title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and △Rsp MRSA Transcriptomes

status: Public on Jan 02 2016

first: Michael

last: Otto

state: MD

address: 9000 Rockville Pike

department: NIAID

institute: NIH

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of gene regulon. The goal of this study is to investigate the genes regulated by Rsp in MRSA BD02-25
Methods: mRNA profiles of wild-type (WT) and Rsp knockout (△Rsp) MRSA at mid-logarithmic growth phase (4h) were generated by deep sequencing, respectively in duplicate samples, using the Hiseq2000 (Illumina, CA) sequencer. The sequence reads that passed quality filters were aligned to S. aureus COL (RefSeq accession number NC_002951.2) using the Burrows-Wheeler Alignment tool (BWA)  followed by ANOVA (ANOVA). Only the consistent data between the two WT or mutant samples were reserved for further analysis. qRT–PCR validation was performed using SYBR Green assays.
Results: Using an optimized data analysis workflow, RNA-seq analyses revealed that 328 genes were up-regulated and 176 genes were down-regulated in △rsp compared with wild type. In order to explain the major relevant changes in △rsp compare to wild-type, the differential expressed genes obtained in RNA-seq with three biological replicates were used to construct a regulation network. 108 up-regulated genes and 33 down-regulated genes in RNA-seq data had gathered in the protein-protein interaction network. 15 modules of biological processes were responsible, including ribosome, metabolism, biofilm formation, cell wall degradation, cytolysis, two-component system and so on. Biological processes related to biofilm formation, such as cell wall degradation and metabolism were up regulated, indicating that the defense systems were activated. However, the genes that responsible for the two-component system and cytolysis were down regulated, suggesting a possible pathway how Rsp controls the virulence.
Conclusions: Our data provide new information to the virulence regulatory network in S. aureus.

overall_design: mRNA profiles of wild-type (WT) and Rsp knockout (△Rsp) MRSA were generated by deep sequencing, in duplicate, using the Hiseq2000 (Illumina, CA) sequencer.

first: Tianmin

last: Li

first: Lei

last: He


title: Correlative Controls of Seeds over Maternal Growth and Senescence in Arabidopsis

status: Public on Jan 01 2016

city: Zurich

first: Samuel

middle: Elias

last: Wuest

address: Winterthurerstrasse 190

department: Institute of Evolutionary Biology and Environmental Studies

country: Switzerland

institute: University of Zurich

type: Expression profiling by high throughput sequencing

summary: Correlative controls (influences of one organ over another organ) of seeds over maternal growth are one of the most obvious phenotypic expressions of the trade-off between growth and reproduction. However, the underlying molecular mechanisms are largely unknown. Here, we characterize the physiological and molecular effects of correlative inhibition by seeds on Arabidopsis thaliana inflorescences, i.e. global proliferative arrest (GPA) during which all maternal growth ceases upon the production of a given number of seeds. We use laser-assisted microdissection and RNA-seq or Affymetrix GeneChip hybridizations to compare sterile growing, fertile growing and fertile arrested meristems or whole inflorescences. In shoot tissues, we detected the induction of stress- and senescence-related gene expression upon fruit production and GPA, and a drop in chlorophyll levels - suggestive of altered source-sink relationships between vegetative shoot and reproductive tissues. Levels of shoot reactive oxygen species, however, strongly decreased upon GPA - a phenomenon that is associated with bud dormancy in some perennials. Indeed, gene expression changes in arrested apical inflorescences after fruit removal resembled changes observed in axillary buds following release from apical dominance. This suggests that GPA represents a form of bud dormancy, and that dominance is gradually transferred from growing inflorescences to maturing seeds - allowing offspring control over maternal resources, simultaneously restricting offspring number.

overall_design: Examination of transcriptomes of four reproductive stages: i) sterile growing plants, ii) fertile growing plants, iii) fertile arrested plants, iv) arrested plants after removal of all fruits from the plant

middle: E


title: Genome-wide maps of chromatin state in ESET+/+ and ESET-/- DP thymocytes

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We generated genome-wide H3K9me3-state maps of DP thymocytes purified from ESET+/+ and ESET-/- mice  by using next generation sequencing.

overall_design: Examination of H3K9 trimethylation in DP thymocytes purified from ESET+/+ and ESET-/- mice.

first: Shoichi

last: Takikita

middle: A

first: Takeshi

last: Otsubo

first: Yuki

middle: I

last: Kawamura

first: Taeko

last: Dohi

first: Kenshiro

last: Oshima

first: Masahira

last: Hattori

first: Tetsuro

last: Toyoda

first: Ryunosuke

last: Muro

first: Toshiyuki

last: Takai

first: John

last: Weis

first: Yoichi

last: Shinkai

first: Harumi

last: Suzuki


title: ETO Family Protein Mtgr1 Mediates Prdm14 Functions in Stem Cell Maintenance

city: Stanford

first: Natalie

last: Nady

state: CA

address: 265 Campus Dr.

department: Chemical and Systems Biology

country: USA

institute: Stanford

summary: Prdm14 is a sequence-specific transcriptional regulator of embryonic stem cell (ESC) pluripotency and primordial germ cell (PGC) formation. It exerts its function, at least in part, through repressing genes associated with epigenetic modification and cell differentiation. Here, we show that this repressive function is mediated through an ETO-family co-repressor Mtgr1, which tightly binds to the pre-SET/SET domains of Prdm14 and co-occupies its genomic targets in mouse ESCs. Structure-guided point mutants abrogated the Prdm14-Mtgr1 association and disrupted Prdm14's function in mESC gene expression and PGC formation in vitro. Altogether, our work uncovers the molecular mechanism underlying Prdm14-mediated repression.

overall_design: Examination of Prdm14 and Mtgr1 occupancy by ChIP-seq and effects on gene expression in mouse embryonic stem cells

first: Nataliya

first: Tomasz

last: Swigut

first: Joanna

last: Wysocka


title: Pluripotent Stem Cells Induced from Mouse Neural Stem Cells and Small Intestinal Epithelial Cells by Small Molecule Compounds

city: Beijing

first: Junqing

last: Ye

address: Yi He Yuan Road #5

country: China

institute: Peking University

summary: Pluripotent stem cells can be generated by pure small molecule compounds. However, only fibroblasts, a heterogeneous cell population, were reported for use in chemical reprogramming, and the efficiency is relatively low, raising the possibility that chemically induced pluripotent stem cells (CiPSCs) are derived from a specific cell subpopulation residing in fibroblast culture. Thus, it is of interest to know whether chemical reprogramming can be induced in other cell types, even using the same chemical cocktail. Here, using lineage tracing, we verify the generation of CiPSCs from fibroblasts. We further demonstrate that neural stem cells (NSCs) and small intestinal epithelial cells (IECs), cell types from the ectoderm and endoderm, respectively, can be chemically reprogrammed into pluripotent stem cells. CiPSCs derived from NSCs and IECs resemble mouse embryonic stem cells (ESCs) in terms of proliferation rate, global gene expression profiling, epigenetic status, self-renewal and differentiation capacity, and germline transmission competency. Interestingly, in the chemical reprogramming process from different cell types, a pluripotency gene Sall4 was commonly expressed in the initial stage, and the same core small molecules were required, suggesting conservatism underlying chemical reprogramming from different cell types. Moreover, the use of these small molecules should be fine-tuned to meet the requirement of reprogramming from different cell types. Together, these findings demonstrate that our reported chemical reprogramming approach can be reproduced in different cell types and suggest that chemical reprogramming is a promising strategy with the potential to be extended to more initial cell types.

overall_design: We analyzed the gene expression profiles of NSC-derived CiPSCs and IEC-derived CiPSCs ,using RNA-Sequencing. NSCs, IECs, and embryonic stem cells (R1) are controls.

first: Jian

last: Ge

first: Yang

last: Zhao

first: Hongkui

last: Deng


title: A novel RAF kinase inhibitor with DFG-out binding mode: high efficacy in BRAF-mutant tumor xenograft models in the absence of normal tissue hyperproliferation

city: Vienna

first: Andreas

last: Schlattl

address: Dr. Boehringer-Gasse 5-11

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

summary:
Purpose: Seek for differential gene expression in vemurafenib-resistant A375 tumors vs. untreated controls to provide a rationale for resistance mechanism
Methods: mRNA profiles of vemurafenib-resistant A375 tumors and untreated control tumors were generated by transcriptome sequencing of A375 melanoma bearing mice. Since our xenograft samples contain a mixture of human and mouse RNAs we mapped RNASeq reads against a hybrid human/mouse genome. We than removed reads of potential mouse origin by taking only reads that map uniquely to human chromosomes. On average 23% of reads were removed as potential mouse reads. We than took the remaining reads (on average 77% per sample) to determine the gene expression levels for each sample. Normalized expression levels of 5 resistant samples were compared to 4 untreated control samples to detect differnetially regulated genes which may contribute to vemurfenib resistance
Results: Expression levels of several genes were consistently altered in all resistant samples. Expression of e.g. genes encoding SPRY2, SPRY4, DUSP6, CCND1, PIK3R3, FGFR1, EPHA4, MCL1, and IGF1R was down-regulated, whereas expression of PDGFC, VEGFC, ABCB9 and KITLG was increased.
Conclusions: Our study reports several differentially expressed genes which may contribute to vemurafenib resistance in A375 tumor bearing mice

overall_design: RNA sequencing of genes expressed in A375 tumors bearing mice treated with vemurafenib until in vivo resistance appeared vs. untreated A375 tumors


title: SIRT6 regulates redox homeostasis in human mesenchymal stem cells by the transactivation of NRF2

status: Public on Jan 04 2016

first: xiaomeng

last: liu

state: Beijing

address: Yiheyuan Road No.5

institute: Biodynamics Optical Imaging Center (BIOPIC), Peking University

summary: We investigated the effect of SIRT6-knockout on gene expression and H3K4me3 modification profile in human mesenchymal stem cells.

overall_design: RNAs isolated from SIRT6+/+ and SIRT6-/- hMSCs at early and late passages were sequenced, respectively. And, H3K4me3 ChIP-seq was performed upon the SIRT6 deleted hMSC and WT at early stage, respectively.

first: Huize

last: Pan

first: Dee

last: Guan

first: Jingyi

last: Li

first: Xiaomeng

last: Liu

first: Guanhui

first: Fuchou

last: Tang


title: Nucleosome free chromatin measured by ATAC-seq in Rice leaves (Oryza sativa)

city: New York

first: Christoph

last: Hafemeister

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Nucleosome free measurement of 14 day old rice leaves (2nd leaf) in heat stress and recovery and dehydration stress and recovery

overall_design: 5 conditions: control (30C, liquid media; at 0.5h, 2h, 4h); Heat (transferred from 30C to 40C; at 0.5h, 2h, 4h); Heat recovery (transferred back to 30C after 2h at 40C; after 2h); Dehydration (roots exposed to air; at 2h); Dehydration recovery (roots returned to liquid media after 1.5h in air; after 2h) Samples: 2 biological replicates.

first: Olivia

last: Wilkins

first: Richard

last: Bonneau

first: Michael

last: Purugganan


title: Microbial community structure of a lotic aquatic system receiving wastewater effluent

city: Charleston

first: Thomas

last: Canam

state: Illinois

address: 600 Lincoln Avenue

department: Biological Sciences

institute: Eastern Illinois University

summary: Total bacterial DNA was isolated from water and sediment samples from a local watershed and 16S rRNA sequences were analyzed using the Illumina MiSeq v3 platform in order to generate snapshots of bacterial community profiles.

overall_design: A total of 56 samples were collected that represent water and sediment samples from 14 sample sites over two different time points (November 18 and 25, 2011).

first: James

middle: M

last: Novak

first: Daniel

middle: B

last: Johnson

first: Karen

middle: F

last: Gaines


title: Comparison of RNA profiling between wild type, med20∆, rrp6∆ and med20∆/rrp6∆ in Schizosaccharomyces pombe

city: Göteborg

first: Jonas

last: Carlsten

address: Medicinaregatan 9A

department: Biomedicin

country: Sweden

institute: University of Gothenburg

summary: Mediator is a co-regulator of RNA polymerase II (Pol II), transducing signals from regulatory elements and transcription factors to the general transcription machinery at the promoter. We here demonstrate that Med20 influences ribosomal protein expression in fission yeast. In addition, loss of Med20 leads to an accumulation of aberrant readthrough tRNA transcripts. The aberrant transcripts are polyadenylated and targeted for degradation by the exosome.  Similarly, other specialized RNA molecules, such as snRNA, snoRNA and rRNA are also accumulated in the absence of Med20.  We suggest that fission yeast Mediator takes part in a regulatory pathway of Pol III transcripts.

overall_design: RNA-sequencing of wt, med20∆, rrp6∆, med20∆/rrp6∆ strains using wt as control. Each strain was sequenced using three biological replicas. The results were analyzed for differential expression.

middle: O

first: Xuefeng

last: Zhu

first: Marcela

middle: D

last: López

first: Tore

last: Samuelsson

first: Claes

last: Gustafsson


title: Ubiquitin-dependent turnover of MYC promotes loading of the PAF complex on RNA Polymerase II to drive transcriptional elongation (ChIP-seq)

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

summary: The MYC transcription factor is an unstable protein and its turnover is controlled by the ubiquitin system. Ubiquitination enhances MYC-dependent transactivation, but the underlying mechanism remains unresolved. Here we show that proteasomal turnover of MYC is dispensable for recruitment of RNA polymerase II (RNAPII), but is required to promote transcriptional elongation at MYC target genes. Degradation of MYC stimulates histone acetylation and recruitment of BRD4 and P-TEFb to target promoters, leading to phosphorylation of RNAPII CTD and the release of elongating RNAPII. In the absence of degradation, the RNA polymerase II-associated factor (PAF) complex associates with MYC via interaction of its CDC73 subunit with a conserved domain in the amino-terminus of MYC ("MYC box I"), suggesting that a MYC/PAF complex is an intermediate in transcriptional activation. Since histone acetylation depends on a second highly conserved domain in MYCs amino-terminus ("MYC box II"), we propose that both domains co-operate to transfer elongation factors onto paused RNAPII.

overall_design: ChIP-Seq experiments for MYC-HA (HA-IP) and RNAPII (total,Ser2p,Ser5p) performed in IMEC primary breast epithelial cells. Input-samples were sequenced as controls. The following antibodies were used: HA (Abcam; ab 9110)/ total RNAPII (Santa Cruz; sc-899x)/ Ser2p RNAPII (Abcam; ab 5095)/ Ser5p RNAPII (Covance; MMS-128P)

first: Laura

last: Jaenicke

first: Björn

last: von Eyss

first: Anne

last: Carstensen

first: Wenshan

last: Xu

first: Nikita

last: Popov


title: Hypothalamic reprogramming by sperm microRNA

city: Philadelphia

first: Ali

last: Rodgers

state: PA

address: 380 S. University Ave, 476 Hill Pavilion

department: Biomedical Sciences

institute: University of Pennsylvania, School of Veterinary Medicine

summary: Nine microRNAs (miRs) previously identified as increased in the sperm of stressed sires were microinjected into C57/Bl6:129S6/SvEvTac mouse single cell zygotes to examine the hypothesis that specific sperm miRs function postfertilization to alter offspring stress responsivity. Derived mice were exmined for hypothalamic-pituitary-adrenal axis stress response in adulthood, and the paraventricular nucleus of the hypothalamus was subsequently collected for gene expression analysis by next gen sequencing. Similar to what we reported previously in our paternal stress model, the majority of diffferenitally expressed genes in the PVN exhibited decreased expression, supporting that an increase of specific sperm miRs in the zygote can elicit long-term genetic reprogramming. Futher, marked changes in the expression of extracellular matrix and collagen gene sets suggested altered blood-brain barrier permeability with potential consequences for neuroendocrine function.

overall_design: mRNA profiling of paraventricular nucleus from adult male mice derived from zygote microinjection of nine miRs (multi-miR; miR-29, miR-30a, miR-30c, miR-32, miR-193-5p, miR-204, miR-375, miR-532-3p, miR-698) or PBS. Six biological replicates per group (12 total cDNA libraries) were multiplexed and sequenced on two identical HiSeq2000 lanes (Illumina).

first: Christopher

middle: P

last: Morgan

first: N

last: Leu

first: Tracy

middle: L

last: Bale


title: No evidence for a C. elegans small RNA response to feeding with OxyS-expressing bacteria

status: Public on Jan 03 2016

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

country: United Kingdom

institute: Imperial College London

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNA sequencing shows that there are no Caenorhabditis elegans endo siRNAs made against the OxyS non-coding RNA.

sample_organism:
Escherichia coli
Caenorhabditis elegans

platform_organism:
Escherichia coli
Caenorhabditis elegans

overall_design: Sequencing of small RNAs from C. elegans fed bacteria overexpressing the non-coding RNA OxyS, control samples fed either standard E. coli or one without the OxyS RNA, an rde-4 deletion mutant deficient in endo siRNA production and the OxyS-overexpressing bacteria itself. 5' independent samples were treated with the enzyme RNA 5' polyphosphatase to remove 5'  triphosphate; 5' dependent samples were not treated with 5' polyphosphatase.


title: Genetic code expansion in stable cell lines enables encoded chromatin modification

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

institute: Karolinska Institutet

summary: Genetically encoded unnatural amino acids provide powerful strategies for  modulating the molecular functions of proteins in mammalian cells. However this  approach has not been coupled to genome-wide measurements, because efficient  unnatural amino acid incorporation is limited to readily transfectable cells and  leads to very heterogeneous expression. We demonstrate that rapid piggybac  integration of the orthogonal pyrrolysyl-tRNA synthetase (PylS)/tRNAPyl  CUA pair  (and its derivatives) into the mammalian genome enables efficient, homogeneous  unnatural amino acid incorporation into target proteins in diverse cells, and we  reveal the distinct transcriptional responses of ES cells and MEFs to amber  suppression. Genetically encoding Nε-acetyl-lysine in place of six lysine residues in  histone H3, that are known to be post-translationally acetylated, enables deposition  of pre-acetylated histones into cellular chromatin, via a synthetic pathway that is  orthogonal to enzymatic modification, allowing us to determine the consequences of  acetylation at specific amino acids in histones on gene expression.

overall_design: mRNA was sequenced using polyA-enrichment and Truseq library preparation protocol. Two biological replicates were sequences for each cell line and condition

first: Jason

middle: W

last: Chin


title: RNA-seq from animals treated with RNAi against prp-8, prp-6, and prp-31

city: Hospitalet de Llobregat

first: Julián

last: Cerón

state: Barcelona

address: Gran via 199, Hospital Duran i Reynals, planta 3

department: Cancer and Human Molecular Genetics

country: Spain

institute: IDIBELL

summary: Transcriptome analysis of a population of control animals and RNAi-treated to partially inactivate genes that are homologs to human genes causing Retinitis Pigmentosa. RNA-seq analyses were performed at L3 larval stage in wild type, and smg-1(r861) mutants that have a defective Non-mediated decay pathway.  RNA-seq experiments were also performed in adults glp-4(bn2) mutants that lack of germline.

overall_design: synchronized N2 and smg-1(r861) L1 larvae fed for 24 hours at 20 °C with the RNAi clones of prp-6, prp-8, prp-31 and gfp; and 5-day adult glp-4(bn2) worms grown at 25 °C and fed first, for 72 hours with OP50 and next, for 48 more hours with the RNAi clones of prp-8, prp-31 and gfp

middle: C

last: Madrigal

first: David

last: Aristizábal-Corrales


title: Adult mouse cortical cell taxonomy by single cell transcriptomics

city: Seattle

first: Lucas

middle: T

last: Gray

state: WA

address: 615 Westlake Ave N

department: Molecular Genetics

institute: Allen Institute for Brain Science

summary: Nervous systems are composed of numerous cell types, but the extent of cell type diversity is poorly understood. Here, we construct a cellular taxonomy of one cortical region, primary visual cortex, in adult mice based on single cell RNA-sequencing. We identify 49 transcriptomic cell types including 23 GABAergic, 19 glutamatergic and 7 non-neuronal types.

overall_design: Single-cell RNA-Seq of adult mouse primary visual cortex

first: Bosiljka

last: Tasic

first: Vilas

last: Menon

first: Thuc

middle: N

last: Nguyen

first: Tae

middle: K

last: Kim

first: Zizhen

last: Yao

first: Michael

last: Hawrylycz

first: Christof

last: Koch

first: Hongkui

last: Zeng


title: The genomes of the ancestral species of peanut - a remarkable case of living archaeology

city: East Lansing

first: Chad

middle: E.

last: Niederhuth

state: M

address: 612 Wilson Road

department: Plant Biology

institute: Michigan State University

type: Methylation profiling by high throughput sequencing

summary: Peanut (Arachis hypogaea) has a large (~2.7 Gbp) allotetraploid genome with closely related component genomes making its genome very challenging to assemble. Here we report genome sequences of its diploid ancestors (A. duranensis and A. ipaënsis). We show they are similar to the peanut’s A- and B-genomes and use them use them to identify candidate disease resistance genes, create improved tetraploid transcript assemblies, and show genetic exchange between peanut’s component genomes. Based on remarkably high DNA identity and biogeography, we conclude that A. ipaënsis may be a descendant of the very same population that contributed the B-genome to cultivated peanut.

sample_organism:
Arachis duranensis
Arachis ipaensis

platform_organism:
Arachis duranensis
Arachis ipaensis

overall_design: Whole Genome Bisulphite Sequencing of the peanut species Arachis duranensis and Arachis ipaensis.

middle: E

first: Robert

last: Schmitz


title: Rice gene expression in heat stress and dehydration stress - time series

first: Christoph

last: Hafemeister

summary: Transcriptome measurements of 14 day old rice leaves (2nd leaf) in heat stress and recovery and dehydration stress and recovery - samples collected every 15 minutes for up to 4h - 480 samples (240 conditions, 2 biological replicates)

overall_design: 5 conditions: control (30C, liquid media); Heat (transferred from 30C to 40C; up to 4h); Heat recovery (transferred back to 30C after 2h at 40C; up to 2h); Dehydration (roots exposed to air; up to 2.25h); Dehydration recovery (roots returned to liquid media after 1.5h in air; up to 3.5h) Samples: every 15 minutes, 2 biological replicates.  Dataset includes 475 samples.

first: Olivia

last: Wilkins

first: Richard

last: Bonneau

last: Purugganan


title: Splicing analyses of mESCs, mNPCs, and mMNs

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

summary: PTBP1 and PTBP2 control alternative splicing programs during neuronal development, but the cellular functions of most PTBP1/2-regulated isoforms remain unknown. We show that PTBP1 guides developmental gene expression by regulating the transcription factor Pbx1. We identify exons that are differentially spliced when mouse embryonic stem cells (ESCs) differentiate into neuronal progenitor cells (NPCs) and neurons, and transition from PTBP1 to PTBP2 expression. We define those exons controlled by PTBP1 in ESCs and NPCs by RNA-seq analysis after PTBP1 depletion and PTBP1 crosslinking-immunoprecipitation. We find that PTBP1 represses Pbx1 exon 7 and the expression of its neuronal isoform Pbx1a in ESC. Using CRISPR-Cas9 to delete regulatory elements for exon 7, we induce Pbx1a expression in ESCs, finding that this activates transcription of specific neuronal genes including known Pbx1 targets. Thus PTBP1 controls the activity of Pbx1 and suppresses its neuronal transcriptional program prior to differentiation.

overall_design: HB9-GFP mESCs were differentiated into mNPCs and mMNs. Poly-A RNA was isolated from isolated populations of mESCs, mNPCs, and mMNs for RNA-sequencing and splicing analyses.

first: Anthony

last: Linares


title: Ptpb1 iCLIP in 46C mESCs and mNPCs

overall_design: 46C mESCs and mNPCs were cross-linked at 100 mJ/cm2. Cell pellets were collected and flash-frozen for iCLIP library preparation. Libraries were subjected to 100 single-end RNA-sequencing.


title: Splicing analyses of 46C mNPCs following PTBP depletion

overall_design: 46C mESCs were differentiated in mNPCs. The mNPCs were treated with 10 nM control, Ptbp1, Ptbp2, or Ptbp1 and Ptbp2 siRNAs for 48 hours. The knockdowns were performed using 2 independent sets of siRNAs. Poly-A RNA was isolated for RNA-sequencing and splicing analyses.


title: Cells with Surface Expression of CD133highCD71low are Enriched for Colony-Forming Progenitor Cells in the Adult Murine Pancreas

city: Duarte

first: Xiwei

last: Wu

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

institute: Beckman Research Institute

summary: Previously, we identified tripotent colony-forming progenitor cells in the adult murine pancreas that were capable of self-renewal and differentiation into duct, acinar and endocrine cells in vitro. However, the incidence of these progenitor cells was low (~1% among pancreatic cells in adult 2-4 month-old mice). The goal of the current study was to find cell-surface markers that can distinguish and enrich pancreatic colony-forming progenitor cells. It was found that pancreatic cells could be divided into CD133+CD71- , CD133highCD71low and CD133lowCD71low and CD133-CD71- cells. CD133highCD71low cells, but not other cell populations, were the most enriched for colony-forming progenitors. Interestingly, both CD133+CD71- and CD133highCD71low cells expressed ductal markers as shown by gene expression RT-PCR analysis. To further characterize CD133+CD71- (designated as R1 cells) and CD133highCD71low (designated as R2 cells) ductal cell populations, genome-wide gene expression analysis using RNA-seq was performed. The genes that were differentially expressed by R1 and R2 cells are deposited here. Subsequent pathway analysis of the RNA-seq data revealed that R2 and R1 cells have propensity for cell migration and immune response, respectively. These gene expression analyses suggested ductal cells of the adult pancreas are heterogeneous in nature.

overall_design: Two populations of cells are sorted from the pancreas of adult 2-4 month old C57Bl/6 mice and their RNA profiles are determined. These cell populations are CD133(high)CD71(low) cells (3 samples) and CD133(positive)CD71(negative) (2 samples).

first: Liang

last: Jin

first: Dan

last: Gao

first: Tao

last: Feng

first: Jacob

middle: R

last: Tremblay

first: Nadiah

last: Ghazalli

first: Angela

last: Luo

first: Jeffrey

last: Rawson

first: Janine

last: Quijano

first: Jing

last: Chai

first: Lena

last: Wedeken

first: Jasper

last: Hsu

first: Jeanne

last: LeBon

first: Stephanie

last: Walker

first: Hung-Ping

last: Shih

first: Alborz

last: Mahdavi

first: David

middle: A

last: Tirrell

first: Arthur

last: Riggs

first: H

last: Ku


title: The splicing regulator PTBP1 controls the activity of the transcription factor Pbx1 during neuronal differentiation

first: Chia-ho

last: Lin

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

overall_design: Refer to individual Series


title: Gene expression analyses of HB9-GFP D2 mMN cultures following Pbx1 exon 7 inclusion

overall_design: HB9-GFP mESC were transiently transfected with Cas9 and guide RNA sequences to generate heterozygous deletions at the Pbx1 intron 6 locus (Pbx1 I6 +/-). Wild type and  (n=3) or Pbx1 I6 +/- (n=5) clones were differentiated in MN media. Samples were harvested at Day 2 of differentiation, and poly-A RNA was isolated for RNA-sequencing and gene expression analyses.

first: Anthony

last: Linares


title: Splicing analyses of 46C mESCs following PTBP depletion

overall_design: 46C mESCs were treated with 20 nM control, Ptbp1, Ptbp2, or Ptbp1 and Ptbp2 siRNAs for 72 hours. The knockdowns were performed using 2 independent sets of siRNAs, including one biological replicate. Poly-A RNA was isolated for RNA-sequencing and splicing analyses.


title: ChIP-seq of circadian transcription factors in MLL-AF9 leukemia cell lines

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

summary: We performed ChIP-seq of two core circadian TFs which were found to be important in leukemia proliferation, in order to identify potential target genes regulated by the circadian rhythm.

overall_design: Here, we performed ChIP-seq for the core circadian transcription factors CLOCK and ARNTL (BMAL1) in NOMO-1 and THP-1 cells.

first: Monkia

last: Kowalczyk

first: Rishi

last: Puram


title: A comprehensive examination of dynamic gene expression changes in the mouse brain during pregnancy and the postpartum period

city: Tallahassee

first: Michelle

last: Arbeitman

state: FL

address: 1115 West Call Street

department: Department of Biomedical Sciences

institute: Florida State University

summary: The developmental transition to motherhood requires gene expression changes that alter the brain to prepare and drive the female to perform maternal behaviors. Furthermore, it is expected that the many physiological changes accompanying pregnancy and postpartum stages will impact brain gene expression patterns. To understand how extensive these gene expression changes are, we examined the global transcriptional response broadly, by examining four different brain regions: hypothalamus, hippocampus, neocortex, and cerebellum.  Further, to understand the time course of these changes we performed RNA-sequencing analyses on mRNA derived from virgin females, two pregnancy time points and three postpartum time points.  We find that each brain region and time point shows a unique molecular signature, with only 49 genes differentially expressed in all four regions, across the time points.  Additionally, several genes previously implicated in underlying postpartum depression change expression. This study serves as a comprehensive atlas of gene expression changes in the maternal brain in the cerebellum, hippocampus, hypothalamus, and neocortex. At each of the time points analyzed, all four brain regions show extensive changes, suggesting that pregnancy, parturition, and postpartum maternal experience substantially impacts diverse brain regions.

overall_design: Libraries were prepared from three independent biological replicates, mRNA for each biological replicate was derived from a single mouse brain, with each mouse brain being used to collect all four brain regions.

first: Surjyendu

last: Ray

first: Ruei-Ying

last: Tzeng

first: Lisa

middle: M

last: DiCarlo

first: Joseph

last: Bundy

first: Cynthia

last: Vied

first: Gary

last: Tyson

first: Richard

last: Nowakowski


title: Genome-wide analysis of enzalutamide- and/or olaparib-responsive gene expression in prostate cancer cells

city: Houston

first: Likun

last: Li

state: TX

address: 1515 Holcombe Blvd

department: GU Meducal Oncology

institute: MD Anderson Cancer Center

summary: Analysis of enzalutamide- and/or olaparib-responsive gene expression in prostate cancer cells. The hypothesis tested in the present study was that enzalutamide influences the expression of genes that are involved in important bioprocesses in prostate cance rcells, including DNA damage response genes and this effect may synergize with poly(ADP-ribose) polymerase inhibitor olaparib in cytotoxicity to prstate cancer cells.

overall_design: prostate cancer cells were pretreated with enzalutamide or vehicle control DMSO for 24 h, followed by treatment with enzalutamide, olaparib, enzalutamide+olaparib, or vehicle control DMSO for 48 h. Gene expression in enzalutamide+olaparib-treated cells was compared with taht in vehicle control- and single agent-treated cells.

first: Hyun-Sung

last: Lee

first: Ju-Seog

first: Timothy

last: Thompson


title: ADAR2 affects mRNA coding sequence edits but not gene expression or splicing in vivo

city: Bethesda

first: Allissa

last: Dillman

address: Center for Cancer Research National Cancer Institute Building 41, Room B626

department: Center for Cancer Research

institute: NCI

summary: Adenosine deaminases (ADARs) are RNA binding proteins that bind to double stranded RNA and convert adenosine to inosine.  Editing creates multiple isoforms of neurotransmitter receptors, including AMPA-subtype Glutamate channels such as Gria2 that is edited to introduce a Q to R amino acid change.  Adar2 knock out mice die of seizures shortly after birth, but if the Gria2 Q/R editing site is mutated to mimic the edited version then the animals are viable. We performed RNA-Seq on the frontal cortices of Adar2-/- Gria2R/R mice and their Adar2+/+ Gria2R/R littermates, quantifying overall gene expression, splicing, and A to I editing in a transcriptome-wide fashion.  We found 56 editing sites whose level of editing was significantly diminished in the Adar2 deficient animals. The majority of Adar2 responsive editing sites were in the coding regions of genes. Interestingly, other than Adar2 expression, there were only two additional statistically significant differentially expressed genes, Flnb and Cdh13.  There were also only three exons that showed statistically significant differences in expression levels between the two genotypes.  This work illustrates that ADAR2 is important in site-specific changes of protein coding sequences but has only modest effects on gene expression or splicing in vivo.

overall_design: 6 ADAR2 Knock out frontal cortices and 6 litter mate control frontal cortices from male mice

first: Mark

last: Cookson

first: Dagmar

last: Galter


title: A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways [mESCs]

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

summary: To characterize the largely unknown functions of oxidised methylcytosines (oxi-mC; 5hmC/5fC/5caC) in DNA, several sequencing protocols have been recently developed. Quantitative analysis is complicated because DNA methylation modifications need to be deconvoluted from the data which is affected by several experimental parameters, including e.g. imperfect bisulphite conversion, oxidation efficiencies, various chemical labeling and protection steps, and sequencing errors. Here, we present a hierarchical generative model, Lux, for integrative analysis of any combination of BS-seq and “oxi-mC”-seq (BS-seq/oxBS-seq/TAB-seq/fCAB-seq/CAB-seq/redBS-seq/MAB-seq) data. We show that Lux improves quantification and comparison of methylation levels over existing methods and that Lux can easily process any oxi-mC-seq data sets to quantify all cytosine modifications simultaneously together with their experimental parameters. Application of Lux to targeted data from Tet2 knockdown ESCs and T cells during development demonstrates DNA modification quantification at unprecedented detail, quantifies active demethylation pathway and reveals 5hmC localization in putative regulatory regions.

overall_design:
Examine the distribution of C, 5mC, and 5hmC in ES and Tet2 knock-down cells within selected loci.
Half of the samples are measured using the traditional bisulphite-seq protocol but the other half is measured using the oxidative bisulphite-seq protocol (oxBS-seq).

first: Yun

last: Huang

first: Anjana

last: Rao


title: A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways [T-cells]

overall_design:
Examine the distribution of C, 5mC, and 5hmC in DP, CD4 SP, and naïve CD4 T cells within selected loci.
Half of the samples are measured using the traditional bisulphite-seq protocol but the other half is measured using the oxidative bisulphite-seq protocol (oxBS-seq).

first: Ageliki

last: Tsagaratou


title: A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways


title: RNA seq of pancreatic islets isolated from free fatty acid receptor 3 knockout (Ffar3 KO) and wildtype (Ffar3 WT) male mice

city: Chicago

first: Brian

last: Layden

address: 303 E Chicago

institute: Northwestern

summary: The short chain fatty acid (SCFA) receptor (free fatty acid receptor-3; FFAR3) is expressed in pancreatic beta cells; however, its role in insulin secretion is not clearly defined. Here, we examined the role of FFAR3 in insulin secretion. Using islets from global knockout FFAR3 (Ffar3-/-) mice, we explored the role of FFAR3 and ligand-induced FFAR3 signaling on glucose stimulated insulin secretion. RNA sequencing was also performed to gain greater insight into the impact of FFAR3 deletion on the islet transcriptome. First exploring insulin secretion, it was determined that Ffar3-/- islets secrete more insulin in a glucose-dependent manner as compared to wildtype (WT) islets. Next, exploring its primary endogenous ligand, propionate, and a specific agonist for FFAR3, signaling by FFAR3 inhibited glucose-dependent insulin secretion, which occurred through a Gαi/o pathway. To help understand these results, transcriptome analyses by RNA-sequencing of Ffar3-/- and WT islets observed multiple genes with well known roles in islet biology to be altered by genetic knockout of FFAR3. Our data shows that FFAR3 signaling mediates glucose stimulated insulin secretion through Gαi/o sensitive pathway. Future studies are needed to more rigorously define the role of FFAR3 by in vivo approaches.

overall_design: Analysis of total RNA from 3 biological replicates of pancreatic islets isolated from free fatty acid receptor 3 knockout (Ffar3 KO) and wildtype (Ffar3 WT) male mice

first: Medha

last: Priyadarshini


title: Myelodysplastic syndrome: NUP98-HoxD13 (NHD13) expression effect on hematopoietic stem cells

city: Clayton

first: David

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

country: Australia

institute: Monash University

summary: Analysis of Lin-c-Kit+Sca-1- haematopoietic stem cells (HSCs) expressing the Nup98-HoxD13 (NHD13) fusion gene. NHD13 induces myelodysplastic syndrome (MDS) in mice. Results provide insight into the molecular basis of the myelodysplastic phenotype

overall_design: WT mouse HSCs were compared to an NHD13 mutant sequenced in triplicate on a HiSeq 2000

first: Andrew

last: Guirguis

last: Curtis


title: Lysophosphatidic acid receptor expression identifies a pure population of adult hippocampal stem cells with an immune cell-related transcriptional profile

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: Lysophosphatidic acid receptor 1 (LPA1) is a phospholipid which has been linked to adult hippocampal neurogenesis and learning deficits. Here we investigated whether LPA acts directly on the hippocampal stem cells and whether LPA1 could be a functional marker for their prospective isolation. Our results reveal that exogenous LPA increases precursor potential in vitro and net neurogenesis in vivo, an effect that is mediated by Akt activation. Using a mouse reporter line, immunohistochemistry and flow cytometry followed by in vitro cell culture, we show that, in contrast to the subventricular zone, neural precursor cells in the adult mouse dentate gyrus express LPA1-GFP. Fluorescence-activated cell sorting for LPA1-GFP in combination with Prominin-1 and epidermal growth factor receptor expression allowed the efficient isolation of a very pure population of hippocampal stem cells. Transcriptional analysis revealed a profile suggesting immune response and cytokine signaling as molecular regulators of adult hippocampal neural stem cells.

overall_design: RNA from cells sorted (FACS) from the dentate gyrus of adult LPA1-GFP (lysophosphatidic acid receptor) reporter mice. Sorting was based on the markers EGFR (Egfr), LPA1 (Lpar1) and Prominin1 (Prom1). From each of 4 replicates, 3 populations (stem cells, progenitor cells, niche cells) were sequenced.

first: Tara

last: Walker

first: Rupert

last: Overall


title: Dissection of the translational impacts of the PERK pathway

city: Durham

last: Reid

state: NC

address: 436 Nanaline Duke Bldg., Box 3709 DUMC

department: Biochemistry

institute: Duke University

summary: Disruptions of protein homeostasis in the endoplasmic reticulum (ER) elicit activation of the unfolded protein response (UPR), a translation- and transcription-coupled proteostatic stress response pathway. The primary translational control arm of the UPR is initiated by the PERK-dependent phosphorylation of eIF2α, leading to a large-scale reprogramming of translation and subsequent activation of an ATF4-mediated transcriptional program. It has remained challenging, however, to accurately evaluate the contribution of each component of the eIF2α/ATF4 pathway to the remodelling of transcription and translation. Here, we have used mouse embryonic fibroblasts containing either a knock-in of the non-phosphorylatable eIF2α S51A mutant or knock-out for ATF4 by ribosome profiling and mRNA-seq to define the specific contributions of eIF2α phosphoryation and ATF4 in controlling the translational and transcriptional components of the UPR. These studies show that the transcriptional and translational targets of each P-eIF2α, ATF4, and the other UPR gene expression programs overlapped extensively, leading to a core set of UPR genes whose robust expression in response to ER stress is driven by multiple mechanisms. The identification of other, more factor-specific targets illustrated the potential for functional specialization of the UPR. As the UPR progressed temporally, cells employed distinct combinations of transcriptional and translational mechanisms, initiated by different factors, to adapt to ongoing stress. These effects were accompanied by a buffering effect where changes in mRNA levels were coupled to opposing changes in ribosome loading, a property which makes cooperation between transcription and translation essential to confer robust protein expression.

overall_design:
Translational analysis by ribosome profiling and mRNA-seq of PERK pathways mutants during the UPR.
Mouse embryonic fibroblasts (MEFs) lacking components of the PERK pathway (eIF2a phosphorylation and ATF4) were subjected to ER stress and analyzed by ribosome profiling.

first: Angeline

middle: S

last: Tay

first: Shirish

last: Shenolikar

first: Christopher

last: Nicchitta


title: Expression profiling of small RNAs in developing wheat grains

city: Beijing

first: Tian

last: Li

address: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

summary: We aimed to identify differentially expressed miRNAs during wheat grain development by using high-throughput sequencing approach. Four small RNA libraries were constructed from wheat grains collected at 7, 14, 21 and 28 days post anthesis (DPA). A total of 165 known miRNAs and 37 novel miRNAs were identified in four small RNA libraries. Moreover, a miRNA-like long hairpin locus was first identified to produce 21~22-nt phased siRNAs. A comparison of the miRNAomes revealed that 55 miRNA families were differentially expressed during the grain development.

overall_design: Examination of 4 different small RNA expression profilings in the 4 developmental stages of wheat grains.

first: Xueyong

last: Zhang


title: Small RNA and degradome sequencing reveal complex roles of miRNAs and their targets in the developing grains of wheat (Triticum aestivum L.)


title: Degradome sequencing analysis in developing wheat grains

summary: We aimed to identify targets of miRNAs during wheat grain development by using degradome sequencing approach. Two degradome libraries were constructed from wheat grains.

overall_design: Verification of miRNA targets from two degradome libraries in developing wheat grains.


title: Smyd3 is a transcriptional potentiator of multiple cancer-promoting genes and required for liver or colon cancer development

city: Vassilika Vouton, Herakleion

first: Iannis

last: Talianidis

state: Crete

address: 100 N. Plastira Str

department: Institute of Molecular Biology and Biotechnology

country: Greece

institute: Foundation for Research and Technology - Hellas

summary: Smyd3 is a histone methyltransferase implicated in tumorigenesis. Here we show that Smyd3 expression in mice is required but not sufficient for chemically induced liver and colon cancer formation. In these organs Smyd3 is functioning in the nucleus as a direct transcriptional activator of several key genes involved in cell proliferation, epithelial-mesenchymal transition, JAK/Stat3 oncogenic pathways, as well as of the c-myc and b-catenin oncogenes. Smyd3 specifically interacts with H3K4Me3-modified histone tails and is recruited to the core promoter regions of many but not all active genes. Smyd3 binding density on target genes positively correlates with increased RNA Pol-II density and transcriptional outputs. The results suggest that Smyd3 is an essential transcriptional potentiator of a multitude of cancer-related genes.

overall_design: Standard Smyd3-deficient (Smyd3-KO) mice were generated using gene-trap ES cell clones (AS0527 from International Gene Trap Consortium), in which a selection cassette, containing the splice acceptor site from mouse EN2 exon 2 followed by the beta-galactosidase and neomycin resistance gene fusion gene and the SV40 polyadenylation sequence was inserted into the 5th intron of the Smyd3 gene. The resulting mice were devoid of Smyd3 mRNA and protein in all tissues, including liver and colon. For the generation of Smyd3-Tg mice the open reading frame of the mouse Smyd3 cDNA, which contained 3 Flag epitopes at the 3’ end was inserted into the StuI site of the pTTR1-ExV3 plasmid (Yan et al, 1990). The 6.8 kb HindIII fragment containing the mouse transthyretin enhancer/promoter, intron 1, Smyd3 cDNA, three Flag epitopes and SV40 poly-A site was used to microinject C57Bl/6 fertilized oocytes. Founder animals were identified by Southern blotting and crossed with F1 mice to generate lines. Specific overexpression in the liver was tested by RT-PCR analysis in different tissues.

first: Michalis

last: Sarris

first: Panagiotis

last: Moulos

first: Anna

last: Haroniti


title: Expression profiling of E14 cells overexpressing Hk2/Pkm2

city: Seoul

first: Hyunsoo

last: Kim

address: 103 Daehakro, Jongro-gu

country: South Korea

institute: Seoul  National University

summary:
Purpose: In this study, we compared transcriptome profiling (RNA-seq) between normal mouse embryonic stem cell (E14) and Hexokinase2 (Hk2)/ Pyruvate Kinase M2 (Pkm2) overexpressed E14 cell.
Result: Using an optimized data analysis workflow, we mapped over 4 billion sequence reads per sample to the mouse genome (build mm9) and identified  28698 transcripts in 5 samples.
Conclusion: Our study represents the first detailed analysis of Hk2/ Pkm2 overexpressed E14 cell transcriptomes, generated by RNA-seq technology

overall_design: We compared transcriptome profiling (RNA-Seq) between normal mouse embryonic stem cell (E14) and  E14 cells over-expressing Hexokinase2 (Hk2)/Pyruvate Kinase M2 (Pkm2)

first: Hong-Duk

last: Youn


title: Allele-specific regulation of gene expression through enhancer function and transcriptional elongation control at imprinted loci

city: Kansas City

first: Joan

last: Conaway

state: MO

institute: Stowers Institute

summary: Genomic imprinting is a critical developmental process characteristic of parent-of-origin- specific gene expression. Here, we have identified the AFF family protein, Aff3, as a factor that functionally interacts with imprinted loci. Indeed, our genome-wide studies demonstrate that Aff3 specifically binds both imprinting control regions (ICRs) and enhancers within imprinted loci in an allele-specific manner. We have identified the molecular regulators involved in the recruitment of Aff3 to ICRs to impede transcription through the ICR, and provide a mechanism requiring Aff3 within the Super Elongation Complex-like 3 (SEC-L3) in the expression of an imprinted polycistronic transcript spanning the Dlk1-Dio3 locus. Our study also shows that DNA methylation at the ICR reinforces silencing of its related enhancers by controlling the binding and activity of Aff3 in an allele-specific manner.  This study provides molecular details about the regulation of dosage-critical imprinted gene expression through Aff3’s function in transcriptional elongation control.

overall_design: ChIP-seq of Aff3 in different mES cells. ChIP-seq of Aff3, PolII, H3K9me3 in uniparental MEF cell lines. ChIP-seq of H3K27ac and PolII in mES cells after Aff3 shRNA and non-targeting shRNA. ChIP-seq of H3K27ac in wild type and Zfp57 knockout ES cells. Total RNA-seq and nascent RNA-seq of mES cells after Aff3 shRNA and non-targeting shRNA. Total RNA-seq of uniparental MEF cells after Aff3 shRNA and non-targeting shRNA.

first: Zhuojuan

last: Luo

first: Xin

last: Gao

first: Ali

last: Shilatifard


title: RNA-Seq studies identify cancer-related genes differentially regulated during inflammation-driven lung tumorigenesis and modulated by chemopreventive agents

city: Minneapolis

first: Fekadu

last: Kassie

state: MN

address: 425 East River Road, 560E MCRB

department: Veterinary Clinical Sciences

institute: University of Minnesota

summary:
Purpose: Chronic pulmonary inflammation in the form of chronic obstructive pulmonary disease (COPD) has been consistently shown to increase the risk of lung cancer. Therefore, identification of chemopreventive agents with anti-inflammatory effects, in addition to antiproliferative and apoptotic activities, is indispensable. Recently, we found that combinations of silibinin (Sil) and indole-3-carbinol (I3C) significantly inhibited lung tumorigenesis induced by 4-(methylnitro-samino)-1-(3-pyridyl)-1-butanone (NNK) and enhanced by chronic treatment with the inflammatory agent lipopolysaccharide (LPS). In this study, we described gene expression profiling of lung tissues using RNA-seq to determine the gene expression signature in inflammation-driven lung tumors and modulation of this signature by the chemopreventive agents Sil and I3C.
Methods: Total RNA extracted from lung tissues of control and treated mice were processed for mRNA sequencing, in triplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed for transcript abundance at the gene level using CLC Bio Genomics Workbench and differential gene expression analysis was performed using the built-in Empirical Analysis of Differential Gene Expression (DGE) based on 'Exact Test' method. qRT–PCR validation was performed using SYBR Green assays.
Results and conclusions: We found that 330, 2,957, and 1,143 genes were differentially regulated in mice treated with NNK, LPS, and NNK + LPS, respectively. The expression of inflammation-and immunity-related genes was significantly more deregulated in lung tissues of mice treated with LPS alone compared to mice treated with NNK + LPS. Among 1,143 genes differentially regulated in the NNK + LPS group, the expression of 162 genes and associated signaling pathways were significantly modulated by I3C and/or Sil + I3C. These genes include cytokines, chemokines, and genes with a well-established role in inflammation and/or tumorigenesis such as c-ros oncogene 1 (Ros1), the EGFR ligands amphiregulin and epiregulin, Cyp1a1, and the circadian rhythm genes Arntl, and Npas2. To our knowledge, this is the first report that provides insight into genes that are differentially expressed during inflammation-driven lung tumorigenesis and the modulation of these genes by chemopreventive agents.

overall_design: Lung tissue mRNA profiles of mice treated with control vehicle, NNK, LPS, NNK+LPS, or NNK+LPS supplemented with chemopreventive agent(s) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.


title: Multiple Sclerosis Pattern II Demyelinating Lesions

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

overall_design: Refer to individual Series


title: Transcriptomic analysis of Plasmodium PBANKA, PBSLTRiP-KO, PB268-KO parasite infected and uninfected host cell

city: New Delhi

first: Agam

middle: Prasad

last: Singh

state: Delhi

address: Aruna Asaf Ali Marg

department: IDL

country: India

institute: NII

summary: Liver stage of malaria parasite exports SLTRiP and PB268 to the cytosol of parasite infected host cell. To know the host genes perturbed by WT-PBANKA, SLTRiP-KO and PB268-KO parasite growth, we did transcriptomic sequencing of infected host cells.  We did mRNA sequencing of four samples for comparative analysis of WT and PB-knockout parasites infected host cells at 22 hours of post sporozoites infection.

overall_design: mRNA profiles of Plasmodium PBANKA, PBSLTRiP-KO, PB268-KO parasite infected and uninfected HepG2 cells after  22hrs of sporozoites infections  were generated by deep sequencing using Illumina GAIIx.

first: D

last: Jaijyan

first: A

last: Pandit


title: Macrophage Precursor Cells from the Left Atrial Appendage of the Adult Heart Spontaneously Reprogram  into a C-kit+/CD45- Stem Cell-Like Phenotype

city: Jerusalem

first: Jussi

last: Leinonen

address: Kiryat Hadassah p.o.b 12000

department: Cardiovascular Research Center, Heart Institute

country: Israel

institute: Hadassah-Hebrew University Medical Center

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


title: Hey target gene regulation in murine ES cells and cardiomyocytes [high throughput sequencing]

city: Wuerzburg

first: Manfred

last: Gessler

address: Am Hubland

department: Developmental Biochemistry

institute: Biocenter, University of Wuerzburg

summary: We used an in vitro cardiomyocyte differentiation system with inducible Hey1 or Hey2 expression to study target gene regulation in cardiomyocytes (CM) generated from murine embryonic stem cells (ESC). The effects of Hey1 and Hey2 are largely redundant, but cell type specific. The number of regulated genes is comparable between ESC and CM, but the total number of binding sites is much higher, especially in ESC, targeting mainly genes involved in transcriptional regulation and developmental processes. Repression by Hey generally correlates with the extent of Hey-binding to target promoters, subsequent Hdac recruitment and lower histone acetylation. Functionally, treatment with the Hdac inhibitor TSA abolished Hey target gene regulation. However, in CM the repressive effect of Hey-binding is lost for a subset of genes. These lack Hey-dependent histone deacetylation in CM and are enriched for binding sites of cardiac specific activators like Srf, Nkx2-5, and Gata4.

overall_design: ES cells and cardiomyocytes with Hey1 or Hey2 overexpression were compared to control cells

first: David

last: Weber

first: Julia

last: Heisig

first: Susanne

last: Kneitz


title: Dual roles of RNF2 in melanoma progression

first: Kadir

middle: Caner

last: Akdemir


title: Next Generation Sequencing of Pattern II Demyelinating Brain Lesions from a Multiple Sclerosis Patient

summary: Multiple sclerosis is a chronic inflammatory demyelinating disease of the central nervous system with marked heterogeneity in several aspects including pathological processes. Four histopathological patterns of MS have been described. Pattern II is characterized by infiltrating macrophages and T-cells and by antibody and complement deposition. Transcriptome analysis of three patern II demyelinating brain lesions from a multiple sclerosis patient using RNA sequencing demonstrated the presence of mRNA transcripts for genes specific of activated macrophages, T and B cells as well as genes coding for immunoglobulins, complement proteins and some pattern II associated proteins, providing additional evidence supporting pattern II demyelination.

overall_design: Examination of 3 different demyelinating lesions identified by Immunohistopathology.

first: Roland

last: Martin

first: Mireia

last: Sospedra

first: Raquel

last: Planas


title: Irp2 mediates cigarette smoke-induced bronchitis and emphysema via regulation of cytochrome c oxidase and mitochondrial iron loading

city: New York

first: Augustine

middle: MK

last: Choi

state: NY

address: 525 East 68th Street, Room M-522, Box 130

department: Department of Medicine

institute: Weill Cornell Medical College

summary: Chronic obstructive pulmonary disease (COPD), the fourth leading cause of death globally, is influenced by both cigarette smoking and genetic determinants.  We have previously identified iron-responsive element binding protein 2 (IRP2) as a candidate COPD susceptibility gene based on genetic association studies, with IRP2 increased in the lungs of COPD patients. Here we demonstrate that mice deficient in IRP2 are protected from cigarette smoke (CS)-induced COPD. Using RIP-Seq, RNA-Seq, gene expression and pathway analysis, we identify IRP2 as a regulator of mitochondrial function in the lung. We show that an increase in IRP2 results in a cytochrome c oxidase (COX)-dependent alteration in oxidative capacity and mitochondrial-iron dysfunction involving frataxin. We demonstrate that mice with impaired COX or frataxin activity have altered responses to CS and show that overexpressing IRP2 in vivo alters mitochondrial dynamics. These data suggest a critical role of the mitochondria-iron axis in mediating the pathogenesis of COPD.

overall_design: 1.5 X106 Beas2B cells (purchased from ATCC) with or without 10 μM DFO (16 h) (15 cm2 dishes) were washed with ice cold PBS and collected into 2 ml eppendorfs by scraping. RNA immunoprecipitation was carried out using the Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore, Billerica, MA). 4 μg of Irp2 (7H6: sc-33682, Santa Cruz, Dallas, Texas) or 4 μg of IgG rabbit control antibody (sc-2749, Santa Cruz) were added to supernatants and incubated overnight at 4°C. RNA was extracted from Magna RIP™ beads by Trizol extraction. Samples were prepared for RNA-Seq using the TruSeq RNA-Seq Lib Prep Reagent (Illumina, San Diego, CA) and performed on the Illumina HiSeq2000 platform.

first: Suzanne

last: Cloonan

first: Kimberly

last: Glass


title: Dual roles of RNF2 in melanoma progression [ChIP-seq]

institute: MD Anderson Cancer Center

summary:
Epigenetic regulators have emerged as critical factors governing the biology of cancer. Here, in the context of melanoma, we show that RNF2 is prognostic, exhibiting progression-correlated expression in human melanocytic neoplasms.
Through a series of gain of function and loss of function studies, we establish that RNF2 is oncogenic and pro-metastatic. Mechanistically, RNF2-mediated invasive behavior is dependent on its ability to mono-ubiquitinate H2AK119 at the promoter of LTBP2, resulting in silencing of this negative regulator of TGFβ signaling. In contrast, RNF2's oncogenic activity did not require its catalytic activity nor derives from its canonical gene repression function, rather RNF2 drives proliferation through direct transcriptional up-regulation of the cell cycle regulator CCND2. In summary, RNF2 regulates distinct biological processes in the genesis and progression of melanoma via distinct molecular mechanisms, underscoring the complex and multi-faceted actions of epigenetic regulators in cancer.

overall_design: RNF2 is overexpressed in immortalized human melanocytes HMEL-BRAFV600E to address impact of RNF2 overexpression in melanoma and identify RNF2 target genes. ChIP was performed to identify RNF2 binding sites using antibody against the V5 tag.

first: Kunal

last: Rai


title: Transcriptional responses of an indigenous and an invasive whitefly to different host plants reveal their different capacity of adaptation

city: Hangzhou

first: Xiaowei

last: Wang

address: 866 Yuhangtang Road

department: Insect Sciences

institute: Zhejiang University

summary: The whitefly Bemisa tabaci is a species complex with global distribution and extensive genetic diversity. In this species complex, Middle East-Asia Minor 1 (MEAM1, previously referred to as the ‘B biotype’) species has been spreading rapidly in tropical and subtropical regions. we analyzed the transcriptional responses of the invasive MEAM1 and the indigenous Asia II 3 species of B. tabaci complex during host plant shift (from cotton to tobacco) using the Illumina sequencing technology.The different gene expression pattern of energy and carbonhydrate metabolism and detoxification metabolism between MEAM1 and Asia II 3 were the main reasons of their different capacity of adapation.

overall_design: The global transcriptional difference between the invasive whitefly Bemisia tabaci species (MEAM1) and the indigenous whitefly species (Asia II 3) on cotton and tobacco were analyzed using the Illumina sequencing technology.

first: Hong-Xing

last: Xu

first: Hong

last: Yue

first: Yong-Liang

first: Xiao-Wei

first: Shu-Sheng

last: Liu


title: Widespread RNA Binding by Chromatin Associated Proteins

city: Cambridge

first: David

last: Kelley

address: 7 Divinity Ave.

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: Recent evidence suggests that RNA interaction can regulate the activity and localization of DNA binding proteins, particularly chromatin-associated proteins. However, it is unknown if these observations are specialized instances for a few key RNAs and chromatin factors in specific contexts, or a general mechanism underlying the establishment of chromatin state and regulation of gene expression. Here, we introduce formaldehyde RNA ImmunoPrecipitation (fRIP-Seq), a sensitive method for cataloging RNA-protein interactions, to survey the RNA associated with a panel of 24 chromatin-associated and traditional RNA binding proteins. For each protein that reproducibly bound measurable quantities of bulk RNA (90% of the panel), we detected enrichment for hundreds to thousands of both noncoding and mRNA transcripts. We found that the enriched sets of RNA share biochemical, functional, and epigenetic properties. Thus, these data provide strong evidence that non-random RNA association is a common feature across diverse classes of chromatin modifying complexes.

overall_design: RNA associated with 24 different proteins using fRIP was compared to total RNA-seq

last: Hendrickson


title: Defining principles of gene and regulatory element imprinting in mouse trophoblast stem cells

city: Chapel Hill

first: J

middle: Mauro

last: Calabrese

address: 120 Mason Farm Road

department: Pharmacology

institute: UNC-Chapel Hill

summary: An undefined number of mammalian genes are expressed preferentially from one parental allele, in a process termed genomic imprinting. To shed light on the general principles of this process in a single cell type, we profiled allelic gene expression, DNaseI hypersensitivity (DHS), and CTCF binding in genetically defined murine trophoblast stem cells (TSCs). The data deposited in this entry are from CTCF ChIP-Seq and DNase-Seq experiments performed in the BC.1 cell line. All other data has been previously deposited as part of GEO Series GSE39406.

overall_design: The F1 TSC line profiled was generated from a cross between a C57BL/6J (B6) female and CAST/EiJ (Cast) male mouse.


title: Macrophage Precursor Cells from the Left Atrial Appendage of the Adult Heart Spontaneously Reprogram  into a C-kit+/CD45- Stem Cell-Like Phenotype [RNA-Seq]

first: Jussi

last: Leinonen

summary: The developmental origin of the c-kit expressing progenitor cell pool in the adult heart has remained elusive. Recently, it has been discovered that the injured heart is enriched with c-kit+ cells, which also express the hematopoietic marker CD45. In this study, we characterize the phenotype and transcriptome of the c-kit+/CD45+ cell population, originating from the left atrial appendage. These cells are defined as cardiac macrophage progenitors. We also demonstrate that the c-kit+/CD45+ progenitor cell population activates heart development, neural crest and pluripotency associated pathways in vitro, in conjunction with CD45 down-regulation, and acquire a c-kit+/lin- phenotype. This spontaneous reprogramming progresses further to a highly proliferative, partially myogenic phenotype. Our data suggests that c-kit+/lin- cells and cardiac macrophages have a common lineage origin possibly resolving some current conundrums in the field of cardiac regeneration.

overall_design: Two different stem cell types were grown by altering the tissue digestion protocol, from which one type was spontaneously transdifferentiating to other cell types. To investigate their transcriptional profiles we prepared RNA from two cell sorted replicates per cell type (A, B, C1, C2, C3).

middle: V

first: Ronen

last: Beeri


title: Hey target gene regulation in murine ES cells and cardiomyocytes

first: Manfred

last: Gessler


title: Transcriptome sequencing analysis of swamp eel

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: The swamp eel or rice field eel (Monopterus albus) taxonomically belongs to the family Synbranchidae of the order Synbranchiformes (Neoteleostei, Teleostei, Vertebrata). It is not only an economically important freshwater fish in aquacultural production, but also an increasingly known model species for biological studies. Understanding molecular mechanisms underlying sex change is a major area of interest. The swamp eel thus offers a powerful system for studying sexual development and adaptive evolution in vertebrates.The whole genome sequencing provides valuable resources for sex control in fish production, species protection through manipulating sex reversal genes, and potentially enabling effective population control and promoting reproduction health in human.

overall_design: High throughput sequencing was employed for three samples,three kind s of sex gonad from swamp eel, testis,ovotestis and ovary, no replicates.

first: Rongjia

last: Zhou

first: Majing

last: Luo


title: Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals (ICSI)

status: Public on Dec 31 2015

city: Santa Cruz

first: Upasna

last: Sharma

state: California

address: 1156 High St

department: MCD Biology

institute: UCSC

summary: Parental dietary conditions can influence the metabolic traits of offspring. In mice, paternal consumption of low protein diet alters cholesterol and lipid metabolism of progeny. Here, we examine RNA species expressed in male reproductive tissues of mice. Protein restriction leads to altered levels of multiple small RNAs in mature sperm, as well as throughout the male reproductive tract, with decreased levels of let-7 family members and increased levels of 5’ fragments of tRNA-Gly isoacceptors. Intriguingly, tRNA fragments are scarce in the testis, but their levels increase in sperm during post-testicular maturation in the epididymis. We find that epididymosomes – extracellular vesicles which fuse with sperm during epididymal transit – exhibit RNA payloads closely matching those of mature sperm, and can deliver tRNA fragments to immature sperm in vitro both in mouse and in bull. Finally, we show that tRNA-Gly-GCC fragments play a role in repressing genes associated with the endogenous retroelement MERVL, both in ES cells and in preimplantation embryos. Our results shed light on small RNA biogenesis during post-testicular sperm maturation, and link tRNA fragments to regulation of endogenous retroelements active in the early embryo.

overall_design: Zygotes were generated by ICSI from oocytes/females fed a Control diet and sperm/males fed either a Control or Low Protein diet. The sperm was isolated from either the Rete testis or the Cauda epididymis and injected either as a whole sperm or just the sperm head. Following fertilization by ICSI the zygotes developed for 28 hours (2C stage) and were harvested for single-embryo RNA-Seq.

first: Colin

last: Conine

first: Oliver

last: Rando


title: Identification of Magnaporthe oryzae elicited small RNAs and expression profiles in resistant and susceptible rice cultivars

city: Guangzhou

first: Jingxin

last: Zhang

state: Guangdong

institute: Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P.R.China

summary: To identify blast pathogen elicited miRNAs, four sRNA libraries were constructed: 8749036, A library, susceptible rice cultivar Zhonger-Ruanzhan; 12157795, B library, mock-treated blast resistant line H4; 9937360, C library, blast-treated susceptible rice cultivar Zhonger-Ruanzhan; and 11138187 clean reads, D library, blast-treated blast resistant line H4. The Short Oligonucleotide Analysis Package (SOAP; Beijing Genomics Institute) matched 85.46% (A, 7476714), 79.35% (B, 9647324), 77.70% (C, 7721715) and 76.10% (D, 8476386) sRNA reads to the genome. After removing other RNA categories matched to NCBI Genbank, Rfam database, known rice miRNA precursor, repeat associated RNA and siRNA, the remaining reads: 1681359(A); 3829741(B); 3182403(C); and 3970132(D), were used for further novel miRNA prediction. Since some miRNAs were tissue-specific, time-specific or stress-induced, only 291, 210, 164 and 220 registered miRNAs were identified in libraries A, B, C and D respectively. Thirty-one (A, 9385 reads), 399(B, 41024 read), 351(C, 36622 reads) and 333(D, 38064 reads) unique sRNAs were projected to be candidate miRNAs.

overall_design: Examination of mock-treated rice cultivar, mock-treated blast resistant rice line H4, blast-treated susceptible rice cultivar, and blast-treated blast resistant rice line H4.

first: Zhang

last: Jingxin


title: Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals (smallRNA-seq)

overall_design: Small RNA (<40nt) profile of various tissues and cells was examined by deep sequencing

middle: C

middle: J


title: Auxin-independent NAC pathway regulates cell wall metabolism in response to explant-specific wounding during regeneration in Arabidopsis I

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

summary: In this study, through a genome-wide transcriptome analysis of wounding in the leaf explant, we identified NAC1 (petunia NAM and Arabidopsis ATAF1, ATAF2, and CUC2) family transcription factor gene  that acts in response to wounding and functions in regulation of cell wall metabolism.

overall_design: RNA-Seq analysis of the genes up-regulated by NAC1

first: Xiaodong

last: Chen

first: Jingfei

last: Cheng

first: Guifang


title: Identification of MEDIATOR16 as the Arabidopsis COBRA suppressor, MONGOOSE1

city: BERKELEY

first: Nadav

last: Sorek

state: CALIFORNIA

address: 2151 BERKELEY WAT

department: PMB

institute: UC BERKELEY

summary: RNAseq data for Col-0. cob-6, sfr6-3 and cob-6sfr6-3

overall_design: 7 days old seedlings grown in 24h light with 0

first: Chris

last: Somerville


title: Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder

city: Riverside

first: Junchao

last: Shi

state: CA

address: 900 University Ave

department: Division of Biomedical Sciences, School of Medicine

institute: University of California, Riverside

summary: Increasing evidences indicate diet-induced metabolic disorder could be paternally inherited, but the exact sperm epigenetic carrier remains unclear. Here, in a paternal high-fat diet (HFD) mouse model, we revealed that a highly enriched subset of sperm small RNAs (30-34 nt) that derived from the 5’ halves of tRNAs (tsRNAs), exhibit changes in both expression profiles and RNA modifications. Injection of sperm tsRNAs from HFD male but not synthetic tsRNAs lacking RNA modifications, into normal zygotes generated metabolic disorders in the F1 offspring. Injection of HFD sperm tsRNAs derails gene expression in both early embryos and islets of F1 offspring, enriched in metabolic pathways, but unrelated to DNA methylation at CpG-enriched region. Collectively, we uncover sperm tsRNAs as a type of “epigenetic carrier” that mediate intergenerational inheritance of acquired traits.

overall_design: Mature sperm small-RNA profiles between High-fat-diet (HFD) and Normal-diet (ND) males; Transcriptional profiles of 8-cell embryos and balstocysts that developed from zygotes that injected with sperm RNAs from HFD vs ND males. Transcriptional profiles and RRBS profiles of islets of F1 offsrping that generated from zygotes that injected with sperm RNAs from HFD vs ND males.

first: Qi

first: Enkui

last: Duan


title: Auxin-independent NAC pathway regulates cell wall metabolism in response to explant-specific wounding during regeneration in Arabidopsis

overall_design: Refer to individual Series


title: Gene expression data from adipocytes of insulin resistant mice

city: Charlottesville

first: Annamalai

last: Muthiah

state: VA

address: 857, Swan Ridge Road

institute: University of Virginia

summary:
We developed a novel network inference approach, Biologically Anchored Knowledge Expansion (BAKE), to analyze large volume gene expression data obtained from a mouse model of insulin resistance progression.
Both genetic aspects and dietary factors, specifically high caloric high-fat high-sugar diets, contribute to the progression of insulin resistance. To mimic genetic predisposition, we used a mouse model with double heterozygous deletion of early insulin signaling pathway intermediates, insulin receptor (IR) and insulin receptor substrate 1 (IRS1) genes. These mice were fed with high-fat (Western) or low-fat (Chow) diet for 8 and 16 weeks starting at 8 weeks of age. Gene expression data was collected from adipocytes isolated from these mice. Applying BAKE analysis to the adipocyte gene expression data, we demonstrate that we can accurately discover a novel regulatory gene in the insulin signaling pathway.

overall_design: The mouse model of double heterozygous deletion of insulin receptor (IR) and insulin receptor substrate 1 (IRS1) was originally introduced as a polygenic model to study the development of type 2 diabetes. This mouse model, on an atherosclerosis-prone ApoE null background (IR+/- IRS1+/- ApoE-/-), also shows increased atherosclerotic lesions due to impaired insulin signaling.  For our study we used female double heterozygous mice (IR+/- IRS1+/-, 'Dhet' mice or 'D’ mice) on an ApoE null background (ApoE-/-, ‘E’) fed with a Western (high-fat) diet for 8 (DW8, n=5) and 16 (DW16, n=9) weeks starting at 8 weeks of age or with a Chow (low-fat) diet (DC8, n=7; DC16, n=5). There were also ApoE null mice (ApoE-/-, 'E’) fed either Western diet for 8 (EW8, n=6) and 16 (EW16, n=8) weeks or Chow diet for 16 weeks (EC16, n=5) starting at 8 weeks of age.

first: Lee

last: Jae

first: Keller

last: Susanna


title: Identification and Characterization of Cryptic Extremophile Traits by Experimental Evolution

city: Lincoln

first: Paul

last: Blum

state: NE

address: 1901 Vine St.

department: School of Biological Sciences

institute: University of Nebraska-Lincoln

summary: Extremely thermoacidophilic Crenarchaeota belonging to the family Sulfolobales flourish in hot acidic habitats that are strongly oxidizing. However, the pH extremes of these habitats often exceed the acid tolerance of type species and strains. Here, experimental evolution was used to test whether such organisms harbor additional thermoacidophilic capacity. Three distinct cell lines derived from a single type species were subjected to high temperature serial passage while culture acidity was gradually increased. A 178-fold increase in thermoacidophily was achieved after 29 increments of shifted culture pH resulting in growth at pH 0.8 and 80°C. These strains are named super acid resistant crenarchaeota (SARC). Mathematical modeling using growth parameters predicted the limits of acid resistance while genome and transcriptome resequencing provided insights into the underlying mechanisms responsible for evolved thermoacidophily. Transcriptomics of the evolved strains indicates that their unique phenotype may be due to an increased rate of membrane turnover under strong acid conditions.

overall_design: 6 Samples were analyzed: 2 replicate control samples [SULA] and 2 replicate experimental samples [SULC and SULB]

first: Samuel

last: McCarthy

first: Tyler

last: Johnson

first: Benjamin

last: Pavlik

first: Sophie

last: Payne

first: Wendy

last: Schackwitz

first: Joel

last: Martin

first: Anna

last: Lipzen


title: Assessment of ability of hTSLP to maintain primary CRLF2 B-ALL cells in a xenograft model in a state more similar to the parent leukemia

city: Loma Linda

first: Kimberly

address: 11085 Campus Street, Mortensen Hall, First Floor

institute: Loma Linda University

summary: Xenograft models represent an excellent method for expanding primary leukemias, but their ability to preserve the gene expression profile of the parent leukemia may also depend on providing microenvironmental factors that are not cross-reactive between human and mouse. Here we focused on leukemias with a CRLF2 mutation, and the ability of human TSLP to stimulate these cells.

overall_design: Three different classes of samples were analyzed. 1) The primary leukemia sample without any culture or treatment 2) Xenograft samples (2) of the primary leukemia that were exposed to TSLP in vivo for 2 weeks, 9 weeks post-engraftment and 3) Xenograft samples (2) of the primary leukemia that were NOT exposed to TSLP in vivo for 2 weeks, 9 weeks post-engraftment.


title: EBF2 promotes the recruitment of beige adipocytes in white adipose tissue

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: The induction of beige/brite adipose cells in white adipose tissue (WAT) is associated with protection against high fat diet-induced obesity and insulin resistance in animals. The helix-loop-helix transcription factor Early B-Cell Factor-2 (EBF2) regulates brown adipose tissue development. We examined the role of EBF2 in beige fat cell biogenesis by comparing transcriptome in wildtype and EBF2-overexpressing mice in the adipose tissue.

overall_design: Four control replicates (wildtype) and four experimental replicates (Fabp4-Ebf2) mice were analyzed

first: Rachel

last: Stine

first: Suzanne

middle: N

last: Shapira

first: Jeff

last: Ishibashi

first: Sona

last: Rajakumari

first: Matthew

last: Harms

first: Kyoung-Jae

last: Won

first: Patrick

last: Seale


title: Mdm2 enhances stemness-promoting chromatin modifications through the Polycomb Repressor Complex 2 in a p53-Independent Manner [RNA-Seq]

city: Goettingen

first: Magdalena

last: Wienken

address: Justus-von-Liebig-Weg 11

institute: University Medical Center Goettingen

summary: The Mdm2 oncoprotein ubiquitinates and antagonizes p53 but may also carry out p53-independent functions. Here we report that Mdm2 is required for the efficient generation of induced pluripotent stem cells (iPSCs) from murine embryonic fibroblasts, in the absence of p53. Similarly, Mdm2 depletion in the context of p53 deficiency also promoted the differentiation of human mesenchymal stem cells and diminished clonogenic survival of cancer cells. Most of the Mdm2-controlled genes also responded to the inactivation of the Polycomb Repressor Complex 2 (PRC2) and its catalytic component EZH2. Mdm2 physically associated with EZH2 on chromatin, enhancing the trimethylation of Histone 3 at lysine 27 and the ubiquitination of Histone 2A at lysine 119 (H2AK119) at its target genes. Removing Mdm2 simultaneously with the H2AK119 E3 ligase Ring1B/RNF2 further induced these genes and synthetically arrested cell proliferation. In conclusion, Mdm2 supports the Polycomb-mediated repression of lineage specific genes independent of p53.

overall_design: Expression profiling by high throughput sequencing of p53 ko MEFs, p53Mdm2 ko MEFs, p53ko Mdm2 C462A ki MEFs.

first: Antje

last: Dickmanns

first: Matthias

last: Dobbelstein


title: Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals (IVF)

first: Upasna

last: Sharma

overall_design: IVF was carried out using oocytes from females fed Control diet (C) and sperm from males fed Control diet or Low Protein diet (LP).  Zygotes were then developed 2 cell (2C), 4 cell (4C), 8 cell (8C), Morula (M) or Blastocyst (B) embryonic developmental stages when single embryo RNA seq was carried out to study gene expression changes.

first: Jeremy

last: Shea

first: Alan

last: Derr

first: Oliver

last: Rando


title: Mdm2 enhances stemness-promoting chromatin modifications through the Polycomb Repressor Complex 2 in a p53-Independent Manner [ChIP-Seq]

overall_design: H3K27me3 and H2Ak119ub1 ChIP-Seq


title: SMN and Symmetric Arginine Dimethylation of RNAP II CTD Control Termination

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

summary: The C-terminal domain (CTD) of the RNA polymerase II (RNAPII) subunit POLR2A is a platform for modifications specifying the recruitment of factors that regulate transcription, mRNA processing, and chromatin remodeling.  Here, we show that a CTD arginine residue (R1810 in human) that is conserved across vertebrates is symmetrically dimethylated (me2s).  This R1810me2s modification requires Protein Arginine Methyltransferase 5 (PRMT5) and recruits the Tudor domain of the Survival of Motor Neuron (SMN) protein, which is mutated in spinal muscular atrophy (SMA).  SMN interacts with Senataxin, which is sometimes mutated in Ataxia Oculomotor Apraxia 2 (AOA2) and Amyotrophic Lateral Sclerosis (ALS4).  Because R1810me2s and SMN, like Senataxin, are required for resolving RNA-DNA hybrids, created by RNA polymerase II, that form ‘R-loops’ in transcription termination regions, we propose that R1810me2s, SMN, and Senataxin are components of a pathway for R-loop resolution in which defects can influence transcription termination and may contribute to neurodegenerative disorders.

overall_design: ChIP of RNAPII in Raji cells expressing shRNG against SMN or GFP; ChIP against RNAPII in Raji cells where endogenous RNAPII has been replaced with wt or R1810A mutant amanitin-resistant protein; and ChIP of SMN in HEK293 cells.

first: Dorothy

middle: Y

last: Zhao

first: Gerald

last: Gish

first: Yue

last: Li

first: Zuyao

last: Ni

first: Frank

middle: W

last: Schmitges

first: Guoqing

last: Zhong

first: Ke

last: Liu

first: Weiguo

first: Jason

last: Moffat

first: Masoud

last: Vedadi

first: Jinrong

last: Min

first: Tony

last: Pawson

first: Benjamin

last: Blencowe

first: Jack

middle: F

last: Greenblatt


title: Transcriptomic profiling of S. cerevisiae wild type and aft2 mutant in response to exposure to selenite

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

institute: UNIVERSITAT AUTONOMA BARCELONA

summary: The yeast S. cerevisiae does not require selenium for growth, so it is an excellent model to investigate the toxicity of this element without interference from its requirement as growth factor as occurs in animal cells. Exposure to selenite interferes with the yeast iron metabolism. Aft2 is a transcription factor related (with Aft1) to maintenance of iron homeostasis. We have found that aft2 cells are highly sensitive to selenite (a common environmental source for selenium). In these experiments we investigate the transcriptional response to a sub-lethal dose of selenite in wild type and aft2 cells. Our results show that the aft2 mutation strongly potentiates the transcriptional response to selenite, showing induction of many genes related to the responses to oxidative stress and DNA damage.

overall_design: Wild type (W303-1A) background and its MML1086 derivative (Daft2) were exposed to 1 mm selenite and samples taken at time 0, 1, 3 and 5 h of selenite treatment. Two biological replicates were prepared for each time-point. Therefore, there are 8 samples per replicate (4 samples for WT and 4 samples for aft2 cells). The WT strain is used here as reference.

first: Joaquín

last: Ariño

first: David

last: Canadell

first: Albert

last: Serra-Cardona

first: María

last: Pérez-Sampietro

first: Celia

last: Casas

first: Enrique

last: Herrero


title: Circadian regulation of gene expression in the SCN

city: Philadelphia

first: Heather

last: Ballance

state: PA

address: 3400 Civic Center Blvd. Building 421

institute: University of Pennsylvania

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


title: Auxin-independent NAC pathway regulates cell wall metabolism in response to explant-specific wounding during regeneration in Arabidopsis II

first: Lin

last: XU

overall_design: RNA-Seq analysis of the wound site of leaf explants and leaf residu

first: Xiaodong

last: Chen

first: Jingfei

last: Cheng

first: Guifang

last: Zhang


title: Whole Genome Bisulfite sequencing of Arabidopsis thaliana High and Low phosphate methylomes

city: Irapuato

first: Luis Rafael

middle: Herrera

last: Estrella

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera León

department: LANGEBIO

country: Mexico

institute: LANGEBIO CINVESTAV

summary: Pi availability is a significant limiting factor for plant growth in both natural and agricultural systems. To cope with such limiting conditions, plants have adapted developmental and biochemical strategies to enhance Pi acquisition and to avoid starvation. A myriad of genes that are involved in the regulation and display of these strategies have been identified. However, the possible epigenetic components regulating the phosphate starvation responses have not been thoroughly investigated. DNA methylation is a major epigenetic mark involved in diverse biological processes and it may play a critical role in Pi starvation stress adaptation, also changes in DNA methylation can lead to a unique gene expression pattern in response to specific developmental and environmental conditions. Here in we demonstrate that non-CpG DNA methylation is required for proper expression of a number of Pi-limitation responsive genes in Arabidopsis thaliana and results in altered morphologic and physiologic phosphate starvation responses.Our data suggest that DNA methylation is involved in the modulation of Pi starvation responses via the transcriptional regulation of a set of phosphate-starvation responsive genes.

overall_design: Analysis of 8 different treatments, 2 different Organs (Root and Shoot), 2 different Phosphate treatments (High Pi, Low Pi), 2 different Times (Short Term, Long Term), 2 biological replicates for treatment

first: Lenin

last: Yong-Villalobos

first: Luis

middle: R

last: Herrera-Estrella

first: Octavio

last: Martinez-de la Vega


title: Gene expression analysis of CD4+ and CD4- ILC1 subsets by RNAseq

city: Seattle

first: Scott

last: Presnell

state: WA

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

summary: Innate lymphoid cell (ILC) subsets that mirror helper T cells in their effector cytokine profiles have recently emerged as central players in both homeostatic and inflammatory conditions.  Like their Th1, Th2 and Th17/Th22 helper T cell counterparts, ILC subsets are categorized based on their expression of specific transcription factors and effector cytokines:  group 1 ILC (ILC1) express T-bet and IFN-γ; group 2 ILC (ILC2) express GATA-3 and type 2 effector cytokines such as IL-13 and IL-5; and group 3 ILC (ILC3) express RORgt and the cytokines IL-22 and/or IL-17.  Under this nomenclature, natural killer (NK) cells and lymphoid tissue inducers (LTi) are considered ILC1 and ILC3, respectively.  ILC1 contain both CD4+ and CD4- populations, but whether this phenotypic characteristic reflects functional differences between these two populations is unknown.  These studies examine the gene expression profiles of CD4+ vs CD4- ILC1 in a cohort of healthy control subjects.

overall_design: ILC subsets were isolated from the peripheral blood of healthy control subjects.  cDNA was isolated and amplified from sorted populations, and gene expression was analyzed by RNAseq

first: Florence

last: Roan

first: Thomas

middle: A

last: Stoklasek

first: Elizabeth

last: Whalen

first: Jeffrey

last: Bluestone

first: Michael

last: Mason

first: Steven

last: Ziegler


title: The histone H3 lysine 4 presenter WDR5 induces N-Myc target gene transcription and promotes neuroblastoma

city: Randwick

first: Tao

last: Liu

state: NSW

address: Lowy Cancer Research Centre

institute: Children's Cancer Institute Australia


title: BMAL1 Activates Clock Gene Expression by Regulating Transcription Initiation

city: Beijing

first: xiong

middle: will

last: wei

address: 7 Science Park Road ZGC Life Science Park

institute: NIBS,Beijing

summary: We showed that Bmal1 mainly regulates clock gene initiation, with this functioning being highly conserved across species.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: compare RNA-seq and chip-seq between wildtype and mutant cells

first: Xiong

last: Wei


title: Cryptochromes interact directly with PIFs to control plant growth in limiting blue light

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Sun-loving plants have the ability to detect and avoid shading through sensing of both blue and red light wavelengths. Higher plant cryptochromes (CRYs) control how plants modulate growth in response to changes in blue light. For growth under a canopy, where blue light is diminished, CRY1 and CRY2 perceive this change and respond by directly contacting two bHLH transcription factors, PIF4 and PIF5. These factors are also known to be controlled by phytochromes, the red/far-red photoreceptors; however, transcriptome analyses indicate that the gene regulatory programs induced by the different light wavelengths are distinct. Our results indicate that CRYs signal by modulating PIF activity genome-wide, and that these factors integrate binding of different plant photoreceptors to facilitate growth changes under different light conditions.

overall_design: We performed whole-genome chromatin immunoprecipitation with sequencing (ChIP-Seq) analysis on 5 day old Flash-CRY2, PIF4-Flash and PIF5-Flash treated in low blue-light for 16h.

first: Joanne

last: Chory

first: Ullas

last: Pedmale

first: Shao-shan

last: Huang

first: Mark

last: Zander


title: Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals

city: Santa Cruz

first: Upasna

last: Sharma

address: 1156 High St

institute: UCSC

first: Colin

last: Conine

first: Oliver

last: Rando


title: Circadian regulation of gene expression in the SCN (RNA-seq)

first: Heather

last: Ballance

summary: We performed a circadian RNA expression profile of the mammalian biological clock, the suprachiasmatic nucleus (SCN) in C57/BL6 mice, at 2-hour resolution using microarrays, and at 6-hour resolution using RNA-seq.

overall_design: 8 samples total covering 8 time points, with no replicates. SCN samples from mouse brains collected every 6 hours for 2 days (8 samples total).


title: RNA-seq analysis between mouse UPS tumors (KP) and mouse UPS tumors without HIF-2alpha (KPH2)

first: M. Celeste

last: Simon

address: 421 Curie Blvd.

summary: Purpose: determine RNA expression differences in an unbiased fashion between UPS tumors derived from LSL-KrasG12D;Trp53-/- (KP) mice, and  UPS tumors derived from LSL-KrasG12D;Trp53-/-;Epas1-/- (KPH2) mice. Epas1 encodes HIF-2alpha protein.

overall_design: RNA-seq was performed on KP (n = 4) and KPH2 (n = 4) derived UPS tumors using Illumina HiSeq 2000.

last: Nakazawa

first: M


title: Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals (single embryo)

summary: Parental dietary conditions can influence the metabolic traits of offspring. In mice, paternal consumption of low protein diet alters cholesterol and lipid metabolism of progeny. Here, we examine RNA species expressed in male reproductive tissues of mice. Protein restriction leads to altered levels of multiple small RNAs in mature sperm, as well as throughout the male reproductive tract, with decreased levels of let-7 family members and increased levels of 5’ fragments of tRNA-Gly isoacceptors. Intriguingly, tRNA fragments are scarce in the testis, but their levels increase in sperm during post-testicular maturation in the epididymis. We find that epididymosomes – extracellular vesicles which fuse with sperm during epididymal transit – exhibit RNA payloads closely matching those of mature sperm, and can deliver tRNA fragments to immature sperm in vitro both in mouse and in bull. Finally, we show that tRNA-Gly-GCC fragments play a role in repressing genes associated with the endogenous retroelement MERVL, both in ES cells and in preimplantation embryos. Our results shed light on small RNA biogenesis during post-testicular sperm maturation, and link tRNA fragments to regulation of endogenous retroelements active in the early embryo.

overall_design: Zygotes were generated by IVF from animals fed a control diet. These embryos were then microinjected with various combinations of small RNAs and control RNA (HIS3.3::GFP). Follwoing injections the zygotes were developed and allowed to develop until 2 cell (2C) or 4 cell (4C) stage when single embryo RNA seq was carried out to study gene expression changes

first: Ana

last: Boskovic


title: The histone H3 lysine 4 presenter WDR5 induces N-Myc target gene transcription and promotes neuroblastoma [ChIP-Seq]

summary:
WDR5 is an important co-factor for N-Myc-regulated transcriptional activation and tumorigenesis
Using ChIP-Seq, We profiled key epigenetic marks H3K4 trimethylation in BE(2)-C neuroblastoma cells transfected with control siRNA or WDR5 siRNA-1 at N-Myc target gene promoters
The results showed knockdown WDR5 significantly reduced H3K4me3 at 93.2% of N-Myc binding promoters, but only at 53.5% of N-Myc non-binding promoters.

overall_design: Identification of Histone H3K4 trimethylation and N-Myc binding sites in BE(2)-C cells transfected with control siRNA or WDR5 siRNA-1.

first: Yuting

last: Sun


title: Expression of AWR5 in wild type and cdc55 deletion mutant at 6 h of induction

first: JOAQUIN

last: ARINO

summary: Expressing the type III effector AWR5 of the phytopathogen Ralstonia solanacearum in yeast cells causes cessation of growth and transcriptional changes reminiscent of inhibition of the TOR pathway. Deletion of cdc55, a regulatory subunit of the PP2A Ser/Thr protein phosphatase eliminates the strong growth defect caused by AWR5 expression. This experiments aims to identify the impact of the cdc55 mutation in the transcriptome of AWR5-expressing cells.

overall_design: induction of AWR5 in JA-100 CDC55 tetO:AWR5-GFP and JA-100 cdc55 tetO:AWR5-GFP

first: Joaquin

last: Ariño

first: Crina

last: Popa

first: Sergio

last: Gil

first: Laura

last: Tatjer

last: Tabuchi

first: Núria

last: Coll

first: Marc

last: Valls