title: METTL9 methylates H2B a-N-proline and suppresses human retrotransposition

city: Beer-Sheva

first: Eitan

last: Rubin

address: Building 39 room 005

institute: Ben Gurion University of the Negev

summary: The methylation of residues within histones plays a central role in regulating genome function; however, little is known about the biological importance of a-N-terminal histone methylation. Here we explored the function of the previously uncharacterized a-N methylation of mammalian histone 2B proline 1 (H2BP1me). Genome-wide analyses revealed an enrichment of H2BP1 methylation at certain transposable elements (TEs) and repetitive genomic sequences. We identified a novel histone methyltransferase, METTL9, which specifically methylates H2BP1. Depletion of METTL9 led to reduced H2BP1me2 levels, an accumulation of gH2A.X, expression activation of some TEs, and increased retrotransposition of a human LINE-1 containing a reporter gene; the latter being a unique feature amongst histone modifiers described to date. These data suggest that reduced H2BP1 methylation may lead to increased TE activity and genome instability.   Indeed, decreased levels of H2BP1 methylation in colon tumors correlated with an increase in LINE-1 protein expression. Furthermore, METTL9 depletion in cultured cells led to an enhancement of cellular proliferation, invasion, and migration, suggesting that a loss of H2BP1 methylation could play a role in cancer progression. Thus, we have identified a new role for H2BP1 N-terminal histone methylation in regulating chromatin function and perhaps disease progression, thereby highlighting the role of METTL9 as a novel guardian of genomic stability.

overall_design: H2B Proline (e.g. mono methyl and demethyl) methylation were Chiped and sequenced

first: Idan

last: Cohen

first: Robert

last: Schneider


title: Polycomb- and Methylation-Independent Roles of EZH2 as a Transcription Activator [RNA-seq]

status: Public on Dec 01 2018

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

country: USA

institute: Emory University

type: Expression profiling by high throughput sequencing

summary: EZH2 induces active transcription of the AR gene, thereby increasing AR level and promoting AR signaling. Importantly, EZH2-mediated activation of AR requires EZH2 protein occupancy at the AR gene promoter, but is independent of PRC2 as well as its histone methyltransferase activity

overall_design: RNA-seq examination of combinatorial effects of ENZ+EPZ in prostate cancer cells signaling pathway

first: Jung

last: Kim


title: Human Sperm Epigenomes and Transcriptomes Reveal Novel Features of Enhancers, Sex Chromosomes, piRNAs, Gametogenesis, and Inherited Small RNAs

status: Public on Dec 03 2018

city: Bethesda

first: Andrew

middle: J

last: Oler

state: MD

address: 31 Center Drive, Room 3B62E

department: Bioinformatics and Computational Biosciences Branch (BCBB)

institute: NIAID/NIH

type: Methylation profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RNA-seq of WT, hrr25as, and hrr25is treated with inhibitors

status: Public on Dec 02 2018

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

summary: The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) orchestrates dynamic recruitment of specific cellular machines during different stages of transcrption. Signature phosphorylation patterns of Y1S2P3T4S5P6S7 heptapeptide repeats of the CTD engage specific "readers." While phospho-Ser5 and phospho-Ser2 marks are ubiquitous, phospho-Thr4 is reported to only impact specific genes. Here, we investigate the transcriptome in WT cells, hrr25as cells, or hrr25is cells in the presence or absence of ATP analog inhibitors.

overall_design: Total RNA was collected from WT, hrr25as, and hrr25is cells treated with either DMSO or CMK.

first: Nemec

last: CM

first: Ansari

last: AZ


title: Characterizing the Key Metabolic Pathways of the Neonatal Mouse Heart Using a Quantitative Combinatorial Omics Approach

city: Helsinki

first: Matti

last: Kankainen

address: PL0056 (Viikinkaari 5)

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

summary: The heart of new-born mouse has exceptional capacity to regenerate from myocardial injury. However, the mouse heart loses this capacity within the first week of its life. In order to elucidate the molecular mechanisms taking place in the mouse heart during the loss of its regenerative potential, a systematic comparison of 1-day and 7-day-old mouse hearts was performed at the proteomic, metabolomic, and transcriptomic levels.

overall_design: RNA-seq gene expression of hearts of postnatal day 1 and day 7 Hsd:ICR(CD-1®) male mice

first: Esko

last: Kankuri

first: Eero

last: Mervaala

first: Maciej

last: Lalowski


title: General and sequence-specific roles for DNA in glucocorticoid receptor DNA-binding stoichiometry

city: Iowa City

first: Miles

middle: A

last: Pufall

state: IA

address: 51 Newton Rd., BSB Rm 4-430

department: Biochemistry

institute: University of Iowa

summary: The glucocorticoid receptor (GR) binds to DNA in at least three stoichiometric ratios to regulate gene expression. The dimeric binding of GR to a 15 base pair core sequence has been well studied, and is associated with activation of gene expression. Monomeric GR has been associated with repression. GR has also been shown to form tetramers on DNA in live cells. The role of DNA sequence in directing DNA-binding stoichiometry and subsequent gene regulation is not clear. We took an unbiased approach using SELEX-seq to calculate comprehensive monomeric- and dimeric-binding profiles for GR. The monomeric site is composed of a canonical half-site, but is distinguished from the dimer site by a downstream TTTg motif and the absence of a second half-site. To probe the mechanism of how this motif favors monomeric binding, we performed Spec-/Coop-seq. The TTTg increases monomeric affinity while decreasing cooperative dimeric binding. Crystal structures indicated that TTTg results in a narrowed minor groove bringing residues Y455 and K471 of GR into the proximity of DNA, increasing affinity. Interestingly, although monomeric binding is more often associated with repression of gene expression than dimeric binding, the trend is not significant. Consistent with live-cell imaging, a meta-analysis of GR:DNA structures reveals that, regardless of binding sequence, GR binds to DNA as a dimer of dimers using highly similar interfaces. This suggests that the functional stoichiometry of GR in the cell is tetrameric, and that sequence may modulate GR activity.

overall_design: Two ChIP-seq samples.  GR was ChIPed from SUP-B15 cells in the presence of vehicle (0.02% ethanol) or 1µM dexamethasone.

first: Mimi

last: Fang


title: Mutant IDH1 promotes glioma formation in vivo

city: Salt Lake City

first: Sheri

last: Holmen

state: UT

address: 2000 Circle of Hope Dr.

department: Surgery

institute: University of Utah


title: Analysis of transcriptome between clv3 and mpclv3

status: Public on Dec 04 2018

city: Hefei

first: Zhong

last: Zhao

state: Anhui

address: Huangshan Road 443

department: School of Life Sciences

country: China

institute: University of Science and Technology of China

summary: The targets of AUXIN REPONSE FACTOR5/MONOPTEROS (ARF5/MP) were reported in many studies which mainly concerned to the flower initiation. But most of these targets are expressed in periphery zone (PZ), how MP regulate the stem-cell activity is unclear. In order to specifically identify the targets of MP in stem cells, as clv3 mutant enrich lots of stem cells, thus we performed transcriptomes of clv3 and mpclv3. This method will enhance the resolution of MP targets specific in stem cells. And it will also avoid the severe morphologic difference between WT and mp single mutant.

overall_design: Examination of transcriptome profile in 2 genotypes with 2 biological replicates each.

first: Linjie

last: Luo

first: Jian

last: Zeng


title: Mutant IDH1 promotes glioma formation in vivo [RNA-seq]

summary: RNA was isolated from FFPE samples of IDH1 mutant, WT tumors and normal brains

overall_design: Determination of the glioma subtype in IDH1 mutant and WT tumors

first: Beatrice

last: Philip

first: Mark

middle: R

last: Silvis

first: Diana

middle: X

first: Clifford

middle: H

last: Shin

first: James

middle: P

last: Robinson

first: Gemma

middle: L

first: Stephanie

middle: N

last: Angel

first: Adam

middle: E

last: Welker

first: Sheryl

last: Tripp

first: Joshua

last: Sonnen

first: Matthew

middle: W

last: VanBrocklin

first: Richard

last: Gibbons

first: Ryan

last: Looper

first: Howard

last: Colman


title: Expression profiling of mouse eosinophils and myeloid progenitors

city: Parkville

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: We have sequenced using single end and paired end sequencing GMPs, CMPs, EoPs, SiglecF+IL5ra- GMPs and eosinophils to be able to characterise this new subset of GMPs and to be able to give it some context within a lineage trajectory analysis

overall_design: RNA-seq was performed on GMPs (n=2), CMPs (n=2), EoPs (n=2), Eosinophils (n=3) and SiglecF+IL5ra- GMPs isolated from C57BL/6 (n=5) and Myb hypomorphic Plt4/Plt4 mice (n=4).

first: Kirsten

last: Fairfax

first: Jessica

last: Bolden

first: Carolyn

last: de Graaf

first: Douglas

last: Hilton


title: Mutant IDH1 promotes glioma formation in vivo [Bisulfite-seq]

first: Sheri

last: Holmen

summary: Genomic DNA from IDH1 mutant and WT tumors were used to detect genome wide methylation using Agilent SureSelect XT Mouse Methyl-Seq Enrichment System capture kit following manufacturer’s recommendations.

overall_design: Whole genome methylation analysis on IDH mutant and WT cell lines

first: Beatrice

last: Philip

first: Mark

last: Yu


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and mutant E. coli K-12 MG1655 Transcriptomes

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

institute: University of Queensland

summary: The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of wild-type E. coli K-12 MG1655 and triclosan induced E. coli mutants in response to 0.2 mg/L triclosan for 8 h, in triplicate, using Illumina HiSeq 2500.The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

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

overall_design: Bacterial mRNA profiles of wild-type E. coli K-12 MG1655 and triclosan induced E. coli mutants in response to 0.2 mg/L triclosan for 8 h, in triplicate, using Illumina HiSeq 2500

first: Ji

last: Lu

first: Min

last: Jin

first: Likai

last: Mao


title: Degradation of unmethylated miRNA/miRNA*s by a DEDDy-type 3’ to 5’ exoribonuclease ATRIMMER2 in Arabidopsis

city: Nashville

first: Yongchao

last: Dou

state: Tennessee

address: 2525 west end

institute: vanderbilt medical center

summary: 3’ end methylation catalyzed by HUA ENHANCER1 (HEN1) is a crucial step of small RNA stabilization in plants, yet how unmethylated small RNAs undergo degradation remains largely unknown. Using a reverse genetic approach, we here show that ATRIMMER2 (ATRM2), a DEDDy-type 3’ to 5’ exoribonuclease, acts in the degradation of unmethylated miRNAs and miRNA*s in Arabidopsis. A loss-of-function mutations in ATRM2 partially suppress the morphological defects caused by HEN1 malfunction, with restored levels of a subset of miRNAs and receded expression of corresponding miRNA targets. Loss of ATRM2 has negligible effect on miRNA trimming, and further increase the fertility of hen1 heso1 urt1, a mutant with an almost complete abolishment of miRNA uridylation, indicating that ATRM2 may neither be involved in 3’ to 5’ trimming nor be the enzyme that specifically degrades uridylated miRNAs. Notably, the fold changes of miRNAs and their corresponding miRNA*s were significantly co-regulated in hen1 atrm2 as compared with those in hen1. Unexpectedly, we also observed a markedly increase of 3’ to 5’ trimming of several miRNA*s but not miRNAs in ATRM2 compromised backgrounds. These data suggest an action of ATRM2 on miRNA/miRNA* duplexes, and the existence of an unknown exoribonuclease for specific trimming of miRNA*. This asymmetric effect on miRNA/miRNA* is likely related to ARGONAUTE (AGO) proteins, which can distinguish miRNAs from miRNA*s. Finally, we show that ATRM2 colocalizes and physically interacts with ARGONAUTE1 (AGO1). Taken together, our results suggest that ATRM2 may be involved in the surveillance of unmethylated miRNA/miRNA* duplexes during the initiation step of RISC assembly.

overall_design: Examination of total and  AGO1-associated small RNAs in different genotypes

first: Xiaoyan

last: Wang

first: Ning

last: Jiang

first: Guodong

last: Ren


title: HMGA2 Promotes Long-Term Engraftment and Myelo-Erythroid Differentiation of Human Hematopoietic Stem and Progenitor Cells

city: Sydney

first: Dominik

last: Beck

state: NSW

address: Level 10, UTS Building 11 (CB11 81-113, Broadway, Ultimo)

department: School of Biomedical Engineering

institute: University of Technology Sydney

summary: Identification of determinants of fate choices in hematopoietic stem cells (HSCs) is essential in order to improve the clinical use of HSCs and to enhance our understanding of the biology of normal and malignant hematopoiesis. Here we show that high mobility group AT hook 2 (HMGA2), a non-histone chromosomal binding protein, is highly and preferentially expressed in HSCs and the most immature progenitor cell subsets of fetal, neonatal and adult human hematopoiesis. Knockdown of HMGA2 by shRNA impaired the long-term hematopoietic reconstitution of cord blood (CB) derived CB CD34+ cells. Conversely, overexpression of HMGA2 in CB CD34+ cells led to an overall enhanced reconstitution in serial xenotransplantation assays accompanied by a skewing towards the myeloerythroid lineages. RNA-Seq analysis showed that enforced HMGA2 expression in CD34+ cells induced gene expression signatures associated with differentiation towards megakaryocyte-erythroid and myeloid lineages, as well as signatures associated with growth and survival, which at the protein level were coupled with a strong activation of AKT. Taken together our findings demonstrate a key role of HMGA2 in regulation of both proliferation and differentiation of human HSPCs.

overall_design: RNA-Seq  on control and HMGA2 transduced CD34+ cells.

first: Praveen

last: Kumar

first: Jonas

last: Larsson

first: Julie

last: Thoms


title: Human Sperm Epigenomes and Transcriptomes Reveal Novel Features of Enhancers, Sex Chromosomes, piRNAs, Gametogenesis, and Inherited Small RNAs (RNA-Seq)

first: Andrew

last: Oler

summary: To better understand the paternally inherited epigenome and transcriptome, we profiled multiple histone modifications, histone H3.3 variant, cytosine DNA methylation at base-pair resolution, and small RNA transcriptomes. We report new and surprising features of enhancers, pluripotency factor targets, spermiogenesis genes, piRNA clusters, CpG islands, partially methylated domains, imprinted loci, repetitive elements and sex chromosomes. First, we find that enhancers for embryonic transcription factors bear H3K27me3, but low H3K14ac and DNA methylation -- consistent with poising for future activation -- whereas enhancers near genes active in gametogenesis have high H3K27ac/H3K14ac, consistent with past activation. Second, binding site regions (in ES cells) for the pluripotency factors SOX2 and NANOG are DNA methylated in sperm, suggesting a need for zygotic demethylation/reprogramming. Unexpectedly, genes for spermiogenesis (but not spermatogenesis), and almost half of piRNA cluster promoters, bear both H3K4me3 and DNA methylation, a co-incidence not previously observed in mammals. Furthermore, we find major assymetries in H3.3 and H3K9me3 density between the X and Y chromosomes after MSCI. Lastly, deep sequencing reveals >10-fold increase in the known repertoire of retained/inherited miRNAs and piRNAs than previous estimates. Thus, the paternal epigenome contributes a mosaic of epigenetic regions that reflect past gametogenesis or poising for subsequent embryonic developmental regulation -- and a complex repertoire of small RNAs.

overall_design: Total RNA was extracted from the sperm of two independent fertile donors and subjected to directional RNA-seq using both small RNA-seq and mRNA-seq Illumina protocols.

first: Saher

middle: S

last: Hammoud

first: David

last: Nix

last: Carrell

first: Bradley

last: Cairns


title: ASXL2 is recurrently mutated in t(8;21) AML and regulates hematopoietic development

city: Singapore

first: Phillip

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute


title: Transcriptome analysis of Envelope and VaWRKY12 overexpressing callus lines generated from Vitis amurensis

city: Wuhan

first: langlang

last: zhang

state: HuBei

address: Cross road of Jiufeng 1 and Guanggu 7 road

institute: Wuhan Botanical Garden, Chinese Academy of Sciences

summary: To investigate the downstream genes of VaWRKY12 during cold stress response in grapevine, RNA-Seq was carried out on three biological replicates of EV (4EV-1, 4EV-2 and 4EV-3) and 3 transgenic callus lines (4#OE-1, 4#OE2 and 4#OE3) undercold treatment conditions

overall_design: Examination of gene expression changes after overexpression of VaWRKY12 in grapevine under cold treatment and identification of VaWRKY12 downstream genes.

first: Langlang

last: Zhang

first: Shaohua

last: Li

first: Haiping

last: Xin


title: Genome-Wide Identification of ABA Responsive microRNAs in the stem of Populus euphratica

city: Beijing

first: Conglong

last: Lian

address: 35 Tsinghua Eastern Road

institute: Beijing Forestry University

summary: More then 10 million raw reads were acquiredIn total, 247 unique mature sequences which contain 149 conserved miRNA and 98 novel miRNAs were identified.

overall_design: Nine sRNA libraries derived from three groups (control, ABA for 1 day and ABA for 4 days) with three librariesas biological replicate.

first: Xinli

last: Xia


title: ASXL2 is recurrently mutated in t(8;21) AML and regulates hematopoietic development [RNA_Seq_Asxl2_knockout]

summary: Chromosomal translocation t(8;21) (q22;q22) leading to generation of oncogenic RUNX1-RUNX1T1 (AML1-ETO) fusion is a cytogenetic abnormality observed in about 10% of acute myelogenous leukemia (AML). To uncover somatic mutations that cooperate with t(8;21)-driven leukemia, we performed targeted and whole exome sequencing of newly-diagnosed and relapsed AML samples. We identified high frequency of truncating alterations in ASXL2 along with recurrent mutations of KIT, TET2, MGA, FLT3, and DHX15 in this subtype of AML.  To investigate in-depth the role of ASXL2 in normal and malignant hematopoiesis, we utilized a mouse model of ASXL2 deficiency. Loss of ASXL2 caused progressive hematopoietic defects characterized by myeloid cell expansion, splenomegaly, extramedullary hematopoiesis and poor reconstitution ability in transplantation models. A parallel analysis of young and >1-year old Asxl2-deficient mice revealed age-dependent changes in the hematopoietic compartment leading to perturbations affecting not only myeloid and erythroid differentiation but also maturation of lymphoid cells. Our studies also suggest that expression of truncated ASXL2 protein confers proliferative advantage to mouse myeloid progenitors. Overall, these findings establish a critical role of ASXL2 in maintaining steady state hematopoiesis and provide insights into how its loss/mutation primes leukemic growth of myeloid cells.

overall_design: Bone marrow derived LSK cells from young (8-12 weeks old) and >1-year old Asxl2 WT and knockout mice were analyzed for gene expression changes.

first: Vikas

last: Madan

first: Lin

last: Han

first: H


title: ASXL2 is recurrently mutated in t(8;21) AML and regulates hematopoietic development [RNA_Seq_Asxl2_mutant]

overall_design: Gene expression analysis of bone marrow derived Lin- Kit+ cells expressing either mutant or full-length ASXL2


title: TP63-driven super-enhancer-associated LINC01503 promotes the malignancy of esophageal squamous cell carcinoma (4C-Seq)

summary: Background & Aims: Lineage-specific expression of long non-coding RNAs (lncRNAs)  has been observed recently. However, the underlying mechanism of such specific  transcription regulation is unclear. The aim of this study is to identify squamous cell carcinoma (SCC) lineage-specific lncRNAs and to investigate the mechanisms for their  expression and function.  Methods: Expression characteristics and functions of four candidate SCC-specific  lncRNAs were explored. qRT-PCR assays were employed to measure the expression  of LINC01503 in 113 tumor/normal matched esophageal SCC (ESCC) cases and its  association with survival was determined. The mechanisms underlying LINC01503  function and regulation in ESCC cells were examined using molecular biological  methods.  Results: Using SCC as a model, we identified a novel super-enhancer (SE)-driven  lncRNA, LINC01503, which was uniquely expressed in SCCs such as those from  esophagus (ESCC) and head and neck (HNSC). LINC01503 was up-regulated in  SCCs and its high expression correlated with poor clinical outcomes. SCC master  transcriptional factor TP63 directly bound to a SE at LINC01503 locus and activated its  transcription. LINC01503 exhibited strong oncogenic functions in ESCC cell models  both in vitro and in vivo. ERK2 and EBP-1 were identified as interacting proteins  mediating the effects of LINC01503. Specifically, LINC01503 protected ERK2 from  dephosphorylation by DUSP-6, leading to the activation of ERK/MAPK pathway.  Similarly, LINC01503 interfered the interaction between EBP-1 and PI3K p85,  enhancing Akt signaling pathway.  Conclusions: These results demonstrated that LINC01503 is a lineage-specific  oncogene in ESCC, which may serve as a potential biomarker and therapeutic target  for SCC patients.

overall_design: 4C sequencing of TE7 Esophageal Squamous Cell Carcinoma Cell Line

first: Jianjun

last: Xie

first: Yan-Yi

last: Jiang

first: De-Chen

last: Lin


title: TP63-driven super-enhancer-associated LINC01503 promotes the malignancy of esophageal squamous cell carcinoma

overall_design: Refer to individual Series


title: TP63-driven super-enhancer-associated LINC01503 promotes the malignancy of esophageal squamous cell carcinoma (ChIP-Seq)

overall_design: ChIP sequencing of Esophageal Squamous Cell Carcinoma Cell Lines


title: Transcriptional profile of human STAT1-/- fibroblasts expressing IFI6 or empty control vector

city: Dallas

first: John

last: Schoggins

state: Texas

address: 5323 Harry Hines Blvd

department: Department of Microbiology

institute: UT Southwester Medical Center

summary: Detection of viral infection by pattern-recognition receptors triggers production of interferon. Secreted interferon binds to cognate receptors, triggering JAK/STAT signaling, resulting in the transcription and production of hundreds of interferon-stimulated genes (ISGs). Our lab identified interferon alpha inducible protein 6 (IFI6) as an ISG that potently suppresses replication of viruses from the Flavivirus genus. To test whether the inhibitory effects of IFI6 were due to activating expression of other antiviral ISGs, we overexpressed IFI6 and a control vector and examined global transcription using RNA-Seq.

overall_design: Human STAT1-deficient fibroblasts stably expressing IFI6 or empty control vector in biological triplicate.

first: R

middle: B

last: Richardson

first: Maikke

last: Ohlson

first: Jennifer

last: Eitson

first: Ian

last: Boys

first: Katrina

last: Mar

first: Pamela

middle: C

last: De La Cruz-Rivera

first: Ashwani

last: Kumar

first: Chao

last: Xing


title: Gene expression profiles of mouse splenic CD4+Foxp3-PD-1hi T cells in comparison with Tregs and Tconv

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Differential gene expression in mouse splenic CD4+Foxp3-PD-1hi T cells

overall_design: 5 RNA samples from mouse splenic CD4+Foxp3-PD-1- T cells (double_negative), 5 RNA samples from mouse splenic Foxp3+Tregs (GFP_plus), 3 RNA samples from mouse splenic CD4+Foxp3-PD-1hi T cells (PD1_plus)

first: Roberta

last: Zappasodi

first: Taha

last: Merghoub

first: Jedd

middle: D

last: Wolchok


title: Polycomb- and Methylation-Independent Roles of EZH2 as a Transcription Activator [ChIP-seq]

first: Jindan

last: Yu

summary: EZH2 induces active transcription of the AR gene, thereby increasing AR level and promoting AR signaling. Importantly, EZH2-mediated activation of AR requires EZH2 protein occupancy at the AR gene promoter, but is independent of PRC2 as well as its histone methyltransferase activity

overall_design: ChIP-seq examination of EZH2 binding sites in LNCaP cells

first: Jung

last: Kim


title: H3K9 methyltransferase G9a negatively regulates UHRF1 transdcription during leukemia cell differentiation.

status: Public on Dec 31 2018

city: Seoul

first: Kee-Beom

address: Heusokdong

country: South Korea

institute: Chung-Ang University

summary: Posttranslational modifications of histone N-terminal tails influence the status of chromatin and eventually control the transcriptional outcome of a particular gene. As a histone H3K9 methyltransferase (HMTase) in higher eukaryotes, G9a-mediated transcriptional repression is the major epigenetic silencing machinery. UHRF1 (ubiquitin-like with PHD and ring finger domains I) binds to hemi-methylated DNA and plays essential role in maintenance of DNA methylation by recruiting DNMT1. Here, we provide evidence that UHRF1 is transcriptionally downregulated by H3K9 HMTase G9a. We found that increased expression of G9a along with transcription factor YY1 specifically represses UHRF1 transcription. We uncovered showed that G9a regulates UHRF1-mediated H3K23 ubiquitylation and proper DNA replication maintenance by FACS analysis and propose that H3K9 HMTase G9a is a specific epigenetic regulator of UHRF1.

overall_design: Identification of Histone 3 acetylation (Acetyl-H3) marks, RNA polymerase II (PolII) binding sites, Histone deacetylase 2 (HDAC2), Histone 3 lysine 27 trimethylation (H3K27-me3) marks, and Histone 2A lysine 119 ubiquitination (H2AK119-ub) marks in HL-60 cells treated with 32 nM 12-O-tetradecanoylphorbol 13-acetate (TPA) or solvent control.

first: Hye-Ju

last: Son

first: Sang-Beom

last: Seo


title: Folate modulation induces chromosomal instability and higher proliferation of immortalized human keratinocytes

city: Heidelberg

first: Thorsten

last: Zenz

address: Im Neuenheimer Feld 460

department: Department of Translational Oncology

country: Germany

institute: German Cancer Research Center (DKFZ)

summary: Gene expression variation upon folate deficiency and repletion in human foreskin keratinocytes immortalized by HPV16E6E7

overall_design: Effects of folate modulation on several cellular events such as DNA stability

first: Claudia

last: Savini

first: Agnes

last: Hotz-Wagenblatt

first: Frank

last: Rösl


title: Gene expression profiles of human circulating CD4+CD25-PD-1hi T cells in comparison with Tregs and Tconv

summary: Differential gene expression in human circulating CD4+CD25-PD-1hi T cells

overall_design: 5 RNA samples from human circulating CD4+CD25-PD-1- T cells (double_negative), 5 RNA samples from human circulating CD25hi Tregs (CD25_plus), 5 RNA samples from human circulating CD4+CD25-PD-1hi T cells (PD1_plus).


title: RNA-seq of mRNAs from spleen and bursa of Fabricius of white leghorn chickens (specific pathogen-free)

city: Guangzhou

first: Wenwu

last: Zhang

address: Wushan street, Tianhe District, Guangzhou 510642, Guangdong, China

institute: South China Agricultural University

summary: We have used RNA-seq to examine mRNAs from chicken spleen and bursa of Fabricius of three different condition (non-immunized and non-heat-stressed (24 ± 1℃ for 3 h), immunized (Newcastle disease vaccine) and non-heat-stressed, and immunized and heat-stressed (36 ± 1℃ for 3 h)). To clarify how chicken immune systems responded to heat stress with and without immunization.

overall_design: To assess mRNA expression during chicken immune systems responded to heat stress with and without immunization, we sequenced and analyzed spleen and bursa of Fabricius at three groups: 1) non-immunized and non-heat-stressed, 2) immunized and non-heat-stressed, and 3) immunized and heat-stressed.

first: Xiquan

first: Qingbin

last: Luo


title: Transcript leader elements contribute to competitive discrimination of mRNAs by the translational machinery

city: Baltimore

first: Boris

last: Zinshteyn

state: Maryland

address: 725 N Wolfe St, PCTB 714

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: Pools of yeast transcript leaders display differential ribosome recruitment in yeast lysates.

overall_design: Ribosome-association measurements (CIVIT-seq) of native and mutant transcript leader sequences.

first: Maria

middle: F

last: Rojas-Duran

first: Wendy

middle: V

last: Gilbert


title: miRNAs in adipose tissue derived exosomes (Exo-AT) and adipose  stem cells derived exosomes (Exo-ADSCs)

city: cheng du

first: Yan

address: No. 14, 3rd Sec., Ren Min Nan Road, Chengdu 610041, Sichuan Province, P.R. China

institute: West China School of Stomatology, Sichuan University

summary: The emerging evidences support that exosome cargo miRNAs function as important regulators in cell differentiation. Therefore, in order to figure out the mechanism that Exo-AT mediated adipogenesis, we profiled miRNAs in Exo-AT using high-throughput sequencing (miRNA-seq). After trimming low-quality reads, contaminants, adaptors, and reads smaller than 15 nt, the remaining reads were mapped to merged pre-miRNA data bases. To identify the conserved miRNAs in Exo exosomes, miRNAs were aligned to miRBase v21. 148 and 154 types of known miRNAs in Exo-ADSCs and Exo-AT, respectively, were identified in the two replicates. Among these miRNAs, 103 miRNAs were simultaneously detected in both Exo-ADSCs and Exo-AT. Compared to Exo-ADSCs, 45 conserved miRNAs were enriched (expressed ≥ 2 folds, FDR<0.05) in Exo-AT. KEGG Pathway analysis was performed for the targets of the most 20 enriched miRNAs in Exo-AT (compared with Exo-ADSCs) to determine their potential function. Data showed that pathways that regulate adipogenesis such as Wnt signaling pathway, Insulin signaling pathway, MAPK signaling pathway, TGF-ß signaling pathway were enriched significantly for targets of Exo-AT miRNAs. Furthermore, 14 of 45 enriched miRNAs in Exo-AT (31.11%, such as miR-30a-5p, miR-148a-3p) were reported to participate in regulation of adipogenesis while 8 miRNAs (17.78%, such as miR-93-5p, miR-150-3p) that negatively control osteoblastic differentiation of MSC have been described.

overall_design: Detection of miRNAs in Exo-AT and Exo-ADSCs

first: Mei


title: Differentially expressed genes during axolotl jaw regeneration identified by RNA-seq

city: Essen

first: Susanne

last: Horn

address: Hufelandstr. 55

department: Klinik für Dermatologie

institute: Universitätsklinikum Essen

summary: Human diseases like oral cancer or injuries may cause irreversible substantial jaw defects. Axolotls are of special interest in regenerative maxillofacial research due to their unique ability to completely renew amputated jaws. Here we performed differential gene expression analyses based on RNA-seq for regenerating jaw tissue of the Mexican axolotl (Ambystoma mexicanum) to identify key players in this regenerative process. Within differentially expressed genes (p<0.001) we use enrichment and network analyses to identify increased expression of structural components crucial for tissue repair (Thbs3, Thbs4 and Col3a1) as well as for extracellular matrix structure (further collagens and Matn4).  Genes of enzymatic function (AldoA, AldoC, Eno1, Ckm and Ak6) as well as muscle components (Atp2A1, Pvalb, Tpm3) are down-regulated. This first RNA-seq study on axolotl jaw tissue can help to elucidate the general molecular mechanisms underlying mandible regeneration and offer a chance for new regenerative strategies focusing on morphologically and functionally adequate replacement of these complex tissues.

overall_design: Examination of gene expression in four regenerated axolotl jaws compared to the pre-surgery jaw tissue

first: Horn

last: Susanne

first: Kramer

last: Julia


title: Mouse Embryonic 12.5 mouse heart transcriptome

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Mouse e12.5 hearts mRNA were sequenced using the illumina NGS platform in order to create an expression profile of developing heart that could be intergrated with other studies.

overall_design: Examination of expression profile of 2 replicate E12.5 mouse heart

first: Edward

last: Morrisey


title: Functional Genomic Analyses of hepatic tissue after FTO knockout

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

summary: To explore the molecular mechanism underlying glucose regulation by hepatic FTO, we analyzed transcriptome changes in hepatic tissue after FTO knockout.

overall_design: analyzing transcriptome change in hepatic tissues of hepatic FTO knockout mice, compared to wildtype control

first: Shiming

last: Peng

first: Dapeng

last: Ju

first: Nannan

last: Hou

first: Niu

last: Huang

first: Eric

first: Huanwei

first: Tao

last: Cai


title: Functional Genomic Analyses of hepatic tissue after FOXO1 knockout

summary: To explore the molecular mechanism underlying glucose regulation, we analyzed transcriptome changes in hepatic tissue after FOXO1 knockout.

overall_design: Analyzing transcriptome change in hepatic tissues of hepatic FOXO1 knockout mice,compared to wildtype control


title: Transcriptome analysis identifies the dysregulation of ultraviolet target genes in human skin cancers

first: Liang

last: Liu

address: 1150 St. Nicholas Avenue

institute: Columbia University

summary: In this study, we performed RNA-Seq studies to generate a transcriptomic cohort containing UV-responsive genes in human skin cells exposed to different UVR conditions. We then performed rigorous bioinformatics analysis to define a UV gene expression signature that is conserved among cells from different donors. We further demonstrated that the UV signature genes are significantly enriched in genes dysregulated in human skin squamous cell carcinomas.

overall_design: UV-responsive genes were identified by characterzing the differentially expressed genes between UV-irradiated human keratinocytes and non-irradiated control keratinocytes.

first: Yao

last: Shen


title: Genome-nuclear lamina interactions in the heart at embryonic days E9.5 and E12.5

summary: Lamin B1 ChIP-seq analysis of microdissected whole hearts from E9.5 and E12.5 CD1 embryos. Results provide insight into in vivo genome-nuclear lamina interactions over the course of embryonic development. Progenitor cells require coordinated expression of lineage-specific genes to regulate differentiation into daughter cell types. Epigenetic regulators are ideally positioned to synchronize transcription of disparate genomic loci. Using cardiac development to model progenitor cell behavior, we map genome- lamina interactions in vivo to reveal dynamic changes during cardiac development and propose that Hdac3 mediates chromatin organization and gene positioning in cardiac progenitors to regulate fate decisions.

overall_design: Examination of Lamin B1 occupancy in embryonic hearts at 2 different time points. 4 biological replicates at E9.5, 3 biological replicates at E12.5.

first: Jonathan

last: Epstein

first: Mudit

last: Gupta


title: Context dependent Histone H3 Lysine 4 methylation is necessary for repression and is a requisite modification for facultative heterochromatin at distinct loci

status: Public on Nov 30 2018

city: New Brunswick

first: William

middle: J.

last: Belden

state: NJ

address: 59 Dudley Rd

department: Animal Sciences

institute: Rutgers, The State University of New Jersey

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

overall_design: Refer to individual Series


title: Context dependent Histone H3 Lysine 4 methylation is necessary for repression and is a requisite modification for facultative heterochromatin at distinct loci [RNA-seq]

summary: Sensing and responding to light provides organisms an adaptive advantage, in part by altering gene expression.  The complement of light-activated genes in model organisms is largely known, and some of the mechanisms by which proteins modulate the light response are likewise well defined.  However, how light alters post translation modifications to chromatin and how changes in chromatin facilitates and/or inhibit changes in gene expression has not been examined in depth.  Nor is know how specific chromatin-modifiers assist in modulating the light response or the extent of the defects in strains lacking certain chromatin modifications.  Using a combination of RNA-seq and ChIP-seq we examines H3K4 methylation and H3K9 methylation and found paradigm changing properties beyond the consensus that H3K4me3 is a solely a mark for activation and H3K9me3 marks silent heterochromatin domains.

overall_design: Samples consist of different strains and harvest times.

first: Willam

middle: J

first: Qiaoqiao

last: Zhu

first: Mukund

last: Ramakrishnan

first: Jinhee

last: Park


title: Effects of losmapimod on non-specific inflammatory response in aged skin.

city: Lancaster

first: Barbara

middle: Bo-Ju

last: Shih

address: Bailrigg

department: Biomedical and Life Sciences

country: United Kingdom

institute: Lancaster University

summary: We have previously demonstrated older skin exhibits increased sterile inflammation 6 hours after saline-injection. In this work, we examined whether p38MAPK inhibitor in vivo would attenuate this non-specific inflammatory response towards saline in elder individuals (≥65 years).

overall_design: Skin mRNA profiles 6 hours after saline injection were studied before and after losmapimod treatment.

first: Akbar

last: Arne

first: Vukmanovic-Stejic

last: Milica


title: Single cell RNA-Seq analysis provide deeper molecular insights into abnormal maturation of tubastatin A-treated mouse oocytes

first: Yun-Jung

last: Choi

address: 120 Neungdon-ro,Gwangjib-gu

department: Animal biotechnology

institute: KONKUK University

summary: In our previous study, we observed that Tub-A treatment induced an increased level of the acetylation of alpha-tubulin, and a failure of spindle migration and actin cap formation. Most Tub-A treated oocytes were arrested in an MI-like or a GVBD-like stage and decreased mTOR (spindle formation factor) and mDia1 (inhibitor of actin assembly) in an HDAC6 expression-dependent manner. We wonder if TubA only affects HDAC6 expression. Therefore the purpose of this study is to clarify the cause of the phenomenon through RNA-seq analysis.

overall_design: Oocyte collection and culture: GV oocytes from Hybrid B6D2F1 (C57BL/6 x DBA) female mice (6-8 weeks old) were selected and maintained in M16 medium. Tubastatin A treatment: Tubastatin A HCl (Catalogue no. 27108) was obtained from BPS Bioscience (San Diego, USA). The compound was dissolved in DMSO and further diluted in saline to the 10 and 20uM concentration.

first: Jin-Hoi

last: Kim


title: Context dependent Histone H3 Lysine 4 methylation is necessary for repression and is a requisite modification for facultative heterochromatin at distinct loci [ChIP-seq]

overall_design: Samples consist of different strains, harvest times, and antibodies.


city: Hachioji

first: Yoshihiro

last: Hayashi

state: Tokyo

address: 1432-1 Horinouchi

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

summary: The MLL-PTD mutation is found in patients with MDS and AML, and not in other haematological malignancies. Previously, we showed that Mll-PTD knock-in heterozygous mice present with several MDS-associated features, such as increased self-renewal and apoptosis in HSPCs, expansion of the myeloid progenitor population, ineffective haematopoiesis, and skewed myeloid differentiation. MLL is an epigenetic regulator: its C-terminal Su[var]3–9, enhancer of zeste, trithorax (SET) domain has methyltransferase activity on lysine 4 on histone 3 (H3K4), which is retained in the MLL-PTD mutant. To clarify the effects of MLL-PTD on target gene regulation, we performed H3K4me3 ChIP-Seq analysis of LSKs isolated from WT and Mll-PTD knock-in heterozygous mice.

overall_design: Chromatin immunoprecipitation sequencing for H3K4me3 in LSK cells from WT and Mll-PTD knock-in heterozygous mice.

first: Gang


title: RNA-sequencing of wild-type (HHY168 background), REB1-FRB, and BDP1-FRB  Saccharomyces cerevisiae strains

city: Los Angeles

first: Kevin

last: Roy

state: CA

address: 607 Charles E. Young Drive East

department: Chemistry and Biochemistry

institute: UCLA

summary: FRB-tagged Reb1p and Bdp1p were depleted from the nucleus using the anchor away technique (Haruki et al., Mol Cell, 2008, 31:925-932), and RNA-sequencing was used to assay the impact of these factors on alternative poly(A) site selection.

overall_design:
RNA-sequencing of biological replicates of WT, REB1-FRB and BDP1-FRB treated for 60 minutes with rapamycin.
Biological replicates of WT, REB1-FRB and BDP1-FRB treated for 60 minutes with rapamycin.

first: Guillaume

last: Chanfreau


title: Genome-wide Identification of APETALA1 Regulated Genes during Early Flower Development in Arabidopsis

city: No.12 Zhongguancun South Street, Haidian

first: Jun

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

summary: Plant inﬂorescence-to-ﬂoral phase transition is an important developmental stage, in which ﬂoral cell identities and many traits of reproductive organs are determined. Two MADS-domain transcription factors, APETALA1 (AP1) and CAULIFLOWER (CAL), have been known as master regulators controlling the early stage of the phase transition in Arabidopsis. In plants with loss-of-function alleles of ap1 and cal double mutations, flower development is heavily delayed at the ﬂower initiation stage and accumulate a large number of inﬂorescence-like meristem cells compared to wild-type plants, resulting in a cauliﬂower-like phenotype. To facilitate investigation on molecular mechanisms during inﬂorescence-to-ﬂoral phase transition, an inducible system of synchronized ﬂoral development has been developed, in which ap1,cal inﬂorescence-like meristem cells express a fusion protein of AP1 and the hormone-binding domain of the rat glucocorticoid receptor (GR) driven by 35S constitutive promoter.  When inflorescences of 35S:AP1-GR ap1,cal plants are treated by steroid hormone dexamethasone as the activator to allow the AP1-GR fusion protein translocate into nucleus, inﬂorescence-to-ﬂoral phase transition is triggered and plants start to produce hundreds of relatively synchronized ﬂoral buds.  To explore molecular basis at early stage of flower development in Arabidopsis, we used the inducible system of synchronized ﬂoral development (35S:AP1-GR ap1,cal) to profile transcriptome change of meristem cells during inﬂorescence-to-ﬂoral phase transition by strand-specific RNA-sequencing.

overall_design: Inflorescences of 35S:AP1-GR ap1,cal plants were treated with dexamethasone (Dex) for 2 hours as the actviator for induction of ﬂoral development as well as cycloheximide (Cyc) for 2 hours as mock treatment for inhibition of translation elongation. RNA libraries derived from non-treatment, 2-hour mock (Cyc) treatment and 2-hour inducer (Dex + Cyc) treatment samples with 3 biological replicates were sequenced by Illumina HiSeq 2500 with strand-specific RNA-sequencing protocol.

first: Kian

last: Hong

first: Hui-Wen

last: Wu

first: Shulin

last: Deng

first: Huan

last: Wang

first: Nam-Hai

last: Chua


title: Accelerated functional evolution of regulatory lncRNAs in the human lineage

city: Barcelona

first: Roderic

last: Guigó

state: Catalonia

address: doctor aiguader 88

department: Bioinformatics and Genomics

country: Spain

institute: Center for Genomic Regulation (CRG)

summary: Long noncoding RNA sequences evolve relatively rapidly, but it is unclear whether this is due to relaxed constraint or accelerated evolution. Here, we trace the recent evolutionary history of human lncRNAs, using genomes of multiple individuals from all great ape species to map fixed lineage-specific nucleotide variants. We find that the lower conservation of lncRNAs compared to protein coding genes partially arises from lncRNA’s more recent evolutionary origin. We identify more than one hundred lncRNAs that show some evidence of accelerated evolution in at least one primate species, including 17 in human. Several of these display transcriptional regulatory activity in an RNA-specific reporter assay. By experimentally reconstructing the ancestral lncRNA sequence, we find that this activity has been altered by human-specific nucleotide substitutions. Functional analysis of accelerated lncRNAs with specific expression in blood suggests lncRNAs have participated in adaptive regulatory changes in the immune system during recent human evolution. Together our results provide evidence that accelerated evolution of lncRNAs may have contributed, through regulatory changes, to human-specific phenotypes.

overall_design: We compared expression changes in BLaER1 cells caused by knocking down HAL7 gene (ENSG00000228427.1, RP5-1091N2.9) using GapmeR design tool (Exiqon, Denmark)

first: Marta

last: Melé

first: Carme

last: Arnan

first: Alexandre

last: Esteban

first: Rory

last: Johnson


title: PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice

city: Milano

first: Fabio

last: Fornara

address: Via Celoria 26

department: Department of Biosciences

country: Italy

institute: University of Milan

summary: Flowering of several plant species is induced by exposure to specific photoperiods that promote the expression of florigenic proteins in the leaves and their subsequent translocation to the shoot apex, where they commit the meristem to a reproductive fate. Transition to reproductive growth at the apex is often accompanied by stem elongation, to expose flowers above the leaves and facilitate fertilization. However, how growth and inflorescence formation are coupled and how photoperiodic signals coordinate these processes at the apex is still unclear. We studied these mechanisms in rice, a short day plant. Here, we show that HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1), encoding components of the rice florigenic signal, are sufficient to repress expression of PREMATURE INTERNODE ELONGATION 1 (PINE1) at the shoot apex during the transition to flowering, thus promoting culm elongation. PINE1 encodes a nuclear C2H2 zinc finger transcriptional repressor that controls the mRNA abundance of GA3ox2, a gibberellin (GA) biosynthetic gene. These data uncover the existence of a regulatory network coordinating multiple aspects of phase transition, and indicate that GA-induced growth and activity of florigenic proteins at the shoot apex need to be strictly coupled.

overall_design:
In this study, we investigated the transcriptional reprogramming at the shoot apex of rice plants during floral transition, when plants switch from vegetative to reproductive growth, after exposure to inductive photoperiodic conditions. After continuous growth under long days, we treated two temperate japonica cultivars (Nipponbare and Taichung 65) with four conditions: 1) 0 short days (continuous long day conditions), 2) 4 short days, 3) 8 short days, and 4) 12 short days.

Some of the samples in this study were merged for data analysis. The merged samples are:
GSM2402823 and GSM2402824
GSM2402826 and GSM2402827
GSM2402828, GSM2402829 and GSM2402830
GSM2402840 and GSM2402841
GSM2402847, GSM2402848 and GSM2402849
Only one processed data file is included for each set of merged samples. Please see the Description field of these samples to find the location of the processed data file.

first: Jorge

last: Gómez-Ariza

first: Martina

last: Landini

first: Vittoria

last: Brambilla

first: Roshi

last: Shrestha

first: Remo

last: Chiozzotto

first: Francesca

last: Galbiati

first: Elisabetta

last: Caporali


title: Skeletal-muscle specifc Gprc6a-/- mice.

first: Paula

last: Mera

department: Genetics and Develoment

summary: Gprc6a|Mck-/- (Gcrp6a skeletal muscle specific knockout)(n=4) are compared to Gprc6afl/fl (WT) mice (n=4). Gprc6a is the osteocalcin receptor.

overall_design: Gprc6a/Mck-/- vs Gprc6afl/fl

first: Kathrin

last: Laue

first: Mathieu

last: Ferron

first: Cyril

last: Confavreux

first: Jianwen

last: Wei

last: Galan-Diez

first: Alain

last: Lacampagne

first: Sarah

last: Mitchell

first: Julie

middle: A

last: Mattison

first: Yun

last: Chen

first: Justine

last: Bacchetta

first: Pawel

last: Szulc

first: Richard

last: Kitsis

first: Rafael

last: de Cabo

last: Friedman

first: Christopher

last: Torsitano

first: Timothy

last: McGraw

first: Michelle

last: Puchowicz

first: Irwin

last: Kurland

first: Gerard

last: Karsenty


title: NANOG assists in the establishment and maintenance of pluripotency by amplifying multiple signaling pathways

status: Public on Nov 29 2018

city: Rotterdam

first: Catherine

last: Dupont

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

summary: Identification of NANOG transcribed factors during the establishment of pluripotency

overall_design: RNA sequencing of E3.5 wildtype and Nanog null embryos and ES cells, TS cells and XEN cells

first: Joke

last: van Bemmel

first: Cheryl

middle: M

last: Maduro

first: Wilfred

last: van Ijcken

first: Mirjam

last: van den Hout

first: M

last: Ghazvini

first: Benjamin

last: Schwarz

first: Konrad

last: Hochedlinger

first: Joost

middle: H

last: Gribnau


title: Centromeric DNA destabilizes H3 nucleosomes to promote CENP-A deposition during the cell cycle

city: Edinburgh

first: Robin

last: Allshire

state: Midlothian

address: Max Born Cresent

institute: The University of Edinburgh


title: H3K9 methyltransferases and demethylases control lung tumor-propagating cells and lung cancer progression

city: New York

first: Hideo

last: Watanabe

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: We have identified the histone methyltransferases G9a/Glp as suppressors of aggressive lung tumor-propagating cells (TPCs). Chemically inhibiting G9a/Glp promoted TPC phenotypes in lung adenocarcinoma cells, and caused chromatin changes at genes associated with the differentiation of stem cells. G9a/Glp inhibition in lung progenitor cell organoid cultures disrupted alveolar differentiation. Depleting G9a during tumorigenesis enriched for TPCs, accelerating disease progression and metastasis.  Demethylase inhibition decreased lung adenocarcinoma progression in vivo.

overall_design: Genome-wide maps of histone H3K27 acetylation and H3K9 dimethylation in CK1750 and Tnm2 cells treated with either DMSO or a G9a/GLP inhibitor, UNC0638.

first: Sam

last: Rowbotham

first: Carla

last: Kim


title: Centromeric DNA destabilizes H3 nucleosomes to promote CENP-A deposition during the cell cycle (part 2)

summary: Centromeres are the regions of eukaryotic chromosomes where kinetochores are assembled and direct the correct segregation of chromosomes.  Active centromeres are defined by presence of nucleosomes containing CENP-A, a histone H3 variant, which alone is sufficient to direct kinetochore assembly.  Once assembled at a location CENP-A chromatin and the kinetochore is maintained at that location though a positive feedback loop where kinetochore proteins recruited by CENP-A promote deposition of new CENP-A following replication.  Although CENP-A chromatin itself is a heritable entity, it is normally associated with specific sequences such as human alpha satellite arrays.  Such analyses suggest that properties of centromeric DNA itself may favour assembly of CENP-A rather than H3 nucleosomes.  To investigate the innate properties of centromeric DNA we have examined histone dynamics on this DNA assembled in CENP-A chromatin at endogenous centromeres and when assembled only in H3 chromatin at an ectopic location. We demonstrate that H3 occupancy on centromeric DNA is innately low while H3 turnover is high.  Moreover, even at an ectopic location centromeric DNA programs H3 deposition in S phase and its eviction during G2 when CENP-A is otherwise deposited.  G2 accumulation of RNAPII on centromeric DNA during G2 is consistent with transcription-coupled destabilisation of H3 nucleosomes to favour CENP-A deposition.

overall_design: ChIP-Seq samples of HA and T7 tagged CENP-ACnp1, Phospho Serine 2 RNA Polymerase II  prepared from  cell cycle synchronized populations of fission yeast. ChIP-Nexus samples were preprared for histone H3 and H4 from wild type strain and strain bearing an ectopically inserted central core DNA.

first: Manu

last: Shukla

first: Pin

last: Tong


title: Centromeric DNA destabilizes H3 nucleosomes to promote CENP-A deposition during the cell cycle (part 1)

overall_design: ChIP-Nexus samples were preprared for histone H3 and H4 from wild type strain and strain bearing an ectopically inserted central core DNA.


title: MBD3 expression and DNA binding patterns are altered in a rat model of temporal lobe epilepsy

city: Warsaw

first: Katarzyna

last: Lukasiuk

address: 3 Pasteur Street

department: Department of Molecular and Cellular Neurobiology

country: Poland

institute: Nencki Institute of Experimental Biology Polish Academy of Sciences

summary: Examine involvement of MBD3 (methyl-CpG-binding domain protein 3), a protein involved in reading DNA methylation patterns, in epileptogenesis and epilepsy.

overall_design: Examination of MBD3 binding differences in stimulated rats compared to sham operated animals in focal stimulation model of epilepsy.

first: Joanna

last: Bednarczyk

last: Dębski

first: Anna

last: Bot


title: AhR activity directs BRAF inhibitors resistance in metastastic melanoma

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: BRAF oncogene is mutated in ~50% of human cutaneous melanomas. The BRAF V600E mutation leads to constitutive activation of the mitogen-activated protein kinase (MAPK) pathway fuelling cancer growth. The inhibitors of BRAF V600E (BRAFi), lead to massive and high response rate. However, BRAFi-resistant cells that operate as a cellular reservoir for relapses severely limits the duration of the clinical response. The recent depiction of these resistant cells did not identify druggable targets to ensure long-term survival under BRAFi. Here, we identify the aryl hydrocarbon receptor (AhR) as a target to eradicate resistant cells. We show that BRAFi bind to AhR on a new site, named beta-pocket, and reprogram gene expression independently of its partner ARNT. beta-pocket activation induces a pigmentation signature, which is associated to BRAFi-induced cell death of sensitive BRAF V600E melanoma cells and tumour shrinkage. Intriguingly, in resistant cells, BRAFi does not induced a pigmentation signature since these cells display another AhR program; AhR-ARNT dependant. By this way, AhR directs several key BRAFi-resistant genes. At single cell level, this constitutive activation of AhR-ARNT is identified in rare cells before BRAFi-treatment of melanoma tumours and an enrichment of these alpha-cells is observed under BRAFi. Our data strongly suggest that an endogenous AhR ligand activates AhR-ARNT via the canonical AhR pocket (alpha-pocket), thus favouring BRAFi-resistant gene expression. Importantly, we identify the clinically compatible AhR antagonist, the resveratrol (RSV), able to abrogate the deleterious constitutive activation of AhR and to reduce the cellular reservoir for the relapse. Taken together, this work reveals that constitutive AhR signalling drives BRAFi resistance and constitutes a therapeutic target to achieve long-term patient survival under BRAFi. More broadly, the constitutive activation of AhR by endogenous ligands is in line with the ability of UV radiations to generate potent AhR ligands and to favour melanoma onset.

overall_design: Total RNA isolated from 12 human melanoma cell lines (501Mel) after different treatments was subjected to multiplexed RNA-sequencing using Illumina NextSeq500 sequencing tehnology.

first: S

last: Corre

first: B

last: Mari

first: K

first: P

last: Barbry


title: Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate (Capture Hi-C)

status: Public on Nov 28 2018

city: La Jolla

first: Ramya

last: Raviram

address: 9500 Gilman Drive

institute: University of California San Diego

summary: The organization of chromatin in the nucleus plays an essential role in gene regulation. About half of the mammalian genome comprises transposable elements. Given their repetitive nature, reads associated with these elements are generally discarded or randomly distributed among elements of the same type in genome-wide analyses. Thus, it is challenging to identify the activities and properties of individual transposons. As a result, we only have a partial understanding of how transposons contribute to chromatin folding and how they impact gene regulation. Using adapted PCR and Capture-based chromosome conformation capture (3C) approaches, collectively called 4Tran, we take advantage of the repetitive nature of transposons to capture interactions from multiple copies of endogenous retrovirus (ERVs) in the human and mouse genomes. With 4Tran-PCR, reads are selectively mapped to unique regions in the genome. This enables the identification of transposable element interaction profiles for individual ERV families and integration events specific to particular genomes. With this approach, we demonstrate that transposons engage in long-range intra-chromosomal interactions guided by the separation of chromosomes into A and B compartments as well as topologically associated domains (TADs). In contrast to 4Tran-PCR, Capture-4Tran can uniquely identify both ends of an interaction that involve retroviral repeat sequences, providing a powerful tool for uncovering the individual transposable element insertions that interact with and potentially regulate target genes. 4Tran provides new insight into the manner in which transposons contribute to chromosome architecture and identifies target genes that transposable elements can potentially control.

overall_design: We adapted the capture Hi-C protocol by using a biotinylated oligo that hybridized to the consensus sequence of MER41 elements. We used this on HeLa cells (treated or not with Interferon gama) to identify chromosomal interactions from these elements.

first: Jane

last: Skok


title: Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate (Hi-C)

overall_design: We used the Hi-C protocol to identify chromosomal interactions from HeLa cells treated with interferon gamma.


title: Inhibition of MEK and ATR induces synergistic killing of a Mll-Af4 B-ALL model harboring activated Ras mutation

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: Infant B-acute lymphoblastic leukemias (B-ALL) that harbor MLL-AF4 rearrangements are associated with a poor prognosis.  One important obstacle to progress for this patient population is the lack of models that faithfully recapitulate the short latency and aggressiveness of this disease.  While current mouse models of Mll-Af4 can generate acute leukemia, not all are lymphoid, and the long latency to disease does not reflect what is seen in patients.  Recent whole genome sequencing of MLL-AF4 B-ALL samples revealed a high frequency of mutations in proto-oncogenes involved in signaling pathways.  Here, we demonstrate that the expression of activating mutant N-RasG12D cooperates with Mll-Af4 to generate a highly aggressive, serially transplantable B-ALL in mice.  We used our novel mouse model to test the sensitivity of Mll-Af4/N-RasG12D leukemia to small molecule inhibitors, and found that dual targeting of the downstream effectors of Ras and the DNA damage response pathway through ATR inhibition induced long-term durable responses in both mouse and patient derived xenografts with both mutations in vivo. Our studies suggest that this mouse model of Mll-Af4/N-Ras B-ALL is not only a powerful tool to explore the molecular and genetic pathogenesis of this disease subtype, but also is an important  preclinical discovery platform for novel therapeutics that might be used to treat patients with this disease.

overall_design: RNA sequencing of a mouse model of MLL-AF4/NRAS-driven acute lymphoblastic leukemia compared with wild type ProB cells.

last: Chu

middle: P

first: Scott

last: Armstrong


title: Next generation sequencing facilitates quantitative analysis of murine high-grade glibablastoma Transcriptomes after VEGF-A blockade In Vivo.

city: Gainesville

first: Jianping

last: Huang

state: FL

address: 1149 Newell Dr

department: neurosurgery

institute: UF

summary: The goals of this study are to compare immunogenic profiling of tumor tissue from GL261 burden mice were treated with different dose VEGF-A antibody from Day10 after tumor implantation to the endpoint. The treatment doses are 0ug, 50ug, 100ug and 200ug.

overall_design: mRNA profiles of  healthy brain tissue  and tumors tissure  harvested from GL261 burden mice after VEGF-A blockade treatment were generated by RNA sequencing. There are 3 individual samples in each treatmen group.

first: Long

last: Yu

first: Huang

last: Jianping

first: Lin

last: Zhiguo

first: Michell

last: Duane

first: Yang

last: Changlin


title: Transcriptome signatures of human induced pluripotent stem cell-derived cardiomyocytes classify cardiomyocyte subtype populations

city: Stanford

first: Jared

last: Churko

address: 265 Campus Dr G1105 SIM1

department: Radiology

institute: Stanford

summary: We profiled the transcriptome of cardiomyocytes from hiPSCs throughout differentiation and at a single cell level to identify subpopulations. We further studied on the transcription factors NR2F2, TBX5, and HEY2 in these subpopulations.

overall_design: Cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs) have become a powerful tool for human disease modeling and therapeutic testing. However, their use remains limited by their immaturity and heterogeneity. To characterize the source of this heterogeneity, we performed bulk RNA-seq on hiPSCs undergoing differentiation into cardiomyocytes over an extended time course followed by single-cell RNA-seq at a later time point (day 30).  These analyses identified novel single-cell populations, characterized by the distinct or overlapping expression of TBX5, NR2F2, HEY2, ISL1, JARID2, and HOPX transcription factors. Analysis of RNA-seq data from hiPSC-CMs both during differentiation in vitro and from human heart tissues suggests these transcription factors underlie physiologically distinct lineages. Using CRISPR genome editing and ChIP-seq, in conjunction with patch clamp, calcium imaging, CYTOF, and single-cell Western analysis, we now demonstrate that these transcription factors play an essential role in specification of early atrial (NR2F2) and late ventricular (HEY2) cardiomyocytes. We RNA-sequenced NR2F2, TBX5, HEY2 gene edited lines as well as day 30 hiPSC-CMs overexpressing NR2F2, TBX5, and HEY2.  These new targets, sequencing data, and methods provide a platform for improved investigation of in vitro cardiac heterogeneity.


title: Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: A novel single-strands RNA virus in Nesidiocoris tenuis

status: Public on Nov 27 2018

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: RNA was isolated from  adults using the TRIzol (Invitrogen) reagent by following the company manual. Poly(A) mRNA was isolated from 20 µl total RNA using Oligo (dT) magnetic beads and then was broken into short fragments (about 200bp) in the presence of fragmentation buffer at 94 °C for 5 min. The mRNA samples were used to construct the cDNA libray with mRNA-Seq assay.The libraries were sequenced using HiSeq4000 (Illumina) in paired-end mode, creating reads with a length of 150 bp.

overall_design: Detection of genes and microbial species

first: Yanhui

last: Lu

first: Pengjun

last: Xu


title: The Photorespiratory BOU Gene Mutation Alters Sulfur Assimilation and Its Crosstalk With Carbon and Nitrogen Metabolism in Arabidopsis thaliana

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

summary: This study was aimed at elucidating the significance of photorespiratory serine (Ser) production for cysteine (Cys) biosynthesis. For this purpose, sulfur (S) metabolism and its crosstalk with nitrogen (N) and carbon (C) metabolism were analyzed in wildtype Arabidopsis and its photorespiratory bou-2 mutant with impaired glycine decarboxylase (GDC) activity. Foliar glycine and Ser contents were enhanced in the mutant at day and night. The high Ser levels in the mutant cannot be explained by transcript abundances of genes of the photorespiratory pathway or two alternative pathways of Ser biosynthesis. Despite enhanced foliar Ser, reduced GDC activity mediated a decline in sulfur flux into major sulfur pools in the mutant, as a result of deregulation of genes of sulfur reduction and assimilation. Still, foliar Cys and glutathione contents in the mutant were enhanced. The use of Cys for methionine and glucosinolates synthesis was reduced in the mutant. Reduced GDC activity in the mutant downregulated Calvin Cycle and nitrogen assimilation genes, upregulated key enzymes of glycolysis and the tricarboxylic acid (TCA) pathway and modified accumulation of sugars and TCA intermediates. Thus, photorespiratory Ser production can be replaced by other metabolic Ser sources, but this replacement deregulates the cross-talk between S, N, and C metabolism.

overall_design: Arabidopsis thaliana plants [Wildtype Col-0 and a mutant line in Col-0 background, bou-2 (At5g46800) were grown in biological triplicates under high CO2 (3000 ppm) for 35 days, 12 hr light / 12 hr dark and then shifted to ambient CO2 24 hours before harvesting. Samples for RNASeq were taken two hours before ("end of night", EON) and two hours after ("beginning of day", BOD) the onset of light.

first: Sladja

last: Samuilov

first: Dominik

last: Brilhaus

first: Samantha

last: Flachbart

first: Nadine

last: Rademacher

first: Leila

last: Arab

first: Franziska

last: Kuhnert

first: Stanislav

last: Kopriva

first: Tabea-Mettler

last: Altmann

first: Heinz

last: Rennenberg


title: MNase-seq analysis of wild type and asf1 mutant of Sordaria macrospora

status: Public on Nov 26 2018

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

institute: Ruhr-University Bochum

summary: The aim of this analysis was to analyze nucleosome distribution in the filamentous ascomycete Sordaria macrospora by micrococcal nuclease digestion and sequencing.

overall_design: Two independent biological replicates were performed and sequenced each for the wild type and the developmental mutant asf1.

first: David

last: Schumacher


title: Hawaiian picture wing Drosophila sproati exhibit adaptive population divergence along a narrow climatic gradient on Hawaii Island

city: Hilo

first: M. Renee

last: Bellinger

state: Hawaii

address: 200 W. Kawili St.

department: Biology

institute: University of Hawaii

summary:
D. grimshawi microarray used to text for gene expression differences between two populations subjected to control or low-intensity heat for one week during maturation
Anthropogenic influences on global processes and climatic conditions are increasingly affecting ecosystems throughout the world. Hawaii Island’s native ecosystems are well-studied and local long-term climatic trends well-documented, making these ecosystems ideal for evaluating how native taxa may respond to a warming environment. This study documents adaptive divergence of populations of a Hawaiian picture wing Drosophila, D. sproati, that are separated by only 7km and 365m in elevation. Representative laboratory populations show divergent behavioral and physiological responses to an experimental low-intensity increase in ambient temperature during maturation. The significant interaction of source population by temperature treatment for behavioral and physiological measurements indicates differential adaptation to temperature for the two populations. Significant differences in gene expression among males were mostly explained by the source population, with eleven genes in males also showing a significant interaction of source population by temperature treatment. The combined behavior, physiology, and gene expression differences between populations illustrates the potential for local adaptation to occur over a fine spatial scale and exemplifies nuanced response to climate change.

overall_design: 44 Drosophila sproati flies from low- and high-elevation populations were raised for six generations in a controlled climate. During the 6th generation each population was split into two groups, one held at the control 18C, and the other group expoosed to 24C during their 3rd week of maturation. Gene expression was measured at week four.

first: M

middle: R

first: Donald

last: Price

first: Jonathan

last: Eldon


title: Gene expression in developmental mutants of Sordaria macrospora

summary: The aim of this analysis was to analyze gene expression in developmental mutants of the filamentous ascomycete Sordaria macrospora. RNA was isolated from total mycelia, or young fruiting bodies (protoperithecia) were isolated by laser microdissection and RNA was extracted, amplified and used for RNA-sequencing.

overall_design: Two independent biological replicates were performed and sequenced.


title: Gene expression of HCT116 colorectal cancer cells after treament with Thymoquinone (TQ), 5-Fluorouracil (5-FU),  Combination of the individual compounds (Combi) and the Hybrid compound (SARB).

status: Public on Nov 24 2018

city: Erlangen

first: Benardina

last: Ndreshkjana

address: Universitätsstraße 22

department: Experimental Tumor Pathology

institute: Uniklinikum Erlangen

summary: Cancer stem cells (CSCs) residing in colorectal cancer tissues have tumorigenic capacity and contribute to chemotherapeutic resistance and disease relapse. It is well known that the survival of colorectal CSCs after 5-Fluorouracil (5-FU)-based therapy leads to cancer recurrence. Thus CSCs represent a promising drug target. Here, we designed and synthesized novel hybrid molecules linking 5-FU with the plant-derived compound thymoquinone (TQ) and tested the potential of individual compounds and their combination to eliminate colorectal CSCs. SARB hybrid showed augmented cytotoxicity against colorectal cancer cells.  Data obtained via Nanostring nCounter Gene Expression Assay (Pan Cancer Pathway Panel). Nanostring analysis revealed a unique signature of dysregulated gene expression in response to the combination of TQ and 5-FU (Combi) and SARB treatment. Importantly, two principle stem cell regulatory pathways WNT/ß-Catenin and PI3K/AKT were found to be downregulated after hybrid treatment.

overall_design: In this study three biological replicates of each treatment and of the untreated control cells were included.  HCT116 cells were treated for 24 h with the individual compounds, the combination of them and with the hybrid compound. We aimed to reveal differences in gene expression between treated and untreated cells as well as the differences on gene expression among different treatments.

first: Aysun

last: Çapci Karagoez

first: Volker

last: Klein

first: Pithi

last: Chanvorachote

first: Julienne

middle: K

last: Muenzner

first: Kerstin

last: Huebner

first: Sara

last: Steinmann

first: Katharina

last: Erlenbach-Wünsch

first: Carol

middle: I

last: Geppert

first: Abbas

last: Agaimy

first: Farah

last: Ballout

first: Chirine

last: El-Baba

first: Hala

last: Gali-Muhtasib

first: Arndt

last: Hartmann

first: Svetlana

last: Tsogoeva

first: Regine

last: Schneider-Stock


title: Dynamic control of translation during adult neurogenesis

status: Public on Nov 23 2018

city: Heidelberg

first: Avni

last: Baser

address: Im Neuenheimer Feld 581

department: Molecular Neurobiology

institute: DKFZ

summary: Here we applied RNAseq and RIBOseq, the deep sequencing of ribosome-associated transcripts, to investigate the relation of RNA abundance and translation at four stages of neurogenic differentiation.

overall_design: RNAseq and RIBOseq of four stages of neural differentiation.

first: Bernd

last: Fischer

first: Ana

last: Martin-Villalba


title: Transcriptome of U251 cells overexpression complement component 7

status: Public on Nov 22 2018

city: Kunming

first: Yong-Gang

last: Yao

state: Yunnan

address: 32 Jiaochang Donglu

department: Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province

institute: Kunming Institute of Zoology

summary: We identified a rare coding variant (p.K420Q) in the complement component 7 (C7) gene affecting the risk of Alzheimer's disease. To investigate the cellular effects of the mutant, we performed RNA-seq in cell line overexpression wilt-type and mutant C7.   U251 glioma cells with stable expression of mutant APP (K670N/M671L) (U251-APP cells), which produce Aβ42 under Dox inducing, were used as the model cell. Total RNA of U251-APP cells overexpressing wild type and mutant C7 proteins were subjected to transcriptome sequencing using Illumina Hiseq 4000 platform.

overall_design: C7 overexpression was performed in U251 cell with a stably expression of mutant APP (U251-APP cells) with three biological triplicates for each condition (vector, wild-type, and mutant).

first: Deng-Feng

last: Zhang

first: Yu

last: Fan

first: Min

last: Xu


title: Integrated Genetic and Proteomic Analysis Identifies PLK1 as a Candidate Therapeutic Target for SETD2-Deficient Clear Cell Renal Cell Carcinoma

city: Riverside

first: LIN

last: LI

state: California

address: 501 Big Springs Road, University of California at Riverside

department: Department of chemistry

institute: UC, riverside

summary: We systematically analyzed the alterations in histone epigenetic marks (H3K36me3 and H4K16ac), mRNA transcriptome evoked by SETD2 depletion.

overall_design: Examination of 2 different histone modifications and mRNA expression in WT and SETD2 KO cells

first: Lin

last: Li

first: Yinsheng

last: Wang


title: Concomitant BCORL1 and BRAF mutations in vemurafenib-resistant melanoma cells

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

summary: BRAF is the most frequently mutated gene in melanoma. Constitutive activation of mutant BRAFV600E leads to aberrant Ras-independent MAPK signaling and cell transformation. Inhibition of mutant BRAF is a current front-line therapy for such cases, with improved survival compared with chemotherapy. Unfortunately, reactivation of MAPK signaling by several mechanisms has been shown to cause drug resistance and disease recurrence. In this work, we describe the co-occurrence of an in-frame deletion within an amplified BRAFV600E locus, and a missense point mutation of the transcriptional repressor BCORL1, in vemurafenib-resistant A375 melanoma cells. Functional data confirmed that truncated p47BRAFV600E and mutant BCORL1Q1076H both contribute to resistance. Interestingly, either endogenous BCORL1 silencing or ectopic BCORL1Q1076H expression mimicked the effects of a CRISPR/Cas9-edited BCORL1Q1076H locus, suggesting a change-of-function mutation. Transcriptomic data confirmed this hypothesis. Finally, we show that the pan-RAF inhibitor sorafenib is not affected by expression of BRAF deletion variant and effectively synergizes with vemurafenib to block resistant cells, suggesting a possible intervention for this class of mutants.

overall_design: Nine total samples: 3 parental plus 3 BCORL1-WT and 3 BCORL1-MUT overexpressing cells

last: Mologni

first: Rocco

last: Piazza

first: Carlo

last: Gambacorti-Passerini


title: Next generation sequence analysis for transcriptome of Drosophila melanogaster third instar larval eye discs expressing activated Ras either alone or along with changes in hsromega  lncRNA levels

city: varanasi

first: subhas chandra

last: lakhotia

state: uttar pradesh

address: cytogenetics lab, department of Zoology BHU

department: Department of Zoology

country: India

institute: Brown University

summary:
Purpose: While studying possible interaction between ras and hsrω genes we found that down- or up- regulation hsrω RNA levels results in further enhancement in activity hyperactive Ras protein in eye discs of Drosophila melanogaster. In order to find out reason underlying this phenomena we checked difference in gene expression between eye discs expressing activated Ras along with alterations in hsrω RNA levels and those expressing activated Ras alone.
Method: Eye disc RNA profiles of wandering late third instar larvae of sev-GAL4>UAS-GFP, sev-GAL4>UAS-hsrωRNAi, sev-GAL4>EP3037, sev-GAL4>UAS-RasV12, sev-GAL4>UAS-hsrωRNAi UAS-RasV12 and sev-GAL4>EP3037 UAS-RasV12 were generated by sequencing, in triplicate, using Illumina Hiseq2500 platform using 50bp pair-end reads, 12 samples per lane and each sample run across 2 lanes. This resulted in a sequencing depth of ~20 million reads. The resulting sequencing FastQ files were mapped to the Drosophila genome (dm6) using Tophat with Bowtie. The aligned SAM/BAM file for each was processed for guided transcript assembly using Cufflink 2.1.1 and gene counts were determined. Mapped reads were assembled using Cufflinks. Transcripts from all samples were subjected to Cuffmerge to get final transcriptome assembly across samples. In order to ascertain differential expression of gene transcripts between different samples, Cuffdiff 2.1.1 was used (Trapnell et al., 2012).
Result: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the Drosophila genome (dm6) and identified  15,905 transcripts with TopHat workflow in each genotypes studied. The sev-GAL4 driven expression of activated Ras in eye discs resulted in differential expression of many genes, with 374 genes being down-regulated and 138 up-regulated, when compared with those in sev-GAL4>UAS-GFP eye discs. Compared to only Ras expressing eye discs in case of down regulation of hsrω RNA in activated Ras background 148 gene were up-regulated while 434 were down-regulated. In eye discs expressing activated Ras alongwith over expression of hsrω RNA, 192 genes were up-regulated and 470 down-regulated compared to only activated Ras expressing eye discs. Some of these (11 genes) were validated using qRT-PCR.
Conclusion: In activated Ras expressing eye discs, besides the expected increase in levels of transcripts of genes involved in cell growth, proliferation and differentiation, transcripts of many genes involved in RNA biosynthesis, metabolism and processing were up-regulated when compared with sev-GAL4>UAS-GFP eye discs. Levels of transcripts of none of the known members of Ras/Raf/MAPK signaling pathway were found to be significantly affected by changes in hsrω transcript levels in activated Ras expression background. Interestingly, several sn/snoRNAs along with a scaRNAs and some members of the RNA processing machinery were differentially expressed in activated Ras background and were further affected when the hsrω RNA levels were down-or up-regulated. In addition, while down-regulation of hsrω activity resulted in up-regulation of a few positive modulators of Ras signaling pathway, up-regulation of these transcripts caused down-regulation of the negative regulators of Ras/Raf/MAPK pathway, and thus resulting in increase in Ras activity in either cases.

overall_design: Eye discs mRNA profiles of wandering late third instar larvae of sev-GAL4>UAS-GFP, sev-GAL4>UAS-RasV12, sev-GAL4>UAS-hsrωRNAi UAS-RasV12 and sev-GAL4>EP3037 UAS-RasV12 third instar larvae  were generated by sequencing, in triplicate, using Illumina Hiseq2500 platform.

first: Subhash

last: Lakhotia

first: Mukulika

last: Ray


title: Transcriptomic analysis of intestinal epithelial Sox4 knockout

city: Atlanta

first: Adam

last: Gracz

state: GA

address: 615 Michael St. NE

department: Medicine

institute: Emory University

summary: Sox4 is expressed in intestinal stem cells (ISCs) and early intestinal progenitors. The regulatory role for Sox4 in intestinal homeostasis is currently unknown. Here, we used RNA-seq to determine the role of Sox4 in the intestinal epithelium using a conditional knockout model.

overall_design: Intestinal epithelium was isolated from adult (6wk) male mice. FACS was used to isolate CD326+ (epithelium-only) cells that were either CD44- (villus enriched) or CD44+ (crypt enriched). 50,000 cells were collected per population. Control mice (Sox4floxed/floxed) were compared to conditional knockout mice (Sox4floxed/floxed:villinCre), which drive recombination of the floxed Sox4 allele starting at E10.5. All mice used were littermates, with 2 biological replicates per control and knockout group.

first: Scott

middle: T

last: Magness


title: Next-generation RNA sequencing to determine changes in gene expression during breast cancer progression

city: bethesda

first: Stefan

last: Ambs

state: md

address: 37 convent cir

institute: NIH

summary:
Purpose: The goal of the study is to compare NGS-derived transcriptome in an isogenic breast cancer progression model cell line system. By comparing the protein-coding and noncoding gene expression of normal versus tumorigenic breast cancer cell lines, we will be able to identify genes that show aberrant expression during breast cancer progression.
Methods: We isolated poly A + RNA from four isogenic mammary epithelial cell lines showing various stages of breast cancer progression. The model system comprises of 4 isogenic cell lines, categorized as M1-M4. M1 represents the normal, non-tumorigenic, immortalized MCF10A cells. Transfection of MCF10A with activated T24-HRAS and selection by xenografting generated the M2 (MCF10AT1k.cl2) cell line, which is highly proliferative and gives rise to premalignant lesions with the potential for neoplastic progression. M3 (MCF10Ca1h) and M4 (MCF10CA1a.cl1) were derived from occasional carcinomas arising from xenografts of M2 cells. M3 gives predominantly well-differentiated low-grade carcinomas on xenografting, while M4 gives rise to relatively undifferentiated carcinomas and colonizes to the lung upon injection of these cells into the tail vein. We performed paired-end deep sequencing (190-260 million reads/sample) of poly A+ RNA isolated from these cells that were cultured as 3D acini in biological duplicates. Reads of the samples were trimmed for adapters and low-quality bases using Trimmomatic software before alignment with the reference genome (Human - hg19) and the annotated transcripts using STAR. The average mapping rate of all samples is 96%. Unique alignment is above 87%. There are 3.74 to 4.07% unmapped reads. The mapping statistics are calculated using Picard software. The samples have 0.59% ribosomal bases. Percent coding bases are between 67-72%. Percent UTR bases are 23-26%, and mRNA bases are between 94-96% for all the samples. Library complexity is measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility. The samples have 31-52% non-duplicate reads. In addition, the gene expression quantification analysis was performed for all samples using STAR/RSEM tools. Both the normalized count and the raw count are provided as part of the data delivery.
Results: Using an optimised data analysis workflow, we mapped ~190-250 million reads/sample and identified expression of 17396 protein-coding genes and 11509 long noncoding RNA genes. We initially compared gene expression between M1 and M4 cells. 4668 genes (2815 protein coding and 1853 lncRNAs) showed ~2 fold change in their expression between M1 and M4 cells in both biological repeats. 1159 out of the 1853 deregulated lncRNAs showed 2-fold upregulation in M4 cells in both repeats. On the other hand, 694 of lncRNAs displayed reduced levels in M4 compared to M1 cells. Further, we noticed that natural antisense transcripts (NATs) comprised one of the largest types of lncRNAs (504 out of 1853) that showed deregulation in M4 cells.
Conclusion: Our study revealed differential expression of thousands of protein-coding and long noncoding RNAs during breast cancer progression using the isogenic cell line model system. This data set will act as a rich resource for downstream mechanistic studies to determine the role of these differentially expressed genes in breast cancer progression.

overall_design: Poly A+ RNA from M1, M2, M3 and M4 cells (all grown in 3D acini in matrigel as biological duplicates) for 8-10 days were sequenced on HiSeq using Illumina TruSeq mRNA Prep Kit RS-122-2101 and paired-end sequencing. The samples have 163 to 256 million pass filter reads with a base call quality of above 94% of bases with Q30 and above.

first: Kannanganattu

last: Prasanth

first: Ashish

last: Lal

first: Tang

last: Wei


title: Estradiol-regulated Dependence Receptor UNC5A Restricts Estradiol Signaling and Luminal to Basal Transition and Metastasis of Breast Cancer

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: C218C, 980 West Walnut St

institute: Indiana University School of Medicine

summary: Estrogen receptor alpha (ERα)-positive breast cancers, while initially being responsive, eventually develop resistance to ERα targeted therapies through ERα-dependent and ERα-independent mechanisms.  Through functional genomic studies we report heretofore unrecognized role for the axon guidance dependence receptor UNC5A in fine-tuning estradiol (E2) and anti-estrogen response.  Knockdown of the estradiol-inducible UNC5A caused unrestricted ERα signaling as evident from deregulated E2-regulated gene expression and E2-independent tumorigenesis accompanied with multi-organ metastatic spread in xenograft models.  UNC5A-knockdown cells displayed luminal/basal hybrid phenotype characterized by elevated expression of basal/stem cell enriched ∆Np63 and ITGA6 (CD49f), anti-apoptotic BCL2, and the lymphangiogenic factor NTN4 but lower expression of luminal/alveolar differentiation-associated factor ELF5 while maintaining functional ERα.  Thus, UNC5A is a new regulator of ERα with a tumor/metastasis suppressive activity. Significance:  ERα signaling network plays a significant role in ~70% of breast cancers.  While the signaling molecules that partner with ERα to augment E2-dependent signaling and promote breast cancer progression have been well studied, negative feedback proteins that attenuate ERα signaling and their contribution to breast cancer progression are yet to be identified.  This study reports E2-inducible UNC5A as a critical attenuator of ERα signaling and its reduced expression in primary breast cancer is associated with poor outcome.  UNC5A potentially controls ERα signaling by restricting PI3K/AKT:ERα crosstalk needed for E2-independent activity while simultaneously maintaining ERα-dependent luminal differentiation program.  These findings have important implications in developing strategies to combat anti-estrogen resistance and to improve clinical utility of PI3K/AKT inhibitors.

overall_design: UNC5A expression was knocked down in MCF-7 and T47D cells by shRNA and stable cells expressing shRNA were generated. The vector expressing cells served as controls (pLKO). Cells were treated with vehicle (ethanol) or estradiol (0.1 nM) for three hours. Total RNA was prepared using RNAeasy kit from Qiagen and subjected to RNA-seq

first: Poornima

last: Bhat-Nakshatri


title: Unique mRNA expressed during grapevine floral development

city: Glen Osmond

first: Mark

middle: Raymond

last: Thomas

state: SA

address: PO Box 350

department: Plant Industry

institute: CSIRO

summary: The aim of the work was the identification of floral specific genes in grapevine.

overall_design: mRNA-Seq datasets were produced from 3 different developmental stages of inflorescences, tendrils and leaves at node positions 1, 2 & 3 from the shoot apex on grapevine plants. Two biological replicates were used for inflorescence structures using different picovine genotypes (06C021V0046, 06C008V0003). Leaf samples were pooled prior to sequencing.

first: Ying

last: Zhu

first: Pat

last: Corena


title: Discovery of new small RNA molecules expressed in the grape berry. Comparison of pre- and post-véraison berries and heat stress effects.

summary: The aim of the present work was the quantitative profiling of small RNAs involved in berry development and responding to heat stress and the identification of chromosome location and putative gene targets.

overall_design: Small RNA datasets were produced for heat stressed berries on grapevine L1 microvine plants. Two biological replicates were used for each temperature treatment and berry development stage.

first: Christopher

last: Davies


title: Heat stress effects on gene expression in the grape berry. Comparison of pre- and post-véraison berries and microarray versus mRNA-seq datasets.

summary: The aim of the work was the identification of grapevine genes in the berry that respond to heat stress.

overall_design: mRNA-Seq datasets were produced for heat stressed berries on grapevine L1 microvine plants. Two biological replicates were used for each each temperature treatment and berry developmental stage.


title: Toxoplasma controls host cyclin E expression through the use of a novel MYR1-dependent effector protein, HCE1

first: Adit

last: Naor

address: 300 Pasteur Drive Stanford, D305 Fairchild Building

summary: Toxoplasma gondii is an obligate intracellular parasite that must establish a favorable environment in the host cells in which it replicates. To do this, it controls key host cell processes by MYR-dependent translocation of dense granule proteins from the parasitophorous vacuole into the host cytosol. Using RNASeq, we previously reported that mutants lacking the MYR translocation apparatus fail to elicit a key set of host responses related to regulation of the cell cycle, including cyclin E and other targets of E2F transcription factors. As no previously reported effector was known to mediate such an effect, we report here our application of a set of criteria to proteins secreted by Toxoplasma leading to our discovery of a novel effector protein that induces the host to produce cyclin E. This inducer of Host Cyclin E (HCE1) is exported from the parasitophorous vacuole in a manner dependent on MYR1 and ASP5, another component of the export system, where it then localizes to the host’s nucleus. HCE1 expression is important for parasite growth as those lacking it produce plaques that are ~35% smaller in area than wild type parasites. RNASeq of host cells infected with parasites lacking HCE1 compared to those infected with wild type parasites shows a complete loss of the parasite’s ability to modulate key host cell cycle genes including those related to the E2F axis. Immunoprecipitation of HCE1 from infected host cells shows that HCE1 efficiently binds elements of the cyclin E regulatory complex: DP1 and its partners E2F3 and E2F4. Expression of HCE1 in Neospora caninum, which is not otherwise capable of up-regulating cyclin E, or in uninfected HFFs, shows nuclear localization of the expressed protein and results in strong cyclin E up-regulation. Thus, HCE1 is a novel, stand-alone effector protein that is necessary and sufficient to impact the E2F-axis of transcription resulting in co-opting of host functions to Toxoplasma’s advantage.

overall_design: RNASeq of human foreskin fibroblasts, infected with Toxoplasma, harvested 6 hours post infection. Samples are: Mock infected, infected with a WT RH, RH∆myr1,  RH∆239010

first: John

last: Boothroyd


title: Dynamic microRNA regulatory networks in establishing the Cellular specificity of developing human brains

status: Public on Nov 21 2018

city: Santa Barbara

first: Kenneth

middle: S.

last: Kosik

address: UC Santa Barbara

department: NRI

institute: UCSB

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

overall_design: Refer to individual Series


title: Unique small RNA expressed during grapevine floral development

summary: The aim of the work was the identification of floral specific small RNAs in grapevine.

overall_design: Small RNA datasets were produced from 3 different developmental stages of inflorescences, tendrils and leaves at node positions 1, 2 & 3 from the shoot apex on grapevine plants. Two biological replicates were used for inflorescence structures using different picovine genotypes (06C021V0046, 06C008V0003). Leaf samples were pooled prior to sequencing.


title: Transcriptomes of normal liver and spontaneous hepatocellular carcinoma in C3HeB/FeJ male mice

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: The goal of this study was to identify and analyze differential gene expression between normal liver and tumor tissue responding or not to potential treatments. A second goal was to compare the mouse results with that from analysis of human differential gene expression for normal liver and hepatocellular carcinoma.

overall_design: Mice were allowed to reach 10-months-old then assessed for the presence of tumors.  Animals with tumors were subjected to treatment protocols to be described else where.  After six 28-day cycles of treatment, mice were euthanized and tissue collected for RNA isolation that was used for next generation sequencing by Beckman Coulter.  Results were analyzed using Pigengene package.

first: Jessica

last: Zavadil

first: Christi

last: Walter

first: Habil

last: Zare


title: Dynamic microRNA regulatory networks in establishing the Cellular specificity of developing human brains (miRNA-seq)

summary: MicroRNAs (miRNAs) regulate many neurodevelopmental events, including proliferation, neurogenesis, neuronal migration, and cell survival. Individual miRNAs interact with hundreds of mRNA transcripts, but the precise landscape of these interactions in the context of cell-type-specificity has not been determined. Here, we used multiple parallel approaches, including AGO2-HITS-CLIP, combined mRNA and miRNA single-cell profiling and bipartite network analysis, to reveal a non-uniformity of miRNA-mRNA interactions that supports both defined cell-type identities as well as their dynamic transitions during human brain development at stages of peak neurogenesis. miRNA-mRNA clusters dynamically exploit the redundancy of the miRNA target code to differentially cluster across transitions in brain development. Using cell-type-specific functional properties of miRNA-mRNA interactions, we identify the role of great ape-specific miR-2115 in regulating cortical progenitor cell proliferation by targeting a radial glia enriched gene, origin recognition complex subunit 4 (ORC4). Together, our study suggests that miRNAs contribute to cell identity by regulating the expression of cell-type-specific transcripts.

overall_design: AGO2-HITS-CLIP was performed on human prenatal brain tissue samples and miRNA and mRNA libraries were prepared separately from the band corresponding to AGO2:miRNA:mRNA complex (130 kDa). Libraries were sequenced on Ion Torrent platform.

first: Neha

last: Rani

first: Tomasz

last: Nowakowski

first: Hongjun

last: Zhou

middle: S