title: Newly identified Aspergillus nidulans PKA targets play a role in carbon-catabolite repression

status: Public on Jul 04 2018

city: Ribeirão Preto

first: Liliane

middle: Fraga Costa

last: Ribeiro

state: São Paulo

address: 3900, Bandeirantes avenue

country: Brazil

institute: University of São Paulo

summary: A transcriptomic assessment of a kinase deletion mutant (ΔpkaA) and a control strain revealed many cellular activities this kinase is impacting. Studies were conducted in the model filamentous fungi, Aspergillus nidulans¸ under rich growth conditions. PkaA is a known kinase that mediates a wide range of processes including: nutrient sensing, stress responses, regulation of metabolism, as well as development and pathogenicity. Here, fungi were grown in rich media containing glucose. The comparison between the control strain and the deletion mutant transcript levels revealed previously unknown targets, such as the transcription factor CreA, the main repressor responsible for carbon catabolite repression (CCR).

overall_design: A control strain and deletion mutant grown in rich media (2 biological replicates and 2 technical replicates) were analyzed to determine unknown functions and targest of PkaA using RNA-seq.

middle: F

first: Jyothi

last: Kumar

first: Steven

last: Harris

first: Mark

last: Marten


title: Chromosomal deletions drove parallel domestication of plant architecture in Asian and African rice

city: Beijing

first: Ma

last: Xin

state: --- Select a state ---

address: 2 Yuanmingyuan West Road, Haidian District, Beijing, China, 2 Yuanmingyuan West Road, Haidian District, Beijing, China

country: China

institute: China Agricultural University

type: Expression profiling by high throughput sequencing

summary: Improving the yield by modifying plant architecture is key to progressive crop domestication. Here, we show that a 110-kb deletion on the short arm of chromosome 7 promotes the critical transition from semi-prostrate growth and low yield in wild rice (Oryza rufipogon), to erect growth and high yield in Asian cultivated rice (O. sativa). The microdeletion harbors a tandem repeat of seven putative Cys2-His2 zinc-finger genes. Three of these genes regulate the plant architecture in O. rufipogon and are closely linked to the previously identified PROSTRATE GROWTH 1 (PROG1) gene. Therefore, we refer to this locus as RICE PLANT ARCHITECTURE DOMESTICATION (RPAD). Furthermore, a similar but independent 113-kb deletion was detected at the RPAD locus in African cultivated rice. These results indicate that the deletions, coupled with the loss of a tandem repeat of zinc-finger genes, drove the parallel domestication of plant architecture in Asian and African rice.

overall_design: Total RNA was isolated from tiller bases of the CP-PROG1, CP-ZnF5, CP-ZnF7, CP-ZnF8 transgenic lines and the control plants at 50 days after sowing, in triplicate, using Illumina system Hiseq2500.For transcriptome analysis, total RNAs of ten tissues from DXCWR，eight tissues from IRGC104165 and eight tissues from W1411 were isolated respectively, using TRIzol (Invitrogen, USA) according to the instructions.

first: Lu

middle: B

last: Tan


title: Transcriptome targets of PCBP1 in T cells

city: Shanghai

first: Xing

last: Chang

address: 320 Yueyang road

institute: Shanghai Institute for Biological Sciences

summary: Iron deposition is frequently observed in human autoinflammatory diseases, such as in the brain of patients with multiple sclerosis or in the synovial fluid of patients with rheumatoid arthritis1-5.  Yet, the functional outcome of excessive iron in inflammatory conditions is largely unknown. Granulocyte macrophage colony-stimulating factor (GM-CSF) is a proinflammatory cytokine promoting myeloid cell maturation and activation6 and is essential for the pathogenesis of many autoimmune diseases, including autoimmune encephalomyelitis7-10. Post-transcriptional regulation of GM-CSF is mediated primarily through its 3’ untranslated region (3’UTR) via interaction with specific RNA-binding proteins11. Here we show that a RNA-binding protein PCBP1 senses intracellular iron and post-transcriptionally promotes GM-CSF production. In a short hairpin (sh) RNA screening, we found that Poly(rC) binding protein 1 (PCBP1) enhanced GM-CSF 3’UTR activity and its endogenous mRNA stability. PCBP1 deficiency in autoreactive T cells resulted in a compromised production of GM-CSF and other proinflammatory cytokines, abolishing their capacity in inducing experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis. Using Crosslinking and Immunoprecipitation (CLIP)12, we demonstrated that PCBP1 promoted mRNA stability by recognizing CU rich elements in the 3’UTRs of pro-inflammatory cytokines. Furthermore, iron depletion induced rapid caspase-mediated proteolysis of PCBP1 and inhibited the production of GM-CSF and a module of 24 cytokines in primary murine and human T cells. Our study thus demonstrates that PCBP1 is critical for the post-transcriptional regulation of proinflammatory cytokines, and indicates that sensing iron may represent a simple yet effective means to adjust the inflammatory response to tissue homeostatic alterations.

overall_design: We apply high-throughput RNA seq analysis to determine the transcriptome change in murine Th1 cells after either shRNA mediated knockdown of PCBP1 or depletion of intracellular iron by an iron chelator ciclopirox olamine.

first: ZhiZhang

last: Wang


title: Generation of muscle stem cells from pluripotent stem cells

status: Public on Jul 05 2018

city: Minneapolis

first: Sunny

middle: Sun-Kin

last: Chan

state: MN

department: Pediatrics

country: USA

institute: University of Minnesota

summary: We have developed a method to generate muscle stem cells from pluripotent stem cells via teratoma formation.  The goal of this study is to compare the transcriptome of a7+ VCAM+ myogenic cells derived from pluripotent stem cells versus satellite cells

overall_design: RNA from a7+ VCAM+ myogenic cells derived from teratoma, transplanted muscles, E14.5 mouse embryos, and hindlimbs of 8-week-old mice.  In 3 biological replicates

middle: S

first: Michael

last: Kyba


title: Cell type-specific HITS-CLIP reveals differential RNA processing in motor neurons

city: New York

first: Yuan

last: Yuan

state: NY

address: 1230 York Ave

department: Laboraotry of Molecular Neuro-Oncology

institute: The Rockefeller University

summary: We report cell type specific Nova HITS-CLIP using BAC-transgenic lines expressing GFP-Nova under the motor neuron specific choline acetyltransferase (Chat) promoter.  By comparing transcriptome wide Nova binding map in motor neurons and that in the whole spinal cord, we identified differential Nova binding sites in motor neurons, which correlate with motor neuron specific RNA processing.

overall_design: 14 total samples were analyzed.  For HITS-CLIP, 4 biological replicates were performed for each BAC-transgenic line, as well as the whole spinal cord.  For RNA-seq,  2 biological repliates were performed on the whole spinal cord.

first: Hemali

last: Phatnani

first: Tom

last: Maniatis

first: Robert

last: Darnell


title: The dual methyltransferase METTL13 targets N-terminus and Lys55 of eEF1A and regulates codon-specific translation rates

city: Muenster

first: Benedikt

middle: Sebastian

last: Nilges

address: Von-Esmarch-Straße 54

department: RNA Biology Group

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

summary: Eukaryotic elongation factor 1 alpha (eEF1A) delivers aminoacyl-tRNA to the ribosome and thereby plays a key role in protein synthesis. Human eEF1A is post-translationally methylated on several lysine residues as well as on the N-terminus and until recently the responsible methyltransferases were largely elusive. Using mass spectrometry based screens, gene targeted cells and in vitro enzymology we identify the human methyltransferase like proteins 13 (METTL13), which contains two distinct methyltransferase domains, as an enzyme catalyzing both dimethylation of Lys55 and trimethylation of the N-terminus of eEF1A. Moreover, through ribosome profiling we demonstrate that loss of METTL13 function alters translation dynamics and results in changed translation rate of specific codons. In line with the established descriptive nomenclature for this type of enzymes we suggest that METTL13 is redubbed eEF1A dual methyltransferase (eEF1A-DMT / EEF1ADMT).

overall_design: ribosome profiling and poly(A) RNA sequencing of wildtype and MELL13-KO cells. Libraries were prepared as triplicates, except for wt ribosome profiling libraries that are duplicates only.

first: Magnus

middle: E

last: Jakobsson

first: Jędrzej

middle: M

last: Małecki

first: Levon

last: Halabelian

first: Rita

last: Pinto

first: Srikanth

last: Kudithipudi

first: Stephanie

last: Munk

first: Erna

last: Davydova

first: Fawzi

middle: R

last: Zuhairi

first: Cheryl

middle: H

last: Arrowsmith

first: Albert

last: Jeltsch

first: Sebastian

middle: A

last: Leidel

first: Jesper

middle: V

last: Olsen

first: Pål

middle: Ø

last: Falnes


title: Repression of Human and Mouse Brain Inflammaging Transcriptome by Broad Gene Body Histone Hyperacetylation

first: Jing-Dong

middle: Jackie

last: Han

address: 5 Yiheyuan Rd, Haidian District

institute: Peking University

type: Genome binding/occupancy profiling by high throughput sequencing

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: RNAseq data from FACS-sorted microglia from mouse brain from control mice (uninjected) or LPS-injected mice in the context of A20 knockout

status: Public on Jul 03 2018

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

summary: Using RNAseq, we compared the mRNA profiles of microglia in wild type or microglia-specific A20 knockout mice. These mice were either untreated or intraperitoneally injected with LPS (3.5 mg/kg).

overall_design: Microglial mRNA profiles were generated from wild type or microglia-specific A20 knockout mice either untreated or injected with LPS.

first: Sofie

last: Voet

first: Nora

last: Hagemeyer

first: Marco

last: Prinz

first: Geert

last: van Loo


title: Repression of Human and Mouse Brain Inflammaging Transcriptome by Broad Gene Body Histone Hyperacetylation (ChIP-seq)

summary: ChIP-seq data of human prefrontal cortex and mouse brain during aging and/or SAHA treatment were generated.

overall_design: For ChIP experiment, human brain samples with similar age were pooled together, mouse brain samples were processed individually. After purified input and IP DNA, library construction and high-throughput sequencing was done.


title: RNAseq data from FACS-sorted CD45hi cells from mouse brain from control mice (uninjected) or LPS-injected mice in the context of A20 knockout

summary: Using RNAseq, we compared the mRNA profiles of CD45hi cells in the brain of wild type or myeloid-specific A20 knockout mice. These mice were either untreated or intraperitoneally injected with LPS (3.5 mg/kg).

overall_design: CD45hi mRNA profiles were generated from wild type or brain cells-specific A20 knockout mice either untreated or injected with LPS.


title: Transcriptional profile of monocytes in the colon in response to C. rodentium infection

status: Public on Jul 02 2018

first: Patricia

middle: K

last: Martin

department: Pathology

institute: NYU School of Medicine

overall_design: Eight samples have been analyzed. All are from Cd11b+Ly6C+ inflammatory monocytes sorted from colonic tissue 9 days after C. rodentium infection from Atg16L1HM(4) and WT(4) mice.

first: Ken

last: Cadwell

last: Marton

first: Eugene

last: Rudensky


title: KAP1 facilitates reinstatement of heterochromatin after DNA replication

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

summary: During cell division, not only is the genome duplicated, but the maintenance of chromatin features on the parental DNA and their propagation onto daughter strands is a challenge. The loss of epigenetic marks on heterochromatin, typically enriched in repetitive elements, could lead to genome instability and chromosomal rearrangements via recombination. How they are maintained across cell division and most importantly which critical molecular players are involved is poorly understood. KAP1 is known to act as a scaffold for a repressor complex that mediates local heterochromatin formation, and plays an important role during DNA repair. Here we identify in KAP1 a novel role for the replication of heterochromatic regions. First, we observed that KAP1 associates with several DNA replication factors including PCNA, MCM3 and MCM6. Second, we found that these interactions are modulated by KAP1 phosphorylation during S phase. Finally we could demonstrate that KAP1 recruits HP1 and the histone-lysine methyltransferases Suv39h1 and Suv420h1. Based on these data, we propose a model for KAP1 involvement in maintaining heterochromatin during DNA replication and thereby preventing genome instability.

overall_design: Histone modification ChIP-seqs (H3K9me3, H4K20me3) in MEF cells for two conditions (WT and KAP1 KO) and KAP1 ChIP-seq in MEF WT.

first: Suk

last: Jang

last: Pontis


title: ATRA mediated regulation of chromatin state

city: Buffalo

first: AC

last: CHANG

address: Elm and Carlton

institute: RPCI

summary: Genome-wide ChIP is performed to examine ATRA-mediated regulation of Tet2 chromatin complex associtaion on different promoter regions.

overall_design: Tet2/RAR complex bound chromatin in ATRA or mock-treated MCF12A cells were examined

first: C

last: Chang


title: Transcriptome targets of PCBP1 in T cells identified with CLIP

first: Xing

overall_design: We apply CLIP and high throughput sequencing to identify PCBP1 -binding RNA in Jurkat T cells.

first: ZhiZhang

last: Wang


title: Expression analysis in mouse jejunum enteroids following over-expression of the zinc finger transcription factor PLAGL2

status: Public on Jul 01 2018

city: Saint Louis

first: Blair

last: Madison

state: MO

address: 660 S Euclid Ave

department: Medicine

institute: Washington University School of Medicine

summary: We examined mRNA level changes in two mouse enteroids clones expressing different levels of PLAGL2 from a constitutive Piggybac transposon vector.

overall_design: Expression analysis, PLAGL2 O/E vs. GFP O/E


title: Repression of Human and Mouse Brain Inflammaging Transcriptome by Broad Gene Body Histone Hyperacetylation (RNA-seq)

last: Han

summary: RNA-seq data of human prefrontal cortex and mouse brain during aging and/or SAHA treatment were generated.

overall_design: For RNA extraction, human brain samples with similar age were pooled together, mouse brain samples were extract individually. After RNA extraction by TRIzol, library construction and high-throughput sequencing was done.


title: MicroRNA-based prognostic model for early-stage oral cancer patients

first: Angela

last: Yoon

address: 630 West 168th Street, PH15W-1562

institute: Columbia University Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: The aim of our study is to develop a miRNA marker panel prognostic of 5-year survival in early-stage OSCC patients. We assessed differential expression of miRNAs genome-wide via deep sequencing in 100 tumor tissue samples. We also attempted to identify deregulated miRNA expression signatures that may serve as the prognostic markers.

overall_design: Identify miRNAs differentially expressed in the poor prognosis group (those who had recurrence and/or died of cancer) compared to the favoarble prognosis group (those who had 5-year cancer-free survival)

middle: J

first: Dominic

last: LaRoche


title: 16S profile of stool from conventional unifected and C.rodentium infected mice

summary: We aim to determine if mice in our mouse colony had similar of different microbiomes.  To do this, we perfromed 16S sequencing of stool from unifected mice of the gentotypes listed below.  We also looked at how infection causes dysbiosis of the mircobiome, measuring 16S sequencing over a C.rodentium infection timecourse.

overall_design: The 16S profile of 3-4 mice were analyzed for each genotype and condition listed

first: Frank

last: Yeung


title: Gene dosage effect of CUX1 in a murine model disrupts HSC homeostasis and controls the severity and mortality of MDS.

city: Chicago

first: Megan

middle: E.

last: McNerney

state: Illinois

address: 900 East 57th Street, KCBD 5128

institute: The University of Chicago

summary: Monosomy 7 (-7) and del(7q) are high-risk cytogenetic abnormalities common in myeloid malignancies. We previously reported that CUX1, a homeodomain-containing transcription factor encoded on 7q22, is frequently inactivated in myeloid neoplasms, and CUX1 myeloid tumor suppressor activity is conserved from humans to Drosophila. CUX1-inactivating mutations are recurrent in clonal hematopoiesis of indeterminate potential as well as myeloid malignancies, in which they independently carry a poor prognosis. To determine the role for CUX1 in hematopoiesis, we generated 2 short hairpin RNA-based mouse models with ∼54% (Cux1mid) or ∼12% (Cux1low) residual CUX1 protein. Cux1mid mice develop myelodysplastic syndrome (MDS) with anemia and trilineage dysplasia, whereas CUX1low mice developed MDS/myeloproliferative neoplasms and anemia. In diseased mice, restoration of CUX1 expression was sufficient to reverse the disease. CUX1 knockdown bone marrow transplant recipients exhibited a transient hematopoietic expansion, followed by a reduction of hematopoietic stem cells (HSCs), and fatal bone marrow failure, in a dose-dependent manner. RNA-sequencing after CUX1 knockdown in human CD34+ cells identified a -7/del(7q) MDS gene signature and altered differentiation, proliferative, and phosphatidylinositol 3-kinase (PI3K) signaling pathways. In functional assays, CUX1 maintained HSC quiescence and repressed proliferation. These homeostatic changes occurred in parallel with decreased expression of the PI3K inhibitor, Pik3ip1, and elevated PI3K/AKT signaling upon CUX1 knockdown. Our data support a model wherein CUX1 knockdown promotes PI3K signaling, drives HSC exit from quiescence and proliferation, and results in HSC exhaustion. Our results also demonstrate that reduction of a single 7q gene, Cux1, is sufficient to cause MDS in mice.

overall_design: RNA-seq after CUX1 knockdown in primary human cord blood CD34+ hematopoietic stem cells.


title: Increasing miRNA sequencing accuracy using an RNA circularization approach

city: Santa Cruz

first: Sergio

last: Barberan-Soler

state: CA

address: 2161 Delaware Avenue

institute: Somagenics Inc

summary: Accurate quantification of all microRNAs (miRNA) is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We have developed a new method of preparation of small RNA sequencing libraries (RealSeq®-AC) that ligates miRNAs with a single combo adapter and then circularizes the ligation products. When compared to other methods, RealSeq®-AC provided greatly reduced sequencing bias and allowed the identification of the largest variety of miRNAs in biological samples.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: The accuracy of detection of miRNAs was evaluated by sequencing miRNA-seq libraries in technical triplicates for each kit by using a synthetic pool of miRNAs (miRXplore pool, Miltenyi Biotec) and also a reference total RNA sample (Human Brain). The coverage of miRNA detection was evaluated by sequencing libraries prepared with TruSeq, RealSeq-AC, NEXTFlex, and QIAseq kits using a Universal miRNA Reference Kit (Agilent).

first: Sergei

last: Kazakov


title: Pre-microRNA-derived sequences in the supraspliceosome

city: Jerusalem

first: Shelly

last: Mahlab-Aviv

address: The Edmond J. Safra Campus - Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

summary: We report the presence of microRNA in the supraspliceosome in six different HeLa samples. After the extraction of the supraspliceosome we subjected its small RNA content to NGS. We identified 304 sequences derived from pre-miRNAs. About two thirds of them are mature miRNAs, which likely shuttled back from the cytoplasm, whereas the rest account for various defined regions of the pre-miRNA. Out of these 304 pre-miRNA-derived sequences, 95 were undetected in cellular extract, and the abundance of additional 58 strongly differed from that in cellular extract.

overall_design: Examination of presence of miRNA in the supraspiceosome in six different HeLa nuclear samples and one HeLa cellular sample.

first: A

last: Peretz

first: L

last: Carmel

first: R

last: Sperling

first: M

last: Linial


title: Iron-mediated stabilization of PCBP1 post-transcriptionally promotes GM-CSF production during autoimmune pathogenesis


title: RNA sequencing of 13 T-cell acute lymphoblastic leukemia patients (5 TCRAD-MYC translocated T-ALL_8TAL1-LMO2 T-ALL)

city: Gent

first: Gloria

last: Milani

address: Pintelaan 185

country: Belgium

institute: Gent University

summary: RNA sequencing analysis revealed a different expression profile between two different T-ALL subgroups, namely MYC-TCRAD translocated T-ALL vs TAL1-LMO2 T-ALL.

overall_design: RNA sequencing in T-cell acute lymphoblastic leukemia patients with and without MYC-TCRAD translocation using the QuantSeq technology

first: Juliette

last: Roels

first: Pieter

last: Van Vlierberghe


title: Microglia-expressed A20 regulates synapse formation and inhibits inflammasome-dependent neuroinflammation

first: Ori

last: Staszewski


title: Genetic characterization and therapeutic targeting of MYC rearranged T-cell acute lymphoblastic leukemia

summary: T-cell acute lymphoblastic leukemia (T-ALL), an aggressive hematological tumor that arises from T-cell precursor cells, is often characterized by T cell receptor (TCR) translocations that drive aberrant activation of specific proto-oncogenes. Here, we performed a detailed molecular genetic characterization of a rare but aggressive genetic subtype of human T-ALL, ie. patients that present with a t(8;14)(q24;q11) translocation, in which high MYC levels are driven by enhancer elements of the TCR a/d locus (TCRAD-MYC). Notably, analysis of an extensive series of primary leukemia samples confirmed that TCRAD-MYC translocation positive T-ALLs represent a NOTCH1 independent subtype of T-cell leukemia characterized by aberrant activation of the TAL1 and/or LMO2 transcription factor oncogenes and frequent activation of the PI3K/AKT signaling pathway. From a therapeutic perspective, in vivo drug treatment experiments using primary patient derived xenografts revealed that TCRAD-MYC positive T-ALLs are sensitive to BET bromodomain inhibition, providing a rationale to develop BRD4 inhibitors as an adjuvant therapy for this rare, but genetically well-defined, high-risk subtype of human leukemia.

overall_design: We performed H3K27ac chromatin immunoprecipitation (ChIP) sequencing analysis on the t(8;14)(q24;q11) positive MOLT16 cells to study the enhancer landscape in proximity of the TCRAD locus, which is involved in TCRAD-MYC translocation in a rare T-ALL subgroup.

last: Milan

first: Wouter

last: Van Loocke

first: Filip

last: Matthijssens


title: H3.3K27M mutant proteins reprogram epigenome by sequestering the PRC2 complex to poised enhancers

first: zhiguo

last: zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

summary: Expression of histone H3.3K27M mutant proteins in diffuse intrinsic pontine glioma (DIPG) results in a global reduction of tri-methylation of H3K27 (H3K27me3), and paradoxically, H3K27me3 peaks remain at hundreds of genomic loci, a dichotomous change that lacks mechanistic insights. Here we show that the PRC2 complex is sequestered at poised enhancers, but not at active promoters with high levels of H3.3K27M proteins, thereby contributing to the global reduction of H3K27me3. Moreover, the levels of H3.3K27M proteins are low at the retained H3K27me3 peaks and consequently having minimal effects on the PRC2 activity at these loci. H3K27me3-mediated silencing at specific tumor suppressor genes, including Wilms Tumor 1, promotes proliferation of DIPG cells. These results support a model in which the PRC2 complex is redistributed to poised enhancers in H3.3K27M mutant cells and supports the proliferation of DIPG cells in part through silencing of tumor suppressor gene WT1.

overall_design: To analyze how H3K27me3 are altered throughout the epigenome in H3.3K27M mutant cells, we performed H3K27me3, H3.3K27M, and EZH2 ChIP-seq in SF7761 and SF8628 cell lines and tissue samples. To gain further insight into the impact of H3.3K27M mutant proteins on H3K27me3, we also introduce the same heterozygous mutation at the H3F3A gene in mouse embryonic stem cells (ES) using the CRISPR/Cas9 genome editing technology. And performed H3K27me3, H3.3K27M, and EZH2 ChIP-seq in WT and H3.3K27M mouse embryonic stem cells.

first: Dong

last: Fang

first: Haiyun

last: Gan

first: Jeong

last: Lee

first: Hui

last: Zhou

first: Jann

last: Sarkaria

first: Zhiguo

last: Zhang


title: Common lymphoid progenitor derivation of plasmacytoid dendritic cells is mediated by Bcl11a

city: Austin

first: Joseph

middle: D

last: Dekker

state: TX

address: 2506 Speedway Blvd, NMS 1.264

department: Molecular Biosciences

institute: University of Texas at Austin

summary: Plasmacytoid dendritic cells (pDC) specialize in type I interferon production to coordinate innate and adaptive immunity. We identify two pDC subsets in vivo, evaluate their genome-wide expression, and demonstrate a developmental requirement for Bcl11a to provide insight into this enigmatic cell type.

overall_design: We separated plasmacytoid dendritic cells that were derived from either the common lymphoid progenitor or the common myeloid progenitor by flow cytometry, collected RNA, and ran RNA-seq.


title: Novel applications of next generation sequencing tools to assess the health of Steller sea lion (Eumetopias jubatus) populations

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Some rookeries of the western distinct population segment (WDPS) of Steller sea lions (Eumetopias jubatus) in the Aleutian Islands (Alaska, USA) have experienced continued declines since the initial collapse of the population in the 1970-1980s. Several theories have been put forward to explain the decline and lack of subsequent recovery including predation, nutritional stress, contaminants, and infectious disease agents, but thus far a primary cause has not been identified. Examining gene expression profiles of organisms has been promoted as a way to assess several health indicators related to toxicoses, infection, and nutritional stress using recent advances in metagenetics (next-generation sequencing) analyses. Next-generation sequencing may provide a more refined and adaptable method of investigating sea lion health under difficult research field collections. Here we suggest that the application of next-generation sequencing tools has the potential to evaluate the transcriptomic (gene expression) profile of animals from declining rookeries. We show that high quality RNA can be obtained from wildlife populations despite logistically challenging field conditions. We compared RNA expression in whole blood using whole transcriptome sequencing (RNA-Seq) among animals with relatively high concentrations of total mercury ([THg]) to animals with lower concentrations. There did not appear to be significant changes in gene expression in animals with high [THg] in whole blood, despite some animals having concentrations above thresholds of concern for model organisms. We did find evidence of a bias toward downregulation of some genes in animals with higher [THg].

overall_design: Steller sea lion pups were captured  on 2 rookery islands in the WDPS (Agattu Island/Gillon Point, and Ulak Island/Hasgox Point) during June 24 - July 17, 2013 and June 18 - July 5, 2015. Blood samples were then collected via the caudal gluteal vein for THg analysis (Vacuette Trace Element, Geiner Labortechnik, Kremsmünter, Austria) and for RNA stabilization and collection (PaxGene? RNA, PreAnalytiX, Hombrechtikon Switzerland).  Blood was stored at approximately -15°C for the duration of the cruise (approximately 3 weeks), and placed in a -80°C freezer upon arrival at UAF. RNA-Seq samples were selected from Agattu (n= 18) and Ulak (n=6) Islands, both of which have declining pup counts from 2000 to present (Figure 1b, Fritz et al., 2015). In order to maximize study efficacy while working with limited funding, we decided to analyze samples with high and low [THg] (extremes) rather than treating [THg] as a continuous variable. We selected six individuals with the highest [THg] and lowest [THg] from each year of sampling (2013 and 2015).

first: John

last: Harley

middle: W

first: Lorrie

last: Rea

first: Theo

last: Bammler

first: Terry

last: Kavanagh

first: Brian

last: Fadely

first: Tom

last: Gelatt

first: Todd

last: O'Hara


title: Identification of genes associated with TGF-beta/Smad3-mediated macrophage-myofibroblast transition (MMT) by single-cell RNA sequencing

city: Hong Kong

first: Hui-Yao

last: Lan

address: Prince of Wales Hospital, Shatin, N.T.

department: Li Ka Shing Institute of Health Sciences, Department of Medicine & Therapeutics, CUHK-Shenzhen Research Institute

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: In this study, we conducted single-cell RNA sequencing (scRNA-Seq) to identify the Smad3-dependent transcriptomes related to MMT in TGF-beta1-treated bone marrow-derived macrophages in vitro, where Smad3-KO group serves as a negative control.

overall_design: The bone marrow macrophages of Smad3-WT or -KO mice were stimulated with 5ng/ml of TGF-beta1 for 5 days. Then the a-SMA negative or positive F4/80-expressing cells were flow sorted and subjected to single-cell RNA sequencing analysis.

first: Patrick

last: Tang

first: Shuang

first: Xiao

last: Huang

first: Ka

middle: F

last: To

first: Ronald

middle: C

last: Ma

first: Tin

middle: L

middle: Y


title: Global transcriptome analysis of BJAB cells that are modulated by EBV infection or (and) EBV BART6-3p mimics.

city: Changsha

first: Jian

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

institute: Central South University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using transcriptome profiling (RNA-seq) to evaluate the effects of EBV infection or (and) EBV BART6-3p mimics on the global transcriptome of the BJAB cells.
Methods: BJAB cells were transfected with negative control mimics or BART6-3p mimics for 48 h and then infected with EBV virons for 2h. RNAs were extracted by Trizol and sequenced by Solexa high-throughput sequencing service (Oebiotech, Shanghai, China). Data were extracted and normalized according to the manufacturer’s standard protocol.
Results: Log-fold changes of up- or down-regulated mRNAs between the control and experiment group were selected with a significance threshold of p<0.05. There are 408 mRNAs were up-regulated and 263 were down-regulated in “EBV infection” group cells comparing to “Mock” group cells. There are 385 mRNAs were up-regulated and 246 were down-regulated in “EBV infection + Bart6-3p mimics” group cells comparing to “EBV infection + negative control mimics” group cells.
Conclusions: Our study describes the global transciptome changes of BJAB cells induced by EBV infection or (and) EBV 6-3p mimics.

overall_design: BJAB cells mRNA profiles of “mock” (no infection, no treatment), “EBV infection”, “EBV infection + negative control mimics”, and “EBV infection + BART6-3p mimics” were generated by RNA sequecning, using Solexa high-throughput sequencing service (Oebiotech, Shanghai, China).

first: Yuanjun

last: Lu


title: Systemic gain and loss of chromatin architecture throughout zebrafish development [Hi-C]

city: Utrecht

first: Robin H.

last: van der Weide

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Chromosomes are three-dimensional structures in the nucleus that are organized at multiple levels. Studies in mammals have shown that chromosomes segregate in active and inactive compartments (A and B, resp.). A compartments have high transcription activity, high GC-content and replicate early in S-phase. B compartments on the other hand are transcriptionally inactive, have low CG content are often found at the nuclear periphery. Every compartment is further divided into megabase-sized Topologically Associated Domains (TADs), the functional units of gene regulation. Regions within such a domain preferentially interact with each other. TAD positions are conserved between mouse and human genomes. However, it is unclear if non-mammalian vertebrates also show these organizational features and how these change throughout development. We have generated Hi-C maps for zebrafish embryos and show that the structural features of mammalian genomes (A/B-compartments and TADs) are also found in this species. We find that the genes within TADs show spatial co-expression. Moreover, the order of genes within a TAD is conserved to other vertebrate species. One of the key features of development is the switch from maternally loaded mRNAs to the transcriptional activation of the zygotic genome, known as Zygotic Genome Activation (ZGA). Prior to ZGA we see both TADs and compartments. Paradoxically, after the initiation of transcription, TADs and compartments completely disappear. These features are progressively re-established in the following developmental stages. Our results show that chromosome conformation can be formed independent of transcription. Analysis of active enhancer and promoter marks after ZGA showed that promoters and enhancers are enriched at future TAD-boundaries. Later in time, when TADs are present, the enrichment of active enhancers at the TAD-boundaries is lost. These data suggest that proximal enhancer-promoter interactions are needed for gene regulation when TADs are not in place. The loss of both TADs and compartments represent an interesting avenue for the further study of factors involved in the formation of the structural features of vertebrate chromosomes.

overall_design: Embryos of 2.3, 4, 8 and 24 hours after fertilisation were processed for Hi-C

first: Robin

first: Elzo

last: de Wit


title: Propargite, an environmental chemical, interacts with GWAS identified diabetes genes to impact human pancreatic β-cell death

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

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

overall_design: Refer to individual Series


title: Propargite, an environmental chemical, interacts with GWAS identified diabetes genes to impact human pancreatic β-cell death [PTPN2 knockout]

summary: This paper describes the first time a high-content environmental chemicals screen using pancreatic β-like cells derived from human pluripotent stem cells (hPSCs), and discovered that a commonly used pesticide, propargite, induces pancreatic β-cell DNA damage and necrosis. More interestingly, we found out the genetic background of β-like cells affects their response to propargite-induced toxicity, based on isogenic hPSC platform, including for variants GWAS identified associated with T1D, since isogenic GSTT1-/- and PTPN2-/- pancreatic β-like cells are hypersensitive to propargite-induced β-cell death both in vitro and in vivo. In summary, our study identified an environmental chemical that contributes to the loss of β-cells and provides an innovative platform for using hPSC-derived cells to explore gene-environment interactions that impact diabetes disease progression.

overall_design: RNA-seq was used to compare the gene expression for two wildtype hESC (PTPN2+/+-1 and PTPN2+/+-2) and two PTPN2 knockout hESC (PTPN2-/--1 and PTPN2-/--2) derived INS-GFP+ cells.

first: Ting

last: Zhou

first: ChiNok

last: Chong

first: Lei

last: Tan

first: Sadaf

last: Amin

first: Suranjit

last: Mukherjee

first: Zaniar

last: Ghazizadeh

first: Hui

last: Zeng

first: Min

last: Guo

first: Miguel

last: Crespo

first: Tuo

last: Zhang

first: Reyn

last: Kenyon


title: Genetic determinants of co-accessible chromatin regions in activated T cells across humans

city: HOUSTON

first: Aviva

middle: P

last: Aiden

address: 2205 MARONEAL ST

institute: BCM

summary: Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease. One possible mechanism is that genetic variants affect the activity of one or more cis-regulatory elements leading to gene expression variation in specific cell types. To identify such cases, we analyzed Assay for Transposase-Accessible Chromatin (ATAC-seq) and RNA-seq profiles from activated primary CD4 + T cells of up to 105 healthy donors. We found that regions of chromatin accessibility (ATAC-peaks) are co-accessible at kilobase and megabase scales, in patterns consistent with the 3D organization of chromosomes measured by in situ Hi-C in T cells. Genetic variants located within ATAC-peaks often affected the accessibility of the corresponding peak and any co-accessible peaks. They also disrupt binding sites for transcription factors important for CD4 + T cell differentiation and activation, overlap and mediate expression QTLs from the same cells, and are enriched for autoimmune disease variants. Our results provide insights into how natural genetic variants modulate cis-regulatory elements, in isolation or in concert, to influence gene expression in primary immune cells that play a key role in many human diseases.

overall_design:
In situ HiC in activated primary CD4 + T cells
NOTE: Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.

first: Rachel

last: Gate


title: In utero exposure to therapeutic doses of acetaminophen and ibuprofen accelerates germ cell differentiation in the mouse embryonic testis

city: Montpellier

first: Brigitte

last: Boizet-Bonhoure

address: 141 rue de la Cardonille

department: Genetic and Development

country: France

institute: CNRS

summary: NSAIDs and ACE that affect prostaglandin synthesis are widely used by pregnant women. Epidemiological studies have hypothesized a potential relation of testis dysgenesis syndromes such as cryptorchidism and hypospadias to exposure to these molecules during both the first and the second trimesters of gestation. To decipher whether the embryonic gonads themselves are targets for these molecules, we analysed the impact of precocious in utero exposure to NSAIDs and ACE alone or in combination on the early development of the testis during sex determination, using therapeutic doses similar to those administrated in human medications. We found that in utero exposure to ACE, aspirin or ibuprofen affects the germ cell proliferation in embryonic testis. The whole transcriptome of 13.5 dpc (days post coïtum) treated testis suggests different mechanisms of action of these drugs and a functional interaction between both molecules used in combination, in accelerating the germ cell differentiation. We identified that ACE and ibuprofen exposure through the up-regulation of Dnmt3L expression induces advanced epigenetic reprograming of the germline and enhanced glycogen storage within the testis cords through the activation of extracellular matrix genes expression. In addition, we identified for the first time the prostaglandin production pattern in the embryonic gonad and showed that PGD2, PGE2 and PGI2 were the targets of ACE and NSAIDs drugs. These features might affect the formation and maturation of postnatal testis and secondary reproductive organs leading to male infertility in adult age.

overall_design: examination of the impact of in utero exposure to NSAIDs and ACE on testis organogenesis

first: Moïra

last: Rossito

first: Alain

last: Pruvost

first: Candice

last: Marchive

first: Aurélie

last: Ghettas

first: Francis

last: Poulat

first: Pascal

last: Philibert


title: Analysis of HER2 genomic binding in breast cancer cells identifies a global role in direct gene regulation [RNA-Seq]

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

summary: HER2 is a transmembrane receptor tyrosine kinase, which plays a key role in breast cancer due to a common genomic amplification. It is used as a marker to stratify patients in the clinic and is targeted by a number of drugs including Trastuzumab and Lapatinib. HER2 has previously been shown to translocate to the nucleus. In this study, we have explored the properties of nuclear HER2 by analysing the binding of this protein to the chromatin in three breast cancer cell lines. We find genome-wide re-programming of HER2 binding after treatment with the growth factor EGF. Over 4,000 HER2 binding sites are found in all three breast cancer cell lines, and these occur near genes involved in protein kinase activity and signal transduction. HER2 was shown to co-localise at a subset of regions demarcated by H3K4me1, a hallmark of functional enhancer elements and HER2/H3K4me1 co-bound regions were enriched near EGF regulated genes providing evidence for their functional role as regulatory elements. A chromatin bound role for HER2 was verified by independent methods, including Proximity Ligation Assay (PLA), which confirmed a close association between HER2 and H3K4me1. Interestingly, HER2 bound to the ErbB2 gene itself indicating a potential self-regulatory mechanism for HER2. Mass spectrometry analysis of the chromatin bound HER2 complex identified EGFR and STAT3 as interacting partners. These findings reveal a global role for HER2 as a chromatin-associated factor that binds to enhancer elements to elicit direct gene expression events in breast cancer cells.

overall_design: RNAseq in the SKBR3 cells, in asynchronous cells and asynchronous cells treated with EGF for 3 hours (5 reps were performed).

first: Aisling

middle: M

last: Redmond

first: Omarjee

last: Soleilmane

first: Muriel

last: Le Romancer

middle: S


title: RNA-Seq matched to ribosome profiling over a zebrafish developmental timecourse

first: Guo-Liang

last: Chew

state: MA

address: 16 Divinity Ave BL 1019

department: Dept of Molecular and Cellular Biology

institute: Harvard University

summary: RNA-Seq data that is sample matched to a previous ribosome profiling dataset GSE46512

overall_design: RNA-Seq over 8 stages in early zebrafish development, matched to ribosome profiling data in : 2-4 cell, 256 cell, 1K cell, Dome, Shield, Bud, 28hpf and 5dpf

first: Andrea

last: Pauli

first: Alexander

last: Schier


title: Propargite, an environmental chemical, interacts with GWAS identified diabetes genes to impact human pancreatic β-cell death [propargite treatment]

city: New York

first: Shuibing

last: Chen

overall_design: RNA-seq was used to compare the gene expression in DMSO, DMSO+GSH, Propargite and Propargite+GSH  treated  hESC derived INS-GFP+ cells.

first: Ting

last: Zhou

first: ChiNok

last: Chong

first: Lei

last: Tan

first: Sadaf

last: Amin

first: Suranjit

last: Mukherjee

first: Zaniar

last: Ghazizadeh

first: Hui

last: Zeng

first: Min

last: Guo

first: Miguel

last: Crespo

first: Tuo

last: Zhang

first: Reyn

last: Kenyon


title: Global analysis of gene expression changes following LINE1 inhibition

status: Public on Jun 30 2018

city: London

first: Michelle

last: Percharde

address: Du Cane Road

department: Imperial College London

institute: MRC Laboratory of Medical Sciences


title: Global analysis of gene expression changes following LINE1 inhibition [I]

summary: Transposable elements make up nearly half of mammalian genomes, yet are generally described as ‘junk DNA’ or genome parasites. The LINE1 retrotransposon is the most abundant class and is thought to be deleterious for cells, but it is paradoxically expressed at high levels during early development. Here, we report that LINE1 plays essential roles in mouse embryonic stem (ES) cells and pre-implantation embryos. In ES cells, LINE1 acts as a nuclear RNA scaffold that recruits Nucleolin and Kap1/Trim28  to repress Dux, the master activator of a gene expression program specific to the 2-cell stage. In parallel, LINE1 RNA mediates binding of Nucleolin and Kap1 to rDNA, thereby promoting rRNA synthesis and ES cell self-renewal. In embryos, LINE1 RNA is required for silencing of Dux, proper synthesis of rRNA and exit from the 2-cell stage. These results reveal an essential partnership between nuclear LINE1 RNA and chromatin factors in the regulation of transcription, developmental potency and ES cell self-renewal.

overall_design: 3 replicates each of E14 ES cells two days after nucleofection with Lissaminated ASOs - RC (control) or LINE1, purified according to Lissamine+ using flow cytometry then lysed for RNA extraction and library generation (6 samples total)

last: Ramalho-Santos


title: Differential Matrix metalloprotease (MMP) Expression Profiles Found in Aged Gingiva

city: Gwangju

first: Tae Hoon

last: Lee

address: 300 Yongbong-Dong

department: School of Dentistry

country: South Korea

institute: Chonnam National University

summary: The periodontium undergoes age-related cellular and clinical changes, but the involved genes are not yet known. Here, we investigated age-related genetic changes in gingiva at the transcriptomic level. Genes that were differentially expressed between young and old human gingiva were identified by RNA sequencing and verified by real-time PCR. A total of 1939 mRNA transcripts showed significantly differential expression between young and old gingival tissues. Matrix metalloprotease (MMP) regulation was the top pathway involved in gingival aging. MMP3, MMP9, MMP12, and MMP13 were upregulated in old gingival tissues, concomitantly with interleukin-1 beta (IL1B) expression. In vitro experiments using human gingival fibroblasts (hGFs) showed that MMP12 was upregulated in old hGFs compared to young hGFs. Moreover, the MMP3, MMP9 and IL1B levels were more highly stimulated by infection with the oral bacterium, Fusobacterium nucleatum, in old hGFs compared to young hGFs. Collectively, these findings suggest that, in gingiva, the upregulation of MMP12 may be a molecular hallmark of natural aging, while the  upregulations of MMP3, MMM9, and IL1B may indicate externally (e.g., infection)-induced aging. These findings contribute to our understanding of the molecular targets involved in gingival aging.

overall_design: Gingival mRNA profiles of young and old human gingiva were generated by deep sequencing using HiSeq 2000 sequencing system (Illumina).

first: Suhee

last: Kim

first: Seon-Kyu

first: Ki-Sun

last: Kwon

first: Taehoon


title: Folic acid supplementation alters the DNA methylation profile and improves insulin resistance in high-fat-diet-fed mice

city: Beijing

first: Wei

last: Li

address: NO.2, Yabao road

institute: Capital of Pediatrics Institute

type: Methylation profiling by high throughput sequencing

summary: Folic acid (FA) supplementation may protect from obesity and insulin resistance, the effects and mechanism of FA on chronic high-fat-diet-induced obesity-related metabolic disorders are not well elucidated. We adopted a genome-wide approach to directly examine whether FA supplementation affects the DNA methylation profile of mouse adipose tissue and identify the functional consequences of these changes. Mice were fed a high-fat diet (HFD), normal diet (ND) or an HFD supplemented with folic acid (20 μg/ml in drinking water) for 10 weeks, epididymal fat was harvested, and genome-wide DNA methylation analyses were performed using methylated DNA immunoprecipitation sequencing (MeDIP-seq). Mice exposed to the HFD expanded their adipose mass, which was accompanied by a significant increase in circulating glucose and insulin levels. FA supplementation reduced the fat mass and serum glucose levels and improved insulin resistance in HFD-fed mice. MeDIP-seq revealed distribution of differentially methylated regions (DMRs) throughout the adipocyte genome, with more hypermethylated regions in HFD mice. Methylome profiling identified DMRs associated with 3787 annotated genes from HFD mice in response to FA supplementation. Pathway analyses showed novel DNA methylation changes in adipose genes associated with insulin secretion, pancreatic secretion and type 2 diabetes. The differential DNA methylation corresponded to changes in the adipose tissue gene expression of Adcy3 and Rapgef4 in mice exposed to a diet containing FA. FA supplementation improved insulin resistance, decreased the fat mass, and induced DNA methylation and gene expression changes in genes associated with obesity and insulin secretion in obese mice fed a HFD.

overall_design: Mice were fed a ND, HFD, or FAD for 10 weeks, epididymal fat was harvested, and genome-wide DNA methylation analyses were performed using methylated DNA immunoprecipitation sequencing (MeDIP-seq).

first: Renqiao

last: Tang

first: Jianxin

last: Wu


title: Transcript levels of genes in the wild type CAI4 as well as the gdt1/gdt1,the pmr1/pmr1 and the gdt1/gdt1 pmr1/pmr1 mutants

city: Zibo

first: Linghuo

last: Jiang

address: 266 West Road Xincun

institute: Shandong University of Technology

summary: We report the expression levels of transcripts of 5,901 genes in log-phase growing cells of the wild type CAI4 as well as the gdt1/gdt1, the pmr1/pmr1, and the gdt1/gdt1 pmr1/pmr1 mutants.We find that as compared to the wild type, there are 249, 446 and 440 differentially expressed genes (DEGs) in the gdt1/gdt1, the pmr1/pmr1 and the gdt1/gdt1 pmr1/pmr1 mutants, respectively. Deletion of CaGDT1 does not affect the transcript level of CaPMR1, and vice versa. There are 105 shared DEGs between the gdt1/gdt1 and the pmr1/pmr1 mutants, which accounts for 42% (105/249) of total DEGs due to deletion of CaGDT1 or 24% (105/446) of total DEGs due to deletion of CaPMR1.

overall_design: RNA sequencing of four strains, the wild type CAI4, the gdt1/gdt1, the pmr1/pmr1, and the gdt1/gdt1 pmr1/pmr1 mutants, which carried the pCR4 vector with a URA3 marker and were grown to log phase in SD-URA medium at 30oC.

first: Yi

last: Yang


title: Transcription start site positioning is not affected by +1 nucleosome depletion

city: Copenhagen

first: Axel

last: Thieffry

state: Hovedstaden

address: Lersø Parkallé 42-44

department: R&D

country: Denmark

institute: BioPhero-FMC

summary: The relationship between the positioning of nucleosomes and transcription start sites (TSSs) is unclear. Here, we report that deletion of the Fun30 class chromatin remodelers Fft2 and Fft3 leads to depletion of +1 nucleosome occupancy. Strikingly, in the vast majority of cases, this depletion had no impact on the placement of the TSS, favoring a model where TSS placement is primarily DNA sequence-driven.

overall_design: 5'-Cap Analysis of Gene Expression (CAGE) of S. pombe wild type and fft2fft3 double mutant cells, in triplicates.

first: Babett

last: Steglich

first: Jenna

last: Persson

first: Mette

last: Boyd

first: Jette

last: Bornholdt

first: Punit

last: Prasad

first: Olaf

last: Nielsen

first: Karl

last: Ekwall

first: Albin

last: Sandelin


title: Analysis of HER2 genomic binding in breast cancer cells identifies a global role in direct gene regulation [ChIP-exo]

first: Jason

last: Carroll

overall_design: ChIPexo of HER2 in three breast cancer cell lines (SKBR3, BT474 & T47D), in asynchronous cells and asynchronous cells treated with EGF for 3 hours. ChIPseq of H3K4me1 in two breast cancer cell lines (SKBR3 & BT474) in asynchronous cells.

first: Aisling

last: Redmond

first: Omarjee

last: Soleilmane

first: Muriel

last: Le Romancer


title: Analysis of HER2 genomic binding in breast cancer cells identifies a global role in direct gene regulation


title: The epigenetic and transcriptional basis of a developmental transition from brown to white adipose tissue

city: Darlinghurst

first: Aaron

last: Statham

state: NSW

address: 384 Victoria St

department: Cancer Department

country: Australia

institute: Garvan Institute of Medical Research

summary:
Brown and white adipose tissues are functionally and morphologically distinct. Theformer tissue has a primary role in maintaining thermogenesis in new born mammals while the latter acts as an energy storage vehicle that enhances survival when food is limiting. Both tissues are involved in maintaining energy homeostasis in adults and are strongly implicated in chronic metabolic diseases associated with obesity in humans. The perirenal adipose depot in sheep undergoes a relatively rapid transition from brown to white adipose tissue between late gestation and a few weeks after birth. However, little is known about this developmental process in terms of mechanism, changes in gene expression and epigenetic architecture.
Citation: Tony Vuocolo, Aaron Statham, Denis C. Bauer, Sean McWilliam, Shalima Nair, Janna L Morrison, Song Zhang, Michael Buckley, Isabella C McMillen, Susan Clark, Ross L Tellam.  "The epigenetic and transcriptional basis of the developmental transition from brown to white adipose tissue" ( submitted).

overall_design: Whole genome bisulfite sequencing was performed upon PRAT from sheep fetuses at 132 days of gestation (132 d post conception (dpc); term =150±3d) and lambs 80 days after birth. Libraries were prepared using the “Whole-Genome Bisulfite sequencing for Methylation Analysis” protocol published by Illumina, and were sequenced one lane each on the HiSeq 2500. Three biological replicates for each developmental time point were analysed. The sequence reads that passed quality filters were mapped to sheep genome Ovis_aries Oar_v3.1.74.

first: Ross

last: Tellam


title: RNA-seq expression profiling of Suz12-deleted or wild-type organoids derived from basal or luminal mouse mammary epithelial cells.

status: Public on Jun 28 2018

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: Total RNA was extracted from organoids grown from single sorted luminal or basal populations from the mammary glands of Rosa26-creERT2 Suz12 flox female mice. Cultures were treated with 4-hydroxytamoxifen to induce deletion of Suz12.

overall_design: Two biological replicates were prepared of the basal-derived organoids and three biological replicates of luminal-derived organoids. Wild-type and Suz12-deleted samples were prepared from both basal and luminal organoids. RNA sequencing was carried out on an Illumina Nextseq 500 to produce 20-65 million 80 bp reads per sample.

first: Ewa

last: Michalak

first: Jane

middle: E

last: Visvader

first: Yifang

last: Hu


title: Transcriptomic analysis reveals candidate genes regulating infection-related developments and host interactions of Colletotrichum fructicola

status: Public on Jun 29 2018

city: Yangling

first: bo

last: wang

state: Shaanxi

address: No. 3 Taicheng Road

institute: Northwest A&F University

summary: RNA sequencing was applied to compare the transcriptome profiles of conidium, appressoruim, infected apple leaf (IL), and cellophane infectious hyphae (CIH)

overall_design: For each sample type, three independent libraries were generated, sequencing was performed on an Illumina Hiseq 4000 platform with a 150 bp pair-ended strategy

first: Xiaofei

last: Liang

first: Guangyu

last: Sun


title: Screening microRNA-196 targets in 11q23-translocation acute myeloid leukemia reveal mechanisms maintaining leukemia stemness with therapeutic potential

city: Cincinnati

first: H. Leighton

last: Grimes

state: OH

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

institute: Cincinnati Childrens Hospital Medical Center


title: RNA-seq and ATAC-Seq profiling of Suz12-deleted or wild-type organoids derived from basal or luminal mouse mammary epithelial cells


title: Transcriptome profiling based study of early gene responses in susceptible and tolerant rat lung tissues during acute hypobaric hypoxia

city: New Delhi

first: Prakash

middle: Chand

last: Sharma

state: Delhi

address: Sector 16-C, Dwarka

department: University School of Biotechnology

country: India

institute: GGS indraprastha University

summary:
Aim: Acute hypobaric hypoxia occurs during fast ascent and brief sojourns to high altitudes. We aimed to elucidate early phase molecular mechanisms during hypobaric hypoxia that may contribute towards differential physiological responses in susceptible and tolerant rats.
Methods: Sprague-Dawley rats representing susceptible, normal (moderate) and tolerant male and female groups were subjected to simulated acute hypobaric hypoxia for one hour at 9144 m and 24°C. The lung tissue samples were subjected to high throughput mRNA-seq based transcriptome profiling. Differential gene expression of selected genes was validated by qRT-PCR.
Results: The cellular mechanisms found to be playing significant role in hypobaric hypoxia included MAPK, p53 and JAK-STAT signaling, and hypometabolism. Upregulated expression of early response genes including Dusp1, Cdkn1a, Txnip, Rgs1 and Rgs2 in susceptible rats indicated a progression towards growth arrest and apoptosis, while elevated expression of cell adhesion molecules, wound healing and repair bioprocesses was found in tolerant males. Upregulated Kcnj15 and Vsig4 variants in tolerant females suggested hypoxia adaptation by fluid reabsorption to avoid edematous conditions and suppression of T cell proliferation to avoid acute lung inflammation.
Conclusion: The differential gene expression patterns in different experimental sets elucidated the physiological mechanisms associated with progressive damage in the lung tissues of susceptible and normal (moderate) rats, and tissue protective measures in tolerant rats during acute hypobaric hypoxia.

overall_design: Transcriptome sequencing of 5 Sprague Dawley rat lung samples including 1 sample of normoxia as reference using Genome Analyser IIx

first: Anju

last: Bansal

first: Priyanka


title: Transcriptome deep sequencing to reveal the gene regulation of variegated mutation in Phalaenopsis aphrodite subsp. formosana

city: Pingtung County

first: Chi-Chu

last: Tsai

address: 2-6 Dehe Rd., Dehe Village, Changjhih Township

department: Crop Improvement Section

country: Taiwan

institute: Kaohsiung District Agricultural Research and Extension Station

summary: Phalaenopsis aprodite subsp. formosana is one of the most important species for Phalaenopsis breeding. A mutant line with variegated leaf is found in this species. The green leaves bear unstable yellow sectors. In order to investigate the molecular mechanism of the variegated mutant line, we sequenced the transcriptome of variegated mutant by Illumina's Solexa sequencing technology. The sequence analysis results showed 22,598 unigenes by de novo assembly method, and the average unigene length was 1,286 bp. The bioinformatics tools were used to screen the differential expression between green and yellow sectors of leaves. There were 389 differentially expressed unigenes were identified. In addition, Gene ontology (GO) and KEGG pathway analyses revealed diverse biological functions and processes from differentially expressed genes. In transcriptome analysis, seven differential expression gene between the green and yellow sectors of leaves can be identified as CHLM, CRD1, POR, CLH, SGR, psbA and Lhcb6 by RNA deep sequencing. The expression of candidate genes was confirmed using semi-quantitative reverse transcription (RT) PCR and real-time RT PCR. The result showed that the significantly differential expression of CLH and SGR between green and yellow sectors was confirmed. It is suggested that the overexpressed SGR gene promotes the function of chlorophyllase, leading to the rapid degradation of chlorophyll in yellow sector. It causes the chlorophyll to not accumulate in the yellow sector, as a result, the variegated leaves are shown.

overall_design: Examination of two different color sectors of leaves

first: Yu-Shiums

last: Lin

first: Po-Han

last: Chen


title: Heads and thoraxes of 10 d old female Drosophila melanogaster flies

status: Public on Jun 27 2018

first: Nina

middle: Evgenjevna

last: Gubina

address: 77 Massachusetts Ave, 56-670

department: CEHS

institute: MIT

summary: The aim of this study was to use unbiased transcriptomic analysis to characterize new traits that may explain differences in longevity between short- and long-lived wild-type backgrounds of Drosophila melanogaster – Dahomey and Oregon R, respectively. For the experiment we chose young flies (10 days old) to capture the difference in basal gene expression related to the genotype rather than to age-dependent functional decline. As a source for RNA extraction we used heads and thoraxes (combined) as tissues the most sensitive to aging. The expression of 3939 genes was changed (nearly 26% of the transcriptome, p-value < 0.05), with 1970 being upregulated and 1969 genes being downregulated in the Dahomey background compared to Oregon R. We found that young short-lived Dahomey flies have the traits previously associated with shorten lifespan such as increased lipo-oxidative stress, increased Tor signaling and loss of proteostasis and mitochondrial complex I activity.  We hypothesized that all these characteristics are caused by an increase in octopamine signaling that promotes foraging behavior even under laboratory conditions where nutrients are in excess.  Our results highlight the importance of controlling the genetic background in aging studies as well as interrogating several different pathways before making conclusions about what causes differences in longevity between different groups or individuals.

overall_design: mRNA profiles from two fruit fly strains were generated using Illumina HiSeq 2500 with paired-end chemistry. mRNA was obtained from heads + thoraxes of 10 days old mated females, 60 flies per sample, 4 samples for each strain. Depth of sequencing — 90 mln reads for each sample.

first: Tommi

last: Rantapero

first: Matti

last: Nykter

first: Alberto

last: Sanz


title: ChIP-seq for HrpR, HrpS, and HrpL

city: Hong Kong

first: Xin

last: Deng

address: To Yuen Building

department: Biomedical Sciences

institute: City University of Hong Kong

summary: The type III secretion system (T3SS) is the main machinery for Pseudomonas syringae and other Gram-negative bacteria to invade plant cells. HrpR/HrpS heterodimer are key factors to activate HrpL which induces all T3SS genes by binding to a ‘hrp box’ in promoters. However, the molecular mechanisms of HrpRS on T3SS or non-T3SS genes have not been fully understood. Following by chromatin immunoprecipitation coupled to high-throughput DNA sequencing (ChIP-seq), we found that HrpRSL had 8, 38, and 36 targets on the genome, respectively. HrpS directly bound to the promoter regions of T3SS genes (hrpK1, hrpA2 and hopAJ1) as well as a group of non-T3SS genes (PSPPH_1496, PSPPH_1525, PSPPH_3494 and PSPPH_3495). Subsequent biochemical and genetic assays showed that HrpS independently regulated these genes in a hrpL deletion strain. In addition, a HrpS-binding motif (GTGCCAAA) in the hrpL promoter was identified by truncation, which was verified by EMSA in vitro and lux-reporter assay in vivo. On the contrary, HrpR alone couldn’t activate hrpL. Overall, our results demonstrated that HrpS directly regulated a group of T3SS and non-T3SS genes, which is independent on HrpL. HrpS functions as the center of the regulatory cascade in T3SS. This work deciphered the key HrpRSL-T3SS regulatory network, which provides insights to develop new strategies to control P. syringae infection in the future.

sample_organism: Pseudomonas savastanoi pv. phaseolicola 1448A

overall_design: ChIP-seq for HrpR, HrpS, and HrpL


title: Decreased TGFBR3/Betaglycan expression enhances the metastatic abilities of renal cell carcinoma cells through TGF-b-dependent and independent mechanisms

city: Wakayama

first: Shogo

last: Ehata

state: Wakayama

address: Kimiidera 811-1

department: School of Medicine

country: Japan

institute: Wakayama Medical University

summary: It is unclear how the loss of TGF-b signaling components affects metastatic abilities in clear cell renal cell carcinoma (ccRCC). In this study, we identified that low TGFBR3 expression in ccRCC cells enhanced primary tumor formation and lung metastasis. In the presence of TGFBR3, TGF-b2 decreased the aldehyde dehydrogenase (ALDH)-positive ccRCC cell population, in which renal cancer-initiating cells are enriched. Loss of TGFBR3 also enhanced cell migration in cell culture and induced expression of several mesenchymal markers in a TGF-b-independent manner. Increased lamellipodium formation by FAK-PI3K signaling was observed with TGFBR3 downregulation, and this contributed to TGF-b-independent cell migration in ccRCC cells. Taken together, our findings reveal that loss of TGFBR3 endows ccRCC cells with multiple metastatic abilities through TGF-b-dependent and independent pathways.

overall_design: Target genes for TGF-b2 and TGFBR3 in ccRCC cells were identified.

first: Jun

last: Nishida

first: Kohei

last: Miyazono


title: RNAseq analysis of bone marrow endothelial cells

city: Bronx

first: Chunliang

last: Xu

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Although endothelial cells (ECs) have been shown to contribute to HSC maintenance in bone marrow (BM), differential contributions of EC subtypes remain unknown, owing to the lack of methods to separate with high purity arterial (AEC) from sinusoidal (SEC) endothelial cells. We show that combination of podoplanin (PDPN) and Sca-1 expression distinguishes AEC from SEC where Sca1brightPDPN—CD45—Ter119— cells exhibit an arterial gene signature and PDPN+Sca1dimCD45—Ter119— marks sinusoids. PDPN can be substituted for antibodies against the adhesion molecules ICAM1 or E-selectin that also mark SEC. We performed functional analysis of these different types of endothelial cells and found that SCF secreated from AECs regulate HSCs.

overall_design: We sorted live, singlet, CD45-Ter119-CD31+PDPN-Sca-1brightNestin-GFPdim artery endothelial cells (AECs), and live, singlet, CD45-Ter119-CD31+PDPN-Sca-1bright Nestin-GFPbright AECs and  live, singlet, CD45-Ter119-CD31+PDPN+Sca-1dim sinusoidal endotehlial cells(SECs) from digested bone marrow cells from Nestin-GFP. RNA was extracted, amplification and sequenced on Hiseq 2500 in Single Cell Genomics and Epigenomics core facility at Albert Einstein College of Medicine.

first: Paul

last: Frenette


title: The arrhythmogenic cardiomyopathy-specific coding and non-coding transcriptome in human cardiac stromal cells

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary: Background: Arrhythmogenic cardiomyopathy (ACM) is a genetic autosomal disease characterized by abnormal cell-cell adhesion, cardiomyocyte death, progressive fibro-adipose replacement of the myocardium, arrhythmias and sudden death. Several different cell types contribute to the pathogenesis of ACM, including, as recently described, cardiac stromal cells (CStCs). In the present study, we aim to identify ACM-specific expression profiles of human CStCs derived from endomyocardial biopsies of ACM patients and healthy individuals employing TaqMan Low Density Arrays for miRNA expression profiling, and high throughput sequencing for gene expression quantification. Results: We identified 5 miRNAs and 272 genes as significantly differentially expressed. Both the differentially expressed genes as well as the target genes of the ACM-specific miRNAs were found to be enriched in cell adhesion related biological processes. Functional similarity and protein interaction based network analyses performed on the identified deregulated genes, miRNA targets and known ACM-causative genes revealed clusters of highly related genes involved in cell adhesion, extracellular matrix organization, lipid transport and ephrin receptor signaling. Conclusions: We determined for the first time the coding and non-coding transcriptome characteristic of ACM cardiac stromal cells, finding evidence for a potential contribution of miRNAs to ACM pathogenesis or phenotype maintenance. Besides known pathways, we identified also deregulation of genes encoding ephrin receptors and ephrins, thus suggesting a potential involvement of Eph-ephrin signaling in CStCs from ACM hearts.

overall_design: Expression profiles of cardiac stromal cells from 3 ACM patients were compared against those of cardiac stromal cells from 3 healthy individuals.

first: Viviana

last: Meraviglia

first: Hagen

last: Blankenburg

first: Chiara

last: Piubelli

first: Peter

last: Pramstaller

first: Adolfo

last: Paolin

first: Elisa

last: Cogliati

first: Giulio

last: Pompilio

first: Elena

last: Sommariva

first: Francisco

last: Domingues

first: Alessandra

last: Rossini


title: Germline DNA replication timing shapes mammalian genome composition

status: Public on Jun 26 2018

city: Jerusalem

first: Itamar

last: Simon

state: APO/FPO IRAQ / AFGHANISTAN / MIDDLE EAST

address: Hadassah Ein Kerem

department: Microbiology and Molecular Genetics

institute: Hebrew University medical school

summary: DNA Replication Timing (RT) has been suggested to play an important role in shaping the mammalian genome by affecting mutation rates. Previous analyses were limited in that they relied on somatic DNA RT profiles, while to fully understand the influences of RT on the mammalian genome, germ cell RT information is necessary, as only germline mutations are passed to offspring and thus affect genomic composition. Using an improved RT mapping technique that allows mapping the RT from limited amounts of cells, we measured RT from two stages in the mouse germline - primordial germ cells (PGCs) and spermatogonial stem cells (SSCs).

overall_design: Examination of replication timing in somatic and germ cells

first: Britny

last: Blumenfeld

first: Yishai

last: Yehuda


title: Next Generation Sequencing Facilitates Quantitative Analysis of human patient derived primary Glioblastoma (GBM) cancer cell Transcriptomes

first: Biplab

last: Dasgupta

address: 3333 Burnet ave

institute: CCHMC

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare GBM transcriptome profiling (RNA-seq) after shRNA based knockdown of PRKAB1 and to compare gene expression by optimal high-throughput data analysis

overall_design: Methods: Total RNA profiles of two GBM cells (scramble and PRKAB1 sh RNA treated) were generated by deep sequencing, in triplicate, using Illumina Hiseq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays

first: Rishi

middle: R

last: Chhipa


title: Global analysis of gene expression changes following LINE1 inhibition [II]

first: Michelle

last: Percharde

address: Du Cane Road

institute: MRC Laboratory of Medical Sciences

summary: Transposable elements make up nearly half of mammalian genomes, yet are generally described as ‘junk DNA’ or genome parasites. The LINE1 retrotransposon is the most abundant class and is thought to be deleterious for cells, but it is paradoxically expressed at high levels during early development. Here, we report that LINE1 plays essential roles in mouse embryonic stem (ES) cells and pre-implantation embryos. In ES cells, LINE1 acts as a nuclear RNA scaffold that recruits Nucleolin and Kap1/Trim28  to repress Dux, the master activator of a gene expression program specific to the 2-cell stage. In parallel, LINE1 RNA mediates binding of Nucleolin and Kap1 to rDNA, thereby promoting rRNA synthesis and ES cell self-renewal. In embryos, LINE1 RNA is required for silencing of Dux, proper synthesis of rRNA and exit from the 2-cell stage. These results reveal an essential partnership between nuclear LINE1 RNA and chromatin factors in the regulation of transcription, developmental potency and ES cell self-renewal.

overall_design: 3 replicates each of E14 ES cells two days after nucleofection with Lissaminated ASOs - RC (control) or LINE1 and the indicated siGenome siRNAs, used for RNA extraction and library generation (15 samples total)

first: Miguel

last: Ramalho-Santos


title: Transcriptomic Analysis of Drought Stress Responses in Agropyron mongolicum Keng

city: Ardmore

first: Kiran

last: Mysore

state: Oklahoma

address: 2510 Sam Noble Parkway

institute: Noble Research Institute

summary: The transcriptome profiling of three samples in A. mongolicum Keng were studied using next-generation RNA sequencing under different drought stress conditions. This study aimed to identify genes of A. mongolicum Keng metabolism pathways that might be involved in this plant’s response to water deficit. 14.33 Gb high quality reads were assembled into 92,752 unigenes (unique transcripts), with a mean length of 1,303 bp. 76.26% had homologous genes in function databases.

overall_design: Transcriptomes of three different samples, including the control (C), 5-day drought, 15-day drought stress were sequenced using Illumina HiSeq 2000 system.

first: Yan

last: Zhao

first: Liang

last: Sun


title: Dynamic methylome remodeling throughout mammalian fetal development

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Genetic studies have revealed an essential role for cytosine DNA methylation in gene regulation. However, its spatiotemporal distribution in the developing embryo remains obscure. Here, we profiled the DNA methylation landscape of 12 mouse tissues/organs at 8 developmental stages spanning from early embryo to birth. In-depth analysis of such spatiotemporal epigenome maps uncovered widespread regulatory DNA element dynamics during embryogenesis. We systematically delineated methylation variants that likely drive gene transcription, whose human counterparts are enriched for genetic risk factors of human diseases. Strikingly, these predicted regulatory elements predominantly lose CG methylation during fetal development, whereas the trend is reversed after birth. Key transcription factors, essential for early tissue/organ development, accumulate non-CG methylation within their gene bodies, coinciding with transcriptional repression during late stage fetal development. These spatiotemporal epigenomic datasets provide a valuable resource for studies of gene regulation during mammalian tissue/organ progression and the possible origins of human developmental diseases.

overall_design: RNA-seq data (in replicate) of forebrain, midbrain, hindbrain and liver in mouse embryos from embryonic day 10.5 (E10.5) to postnatal day 0 (P0)

first: Yupeng

last: He

first: Manoj

last: Hariharan

first: Rosa

middle: G

last: Castanon

last: Nery


title: De novo transcriptome assembly databases in the butterfly orchid Phalaenopsis equestris

city: Shenzhen

first: Zhong Jian

last: Liu

address: No.889 Wangtong Road

country: China

institute: Shenzhen Key Laboratory for Orchid Conservation and Utilization

summary: Orchidaceae are renowned for their spectacular flowers as well as other reproductive and ecological adaptations. After the genome of the tropical epiphytic orchid Phalaenopsis equestris was sequenced, we combined Trinity data for de novo assembly and Illumina HiSeq1500 data for RNA-Seq analysis to characterize the transcriptomes of four different organs for a better understanding of the molecular mechanisms driving these characteristics. We present four de novo assembled transcripts reconstructed from RNA collected from the root, stem, leaf, and flower of Phalaenopsis equestris. These sets of transcripts greatly enrich the available data for Phalaenopsis equestris. Here, we present two databases, and each dataset allows for a different type of search for candidate homologues. The first dataset consists of the sets of assembled unigenes, which enable a sequence-based search. A comprehensive analysis of the assembled unigenes revealed the unigenes from root, stem, leaf, and flower with high e-values aligned versus the Nr, Swiss-Port, KEGG, COG, and GO database, respectively. This analysis enabled the production of a second database, which includes sequences correlated with annotated transcript names as well as the confidence of the best hit from BLAST.

overall_design: Transcriptome analysis of Phalaenopsis equestris root, stem, leaf and flower were by deep sequencing using Illumina Hiseq 1500. De novo transcriptome reconstruction was performed using Trinity (version trinityrnaseq-r2013-02-25). Trinity was applied using the inchworm method with a minimum contig length of 200 nucleotides. The default settings for Trinity paired-end assembly were used for the remaining parameters. The assembly were further spliced and assembled to acquire non-redundant unigenes that were as long as possible. BLASTx (e-value <0.00001) was performed to annotate the unigenes based on protein databases, including Nr, Swiss-Port, KEGG, and COG. The blast2go program was employed to obtain GO annotations from the annotations result of Nr protein databases for the unigenes with the max_target_seqs =10 parameter. The CDSs (coding DNA sequences) and protein sequences of all unigenes were predicted using BLASTX, ESTScan, and the Markov model. First, we performed BLASTx alignment (E-value b 10−5) between unigenes and protein databases such as Nr, SwissProt, KEGG, and COG. The best alignment results were used to determine the sequence direction of the unigenes. Unigenes with sequences that produced matches in only one database were not searched further. When a unigene would not align to any database, ESTScan10 was used to predict coding regions and determine the sequence direction. If the above two methods still could not predict the CDSs of the unigenes, we used a fifth-order Markov model to predict the CDSs.

first: Shance

last: Niu

first: Zhong-Jian


title: Screening microRNA-196 targets in 11q23-translocation acute myeloid leukemia reveal mechanisms maintaining leukemia stemness with therapeutic potential [RNA-seq]

first: H. Leighton

last: Grimes

country: USA

summary: microRNA are aberrantly expressed in acute myeloid leukemia (AML), and clinically may have diagnostic, prognostic, and therapeutic value. We identify one such microRNA, miR-196b, is essential for MLL-AF9 leukemia initiation and maintenance. To discover how miR-196b contributes to leukemogenesis, we utilized multiple unbiased approaches that identified and functionally screened miR-196b target activity in AML. Our studies resolved how conflicting networks of miRNA-regulated targets are integrated during leukemogenesis. This work uncovered two miR-196b direct targets, the cell cycle regulator Cdkn1b (p27Kip1) and Polycomb group member Phc2, that independently cooperate with MLL-AF9 to promote leukemogenesis by regulating stem cell transcriptional programs. Finally, we found that therapeutic disruption of miR-196b direct targeting of Cdkn1b suppresses leukemogenesis.

overall_design: To identify the gene expression changes assoicated with knockdown of Cdkn1b and knockdown of Phc2 in murine MLL-AF9 leukemia cells.

first: Sara

last: Meyer

first: Andrew

last: Rogers

first: Emily

last: Orr

first: John

last: Doench

first: Bruce

middle: J

last: Aronow

first: Ashish

last: Lal

first: Judy

last: Lieberman

first: Edwina

last: McGlinn

first: Nathan

last: Salomonis

first: H


title: Transcriptome analysis of Gata6-AS depleted XEN cells

city: White Plains

first: Mary

last: Donohoe

state: New York

address: 785 Mamaroneck Ave

department: Burke Medical Research Institute

institute: Weill Cornell Medical Colledge

summary: RNA-seq was performed to identify the target genes of Gata6-AS.

overall_design: PS10 cells were transfected with Gata6-AS targeting or control locked siRNA and subjected to RNA-seq.

first: Yasunao

last: Kamikawa


title: Endogenous transcripts control miRNA levels and activity in mammalian cells by a target-dependent miRNA degradation mechanism [RNA-Seq]

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

institute: Istituto Italiano di Tecnologia

summary: Little is known about how miRNAs are turned over, in particular in mammalian cells. A target-dependent miRNA degradation mechanism (TDMD) has been recently suggested, in which RNA targets may induce miRNA degradation. However, endogenous RNA targets involved in TDMD have not been yet identified. During serum stimulation of quiescent fibroblasts, a deep change of miRNA expression occurs in few hours. We scanned the mammalian genome for targets eligible for TDMD and found a dominant miRNA:target pair, consisting of a target (SerpinE1) extraordinarily induced upon serum stimulation and two matched miRNAs (miR-30b/c) quickly downregulated. We verified directly the occurrence of TDMD by interfering specifically with the miR-:target interaction, keeping target and miRNA expression at endogenous levels, using CRISPR/cas9 mediated deletion of the miR-30 responsive element (MRE) of SerpinE1. In MRE-KO cells, we observed the stabilization of the predicted miRNAs, with no evidence of alterations in precursors or unrelated miRNAs, suggesting that TDMD is occurring and has been disrupted by a single MRE deletion. At molecular level miRNA degradation occurs within physiological ranges of target expression (upon 1000 copies per cells) and is accompanied by modification on 3’ends (tailing, mostly through adenylation). TDMD suppression was sufficient to shift the activity of miR-30b/c towards other shared targets, modulate significantly gene expression and, thus, influence cellular functions, including cell proliferation, apoptosis, and adhesion. In conclusion, these data strongly support the existence of a novel and sophisticated regulatory layer of miRNA and gene expression mediated by specific endogenous targets in mammalian cells.

overall_design: mRNA regulation in wild type and MRE_KO cells (where the miR-30 microRNA responsive element within Serpine1 3'UTR was deleted by CRISPR/Cas9 genome editing) in asynchronously growing conditions.

last: Ghini

first: Matteo

last: Marzi


title: Endogenous transcripts control miRNA levels and activity in mammalian cells by a target-dependent miRNA degradation mechanism [miRNA-Seq]

overall_design: miRNA regulation in wild type and MRE_KO cells (where the miR-30 microRNA responsive element within Serpine1 3'UTR was deleted by CRISPR/Cas9 genome editing


title: PP1-NIPP1 wild type and mutant overexpression in Flip-In™ T-Rex Hela cells

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

summary: RNAi-seq of stable Flp-In™ T-Rex Hela cells that inducibly expressed PP1-NIPP1 and mutants.

overall_design: Four cell types are investigated under two conditions in three independent experiments, resulting in 24 samples in total (i.e. 4x2x3). The four cell types are: (1) Flp-In™ T-Rex Hela cells with doxycycline-inducible EGFP transgene, (2) Flp-In™ T-Rex Hela cells with doxycycline-inducible EGFP-PP1-NIPP1 transgene, (3) Flp-In™ T-Rex Hela cells with doxycycline-inducible EGFP-PP1m-NIPP1 transgene (PP1 is mutated at Aa 64, i.e. D64A), (4) Flp-In™ T-Rex Hela cells with doxycycline-inducible EGFP-PP1-NIPP1m transgene (NIPP1 is mutated at the position AA 68-71, i.e. alanine mutation of NIPP1 residues 68-71). The two conditions are (1) not exposed to doxycycline, (2) treated with doxycycline. Three replicates are collected from three independent experiments.

first: Claudia

last: Winkler

first: Aleyde

last: Van Eynde


title: Regulation of gene expression under extreme desiccation: hijacking of heat shock regulatory system.

city: Moscow

first: Pavel

last: Mazin

address: Skolkovo Innovation Center, Building 3

department: Biomed

country: Russia

institute: Skolkovo Institute of Science and Technology

summary: Polypedilum vanderplanki is а striking and unique example of an insect that can survive almost complete water loss. Its genome and series of dehydration-rehydration transcriptomes, together with the genome of P. nubifer (congeneric desiccation-sensitive midge), were recently released. Here, using series of data reflecting detailed transcriptome changes in the process of anhydrobiosis, as well as developmental series, we have identified hundreds of new genes and have demonstrated that up to 53% of genes undergo alternative splicing (AS) and that AS plays a prominent role in the desiccation response. We have shown that the TCTAGAA DNA motif, which closely resembles the binding motif of the D. melanogaster heat shock transcription activator (HSTF), is significantly enriched in promoter regions of desiccation-induced genes, such as LEA, thioredoxins or trehalose metabolism-related genes in P. vanderplanki, but not in P. nubifer. Unlike desiccation-senseitive P. nubifer, P. vanderplanki exhibits double TCTAGAA sites upstream of the HSTF gene, that is a likely explanation for the much stronger activation of HSTF in P. vanderplanki compared to P. nubifer under desiccation. Thus, our results show that rewiring of the heat shock regulatory system is an important evolutionary mechanism of desiccation adaptation in P. vanderplanki.

overall_design: Examination of P. vanderplanki larva transcription changes under dehydration-rehydration cycle

first: Elena

last: Shagimardanova

first: Alexander

last: Cherkasov

first: Roman

last: Sutormin

first: Vita

last: Stepanova

first: Alexey

last: Stupnikov

first: Maria

last: Logacheva

first: Aleksey

last: Penin

first: Takahiro

last: Kikawada

first: Richard

last: Cornette

first: Mikhail

last: Gelfand

first: Oleg

last: Gusev


title: MiR-34a controls proliferation and plasticity of early-progenitors in the normal mammary gland and in breast cancer

first: Francesco

last: Nicassio

summary: The miR-34 is a tumor-suppressor miRNA family involved in various human cancers, including breast. However, the role of such miRNAs in the control of mammary stem cells (MaSCs), early-progenitors and their tumor counterparts,  (CSCs) lies largely unexplored. Here, we identified miR-34a as directly regulated by TP53 in primary mouse mammospheres. Expression of miR-34a is induced upon luminal commitment and differentiation and able to inhibit the expansion of the MaSCs/early-progenitor pool in a p53-independent fashion. Loss of function approaches revealed that miR-34 negatively controls both proliferation and fate commitment in mammary progenitors by modulating several pathways involved in epithelial cell plasticity and luminal-to-basal conversion. In particular, miR-34a negatively regulates Wnt/b-catenin signaling pathway, targeting multiple upstream regulators and, thus, modulating the expansion of the MaSCs/early-progenitor pool. These multiple roles of miR-34a were maintained in a model of human breast cancer, where chronic expression of miR-34a in triple-negative mesenchymal-like cells (enriched in CSCs) reduced tumor growth, restricted CSC pool and inhibited tumor propagation by promoting a luminal-like differentiation program.

overall_design: gene expression by deep-sequencing in mammary epithelial undifferentiated Sca high cells, differentiatied Sca low cells and in Sca high cells upon miR-34a induction. Each sample is analyzed in triplicate

first: Paola

last: Bonetti


title: RNA-seq of MDA-MB-231 cells with TET1 knockout

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

institute: Coriell Institute

summary: DNA hypermethylation is known to contribute to the formation of cancer.  However, DNA hypomethylation has received far less attention and the factors controlling the balance between hypo and hypermethylation and its impact on tumorigenesis remains unclear.  Triple negative breast cancer (TNBC), a subtype of breast cancer that does not overexpress the hormone receptors or HER2/NEU, is one of the most hypomethylated cancers observed.  Importantly, TNBCs are often a therapeutic challenge because of advanced presentation and lack of targeted therapies. TET1 is a DNA demethylase that regulates DNA methylation, hydroxymethylation and gene expression.  We found that TET1 is specifically overexpressed in TNBC, where it is associated with hypomethylation and a worse overall survival.  Further, we uncover an intricate network connecting TET1 expression to maintaining activation of cancer specific pathways, including PI3K, EGFR and PDGF.  In TET1 KO cells, we observed reduced phospho-4EBP1 and decreased expression of genes in the PI3K pathway, suggesting loss of PI3K-mTOR activity is concomitant with loss of TET1.  Additionally, TET1 KO cells have reduced cellular proliferation and migration.  Our work establishes TET1 as an oncogene that contributes to the aberrant hypomethylation observed in cancer and suggests TET1 could serve as a novel druggable target for therapeutic intervention.

overall_design: Triplicates were performed for a total of 12 samples. Fold change of each gene was calculated by comparing changes in expression in KO compared to the empty vector control samples

first: Charly

last: Good

first: Shoghag

last: Panjarian

first: Andrew

last: Kelly

first: Bela

last: Patel

first: Jaroslav

last: Jelinek

first: Jean-Pierre

last: Issa


city: Toronto

first: Norman

last: Rosenblum

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

summary:
Purpose: To analyze the mRNA content of Foxd1Cre;Smo(flox/-) mutant kidneys.
Methods: We collected E13.5 wildtype and Foxd1Cre;Smo(flox/-) mutant kidneys and isolated RNA to do RNA-Seq.
Results: Identified differentially expressed transcripts in Foxd1Cre;Smo(flox/-) mutant kidneys compared to wildtype controls.
Conclusions: Our work provides novel insight into how Hedgehog signaling from stromal cells influences renal development.

overall_design: RNA sequencing of Foxd1Cre;Smo(flox/-) mutant kidneys compared to controls.

first: Christopher

last: Rowan

first: Winny

last: Li


title: Extracellular matrix components HAPLN1, lumican and collagen I cause hyaluronic acid-dependent folding of the developing human neocortex

city: Dresden

first: Holger

last: Brandl

state: Choose One...

address: Pfotenhauerstrasse 108

department: Bioinformatics Service

country: Germany

institute: Max Planck Institute of Molecular Cell Biology and Genetics

summary: Neocortical expansion, thought to underlie the cognitive traits unique to humans, is accompanied by cortical folding. This folding starts around gestational week (GW) 20, but what causes it remains largely unknown. Extracellular matrix (ECM) has been previously implicated in neocortical expansion. Here, we investigate the potential role of ECM in the formation of neocortical folds. We focus on three specific ECM components localized in the human fetal cortical plate (CP): hyaluronan and proteoglycan link protein 1, lumican and collagen I (collectively, HLC). Addition of HLC to cultures of human fetal neocortex (11-22 GW) caused local changes in tissue stiffness and induced CP folding. HLC-induced folding increased CP hyaluronic acid (HA), required the HA-receptor CD168 and downstream ERK signaling, and was prevented/reversed by hyaluronidases. HLC did not induce CP folding in cultures of developing mouse and ferret neocortex. Together, our data suggest a human-specific role of ECM in neocortical folding.

overall_design: Gene expression profiles of the cortical plate of fetal human neocortex after 16 hours of control or HLC-treatment were generated by RNA-seq and analyzed. The cortical plate was isolated by laser capture microdissection.

first: Katherine

last: Long

first: Wieland

middle: B

last: Huttner


title: Genome-wide analysis reveals dual roles for Ikaros in regulation of macrophage chromatin state and inflammatory gene expression [ChIP-seq]

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

summary: Macrophage activation by bacterial LPS leads to induction of a complex inflammatory gene program dependent on numerous transcription factor families. Here we describe an unexpected role for the lymphoid lineage-determining factor Ikaros in the macrophage LPS response using comprehensive genomic analysis of Ikaros-dependent transcription, DNA binding, and chromatin accessibility. Ikaros exhibited dual repressor and activator roles in LPS-induced gene expression. Consistent with the described function of Ikaros as transcriptional repressor, Ikzf1-/- cells showed enhanced induction for select responses. In contrast, we observed a dramatic defect in expression of delayed response genes and ChIP-seq analyses support a key role for Ikaros in sustained NF-kB chromatin binding. Furthermore, in the absence of Ikaros, a constitutively open chromatin state was coincident with dysregulation of LPS-induced chromatin dynamics, gene expression, and cytokine responses. Our data suggest a central role for Ikaros in coordinating the complex macrophage transcriptional program in response to pathogen challenge.

overall_design: RNA-seq time course (0h, 2h, 4h, 10h) and DNase-seq time course (0h, 3h, 8h) sample replicates from WT and Ikzf KO macrophages; RelA/Ikaros ChIP-seq time course (0h, 3h, 8h) sample replicates and input control DNA samples

first: Kyu-Seon

last: Oh

first: Rachel

middle: A

last: Gottschalk

first: Nicolas

last: Lounsbury

first: Jing

last: Sun

first: Ze

last: Wang

first: Bhaskar

last: Dutta

first: Gordon

last: Hager

first: Myong-Hee

last: Sung

first: Iain

middle: D

last: Fraser


title: Sequencing artifacts produced by mispriming during reverse transcription in multiple RNA-seq technologies

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary: The quality of RNA sequencing data relies on specific priming by the primer used for reverse transcription (RT-primer). Non-specific annealing of the RT-primer to the RNA template can generate reads with incorrect cDNA ends and can cause misinterpretation of data (RT mispriming). This kind of artifact in RNA-seq based technologies is underappreciated and currently no adequate tools exist to computationally remove them from published datasets. We show that mispriming can occur with as little as 2 bases of complementarity at the 3' end of the primer followed by intermittent regions of complementarity. We propose an experimental solution to avoid RT-mispriming by performing RNA-seq using thermostable group II intron derived reverse transcriptase (TGIRT-seq).

overall_design: RIP-seq and short RNA seq to identify RNAs interacting with EZH2 in T98G, U87MG and K562 cells.

first: Vishwanath

first: Haridha

last: Shivram


title: Genome-wide analysis reveals dual roles for Ikaros in regulation of macrophage chromatin state and inflammatory gene expression [Dnase-seq]

middle: W