title: Metallothionein I as a direct link between therapeutic hematopoietic stem/progenitor cells and cerebral protection in stroke

city: Osakasayama

first: Seiichi

last: Omura

state: Osaka

address: 377-2 Ohnohigashi

department: Department of Microbiology

institute: Kindai University Faculty of Medicine

summary:
Background: Increasing evidence indicates stem cell transplantation may be an effective stroke treatment but little is known about the direct impact of transplanted cells on injured brain tissue. We investigated the effects of lineage negative murine hematopoietic stem/progenitor cells (HSPCs) on the cerebral microcirculation following ischemia-reperfusion injury (I/RI). Following subsequent evaluation of the mRNA transcriptome of the explanted HSPCs, we assessed whether metallothionein (MT)-1, (increased in explanted HSPCs from I/R mice) administration was able to evoke similar neuro-protection following cerebral I/RI.
Methods and Results: Murine HSPCs administered intravenously 24 hours (h) post cerebral I/R were selectively recruited to the brain of I/RI mice. Mice treated with HSPCs displayed decreased disease severity for up to 2-weeks post cerebral I/R, as evidenced by decreased mortality rate, decreased infarct volume, improved functional outcome, reduced microglial activation and elevated plasma levels of anti-inflammatory interleukin-10. Using confocal intravital microscopy, we found that transplanted cells had emigrated into the brain parenchyma and that RNA-seq analysis of explanted HSPCs indicated significantly increased levels of metallothionein transcripts, in particular MT-1. We further determined that treatment of mice with MT-1 significantly reduced neurological score and IV.
Conclusions: These studies provide further evidence for HSPCs as a promising therapeutic strategy in promoting repair following cerebral I/RI, potentially via a MT-1 mechanism.

overall_design: Murine HSPCs were administered into mice with I/RI intravenously 24 hours post cerebral I/R and selectively recruited to the brain.  RNA profiles of explanted HSPCs were determined by RNA sequencing.

first: Helen

last: Smith

first: Shantel

last: Vital

first: Felix

last: Becker

first: Ikuo

last: Tsunoda

first: Felicity

last: Gavins


title: RNA sequencing Facilitates Quantitative Analysis of luminal breast cancer cells and basal breast cancer cells Transcriptomes

status: Public on Feb 20 2018

city: Shanghai

first: Lixing

last: Zhan

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

country: China

institute: Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: We conduct transcriptome comparison of lumianl breast cancer cells and basal cells to gain genomic insights on the biological processes. More than 3000 known genes were found changed in basal breast cancer cells. Ingenuity Pathway Analysis _IPA_ and Gene Set Enrichment Analysis _GSEA_ show that the prominent altered pathways in basal cells are related to regulation of actin-based motility, JAK/STAT3 signaling pathway.

overall_design: Genome-wide expression profiling of luminal breast cancer cellsMCF-7,T47D,BT-474 and basal breast cancer cells SUM-159,HBL-100,BT-549.  Total RNA was isolated . Each is tested in duplicate.

first: Renxu

last: Chang


title: The FlbA-regulated transcription factor FusR of Aspergillus niger is involved in production of fumonisin

status: Public on Feb 21 2018

city: Utrecht

first: Robin

last: Ohm

address: Padualaan 8

country: Netherlands

institute: Utrecht University

summary: Colonies of Aspergillus niger secrete proteins throughout the colony except for the sporulating zone. Inactivation of flbA results in colonies that are unable to reproduce asexually and that secrete proteins throughout the mycelium. In addition, the ΔflbA strain shows cell lysis and has thinner cell walls. This pleiotropic phenotype is associated with differential expression of 38 transcription factor genes. Here, the impact of inactivation of one of these regulatory genes, fusR, was assessed. Mycelium of ΔfusR and its control strain MA234.1 was subjected to whole genome expression analysis, which revealed that 10 out of 15 genes of the fumonisin biosynthetic gene cluster were strongly downregulated in ΔfusR.

overall_design: mRNA profiles from ΔfusR and the control strain MA234.1 were generated by Illumina Hiseq using duplicate samples from liquid shaken cultures.

first: David

last: Aerts

first: Esther

middle: E

last: Hauer

middle: A

first: Han

last: Wösten


title: Retinoic Acid Induced Transcriptional Repressor HIC1 is Required for Suppressive Function of Human Induced Regulatory T cells [RNA-Seq 2]

city: Espoo

first: Sini

last: Rautio

address: Konemiehentie 2

country: Finland

institute: Aalto University

summary: Human CD4 positive T cells were isolated from cord blood using CD4 positive isolation kit from Dynal.  Cells were activated with plate bound anti-CD3 and soluble anti-CD28 in presence (iTreg) or absence (Th0) of IL2, TGF beta and ATRA. The cells were harvested at 0, 0.5, 1, 2, 4, 6, 12, 24, 48, and 72 hours.

overall_design: Comparing the gene expression in activated CD4+ cells and iTreg differentiated cells in human. 9 time points, 3 replicates for each time point.

first: Riitta

last: Lahesmaa


title: Genome-wide small RNAtranscriptome analysis during dehydration and recovery in gametophores of  Physcomitrella patens

status: Public on Feb 22 2018

city: Beijing

first: Lihong

last: Xiao

address: No.105 North Road of West 3rd-ring Road.Haidian District

institute: Capital Normal University

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNA transcript abundances were analyzed with samples taken from hydrated (HD), moderate dehydration (MDH), desiccated (SDH), partially recovered (PRE) and fully recovered (FRE) gametophores of P. patens by using next generation sequencing. Totally, 147 microRNAs were identified as differentially expressed miRNAs.The results provided insight for exploring the mechanisms of desiccation tolerance and their evolution.

overall_design: Examination of miRNA transcript abundances in hydrated (HD), moderate dehydration (MDH), desiccated (SDH), partially recovered (PRE) and fully recovered (FRE) gametophores, for each treatment, two biological replicates were included.


title: Single cell transcriptome datasets of murine B cell commitment

city: Yokohama

first: Tomokatsu

last: Ikawa

state: Kanagawa

address: 1-7-22, Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

summary: To identify the “time-lapse” TF networks during B lineage commitment, we established multipotent progenitors harboring a tamoxifen-inducible form of Id3, an in vitro system where virtually all cells became B cells within 6 days by simply withdrawing 4-OHT. In this study, single cell transcriptomic analysis at pre- and post-commitment was performed using the culture system. In addition, we also performed single cell RNA-seq analysis of B cell precursor populations (LMPP, CLP and pro-B cells) in murine bone marrow.

overall_design: Single cell transcriptomic profiles of multipotent and B committed cells in iLS system and BM-derived B cell precursor populations  were analyzed using Chromium Single Cell 3' Solution system (10x genomics).

first: Tomohiro

last: Miyai

first: Yukie

last: Kashima

first: Yutaka

last: Suzuki

first: Eiryo

last: Kawakami


title: Impact of hypothermic preservation of mouse kidney resident immune cells

city: Stanford

first: Wanxin

last: Wang

state: CA

address: James H Clark Center, 318 Campus Drive, room E300

country: USA

institute: Stanford Univeristy

summary: With the growing interest in studying primary tissue samples by single cell transcriptome analysis, there is an emerging demand for a preservation strategy that enables sample transportation and storage. In this study, we describe a simple and general strategy that preserves primary tissues at hypothermic temperature. Using FACS and single-cell RNAseq, we demonstrated the effectiveness of this strategy in maintaining cell viability, cell population heterogeneity, and cell transcriptome integrity for primary tissues that underwent up to 3 days of preservation.

overall_design: Examine the impact of hypothermic preservation on mouse kidney resident immune cells over up to 4 days at single-cell resolution

first: Stephen

middle: R

last: Quake


title: Translational control of ERK signalling pathway by the mRNA cap-binding protein 4EHP

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: microRNA (miRNA)-mediated gene silencing is commonly deregulated in a wide variety of diseases. Therefore, a better understanding of how miRNAs govern the translation and stability of mRNAs is of paramount importance. We recently demonstrated that the cap-binding protein 4EHP is recruited by the miRNA machinery to effect translational repression. However, the impact of 4EHP on regulation of endogenous mRNAs and its role in cell biology is debated. Herein, using the ribosome profiling assay, we identify a subset of endogenous mRNAs that are sensitive to translational repression by 4EHP. We show that expression of DUSP6, a phosphatase that reverses ERK1/2 phosphorylation, is regulated by 4EHP. This regulation, which occurs exclusively at the level of mRNA translation, without affecting the stability of Dusp6 mRNA, is engendered through 4EHP- and miRNA-dependent elements in Dusp6 3´UTR. Consequently, 4EHP protein controls ERK1/2 phosphorylation, promotes cell growth and inhibits apoptosis. Our data reveal a crucial role for translational control mechanisms in the regulation of the ERK pathway.

overall_design: Ribosome profiling and mRNA-seq in 4EHP KO and WT MEFs.

first: Seyed

middle: M

last: Jafarnejad


title: Gene expression profile of human placenta from T. Cruzi infected mothers

city: Buenos Aires

first: Natalia

middle: Anahí

last: Juiz

address: 2490, Vuelta de Obligado

country: Argentina

institute: INGEBI-CONICET

summary: Background. More than one million women in fertile age are infected with Trypanosoma cruzi worldwide. Anti-T.cruzi seropositivity in mothers has been associated with adverse pregnancy outcome but there is still a knowledge gap regarding this effect. Our aim was to compare the gene expression profile of term placental environment from T. cruzi seropositive (SP) and seronegative (SN) mothers.   Methods. A RNA-Seq was performed in 9 pools of 2 different placental RNA samples each: 3 belonging to placentas from SN and 6 from SP. Each pool consisted of a binomial of a female/male newborn and a vaginal/caesarean delivery. None of the newborns resulted infected.  Results.  Only 42 genes showed a significant fold change between SP and SN groups. Among the down-regulated genes were KISS1 and CGB5. In the up-regulated genes group were: KIF12, HLA-G, PRG2, TAC3, FN1 and ATXN3L. To identify pathways significantly associated with maternal T. cruzi-infection, a gene-set association analysis was implemented. The placental environment transcriptomic profile of SP consisted of an enrichment in immunological genes sets (inflammatory response and lymphocytic activation were over-expressed) whereas numerous biosynthetic processes were down-regulated.   Conclusions. It is worth noting that several differentially expressed genes in SP placentas code for proteins associated to preeclampsia and miscarriage. This first transcriptomics study in human term placental environment from non-infected deliveries shows a placental response that may affect the faetus while protecting it from the parasite infection; this host response  could be responsible for the low rate of congenital transmission observed in human chronic Chagas disease.    Background. More than one million women in fertile age are infected with Trypanosoma cruzi worldwide. Anti-T.cruzi seropositivity in mothers has been associated with adverse pregnancy outcome but there is still a knowledge gap regarding this effect. Our aim was to compare the gene expression profile of term placental environment from T. cruzi seropositive (SP) and seronegative (SN) mothers.   Methods. A RNA-Seq was performed in 9 pools of 2 different placental RNA samples each: 3 belonging to placentas from SN and 6 from SP. Each pool consisted of a binomial of a female/male newborn and a vaginal/caesarean delivery. None of the newborns resulted infected.  Results.  Only 42 genes showed a significant fold change between SP and SN groups. Among the down-regulated genes were KISS1 and CGB5. In the up-regulated genes group were: KIF12, HLA-G, PRG2, TAC3, FN1 and ATXN3L. To identify pathways significantly associated with maternal T. cruzi-infection, a gene-set association analysis was implemented. The placental environment transcriptomic profile of SP consisted of an enrichment in immunological genes sets (inflammatory response and lymphocytic activation were over-expressed) whereas numerous biosynthetic processes were down-regulated.   Conclusions. It is worth noting that several differentially expressed genes in SP placentas code for proteins associated to preeclampsia and miscarriage. This first transcriptomics study in human term placental environment from non-infected deliveries shows a placental response that may affect the faetus while protecting it from the parasite infection; this host response  could be responsible for the low rate of congenital transmission observed in human chronic Chagas disease.

overall_design: Serodiagnosis of pregnant women was done by means of conventional serological methods and carried out by the respective health centres based on routine assays. In maternal and umbilical cord blood samples T. cruzi presence was tested using multiplex Real Time PCR as previously described [6]. Maternal infection with other pathogens that produce congenital transmission and adverse pregnancy outcome were considered as exclusion criteria, as well as missing data or incorrect sampling.  Fresh normal placentas were obtained after labour from vaginal or caesarean deliveries and placed within 24 hours at 4°C. Each placenta was dissected and the middle section [7] at 2 cm distance from the umbilical cord was isolated and placed into RNAlater solution (Applied Biosystems, Foster City, CA). Total RNA was extracted with TRIzol reagent (Invitrogen, Carlsbad, CA) and stored at −80°C until used.   Transcriptomic studies. A RNA-Seq experiment was done in 9 pools of 2 different placental RNA samples each: 3 pools (C1, C2 and C3) belonging to placentas from seronegative mothers (SN) and 6 pools (TC4 to TC9) from seropositive mothers (SP). Each pool consisted of a binomial of a female/male newborn and a vaginal/caesarean delivery. The cDNA Libraries were prepared according to Illumina's TruSeq Stranded Total RNA with Ribo-Zero Gold for Human and a Hiseq 2.500 Illumina platform with 100 bp paired-end reads was used for sequencing

first: Alejandro

middle: G

last: Schijman


title: Effects on gene expression of doxorubicin in human stem cells-derived cardiomyocytes

city: Singapore

first: Manvendra

middle: K.

last: Singh

address: 8 College Road

department: Programme in Cardiovascular & Metabolic Disorders

country: Singapore

institute: Duke-NUS MEDICAL SCHOOL

summary:
To gain into the molecular mechanisms and pathways involved in doxorubicin induced cardiotoxicity, we performed whole genome transcriptome profiling via RNA-seq in hESCs-derived CMs treated with doxorubicin or vehicle only control.
Cells were treated with 0, 1 or 2.5 μM of doxorubicin for 16 hours and RNA was isolated for high throughput sequencing

overall_design: To identify genes that are significantly regulated by doxorubicin treatment, we analyzed read count data from RNA-seq using edgeR software. We also performed KEGG pathway analysis and GO analysis

first: Agnes

last: Maillet

first: Liam

last: Brunham

first: Sujoy

last: Ghosh

first: Xiaron

last: Chai

first: Veerabrahma

middle: P

last: Seshachalam


title: Genome-wide analysis of gene expression in mouse embryonic stem cells when individual glycogen synthase kinase 3 (GSK3) paralog is inhibited via chemical genetic approach

city: Los Angeles

first: Liang

last: Hu

address: 1425 San Pablo Street

department: Department of Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

summary: Analysis of downstream targets when individual GSK3 paralog is inhibited at gene expression level. The hypothesis tested in the present study was that GSK3α and GSK3β have different targets. Results provide important information of the downstream targets of GSK3α and GSK3β.

overall_design: Total RNA obtained from two transgenic embryonic stem cell lines subjected to analog inhibitor treatment for 2 hrs compared to control groups.

first: Xi

last: Chen


title: Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B cell programming  [RNA-Seq-Cre]

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

summary: EBF1 is essential for B cell specification and commitment. To explore the dynamics of EBF1 initiated B cell programming, we performed EBF1 ChIP-seq, ATAC-seq, bisulfite-seq, RNA-seq and several histone ChIP-seq analyses at different stages of the transition from Ebf1-/- pre-pro-B to pro-B triggered by EBF1 restoration. We also performed Pax5 ChIP-seq in Ebf1-/- pre-pro-B cell and EBF1-restored pro-B cell to study the pioneering function of EBF1 that allows other transcription factors to access certain chromatin sites.

overall_design: Time series RNA-Seq analysis during the differentiation from Ebf1-deficient pre-pro-B cell to EBF1-restored pro-B cell.

first: Rui

last: Li

first: Senthilkumar

last: Ramamoorthy

first: Chavez

last: Lukas

first: Rudolf

last: Grosschedl


title: Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B cell programming  [Histone-ChIP-Seq-Cre]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Time series histone ChIP-Seq analysis during the differentiation from Ebf1-deficient pre-pro-B cell to EBF1-restored pro-B cell.


title: Profiling of differential RNAs in alpha amanitin treated SORBS2-depleted ovarian cancer cells and control-treated SORBS2-depleted

city: Chengdu

first: Shengtao

last: Zhou

address: #17, Renmin South Road

department: Department of Obstetrics and Gynecology

institute: West China Second Hospital, Sichuan University

summary: In this study, we examined the differential RNA profile of alpha  amanitin-treated SORBS2-depleted ovarian cancer cells compared with control-treated SORBS2-depleted cells

overall_design: We used RNA sequencing to compare the differential RNAs of  alpha  amanitin-treated SORBS2-depleted ovarian cancer cells compared with control-treated SORBS2-depleted cells


title: Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B cell programming  [ATAC-Seq-Cre]

overall_design: Time series ATAC-Seq analysis during the differentiation from Ebf1-deficient pre-pro-B cell to EBF1-restored pro-B cell.


title: Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B cell programming  [EBF1-ChIP-Seq-Tet-On]

overall_design: EBF1 ChIP-Seq analysis at the early time point after EBF1 restoration in Ebf1-deficient B cell progenitors.


title: Comparsion of the transcriptome profiles in normal and age-related macular degneration in retina and RPE-Choroid-Scleral (RCS) tissues

city: Philadelphia

first: Venkata

middle: Ramana Murthy

last: Chavali

state: PA

address: 3620 Hamilton Walk

institute: University of Pennsylvania

summary: Analysis of retinal and RCS tissues revealed a significant differential expression of noncoding RNA and anti-sense transcripts in AMD when compared to the normal tissues.

overall_design: The retinal and RPE-Choroid-Scleral tissue punches from Eight normal and Eight age-related macular degeneration donor eye samples were obtained and processed within 8hrs from the time of death. The total RNA was isolated using Qiagen All prep kit and RNA libraries were made using Illumina Stranded-Sequencing Ribozero kit. The prepared RNA libaries were multiplexed and PE100bp sequencing was performed on Illumina HiSeq2000. The complete RNA transcriptome is analyzed by a standardized in-house bioinformatic pipeline and the results are interpreted.

first: Eun

middle: J

last: Kim

first: Gregory

last: Grant


title: Retinoic Acid Induced Transcriptional Repressor HIC1 is Required for Suppressive Function of Human Induced Regulatory T cells [RNA-Seq 1]

first: Sini

last: Rautio

summary: Comparing the gene expression in control siRNA samples and HIC1 siRNA samples

overall_design: Two time points; 48h and 72h. For each time point 3 replicates from HIC1 siRNA and 3 replicates from NT siRNA.

first: Riitta

last: Lahesmaa


title: Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

city: Athens

first: Stephen

middle: Patrick

last: LaVoie

state: Ga

address: 527 Biological Sciences Bldg.

department: Microbiology

institute: University of Georgia

summary: Gene expression changes during exponential growth of E. coli MG1655 were compared by RNA-seq after sub-acute exposure to inorganic mercuric chloride (HgCl2) or to the organomercurial, phenylmercuric-acetate (PMA). Differential gene expression revealed common and distinct responses to the mercurials from initial growth stasis through subsequent recovery. Sub-acute mercurial exposures affected expression of ~45% of all genes, many reflecting distinct biochemical damage by each mercurial and the corresponding cellular resources available for recovery of normal growth.

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

overall_design: RNA-Seq and differential gene expression analysis were used to compare the effects of sub-acute inorganic and organic mercury exposure in E. coli throughout recovery. Sub-acute exposure was operationally defined as the concentration of mercury that clearly inhibited growth relative to the unexposed control, but allowed cells to resume growth within 1 hour or approximately one generation in Neidhart MOPS minimal medium. The effects of exposure to HgCl2 (n=3) or PMA (n=3) were examined in E. coli and differential gene expression was determined for each condition by performing pair-wise comparisons to unexposed E. coli culture (n=3) at corresponding time point (10, 30, and 60 min) following exposure. Comparisons were also made to determine differential expression in unexposed culture over time, not influenced by mercury exposure.

first: Anne

middle: O

last: Summers


title: Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B cell programming  [EBF1-ChIP-Seq-Cre]

overall_design: Time series EBF1 ChIP-Seq analysis during the differentiation from Ebf1-deficient pre-pro-B cell to EBF1-restored pro-B cell.


title: Profiling of SORBS2-bound RNAs

summary: In this study, we found that RNA binding protein SORBS2 could significantly reduce the metastatic potential of ovarian cancer. We examined the global profile of SORBS2-bound RNAs in ovarian cancer during metastasis.

overall_design: We used RNA immunoprecipitation followed by RNA sequencing to compare the RNAs bound by SORBS2 in ovarian cancer.


title: RNA sequencing of human bronchial epithelial cell transcriptomes after repopulation and differentiation on bronchial scaffolds from COPD patients and healthy donors

city: Mölndal

first: Lisa

last: Öberg

address: Pepparedleden 1

department: Translational Science and Experimental Medicine

country: Sweden

institute: Research and Early Development, Respiratory Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden

summary: Chronic obstructive pulmonary disease (COPD) is a serious global health problem characterized by chronic airway inflammation, progressive airflow limitation and destruction of lung parenchyma. Remodeling of the bronchial airways in COPD includes changes in both the bronchial epithelium and the subepithelial extracellular matrix (ECM). To explore the impact of an aberrant ECM on epithelial cell phenotype in COPD we developed a new ex vivo model, in which normal human bronchial epithelial (NHBE) cells repopulate and differentiate on decellularized human bronchial scaffolds derived from COPD patients and healthy individuals. By using transcriptomics, we show that bronchial ECM from COPD patients induces differential gene expression in primary NHBE cells when compared to normal bronchial ECM. The gene expression profile indicated altered activity of upstream mediators associated with COPD pathophysiology, including hepatocyte growth factor, transforming growth factor beta 1 and platelet-derived growth factor B, which suggests that COPD-related changes in the bronchial ECM contribute to the defective regenerative ability in the airways of COPD patients.

overall_design: Normal bronchial epithelial (NHBE) cells were seeded on decellularized bronchial scaffolds from 3 COPD patients and 3 healthy donors. Differentiation was induced 4 days later and repopulated scaffolds were collected after 0, 7, 14, 21, 28 and 35 days of differentiation.

first: Ulf

last: Hedström

first: Oskar

last: Hallgren

first: Amy

last: DeMicco

first: Outi

last: Vaarala

first: Gunilla

last: Westergren-Thorsson

first: Xiaohong


title: Genome-wide small RNAs expression analysis of Y-chromosome aneuploidy strains of Drosophila melanogaster

city: Boston

first: Bernardo

last: Lemos

state: MA

address: 655 Huntington Avenue

department: Environmental Health

institute: Harvard T.H. Chan School of Public Health

summary: Y-chromsome aneuplody strains were generated for 2 distinct Y chromosome (Ycongo and Yohio), and expression profile analized by RNA-seq

overall_design: CONTRAST 1: X^X (control) vs X^XYohio; CONTRAST 2: X^X (control) vs X^XYcongo; CONTRAST 3: X^Y (control) vs X^YYohio; CONTRAST 4: X^Y (control) vs X^YYcongo

first: Alan

last: Branco

first: Meng

last: Wang


title: Transcriptional response to Activating transcription factor 3 (Atf3) activity in the Drosophila eye antenna imaginal disc (EAD) epithelium.

city: Cologne

first: Mirka

last: Uhlirova

state: NRW

address: Joseph-Stelzmann Str. 26

department: Institute for Genetics

institute: CECAD Research Center  Cologne

summary: Here we describe the transcriptional response to Atf3 expression in the EAD. Atf3 is a cell polarity response gene acting downstream of the membrane-associated Scribble polarity complex. Loss of the neoplastic tumor suppressors Scribble or Dlg1 induces Atf3 expression via aPKC signaling. Using ChIP-seq we have determined that Atf3 targets are enriched for roles in cytoarchitecture. Gain of Atf3 function interferes with organization of the microtubule network, thereby disturbing vesicular trafficking processes including endocytosis, and consequently alters the distribution of key polarity proteins along the apicobasal axis. Conversely, removal of Atf3 from cells lacking Dlg1 suppresses trafficking defects and restores both the normal localization of polarity determinants and epithelial differentiation. These results thus establish loss of polarity as a novel cue that induces Atf3 and demonstrate that gain of Atf3 function drives specific hallmarks of epithelial cells deficient for the Scribble polarity module.

overall_design: Examination of mRNA expression following gain of Drosophila Atf3 function in the EAD. Using four biological replicates, RNA from mosaic EAD overexpressing Atf3 (FRT82B atf3) was isolated and single-end sequenced on the Illumina NextSeq 500 instrument at 75 bp read length. FRT82B samples (GSM1591021,GSM1591022,GSM1591023,GSM1591024) from Kuelshammer et al., 2015 Disease Models and Mechanisms (GEO accession number GSE65261) were used as control.

first: Colin

middle: D

last: Donohoe

first: Andreia

last: Correia

first: Marek

last: Jindra

first: Prerana

last: Wagle

first: Peter

last: Frommolt


title: Transcriptional repressor HIC1 contributes to suppressive function of human induced regulatory T cells

first: Sini

last: Rautio

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

overall_design: Refer to individual Series


title: Integrative analysis of 3D nucleome and chromatin accessibility reveals a chromatin barrier established for T-lineage commitment during early T cell development [ChIP-Seq]

city: Pasadena

first: Satoshi

last: Hirose

address: 1200 E. California

department: Biology and Bioengineering

institute: California Institute of Technology

summary: Hematopoiesis consists of step-wise commitment of multiple distinct intermediate differentiation stages before mature blood cells are generated1,2. Early progenitor cells have multiple cell fate potentials and retain plasticity to differentiate to alternative lineages, while later stages are fully committed to certain cell lineages and rarely alter their fates3,4. Although extensive studies have been performed on regulatory pathways in mature blood cells5-8, few have examined chromatin re-organization underlying the transcription programs in early progenitors of hematopoiesis. In particular, what roles chromatin organization plays in the cell fate commitment during the differentiation of early hematopoietic progenitor cells remains unclear. Here, we carried out an integrative analysis of 3D nucleome, chromatin accessibility and gene expression during early T cell development from hematopoietic stem cells (HSC) to CD4/CD8 double positive (DP) T cells. Analysis of these data sets revealed extensive A/B compartment flips and dynamic changes of chromatin accessibility at regulatory regions including promoters and enhancers during the development process. Remarkably, both the compartment flip and changes in chromatin accessibility display a monotonic pattern. While gradual and progressive changes in chromatin re-organization was observed at most development stages, an abrupt and striking genome-wide change in A/B compartment structure and chromatin accessibility occurred during the transition from double negative stage 2 (DN2) to DN3, which was accompanied with the loss of cell fate plasticity of DN3 to differentiate to alternative lineages, suggesting that a chromatin barrier is established at the DN3 stage to lock the cells in the T cell fate. The binding of PU.1, a key factor for the fate choice of early progenitor cells, and BCL11B, critically required for T cell commitment at late stages, was associated with increased long-distance interaction and chromatin accessibility and may coordinately contribute to the establishment of the 3D nucleome structure required for the lineage differentiation and commitment.

overall_design: To understand the contribution  of chromatin  interaction landscape to early development stages of hematopoesis, we generated genome-wide profiles of chromatin interaction (with an improved HiC protocal), chromatin accessibility (with scDNase-Seq) and gene expression (with RNA-Seq) from hematopoietic stem cells (HSC) and its immediate progeny (MPP) to common lymphocyte progenitor cells (CLP), early T progenitor cells (ETP or DN1), double negative stage 2 (DN2), DN3, DN4 and double positive (DP) cells.

first: Hu

last: Gangqing

first: Cui

last: Kairong

first: Fang

last: Difeng

first: Hirose

last: Satoshi

first: Wang

last: Xun

first: Zhu

last: Jingfang

first: Ellen

middle: V

last: Rothenberg

first: Zhao

last: Keji


title: Deciphering the direct transcriptional targets of the Drosophila Activating transcription factor 3 (Atf3) via ChIp-seq: Atf3 bridges the gap between cell polarity and the nucleus

summary: Epithelial structure and function are governed by evolutionarily conserved signaling programs. The Drosophila Activating transcription factor 3 (Atf3) prevents epithelial cell replacement during abdominal morphogenesis, yet its transcriptional targets are unknown. Here we demonstrate that Atf3 positively and negatively regulates target genes central to cytoskeleton dynamics and adhesion. Epithelial clones overexpressing Atf3 are enriched for basolateral proteins at the expense of apical identity.  Strikingly, Atf3 functions downstream of the Scrib polarity module. Depleting either scrib or dlg1 induces atf3 expression, while loss of atf3 suppresses differentiation and polarity defects in cells deficient for the Scrib complex

overall_design: Identification of Atf3 transcirptional targets in adult Drosospohila. In three Atf3 biological replicates, an Atf3::GFP fusion protein expressed from a germline-integrated, recombineered bacterial artificial chromosome (BAC) in an atf3 mutant backround. Three biological replicates which did not contain the BAC served as control. One chromatin input sample each from Atf3 and control samples served as a reference.

first: Corinna

last: Klein

first: Bianca

middle: H

last: Habermann


title: Integrative analysis of 3D nucleome and chromatin accessibility reveals a chromatin barrier established for T-lineage commitment during early T cell development

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University


title: IL-4 effect on mouse bone marrow-derived macrophages

status: Public on Feb 19 2018

city: Daejeon

first: Saet-Byel

last: Jung

address: 266, Munhwa-ro, Jung-gu

department: School of medicine

country: South Korea

institute: Chungnam national university

summary: Analysis of BMDMs activated with IL-4. Results provide insight into the molecular effects and secretory effects of IL-4-induced anti-inflammation in macrophages.

overall_design: BMDMs treated with IL-4 for 18 hours


title: Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B cell programming  [ATAC-Seq-Tet-On]

first: Pierre

last: Cauchy

overall_design: ATAC-Seq analysis at the early time point after EBF1 restoration in Ebf1-deficient B cell progenitors.

first: Rui

last: Li

first: Senthilkumar

last: Ramamoorthy

first: Chavez

last: Lukas

first: Rudolf

last: Grosschedl


title: Integrative analysis of 3D nucleome and chromatin accessibility reveals a chromatin barrier established for T-lineage commitment during early T cell development [Dnase-Seq, HiC-Seq, Mnase-Seq, RNA-Seq]

summary: Hematopoiesis consists of step-wise commitment of multiple distinct intermediate differentiation stages before mature blood cells are generated. Although extensive studies have been performed on regulatory pathways in mature blood cells, few have examined chromatin reorganization underlying the changes in transcription programs from early progenitors of hematopoiesis to mature immune cells. In particular, what roles chromatin organization plays in the cell fate commitment during the differentiation of early hematopoietic progenitor cells to committed T cells remains unclear. Here, we carried out an integrative analysis of 3D nucleome, chromatin accessibility and gene expression from hematopoietic stem cells (HSC) to CD4/CD8 double positive (DP) T cells. Analysis of these data sets revealed extensive reorganization of A/B compartments, topologically associating domains (TADs), and chromatin accessibility at transcriptional regulatory regions during the development process. Remarkably, all three levels of chromatin organization display a monotonic pattern of change. While gradual and progressive changes in chromatin reorganization was observed at most development stages, an abrupt genome-wide change in A/B compartment structure, TAD domain scores and chromatin accessibility occurred during the transition from double negative stage 2 (DN2) to DN3, which was accompanied with the loss of cell fate plasticity of DN3 to differentiate to alternative lineages, suggesting that a chromatin barrier is established at the DN3 stage to lock the cells in the T cell fate. This chromatin barrier may be reinforced by another genome-wide reorganization of chromatin at the DN4-to-DP transition. The binding of PU.1, a key factor for the fate choice of early progenitor cells, and BCL11B, critically required for T cell commitment at later stages, was associated with increased long-distance interaction and chromatin accessibility. Deletion of Bcl11b led to decreased chromatin interaction for BCL11B target genes, suggesting that it may contribute to the establishment of the 3D nucleome structure required for the lineage differentiation and commitment.

overall_design: To understand the contribution  of chromatin  interaction landscape to early development stages of hematopoesis, we generated genome-wide profiles of chromatin interaction (with an improved HiC protocal), chromatin accessibility (with scDNase-Seq) and gene expression (with RNA-Seq) from hematopoietic stem cells (HSC) and its immediate progeny (MPP) to common lymphocyte progenitor cells (CLP), early T progenitor cells (ETP or DN1), double negative stage 2 (DN2), DN3, DN4 and double positive (DP) cells. To examine the impact of BCL11B on gene expression, we conditionally knocked out Bcl11b in  DP cells and mearured the expression change by RNA-Seq. To examine the effect of BCL11B  on chromatin interaction and accessibility, we conditional knocked out Bcl11b in Naive CD4+ T cells and measured change in chromatin interaction by Hi-C, chromatin accessibility by scDNase-Seq, and expression by RNA-Seq.

first: Hu

last: Gangqing

first: Wangsa

last: Darawalee

first: Jin

last: Wenfei

first: Ried

last: Thomas

first: Liu

last: Pentao

first: Rothenberg

last: Ellen


title: COMBINING BET AND MEK INHIBITORS SYNERGISTICALLY TARGETS   NRAS MUTANT MELANOMA

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Nearly 30% of all malignant melanomas harbor somatic mutations in NRAS.  However, there are currently no effective targeted therapies for this tumor type. The bromodomain and extra terminal domain (BET) family of proteins are transcriptional regulators that serve as scaffolds to facilitate gene transcription by binding to acetylated lysine residues in the N-terminal tail of histones.  BET/BRD proteins have emerged as therapeutic targets in a broad range of tumors.  We found that BET proteins are overexpressed in NRAS mutant melanoma, and that high levels of BET family member BRD4 are associated with poor patient survival, suggesting that BRD4 plays a key role in melanoma. Consequently, we hypothesized that these epigenetic regulators constitute potential vulnerabilities that can be exploited for melanoma treatment.  We found that genetic or pharmacological inhibition of BET/BRD proteins decreases viability and inhibits proliferation of NRAS mutant melanoma cells, as well as BRAF/MEK-inhibitor resistant melanoma cells harboring concurrent BRAF/NRAS mutations.  However, BET inhibitors when used as single agents were either cytostatic (in vitro) or ineffective (in vivo).  We therefore evaluated combinations that could maximize the efficacy of BET inhibitors in NRAS mutant melanoma. Here we report that co-targeting BET and MEK synergistically restrained tumor growth and significantly prolonged the survival of NRAS-mutant tumor bearing mice. RNA-sequencing and RPPA analysis revealed that co-treatment with BETi/MEKi synergistically downregulated cell cycle regulators and activated caspase-7. This study demonstrates that combined BET and MEK inhibition elicits robust synergistic therapeutic effects and supports the clinical utility of this combination therapy for NRAS mutant melanoma patients.

overall_design: Examination of transcriptome changes for BET and MEK inhibitors and their combination

first: Jessie

last: Villanueva

first: Ileabett

last: Echevarría-Vargas


title: Transcriptomic analysis of paired patient isolates of Acinetobacter baumannii following failed colistin treatment

city: Clayton

first: David

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

country: Australia

institute: Monash University

summary: Colistin is a crucial last-line drug used for the treatment of life-threatening infections caused by multi-drug resistant strains of the Gram-negative bacteria, Acinetobacter baumannii. However, colistin resistant A. baumannii isolates can be isolated following failed colistin therapy. Resistance is most often mediated by the addition of phosphoethanolamine (pEtN) to lipid A by PmrC, following missense mutations in the pmrCAB operon encoding PmrC and the two-component signal transduction system PmrA/PmrB. We recovered an isogenic pair of A. baumannii isolates from a single patient before (6009-1) and after (6009-2) failed colistin treatment that displayed low/intermediate and high levels of colistin resistance, respectively. To understand how increased colistin-resistance arose, we genome sequenced each isolate which revealed that 6009-2 had an extra copy of the insertion sequence element ISAba125 within a gene encoding an H-NS-family transcriptional regulator. Consequently, transcriptomic analysis of the clinical isolates identified was performed and more than 150 genes as differentially expressed in the colistin-resistant, hns mutant, 6009-2. Importantly, the expression of eptA, encoding a second lipid A-specific pEtN transferase, but not pmrC, was significantly increased in the hns mutant. This is the first time an H-NS-family transcriptional regulator has been associated with a pEtN transferase and colistin resistance.

overall_design: mRNA profiles of two isolates taken from a single patient, one before and one after colistin treatment, cDNA libraries were sequenced on an Illumina HiSeq 2000

first: D

last: Deveson Lucas

first: J

last: Boyce


title: ADAM17 is required for EGF-R induced intestinal tumors via IL-6 trans-signaling

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

institute: Institute of Clinical Molecular Biology

summary: Colorectal cancer is treated with antibodies blocking epidermal growth factor receptor (EGF-R) but therapeutic success is limited. EGF-R is stimulated by soluble ligands, which are derived from transmembrane precursors by ADAM17-mediated proteolytic cleavage. In mouse intestinal cancer models in the absence of ADAM17, tumorigenesis was almost completely inhibited and the few remaining tumors were of low grade dysplasia. RNA-Seq analysis demonstrated downregulation of STAT3 and Wnt pathway components. Since EGF-R on myeloid cells, but not on intestinal epithelial cells is required for intestinal cancer and IL-6 is induced via EGF-R stimulation, we analyzed the role of IL-6 signaling. Tumor formation was equally inhibited in IL-6 -/- and sgp130Fc transgenic mice, in which only trans-signaling via soluble IL-6R is abrogated. ADAM17 is needed for EGF-R-mediated induction of IL-6 synthesis, which via IL-6 trans-signaling induces ß-catenin dependent tumorigenesis. Our data reveal the possibility of a novel strategy for treatment of colorectal cancer, which could circumvent intrinsic and acquired resistance to EGF-R blockade.

overall_design: RNA sequencing of tumor tissue and surrounding unaffected tissue of Apc Min/+ and Apc Min/+ ::ADAM17 ex/ex

first: Stefan

last: Rose-John

first: Philip

last: Rosenstiel


title: Identification of the RB loss-induced transcriptome in prostate cancer [RNA]

first: Christopher

last: McNair

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University

summary: The retinoblastoma protein (RB) is preferentially lost in the progression to castrate resistant prostate cancer (CRPC).  However, the alterations associated with such loss have been scantly described.  The current study aims to provide molecular mechanisms underlying Rb loss-driven CRPC phenotypes

overall_design: Transcriptional alterations upon RB loss were assessed in hormone deficient conditions through RNA-Seq of shCON and shRB LNCaP prostate cancer cells

first: Karen

middle: E

last: Knudsen


title: Distinct, OR-specific subsets of axon guidance molecules govern early olfactory map formation

first: Junhyong

last: Kim

address: 433 S University Avenue

department: Biology

summary: We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified, suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting.

overall_design: Single-cell RNASeq of OMP-expressing olfactory sensory neurons was performed by capture on Fluidigm-C1 followed by sequencing on Illumina HiSeq2500

first: Puneet

last: Dang

first: Stephen

middle: A

last: Fisher

first: Derek

last: Stefanik

first: Jonathan

last: Raper


title: Transcription profiling of lettuce in response to UV-B radiation

status: Public on Feb 18 2018

city: Shanghai

first: lili

last: zhang

address: 2901 Beidi Rd

institute: Shanghai Academy of Agricultural Sciences

summary: UV-B radiation is one of the major environmental stresses that triggers a variety of plant responses. However, limited information is available regarding plant biological reactions which help to circumvent the potentially harmful effects of UV-B radiation in lettuce (Lactuca sativa L.). In this study, RNA-seq was performed to identify differentially expressed genes in response to UV-B radiation.

overall_design: The lettuce cultivar Shenxuan 5 was used in this study. Four week-old healthy seedlings were exposed to UV-B radiation (310 nm light-emitting diode, T9E31C, Seoul Optodevice, 0.3Wm-2). Devices for supplemental UV-B radiation were suspended above and perpendicular to the planted rows (rows oriented in an east-west direction to minimize shading). Samples were collected at four time points: 0h, 6h, and 24h of UV-B radiation and 12h of recovery under normal conditions after 24h of UV-B radiation. Two biological replicates were used for each time points

first: Lili

last: Zhang

first: Fanrong

last: Gong


title: Genome-wide gene and small RNA expression analysis of Y-chromosome aneuploidy strains of Drosophila melanogaster

first: Bernardo

last: Lemos


title: Next Generation Sequencing Facilitates Quantitative Analysis of overexpression ydeH and ydeH (E208,209A) Transcriptomes in Mycobacterium smegmatis

city: Wuhan

first: Weihui

last: Li

address: 1 str Sizisan

institute: Huazhong Agricultural University

summary: Compare the gene expression difference between these two strains by RNA sequencing in Mycobacterium smegmatis

overall_design: Two samples in triplicate are analyzed. The control sample is the overexpression ydeH(E208,209A) in Mycobacterium smegmatis

first: Zhengguo

last: He


title: A RNA-Seq Analysis of the Response of Photosynthetic System to Low Nitrogen Supply in Maize Leaf

status: Public on Feb 16 2018

city: zheng zhou

first: xiaohuan

last: mu

address: zhengzhou long zi hu

institute: Henan Agricultural University

summary: Using Digital Gene Expression technology to compare the genome-wide gene expression profiles about photosynthesis in two nitrogen treatment.

overall_design: Using an integrated approach including RNA-seq and chlorophyll fluorescence to investigated photosythesis in response to LN stress in maize.Two biological replicates were generated for each treatment.

first: Xiaohuan

last: Mu

first: Qinwu

last: Chen

first: Fanjun

first: Lixing

last: Yuan

first: Guohua

last: Mi


title: Drosha drives the formation of DNA:RNA hybrids around DNA break sites to facilitate DNA damage repair

city: New York

first: Ben

middle: R

last: Hawley

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

summary: The microRNA biogenesis enzyme Drosha was found to be important for DNA repair and this function appears to be distinct to its role in miRNA-mediated repression. Novel small RNAs were reported previously to be produced from the sequences around a DNA break. Utilising an endonuclease system (AsiSI) we were unable to detect such small RNA around 100 cuts within the endogenous genome. Sequencing of R-loops (DNA:RNA hybrids) was performed and an increase in R-loop formation was observed around many DNA break sites. Loss of Drosha appears to perturb this damage dependent formation of R-loops. RNase H1 over-expression appears to reduce repair at these break sites. Drosha appears to be important for facilitating R-loop formation at DNA break sites to aid in the repair process.

overall_design:
Small RNA sequencing from cells that have been DNA damaged by AsiSI endonuclease at various time points, as well as 5'-triphosphate small RNA (i.e. 5'-monophosphate depleted).
4-thiouridine total RNA PE sequencing to determine transcriptional activity within these cells.
DNA:RNA hybrid immunoprecipitation (DRIP) followed by PE sequencing of the genomic fragments, following DNA damage induced by the AsiSI endonuclease with and without siRNA against the microRNA biogenesis enzyme Drosha.

first: Wei-Ting

last: Lu

first: George

middle: L

last: Skalka

first: Robert

last: Baldock

first: Ewan

last: Smith

first: Aldo

middle: S

last: Bader

first: Michal

last: Malewicz

first: Felicity

middle: Z

last: Watts

first: Ania

last: Wilczynska

first: Martin

last: Bushell


title: Plant-specific histone residue F41 restricts H3.1 distribution in heterochromatin

city: Madison

first: Xuehua

last: Zhong

state: WI

address: 330 N. Orchard St.

department: Epigenetics

institute: Wisconsin Institute for Discovery

summary: The plant specific H3.1F41 plays crucial role in H3.1 genome-wide deposition pattern.

overall_design: We made single and double mutant transgenic lines between histone 3 variants H3.3 and canonical H3.1 in Arabidopsis. The mutated constracts were fused with FLAG tag and transformed into Arabidopsis driven by their endougenous promoter. ChIP seq experiments were did by anti FLAG tag (Sigma (M8823)).

first: Li


title: SAGE analysis of alveolar macrophages from metastatic lung and untreated lung

city: Yoshida-gun

first: Takuto

last: Nosaka

state: Fukui

address: 23-3 Matsuoka, Eiheiji-cho

department: Second Department of Internal Medicine

institute: University of Fukui

summary: Macrophages in lungs can be classified into two subpopulations, alveolar macrophages (AMs) and interstitial macrophages (IMs), which reside in the alveolar and interstitial spaces, respectively. Accumulating evidence indicates the involvement of IMs in lung metastasis but the roles of AMs in lung metastasis still remain elusive. An intravenous injection of a mouse hepatocellular carcinoma (HCC) cell line, BNL, caused lung metastasis foci with infiltration of AMs and IMs. Comprehensive determination of arachidonic acid (AA) metabolite levels revealed increases in leukotrienes (LTs) and prostaglandins in lungs in this metastasis model. A 5-lipoxygenase (LOX) inhibitor but not a cyclooxygenase inhibitor reduced the numbers of metastatic foci, particularly those with larger sizes. A major 5-LOX metabolite, LTB4, augmented in vitro cell proliferation of human HCC cell lines as well as BNL cells. Moreover, in this lung metastasis course, AMs exhibited higher expression levels of the 5-LOX and LTB4 than IMs. Consistently, 5-LOX-expressing AMs increased in the lungs of human HCC patients with lung metastasis, compared with those without lung metastasis. Furthermore, intratracheal clodronate liposome injection selectively depleted AMs but not IMs, together with reduced LTB4 content and metastatic foci numbers in this lung metastasis process. Finally, IMs in mouse metastatic foci produced CCL2, thereby recruiting blood-borne, CCR2-expressing AMs into lungs. Thus, AMs can be recruited under the guidance of IM-derived CCL2 into metastatic lungs and can eventually contribute to the progression of lung metastasis by providing a potent AA-derived tumor growth promoting mediator, LTB4.

overall_design: Total RNA was extracted from AMs of untreated mice and mice injected intravenously with BNL cells. The resultant total RNAs were subjected to SAGE

first: Hideaki

last: Yurino

first: Shinichi

last: Hashimoto


title: Zebrafish heart regeneration

city: Pittsburgh

first: Michael

last: Tsang

address: 3501 Fifth Ave

department: Developmental Biology

institute: University of Pittsburgh

summary: The study compares gene expression profile at 20 days post amputation of the zebrafish ventricular heart between dusp6 mutant and WT siblings.

overall_design: Ventricular resection was performed and 20 dpa, hearts were extracted.

first: Maria

last: Missinato


title: Interleukin 4 modulates microglia homeostasis and attenuates the early slowly progressive phase  of Amyotrophic Lateral Sclerosis

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

summary: CNS-delivery of Interleukin 4 (IL-4) - via a lentiviral-mediated  gene therapy strategy - skews microglia to proliferate, inducing these cells to adopt the phenotype of  slowly proliferating cells. Transcriptome analysis revealed that IL-4-treated microglia express a broad  number of genes normally encoded by embryonic microglia.

overall_design: RNAseq analysis of sorted microglia from mice receiving IL-4 gene therapy

middle: M

first: Chiara

last: Rossi

first: Luca

last: Muzio


title: Long non-coding RNAs and mRNAs profiling during spleen development in pig

city: chengdu

first: Mingzhou

last: Li

state: Sichuan

address: No.211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

summary: We describe a total 222.19 Gb of pig RNA-seq sequences generated from the 18 libraries

sample_organism:
Sus scrofa
Sus scrofa domesticus

platform_organism:
Sus scrofa
Sus scrofa domesticus

overall_design: Examination of 5 development stages of pig spleen including one wild boar sample

first: Tiandong

last: Che


title: Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B cell programming  [Bisulfite-Seq-Cre]

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

type: Methylation profiling by high throughput sequencing

summary: EBF1 is essential for B cell specification and commitment. To explore the dynamics of EBF1 initiated B cell programming, we performed EBF1 ChIP-seq, ATAC-seq, bisulfite-seq, RNA-seq and several histone ChIP-seq analyses at different stages of the transition from Ebf1-/- pre-pro-B to pro-B triggered by EBF1 restoration. We also performed Pax5 ChIP-seq in Ebf1-/- pre-pro-B cell and EBF1-restored pro-B cell to study the pioneering function of EBF1 that allows other transcription factors to access certain chromatin sites.

overall_design: Time series whole genome bisulfite-Seq analysis during the differentiation from Ebf1-deficient pre-pro-B cell to EBF1-restored pro-B cell.

first: Rui

first: Senthilkumar

last: Ramamoorthy

first: Chavez

last: Lukas

first: Rudolf

last: Grosschedl


title: Search for genes affected by mgtC leader expression in Salmonella enterica serovar Typhimurium 14028s (2)

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

summary: A set of genes are highly downregulated in the presence of extra copy of the mgtC leader. Provide a hint of potental target of the leader RNA.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: RNA expression profile of cells harboring a plasmid with the mgtC leader versus the empty vector, grown in minimal media, using Illumina NextSeq 500.

first: Eun-Jin

last: Lee

first: Daesil

last: Nam


title: TGF-b utilizes a novel receptor activation mechanism to phosphorylate SMAD1/5 and regulate epithelial-to-mesenchymal transition

city: London

first: Caroline

last: Hill

address: 1 Midland Road

department: Developmental Signalling

country: United Kingdom

institute: Francis Crick Institute

summary: TGF-b treatment leads to the transcriptional regulation of many genes. However, the proportion of those that are dependent on SMAD1/5 is unknown. Here, we compared the transcriptional profile after TGF-b treatment in a parental clone and one in which SMAD1/5 had been deleted by CRISPR/Cas9 to identify SMAD1/5 dependent genes.

overall_design: NMuMG parental clone or DSMAD1/5 Clone 1, untreated or treated with TGF-b for 48 hr, n=3 in each group.

first: Anassuya

last: Ramachandran

first: Probir

last: Chakravarty

first: Pedro

last: Vizan

first: Debipriya

last: Das

first: Janis

last: Voyt

first: Katherine

middle: W

last: Rogers

first: Patrick

last: Müller

first: Andrew

middle: P

last: Hinck

first: Gopal

last: Sapkota


title: Transcriptome profiling of HepG2 cells upon treatment of the menin-MLL inhibitor MI-503 or DMSO

city: Gaithersburg

first: Jingya

last: Wang

state: Maryland

address: 1 Medimmune Way

department: Early respiratory and immunology

institute: Astrazeneca

summary: Hepatocellular carcinoma (HCC) accounts for the majority of malignant liver tumors and results in many deaths each year, emphasizing the need for new therapies. The protein-protein interaction between menin and histone methyltransferase Mixed Lineage Leukemia 1 (MLL1) plays an important role in the development of HCC, implying that pharmacologic inhibition of this interaction could lead to new therapeutic strategy for the HCC patients. Therefore, we performed RNA sequencing experiment to determine the transcriptome change in the HepG2 cells upon treatment of MI-503, a small molecule inhibitor of the menin-MLL1 interaction with optimized drug-like properties

overall_design: HepG2 cells were plated in the 12-well plates at the initial concentration of  0.4x106 cells/ml and treated with 3 μM MI-503 or DMSO (0.25%) in triplicates. After 3 days of  treatment viable cell number was adjusted to the original concentration in the DMSO treated  samples and the same dilution factor was used to adjust cell number in the MI-503 treated cells.  Media was changed and compound or DMSO was re-supplied at that time. Cells were harvested  after 3 more days of incubation.

first: Jolanta

last: Grembecka

first: Tomasz

last: Cierpicki


title: Increased Susceptibility to AKI in a Mouse Model of Presymptomatic Cardiomyopathy

city: Cincinnati

first: Keri

middle: Anne

last: Drake

state: Ohio

address: 3333 Burnet Avenue

department: Nephrology

institute: Cincinnati Children's Hospital Medical Center

summary: The early events that signal renal dysfunction in presymptomatic heart failure are unclear. To evaluate this, we performed RNA-seq on kidneys from transgenic mice with cardiac-specific overexpression of mutant alpha-B-crystallin, which develop slowly progressive cardiomyopathy. Presymptomatic transgenic mice display an increase in serum creatinine and in urinary neutrophil gelatinase-associated lipocalin (NGAL), but lack chronic interstitial fibrosis.  Presymptomatic transgenic mouse kidneys exhibited a worsened response to ischemia-reperfusion injury based on serum creatinine, urine NGAL, tubule dilation and cast score, and apoptosis. Our findings demonstrate functional renal impairment, urinary biomarker elevations, and gene expression changes that occur in early presymptomatic heart failure, which dramatically increase the susceptibility to subsequent acute kidney injury.

overall_design: mRNA profiles were generated by performing RNA-seq on adult kidney tissue from transgenic mice (FVB/N mice that overexpress CryAB containing the R120G missense mutation driven by the cardiomyocyte-specific α-myosin heavy chain promoter. We performed analysis in triplicate of kidneys from transgenic animals (prior to the onset of heart failure) vs. age-matched, sex-matched (male) control mice by deep sequencing using Illumina Hi-Seq 2500.

first: Prasad

last: Devarajan


title: Salt-stress and CTD phosphatase-like 4 mediate switching of snRNA to mRNA transcription in Arabidopsis thaliana

city: College Station

first: Akihito

last: Fukudome

state: Texas

address: Dept. Horticultural Sciences MS2133 Texas A&M Univ.

institute: Texas A&M University

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

overall_design: Refer to individual Series


title: Ezh2 and Runx1 Mutations Collaborate to Initiate Lympho-Myeloid Leukemia in Early Thymic Progenitors [Human cell line RNA-seq]

city: Oxford

first: Christopher

last: Booth

state: Oxfordshire

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Understanding the specific cell populations responsible for propagation of leukemia is an important step for development of effective targeted therapies. Recently, the lymphoid-primed multipotent progenitor (LMPP) has been proposed to be a key propagating population in acute myeloid leukemia (AML; PMID 21251617). We have also shown that LMPPs share many functional and gene expression properties with early thymic progenitors (ETPs; PMID 22344248). This finding is of particular interest as ETP leukemias have recently been described: a distinct and poor prognostic disease entity with a transcriptional profile reminiscent of murine ETPs, showing co-expression of hematopoietic stem cell (HSC) and myeloid markers (PMID 19147408). Together, this raises the question whether ETPs can act as a leukemia-initiating/propagating cell population; however, relevant disease models to test this hypothesis are currently lacking. Analysis of the genetic landscape of ETP leukemias has revealed frequent coexistence of inactivating mutations of EZH2 and RUNX1 (PMID 22237106). We therefore generated mice with deletions of Ezh2 and Runx1 specifically targeted to early lymphoid progenitors using Rag1Cre (Ezh2fl/flRunx1fl/flRag1Cre+; DKO mice). As anticipated, HSCs lacked significant recombination in DKO mice whereas close to 100% of purified ETPs (Lin-CD4-CD8-CD44+CD25-Kit+Flt3+) showed deletion of Ezh2 and Runx1. Strikingly, despite a 16-fold reduction in thymus cellularity caused by a block in thymocyte maturation at the DN2-DN3 transition, absolute numbers of ETPs within the thymus of DKO mice were markedly expanded (12-fold; p<0.0001). In contrast, Ezh2 or Runx1 deletion alone had no impact on numbers of ETPs. RNA-sequencing of the expanded ETPs in DKO mice revealed upregulation of HSC- and myeloid-associated transcriptional programs, reminiscent of ETP leukaemia e.g. Pbx1 (log2FC=3.0; p<0.0001) and Csf3r (log2FC=1.9; p=0.0038). Single-cell gene expression analysis confirmed co-expression of HSC and myeloid programs with lymphoid genes within individual DKO ETPs. Further, some key regulators of T-cell maturation which are aberrantly expressed in ETP leukemia were also disrupted in DKO ETPs e.g. Tcf7 (log2FC=-9.5; p<0.0001). Gene expression associated with aberrant Ras signalling was also present. However, despite a continued expansion of the ETP population with age, we did not observe leukemia in DKO mice with over 1 year of follow-up. Since ETP leukemias frequently feature activating mutations in genes regulating RAS signaling, we hypothesised that the expanded “pre-leukemic” ETPs in DKO mice would be primed for leukemic transformation by signalling pathway mutation. We therefore crossed DKO mice with a Flt3ITD/+ knock-in mouse line, as internal tandem duplications (ITD) of FLT3 are frequent in ETP leukemias. Ezh2fl/flRunx1fl/flRag1Cre+Flt3ITD/+ (DKOITD) mice showed dramatically reduced survival (median 9.3 weeks) resulting from an aggressive, fully penetrant acute leukemia showing a predominantly myeloid phenotype (e.g. Mac1) but with co-expression of some lymphoid antigens (e.g. intracellular CD3). Crucially, this leukaemia could be propagated in wild-type recipients upon transplantation of the expanded ETPs. DKOITD ETPs were transcriptionally very similar to DKO ETPs, retaining expression of lymphoid alongside HSC- and myeloid-associated genes. Finally, in a lympho-myeloid cell line model (EML cells) we demonstrated that Ezh2 inactivation-induced loss of H3K27me3 is associated with a corresponding increase in H3K27Ac, a transcriptional activating signal that recruits bromodomain proteins. As such, we reasoned that our ETP leukemia model might be sensitive to bromodomain inhibitors such as JQ1. Indeed, we observed high sensitivity of expanded DKOITD ETPs to JQ1, raising the possibility of a new therapeutic approach for ETP leukemias. This novel mouse model of ETP-propagated leukemia, driven by clinically relevant mutations, provides intriguing evidence that leukemias with a predominant myeloid phenotype, but co-expressing lymphoid genes, may initiate within a bona fide early lymphoid progenitor population. Since the functional characteristics of the cell of origin of a leukaemia may direct its progression and response to therapy, these findings could have important implications for future stratification and treatment of both AML and ETP leukemias.

overall_design: RNA-sequencing of the LOUCY and JURKAT human leukemia cell lines. Cells were either untreated, treated with DMSO, or treated with the BET inhibitors JQ1 or I-BET151. Samples were obtained from two independent experiments.

first: Neil

last: Ashley

first: Sten

last: Jacobsen

first: Adam

middle: J

last: Mead


title: Gene expression profiling of the Arabidopsis Mediator MED5 mutant ref4-3 and suppressors thereof

city: West Lafayette

first: Clint

last: Chapple

state: IN

address: 175 S. University St.

department: Department of Biochemistry

institute: Purdue University

summary:
Purpose:  To identify changes in gene expression in the ref4-3 mutant that contribute to the mutant’s altered growth and metabolite accumulation by comparing differential gene expression in ref4-3 and suppressors of ref4-3.
Methods: Gene expression profiles were generated from 18-day-old, pooled Arabidopsis rosettes in biological quadruplicate, by paired-end sequencing of 100 bp fragments using Illumina HiSeq 2500. The sequence reads that passed quality filters were aligned to the TAIR10 reference genome using TopHat. Gene counts were determined using HTseq-count. Differential expression analysis was performed using edgeR.
Results: We identified 14,688 genes that were differentially expressed across the 10 genotypes (ANOVA, FDR <0.05).

overall_design: Gene expression profiles of wild type and Mediator single or double mutants were generated in biological quadruplicate from 18-day-old Arabidopsis rosettes by deep sequencing using Illumina HiSeq 2500.

first: Whitney

last: Dolan


title: The 19S proteasome subunit Rpt4 is directly involved in the regulation of heterochromatin spreading

city: Daejeon

first: Hogyu David

last: Seo

address: 291 Daehak-ro

institute: KAIST

summary: The non-proteolytic role of the proteasome in heterochromatin regulation

overall_design: For ChIP experiment : ChIP against H3K9me2, anti-FLAG was performed for a wild type strain and strains lacking Clr4 and FLAG-tagged Rpn1 and Pre1. For sRNA experiment : Total RNA was prepared from cells arrested in mid-log phase followed by sRNA isolation.

first: H

middle: D

first: Y

last: Choi

first: M

last: Kim

first: K

last: Kang

first: T

last: Urano

first: D

last: Lee


title: Salt-stress and CTD phosphatase-like 4 mediate switching of snRNA to mRNA transcription in Arabidopsis thaliana [im-nc]

summary: RNA polymerase II C-terminal domain (CTD) phosphorylation regulates transcription of both protein-coding mRNAs and non-coding RNAs (ncRNAs). However, understanding about CTD-phosphoregulation in plant ncRNA transcription is still obscure.  Here we used Arabidopsis CTD phosphatase-like 4 knock-down lines (CPL4RNAi) and show that CPL4 functions in a genome-wide, conditional 3'-extensions of small nuclear RNA (snRNA) and biogenesis of novel snR-DPGs, which are protein-coding snRNA-mRNA fusion transcripts (snR-Downstream Protein-coding Gene).  Production of snR-DPG is dependent on pol II snRNA promoter (PIIsnR), and CPL4RNAi promotes readthrough of snRNA 3’-end processing signal and pol II transcription downstream of snRNA.  Also discovered was a novel unstable ncRNASSP14, which is driven by a PIIsnR and is conditionally 3'-extended to produce mRNA.  In wild type, the snRNA-to-snR-DPG switching is induced by salt stress, and is associated with alteration of CTD phosphorylation status in the transcribing pol II complex. The snR-DPG transcripts occur widely in plants, suggesting that the transcriptional snRNA-to-snR-DPG switching is a previously unknown mechanism ubiquitous in plants to regulate gene expression in response to environmental stresses.

overall_design: Examination of two genotypes (Col and hen2-4) in biological triplicate

first: Hisashi

last: Koiwa


title: Structure-function Analysis of Rice Immune Receptor BPH14 Reveals Planthopper-resistance Mediated through Protein-protein Interaction with WRKY46/72

city: wuhan

first: Liang

last: Hu

address: bayi street

institute: wuhan university

summary: BPH14 is the first planthopper-resistance gene which encodes a coiled-coil–nucleotide-binding site–leucine-rich repeat (CC-NB-LRR) protein. Here, we analysed the function of BPH14 domains and characterized the possible molecular mechanisms underlying BPH14-mediated BPH resistance. In this study, we found BPH14 form homo-complexes and interacted with WRKY46 and WRKY72, to enhance WRKYs accumulation and increase WRKYs-dependent transactivation activity. We performed chromatin immunoprecipitation (ChIP) analysis to identify the candidate promoters that interacted with the WRKY46 or WRKY72 directly in rice protoplasts. After the ChIP test, the enrichment of specific DNA fragments in the immune precipitant were determined by ChIP sequencing. Two candidate genes RLCK281 and SCalS5 were confirmed by yeast one-hybrid system and EMSAs. These data would advance our understanding about the mechanisms underlying the characteristics of BPH14-dependent BPH resistance in the future.

overall_design: The chromatin immunoprecipitation experiment was performed, following a previously reported protocol (Gendrel et al., 2005) with several modifications. Approximately 9 × 106 cells in each sample from rice protoplasts transfected with WRKY46-Myc or WRKY72-Myc were used as a starting material and proteins were immunoprecipitated using antibodies against Myc (MBL, M192-3). The precipitated DNA was purified with the Qia quick PCR purification kit (Qiagen, Germany) and processed further for ChIP-seq data processing and analysis.

first: Guangcun

last: He


title: Defining the Transcriptional Landscape during Cytomegalovirus Latency with Single-Cell RNA Sequencing

status: Public on Feb 17 2018

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

institute: Weizmann Institute

summary: Primary infection with human cytomegalovirus (HCMV) results in a lifelong infection due to its ability to establish latent infection, with one characterized viral reservoir being hematopoietic cells. Although reactivation from latency causes serious disease in immunocompromised individuals, our molecular understanding of latency is limited. Here, we delineate viral gene expression during natural HCMV persistent infection by analyzing the massive transcriptome sequencing (RNA-seq) atlas generated by the Genotype-Tissue Expression (GTEx) project. This systematic analysis reveals that HCMV persistence in vivo is prevalent in diverse tissues. Notably, we find only viral transcripts that resemble gene expression during various stages of lytic infection with no evidence of any highly restricted latency-associated viral gene expression program. To further define the transcriptional landscape during HCMV latent infection, we also used single-cell RNA-seq and a tractable experimental latency model. In contrast to some current views on latency, we also find no evidence for any highly restricted latency-associated viral gene expression program. Instead, we reveal that latency-associated gene expression largely mirrors a late lytic viral program, albeit at much lower levels of expression. Overall, our work has the potential to revolutionize our understanding of HCMV persistence and suggests that latency is governed mainly by quantitative changes, with a limited number of qualitative changes, in viral gene expression.

overall_design: The MARS-seq protocol was used for single cell RNA-seq of CD14+ cells infected with TB40/E strain of HCMV in several days post infection. 10x genomics was used for single cell RNA-seq of CD34+ cells infected with TB40/E strain of HCMV.

first: Miri

last: Shnayder

first: Michal

last: Schwartz

first: Aharon

last: Nachshon

first: Alina

last: Boshkov

first: Amit

last: Binyamin

first: Itay

last: Maza


title: Gene expression signature of colorectal cancer patients

city: Guangzhou

first: Huanliang

last: Liu

address: 26 Yuancun Er Heng Road

institute: Guangdong Institute of Gastroenterology and the Sixth Affiliated Hospital, Sun Yat-sen University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: lncRNAs contributes to the development of colorectal cancer (CRC). Analysis of tumor tissues and adjacent non-tumor tissues from 6 colorectal cancer patients was conducted. Results indicate insight into molecular signature of the tumorigenesis of CRC.

overall_design: Microarray analysis was conducted to identify the differentially expressed lncRNAs and mRNAs between tumor tissues and adjacent non-tumor tissues in 6 CRC patients.


title: Chemoprevention with COX2 and EGFR inhibition in FAP patients: mRNA signatures of duodenal neoplasia

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

summary: RNA sequencing of duodenal polyps in FAP patients treated with plabebo or the drug combination, erlotinib + sulindac

overall_design: 69 duodenal RNA sequencing datasets (17 baseline uninvolved from 17 FAP patients, 10 endpoint uninvolved and 16 polyp from 10 FAP patients on placebo, 10 endpont uninvolved and 16 polyp from 10 FAP patients on drug)

first: Don

last: Delker

first: Deb

last: Neklason


title: A naturally unique variation in Al-activated malate transporter 9 determines fruit malate in cultivated tomato

city: Wuhan City

first: JIE

last: YE

state: Hubei Province

address: No. 1, Shizishan Road

institute: Huazhong Agricultural University

summary:
Purpose: Understanding the mechanism of malate accumulation in plants is beneficial for both plant nutrient and human health. However, little is known regarding regulation of malate accumulation in horticulture plants such as tomato. The goals of this study are to investigate potential regulation network of Al-Activated Malate Transporter 9 (ALMT9) which is the major locus responsible for the variation in fruit malate concentration observed in cultivared tomato.
Methods: The transcriptomes of fruit at ripening stage  from CK and SlALMT9 overexpressing line1 were evaluated using single-ended sequencing of Illumina HiSeq 2500. Raw sequences were filtered and the resulting sets of clean reads were used for the following analysis by tophat and edgeR software.
Results: Among 1,887 differentially expressed genes, some structural genes involved in sugar and organic acid metabolism were differently expressed in SlALMT9 overexpressing line, which partially coincide with changes of sugar and organic acid concentration. PR genes was also altered in the OX lines, in agreement with previous study that tomato fruit malate is involved in pathogen infection. Three members of malate transporters, MATE (multidrug and toxin efflux), were up-regulated (SlMATE5 and 6) or down-regulated (SlMATE9) . Besides, three sugar transport proteins and four vacuole membrane or plasma membrane proteins were up-regulated in OX line
Conclusions: Using RNA-seq analysis, 1,887 differentially expressed genes was revealed. Among them, several genes related to sugar and organic acid metabolism and transport, pathogen resistances were identified. This transcriptome study provides insight into the regulatory mechanism of fruit malate accumulation and the effect of the SlALMT9 to primary metabolism.

overall_design: Investigate the potential regulation network of SlALMT9 in ripening tomato fruit by Illumina sequencing platform.

first: Jie

last: Ye

first: Zhibiao


title: Response of potato sRNAome to PVYNTN infection [degradome-Seq]

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary: We aimed at unraveling the role of small RNAs in a complex immune signaling network controlling defense responses that render the plant tolerant to viral infection. We have identified and quantified miRNAs, phasiRNA and virus-derived small RNAs in both, the PVYNTN-tolerant cv. Désirée and its susceptible transgenic counterpart impaired in accumulation of salicylic acid (NahG-Désirée). We have constructed a small RNA regulatory network using in silico prediction results as well as degradome sequencing to link our data to the physiological response (target transcript abundances and hormone levels).

overall_design: Degradome-seq data of PVYNTN-infected (PVY) and mock (MOCK) inoculated potato plants of cv. Désirée and NahG-Désirée. Samples were obtained by pooling RNA samples of three plants per treatment.

first: Maja

last: Križnik

first: David

last: Dobnik

first: Kristina

last: Gruden


title: Response of potato sRNAome to PVYNTN infection


title: Response of potato sRNAome to PVYNTN infection [smallRNA-Seq]

overall_design: small RNA-seq data of PVYNTN-infected (PVY1, PVY2, PVY3) and mock (mock1, mock2, mock3) inoculated potato plants of cv. Désirée and NahG-Désirée. Three plants per treatment were used.


title: Zone dependent distinctive gene expression profile of the normal human liver tissue

city: Los Angeles

first: Meng

last: Li

state: CA

address: 2003 Zonal Avenue

institute: University of Southern California

summary: The regulatory mechanisms that shapes the hepatic zonation is not well understood. In addition, the concept and significance of of hepatic zonation is well established in rodens, however, its relavence to human liver biology remain elusive. We conducted a comprehensive transcriptome analysis of each zonation within normal human liver vis Laser Capture Microdissection approach. Here,  we report a poly A RNA sequencing data of the individual zone of liver tissue as well as the whole liver of the corresponding subjects.

overall_design: The RNA samples were collected from each zone within hepatic lobule by a Laser Captured Microdissection approach. This study examined the gene expression profile in each zone of the normal human liver.

first: Takeshi

last: Saito


title: Profiling DNA Methylation Differences Between Inbred Mouse Strains on the Illumina Human Infinium MethylationEPIC Microarray

status: Public on Feb 15 2018

city: Memphis

first: Khyobeni

last: Mozhui

state: TN

address: 66 N. Pauline Street, #631

department: Preventive Medicine

institute: University of Tennessee Health Science Center

summary: We used the Illumina Infinium MethylationEPIC to measure DNA methylation in mouse liver samples. We identified 13,665 conserved probes and compared methylation signal with sequecing based data (MBD-seq and RRBS)

overall_design: Mouse tissue were from two different inbred strains (C57BL/6J and DBA/2J) and from 3 age groups classified as young (4 months), mid (11–12 months) and old (24 months).


title: Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance.

city: Clayton

first: Patrick

last: Western

address: 27-31 Wright Street

department: Centre for Reproductive Health

institute: Hudson Institute of Medical Research

summary: Background: Defining the mechanisms that establish and regulate the transmission of epigenetic information from parent to offspring is critical for understanding disease heredity. Currently, the molecular pathways that regulate epigenetic information in the germline and its transmission to offspring are poorly understood. Results: Here we provide evidence that Polycomb Repressive Complex 2 (PRC2) regulates paternal inheritance, both at the phenotypic and molecular levels. Reduced PRC2 function in mice resulted in male sub-fertility and altered epigenetic and transcriptional control of retrotransposed elements in fetal male germ cells. Males with reduced PRC2 function produced offspring that over-expressed retrotransposed pseudogenes and had altered preimplantation embryo cleavage rates and cell cycle control. Conclusion: This study reveals a novel role for the histone modifying complex, PRC2, in epigenetic inheritance, with important implications for understanding disease inheritance.

overall_design: ChIPseq experiment using H3K27me3 specific antibody. Eight replicates of OCT4GFP FACS purified E15.5 fetal male germ cells from Eedwt/wt (n=4) and Eedhypo/hypo (n=4) mice were compared, using Eedwt/wt samples as control vs Eedhypo/hypo germ cells as test samples.

first: Jessica

last: Stringer


title: Low carbohydrate diet study for non-alcoholic fatty liver disease patients

city: Solna

first: Adil

last: Mardinoglu

address: Tomtebodavägen 23B

department: Systems biology

institute: SciLifeLab, KTH

summary: We performed a short-term dietary intervention with a low-carbohydrate diet in obese subjects with NAFLD

overall_design: Transcriptomes were generated from liver biopsies of seven non-alcoholic fatty liver disease patients before/after low carbohydrate diet

first: Sunjae

last: Lee


title: Sequence variation within similar cis-elements promotes context-specific functions of two Drosophila GA-binding transcription factors

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

type: Genome binding/occupancy profiling by array


title: Salt-stress and CTD phosphatase-like 4 mediate switching of snRNA to mRNA transcription in Arabidopsis thaliana [CPL4(Oto)]

first: Akihito

last: Fukudome

overall_design: Examination of two genotypes (wild-type and CPL4 knockdown) in biological triplicate

first: Hisashi

last: Koiwa


title: H3K27Ac in MCF7 Y537S ER mutant cells and RNAseq with and without treatment with THZ1

first: Rinath

last: Jeselsohn

state: MD

address: 450 Brookline Ave, D728

department: Medical Oncology

institute: DFCI

summary:
H3K27Ac ChIP-seq in MCF7 Y537S ER mutant cells
RNAseq analysis of MCF7 Y537S ER mutant cells treated with veh and THZ1

overall_design:
H3K27ac ChIP-seq in MCF7 cells with DOX-inducible expression of the Y537S ER mutant in cells without induction of the mutation in E2 stimulated conditions and cells with DOX induction of the mutation in hormone deprived conditions
RNAseq of cells with DOX-induced expression of the Y537S mutation with veh treatment and THZ1 treatment for 6 hrs and 24 hrs

first: Myles

last: Brown


title: Luminal subtype-specific circRNAs in breast cancer cells by a novel tool for external data analysis.

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

summary: Circular RNAs are molecules present in all eukaryotes that are generated from a large number of genes by a particular processing of transcripts. We have exploited poly(A-) RNA-Seq data generated in our lab in MCF-7 breast cancer cells to define a compilation of exonic circRNAs more comprehensive than previously existing lists. Development of novel computational algorithms allowed us to quantitatively evaluate expression of these circRNA also in publicly available data. We report here novel findings with important implications both for circRNA biogenesis and as specific markers for breast cancer. We observed and confirmed by ChIP analysis that exons involved in circularization events display significantly higher levels of the histone post-transcriptional modification H3K36me3 than non-circularizing exons. This suggests a clear link with a published alternative splicing mechanism in the circRNA biogenesis mechanism. We also found that circRNAs contain an unexpectedly elevated number of Ago binding sites, revamping the hypothesis of circRNAs acting as miRNA sponges in some cases. Finally, we report that a subset of MCF-7 circRNAs are specific to tumor versus normal tissue, while others can differentiate the Luminal tumor subtype, thus suggesting that circRNAs can be exploited as novel biomarkers and drug targets for breast cancer.

overall_design: The RNA-seq datasets were obtained from libraries generated with the TruSeq stranded library preparation kit (Illumina) using as input material RNA depleted of both poly(A+) and ribosomal RNAs fractions. Pool of 12 libraries (pooled at equimolar concentration) was generated, quantified and run on the HiSeq2000 (Illumina) sequencer in 50 nts paired-end sequencing mode following manufacturer instruction. A total of 12 datasets, with an average depth from 30.7 to 116.1 million paired-end reads, were obtained, composed of triplicates of four MCF-7 culture conditions: i) hormone-deprived (HD) media ii) HD+ 17b-estradiol (6h) iii) medium added of FSC 5% iv) double-stranded RNA complementary to ESR1 mRNA (siRNA) (48h).

first: Lucia

middle: T

last: Coscujuela

first: Valentina

last: Miano

first: Carlo

last: De Intinis

first: Mariangela

last: Arigoni

first: F

last: Riccardo

first: Raffaele

last: Calogero

first: Marco

last: Beccuti

first: Francesca

last: Cordero

first: Michele

last: De Bortoli


title: Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone [single-cell RNA-Seq]

city: New York

first: Frederique

last: Ruf-Zamojski

state: NY

address: 1468 Madison Avenue

department: Neurology

institute: Mount Sinai Medical Center

summary: The LβT2 mouse pituitary cell line has many characteristics of a mature gonadotrope and is a widely used model system for studying developmental processes and the response to gonadotropin-releasing hormone (GnRH). The global epigenetic landscape, which contributes to cell-specific gene regulatory mechanisms, and the single-cell transcriptome response variation of LβT2 cells have not been previously investigated. Here, we integrate the transcriptome and genome-wide chromatin accessibility state of LβT2 cells during GnRH stimulation. Additionally, we examine cell-to-cell variability in the transcriptional response to GnRH using gel-in-emulsion Drop-seq technology. Analysis of a bulk RNA-seq dataset obtained 45 minutes after exposure to either GnRH or vehicle identified 112 transcripts that were regulated > 4-fold by GnRH (FDR < 0.05). The top regulated transcripts constitute, as determined by Bayesian massive public data integration analysis, a human pituitary-relevant coordinated gene program. Chromatin accessibility (ATAC-seq) datasets generated from GnRH-treated LβT2 cells identified more than 58,000 open chromatin regions, some containing notches consistent with bound transcription factor footprints. Study of the most prominent open regions showed that 75% were in transcriptionally active promoters or introns, supporting their involvement in active transcription. Lhb, Cga, and Egr1 showed significantly open chromatin over their promoters. While Fshb was closed over its promoter, several discrete significantly open regions were found at -40 to -90 kb, which may represent novel upstream enhancers. Chromatin accessibility determined by ATAC-seq was associated with high levels of gene expression determined by RNA-seq. We obtained high quality single-cell gel-in-emulsion Drop-seq transcriptome data, with an average of >4000 expressed genes/cell, from 1992 vehicle- and 1889 GnRH-treated cells. While the individual cell expression patterns showed high cell-to-cell variation, representing both biological and measurement variation, the average expression patterns correlated well with bulk RNA-seq data. Computational assignment of each cell to its precise cell cycle phase showed that the response to GnRH was unaffected by cell cycle. To our knowledge, this study represents the first genome-wide epigenetic and single-cell transcriptomic characterization of this important gonadotrope model. The data have been deposited publicly and should provide a resource for hypothesis generation and further study.

overall_design: GEM Drop-seq was performed on two samples of LβT2 cells: one control sample (vehicle-treated for 40 min) and one GnRH-treated (2 nM GnRH for 40 min).

first: Miguel

last: Fribourg

first: Yongchao

last: Ge

first: Venugopalan

last: Nair

first: Hanna

last: Pincas

first: Elena

last: Zaslavsky

first: German

last: Nudelman

first: Stephanie

last: Tuminello

first: Hideo

last: Watanabe

first: Judith

last: Turgeon

first: Stuart

middle: C

last: Sealfon


title: TGF-beta signalling through SMAD1/5 is required for epithelial-to-mesenchymal transition

city: London

first: Caroline

last: Hill

address: 1 Midland Road

institute: Francis Crick Institute

summary: TGF-beta treatment leads to SMAD1/5 phosphorylation. However, the ability of SMAD1/5 to bind chromatin downstream of TGF-beta signalling is unknown. We performed ChIP-sequencing for pSMAD1/5 and SMAD3 to identify binding sites for pSMAD1/5 upon TGF-beta stimulation and identified preferential pSMAD1/5 binding at SMAD1/5:SMAD4 consensus sites.

overall_design: MDA-MB-231 cells untreated or treated with TGF-beta for 1 h and then examined with a SMAD3 or pSMAD1/5 antibody. The SMAD3 acts as a control as it is well known that SMAD3 is required for transcriptional regulation of many TGF-beta target genes.

first: Anassuya

last: Ramachandran

first: Probir

last: Chakravarty

first: Pedro

last: Vizan

first: Debipriya

last: Das

first: Janis

last: Voyt

first: Andrew

last: Hinck

first: Gopal

last: Sapkota


title: Bypassing drug-resistance mechanisms of prostate cancer with small-molecules that target androgen receptor chromatin interactions

city: Minneapolis

first: Scott

last: Dehm

state: MN

address: 8806 420 Delaware

department: Masonic Cancer center

institute: University of Minnesota

summary: Human androgen receptor (AR) is a hormone-activated transcription factor that is an important drug-target in the treatment of prostate cancer. Current small molecule AR-antagonists (such as Enzalutamide) compete with male hormones that bind to the steroid binding pocket of the AR ligand binding domain (LBD). In castration-resistant prostate cancer (CRPC), drug-resistance can manifest through AR-LBD mutations that convert AR-antagonists into agonists, or by expression of AR-variants lacking the LBD. Such treatment resistance underscores the importance of novel ways of targeting the AR.  In this study, we tested whether VPC14449, a small molecule inhibitor that was rationally designed to selectively target the AR DNA binding domain (DBD), could directly interfere with AR-DNA interactions.  Using ChIP-seq in cell line models expressing AR or AR variants, we found that genome-wide chromatin binding of AR was dramatically impacted by VPC14449 (although with lesser effect on AR variants).

overall_design: AR and AR variant ChIP-seq in R1-AD1 and R1-D567 prostate cancer cells with VPC14449 treatment

first: Rendong

last: Yang

first: Meixia

last: Che


title: Role of remodeling and spacing factor 1 in histone H2A ubiquitination mediated gene silencing

city: Birmingham

first: Hengbin

last: Wang

state: AL

address: 720 20th St S Kaul Bldg 430

department: Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: Posttranslational modification of histones plays important roles in regulating chromatin-based nuclear processes. Histone H2A ubiquitination (H2Aub) is a prevalent modification and has been primarily linked to gene silencing; however, the mechanism by which H2Aub represses gene expression remains largely unclear. Here we report the identification of RSF1 (remodeling and spacing factor 1), a subunit of the RSF (remodeling and spacing factor) complex, as a novel H2Aub binding protein which mediates the repressive function of H2Aub on gene expression. RSF1 preferentially associates with H2Aub nucleosomes through a previously uncharacterized region designated as the ubiquitinated H2A binding (UAB) motif. RSF1 interacts with H2Aub nucleosomes specifically and the UAB motif is required for RSF1 to interact with H2Aub nucleosomes in vitro and in vivo. Genes regulated by RSF1 overlap significantly with genes regulated by RNF2 or Ring1B, the catalytic subunit of Polycomb repressive complex 1, in both human and mouse cells. RSF1 binds to gene promoter regions, and over 92% of H2Aub enriched genes, including the classic PRC1 target Hox genes, are co-bound by RSF1. Reduction of H2Aub levels by Ring1B knockout results in a significant reduction of RSF1 binding. RSF1 knockout does not affect RNF2/Ring1B or H2Aub levels but results in re-expression of H2Aub target genes, accompanied by a reduction in the spacing and stability of H2Aub nucleosomes. The direct role of RSF1 in repressing H2Aub target gene expression is further demonstrated by chromatin based in vitro transcription assay. Finally, RSF1 regulates Xenopus early embryonic development and gene expression in a fashion similar to that of PRC1 subunit Ring1A. Therefore, this study identifies RSF1 as a novel H2Aub binding protein and reveals that RSF1 contributes to H2Aub mediated gene silencing by maintaining a regular spaced, stable nucleosome array at promoter regions.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of binding pattern of RSF1, gene expression profiles and nucleosome position in wildtype and RSF1 knock out mouse embryonic stem cells. And binding pattern of RSF1 and gene expression profiles in wildtype and RSF1 knock down HeLa cells.

first: Zhuo

last: Zhang

first: Amanda

last: Jones

first: Wei

last: Wu

first: Jinman

last: Kim

first: Yue

last: Kang

first: Xiaobao

last: Bi

last: Gu

first: Matthew

middle: B

last: Renfrow

first: Marina

middle: N

last: Vassylyeva

first: Dmitry

last: Vassylyev

first: Keith

last: Giles

first: Dongquan

last: Chen

first: Yufeng

last: Tong

first: Chuan

middle: F

last: Liu

first: Woojin

last: An

first: Chenbei

last: Chang

first: Jianjun

last: Luo


title: ChIP-Seq of H3K9me3 and H3K36me3 after GFP or dKDM4A RNAi of S2 cells

city: berkeley

first: serafin

last: colmenares

address: 1 cyclotron road MS977R180A

institute: lawrence berkeley national lab

summary: Analysis of H3K9me3 and H3K36me3 levels in unique and repetitive regions of Drosophila genome after GFP (control) or dKDM4A RNAi of S2 cells

overall_design: After 5 days of RNAi, chromatin was prepared by fixation of 2x10^7 S2 cells with 1% paraformaldehyde for 10 minutes and shearing with Bioruptor sonicator (30 cycles). ChIP was performed by overnight incubation of chromatin with Protein-A Dynabeads and 5 ug of either anti-H3K36me3 or anti-H3K9me3 ChIP-grade antibody (Abcam). Library construction was conducted using TruSeq DNA sample preparation kit (Illumina). All sequencing data were obtained from the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley.

first: Serafin

middle: U

last: Colmenares

first: Gary

middle: H

last: Karpen


title: Spindle-localized mRNA translation mediated by CPEB1 and CPEB4 controls mitotic progression

city: Bariloche

first: Nicolas

last: Bellora

state: Rio Negro

address: Quintral 1250

department: IPATEC

institute: CONICET

summary: Sequencial functions of CPEB1 and CPEB4 in the localization of repressed mRNAs to the mitotic spindle and their subsequent phase-specific activation to promote cell phase transitions and correct chromosome segregation

overall_design: RNA-seq of total and spindle-associated mRNAs in Hela S3 cells

first: Rosa

last: Pascual

first: Raul

last: Mendez


title: Genome-wide gene expression analysis of Y-chromosome aneuploidy strains of Drosophila melanogaster

first: Bernardo

last: Lemos

address: 655 Huntington Avenue

department: Environmental Health

institute: Harvard T.H. Chan School of Public Health

summary: Y-chromosome aneuploidy strains were generated for 2 distinct Y chromosomes (Ycongo and Yohio), and expression profile analyzed by RNA-seq.

overall_design: CONTRAST 1: X^X (control) vs X^XYohio; CONTRAST 2: X^X (control) vs X^XYcongo; CONTRAST 3: X^Y (control) vs X^YYohio; CONTRAST 4: X^Y (control) vs X^YYcongo.

first: Alan

last: Branco


title: RNA-seq of S2 cells after GFP (control), dKDM4A, or HP1a RNAi

summary: Analysis of transcriptional changes from genes and repetitive elements after dKDM4A and HP1a RNAi of S2 cells

overall_design: After 5 days of RNAi, total RNA was harvested using Trizol reagent from 5 x 106 S2 cells, and mRNA was purified using oligo-dT-conjugated magnetic beads. Library construction was conducted using TruSeq RNA sample preparation kits (Illumina). All sequencing data were obtained from the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley.