title: ORFome decay in 293t and k562

city: Kansas City

summary:
mRNA translation decodes nucleotide into amino acid sequences. However, translation has also been shown to affect mRNA stability depending on codon composition in model organisms, although universality of this mechanism remains unclear. Here, using three independent approaches to measure exogenous and endogenous mRNA decay, we define which codons are associated with stable or unstable mRNAs in human cells. We demonstrate that the regulatory information affecting mRNA stability is encoded in codons and not in nucleotides. Stabilizing codons tend to be associated with higher tRNA levels and higher charged/total tRNA ratios. While mRNAs enriched in destabilizing codons tend to possess shorter poly(A)-tails, the poly(A)-tail is not required for the codon-mediated mRNA stability. This mechanism depends on translation; however, the number of ribosome loads into a mRNA modulates the codon-mediated effects on gene expression. This work provides definitive evidence that translation strongly affects mRNA stability in a codon-dependent manner in human cells.
293T cells and k562 cells were infected with ORFome library to decay exodogenous gene mRNA decay. Stable infected cells were treated with actinmycin D at 6 well plate and samples were collected in duplicate every hour 0-6h for RNA-seq

overall_design: The 96 well format ORFome library was pool together using an automatic robot.  First in 20 bins were created based in ORF size, then those 20 were pooled in 5 groups, grown, DNA maxi-preparation done. After quantification, the five groups were mixed into a single cocktail. The ORFome cocktail was transfected with lentivirus vector: Pax2 and VSV-G into 293T cells for virus packing. Media containing virus were filtered and ultracentrifuged to enrich virus for infection. 293T cells and k562 cells were infected and selected with puromycin for a week, at the concentration of 293T(2ug/ml), K562(0.75ug/ml). Then, cells were treated with Actinomycin D (5ug/ml) at 6 well plate and samples were collected in duplicate every hour 0-6h for RNA-seq.  Specific oligos were used to target the surrounding barcode region of ORFome to generate library and sequenced.


title: ATAC-Me captures spatiotemporal dynamics of DNA methylation across the chromatin accessible genome

status: Public on May 01 2019

city: Nashville

first: Emily

last: Hodges

state: TN

address: 2212 Garland Ave.

department: Biochemistry

country: USA

institute: Vanderbilt University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: DNA methylation of enhancers is dynamic, cell-type specific, and vital for cell fate progression. However, current models inadequately define its role within the highly ordered steps of gene regulation. An analysis of independent datasets show an unanticipated overlap between DNA methylation and chromatin accessibility at enhancers of steady state stem cells, suggesting that two opposing features might exist concurrently. To temporally define the relationship between these two events, we developed ATAC-Me, which probes accessibility and methylation from a single library preparation. We identified waves of accessibility, both transient and persistent, occurring rapidly across thousands of myeloid enhancers as monocyte cells transition to a macrophage state. Persistent methylation states were observed at a majority of these sites while transcriptional responses of nearby genes tracked closely with accessibility. ATAC-Me uncovers a significant disconnect between chromatin accessibility, DNA methylation status, and gene activity. This unexpected observation highlights the value of ATAC-Me in constructing precise molecular timelines for understanding the role of DNA methylation in gene regulation.

overall_design: RNA-seq and ATAC-Me-seq libraries were generated for 5 time points of PMA stimulated THP-1 monocytes (0, 0.5, 1, 2, 24hrs), in biological replicate. Standard ATAC-seq libraries were generated at two time points (0, 24hr) in biological replicate. WGBS libraries were generated at two time points (0, 24 hr).

first: Kelly

middle: R

last: Barnett

middle: C


title: An Excitatory Circuit in Perioculomotor Midbrain for Non-REM Sleep Control

city: Berkeley

first: Zhe

last: Zhang

state: CA

address: University of California Berkeley

department: MCB

institute: University of California, Berkeley

summary: The perioculomotor (pIII) region of the midbrain was postulated as a sleep-regulating center in the 1890s but largely neglected in subsequent studies. Using activity-dependent labeling and gene-expression profiling, we identified pIII neurons that promote non-REM (NREM) sleep.

overall_design: RNA-Seq profiling identifies transcripts enriched in RS-eGFP neurons.

first: Yang

last: Dan


title: H3K27 ChIP-sequencing of NNMT overexpression in normal fibroblasts

city: Chicago

first: Mark

middle: Adam

last: Eckert

state: IL

address: 929 East 57th St, W107

department: OB/GYN

institute: University of Chicago

summary: High grade serous carcinoma (HGSC) arising from either the fallopian tube or ovary has a poor prognosis primarily due to its early dissemination throughout the abdominal cavity. Genomic and proteomic approaches have provided snapshots of the proteogenomics of ovarian cancer (OvCa)1,2, but a systematic examination of both the tumor and stromal compartments is critical to understanding OvCa metastasis. We developed a label-free proteomic workflow to analyze as few as 5,000 formalin-fixed, paraffin embedded cells microdissected from each compartment. The tumor proteome was comparatively stable during progression from in situ lesions to metastatic disease; however, the metastasis-associated stroma was characterized by a highly conserved proteomic signature, prominently including the methyltransferase nicotinamide N-methyltransferase (NNMT) and the proteins it regulates. Stromal NNMT expression was necessary and sufficient for several functional aspects of the cancer associated fibroblast (CAF) phenotype, including the expression of CAF markers and the secretion of cytokines and oncogenic extracellular matrix. Stromal NNMT supported OvCa migration, proliferation, and in vivo growth and metastasis. Expression of NNMT in CAFs led to a depletion of S-adenosyl methionine (SAM) and a reduction in histone methylation associated with extensive gene expression changes in the tumor stroma. This work supports the use of ultra-low input proteomics to identify candidate drivers of disease phenotypes and reveals that NNMT is a central, metabolic regulator of CAF differentiation and cancer progression in the stroma and a novel treatment target.

overall_design: Three biological replicates of normal murine 3T3 fibroblasts expressing either control or NNMT overexpression construct were grown for 48 hours in physiological levels of methionine before chromatin was extracted and subjected to H3K27me3 chromatin immunoprecipitation sequencing. Input controls for both control and NNMT overexpressing cells were also included.

middle: A

first: Ernst

last: Lengyel


title: Gene-expression patterns at transcriptional ans translational levels in the tissues of colorectal cancer are different from that in the correspondent adjacent regions

city: Memphis

first: Qingfei

last: Pan

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St. Jude Children's Research Hospital

summary: In the interest of gene expression status responsive to CRC, the colorectal tissues from the tumor and adjacency were isolated from the AOM/DSS mouse model, and then the transcriptomes and proteomes in these tissues were quantitatively profiled using next generation sequencing (NGS) and liquid chromatography mass spectrometry (LC-MS). The mutations in the transcriptomes exhibited huge diversity at either site or gene, while a few of mutated peptide were identified in these CRC tissues. Surprisingly, the inconsistent mutations in the gene expression transcriptional products were poorly supported by the genomic data at somatic mutations from the same mouse model. However, quantitative transcriptomic and proteomic data unveiled in the common and clearly differential patterns that enabled a distinction between the tumor and adjacent tissues, implying gene expression status as the sensitive indicators to characterize the CRC-related molecular features. The differentially expressed genes (DEGs) were enriched in the process of environmental information, while the differentially expressed proteins (DEPs) were concentrated in the metabolic pathways. Analysis towards the abundance of expressed products further clarified that most transcripts at lower abundance belonged to the genes within signaling pathways and most transcripts and proteins at higher abundance came from the genes located functioned in metabolism. Collecting transcriptomic and proteomic data in the cancer genome atlas (TCGA) and adopting the similar analysis strategy, the gene expression patterns were compared between human and mouse CRC. The functional themes of the cancer-related genes derived from transcriptomic as well as proteomic evidence in the mouse CRC were quite similar to that in human CRC. The CRC model upon the AOM/DSS mouse is therefore well mimic to human CRC.

overall_design: Mutation detection and gene expression profiles of CRC and matched-normal tissues from AOM/DSS mice at both transcritomics and proteomics levels.

last: Fan


title: BDE-47 Transcriptomic Alterations in Human Embryonic Stem Cell-derived Neural Precursor Cells

city: SAN FRANCISCO

first: Joshua

middle: F

last: Robinson

address: 513 Parnassus Ave HSE16

department: Obstretrics, Gynecology and Reproductive Sciences

institute: University of California, San Francisco

summary: Transcriptomic characterization of BDE-47 exposures in human neural precursor cells

overall_design: Transcriptome of human neural precursor cells exposed to BDE-47 (10 or 1μM) or vehicle for 24h.

first: H

last: Chen

first: J


title: RNA sequencing of NNMT overexpression in 3T3 fibroblasts

overall_design: Three biological replicates of normal murine 3T3 fibroblasts expressing either control or NNMT overexpression construct were grown for 48 hours in physiological levels of methionine before RNA was collected and sequenced to identify genes differentially regulated in response to NNMT.


title: Effect of ubiquitin-activating enzyme inhibition on multiple myeloma cell line MM1.S

city: Houston

first: Zhiqiang

last: Wang

state: Texas

address: 7455 Fannin St.

department: Lymphoma and Myeloma

institute: University of Texas MD Anderson Cancer Center

summary:
Resistance to proteasome inhibitors has prompted interest in blocking upstream components of the ubiquitin-proteasome pathway for the treatment of multiple myeloma (MM). We therefore evaluated the activity of TAK-243, a novel and specific inhibitor of E1 ubiquitin activating enzyme (UAE) activity, in the MM cell line MM1.S.
Treatment of MM1.S with 25 nM TAK-243 for 24 hr caused extensive changes in gene expression, highly uniform between triplicates.

overall_design:
Cells were incubated for 24 hr in triplicate with either DMSO control or 25 nM TAK-243.

The submitter did not provide the normalized data.

first: Junling

last: Zhuang

first: Fazal

last: Shirazi

first: Isere

last: Kuiatse

first: Hua

first: R

middle: E

last: Davis

first: Robert

middle: Z

last: Orlowski


title: Total uterus transcriptome after depletion of regulatory T cells at E8 of murine pregnancy

city: Paris

first: Felipe

middle: Leal

last: Valentim

state: Île-de-France

address: Bâtiment Cervi, 4ème étage, pièce 052

country: France

institute: INSERM/UPMC

summary: Regulatory T cells (Tregs) contribute to successful pregnancy by promoting maternal-fetal tolerance. We depleted Tregs using diphtheria toxin (DT) in the Foxp3DTR mouse model after allogenic mating with BALB/c males and we performed a complete NGS transcriptome analysis by RNA-seq at 100 million reads/sample of total uterine tissues at day 8 post coitum from control (PBS1X treated) and diphtheria toxin (DT) treated mice.

overall_design: Total uterine tissues mRNA profiles of 8 days post coitum pregnant, 8 weeks old, Foxp3DTR females after allogenic mating with BALB/c males. Samples  were generated by deep sequencing using NextSeq Illumina , in quadruplicate, for control (PBS1X treated) and diphtheria toxin (DT) treated mice.

first: Laura

middle: M

last: Florez

first: Gwladys

last: Fourcade

last: Leal-Valentim

first: Pierre

last: Barennes

first: Encarnita

last: Mariotti-Ferrandiz

first: David

last: Klatzmann


title: A vitamin-C-derived DNA modification catalysed by an algal TET homologue

city: Shanghai

first: Guoliang

last: Xu

address: 320 Yueyang Road

country: China

institute: Shanghai institute of biochemistry and cell biology

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

overall_design: Refer to individual Series


title: Endothelial Sash1 is required for alveolar surfactant production through nitric oxide signaling

city: Vancouver

first: Aly

last: Karsan

state: BC

address: W10th Ave

department: Genome Sciences Centre

country: Canada

institute: BC Cancer Agency

summary: Sash1 acts as a scaffold in TLR4 signaling. We generated Sash1-/- mice, which die in the perinatal period due to respiratory distress. Constitutive or endothelial-restricted Sash1 loss leads to a reduction of surfactant-associated protein synthesis. We show that Sash1 interacts with β-arrestin 1 downstream of the TLR4 pathway to activate Akt and eNOS in microvascular endothelial cells. Generation of nitric oxide downstream of Sash1 in endothelial cells activated cGMP in adjacent alveolar type 2 cells to induce transcription of surfactant genes. Thus we identify a critical cell nonautonomous function for Sash1 in embryonic development in which endothelial Sash1 affects alveolar type 2 cells and promotes pulmonary surfactant production through nitric oxide signaling. Lack of pulmonary surfactant is a major cause of respiratory distress and mortality in preterm infants, and these findings identify the endothelium as a potential target for therapy.

overall_design: E18.5 lung endothelial cells from wild-type compared to Sash1-knockout

first: Patrick

last: Coulombe

first: Grigorios

last: Paliouras


title: Heterogeneity and evolution in acute myeloid leukemia initiating cells

city: Cleveland

last: Wald

state: OH

address: Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road

department: Pathology

institute: Case Western Reserve University

summary: Little is currently known about the heterogeneity of leukemic initiating cells and how they evolve during AML disease progression. AML exhibits extremely few DNA mutations (an average of 13 per patient); therefore, it is likely that RNA based changes also play crucial roles in the development and progression of AML. We have optimized a method to robustly and cost-effectively perform single cell RNA sequencing on AML initiating cells (CD34+CD38-CD45RA+CD90-Lin-7AAD-). We completed a study on serial diagnosis/relapse samples from five AML patients, which revealed strong evidence of the evolution of RNA based changes in AML initiating cells.

overall_design: Single cell RNA sequencing of acute myeloid leukemia cells from five patients (matched diagnosis and relapse bone marrow samples)

first: L

last: Stetson


title: The Lin28/let-7 pathway regulates the mammalian caudal body axis elongation program

city: Boston

first: Edroaldo

last: Lummertz da Rocha

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

summary: The heterochronic genes Lin28a/b and let-7 are well-established regulators of invertebrate development, however their functions in patterning the mammalian body plan remain unexplored. In this study, we discovered a novel function of Lin28/let-7 in controlling caudal vertebrae number during body axis formation. We found that FoxD1-driven overexpression of Lin28a or LIN28B led to a striking increase in caudal vertebrae number, whereas loss of Lin28a stunted tail formation. Accordingly, perturbation of the let-7 microRNA family led to the opposite phenotypes. We further show that overexpressing Lin28a in embryos resulted in increased tail bud cell proliferation, whereas Lin28a KO decreased cellular proliferation. This was accompanied by a transcriptional shift, including down-regulation of the neural marker Sox2, and resulted in a pro-mesodermal phenotype with decreased proportions of neural tissue relative to mesoderm in Lin28a-overexpressing embryos. Strikingly, Lin28a KO and let-7 over-expression demonstrated opposite effects, suggesting that the Lin28/let-7 pathway acts upstream of the signaling pathways controlling the self-renewal and cell fate commitment of neuro-mesodermal progenitors. We propose that Lin28a/b activity controls the pool of caudal progenitors during tail development, promotes their self-renewal potential, is involved in controlling the balance of neural versus mesodermal cell fate decisions, and that progressive down-regulation of Lin28a allows for species-specific vertebral formula to be achieved. These findings suggest that Lin28/let-7 play a role in the regulation of tail length through heterochrony of the body plan.

overall_design: Study the role of Lin28/let7 pathway in the caudal body axis elongation program

first: Daisy

last: Robinton


title: Gene profile beween CD19 normal and deletion of resting B cells in spleen of sirt1 conditional knockout mouse

city: Daejeon

first: Seong-Lan

last: Yu

address: Gasuwon-dong

department: Myunggok Medical Research Institute

country: South Korea

institute: Konyang university

overall_design: Total RNA that obtained from CD19 normal and deleted resting B cells in sirt1 conditional knockout mouse were hybridized using Affymetrix.

first: Younghwan

last: Han

first: Seok-Rae

last: Park

first: Jae

last: Kang


title: Cytokine induced NK memory transcriptional profile characterization

city: Worcester

first: Alan

middle: G

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

summary: By comparing CD94-CD56dim NK cell with or without primary stimulation treatment after 5 days, cytokine induced NK memory related molecules were identified.

overall_design: Sorted CD94-CD56dim NK cells were primary stimulated or without for 16 hrs, then cultured in low dose IL-15 (5ng/ml) for 5 days, then cells were subjected RNA-Seq.

first: Yetao

last: Wang

first: Lawrence

last: Lifshitz

first: Alper

last: Kucukural

last: McDonel

first: Manuel

last: Garber

first: Jeremy

last: Luban


title: Unraveling a mechanism driving poor-prognosis prostate cancer: overexpression of the DNA repair gene, ribonucleotide reductase small subunit M2

first: Matthew

last: Freedman

address: 450 Brookline Avenue

institute: Dana Faber Cancer Institute

summary: FOXM1 activated RRM2 drives poor outcomes in major PC subtype classifications (PCS and PAM50 classifiers),and targeting RRM2 and its key TFs (e.g. FOXM1) abrogate PC progression.

overall_design: Examination of AR and K27ac ChIP-seq in 4 patient tumors and normals

first: Mark

last: Pomerantz

first: Connor

last: Bell

first: Edward

last: O’Connor

first: Matt

middle: L

first: Henry

middle: W

last: Long

first: Xintao

last: Qiu


title: Subdivision of ancestral scale genetic program underlies origin of feathers and avian scutate scales

city: Heidelberg

first: Jacob

last: Musser

address: Meyerhofstrasse 1

country: Germany

institute: European Molecular Biology Laboratory

summary: Birds and other reptiles possess a diversity of feather and scale-like skin appendages. Feathers are commonly assumed to have originated from ancestral scales in theropod dinosaurs. However, most birds also have scaled feet, indicating birds evolved the capacity to grow both ancestral and derived morphologies. This suggests a more complex evolutionary history than a simple linear transition between feathers and scales. We set out to investigate the evolution of feathers via the comparison of transcriptomes assembled from diverse skin appendages in chicken, emu, and alligator. Our data reveal that feathers and the overlapping ‘scutate’ scales of birds share more similar gene expression to each other, and to two types of alligator scales, than they do to the tuberculate ‘reticulate’ scales on bird footpads. Accordingly, we propose a history of skin appendage diversification, in which feathers and bird scutate scales arose from ancestral archosaur body scales, whereas reticulate scales arose earlier in tetrapod evolution. We also show that many “feather-specific genes” are also expressed in alligator scales. In-situ hybridization results in feather buds suggest that these genes represent ancestral scale genes that acquired novel roles in feather morphogenesis and were repressed in bird scales. Our findings suggest that the differential reuse, in feathers, and suppression, in bird scales, of genes ancestrally expressed in archosaur scales has been a key factor in the origin of feathers – and may represent an important mechanism for the origin of evolutionary novelties.

sample_organism:
Alligator mississippiensis
Dromaius novaehollandiae
Gallus gallus

overall_design: In chicken and emu we sampled two biological replicates for epidermis from each of five skin tracts at two developmental stages (placode and morphogenesis): dorsal and femoral/flank feathers, scutate scales, reticulate scales, and claws. In chicken, we additionally sampled a single biological replicate from dermis from all 5 skin tracts at both developmental stages. In alligator we sampled two biological replicates for epidermis from 3 skin tracts at two developmental stages (placode and morphogenesis): dorsal scales, femoral scales, and claws.


title: Childhood Cerebellar Tumors Mirror Conserved Fetal Transcriptional Programs

city: Toronto

first: Maria

last: Vladoiu

state: Ontarion

address: 555 University Ave

department: DSCB

institute: Hospital for Sick Children

summary: The study of the origin and development of cerebellar tumours has been hampered by the complexity and heterogeneity of cerebellar cells that change over the course of development. We used single-cell transcriptomics to study >60,000 cells from the developing murine cerebellum, and show that different molecular subgroups of childhood cerebellar tumours mirror the transcription of cells from distinct, temporally restricted cerebellar lineages. Sonic Hedgehog medulloblastoma transcriptionally mirrors the granule cell hierarchy as expected, whereas Grp3-MB resemble Nestin+ve stem cells, Group 4 medulloblastomas resemble unipolar brush cells, and PFA/PFB ependymoma and cerebellar pilocytic astrocytoma resemble the pre-natal gliogenic progenitor cells. Furthermore, single-cell transcriptomics of human childhood cerebellar tumours demonstrates that many bulk tumours contain a mixed population of cells with divergent differentiation. Our data highlight cerebellar tumours as a disorder of early brain development, and provide a proximate explanation for the peak incidence of cerebellar tumours in early childhood.

overall_design: 9 mouse hindbrains from different developmental stages were processed for single cell mRNA sequencing. No technical or biological replicates were used.

first: Michael

middle: D

last: Taylor


title: Effect of hyper-and hypoactivation of Notch signaling in IL-4-stimulate THP-1

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

summary: MSCV-GFP-IRES (IRES), MSCV-GFP-Myc-NIC1 (NIC1) and MSCV-GFP-DNMAML (DNMAML) were retrovirally transduced in to THP-1 cell (pCL-Ampho was used as packaging plasmid). GFP positive cells were sorted for selective desired cell. Then IRES, NIC1 and DNMAML overexpressing THP-1 were pretreated with PMA (5ng/ml) for 48 h before stimulation with IL-4 (20 ng/ml) for 3 h.

overall_design: IL-4-stimulated NIC1, IRES or DNMAML overexpressing THP-1

first: Naunpun

last: Sangphech


title: Biological significance of EZH2 in uterine cancer

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary:
Change of gene expression profile by EZH2 silencing
EZH2 is overexpressed in a number of malignancies, and is an attractive target for cancer treatment. The overexpression of EZH2 was significantly associated with disease free survival and overall survival of patients with ovarian cancer. EZH2 silencing resulted in decreased cell viability and invasion ability, and increased apoptosis. EZH2 silencing significantly enhanced cytotoxicity of paclitaxel, docetaxel and cisplatin in Hec-1A and Ishikawa cells. EZH2 silencing using siRNA incorporated into chitosan nanoparticles (siRNA/CH) resulted in significant inhibition of tumor growth compared to control siRNA/CH. Moreover, EZH2 siRNA/CH in combination with taxanes showed robust anti-tumor effects compared to monotherapy groups. These effects were associated with decreased tumor cell proliferation and angiogenesis, and increased tumor cell apoptosis. Genomic analyses revealed that EZH2 gene silencing resulted in decreased expression of many genes associated with tumor growth.

overall_design: Gene expression profile of EZH2 silencing by EZH2 siRNA compared with control siRNA in Hec-1A cells

first: Ju-Won

last: Roh

first: Jongseung

first: Anil

last: Sood


title: Myocardial Differentiation is Dependent upon Endocardial Signalling During Early Cardiogenesis in vitro

city: London

first: Rebecca

middle: J

last: Oakey

address: Great Maze Pond

department: Medical and Molecular Genetics

country: United Kingdom

institute: King's College London

summary: The endocardium interacts with the myocardium to promote proliferation and morphogenesis during the later stages of heart development. However, the role of the endocardium in early cardiac ontogeny remains under-explored. Given the shared origin, subsequent juxtaposition, and essential cell-cell interactions of endocardial and myocardial cells throughout heart development, we hypothesized that paracrine signaling from the endocardium to the myocardium is critical for initiating early differentiation of myocardial cells. To test this, we generated an in vitro, endocardial-specific ablation model using the diphtheria toxin receptor under the regulatory elements of the NFATc1 genomic locus (NFATc1-DTR) Early treatment of NFATc1-DTR embryoid bodies with diphtheria toxin efficiently ablated endocardial cells, which significantly attenuated the percent of beating EBs in culture and expression of early and late myocardial differentiation markers. The addition of Bmp2 during endocardial ablation partially rescued myocyte differentiation, maturation and function. Therefore, we conclude that early stages of myocardial differentiation rely on endocardial paracrine signaling mediated in part by Bmp2. Our findings provide novel insight into early endocardial-myocardial interactions that can be explored to promote early myocardial development and growth.

overall_design: RNA-seq was performed on FACS isolated endocardial and endothelial cells from embryoid body cultures

first: Saint-Jean

last: Leshana

first: Nikolaos

last: Barkas

first: Cristina

last: Harmenlink

first: Kevin

last: Tompkins

first: Scott

middle: H

last: Baldwin


title: Impact of poly herbal formulation (PHF) on transcriptome profiling of chickens

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: To delineate the mechanism of action of feed efficiency enhancement, we have evaluated the influence of PHF on gene expression profiles in chicken.

overall_design:
Organism : Gallus gallus, Agilent's Chicken Gene Expression  8x60k Array (AMADID: 049081) designed by Genotypic Technology Private Limited, Bangalore
Birds were supplemented with PHF for 42 days and breast muscle were collected.

first: Saravana

last: Kumar


title: Gene expression comparison of exhausted CD8 T cells that respond or do not respond to PD-1 blockade

first: Pablo

last: Penaloza-Macmaster

state: Illinois

address: 303 E. Chicago Avenue

department: Microbiology-Immunology

institute: Northwestern University

summary:
CD8 T cells that respond to PD-1 blockade (during the early stage of infection) have enriched CD28 costimulation genes
During the early stages of chronic infection PD-1 blockade is effective are rescuing exhausted CD8 T cells. However during the later stages of chronic infection PD-1 blockade is not able to induce a significant rescue of exhausted T cells. In order to understand the transcriptional basis of these difference we performed an RNA comparison. There is enrichment in several genes and pathways, and we hypothesize that these could be exploited for optimizing immune checkpoint therapies during the later stages of chronic infection.

overall_design: We FACS-sorted exhausted CD8 T cells from chronically infected mice (lifelong model of LCMV Cl-13 infection) at 2 different times when PD-1 blockade is effective or when PD-1 blockade is not effective

last: Penaloza-MacMaster


title: Invasive mechanisms for exotic Ageratina adenophora to customize soil microbe

city: beijing

first: zhao

last: mengxin

address: Haidian District Zhongguancun Street

institute: tsinghua university

summary: Understanding the mechanisms underlying the establishment of invasive plants is critical in community ecology. According to a widely accepted theory, plant-soil-microbe interactions mediate the effects of invasive plants on native species, thereby affecting invasion success. However, the roles and molecular mechanisms associated with such microbes remain elusive. Using high throughput sequencing and a functional gene microarray, we found that soil taxonomic and functional microbial communities in plots dominated by Ageratina adenophora developed to benefit the invasive plant.  There were increases in nitrogen-fixing bacteria and labile carbon degraders, as well as soil-borne pathogens in bulk soil, which potentially suppressed native plant growth. Meanwhile, there was an increase of microbial antagonism in the A. adenophora rhizosphere, which could inhibit pathogenicity against plant invader. These results suggest that the invasive plant A. adenophora establishes a self-reinforcing soil environment by changing the soil microbial community. It could be defined as a ‘bodyguard/mercenary army’ strategy for invasive plants, which has important insights for the mitigation of plant invasion.

overall_design: Eighteen samples were collected from three plots. In each plot, rhizosphere and bulk soil samples from monoculture Ageratina adenophora, multiculture of Ageratina adenophora and native plants, and native plants, respctively, were collected.

first: Mengxin

last: Zhao

first: Fanghao

last: Wan

first: Jizhong

last: Zhou

first: Xiaofei

last: Lu


title: Fgf10 knock-down effects in hyperoxia

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: Our previous data obtained by using immunohistochemistry showed, that Fgf10+/- (50% Fgf10 expression compared to WT) in hyperoxic condition at postnatal day 3 (P3) compared to WT  has less vessel count in the lung and less muscularization of small capillaries in the lung. Furthermore, Fgf10+/- showed a drastic increase in mortality upon hyperoxic lung injury. Main question to be answer by this experiment is as followed: Does Fgf10+/-  mice after hyperoxia from P0-P3 show different expression profiles at P3 compared to WT? To adress this question we harvest lungs at P3 from WT and Fgf10+/- after hyperoxia treatment from P0-P3. For this the mice were sacrificed by Ketamin/ Dormitor ip, lungs were perfused transcardiac with PBS and directly frozen in liquid nitrogen.

overall_design: Comparison of 2 groups with 4 independent samples each.

first: Saverio

last: Bellusci

first: Chao

last: Cho-Ming


title: Fgf10 knock-down effects in normoxia

summary: Our previous data obtained by using immunohistochemistry showed, that Fgf10+/- (50% Fgf10 expression compared to WT) in hyperoxic condition at postnatal day 3 (P3) compared to WT  has less vessel count in the lung and less muscularization of small capillaries in the lung. Furthermore, Fgf10+/- showed a drastic increase in mortality upon hyperoxic lung injury. Main question to be answer by this experiment is as followed: Does Fgf10+/-  mice in normoxia from P0-P3 show different expression profiles at P3 compared to WT? To adress this question we harvest lungs at P3 from WT and Fgf10+/- . For this the mice were sacrificed by Ketamin/ Dormitor ip, lungs were perfused transcardiac with PBS and directly frozen in liquid nitrogen.


title: Expression data from developing hematopoietic stem and progenitor cells

city: Kumamoto

first: Tomomasa

last: Yokomizo

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

summary:
In the mouse embryo during midgestation, hematopoietic stem cells (HSCs) are generated from aortic endothelium through the transdifferentiation process known as endothelial-to-hematopoietic transition, or EHT. During EHT, flat-shaped hemogenic endothelium transform into round-shaped hematopoietic cells, which subsequently form cell aggregates, called hematopoietic clusters.
To understand HSC specification during ontogeny and to search for nascent HSC markers, we performed single-cell microarray analysis of developing HSC populations.

overall_design: Using cell sorter, we collected 85 single cells from 5 different populations: E10.5 endothelial cells, E10.5 hemogenic endothelial cells, E10.5 hematopoietic clusters, E12.5 hematopoietic clusters and E14.5 fetal liver HSCs.

first: T

first: J

last: Matsuo

first: A

last: Shimono

first: S

last: Mori


title: SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development [Bisulfite-seq]

city: Beijing

first: Wei

last: Xie

address: Haidian District

department: School of Life Science

institute: Tsinghua University

summary: The oocyte epigenome plays critical roles in mammalian gametogenesis and embryogenesis. Yet, how it is established remains elusive. Here, we report that histone-lysine N-methyltransferase SETD2, an H3K36me3 methyltransferase, is a crucial regulator of the mouse oocyte epigenome. Deficiency in Setd2 leads to extensive alterations of the oocyte epigenome, including the loss of H3K36me3, failure in establishing the correct DNA methylome, invasion of H3K4me3 and H3K27me3 into former H3K36me3 territories and aberrant acquisition of H3K4me3 at imprinting control regions instead of DNA methylation. Importantly, maternal depletion of SETD2 results in oocyte maturation defects and subsequent one-cell arrest after fertilization. The preimplantation arrest is mainly due to a maternal cytosolic defect, since it can be largely rescued by normal oocyte cytosol. However, chromatin defects, including aberrant imprinting, persist in these embryos, leading to embryonic lethality after implantation. Thus, these data identify SETD2 as a crucial player in establishing the maternal epigenome that in turn controls embryonic development.

overall_design:
Mouse GO_P7, GO_P10, GO_P14, FGO, MII oocyte, zygote, late 2-cell, 8-cell and ICM from E3.5 blastocyst were obtained and performed STAR ChIP-seq to determine the H3K36me3 distribution. FGO in Dnmt3L KO mice and Setd2 maternal KO mice were collected and conducted STAR ChIP-seq, STEM-seq and RNA-seq to explore the cross talk between histone modifications. STAR ChIP-seq and RNA-seq were performed in Setd2 maternal KO zygote to test if abnormal H3K4me3 and transcription can be inherited in mutant embryo.
GO = growing oocyte
FGO = full grown oocyte

first: Qianhua

last: Xu

first: Yunlong

last: Xiang


title: SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development [RNA-seq]

overall_design:
Mouse GO-P7, GO-P10, GO-P14, FGO, MII oocyte, zygote, late 2-cell, 8-cell and ICM from E3.5 blastocyst were obtained and performed STAR ChIP-seq to determine the H3K36me3 distribution. FGO in Dnmt3L KO mice and Setd2 maternal KO mice were collected and conducted STAR ChIP-seq, STEM-seq and RNA-seq to explore the cross talk between histone modifications. STAR ChIP-seq and RNA-seq were performed in Setd2 maternal KO zygote to test if abnormal H3K4me3 and transcription can be inherited in mutant embryo.
GO = growing oocyte
FGO = full grown oocyte


title: Fgf10 knock-down effects in hyperoxia and normoxia

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

overall_design: Refer to individual Series


title: Array comparative genomic hybridization of canine diffuse large B-cell lymphoma (cDLBCL)

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

type: Genome variation profiling by genome tiling array

summary: The aim of this work was to identify copy number variations (CNVs) by high-resolution array comparative genomic hybridization (aCGH) on 50 dogs with newly diagnosed DLBCL.

overall_design: The DNA obtained from 50 cDLBCL specimens together with the paired skin biopsies were analyzed using a Agilent-025522 SurePrint G3 Canine CGH Microarray 4x180K (GPL10156). Tumor and reference DNA samples were labelled independently with cyanine 5-deoxyuridine triphosphate (dUTP) and cyanine 3-dUTP, respectively, using SureTag Complete DNA Labeling Kit. Oligo aCGH analysis was performed following the manufacturer’s recommendations, using an Oligo aCGH/ChIP-on-chip Hybridization Kit (Agilent Technologies).

first: Ferraresso

last: Serena

first: Aresu

last: Luca


title: DNA methyaltion analysis in decidualization

city: Ube

first: Ryo

last: Maekawa

address: Minami-Kogushi 1-1-1

department: Department of Obstetrics and Gynecology

institute: Yamaguchi University School of Medicine

type: Methylation profiling by genome tiling array

summary: DNA methylation status was examined by Illumina 450k in non-decidualized and decidualized ESCs.

overall_design: a set of examination in a non-decidualized ESC and a decidualized ESC was examined by Illumina 450k.

first: Kosuke

last: Jozaki


title: DNA methylation prevents REF6 binding in Arabidopsis

first: Xiaofeng

last: Cao

address: No.1 West Beichen Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: RELATIVE OF EARLY FLOWERING 6 (REF6/JMJ12), a Jumonji C (JmjC)-domain-containing histone demethylase, directly recognizes the CTCTGYTY motif by its zinc-finger domains to demethylate H3K27me3 at specific loci in Arabidopsis genome. Here we show that the recognition of CTCTGYTY motif by REF6 is prevented by DNA methylation. REF6 prefers to bind DNA hypo-methylated regions in vivo. DNA cytosine-methylation decreases REF6 binding affinity in vitro, and the crystal structure of ZnF-clusters showed that REF6 prefers unmethylated DNA sequences. Furthermore, REF6 displayed ectopic binding on multiple new target loci in drm1 drm2 cmt2 cmt3 (ddcc) quadruple mutants, where non-CG methylation was largely diminished. Collectively, this study reveals a novel targeting crosstalk between an H3K27me3 demethylase and DNA methylation.

overall_design: All mutant lines used in this study were in the Columbia ecotype background. Whole seedlings of 10 days after germination were harvested for ChIP-seq. ChIP-Seq experiments with anti-REF6 antibody were performed with three samples: Col (WT), ddcc (drm1-2; drm2-2; cmt2-7; cmt3-11 quadruple mutant), ref6-5 (mutant,Negative control). ChIP-Bisulfite-Seq experiments with anti-REF6 antibody were performed with three samples: Col (WT), ddcc (drm1-2; drm2-2; cmt2-7; cmt3-11 quadruple mutant), ref6-5 (mutant,Negative control).

first: Qi

last: Qiu

first: Hailiang

last: Mei

first: Qingqing

last: Yao

first: Xian

last: Deng

first: Kaixuan

last: He

first: Jinbiao

last: Ma


title: RNA-seq analysis of kinase deletion mutant (ΔmpkA) and parental strain Aspergillus nidulans reveal novel cellular functions of MpkA.

city: Baltimore

first: Mark

middle: R.

last: Marten

state: MD

address: 1000 Hilltop Circle

department: Chemical, Biochemical, and Environmental Engineering

institute: University of Maryland Baltimore County

summary: A transcriptomic assessment of a kinase deletion mutant (ΔmpkA) and a control strain revealed many cellular activities this kinase is impacting. Studies were conducted in the model filamentous fungi, Aspergillus nidulans¸ under rich growth conditions. MpkA is a known kinase involved in the cell wall integrity signaling pathway. This pathway is activated upon cell wall stress and regulates production of cell wall related genes. Here, fungi were grown under non-stressful conditions. The comparison between the control strain and the deletion mutant transcript levels revealed previously unknown functions, such as iron starvation, that MpkA may be involved with.

overall_design: A control strain and deletion mutant grown in non-stressful conditions (2 biological replicates and 2 technical replicates) were analyzed to determine alternative, unknown functions of MpkA using RNA-seq.

first: Chelius

last: Cynthia

first: Kumar

last: Jyothi

first: Steven

last: Harris


title: Microarray analysis of NNMT overexpression and knockdown in stromal cells

city: Chicago

last: Eckert

address: 929 East 57th St, W107

department: OB/GYN

institute: University of Chicago

summary: Analysis of gene expression in human CAFs with control (shCtrl) or shRNA against NNMT (shNNMT) expression or normal fibroblasts expressing control (Ctrl) or NNMT overexpression (NNMT) constructs. Cells were infected with lentivirus to express the indicated shRNA  construct. Hypothesis is that knockdown of NNMT will affect expression of genes via regulation of histone methylation status.

overall_design: Total RNA was collected from human cancer associated fibroblasts expressing the indicated shCtrl or shNNMT constructs or from normal WI-38 fibroblasts expressing Ctrl or NNMT constructs and expression analyzed with Affymetrix microarray.


title: Mouse model of MCC deficiency reveals novel pathways altered by colon barrier destruction in colitis-associated cancer

city: Sydney

first: Daniel

last: Roden

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute

summary: Chronic inflammation is a well-known risk factor but the early events by which inflammation promotes colitis-associated cancer (CAC) are still poorly understood. Here we developed a new model to profile early carcinogenesis, using mice deficient for the tumor suppressor ‘Mutated in colorectal cancer’ (MCC). We generated mice with loss of MCC expression in colonic/intestinal epithelial cells (MccΔIEC) and gave them a diet containing the drug sulindac, which acts as a mild irritant in the mouse proximal colon causing foci of tissue damage with chronic inflammation. The genomic expression profiles were analyzed by Mouse Transcriptome Arrays (10 weeks) and tissue by histopathology at 20 weeks. MccΔIEC mice exposed to sulindac developed colon lesions with adenocarcinoma (59%) and down-regulation of E2F targets, such as the DNA mismatch repair genes. MCC-proficient mice also developed lesions, but these showed up-regulation of E2F pathways and progressed to cancer less frequently (19%). The most highly activated pathway in both groups was Interferon-Gamma-Response, in particular the p47-GTPase family of anti-microbial host defense genes that are homologs of the Crohn’s Disease susceptibility gene IRGM.

overall_design: Gene expression analysis of the inflammatory colonic lesions induced by a diet containing the drug sulindac and compared with matching tissue from control-fed mice of the same genotype.

first: Phuong

middle: N

last: Tran

first: Maija

last: Kohonen-Corish


title: Resident effector memory Tregs of the uterus regulate trophic functions during mouse early pregnancy

city: Paris

first: Felipe

last: Valentim

address: Bâtiment Cervi, 4ème étage, pièce 052

institute: INSERM/UPMC

summary: Regulatory T cells (Tregs) contribute to successful pregnancy by promoting maternal-fetal tolerance. We identified a novel population of CD25-Foxp3+ resident uterine Tregs in non-pregnant mouse uterus. They have phenotypic and migration properties of tissue-resident effector-memory T cells (Trm), thus identifying regulatory Trm (regTrm). Lack of CD25 expression in regTrm is caused by the IL-2-deprived uterine microenvironment. We performed a complete transcriptome analysis by RNA-seq to determined whether uterine regTrm have a unique molecular signature, as has been described for other tissue Tregs. For this, we purified CD25- regTrm from non-pregnant and pregnant uterus at day 6 to 8 of pregnancy, and we compared them to CD4+Foxp3- (CD4conv) T cells from non-pregnant uterus and to CD25+ Tregs from paraaortic uterine draining lymph nodes. We used criteria of (i) a two-fold or greater change in expression and (ii) a p-value <0.05 (cut-off at 5% FDR) to determine differentially expressed genes (DEGs). DEGs were annotated  by their functional relevance in pregnancy using ingenuity pathway analysis (IPA) and using the PubMed Query: (Gene main name OR Gene Synonymous 1 OR Gene Synonymous 2 OR …) AND "pregnancy" OR “regulatory T cells” OR "uterus". We found that uterine regTrm have a unique transcriptional profile, impregnated with a uterine signature comprising up-regulation of genes related to the endometrium and to uterine receptivity. Pregnancy triggers regTrm expression of genes involved in trophic functions such as uterine development, extracellular matrix remodeling, hypoxia and vasculogenesis.

overall_design: Samples from regulatory T cells mRNA profiles from uterus of non-pregnant and pregnant BALB/c foxp3<gfp> mice  at day 6 to 8 of pregnancy, and from paraaortic lymph nodes of non-pregnant mice.  Data were generated by RNA sequencing, in quadruplicate, using Illumina NextSeq.

first: Laura

last: Florez

first: Gwladys

last: Fourcade

last: Leal-Valentim

first: Federica

last: Martina

first: Encarnita

last: Mariotti-Ferrandiz

first: David

last: Klatzmann


title: A phosphoproteomic and transcriptomic analysis of carnosine’s action on signaling in glioblastoma

city: Leipzig

first: Henry

last: Oppermann

address: Liebigstraße 19

department: Klinik und Poliklinik für Neurochirurgie

institute: Universitätsklinikum Leipzig

summary: Previous studies demonstrated that carnosine affects signaling molecules of different pathways in a number of experimental models. However, the primary targets of carnosine are still unknown and its effect on complex signal transduction has not been revealed. This is especially the case for pathways that could be responsible for the anti-neoplastic effect of the dipeptide. Therefore, we performed a phosphoprotein antibody array and RNA-seq experiments with U87 glioblastoma cells treated with 50 mM carnosine for 24h, in order to obtain a precise and coherent picture of carnosine’s influence on signal transduction in single tumor cells.

overall_design: mRNA of U87 Glioblastoma cells treated with or without carnosine was analyzed by deep sequencing

first: Kristin

last: Reiche

first: Conny

last: Blumert


title: Dopamine receptor allows selective targeting of neoplastic progenitors in human acute myeloid leukemia

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

summary: Dopamine receptor (DRD) antagonist thioridazine (TDZ) has been traditionally prescribed as an anti-psychotic drug. Recent observations have revealed anti-neoplastic effects of TDZ in a variety of neural and non-neural cancers including acute myeloid leukemia (AML). However, the basis of TDZ effects on transformed tissues is not fully understood. We used AML as a model system to study the anti-neoplastic properties of TDZ, as well as the downstream mechanism of action for DRDs in the context of cancer. Our study defines a role for DRDs in regulating neoplastic properties and suggests DRD2 as an attractive therapeutic target for AML.

overall_design: Xenografted AML samples were obtained after in vivo treatment with Thioridazine (TDZ) for 21 days. The human leukemic cells (hCD45+CD33+) were FACS-purified and RNA was extracted. Gene expression profiles were compared between TDZ- versus vehicle (captisol 30%)-treated matched xenografts.

first: Lili

last: Aslostovar

first: Yannick

last: Benoit

first: Allison

last: Boyd

first: Zoya

last: Shapovalova

first: Jennifer

last: Reid


title: circRNA-sequencing for renal cell carcinoma and control

city: Shenyang

first: Chengcheng

last: Lv

state: Liaoning

address: 44. Xiaoheyan Road

department: Department of Urology Surgery

institute: Liaoning Cancer Hospital and Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: We aim to identify profiling of circRNAs in renal tissue from renal cell carcinoma patients. In this study, seven paired frozen carcinoma tissues as well as normal tissues from  patients with renal cell carcinoma were used for circRNA profiling by second generation of RNA sequencing.

overall_design: normal control group and renal cell carcinoma group

first: Yu

last: Zeng

first: Qingzhuo

last: Dong

first: Zi

last: Yu

first: Gejun

last: Zhang


title: Rewiring of a sigma factor regulatory network in P. aeruginosa by a naturally occurring single nucleotide polymorphism

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

institute: Technische Universität Braunschweig

summary: Transcriptional regulatory networks represent an important organizational element in the bacterial cell where signals from the cell state and the outside environment are integrated in terms of activation and inhibition of gene transcription. How these networks evolve is not well understood, and the effects of natural occurring polymorphisms within network components are often not known. Here, we systematically investigate the functional consequences of an amino acid substitution in the sigma factor protein RpoN in the opportunitic pathogen Pseudomonas aeruginosa. While RpoN is known to be important for virulence gene expression in P. aeruginosa, the particular amino acid substitution is important for ecological success of the bacteria in cystic fibrosis infections. We use Chromatin Immunoprecipitation coupled to deep sequencing (ChIP-seq), transcriptional profiling as well as in vitro protein-DNA interaction studies and show that the rpoN mutation results in reduced connections to only parts of the RpoN controlled regulatory network. On the other hand, the mutation results in activation of other sigma factor regulons. Finally, our results also show that the rpoN mutation results in a rewiring of the RpoN network in terms of increased connectivity and positive regulatory effect on a virulence associated locus. This molecular pleiotropy could not have been predicted from in silico analyses alone, and this work thus underlines the importance of achieving a molecular understanding of the effects of polymorphisms in regulator network components

overall_design: ChIP-seq experiments, transcriptome profiling and in vitro DNA interaction abbility of the sigma factor RpoN and its single amino acid substitution mutant, RpoN(DK2)

first: Eva

middle: K

last: Andresen

first: Sebastian

last: Schulz

first: Susanne

last: Haussler

first: Tino

last: Krell

first: Maher

last: Hachem

first: Lars

last: Jelsbak


title: The LKB1/AMPK pathway is a central mediator of the hepatic xenobiotic response

city: La Jolla

first: Ruth

middle: T

state: CA

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute

summary: The serine/threonine kinase LKB1 is a tumor suppressor gene which also plays key roles in metabolic function in peripheral tissues through its direct phosphorylation and activation of the AMP-activated protein kinase (AMPK).  The LKB1/AMPK pathway plays key roles in the liver in suppressing transcriptional programs of gluconeogenesis and lipogenesis, and hepatic LKB1 is required for the ability of the type 2 diabetes agent metformin to lower blood glucose levels in mice.  To more broadly define how the LKB1/AMPK pathway controls hepatic metabolism, transcriptional profiling was employed using mice with an inducible liver-specific deletion of Lkb1.  Unexpectedly, LKB1/AMPK signaling broadly controls the expression of many phase I xenobiotic metabolism genes, including several members of the cytochrome P450 family. In particular, expression of CYP2E1, an important mediator of drug detoxification, was markedly reduced upon LKB1 loss.  LKB1 liver-specific knockout mice exposed to hepatocarcinogens, exhibited marked resistance to carcinogen-induced hepatocyte apoptosis, proliferation, senescence, and liver fibrosis and tumorigenesis.

overall_design: Total RNA obtained from livers of wild-type and LKB liver-specific knockout mice treated with CCL4, AICAR, or control mineral oil or saline.

first: Rebecca

last: Kohnz

first: Reuben

last: Shaw


title: Immunomodulatory mechanism of Cordyceps militaris polypeptide through regulating gene in mice

city: jilin city

first: guangyu

last: xu

address: Binjiang Road 3999,jilin city,132013

institute: College of Pharmacy, Beihua University

summary: Cordyceps militaris and Cordyceps sinensis belong to belong to the same genus, but the different species, with immunity improvement, antibacterial, and antihypertensive effect, and the studies on the functions of Cordyceps militaris mainly focus on those of its polysaccharides and polypeptides. The latest studies have found that some of the polypeptides with immunomodulatory effect can widely regulate immune functions at multiple levels, improve immunity, and enhance immune functions to ensure the healthy body, showing an important significance. Cordyceps militaris polypeptide prepared with the enzymolysis method was taken as the research object in this study. The differentially expressed genes and the related cell signal transduction pathway were screened by mRNA expression microarray. STEM 1.3.6 software was used for the clustering of the gene functions, and David and KEGG database were applied for the analysis of the related functions. 1748 differentially expressed genes were selected finally and three of them were validated by qPCR. The results showed that gene Hist1h2bp, Ctsg, and Elane were involved in the regulation of Cordyceps militaris on the immune activity of mice. Gene Hist1h2bp, Ctsg and Elan may be the potential targets of Cordyceps militaris polypeptide, which may provide an important theory basis for the further research and development of Cordyceps militaris polypeptide.

overall_design: The experimental animals were fed under the conditions with a relative humidity of 40-70%, at 20±1℃ and in a sterile environment, with ad libitum access to water and food. After they adapted to the environment for one week, the mice were randomly divided into blank control group, model group, and low-, medium- and high-dose Cordyceps militaris polypeptide (CMP) groups. Mice in low-, medium- and high-dose Cordyceps militaris polypeptide were orally given 32, 160 and 800 mg/kg once daily continuously for 45 days, respectively, and those in the blank control group and model group were given equal volume of distilled water in the same way. In addition to those in the blank control group, mice in the other groups were injected with 40 mg/kg of cyclophosphamide intraperitoneally once daily, successively for 2 day for the establishment of mice immunodeficiency model. The mice's body weights were measured every week regularly for the observation on changes in their body weights and their general states were also observed at the same time. We choose best group(high-dose group) to do mRNA  expression microarray.

first: guangxin

last: yuan


title: Transcriptome profiles in MRC5 and CS1AN cell lines upon UV irradiation

status: Public on Apr 30 2019

city: Guangzhou

first: Yuming

last: Wang

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

institute: Guangzhou medical university

summary: Cockayne syndrome (CS) is mainly caused by mutations in CSB gene encoding a protein belonging to SWI/SNF chromatin remodeling family. CS1AN cells derived from CS patients carrying mutations in CSB gene are useful for the study of nucleotide excision repair (NER) upon UV- or oxidative stress-induced DNA damage. However, establishment of isogenic cells endogenously expressing wild type CSB is tedious and difficult. Normal fibroblast MRC5 has been widely used to study cellular reponse to stress. This study was designed to systematically analyze the features of these two cell lines during DNA damage and repair pathways, aiming to provide a reference for application of these two cell lines as in vitro model. We show that CS1AN is hypersensitive to UV irradiation compared to MRC5. We found that CSB is essential for regulating gene expression in response to DNA damage.

overall_design: mRNA profiles of MRC5 and CS1AN cells with or without UV exposure were generated by deep sequencing, using Illumina HiSeq X Ten in paired-end mode.

first: Zhenzhen

last: Wu

first: Lingyun

last: Liu

first: Yingying

last: Xu

first: Xun

last: Zhu


title: Transcriptome-wide Association study identifies putative Elicitors/Suppressor of Puccinia graminis f. sp. tritici that Modulate Barley rpg4-mediated Stem Rust Resistance

city: Fargo

first: Robert

last: Brueggeman

state: ND

address: 306 Walster Hall, North Dakota State University

department: Plant Pathology

institute: North Dakota State University

summary:
Transcriptomic profiling was done on barley samples incoulated with different Puccinia graminis f. sp. tritici (Pgt) isolates of varying virulence profile on barley stem rust resistance gene rpg4/5 and Rpg1.
Several differentally expressed host and pathogen genes were identified while comparing gene expression profiles between group of samples inoculated with isoaltes of varying virulence.
Several variants with genes of pathogen were idnetified that are possibly associated with virulence to rpg4/5.

sample_organism:
Hordeum vulgare
Puccinia graminis f. sp. tritici

overall_design: Suceptible barley cv. Harrignton were treated with 24 Pgt isolates, indivdually and samples were collected 5 days post inoculation.

first: Roshan

last: Sharma Poudel


title: Hominid-specific transposable elements and KRAB-ZFPs facilitate human embryonic genome activation and transcription in naïve hESCs [ChIP-seq]

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

country: Switzerland

institute: EPFL

summary: Transposable elements (TEs) are key to the evolutionary turnover of regulatory sequences. How they can play such an essential role in spite of their genotoxic potential is unknown. Here, we demonstrate that KRABcontaining zinc finger proteins control the timely and pleiotropic engagement of TE-derived cis-regulators of transcription. We first observed that evolutionary recent TEs of the SVA, HERVK and HERVH subgroups are major contributors to chromatin opening during human embryonic genome activation and act as KLF-stimulated enhancers in naïve embryonic stem cells. We then found that KZFPs of corresponding evolutionary ages are simultaneously induced and repress the transcriptional activity of these TEs. We finally determined that the same KZFP-controlled TE-based enhancers later serve as developmental and tissue-specific regulators of gene expression. Thus, by taming the transcriptional impact of TEs during early embryogenesis, KZFPs allow for their genome-wide incorporation into transcriptional networks, thereby contributing to the species-specificity of human genome regulation.

overall_design: Chromatin immunoprecipitation of KLF4, H3K27ac, H3K9me3 in hESC

last: Pontis


title: Hominid-specific transposable elements and KRAB-ZFPs facilitate human embryonic genome activation and transcription in naïve hESCs [RNA-seq]

overall_design: RNA-seq was performed in WIBR3dPE hESC in KN/2iL media or in Induced Neurons upon dCAS9-KRAB overexpression containing or not a guide RNA targeting LTR7YB or SVA/LTR5Hs or overexpressing ZNF611; in H1 primed hESC overexpressing GFP, KLF4 or KLF17


title: LNK suppresses interferon signaling in M202 melanoma cells

city: Singapore

first: SIQIN

last: ZHOU

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary: LNK attenuates IFN-γ (2,000 U/ml, 24 hours) induced gene expression in M202 melanoma cells.

overall_design: mRNA profiles of Control (GFP) and LNK overexpressing M202 cells were generated by microarray using  Illumina Human HT-12 v4 Expression BeadChip

first: Ling-Wen

last: Ding

first: Qiao-Yang

last: Sun

first: Jarem

last: Edwards

first: Lucia

last: Fernández

first: Xue-Bin

last: Ran

first: Si-Qin

last: Zhou

first: Richard

last: Scolyer

first: James

middle: S

last: Wilmott

first: John

last: Thompson

first: Ngan

last: Doan

first: Jonathan

last: Said

first: Nachiyappan

last: Venkatachalam

first: Jin-Fen

last: Xiao

first: Xin-Yi

last: Loh

first: Maren

last: Pein

first: Liang

first: David

last: Mullins

first: Henry

last: Yang

first: De-Chen

last: Lin

first: H

middle: P

last: Koeffler


title: Dragotcytosis: Elucidation of the Mechanism for Cryptococcus neoformans Macrophage-to-Macrophage Transfer

first: Anne

middle: E.

last: Jedlicka

address: 615 N. Wolfe street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins University, School of Public Health

summary:
Abstract:  Cryptococcus neoformans is a pathogenic yeast capable of a unique and intriguing form of cell-to-cell transfer between macrophage cells. The mechanism for cell-to-cell transfer is not understood. Here we imaged macrophages with CellTracker Green CMFDA-labeled cytosol to ascertain whether cytosol was shared between donor and acceptor macrophages. Analysis of several transfer events detected no transfer of cytosol from donor to acceptor macrophages. However, blocking Fc and complement receptors resulted in a major diminution of cell-to-cell transfer events. The timing cell-to-cell transfer (11.17 min) closely approximated the sum of phagocytosis (4.18 min) and exocytosis (6.71 min) times. We propose that macrophage cell-to-cell transfer represents a non-lytic exocytosis event followed by phagocytosis into a macrophage that is in close proximity and name this process Dragotcytosis (Dragot is a Greek surname meaning ‘Sentinel’) as it represents sharing of a microbe between two sentinel cells of the innate immune system.
Microarrays were used to assess whether incubation of Bone Marrow-derived macrophages (BMDMs) with receptor blocking antibodies had an effect on their transcriptional profiles.

overall_design: BMDMs incubated with or without the Fc receptor blocking antibody were processed in triplicate for each condition.

first: Quigly

last: Dragotakes

first: Man

last: Fu

first: Arturo

last: Casadevall


title: mRNA transcription profile of potato (Solanum tuberosum L.) exposed to ultrasound during different stages of in vitro plantlet development

city: Martonvásár

first: Norbert

middle: Tibor

last: Hidvégi

address: Brunszvik street 2.

department: Department of Biological Resources

country: Hungary

institute: HUN-REN Centre for Agricultural Research Agricultural Institute

summary: Ultrasound (US) can influence plant growth and development. To better understand the genetic mechanism underlying the physiological response of potato to US, single-node segments of four-week-old in vitro plantlets were subjected to US at 35 kHz for 20 min. Following mRNA purification, 10 cDNA libraries were assessed by RNA-seq and significantly differentially expressed genes (DEGs) were categorized by gene ontology (GO) or Kyoto Encyclopedia of Genes and Genomes (KEGG) identifiers. The expression intensity of 40,430 genes from a total pool of 45,112 genes were studied. From these, several hundred genes associated with biosynthesis, carbohydrate metabolism and catabolism, cellular protein modification, and response to stress, and expressed mainly in the extracellular region, nucleus, and plasma membrane, were either up- or down-regulated in response to US. This study examines how some processes evolved over time (0 h, 24 h, 48 h, 1 week and 4 weeks) after an abiotic stress (US) was imposed on in vitro potato explants, and provides important clues to the temporal dynamics in enzyme and DEG profiles in response to this stress as the explant becomes established in vitro. Despite this abiotic stress, plantlets survived.

overall_design: mRNA transcription profile of potato (Solanum tuberosum L.) under US stress conditions.

first: Judit

last: Dobránszki

first: Andrea

last: Gulyás

first: Jaime

middle: A

last: Teixeira da Silva


title: CUT&Tag for efficient epigenomic profiling of small samples and single cells

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Many chromatin features play critical roles in regulating gene expression. A complete understanding of gene regulation will require the mapping of specific chromatin features in small samples of cells at high resolution. Here we describe Cleavage Under Targets and Tagmentation (CUT&Tag), an enzyme-tethering strategy that provides efficient high-resolution sequencing libraries for profiling diverse chromatin components. In CUT&Tag, a chromatin protein is bound in situ by a specific antibody, which then tethers a proteinA-Tn5 transposase fusion protein. Activation of the transposase efficiently generates fragment libraries with high resolution and exceptionally low background. All steps from live cells to sequencing-ready libraries can be performed in a single tube on the benchtop or a microwell in a high-throughput pipeline, and the entire procedure can be performed in one day. We demonstrate the utility of CUT&Tag by profiling histone modifications, RNA Polymerase II and transcription factors on low cell numbers and single cells.

overall_design: CUT&Tag followed by Illumina sequencing

first: Hatice

last: Kaya-Okur

first: Steven

last: Wu

first: Erica

last: Pledger

first: Kami

last: Ahmad


title: Changes in the maize (B73) 1-cm primary root growth zone transcriptome induced by mild (-0.03 MPa) or severe water-deficit stress (-1.6 MPa)

city: Columbia

first: Melvin

middle: John

last: Oliver

state: Missouri

address: 206 Curtis Hall

department: Plant Genetics Unit

institute: USDA-ARs

summary: Transcriptome sequencing (RNA-seq) was used to profile genome-wide transcript abundance in the primary root growth zone (PRGZ) of maize seedlings grown in different water deficit treatments: well-watered (-0.02 MPa), mild water deficit stress (-0.3 MPa), or severe water deficit stress (-1.6 MPa). For each water deficit treatment, the PRGZ transcriptome was profiled at 26 hours after initiation of the water deficit treatment. By comparing the abundance of each transcript under mild or severe water deficit stress relative to its abundance under well-watered conditions, we identified transcripts that are differentially regulated in the PRGZ in response to the two levels of water deficit stress.

overall_design: For each of the three treatments (well-watered, mild water deficit, and severe water deficit), three biological replicates consisting of 5 x 1-cm primary root growth zone segments of maize seedlings were examined by RNA-seq.

first: Candace

last: Seeve


title: U373MG edaravone and carnosic acid

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: We investigated the gene expression profiles of U373MG human astrocytoma cells treated with vehicle (DMSO) or edaravone or carnosic acid) or both edaravone and carnosic acid. Edaravone is a free radical scavenger sold as radicut. Carnosic acid is a phytochemical found in rosemary and sage.

overall_design: U373MG cells cultured in DMEM-3% FBS were administrated with 1 mM edaravone or 50 microM carnosic acid for 24 h, then the cells were harvested for RNA preparation.

first: J

last: Mimura

first: K

last: Itoh


title: Next Generation Sequencing analysis atg5 gene expression in zebrafish model

city: beijing

first: zhanying

last: hu

address: 1# tiantanxili, dongcheng district

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College

summary:
Purpose: study of function of ATG5 protein on zebrafish larvae development
Methods: Using morpholino oligos for atg5 gene knock down and overexpression, injected into one- to four-cell-stage embryos,extracted total RNA, then sending to RNA sequencing.
Results: we compared to Wildtype, 5MO and atg5 mRNA groups, we analyza autophagy related gene mRNA expression, there are obvious different.
Conclusion: our study showed the function of autophagy related gene 5 on zebrafish larvae, it has an important significant for understanding the affection of autophagy on embryo development

first: Zhanying

last: Hu


title: Transcriptional response of HT-29 intestinal epithelial cells to bovine glycomacropeptide.

city: Fermoy

first: Rita

last: Hickey

state: County Cork

address: Moorepark

department: Food Bioscience

country: Ireland

institute: Teagasc Food Research Centre

summary: We have employed whole genome microarray analysis to determine the transcriptional response of intestinal epithelial cells following treatment with bovine glycomacropeptide (GMP)

overall_design: HT-29 intestinal epithelial cells were exposed to  glycomacropeptide for 24 hours after which the cells were harvested for RNA extraction. Three independent biological replicates were performed for each exposure.

first: Shane

last: Feeney

first: John

last: O'Callaghan

first: Michelle

last: Kilcoyne

first: Lokesh

last: Joshi

middle: M


title: Transcriptional profiling of the cardiac left ventricle during pregnancy and the early post-partum period

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: Comparative analysis was done to identify genes and pathways affected in the heart left ventricle during different stages of pregnancy. Microarray profiling was done on nonpregnant, pregnant, and early post-partum mice, with diestrus females serving as reference.

overall_design: Two replicates of each type of sample were analyzed (n=2). The diestrus sample serves as reference for three pregnancy-related states (pregnant day 12, pregnant day 19, and post-partum day 1.5).

first: Holly

last: LaVoie


title: Analysis of NR4A-specific gene expression in human alveolar rhabdomyosarcoma in response to specific gene knockdown

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: By knocking down the three NR4A family members in single, double, or triple combinations and comparing the gene expression profiles, putative targets that are specific or shared among the NR4A members have been identified

overall_design: Gene expression in Rh30 rhabdomyosarcoma cells transfected with non-targeting siRNA or siRNA pools specific for each NR4A family member have been compared, in triplicate

first: Jordan

last: Beard

first: Taosheng

last: Chen


title: Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. (ATAC-seq)

city: Nijmegen

first: Hendrik

middle: G

last: Stunnenberg

address: Geert Grooteplein 30

country: Netherlands

institute: Radboud University

summary: The mechanisms underlying enhancer activation and the extent to which enhancer-promoter rewiring contributes to spatiotemporal gene expression are not well understood. Using integrative and time resolved analyses we show that the extensive transcriptome and epigenome resetting during the conversion between ‘serum-’ and ‘2i’-states of mouse embryonic stem cells (ESCs) takes place with minimal enhancer-promoter rewiring that becomes more evident in primed-state pluripotency. Instead, differential gene expression is strongly linked to enhancer activation via H3K27ac. Conditional depletion of TFs and allele-specific enhancer analysis reveals an essential role for Esrrb in H3K27-acetylation and activation of 2i-specific enhancers. Restoration of a polymorphic ESRRB motif using CRISPR/Cas9 in a hybrid ESC-line, restores ESRRB binding and enhancer H3K27ac in an allele-specific manner but has no effect on chromatin interactions. Our study shows that enhancer activation in serum- and 2i-ESCs is largely driven by TF-binding and epigenetic marking in a hardwired network of chromatin interactions.

overall_design: Time course analysis of mouse ESCs during transition between serum and 2i-cultured ESCs followed by integrative analysis of chromatin accessibility by ATAC-seq.


title: Genome-wide characterization of BCL6/STAT5-switch target genes identifies reprogramming of DNA damage response as a novel branch of RAC1/PAK1 signalling

city: Lisbon

first: Andreia

middle: Jesus

last: Amaral

state: Estremadura

address: Camp Grande

department: Gene Expression and Bioinformatics Unit

country: Portugal

institute: Center for Biosystems, Integrative and Functional Genomics

summary: The RAC1 GTPase and its effector PAK1 have been found to be overexpressed or hyperactivated in colorectal cancer (CRC), one of the most prevalent types of cancer in the world. This overexpression frequently correlates with chemoresistance and less favourable prognoses. We previously showed that the activation of RAC1/PAK1 signalling promotes a switch between the BCL6 transcriptional repressor and the STAT5 transcriptional activator at a subset of pro-proliferative gene promoters. Here we used ChIP-Seq, under conditions of pathway inhibition and stimulation, to identify the BCL6/STAT5-switch binding sites throughout the genome. Using a knowledge-driven pipeline for ChIP-Seq data analysis, we identify 3774 genomic features associated to the switch-motif, with a significant enrichment in protein-coding genes involved in DNA damage repair pathways. Stimulation of RAC1/PAK1 signalling in DLD-1 CRC cells increased the expression of these genes and significantly enhanced DNA repair in response to damage induced by alkylating agents. Our results reveal a new transcriptional reprogramming mechanism whereby the alternate binding of a repressor and an activator protein to low-affinity motifs is used to coordinate a transcriptional  response to DNA damage. This mechanism may link the upregulation of the RAC1/PAK1 pathway  to the chemoresistant phenotype of aggressive CRCs.

overall_design: Examination of Chip-seq binding sites in STAT5 and BCL6 transcription factors, activated STAT5, activated BCL6, inhibited STAT5, inhibited BCL6

first: A

first: P

last: Matos


title: Wnt5a and its downstream transcription factor Stat3 are therapeutic targets for diffuse intrinsic pontine gliomas

status: Public on Apr 29 2019

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

country: USA

institute: Columbia University

summary: Understand how Wnt5a depletion affects the growth of diffuse intrinsic pontine gliomas

overall_design: SF7761 and SF8628 cells are H3.3K27M mutant diffuse intrinsic pontine glioma cells, SF9427 is glioblastomas with wild type histone H3. Every cell line was treated with None-target control shRNA, two shRNAs against Wnt5a

first: Dong

last: Fang

first: Haiyun

last: Gan

first: Liang

last: Zhang

first: Tatiana

last: Kaptzan

first: Xiaoyue

first: Xu

last: Hua

first: Hui

last: Zhou

first: David

last: Daniels

first: Zhiguo


title: Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. (4C-seq)

overall_design: Time course analysis of mouse ESCs during transition between serum and 2i-cultured ESCs followed by integrative analysis of transcriptome, epigenome and 3D-chromatin organization


title: Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. (RNA-seq)

overall_design: Time course analysis of mouse ESCs during transition between serum and 2i-cultured ESCs followed by integrative analysis of transcriptome by RNA-seq.


title: Gene expression of blood and cerebellum of Mecp2-null and WT male mice

city: Dublin

first: Albert

last: Sanfeliu

address: Trinity Translational Medicine Institute, St James's Hospital, James's Street

department: Psychiatry

institute: Trinity College Dublin

summary: In order to find a relationship between gene expression of blood and brain in Rett Syndrome (RTT), we performed RNA sequencing on from cerebella and blood of 7 week-old male Mecp2-null mice (a model of RTT) and WT controls.

overall_design: Transcriptional profiles were generated from cerebellum and blood of 3 Mecp2-null and 3 WT 7 week-old male mice, by RNAseq performed on an Illumina HiSeq 2000 System, generating approximately 60 million 2x75bp paired-end reads/sample. Blood and cerebellum samples originate from the same animal

first: Karsten

last: Hokamp

first: Daniela

last: Tropea

first: Michael

last: Gill


title: Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate [Baf60c_RNA-seq]

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Generation of widely differing and specialized cell types from a single totipotent zygote involves large-scale transcriptional changes and chromatin reorganization. Pioneer transcription factors play key roles in programming the epigenome and facilitating recruitment of additional regulatory factors during successive cell lineage specification and differentiation steps. Here we show that Isl1 acts as a pioneer factor driving cardiomyocyte lineage commitment by shaping the chromatin landscape of cardiac progenitor cells. Using an Isl1 hypomorphic mouse line which shows congenital heart defects, genome-wide profiling of Isl1 binding together with RNA- and ATAC-sequencing of cardiac progenitor cells and their derivatives, we uncover a regulatory network downstream of Isl1 that orchestrates cardiogenesis. Mechanistically, we show that Isl1 binds to compacted chromatin and works in concert with the Brg1-Baf60c-based SWI/SNF complex to promote permissive cardiac lineage-specific alterations in the chromatin landscape not only of genes with critical functions in cardiac progenitor cells, but also of cardiomyocyte structural genes that are highly expressed when Isl1 itself is no longer present. Thus, the Isl1/Brg1-Baf60c complex plays a crucial role in orchestrating proper cardiogenesis and in establishing epigenetic memory of cardiomyocyte fate commitment

overall_design: Nkx2.5GFP reporter ES cell line stably transfected with Baf60cSh constructs were generated. Baf60c knockdown ES cell lines were differentiated into cardiovascular progenitors. Genomewide RNA-seq profiles were generated.

first: Julio

last: Cordero

first: Rui

last: Gao


title: Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency.

first: Hendrik

last: Stunnenberg

summary:
The mechanisms underlying enhancer activation and the extent to which enhancer-promoter rewiring contributes to spatiotemporal gene expression are not well understood. Using integrative and time resolved analyses we show that the extensive transcriptome and epigenome resetting during the conversion between ‘serum-’ and ‘2i’-states of mouse embryonic stem cells (ESCs) takes place with minimal enhancer-promoter rewiring that becomes more evident in primed-state pluripotency. Instead, differential gene expression is strongly linked to enhancer activation via H3K27ac. Conditional depletion of TFs and allele-specific enhancer analysis reveals an essential role for Esrrb in H3K27-acetylation and activation of 2i-specific enhancers. Restoration of a polymorphic ESRRB motif using CRISPR/Cas9 in a hybrid ESC-line, restores ESRRB binding and enhancer H3K27ac in an allele-specific manner but has no effect on chromatin interactions. Our study shows that enhancer activation in serum- and 2i-ESCs is largely driven by TF-binding and epigenetic marking in a hardwired network of chromatin interactions.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate

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


title: Characterization and comparative analyses of transcriptomes of cloned and in vivo fertilized porcine pre-implantation embryos

city: Guangzhou

first: Xiaoyan

last: He

address: No.483 Wushan Road, Tianhe District

country: China

institute: South China Agricultural University

summary: By using RNA-Seq technology, we get genome-wide transcriptome profiles of cloned and in vivo fertilized porcine embryos, from the oocyte to the blastocyst stages. We identified differentially expressed genes between the cloned and in vivo fertilized embryos from distinct stages of development and uncovered associated cellular signaling pathways and upstream transcription factors.

overall_design: We get transcriptome of  cloned and in vivo fertilized porcine embryos in seven consecutive points in time. Our findings provided a valuable resource for further discovery of the epigenetic reprogramming mechanisms in pig embryos.


title: Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. (ChIP-seq)

overall_design: ChIP-seq analysis of H3K27ac, ESRRB, GFP, CTCF, YY1, SMC1 in E14- or F1-ESCs cultured in 2i, serum or EpiLSC medium. ChIP-seq analysis for H3K27ac in Tamoxifen inducible Nr5a2 or Esrrb- KO ESCs.


title: The landscape of global-long range interactions in mouse and human blood cell lines mediated by Yy1, GATA1, and CTCF during differentiation

city: Minneapolis

first: Marissa

last: Macchietto

address: 117 Pleasant Street SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota, Minneapolis

summary: Abstract: A network of interactions between functional DNA elements regulates gene expression in a precise spatio-temporal pattern during development.  This regulation is implemented through many-to-many looping interactions of DNA elements mediated by specific transcription factors such as Ctcf, Gata1 and Yy1. We carried out RNA polymerase II ChIA-PET and DNase-seq in Mouse Erythroleukemia (MEL) cells to capture genomewide changes in the resulting chromatin interaction graphs (CIGs) during DMSO-induced hemoglobin activation.  We found that the change of interactions in CIGs is positively correlated to the change of a corresponding genes’ expression as measured by RNA-seq. DNase footprints and ChIP-seq data indicate that these long-range interactions are controlled through distinct combinations of transcription factors before and after differentiation, with Ctcf or cohesin only mediating half of these interactions, and Gata1 and/or Yy1 interactions accounting for an additional 40% of detected interactions. Strikingly, while  Ctcf and Gata1–mediated interactions were enriched in genes involved in erythrocyte differentiation and mitochondrial regulation, Yy1-mediated interactions were enriched for genes involved in RNA processing, translation, and histone remodeling.  We further found that about two-thirds of MEL DNA elements with long-range interactions as well 35% of these interactions are conserved in human K562 cells and show similar combinations of factor occupancy.   Taken together, our study identifies that a large set of long-range interactions between active enhancers and promoters involving RNA Pol II are mediated by factors other than cohesin and Ctcf in both human and mouse.

overall_design:
PU.1 ChIP-Seq, RNA-Seq, DNase-Seq, ChIA-PET
The 'MEL_foot_1kb_DHS_cohesin_pol2_peak_blacklistfiltered.bed contains the locations and names of the 1kb vertices used to characterize and quantitate the long-range interaction edges between vertices from the ChIA-PET data.
It was generated from the hotspot bed file of MEL DNase-seq data. After incorporating anti-pol2 and cohesin ChIP-seq peaks from ENCODE consortium, the merged DNase-seq hotspots and ChIP-seq peaks were expanded to 1kb in order to make the 1kb vertices.

first: Weihua

last: Zeng

first: Ricardo

last: Ramirez

first: Camden

last: Jansen

first: Shan

last: Jiang

first: Ana

last: Conesa

first: Ali

last: Mortazavi


title: LNK suppresses interferon signaling in melanoma

first: SIQIN

last: ZHOU

address: 14 Medical Drive

institute: Cancer Science Institute of Singapore

summary: LNK (SH2B3) is a key negative regulator of JAK-STAT signaling which has been extensively studied in malignant hematopoietic diseases. We found that LNK is significantly elevated in cutaneous melanoma; this elevation is correlated with hyperactive signaling of the RAS-RAF-MEK pathway. Elevated LNK enhances cell growth and survival in adverse conditions. Forced expression of LNK inhibits signaling by interferon-STAT1 and suppresses interferon (IFN) induced cell cycle arrest and cell apoptosis. In contrast, silencing LNK expression by either shRNA or CRISPR-Cas9 potentiates the killing effect of IFN. The IFN-LNK signaling is tightly regulated by a negative feedback mechanism; melanoma cells exposed to IFN upregulate expression of LNK to prevent overactivation of this signaling pathway. Our study reveals an unappreciated function of LNK in melanoma and highlights the critical role of the IFN-STAT1-LNK signaling axis in this potentially devastating disease. LNK may be further explored as a potential therapeutic target for melanoma immunotherapy.

overall_design: mRNA profiles of Control and LNK knockdown (by CRISPR-Cas9, sgLNK-1, sgLNK-2) were generated by deep sequencing using BGISEQ-500.

first: Ling-Wen

last: Ding

first: Qiao-Yang

last: Sun

first: Jarem

last: Edwards

first: Lucia

last: Torres Fernández

first: Xue-Bin

last: Ran

first: Si-Qin

last: Zhou

first: Richard

last: Scolyer

first: James

last: Wilmott

first: John

middle: F

last: Thompson

first: Ngan

last: Doan

first: Jonathan

middle: W

last: Said

first: Nachiyappan

last: Venkatachalam

first: Jin-Fen

last: Xiao

first: Xin-Yi

last: Loh

first: Maren

last: Pein

first: Liang

last: Xu

first: David

last: Mullins

first: Henry

last: Yang

first: De-Chen

last: Lin

first: H

last: Koeffler


title: CHD4 is essential for transcriptional repression and lineage progression in B lymphopoiesis

city: Denver

middle: R

last: Hagman

state: Colorado

address: 1400 Jackson St

department: Biomedical Research

institute: National Jewish Health


title: Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate [CPC_ATAC-seq]

first: Gergana

last: Dobreva

overall_design: Genome wide ATAC-sequencing profiles in cardiac progenitors derived from control and Isl1 knockdown.

first: Julio

last: Cordero

first: Rui

last: Gao


title: Tbet regulates the accessible chromatin of Be1 B cells

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To investigate the role of Tbet in B cell differentiation to "effector-like" antibody secreting cells (ASC's) we utilized an ex vivo culture system to differentiate B cells in the presence of Th1 (Be1) or Th2 (Be2) polarized T cells. To determine the role of Tbet in Be1 cell differentiation we performed ATAC-seq on Wt Be1 and Tbet negative (TbetNeg) Be1 cells and Wt Be2 and Tbet negative (TbetNeg) Be2 cells.  Collectively, these data show that T-bet serves as master regulator for the Be1 cell fate and is required to program chromatin accessibility during ASC differentiation in Be1 cells.

overall_design: ATAC-seq on wild-type Be1 and Be2 and Tbet-deficient Be1 and Be2 B cells at day 2 of ex vivo differentiation.

first: C

middle: D

first: F

middle: E

last: Lund

first: S

middle: L

last: Stone

first: B

last: Mousseau

first: J

last: Boss


title: CUT&Tag for efficient epigenomic profiling of small samples and single cells (908 single cells)

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

institute: Fred Hutchinson Cancer Research Center

summary: Many chromatin features play critical roles in regulating gene expression. A complete understanding of gene regulation will require the mapping of specific chromatin features in small samples of cells at high resolution. Here we describe Cleavage Under Targets and Tagmentation (CUT&Tag), an enzyme-tethering strategy that provides efficient high-resolution sequencing libraries for profiling diverse chromatin components. In CUT&Tag, a chromatin protein is bound in situ by a specific antibody, which then tethers a proteinA-Tn5 transposase fusion protein. Activation of the transposase efficiently generates fragment libraries with high resolution and exceptionally low background. All steps from live cells to sequencing-ready libraries can be performed in a single tube on the benchtop or a microwell in a high-throughput pipeline, and the entire procedure can be performed in one day. We demonstrate the utility of CUT&Tag by profiling histone modifications, RNA Polymerase II and transcription factors on low cell numbers and single cells.

overall_design: Single-cell CUT&Tag using ICELL8 platform followed by Illumina sequencing. 908 samples of H3K27me3 in K562 cells.

first: Hatice

last: Kaya-Okur

first: Steven

middle: J

last: Wu

first: Erica

last: Pledger

first: Kami

last: Ahmad


title: L-lactate induces specific genome wide alterations of gene expression in cultured bovine granulosa cells

city: Dummerstorf

first: Jens

last: Vanselow

address: Wilhelm-Stahl-Allee 2

department: Reproductive Biology

institute: Leibniz Institute for Farm Animal Biology

summary:
Background:
Previously, we could show that L-lactate affects cultured bovine granulosa cells (GC) in a specific manner driving the cells into an early pre-ovulatory phenotype. Here we studied genome wide effects in L-lactatetreated GC to further elucidate the underlying mechanisms that are responsible for the L-lactate induced transformation. Cultured estrogen producing GC treated either with L-lactate or vehicle control were subjected to mRNA microarray analysis.
Results:
The analysis revealed 487 differentially expressed clusters, representing 461 annotated genes. Of these, 333 (= 318 genes) were identified as up- and 154 (= 143 genes) as down-regulated. As the top up-regulated genes we detected TXNIP, H19 and AHSG as well as our previously established marker transcripts RGS2 and PTX3. The top down-regulated genes included VNN1, SLC27A2 and GFRA1, but also MYC and the GC marker transcript CYP19A1. Pathway analysis with differentially expressed genes indicated “cAMP-mediated signaling” and “Axon guidance signaling” among the most affected pathways. Furthermore, estradiol, progesterone and Vegf were identified as
potential upstream regulators. An effector network analysis by IPA provided first hints that processes of “angiogenesis” and “vascularization”, but also “cell movement” appeared to be activated, whereas “organismal death” was predicted to be inhibited.
Conclusions:
Our data clearly show that L-lactate alters gene expression in cultured bovine GC in a broad, but obviously specific manner. Pathway analysis revealed that the mode of L-lactate action in GC initiates angiogenic processes, but also migratory events like cell movement and axonal guidance signaling, thus supporting the transformation of GC into an early luteal phenotype.

overall_design: Bovine granulosa cells were aspirated from small to medium sized follicles (<6mm), cultered under FSH and IGF-1 stimulation under serum free conditions to induce estradiol production and were treated with L-lactate, NaCl as vehicle control or left untreated.  After 8 days in culture RNA was isolated and subjected to mRNA microarray analysis using Bovine Gene 1.0 ST Arrays (Affymetrix, St. Clara, CA, USA).

first: Anja

last: Baufeld

first: Dirk

last: Koczan


title: CUT&Tag for efficient epigenomic profiling of small samples and single cells (807 single cells)

city: Seattle

overall_design: Single-cell CUT&Tag using ICELL8 platform followed by Illumina sequencing. 393 (replicate 1) and 414 (replicate 2) samples of H3K4me2 in K562 cells.


title: Gene expression in oligodendrocytes during remyelination reveals cholesterol homeostasis as a therapeutic target in multiple sclerosis.

city: Los Angeles

first: Yuichiro

last: Itoh

state: California

address: 635 Charles E. Young Drive South

department: Neurology

institute: UCLA

summary: Regional differences in neurons, astrocytes, oligodendrocytes, and microglia exist in the brain during health, and regional differences in the transcriptome may occur for each cell type during neurodegeneration. Multiple sclerosis (MS) is multifocal, and regional differences in the astrocyte transcriptome occur in experimental autoimmune encephalomyelitis (EAE), an MS model. MS and EAE are characterized by inflammation, demyelination, and axonal damage, with minimal remyelination. Here, RNA-sequencing analysis of MS tissues from six brain regions suggested a focus on oligodendrocyte lineage cells (OLCs) in corpus callosum. Olig1-RiboTag mice were used to determine the translatome of OLCs in vivo in corpus callosum during the remyelination phase of a chronic cuprizone model with axonal damage. Cholesterol-synthesis gene pathways dominated as the top up-regulated pathways in OLCs during remyelination. In EAE, remyelination was induced with estrogen receptor-β (ERβ) ligand treatment, and up-regulation of cholesterol-synthesis gene expression was again observed in OLCs. ERβ-ligand treatment in the cuprizone model further increased cholesterol synthesis gene expression and enhanced remyelination. Conditional KOs of ERβ in OLCs demonstrated that increased cholesterol-synthesis gene expression in OLCs was mediated by direct effects in both models. To address this direct effect, ChIP assays showed binding of ERβ to the putative estrogen-response element of a key cholesterol-synthesis gene (Fdps). As fetal OLCs are exposed in utero to high levels of estrogens in maternal blood, we discuss how remyelinating properties of estrogen treatment in adults during injury may recapitulate normal developmental myelination through targeting cholesterol homeostasis in OLCs.

overall_design: The mice expressing HA-tagged ribosomal protein RPL22 in oligodendrocytes were generated by crossing RiboTag mice with Olig1-Cre mice. Oligodendrocyte specific RNA was isolated as the co-immunoprecipitation with anti-HA antibody.


title: Expression data of murine capillary endothelial cells after MICAL2 gene knock-down by means of shRNA-expressing lentiviral vectors.

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

summary:
Molecules interacting with CasL 2 (MICAL2) belongs to a three-member family of multi-domain flavoprotein monooxygenase enzymes that catalyze actin oxidation-reduction reactions destabilizing F-actin in cytoskeletal dynamics. MICAL2 is over-expressed, being a negative prognostic factor, in aggressive gastric, kidney, prostate, bladder, breast and endometrial human cancer. MICAL2 is expressed in cancer-associated neo-angiogenic capillaries. The study of MICAL2 knock-down in endothelial cells shed light on the transcriptional impact of the gene on endothelial cell biology.
To explore the transcriptional impact of the lack of Mical2 in endothelial cells, we performed genome-wide expression profiling of Mical2 knock-down SVEC4-10 (ATTC CRL-2181) cells (M2KD). Reference cells were: Mical3 knock-down (M3KD), obtained with same strategy; untreated SVEC4-10 cells ((WT), and cells transduced with insert-free viral vector (empty).

overall_design: Gene expression profiling was performed to identify transcripts modulated by the absence of the F-actin modifying redox enzyme MICAL2 that affects the pro-angiogenic and therefore pro-cancer  activity of endothelial cells.

first: Debora

last: Angeloni

first: Enrico

last: Tagliafico


title: CUT&Tag for efficient epigenomic profiling of small samples and single cells (965 single cells)

overall_design: Single-cell CUT&Tag using ICELL8 platform followed by Illumina sequencing.  H3K27me3 in 486 H1 cells and 479 K562 cells.