title: Mettl3-mediated mRNA m6A methylation promotes dendritic cell activation

city: Beijing, China

first: Huamin

last: Wang

address: Three N0. 5 dongdan street, Dongcheng District, Beijing

department: Department of Immunology

institute: Peking Union Medical College, Chinese Academy of Medical Sciences,


title: Extracellular matrix (ECM) stiffness and collagen-1 (col-1) responsive genes in 3D cultured mammary epithelial cells

status: Public on Mar 25 2019

city: Stanford

first: Jessica

middle: Kay

last: Chang

state: CA

address: 300 Pasteur Drive, Alway Building M311

department: Genetics

country: USA

institute: Stanford University

type: Expression profiling by high throughput sequencing

summary: We report the expression profiles of MCF10A cells encapsulated in hydrogels of varying stiffness and composition. Cells were encapsulated for 7 days in either 1.) soft alginate and reconstituted basement membrane (rBM), 2.) stiff alginate and rBM, 3,) soft col-1 and rBM, or 4.) stiff col-1. We find global gene expression changes in response to enhanced ECM stiffness, independent of expression changes in response to col-1 exposure. These results provide a comprehensive study of the gene expression changes associated with increased ECM stiffness in addition to the gene expression changes associated with increased col-1 concentration in combination with, and independent of, ECM stiffness.

overall_design: Expression profiling of MCF10A cells in four hydrogel conditions were sequenced in duplicate via Illumina HiSeq.

first: Joanna

middle: Y

last: Lee

first: Ovijit

last: Chaudhuri


title: Nuclear miCLIP and Nuclear NKAP iCLIP

status: Public on Mar 24 2019

city: Guangzhou

first: Liang

middle: Jia

last: Zhang

address: 651 Dongfeng Road East, Yuexiu District,

country: China

institute: SYSUCC

summary: To identify m6A sites on endogenous nuclear RNAs, we performed miCLIP to identify m6A sites in PANC-1 cells. To identify NKAP binding sites on endogenous nuclear RNAs, we performed iCLIP for flag-tag NKAP to analyze the nuclear RNA binding with NKAP in the same cells.

overall_design: PRJNA477937;SRP151346;PANC-1 cells overexpressing FLAG-tag NKAP were subjected to the iCLIP procedure on immunoprecipitated NKAP associated RNA obtained from the nuclear fraction (Licatalosi D, et al. 2008, Nature 456:464-U22).

first: Jialiang

first: Ying

last: Ye

first: DongXin

last: Lin


title: Genetic disarray follows mutant KLF1-E325K expression in a congenital dyserythropoietic anemia patient

status: Public on Mar 23 2019

city: New York

first: James

middle: J

last: Bieker

state: NY

address: One Gustave Levy Place

department: Cell, Developmental, and Regenerative Biology

institute: Mount Sinai School of Medicine

summary: Congenital dyserythropoietic anemia (CDA) type IV is caused by a heterozygous mutation, Glu325Lys (E325K), in the KLF1 transcription factor. A molecular understanding of this disease is absent, partly due to its rarity. We expanded erythroid cells from a patient’s peripheral blood and analyzed its global expression pattern. We find that a large number of erythroid pathways are disrupted, particularly those related to membrane transport, globin regulation, and iron utilization. The altered genetics lead to significant deficits in differentiation. Glu325 is within the KLF1 zinc finger domain at an amino acid critical for site specific DNA binding. The change to Lys is predicted to significantly alter the target site recognition sequence, both by subverting normal recognition and by enabling interaction with novel sites. Consistent with this, we find high level ectopic expression of genes not normally present in the red cell. These altered properties explain the patients’ clinical and phenotypic features and elucidate the dominant character of the mutation.

overall_design: Samples from one patient and one healthy individual; each analyzed at three different time points of erythroid expansion/differentiation

first: Antanas

last: Planutis


title: Deciphering the role of ancient genome fossils in mammalian development

status: Public on Mar 21 2019

city: South San Francisco

first: Rohit

last: Reja

address: 1 DNA Way

institute: Genentech

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Peg10 regulation of TSC differentiation

status: Public on Mar 22 2019

summary:
The prevailing dogma that approximately 50% of our genome is “junk” DNA composed of transposable elements and retroviral insertions has recently been challenged. It has become evident that our genome has taken advantage of these transposable elements and uses them as a source of DNA to generate novel genes, which subsequently allow the organism to evolve. This process is termed “domestication of transposable elements” and the majority of these genes have been found to be essential for the existence of the organism.
One of these developmentally essential domesticated genes: Peg10 (paternally expressed gene 10), was derived from a Ty3/gyspy LTR retrotransposon, yet lost its ability to transpose due to mutational events during its domestication. Remarkably, Peg10 has successfully maintained its Gag and Pol-like domains for millions of years.
Peg10 orthologues are expressed in eutherian mammals and are essential for placentogenesis. To address the functional mechanisms of Peg10 we studied it in Trophoblast Stem Cells (TSCs). We find that the Gag of Peg10 is fully active: it promotes budding of vesicles, akin to the viral counterpart that catalyzes the budding of viruses. TSCs, deleted for Peg10, fail to differentiate into placental lineages, underscoring a critical role in lineage specification. This paper discusses our efforts to characterize the contents of Peg10 vesicles and whether such vesicles regulate lineage specification.

overall_design: RNA was extracted from following genotypes - wildtype TSCs (WT_TSC), Peg10 knockout TSCs (KO_TSC), wildtype TSCs differentiated in 20% oxygen (WT_TSC_diff), Peg10 knockout TSCs differentiated in 20% oxygen (KO_TSC_diff),  wildtype TSCs differentiated in 2% oxygen (WT_diff_2O2),and Peg10 knockout TSCs differentiated in 2% oxygen (KO_diff_2O2). Cells are kept in the pluripotent state by growing them on CellStart/Fgf4/Heparin. The cells were differentiated in two different conditions: 20% oxygen and 2% oxygen. The samples were collected at 10th day following differentiation. Cells are harvested and RNA is isolated using the Qiagen RNeasy kit. RT-PCR was performed for several differentiation markers to validate the success of the assay.

first: R


title: Peripheral and systemic antigens elicit an expandable pool of resident memory CD8+ T cells in the bone marrow

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

country: Netherlands

institute: Sanquin

summary: Bone marrow (BM) has been put forward as a major reservoir for memory CD8+  T cells. In order to fulfill that function, BM should "store" memory CD8+ T cells, which in biological terms would require these "stored" memory cells to be in disequilibrium with the circulatory pool. This issue is a matter of ongoing debate. Here, we unequivocally demonstrate that murine and human BM harbors a population of tissue-resident memory CD8+ T (TRM ) cells. These cells develop against various pathogens, independently of BM infection or local antigen recognition. BM CD8+ TRM cells share a transcriptional program with resident lymphoid cells in other tissues; they are poly-functional cytokine producers and dependent on IL-15, Blimp-1 and Hobit. CD8+ TRM cells reside in the BM parenchyma, but are in close contact with the circulation. Moreover, this pool of resident T cells is not size-restricted and expands upon peripheral antigenic re-challenge. This works extends the role of the BM in the maintenance of CD8+ T cell memory to include the preservation of an expandable reservoir of functional, non-recirculating memory CD8+ T cells, which develop in response to a large variety of peripheral antigens. This article is protected by copyright. All rights reserved.

overall_design: In total 3 sorts were done, and for each sort the 8 T cell populations were isolated from a pool of 6 mice. The quality of the RNA sample of RM T cells of sort 4 was poor and therefore removed from analysis.

first: M

middle: F

last: Pascutti

first: S

last: Geerman

first: B

middle: A

last: Nolte


title: Bap1 and RNF2 ChIP-seq in mES cells

status: Public on Mar 26 2019

summary: Malignancies arising from mutation of tumor suppressor genes display an unexplained tissue  proclivity. For example, tumor suppressor BAP1 encodes a ubiquitously expressed deubiquitinase  for histone H2A but germline mutations predominantly cause uveal melanomas and  mesotheliomas. We show that BAP1 inactivation causes apoptosis in mouse embryonic stem cells,  fibroblasts, liver and pancreas, whereas melanocytes and mesothelial cells remain viable. E3 ligase  RNF2, which silences genes by monoubiquitinating H2A, promoted apoptosis in BAP1-deficient  cells by suppressing the pro-survival genes Bcl-2 and Mcl-1. Our data argue that BAP1 modulates  gene expression by countering H2A ubiquitination, but its loss only promotes tumorigenesis in  cells that do not engage an RNF2-dependent apoptotic program. We propose that intolerance of  BAP1 loss, and perhaps the loss of other tumor suppressors, restricts the mutant tumor spectrum.

overall_design: ChIP-seq was performed on the following genotypes: BAP1-C91A mutant, BAP1-FLAG tag, BAP1 ChIP in BAP1 knock out, RNF2 wildtype, RNF2 ChIP in RNF2 knock out background, and RNF2 ChIP in BAP1 knock out background. Each experiement includes a corresponding input sample.

last: He


title: Leukodystrophy-associated POLR3A mutations down-regulate the RNA polymerase III transcript and important regulatory RNA BC200

status: Public on Mar 20 2019

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

country: Canada

institute: Université de Sherbrooke

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA polymerase III (Pol III) is an essential enzyme responsible for the synthesis of several small non-coding RNAs, a number of which are involved in mRNA translation. Recessive mutations in POLR3A, encoding the largest subunit of Pol III, cause POLR3-related hypomyelinating leukodystrophy (POLR3-HLD), characterized by deficient central nervous system myelination. Identification of the downstream effectors of pathogenic POLR3A mutations has been so far elusive. Here, we used CRISPR-Cas9 to introduce the POLR3A mutation c.2554A>G (p.M852V) into human cell lines and assessed its impact on Pol III biogenesis, nuclear import, DNA occupancy, transcription, and protein levels. Transcriptomic profiling uncovered a subset of transcripts vulnerable to Pol III hypofunction, including a global reduction in tRNA levels. The brain cytoplasmic BC200 RNA (BCYRN1), involved in translation regulation, was consistently affected in all our cellular models, including patient-derived fibroblasts. Genomic BC200 deletion in an oligodendroglial cell line led to major transcriptomic and proteomic changes, having a larger impact than those of POLR3A mutations. Upon differentiation, mRNA levels of the MBP gene, encoding myelin basic protein, were significantly decreased in POLR3A-mutant cells. Our findings provide the first evidence for impaired Pol III transcription in cellular models of POLR3-HLD and identify several candidate effectors, including BC200 RNA, having a potential role in oligodendrocyte biology and involvement in the disease.

overall_design:
Gene expression profiling of Pol III transcripts in control and POLR3A-mutated cell lines (HEK293 and MO3.13) using RNA-seq and small RNA-seq;
ChIP-seq of FLAG-tagged POLR3A-WT and mutated POLR3A-M852V

first: Claudia

last: Kleinman


title: Signal sequences in the viral genome regulate the generation of copy-back defective viral genomes

status: Public on Mar 19 2019

city: St Louis

first: Carolina

middle: B

last: Lopez

state: MO

address: 425 S Euclid Ave

institute: Washington University in St. Louis

summary: We developed VODKA (Viral Opensource DVG Key Algorithm) to identify cbDVGs from RNA-Seq data from infected samples and used these DVG sequences to identify signals that regulate cbDVG generation. We applied VODKA to datasets from RSV-positive patients. VODKA identified common cbDVGs across multiple samples in both patients, and predicted specific genomic loci that mediate cbDVG formation.

overall_design: Total RNA was extracted from 2 RSV positive pediatric samples. RNAs were then used for preparation for the library used in RNA-seq to generate this dataset.

first: Yan

last: Sun


title: LncRNA expression profiling of the early mesoderm reveals LncCPR as a novel regulator of cardiogenesis in mice

city: houston

last: Soibam

address: one main street

institute: university of houston-Downtown

summary: Whole mount in situ hybridization analysis of the 17 lncRNAs revealed that lncRNAs 2410006H16Rik and 4930500J02Rik were expressed in mouse hearts at E9.5. 4930500J02Rik, renamed Long Noncoding Cardiac-promoting RNA (LncCPR), was also enriched in postnatal and adult heart tissue. We hypothesized that the loss of LncCPR expression would directly affect cardiogenesis. To test this hypothesis, we performed functional studies of ESC differentiation after knocking out the LncCPR gene with the CRISPR/Cas9 system. We profiled the transcriptome of mouse ES cells after the loss of LncCPR expression. We found the downregulation of Mesp1 and cardiac transcription factors, as well as a significant reduction in contractility and levels of cardiac structural protein TNNT2. Our findings indicate that LncCPR is a novel, specific regulator of Mesp1, and therefore, of early cardiogenesis.

overall_design: mRNA profiles of control and LncCPR knockout mouse ES cells were generated by Hiseq 2000 at  6 different time points (day 0, 3, 5, 8, 10 and 12) during differentiation

first: Robert

last: Schwartz

first: Ashley

last: Benham


title: In vivo generation of post-infarct human cardiac muscle by laminin-promoted cardiovascular progenitors

city: Singapore

first: Aida

last: Moreno-Moral

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

summary:
This SuperSeries is composed of the SubSeries listed below and contains: bulk RNA-seq of two time series of a xeno-free human cardiomyocyte differentiation protocol starting from HS1001 and H1 hECSs until day 94 cardiomyocytes, single cell sequencing of cardiovascular progenitors (H1 and HS1001-derived cardiovascular progenitors at day 9 and 11) and bulk RNA-Seq of H1 hECSs that have been transferred to a LN-221 matrix.
Regeneration of injured human heart muscle is limited and an unmet clinical need. There are no methods for the reproducible generation of clinical quality stem-cell-derived cardiovascular progenitors (CVPs). We identified laminin-221 (LN-221) as the most likely expressed cardiac laminin. We produced it as human recombinant protein, and showed that LN-221 promotes differentiation of pluripotent hESCs towards cardiomyocyte lineage and downregulates pluripotency and teratoma associated genes. We developed a chemically defined, xeno-free laminin-based differentiation protocol to generate CVPs. We show high reproducibility of the differentiation protocol using time-course bulk RNA sequencing developed from different hESC lines. Single-cell RNA sequencing of CVPs derived from hESC lines supported reproducibility and identified three main progenitor subpopulations. These CVPs were transplanted into myocardial infarction mice, where heart function was measured by echocardiogram and human heart muscle bundle formation was identified histologically. This method may provide clinical quality cells for use in regenerative cardiology.


title: Transcriptome Sequencing and Gene Expression Analysis of Trichophyton mentagrophytes under Different Culture Conditions

city: HANGZHOU

first: Chenwen

last: Xiao

address: Shiqiao Road 145 JiangGan District

department: Institute of Animal Husbandry and Veterinary Science

institute: Zhejiang Academy of Agricultural Sciences

summary: Our study provides considerable gene expression information of Trichophyton mentagrophytes at the transcriptional level, which will help accelerate the research on the antifungal medicine development. Additionally, we have demonstrated the feasibility of using the Illumina sequencing based DGE system for gene expression profiling, and have shed new light on functional studies of the genes involved in antifungal mechanisms of berberine hydrochloride and clotrimazole.

overall_design: Berberine hydrochloride (BC) (HPLC > 98 %, Lot Number:20130306) was purchased from Yuan Ye Biological technology co., Ltd, Shanghai, China. The BC treated group (three samples) was subject to medicinal stress dose which means 1/2 MIC (minimum inhibitory concentration) dose (1 mg/mL berberine in DMSO), Clotrimazole (CLO) (99 % pure, Lot No. 23593-75-1) was purchased from BaDaTong Medical Company (TaiZhou, Zhejiang Province, China). And clotrimazole treated group (three samples) was subject to medicinal stress dose which means 1/2 MIC (minimum inhibitory concentration) dose (0.5 μg/mL Clotrimazole in DMSO),while the control group was fed with DMSO (Purity>99%) which was purchased from Sangon Biotech co., Ltd Shanghai, China only. Each group has three repeats. After 6 h incubation (28°C,150 rpm), the seeds were filtered with gauze and frozen after treatment for RNA isolation and further analysis.

first: Xiao

middle: C

last: Wen

first: Bao

middle: G

last: Lian


title: Characterization of Epigenetic Regulation in an Extraterrestrial Environment: The Arabidopsis Spaceflight Methylome [RNA-seq]

city: Gainesville

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

summary: When germinated and grown on-board the ISS (International Space Station), plant do not exhibit abnormal structures but they do have altered growth habits and this project aims to investigate the molecular mechanisms that provide the foundation for the altered growth habits observed in orbit. APEX03-2 (Advanced Plant Experiment 03-2), also known as TAGES-ISA (Transgenic Arabidopsis Gene Expression System-Intracellular Signaling Architecture) specifically addresses the growth and molecular changes that occur in Arabidopsis thaliana plants during spaceflight by using molecular and genetic tools, and by asking fundamental questions regarding root structure, growth and cell wall remodeling may be answered. This investigation advances the fundamental understanding of the molecular biological responses to extraterrestrial environments. This understanding helps to further define the impacts of spaceflight on biological systems to better enable NASA’s future space exploration goals. https://www.nasa.gov/mission_pages/station/research/experiments/1059.html

overall_design: APEX03-2 also identified as TAGES-Isa (Transgenic Arabidopsis Gene Expression System—Intracellular Signaling Architecture) was launched on SpaceX mission CRS-5 on 10 January 2015. Dry, sterilized Arabidopsis seeds were planted aseptically on the surface of 10 cm2 solid media plates and remained dormant until removed from cold stowage and exposed to light at the initiation of the experiment on the ISS (International Space Station). The plates were grown in the Vegetable Production System (VPS/Veggie) hardware on the Columbus Module of the ISS with overhead LED lighting of the VPS. After 11 days after sowing (DAS) seedlings were harvested by an astronaut into KFT (Kennedy Fixation Tube) containing RNAlater solutions. Upon return to Earth, the harvested material was used to compare the transcriptomes and methylomes of the WS genotype between spaceflight and ground control samples.

first: Collin

middle: E

last: LeFrois

first: Mingqi

last: Zhou

first: Anna-Lisa

last: Paul


title: Paired TCR and transcriptome analysis of single T cells characterizes clonally expanded human conventional and unconventional CD8+ T cells

first: Michael

last: Sikora

address: 450 Serra Mall

summary:
Purpose: Single cell RNAseq has revolutionized our understanding of the heterogeneity of immune system. The goal of this study is to characterize functions of Mycobacterium tuberculosis (Mtb) specific CD8+ T cell clones using single cell RNAseq
Methods: PBMCs from Mtb exposed patients were stimulated ex vivo with Mtb lysate for 12 hours. Activated CD8+ T cells were selected and single cell sorted based on the upregulation of activation markers, including CD154 and CD137.
Results: Using an optimized Smart-seq2 protocol, we could successfully combine TCR sequencing with transcriptome sequencing on single T cell. TCR sequence analysis allows us to preferentially identify and select expanded conventional CD8+ T cells as well as invariant natural killer T (iNKT) cells and mucosal-associated invariant T (MAIT) cells. In summary, we analyzed 921 single cells with 2,500-3000 detected genes for each cell. The iNKT and MAIT cells have a nearly superimposable transcriptional pattern, indicating that they are variations of the same cell type, and differ considerably from conventional CD8+ T cells. While there are no distinct gene expression differences between clonally expanded versus unique iNKT or MAIT cells, highly expanded conventional CD8+ T cells downregulate the interleukin-2 (IL-2) receptor alpha (IL2RA, or CD25) protein and show signs of senescence. This suggests inherent limits to clonal expansion that act to diversify the T cell response repertoire.
Conclusions: we combine targeted TCR sequencing with a sensitive RNA-seq protocol that yields both paired TCR sequences and extensive transcriptional information on single T cells. This enables the selection of rare, clonal and specific T cell subtypes, enabling analysis of their transcriptomes. Our targeted approach allowed us to efficiently and economically select clonal cells with a sensitive clone size dynamic range. And by using a short ex vivo stimulation (12~24 hours) to identify pathogen-responsive T cells, we could circumvent long-term ex vivo culture artifacts. By leveraging single cell analysis of clonal T cells in additional contexts we may improve our understanding of immune system responses to diseases such as cancer, additional infections, as well as aid in vaccine development.

overall_design: Parellel single cell TCR and RNA-seq to study the transcriptome of clonally expanded conventional and unconventional cells responding to Mycobacterium tuberculosis

middle: S

last: Islam

first: Huang

last: Huang


title: A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and postnatal growth retardation in mice

status: Public on Mar 18 2019

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

type: Methylation profiling by high throughput sequencing

summary: DNA methyltransferases (DNMTs) deposit repressive DNA methylation, which regulates gene expression and is essential for mammalian development. Histone post-translational modifications can recruit DNMTs to DNA. The PWWP domains of DNMT3A and DNMT3B are posited to interact with histone 3 lysine 36 trimethylation (H3K36me3); however, the functionality of this interaction for DNMT3A remains untested in vivo. Here we present a mouse model carrying a D329A point mutation in the DNMT3A PWWP domain. The mutation causes dominant postnatal growth retardation. At the molecular level, it results in aberrant progressive acquisition of DNA methylation across domains marked by bivalent chromatin, resulting in de-repression of important developmental regulatory genes in adult hypothalamus. Evaluation of non-CpG methylation further demonstrates the altered recruitment and activity of mutant DNMT3A at bivalent domains. This work provides key molecular insights into analogous growth phenotypes observed in humans with congenital mutations in the DNMT3A PWWP domain.

overall_design: There are at least two biological replicates per genotype per experiment, and a wild-type (reference) and mutant mouse comparison is always included.

first: Gintarė

last: Sendžikaitė

first: Courtney

last: Hanna

first: Kathleen

last: Stewart-Morgan

first: Elena

last: Ivanova

first: Gavin

last: Kelsey


title: RNAseq of cell lines with knocked in ESR1 mutations

city: Boston

first: Rinath

last: Jeselsohn

state: MD

address: 450 Brookline Ave, D728

department: Medical Oncology

institute: DFCI

summary: The study was designed to investigae the transcriprional changes induced by the Y537S, D538G and E380Q ESR1 mutations

overall_design: MCF7 cells were designed to express the Y537S, D538G and the E380Q mutations. Cells were generated using TALEN technology and homologous recombination


title: Loss of RNA-binding protein Sfpq causes long-gene transcriptopathy in skeletal muscle and severe muscle mass reduction with metabolic myopathy (Primary culture, rRNA depleted RNA-seq)

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

summary: Growing evidences are suggesting that extra-long genes in mammals are vulnerable for full-gene length transcription and dysregulation of long genes is a mechanism underlying human genetic disorders. Skeletal muscle expresses Dystrophin which is 2.26 Mbp in length; however, how long-distance transcription is achieved is totally unknown. We had discovered RNA-binding protein SFPQ preferentially binds to long pre-mRNAs and specifically regulates the cluster of neuronal genes > 100 kbp. Here we investigated the roles of SFPQ for long gene expression, target specificities, and also physiological functions in skeletal muscle. Loss of Sfpq selectively downregulated genes >100 kbp including Dystrophin and caused progressive muscle mass reduction and metabolic myopathy characterized by glycogen accumulation and decreased abundance of mitochondrial oxidative phosphorylation complexes. Functional clustering analysis identified metabolic pathway related genes as the targets of SFPQ. These findings indicate target gene specificities and tissue-specific physiological functions of SFPQ in skeletal muscle.

overall_design: We analyzed rRNA-depleted RNA profiles including transcribing RNAs in primary myoblasts obtained from skeletal muscles of 1-month-old SfpqSM-KO (n=1) and control (n=1) mice under differentiated condition using Ion-proton.

first: Motoyasu

last: Hosokawa

first: Akihide

last: Takeuchi

last: Iida

first: Masatoshi

last: Hagiwara


title: IDH1-R132H Low Grade Glioma animal brain tumors

city: Ann Arbor

first: Richard

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan


title: Loss of RNA-binding protein Sfpq causes long-gene transcriptopathy in skeletal muscle and severe muscle mass reduction with metabolic myopathy


title: Glucose metabolism induced chromatin remodeling in pulmonary artery endothelial cell [RNA-Seq]

first: Kazuya

last: Miyagawa

state: California

address: 269 Campus Drive

department: Pediatrics

institute: Stanford Universtiy

summary: Maintaining endothelial cells (EC) as a monolayer in the vessel wall depends on a gene expression profile and the metabolic state, features influenced by contact with neighboring cells eg, pericytes and smooth muscle cells (SMC). Dysfunctional bone morphogenetic protein receptor 2 (BMPR2) signaling disrupts EC metabolism and monolayer formation and is associated with vascular diseases such as pulmonary arterial hypertension. We show that BMPR2 in either EC or SMC is required for contact-dependent activation of Notch1 in EC. Notch1, through the glycolysis inducer PFKFB3, mediates an increase in the citrate pool and histone acetylation required for Notch1 and MYC target gene expression. This maintains Notch1-dependent EC proliferative capacity, coordinating with Notch1 activation of mitochondria. We report how Notch1 and p300 binding to chromatin and H3K27ac status are influenced by glucose metabolism and regulate gene expression in endothelial cells.

overall_design: Examination of RNA-sequencing in pulmonary artery endothelial cells with or without PFKFB3 silencing in contact co-culture with pulmonary artery smooth muscle cells.

first: Minyi

last: Shi

middle: P

last: Snyder

first: Marlene

last: Rabinovitch


title: Genome Wide Transcriptional Modelling of a 24hour timecourse of T-helper cell differentiation

city: London

first: Tessa

last: Crompton

address: 30 Guilford Street

department: Immunobiology

institute: UCL

summary: In this study we used Genome Wide Transcriptional Modelling (GWTM) to investigate the temporal transcriptional changes during CD4 Th0, Th1 and Th2 differentiation in the first 24 hours after T cell activation.  We measured the transcriptional response by RNA seq every four hours for a 24 hour time course.

overall_design: WT CD4 T cells were isolated and purified from adult murine spleen. The purified CD4 cells were then set up in culture under three different conditions: Th0, Th1 and Th2. Cells were extracted at 4 hour timepoints during a 24hour timecourse and RNA was extracted for each timepoint under each condition. This RNA was further sequenced to analyse the genome wide transcriptional changes through time under each of the three conditions.

first: Anisha

last: Solanki

first: Martino

last: Barenco


title: RB constrains lineage fidelity and multiple stages of tumour progression and metastasis

city: Philadelphia

first: David

middle: M

last: Walter

state: PA

address: 421 Curie Blvd, Rm 745

department: Cancer Biology

institute: University of Pennsylvania

summary: RNA-Sequencing analysis of murine lung adenocarcinoma cell lines in the presence and absence of Rb. Cell lines were derived from KP tumours and KPRbTR tumours where Rb is trapped and lacks expression due to the XTR system. Cell lines were then subject to RNA-Seq to identify gene expression differences following loss of Rb expression.

overall_design: 4 KP and 4 KPRbTR cell lines were derived from murine lung tumours, and were then subjected to paired-end RNA-Sequencing to identify changes in the presence and absence of Rb.

first: Travis

last: Yates

first: Miguel

last: Ruiz-Torres

first: Caroline

last: Kim-Kiselak

first: A

last: Gudiel

first: Charuhas

last: Deshpande

first: Walter

middle: Z

last: Wang

first: Michelle

last: Cicchini

first: Kate

middle: L

last: Stokes

first: John

middle: W

last: Tobias

first: Elizabeth

last: Buza

last: Feldser


title: Characterization of Epigenetic Regulation in an Extraterrestrial Environment: The Arabidopsis Spaceflight Methylome

first: Robert

last: Ferl

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


title: Glucose metabolism induced chromatin remodeling in pulmonary artery endothelial cell

city: Stanford

first: Kazuya

last: Miyagawa


title: Glucose metabolism induced chromatin remodeling in pulmonary artery endothelial cell [ChIP-Seq]

overall_design: Examination of Notch1, p300 and H3K27ac ChIP-sequencing in pulmonary artery endothelial cells with or without PFKFB3 silencing in contact co-culture with pulmonary artery smooth muscle cells.

first: Minyi

last: Shi

first: Zhixin

last: Zhao

first: Michael

last: Snyder

first: Marlene

last: Rabinovitch


title: A co-expression analysis of the placental transcriptome in association with maternal pre-pregnancy BMI and newborn birth weight

status: Public on Mar 16 2019

city: Diepenbeek

first: Tim

last: Nawrot

address: Agoralaan building D

department: Centre for Environmental Sciences

country: Belgium

institute: Hasselt University

summary: We conducted a genome-wide placental transcriptome study aiming at the identification of functional pathways representing the molecular link between maternal pre-pregnancy BMI and fetal growth. We used RNA microarray (Agilent 8 X 60 K), medical records, and questionnaire data from 183 mother-newborn pairs from the ENVIRONAGE birth cohort study (Flanders, Belgium). We applied a weighted gene co-expression network analysis (WGCNA) and identified genes modules and hub genes that were associated with maternal BMI as well as newborn birth weight. Modules of interest were further characterized by gene ontology (GO) and pathway enrichment analyses. We assessed the mediating effects of modules and hub genes in the association between maternal BMI and newborn weight.

overall_design: Epidemiologic study

first: B

last: Cox

first: M

last: Tsamou

first: K

last: Vrijens

last: Neven

first: E

last: Winckelmans

first: T

last: de Kok

last: Plusquin


title: Grape Proanthocyanidins Modulate MicroRNA Expression in Human pancreatic cancer cells

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Mi(cro)RNAs are small non-coding RNAs of 18-25 nucleotides in length that modulate gene expression at the posttranscriptional level. Grape seed proanthocyanidins (GSPs), a biologically active component of grape seeds, have been shown to have positive effects on anti-cancer. In current study, to explore whether GSPs can regulate miRNA expression and possible molecular mechanisms involved in anti-cancer, we prepared the pancreatic cancer (PC) cells samples (SS3, SS12 and SS24) at 3, 12 and 24h after GSPs treatments respectively; and control samples (SC3, SC12 and SC24) were also collected accordingly. miRNA-seq transcriptome comparisons were performed, and 26, 85 and 85 differentially expressed (DE) miRNA were identified among SS3 vs. SC3, SS12 vs. SC12 and SS24 vs. SC24 respectively, indicating the GSPs treatments could modulate the expression of miRNAs globally. Subsequently, 74, 598 and 1204 target genes of these DE miRNAs were predicted in three comparisons, and GO and KEGG analysis revealed that multiple target genes were associated with proliferation and apoptosis of PC cells. Moreover, interaction network analyis of DE miRNAs and target genes associated with PC were also carried out, and fabulous co-expression relationships further suggested that GSPs treatment could probably repress the  proliferation of PC cells by modulating the miRNAs expression

overall_design: Transcriptome change of PANC-1 cells post Proanthocyanidins (20 μg/ml) exposure at 3, 12 and 24h  were investigated. A biological replicate sequencing was carried out.

first: Zhanjiang

last: Han


title: Identification of ChIP-seq and RIME grade antibodies for estrogen receptor alpha

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

summary: Estrogen Receptor alpha (ERα) is a key driver of most breast cancers, and it is the target of endocrine therapies used in the clinic to treat women with ERα positive (ER+) breast cancer. ChIP-seq (chromatin immunoprecipitation coupled with deep sequencing) has improved our understanding of ERα function during breast cancer progression and in response to anti-estrogens. A critical component of the ChIP-seq protocol is the antibody that is used to pull down the bait protein. To date, most of the ChIP-seq experiments for the study of ERα have been performed using the sc-543 antibody from Santa Cruz Biotechnology. However, this antibody has been discontinued, thereby severely impacting the study of ERα in normal physiology as well as diseases such as breast cancer and ovarian cancer. Here, we compare the sc-543 antibody with other commercially available antibodies, and we show that 6-935 (EMD Millipore) and ab3575 (Abcam) antibodies can successfully replace the sc-543 antibody for ChIP-seq experiments.

overall_design: ChIP-seq in breast cancer cell lines to identify high-quality, ChIP-grade antibodies for ERα.

first: Silvia

last: Glont

first: Evangelia

middle: K

last: Papachristou

first: Ashley

last: Sawle

first: Kelly

last: Holmes

first: Rasmus

last: Siersbaek


title: RNA-seq of RKO cells with cTAZ KO or putback

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

summary: RKO cells with cTAZ KO or putback were subjected to RNA isolation and RNA-seq analyses were generated by deep sequencing using Illumina Hiseq.

overall_design: RNA-seq analyses of RKO cells with cTAZ KO or putback by deep sequencing using Illumina Hiseq.

first: Faxing

last: Yu


title: A Chemical Toolbox for the Study of Bromodomains and Epigenetic Signaling

city: Oxford

first: Panagis

last: Filippakopoulos

state: Oxfordshire

address: ORCRB - Roosevelt Drive

department: Nuffield Department of Medicine

institute: Oxford University

summary: Bromodomains (BRDs) are evolutionary conserved epigenetic protein interaction modules which recognize (“read”) acetyl-lysine, however their role(s) in regulating cellular states and their potential as targets for the development of targeted treatment strategies is poorly understood. Here we present a set of 25 chemical probes, selective tool small molecule inhibitors, covering 29 human bromodomain targets. We comprehensively evaluate the selectivity of this probe-set using BROMOscan® and demonstrate the utility of the set in studies of muscle cell differentiation and triple negative breast cancer (TNBC). We identified cross talk between histone acetylation and the glycolytic pathway resulting in a vulnerability of TNBC cell lines to inhibition of BRPF2/3 BRDs under conditions of glucose deprivation or GLUT1 inhibition. This chemical probe set will serve as a resource for future applications in the discovery of new physiological roles of bromodomain proteins in normal and disease states and as a toolset for bromodomain target validation.

overall_design:
C2C12 mouse myoblast cells were grown in DMEM containing 20% FBS. For differentiation experiments in the presence and absence of mentioned drugs, 0.3x106 cells were seeded and allowed to grow for 36 hrs before switching to differentiation media (DMEM containing 2% horse serum, 10 µg/ml insulin and 10 µg/ml Transferrin). Indicated drugs were added at the time of differentiation at 0.5 μM (JQ1, LP99) or 2 μM (GSK2801, BAZ2ICR, BSP) for 12h before they were harvested for extraction of total RNA. Total RNA was extracted using PureLinkTM RNA kit as per the manufacturer’s protocol.
Raw CEL data were processed in R (v.3.5.1) using Bioconductor (v.3.7) and the oligo package (v.1.44). Quality controls were carried out using the arrayQualityMetrics package (v.3.36.0) taking into account array intensity distributions, distance between arrays and variance mean-dependence. Principal component analysis was used to decide which arrays to process together. On this basis one of the three arrays treated with BSP was considered to be an outlier and was discarded (sample 'BSP_rep3', file 'BSP_rep3.CEL'), with the rest of the analysis performed without taking it into account. Background correction and normalization were carried out employing the Robust Multichip Array (RMA) method implemented in the oligo package. Data were filtered using the genefilter package (v.1.62.0) employing the nsFilter function and an interquartile range (IQR) cut-off of 0.28 (or >log(1.2), determined by the midpoint of the shortest interval containing half of the data. Probe sets that did not have an Entrez gene identifier were also removed. From the 29129 features available on the Clariom S Mouse HT chip, 14538 remained after filtering.
A linear model was applied employing the limma package (v.3.36.2) followed by empirical Bayesian analysis to determine differential expression between not-treated and treated samples. Genes were considered differentially expressed if the adjusted P-value, calculated using the Benjamini–Hochberg method  in order to minimize false discovery rate, was less than 0.05 and the mean level of expression was greater than 1.5-fold. Data were annotated using the clariomsmousehttranscriptcluster.db annotation data (https://www.bioconductor.org/packages/release/data/annotation/html/clariomsmousehttranscriptcluster.db.html).

first: Kiran

last: Nakka

first: Jeffrey

last: Dilworth


title: Characterization of Epigenetic Regulation in an Extraterrestrial Environment: The Arabidopsis Spaceflight Methylome [Bisulfite-seq]

first: Robert

last: Ferl

overall_design: APEX03-2 was launched on SpaceX mission CRS-5 on 10 January 2015. Dry, sterilized Arabidopsis seeds were planted aseptically on the surface of 10 cm2 solid media plates and remained dormant until removed from cold stowage and exposed to light at the initiation of the experiment on the ISS (International Space Station). The plates were grown in the Vegetable Production System (VPS/Veggie) hardware on the Columbus Module of the ISS with overhead LED lighting of the VPS. After 11 days after sowing (DAS) seedlings were harvested by an astronaut into KFT (Kennedy Fixation Tube) containing RNAlater solutions. Upon return to Earth, the harvested material was used to compare the transcriptomes and methylomes of the WS genotype between spaceflight and ground control samples.

first: Collin

last: LeFrois

first: Mingqi

last: Zhou

first: Anna-Lisa

last: Paul


title: Differential gene expression in IDH1-R132H  Low Grade Glioma animal brain tumors brain in response to 10 Gy of radiation

first: Richard

last: McEachin

summary:
IDH1-R132H is expressed in Low Grade Glioma (LGG) in combination with loss of function mutation in ATRX and TP53 genes. IDH1-R132H results in gain of function with production
of 2-hydroxygluatrate, that in turn generates a hypermethylatyed phenotype in DNA and histone with consequences in epigenetic regulation of gene expression. Here we will
compare the gene expression profile between IDH1-R132H and IDH1 Wt LLG animal brain tumors in reponse to radiation

overall_design: Evaluate differential gene expression between Brain DH1-R132H and IDH1 wt in response to 10Gy ionizing radiation at 14 days after tumor neurospheres implantation

first: Felipe

last: Nunez

first: Maria

last: Castro

first: P

middle: R

last: Lowenstein


title: mitoCPR - a surveillance pathway that protects mitochondria in response to mitochondrial import stress [human]

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Mitochondrial functions are essential for cell viability and rely on protein import into the organelle. Physiological perturbations and disease conditions can lead to mitochondrial import defect. We find that in budding yeast, mitochondrial import defects result in activation of a surveillance mechanism, which we termed mitoCPR. The mitoCPR is aimed at ameliorating mitochondrial import and protecting mitochondria during import stress. This is mediated by the mitoCPR effector, Cis1, which associates with mitochondria to reduce the accumulation of mitochondrial preproteins at the organelle's surface. Clearance of preproteins depends on the AAA-ATPase Msp1 and the proteasome, suggesting that Cis1 facilitates the degradation of unimported proteins that accumulate at the mitochondrial surface. We further show that mitoCPR is critical for maintaining mitochondrial functions during mitochondrial import stress and provide evidence that it is an ancient, conserved mitochondrial protection mechanism.

overall_design: Three replicates each of WT control, rho0 (lacking mitochondrial DNA) and CCCP-treated (to induce mitochondrial protein import stress) were compared.

first: Hilla

last: Weidberg

first: Angelika

last: Amon


title: The E3 Ubiquitin Ligase UBE3A Antagonizes Steatosis by Targeting the Pro-Steatotic Epigenetic Regulator MLL4 for Degradation

city: Gwangju

first: JANGHYUN

last: KIM

state: Gwangju

address: 33, YONGBONG-RO, BUK-GU, GWANGJU

department: Oral pathology

country: South Korea

institute: CNUDH

summary: Regulation of the stability of epigenetic regulators offers unique opportunities for epigenetic therapies. However, this strategy has been poorly explored. Here we report that the E3 ubiquitin ligase UBE3A binds and ubiquitylates the histone H3-lysine 4-methyltransferase MLL4 (aka KMT2D) as a new substrate for degradation. Using Ube3a knockout and UBE3A-overexpressing transgenic mouse models, we show that, in the liver, UBE3A levels are inversely correlated with levels of MLL4, its functional surrogate marker H3-lysine 4-monomethylation, and expression of the recently identified steatosis target genes of MLL4. Consistently, Ube3a knockout mice are highly susceptible to high-fat diet-induced steatosis relative to their littermate control mice, and this phenotype is rescued by deletion of a copy of Mll4. Therefore, UBE3A indirectly exerts an epigenetic gene regulation activity through targeting MLL4 for degradation. Also this UBE3A-MLL4 axis presents a novel therapeutic venue for treating various MLL4-directed pathogeneses.

overall_design: RNA samples from wild-type and Ube3a het or Ube3a TG homo livers treated with high-fat diet were prepared for sequencing according to the Illumina protocol, and sequenced on the Illumina HiSeq 2500. We then compared the transcriptome changes between WT and Ube3a het or TG livers after high-fat diet. And then we identified gene whose expression is altered by high-fat diet in Ube3a mutant liver compared to wild-type. The Ube3a TG homo samples overexpress Ube3a. The Ube3a het samples have one knockout and one wt allele, so they express half amount of Ube3a.

first: J

middle: H

last: Kim

last: Lee


title: Differential gene expression in IDH1-R132H Tumor Neurospheres generated from a mouse model of Low Grade Glioma

summary:
IDH1-R132H is expressed in Low Grade Glioma (LGG) in combination with mutation in ATRX and TP53 genes. IDH1-R132H results in gain of function with production
of 2-hydroxygluatrate, that in turn generates a hypermethylatyed phenotype in DNA and histone with consequences in epigenetic regulation of gene expression. Here we will
compare the gene expression profile between IDH1-R132H and IDH1 Wt tumor neurospheres.

overall_design: Evaluate differential gene expression between tumor neurospheres IDH1-R132H and IDH1 wt.

middle: J


title: The histone chaperone CAF-1 cooperates with the DNA methyltransferases to maintain Cd4 silencing in cytotoxic T cells [MBD-seq]

status: Public on Mar 14 2019

city: New York

first: Craig

last: Thompson

address: 411 East 67th Street RRL 469

institute: Memorial Sloan Kettering Cancer Center

summary: The transcriptional repression of alternative lineage genes is critical for cell fate commitment. Mechanisms by which locus-specific gene silencing is initiated and heritably maintained during cell division are not clearly understood. To study the maintenance of silent gene states, we investigated how the Cd4 gene is stably repressed in CD8+ T cells. Through CRISPR and shRNA screening, we identified the histone chaperone CAF-1 as a critical component for Cd4 repression. We found that the large subunit of CAF-1, Chaf1a, requires the N-terminal KER domain to associate with the histone deacetylases HDAC1/2 and the histone demethylase LSD1, enzymes that also participate in Cd4 silencing. When CAF-1 was lacking, Cd4 derepression was markedly enhanced in the absence of the de novo DNA methyltransferase Dnmt3a, but not the maintenance DNA methyltransferase Dnmt1. In contrast to Dnmt1, Dnmt3a deficiency did not significantly alter levels of DNA methylation at the Cd4 locus. Instead, Dnmt3a deficiency sensitized CD8+ T cells to Cd4 derepression mediated by compromised functions of histone modifying factors, including the enzymes associated with CAF-1. Thus, we propose that the heritable silencing of the Cd4 gene in CD8+ T cells exploits cooperative functions among the DNA methyltransferases, CAF-1, and histone modifying enzymes.

overall_design: There are 3 samples total consisting of Cas9Tg CD8+ T cells electroporated with sgRNA. Control sgRNA (Olfr2) CD8+CD4- T cells, Dnmt1 sgRNA treated CD8+CD4+ and Dnmt3a sgRNA treated CD8+CD4+ T cells were processed for genome-wide DNA methylation analysis as described in the methods.

last: Ng

first: Martin

last: Aichinger

first: Tung

last: Nguyen

first: Christy

last: Au

first: Tariq

last: Najar

first: Lin

last: Wu

first: Kai

last: Mesa

first: Lao

last: Will

first: Jean-Pierre

last: Quivy

first: Hubert

last: Benjamin

first: Genevieve

last: Almouzni

first: Johannes

last: Zuber

first: Dan

last: Littman


title: CD8+ T cells regulate tumor ferroptosis during cancer immunotherapy

first: Weimin

last: Wang

state: Michigan

address: 109 Zina Pitcher Place

department: Surgery

summary: CD8+ T cells activated by cancer immunotherapy execute tumor clearance mainly by inducing cell death through perforin-granzyme- and Fas/Fas ligand-pathways. Ferroptosis is a form of cell death that differs from apoptosis and results from iron-dependent lipid peroxide accumulation. Although it was mechanistically illuminated in vitro, emerging evidence has shown that ferroptosis may be implicated in a variety of pathological scenarios. However, the involvement of ferroptosis in T cell immunity and cancer immunotherapy is unknown. Here, we find that immunotherapy-activated CD8+ T cells enhance ferroptosis-specific lipid peroxidation in tumor cells, and in turn, increased ferroptosis contributes to the anti-tumor efficacy of immunotherapy. Mechanistically, IFNg released from CD8+ T cells downregulates expression of SLC3A2 and SLC7A11, two subunits of glutamate-cystine antiporter system xc-, restrains tumor cell cystine uptake, and as a consequence, promotes tumor cell lipid peroxidation and ferroptosis. In preclinical models, depletion of cyst(e)ine by cyst(e)inase in combination with checkpoint blockade synergistically enhances T cell-mediated anti-tumor immunity and induces tumor cell ferroptosis. Thus, T cell-promoted tumor ferroptosis is a novel anti-tumor mechanism. Targeting tumor ferroptosis pathway constitutes a therapeutic approach in combination with checkpoint blockade.

overall_design: Human HT-1080 mRNA profiles treated by IFNg for 8 hours was determined by RNA-Seq.

first: Jing

last: Li

first: Weiping

last: Zou


title: The medium-chain free fatty acid receptor GPR84 is expressed in pro-inflammatory macrophages and mediates inflammatory sequelae in endometriosis

status: Public on Mar 15 2019

first: Udo

last: Oppermann

address: Botnar Research Centre, Nuffield Orthopaedic Centre, Windmill Road

department: Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences

institute: University of Oxford

summary: RNA sequencing was used to investigate the transcriptomic response of primary human macrophages to stimulation of GPR84 and the effect of inhibition of this receptor with a range of antagonists.

overall_design: RNA-seq of polyA-selected RNA from five healthy human donor macrophages exposed to a combination of agonists and antagonists for GPR84.

first: Edward

last: Hookway


title: mitoCPR - a surveillance pathway that protects mitochondria in response to mitochondrial import stress

first: Charles

last: Whittaker

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens

overall_design: Refer to individual Series


title: Bone marrow-derived and dental pulp-derived human mesenchymal stem cell RNA-Seq

status: Public on Mar 17 2019

city: Taichung

first: Shih-Chieh

last: Hung

address: No. 120, Wuyi Street, North District

department: Integrative Stem Cell Center

country: Taiwan

institute: China Medical University Hospital

summary: Lineage commitment and tumorigenesis specify adult stem cells from different tissues or organs. To gain insight into the mechanism of this programming, phenotypic, functional and transcriptome analyses were performed in mesenchymal stem cells derived from human dental pulp (DPSCs) and bone marrow (BMSCs). DPSCs and BMSCs had similar morphologies and flow cytometric profiles, and were capable of tri-lineage differentiation into osteoblast, adipocyte and chondocyte. However, compared with BMSCs, DPSCs increased in osteogenic potential, decreased in adipogenic potential, and formed dentin-pulp-like complexes in vivo. Genome-wide RNA-seq and differential expression analysis revealed that signalings such as, phosphatase and tensin homolog (PTEN)/PI3K/AKT pathway, and cancer-related pathway were different in both cells. Differential PTEN expression, higher in DPSCs than BMSCs, was responsible for the lineage commitment and tumorigenesis differences in both cells. Besides, BMSCs decreased in PTEN DNA methylation compared to DPSCs, which was mediated by increased DNA (cytosine-5) methyltransferase 3B (DNMT3B) expression. Furthermore, histone methyltransferase G9a mediated repressive epigenetic mark H3K9Me2 was selectively enriched in BMSCs. Moreover, DPSCs were more resistant to oncogenic transformation than BMSCs. To link lineage commitment with tumorigenesis, we demonstrated that DPSCs were more resistant to oncogenic transformation than BMSCs and PTEN deficiency increased the sensitivity of DPSCs for tumorigenic transformation. The results help understanding the roles of the epigenetic factors in lineage commitment and tumorigenesis and also for therapeutic uses of adult stem cells.

overall_design: RNA-Seq of bone marrow-derived and dental pulp-derived mesenchymal stem cells with 3 biological replicates


title: BRD9 defines a novel SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors

first: Peter

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School


title: BRD9 defines a novel SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors [RNA-seq]

summary: Bromodomain-containing protein 9 (BRD9) was recently identified to be associated with the chromatin remodeling SWI/SNF(BAF) complex, yet its function within the complex has remained unclear. Here, using genome-scale CRISPR-Cas9 screens, we found that BRD9 constitutes a specific vulnerability in highly malignant pediatric rhabdoid tumors, which are driven by inactivating mutations of SMARCB1 subunit of SWI/SNF complexes. Surprisingly, we found that BRD9 does not belong to the previously identified BAF or PBAF complexes, but instead is found exclusively in a novel of SWI/SNF sub-complex.  We show that BRD9-containing complexes lack SMARCB1, which had previously been considered a core subunit present in all SWI/SNF variants.  We recently demonstrated that both SMARCB1-containing and ARID1A-containing SWI/SNF complexes preferentially function at enhancers, but here we show that BRD9-containing complexes are located at active promoters as well as enhancers. We show that loss of SMARCB1, as observed in rhabdoid tumors, results in increased BRD9 interaction with SWI/SNF core subunit SMARCC1, consistent with competition between SMARCB1 and BRD9 in the formation of SWI/SNF complexes.  Underlying the dependency, we demonstrate that BRD9, via its DUF3512 domain, is essential for maintaining the integrity of its sub-complex, which predominates in the absence of SMARCB1.  Taken together, our results reveal a BRD9-containing SWI/SNF subcomplex which is required for the survival of SMARCB1-mutant rhabdoid tumors.

overall_design: RNA-seq for G401 cell before and after Knockout BRD9

first: Xiaofeng

first: Su

last: Roberts


title: mitoCPR - a surveillance pathway that protects mitochondria in response to mitochondrial import stress [yeast]

overall_design: Two replicates each of WT controls, Psd1_oe2 samples (overexpressing Psd1) and Psd1_oe_Pdr3_ko2 samples (overexpressing Psd1 with a Pdr3 deletion) were compared.

first: Hilla

last: Weidberg

first: Angelika

last: Amon


title: BRD9 defines a novel SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors [ChIP-seq]

overall_design: ChIP-seq of BRD9 and two histone modifications: H3K27ac, H3K4m3, in G401 before and after KO BRD9


title: Epigenetic modulation of β-cells by interferon-α via PNPT11-miR-26a-TET2 triggers autoimmune diabetes

first: Weijia

last: Zhang

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

type: Methylation profiling by genome tiling array


title: Regulation of T-cell receptor signaling induced gene expression by the zinc finger transcription factor Ikaros.

city: Los Angeles

first: Ameya

last: Champhekar

address: 700 Tiverton Ave, 11-272 Factor Bldg

department: Medicine, HemOnc Division

institute: University of California, Los Angeles

summary: Ikaros is critical in setting the threshold for T-cell activation and proliferation. Here we used mature CD8+ T cells from mice lacking the zinc finger 4 of Ikaros (Ikaros-Zn4-/-) to study its role in regulating gene expression at early time points after T-cell receptor stimulation.

overall_design: Transcriptome profiling was performed using WT and Ikaros-Zn4-/- naïve CD8+ T cells that were stimulated for 0, 30 or 120 minutes.

first: S

last: Wadsworth

first: A

middle: T

last: Smale


title: Transcriptomic profiling of Yersinia enterocolitica O:3 and O:8 reveals serotype-specific expression differences leading to largely different YstA toxin levels

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

country: Germany

institute: Helmholtz Centre for Infection Research

summary: The enteric pathogen Yersinia enterocolitica is a the most common gram-negative zoonotic pathogen that causes a variety of gut-associated diseases named yersiniosis ranging from enteritis, watery diarrhea, mesenteric lymphadenitis to post infectious extraintestinal sequelae such as reactive arthritis human yersiniosis. The species Y. enterocolitica comprises a diverse group of about 70 serotypes of which only 11 are harmful to humans. Among the pathogenic strains are the highly mouse-virulent 1B/O:8 strains (YeO:8). This bioserotype, in particular YeO:8 strain 8081v has been used to study the pathogenesis of Y. enterocolitica using mouse infection models. However, by far the most frequent cause of human yersiniosis in Europe and Japan (>90%) is Y. enterocolitica bioserotype O:3 (YeO:3), which is also frequently found in pigs and pork products.   In this study a comparative RNA-seq-based transcriptomic approach was used to identify serotype/isolate-specific differences in the transcriptome of the isolates YeO:8 8081v and YeO:3 Y1 under infection-relevant conditions. This strategy allowed the generation of the first in-depth single-nucleotide resolution transcriptome of Y. enterocolitica, revealed major differences in the temperature- and growth phase-dependent expression profiles, and led to the discovery of changes that modulate transcripts levels of important virulence-relevant traits. Additionally a comprehensive map of transcriptional start sites for Y. enterocolitica was generated using cDNA libraries based on samples enriched for primary transcripts.

overall_design: RNA of Y. enterocolitica Y1 (YeO:3) and 8081v (YeO:8) from in vitro cultures

first: Carina

last: Schmühl

first: Petra

last: Dersch


title: The histone chaperone HIRA promotes the induction of host innate immune defences in response to HSV-1 infection

status: Public on Mar 12 2019

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

institute: University of Glasgow

summary: Host innate immune defences play a critical role in restricting the intracellular propagation and pathogenesis of invading viral pathogens. Here we show that the histone H3.3 chaperone HIRA (histone cell cycle regulator) associates with promyelocytic leukaemia nuclear bodies (PML-NBs) to stimulate the induction of innate immune defences against herpes simplex virus 1 (HSV-1) infection. Following the activation of innate immune signalling, HIRA localized at PML-NBs in a Janus-Associated Kinase (JAK), Cyclin Dependent Kinase (CDK), and Sp100-dependent manner. RNA-seq analysis revealed that HIRA promoted the transcriptional upregulation of a broad repertoire of host genes that regulate innate immunity to HSV-1 infection, including those involved in MHC-I antigen presentation, cytokine signalling, and interferon stimulated gene (ISG) expression. ChIP-seq analysis revealed that PML, the principle scaffolding protein of PML-NBs, was required for the enrichment of HIRA onto ISGs, identifying a role for PML in the HIRA-dependent regulation of innate immunity to virus infection. Our data identifies independent roles for HIRA in the intrinsic silencing of viral gene expression and the induction of innate immune defences to restrict the initiation and propagation of HSV-1 infection, respectively. These intracellular host defences are antagonized by the HSV-1 ubiquitin ligase ICP0, which disrupts the stable recruitment of HIRA to infecting viral genomes and PML-NBs at spatiotemporally distinct phases of infection. Our study highlights the importance of histone chaperones to regulate multiple phases of intracellular immunity to virus infection, findings that are likely to be highly pertinent in the cellular restriction of many clinically important viral pathogens.

overall_design: Enrichment assay of HIRA protein by ChIP-seq in positively/negatively interferon stimulated cells, with/without PML hairpin

first: Steven

last: McFarlane

first: Anne

last: Orr

first: Ashley

middle: D

last: Adams

first: Taranjit

last: Rai

first: Chris

last: Boutell


title: Epigenetic modulation of β-cells by interferon-α via PNPT11-miR-26a-TET2 triggers autoimmune diabetes [RNA-seq]

state: NY

summary: Type 1 diabetes (T1D) is caused by autoimmune destruction of pancreatic β cells. Mounting evidence supports a central role for β-cell alterations in triggering the activation of self-reactive T-cells in T1D. However, the early deleterious events that occur in β cells, underpinning islet autoimmunity are not known. We hypothesized that epigenetic modifications induced in β cells by inflammatory mediators play a key role in initiating the autoimmune response. We analyzed DNA methylation (DNAm) patterns and gene expression in human islets exposed to IFNα, a cytokine associated with T1D development. We found that IFNα triggers DNA demethylation and increases expression of genes controlling inflammatory and immune pathways. We then demonstrated that DNA demethylation was caused by up-regulation of the exoribonuclease, PNPase Old-35 (PNPT1), which caused degradation of miR-26a. This in turn promoted the up-regulation of ten-eleven translocation TET2 enzyme and increased 5-hydoxymethylcytosine levels in human islets and pancreatic β-cells. Moreover, we showed that specific IFNα expression in the β cells of IFNα-INS1CreERT2 transgenic mice, led to development of T1D that was preceded by increased islet DNA hydroxymethylation through a PNPT1/TET2-dependent mechanism. Our results suggest a new mechanism through which IFNα regulates DNAm in β cells, leading to changes in expression of genes in inflammatory and immune pathways that can initiate islet autoimmunity in T1D.

overall_design: We exposed human pancreatic islets from three donors to 2000 IU IFNα and assessed gene expression by RNAseq. The cDNA library was prepared using Illumina TruSeq RNA Sample Prep Kits. Next generation sequencing was performed on Illumina HiSeq2000 using the Single-Read Cluster Generation kit v2 and SBS Sequencing kit v3. Image analysis and base calling were conducted using the SDS 2.5/RTA1.5 software.

first: Mihaela

last: Stefan-Lifshitz

first: Esra

last: Karakose

first: Lingguang

last: Cui

first: Abora

last: Ettela

first: Zhengzi

last: Yi

first: Yaron

last: Tomer


title: SALL3 regulates propensity of human induced pluripotent stem cells to differentiate into distinct cell lineages [Affymetrix]

city: Setagaya

first: Takuya

last: Kuroda

state: Tokyo

address: 1-18-1 Kamiyoga

department: Division of cell-based therapeutic products

institute: National Institute of Health and Sciences

summary:
The expression of SALL3 in hiPSCs correlated positively with ectoderm differentiation capacity and negatively with mesoderm/endoderm differentiation capacity.
We investigated reference gene expression in human iduced pluripotent stem cells infected shRNA to SALL3.

overall_design: Total RNAs were extracted from undifferentiated state of 253G1 cells infected control shRNA or SALL3 shRNA, and we obtained the transcript expression profiles using Affymetrix microarrays.

first: T

first: S

last: Yasuda

first: Y

last: Sato


title: Molecular mapping of nuclear lamina interactions in the mammalian embryo reveals de novo establishment of nuclear architecture

status: Public on Mar 13 2019

city: UTRECHT

first: Jop

last: Kind

state: utrecht

address: Upssalalaan 8

institute: Hubrecht Institute

summary: We generated high-resolution maps of genome-lamina interactions for different stages of the pre-implantation mouse embryo, including oocyte, zygote, 2cell stage and 8cell stage and additionally mouse ES cells. We find that LAD domains are already present at the zygote stage, but not in the oocyte, concluding that genome-nuclear lamina interactions  are not inherited from the maternal germline, but  instead are established de novo rapidly after fertilisation. By using a hybrid genetic background, we were able to identify parental-specific genome-nuclear lamina interaction, allowing us to show that the parental genomes have different features, which are globally resolved at the 8-cell stage. We blocked replication in zygotes by treatment with aphidicolin and found that LAD establishment was unaffected. Moreover, we ectopically expressed Kdm5b in zygotes and show that paternal LAD formation is impaired, suggesting that this mechanism is dependent upon de novo H3K4 methylation. Altogether, our data suggest a step-wise assembly model whereby early LAD formation precedes consolidation of TADs and reveals non-inheritance  of nuclear organisation from the germline.

overall_design: DamID profiles (Dam-lamin B1 and/or Dam alone) were generated for population of cells (15,20,24 cells, triplicate) and for single cells for all the stages studied (oocyte, zygote, 2cell stage and 8cell stage ES cells) and for the additional experiments (treatment with aphidicolin/DMSO, injection with WT_Kdm5b/MUTANT_Kdm5b mRNA). The libraries were sequenced using Illumina hiseq 2500 platform.

first: Máté

last: Borsos

first: Sara

last: Perricone

first: Tamás

last: Schauer

first: Julien

last: Pontabry

first: Kim

last: de Luca

first: Sandra

last: de Vries

first: Maria-Elena

last: Torres-Padilla


title: Epigenetic modulation of β-cells by interferon-α via PNPT11-miR-26a-TET2 triggers autoimmune diabetes [methylation array]

first: Weijia

last: Zhang

overall_design: To characterize DNAm changes induced by IFNα, we exposed human pancreatic islets from three donors to 2000 IU IFNα and analyzed the DNAm patterns for a total of 485,577 CpG sites, using the Infinium HumanMethylation450 BeadChip.

first: Mihaela

last: Stefan-Lifshitz

first: Esra


title: Loss of TET2 and TET3 in regulatory T cells unleashes effector function

city: La Jolla

first: Anjana

last: Rao

address: 9420 Athena Cir

department: Signaling and Gene Expression

institute: La Jolla Institute for Allergy and Immunology

summary: We studied the effects of loss of TET proteins in regulatory T cells in mice and compared the transcriptional profiles in Treg cells and CD4+ T cells isolated from WT and Tet2/3 DKO mice

overall_design: Transcriptional profiles were generated for CD4+Foxp3+ Treg cells and CD4+Foxp3- T cells isolated from WT and Tet2/3 DKO mice

first: Xiaojing

last: Yue

first: Daniela

last: Samaniego-Castruita


title: Mast cell cytonemes as a defense mechanism against Coxiella burnetii

city: marseille

first: Amira

last: Ben Amara

address: 27  Boulevard Leï Roue

country: France

institute: IHU-CRCM

summary: Mast cells (MCs) are critical mediators of inflammation; however, their microbicidal activity against invading pathogens remains largely unknown. Here, we describe a nonpreviously reported antibacterial mechanism used by MCs against Coxiella burnetii, the agent of Q fever. We show that C. burnetii interaction with MCs does not result in bacterial uptake but rather induces the formation of extracellular actin filaments named cytonemes. MC cytonemes express cathelicidin and neutrophil elastase and mediate the capture and destruction of entrapped bacteria. We provide evidence that MC cytoneme formation and microbicidal activity are dependent on the cooperation of the scavenger receptor CD36 and Toll-like receptor 4. Taken together, our results suggest that MCs use an extracellular sophisticated mechanism of defense to eliminate intracellular pathogens, such as C. burnetii, before their entry into host cells.

overall_design: The human mast cell line HMC-1.2 was cultured in Iscove's Modified Dulbecco's Medium (IMDM, Life Technologies) supplemented with 10% fetal bovine serum (FBS), 100 IU/ml penicillin and 50 µg/ml streptomycin (Life Technologies) at 37°C.

first: Soraya

last: Mezouar

first: Joana

last: Vitte

first: Laurent

last: Gorvel

first: Benoit

last: Desnues

first: Jean-Louis

last: Mege


title: BRD9 defines a novel SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors [RNA-seq 2]

city: Boston

first: Peter

last: Park

first: Xiaofeng

last: Wang

first: Su

first: Charles

last: Roberts


title: Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders

city: Rochester

first: Purna

last: Kashyap

state: MN

address: 200 1st St SW

institute: Mayo Clinic

summary: Small intestinal bacterial overgrowth (SIBO) has been implicated in symptoms associated with functional gastrointestinal disorders (FGIDs), though mechanisms remain poorly defined and treatment involves non-specific antibiotics. Here we show that SIBO based on duodenal aspirate. culture reflects an overgrowth of anaerobes, does not correspond with patient symptoms, and may be a result of dietary preferences. Small intestinal microbial composition, on the other hand, is significantly altered in symptomatic patients and does not correspond with aspirate culture results. In a pilot interventional study we found that switching from a high fiber diet to a low fiber, high simple sugar diet triggered FGID-related symptoms and decreased small-intestinal microbial diversity and small-intestinal permeability. Our findings demonstrate that characterizing small intestinal microbiomes in patients with gastrointestinal symptoms may allow a more targeted antibacterial or a diet-based approach to treatment.

overall_design: A host duodenal RNA sequencing study in conjuction with a microbial analysis of small bowel aspirates following dietary intervention to reduce fiber intake for 1 week.   Aspirates were collected during research endoscopy and submtttied for for 16S microbial identification (european

first: Kevin

last: Thompson


title: The susceptibility of sea-island cotton recombinant inbred lines to Fusarium oxysporum f. sp. vasinfectum infection is characterized by altered expression of long noncoding RNAs

city: wuhan

first: dong

last: chen

address: GaoXin 2nd Road

institute: ablife

summary: Disease resistance is one of the most complicated yet important plant traits. The potential functions of long noncoding RNAs (lncRNAs) in response to pathogenic fungi remain unclear. In this study, we sequenced the transcriptomes of four different sea-island cotton (Gossypium barbadense) recombinant inbred lines (RILs) with susceptible, highly susceptible, highly resistant, or super highly resistant phenotypes and compared their responses to Fusarium oxysporum f. sp. vasinfectum (Fov) infection with those of their susceptible and resistant parents. Infection-induced protein coding genes were highly enriched in similar disease resistance-related pathways regardless of fungal susceptibility. In contrast, we found that the expression of a large number of Fov infection-induced lncRNAs was positively correlated with plant susceptibility. Bioinformatics analysis of potential target mRNAs of lncRNAs with both trans-acting and cis-acting mechanisms showed that mRNAs co-expressed or co-located with Fov-regulated lncRNAs were highly enriched in disease resistance-related pathways, including glutathione metabolism, glycolysis, plant hormone signal transduction, anthocyanin biosynthesis, and butanoate metabolism. Together these results suggest that lncRNAs could play a significant role in the response to pathogenic fungal infection and the establishment of disease resistance. The transcriptional regulation of these infection-susceptible lncRNAs could be coordinated with infection-susceptible mRNAs and integrated into a regulatory network to modulate plant-pathogen interactions and disease resistance. Fov-susceptible lncRNAs represent a novel class of molecular markers for breeding of Fov-resistant cotton cultivars.

overall_design: Examination between resistant and susceptible cotton before and after infected with Fov

first: Yi

first: Yanying

last: Qu


title: Regulation of mesenchymal stem to transit amplifying cell transition in the continuously growing mouse incisor [Ring1b ChIP]

city: London

first: Paul

middle: T.

last: Sharpe

state: Please select one below:

address: Guy's hospitial

department: Centre for Craniofacial and Regenerative Biology

institute: King's College London

summary:
Regulation of transit amplifying cell formation from self-renewing stem cell is fundamental process for cell replacement in a controlled way. Here we analyse the properties of a population of mesenchymal TACs in the continuously growing mouse incisor to identify key components of the molecular regulation that drives proliferation. We show that the polycomb repressive complex 1 acts as a global regulator of the TAC phenotype by its direct action on the expression of key cell cycle regulatory genes and also by regulating Wnt/b-catenin signalling activity. We also identify an essential requirement for TACs in maintaining the mesenchymal stem cells, indicative of a positive feedback mechanism.
Analysing the properties of mesenchymal transit amplifying cells population and identifing key components of the molecular regulation that drives proliferation.

overall_design: Ring1b ChIP-seq and input sample

first: Zhengwen

last: An

first: Basem

last: Akily

first: Maja

last: Sabalic

first: Guo

last: Zong


title: Ikaros regulates gene expression downstream of TCR signaling

first: Ameya

last: Champhekar

summary: The transcription factor Ikaros plays a critical role during lymphocyte differentiation, proliferation and activation. The deletion of Ikaros zinc finger 4 (Ikaros-Zn4-/-) results in the lowering of activation threshold and increased proliferation of mature T cells. Here we used CD8+ T cells from homozygous Ikaros-Zn4-/- mice to investigate its role in regulating gene expression downstream of T-cell receptor signaling.

overall_design: Naïve CD8+ T cells from WT or homozygous IkarosZn4-/- mice were stimulated with plate-bound anti-CD3 and anti-CD28 antibodies. Cells were used immediately (0 hour) or harvested 12 and 24 hours after stimulation and used for expression profiling.

first: A

first: S

last: Smale


title: Next Generation Sequencing (RNA-Sequencing) for the analysis of RUNX3 targets in H460, H460-ERT2-RUNX3 WT and H460-ERT2-RUNX3 MT(K94/171R mutation)

city: Cheongju

first: Jung-Won

last: Lee

address: 1, Chungdae-ro

department: Department of Biochemistry, School of Medicine

institute: Institute for Tumor Research

summary:
Purpose: The goal of this study is to compare the gene expression profiles of H460, H460-ERT2-RUNX3-WT and H460-ERT2-RUNX3-MT(K94/171R) cells.
Methods: H460, H460-ERT2-RUNX3 WT, and H460-ERT2-RUNX3-MT(K94/171R) cells were serum-starved for 24 hr, and then stimulated with 10% serum or 10% serum + 1 uM 4-OHT for 0, 8, or 16 hr. RNA was extracted from the cells. Isolated total RNA was processed for preparation of an RNA-seq library using the Illumina TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, CA, USA). Quality and size of libraries were assessed using the Agilent 2100 Bioanalyzer DNA kit (Agilent, Santa Clara, CA, USA). All libraries were quantified by qPCR using a CFX96 Real Time System (Bio-Rad, Hercules, CA, USA) and sequenced on NextSeq500 sequencers (Illumina). Sequencing adapters and low-quality bases in the raw reads were trimmed using the Cutadapt software. The cleaned high-quality reads were mapped to the human reference genome hg19 (https://genome.ucsc.edu) using STAR software. Genes differentially expressed between two selected biological conditions were identified by Cuffdiff in the Cufflinks package (http://cole-trapnell-lab.github.io/cufflinks/papers/).
Results: RNA-Sequencing Data suggest that the R-point defends against oncogenic K-RAS–induced tumorigenesis not only by regulating intracellular programs (cell cycle, apoptosis, and metabolic pathways), but also by regulating extracellular programs (inflammatory response and immune response).

overall_design:
Compare the gene expression profiles of H460, H460-ERT2-RUNX3-WT and H460-ERT2-RUNX3-MT(K94/171R) cells.
Isolated total RNA was processed for preparation of an RNA-seq library using the Illumina TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, CA, USA). Quality and size of libraries were assessed using the Agilent 2100 Bioanalyzer DNA kit (Agilent, Santa Clara, CA, USA). All libraries were quantified by qPCR using a CFX96 Real Time System (Bio-Rad, Hercules, CA, USA) and sequenced on NextSeq500 sequencers (Illumina). Sequencing adapters and low-quality bases in the raw reads were trimmed using the Cutadapt software. The cleaned high-quality reads were mapped to the human reference genome hg19 (https://genome.ucsc.edu) using STAR software. Genes differentially expressed between two selected biological conditions were identified by Cuffdiff in the Cufflinks package (http://cole-trapnell-lab.github.io/cufflinks/papers/). For cell line studies, heatmaps were analyzed by the log-rank test using the PermutMatrix software. Gene clustering was analyzed using DAVID Bioinformatics Resources 6.8.

first: Suk-Chul

last: Bae


title: YAP/TAZ as new regulatory hub of VEGF signaling

city: Heidelberg

first: Carmen

last: Ruiz de Almodovar

address: Im Neuenheimer Feld 328

institute: Heidelberg University Biochemistry Center (BZH)

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: ChIP-seq analysis of myeloma cell lines

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

summary: ARP1, MM1S, and RPMI8226 myeloma cells lines were analyzed by ChIP-seq using antibodies against BRD4, MED1, IKZF1, ETV4

overall_design: BRD4, MED1, IKZF1, ETV4 ChIP-seq was performed in ARP1, MM1S, and RPMI8226 as detailed below

first: Paola

last: Neri

first: Nizar

last: Bahlis


title: Genome-wide Methylation in Cordblood CD4+ Cells from Newborns Exposed vs. Unexposed to Maternal Tobacco Smoke During Pregnancy

first: Carrie

last: Breton

state: CA

address: 2001 N Soto St

department: Preventive Medicine

institute: University of Southern California

summary: We generated genome-wide methylation levels, using whole-genome bisulfite sequencing, for sorted CD4+ cells from cordblood of newborns exposed vs. unexposed to tobacco smoke in utero

overall_design: Comparison of genome-wide methylation levels in 10 prenatal tobacco smoke-exposed newborns matched to 10 unexposed newborns

first: Caitlin

last: Howe


title: YAP/TAZ as new regulatory hub of VEGF signaling [ChIP]

summary:
VEGF is a major driver of blood vessel formation.
However, the signal transduction pathways culminating into the biological consequences of VEGF signaling are partially understood.
Here we show that the Hippo pathway effectors YAP and TAZ, work as a regulatory hub in mediating VEGF-VEGFR2 signaling during angiogenesis.
We demonstrate that YAP/TAZ are essential for vascular development as endothelium specific deletion of YAP/TAZ leads to impaired vascularization and embryonic lethality.
Mechanistically, we show that VEGF activates YAP/TAZ via its effects on actin cytoskeleton remodeling, and that activated YAP/TAZ induce a transcriptional program that results in the expression of a set of genes to further control cytoskeleton dynamics, and thus ensure a proper angiogenic response.
YAP/TAZ deletion also results in VEGFR2 trafficking defects from the Golgi to the plasma membrane.
Together, our study establishes YAP/TAZ as a central regulatory hub that mediates VEGF signaling, and hence, regulates angiogenesis.

overall_design: Human brain microvascular endothelial cells (HBMECs) with or without VEGF treatment were performed for YAP/TAZ ChIP-seq

first: Xiaohong

last: Wang

first: Aida

last: Freire

first: Géza

last: Schermann

first: Ivan

last: Moya

first: Ying

last: Shen

first: Laura

last: Castro

first: Severino

last: Urban

first: Gergely

last: Solecki

first: Frank

last: Winkler

first: Alba

last: Diz-Muñoz

first: Thomas

last: Schmidt

first: Tamás

last: Fischer

first: Georg

last: Halder

last: de Almodóvar


title: RNA sequencing analysis of selumetinib-resistant CRC cells lines

status: Public on Mar 11 2019

city: Waltham

first: Aleksandra

last: Markovets

state: Massachusetts

address: 35 Gatehouse Dr.

department: Oncology, iMED

institute: AstraZeneca

summary: RNA sequencing analysis to compare parental colorectal cancer cell lines and their selumetinib-resistant derivatives and identify expression changes and/or mutations that might contribute to resistance

overall_design: RNA sequencing analysis in 5 colorectal cancer cell lines and comparison to selumetinib-resistant derivatives

first: Jonathan

last: Dry


title: Copy number analysis of selumetinib-resistant CRC cells lines

summary: Copy number analysis to compare parental colorectal cancer cell lines and their selumetinib-resistant derivatives and identify gene copy changes that might contribute to resistance

overall_design: Array comparative genomic hybridisation analysis in 5 colorectal cancer cell lines and comparison to selumetinib-resistant derivatives


title: Transcriptomic analysis of strains evolved for anaerobic xylose utilization

city: Madison

first: Kevin

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison


title: Condensin II Counters Cohesin and RNA Polymerase II in 3D Chromatin Organization

city: Omaha

first: M

middle: Jordan

last: Rowley

state: NE

address: 601 S Saddle Creek Rd

department: GCBA

institute: Univ of Nebraska Medical Center

summary: CTCF is present at the anchors of thousands of loops likely formed via cohesin-mediated loop extrusion in mammalian cells. Interaction domains present in D. melanogaster chromosomes form via the segregation of active and inactive chromatin in the absence of CTCF looping, but the role of transcription versus other architectural proteins in chromatin organization is unclear. Here we find that positioning of RNAPII via transcription elongation is essential in the formation of gene loops, which in turn interact to form compartmental domains. Inhibition of transcription elongation or depletion of cohesin decreases gene looping and formation of active compartmental domains. In contrast, depletion of condensin II, which also localizes to active chromatin, results in increased gene looping, formation of compartmental domains, and stronger intra-chromosomal compartmental interactions. Condensin II has a similar role in maintaining inter-chromosomal interactions responsible for pairing between homologous chromosomes, whereas inhibition of transcription elongation or cohesin depletion has little effect on homolog pairing. The results suggest distinct roles for cohesin and condensin II in the establishment of 3D nuclear organization in Drosophila.

overall_design:
Hi-C after 3 hours Flv treatment
HiChIP for RNAPII or Rad21
Hi-C after knockdown of Slimb
ChIP-seq under normal conditions
ChIP-seq after knockdown of Rad21 or Cap-H2
ChIP-seq after 3 hours Flv treatment

first: Jordan

first: Xiaowen

last: Lyu

first: Vibhuti

last: Rana

first: Masami

last: Ando-Kuri

first: Rachael

last: Karns

first: Giovanni

last: Bosco

first: Victor

last: Corces


title: Differential expression analysis of a hyperthermophilic archeaon Methanocaldococcus jannaschii upon hydrogen limitation and hydrogen syntrophy with Thermococcus paralvinellae

city: Amherst

first: Begum

middle: D.

last: Topcuoglu

address: 336 North Pleasant St., Apt:3B

department: Microbiology

institute: University of Massachusetts

summary: The purpose of this experiment was to compare the transcriptomes of M. jannaschii using RNA-Seq gene expression analyses to understand the physiology of this organism when it is grown under H2-replete, H2-limited and H2-syntrophy conditions. The RNA-seq reads were mapped to both M. jannaschii and T. paralvinellae genomes using BBSplit from BBMap package. BBSplit is an aligner tool that bins sequencing reads by mapping to them multiple references simultaneously and separates the reads that map to multiple references to a special "ambiguous" file for each of them. For further analyses we removed all ambiguously mapped reads to both genomes and worked with only the reads that unambiguously map to M. jannaschii genome. The mapped reads for M. jannaschii were then aligned to the M. jannaschii genome again and sorted using the STAR aligner version 2.5.1b . Aligned sequence reads were assigned to genomic features and quantified using featureCounts read summarization tool. Genes that were differentially expressed were identified using ‘DESeq2’ in the Bioconductor software framework in R. The differential gene expression analyses  showed that the enzyme responsible for the reduction of methenyl group to a methylene group during carbon fixation switches from a H2-dependent enzyme to a coenzyme F420-dependent enzyme with decreasing H2 availability and into syntrophy. During syntrophy, the genes for energy generation on the membrane decreased in their expression levels.

sample_organism:
Methanocaldococcus jannaschii
Thermococcus paralvinellae

overall_design: Total RNA was extracted from 13 cell pellets from 4 different conditions.1. M. jannaschii was grown in monoculture on high H2 in a chemostat in biological triplicates. 2. M. jannaschii was grown in monoculture on low H2 in a chemostat in biological triplicates. 3. M. jannaschii in co-culture with T. paralvinellae was grown in the bottles with maltose in 3 biological and 2 technical replicates. 4. M. jannaschii in co-culture with T. paralvinellae was grown in the bottles with formate in 4 biological and 1 technical replicates. Technical replicates were pooled for larger RNA yields.

first: Cem

last: Meydan


title: Highly resolved systems biology to dissect the etioplast-to-chloroplast transition in tobacco leaves

status: Public on Mar 09 2019

city: Potsdam-Golm

first: Tegan

last: Armarego-Marriott

address: Am Muehlenberg, 1

institute: Max Planck Institute of Molecular Plant Physiology

summary: Upon exposure to light, plant cells quickly acquire photosynthetic competence by converting pale etioplasts into green chloroplasts. This developmental transition involves the de novo biogenesis of the thylakoid system, and requires reprogramming of metabolism and gene expression. Etioplast-to-chloroplast differentiation involves massive changes in plastid ultrastructure, but how these changes are connected to specific changes in physiology, metabolism and expression of the plastid and nuclear genomes is poorly understood. Here a new experimental system in the dicotyledonous model plant tobacco (Nicotiana tabacum) that allows us to study the leaf de-etiolation process at the systems level. We have determined the accumulation kinetics of photosynthetic complexes, pigments, lipids and soluble metabolites, and recorded the dynamic changes in plastid ultrastructure and in the nuclear and plastid transcriptomes. Our data describe the greening process at high temporal resolution, resolve distinct genetic and metabolic phases during de-etiolation, and reveal numerous candidate genes that may be involved in light-induced chloroplast development and thylakoid biogenesis.

overall_design: Time-course transcriptome profiling by RNA-sequencing of de-etiolating tobacco leaves

first: Łucja

last: Kowalewska

first: Asdrubal

last: Burgos

first: Axel

first: Wolfram

last: Thiele

first: Alexander

last: Erban

first: Deserah

last: Strand

first: Sabine

last: Kahlau

last: Hertle

first: Joachim

last: Kopka

first: Dirk

last: Walther

first: Ziv

last: Reich

first: Mark

last: Aurel Schoettler

first: Ralph

last: Bock


title: The long noncoding RNA Pnky is a trans-acting regulator of cortical development in vivo

status: Public on Mar 08 2019

city: San Francisco

first: Tomasz

last: Nowakowski

state: Ca

institute: UCSF

summary: While it is now appreciated that certain long noncoding in vivo, particularly with genetic strategies that establish cis versus trans mechanisms.  Pnky is a nuclear-enriched lncRNA that is transcribed divergently from the neighboring proneural transcription factor Pou3f2.  Here we show that conditional deletion of Pnky from the developing cortex regulates the production of projection neurons from neural stem cells (NSCs) in a cell-autonomous manner, altering postnatal cortical lamination.  Surprisingly, Pou3f2 expression is not disrupted by deletion of the entire Pnky gene.  Moreover, expression of Pnky from a BAC transgene rescues the differential gene expression and increased neurogenesis of Pnky-knockout NSCs, as well as the developmental phenotypes of Pnky-deletion in vivo.  Thus, despite being transcribed divergently from a key developmental transcription factor, the lncRNA Pnky regulates development in trans.

overall_design: Set 1: Differential expression of acutely-dissected cortical tissue from E12.5 embryos. Biological triplicate samples of Pnky(fl/fl);Emx1-Cre and controls. Set 2: Differential expression in cultured NSCs performed by dissecting cortex from E12.5 Pnky(+/+), Pnky(fl/fl),  and Pnky(fl/fl);BAC-Pnky mice in biological triplicate. Recombination was induced by Ad:Cre and cultured for 3 days prior to RNA extraction. Group-specific condition effects were analyzed by RNA-seq.

first: Ryan

middle: N

last: Delgado


title: Epidermal overexpression of ∆NLef1 leads to deregulation of epidermal stem cell fate

first: Giacomo

last: Donati

address: Guy's Hospital, Great Maze Pond

summary: In adult K14ΔNLef1 mouse, the overexpression of ∆NLef1, a B-catenin dominat negative, in basal keratinocytes leads to the conversion of hair follicles into multilayered epithelial cysts and ectopic sebaceous gland. To uncover in vivo changes in gene expression associated to ΔNLef1 activity, we compared the expression profiles of basal keratinocytes (Itga6+) and bulge stem cells (cd34+/itga6+) in wild type and K14ΔNLef1 transgenic mice. Cells were collected from 9.5 week old mice, when the hair follicle are in the resting (telogen) phase of the hair growth cycle. At this stage the ΔNLef1 phenotype is not yet evident enabling us to detect early molecular events.

overall_design: We compared the expression profiles of basal keratinocytes (Itga6+) and bulge stem cells (cd34+/itga6+) in wild type and K14ΔNLef1 transgenic 9.5 week old mice. Three biological replicates for each cell population were analyzed.

first: Fiona

last: Watt


title: RNA-seq identifies a distinct response in macrophages stimulated with early secreted antigenic target 6-KDa from Mycobacterium tuberculosis

status: Public on Mar 10 2019

city: Chongqing

first: Fake

last: Li

state: Chongqing

address: Changjiangzhilu 10 Yuzhong District

department: Clinical Laboratory Medicine

institute: Daping Hospital

summary:
Purpose: The goals of this study are to obtain the NGS-derived transcriptome profiling (RNA-seq) for THP-1 macrophages response to early secreted antigenic target 6-KDa (ESAT6) from Mycobacterium tuberculosis
Methods: mRNA profiles of THP-1 macrophages treated with ESAT6 were generated by deep sequencing, using Illumina Hiseq3000. The sequence reads that passed quality filters were first mapped to the latest UCSC transcript set using Bowtie2 (version 2.1.0). Then the gene expression level was estimated using RSEM (RNA-Seq by Expectation Maximization, v1.2.15), and normalized with TMM (trimmed mean of M-values) to identify differentially expressed genes (DEGs) using the edgeR package edgeR. qRT–PCR validation was performed using SYBR Green assays.
Results: Using an optimized data analysis workflow, we mapped about 23 million sequence reads per sample to the human genome (GRCh38/hg38) and identified 25,343 transcripts.
Conclusions: Our study represents the first detailed analysis of transcriptomes for macrophages response to ESAT6, generated by RNA-seq technology.

overall_design: NGS-derived transcriptome profiling (RNA-seq) for THP-1 macrophages response to early secreted antigenic target 6-KDa (ESAT6) from Mycobacterium tuberculosis.

first: Ming

last: Chen


title: Regulation of mesenchymal stem to transit amplifying cell transition in the continuously growing mouse incisor [Histone ChIP]

first: Paul

last: Sharpe

overall_design: Histone ChIPseq without input sample (SICER algorithm used for analysis does not reqire input sample)

first: Zhengwen

last: An

first: Basem

last: Akily

first: Maja

last: Sabalic

first: Guo

last: Zong


title: Gene Expression In Blood From an Individual With β-Thalassemia: an RNA Sequence Analysis

city: Northridge

first: Aida

last: Metzenberg

address: 18111 Nordhoff Street

department: Biology

institute: California State University, Northridge

summary: Background: The thalassemias are highly diverse at both the molecular and clinical levels. Many of the HBB mutations that result in β-thalassemia are missense mutations in the coding region of the β-globin gene, but a few cause alternative splicing, and interfere with normal processing of the β-globin transcripts. Transcriptome profiling in individuals affected with β-thalassemia, especially in individuals who carry novel mutations in the HBB, may improve our understanding of the heterogeneity and molecular mechanisms of the disease. Methods: Members of a family with a daughter affected with thalassemia intermedia, although her mother was not clinically affected, were examined for physical characteristics, hematological parameters and β-globin gene sequences. We also characterized genome-wide gene expression in the family using RT-qPCR and high-throughput RNA-sequencing mRNA expression profiling of blood. Results: Clinical findings, hematological indices, DNA and RNA sequence analysis of individuals with β-thalassemia, including the description of a novel mutation in the β-globin gene, which introduces a cryptic donor splice site. More than 300 genes are differentially expressed in β-thalassemic blood with many of the DEGs involved in pathways relevant to the clinical management of β-thalassemia. β-thalassemia shows important similarities and differences with sickle cell disease at the transcriptome level. Conclusions: We described the down-regulation of the β-globin gene in β-thalassemia by RNA-sequencing analysis using a sample from an affected individual and her mother, who have a novel mutation in the HBB that creates a cryptic donor splice site. The daughter has a typical β-thalassemia allele as well, and an unexpectedly severe phenotype. The DEGs are enriched in pathways that are directly or indirectly related to β-thalassemia such as hemopoiesis, heme biosynthesis, response to oxidative stress, inflammatory responses, immune responses, control of circadian rhythm, apoptosis, and other cellular activities. We compare our findings with published results of RNA-Sequencing analysis of sickle cell disease (SCD) and erythroblasts from a KLF1-null neonate with hydrops fetalis, and recognize similarities and differences in their transcriptional expression patterns.

overall_design: Total RNA was isolated from blood using EDTA as an anticoagulant and Trizol reagent (Sigma-Aldrich, Germany). 500ng of the total RNA from each of the daughter (sample D), mother (sample M), and a control individual with normal hematological indices (sample N) was used for RNA-Sequencing library preparation, and the quality of RNA was determined with Bioanalyzer 2100. Libraries for RNA-sequencing were prepared with a KAPA Stranded RNA-sequencing Kit (Illumina), following the manufacture’s instructions. Sequencing was performed on an Illumina HiSeq 2500 system for pair-ended reads with a length of 100 bp (2x100 bp). Pre-processing and data quality control were performed using Illumina proprietary software.

first: Forough

last: Taghavifar

first: Mohammad

last: Hamid

first: Gholamreza

last: Shariati

first: Stan