title: Mechanism of in vivo activation of the MutLgamma-Exo1 complex for meiotic crossover formation

city: PARIS

first: Valerie

last: Borde

address: 26 rue d'Ulm

institute: Institut Curie

summary: Programmed DNA double-strand breaks (DSBs) initiate meiotic recombination and their subsequent repair culminates in crossover (CO) formation. COs result from the asymmetric cleavage of double-Holliday junction (dHJ) intermediates, that requires the MutLγ complex together with a non-catalytic function of Exo1, an activity essential for fertility but at risk of generating unwanted chromosome rearrangements. Here we show how crossover formation by MutLγ is activated at the right time and at the right place. MutLγ forms a constitutive complex with Exo1, and in meiotic cells transiently contacts the upstream MutSγ (Msh4-Msh5) heterodimer. MutLγ associates with DSB hotspots at a late step in the recombinational repair, once recombination intermediates have been stabilized and engaged in the crossover repair pathway. MutLγ-Exo1 is recruited to DSB hotspots independently of the polo-like Cdc5 kinase, but to activate dHJ resolution, Cdc5 is recruited to the recombination intermediates and interacts individually with both MutLγ and Exo1, suggesting their direct modification. in vivo, MutLγ occupancy is restrained on recombination intermediates, and genome-wide, MutLγ associates with the vast majority of DSB hotspots, but at a lower frequency in centromeres, consistent with a strategy to reduce at-risk crossover events in these regions, and in late replicating regions. Our data highlight the highly temporally and spatially control of the activity of this constitutive, potentially harmful, nuclease

overall_design: 9 samples total: 2 independent replicates of Mer3-Flag ChIP at 4 h in meiosis and their control untagged anti-Flag ChIP at 4 h in meiosis; 2 Mlh3-Myc8 ChIP at 5 h and 5h30 in pCUP1-IME1-synchronized meiosis and their corresponding controls spo11∆ Mlh3-Myc8 ChIP at 5 h and 5h30 in pCUP1-IME1-synchronized meiosis; 1 exo1∆ Mlh3-Myc8 ChIP at 5h30 in pCUP1-IME1 synchronized meiosis and its corresponding control spo11∆ Mlh3-Myc8 ChIP at 5h30 in pCUP1-IME1 synchronized meiosis.

first: Valérie


title: Histone Demethylases KDM3A and KDM4C regulate mesenchymal stromal cell senescence and bone aging through condensin-mediated heterochromatin organization

status: Public on Dec 01 2019

city: Hong Kong

first: HUANG

last: BIAO

address: Shatin, N. T, Hong Kong

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

type: Expression profiling by high throughput sequencing

summary: Epigenomic changes and stem cell exhaustion are two hallmarks of aging. Accumulating evidence suggest that MSC senescence could perpetuate aging or age-related diseases. Here we report that two H3K9 demethylases KDM3A and KDM4C regulate heterochromatin reorganization via transcriptionally activating condensin components NCAPD2 and NCAPG2 in aging MSCs. Suppression of KDM3A or KDM4C leads to robust DNA damage response and aggravates cellular senescence, whereas overexpression of KDM3A/KDM4C or NCAPD2 directly promotes heterochromatin reorganization and blunts DNA damage response. MSCs derived from kdm3a-/- mice exhibit compromised heterochromatin organization machinery and are more susceptible to genotoxic damage, which are associated with accelerated bone aging. Consistently, analysis of human bone marrow MSCs and transcriptome database for other human adult stem cells reveals inverse correlation of KDM3A and KDM4C with aging. Taken together, the present finding unveils a novel function of histone demethylases as a surveillance mechanism to restrain DNA damage accumulation via transcriptionally activating condensins during stem cell aging, which provides potential targets for the diagnosis and intervention of human aging and geriatric diseases.

overall_design: hUCMSCs were treated with siKDM3A, siKDM4C, siNC or KDM3A, KDM4C, control vector plasmids

first: Biao

last: Huang

first: Bin

last: Wang

first: Wayne

middle: Y

last: Lee

first: Kam

middle: T

last: Leung

first: Zhenqing

last: Liu

first: Rui

last: Chen

first: Liu

last: Shi

first: Lai

middle: L

last: Tsang

first: Hailong

first: Baohua

first: Yechun

last: Ruan

first: Hsiao

middle: C

last: Chan

first: Gang

last: Li

first: Xiaohua

last: Jiang


title: The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome [Hi-C seq]

city: Providence

first: Erica

last: Larschan

address: 185 Meeting St.

country: USA

institute: Brown University

summary:
Hi-C and 4C-seq anlaysis of Drosophila S2 cells
Drosophila dosage compensation is an important model system for defining how active chromatin domains are formed. The Male-specific lethal dosage compensation complex (MSLc) increases transcript levels of genes along the length of the single male X-chromosome to equalize with that on the two female X-chromosomes. The strongest binding sites for MSLc cluster together in three-dimensional space independent of MSLc because clustering occurs in both sexes. CLAMP, a non-sex specific, ubiquitous zinc finger protein, binds synergistically with MSLc to enrich the occupancy of both factors on the male X-chromosome. Here, we demonstrate that CLAMP promotes the observed clustering of MSLc bindings sites. Genome-wide, CLAMP promotes interactions between active chromatin regions and represses interactions between inactive chromatin regions. Moreover, the X-enriched CLAMP protein promotes longer-range interactions on the active X-chromosome than autosomes. Overall, we define how long-range interactions, mediated by a locally-enriched ubiquitous transcription factor, generate a three-dimensional active chromatin domain.

overall_design: Biological duplicated Hi-C experiments of Drosophila S2 cells after RNAi of gfp (control) or clamp.

first: William

last: Jordan


title: The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome

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

overall_design: Refer to individual Series


title: miR-611 overexpression effect on tongue cancer cells

city: Beijing

first: shuai

last: chen

state: Beijing

address: No. 22, Zhongguancun South Street, Haidian District,

department: Department of Oral Pathology

country: China

institute: Peking University School and Hospital of Stomatology

summary:
Analysis of SCC-15 tongue cancer cells overexpressing miR-611. miR-611 is frequently upregulated in primary tongue cancer. Results provide insight into the role of miR-611 in the pathogenesis of tongue cancer.
We used micorarrays to detailed the genes regulated by miR-611 in SCC-15 cells.

overall_design: We trasfected SCC-15 cells with miR-NC (control) or miR-611 mimics (30nM). 36 hours later,  RNA was extracted by Qiangen RNA Isolation Kit.

first: Shuai

first: Heyu

last: Zhang

first: Tiejun


title: Transpositional scaling and niche transitions restore organ size and shape during zebrafish fin regeneration

city: Eugene

first: Gabriel

last: Yette

state: Oregon

address: 1229 University of Oregon 1318 Franklin Blvd

department: Biology- Institute of Molecular Biology

institute: University of Oregon

summary: Regenerating zebrafish fins have distal progenitor and proximal re-differentiation zones. A Wnt-producing "niche" population maintains distal cells in progenitor states. We sought to define molecular markers of niche cells to study their origins and fates and how they contribute to fin size and shape restoration.

overall_design: We used RNA-Seq to compare gene expression between three replicates of microdissected distal vs. proximal regenerating fin tissue, as distinguished by distal shha:gfp expression. Each replicate consisted of pooled tissue from four caudal fins.

first: Scott

last: Stewart

middle: A

first: Astra

last: Henner

first: Heather

middle: K

last: Le Bleu

first: Joshua

last: Braunstein

first: Jad

last: Chehab

first: Michael

middle: J

last: Harms

first: Kryn

last: Stankunas


title: The vitamin B12 processing enzyme, mmachc, is essential for zebrafish survival, growth and retinal morphology

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: Cobalamin C deficiency (cblC), the most common inborn error of intracellular cobalamin metabolism, is caused by mutations in MMACHC, a gene responsible for the processing and intracellular trafficking of vitamin B12. This recessive disorder is characterized by a failure to metabolize cobalamin into adenosyl- and methylcobalamin, which results in the biochemical perturbations of methylmalonic acidemia, hyperhomocysteinemia, and hypomethioninemia caused by impaired activity of the downstream enzymes, methylmalonyl-CoA mutase and methionine synthase. Cobalamin C deficiency can be accompanied by a wide spectrum of clinical manifestations, including progressive blindness, and in mice, manifests with very early embryonic lethality. Because zebrafish harbor a full complement of cobalamin metabolic enzymes, we used genome editing to study loss of mmachc function. mmachc homozygotes survived the embryonic period but perished in early juvenile life. The mutants displayed metabolic and clinical features of cblC deficiency including methylmalonic acidemia, severe growth retardation, and lethality. Clinical and metabolic parameters improved when the mutants were raised in water supplemented with small molecules used to treat patients, including hydroxocobalamin, methylcobalamin, methionine, and betaine. Furthermore, mmachc mutants, some bred to express rod and or cone fluorescent reporters, manifested a retinopathy and thin optic nerves. Expression analysis using whole eye mRNA revealed dysregulation of genes involved in phototransduction and cholesterol metabolism. Zebrafish with mmachc deficiency recapitulate the phenotypic and biochemical features of the human disorder, including ocular pathology, and a show a response to established treatments

overall_design: mmachc heterozygous and mutant zebrafish whole eyes N=3 pools were studied by microarray at two timepoints 7 and 28 days post fertilization.

first: Jennifer

last: Sloan

first: Abdel

first: Charles

last: Venditti


title: The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome [4C-seq]

first: Erica

overall_design: Biological duplicated 4C-seq experiments of various CES in Drosophila S2 cells after RNAi against gfp (control), clamp, msl2, or trl

first: William


title: Gene expression profile in endometrial organoids cultured in normal follicular phase vs PCOS-like hormone profile

city: Chicago

first: Julie

last: Kim

state: IL

address: 303 E. Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

summary: We generated scaffold-free endometrial organoids from human primary endometrial tissues. These organoids were subjected to stepwise hormone treatments for 14 days mimicking the proliferative phase of menstrual cycle or with constantly high testosterone mimicking PCOS conditions

overall_design: Organoids from 4 patients were cultured in normal follicular phase and PCOS hormone profiles for 14 days and then subjected for RNAseq to determine genes differentially expressed in organoids cultured in PCOS condition.


title: Transcriptional effects of prostaglandins inhibition in the early canine Corpus Luteum

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

summary: The absence of luteolytic signal on non-pregnant bitches leads to the existence of a physiological pseudopregnancy maintained by a long lasting luteal function. During the diestrus, hormonal regulation of the canine CL changes. While in later stages prolactin is the main luteotropic hormone, in earlier stages the CL is independent from hypophysary hormones. At this time, prostaglandins are among the main luteotropic factors. In the present project, the aim was to further understand the effects of prostaglandins withdrawal on luteal function. In the present project, next generation sequencing (NGS), RNA-seq, was applied to explore the modulatory role of prostaglandins in the canine corpus luteum (CL) during the first half of diestrus. For this, transcriptome analysis of genes differently expressed in the CL of bitches treated in vivo with a COX2 inhibitor (Previcox, Merial) was performed. Additionally, by using just control samples, effects dependent on time were also explored and used as primary validation of results. Higher represented differentially expressed genes (DEG, p<0.01, FDR<0.1) in mature CL (days 20 and 30) referred to steroidogenesis, while in early CL (days 5 and 10) to proliferation and immune system. Then, treatment effects were investigated at each time point. No gene was concomitantly affected in all investigated groups. Thus, clearly, the effects were dioestrus stage-dependent. Higher numbers of DEG were found on day 20 (n=1741), mainly related to increased immune function, while on day 30 (n=552) they were related to decreased steroidogenesis and vascularization. Low numbers of DEG were found in early CL. Our results suggest the presence of strong compensatory effects in the early CL and multidirectional effects towards luteal gonadotropin-dependency after COX2-inhibition.

overall_design: Bitches of various breeds and ages were observed for the onset of spontaneous estrus by vaginal cytology and P4 assay. The day of ovulation (day 0) was considered when circulation P4 levels exceeded 5ng/ml. The animals were then randomly assigned to four treatment groups and five control groups. Animals from treated groups (TG) received, orally, 10mg/kg of firocoxib (Previcox, Merial Ltd) for 5 (n=4), 10 (n=3), 20 (n=3) and 30 (n=3) days. Animals from control groups (CG) remained untreated for 5 (n=4), 10 (n=3), 20 (n=3) and 30 (n=3) days. Ovariohysterectomy was performed on the last day of treatment for collection of CL. To evaluate treatment-induced effects, analysis of differentially expressed genes was performed by comparing treated with control groups at each time-point (Days 5, 10, 20 and 30). Time-dependent effects were analyzed by comparing differently expressed genes on days 20+30 with days 5+10.

first: Miguel

last: Tavares Pereira

first: Mariusz

middle: P

last: Kowalewski


title: RNA-seq on tomato infected with Xanthomonas euvesicatoria

city: Tuebingen

first: Dousheng

last: Wu

address: Auf der Morgenstelle 32

department: General Genetics

country: Germany

institute: Tuebingen University

summary: Transcription activator-like effectors (TALEs) from Xanthomonas activate host susceptibility genes to promote disease. We report here the tomato transcriptome changes after inoculation with Xanthomonas strains delivering Brg11*, a TALE-like effector from Ralstonia solanacearum or delivering the Brg11-derivative lacking the DNA binding domain as a control. After diffenential gene expression analysis we identified 117 genes were up-regulated and 8 genes were down-regulated by Brg11. This provides us a candidate gene list facilitating identification of Brg11 direct target genes in tomato.

overall_design: Tomato infected with two Xanthomonas strains, one strain expresses our effector of interest and the other strain expresses a non-functional mutant of the effector as a negative control

first: Thomas

last: Lahaye


title: Ranking of nanomaterial potency to induce pathway perturbations associated with lung (Day 28, Group 2)

city: Ottawa

first: Sabina

last: Halappanavar

state: Ontario

address: 251 Sir Frederick Banting Driveway, Building 22

country: Canada

institute: Health Canada

overall_design: This experiment examined the the lung transcriptomic responses to single intratracheal instillation of NRCWE-046, NRCWE-047, NRCWE-048 and NRCWE-049 (CNT). Four diferent doses were selected: 18 and 54 µg/animal. Samples were collected at   day 28 post-exposure

first: Luna

last: Rahman

first: Jake

last: Nikota

first: Sarah

middle: S

last: Poulsen

first: Yaobo

last: Ding

first: Petra

last: Jackson

first: Hakan

last: Wallin

first: Otmar

last: Schmid

first: Ulla

last: Vogel

first: Andrew

last: Williams


title: Ranking of nanomaterial potency to induce pathway perturbations associated with lung (Day 28, Group 1)

summary: This experiment examined the the lung transcriptomic responses to single intratracheal instillation of NRCWE-046, NRCWE-047, NRCWE-048 and NRCWE-049 (CNT).

overall_design: This experiment examined the the lung transcriptomic responses to single intratracheal instillation of NRCWE-043, NRCWE-044 and NRCWE-045 (CNT). Four diferent doses were selected: 18 and 54 µg/animal. Samples were collected at  day 28 post-exposure


title: Ranking of nanomaterial potency to induce pathway perturbations associated with lung


title: Ranking of nanomaterial potency to induce pathway perturbations associated with lung (Day 1, Group 2)

overall_design: Four diferent doses were selected: 18 and 54 µg/animal. Samples were collected at day 1 a post-exposure


title: Ranking of nanomaterial potency to induce pathway perturbations associated with lung (Day 1, Group 1)

summary: This experiment examined the the lung transcriptomic responses to single intratracheal instillation of NRCWE-043, NRCWE-044 and NRCWE-045 (CNT).

overall_design: Four diferent doses were selected: 18 and 54 µg/animal. Samples were collected at day 1  post-exposure

first: Halappanavar

last: Sabina


title: Development of gene expression signatures for liver cirrhosis

city: guangzhou

first: leijia

last: Li

address: Tianhe road

institute: The third affiliated hospital of sun yat-sen university

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

summary: We sought to identify sensitive and noninvasive biomarkers for development and progression of post HBV infection liver cirrhosis.

overall_design: To explore the different expression of lncRNAs in whole blood of healthy people, patients with hepatitis B infection and patients with post HBV infection liver cirrhosis.

first: Leijia

first: Bin


title: Netrin-1 signalling function in mouse pluripotent stem cells [RRBS]

status: Public on Dec 02 2019

city: Lyon

first: Fabrice

last: Lavial

address: 28 rue Laennec

country: France

institute: CRCL

type: Methylation profiling by high throughput sequencing

summary: We describe here the consequences of the activation of the netrin-1 signalling pathway in mouse embryonic stem cells (mESC).

overall_design: Comparison of DNA methylation profiles of WT mESC and mESC exogenously expressing netrin-1 by reduced representation bisulphite sequencing.


title: A non-catalytic function of carbonic anhydrase IX contributes to the glycolytic phenotype and pH regulation in human breast cancer cells

city: Louisville

first: Christopher

last: Frost

state: KY

address: 139 LSB

department: Biology

institute: University of Louisville

summary: We have hypothesized that carbonic anhydrases (CAs) play a role in stabilizing both intracellular and extracellular pH to a value that favors cancer progression and metastasis. This is likely in cooperation with the ion transport family.  Here, we examined the expression pattern of selected ion transporters, glucose transporters, and carbonic anhydrases in a triple negative cell model of human breast cancer (UFH-001) and the effect of hypoxia.  Heat map analysis of RNA transcripts from normoxic and hypoxic cells were significantly different.  Additionally, our results show that transcription of the MCT1 monocarboxylate transporter, but not that of MCT4, was sensitive to hypoxia.  Both MCT1 and MCT4 were robustly expressed at the protein level, but neither were significantly upregulated by hypoxia. Only low levels of the vATPase and NHE1 transcripts were detected, which is consistent with little to no detectable signal at the protein level. Our data also show high transcript levels of the GLUT1-glucose transporter, CAII and CAIX.  Only GLUT1 and CAIX transcription were significantly increased by exposure to hypoxia.  CAXII transcripts levels were very low, confirming the lack of expression at the protein level.  Yet, CAXII transcription was significantly increased by hypoxia.  Overall protein levels of our proteins of interest matched transcription patterns.  These studies show a coordinate expression at both the transcriptional and translational levels of the monocarboxylate transporters, the GLUT1 transporter and CAIX in the aggressive triple negative UFH-001 breast cancer cells.

overall_design: Examination of UFH-001 Triple Negative Breast Cancer cell line under normoxic and hypoxic conditions

first: Susan


title: Cyclic LSD1 recruitment and dynamic H3K4 methylation establish TRIM24-activated estrogen response

city: Irvine

first: Jiejun

last: Shi

state: CA

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The role of histone lysine methylation in estrogen receptor-alpha (ERα)-activated transcription is highly context-specific and poorly understood. Here, we show that lysine demethylase 1 (LSD1) mediates loss of H3 lysine 4 dimethylation (H3K4me2) in coordination with tripartite-motif-containing protein 24 (TRIM24)- regulated growth of breaset cancer-derived cells. We performed global profiling of histone H3K4me2 in comparison to genome-wide binding of TRIM24 in MCF7 cells when estrogen is depleted or added.  We found specific subsets of genes with functions in transcription and cell proliferation are depleted of H3K4me2 at TRIM24 binding sites.  Chromatin immunoprecipitation (ChIP) analyses over a time course of estrogen induction revealed cyclic demethylation of H3K4me2, LSD1, TRIM24 and ERα binding. Inhibition of LSD1 enzymatic activity led to increased H3K4me2 and decreased estrogen response of TRIM24-dependent genes. Additon of a small molecule inhibitor of the TRIM24 bromodomain or depletion of TRIM24 expression amplified the impact of LSD1 inhbition as measured by survival and proliferation of MCF7 cells, suggesting that combinatorial inhibition of LSD1 and TRIM24 may be effective in targeting ER-positive breast cancers.

overall_design: TRIM24 ChIP-seq with and without Estrogen (E2) in MCF7 human breast cancer-derived cell lines

first: Abhinav

last: Jain


title: Landscape of mouse mast cell chromatin: a rich resource for identification of novel mediators and genetic drivers of allergic and inflammatory diseases

city: Singapore

first: Jingxian

last: Zhang

state: Singpaore

address: 61 Biopolis Drive Proteos

department: IMCB

country: Singapore

institute: Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore


title: TIP60-dependent acetylation on H2AZ lysine 7 regulates the transcriptional program for genome stability [RNA-seq]

first: Roberto

last: Tirado-Magallanes

email: e0056363@nus.edu.sg, rtmag4@gmail.com

state: Singapore

address: 14 Medical Dr

institute: Cancer Science Institute of Singapore

summary: TIP60 mediated acetylation of H2AZ on gene promoter results in change in transcriptional landscape, and further regulates expression of genes involved in the maintenance of genome stability.

overall_design: Examination of global transcription profiles in TIP60-WT and TIP60-knockDown cells.

first: Yanzhou


title: TIP60-dependent acetylation on H2AZ lysine 7 regulates the transcriptional program for genome stability

overall_design: Refer to individual Series


title: Microbiome and Inflammatory Interactions in Obese and Severe Asthmatic Adults

city: Collegeville

first: David

last: Mayhew

state: PA

address: 1250 South Collegeville Road

department: Target Sciences, Computation Biology, R&D

institute: GlaxoSmithKline

summary: In order to better understand the systemic immunological responses in a clinical cohort of obese and non-obese asthmatics and healthy subjects, we sought to analyze gene expression from whole blood.  We collected whole blood samples from 156 donors and performed gene expression analysis of these samples and identified differentially expressed genes (DEGs) in each obese and/or asthma group relative to healthy volunteers.

overall_design: Total mRNA was extracted from peripheral blood using Qiagen RNeasy kit (Qiagen, Valencia, CA) and quantified by NanoDrop (Thermo Fisher Scientific, Waltham, MA). RNA integrity was confirmed using the Agilent 2100 BioAnalyzer (Agilent, Palo Alto, CA).  Samples were normalized to the lowest concentration sample, and cDNA was made using Superscript Vilo cDNA synthesis Master Mix (Invitrogen Life Technologies, Grand Island, NY). The cDNA samples were then labeled with biotin with the FL-Ovation cDNA Biotin Module V2 and hybridized to a Human Genome U133 Plus 2.0 Array using a Genechip Hybridization Kit. The microarray chips were washed and stained using a Genechip Hybridization Wash and Stain Kit and then scanned using a Genechip Scanner. All reagents and readers were used according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).  The microarray gene expression data were analyzed using ArrayStudio 7.0 (OmicSoft, Cary, NC). Data from .CEL files from Human Genome U133 Plus 2.0 Affymetrix chips were normalized using robust multiarray averaging and scaled to a mean target intensity of 150. Differentially expressed transcripts were identified by comparing each asthma and obesity group to the non-obese non-asthmatic group.

middle: N

last: Michalovich

first: Liam

last: O'Mahony


title: TIP60 represses activation of endogenous retroviral elements

summary: We found that the loss of TIP60 de-represses retrotransposon elements genome-wide, which in turn activate the cellular response to pathogens mediated by STING, culminating in an induction of Interferon Regulatory Factor 7 (IRF7) and associated inflammatory response.

overall_design: SRA accession: SRP128080 ; BioProject accession: PRJNA428558

first: Deepa

last: Rajagopalan

first: Sudhakar

last: Jha


title: TIP60-dependent acetylation on H2AZ lysine 7 regulates the transcriptional program for genome stability [ChIP-seq]

overall_design: Examination of acetylated H2AZ and H2AZ binding signal in TIP60-WT and TIP60-knockDown cells.


title: Analysis of transcriptional responses of Saccharomyces cerevisiae to mannitol and 4-deoxy-L-erythro-5-hexoseulose uronate (DEH).

city: Uji city

first: Fumiya

last: Matsuoka

state: Kyoto prefecture

address: Gokasyo

department: Agriculture

country: Japan

institute: Kyoto University

summary:
We constructed S. cerevisiae BY_DEH+ strain which is able to assimilate both 4-deoxy-L-erythro-5-hexoseulose uronate (DEH, a monouronic acid produced by digestion of alginate with exo-type alginate lyase) and mannitol from BY4742 strain and improved its ability to assimilate DEH through an adaptive evolution (Matsuoka et al. Sci. Rep. 2017, 7, 4206).
To examine transcriptional responses of the yeast to DEH and mannitol, gene expressions of the evolved strain (BY_DEH++ strain) in DEH medium, mannitol medium, and glucose medum were analyzed.
For revealing the mechanisms underlying the adaptive evolution, gene expressions of both BY_DEH+ strain and BY_DEH++ strain in both DEH medium and glucose medium were measured.

overall_design: Cap analysis of gene expression (CAGE) of BY_DEH+ strain cultured in DEH medium and glucose medium and BY_DEH++ strain cultured in DEH medium, mannitol medium, and glucose medium.

first: Takayuki

last: Kashihara

first: Shigeyuki

last: Kawai


title: miRNA expression in ovarian cancer stem cells

city: Columbus

first: Qi-En

last: Wang

state: OH

address: 420 W.12th Avenue

department: Radiation Oncology

institute: The Ohio State University

summary: Cancer stem cells (CSCs) are considered to play a central role in the cancer progression, metastasis and the development of drug resistance. MicroRNAs (miRNAs) have important roles in regulating CSC properties and are considered to be potential therapeutic targets. Diverse aberrantly expressed miRNAs have been reported in ovarian cancer cells. However, there have been few reports about miRNAs that were associated with stemness and progression of ovarian cancer. In this study, we enriched ovarian CSCs by using sphere culture of two ovarian cancer cell lines Kuramochi and SKOV3, and screened crucial miRNAs associated with characteristics and maintenance of CSCs by using miRNA nanoString nCounter assay.

overall_design: miRNA expression was determined in both adherent and sphere cultured ovarian cancer cell lines Kuramochi and SKOV3.

first: A

last: Srivastava

first: Q

middle: E


title: transcriptomic assay on embryos after barley seeds gamma_irradiation-Molecular mechanisms of growth stimulation after low-dose irradiation of barley seeds

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: 4plex_barley_2017_01 - transcriptomic assay on embryos after barley seeds gamma_irradiation - Why radiation exposure on seeds at low doses causes stimulation of plant growth after germination?  - Barley dry seeds of variety “Nur” were irradiated by gamma-rays (Co-60) at doses 20 Gy (stimulatory) and 100 Gy (inhibitory). Immediately after irradiation we put seeds for germination to Petri dishes containing water filter paper; embryos were taken 2h after irradiation, embryos with embrionic roots were taken 24 and 48h after irradiation. The following comparisons have been made: non-irradiated (0 Gy), 2h vs. 20 Gy, 2h; 0 Gy, 24h vs. 20 Gy, 24h; 0 Gy, 48h vs. 20 Gy, 48h; 0 Gy, 24h vs. 100 Gy, 24h. Three independent biological replicates were used.

overall_design: 12 dye-swap - dose response,treated vs untreated comparison

first: Polina

last: Volkova

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Epigenetic Inactivation of Cysteine Dioxygenase Type 1 Contributes to ROS-dependent Progression of Colorectal Cancer

city: Guangzhou

first: Huichuan

last: Yu

state: Guangdong

address: 26 Yuancun Erheng Road

institute: Sun Yat-sen University

summary: We performed a comprehensive investigation to understand the clinical and biologic significance of CDO1 methylation under various circumstances in CRC tissues and cell lines. The restoration of CDO1 function impaired ROS detoxification and changed the effect of ROS on cell viability. We performed RNA-seq which reveals the differential transcriptome profiles to interpret those changes following the restoration of CDO1 function.

overall_design: Examination of gene expression profiles between CDO1-overexpression KM12 and mock cells with three replicates each group.

first: Yanxin

last: Luo


title: Identifying the impact of intergenic variants from meta-GWAS of Rheumatoid Arthritis

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

summary: We performed an analysis of 489 GWAS variants that are associated with RA disease or are markers of RA drug efficacy. These variants were analyzed for: 1) their spatial interactions in three-dimensions, as captured by proximity ligation; 2) chromatin markers of regulatory functions (DNAse Hypersensitivity Sites, transcription factor binding site motifs, luciferase allele-specific SNP enhancer activity); and 3) their ability to affect linked gene expression (i.e. act as an eQTL). SNPs rs3184504, rs653178, and rs11545078 show evidence of differential long distance spatial associations in HL-60/S4 cells in undifferentiated versus differentiated cell states. RA associated variants at the SH2B3 locus (rs3184504/rs653178)) have a spatially-reinforced eQTL with BAZ2A, ~60Mb away, which affects platelet formation. Similarly, a variant at the GGH locus, which is associated with methotrexate toxicity, forms an inter-chromosomal spatially-reinforced eQTL with MGEA5, which is overexpressed in peripheral blood mononuclear cells.

overall_design: Hi-C library preparation was adapted from Lieberman-Aiden et al. 2009. Genome-wide Hi-C analysis and contact maps were generated for each of the three cell types. The analysis pipeline included three programs for sequence alignment and analysis. The raw sequence files were aligned using bowtie and analyzed using HiCup v0.5.826 to produce a filtered set of mapped chromosome interactions. Following alignment, HOMER was used to identify significant structural interactions in each of the three cell types for both 75- and 500-kb bin sizes (both intra- and inter-chromosomal interactions).

first: William

last: Schierding

first: Ralph

last: Grand

first: Cameron

last: Eckblad

first: Katlin

last: Toth

first: Wayne

last: Cutfield

first: Jörg

last: Langowski

first: Ada

last: Olins

first: Donald

last: O’Sullivan


title: Epigenetic profiling of human CD34+ derived mast cells [ChIP-Seq]

first: Jingxian

last: Zhang

summary: The chromatin landscape of human mast cells is extensively reorganized upon FcεRI crosslinking

overall_design: Human mast cells were generated from peripheral blood-derived CD34+ cells with recombinant hIL-3, hIL-6 and hSCF. Cells were left untreated or sensitized overnight with myeloma IgE (0.5 μg/ml) and treated with anti-IgE (1 μg/ml) for 2h. H3K4me3 and H3K27Ac CHIP-seq were performed.

first: Gokhan

last: Cildir


title: Transcriptomic profiling of human CD34+ derived mast cells [RNA-Seq]

summary: Transcriptome of human mast cells is extensively reorganized upon FcεRI crosslinking

overall_design: Human mast cells were generated from peripheral blood-derived CD34+ cells with recombinant hIL-3, hIL-6 and hSCF. Cells were left untreated or sensitized overnight with myeloma IgE (0.5 μg/ml) and treated with anti-IgE (1 μg/ml) for 2h.


title: FOXA1 in HER2+ endometrial cancer patients predicts good outcome

city: Oslo

first: Siv

last: Gilfillan

address: Gaustadaleen 21

department: Norwegian Center for Molecular Medicine

country: Norway

institute: University of Oslo

summary: ChIP-seq of endometrial cancer cell lines Ishikawa (Ish) and Hec1a (Hec) cells

overall_design: Cell lines x-linked and ChIP-seq with FOXA1 antibody

first: Mari

last: Halle

first: Ingvild

last: Tangen

first: Sachin

last: Sign

first: Madhumohan

middle: R

last: Katika

first: Helga

middle: B

last: Salvesen

first: Camilla

last: Krakstad

first: Antoni

last: Hurtado


title: Wnt-Induced Stabilization of KDM4C Is Required for Wnt/beta-Catenin Target Gene Expression and Tumorigenesis

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

summary: Wnt/beta-catenin signaling is essential for stem cell regulation and cancer formation by activation of target genes transcription. For transcriptional activation, the histone around promoters needs to be modified to remove transcriptional repressors; however, the underlying mechanisms remain largely unknown. Here, we report that Wnt signal erases TCF4-associated H3K9me2/me3 by recruitment of KDM4C through β-catenin to activate gene transcription. In the absence of Wnt3a, PKR phosphorylates KDM4C which induces its ubiquitination and degradation. Wnt3a stabilizes KDM4C through inhibition of GSK3-dependent PKR kinase activity. Stabilized KDM4C accumulates in nucleus. Through interaction with β-catenin, KDM4C binds to and demethylates TCF4-associate Histone H3K9 which leads to HP1 removal and transcription activation. KDM4C-dependent H3K9 demethylation is essential for Wnt-induced gene expression and tumorigenesis. Importantly, KDM4C levels directly correlate with Wnt signaling activation in human glioblastomas. These findings demonstrate a pivotal epigenetic regulation mechanism for Wnt/β-catenin signaling activation in tumorigenesis.

overall_design: KDM4C and TCF4 ChIP-seq with Wnt treatment

first: Yao-Hui

last: Chen


title: HCT116 (CRC): control siRNA vs. ZNF746 siRNA Transfected

city: Seoul

first: Hyemin

last: Lee

address: Kyunghee-dae-ro 26

country: South Korea

institute: Kyunghee Univ

summary:
Transcriptional profiling of HCT116 cells compared to untreated control with HCT116 cells transfected with ZNF746 siRNA plasmid. Goal was to determine the effects of ZNF746 gene transfection on CRC progression.
Two-condition experiment, HCT116 vs. ZNF746 siRNA.

overall_design: Sung-Hoon, Kim


title: An optimization system for isolating and sequencing of single human colon cancer cells

city: Hangzhou

first: Ling

last: Yang

address: 34th, Yanguan alley

institute: Hangzhou cancer institute

summary: Single cell sequencing (SCS) is a promising approach for precisely digging into the genetic heterogeneity at single cells level. Single cell whole genome/exome sequencing (scWGS/scWES) and single cell whole transcriptome sequencing (scRNA-seq) are methods of SCS and have been applied in various studies of solid tumors, e.g. liver cancer, breast cancer. However, no scRNA-seq-related studies of human colon-cancer tissue-samples have been conducted. In this study, we developed a modified and efficient colon-cancer-tissue SCSs system (named CCTSs-SCSs system) by combining four optimization technologies: tissue digestion, live and intact single-cells capture, single-cell RNA or genome amplification and sequencing, and bioinformatics analysis. This advanced system is applicable to both scRNA-seq and scWGS/scWES. Using this system, we successfully completed several single cells scRNA-seq and scWES, and found three key points of this system: an improved digestion system, FACS-based dead-cell-removal method for scRNA-seq, 20 cycles for scRNA amplification. Our CCTSs-SCSs system provides a reliable and efficient method of scRNA-seq or scWGS/scWES for human colon cancer tissue and contributes to single-cell level and precise studies for colon cancer.

overall_design: 5 cells for beads-based DCR kit, and 5 cells for FACS-based DCR kit

first: Xiaoyan


title: Cell subpopulations in cultures of rat's olfactory mucosa

city: Rouen cedex

first: Celine

last: Derambure

address: 22 Bvd Gambetta

institute: INSERM U905

summary: In order to improve our knowledge of olfactory ensheathing cells of the olfactory mucosa, we performed a wide microarray experiment to characterize the cell subpopulations found in primary olfactory mucosa cell cultures (CD90, P75 and TRKA cells). The consequences of the conditionning of TRKA cells by FBS deprivation and TGF-a supplementation was also studied.

overall_design: One-color experiment, 4 cells populations : CD90, p75, TRKA and TGF-a induced TRKA. Biological replicates: 4 .

first: Nicolas

last: Bon-Mardion

first: Céline


title: Comprehensive transcriptomes of mouse pancreatic beta cells that transdifferentiated from delta cells

city: Davis

first: Mark

middle: O.

last: Huising

address: One Shields Avenue

department: Neurobiology, Physiology and Behavior

institute: University of California, Davis

summary: Rodent models are widely used to study diabetes. Yet, significant gaps remain in our understanding of mouse islet physiology, including the maintenance of mature endocrine cell fate. We generated comprehensive transcriptomes beta cells that transdifferentiated from delta cells using a triple transgenic mouse models generated for this purpose.

overall_design:
FACS purified beta cells with a delta cell lineage label that reflect beta cells that transdifferentiated from alpha cells, along with delta cells and beta cells [GSE80673] from the same islets. Islets were isolated from triple transgenic offspring of a cross between mIns1-H2b-mCherry (Jax # 028589) and Sst-cre (alpha) cells and a floxed YFP allele to lineage-label delta cells. Islets from replicate groups of 10 to 12 triple transgenic animals for each group were pooled by sex to obtain sufficient material. Pooled islets were dissociated, sorted and collect in Trizol for RNA isolation and library construction.
Islets from replicate groups of 10 to 12 bitransgenic females for each group were pooled to obtain sufficient material. Pooled islets were dissociated, sorted and collect in Trizol for RNA isolation and library construction.

first: Talitha

last: van der Meulen

first: Alex

last: Mawla

middle: O


title: Genome-wide analysis of human endothelium response to Staphylococcus aureus blood isolates infection.

city: Münster

first: Dzmitry

last: Sinitski

address: Vesaliusweg 2-4

department: Anatomy and Vascular Biology

institute: University of Münster

summary: Analysis of strain-specific HUVEC gene expression as a response to infection by selected sepsis isolates of Staphylococcus aureus. Previous study showed great heterogeneity of endothelium pro-inflammatory response, cell death induction and translocation of bacteria through the endothelium barrier. The focus of this study was to investigate different endothelial gene expression patterns which might correspond to activation of different pathways determining various behaviour of the endothelium to the infection. Results give important information on strain-specific endothelium gene response to Staphylococcus aureus infection and give hints about important key players involved in strain-specific endothelium responses.

overall_design: Total RNA obtained from human umbilical cord endothelial cells infected with respective Staphylococcus aureus strain. Expression of infected endothelial cells were compared to mock infection control and tumor necrosis factor alpha treatment control.

first: Nadzeya

last: Kramko

first: Frank

last: Ruhle

first: Anika

last: Witten

first: Monika

last: Stoll

first: Hans

last: Schnittler


title: Landscape of human mast cell chromatin: a rich resource for identification of novel mediators and genetic drivers of allergic and inflammatory diseases

first: Jingxian

last: Zhang

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

overall_design: Refer to individual Series


title: Transcriptomic profiling of bone marrow derived mast cells (BMMCs) [RNA-seq]

summary: Allergy is one of the least understood immunological response partly due to the diversity of allergens and the complexity of immune response against them. In allergic responses, mast cells are key players with their ability to rapidly degranulate and also generate de novo lipids and transcripts. Although the molecular details of degranulation in mast cell were studied in allergic inflammation, the transcriptional response involving chromatin remodeling, enhancer dynamics and long non-coding RNA (lncRNA) expression are largely unexplored. Here, using mouse bone marrow derived mast cells (BMMCs), we characterized the steady state, immunoglobulin E (IgE) and antigen (Ag) mediated epigenetic changes in mast cell chromatin and described the enhancer, super-enhancer and mRNA, lncRNA catalogue in these cells.

overall_design: BMMCs are generated from mouse bone marrow cells with IL-3 and SCF. Cells were left untreated or sensitized overnight with DNP-IgE (0.5 ug/ml) and treated with DNP-BSA (50 ng/ml) for 2h. RNA was isolated and RNA-seq was performed

first: Gokhan

last: Cildir


title: Epigenetic profiling of mouse bone marrow derived mast cells (BMMCs) [ChIP-seq]

overall_design: BMMCs were generated from mouse bone marrow cells with IL-3 and SCF. Cells were left untreated or sensitized overnight with DNP-IgE (0.5 ug/ml) and treated with DNP-BSA (50 ng/ml) for 2h. H3K4me1, H3K4me3 and H3K27Ac CHIP-seq was performed.


title: Gene expression of Tetrahymena thermophila SB210 under the arsenic exposure

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

institute: Institute of hydrobiology, CAS

summary:
To identified the differential expressed genes between the  arsenic exposure cells and wild type cells
As is a well- known carcinogen, it receives special attention. Due to its ubiquitous distribution in the environment, a unicellular model system related to the environment will be useful in toxicological research of arsenic. The eukaryotic protist Tetrahymena thermophila is a well-established model in classical toxicology and now a potential model at genomic level. In the present study, Tetrahymena thermophila was inbred with arsenate. With the use of microarray technique, the genes differentially expressed at 4 time points in exposure to arsenate were screened out. The major biological processes involved and their changes over time were identified with enrichment analysis and transformed expression data. Characteristics of arsenic toxicity and response to arsenic were identified, proving T. thermophila a good unicellular model for arsenic toxicological research at genomic level.

overall_design: Total 4 arsenic exposure samples, and 4 wild type samples as controls


title: Milk- and soy-based diets have differential effects on colitis and colon gene expression in the Il10-/- mouse

city: Palmerston North

first: Anna

last: Moore

address: Tennent Drive

institute: AgResearch Ltd

summary:
Milk and soy are reported to contain bioactive molecules with antibacterial and immunomodulatory actions, which may be beneficial to people with IBD. The aim of this study was to determine whether diets containing ruminant milk or soy solids reduce intestinal inflammation in Il10-/- mice. Male Il10-/- mice and C57BL/6J mice were fed diets containing 40% (w/w) sheep, goat, or cow whole milk powder, 40% (w/w) soy solids (NOW® Foods Soy Milk Powder, Instant), or one of two control diets (casein-free modified-AIN76A or standard AIN76A) from 4 to 11 weeks of age. Diets were based on AIN76A, which was included as an inter-experimental control for inflammation. For all diets except AIN76A, total protein, fat, carbohydrate and energy were kept as similar as possible. Weight and food intake were measured throughout the experiment (three times weekly), and intestinal tissue was taken for histopathology evaluation of inflammation and analysis of gene expression.
Analysis of mouse weight and feed intake both showed a significant strain-diet interaction: Il10-/- mice fed the cow and goat milk diets ate less and gained less weight than all the other diet groups. This diet effect was not evident for the C57BL/6J mice. Il10-/- mice on the cow and goat milk diets had reduced colon histological injury scores relative to those on the other diets. Il10-/- mice on the cow and goat milk diets also had reduced expression of many immune/inflammatory-related genes and pathways.

overall_design: 6x2 factorial design. Two strains of mouse (Il10 knockout mouse and the background strain C57BL/6J) were sampled at 12 weeks of age after feeding of milk, soy and control diets for 6 weeks, and intact proximal colon and colon epithelium harvested from each mouse (6 mice per group).

last: Russ

first: Nicole

last: Roy

first: Gordon

middle: W

last: Reynolds

first: Rachel

last: Anderson

first: Matthew

last: Barnett

first: Warren

last: McNabb

first: Wayne

last: Young

first: Paul

last: MacLean

first: Zaneta

last: Park

first: Leigh

last: Ryan


title: Differentiation to extra-embryonic primitive endoderm from naïve human ESCs on mouse embryonic fibroblasts (MEFs) or laminin-511 (LN511) substrates

status: Public on Nov 30 2019

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: DanStem

country: Denmark

institute: Copenhagen University

summary: Embryonic stem cells (ESCs) can exist in at least two states that transcriptionally resemble different stages of embryonic development. Naïve ESCs resemble peri-implantation stages and primed ESCs the pre-gastrulation epiblast. In mouse, primed ESCs give rise to definitive endoderm in response to pathways downstream of Nodal and Wnt signalling. However, when these cytokines are applied to naïve ESCs, they differentiate to a cell type that approximates early primitive endoderm (PrE), the blastocyst stage progenitor layer that gives rise to the extra-embryonic endoderm. Here, we apply this context dependency to human ESCs, showing that these cytokines drive the differentiation of naïve pluripotent cells to generate extra-embryonic PrE, or hypoblast, and, as in mouse, expanded as an in vitro model for naïve extra-embryonic endoderm (nEnd) in defined conditions. Consistent with observations made in mouse, human PrE differentiation is dependent on FGF signalling in vitro, and we show, that by inhibiting FGF receptor signalling, we could simplify naïve pluripotent culture such that inhibitor requirements closer resembled those used in mouse. These nEnd cultures represent stable extra-embryonic endoderm, or human hypoblast, cell lines.

overall_design: Naïve embryonic stem cells were cultured in naïve medium for 5 days and extra-embryonic endoderm was differentiated in differentiation medium for 7 days, after which total RNA was isolated. Microarray was performed on total RNA labelled, hybridised and scanned using Agilent materials and instruments.

first: Joshua

first: Madeleine

last: Linneberg-Agerholm

first: Yan

middle: F

last: Wong


title: RNA sequencing of 112kb congenic and C57BL/6J (B6) wild-type littermates reveals differential splicing

city: Boston

first: Camron

middle: D

last: Bryant

state: MA

address: 72 East Concord St

department: Pharmacology

institute: Boston University School of Medicine

summary: The 112kb congenic was identified via routine monitoring of the proximal and distal SNP sites of the heterozygous Line 4a C57Bl/6J (B6J)-DBA/2J (D2J) congenic offspring (PMID: 26658939). The 112kb congenic was identified via routine monitoring of the proximal and distal SNP sites of the heterozygous Line 4a C57Bl/6J (B6)-DBA/2J (D2) congenic offspring (Yazdani et al. 2015). Like the Line4a congenic, the original mouse of interest possessed a D2J SNP site at the proximal end of the D2J interval (rs29383600; mm9 - chr11:50,186,508, mm10 - chr11:50,373,006). To identify the distal D2J boundary of this new congenic, we generated a list of known SNPs within a roughly 55kb interval spanning downstream from the distal end of the originally characterized 206kb “critical interval” harboring Hnrnph1 and Rufy1 (mm9 - chr11:50,295,887-50,352,284, mm10 - chr11:50,482,385-50,538,782). Starting from the upstream portion of the interval, PCR primers were designed to every five SNPs, and 200bp region around each SNP was amplified, run on a 1.5% agarose gel, visualized for band specificity. Single appropriately-sized bands were then excised and gel purified (Promega Wizard SV Gel and PCR Clean-Up System, Cat A9281), and prepared for sanger sequencing (Genewiz). Using the SNP data from the Mouse Genome Project (Sanger Institute) for reference, the sequenced SNPs were deemed as either heterozygous for B6J and D2J SNPs or homozygous/wildtype B6J. The final SNP we identified as D2 was rs29459915 (mm9 - chr11:50,297,762, mm10 - chr11:50,484,260), and the first SNP we identified as B6 was rs254771403 (mm9 - chr11:50,300,250, mm10 - chr11: 50,486,748).

overall_design: For this study, 3mm punches from both striatal hemispheres were collected and pooled from 16 mice (8 wild-type and 8 112kb congenics), and RNA was extracted and prepared for cDNA library preparation using the Illumina TruSeq (oligo-dT; 50bp single-end reads).

first: Neema

last: Yazdani

first: Eric

last: Reed

first: Qiu

last: Ruan


title: Uterine infection alters bovine endometrium, oviduct and granulosa transcriptome three months later

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: UNIVERSITY OF FLORIDA

summary: Here we tested the hypothesis that intrauterine infusion of pathogenic bacteria leads to changes in the transcriptome of the reproductive tract in dairy cattle three months later. We used virgin Holstein heifers to avoid the confounding effects of periparturient problems, metabolic stress and lactation. Animals were infused intrauterine with endometrial pathogenic bacteria Escherichia coli and Trueperella pyogenes to induce clinical endometritis (n = 4) and compared with control animals (n = 6). Three months after infusion, the caruncular and intercaruncular endometrium, isthmus and ampulla of the oviduct, and granulosa cells from dominant ovarian follicles were profiled by RNA-sequencing. Compared with control, bacterial infusion altered the transcriptome of all the tissues. Most differentially expressed genes were tissue-specific, with 109 differentially expressed genes unique to the caruncular endometrium, 57 in the intercaruncular endometrium, 65 in the isthmus, 298 in the ampulla, and 83 in granulosa cells. Surprisingly, despite infusing the bacteria into the uterus, the granulosa cells had more predicted upstream regulators of differentially expressed genes than all the other tissues combined. In conclusion, there was evidence of long-term changes to the transcriptome of the endometrium, oviduct and even the granulosa cells after intrauterine infusion of pathogenic bacteria, which implies that all these tissues contribute to the infertility that persists after endometritis.

overall_design: The present study aimed to explore whether uterine infection with bacteria that cause endometritis leads to long-term changes in the reproductive tract. Specifically, we tested the hypothesis that intrauterine infusion of pathogenic bacteria leads to changes in the transcriptome of the reproductive tract in dairy cattle three months later. To test this hypothesis, we exploited a model of clinical endometritis in virgin Holstein heifers, which allowed us to avoid the confounding effects of periparturient problems, metabolic stress and lactation (Piersanti et al. 2019b). We infused animals intrauterine with control vehicle or with E. coli and T. pyogenes to induce endometritis, and collected endometrium, oviduct and granulosa cells three months later. We then compared the transcriptomes of each of these tissues between bacteria-infused and control animals using RNA-sequencing (RNAseq) and pathway analysis.

first: A

last: Horlock

first: R

middle: L

last: Piersanti

first: F

middle: H

last: Yu

first: J

last: Block

last: Santos

last: Bromfield

first: I

last: Sheldon


title: Patient-derived scaffolds of colorectal cancer metastases as an organotypic 3D model of liver metastatic colonization

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

summary:
The liver is the most common site for colorectal cancer (CRC) metastasis and new tissue culture models are needed to study hepatic metastasis from CRC as none of the current models mimic the biological, biochemical and structural characteristics of the metastatic microenvironment. Decellularization provides a novel approach for the study of cancer extracellular matrix (ECM) as decellularized scaffolds retained their tissue-specific features and biological properties. In the present study we created a 3D model of CRC and matched CRC liver metastasis (CRLM) using patient-derived decellularized ECM scaffolds seeded with HT-29 CRC cell line. Here we show increased HT-29 cell proliferation and migration capability when cultured in cancer-derived scaffolds compared to same-patient healthy colon and liver tissues. CRLM scaffolds also induced activation of epithelial-mesenchymal transition (EMT) with cancer cells showing loss of E-cadherin expression and increased Vimentin expression. EMT was confirmed by gene expression profiling, with the most represented biological processes in CRLM-seeded scaffolds involving demethylation, deacethylation, cellular response to stress metabolic processes, response to oxygen level and to starvation. The complex 3D culture environment reduced the HT-29 cell response to anti-CRC drug 5-FU when used at standard IC50 determined in 2D cultures. In conclusion, our 3D culture system with patient-derived tissue-specific decellularized ECM better recapitulates the metastatic microenvironment compared to conventional 2D culture conditions and represents a relevant approach for the study of liver CRC metastasis formation and progression.
Transcriptomic analysis was performed comparing the global gene expression profiles of HT29 cells grown on CRLM and HL scaffolds. The transcriptomic profile of each 3D subtype was compared with HT29 cells grown in plastic. Hierarchical clustering analysis revealed that the gene expression signature of recellularized CRLM scaffolds was more comparable to recellularized HL scaffolds, than to HT29 cells grown in 2D. Gene set enrichment analysis (GSEA) of the differently expressed genes (DEG) up-regulated in recellularized CRLM scaffolds compared to HT29 grown in 2D revealed that genes involved in demethylation, deacethylation and metabolic process belong to the most enriched biological pathways in repopulated-CRLM scaffolds. Comparing the DEG between recellularized CRLM scaffolds vs HT29 grown in 2D with a series of a-priori defined gene-set, called Hallmark, we obtained concordant results with the “HYPOXIA” and “EPITHELIAL_MESENCHYMAL_TRANSITION” pathway, enriched in recellularized CRLM, supporting the idea that 3D culture models are the ability to re-create a complex environment in terms of oxygen tension, nutrients, and metabolic gradient, similarly to the in vivo environment.

overall_design: Gene expression was measured on Affymetrix ClariomS in 4 CRLM recellularized, HL-recellularized and HT29 adenocarcinoma cells  grown in plastic

first: Silvia

last: Bresolin

first: Marco

last: Agostini


title: Candidate genes mediated by estrogen-related receptor gamma (ERRγ) in pancreatic β cells

city: beijing

first: zhou

last: lei

address: No. 5, Summer Palace Road

institute: peking university

summary: Recent studies have established the importance of ERRγ as a required participant for insulin secretion in pancreatic β cells. Key downstream genes of ERRγ remain unclear in the pancreatic β cell. To understand the molecular role of ERRγ and elucidate potential key candidate genes involved in pancreatic β cells, the eukaryotic expression plasmid containing mouse ERRγ was constructed and transfected into NIT-1 pancreatic β cells. Overexpression of ERRγ was confirmed by Q-RT-PCR and western blot. RNA-seq was conducted to get the gene expression profiling between the experimental cells and control cells. Differentially expressed genes (DEGs) were identified and subsequently analyzed by gene ontology (GO) enrichment analysis and kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis. We found that overexpression of ERRγ in pancreatic β cells enables regulation of the expression of certain genes involved in cell apoptosis and mitochondrial function, such as TFPT, Bcl7c, Dap, Thoc6, Ube2d3, ATP5H, MPV17, and NDUFA6. GO analysis revealed that the DEGs were mainly enriched in biological regulation, cell, and binding. KEGG pathway analysis demonstrated that DEGs were significantly enriched in infectious diseases, translation annd signal transduction. This study helps to further understand and reposition the molecular mechanisms of ERRγ in pancreatic β cells.

overall_design: Examination the molecular role of ERRγ and elucidate potential key candidate genes involved in pancreatic β cells,

first: li

middle: p

last: feng


title: RNA-seq transcriptome analysis in NCI-H209 and NCI-H441 cells transfected with TTF-1/NKX2-1 or ASCL1 siRNAs.

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo

summary: Although Thyroid transcription factor-1 (TTF-1, encoded by NKX2-1 gene) is highly expressed in small cell lung carcinoma (SCLC) and lung adenocarcinoma (LADC), difference in the functional roles of TTF-1 between SCLC and LADC remains to be elucidated. The aim of this study was to clarify the differences in the TTF-1 binding regions and functional roles in SCLC and LADC. Employing chromatin immunoprecipitation-sequencing (ChIP-seq) , here we compared the genome-wide TTF-1-binding profiles and the TTF-1-mediated transcriptional programs in a SCLC and a LADC cell lines. We also investigated ASCL1 binding regions in SCLC cells. To validate whether the changes in TTF-1 or ASCL1 binding to the genome indeed resulted in changes in target gene expression, we performed RNA-seq transcriptome analyses in H209 cells with TTF-1 or ASCL1 knockdown. Data were also obtained from H441 cells transfected with TTF-1 siRNAs.

overall_design: RNA-seq transcriptome analyses performed in a small cell lung carcinoma NCI-H209 cells with TTF-1 or ASCL1 knockdown. RNA-seq data were also obtained from a lung adenocarcinoma NCI-H441 cells transfected with TTF-1 siRNAs.

first: Satoshi

last: Hokari

first: Yusuke

last: Tamura

first: Masato

last: Morikawa

first: Kohei

last: Miyazono


title: Long range inter-chromosomal interaction of Oct4 distal enhancer loci regulates ESCs pluripotency [DNA-seq]

city: Los Angeles

first: Byoung San

last: Moon

state: California

address: 1425 San Pablo St. 409B

institute: University of Southern California

summary: Nuclear architecture underlies the transcriptional programs within the cell to establish cell identity. As previously demonstrated, long-range chromatin interactions of the Oct4 distal enhancer (DE) are correlated with active transcription in naïve state embryonic stem cells. Here, we identify and characterize extreme long range interactions of the Oct4 DE through a novel CRISPR labeling technique we developed and chromosome conformation capture to identify lethal giant larvae 2 (Llgl2) and growth factor receptor-bound protein 7 (Grb7) as putative functional interacting target genes in different chromosomes. We show that the Oct4 DE directly regulates expression of Llgl2 and Grb7 in addition to Oct4. Expression of Llgl2 and Grb7 closely correlates with the pluripotent state, where knock down of either result in loss of pluripotency, and overexpression enhances somatic cell reprogramming. We demonstrated that biologically important interactions of the Oct4 DE can occur at extreme distances that are necessary for the maintenance of the pluripotent state.

overall_design: We constructed a targetable live cell labeling system combining the principles of CRISPR-Cas9 and DamID to track long range chromatin interactions at the Oct4 DE

first: David

last: Huang

first: Byoung-San

first: Fan

last: Gao

first: Wange

last: Lu


title: Identification of the genes regulated by the two-component system response regulator NarP of Actinobacillus pleuropneumoniae by DNA-affinity-purified (DAP) sequencing

city: Wuhan

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

institute: Huazhong Agricultural University

summary: Identification of the direct target genes of a response regulators (RRs) of a bacterial two-component system (TCS) is critical to understand the roles of the TCS in bacterial environmental adaption and pathogenesis. A. pleuropneumoniae is an important respiratory bacterial pathogen causing great economic losses to swine industry worldwide. The triggering signal(s) and targets of the RR NarP belonging to the TCS NarQ/NarP of A. pleuropneumoniae are still unknown. In the present study, a DNA-affinity-purified sequencing (DAP-Seq) approach was established. The upstream regions of a total of 131 candidate genes from the genome of A. pleuropneumoniae were shown to be co-purified with the activated NarP protein. Electrophoretic mobility shift assay results confirmed the interactions of NarP with the promoter regions of five selected target genes, including dmsA, pgaA, ftpA, cstA and ushA. Then, the EMSA-confirmed target genes were shown to be significantly up-regulated in the narP deleted mutant in the presence of additional nitrate, while the transcriptional changes were restored in the complemented strain. The NarP binding motif in the upstream regions of the target gene dmsA and ftpA were further identified and confirmed by EMSA using the truncated binding motif. The NarP binding sites were present in a total of 25.2% of the DNA fragments captured by DAP-Seq. These results demonstrated that the DAP-Seq method established in this study was effective to explore the direct targets of RRs of bacterial TCSs, and indicated that the A. pleuropneumoniae NarP could be a repressor in response to nitrate.

overall_design: The potential NarP binding sites were acquired by DNA-affinity-purified sequencing (DAP-Seq). The genomic DNA were extracted and fragmented, the paired-end adapters were added on both ends. The adapter-containing DNA fragments were then subject to DNA affinity purification by incubation with the purified activated protein NarP with His tag and applied to Ni-NTA resin. The resin was washed and the protein was eluted. The DNA bound to NarP was purified and sequenced. A incubation using DNA fragments without any protein was used as a control. Afterwards, the peaks generated by the sequenced data analysis were used to predict binding sites of NarP and be further validated.

first: Rui

last: Zhou

first: Qiuhong

last: Zhang

first: Qi


title: The vegetative transcriptome of Arabidopsis thaliana

city: Ithaca

first: Matthew

last: Willmann

state: NY

address: B18 Weill Hall, 237 Tower Road

department: School of Integrative Plant Science

institute: Cornell University

summary: Plants grow continuously and undergo numerous changes in their vegetative morphology and physiology during their life span.  The molecular basis of these changes is largely unknown.  To provide a more comprehensive picture of shoot development in Arabidopsis, microarray analysis was used to profile the mRNA content of shoot apices of different ages, as well as leaf primordia and fully-expanded leaves from 6 different positions on the shoot, in early-flowering and late-flowering genotypes.  This extensive dataset provides a new and unexpectedly complex picture of shoot development in Arabidopsis.  At any given time, the pattern of gene expression is different in every leaf on the shoot, and reflects the activity at least 6 developmental programs.  Three of these are specific to individual leaves (leaf maturation, leaf aging, leaf senescence), two occur at the level of the shoot apex (vegetative phase change, floral induction), and one involves the entire shoot (shoot aging).  Our results demonstrate that vegetative development is a much more dynamic process that previously imagined, and provide new insights into the underlying mechanism of this process.

overall_design: Samples were collected from FRI;FLC and FRI;flc-3 of four growth time points—shoot apices with all primordia under 1 mm (120 apices for days 4 and 6, 60 for day 9, and 30 for days 11 and 14, and 24 for day 21), 1 mm leaf primordia (30 primordia per replicate, 60 for leaves 1/2), fully expanded leaves (9 leaves per replicate, 18 for leaves 1/2), and leaves past full expansion (leaves 3, 5, and 7 collected at the same point as fully-expanded leaf 9).  Six-day-old shoot apices were also harvested for FRI;FLC;35S::miR156mimic.  To determine the point of full expansion, leaves from 8 representative plants of each genotype were measured daily until the average daily increase in total leaf length was less than 1 mm on each of two consecutive days, with the second day called the point of full expansion.  Two microarray experiments were done with fully-expanded leaves of FRI;flc-3 and FRI;FLC, the first set (called experiment 1, throughout) collected from the same plants as the leaf primordia and the second (experiment 2) at the same time as the shoot apices, leaves past full expansion, and FRI;FLC;35S::mir156mimic.  Equal collections were made at three different times in the day—4-5 hours, 8-9 hours, and 11.5-12.5 hours after the subjective dawn—and pooled to minimize the effects of circadian rhythms on the data.  Three replicates were used for all conditions except there were only two shoot apex day 6 replicates for FRI;FLC and one for FRI;flc-3.

first: R

last: Poethig


title: TTF-1/NKX2-1 and ASCL1 binding regions in a small cell lung carcinoma cell line, NCI-H209

summary: Although Thyroid transcription factor-1 (TTF-1, encoded by NKX2-1 gene) is highly expressed in small cell lung carcinoma (SCLC) and lung adenocarcinoma (LADC), difference in the functional roles of TTF-1 between SCLC and LADC remains to be elucidated. The aim of this study was to clarify the differences in the TTF-1 binding regions and functional roles in SCLC and LADC. Employing chromatin immunoprecipitation-sequencing (ChIP-seq) , here we compared the genome-wide TTF-1-binding profiles and the TTF-1-mediated transcriptional programs in a SCLC and a LADC cell lines. We also investigated ASCL1 binding regions in SCLC cells.

overall_design: TTF-1 and ASCL1 ChIP-seq analysis was performed in a small cell lung carcinoma cell line, NCI-H209.


title: Receptor-specific interactome as a hub for rapid cue-induced selective translation in axons

status: Public on Nov 29 2019

city: Cambridge

first: Christine

last: Holt

address: Anatomy Bldg., Downing St.

department: Department of PDN

country: United Kingdom

institute: University of Cambridge

summary: During neuronal wiring, extrinsic cues trigger the local translation of specific mRNAs in axons via cell surface receptors. The coupling of ribosomes to receptors has been proposed as a mechanism linking signals to local translation but it is not known how broadly this mechanism operates, nor whether it can selectively regulate mRNA translation. We report that receptor-ribosome coupling is employed by multiple guidance cue receptors and this interaction is mRNA-dependent. We find that different receptors bind to distinct sets of mRNAs and RNA-binding proteins. Cue stimulation induces rapid dissociation of ribosomes from receptors and the selective translation of receptor-specific mRNAs in retinal axon growth cones. Further, we show that receptor-ribosome dissociation and cue-induced selective translation are inhibited by simultaneous exposure to translation-repressive cues, suggesting a novel mode of signal integration. Our findings reveal receptor-specific interactomes and provide a general model for the rapid, localized and selective control of cue-induced translation.

overall_design: The profiling of mRNAs binding with DCC or Nrp1 in SH-SY5Y cells

first: Max

last: Koppers

first: Roberta

last: Cagnetta

first: Toshiaki

last: Shigeoka

first: Lucia

middle: C

last: Wunderlich

first: Sixian

last: Zhao

first: Michael

last: Minett

first: Anai?s

last: Bellon

first: Clemens

last: Kaminski

first: John

middle: G

last: Flanagan


title: An integrated transcriptome analysis of immunological responses in pearl sac of pearl mussel Hyriopsis cumingii after mantle implantation

city: Shanghai

first: weiwei

last: Qi

address: No 99 Shangda Road

institute: Shanghai  University

summary: Our findings help us gain new insight into the immunological reactions induced by transplantation in pearl mussels and markedly bring us more clues about pearl sac formation, contributing to the novel development of management strategies for pearl culture.

overall_design: Ten samples at 0h,2 h, 6 h, 12 h, 24 h, 48 h, 96 h, 7 D, 14 D and 30 D during pearl sac formation after implantation

first: Dandan

last: Huang

first: Zhiyi

last: Bai

first: Jiexuan

last: Shen

first: Jia-Le


title: Effects of CRISPR/Cas9-mediated deletion of Safb1 and Safb2 genes on the mature miRNA transcriptome

status: Public on Nov 28 2019

city: Innsbruck

first: Sebastian

last: Herzog

address: Innrain 80-82

department: Institute of Developmental Immunology

country: Austria

institute: Medical University of Innsbruck, Biocenter

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are 20-25 nucleotides (nt) RNAs that are predicted to post-transcriptionally silence expression of >60% of all protein coding genes in mammals. As such, they form an additional layer of gene regulation that controls most if not all biological processes. MiRNAs are generated from primary transcripts containing single or multiple clustered stem-loop structures that are thought to be recognized and cleaved by the DGCR8/DROSHA Microprocessor complex as independent entities. Contrasting this view, we find that the primary miR-15a stem-loop within the bicistronic miR-15a-16-1 cluster is a poor Microprocessor substrate and is consequently not processed on its own, but that the presence of the neighboring primary miR-16-1 stem-loop on the same transcript can compensate for this deficiency in cis. Using a CRISPR/Cas9 screen, we identify SAFB2 (scaffold attachment factor B2) as an essential co-factor in this miR-16-1-assisted primary miR-15 cleavage. Small RNA sequencing further revealed that deletion of Safb1 and 2 genes reduces not only miR-15a levels, but also affects other clustered miRNAs, among them miR-15b, miR-181b and miR-92a. We therefore postulate a model in which SAFB2 enables processing of suboptimal substrates in a subset of clustered pri-miRNA transcripts.

overall_design: Comparison of control CRISPR/Cas9 cells and Safb1/Safb2 CRISPR/Cas9 cells (independent knockout clones per group; 2 different cell lines)


title: Transcriptomic profile of T cell acute lymphoblastic leukemia (T-ALL) cell from patients in CHCQMU

city: Chongqing

first: Yi

last: Shu

address: 136 2nd Zhongshan Rd

institute: Children's Hospital, Chongqing Medical University

summary: The T cell acute lymphoblastic leukemia cells and normal T cells were collected from the patients in CHCQMU.  Then the RNA-seq were conducted to compare the transcriptomic different between those two types of cells.

overall_design: mRNA profiles of T cell acute lymphoblastic leukemia cells (T-ALL) and normal T cells were generated by deep sequencing using Illumina HiSeq X Ten.

first: Lin

last: Zou


title: Single-cell profiles of retinal neurons differing in resilience to injury reveal neuroprotective genes - Adult control RGCs treated with Actinomycin

status: Public on Nov 27 2019

first: Wenjun

last: Yan

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

summary: Neuronal types in the central nervous system differ dramatically in their resilience to injury or insults. Here we studied selective resilience in mouse retinal ganglion cells (RGCs) following optic nerve crush (ONC), which severs their axons and leads to death of ~80% of RGCs in 2 weeks. To identify expression programs associated with differential resilience, we first used single-cell RNA-seq (scRNA-seq) to generate a comprehensive molecular atlas of 45 RGC types in adult retina. We tracked their survival after ONC, characterized transcriptomic, morphological, and physiological changes that preceded degeneration, and identified genes selectively expressed by each type. Finally, loss- and gain-of-function assays in vivo showed that manipulating some of these genes improved neuronal survival and axon regeneration following ONC. This study provides a systematic framework for parsing type-specific responses to injury, and demonstrates that these responses can be used to reveal molecular targets for intervention.

overall_design: In these experiments, we FACS sorted for retinal ganglion cells using a combination of a transgenic reporter (VGLUT2) and a surface protein (CD90) from dissociated retinas of adult (6-8 wk old) mice.

first: Irene

last: Whitney

first: Inbal

last: Benhar

first: Nicholas

last: Tran

first: Karthik

last: Shekhar

first: Anne

last: Jacobi

first: Zhigang

last: He

first: Aviv

last: Regev

first: Joshua

last: Sanes


title: Single-cell profiles of retinal neurons differing in resilience to injury reveal neuroprotective genes - Atlas of adult mouse retinal ganglion cells [Smart-seq2]

overall_design: In this experiment, we FAC sorted for GFP expressing cells in the W3-GFP mouse line that were also positive for the  retinal ganglion cell surface protein CD90 from dissociated cells from retinas of postnatal day 15 mice


title: SOX9+/PTF1A+ Cells Define the Tip Progenitor Cells of the Human Fetal Pancreas of the Second Trimester

city: Duarte

first: Teresa

last: Ku

address: 1500 E Duarte Rd

department: Translational Research and Cellular Therapeutics

institute: City of Hope - Beckman Research Institute

summary: Significant progress has been made in recent years in characterizing human multipotent progenitor cells (hMPCs) of the early pancreas; however, the identity and persistence of these cells during the second trimester, after the initiation of branching morphogenesis, remain elusive. Additionally, studies on hMPCs have been hindered by few isolation methods that allow for the recovery of live cells. Here, we investigated the tip progenitor domain in the branched epithelium of human fetal pancreas between 13.5 and 17.5 gestational weeks by immunohistological staining. We also used a novel RNA‐based technology to isolate live cells followed by gene expression analyses. We identified cells co‐expressing SOX9 and PTF1A, two transcription factors known to be important for pancreatic MPCs, within the tips of the epithelium and observed a decrease in their proportions over time. Pancreatic SOX9+/PTF1A+ cells were enriched for MPC markers, including MYC and GATA6. These cells were proliferative and appeared active in branching morphogenesis and matrix remodeling, as evidenced by gene set enrichment analysis. We identified a hub of genes pertaining to the expanding tip progenitor niche, such as FOXF1, GLI3, TBX3, FGFR1, TGFBR2, ITGAV, ITGA2, and ITGB3. YAP1 of the Hippo pathway emerged as a highly enriched component within the SOX9+/PTF1A+ cells. Single‐cell RNA‐sequencing further corroborated the findings by identifying a cluster of SOX9+/PTF1A+ cells with multipotent characteristics. Based on these results, we propose that the SOX9+/PTF1A+ cells in the human pancreas are uncommitted MPC‐like cells that reside at the tips of the expanding pancreatic epithelium, directing self‐renewal and inducing pancreatic organogenesis.

overall_design: Total RNAs were extracted individual cells obtained following dissociation of freshly obtained human fetal pancreas tissue.

first: Valentina

last: Villani

first: Matthew

last: Thornton

first: Heather

last: Zook

first: Christiana

middle: J

last: Crook

first: Brendan

last: Grubbs

first: Giuseppe

last: Orlando

first: Roger

last: De Filippo

first: Hsun

middle: T

first: Laura

last: Perin


title: MeCP2 represses the rate of transcriptional initiation of highly methylated long genes (ChIP-Seq II)

status: Public on Nov 26 2019

first: Lisa

middle: D.

last: Boxer

address: 220 Longwood Ave., Goldenson Bldg Rm 405

department: Neurobiology

institute: Harvard Medical School

summary: Mutations in the methyl-DNA-binding repressor protein MeCP2 cause the devastating neurodevelopmental disorder Rett syndrome. It has been challenging to understand how MeCP2 regulates transcription because MeCP2 binds broadly across the genome, and MeCP2 mutations are associated with widespread small-magnitude changes in neuronal gene expression. We demonstrate here that MeCP2 represses nascent RNA transcription of highly methylated long genes in the brain through its interaction with the NCoR co-repressor complex. By measuring the rates of transcriptional initiation and elongation directly in the brain, we find that MeCP2 has no measurable effect on transcriptional elongation, but instead represses the rate at which Pol II initiates transcription of highly methylated long genes. These findings suggest a new model of MeCP2 function in which MeCP2 binds broadly across highly methylated regions of DNA, but acts at transcription start sites to attenuate transcriptional initiation.

overall_design: ChIP-seq was performed from WT and MeCP2 KO forebrain for H3K36me3 (n=10), H3K27ac (n=10), MeCP2 Ab1 (n=2), MeCP2 Ab2 (n=2), and pre-immune serum for MeCP2 Ab1 (n=2) with input controls. ChIP-seq was performed from WT and MeCP2 R306C forebrain for H3K9ac (n=5), H3K27ac (n=2), H4K12ac (n=3), and MeCP2 (n=4) with input controls. ChIP-seq was peformed from WT cortical neurons for YY1, and from WT forebrain for H3K79me2 (n=2) with input controls.

first: William

last: Renthal

first: Marty

last: Yang

first: Michael

middle: E

last: Greenberg


title: The Integrator complex terminates promoter-proximal transcription at protein-coding genes

first: Karen

last: Adelman

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

summary: The transition of RNA polymerase II (Pol II) from initiation to productive elongation is a central, regulated step in metazoan gene expression. At many genes, Pol II pauses stably in early elongation, remaining engaged with the 25-60 nucleotide-long nascent RNA for many minutes while awaiting signals for release into the gene body. However, a number of genes display highly unstable promoter Pol II, suggesting that paused polymerase terminates transcription at these promoters and releases a short, non-functional RNA. Here, we investigate the mechanisms driving Pol II instability and discover that the Integrator complex targets paused Pol II and terminates transcription at selected genes. Specifically, Integrator utilizes its RNA endonuclease activity to cleave nascent RNA and destabilize elongating polymerase. Our findings uncover a previously unappreciated mechanism of metazoan gene repression, wherein promoter paused Pol II is prevented from entering productive elongation through regulated termination.

overall_design:
RNAseq experiments: 3 biological replicates were generated for Control (B-galactosidade treated) or IntS9-depletion (treated with double stranded RNA for IntS9) in DL1 cells. RNAi treatments were carried for 60h.
3 biological replicates were generated for Control (B-galactosidade treated) in Flag-tagged eGFP control line transgenes or IntS11-depletion (treated with double stranded RNA for IntS11) in Flag-tagged IntS11WT, E203Q mutant, and the eGFP control DL1 cell line transgenes. RNAi treatments were carried for 60h along with a final concentration of 100 μM CuSO4 to induce transgene expression.
PRO-seq: 3 biological replicates were generated using DL1 cells treated with Bgal or IntS9 dsRNA for 60h.
ChIP-seq: 3 biological replicates using untreated DL1 cells were generated for Input, IntS1 and IntS12 ChIP-seq datasets.
ATAC-seq: 3 biological replicates using untreated S2 cells were generated.

first: Nathan

last: Elrod

first: Telmo

last: Henriques

first: Kai-Lieh

last: Huang

first: Deirdre

last: Tatomer

first: Jeremy

last: Wilusz

first: Eric

last: Wagner


title: MeCP2 represses the rate of transcriptional initiation of highly methylated long genes (RNA-Seq II)

overall_design: Total RNA-seq was performed on whole-cell, nuclear, and chromatin-associated RNA from forebrain tissue from 10 8-week-old MeCP2 KO and 10 WT mice and 10 8-12 week-old MeCP2 R306C and 10 WT mice. Total RNA-seq was performed on whole-cell RNA from forebrain tissue from 10 1-week-old MeCP2 R306C and 10 WT mice. Total RNA-seq was performed on visual cortex tissue from 6 8-12 week-old Dnmt3a cKO and 6 WT mice.

first: Benyam

last: Kinde


title: Comparative Analysis of TTF-1 Binding DNA Regions in Small Cell Lung Cancer and Non-Small Cell Lung Cancer

first: Daizo

last: Koinuma

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

overall_design: Refer to individual Series


title: MeCP2 represses the rate of transcriptional initiation of highly methylated long genes (HiC)

overall_design: Hi-C was performed from forebrain tissue from 3 WT and 3 MeCP2 KO mice.

first: Boyan

last: Bonev


title: RASSF2 knockdown in THP-1 AML cells

city: La Jolla

first: Sam

last: Stoner

address: 3855 Health Sciences Dr 0815

institute: University of California, San Diego

summary: Large-scale chromosomal translocations are frequent oncogenic drivers in acute myeloid leukemia (AML). These translocations often occur in critical transcriptional/epigenetic regulators and contribute to malignant cell growth through alteration of normal gene expression. Despite this knowledge, the specific gene expression alterations that contribute to the development of leukemia remain incompletely understood. Here, through characterization of transcriptional regulation by the RUNX1-ETO fusion protein, we have identified Ras-association domain family member 2 (RASSF2) as a critical gene that is aberrantly transcriptionally repressed in t(8;21)-associated AML. Based on this, we performed molecular and functional characterization of RASSF2 in AML cells.

overall_design: RNA-seq in THP-1 AML cells transduced with two independent RASSF2-targeting shRNAs or control shRNA

first: Samuel

middle: A

first: Dong-er

last: Zhang


title: Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle

city: Lausanne

first: David

middle: Michael

last: Suter

address: EPFL SV-IN Station 19

department: Institute of Bioengineering

institute: École polytechnique fédérale de Lausanne


title: Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle [MD-OCT4 ChIP-seq]

summary: The pioneer activity of transcription factors allows for opening of inaccessible regulatory elements and has been extensively studied in the context of cellular differentiation and reprogramming. In contrast, the function of pioneer activity in self-renewing cell divisions and across the cell cycle is poorly understood. Here we assessed the interplay between OCT4 and SOX2 in controlling chromatin accessibility of mouse embryonic stem cells. We found that OCT4 and SOX2 operate in a largely independent manner even at co-occupied sites, and that their cooperative binding is mostly mediated indirectly through regulation of chromatin accessibility. Controlled protein degradation strategies revealed that the uninterrupted presence of OCT4 is required for post-mitotic re-establishment and interphase maintenance of chromatin accessibility, and that highly OCT4-bound enhancers are particularly vulnerable to transient loss of OCT4 expression. Our study sheds light on the constant pioneer activity required to maintain the dynamic pluripotency regulatory landscape in an accessible state.

overall_design: ZHBTc4 cells expressing Ypet-MD and SNAP-MD-OCT4 or SNAP-MD*-OCT4 were treated with doxycycline for 40 hours, stained with Hoechst, fixed, sorted for different cell cycle phases, and subjected to ChIP-seq

first: Elias

last: Friman


title: RNAseq analysis of developing chick somites

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

institute: University of East Anglia

summary: Illumina sequencing was used to characterize the transcriptome of somites dissected from chick embryos HH stage 14-16. Somites were treated as follows: uninjected, injected with antagomiR-206 or with scrambled antagomiR. Transcripts were mapped to the chicken genome.

overall_design: Differential analysis of transcriptomes in presence or absence of a miR-206 antagonist.

first: Katarzyna

last: Goljanek-Whysall

first: Helio

last: Pais

first: Irina

last: Mohorianu

first: Andrea

last: Münsterberg


title: Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle [MD-OCT4 ATAC-seq]

overall_design: ZHBTc4 cells expressing Ypet-MD and SNAP-MD-OCT4 or SNAP-MD*-OCT4 were treated with doxycycline for 40 hours, stained with Hoechst, sorted for different cell cycle phases, and subjected to ATAC-seq


title: Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle [OCT4OFF SOX2OFF ChIP-seq]

overall_design: ZHBTc4 and 2TS22C mouse embryonic stem cell lines were grown in the presence or absence of doxycycline and subjected to ChIP-seq


title: Human JNK1 haploinsufficiency: a novel genetic etiology of chronic mucocutaneous candidiasis and connective tissue disorder

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

summary: Genetic etiologies of chronic mucocutaneous candidiasis (CMC) disrupt human IL-17A/F-dependent immunity at mucosal surfaces, whereas those of connective tissue disorders (CTD) often impair the TGF-β-dependent homeostasis of connective tissues. The signaling pathways involved are incompletely understood. We report a three-generation family with an autosomal dominant (AD) combination of CMC and a novel CTD that clinically overlaps with Ehlers-Danlos syndrome (EDS). The patients are heterozygous for a private splice-site variant of MAPK8, the gene encoding c-Jun N-terminal kinase 1 (JNK1), a component of the MAPK signaling pathway. This variant is loss-of-expression and loss-of-function in the patients’ fibroblasts, which display AD JNK1 deficiency by haploinsufficiency. These cells have impaired, but not abolished, responses to IL-17A and IL-17F. Moreover, the development of the patients’ TH17 cells was impaired ex vivo and in vitro, probably due to the involvement of JNK1 in the TGF-β-responsive pathway and further accounting for the patients’ CMC. Consistently, the patients’ fibroblasts displayed impaired JNK1- and c-Jun/ATF2-dependent induction of key extracellular matrix (ECM) components and regulators, but not of EDS-causing gene products, in response to TGF-β. Furthermore, they displayed a transcriptional pattern in response to TGF-β different from that of fibroblasts from patients with Loeys-Dietz syndrome and mutations of TGFBR2 or SMAD3, further accounting for the patients’ complex and unusual CTD phenotype. This experiment of Nature indicates that the integrity of the human JNK1-dependent MAPK signaling pathway is essential for IL-17A- and IL-17F-dependent mucocutaneous immunity to Candida, and for the TGF-β-dependent homeostasis of connective tissues.

overall_design: Examination of gene expression in dermal fibroblasts from healthy controls and MAPK8-heterozygous patients treated with TGF-β1

first: Juan

last: Li

first: Marco

last: Ritelli

first: Cindy

middle: S

last: Ma

first: Geetha

last: Rao

first: Emilie

last: Corvilain

first: Salim

last: Bougarn

first: Sophie

last: Cypowyj

first: Lucie

last: Grodecká

first: Romain

last: Lévy

first: Vivien

last: Béziat

first: Lei

last: Shang

first: Kathryn

last: Payne

first: Danielle

last: Avery

first: Mélanie

last: Migaud

first: Soraya

last: Boucherit

first: Sabri

last: Boughorbel

last: Guennoun

first: Maya

last: Chrabieh

first: Franck

last: Rapaport

first: Benedetta

last: Bigio

first: Yuval

last: Itan

first: Bertrand

last: Boisson

first: Valérie

last: Cormier-Daire

first: Delfien

last: Syx

first: Fransiska

last: Malfait

first: Nicoletta

last: Zoppi

first: Laurent

last: Abel

first: Tomáš

last: Freiberger

first: Harry

last: Dietz

first: Nico

last: Marr

first: Stuart

last: Tangye

first: Marina

last: Colombi

first: Jean-Laurent

last: Casanova

first: Anne

last: Puel


title: Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle [OCT4-AID ATAC-seq]

first: David

last: Suter

overall_design: ZHBTc4 cells expressing Ypet-MD and mCherry-OCT4-AID were treated with doxycycline for 24 hours before treatment with different IAA regimes, stained with Hoechst, sorted for different cell cycle phases, and subjected to ATAC-seq

first: Elias

last: Friman


title: Inducible three-factor direct reprogramming to nephron progenitors using piggyBac transposons

city: Parkville

first: Andrew

last: Lonsdale

state: VIC

address: 50 Flemington Rd

country: Australia

institute: Murdoch Children's Research Institute

summary: All nephrons in the mammalian kidney arise from a transient nephron progenitor population that is lost after birth. The recreation of nephron progenitors (NPs) and/or their maintenance in culture has been a major focus of renal regenerative strategies. Using a lentiviral screening approach, we previously generated an induced nephron progenitor (iNP) state in vitro using a pool of six transcription factors (SIX1, SIX2, HOXA11, OSR1, EYA1, SNAI2). Here, using an inducible piggyBac transposon system, we demonstrate efficient reprogramming to iNPs with only three transcription factors (SNAI2, EYA1 and SIX1). Coupled with maintenance in culture conditions supportive of this progenitor state, the resulting population can contribute to developing nephrons in vitro, ex vivo and in vivo. This approach provides a rapid and efficient method for the generation of NPs from human somatic cells.

overall_design: RNA-seq of three replicates each of nephron progenitors with inducible transcript factors  across uninduced sample, induced sample on HGM media and induced samples on NPSR media

first: Jessica

last: Vanslambrouck


title: Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle [OCT4OFF SOX2OFF ATAC-seq]

overall_design: ZHBTc4 and 2TS22C mouse embryonic stem cell lines were grown in the presence or absence of doxycycline and subjected to ATAC-seq


title: MeCP2 represses the rate of transcriptional initiation of highly methylated long genes (NanoString)

city: Boston

first: Lisa

last: Boxer

country: USA

summary: Mutations in the methyl-DNA-binding repressor protein MeCP2 cause the devastating neurodevelopmental disorder Rett syndrome. It has been challenging to understand how MeCP2 regulates transcription because MeCP2 binds broadly across the genome, and MeCP2 mutations are associated with widespread small-magnitude changes in neuronal gene expression. Using multiple approaches, we demonstrate that MeCP2 represses nascent RNA transcription of highly methylated long genes in the brain through its interaction with the NCoR co-repressor complex. By measuring the rates of transcriptional initiation and elongation in the brain directly, we find that MeCP2 has no measurable effect on transcriptional elongation, but instead represses the rate at which Pol II initiates transcription of highly methylated long genes. These findings suggest a new model of MeCP2 function in which it binds broadly across highly methylated regions of DNA, but acts from a distance to attenuate transcriptional initiation.

overall_design: RNA was extracted from forebrain tissue from 10 MeCP2 KO and 10 WT littermate control mice, and 10 MeCP2 R306C and 10 WT littermate control mice. Expression of 200 genes was quantified by Nanostring nCounter.

first: William

last: Renthal

first: Michael

last: Greenberg


title: MeCP2 represses the rate of transcriptional initiation of highly methylated long genes (FP PRO-Seq)

overall_design: Flavopiridol (FP) was injected for 0, 20, 40, or 60 minutes into MeCP2 KO or WT mice (n = 2 or 3), followed by nuclei isolation from forebrain tissue and Precision Run-On sequencing (PRO-seq) to measure rates of transcriptional elongation and initiation.

first: Benyam

last: Kinde


title: MeCP2 represses the rate of transcriptional initiation of highly methylated long genes (PRO-Seq)

overall_design: Precision Run-On sequencing (PRO-seq) was performed from the forebrain of 5 MeCP2 KO and 5 WT littermate control mice, 5 R306C and 5 WT littermate control mice, and 3 Dnmt3a cKO and 3 WT littermate control mice.


title: Hypomethylation of STAT1 and HLA-DRB1 is associated with type-I interferon-dependent HLA-DRB1 expression in lupus CD8+ T cells

city: Pittsburgh

first: Amr

last: Sawalha

address: 4401 Penn Avenue

institute: University of Pittsburgh

summary: Systemic lupus erythematosus (SLE) is a chronic relapsing autoimmune disease characterized by the production of autoantibodies and multiple organ involvement. In this study, we investigated genome-wide DNA methylation changes in the CD8+ T cells from 8 pairs of lupus patients compared to age, sex, and ethnicity matched healthy controls.

overall_design: Illumina Infinium MethylationEPIC array of genomic DNA from CD8+T cells extracted from whole blood from 8 systemic lupus erythematosus (SLE) patients and 8 healthy controls (CON) matched by age, sex and ethnicity.

first: Patrick

last: Coit


title: MeCP2 represses the rate of transcriptional initiation of highly methylated long genes (ChIP-Seq I)

overall_design: ChIP-seq was performed from WT and MeCP2 KO forebrain for H3K36me3 (n=10) and H3K27ac (n=10) with input controls. ChIP-seq was performed from WT and MeCP2 R306C forebrain for H3K9ac (n=5), H3K27ac (n=2), H4K12ac (n=3), and MeCP2 (n=4) with input controls. ChIP-seq was peformed from WT cortical neurons for YY1, and from WT forebrain for H3K79me2 (n=2) with input controls.


title: Naphthoquinone-based aerobic respiration in E. coli

status: Public on Nov 25 2019

city: San Diego

first: Amitesh

last: Anand

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

summary: We performed evolution of Escherichia coli K12 MG1655 to study how the system adapts to loss of ubiC gene involved in ubiquinone biosynthesis. RNA-Seq was performed to examine the underlying transcriptional rewiring.

overall_design: Growth of E. coli with various supplements was performed with biological duplicates. Total RNA was extracted from mid-log phase culture for RNA-Seq library preparation.


title: MeCP2 represses the rate of transcriptional initiation of highly methylated long genes

overall_design: Refer to individual Series