title: SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: Severe acute respiratory syndrome coronavirus (SARS-CoV) causes lethal disease in humans, which is characterized by exacerbated inflammatory response and extensive lung pathology. To address the relevance of small non-coding RNAs in SARS-CoV pathology, we deep sequenced RNAs from the lungs of infected mice and discovered three 18–22 nt small viral RNAs (svRNAs). The three svRNAs were derived from the nsp3 (svRNA-nsp3.1 and -nsp3.2) and N (svRNA-N) genomic regions of SARS-CoV. Biogenesis of CoV svRNAs was RNase III, cell type, and host species independent, but it was dependent on the extent of viral replication. Antagomir-mediated inhibition of svRNA-N significantly reduced in vivo lung pathology and pro-inflammatory cytokine expression. Taken together, these data indicate that svRNAs contribute to SARS-CoV pathogenesis and highlight the potential of svRNA-N antagomirs as antivirals.

overall_design: Strand-specific, single-end, reads were generated for detecting smallRNAs (18 nts or more) in lung (mouse). Three or four replicates were prepared per sample type.

first: Lucía

last: Morales

middle: C

first: Raúl

last: Fernández-Delgado

first: Benjamin

last: tenOever

first: Luis

last: Enjuanes

first: Isabel

last: Sola


title: Analysis of transcriptional and epigentic changes induced by loss of Phf8 [RNA-seq]

status: Public on Feb 14 2017

city: Boston

first: Ryan

last: Walsh

state: Massachusetts

address: 185 Cambridge St. CPZN 4100

country: USA

institute: Harvard

type: Expression profiling by high throughput sequencing

summary: Phf8 is a histone demethylase with links to human behavior. Here we have performed a transcriptional analysis of Phf8 knockout embryonic stem and neural projenitor cells in vitro along with an analysis of the prefrontal cortex and ventral striatum in vivo. Our results suggest that knockout of Phf8 is largely compensated for. However, we did observe a misregulation of serotonin receptors in the prefrontal cortex, which may have disease implications.

overall_design: mRNA was generated from WT and KO ESCs and NPCs in culture or from prefrontal corteces and ventral striata dissected from adult WT or KO mice.

first: Konrad

last: Hochedlinger

middle: M


title: Analysis of gene expression in the  "clock rescue" and rpaA- "clock rescue" strains of Synechococcus elongatus PCC7942 with RNA sequencing in light/dark conditions

status: Public on Feb 15 2017

city: Cambridge

first: Anna

last: Puszynska

state: MA

address: 455 Main street

institute: Whitehead Institute for Biomedical Research

summary: The transcription factor RpaA is the master regulator of circadian transcription in cyanobacteria, driving genome-wide oscillations in mRNA abundance. Deletion of rpaA has no effect on viability in constant light conditions, but renders cells inviable in cycling conditions when light and dark periods alternate.  We investigated the mechanisms underlying this viability defect. We performed RNA-seq experiment using the rpaA- “clock rescue” and “clock rescue” strains and we show that the rpaA- “clock rescue” strain is defective in transcription of genes crucial for utilization of carbohydrate stores at night.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Enriched mRNA was prepared from synchronized rpaA- “clock rescue” and “clock rescue” S. elongatus cells at twelve indicated time points using the Illumina TruSeq Stranded mRNA Sample Prep Kit and Illumina HiSeq technology. Gene expression in the rpaA- “clock rescue” strain was compared at each time point to the control “clock rescue” strain.

first: Erin

middle: K

last: O'Shea


title: Analysis of histone methylation in the neocortex of Phf8 KO mice, and transcriptional/epigentic changes induced by loss of Phf8

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The conserved protein Seb1 from fission yeast is recruited to the chromatin during active Pol II transcription

city: Oxford

first: Beth

last: Watts

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

summary: The protein Seb1 from fission yeast contains a conserved CTD-interacting domain (CID) with which it can bind to phosphorylated forms of the Pol II C-terminal domain (CTD) during active transcription. It mainly interacts with Ser2P-CTD but also with Ser5P-CTD. Here, we show the recruitment profile of the protein to chromatin using ChIP-Seq which is mediated mainly via binding to the Pol II-CTD. In addition, it can also interact with nascent RNA via its RNA recognition motif (RRM) domain.

overall_design: Two inputs and two immunoprecipitated Seb1-TAP samples were used to perform ChIP-seq. An untagged control (called WT) is also provided.

first: B

middle: R

first: S

last: Wittmann

first: L

last: Vasiljeva


title: Gene expression profiling of histone deacetylase inhibition in triple-negative breast cancer

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

summary: Analysis of changes in gene expression levels after after prolonged exposure of triple-negative breast cancer cell lines to low doses of Panobinostat (LBH589), a pan-histone deacetylase inhibitor.

overall_design: RNA-sequencing was performed after 96 hours and 4 weeks of incubation 10 nmol/L of LBH589 of two triple-negative breast cancer cell lines (HCC1806 and MDA-MB-231). All the expreiments were performed in biological triplicates

first: Diego

last: Marzese

first: Matthew

middle: P

last: Salomon

middle: S

first: Matias

middle: A

last: Bustos


title: Applied topology delineates developmental progression with single-cell resolution

city: Philadelphia

first: Pablo

middle: G

last: Camara

state: PA

address: 3700 Hamilton Walk

institute: University of Pennsylvania

summary: Cellular lineage commitment and terminal cellular differentiation result from the induction of dynamically regulated transcriptional programs. We report an unbiased approach to studying this process that combines temporal single cell RNA-sequencing and topology-based computational analyses (single cell Topological Data Analysis (scTDA)). scTDA is a non-linear, model-independent, statistical framework particularly tailored to capture high-dimensional continuous relationships, allowing for unsupervised characterization of transient cellular states. We analyzed single-cell RNA-seq data from murine embryonic stem cells (mESCs) as they differentiate in vitro in response to inducers of motor neuron differentiation. scTDA resolved asynchrony and continuity in cellular identity over time, and identified four transient states (pluripotent, precursor, progenitor, and fully differentiated cells) based on dynamic changes in stage-dependent combinations of transcription factors, RNA-binding proteins and long non-coding RNAs. scTDA is applicable to a broad range of problems that involve asynchronous or stochastic cellular responses to developmental cues or environmental perturbations.

overall_design: Single cell RNA sequencing of 2,744 individual cells, spanning 2 biological (non-technical) replicates. Cells were sampled daily across days 2 through 6 of the in vitro differentiation of mESCs into motor neurons.

first: Abbas

middle: H

last: Rizvi

first: Elena

last: Kandror

first: Thomas

middle: J

last: Roberts

first: Ira

last: Schieren

first: Tom

last: Maniatis

first: Raul

last: Rabadan


title: A novel target of CD274 involvement in AML development

city: Shanghai

first: Xianghua

last: Yi

address: NO.389, Xincun Rd, Putuo distrct

department: pathology

country: China

institute: Tongji hospital

summary: We report abonormally expressed genes of MLL-AF9 induced CD274-/- AML mice by RNA-seq analysis. Cyclin D2 was found down-regulated in CD274 depleted AML LSCs, suggesting it might be a novel target gene of CD274 involvement in AML advancement.

overall_design: Examination of differentially expressed genes in AML LSCs of wild type and CD274 knockout mice. Verification the function of selected gene in pathogenesis of AML involvement CD274 dysfunction.

first: Junke

last: Zheng

first: Aibin

last: Liang


title: Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression [RNA-Seq]

city: Wuhan

first: Yang

last: Zhou

state: Hubei

address: Shizishanjie #1

department: College of animal science

institute: Huazhong Agricultural University

summary: As a key epigenetic modification, DNA methylation is essential for normal development by regulating processes like gene expression, genomic imprinting, and suppression of repetitive elements. However, DNA methylation in the cattle genome is not well understood. Here we presented the first single-base-resolution maps of DNA methylation in 10 diversely somatic tissues harvested from the sequenced Hereford cow L1 Dominette 01449 and her relatives using reduced representation bisulphite sequencing (RRBS). In total, we observed 1,868,049 high accuracy cytosines that located in the CG enriched regions. Similar to the methylation patterning in other species, the CG context was predominant methylated. Widespread differences were identified between the methylation patterns of CG and non-CG contexts. They were distributed differentially among the genomic features, including the genic regions, CpG islands, and repetitive sequences. Autocorrelation analysis among adjacent residues illustrated that methylation level of CGs were highly correlated in a region. In contrast, weak or no correlation was found among non-CGs or between CGs and non-CGs. The distinct distribution and low correlation of CG and non-CG methylation suggested that non-CG methylation may be independent from CG methylation and may be mediated by different mechanisms. We also detected 798 tissue-specific differentially methylated cytosines (tDMC) and 131 tissue-specific differentially methylated CpG islands. Combined analysis with the RNA-seq data, we discovered several non-CGs in tDMCs also highly correlated with gene expression, which implied the potential function of non-CG methylation in somatic cells in addition to pluripotent cells. In summary, we showed that non-CGs exist in bovine tissues and some of them were correlated with tissue-specific functions. This study provided essential information for the cytosine methylation patterning in bovine somatic tissues.

overall_design: We applied RNA_seq for 8 different tissues to detect the effects of methylation on gene expression.

first: Tad

last: Sonstegard

first: Leeson

last: Alexander

first: Steven

last: Schroeder

first: George

middle: E

last: Liu


title: Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression

type: Methylation profiling by high throughput sequencing


title: Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Merino and Small Tail Han sheep

city: Changchun

first: Limin

last: Sun

state: Jilin

address: Xincheng Street 2888,Jingyue Distric

institute: Jilin Agricultural University

summary: We aimed to evaluate the transcriptome regulators associated with muscle growth and development between the Qianhua Mutton Merino (QHMM) and  Small Tail Han (STH) sheep.We used RNA-Seq to obtain the transcriptome profiles of the longissimus muscle from the QHMM and STH.The genome-wide transcriptome analysis of QHMM and STH muscle in present study is reported first time.

overall_design: Muscle mRNA profiles of Qianhua Mutton Merino (QHMM) and  Small Tail Han (STH) sheep were generated by deep sequencing, three replicates in each sheep breed, using ABI Ion Proton instrument .

first: Huaizhi

last: Jiang


title: Identification and Comparative Analysis of Drought Responsive microRNA Targets in Mulberry (Morus alba L.) by Degradome Sequencing

city: zhenjiang

first: li

middle: rui

last: xue

state: jiangsu

address: sibaidu

department: School of Biology and Technology

institute: Jiangsu University of Science and Technology

summary: MicroRNAs (miRNAs) are endogenous non-coding small RNAs containing 21-24 nucleotides, and play an important function in the course of stand up to adversity. Identification of miRNA target mRNAs is essential for their functional analysis. In order to anatomize miRNA guided gene regulation under drought stress, we performed a transcriptome-wide experimental method using high throughput degradome sequencing to directly detect drought stress responsive miRNA targets in mulberry. In this study, drought library (DL) and contrast library (CL) which captured the cleaved mRNA were constructed from mulberry for sequencing by Illumina sequencer, and 409, 373 target genes for 30 conserved miRNA families and 990, 950 target genes for 199, 195 novel miRNAs were identified in CL and DL, respectively. Among those conserved miRNA families in DL, mno-miR156, mno-miR172 and mno-miR396 refer to the highest number of targets, indicating that mno-miR156, mno-miR172 and mno-miR396 families and their target genes might play a key important function in corresponding to drought stress in mulberry. By construction and analysis of miRNA-target network, we found that the DL independent networks consist of 838 miRNA-mRNA pairs (63.34%). Besides, the expression patterns of 11 target genes and 12 correspondent miRNAs were compared and analyzed by qRT-PCR. In addition, 5 of 6 miRNA targets were further verified by RNA ligase-mediated 5’ rapid amplification of cDNA ends (RLM-5’ RACE). Gene ontology (GO) annotations and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis showed that these target transcripts were implicated in a broad range of biological processes and various metabolic pathways. The characterization of target genes and the associated miRNAs in response to drought exposure provides a framework for understanding the molecular mechanism of resistance to drought in plants.

overall_design: Identification of miRNA targets in mulberry leaves. There are two RNA samples, one comes from untreated control mulberry, and the other comes from mulberry treated with drought stress for 15 d.

first: Ruixue

last: Li

first: Weiguo

last: Zhao


title: Sequential loss of plasticity during trophectoderm and inner cell mass lineage segregation in the mouse embryo

city: Stockholm

first: Sophie

last: Petropoulos

address: liniskt Forskningscentrum  Novum

country: Sweden

institute: Karolinska Institutet

summary: We report the whole transcriptome data of single-cells derived from the early 16-cell stage to the 64-cell stage in the mouse embryo.

overall_design: RNA from 262 cells from 36 mouse embryos (16- to 64-cell stage)

first: Eszter

last: Posfai

first: Flavia

last: Barros

first: John

last: Schell

first: Rickard

last: Sandberg

first: Fredrik

last: Lanner

first: Janet

last: Rossant


title: Streptomyces exploration is triggered by fungal interactions and volatile signals

city: Hamilton

first: stephanie

middle: erin

last: jones

state: ON

address: 1280 Main St W

department: Biology

country: Canada

institute: McMaster University

summary: We discovered the bacteria Streptomyces venezuelae can display a new form of growth termed exploration, and we used NGS to compare transcriptome profiles of cells demonstrating exploration versus static cells (not demonstrating exploration)

overall_design: RNA profiles of 14-day old S. venezuelae explorer cells and 1-day old S. venezuelae static cells were generated by deep sequencing in duplicate using Illumina HiSeq

first: Stephanie

last: Jones

first: Marie

last: Elliot


title: Gene expression profiling of dsDNA-transfected reconstituted mouse embryonic fibroblasts

city: Miami

first: Glen

last: Barber

state: FL

address: 1550 NW 10th Ave, Room 511

department: Cell Biology

institute: University of Miami

summary: Analysis of dsDNA-induced innate immune response at gene expression level. The hypothesis tested in this study was that K224R mutation significantly inhibits hSTING activity. Results provide important information of the response of hSTING and its variants to cytosolic dsDNA, such as induction of type I IFN genes and proinflammatory cytokine genes.

overall_design: Sting-/- MEFs were reconstituted with wild type hSTING, hSTING-K224R or hSTING-K289R. Total RNA obtained from dsDNA-transfected MEFs was compared to mock-transfected MEFs.

first: Guoxin

last: Ni

first: Loida

last: Navarro

first: Anthony

last: Griswold


title: MicroRNAs Expression in the Ileal Pouch of Patients with Ulcerative Colitis is Robustly Up-Regulated and Correlates with Disease phenotypes

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

type: Non-coding RNA profiling by high throughput sequencing

summary: Gene expression alterations are associated with disease behavior in inflammatory bowel disease (IBD). microRNAs (miRNAs) are dominant in the regulation of gene expression, and may affect IBD phenotype. Our aim was to assess mucosal miRNA expression in IBD and the correlation with intestinal inflammation. Sixty-one subjects were recruited. The ileum of unoperated UC patients was comparable with NC. There were significant miRNA expression alterations (fold change ≥2, corrected P ≤.05) in NP (n = 6), CP (n = 40) and CLDP (n = 139), but only two expression alterations were noted in CD. More than 90% of the altered miRNAs were up-regulated, and many were predicted to be associated with significantly decreased transcripts. miRNAs alterations were generally clustered with disease phenotypes. Ileal inflammation causes increased miRNA expression. miRNA alterations correlate with IBD phenotype, apparently by controlling the down-regulation of specific mRNAs.

overall_design:
Pouchitis is a model for ileal  Inflammatory Bowel Disease (IBD) and may enable the detection of miRNAs associated with intestinal inflammation.
Control/disease samples: Crohn's-like disease of the pouch (CLDP), chronic pouchitis (CP-P), Ileal Crohn's disease (IlealCD), normal control (NC), normal pouch (NP-P), ulcerative colitis (UC).

first: Shay

last: Ben-Shachar

first: Henit

last: Yanai

first: Hadas

last: Sherman Horev

first: Hofit

last: Elad

first: Liran

last: Baram

first: Ofer

last: Issakov

first: Hagit

last: Tulchinsky

first: Noam

last: Shomron

first: Iris

last: Dotan


title: Transcriptome profiling of drought responsive noncoding RNAs and their target genes in rice

city: Pyeongchang

first: Pil Joong

last: Chung

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

country: South Korea

institute: Seoul National University

summary: RNA-seq analyses of leaves from drought stressed rice plants was performed, producing differential expression profiles of genes containing coding RNAsand noncoding RNAs.

overall_design: Water-deficit stressed leaves mRNA profiles of 5-week old wild type rice were generated by deep sequencing using Illumina Hiseq 2500.

first: Pil

first: Ju-Kon

last: Kim


title: A Novel RNA Sequencing Data Analysis Method for Cell Line Authentication

first: Erik

last: Fasterius

address: AlbaNova University Center

department: Proteomics and nanotechnology

institute: KTH Royal Institute of Technology

summary: We have developed a novel analysis method that can interrogate the authenticity of biological samples used for generation of transcriptome profiles in public data repositories. The method uses RNA sequencing information to reveal mutations in expressed transcripts and subsequently confirms the identity of analysed cells by comparison with publicly available cell-specific mutational profiles. Cell lines constitute key model systems widely used within cancer research, but their identity needs to be confirmed in order to minimise the influence of cell contaminations and genetic drift on the analysis. Using both public and novel data, we demonstrate the use of RNA-sequencing data analysis for cell line authentication by examining the validity of COLO205, DLD1, HCT15, HCT116, HKE3, HT29 and RKO colorectal cancer cell lines. We successfully authenticate the studied cell lines and validate previous reports indicating that DLD1 and HCT15 are synonymous. We also show that the analysed HKE3 cells harbour an unexpected KRAS-G13D mutation and confirm that this cell line is a genuine KRAS dosage mutant, rather than a true isogenic derivative of HCT116 expressing only the wild type KRAS. This authentication method could be used to revisit the numerous cell line based RNA sequencing experiments available in public data repositories, analyse new experiments where whole genome sequencing is not available, as well as facilitate comparisons of data from different experiments, platforms and laboratories.

overall_design: RNA-sequencing of three colorectal cancer cell lines (HCT116, HKE3 and RKO) with either three (HCT116, RKO) or four (HKE3) replicates each.

first: Cristina

last: Al-Khalili Szigyarto

first: Mathias

last: Uhlén


title: Changes in relative transcript amounts caused by ∆phoU2::kanrpsL+ and double ∆phoU2::kanrpsL+ ∆phoU1::Pcerm mutations in Streptococcus pneumoniae

city: Bloomington

first: Malcolm

last: Winkler

state: IN

address: 1001 E. Third Street

institute: Indiana University

summary: Unlike most bacteria, Streptococcus pneumoniae (pneumococcus) has two evolutionarily distinct ABC transporters (Pst1 and Pst2) for inorganic phosphate (Pi) uptake. The genes encoding a two-component regulator (PnpRS) are located immediately upstream of the pst1 operon. Both the pst1 and pst2 operons encode putative PhoU regulators (PhoU1 and PhoU2) at their ends.his study addresses why S. pneumoniae contains dual Pi uptake systems and the regulation and contribution of the Pst1 and Pst2 systems in conditions of high (mM) Pi amount and low (μM) Pi amount. To determine whether PhoU1 or PhoU2 regulates pnpRS, pst1, or pst2 operons. we performed RNA-Seq analyses of ΔphoU2::kanrpsL+ sinlge mutant and ΔphoU2::kanrpsL+ ΔphoU1::Pcerm double mutant compared to the isogenic encapsulated strain cep::kanrpsL+. Unexpectedly, only ΔphoU2::kanrpsL+ indulces the pst1 operon, but not pst2 or pnpRS operon. Addtional PhoU1 deletion has no effect on pst1, pst2, or pnpRS operons.

overall_design: RNA was prepared from cultures of strains IU3116 (cep::kanrpsL+), IU6139 (∆phoU2::kanrpsL+), and IU6173 (∆phoU2::kanrpsL+ ∆phoU1::Pcerm) grown exponentially in BHI media at 37ºC to OD620 ≈0.15 to 0.2. Three independent biological replicates of RNA were prepared for each strain or condition. cDNA libraries were sequenced and the sequencing results were used as the data base for differential expression analysis.

first: Jiaqi

last: Zheng

first: Dhriti

last: Sinha

first: Kurt

last: Zimmer

first: Douglas

middle: B

last: Rusch


title: Analysis of histone methylation in the neocortex of Phf8 KO mice [ChIP-seq]

first: Ryan

last: Walsh

summary: Phf8 is a histone demethylase with links to human behavior. To gain insight into Phf8's function in the brain, we have performed ChIP-seq for the histone methylation marks H3K4me3, H3K4me1, H3K27me2 and H3K9me2.

overall_design: ChIP-seq was performed on neuronal chormatin isolated from the neocortex of WT and KO mice.

first: Konrad

last: Hochedlinger


title: A Method for High-throughput Production of Sequence-verified DNA Libraries and Strain Collections

city: Palo Alto

first: Robert

middle: Peter

address: 3165 Porter Drive

institute: Stanford University

summary: The low costs of array-synthesized oligonucleotide libraries are empowering rapid advances in quantitative and synthetic biology. Unfortunately, high synthesis error rates, uneven representation, and lack of access to individual oligonucleotides limit the true potential of these libraries. We have developed a cost-effective method called Recombinase Directed Indexing (REDI) to address these problems. The method involves integration of a complex library into yeast, site-specific recombination to index (i.e. barcode) library DNA, and then next-generation sequencing to identify clones containing the DNA of interest. We used REDI to generate a molecular probe library (n = ~3,300) that exhibited >96% purity and remarkable uniformity (>95% of probes were within 2-fold relative abundance of the median). Moreover, each sequence-verified probe was readily accessible. We also used REDI to rapidly create an arrayed collection of ~9,000 strains for CRISPR interference in yeast and demonstrate the utility of this collection for highly sensitive phenotypic screening. Our approach will enable a variety of applications requiring accurate, high-quality DNA libraries.

overall_design: 102 samples, some of which are replicates.

first: Justin

middle: D

last: Smith

first: Ulrich

last: Schlecht

first: Weihong

last: Xu

first: Sundari

last: Suresh

first: Joe

last: Horecka

first: Michael

last: Proctor

first: Raeka

last: Aiyar

first: Richard

last: Bennett

first: Angela

last: Chu

first: Yong

last: Li

first: Kevin

last: Roy

first: Ronald

middle: W

last: Davis

first: Lars

last: Steinmetz

last: Hyman

first: Sasha

middle: F

last: Levy

last: StOnge


title: Identification and characterization of sex-biased microRNAs in Bactrocera dorsalis (Hendel)

first: Wei

last: Peng

address: Shizishan Street No. 1, Hongshan District, Wuhan,Hubei  430070, P.R. China

summary: We constructed four small RNA libraries from whole body of females, males (except ovaries and testes) and ovaries, testes of B. dorsalis for deep sequencing. The data analysis revealed 314 known and 221 novel miRNAs from these libraries. 14 female-biased and 12 male-biased miRNAs that may be involved in sexual differentiation were found by comparing the miRNA expression profiles in the four libraries.

overall_design: Small RNA profiles from whole body of females, males (except ovaries and testes) and ovaries, testes of 12-day old adult Bactrocera dorsalis were generated by Illumina deep sequencing.

first: Hongyu

last: Zhang


city: Pretoria

first: Daniel

last: Bellieny-Rabelo

state: Gauteng

address: Lynnwood Rd, Hatfield, Pretoria

department: Department of Biochemistry, Genetics and Microbiology

country: South Africa

institute: University of Pretoria

summary:
Purpose: This RNA-Seq study aims on elucidate the major trends in the transcriptional profile of soybean embryonic axes during germination.
Methods: Soybean seeds were germinated in soaked cotton at 28ºC. In addition to dry seeds, seeds were harvested at 3, 6, 12, 24 hours after imbibition. Then the embryonic axes were separated from the cotyledons for RNA extraction. For each biological sample, 20 seeds were used.
Results:  Identification of genes and pathways involved in metabolism, hormone signaling and transcriptional regulation.

overall_design: Large-scale analysis of soybean embryonic axis in five time points during germination: dry, 3, 6, 12 and 24 hours after imbibition.

first: Thiago

middle: M

last: Venancio


title: Plasma cell mutation analysis

city: Atlanta

first: Caitlin

middle: Darcy

last: Bohannon

state: GA

address: 210 Dowman Drive

department: Immunology

institute: Emory University

summary: Here we use 454 sequencing to determine the number and location of mutations in IgM plasma cells.

overall_design: Heavy chain sequences from NP-specific plasma cells were analyzed for mutation.

first: Joshy

last: Jacob


title: Quantitative Analysis of ZF4 cells Transcriptomes when Infected with Edwardsiella tarda

city: Qingdao

first: Zejun

last: Zhou

address: 7 Nanhai Road

institute: Institute of Oceanology, Chinese Academy of Sciences

summary: Edwardsiella tarda is a Gram-negative bacterial pathogen that can infect a wide range of freshwater and marine fish. However, the immune evasion mechanisms of Edwardsiella tarda is not fully understood. We found that Edwardsiella tarda infection generally significantly upregulated and downregulated a lot of immune-related genes of zebrafish ZF4 cells using RNA-seq technology.

overall_design: Examination of  the different expressed genes of ZF4 cells in response to the Edwardsiella tarda infection.


title: RNA-seq analysis reveals profound changes in transcript profiles between siCon- and siH19-transfected EVT cells

city: Farmington

first: Tingting

last: Geng

state: CT

address: 263 Farmington Avenue

department: Department of Immunology

institute: Uconn Health

summary: We used high throughput sequencing to analyze the transcriptional profiling of EVT. By comparing the transcriptional profiling of EVT with or without H19 knockdown, numerous genes showed significantly altered expression as a result of H19 repression.

overall_design: HTR cells were transfected with either control siRNA or siH19. 48h later after transfection, total RNA was extracted for library preparation and RNA-seq analysis to compare trancript profiles between siCon and siH19 cells.

first: Yingqun

last: Huang


title: Genome-wide analysis of tumor suppressive programs during p53-induced regression of Myc-driven lymphomas [DNaseI-seq]

city: Milan

first: Marco

middle: J.

last: Morelli

address: via Adamello 16

department: Center for Genomic Science of IIT@SEMM

country: Italy

institute: Istituto Italiano di Tecnologia

summary: The tumor suppressor p53 is a transcription factor that controls the response to stress. Here, we dissected the transcriptional programs triggered upon restoration of p53 in Myc-driven lymphomas, based on the integrated analysis of p53 genomic occupancy and gene regulation. p53 binding sites were identified at promoters and enhancers, both characterized by the pre-existence of active chromatin marks. p53 recruitment at these sites was mainly mediated through protein-protein or protein-chromatin interactions and, only for a small fraction, through recognition of the 20 base-pair p53 consensus motif. At promoters, p53 binding to the consensus motif was associated with gene induction, but not repression, indicating that the latter was most likely indirect. p53 also targeted unmarked distal sites devoid of activation marks, at which binding was prevalently driven by recognition of the consensus motif. At all sites, our data highlighted a functional role for the canonical, unsplit consensus element, but did not provide evidence for p53 recruitment by split motifs. Altogether, our data highlight key features of genome recognition by p53 and provide unprecedented insight into the pathways associated with p53 re-activation and tumor regression.

overall_design: Mapping accessible chromatin regions in lymphoma T6


title: Genome-wide analysis of tumor suppressive programs during p53-induced regression of Myc-driven lymphomas [RNA-Seq]

overall_design: Total RNA profiling of gene expression in Eµ-myc lymphomas following p53 restoration by Illumina sequencing


title: Genome-wide analysis of tumor suppressive programs during p53-induced regression of Myc-driven lymphomas [ChIP-Seq]

overall_design: Mapping p53 binding sites in Eµ-myc lymphomas following p53 restoration.


title: Genome-wide analysis of tumor suppressive programs during p53-induced regression of Myc-driven lymphomas

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

overall_design: Refer to individual Series


title: Transcriptome analysis of Synechococcus elongatus PCC 7942 for nitrogen starvation response using RNA sequencing

city: Seoul

first: Han

middle: Min

last: Woo

address: Hwarangno 14-gil 5, Seongbuk-gu

department: Clean Energy Research Center

institute: Korea Institute of Science and Technology

summary: We reported transcriptome analysis of S. elongatus PCC 7942 for nitrogen starvation response by performing RNA-sequencing. As a result, we identified differentially express genes and confirmed physiological response changes for up or down regulation genes. among differentially expressed genes (p value < 0.01) during N starvation

platform_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: RNA-Seq analysis of S. elongatus PCC 7942 for nitrogen starvation response

first: Sun

middle: Y

last: Choi

first: Byeonghyeok

last: Park

first: In-Geol


title: The dose-dependent role of PU.1 in Myeloid differentiation

city: LONDON

first: Rodney

last: DeKoter

state: Ontario

address: 1151 Richmond street

department: Microbiology and Immunology

institute: University of Western Ontario


title: The dose-dependent role of PU.1 in Myeloid differentiation [ChIP-Seq]

summary: A doxycycline-inducible system was used to induce PU.1 expression in cultured myeloid cell lines. The parent cell line used was BN (Kamath et al., Leukemia 22:1214-1225, 2008).

overall_design: ChIP-seq using an anti-PU.1 antibody was prepared from uninduced cells (2) and cells induced with 1000 ng/ml doxycycline for 72 hours (2)

first: Lauren

last: Solomon


title: Transcriptional profiles of drought-related genes in modulating metabolic processes in Lolium multiflorum

city: Chengdu

first: Xinquan

state: Sichuan

address: NO. 211 Huimin Road   Wenjiang District

department: Department of Grassland Science

institute: Sichuan Agricultural University

summary: Drought is a major environmental stress that limits growth and development of cool-season annual grasses. Drought transcriptional profiles of resistant and susceptible lines were studied to understand the molecular mechanisms of drought tolerance in annual ryegrass (Lolium multiflorum L.). A total of 4,718 genes exhibited significant differential expression in two L. multiflorum lines. Additionally, up-regulated genes associated with drought response in the resistant lines were compared with susceptible lines. Gene ontology enrichment and pathway analyses revealed that genes partially encoding drought-responsive proteins as key regulators were significantly involved in carbon metabolism, lipid metabolism, and signal transduction. Comparable gene expression was used to identify the genes that contribute to the high drought tolerance in resistant lines of L. multiflorum.

overall_design:
A total of 12 samples are analyzed.And ten individual plants were pooled to create one treatment, and two biological replicates were used for all RNA-Seq experiments from each treatment.
Please note that Unigenes of all samples are provided in fasta format (series supplementary file)

first: Ling

last: Pan


title: Transcriptome profiling of Drosophila Wild Type and Sox21a-/- intestinal progenitor cells

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling (RNA-seq) of intestinal progenitor cells in Drosophila wild type and Sox21a mutant midgut.
Methods: mRNA profiles of intestinal progenitor cells isolated from 7-day-old wild-type (WT) and Sox21a knockout (Sox21a−/−) Drosophila midgut were generated by deep sequencing using Illumina HiSeq 4000.
Results: Each sequencing experiment generated an average 11.18 million raw reads, and 86% was successfully mapped for each experiment. 7608 transcripts were identified in the progenitor cells of WT and Sox21a−/− Drosophila midgut with TopHat workflow. 389 genes of the transcripts showed differential expression between the WT and Sox21a−/− progenitor cells, with a fold change ≥2.0 and p value <0.05.  Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to intestinal function.

overall_design: mRNA profiles of intestinal progenitor cells isolated from 10-day-old wild-type (WT) and Sox21a knockout (Sox21a−/−) Drosophila adult midgut were generated by deep sequencing using Illumina HiSeq 4000.

first: Jun

last: Chen

first: Rongwen

last: Xi


title: Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression [RRBS-Seq]

city: Wuhan

first: Yang

address: Shizishanjie #1

institute: Huazhong Agricultural University

summary: As a key epigenetic modification, DNA methylation is essential for normal development by regulating processes like gene expression, genomic imprinting, and suppression of repetitive elements. However, DNA methylation in the cattle genome is not well understood. Here we presented the first single-base-resolution maps of DNA methylation in 10 diversely somatic tissues harvested from the sequenced Hereford cow L1 Dominette 01449 and her relatives using reduced representation bisulphite sequencing (RRBS). In total, we observed 1,868,049 high accuracy cytosines that located in the CG enriched regions. Similar to the methylation patterning in other species, the CG context was predominant methylated. Widespread differences were identified between the methylation patterns of CG and non-CG contexts. They were distributed differentially among the genomic features, including the genic regions, CpG islands, and repetitive sequences. Autocorrelation analysis among adjacent residues illustrated that methylation level of CGs were highly correlated in a region. In contrast, weak or no correlation was found among non-CGs or between CGs and non-CGs. The distinct distribution and low correlation of CG and non-CG methylation suggested that non-CG methylation may be independent from CG methylation and may be mediated by different mechanisms. We also detected 798 tissue-specific differentially methylated cytosines (tDMC) and 131 tissue-specific differentially methylated CpG islands. Combined analysis with the RNA-seq data, we discovered several non-CGs in tDMCs also highly correlated with gene expression, which implied the potential function of non-CG methylation in somatic cells in addition to pluripotent cells. In summary, we showed that non-CGs exist in bovine tissues and some of them were correlated with tissue-specific functions. This study provided essential information for the cytosine methylation patterning in bovine somatic tissues.

overall_design: We applied RRBS analysis (MspI,~40-220bp size fraction) for 10 highly diverse tissues (90 d lactating gland, mammary, nucleated blood cells, skeletal muscle near ceasarian, frontal cortex, uterus intercaruncular, whole testes, abomasum, ileum, rumen) from the Hereford cow L1 Dominette 01449 and her relatives.

first: George

last: Liu


title: A spatio-temporal characterization of the transcriptional landscape of epidermal development

city: New York

first: Amma

last: Asare

state: New York

address: 1230 York Ave

institute: Rockefeller University

summary: The mouse epidermis develops from a single layer of cells at e9.5 to a fully formed organ at birth capable of performing essential functions. The regularity of the epidermal differentiation program creates an excellent system to explore the mechanisms required for this transition from transit amplifying/ stem cell to differentiated cell and to identify key regulators in this biological process. Here we use FACS sorting of transgenic mice to separate the developing epidermis into its differentiating populations. Though many key players in epidermal differentiation have been identified, the challenge of examining the process in vivo has limited discovery of novel associated pathways and proteins. With this profiling we aim to create a map of epidermal development for identificatin of novel regulators of this process.

overall_design: Epidermal keratinocytes were purified from embryonic mouse backskin via FACS sorting at multiple time points during development. RNA was extracted, cDNA libraries created and RNA sequencing was run on the samples.

first: Elaine

last: Fuchs


title: Transcriptome of inner bark in Hevea brasiliensis

city: Danzhou

first: Wu

last: Shaohua

state: Hainan

address: Baodao Xincun

department: Rubber Research Institute

institute: Chinese Academy of Tropical Agricultural Sciences

summary: We report transcriptome data of four kinds of bark samples from the Hevea brasiliensis clone CATAS7-33-97 by use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly. The output of sequenced data showed that a total of 323,842,182 clean reads with average length of 90 nt were generated in four samples. Totally 67,873 uingenes with an average length of 750 nt and a N50 of 1,222 nt were assembled through transcriptome de novo assembly. The all assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. The comparative analysis of the transcriptome data performed with the criteria of FDR ≤ 0.001 and |log2 Ratio| ≥ 1. As a result, 15,780 different expression unigenes (8,646 up and 7,134 down ) were detected in early libraries (Control-A versus COR-A) upon coronatine treatment, and 19,824 different expression unigenes (7,711 up and 12,113 down) were detected in late libraries (Control-B versus COR-B) upon coronatine treatment. Functional analysis of different expression unigenes showed that mass of unigenes were annotated in multiple signaling pathways. Comparative transcriptome analysis of inner bark in response to coronatine reveals a new insight into the signal networks for the secondary laticifer differentiation from vascular cambia in rubber tree.

overall_design: The transcriptome of bark in response to coronatine in Hevea brasiliensis

first: Shaohua

last: Wu

first: Shixin

last: Zhang

first: Weimin

last: Tian


title: Transcriptome analysis of wild-type and VaERF73 overexpressing Arabidopsis

first: Xiaoming

last: Sun

address: Lumo road, No. 1

institute: Wuhan Botanical Garden, Chinese Academy of Sciences

summary: To gain the possible direct or indirect targets of VaERF73, RNA-Seq was carried out on two biological replicates of wild-type and 3 transgenic Arabidopsis lines mixture (OE1, OE2 and OE3) under normal conditions. The fold change analysis showed that 140 significantly differentially expressed genes were expressed > 2-fold in the transgenic as compared with WT plants. Among these changed genes, 89 genes were up-regulated while 51 genes down-regulated.

overall_design: Examination of gene expression changes after overexpression of VaERF73 in Arabidopsis and identification of VaERF73 downstream genes.

last: Li

first: Haiping

last: Xin


title: Effects of NSD2 depletion on gene expression and H3K36me2 in a lung cancer cell line

city: Majadahonda

first: Maria

last: Barrero

state: Madrid

address: Crta. Majadahonda-Pozuelo KM 2.2

institute: ISCIII

summary: The histone methyltransferase NSD2/WHSC1/MMSET is overexpressed in a number of solid tumors but its contribution to the biology of these tumors is not well understood. Here, we describe that NSD2 contributes to the proliferation of a subset of lung cancer cell lines by supporting oncogenic RAS transcriptional responses. Co-treatment with MEK and BRD4 inhibitors causes co-operative inhibitory responses on cell growth. While these inhibitors converge in the downregulation of genes associated with cancer-acquired super-enhancers, NSD2 inhibition complements their action by affecting the expression of clusters of genes embedded in megabase-scale regions marked with H3K36me2. Thus, combinatorial therapies using MEK or BRD4 inhibitors together with NSD2 inhibition ensure a more comprehensive inhibition of oncogenic RAS-driven transcription programs.

overall_design: H1299 cells were transduced with doxycycline (dox) inducible shRNAs (sh3 or sh5) againts NSD2 and with non target shRNA (shNT). Changes in gene expression (RNA-seq) and H3K36me2 (ChIP-seq) caused by depletion of NSD2 and indicated treatments were assessed. Two replicates (Rep) for RNA-seq and three replicates for ChIP-seq were included.

first: Veronica

last: Garcia-Carpizo

first: Osvaldo

last: Graña


title: Interaction between cyclooxygenase-2 and caspase-3 abolishes the cleavage of RNA-binding protein HuR and promotes drug resistance in oral squamous cell carcinoma

city: Charleston

first: Gary

last: Hardiman

state: SOUTH CAROLINA

address: 135 Cannon Street, Suite 303 MSC835

institute: MUSC

summary: Here, we show that HuR cleavage is dependent on active caspase-3 in oral cancer cells treated with ionizing radiation and the chemotherapeutic drug paclitaxel.  We determined that oral cancer cells overexpressing cyclooxygenase-2 (COX-2) limited the cleavage of both caspase-3 and HuR, which in turn, reduced the rate of apoptosis in paclitaxel treated cells. Specific inhibition of COX-2 by celecoxib promoted apoptosis through activation of caspase-3 and cleavage of HuR in paclitaxel-resistant oral cancer cells.  In addition, oral cancer cells overexpressing cellular HuR increased the half-life of COX-2 mRNA and promoted COX-2 expression, exhibiting enhanced tumor growth in vivo in comparison with the cleavable form of HuR.  Finally, our RNP IP and RNA transcriptome analysis of HuR under IR revealed that the HuR cleavage product-1 (HuR-CP1) associates and promotes the expression of mRNAs encoding proteins involved in apoptosis.

overall_design: 4 samples: The GFP plasmid vectors containing full-length HuR, HuR-D226A, HuR-CP1 were expressed in oral cancer cells. GFP empty vector served as a control. HuR RNP IP was performed and RNA sequencing carried out.

first: Viswanathan

last: Palanisamy


title: Transcriptome analysis of eosinophilic and noneosinophilic chronic rhinosinusitis with nasal polyps reveals distinct lncRNA expression profiles

first: Weiqing

last: Wang

address: No.1 Shuai Fu Yuan Street

department: Department of Otolaryngology

institute: Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College

summary:
Background: The pathogenesis of chronic rhinosinusitis with nasal polyps (CRSwNP) remains unclear. Long noncoding RNAs (lncRNAs) play pivotal roles in various biological processes, but their roles in CRSwNP have not been explored. We performed systematic transcriptome analysis of mRNAs and lncRNAs of eosinophilic and noneosinophilic CRSwNP to deepen our understanding of the disease mechanism.
Methods: We analyzed expression profiles of mRNAs and lncRNAs with next-generation high-throughput RNA sequencing in patients with eosinophilic CRSwNP (n=3), noneosinophilic CRSwNP (n=3), and healthy control subjects (n=3). Results were verified by quantitative reverse transcription polymerase chain reaction (qRT-PCR) in an independent cohort of patients. The dysregulated mRNAs and lncRNAs were identified and characterized via bioinformatics analysis.
Results: A total of 1917 novel lncRNA transcripts and 280 known lncRNA transcripts were identified. Sample groups were separated by unsupervised hierarchical clustering on differentially expressed lncRNAs or mRNAs. The qRT-PCR results of five dysregulated lncRNAs were consistent with the RNA-seq data. The dysregulated genes were significantly overrepresented in immune response and extracellular environment related terms in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The predicted functions of dysregulated lncRNAs were highly consistent with those of dysregulated mRNAs.
Conclusion: The cross talk between inflammation and immune response and microenvironment is the key pathogenesis mechanism of CRSwNP. Patients with eosinophilic CRSwNP compared with noneosinophilic CRSwNP has distinct gene expression profiles. This highlights the necessity of designing personalized therapeutic strategies and suggests developing specific molecular biomarkers.

overall_design: Ribosomal RNA (rRNA) removed total RNA sequencing carried out in 3 groups of samples: ECRSwNP, non-ECRSwNP, CTRL.

first: Wei

last: Lv

first: Jianmin

first: Zhiqiang

last: Gao


title: Dramatic Increase in Cell-subset Specific Methylation Accompanies Mammalian Brain Development [hairpin BS-Seq]

city: Bethesda

first: Mingan

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

summary:
Purpose: This study aims to identify cell-subset specific methylated (CSM) loci in mammalian brain methylomes and to uncover epigenetic regulatory networks associated with brain development.
Methods: To generate methylation data from DNA double strands simultaneously, genome-scale hairpin bisulfite sequencing technique was used for the assessment of the levels of asymmetric DNA methylation in the human frontal cortical gray and white matters
Results and conclusion: CSM loci increase dramatically during early stages of brain development. They are overrepresented in cis-regulatory elements such as active enhancers and promoters, and are enriched for GWAS variants associated with neurological-disorder-related diseases/traits. Co-methylated CSM clustering analysis indicated that the CSMs hypo-methylated in neurons are enriched for EGR1 binding sites.Our results show the functional relevance of CSM loci identified and provide insights into epigenetic complexity of mammalian brains.

overall_design: We first explored asymmetric DNA methylation in human fetal and adolescent brain tissues using genome-scale hairpin bisulfite sequencing technique. Based on the finding that brain methylomes are with exceeding high methylation fidelity, we developed an analytical procedure to identify CSM loci and applied it to human and mouse brain methylomes throughout the life span. We further explored the functional relevance of CSM loci via integrative “omics” analysis with ChIP-Seq data for histone modifications, transcription factor (TF) bindings and GWAS disease/trait associated variants.

first: Ming-an

first: Zhixiong

first: Hehuang

last: Xie


title: RNA sequencing of LPS treated mouse bone marrow stromal cells

city: Indianapolis

first: Yunlong

last: Liu

address: 410 West 10th Street, HS 5000

institute: IUPUI

summary:
Background: Lipopolysaccharide (LPS) is a gram-negative bacterial antigen that triggers a series of cellular responses. LPS pre-conditioning was previously shown to improve the therapeutic efficacy of bone marrow stromal cells/bone-marrow derived mesenchymal stem cells (BMSCs) for repairing ischemic, injured tissue.
Results: In this study, we systematically evaluated the effects of LPS treatment on genome-wide splicing pattern changes in mouse BMSCs by comparing transcriptome sequencing data from control vs. LPS-treated samples, revealing 197 exons whose BMSC splicing patterns were altered by LPS. Functional analysis of these alternatively spliced genes demonstrated significant enrichment of phosphoproteins, zinc finger proteins, and proteins undergoing acetylation. Additional bioinformatics analysis strongly suggest that LPS-induced alternatively spliced exons could have major effects on protein functions by disrupting key protein functional domains, protein-protein interactions, and post-translational modifications.
Conclusion: Although it is still to be determined whether such proteome modifications improve BMSC therapeutic efficacy, our comprehensive splicing characterizations provide greater understanding of the intracellular mechanisms that underlie the therapeutic potential of BMSCs.

overall_design: 6 samples (3 untreated wild type samples, 3 LPS treated wild type samples)

first: Yue

first: Hongyu


title: Response to ibrutinib treatment in an Eµ-TCL1 mouse model of  CLL harboring a p53 alteration

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

summary: Deletion of the short arm of chromosome 17 (17p-) is one of the most critical genetic variants used in B-CLL risk stratification. The tumor suppressor TP53 maps to this region, and its loss or mutation significantly accelerates B-CLL progression, hampers response to chemotherapy, and shortens survival. While florescent in situ hybridization (FISH) analyses for 17p deletions are routinely performed during clinical diagnoses, mutational analyses of the TP53 gene is not widely available and thus its mutational status is often unknown in patients with CLL. Given the limited clinical data that exists for frontline treatment of patients with CLL harboring TP53 mutations, there is a great need to identify novel treatment strategies for this subset of patients. Herein, we use a CLL mouse model (Eμ-TCL1) in the presence or absence of a common TP53 hot-spot mutation (p53R172H, corresponding to p53R175H in humans) to study its impact on disease progression, survival, response to therapy, and dynamic loss of the remaining wild-type Trp53 allele during the course of B-CLL following BTK inhibitor (ibrutinib). We show that ibrutinib was effective in increasing survival and activated gene and cellular programs outside of the p53 pathway in both settings, and thus, did not place selective pressure on the remaining wild type Trp53 allele. These data demonstrate the potent effect of BTK-inhibition in B-CLL and more importantly, provide evidence that ibrutinib acts as an effective treatment for aggressive forms of B-CLL with TP53 mutation and potentially chemo-resistant refractory disease.

overall_design: Examination of ibrutinib's impact on malignant B-cells with and without a fully finctional p53 pathway

first: Hun

last: Lee

first: Miguel

last: Gallardo

first: Huaxian

last: Ma

first: Xiaoping

last: Su

first: Sean

last: Post


title: Distinct NSun methylases control cytosine-5 methylation of messenger, mitochondrial and transfer RNA: implications for human diseases [Bisulfite-Seq dermal fibroblasts]

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

summary: Aberrant post-transcriptional methylation is implicated in a wide range of human diseases, yet the specific enzymes responsible for site- and substrate-specific methylation remain largely unknown. Here, we use our recently developed catalysis-dependent RIP sequencing approach (miCLIP) and RNA bisulfite sequencing to map C5-methylcytosine (m5C) in the human transcriptome. We identified two novel m5C methylases NSun3 and NSun6, both of which have strong substrate specificity. In contrast to the previously characterized NSun2, which displays some preference to methylating transfer RNAs (tRNA), NSun6 predominantly targeted 3’ UTRs of messenger RNAs (mRNA), and NSun3 mainly methylated mitochondrial RNAs (mtRNA). Consistent with the miCLIP-predicted RNA target specificity, whole exome sequencing identified NSUN3 loss-of-function mutations in a patient presenting with combined respiratory chain complex deficiency. Functional studies of the patient fibroblast cell line revealed that loss of the NSun3 protein resulted in severe mitochondrial translation defects, which were rescued by expression of wild-type NSun3. In summary, our results reveal how highly conserved NSun m5C methylases partition their substrate specificities to remodel the sequences of particular ribonucleotide classes.

overall_design: Identification of methylation of mitochondrial RNA in human dermal fibroblasts by bisulfite sequencing

first: Lindsey

last: van Haute


title: Expression Profiling of E. coli K-12 BW25113 in Minimal Media with Glucose and Amino Acid Supplementations

city: La Jolla

first: Bernhard

last: Palsson

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

summary: mRNA sequencing was performed on E. coli K-12 MG1655 with Glucose supplemented on Glycine and L-Threonine

overall_design: Growth of E. coli with 2 different amino acid supplementations was analyzed in biological duplicates.

first: Ali

last: Ebrahim

first: Edward

last: O'Brien

first: Donghyuk

last: Kim

first: Joshua

middle: A

last: Lerman

first: Aarash

last: Bordbar

first: Adam

last: Feist


title: Expression Profiling of E. coli K-12 BW25113 in Minimal Media with Different Carbon Sources

summary: mRNA sequencing was performed on E. coli K-12 BW25113 grown on Glucose, Pyruvate, Fumarate, and Acetate.

overall_design: Growth of E. coli on 4 different carbon sources was analyzed in biological duplicates.


title: Bmi1 defines long-term adult cardiac stem cells in heart homeostasis and repair

city: Madrid

first: Antonio

last: Bernad

address: Melchor Fernandez Almagro, 3

institute: Spanish Cardiovascular Research Center

summary: We have found the existence of a Bmi1+ population in the adult heart contributing to the organ low-rate turnover and repair with the generation of new cardiomyocytes. We show that the Bmi1+ population is a sub-population of the cardiac Sca-1+ progenitor cells.  We have analyzed the gene profile by deep-sequencing (RNA-Seq) of Bmi1+ and Sca-1+Bmi1- cells in homeostatic heart condition. On the other hand, we have compared gene profile by deep-sequencing (RNA-Seq) of Bmi1+ cells in homeostatic condition versus Bmi1+ cells 5 days after myocardial infarction (MI).  Analysis of RNA-Seq data revealed a differential expression signature between both subsets of cardiac stem/progenitors cells in homeostatic condition and also differences between Bmi1+ cells after AMI versus homeostatic condition.

overall_design: Examination of gene profile of 2 different cardiac stem /progenitors subsets (Bmi1+ and Sca-1+Bmi1-) co-existing inthe adult heart under steady state. Examination of gene profile of Bmi1+ cardiac stem cells in homeostatic condition versus MI


title: The dose-dependent role of PU.1 in Myeloid differentiation [small RNA-Seq]

first: Rodney

last: DeKoter

summary: A doxycycline-inducible system was used to induce PU.1 expression in cultured myeloid cell lines. The parent cell line used was BN (Kamath et al., Leukemia 22:1214-1225, 2008). Induction of PU.1 expression was previously demonstrated to lead to cell cycle exit and decreased expression of cell cycle genes. The goal of this study is expression profiling of small RNAs in cells with reduced or elevated PU.1 expression.

overall_design: MiRNA expression profilers were generated by sequencing small RNAs from uninduced cells (3) and cells induced with 1000 ng/ml doxycycline for 72 hours (3). Reads were aligned to MirBase and differential expression determined using DeSeq2.

first: Lauren

last: Solomon


title: SIR2 Suppresses Replication Gaps and Genome Instability in Yeast by Balancing Replication Between Repetitive and Unique Sequences

status: Public on Feb 13 2017

city: Seattle

first: Eric

middle: Jan

last: Foss

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: Replication gaps that persist into mitosis likely represent important threats to genome stability, but experimental identification of these gaps has proved challenging.  We have developed a technique that allows us to explore the dynamics by which genome replication is completed prior to mitosis.  Using this approach, we demonstrate that excessive allocation of replication resources to origins within repetitive regions, induced by SIR2 deletion, leads to persistent replication gaps and genome instability.  Conversely, the weakening of replication origins in repetitive regions suppresses these gaps.  Given known age- and cancer-associated changes in chromatin accessibility at repetitive sequences, we suggest that replication gaps resulting from misallocation of replication resources underlie age- and disease-associated genome instability.

overall_design: flow sort yeast according to DNA content into G1, S, early G2 and late G2, isolate DNA, and subject DNA to Illumina single end sequencing

last: Bedalov


title: The RNA-induced transcriptional silencing complex is targeted to chromatin exclusively via base-pairing interactions with nascent transcripts

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Small RNAs are implicated in chromatin modification and transcriptional gene silencing across the eukaryotic kingdom. Although well understood, fundamental mechanistic aspects of RNA-mediated chromatin regulation have remained obscure. It has not been possible to unambiguously distinguish whether small RNA loaded Argonaute proteins target the nascent transcript or the underlying DNA sequence. Here, we demonstrate that transcription of the target locus is indispensable for the formation of heterochromatin in fission yeast. Yet, high transcriptional activity opposes RNA-directed chromatin silencing. We further find that pre-mRNA splicing is compatible with RNA-directed heterochromatin formation. Small RNAs complementary to promoter distal introns trigger the formation of stable heterochromatin irrespective of pre-mRNA splicing. However, targeting a functional intron close to the 5’ end of a transcript results in a bistable chromatin state. Together, our results disprove siRNA-DNA base-pairing and provide mechanistic insights that will inform the experimental design of small RNA-directed chromatin silencing studies in multicellular organisms.

overall_design: The study comprises of 8 small RNAs sequencing data sets from cells expressing a ura4-cox4 hairpin construct that gives rise to siRNAs against 4 engeneered target genes. Experiments were performed in wt and leo1 mutant cells.

first: Yukiko

last: Shimada

first: Marc

last: Bühler


title: Histone modification (H3K4me3 and H3K27me3) during vascular endothelial cell differentiation from mouse embryonic stem cells

city: Tokyo

first: Yasuharu

last: Kanki

address: 4-6-1 Komaba, Meguro-ku

country: Japan

institute: The University of Tokyo

summary: Although studies of the differentiation from mouse embryonic stem (ES) cells to vascular endothelial cells (ECs) provide an excellent model for investigating the molecular mechanisms underlying vascular development, temporal dynamics of gene expression and chromatin modifications have not been well studied. Herein, using transcriptomic and epigenomic analyses based on the H3K4me3 and H3K27me3 modifications at a genome-wide scale, we analyzed the EC differentiation steps from ES cells and crucial epigenetic modifications unique to ECs. We determined that Gata2, Fli1, Sox7, and Sox18 are master regulators of EC induced following expression of the hemangioblast commitment pioneer factor, Etv2. These master regulator gene loci were repressed by H3K27me3 under the mesoderm period, but rapidly transitioned to the histone modification switching from H3K27me3 to H3K4me3 after treatment with vascular endothelial growth factor (VEGF). SiRNA knockdown experiments indicated that these regulators are indispensable not only for proper EC differentiation but also for blocking the commitment to other closely aligned lineages. Collectively, our detailed epigenetic analysis might provide an advanced model for understanding temporal regulation of chromatin signature and resulting gene expression profiles during EC commitment. These studies would lead the future development of methods to amplify the vascular endothelium for regenerative medicine.

overall_design: We prepared Flk-positive mesoderm cells, and 6 and 48 hours after with or without VEGF treatment cells. Cells were collected and cross-linked with 1% formaldehyde for 10min. After neutralization by using 0.2M glycine for 5min, cells were collected, re-suspended in SDS lysis buffer (10 mM Tris-HCl, 150 mM NaCl, 1% SDS, 1mM EDTA; pH 8.0, protease inhibitor cocktail), and fragmented by sonication (Sonifer 250, Branson; 10min, 60% duty, output level 4). The sonicated solution was diluted in ChIP dilution buffer (20 mM Tris-HCl (pH 8.0), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100) to a volume of 10.3ml, and 10ml was used for IP,whereas 300 ul was used as INPUT. Specific antibodies were bound with Dynabeads Magnetic beads (Life technologies, Madison, WI, USA) and applied to the diluted sonicated solution for immunoprecipitation. Antibodies against H3K4me3 (kindly gifted by Dr. Kimura (Tokyo Institute of Technology, Japan)) and H3K27me3 (07-449, Millipore, Billerica, MA, USA) were used. The prepared DNA was quantified using Q-bit (Life Technologies) and more than 10 ng of DNA was processed for the ChIP-seq assay. ChIP-DNA was prepared for sequencing according to a modified version of the genomic DNA protocol (Illumina, San Diego, CA, USA).

first: Takashi

last: Minami


title: NRSF/REST ChIP-seq binding profile in the rat paraventricular nucleus (PVN) of the hypothalamus

city: Irvine

first: Tallie

middle: Z.

last: Baram

state: California

address: Medical Sciences I, ZOT 4475

institute: University of California-Irvine

summary: We report genome-wide changes in NRSF binding following early life events that may be associated with resilience

overall_design: Examination of NRSF binding in vehicle incubated and ionotropic glutamate receptor antagonist exposed PVN explants

middle: Z

first: Akanksha

last: Singh-Taylor


title: A bacterial global regulator forms a prion

city: Boston

first: Ann

last: Hochschild

state: MA

address: 4 Blackfan Circle

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Prions are self-propagating protein aggregates that act as protein-based genetic elements in fungi. Although prevalent in eukaryotes, prions have not been identified in bacteria. Here we demonstrate that a bacterial protein, transcription terminator Rho of Clostridium botulinum (Cb-Rho), can form a prion. Specifically, we identify a candidate prion-forming domain (cPrD) in Cb-Rho and show that it confers amyloidogenicity on Cb-Rho and can functionally replace the PrD of a yeast prion-forming protein. Furthermore, we show that its cPrD enables Cb-Rho to access alternative conformations in bacteria, a soluble form that terminates transcription efficiently and an aggregated, self-propagating prion form that is functionally compromised, causing genome-wide changes in the transcriptome. Thus, Cb-Rho functions as a protein-based genetic element in bacteria, suggesting that the emergence of prions predates the evolutionary split between eukaryotes and bacteria.

overall_design: Transcription profiling of cells descended from two blue (prion-containing) colonies and three pale (prion-lacking) colonies reveals genome-wide readthrough of Rho-dependent terminators in cells containing the Rho prion

first: Andy

middle: H

last: Yuan


title: Nucleotide pools dictate the identity and frequency of ribonucleotide incorporation in mitochondrial DNA

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

institute: University of Gothenburg

summary: Previous work has demonstrated the presence of ribonucleotides in human mitochondrial DNA (mtDNA) and in the present study we use a genome-wide approach to precisely map the location of these. We find that ribonucleotides are distributed evenly between the heavy- and light-strand of mtDNA. The relative levels of incorporated ribonucleotides reflect that DNA polymerase γ discriminates the four ribonucleotides differentially during DNA synthesis. The observed pattern is also dependent on the mitochondrial deoxyribonucleotide (dNTP) pools and disease-causing mutations that change these pools alter both the absolute and relative levels of incorporated ribonucleotides. Our analyses strongly suggest that DNA polymerase γ-dependent incorporation is the main source of ribonucleotides in mtDNA and argues against the existence of a mitochondrial ribonucleotide excision repair pathway in human cells. Furthermore, we clearly demonstrate that when dNTP pools are limiting, ribonucleotides serve as a source of building blocks to maintain DNA replication and genome stability. Increased levels of embedded ribonucleotides in patient cells with disturbed nucleotide pools may constitute to a pathogenic mechanism that affects mtDNA stability and impair new rounds of mtDNA replication

overall_design: Mapping mitochondrial ribonucleotides in human cells (HeLa cells, healthy fibroblast cells as well as fibroblast cells from patients with mutations in TK2, MPV17 and DGUOK), via HydEn-seq (end sequencing of genomic fragments generated by alkaline hydrolysis). The genomic DNA of these cells were also digested with the ristriction enzyme HincII to allow for an estimation of the abosulte number of mitochondrial ribonucleotides in these lines.

first: Anna-Karin

last: Berglund

first: Clara

last: Navarrete

first: Martin

middle: K

last: Engqvist

first: Emily

last: Hoberg

first: Zsolt

last: Szilagyi

first: Robert

last: Taylor

first: Claes

last: Gustafsson

first: Maria

last: Falkenberg

first: Anders

middle: R


title: JMJD5/PHF8 regulates H3K36me2 and it is required for late steps of homologous recombination and genome integrity

city: Copenhagen

first: Anna Elisabetta

last: Salcini

address: Ole Maaloes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: The eukaryotic genome is organized in a three-dimensional structure called chromatin, constituted by DNA and associated proteins, the majority of which are histones. Post-translational modifications of histone proteins greatly influence chromatin structure and regulate many DNA-based biological processes. Methylation of lysine 36 of histone 3 (H3K36) is a post-translational modification functionally relevant during early steps of DNA damage repair. Here, we show that the JMJD-5 regulates H3K36 di-methylation and it is required at late stages of double strand break repair mediated by homologous recombination. Loss of jmjd-5 results in hypersensitivity to ionizing radiation and in meiotic defects, and it is associated with aberrant retention of RAD-51 at sites of double strand breaks. Analyses of jmjd-5 genetic interactions with genes required for resolving recombination intermediates (rtel-1) or promoting the resolution of RAD-51 double stranded DNA filaments (rfs-1 and helq-1) suggest that jmjd-5 prevents the formation of stalled postsynaptic recombination intermediates and favors RAD-51 removal. As these phenotypes are all recapitulated by a catalytically inactive jmjd-5 mutant, we propose a novel role for H3K36me2 regulation during late steps of homologous recombination critical to preserve genome integrity.

overall_design: RNA sequencing of N2 and jmjd-5(tm3735) at 20C and 25C at generation 1 (G1) and generation 6 (G6)

first: Pier

middle: G

last: Amendola

first: Nico

last: Zaghet

first: João

middle: J

last: Ramalho

first: Jens

middle: V

last: Johansen

first: Mike

last: Boxem

first: Anna

middle: E


title: Effects of in vivo expansion of mouse embryonic stem cells

first: Elisa

last: Varela

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

institute: CNIO

summary: Whe embryonic stem cells are in vitro expanded threir telomereres lengthen, in the absence of genetic manipulations,  concomitant with the loss of heterochromatic marks. In order to analyze whether there would be changes in gene expression during in vitro expansion we performed RNA-seq and found no substantial differences in gene expression at passage 6 or 16.

overall_design: Embryonic stem (ES) cells were derived from blastocysts expressing GFP in the Rosa26 locus. Four independent lines of ES were in vitro expanded to passage 16. Total RNA was extracted from each independent clones, RNA was extracted and prepared for RNA-seq.

first: Osvaldo

last: Graña

last: Blasco


title: Targeting the Creatine Kinase Pathway in EVI1-Positive Acute Myeloid Leukemia

city: Cambridge

first: Gabriela

last: Alexe

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

summary:
Purpose: Identify new targets in EVI1-Positive Acute Myeloid Leukemia
Methods: Treatment with cyclocreatine  of EVI1-driven AML cell lines TF-1,  UT-7 and UCSD-AML1. Cyclocreatine was purchased from Sigma-Aldrich (Sigma). TF-1, UT-7 and UCSD-AML1 cells were treated in quadruplicate with either vehicle or 3 mM cyclocreatine for 24 hours. Total RNA was extracted and profiled by RNA sequencing (HiSeq, Illumina) at BioMicroCenter from Massachusetts Institute of Technology (Cambridge, MA, USA).
Results: Alteration of arginine-creatine metabolism by the small-molecule cyclocreatine selectively decreased the viability, promoted cell cycle arrest and apoptosis of EVI1-positive AML cells.
Conclusions: Targeting CKMT1 is a promising therapeutic strategy for the EVI1-driven AML subtype that is highly resistant to current treatment regimens.

overall_design: mRNA profiles for the EVI1-driven AML cell lines TF-1, UT-7 and UCSD-AML1 treated with either 3mM cyclocreatine for 24 hours or with vehicle  were generated in quadruplicate  by RNA sequencing (HiSeq, Illumina) at the BioMicroCenter from Massachusetts Institute of Technology (Cambridge, MA, USA).

first: Kimberly

last: Stegmaier


title: Effects of the expression of a samble mutant of Kif1-Binding Protein (KBP) on the transcriptome of self-renewing ES cells

city: New York

first: Igor

last: Dolgalev

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: Mouse ES cells were stably transduced with a lentivirus expressing either wild-type KBP or the stable mutant KBP(KK/RR) and maintained in self-renewing growth conditions. RNA-seq was performed to assess mRNA expression differences caused by the stabilization of KBP.

overall_design: 6 samples [a triplicate set for ES cells expressing wild-type KBP and a triplicate set expressing KBP(KK/RR)] were analyzed.

first: Valerio

last: Donato

first: Michele

last: Pagano


title: BCL11B AND COMBINATORIAL RESOLUTION OF CELL FATE IN THE T-CELL GENE REGULATORY NETWORK

city: Isehara

first: Hiroyuki

last: Hosokawa

state: Kanagawa

address: 143 Shimokasuya

institute: Tokai University School of Medicine

summary: T-cell development from hematopoietic progenitors depends on multiple transcription factors, mobilized and modulated by intrathymic Notch signaling. Key aspects of T-cell specification network architecture have been illuminated through recent reports defining the roles of transcription factors PU.1, GATA-3, and E2A, their interactions with Notch signaling, and roles of Runx1, TCF-1, and Hes1, providing the basis for a comprehensively updated model of the T-cell specification gene regulatory network (GRN). However, the role of lineage commitment factor Bcl11b has been unclear. We use Self-Organizing Maps (SOM) on 63 RNA-seq datasets from normal and perturbed T-cell development to identify positive and negative regulation targets of Bcl11b during commitment and relate them to other regulomes. Both activation and repression targets can be bound by Bcl11b in vivo, but both depend strongly on developmental context. The newly clarified role of Bcl11b distinguishes discrete components of commitment, resolving how innate lymphoid cell, myeloid and dendritic, and B cell fate alternatives are excluded by different mechanisms.

overall_design: Ten million of BM-derived DN3 cells were fixed with 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min at RT followed by additional 10 min with addition of formaldehyde up to 1%. The reaction was quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed with HBSS (Gibco). Pelleted nucleus were dissolved in lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8) and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30sec sonication followed by 30sec rest, with max power. Six μg per 10^7 cells of anti-Bcl11b Abs (a mixture of A300-383A (Bethyl), A300-385A (Bethyl), ab18465 (Abcam) and 12120 (CST)) were hybridized to Dynabeads Protein A/G (Invitrogen) and added to the diluted chromatin complex. They were incubated over night at 4°C, then washed and eluted for 6hr at 65°C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, and 50 μg proteinase K). Precipitated chromatin fragments were cleaned up using Zymo ChIP DNA Clean & Concentrator. ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (NEB #E6240) following manufacturer’s instructions. Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt following manufacturer's instructions. Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4 and produced approximately 30 million reads per sample.

first: William

last: Longabaugh

first: Weihua

last: Zeng

first: Jingli

last: Zhang

first: Camden

last: Jansen

first: Long

last: Li

first: Maile

last: Romero-Wolf

first: Pentao

last: Liu

first: Hao

last: Kueh

first: Ali

last: Mortazavi

first: Ellen

last: Rothenberg


title: RNA sequencing of MDA-MB231 and U2OS cancer cell lines exposed to the alkylating agent methyl methanesufonate (MMS) and classical chemotherapeutics

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Understanding the mechanisms by which cells respond to chemotherapeutics is key to identifying means to improve therapy effiicacy while reducing systemic toxicity of these widely used classes of drugs. While determining the role of NRF2-GSH and ER stress in cells exposed to alkylating compounds such as methyl-methanesulfonate (MMS), we asked if these pathways could also be a general cell damage response relevant to other clinically used chemotherapeutics or if it is an alkylation specific response. With this intent, we performed RNA sequencing of MDA-MB231 breast cancer and U2OS osteosarcoma cells lines treated for 8 hours with a topoisomerase II inhibitor etoposide (20 µM), the antimitotic beta-tubulin-interacting drug paclitaxel (0.2 µM), doxorubicin (1 µM) and compared to MMS (40 µg/mL) treated cells. Doses represent IC50 level after 72 hours exposure. We observed that even though non-alkylating drugs, especially etoposide, caused an increase in the mRNA expression of some NRF2 and ER stress signaling markers, the number and magnitude of upregulation of genes markers in either pathway was more pronounced in alkylation treatments compared to other drugs. This indicates that alterations in NRF2 and ER stress pathways could be more likely associated with differential sensitivity to alkylating chemotherapies.

overall_design: MDA-MB231 breast cancer and U2OS osteosarcoma cells lines were treated with the 72 h IC50  dose of etoposide (20 µM), paclitaxel (0.2 µM),  doxorubicin (1 µM) or  MMS (40 µg/mL) for 8 h, and RNA was extracted and analyzed.

first: Aparna

last: Gorthi

first: Alfeu

last: Zanotto-Filho

first: Alexander

last: Bishop


title: Vascular endothelial cells differentiation from mouse embryonic stem cells

first: Yasuharu

last: Kanki

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

overall_design: Refer to individual Series


title: Interaction with ZMYND11 mediates opposing roles of Ras-responsive transcription factors ETS1 and ETS2

city: North Chicago

first: Josh

last: Plotnik

state: IL

address: 1 North Waukegan Rd, AP10/210A

institute: AbbVie Inc.


title: Proteome-wide identification of protein poly(ADP-ribosyl)ation targets reveals an important role of FHA domain protein DAWDLE in Arabidopsis immunity

city: Riverside

first: Brandon

last: Le

address: 3401 Watkins Drive

department: Institute for Integrative Genome Biology

institute: University of California, Riverside

summary: Protein poly(ADP-ribosyl)ation (PARylation) primarily catalyzed by poly(ADP-ribose) polymerases (PARPs) plays a crucial role in controlling various cellular responses. However, PARylation targets and their functions remain largely elusive. In this study, we deployed an Arabidopsis protein microarray coupled with in vitro PARylation to globally identify PARylation targets in plants. In line with nuclear localization of Arabidopsis PARPs, 56% of PARylation targets are predicted to localize in nucleus. Consistent with the essential role of protein PARylation in plant innate immunity, forkhead-associated (FHA) domain protein DAWDLE (DDL), one of the PARylation targets, positively regulates plant defense to both adapted and non-adapted pathogens. Arabidopsis PARP2 interacts and PARylates DDL, which was enhanced upon treatment of microbe-associated molecular pattern. Mass spectrometry and mutagenesis analysis identified multiple PARylation sites of DDL by PARP2. Genetic complementation assays indicate that DDL PARylation is required for its function in plant immunity. In contrast, DDL PARylation appears to be dispensable for its previously reported function in plant development likely mediated by the regulation of microRNA biogenesis. Our study uncovers many previously unknown PARylation targets and points to the distinct functions of DDL in plant immunity and development mediated by protein PARylation and small RNA biogenesis respectively.

overall_design: Two mutants (parg1-1 and parp1parp2) and one wild type control with and without treatment with 100nM flg22 (total 6 samples)

first: Baomin

last: Feng

first: Yu

last: Yu

first: Xuemei

first: Ping

last: He


title: RNA-seq of mycorrhizal Medicago truncatula roots under K+ deprivation

city: Madison

first: Jean-Michel

last: Ané

state: WI

address: 1550 Linden Drive

department: Bacteriology

institute: University of Wisconsin-Madison

summary: Arbuscular mycorrhizal (AM) associations enhance the phosphorous and nitrogen nutrition of host plants, but little is known about their role in potassium (K+) nutrition. Medicago truncatula plants were co-cultured with the AM fungus Rhizophagus irregularis under high and low K+ regimes for six weeks. We determined how K+ deprivation affects plant development, mineral acquisition, and how these negative effects are tempered by the AM colonization. The transcriptional response of AM roots under K+ deficiency was analyzed by whole genome RNA-seq. K+ deprivation decreased root biomass, external K+ uptake, and modulated oxidative stress gene expression in M. truncatula roots. AM colonization induced specific transcriptional responses to K+ deprivation that seem to temper these negative effects. A gene network analysis revealed putative key regulators of these responses. This study confirmed that AM associations provide some tolerance to K+ deprivation to host plants, revealed that AM symbiosis modulates the expression of specific root genes to cope with this nutrient stress, and identified putative regulators participating in these tolerance mechanisms.

overall_design: Medicago truncatula were inoculated or not with the arbuscular mycorrhizal fungus Rhizophagus irregularis and watered with a high (3.75 mM) or low (0.05 mM) potassium solution for six weeks. RNAs from three to four biological replicates composed of four plants each were sequenced.

first: Kevin

last: Garcia


summary: Aberrant activation of RAS/MAPK signaling is a driver of over one third of all human carcinomas. The homologous transcription factors ETS1 and ETS2 mediate the activation of gene expression programs downstream of RAS/MAPK signaling. ETS1 is important for oncogenesis in many tumor types. However, ETS2 can act as an oncogene in some cellular backgrounds, and as a tumor suppressor in others, and the molecular mechanism responsible for this cell-type specific function remains unknown. Here, we show that ETS1 and ETS2 regulate a cell migration gene expression program in opposite directions, and provide the first comparison of the ETS1 and ETS2 cistromes. This genomic data, and an ETS1 deletion line are used to show that the opposite function of ETS2 is due to binding site competition and a weaker activation function of ETS2 compared to ETS1. This weaker activation was mapped to the ETS2 N-terminus and a specific interaction with the co-repressor BS69 (ZMYND11). Gene expression data from tumor cohorts was then used to show that BS69 expression level in tumors correlates with oncogenic and tumor suppressive roles of ETS2. Therefore, these data indicate a novel and specific mechanism allowing ETS2 to switch between oncogenic and tumor suppressive functions in a cell-type specific manner.

overall_design: ChIP-sequencing

first: Joshua

middle: P

first: Peter

middle: C

last: Hollenhorst


title: ROLE OF FATTY ACID ß-OXIDATION IN LYMPHANGIOGENESIS

city: Leuven

first: Bernard

last: Thienpont

address: herestraat 42

country: Belgium

institute: KULeuven

summary: Lymphatic vessels are involved in fluid drainage and are critical for health. To date, only genetic signaling pathways have been implicated in lymphatic development, and a role for metabolism has not been described. Here, we report that transcription factor Prox1 increases fatty acid ß-oxidation (FAO) through upregulation of CPT1a, a rate-controlling step of FAO. Lymphatic endothelial cells (LECs) oxidize fatty acids to proliferate and migrate. By providing acetyl-CoA, FAO is also critical for the maintenance of differentiated LECs through the regulation of histone acetylation of key lymphangiogenic genes. Loss of CPT1a in LEC precursors causes lymphatic defects in vivo, while restoration of acetyl-CoA by supplementing acetate to replenish cellular acetyl-CoA levels rescues this process.

overall_design: We have profiled Prox1 binding sites in programmed lymphatic endothelial cells using ChIP-seq by overexpressing a FLAG-tagged PROX1 or a normal PROX1 (2 replicates each). We have also profiled the overlap of PROX1 binding with p300 binding sites in these cells as determined using ChIP-seq (2 replicates). Finally, we have investigated changes in acetylation of histone 3 lysine 9 (H3K9ac) in response to Prox1 overexpression and Cpt1a knockdown (3 replicates)

first: Brian

last: Wong

first: Xingwu

last: Wang

first: Annalisa

last: Zecchin

first: Ivo

last: Cornelissen

first: Melissa

last: García-Caballero

first: Silvia

last: Blacher

first: Stefan

last: Vinckier

first: Marlen

last: Knobloch

first: Cathrin

last: Pollman

first: Hui

last: Zhao

first: Sabine

last: Wyns

first: Bieke

last: Tembuyser

first: Martin

last: Lippens

first: Aernout

last: Luttun

first: Sarah-Maria

last: Fendt

first: Sebastian

last: Jessberger

first: Bart

last: Ghesquière

first: Friedemann

last: Kiefer

first: Agnès

last: Noel

first: Lieve

last: Moons

first: Mieke

last: Dewerchin

first: Diether

last: Lambrechts

last: Carmeliet


title: Regulation of Transcription Factor Yin Yang 1 by SET7/9-mediated Lysine Methylation [ChIP-Seq]

city: Ganzhou

first: Wenjuan

last: Zhang

state: Jiangxi

address: No. 23, Qingnian Road

department: First Affiliated Hospital

institute: Gannan Medical University

summary: Yin Yang 1 (YY1) is a multifunctional transcription factor shown to be critical in a variety of biological processes. Although it has been reported to be regulated by multiple types of post-translational modifications (PTMs), whether YY1 is methylated, which enzyme methylates YY1, and hence the functional significance of YY1 methylation remain completely unknown. Here we reported the first methyltransferase, SET7/9 (KMT7), capable of methylating YY1 in vitro and in vivo at two highly conserved lysine (K) residues, K173 and K411, located in two distinct domains, one in the central glycine-rich region and the other in the very carboxyl-terminus. Functional study revealed that SET7/9-mediated YY1 methylation regulated YY1 DNA-binding activity both in vitro and at specific genomic loci in cultured cells. Consistently, SET7/9-mediated YY1 methylation was shown to involve in YY1-regulated gene transcription and cell proliferation. Our findings revealed a novel regulatory strategy, methylation by lysine methyltransferase, imposed on YY1 protein, and linked YY1 methylation with its biological functions.

overall_design: The YY1 ChIP-seq in this study was designed to reveal YY1 genomic binding sites in HeLa cells.

first: Wen

last: Liu

first: Wen-Juan


title: Regulation of Transcription Factor Yin Yang 1 by SET7/9-mediated Lysine Methylation


title: The Roles of Arabidopsis CDF2 in Transcriptional and Posttranscriptional Regulation of Primary MicroRNAs

city: Shanghai

first: Zhenfei

last: Sun

address: Dongchuan Road 500

institute: Shanghai Jiaotong University

summary: The precise regulation of microRNA (miRNA) transcription and processing is important for eukaryotic development. Plant miRNAs are first transcribed as stem-loop primary miRNAs (pri-miRNAs) by RNA polymerase II，then cleaved in the nucleus into mature miRNAs by Dicer-like 1 (DCL1). We identified a cycling DOF transcription factor, CDF2, which interacts with DCL1 and regulates the accumulation of a population of miRNAs. CDF2 binds directly to the promoters of some miRNAs and works as a transcription activator or repressor for these miRNA genes. CDF2 binds preferentially to the pri-miRNAs regulated by itself and suppresses DCL1-mediated pri-miRNA processing. Genetically, CDF2 works in the same pathway as miR156 or miR172 to control flowering. We conclude that CDF2 regulates a group of pri-miRNAs at both the transcriptional and posttranscriptional levels to maintain proper levels of their mature miRNAs to control plant development.

overall_design: Examination of small RNA populations in Arabidopsis Wild Type and cdf2 mutant or Wild Type and dcl1-9 mutant

first: Yuda

last: Fang


title: Analysis of Wild Type and Top2b-/- Retinal Transcriptomes

status: Public on Feb 12 2017

city: Piscataway

first: Li

last: Cai

address: 599 Taylor Road

institute: Rugers, the Stage U of NJ

summary:
Purpose: Identify Top2b-dependent genes by comparing retinal transcriptome profiling (RNA-seq)
Methods: Retinal mRNA profiles of neonatal (postnatal day 0 and 6) wild-type (WT) and Topoisomerase IIbeta (Top2b) conditional knockout (Top2b−/−, or cKO) mice were generated using the SOLiD System (Applied Biosystems). Data analysis was performed according to published protocols (Trapnell et al., 2012) with minor modifications. Briefly, colorspace data of raw 50 bp reads was aligned to the mouse genome (mm9 or GRCm37) using Bowtie (Langmead et al., 2009). Gene expression levels were analyzed with Cufflinks, with differentially expressed genes determined by Cuffdiff (Trapnell et al., 2010).
Results: After sequencing, ~120 million 50 bp reads for each time point and each group were obtained and mapped to the mouse genome (MGI, as of Feb 15, 2012). Over 62,000 transcripts were identified; these include ~22,000 annotated genes (including alternative-spliced variants) which cover 76% of the whole mouse genome. Among all the annotated genes, 8.80% (1,935/22,000) for P0 and 1.25% (274/22,000) for P6 showed differential expression between the control and cKO samples (p-value ≤ 0.05, q-value ≤ 0.05).
Conclusions: All genes with differential expression levels in Top2b cKO samples are direct or indirect dependent to Top2b.

overall_design: RNA-seq of WT and Top2b cKO mice at P0 and P6

first: Ying

last: Li


title: Comparison of expression profiles between WT and MG-G1 adult bone marrow LSK cells

city: Sendai

first: Lei

last: YU

state: Miyagi

address: 2-1 Seiryo-cho, Aoba-ku

department: Department of Medical Biochemistry

institute: Tohoku University School of Medicine

summary: GATA1 is repressed in hematopoietic stem cells. To understand the significance of Gata1 gene silencing in HSC  we generated GATA1-HSC overexpressing mice (MG-G1). RNA-seq was performed to analyze the gene expression profiles between MG-G1 and WT adult bone marrow LSK cells to examine the consequence of GATA1 overexpression upon HSC.

overall_design: mRNA profiles from MG-G1 and WT LSK cells were generated by deep sequencing in triplicate.

last: Yu

first: Jun

last: Takai

first: Akihito

last: Otsuki

first: Fumiki

last: Katsuoka

first: Mikiko

last: Suzuki

first: Saori

last: Katayama

first: Masahiro

last: Nezu

first: James

middle: D

last: Engel

first: Takashi

last: Moriguchi

first: Masayuki

last: Yamamoto


title: A renal cancer-associated, renal tubule-specific, HIF-binding enhancer of oncogenic MYC and PVT1 expression

city: Oxfors

last: Platt

address: Roosevelt Drive

institute: University of Oxford

summary: Clear cell renal cell carcinoma is characterized by loss of function of the von Hippel-Lindau tumor suppressor gene (VHL) and unrestrained activation of hypoxia inducible transcription factors (HIF). Genetic and epigenetic determinants can impact on HIF pathways. A recent genome-wide association study identified single nucleotide polymorphisms (SNPs) in an intergenic region on chromosome 8 that modify the risk of developing renal cancer. The SNPs are located in a putative regulatory region between the oncogenes MYC and PVT1. Using capture C assay and genome editing we show that HIF-binding to this regulatory element is necessary to trans-activate MYC and PVT1 expression specifically in cells of renal tubular origins. Moreover, we demonstrate that the risk associated polymorphisms increase chromatin accessibility and activity as well as binding of HIF to the enhancer. These findings further strengthen the hypothesis that genetic variation at HIF-binding sites modulates the oncogenic transcriptional output of the VHL-HIF axis and provide a functional explanation for disease associated effects of SNPs in ccRCC.

overall_design: We utilized Capture-C with a capture region that incorporates the SNP of interest. Studying the interactions made between this and the rest of the genome.

first: Johannes

last: Schödel

first: David

last: Mole


title: MicroRNAs and targets in senescent fruit of litchi during ambient storage and post cold storage shelf-life.

city: GUANGZHOU

first: HONG

last: ZHU

state: GUANGDONG

address: 723 XINGKE RD.TIANHE DISDRICT

institute: SOUTH CHINA BOTANICAL GARDEN,CHINESE ACADEMY OF SCIENCES

summary:
Background: Litchi has high commercial value for its bright color and rich nutrients. However, it deteriorates with the pericarp turning brown within 1-2 days after harvest. The factors that mediate litchi fruit senescence are complicated. MicroRNAs act as negative regulators involving in almost every physiological process. To understand the mechanism of litchi fruit senescence and pericarp browning from miRNA level, five small RNA libraries and a degradome library from the pericarp of litchi fruit stored at ambient and post cold shelf-life were sequenced.

Results: By aligning the sRNA reads onto litchi unigene assembly, 296 miRNAs belonging to 49 known miRNA families were first identified from litchi. In addition, eleven litchi-specific miRNAs were identified. Among these, 167 known miRNAs were identified to cleave 197 targets, and three litchi-specific miRNAs were found to have five targets. Through combined analysis of stem-loop quantitative real-time polymerase chain reaction (qRT-PCR) and transcriptome profiling, 14 miRNA-target pairs were found to be actively involved in litchi fruit senescence-related processes, including energy regulation, anthocyanin metabolism, hormone signaling, and pathogen-infection defense.

Conclusions: A network of miRNA-target that regulates litchi fruit senescence has been proposed, revealing the miRNA-mediated regulation in senescent litchi fruit. This will aid to develop new strategies to postpone the senescence of litchi fruit and other horticultural products.

overall_design:
Examination of miRNAs in litchi pericarp tissue at 5 specific stages relating to ambient and post cold storage.
Table S1.xlsx: statistics of sRNA sequences from litchi pericarp
Table S2.xlsx: conserved miRNAs identified from litchi pericarp
Table S3.xlsx: predicted candidate litchi-specific miRNAs
Table S4.xlsx: detailed table of degradome sequencing data

first: Furong

last: Yao

first: Hong

last: Zhu

first: Hongxia

last: Qu


title: Maize seedling mRNA-seq of splicing factor mutants and their wild-type siblings

city: Gainesville

first: A.

middle: Mark

last: Settles

state: FL

address: 1301 Fifield Hall

department: Horticultural Sciences

institute: University of Florida

summary: The maize Rough endosperm3 (Rgh3) gene encodes an ortholog of the human essential splicing factor, ZRSR2. To test whether a mutation in Rgh3 affects mRNA splicing, we compared rgh3 mutants and wild-type sibling transcriptomes in an RNA-seq experiment. Twelve libraries were constructed with mRNA extracted from the roots and shoots of three seedlings of each genotype. The libraries were multiplexed and sequenced on one lane of the HiSeq 2000 platform. The run produced 149 million paired-end 100 bp reads that mapped to 35,028 genes. Two approaches were used to analyze the dataset. In the first approach, Mosaik2, FreeBayes, GSNAP, and Cufflinks were used to identify differences in transcript isoform abundance in a SNP-tolerant fashion. During reverse-transcription PCR validation, six examples of intron retention were found to occur more frequently in rgh3 seedlings, and all six introns were members of a rare class of introns called U12-type introns. The second approach utilized a t-test to determine whether more reads were mapped to U12-type introns in rgh3 libraries relative to wild-type libraries. Out of all U12-type introns within genes that are expressed at a early seedling stage, 43% exhibit splicing defects in rgh3 mutants. These U12-type intron splicing defects include intron retention and cryptic splice site activation. We report that the rgh3 mutation specifically impairs the U12-type intron splicing.

overall_design: Libraries were built from three replicates of each: wild-type roots, wild-type shoots, rgh3 roots, and rgh3 shoots

first: A

middle: M

first: Christine

last: Gault