title: Next-generation sequencing facilitates quantitative analysis of the transcriptomes of FOXG1 100% dosage, FOXG1 60% dosage, FOXG1 30% dosage, and FOXG1 0% dosage GABA interneurons derived from human embryonic stem cells

status: Public on Sep 18 2018

city: Beijing

first: Baoyang

last: Hu

state: Select State/Province

address: Beichenxilu

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology

summary:
Next-generation sequencing facilitates quantitative analysis of the transcriptomes of FOXG1 100% dosage GABA interneurons, FOXG1 60% dosage GABA interneurons, FOXG1 30% dosage GABA interneurons, and FOXG1 0% dosage GABA interneurons derived from human embryonic stem cells.
We report a genetic manipulation system that enable precise dosage control of FOXG1 protein in human pluripotent stem cells (hPSCs). Using this system, we explored how the various reduced dosage affect human ventrol GABA interneuron development. We employed RNA seq on hPSC-derived GABA interneurons (day 60) to invest the expression pattern under different FOXG1 dosage conditions. RNA-Seq on GABA interneurons (Day 60) indicates that compared to the FOXG1 100% group, variable insufficiency of FOXG1 produces more than 1000 differently expressed genes (DEGs), and more DEGs in the group with less FOXG1 dosage. Heat map on Pearson Correlation indicates that groups with more discriminated FOXG1 exhibit much weaker correlation. Venn diagram reveals that each group has a set of distinct DEGs, suggesting that each FOXG1 protein dosage could results in different expression pattern during differentiation. The DEGs can be divided into two clusters, with one showing dosage-dependent regulation by FOXG1 and the other one typical binary. Key regulatory genes for GABA interneuron induction (NKX2-1, NKX6-2, GAD1, etc.) and for functional GABAergic-speciﬁc synapse formation (GABBR1, GABRA1, GABRB1, GABRG1, GABRQ, SHANK1, etc.) are down regulated along with reduction of FOXG1 protein.

overall_design: The genetic manipulation system we built, which we call it SPIDe, is controlled by a small molecule (ASV). During the differentiation procedure from hPSCs to cortical GABA interneuron, treat the cells with ASV to induce FOXG1 protein degradation and then collect the samples on day 60 for RNA-seq.

first: Wenliang

last: Zhu


title: Dose-dependent transcriptomic responses of zebrafish embryos to Bisphenol A

status: Public on Sep 19 2018

city: Barcelona

first: Rubén

middle: Francisco

last: Martínez López

state: Cataluña

address: Carrer Jordi Girona, 18-26

department: Environmental Toxicology

country: Spain

institute: IDAEA-CSIC

type: Expression profiling by high throughput sequencing

summary:
Purpose: the goal of this project is to study the effects of the bisphenol A (BPA) in the transcriptome profiling (RNA-seq) of exposed zebrafish larvae.
Methods: Total RNA was isolated from the samples using AllPrep DNA/RNA Mini Kit (Qiagen, CA, USA) as described by the manufacturer. Three high quality sample per condition were chosen to the mRNA enrichment using KAPA Stranded mRNA-Seq Kit Illumina® Platforms (Kapa Biosystems). Transcriptomic profiles were generated by deep sequencing using Illumina TruSeq SBS Kit v3-HS (pair-ended; 2x76bp) on a HiSeq2000 sequencing system. Images analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA.
Statistical analysis: RNA-seq reads were aligned to the D. rerio reference genome (GRCz10) using STAR version 2.5.1b . Genes annotated in GRCz10.84 were quantified using RSEM version 1.2.28 with default parameters. Differential expression analysis between all BPA conditions was performed with the DESeq2 (v.1.10.1) R package with the Likelihood ratio test option. ANOVA-PLS was performed on the normalized data using the lmdme package in R (v. 1.0.136, R Core Team).
Results: We generated on average 40 million paired-end reads for each sample and identified aproximatelly 25000 transcripts. 2539 differentially expressed genes (DEGs) were detected which could be divided in 3 clusters including 960, 1132 and 447 genes, respectively. Affected metabolic pathways were analyzed from the DEGs: liver development, lipid transport, lysosome and protein glycosylation, metabolic pathways for lipids, glutathione, retinol, and steroid hormones, and cytochrome P450-mediated metabolism in adittion to protein ubiquitination and glycolysis/gluconeogenesis pathways' were down or upregulated.
Conclusions: The results suggest the interaction of BPA with different signaling pathways, being the estrogenic and retinoid receptors two likely BPA targets.  We concluded that our analysis allowed us the identification of underlying molecular mechanisms occurring simultaneously at the exposed animals. While this approach is very useful to analyze the effects of compounds, like BPA, able to interact with different cellular targets, we believe that it can be also applied to the characterization of the different toxic components present in complex natural mixtures.

overall_design: Whole embryo (5 dpf; wild type zebrafish) mRNA profiles of 4 groups (control, 0.1, 1 and 4 ppm of BPA) were generated by deep sequencing, in triplicate, using Illumina TruSeq SBS Kit v3-HS (pair-ended) on a HiSeq2000 sequencing system.

last: Martínez

first: Anna

last: Esteve-Codina

first: Laia

last: Herrero-Nogareda

first: Elena

last: Ortiz-Villanueva

first: Carlos

last: Barata

first: Romà

last: Tauler

first: Demetrio

last: Raldúa

first: Benjamin

last: Piña

last: Navarro-Martín


title: Ursolic acid attenuates hepatic steatosis, fibrosis, and insulin resistance by modulating the circadian rhythm pathway in diet-induced obese mice

status: Public on Sep 21 2018

city: Daegu

first: Myung-Sook

last: Choi

address: 1370, Sankyuk-Dong, Buk-gu

department: Food and Nutrition

country: South Korea

institute: Kyungpook National University

summary: Background/Objectives: The aim of the current study was to elucidate the effects of long-term supplementation with dietary ursolic acid (UR) on obesity and associated comorbidities, such as hepatic fibrosis, by analyzing transcriptional and metabolic responses, focusing on the role of UR in the modulation of the circadian rhythm pathway in particular. Subjects/Methods: C57BL/6J mice were divided into three groups and fed a normal diet, high-fat diet (HFD), or high-fat + 0.05% (w/w) UR diet for 16 weeks. Results: Oligonucleotide microarray profiling revealed that the liver transcriptome was more significantly altered by UR supplementation than that of the skeletal muscle and epididymal white adipose tissue, suggesting that UR is an effective regulator of the liver transcriptome. Furthermore, Kyoto Encyclopedia of Genes and Genomes pathway mapper analyses showed that canonical pathways associated with the “circadian rhythm” and “extracellular matrix (ECM)-receptor interactions” were effectively regulated by UR in the liver. UR altered the expression of various clock and clock-controlled genes (CCGs), which may be linked to the improvement of hepatic steatosis and fibrosis via lipid metabolism control and detoxification enhancement. UR reduced excessive reactive oxygen species production via an increase in plasma paraoxonase activity, adipokine/cytokine dysregulation, and ECM accumulation in the liver, which also contributed to improve hepatic lipotoxicity and fibrosis. In addition, UR treatment improved and normalized pancreatic islet dysfunction, and suppressed hepatic gluconeogenesis, thereby reducing obesity-associated insulin resistance in HFD-fed mice. Conclusions: Therapeutic approaches targeting hepatic circadian clock and CCGs using UR may ameliorate the deleterious effects of diet-induced obesity and associated complications such as hepatic fibrosis.

overall_design: Total RNA of liver, skeletal muscle and adipose tissues was obtained from normal diet, high-fat diet and ursolic acid added high-fat diet-fed mice and mRNA expression-associated with lipid metabolism and inflammation was measured.

first: Eun-Young

last: Kwon

first: Su-Kyung

last: Shin


title: Associative appetitive olfactory conditioning with Sucrose or Sorbose in Drosophila at 4 hours post training.

status: Public on Sep 15 2018

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

country: USA

institute: Stowers Institute

summary: To obtain a comprehensive view of genes contributing to long-term memory we performed mRNA sequencing from single Drosophila heads following behavioral training that produces long-lasting memory.

overall_design: Drosophila were starved and trained with an appetitive conditioning paradigm involving Sucrose or Sorbose, and then collected prior to or 4 hours post-training, 4 to 6 replicates each, for RNA-Seq analysis of the fly heads with an Illumina HiSeq 2000.

first: Kausik

last: Si

first: Raquel

last: Azpeleta

first: Jason

last: Gill

first: Jianping

last: Wu

first: Ryan

last: Welte


title: Butyrivibrio hungatei MB2003 and Butyrivibrio proteoclasticus B316T grown in mono- and co-cultures on xylan or pectin

status: Public on Sep 27 2018

city: Palmerston North

first: Nikola

last: Palevich

state: Manawatu

address: Tennent Drive, Agresearch, Grasslands

country: New Zealand

institute: AgResearch

summary: Rumen bacterial species belonging to the genera Butyrivibrio are important degraders of plant polysaccharides, particularly hemicelluloses (arabinoxylans) and pectin. Currently, four distinct species are recognized which have very similar substrate utilization profiles, but little is known about how these microorganisms are able to co-exist in the rumen. To investigate this question, Butyrivibrio hungatei MB2003 and Butyrivibrio proteoclasticus B316T were grown alone or in co-culture on the insoluble substrates, xylan or pectin, and their growth, release of sugars, fermentation end products and transcriptomes were examined. In single cultures, B316T was able to degrade and grow well on xylan and pectin, while MB2003 was unable to utilize either of these insoluble substrates to support significant growth. Co-cultures of B316T grown with MB2003 revealed that MB2003 showed almost equivalent growth to B316T when either xylan or pectin were supplied as substrates. The effect of co-culture on the transcriptomes of B316T and MB2003 was very marked; B316T transcription was largely unaffected by the presence MB2003, but MB2003 expressed a wide range of genes encoding carbohydrate degradation/metabolism and oligosaccharide transport/assimilation in order to compete with B316T for the released sugars. These results suggest that B316T has a role as an initiator of the primary solubilization of xylan and pectin, while MB2003 competes effectively as a scavenger for the released soluble sugars to enable its growth and maintenance in the rumen.

sample_organism:
Butyrivibrio proteoclasticus
Butyrivibrio hungatei

overall_design: Transcriptional profiling of B. hungatei MB2003 and B. proteoclasticus B316T grown in mono- and co-cultures on xylan and pectin substrates in triplicate.

first: Graeme

middle: T

last: Attwood

first: William

middle: J

last: Kelly

first: Jasna

last: Rakonjac


title: Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation [Microarray]

status: Public on Sep 13 2018

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

summary: Self-renewal of embryonic stem cells (ESCs) cultured in serum-LIF is incomplete with some cells initiating differentiation. While this is reflected in heterogeneous expression of naive pluripotency transcription factors (TFs), the link between TF heterogeneity and differentiation is not fully understood. Here we purify ESCs with distinct TF expression levels from serum-LIF cultures to uncover early events during commitment from naïve pluripotency. ESCs carrying fluorescent Nanog and Esrrb reporters show Esrrb downregulation only in NANOGlow cells.  Independent Esrrb reporter lines demonstrate that ESRRBnegative ESCs cannot effectively self-renew. Upon ESRRB loss, pre-implantation pluripotency gene expression collapses. ChIP-Seq identifies different regulatory element classes that bind both OCT4 and NANOG in ESRRBhigh cells. Class I elements lose NANOG and OCT4 binding in ESRRBnegative ESCs and associate with genes expressed preferentially in naïve ESCs. In contrast, class II elements retain OCT4 but not NANOG binding in ESRRBnegative cells and associate with more broadly expressed genes. Therefore, mechanistic differences in TF function act cumulatively to restrict potency during exit from naïve pluripotency.

overall_design: Microarray gene expression analysis of mouse ESCs and EpiSCs. ESCs were sorted by Esrrb expression level into High / Medium / Negative. 3 replicates per group. 12 samples total.

first: Nicola

last: Festuccia

first: Andrea

last: Corsinotti

first: Alessia

last: Gagliardi

first: Douglas

last: Colby

first: Simon

middle: R

last: Tomlinson

first: Ian

last: Chambers


title: Associative appetitive olfactory conditioning with Sucrose in Drosophila at 1 and 4 hours post training

first: Chris

last: Seidel

overall_design: Drosophila trained with an appetitive conditioning paradigm using Sucrose were collected prior to starvation, training, and 1 or 4 hours post-training, 5 to 6 replicates each, for RNA-Seq analysis of the fly heads with an Illumina HiSeq 2000.


title: Transcriptomic profiles of tissues from rats treated with drug combinations [Study 1]

status: Public on Sep 11 2018

city: Bethesda

first: Myrtle

last: Davis Millin

state: MD

address: 31 Center Drive

institute: The National Cancer Institute

summary: Combinations of anticancer agents may have synergistic anti-tumor effects, but enhanced toxicity often limit their clinical use. The risk that combinations of two or more drugs will cause adverse effects that are more severe than drugs used as monotherpies can be hypothesized from comprehensive analysis of each compound’s activity.  We generated microarray gene expression data following a single dose of agents administered individually with that of the agents administered in a combination.  The key objective of this initiative is to generate and make publicly available key high-content gene expression data sets for mechanistic hypothesis generation for several anticancer drug combinations.  The expectation is that availability of tissue-based genomic information that are derived from target tissues will facilitate the generation and testing of mechanistic hypotheses.  The view is that availability of these data sets for bioinformaticians and other scientists will contribute to analysis of these data and evaluation of the approach.

overall_design: Study 1 (originally study #3): Gene expression data from the bone marrow, heart and liver of Sprague-Dawley rats after after exposure to Temsirolimus at 0.3 mg/kg (i.v) or vehicle control (i.v) followed by either Sunitinib at 5 mg/kg (orally) or Sorafenib at 25 mg/kg (orally) or vehicle control (orally).

last: Davis

first: Pierre

last: Bushel


title: Transcriptomic profiles of tissues from rats treated with drug combinations [Study 3]

overall_design: Study 3 (originally study #5): Gene expression data from the skin heart and liver of Sprague-Dawley rats after after exposure to Gemcitabine at 20 mg/kg (i.v) or vehicle control (i.v) followed by either Erlotinib at 150 mg/kg (orally) or Sorafenib at 25 mg/kg (orally) or vehicle control (orally).


title: The expression of MHC class II molecules on murine breast tumors delays T cell exhaustion, expands the T cell repertoire and slows tumor growth

status: Public on Sep 08 2018

city: Huntsville

first: Dmytro

last: Starenki

state: Alabama

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: Transfection with the human class II transcriptional activator (hCIITA) promotes MHCII expression on TS/A breast cancer cells. Using a murine breast tumor line, we showed that MHCII-expressing tumors grew more slowly than controls and recruited more functional CD4+ and CD8+ T cells. Additionally, MHCII-expressing tumors contained more TCR clonotypes expanded to a larger degree than control tumors.  Functional CD8+ T cells in tumors depended on CD4+ T cells.  However, both CD4+ and CD8+ T cells eventually became exhausted, even in MHCII-expressing tumors. Treatment with anti-CTLA4, but not anti-PD-1 or anti-TIM-3, promoted complete eradication of MHCII-expressing tumors.  These results suggest tumor cell expression of MHCII facilitates the local activation of CD4+ T cells, indirectly helps the activation and expansion of CD8+ T cells and, in combination with the appropriate checkpoint inhibitor, promotes tumor regression.

overall_design: To test whether local MHCII expression promoted T cell clonal expansion or accumulation, we harvested 12 control and 12 MHCII-expressing whole tumor samples and sequenced the CDR3 region of the TCRbeta chain to identify unique T cell clones.

first: Tyler

last: McCaw

first: Mei

last: Li

first: Sara

last: Cooper

first: Mingyong

last: Liu

first: Selene

last: Meza-Perez

first: Rebecca

middle: C

last: Arend

first: Donald

last: Buchsbaum

first: Andres

last: Forero

first: Troy

middle: D

last: Randall


title: RNA-seq for transcriptome analysis in myoblasts, myotubes and osteoblasts trans-differentiated from C2C12 myoblasts

city: Suwon

first: Jinyoung

last: Park

address: Seobu-ro 2066, Jangan-gu

institute: Sungkyunkwan University

summary: We performed total transcriptome analysis by RNA-seq to find novel long non-coding RNAs which are differentiatlly expressed in myogenesis or osteogenesis.

overall_design: Total RNA extracted from C2C12 myoblasts, 3-days differentiated myotubes, and 3-days trans-differentiated osteoblasts using BMP2 was used for transcriptome analysis.

first: J

first: E-J

last: Cho


title: Inhibition of Enhancer of Zeste Homologue 2 attenuates TGF-β dependent hepatic stellate cell activation and liver fibrosis

status: Public on Sep 07 2018

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

summary: We report the effect of TGFβ  vs PDGF 2h treatment in hepatic stellate cells. We also report the effect of TGFβ treatment for 48h in human hepatic stellate cells.

overall_design: RNA sequencing was performed after treating human hepatic stellate cells with TGFβ and PDGF for 2h and also with TGFβ for 48h

first: Rosa

middle: M

last: Mateos

first: Thiago

last: De Assuncao

first: Juan

middle: P

last: Arab

first: Nidhi

last: Jalan-Sakrikar

first: Usman

last: Yaqoob

first: Thomas

last: Greuter

first: Vikas

last: Verma

first: Cao

last: Sheng

first: Robert

last: Huebert

first: Vijay

last: Shah


title: Transcriptomic profiles of tissues from rats treated with drug combinations

first: Myrtle

last: Davis Millin

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

overall_design: Refer to individual Series


title: Transcriptomic profiles of tissues from rats treated with drug combinations [Study 2]

overall_design: Study 2 (originally study #4): Gene expression data from the kidney, heart and liver of Sprague-Dawley rats after after exposure to Oxaliplatin at 15 mg/kg (i.v) or vehicle control (i.v) followed by either Sunitinib at 5 mg/kg (orally) or Sorafenib at 25 mg/kg (orally) or vehicle control (orally).

last: Davis

first: Pierre

last: Bushel


title: ETMR-like infantile cerebellar embryonal tumors in the extended morphologic spectrum of DICER1-related tumors

city: Paris

first: Julien

last: Masliah-Planchon

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Description of two cases of ETMR-like cerebellar tumors with DICER1 mutations

overall_design: Two cerebellar tumors

first: Franck

last: Bourdeaut


title: Meta-analysis Identifies MHC Loci in or near HLA-DRB1, HLA-DQA1, HLA-C as Associated with Leprosy in Chinese Han Population

status: Public on Sep 30 2018

city: Hefei

first: Xuelei

last: Zhang

state: China

address: Science and teaching building, Meishan Road 81, Hefei230032, Anhui Province, China

department: Dermatology

country: China

institute: Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University

summary: Leprosy is a chronic granulomatous disease caused by infection with Mycobacterium leprae. Genetic association studies indicated that leprosy risk is strongly associated with variation within the major histocompatibility complex (MHC) region, but the full number of variants in this region has yet to be elucidated. To identify further susceptibility loci or loss of function variants for this disease, we performed fine-mapping analysis of the MHC region using a Han Chinese reference panel (n= 10,689 patients, 29,948 genetic markers) in the data sets from our previous leprosy studies. Then, a fixed-effect meta-analysis was carried out separately for Chinese (case=2,901, control=3,801) and North Chinese (case=1,983, control=2,635) participants. The meta-analysis of Chinese participants identified 10 HLA-type or amino acid variants with lower than the genome-wide significant susceptibility signal. Next, gene-by-gene step-wise conditional analysis was performed in the combined dataset of these cohorts. Finally, we identified four new independent susceptibility loci (HLA-DQA1, HLA-C, rs3129063, and rs58327373) and confirmed one previously reported locus (HLA-DRB1) that significantly associated with leprosy in the Chinese Han population. Thus the results of this study increase knowledge about leprosy risk variants and illustrate the value of HLA imputation for fine mapping of causal variants in the MHC.

overall_design: To identify further susceptibility loci or loss of function variants for this disease, we performed fine-mapping analysis of the MHC region (29–34 Mb at chromosome 6)  using a Han Chinese reference panel (n= 10,689 patients, 29,948 genetic markers) in the data sets from our previous leprosy studies. Then, a fixed-effect meta-analysis was carried out separately for Chinese (case=2,901, control=3,801) and North Chinese (case=1,983, control=2,635) participants. This series includes the 728 cases and 1276 controls hybridized on Illumina Human610-Quad BeadChip in GWAS 1.


title: Gene expression analysis of liver samples at birth

status: Public on Sep 01 2018

city: Boston

first: Mary

middle: Frances

last: Lopez

state: Massachusetts

address: 3 blackfan circle, center for life sciences-16

department: Encrocrinology

institute: Boston Children's Hospital

summary: The present study aims to characterize the metabolic and transcriptional consequences of Igf2 deficiency in the newborn livers by gene expression analysis, Histological, triglyceride an Pathway Analysis.

overall_design: Livers were collected from mice. Total RNA isolated.  Samples where given to the microarray facility.

first: Joel

middle: N

last: Hirschhorn

middle: F


title: Transcriptome analysis of rhesus monkey MII oocytes and embryos

status: Public on Sep 09 2018

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

department: Animal Sciences

institute: Michigan State University


title: Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements [HMEPIC array]

city: Darlinghurst

first: Timothy

middle: John

last: Peters

state: NSW

address: 384 Victoria St

department: Immunology

country: Australia

institute: Garvan Institute of Medical Research

type: Methylation profiling by genome tiling array

summary: We empirically assess the measurement precision and sensitivity of a suite of DNA methylation technologies via a consensus modelling method called the row-linear model.

overall_design: Illumina HMEPIC microarrays were used to assay visceral (omental) adipocytes (VA).

first: T


title: CsGSTF1 is able to rescue the anthocyanin deficient phenotype of tt19-8 mutant

status: Public on Aug 30 2018

city: Hangzhou

first: Kang

last: Wei

address: Meiling South Road

institute: Tea Research Institute Chinese Academy of Agricult

summary: We reported gene expression difference between tt19 knock out line and two lines overexpressing CsGSTF1

overall_design: Nine samples examined.


title: Genome wide methylation analysis of 16 melanoma cell lines

status: Public on Aug 31 2018

city: Callaghan

first: Nikola

last: Bowden

address: University Dr

department: School of Medicine and Public Health

institute: University of Newcastle

summary: Genome wide DNA methylation profiling of  sixteen melanoma cell lines. The Illumina Infinium MethylationEPIC DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs from the cell lines at baseline.

overall_design: Bisulphite converted DNA from the 16 samples were hybridised to the Illumina Infinum Methylation EPIC beadchip

last: Budden

middle: A


title: Gene expression of DBTRG-05MG treated with dbcAMP or miR-1275 mimics

status: Public on Aug 29 2018

city: Guangzhou

first: liu

last: xincheng

address: zhongshan Road 74 Street

institute: sysu

type: Non-coding RNA profiling by high throughput sequencing

summary: Samples 1-5 were the microRNA-seq data of DBTRG-05MG treated with dbcAMP at 0/6/12/24/48 hours. Sample 6-17 were the analysis of DBTRG-05MG cells treated with control-media, dbcAMP, miR-1275 mimics and combined dbcAMP and miR-1275 mimics on day3.

overall_design: DBTRG-05MG tumor cells were treated with dbcAMP at 0/6/12/24/48 hours and microRNA-seq was performed. DBTRG-05MG tumor cells were treated with cultured media (RPMI1640), 1 mol/L dbcAMP, miR-1275 and the combination of dbcAMP and miR-1275 for 3 days, respectively. We used RNA-seq to detail the role miR-1275 played in the differentiation induced by dbcAMP.

first: J

middle: L

last: Mai

first: X

last: Liu


title: Critical role of the UBL-domain in stimulating the E3 ubiquitin ligase activity of UHRF1 towards chromatin

city: Planegg-Martinsried

first: Christopher

middle: B

last: Mulholland

state: Bavaria

address: Großhaderner Str. 2

department: Biologie II, Human Biologie und BioImaging

country: Germany

institute: Ludwig-Maximilians-Universität München

type: Methylation profiling by high throughput sequencing

summary: The RING E3 ubiquitin ligase UHRF1 controls DNA methylation through its ability to target the maintenance DNA methyltransferase DNMT1 to newly replicated chromatin. DNMT1 recruitment relies on ubiquitylation of histone H3 by UHRF1, however, how UHRF1 deposits ubiquitin onto the histone is unknown. Here, we demonstrate that the ubiquitin-like domain (UBL) of UHRF1 is essential for RING-mediated H3 ubiquitylation. Using chemical crosslinking and mass spectrometry, biochemical assays and recombinant chromatin substrates we show that the UBL participates in structural rearrangements of UHRF1 upon binding to chromatin and the E2 ubiquitin conjugating enzyme UbcH5a/UBE2D1. Similar to ubiquitin, the UBL exerts its effects through a hydrophobic patch that contacts a regulatory surface on the “backside” of the E2 to stabilise the E2-E3-chromatin complex. Our analysis of the enzymatic mechanism of UHRF1 uncovers an unexpected function of the UBL-domain and defines a new role for this domain in DNMT1-dependent inheritance of DNA methylation.

overall_design: Multiplex bisulfite PCR and next generation sequencing of 16 samples (biological quadruplicates from four genotypes)


title: Expression data from murine hepatic stellate cells

city: Setagaya

first: Keisuke

last: Oboki

state: Tokyo

address: 2-1-6 Kamikitazawa

department: Center for Medical Research Cooperation

country: Japan

institute: TOKYO METROPOLITAN INSTITUTE of MEDICAL SCIENCE

summary:
Wnt/β-catenin is involved in every aspect of embryonic development and in the pathogenesis of many human diseases, and is also implicated in organ fibrosis. However, the role of β-catenin-mediated signaling on liver fibrosis remains unclear. To explore this issue, the effects of PRI-724, a selective inhibitor of the cAMP-response element-binding protein-binding protein (CBP)/β-catenin interaction, on liver fibrosis were examined using carbon tetrachloride (CCl4)- or bile duct ligation (BDL)-induced mouse liver fibrosis models. Following repetitive CCl4 administrations, the nuclear translocation of β-catenin was observed only in the non-parenchymal cells in the liver. PRI-724 treatment reduced the fibrosis induced by CCl4 or BDL, accompanied by the suppression of S100A4 expression, a CBP/β-catenin transcript. C-82, an active form of PRI-724, inhibited the activation of isolated primary mouse quiescent hepatic stellate cells (HSCs) and promoted cell death in culture-activated HSCs. During the fibrosis resolution period, an increase in F4/80+ CD11b+ and Ly6Clow CD11b+ macrophages was induced by CCl4 and was sustained for two weeks thereafter, even after having stopped CCl4 treatment. PRI-724 accelerated the resolution of CCl4-induced liver fibrosis, and this was accompanied by increased matrix metalloproteinase (MMP)-9, MMP-2, and MMP-8 expression in intrahepatic leukocytes. These results suggest that the inhibition of CBP/β-catenin suppresses liver fibrosis through the inhibition of HSCs activation, the induction of activated HSC death, and the production of MMPs from macrophages. Thus, targeting the CBP/β-catenin interaction may become a new therapeutic strategy in treating liver fibrosis.
We used microarrays to detail the global change of gene expression by PRI-724 (C-82)-treatment in culture-activated murine hepatic stellate cells.

overall_design: RNA was extracted from murine hepatic stellate cells in the presense/absence of PRI-724 (C-82) and was hybridized on Affymetrix microarrays. We compared gene expression levels among quiescent and PRI-724-treated or vehcle-treated culture-activated hepatic stelalte cells. Moreover, we juxtaposed hepatic stellate cells from young and old mice under the same experimantal condition.

first: Yosuke

last: Osawa


title: Transcriptional profiling of irritant contact dermatitis (ICD) in a mouse model identifies specific patterns of gene expression and immune-regulation

status: Public on Sep 04 2018

city: Oklahoma City

first: Lerin

last: Luckett-Chastain

state: OK

address: 1110 N. Stonewall

department: Pharmaceutical Science

institute: OUHSC

summary: Irritant contact dermatitis (ICD) is a non-immunological, cutaneous inflammatory response to a variety of triggers that requires no sensitization and accounts for up to 80% of occupational dermatitis cases.  Numerous inflammatory cytokines play critical roles in the mechanism and severity of ICD, one being interleukin-6 (IL-6). Therefore, to investigate the influence of this pleotropic cytokine transcriptome analysis (MiSeq) was employed examining irritant-exposed and control skin samples from C57 and IL-6KO mice to gain a better understanding of the immunological mediators of ICD and what role IL-6 plays.  Overall, this study offers new insight into the pathogenesis of ICD, indicates new mediators/markers that may influence the variability of responses to irritants and potential targets for therapeutic manipulation.

overall_design: Examination of non-treated skin (C57 and IL-6KO, control samples), and 7 day BKC treated skin (C57-BKC and KO-BKC) in C57 and IL-6KO mouse skin. There are 3 replicates per group for a total of 12 samples and MiSeq analysis was performed.

first: Randle

last: Gallucci


title: Yap regulates glucose utilization and sustains nucleotide synthesis to enable organ growth

status: Public on Aug 25 2018

first: Wolfram

last: Goessling

state: MA

address: 77 Avenue Louis Pasteur

department: Department of Medicine, Division of Genetics

institute: Brigham and Women's Hospital

summary: The Hippo pathway and its nuclear effector Yap regulate organ size and cancer formation. While many modulators of Hippo activity have been identified, little is known about how Yap target genes mediate these growth effects. Here, we show that defects in hepatic progenitor potential and liver growth in yap-/- mutant zebrafish are caused by impaired glucose transport and nucleotide biosynthesis: transcriptomic and metabolomic analyses reveal that Yap directly regulates expression of glucose transporter glut1, causing decreased glycolytic flux into anabolic nucleotide biosynthesis in yap-/- mutants and impaired glucose tolerance in adults. Nucleotide supplementation improved Yap-deficient phenotypes, indicating functional importance of glucose-fuelled nucleotide biosynthesis. Yap-regulated Glut1 expression and glucose uptake are conserved in mammals. Our results identify Glut1 as a direct Yap target enhancing glucose uptake and utilization for anabolic nucleotide biosynthesis, which are required for organ growth. Our findings demonstrate the central role of Hippo signalling in metabolic homeostasis

overall_design: WT, yap-/- and yap-/-;taz-/- mutant larvae at 3 dpf, 4 replicates each.

first: Yariv

last: Houvras


title: Small non-coding RNA expression in developing mouse nephron progenitors

status: Public on Aug 21 2018

city: Pittsburgh

first: Andrew

middle: Scott

last: Clugston

state: PA

address: 872 Mirror Street

department: Integrative Systems Biology

institute: University of Pittsburgh

summary: The overall goal of this study is to determine the small non-coding RNA expression profile in developing mouse nephron progenitors and whole kidney. Using a limited digestion and negative selection approach, an enriched fraction of nephron progenitors were isolated from E15.5 whole kidney samples followed by small RNA-Sequencing (sRNA-Seq). A total of 3 biological replicates of mouse nephron progenitors and whole kidney samples were used for the sRNA-Seq. The NEBNext Multiplex Small RNA Library Prep Kit allowed us to prepare sequencing libraries from as little as 100ng total RNA. Multiplex sequencing was performed using the Illumina NextSeq 550 system with 50bp single reads, resulting in approximately 18 million reads per sample. Reads were aligned to the mm10 genome using Bowtie2, and the miRDeep2 software package was used to identify and quantify known and novel micro RNA (miRNA) within our sRNA-seq libraries. Differential expression analysis of miRNA expression between nephron progenitor and whole kidney samples identified 162 differentially expressed miRNAs (padj <= 0.05).

overall_design: 3 biological replicates of nephron progenitors and whole kidney samples were used for the sRNA-Seq. Each replicate consists of material pooled from a single litter of embryos.

first: Yu

last: Phua

first: Kevin

middle: H

last: Chen

first: Jacqueline

last: Ho

first: Dennis

last: Kostka


title: Preclinical and phase I clinical studies of KW-2450, a dual IGF-1R/IR tyrosine kinase inhibitor, in combination with lapatinib and letrozole.

status: Public on Aug 26 2018

city: Sunto-gun

first: Toshio

last: Ota

state: Shizuoka-ken

address: 1188, Shimotogari, Nagaizumi-cho

department: Translational Research Unit

institute: Kyowa Hakko Kirin Co. Ltd.

summary:
KW-2450 is an oral dual insulin-like growth factor-1 receptor/insulin receptor tyrosine kinase inhibitor. We investigated the in vitro and in vivo preclinical activity of KW-2450 plus lapatinib and letrozole and conducted a phase I trial of the triple-drug combination in one male and 10 postmenopausal female patients with advanced/metastatic hormone receptorpositive, human epidermal growth factor receptor 2 (HER2)-positive breast cancer.
A series of in vitro and in vivo animal studies was undertaken of KW-2450 in combination with lapatinib and hormonal agents. The phase I trial was conducted to establish the safety, tolerability, and recommended phase II dose (RP2D) of KW-2450 administered in combination with lapatinib and letrozole.
Preclinical studies showed KW-2450 and lapatinib act synergistically to induce in vitro apoptosis and inhibit growth of HER2-positive MDA-MB-361 and BT-474 breast cancer cell lines. This combined effect was confirmed in vivo using the MDA-MB-361 xenograft model. KW-2450 showed synergistic in vitro growth inhibition with letrozole and 4-hydroxytamoxifen in ER-positive MCF-7 breast cancer cells and MCF-7-Ac1 aromatase-transfected MCF-7 cells. In the phase I study, dose-limiting toxicity (DLT; grade 3 rash and grade 3 hyperglycemia, respectively) occurred in two of three patients at the dose of KW-2450 25 mg/day plus lapatinib 1500 mg/day and letrozole 2.5 mg/day. The RP2D of the triple-drug combination was established as KW-2450 25 mg/day, lapatinib 1250 mg/day, and letrozole 2.5 mg/day with no DLT at this dose level.

overall_design: Breast cancer cell line MDA-MB-361 was treated with DMSO, 100 nM KW-2450, 100 nM Lapatinib or 100 nM KW-2450 + 100 nM Lapatinib for 48 hours.

first: Hiroshi

last: Umehara

first: Yoshimi

last: Maekawa

first: Fumito

last: Koizumi

first: Makiko

last: Shimizu

first: Tamer

last: Fouad

first: Jie

last: Willey

first: Hidekuni

last: Kaito

first: Norihiko

last: Shiraishi

first: Daisuke

last: Nakashima

first: Shiro

last: Akinaga

first: Naoto

last: Ueno


title: Characterizing the gene expression profile of Prox1+ intestinal adenoma organoid cells

city: Budapest

first: Zoltan

last: Wiener

address: Ulloi ut 26

country: Hungary

institute: Semmelweis University

summary: We isolated and selected intestinal adenoma organoids from Apcmin/+; Rosa26LSL-TdTomato; Prox1-CreERT2 mice. After the selection procedure without growth factors, we induced CreERT2 activity and the transcription of tdTomato to label Prox1+ cells by 300 nM 4-hydroxytamoxifen for 16h.  tdTomato+ (Prox1+) and tdTomato- cells (enriched for Prox1- cells) were FACS sorted and total RNA was isolated.

overall_design: Total RNA obtained from tdTomato+ (Prox1+) cells was compared to the tdTomato- cell population (enriched for Prox1- cells) after FACS sorting.

first: Jenny

last: Högström

first: Zoltán

first: Kari

last: Alitalo


title: Dot6 is a major regulator of cell size and a transcriptional activator of ribosome biogenesis in the opportunistic yeast Candida albicans

status: Public on Aug 28 2018

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

country: Canada

institute: Universite de Montreal

summary: In most species, size homeostasis appears to be exerted in late G1 phase as cells commit to division, called Start in yeast and the Restriction Point in metazoans. This size threshold couples cell growth to division and thereby establishes long-term size homeostasis. Our former investigations have shown that hundreds of genes markedly altered cell size under homeostatic growth conditions in the opportunistic yeast Candida albicans, but surprisingly only few of these overlapped with size control genes in the budding yeast Saccharomyces cerevisiae. Here, we investigated one of the divergent potent size regulators in C. albicans, the Myb-like HTH transcription factor Dot6. Our data demonstrated that Dot6 is a negative regulator of Start and also acts as a transcriptional activator of ribosome biogenesis (Ribi) genes. Genetic epistasis uncovered that Dot6 interacted with the master transcriptional regulator of the G1 machinery, SBF complex, but not with the Ribi and cell size regulators Sch9, Sfp1 and p38/Hog1. Dot6 was required for carbon-source modulation of cell size and it is regulated at the level of nuclear localization by TOR pathway. Our findings support a model where Dot6 acts as a hub that integrate directly growth cues via the TOR pathway to control the commitment to mitotic division at G1.

overall_design: To investigate the role of Dot6 in Start control in C. albicans, we performed genome-wide transcriptional profiling by microarray. G1-cells of both dot6 mutant and the parental WT strain (SFY87) were collected by centrifugal elutriation, grown for 10 min at 30°C in fresh YPD medium and their transcriptomes were characterized.

first: Julien

last: Chaillot

first: Jaideep

last: Malick


title: Junction Usage Model (JUM) is a computational method for comprehensive annotation-free analysis of alternative pre-mRNA splicing patterns

city: Berkeley

first: Qingqing

last: Wang

state: CA

address: 161 Koshland Hall, UC Berkeley

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: Alternative pre-mRNA splicing (AS) greatly diversifies metazoan transcriptomes and proteomes and is crucial for gene regulation. Current computational analysis methods of AS from Illumina RNA-seq data rely on pre-annotated libraries of known spliced transcripts, which hinders AS analysis with poorly annotated genomes and can further mask unknown AS patterns. To address this critical bioinformatics problem, we developed a method called the Junction Usage Model (JUM) that uses a bottom-up approach to identify, analyze and quantitate global AS profiles without any prior transcriptome annotations. JUM accurately reports global AS changes in terms of the five conventional AS patterns and an additional "Composite" category composed of inseparable combinations of conventional patterns. JUM stringently classifies the difficult and disease-relevant pattern of intron retention, reducing the false positive rate of IR detection commonly seen in other annotation-based methods to near negligible rates. When analyzing AS in RNA-samples derived from Drosophila heads, human tumors and human cell lines bearing cancer-associated splicing factor mutations, JUM consistently identified ~ twice the number of novel AS events missed by other methods. Computational simulations showed JUM exhibits a 1.2-4.8 times higher true positive rate at a fixed cut-off of 5% false discovery rate. In summary, JUM provides a new framework and improved method that removes the necessity for transcriptome annotations and enables the detection, analysis and quantification of AS patterns in complex metazoan transcriptomes with superior accuracy.

overall_design: Computationally simulated RNA-seq datasets that model the cellular conditions in Drosophila S2 cells when a splicing factor PSI is knocked down (testgroup2) versus the control condition when a non-targeting siRNA is transfected into the same cell line type (testgroup 1). Three levels of splicing changes were simulated (60% - testgroup2_0.8; 40% - testgroup2_0.6; 20%-testgroup2_0.4). Three replicates were simulated for each condition.

first: Donald

last: Rio


title: Genome-wide maps of LDL1pro::LDL1:GFP in 14 days old arabidopsis

status: Public on Aug 19 2018

city: Taipei

first: Fu-Yu

last: Hung

address: Institute of Plant Biology, National Taiwan University

country: Taiwan

institute: NTU, IPB

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of H3K4 demethylase LDL1 in 14 days old arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we generated genome-wide LDL1-binding maps of 14 days old arabidopsis. To reveal bound genes by LDL1, chimeric protein LDL1-GFP was expressed under LDL1 promoter in ldl1 (LDL1pro:LDL1:GFP/ ldl1). ChIP was performed using anti-GFP antibody (ab290; ABCAM), and ChIP DNA were analyzed by Illumina HiSeq 2500.

overall_design: Chromatin immunoprecipitation was performed for LDL1pro::LDL1:GFP-expressing Arabidopsis. ChIP DNA was analyzed by Illumina HiSeq 2500.

first: Keqiang

last: Wu


title: AmpliSeq Transcriptome Analysis of cells stimulated with polyIC in presence of GFP or NS5 protein

status: Public on Aug 18 2018

city: San Francisco

first: A.

middle: Jeremy

last: Willsey

address: 675 Nelson Rising Lane

department: Psychiatry

institute: UCSF

summary: We compared polyIC stimulated cells in the presence of either GFP or NS5 protein

overall_design: A549 cells presence with GFP- or NS5-expressing plasmid using Polyjet (Signagen) according to manufacturer instructions, and 30 hours later stimulated with polyIC (Tocris) as previously described (Marazzi et al., 2012). At 12 hours post-stimulation, total cellular RNA was purified by RNeasy column (Qiagen).

first: Priya

middle: S

last: Shah

first: A

first: Nevan

last: Krogan


title: Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [4C-seq]

status: Public on Aug 15 2018

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

institute: CABD/CSIC

summary: What genomic changes led to the origin of vertebrates remains a mystery. On the one hand, animal evolution is thought to be driven mostly by changes in the cis-regulatory regions of a shared conserved and toolkit of developmental genes. On the other hand, vertebrates experienced two rounds of whole genome duplication (WGD) that increased their gene repertoire, particularly of regulatory genes controlling embryo development. To shed light into the origin and evolution of the vertebrate regulatory genome, we have generated an unprecedented transcriptomic and epigenomic resource for the non-duplicated genome of the European amphioxus, a closely related invertebrate chordate. These data include RNA-seq for more than 35 developmental stages and adult tissues, CAGE-seq, ChIP-seq, bisulphite-seq and ATAC-seq for several developmental stages and adult tissues. By comparing these data sets with equivalent novel and previously available data for various vertebrate species, especially zebrafish, we uncovered multiple conserved and vertebrate-specific regulatory landmarks. We first identify a conserved chordate phylotypic stage, a developmental period in which different chordate species show the highest gene expression similarity. We also shed light on the origin of enhancer demethylation in vertebrates, by identifying, for the first time in an invertebrate species, differentially methylated enhancers. Furthermore, we show that conserved clusters of co-expressed and tissue-specific genes display similar enrichments for cis-regulatory motifs between amphioxus and vertebrates. Finally, we study the impact of vertebrate WGDs on the evolution of gene regulation, providing the first genome-wide quantitative assessment of sub-functionalization and neo-functionalization processes after the vertebrate WGDs; changing the way in which these evolutionary mechanisms have been traditionally understood.

overall_design: 4C-Seq experiments using developmental genes promoters as baits in zebrafish (24hpf), mice (E9.5) and amphioxus (15hpf) whole embryos.

first: Firmpas

last: Panos

first: Acemel

last: Rafael D.

first: Naranjo

last: Silvia

middle: J

first: Maeso

last: Ignacio

first: José

last: Gómez-Skarmeta


title: Combinatorial Smad2/3 Activities Downstream of Nodal Signaling Maintain Embryonic/Extra-Embryonic Cell Identities during Lineage Priming [array]

status: Public on Aug 14 2018

city: Oxford

first: Anna

middle: Dorothea

last: Senft

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

summary: Epiblast cells in the early post-implantation stage mammalian embryo undergo a transition described as lineage priming before cell fate allocation, but signaling pathways acting upstream remain ill defined. Genetic studies demonstrate that Smad2/3 double-mutant mouse embryos die shortly after implantation. To learn more about the molecular disturbances underlying this abrupt failure, here we characterised Smad2/3-deificient embryonic stem cells (ESCs). We found that Smad2/3 double-knockout ESCs induced to form epiblast-like cells (EpiLCs) display changes in naïve and primed pluripotency marker gene expression, associated with the disruption of Oct4-bound distal regulatory element. In the absence of Smad2/3, we observed enhanced Bmp target gene expression and de-repression of extra-embryonic gene expression. Cell fate allocation into all three embryonic germ lakers is disrupted. Collectively, these experiments demonstrate that combinatorial Smad2/3 functional activities are required to maintain distinct embryonic and/or extra-embryonic cell identity during lineage priming in the epiblast before gastrulation.

overall_design: Total RNA was obtained from wild type, Smad2 KO, Smad3 KO or Smad2/3 DKO undifferentiated embryonic stem cells (ESCs) and embryoid bodies (EBs) differentiated from 100 ESCs each in the absence of LIF for two or three days (d2 and d3 EBs). Biotyinylated cRNA (1500 ng) was randomly hybridised to Illumina WG6_V2 arrays.

first: Ita

last: Costello

first: Hamish

middle: W

last: King

first: Arne

last: Mould

first: Elizabeth

middle: K

last: Bikoff

last: Robertson


title: Gene expression analysis of HL-60 cells treated with antimicrobial peptide ChMAP-28

status: Public on Aug 11 2018

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

summary: Antimicrobial peptide ChMAP-28  is a peptide of innate immunity of the goat Capra hircus. The goal of this research  was to evaluate possible changes in the molecular signaling pathways in HL-60 leukemia cells  and also to correlate this effect with the cytotoxic activity of the peptide.

overall_design: HL-60 cell line obtained from ATCC®. Cells were treated with three different concentration (less, equal or more IC50) of cytotoxic antimicrobial peptide of caprine origin ChMAP-28.

last: Emelianova

first: Denis

last: Kuzmin

first: Pavel

last: Panteleev

first: Maksim

last: Sorokin

first: Anton

last: Buzdin


title: A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo [bulk RNA-seq]

city: Baltimore

first: Patrick

last: Cahan

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

summary: We report the application of bulk high-throughput transcriptional profiling of differentiating mouse embryoid bodies.

overall_design: We examine four time points of the embryoid body directed differentiation protocol by bulk RNA sequencing: day 0, 2, 4, and 6.

first: Abby

last: Spangler


title: Systematic Interrogation of Human Promoters

status: Public on Aug 08 2018

city: Cambridge

first: Shira

last: Weingarten-Gabbay

address: 75 Ames St

institute: The Broad Institute

summary: Despite much research, our understanding of the architecture and cis-regulatory elements of human promoters is still lacking. Here, we devised a high-throughput assay to quantify the activity of ~15,000 fully designed sequences that we integrated and expressed from a fixed location within the human genome. We used this method to investigate thousands of native promoters and pre-initiation complex (PIC) binding regions followed by in-depth characterization of the sequence motifs underlying promoter activity including core promoter elements and TF binding-sites. We find that core promoters drive transcription mostly unidirectionally, and that sequences originating from promoters exhibit stronger activity than those originating from enhancers. Testing multiple synthetic configurations of core promoter elements, we dissect the motifs that positively and negatively regulate transcription as well as the effect of their combinations and distances, including a 10bp periodicity in the optimal distance between the TATA and the Initiator. By comprehensively screening 133 TF binding-sites, we find that in contrast to core promoters, TF binding-sites maintain similar activity levels in both orientations supporting a model by which divergent transcription is driven by two distinct unidirectional core promoters sharing bidirectional TF binding-sites. Finally, we find a striking agreement between the effect of binding site multiplicity of individual TFs in our assay and their tendency to appear in homotypic clusters throughout the genome. Overall, our study systematically assays the elements that drive expression in core- and proximal- promoter regions and shed light on organization principles of regulatory regions in the human genome.

overall_design: High-throughput measurements of fully designed promoters in human cells from a fixed location in the genome

first: Ronit

last: Nir

first: Shai

last: Lubliner

first: Eilon

last: Sharon

first: Yael

last: Kalma

first: Adina

last: Weinberger

first: Eran

last: Segal


title: The spatial and temporal dynamics of the nuclear RNAi-targeted retrotransposon transcripts in Caenorhabditis elegans [RNA-seq]

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

summary: Small RNA-guided chromatin silencing, also referred to as nuclear RNAi, plays an essential role in genome surveillance in eukaryotes and provides a unique paradigm to explore the complexity in RNA-mediated chromatin regulation and transgenerational epigenetics. A well-recognized paradox in this research area is that transcription of the target loci is necessary for the initiation and maintenance of the silencing at the same loci. How the two opposing activities (transcriptional activation and repression) are coordinated during animal development is poorly understood.  To resolve this gap, we took single-molecule RNA imaging, deep-sequencing, and genetic approaches towards delineating the developmental regulation and subcellular localization of RNA transcripts of two exemplary endogenous germline nuclear RNAi targets in C. elegans, Cer3 and Cer8 LTR retrotransposons.  By examining the wild type and a collection of mutant strains, we found that transcription and silencing cycle of Cer3 and Cer8 is tightly coupled with the early embryogenesis and germline mitotic and meiotic cell cycles.  Strikingly, Cer3 and Cer8 transcripts are exclusively localized in the nuclei of germ cells in both wild type and germline nuclear RNAi-defective mutant animals. RNA-sequencing analysis found that this nuclear enrichment feature is a general feature for the endogenous targets of the germline nuclear RNAi pathway.  In addition, the germline and somatic repressions of Cer3 have different genetic requirement for the three H3K9 histone methyltransferases, MET-2, SET-25, and SET-32, in conjunction with the nuclear Argonaute protein WAGO-9/HRDE-1. These results provide a first comprehensive cellular and developmental characterization of the nuclear RNAi-targeted endogenous targets throughout animal reproductive cycle. Altogether, these results support a model in which (1) both the transcriptional activation and repression steps of the germline nuclear RNAi pathway are tightly coupled with animal development, (2) the endogenous targets exhibit a hallmark of nuclear enrichment of their transcripts, and (3) different heterochromatin enzymes play distinct roles in somatic and germline silencing of the endogenous targets.

overall_design: 12 rRNA-removed RNA-seq libraries

first: Julie

middle: Z

last: Ni

middle: G


title: The spatial and temporal dynamics of the nuclear RNAi-targeted retrotransposon transcripts in Caenorhabditis elegans [ncRNA-seq]

overall_design: 2 small RNA-seq libraries


title: Gene expression of NonA RNAi knockdown in dvpdf cells in Drosophila

city: waltham

first: weifei

last: luo

address: 415 South st

department: Department of Biology

institute: Brandeis University

summary: We downregulated NonA in dvpdf cells by RNAi. 50-100 GFP-labeled dvpdf cells from 50-60 fly brians were manually isolated. mRNA sequecing libraries were prepared according to Nagoshi et al 2010, Abruzzi et al 2016.

overall_design: Examination of gene expression in Drosophila dvpdf cells.

first: Weifei

last: Luo


title: The spatial and temporal dynamics of the nuclear RNAi-targeted retrotransposon transcripts in Caenorhabditis elegans

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

overall_design: Refer to individual Series


title: Abundantly present miRNAs in milk-derived extracellular vesicles are conserved between mammals

city: Utrecht

first: Martijn

last: van Herwijnen

address: Yalelaan 2

department: Biochemistry & Cell Biology

country: Netherlands

institute: Utrecht University

summary: Mammalian milk is not only a source of nutrition for the newborn, but also contains various components that regulate further development. For instance, milk is an abundant source of microRNAs (miRNAs), which are evolutionary conserved small non-coding RNAs that are involved in post-transcriptional regulation of target mRNA. MiRNAs present in milk can occur in extracellular vesicles (EV), which are nanosized membrane vesicles released by many cell types as a means of intercellular communication. The membrane of EV protects enclosed miRNAs from degradation and harbors molecules that allow specific targeting to recipient cells. Although several studies have investigated the miRNA content in milk EV from individual species, little is known about the evolutionary conserved nature of EV-associated miRNAs among different species. In this study, we profiled the miRNA content of purified EV from human and porcine milk. These data were compared to published studies on EV from human, cow, porcine and panda milk to assess the overlap in the top 20 most abundant miRNAs.   Interestingly, several abundant miRNAs were shared between species (e.g. let-7 family members let-7a, let-7b, let-7f, and miR-148a). Moreover, these miRNAs have been implicated in immune-related functions and regulation of cell growth and signal transduction.   The conservation of these miRNA among species, not only in their sequence homology , but also in their incorporation in milk EV of several species, suggests that they are evolutionarily selected to regulate cell function in the newborn.

sample_organism:
Homo sapiens
Sus scrofa

platform_organism:
Homo sapiens
Sus scrofa

overall_design: EV were purified from a pool of 4 human milk donors, and from the milk of two pigs. RNA was isolated from these EV, treated with DNAse and subjected to NebNext (human) or TruSeq (pig) library preparation.

first: Marca

last: Wauben


title: Genome-wide analysis of altered gene expression pattern upon Atad3a deletion in mouse bone marrow lineage negative progenitor cells

status: Public on Aug 05 2018

city: Houston

first: Guoxiang

last: Jin

state: TX

address: 1515 Holcombe

department: Molecular&Cellular Oncology

institute: MD Anderson Cancer Center

summary: We sought to identify the altered expression of lineage specific markers including Gata1, Epor, Klf1, Tal1, Lmo2, Rag1, Ebf1, Irf8 and Csf2ra upon Atad3a deletion in the lineage negative cells

overall_design: Total RNA isolated from control (Atad3afl/fl) and Atad3a deletion (Atad3afl/flMx1Cre) lineage negative cells was analyzed by illumina mouse WG-6 V2 array. Each group has two replicates.

first: Hui-Kuan

last: Lin


title: Interdependent nutrient availability and   steroid hormone signals facilitate root growth plasticity

status: Public on Aug 01 2018

city: Haifa

first: Sigal

last: Savaldi-Goldstein

address: Technion City

country: Israel

institute: Technion

summary: Plants acquire essential elements from inherently heterogeneous soils, in which phosphate and iron availabilities vary.  Consequently, plants developed adaptive strategies to cope with low iron and low phosphate levels, including alternation between root growth enhancement and attenuation. How this adaptive response is achieved remains unclear. Here, we found that low iron accelerates the root growth of Arabidopsis thaliana by activating brassinosteroid signaling, whereas low-phosphate-induced high iron accumulation inhibited it.  Altered hormone signaling intensity also modulated iron accumulation in the root elongation and differentiation zones, constituting a feedback response between brassinosteroid and iron. Surprisingly, the early effect of low iron levels on root growth required the brassinosteroid receptor but the hormone ligand was negligible. The brassinosteroid receptor inhibitor BKI1, the transcription factors BES1/BZR1 and the ferroxidase LPR1, stood at the base of this feedback loop.  Hence, shared brassinosteroid and iron regulatory components link nutrient status to root morphology, thereby driving the adaptive response.

overall_design: Arabidopsis (Arabidopsis thaliana) lines in the Columbia-0 (Col-0) background, wild type and bzr1-D mutant, were germinated on one-half-strength Murashige and Skoog medium supplemented with 0.2% (w/v) sucrose for 6 days. Seedlings were then transferred for 24h to medium with either adequate (0.625 mM) or deficient (1µM) Pi levels (as described in Singh et al, Plant Phys, 2014). 8 samples of mRNA from two biological replicates were collected (i.e. from roots of 7-day-old seedlings). Samples were sequenced on an Illumina HiSeq 2500, to obtain 50 bp single end reads.

first: Amar

middle: P

last: Singh


title: HITS-CLIP of SMN

city: Ames

first: Ravindra

middle: N

state: IA

address: 2034 Veterinary Medicine

department: Biomedical Sciences

institute: Iowa State University

summary: We performed HITS-CLIP to determine cellular RNA targets of the SMN protein. Three replicates were performed in SH-SY5Y cells.

overall_design: HITS-CLIP of SMN

first: Eric

last: Ottesen

first: Diou

first: Natalia


status: Public on Jul 31 2018

city: Oklahoma City

first: Hiroshi

middle: Y

last: Yamada

state: Oklahoma

department: Medicine

institute: OUHSC

summary: Brain RNAseq, comparing wild type and Sgo1 mouse (all 24 months of age)

overall_design: Total RNA were collected from cerebrum extract of 24 months old wild type C57BL6 (n=3) and Shugoshin1 haploinsufficient mouse (n=3), and RNA-sequenced with Illunima sequencer.


title: Exon Level Expression Profiling of Diabetic Nephropathy

city: Nanjing

first: Jingsong

last: Shi

address: No.305, Zhongshan East Road

department: National Clinical Research Center of Kidney Disease

institute: Jinling Hospital, Nanjing University School of Medicine

summary:
Transcriptome comparison of glomeruli from kidneys with diabetic nephropathy (DN) and glomeruli from the unaffected portion of tumor nephrectomies.
Transcritomics profile of glomeruli in DN patients explored SRGAP2 was strongly associated with proteinuria and involved in podocyte cytoskeleton organization

overall_design: We applied high-throughput transciptomics method and tested the gene expression profile of microdissected glomeruli from type 2 DN patients. RNA was processed using the Affymetrix® microarray platform (Human Transcriptome Array 2.0, HTA 2.0). Array data was processed by Affymetrix Expression Console software. No techinical replicates were performed.

first: Zhihong

last: Liu

first: Song

last: Jiang

first: Yu

last: Pan

first: Qing

last: Hou

first: Dandan

last: Qiu

first: Yinhui

last: Lu


title: De novo mutations of MSL3 cause a novel X-linked syndrome due to impaired histone H4 lysine 16 acetylation

status: Public on Aug 06 2018

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Epigenetic regulation by histone acetylation plays a key role in cellular homeostasis and its misregulation is associated with human disease. The Male Specific Lethal (MSL) complex associated MOF/KAT8 histone acetyl-transferase is responsible for bulk Histone 4 Lysine 16 acetylation (H4K16ac) in flies and mammals. H4K16ac is a peculiar case amongst the many histone tail modifications in directly affecting higher order chromatin compaction. Yet, its importance during human development and a potential involvement in human pathologies remains largely unknown. Here, we uncover that pathogenic variants in MSL3, a component of the MSL complex, are causative for a new recognizable X-linked syndrome affecting both male and female individuals. Common clinical features of the syndrome include a global delay in developmental milestones and speech, a progressive gait disturbance and recognizable dysmorphism. Using skin biopsies and patient-derived primary fibroblasts, we demonstrate that de novo variants or deletions of MSL3 affect the assembly and enzymatic activity of the MSL complex, hence globally impacting H4K16ac levels in vivo. Transcriptome analysis from patient cells showed misregulation of cellular pathways involved in morphogenesis, cellular shape and cell migration. Using RNAi and MSL3 reintroduction experiments, we phenocopy acute responses occurring on H4K16ac-sensitive MSL target genes, supporting that this syndrome is caused by the loss of MSL3. Finally, we use HDAC inhibitors to rebalance acetylation levels and are able to alleviate both molecular and cellular phenotypes of MSL3 patients cells. Taken together, we characterize a novel syndrome, which is caused by mutations of an epigenetic regulator, allowing us for the first time to unravel the crucial role of H4K16ac during human development.

overall_design: RNA sequencing of human primary fibroblasts from control and patients with various truncations of MSL3 with and without panobinostat treatment

first: Giuseppe

last: Semplicio

first: Maria

middle: F

last: Basilicata


title: ALDH2 over expression in HCC cell line

city: Shanghai

first: Gang

address: 320 Yueyang Rd, Shanghai

institute: Shanghai Institutes for Biological Sciences

summary: mRNA levels of MHCCLM3 cell line over expressing ALDH2 and GFP were evaluated with Aligent microarray

overall_design: RNA from HCC cell line with over expression of ALDH2 and GFP were extracted, and evaluated with Aligent Human 4x44 microaaray

first: G

first: L

first: W

last: Zhou


title: Coordinated analysis of hepatic host responses to Dengue virus infection reveals a role for Hsp90 in viral replication

city: New York

first: Angela

last: Rasmussen

state: NY

department: Center for Infection and Immunity

institute: Columbia University

summary: Dengue virus (DENV) is a flavivirus transmitted by mosquitoes, and is the most prevalent arboviral pathogen in the world. The extent of acute DENV hepatitis has been linked to severe outcomes such as vascular leakage and hemorrhage, although the means by which hepatic responses to infection contribute to virus replication and disease are not well understood. We conducted an integrated transcriptomic, proteomic, and phosphoproteomic survey of hepatic cellular responses to DENV infection to identify host processes associated with increased inflammation, reduced coagulation factor synthesis, regulation of cell cycle progression and apoptosis, and translational control. Integration of these data sets into a comprehensive network model revealed modulation of several critical host signaling pathways, including PI3K/Akt, Ras/Raf/MAPK, Hsp90, and mTOR signaling. Experimental testing of these pathways demonstrated that Hsp90 inhibition impairs DENV replication, suggesting that heat shock responses may contribute significantly to hepatic infection.

overall_design: Huh7 human hepatoma cells were mock-infected or infected with dengue virus 2/New Guinea C strain (MOI=10) and total RNA was extracted from cells collected at 24 and 48h post-infection

middle: L

first: Nurcan

last: Tuncbag

first: Michael

last: Katze

first: Alejandro

last: Wolf-Yadlin

first: Ernest

last: Fraenkel


title: Caenorhabditis elegans heterochromatin factor SET-32 plays an essential role in transgenerational initiation of nuclear RNAi-mediated epigenetic silencing

status: Public on Jul 26 2018

first: Sam

last: Gu


title: Caenorhabditis elegans heterochromatin factor SET-32 plays an essential role in transgenerational initiation of nuclear RNAi-mediated epigenetic silencing (sRNA-Seq)

summary: Epigenetic inheritance contributes fundamentally to transgenerational physiology and fitness. Mechanistic understanding of RNA-mediated chromatin modification and transgenerational epigenetic inheritance, which in C. elegans can be triggered by exogenous double-stranded RNA (exo-dsRNA) or facilitated by endogenous small interfering RNAs (endo-siRNAs), has mainly been limited to the post-initiation phases of silencing. Indeed, the dynamic process by which nuclear RNAi engages a transcriptionally active target, before the repressive state is stably established, remains largely a mystery. Here we found that the onset of exo-dsRNA-induced nuclear RNAi is a transgenerational process, and that establishment requires SET-32, one of the three putative histone methyltransferases (HMTs) that are required for H3K9me3 deposition at the nuclear RNAi targets. We also performed multigenerational whole-genome analyses to examine the establishment of silencing at endogenous targets of germline nuclear RNAi. The nuclear Argonaute (AGO) protein HRDE-1 is essential for the maintenance of nuclear RNAi. Repairing a loss-of-function mutation in hrde-1 by CRISPR restored the silencing of endogenous targets in animals carrying wild type set-32. However, for numerous endogenous targets, repairing the hrde-1 mutation in a set-32;hrde-1 double mutant failed to restore their silencing states in up to 20 generations after the hrde-1 repair, using a similar genome editing approach.  We found that despite a prominent role in the establishment of silencing, however, set-32 is completely dispensable for the maintenance of silencing once HRDE-1-dependent gene repression is established.  Our study indicates that: 1) initiation and maintenance of siRNA-guided transcriptional repression are two distinct processes with different genetic requirements; and 2) the rate-limiting step of the establishment phase is a transgenerational, chromatin-based process. In addition, our study reveals a novel paradigm in which a heterochromatin factor primarily functions to promote the initiation of transgenerational silencing, expanding mechanistic understanding of the well-recognized role of heterochromatin in epigenetic maintenance.

overall_design: 16 samples were analyzed using small RNA-seq

first: Natallia

last: Kalinava


title: NonA-ADAR TRIBE RNA target identification in Drosophila Brains

first: weifei

last: luo

summary: We identified about NonA TRIBE RNA target in Drosopjila Brains

overall_design: We employed our TRIBE method to investigate NonA TRIBE target in fly brains. The expression of NonA_ADAR fusion protein is controlled by an inducible promotor elev-gsg. Nascent RNAs were prepared from 4 control and 3 experiment samples.

first: Weifei

last: Luo

first: Aoife

last: Mcmahan


title: Comparison of gene expression profile of T follicular helper cells and germinal center B cells from neonatal and adult mice

city: White Oak

first: Mustafa

last: Akkoyunlu

state: MD

address: 10903 New Hampshire Ave,

institute: FDA

summary: Vaccines that require T-cell help for the production of antibodies need to be administered three to four doses during the first 15 months of life in order to afford protection. Diminished antibody responses in newborns have been considered as a consequence of impaired T follicular helper (TFH) development and germinal center B cell (GC BC) formation upon immunization. To gain further insight into the transcriptional program for the induction and/or inhibition of TFH cell development, we screened 561 immune-related genes using the nCounter® Immunology Panel array.

overall_design: Analysis of in vivo follicular helper CD4 T cells (CD4+CXCR5+PD-1+), versus non-follicular helper CD4 T cells (CD4+CXCR5-PD-1-) and germinal center B cells (B220+GL-7-FAS-), versus non-germinal center B cells (B220+GL-7-FAS-), 10 days after immunization with sheep red blood cells to adult mice (8 week-old) and neonatal mice (5 day-old).

first: Jiyeon

last: Yang

first: Shafiuddin

last: Siddiqui

first: Derek

middle: D

last: Ireland


title: Identification of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome-associated DNA methylation patterns

status: Public on Jul 23 2018

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

summary:
Background: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex condition that involves multiple organ systems and is characterized by an abrupt or delayed onset of persistent/relapsing symptomatology such as debilitating fatigue, immune dysfunction, neurological problems, and other symptoms not curable for at least 6 months. Disruption of DNA methylation patterns has been tied to various immune and neurological diseases; however, the status of this epigenetic mark in ME/CFS remains uncertain. This study aimed at identifying changes in the DNA methylation patterns that are causative of changes in the regulation of gene expression in ME/CSF patients. Such changes may be also used for diagnostic purposes and be indicative of potential therapeutic targets.
Methods: Peripheral blood mononuclear cells (PBMCs) from 13 ME/CFS patients and 12 healthy controls (HC) were used to extract genomic DNA and measure global DNA methylation, and the methylation status at 850,000 CpG sites was assessed using Illumina MethylationEPIC microarrays.
Results: Global DNA methylation levels of ME/CFS patients were similar to those of HC. However, microarray-based genome-wide technology allowed detection of 17,296 differentially methylated CpG sites in 6,368 genes across promoters, gene regulatory elements and within coding regions of genes. Analysis of DNA methylation in promoter regions found 307 differentially methylated promoters (DMP); genes associated with DMP participate in at least 15 different pathways mostly related to cell signaling with a strong immune component.
Conclusions: This is the first study that has explored genome-wide epigenetic changes associated with ME/CFS using the new MethylationEPIC microarrays covering about 850,000 CpG sites. Our results are consistent with dysregulation of the immune system in ME/CFS and suggest a role of this epigenetic modification on the DNA pathobiology of ME/CFS.

overall_design: Genomic DNA from 25 peripheral blood mononuclear cells (PBMC) samples (13 ME/CFS, 12 controls) were bisulfite-converted and hybridised to the Illumina MethylationEPIC microarrays. GenomeStudio idat files were generated and the data was analyzed using the RnBeads R package.

first: Malav

last: Trivedi

first: Elisa

last: Oltra

first: Leonor

last: Sarria

first: Natasha

last: Rose

first: Vladimir

last: Beljanski

first: Mary

middle: A

last: Fletcher

first: Nancy

last: Klimas


title: Caenorhabditis elegans heterochromatin factor SET-32 plays an essential role in transgenerational initiation of nuclear RNAi-mediated epigenetic silencing (ChIP-Seq)

first: Sam

last: Gu

overall_design: Pol II and H3K9me3 ChIP-seq


title: Genome-wide analysis of EMT induced gene expression in accelerating mouse KrasG12D lung tumorigenesis

status: Public on Jul 24 2018

first: Hailun

last: Wang

address: 1550 Orleans Street

institute: Johns Hopkins University

summary: Analysis of EMT induced acceleration of mouse KrasG12D lung tumorigenesis at gene expression level. Results revealed that EMT activated important metabolism pathways including hexosamine biosysthesis pathway to suppress cell senescence and accelerate tumorigenesis.

overall_design: Total RNA obtained from isolated mouse lung tumors with EMT genes overexpression.

first: Kekoa

last: Taparra

first: Russell

last: Williams

first: Phuoc

middle: T

last: Tran


city: suzhou

first: Yi

state: Jiangsu

address: 199 Renai Road

department: Institutes of Biology and Medical Sciences

institute: Soochow University

summary: Myeloid-derived suppressor cells (MDSCs) represent a group of immature myeloid cells composed of myeloid progenitor cells and immature myeloid cells that can negatively regulate immune responses by inhibiting T cell function. Our lab and other groups have shown that injection of a lethal or sublethal dose of LPS into mice can result in the expansion of MDSCs in the bone marrow, spleen and blood. Until now, the molecular mechanisms responsible for this expansion were poorly studied. Specifically, the role of the individual microRNAs (miRNAs) involved remained largely unknown. We performed microarray analysis to compare the miRNA expression profiles of Gr-1+CD11b+ cells sorted from the bone marrow of LPS-injected and PBS-injected mice. We identified let-7e, which was highly upregulated in the LPS-treated group, as a potent regulator of LPS-induced MDSC expansion. Furthermore, let-7e overexpression in bone marrow chimeric mice leads to a noticeable increase in the population of Gr-1+CD11b+ cells, which results from reduced cellular apoptosis. Further studies showed that let-7e can directly target caspase-3 to inhibit cell apoptosis, and upregulation of let-7e in LPS-stimulated MDSCs could be due to the relieved repression of let-7e transcription exerted by downregulated GATA2. Our findings suggest that LPS expands MDSCs by inhibiting apoptosis through the regulation of the GATA2/let-7e axis.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Mice were injected (ip) with 100ng LPS(L3024-10MG, Sigma) dissolved in PBS, with mice injected with PBS as control group. Thirty hours later, mice were sacrificed and Gr-1+CD11b+ cells were sorted from bone marrow by flow cytometer.Total RNA was harvested using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions. After having passed RNA quantity measurement using the NanoDrop 1000, these two samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.18.0). Following the washing steps the slides were scanned by the Agilent Scanner G2505C.

first: Jinping

last: Zhang


title: cGMP-dependent protein kinase 1 (cGK1) modulates human hepatic stellate cell activation

status: Public on Sep 11 2018

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

institute: Universitätsklinikum Tübingen

summary: The activation of hepatic stellate cells (HSC) plays a crucial role in non-alcoholic fatty liver disease (NAFLD), which could further develop to non-alcoholic steatohepatitis (NASH) and liver fibrosis/cirrhosis. Since cGMP-dependent protein kinase 1 (cGK1) deficient (cGK1-KO) mice displayed hepatic insulin resistance we hypothesized that cGK1 modulates HSC activation and its metabolic consequences. First, retinol storage and gene expression were studied in cGK1-KO mice. Second, we investigated the effects of cGK1-silencing on gene expression in the human stellate cell line LX2. Finally, cGK1 expression was investigated in human liver biopsies covering a wide range of liver fat content. Retinyl-ester level in the liver of cGK1-KO mice was lower compared to wild-type animals, which was associated with increased inflammatory gene expression. mRNA regulation in cGK1-silenced LX2 cells showed stronger stellate cell activation profile, altered matrix degradation and elevated chemokine level. On the other hand, activation of LX2 cells suppressed cGK1 expression, which was associated with human data, showing a negative correlation between cGK1 mRNA and liver fat content in liver biopsies. These results suggest that the lack of cGK1 could possibly lead to stellate cell activation, which elevates chemokine expression and inflammatory processes, which in turn disturbs hepatic insulin sensitivity.

overall_design: We performed gene expression microarray analysis on liver tissue derived from 2 months old, male cGK1-KO smooth muscle rescue and control mice

first: Andras

last: Franko

first: Marketa

last: Kovarova

first: Susanne

last: Feil

first: Robert

last: Wagner

first: Alfred

last: Königsrainer

first: Marc

last: Ruoß

first: Andreas

last: Nussler

first: Cora

last: Weigert

first: Hans-Ulrich

last: Häring

first: Stefan

last: Lutz

last: Peter


title: WDR-23 and SKN-1 Nrf2 coordinate with the BLI-3 dual oxidase in response to iodide-triggered oxidative stress

status: Public on Jul 18 2018

city: Changsha

first: Long

last: Ma

state: Hunan

address: Xiangya Road No.110

institute: Central South University

summary: Excess iodide could lead to larve arrest to C. elegans, we screened for mutants that can survive in excess iodide and identified gain-of-function mutations in skn-1 and loss-of-function mutations in wdr-23 and bli-3. Genetic study uncover that wdr-23(lf) can interact with bli-3 mutations in a manner different from skn-1(gf). Transcriptome studies suggest that excess iodide causes developmental arrest largely independent of changes in gene expression, and wdr-23(lf) could affect the expression of a subset of genes by a mechanism different from SKN-1 activation.

overall_design: L1 mRNA profiles of wild type (WT), wdr-23(mac35lf) and skn-1(mac53gf) C. elegans with or without iodide treatment were generated in triplicate.

first: Zhaofa

last: Xu


title: Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish

status: Public on Jul 15 2018

city: Worcester

first: Charles

last: Sagerstrom

address: 364 Plantation Street

department: Biochemistry and Molecular Pharmacology

institute: UMass Medical School

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

overall_design: Refer to individual Series


title: Caenorhabditis elegans heterochromatin factor SET-32 plays an essential role in transgenerational initiation of nuclear RNAi-mediated epigenetic silencing (RNA-Seq)

city: Piscataway

first: Sam

last: Gu

institute: Rutgers University

overall_design: 23 samples were analyzed using RNA-seq

first: Natallia

last: Kalinava


title: Kinase-dependent structural role of DNA-PKcs during immunoglobulin class switch recombination

city: New Yprk

first: Zhengping

last: Shao

state: New York

address: 1130 St. Nicholas Ave

department: ICG

institute: Columbia University Medical Center

summary: The catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) is a classical nonhomologous end-joining (cNHEJ) factor. Loss of DNA-PKcs diminished mature B cell class switch recombination (CSR) to other isotypes, but not IgG1. Here, we show that expression of the kinase-dead DNA-PKcs (DNA-PKcsKD/KD) severely compromises CSR to IgG1. High-throughput sequencing analyses of CSR junctions reveal frequent accumulation of nonproductive interchromosomal translocations, inversions, and extensive end resection in DNA-PKcsKD/KD, but not DNA-PKcs-/- B cells. Meanwhile, the residual joints from DNA-PKcsKD/KDcells and the efficient Sμ-Sγ1 junctions from DNA-PKcs-/- B cells both display similar preferences for small (2–6 nt) microhomologies (MH). In DNA-PKcs-/- cells, Sμ-Sγ1 joints are more resistant to inversions and extensive resection than Sμ-Se and Sμ-Sμ joints, providing a mechanism for the isotype-specific CSR defects. Together, our findings identify a kinase-dependent role of DNA-PKcs in suppressing MH-mediated end joining and a structural role of DNA-PKcs protein in the orientation of CSR.

overall_design:
To ascertain how different DNA-PKcs mutations (null vs KD) affect CSR in an isotype dependent manner, we employed the High Throughput Genome Translocation Sequencing (HTGTS) (1) method to analyze CSR junctions in DNA-PKcsKD/KD and DNA-PKcs-/- B cells with preassembly IgH and L chains (HL). We measured switching efficiency, efficiency and size of small MH in DNA-PKcs-/- and DNA-PKcsKD/KD  B cells in contrast to cNHEJ-deficient Xrcc4-/- B cells, as well as insertions and deletions than both Sμ-Sμ and Sμ-Sε junctions. Finally our analyses also identified long MH mediated inter-chromosomal translocations in DNA-PKcsKD/KD B cells and a reduced number of G mutations in 5’Sμ in repair deficient B cells.
Since all our experimental mice carry the preassembled IgH on the 129  ackground, we replaced the IgH switch region (from JH4 to the last Cα exon, chr12 114, 494, 415–114, 666, 816) of the C57/BL6-based mm9 with the corresponding region in the AJ851868.3 (NCBI gene accession no. AJ851868.3) 129 IgH sequence (1415966–1592715) to generate the mm9sr (switch region replacement) genome.  1. Hu J, et al. (2016) Detecting DNA double-stranded breaks in mammalian genomes by linear amplification-mediated high-throughput genome-wide translocation sequencing. Nat Protoc 11:853–871.

first: Jennifer

last: Crowe

first: Xiaobin

middle: S

last: Wang

first: Shan

last: Zha


title: Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli

status: Public on Jul 16 2018

city: Trondheim

first: Christina

middle: Gabrielsen

last: Aas

address: Erling Skjalgssons gt 1

department: Dept. of Medical Microbiology

country: Norway

institute: St. Olavs University Hospital

summary: We have used RNA sequencing to compare transcriptomes of 30 stx2a and eae positive STEC strains of non-O157 serogroups isolated from children < 5 years of age. The strains were from children with HUS (HUS group, n=15), and children with asymptomatic or mild disease (non-HUS group, n=15), either induced with mitomycin C or non-induced, to reveal potential differences in gene expression levels between groups. When the HUS and non-HUS group were compared for differential expression of protein-encoding gene families, 399 of 6119 gene families were differentially expressed (log2 fold change ≥ 1, FDR < 0.05) in the non-induced condition, whereas only one gene family was differentially expressed in the induced condition. Gene ontology and cluster analysis showed that several fimbrial operons, as well as a putative type VI secretion system (T6SS) were more highly expressed in the HUS group than in the non-HUS group, indicating a role of these in the virulence of STEC strains causing severe disease.

overall_design:
Comparison of 30 non-O157 STEC strains, one group of strains having caused HUS (n=15) and one causing no or mild disease (n=15), induced with mitomycin c or non-induced, at exponential growth in SILAC medium.

Please note that locations of genomic features are provided in associated .gtf file for each sample pair (i.e. non-induced and induced samples; e.g.  *nIND.HUS and *IND.HUS), linked to the corresponding uninduced sample records.

last: Ås

first: Finn

last: Drabløs

first: Kjersti

last: Haugum

first: Jan

middle: E

last: Afset


title: Biogenesis of a young, 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation

status: Public on Jul 06 2018

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: Phased, secondary siRNAs (phasiRNAs) represent a class of small RNAs in plants generated via distinct biogenesis pathways, predominantly dependent on the activity of 22 nt miRNAs. Most 22 nt miRNAs are processed by DCL1 from miRNA precursors containing an asymmetric bulge, yielding a 22/21 nt miRNA/miRNA* duplex. Here we show that miR1510, a soybean miRNA capable of triggering phasiRNA production from numerous NB-LRRs, previously described as 21 nt in its mature form, primarily accumulates as a 22 nt isoform via monouridylation. We demonstrate that in Arabidopsis, this uridylation is performed by HESO1. Biochemical experiments showed that the 3' terminus of miR1510 is only partially 2'-O-methylated, because of the terminal mispairing in the miR1510/miR1510* duplex that inhibits HEN1 activity in soybean. miR1510 emerged in the Phaseoleae ~41 to 42 MYA with a conserved precursor structure yielding a 22 nt monouridylated form, yet a variant in mung bean is processed directly in a 22 nt mature form. This analysis of miR1510 yields two observations: (1) plants can utilize post-processing modification to generate abundant 22 nt miRNA isoforms to more efficiently regulate target mRNA abundances; (2) comparative analysis demonstrates an example of selective optimization of precursor processing of a young plant miRNA.

sample_organism:
Arabidopsis thaliana
Cajanus cajan
Vigna radiata

overall_design: Small RNA sequencing from pigeon pea, mung bean, and Arabidopsis (with soybean MIR1510a transgene) leaves.

middle: C

first: Qili

last: Fei


title: RNA Seq of wild-type and VPS35-D620N-expressing SH-SY5Y cells

status: Public on Jul 11 2018

city: Boise

first: Brad

last: Morrison

state: ID

address: 1910 university dr., mail stop: 1515

department: Biological Sciences

institute: Boise State University

summary: SH-SY5Y were created to stably express wild-type or VPS35-D620N (CMV-promoter driven) using a lentiviral vector (Vira power). Non-transduced cells were eliminated with blasticidin resistance gene included in viral cassette

overall_design: Wild-type VPS35 and VPS35 D620N-expressing SH-SY5Y cells were differentiated with 10uM all-trans retinoic acid for 7 days and RNA extracted using Qiagen RNEasy kit. There are 3 independent experiments (replicates 1-3)

first: Abir

last: Rahman


title: Dll and Sp1 ChIP-seq data from Drosophila third instar leg imaginal discs

city: Duluth

first: Matthew

last: Slattery

state: MINNESOTA

address: 1035 University Drive, SMed 219

institute: University of Minnesota Medical School

summary: Animal limb development relies on the establishment of organizing centers, which govern limb outgrowth and patterning by regulating the spatial and temporal expression of secreted signaling molecules. On a molecular level the establishment of organizing centers occurs via cis regulatory modules (CRMs), also known as transcriptional enhancers, that integrate upstream temporal and spatial inputs. We elucidated the mechanism that governs the establishment of an Epidermal Growth Factor Receptor (EGFR) organizing center (EOC) during leg development in Drosophila melanogaster. We find that EGFR activation occurs by sequential activation of the EGFR ligand Vein (Vn) and the EGFR ligand-processing protease Rhomboid (Rho), each through single CRMs. These CRMs integrate in a distinct manner inputs from the Wingless (Wg) and Decapentaplegic (Dpp) signaling pathways, and from the leg selector transcription factors Distal-less (Dll) and Sp1. Elimination of the vn (vnE) and rho (rhoE) EOC enhancers eliminates the expression of these genes in the center of the leg imaginal discs, respectively.  A vnE rhoE double deficiency, but not single deletions, demonstrates an absolute requirement of these CRMs for specifying the most distal, but not more proximal, leg fates. In addition, the cis-regulatory logic of vnE and rhoE transcends the leg EOC developmental program, because genomic regions with similar inputs, based on predicted and genome-wide binding by the transcription factors that establish the EOC, faithfully predicts novel CRMs active in the distal leg. The combinatorial input of Wg, Dpp, Dll and Sp1 at these CRMs reveals a molecular signature for coordinating gene expression in the Drosophila leg that might be analogous to many other multi-cellular systems.

overall_design: Triplicate pools of 100 yw and 100 recombineered Sp1-GFP (BAC) L3 wandering larvae were used to perform independent chromatin IPs. The Sp1-GFP (BAC) is a GFP-tagged Sp1 in BAC clone CH321-64M02 inserted in landing site VK00033 (gift from Dr. Rebecca Spokony). All 6 leg discs from each larva were used as material for each IP. Chromatin from the yw larvae pools was immuno-precipitated with goat anti-Dll antibody (sc-15858, Santa Cruz Biotechnology, 1.5 µg/ml for IP) while chromatin from the Sp1-GFP  larvae pools was immuno-precipitated with rabbit anti-GFP antibody (ab290, Abcam, 1∶300 dilution for IP). DNA from non-immunoprecipitated 10% chromatin input was isolated from each pool as reference control.

first: Mann

last: Richard

first: Voutev

last: Roumen


title: Segregation of the mammalian germline and soma is policed by Otx2

city: Jinan

first: Detian

last: Yuan

address: Wenhuaxi 44

institute: Shandong University

summary: The successful segregation of germ cells from somatic lineages is vital for sexual reproduction and species survival. In the mouse, primordial germ cells (PGCs), precursors of all germ cells, are induced from the post-implantation epiblast. Induction requires BMP4 signalling to prospective PGCs and the intrinsic action of PGC transcription factors (TFs). However, the molecular mechanisms connecting BMP4 action to induction of PGC TFs that are responsible for segregation of PGCs from somatic lineages are unknown. Here we show that the transcription factor OTX2 is a key regulator of these processes. Down-regulation of Otx2 precedes the initiation of the PGC programme both in vitro and in vivo. Deletion of Otx2 in vitro dramatically increases PGCLC differentiation efficiency and prolongs the period of PGC competence. In the absence of Otx2 activity, PGCLC differentiation becomes independent of the otherwise essential cytokine signals, with germline entry initiating even in the absence of the PGC TF Blimp1. Deletion of Otx2 in vivo increases PGC numbers. These data demonstrate that Otx2 acts repressively upstream of PGC TFs and functions as a roadblock to prevent the untimely entry of pluripotent stem cells into the PGC lineage, thereby ensuring correct spatio-temporal segregation of the germline and soma.

overall_design: In order to test whether PGCLCs induced from Otx2GFP/lacZ (hereinafter refer to as Otx2-/-)  and Otx2GFP/lacZ;Blimp1-/-  (Otx2-/-; BLimp1-/-) line in the presence or absence of cytokines are bona fide PGCs, we isolated samples from competent EpiLCs, and SSEA1+; CD61+ population sorted from aggregates at day 6 of PGCLC induction from wildtype E14Tg2a, Otx2-/- and Otx2-/-; BLimp1-/- cell lines, yielding a total of 21 samples. The RNAs were extracted and labelled for microarray analysis and the global transcriptional programs during PGCLC induction of the three lines were compared.

first: Jingchao

last: Zhang

first: Man


title: Potential role of gas6 in zebrafish hindbrain development

first: Charles

last: Sagerstrom

state: MA

summary: identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish

overall_design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit (Qiagen). Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina). All libraries were analyzed for quality on a bioanalyzer prior to sequencing (Agilent 2100 BioAnalyzer).

first: Priyanjali

last: Ghosh


title: CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [gDNA]

city: Urbana

first: Alan

last: Luu

state: Illinois

address: 1110 W Green St.

department: Physics

institute: University of Illinois at Urbana Champaign

summary: CRISPR gene editing has revolutionized biomedicine and biotechnology by providing a simple means to engineer genes in vivo by introducing mutations at target sites in the genomic DNA of living cells. However, given the stochasticity of cellular DNA repair mechanisms and the potential for introducing mutations at off-target sites, technologies capable of introducing targeted changes with increased precision, such as cytidine deaminase single-base editors, are preferred. We here present a versatile method termed CRISPR-SKIP that utilizes cytidine deaminase single-base editors to program de-novo exon skipping by mutating target DNA bases within splice acceptor sites. Given its simplicity and precision, CRISPR-SKIP will be broadly applicable in gene therapy and synthetic biology.

overall_design: Four exons were targeted by CRISPR-SKIP. For each exon, genomic DNA at the splice acceptor of two control samples and two treated samples were sequenced. Rate of G to A conversion of intronic flanking G was quantified.

first: Michael

last: Gapinske

first: Jackson

last: Winter

first: Wendy

last: Woods

first: Kurt

last: Kostan

first: Nikhil

last: Shiva

first: Jun

last: Song

first: Pablo

last: Perez-Pinera


title: Changes of misregulated genes in colon tissues after Setd2 disruption

status: Public on Jul 07 2018

first: Li

last: Li

address: 1954 Huashan Road

department: State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University

summary: Analysis of expression levels of misregulated genes.  Results provide important information of the gene regulation and signaling pathway of setd2.

overall_design: Total RNA were obtained and purified from isolated colon tissues from both 6-week-old control and KO mice.

first: Wenjun

last: Liu


title: SALL4 Crud ChIP sequencing-WT and RNA-seq of SNU398 cells treated with therapeutic SALL4 peptides

status: Public on Jul 05 2018

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary: SALL4 is a nuclear factor central to the maintenance of stem cell pluripotency and is a key component in HCC, a malignancy with no effective treatment. In cancer cells, SALL4 associates with NuRD to silence tumor suppressor genes such as PTEN. Here, we design a potent therapeutic SALL4 peptide (FFW) capable of antagonizing the SALL4-NURD interaction using systematic truncation and amino acid substitution studies. To understand the pathways affected by the peptide treatment, we performed RNA sequencing on cells treated with different peptides. Furthermore,  to identify SALL4 DNA binding targets, we have performed CRUD-ChIP sequencing with SALL4 and H2K27Ac antibodies on HCC cell line SNU398.

overall_design: For RNA sequencing, SNU398 were treated with 30μM of PEN, PEN-MUT, PEN-WT, or PEN-FFW for 8hrs and paired-end RNA-seq was performed for the treated samples. RNA-seq reads of each sample were mapped to hg19 using the STAR aligner.For Chip-sequencing, SNU398 cells were SNU398 cells were harvested and fixed. Only insoluble chromatin fractions were used for perfoming ChIP protocol, we renamed the protocol as CRUD-ChIP.

first: Liu

middle: B

last: Hui

first: Tan

middle: H

last: Kee

first: Wu

last: Chan-suo

last: Jia

first: Chai

first: Daniel

last: Tenen