title: The miR-155/PU.1 axis acts on Pax5 to enable efficient terminal B cell differentiation [ChIP-Seq]

first: Simon

last: Andrews

overall_design: Sequencing analysis of PU.1 binding in B cells using Illumina ChIP-seq sample prep kit and Illumina platform. Cells were from ex-vivo LPS and IL-4 activated (96h) splenic B cells from wild type, PU.1[155-/155-] and miR-155[-/-] mice.

first: Dong

last: Lu

first: Rinako

last: Nakagawa

first: Sandra

last: Lazzaro

first: Philipp

last: Staudacher

first: Cei

last: Abreu-Goodger

first: Tom

last: Henley

first: Sara

last: Boiani


title: Genome-wide mapping of DEK binding in the U937 cell line

status: Public on Sep 26 2014

city: Lund

first: Carl

last: Sanden

address: BMC B13, Klinikgatan 26

department: Department of Hematology

country: Sweden

institute: Lund University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We find that the DEK oncoprotein preferentially binds close to the transcription start sites of highly and ubiquitously expressed genes.

overall_design: Sequencing of DNA precipitated by an antibofy against the DEK oncoprotein (ChIP-seq).

last: Sandén

first: Linnea

last: Järvstråt

first: Björn

last: Nilsson

first: Urban

last: Gullberg


title: The role of HIF-1 in beta-glucan induced response in myeloid cell

city: Nijmegen

first: Shih-Chin

last: Cheng

address: Geert Grooteplein Zuid 10

department: Department of Internal Medicine

country: Netherlands

institute: Radboudumc

type: Expression profiling by high throughput sequencing

summary: beta-glucan induced glycolysis in HIF-1 depedent manner. We reported that beta-glucan injection in mice led to upregulated glycolysis. HIF-1a plays a major role in this process.

overall_design: Mice receives beta-glucan via ip for 4 days. Splenocytes were isolated for RNA sequencing.

first: Mihai

last: Netea


title: Epigenetic programming during monocyte to macrophage differentiation and trained innate immunity

first: Hindrik

last: Kerstens

address: Geert Grooteplein Zuid 26

department: Molecular Biology

institute: Radboud University

summary: Monocyte differentiation into macrophages represents one of the cornerstone processes in innate host defense. In addition, immunological imprinting of either tolerance or trained immunity after an initial infection determines the functional fate of innate immune cells and the susceptibility of the host to secondary infections. Here we comprehensively characterize the epigenetic profiles of these functional states relative to healthy adult naïve monocytes. Inflammatory and metabolic pathways are strongly modulated in the derived macrophages, including decreased activation of inflammasome components. The cAMP-dependent signaling pathway is remodeled and adrenergic signaling was functionally implicated in trained innate immunity induction in vivo. Interestingly, -Glucan trains innate immune cells through extensive remodeling of distal regulatory region-bound histone acetylation, resulting in a sizeable exclusive epigenomic signature. Accordingly, genome-wide transcription factor footprint analysis reveals a specific transcription factor repertoire at trained cell-specific enhancers when recouped with epigenetic data, forming a rich hypothesis generator to manipulate innate immunity.

overall_design: Monocytes were pre-incubated either with cell culture medium (RPMI), β-glucan (5µg/mL) or with LPS (100ng/mL), for 24 hours in a total volume of 10 mL. After a wash-out, cells were cultured in RPMI supplemented with 10% human pool serum. Monocytes were collected at different time points (0 h and 6 d after treatment) and counted before further treatment for chromatin immunoprecipitation, RNA or DNaseI treatment. Different donor Buffycoats (BC) were used as independent replicates. Replicates were generated for all the profiles including ChIPseq,RNAseq and DNaseIseq.

first: Sadia

last: Saeed

first: Jessica

last: Quintin

first: Nagesha

middle: A

last: Rao

first: Hinri

first: Ali

last: Aghajanirefah

first: Filomena

last: Matarese

first: Jacqueline

last: Ratter

first: Kim

last: Berentsen

first: Martijn

last: van der Ent

first: Nilofar

last: Sharifi

first: Eva

last: Janssen-Megens

first: Menno

last: Ter Huurne

first: Amit

last: Mandoli

first: Aylwin

last: Ng

first: Frances

last: Burden

first: Kate

last: Downes

first: Mattia

last: Frontini

first: Vinod

last: Kumar

first: Evangelos

middle: J

last: Giamarellos-Bourboulis

first: Willem

middle: H

last: Ouwehand

first: Jos

middle: W

last: van der Meer

first: Leo

last: Joosten

first: Cisca

last: Wijmenga

first: Joost

last: Martens

first: Ramnik

last: Xavier

first: Colin

last: Logie

middle: G

first: Hendrik

last: Stunnenberg


title: R-loops induce repressive chromatin marks over mammalian gene terminators

status: Public on Sep 29 2014

city: Oxford

first: Kinga

last: Kamieniarz-Gdula

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

summary: The formation of R-loops is a natural consequence of the transcription process, caused by invasion of the DNA duplex by nascent transcripts. These structures have been considered rare transcriptional by-products with potential harmful effects on genome integrity, due to the fragility of the displaced DNA coding strand. However R-loops may also possess beneficial effects as their widespread formation has been detected over CpG island promoters in human genes. Furthermore we have previously shown that R-loops are particularly enriched over G-rich terminator elements. These facilitate RNA polymerase II (Pol II) pausing prior to efficient termination. Here we reveal an unanticipated link between R-loops and RNA interference (RNAi)-dependent H3K9me2 formation over pause site termination regions of mammalian protein coding genes. We show that R-loops induce antisense transcription over these pause elements which in turn lead to the generation of double-strand RNA (dsRNA) and recruitment of Dicer, Ago1, Ago2, and G9a histone lysine methyltransferase (HKMT). Consequently an H3K9me2 repressive mark is formed and Heterochromatin Protein 1γ (HP1γ) is recruited, that reinforces Pol II pausing prior to efficient transcriptional termination. We predict that R-loops promote a chromatin architecture that defines the termination region for a substantial subset of mammalian genes.

overall_design: PolIIS2ph ChIP-seq and input in untreated condition and treated with BIX and RNaseH1 overexpression in HeLa cells. The 4 samples have been multiplexed, pooled and sequenced on 3 lanes of Illumina HiSeq2000.

first: Konstantina

last: Skourti-Stathaki

first: Nicholas

last: Proudfoot


title: Epigenetic Repogramming by an Environmental Carcinogen Through Chromatin Domain Disruption [RNA-Seq]

city: Duarte

first: Dustin

middle: E

last: Schones

state: CA

address: 1500 Duarte Rd

department: Cancer Biology

country: USA

institute: City of Hope

summary: Alterations in chromatin modifications, including DNA methylation and histone modification patterns, have been characterized under exposure of several environmental pollutants, including nickel. As with other carcinogenic metals, the mutagenic potential of nickel compounds is low and is not well correlated with its carcinogenic effects. Nickel exposure, however, is associated with alterations in chromatin modifications and related transcriptional programs, suggesting an alternative pathway whereby nickel exposure can lead to disease. To investigate the extent to which nickel exposure disrupts chromatin patterns, we profiled several histone modifications, including H3K4me3, H3K9ac, H3K27me3 and H3K9me2 as well as the insulator binding protein CTCF and the transcriptomes of control BEAS-2B cells and cells treated with nickel for 72 hours. Our results show significant alterations of the repressive histone modification H3K9me2 in nickel-exposed cells with spreading of H3K9me2 into new domains associated with gene silencing. We furthermore show that local regions of active chromatin can protect genes from nickel-induced H3K9me2 spreading. Interestingly, we show that nickel exposure selectively disrupts weaker CTCF sites, leading to spreading of H3K9me2 at these regions. These results have major implications in the understanding of how environmental carcinogens can affect chromatin dynamics and the consequences of chromatin domain disruption in disease progression.

overall_design: Treat BEAS-2B cells with NiCl2 for 72 hours and compare histone modification, CTCF binding to control BEAS-2B cells to see how they regulated gene expression by RNA-seq

first: Suresh

last: Cuddapah

first: Beisi

last: Xu

first: Cynthia

last: Jose


title: Epigenetic Repogramming by an Environmental Carcinogen Through Chromatin Domain Disruption [ChIP-Seq]


title: Reconstitution of CPSF active in polyadenylation: Recognition of the polyadenylation signal by WDR33

status: Public on Sep 25 2014

city: Basel

first: Andreas

middle: R

last: Gruber

address: Klingelbergstrasse 50-70

department: Biozentrum

country: Switzerland

institute: University of Basel

summary: Cleavage and polyadenylation specificity factor (CPSF) is the central component of the 3' processing machinery for polyadenylated mRNAs in metazoans: CPSF recognizes the polyadenylation signal AAUAAA, providing sequence specificity in both pre-mRNA cleavage and polyadenylation, and catalyzes pre-mRNA cleavage. Here we show that of the seven polypeptides that have been proposed to constitute CPSF, only four, CPSF160, CPSF30, hFip1 and WDR33, are necessary and sufficient to reconstitute a CPSF subcomplex active in AAUAAA-dependent polyadenylation, whereas CPSF100, CPSF73 and symplekin are dispensable. WDR33 is required for binding of reconstituted CPSF to AAUAAA-containing RNA and can be specifically UV-crosslinked to such RNAs, as can be CPSF30. Transcriptome-wide identification of WDR33 targets by PAR-CLIP shows that WDR33 specifically binds the AAUAAA signal in vivo in contrast to any of the five other CPSF subunits tested before. Thus, our data indicate that the CPSF subunit that is mainly responsible for recognizing the polyadenylation signal is WDR33 and not CPSF160, as suggested by previous studies.

overall_design: Transcriptome-wide profiling of WDR33 binding sites using PAR-CLIP in HEK293 cells.

first: Lars

last: Schönemann

first: Uwe

last: Kühn

first: Georges

last: Martin

first: Peter

last: Schäfer

first: Walter

last: Keller

first: Mihaela

last: Zavolan

first: Elmar

last: Wahle


title: Characterization of the coding and noncoding transcriptome in undifferentiated and differentiating mouse embryonic stem cells

city: Lausanne

first: Frederic

last: Burdet

address: Quartier Sorge - Batiment Amphipole

institute: Swiss Institute of Bioinformatics

summary: RNA (poly(A)+ fraction) has ben isolated from undifferentiated mouse embryonic stem cells and from embryonic stem cells induced to differentiate using the hanging drop model, 6 days following iinduction of differentiation. Profiling of the transcritome at these two stages of differentiation using deep RNA sequencing allows identifying modulated coding and noncoding transcripts upon induction of differentiation.

overall_design: RNA profiling of mouse embryonic stem cells at two stages of differentiation, i.e. undifferntiated state and at day 6 after induction of differentiation. Two conditions, three biological replicates per condition

first: Iole

last: Pezzuto

first: Samir

last: Ounzain

first: Thierry

last: Pedrazzini

first: Mark

last: Ibberson

first: Jerome

last: Dauvillier

first: Ioannis

last: Xenarios


title: The miR-155/PU.1 axis acts on Pax5 to enable efficient terminal B cell differentiation

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

institute: The Babraham Institute

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

overall_design: Refer to individual Series


title: Population- and sex-biased gene expression in the excretion organs of Drosophila melanogaster

city: Planegg

first: John

last: Parsch

state: BY

address: Grosshaderner Str. 2

department: Biology II

country: Germany

institute: University of Munich (LMU)

summary: We used RNA-seq to investigate gene expression variation in Malpighian tubules, which have a function analogous to that of human kidneys. In order to characterize population differentiation, we sequenced the Malpighian tubule transcriptomes of flies derived from two populations, one from sub-Saharan Africa (Zimbabwe) and one from Europe (the Netherlands). Males and females were examined separately. Overall, we found a high amount of differential expression between sexes (2,308 genes) and populations (2,474 genes). Although most of the differentially expressed genes were consistent between sexes and populations, there were 615 genes showed sex-biased expression in only one population and 557 genes showed population-biased expression in only one sex.

overall_design: mRNA expression profiles of Drosophila melanogaster Malpighian tubules from adult males and females from a European and an African population (2 biological replicates per sex and population)

first: Ann

middle: K

last: Huylmans


title: G9a/GLP-dependent H3K9me2 patterning alters chromatin structure at CpG islands in hematopoietic progenitors.

first: Dustin

last: Schones

address: 1500 E Duarte Rd.

summary: We profiled chromatin accessibility across the genome of HSPCs treated with either a small molecule inhibitor of G9a/GLP or DMSO. We observed that chromatin accessibility is dramatically altered at the regions of H3K9me2 nucleation. We have characterized the regions of H3K9me2 nucleation, revealing that H3K9me2 is nucleated in HSPCs at CpG islands (CGIs) and CGI-like sequences across the genome. Our analysis furthermore revealed a bias of H3K9me2 nucleation towards regions with low rates of C->T deamination, which typically lack DNA methylation. Lastly we examined the interaction of H3K9me2 and DNA methylation and determined that chromatin accessibility changes upon loss of H3K9me2 are dependent on the presence of DNA methylation.

overall_design: Examination of chromatin remodeling with FAIRE-seq in HSPCs treated with either a small molecule inhibitor of G9a/GLP or DMSO

first: Xiaoji

last: Chen

first: Candi

last: Trac

first: Ryan

last: Setten

first: Patrick

last: Paddison


title: TAF4 promotes pre-initiation complex formation and HNF4A occupancy of regulatory elements required to activation post-natal gene expression programme in hepatocytes

city: Illkirch

first: Irwin

last: Davidson

address: 1 rue Laurent Fries

department: Functional Genomics

country: France

institute: IGBMC


title: TAF4 promotes pre-initiation complex formation and HNF4A occupancy of regulatory elements required to activation post-natal gene expression programme in hepatocytes (ChIP-seq)

summary: The nuclear receptor HNF4A regulates embryonic and post-natal hepatocyte gene expression. Using hepatocyte-specific inactivation in mice, we show that the TAF4 subunit of TFIID acts as a cofactor for HNF4A in vivo and that HNF4A interacts directly with the TAF4-TAF12 heterodimer in vitro. In vivo, TAF4 is required to maintain HNF4A-directed embryonic gene expression at post-natal stages and for HNF4A-directed activation of post-natal gene expression. TAF4 promotes HNF4A occupancy of functional cis-regulatory elements located adjacent to the transcription start sites of post-natal expressed genes and for pre-initiation complex formation required for their expression. Promoter-proximal HNF4A-TFIID interactions are therefore required for pre-initiation complex formation and stable HNF4A occupancy of regulatory elements as two concomitant mutually dependent processes.

overall_design: Examination of PIC, H3k4me3, Ctcf and Hnf4a occupancy in wild-type and Taf4-/- livers by deep sequencing

first: Daniil

last: Alpern


title: High-resolution transcriptome analysis with long-read RNA sequencing

first: Hyunghoon

last: Cho

state: MA

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology

summary: Ongoing improvements to next generation sequencing technologies are leading to longer sequencing read lengths, but a thorough understanding of the impact of longer reads on RNA sequencing analyses is lacking. To address this issue, we generated and compared two RNA sequencing datasets of differing read lengths -- 2x75 bp (L75) and 2x262 bp (L262) -- and investigated the impact of read length on various aspects of analysis, including the performance of currently available read-mapping tools, gene and transcript quantification, and detection of allele-specific expression patterns. Our results indicate that, while the scalability of read-mapping tools and the cost-effectiveness of long read protocol is an issue that requires further attention, longer reads enable more accurate quantification of diverse aspects of gene expression, including individual-specific patterns of allele-specific expression and alternative splicing.

overall_design: Two RNA-Seq datasets of differing read lengths (2x262 bp and 2x75 bp)

first: Joe

last: Davis

first: Xin

last: Li

first: Kevin

middle: S

last: Smith

first: Alexis

last: Battle

first: Stephen

middle: B

last: Montgomery


title: TAF4 promotes pre-initiation complex formation and HNF4A occupancy of regulatory elements required to activation post-natal gene expression programme in hepatocytes (RNA-seq)

overall_design: RNA profiles in wild-type and Taf4-/- livers by deep sequencing


title: Pneumococcus rolls epigenetic dice with a six phase random switch that controls virulence

city: Leicester

first: Marco Rinaldo

last: Oggioni

address: University Road

department: Genetics

institute: University of Leicester

summary: We sequenced mRNA form 4 Streptococcus pneumoniae which expressed only a single HsdS variant of the phase variable type I restriction modification system. Samples were from mid log exponential growth phase in standard glucose containing growth medium.

overall_design: Examination of the mRNA profiles for evaluation of epigenetic regulation by a phase variable restriction modification system

first: L

last: Furi

first: M


title: Transcriptional changes in dormant and non_dormant potato meristems

status: Public on Sep 24 2014

city: Erie

first: Michael

last: Campbell

state: PA

address: 4205 College Drive

department: School of Science

institute: Penn State Erie

summary: RNA was sequenced from meristems excised from dormant and non-dormant potato tubers harvested from four different harvest years.

overall_design: Expression based on mapped RNA-sequences was accomplished from excised meristems from fall harvested (dormant tubers) and the same harvested tubers were stored under standard commercial conditions until sprouting was present (non-dormant). The experiment was replicated for four different harvest years.


title: mRNA profiles of WTAP siRNA-treated HUVECs

city: Kawasaki

first: Horiuchi

last: Keiko

state: Kanagawa

address: 1-396 Kosugi-cho, Nakahara-ku,

department: Protein-Protein Interaction

country: Japan

institute: Institute for Advanced Medical Sciences, Nippon Medical School

summary:
To examine the role of WTAP in splicing regulation, we performed high-throughput mRNA sequencing (RNA-seq) on RNA isolated from control, WTAP or Virilizer siRNA-treated HUVECs, yielding 12 million uniquely mapped 75nt pair-end tags from each sample.
MapSplice software was used for differential expression and differences in transcript splice junctions .

overall_design: mRNA profiles of control, WTAP or Virilizer siRNA-treated HUVECs were generated by deep sequencing using Illumina GAII.

first: Keiko

last: Horiuchi

first: Takao

last: Hamakubo


title: Genome-wide identification of PPARG binding sites in NCI-H2347 and NCI-H1993 cell lines

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: While the regulation of metabolic enzymes by oncogenic drivers or tumor suppressors has been intensively studied over recent years, our understanding of how metabolic processes directly regulate cell proliferation has remained fragmentary. Here we show how the alteration of metabolism directly affects cell cycle progression in cancer cells. We found that activation of the nuclear receptor peroxisome-proliferation activated receptor gamma (PPARγ), a transcriptional master regulator of lipid metabolism, inhibits the growth of lung adenocarcinoma cells by triggering a metabolic switch that inhibits pyruvate oxidation and reduces glutathione levels. These PPARγ-induced metabolic changes result in a marked increase of reactive oxygen species (ROS) levels that lead to rapid hypophosphorylation of retinoblastoma protein (RB) and cell cycle arrest. Both of these changes can be prevented by suppressing pyruvate dehydrogenase kinase 4 (PDK4) or β-oxidation of fatty acids. Thus, we provide a mechanism that directly links metabolic changes to inhibition of cancer cell cycle progression by altering ROS levels.

overall_design: We generated PPARG-LAP BAC transgenic NCI-H2347 and NCI-H1993 cell lines using the BAC-transgenesis approach. Cells at 80% confluency (~1-1.5x107) were cross-linked with 1% formaldehyde for 10 minutes at 37°C, and quenched with 125 mM glycine at room temperature for 5 minutes. The fixed cells were washed twice with cold PBS, scraped, and transferred into 1 ml PBS containing protease inhibitors (Roche). After centrifugation at 700 g for 4 minutes at 4°C, the cell pellets were resuspended in 100 μl ChIP lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl [pH 8.1] with protease inhibitors) and sonicated at 4°C with a Bioruptor (Diagenode) (30 seconds ON and 30 seconds OFF at highest power for 12 minutes). The sheared chromatin with a fragment length of ~200 – 600 bp) was centrifuged at 10,000 g for 10 minutes at 4°C). 100 μl of the supernatant was used for ChIP or as input. A 1:10 dilution of the solubilized chromatin in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl 16.7 mM Tris-HCl [pH 8.1]) was incubated at 4°C overnight with 6 μg/ml of a goat anti-GFP (raised against His-tagged full-length eGFP and affinity-purified with GST-tagged full-length eGFP). Immunoprecipitations were carried out by incubating with 40 μl pre-cleared Protein G Sepharose beads (Amersham Bioscience) for 1 hour at 4°C, followed by five washes for 10 minutes with 1ml of the following buffers: Buffer I: 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.1], 150 mM NaCl; Buffer II: 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.1], 500 mM NaCl; Buffer III: 0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl [pH 8.1]; twice with TE buffer [pH 8.0]. Elution from the beads was performed twice with 100 μl ChIP elution buffer (1% SDS, 0.1 M NaHCO3) at room temperature (RT) for 15 minutes. Protein-DNA complexes were de-crosslinked by heating at 65°C in 192 mM NaCl for 16 hours. DNA fragments were purified using QiaQuick PCR Purification kit (Qiagen) and eluted into 30 μl H2O according to the manufacturer’s protocol after treatment with RNase A and Proteinase K.

first: Nishi

last: Srivastava

first: Rahul

last: Kollipara


title: mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues

last: Eichhorn

address: 9 Cambridge Center

department: Biology

institute: Whitehead Institute for Biomedical Research

type: Non-coding RNA profiling by high throughput sequencing

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transcription profile of phm3 damp strain during growth in no phosphate medium

city: rehovot

first: Noam

last: Vardi

address: herzel 235

department: molecular genetics

country: Israel

institute: Weizmann Institute of Science

summary:
Depletion of essential nutrients triggers regulatory programs that prolong cell growth and survival. Starvation-induced processes increase nutrient transport, mobilize nutrient storage, and recycle nutrients between cellular components.  This leads to an effective increase in intracellular nutrients, which may act as a negative feedback that down-regulates the starvation program. To examine how cells overcome this potential instability, we followed the transcription response of budding yeast transferred to medium lacking phosphate. Genes were induced in two temporal waves. The first wave was stably maintained and persisted even upon phosphate replenishment, indicating a positive feedback loop. This commitment was abolished after two hours with the induction of the second expression wave, coinciding with the reduction in cell growth rate. We identify genes that mediate this loss of commitment, and show that the overall temporal stability of the expression response depends on the sequential pattern of gene induction. Our results emphasize the key role of gene expression dynamics in optimizing cellular adaptation.
phm3 damp cells were grown at high Phosphate medium, washed and transferred to no phosphate medium. Sample were taken every 15 minuets for 6 hours

overall_design: 25 samples were taken during the time course. Expression data was normalized to the first time point (cells grown at high phosphate medium)


title: The RtcB RNA ligase is an essential component of the metazoan unfolded protein response.

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

summary: RNA ligation can regulate RNA function by altering RNA sequence, structure and coding potential. For example, the function of XBP1 in mediating the unfolded protein response requires RNA ligation, as does the maturation of some tRNAs. Here, we describe a novel in vivo model in C. elegans for the conserved RNA ligase RtcB, and show that RtcB ligates the xbp 1 mRNA during the IRE 1 branch of the unfolded protein response. Without RtcB, protein stress results in the accumulation of unligated xbp-1 mRNA fragments, defects in the unfolded protein response, and decreased lifespan. RtcB also ligates endogenous pre tRNA halves, and RtcB mutants have defects in growth and lifespan that can be bypassed by expression of pre-spliced tRNAs. In addition, animals that lack RtcB have defects that are independent of tRNA maturation and the unfolded protein response. Thus, RNA ligation by RtcB is required for the function of multiple endogenous target RNAs including both xbp-1 and tRNAs. RtcB is uniquely capable of performing these ligation functions, and RNA ligation by RtcB mediates multiple essential processes in vivo.

overall_design: 4 paired-end RNA-seq reads. Control worms have pre-spliced tRNAs, RtcB-null have mutated RtcB, +/- tunicamycin treatment

first: Marc

last: Hammarlund

first: Sally

last: Peach


title: Evidence of a critical role for cellodextrin transporter 2 (CDT-2) in both cellulose and hemicellulose degradation and utilization in Neurospora crassa

city: Tianjin

first: Pengli

last: Cai

address: Xiqi Dao 32, Tianjin Airport Economic Area

country: China

institute: Tianjin Institute of Industrial Biotechnology, CAS

summary: CDT-1 and CDT-2 are two cellodextrin transporters discovered in the filamentous fungus Neurospora crassa. Previous studies focused on characterizing the role of these transporters in only a few conditions, including cellulose degradation, and the function of these two transporters is not yet completely understood. In this study, we show that deletion of cdt-2, but not cdt-1, results in growth defects not only on Avicel but also on xylan. cdt-2 can be highly induced by xylan, and this mutant has a xylodextrin consumption defect. Transcriptomic analysis of the cdt-2 deletion strain on Avicel and xylan showed that major cellulase and hemicellulase genes were significantly down-regulated in the cdt-2 deletion strain and artificial over expression of cdt-2 in N. crassa increased cellulase and hemicellulase production. Together, these data clearly show that CDT-2 plays a critical role in hemicellulose sensing and utilization. This is the first time a sugar transporter has been assigned a function in the hemicellulose degradation pathway. Furthermore, we found that the transcription factor XLR-1 is the major regulator of cdt-2, while cdt-1 is primarily regulated by CLR-1. These results deepen our understanding of the functions of both cellodextrin transporters, particularly for CDT-2. Our study also provides novel insight into the mechanisms for hemicellulose sensing and utilization in N. crassa, and may be applicable to other cellulolytic filamentous fungi.

overall_design: N. crassa was pregrown in Sucrose and transferred to Avicel (cellulose) or Xylan(hemicellulose) media. Up regulated and down regulated genes expressions were compared with wild type strain on two conditions (Avicel and xylan) respectively.

first: Chaoguang

last: Tian

first: Ruimeng

last: Gu

first: Bang

last: Wang

first: Jingen

last: Li

first: Li

last: Wan

first: Yanhe

last: Ma


title: Transcription profile of pho90_OX strain during growth in no phosphate medium

summary:
Depletion of essential nutrients triggers regulatory programs that prolong cell growth and survival. Starvation-induced processes increase nutrient transport, mobilize nutrient storage, and recycle nutrients between cellular components.  This leads to an effective increase in intracellular nutrients, which may act as a negative feedback that down-regulates the starvation program. To examine how cells overcome this potential instability, we followed the transcription response of budding yeast transferred to medium lacking phosphate. Genes were induced in two temporal waves. The first wave was stably maintained and persisted even upon phosphate replenishment, indicating a positive feedback loop. This commitment was abolished after two hours with the induction of the second expression wave, coinciding with the reduction in cell growth rate. We identify genes that mediate this loss of commitment, and show that the overall temporal stability of the expression response depends on the sequential pattern of gene induction. Our results emphasize the key role of gene expression dynamics in optimizing cellular adaptation.
pho90_OX cells were grown at high Phosphate medium, washed and transferred to no phosphate medium. Sample were taken every 15 minuets for 6 hours


title: 5mC Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming during Differentiation

first: Gary

middle: Chung

last: Hon

state: TX

address: 5323 Harry Hines Blvd.

department: OB/GYN

institute: UT Southwestern

type: Methylation profiling by high throughput sequencing

summary:
In mammals, cytosine methylation (5mC) is widely distributed throughout the genome but is notably depleted from active promoters and enhancers. While the role of DNA methylation in promoter silencing has been well documented, the function of this epigenetic mark at enhancers remains unclear. Recent experiments have demonstrated that enhancers are enriched for 5-hydroxymethylcytosine (5hmC), an oxidization product of the Tet family of 5mC dioxygenases and an intermediate of DNA demethylation. These results support the involvement of Tet proteins in the regulation of dynamic DNA methylation at enhancers. By mapping DNA methylation and hydroxymethylation at base resolution, we find that deletion of Tet2 causes extensive loss of 5hmC at enhancers, accompanied by enhancer hypermethylation, reduction of enhancer activity, and delayed gene induction in the early steps of differentiation. Our results reveal that DNA demethylation modulates enhancer
activity, and its disruption influences the timing of transcriptome reprogramming during cellular differentiation.

overall_design: We performed traditional bisulfite sequencing, TAB-Seq, RNA-Seq, and ChIP-Seq for 6 histone modifications in two biological replicates of wild-type, Tet1-/-, and Tet2-/- mouse ES cells. We also performed RNA-Seq analysis during a timecourse of differentiation to neural progenitor cells.

first: Bing

last: Ren


title: Transcription profile of Δvip1 strain during growth in no phosphate medium

summary:
Depletion of essential nutrients triggers regulatory programs that prolong cell growth and survival. Starvation-induced processes increase nutrient transport, mobilize nutrient storage, and recycle nutrients between cellular components.  This leads to an effective increase in intracellular nutrients, which may act as a negative feedback that down-regulates the starvation program. To examine how cells overcome this potential instability, we followed the transcription response of budding yeast transferred to medium lacking phosphate. Genes were induced in two temporal waves. The first wave was stably maintained and persisted even upon phosphate replenishment, indicating a positive feedback loop. This commitment was abolished after two hours with the induction of the second expression wave, coinciding with the reduction in cell growth rate. We identify genes that mediate this loss of commitment, and show that the overall temporal stability of the expression response depends on the sequential pattern of gene induction. Our results emphasize the key role of gene expression dynamics in optimizing cellular adaptation.
Δvip1 cells were grown at high Phosphate medium, washed and transferred to no phosphate medium. Sample were taken every 15 minuets for 6 hours


title: Sequential feedback induction stabilizes the phosphate starvation response in budding yeast


title: Transcription profile of Δphm3 strain during growth in no phosphate medium

summary:
Depletion of essential nutrients triggers regulatory programs that prolong cell growth and survival. Starvation-induced processes increase nutrient transport, mobilize nutrient storage, and recycle nutrients between cellular components.  This leads to an effective increase in intracellular nutrients, which may act as a negative feedback that down-regulates the starvation program. To examine how cells overcome this potential instability, we followed the transcription response of budding yeast transferred to medium lacking phosphate. Genes were induced in two temporal waves. The first wave was stably maintained and persisted even upon phosphate replenishment, indicating a positive feedback loop. This commitment was abolished after two hours with the induction of the second expression wave, coinciding with the reduction in cell growth rate. We identify genes that mediate this loss of commitment, and show that the overall temporal stability of the expression response depends on the sequential pattern of gene induction. Our results emphasize the key role of gene expression dynamics in optimizing cellular adaptation.
Δphm3 cells were grown at high Phosphate medium, washed and transferred to no phosphate medium. Sample were taken every 15 minuets for 6 hours


title: Metabolic regulation of cancer cell proliferation is mediated by reactive oxygen species

last: Kittler


title: Transcription profile of BY4741 (Wild type) during growth in no phosphate medium

summary:
Depletion of essential nutrients triggers regulatory programs that prolong cell growth and survival. Starvation-induced processes increase nutrient transport, mobilize nutrient storage, and recycle nutrients between cellular components.  This leads to an effective increase in intracellular nutrients, which may act as a negative feedback that down-regulates the starvation program. To examine how cells overcome this potential instability, we followed the transcription response of budding yeast transferred to medium lacking phosphate. Genes were induced in two temporal waves. The first wave was stably maintained and persisted even upon phosphate replenishment, indicating a positive feedback loop. This commitment was abolished after two hours with the induction of the second expression wave, coinciding with the reduction in cell growth rate. We identify genes that mediate this loss of commitment, and show that the overall temporal stability of the expression response depends on the sequential pattern of gene induction. Our results emphasize the key role of gene expression dynamics in optimizing cellular adaptation.
Wild type cells were grown at high Phosphate medium, washed and transferred to no phosphate medium. Sample were taken every 15 minuets for 6 hours


title: Transcription profile of pho85 damp strain during growth in no phosphate medium

summary:
Depletion of essential nutrients triggers regulatory programs that prolong cell growth and survival. Starvation-induced processes increase nutrient transport, mobilize nutrient storage, and recycle nutrients between cellular components.  This leads to an effective increase in intracellular nutrients, which may act as a negative feedback that down-regulates the starvation program. To examine how cells overcome this potential instability, we followed the transcription response of budding yeast transferred to medium lacking phosphate. Genes were induced in two temporal waves. The first wave was stably maintained and persisted even upon phosphate replenishment, indicating a positive feedback loop. This commitment was abolished after two hours with the induction of the second expression wave, coinciding with the reduction in cell growth rate. We identify genes that mediate this loss of commitment, and show that the overall temporal stability of the expression response depends on the sequential pattern of gene induction. Our results emphasize the key role of gene expression dynamics in optimizing cellular adaptation.
pho85 damp cells were grown at high Phosphate medium, washed and transferred to no phosphate medium. Sample were taken every 15 minuets for 6 hours


title: Humanized Foxp2 Accelerates Making Transitions From Declarative to Procedural Learning

city: Martinsried

first: Cemil

last: Kerimoglu

address: Grosshaderner Strasse 2

institute: Ludwig-Maximilians University Munich

summary:
Purpose: Foxp2 is the first and for now the only gene connected to speech and language in humans. Two aminoacid substitutions took place in this protein during recent human evolution, after our split from the last common ancestor with chimpanzees, and are most likely to have undergone positive selection in human lineage (Enard et al., 2002).
Methods: Transgenic mice in which the wild-type (murine) version of Foxp2 was replaced with the one bearing two human-specific amino acid substitutions (i.e. "humanized" Foxp2) - Foxp2hum/hum, have been compared to their wild-type (WT) counterparts in terms of behavior, electrophysiology and striatal gene expression. The latter was analyzed through RNA-sequencing performed on pooled indexed libraries on three flow cells on Illumina GAIIx.  The reads were mapped to mouse genome (mm9) by TopHat 1.4.1 and were counted using Bedtools. mRNA profiles were obtained with more than 20 million reads for every sample. Differential gene expression was analyzed with DESeq using multifactor model (Anders and Huber, 2010).
Results: Wild-type and Foxp2hum/hum mice did not show any significant differences in expression at individual gene level, neither in dorsomedial nor in dorsolateral striatum. However, when genes were grouped into functional categories and analyzed accordingly, this revealed a significant downregulation of functional categories related to synaptic signalling and plasticity in dorsomedial striatum of Foxp2hum/hum mice.

overall_design: RNA-sequencing was performed on dorsomedial and dorsolateral striatum of wild-type and Foxp2hum/hum mice, on three flow cells Illumina GAIIx. The libraries from each sample were indexed and pooled together.

first: C

first: S

last: Schreiter

first: M

last: Dannemann

first: W

last: Enard


title: The Brucella abortus virulence regulator, LovhK, is a sensor kinase in the general stress response signaling pathway

city: Chicago

first: Sean

last: Crosson

state: IL

address: 929 E 57th St. GCIS-W125

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: We sequenced the transcriptomes of B. abortus 2308 wild type, rpoE1, and lovhK deletion strains to assess gene expression in response to oxidative stress. The data represent 2 independent biological replicates of each strain.

overall_design: Illumina RNA-seq of total mRNA isolated from wild type, rpoE1, and lovhK deletion strains that were each exposed to 5 mM hydrogen peroxide for 10 min.

first: H

last: Kim


title: Identification of a dynamic core transcriptional network in t(8;21) AML regulating differentiation block and self-renewal [ChIP-Seq]

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

summary: The leukemogenic fusion protein RUNX1/ETO impairs myeloid differentiation and drives malignant self-renewal. Here we use digital footprinting and ChIP-sequencing to identify the core RUNX1/ETO responsive transcriptional network of t(8;21) cells. We show that the transcriptional programme underlying leukemic propagation is regulated by a dynamic equilibrium between RUNX1/ETO and RUNX1 complexes, which bind in a mutually exclusive fashion to identical genomic sites. Perturbation of this equilibrium by RUNX1/ETO knockdown results in a global reassembly of transcription factor complexes within pre-existing open chromatin and the formation of a new C/EBP-alpha-dominated transcriptional network driving myeloid differentiation. Our work demonstrates that the block in myeloid differentiation in t(8;21) is caused by the dynamic balance between RUNX1/ETO and RUNX1 activities and the repression of C/EBP-alpha and highlights the core targets of epigenetic reprogramming in t(8;21) AML.

overall_design: ChIP-sequencing and DNAse1-sequencing  was used for the identification of a dynamic core transcriptional network in t(8;21) AML

first: Anetta

last: Ptasinska

first: Jason

last: Piper

first: Anna

last: Pickin

first: Maria

last: Imperato

first: Maarten

last: Hoogenkamp

first: Pierre

last: Cauchy

first: Natalia

last: Martinez-Soria

first: Sally

last: James

first: Mengchu

last: Wu

first: Sascha

last: Ott

first: Dan

last: Williamson

first: Daniel

last: Tenen

first: David

last: Westhead

first: Peter

last: Cockerill

first: Olaf

last: Heidenreich

first: Constanze

last: Bonifer


title: Genome-wide analysis of Botrytis cinerea genes targeting plant cell walls of different hosts [grape]

city: Berkeley

first: Abraham

last: Morales-Cruz

state: California

address: 1 Cyclotron Road

institute: Joint Genome Institute

summary: The cell wall is among the first plant structures encountered by necrotrophic fungal pathogens, such as Botrytis cinerea. The composition of plant cell walls varies depending on the species, type of cell or tissue, and stage of development. Cell walls are important reservoirs of energy-rich sugars for pathogens, but also are barriers that impair colonization of host tissues. Growing fungal hyphae secrete enzymes that hydrolyze cell wall polysaccharides. Degradation of wall polysaccharides provides nutrients for the pathogen and improves the access of secreted Botrytis enzymes to all host cell wall targets and cytoplasmic constituents. Destruction of host cell walls results in tissue maceration, a hallmark of diseases caused by Botrytis. The Botrytis genome encodes 1,155 predicted carbohydrate-active enzyme (CAZy) genes; products of 275 are potentially secreted. Transcriptome sequencing identified Botrytis CAZy genes expressed during infections of lettuce leaves, ripe tomato fruit and grape berries. On all three hosts, Botrytis expresses a common group of 229 predicted CAZy genes including 28 pectin-modifying enzymes, 21 hemicellulose-modifying proteins, 18 enzymes targeting pectin and hemicellulose side-branches, and 16 enzymes that may degrade cellulose. Pectin polysaccharides are abundant in grape and tomato cell walls, but lettuce leaf walls are predominantly hemicelluloses and cellulose. These results suggest that Botrytis targets similar wall polysaccharide networks; e.g., pectins, on leaves and fruit, but also attacks unique host wall polysaccharide substrates The diversity of the Botrytis CAZy proteins may be partly responsible for its wide host range.

sample_organism:
Vitis vinifera
Botrytis cinerea

platform_organism:
Vitis vinifera
Botrytis cinerea

overall_design:
4 biological replicates consisting of groups of infected berries from different plants.
The experimental design consists of 4 biological replicates sequenced with RNAseq, each replicate corresponded to independent pools of 10-15 berries harvested from adjacent grapevines.

first: Barbara

last: Blanco-Ulate

first: Katherine

middle: C

last: Amrine

first: Dario

last: Cantu


title: Genome-wide transcriptional profiling of Botrytis cinerea genes targeting plant cell walls during infections of different hosts

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

sample_organism:
Vitis vinifera
Botrytis cinerea
Botrytis cinerea B05.10

overall_design: Refer to individual Series


title: The systematic shortening of 3’ UTRs has limited influence on the relative change in protein abundance in proliferating cells

first: Andreas

last: Gruber

address: Klingelbergstrasse 50-70

institute: University of Basel

summary: Alternative polyadenylation is an important cellular mechanism that enables generation of  mRNA isoforms that differ in their 3' untranslated regions (3' UTRs) and consequently in their susceptibility to miRNA and RNA binding protein mediated regulation. A dramatic change in polyadenylation site usage, leading to the systematic expression of short 3’ UTR isoforms is known to occur upon induction of proliferation in resting cells. To understand the functional consequences of short 3’ UTR isoform expression we used 3' end sequencing and quantitative mass spectroscopy to determine polyadenylation site use, mRNA and protein levels in murine and human naive and activated T cells. We found that while the process and its impact on the susceptibility to miRNA and RNA binding protein mediated regulation are evolutionarily conserved, the conservation is poor at the level of individual orthologous genes. Contrary to the common belief, we did not find that transcriptome-wide 3' UTR shortening leads to a matched increase in mRNA and protein levels of genes with tandem polyadenylation sites.

overall_design: 3' ends of transcripts were profiled by high-throughput sequencing in murine and human naive and activated T cells.

first: Georges

last: Martin

first: Philipp

last: Müller

first: Alexander

last: Schmidt

first: Rafal

last: Gumienny

first: Rajesh

last: Jayachandran

first: Jean

last: Pieters

first: Walter

last: Keller

first: Erik

last: van Nimwegen

first: Mihaela

last: Zavolan


title: Transcription profile of Δphm4 strain during growth in no phosphate medium

first: Noam

last: Vardi

summary:
Depletion of essential nutrients triggers regulatory programs that prolong cell growth and survival. Starvation-induced processes increase nutrient transport, mobilize nutrient storage, and recycle nutrients between cellular components.  This leads to an effective increase in intracellular nutrients, which may act as a negative feedback that down-regulates the starvation program. To examine how cells overcome this potential instability, we followed the transcription response of budding yeast transferred to medium lacking phosphate. Genes were induced in two temporal waves. The first wave was stably maintained and persisted even upon phosphate replenishment, indicating a positive feedback loop. This commitment was abolished after two hours with the induction of the second expression wave, coinciding with the reduction in cell growth rate. We identify genes that mediate this loss of commitment, and show that the overall temporal stability of the expression response depends on the sequential pattern of gene induction. Our results emphasize the key role of gene expression dynamics in optimizing cellular adaptation.
Δphm4 cells were grown at high Phosphate medium, washed and transferred to no phosphate medium. Sample were taken every 15 minuets for 3.75 hours

overall_design: 16 samples were taken during the time course. Expression data was normalized to the first time point (cells grown at high phosphate medium)


title: Genome-wide analysis of Botrytis cinerea genes targeting plant cell walls of different hosts [tomato]

overall_design: 3 biological replicates consisting of groups of infected tomato fruits from different plants

first: John

middle: M

last: Labavitch

first: Ann

middle: L

last: Powell


title: Genome-wide DNase-Seq and methylation profiles in Hodgkin's and non-Hodgkin's lymphoma

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg


title: Identification of a dynamic core transcriptional network in t(8;21) AML regulating differentiation block and self-renewal [RNA-Seq]

first: Salam

last: Assi

summary: The leukemogenic fusion protein RUNX1/ETO impairs myeloid differentiation and drives malignant self-renewal. Here we use digital footprinting and ChIP-sequencing to identify the core RUNX1/ETO responsive transcriptional network of t(8;21) cells. We show that the transcriptional programme underlying leukemic propagation is regulated by a dynamic equilibrium between RUNX1/ETO and RUNX1 complexes, which bind in a mutually exclusive fashion to identical genomic sites. Perturbation of this equilibrium by RUNX1/ETO knockdown results in a global reassembly of transcription factor complexes within pre-existing open chromatin and the formation of a new C/EBP-dominated transcriptional network driving myeloid differentiation. Our work demonstrates that the block in myeloid differentiation in t(8;21) is caused by the dynamic balance between RUNX1/ETO and RUNX1 activities and the repression of C/EBP and highlights the core targets of epigenetic reprogramming in t(8;21) AML.

overall_design:
ChIP-sequencing, DNAse1-sequencing and RNA-sequncing was used for the identification of a dynamic core transcriptional network in t(8;21) AML
This submission represents the RNA-Seq component of the study

first: Anetta

last: Ptasinska

middle: A

first: Jason

last: Piper

first: Anna

last: Pickin

first: Maria

last: Imperato

first: Maarten

last: Hoogenkamp

first: Natalia

last: Martinez-Soria

first: Sally

last: James

first: Mengchu

last: Wu

first: Sascha

last: Ott

first: Dan

last: Williamson

first: Daniel

last: Tenen

first: David

last: Westhead

first: Peter

last: Cockerill

first: Olaf

last: Heidenreich

first: Constanze

last: Bonifer


title: Genome-wide Dnase-Seq profiles in Hodgkin's and non-Hodgkin's lymphoma

first: Pierre

last: Cauchy

summary: We report corresponding gene expression, promoter methylation patterns of differential DHSs as well as differentially occupied TF binding motifs using surrounding DNAseI cut profiles. Overall, our study provides a framework for model studies of HL and NHL pathologies.

overall_design: Examination of genome-wide DNaseI hypersensitive sites in  L1236, L428, L591, Reh and Namalwa cell lines.

first: Amine

last: Bouhlel

first: Stephan

last: Kreher

first: Karl

last: Köcher

first: Björn

last: Lamprecht

middle: N

last: Mathas


title: Epigenetic Repogramming by an Environmental Carcinogen Through Chromatin Domain Disruption

city: Duarte

first: Dustin

last: Schones

address: 1500 Duarte Rd

institute: City of Hope

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

Histone modifications associated with gene silencing typically mark large contiguous regions of the genome forming repressive chromatin domain structures. Since the repressive domains exist in close proximity to active regions, maintenance of domain structure is critically important. This study shows that nickel, a nonmutagenic carcinogen, can disrupt histone H3 lysine 9 dimethylation (H3K9me2) domain structures genome-wide, resulting in spreading of H3K9me2 marks into the active regions, which is associated with gene silencing. Our results suggest inhibition of DNA binding of the insulator protein CCCTC-binding factor (CTCF) at the H3K9me2 domain boundaries as a potential reason for H3K9me2 domain disruption. These findings have major implications in understanding chromatin dynamics and the consequences of chromatin domain disruption during pathogenesis.

overall_design:
Investigations into the genomic landscape of histone modifications in heterochromatic regions have revealed histone H3 lysine 9 dimethylation (H3K9me2) to be important for differentiation and maintaining cell identity. H3K9me2 is associated with gene silencing and is organized into large repressive domains that exist in close proximity to active genes, indicating the importance of maintenance of proper domain structure. Here we show that nickel, a nonmutagenic environmental carcinogen, disrupted H3K9me2 domains, resulting in the spreading of H3K9me2 into active regions, which was associated with gene silencing. We found weak CCCTC-binding factor (CTCF)-binding sites and reduced CTCF binding at the Ni-disrupted H3K9me2 domain boundaries, suggesting a loss of CTCF-mediated insulation function as a potential reason for domain disruption and spreading. We furthermore show that euchromatin islands, local regions of active chromatin within large H3K9me2 domains, can protect genes from H3K9me2-spreading–associated gene silencing. These results have major implications in understanding H3K9me2 dynamics and the consequences of chromatin domain disruption during pathogenesis.

Refer to individual Series


title: U2AF1 mutations alter splice site recognition in hematological malignancies

status: Public on Sep 23 2014

city: Seattle

first: Janine

middle: O

last: Ilagan

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: Whole-exome sequencing studies have identified common mutations affecting genes encoding components of the RNA splicing machinery in hematological malignancies. Here, we sought to determine how mutations affecting the 3' splice site recognition factor U2AF1 altered its normal role in RNA splicing. We find that U2AF1 mutations influence the similarity of splicing programs in leukemias, but do not give rise to widespread splicing failure. U2AF1 mutations cause differential splicing of hundreds of genes, affecting biological pathways implicated in myeloid disease such as DNA methylation (DNMT3B), X chromosome inactivation (H2AFY), the DNA damage response (ATR, FANCA), and apoptosis (CASP8). We show that U2AF1 mutations alter the preferred 3' splice site motif in vivo, in cell culture, and in vitro. Mutations affecting the first and second zinc fingers give rise to different alterations in splice site preference and largely distinct downstream splicing programs. These allele-specific effects are consistent with a computationally predicted model of U2AF1 in complex with RNA. Our findings suggest that U2AF1 mutations contribute to pathogenesis by causing quantitative changes in splicing that affect diverse cellular pathways, and give insight into the normal function of U2AF1’s zinc finger domains.

overall_design: mRNA profiles of K562 cells expressing U2AF1 WT, mutants and knockdown of U2AF1 generated by deep sequencing.

first: Aravind

last: Ramakrishnan

first: Brian

last: Hayes

first: Michele

last: Murphy

first: Ahmad

last: Zebari

first: Philip

last: Bradley

first: Robert


title: mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues (sequencing)

city: Cambridge

first: Stephen

last: Eichhorn

summary: MicroRNAs (miRNAs) regulate target mRNAs through a combination of translational repression and mRNA destabilization, with mRNA destabilization dominating at steady state in the few contexts examined globally. Here, we extend the global steady-state measurements to additional mammalian contexts and find that regardless of the miRNA, cell type, growth condition, or translational state, mRNA destabilization explains most (66%–>90%) miRNA-mediated repression. We also determine the relative dynamics of translational repression and mRNA destabilization for endogenous mRNAs as a miRNA is induced. Although translational repression occurs rapidly, its effect is relatively weak, such that by the time consequential repression ensues, the effect of mRNA destabilization dominates. These results imply that consequential miRNA-mediated repression is largely irreversible and provide other insights into the nature of miRNA-mediated regulation. They also simplify future studies, dramatically extending the known contexts and time points for which monitoring mRNA changes captures most of the direct miRNA effects.

overall_design: 85 samples from a variety of cell types and species

middle: W

first: Huili

last: Guo

first: Sean

last: McGeary

first: Ricard

last: Rodriguez-Mias

first: Chanseok

last: Shin

first: Daehyun

last: Baek

first: Shu-hao

last: Hsu

first: Kalpana

last: Ghoshal

first: Judit

last: Villén

first: David

middle: P

last: Bartel


title: Single Cell RNA-sequencing of Pancreatic Circulating Tumor Cells

status: Public on Sep 22 2014

city: Boston

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: Circulating Tumor Cells (CTCs) are shed from primary tumors into the bloodstream, mediating the hematogenous spread of cancer to distant organs. Using a pancreatic cancer mouse model, we applied a microfluidic device to isolate CTCs independently of tumor epitopes, subjecting these to single cell RNA-sequencing. This study was conducted to determine the heterogeneity of pancreatic CTCs and to compare these CTCs to matched primary tumors, cell line controls (NB508 cancer cell line and MEF non-cancer cell line), primary tumor single cells, and normal leukocytes/WBCs.

overall_design: We profiled RNA from 75 single cells circulating in mouse blood enriched for circulating tumor cells from 5 mice, 12 single cells from a mouse embryonic fibroblast cell line, 16 single cells from the nb508 mouse pancreatic cancer cell line, 12 single mouse white blood cells, 18 single GFP lineage-traced circulating tumor cells from two mice, 20 single GFP lineage-traced cancer cells from the primary pancreatic tumor of a mouse, and 34 dilutions to 10 or 100 picograms of total RNA from mouse primary pancreatic tumors from 4 mice.

middle: T

last: Ting

first: Ajay

last: Shah

last: Miyamoto

last: Brannigan

first: Kristina

last: Xega

first: Jordan

last: Ciciliano

last: Zhu

first: Olivia

last: MacKenzie

first: Julie

last: Trautwein

first: Mohammad

last: Shahid

first: Haley

last: Ellis

last: Qu

first: Nabeel

last: Bardeesy

first: Miguel

last: Rivera

first: Ravi

last: Kapur

first: Sridhar

last: Ramaswamy

first: Toshi

last: Shioda

first: Mehmet

last: Toner

first: Shyamala

last: Maheswaran

first: Daniel

last: Haber


title: Tet proteins in DNA demethylation and cell fate restriction

first: Lan

last: Jiang

state: Massachusetts

address: 200 Longwood Ave

institute: Boston Children Hospital

summary: DNA methylation at 5-position of cytosine (5mC) is one of the best studied epigenetic modifications that plays important roles in diverse biological processes. Iterative oxidation of 5mC by the Ten-eleven translocation (Tet) family of proteins generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), which can be further processed by DNA repair proteins leading to DNA demethylation. Functional characterization of the Tet proteins has been complicated by the redundancy between the three Tet proteins. Using the CRISPR/Cas9 technology, we have generated mouse embryonic stem cells (ESCs) deficient for all three Tet proteins (TKO). Whole genome bisulphite sequencing (WGBS) analysis revealed that Tet-mediated DNA demethylation mainly occurs distal enhancers as well as promoters that significantly overlap with 5hmC, 5fC and 5caC. Characterization of the Tet TKO ESCs revealed a function for Tet proteins in cell fate restriction as Tet TKO ESCs tend to adopt both primed pluripotent stem cell-like state and 2-cell embryo-like state. In addition, Tet TKO ESCs exhibit elongated telomeres. Thus, our study reveals a role of Tet proteins not only in DNA demethylation, but also in cell fate restriction and telomere maintenance.

overall_design: 2 samples for WGBS and 2 samples for RNA-seq

first: Falong

last: Lu

first: Yuting

last: Liu

first: Shinpei

last: Yamaguchi

first: Yi

last: Zhang


title: DNA hypomethylation bypasses the interploidy hybridization barrier in Arabidopsis

city: Uppsala

first: Juan

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

institute: SLU

summary: Plants of different ploidy levels are separated by a strong postzygotic hybridization barrier that is established in the endosperm. Deregulated parent-of-origin specific genes are causal for the response to interploidy hybridizations, revealing an epigenetic basis of this phenomenon. In this study we present evidence that paternal hypomethylation can bypass the interploidy hybridization barrier by alleviating the requirement of the epigenetic Polycomb Repressive Complex 2 (PRC2) in the endosperm. Bypass of the barrier is mediated by suppressed expression of imprinted genes. We show that hypomethylated pollen causes redistribution of CHG methylation to PRC2 target genes, revealing that different epigenetic modifications can functionally substitute for each other. Our work presents a method and the underlying mechanism for the generation of viable triploids, providing an impressive example for the potential of epigenome manipulations for plant breeding.

overall_design: Examination of DNA methylation in Arabidopsis endosperm, embryo, and pollen, and gene expresion in seeds

first: Claudia

last: Köhler


title: Identification of a dynamic core transcriptional network in t(8;21) AML regulating differentiation block and self-renewal

first: Salam

last: Assi


title: Dynamic miRNA Expression Patterns During Retina Regeneration in Zebrafish: Loss of Dicer Inhibits Regeneration

status: Public on Sep 20 2014

city: Nashville

first: James

middle: G

last: Patton

state: TN

address: 1161 21st avenue south

department: Biological Sciences

institute: Vanderbilt University

summary: Background: Adult zebrafish spontaneously regenerate their retinas after damage. Although a number of genes and signaling pathways involved in regeneration have been identified, the extent of mechanisms regulating regeneration is unclear. Small non-coding RNAs, microRNAs (miRNAs), that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. Results: To investigate the requirement of miRNAs during zebrafish retinal regeneration, we knocked down the expression of the miRNA-processing enzyme Dicer in retinas prior to light-induced damage. Dicer loss significantly reduced proliferation of Müller glia-derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in retina regeneration, we collected retinas at different stages of light damage and performed small RNA high-throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. To validate the roles of differentially expressed miRNAs, we knocked down 6 different miRNAs that were upregulated in expression during regeneration and demonstrated that they have distinct effects on neuronal progenitor cell proliferation and migration during retina regeneration. Conclusions: miRNAs are necessary for retinal regeneration. miRNA expression is dynamic during regeneration. miRNAs function during initiation and progression of retinal regeneration.

overall_design: Identification of miRNAs before, during and after completion of zebrafish retinal regeneration

first: Kamya

last: Rajaram


title: Dysregulation of gene expression as the cause of Cockayne syndrome neurologic disease

city: London

first: Yuming

last: Wang

address: South Mimms

department: Mechanisms of Transcription Laboratory

institute: Cancer Research UK


title: Genome wide profiling of RNA Pol II and CSB in CS1AN cells or wild type CSB reconstituted cells [ChIP-seq]

summary: We report how CSB affects globally the density of RNA Pol II at TSS and how this effect correlates with the gene expression alterations observed from microarray analysis. We also show globally the distribution of CSB.

overall_design: RNA Pol II and CSB ChIP-Seq in CS1AN cells and CSB reconstituted wild type cells, in duplicate, using Illumina GAIIx

first: Probir

last: Chakravarty

first: Jesper

middle: Q

last: Svejstrup


title: The histone H3.3K27M mutation in pediatric glioma reprograms H3K27 methylation and gene expression

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

summary: Recent studies have identified a Lys 27-to-methionine (K27M) mutation at one allele of H3F3A, one of the two genes encoding histone H3 variant H3.3, in 60% of high-grade pediatric glioma cases. The median survival of this group of patients after diagnosis is ∼1 yr. Here we show that the levels of H3K27 di- and trimethylation (H3K27me2 and H3K27me3) are reduced globally in H3.3K27M patient samples due to the expression of the H3.3K27M mutant allele. Remarkably, we also observed that H3K27me3 and Ezh2 (the catalytic subunit of H3K27 methyltransferase) at chromatin are dramatically increased locally at hundreds of gene loci in H3.3K27M patient cells. Moreover, the gain of H3K27me3 and Ezh2 at gene promoters alters the expression of genes that are associated with various cancer pathways. These results indicate that H3.3K27M mutation reprograms epigenetic landscape and gene expression, which may drive tumorigenesis.

overall_design: We performed chromatin-immunoprecipitation of H3K27me3, H3K4me3, and EZH2 in SF7761 and NSC cell lines. And do RNA-seq in SF7761, SF8828 and NSC cell lines. SF7761 and SF8628 cell lines from patients harboring the histone H3.3 K27M mutation were obtained from Hashizume et al. (2012). NSCs (N7800-100) were purchased from Invitrogen and cultured and maintained in NSC medium (A10509-01, StemPro NSC SFM, Invitrogen).

first: Kui-Ming

last: Chan

first: Haiyun

last: Gan

first: Zhiguo


title: Low MITF/AXL ratio predicts early resistance to multiple targeted drugs in melanoma

status: Public on Sep 19 2014

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

institute: Netherlands Cancer Institute

summary: Increased MITF expression contributes to melanoma progression and resistance to BRAF pathway inhibition. We show that, unexpectedly, lack of MITF is associated with more severe resistance to a range of inhibitors. Indeed, the presence of endogenous MITF was essential for robust drug responses. Both in primary and acquired resistance, MITF levels inversely correlated with expression of several activated receptor tyrosine kinases, most commonly AXL. The MITF-low/AXL-high/drug resistance phenotype was seen in roughly half of BRAF mutant and the majority of NRAS mutant melanoma cell lines. The dichotomous behavior of MITF in drug response was corroborated in vemurafenib-resistant biopsies, including MITF high and low clones in a relapsed patient. Drug cocktails containing AXL inhibitor enhanced melanoma cell elimination by BRAF or ERK inhibition. Our results demonstrate that a low MITF/AXL ratio predicts early resistance to multiple targeted drugs, and warrant clinical validation of AXL inhibitors to combat resistance of BRAF and NRAS mutant MITF-low melanomas.

overall_design: Experssion analysis by RNAseq of 14 melanoma cell lines.

first: Judith

last: Müller

first: Daniel

last: Peeper


title: Human Pancreatic CTCs Express the ECM Protein SPARC

first: Ben

last: Wittner

summary: Circulating Tumor Cells (CTCs) are shed from primary tumors into the bloodstream, mediating the hematogenous spread of cancer to distant organs. To determine the relevance of ECM protein expression to human disease, CTCs were isolated from the blood of metastatic PDAC patients and subjected to single cell RNA-sequencing.  Analysis of 7 pancreatic CTCs from 3 patients revealed that the majority expressed keratins defining their epithelial origin.  A total of 13 of 60 extracellular protein genes enriched in mouse CTCs (see GEO GSE51372) were expressed at high levels (>100 rpm) in at least one human pancreatic CTC.  Human SPARC was the only gene found at high levels in all human pancreatic CTCs.

overall_design: To achieve a deep RNA sequencing profile of CTCs at the single cell level, we applied a novel inertial focusing-enhanced device, the CTC-iChip, which allows high efficiency negative depletion of normal blood cells, leaving unattached CTCs in solution where they can be selected and analyzed as single cells (Pubmed ID 23552373). CTCs were then subjected to single cell RNA-sequencing (Pubmed ID 20203668).

first: David

last: Ting

middle: S

first: Ajay

last: Shah

last: Miyamoto

first: Brian

last: Brannigan

first: Kristina

last: Xega

first: Jordan

last: Ciciliano

first: Huili

last: Zhu

first: Olivia

last: MacKenzie

first: Julie

last: Trautwein

first: Mohammad

last: Shahid

first: Haley

last: Ellis

last: Qu

first: Nabeel

last: Bardeesy

first: Miguel

last: Rivera

first: Ravi

last: Kapur

first: Sridhar

last: Ramaswamy

first: Toshi

last: Shioda

first: Mehmet

last: Toner

first: Shyamala

last: Maheswaran

last: Haber


title: Quantitative trait loci mapping and transcriptome analysis reveal candidate genes regulating the response to ozone in Arabidopsis thaliana

city: Beijing

first: Yuxin

last: Hu

address: No.20 Nanxincun, Xiangshan

department: Key Laboratory of Plant Molecular Physiology

institute: Institute of Botany, CAS

summary: The formation of Reactive oxygen species (ROS) has been detected in all cellular departments and even in apoplastic space of plants. As multifaceted molecule, ROS are known to accumulate in response to various stresses, and ROS burst accompanied with transcriptomic reprogramming leading to defense response or programmed cell death. Acute ozone exposure has been used as a noninvasive tool to study ROS burst induced defense response and cell death for a long time. Moreover the variation of ozone sensitivity in different Arabidopsis accessions highlights the flexibility of complex genetic architecture to adapt to specific stresses. In this study, we combine classic Quantitative Trait Loci (QTL) mapping and RNA-seq to identify the cause QTLs and potential gene candidates in response to ozone. RNA sequencing was performed on both control and ozone treated 3 weeks old accessions C24 (ozone tolerant), Te (ozone sensitive) and on a RIL line CT101 (a hypersensitive line of RIL population from reciprocal cross between C24 and Te), in triplicate. We identified 69 potential genes candidates inside the QTL regions and about 200 potential genes outside QTL region in response to ozone by comparing control to treatment within same genotype or comparing control between genotypes.

overall_design: Transcriptome profiling of ozone response using two arabidopsis accessions C24 and Te with different ozone sensitivity

first: Enjun

last: Xu

first: Lauri

last: Vaahtera

first: Hanna

last: Hõrak

first: Dirk

middle: K

last: Hincha

first: Arnd

last: Heyer

first: Mikael

last: Brosché


title: Whole genome expression analysis in the third-instar larval midgut of Drosophila melanogaster

city: Canberra

first: Stephen

middle: Leslie

last: Pearce

state: ACT

address: Clunies Ross St, Black Mountain

department: Ecosystem Sciences

country: Australia

institute: CSIRO

summary: Survival of insects on a substrate containing toxic substances such as plant secondary metabolites or insecticides is dependent on the metabolism or excretion of those xenobiotics. The primary sites of xenobiotic metabolism are the midgut, Malpighian tubules and fat body. In general, these organs are treated as single tissues by online databases, but several studies have shown that gene expression within subsections of the midgut is compartmentalized. In this article, RNA sequencing analysis was used to investigate whole-genome expression in subsections of the third-instar larval midgut. The results support functional diversification in subsections of the midgut. Analysis of the expression of gene families that are implicated in the metabolism of xenobiotics suggests that metabolism may not be uniform along the midgut. These data provide a starting point for investigating gene expression and xenobiotic metabolism in the larval midgut.

overall_design: Examination of expression in eight samples corresponding to compartments of gene expression in the midgut

first: Thomas

last: Harrop

first: Phillip

middle: J

last: Daborn

first: Philip

last: Batterham


title: Gene expression profile of the Myd88 gene depletion on mouse salivary glands

city: Mizuho

first: Takeshi

last: Into

state: Gifu

address: Hozumi 1851-1

department: Department of Oral Microbiology

institute: Asahi University School of Dentistry

summary: MyD88 is an important adaptor protein for signal transduction downstream of Toll-like receptors and TACI, receptors for regulation of innate immunity and B cell responses, respectively. The surfaces of oral mucosa are protected from infections by antimicrobial proteins and natural immunoglobulins that are constantly secreted in saliva, serving as principal innate immune defense in the oral cavity. Although MyD88-mediated signaling has a regulatory role in the intestinal mucosal immunity, its specific role in the oral cavity has been remained elusive. To identify the specific roles of MyD88-dependent signaling in gene expression profiles in salivary glands, we performed microarray analysis of the major salivary gland tissues (submandibular gland plus sublingual gland) from control (wild-type C57BL/6) mice and C57BL/6 background Myd88-null mice using Agilent Whole Mouse Genome Oligo Microarrays (8x60K, Design ID 028005).

overall_design: Total RNA was extracted from the major salivary gland tissues (submandibular gland plus sublingual gland) of wild-type and Myd88-null mice using using Trizol reagent (Life Technologies, Rockville, MD, USA) according to the manufacturer's instructions. 100 ng of all RNA samples was used as template to produce Cy3-labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, USA) following the manufacturer’s protocol. Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (8x60K, Design ID 028005) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT. Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies). The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

first: Toshiya

last: Takigawa

first: Shumpei

last: Niida

first: Ken-ichiro

last: Shibata


title: Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signalling in target cells

first: Stefano

last: Pluchino

address: Forvie Site, Robinson Way

department: Brain Repair Centre

institute: University of Cambridge

summary: The idea that stem cell therapies work only via cell replacement is challenged by the observation of consistent intercellular molecule exchange between the graft and the host. Here we defined a mechanism of cellular signaling by which neural stem/precursor cells (NPCs) communicate with the microenvironment via extracellular vesicles (EVs), and we elucidated its molecular signature and function. We observed cytokine-regulated pathways that sort proteins and mRNAs into EVs. We described induction of interferon gamma (IFN-γ) pathway in NPCs exposed to proinflammatory cytokines that is mirrored in EVs. We showed that IFN-γ bound to EVs through Ifngr1 activates Stat1 in target cells. Finally, we demonstrated that endogenous Stat1 and Ifngr1 in target cells are indispensable to sustain the activation of Stat1 signaling by EV-associated IFN-γ/Ifngr1 complexes. Our study identifies a mechanism of cellular signaling regulated by EV-associated IFN-γ/Ifngr1 complexes, which grafted stem cells may use to communicate with the host immune system.

overall_design:
polyA RNA profiling of Neural Stem/Progenitor cells (NPCs) cultured in basal/Th1/Th2 conditions, of Exosomes derived from NPCs cultured in basal/Th1/Th2 conditions and of EVs derived from NPCs cultured in Basal/Th1/Th2 conditions.
Total RNA was purified using Trizol. Purity and integrity were confirmed by BioAnalyser (Agilent). Paired End library construction and poly-A selection were performed by EASIH (The Eastern Sequence and Informatics Hub, University of Cambridge, Cambridge) according to the Illumina standard protocol. Sequencing was performed by EASIH using Illumina GAII.

first: Chiara

last: Cossetti

first: Nunzio

last: Iraci

first: Tim

middle: R

last: Mercer

first: Tommaso

last: Leonardi

first: Emanuele

last: Alpi

first: Denise

last: Drago

first: Clara

last: Alfaro-Cervello

first: Harpreet

last: Saini

first: Matthew

last: Davis

first: Julia

last: Schaeffer

first: Beatriz

last: Vega

first: Matilde

last: Stefanini

first: CongJian

last: Zhao

first: Werner

last: Muller

first: Jose-Manuel

last: Garcia-Verdugo

first: Suresh

last: Mathivanan

first: Angela

last: Bachi

first: Anton

last: Enright

first: John

last: Mattick


title: Differential gene expression in ahr-1 mutants compared to wild-type C. elegans

city: Kuopio

first: Vuokko

last: Aarnio

department: A. I. Virtanen Institute, Department of Neurobiology

country: Finland

institute: University of Eastern Finland

summary: The aryl hydrocarbon receptor (AHR) functions in higher organisims in development, metabolism and toxic responses. Its Caenorhabditis elegans (C. elegans) ortholog, AHR-1, facilitates neuronal development, growth and movement. We investigated the effect of AHR mutation on the transcriptional profile of L4 stage C. elegans using RNA-seq and quantitative real-time PCR in order to understand better AHR-1 function at the genomic level. Illumina HiSeq 2000 sequencing yielded 51.1, 61.2 and 54.0 million reads from wild-type controls, ahr-1(ia03) and ahr-1(ju145) mutants, respectively, providing detection of over 18,000 transcripts in each sample. Fourteen transcripts were over-expressed and 125 under-expressed in both ahr-1 mutants when compared to wild-type. Under-expressed genes included soluble guanylate cyclase (gcy) family genes, some of which were previously demonstrated to be regulated by AHR-1. A neuropeptide-like protein gene, nlp-20, and an F-box domain protein gene fbxa-192 and its pseudogenes fbxa-191 and fbxa-193 were also under-expressed. Conserved xenobiotic response elements were identified in the 5' flanking regions of some but not all of the gcy, nlp-20 and fbxa genes. These results extend previous studies demonstrating control of gcy family gene expression by AHR-1, and furthermore suggest a role of AHR-1 in regulation of a neuropeptide gene as well as pseudogenes.

overall_design: One sample was created from each of the following strains: wild-type N2, ahr-1(ia03) mutant and ahr-1(ju145) mutant. In data analysis, each mutant sample was individually compared to the wild-type sample to find differentially expressed genes.

first: Liisa

last: Heikkinen

first: Juhani

last: Peltonen

first: Gundars

last: Goldsteins

first: Merja

last: Lakso

first: Garry

last: Wong

first: Igor

last: Antoschechkin

first: Paul

last: Sternberg


title: PROX1 ChIP-seq analysis of human colorectal cancer cells SW480R

status: Public on Sep 18 2014

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: We performed ChIP-seq data in SW480R cells.

overall_design: Pools of three independent ChIP experiments and input DNA were used for sequencing.

first: Tatiana

middle: V

last: Petrova

last: Zangger

first: Mauro

last: Delorenzi

first: Simone

last: Ragusa


title: Analysis of gastric microbiota by pyrosequencing in Korea

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

summary: Sequencing of 16S ribosomal RNA (rRNA) gene, which has improved the characterization of microbial community, has made it possible to detect a low level Helicobacter pylori (HP) sequences even in HP-negative subjects which were determined by a combination of conventional methods. This study was conducted to obtain a cutoff value for HP colonization in gastric mucosa biopsies and gastric juices by the pyrosequencing method. Corresponding author: Nayoung Kim, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoungnam, Gyeonggi-do, Korea; Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea (Tel., +82-31-787-7008; e-mail, nayoungkim49@empas.com).

overall_design: Microbial DNA from gastric mucosal samples [gastric antrum (n=63, mucosal biopsy), follow-up sample on gastric antrum (n=16, mucosal biopsy), and gastric body (n=18, mucosal biopsy)] and gastric juices (n=4, not mucosal biopsy) was amplified by nested PCR using universal bacterial primers, and the 16S rRNA genes were pyrosequenced.

first: Hyun

last: Jo

first: Nayoung

first: Jaeyeon

first: Ji

middle: H

last: Park

first: Ryoung

last: Nam

first: Yeong-Jae

last: Seok

first: Yeon-Ran

first: Joo

first: Jung

middle: M

first: Dong

last: Lee

middle: C

last: Jung


title: The splicing factor RBM4 controls apoptosis, proliferation, and migration to suppress tumor progression

city: Chapel Hill

first: Zefeng

last: Wang

state: NC

address: 4113 Genetic Medicine

department: Pharmacology

institute: UNC

summary: Gene expression and splicing switches upon RBM4 overexpression

overall_design: 2 Samples

first: Yang

first: Dan

last: Chen

first: Haili

last: Qian

first: Yihsuan

last: Tsai

first: Shujuan

last: Shao

first: Quentin

last: Liu

first: Daniel

last: Dominguez


title: Structural basis of YTH domain as m6A reader

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E. 57th. Street

department: Chemistry

institute: The University of Chicago

summary: The N6-methyladenosine (m6A) is the most abundant internal modification in almost all eukaryotic messenger RNAs, and is dynamically regulated. Therefore, identification of m6A readers is especially important in determining the cellular function of m6A. YTHDF2 has recently been characterized as the first m6A reader that regulates the cytoplasmic stability of methylated RNA. Here we show that YTHDC1 is a nuclear m6A reader and report the crystal structure of the YTH domain of YTHDC1 bound to m6A-containing RNA. We further determined the structure of another YTH domain, YTHDF1, and found that the YTH domain utilizes a conserved aromatic cage to specifically recognize the methyl group of m6A. Our structural characterizations of the YTHDC1-m6A RNA complex also shed light on the molecular basis for the preferential binding of the GG(m6A)C sequence by YTHDC1 and confirm the YTH domain as a specific m6A RNA reader.

overall_design: PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) was applied to human YTHDC1 protein to identify its binding sites.

first: Chao

last: Xu

first: Xiao

first: Ke

first: Ian

middle: A

last: Roundtree

first: Wolfram

last: Tempel

first: Yanjun

last: Li

first: Zhike

last: Lu

first: Jinrong

last: Min


title: Characterization of stress-responsive lncRNAs in Arabidopsis thaliana

first: Zhi

middle: John

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

summary: We sequenced the total RNA from a tissues mixed sample (inflorescences, rosette leaves, cauline leaves and stems) of Arabidopsis thaliana. After total RNA extraction, the same amount of tissue RNA were mixed. Ribosomal RNAs were deleted from the mixed tissue total RNAs using RiboMinus™ Plant Kit repeated three times.   We also sequenced 9 poly(A)- RNAs from seedlings treated with different stress conditions at different times. The poly(A)- RNAs were collected by removing poly(A)+ RNAs four times . Then rRNAs were removed from poly(A)- RNAs three times.

overall_design: Sequencing of total RNAs from the mixed tissues sample is taken as an example of collecting novel transcripts from high-throughput data, which could be clarified by noncoding scores derived from our integrative models. Sequencing of nonpolyA RNAs are used for identifing stress-responsive nonpolyA lncRNAs and for validation of predicted lncRNAs.

last: Di

first: Jiapei

last: Yuan


title: Hematopoietic cell differentiation is required for initiation of acute myeloid leukemia

status: Public on Sep 17 2014

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

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

overall_design: Refer to individual Series


title: Deletion of human tarbp2 reveals cellular microRNA targets and cell cycle function of TRBP

status: Public on Sep 16 2014

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

summary: TRBP has two known functions as Dicer co-factor and PKR inhibitor. However, the role of TRBP in miRNA biogenesis is controversial and its regulation of PKR in mitosis remains unexplored. Here, we generate TRBP KO HeLa cells and find that TRBP depletion alters Dicer processing sites of a subset of miRNAs, but does not affect Dicer stability, miRNA abundance, or Argonaute loading. By generating PACT, another Dicer interactor, and TRBP/PACT double-KO cells, we further show that TRBP and PACT do not functionally compensate each other and that only TRBP contributes to Dicer processing. We also report that TRBP is hyperphosphorylated by JNK in M phase when PKR is activated by cellular dsRNAs. Hyperphosphorylation potentiates the inhibitory activity of TRBP on PKR, suppressing PKR in M-G1 transition. By generating the first human TRBP KO, our study clarifies the role of TRBP and unveils negative feedback regulation of PKR through TRBP phosphorylation.

overall_design: small RNAs of wild type, TRBP knockout, PACT knockout and TRBP/PACT double knockout cells were sequenced by Illumina Miseq.

first: Yoosik

last: Kim

first: Jinah

last: Yeo

first: Jung Hyun

last: Lee

first: V

middle: N


title: Next generation sequencing of advanced non-castrate prostate cancer treated with docetaxel chemotherapy

city: Sheffield

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

institute: University of Sheffield

summary: Early chemotherapy for advanced/metastatic non-castration resistant prostate cancer (PCa) may improve overall patient survival.  We studied the safety, tolerability and early efficacy of up-front docetaxel chemotherapy and androgen deprivation therapy (ADT) versus ADT alone for patients with newly-diagnosed advanced/metastatic PCa.  As proof of concept, we undertook in vivo gene expression profiling by next generation RNA sequencing (RNA-Seq).

overall_design: Tumour biposies from 6 patients were taken before and after treatment with combined ADT and docetaxcel for 6 weeks

first: Prabhaker

last: Rajan

first: Jacqueline

last: Stockley

first: Janis

last: Fleming

first: Mark

last: Davis

first: Albiruni

last: Abdul Razak

first: David

last: Sims

first: Chris

middle: P

last: Ponting

first: Andreas

last: Heger

first: Craig

last: Robson

first: Rhona

last: McMenemin

middle: D

last: Pedley

first: Hing

middle: Y

last: Leung


title: Lineage reprogramming of adult mouse liver cells and B-lymphocytes to neural stem-like cells using defined factors

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research


title: Ebf2 is a selective marker of brown and beige adipogenic precursor cells

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center


title: Methylome sequencing of Burkholderia pseudomallei strains Bp33 and Bp35

status: Public on Sep 15 2014

first: Tannistha

last: Nandi

address: 60 Biopolis Street, Genome, #02-01

department: Cancer Therapeutics & Stratified Oncology

institute: Genome Institute of Singapore

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of DNA methylations in Burkholderia pseudomallei.

overall_design: SMRTbell™ sequencing

first: Patrick

last: Tan


title: Comprehensive mouse alpha and beta cell transcriptomes

city: Davis

middle: O.

last: Huising

state: CA

address: One Shields Avenue

department: Neurobiology, Physiology and Behavior

institute: University of California, Davis

summary: Rodent models are widely used to study diabetes. Yet, significant gaps remain in our understanding of mouse islet physiology that reduce their accuracy as a model for human islet disease. We generated comprehensive transcriptomes of mouse beta and alpha cells using a novel bitransgenic mouse model generated for this purpose. This enables systematic comparison across thousands of genes between the two major endocrine cell types of the islets of Langerhans whose principal hormones are of cardinal importance for glucose homeostasis. Our data leveraged against similar data for human beta cells reveal a core common beta cell transcriptome of 9900+ genes and marked differences in the repertoire of receptors and long non-coding RNAs between mouse and human beta cells. The comprehensive comparison of the (dis)similarities between mouse and human beta cells represents an invaluable resource to boost the effectiveness by which rodent models offer guidance in finding cures for human diabetes.

overall_design: FACS purified alpha and beta cells from the same islets. Islets were isolated from bitransgenic offspring of a cross between mIns1-H2b-mCherry and S100b-eGFP transgenic reporter mice that mark beta and alpha cells, respectively. Islets from two replicate groups of 10 or 11 animals were pooled by sex to obtain sufficient material. Pooled islets were dissociated, sorted and collect in Trizol for RNA isolation and library construction.

last: Benner

middle: O


title: Intron evolution in Saccharomycetaceae

city: Bordeaux

first: Katarzyna

middle: B

last: Hooks

address: 146, rue Léo Saignat

department: CBIB

institute: Univ. Bordeaux

summary:
Purpose: Saccharomyceatacea yeast are intron-poor species and they contain on average 300 introns in their genomes. We designed RNAseq experiment to investigate if splicing patterns in related yeast species are similar.

Methods: Total RNA was extracted from wild type cells and processed by the RiboMinus Transcriptome Isolation Kit for Yeast and Bacteria (Invitrogen) to deplete the rRNA. cDNA libraries were prepared according to manufacturer's protocol and sequenced by SOLiD. Sequence reads were filtered and processed by TopHat.

Results: We found 216, 163, 200 and 155 predicted introns with canonical splice signals in S. cerevisiae, S. kudriavzevii, S. bayanus and N. castellii respectively. Three introns in S. cerevisiae, four in S. bayanus and ten in S. castellii are novel compared to Saccharomyces Genome Database (SGD) annotations. The expression of introns and splicing shows very high correlation between species.

Conclusion: Transcripts with introns in yeast species tested show similar levels of expression and splicing. We found few novel introns, which are conserved in yeast genomes.

sample_organism:
Saccharomyces cerevisiae
Naumovozyma castellii
Saccharomyces kudriavzevii
Saccharomyces uvarum

overall_design: Total RNA profiles from wild type yeast S. cerevisiae, S. kudriavzevii, S. bayanus and N. castellii generated by RNAseq using SOLiD.

first: Samina

last: Naseeb


title: RNA-seq from control and macroH2A1-depleted IMR90 primary human lung fibroblasts

city: Bronx

first: Matthew

middle: Jon

last: Gamble

address: 1300 Morris Park Ave / Golding 203

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: The histone variant macroH2A1 and the poly(ADP-ribose) polymerase PARP-1 both regulate gene transcription by modulating chromatin structure and function. Of the two macroH2A1 splice variants, macroH2A1.1 and macroH2A1.2, the former is often suppressed in cancer and has the unique ability to interact with poly(ADP-ribose). Using ChIP-seq in primary lung fibroblasts, we demonstrate that macroH2A1 is incorporated into either of two spatially and functionally distinct types of chromatin; the first is marked by H3 K27 trimethylation, while the second contains a set of nine histone acetylations. MacroH2A1-regulated genes are involved in cancer progression are specifically found in macroH2A1-containing acetylated chromatin. Through the recruitment of PARP-1, macroH2A1.1 promotes the acetylation of H2B K12 and K120 which plays a key role in the regulation of macroH2A1 target genes in primary cells. The macroH2A1/PARP-1 pathway regulating H2B K12 and K120 acetylation is disrupted in cancer cells, in part, explaining macroH2A1’s role in cancer suppression.

overall_design: Three biological replicates of RNA-seq from cells expressing shRNA directed against macroH2A1 or luciferase as a control

first: Hongshan

last: Chen


title: RNA-seq Experiments from Saccharomyces cerevisiae

city: Philadelphia

first: Shelley

middle: L

last: Berger

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Departments of Cell & Developmental Biology; Biology; Genetics

institute: University of Pennsylvania

summary: RNA-seq Experiments from Calorie Restricted and Non-Restricted WT Yeast

overall_design: We used RNA-seq to study transcriptome changes under Calorie Restricted and Non-restricted Saccharomyces cerevisiae

first: Weiwei

last: Dang

first: Kajia

last: Cao

first: Jean

last: Dorsey


title: The BCL6 RD2 domain governs commitment of activated B-cells to form germinal centers

status: Public on Sep 14 2014

city: New York

first: Yanwen

last: Jiang

institute: Weill Cornell Medical College

summary: Our data demonstrated that Bcl6 directly binds and represses trafficking receptors S1pr1 and Grp183 by recruiting Hdac2 through the RD2 domain.  Deregulation of these genes impairs B-cell migration and may contribute to the Germinal Center failure in Bcl6RD2MUT mice.

overall_design: RNAseq was performed in endogenous BCL6-depleted OCI-LY1 cells rescued with either WT or RD mutant BCL6 (N=3 for each group).

first: Chuanxin

last: Huang

first: Ann

last: Haberman

first: Ari

last: Melnick


title: MacroH2A1 ChIP-seq from IMR90 human primary lung fibroblasts

overall_design: Two biological replicates of the macroH2A1 ChIP and two corresponding input samples were sequenced

middle: J


title: Exploring the role of macroH2A1 in transcription regulation in IMR90 primary human lung fibroblasts with RNA-seq and ChIP-seq


title: RNA-seq analysis of diabetes induced changes in macrophage transcriptome

city: Duarte

first: Nancy

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

summary: Macrophage dysfunction and polarization plays key role in chronic inflammation associated with diabetes and its complications. However, the effect of diabetes on macrophage transcriptome including long non-coding RNAs is not known. Here, we analyzed global changes in transcriptome of bone marrow macrophages isolated from type 2 diabetic db/db mice and control littermates db/+ mice using high throughput RNA-seq technique. Data analysis showed that expression of genes relevant to fibrosis, cell adhesion and inflammation were altered in diabetic db/db mice relative to control db/+ mice. Furthermore, expression of several known and novel long non coding RNAs and nearby genes was altered in db/db mice. Gene ontology and IPA showed activation of signaling netwroks relevant to  fibrosis, cell adhesion and inflammatory pathways . This study for the first time demonstrated that diabetes profoundly affects macrophage transcriptome including expression of long non coding RNAs and altered the levels of genes relevant to diabetes complications.

overall_design: Bone marrow macrophages were isolated from 12 weeks old type 2 diabetic male db/db mice and control littermates db/+ mice. These were differentiated in culture for 7-8 days in the presence of 10  ng/ml of MCSF-1  (BMMC) or 20 ng/ml of GM-CSF (BMGM). Then RNA was extracted and used for RNA-seq.

first: Natarajan

last: Rama

first: Reddy

last: Marpadga

first: Chen

last: Nancy