title: Chickpea Transcriptome Atlas II - Abiotic Stress

status: Public on Aug 27 2014

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary: In this study, we aim to present a global view of transcriptome dynamics during various abiotic stresses in chickpea. We generated about 252 million high-quality reads from eight libraries (control, desiccation, salinity and cold stress samples for roots and shoots) using Illumina high-throughput sequencing GAII platform. We mapped the reads to the desi chickpea genome for estimation of their transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample.

overall_design: We collected different tissue samples (root and shoot tissues of 10-day-old seedlings subjected to control (kept in water), desiccation (transferred on folds of tissue paper), salinity (transferred to beaker containing 150 mM NaCl solution) and cold (kept in water at 4 ± 1°C) stress for 5 h. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to annotated chickpea genome using TopHat and fragments per exon kilobase per million (FPKM) was calculated using Cufflinks software for each gene in all the sample to measure their gene expression. Differential expression analysis was performed using Cuffdiff software. The differentially expressed genes during various abiotic stress conditions were identified.

first: Garg

last: Rohini

first: Jain

last: Mukesh


title: Genome wide RNA Sequencing of whole C. elegans RNA

city: Chicago

first: Navdeep

last: Chandel

state: IL

address: 240 E. Huron St.

department: Pulmonary and Critical Care Medicine

country: USA

institute: Northwestern University

type: Expression profiling by high throughput sequencing

summary: We report genes induced under transient hypoxia in an ELT-2 dependent manner

overall_design: Adult C. elegans were exposed to transient hypoxia and fed ELT-2 RNAi. Normoxia and Empty Vector RNAi were performed as controls

first: Michael

last: Schieber


title: Genome Sequencing and Comparative Transcriptomics of Race1 and Race4 of Banana pathogen: Fusarium oxysporum f.sp. Cubense

city: Shenzhen

first: Fan

middle: ding

last: ding

address: yantian shashen Road

country: China

institute: EasyATCG

summary: Deep sequencing of mRNA from Fusarium oxysporum f. sp. Cubense 1 and 4  after infecting Musa acuminata 0h and 48h.

overall_design: Analysis of ploy(A)+ RNA of different hours after infecting of Musa acuminata

first: JunSheng

last: Huang

first: XiaoDong

last: Fang

first: Lijia

last: Guo

first: Laying

last: Lang

first: Huicai

last: Zeng

first: Guofen

last: Wang

first: Ming

last: Peng


title: Translational profiling in the unfolded protein response

status: Public on Aug 28 2014

city: Durham

first: David

last: Reid

state: NC

address: 436 Nanaline Duke Bldg., Box 3709 DUMC

department: Biochemistry

institute: Duke University

summary: The unfolded protein response (UPR) couples cellular translation rates and gene expression to the protein folding status of the endoplasmic reticulum (ER). Upon activation, the UPR machinery elicits a general suppression of protein synthesis and activation of stress gene expression, which act coordinately to restore protein folding homeostasis. We report here that UPR activation promotes the release of signal sequence-encoding mRNAs from the ER to the cytosol as a mechanism to decrease protein influx into the ER.  This release of mRNA begins rapidly, then gradually recovers with ongoing stress. Upon release into the cytosol, these mRNAs have divergent fates: some synthesize full-length proteins, while others are translationally inactive and retain nascent protein chains. Together, these findings identify the dynamic subcellular localization of mRNAs and translation as a regulatory feature of the cellular response to protein folding stress.

overall_design: Cells were treated with a timecourse of Thapsigargin or DTT, then fractionated and analyzed by mRNA-seq or ribosome profiling

middle: W

first: Christopher

middle: V

last: Nicchitta


title: Dormancy within Staphylococcus epidermidis biofilms: a transcriptomic analysis by RNA-seq

city: Braga

first: Virginia

last: Carvalhais

state: Braga

address: Campus de Gualtar

department: Centre of Biological Engeneering

country: Portugal

institute: University of Minho

summary: We sequenced mRNA from three independent biological replicates of Staphylococcus epidermidis biofilms with different proportion of dormant cells.

overall_design: Whole trancriptome analysis of Staphylococcus epidermidis biofilms with prevented and induced dormancy.

first: V

first: A

last: França

first: F

last: Cerca

first: R

last: Vitorino

first: G

middle: B

last: Pier

first: M

last: Vilanova

first: N


title: A high-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast

status: Public on Aug 31 2014

city: Pittsburgh

first: Zheng

last: Kuang

state: PA

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Under continuous, glucose-limited conditions, budding yeast exhibit robust metabolic cycles associated with major oscillations of gene expression and metabolic state. However, how such fluctuations might be coordinately linked to changes in chromatin status is less well understood. Here, we examine the correlated genome-wide transcription and chromatin states across the yeast metabolic cycle (YMC) at unprecedented temporal resolution, revealing a "just in time supply chain" by which specific cellular processes such as ribosome biogenesis are coordinated in time with remarkable precision. We identify distinct chromatin and splicing patterns associated with different gene categories and determine the relative timing of chromatin modifications to maximal transcription. Additionally, we interrogate chromatin modifier occupancy and observe subtly distinct spatial and temporal patterns compared to the modifications themselves. Furthermore, we identify multiple lysine mutants in H3 or H4 tails that disrupt metabolic cycling, supporting a potentially cooperative role of histone modifications in the YMC.

overall_design: 16 time points RNA-seq and ChIP-seq of 8 histone marks over one metabolic cycle, 14 time points ChIP-seq of 3 chromatin modifiers over one metabolic cycle

first: Ling

last: Cai

first: Xuekui

last: Zhang

first: Hongkai

last: Ji

first: Benjamin

middle: P

last: Tu

first: Jef

middle: D

last: Boeke


title: A new transcription factor for mitosis: In S. pombe, the RFX transcription factor Sak1 works with forkhead factors to regulate mitotic expression (ChIP-Seq)

status: Public on Aug 25 2014

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: Mitotic genes are one of the most strongly oscillating groups of genes in the eukaryotic cell cycle. Understanding the regulation of mitotic gene expression is a key issue in cell cycle control but is poorly understood in most organisms. Here, we find a new mitotic transcription factor, Sak1, in the fission yeast S. pombe.  Sak1 belongs to the RFX family of transcription factors, which have not previously been connected to cell cycle control.  Sak1 binds upstream of mitotic genes in close proximity to Fkh2, a forkhead transcription factor previously implicated in regulation of mitotic genes. We show that Sak1 is the major activator of mitotic gene expression and also confirm the role of Fkh2 as the opposing repressor. Sep1, another forkhead transcription factor, is an activator for a small subset of mitotic genes involved in septation. From yeasts to humans, forkhead transcription factors are involved in mitotic gene expression, and it will be interesting to see whether RFX transcription factors may also be involved in other organisms.

overall_design: 3 test samples were analyzed; 1 control (no-tag) sample was processed (each sample has 2 replicate experiments)

first: Bruce

last: Futcher

first: Janet

last: Leatherwood


title: A new transcription factor for mitosis: In S. pombe, the RFX transcription factor Sak1 works with forkhead factors to regulate mitotic expression

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

overall_design: Refer to individual Series


title: Stress response of Salmonella Typhimurium to acidified nitrite

city: Freising

first: Stefanie

last: Müller-Herbst

address: Weihenstephaner Berg 3

department: ZIEL, Department of Microbiology

country: Germany

institute: Technical University Munich

summary: The antimicrobial action of the curing agent NaNO2, which is added as a preservative to raw meat products, depends on its conversion to nitric oxide and other reactive nitrogen species under acidic conditions. In this study, we applied RNA-sequencing to analyze the acidified NaNO2 shock and adaptive response of Salmonella Typhimurium, a frequent contaminant in raw meat. Upon a 10 minute exposure to 150 mg/l NaNO2 in LB pH 5.5 acidified with lactic acid, genes involved in nitrosative stress protection together with several other stress related genes were induced. To the contrary, genes involved in translation, transcription, replication and motility were down-regulated. Induction of stress tolerance and reduction of cell proliferation obviously promote survival under harsh acidified NaNO2 stress. The subsequent adaptive response was characterized by up-regulation of NsrR-regulated genes and iron-uptake systems and down-regulation of genes involved in anaerobic respiratory pathways. Strikingly, amino acid decarboxylase systems, which contribute to acid tolerance, displayed increased transcript levels in response to acidified NaNO2. The induction of systems known to be involved in acid resistance indicates a nitrite mediated increase of acid stress.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Transcriptome of Salmonella Typhimurium 14028, treated at OD600 = 0.80-0.85 with 150 mg/l NaNO2 (acidified by lactic acid in the growth medium) for 10 min (shock response) or until an OD600 = 1.45-1.55 is reached (1.5 - 2.0 h, adaptation response), was compared to respective control cultures without NaNO2. Amplified cDNA libraries for sequencing on the SOLiD 5500xl system were prepared from one culture per condition.

first: Anna

last: Mühlig

first: Siegfried

last: Scherer


title: PSI-seq to Identify Sites of Pseudouridylation in S. cerevisiae

status: Public on Aug 24 2014

city: Stanford

first: Alexander

middle: F

last: Lovejoy

state: CA

address: 279 Campus Drive

institute: Stanford University

summary: Using a technique based on the ability of CMC to specifically label pseudouridines and to stop reverse transcriptase, we provide a transcriptome-wide map of pseudouridylation in S. cerevisiae under log phase and heat shock conditions

overall_design: 4 conditions: log phase (2x), heat shock, and stationary phase. For each condition, there are 4 libraries: natural RNA + or - CMC treatment and in vitro transcribed RNA + or - CMC treatment

first: Daniel

last: Riordan

first: Patrick

middle: O

last: Brown


title: Temporally defined neocortical translation and polysome assembly is determined by the RNA-binding protein, Hu antigen R

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Precise spatiotemporal control of mRNA translation machinery is essential to proper development of highly complex systems like the neocortex. Here, we show that an RNA-binding protein, Hu antigen R (HuR), regulates both neocorticogenesis and specificity of neocortical translation machinery in a developmental stage-dependent manner in mice. Neocortical absence of HuR alters the phosphorylation states of the initiation and elongation factors of the core translation machinery. In addition, HuR regulates the temporally specific positioning of functionally related mRNAs into the active translation sites, the polysomes. HuR also determines the specificity of neocortical polysomes by defining their combinatorial composition of ribosomal proteins and initiation and elongation factors. For some of the HuR-dependent proteins, the association with polysomes depends on the eIF2 alpha kinase 4 (eIF2ak4), which associated with HuR in prenatal developing neocortices. Finally, we found that deletion of HuR prior to embryonic day 10 (E10) disrupts both neocortical lamination and formation of the main neocortical commissure, the corpus callosum. Our study identifies a crucial role for HuR in neocortical development as a translational gatekeeper for functionally related mRNA subgroups and polysomal protein specificity.

overall_design: Cortex was dissected from WT and HuR cKO mouse pups at embryonic day 13 (E13) or the day of birth (P0).

first: Mladen

middle: R

last: Rasin

first: Matthew

middle: L

last: Kraushar

first: Kevin

last: Thompson


title: P493-6 treated with KJ-Pyr-9 and/or Doxycycline

city: La Jolla

first: Jonathan

middle: Ross

address: 10550 North Torrey Pines Road, BCC239

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

summary: In a fluorescence polarization screen for MYC-MAX interaction, we have identified a novel small molecule inhibitor of MYC, KJ-Pyr-9, from a Kröhnke pyridine library. The Kd of KJ-Pyr-9 for MYC in vitro is 6.5 ± 1.0 nM as determined by backscattering interferometry; KJ-Pyr-9 also interferes with MYC-MAX complex formation in the cell as shown in a protein fragment complementation assay. KJ-Pyr-9 specifically inhibits MYC-induced oncogenic transformation in cell culture; it has no or only weak effects on the oncogenic activity of several unrelated oncoproteins. KJ-Pyr-9 preferentially interferes with the proliferation of MYC-overexpressing human and avian cells and specifically reduces the MYC-driven transcriptional signature. In vivo, KJ-Pyr-9 effectively blocks the growth of a xenotransplant of MYC-overexpressing  human cancer cells.

overall_design: 4 treatment groups analyzed in triplicate: no treatment(control), 20uM KJ-Pyr-9, 0.1ug/mL doxycycline and KJ-Pyr-9 in combination with doxycycline

first: Peter

middle: K

last: Vogt


title: Cell type-specific ribosome profiling in vivo.

last: Sims

state: NEW YORK

address: 3960 Broadway blvd

institute: Columbia Medical Center

summary: We report cell-type specific ribosome profiling in a mouse glioma model.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We report a strategy for cell-type specific ribosome profiling in vivo. Our strategy was applied to the characterization of a mouse glioma model.

middle: A

first: Christian

last: Gonzalez

first: Nicholas

last: Hornstein


title: Identification of circulating miRNAs in a mouse model of nerve allograft transplantation under FK506 immunosuppression by Illumina small RNA deep sequencing

status: Public on Aug 22 2014

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: This study aimed to establish the expression profile of circulating microRNAs (miRNAs) during nerve allotransplantation.

overall_design: Experimental design  Male Balb/c and C57BL/6 mice (age, 10–12 weeks; weight, 30–35 g) were purchased from BioLasco (Yi-Lan, Taiwan). The Balb/c mice served as sciatic nerve allograft donors. The C57BL/6 mice were randomized into the group of nerve allograft transplantation with FK506 treatment and the group without FK506 treatment. These species of mice were selected on the basis of disparity at the MHC locus and prior experience with reciprocal rejection of grafts between these murine strains [18]. The mice were anesthetized by intraperitoneal injection of an anesthetic cocktail consisting of 0.1 mg/g ketamine and 0.01 mg/g xylazine. The anesthetized mice were restrained in a supine position on a heated pad to maintain the body temperature at 37°C. Under aseptic conditions, with sterile povidone/iodine preparation and 70% ethanol and sterile instruments and drapes, the skin over the proximal right hindlimb was incised, and the underlying biceps femoris muscle was bluntly dissected to expose the sciatic nerve. An established mouse sciatic nerve allotransplantation model was used. In brief, 1-cm Balb/c donor sciatic nerve grafts were transplanted in reverse orientation into 0.5-cm sciatic nerve gaps created in the recipient Balb/c mice. Tension-free repair was then performed under an operating microscope with three 11–0 nylon (Ethicon Inc., Somerville, NJ) interrupted epineurial sutures under 40X magnification. The muscle was closed with 5–0 vicryl sutures, and the skin with interrupted 5–0 nylon sutures. The animals were monitored to ensure appropriate feeding and diet after surgery. FK506 was administered subcutaneously at 1 mg/(kg-d) throughout the experimental course. At 3, 7, and 14 d after initial surgery (n = 3 animals per group at each time point), the whole blood samples were collected at the indicated times in tubes containing anticoagulant. (F)3d, (F)7d and (F)14d were used to indicate the serum samples of allotransplantation mice with FK506 immunosuppression for 3, 7, and 14 d, respectively. (N)3d, (N)7d and (N)14d were used to indicate the serum samples of allotransplantation mice without FK506 immunosuppression and sacrificed at postoperative 3, 7, and 14 d, respectively. After the whole blood samples were incubated at room temperature for 15 min, they were centrifuged at 3,000 ×g for 10 min, white blood cells were slowly removed from the corresponding layers, and the serum was extracted and stored at –80°C before processing for RNA analyses. Small RNA libraries generated from the serum of mice of above groups were analyzed using an Illumina HiSeq2000 Sequencer.

first: Cheng-Shyuan

last: Rau


title: The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger

city: Nottingham

first: David

last: Archer

address: University Park

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

summary: Fungi are an important source of enzymes for saccharification of plant polysaccharides and production of biofuels. Understanding of the regulation and induction of expression of genes encoding these enzymes is still incomplete. To explore the induction mechanism, we analysed the response of the industrially important fungus Aspergillus niger to wheat straw, with a focus on events occurring shortly after exposure to the substrate. RNA sequencing showed that over a third of the genes induced after 6 h of exposure to wheat straw were also induced during 6 h of carbon starvation, indicating that carbon starvation is probably an important factor in the early response to wheat straw. The up-regulation of the expression of a high number of genes encoding CAZymes that are active on plant-derived carbohydrates during early carbon starvation suggests that these enzymes could be involved in a scouting role during starvation, releasing inducing sugars from complex plant polysaccharides.

overall_design: Eight samples in total consisting of duplicate shake flask Aspergillus niger cultures from four conditions: 48h glucose, 6 h starvation, 6 h wheat straw, 24 h starvation

first: Jolanda

middle: M

last: van Munster

first: Paul

last: Daly

first: Stephane

last: Delmas

first: Steven

middle: T

last: Pullan

first: Martin

middle: J

last: Blythe

first: Sunir

last: Malla

last: Kokolski

first: Emelie

middle: C

last: Noltorp

first: Kristin

last: Wennberg

first: Richard

last: Fetherston

middle: G

last: Beniston

first: Xiaolan

last: Yu

last: Dupree


title: Three-dimensional proximity mapping of the DRGFP DNA double-strand break site in U2OS cells

city: Bethesda

first: Philipp

last: Oberdoerffer

state: MD

address: 41 Library Drive

department: CCR

institute: National Cancer Institute

summary: We mapped the DNA sequences located in physical proximity to an I-SceI endonuclease-dependent DNA double-strand break (DSB) site to be able to study the impact of DSBs on the break-associated chromatin micro-environment. The I-SceI DSB site is part of a DRGFP transgene that serves as a reporter for homology-directed DSB repair and was stably integrated into U2OS human osteosarcoma cells (Pierce et al., Genes Dev, 1999). DRGFP-U2OS cells were modified to carry a stable Doxycycline (Dox)-inducible I-SceI transgene (TRE-I-SceI) as well as the Tet-ON vector from Contech. Circular chromosome conformation capture (4C) was used to identify DSB-proximal DNA. 4C amplified DNA was subjected to Illumina Hi-Seq 200 100 bp paired end sequencing and reads were mapped to the human genome. The resulting genome-wide map of I-SceI/DRGFP-proximal DNA allows for the investigation of changes in DSB-surrounding chromatin features following I-SceI-mediated DSB induction.

overall_design: 4C library of I-SceI (DRGFP)-proximal DNA contacts in DRGFP-U2OS cells was generated using Illumina Hi-Seq 2000 sequencing, data sets are from two independent experiments.

first: Ofir

last: Hakim

first: Parthav

last: Jailwala

first: Myong-Hee

last: Sung

first: Simran

last: Khurana


title: Genome-wide map of regulatory interactions in the human genome

status: Public on Aug 21 2014

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors.

For data usage terms and conditions, please refer to https://www.encodeproject.org/about/data-use-policy

overall_design: Chromatin interactions identified by ChIA-PET for 4 different histone modifications (H3K4me1, H3K4me2, H3K4me3, H3K27ac), RAD21 and RNAPII in the K562 cell line, two biological replicates each. Additionally, chromatin interactions were identified by ChIA-PET in the GM12878 cell line for RAD21.

first: Nastaran

last: Heidari

first: Doug

middle: H

last: Phanstiel

first: Chao

last: He

first: Fabian

last: Grubert

first: Fereshteh

last: Jahanbani

first: Maya

last: Kasowski

first: Michael

middle: Q

last: Zhang

last: Snyder


title: The G-protein Alpha Subunit Gsα Is A Tumor Suppressor In Sonic Hedgehog-driven Medulloblastoma [RNA-Seq]

city: Cincinnati

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

summary:
Medulloblastoma, the most common malignant pediatric brain tumor, is highly heterogeneous with distinct molecular subtypes and cellular origins. Although current treatments improve survival rates, patients suffer severe treatment-related side effects and often relapse of tumors carrying resistance mutations, underscoring an urgent need for alternative targeted therapies. Currently, the genetic alterations underlying this disease are not fully understood. Here we identify GNAS, encoding the G-protein Gs-alpha, as a potent tumor suppressor gene in medulloblastoma. GNAS specifically defines a subset of aggressive Sonic Hedgehog (Shh)-group medulloblastomas. Gnas loss-of-function in distinct lineage progenitors of the developing hindbrain suffices to initiate medulloblastoma. We find that Gs-alpha is highly enriched at primary cilia of granule neuron precursors and suppresses Shh signaling not only by regulating classic cAMP-dependent pathway but also controlling ciliary trafficking of Smoothened. Concurrent cAMP elevation and Smoothened inhibition robustly arrests tumor cell growth in Gnas mutants. We further reveal oligodendrocyte progenitors as a novel cellular origin for anatomically-distinct Shh-associated medulloblastomas. Together, we identify a previously unrecognized tumor suppressor function of Gs-alpha in medulloblastoma partially mediated through inhibiting Shh signaling, and uncover Gs-alpha as a molecular link across disparate cells of origin among Shh-group medulloblastomas, pointing to G- protein modulation as a potential therapeutic avenue.
Purpose: To known the gene expression profile of Medulloblastoma which drived by Gnas mutation
Methods: mRNAs isolated from the cerebellum of control and Gnas mutants
Results:Upregulation of Shh Signaling components in tumors
Conclusions: The deletion of Gnas in hGFAP and Olig1 possitive cells result in substantial upregulation of shh signaling and formation of Medulloblastoma

overall_design: cerebellum mRNA profiles of 3 60-day old wild type (Ctrl) and 8 Olig1Cre driven Gsa conditional knockout or 8 hGFAPCre driven conditional knockout mice were generated by deep sequencing using Illumina Hiseq2000


title: The G-protein Alpha Subunit Gsα Is A Tumor Suppressor In Sonic Hedgehog-driven Medulloblastoma

type: Genome variation profiling by genome tiling array


title: Selection of epigenetic variation in Arabidopsis

status: Public on Sep 01 2014

city: Zürich

first: Christian

last: Heichinger

state: Zürich

address: Zollikerstrasse 107

department: Institute of Plant Biology

country: Switzerland

institute: Zürich University

type: Methylation profiling by high throughput sequencing

type: Genome variation profiling by high throughput sequencing


title: Sequestration of a two-component response regulator by a riboswitch regulated non-coding RNA

city: Paris

first: Jeffrey

last: Mellin

address: 25 rue Docteur Roux

country: France

institute: Institut Pasteur

summary: Riboswitches are ligand-binding elements contained within the 5’ untranslated regions of bacterial transcripts, which generally regulate expression of downstream open reading frames. Here we show that in Listeria monocytogenes, a Vitamin B12-binding (B12) riboswitch controls expression of a non-coding regulatory RNA, Rli55.  Rli55 in turn controls expression of the eut genes, which enable ethanolamine utilization and require B12 as a cofactor. Defects in ethanolamine utilization, or in its regulation by Rli55, significantly attenuate Listeria virulence in mice. Rli55 functions by sequestering the two-component response regulator, EutV via a EutV binding-site contained within the RNA. Thus Rli55 is a riboswitch-regulated member of the small group of regulatory RNAs that function by sequestering a protein and reveals a unique mechanism of signal integration in bacterial gene regulation.

overall_design: RNA-Seq and CLIP-Seq to investigate the sequestration of EutV by rli55

first: Mikael

last: Koutero

first: Daniel

last: Dar

first: Marie-Anne

last: Nahori

first: Rotem

last: Sorek

first: Pascale

last: Cossart


title: Ras-induced epigenetic inactivation of RRAD promotes glucose uptake in a human ovarian cancer model (RRBS-Seq]

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

summary: Ras-related associated with diabetes (RRAD) is a small Ras-related GTPase that is frequently inactivated by DNA methylation of the CpG island in its promoter region in cancer tissues. However, the role of the methylation-induced RRAD inactivation in tumorigenesis remains unclear. In this study, the Ras regulated-transcriptome and epigenome were profiled by comparing T29H (a RasV12-transformed human ovarian epithelial cell line) with T29 (an immortalized but non-transformed cell line) through Reduced representation bisulfite sequencing (RRBS-seq) and Digital gene expression (DGE) . We found that RasV12-mediated oncogenic transformation was accompanied by RRAD promoter hypermethylation and a concomitant loss of RRAD expression. In addition, we found that the RRAD promoter was hypermethylated and its transcription was reduced in ovarian cancer versus normal ovarian tissues. Treatment with the DNA methyltransferase inhibitor 5-aza-2′-deoxycytidine (5-aza-dC) resulted in demethylation in RRAD promoter and restored RRAD expression in T29H cells. By employing knockdown and overexpression techniques in T29 and T29H, respectively, we found that RRAD inhibited glucose uptake and lactate production by repressing the expression of glucose transporters. Finally, RRAD overexpression in T29H cells inhibited tumor formation in nude mice, suggesting RRAD is a tumor suppressor gene. Our results indicate that RasV12-mediated oncogenic transformation induces RRAD epigenetic inactivation, which in turn promotes glucose uptake and may contribute to ovarian cancer tumorigenesis

overall_design: Reduced representation bisulfite sequencing (MspI,~40-220bp size fraction) data for two cell lines (T29 and T29H) were generated by deep sequencing, in two replicates, using Illumina HiSeq 2000.

first: Yan

last: Wang

first: Zhong

middle: S

last: Sun


title: Ras-induced epigenetic inactivation of RRAD promotes glucose uptake in a human ovarian cancer model


title: mRNA expression in HEK-293 /STF cells

status: Public on Aug 20 2014

city: Baltimore

first: Yulian

last: Zhou

address: 725 N. Wolfe Street

institute: JHMI

summary: Canonical Wnt signaling in endothelial cells (ECs) is required for vascularization of the central nervous system (CNS) and for formation and maintenance of barrier properties unique to CNS vasculature. Gpr124 is an orphan member of the adhesion G-protein-coupled receptor family that is expressed in ECs and is essential for CNS angiogenesis and barrier formation via an unknown mechanism. Using canonical Wnt signaling assays in cell culture and genetic loss- and gain-of-function experiments in mice, we show that Gpr124 functions as a co-activator of Wnt7a- and Wnt7b-stimulated canonical Wnt signaling via a Frizzled receptor and Lrp co-receptor, and that Gpr124-stimulated signaling functions in concert with Norrin/Frizzled4 signaling to control CNS vascular development.  These experiments identify Gpr124 as a ligand-specific co-activator of canonical Wnt signaling.

overall_design: Total mRNA from HEK-293/STF cells was subjected to RNAseq

first: Amir

last: Rattner

first: Jeremy

last: Nathans


title: Ras-induced epigenetic inactivation of RRAD promotes glucose uptake in a human ovarian cancer model [DGE-Seq]

overall_design: DGE-seq data for two cell lines (T29 and T29H) by were generated by deep sequencing using Illumina GAIIx.


title: methylSig: a whole genome DNA methylation analysis pipeline

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

summary: DNA methylation plays critical roles in gene regulation and cellular specification without altering DNA sequences.  The wide application of reduced representation bisulfite sequencing (RRBS) and whole genome bisulfite sequencing (bis-seq) opens the door to study DNA methylation at single CpG site resolution. One challenging question is how best to test for significant methylation differences between groups of biological samples in order to minimize false positive findings. Current methods to analyze genome-wide bisulfite sequencing data use a smoothing approach or a simple statistical test based on the binomial distribution.

overall_design: Comparative DNA methylation profiling in AML blasts and normal CD34(+) control cells

first: Yongseok

last: Park

first: Maureen

last: Sartor

middle: E


title: RNA-seq Reveals Regional Differences in Transcriptome Response to Heat Stress in the Marine Snail Chlorostoma funebralis

first: Lani

last: Gleason

address: 8750 Biological Grade

department: Marine Biology Research Division

institute: Scripps Institution of Oceanography

summary: Southern California (USA) populations of the intertidal marine snail Chlorostoma (formerly Tegula) funebralis are generally exposed to higher air and water temperatures than northern California populations.  Previous studies have shown that southern populations are more tolerant of heat stress than northern populations.  To assess the potential role of gene regulation in these regional differences, we examined transcriptome responses to thermal stress in two southern and two northern populations of C. funebralis.  Snails from the four populations were acclimated to a common lab environment, exposed to a heat stress representative of natural low tide conditions, and then analyzed using RNA-Seq to characterize changes in gene expression associated with stress and differences in expression across geographic regions.  Changes in expression following stress were dominated by genes involved in apoptosis, the inflammatory response, response to mis and unfolded proteins, and ubiquitination of proteins.  Heat shock proteins (Hsps) were up-regulated in both northern and southern populations.  However, while the magnitude of the response was significantly greater in northern populations for the majority of Hsp70s, the southern populations showed a greater up-regulation for roughly half of the Hsp40s, which are co-chaperones for Hsp70s.  Differential expression analysis of the control versus treatment genes in the northern and southern populations respectively revealed that 56 genes, many involved in the inflammation and immune response, responded to heat stress only in the northern populations.  Moreover, several of the molecular chaperones and antioxidant genes that were not differentially expressed in the southern populations instead showed higher constitutive expression under control conditions compared to the northern populations.  The expression levels of some of these constitutive genes such as superoxide dismutase were also found to positively correlate with survival following heat stress.  This suggests that expression of these genes has evolved a degree of “frontloading” that may contribute to the higher thermal tolerance of southern populations.

overall_design: mRNA profiles of northern and southern California heat-stressed and control C. funebralis were generated by 100bp paired end sequencing, in duplicate, using Illumina HiSeq2000.

middle: U

first: Ron

last: Burton


title: Cfp1 is required for gene expression dependent H3K4me3 and H3K9 acetylation in embryonic stem cells (ChIP-Seq)

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

summary: Trimethylation of histone H3 lysine 4 (H3K4me3) accumulates at promoters in a gene activity dependant manner. The Set1 complex is responsible for most H3K4me3 in somatic cells and contains the conserved subunit Cfp1, which is implicated in targeting the Set1 complex to CpG islands in mammals. In mouse embryonic stem cells, Cfp1 is necessary for H3K4me3 accumulation at constitutively active gene promoters, but is not required to maintain steady-state transcription of the associated gene. Here we show that Cfp1 is instrumental for targeting H3K4me3 at promoters upon rapid transcriptional induction in response to external stimuli. Surprisingly, H3K4me3 accumulation is not required to ensure appropriate transcriptional output but rather plays gene specific roles. We also show that Cfp1 dependant H3K4me3 deposition contributes to H3K9 acetylation genome wide; suggesting that Cfp1 dependant H3K4me3 regulates overall H3K9 acetylation dynamics and is necessary for histone acetyl transferase recruitment. Finally, we observe increased antisense transcription at start and end of genes that requires Cfp1 for accurate H3K4me3 and H3K9ac deposition. Our results assign a key role for Cfp1 in establishing a complex active promoter chromatin state and shed light on how chromatin signalling pathways provide context dependant outcomes.

overall_design: wt (wtES) or Cfp1-/- (Cfp1null) ES cells were treated or not with doxorubicin (Dox) at 1uM for 6h. H3K4me3 (2 replicates) and H3K9,K14ac (H3ac, 1 replicate) occupancy was analyzed in each condition by ChIP-Seq. Input DNA for each cell line was alos sequenced alongside.

first: Thomas

last: Clouaire

first: Adrian

last: Bird


title: RNAseq analyses of pathogenic Burkholderia glumae under in vitro and in vivo conditions

city: Busan

first: Jungwook

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

country: South Korea

institute: Pusan National University

summary: We analyzed B. glumae transcriptome from infected rice tissue using an RNAseq technique. To identify unique expression of B. glumae genes within rice tissues, we compared in vivo transcriptome data of B. glumae to in vitro data. To accomplish this, we analyzed differentially expressed genes (DEGs) and identified 2,906 transcripts that were significantly altered.

overall_design: Three in vitro (culture) and three in vivo (in plant) RNAseqs in B. glumae

first: Young-Su

last: Seo


title: Cfp1 is required for gene expression dependent H3K4me3 and H3K9 acetylation in embryonic stem cells (RNA-Seq)

overall_design: wt (wtES) or Cfp1-/- (Cfp1null) ES cells were treated or not with doxorubicin (Dox) at 1uM for 6h and rRNA depleted total RNA was prepraed and analyzed by strand-specific RNA-Seq in 2 biological and 2 technical replicates per condition.


title: Comparison of Poly(A) capture versus Ribosomal RNA depletion methods for RNA-seq

city: Chapel Hill

first: Charles

middle: M.

last: Perou

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary:
Methods: RNA-sequencing was performed on matched samples obtained across several different gene expression measurement methods including: (a) fresh-frozen (FF) RNA samples by mRNA-seq, Ribo-zero and DSN and (b) FFPE samples by Ribo-zero and DSN. We also assayed the matched samples with Agilent microarray. RNA-seq data was compared on the rRNA-removal efficiency, genome profile, library complexity, coverage uniformity and quantitative cosinstency across protocols and with microarray data.
Results: Compared to mRNA-seq, Ribo-zero provides equivalent percentage of rRNA component, genome-based mapped reads, and consistent quantification of transcripts. Moreover, Ribo-zero and DSN protocols achieve concordant transcript profiling in FFPE samples, and provide substantially more information on non-poly(A) RNA, which cannot be captured by mRNA-seq.  Therefore, our study provides evidence that RNA-sequencing can generate accurate and reproducible transcript quantification using FFPE tissues.

overall_design:
mRNA profile of 11 breast tumors were assayed by Agilent microarray, and by RNA-sequencing on libraries including:  (a) fresh-frozen (FF) RNA samples by mRNA-seq, Ribo-zero and DSN and (b) FFPE samples by Ribo-zero and DSN, using Illunia HiSeq2000 2x50bp.

RNA-Seq raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns:
http://www.ncbi.nlm.nih.gov/gap/?term=phs000676

first: Wei

last: Zhao


title: Cfp1 is required for gene expression dependent H3K4me3 and H3K9 acetylation in embryonic stem cells

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

overall_design: Refer to individual Series


title: Profiling the circulating miRNAs in mice exposed to gram-positive and gram-negative bacteria by Illumina small RNA deep sequencing

status: Public on Aug 19 2014

first: Ching-Hua

last: Hsieh

summary: We profiled the expression of circulating microRNAs (miRNAs) in mice exposed to  gram-positive and gram-negative bacteria using Illumina small RNA deep sequencing. Recombinant-specific gram-negative pathogen Escherichia coli (Xen14) and gram-positive pathogen Staphylococcus aureus (Xen29) were used to induce bacterial infection in mice at a concentration of 1 × 108 bacteria/100 μL of phosphate buffered saline (PBS). Small RNA libraries generated from the serum of mice after exposure to PBS, Xen14, Xen29, and Xen14+Xen29 via the routes of subcutaneous injection (I), cut wound (C), or under grafted skin (S) were analyzed using an Illumina HiSeq2000 Sequencer. Following exposure to gram-negative bacteria alone, no differentially expressed miRNA was found in the injection, cut, or skin graft models. Exposure to mixed bacteria induced a similar expression pattern of the circulating miRNAs to that induced by gram-positive bacterial infection. Upon gram-positive bacterial infection, 9 miRNAs (mir-193b-3p, mir-133a-1-3p, mir-133a-2-3p, mir-133a-1-5p, mir-133b-3p, mir-434-3p, mir-127-3p, mir-676-3p, mir-215-5p) showed upregulation greater than 4-fold with a p-value < 0.01. Among them, mir-193b-3p, mir-133a-1-3p, and mir-133a-2-3p presented the most common miRNA targets expressed in the mice exposed to gram-positive bacterial infection.

overall_design: Male C57BL/6 mice (age, 10–12 weeks; weight, 30–35 g) were purchased from BioLasco (Yi-Lan, Taiwan). The mice were anesthetized by intraperitoneal injection of an anesthetic cocktail consisting of 0.1 mg/g ketamine and 0.01 mg/g xylazine. The anesthetized mice were restrained in a supine position on a heated pad to maintain body temperature at 37°C. Recombinant-specific gram-negative pathogen Escherichia coli (Xen14) and gram-positive pathogen Staphylococcus aureus (Xen29) purchased from Caliper (Caliper, USA) were used to induce bacterial infection in the mice at a concentration of 1 × 108 bacteria/100 μL of phosphate buffered saline (PBS). To create mixed gram-negative and gram-positive bacterial infection, 1 × 108 Xen14 bacteria and 1 × 108 Xen29 bacteria/100 μL of PBS were used for wound contamination. Three animal models were used to create bacterial infection routes: subcutaneous injection (hereafter referred to as (I)), cut wound (hereafter referred to as (C)), and skin grafting (hereafter referred to as (S)). In the (I) model, E. coli and/or S. aureus suspensions were injected subcutaneously into the backs of the mice using an Fr. 25 needle. In the (C) model, a 1 cm incision wound was created in the midline of the back, smeared with E. coli and/or S. aureus suspension, and the wound was closed directly with a 4-0 nylon suture. In the (S) model, a 1×1 cm rectangular full- thickness skin graft was lifted from the backs of the mice, E. coli and/or S. aureus suspensions were spread over the wound bed, and the skin graft was reattached and closed with a 4-0 nylon suture. An additional group of animals in each of these three models was inoculated with PBS to serve as a negative control. Small RNA libraries generated from the serum of mice after exposure to PBS, Xen14, Xen29, and Xen14+Xen29 via the routes of subcutaneous injection (I), cut wound (C), or under grafted skin (S) were analyzed using an Illumina HiSeq2000 Sequencer.

first: Cheng-Shyuan

last: Rau


title: RNA-Seq analysis of the multipartite genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock

city: Cuernavaca

first: Gamaliel

last: Lopez

state: Morelos

address: Ave. Universidad s/n, Chamilpa

department: Genómica Evolutiva

country: Mexico

institute: Centro de Ciencias Genómicas

summary:
Background
Regulation of transcription is essential for any organism and Rhizobium etli (a multi-replicon, nitrogen-fixing symbiotic bacterium) is no exception. This bacterium is commonly found in the rhizosphere (free-living) or inside of root-nodules of the common bean (Phaseolus vulgaris) in a symbiotic relationship. Abiotic stresses, such as high soil temperatures and salinity, compromise the genetic stability of R. etli and therefore its symbiotic interaction with P. vulgaris. However, it is still unclear which genes are up- or down-regulated to cope with these stress conditions. The aim of this study was to identify the genes and non-coding RNAs (ncRNAs) that are differentially expressed under heat and saline shock, as well as the promoter regions of the up-regulated loci.

Results
Analysing the heat and saline shock responses of R. etli CE3 through RNA-Seq, we identified 756 and 392 differentially expressed genes, respectively, and 106 were up-regulated under both conditions. Notably, the set of genes over-expressed under either condition was preferentially encoded on plasmids, although this observation was more significant for the heat shock response. In contrast, during either saline shock or heat shock, the down-regulated genes were principally chromosomally encoded. Our functional analysis shows that genes encoding chaperone proteins were up-regulated during the heat shock response, whereas genes involved in the metabolism of compatible solutes were up-regulated following saline shock. Furthermore, we identified thirteen and nine ncRNAs that were differentially expressed under heat and saline shock, respectively, as well as eleven ncRNAs that had not been previously identified. Finally, using an in silico analysis, we studied the promoter motifs in all of the non-coding regions associated with the genes and ncRNAs up-regulated under both conditions.

Conclusions
Our data suggest that the replicon contribution is different for different stress responses and that the heat shock response is more complex than the saline shock response. In general, this work exemplifies how strategies that not only consider differentially regulated genes but also regulatory elements of the stress response provide a more comprehensive view of bacterial gene regulation.

overall_design: mRNA of nine independent cultures of wild type strain Rhizobium etli CE3  were sequenced using Illumina GAIIx.  Our parameters were: all cultures were taken from exponential phase, at 30°C for 30min in control condition; 42°C for 30min for the culture subject to heat -shock, and 30min at 30°C in supplementary PY medium with 80mM NaCl for the saline shock condition.

last: López-Leal

middle: L

last: Tabche

first: Santiago

last: Castillo-Ramírez

first: Alfredo

last: Mendoza-Vargas

first: Miguel

last: Ramírez-Romero

first: Guillermo

last: Dávila


title: RNA-seq of poly(A)-/ribo- or poly(A)+ RNAs from human and mouse ES cells

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: We have used RNA-seq to examine circular RNAs from poly(A)-/ribo- RNAs in human and mouse embryonic stem cells, and from from RNase R treated poly(A)-/ribo- RNAs in mouse embryonic stem cells.

overall_design: In order to identify novel circular RNAs from different species

first: Qing-Fei

last: Yin

first: Hua-Hong

last: Fang

first: Xiao-Ou

last: Zhang

first: Ling-Ling

last: Chen


title: Role of de novo DNA methyltransferases in hematopoietic stem cells (RNA-seq)

city: Houston

first: deqiang

last: sun

state: TX

address: 2121 W Holcombe Blvd

institute: Texas A&M University

summary: To investigate the global transcriptome expression in Dnmt3ab dKO HSCs, we performed high-throughput sequencing of Poly A+ RNA (RNA-Seq) from purified HSCs (SP-KSL-CD150+). With biological duplicates, more than 200 million reads in total for each genotype of HSC were obtained.

overall_design: Mouse hematopoietic stem cell mRNA profiles of Dnmt3ab Dko HSCs, generated by deep sequencing, in duplicate, using Illumina Hiseq 2000

first: Deqiang

last: Sun

last: Wei


title: RNA-seq transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis

status: Public on Aug 18 2014

city: Dublin

first: David

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

summary: In the present study, we have analyzed the peripheral blood leukocyte (PBL) transcriptome of eight natural M. bovis-infected and eight age- and sex-matched non-infected control Holstein-Friesian animals using RNA-seq. In addition, we compared gene expression profiles generated using RNA-seq with those previously generated using the high-density Affymetrix® GeneChip® Bovine Genome Array platform from the same PBL-extracted RNA

overall_design: Identify changes occuring at the transcriptome level of PBL in response to M. bovis

first: Kirsten

last: McLoughlin

first: Nicolas

last: Nalpas

first: Kévin

last: Rue-Albrecht

first: John

last: Browne

last: Magee

first: Kate

last: Killick

first: Stephen

last: Park

first: Karsten

last: Hokamp

first: Kieran

last: Meade

first: Cliona

last: O'Farrelly

first: Eamonn

last: Gormley

middle: V

last: Gordon


title: A genome-wide perspective of miRNAome in response to high temperature, salinity and drought stresses in Brassica juncea (Czern) L.

city: New Delhi

first: Gopal

last: Joshi

state: Delhi

address: First Floor

department: Department of Botany

institute: Delhi University

summary:
Purpose: To identify high temperature, sailinity and drought-responsive miRNAs at genome wide level in B. juncea var varuna.
Results: In this study four small RNA libraries viz. B. juncea control (BJC), B. juncea high temperature stressed (BJH), B. juncea salinity stressed (BJS) and B. juncea drought stressed (BJD) were prepared and sequenced. With the help of UEA sRNA workbench software package 51 conserved miRNAs belonging to 30 miRNA families were identified. As there was limited genomic information available for B. juncea, we generated and assembled its genome sequence at a very low coverage. Using the generated sequence and other publically available Brassica genomic/transcriptomic resources as mapping reference, 126 novel (not reported so far in any plant species) were discovered for the first time in B. juncea. Further analysis also revealed existence of 32 and 37 star sequences for conserved and novel miRNAs, respectively. The expression of a few selected conserved and novel miRNAs under conditions of different abiotic stresses was revalidated through universal TaqMan based real time PCR. Putative targets of identified conserved and novel miRNAs were predicted in B. rapa to gain insights into functional roles manifested by B. juncea miRNAs. Furthermore, SPL2-like, ARF17-like and a NAC domain containing protein were experimentally validated as targets of miR156, miR160 and miR164 respectively. Investigation of gene ontologies linked with targets of known and novel miRNAs forecasted their involvement in various biological functions.
Conclusions: We have generated in this study, the first comprehensive abiotic stress influenced small RNA dataset in B. juncea. The combinatorial approach of NGS and computational methods led to the discovery of 51 conserved and 126 novel miRNAs. The present study provides a holistic view of B. juncea miRNAome under conditions of high temperature, salinity and drought. The catalogue of miRNA sequences, their expression and putative targets, generated in this study can be utilized to design crop improvement strategies in B. juncea and related species.

overall_design: Total four small RNA libraries were prepared and sequenced independently  [B. juncea control (BJC), B. juncea high temperature stressed (BJH), B. juncea salinity stressed (BJS) and B. juncea drought stressed (BJD)] on Illumina GAIIx

first: Ankur

middle: R

last: Bhardwaj

first: Ritu

last: Pandey

first: Shailendra

last: Goel

first: Arun

last: Jagannath

first: Amar

last: Kumar

first: Surekha

last: Katiyar-Agarwal

first: Manu

last: Agarwal


title: Transcriptome Sequencing from Diverse Human Populations Reveals Differentiated Regulatory Architecture

city: Stanford

first: Carlos

middle: D.

last: Bustamante

address: 300 Pasteur Drive

institute: Stanford University

summary: To understand the full range of expression variation, alternative splicing, and the genetics of regulatory variation in humans, we have sequenced the genomes, exomes, and transcriptomes of 45 individuals in the Human Genome Diversity Panel (HGDP) from seven worldwide populations that span the geographic breadth of human migration history. We find few genes that are systematically differentially expressed among populations. Further, allelic expression analysis indicates that previously mapped common regulatory variants identified in eight HapMap3 populations have similar effects across HGDP populations, suggesting that the cellular effects of common variants are shared even across very diverse populations. In contrast, comparisons of alternative splicing across pairwise populations reveal highly significant differences, with ~20% of alternatively spliced exons varying significantly by population. Greater genomic differences are associated with significantly more splicing variability overall. Together, these results provide a resource and an estimate for the degree of sharing of gene expression, alternative splicing, and regulatory genetics across populations.

overall_design: Lymphoblastoid cell line mRNA profiles of 45 human samples from the Human Genome Diversity Panel sequenced on an Illumina HiSeq 2000, each sample library was sequenced in duplicate to produce a merged sample bam.

first: Alicia

last: Martin

first: Helio

middle: A

last: Costa

first: Tuuli

last: Lappalainen

first: Brenna

last: Henn

first: Jeffrey

last: Kidd

first: Muh-Ching

last: Yee

first: Fabian

last: Grubert

first: Howard

last: Cann

first: Michael

last: Snyder

middle: B

last: Montgomery

middle: D


title: Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis

city: Columbus

first: Dominik

last: Jäger

state: Ohio

address: 484 12th West Ave

institute: The Ohio State University

summary:
Background:  Prokaryotes have relatively small genomes, densely-packed and apparently dominated by protein-encoding sequences.  However, data now generated by high throughput RNA sequencing (RNA-seq) reveal surprisingly more-complex transcriptomes with many previously unrecognized and unanticipated non-coding small and antisense transcripts.  To date, such studies have investigated primarily Bacteria.  Here, we report the transcripts present in Thermococcus kodakarensis, a model hyperthermophilic Archaeon, synthesized under different growth and metabolic conditions.

Results:  cDNA libraries, generated from RNA preparations isolated from cells growing in media with sulfur or pyruvate, with sulfur to stationary phase, and growing with pyruvate but with sulfur added 20 min before RNA isolation, have been deep-sequenced.  The results identify >2,700 sites of transcription initiation, establish a genome-wide map of transcripts, and consensus sequences for transcription initiation and post-transcription regulatory elements in T. kodakarensis.  Primary transcription start sites (TSS) are identified upstream of 1,254 annotated genes, including ~78 % of those predicted by promoter locations, and an additional 644 primary TSS and their promoters have been identified within genes.  Most of the mRNAs have a 5'-untranslated region (5'-UTR) between 10 and 50 nt long (median length = 16 nt), ~20 % have 5'-UTRs from 50 to 300 nt long, ~14 % are leaderless with 5'-UTRs ≤8 nt, and ~50% contain a consensus ribosome binding sequence.  The results also identify TSS for 1,018 antisense transcripts, most with sequences complementary to either the 5'- or 3'-region of a sense mRNA.  The data confirm the presence of transcripts from all three CRISPR loci, the RNase P and 7S RNAs, all tRNAs and rRNAs and 69 snoRNAs predicted to be encoded in the T. kodakarensis genome.  Two transcripts, putatively identified as riboswitches, were present in RNA preparations isolated from growing but not from stationary phase cells.  The procedure used is designed to identify TSS but, assuming that the number of cDNA reads correlates with transcript abundance, the data obtained also provide a semi-quantitative overview of global operon expression. They document substantial differences in gene expression under different physiological conditions and are consistent with previous observations of substrate-dependent specific gene expression.   Many previously unrecognized and unanticipated small RNAs have been identified, some with relative low GC contents (≤50%) and sequences that do not fold readily into base-paired secondary structures, contrary to the classical expectations for non-coding RNAs in a hyperthermophile.

Conclusion:  We have identified >2,700 TSS that include almost all of the primary sites of transcription initiation upstream of annotated genes, and also many secondary sites, sites within genes and sites resulting in antisense transcripts.  The T. kodakarensis genome is small (~2.1 Mbp) and tightly packed with protein-encoding genes, but the results reveal the presence of many non-coding RNAs and predict extensive RNA-based regulation in T. kodakarensis.

overall_design: cDNA libraries were generated and sequenced from RNA isolated from T. kodakarensis cells growing exponentially (Sexp) and to stationary phase (Sstat) in ASW-YT medium with sulfur, growing exponentially in ASW-YT with pyruvate (Pexp), and from cells growing exponentially in pyruvate but 20 min after sulfur addition (PS).  The cDNAs were generated after first incubating the RNA preparations with terminator exonuclease (TEX).  TEX does not degrade primary transcripts with a 5'-triphosphate (Sharma et al., 2010) but does digest RNAs generated by transcript processing that have a 5'-monophosphate.  As a control and to fully document all transcripts, a cDNA library (C) was also generated and sequenced from an aliquot of an RNA preparation isolated from the cells growing exponentially with sulfur that was not exposed to TEX digestion.

first: Konrad

last: Förstner

first: Cynthia

middle: M

last: Sharma

first: Thomas

middle: J

last: Santangelo

first: John

middle: N

last: Reeve


title: Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

city: Berkeley

first: Nicholas

middle: T

last: Ingolia

email: ingolia@berkeley.edu, nick@ingolia.org

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: Ribosome profiling suggests that ribosomes occupy many regions of the transcriptome thought to be non-coding, including 5' UTRs and lncRNAs. Apparent ribosome footprints outside of protein-coding regions raise the possibility of artifacts unrelated to translation, particularly when they occupy multiple, overlapping open reading frames (ORFs). Here we show hallmarks of translation in these footprints: co-purification with the large ribosomal subunit, response to drugs targeting elongation, trinucleotide periodicity, and initiation at early AUGs. We develop a metric for distinguishing between 80S footprints and nonribosomal sources using footprint size distributions, which validates the vast majority of footprints outside of coding regions. We present evidence for polypeptide production beyond annotated genes, including induction of immune responses following human cytomegalovirus (HCMV) infection. Translation is pervasive on cytosolic transcripts outside of conserved reading frames, and direct detection of this expanded universe of translated products enables efforts to understand how cells manage and exploit its consequences.

overall_design: Ribosome profiling to verify that true ribosome footprints shift in response to different elongation inhibitors (CHX vs Emetine) and co-purify with an affinity-tagged large ribosomal subunit (bound vs input)

first: Gloria

last: Brar

first: Noam

last: Stern-Ginossar

last: Harris

first: Gaëlle

last: Talhouarne

first: Sarah

last: Jackson

first: Mark

last: Wills

first: Jonathan

last: Weissman


title: Transcriptome profiling in human T-ALL

city: New York

last: Trimarchi

state: NY

address: 550 First Ave Smilow 1307

department: Pathology

institute: NYU School of Medicine

summary: Genome-wide mapping and characterization of novel Notch-regulated long non-coding RNAs in acute leukemia

overall_design: Total RNA was extracted from samples using the RNeasy Plus mini kit (Life Technologies, Carlsbad, CA). Samples were then subject to PolyA  selection (Figures 1E, 5F and 5G only) using oligo-dT beads (Life Technologies, Carlsbad, CA) or rRNA removal (all other samples) using the Ribo-Zero kit (Epicentre, Madison, WI)  according to the manufacturers instructions. The resulting RNA samples were then used as input for library construction using the dUTP method as described by Parkhomchuck et al, 2009. RNA libraries were then sequenced on the Illumina HiSeq 2000 or 2500 using 50bp paired-end reads.


title: Role of de novo DNA methyltransferases in hematopoietic stem cells (WGBS)

first: deqiang

last: sun

summary: To investigate the global DNA methylation changes in Dnmt3a-KO and Dnmt3ab-dKO HSCs compared to control HSCs, we performed whole genome bisulfite sequencing

overall_design: Mouse hematopoietic stem cell DNA methylation profiles of control, Dnmt3a-KO and Dnmt3ab-dKO HSCs  were generated generated by deep sequencing, in duplicate, using Illumina Hiseq 2000

first: Li

last: Wei


title: Promoter Decommissioning by the NuRD Chromatin Remodeling Complex Triggers Synaptic Connectivity in the Mammalian Brain

city: Boston

first: Martin

last: Hemberg

state: MA

address: 300 Longwood Avenue

department: Ophthalmology

institute: Boston Children's Hospital

summary: Precise control of gene expression plays fundamental roles in brain development, but the roles of chromatin regulators in neuronal connectivity have remained poorly understood. Here, we find that depletion of the nucleosome remodeling and deacetylation (NuRD) complex in the cerebellar cortex by in vivo RNAi in rats and conditional knockout of the core NuRD subunit Chd4 in mice profoundly impairs the establishment of granule neuron parallel fiber/Purkinje cell synapses. In RNA-Seq analyses of Chd4 conditional knockout mice, we identify a set of nearly 200 genes that are repressed by the NuRD complex in the cerebellum in vivo. Genome-wide ChIP-Seq analyses reveal that the NuRD complex selectively decommissions the promoters of NuRD-repressed genes in the cerebellum in vivo by inducing the deacetylation of histone H3K9/14 and H3K27 and demethylation of H3K4 at these genes. Importantly, temporal control of promoter decommissioning and repression of NuRD target genes upon maturation of the cerebellum requires the NuRD complex. Finally, in a targeted in vivo RNAi screen of NuRD-repressed target genes, we identify the transcription factor Nhlh1, the RNA-binding protein Elavl2, and the presynaptic regulator Cplx3 as negative regulators of presynaptic differentiation in the cerebellar cortex. Together, these findings define NuRD-dependent promoter decommissioning as a developmentally regulated programming mechanism that releases the brake on presynaptic differentiation and thereby drives synaptic connectivity in the mammalian brain.

overall_design: Three distinct histone modifications using postnatal day 6 or day 22 cerebella from wild type (WT) or Chd4 conditional knockout (cKO) mice were examined in duplicate using libraries prepared with the Illumina ChIP-Seq DNA Sample Prep Kit and sequenced on the Illumina HiSeq 2000 platform.

first: Tomoko

last: Yamada

first: Yue

last: Yang

first: Toshimi

last: Yoshida

first: Ha

middle: Y

last: Cho

first: J

middle: P

last: Murphy

first: Diasynou

last: Fioravante

first: Wade

middle: G

last: Regehr

first: Steven

last: Gygi

first: Katia

last: Georgopoulos

first: Azad

last: Bonni


title: Chromosomal Architecture of Arabidopsis and its Implication in Transposon Intergration

city: Zurich

first: Stefan

last: Grob

address: Zollikerstrasse 107

institute: University of Zurich

summary: Efficient storing and readout of genetic information is not only dependent on tight epigenetic regulation but also on the spatial organization and folding of chromosomes. Although the epigenome of the model plant Arabidopsis has been extensively studied, its interplay with chromosomal architecture is less well understood. We show that chromosomal architecture is tightly linked to the epigenetic state and furthermore how physical constraints such as nuclear size influence folding principles of chromatin. In addition to global principles of chromatin organisation, we describe a novel nuclear structure, termed KNOT, in which genomic regions of all five Arabidopsis chromosomes highly interact. These regions are characterized as heterochromatic islands within the euchromatin and likely represent preferred landing sites for transposons, suggesting a novel transposon defence mechanism in the Arabidopsis nucleus.

overall_design: HiC experiments were performed on Arabidopsis thaliana Col-0 wildtype, homozygous crwn1-1, and homozygous crwn4-1 14-day-old seedlings


title: A Comprehensive Genome-wide Study on Tissue- and Abiotic Stress-specific miRNAs in Triticum aestivum

first: Gopal

last: Joshi

summary:
Purpose: To identify abiotic stress responsive and tissue specific  miRNAs at genome wide level in wheat (Triticum aestivum)
Results: Small RNA libraries were constructed from four tissues (root, shoot, mature leaf and spikelets) and three stress treatments of wheat seedlings (control, high temperature, salinity and water-deficit). A total of 59.5 million reads were obtained by high throughput sequencing of eight wheat libraries, of which 32.5 million reads were found to be unique. Using UEA sRNA workbench we identified 47 conserved miRNAs belonging to 20 families, 1030 candidate novel and 51 true novel miRNAs. Several of these miRNAs displayed tissue specific expression whereas few were found to be responsive to abiotic stress treatments. Target genes were predicted for miRNAs identified in this study and their grouping into functional categories revealed that the putative targets were involved in diverse biological processes. RLM-RACE of predicted targets of three conserved miRNAs (miR156, miR160 and miR164) confirmed their mRNA cleavage, thus indicating their regulation at post-transcriptional level by corresponding miRNAs. Expression profiling of confirmed target genes of these miRNAs was also performed.
Conclusions: This is the first comprehensive study on profiling of miRNAs in a variety of tissues and in response to several abiotic stresses in wheat. Our findings provide valuable resource for better understanding on the role of miRNAs in stress tolerance as well as plant development. Additionally, this information could be utilized for designing wheat plants for enhanced abiotic stress tolerance and higher productivity.

overall_design: Total eight (three stress, one control and four tissue specific small RNA libraries were pepared and sequenced independently  [wheat control (WC), wheat high temperature stressed (WHTS), wheat salinity stressed (WSS) and wheat drought stressed (WDS), wheat shoot(WSH), wheat leaf (WLF), wheat flower(WFL), wheat root(WRT)] on Illumina GAIIx

first: Ritu

last: Pandeya

first: Ankur

last: Bhardwaj

first: Manu

last: Agarwal

first: Surekha

last: Katiyar-Agarwal


title: Role of de novo DNA methyltransferases in hematopoietic stem cells

first: deqiang

last: sun


title: Moderate stress acclimation provides immunity to stress by rewiring regulatory networks and inducing genes with protective functions in Cassava

city: Saint Louis

first: Weixiong

last: Zhang

state: MO

address: Campus Box 1045 One Brookings Drive

institute: Washington university in St Louis

summary: Stress acclimation is an effective mechanism that plants acquired for adaption to dynamic environmental conditions. After undergoing cold acclimation, plants become more tolerant to cold stress. In order to understand the mechanism of cold acclimation, we performed a systematic, comprehensive study of cold response and acclimation in Cassava (Manihot esculenta), a staple crop and major food source in the tropical regions of the world. We profiled mRNA genes and small-RNA species, using next generation sequencing, and performed an integrative analysis of the transcriptome and microRNAome of Cassava across the normal condition, a moderate cold stress at 14°C, a harsh stress at 4°C after cold acclimation at 14°C, and a cold shock from 24°C to 4°C. Two results from the analysis were striking. First, the moderate stress and cold shock, despite a difference of 10°C between the two, triggered comparable degrees of perturbation to the transcriptome; in contrary, further harsh stress after cold acclimation resulted in a much smaller degree of transcriptome variation. Second and more importantly, about two thirds of the up- or down-regulated genes after moderate stress reversed their expression to down- or up-regulation, respectively, under harsh stress after cold acclimation, resulting in a genome-wide rewiring of regulatory networks. MicroRNAs, which are key post-transcriptional gene regulators, were major players in this massive rewiring of genetic circuitry. Further, a function enrichment analysis of the perturbed genes revealed that cold acclimation helped the plant to develop immunity to further harsh stress by exclusively inducing genes with functions of nutrient reservoir; in contrast, many genes with functions of viral reproduction were induced by cold shock. Our study revealed, for the first time, the molecular basis of stress acclimation in plants, and shed lights on the role of microRNA gene regulation in cold response and acclimation in Euphorbia.

overall_design: Three organs/tissues (folded leaf, fully expanded leaf and roots) of Cassava cultivar SC124 harvested at 6h, 24h and 5d for three cold treatments of CA, CCA and CS, for gene expression profiling at the stages of initial response, secondary response, and functional adaption to cold stresses. Total RNA of each sample was isolated individually, and then pooled with an equal amount from each sample into one for profiling. As a result, four mRNA libraries and four small-RNA libraries, corresponding to the conditions of CA, CCA, CS and NC, were constructed.

first: Changyin

last: Zeng

first: Zheng

last: Chen

first: Jing

last: Xia

first: Kevin

first: Xin

first: Yufei

last: Zhou

first: Weiping

last: Bo

first: Shun

last: Song

first: Ruiju

first: Zi

last: Guo

first: Bin

last: Wang

first: Junfei

first: Hai

last: Peng

first: Wenquan

first: Ming


title: AA Effector CD8 T cell profiling

status: Public on Aug 17 2014

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 200 Hawkins Dr, 40025 PFP

institute: University of Iowa

summary: Flow sorted CD3+CD8+CD44+CXCR3+NKG2D+ lymph node cells from C3H/HeJ mice with alopecia were flow sorted and profiled in relation to CD3+CD8+CD44+CXCR3+NKG2D- lymph node cells from the same host

overall_design: Cell populations were sorted from three separate mice

first: Jane

middle: E

last: Cerise

first: Angela

last: Christiano


title: Wound-induced neoblast specialization in S. mediterranea

city: Cambridge

first: Kellie

last: Kravarik

address: 9 Cambridge Center

department: Biology Department

institute: Whitehead Institute, MIT

summary: We report the expression of mRNA transcripts in X1 neoblast isolated by FACS followin amputation of the head (anterior wounding) and amputation of the pharyx and tail (posterior wounding) at 0 and 48 hours

overall_design: RNA-sequencing of pre-pharyngeal X1 cells from anterior and posterior facing wounds at 0 and 48 hrs after wounding in S. mediterranea

first: Scimone

last: M. Lucila

first: Sylvain

middle: W

last: Lapan

first: Peter

last: Reddien


title: Single-base-resolution Methylomes of Populus trichocarpa Reveal the Association between DNA Methylation and Drought Tolerance

city: Beijing

first: dan

last: liang

address: No. 35 Qinghua East Road

institute: Beijing Forestry University

summary: DNA methylation is an important biological form of epigenetic modification, playing key roles in plant development and environmental responses. In this study, we examined single-base resolution methylomes of Populus under control and drought stress conditions using high-throughput bisulfite sequencing for the first time. Our data showed methylation levels of methylated cytosines, upstream2kp, downstream2kb, and repeatitive sequences significantly increased after drought treatment in Populus. Interestingly, methylation in 100 bp upstream of the transcriptional start site (TSS) repressed gene expression, while methylations in 100 – 2000bp upstream of TSS and within the gene body were positively associated with gene expression. Integrated with the transcriptomic data, we found that all cis-splicing genes were non-methylated, suggesting that DNA methylation may not associate with cis-splicing. However, our results showed that 80% of trans-splicing genes were methylated. Moreover, we found 1156 transcription factors (TFs) with reduced methylation and expression levels and 690 TFs with increased methylation and expression levels after drought treatment. These TFs may play important roles in Populus drought stress responses through the changes of DNA methylation. Taken together, these findings may provide valuable new insight into our understanding of the interaction between gene expression and methylation of drought responses in Populus.

overall_design: Methylomes of Poplar response to drought

first: Dan

last: Liang


title: Small RNAs as important regulators for the hybrid vigour of super-hybrid rice

first: Zhen

last: Zhu

address: No.1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology

summary: Heterosis is an important biological phenomenon; however, the role of small RNA (sRNA) in heterosis of hybrid rice remains poorly described. Here, we performed sRNA profiling of F1 super-hybrid rice LYP9 and its parents using high-throughput sequencing technology, and identified 355 distinct mature microRNAs and trans-acting small interfering RNAs, 69 of which were differentially expressed sRNAs (DES) between the hybrid and the mid-parental value. Among these, 34 DES were predicted to target 176 transcripts, of which 112 encoded 94 transcription factors. Further analysis showed that 67.6% of DES expression levels were negatively correlated with their target mRNAs either in flag leaves or panicles. The target genes of DES were significantly enriched in some important biological processes, including the auxin signalling pathway, in which existed a regulatory network mediated by DES and their targets, closely associated with plant growth and development. Overall, 20.8% of DES and their target genes were significantly enriched in quantitative trait loci of small intervals related to important rice agronomic traits including growth vigour, grain yield, and plant architecture, suggesting that the interaction between sRNAs and their targets contributes to the heterotic phenotypes of hybrid rice. Our findings revealed that sRNAs might play important roles in hybrid vigour of super-hybrid rice by regulating their target genes, especially in controlling the auxin signalling pathway. The above finding provides a novel insight into the molecular mechanism of heterosis.

overall_design: We constructed six sRNA sequencing libraries and six mRNA sequencing libraries of flag leaves and panicles of the super-hybrid rice Liangyou-pei9 (LYP9) combination at the grain-filling stage. The above hybrid rice combination includes F1 hybrid LYP9 and its parental lines including the male-sterile line Peiai64s (PA64s) and the restorer line 93-11.

first: Lei

last: Zhang

first: Yonggang

first: Xiaoli

last: Wei

first: Yan

last: Dai

first: Dawei

last: Yuan

first: Yufei

last: Lu

first: Yangyang

last: Pan


title: Genome Wide Mapping of Foxo1 Binding-sites in Murine T Lymphocytes

first: Willey

last: Liao

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

summary: The Forkhead box O (Foxo) family of transcription factors has a critical role in controlling the development, differentiation, and function of T cells. However, the direct target genes of Foxo transcription factors in T cells have not been well characterized. In this study, we focused on mapping the genome wide Foxo1-binding sites in naïve CD4+ T cells, CD4+ T cells, and Foxp3+ regulatory T (Treg) cells. By using chromatin immunoprecipitation coupled with deep sequencing (ChIP-Seq), we identified Foxo1 binding sites that were shared among or specific to the three T cell populations. Here we describe the experiments, quality controls, as well as the deep sequencing data. Part of the data analysis has been published by Ouyang W et al. in Nature 2012  (1) and Kim MV et al. in Immunity 2013 (2), and the associated data set were uploaded to NCBI Gene Expression Omnibus.

overall_design: ChIP DNAs were prepared from T cells isolated from C57BL/6 mice using Foxo1 antibody and T cells isolated from Foxo1tag/tagbirA mice using Streptavin-coated beads. ChIP-seq libraries were prepared following a standard protocol.

first: Will

first: Weiming

last: Ouyang

first: Michael

middle: Q

first: Ming

middle: O

last: Li


title: Adenovirus Small E1A Employs the Lysine Acetylases p300/CBP and Tumor Suppressor Rb to Repress Select Host Genes and Promote Productive Virus Infection [RB1_ChIP_2]

status: Public on Aug 15 2014

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

institute: UCSD

summary: Oncogenic transformation by adenovirus small e1a depends on simultaneous interactions with the host lysine acetylases p300/CBP and the tumor suppressor RB. How these interactions influence cellular gene expression remains unclear. We find that e1a displaces RBs from E2F transcription factors and promotes p300 acetylation of RB1 K873/K874 to lock it into a repressing conformation that interacts with repressive chromatin-modifying enzymes. These repressing p300-e1a-RB1 complexes specifically interact with host genes that have unusually high p300 association within the gene body. The TGF?-, TNF-, and interleukin-signaling pathway components are enriched among such p300-targeted genes. The p300-e1a-RB1 complex condenses chromatin in a manner dependent on HDAC activity, p300 lysine acetylase activity, the p300 bromodomain, and RB K873/K874 and e1a K239 acetylation to repress host genes that would otherwise inhibit productive virus infection. Thus, adenovirus employs e1a to repress host genes that interfere with viral replication.

overall_design: Examination of RB1 rearrangements by adenoviral e1a as well as mutant e1as in IMR90

first: Roberto

last: Ferrari

first: Dawie

last: Gou

first: Gauri

last: Jawdekar

first: Sarah

last: Johnson

first: Miguel

last: Nava

first: Trent

last: Su

first: Ahmed

last: Yousef

first: Nathan

last: Zemke

first: Matteo

last: Pellegrini

first: Siavash

middle: K

last: Kurdistani

first: Arnold

last: Berk


title: Adenovirus Small E1A Employs the Lysine Acetylases p300/CBP and Tumor Suppressor Rb to Repress Select Host Genes and Promote Productive Virus Infection

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

Oncogenic transformation by adenovirus small e1a depends on simultaneous interactions with the host lysine acetylases p300/CBP and the tumor suppressor RB. How these interactions influence cellular gene expression remains unclear. We find that e1a displaces RBs from E2F transcription factors and promotes p300 acetylation of RB1 K873/K874 to lock it into a repressing conformation that interacts with repressive chromatin-modifying enzymes. These repressing p300-e1a-RB1 complexes specifically interact with host genes that have unusually high p300 association within the gene body. The TGF?-, TNF-, and interleukin-signaling pathway components are enriched among such p300-targeted genes. The p300-e1a-RB1 complex condenses chromatin in a manner dependent on HDAC activity, p300 lysine acetylase activity, the p300 bromodomain, and RB K873/K874 and e1a K239 acetylation to repress host genes that would otherwise inhibit productive virus infection. Thus, adenovirus employs e1a to repress host genes that interfere with viral replication.

overall_design: Refer to individual Series


title: Adenovirus Small E1A Employs the Lysine Acetylases p300/CBP and Tumor Suppressor Rb to Repress Select Host Genes and Promote Productive Virus Infection [Pol2_ChIP]

overall_design: Examination of POL II rearrangements by adenoviral e1a in IMR90

middle: R


title: Adenovirus Small E1A Employs the Lysine Acetylases p300/CBP and Tumor Suppressor Rb to Repress Select Host Genes and Promote Productive Virus Infection [RB1_ChIP]

overall_design: Examination of RB1 rearrangements by adenoviral e1a in IMR90


title: Adenovirus Small E1A Employs the Lysine Acetylases p300/CBP and Tumor Suppressor Rb to Repress Select Host Genes and Promote Productive Virus Infection [p300_ChIP]

overall_design: Examination of P300 IMR90 before and after infection with dl1500


title: Adenovirus Small E1A Employs the Lysine Acetylases p300/CBP and Tumor Suppressor Rb to Repress Select Host Genes and Promote Productive Virus Infection [RNA-seq]

overall_design: Examination of transcriptome by mRNA sequencing before and after infection by adenoviral e1a expressing vectors in growth arrested IMR90


title: Transcriptional profiling in Finger millet (Eleusine coracana) genotypes provides insights into the molecular basis of salinity tolerance in tolerant genotype.

city: Coimbatore

first: Raveendran

last: Muthurajan

state: Tamil Nadu

address: Tamil Nadu Agricultural University

department: Department of Plant Biotechnology

institute: Tamil Nadu Agricultural University

summary: In present study we compared transcriptional response to salinity stress between susceptible CO 12 and tolerant genotype trichy 1 of finger millet. We found out that several functional group of genes like transporters, transcription factors, genes involved in cell signalling, osmotic homeostasis, compatible solutes biosynthesis were upregulated more in tolerant genotype as compared to susceptible genotype in response to salinity stress. Salnity inhibited photosynthetic capacity and photosynthesis related genes more in susceptible genotype as compared to tolerant genotype. Identified genes are excellent targets for further functional studies in order to understand more specific molecular mechanisms of salt tolerance in two genotypes of finger millet and can be further used for developing salinity tolerant crops through genetic engineering.

overall_design: 4 samples were examined:- CO12 without salinity stress, CO12 exposed to salinity stress, Trichy 1 without salinity stress, Trichy 1 exposed to salinity stress

first: Hifzur

last: Rahman

first: Jagadeesh

middle: S

last: Nallathambi

first: Sethil

last: Natesan


title: Adenovirus Small E1A Employs the Lysine Acetylases p300/CBP and Tumor Suppressor Rb to Repress Select Host Genes and Promote Productive Virus Infection [H3k27ac_ChIP]

overall_design: Examination of H3K27ac IMR90 before and after infection with dl1500

middle: A


title: Suppression of the FOXM1 transcriptional program via novel small molecule inhibition

first: Giovanni

last: Marsico

address: Robinson Way

institute: CRUK Cambridge Institute

summary: The transcription factor FOXM1 binds to sequence-specific motifs on DNA (C/TAAACA) through its DNA binding domain (DBD), and activates proliferation- and differentiation-associated genes. Aberrant overexpression of FOXM1 is a key feature in oncogenesis and progression of many human cancers. Herein we identify novel inhibitors of FOXM1 that block DNA binding from a high-throughput screen applied to a library of 54,211 small molecules. One compound, FDI-6 (NCGC00099374) is studied in depth and is shown to bind directly to FOXM1 protein, displace the transcription factor from genomic targets in MCF-7 breast cancer cells, and induce concomitant transcriptional down-regulation. Global transcript profiling of MCF-7 cells by RNA-seq shows that FDI-6 specifically down regulates FOXM1-activated genes with FOXM1 occupancy confirmed by ChIP-seq. This small molecule mediated effect is selective for FOXM1-controlled genes with no effect on genes regulated by homologous forkhead family factors.

overall_design: 12 samples, 100 single-ended RNAseq libraries: 3 replicates for untreated (0 hours); 3 replicates for 3 hours treatment; 3 replicates for 6 hours treatment; 3 replicates for 9 hours treatment. Treatment: compound FDI-6 inhibiting binding of FOXM-1 to DNA.

first: Michael

middle: V

last: Gormally

first: Thomas

last: Dexheimer

first: Deborah

last: Sanders

first: Christopher

last: Lowe

first: Dijana

last: Matak-Vinković

first: Ajit

last: Jadhav

first: Ganesha

last: Rai

first: David

last: Maloney

first: Anton

last: Simeonov

first: Shankar

last: Balasubramanian


title: Analysis of the RNA-Seq data of castration resistant prostate cancer (CRPCa)

status: Public on Aug 16 2014

first: hao

last: zhao

address: 1 Baylor Plaza

institute: BAYLOR COLLEGE OF MEDICINE

summary: Prostate cancer is the second leading cancer that causes the death of American men. In this study, we  perform an integrative analysis of the whole-transcriptome of metastatic prostate cancer clinical samples. Specifically, we prepare our samples using an innovative protocol NuGEN, which captures the profile of the total RNA, rather than only the mRNA as the popular polyA selection protocol does. Unexpectedly high intronic expressions are observed including the gene AR (Androgen Receptor) and KLK3/PSA, a marker of prostate cancer. Further, certain amount of reads can be found to be across the intron-exon boundaries, suggesting that they come from unspliced pre-mRNAs.  Interestingly, we also observe high splicing on a non-coding RNA MALAT-1. We believe that the aberrant splicing patterns are associated with prostate cancer development.

overall_design: Analysis of 8 clinical samples of metastatic prostate cancer patients

first: Adam

last: Sowalsky

first: Hao

last: Zhao

first: Wei

last: Li

first: Steven

last: Balk


title: The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome

city: Castanet Tolosan

first: Erika

last: Sallet

address: 24 Chemin de Borde Rouge, CS 52627

department: Plant Health and the Environment

institute: INRA/CNRS

summary: Plants show a remarkable plasticity to adapt their root architecture to biotic and abiotic constraints of the soil  environment. Although some of these modifications are fine-tuned by miRNAs, there are still shadow zones in these regulations. In the model legume Medicago truncatula, we analyzed the small RNA (smRNA) transcriptome of roots submitted to symbiotic and pathogenic interactions. Mapping on the genome and prediction of pre-miRNA hairpins allowed the identification of 416 candidates. Out of them, we found known and novel variants of 77 miRNA families, already reported in miRBase. In addition, thanks stringent criteria of miRNA prediction, 53 mtr-miRNAs were discovered, including 27 putative miRtrons. Exploring polymorphism in 26 M. truncatula ecotypes, higher polymorphism was observed in conserved rather than legume-specific miRNA genes. An average of 19 targets, mainly involved in environmental responses and signaling, was predicted per novel miRNA. In addition, taking advantage of our large number of smRNA libraries, we identified sets of miRNAs responsive to root pathogens or to symbiotic interactions and the related Nod and myc-LCO signals.

overall_design: 23 libraries of small RNA (smRNA)  of roots submitted to symbiotic and pathogenic interactions.

first: Damien

last: Formey

first: Christine

last: Lelandais-Brière

first: Cécile

last: Ben

first: Laurent

last: Gentzbittel

first: Pilar

last: Bustos-Sanmamed

first: Christophe

last: Roux

first: Andreas

last: Niebel

first: Florian

last: Frugier

first: Jean

last: Combier

first: Caroline

last: Hartmann

first: Patrick

last: Wincker

first: Jérôme

last: Gouzy

first: Martin

last: Crespi


title: A post-translational regulatory switch on UPF1 controls targeted mRNA degradation.

city: Bridgewater

first: Wencheng

state: NJ - New Jersey

institute: PTC Therapeutics

summary: Nonsense-mediated mRNA decay (NMD) controls the quality of eukaryotic gene expression and also degrades physiologic mRNAs. How NMD targets are identified is incompletely understood. A central NMD factor is the ATP-dependent RNA helicase UPF1. Neither the distance in space between the termination codon and the poly(A) tail nor the binding of steady-state, largely hypophosphorylated UPF1 is a discriminating marker of cellular NMD targets, unlike for PTC-containing reporter mRNAs when compared to their PTC-free counterparts. Here, we map phosphorylated UPF1 (p-UPF1) binding sites using transcriptome-wide footprinting or DNA oligonucleotide-directed mRNA cleavage to report that p-UPF1 provides the first reliable cellular NMD-target marker. p-UPF1 is enriched on NMD target 3'UTRs along with SMG5 and SMG7 but not SMG1 or SMG6. Immunoprecipitations of UPF1 variants deficient in various aspects of the NMD process in parallel with FRET experiments reveal that ATPase/helicase-deficient UPF1 manifests high levels of RNA binding and disregulated hyperphosphorylation, whereas wild-type UPF1 releases from nonspecific RNA interactions in an ATP hydrolysis-dependent mechanism until an NMD target is identified. 3'UTR-associated UPF1 undergoes regulated phosphorylation on NMD targets, providing a binding platform for mRNA degradative activities. p-UPF1 binding to NMD target 3'UTRs is stabilized by SMG5 and SMG7. Our results help to explain why steady-state UPF1 binding is not a marker for cellular NMD substrates and how this binding is transformed to induce mRNA decay.

overall_design: RIP-seq experiments for p-UPF1, control IPs using rabbit IgG and additional control sample without IP were performed in duplicates

first: Tatsuaki

last: Kurosaki

first: Mainul

last: Hoque

first: Maximilian

last: Popp

first: Dmitri

last: Ermolenko

first: Bin

last: Tian

first: Lynne

last: Maquat