canine osteosarcoma tumors with distinctly different biological behaviors for heterotypic in vivo modeling. NGS was used to compare the transcriptome profiles of the xenograft tumors to the transcriptome profiles of the parental cell lines and to study the tumor microenvironment of the xenograft tumors. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to a HISAT2 index for mapping which was built from a multi-sequence fasta file containing both the canine (canFam3) and murine (mm10) genomes with the HISAT2 aligner (2.0.2-beta) using default parameters. Rsubread featureCounts (1.4.6) was used to estimate transcript abundance using default parameters. The Bioconductor package ‘edgeR’ (version 3.12.1)  was used for differential gene expression analysis and Partek Genomic Suite (version 6.6) was used for clustering and visualization. Qiagen's Ingenuity Pathway Analysis application (version 01-04) and Thomson Reuter's MetaCore software suite were used for pathway and upstream regulator analysis with differentially expressed genes.

Results: We document that orthotopic canine osteosarcoma xenografts preserve the biological, molecular, and heterotypic biology observed in the tumors from which they were derived. The data also provide insight into the tumor-host interactions and identify targets that could play a role in treatment strategies.

Conclusions: Our study represents the first detailed analysis of xenograft transcriptomes with an approach that allows for accurate examination of tumor-intrinsic properties, as well as organotypic tumor-stromal interaction that may influence tumor progression.

sample_organism:
Canis lupus familiaris
Mus musculus

platform_organism:
Canis lupus familiaris
Mus musculus

overall_design: mRNA profiles of xenograft tumor from cell lines derived from two spontaneous canine osteosarcoma tumors with different biological behavior (OS-1 and OS-2) were generated by deep sequencing, in quarduplicate, using Illumina HiSeq 2500.

middle: C

first: Hirotaka

last: Tomiyasu

first: John

middle: R

last: Garbe

first: Ingrid

last: Cornax

first: Clarissa

last: Amaya

first: M

middle: G

last: O’Sullivan

first: Subbaya

last: Subramanian

first: Brad

last: Bryan

first: Jaime

middle: F

last: Modiano


title: Fat cells regenerate from myofibroblasts during wound healing

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

summary: We report transcriptomes of myofibroblasts from mouse skin wounds. Myofibroblasts were FACS sorted as Zombie-neg;tdTomato-hi cells from Sm22-Cre;TdTomato mice. We identified and analyzed 4,120 differentially expressed transcripts across four post-wounding time points, day 12, day 15, day 21 and day 26.

overall_design: Examination of FACS sorted wound myofibroblasts from four consecutive post-wounding time points

first: Christian

last: Guerrero-Juarez

first: George

last: Cotsarelis


title: Collagen XVII/Laminin-5 Activates Epithelia-to-Mesenchymal Transition and is Associated with Poor Prognosis in Lung Cancer

city: Taipei

first: Chen-Chi

last: Liu

address: No. 155, Sec. 2, Li-Nong Street

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang-Ming University School of Medicine

summary: We searched for candidate genes responsible for Epithelial-to-mesenchymal transition (EMT) by microarray analysis of cultured lung cancer cells with or without the property of spheroid formation. We found increased expression of a variety of adhesion molecules in cancer stem-like cells, including Collagen XVII. Further functional assays and signaling pathway were also investigated.

overall_design: A549 cells were cultured in serum-free medium supplemented with EGF and bFGF (Daoy medium) for 12 days. Control was A549 cells cultured in DMEM with supplemented with 10% FBS. Cells were harvested for RNA extraction and hybridization on Affymetrix Microarray. Differentially expression genes between treatment and control were identified for functional study.

first: Jiun-Han

last: Lin

first: Tien-Wei

last: Hsu

first: Jer-Wei

last: Chang

first: Kelly

last: Su

first: Jyuan-Wei

first: Han-Shui

first: Shih-Chieh

last: Hung


title: Functional Haploid Human Oocytes Generated from Polar Body Genomes

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Investigating Conservation of the Cell-Cycle-Regulated Transcriptional Program in the Fungal Pathogen, Cryptococcus neoformans

city: Hanover

first: Christina

last: Kelliher

state: NH

address: 7400 Hinman

department: Molecular & Systems Biology

institute: Geisel School of Medicine at Dartmouth

summary: Cell-cycle transcript dynamics from two species of wild-type budding yeast growing at 30 degrees Celsius in rich media: Saccharomyces cerevisiae (BF264-15D background) and Cryptococcus neoformans var. grubii (H99F background). We compared programs of cell-cycle-regulated genes between distantly related budding yeasts.

sample_organism:
Saccharomyces cerevisiae
Cryptococcus neoformans

overall_design: One time course experiment for each yeast over multiple cell cycles

first: Adam

last: Leman

first: Crystal

middle: S

last: Sierra

first: Steven

middle: B

last: Haase


title: Functional Haploid Human Oocytes Generated from Polar Body Genomes (RNA-Seq)

summary: Oocyte defects lie at the heart of some forms of infertility and could potentially be addressed therapeutically by alternative routes for oocyte formation. Here, we describe the generation of functional human oocytes following nuclear transfer of first polar body (PB1) genomes from metaphase II (MII) oocytes into enucleated donor MII cytoplasm (PBNT). The reconstructed oocytes supported the formation of de novo meiotic spindles and, after fertilization with sperm, meiosis completion and formation of normal diploid zygotes. While PBNT zygotes developed to blastocysts less frequently (42%) than controls (75%), genome-wide genetic, epigenetic, and transcriptional analyses of PBNT and control ESCs indicated comparable numbers of structural variations and markedly similar DNA methylation and transcriptome profiles. We conclude that rescue of PB1 genetic material via introduction into donor cytoplasm may offer a source of oocytes for infertility treatment or mitochondrial replacement therapy for mtDNA disease.

overall_design: RNA sequencing collected from PBNT1 and hESO-14

first: Manoj

last: Hariharan

first: Ryan

last: O'Neil

first: Rosa

last: Castanon

last: Nery


title: m6A controls neurogenesis and sex determination in Drosophila via its nuclear reader protein YT521-B [MeRIP-Seq, S2R+ cells]

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

summary: N6-methyladenosine RNA (m6A) is the most abundant internal mRNA modification in mammals. While its role in the regulation of posttranscriptional gene expression is beginning to be unveiled, its function during development of complex organisms is poorly understood. Here, we identify Spenito as a novel member of the methyltransferase complex and show that m6A in Drosophila is necessary for proper synaptic growth, and in regulation of early steps of pre-mRNA splicing. Splicing of Sex-lethal and of its downstream targets are defective in animals lacking m6A, revealing also important roles in sex determination and dosage compensation. Finally, we implicate the nuclear m6A reader protein, YT521-B, as a crucial effector of m6A modifications in vivo. Altogether, our work provides important novel insights into m6A biology through identification and characterization of both m6A-writing and -reading proteins in Drosophila and their effects on splicing, neurogenesis and sex-determination within the context of the whole animal.

overall_design: meRIP-Seq in S2R+ cells (2 conditions, duplicates)

first: Tina

last: Lence

first: Junaid

last: Akhtar

first: Marc

last: Bayer

first: Katharina

last: Schmid

first: Laura

last: Spindler

first: Cheuk

middle: H

last: Ho

first: Nastasja

last: Kreim

first: Miguel

last: Andrade-Navarro

first: Burkhard

last: Poeck

first: Mark

last: Helm


title: Functional Haploid Human Oocytes Generated from Polar Body Genomes (Bisulfite-Seq)

first: Joseph

last: Ecker

overall_design: Whole-genome single-base resolution methyl-C sequencing collected from PBNT1 and hESO-14


title: m6A controls neurogenesis and sex determination in Drosophila via its nuclear reader protein YT521-B [RNA-Seq, heads]

overall_design: RNA-Seq in female adult heads (3 conditions, triplicates)


title: A multi-step transcriptional and chromatin cascade underlies motor neuron programming (Histone modification ChIP-seq)

first: Shaun

last: Mahony

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Histone modifications were characterized during the direct programming of ES cells into motor neurons using over-expression of Ngn2-Isl1-Lhx3 programming factors. ChIP-seq experiments were performed targeting H3K4me3, H3K4me2, H3K4me1, H3K27ac and H3K27me3 at various time-points during the programming process. Input sequencing at each time-point was performed as a control. Input experiments are provided under GEO accession number: GSE80321

first: Silvia

last: Velasco

first: Mahmoud

last: Ibrahim

first: Akshay

last: Kakumanu

first: Görkem

last: Garipler

first: Mohamed

last: Al-Sayegh

first: Antje

last: Hirsekorn

first: Rahul

last: Satija

first: Uwe

last: Ohler

first: Esteban

last: Mazzoni


title: Telomeric retrotransposon HeT-A contains a bidirectional promoter that initiates divergent transcription of piRNA precursors in Drosophila germline

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

type: Non-coding RNA profiling by high throughput sequencing

summary: PIWI-interacting (pi) RNAs provide silencing of transposable elements (TE) in the germline. Drosophila telomeres are maintained by transpositions of specialized telomeric retroelements. piRNAs generated from sense and antisense transcripts of telomeric elements provide telomere length control in the germline. Previously, we have found that antisense transcription of the major telomeric retroelement HeT-A is initiated upstream of the HeT-A sense transcription start site. Here, we performed a deletion analysis of the HeT-A promoter and show that common regulatory elements are shared by sense and antisense promoters of HeT-A. Therefore, the HeT-A promoter is a bidirectional promoter capable of processive sense and antisense transcription. Ovarian small RNA data shows that a solo HeT-A promoter within an euchromatic transgene initiates divergent transcription of transgenic reporter genes and subsequent processing of these transcripts into piRNAs. These events lead to the formation of a divergent uni-strand piRNA cluster at solo HeT-A promoters, in contrast to endogenous telomeres that represent strong dual-strand piRNA clusters. Solo HeT-A promoters are not immunoprecipitated with Heterochromatin Protein 1 (HP1) homolog Rhino, a marker of the dual-strand piRNA clusters, but are associated with HP1 itself, which provides piRNA-mediated transcriptional repression of the reporter genes. Unlike endogenous dual-strand piRNA clusters, the solo HeT-A promoter does not produce overlapping transcripts. In a telomeric context, however, bidirectional promoters of tandem HeT-A repeats provide read-through transcription of both genomic strands, followed by Rhi binding. These data indicate that Drosophila telomeres share properties of uni-strand and dual-strand piRNA clusters.

overall_design: The fractions of small RNAs (19-29 nt) from ovaries of 3 transgenic strains of Drosophila melanogaster were sequenced using Illumina HiSeq 2000.

first: Natalia

last: Akulenko

first: Alla

last: Kalmykova


title: Gamma oscillations attenuate amyloid pathology and trigger a protective microglia response in a mouse model of Alzheimer's disease

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

summary: Gamma oscillations (20-50Hz) are a common local field potential signature in many brain regions that are generated by a resonant circuit between fast-spiking parvalbumin (PV)-positive interneurons and pyramidal cells. Changes in the magnitude and frequency of gamma have been observed in several neuropsychiatric disorders.  However, it is unclear how disruptions in gamma oscillations affect cellular pathologies seen in these disorders. Here, we investigate this using the 5XFAD mouse model of Alzheimer’s disease (AD) and find reduced power and magnitude of behaviorally driven gamma oscillatory activity — even before the onset of plaque formation or measurable cognitive decline. Because of the early onset, we aimed to determine if exogenous manipulations of gamma could influence the progression of disease pathology. We find that driving PV-positive neurons at gamma frequency (40Hz) using channelrhodopsin-2 reduced total levels of amyloid-β (Aβ) 40 and 42 isoforms in the hippocampus of 5XFAD mouse. Driving PV-positive neurons at other frequencies, or driving excitatory neurons, did not reduce Aβ levels.  Furthermore, driving PV-positive neurons reduced enlarged endosomes in hippocampal neurons and cleavage intermediates of APP in 5XFAD mouse. Gene expression profiling revealed a neuroprotective response with morphological transformation of microglia and markedly increased phagocytosis of Aβ by microglia. Inspired by these observations, we designed a non-invasive light-flickering paradigm that drives 40Hz gamma activity in mouse visual cortex. The light-flickering paradigm profoundly reduced Aβ40 and Aβ42 levels in the visual cortex of pre-symptomatic mice and greatly mitigated plaque load in the visual cortex of aged, symptomatic mice. This reduction was completely blocked by a GABA-A antagonist, providing further support for an essential role of GABAergic signaling in mediating neuroprotective gamma activity. Overall, our findings uncover a dramatic and previously unappreciated function of the brain’s endogenous gamma rhythms in reducing the production and increasing the clearance of Aβ  peptides, whose accumulation is believed to drive the pathogenesis of AD.

overall_design: Two to four weeks following virus injection and implant placement, hippocampal CA1 neurons were optigenetically manipulated. During the experiment, 1mW of optical stimulation was delivered for 1h using a 40Hz stimulation protocol.

first: Hannah

last: Iaccarino

first: Annabelle

last: Singer

first: Fan

last: Gao


title: A multi-step transcriptional and chromatin cascade underlies motor neuron programming (single-cell RNA-seq)

first: Shaun

last: Mahony

overall_design: Gene expression was characterized by single-cell RNA-seq during the direct programming of ES cells into motor neurons using over-expression of Ngn2-Isl1-Lhx3 programming factors.


title: Sutherlanida extract inhibits Hedgehog signaling target genes

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

summary:
Sutherlandia frutescens (L) R. Br. (Sutherlandia) is a South African botanical that is traditionally used to treat a variety of health conditions, infections and diseases, including cancer.
We hypothesized Sutherlandia might act through Gli/ Hedgehog (Hh)-signaling in prostate cancer cells and used RNA-Seq transcription profiling to profile gene expression in TRAMPC2 murine prostate cancer cells with or without Sutherlandia extracts.
We found 50% of Hh-responsive genes can be repressed by Sutherlandia ethanol extract, including the canonical Hh-responsive genes Gli1 and Ptch1 as well as newly distinguished Hh-responsive genes Hsd11b1 and Penk.

overall_design: Using mouse prostate cancer TRAMPC2 cells, we treated TRAMPC2 cells with  Hh ligand conditioned medium (Hh-CM), 8ug/ml or 80ug/ml Sutherlandia, co-treatment of Hh-CM with 8ug/ml or 80ug/ml Sutherlandia for 8 or 24 hrs and performed gene expression profiling using RNA-Seq. Control experiment were set up for both 8hr and 24hr treatment by treating the cells with ethanol only. We have done 2 biological replicate for each treatment.

first: Lu

last: Yuan

first: Lubahn

last: Dennis


title: MicroRNA regulatory mechanisms on Citrus sinensis leaves to magnesium-deficiency

city: Fuzhou

first: Chen

last: Lisong

address: Shangdian street NO.15

country: China

institute: Fujian Agriculture and Forestry University

summary: In China, magnesium (Mg)-deficiency often occurs in citrus orchards, and is responsible for the loss of yield and poor fruit quality. However, very limited data are available on Mg-deficiency-responsive microRNAs (miRNAs) in higher plants. Using Illumina sequencing, we isolated 93 (91 known and 2 novel) up- and 90 (83 known and 7 novel) down-regulated miRNAs from Mg-deficient Citrus sinensis leaves. In addition to the remarkable metabolic flexibility as indicated by the great alteration of miRNA expression, the adaptive responses of leaf miRNAs to Mg-deficiency might also involve the following aspects: (a) accelerating protein turnover and amino acid biosynthesis by repressing the expression of miR2919, miR7812, miR5904 and miR5742; (b) up-regulating stress-related genes by down-regulating miR2919, miR164 and miR7812; (c) enhancing cell transport due to decreased expression of miR2919, miR3946, miR7533, miR1222, miR779, miR6143 and miR2868 and increased expression of miR395, miR1077, miR1160 and miR8019; (d) activating lipid metabolism-related genes by repressing miR158, miR1222, miR7533 and miR3946; (e) inducing cell wall-related genes by decreasing miR7533, miR779 and miR2868 expression; and (f) maintaing primary meristems by down-regulating miR6135. To conclude, we identified some candidate miRNAs that might contribute to Mg-deficiency tolerance. Our results are usefult not only for increasing our understaning of the molecular mechanisms on plant Mg-deficiency tolerance at post-transcriptional level, but also for obtaining the key miRNAs for plant Mg-deficiency tolerance.

overall_design: Two libraries were constructed from Citrus sinensis (L.) Osbeck leaves subjected to 0(0 mM MgSO4，Mg-deficient，LD) or 1(Mg-sufficient,control, LS) mM MgSO4   for 16 weeks, and sequenced by Illumina sequencing. Size fractionated small RNAs (16-30 bp) from total RNA extracts was ligated to 5' and 3' adapters, and reverse transcribed. After PCR amplification the sample was subjected to Solexa sequencing. The clean tags were used for further analysis.

first: Cui-Lan

last: Ma

first: Yi-Ping

last: Qi


title: A multi-step transcriptional and chromatin cascade underlies motor neuron programming (transcription factor ChIP-seq)

overall_design: Transcription factor binding was characterized during the direct programming of ES cells into motor neurons using over-expression of Ngn2-Isl1-Lhx3 programming factors. ChIP-seq experiments were performed targeting Lhx3 (FLAG epitope tag), Isl1, Ngn2, Oct4, Onecut2, and Ebf2 at various time-points during the programming process. Input sequencing at each time-point was performed as a control.

first: Silvia

last: Velasco

first: Mahmoud

last: Ibrahim

first: Akshay

last: Kakumanu

first: Görkem

last: Garipler

first: Mohamed

last: Al-Sayegh

first: Antje

last: Hirsekorn

first: Rahul

last: Satija


title: Adipose Angiotensin AT2 Receptors Modulate Thermogenesis

city: Iowa City

first: Henry

last: Keen

state: IA

department: Pharmacology

institute: University of Iowa

summary: The brain renin-angiotensin system (RAS) stimulates resting metabolic rate in part through a mechanism involving suppression of the circulating RAS.  This effect appears to be mediated through a reduction in  angiotensin AT2 receptor (AT2R) signaling within inguinal fat.  To examine the molecular mechanisms underlying this effect, mice with hyperactivity of the brain RAS (“sRA” mice, expressing human renin via the synapsin promoter and human angiotensinogen via its own promoter) and littermate controls were chronically infused with vehicle or the AT2R specific agonist, CGP-42112a (CGP, 90 ng/hr, 8 wk, sc).  To identify altered signaling pathways, total RNA was isolated from inguinal adipose tissue and transcript abundance was quantitated by RNA-Seq.

overall_design: Four groups of mice were studied: controls receiving either a saline infusion (CON) or a specific angiotensin type 2 receptor agonist (CON_CGP),  transgenic mice with specific activation of the brain renin-angiotensin receiving either a saline infusion (SRA) or a specific angiotensin type 2 receptor agonist (SRA_CGP).  A sample size of N=3-4 was used for each of the four groups.

first: Nicole

middle: K

last: Littlejohn

middle: L

first: Xuebo

last: Liu

first: Curt

middle: D

last: Sigmund

first: Justin

last: Grobe


title: LncPRESS1 is a p53-regulated lncRNA that safeguards pluripotency by disrupting SIRT6 mediated de-acetylation of histone H3K56

city: Houston

first: Yuanxin

last: Xi

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

summary: Recent evidence suggests that lncRNAs play an integral regulatory role in numerous functions, including determination of cellular identity. We determined global expression (RNA-seq) and genome wide profiles (ChIP-seq) of histone post-translational modifications and p53 binding in human embryonic stem cells (hESCs) undergoing differentiation to define a high-confidence set of 40 lncRNAs, which are p53 transcriptional targets. We focused on lncRNAs, highly expressed in pluripotent hESCs and repressed by p53 during differentiation, to identify lncPRESS1 as a p53-regulated transcript that maintains hESC pluripotency in concert with core pluripotency factors. RNA-seq of hESCs depleted of lncPRESS1 revealed that lncPRESS1 controls a gene network that promotes pluripotency. Further, we found that lncPRESS1 physically interacts with SIRT6 to prevent SIRT6 chromatin localization and maintain high levels of histone H3K56 and H3K9 acetylation at promoters of pluripotency genes. In summary, we describe a novel pluripotency-specific lncRNA that safeguards the hESC state by disrupting SIRT6 activity

overall_design: TP53 KD RNA-seq with and without RA, lncRNA KD RNA-seq in H9 human Embryonic Stem cells (hESCs)

first: Abhinav

last: Jain


title: m6A controls neurogenesis and sex determination in Drosophila via its nuclear reader protein YT521-B

first: Jean-Yves

last: Roignant


title: Adaptation of Propionibacterium freudenreichii to long-term survival under gradual nutritional shortage

city: Rennes

first: Hélène

last: Falentin

address: 65 rue de St Brieuc

department: Microbiologie

country: France

institute: INRA

summary: Propionibacterium freudenreichii CIRM-BIA138 was grown for 11 days in YEL medium at 30°C without any addition of nutrients. RNA was extracted  from bacteria harvested 24 H post-inoculation (exponential phase) and 72 H post-inoculation and was depleted from  ribosmic sequences. RNA samples were sequenced on Hiseq 2000 generating single reads of 50 bp.

overall_design: Comparison of genes expressed in stationary growth phase (biological triplicate) in a context of nutritional shortage with those expressed in exponential growth phase (biological triplicate).

first: Flavia

last: Aburjaile


title: Genetic and genomic response to selection for food consumption in Drosophila melanogaster

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

summary: Food consumption is critical for animal survival and reproduction. The biomedical and economic consequences of metabolic diseases arising from excessive food intake, however, are a burden for human society. While the role of neuroendocrine feedback loops, food sensing modalities, and physiological state in regulating food intake are increasingly well understood, other genetic mechanisms remain elusive. Here, we applied ten generations of artificial selection for high and low food consumption in replicate populations of Drosophila melanogaster. The phenotypic response to selection was highly asymmetric, with efficient selection and an average realized heritability of 0.15 in the lines selected for high food consumption. To further nominate candidate genes contributing to response to selection for feeding behavior, we evaluated differences in genome wide gene expression between the selection lines using whole-fly RNA sequencing. We identified 1,631 differentially expressed genes in the analysis pooled across sexes, and 1,267 (2,321) differentially expressed genes in females (males).

overall_design: We applied an ‘evolve and re-sequence’ approach, combined with analysis of divergence in genome wide gene expression to identify strong candidate genes affecting transcriptional regulation of food consumption. We performed ten generations of replicated, divergent artificial selection for high and low food consumption using an advanced intercross population (AIP) derived from as subset of Drosophila Genetic Reference Panel (DGRP) lines as the base population. We performed RNA sequencing of pools of individuals from two replicate lines for both high and low selection at two generations (G9 and G10).

first: Megan

middle: E

last: Garlapow

first: Shanshan

last: Zhou

first: Alexander

middle: W

last: Gearhart

first: Kairsten

last: Fay

first: Wen

last: Huang

first: Tatiana

last: Morozova

first: Gunjan

last: Arya

first: Lavanya

last: Turlapati

first: Genevieve

last: St. Armour

first: Yasmeen

middle: N

last: Hussain

first: Sarah

last: McAdams

first: Sophia

last: Fochler

first: Trudy

last: Mackay


title: RNA sequencing of synaptic and cytoplasmic Upf1-bound transcripts supports contribution of nonsense-mediated decay to epileptogenesis

status: Public on Dec 06 2016

city: Dublin

first: David

last: Henshall

address: 123 St Stephens Green

country: Ireland

institute: Royal College of Surgeons in Ireland

summary: Immunoprecipitation of Upf1-bound RNA from the cytoplasmic and synaptosomal compartments followed by RNA sequencing identified unique populations of NMD-associated transcripts and altered levels after status epilepticus.

overall_design: We sequenced Upf1-bound mRNA transcripts in neurossynaptosome and cytoplasm compartments of the hippocampus in control mice and in mice that underwent status epilepticus.

first: Claire

middle: M

last: Mooney

first: Catherine


title: RAD51 ChIP-seq post treatment with CX-5461

city: Vancouver

first: Steven

last: McKinney

state: BC

address: 675 West 10th Ave

department: Molecular Oncology

country: Canada

institute: British Columbia Cancer Agency

summary: We discovered two small molecule drugs - CX-5461 and CX-3543 - with specific toxicity against BRCA deficiencies in cancer cells and xenograft models. Both CX-5461 and CX-3543 have been previously recognized as RNA pol I inhibitors. CX-5461 is in advanced phase 1 trials for treatment of lymphoma and leukemia through rDNA transcription inhibition in a p53-dependent mechanism. We have discovered a novel activity of CX-5461, as a stabilizer of G-quadruplex DNA sequences inside cells the same as CX-3543. We found that BRCA1 and BRCA2 deficiency markedly increases (one log order) sensitivity to CX-5461 and a related drug CX-3543 in human cancer cell lines and polyclonal patient derived xenograft models, providing a direct therapeutic hypothesis, including PDX tumours resistant to PARP inhibition. We show that in epithelial cells, exposure to CX-5461 and CX-3543 blocks replication forks and induces ssDNA gaps or breaks. The BRCA and NHEJ pathways are required for the repair of CX-5461 and CX-3543 induced DNA damage and failure to do so leads to lethality. RNA pol I inhibition is not a required component of the cell killing mechanism in these tumours, because BRCA2 deficient cells are not more sensitive to BMH-21, a more potent rDNA transcription inhibitor. These data strengthen the concept of G4 targeting as a therapeutic approach, specifically for targeting HR and NHEJ deficient cancers and other tumors deficient for DNA damage repair. Since CX-5461 is already in advanced phase 1 trials for other indications, this has resulted in immediately testable translational implications (Canadian trial, NCT02719977, opened May 2016) as no phase-1 eligible G4 stabilizers have been described to date.

overall_design:
Examination of the chromatin loci bound by RAD51 post treatment with CX-5461 at a whole-genome level and analyzing whether it is enriched at G-quadruplex forming sequences.
We report the ChIP-seq results using RAD51 antibody with and without CX-5461 treatment (10-7M 24hour) and compare with IgG ChIP-seq with and without CX-5461 treatment.

first: Hong

last: Xu

first: Daniel

last: Lai

first: Samuel

last: Aparicio


title: A novel small molecule that disrupts the oocyte-to-embryo transition in C. elegans

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

summary: The complex cellular events that occur in response to fertilization are essential for mediating the oocyte-to-embryo transition.  Here, we describe a comprehensive small molecule screen focused on identifying compounds that affect the oocyte-to-embryo transition in C. elegans.  We identify a single novel compound that disrupts early embryogenesis with remarkable stage- and species-specificity.  The compound, named C22, primarily impairs eggshell integrity, leading to osmotic sensitivity and embryonic lethality.  We show that this phenotype is dependent upon the upregulation of the LET-607/CREBH transcription factor.  We then demonstrate that LET-607 candidate gene targets primarily encode factors involved in diverse aspects of protein trafficking.  Together, our data suggest that in the presence of C22, one or more key components of the eggshell are inappropriately processed, leading to permeable, inviable embryos.  The remarkable specificity and reversibility of this compound will facilitate further investigation into the role and regulation of protein trafficking in the early embryo, as well as serve as a tool for manipulating the life cycle for other studies such as aging.

overall_design: This data submission includes a single ChIP-seq sample for one factor called LET-607 in C. elegans (CREBH in human).  These samples were done in replicate, with input, yielding three sequence files per sample (two replicates, and one input fastq file). In addition, we are submitting two wig files for the dataset, consisting of one normalized wig file for the combined duplicate IP and one normalized wig file for the input sequence.

last: Weicksel

first: Assaf

last: Mahadav

first: Mark

last: Moyle

first: Patricia

last: Cipriani

first: Michelle

last: Kudron

first: Zachary

last: Pincus

first: Shirin

last: Bahmanyar

first: Laura

last: Abriola

first: Janie

last: Merkel

last: Gutwein

first: Anita

last: Fernandez

first: Fabio

last: Piano

first: Krstin

last: Gunsalus


title: Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding [RNA-seq]

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

institute: University of Geneva

overall_design: RNA-seq

first: Robert

last: Schöpflin


title: Identification of rare, dormant and therapy resistant stem cells in acute lymphoblastic leukemia

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

country: Germany

institute: Ludwig-Maximilians University Munich

summary: Tumor relapse is associated with dismal prognosis, but responsible biological principles remain incompletely understood. To isolate and characterize relapse-inducing cells, we used genetic engineering and proliferation-sensitive dyes in patient-derived xenografts of acute lymphoblastic leukemia (ALL). We identified a rare subpopulation that resembled relapse-inducing cells with combined properties of long-term dormancy, treatment resistance, and stemness. Single-cell and bulk expression profiling revealed their similarity to primary ALL cells isolated from pediatric and adult patients at minimal residual disease (MRD). Therapeutically adverse characteristics were reversible, as resistant, dormant cells became sensitive to treatment and started proliferating when dissociated from the in vivo environment. Our data suggest that ALL patients might profit from therapeutic strategies that release MRD cells from the niche.

overall_design: Gene expression profiles from two PDX ALL Samples (ALL-199 & ALL-265) were generated for either dormant (LRC) vs. dividing (non-LRC) cells or drug treated vs. non-treated cells. For single cell analysis one mouse were analyzed for each condition.

first: Erbey

last: Özdemir


title: In Vitro Derivation and Propagation of Spermatogonial Stem Cell Activity from Mouse Pluripotent Stem Cells

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

summary: The in vitro derivation and propagation of spermatogonial stem cells (SSCs) from pluripotent stem cells (PSCs) is a key goal in reproductive science. We show here that when aggregated with embryonic testicular somatic cells (reconstituted testes), primordial germ cell-like cells (PGCLCs) induced from mouse embryonic stem cells differentiate into spermatogonia-like cells in vitro and are expandable as cells that resemble germline stem cells (GSCs), a primary cell line with SSC activity. Remarkably, GSC-like cells (GSCLCs), but not PGCLCs, colonize adult testes and, albeit less effectively than GSCs, contribute to spermatogenesis and fertile offspring. Whole-genome analyses reveal that GSCLCs exhibit aberrant methylation at vulnerable regulatory elements, including those critical for spermatogenesis, which may restrain their spermatogenic potential. Our study establishes a strategy for the in vitro derivation of SSC activity from PSCs, which, we propose, relies on faithful epigenomic regulation.

overall_design: Transcriptome analysis of mouse GSCs and GSCLCs using SC3-seq technology

first: Yukiko

last: Ishikura

first: Hiroshi

last: Ohta

first: Katsuhiko

last: Hayashi

first: Tomonori

last: Nakamura

first: Ikuhiro

last: Okamoto

first: Takuya

last: Yamamoto

first: Kazuki

last: Kurimoto

first: Kenjiro

last: Shirane

first: Hiroyuki

last: Sasaki

first: Mitinori

last: Saitou


title: Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding [ChIP-seq]

overall_design:
ChIP-seq of CTCF,  H3K4me1, H3K4me3, H3K27Ac, H3K27me3 and RAD21 on embryonic limb bud.

Bigwig files for data of merged replicates are available on the "Rep1" samples.


title: FOXA1 directs H3K4 monomethylation at enhancers via recruitment of the methyltransferase MLL3

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

summary: We performed MLL3 ChIP-seq in breast cancer cells and unexpectedly found that MLL3 binds mostly at non-promoter regions enhancers, in contrast to the prevailing hypothesis. MLL3 was shown to occupy regions marked by FOXA1 occupancy and as expected, H3K4me1 and H3K4me2. MLL3 binding was dependent on FOXA1, indicating that FOXA1 recruits MLL3 to chromatin. Motif analysis and subsequent genomic mapping revealed a role for Grainy head like protein-2 (GRHL2) which was shown to co-occupy regions of the chromatin with MLL3. Regions occupied by all three factors, namely FOXA1, MLL3 and GRHL2, were most enriched in H3K4me1.  MLL3 silencing decreased H3K4me1 at enhancer elements, but had no appreciable impact on H3K4me3 at enhancer elements. We identify a complex relationship between FOXA1, MLL3 and H3K4me1 at enhancers in breast cancer and propose a mechanism whereby the pioneer factor FOXA1 can interact with a chromatin modifier MLL3, recruiting it to chromatin to facilitate the deposition of H3K4me1 histone marks, subsequently demarcating active enhancer elements.

overall_design: ChIPseq of MLL3, FOXA1, GRHL2, H3K4me3, H3K4me1 in asynchronous MCF7 cells

first: Kamila

last: Jozwik

first: Igor

last: Chernukhin

first: Sankari

last: Nagarajan

first: Aurelien

middle: A

last: Serandour


title: RPA interacts with HIRA and regulates H3.3 deposition at gene regulatory elements in mammalian cells

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

summary: The incorporation of histone variant H3.3 has been implicated in the formation and maintenance of specialized chromatin structure in metazoan cells. H3.3 is enriched in promoters, regulatory elements and genebody, and HIRA is required for H3.3 enrichment in these regions. But the mechanism of regulating H3.3 deposition by HIRA remains elusive. By screening a custom library of small hairpin RNAs (shRNAs) targeting known chromatin regulators, we identify single-stranded DNA binding protein RPA as being critically required for deposition of newly synthesized H3.3. RPA interacts with HIRA and H3.3 and co-localizes with HIRA at gene promoters and some regulatory elements across genome wide. Deletion of RPA dramatically reduces the enrichment of HIRA and newly synthesized H3.3 at these regions and reduced nascent anti-sense transcription. Taken together, our data demonstrate that RPA functions as new regulator of H3.3 deposition in promoter and some regulatory elements by recruiting HIRA and reveal a novel mechanism for RPA in chromatin and gene regulation.

overall_design: We performed RPA1 and RPA2 ChIP-seq to find the RPA binding regions. mRNA-seq and BrU-seq were performed after shHIRA or shRPA1.

first: Honglian

last: Zhang

first: Haiyun

last: Gan

first: Jeong-Heon

last: Lee

first: Zhiguo


title: Partially exhausted CD8+ T cells are associated with clinically beneficial response to Teplizumab in new onset type I diabetes (single-cell RNA-seq of sorted CD8+ T-cells)

city: Seattle

first: Scott

last: Presnell

state: WA

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

summary: Biologic agents active in other autoimmune settings have had variable effectiveness in newly diagnosed type 1 diabetes (T1D) where treatment across therapeutic targets is accompanied by transient stabilization of C-peptide levels in some patients, followed by progression at the same rate as in control groups. Why disparate treatments lead to similar clinical courses is currently unknown. Here, we use integrated systems biology and flow cytometry approaches to elucidate immunologic mechanisms associated with C-peptide stabilization in T1D subjects treated with the anti-CD3 monoclonal antibody, teplizumab. This work is part of the Immune Tolerance Network AbATE study (Autoimmunity-Blocking Antibody for Tolerance in Recently Diagnosed Type 1 Diabetes); data are also available through the ITN TrialShare portal: https://www.itntrialshare.org/project/Studies/ITN027AIDB/Study%20Data/begin.view?.

overall_design: We performed single-cell RNA-seq on 219 captured and sorted CD8+ T-cells from 3 responders at visit month 6 (N = 87, 75, 57); we sorted cells with and without EOMES-associated inhibitory receptors (TIGIT, KLRG1)); prior to RNA extraction, cells were stimulated with anti-CD3 and anti-CD28.

first: S

last: Long

first: Jerill

last: Thorpe

first: Hannah

last: DeBerg

first: Vivian

last: Gersuk

first: James

last: Eddy

first: Kristina

last: Harris

first: Mario

last: Ehlers

first: Kevan

middle: C

last: Herold

first: Gerard

middle: T

last: Nepom

first: Peter

last: Linsley


first: Yukihiro

last: Yabuta

overall_design: Transcriptome analysis of mouse GSCs and GSCLCs using SC3-seq technology.

first: Yukiko

last: Ishikura

first: Hiroshi

last: Ohta

first: Katsuhiko

last: Hayashi

first: Tomonori

last: Nakamura

first: Ikuhiro

last: Okamoto

first: Takuya

last: Yamamoto

first: Kazuki

last: Kurimoto

first: Kenjiro

last: Shirane

first: Hiroyuki

last: Sasaki

first: Mitinori

last: Saitou


title: Characterization of EZH2-deficient human embryonic stem cells [ChIP-seq and bulk RNA-seq]

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: Here we analyze histone modifications and transcriptome profiles of EZH2-deficient human embroynic stem cells

overall_design: Histone modifications (H3K27me3, H3K4me3, H3K27ac and H3K4me1) and transcriptome (mRNA-Seq) from EZH2-/- (Null), Ezh2-/- +EZH2 (Null + EZH2), Ezh2 -/+ (Het) and EZH2 +/+ (WT) human ESC

first: Adam

last: Collinson

last: Rugg-Gunn


title: Characterisation of EZH2-deficient human embryonic stem cells

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

overall_design: Refer to individual Series


title: Heterogeneous nuclear ribonucleoprotein C1/C2 links transcriptional and splicing actions of 1,25-dihydroxyvitamin D

city: Los Angeles

first: Yi

last: Xing

address: 650 Charles E. Young Dr. South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: UCLA

summary: Heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNPC1/C2) functions as an RNA splicing regulator through co-transcriptional association with nascent mRNA. HnRNPC1/C2 can also bind to double-stranded DNA as a vitamin D response element-binding protein (VDRE-BP), thereby regulating transcriptional activity of the vitamin D receptor (VDR) bound to 1,25-dihydroxyvitamin D (1,25(OH)2D). In this way hnRNPC1/C2 may act as a coupling factor for 1,25(OH)2D-directed transcription and RNA splicing. Studies using MG63 osteoblastic cells confirmed that 1,25(OH)2D-VDR mediated induction of the gene for the enzyme 24-hydroxylase (CYP24A1), involved CYP24A1-specific chromatin and RNA immunoprecipitation of hnRNPC1/C2. Furthermore, small interfering (siRNA) knockdown of hnRNPC1/C2 in MG63 cells and was associated with dysregulated expression of CYP24A1 and an alternatively spliced form of CYP24A1 (CYP24A1-variant 2). Genome-wide analysis of RNA expression and alternative splicing indicated that dual role of hnRNPC1/C2 in directing 1,25(OH)2D-mediated gene expression is not restricted to the classical VDR-target CYP24A1. Knockdown of hnRNPC1/C2 resulted in 3500 differentially expressed genes (DEG), and treatment with 1,25(OH)2D 324 DEG. A further 87 DEG were only observed in 1,25(OH)2D-treated cells in hnRNPC1/C2 knockdown cells. HnRNPC1/C2 knockdown or 1,25(OH)2D treatment also induced alternative splicing (AS) (5039 and 310 AS events respectively). Combined hnRNPC1/C2 knockdown and 1,25(OH)2D treatment resulted in significant overlap between DEG and AS genes, but this was not observed for 1,25(OH)2D treatment alone. These data indicate that hnRNPC1/C2 can act to couple transcriptional and splicing responses to 1,25(OH)2D by binding to both DNA and RNA.  Similar mechanisms may also exist for other members of the hnRNP and steroid receptor family.

overall_design: Human MG63 osteosarcoma cells (American Type Culture Collection, CRL-1427) were cultured in Dulbecco’s modified Eagle medium (DMEM, high glucose, Gibco, 11995-065) supplemented with 10% Fetal Bovine Serum (FBS) cultured at 37oC with 5% CO2. Crystalline 1,25-dihydroxyvitamin D3 (1,25(OH)2D3, Enzo Life Sciences, BML-DM200-0050) was reconstituted in ethanol. Ethanol (0.1%) was used as vehicle treatment. RNA-seq analysis was carried out using total RNA extracted from MG63 cells using RNAeasy mini kit (Qiagen, 74104), with on-column DNase treatment to remove contaminating genomic DNA. cDNA libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit (illumina). High-throughput sequencing was performed using an Illumina HiSeq2500 (paired-end, non-strand-specific 107-bp read length). Knockdown and control samples were sequenced together in two flowcells on four lanes.

first: John

last: Adams

first: Martin

last: Hewison


title: Probing Hemogenic Precursors with Endoglin Regulatory Elements uncovers LRP2 as a Regulator of Hematopoiesis

city: Sydney

first: Dominik

last: Beck

state: NSW

address: Level 10, UTS Building 11 (CB11 81-113, Broadway, Ultimo)

department: School of Biomedical Engineering

country: Australia

institute: University of Technology Sydney

summary: Different combinations of Endoglin tissue specific enhancers define hemangioblast and hemogenic endothelium cell fractions

overall_design: We generated a series of embryonic stem cell lines, each targeted with reporter constructs driven by tissue specific promoter/enhancer combinations of Endoglin (ENG). The Eng promoter (P) when combined with the -8/+7/+9kb enhancers targeted cells in FLK1 mesoderm that were enriched for blast colony forming potential, whereas the P/-8kb enhancer targeted TIE2+/c-KIT+/CD41- HE cells that were enriched for hematopoietic potential. These cell fractions were isolated and their transcriptomes profiled by RNA-seq.

first: Rabab

last: Nasrallah

first: Jason

last: Wong

last: Pimanda


title: Chromatin immunoprecipitation and sequencing of pPLT2::PLT2-YFP in the root of plt1plt2 double mutant

city: Wageningen

first: Luca

last: Santuari

address: Droevendaalsesteeg 1

department: Plant Sciences Group

country: Netherlands

institute: Wageningen University

summary: Organ formation in animals and plants relies on precise control of cell state transitions to turn stem cell daughters into fully differentiated cells. In plants, cells cannot rearrange due to shared cell walls. Thus, differentiation progression and the accompanying cell expansion must be tightly coordinated. PLETHORA (PLT) transcription factor gradients were shown to guide the progression of cell differentiation at different positions in the Arabidopsis root. While well-described transcription factor gradients in animals specify distinct cell fates within an essentially static context, the PLT gradient is unique in its ability to control cell differentiation in a growing organ during continuous production and expansion of cells. To understand the output of these gradients we studied the gene set transcriptionally controlled by PLTs. Our work reveals how the PLT gradient regulates cell state by region-specific induction of cell proliferation genes and repression of differentiation. Moreover, PLT targets include major patterning genes and autoregulatory feedback components, reinforcing their role as master regulators of organ development.

overall_design: Two replicates were performed for the IP and sequenced along with the Input DNA.


title: In planta expression profiles of five Fusarium fujikuroi species complex (FFC) isolates revealed common and different sets of up-regulated genes

city: Freising

first: Ulrich

last: Guldener

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

institute: Technische Universität München

summary: The five FFC strains analyzed are able to penetrate maize roots and grow invasively, the efficiency of this growth as well as the ability to subsequently grow in other parts of maize plants differ significantly. To gain insight into these differences, we examined the transcriptome of the five isolates in infected maize roots with that of in vitro (CM agar) growing fungi by a RNA sequencing approach.

sample_organism:
Zea mays
Fusarium mangiferae
Fusarium verticillioides 7600
Fusarium proliferatum
Fusarium proliferatum ET1
Fusarium fujikuroi IMI 58289

overall_design: To get insight into the transcriptional changes during maize root infection we compared the transcriptome of the five isolates in infected maize roots with that of in vitro (CM agar) growing fungi by a RNA sequencing approach. The maize seedlings were grown in sterile vermiculite in glass tubes and artificially inoculated with conidia suspensions of the five strains. Root samples were taken 4, 10 and 20 dpi for RNA isolation. In addition, the maize gene expression of uninfected seedlings (sample 21) was compared with maize gene expression in response to infection by the five isolates.

last: Münsterkötter

first: Eva-Maria

last: Niehaus

last: Güldener

first: Bettina

last: Tudzynski


title: Characterisation of EZH2-deficient human embryonic stem cells [single cell RNA-seq]

city: Cambridge

summary: Here we analyse single cell transcriptome profiles of EZH2-deficient human embroynic stem cells

overall_design: Single cell transcriptome (mRNA-Seq) from Ezh2-/- (Null)  and EZH2+/+ (WT) human ESC

first: Peter


title: The PLETHORA gene regulatory network guides growth and cell differentiation in Arabidopsis roots

summary:
Organ formation in animals and plants relies on precise control of cell state transitions to turn stem cell daughters into fully differentiated cells. In plants, cells cannot rearrange due to shared cell walls. Thus, differentiation progression and the accompanying cell expansion must be tightly coordinated across tissues. PLETHORA (PLT) transcription factor gradients are unique in their ability to guide the progression of cell differentiation at different positions in the growing Arabidopsis root, which contrasts with well-described transcription factor gradients in animals specifying distinct cell fates within an essentially static context. To understand the output of the PLT gradient, we studied the gene set transcriptionally controlled by PLTs. Our work reveals how the PLT gradient can regulate cell state by region-specific induction of cell proliferation genes and repression of differentiation. Moreover, PLT targets include major patterning genes and autoregulatory feedback components, enforcing their role as master regulators of organ development.

This SuperSeries is composed of the SubSeries listed below.


title: Ultra-fast transcriptional responses in plants

city: Denton

first: Rajeev

middle: K.

last: Azad

state: Texas

address: 1155 Union Circle #305220

institute: University of North Texas

summary: Transcriptome of plants exposed to 0, 20 and 60 sec light stress was analyzed using Illumina HiSeq2000. We found that mRNA accumulation of more than 700 transcripts in plants occurs as early as 20-60 sec following light stress application

overall_design: Three independent biological replicates, each composed of leaves pooled from at least 30 different plants, were used per experimental condition (0, 20 and 60 sec high light)

first: Nobuhiro

last: Suzuki

first: Amith

last: Devireddy

first: Gad

last: Miller

first: Elena

last: Shulaev

first: Vladimir

first: Ron

last: Mittler


title: Characterization of transcriptome changes induced in 3T3L1 adipocytes by expression of Adenovirus subtype 5 protein E4-ORF1

status: Public on Dec 05 2016

first: natasha

last: chaudhary

address: 1300 York Avenue

department: Biochemistry

institute: Weill Cornell Medicine

summary: Insulin activation of phosphoinositol 3-kinase (PI3 kinase) regulates metabolism, including the translocation of the Glut4 glucose transporter to plasma membrane and inactivation of FoxO1 transcription factor. Adenoviral protein E4-ORF1 stimulates cellular glucose metabolism by mimicking growth factor activation of PI3 kinase. We have used E4-ORF1 to dissect PI3 kinase-mediated signaling in adipocytes. E4-ORF1 activation of PI3 kinase recapitulates insulin-regulation of FoxO1 but not regulation of Glut4. This uncoupling of PI3 kinase effects occurs despite E4-ORF1 activating PI3 kinase and downstream signaling to levels achieved by insulin. Although, E4-ORF1 does not fully recapitulate insulin’s effects on Glut4, it enhances insulin-stimulated insertion of Glut4-containing vesicles to the plasma membrane independent of Rab10, a key regulator of Glut4 trafficking. E4-ORF1 also stimulates plasma membrane translocation of ubiquitously expressed Glut1 glucose transporter an effect that is likely essential for E4-ORF1 to promote an anabolic metabolism in a broad range of cell types.

overall_design: mRNA profiles of wild type and E4-ORF1 stably expressing adipocytes generated by deep sequencing, in triplicate, using Illumina HTDNA sequencing.

first: Natasha

last: Chaudhary

first: Eva

last: Gonzalez

first: Sung-Hee

last: Chang

first: Fuqiang

last: Geng

first: Shahin

last: Rafii

first: Naseer

last: Altorki

first: Timothy

last: McGraw


title: Characterization of small RNAs and genes in maize anthers (ms23 sterile)

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary:
Successful male gametogenesis involves orchestration of sequential gene regulation for somatic differentiation in pre-meiotic anthers.  We report here the cloning of Male Sterile23 (Ms23), encoding an anther-specific predicted basic helix-loop-helix (bHLH) transcription factor required for tapetal differentiation; transcripts localize initially to the precursor secondary parietal cells then predominantly to daughter tapetal cells.  In knockout ms23-ref mutant anthers, five instead of the normal four wall layers are observed.  Microarray transcript profiling demonstrates a more severe developmental disruption in ms23-ref than in ms32 anthers, which possess a different bHLH defect. RNA-seq and proteomics data together with yeast two-hybrid assays suggest that MS23 along with MS32, bHLH122, and bHLH51 act sequentially as either homo- or heterodimers to choreograph tapetal development. Among them, MS23 is the earliest-acting factor, upstream of bHLH51 and bHLH122, controlling tapetal specification and maturation. In contrast, MS32 is constitutive and independently regulated and is required later than MS23 in tapetal differentiation.
We characterized a maize (Zea mays) mutant line, ms23-ref, which the tapetal cells lack a dense cytoplasm and are not Binucleate -- the two characteristics of normal TP during meiosis. The meiocytes in ms23-ref fail to progress beyond meiotic prophase I. By profiling the small RNA population in ms23 mutants, we investigated the impact of ms23 mutation on small RNAs abundance in 0.4 mm, 0.7 mm, 1.0 mm, 1.5 mm and 2.0 mm anther. We also investigated the transcript abundance that were impacted in ms23 mutant by transcriptome profiling. The result provides an avenue for future research to understand the genetic networks and protein interactions among ms23, important for tapetal development in maize anther.

overall_design: We generated integrative maps of small RNA profiles (sRNA-seq) and transcriptome (RNA-seq) profiles to characterize the sRNA and genes from maize anther (0.4 mm, 0.7 mm, 1.0 mm, 1.5 mm and 2.0 mm) of ms23 mutant.

first: Siwaret

last: Arikit

first: Jixian

last: Zhai


title: ChIP-seq of H3K27ac, H3K9me3, and HA tag for ATFs on MEF-derived cells

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

summary: We tested a genome-scale artificial transcription factor (ATF) library in reprogramming mouse embryonic fibroblasts to induced pluripotent stem (iPS) cells. Three combinations of ATFs (C2, C3, and C4) could induce pluripotency when expressed with Sox2, Klf4, and c-Myc. The transcriptional profiles of ATF-induced iPS cells are similar to that of iPS cells induced with Oct4, Sox2, Klf4, and c-Myc and mouse embryonic stem cells, exhibiting up-regulation of pluripotency markers and down-regulation of fibroblast markers. We performed ChIP-seq on the active histone mark H3K27ac and the repressive histone mark H3K9me3 in C2+SKM iPS cells, C3+SKM iPS cells, in Oct4+SKM to validate the total transcriptome results. In addition, the ATFs from C2 were chromatin immunoprecipitated to determine where they are bound in the genome at an intermediate stage before being fully reprogrammed to iPS cells. This study provides a proof-of-principle that a gene-activating ATF library can be used to identify cell fate-defining transcriptional networks in an unbiased manner.

overall_design: For mapping histone marks across the genome, C2+SKM iPS cells, C3+SKM iPS cells, and Oct4+SKM iPS cells were collected in duplicate. Input for C2_OSKM serves as the control for C2+SKM iPS cells and Oct4+SKM iPS cells. Input for C3 serves as the control for C3+SKM iPS cells. For mapping ATF occupancy in the genome, C2+SKM cells were collected 20 days after transduction in duplicate. These cells still express the ATFs and are not fully reprogrammed. Input and Empty+SKM serve as negative controls, with the latter capturing any non-specific interactions of the HA antibody to protein-DNA complexes.

middle: Z

first: Asuka

last: Eguchi


title: Functional genomics of artificial transcription factor-induced iPS cells

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Survival in quiescence requires the euchromatic deployment of Clr4/SUV39H by Argonaute-associated small RNAs [siRNA-Seq]

city: Charlestown

first: Richard

last: Joh

state: MA

department: Center for Cancer Research

institute: Mass General Hospital

summary: Cellular quiescence (G0) is a ubiquitous stress response through which cells enter a state of reversible dormancy, acquiring distinct properties including reduced metabolism, resistance to stress and long life. G0 entry involves dramatic changes to the chromatin landscape and transcriptional program of cells, but the mechanisms coordinating these processes remain poorly understood. Using the fission yeast, here we track the G0-associated chromatin and transcriptional changes temporally. We show that as cells enter G0, their survival and global gene expression programs become increasingly dependent on Clr4/SUV39H, the sole histone H3 lysine 9 (H3K9) methyltransferase, and RNA interference (RNAi) proteins. Notably, G0 entry results in RNAi-dependent H3K9 methylation of several euchromatic regions, prior to which Argonaute 1-associated small RNAs from these regions emerge. Overall our data reveal a new function for constitutive heterochromatin proteins in establishing the global G0 transcriptional program and suggest that stress-induced alterations in Argonaute-associated sRNAs can specify the deployment of transcriptional regulatory proteins to unique sites in eukaryotic genomes.

overall_design: Comparison of Ago1-associated small RNA in wt at 0 and 24h into N starvation (3 replicates)

middle: I

first: Jasbeer

middle: S

last: Khanduja

first: Isabel

last: Calvo

first: Meeta

last: Mistry

first: Christina

last: Palmieri

first: Andrej

last: Savol

first: Shannan

last: Sui

first: Ruslan

last: Sadreyev

first: Martin

last: Aryee

first: Mo

last: Motamedi


title: Survival in quiescence requires the euchromatic deployment of Clr4/SUV39H by Argonaute-associated small RNAs


title: Global transcriptional profiling of HEK293 cells transfected with ATFs, mouse embryonic fibroblasts, and mouse iPS cells derived with artificial transcription factors

summary: We tested various architectures of artificial transcription factors (ATFs) in HEK293 cells to test the contribution of the interaction domain, nuclear localization domain, size of DNA-binding domain, and activation domain. Then we made a genome-scale ATF library and tested it in reprogramming mouse embryonic fibroblasts to induced pluripotent stem (iPS) cells. Three combinations of ATFs (C2, C3, and C4) could induce pluripotency when expressed with Sox2, Klf4, and c-Myc. We harvested polyadenylated RNAs from 11 cell types derived with different sets of factors. The transcriptional profiles of ATF-induced iPS cells are similar to that of iPS cells induced with Oct4, Sox2, Klf4, and c-Myc and mouse embryonic stem cells, exhibiting up-regulation of pluripotency markers and down-regulation of fibroblast markers. Comparisons of cells undergoing reprogramming at an intermediate stage before becoming fully reprogrammed suggest that ATFs activate a different set of genes than the set activated by Oct4. This study provides a proof-of-principle that a gene-activating ATF library can be used to identify cell fate-defining transcriptional networks in an unbiased manner.

overall_design: Total RNA was collected from HEK293 cells from 5 different conditions (n=1), and poly-adenylated transcripts were sequenced. Total RNA was collected from 11 different mouse conditions (n=3 or 4), and poly-adenylated transcripts were sequenced.


title: Survival in quiescence requires the euchromatic deployment of Clr4/SUV39H by Argonaute-associated small RNAs [RNA-Seq]

overall_design: Comparison of wt and clr4D transcriptome under N starvation (2 biological replicates)


title: Survival in quiescence requires the euchromatic deployment of Clr4/SUV39H by Argonaute-associated small RNAs [sRNA-Seq]

overall_design: Comparison of wt/ago1D/clr4D/dcr1D small RNA under N starvation


title: Survival in quiescence requires the euchromatic deployment of Clr4/SUV39H by Argonaute-associated small RNAs [ChIP-Seq]

overall_design: Comparision of H3K9me2 peaks in wt/clr4D/ago1D


title: Chromatin Binding of Gcn5 in Drosophila is Largely Mediated by CP190

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen


title: Chromatin Binding of Gcn5 in Drosophila is Largely Mediated by CP190 [ChIP-seq]

summary: 80% of the genomic binding sites of the histone acetyltransferase Gcn5 are colocalizing with CP190 binding. Depletion of CP190 reduces the number of Gcn5 binding sites and binding strength to chromatin. Binding dependency was further supported by Gcn5 mediated co-precipitation of CP190

overall_design: Gcn5 ChIP-Seq in Kc cells treated either with GFP RNAi or CP190 RNAi


title: Chromatin Binding of Gcn5 in Drosophila is Largely Mediated by CP190 [RNA-seq]

overall_design: RNA-seq expression profiles of drosophila S2 mRNA after depletion of CP190 and Gcn5


title: Human tumorigenesis induced by an endogenous DNA transposase

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: Genomic rearrangements are a hallmark of childhood cancers, but the mutational processes underlying most of these variants remain unknown. We identified piggyBac transposable element derived 5 (PGBD5) as a highly expressed, enzymatically active domesticated human DNA transposase in a large subset of pediatric solid tumors, including rhabdoid tumors. Ectopic expression of PGBD5 in primary human cells was sufficient to induce fully penetrant cell transformation both in vitro and in immunodeficient mice in vivo. This activity required specific catalytic aspartic acid residues in the PGBD5 transposase domain as well as cellular non-homologous end-joining DNA repair, and was associated with distinct structural rearrangements defined by specific DNA sequence motifs. Similar genomic alterations, some recurrent, were found in primary human rhabdoid tumors. Thus, PGBD5 represents a new class of developmental oncogenic mutators in childhood solid tumors.

overall_design: ChIP-sequencing of PGBD5 and histone modifications in human rhadboid tumor cells and immortalized retinal epithelium.

first: Anton

middle: G

last: Henssen

middle: P

first: Alex

last: Kentsis


title: A-to-I RNA editing promotes developmental-stage specific gene and lncRNA expression

city: Haifa

first: Ayelet

last: Lamm

address: Technion st

department: Biology

country: Israel

institute: Technion

summary: A-to-I RNA editing is a conserved and widespread phenomenon in which adenosine (A) is converted to inosine (I) by adenosine deaminases (ADARs) in double-stranded RNA regions. Although human RNAs contain millions of A-to-I editing sites, most of these occur in noncoding regions and their function is unknown. Knockdown of ADAR enzymes in C. elegans causes defects in normal development but is not lethal as it is in human and mouse, making C. elegans an ideal organism for studying the regulatory effects of RNA editing on the transcriptome. Previous studies in C. elegans indicated competition between RNA interference (RNAi) and RNA editing mechanisms, with the observation that lack of both mechanisms can suppress defects observed when only RNA editing is absent. To study the effects of RNA editing on gene expression and function, we established a novel screen that enabled to identify thousands of RNA editing sites in non-repetitive regions in the genome. These include dozens genes that are edited at their 3’UTR region. We found that these genes are mainly germline and neuronal genes and that they are downregulated in the absence of ADAR enzymes. Moreover, we discovered that almost half of these genes are edited in a developmental-specific manner. In addition, we found that many pseudogenes and other lncRNAs are also extensively downregulated in the absence of ADARs in embryo but not L4 larva developmental stage, while this downregulation is not observed in additional knockout of RNAi.  Taken together, our results suggest a role for RNA editing in normal growth and development by regulating silencing via RNAi.

overall_design: RNA-seq samples were generated from:  1. wildtype (N2) at embryo stage  2. wildtype (N2) at L4 stage  3. ADAR mutant (BB21 or BB4) worms at L4 stage   4. ADAR mutant (BB21 or BB4) worms at embryo stage   5. ADAR mutant and RNAi mutant (BB23, BB24) at embryo stage   RNA in high and low molecular weight fractions was extracted by mirVana kit (ambion).   mRNA was sequenced from the high molecular weight fraction by means of Illumina   TruSeq® RNA Sample Preparation kit automated by Agilent Bravo Automated Liquid Handling Platform. The resulting libraries were sequences with an Illumina HiSeq 2500.

first: Dean

last: Light


title: Xist-dependent imprinted X inactivation and the early developmental consequences of its failure

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

summary: In Mammals, the difference in sex-chromosome constitution between males (XY) and females (XX) has led to the evolution of dosage compensation strategies, including silencing of an entire X chromosome in females. In mice, X chromosome inactivation (XCI) first occurs in the pre-implantation embryo. Here the non-coding Xist RNA is expressed only from the paternal allele and the paternal X (Xp) becomes inactivated. The Xp is reactivated in the inner cell mass and this is followed by random XCI in the embryo proper, while in extra-embryonic tissues the Xp remains inactive. Although random XCI initiation is thought to be fully Xist-dependent in the mouse, initiation of imprinted XCI was reported to be Xist-independent. Furthermore, the chromosome-wide dynamics of XCI in early embryos of reciprocal inter-specific crosses, which better reflect a natural situation, have never been investigated. Here we report that the expression dynamics of X-linked genes depends both on strain and parent of origin, as well as on X chromosome location, using single-cell RNA-sequencing (scRNAseq) of early mouse embryos. We also demonstrate that initiation of imprinted XCI absolutely requires Xist and that its absence leads to genome-wide transcriptional misregulation in the early blastocyst, with massive over-expression of specific genes such as Rhox5 and failure to activate the extra-embryonic pathway essential for early post-implantation development. This study provides important insights into the transcriptional and allelic dynamics of the X chromosome and the first evidence of dosage compensation failure as early as the blastocyst stage.

overall_design: 182 single-cells RNAseq from oocytes and hybred males and females pre-implantation embryos, with or without deletion of the paternal Xist allele.

first: Maud

last: Borensztein

first: Laurène

last: Syx

first: Ivaylo

last: Vassilev

first: Chong-Jian

last: Chen

first: Edith

last: Heard


title: Extensive regulation of diurnal transcription and metabolism by glucocorticoids [RNA-Seq]

city: Eggenstein-Leopoldshafen

first: Thomas

last: Dickmeis

address: Hermann-von-Helmholtz-Platz 1

department: ITG

institute: KIT

summary: Altered daily patterns of hormone action are suspected to contribute to metabolic disease. It is poorly understood how the adrenal glucocorticoid hormones contribute to the coordination of daily global patterns of transcription and metabolism. Here, we examined diurnal metabolite and transcriptome patterns in a zebrafish glucocorticoid deficiency model by RNA-Seq, NMR spectroscopy and liquid chromatography-based methods. We observed dysregulation of metabolic pathways including glutaminolysis, the citrate and urea cycles and glyoxylate detoxification. Constant, non-rhythmic glucocorticoid treatment rescued many of these changes, with some notable exceptions among the amino acid related pathways. Surprisingly, the non-rhythmic glucocorticoid treatment rescued almost half of the entire dysregulated diurnal transcriptome patterns. A combination of E-box and glucocorticoid response elements is enriched in the rescued genes. This simple enhancer element combination is sufficient to drive rhythmic circadian reporter gene expression under non-rhythmic glucocorticoid exposure, revealing a permissive function for the hormones in glucocorticoid-dependent circadian transcription. Our work highlights metabolic pathways potentially contributing to morbidity in patients with glucocorticoid deficiency, even under glucocorticoid replacement therapy. Moreover, we provide mechanistic insight into the interaction between the circadian clock and glucocorticoids in the transcriptional regulation of metabolism.

overall_design: RNA-Seq from total RNA of zebrafish larvae during (5 dpf) the diurnal cycle. Time-series mRNA profiles of untreated wild type (WT), rx3t25327/t25327 [rx3 strong] and rx3t25181/t25181 [rx3 weak] mutant larvae as well as dexamethasone treated WT and rx strong larvae were generated by deep sequencing.

first: Benjamin

last: Weger

first: Meltem

last: Görling

first: Andrea

last: Schink

first: Cédric

last: Gobet

first: Céline

last: Keime

first: Gernot

last: Poschet

first: Bernard

last: Jost

first: Nils

last: Krone

first: Rüdiger

last: Hell

first: Frédéric

last: Gachon

first: Burkhard

last: Luy


title: RNA Sequencing Facilitates Quantitative Analysis of Primary Microglia Transcriptomes

status: Public on Dec 04 2016

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

summary: Using RNA-seq, we report here that primary microglia (PM) cells have a distinct transcriptomic signature and express a unique cluster of transcripts in response to 4 hrs LPS.

overall_design: Examination of effects of LPS-stimulated PM microglial cells, were generated by deep sequencing on an Illumina HiSeq 2000(101 cycles PE lane).

first: YoungGyu

first: JinChoul


title: Methylation of H3K9 by G9a/GLP protects against pathological cardiac hypertrophy

first: Felix

last: Krueger

summary: The heart adapts to increased workload through hypertrophic growth of cardiomyocytes.  Although beneficial when induced physiologically by exercise, pathological cues including hypertension cause reexpression of fetal genes and dysfunctional hypertrophy, with lasting consequences for cardiac health. We hypothesised that these differences are driven by changes in chromatin-encoded cellular memory. We generated genome-wide maps of transcription and of two stable epigenetic marks, H3K9me2 and H3K27me3, specifically in hypertrophied cardiomyocytes, by selectively flow-sorting their nuclei. This demonstrated a pervasive loss of euchromatic H3K9me2 specifically upon pathological but not physiological hypertrophy, derepressing genes associated with pathological hypertrophy. Levels of the H3K9 methyltransferases, G9a and GLP, were correspondingly reduced. Importantly, pharmacological or genetic inactivation of these enzymes was sufficient to induce pathological hypertrophy and the dedifferentiation associated with it. These findings suggest novel therapeutic opportunities by defining an epigenetic state of cardiomyocytes, acquired during maturation, which is required for maintaining cardiac health.

overall_design: Examination of 2 different histone modifications and RNA expression in cardiomyocyte nuclei flow-sorted from hypertrophic rat hearts

last: Thienpont

first: Jan

last: Aronsen

first: Emma

middle: L

last: Robinson

first: Hanneke

last: Okkenhaug

first: Elena

last: Loche

first: Arianna

last: Ferrini

first: Patrick

last: Brien

first: Olaf

last: Bergmann

first: Asmita

last: Tingare

first: Ivar

last: Sjaastad

first: Wolf

last: Reik

first: Llewelyn

last: Roderick


title: Anaylsis of the effect of down-regulation of the EWS-FLI1 fusion protein in Ewing Sarcoma cells by RNA-seq.

city: Oxford

first: Helio

last: Pais

address: Jonh Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: We generated A673 Ewing Sarcoma cell lines which stably express shRNA targeting the EWS-FLI1 fuison protein or Luciferase as a control to study the effect of EWS-FLI1 on the transcriptome. The vectors used to generate the cell lines were a gift from Stephen Lessnick and were first published in PMID 16697960

overall_design: We analysed five A673 cell lines in which the EWS-FLI1 fusion is down-reagulated by shRNA and three control cell lines which express shRNA targeting Luciferase.

first: Terence

last: Rabbitts

first: Jennifer

last: Town


title: RNA Sequencing Facilitates Quantitative Analysis of BV-2 Transcriptomes

first: Young Gyu

last: Chai

summary: Using RNA-seq, we report here that BV-2 microglial cells have a distinct transcriptomic signature and express a unique cluster of transcripts in response to 4 hrs LPS.

overall_design: Examination of effects of LPS-stimulated BV-2, were generated by deep sequencing on an Illumina HiSeq 2000(101 cycles PE lane).

first: YoungGyu

first: Jin


title: Impact of melatonin on gene expression in colonic epithelium of pinealectomized rats

city: Prague 4

first: Martin

last: Sládek

address: Videnska 1083

country: Czech Republic

institute: Institute of Physiology of the Czech Academy of Sciences

summary: To examine the effect of melatonin on global gene expression in the colonic epithelium, we used RNA-seq analysis to identify differentially expressed genes (DEGs) in samples from three melatonin-treated (MEL4-6) versus three vehicle-treated pinealectomized rats (VEH1-3) injected i.p. at the beginning of subjective night and sacrificed 4 h later. More than 12 050 expressed genes were identified in each sample out of 18 258 genes in the database. A surprisingly small number of significant DEGs (49) was identified. The GO pathways analysis revealed that the largest group of the DEGs was associated with immune system response.  Most DEGs (47) identified by RNA-seq were independently analyzed by RT-qPCR and the correlation between both methods indicates reliability of the data.

overall_design: To avoid a potential masking effect of endogenous pineal melatonin rhythm, we performed the study on six pinealectomized adult male Wistar rats. We injected the animals i.p. with either melatonin (MEL, 1mg/kg of body weight, n = 3) or vehicle (VEH, 2.5% ethanol in PBS, n = 3) solution at the beginning of subjective night, sacrificed them 4 h later, isolated total RNA from the colonic inner epithelial layer and subjected the samples to RNA-seq differential expression analysis on HiSeq 4000 (Illumina) by BGI International (Shenzhen, China).

first: Alena

last: Sumová


title: Transcriptome and network analyses in Saccharomyces cerevisiae reveal that amphotericin B and lactoferrin synergy disrupt metal homeostasis and stress response

first: Chi Nam Ignatius

last: Pang

address: School of Biotechnology and Biomolecular Sciences, UNSW Australia

department: The NSW Systems Biology Initiative

institute: The University of New South Wales

summary: Invasive fungal infections (IFIs) are difficult to treat. Few effective antifungal drugs are available and many have problems with toxicity, efficacy and drug-resistance. To overcome these challenges, existing therapies may be enhanced using more than one agent acting in synergy. Previously, we have found amphotericin B (AMB) and the iron chelator, lactoferrin (LF), were synergistic against Cryptococcus neoformans and Saccharomyces cerevisiae. This study investigates the mechanism of AMB+LF synergy, using RNA-seq and network analyses. Genes involved in iron homeostasis showed increased expression upon treatment with AMB alone. Unexpectedly, AMB+LF treatment did not lead to increased expression of iron or zinc homeostasis genes however we observed decreased expression of oxidative stress response genes. Addition of iron or zinc to AMB+LF treated cells did not rescue the synergy, supporting the likelihood that the mechanism of synergy involves more than iron and zinc chelation. We clustered genes based on patterns of co-expression and found by network analysis that many genes involved in iron and zinc homeostasis, which have dysregulated expression upon AMB+LF treatment, are targets of transcription factors Aft1p and Zap1p. Hypothesizing that these might play a key role in the synergistic response, knock-out mutants of Aft1 and Zap1 were tested for increased sensitivity to AMB and oxidative stress. Both mutants showed hypersensitivity towards these treatments. Our results suggest the mechanism of AMB+LF synergy involves disruption to oxidative stress response, in addition to chelation of iron and zinc. Since Zap1 is conserved in C. neoformans and contains a putative drug binding domain, we suggest novel Zap1 binding molecules could be combined with existing antifungals to serve as synergistic antifungal treatments for this species.

overall_design: We extracted mRNA from S. cerevisiae treated with i) AMB only (0.03 µg/mL), ii) LF only (2 µg/mL), iii) a combination of AMB + LF (0.03 µg/mL and 2 µg/mL, respectively) or iv) corresponding matching untreated controls. ID20 (inhibition of cell growth by 20%) was chosen as the time point for RNA isolation from all treatments, as at this point cells are stressed but there should be few confounding effects of cell death, allowing a direct comparison among treatments. The ID20 for AMB of 60 minutes, and AMB-LF of 50 minutes. The same incubation times were applied to each of the matched control samples. RNA-seq data were generated using Illumina HiSeq 2000 and Illumina NextSeq 500 with biological triplicates multiplexed and randomized across two sequencing lanes. Using EdgeR, we identified differentially expressed genes by comparing AMB treatment with the matched control. We also compared AMB + LF treatment with its matched control. Please refer to the manuscript for more details regarding the experimental methods.

first: Chi

first: Yu

last: Lai

first: Leona

last: Campbell

first: Sharon

last: Chen

first: Dee

last: Carter

first: Marc

middle: R

last: Wilkins


title: Three Distinct Cell Types Express Extracellular Matrix Proteins In Different Niches During Skeletal Muscle Fibrosis

city: La Jolla

first: Kavitha

last: Mukund

state: California

address: 9500 Gilman Drive #0412

institute: University of California, San Diego

summary: Tissue extracellular matrix provides structural support and creates unique niches for resident cells . However, the identities of cells responsible for creating specific ECM niches have not been determined. In striated muscle, the identity of these cells becomes important in disease when ECM changes result in fibrosis and subsequent increased tissue stiffness and dysfunction. Here we describe a novel approach to isolate and identify cells that maintain ECM niches in both healthy and fibrotic muscle. Using a collagen I reporter mouse, we show that there are three distinct cell populations that express collagen I in both healthy and fibrotic skeletal muscle. Interestingly, the number of collagen I expressing cells in all three cell populations increase proportionally in fibrotic muscle indicating that all cell types participate in the fibrosis process. Furthermore, it is shown that the ECM gene expression profile is not qualitatively altered in fibrotic muscle. This suggests that muscle fibrosis in this model results from an increased number of collagen I expressing cells and not the initiation of a specific fibrotic gene expression program. Finally, in fibrotic muscle, we show that these collagen I expressing cell populations differentially express distinct ECM proteins – fibroblasts express the fibrillar components of ECM, fibro/adipogenic progenitors cells differentially express basal laminar proteins and skeletal muscle progenitor cells differentially express genes important for the satellite cell niche.

overall_design: RNA sequencing was performed on Illumina HiSeq 2500 (rapid run mode). 2 to 4 biological replicates for each cell type (FAP, SMP and FB) under each condition (DKO and WT) were multiplexed across two lanes (total samples=20). 100 base-paired reads per sample with an average of 22 million reads per sample were obtained.  RNA read mapping and the initial quality control was performed using the OSA algorithm (16) to the mouse reference genome version mm10, with Refseq annotation.

first: Mark

last: Chapman

first: Shankar

last: Subramaniam

first: David

last: Brenner

first: Richard

last: Lieber


title: A multi-step transcriptional and chromatin cascade underlies motor neuron programming

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

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

overall_design: Refer to individual Series


title: SETX attenuates the antiviral innate immune response and controls viral biogenesis (ChIP-Seq)

status: Public on Dec 03 2016

city: New York

first: Ivan

last: Marazzi

address: 1468 Madison Avenue

department: Department of Microbiology

institute: Icahn School of Medicine at Mount Sinai

summary: The innate immune response is the first line of defense against pathogens, and factors that control this cellular response represent targets for treating both infectious and inflammatory diseases. Here, we reveal a novel role for the human helicase SETX, also previously implicated in amyotrophic lateral sclerosis (ALS4) and ataxia with oculomotor apraxia (AOA2), in controlling the magnitude of the antiviral response. Cells depleted for SETX and AOA2 patient-derived SETX-null cells show increased expression of antiviral mediators in response to infection. Mechanistically, this effect is achieved through SETX-mediated inhibition of RNAPII transcription of antiviral genes, and depends on SETX helicase activity. Our results suggest that SETX helps maintain the delicate balance between controlling viral infection and avoiding the potentially detrimental effects of an excessive antiviral response. More broadly, the observation that SETX can regulate the transcriptional activity of specific genes may have important implications for disorders where SETX function is compromised.

overall_design: A549 cells that were transfected with either control non-targeting or SETX-specific siRNAs were infected with the Influenza A virus (A/PR/8/34(ΔNS1) strain) at a multiplicity of infection (MOI) of 3. 4 hours post infection, cells were collected and used to prepare ChIP libraries. Uninfected cells were used as controls.

first: Matthew

last: Miller

first: Alexander

last: Rialdi

first: Jessica

middle: Y

last: Ho

first: Luis

last: Martinez-Gil

first: Natasha

last: Moshkina

first: Micah

last: Tilove

first: Ana

last: Maestre

first: Olivier

last: Bequerel

first: Alicia

last: Feagins

first: Christopher

last: Basler

last: Fernandez-Sesma

last: Lavin

first: Harm

last: van Bakel


title: A High Resolution Profile of NMD Substrates in Yeast

status: Public on Dec 02 2016

city: Worcester

first: Allan

last: Jacobson

address: 368 Plantation Street Albert Sherman Center AS8-1014

department: MaPS

institute: UMASS Medical School

summary: We report a high resolution catalouge of NMD substrates using RNA-Seq. We discovered several hundred new substrates for NMD. Using published ribosome footprint profiling data, we measured ribosome densities of normal-looking NMD substrates and non-NMD substrates. NMD substrates exhibited a striking difference in normalized ribosome occupancy in wild-type and UPF1 cells. We also found that normal looking NMD substrates have higher ratio of out of frame reads, lower codon optimalites and a higher propensity to have long stretches of non-optimal codons.

overall_design: Total RNA profilies of 7 different yeast strains grown in rich media.

first: Alper

last: Celik

last: Baker

first: Feng

last: He


title: The dynamic three-dimensional organization of the diploid yeast genome

city: Stanford

first: Seungsoo

last: Kim

state: CA

address: 265 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

summary: The budding yeast Saccharomyces cerevisiae is a long-standing model for the three-dimensional organization of eukaryotic genomes1,2, and recent high-throughput chromatin conformation capture (Hi-C)2 methods have allowed systematic and unbiased measurement of this organization. Using polymer modeling, some groups have suggested that yeast genome conformation is simple and dominated by its Rabl-like orientation (anaphase-like polarization)3,4. Others have argued that yeast genome conformation is influenced by homolog pairing in diploids5–7 and environment-induced gene relocalization8–13, but the generality and extent of these phenomena remain unclear14. Here, we perform Hi-C on diverged Saccharomyces hybrid diploids to obtain the first global view of chromosome conformation in diploid budding yeasts. Previous studies of homolog pairing have attempted to control for the Rabl-like orientation14, but genomic analysis combined with polymer modeling reveals underappreciated contributions of the Rabl-like orientation to homolog proximity. After controlling for these features, we observe a residual signature of homolog proximity, particularly in saturated phase. From these same data, we also identify known and unexpected inducible gene repositioning. We observe that GAL1 shifts away from the centromere cluster upon galactose induction, consistent with reports of peripheral relocalization8,15. Surprisingly, under galactose induction and saturated phase, we observe a localized increase in homologous interactions between the HAS1 alleles, mediated by association with nuclear pore complexes. The discovery of this conformational change in such well-studied conditions suggests that our understanding of inducible genome reorganization remains incomplete. Together, these results reveal that the diploid yeast genome displays dynamic and complex 3D organization.

sample_organism: Saccharomyces cerevisiae x Saccharomyces uvarum

sample_organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

sample_organism: Saccharomyces paradoxus x Saccharomyces uvarum

overall_design: Hi-C, RNA-seq, and Nup60-TAP ChIP-seq on yeast strains under exponential growth in glucose and galactose, and saturated culture

last: Liachko

first: Donna

last: Brickner

first: Kate

last: Cook

first: William

last: Noble

first: Jason

middle: H

first: Jay

last: Shendure

first: Maitreya

middle: J

last: Dunham


title: Arabidopsis BIC1 inactivates CRY2 by suppressing the blue light-dependent cryptochrome dimerization

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

summary: Cryptochromes are blue-light receptors in plants and animals. Homodimers are the physiologically active form of plant cryptochromes that mediates blue light regulation of gene expression and photomorphogenesis, but how light regulates the photoreceptor activation and inactivation remains unclear. We identified an Arabidopsis protein BIC1 (Blue-light Inhibitor of Cryptochromes 1) that inhibits all photoreactions of plant cryptochrome 2 (CRY2) examined, allowing direct tests of the photoactivation and inactivation mechanisms of CRY2. We found that blue light stimulates homodimerization of CRY2, whereas BIC1 binds to CRY2 to suppress CRY2 dimerization and the interaction of CRY2 with its signaling partners. We further show that cryptochromes and phytochromes mediate light induction of BIC1 transcription, evoking the negative feedback circuitry to control homeostasis of the active cryptochromes under the broad spectra of solar radiation in nature.

overall_design: RNA-seq of BIC1 overexpression (BIC1ox), cry1cry2 mutant, and wild type seedlings exposed to 2h blue light or dark.

first: Qin

last: Wang

first: Zecheng

last: Zuo

first: Xu

first: Yoshito

last: Oka

first: Chentao

last: lin


title: Coop-seq: quantitative measurement of cooperative binding between transcription factors to hundreds of variants simultaneously

first: Gary

middle: D.

last: Stormo

address: 4515 McKinley Ave. Room 4208.

department: Genetics

institute: Washington University School of Medicine

summary:
Cooperative binding of transcription factors is known to be important in the regulation of many promoters and enhancers, but current methods to measure cooperativity parameters have been laborious and therefore limited to studying only a few sequence variants at a time. Coop-seq (cooperativity by sequencing) is capable of efficiently and accurately determining the cooperativity parameters for hundreds of different DNA sequences in a single experiment, which we demonstrate using members of the Sox and POU families of transcription factors.
Spec-seq directly measures specificity by sequencing. We run an EMSA experiment on TF of interest with a library of DNA targets. Then we extract and sequence the bound and unbound portion of the DNA separately. Finally we count the occurences of each variant in the library and calculate the ratio and the relative binding energy.

overall_design: 6 independent Spec-seq experiments and 12 independent Coop-seq experiments and their replicates.

first: Yiming

middle: K

last: Chang

middle: D


title: RNA-sequencing of human intestinal enteroids infected with or without human rotavirus (strain Ito)

city: Houston

first: Lukas

last: Simon

address: 1 Baylor Plaza

department: THINC

institute: Baylor College of Medicine

summary: We report the human intestinal epithelial host transcriptional response to human enteric virus infection using primary human intestinal enteroids cultures as a model system.

overall_design: Human intestinal enteroids from two different individuals were mock-infected or human rotavirus (strain Ito) infected.  At 6 hpi, total RNA was extracted.  The RNA was rRNA-reduced and then sequenced.

first: Mary

last: Estes

first: Chad

middle: A

last: Shaw

middle: M

first: Kapil

last: Saxena