title: Analysis of transcriptional differences between ZIKV-infected Ifnar-/- and Ifnar+/- placentas

first: Akiko

last: Iwasaki

summary:
Purpose: While type I interferons (IFN) are important for control of viral replication, we see that, upon infection of Ifnar-/- females were crossed to Ifnar+/- males with ZIKV, only Ifnar+/- fetuses are resorbed or develop severe growth restriction. To identify how IFN may be altering placenta development, we performed RNAsequencing on infected and uninfected Ifnar-/- and Ifnar+/- placentas.
Methods: Ifnar-/- females were crossed to Ifnar+/- males and infected intravaginally with Cambodian ZIKV at E5.5. Placentas were harvested from infected and uninfected pregnant dams at E10.5.
Results/ Conclusions: Comparison of ZIKV-infected Ifnar-/- and Ifnar+/- shows an elevated interferon stimulated gene (ISG) signature in Ifnar+/- placentas but does not reveal any underlying developmental defects that may be causing defects in placenta development.

overall_design: MRNA profiles from 3 placentas per genotype from uninfected and 5 placentas per genotype of infected were generated using Illumina NextSeq 500.

first: Laura

last: Yockey


title: Differential expression of genes in fetal brain as a consequence of maternal protein deficiency and nematode infection

status: Public on Dec 31 2017

city: Sainte Anne de Bellevue

first: Manjurul

last: Haque

state: Quebec

address: Institute of Parasitology, Mac campus

department: Institute of Parasitology

country: Canada

institute: McGill University

type: Expression profiling by high throughput sequencing

summary: Maternal dietary protein deficiency and nematode infection during early pregnancy have negative impacts on both maternal placental gene expression and fetal growth in the mouse. Here we used next-generation RNA sequencing to test our hypothesis that maternal protein deficiency and/or nematode infection also alter the expression of genes in the developing fetal brain. Outbred pregnant CD1 mice were used in a 2x2 design with two levels of dietary protein (24% and 6%) and two levels of infection (repeated sham and Heligmosomoides bakeri beginning at gestation day 5). Pregnant dams were euthanized on gestation day 18 to harvest the whole fetal brain. Four fetal brains from each treatment group were analyzed using RNA Hi-seq sequencing and the differential expression of genes was determined by edgeR package using NetworkAnalyst. In response to maternal H. bakeri infection, 96 genes (88 up-regulated and 8 down-regulated) were differentially expressed in the fetal brain. Differentially expressed genes were involved in metabolic processes, developmental processes and immune system according to the PANTHER classification system. Among the important biological functions identified, several upregulated genes have known neurological functions including neurodevelopment (Gdf15, Ing4), neural differentiation (miRNA let-7), synaptic plasticity (via suppression of NF-κβ), neuro-inflammation (S100A8, S100A9) and glucose metabolism (Tnnt1, Atf3). However, in response to maternal protein deficiency, brain specific serine protease (Prss22) was the only upregulated gene and only one gene (Dynlt1a dynein light chain) responded to the interaction of maternal nematode infection and PD.  In conclusion, maternal exposure to GI nematode infection from day 5 to 18 of pregnancy may influence developmental programming of the fetal brain.

overall_design: 2 X 2 factorial design with two types of dietary protein and two levels of infection

first: Lisa

last: Starr

first: Kristine

middle: G

last: Koski

first: Marilyn

middle: E

last: Scott


title: Assesment of Foxg1 targets via RNAseq at E13.5 of mouse cortex

city: Freiburg

first: Henriette

last: Franz

address: Alberstr: 17

department: Anatomy and Cellbiology

country: Germany

institute: University Freiburg

summary: Cortical development is under control of transcriptional programs that are orchestrated by activation of key determinants such as transcription factors. But stable inheritance of temporo-spatial activity of factors influencing cell fate and regionalization in different layers is only partly understood. We report that chromatin methylation at H3K79 transmits cell fate and layering information from early to late progenitors. Activity of DOT1L, mediating H3K79 methylation, prevents premature cell cycle exit by increasing expression of genes regulating asymmetric cell division (Vangl2, Cenpj). Transcriptional programs characteristic for upper layer neurons are less active in Dot1l-deficient mice already at developmental stages that precede upper layer neuron generation. DOT1L activates expression of many key determinants such as Cux1, Cux2, Satb2 or Pou3f3. Additionally, DOT1L affects transcription of Sox family members, suggesting an evolutionary conserved mechanism. In part, DOT1L and H3K79me2 replace inactivating H3K9me3 at Sox family promoters and allow for transcriptional activation during neural differentiation.

first: Tanja

last: Vogel

first: Pavankumar

last: Videm

first: Rolf

last: Backofen

first: Ganeshkumar

last: Arumugam

first: Christine

last: Hacker

first: Stefan

last: Weise


title: DOT1L and H3K79 methylation refer layer identity by controlling temporo-spatial expression of key transcription factors in cortical development

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Assesment of DOT1L direct targets via RNAseq at E14.5 of mouse cortex

first: Nicole

last: Hellbach


title: Assesment of DOT1L direct targets via ChIP of H3K79me2 at E12.5 of mouse cortex

first: Fabian

last: Kilpert

first: Thomas

last: Manke

first: Stefanie

last: Heidrich


title: microRNA-triggered transposon small RNAs mediate genome dosage response (RNA-Seq)

city: Versailles

first: Filipe

last: Borges

address: Route de St-Cyr (RD10)

country: France

institute: Institut Jean-Pierre Bourgin - INRAE

summary: Chromosome dosage plays a significant role in reproductive isolation and speciation in both plants and animals, but underlying mechanisms are largely obscure. Transposable elements can promote hybridity through maternal small RNA, and have been postulated to regulate dosage response via neighboring imprinted genes. Here, we show that a highly conserved microRNA in plants, miR845, targets the tRNAMet primer-binding site (PBS) of LTR-retrotransposons in Arabidopsis pollen, and triggers the accumulation of 21 to 22-nucleotide small RNA in a dose dependent fashion via RNA polymerase IV. We show that these epigenetically activated small-interfering RNAs (easiRNAs) mediate hybridization barriers between diploid seed parents and tetraploid pollen parents  (“the triploid block”), and that natural variation for miR845 may account for “endosperm balance” allowing formation of triploid seeds. Targeting the PBS with small RNA is a common mechanism for transposon control in mammals and plants, and provides a uniquely sensitive means to monitor chromosome dosage and imprinting in the developing seed.

overall_design: RNA-seq of Arabidopsis pollen

first: Robert

middle: A

last: Martienssen


title: A Highly Conserved GAD-1 Is Required for Pre-mRNA Splicing and Transcription Elongation by Forming Spliceosome with NineTeen Complex

city: Hong Kong

first: Runsheng

last: Li

address: To Yuen Building, 31 To Yuen Street, City University of Hong Kong

country: Hong Kong

institute: City University of Hong Kong

summary: Pre-mRNA splicing requires assembly of spliceosome that consists of hundreds of factors forming various dynamic complexes with or without small nuclear RNAs (snRNAs). Systematic identification of the splicing factors remains a significant challenge especially in vivo. In our genetic screening for the factors required for division asynchrony during Caenorhabditis elegans embryogenesis, we identified a highly conserved but uncharacterized essential protein, GAD-1, that is necessary for setting cell cycle length of intestine progenitors, a function that is shared with many other factors involved in transcription, pre-mRNA splicing or polyadenylation, suggesting its potential role in mRNA biogenesis. Co-immunoprecipitation followed by mass spectrometry reveals that GAD-1 mainly interacts with non-snRNP type of splicing complex called NineTeen Complex (NTC). Consistent with this, RNA-seq analysis demonstrates pervasive defects in pre-mRNA splicing in gad-1 mutants. Transgenic reporter assay shows its ubiquitous and nuclear expression across developmental stages. Immunostaining of the C-terminal domain of RNA polymerase II demonstrates a GAD-1’s role in transcription elongation. In agreement with this, depletion of GAD-1 and its interacting partners inhibits expression of both ubiquitous and tissue-specific genes, supporting that both GAD-1 and many of its interacting proteins are novel components of NTC or its associated spliceosome. Taken together, we identify GAD-1 and its multiple interacting partners as novel components of spliceosome in vivo through which they regulate pre-mRNA splicing and transcription elongation.

overall_design: Mix-stage embryo samples were collected from strain BW1943 (gad-1(ct226) dpy-11(e224) V) at 16 °C and 25 °C by bleaching. Total RNAs were extracted using TRIzol (Invitrogen) following the manufacturer’s instructions. mRNA purification and fragmentation, cDNA synthesis, end repairing, adapters ligation, and DNA fragment enrichment were performed using Illumina’s TruSeq Stranded mRNA Library Preparation Kit based on the Kit’s manual. Each library was sequenced to obtain pair-end (2×150 bps) reads using Illumina HiSeq 2500. We obtained approximately 20 million reads of high-quality score (>30 mean quality score) on average per library.

first: Zhongying

last: Zhao


title: RNA-seq comparison of gene induction in RIG-I stimulated old and young human monocytes

city: New Haven

first: Ryan

last: Molony

state: CT

address: 300 Cedar Street

country: USA

institute: Yale University

summary: Goal: The goal of this study was to compare gene induction in old and young human monocytes upon stimulation of these cells with a RIG-I specific ligand, based on previously published results which indicated impaired interferon responses in monocytes from older individuals upon influenza virus infeciton.

overall_design: Methods: We isolated monocytes from human donor peripheral blood of young (n = 2) or old (n =3) donors. Cells were then transfected with a 14bp hairpin RNA construct bearing a 5'-ppp motif that specifically stimulates RIG-I. After 6 hours, total RNA was collected from stimulated cells and RNA was purified using the RNeasy kit (Qiagen) according to manufacturer's protocols.  RNA was isolated from cellular lysates in the same manner as for qPCR experiments. RNA sequencing was performed by the HudsonAlpha Institute for Biotechnology. RNA samples were sequenced using an Illumina HiSeq 2500 machine, with 125 base pair reads. The raw reads of RNA-seq experiments were trimmed off sequencing adaptors and low quality regions by btrim.  The trimmed reads were mapped to human genome (GRCh37) by tophat2 .  The counts of reads for each gene were based on Ensembl annotation (release 70). After the counts are collected, the differential expression analysis was done by DEseq2, which calculated the adjusted p-values.

middle: D

first: Jenny

middle: T

last: Nguyen

first: Yong

last: Kong

first: Ruth

middle: R

last: Montgomery

first: Albert

middle: C

last: Shaw

first: Akiko

last: Iwasaki


title: Androgen receptor RIP-seq of LNCaP cells treated with androgen hormone

city: São Paulo

first: Lucas

middle: Ferreira

last: daSilva

state: São Paulo

address: Av. Vital Brasil 1500

department: Parasitology

country: Brazil

institute: Instituto Butantan

summary: In this work we reported in a high-throughput way (RIP-seq) the RNAs associated with androgen receptor after treatment with androgen hormone. We used a large compilation of lincRNAs to describe the differences between lincRNAs associated to androgen receptor from those who are non-associated with androgen receptor. By integrating different data sources (DNA-seq Seq and CHIP-seq) was possible to describe transcription factors and histone marks diffrentially enriched at the promoter and vicinity of androgen associated lincRNA loci.

overall_design: The LNCaP cell were cultivated by 6 hours in a medium containing 0.1 nM of synthetic androgen hormone (R1881). After this process RNA was immunopreciptated with anti-AR (2 biological replicates) or Anti-IgG (2 biological replicates).

middle: F

first: Felipe

last: Beckedorff

first: Murilo

middle: S

last: Amaral

first: Sergio

last: Verjovski-Almeida


title: Neuronal activity, TGFβ signaling and unpredictable chronic stress affect transcription of Gadd45 family members in vitro and in vivo [MeDIP-Seq]

first: Henriette

last: Franz

type: Methylation profiling by high throughput sequencing

summary: Neuronal activity is altered in several neurological and psychiatric diseases. Upon depolarization not only neurotransmitters are released but also cytokines and other activators of signaling cascades. Unraveling their complex implication in transcriptional control in receiving cells will contribute to understand specific central nervous system (CNS) pathologies and will be of therapeutical interest. In this study we depolarized mature hippocampal neurons in vitro using KCl and revealed increased release not only of Brain-derived neurotrophic factor (BDNF), but also of Transforming growth factor beta (TGFB). Neuronal activity together with BDNF and TGFB controls transcription of DNA modifying enzymes specifically members of the DNA-damage-inducible (Gadd) family, Gadd45a, Gadd45b, and Gadd45g. MeDIP followed by massive parallel sequencing and transcriptome analyses revealed less DNA methylation upon KCl treatment. Thereby, psychiatric disorder-related genes, namely Tshz1, Foxn3, Jarid2, Per1, Map3k5, and Arc are transcriptionally activated and demethylated upon neuronal activation. To analyze whether misexpression of Gadd45 family members can be associated with psychiatric diseases, we applied unpredictable chronic mild stress (UCMS) as established model for depression to mice.UCMS lead to a reduced expression of Gadd45 family members. Taken together, our data demonstrate that Gadd45 family members are new putative targets for UCMS treatments.

overall_design: Definition of activity dependent targets on transcriptional and DNA methylation level

first: Patrick

last: Bovio

first: Daniela

last: Grassi

first: Tanja

last: Vogel

first: Riccardo

last: Vezzali


title: Epigenomic analysis of Atrx deficiency in murine glioma cells of orgin [H3.3 ChIP]

city: Houston

first: Jason

last: Huse

state: TX

address: 1515 Holcombe Blvd

department: Department of Pathology

institute: University of Texas MD Anderson Cancer Center

summary: The chromatin regulator ATRX is inactivated in large subsets of adult and pediatric glioma.  Whether and how ATRX deficiency promotes oncogenesis by epigenomic dysregulation remains unclear.  We found that Atrx loss, especially when coupled with Tp53 inactivation, promoted cell motility and modulated differentiation state in primary murine neuroepithelial progenitors, recapitulating characteristic disease phenotypes and molecular features.  Moreover, Atrx deficiency induced widespread shifts in chromatin accessibility, histone composition, and gene transcription at vacant Atrx binding sites distributed across the genome.  Finally, target genes mediating Atrx-deficient phenotypes in vitro exhibited similarly selective misexpression in ATRX-mutant human glioma tissues and cell lines.  These findings demonstrate that, in appropriate physiological contexts, ATRX deficiency and its epigenomic sequelae are sufficient to induce disease-defining oncogenic phenotypes.

overall_design: Examination of H3.3 compositional changes genome-wide arising in the setting of Atrx deficiency in murine neuroepithelial progenitor cells (NPCs)

first: Carla

last: Danussi

first: Promita

last: Bose

first: Kasthuri

last: Kannan


title: Whole-genome bisulfite-seq (WGBS) on Lin-Sca1+Kit+ (LSK) bone marrow cells from wild-type C57BL/6J mice

city: Vancouver

first: Aly

last: Karsan

state: British Columbia

address: 675 West 10th Avenue

department: Michael Smith Genome Sciences Centre

institute: BC Cancer Agency

summary: Hematopoietic stem cells (HSC) are heterogeneous in their ability to durably reconstitute the blood system. Epigenome surveys along the hematopoietic hierarchy and within the HSC compartment have revealed distinct epigenomic states associated with functionally defined hematopoietic cell types. However, the degree to which epigenomic states vary within functionally defined hematopoietic populations is still largely unknown. To address this question we performed single-cell genome-wide DNA methylation profiling of linage negative Sca+cKit+ (LSK) and EPCR+CD45+CD48-CD150+ (ESLAM) hematopoietic stem cell populations purified from adult mouse bone marrow. For this we developed a bisulfite based whole genome protocol suitable for use on single index sorted mammalian cells. Analysis of the resulting data from 148 single cells revealed that the methylomes of single HSCs show characteristics consistent with those defined from bulk populations. Comparing methylation states across single HSCs revealed a significant reduction in CpG state adjacency compared to bulk estimates and that on average 13% of CpGs exist in the opposite methylation state between any two cells within both surface marker defined HSC containing populations. Utilizing a novel analytical approach designed to address missing data inherent in single cell assays we identified an epigenetically distinct subpopulation of cells present in both the LSK and ESLAM populations. Enrichment analysis of genes associated with this distinct epigenetic state revealed pathways consistent with hematopoietic stem cell function, and integration with single-cell RNA-seq data defined putative surface proteins that mark this population, including the previously identified hematopoietic marker, NRXN1.

overall_design: One sample, no controls

first: Joanna

last: Wegrzyn

first: Kieran

last: O'Neill

first: Jenny

last: Li


title: Next generation sequencing of Pseudomonas aeruginosa PAO1 in the presence of Copper Nanoparticles Stress

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

summary:
Purpose: The intensive use of metal-based nanoparticles results in their continuous release into the environment and the subsequent destroying microbial biodiversity and causing occurrence of antibiotic resistant determinants. Although previous studies have indicated that nanoparticles may be toxic to microorganisms, there is a scarcity of data available to assess the underlying molecular mechanisms of inhibitory and biocidal effects of nanoparticles on microorganisms, which is a critical gap in our comprehensive understanding of the impacts of nanoparticles on microbial ecosystems.
Methods: By combining the global activated/suppressed gene profiles and detected physiological responses, we detected the microbial response to CuO NPs exposure and revealed potential mechanisms of CuO NPs on this prevalent opportunistic pathogen and environmentally relevant denitrifier.
Results:Our results indicate that nanoparticles could react directly with the biological membrane, but also change gene expressions. Transmission electron microscopy (TEM) results indicate that CuO nanoparticles not only damaged the structure of the bacterial membrane but also entered the cells. Planktonic cells of P. aeruginosa are energetically compromised after exposure to a sublethal level (1 and 10 mg/L) of CuO nanoparticles. Respiration was likely inhibited as denitrification activity was severely depleted in terms of decreased transcript levels of most denitrification genes. In addition, and of high concern, bacteriophage genes were activated and it is speculated that phage mediated cell lysis. Meanwhile, CuO NP exposure induced significantly up-regulated expressions of metal resistance gene, resistance-nodulation-division, P-type ATPase efflux and cation diffusion facilitator transporters, which can form an integrated network controlling metals concentrations in the cytoplasm and periplasm P. aeruginosa.
Conclusion: Based on our results, it is evident that the response of bacteria under the exposure of nanoparticles is very complex, though a clear and comprehensive understanding of the true mechanisms of inhibition or toxicity is still lacking. Our findings will provide insights on whole picture regarding the fundamental mechanisms of microbial susceptibility, tolerance and resistance to exposure of CuO NPs, as well highlight to re-estimate potential risks of CuO NP to public health and environment.

overall_design: mRNA profiles of P.aeruginosa PAO1 towards CuO NPs stress were generated by next generation sequencing via Illumina 2000.

first: Shuhong

last: Gao


title: Neuronal activity, TGFβ signaling and unpredictable chronic stress affect transcription of Gadd45 family members in vitro and in vivo


title: Convergent exaptation of Alu and B/ID SINEs for Staufen-mediated mRNA decay

city: Santa Cruz

first: Manuel

last: Ares

state: CA

address: 1156 High Street

department: MCDB

institute: UC Santa Cruz

summary: Identifying orthologous mRNAs subject to SMD in both mouse and human myoblasts using siRNA depletion of Staufen or Upf1

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: mRNAs subject to Staufen-mediated decay should increase in level upon depletion of either Staufen or Upf1. Cultured myoblasts (mouse or human) treated with control, Staufen, or Upf1 siRNAs were extracted and RNA was purifed, polyA selected and sequenced. Changes in level were detected by DESEQ analysis.

first: Lucas

last: Bronwyn

first: Ares

last: Manuel

first: Shiue

last: Lily

first: Katzman

last: Sol

first: Maquat

last: Lynne


title: B cell differentiation is limited by de novo DNA methylation [ATAC-seq]

city: Atlanta

first: Benjamin

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

summary: B cells provide humoral immunity by differentiating into antibody-secreting plasma cells, a process that requires cell division and is linked to DNA hypomethylation and gene regulation. Conversely, accumulation of DNA methylation in B cell differentiation is less apparent. To determine the role of de novo DNA methylation in B cell differentiation, the de novo DNA methyltransferases, Dnmt3a and Dnmt3b, were deleted in B cells resulting in phenotypically normal B cell development in the bone marrow, spleen and lymph nodes. However, upon immunologic challenge, mice deficient for Dnmt3a and Dnmt3b (Dnmt3-deficient) accumulated more antigen-specific B cells and bone marrow chimeras showed this was cell-autonomous. Additionally, a five-fold increase in splenic and bone marrow plasma cells was observed. Molecular analysis revealed that Dnmt3-deficient bone marrow plasma cells failed to repress gene expression to the same level as their Dnmt3ab-sufficient counterparts. This was coupled with a failure of Dnmt3-deficient germinal center B cells and plasma cells to gain and/or maintain DNA methylation at several thousand loci that were clustered in enhancers of genes that function in B cell activation and homing. Analysis of chromatin accessibility showed Dnmt3-deficient plasma cells had increased accessibility at several genes involved in hematopoiesis and B cell differentiation. These data show that de novo DNA methylation limits B cell activation, proliferation and differentiation, and support a model whereby DNA methylation represses the aberrant transcription of genes silenced in B cell differentiation to maintain plasma cell homeostasis.

overall_design:
Naïve lymph node B cells (B220+ GL7- Fas-), Phycoerythrin-specific germinal center B cells (B220+ GL7+ Fas+ PE+), and bone marrow plasma cells (CD138+) were compared between Cd19cre/wtDnmt3afl/flDnmt3bfl/fl (Dnmt3-deficient) and littermate control Cd19wt/wtDnmt3afl/flDnmt3bfl/fl (Dnmt3-sufficient) mice using RRBS, RNA-seq, and ATAC-seq. Naïve lymph node B cells were taken from naïve mice, whereas PE-specific germinal center B cells and bone marrow plasma cells were isolated from mice that had been immunized with phycoerythrin 30 days prior.
This Series includes the ATAC-seq component of the study.


title: B cell differentiation is limited by de novo DNA methylation [RNA-seq]

overall_design:
Naïve lymph node B cells (B220+ GL7- Fas-), Phycoerythrin-specific germinal center B cells (B220+ GL7+ Fas+ PE+), and bone marrow plasma cells (CD138+) were compared between Cd19cre/wtDnmt3afl/flDnmt3bfl/fl (Dnmt3-deficient) and littermate control Cd19wt/wtDnmt3afl/flDnmt3bfl/fl (Dnmt3-sufficient) mice using RRBS, RNA-seq, and ATAC-seq. Naïve lymph node B cells were taken from naïve mice, whereas PE-specific germinal center B cells and bone marrow plasma cells were isolated from mice that had been immunized with phycoerythrin 30 days prior.
This Series includes the RNA-seq component of the study.


title: Epigenomic analysis of Atrx deficiency in murine glioma cells of orgin [Atrx ChIP]

first: Jason

last: Huse

overall_design: Examination of ATRX binding sites in Tp53+/+ and Tp53-/- neuroepithelial progenitor cells (NPCs)


title: Growth is required for perception of water availability to pattern plant root branches

city: Stanford

first: Jose

middle: Ramon

last: Dinneny

state: United States

address: 260 Panama St

department: Plant Biology

institute: Carnegie Institution for Science, Department of Plant Biology

summary: Lateral root branching in higher plants is promoted in regions locally contacting a source of water, and suppressed in regions exposed to low water availability. We found that developmental competence to respond to this environmental signal is limited to growing tissues. We profiled gene expression in regions of the maize primary root exposed to low and high water availability both within and outside of the zone of competence.

overall_design: Maize primary roots were grown along an agar surface. Roots were manually dissected longitudinally to separate the size exposed to air (Air) from the side contacting agar (Contact). These tissue sections were then cut radially into segments 0-5 mm from the root tip for the developmentally competent zone (Competent) and 5-15 mm from the root tip for the developmentally fixed zone (Fixed). Matching tissue types from 2 primary roots were pooled for each biological replicate. RNA was profiled from 3 biological replicates.

first: Neil

last: Robbins

first: José


title: B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation

summary: B cells provide humoral immunity by differentiating into antibody-secreting plasma cells, a process that requires cellular division and is linked to DNA hypomethylation. Conversely, little is known about how de novo deposition of DNA methylation affects B cell fate and function. Here we show that genetic deletion of the de novo DNA methyltransferases Dnmt3a and Dnmt3b (Dnmt3-deficient) in mouse B cells results in normal B cell development and maturation, but increased cell activation and expansion of the germinal center B cell and plasma cell populations upon immunization. Gene expression is mostly unaltered in naive and germinal center B cells, but dysregulated in Dnmt3-deficient plasma cells. Differences in gene expression are proximal to Dnmt3-dependent DNA methylation and chromatin changes, both of which coincide with E2A and PU.1-IRF composite-binding motifs. Thus, de novo DNA methylation limits B cell activation, represses the plasma cell chromatin state, and regulates plasma cell differentiation.

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

Refer to individual Series


title: Multiple regulatory modules are required for scale-to-feather conversion

city: Los Angeles

first: Ping

last: Wu

address: 2011 Zonal Ave HMR313A

department: Pathology

institute: University of Southern California


title: Chicken embryonic E16 scutate scale and feather samples

summary: Feather evolution enabled feathered dinosaurs and early Mesozoic birds to venture into new ecological niches. Studying how feathers and scales are specified provides insight into how a new organ evolves. We use genome-wide analyses to identify feather-associated genes and test their feather-forming ability by expressing them in chicken and alligator scales. Intermediate morphotypes revealed five cardinal morphogenetic events: localized growth zone, follicle invagination, branching, feather keratin differentiation and dermal papilla formation. In contrast to molecules known to induce feathers on scales (retinoic acid, beta-catenin), we identify novel scale-feather converters (Sox2, Zic1, Grem1, Spry2, Sox18) which induce only one or several of the five regulatory modules. Some morphotypes resemble filamentous appendages found in feathered dinosaur fossils, while others demonstrate some characteristics of modern feathers. We propose that at least five morpho-regulatory modules were used to diversify ancient reptile scales. The regulatory combination and hierarchical integration led to extant feather forms.

overall_design: Scale samples treated with gene misexpression or retinoic acid were collected at E16. RNA-seq was performed to study the gene expression profiles of the treated samples, compared to the GFP control and normal feather samples. There are 2-3 replicates for each sample group.


title: B cell differentiation is limited by de novo DNA methylation [RRBS]

overall_design:
Naïve lymph node B cells (B220+ GL7- Fas-), Phycoerythrin-specific germinal center B cells (B220+ GL7+ Fas+ PE+), and bone marrow plasma cells (CD138+) were compared between Cd19cre/wtDnmt3afl/flDnmt3bfl/fl (Dnmt3-deficient) and littermate control Cd19wt/wtDnmt3afl/flDnmt3bfl/fl (Dnmt3-sufficient) mice using RRBS, RNA-seq, and ATAC-seq. Naïve lymph node B cells were taken from naïve mice, whereas PE-specific germinal center B cells and bone marrow plasma cells were isolated from mice that had been immunized with phycoerythrin 30 days prior.
This Series includes the RRBS component of the study.


title: Chicken embryonic feather and scale samples

overall_design: RNA-seq was performed to study the gene expression profiling between the feather-forming and scale-forming regions. There are 2 replicates for each sample group.


title: ChIP-seq for embryonic chicken feather and scale samples

overall_design: H3K27ac ChIP-seq was performed to compare the feather-forming and scale-forming regions. There are 2 replicates for each sample group.


title: Developmental Exposure To PCB153 Alters Genes Related To Circadian Rhythm And Metabolism In Zebrafish (Danio rerio)

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

summary: Polychlorinated biphenyls (PCBs) are persistent and ubiquitously distributed environmental pollutants. Based on their chemical structure, PCBs are classified into non-ortho substituted and ortho-substituted congeners. Non-ortho-substituted PCBs are structurally similar to dioxin or TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) and their mode of action and toxic effects are well established. In contrast, much less is known about the effects of ortho-substituted PCBs. Studies conducted so far have focused on tissue-specific effects but there is limited knowledge about the effects on the whole organism, particularly the sensitive developmental stages in vertebrates. Hence, in this study we investigated the effects of exposure to an environmentally relevant ortho-substituted PCB (2,2’,4,4’,5,5’-hexachlorobiphenyl; PCB153) on zebrafish embryos. We exposed zebrafish embryos to either DMSO (0.1%; solvent control) or three different concentrations of PCB153 (0.1, 1 and 10 μM) from 4 hours post-fertilization (hpf) to 120 hpf. At the end of the exposure, larvae were sampled for determining transcriptional changes (RNA sequencing) and the remaining embryos were maintained in contaminant-free environment. At 7 and 14 days post-fertilization (dpf), zebrafish larvae were assessed for locomotory behavior. We did not observe any overt phenotypes during the exposure period, but observed a spinal phenotype in the 10μM PCB153 treated group starting at 7 dpf. This phenotype was observed in a dose-dependent manner and majority of the embryos with this phenotype died by 14 dpf. RNA sequencing of 5 dpf larvae exposed to PCB153 also revealed dose-dependent changes in gene expression patterns. A total of 633, 2227, and 3378 differentially expressed genes were observed in 0.1, 1 and 10 μM PCB153 treated embryos, respectively. Among these, 301 genes were common to all treatment groups, and KEGG pathway analysis revealed enrichment of genes related to circadian rhythm, FOXO signaling and insulin resistance pathways. We are currently investigating the functions of genes that are uniquely altered by different PCB153 concentrations. Overall, these results suggest that developmental exposure to PCB153, a PCB congener highly prevalent in the environment, targets multiple physiological processes including photoperiod regulation and metabolism. [Funded by NIH P01ES021923 and NSF OCE-1314642].

overall_design: A total of 16 samples were sequenced. It includes 4 different treatments at a single developmental time point. Each treatment had 4 biological replicates.

first: Keegan

last: Krick

first: Mark

last: Hahn


title: Transcriptome analysis for anatomically separate psoriatic plaques highlight individualized expression patterns

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: To evaluate the transcriptomes of lesional skin from different body parts of the same individual.  Specifically, we conducted a transcriptomic study to investigate expression variability for diseased samples taken from different anatomic regions of same patient, and to compare the variability to between individuals variability.

overall_design: 5 psoriasis patients, each with 4 psoriatic and 1 uninvolved skin biopsies. Totally 25 RNA-seq experiments conducted.

first: Johann

last: Gudjonsson


title: Profiling gene expression of the host response to an irradiated sporozoite immunization and Plasmodium vivax malaria challenge

first: Monica

middle: L.

last: Rojas-Peña

address: 310 Ferst Dr.

department: School of Biology

institute: Georgia Institute of Technology

summary: We report an initial understanding of the modular immune response to a P. vivax malaria challenge after protection with PvRAS. By contrasting blood samples drawn at baseline, following immunization but pre-challenge, and at the first day of diagnosis of malaria in affected subjects.

overall_design: RNA-seq analysis was performed for 20 individuals (5 Duffy Fy(-) and 15 Duffy Fy (+) from Cali Colombia) 3 Control, 5 Duffy Fy(-) and 12 PvRAS immunized for three of the time points, namely the diagnosis day, baseline and pre-challenge day.

middle: L

first: Dalia

last: Arafat

first: Swetha

last: Garimalla

first: Myriam

last: Arévalo-Herrera

first: Sócrates

last: Herrera

first: Juan

middle: M

last: Velasquez

first: Greg

last: Gibson


title: Altered basal and TCDD-induced gene expression in zebrafish embryos made AHRRa-null by ZFN-mediated gene targeting

summary: The aryl hydrocarbon receptor (AHR) repressor (AHRR), a bHLH-PAS protein, is a transcriptional repressor of AHR and other transcription factors (HIF, ER) and is regulated by an AHR-dependent mechanism. However, the physiological and toxicological roles of AHRR are not well understood. We demonstrated earlier that knockdown of AHRRa (one of two AHRR paralogs) in zebrafish embryos using morpholino anti-sense oligonucleotides results in developmental phenotypes such as pericardial edema, craniofacial malformations, and cardiac deformities, similar to effects caused by exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). AHRRa morphants also exhibit down-regulation of genes associated with photoreceptor development. To characterize the AHRRa function further, we used ZFN (zinc finger nuclease) technology to generate a line of zebrafish with a 7-bp deletion in exon 3 of AHRRa, leading to a truncated AHRR (110 aa, of which 38 are from AHRRa, compared to the 550-aa wild-type (wt) AHRRa). The mutant AHRRa protein, which contains basic regions but lacks the HLH and PAS domains, did not repress AHR in vitro, suggesting that it is inactive (null). Unlike AHRRa morphants, AHRRa-null fish did not display a TCDD-like phenotype; exposure to TCDD caused defects similar to those in TCDD-exposed wt embryos. RNA-sequencing revealed that basal expression of 562 genes differed significantly between the null and wt embryos, including down-regulation of genes associated with photoreceptor development, as seen in AHRRa morphants. TCDD-induced gene expression patterns for the prototypic AHR target genes were similar for null and wt embryos. However, 22 genes were differentially regulated by TCDD in the AHRRa-null embryos as compared to wt embryos (>2-fold; 5% FDR). We are currently investigating the link between these differentially expressed genes and the function of AHRRa in development and AHR signaling. [Supported by NIH R01ES006272]

overall_design: Ahrra-null and wild type embryos were exposed to either solvent control or 2nM TCDD for 1 hour at 6 hours post-fertilization and subsequently reared in clean water until 72 hpf. At 72 hpf, embryos were sampled for gene expression profiling.

first: Sibel

middle: I

last: Karchner

first: Diana

last: Franks


title: Molecular effects on individual and combined toxicity of OTA and CTN against human embryonic kidney 293 cells

city: GUANGZHOU

first: HONG

last: ZHU

state: GUANGDONG

address: 723 XINGKE RD.TIANHE DISDRICT

country: China

institute: SOUTH CHINA BOTANICAL GARDEN,CHINESE ACADEMY OF SCIENCES

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the transcriptome and miRNAome of human embryonic kidney 293 cells upon the administration of ochratoxin A (OTA) and citrinin (CTN), to compare the individual and combined toxicity of these two mycotoxins. We identified largely differentially expressed miRNAs and corresponding genes, and the correlations between miRNAs and their target genes associated with apoptotic signaling were furthermore analyzed by pmi-RB-REPORT luciferase assay system. We concluded that hsa-miR-1-3p plays an essential role in promoting OTA and CTN-induced renal cytotoxicity.

overall_design: Examination of miRNAs with targets and identification of differentially expressed genes in control and mycotoxin-treated human kidney cells.

first: Liang

last: Gong

first: Hong

last: Zhu

first: Taotao

last: Li

first: Yueming

last: Jiang

first: Xuewu

last: Duan


title: RNA-seq of Human neural progenitor cells exposed to lead (Pb) reveals transcriptome dynamics, splicing alterations and Pb disease risk associations

city: Cleveland

first: Peng

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

summary: We use time series RNA-seq to conduct a genome-wide survey of the temporal transcriptome response of human embryonic stem (ES) cell-derived neural progenitor cells (NPCs) exposed to lead.

overall_design: NPCs were derived from human embryonic stem cells (hESCs) with a modified protocol from a previously reported protocol (Chambers et al. 2009) (Methods). We used lead acetate to treat NPCs at two different concentrations, 3 μM and 30 μM.

first: Zhonggang

last: Hou

first: Jennifer

last: Bolin

first: James

last: Thomson

first: Ron

last: Stewart


title: The myelin protein PMP2 is regulated by SOX10 and drives melanoma cell invasion

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

summary: The transcription factor SRY(sex related protein-Y)-box10 (SOX10) plays a key role in the development of melanocytes and peripheral glial cells from neural crest precursors. Recently, we and other groups found SOX10 to be involved in melanoma initiation, proliferation, invasion, and survival. However, specific mediators which impart the oncogenic role of SOX10 in melanoma remain widely unknown. To identify potential target genes of SOX10, we performed RNA sequencing to analyze genome-wide expression alterations after ectopic expression of SOX10. Among nine genes differentially regulated by SOX10, only peripheral myelin protein 2 (PMP2) was found upregulated in several other melanoma cell lines. PMP2 is one of the most abundant myelin proteins in glial cells and is necessary for the formation and maintenance of the myelin sheath. We detected PMP2 expression in a subset of human melanoma cell lines while it was absent in human melanocytes and fibroblasts. Direct binding of SOX10 to the PMP2 promoter was shown by chromatin immunoprecipitation and electrophoretic shift assay. In three-dimensional spheroid assays, we found that PMP2 overexpression increased melanoma cell invasion. In conclusion, we identified PMP2 as target gene of SOX10 and propose a novel role for PMP2 in melanoma cell invasion.

overall_design: RNA sequencing was performed with 1205Lu metastatic melanoma cells transiently transfected with a vector for SOX10 overexpression (pCMV6-SOX10) or a control vector (pCMV6) in three biological replicates.

first: Saskia

last: Graf

first: Claudia

last: Kammerbauer

first: Robert

last: Besch

first: Carola

last: Berking


title: miRNA expression profiles of early lactation and early involution in dairy goat mammary gland tissues

city: Taian

first: zb

last: Ji

address: Daizong street

institute: shandong agricultural university

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of miRNA expression files. The goals of this study are to obtain the miRNA expression files in dairy goat mammary gland at early lactation (10th day after parturition) and early involution (5th day after forced weaning at late lactation, 218 day after parturition).

overall_design: RNA were extracted respectively from five dairy goats in early lactation and early involution using TRIzol reagent and were equivalent mixed into a pool from the same stage. miRNA profiles of eary lacation and early involution in dairy goat mammary gland tissues were generated by deep sequencing using Illumina/Solex seqing technology.

first: Zhibin


title: mRNA profile of dG9a-depleted adult Drosophila melanogaster under starvation

city: matsugasakihashigami tyo

first: Kohei

last: Shimaji

department: Applied biology

country: Japan

institute: Kyoto Institute of Technology

summary: dG9a-depletion decreases the starvation resistance in the adult stage of Drosophila melanogaster. To determine which genes are regulated by dG9a under starvation stress, we examined mRNA levels by performing RNA-sequence analysis using 0 h and 12  h starved dG9a null mutant and wild type as a control.

overall_design: mRNA profiles of 0 h and 12 h starved wild type (CantonS) and dG9a-depleted (dG9aRG5) strain

first: Kouhei

first: Yasuyuki

last: Ohkawa

first: Tetsuya

last: Sato

first: Mikita

last: Suyama

first: Masamitsu

last: Yamaguchi


title: The role of PRMT5/WDR77 complex in promoting breast cancer oncogenesis [RNA-Seq]

city: New York

first: Martin

middle: J.

last: Walsh

state: NY

address: One Gustave L. Levy Pl.

department: Structural and Chemical Biology

institute: Mount Sinai School of Medicine

summary: Comprehensive RNA-seq experiments in control and PRMT5 and WDR77 shRNA infected cells delineate the role of PRMT5/WDR77 complex in promoting breast cancer oncogenesis

overall_design: RNA-seq was used to measure gene expression levels in scrambled control, PRMT5 and WDR77 short hairpin RNA (shRNA) infected human breast cancer cells

first: Madhumitha

last: Rengasamy

first: Fan

last: Zhang

first: Weijia

middle: J


title: T47D xenografts treated with various combinations of ER- and PR-targeting therapies

city: Chicago

first: Hari

last: Singhal

state: IL

address: 929 E 57th St

department: Ben May Department for Cancer Research

institute: University of Chicago

summary: Major roadblocks to developing effective progesterone receptor (PR)-targeted therapies in breast cancer include the lack of highly-specific PR modulators, a poor understanding of the pro- or anti-tumorigenic networks for PR isoforms and ligands, and an incomplete understanding of the cross talk between PR and estrogen receptor (ER) signaling. Through genomic analyses of xenografts treated with various clinically-relevant ER and PR-targeting drugs, we describe how the activation or inhibition of PR differentially reprograms estrogen signaling, resulting in the segregation of transcriptomes into separate PR agonist and antagonist-mediated groups. These findings address an ongoing controversy regarding the clinical utility of PR agonists and antagonists, alone or in combination with tamoxifen, for breast cancer management. Additionally, the two PR isoforms PRA and PRB, bind distinct genomic sites and interact with different sets of co-regulators to differentially modulate estrogen signaling to be either pro- or anti-tumorigenic. Of the two isoforms, PRA inhibited gene expression and ER chromatin binding significantly more than PRB. Differential gene expression was observed in PRA and PRB-rich patient tumors and importantly, PRA-rich gene signatures had poorer survival outcomes. In support of antiprogestin responsiveness of PRA-rich tumors, gene signatures associated with PR antagonists, but not PR agonists, predicted better survival outcomes. This better patient survival associated with PR antagonists versus PR agonists treatments was further reflected in the higher anti-tumor activity of combination therapies of tamoxifen with PR antagonists and modulators. The study suggests that distinguishing common effects observed due to concomitant interaction of another receptor with its ligand (agonist or antagonist) from unique isoform and ligand-specific effects will guide the development of biomarkers for patient selection and translation of PR-targeted therapies to the clinic.

overall_design: For the xenograft studies involving PR agonists (progesterone, MPA and R5020), PR antagonists (CDB4124, CDB4453 and EC313) and SERMs (tamoxifen, raloxifene, bazedoxifene and fulvestrant), mice harboring T47D xenografts were injected intra-peritoneal for three weeks with 10 mg/kg/day of the respective drugs. Five injections per week were administered. At the end of the duration of the experiment, mice were sacrificed; tumors were excised, weighed, fixed and snap-frozen for later analyses. RNA-seq was performed on these harvested xenografts.


title: Transcriptome-Based Network Analysis on Gene Expression Regulated by CO2 Deprivation in Chlorella pyrenoidosa

city: Shanghai

first: Jianhua

last: Fan

address: 130 Meilong Road

institute: East China University of Science & Technology

summary: The understanding of molecular events occurring in green alga during CO2 deprivation, are still largely unknown. To well grasp its cellular metabolism, particularly the regulation of biosynthesis and degradation pathways of lipid, protein and carbohydrates, as well as the diverse trophic adaptation affecting carbon partitioning during the transition process, we sequenced the transcriptome (RNA-seq) in four time points to discover how transcriptional changes in C. pyrenoidosa modulate metabolic flux trends leading to intracellular components dynamic reassortment.

overall_design: Two independent biological experiments (biological replicates) were carried out in the same batch. In total, eight samples collected at four time points (0-, 1-, 4, 24-h from CO2 deprivation process were used for mRNA-Seq library preparation and then submitted to HiSeq 2000 (Illumina, USA) for sequencing.

first: Hui

last: Xu


title: The role of PRMT5/WDR77 complex in promoting breast cancer oncogenesis [RNA-Seq_HPTB]

summary: Comprehensive RNA-seq experiments in DMSO and HPTB (inhibitor of PRMT5) treated cells delineate the role of PRMT5 complex in promoting breast cancer oncogenesis

overall_design: RNA-seq was used to measure gene expression levels in DMSO and HPTB (inhibitor of PRMT5) treated human breast cancer cells


title: DNA methylation profile for male SD rats treated with high fat diet (HFD) and DNA methyltransferase (DNMT) inhibitor 5-aza-2′-deoxycytidine (5-AzaD) by RRBS

first: Xia

last: Yang

address: 2000 Terasaki Life Sciences Bldg, 610 Charles E. Young Drive East

department: IBP

institute: UCLA

summary: To investigate the effects of HFD on affecting the DNA methylation, as well as the methylation inhibitor 5-AzaD reversing such effects in the frontal cortex of male SD rats by sequencing the methylome (RRBS).

overall_design: Male Sprague–Dawley (SD) rats of 11 weeks old were randomly assigned to (1) chow diet or HFD group, where they received the respective diet for 7 weeks. Among these, the HFD group was further split into (2) HFD only, (3) HFv (10 days i.p. injection of PBS vehicle in addition to high fat diet) and (4) In (10 days i.p. injection of 5-AzaD in PBS in addition to high fat diet). Thus, in total there were 4 groups in the study.   At the end of study, the rats were sacrificed by decapitation. Frontal cortex were dissected out, flash frozen, and stored at -70°C for later transcriptome and DNA methylome sequencing experiments. All experiments were performed in accordance with the United States National Institutes of Health Guide for the Care and Use of Laboratory Animals and were approved by the University of California at Los Angeles Chancellor’s Animal Research Committee.

first: Qingying

last: Meng

first: Fernando

last: Gomez-Pinilla


title: The role of PRMT5/WDR77 complex in promoting breast cancer oncogenesis

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

overall_design: Refer to individual Series


title: The role of PRMT5/WDR77 complex in promoting breast cancer oncogenesis [ChIP-Seq]

summary: The PRMT5/WDR77 complex is known to regulate alternative splicing through the symmetric dimethylation of spliceosome proteins in the cytoplasm. Overexpression of this complex is observed in different types of cancer including breast cancer, where it shows increased nuclear accumulation.To understand the nuclear role and the chromatin binding properties of PRMT5 we performed genome-wide ChIP-Seq analysis in the breast cancer cell line MDA-MB-231.

overall_design: Analysis of genome-wide binding of PRMT5 by chromatin immunoprecipitation followed by high throughput sequencing in MDA-MB-231 cells


title: Genome-wide changes in DNase-hypersensitivity during osteoblastogenesis reveal differential usage of DNA motifs and define novel cis-regulatory regions that control gene expression during differentiation [ChIP-Seq]

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

summary: Gene regulation during the process of osteoblastogenesis has been well-described, yet the discovery of novel regulatory regions has been limited by how we currently predict the locations of functional cis-regulatory modules.  Historically, the de novo identification of sequences critical for the control of gene expression relied primarily on sequence conservation in promoters.  Queries for binding motifs were based on position weight matrices of known transcription factors and the identification of disease-causing, non-coding mutations near critical genes.  However, we now must consider that regulatory elements also rely on 3-dimensional chromosomal interactions between far-distal regions, epigenetic chromosomal modifications, and RNA:DNA interactions.  Traditionally, DNaseI-hypersensitivity assays have been used for the identification of regulatory regions via preferential digestion at chromatin depleted or displaced of nucleosomes, as a result of transcription factor occupancy.  We probed DNase hypersensitivity on a genome-wide scale to determine whether osteogenic differentiation and/or bone-related gene regulation is marked by the presence of commonly utilized DNA motifs within active cis-regulatory modules.  We thus sought to evaluate the gain or loss of motif representation within hypersensitive regions during osteoblastogenesis, from day-0 (growth-phase) to day-28 (mineralizing) MC3T3 cultures.  We find that differentiation is marked by an increased enrichment of NFkB-p65, MEF2, and bHLH/E-box motifs within hypersensitive regions, while CTCF, NF1, TEAD, and AP1 motifs decrease.  Furthermore, grouping hypersensitive regions based on genomic positioning (promoters, introns, exons, and far-distal regions) reveals significant differences in motif abundance in first introns versus other genomic positions.  This finding suggests that the regulation conferred within first intron sequences may be somewhat distinct.  Interestingly, the majority of motifs that were enriched, regardless of genomic position or differentiation time-point, were not completely matched to currently known transcription factor motifs (curated in the JASPAR database).  Taken together, the changes in DNase-hypersensitive regions during osteoblastogenesis and the enrichment of distinct motifs within these regions indicate that osteoblasts utilize unique sets of motif rules for transcription factor binding or that regulatory control operates through undiscovered factors.

overall_design: To identiy the genome-wide occupancy of Ctcf, DNA bound by Ctcf at the prolieration, matrix deposition, and mineralization stages were recovered by Ctcf ChIP. Libraries of purified DNA were generated using Illumina SR adapters (Illumina) following manufacturer’s manual, and were selected for the inserted fragments of 200 ± 50 bp, and sequenced 36 bases on an Illumina Genome Analyzer II. Base calls and sequence reads were generated by Illumina CASAVA software (version 1.6, Illumina). Two independent biological repeats of Ctcf ChIP-Seq libraries were prepared for each time point, and two Input libraries were prepared with sonicated DNA from day 9 MC3T3-E1 cells.

first: Hai

last: Wu

first: Phillip

middle: W

last: Tai

first: Troy

last: Whitfield

first: Andre

last: van Wijnen

first: Janet

last: Stein

first: Gary

first: Jane

middle: B

last: Lian


title: Male SD rats treated with high fat diet (HFD) and DNA methyltransferase (DNMT) inhibitor 5-aza-2'-deoxycytidine (5-AzaD)


title: Gene expression profile for male SD rats treated with high fat diet (HFD) and DNA methyltransferase (DNMT) inhibitor 5-aza-2′-deoxycytidine (5-AzaD) by RNA-Seq

summary: To investigate the effects of HFD on affecting the gene expressions, as well as the methylation inhibitor 5-AzaD reversing such effects in the frontal cortex of male SD rats by RNA-Seq.


title: Identification of p66Shc promoter interactional DNA fragments using Circularized Chromosome Conformation Capture coupled with next-generation sequencing (4C-seq)

status: Public on Dec 30 2017

city: Tianjin

first: Zhe

last: Liu

address: Heping District Qixiangtai Road No. 22

institute: Tianjin Medical University

summary: p66Shc is encoded by the SHC1 gene, which contains two tandem promoters that generate three proteins (p46, p52 and p66). More recently, p66Shc was found to localize to focal adhesions that reports cell attachment and is required for anoikis through a RhoA-dependent mechanosensory test (Ma et al., J Cell Biol, 179, 23-31). Consistent with its role in anoikis, p66Shc is expressed in normal epithelial and endothelial cells but not in hematopoietic cells that survive in unanchored conditions. To uncover the epigenetic regulation mechanisms of p66Shc expression, here we performed 4C-seq assays with p66Shc promoter as a bait in HUVEC and U937 cells. Our results identify different p66Shc promoter interactional DNA fragments in different cell types.

overall_design: 4C-seq analysis of p66Shc promoter with putative interactional DNA fragments in HUVEC and U937 cells.

first: Xichuan

last: Li

first: Zhenzhen

last: Lin


title: Investigating the Regulation of Hypopharyngeal Gland Activity in Honeybees Undergoing Harsh Winter Conditions through RNA-seq Transcriptomics Combined with iTRAQ-based Comparative Proteomics

city: Yangzhou

first: Zhenguo

address: 88 South University Ave.

institute: Yangzhou University

summary: The honeybee model organism, Apis mellifera carnica, is a hymenopteran with a remarkable ability to withstand cold winters by instinctively entering into hibernation in the hive. Hibernation is characterized by a significant reduction in the metabolic rate, triggered by a drop in the ambient temperature and a shortage of reserves. It provides a token cue that initiates an alternative developmental program that leads to dormancy and switches social behaviors. The age-dependent changes in the generic proteins and substance composition of royal jelly (RJ) have been well documented. However, the molecular mechanism of RJ secretion and the biological consequences of regulation by the hypopharyngeal gland (HG) according to the season remain to be addressed. In this study, large-scale transcriptomic and proteomic approaches were used to detect statistically significant changes in the honeybee proteome and to explore the mechanistic basis for the HG regulation that accompanies hibernation in the winter and arousal in the spring. HG activity was associated with hundreds of gene and protein expression changes in the winter-spring cycle. A systematic study of HG activity and secretion identified 21,441 genes and 2,156 proteins at three time points (i.e., A, winter bees; B, spring bees; and C, retired bees). Of these, 737 genes and 698 proteins were qualified and compared to reveal differential expression patterns, including 197 up-regulated and 291 down-regulated DEGs in group A vs. B, 118 up-regulated and 259 down-regulated DEGs in group A vs. C, and 106 up-regulated and 53 down-regulated DEGs in group B vs. C, respectively. The results were validated by qPCR.Honeybee HG activity was associated with multiple genes regulation.The results present the first global pictures of the regulation of HG activity in winter bee.

overall_design: The 3 samples at given time (A,winter bee; B,spring bee; and C, retired bee) are collected to reveal the mechanism of the regulation of HG activity and RJ secretion, the differentially expressed genes involved in the Metabolic process and protein processing in endoplasmic reticulum related DEGs were identified and the shifts appeared to show dormancy-induced transcriptional changes across the winter. 30 pooled heads of each samples were pooled as one biologiacl repeat.

first: Ting

last: Ji

first: Jie

last: Shen

first: Fang

first: Qin

last: Liang

first: Liming

first: Guohong

last: Chen


title: PR isoform-specific ER and PR chromatin binding and gene expression observed in-vitro in breast cancer cells.

first: Hari

last: Singhal

summary: Major roadblocks to developing effective progesterone receptor (PR)-targeted therapies in breast cancer include the lack of highly-specific PR modulators, a poor understanding of the pro- or anti-tumorigenic networks for PR isoforms and ligands, and an incomplete understanding of the cross talk between PR and estrogen receptor (ER) signaling. Through genomic analyses of xenografts treated with various clinically-relevant ER and PR-targeting drugs, we describe how the activation or inhibition of PR dictates distinct ER and PR chromatin binding and differentially reprograms estrogen signaling, resulting in the segregation of transcriptomes into separate PR agonist and antagonist-mediated groups. These findings address an ongoing controversy regarding the clinical utility of PR agonists and antagonists, alone or in combination with tamoxifen, for breast cancer management. Genomic analyses of the two PR isoforms, PRA and PRB, indicate that these isoforms bind distinct genomic sites and interact with different sets of co-regulators to differentially modulate gene expression as well as pro- or anti-tumorigenic phenotypes. Of the two isoforms, PRA inhibited gene expression and ER chromatin binding significantly more than PRB. Of note, the two isoforms reprogrammed estrogen activity to be either pro or anti-tumorigenic. In concordance to the in-vitro observations, differential gene expression was observed in PRA and PRB-rich patient tumors and importantly, PRA-rich gene signatures had poorer survival outcomes. In support of antiprogestin responsiveness of PRA-rich tumors, gene signatures associated with PR antagonists, but not PR agonists, predicted better survival outcomes. This differential of better patient survival associated with PR antagonists versus PR agonists treatments was further reflected in the higher anti-tumor activity of combination therapies of tamoxifen with PR antagonists and modulators. Knowledge of various determinants of PR action and their interactions with estrogen signaling to differentially modulate breast cancer biology should serve as a guide to the development of biomarkers for patient selection and translation of PR-targeted therapies to the clinic.

overall_design: For in-vitro experiments, cells were grown in steroid-deprived RPMI for 48 hours to 80% confluence, before being treated for with the hormones of interest (vehicle, 10 nM estrogen, 10 nM R5020 or both estrogen +R5020). Cells were then fixed with 1% formaldehyde for 10 minutes and the crosslinking was quenched with 0.125 M glycine for 5 minutes. Fixed cells were suspended in ChIP lysis buffer (1 ml 1M Tris pH 8.0; 200 µl 5M NaCl; 1 ml 0.5M EDTA; 1 ml NP-40; 1 g SDS, 0.5 g deoxycholate) and sheared in the Diagenode Biorupter for 20 minutes (30 second cycles). 100 µl of sheared chromatin was removed as input control.  A 1:10 dilution of sheared chromatin in ChIP dilution buffer (1.7 ml 1M Tris pH 8.0; 3.3 ml 5M NaCl; 5 ml 10% NP-40; 200 µl 10% SDS; to 100 ml with H2O), 4 µg antibody and 30 µl magnetic DynaBeads were incubated in a rotator at 4oC overnight. Chromatin was immunoprecipitated overnight using anti-ER (Santa Cruz Biotechnology HC-20), anti-PR (in-house made KD68) or rabbit IgG (Santa Cruz Biotechnology SC-2027). Next, the immunoprecipitated chromatin was washed with ChIP wash buffer I (2 ml 1M Tris pH 8.0; 3 ml 5M NaCl; 400 µl 0.5M EDTA; 10 ml 10% NP-40; 1 ml 10% SDS; to 100 ml with H2O), ChIP wash buffer II (2 ml 1M Tris pH 8.0; 10 ml 5M NaCl; 400 µl 0.5M EDTA; 10 ml 10% NP-40; 1 ml 10% SDS; to 100 ml with H2O), ChIP wash buffer III (1 ml 1M Tris pH 8.0; 5 ml of 5M LiCl; 200 µl 0.5M EDTA; 10 ml 10% NP-40; 10 ml 10% deoxycholate; to 100 ml with H2O) and TE (pH 8.0). Elution was performed twice from beads by incubating them with 100 µl ChIP-elution buffer (1% SDS, 0.1 M NaHCO3) at 65oC for 15 minutes each. The eluted protein-DNA complexes were de-crosslinked overnight at 65oC in 200 µM NaCl. After de-crosslinking, the mixture was treated with proteinase K for 45 minutes followed by incubation with RNase A for 30 minutes. Finally, DNA fragments were purified using Qiagen PCR purification kit and reconstituted in 50 µl nuclear-free water. Real time PCR was performed using SYBR green.  For ChIP-seq library preparations, libraries were prepared using KapaBiosystems LTP library preparation kit (#KK8232) according to the manufacturer’s protocol.

first: Geoffrey

last: Greene


title: Transcriptome analysis of buckwheat seed developmental

city: Hefei

first: cong

middle: bing

last: fang

state: Anhui

address: No. 130 Changjiang West Road

department: School of Horticulture

institute: Anhui Agricultural University

summary: Combining the Solexa/ Illumina RNA-seq high-throughput sequencing approach with Digital Gene Expression (DGE) analysis results in a powerful transcriptomic study. This publication reports the transcriptome profiling analysis of Fagopyrum esculentum Moench. using RNA-seq and DGE in order to better understand the molecular mechanisms underlying biological aspects of buckwheat, especially seed development and maturation.

overall_design: 5 samples examined: buckwheat seed developmental stage 1(ss1), buckwheat seed developmental stage 2(ss2), buckwheat seed developmental stage 3(ss3), buckwheat seed developmental stage4(ss4), buckwheat seed developmental stage 5(ss5).

first: Congbing

last: Fang


title: Global mRNA expression profile in cardiac progenitor cells generated by ISX-9

city: Tampa

first: Wanling

last: xuan

state: FL

address: 12901 Bruce B Down Blvd

department: DPS

institute: University of South Florida

summary: We developed a strategy to generate cardiac progenitor cells from human induced pluripotent stem cells using a novel small molecule. mRNA-sequencing results showed different gene expression profile among undifferentiated  human induced pluripotent stem cells(hiPSCs), DMSO and ISX-9 treated hiPSCs.In comparsion with DMSO treated cells or undifferentiated hiPSCs, ISX-9 upregulated the genes related to WNT and cytoskeleton remodeling and TGF-β signaling, which are involved in heart development and cardiac differentiation. In addition, the genes related to cardiac differentiation signaling pathways were upregulated by ISX-9 including development of PIP3 signaling in cardiomyocyte myocytes, muscle contraction and NF-AT hypertrophy signaling.

overall_design: Examination of global mRNA expression profile in  undifferentiated hiPSCs, and monolayer hiPSCs treated with ISX-9 or DMSO(n=4).

last: Xuan

first: Muhammad

last: Ashraf


title: Global miRNA expression profile in cardiac progenitor cells generated by ISX-9

summary: We developed a strategy to generate cardiac progenitor cells from human induced pluripotent stem cells using a novel small molecule.miRNA-sequencing results showed different miRNA expression profile among undifferentiated  human induced pluripotent stem cells(hiPSCs), DMSO and ISX-9 treated hiPSCs.In comparsion with DMSO treated cells, ISX-9 upregulated several myogenic miRNAs and cardiac hypertrophy related-miRNAs including miR-335, miR-21, miR-30c,miRNA-181a and miR-214.

overall_design: Examination of global miRNA expression profile in  undifferentiated hiPSCs, and monolayer hiPSCs treated with ISX-9 or DMSO(n=4).


title: Methylomes of wild-type and MeCP2 knockout brain cells

city: Cambridge

first: Rahul

last: Karnik

address: 419 Broadway

summary: By performing whole genome methylome analysis in MeCP2 knock-out mice brain, we identify both hypo- and hypermethylated regions overlapping with MeCP2 binding sites. Hypermethylation was mainly observed at CpG promoters, suggesting that MeCP2 contributes to the protection of these regions from methylation in brain.

overall_design: Whole genome bisulfite sequencing profiles were generated for wild type and MeCP2 KO cells, 1 replicate each.

first: Alex

last: Meissner

first: Albert

last: Jeltsch


title: Social status alters immune regulation and response to infection [PBMC_ATACseq]

city: Tempe

first: Noah

last: Snyder-Mackler

state: AZ

address: 427 East Tyler Mall

institute: Arizona State University

summary:
Social status is one of the strongest predictors of disease risk and mortality in humans, and often influences Darwinian fitness in social mammals more generally. To understand the biological basis of these effects, we combined a functional genomics approach with sequential social status manipulations in rhesus macaques to investigate how social status alters immune function. We demonstrate causal, but largely plastic, effects of social status on immune cell proportions, cell type-specific gene expression levels, and the gene expression and cytokine response to infection. Further, we identify specific transcription factor signaling pathways that explain these differences, particularly status-associated polarization of the TLR4 signaling pathway towards pro-inflammatory versus anti-viral responses. Our findings provide an unprecedented level of insight into the direct biological effects of social inequality on immune function, thus contributing to an improved understanding of social gradients in health and the evolution of social hierarchies.
For social status, please refer to table S1 in the manuscript.

overall_design: ATAC-seq of PBMCs from 3 female rhesus macaques

first: Jenny

last: Tung


title: Production of Red Flower Rapeseed by Ectopic Expression of OvPAP2 Identified in Brassica napus-Orychophragmus violaceus Addition Line by Comparative Transcriptome Analysis

city: Wuhan

first: wenqin

last: fu

state: Hubei

address: No.1,Shizishan Street

department: College of Plant Science and Technology

institute: Huazhong Agricultural University

summary: Oilseed rape is both an important oleaginous crop and agriculture sightseeing crop whereas has relatively scanty flower color. As natural ﬂavonoids, Anthocyanin are responsible for the attractive red, purple, and blue colors of various tissues in higher plants, especially for the ornamental plants flower. One Brassica napus-Orychophragmus violaceus disomic addition line (M4) obtained previously exhibits red petals whichresult from anthocyanin biosynthesis. Transcriptome analysis of M4, B. napus (H3), natural individuals of O. violaceus with purple petals (OvP) and white petals (OvW) revealed that most of structural genes for the anthocyanin synthesis were up-regulated in both M4 and OvP, especially key gene ANS in the last step. Reads assembling and sequence alignment showed that the regulatory DEG PAP2 in M4 was from the transcript of O. violaceus. OvPAP2 was transformed into Arabidopsis thaliana and B. napus driven by the CaMV35S promoter and the rape petal-specific prompter XY355. Transgenic A. thaliana plants showed different levels of purple pigments in most of the organs, including the petals, and transgenic B. napus flowers exhibited restricted accumulation of anthocyanins in stamens when driven by CaMV35S promoter, but generated both red petals and anthers driven by the XY355 promoter. These results provided a platform for expounding the anthocyanin biosynthesis pathway in B. napus petals and give a successful case for flower color modification of the agriculture sightseeing rape.

sample_organism:
Brassica napus
Orychophragmus violaceus

platform_organism:
Brassica napus
Orychophragmus violaceus

overall_design: The petals on half-open flowers were collected in liquid nitrogen from four samples：The disomic addition line with red petals (designated as M4), donor B. napus cv. Huashuang 3 (designated as H3), the wild type O. violaceus with purple petals (designated as OvP) and it’s natural mutant with white petals (designated as OvW) , respectively, and kept at -80°C. Total RNA from the four samples were extracted and sequencing was performed using Illumina HiSeq 2000.

first: Wen-qin

last: Fu

first: Dao-zong

first: Qi

last: Pan

first: Feng-feng

last: Li

first: Zhi-gang

last: Zhao

first: Xian-hong

last: Ge

first: Zai-yun


title: Global expression profiles in cardiac progenitor cells generated by ISX-9


title: Mosquito hematophage-mediated GABAergic activation facilitates acquisition of mosquito-borne viruses (infection)

city: Beijing

first: Yibin

last: Zhu

address: Biotechnology building

department: School of Medicine

institute: Tsinghua University

summary: Gene regulation by infection flavivirus, alphavirus and orthobunyavirus in Aedes aegypti

overall_design: Mosquitoes were microinjected with 100 M.I.D.50 viruses, respectively, extracted total RNA at day1 and day6

first: Rudian

last: Zhang


title: Mosquito hematophage-mediated GABAergic activation facilitates acquisition of mosquito-borne viruses (dsRNA knocked-down)

summary: Two independent dsRNAs to knocked-down the AaGABAA-R1 gene in A. aegypti

overall_design: Total RNA was extracted with TRIzol  from the GFP dsRNA and AaGABAA R1 dsRNAs inoculated mosquitoes on 3 days post dsRNA treatment


title: Cell type-specific regulation by intragenic CpG islands

city: Seoul

first: Jungwoo

last: Lee

address: 50 Yonsei-ro Seodaemun-gu

country: South Korea

institute: Yonsei University


title: Nucleosome locations in human oral keratinocytes

city: Camperdown

first: Guy

last: Lyons

state: NSW

address: Room W350 Blackburn Bldg D06

department: Dermatology

institute: University of Sydney

summary: Miccrococcal nuclease sequencing (MNase-seq) of chromatin from control and Snail2-expressing oral keratinocytes

overall_design: MNase-seq was performed on sub-confluent HN13(TVA) cells that stably expressed either Snail2-Cerulean (Snail2) or EYFP (Control). Two biological replicates of each were analyzed.

first: J

middle: G

first: Naomi

last: Delic


title: Cell type-specific regulation by intragenic CpG islands [RNA-seq]

summary: We wanted to emphisize the role of intragenic CpG island in various cell differentiation. We especially examined the effect of DNA methyltransferase (DNMT) in the neural differentiation from mouse ES cell. Therefore, we performed the transcriptome analysis of mouse ES cell, ESC-derived NPC, and also in DNMT double knockout (DKO) conditions. By utilizing these result, we confirmed the genes regulated by intragenic CpG island methylation have effect in NPC differentation.

overall_design: 4 RNA-seq data from mouse ES cell, mouse ES cell-derived NPC, DNMT3A/B DKO mouse ES cell, and DNMT3A/B DKO mouse ES cell-derived NPC

first: Sun-Min

first: Kyung-Min

last: Noh


title: Cell type-specific regulation by intragenic CpG islands [WGBS]

summary: We wanted to emphisize the role of intragenic CpG island in various cell differentiation. We especially examined the effect of DNA methyltransferase (DNMT) in the neural differentiation from mouse ES cell. Therefore, we performed the Whole-Genome Bisulfite Sequencing (WGBS) analysis of mouse ES cell, ESC-derived NPC, and also in DNMT double knockout (DKO) conditions. By utilizing these result, we confirmed the genes regulated by intragenic CpG island methylation have effect in NPC differentation.

overall_design: 4 WGBS data from mouse ES cell, mouse ES cell-derived NPC, DNMT3A/B DKO mouse ES cell, and DNMT3A/B DKO mouse ES cell-derived NPC


title: Genome-wide maps of chromatin state in human primary airway smooth muscle cells.

city: London

first: Paul

last: Lavender

address: 5th Floor, Tower Wing, Great Maze Pond

department: School of Immunology and Microbial Sciences

country: United Kingdom

institute: King's College London

summary: We generated genome-wide chromatin-state maps of human airway smooth  muscle cells. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed,  Lysine 4 monomethylation was used to highlight the location of potential regulatory domains in these cells.

overall_design: Examination of 3 different histone modifications in primary human cells.

first: Venu

last: Pullabhatla


title: RNAseq of ground state mouse embryonic stem cells.

first: Bo

last: Wen

address: 130 DongAn Road

department: Institutes of Biomedical Sciences

institute: Fudan University

summary: lncRNA profiles of ground state mouse embryonic stem cells cultured in 2i condition.

overall_design: lncRNA profiles of ground state mouse embryonic stem cells were generated by deep sequencing, in duplicate, using Illumina HiSeq 3000. The sequence reads that passed quality filters were analyzed at the gene level by Tophat and Cufflinks.

first: Pin

last: Lv


title: Low affinity TCRs support regulatory T cell function in autoimmunity

status: Public on Dec 29 2017

city: Houston

first: Maria

last: Bettini

state: TX

address: 1102 Bates St

institute: Baylor College of Medicine

summary: Low affinity Tregs are important for controlling autoimmune diabetes.

overall_design: High and low affinity Tregs were isolated from the spleen and pancreatic islets of two-TCR retrogenic mice expressing the insulin-specific TCRs 4-8 and 12-4.4m1.

first: Mara

last: Sprouse

first: Marissa

middle: A

last: Scavuzzo

first: Malgorzata

last: Borowiak


title: miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2

status: Public on Dec 28 2017

first: Rasmus

last: Moeller

address: 1 Gustave L. Levy Place

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

summary: We introduce target sites for the microRNA (miRNA) miR-142 into the 3’-untranslated region of the human cytomegalovirus (HCMV) IE2 to study the transcriptional effect of IE2 knock-down on both viral and host genes in cells that express miR-142. When comparing transcriptional data from miR-142 expressing macrophages infected with HCMV to macrophages infected with IE2-miR-142 targeted HCMV, we see a knock-down of IE2 and differential regulation of predicted viral targets of IE2 including IE1, vIL-10 and US29. We then generated fibroblasts expressing miR-142 to study the knock-down of IE2 in a different cellular system and find drastic differences in loss of IE2 on the host transcriptional profile in the two different cell types.

overall_design: BW series: Fibroblasts (MRC-5) and macrophages (THP-1) infected with HCMV and miR-142 targeted HCMV for 24h to see immediate effect of IE2-knock down. CK series: Fibroblasts and macrophages infected with HCMV and miR-142 targeted HCMV for 9 days done in duplicate. EX series: miR-142 expressing fibroblasts infected with HCMV and miR-142 targeted HCMV for 9 days done in duplicate.

last: Møller

first: Maryline

last: Panis

first: Domenico

last: Tortorella

first: Benjamin

middle: R

last: tenOever


title: Mosquito hematophage-mediated GABAergic activation facilitates acquisition of mosquito-borne viruses

first: Yibin

last: Zhu

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

overall_design: Refer to individual Series


title: Tyrosine-1 of RNAPII CTD controls global termination of gene transcription in mammals

city: Macclesfield

first: Muhammad

middle: Ahmad

last: Maqbool

address: Alderley Park

department: Cancer Research UK Manchester Institut

institute: University of Manchester

summary: The carboxy-terminal domain (CTD) of RNA polymerase (Pol) II is composed of a repetition of YSPTSPS heptads and functions as a loading platform for protein complexes that regulate transcription, splicing and maturation of RNAs. Here, we studied mammalian CTD mutants to analyze the function of tyrosine1 residues in the transcription cycle. Mutation of 3/4 of the tyrosine residues (YFFF mutant) resulted in a massive read-through transcription phenotype in antisense direction of promoters as well as in 3' direction several hundred kb downstream of genes. The YFFF mutant shows reduced Pol II at promoter-proximal pause sites, a loss of interaction with the Mediator and Integrator complexes and impaired recruitment of these complexes to chromatin. Consistent with these observations, Pol II loading at enhancers and maturation of snRNAs are altered in the YFFF context genome wide. We conclude that tyrosine1 residues of the CTD control termination of transcription by Pol II.

overall_design: This study was performed in a human Raji cell line. It contains ChIP-seq data for RNA Pol II, H3K4me1, H3K4me3, H3K27ac, RNA-seq data for Total RNA, polyA-RNA, nascent RNA and MNase-seq data. All sequencing were performed in paired-end sequencing runs, 4 replicates for the input genomic DNA.

first: Nilay

last: Shah

first: Yousra

last: Yahia

first: Amal

last: Makrini

first: Ignasi

last: Forné

first: Tim-Michael

last: Decker

first: David

last: Martin

first: Roland

last: Schüller

first: Stefan

last: Krebs

first: Helmut

last: Blum

first: Axel

last: Imhof

first: Dirk

last: Eick

first: Jean-Christophe

last: Andrau


title: The C. elegans transcriptome is regulated by environmental and developmental history

status: Public on Dec 27 2017

city: Syracuse

first: Maria

last: Ow

address: 107 College Place

department: Biology

institute: Syracuse University

summary: We show that C. elegans adults that passed through the stress-resistant dauer stage due to starvation exhibit opposite transcriptional profiles compared to adults that entered dauer due to crowding, and are distinct from animals that bypassed dauer. These “seesaw” trends in gene expression extend to a majority of genes in the genome and, based upon the direction of change, are enriched on different chromosomes.

overall_design: mRNA-seq was performed on the Illumina platform to measure gene expression in wild-type N2 and WM193 csr-1(tm892); neIs20 [(pie-1::3xFLAG::csr-1 + unc-119(+)] adults (24 hours post-L4 stage) that had continously developed (CON) or transiently passed through the dauer stage (PD). The PD samples experienced either starvation or high pheromone (crowding) dauer-inducing conditions.

first: Sarah

middle: E

last: Hall

middle: C


title: Effect of RBP2 on MCF7 breast cancer cells (RNA-seq)

first: Hee-Joo

last: Choi

address: 222 Yangshimri-ro, Seongdonggu

institute: Hanyang University

summary: RNA-sequencing analysis of RBP2 overexpressing MCF7 cell lines. RBP2 (also known as JARID1A), a member of the JARID1 family of histone H3 lysine K4 demethylases, has been considered to have an oncogenic potential in several cancer including breast cancer. Results provide insight into the transcriptional regulation of RBP2 in estrogen receptor positve breast cancer.

overall_design: MCF7 cells stably infected with lentiviruses encoding either control (pLVX vector) or RBP2 (pLVX-RBP2) were cultured in phenol-red free DMEM containt 10% FBS for 48h. Total RNA was isolated from the cultures using Trizol reagent. For each of the 2 conditions, 3 biological replicates were included. In total, 6 RNA-sequencin samples were analyzed; 3 controls and 3 RBP2 overexpressing cells.

first: Gu

last: Kong


title: Genome sequences of Chlorella sorokiniana UTEX 1602 and Micractinium conductrix SAG 241.80: implications to maltose excretion by a green alga

city: Saint Paul

first: Brett

last: Barney

state: MN

address: 1500 Gortner Avenue

department: Bioproducts and Biosystems Engineering

institute: University of Minnesota

summary: Micractinium conductrix SAG 241.80 secretes sugars (especially maltose) at pH 5.7 while very little sugar is found at pH 7.6. Another algae, Chlorella sorokiniana does not secrete sugars at either pH. We evaluated the transcriptional profiles of both species of algae at pH 5.7 and 7.6 to make comparisons in the regulation of potential genes involved in these pathways.

sample_organism:
Chlorella sorokiniana
Micractinium conductrix

overall_design: Micractinium conductrix was grown in modified freshwater SAG medium and Chlorella sorokiniana was grown in a modified freshwater medium and both were grown at both pH 5.7 and pH 7.6. All samples were harvested at similar times and total RNA was extracted. Libraries were constructed and sequenced using HiSeq 2500 Illumina sequencing technique.

first: Matthew

last: Arriola

first: Natarajan

last: Velmurugan

first: Mary

middle: H

last: Plunkett

first: Hanna

last: Hondzo

first: Ying

last: Zhang


title: Maturation of hematopoietic stem cells from pre-hematopoietic stem cells is accompanied by upregulation of programmed death ligand 1

status: Public on Dec 26 2017

city: Philadelphia

first: Long

last: Gao

state: PA

address: 4002 Colket Translational Research Building (CTRB) 3501 Civic Center Boulevard

institute: The Children’s Hospital of Philadelphia

summary: Hematopoietic stem cells (HSCs) in the fetal liver mature from pre-HSCs that originate in the major arteries of the embryo. To generate HSCs from other cell sources it will be necessary to reproduce the maturation of HSCs from pre-HSCs ex vivo. We refined the markers used to purify pre-HSCs and HSCs matured ex vivo, and compared the transcriptomes of pre-HSCs, ex vivo matured HSCs, and fetal liver HSCs. We found that maturation of pre-HSCs into HSCs in vivo or ex vivo is accompanied by the downregulation of genes involved in embryonic development and vasculogenesis, and upregulation of genes involved in hematopoietic organ development, lymphoid development, and immune responses. Ex vivo matured HSCs more closely resemble fetal liver HSCs than pre-HSCs, but are not their molecular equivalents. We show that functional ex vivo-matured and fetal liver HSCs increase the expression of programmed death ligand 1 (PD-L1). PD-L1 does not mark all pre-HSCs, but cell surface PD-L1 was present on functional HSCs after ex vivo culture. PD-L1 signaling, however, is not required for engraftment of embryonic HSCs. Hence, up-regulation of PD-L1 is a correlate of, but not a requirement for HSC maturation.

overall_design: Cells were sorted into Trizol-LS. Total RNA was prepared using RNeasy micro kit (Qiagen, Valencia, CA, USA). DNase treatment was performed either on-column (Qiagen) or using DNA-free DNA Removal Kit (Life Technologies). Total RNA was quantified with RNA HS Kit (Q32852) for Qubit fluorometer (Life Technologies) and analyzed for integrity using RNA 6000 Pico Kit (5067-1513) for 2100 Bioanalyzer (Agilent). mRNA was isolated from total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, NEB). PolyA-selected mRNA was fragmented to average size of 300 nt, reverse transcribed to generate double-stranded cDNA, and converted to a paired end library using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) according to manufacturer's instructions including the optional double size selection procedure using Agencourt AMPure XP beads. Prepared libraries were quantified with dsDNA HS Kit (Q32851) for Qubit and the size distribution was assessed using High Sensitivity DNA Kit (5067-462) for Bioanalyzer. Libraries were sequenced on Illumina HiSeq2500 in paired-end mode with the read length of 75 nt.

first: Joanna

last: Tober

first: Marijke

last: Maijenburg

first: Yan

last: Li

first: Brandon

middle: K

last: Hadland

first: Peng

first: Kodai

last: Minoura

first: Irwin

last: Bernstein

first: Kai

last: Tan

first: Nancy

last: Speck


title: Transcriptome analysis of Agrobacterium sp. ATCC 31749 wild strain and ΔfnrN based on RNA-seq

city: 无锡

first: 王

last: 永远

state: 江苏省

address: 滨湖区蠡湖街道1800号

institute: 江南大学

summary: Purpose:first,we want to find the genes revelant to curdlan synthesis and oxygen regulation, second, we want to research the function of fnrN gene in Agrobacterium sp. ATCC 31749. Method: samples of cell growth phase, curdlan-producing phase (normoxia) and curdlan-producing phase (micro-oxygen treated) in both Agrobacterium sp. ATCC 31749 wild strain and ΔfnrN strain were collectecd to extract mRNA. Each sample was treated in duplicate. The softwares we used include fastqc, trimmomatic, TopHat2 and Cufflinks. Illumina Hiseq4000 was used to complete the research.

overall_design: 12 samples: samples of cell growth phase, curdlan-producing phase (normoxia) and curdlan-producing phase (micro-oxygen treated) in both Agrobacterium sp. ATCC 31749 wild strain and ΔfnrN strain were collectecd to extract mRNA. Each sample was treated in duplicate.

first: Zhiyong

last: Zheng

first: Yongyuan

last: Wang


title: AP-1 transcription factors and the BAF complex mediate signal-dependent enhancer selection

city: Boston

first: Michael

last: Greenberg

address: 200 Longwood Ave

institute: Harvard Medical School

summary: Enhancer elements are regulatory sequences within genomes that direct the selective expression of genes so that genetically identical cells can differentiate and acquire the highly specialized forms and functions required to build a functioning animal. To differentiate, cells must select from among the ~10^6 enhancers encoded in the genome the thousands of enhancers that drive the gene programs that impart their distinct features. We used a genetic approach to identify transcription factors (TFs) required for enhancer selection in fibroblasts. This revealed that the broadly expressed, growth factor-inducible TFs Fos/Jun (AP-1) play a central role in enhancer selection. Fos/Jun selects enhancers together with cell type-specific TFs by collaboratively binding to nucleosomal enhancers and directing recruitment of the SWI/SNF (BAF) chromatin remodeling complex to establish accessible chromatin. These experiments demonstrate how environmental signals acting via Fos/Jun and BAF coordinate with cell type-specific TFs to select enhancer repertoires that enable differentiation during development.

overall_design: Genome-wide maps of H3K27ac, H3K4me1/2, AP-1 transcription factors, Smarca4, and chromatin accessibility before and after serum stimulation for the indicated times in primary mouse embryonic fibroblasts.

first: Emi

last: Ling

first: Thomas

last: Vierbuchen


title: RNA-sequencing analysis of wild-type and osvil2 mutant panicles

city: Shanghai

first: liang

last: wanqi

address: 800 Dongchuan Road

department: Department of Bioscience and Biotechnology,School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

summary: Oryza sativa VIN3-LIKE2 (OsVIL2) acts as an epigenetic regulator together with Polycomb Repressive Complex2 (PRC2), which mediates trimethylation of histone H3 lysine 27 (H3K27me3) on target chromatin. T-DNA mutants of OsVIL2 displayed abnormal spikelet development. To understand function of OsVIL2 during spikelet development, RNA-sequencing was conducted in developing panicles of wild-type (WT) and osvil2 mutants.

overall_design: RNA-sequencing assays were performed to identify genes differentially expressed in osvil2 during early spikelet development. Two stages were examined: developing panicles in the length of 2 mm containing spikelets mostly at Sp4 or earlier, and developing panicles in the length of 4 mm containing spikelets at mainly Sp7 or younger.

first: Hyeryung

last: Yoon

first: Jungil

last: Yang

first: Wanqi

last: Liang

first: Dabing

first: Gynheung

last: An


title: Developmental emergence of adult neural stem cells as revealed by single cell transcriptional profiling

city: Toronto

first: Freda

last: Miller

state: ON

address: 686 Bay St

institute: Hospital for Sick Children

summary: Adult neural stem cells (NSCs) derive from embryonic precursors, but little is known about how or when this occurs. We have addressed this issue using single cell RNAseq at multiple developmental timepoints to analyze the embryonic murine cortex, one source of adult forebrain NSCs.  We computationally identify all major cortical cell types, including the embryonic radial precursors (RPs) that generate adult NSCs.  We define the initial emergence of RPs from neuroepithelial stem cells at E11.5.  We show that by E13.5 these RPs express a transcriptional identity that is maintained and reinforced throughout their transition to a non-proliferative state between E15.5 and E17.5.  These slowly-proliferating late embryonic RPs share a core transcriptional phenotype with quiescent adult forebrain NSCs. Together, these findings support a model where cortical RPs maintain a core transcriptional identity from embryogenesis through to adulthood, and where the transition to a quiescent adult NSC occurs during late neurogenesis.

overall_design: We applied the high-throughput single-cell mRNA sequencing technique, Drop-seq, to the embryonic mouse cortex. 2000-5000 single cells from wildtype CD1 embryos of gestational ages E11.5, E13.5, E15.5 and E17.5 were characterized.

first: Scott

last: Yuzwa

last: Borrett

first: Brendan

middle: T

last: Innes

first: Anastassia

last: Voronova

first: Troy

last: Ketela

first: David

last: Kaplan

first: Gary

middle: D

last: Bader


title: Prevention of tuberculosis in rhesus macaques by a cytomegalovirus-based vaccine

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

institute: Regeneron

summary: RhCMV-based TB vaccines are able to elicit and maintain immune effector responses that can control Mtb at the earliest stages of infection, and the protection afforded by this vaccine can be complete, if not sterilizing. To our knowledge, this is the first demonstration of complete prevention of TB disease in Rhesus Macaques (RM) by a long-acting vaccine after highly pathogenic (Erdman strain) Mtb challenge.

overall_design: To test the hypothesis whether vaccination with RhCMV/TB would elicit more effective immunity than BCG, and/or enhance the efficacy of BCG, we vaccinated 3 groups of RM (n=7/group; all naturally RhCMV-infected and therefore RhCMV infected at study assignment) with the following vaccines: 1) RhCMV/TB alone  2) CMV alone and 3)BCG + CMV. We will refere to this as Study 1. To confirm and further characterize RhCMV/TB efficacy, we performed a second larger Mtb challenge study (n=9/group; all RhCMV+ at assignment) in which we compared the same 68-1 RhCMV/TB-9 Ag vaccine used in Study 1 (group 1) with an analogous RhCMV/TB-9 Ag vaccine based on the 68-1.2 RhCMV backbone (group 2), and a single 68-1 RhCMV/TB-6 Ag vector expressing a single 6 Ag Mtb polyprotein (Ag85A; ESAT-6; Rv3407; Rv2626; Rpf A; Rpf D) (group 3)

first: Smitha

last: Shankar

first: Louis

last: Picker


title: The Escherichia coli nucleoid is shaped around replication and transcription

status: Public on Dec 25 2017

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland


title: Rlim-independent XCI in female embryonic stem cells in vitro

city: Worcester

first: Ingolf

last: Bach

state: MA

address: 364 Plantation St

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

summary: The transcriptomes of differentiated and undifferentiated E14 (male), Pgk12.1 (female; WT) and Pgk12.1 with a KO of Rlim (RlimKO) were elucidated and examined for differences in X chromosome inactivation. No significant differences between wt and RlimKO with respect to Xist expression and global X-silencing was detected. Results confirm that Rlim is not required for XCI in female ESCs.

overall_design: Transciptomes of female WT (Pgk12.1) and female RlimKO ESCs were compared to those of male ESCs (E14). State of XCI in undifferentiated and differentiated ESCs was determined by comparing expression of Xist and expression of X-linked genes female versus male.

first: Feng

last: Wang


title: The Escherichia coli nucleoid is shaped around replication and transcription [RNA-Seq]

summary: The Escherichia coli nucleoid is confined within a rod shaped cell many times smaller than the outstretched chromosome. While extensive compaction is necessary for this process, the chromosome must at the same time remain accessible to essential cellular processes such as replication and transcription. Currently, the individual contributions of cellular confinement, chromosome topology, replication and transcription on nucleoid organization are not well understood. Here we synchronize E. coli cells in stationary phase, where replication has ceased, each cell contains only one copy of the chromosome, and transcription is minimal. We then release the cells and capture chromosome contacts and transcription immediately following release and through-out one cell cycle. Polymer models of confined and topologically constrained circular polymers revealed that cellular confinement and topology do not contribute extensively to the organization of the E. coli nucleoid. Rather, local nucleoid structure is established concurrent with replication, and higher order organization is formed by the replication dependant clustering of linearly distant SeqA bound sites and cell cycle specific gene transcription.

overall_design: There are four samples, two biological replicates at t=0, one sample each at t=1 and t=2 hours following release of E. coli cells from the stationary phase.

first: Rachel

last: Bowden

middle: M


title: Genome-wide analysis of RNA-binding protein PSF-associated transcripts in prostate cancer

status: Public on Dec 24 2017

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

summary: Prostate cancer is the most common cancer in men and androgen receptor (AR) downstream signalings promote prostate cancer cell proliferation. PSF is an RNA-binding protein which is involved in AR signaling. To investigate the role of PSF, we performed RNA immunoprecipitation (RIP) and crosslinking immunoprecipitation (CLIP) sequence analysis in AR-positive prostate cancer cell line, LNCaP. In addition, we used hormone-refractory prostate cancer model cells 22Rv1 and long term androgen deprivation (LTAD) cells to explore the differences of PSF function in prostate cancer progression.

overall_design: RIP and CLIP sequence analysis of PSF in three prostate cancer cell lines.

first: Ken


title: Transcriptome analysis of RGA1 mutant (d1) by RNA-seq

status: Public on Dec 23 2017

city: University Park

first: Zhao

last: SU

address: 354 N. Frear

institute: The Penn State University

summary: We applied RNA-seq to 60-day-old rice (Oryza sativa) flag leaf tissue to investigate the effect of RGA1 mutation on the transcriptome in d1 as compared to wild type plant.

overall_design: Two biological replicates of rice leaf blades, sampled flag leaf at the region of maximum width, were collected from two-month-old WT and d1 plants grown as described above and immediately frozen in liquid nitrogen. Total RNA was extracted from each sample using the NucleoSpin RNA Plant kit. After examination of the quality (Bioanalyzer, Agilent) and quantity (NanoDrop 2000, ThermoFisher) of each RNA sample, aliquots of total RNA were submitted to the Genomics Core Facility at Penn State University for cDNA library preparation and next generation sequencing on a Hiseq 2500 (Illumina). Approximately 40 million 150 bp single-end sequencing reads were obtained for each library.

last: Su

first: Ángel

last: Ferrero-Serrano

first: Sarah

last: Assmann