title: Development of Pathway Preferential Estrogens Affording Beneficial Metabolic and Vascular Actions without Reproductive Tissue Stimulation in Mice

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

summary: There is great medical need for estrogens having favorable pharmacological profiles, supporting desirable activities for menopausal women such as metabolic and vascular protection but lacking stimulatory activities on the breast or uterus. Here, we report the development of structurally novel estrogens with favorable target tissue-selective estrogenic activity. Through a process of structural alteration of the hormone estradiol that preserves essential chemical and physical features of estradiol but greatly moderates its binding affinity for the estrogen receptors (ERs), we obtained Pathway Preferential Estrogens (PaPEs) capable of having interaction with ER that is sufficient to activate the extranuclear-initiated signaling pathway preferentially over the direct nuclear-initiated pathway. PaPE modulate a pattern of gene regulation and cellular and biological processes that result in essentially no stimulation of reproductive and mammary tissues and breast cancer cells, but have a favorable pattern of activity on metabolic tissues and the vasculature. The structural permutation process represents a novel approach to govern the balance in utilization of extranuclear vs. nuclear pathways of ER action to obtain tissue-selective/non-nuclear pathway-preferential estrogens, which should prove to be beneficial for postmenopausal hormone replacement. The approach may also have broad applicability for other members of the nuclear hormone receptor superfamily.

overall_design: 24 samples; inhibitor and time course experiments

last: Madak-Erdogan


title: 5-Hydroxymenthylation-associated Epigenetic Modifiers in Alzheimer's disease

status: Public on Jul 20 2016

city: Atlanta

first: Peng

last: Jin

state: GA

address: 615 Michael St

country: USA

institute: Emory University

type: Methylation profiling by high throughput sequencing

summary: Alzheimer's disease (AD) is a chronic neurodegenerative disorder characterized by progressive deterioration of cognitive function. Evidence suggests a role for epigenetic regulation, in particular the cytosine modifications 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC,) in AD. 5hmC is highly enriched in the nervous system and displays neurodevelopment and age-related changes. To determine the role of 5hmC in AD, we performed genome-wide analyses of 5hmC in DNA from prefrontal cortex of post-mortem AD as well as RNA-Seq to correlate changes in methylation status with transcriptional changes. We also utilized the existing AD fly model to further test the functional significance of these epigenetically altered loci. We identified 325 genes containing differentially hydroxymethylated loci (DhMLs) in both the discovery and replication datasets, and these are enriched for pathways involved in neuron projection development and neurogenesis. Of the 325 genes identified, 140 also showed changes in gene expression by RNA-Seq. Proteins encoded by genes identified in the current analysis form direct protein-protein interactions with AD-associated genes, expanding the network of genes implicated in AD. Furthermore, we identified AD-associated single nucleotide polymorphisms (SNPs) located within or near DhMLs, suggesting that these SNPs may identify regions of epigenetic gene regulation that play a role in AD pathogenesis. Finally using the existing AD fly model we showed that some of these genes could modulate the toxicity associated with AD. Our data implicate neuron projection development and neurogenesis pathways as potential targets in AD.  These results indicate that incorporating epigenomic and transcriptomic data with GWAS data can expand the known network of genes involved in disease pathogenesis. Combination of epigenome profiling and Drosophila model enables us to identify the epigenetic modifiers of Alzheimer's disease.

overall_design: University of Kentucky Alzheimer's Disease Research Center (3 control, 3 Alzheimer's) and Emory University Alzheimer's Disease Research Center (2 control, 2 Alzheimer's)

first: Alison

middle: I

last: Bernstein

first: Yunting

last: Lin

first: R

middle: C

last: Street

first: Li

first: Marla

last: Gearing

first: James

middle: L

last: Lah

first: Peter

middle: T

last: Nelson

first: Allan

last: Levey

first: Jennifer

middle: G

last: Mulle

first: Ranhui

last: Duan


title: The Nuclear Receptor Rev-erb alpha Regulates Adipose Tissue-Specific FGF21 Signaling

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

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Perlman syndrome nuclease DIS3L2 controls cytoplasmic non-coding RNAs and provides surveillance pathway for maturing snRNAs

status: Public on Jul 19 2016

city: Warszawa

first: Tomasz

middle: M.

last: Kuliński

state: Mazowieckie

address: ul. Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: The exosome-independent exoribonuclease DIS3L2 is mutated in Perlman syndrome. Here we used extensive global transcriptomic and targeted biochemical analyses to identify novel DIS3L2 substrates in human cells. We show that DIS3L2 regulates pol II transcripts, comprising selected canonical and histone-coding mRNAs, and a novel FTL_short RNA from the ferritin mRNA 5' UTR. Importantly, DIS3L2 contributes to surveillance of pre-snRNAs during their cytoplasmic maturation. Among pol III transcripts, DIS3L2 particularly targets vault and Y RNAs and an Alu-like element BC200 RNA, but not Alu repeats, which are removed by exosome-associated DIS3. Using 3' RACE-Seq, we demonstrate that all novel DIS3L2 substrates are uridylated in vivo by TUT4/TUT7 poly(U) polymerases. Uridylation-dependent DIS3L2-mediated decay can be recapitulated in vitro, thus reinforcing the tight cooperation between DIS3L2 and TUTases. Together these results indicate that catalytically inactive DIS3L2, characteristic of Perlman syndrome, can lead to deregulation of its target RNAs to disturb transcriptome homeostasis.

overall_design:
To investigate DIS3L2 functions genome-wide, total RNA samples were collected from model cell lines producing either WT or mut DIS3L2 three days after induction with doxycycline. The RNA samples were rRNA-depleted before preparation of strand-specific total RNA libraries according to the standard TruSeq (Illumina) protocol. TruSeq library preparation favours RNA molecules longer than 200 nt, and shorter transcripts are suboptimal for sequencing via this protocol. Thus, to obtain information about potential DIS3L2 RNA substrates with lengths between 20 and 220 nt, another RNA-Seq was carried out in parallel (with size selection through gel purification).
The stable inducible HEK293 cell lines producing DIS3L2 variants were obtained using “pAL_01” and “pAL_02” plasmid constructs and the Flp-In™ T-REx™ system according to the manufacturer’s guidelines. “pAL_01” and “pAL_02” plasmids are vectors for co-expression of recoded C-terminal FLAG-tagged DIS3L2 [wild type (WT) variant or its catalytic mutant counterpart (mut), respectively] and sh-miRNAs directed against endogenous DIS3L2 mRNA.

first: Anna

last: Labno

first: Zbigniew

last: Warkocki

last: Kulinski

first: Pawel

middle: S

last: Krawczyk

first: Krystian

last: Bijata

first: Rafal

last: Tomecki

first: Andrzej

last: Dziembowski


title: Biological characterization of virulent therapeutic bacteriophage PAK_P3 infecting Pseudomonas aeruginosa.

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

summary: We have isolated and characterized several bacteriophages infecting Pseudomonas aeruginosa distantly related to Felix O1 virus and proposed they form a new subfamily named Felixounavirinae. The infectious cycle of bacteriophages belonging to this subfamily has not been studied yet in terms of gene expression. The present study reports the RNA-Seq analysis of bacteriophage PAK_P3 infecting PAK strain of P. aeruginosa.

sample_organism:
Pseudomonas aeruginosa
Pseudomonas phage PAK_P3

overall_design: RNA profile of Host and Phage at 0min, 3.5min and 13 min after infection of Pseudomonas aeruginosa PAK strain with the Pseudomonas phage PAK P3. Three biological replicates for each time point.

first: Anne

last: Chevallereau

first: Marc

last: Monot

first: Bob

last: Blasel


title: Inactivation of Oncogenic cAMP-specific Phosphodiesterase 4D by miR-139-5p in Response to p53 Activation

city: New Orleans

first: HUA

last: LU

state: LA

address: 1430 Tulane Ave

department: Biochemistry and Molecular Biology

institute: TULANE UNIVERSITY

summary: Investigation of microRNA expression level changes in human colon cancer cell lines in response to p53 activation by Inauhzin (INZ), and identification of novel p53 target microRNAs.

overall_design: HCT116 p53+/+ and HCT116 p53-/- cells were treated with DMSO or 4μM INZ and harvested at 18 hours post treatment. Cells were then homogenized in TriZol reagents. Duplicates were included for each sample. Total RNA was extracted by following the manufacturer’s standard instructions (Invitrogen).

first: Bo

last: Cao

first: Hua

last: Lu


title: Azithromycin effects on lung microbiome in COPD patient

city: New York

first: Leopoldo

middle: Nicolas

last: Segal

state: NY

address: 462 First Avenue NBV 6N5-6N8

department: Medicine

institute: NYU School of Medicine

summary: Azithromycin (AZM) reduces pulmonary inflammation and exacerbations in chronic obstructive pulmonary disease patients with emphysema. The antimicrobial effects of AZM on the lung microbiome are not known and may contribute to its beneficial effects.  Methods. Twenty smokers with emphysema were randomized to receive AZM 250 mg or placebo daily for 8 weeks. Bronchoalveolar lavage (BAL) was performed at baseline and after treatment. Measurements included: rDNA gene quantity and sequence. Results. Compared with placebo, AZM did not alter bacterial burden but reduced α-diversity, decreasing 11 low abundance taxa, none of which are classical pulmonary pathogens. Conclusions. AZM treatment the lung microbiome

overall_design:
Randomized trial comparing azithromycin (AZM) treatment with placebo for eight weeks. Bronchoalveolar lavage (BAL) samples were obtained before and after treatment to explore the effects of AZM on microbiome, in the lower airways. 16S rRNA was quantified and sequenced (MiSeq)
The amplicons from total 39 samples are barcoded and the barcode is provided in the metadata_complete.txt file.

first: Michael

last: Weiden


title: RNA-seq Analysis of MoRFX1-dependent Genes in Magnaporthe oryzae 70-15

city: Hangzhou

first: Jianping

state: Zhejiang

address: 866 Yuhantang Road

department: College of Life Sciences

country: China

institute: Zhejiang University

summary:
Purpose: The goals of this study are to find out the genes regulated directly or indirectly by the regulatory factor X protein MoRfx1 by RNA-seq in the rice blast fungus
Methods: Mycelial mRNAs of the wild type strain 70-15, ΔMorfx1 incubated in H2O at 25˚C for 4 h, in triplicate independently for each strain, were extracted and isolated by RNeasy Plant mini kit (QIAGEN) and AMPure XP beads (Beckman). RNA-sequencing libraries were constructed using NEBNext RNA sample preparation kit (NEB). Samples were sequenced in a 1 x 100 nt way on Illumina Hiseq2500 instrument using TruSeq PE Cluster Kit v3 - cBot - HS (Illumina) and TruSeq SBS Kit v3-HS (Illumina).The M. oryzae genome database (MG8) (www.broadinstitute.org) was used as a reference gene database. Genome-wide transcript levels of genes were quantified in fragments per kilobase of exon model per million mapped reads (FPKM) (Trapnell 2010). Gene Ontology (GO) enrichment analyses for differentially expressed genes were performed using hypergeometric test with topGO, and p-values were adjusted with Bonferroni for multiple testing (Alexa 2006). And we selected FDR < 0.05 as enrichment terms.
Results and Conclusions: We identified 1735 genes regulated by Morfx1 through RNA-seq.

overall_design: Mycelial mRNA profiles of wild type strain 70-15 (WT), ΔMorfx1 incubated in H2O for 4 h were generated, in biologic triplicate, by Illumina Hiseq2500 in a 1 x 100 nt way

first: Jian

middle: P

first: Hui

middle: J

first: Li

last: Zhang

first: Peng

middle: Y

last: Huang

first: Fu

last: Lin

first: Dan

middle: D

last: Sun


title: Small RNA sequencing in tomato roots with and without Rhizophagus irregularis

city: Nanjing

first: Ping

last: Wu

address: 163 Xianlin Avenue

institute: Nanjing University

summary: Arbuscular mycorrhizal symbiosis is a predominant relationship between plant and arbuscular mycorrhizal fungi. To idendify arbuscular mycorrhiza responsive miRNAs, small RNA libraries were constructed in tomato roots colonized with Rhizophagus irregularis and without Rhizophagus irregularis. We identify miRNAs in tomato roots and provide a new profile of tomato miRNAs. And we found that some miRNAs were responsive to arbuscular mycorrhiza by comparing miRNAs in treatment with that in control.

overall_design: Examination of arbuscular mycorrhiza responsive miRNAs in tomato through high-throughput small RNA sequencing of  roots with Rhizophagus irregularis and that without Rhizophagus irregularis

first: Jianqun

last: Chen


title: RNA-Seq analysis of human adult peripheral blood populations

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

summary: Generate transcriptomic atlas of healthy peripheral blood subpopulations

overall_design:
RNA-Seq performed on sorted granulocytes, monocytes, B-cells, T-cells, total WBC, CD34+ cells
Leucegene Project, IRIC

first: Caroline

last: Pabst

first: Jonathan

last: Yeh


title: Vicious circle of LSD1 and TGF β1 promotes EMT of gastric cancer

city: Zhengzhou

first: Jinlian

last: Ma

state: Henan

address: 100 Kexue Avenue

department: School of Pharmaceutical Sciences

institute: Zhengzhou University

summary: Vicious circle of some key proteins is critical in the process of tumor development. Nevertheless, the mechanism of how the epigenetic modifiers are involved in was seldom reported and has not been clearly illustrated. We found the expression of lysine specific demethylase 1 (LSD1), the first identified histone lysine demethylase, is positively correlated with transforming growth factor beta 1 (TGF β1) in gastric cancer tissues and can be promoted by TGF β1 activated (p-EKR)-(NF-κB)-p300 signaling pathway, which resulted in the progression of epithelial-mesenchymal transition (EMT) in human gastric cancer cells. On the other hand, abrogation of LSD1 leads to the down regulation of TGF β1 as well as the EMT. But in benign cells, this circle was blocked by TGF β1 induced inactivation of ERK, which suggested the distinct roles of TGF β1 against LSD1 in gastric cancer cells and benign cells. This vicious cycle may illustrate a novel mechanism for EMT in gastric cancer mediate by TGF β1 and LSD1 but not in benign cells and may serve as a new strategy for the prevention of EMT for gastric cancer.

overall_design: Nuclear extracts prepared from MGC803 cells stably expressing Lenti-CAS9-sgRNA-puro for LSD1 or empty vector were used in immunoprecipitation reactions with antibodies against H3K4me2 and H3K9me2. Sequencing libraries were prepared using the TruSeq DNA Sample Prep Kit (Illumina) and sequencing was performed on a HiSeq2000 (Illumina).

first: Yichao

last: Zheng


title: localization of Scc2 between wild type and scc4-m35 cells in S-phase

status: Public on Jul 21 2016

city: Edinburgh

first: Alastair

middle: Robert

last: Kerr

state: Midlothian

address: 2.21 Michael Swann Building, Kings Buildings, Mayfield Road

department: Wellcome Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

summary: Wild-type (AM15307) and scc4-m35 (AM15311) cells carrying SCC2-3FLAG were fixed for 2 hr, 15 min following an a-factor arrest. Samples were harvested, anti-HA ChIP was performed and both input and IP samples were sequenced for both strains.

overall_design:
ChIP-seq for S. cerevisiae Scc2-3FLAG in S-phase cells in Wild type and in scc4-m35 mutant
Vasso Makrantoni: experiments and Alastair Kerr: ChIP Seq Data analysis

first: Vasso

last: Makrantoni


title: Snapshot and temporal scRNA-seq of progenitor cells to dissect human embryonic stem cells entry into endoderm progenitors

city: Madison

first: Ning

last: Leng

state: WI

address: 330 N Orchard St

institute: Morgridge Institute for Research

summary: Human pluripotent stem cells (hPSCs) offer a unique cellular model to study lineage specifications of the primary germ layers during human development. We profiled single-cell RNA-seq (scRNA-seq) on four lineage-specific progenitor cells derived from hESCs. Our scRNA-seq analyses revealed each type of progenitors display various extend of heterogeneity. Specifically, definitive endoderm cells (DECs) not only show a greater degree of heterogeneity, but are also enriched in metabolic signatures. Followed by detailed temporal scRNA-seq profiling along DEC differentiation, we reconstructed a differentiation trajectory using a novel statistical pipeline named Wave-Crest. Wave-Crest further identifies candidate regulators during the transitioning phase from Brachyury (T)+ mesendoderm towards CXCR4+ DEC state. To functionally test identified novel regulators; we generated a live cell monitoring system, a T-2A-EGFP knock-in reporter cell line via CRISPR/CAS9. We demonstrated that, among the top candidate genes, KLF8 plays a pivotal role modulating mesendoderm to DEC differentiation. In this submission, 1810 raw fastq files are provided; 212 are re-analysis from GSE64016. Four expected count matrices are provided - 1) 1018 single cells from snapshot progenitors; 2) 758 single cells from time couse profiling; 3) 19 bulk RNA-seq sample from snapshot progenitors; 4) 15 bulk RNA-seq sample from time course profiling.

overall_design: Total 1018 single cells from snapshot progenitors and 758 single cells from time couse profiling. Matchd population bulk RNA-seq samples for both the progenitors snapshot (19 samples) and time course profiling (15 samples) also included in this submission. These data set are used to detect the transitioning phase from mesendoderm to definitive endoderm.

first: Li-Fang

last: Chu


title: GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes.

city: Nankang, Taipei

first: Der-Hwa

state: Taiwan

address: 128, Sec2, Academia Rd.

department: Insititute of Molecular Biology

country: Taiwan

institute: Academia Sinica


title: RNA-seq profiles of Arabidopsis thaliana wild-type and fip37-4 LEC1:FIP37

status: Public on Jul 25 2016

city: Singapore

first: Hao

last: Yu

address: Science Drive 4

country: Singapore

institute: National University of Singapore

summary: N6-methyladenosine (m6A) represents the most prevalent internal modification on messenger RNA, and requires a multicomponent m6A methyltransferase complex in mammals. How their plant counterparts determine the global m6A modification landscape and its molecular link to plant development remain elusive. Here we show that FKBP12 INTERACTING PROTEIN 37 KD (FIP37) is a core component of the m6A methyltransferase complex, which underlies control of shoot stem cell fate in Arabidopsis. The mutants lacking FIP37 exhibit massive overproliferation of shoot meristems and a transcriptome-wide loss of m6A RNA modifications. We further demonstrate that FIP37 mediates m6A RNA modification on key shoot meristem genes inversely correlated with their mRNA stability, thus confining their transcript levels to prevent shoot meristem overproliferation. Our results suggest an indispensable role of FIP37 in mediating m6A mRNA modification, which is required for maintaining the shoot meristem as a renewable source for continuously producing all aerial organs in plants.

overall_design: RNA-seq in Arabidopsis thaliana (Col-0) wild-type and  fip37-4 LEC1:FIP37, three replicates for each sample

first: Lisha

last: Shen

first: Zhe

last: Liang

first: Xiaofeng

last: Gu

first: Ying

first: Zhiwei

middle: N

last: Teo

first: Xingliang

last: Hou

first: Weiling

middle: M

last: Cai

first: Peter

last: Dedon

first: Lu

last: Liu


title: Glutamine Deficiency Occurs in Regions of Solid Tumours and Promotes Dedifferentiation through Inhibition of Histone Demethylation

status: Public on Jul 18 2016

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 East Duarte Road

department: Department of Computational & Quantitative Medicine

institute: Beckman Research Institute of City of Hope, Center for Informatics

summary: We sequenced mRNA from the core regions and the peripheral regions of  melanoma xenograft tumors

overall_design: Examination of mRNA levels in samples from core and peripharal regions within the same tumor

first: Mei

last: Kong

first: Min

last: Pan


title: GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes.[ChIP-seq]

last: Huang

summary: Promoter-proximal pausing of RNA polymerase II (RNA-Pol) is a rate-limiting step primed for rapid and synchronous induction of genes involved in critical physiological processes. Its underlying mechanisms are not fully understood. Using cytogenetic, genomic and genetic approaches, we provide evidence to support a direct role of a prevalent upstream GAGA binding factor (GAF) in transcriptional pausing of Hsp70 and many developmental regulators in Drosophila. For GAF target genes, the abundance of paused RNA-Pol and GAF is closely correlated. Promoters with higher GAF occupancy show stronger reduction of paused RNA-Pol in Gaf mutants. In addition, nucleosome organization is preferentially affected in the upstream region by GAF in a dosage-dependent manner. Genetic assays using a dominant eye phenotype caused by GAF overexpression suggests that GAF cooperates with nucleosome remodeler NURF, pausing factor NELF and an upstream binding factor BAB1. Thus, GAF plays a critical role in a regulatory network to facilitate transcriptional pausing through modulation of upstream nucleosomes.

overall_design: Examination of GAGA factor distribution in WT Drosophila third instar tissue and examination of RNA Pol II distribution in WT and GAF mutant Drosophila third instar tissue.

first: Shih-Ying

last: Tsai


title: Localizing gene regulation by RNA-seq reveals a staggered wood decay mechanism for the brown rot fungus Postia placenta

city: saint paul

first: Jonathan

last: Schilling

state: minnesota

address: 2004 folwell ave

institute: University of Minnesota

summary: Wood-degrading brown rot fungi are essential recyclers of plant biomass in forest ecosystems. Their efficient cellulolytic systems, which have potential biotechnological applications, apparently depend on a combination of two mechanisms: lignocellulose oxidation by reactive oxygen species (ROS) and polysaccharide hydrolysis by a limited set of glycoside hydrolases (GHs). Given that ROS are strongly oxidizing and non-selective, these two steps are likely segregated. A common hypothesis has been that brown rot fungi use a concentration gradient of chelated metal ions to confine ROS generation inside wood cell walls before enzymes can infiltrate. We examined an alternative: that lignocellulose-oxidation (LOX) components involved in ROS production are differentially expressed by brown rot fungi ahead of GH components. We used spatial mapping to resolve a temporal sequence in Postia placenta, sectioning thin wood wafers colonized directionally. Among sections, we measured gene expression by whole transcriptome sequencing (RNAseq) and assayed relevant enzyme activities. We found a marked pattern of LOX upregulation in a narrow (5-mm; 48-hr) zone at the hyphal front, which included many genes likely involved in ROS generation. Upregulation of GH5 endoglucanases and many other GHs clearly occurred later, behind the hyphal front, with notable exceptions of two likely expansins and a GH28 pectinase. Our results support a staggered mechanism for brown rot that is controlled by differential expression rather than microenvironmental gradients. This mechanism likely results in an oxidative pretreatment of lignocellulose, possibly facilitated by expansin- and pectinase-assisted cell wall swelling, before cellulases and hemicellulases are deployed for polysaccharide depolymerization.

overall_design: We sequenced mRNA from 9 Postia placenta samples taken from 3 wood sections of wafer design, with 3 bioreplicates for each wood section, to compare the gene expression during brown rot processes. Three wood sections of the wafer are representing early to late decay stages.

first: Jiwei

last: Zhang

first: Kenneth

middle: E

last: Hammel

first: Melania

last: Figueroa


title: GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes. [MNase-seq]

first: Der-Hwa

overall_design: MNase digested chromatin from wild type and GAF mutant lines


title: RNA-Seq analysis of primary AML specimens exposed to AhR modulating agents

first: Guy

last: Sauvageau

summary: The goal of the study was to identify genes that are directly or indirectly coregulated by the AhR pathway in primary human AML cells. Patient AML cells were treated for 16 hours with the two indirubin derivatives 6-bromoindirubin-3'oxime (BIO), 1-Methyl-6-bromoindirubin-3'oxime (MeBIO), the AHR-antagonist SR1 (StemReginin1), combinations of BIO+SR1 and MeBIO+SR1 or DMSO alone at indicated concentrations prior to RNA extraction for sequencing.

overall_design:
RNA-Seq performed on 5 primary AML samples fresh (t0) and after exposure to AhR-agonists (2), -antagonist (1), and DMSO

Contributor: Leucegene Project, IRIC

first: Caroline

last: Pabst

first: Josee

last: Hebert


title: Next Generation Sequencing and Quantitative Analysis of Wild Type and p110gamma-/- macrophages

city: La Jolla

first: Roman

last: Sasik

address: 9500 Gilman Dr.

department: Center for Computational Biology and Bioinformatics

institute: UCSD

summary:
Purpose: The goals of this study were to identify quantitative gene expression differences between macrophages derived from wild type and PI3Kgamma null macrophages
Methods: mRNA profiles of MCSF, IL4 and IFNg/LPS stimulated macrophage  wild-type (WT) and PI3Kinase gamma knockout (p110g-/-) mice were generated by single read deep sequencing, in triplicate, using Illumina  HiSeq2000. The sequence reads that passed quality filters were aligned to mouse transcriptome using the bowtie2 aligner. Gene-level summaries were normalized and analyzed for differential expression using DESeq. qRT–PCR validation was performed using SYBR Green assays.
Conclusions: Our study represents the first detailed analysis of the role of p110g in the control of the macrophage immune response, with biological replicates, generated by RNA-seq technology.

overall_design: mRNA profiles of  wild type (WT) and p110g-/- macrophages were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: Judith

middle: A

last: Varner


title: Regulation of highly expressed hCINAP on translatome

city: Beijing

first: Dongmei

last: Bai

address: Haidian

institute: Peking University

summary: hCINAP is essential for human 18S rRNA processing and ribosome assembly. hCINAP is highly expressed in human cancers and promotes cancer cell growth. To connect the role of hCINAP in ribosome biogenesis and tumor growth, genome-wide polysome profiling was performed to detect the regulation of hCINAP on ribosome assembly and translation control. The results showed taht hihgly expressed hCINAP promotes ribosome biogenesis and selectively modulates cancer-associated translatome to promote malignancy. This result provides important insights into the molecular mechanism underlying the role of hCINAP in tumorigenesis.

overall_design: For the transcriptional profile, MCF7 cells transfected with control vector or GFP-hCINAP were collected and total RNA was extracted. For the polysoem profile, MCF7 cells with stably expressed GFP or GFP-hCINAP were subjected to surcose gradient fractionation. Ribosome profiles were obtained by measuring the absorbance of the sucrose gradient at a wavelength of 254 nm using a BioComp Gradient Fractionator. The fractions corresponding to subpolysome and polysome were collected and RNA was extracted. The cDNA library was generated and sequenced via Illumina HiSeqTM 2000. The clean reads were mapped to the UCSC hg19 reference genome and FPKM was assigned to calculate expression levels. The recruitment to polysome of each mRNA was calculated according to their FPKM values in the monsome and polysome.

first: Xiaofeng

last: Zheng


title: Expansion of GA dinucleotide repeats increases the density of CLAMP binding sites on the X-chromosome to promote Drosophila dosage compensation

status: Public on Jul 17 2016

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

type: Genome binding/occupancy profiling by array

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

sample_organism:
Drosophila melanogaster
Drosophila miranda

overall_design: Refer to individual Series


title: Macrophage Gene Expression Upon Infection with Anaplasma phagocytophilum in the Presence and Absence of the Tick Salivary Protein SL2

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

summary: Previously, we observed that a tick salivary protein named sialostatin L2 (SL2) mitigates caspase 1-mediated inflammation upon Anaplasma phagocytophilum infection. Here we are performing next-generation sequencing to determine the global effect of SL2 upon A. phagocytophilum infection of macrophages.

overall_design: BMDMs were treated by 4 different conditions (including non-treated, treated by SL2, treated by Anaplasma, and by Anaplasma and SL2, each treatment was performed in triplicate) followed by the extraction of total RNA and deep sequencing by Illumina

first: Joao

last: Pedra

first: Xiaowei

last: Wang


title: Expansion of GA dinucleotide repeats increases the density of CLAMP binding sites on the X-chromosome to promote Drosophila dosage compensation [ChIP-Seq]

summary: ChIP-seq was performed to compare binding the genome-wide binding profile of the CLAMP transcription factor in two different Drosophila species.

platform_organism:
Drosophila melanogaster
Drosophila miranda

overall_design: ChIP seq experiments compare the binding profile of CLAMP in female larvae to identify conservation of its binding sequence.

first: E

last: Larschan


title: Massive redeployment of PRC1 proteins suppresses tumor formation during Drosophila development

city: Montpellier

first: Giacomo

last: Cavalli

address: IGH - CNRS, 141, rue de la Cardonille

institute: CNRS

summary: Polycomb group proteins form two main complexes, PRC2 and PRC1, which generally coregulate their target genes. Here, we show that PRC1 components act as neoplastic tumor suppressors independently of PRC2 function. By mapping the distribution of PRC1 components and the histone H3K27me3 mark, we identify genes that acquire PRC1 and H3K27me3 in larvae, and a much larger set of genes bound by PRC1 in the absence of H3K27me3 in larval tissues. These genes massively outnumber canonical targets and they are preeminently involved in the regulation of cell proliferation, signaling and polarity. Mutation in PRC1 components specifically deregulates this set of genes, whereas canonical targets are derepressed in both PRC1 and PRC2 mutants. In human ES cells, PRC1 components colocalize with H3K27me3 like in Drosophila embryos, whereas they are selectively recruited to a large set of proliferation and signaling-associated genes in differentiated cell types, showing that the redeployment of PRC1 components during development is evolutionarily conserved.

overall_design: Comparative study of Polycomb group proteins and histon marks during development with ChIP-Seq and RNA-Seq data in eye discs and wing discs (L3 stage) in Drosophila

first: Anna

last: Delest

first: Vincent

last: Loubière

first: Aubin

last: Thomas

first: Boyan

last: Bonev

first: Bernd

last: Schuttengruber

first: Anne-Marie

last: Martinez


title: Structural organization of the inactive X chromosome

city: Worcester

first: Bryan

middle: R

last: Lajoie

address: 368 Plantation St.

department: Program in Systems Biology

institute: UMMS

summary: X-chromosome inactivation (XCI) entails a massive structural reorganization of the inactive X (Xi). However the molecular architecture of the Xi is unknown. Here we show that the Xi lacks typical autosomal features such as active/inactive compartments and topologically associating domains (TADs), except around a small number of genes that escape XCI and remain expressed. Escaping genes form TADs and retain DNA accessibility at promoter-proximal and CTCF binding sites, indicating that these loci can avoid Xist-mediated erasure of chromosomal structure. We further show that genesilencing competent Xist RNA is sufficient to induce segregation of the Xi into two ‘mega-domains’ separated by a boundary that includes the DXZ4 macrosatellite. Deletion of this boundary prior to XCI results in fusion of the megadomains and altered patterns of escape that correlate with changes in TAD structure following differentiation and XCI . Our results suggest a critical role for the boundary locus and Xist RNA in shaping the structure of the Xi and modulating escape from XCI. Our findings also point to roles of transcription and CTCF binding in TAD formation in the context of facultative heterochromatin.

overall_design:
Allele specific Hi-C, Allele specific ATAC-seq and Allele specific RNA-seq.  Mouse 129/cast female.

Processed data for two reanalyzed RNA-seq Samples, GSM1305895 and GSM1305900, are included in this study and are linked to the Series record, GSE72697_rpkm_bedGraph_ESC.tar.gz and GSE72697_rpkm_bedGraph_NPC-deltaFT.tar.gz.

first: Luca

last: Giorgetti

first: Ava

middle: C

last: Carter

first: Mikael

last: Attia

first: Ye

last: Zhan

first: Jin

last: Xu

first: Chong Jian

last: Chen

first: Noam

last: Kaplan

first: Howard

last: Chang

first: Edith

last: Heard

first: Job

last: Dekker


title: Deletion of DXZ4 on the human inactive X chromosome eliminates superdomains and impairs gene silencing

city: Cambridge

first: Miriam

last: Huntley

address: 29 Oxford Street

institute: Harvard University

summary: During interphase, the inactive X chromosome (Xi) adopts an unusual 3D configuration known as the Barr body and is largely transcriptionally silent. Despite the importance of X inactivation, little is known about the 3D configuration of Xi and its relationship to gene silencing. We recently showed that in humans, Xi exhibits two distinctive structural features. First, Xi is partitioned into two huge intervals, called superdomains, such that pairs of loci in each superdomain show an enhanced contact frequency with one another. The boundary between the two superdomains lies near DXZ4, a macrosatellite repeat spanning ~300kb, whose Xi allele extensively binds the protein CTCF. Second, Xi exhibits extremely large loops, up to 77Mb long, called superloops. DXZ4 lies at the anchor of several superloops. Here, we use 3D mapping to study the structure of Xi, focusing on the role of DXZ4. We show that superloops and superdomains are conserved across mammals. We develop a novel variant of our in situ Hi-C protocol, dubbed COLA (COncatemer Ligation Assay) to probe the higher order structures formed by the superloops. In COLA, in situ proximity ligation of multiple extremely short fragments produced by the enzyme CviJI is used to efficiently map simultaneous proximity among three or more loci. Using data from Hi-C and COLA, we demonstrate that DXZ4 and other superloop anchors tend to co-locate simultaneously within the same cells, a result that is confirmed by 3D-FISH. Finally, we examine the effects of deleting DXZ4 from Xi in human cells. Using in situ Hi-C, microscopy, and RNA-FISH, we show that superdomains and superloops disappear; that Xi frequently dissociates into multiple separate structures; and that transcriptional silencing on Xi is compromised. Deletion of DXZ4 from the active X chromosome (Xa) has no such effect. Thus, DXZ4 is essential for proper folding and silencing of Xi.

sample_organism:
Macaca mulatta
Homo sapiens
Mus musculus

overall_design:
Hi-C protocol was used on wildtype and DXZ4-deleted cells to examine the structure of Xi. A novel variant of our in situ Hi-C protocol, dubbed COLA (COncatemer Ligation Assay), was developed to probe the higher order structures formed by the superloops.

This series also includes RNA-seq data on Retinal Pigmented Epithelial Cells (hTERT-RPE1).

The samples starting with the prefix 'RaoHuntley-2014' were generated as part of the study described in GSE63525 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525).

first: Emily

last: Darrow

middle: H

first: Erez

last: Lieberman Aiden


title: Widespread and adaptive alterations in genome-wide gene expression associated with ecological divergence of two Oryza species

first: Jie

last: Guo

state: Beijing

address: No.20 Nanxincun, Xiangshan

institute: Institute of Botany, Chinese Academy of Sciences

summary: Ecological speciation is a common mechanism by which new species arise. Despite great efforts, the role of gene expression in ecological divergence and speciation is poorly understood. Here, we conducted a genome-wide gene expression investigation of two Oryza species that are evolutionarily young and distinct in ecology and morphology. Using digital gene expression (DGE) technology and the paired-end RNA sequencing (RNA-Seq) method, we obtained 21,415 expressed genes across three reproduction-related tissues at two critical developmental stages. Of them, ~8% (1717) differed significantly in expression levels between the two species and these differentially expressed genes are randomly distributed across the genome. Moreover, 62% (1064) of the differentially expressed genes exhibited a signature of directional selection in at least one species. Importantly, the genes with differential expression between species evolved more rapidly at the 5’flanking sequences than the genes without differential expression relative to coding sequences, suggesting that cis-regulatory changes are likely adaptive and play an important role in the ecological divergence of the two species. Finally, we showed evidence of significant differentiation between species in phenotype traits and observed that genes with differential expression were overrepresented with functional terms involving phenotypic and ecological differentiation between the two species, including reproduction- and stress-related characteristics. Our findings demonstrate that ecological speciation is associated with widespread and adaptive alterations in genome-wide gene expression and highlight the dominant role of regulatory evolution in ecological divergence and adaptation.

sample_organism:
Oryza rufipogon
Oryza nivara

platform_organism:
Oryza rufipogon
Oryza nivara

overall_design:
We selected accessions representing typical Oryza rufipogon and O. nivara, which were sampled exclusively from South and Southeast Asia where the two species overlap. We chose to collect three types of tissues, i.e., flag leaves at the heading stage (2–7 cm above the primary branch) (L), panicles at the heading stage (H) and panicles at the flowering stage (10–15 cm above the primary branch) (F). Sample collection was repeated twice in two consecutive years (2009 and 2010) under the same controlled conditions.
A total of 36 samples were sequenced by Illumina’s digital gene expression (DGE) system, with each type of tissues collected from six individuals of each species as biological replicates. To access the quality of DGE technology, we also selected six samples representing three tissues from each of two individuals (one individual per species) for paired-end RNA-Seq sequencing.

first: Rong

last: Liu

first: Lei

last: Huang

first: Xiao-Ming

last: Zheng

first: Ping-Li

first: Yu-Su

last: Du

first: Zhe

last: Cai

first: Lian

last: Zhou

first: Xing-Hua

last: Wei

first: Fu-Min

last: Zhang

first: Song

last: Ge


title: Mapping the Chromatin State Dynamics in Myoblasts

city: Corvallis

first: Chrissa

last: Kioussi

state: Oregon

address: 1601 SW Jefferson Way

department: College of Pharmacy

institute: Oregon State University

summary: The chromatin state in developing body parts provides a zip code to cellular populations that direct their cell fates. We used antibodies for H3K4me3, H3K27me3 and Pol2, to identify the chromatin state signature of the Pitx2-null mouse forelimb during mid-gestation, at embryonic day 12. The families of genes marked included those related to transcription, transcriptional regulation, and embryonic organ development. Transcription factors specific for muscle development were characterized by bivalent chromatin, as E12 is a transition time point from embryonic to fetal myogenesis. The identified chromatin state of muscle specific genes was in strong correlation with their observed expression profile.

overall_design: Examination of the histone marks H3K4me3, H3k27me3, and Pol2 in whole E12.5 forelimb tissues from Pitx2 null mice using the Illumina HiSeq 2000

first: Diana

last: Eng

first: Arun

last: Singh


title: Gene Expression Profiling Using Huntington Disease Cell Culture Model

status: Public on Jul 15 2016

city: Ashburn

state: Virginia

address: 19700 Helix Dr.

department: Janelia Farm Research Campus

institute: Howard Hughes Medical Institute

summary: To identify genes affected by mutant huntington protein, we performed mRNA-seq experiments with Striatal STHdh Q7/Q7, Q7Q111, and Q111/Q111 cells. We also tested the effect of Sp1 overexpression on rescuing gene expression in Q111/Q111 cells.

overall_design: Striatal STHdh Q7/Q7, Q7/Q111 and Q111/Q111 cells were used for the mRNA-seq in replicates. After Sp1 transient overexpression in Q111/Q111 cells, cells were collected for mRNA-seq analysis.

first: Li

last: Li

first: Liu

last: Zhe


title: Gene expression data of islets from WT and βRapKO mice

city: Shanghai

first: Qicheng

last: Ni

address: 197 Ruijin 2nd Road

institute: Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine

summary: The mechanistic target of rapamycin complex 1 (mTORC1) regulates beta cell growth and mass; yet it remains unclear whether it also directs beta cell functional maturation. To understand the global molecular basis of the phenotype caused by the loss of Raptor in beta cells, we isolated pancreatic islets from 8-week-old βRapKO and WT mice. We compared gene-expression profile by Affymetrix microarray of islets, which revealed that a number of mRNAs were dys-regulated in Raptor-deficient islets.

overall_design: To understand the global molecular basis of the phenotype caused by the loss of Raptor in beta cells, we isolated pancreatic islets from 8-week-old βRapKO and WT mice.  Then mice were sacrificed and total RNAs were isoloated from islets. Affymetrix array hybridisation and scanning were performed using Mouse Genome 430 2.0 chips.We included at least 4-5 independent biological replicates, each composed of RNA isolated from islets of 5 animals with the same genotype.

first: Qidi

last: Wang


title: High-resolution Sp1 DNA-binding Site Mapping by ChIP-exo in STHdh Q7/Q7 cells

summary: Mapping ultra-high resolution of Sp1:DNA interaction would provide us with valuable new mechanistic insights into Sp1-mediated gene regulatory network in Huntington Disease cell culture model.

overall_design: STHdh Q7/Q7 cells were directly fixed and used for the ChIP-exo experiment.


title: Chromatin targets of androgen receptor and PIAS1 in molecular apocrine breast cancer cells [ChIP-seq]

city: Kuopio

first: Sari

last: Toropainen

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: The majority of breast cancer subtypes express androgen receptor (AR) in addition to estrogen receptor a (ERa). Depending on the breast cancer subtype androgen signaling has either stimulatory or inhibitory roles in breast cancer cell growth. We have mapped AR cistrome in ERa negative human molecular apocrine breast cancer MDA-MB453 cells and analyzed it in relation to the androgen-regulated transcriptome in the same cells. We have also examined the effect of silencing of the coregulator SUMO ligase PIAS1 on the androgen-regulated transcriptome and AR cistrome in MDA-MB453 cells. Our results show that the MDA-MB453 cells share with VCaP prostate cancer cells a core AR cistrome and target gene signature linked to cancer cell growth and that PIAS1 acts as an AR target gene-selective coregulator in MDA-MB453 cells.

overall_design: All ChIP-seq samples were collected from cells treated with 10 nM R1881 (synthetic androgen methyltrienolone) for 2 h. In addition, AR ChIP-seq samples were collected from cells exposed to control siRNA (siNON, Dharmacon Non-targeting pool) or PIAS1 siRNA (siPIAS1, Dharmacon ON-TARGETplus SMARTpool for human PIAS1). IgG sample was collected from siNON and siPIAS1 cells and used as background control. Biological duplicate samples of the AR, PIAS1 and single IgG ChIP-seq samples were analyzed by using Solexa/Illumina 1.5.

first: Marjo

last: Malinen

first: Tiina

last: Jääskeläinen

first: Miia

last: Rytinki

first: Biswajyoti

last: Sahu

first: Olli

last: Jänne

first: Jorma

last: Palvimo


title: RNA-sequencing study of peripheral blood monocytes for chronic periodontitis

status: Public on Jul 16 2016

city: New Orleans

first: Yao-Zhong

last: Liu

address: 1440 Canal Street, Suite 2001

department: Dept. of Biostatistics and Bioinformatics

institute: Tulane University School of Public Health

summary: We confirmed immune response as the key mechanism and provided solid evidence for novel genes (e.g., FCAR and CUX1) and distinct biological processes (e.g., endocytosis, cytokine production and apoptosis) as potentially new important factors/mechanisms contributing to chronic periodontitis pathogenesis.

overall_design: We performed an RNA-sequencing (RNA-seq) study of peripheral blood monocytes (PBMs) in 5 non-smoking moderate to severe CP (case) subjects vs. 5 controls. We replicated the DEx transcripts/isoforms using an independent microarray dataset. We also pathway-based analysis on the identified/replicated DEx transcripts/isoforms using DAVID performed (Database for Annotation, Visualization and Integrated Discovery).

first: Pooja

last: Maney

first: Jyoti

last: Puri

first: Yu

last: Zhou

first: Hong-Wen

last: Deng


title: Chromatin targets of androgen receptor and coregulator PIAS1 in molecular apocrine breast cancer cells


title: High Resolution Mapping of RNA Polymerases Identifies Mechanisms of Sensitivity and Resistance to BET Inhibitors in t(8;21) AML

city: Nashville

first: Scott

middle: W

last: Hiebert

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

summary: Bromodomain and extra-terminal domain (BET) family inhibitors offer a new approach to treating hematological malignancies. We used precision nuclear run-on transcription sequencing (PRO-seq) to create high-resolution maps of active RNA polymerases across the genome in t(8;21) acute myeloid leukemia (AML) that are exceptionally sensitive to BET inhibitors. PRO-seq identified over 1400 genes showing impaired release of promoter-proximal paused RNA polymerases, including the stem cell factor receptor tyrosine kinase KIT that is mutated in t(8;21) AML. PRO-seq also identified an enhancer 3’ to KIT. Chromosome conformation capture confirmed contacts between this enhancer and the KIT promoter and CRISPRi-mediated repression of this enhancer impaired cell growth. PRO-seq also identified microRNAs, including MIR29C and MIR29B2 that target the anti-apoptotic factor MCL1 and were repressed by BET inhibitors. MCL1 protein was up-regulated, and inhibition of BET proteins sensitized t(8:21)-containing cells to MCL1 inhibition, suggesting a potential mechanism of resistance to BET inhibitor-induced cell death.

overall_design:
Kasumi-1 cells were treated with DMSO, 250 nM JQ1, and 125 nM MS417 for 1 and 3 hours, and PRO-seq was performed to study transcriptional changes.
Kasumi-1 cells were treated with 250 nM JQ1 for 0, 15, and 30 minutes, and PRO-seq was performed. Two biological replicates were included for each time point.
Primary AML patient cells were treated with DMSO and 250 nM JQ1 for 1 hour, and PRO-seq was performed to confirm trancriptional effects of BET inhibitors.

first: Yue

last: Zhao

first: Pankaj

last: Acharya


title: RNA-sequencing based transcriptome-wide expression profiling of Cynomolgus monkey and human IPSCs in vitro differentiated into endothelial cells

city: Basel

first: Tobias

last: Heckel

address: Grenzacherstr. 124

department: pRED

country: Switzerland

institute: Roche

summary:
We report a macaque in vitro endothelial cell system using induced pluripotent stem cells (IPSCs) from Cynomolgus monkey (Macaca fascicularis). Based on a protocol adapted for human IPSCs we directly differentiated macaque IPSCs into endothelial cells under chemically defined conditions. The resulting endothelial cells can be enriched using magnetic cell sorting and display endothelial marker expression and function. RNA sequencing revealed that the differentiation process closely resembled vasculogenesis. Moreover, we show that endothelial cells derived from macaque and human IPSCs are highly similar regarding gene expression patterns and key endothelial functions such as inflammatory responses. These data demonstrate the power of IPSC differentiation technology to generate defined cell types such as endothelial cells as translational in vitro model to compare cell type specific responses across species.
For more detail see also: Eva C Thoma, Tobias Heckel, David Keller, Nicolas Giroud, Brian Leonard, Klaus Christensen, Adrian Roth, Cristina Bertinetti-Lapatki, Martin Graf, Christoph Patsch. "Establishment of a translational endothelial cell model using directed differentiation of induced pluripotent stem cells from Cynomolgus monkey" (under submission)

sample_organism:
Macaca fascicularis
Homo sapiens

platform_organism:
Macaca fascicularis
Homo sapiens

overall_design: mRNA expression profiles of Cynomolgus monkey and human IPSC and in vitro differentiated IPSC-derived endothelial cells measured by deep RNA-sequencing on an Illumina HiSeq2500 instrument

first: Nicolas

last: Giroud

first: Eva

last: Thoma

first: Christoph

last: Patsch


title: Chromatin Remodeling Inactivates Activity Genes and Regulates Neural Coding

city: Evanston

last: Yang

state: IL

address: 2200 Campus Dr

department: Neurobiology

institute: Northwestern University

summary: Activity-dependent transcription influences neuronal connectivity, but the roles and mechanisms of inactivation of activity-dependent genes have remained poorly understood. Genome-wide analyses in the mouse cerebellum revealed that the nucleosome remodeling and deacetylase (NuRD) complex deposits the histone variant H2A.z at promoters of activity-dependent genes, thereby triggering their inactivation. Purification of translating mRNAs from synchronously developing granule neurons (Sync-TRAP) showed that conditional knockout of the core NuRD subunit Chd4 impairs inactivation of activity-dependent genes when neurons undergo dendrite pruning. Chd4 knockout or expression of NuRD-regulated activity genes impairs dendrite pruning. Imaging of behaving mice revealed hyperresponsivity of granule neurons to sensorimotor stimuli upon Chd4 knockout. Our findings define an epigenetic mechanism that inactivates activity-dependent transcription and regulates dendrite patterning and sensorimotor encoding in the brain.

overall_design: One or two replicates of the histone modifications (H3K27me3 and H2A.z), total histone proteins (H2A.z and H3), and ATPase Chd4 using postnatal day 22 cerebella from wild type (WT) or Chd4 conditional knockout (cKO) mice were examined using libraries prepared with the Illumina ChIP-Seq DNA Sample Prep Kit. Four replicates of total RNA were extracted from postnatal day 27-28 cerebella from rotarod-trained or control homecage mice, or Chd4 cKO or WT mice using Trizol and reverse-transcribed with oligo-dT priming. Three replicates of immunoprecipitated Sync-TRAP RNA or the input control using postnatal day 12 Chd4 cKO or WT cerebella were purified and amplified with Ovation RNA-Seq System V2 (NuGEN). All samples were sequenced on the Illumina HiSeq 2000 platform.

first: Tomoko

last: Yamada

first: Kelly

middle: K

last: Hill

first: Martin

last: Hemberg

first: Naveen

last: Reddy

first: Ha

last: Cho

first: Arden

last: Guthrie

first: Anna

last: Oldenborg

first: Shane

last: Heiney

first: Shogo

last: Ohmae

first: Javier

middle: F

last: Medina

first: Timothy

last: Holy

first: Azad

last: Bonni


title: TWIST1 drives cisplatin resistance and cell survival in an ovarian cancer model, via upregulation of GAS6, L1CAM, and Akt signalling

city: DOWNERS GROVE

first: Cai

last: Roberts

address: 555 31ST STREET, SCIENCE HALL 322-E

department: Pharmacology

institute: Midwestern University

summary: We created two cell lines derived from Ovcar8 by stably transfecting with an eGFP-firefly luciferase fusion protein and either an additional copy of the gene TWIST1 or an shRNA against TWIST1, under the control of the CMV promoter. RNA sequencing was used to look for differential expression of genes that may impact cisplatin resistance in epithelial ovarian cancer.

overall_design: RNA-seq for differential expression between two cell lines differing in expression of gene of interest. Run as biological replicates and technical triplicates.

first: Michelle

last: Tran

first: Mary

last: Pitruzzello

first: Wei

last: Wen

first: Joana

last: Loeza

first: Thanh

last: Dellinger

first: Gil

middle: G

last: Mor

first: Carlotta

last: Glackin


title: ER stress increases alternative splicing of SRFS3’s poison exon.

city: San Diego

first: Brian

middle: Patrick

last: James

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Mouse fibroblasts stressed with 1mM dithiothreitol for 4 hours were interogated for stress-induced alternative mRNA spliceforms

overall_design: mRNA-Seq Untreated fibroblasts versus dithiothrietol stressed fibroblasts; wild-type, Ire1α-null and Xbp1-null lines were compared.

first: Justin

last: Hassler


title: Chromatin Immunoprecipitation sequencing of heterochromation associated proteins in Tetrahymena

city: Vienna

first: Kensuke

last: Kataoka

address: Dr. Bohr Gasse 3

country: Austria

institute: IMBA

summary: In the ciliated protozoan Tetrahymena, de novo heterochromatin body formation is accompanied by programmed DNA elimination. We previously reported that dephosphorylation of the HP1-like protein Pdd1p is required for the formation of heterochromatin bodies during the process of programmed DNA elimination in the ciliated protozoan Tetrahymena. Here, we show that the heterochromatin body component Jub4p is required for Pdd1p phosphorylation, heterochromatin body formation and DNA elimination. Moreover, our analyses of unphosphorylatable Pdd1p mutants demonstrate that Pdd1p phosphorylation is required for heterochromatin body formation and DNA elimination, while it is dispensable for local heterochromatin assembly. Therefore, both phosphorylation and the following dephosphorylation of Pdd1p are necessary to facilitate the formation of heterochromatin bodies. We suggest that Jub4p-mediated phosphorylation of Pdd1p creates a chromatin environment that is a prerequisite for subsequent heterochromatin body assembly and DNA elimination.

overall_design: New macronuclei (MACs) of exconjugants were isolated from wild-type and various mutant cells at 12 hpm (hours post-mixing), sheared chromatin was immunoprecipitated andprecipitated DNA was analyzed by high-throughput sequencing

first: Tomoko

last: Noto

first: Kazufumi

last: Mochizuki


title: Gene Expression Profiling Using Huntington Disease Cell Culture Model and High-resolution Sp1 DNA-binding Site Mapping by ChIP-exo in STHdh Q7/Q7 cells

first: Zhe

last: Liu

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

overall_design: Refer to individual Series


title: Jub4p-mediated phosphorylation of Pdd1p is a prerequisite for heterochromatin body assembly and DNA elimination


title: Transcriptome of liver tissue in 5 week old Stabilin-1 knock-out mice

city: Turku

first: Kati

last: Elima

address: Tykistökatu 6

department: MediCity

institute: University of Turku

summary: Stabilin-1/CLEVER-1 is a multidomain protein present in lymphatic and vascular endothelial cells and in M2 immunosuppressive macrophages. Stabilin-1 functions in scavenging, endocytosis and leukocyte adhesion to and transmigration through the endothelial cells.

overall_design: The transcriptome of liver tissue in 5wk old Stab1 knock-out mice was compared to that of corresponding wild type mice


title: To russet or not to russet: MdMyb93 as a regulator of suberin deposition in apple fruits

city: Belvaux

first: Sylvain

last: Legay

address: 41, rue du Brill

department: ERIN department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology

summary: • A comparison of the transcriptomes of russeted vs. waxy apple exocarps previously highlighted a tight relationship between a gene encoding a MYB-type transcription factor, MdMYB93, and some key suberin biosynthetic genes. The present work assesses the role of this transcription factor in the suberization process.  • A phylogenetic analysis of MdMYB93 and Arabidopsis thaliana MYBs was performed and the function of MdMYB93 was further investigated using Agrobacterium-mediated transient overexpression in Nicotiana benthamiana leaves. An RNA-Seq analysis was performed to highlight the MdMYB93-regulated genes. UPLC-TripleTOF and GC-MS were used to investigate alterations in phenylpropanoid, soluble free lipid, and lipid polyester contents.  • A massive accumulation of suberin and its biosynthetic precursors in MdMYB93 agro-infiltrated leaves was accompanied by a remobilization of phenylpropanoids and an increased amount of lignin precursors. Gene expression profiling displayed a concomitant alteration of lipid and phenylpropanoid metabolism, cell wall development, and extracellular transport, with a large number of induced transcripts predicted to be involved in suberin deposition.  • The present work supports a major role of MdMYB93 in the regulation of suberin deposition in russeted apple skins, from the synthesis of monomeric precursors, their transport, polymerization, and final deposition as suberin in primary cell wall.

overall_design: In order to draw a consistent picture of a gene expression profile of the MYB93 induced was performed comparing of 4 biological replicates of Nicotiana benthamiana leaves infiltrated with Pearleygate103 35S::MdMYB93 and 4 biological replicates of control plants infiltrated with P19 only.

first: Gea

last: Guerriero

first: Christelle

last: André

first: Cédric

last: Guignard

first: Emmanuelle

last: Cocco

first: Sophie

last: Charton

first: Marc

last: Boutry

first: Owen

last: Rowland

first: Jean-Francois

last: Hausman


title: Targeting evasion from Antiangiogenic therapy

city: Lausanne

first: Sadegh

last: Saghafinia

address: Route Cantonale

department: SV

institute: EPFL

summary: Abstract: Therapeutic targeting of tumor angiogenesis with VEGF inhibitors results in demonstrable but transitory efficacy in certain human tumors and mouse models of cancer, limited by unconventional forms of adaptive/evasive resistance.  In one such mouse model, potent angiogenesis inhibitors elicit compartmental reorganization of cancer cells around remaining blood vessels. The glucose and lactate transporters GLUT1 and MCT4 are induced in distal hypoxic cells in a HIF1α-dependent fashion, indicative of glycolysis. Tumor cells proximal to blood vessels instead express the lactate transporter MCT1, and p-S6, the latter reflecting mTOR signaling.  Normoxic cancer cells import and metabolize lactate, resulting in upregulation of mTOR signaling via glutamine metabolism enhanced by lactate catabolism. Thus metabolic symbiosis is established in the face of angiogenesis inhibition, whereby hypoxic cancer cells import glucose and export lactate, while normoxic cells import and catabolize lactate.  mTOR signaling inhibition disrupts this metabolic symbiosis, associated with upregulation of the glucose transporter GLUT2.

overall_design: Examination of sunitinib monotherapy and sunitinib/rapamycin combination therapy versus sham-treated controls

first: Elizabeth

last: Allen

first: Leanne

last: Li

first: Douglas

last: Hanahan


title: RNA-seq of naive and primed ES cells

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Here we propose a set of molecular criteria for evaluating the naive human pluripotent state. We show by RNA-seq that transcription of transposable elements provides a sensitive measure of the concordance between pluripotent stem cells and early human development.

overall_design: RNA-seq of 4 naive ES samples in 4i/LA, 3 naive ES samples in 5i/LA, 2 transgene-dependant naive ES cell samples, and 5 primed ES cell samples (in hESM)

last: Friedli

first: Evarist

last: Planet

first: Julien

last: Duc

first: Didier

last: Trono


title: Transcriptome analysis of SF3B1-mutation induced changes in K562 cells

city: NEW HAVEN

first: MANOJ

last: PILLAI

state: CT

address: 300 GEORGE STREET #786

institute: YALE UNIVERSITY

summary: Using RNA-Seq, we determined changes to gene expression and splicing on inducible expression of SF3B1-WT and SF3B1-MUT (K700E) in K562 cells.

first: Anil

last: Kesarwani

first: Manoj

last: Pillai


title: Long non-coding RNAs in B cells

city: Farmington

first: Jethro

last: Johnson

address: 10 Discovery Drive

institute: Jackson Laboratory for Genomic Medicine


title: Long non-coding RNAs in B cells (RNA-Seq)

summary: Using RNA sequencing and de novo transcript assembly, we identified 4516 lncRNAs expressed in 8 different stages of B cell development and activation. Chromatin immuno-precipitation sequencing was used to classify a substantial fraction (38%) of these lncRNAs as enhancer-associated or promoter-associated RNAs (eRNAs or pRNAs).

overall_design: A catalogue of lncRNAs expressed in eight murine B cell populations

first: Tiago

last: Brazao


title: Discovery of Telomere Repeat-binding Zinc finger protein in the malaria parasite Plasmodium falciparum

city: Nijmegen

first: Christa

last: Toenhake

state: Netherlands

address: Geert Grooteplein 28

country: Netherlands

institute: Radboud University

summary: ChIP-seq experiments were performed for the putative Telomere Repeat-binding Zinc finger protein (PfTRZ) in the malaria parasite Plasmodium falciparum strain 3D7. The gene encoding this factor (PF3D7_1209300) was endogenously tagged with either a GFP- or a 3xHA-tag and these transgenic parasite lines were used in ChIP-sequencing experiments. Sequencing of the ChIP and input libraries showed enrichment of PfTRZ at all telomere-repeat containing chromosome ends (reference genome Plasmodium falciparum 3D7 from PlasmoDB version 6.1) as well as in all upsB var promoters.In addition,PfTRZ was enriched at seven additional, intra-chromosomal sites and called in the PfTRZ-HA ChIP-seq only.

overall_design: Plasmodium falciparum 3D7 parasites were generated with -GFP or -3xHA C-terminal tagged TRZ (PF3D7_1209300). Nuclei were isolated from formaldehyde cross-linked schizont-stage transgenic parasites and used to prepare chromatin. Chromatin immunoprecipitations were performed using mouse anti-GFP (Roche Diagnostics, #11814460001) or rat anti-HA 3F10 (Roche Diagnostics, #12158167001). Sequencing libraries were prepared according to a Plasmodium-optimized library preparation procedure including KAPA polymerase-mediated PCR amplification.

first: Richárd

last: Bártfai


title: Gene expression and methylation profile for male SD Rats upon fructose and DHA treatment

city: Los Angeles

first: Xia

last: Yang

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

department: IBP

institute: UCLA


title: Differential Chromosomal Localization of Centromeric Histone CENP-A Contributes to Nematode Programmed DNA Elimination

city: Aurora

first: Jianbin

last: Wang

state: CO

address: 12801 East 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado Denver

summary: The stability of the genome is paramount to organisms. However, diverse eukaryotes carry out programmed DNA elimination in which portions or entire chromsomes are lost in early development or during sex determination. During early development of the parasitic nematode, Ascaris suum, 13% of the genome is eliminated. How different genomic segments are reproducibly retained or discarded is unknown. Here, we show that centromeric histone CENP-A localization plays a key role in this process. We show that Ascaris chromosomes are holocentric during germline mitoses, with CENP-A distributed along their length. Prior to DNA elimination in the four-cell embryo, CENP-A is significantly diminished in chromosome regions that will be lost. This leads to the absence of kinetochores and microtubule attachment sites necessary for chromosome segregation, resulting in loss of these regions upon mitosis. Our data suggest that changes in CENP-A localization specify which portions of chromosomes will be lost during programmed DNA elimination.

overall_design: A total of 62 samples are analyzed. These include: (1). CENP-A ChIP-seq on 12 developmental stages with input and replicates (12 x 2 x 2 samples); (2). CENP-C ChIP-seq on 3 developmental stages with input and replicates (total 8 samples); and (3). Histone marks ChIP-seq with 6 samples

first: Yuanyuan

last: Kang

first: Richard

last: Davis


title: Modulation of global transcriptional regulatory networks as a strategy for increasing kanamycin resistance of EF-G mutants

status: Public on Jul 14 2016

city: Bangalore

first: Aalap

last: Mogre

state: Karnataka

address: NCBS, GKVK, Bellary Road

country: India

institute: National Centre for Biological Sciences

summary: Evolve and resequence experiments have provided us a tool to understand bacterial adaptation to antibiotics by the gain of genomic mutations. In our previous work, we used short term evolution to isolate mutants resistant to the ribosome targeting antibiotic kanamycin. We had reported the gain of resistance to kanamycin via multiple different point mutations in the translation elongation factor G (EF-G). Furthermore, we had shown that the resistance of EF-G mutants could be increased by second site mutations in the genes rpoD / cpxA / topA / cyaA. In this work we expand on our understanding of these second site mutations. Using genetic tools we asked how mutations in the cell envelope stress sensor kinase (CpxAF218Y) and adenylate cyclase (CyaAN600Y) could alter their activities to result in resistance. We found that the mutation in cpxA most likely results in an active Cpx stress response. Further evolution of an EF-G mutant in a higher concentration of kanamycin than what was used in our previous experiments identified the cpxA locus as a primary target for a significant increase in resistance. The mutation in cyaA results in a loss of catalytic activity and probably results in resistance via altered CRP function. Despite a reduction in cAMP levels, the CyaAN600Y mutant has a transcriptome indicative of increased CRP activity, pointing to an unknown non-catalytic role for CyaA in gene expression. From the transcriptomes of double and single mutants we describe the epistasis between EF-G mutant and these second site mutations. We show that the large scale transcriptomic changes in the topoisomerase I (FusAA608E-TopAS180L) mutant likely result in supercoiling changes in the cell. Finally, genes with known roles in aminoglycoside resistance were present among the mis-regulated genes in the mutants.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Deep sequencing of rRNA depleted RNA isolated from populations of kanamycin resistant mutants growing exponentially in Luria-Bertani broth.

first: Aswin

middle: S

last: Seshasayee


title: Analyses of Early- and Late-scnRNAs of Tetrahymena

first: Kensuke

last: Kataoka

overall_design: 26 to 32-nt small RNAs from various mutants were analyzed by high-throughput sequencing

first: Tomoko

last: Noto

first: Kazufumi

last: Mochizuki


title: Differential gene expression m39 vs. siblings

city: Pittsburgh

first: Miler

middle: T

last: Lee

state: PA

address: 4249 Fifth Ave.

department: Biological Sciences

institute: University of Pittsburgh

summary: RNAseq analysis of cloche m39 mutant zebrafish embryos and wild type siblings at 90% epiboly - tailbud stage

overall_design: In order  to isolate the cloche gene, RNAseq was performed on a deletion allele of the zebrafish cloche mutant.  RNA was extracted from individual embryos at a stage the cloche gene was predicted to be expressed based on previous literature. RNA from the respective genoptypes was then pooled and subjected to RNAseq analysis.

first: Didier

last: Stainier

first: Sven

last: Reischauer

first: Oliver

last: Stone

first: Alethia

last: Villasenor


title: Long non-coding RNAs in B cells (ChIP-Seq)

first: Jethro

last: Johnson

first: Tiago

last: Brazao


title: Widely Interspaced Zinc Finger Motifs, Wiz, binds active promoters and CTCF-binding sites and is required for normal neural function in the mouse

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

country: Australia

institute: SAiGENCI

summary: Mice heterozygous for a null mutation in Widely-interspaced zinc finger, Wiz, were produced in a screen for modifiers of epigenetic reprogramming; expression of the GFP reporter transgene decreased in mutants, suggesting a role in transcriptional activation (Daxinger et al., 2013). These mice are viable and fertile, with no overt abnormalities and homozygosity for the mutation is embryonic lethal (Daxinger et al, 2013). Wiz is expressed at high levels in the brain, both in the embryo and in the adult, but there have been no reports of its role in neural tissue. To address this, ChIP-seq, using an anti-Wiz antibody, was carried out in adult cerebellum. Wiz peaks were found at tens of thousands of sites across the genome, many of which are gene promoters that show enrichment for the pioneer transcription factor CTCF. RNA-seq, using WizMommeD30/+ and Wiz+/+ mice, revealed that some genes were affected by haploinsufficiency of Wiz; ~30 in the brains of mid-gestation embryos and ~80 in adult cerebellum. Most genes that were deregulated in embryonic brain of heterozygous mutants decreased in expression and include a group of clustered protocadherin genes that were also down-regulated in adult cerebellum. The enhancer of this gene cluster has a strong Wiz peak in the ChIP-seq data and has been reported, by others, to be activated by CTCF in neurons.

overall_design: Examination of Wiz binding using ChIP sequencing and the result of Wiz haploinsufficiency using RNA sequencing, in mouse neural tissues.

first: Lexie

last: Prokopuk

first: Haoyu

last: Wu

first: Lucia

last: Daxinger

first: Harald

last: Oey

first: Alex

last: Spurling

first: Adam

middle: J

last: Lawther

first: Matthew

last: Hale

first: Emma

last: Whitelaw


title: Tip5/Baz2a Regulates Chromatin Architecture and Gene Expression to Maintain Self-renewal and Pluripotency of Embryonic Stem Cells.

city: San Francisco

first: Hunter

last: Richards

address: 513 Parnassus Ave., HSW 863

department: Orofacial Sciences

institute: UCSF


title: Tip5/Baz2a Regulates Chromatin Architecture and Gene Expression to Maintain Self-renewal and Pluripotency of Embryonic Stem Cells [ChIP-seq]

summary: It is unclear how gene networks that regulate self-renewal and pluripotency of embryonic stem (ES) cells are established. We searched for factors that contribute to forming functional chromatin architecture in ES cells and identified Tip5 (also called Baz2a) as a genome organizer, folding chromatin and recruiting chromatin remodeling/epigenetic factors to genes. Tip5 binds specialized genomic sequences called base-unpairing regions (BURs) and localizes near heterochromatin. Through chromatin looping Tip5 recruits the polycomb-repressive complex 2 (PRC2) subunits and Jarid2 to target genes far from Tip5-bound BURs and alters their histone profiles. In ES cells Tip5 represses PRC2-bound developmental genes and regulates non-PRC2-bound genes that are enriched for G-protein coupled receptor signaling. Tip5 knockdown caused misexpression of these genes important for ES cell maintenance, leading to rapid ES cell differentiation and impaired pluripotency. These data suggest that Tip5 regulates multiple processes through ES cell-specific genome organization to maintain ES cell stemness.

overall_design: Genome occupancy profiles of Tip5, Jarid2, Suz12, and relevant histone modifications, were determined for E14 and E14 Tip5-knockdown ES cells.

first: Hye-Jung

last: Han


title: Genome-wide characterization of histone mark co-occurrence at single molecule resolution

status: Public on Jul 13 2016

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Histone modifications play an important role in chromatin organization and transcriptional regulation. Specific combinations of these modifications to the histone tails have been associated with different functional genomic elements: for example, promoters, enhancers and insulators. Despite the enormous amount of genome-wide histone modification data collected in different cells and tissues, little is known about co-occurrence of modifications on the same nucleosome. Here we present a novel, genome-wide quantitative method for combinatorial indexed chromatin immunoprecipitation (Co-ChIP) to characterize the co-occurrence of histone modifications. Using Co-ChIP, we characterize the genome-wide co-occurrence of 15 chromatin marks (70 pairwise combinations), and find unexpected dynamics between the different marks, including co-occurrence of H3K9me1-H3K27ac in super-enhancers. Finally, we apply Co-ChIP to characterize the distribution of the bivalent H3K4me3-H3K27me3 domain in distinct mouse embryonic stem cell (mESC) states as well as in four adult tissues. We observe dynamic changes in 5786 regions and discover both loss and de novo gain of bivalency in key tissue-specific regulatory genes, suggesting a crucial role for bivalent domains following development. Taken together, we demonstrate that Co-ChIP enables routine single molecule characterization of histone mark co-occurrence and probes the previously hidden dynamic interactions of histone modifications.

overall_design:
CoChIP is a modular protocol in which every step has been optimized to minimize noise. 1) Cells are cross-linked and frozen in aliquots of 10-20 million cells; 2) Chromatin is sheared; 3) Immobilized on specific antibody-coated magnetic beads; 4) Bead-immobilized chromatin is indexed by ligation of sequencing adaptors; 5) The indexed chromatin is released from the antibody-coated magnetic beads using antibody-denaturing conditions and pooled together with other samples in a single tube; 6) The chromatin pool is washed to remove antibody-denaturing elements; 7) The chromatin pool is subjected to a second chromatin immunoprecipitation step; 8) RNA and proteins are degraded and DNA is reverse crosslinked; 9) ChIPed DNA, which contains P5 and P7 Illumina sequences, is purified using SPRI AMPure XP beads; and 10) DNA is amplified by PCR.
Genome-wide co-occurrence of 14x6 chromatin marks in bone-marrow-derived dendritic cells. Co-occurrence of H3K4me3 and H3K27me3 in 4 adult tissues (lung/kidney/liver/brain) and primed/naïve mESC.

first: Assaf

last: Weiner

first: David

last: Lara-Astiaso

first: Eyal

last: David


title: The transcriptional repressor Polycomb group factor 6 (PCGF6) negatively regulates dendritic cell activation and promotes quiescence

city: Montreal

first: Genevieve

last: Deblois

state: Quebec

address: 2950, chemin de Polytechnique

institute: Université de Montréal

summary: We identified that DC activation and immunogenicity are regulated by the transcriptional repressor polycomb group factor 6 (PCGF6). Pcgf6 is rapidly downregulated upon stimulation and this downregulation is necessary to permit full DC activation. Silencing PCGF6 expression enhanced both spontaneous and stimulated DC activation. We show that PCGF6 associates with the H3K4me3 demethylase JARID1c, and together they negatively regulate H3K4me3 levels in DCs. Our results identify two key regulators – PCGF6 and JARID1c – that temper DC activation, and implicate active transcriptional silencing via histone demethylation as a previously unappreciated mechanism for regulating DC activation and quiescence

overall_design: ATAC-seq analysis of BMDCs transduced with either control vectors, cDNA to over-express, or hpRNA to knockdown Pcgf6.

first: Connie

last: Krawczyk

first: Mathieu

last: Lupien


title: TE-associated chromatin variation in mice livers

city: Duarte

first: Juan

last: Du

address: 1500 E. Duarte Rd

institute: Beckman Research Institute, City of Hope

summary:
Chromatin accessibility is a hallmark of active regulatory function in the genome and variation of chromatin accessibility across individuals has been shown to contribute to complex traits and disease susceptibility. However, the mechanisms responsible for chromatin variation among different individuals and how this variation contributes to phenotypic diversity remain poorly understood.
We examined chromatin accessibility variation in liver tissue from seven strains of adult mice that have phenotypic diversity in response to a high-fat/high-sucrose diet. Remarkably, nearly 40% of the loci with the greatest degree of chromatin variability across the strains are associated with transposable elements (TEs), with evolutionarily younger TEs being particularly enriched for regions of chromatin variation. We found that evolutionary younger and older TEs have differential chromatin accessibility profiles and are enriched for binding sites of different transcription factors, indicating the role of TEs in the evolution of regulatory networks in the liver. We also demonstrate that TE polymorphisms and epigenetic regulation of TEs contribute to regulatory variation across different strains through providing binding sites for liver transcription factors. Intriguingly, variable chromatin loci that are associated with liver metabolism are primarily TE-associated.
We demonstrate that TEs contribute to regulatory variation in liver and have downstream effects on metabolism. Our data reveal TEs as a novel and important contributor to regulatory and phenotypic variation in the liver and suggest that regulatory variation at TEs is a major contributor to phenotypic variation in populations.

overall_design: Examination of chromatin accessibility with FAIRE-seq in livers of male mice (A/J, AKR/J, BALB/cJ, C57BL/6J, C3H/HeJ, CBA/J, DBA/2J, BXH2/TyJ, and BXH19/TyJ) fed a high-fat, high-sucrose diet.

first: Amy

last: Leung

first: Candi

last: Trac

first: Michael

last: Lee

first: Brian

last: Parks

first: Aldons

last: Lusis

first: Rama

last: Natarajan

first: Dustin

last: Schones


title: Regulation of Gene Expression During Electron Acceptor Limitation and Bacterial Nanowire Formation in Shewanella oneidensis MR-1

city: University Park

first: John

last: Golbeck

state: Pennsylvania

address: 328 South Frear Laboratory

department: Department of Biochemistry and Molecular Biology

institute: The Pennsylvania State University

summary: In limiting oxygen as an electron acceptor, the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 rapidly forms nanowires, extensions of its outer membrane containing the cytochromes MtrC and OmcA needed for extracellular electron transfer. RNA-Seq analysis was employed to determine differential gene expression over time from cultures maintained in a chemostat and limited for oxygen. We identified 465 genes with decreased expression and 677 genes with increased expression. The coordinated increased expression of heme biosynthesis, cytochrome maturation, and transport pathways indicates that S. oneidensis MR-1 increases cytochrome production, including transcription of genes encoding MtrA, MtrC and OmcA, and properly positions these decaheme cytochromes in or near the outer membrane during nanowire formation. In contrast, the expression of the mtrA and mtrC homologs mtrF and mtrD either remain unaffected or decrease during nanowire formation. The ompW gene, encoding a small outer membrane porin, has 50-fold higher expression during oxygen limitation, and it is proposed that OmpW plays a role in cation transport to maintain electrical neutrality during electron transfer. The genes encoding the anaerobic respiration regulator CRP and the extracytoplasmic function sigma factor RpoE are among transcription factor genes with increased expression. RpoE could function by signaling the initial response to oxygen limitation. Our results show that RpoE activates transcription from promoters upstream of mtrC and omcA. The transcriptome and mutant analysis of S. oneidensis MR-1 nanowire production are consistent with independent regulatory mechanisms for extending the outer membrane into tubular structures and for ensuring the electron transfer function of the nanowires.

overall_design: RNA-seq to identify temporal changes (5 timepoints) in gene expression in S. oneidensis MR-1 during nanowire formation in a chemostat.

first: Sarah

last: Barchinger

first: Sahand

last: Pirbadian

first: Christine

last: Sambles

first: Carol

last: Baker

first: Kar

first: Nigel

last: Burroughs

first: Mohamed

middle: Y

last: El-Naggar


title: Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNAseq

city: Stanford

first: Stephen

last: Quake

state: CA

address: 450 Serra Mall

institute: Stanford Department of Bioengineering

summary: The striatum contributes to many cognitive processes and disorders, but its cell types are incompletely characterized. We show that microfluidic and FACS-based single-cell RNA sequencing of mouse striatum provides a well-resolved classification of striatal cell type diversity. Transcriptome analysis revealed 10 differentiated distinct cell types, including neurons, astrocytes, oligodendrocytes, ependymal, immune, and vascular cells, and enabled the discovery of numerous novel marker genes. Furthermore, we identified two discrete subtypes of medium spiny neurons (MSN) which have specific markers and which overexpress genes linked to cognitive disorders and addiction. We also describe continuous cellular identities, which increase heterogeneity within discrete cell types. Finally, we identified cell type specific transcription and splicing factors that shape cellular identities by regulating splicing and expression patterns. Our findings suggest that functional diversity within a complex tissue arises from a small number of discrete cell types, which can exist in a continuous spectrum of functional states.

overall_design: We measured the transcriptome of 1208 single striatal cells using two complementary approaches; microfluidic single-cell RNAseq (Mic-scRNAseq) and single cell isolation by FACS (FACS-scRNAseq) (Table S1). We sampled cells either randomly or enriched specifically for MSNs or astrocytes using FACS from D1- tdTomato (tdTom)/D2-GFP or Aldhl1-GFP mice, respectively

first: Geoffrey

middle: M

last: Stanley

first: Barbara

last: Treutlein


title: mRNA expression data from human parthenogenetic haploid ESCs (hPGES), normal ESCs (H9) and human fibroblast

city: shanghai

first: cuiqing

last: zhong

address: yueyang road 320

institute: institute of biochemistry and cell biology

summary: Here we report the derivation of human haploid ESCs from parthenogenetic haploid embryos. We used RNA-seq to compare the gene expression levels among human parthenogenetic haploid ESCs (hPGES), normal human ESCs (H9) and human forskin fibroblasts and identified that these cells  express conventional ESCs pluripotent markers and most maternally imprinted genes were  down-regulated.

overall_design: To avoid the influence of diploidized cells on the expression profile, we collected samples from FACS of cells at G1/G0 stage by staining Hochest 33342. We used normal human ESCs and human fibroblast as control. Gene expression profiles of all the cell lines were analysed on illumina Hiseq 2500.

first: Jinsong

last: Li


title: Microglia development follows a stepwise program to regulate brain homeostasis - RNA seq

first: Ido

last: Amit

summary: Microglia play important roles in life-long brain maintenance and in pathology, but are also crucial in the developing central nervous system; yet their regulatory dynamics during development have not been fully elucidated. Genome-wide chromatin and expression profiling coupled with single-cell transcriptomic analysis throughout development reveal that microglia undergo three temporal developmental stages in synchrony with the brain: early, pre-, and adult microglia, which are under the control of distinct regulatory circuits. Knockout of the transcription factor MafB caused disruption of homeostasis in adulthood and increased inflammation. Environmental perturbations, such as the microbiome or prenatal immune activation, led to dysregulation of the developmental program, particularly in terms of inflammation. Together, our work identifies a stepwise developmental program of microglia integrating immune response pathways that may be associated with several neurodevelopmental disorders.

overall_design: Yolk sac progenitors (CD45+CD11B+CX3CR1-GFP+), microglia from early brain (CD45+CD11B+CX3CR1-GFP+), and microglia from later stages (CD45intCD11BintCX3CR1-GFP+) were isolated from CX3CR1+ C57BL/6J mice or microglia from perturbation models (CD45intCD11Bint) from mice of C57BL/6J background


title: Microglia development follows a stepwise program to regulate brain homeostasis

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

overall_design: Refer to individual Series


title: Dnmt3a and Dnmt3b associate with enhancers to regulate human epidermal stem cell homeostasis

city: Barcelona

first: Debayan

last: Datta

state: Barcelona

address: C. Baldiri Reixac 10

department: Oncology

country: Spain

institute: IRB Barcelona

summary: Here, we show that Dnmt3a and Dnmt3b show non-overlapping and unique patterns of genomic localization in human epidermal stem cells and their differentiated counterparts. Dnmt3a, but not Dnmt3b, binds to the TSSs of a cohort of genes required for the interaction of stem cells with their underlying stroma. Unexpectedly, TSSs bound by Dnmt3a are highly transcribed and are devoid of DNA-methylation. Conversely, Dnmt3b specifically decorates the genebody of genes that establish the stem cell and differentiated signatures. Genic occupation by Dnmt3b correlates with high levels of DNA-methylation, broad domains of histone H3K4me3 8, and robust transcription. Intriguingly, both proteins also bind to the most active subset of enhancers, and are required for the production of their associated bidirectional enhancer RNAs 9. We show that typical and super-enhancers are very dynamically regulated during the linear transition of epidermal stem cells to differentiated keratinocytes. Interestingly, Dnmt3a and Dnmt3b show a strong preference for the super-enhancers that define the ectodermal lineage, but importantly, that also establish the functional traits associated to the stem cell and differentiated states. These enhancers contain very low levels of DNA-methylation, but high amounts of DNA-hydroxymethylation. Depletion of either protein completely impairs human epidermal stem cell self-renewal by inducing their spontaneous differentiation.

overall_design: Examination of genome wide localization of Dnmt3A and Dnmt3B and their overlap within genomic regulatory regions in a DNA-methylation dependent and independent manner. Genome wide total RNA quantification of Wild Type Human EpiSC and its Differentiated counterparts.

first: Lorenzo

last: Rinaldi

first: Judit

last: Serrat

first: Lluis

last: Morey

first: Guiomar

last: Solanas

first: Alexandra

last: Avgustinova

first: Enrique

last: Blanco

first: Jose

middle: I

last: Pons

first: David

last: Gomez

first: Alex

last: Von Kriegsheim

first: Luciano

last: di Croce

first: Salvador

last: Benitah


title: Small RNA Deep Sequencing Analysis of Mouse T follicular helper (TFH) cells

city: La Jolla

first: Changchun

last: Xiao

state: California

address: 10550 North Torrey Pines Road

department: Immunology & Microbial Science

country: USA

institute: The Scripps Research Institute

summary: Small non-coding RNAs, esp. microRNAs (miRNAs), play critical roles in a large diversity of biological processes. The goal of this study is to perfrom small RNA deep sequencing analysis of mouse T follicular helper cells and to identify miRNAs that are highy and specifically expressed in these cells.

overall_design: Two to three month old C57BL/6 mice were immunized with OVA/alum/LPS intraperitoneally. On day 7 after immunization, naïve (CD4+CD44-CXCR5-PD1-), pre-TFH (CD4+CXCR5intPD1lo), and TFH (CD4+CXCR5hiPD1hi) cells were FACS-sorted from splenocytes. Total RNA was extracted using the TRIzol reagent and subjected to standard small RNA deep sequencing analysis.

first: Seung

last: Kang

first: Mohsen

last: Sabouri‐Ghomi


title: Replicates, Read Numbers, and Other Important Experimental Design Considerations for Microbial RNA-seq Identified Using Bacillus thuringiensis Datasets.

city: Oak Ridge

first: Steven

last: Brown

address: 1 Bethel valley road

institute: ORNL

summary: RNA-seq has recently become a popular choice for gene expression studies. It is revolutionizing the fields of genomics and transcriptomics by enabling a wide range of applications along with high genome coverage and the ability to detect weakly expressed genes, which makes it an attractive alternative to microarrays. However, the field of RNA-Seq analysis is still evolving. In this study transcriptomic data from Bacillus thuringiensis strains ATCC10792 and CT43, grown in two Luria broth medium lots on four dates was obtained from Illumina High-Seq2000 and analyzed using DESeq2. Genome coverages across samples ranged from 87-450X with medium lots and culture dates as major variation sources. Significantly differentially expressed genes (5% FDR, two-fold change) were detected between cultures grown in different medium lots as well as on different dates for both ATCC10792 and CT43. Genes related to iron acquisition and metabolism were also consistently differentially expressed for both strains, in different media lots. RNA-seq is highly sensitive and can identify differential gene expression at predictive biology levels. The noise in data can be controlled and minimized with appropriate experimental design, number of replicates and reads. Here we outline some experimental design parameters for an efficient and cost effective microbial transcriptomics study.

overall_design: Transcriptomic data from Bacillus thuringiensis strains ATCC10792 & CT43 grown with media from different lots and collected on different dates.

first: Punita

last: Manga

middle: D

first: Dawn

last: Klingeman

first: Tse-Yuan

last: Lu

first: Tonia

middle: L

last: Mehlhorn

first: Dale

middle: A

last: Pelletier

first: Loren

last: Hauser

first: Charlotte

last: Wilson


title: Microglia development follows a stepwise program to regulate brain homeostasis - ChIP-seq

first: Ido

last: Amit

overall_design: Yolk sac progenitors (CD45+CD11B+CX3CR1-GFP+), microglia from early brain (CD45+CD11B+CX3CR1-GFP+), and microglia from later stages (CD45intCD11BintCX3CR1-GFP+) were isolated from CX3CR1+ C57BL/6J  mice


title: Microglia development follows a stepwise program to regulate brain homeostasis - Single Cell RNA-seq


title: Molecular signatures of neural connectivity in the olfactory cortex

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

summary:
Purpose:This work aimed to identify the genetic profiles of piriform projection neurons and characterize their spatial organization within the piriform cortex.
Methods: We microdissected the three layers of pirifrom cortex by laser capture (LMD) and performed RNA deep sequencing in order to identify layer-specific molecular markers, we then validated these data by using RNA in situ hybridization and immunohistochemistry.We next performed anterograde neural tracing experiments to identify piriform target regions, and retrograde neural tracing experiments to analyze how piriform projection neurons are organized within piriform cortex.We then combined the analysis of patterns of gene expression with retrograde tracing experiments to identify molecular signatures of the different subclasses of piriform projecting neurons.
Results:We show that layers and sub-layers of the piriform cortex can be discriminated by gene expression patterns in adult piriform cortex. We observe that neurons projecting to distinct target areas are localized in distinct layers and express specific genes. We demonstrate that these molecular signatures of piriform projection neurons are maintained in reeler mice, in which cortical lamination is lost and neural positioning is scrambled, suggesting that piriform output connectivity strictly depends on the molecular programm, rather than a proper lamination of the cortex.
Conclusion:These results provide important insights into the principles underling the piriform connectivity.

overall_design: 3 replicates per each layer (three layers) of piriform cotrex were used for the RNA deep sequancing

first: Assunta

last: Diodato

first: Alexander

last: Fleischmann

first: Juliette

last: Pouch

first: Sandrine

last: Perrin


title: Dynamic competing histone H4 K5K8 acetylation and butyrylation are hallmarks of highly active gene promoters

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

institute: INSERM-UGA

summary: Newly discovered histone lysine acylations increase the functional diversity of nucleosomes well beyond acetylation. Here, we focus on histone butyrylation in the context of sperm cell differentiation. Specifically, we investigate the butyrylation of histone H4 lysine 5 and 8 at gene promoters, where acetylation guides the binding of Brdt, a bromodomain-and-extra-terminal protein, thereby mediating stage-specific gene expression programs. Genome-wide mapping data show that highly active Brdt-bound gene promoters systematically harbour competing histone acetylation and butyrylation marks at H4 K5 and K8. Histone butyrylation, despite acting as a direct stimulator of transcription, competes with acetylation, especially at H4 K5, to prevent Brdt binding.  The observed in vivo H4 K5K8 acetylation butyrylation state at active promoters is reproduced in vitro where p300 indistinctly acetylates and butyrylates H4 K5 and K8.  Altogether, highly active gene promoter regions are characterized by alternating H4 acetylation and butyrylation sustaining direct gene activation and a dynamic bromodomain binding.

overall_design: Examination of 4 different histone modifications, butyrylation of H4K5 and of H4K8, and acetylation of H4K5 and H4K8, in mouse spermatogenic cells at 2 stages: spermatocytes and round spermatids.

first: Guillaume

last: Charbonnier

first: Denis

last: Puthier

first: Di

last: Zhang

first: Afsaneh

last: Goudarzi

first: He

last: Huang

last: Barral

first: Okwang

last: Kwon

first: Shankang

last: Qi

first: Zhanyun

last: Tang

first: Thierry

last: Buchou

first: Emilie

last: Montellier

first: Jonathan

last: Gaucher

last: Curtet

first: Alexandra

last: Debernardi

first: Carlo

last: Petosa

first: Daniel

last: Panne

first: Robert

last: Roeder

first: Yingming

last: Zhao

first: Saadi

last: Khochbin


title: Za and Zaa binding profiles in HeLa cells

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

summary: Genome-wide positions of Z-DNA are mapped. ChIP was performed against transiently expressing Flag-Za or Flag-Zaa using Flag antibody in HeLa cells. Za and Zaa ChIP DNA and fragmented genomic DNA were used for sequencing library construction. Each library was sequenced on Illumina GAIIx and HiSeq 2500 and sequenced reads were mapped and normalized.

overall_design: The information of Za and Zaa binding sites in HeLa cells transiently expressing Za or Zaa was generated by deep sequencing, using Illumina GAIIx and HiSeq 2500.

first: So-I

last: Shin

first: Jihwan

last: Park

first: Seong

last: Seo

first: Chae

last: Lim

first: Hyeongrin

last: Jeon