title: Analysis of small RNAs revealed differential expressions during the development of pollen and embryo sac and their targets may associate with fertility in autotetraploid rice

city: Guangzhou

first: andyslee

last: Li

address: Wushan 483

institute: South China Agricultural University

summary: Background: Partial pollen and embryo sac sterilities are the two main reasons for low fertility in autotetraploid rice. Our previous study revealed that small RNAs changes may associate with pollen fertility in autotetraploid rice. However, knowledge on comparative analysis between the development of pollen and embryo sac by small RNAs in autotetraploid rice is still unknown. In the present study, WE-CLSM (whole-mount eosin B-staining confocal laser scanning microscopy) and high-throughput sequencing technology was employed to examine the cytological variations and to analyze small RNAs changes during pollen and embryo sac development in autotetraploid rice compared with its diploid counterpart. Results: A total of 321 and 368 differentially expressed miRNAs (DEM) were detected during development of pollen and embryo sac in autotetraploid rice, respectively. Gene Ontology enrichment analysis on the targets of miRNAs-enriched during the development of pollen and embryo sac in autotetraploid rice revealed 30 prominent functional gene classes, such as cell differentiation and signal transduction during embryo sac development. However, only 7 prominent functional gene classes, such as flower development and transcription factor activity, were detected during pollen development. The expression levels of 39 DEM, which revealed interaction with meiosis-related genes, showed opposite expression levels in pollen and embryo sac development. Of these DEM, osa-miR1436_L+3_1ss5CT and osa-miR167h-3p were associated with the female meiosis, while osa-miR159a.1 and osa-MIR159a-p5 were related with the male meiosis. 21nt-phasiRNAs were detected both during pollen and embryo sac development, while 24nt-phasiRNAs were found only in pollen development, which displayed down-regulation in autotetraploid compared to diploid rice and their spatial-temporal expression patterns were similar to osa-miR2275d. 24nt TEs-siRNAs were found to be up-regulated in embryo sac but down-regulated in pollen development. Conclusion: The above results not only provide the small RNAs changes during four landmark stages of pollen and embryo sac development in autotetraploid rice but also have identified specifically expressed miRNAs, especially meiosis-related miRNAs, pollen-24nt-phasiRNAs and TEs-siRNAs in autotetraploid rice. Together, these findings provide a foundation for understanding the effect of polyploidy on small RNAs expression patterns during pollen and embryo sac development that may lead to different abnormalities in autotetraploid rice.

overall_design: To investigate the small RNAs associated with the pollen and embryo sac development of autotetraploid and diploid (CK) rice, anthers with four pollen development stages, including pre-meiotic interphase (PMA), meiosis (MA), single microspore stage (SCP) and bi-cellular pollen stage (BCP), and the ovary tissues were collected with their corresponding embryo sac development stages (i.e. megasporocyte formation stage (MF), megasporocyte meiosis stage (MM), functional megaspore formation stage (FMF) and eight-nucleate embryo sac developing-stage (EES)), were selected to construct 16 libraries and sequenced by Solexa high-throughput sequencing technology.

first: Xiang

first: Xiangdong

last: Liu


title: N6-methyladenosine Recruits HNRNPG for Alternative Splicing Regulation

status: Public on Mar 09 2017

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

country: USA

institute: University of Chicago

type: Expression profiling by high throughput sequencing

summary: Understanding how RNA-binding proteins interact with RNA transcripts for splicing regulation is fundamental to human biology and disease. N6-methyladenosine (m6A), the most abundant and dynamic internal modification of eukaryotic messenger RNA (mRNA), is important for RNA splicing, but its detailed mechanism remains unclear. We find the splicing factor heterogeneous nuclear ribonucleoprotein G (HNRNPG) selectively binds m6A-modified RNA in vitro and in vivo. Transcriptome-wide identification of HNRNPG binding sites reveals the binding sequence specificity of HNRNPG (AGRAC, R=A/G), which embeds the m6A consensus motif. The m6A methylation makes the binding sequence more accessible to facilitate HNRNPG binding. In total, we identify 13,191 high-confidence m6A sites recruiting HNRNPG in HEK293T cells. Furthermore, m6A writers depletion decreases HNRNPG binding at m6A sites, and consequently cause alternative splicing changes similar as HNRNPG depletion on the m6A-containing RNA transcripts. These findings indicate that m6A RNA methylation facilitates HNRNPG binding to regulate mRNA alternative splicing.

overall_design: Measure the m6A methylated HNRNPG binding sites transcriptome-wide by PAR-CLIP-MeRIP; measure the differential HNRNPG occupancies upon METTL3/METTL14 knockdown by PAR-CLIP; measure RNA abundance and splicing level changes upon HNRNPG, METTL3 and METTL14 knockdown

first: Nian

first: Marc

last: Parisien

first: Qing

last: Dai

first: Katherine

last: Zhou

first: Luda

last: Diatchenko


title: Transcriptome analysis of TOR inhibited cotton seedlings using RNA-Seq

status: Public on Mar 08 2017

city: Anyang

first: Yun

last: Song

state: Henan

address: Huanghe Street No. 83

country: China

institute: Institute of cotton research of CAAS

summary: Next-generation sequencing (NGS) was used to analysis the expression profiling of cotton seedlings under TOR inhibition by AZD. TOR inhibition significantly altered the expression levels of anabolic and catabolic processes related genes, photosynthesis and phytohormone signaling pathways related genes. Expression profiling analysis reveals that TOR is a key player in cotton seedlings growth.

overall_design: mRNA profiles of DMSO and AZD treated cotton seedlings were generated by deep sequencing, in triplicate, using Illumina Hiseq 4000 platform.

first: Xueyan

last: Zhang

first: Maozhi

last: Ren

first: Fuguang


title: Expression profiling of cochlear ducts  from P8 Gfi1cre/+ and Gfi1+/+ mice

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

summary: The Gfi1-Cre mouse is commonly used for conditional hair cell-specific gene deletion/activation in the inner ear. However, we have shown that these mice produce a pattern of recombination that is not strictly limited to hair cells, and that Gfi1cre/+  mice exhibit an early onset progressive hearing loss as compared with their wildtype littermates. Here we performed a transcriptome analysis of Gfi1cre/+ and Gfi1+/+ cochlea to detect potential changes in gene expression that could contribute to their hearing loss phenotype, or that could potentially confound downstream analysis of conditional gene deletion using these mice.

overall_design: Trancriptome profiles of P8 cochlear duct from mice of two genotype - Gfi1cre/+ and Gfi+/+ controls - were measured.  Gene expression levels were recorded in independent triplicates using polyA-enriched RNA-seq

first: Maggie

last: Matern

first: Ronna

last: Hertzano


title: Chemical warfare does not always win – rapid evolution of increased virulence in Beauveria bassiana

city: Gießen

first: Gerrit

last: Joop

address: Heinrich-Buff-Ring 26-32

department: Institute for Phytopathology and Applied Zoology

country: Germany

institute: University of Gießen

summary: Virulence is a key trait under selection during host-parasite coevolution. In order to obtain increased fitness, parasites are predicted to increase their ability to circumvent and overcome host immunity. A particular challenge for pathogens are external immune systems, found among various invertebrates. Such external immune systems are chemical defence systems comprised of highly potent antimicrobial compounds released by prospective hosts into the environment. We carried out a coevolution experiment with the entomopathogenic fungus, Beauveria bassiana, and the red flour beetle, Tribolium castaneum, which has a well-documented external immune system.  Surprisingly, after just seven transfers of experimental evolution we saw a significant increase in virulence in all B. bassiana. This increase in virulence was mainly the result of the B. bassiana isolates evolving resistance to the external immune defences of the T. castaneum beetles, but not obviously through the increased production of toxins or other harmful substances. Furthermore, transcriptomic analyses of B. bassiana RNA-seq data implicates up-regulation of genes responsible for resistance to oxidative stress underlying the observed resistance. We conclude that external immunity acts as a powerful selective force for virulence evolution, with an increase in virulence being achieved apparently entirely by overcoming these defences, most likely due to elevated oxidative stress resistance.

overall_design: mRNA profiles of Beauveria bassiana (ancestral: A and evolved isolates:BI5 & BI3) exposed to either 10µl of Methyl-para-benzoquinone (MBQ, quinone, 0.11µg per ml diluted in methanol) or methanol at 72h or 96h were generated by deep sequencing, in triplicate or single, using Illumina HiSeq2000.

first: Charlotte

last: Rafaluk

first: Wentao

last: Yang

first: Andreas

last: Mitschke

first: Philip

last: Rosenstiel

first: Hinrich

last: Schulenburg


title: APOBEC Signature Mutation Forms an Oncogenic Enhancer Upstream of LMO1 in T-ALL

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Oncogenic driver mutations are those that provide a proliferative or survival advantage to neoplastic cells resulting in clonal selection. Although most cancer causing mutations have been detected in the protein-coding regions of the cancer genome, driver mutations have recently also been discovered within noncoding genomic sequences. Thus, a current challenge is to gain precise understanding of how these unique genomic elements function in cancer pathogenesis, while clarifying mechanisms of gene regulation and identifying new targets for therapeutic intervention. Here we report a C-to-T single nucleotide transition that occurs as a somatic mutation in noncoding sequences 4 kb upstream of the transcriptional start site of the LMO1 oncogene in primary samples from patients with T-cell acute lymphoblastic leukaemia. This single nucleotide alteration conforms to an APOBEC-like cytidine deaminase mutational signature, and generates a new binding site for the MYB transcription factor, leading to the formation of an aberrant transcriptional enhancer complex that drives high levels of expression of the LMO1 oncogene. Since APOBEC-signature mutations are common in a broad spectrum of human cancers, we suggest that noncoding nucleotide transitions such as the one described here may activate potent oncogenic enhancers not only in T-lymphoid cells but in other cell lineages as well.

overall_design: ChIP-Seq for LMO1 in Jurkat T cell leukemia cells

first: Zhaodong

last: Li

first: Brian

middle: J

last: Abraham

first: Alla

last: Berezovskaya

first: Nadine

last: Farah

first: Yu

last: Liu

first: Theresa

last: Leon

first: Adele

last: Fielding

first: Shi

middle: H

last: Tan

first: Takaomi

last: Sanda

first: Abraham

middle: S

last: Weintraub

first: Benshang

first: Shuhong

last: Shen

first: Jinghui

first: Marc

middle: R

last: Mansour

first: A

middle: T

last: Look


title: Transcriptomic comparison of wild-type and ptvR deletion mutant of Streptococcus pneumoniae D39

city: Beijing

first: Jing-Ren

last: Zhang

state: Beijing

address: Qinghuayuan Street

department: Center for Infectious Disease Research, School of Medicine

institute: Tsinghua University

summary: Reversible or phenotypic tolerance to antibiotics within microbial populations has been implicated in treatment failure of chronic infections and development of persister cells. However, the molecular mechanisms regulating phenotypic drug tolerance are largely unknown. In this study, we identified a four-gene operon in Streptococcus pneumoniae that contributes to phenotypic tolerance to vancomycin (ptv). RNA-Seq, qRT-PCR, and luciferase reporter experiments revealed that transcription of the ptv operon (consisting of ptvR, ptvA, ptvB and ptvC) is induced by pneumococcal exposure to vancomycin. Further investigation showed that the transcription of the ptv operon is repressed by PtvR, a PadR-family repressor; transcriptional induction of the ptv operon by vancomycin is achieved by transcriptional de-repression of this locus. Importantly, de-repression of ptvABC significantly enhanced the levels of vancomycin-tolerant pneumococci. Gene fusion and deletion analyses revealed that PtvA, PtvB and PtvC are membrane-associated proteins, and all required for the PtvR-regulated phenotypic tolerance to vancomycin. Finally, gel-shifting test with recombinant PtvR uncovered that PtvR represses the transcription of the ptv operon by binding to two palindromic sequences of the ptv promoter. Together, the ptv locus represents a novel inducible system for pneumococcal response to stressful conditions, including those caused by antibiotics.

overall_design: Pairwise comparison of wild-type and ptvR knockout mutant of Streptococcus pneumoniae D39 (RNA-seq), analyzing the effect of ptvR deletion on the transcriptome. It was performed with deep sequencing, using an Illumina HiSeq 2500 machine with 125 nt single-end reads.

first: Xue

first: Jing-Wen

first: Zhixing

last: Feng

first: Youfu

last: Luo

first: Jan-Willem

last: Veening


title: Global analysis of translation termination in E. coli using release factor manipulations

city: San Francisco

first: Natalie

last: Baggett

state: CA

address: 600 16th Street, S376

department: Microbiology and Immunology

institute: UCSF

summary: Terminating protein translation accurately and efficiently is critical for both protein fidelity and ribosome recycling for continued translation. The three bacterial release factors (RFs) play key roles:  RF1 and 2 recognize stop codons and terminate translation; and RF3 promotes disassociation of bound release factors. Probing release factors mutations with reporter constructs containing programmed frameshifting sequences or premature stop codons had revealed a propensity for readthrough or frameshifting at these specific sites, but their effects on translation genome-wide have not been examined. We performed ribosome profiling on a set of isogenic strains with well-characterized release factor mutations to determine how they alter translation globally.  Consistent with their known defects, strains with increasingly severe release factor defects exhibit increasingly severe accumulation of ribosomes over stop codons, indicative of an increased duration of the termination/release phase of translation. Release factor mutant strains also exhibit increased occupancy in the region following the stop codon at a significant number of genes.  Our global analysis revealed that, as expected, translation termination is generally efficient and accurate, but that at a significant number of genes (≥ 50) the ribosome signature after the stop codon is suggestive of translation past the stop codon. Even native E. coli K-12 exhibits the ribosome signature suggestive of protein extension, especially at UGA codons, which rely exclusively on the reduced function RF2 allele of the K-12 strain for termination. Deletion of RF3 increases the severity of the defect.  We unambiguously demonstrate readthrough and frameshifting protein extensions and their further accumulation in mutant strains for a few select cases. In addition to enhancing recoding, ribosome accumulation over stop codons disrupts attenuation control of biosynthetic operons, and may alter expression of some overlapping genes.  Together, these functional alterations may either augment the protein repertoire or produce deleterious proteins.

overall_design: Samples of WT, ∆RF3, RF2B, and RF2B∆RF3 were analyzed by ribosome profiling and RNA-seq. Over 4 experiments there are 4 replicates of WT, 2 replicates of ∆RF3, 2 replicates of RF2B and 5 replicates of RF2B∆RF3. One experiment (both ribosome profiling and RNA-seq) was performed in minimal media with a single sample for WT and ∆RF3

first: Yan

first: Carol

last: Gross


title: Definition of the Ras/ERK signal induced chromatin modification at target gene promoters

city: London

first: Francesco

last: Gualdrini

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Francis Crick Institute

summary: Specific spectra of chromatin modifications are associated with different transcriptional states and gene regulatory elements, but relatively little is known about how such chromatin modifications are established. In particular the relationship of chromatin modifications to the activity of specific transcription factors and the signalling pathways that control them remain largely unclear.  We investigated the relationship between chromatin modifications and transcription in response to Ras/ERK activationby stimulating cells with TPA  (12-O-tetradecanoyl phorbol-13-acetate) for 30 minutes. Oncogenic active Ras is known to mediate the cellular response to multiple growth factors leading to the activation of immediate-early genes (IE). A key player in IE gene response is the SRF transcriptional network that we identified being crucial to mediate allegedly the entire transcriptional response downstream of Ras/ERK. The Serum response factor (SRF) is a transcription factor with low intrinsic transcriptional activity and requires the recruitment of one of two families of co-activators: the MRTFs (myocardin-related transcription factors) and the TCFs (ternary complex factors). In particular the TCF, member of the wide family of ETS transcription factors, are specifically activated by MAPK signalling downstream of Ras. Cells lacking all three TCFs are defective in responding to Ras/MAPK signalling. We analysed changes in 5 main histone modifications (H3K9acS10ph, H4K16ac, H3K27ac, H3K9acK14ac and H3K4me3) associated with active transcription by ChIP-seq in Mouse Embryonic Fibroblasts (MEFs) derived from wild type mice (MEF WT) or animals lacking all three TCFs (TCF KO). In addition the distribution of the 5 modifications have been assessed in TCF KO cells reconstituted with Elk-1 (one of the member of the TCF factos) variants.

overall_design: Chromatin immunoprecipitation (ChIP-seq) in Mouse Embryonic Fibroblasts (MEFs) derived from wild type mice (MEF WT) or animals lacking all three TCFs (TCF KO) after TPA (12-O-tetradecanoyl phorbol-13-acetate)  using antibodies against H3K9acS10ph, H4K16ac, H3K27ac, H3K9acK14ac and H3K4me3 histone modifications.  In addition the distribution of the 5 modifications have been assessed in TCF KO cells reconstituted with Elk-1 (one of the member of the TCF factos) variants. Distribution of reads around the TSS of all Ref-seq annotated genes (-2Kb to +1Kb) have been investigated. Each sample has been normalised/standardised to a reference set of TSSs of genes that are constitutively active and invariant across the conditions used. The scaling factors have been compared to a second method of normalisation that involve the identification of those TSSs which frequency distribution of the differences across samples can be approximated to a normal-gaussian distribution.

first: Gualdrini

last: Francesco

first: Cyril

last: Esnault

first: Stuart

last: Horswell

first: Phil

last: East

first: Gavin

last: Kelly

first: Aengus

last: Stewart

first: Nik

last: Matthews

first: Richard

last: Treisman


title: Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes in S. cerevisiae (HTS)

city: Los Angeles

first: Andrew

middle: Zachary

last: Ostrow

state: California

address: 1050 Childs Way

department: Biological Sciences

institute: University of Southern California

summary: Forkhead Box (Fox) proteins share the Forkhead domain, a winged-helix DNA binding module, which is conserved among eukaryotes from yeast to humans. These sequence-specific DNA binding proteins have been primarily characterized as transcription factors regulating diverse cellular processes from cell cycle control to developmental fate, deregulation of which contributes to developmental defects, cancer, and aging. We recently identified S. cerevisiae Fkh1 and Fkh2 as required for the clustering of a subset of replication origins in G1 phase and for the early initiation of these origins in the ensuing S phase, suggesting a mechanistic role linking the spatial organization of the origins and their activity. Here we show that Fkh1 and Fkh2 share a unique structural feature of human FoxP proteins that enables FoxP2 and FoxP3 to form domain-swapped dimers capable of bridging two DNA molecules in vitro. Accordingly, Fkh1 self-associates in vitro and in vivo in a manner dependent on the conserved domain-swapping region, strongly suggestive of homo-dimer formation. Fkh1- and Fkh2-domain-swap-minus (dsm) mutations are functional as transcription factors yet are defective in replication origin timing control. Fkh1-dsm binds replication origins in vivo but fails to cluster them, supporting the conclusion that Fkh1 and Fkh2 dimers perform a structural role in the spatial organization of chromosomal elements with functional importance.

overall_design: S. cerevisiae strains with various Forkhead protein mutations and deletions were examined by BrdU-IP-Seq, RNA-Seq, and 4C-Seq.

first: A

middle: Z

first: Reza

last: Kalhor

last: Gan

first: Sanda

middle: K

last: Villwock

first: Linke

last: Christian

first: Barberis

last: Matteo

first: Lin

last: Chen

first: Oscar

middle: M

last: Aparicio


title: Analysis of differential gene expression in the Streptococcus sanguinis brpT mutant

city: Richmond

first: Ping

last: Xu

state: VA

address: 521 North 11th street

department: Philips Institute for Oral Health Research

institute: Virginia Commonwealth Univ. School of Dentistry

summary: Gene expression profile of the Streptococcus sanguinis TetR family transcriptional regulator, brpT, deletion mutant compared to the wild-type strain SK36

overall_design: Experiment: brpT mutant vs. wild-type SK36. Biological replicates (1-5) independently grown and prepared for each sample.

first: Victoria

middle: N

last: Stone


title: Low-Cell-Number, Single-Tube Amplification (STA) of RNAs Revealed miRNA Changes from Pluripotency to Endothelium

city: Tainan

first: Po-Min

last: Chiang

state: TAIWAN

address: No. 35, Xiaodong Road,, Rm. 7068

department: Institute of Clinical Medicine

country: Taiwan

institute: National Cheng Kung University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Non-coding RNAs (ncRNAs) are essential components in cellular machineries for translation and splicing. In addition to their housekeeping functions, ncRNAs are involved in cell type-specific regulation of translation, mRNA stability, genome structure and accessibility. To decipher their functions in different cell types, a method to comprehensively quantify them in a sensitive manner is highly desirable. Using miRNA as an example, we showed that cDNA from total RNA could be amplified and specifically detected from a few cells within a single tube. The sensitivity of the system was maximized by avoiding purification from cell lysis to amplified cDNA and by optimizing the buffer conditions. With 100 human embryonic stem cells (hESCs) and their differentiated endothelial cells as input for high-throughput sequencing, the single-tube amplification (STA) system revealed both well-known and other miRNAs selectively enriched in each cell type. The selective enrichment of the miRNAs was further verified by qPCR with 293FT cells and a human induced pluripotent stem cell (hiPSC) line. In addition, the STA system was capable of detecting miRNA expression down to single cells, albeit with some loss of sensitivity and power. Finally, the detection of other non-miRNA transcripts indicated that the STA target was not limited to miRNA, but extended to other ncRNAs and mRNAs as well. Overall, STA offered a simple and extremely sensitive way to collect the quantitative miRNA and other RNA information from individual cells.

Grant ID: MOST-104-2314-B-006-038-MY3
Funding source: Ministry of Science and Technology, Taiwan
Grantee First Name: Po-Min
Grantee Last Name: Chiang

overall_design: total RNA from 3 types of cells was amplified and sequenced using HiSeq2500 platform


title: A systems level approach reveals new gene regulatory modules in the developing ear

first: Jingchen

address: International Bioisland

institute: Maijing Gene Diagnostics

summary: The vertebrate inner ear arises early in development from a thickened epithelium, the otic placode. Specification toward an otic fate requires diverse signals and complex transcriptional inputs that act sequentially and/or in parallel. To uncover and integrate novel genes with known molecular players in the gene regulatory network (GRN) underlying otic development, we have performed transcriptome analyses of the presumptive otic region at sequential early stages of commitment toward inner ear identity. Our results identify hundreds of genes enriched at specific developmental time points, revealing dynamic changes in gene expression as a function of time during the transition from progenitor to committed otic state. Initial functional analysis of selected enriched transcription factors demonstrates a genetic hierarchy amongst these genes underlying this critical transition. Our results not only characterize the otic transcriptome in unprecedented detail but also identify new links in the GRN responsible for development of the presumptive inner ear.

overall_design: 3 different biological samples at various developmental stages (5-6 somite stage, 8-9 somite stage, 11-12 somite stage) are included. Two additional samples (a whole embryo at somite stage 3, and posterior pre-placodal region at Hamburger-Hamilton stage 6 (HH6)) are used as reference for different comparisons.

first: Monica

last: Tambalo

first: Meyer

last: Barembaum

first: Marcos

last: Simoes-Costa

first: Marianne

middle: E

last: Bronner

first: Andrea

last: Streit

first: Ramya

last: Ranganathan


title: Whole-genome DNA methylation profiling identifies epigenetic signatures of uterine carcinosarcoma

city: SAINT LOUIS

first: Ting

last: Wang

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

type: Methylation profiling by high throughput sequencing

summary: Uterine carcinosarcoma (UCS) is a form of endometrial cancer simultaneously exhibiting carcinomatous and sarcomatous elements, but the underlying molecular and epigenetic characteristic of this disease is poorly understood. We generated complete DNA methylomes for both the carcinomatous and the sarcomatous components of three UCS samples separated by laser capture microdissection and compared DNA methylomes of UCS with that of normal endometrium as well as methylomes derived from endometrioid carcinoma, serous endometrial carcinoma, and endometrial stromal sarcoma. We identified epigenetic lesions specific to carcinosarcoma, and specific to two components. Hallmarks of DNA methylation abnormality of UCS included global hypomethylation, especially in repetitive elements, and hypermethylation of tumor suppressor gene promoters. Among these, aberrant DNA methylation of MIR200 genes is a key feature of UCS. The carcinoma component of UCS was characterized by hypermethylation of promoters of EMILIN1, NEFM and CLEC14A, genes that are associated with tumor vascularization. In contrast, DNA methylation changes of PKP3, FAM83F and TCP11 were more characteristic of the sarcoma components. Our findings highlight the epigenetic signatures that distinguish the two components of UCS, providing a valuable resource for investigation of these diseases.

overall_design: We used laser capture microdissection (LCM) to separate the two components of uterine carcinosarcoma (UCS) samples from 3 patients. We used two complementary next-generation sequencing-based methods, methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylation-sensitive restriction enzyme digestion sequencing (MRE-seq), to construct genome-wide DNA methylation maps at single-CpG resolution in these components. We also generared methylome of endometrial stromal sarcoma (ESS).

first: Jing

last: Li

first: Xiaoyun

last: Xing

first: Daofeng

first: Ian

last: Hagemann


title: Gene expression profile of TGFbeta treated human coronary smooth muscle cell (HCASM)

city: Augusta

first: Xiaochun

last: Long

state: GA

address: 1460 Laney Walker Blvd, CL-3004

department: Vascular Biology Center

institute: Augusta University

summary: TGFbeta induces VSMC gene expression in human coronary artery smooth muscle cell (HCASM)

overall_design: Subconfluent human coronary artery smooth muscle cells (HCASM) were starved overnight followed by TGFbeta treatment for 24 hours. RNA was then extracted for deep-sequencing.

first: Joseph

last: Miano


title: Sox17 drives functional engraftment of endothelium converted from nonvascular cells

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

summary: Transplanting vascular endothelial cells (ECs) to support metabolism and express regenerative paracrine factors is a strategy to treat vasculopathies and to promote tissue regeneration. However, transplantation strategies have been challenging to develop because ECs are difficult to culture and little is known about how to sustain their vascular identity and direct them to form long-lasting new vessels or engraft into existing ones. We found that multiple non-vascular cell types transiently expressed EC markers after enforced expression of the transcription factors, Etv2, Erg, and Fli1. However, only mid-gestational amniotic cells could be converted to cells that maintained EC gene expression and proliferated in culture to yield billions of vascular cells. Even so, these converted cells performed sub-optimally in assays of EC function. We used constitutive Akt signaling to mimic the shear forces of the vascular environment and promote EC survival in an effort to correct the deficiencies of the converted cells. Akt signaling increased gene expression of EC morphogenesis genes, including Sox17, shifted the genomic targeting of Fli1 to favor nearby Sox consensus sites, and enhanced the in vivo vascular function of EC-like converted cells. Enforced expression of Sox17 was dispensable for broad EC gene activation, but indispensable for vascular engraftment and reperfusion of ischemic tissue. Our results identify a transcription factor network comprised of Ets and Sox17 factors that specifies and sustains endothelial cell fate and function. This work shows that the commonly used criterion of transcriptional similarity for cell conversion can fail to predict in vivo vascular function. Our approach shows that stringent functional testing in vitro and in vivo is necessary to validate engineered endothelial cell grafts.

overall_design: Transcriptome sequencing of endothelial cells and amniotic cells

first: Will

last: Schachterle

first: Shahin

last: Rafii


title: Histone H3 Lysine 4 trimethylation (H3K4me3) ChIP-Seq to identify actively transcribing genes and their active promoter regions in the narrower and wider vanes of primary remiges, respectively

city: Arlington

first: Ang

state: TX

address: 655 W Mitchell St, SEIR 244

department: Kinesiology

institute: University of Texas at Arlington

summary: Purpose: One goal of this study is to identify actively transcribing genes in the mesenchyme (pulp) corresponding to the narrow (lateral) and wide (medial) vane of primary remiges. The other is to pinpoint the  active promoter regions of these genes.

overall_design: 15 primary remige follicles were collected, cut into the lateral and medial halves and shorted treated in 2x CMF to separate epithelium and mesenchyme. The mesenchymal cells were dissociated by 0.35% collagenase digestion. Then we conduct formaldehyde crosslinking, sonication, IP, reverse crosslinking and removal of protein/RNA. The library preparation and sequencing were done at USC epigenome center.


title: Next Generation Sequencing Facilitates identification of crucial genes for feather vane shape variations

summary: Purpose: The goals of this study is to identify crucial genes associated with narrow and wide vane sizes in feather epithelium and mesenchyme (pulp)

overall_design: proximal follicles of 3 primary remiges from Spafas white leghorn chickens into the lateral and medial halves and separated the epithelium from the mesenchyme in 2xCMF solution.  For dorsal plumes and breast plumes, 25 proximal follicles were used, respectively. Total RNA was extracted using Trizol reagent. 4 µg RNA was used for library construction by TruSeq RNA Sample Prep Kit Version2 (Illumina). Two biological replicates were sent for sequencing (50bp, single end) with Illumina HiSeq 2000 in the USC Epigenome Center.


title: Histone H3 Lysine 4 trimethylation (H3K4me3) ChIP-Seq and RNA-seq of narrower and wider vanes of primary remiges

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

overall_design: Refer to individual Series


title: Identification of circular RNAs and their targets in leaves of Triticum aestivum L. under dehydration stress

city: Zhengzhou

first: Ming

last: Yang

address: Wenhua Road No.95

institute: Henan Agricultural University

summary: circRNA sequencing for 2 samples

overall_design: Examing 2 conditions

first: Y

first: B

last: Suo

first: M

first: S

last: Wei

first: H

last: Zhao


title: Altered hepatic lipid metabolism in mice lacking both the melanocortin type 4 receptor and low density lipoprotein receptor

city: Leipzig

first: Torsten

last: Schöneberg

address: Johannisallee 30

department: Institute of Biochemistry, Medical Faculty

institute: Leipzig University

summary: In this study we investigated the effect of normal chow (0 % cholesterol) or a semisynthetic diet (high sugar, 0.02 % cholesterol) fed to mice lacking either Mc4r, Ldlr or both and wildtype animals (total of 4 genotypes) by generating an expression profile of their livers after 6 months by RNA sequencing.

overall_design: We investigated mice lacking either Mc4r, Ldlr or both and wildtype animals fed with normal chow or a semisynthetic diet with 10 replicates for each of the 8 resulting groups (4 genotypes * 2 diets).

first: Angela

last: Schulz

first: Joachim

last: Thiery

first: Albert

last: Ricken

first: Jürgen

last: Schiller

first: Wieland

last: Kiess

first: Daniel

last: Teupser

last: Huster

first: Antje

last: Garten

first: Melanie

last: Penke

first: Yulia

last: Popkova

first: Vera

last: Lede

first: Andrej

last: Meusel

first: Christin

last: Franke


title: Genome-wide profiling of DNA methylation patterns in iAs-transformed cells

city: Grand Rapids

first: Yvonne

middle: Nsokika

last: Fondufe-Mittendorf

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

summary: To examine the global impact of iAs on DNA methylation patterns. Genomic DNA was Bisulfite converted and analyzed using Mini methly-seq.

overall_design: DNA from both NT and iAs-transformed cells were bisulfite converted and used for analysis through Minimethyl-seq

first: Matthew

last: Rea

first: Meredith

last: Eckstein

first: Rebekah

last: Eleazer

first: Caroline

last: Smith


title: Transcriptomic and anatomic parcellation of 5-HT3AR expressing cortical interneuron subtypes revealed by single-cell RNA sequencing

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

summary: Cortical GABAergic interneurons constitute a highly diverse population of inhibitory neurons that are key regulators of cortical microcircuit function. An important and heterogeneous group of cortical interneurons specifically expresses the serotonin receptor 3A (5-HT3AR) but how this diversity emerges during development is poorly understood. Here we use single-cell transcriptomics to identify gene expression patterns operating in Htr3a-GFP+ interneurons during early steps of cortical circuit assembly. We identify 3 main molecular types of Htr3a-GFP+ interneurons, each displaying distinct developmental dynamics of gene expression. The transcription factor Meis2 is specifically enriched in a type of Htr3a-GFP+ interneurons spatially confined to the cortical white matter. These MEIS2 expressing interneurons appear to originate from a restricted region located at the embryonic pallial-subpallial boundary. Overall, this study identifies MEIS2 as a subclass-specific marker for 5-HT3AR-containing interstitial interneurons and demonstrates that the transcriptional and anatomical parcellation of cortical interneurons is developmentally coupled.

overall_design: Single cell transcriptomics of cortical interneurons FACS sorted according to GFP-Htr3a+. Acquired from mouse brains of 3 different developmental ages: E18, P2, P5

first: Sarah

last: Frazer

first: Mathieu

last: Niquille

first: Christelle

last: Cadilhac

first: Foivos

last: Markopoulos

first: Lucia

last: Gomez

first: Ugo

last: Tomasello

first: Ludovic

last: Telley

first: Anthony

last: Holtmaat

first: Denis

last: Jabaudon

first: Alexandre

last: Dayer


title: Genome-wide expression profiling of Neofusicoccum parvum virulence factors in response to different growth substrates in vitro and during an interaction time course with grapevine stems

city: Davis

first: Mélanie

last: Massonnet

address: 2105 Robert Mondavi Institute-North Building

department: Viticulture and Enology

institute: University of California, Davis

summary: Transcriptome profiling by RNA sequencing determined the genome-wide patterns of expression of N. parvum virulence factors when PDA or grape wood were provided as nutrient source and during an extensive interaction time course with grapevine stem.

sample_organism:
Vitis vinifera
Neofusicoccum parvum

platform_organism:
Vitis vinifera
Neofusicoccum parvum

overall_design: N. parvum UCD646So (ATCC number: MYA-3706) was grown on Potato Dextrose Agar (PDA) or agar containing ground grapevine wood (V. vinifera cv. Cabernet Sauvignon clone FPS 08 and V. vinifera cv. Merlot clone FPS 03). Potted V. vinifera cv. Cabernet Sauvignon clone FPS 19 plants were inoculated with N. parvum UCD646So mycelia. Stems were collected at seven time points: 0 hour post-inoculation (hpi), 3 hpi, 24 hpi, 2 weeks post-inoculation (wpi), 6 wpi, 8 wpi, and 12 wpi from 1 cm below the inoculation site. Three biological replicates were collected from each medium and for each infection time point.

first: Abraham

last: Morales-Cruz

first: Rosa

last: Figueroa-Balderas

first: Daniel

middle: P

last: Lawrence

first: Kendra

last: Baumgartner

first: Dario

last: Cantu


title: DNA Methylation Dynamics in Urological Tumors

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of normal and tumoral urological tissues (Prostate, Kidney and Bladder). The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 27,000 CpGs in urological fresh frozzen tissue samples. Samples included morphologically normal samples of each tissue and tumor samples. Kidney: 6 normal and 17 tumor samples; Bladder: 5 normal and 25 tumor samples; Prostate: 5 Normal and 25 tumor samples.

overall_design: Bisulphite converted DNA from the 83 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.

first: Joao

last: Ramalho-Carvalho


title: Absolute quantification of B cell transcriptome using ERCC spiked-in RNA

city: La Jolla

first: Changchun

last: Xiao

address: 10550 North Torrey Pines Road

department: Immunology & Microbial Science

institute: The Scripps Research Institute

summary: RNA-seq analysis of with known quantity of cell numbers and reference RNA (ERCC) to determine absolute abundance of endogenous mRNA abundances in B cells

overall_design: WT B cells were prepared as described. 3 x 10^6 cells were harvested at indicated time points (naïve, 1.5h, 4.5h, 13.5hr and 25.5hr). We determined the amount of ERCC control needed to cover the whole dynamic range of endogenous mRNA abundance at each time point in a pilot experiment, and added the following amounts of ERCC control into 3 x 10^6 cells before RNA extraction: naïve, 1uL or 0.1uL; 1.5h and 4.5h, 0.5uL; 13.5hr, 1uL; and 25.5hr, 2uL.

first: Hyun

middle: Y

last: Jin


title: DNA Methylation profile for male SD Rats with and without traumatic brain injury (TBI) by RNA-Seq, batch2

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 TBI on affecting DNA methylations in the WBC of male SD rats by RRBS.

overall_design: Male Sprague–Dawley (SD) rats weighing between 200 and 240 g were housed in cages and maintained in environmentally-controlled rooms (22–24C) with a 12-h light/dark cycle. After acclimatization for 1 week on standard rat chow, the rats were subjected to TBI by fluid percussion injury (FPI), sham surgery or non-procedure control.  At 1 week post-surgery the rats were tested for learning abilities, and then were sacrificed by decapitation. The fresh tissues including the hippocampus and white blood cells (WBC) were collected, processed, 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: Ribosome Profiling analysis of Follicular B (FoB) cells purified from WT, miR-17~92 transgenic and  miR-17-92 tKO mice

summary: We have generated a miR-17~92 transgene and fl/fl allele whose expression can be turned on and off conditionally by Cre recombinase. The mice were crossed to CD19-Cre mice to turn on and off the expression of miR-17~92 specifically in B cells and stimulated LPS/IL-4 for 25.5hr. tKO mice were generated in the miR-106a-363-/-;miR-106b-25-/- background, so that all three homologous cluster of miR-17~92 family miRNAs are deleted in B cells.

overall_design: Follicular B(FoB) cells were purified from CD19-Cre;miR-17~92 fl/fl;miR-106a-363;miR-106b~25 mice (tKO1, tKO2, tKO3), WT (WT1, WT2, WT3) and transgenic (TG2, TG2, TG3) mice by MACS depletion of cells positive for CD9, CD43, and CD93 (also known as AA4.1). The purified B cells were stimulated with LPS/IL-4 for 25.5hr in B cell media.


title: Comparison of gene transcription in Ly49G versus Ly49I positive splenic NK cells

city: Bethesda

first: Margaret

middle: C

last: Cam

state: MD

institute: NIH

summary: We report RNA seq of mature, freshly isolated splenic NK cells sorted for the expression of Ly49G or Ly49I.

overall_design: Three biological replicates of sorted Ly49G+/Ly49I- versus Ly49I+/Ly49G- NK cells prepared from the spleens of 20 C57BL/6Ncr mice

first: Stephen

last: Anderson

first: Matthew

middle: V

last: McCullen

first: Hongchuan

last: Li

first: Maggie

first: Shurjo

last: Sen

middle: W

last: McVicar


title: Acriflavine inhibits the epithelial-to-mesenchymal transition in vitro in liver and pancreatic cancer cells (part of study on PANC1 cells treated with CoCl2)

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary:
Background: Epithelial-to-mesenchymal transition (EMT) is considered an important driving mechanism behind aggressive cancer phenotype. This was recently challenged by the finding that cells can metastasize without undergoing EMT. However, the same studies confirmed the important role of the EMT program in drug resistance. The EMT program is largely dependent on the cell’s microenvironment. Acriflavine (ACF) is a heteroaromatic dye with antibacterial and antiviral effects. Recently, ACF was suggested as anticancer agent for its topoisomerase inhibitor activity. ACF further blocks the hypoxia-inducible factor (HIF) pathway, an important driver of cancer aggressiveness. How ACF works in cancer is however unknown.
Aim: Identification of the working mechanism, molecular pathways and signaling of ACF in EMT cancer cells. To this end,  three in vitro models were developed of EMT induction (human pancreatic cancer cells stimulated with TGF-b1, human pancreatic cancer cells stimulated with CoCl2, drug resistance against sorafenib in human liver cancer cells). Only the second model - PANC1 with CoCl2, a model of severe hypoxia - is discussed in this GEO submission.

overall_design: Three conditions were investigated: (1) untreated PANC1 cells (= controls), (2) PANC1 cells treated with only CoCl2, (3) PANC1 cells treated with CoCl2 and ACF. For each condition three biological replicates were profiled.

first: Jeroen

last: Dekervel

first: Ashenafi

last: Bulle

first: Petra

last: Windmolders

first: Diether

last: Lambrechts

first: Eric

last: Van Cutsem

first: Chris

last: Verslype

first: Jos

last: van Pelt


title: Acriflavine inhibits the epithelial-to-mesenchymal transition in vitro in liver and pancreatic cancer cells (part of study on HepG2)

summary: Background: Epithelial-to-mesenchymal transition (EMT) is considered an important driving mechanism behind aggressive cancer phenotype. This was recently challenged by the finding that cells can metastasize without undergoing EMT. However, the same studies confirmed the important role of the EMT program in drug resistance. The EMT program is largely dependent on the cell’s microenvironment. Acriflavine (ACF) is a heteroaromatic dye with antibacterial and antiviral effects. Recently, ACF was suggested as anticancer agent for its topoisomerase inhibitor activity. ACF further blocks the hypoxia-inducible factor (HIF) pathway, an important driver of cancer aggressiveness. How ACF works in cancer is however unknown. Aim: Identification of the working mechanism, molecular pathways and signaling of ACF in EMT cancer cells. To this end,  three in vitro models were developed of EMT induction (human pancreatic cancer cells stimulated with TGF-b1, human pancreatic cancer cells stimulated with CoCl2, drug resistance against sorafenib in human liver cancer cells). Only the third model - drug resistance against sorafenib in HepG2 cells - is discussed in this GEO submission.

overall_design: Three conditions were investigated: (1) untreated HepG2 cells (= controls), (2) HepG2 cells treated with 2.5µM acriflavine, (3) HepG2 cells treated with 5µM acriflavine. For each condition four biological replicates were profiled.


title: Transcriptomic analysis of Plasmodium berghei apiAP2 KO mutants

city: Cambridge

first: Katarzyna

middle: Kinga

last: Modrzynska

address: Genome Campus

department: Malaria program

institute: Wellcome Trust Sanger Institute

summary: During the progress through its complex life cycle, the malaria parasite requires strict control of gene expression but the mechanism controlling this process remain poorly understood and unexplored for therapeutic purposes. A group of the apicomplexa-specific putative transcription factors with AP2 DNA binding domain (apiAP2) has been identified as the major regulators of the parasite transcriptome at multiple stages. The targets and the role of the majority of the members of the family however are unknown.

overall_design: Three independent replicates of each strain + WT control were prepared for schizonts (all strains), as well as gametocytes and ookinetes (ap2-o, ap2-o2, ap2-o3 and wt control). The RNA-seq libraries were prepared using DAFT-seq protocol and sequenced using Illumina 2500 system.

first: Oliver

last: Billker


title: Toxoplasma gondii remodels the cis-regulatory landscape of infected human host cells [HELP-tagging]

city: Bronx

first: John

last: Greally

address: 1301 Morris Park Avenue

institute: Albert Einstein College of Medicine

summary: To study the host DNA methylome of human fibroblasts after infection with T. gondii (Type I-RH).

overall_design: Three biological replicates of uninfected HFFs and three biological replicates of T. gondii (Type I-RH) infected HFFs were sequenced using HELP-tagging.

first: Netha

last: Ulahannan

first: Kami

last: Kim


title: Toxoplasma gondii remodels the cis-regulatory landscape of infected human host cells [RNA-seq]

summary: To study the host transcriptome of human fibroblasts after infection with T. gondii (Type I-RH).

overall_design: Three bioloigcal replicates of uninfected HFFs and three biological replicates of T. gondii (Type I-RH) infected HFFs were sequenced using directional RNA-seq.


title: Toxoplasma gondii  remodels the cis-regulatory landscape of infected human host cells [HELP-GT]

summary: To study the host DNA hydroxymethylome of human fibroblasts after infection with T. gondii (Type I-RH).

overall_design: Three bioloigcal replicates of uninfected HFFs and three biological replicates of T. gondii (Type I-RH) infected HFFs were sequenced using HELP-tagging.


title: Toxoplasma gondii remodels the cis-regulatory landscape of infected human host cells

overall_design: Refer to individual Series


title: Landscape of TOP2A-mediated DNA cleavage across the human genome

city: Shanghai

first: Xiang

last: Yu

state: Shanghai

address: 800 DongChuan

institute: Shanghai Jiao Tong University

summary: Type II topoisomerases orchestrate proper DNA topology and they also are the targets of anticancer drugs that cause leukemias with balanced translocations as secondary cancers.  Here, we develop a novel high-throughput sequencing technology to define TOP2 cleavage sites at single base precision in human cells and use the technology to characterize TOP2A cleavage genome-wide in the K562 leukemia cell line. We find that TOP2A cleavage has functionally conserved local sequence predilections, occurs in cleavage cluster regions (CCRs) and is enriched in introns and lincRNA loci. In coding genes we discover a bias of TOP2A CCRs towards the distal regions of gene bodies and proximal shifts in TOP2A CCRs with TOP2 poisons. We find high TOP2A cleavage levels in the genes involved in translocations associated with TOP2 poisons in leukemia. In addition, we find that large a proportion of genes involved in oncogenic translocations overall contain TOP2A CCRs. The TOP2A cleavage of coding and lincRNA genes is independently associated with both length and transcript abundance. By making comparisons to ENCODE data, we uncover distinct TOP2A CCR clusters that overlap with marks of gene transcription, open chromatin and enhancers. Our findings implicate TOP2A as the DNA damage mediator in oncogenic translocations more broadly than was previously appreciated. They also identify TOP2A as a functional DNA element that contributes to the regulation of transcription elongation and gene activation.

overall_design: Global TOP2A-cleavage cluster region in human K562 cell treated with different TOP2 poisons.

first: James

last: Davenport

first: Brian

middle: D

last: Gregory

first: Carolyn

middle: A

last: Felix


title: DNA Methylation profile for male SD Rats with and without traumatic brain injury (TBI) by RRBS-Seq

city: Los Angeles

first: Xia

last: Yang

first: Qingying

last: Meng

first: Fernando

last: Gomez-Pinilla


title: Toxoplasma gondii remodels the cis-regulatory landscape of infected human host cells [ATAC-seq]

summary: To identify the open chromatin cis-regulatory elements present in uninfected and T. gondii (Type I-RH) infected HFFs.

overall_design: Three bioloigcal replicates of uninfected HFFs and three biological replicates of T. gondii (Type I-RH) infected HFFs.


title: Transcriptomic analysis of  CV. ‘Shine Muscat’  (Vitis vinifera L.) buds during dormant and non dormant period

city: nanjing

first: Muhammad

middle: Khalil

last: Ur Rehman

state: Jaingsu

address: WeiGang No.1

department: Horticulture

institute: Nanjing Agricultural university

summary: We used Illumina RNA-Seq technology to carry out digital gene expression profiling of Dormant and non dormant buds of Shine Muscat Cultivar.127 pathways were annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and metabolic, biosynthesis of secondry metabolite and. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that DEGs were involved in various metabolic processes, including phytohormone metabolism. The newly generated transcriptome and gene expression profiling data provide valuable genetic information for revealing transcriptomic variation during dormant and non dormant period in Grapevine and ultimately helpful in uplifting of table grape industry.

overall_design: Total RNA extracted from 3 samples with three replication for each and compared within all samples

first: Jianmin

last: Tao


title: Difference in miRNA expression profiles of testes tissues from different breeder cock related to dietary intake of Astragalus Polysaccharide

city: Yangling

first: Shengru

last: Wu

address: 22 St.XiNong

department: College of Animal Science and Technology

institute: Northwest A&F University

summary: We generated miRNA expression profiles of testes from breeder cocks fed with control diets and extra Astragalus Polysaccharide.  A total of 663 and 660 miRNAs were expressed in control and APS groups, and there were 16 up-expressed miRNAs and 17 down-expressed miRNAs in APS group, compared with the control group meeting the criteria of P-values<0.05.

first: Xiaochun

last: Ren


title: A molecular basis behind heterophylly in an amphibious plant, Ranunculus trichophyllus

city: Seoul

first: Juhyun

state: Seoul

address: Daehak-ro 1, Gwanak-gu

department: School of Biological Science

country: South Korea

institute: Seoul National University

summary: Transcriptomes for two types of leaves in R. tricophyllus

overall_design: Comparison between terrestrial and aquatic leaves in three replicates

first: Jinseul

last: Kyung

first: Ilha

last: Lee


title: Single cell sequencing of Dgcr8 knockout embryonic stem cells plus/minus miR-294 or let-7

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

summary: We performed Fluidigm C1 single cell sequencing analysis of wild-type and microRNA deficient (Dgcr8 knockout) mouse embryonic stem cells mock treated or transfected with either miR-294 or let-7.

overall_design: Wild-type and Dgcr8 knockout cells grown in naïve culture conditions were mock transfected or transfected with miRNA mimics for let-7b or miR-294, single cells were captured on Fluidigm C1 24 hours post-transfection and then prepared for sequencing on Illumina HiSeq1000 following manufacturer's protocol.

first: Robert

last: Blelloch

first: Diego

last: dii Bernardo


title: RNA sequencing of Hordeum vulgare near isogenic lines

city: Cologne

first: Kurt

last: Stueber

address: Carl von Linne-Weg 10

department: Genome Centre

institute: Max Planck Institute for Plant Breeding Research

summary:
NILs containing five parental lines, three wild barley genotypes ssp. spontaneum: HID 4 (A), Iraq; HID 64 (B), Turkey; and HID 369 (C), Israel,  one ssp. agriocrithon: HID 382(D)) and  cv. Morex (ssp. vulgare, USA).
Purpose: Variant calling to identifie markers associated  with a awn length QTL on the distal part of chromosome 7HL

overall_design: Two NILs differing in awn length were sequenced, one having an introgression from HID382 at position 132.01 – 134.21 cM (POPSEQ map) (RD) and the other from Morex (RM).

first: Agatha

last: Walla

first: Corinna

last: Liller

first: Wilma

last: van Esse

first: Maria

last: von Korff


title: Small RNA sequencing in cells and exosomes identifies eQTLs and 14q32 as a region of active export

city: Stanford

first: Emiy

last: Tsang

address: 300 Pasteur Dr

department: Pathology

institute: Stanford University

summary: Exosomes are small extracellular vesicles that carry heterogeneous cargo, including RNA, between cells. Increasing evidence suggests that exosomes are important mediators of intercellular communication and biomarkers of disease. Despite this, the variability of exosomal RNA between individuals has not been well quantified. To assess this variability, we sequenced the small RNA of cells and exosomes from a 17-member family. Across individuals, we show that selective export of miRNAs occurs not only at the level of specific transcripts, but that a cluster of 74 mature miRNAs on chromosome 14q32 is massively exported in exosomes while mostly absent from cells. We also observe more inter-individual variability between exosomal samples than between cellular ones and identify four miRNA expression quantitative trait loci (eQTLs) shared between cells and exosomes. Our findings indicate that genomically co-located miRNAs can be exported together and highlight the variability in exosomal miRNA levels between individuals as relevant for exosome use as diagnostics.

overall_design: Small RNA-Sequencing of CEPH/UTAH family 1463 cells and exosomes

first: Emily

first: Stephen

middle: B

last: Montgomery


title: Gene expression profile for male SD Rats with and without traumatic brain injury (TBI) by RNA-Seq (CA1 and WBC)

first: Xia

last: Yang

summary: To investigate the effects of TBI on affecting the gene expressions in the hippocampus of male SD rats by RNA-Seq

overall_design: Male Sprague–Dawley (SD) rats weighing between 200 and 240 g were housed in cages and maintained in environmentally-controlled rooms (22–24C) with a 12-h light/dark cycle. After acclimatization for 1 week on standard rat chow, the rats were subjected to TBI by fluid percussion injury (FPI) or sham surgery.  At 1 week post-surgery the rats were tested for learning abilities, and then were sacrificed by decapitation. The fresh tissues including the white blood cells (WBC) isolated from blood, and the Region I of hippocampus proper (CA1) dissected were 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: A porcine gluteus medius muscle genome-wide transcriptome analysis: dietary effects of n-6 and n-3 fatty acids on biological mechanisms

city: Magdalenka

first: Magdalena

last: Ogłuszka

address: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

department: Genomics

country: Poland

summary: The level of n-6 and n-3 polyunsaturated fatty acids may affect many cellular systems and functions via nuclear receptors or the bioactive lipid regulation of gene expression. The objective of this study was to investigate the changes in the muscle transcriptome and the biological functions regulated by increased consumption of n-3 and n-6 fatty acids in the pig gluteus medius muscle. The transcriptome of the gluteus medius muscle was studied for pigs subjected to either a control diet or a diet supplemented with linseed and rapeseed oil to increase polyunsaturated fatty acid content. Next-generation sequencing (NGS) was used to generate the muscle tissue transcriptome database. The results of the NGS indicate a role of the fatty acids in the regulation of the expression of genes essential for muscle tissue development and functioning. Functional analysis revealed that the identified genes were important for a number of biological processes including protein development, signaling, inflammatory response, membranes, and lipid metabolism. The genes that were expressed specifically in only one of the dietary groups were responsible for many of the same processes listed above, indicating that biological processes were strongly modulated and tended to switch between coherent stages in response to increased levels of n-6 and n-3 fatty acids. Several nuclear receptors regulating transcription showed altered expression, including hepatocyte nuclear factor-4α (HNF4alpha), carbohydrate responsive element binding protein (ChREBP), and nuclear factor κB (NFkappaΒ). We suggest that the identified changes were largely due to regulation of those transcription factors. Our results provide strong evidence that n-6 and n-3 fatty acids regulate fundamental metabolic processes in muscle tissue development and functioning.

overall_design: Muscle mRNA profiles of Polish Landrace pig breed fed two different diets were generated by deep sequencing using Illumina MiSeq. Experimental diet was enriched with polyunsaturated fatty acids (omega-6 and omega-3), while standard diet remain as a control. 2 pooled samples, each containing RNA extracts from gluteus medius muscle of 6 individuals, were analyzed.

first: Agnieszka

last: Szostak

first: Marinus

middle: F

last: te Pas

first: Ewa

last: Poławska

first: Paweł

last: Urbański

first: Edyta

last: Juszczuk-Kubiak

first: Tadeusz

last: Blicharski

first: Chandra

last: Shekhar Pareek

first: Jenelle

middle: R

last: Dunkelberger

first: Jarosław

middle: O

last: Horbańczuk

first: Mariusz

last: Pierzchała


title: Acriflavine inhibits the epithelial-to-mesenchymal transition in vitro in liver and pancreatic cancer cells

first: Rekin's

last: Janky

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


title: Contribution of classical end-joining to PTEN inactivation in p53-mediated glioblastoma formation and drug-resistant survival

city: SEONGNAM-SI

first: YOUN JUNG

last: KANG

address: 335 PANGYO-RO

department: MEDICINE

institute: CHA University

summary: RNA-seq profiling of murine  hGFAPCreXrcc4f/fp53f/f malignant gliomas with characteristic features of human glioblastoma multiforme (GBMs). Comparison to control neurospheres generated from the hGFAPCreXrcc4f/fp53f/f postnatal day 1-3 brain.

overall_design: One control neurosphere sample and 6 malignant glioma samples.

first: YOUN

middle: J

first: CATHERINE

last: YAN

first: HIMANSHU

last: SHARMA


title: Gene expression and DNA methylation profiles for male SD Rats with and without traumatic brain injury

first: Xia

last: Yang


title: Analysis of global RNA expression established that zebrafish brain tumors resemble GBMs of the mesenchymal subtype.

city: Nantes

first: Victor

last: GOURAIN

address: 30 Bd Jean Monnet

country: France

institute: Centre de recherche en transplantation et immunologie

summary: Somatic mutations activating MAPK signaling in disorders of brain overgrowth and in diffuse glioma have recently been reported in pediatric neurology. Here we developed a progressive zebrafish model of glioma based on somatic expression of oncogenes that activate MAPK-AKT signalling (H-RASG12V, K-RASG12D, AKT, EGFRv3, BRAFV600E) in neural progenitor cells. Oncogenic HRAS was the most effective in activating MAPK signaling and caused the development of different types of growth disorders in juvenile fish: from benign dysplasia/heterotopia to invasive tumors of the telencephalon, midbrain and cerebellum.  We used this model to clarify the molecular events leading to malignant tumors instead of benign lesions. Specific signatures distinguish benign heterotopia from tumors and establish that tumors require persistent activation of MAPK/ERK. Moreover, analysis of global RNA expression showed that brain tumors expressed a gene signature similar to the mesenchymal glioblastoma subtype

overall_design: We performed transcriptome analysis (RNA-Seq) of 3 UAS:HRASV12G  brains, which carried tumorigenic lesions in the telencephalon, midbrain and IV ventricle  and compared them with tumor free, age matched brains.

first: Marina

last: Mione

last: Gourain

first: Marie

last: Mayrhofer


title: DNA methylation profile for male SD rats with and without traumatic brain injury (TBI) by RRBS

summary: To investigate the effects of TBI on affecting the DNA methylation in the hippocampus of male SD rats by sequencing the methylome (RRBS).

overall_design: Male Sprague–Dawley (SD) rats weighing between 200 and 240 g were housed in cages and maintained in environmentally-controlled rooms (22–24C) with a 12-h light/dark cycle. After acclimatization for 1 week on standard rat chow, the rats were subjected to TBI by fluid percussion injury (FPI) or sham surgery.  At 1 week post-surgery the rats were tested for learning abilities, and then were sacrificed by decapitation. The fresh tissues including the hippocampus 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: Gene expression profile for male SD Rats with and without traumatic brain injury (TBI) by RNA-Seq

summary: To investigate the effects of TBI on affecting the gene expressions in the hippocampus of male SD rats by RNA-Seq..


title: EZH1 in Germ Cells Safeguards the Function of PRC2 during Spermatogenesis

status: Public on Mar 07 2017

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: We previously reported the requirement of Polycomb Repressive Complex 2 (PRC2) for spermatogenesis through transcriptional repression of somatic genes and meiosis-specific genes. To characterize how PRC2's two methyltransferase subunits, EZH1 and EZH2, regulate histone H3 lysine 27 (H3K27) methylation during germ cell development, we generated mouse models with a germline ablation of EZH1 and/or EHZ2. Only the combined loss of EZH1 and EZH2 caused a depletion of global H3K27me3 marks and meiotic arrest in spermatocytes. Genome-wide analysis of H3K27me3 in spermatogenic cells revealed that a noncanonical EZH1-PRC2 could establish and maintain this histone mark on somatic genes and certain meiotic genes. Consistent with it having active enhancers in testis, Ezh1 was not only abundant in highly differentiated spermatocytes but also in actively proliferating progenitor and stem germ cells. Taken together, our findings suggest that the expression level of Ezh1 determines the restoration of H3K27 methylation in the absence of the canonical EZH2-PRC2.

overall_design: ChIP-seq of H3K27me3 in control and Ezh2 mutant spermatogenic cells isolated from 6-wk-old spermatocytes. Ezh2 was ablated in developing germ cells using the Mvh-Cre recombinase.

first: Weipeng

last: Mu

first: Yoichiro

last: Shibata

first: Della

last: Yee

first: Terry

last: Magnuson


title: ICF-specific DNMT3B dysfunction interferes with intragenic regulation of mRNA transcription and alternative splicing (RNA-seq)

city: Munich

first: Miriam

last: Gagliardi

state: Bayern

address: Kraepelinstrasse 2-10

institute: Max Planck Institute of Psychiatry

summary: We performed a transcriptomic and epigenomic study in patient-derived B-cell lines to investigate the genome-scale effects of DNMT3B dysfunction. We highlighted that altered intragenic CpG-methylation impairs multiple aspects of transcriptional regulation, like alternative TSS usage, antisense transcription and exon splicing.

overall_design: Samples used in this study correspond to B-lymphoblastoid cell lines (B-LCL) derived from peripheral blood of individuals affected by ICF1 syndrome and healthy individuals

first: Claudia

last: Angelini

first: Maria

last: Matarazzo


title: ICF-specific DNMT3B dysfunction interferes with intragenic regulation of mRNA transcription and alternative splicing


title: MicroRNA expression in chicken cecum following Salmonella Enteritidis infection

city: Tian'an

first: XIANYAO

last: LI

address: No. 61  Daizong Street,

department: Department of Animal Science

institute: Shandong Agricultural University

summary: White leghorn layers were infected with Salmonella Enteritidis. The cecum were collected at 7 days post infection for total RNA isolation. The significantly expressed microRNAs between infected and non-infected chickens were identified through Solexa sequencing technology.

overall_design: Three libraries were made from each group, in total, six libraries were used for Solexa sequencing.

first: Guixian

last: Wu

first: Xianyao

last: Li


title: MAP3K4 Kinase Activity Controls Chromatin Remodelers for Transitions Between Epithelial and Mesenchymal Phenotypes in Trophoblast Stem Cells

city: Memphis

first: Amy

last: Abell

state: TN

address: 3774 Walker Ave

department: Biological Sciences

institute: The University of Memphis


title: Expression changes in mRNA expression associated with the effects of nutrition on apoptosis and spermatogenesis in the adult testis

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

summary: We tested whether the defects in spermatogenesis and increases in germ cell apoptosis that are induced by under-nutrition are associated with changes in mRNA expression and pre-mRNA alternative splicing in the testis. Groups of 8 male sheep were fed for a 10% increase or 10% decrease in body mass over 65 days. We identified 2,243 mRNAs, including TP53 and Claudin 11, that were differentially expressed in testis from underfed and well-fed sheep (FDR < 0.1), and found that their changes in expression were associated with germ cells, testis size, cell cycle and spermatogenesis variations. Furthermore, pairs of 269 mRNAs and 48 miRNAs were indentified based on target prediction and the negative regulatory effect of miRNAs on mRNA expression with functions involved in abnormal reproductive morphology, apoptosis and male infertility. Nutrition did not affect the total number of alternative splicing junctions, but affected 1,040 alternative splicing events (FDR < 0.05, ∆PSI > 10%). A total of 788 genes, including CREM, MAP2, HIPK3 and TRa2β, were differentially spliced between dietary treatments, with functions related to protein localization, cellular metabolic process, post-translational protein modification and spermatogenesis. In addition, three gene modules were positively correlated with spermatogenesis-related phenotypic traits and negatively related to apoptosis-related phenotypic traits. Among these gene modules, seven (CFLAR, PTPRC, F2R, MAP3K1, EPHA7, APP, BCAP31) were also differentially expressed between nutritional treatments, indicating their potential as markers of spermatogenesis or apoptosis. We conclude that under-nutrition causes changes in mRNAs and pre-mRNA alternative splicing that, at least partly, contribute to disrupted spermatogenesis and increased germ cell apoptosis.

overall_design: Two groups of 8 male sheep were fed for a 10% increase or 10% decrease in body mass over 65 days, and the small RNA expression was profiled.

first: Yongjuan

last: Guan


title: ICF-specific DNMT3B dysfunction interferes with intragenic regulation of mRNA transcription and alternative splicing (RRBS-Seq)


title: RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-feed efficient Nordic dairy cattle

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

summary: The study investigated gene expression patterns in liver tissue to understand the biological functions of genes that are potentially involved in controlling / regulating feed efficiency in Nordic dairy cattle.

overall_design: Comparison of liver transcriptome from 2 cattle breeds (Holstein and Jersey), 2 levels of feed efficiency (FE) (High and low), 2 types of feed diet (Control (C) and High concentrate diet (HC)).  Within each breed, there are 5 High FE and 5 Low FE cows.  Notes: each of the animals received both of the diet (C and HC) after conditioning period (14 to26 days intervals). One cow from Holstein was dropped from the study because of the unsuccessful liver biopsy sampling.

first: Suraya

middle: M

last: Salleh

first: Peter

last: Løvendahl

last: Lund

first: Johanna

middle: K

last: Höglund

first: Dana

last: Olijhoek

first: Gianluca

last: Mazzoni


title: Tamoxifen-associated endometrial tumors expose differential enhancer activity for Estrogen Receptor alpha

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

department: Molecular Pathology

country: Netherlands

institute: Netherlands Cancer Institute

overall_design: Refer to individual Series


title: MAP3K4 Kinase Activity Controls Chromatin Remodelers for Transitions Between Epithelial and Mesenchymal Phenotypes in Trophoblast Stem Cells [RNA-Seq]

summary: MAP3K4 is a serine/threonine kinase that regulates epithelial to mesenchymal transition (EMT). Trophoblast stem (TS) cells lacking MAP3K4 kinase activity (TSKI4 cells) are in an intermediate state of EMT, having reduced epithelial and increased mesenchymal marker expression. Reduced epithelial gene expression in TSKI4 cells was due to loss of H2BK5 promoter acetylation catalyzed by the histone acetyltransferase CBP. Herein, we show that MAP3K4 also regulates the ubiquitination and degradation of the deacetylase HDAC6. Due to the loss of MAP3K4 kinase activity, TSKI4 cells have elevated HDAC6 expression and activity. Knockdown of HDAC6 in TSKI4 cells restores epithelial features, defining HDAC6 as a key regulator of EMT controlled by MAP3K4. HDAC6 promotes EMT by directly deacetylating H2BK5 on promoters of tight junction genes claudin6 and occludin, inhibiting their expression. Thus, MAP3K4 is a master regulator that coordinates chromatin modifiers, CBP and HDAC6, to regulate the transition between epithelial and mesenchymal states.

overall_design: RNA samples from TSWT, TSKI4, and TSKI4 HDAC6 sh2 cells were sequenced.

first: Robert

last: Mobley

first: Deepthi

last: Raghu

first: Lauren

last: Duke

first: Kayley

last: Abell-Hart

first: Jon

middle: S

last: Zawistowski

first: Kyla

last: Lutz

first: Shawn

last: Gomez

first: Sujoy

last: Roy

first: Ramin

last: Homayouni

first: Gary

middle: L

last: Johnson


title: MAP3K4 Kinase Activity Controls Chromatin Remodelers for Transitions Between Epithelial and Mesenchymal Phenotypes in Trophoblast Stem Cells [ChIP-Seq]

first: Amy

last: Abell

overall_design: α-H2BK5Ac ChIP samples from TSWT, TSKI4, and TSKI4 HDAC6 sh2 cells and a TSWT input sample were analyzed.


title: Genome Wide Characterization of Genome Organization in Mouse ES cells

city: Oxford

last: Beagrie

address: Headley Way

department: Molecular Haematology Unit

institute: MRC Weatherall Institute of Molecular Medicine

type: Genome variation profiling by high throughput sequencing

summary: The three-dimensional folding of genomes in the eukaryotic nucleus can influence the expression of genes. We used a new method to determine interactions between different chromatin regions genome-wide. Using a simple statistical model, we determine the subset of those interactions which represent stable contacts. We find an enrichment in contacts between active genes, between Polycomb-repressed genes, between enhancer elements and between enhancers and active genes.

sample_organism:
Mus musculus
other sequences

platform_organism:
Mus musculus
other sequences

overall_design: We used a new method to detect interactions from 490 46C Mouse ES cell derived samples

first: Antonio

last: Scialdone

first: Mita

last: Chotalia

first: Markus

last: Schueler

first: Mario

last: Nicodemi

first: Ana

last: Pombo


title: ICF-specific DNMT3B dysfunction interferes with intragenic regulation of mRNA transcription and alternative splicing (ChIP-Seq)

first: Miriam

last: Gagliardi

first: Claudia

last: Angelini

first: Maria

last: Matarazzo


title: The long non-coding RNA transcriptome of Dictyostelium discoideum development

city: Houston

first: Rafael

last: Rosengarten

state: Texas

address: 2520 Robinhood St #603

institute: Genialis, Inc

summary: This study details the content and dynamics of the long non-coding transcriptome during D. discoideum development, providing an important compendium to the well-characterized protein coding transcriptome. Applying a novel sample preparation method, we isolated antisense and long intergenic non-coding RNAs in addition to mRNAs. We describe the behavior of these different classes of RNAs that have been shown to play important regulatory roles in numerous model systems. Our analyses contribute a wholly different perspective to the most widely appreciated and compelling aspect of Dictyostelium biology—the change in life style from solitary amoebae to differentiated multicellular organisms.

overall_design: RNA-sequencing of rRNA-depleted (Ovation, Nugen)  libraries from Dictyosteloium discoideum developmental time course. Samples were collected every 2 hours during the 24-hour development cycle. Biological replicate 1 consists of all 13 time points. Bio rep 2 consists of 11 time points, with hours 16 and 22 failing to sequence properly. Additionally, hours 0, 4, 8, 12, 16, and 22 were reprocessed with a different rRNA-depletion method (RiboZero, Epictentre) and sequenced.

first: Balaji

last: Santhanam

first: Janez

last: Kokosar

first: Gad

last: Shaulsky


title: upSET, the Drosophila homologue of SET3, is required for viability and the proper balance of active and repressive chromatin marks

city: Boston

first: Peter

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

summary: Chromatin plays a critical role in faithful implementation of gene expression programs. Different post-translational modifications of histone proteins reflect the underlying state of gene activity, and many chromatin proteins write, erase, bind, or are repelled by these histone marks. One such protein is UpSET, the Drosophila homolog of yeast Set3 and mammalian KMT2E (MLL5). Here we show that UpSET is necessary for the proper balance between active and repressed states. Using CRISPR/Cas-9 editing, we generated S2 cells which are mutant for upSET. We found that loss of UpSET is tolerated in S2 cells, but that heterochromatin is misregulated, as evidenced by a strong decrease in H3K9me2 levels assessed by bulk histone post-translational modification quantification. To test whether this finding was consistent in the whole organism, we deleted the upSET coding sequence using CRISPR/Cas-9, which we found to be lethal in both sexes in flies. We were able to rescue this lethality using a tagged upSET transgene, and found that UpSET protein localizes to transcriptional start sites of active genes throughout the genome. Misregulated heterochromatin is apparent by suppressed position effect variegation of the wm4 allele in heterozygous upSET-deleted flies. We show that this result applies to heterochromatin genes generally using nascent-RNA sequencing in the upSET-mutant S2 lines. Our findings support a critical role for UpSET in maintaining heterochromatin, perhaps by delimiting the active chromatin environment.

overall_design: Examination of binding sites for UpSET by ChIPseq. Transcriptome analysis by RNAseq.

first: Mitzi

middle: I

last: Kuroda

first: Kyle

last: McElroy


title: SALL4 ensures oocytes maturation by modulating DNA methylation and histone modifications

city: Shanghai

first: Shaorong

last: Gao

address: No. 1239, Siping Road

institute: Tongji University


title: Gene expression profiles of endothelial cells from mutants and siblings of tsu3994

city: Beijing

first: Jing

last: Chen

address: Medical Building  C121

department: School of Lifesciences

institute: Tsinghua University

summary: Through RNA-seq, we report endothelial cells from mutants had 1063 up-regulated and 132 down-regulated genes (>2.0 fold with false discovery rate <0.001)  when compared to siblings.

overall_design: Examination of gene exprssion profiles of endothelial cells from siblings and mutants of tsu3994

first: Anming

last: Meng


title: Global transcriptional response in Japanese medaka larvae following embryonic exposure to TCDD

city: Raleigh

first: AtLee

last: Watson

state: North Carolina

address: Campus Box 7633

institute: North Carolina State University

summary: A global RNA-Seq analysis was conducted using RNA isolated from the axial region of DMSO- and 0.3 nM TCDD-exposed medaka to identify targets within the osteochondral pathway potentially impacted by TCDD exposure.  In total, 597 genes were significantly up- or down-regulated (q<0.05) and were associated with select pathological states including inflammatory disease, connective tissue disorders, and skeletal and muscular disorders.

overall_design: RNA was isolated from axial tissue (containing vertebrae and surrounding muscle, fat, and dermis) from Japanese medaka larvae. Whole transcriptome libraries from DMSO and TCDD-medaka were generated for downstream RNA-Seq using the Ion Torrent PGM platform.

first: Seth

last: Kullman


title: RNA-sequencing of B cells in the absence of Moz or c-Myb

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Humoral responses of mice specifically deleted for Moz (a histone acetyltransferase) or c-Myb (a transcription factor) in B cells were aberrant. RNA-sequencing analysis was performed to assess gene expression differences compared to wild-type controls in germinal center B cells or plasmablasts.

overall_design: Moz f/f Aicda1-Cre, Aicda1-Cre, Myb f/f Cd23-Cre, Mybf/f (no cre) mice were immunized with NP-KLH precipitated in alum and germinal center B cells were sort-purified. Secondary plasmablasts were sort-purified from immunized mice boosted with NP-KLH in PBS (Myb experiment). Two independent experiments were conducted.

first: Yunshun

first: Kim

last: Good-Jacobson


title: Impact of NCoR1 on global transcriptomic profiling in intestinal epithelial cells during development

city: La Jolla

first: Shujuan

state: CA

address: 9500 Gilman Drive

department: Pharmacology

country: USA

institute: University of California, San Diego

summary: To explore the molecular events engaged following the deletion of NCoR1 in intestinal tissue during development, we performed global transcriptional profiling in wild type (F/FUN) and NCoR1 intestinal deletion (ΔIECUN) mice at neonates (day 12) and adults (week 10) by utilizing RNA-seq technology.

overall_design: Intestine RNA was prepared from F/FUN and DIECUN mice at either 12-day old (neonates) or 10-week old (adults) for RNA-seq. RNA from two mice were pooled and a total three samples per strain were used for RNA-seq studies. Polyadenylated mRNA was purified with the Dynabeads mRNA purification kit (ThermoFisher). The mRNA libraries were prepared for strand-specific sequencing as previously described 58and sequenced using an Illumina HiSeq 2500 by running 36 cycles. Image deconvolution, quality value calculation, and the mapping of exon reads and exon junctions were performed. Sequencing reads were aligned to the Mus musculus (UCSC mm9) genome.

first: Robert

middle: H

last: Tukey


title: ICF-specific DNMT3B dysfunction interferes with intragenic regulation of mRNA transcription and alternative splicing (RIP-seq)

first: Miriam

last: Gagliardi

first: Claudia

last: Angelini

first: Maria


title: Circulating miRNA Associated with Posttraumatic Stress Disorder in a Cohort of Military Combat Veterans

city: Bethesda

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

institute: NIH/JHU

summary:
Objective: Posttraumatic stress disorder (PTSD) affects a high proportion of returning combat veterans, but the biological mechanisms of PTSD remain unclear. Circulating micro RNAs (miRNAs) have been associated with depression, and anxiety disorders, but there is little understanding of how miRNAs may relate to PTSD. In this study we compare profiles of circulating miRNA in combat veterans with and without PTSD in order to better understand biological mechanisms of PTSD.
Methods: Blood from 24 male military service members was collected following deployment to Operation Iraqi Freedom (OIF) or Operation Enduring Freedom (OEF), and subjects were assessed for PTSD symptoms using the PTSD checklist-military version. miRNA was isolated from whole blood and sequenced on the Ion Torrent PGM™ using the Ion 316 Chip v2. Differences in miRNA expression was compared between subjects with PTSD (N=15) and combat matched controls without PTSD (N=9). Significantly different miRNA, according to a FDR≤0.05, were assessed for predictive putative targets, and pathway analysis of related targets was completed.
Results: PTSD was associated with 4 upregulated and 4 downregulated miRNA, including a 2.94 fold increase in miR-19a-3p and a 1.56 fold decrease in miR-15b. Pathway analysis show that PTSD is related to the axon guidance and Wnt signaling pathways, which work together along with the adherens junction and MAPK signaling pathways to support neuronal development through regulation of growth cones. The PTSD associated miRNAs related to transcription factors, including Transcription factor 7 (T-cell specific, HMG-box), Transcription factor 7 like 1, and Transcription factor 7 like 2.
Conclusions: PTSD is associated with miRNAs that regulate biological functions that include neuronal activities, suggesting that they play a role in PTSD symptomatology.

overall_design: miRNA profiling of 24 human blood samples at two time points to study PTSD

first: Heather

last: Rusch


title: The role of retinol dehydrogenase 10 in the retina visual cycle

city: St. Louis

first: Joseph

middle: C

last: Corbo

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine

summary: Pigment regeneration is critical for the function of cone photoreceptors in bright and rapidly-changing light conditions. This process is facilitated by the recently-characterized retina visual cycle, in which Müller cells recycle spent all-trans-retinol visual chromophore back to 11-cis-retinol. This 11-cis-retinol is oxidized selectively in cones to the 11-cis-retinal used for pigment regeneration. However, the enzyme responsible for the oxidation of 11-cis-retinol remains unknown. Here, we sought to determine whether retinol dehydrogenase 10 (RDH10), upregulated in rod/cone hybrid retinas and expressed abundantly in Müller cells, is the enzyme that drives this reaction. We created mice lacking RDH10 either in cone photoreceptors, Müller cells, or the entire retina. In vivo electroretinography and transretinal recordings revealed normal cone photoresponses in all RDH10-deficient mouse lines. Notably, their cone-driven dark adaptation both in vivo and in isolated retina was unaffected, indicating that RDH10 is not required for the function of the retina visual cycle. We also generated transgenic mice expressing RDH10 ectopically in rod cells. However, rod dark adaptation was unaffected by the expression of RDH10 and transgenic rods were unable to use cis-retinol for pigment regeneration. We conclude that RDH10 is not the dominant retina 11-cis-RDH, leaving its primary function in the retina unknown.

overall_design: Retinas from rd7 and wild-type (C57BL/6J) mice at age 21 days were harvested. Two biological replicates per strain were collected. Each replicate consisted of 8 retinas total from two female and two male mice. RNA was extracted with Trizol, polyA-selected, and processed for mRNA-seq. All four samples were sequenced on a single lane of Illumina HiSeq 2000 (1x50 bp). Note that Nr2e3 transcript levels are higher in the rd7 mutant, as previously reported (Chen et al 2006 Hum Mol Genet 15(13):2146-56).

first: Yunlu

last: Xue

first: Susan

middle: Q

last: Shen

first: Vladimir

last: Kefalov


title: Histone modifications in primary intestinal epithelial cells from wild type (F/FUN) and intesinal NCoR1 deletion (ΔIECUN) neonates.

summary: ChIP-seq analyses were carried out in intestinanl epithelial cells (IECs) isolated from F/FUN and ΔIECUN mice to assess histone modifications across the genome, an event that links the actions of corepressors with molecular insight towards a mechanism.

overall_design: Examination of 6 different histone modifications in IECs with or without the presence of NCoR1.


title: SALL4 ensures oocytes maturation by modulating DNA methylation and histone modifications (RRBS)

first: Shaorong

country: China

summary: Splat-like 4 (Sall4) plays important roles in maintaining pluripotency of embryonic stem cells and in various developmental processes. Here, we find that the SALL4 null oocytes fail to undergo maturation to form fully-grown oocytes (FGOs) and subsequent meiosis resumption. We further discover that the loss of maternal SALL4 causes failure in establishment of DNA methylation. Moreover, we demonstrate that SALL4 modulates H3K4me3 and H3K27me3 modifications by regulating the expression of Kdm5b, Kdm6a and Kdm6b. Taken together, SALL4 plays pivotal roles in oocyte epigenetic maturation.

overall_design: In this study, we have 19 RNA-seq data and 18 RRBS data. As for RNA-seq, secondary follicle (SF) stage WT oocyte group have 2 replicates, and SF stage oocyte group have 3 replicates. Early antral follicle (EAF) stage Sall4 KO or WT oocyte group both have 3 replicates. In the microinjection experiments, the control group have 5 replicates, and the experimental group have 3 replicates. As for RRBS, SF WT group have 7 replicates, and SF Sall4 KO group have 5 replicates. EAF WT group have 4 replicates, and EAF Sall4 KO group have 2 replicates.

first: Kai

last: Xu

first: Xia

first: Hui

last: Yang

first: Yiwen

first: Yuanlin

last: He

first: Chenfei

last: Wang

first: Hua

last: Huang

first: Baodong

last: Liu

first: Wenqiang

first: Jingyi

last: Li

first: Xiaochen

last: Kou

first: Yanhong

last: Zhao

first: Kun

first: Linfeng

last: Zhang

first: Zhenzhen

last: Hou

first: Hong

first: Hailin

first: Yong

first: Jing

first: Hengyu

last: Fan

first: Fengchao

first: Yawei

first: Jiayu


title: Genome-wide maps of histone variant H3.3 occupancy in zebrafish cardiomyocytes

first: Michael

last: Tolstorukov

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

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


title: Effect of tcdR mutation in Clostridium difficile sporulation

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

summary: Clostridium difficile is an important nosocomial pathogen and the leading cause of hospital-acquired diarrhea. Antibiotic use is the primary risk factor for the development of C. difficile-associated disease because it disrupts normal protective gut flora and enables C. difficile to colonize the colon. C. difficile damages host tissue by secreting toxins and disseminates by forming spores. The toxin-encoding genes, tcdA and tcdB are part of a pathogenicity locus, which also encodes the gene tcdR that codes for the toxin genes positive regulator. TcdR is an alternate sigma factor that initiates transcription of tcdA and tcdB at their promoters. Alternative sigma factors are known to regulate virulence and virulence associated genes in many pathogenic bacteria. We created a tcdR mutant in the epidemic-type C. difficile R20291 strain in an attempt to identify the global role of tcdR. A site-directed mutation in tcdR affected both toxin production and sporulation in C. difficile R20291. Spores derived from the tcdR mutant were found to be mildly temperature sensitive. Moreover, nearly two fold more taurocholate was needed to germinate spores from the tcdR mutant than the spores prepared from the wild-type parent strain. Comparison of the tcdR mutant transcriptome with the parent strain revealed many differentially expressed late sporulation genes in the tcdR mutant. These data suggests that gene regulatory networks of toxin production and sporulation in Clostridium difficile are linked with each other.

overall_design: Total RNA was extracted from 2 independent biological replicates of ∆tcdR and WT of the R20291 C. difficile strain.

first: Marc

last: Monot

first: Revathi

last: Govind


title: Genome-wide identification of nitric-oxide regulated H3K9/14ac sites in Arabidopsis thaliana

city: Neuherberg/munich

first: Christian

last: Lindermayr

state: Bavaria

address: Ingolstädter Landstrasse 1

department: Biochemical plant pathology

institute: Helmholtz-Zentrum munich

summary: We report on the identification of nitric-oxide regulated H3K9/14ac sites in Arabidopsis. For this purpose liquid grown Arabidopsis seedlings were treated with the natural NO-donor S-nitrosoglutathione (GSNO), GSNO in combination with the NO-scavenger cPTIO, GSH (control) or TSA (positive control). Material was crosslinked and harvested 3h and 16h after onset of the treatments. Then, quantitative analysis of the H3K9/14ac patterns across these treatment was performed using DiffBind. By comparison of the GSNO and GSNO/cPTIO treatment, NO-regulated H3K9/14ac sites were identified. These sites were then annotated to the nearest TSS. GO enrichment analysis revealed that NO affects H3K9/14ac at many stress-responsive and photosynthetic genes.

overall_design: H3K9/14ac maps were generated for Arabidopsis seedlings treated with water (solvent control), GSNO, GSH, TSA or GSNO/cPTIO for 3h and 16h. The experiment was performed in two biological replicates, with input samples for each treatment/timepoint/biological replicate, resulting in a total of 40 samples. All samples were indexed, pooled and sequenced on an Illumina HiSeq2500. To obtain enough reads per sample the library had to be sequenced four times, resulting in at least 16 million reads per sample.

first: A

last: Mengel

first: E

last: Georgii

first: C


title: The coi1-2 mutant has a differential transcriptional program in response to Al stress

city: Qingdao

first: Zhong-Bao

last: Yang

state: Shandong

address: 72# Binhai Road

department: School of Life Science

institute: Shandong University (Qingdao)

summary: To investigate how JA regulates Al-induced inhibition of root growth, a transcriptional analysis through RNAseq was performed by comparing the coi1-2 mutant and WT plants in the presence or absence of Al. In the absence of Al, 149 and 147 genes were up- and down-regulated, respectively, at least 2-fold in the roots of the coi1-2 mutant and WT plants. In the presence of Al, 1747 and 5838 genes were up- and down-regulated, respectively, in the roots of WT plants, while 1449 and 3773 genes were up- and down-regulated, respectively in the coi1-2 mutant. While the comparison of the Al-exposed coi1-2 mutant and WT plants reveals that totally 1187 genes were up-regulated and only 197 genes were down-regulated at least 2-fold.

overall_design: Total RNA obtained from control (non-treated roots) and Al-exposed roots. Six day old plants were treated with and without Al treatment for 24 h, then total RNA was isolated using the RNeasy® Plant Mini Kit (QIAGEN), and then Illumina sequencing was performed.

first: Chunmei

last: He

first: Yanqi

last: Ma

first: Zhaojun

last: Ding


title: Gene Expression Profiling Of TTLL12 Knocked Down Cell With Sendai Virus Treatment

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

summary: Upon virus infection, RIG-I-like receptors in host cells recognize viral RNA and activate type I interferon expression. To investigate the role of protein methylation in the anti-viral signaling pathway, we screened all the SET domain containing proteins and identified TTLL12 as a negative regulator of RIG-I signaling pathway. TTLL12 contains SET and TTL domains, which are predicted to have lysine methyltransferase and tubulin tyrosine ligase activities, respectively. Exogenous expression of TTLL12 represses IFN-β expression induced by SeV. TTLL12 deficiency by RNA interference and CRISPR-gRNA techniques increases the induced IFN-β expression and inhibits virus replication in the cell. Gene expression profiling also indicated that TTLL12 specifically inhibits the expression of the downstream genes of innate immunity pathways. Cell fractionation and fluorescent staining indicated that TTLL12 is localized in the cytosol. The study of various mutants suggested TTLL12’s ability to repress RIG-I pathway is probably not dependent on protein modifications. Instead, TTLL12 directly interacts with VISA, TBK1 and IKKε, and inhibits the interactions of VISA with other signaling proteins. Taken together, our findings demonstrate TTLL12 as a negative regulator of RNA-virus-induced type I IFNs expression through inhibition of the interaction of VISA with other proteins.

overall_design: TTLL12 was knocked down by siRNA in HCT116 and the gene expression profile was studied by RNA sequencing

first: Lin-Gao

last: Ju

first: Yuan

last: Zhu