title: Staphylococcus aureus coordinates leukocidins expression and pathogenesis by sensing metabolic fluxes via RpiRC

city: Tampa

first: Andy

last: Weiss

state: Florida

address: 4202 East Fowler Avenue, ISA2015

department: Department of Cell Biology, Microbiology and Molecular Biology

institute: University of South Florida

summary: Staphylococcus aureus (S. aureus) is a formidable human pathogen that uses secreted cytolytic factors such as hemolysins, leukocidins and cytolytic peptides to injure immune cells and promote infection of its host. Of these secreted molecules, the bicomponent family of pore-forming leukocidins are a potent class of cytolytic proteins with critical contributions to S. aureus pathogenesis. The regulatory mechanisms governing the expression of these toxins are incompletely defined. In this work, we performed a screen to identify transcriptional regulators involved in leukocidin expression in S. aureus USA300. We discovered that a metabolic sensor regulator, RpiRc, is a potent and selective repressor of two leukocidins, LukED and LukSF-PV. Whole genome transcriptomics, S. aureus exoprotein proteomics and metabolomic analyses revealed that RpiRc influences the expression and production of disparate virulence factors, in addition to altering metabolic fluxes in the TCA cycle, glycolysis and amino acid metabolism. Using mutational analyses, we confirmed that RpiRc signals through the accessory gene regulatory quorum-sensing system (Agr) in USA300. Specifically, in wildtype USA300, RpiRc represses the rnaIII promoter resulting in increased production of the repressor of toxins –Rot, which in turn represses leukocidin expression. In fact, deletion of rpiRc phenocopied deletion of rot. We show that RpiRc-mediated regulation of virulence factors is critical for killing of primary human polymorphonuclear leukocytes and for the pathogenesis of bloodstream infection in vivo. Collectively, our results suggest that S. aureus senses metabolic shifts by RpiRc to differentially regulate the expression of leukocidins thereby promoting invasive disease.

overall_design: wild-type AH LAC versus AH LAC carrying the bursa aurealis transposon in the rpiRC gene

first: Divya

last: Balasubramanian

first: Elizabeth

last: Ohneck

first: Jessica

last: Lim-Chapman

first: Min

middle: K

first: Tamara

last: Reyes-Robles

first: Lindsey

middle: N

last: Shaw

first: Desmond

last: Lun

first: Beatrix

last: Ueberheide

first: Bo

last: Shopsin

first: Victor

middle: J

last: Torres


title: Gene expression in PANC-1 and AsPC-1 human pancreatic carcinoma cells under hypoxia, nutrient starvation and low pH culture condition.

status: Public on Jan 25 2017

city: Tokyo

first: Tsuyoshi

last: Osawa

address: 4-6-1 Komaba, Meguro-ku

department: RCAST

country: Japan

institute: The University of Tokyo

type: Expression profiling by high throughput sequencing

summary: The conditions of the tumor microenvironment, such as hypoxia and nutrient starvation, play critical roles in cancer progression. However, the role of acidic extracellular pH in cancer progression is not studied as extensively as that of hypoxia. Here, we show that extracellular acidic pH (pH 6.8) triggered activation of sterol regulatory element-binding protein 2 (SREBP2) by stimulating nuclear translocation and promoter binding to its targets along with intracellular acidification. Interestingly, inhibition of SREBP2, but not SREBP1, suppressed the upregulation of low pH-induced cholesterol biosynthesis-related genes. Moreover, acyl-CoA synthetase short-chain family member 2 (ACSS2), a direct SREBP2 target, provided a growth advantage to cancer cells under acidic pH. Furthermore, acidic pH-responsive SREBP2 target genes were associated with reduced overall survival of cancer patients. Thus, our findings show that SREBP2 is a key transcriptional regulator of metabolic genes and progression of cancer cells, partly in response to extracellular acidification.

overall_design: Cells were treated for 24 h under each condition. RNA-seq reads were aligned to human transcriptome (UCSC gene) and genome (GRCh37/hg19) references respectively using Burrows-Wheeler Aligner. After transcript coordinate was converted to genomic positions, an optimal mapping result was selected either from transcript or genome mapping by comparing the minimal edit distance to the reference. Local realignment was performed within in-house short reads aligner with smaller k-mer size (k=11). Finally, fragments per kilobase of exon per million fragment mapped (FPKM) values were calculated for each UCSC gene while considering strand-specific information.

first: Ayano

last: Kondo

first: Hiroyuki

last: Aburatani


title: PANC-1 and AsPC-1 human pancreatic carcinoma cells under hypoxia, nutrient starvation and low pH culture condition

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Open chromatin region, histone acetylation, and SREBP2 binding in PANC-1 and AsPC-1 human pancreatic carcinoma cells under hypoxia, nutrient starvation and low pH culture condition.

overall_design: For ChIP-seq, PANC-1 cells (1 × 107) were crosslinked with 1% formaldehyde for 10 min at room temperature (RT). Fixation was stopped by adding 0.125 M　glycine. After crosslinking, nuclear pellets were prepared for ChIP. Pre-washed magnetic Dynabeads (Life Technologies, Massachusetts, USA) were incubated with anti-H3K27ac antibody (Millipore, Massachusetts, USA, #07-360) or anti-SREBP2 antibody (Cayman, Michigan, USA) for 6 h by wheel rotating at 4 °C. Sonicated crosslinked nuclear lysates and 8 ml ChIP Dilution buffer were added and incubated overnight at 4 °C by wheel rotating. The beads were washed several times and eluted with elution buffer (1% SDS and 100 mM NaHCO3), the eluent was incubated with pronase (1 mg ml-1) at 42 °C for 2 h and then incubated at 65 °C overnight to reverse the crosslinks. DNA was purified using QIA quick PCR purification kit (QIAGEN, Hilden, Germany).  Formaldehyde-assisted isolation of regulatory elements was performed as described previously (Giresi et al., 2007; Nakaki et al., 2012). Briefly, formalin-crosslinked cell pellets were lysed in SDS lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM ETDA, 1% SDS and proteinase inhibitor cocktail (Nacalai Tesque, Kyoto, Japan) and sonicated by ultrasound homogenizer (Bioruptor UCD-200TM, Cosmo Bio). Samples were subjected to phenol/chloroform extraction twice followed by ethanol precipitation and subsequently purified using QIAquick PCR purification kit (QIAGEN, Hilden, Germany).


title: Genetic Redundancy of GATA Factors in Extraembryonic Trophoblast Lineage Ensures Progression of both Pre and Postimplantation Mammalian Development [ChIP-seq]

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

country: USA

institute: University of kansas medical center

summary: GATA transcription factors are implicated in establishing cell fate during mammalian development. In early mammalian embryos, GATA3 is selectively expressed in the extraembryonic trophoblast lineage and regulates gene expression to promote trophoblast fate. However, trophoblast-specific GATA3 function is dispensable for early mammalian development. Here, using dual conditional knockout mice, we show that genetic redundancy of GATA3 with paralog GATA2 in trophoblast progenitors ensures the successful progression of both pre and postimplantation mammalian development. Stage-specific gene deletion in trophoblasts reveals that loss of both GATA genes, but not either one alone, leads to embryonic lethality prior to the onset of their expression within the embryo proper. Using ChIP-seq and RNA-seq analyses, we define the global targets of GATA2/GATA3 and show that they directly regulate a large number of common genes to orchestrate stem vs. differentiated trophoblast fate. Also, in trophoblast progenitors GATA factors directly regulate BMP4, Nodal and Wnt signaling components that promote embryonic-extraembryonic signaling cross-talk, essential for the development of the embryo proper. Our study provides genetic evidence that impairment of trophoblast-specific GATA2/GATA3 function could lead to early pregnancy failure.

overall_design: ChIPseq profiles of GATA2, GATA3 and IgG in Mouse trophoblast stem cells using Illumina Genome Analyzer IIx

first: Paul

last: Soumen

first: Home

last: Pratik

first: Gunewardena

last: Sumedha


title: Genetic Redundancy of GATA Factors in Extraembryonic Trophoblast Lineage Ensures Progression of both Pre and Postimplantation Mammalian Development


title: Genetic Redundancy of GATA Factors in Extraembryonic Trophoblast Lineage Ensures Progression of both Pre and Postimplantation Mammalian Development [RNA-seq]

overall_design: Gata2f/f;Gata3f/f;UBC-cre/ERT2 mTS cells were cultured in presence or absence of 4-hydroxytamoxifen (4-OHT) in MEF conditioned media FGF4 and heparin.  Deletion of respective genes were confirmed by PCR using genomic DNA from individual samples. Whole cell-lysates were used to prepare RNA using Qiagen RNeasy Mini Kit with on column DNase digestion. RNA-seq analysis were performed using a illumina HiSeq2000 platform.


title: Expression data for hiPSC-derived RPE treated with 10mM Nicotinamide or vehicle

city: Rensselaer

first: Thomas

middle: R

last: Kiehl

state: NY

address: One Discovery Drive

institute: Neural Stem Cell Institute

summary: We did the RNA-seq analysis to examine the global impact of Nicotinamide (NAM) on hiPSC-derived RPE transcriptome in order to better understand the mechanism of action of NAM. NAM inhibited the expression of Age related Macular degeneration (AMD) associated protein transcripts in hiPSC-derived RPE.

overall_design: Seven hiPSC-RPE lines (4 AMD donors and 3 Control donors) that had been cultured with 10mM NAM or vehicle for three weeks were used for RNA extraction and RNA-seq analysis. We treated 4 AMD hiPSC-RPE and 3 Control hiPSC-RPE lines with 10mM NAM or vehicle.

first: Janmeet

last: Saini

first: Sally

last: Temple


title: Transcriptional profiling of Mycobacterium tuberculosis Mmpl3 conditional mutant

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

summary: MmpL3 is an inner membrane transporter of Mycobacterium tuberculosis responsible for the export of trehalose momomycolate, a precursor of the mycobacterial outer membrane component trehalose dimycolate (TDM), as well as mycolic acids bound to arabinogalactan. MmpL3 represents an emerging target for tuberculosis therapy. In this paper, we describe the construction and characterization of an mmpL3 knockdown strain of M. tuberculosis. Downregulation of mmpL3 led to a stop in bacterial division and rapid cell death, preceded by the accumulation of TDM precursors. MmpL3 was also shown to be essential for growth in monocyte-derived human macrophages. Using RNA-seq we also found that MmpL3 depletion caused up-regulation of 47 genes and down-regulation of 23 genes (at least 3-fold change and false discovery rate ≤ 1%). Several genes related to osmoprotection and metal homeostasis were induced, while several genes related to energy production and mycolic acids biosynthesis were repressed suggesting that inability to synthesize a correct outer membrane leads to changes in cellular permeability and a metabolic shiftdown.

overall_design: The mmpL3 conditional mutant (named TB416) was constructed using the TetR/Pip ORR repressible promoter system (PMC2896539). Adding Anhydrotetracycline (Atc) to the cell culture medium represses the gene of interest. The Mycobacterium tuberculosis H37Rv conditional mutant strain was grown till exponential phase with or without ATc [500 ng/ml] in rolling bottles. Two biological replicates per condition were taken. As a control for a possible effect of Atc on cells, a wild-type H37Rv strain, ATc-treated and not treated, was used, one sample per condition.

first: Giulia

last: Degiacomi

first: Jan

last: Madacki

first: Francesca

last: Boldrin

first: Roberta

last: Provvedi

first: Giorgio

last: Palù

first: Jana

last: Kordulakova

first: Stewart

middle: T

last: Cole

first: Riccardo

last: Manganelli


title: POWERDERESS and HDA9 interact and promote histone H3 deacetylation at specific lysine residues in Arabidopsis.

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

country: China

institute: shenzhen university


title: POWERDERESS and HDA9 interact and promote histone H3 deacetylation at specific lysine residues in Arabidopsis. [RNA-Seq]

summary: Histone acetylation is a major epigenetic control mechanism that is tightly linked to the promotion of gene expression. Histone acetylation levels are balanced through the opposing activities of histone acetyltransferases (HATs) and histone deacetylases (HDACs). Arabidopsis HDAC genes (AtHDACs) compose a large gene family, and distinct phenotypes among AtHDAC mutants reflect the functional specificity of individual AtHDACs. However, the mechanisms underlying this functional diversity are largely unknown. Here, we show that POWERDRESS (PWR), a positive regulator of floral stem cell maintenance, interacts with HDA9 and promotes histone H3 deacetylation possibly by facilitating HDA9 function at target chromatin. The PWR SANT2 domain, which is homologous to that of subunits in animal HDAC complexes, showed specific binding affinity to acetylated histone H3. Three lysine residues (K9, K14 and K27) of H3 retained hyperacetylation status in both pwr and hda9 mutants. Genome wide H3K9 and H3K14 acetylation levels were generally elevated, and a large portion of acetylated targets overlapped between the pwr and hda9 mutants. Comparative analysis revealed a correlation between gene expression and histone H3 acetylation status in the pwr and hda9 mutants. In addition, PWR and HDA9 modulated the AGAMOUS-LIKE 19 (AGL19)-mediated flowering time pathway through histone H3 deacetylation. Finally, PWR was shown to physically interact with HDA9. We therefore propose that PWR acts as a subunit in a complex with HDA9 to negatively regulate the acetylation of specific lysine residues of histone H3 at genomic targets.

overall_design: Transcriptome analysis of WT (Col), pwr-2 and hda9-1: three biological replicates for each

first: Yun

last: kim

first: Xuemei

last: Chen


title: ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis

city: Riverside

first: Brandon

last: Le

state: CA

address: 3401 Watkins Drive

department: Institute for Integrative Genome Biology

institute: University of California, Riverside

type: Non-coding RNA profiling by high throughput sequencing


title: ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis [AGO10SDN]

summary: The degradation of small RNAs in plants and animals is associated with small RNA 3’ truncation and 3’ uridylation and thus relies on exonucleases and nucleotidyl transferases. Argonaute proteins associate with small RNAs in vivo and are essential for not only the activities but also the stability of small RNAs. Arabidopsis ARGONAUTE10 (AGO10) maintains stem cell homeostasis in meristems by sequestration of miR165/6, a conserved miRNA acting through AGO1. Here, we report that AGO10 reduces miR165/6 accumulation by enhancing its degradation. This is contrary to the stabilizing effect of all known argonaute proteins on their associated small RNAs. We show that SMALL RNA DEGRADING NUCLEASES (SDNs) are responsible for miRNA 3’ truncation in general and AGO10 promotes the degradation of miR165/6 by SDNs. Our work identifies the exonucleases responsible for miRNA 3’ truncation in vivo and uncovers a mechanism of specificity determination in miRNA turnover. This work, together with previous studies on AGO10, demonstrates that spatially regulated miRNA degradation underlies stem cell maintenance in plants.

overall_design:
Immunoprecipitation of AGO1- and AGO10-RISCs followed by treatment with SDN/SDN-D283A exonucleases (two biological replicates and two treatments for a total of 8 samples).
Immunoprecipitation of AGO1- and AGO10-RISCs followed by Mock treatment that included buffer only (i.e., no SDN) (two biological replicates, a total of 4 samples).

first: Lijuan

last: Ji

first: Yu

last: Yu

middle: H


title: ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis [AGO10OE]

overall_design: Total and AGO1-RISC small RNAs were isolated from AGO10 overexpression lines (Four AGO1-IP samples and five total RNA samples, nine total samples)


title: POWERDERESS and HDA9 interact and promote histone H3 deacetylation at specific lysine residues in Arabidopsis. [ChIP-Seq]

overall_design: Global analysis of the acetylation status of histone H3K9 (two biological replicates) and H3K14 (one replicate) in Col (WT), pwr-2 and hda9-1.


summary:
It is largely unknown how microRNAs (miRNAs) are degraded in vivo or whether active miRNA turnover is critical to specific developmental processes. Arabidopsis ARGONAUTE10 (AGO10) maintains stem cell homeostasis in meristems by repression of miR165/6, a conserved miRNA acting through AGO1. Here, we report that AGO10, through its binding to miR165/6, reduces miR165/6 accumulation by enhancing its decay. We show that AGO10 promotes the 3’ truncation of miR165/6 by SMALL RNA DEGRADING NUCLEASES (SDNs) and that AGO10-bound miR165/6 is more susceptible to degradation by SDN1 than AGO1-bound miR165/6. Our work uncovers a mechanism that governs the stability of miRNAs, establishes the importance of spatially controlled miRNA decay in stem cell homeostasis, and sheds light on the diversification and specialization of Argonaute proteins.
Both biogenesis and degradation contribute to the steady-state levels of microRNAs (miRNAs). miRNA degradation in both plants and animals is associated with 3’ truncation and 3’ uridylation, and in Arabidopsis, the nucleotidyl transferase HEN1 SUPPRESSOR1 is responsible for 3’ uridylation. The SMALL RNA DEGRADING NUCLEASE (SDN) family of 3’ to 5 exonucleases degrades short RNAs in vitro and limits the accumulation of miRNAs in vivo, but it is not known whether SDNs are responsible for the accumulation of 3’ truncated miRNA species in vivo. In addition, there has not been an example of active miRNA turnover being critical to specific developmental processes. Arabidopsis ARGONAUTE10 (AGO10) maintains stem cell homeostasis in meristems by sequestration of miR165/6, a conserved miRNA acting through AGO1. Here, we report that AGO10, through binding to miR165/6, reduces miR165/6 accumulation by enhancing its degradation. We show that SDNs are responsible for the generation of 3’ truncated miRNAs in vivo and AGO10 promotes the 3’ truncation of miR165/6 by SDNs. Our work uncovers a novel mechanism of miRNA degradation mediated by an argonaute protein, which contrasts the known stabilizing effects of most AGO proteins on their associated miRNAs. This work, together with previous studies on AGO10, demonstrates that spatially regulated miRNA degradation underlies stem cell maintenance in plants.

overall_design:
19 samples in total, 3 replicates for control Col, 3 replicates for AGO1IP, AGO10IP and AGO10 OE, 1 for AGO1IP_col, AGO1IP (AGO10 OE), AGO10 OE 4mAGO1, AGO10 OE (I_s), sdn1 sdn2 AGO10 OE (I_s), AGO10 OE (II_f) and sdn1 sdn2 AGO10 OE (II_f)
17 samples in total, 2 replicates for Col, sdn1sdn2, hen1 and hen1sdn1sdn2, 3 replicates for Ler, pnh-2 and ago10-13

first: L

first: X


title: Adaptive chromatin remodeling in glioblastoma stem cell plasticity and drug tolerance

city: Boston

first: Cem

last: Sievers

address: 165 Cambridge Street

department: Molecular Pathology

institute: MGH

summary: Many cancers are postulated to harbor developmental hierarchies in which cells display variability in stem-like character, tumor propagating ability, and proliferation. In glioblastoma (GBM), glioma stem cells (GSCs) reside atop such a tumor cellular hierarchy, and are thought to resist current therapies and thus underlie inevitable relapse. Here we show that GSCs can evade RTK inhibition by reversibly regressing to a slow-cycling state reminiscent of quiescent neural stem cells. This process involves up-regulation of numerous histone demethylases, including KDM6A/B, which remodel the chromatin landscape and are selectively essential for drug persister survival. Chromatin remodeling is accompanied by activation of various neurodevelopmental master regulators and Notch signaling, changes which closely parallel critical aspects of neural stem cell biology. Thus our findings illustrate how cancer cells may hijack native developmental programs for deranged proliferation, adaptation, and tolerance in the face of stress. Our studies highlight key roles for chromatin remodeling and developmental plasticity in GBM biology, and suggest strategies for overcoming therapeutic resistance by targeting epigenetic and developmental pathways.

overall_design:
ChIP-seq for histone modifications and Notch factors in glioblastoma stem cell lines with various drug treatments
RNA-seq in glioblastoma stem cell lines with various drug treatments

first: Brian

last: Liau

first: Bradley

last: Bernstein


title: Characterization of Dopaminergic Neurons Derived from A Tyrosine Hydroxylase Reporter Stem Cell Line

status: Public on Jan 24 2017

city: Bozeman

first: Ninuo

last: Xia

state: Montana

address: 3114 annie street

department: cell biology and neurosciences

institute: Montana State University

type: Methylation profiling by high throughput sequencing

summary: Generation of midbrain dopaminergic (mDA) neurons from human pluripotent stem cells provides a platform for inquiry into basic and translational studies of Parkinson’s disease (PD). However, heterogeneity in differentiation in vitro makes it difficult to identify mDA neurons in culture or in vivo following transplantation. Tyrosine hydroxylase (TH), the first and rate-limiting enzyme for dopamine synthesis, is a well-established marker for mDA neurons. Here, we report the generation of a human embryonic stem cell (hESC) line with a TH-RFP (red fluorescent protein) that was generated via insertion of an RFP sequence downstream of the TH coding sequence. We validated that endogenous TH expression was unaffected by genetic modification; RFP faithfully mimicked TH expression during differentiation. Use of this TH-RFP reporter cell line enabled purification of mDA-like neurons from heterogeneous cultures with subsequent characterization of neuron transcriptional and epigenetic programs (global binding profiles of H3K27ac, H3K4me1 and 5 hydroxymethylcytosine (5hmC)) at four different stages of development.  We anticipate that tools and data described here will contribute to development of mDA neurons for applications in disease modeling and/or drug screening and cell replacement therapies for PD.

overall_design: RNA -seq, ChIP-seq and 5hmC seq of ES cell derived TH+ dopamine neurons

first: Renee

last: Pera


title: The RNA helicase Ded1p suppresses translation initiation from near-cognate start codons

city: Cleveland

first: Ulf-Peter

last: Guenther

state: OH

address: 10900 Euclid Ave

department: Biochemistry/ RNA Center

institute: Case Western Reserve University

summary: The conserved and essential DEAD-box RNA helicase Ded1p from yeast and its mammalian ortholog DDX3 are critical for translation initiation. Mutations in DDX3 are linked to tumorigenesis and intellectual disability, and the enzyme is targeted by diverse viruses. How Ded1p and its orthologs engage RNAs to impact translation initiation has been a longstanding, unresolved question. Here we show that Ded1p associates with the pre-initiation complex at the mRNA entry channel of the small ribosomal subunit and that the helicase unwinds mRNA structure ahead of the scanning pre-initiation complex. Defective Ded1p causes pervasive translation in 5’UTRs, starting from near-cognate initiation codons located 5' of mRNA structures and concomitant decrease of protein synthesis from of the main ORFs. The data indicate that Ded1p functions to suppress translation initiation on near-cognate codons proximal to mRNA structure and show how the helicase is targeted to specific RNA sites without common sequence signatures. Our results reveal a straightforward mechanism for the activation of upstream open reading frames and suggest that mRNA structure and proximal near-cognate initiation codons encode a widespread regulatory program for translation initiation that is sensitive to RNA helicase function.

overall_design: We investigated the molecular mechanism of function of the DEAD-box RNA helicase Ded1p during translation initation.The study includes 38 samples, comprised of high-throughput sequencing approaches determining the binding of Ded1p to mRNAs, changes in RNA secondary structure and ribosome binding in response to a sudden loss of Ded1p. These data is derived from biological replicates of an RNA binding deficient, termperature-sensitive Ded1p mutant (ded1-95), and the corresponding wild-type strain.

first: David

middle: E

last: Weinberg

first: Meghan

middle: M

last: Zubradt

first: Frank

last: Tedeschi

first: Brittany

last: Stawicki

first: Leah

last: Zagore

first: Donny

last: Licatalosi

middle: P

last: Bartel

first: Jonathan

last: Weissman

first: Eckhard

last: Jankowsky


title: Mercury-Induced Epigenetic Transgenerational Inheritance of Abnormal Neurobehavior is Correlated with Sperm Epimutations in Zebrafish

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary: Methylmercury (MeHg) is a ubiquitous environmental neurotoxicant, with human exposures predominantly resulting from fish consumption. Developmental exposure of zebrafish to MeHg is known to alter their neurobehavior.   The current study investigated the direct exposure and transgenerational effects of MeHg, at tissue doses similar to those detected in exposed human populations, on sperm epimutations (i.e., differential DNA methylation regions [DMRs]) and neurobehavior (i.e., visual startle and spontaneous locomotion) in zebrafish, an established human health model. F1 generation embryos were exposed to MeHg (0, 1, 3, 10, 30, and 100 nM) for 24 hours ex vivo. F1 generation control and MeHg-exposed lineages were reared to adults and bred to yield the F2 generation, which was subsequently bred to the F3 generation.  Direct exposure (F1 generation) and transgenerational actions (F3 generation) were then evaluated. Hyperactivity and visual deficit were observed in the unexposed descendants (F3 generation) of the MeHg-exposed lineage compared to control.  An increase in F3 generation sperm epimutations was observed relative to the F1 generation. Investigation of the DMRs in the F3 generation MeHg-exposed lineage sperm revealed associated genes in the neuroactive ligand-receptor interaction and actin-cytoskeleton pathways being effected, which correlate to the observed neurobehavioral phenotypes. Developmental MeHg-induced epigenetic transgenerational inheritance of abnormal neurobehavior is correlated with sperm epimutations in F3 generation adult zebrafish.  Therefore, mercury has the ability to promote the epigenetic transgenerational inheritance of disease in zebrafish, which significantly impacts its environmental health considerations in all species including humans.

overall_design: F1 generation zebrafish embryos were exposed to MeHg.  F1 generation control and MeHg-exposed lineages propogated to the F3 generation. Sperm was collected from both F1 and F3 generation fish. The sperm from two fish was combined to create a single pooled sample. Three pools were collected for both control and MeHg treated groups. The methylation characteristics of the pooled samples was estimated using a methylated DNA immunoprecipitation (MeDIP) followed by PE50 sequencing on an Illumina HiSeq 2500 platform.

last: Carvan III

first: Thomas

middle: A

last: Kalluvila

first: Rebekah

last: Klingler

first: Jeremy

last: Larson

first: Matthew

last: Pickens

first: Francisco

middle: X

last: Mora-Zamorano

first: Victoria

last: Connaughton

first: Ingrid

last: Sadler-Riggleman

first: Daniel

last: Beck


title: Ligand and Target Discovery by Fragment-Based Screening in Human Cells

city: La Jolla

first: Inigo

last: Narvaiza

address: 10010 N Torrey Pines Rd

department: Laboratory of Genetics

institute: Salk Institute

summary: Advances in the synthesis and screening of small-molecule libraries have accelerated the discovery of chemical probes for studying biological processes. Still, only a small fraction of the human proteome has chemical ligands, and the full complement of proteins with potential to be targeted by small molecules remains unknown. Here, we describe a platform that marries fragment-based ligand discovery with quantitative chemical proteomics to map thousands of reversible small molecule-protein interactions directly in human cells, many of which can be site-specifically determined. We advance this knowledge to create ligands that affect the activity of proteins heretofore lacking chemical probes and to identify by phenotypic screening small molecules that promote adipocyte differentiation by engaging the poorly characterized membrane protein PGRMC2. Fragment-based screening in human cells thus provides an extensive proteome-wide map of protein ligandability and facilitates the coordinated discovery of bioactive small molecules and their molecular targets.

overall_design: PolyA+ Rnaseq profilling of 3T3-L1 stably overexpressing Gfp or PGRMC2 treated with dmso and induced to differentiate into adipocytes. RNA samples were collected 24 hours after induction of differentiation.

first: Andrea

last: Galmozzi

first: Christopher

middle: G

last: Parker

first: Benjamin

middle: F

last: Cravatt

first: Enrique

last: Saez


title: Heterochromatin Protein 1γ Regulates Epigenetic Reprogramming in Primordial Germ Cells

city: Beijing

first: Pinchao

last: Mei

address: Dongdansantiao 5hao

department: Dept. Biochem & Mol Biol

institute: Peking Union Medical College & Chinese Academy of Medical Science

summary: Temporal and spatial regulation of trimethylation of histone H3 lysine27 (H3K27me3) is crucial for cell lineage commitment and development. Resetting the ground state of H3K27me3 is important for establishing a proper development program of primordial germ cells (PGCs). The mechanisms that regulate global erasure of epigenetic information in the germ line are not well understood. Here we show that HP1γ suppresses the demethylation activity of Utx through direct interaction in vitro and in vivo. Down-regulation of mammalian heterochromatin protein 1 gamma (HP1γ) coincides with transient loss of H3K27me3 in PGCs on Embryonic Day 10.5 (E10.5). Furthermore, transient abolishment of HP1γ promotes the induction of embryonic stem cells into putative PGCs in vitro. These data reveal a cross-talk between HP1γ and Utx in controlling histone H3K27 methylation status, thereby define HP1γ as a molecular regulator of germ cell epigenetic reprogramming.

overall_design: Examination of H3K27me3 modification and HP1γ in HP1γ-depleted mouse ESCs.

first: Feng

last: Xiong

first: Tiantian

last: Zhang


title: RNA-Seq data from ZR75-1 cells

first: Qinong

last: Ye

address: Taiping Rd.27

institute: Beijing Institute of Biotechnology

summary: We report the transcription factor Six1 directly increases the expression of many glycolytic genes by performing RNA sequencing using Six1 stable knockdown ZR75-1 breast cancer cell line and control cell line.

overall_design: Examination of ZR75-1 cells stably infected with lentivirus carrying Six1 shRNA or control shRNA

first: Ling

last: Li


title: Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific p300 bioChIP-seq

first: Fei

last: Gu

state: MA

address: 320 Longwood Ave.

department: Cardiology

institute: Childrens hospital boston, Harvard Medical School

summary: We report a method for high throughput mapping of transcriptional enhancers, genomic regulatory regions that activate lineage-specific transcription. Since tissue-specific enhancers are bound by the transcriptional co-activator p300, we developed murine knock-in alleles that permit Cre-dependent, lineage-specific p300 in vivo biotinylation and high affinity pulldown on immobilized streptavidin. Subsequent next generation sequencing of p300-bound genomic DNA identified lineage-specific enhancers. By driving this system with lineage-specific Cre transgenes, we mapped enhancers active in embryonic endothelial cells/blood or skeletal muscle. Analysis of these enhancer sequences identified new transcription factor heterodimer motifs that likely regulate transcription in these lineages. Furthermore, we identified candidate enhancers that regulate adult heart- or lung- specific endothelial cell specialization.

overall_design: ES_p300_bioChIP x2, E12.5 forebrain_p300bioChIP x2 and H3K27Ac ChIP x2,  E12.5 heart_p300bioChIP x2 and H3K27Ac ChIP x2, E11.5_embryo_p300_bioChIP x3, E11.5_Tie2Cre_EC_p300-bioChIP x3, E13.5_Myf5Cre_muscle prognitors_p300-bioChIP x3, adult_heart_p300-bioChIP x2, adult heart_lung_p300-bioChIP x3, adult_heart_EC_p300-bioChIP x3, adult_lung_EC_p300-bioChIP x3, E12.5 Cardiomyocyte_ATAC-seq x2, E10.5_Tie2Cre-TRAP x1

first: Pingzhu

last: Zhou

first: Lina

first: Brynn

last: Akerberg

first: Qing

last: Ma

first: Kai

first: Aibin

last: He

first: Zhiqiang

last: Lin

first: Sean

last: Stevens

first: Bin

first: William

last: Pu


title: Unique Genetic Responses Revealed in RNA-seq of the Spleen of Chickens Stimulated with Lipopolysaccharide and Heat

city: Ames

first: Angelica

last: Van Goor

state: Iowa

address: 1221 Kildee Hall

institute: USDA-NIFA

summary: Climate change and disease have large negative impacts on poultry production, but little is known about the interactions of responses to these stressors in chickens. Fayoumi (heat and disease resistant) and broiler (heat and disease susceptible) chicken lines were stimulated at 22 days of age, using a 2x2x2 factorial design including: breed (Fayoumi or broiler), inflammatory stimulus [lipopolysaccharide (LPS) or saline], and temperature (35°C or 25°C). Transcriptional changes in spleens were analyzed using RNA-sequencing on the Illumina HiSeq 2500. Thirty-two individual cDNA libraries were sequenced (four per treatment) and an average of 22 million reads were generated per library. Stimulation with LPS induced more differentially expressed genes (DEG, log2 fold change ≥ 2 and FDR ≤ 0.05) in the broiler (N=283) than the Fayoumi (N=85), whereas heat treatment resulted in fewer DEG in broiler (N=22) compared to Fayoumi (N=107). The double stimulus of LPS+heat induced the largest numbers of changes in gene expression, for which broiler had 567 DEG and Fayoumi had 1471 DEG of which 399 were shared between breeds. Further analysis of DEG revealed pathways impacted by these stressors such as Remodelling of Epithelial Adherens Junctions due to heat stress, Granulocyte Adhesion and Diapedesis due to LPS, and Hepatic Fibrosis/Hepatic Stellate Cell Activation due to LPS+heat.   The genes and pathways identified provide deeper understanding of the response to the applied stressors and may serve as biomarkers for genetic selection for heat and disease tolerant chickens.

overall_design: At 22 days of age, divergent chicken breeds (Fayoumi and broiler) were treated with a thermal treatment (heat stress at 35C, or thermoneutral at 25C as a control) for 3.5 hours, then stimulated subcutaneously with an inflammatory stimulus (LPS, or saline as a control) for another 3.5 hours. Chickens were euthanized and spleens were harvested. A total of 32 indivudally coded cDNA libraries were prepared using TruSeq v2 library preparation kit which selects for polyA mRNA. In this 2x2x2 full factorial design with the factors of breed, thermal treatment, and inflammatory stimulus, there were a total of 8 treatment groups. Each treatment group had a total of 4 animal biological replicates. Therefore, a total of 32 individual barcoded samples were sequenced. A total of 8 individually barcoded cDNA libraries were sequenced per lane using the HiSeq Illumina 2500, and we used 4 lanes total. Reads were mapped to Galgal 2.0.

first: Susan

last: Lamont


title: Genetic variants alter T-bet binding and gene expression in mucosal inflammatory disease

city: London

first: Richard

last: Jenner

address: 72 Huntley Street

department: Cancer Biology

country: United Kingdom

institute: UCL Cancer Institute

summary: The polarization of CD4+ T cells into distinct T helper cell lineages is essential for protective immunity against infection, but aberrant T cell polarization can cause autoimmunity. The transcription factor T-bet (TBX21) specifies the Th1 lineage and represses alternative T cell fates. Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) that may be causative for autoimmune diseases. The majority of these polymorphisms are located within non-coding distal regulatory elements. It is considered that these genetic variants contribute to disease by altering the binding of regulatory proteins and thus gene expression, but whether these variants alter the binding of lineage-specifying transcription factors has not been determined. Here, we show that SNPs associated with the mucosal inflammatory diseases Crohn’s disease, ulcerative colitis (UC) and celiac disease, but not rheumatoid arthritis or psoriasis, are enriched at T-bet binding sites. Furthermore, we identify disease-associated variants that alter T-bet binding in vitro and in vivo. ChIP-seq for T-bet in individuals heterozygous for the celiac disease-associated SNPs rs1465321 and rs2058622 and the IBD-associated SNPs rs1551398 and rs1551399, reveals decreased binding to the minor disease-associated alleles. Furthermore, we show that rs1465321 is an expression quantitative trait locus (eQTL) for the neighboring gene IL18RAP, with decreased T-bet binding associated with decreased expression of this gene. These results suggest that genetic polymorphisms may predispose individuals to mucosal autoimmune disease through alterations in T-bet binding. Other disease-associated variants may similarly act by modulating the binding of lineage-specifying transcription factors in a tissue-selective and disease-specific manner.

overall_design: Correlation of T-bet binding sites and autoimmune disease associate SNPs

first: Katrina

last: Soderquest

first: Arnulf

last: Hertweck

first: Claudia

last: Giambartolomei

first: Stephen

last: Henderson

first: Rami

last: Mohamed

first: Rimma

last: Goldberg

first: Esperanza

last: Perucha

first: Lude

last: Franke

first: Javier

last: Herrero

first: Vincent

last: Plagnol

first: Graham

last: Lord


title: Simultaneous transcriptional and epigenomic profiling from specific cell types within heterogeneous tissues in vivo

first: Evan

last: Rosen

address: 3 Blackfan Cir

department: Endocrinology

institute: Beth Israel Deconess Medical Center

summary:
This study introduces “NuTRAP”, a transgenic mouse that allows simultaneous isolation of cell type-specific translating mRNA and chromatin from complex tissues
Using NuTRAP, we successfully characterize gene expression and epigenomic states of various adipocyte populations in vivo,
To demonstrate general usefulness, we chateraterize histone states of in vivo hepatocytes.

overall_design: We demonstrate the robustness of NuTRAP-based ChIP-seq by performing titration experiments

first: Hyun

last: Roh


title: Pancreas lineage allocation and specifciation are regulated by sphingosine-1-phosphate signalling

city: Dresden

first: Anthony

last: Gavalas

address: Fetscherstr. 105

country: Germany

institute: TU Dresden

summary: Identifying the signals that regulate the survival, lineage allocation and specification of pancreas progenitors will help elucidate the embryonic origins of pancreas dysfunction and provide important cues for the efficient conversion of pluripotent stem cells into fully functional β cells. Several transcription factors regulating the conversion of the early pancreatic progenitors into terminally differentiated cells have been identified but extracellular signals regulating pancreas development are less well understood.    Using a combination of genetic approaches, organotypic cultures of embryonic pancreata and genomics we have found that sphingosine-1-phosphate signalling through plays a key role in this process. S1p signalling stabilizes the Hippo pathway effector YAP to promote progenitor survival, acinar and endocrine specification. Endocrine cell specification relies on Gai subunits revealing an unexpected dependence of lineage specification on selected intracellular signalling components. Independently of YAP stabilization, S1p signalling attenuates Notch levels, thus regulating lineage allocation.   These findings identify S1p signalling as a key pathway coordinating cell survival, lineage allocation and specification during pancreas development.

overall_design: Analysis was carried out at 14.5 dpc embryonic pancreata and in 14.5 dpc embryonic pancreata that have been cultured in air to liquid interface cultures for two days (14.5 + 2). For the 14.5 dpc analysis wild type (14.5 wt) and S1pr2 null (14.5 S1pr2 null) pancreata were analyzed. For the analysis of cultured embryonic pancreata, conditions used were either standard conditions (14.5 + 2) or in the presence of 15 uM of JTE013 (14.5 + 2 + JTE) or in the presence of 15 uM of JTE013 and 50 ng/ml CTGF (14.5 + 2 + JTE + CTGF). Three biological replicates were used for each stage/condition for a total of 15 samples.

first: Ioannis

last: Serafimidis

first: Eva

last: Rodriguez-Aznar

first: Mathias

last: Lesche

first: Kazuaki

last: Yoshioka

first: Yoh

last: Takuwa

first: Andreas

last: Dahl

first: Duojia

last: Pan


title: Activation of a SOX2-dependent transcriptional regulatory circuit drives glioblastoma.

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Overexpression of the transcription factor SRY-related box 2 (SOX2) is characteristic of Glioblastoma (GBM), yet its regulatory network in vivo is poorly understood. Using a human orthotopic tumor model of GBM for ChIP-Seq analysis, we mapped the SOX2 cistrome. Integrative analysis of SOX2 cistrome and GBM transcriptome data identified two transcription factors, oligodendrocyte lineage transcription factor 2 (OLIG2) and zinc finger E-box binding homeobox 1 (ZEB1) as critical SOX2 targets. Their expression is strongly correlated with SOX2 expression in clinical GBM specimens, and all three proteins are frequently co-expressed in primary Glioblastoma cells, even in the setting of EGFR intratumoral heterogeneity. Sox2, Olig2, and Zeb1 expression is activated by the oncogene EGFRvIII in a murine glioma model, and we demonstrate that co-expression of these transcription factors transforms tumor suppressor deficient astrocytes in the absence of an upstream oncogene and that the resulting tumors exhibit the major histopathological features of GBM.

overall_design: A NOD-SCID mouse harboring HOT1 tumor derived from a human glioblastoma patient sample was euthanized. Three slices of tumor sample (~1 mm thick, ~100 mg total) were obtained from the dissected brain within three minutes after sacrificing the mouse, and were immediately placed in 1 ml of pre-warmed DMEM (37C) containing 1% formaldehyde, and homogenized with a POLYTRON for 30 seconds. After 10 minutes of incubation at room temperature 111 µl 1.25 M glycine was added, and after 5 minutes of incubation at room temperature the cells were pelleted by centrifugation at 700g. The cell pellet was washed twice with 1 ml of ice-cold PBS. The cell pellet was then lysed in 1 ml ChIP lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl [pH 8.1] with protease inhibitors, Roche) and sonicated at 4C with a Bioruptor (Diagenode) (30 seconds ON and 30 seconds OFF at highest power for 15 minutes). The sheared chromatin with an average fragment length of ~500 bp was centrifuged at 10,000 g for 10 minutes at 4C. 100 μl of the supernatant was used for ChIP or as input. A 1:10 dilution of the solubilized chromatin in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl 16.7 mM Tris-HCl [pH 8.1]) was incubated at 4C overnight with 6 μg/ml of SOX2 antibody (Cell Signaling Technology, rabbit monoclonal antibody). Immunoprecipitation was carried out by incubating with 40 μl pre-cleared Protein G Sepharose beads (Amersham Bioscience) for 1 hour at 4C, followed by five washes for 10 minutes with 1ml of the following buffers: Buffer I: 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.1], 150 mM NaCl; Buffer II: 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.1], 500 mM NaCl; Buffer III: 0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl [pH 8.1]; twice with TE buffer [pH 8.0]. Elution from the beads was performed twice with 100 μl ChIP elution buffer (1% SDS, 0.1 M NaHCO3) at room temperature (RT) for 15 minutes. Protein-DNA complexes were de-crosslinked by heating at 65C in 192 mM NaCl for 16 hours. DNA fragments were purified using QiaQuick PCR Purification kit (Qiagen) and eluted twice with 30 μl EB buffer according to the manufacturer’s protocol after treatment with RNase A and Proteinase K.

first: Rahul

last: Kollipara

first: Robert

last: Bachoo


title: Generation and Characterization of Acid Tolerant Fibrobacter succinogenes S85

status: Public on Jan 23 2017

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

summary: Microorganisms are key components for plant biomass breakdown within rumen environments. Gram negative Fibrobacter succinogenes have been identified as being active and dominant cellulolytic members of the rumen. In this study, F. succinogenes type strain S85 was adapted for steady state growth in continuous culture at pH 5.75 and confirmed to grow in the range of pH 5.60-5.65, which is lower than has been reported previously. RNA-seq analysis revealed 268 and 829 genes were differentially expressed at pH 6.1 and 5.65 compared to pH 6.7, respectively. Resequencing analysis identified seven single nucleotide polymorphisms (SNPs) in the sufD, yidE, xylE, rlmM, mscL and dosC genes of acid tolerant strains. Due to the absence of a F. succinogenes genetic system, homologues in Escherichia coli were mutated and complemented and the resulting strains were assayed for acid survival. Complementation with wild-type or acid tolerant F. succinogenes sufD restored the function of E. coli SufDSE, suggesting a possible role F. succinogenes sufD was involved in acid homeostasis. Recent genetic engineering developments need to be adapted and applied in F. succinogenes to further our understanding of this species.

sample_organism: Fibrobacter succinogenes subsp. succinogenes S85

overall_design: Chia-wei,Wu

first: Steven

middle: D

last: Brown

first: Thomas

last: Spike


title: Transcriptome analysis of Shank2 mutant mice

city: Seoul

first: Jae-Hyung

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

country: South Korea

institute: Kyung Hee University

summary: Autism spectrum disorders (ASDs) are a group of developmental disorders that cause variable and heterogeneous phenotypes across three behavioral domains such as atypical social behavior, disrupted communications, and highly restricted and repetitive behaviors. In addition to these core symptoms, other neurological abnormalities are associated with ASD, including intellectual disability (ID). However, the molecular etiology underlying these behavioral heterogeneities in ASD is unclear. Mutations in SHANK2 genes are associated with ASD and ID. Interestingly, two lines of Shank2 knockout mice (e6-7 KO and e7 KO) showed shared and distinct phenotypes. Here, we found that the expression levels of Gabra2, as well as of GABA receptor-mediated inhibitory neurotransmission, are reduced in Shank2 e6-7, but not in e7 KO mice compared with their own wild type littermates. Furthermore, treatment of Shank2 e6-7 KO mice with an allosteric modulator for the GABAA receptor reverses spatial memory deficits, indicating that reduced inhibitory neurotransmission may cause memory deficits in Shank2 e6-7 KO mice. This article is part of the Special Issue entitled 'Ionotropic glutamate receptors'.

overall_design: Compare gene expression profiles between wild-type and knock-out mutants mice using RNA-Seq (Illumina platform: Hi-Seq 2500)

first: Nam-Kyung

last: Yu

first: Hye

last: Nam

first: Sung

last: Baek

first: Hyopil

last: Kim

first: Chae-Seok

last: Lim

first: Hyun-Hee

last: Ryu

first: Jungsoo

last: Gim

first: Yong-Seok

first: Bong-Kiun

last: Kaang


title: eIF1 modulates the recognition of sub-optimal translation start sites and steers gene expression control mediated by uORFs

city: Gent

first: Petra

middle: Van

last: Damme

state: East Flanders

address: Albert Baertsoenkaai 3

department: Department of Biochemistry

country: Belgium

institute: University of Gent

summary: Alternative translation initiation mechanisms such as leaky scanning and reinitiation potentiate the polycistronic nature of transcripts. By allowing for reprogrammed translation, these mechanisms can mediate biological responses to stress stimuli. We combined proteomics with ribosome profiling and mRNA sequencing to identify the biological targets of translation control triggered by eukaryotic translation initiation factor 1 (eIF1), a protein implicated in the stringency of start codon selection. We quantified expression changes of over 4,000 proteins and 10,000 actively translated transcripts, leading to the identification of 245 transcripts undergoing translational control mediated by upstream open reading frames (uORFs) upon eIF1 deprivation. The stringency of start codon selection and preference for optimal nucleotide context were largely diminished leading to translational regulation of uORFs with sub-optimal start sites. Affected genes were implicated in energy production and sensing of metabolic stress. Interestingly, knockdown of eIF1 elicited a synergic response from eIF5 and eIF1B.

overall_design: Ribosome profiling and mRNA sequening of human HCT116 cells upon eIF1 knockdown and in control conditions.

first: Daria

last: Fijałkowska

last: Verbruggen

first: Elvis

last: Ndah

first: Veronique

last: Jonckheere

first: Sebastian

last: Tanco

first: Gerben

last: Menschaert

last: Van Damme


title: Pancreas lineage allocation and specifciation are regulated by sphingosine-1-phosphate signalling (13.5 and 15.5 dpc)

first: Anthony

last: Gavalas

overall_design: Analysis was carried out at 13.5 and 15.5 dpc wt embryonic pancreata. Three biological replicates were used for each stage for a total of 6 samples.

first: Ioannis

last: Serafimidis

first: Eva

last: Rodriguez-Aznar

first: Mathias

last: Lesche

first: Kazuaki

last: Yoshioka

first: Yoh

last: Takuwa

first: Andreas

last: Dahl

first: Duojia

last: Pan


title: Regulation of gene transcription and transcription factor chromatin binding by PARP-1 in mouse embryonic stem cells

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

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

overall_design: Refer to individual Series


title: Aire, guardian of immunological tolerance, binds to and activates super-enhancers

status: Public on Jan 22 2017

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School


title: Aire, guardian of immunological tolerance, binds to and activates super-enhancers [ChIP-seq]

summary: ChIP-seq profile of Aire and partners in MECs

overall_design: DAPI-CD45-Ly51loMHCIIhi MECs were single sorted and ChIP-seq profiling was perfomed. For ChIP-seq data analysis Illumina output single-end reads were trimmed to 50bp.

first: Kushagra

last: Bansal

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Aire, guardian of immunological tolerance, binds to and activates super-enhancers [ATAC-seq]

summary: ATAC-seq profiles of MECs and earskin fibroblasts

overall_design: DAPI-CD45-Ly51loMHCIIhi MECs and DAPI-CD45-EpCAM-CD31-Ter-119-Sca-1+ earskin fibroblasts were single sorted and ATAC-seq profiling was perfomed.


title: Genome-wide maps of histone marks, Sox2, Oct4 and PARP-1 in mES cells.

summary: ChIP-seq was performed to analyze genome-wide distribution of PARP-1 and histone marks H3K4me3, H3K27me3 in mES cells, and examine the effect of PARP-1 knockout on Sox2 and Oct4 genome-wide distribution in ES cells.

overall_design: ChIP-seq of  transcription factors were performed in WT or Parp-1-/- mESCs in duplicates, using Illumina HiSeq 2000

first: Ziying

last: Liu

first: W

middle: L


title: Translation of poly(A) tails leads to precise mRNA cleavage and widespread ribosome rescue

city: Bethesda

first: Nicholas

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

summary: Translation of poly(A) tails leads to mRNA cleavage but the mechanism and global pervasiveness of this “nonstop/no-go” decay process is not understood. Here we performed ribosome profiling of short 15-18 nt mRNA footprints to identify ribosomes stalled at 3’ ends of mRNA decay intermediates. We found mRNA cleavage extending hundreds of nucleotides upstream of ribosome stalling in poly(A) and predominantly in one reading frame. These observations suggest that cleavage is closely associated with the ribosome. Surprisingly, ribosomes appeared to stall when as few as 3 consecutive ORF-internal lysine codons were positioned in the A, P, and E sites though significant mRNA degradation was not observed. Endonucleolytic cleavage was widespread, however, at sites of premature polyadenylation and rescue of the ribosomes stalled at these sites was dependent on Dom34. These results suggest this process may be critical when changes in polyadenylation occur during development, tumorigenesis, or when translation termination/recycling is impaired.

overall_design: 14 samples are included in the study (2 mRNA-Seq samples and 12 ribosome footprinting samples). Read sizes were examined for lengths of 15-18 nt or 25-34 nt or both in some cases, reads were aligned by 5' or 3' ends or both in some cases.

first: Rachel

last: Green


title: De novo Assembly and Comparative Analysis of Ten Petal Transcriptome (Brassicaceae) Revealed Phylogenetic Relationships and Genetic control of Flower Color Variation

city: Wuhan

first: Chen

last: Daozong

state: Hubei

address: Shizishan Street · Hongshan District

institute: Huazhong agricultural university

summary: Petal is not only the target of selection by horticulturalists to enhance the ornamental value of plants but also emerged as a unique model system for plant organogenesis studies. It is known that three major groups of pigments, betalains, carotenoids and anthocyanins, are responsible for the attractive natural display of flower colors. While carotenoids and betalains generally yield yellow or red colors, anthocyanins confer a diverse range of color from orange to red to violet and blue. In this study, we collected 11 species (Erysimum cheiri, Malcolmia maritime, Brassica oleracea, Raphanus sativus, Orychophragmus violaceus, Eruca sativa, Orychophragmus violaceus, Iberis amara, Aubrieta x cultorum, Lobularia maritime, Matthiola incana) belong to different tribe in Brassicaceae family with varied flower color and performed petal transcriptome analysis. de novo transcriptome assembly showed that average length of the contigs varied from 631bp in O. violaceus to 1212bp in Matthiola incana which indicated that the complexity of the genomes are different much. Protein homology between these species and those sequenced species in Brassicaceae family are consistent with the known phylogenetic relationships. However, O. violaceus has closer relationships with Sisymbrium irio than expected Brassica species. Clustering analysis of genes in anthocyanin and carotenoids synthesis pathway indicated that while silence or low expression of CCD4 (Carotenoid Cleavage Dioxygenase 4) leading to the yellow color formation in different species, purple or red color variation might result from different genes expression variation. These results not only provide transcriptome data for petal development study but also provide useful information for Brassica flower improvement for ornamental purpose.

sample_organism:
Brassica oleracea
Matthiola incana
Raphanus sativus
Eruca vesicaria subsp. sativa
Erysimum cheiri
Orychophragmus violaceus
Iberis amara
Lobularia maritima
Malcolmia maritima
Aubrieta x cultorum

overall_design: 22 samples were used here, each with two biological replicates. Gene expression value was calculated using the Arabidopsis as reference.

first: Dao-zong

last: Chen

first: Qi

first: Zai-yun

last: Li

first: Xian-hong

last: Ge


title: DDX5-deficiency affects cell fate decisions by regulating lineage specific genes and polycomb repressive complexes

city: Shenzhen

first: Andrew

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology


title: DDX5-deficient affect cell fate decision by regulating lineage specific genes and polycomb repressive complexes [RNA-seq]

summary: RNA-binding proteins (RBPs) are involved in a wide variety of regulatory pathways in mammalian cells. Here, we report that the DEAD-box RBP DDX5 (also known as p68) inhibits induced pluripotency by negatively regulating the expression and function of a non-canonical polycomb complex 1 (PRC1) subunit, RYBP, by modulating microRNA-125b processing. DDX5 loss-of-function, both during reprogramming and the somatic to pluripotent transition, and also in the differentiation of mouse embryonic stem cells, results in the suppression of lineage-specific genes via an RYBP-dependent ubiquitination of histone H2A at K119 (H2AK119ub1). RYBP functions as both transcriptional repressor through PRC1 but also as an activator through its interaction with OCT4 during reprogramming. Diminished DDX5 also potentiates RYBP-mediated recruitment of OCT4 to the promoter of the pluripotency activation gene Kdm2b. These data show that DDX5 down-regulation stimulates silencing of lineage-specific genes by RYBP-PRC1 in the early phase of reprogramming and activation of the pluripotency gene network by RYBP-OCT4 in the later phase of reprogramming.

overall_design: RNA-seq profiles of wild type (WT) and knockout DDX5-/- (also known as p68) mouse ESCs were generated by deep sequencing, Samples were sequenced in triplicate.

first: Huanhuan

first: Ping

last: Lai

first: Hongjie

last: Yao


overall_design: Examination of RYBP and H2AK119ub in WT or DDX5-/- ESCs using ChIP-seq


title: DDX5-deficient affect cell fate decision by regulating lineage specific genes and polycomb repressive complexes [miRNA-seq]

overall_design: Expression profiling of miRNAs in  WT or DDX5-/- ESCs by micro-RNA-seq


title: Whole-genome DNA methylation map of japanese macaque sperm

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

institute: RIKEN

summary: It has been thought that epigenetic changes underlie the evolutionary divergence of phenotype between closely related species. However, the manner in which epigenetic changes are generated remains unknown. Although whole-genome DNA methylation profiles in some somatic tissues and sperm have been reported for humans and chimpanzees, a systematic analysis of these data has been lacking. In this manuscript, therefore, we analyzed these methylomes in detail, identified genomic regions with different DNA methylation levels, and examined the cell-type specificity and its association with changes in genomic sequence. Moreover, we generated a methylation map of Japanese macaque sperm and used it as an out-group to infer the evolutional history of methylation in these regions.

overall_design: Genomic DNA was prepared by a standard procedure from sperm of a male Japanese macaque.  The library for WGBS was constructed by the post-bisulfite adaptor tagging method, and subjected to 100-bp single-end sequencing on Illumina HiSeq1500.

first: Kenji

last: Ichiyanagi


title: Whole-genome DNA methylation maps for human and chimpanzee peripheral blood leukocytes (PBLs).

summary: It has been thought that epigenetic changes underlie the evolutionary divergence of phenotype between closely related species. To study differences in DNA methylation between humans and chimanzees, we collected methylated DNAs from age- and gender-matched PBL samples of the two species, and deeply sequenced.  The map counts were then converted to MEDIPS scores in 100-bp bins, which are related to absolute methylation levels.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: Genomic  DNA samples of PBLs from 4 individuals for each species were pooled, and the pooled samples were flagmented into 200-600 bp by sonication. Methylated DNA fragments were collected by using  the His-tagged MBD1.  The sequence libraries were constructed for total and MBD1-collected DNA fragments by using paired-end sequencing kit (Illumina).  The library was deeply sequenced on Illumina Genome Analyzer II with 75-bp paired-end sequencing.  These reads were aligned to the human (hg19) or chimpanzee (panTro3) genomes using Bowtie.  The aligned results were further processed using MEDIPS, which gave methylation scores in 100-bp windows.


title: PARP-1 Controls the Adipogenic Transcriptional Program by PARylating C/EBPβ and Modulating Its Transcriptional Activity

first: W. Lee

last: Kraus

summary: Poly(ADP-ribosyl)ation (PARylation) is a regulatory post-translational modification of proteins mediated by PARP family members, such as PARP-1.  Although PARP-1 and PARylation have been widely studied, very few examples of definitive biological roles for site-specific PARylation of proteins exist in the literature.  Here we show that C/EBPβ, a key pro-adipogenic transcription factor, is PARylated by PARP-1 at Glu135, as well as two adjacent amino acids (K133 and E139).  PARylation at these sites inhibits C/EBPβ’s DNA binding and transcriptional activities, and attenuates adipogenesis in various cell-based models of adipogenesis.  Interestingly, PARP-1 catalytic activity drops precipitously during the first 48 hours of hormone-induced differentiation, corresponding to a release of C/EBPβ from PARylation-mediated inhibition.  This allows the binding of C/EBPβ to the promoters of pro-adipogenic target genes (e.g., Cebpa, Pparg2), their subsequent expression, and continued differentiation.  In this regard, depletion of PARP-1 or chemical inhibition of its catalytic activity enhances early adipogenic events.  Collectively, our results provide a clear example of how site-specific PARylation of a key transcription factor can affect its molecular and biochemical functions, as well as the biological outcomes that it controls.

overall_design: ChIP-seq (C/EBP beta) were perfomed in 3T3-L1 cells expressing doxycycline inducible HA tagged C/EBP beta LAP wildtype and PARylation site mutant, with or without doxycycline and PARP inhibitor treatment.

first: Xin

last: Luo

first: Keun

middle: W

last: Ryu

first: Dae-Seok

last: Kim

first: Tulip

last: Nandu

first: Lee


title: Transcriptomic, Proteomic, and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish

status: Public on Jan 21 2017

city: Seattle

first: Jeremy

last: Rabinowitz

address: 850 Republican St

institute: University of Washington

summary: Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules, few of which have been identified. Here, we quantified the global abundance of transcripts, proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach, we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions, including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover, 32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus, the identification of proximodistal differences in levels of RNAs, proteins, and metabolites will facilitate future functional studies of positional memory during appendage regeneration.

overall_design: RNA-seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal, middle and distal (15 total samples). Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.


title: Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in Plants

city: Nanchang

first: Dong

last: Wang

state: JiangXi

address: Hong Gu Tan New Road, No. 999

institute: Nanchang University

sample_organism:
Arabidopsis thaliana
Oryza sativa Japonica Group
Zea mays subsp. mays


title: Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in Plants (II)

summary: Long intergenic noncoding RNAs (lincRNAs) are widespread in cellular organisms, however, the origins and functions of many lincRNAs remain to be explored. Transposable elements (TEs) are widely distributed in many eukaryotic genomes, and often account for large fractions of plant and animal genomes. By using strand-specific RNA sequencing, we profiled the expression patterns of lincRNAs in Arabidopsis, rice and maize, and identified TE-associated lincRNAs (TE-lincRNAs). Stress regulation of some TE-lincRNAs was observed in Arabidopsis. Our findings indicate that TE-associated lincRNAs potentially play important roles in plant abiotic stress responses. Moreover, in the Arabidopsis chromatin remodelling mutant ddm1 that has an altered chromatin state, novel lincRNAs including TE-lincRNAs were generated. The novel lincRNAs were inherited in the subsequent generations in the wild type background, suggesting that lincRNAs could act as an adaptive reservoir in eukaryotes.

overall_design: High-depth paired-end RNA-seq from wild type and linRNA mutant Arabidopsis, Each sample contains 3 biological replicates.

first: Jian-Kang

last: Zhu


title: Nucleotide resolution analysis reveals extensive regulation of translation in response to neural depolarization.

city: St Louis

first: Joseph

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

summary: Studies on regulation of gene expression have contributed substantially to understanding mechanisms for long term alterations in neural connectivity in response to activity. Most of these, however, focused on the regulation of mRNA transcription. Here, we utilized high-throughput sequencing coupled with ribosomal footprinting to globally characterize the regulation of translation in neural cells in response to depolarization-mediated neural activity. We identify substantial and complex regulation of translation, with hundreds of transcripts demonstrating changes in ribosome occupancy independent of transcriptional changes. These changes are partially mediated by features in the sequence —notably uAUGs and secondary structure in the 5’UTR— both of which predict downregulation in response to activity. These transcripts are also disproportionately targets of Fmrp and include genes implicated in autism in humans.  Our findings indicate that in neurons activity plays a critical role in regulating mRNA translation across the genome and suggest dysregulation of the process may contribute to disease.

overall_design: 3 replicates were prepared for both  Kcl-stimulated and unstimulated neuronal cultures from P0 FVB mouse cortices.

first: Jasbir

last: Dalal

first: Chengran

last: Yang

first: Darshan

last: Sapkota

first: Allison

last: Lake

first: David

last: O'Brien


title: Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in Plants (I)

platform_organism:
Arabidopsis thaliana
Oryza sativa Japonica Group
Zea mays subsp. mays

overall_design: High-depth paired-end RNA-seq from wild type Arabidopsis, rice, maize and ddm1 mutant Arabidopsis. Each sample contains 3 biological replicates.


title: RNA-Seq Analysis of Gfi1b KO Megakaryocytes

city: Montreal

first: Möröy

last: Tarik

state: Quebec

address: 110 Pine avenue West

country: Canada

institute: Insititut de Recherches Cliniques

summary: Megakaryocytes isolated from Gfi1b flox/flox mice carrying PF4-Cre or not, and from Gfi1b flox/flox mice carrying ROSA-Cre-ERT with or without tamoxifen injection were analyzed for differential expression by RNA-Seq

overall_design: A sample of each Gfi1b wild-type and Knock-Out from each model was analyzed

first: Hugues

last: Beauchemin

first: Tarik

last: Möröy

first: Charles

last: Vadnais


title: miR-182 regulates Slit2-mediated axon guidance by modulating the local translation of a specific mRNA

city: Irapuato

first: Cei

last: Abreu-Goodger

state: Guanajuato

address: Km. 9.6 Libramiento Nte Carr Leon-Irapuato

country: Mexico

institute: Langebio - Cinvestav

summary: During brain wiring, mRNAs are trafficked into axons and growth cones where they are differentially translated in response to extrinsic signals. Differential control of local protein synthesis mediates neuronal compartment-specific behaviors that aid axon guidance.  Yet little is understood about how specific mRNAs are selected for translation. Here we have investigated the local role of microRNAs (miRNAs) in mRNA-specific translation during axon pathfinding of Xenopus laevis retinal ganglion cell (RGC) axons. Profiling experiments revealed a rich repertoire of axonal miRNAs in developing RGC axons and identified miR-182 as one of the most abundant. Loss of miR182 impairs Slit2-induced growth cone repulsion and causes RGC axon targeting defects in vivo. To aid miRNA target prediction, we also profiled mRNA expression in RGC axons. Our results show that miR-182 targets cofilin1 mRNA in RGC growth cones and modulates its local translation in response to Slit2.

overall_design: Two biological replicates, one condition

first: Anaïs

last: Bellon

first: Archana

last: Iyer

first: Simone

last: Bridi

first: Flora

last: Lee

first: Cesaré

last: Ovando-Vázquez

first: Eloina

last: Corradi

first: Sara

last: Longhi

first: Michela

last: Rocuzzo

first: Stephanie

last: Strohbuecker

first: Sindhu

last: Naik

first: Peter

last: Sarkies

first: Eric

last: Miska

first: Christine

last: Holt

first: Marie-Laure

last: Baudet


title: Transcriptome analysis of mouse embryonic stem cells upon PARP-1 knockout.

first: W. Lee

last: Kraus

summary: RNA-seq was performed in both wild type and parp1-/- ES cells to check the effect of PARP-1 depletion on gene expression profile in mESC.

overall_design: Two biological replicates were performed in both wild type and Parp-1-/- conditions.

first: Ziying

last: Liu

first: W


title: RNA-Seq and ATAC-Seq in SMARCD2 k/d NB4 cells with/without ATRA differentiation

status: Public on Jan 20 2017

city: Garching

first: Christian

last: Mertes

state: BY

address: Boltzmannstraße 3

department: Informatics

institute: Technical University Munich

overall_design: Refer to individual Series


title: Genome wide DNA accessibility screen by ATAC-Seq in SMARCD2 k/d NB4 cells with/without ATRA differentiation

summary: We report differential chromatin accessiblity in the human AML cell line NB4 that can be partially differentiated into neutrophil granulocytes by 1µM ATRA for 2d or the vehicle DMSO only ((mock))

overall_design: Chromatin accessibility in CTRL vs SMARCD2-specific shRNA1 and SMARCD2-specific shRNA2

first: Maximilian

last: Witzel

first: Daniel

last: Petersheim

first: Christoph

last: Klein

first: Julien

last: Gagneur


title: RNA sequencing of ID4-GFP Bright and ID4-GFP Dim spermatogonia from postnatal day 8 transgenic Id4-Gfp (LT11) mouse pups

city: Pullman

first: Jon

last: Oatley

address: 1770 NE Stadium Way

institute: Washington State University

summary: Spermatogonia expressing the highest levels of ID4 (ID4-GFP Bright) represent a population highly enriched for spermatogonial stem cells (SSC) while those expressing lower levels (ID4-GFP Dim) are the putative immediate progenitors.  Comparing the transcriptome of these populations can provide insight into the SSC to progenitor transition.

overall_design: Comparison of transcriptomes of ID4-GFP Bright and ID4-GFP Dim spermatogonia from postnatal day 8 mouse pups

first: Aileen

last: Helsel


title: RNA-Seq in SMARCD2 k/d NB4 cells with/without ATRA differentiation

summary: We report differential gene expression in the human AML cell line NB4 that can be partially differentiated into neutrophil granulocytes by 1µM ATRA for 2d or the vehicle DMSO only ((mock))

overall_design: Chromatin accessibility in CTRL vs SMARCD2-specific shRNA1 and SMARCD2-specific shRNA2. All biological samples were sequenced twice, i.e. technical replicates.


title: High-throughput manual-quality annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing (CLS)

city: Barcelona

last: Lagarde

address: Dr. Aiguader 88

department: Bioinformatics and Genomics

country: Spain

institute: CRG

summary: Accurate annotations of genes and their transcripts is a foundation of genomics, but no annotation technique presently combines throughput and accuracy. As a result, the GENCODE reference collection of long noncoding RNAs remains far from complete: many are fragmentary, while thousands more remain uncatalogued. To accelerate lncRNA annotation, we have developed RNA Capture Long Seq (CLS), combining targeted RNA capture with third generation long-read sequencing. We present an experimental re-annotation of the entire GENCODE intergenic lncRNA populations in matched human and mouse tissues. CLS approximately doubles the complexity of targeted loci, both in terms of validated splice junctions and transcript models. Through its identification of full-length transcript models, CLS allows the first definitive measurement of promoter features, gene structure and protein-coding potential of lncRNAs. Thus CLS removes a longstanding bottleneck of transcriptome annotation, generating manual-quality full-length transcript models at high-throughput scales.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA Capture Long-Seq study of 6 tissue samples in human and mouse

first: Barbara

last: Uszczynska-Ratajczak

first: Silvia

last: Carbonell

first: Carrie

last: Davis

first: Thomas

last: Gingeras

first: Adam

last: Frankish

first: Jennifer

last: Harrow

first: Roderic

last: Guigo

first: Rory

last: Johnson


title: Analysis of Thermosynechococcus elongatus BP1 and Meiothermus ruber strain A co-cultured under variable light and oxygen conditions

city: Richland

first: Ryan

middle: Scott

last: McClure

state: Washington

address: 902 Battelle Boulevard

institute: Pacific Northwest National Laboratory

summary: The transcriptional response of the cyanobacteria T. elongatus to co-cultiavation with a heterotrophic partner M. ruber was examined under three varying light levels and three varying oxygen levels.

sample_organism:
Meiothermus ruber
Thermosynechococcus vestitus BP-1

overall_design: Three light levels were examined: low (197 µmol photons m-2 sec-1), mid (1190 µmol photons m-2 sec-1), and high (1995 µmol photons m-2 sec-1) all with oxygen at a partial pressure of zero .  Three oxygen levels were also examined: low (oxygen at 7% of atmosphere), mid (oxygen at 150% of atmosphere) and high (oxygen at 217% of atmosphere) all at a light level of 197 µmol photons m-2 sec-1.  T. elongatus was examined both axenically and with a hetertrophic partner of each of these six conditions.  The high light condition overlaps with the low oxygen condition. Each condition used two biological replicates except for HighLight_LowO2 which used 4 biological replicates for a total of 12 data points

first: Hans

last: Bernstein

first: Meng

last: Markillie


title: ID4 levels dictate the stem cell state in mouse spermatogonia

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


title: E(Pc) ChIP-seq experiment in fruitfly testis somatic gonadal cells and RNA-seq experiment in fruitfly testis

city: baltimore

first: Xin

last: Chen

address: 3400 N Charles St

department: Biology

institute: The Joihns Hopkins University

summary: With the ChIP-seq experiment, we identified direct target genes of E(Pc) specifically in somatic gonadal cells. We found that the E(Pc)-binding genes are enriched with signaling pathway components, consistent with our functional data showing prevailing germline defects even when E(Pc) function is exclusively compromised in somatic gonadal cells. In addition, we also performed RNA-seq to compare transcriptomes between E(Pc) knockdown testes and control testes.

overall_design: For ChIP-seq, we used fly testis expressing GFP-tagged E(Pc) specifically in somatic gonadal cells by Tj promoter driven GAL4>UAS system. ChIP-seq with GFP antibody was performed. For RNA-seq, RNA was purified from Tj-Gal4 or Tj-Gal4/+; UAS-E(Pc) shRNA/+ testes.

first: Lijuan

last: Feng

first: Zhen

last: Shi


title: Whole-genome DNA methylation maps for primate tissues

first: Kei

last: Fukuda

sample_organism:
Macaca fuscata
Pan troglodytes
Homo sapiens


title: Genome-wide mapping of chromatin landscape in cerebellar granule cells

city: Heidelberg

first: Haikun

last: Liu

address: INF 581

institute: DKFZ

summary: We mapped the binding sites of Chd7 in cerebellar granule cells, and compared with the pattern of H3K27ac. To examine the impact of Chd7 loss to Top2b binding, we mapped the binding sites of Top2b in control and Chd7 mutant cells

overall_design: Examine the binding pattern of Chd7, H3K27ac and Top2b

first: Weijun

first: Daisuke

last: Kawauchi


title: Phosphate solubilization and gene expression of phosphate-solubilizing bacterium Burkholderia multivorans WS-FJ9 under different levels of soluble phosphate

city: Nanjing

first: Qingwei

last: Zeng

address: 159 Longpan road

institute: Nanjing Forestry University

summary: Phosphate-solubilizing bacteria (PSB) have the ability to dissolve insoluble phosphate and enhance soil fertility. However, the growth and mineral phosphate solubilization of PSB could be affected by exogenous soluble phosphate and the mechanism has not been fully understood. In the present study, the growth and mineral phosphate-solubilizing characteristics of PSB strain Burkholderia multivorans WS-FJ9 were investigated at six levels of exogenous soluble phosphate (0, 0.5, 1, 5, 10 and 20 mM). The WS-FJ9 strain showed better growth at high levels of soluble phosphate. The phosphate-solubilizing activity of WS-FJ9 reduced as the soluble phosphate concentration increased, as well as the production of pyruvic acid. Transcriptome profiling of WS-FJ9 at three levels of exogenous soluble phosphate (0, 5 and 20 mM) identified 446 differentially expressed genes, among which 44 genes were continuously up-regulated when soluble phosphate concentration increased and 81 genes were continuously down-regulated. Some genes related to cell growth were continuously up-regulated which would account for the better growth of WS-FJ9 at high levels of soluble phosphate. Genes involved in glucose metabolism, including glycerate kinase, 2-oxoglutarate dehydrogenase, and sugar ABC-type transporter were continuously down-regulated which indicates that metabolic channeling of glucose towards phosphorylative pathway was negatively regulated by soluble phosphate.

overall_design: In the present study, the growth and mineral phosphate-solubilizing characteristics of PSB strain Burkholderia multivorans WS-FJ9 were investigated at six levels of exogenous soluble phosphate (0, 0.5, 1, 5, 10 and 20 mM).Transcriptome profiling of WS-FJ9 at three levels of exogenous soluble phosphate (0, 5 and 20 mM) were analysised.

first: Xiaoqin

last: Wu


title: Response to low-level phage predation in Staphylococcus aureus biofilms

city: Oviedo

first: Lucia

last: Fernandez

address: C/ Francisco Pintado Fe 26

institute: Instituto de Productos Lacteos de Asturias (IPLA-CSIC)

summary: An important lesson from the war on pathogenic bacteria has been the need to understand the physiological responses and evolution of natural microbial communities. Bacterial populations in the environment are generally forming biofilms subject to some level of phage predation. These multicellular communities are notoriously resistant to antimicrobials and, consequently, very difficult to eradicate. This has sparked the search for new therapeutic alternatives, including phage therapy. This study demonstrates that S. aureus biofilms formed in the presence of a non-lethal dose of phage phiIPLA-RODI exhibit a unique physiological state that could potentially benefit both the host and the predator. Thus, biofilms formed under phage pressure are thicker and have a greater DNA content. Also, the virus-infected biofilm displayed major transcriptional differences compared to an untreated control. Significantly, RNA-seq data revealed activation of the stringent response, which could slow down the advance of the bacteriophage within the biofilm. The end result would be an equilibrium that would help bacterial cells to withstand environmental challenges, while maintaining a reservoir of sensitive bacterial cells available to the phage upon reactivation of the dormant carrier population.

overall_design: 6 samples were analyzed, correponding to 3 biological replicates of two different conditions (sample with phage and control biofilm)

first: Silvia

last: Gonzalez

first: Ana

middle: B

last: Campelo

first: Beatriz

last: Martinez

last: Rodriguez

first: Pilar

last: Garcia


title: A screen for reactivation of MeCP2 on the inactive X-chromosome identifies BMP/TGF-b superfamily as a regulator of maintenance of XIST expression

first: Eric

middle: Jan

last: Foss

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: X-chromosome inactivation (XCI) is an epigenetic phenomenon that renders one of the two X-chromosomes in female cells transcriptionally silent, ensuring that X-linked gene dosage matches that in males, who have only one copy of the X chromosome.  When a mutation of an X-linked gene is heterozygous, as it is in most girls with Rett syndrome, a neurodevelopmental disorder caused by a mutation MeCP2 gene, the presence of the mutated allele on the active X chromosome entails transcriptional inactivation of the wild type allele on the inactive X, resulting in complete loss of gene function. Reactivation of the silenced wild-type copy of MeCP2 therefore presents a potential therapeutic strategy for Rett syndrome. To identify genes that silence MeCP2 on the Xi that could prove useful therapeutic targets, we carried out a screen for genes whose downregulation reactivated a MeCP2 reporter on the Xi.  The 30 genes we have identified comprise seven functional groups revealing a genetic circuitry required for maintenance of X-chromosome inactivation in differentiated cells and a large number of targets suitable for pharmacologic intervention.

overall_design: select for shRNAs that activate MeCP2 on inactive X that has been fused to Hygromycin-resistance gene

first: Antonio

last: Bedalov


title: Chd7 is indispensable for mammalian brain development through activation of a neuronal differentiation program


title: Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex (Exome-seq)

city: Chapel Hill

first: Gary

last: Johnson

state: NC

address: 4009 Genetic Medicine Building, 120 Mason Farm Road

department: Pharmacology

institute: University of North Carolina School of Medicine

type: Genome variation profiling by high throughput sequencing

summary: Targeting the dysregulated BRaf-MEK-ERK pathway in cancer has increasingly emerged in clinical trial design. Despite clinical responses in specific cancers using inhibitors targeting BRaf and MEK, resistance develops often involving non-genomic adaptive bypass mechanisms.   Inhibition of MEK1/2 by trametinib in triple negative breast cancer (TNBC) patients induced dramatic transcriptional responses, including upregulation of receptor tyrosine kinases (RTKs) comparing tumor samples before and after one week of treatment.  In preclinical models MEK inhibition induced genome-wide enhancer formation involving the seeding of BRD4, MED1, H3K27 acetylation and p300 that drives transcriptional adaptation.  Inhibition of P-TEFb associated proteins BRD4 and CBP/p300 arrested enhancer seeding and RTK upregulation. BRD4 bromodomain inhibitors overcame trametinib resistance, producing sustained growth inhibition in cells, xenografts and syngeneic mouse TNBC models.  Pharmacological targeting of P-TEFb members in conjunction with MEK inhibition by trametinib is an effective strategy to durably inhibit epigenomic remodeling required for adaptive resistance.

overall_design: EpCAM/CD49f-positive and EpCAM/CD49f-negative subpopulations of SUM-229PE cell line (Asterand).

first: Jon

middle: S

last: Zawistowski


title: mRNA profiling of Apis mellifera larvae fed with diets containing quercetin

city: Urbana

first: May

last: Berenbaum

state: Illinois

address: 505 S. Goodwin Avenue

department: Entomology

institute: University of Illinois at Urbana-Champaign

summary: To determine the impact of quercetin on honeybee development and physiology, we conducted an RNASeq analysis of gene expression in neonate larvae exposed for three days to control “bee candy” diet (comprising sucrose and sugar syrup) or diets to which 0.1 mM or 0.25 mM quercetin was added.

overall_design: Three replicates of each treatment: A. mellifera larvae in control diet, A. mellifera larvae in diet with added 0.25mM quercetin, and A. mellifera larvae in diet with added 0.1 mM quercetin

first: Wenfu

last: Mao


title: IL-33 regulates metaplasia and macrophage polarization in the stomach.

city: Huntsville

first: Nripesh

last: Prasad

state: Alabama

address: 601 Genome way

institute: Hudson Alpha Institute for Biotechnology

summary: Alternatively-activated macrophages (M2) are known to play a critical role in intestinalization of spasmolytic polypeptide-expressing metaplasia (SPEM), which is a precursor to gastric adenocarcinoma.  However, the precise mechanism(s) and critical mediators produced by M2 macrophages that lead to SPEM are unknown.  Using established murine models of metaplasia in the stomach, the aim of the present study was to determine how M2 macrophages induce intestinalized SPEM.  Macrophages from the stomach corpus of mice with SPEM (DMP-777-treated) or advanced intestinalized SPEM (L635-treated) were isolated and RNA sequencing was performed. IL-33 was the most upregulated cytokine in macrophages associated with intestinalized SPEM.  L635-treated IL-33 knock out mice did not develop metaplasia, suggesting that IL-33 is required for the induction of SPEM after acute parietal cell loss. While the loss of IL-33 did not reduce macrophage recruitment into the mucosa, infiltrating macrophages were not M2 polarized.  We conclude that IL-33 is necessary for both the induction of mucous metaplasia (SPEM) in the stomach and polarization towards M2 in recruited macrophages.   Our data suggest that the inflammatory pathway in the stomach after parietal cell loss resembles pathways associated with allergy-induced airway inflammation, which implicates novel treatment options for gastritis patients to prevent gastric cancer.

overall_design: FAC sorted macrophages (F4/80 positive cells) isolated from the corpus in mice treated with DMP-777 and L635 to induce SPEM and intestinalized SPEM respectively for RNA sequencing.

first: James

middle: R

last: Goldenring

first: Christine

last: Petersen


title: The mammalian LINC complex controls mechanosensing at a genome-wide level

city: Gainesville

first: Tanmay

last: Lele

state: FL

address: Bldg 723, Room 329

department: Chemical Engineering

institute: University of Florida


title: ATAC-seq of Chd7 WT and mutant cerebellar granule neuron progenitors

first: Haikun

last: Liu

summary: We performed ATAC-seq to profile the open chromatin lanscape in primary Chd7 WT and mutant GNPs. By analyzing the differentiate peaks between WT and mutant, we identified Chd7-dependent maintance of open chromatin at many neuronal genes.

overall_design: ATAC-seq of Chd7 WT and mutant GNPs

first: Weijun

last: Feng

first: Daisuke

last: Kawauchi


title: RNA-seq of Chd7 wild type and mutant granule neuron progenitors

summary: We identified genes that are regulated by Chd7 in GNPs

overall_design: Examination of gene expression in 3 groups of GNPs: Chd7 wild type, Chd7 het mutant and Chd7 hom mutant


title: Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex (RNA-seq)

overall_design: 64 experimental samples; replicates are indicated in sample title


title: Essential role of the transcription factor Bhlhe41 in regulating the self-renewal and BCR repertoire of B-1a cells

status: Public on Jan 19 2017

city: Vienna

first: Maria

last: Fischer

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology

summary: The innate-like B-1a cells provide a first line of defense against pathogens, and yet little is known about their transcriptional control. Here we identified an essential role of the transcription factor Bhlhe41, with a lesser contribution of Bhlhe40, in controlling late stages of B-1a cell differentiation. Bhlhe41/Bhlhe40 mutant B-1a cells were strongly reduced and had an abnormal cell-surface phenotype and altered B-cell receptor (BCR) repertoire, as exemplified by loss of the phosphatidylcholine-specific Vh12/Vk4 BCR. Expression of a pre-rearranged Vh12/Vk4 BCR failed to rescue the mutant phenotype and revealed enhanced proliferation accompanied with increased cell death, implicating Bhlhe41 in controlling the self-renewal of B-1a cells. Bhlhe41 directly repressed the expression of cell cycle regulators and inhibitors of BCR signaling, while activating pro-survival cytokine signaling.

overall_design: 22 samples in total: A) 18 RNA-seq samples in 2 cell types: B-1a cells (WT, DKO, 6 replicates each; Vh12/Vk4 Tg, Vh12/Vk4 Tg DKO, 2 replicates each), B-1b cells (WT, DKO, 1 replicate each) B) 2 ChIP-seq samples in 2 cell types: B-1a cells (Bhlhe41, 1 replicate), pro-B cells (input) C) 2 ATAC-seq samples in 1 cell type: B-1a cells (Vh12/Vk4 Tg, Vh12/Vk4 Tg DKO, 1 replicate each)

first: Taras

last: Kreslavsky

first: Bojan

last: Vilagos

first: Hiromi

last: Tagoh

first: Daniela

middle: K

last: Poliakova

first: Tanja

last: Schwickert

first: Miriam

last: Wöhner

first: Markus

last: Jaritz

first: Siegfried

last: Weiss

first: Reshma

last: Taneja

first: Moritz

middle: J

last: Rossner

first: Meinrad

last: Busslinger


title: Spontaneous single-copy loss of TP53 in human embryonic stem cells markedly increases cell proliferation and survival [RNA-Seq]

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

summary: The potential safety issues related to the acquisition of common genomic aberrations in hPSC cultures are well-recognized, but these risks have not been evaluated for sporadic mutations. Here, we explore whether a sporadic mutation that spontaneously arose in a hESC culture consisting of a single-copy deletion of chr17p13.1 would confer a survival advantage to the mutant cells. Compared to wild-type cells with two normal copies of the chr17p13.1 region, the mutant cells displayed a selective advantage when exposed to stressful conditions, and retained a higher percentage of pluripotent cells after two weeks of in vitro differentiation. Knockdown of TP53, which is a gene encompassed by the deleted region, in wild-type cells mimicked the chr17p13.1 deletion phenotype. RNA sequencing analysis showed differential expression of genes in pathways related to proliferation and differentiation. Thus, phenotypic implications of sporadic mutations must be taken into consideration before using the hPSC for clinical applications.

overall_design: Triplicate cDNA libraries of two mutant WA09 lines with a single-copy deletion of chr17p13.1, and two wild-type WA09 lines, for a total of 12 libraries were sequenced using Illumina HiSeq 2500. The sequence reads were mapped to hg19 reference genome and hits that passed quality filters were analyzed for differential expression.

first: Hadar

last: Amir

first: Louise

middle: C

last: Laurent


title: Spontaneous single-copy loss of TP53 in human embryonic stem cells markedly increases cell proliferation and survival

overall_design: Refer to individual Series


title: Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex

first: Gary

last: Johnson

type: Methylation profiling by genome tiling array


title: Artemisinins target GABA receptor signaling to induce alpha to beta cell transdifferentiation

first: Christoph

last: Bock

address: Lazarettgasse 14

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Type 1 diabetes is characterized by the destruction of pancreatic beta cells, and generating new insulin-producing cells from other cell types is a major aim of regenerative medicine. One promising approach is transdifferentiation of developmentally related pancreatic cell types including glucagon-producing alpha cells. In a genetic model, overexpression of the master regulatory transcription factor Pax4 or loss of its counterplayer Arx are sufficient to induce the conversion of alpha cells to functional beta-like cells. Here we identify artemisinins as small molecules that functionally repress Arx and induce beta-cell characteristics in alpha cells. We show that the protein gephyrin is the mammalian target of these antimalaria drugs. Finally, we demonstrate that gephyrin-mediated enhancement of GABAA receptor signaling is the mechanism of action of these molecules in pancreatic transdifferentiation. Our results indicate that gephyrin is a novel druggable target for the regeneration of pancreatic beta cell mass from alpha cells.

overall_design: Transcriptional dissection of Artemether treated, human pancreatic islets of one donor using single-cell RNA-seq

first: Jin

last: Li

first: Thomas

last: Frogne

first: Monica

last: Courtney

first: Kilian

middle: V

last: Huber

first: Caterina

last: Sturtzel

first: Tamara

last: Casteels

first: Charles-Hugues

last: Lardeau

first: Johanna

last: Klughammer

first: Matthias

last: Farlik

first: Sara

last: Sdelci

first: Igor

last: Baburin

first: Robin

middle: A

last: Kimmel

first: Peter

last: Majek

first: Florian

middle: M

last: Pauler

last: Penz

first: Alexey

last: Stukalov

first: Manuela

last: Gridling

first: Katja

last: Parapatics

first: Charlotte

last: Barbieux

first: Ekaterine

last: Berishvili

first: Andreas

last: Spittler

first: Jacques

last: Colinge

first: Keiryn

last: Bennett

first: Dirk

last: Meyer

first: Steffen

last: Hering

first: Martin

last: Distel

first: Giulio

last: Superti-Furga

first: Patrick

last: Collombat

first: Jacob

last: Hecksher-Sørensen

first: Stefan

last: Kubicek


title: Chromatin regulation by the NuA4 acetyltransferase complex is mediated by essential interactions between Enhancer of Polycomb (Epl1) and Esa1

first: Lorraine

last: Pillus

address: 9500 Gilman Drive

department: Biological Sciences

summary:
Enzymes that modify and remodel chromatin are subunits in broadly conserved macromolecular complexes. One key chromatin modification is the dynamic acetylation of histones by opposing activities of acetyltransferase and deacetylase complexes. Among the acetyltransferases, the NuA4 complex containing Tip60 or its Saccharomyces cerevisiae ortholog, Esa1, is of particular significance because of its roles in crucial genomic processes including DNA damage repair and transcription. The catalytic subunit Esa1 is essential, as are five non-catalytic NuA4 subunits. We found that of these non-catalytic subunits, only deletion of Enhancer of polycomb (Epl1) can
be bypassed by loss of a major deacetylase complex. This is a property shared by Esa1. Non-catalytic complex subunits are often critical for complex assembly, stability, genomic targeting, substrate specificity and regulation. Understanding the essential cellular role of Epl1 has been limited, a limitation now overcome by the discovery of its bypass suppression. Here, we present the first comprehensive in vivo study of Epl1 upon complete cellular loss of Epl1 using the powerful tool of suppression combined
with transcriptional and mutational analyses. Our results highlight functional parallels between Epl1 and Esa1 and further illustrate that the structural role of Epl1 is important for promotion of Esa1 activity. This conclusion is strengthened by our dissection of Epl1 domains required in vivo for interaction with specific NuA4 subunits, histone acetylation, and chromatin targeting. These results provide new insights for the conserved, essential nature of Epl1 and its homologs among organisms, such as EPC1/2 in humans, which
is frequently altered in cancers.

overall_design: Ribodepleted RNA profiles of WT and piccolo-NuA4 bypass strains were generated by RNA-seq, in triplicate, using Illumina Hi-Seq2500

first: Naomi

last: Searle

first: Ana

last: Torres-Machorro