title: Reprogramming by de-bookmarking somatic transcriptional program via targeting the BET bromodomains

status: Public on Aug 22 2016

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: One critical task in pluripotent reprogramming is to erase the somatic transcriptional program of starting cells.  No strategy or theory exists for achieving erasure of somatic gene expression memory.  Here, we present a proof-of-principle strategy in which reprogramming to pluripotency is facilitated by small molecules that erase somatic cell transcription memory.  We show that mild chemical targeting of the acetyllysine-binding pockets of the BET bromodomains, the transcriptional bookmarking domains, robustly enhances reprogramming. Furthermore, we show that chemical targeting of the transcriptional bookmarking BET bromodomains dramatically downregulates specific somatic gene expression programs in both naïve and reprogramming fibroblasts. Chemical blocking of the BET bromodomains also resulted in loss of fibroblast morphology early in reprograming. In this study, we experimentally demonstrate a concept for cell fate conversion: facilitating the conversion by chemically targeting the transcriptional bookmarking BET bromodomains responsible for transcriptional memory.

overall_design: human BJ cells were treated with JQ1 at 50 nM for 48 hours. Differential expression was compared with DMSO treatment. The same treatments and comparsion were conducted for reprogramming BJ cells, which were transduced with OCT4, SOX2, and KLF4. JQ1iPSC5 is a iPSC (induced pluripotent stem cell) line generated in this study using small molecules JQ1.

first: Zhicheng

last: Shao

first: Kejin

last: HU


title: DNA methylation and hydroxymethylation profiles were compared between mouse PGCLCs isolated from 6-day culture embryoid bodies, their precursor cells (ESCs, iPSCs, and EpiLCs), and E12.5 in vivo mouse PGCs.

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

country: USA

institute: MGH Cancer Center

type: Methylation profiling by high throughput sequencing

summary: DNA methylation and hydroxymethylation in the genomes of mouse E12.5 primordial germ cells (PGCs), primordial germ cell-like cells (PGCLCs) isolated from 6-day culture embryoid bodies,  and the precursor pluripotent stem cells [embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs)] and epiblast-like cells (EpiLCs)

overall_design: Mouse PGCs and PGCLCs were enriched as SSEA1+/CD61+ double-positive cells by FACS. Genomic DNA was isolated from mouse PGCs, PGCLCs, ESCs, iPSCs, and EpiLCs. DNA methylation and hydroxymethylation were determined using MBD-seq and hydroxymethylcytosine chemical tagging deep sequencing techniques.

first: Norikatsu

last: Miyoshi

first: Jente

middle: M

last: Stel

first: Haley

last: Ellis

first: Keiko

first: Toshi


title: Characterization and function of Tomato yellow leaf curl virus-derived small RNAs generated in the tolerant and susceptible tomato varieties using deep sequencing

city: Changsha

first: Miao

last: Bai

state: Hunan

address: Hunan Agricultural University, No. 1 Nongda Road, Furong

country: China

institute: Hunan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: High-throughput sequence analysis of small RNAs of TYLCV-tolerant (containing tolerance gene Ty-1) and susceptible varieties indicated that miRNA-like vsRNAs and secondary vsiRNAs are mainly contributed to hotpots. Interestingly, various characteristics of vsRNAs among each sample are consistent, but in different number of expression; Deep sequencing of degradome provided evidence for the function of vsRNAs-mediated viral transcripts slicing; And bisulfite sequencing PCR suggested the geminivirus DNA methylation induced by vsRNAs. Comparison of the expression quantity and trend of viral DNA, mRNA and vsRNA inferred that the quantity of vsRNAs is significantly corresponding to the expression level of viral mRNA. Nevertheless, vsRNAs had finite effect on inhibition of virus replication and expression. Here, we also speculated that by RDR catalysis of vsRNAs amplification, the tolerance gene Ty-1 may take an effective inhibition of viral transcription at the beginning of TYLCV infection.

overall_design:
Examination of 6 different sRNA and 4 degradome library in 2 tomato material.
The main result of our paper is distinguish the host plant sRNA and viral-derived sRNA from the .fa files (MMS_21dpi, 30dpi and TY1S_21dpi, 30dpi).

first: Bing

middle: Y

last: Xie


title: Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution

status: Public on Aug 20 2016

city: Kunming

first: lei

last: shi

state: Yunnan

address: No.17 Longxin Road

institute: Kunming Institute of Zoology

type: Genome variation profiling by high throughput sequencing

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

sample_organism:
Macaca
Macaca fascicularis
Macaca mulatta
Pan troglodytes
Homo sapiens
Hoolock leuconedys

overall_design: Refer to individual Series


title: Whole transcriptome analysis of reaggregated embryoid bodies treated with IWR-1

city: Minneapolis

first: June

last: Baik

state: MN

address: 2231 6th St SE CCRB

institute: University of Minnesota

type: Expression profiling by high throughput sequencing

summary: We identified distict mesodermal sub-populations based on Endoglin (Eng) and Flk1 expression in Brachyury (Bry) positive cells. By using whole-transcriptome analysis, we further characterized these populations and how they changed when Wnt pathway is inhibited

overall_design: Reaggregates mRNA profiles of unsorted, Flk1+ Eng+, and Flk1- Eng+  samples were generated by deep sequencing, in triplicate , using  Ilumina.

first: Rita

last: Perlingeiro

first: Scott

last: Swanson


title: microRNA-222 regulates muscle alternative splicing through Rbm24 during differentiation of skeletal muscle cells

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

summary: A number of microRNAs have been shown to regulate skeletal muscle development and differentiation. MicroRNA-222 is downregulated during myogenic differentiation and its overexpression leads to alteration of muscle differentiation process and specialized structures. By using RNA induced silencing complex (RISC) pulldown followed by RNA sequencing, combined with in silico microRNA target prediction, we have identified two new targets of microRNA-222 involved in the regulation of myogenic differentiation, Ahnak and Rbm24. Specifically, the RNA binding protein Rbm24 is a major regulator of muscle specific alternative splicing and its downregulation by microRNA-222 results in defective exon inclusion impairing the production of muscle-specific isoforms of Coro6, Fxr1 and NACA transcripts. Reconstitution of normal levels of Rbm24 in cells overexpressing microRNA-222 rescues muscle-specific splicing. In conclusion, we have identified a new function of microRNA-222 leading to alteration of myogenic differentiation at the level of alternative splicing, and we provide evidence that this effect is mediated by Rbm24 protein.

overall_design: We built linear models using 2 different experiments and two conditions (miR222 over expression (n=1) and control siRNA(n=2)) with the linear formula (~condition + experiment).

first: Beatrice

last: Cardinali

first: Germana

last: Falcone

first: Fabio

last: Martelli


title: Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution [SNP]

summary: We report the application of DNA sequencing technology for high-throughput sequencing of mix candidate genes' PCR products totally 38 based on DNA from human, chimpanzee, gibbon, macaque and crab eating macaque  profrontal cortex tissues.

sample_organism:
Macaca
Macaca fascicularis
Pan troglodytes
Homo sapiens
Hoolock leuconedys

overall_design: Mix candidate genes PCR products from 1 tissues, 22 individual humans, 2 individual chimpanzees, 1 individual gibbons,15 individual rhesus macaques and 5 crab eating macaques were sequenced by using MiSeq

first: Lei

last: Shi

last: Su


title: Comparison Analysis of microRNAs in Response to EV71 and CA16 Infection in Human Bronchial Epithelial Cells by High-Throughput Sequencing to Reveal Differential Infective Mechanisms

first: Jie

last: Song

address: Number 935 Jiaoling Load

institute: Institute of Medical Biology, Chinese Academy of Medicine Science and Peking Union Medical College

summary: To compare MicroRNA expression in 16HBE infected with EV71 and CA16

overall_design: we defined the following experimental groups: EV71-0h, EV71-6h, EV71-12h, CA16-0h, CA16-6h and CA16-12h

first: Yajie

last: Hu

first: Longding

last: Liu

first: Qihan

last: Li


title: High-throughput miRNA sequencing and identification of biomarkers for forensically relevant biological fluids

city: Richmond

first: Sarah

middle: J

last: Seashols-Williams

state: VA

address: 1015 Floyd Ave Box 843079

department: Forensic Science

institute: Virginia Commonwealth University

summary: In this study, small RNAs were isolated from individual donations of eight forensically relevant biological fluids (blood, semen, vaginal fluid, menstrual blood, saliva, urine, feces, and perspiration) and subjected to next generation sequencing using the Illumina® Hi-Seq platform.  Sequencing reads were aligned and annotated against miRbase release 21, resulting in a list of miRNAs and their relative expression levels for each sample analyzed.  Body fluids with high bacterial loads (vaginal fluid, saliva, and feces) yielded relatively low annotated miRNA counts, likely due to oversaturation of small RNAs from the endogenous bacteria.  Both body-fluid specific and potential normalization miRNAs were identified for further analysis as potential body fluid identification tools for each body fluid.

overall_design: 32 samples - 3-5 replicates of each human biological fluid:  venous blood, urine, semen (normal and vasectomized), vaginal secretions, menstrual secretions, perspiration, feces, saliva

first: Carolyn

last: Lewis

first: Chelsea

last: Calloway

first: Nerissa

last: Peace

first: Ariana

last: Harrison

first: Christina

last: Hayes-Nash

first: Samantha

last: Fleming

first: Qianni

last: Wu

first: Zendra

middle: E

last: Zehner


title: Transcriptional changes induced by Brd4 inhibitor, AZD5153, in cancer cell lines

city: Waltham

first: Huawei

last: Chen

address: 35 Gatehouse Dr

institute: AstraZeneca

summary: We sequenced mRNA from 12 human cancer cell lines treated with DMSO or AZD5153 for 24h to determine compound mechanism of action

overall_design: Measured mRNA levels in cell lines treated with either AZD5153 or DMSO for 24h

first: Raymond

first: Austin

last: Dulak


title: The Long Noncoding RNA SNHG1 Regulates both the Local and Distal Genes in Cancer

city: Beijing

first: Guifeng

last: Wei

state: Beijing

address: 15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Increasing evidence indicates that lncRNAs play important roles in various physiological processes and dysfunction of lncRNAs could be a prevalent cause in human diseases. Here, we functionally characterized the nuclear-enriched lncRNA SNHG1, which is highly expressed in multiple types of cancer. We also provide evidence that SNHG1 promotes cancer cell growth by regulating gene expression both in cis and in trans. SNHG1 was involved in the Akt signaling pathway as it promotes the neighboring transcription of the protein-coding gene SLC3A2 in cis, by binding the Mediator complex to facilitate the establishment of enhancer-promoter interaction. In trans, SNHG1 directly interacted with central domain of FUBP1 and antagonize the binding of FBP-Interacting Repressor FIR to FUBP1, thereby coordinating the expression of the oncogene MYC. Collectively, our findings demonstrate that lncRNA SNHG1 can function both in cis and in trans with distinct mechanisms to regulate transcription, promoting tumorigenesis and cancer progression.

overall_design: Even, Odd probes targeting SNHG1 sequence, and control probes targeting LacZ. Probes was coupled with biotin, the captured DNA was prepared for library then sequencing.

first: Y

last: Sun

first: G

first: H

last: Luo

first: R


title: The ubiquitin ligase HUWE1 regulates hematopoietic stem cell maintenance and lymphoid commitment

city: New York

first: Bryan

last: King

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center


title: Age and diet affect genetically separable secondary injuries that cause acute mortatlity following traumatic brain injury in Drosophia

city: Madison

first: David

last: Wassarman

state: Wisconsin

address: 425 G. Henry Mall, Room 4250

department: Medical Genetics

institute: University of Wisconsin

summary: To identify genes involved in TBI outcomes in Drosophila we compared genome-wide mRNA expression of uninjured and injured flies under both age and diet conditions.

overall_design: Whole male fly mRNA profiles of 0-7 day and 20-27d old Drosophila line w1118 were generated, with or without injury and under two different dietary conditions.  Experiments were preformed in triplicate, using Illumina HiSeq 2500.

middle: A

first: Barry

last: Ganetzky

first: Rebeccah

last: Katzenberger


title: Transcriptome of alfalfa plants under animal grazing

status: Public on Aug 24 2016

city: Hohhot

first: Junjie

last: Wang

state: Inner Mongolia

address: 306 Zhaowuda Road

department: College of Ecology and Environmental Science

institute: Inner Mongolia Agricultural University

summary: By comparing transcriptomes of tolerant and intolerant plants of sickle alfalfa subject to intensive animal grazing, we identified pathways involved in nutrient-responsive signaling, light and wound response, cell wall formation, and energy metabolism.  In these pathways, grazing suppressed 39 genes, but less severe in the tolerant plant, and activated 5 genes all carrying polymorphisms in their homologous transcripts between the tolerant and intolerant plants.  These genes and pathways - responsive to grazing and differentially expressed between the tolerant and intolerant plants – underline a defense mechanism in alfalfa against grazing stresses.

overall_design: We examined transcriptomes of 3 alfalfa plants: grazing tolerant and grazed, grazing tolerant and not grazed, grazing intolerant and grazed, all at single replicate each.

first: Yan

last: Zhao


title: De novo DNA methylation by DNA Methyltransferase 3a controls early effector CD8+ T cell fate decisions following activation

city: Baltimore

first: Christopher

middle: Jordan

last: Gamper

state: MD

address: 1650 Orleans St., CRB I, Rm. 209

department: Oncology

institute: Johns Hopkins University

summary: DNMT3a is a de novo DNA methyltransferase expressed robustly after T cell activation that regulates plasticity of CD4+ T cell cytokine expression. Here we show that DNMT3a is critical for directing early CD8+ T cell effector and memory fate decisions. While effector function of DNMT3a knockout T cells is normal, they develop more memory precursor and fewer terminal effector cells in a T cell intrinsic manner compared to wild-type animals. Rather than increasing plasticity of differentiated effector CD8+ T cells, loss of DNMT3a biases differentiation of early effector cells into memory precursor cells. This is attributed in part to ineffective repression of Tcf1 expression in knockout T cells, as DNMT3a localizes to the Tcf7 promoter and catalyzes its de novo methylation in early effector WT CD8+ T cells. This data identifies DNMT3a as a crucial regulator of CD8+ early effector cell differentiation and effector versus memory fate decisions.

overall_design: Examination of global genomic DNA methylation by MBD-seq in naïve CD8 T cells and CD8 T cells 8 days post Vaccinia-Ova infection, comparing OT1 TCR-Tg CD8 T cells isolated from WT and T cell conditional DNMT3a KO mice.

first: Brian

middle: H

last: Ladle

first: Kun-Po

last: Li

first: Maggie

last: Phillips

first: Alexandra

middle: B

last: Pucsek

first: Azeb

last: Haile

first: Jonathan

middle: D

last: Powell

first: Elizabeth

last: Jaffee

last: Hildeman


title: Decoding the Long Noncoding RNA during Cardiac Maturation: a Roadmap for Functional Discovery [RNA]

city: Los Angeles

first: Marlin

last: Touma

state: CA

address: 650 Charles E Young drive- MRL 3760

department: UCLA-Cardiovascular Research Laboratory

institute: UCLA

summary: Cardiac maturation during perinatal transition of heart is critical for functional adaptation to hemodynamic load and nutrient environment. Perturbation in this process has major implications in congenital heart defects (CHDs). Transcriptome programming during perinatal stages is important information but incomplete in current literature, particularly, the expression profiles of the long noncoding RNAs (lncRNAs) are not fully elucidated

overall_design:
From comprehensive analysis of transcriptomes derived from neonatal mouse heart left and right ventricles, a total of 45,167 unique transcripts were identified, including 21,916 known and 2,033 novel lncRNAs. Among these lncRNAs, 196 exhibited significant dynamic regulation along maturation process. By implementing parallel weighted gene co-expression network analysis (WGCNA) of mRNA and lncRNA datasets, several lncRNA modules coordinately expressed in a developmental manner similar to protein coding genes, while a few of them revealed chamber specific patterns. Out of 2,442 lncRNAs located within 50 KBs of protein coding genes, 11% significantly correlates with the expression of their neighboring genes. The impact of Ppp1r1b-lncRNA on the corresponding partner gene Tcap was validated in cultured myoblasts. While this concordant regulation was also conserved in human infantile hearts.  Furthermore, the Ppp1r1b-lncRNA/Tcap expression ratio was identified as a molecular signature that differentiated CHD phenotypes
RNA dataset: neonatal mouse heart left and right ventricles

first: Xuedong

last: Kang

first: Ashley

last: Cass

first: Fuying

last: Gao

first: Reshma

last: Biniwale

first: Giovanni

last: Coppola

first: Xinshu

last: Xiao

last: Reemtsen

first: Yibin


title: Decoding the Long Noncoding RNA during Cardiac Maturation: a Roadmap for Functional Discovery [lncRNA]

overall_design:
From comprehensive analysis of transcriptomes derived from neonatal mouse heart left and right ventricles, a total of 45,167 unique transcripts were identified, including 21,916 known and 2,033 novel lncRNAs. Among these lncRNAs, 196 exhibited significant dynamic regulation along maturation process. By implementing parallel weighted gene co-expression network analysis (WGCNA) of mRNA and lncRNA datasets, several lncRNA modules coordinately expressed in a developmental manner similar to protein coding genes, while a few of them revealed chamber specific patterns. Out of 2,442 lncRNAs located within 50 KBs of protein coding genes, 11% significantly correlates with the expression of their neighboring genes. The impact of Ppp1r1b-lncRNA on the corresponding partner gene Tcap was validated in cultured myoblasts. While this concordant regulation was also conserved in human infantile hearts.  Furthermore, the Ppp1r1b-lncRNA/Tcap expression ratio was identified as a molecular signature that differentiated CHD phenotypes
lncRNA dataset: neonatal mouse heart left and right ventricles

first: Yan

last: Zhao

last: Wang


title: Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer

status: Public on Aug 23 2016

city: Toronto

first: Mathieu

last: Lupien

state: Ontario

address: 101 College street

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

summary:
Sustained expression of the estrogen receptor-α (ESR1) drives
two-thirds of breast cancer and defines the ESR1-positive
subtype. ESR1 engages enhancers upon estrogen stimulation
to establish an oncogenic expression program1. Somatic
copy number alterations involving the ESR1 gene occur in
approximately 1 % of ESR1-positive breast cancers2–5, suggesting
that other mechanisms underlie the persistent expression of
ESR1. We report significant enrichment of somatic mutations
within the set of regulatory elements (SRE) regulating ESR1 in
7% of ESR1-positive breast cancers. These mutations regulate
ESR1 expression by modulating transcription factor binding
to the DNA. The SRE includes a recurrently mutated enhancer
whose activity is also affected by rs9383590, a functional
inherited single-nucleotide variant (SNV) that accounts for
several breast cancer risk–associated loci. Our work highlights
the importance of considering the combinatorial activity of
regulatory elements as a single unit to delineate the impact of
noncoding genetic alterations on single genes in cancer.

overall_design: RNA-Seq was performed in HCC1419 cells heterozygous for the functional SNV, rs9383590, to determine which genes displayed an allelic imbalance within a 1MB window.

first: Kinjal

last: Desai

first: Swneke

last: Bailey


title: Different microRNA Alterations Contribute to Diverse Outcomes Following EV71 and CA16 Infections: Insights from High-Throughput Sequencing in Peripheral Blood Mononuclear Cells of Rhesus Monkey

status: Public on Aug 19 2016

first: Jie

last: Song

summary: Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) are the predominant etiological agents of hand, foot, and mouth disease (HFMD) and both belong to the human enterovirus A species of the Picornaviridae family. These viruses share similar genetic homology, although the clinical manifestations of HFMD caused by the two viruses have some discrepancies. Furthermore, the underlying mechanisms leading to these differences remain unclear. microRNAs (miRNAs) participate in numerous biological or pathological processes, including host responses to viral infections, by targeting messenger RNAs (mRNAs) for translational repression or degradation. Here, we focused on differences in miRNA expression patterns in peripheral blood mononuclear cells (PBMCs) of rhesus monkeys infected with EV71 or CA16 at different time points using high-throughput sequencing technology. For the first time, this study demonstrated that EV71 and CA16 infection result in specific miRNA expression patterns in PBMCs.

overall_design: The EV71 virus strain (sub-genotype C4, GenBank: EU812515.1) that originated from an epidemic in Fuyang, China in 2008 and the CA16 virus G20 strain (sub-genotype B, GenBank: JN590244.1), which originated from an HFMD patient in Guangxi in 2010, were propagated in PBMCs at a multiplicity of infection (MOI) of 1 the following day. Cells were infected in triplicate and collected at 0, 24 and 48 hours post infection (hpi). Cells infected with EV71 and CA16 for 0 hpi were used as controls. We defined the different experimental groups as EV71-0h, EV71-24h, EV71-48h, CA16-0h, CA16-24h and CA16-48h.

first: Yajie

last: Hu

first: Longding

last: Liu

first: Qihan

last: Li


title: Molecular responses and metabolic reset of apple fruit under postharvest low oxygen stress

city: Pisa

first: Pietro

last: Tonutti

address: Piazza Martiri delal Libertà

department: Life Sciences

institute: Scuola Superiore Sant'Anna

summary: In the present work we report data on the application of an integrated approach on apples held under two levels of low oxygen concentrations  throughout  the initial 2 months of  storage, when, in general, strict control of the effects of the extremely low oxygen concentration is  required for a successful DCA performance.

overall_design: Examination of 4 different condition. Three replicates per condition

first: Benedetto

last: Ruperti

first: Dubravka

last: Cukrov

first: Stefano

last: Brizzolara

first: Hans

last: Van Veen

first: Andrea

last: Zuccolo


title: Regional expression of X. tropicalis transcription factors in early gastrula embryos

city: Irvine

first: Kitt

middle: D.

last: Paraiso

address: 4410 Nat Sci II, University of California, Irvine

department: Department of Developmental and Cell Biology

institute: University of California, Irvine

summary:
Purpose: We wished to obtain spatial expression profiles of transcription factor gene expression and expression of other genes.
Methods: Embryos were dissected and RNA-seq was performed to determine expression levels of genes. Comparisons between explanted regions permits determination of spatial enrichment of gene expression.

overall_design: mRNA-seq performed on 5 dissected regions of NF stage 10.5 X. tropicalis embryos and stage-matched sibling whole embryos. Experiment performed in duplicate.

first: Ira

middle: L

last: Blitz


title: Transcriptional expression level during exponential growth phase in Kluyveromyces marxianus

city: Daejeon

first: Byung-Kwan

last: Cho

address: 291 Daehak-ro

country: South Korea

institute: KAIST

summary: To understand functional roles of ncRNAs during exponential growth phase, we captured transcriptome changes by conducting strand-specific RNA-seq.

overall_design: Directional RNA-seq (dUTP method by TruSeq®) were generated  in two biological replicates by using Illumina MiSeq

first: Yoo-Bok

first: Eunju

last: Lee


title: Phenotype and RNA-Seq-Based Transcriptome Profiling of Staphylococcus aureus biofilms in response to Tea tree oil

city: Changchun

last: Guo

address: Xi’an Road 5333#

institute: Jilin University

summary: RNA sequencing (RNA-Seq) was used in our study to elucidate the mechanism of Tea tree oil (TTO) as a potential antibacterial agent to evaluate differentially expressed genes and functional network analysis in S. aureus ATCC 29213 biofilms.

overall_design: Staphylococcus aureus  biofilm cells were exposed for 60 minutes to TTO at concentration of 1/2×MBIC (1 mg/ml).2 samples including 2 control samples are analyzed.

first: Xingchen

last: Zhao

first: Zonghui

first: Zuojia

first: Rizeng

last: Meng

first: Ce

last: Shi

first: Xiangrong

last: Chen

first: Ziwei

last: Liang


title: Potent and targeted activation of HIV-1 using the CRISPR/Cas9 activator Complex

city: La Jolla

first: Jonathan

middle: Ross

last: Hart

address: 10550 North Torrey Pines Road, BCC239

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

summary: Integration of the HIV-1 provirus in the host genome ensures a persistent supply of latently infected cells. This latent reservoir is recalcitrant to antiretroviral therapy (ART) making lifelong treatment the only option for patients. The “shock and kill” strategy aims to eradicate latent HIV by reactivating proviral gene expression followed by ART treatment. Gene specific transcriptional activation can be achieved using the RNA-guided CRISPR-Cas9 system comprising small guide RNAs (sgRNAs) with a nuclease deficient Cas9 mutant (dCas9) fused to the VP64 transactivation domain (dCas9-VP64).  We engineered this system to target 23 sites within the LTR promoter of HIV-1 and identified a “hotspot” for activation. We studied the functionality of activating sgRNAs to transcriptionally modulate the latent proviral genome across multiple different in vitro latency cell models including several J-Lat, ACH2 J1.1 and the CEM T cell model comprising a single clonal population of integrated mCherry-IRES-Tat from a full-length HIV LTR (LChIT).  While we observed variable responses of latent cell models to well-characterized chemical stimuli, we detected consistent efficient activation of latent virus mediated by activator sgRNAs.  In addition, transcriptome analysis of chemically treated cells revealed massive non-specific gene dysregulation whereas by comparison, dCas9-VP64/sgRNAs induced specific activation of the integrated provirus.  In conclusion, we show the potential for CRISPR-mediated gene activation systems to provide enhanced efficiency and specificity in a targeted latency reactivation strategy. This represents a promising approach to a “functional cure” of HIV/AIDS.

overall_design: Three experimental conditions (sgRNA control, TNF treated and sgRNA against the LTR of HIV-1) were analyzed in triplicate using two sequencing lanes

first: Sheena

last: Saayman

first: Daniel

middle: C

last: Lazar

first: Tristan

last: Scott

middle: R

first: Mayumi

last: Takahashi

first: John

last: Burnett

first: Vicente

last: Planelles

first: Kevin

middle: V

last: Morris

first: Marc

middle: S

last: Weinberg


title: Transcriptome profile analysis of breast muscle tissues from high or low levels of atmospheric ammonia exposed broilers (Gallus gallus)

first: Bao

last: Yi

address: No.2 Yuanmingyuan West Road

department: Institute of Animal Sciences

institute: Chinese Academy of Agricultural Sciences

summary: Abstract: Atmospheric ammonia is a common problem in poultry industry. High concentrations of aerial ammonia cause great harm to broilers' health and production. For the consideration of human health, the limit exposure concentration of ammonia in houses is set at 25 ppm. Previous reports have shown that 25 ppm is still detrimental to livestock, especially the gastrointestinal tract and respiratory tract, but the negative relationship between ammonia exposure and the tissue of breast muscle of broilers is still unknown. In the present study, 25 ppm ammonia in poultry houses was found to lower slaughter performance and breast yield. Then, high-throughput RNA sequencing was utilized to identify differentially expressed genes in breast muscle of broiler chickens exposed to high (25 ppm) or low (3 ppm) levels of atmospheric ammonia. The transcriptome analysis showed that 163 genes (fold change ≥ 2 or ≤ 0.5; P-value < 0.05) were differentially expressed between Ammonia25 (treatment group) and Ammonia3 (control group), including 96 down-regulated and 67 up-regulated genes. qRT-PCR analysis validated the transcriptomic results of RNA sequencing. Gene Ontology (GO) functional annotation analysis revealed potential genes, processes and pathways with putative involvement in growth and development inhibition of breast muscle in broilers caused by aerial ammonia exposure. This study facilitates understanding of the genetic architecture of the chicken breast muscle transcriptome, and has identified candidate genes for breast muscle response to atmospheric ammonia exposure.

overall_design: Breast muscle mRNA profiles of 42-day old Arbor Acres male broilers exposed to 3 ppm (Ammonia3) and 25 ppm (Ammonia25) concentrations of atmospheric ammonia were generated by RNA sequencing, in duplicate, using Illumina HiSeq2000.

first: Liang


title: DNA methylation patterns of lupus patient PBMCs, subdivided based on protein expression of ARID3a

city: Oklahoma City

first: Carol

middle: F.

last: Webb

state: OK

address: 800 Research Parkway, Suite 419

department: Medicine

institute: University of Oklahoma Health Sciences Center

summary: Methyl-seq data was obtained from total peripheral blood mononuclear cells of two patients with systemic lupus erythematosus who were characterized as having>2 standard deviations more ARID3a-expressing B lymphocytes than healthy controls. Similarly, methyl-seq data was also obtained from two SLE patient samples with normal (low) numbers of ARID3-expressing B lymphocytes. Our previous studies showed that increased ARID3a expression in B lymphocytes was associated increased disease activity. Data were generated on an Illumina Hiseq 2000 with paired-end 100bp reads and quality control metrics were assessed with Picard tools.

overall_design: Methylation profiles of genomic DNA from four SLE patient PBMC samples, two with high numbers of ARID3a expressing B cells (ARID3aH) versus two with normal numbers of ARID3a+ B cells (ARID3aN), were generated on an Illumina Hiseq 2000 with paired-end 100bp reads.

middle: F

first: Julie

middle: M

last: Ward


title: Female mice lacking Xist RNA show partial dosage compensation and survive to term

city: Boston

first: Jeannie

last: Lee

address: 185 Cambridge Street

department: Molecular Biology

institute: HHMI, Massachusetts General Hospital, Harvard Medical School

summary: X chromosome inactivation (XCI) compensates for differences in X-chromosome number between male and female mammals. XCI is orchestrated by Xist RNA, whose expression in early development leads to transcriptional silencing of one X-chromosome in the female. Knockout studies have established a requirement for Xist, with inviability of female embryos that inherit an Xist deletion from the father. Here, we report that female mice lacking Xist RNA can, surprisingly, develop and survive to term. Xist-null females are born at lower frequency and are smaller at birth, but organogenesis is mostly normal. Transcriptomic analysis indicates significant overexpression of hundreds of X-linked genes across multiple tissues. Therefore, Xist-null mice can develop to term in spite of a deficiency of dosage compensation. However, the degree of X-autosomal dosage imbalance was less than anticipated (1.14- to 1.36-fold). Thus, partial dosage compensation can be achieved without Xist, supporting the idea of inherent genome balance. Nevertheless, to date, none of the mutant mice has survived beyond weaning stage. Sudden death is associated with failure of postnatal organ maturation. Our data suggest Xist-independent mechanisms of dosage compensation and demonstrate that small deviations from X-autosomal balance can have profound effects on overall fitness.

overall_design: RNA-sequencing of tail-tip fibroblasts (TTFs), spleen, liver and heart tissue from Xist-null and control female mice. Sequencing performed with 50nt read length on Illumina HiSeq2000 or 2500. Data consists of 3 biological replicates for TTFs (6 datasets) and 2 biological replicates for tissues (12 datasets).

first: L

last: Yang

first: J

last: Kirby

first: H

last: Sunwoo

middle: T


title: The exon junction complex regulates the splicing of cell polarity gene dlg1 to control Wingless signaling in development

first: Ruifeng

last: Li

address: Haidian

institute: Peking University

summary: Wingless (Wg)/Wnt signaling is conserved in all metazoan animals and plays critical roles in development. The Wg/Wnt morphogen reception is essential for signal activation, whose activity is mediated through the receptor complex and a scaffold protein Dishevelled (Dsh). We report here that the exon junction complex (EJC) activity is indispensable for Wg signaling by maintaining an appropriate level of Dsh protein for Wg ligand reception in Drosophila. Transcriptome analyses in Drosophila wing imaginal discs indicate that the EJC controls the splicing of the cell polarity gene disc large 1 (dlg1), whose coding protein directly interacts with Dsh. Genetic and biochemical experiments demonstrate that Dlg1 protein acts independently from its role in cell polarity to protect Dsh protein from lysosomal degradation. More importantly, human orthologous Dlg protein is sufficient to promote Dvl protein stabilization and Wnt signaling activity, thus revealing a conserved regulatory mechanism of Wg/Wnt signaling by Dlg and EJC.

overall_design: whole transcriptome RNA-seq to examine mRNAs extracted from wildtype (i.e. overexpressing lacZ) and pre-EJC-defective (i.e. overexpressing tsu RNAi) wing discs, respectively.

first: Min

last: Liu

first: Yajuan

first: Cheng

first: Alan

middle: J

last: Zhu


title: Neonatal Heart Maturation (NHM) SuperSeries GSE85728

first: Marlin

last: Touma

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

overall_design: Refer to individual Series


title: The PAXX and XLF DNA Repair Factors are Functionally Redundant in Joining DNA breaks in a G1-arrested Progenitor B Cell Line

city: Stanford

first: Richard

last: Frock

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

summary: Classical non-homologous end-joining (C-NHEJ) is a major mammalian DNA double strand break (DSB) repair pathway.  Core C-NHEJ factors, such as XRCC4, are required for joining DSB intermediates of the G1 phase-specific V(D)J recombination reaction in progenitor lymphocytes.  Core factors also contribute to joining DSBs in cycling mature B-lineage cells, including DSBs generated during antibody class switch recombination (CSR) and DSBs generated by ionizing radiation (IR).  The XLF C-NHEJ factor is dispensable for V(D)J recombination in normal cells, but, due to functional redundancy, is absolutely required for this process in cells deficient for the ATM DSB response factor. The recently identified PAralogue of XRCC4 and XLF (PAXX) factor has homology to these two proteins and variably contributes to IR-induced DSB repair in human and chicken cells.  We now report that PAXX is dispensable for joining V(D)J recombination DSBs in G1-arrested mouse pro-B cell lines, dispensable for joining CSR-associated DSBs in a cycling mouse B cell line, and dispensable for normal IR-resistance in both G1-arrested and cycling pro-B lines.  However, we find that combined deficiency for PAXX and XLF in G1-arrested pro-B lines abrogates DSB joining during V(D)J recombination and sensitizes the cells to IR exposure.  Thus, PAXX provides core C-NHEJ factor-associated functions in the absence of XLF and vice versa in G1-arrested Pro-B cell lines.  Finally, we also find that PAXX-deficiency has no impact on V(D)J recombination DSB joining in ATM-deficient pro-B lines.  We discuss implications of these findings with respect to potential PAXX and XLF functions in C-NHEJ.

overall_design: Examination of CSR Switch mu-to-alpha junctions from mu bait DSBs using LAM-HTGTS and Illumina Miseq.  Two clones of PAXX-/- and XLF-/- and 1 clone of Ligase4-/- were derived from the parental CH12F3 line; the second Ligase4-/- clone was acquired from Kefei Yu.  Two clones of XLF-/-PAXX-/-CH12 cells were derived from one of the PAXX-/- clones.  Three biological replicates were analyzed for each clone.

first: Vipul

last: Kumar

first: Frederick

middle: W

last: Alt


title: Regulation of stem cell maintenance and lymphoid specification by the ubiquitin ligase Huwe1

status: Public on Aug 18 2016

city: Cambridge

first: Charalampos

last: Lazaris

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

summary: The ubiquitin ligase Huwe1 regulates stem cell quiescence, maintenance and lymphoid specification by controlling the expression of N-Myc.

overall_design: Thirty million human bone marrow CD34+ cells were fixed and used for ChIP and precipitated using 3 micrograms of antibody.

first: Bryan

last: King

first: Francesco

middle: E

last: Boccalatte

first: Elmar

last: Wolf

first: Iannis

last: Aifantis


title: Characterisation of the whole blood mRNA transcriptome in Holstein-Friesian and Jersey calves in response to gradual weaning

city: Dunsany

first: Dayle

last: Johnston

state: Ireland

address: AGRIC

department: Animal and Bioscience Research Department

country: Ireland

institute: Teagasc

summary: The objectives of the study were to use RNA-Seq to examine the effect of (i) breed and (ii) gradual weaning, on the whole blood mRNA transcriptome of artificially reared Holstein-Friesian and Jersey calves. The calves were gradually weaned over 14 days (day (d) -13 to d 0) and mRNA transcription was examined one day before gradual weaning was initiated (d -14), one day after weaning (d 1) and 8 days after weaning (d 8). RNA-seq analysis was carried out on RNA extracted from whole blood. Gradual weaning had no effect on gene expression (P>0.05).There were 550 differentially expressed genes at a false discovery rate of 10% and with a ≥1.5-fold change, between Holstein-Friesian and Jersey  calves on d -14, 490 on d 1, and 411 on d 8. GOseq/KEGG pathway analysis showed that the cytokine-cytokine receptor interaction pathway and the neuroactive ligand-receptor interaction pathway were over-represented between breeds on all days (P<0.01; Q≤0.1). These results demonstrate that the gradual weaning practiced here does not compromise the welfare of artificially-reared dairy calves, evidenced by the lack of expression changes in any genes in response to gradual weaning. These data also suggest differences in cell signalling and immune responses between breeds.

overall_design: Eight Holstein-Friesian and eight Jersey bull calves were group housed indoors and individually fed milk replacer and concentrate using an automatic feeder. Calves were gradually weaned by reducing milk-replacer from 6 litres to 0 litres over 14 days (d) (d -13 to d 0). Calves were blood sampled on d -14, 1, and 8, relative to weaning (d 0). RNA-seq analysis was carried out on RNA extracted from whole blood.

first: Paul

last: Cormican

first: Matthew

last: McCabe

first: David

middle: A

last: Kenny

middle: K

last: Kelly

first: Sinead

last: Waters

first: Mark

last: McGee

first: Bernadette

last: Earley


title: An integrative transcriptomics approach identifies miR-503 as a candidate master regulator of the estrogen response [miRNA-seq]

city: Chapel Hill

first: Jeanette

last: Baran-Gale

state: NC

address: 120 Mason Farm Rd.

institute: University of North Carolina at Chapel Hill

summary: Estrogen receptor α (ERα) is an important biomarker of breast cancer severity and a common therapeutic target. Recent studies have demonstrated that in addition to its role in promoting proliferation, ERα also protects tumors against metastatic transformation. Current therapeutics antagonize ERα and interfere with both beneficial and detrimental signaling pathways stimulated by ERα. The goal of this study is to uncover the dynamics of coding and non-coding RNA (microRNA) expression in response to estrogen stimulation and identify potential therapeutic targets that more specifically inhibit ERα-stimulated growth and survival pathways without interfering with its protective features. To achieve this, we exposed MCF7 cells (an estrogen receptor positive model cell line for breast cancer) to estrogen and prepared a time course of paired mRNA and miRNA sequencing libraries at ten time points throughout the first 24 hours of the response to estrogen. From these data, we identified three primary expression trends—transient, induced, and repressed—that were each enriched for genes with distinct cellular functions. Integrative analysis of paired mRNA and microRNA temporal expression profiles identified miR-503 as the strongest candidate master regulator of the estrogen response, in part through suppression of ZNF217—an oncogene that is frequently amplified in cancer. We confirmed experimentally that miR-503 directly targets ZNF217 and that over-expression of miR-503 suppresses breast cancer cell proliferation. Overall, these data indicate that miR-503 acts as a potent estrogen-induced tumor suppressor microRNA that opposes cellular proliferation and has promise as a therapeutic for breast cancer. More generally, our work provides a systems-level framework for identifying functional interactions that shape the temporal dynamics of gene expression.

overall_design:
Quantification of miRNAs in MCF7 cells responding to estrogen following a period of estrogen starvation.
Three independent biological replicates (30 samples: 3 replicates x 10 time points) of MCF7 cells were exposed to 10nM Estradiol for 0, 1, 2, 3, 4, 5, 6, 8, 12 , or 24 hours, and total RNA was extracted from the samples. Total RNA was used to generate paired RNA and miRNA sequencing. The miRNA libraries were prepared using the Bioo Scientific NextFLEX v2 library preparation kit.

first: Praveen

last: Sethupathy

first: Jeremy

last: Purvis


title: An integrative transcriptomics approach identifies miR-503 as a candidate master regulator of the estrogen response [RNA-seq]

overall_design:
Quantification of mRNAs in MCF7 cells responding to estrogen following a period of estrogen starvation.
Three independent biological replicates (30 samples: 3 replicates x 10 time points) of MCF7 cells were exposed to 10nM Estradiol for 0, 1, 2, 3, 4, 5, 6, 8, 12 , or 24 hours, and total RNA was extracted from the samples. Total RNA was used to generate paired RNA and miRNA sequencing. RNA libraries were prepared using an Illumina TruSeq stranded mRNA library preparation kit.


title: An integrative transcriptomics approach identifies miR-503 as a candidate master regulator of the estrogen response


title: RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells.

city: Durham

first: Rasim

last: Barutcu

address: 6 Davis Drive

institute: ScitoVation

summary: RUNX1 is a transcription factor functioning both as an oncogene and a tumor suppressor in breast cancer. RUNX1 alters chromatin structure in cooperation with chromatin modifier and remodeling enzymes. In this study, we examined the relationship between RUNX1-mediated transcription and genome organization. We characterized genome-wide RUNX1 localization and performed RNA-seq and Hi-C in RUNX1-depleted and control MCF-7 breast cancer cells. RNA-seq analysis showed that RUNX1 depletion led to up-regulation of genes associated with chromatin structure and down-regulation of genes related to extracellular matrix biology, as well as NEAT1 and MALAT1 lncRNAs. Our ChIP-Seq analysis supports a prominent role for RUNX1 in transcriptional activation. About 30% of all RUNX1 binding sites were intergenic, indicating diverse roles in promoter and enhancer regulation and suggesting additional functions for RUNX1. Hi-C analysis of RUNX1-depleted cells demonstrated that overall three-dimensional genome organization is largely intact, but indicated enhanced association of RUNX1 near Topologically Associating Domain (TAD) boundaries and alterations in long-range interactions. These results suggest an architectural role for RUNX1 in fine-tuning local interactions rather than in global organization. Our results provide novel insight into RUNX1-mediated perturbations of higher-order genome organization that are functionally linked with RUNX1-dependent compromised gene expression in breast cancer cells.

overall_design: Hi-C and RNA-seq experiments were conducted in MCF-7  shNS and shRUNX1 cells.  RUNX1 ChIP-seq was conducted in wildtype MCF-7 cells.

first: A

first: Deli

last: Hong

last: Lajoie

first: Rachel

middle: P

last: McCord

first: Andre

last: van Wijnen

first: Jane

middle: B

last: Lian

first: Janet

last: Stein

first: Job

last: Dekker

first: Anthony

middle: N

last: Imbalzano

first: Gary


title: The spectrum and regulatory landscapes of intestinal innate lymphoid cells are shaped by the microbiome (RNA-Seq)

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Innate lymphoid cells (ILCs) are critical modulators of mucosal immunity, inflammation, and tissue homeostasis, but their full spectrum of cellular states and regulatory landscapes remain elusive. Here, we use a combination of genome-wide RNA-seq, ChIP-seq and ATAC-seq to compare the transcriptional and epigenetic identity of small intestinal ILCs, identifying thousands of distinct gene profiles and regulatory elements. Single-cell RNA-seq, cytometry, and imaging analyses reveal functional compartmentalization of cytokine expression and metabolic activity within the three classical ILC subtypes, and highlight transcriptional states beyond the current canonical classification. In addition, using antibiotic intervention and germ-free mice, we characterize the effect of the microbiome on the ILC regulatory landscape, and determine the response of ILCs to microbial colonization at the single-cell level. Together, our work characterizes the spectrum of transcriptional identities of small intestinal ILCs and describes how ILCs differentially integrate signals from the microbial microenvironment to generate phenotypic and functional plasticity.

overall_design: ILC1(CD45+CD3-CD19-GR1-B220-CD127+RORγt-NkP46+), ILC2(CD45+CD3-CD19-GR1-B220-CD127+RORγt-KLRG1+) and ILC3(CD45+CD3-CD19-GR1-B220-CD127+RORγt+) were isolated from small intestine lamina propria of WT C57Bl/6 RORγt-GFP mice, or antibiotics treated mice (vancomycin, ampicillin,kanamycin, and metronidazole)


title: The spectrum and regulatory landscapes of intestinal innate lymphoid cells are shaped by the microbiome (ChIP-Seq)


title: The spectrum and regulatory landscapes of intestinal innate lymphoid cells are shaped by the microbiome (ATAC-Seq)


title: 53BP1 integrates DNA repair and p53-dependent cell fate decisions via distinct mechanisms

city: Oxford

first: Jonathan

middle: Ross

last: Chapman

address: Roosevelt Drive

department: Nuffield Department of Medicine (University of Oxford)

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics

summary: The tumor suppressor protein 53BP1, a pivotal regulator of DNA double-strand break (DSB) repair,  was  first  identified  as  a  p53-interacting  protein  over  two  decades  ago,  however  its direct  contributions  to  p53-dependent  cellular  activities  remain  undefined.  Here,  we  reveal 53BP1 stimulates  genome-wide  p53-dependent  gene  transactivation  and repression  events  in response  to  ionizing  radiation  (IR)  and  synthetic  p53  activation. 53BP1-dependent  p53 modulation requires  both auto-oligomerization and tandem-BRCT domain  mediated bivalent interactions  with  p53  and  the  ubiquitin-specific  protease  USP28.  Loss  of  these  activities results in inefficient p53-dependent cell-cycle checkpoint and exit responses. Furthermore, we demonstrate  53BP1-USP28  cooperation  to  be  essential  for  normal  p53-promoter  element interactions and gene transactivation-associated events, yet dispensable for 53BP1-dependent DSB repair regulation. Collectively, our data provides  a mechanistic  explanation for 53BP1-p53 cooperation in controlling anti-tumorigenic cell fate decisions, and reveal these activities to  be  distinct  and  separable  from  53BP1’s  regulation  of  DNA  double-strand  break  repair pathway choice.

overall_design: We evaluated the transcriptional profiles of two 53BP1Δ cell lines and included a positive (WT) and a negative (p53Δ) controls. These cell lines were treated with Nutlin-3, ionising radiation or mock treated. Three independent replicates were included for each independent condition generating a total of 36 samples.

first: Raquel

last: Cuella-Martin

first: Catarina

last: Oliveira

first: Helen

last: Lockstone

first: Suzanne

last: Snellenberg

first: Natalia

last: Gromulsova


title: The spectrum and regulatory landscapes of intestinal innate lymphoid cells are shaped by the microbiome


title: Id3 Orchestrates Germinal Center B Cell Development

first: Vivek

last: Chandra

address: 9500 Gilman Drive MC0377

department: Department of Molecular Biology

institute: University of California, San Diego

summary: Previous studies have demonstrated that E-proteins induce AID expression in activated B cells. Here we have examined the role of Id3 in germinal center (GC) cells. We found that Id3 expression is high in follicular B-lineage cells but declines in GC cells. Immunized mice depleted for Id3 expression displayed a block in germinal center B cell maturation, showed reduced numbers of marginal zone B cells and class switched cells, were associated with decreased antibody titers and lower numbers of plasma cells. In vitro Id3-depleted B cells displayed a defect in class switch recombination. Whereas AID levels were not altered in Id3-depleted activated B cells, the expression of a subset of genes encoding for signaling components of antigen receptor, cytokine receptor and chemokine receptor mediated signaling was significantly impaired. We propose that during the GC reaction Id3 levels decline to activate the expression of genes encoding for signaling components that mediate B cell receptor and or cytokine-mediated signaling to promote the differentiation of GC B cells.

overall_design: B cells derived from control and CD19-Cre;Id3loxP/loxP mice were activated in vitro in the presence of LPS and IL-4 for 24 or 48 hours. RNA was isolated from naïve as well as activated control and CD19-Cre;Id3loxP/loxP mice and analyzed by RNA-seq, in duiplicate.

first: Shuwen

last: Chen

first: Masaki

last: Miyazaki

first: Kathleen

last: Fisch

first: Aaron

last: Chang

first: Cornelis

last: Murre


title: Egf signaling directs neoblast repopulation by regulating asymmetric cell division in planarians

city: Kansas City

first: Chris

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: The goal of this experiment is to identify target genes of Egf signaling which regulate recovery of the neoblast population following exposure to a sublethal dose of radiation. A large population of highly proliferative stem cells (neoblasts) is required for physiological tissue homeostasis and regeneration after injury in planarians. Recent studies indicate that survival of a few neoblasts after sublethal irradiation results in the clonal expansion of the surviving stem cells and the eventual restoration of tissue homeostasis and regenerative capacity. Many genes are known to be required for the normal function of neoblasts, but the precise mechanisms regulating the population dynamics of these adult pluripotent stem cells remain largely unknown. By coupling RNAi screening and sublethal irradiation, we uncovered a central role for Epidermal Growth Factor (EGF) signaling during in vivo neoblast expansion mediated by Smed-egfr-3 (egfr-3) and its putative ligand Smed-neuregulin-7 (nrg-7). Furthermore, the EGFR-3 protein localizes asymmetrically on the cytoplasmic membrane of neoblasts and the ratio of asymmetric to symmetric cell divisions decreases significantly in egfr-3(RNAi) worms. Our results not only provide the first molecular evidence of asymmetric stem cell divisions in planarian, but also demonstrate that EGF signaling likely functions as an essential regulator of neoblast clonal expansion.

overall_design: Worms were fed on a schedule every three days with RNAi against Egfr3, nrg6, nrg7, or unc22 control. One population (SR) was exposed to a sublethal dose of gamma radiation, another population continued to grow with no treatment (NT). A third population was dissected and X1 cells were isolated (X1). The experiments were performed in quadruplicate for a total of 144 samples.

first: Kai

last: Lei

first: Hanh

last: Vu

first: Ryan

middle: D

last: Mohan

first: Sean

last: McKinney

first: Richard

last: Alexander

first: Kirsten

last: Gotting

first: Jerry

middle: L

last: Workman

first: Alejandro

last: Alvarado


title: Next generation sequencing of antibody heavy chain genes that bind to the hapten NP in sorted memory cells and long-lived plasma cells isolated from mice immunized orally with NP-CT

city: Gothenburg

first: Mats

last: Bemark

address: PO Box 435

department: Departement of microbiology and immunity

country: Sweden

institute: University of Gothenburg

summary: We report that there are differences in V gene usage in memory B cells and long-lived plasma cells after oral immunization. The hapten NP was conjugated to cholera toxin (CT) to create NP-CT, an antigen that is highly immunogenic after oral immunization. The NP hapten induces immune responses dominated by the 1-72 (VH186.2) heavy chain V region. The relationship between NP binding IgA antibody genes from memory B cells from spleen, MLN and Peyer´s patches and long-lived plasma cells from lamina propria and bone marrow that persisted 6-12 months after an oral immunization in three C57BL/6 mice with NP-CT was investigated. Extensive clonal overlap im clones was observed between long-lived memory cells from lamina propria and bone marrow, but very limited overlap was found between memory cells and plasma cells. The data suggest that memory and plasma cells formed through temporarily or anatomically separate processes.

overall_design: RNA was prepared from memory cells and long-lived plasma cells from C57BL/6 mice that had been orally immunized with NP-CT 6-12 months before analysis

first: Nils

middle: Y

last: Lycke


title: Transcriptome analysis of chronic periodontitis patients' gingival tissue

city: Seoul

first: Jae-Hyung

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

institute: Kyung Hee University

summary: We examined the molecular and cellular mechanism for chronic periodontitis in patients' gingival tissue by whole transcriptome sequencing.

overall_design: Compare gene expression profiles between between periodontitis and healthy gingival samples using RNA-Seq (Illumina platform: Hi-Seq 2000)

first: Yong-Gun

last: Kim

first: Minjung

first: Ji-Hyun

last: Kang

first: Hyo-Jeong

first: Jae-Young

first: Youngkyun


title: The pentose phosphate pathway regulates the circadian clock

city: Geneva

first: Guillaume

last: Rey

address: Campus Biotech, Chemin des Mines 9

country: Switzerland

institute: University of Geneva

summary: The circadian clock is a ubiquitous timekeeping system that organizes the behavior and physiology of organisms over the day and night. The clockwork orchestrates a multitude of metabolic processes as illustrated by previous global transcriptomics and proteomics studies, and the existence of daily rhythms of reduction and oxidation (redox) in a range of diverse species. However, the reciprocal question of whether metabolism can alter the clockwork remains largely unaddressed. Here we identify the pentose phosphate pathway (PPP), a critical source of cellular reducing power in the form of NADPH, as an important modulator of circadian oscillations. We show that genetic and pharmacologic inhibition of the PPP perturbs circadian gene expression and metabolic rhythms in human cells. Pharmacologic inhibition of the PPP caused similar effects in mouse tissues, and altered the pattern of rhythmic behavior in Drosophila. These manipulations also altered genome wide DNA-binding activity of the circadian transcription factors BMAL1 and CLOCK through a mechanism likely involving the redox-sensitive histone acetyltransferase p300. Thus, disruption of the PPP regulates circadian rhythms via modulation of NADPH metabolism, highlighting redox reactions as a novel connector of metabolic cycles and transcriptional oscillations in nucleated cells.

overall_design: RNA-Seq time-course experiment in U2OS cells treated with 6AN or control over 48 hours at 4h resolution. ChIP-Seq of BMAL1, CLOCK, H3K4me3 and H3K9ac in U2OS cells treated with 6AN or control for 24h.

first: Utham

last: Valekunja

first: Kevin

last: Feeney

first: Lisa

last: Wulund

first: Nikolay

last: Milev

first: Alessandra

last: Stangherlin

first: Laura

last: Bollepalli

first: Vidya

last: Velagapudi

first: John

middle: S

last: O’Neill

first: Akhilesh

last: Reddy


title: Maize proteome and transcriptome atlas

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: An atlas of RNA and protein expression maps across a diverse set of developmental tissues from Zea mays

overall_design: RNA-seq collected from a variety of maize tissues

first: Robert

last: Schmitz

first: Justin

last: Walley

first: Steven

last: Briggs


title: RNA-seq analysis of the developing chicken retina

city: Charlottesville

first: Stephen

last: Turner

address: 1670 Discovery Drive

institute: Signature Science, LLC

summary: The chicken embryo (Gallus gallus) is a classic model system for studying developmental biology. During chick development, embryonic day 8 (E8) retina are packed with multipotent neuronal precursors on the cusp of differentiation into all retinal cell types. By E18 the retina is nearly fully mature with all major retinal cell types differentiated and expressing cell type-specific genes. Whole retina were harvested from embryonic day 8 (E8), E16, and E18 developing chicken embryos. Whole cornea were also collected from E18 embryos as a reference tissue. Duplicates were obtained for each time point and total RNA was extracted from samples using a Qiagen AllPrep Mini Kit. To characterize differential gene expression in these tissues, Illumina stranded TrueSeq RNA-Seq libraries were prepared from total RNA and 125 PE sequencing reads were obtained. These data will be used to characterize retina-specific patters of gene expression as well as global changes in gene expression between critical developmental time points in the chicken retina.

overall_design: 4 samples in duplicate; 3 developmental time points of the retina E8, E16, E18) and 1 reference tissue (cornea)

first: Raymond

last: Enke

first: Emily

last: Grunwald

first: Sophia

last: Brown

first: Cold Spring Harbor Laboratory

last: DNA Learning Center


title: Genome wide extracellular signal-regulated kinase (ERK) pathway components interaction with human genome

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: Several recent studies, including ours, show that most components of signal  transduction cascades including the extracellular signal-regulated protein kinase (ERK), that once were thought to act predominantly in cytoplasm, are in fact recruited to chromatin and are integral components of transcriptional complexes. However, their distribution along whole genome remains uncovered. Here we investigate genome wide recruitment of the ERK pathway components using chromatin immunoprecipitations (ChIP) followed by deep sequencing, ChIP-Seq.

overall_design: Hela-S3 cells were starved for 48 hours (control) and stimulated with EGF at concentration of 100ng/mL for 20 minutes. Cells were fixed with formaldehyde, chromatin isolated and subjected to ChIP reaction. Two technical replicates of ChIP reaction followed by sequencing were performed.

first: Michal

last: Mikula

first: Joanna

last: Ledwon

first: Magdalena

last: Skrzypczak

first: Marta

last: Grzelak

first: Michalina

last: Dabrowska

first: Maria

last: Kulecka

last: Ginalski

first: Karol

last: Bomsztyk

first: Jerzy

last: Ostrowski


title: Single cell RNAseq of electrophysiologically characterized neurons of the hippocampus

first: Spyros

last: Darmanis

address: Clark Center, E300

department: Bioengineering

summary: Recent advances in single-cell RNAseq technologies are enabling new cell type classifications. For neurons, electrophysiological properties traditionally guide cell type classification but correlating RNAseq data with electrophysiological parameters has been difficult. Here we demonstrate RNAseq of electrophysiologically and synaptically characterized individual, patched neurons in the hippocampal CA1-region and subiculum, and relate the resulting transcriptome data to their electrical and synaptic properties. In this analysis, we explored the hypothesis that precise combinatorial interactions between matching cell-adhesion and signaling molecules shape synapse specificity. In analyzing interneurons and pyramidal neurons that are synaptically connected, we identified two independent, developmentally regulated networks of interacting genes encoding cell-adhesion, exocytosis and signal-transduction molecules. In this manner, our data allow postulating a presumed cell-adhesion and signaling code, which may explain neuronal connectivity at the molecular level. Our approach enables correlating electrophysiological with molecular properties of neurons, and suggests new avenues towards understanding synaptic specificity.

overall_design: These data include 15 tissue samples (including 3 independent replicas in 5 developmental stages) as well as 93 single-cell samples (including CA1 cholecystokinin, parvalbumin, and pyramidal neurons as well as subiculum burst and regular firing pyramidal neurons).

first: Csaba

last: Földy

first: Jason

last: Aoto

first: Robert

last: Malenka

last: Quake

first: Thomas

middle: C

last: Südhof


title: Effect of endophilin A deficiency in mouse hippocampus

status: Public on Aug 17 2016

city: Gottingen

first: Ramon

last: Oliveira Vidal

address: Grisebachstraße 5

department: Bioinformatics

country: Germany

institute: DZNE

summary: We tested how complete or partial loss of endophilin A1, A2 and A3 affects gene expression in mouse hippocampus. Total loss of endophilin (triple knock-outs, TKO) was assessed in newborn mice, since the TKO mice only survive only several hours after birth. Partial loss of endophilin (endoA1,A2 double knock-out, DKO) was assessed between

overall_design: 2-3 weeks of age (p13-21).

first: John

last: Murdoch

first: Christine

middle: M

last: Rostosky

first: Sindhuja

last: Gowrisankaran

last: Vidal

first: Vincenzo

last: Capece

first: Stefan

last: Bonn

first: Nuno

last: Raimundo

first: Ira

last: Milosevic


title: The ubiquitin ligase HUWE1 regulates hematopoietic stem cell maintenance and lymphoid commitment [high-throughput sequencing]

city: New York

first: Bryan

last: King

state: NY

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: We identified the ubiquitin ligase Huwe1 as a crucial regulator of hematopoietic stem cell (HSC) functions. We generated Huwe1 conditional knock-out mice and discovered that the loss of this ligase causes an increased proliferation and stem cell exhaustion, together with a decreased lymphoid specification in vivo. We observed that the ubiquitin ligase Huwe1 is controlling the expression of N-myc at the level of the most immature stem and progenitor hematopoietic populations, mediating the described effects.

overall_design: High-troughput RNA-sequencing of sorted HSC (Lin-Sca+Kit+CD48-CD150+) from wild type or Huwe1 conditional knockout mice (constitutively deleted with Vav-Cre recombinase or inducibly deleted with Mx1-Cre)

first: Francesco

last: Boccalatte

first: Charalampos

last: Lazaris

first: Ioannis

last: Aifantis


title: Genome-wide alterations in DNA methylation identify Leprel2, Foxf1, Mmp25, Igfbp6 and Peg12 as disease-associated genes in murine Achilles tendinopathy

city: Chicago

first: Katie

last: Trella

state: IL

address: 1611 W. Harrison St, Suite 401A

department: Orthopedics

institute: Rush University Medical Center

summary: We partnered with Zymo Research, Inc. to detect genome-wide methylation changes associated with the initiation and progression of tendinopathy induced by TGF-β1 in a murine Achilles tendon model. All genes identified as significantly differentially methylated were present in only one experimental group showing that both the gene identified and its modified methylation status are dependent on the injury time-course and activity level. In summary, we identified five genes (Leprel2, Foxf1, Mmp25, Igfbp6 and Peg12) which demonstrate significant relevance to tendon biology with three exhibiting functions in collagen fibril organization. We postulate that a study of the molecular genomics of these genes in animal and human tendon could further delineate the pathogenesis of this multifactorial disease.

overall_design: Chronic Achilles tendinopathy was induced in WT C57/Bl6 male mice via two injections of TGF-β1 directly into the body of the tendon. Methylome analysis was conducted on the tendon DNA for the acute (3 day) response as well as the chronic response (14 and 28 days) under normal cage activity or with treadmill running and compared to un-injured mice.

first: Jun

last: Li

first: Eleni

last: Stylianou

first: Vincent

last: Wang

first: Jon

last: Frank

first: Jorge

last: Galante

last: Sandy

first: Anna

last: Plaas

last: Wysocki


title: Effect of high fat diet on the rat germ cell transcriptome

first: Michael

last: Morgan

state: Oxfordshire

address: South Parks Road

department: Department of Physiology, Anatomy and Genetics

institute: University of Oxford

summary:
PURPOSE: To examine if a parental high fat diet (HFD) influences metabolic health in two generations of offspring, and alters the germ cell (GC) transcriptome.
PROCEDURE: GC-eGFP Sprague Dawley rats were weaned onto HFD (45% fat) or Control Diet (CD; 10% fat). After metabolic testing, founders (F0) were bred with controls, establishing the F1 generation. Germ cells from F0 males were isolated and their RNA sequenced. F1 rats were bred with control rats at 17 weeks to generate F2 offspring.
FINDINGS: HFD resulted in 9.7% and 14.7% increased weight in male and female F0 respectively. F1 offspring of HFD mothers were heavier than controls. F1 daughters of HFD-fed males were also heavier. F2 male offspring derived from HFD-fed maternal grandfathers were 7.2% heavier, and exhibited increases of 31% in adiposity, 97% in plasma leptin and 300% in luteinising hormone to testosterone ratio. HFD exposure did not alter the F0 GC transcriptome.
CONTROLS: Matched CD was consumed by all animals not consuming the HFD. Animals were compared to a parallel cohort of CD rats.
CONCLUSIONS: HFD consumption by maternal grandfathers results in a disrupted metabolic phenotype in grandsons. This effect is not mediated by alterations to the GC transcriptome.

overall_design: Male rats high fat diet vs. control diet. 4 replicates per condition. SmallRNA seq and mRNAseq for each replicate and condition

first: Thomas

last: Chambers

first: Andreas

middle: H

last: Heger

first: Richard

last: Sharpe

first: Amanda

last: Drake


title: Physiologic expression of Sf3b1K700E causes impaired erythropoieses, aberrant splicing, and sensitivity to pharmacologic spliceosome modulation

first: Silvia

last: Buonamici

state: MA

address: 300 Technology Square #5

institute: H3 Biomedicine

summary: Over 80% of patients with the refractory anemia with ring sideroblasts subtype of myelodysplastic syndrome (MDS) have mutations in Splicing Factor 3B, Subunit 1 (SF3B1). We generated a conditional knock-in mouse model of the most common SF3B1 mutation, Sf3b1K700E. Sf3b1K700E mice develop macrocytic anemia due to a terminal erythroid maturation defect, erythroid dysplasia, and long-term hematopoietic stem cell (LT-HSC) expansion. Sf3b1K700E myeloid progenitors and SF3B1-mutant MDS patient samples demonstrate aberrant 3' splice-site selection associated with increased nonsense-mediated decay. Tet2 loss cooperates with Sf3b1K700E to cause a more severe erythroid and LT-HSC phenotype. Furthermore, the spliceosome modulator, E7017, selectively kills Sf3b1K700E-expressing cells. Thus, Sf3b1K700E expression reflects the phenotype of the mutation in MDS and may be a therapeutic target in MDS.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 15 samples, including 6 mouse and 9 human samples with varying SF3B1 status

last: Seiler

first: Esther

last: Obeng


title: Global assessment of imprinted gene expression in the bovine conceptus by next generation sequencing

city: Columbia

first: Rocío

middle: Melissa

last: Rivera

address: 920 East Campus Drive, ASRC 164

department: Animal Sciences

institute: University of Missouri, Columbia

summary: Genomic imprinting is an epigenetic mechanism that leads to parental-allele-specific gene expression.  Approximately 150 imprinted genes have been identified in humans and mice but less than 30 genes have been described as imprinted in cattle.  For the purpose of de novo identification of imprinted genes in bovine, we determined global monoallelic gene expression in brain, skeletal muscle, liver, kidney and placenta of day ~105 Bos taurus indicus X Bos taurus taurus F1 conceptuses using RNA sequencing.  For this, we developed a bioinformatics pipeline to identify parental-specific SNPs after filtering A-to-I RNA editing sites.  We identified 53 genes subject to monoallelic expression.  A total of 23 are genes known to be imprinted in the cow and 7 are previously-characterized imprinted genes in human and/or mouse that have not be reported to be imprinted in cattle.  Of the remaining 23 genes, we found that 10 are uncharacterized or unannotated transcripts located in known imprinting clusters, whereas the other 13 genes are distributed across the bovine genome and not close to any known imprinting clusters.  To exclude potential cis-eQTL effects on allelic expression, we corroborated the parental specificity of monoallelic expression in day 86 Bos taurus taurus X Bos taurus taurus F1s and identified eight novel imprinted genes in bovine.  Further, we identified 671 candidate A-to-I RNA editing sites and describe imprinted X inactivation in the bovine trophectoderm-derived CT1 cell line.  Our results expand the imprinted gene list in bovine and demonstrate that monoallelic gene expression can be the result of cis-eQTL effect.

sample_organism:
Bos indicus
Bos indicus x Bos taurus

platform_organism:
Bos indicus
Bos indicus x Bos taurus

overall_design: Identification of imprinted genes in brain, kidney, liver, skeletal muscle, and placenta of four day ~105 bovine conceptuses (The RNAseq data of brain, kidney, liver, and skeletal muscle have been deposited in GEO database under accession number: GSE63509)

first: Zhiyuan

last: Chen

first: Darren

last: Hagen

first: Juanbin

first: Christine

middle: G

last: Elsik

first: Tieming

last: Ji

first: Luiz

last: Siqueira

first: Peter

middle: J

last: Hansen


title: Global Genome Repair factors are essential for shaping the DNA methylation landscape in Arabidopsis

city: Strasbourg

first: Jean

last: Molinier

address: 12 rue du General Zimmer

country: France

institute: IBMP-CNRS

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

overall_design: Refer to individual Series


title: Global Genome Repair factors are essential for shaping the DNA methylation landscape in Arabidopsis [small RNA-seq]

summary: We report the small RNA analysis of Arabidopsis plants deficient for the expression DDB2 involved in global genome repair using small RNA sequencing. In addition we performed RNA  immunoprecipitation  (RIP) of DDB2.

overall_design: siRNA sequencing in WT,  ddb2-3 and nrpd1a plants


title: RNA-sequencing of tumor-associated microglia reveals Ccl5 as a stromal chemokine critical for neurofibromatosis-1 glioma growth

city: St Louis

first: Winnie

middle: W

last: Pong

address: 660 S. Euclid Avenue

department: Department of Neurology

institute: Washington University School of Medicine

summary: Solid cancers develop within a supportive microenvironment that promotes tumor formation and continued growth through the elaboration of mitogens and chemokines. Within these tumors, monocytes (macrophages and microglia) represent rich sources of these stromal factors.  Leveraging a genetically-engineered mouse model of neurofibromatosis type 1 (NF1) low-grade brain tumor (optic glioma), previous studies have demonstrated that microglia are important for glioma formation and maintenance. To identify the tumor-associated microglial factors that support glioma growth (gliomagens), we employed a comprehensive large scale discovery effort using optimized advanced RNA-sequencing methods. Candidate gliomagens were prioritized to identify potential secreted or membrane-bound proteins, which were next validated by quantitative RT-PCR and RNA FISH following minocycline-mediated microglial inactivation in vivo. Using these selection criteria, Ccl5 was identified as a highly expressed chemokine in both genetically engineered Nf1 mouse and human optic gliomas. As a candidate gliomagen, recombinant Ccl5 increased Nf1-deficient optic nerve astrocyte growth in vitro. Importantly, consistent with its critical role in maintaining tumor growth, Ccl5 inhibition with neutralizing antibodies reduced Nf1 mouse optic glioma growth in vivo. Collectively, these findings establish Ccl5 as critical stromal growth factor in low-grade glioma maintenance relevant to future microglia-targeted therapies for brain tumors.

overall_design: Nf1 optic glioma associated microglia from mice were flow sorted. Upregulated genes of glioma associated microglia were verified and further examined.

first: Anne

last: Solga

first: Keun-Young

last: Kim

first: Patrick

last: Cimino

first: Jason

last: Walker

first: Todd

last: Wylie

first: Vincent

last: Magrini

first: Malachi

last: Griffith

first: Obi

first: Amy

last: Ly

first: Joseph

middle: A

last: Toonen

first: Mark

last: Ellisman

first: Elaine

last: Mardis

first: David

last: Gutmann


title: Time course analysis of gene expression during hypoxia in S. cerevisiae using RNA-Seq

status: Public on Aug 16 2016

city: Glassboro

last: Hickman

state: NJ

address: 201 Mullica Hill Road

department: Biological Sciences

institute: Rowan University

summary: We used RNA-seq to monitor mRNA levels of all genes in response to hypoxia of wild-type yeast, S. cerevisiae (strain yMH914 with wildtype HAP1).  To gain insights into how gene expression changes over time, cells were subjected to 100% nitrogen gas and collected after 0,5,10,30,60,120,180, and 240 minutes.  Total RNA was extracted and mRNAs were enriched by polyA selection.  The cDNA was prepared into a sequencing library, multiplexed and single-end sequenced by an Illumina HiSeq 2500 sequencer.  After mapping with Tophat2, the number of reads per feature was calculated using HTSeq.

overall_design: RNA-seq analysis of eight time points of a yeast strain grown in hypoxia. There are three biological replicates of the time course.


title: RNA-seq of naive and primed ES cells (NHSM)

city: La Jolla

last: Ecker

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 3 naive ES samples in NHSM (Gafni et al.) and 3 primed ES cell samples (in hESM)

first: Marc

last: Friedli

first: Evarist

last: Planet

first: Julien

last: Duc

first: Didier

last: Trono


title: Proteolysis - hallmark of tumor-initiating cells in polyoma-middle-T-oncogene induced murine mammary carcinomas.

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: Tumor initiating cells (TIC) have been identified and functionally characterized in hematological malignancies as well as in solid tumors such as breast cancer. In addition to their high tumor-initiating potency, TICs are important for metastasis formation and involved in chemotherapy resistance. Here we explored the molecular pathways that enable the tumor initiating potential of a cancer cell subset of the transgenic MMTV-PyMT mouse model for metastasizing breast cancer. The cell population, characterized by the marker profile CD24+CD90+CD45-, revealed a high tumorigenicity compared to CD24-CD90- cancer cells in colony formation assays as well as upon orthotopic transplantation into the mammary fad pad of mice. In addition, these orthotropically grown CD24+CD90+ TICs metastasized to the lungs. Upon cell sorting from primary tumors the transcriptome of TICs was compared with that of CD24-CD90- cancer cells by RNAseq. In addition to more established TIC signatures, such as epithelial-to-mesenchymal transition or mitogen signaling, an upregulated gene set comprising several classes of proteolytic enzymes was uncovered in CD24+CD90+TICs. Accordingly, TICs showed a high intra- and extracellular proteolytic activity. Application of a broad range of protease inhibitors to TICs in a colony formation assay reduced anchorage independent growth and had an impact on the colony morphology in 3D cell culture assays. Proteases have been frequently implicated in tumor growth and progression by shaping the extracellular environment and liberating growth factors, cytokines and chemokines. We conclude that CD24+CD90+ cells of the MMTV- PyMT mouse model possess an upregulated proteolytic signature that is likely to represent a functional hallmark of metastatic TICs of mammary carcinomas.

overall_design: The transcriptome of TICs was compared with that of CD24-CD90- cancer cells by RNAseq.

first: Larissa

middle: E

last: Hillebrand

first: Jochen

last: Hochrein

first: Melanie

last: Börries

first: Thomas

last: Reinheckel


title: FASTmC: predictive models for non-reference-based estimations of DNA methylation

city: Athens

first: Adam

middle: James

last: Bewick

state: GA

address: 120 East Green Street

department: Genetics

institute: University of Georgia

summary: We describe a suite of predictive models, coined FASTmC, for non-reference, cost-effective exploration and comparative analysis of context-specific DNA methylation levels. Accurate estimations of true DNA methylation levels can be obtained from as few as several thousand short-reads generated from whole genome bisulfite sequencing. Our models make high-resolution time course or developmental, and large diversity studies practical regardless of species, genome size and availability of a reference genome.

sample_organism:
Populus trichocarpa
Brassica oleracea
Erythranthe guttata
Sorghum bicolor
Brachypodium distachyon

overall_design: MethylC-Seq data collected from genomic DNA extracted from leaf tissue.

first: Robert

last: Schmitz


title: Effect of Estrogen Receptor Beta Ligand on Gene Expression in White Adipose Tissue

status: Public on Aug 15 2016

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

summary: C57BL/6 male mice were fed with normal diet or high fat diet and treated with vehicle or 30 mg/kg/day s.c. of ER-beta ligand, B-LGND2. Genes differentially expressed by H.F.D. and B-LGND2 are represented in this RNA-Sequencing data

overall_design: n=3/group. White adipose tissue. Mice were fed and treated as indicated above for 9 weeks. WAT was collected, RNA isolated, and expression of genes was measured by RNA-Sequencing.

first: Ramesh

last: Narayanan


title: Single-cell transcriptomes of each cell of the C. elegans embryo until the 16-cell stage

first: Sophia

last: Tintori

address: 29 Washington Pl - rm 951

institute: New York University

summary: A prevalent hypothesis for the cell-to-cell coordination of the phenomena of early development is that a defined mixture of different mRNA species at specific abundances in each cell determines fate and behavior. With this dataset we explore this hypothesis by quantifying the abundance of every mRNA species in every individual cell of the early C. elegans embryo, for which the exact life history and fate is precisely documented.

overall_design: Embryos of the 1-, 2-, 4-, 8- and 16-cell stage were dissected into complete sets of single cells, and each cell from each set was sequenced individually using SMARTer technology. 5-9 replicates were generated for each stage. Most cell identities were unknown upon sequencing, but were deduced from by their transcriptomes post hoc.

first: Erin

last: Osborne Nishimura

first: Patrick

last: Golden

first: Jason

last: Lieb

first: Bob

last: Goldstein


title: A systematic view on Influenza induced host shut-off

city: Rehovot

first: Idit

middle: Anna

last: Gelbart

address: Weizmann Institute of Science

department: Molecular Genetics

institute: Weizmann Institute of Science

summary: Influenza A viruses (IAV) induces drastic host shut-off during infection. We use RNA-seq and ribosome profiling to systematically look at host genes RNA and translation levels along IAV infection. We show that host shutoff is mainly achieved by reduction in cellular mRNAs levels and that the high translation levels of IAV transcripts are driven by their strong accumulation compared to host transcripts. Interestingly, our systematic analysis reveals that host transcripts are affected differently by IAV infection and the extent of cellular mRNAs reduction is strongly related to transcripts’ length and GC content.

sample_organism:
Homo sapiens
Influenza A virus

platform_organism:
Homo sapiens
Influenza A virus

overall_design: Ribosome profiling and mRNA-seq along IAV infection

first: Noam

last: Stern-Ginossar


title: Enriched retinal ganglion cells derived from human embryonic stem cells (RNA-seq)

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

summary: We performed the whole transcriptome analysis in human H9 ES cells and in retinal ganglion cells (RGC) derived from H9 ES cells.

overall_design: RNA-seq in H9 human ESCs and RGC derived from H9 ESCs

first: R

last: Wong

first: A

last: Sharov

first: K

middle: P

last: Gill

first: S

last: Hung


title: Global Genome Repair factors are essential for shaping the DNA methylation landscape in Arabidopsis [BS-seq]

first: Jean

last: Molinier

summary: We report the methylome analysis of Arabidopsis plants deficient for the expression of 2 factors involved in global genome repair using whole genome bisulfite sequencing technology

overall_design: Methylomes of global genome repair deficient Arabidopsis plants

first: Vincent

last: Colot


title: Memory-like CD8 T-cells sustain the immune response to chronic viral infections.

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

institute: University of Lausanne

summary: We have discovered a small subpopulation of virus-specific CD8 T-cells that sustains the T-cell response in chronic infections.  These cells are defined by - and depend on - the expression of the transcription factor Tcf1 (T cell  factor 1) and show key characteristics of central memory cells while lacking an effector signature.  Unlike conventional memory cells, Tcf1+ T-cells display hallmarks of an “exhausted” phenotype,  including the expression of certain inhibitory receptors.

overall_design: Naive Tcf1-GFP+ P14 cells (Naive) were transferred into Vb5 recipient mice  (CD45.1)  prior to infection with LCMV clone 13 (c13). Tcf1-GFP+ P14 cells (chronic Tcf1+) and Tcf1-GFP- P14 cells (chronic Tcf1-) were flow sorted on day 28 post infection. Naive Tcf1-GFP+ P14 cells (Naive) were also  transferred into C57BL/6 hosts (CD45.1.2) prior to infection with LCMV Armstrong (Arm). Tcf1-GFP+ P14 cells (memory Tcf1+) and Tcf1-GFP- P14 cells (memory Tcf1-) were flow sorted on day 28 post infection. Total RNA was extracted, cDNA libraries prepared and sequencing was performed using Illumina HiSeq 2500 technology.

first: Mélanie

last: Charmoy

first: Daniela

last: Pais Ferreira

last: Calderon-Copete

first: Vijaykumar

last: Chennupati

first: Sylvain

last: Pradervand

first: Werner

last: Held


title: Differential Gene Expression Time Course of Normal Human Immortalized (iPrECs) vs Tumorigenic (EMP-iPrECs) Prostate Epithelial Cells during In Vitro Prostate Epithelial Cell Differentiation

city: Tuscon

first: Cindy

middle: K

last: Miranti

state: AZ

address: 1515 N Campbell

department: Department of Cellular and Molecular Medicine University of Arizona Cancer Center

institute: University of Arizona

summary: The first goal of this project was to identify differentially expressed genes associated with human prostate epithelial cells (PrEC) differentiation over a 2+ week time course that are associated with and potentially required for normal PrEC differentiation (J Cell Sci 123:266-76, 2010).  The second goal was to determine how these differentially expressed genes are changed when the same cells are transformed into tumorigenic cells (EMP-iPrECs) through overexpression of Erg, Myc, and shRNA to Pten (Cancer Res 74:3357-68, 2014).  In the iPrECs, we readily identified many genes that were up and down regulated over time during differentiation.  Genes that decreased include many cell cycle genes, and genes that increased include known differentiation markers.  The EMP cells did not differentiate as previously reported and was supported by the general lack of any major changes in gene expression over the EMP time course.  When iPrECs were compared to EMPs, there were over 2000 differentially expressed genes that did not overlap with the differentially expressed genes identified during the normal differentiation time course.  Thus, oncogenic transformation of PrECs results in major gene expression changes and abrogates the differentiation program.

overall_design:
Approach was to collect and isolate polyA-selected RNA from from two cell lines; normal human immortalized PrECs (iPrECs) and transformed human EMP-iPrECs, which had been subjected to an in vitro differentiation assay (J Cell Sci 123:266-76, 2010).  EMP-iPrECs were generated by stable expression of Erg, Myc and shRNA to Pten iPrECs (Cancer Res 74:3357-68, 2014).  Specifically, total RNA was isolated from the cells at specified time points during the course of iPrEC or EMP-iPrEC differentiation. Differentiation in untransformed cells results in a bilayer of epithelial cells- basal and luminal cells. The RNA isolated from the last two time points for iPrECs include only the luminal cells which were dissociated from the basal cells. The EMP-iPrECs did not form a bilayer, therefore all time points contain the whole population. Each time point for each cell line includes biological triplicates.
Michigan State University Research Technology Support Facility Genomics Core

first: Penny

middle: L

last: Berger

first: Mary

last: Winn


title: QUORUM SENSING IN A METHANE-OXIDIZING BACTERIUM

city: Salt Lake City

first: Aaron

last: Puri

state: UT

address: 1390 Presidents Circle

institute: University of Utah

summary: Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Despite this important environmental role, little is known about the molecular details of how these organisms interact in the environment. Many bacterial species use quorum sensing systems to regulate gene expression in a density-dependent manner. We have identified a quorum sensing system in the genome of Methylobacter tundripaludum, a dominant methane-oxidizer in methane enrichments of sediment from Lake Washington (Seattle, WA, USA). We determined that M. tundripaludum primarily produces N-3-hydroxydecanoyl-L-homoserine lactone (3-OH-C10-HSL) and that production is governed by a positive feedback loop. We then further characterized this system by determining which genes are regulated by quorum sensing in this methane-oxidizer using RNA-seq, and discovered this system regulates the expression of a novel nonribosomal peptide synthetase biosynthetic gene cluster. These results identify and characterize a mode of cellular communication in an aerobic methane-oxidizing bacterium.

overall_design: Samples are 2 sets of biological replicates of a Methylobacter tundripaludum strain 21/22 mutant where the acyl-homoserine lactone (AHL) synthase gene mbaI (T451DRAFT_0796) has been deleted. The mutant strain was grown to log (48 hours) or stationary (68 hours) phase in the absence or presence of the AHL 3-OH-C10-HSL.

first: Amy

last: Schaefer

first: Yanfen

last: Fu

first: David

last: Beck

first: E

last: Greenberg

last: Lidstrom


title: Chromatin organization in NPP-13 knockdown C. elegans embryos

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

type: Genome binding/occupancy profiling by genome tiling array


title: Small RNA sequencing in grapevine berries from two varieties (Cabernet Sauvignon and Sangiovese) grown in three different environments and sampled at four developmental stages

city: St. Louis

first: Blake

middle: C.

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary:
Purpose: The goal of this study is to detect the environmental influence on small RNAs population (miRNAs and other smallRNAs) in berries from two different grapevine varieties, evaluating Genotype x Environment interactions.
Methods: The grapevine berries were collected in liquid nitrogen and their small RNA fractions were isolated from total RNA for library construction and subsequent sequencing on an Illumina HiSeq 2000.
Results: Reads were mapped to the reference Vitis vinifera L. genomic sequence V1 (PN40024, (Jaillon et al., 2007) using Bowtie and retaining reads perfectly aligned to the genome. The static clustering analysis was carried out, using a proximity-based pipeline built with custom Perl and database scripts and MySQL database queries, to group and quantify clusters of small RNAs. The identification of annotated (conserved or known) and novel (or specie-specific) miRNAs was carried out applying a conservative and robust pipeline.
Conclusions: Our results show that the distribution of small RNA-producing loci is variable between the two cultivars, and that the level of variation depends on the vineyard. Differently, the profile of miRNA accumulation mainly depends on the developmental stage. One of the environment, Riccione, maximizes the differences between the varieties, promoting the production of more than one thousand specific small RNA loci and modulating their expression depending on the cultivar and the maturation stage.

overall_design: The grapevine berries were collected for the sequencing at four different developmental stages from Cabernet Sauvignon (CS) and Sangiovese (SG) clones grown side by side in three different vineyards. The vineyards are located in three typical wine making italian areas: Bolgheri (Bol), a coastal area of Tuscany, Montalcino (Mont) a mountain area of Tuscany, and Riccione (Ric), a plain area of Emilia-Romagna.

last: Lopes Paim Pinto

first: Lucio

last: Brancadoro

first: Silvia

last: Dal Santo

first: Gabriella

last: De Lorenzis

first: Mario

last: Pezzotti

first: Mario-Enrico

last: Pè

first: Erica

last: Mica


title: Lack of adrenomedullin in mouse endothelial cells results in defective angiogenesis, enhanced vascular permeability, less metastasis, and more brain damage

status: Public on Aug 14 2016

city: Logroño

first: Laura

last: Ochoa-Callejero

state: La Rioja

address: C/Piqueras 98 SPAIN

country: Spain

institute: CIBIR

summary: Adrenomedullin (AM) is a vasodilating peptide involved in the regulation of circulatory homeostasis and in the pathophysiology of certain cardiovascular diseases. AM plays critical roles in blood vessels, including regulation of vascular stability and permeability. To elucidate the autocrine / paracrine function of AM in endothelial cells in vivo. A conditional knockout of AM in endothelial cells (AM EC-KO) was used. The amount of vascularization the matrigel implants was lower in AM EC-KO mice indicating a defective angiogenesis. Moreover, ablation of AM in endothelial cells revealed increased vascular permeability in comparison with wildtype littermates. In addition, AM EC-KO lungs exhibited significantly less tumor growth than littermate WT mice using a syngeneic model of metastasis. Furthermore, following middle cerebral artery permanent occlusion, there was a significant infarct size decrease in animals lacking endothelial AM when compared to their wild type counterparts. AM is an important regulator of EC function, angiogenesis, tumorigenesis and brain response to ischemia. Studies of AM should bring novel approaches to the treatment of vascular diseases.

overall_design: Lung endothelial mRNA profiles of wild type (WT) and adrenomedullin endothelial cell conditional knockout (AM EC-KO) mice were generated by deep sequencing using Illumina GAIIx.

first: Alfredo

last: Martínez


title: Genomic nucleosome organization reconstituted with pure proteins

city: University Park

first: Bongsoo

last: Park

state: PA

address: 453 North Frear Building

institute: Penn State University

summary: Chromatin remodelers regulate genes by organizing nucleosomes around promoters, but their individual contributions are obfuscated by the complex in vivo milieu of factor redundancy and indirect effects. Genome-wide reconstitution of promoter nucleosome organization with purified proteins resolves this problem and is therefore a critical goal. Here we reconstitute four stages of nucleosome architecture using purified components: Yeast genomic DNA, histones, sequence-specific Abf1/Reb1, and remodelers RSC, ISW2, INO80, and ISW1a. We identify direct, specific and sufficient contributions that in vivo observations validate. First, RSC clears promoters by translating poly(dA:dT) into directional nucleosome removal. Second, partial redundancy is recapitulated where INO80 alone, or ISW2 at Abf1/Reb1sites, positions +1 nucleosomes. Third, INO80 and ISW2 each align downstream nucleosomal arrays. Fourth, ISW1a tightens the spacing to canonical repeat lengths. Such a minimal set of rules and proteins establishes core mechanisms by which promoter chromatin architecture arises through a blend of redundancy and specialization.

overall_design: In this study, nucleosomes were assembled using Salt Gradient Dialysis (SGD) on yeast genomic DNA library. Assembled nucleosomes were either left untreated (labelled as "SGD", control), treated with whole cell extract (WCE), mutant extracts (rsc3ts WCE, isw1 isw2 chd1 WCE), purified remodelers; singly or in combinations (RSC, ISW1a, ISW1b, ISW2, INO80, CHD1, SWI/SNF), combinations of mutant extracts and chromatin remodelers or combination of General Regulatory Factors (Abf1, Reb1) and chromatin remodelers. The resulting nucleosome positions were mapped genome-wide using MNase-(anti-H3-ChIP)-Seq.

first: Nils

last: Krietenstein

first: Megha

last: Wal

first: Shinya

last: Watanabe

first: Craig

last: Peterson

first: Benjamin

middle: F

last: Pugh

first: Philipp

last: Korber