title: The nucleosome DNA entry-exit site is important for transcription termination and prevention of pervasive transcription

city: Oakland

first: Mitchell

middle: Alden

last: Ellison

state: PA

address: Langley Hall

department: Biological Sciences

institute: University of Pittsburgh

summary: Compared to the initiation and elongation stages of transcription, the role of chromatin in transcription termination is poorly understood. Through a yeast genetic screen, we identified histone H3 and H4 substitutions that cause transcription to read through the terminator of a small noncoding gene. The substitutions map to the nucleosome DNA entry-exit site, a region that controls nucleosome stability and certain histone modifications. Genome-wide studies on the strongest mutants revealed evidence of transcription read-through of noncoding and coding genes and reduced nucleosome occupancy. Replacement of the native sequence downstream of a gene with a “superbinder” sequence that increases nucleosome occupancy in vivo increased termination efficiency and suppressed the effect of a DNA entry-exit site substitution at this locus. Our results highlight the importance of the DNA entry-exit site in maintaining the integrity of the transcriptome and suggest that nucleosomes can facilitate termination by serving as a barrier to RNA polymerase.

overall_design: RNA-seq, 4tU-seq, ChIP-seq, and MNase seq on S. cerevisiae Histone H3 Mutants in biological duplicate

first: A

middle: E

last: Hildreth

first: Alex

last: Francette

first: Julia

last: Seraly

first: Lauren

last: Lotka

first: Karen

last: Arndt


title: An endogenous retrovirus-derived long non-coding RNA promotes fetal cardiomyocyte migration in primates

status: Public on Aug 11 2020

city: Stanford

first: Lei

last: Tian

state: CA

address: 1215 Welch Rd

country: USA

institute: Stanford's Postdoctoral Scholar programs

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The protein-coding gene networks regulating heart development are well known. Less understood are the roles of long non-coding RNAs (lncRNAs), many of which are poorly conserved due to their origins from transposable elements (TEs) such as endogenous retroviruses (ERVs). Here, we report hundreds of ERV elements from the primate-specific MER41 family are expressed in pluripotent cell-derived cardiomyocytes and fetal heart, some of which are regulated by the cardiogenic transcription factor TBX5. The most significant of these are located within BANCR, an lncRNA exclusively expressed in primate fetal cardiomyocytes in normal physiology. Surprisingly, BANCR promotes cellular movement in fetal cardiomyocytes, which is due in part to Rho GTPase and ephrin receptor signaling. We postulate that ERV-derived BANCR is a recent evolutionary mechanism for enabling larger heart sizes in primates, and underscores the remarkable retroviral origins of humans.

sample_organism:
Macaca mulatta
Gorilla gorilla
Pan troglodytes
Homo sapiens
Mus musculus

overall_design:
We performed RNA-seq of human fetal tissues, and iPSCs and cardiomyocytes derived from iPSCs (iPSC-CMs) in both human and non-human primate cell lines (chimpanzee, gorilla, rhesus macaque).
We also performed both RNA- and ATAC-seq of hESC-CMs with constitutive BANCR shRNA knockdown (BKD), lentiviral constitutive over-expression (BOE), as well as H3K27ac HiChIP in human iPSC-CMs. RNA-seq was also performed on E16 transgenic mouse embryo hearts with human BANCR expression, and compared with littermate control hearts.
YAP1 ChIP-seq was performed with anti-YAP1 antibody (Novus; NB110).

first: Kitchener

middle: D

last: Wilson

first: Mohammed

last: Ameen

first: Yue

last: Zhang

first: Maxwell

last: Mumbach

first: Hongchao

last: Guo

first: Joseph

middle: C

last: Wu


title: A transcriptomic atlas of murine and human alopecia areata identifies immune cell profiles predictive of human disease state.

status: Public on Aug 10 2020

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 500 Newton Road

department: Dermatology

institute: University of Iowa

summary: Alopecia areata (AA) is one of the most common autoimmune conditions, presenting initially with loss of hair without overt skin changes. The unremarkable appearance of the skin surface contrasts with the complex immune activity occurring at the hair follicle. AA pathogenesis is due to the loss of immune privilege of the hair follicle leading to autoimmune attack. Although the literature has focused on CD8+ T cells, vital roles for CD4+ T cells and antigen-presenting cells have been suggested. Here, we use single-cell sequencing to reveal distinct expression profiles of immune cells in AA. We found clonal expansions of both CD4+ and CD8+ T cells, with shared clonotypes across varied transcriptional states. These data were used to generate highly predictive models of human AA disease. Finally, single-cell sequencing of T cells in human AA recapitulated the clonotypic findings and the gene expression of the predictive models.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: CD45+ immune cells were isolated from skin and lymph nodes of mice with AA and control, while in humans CD45+ T cells were isolated from AA skin. Single-cell suspensions were processed with the Chromium Single Cell 5-prime Library & Gel Bead Kit and the 10x Genomics TCR Immunprofiling kit.

first: Nicholas

last: Borcherding


title: Distinct and overlapping roles of STAG1 and STAG2 in cohesin localization and gene expression in embryonic stem cells

city: Chapel Hill

first: Jill

last: Dowen

state: NC

address: 250 Bell Tower Drive

institute: University of North Carolina at Chapel Hill

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

overall_design: Refer to individual Series


title: Mechanism of Mitochondrial Dysfunction in Spinal and Bulbar Muscular Atrophy [AR ChIP-seq]

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Spinal and bulbar muscular atrophy (SBMA) is a neuromuscular disorder caused by a polyglutamine expansion in the androgen receptor (AR). Previous studies have shown that transcriptional dysregulation and mitochondrial impairment occur in SBMA. We used gene-expression analysis and ChIP-sequencing to map transcriptional changes in SBMA induced pluripotent stem cell-derived motor neurons. The SBMA cells had decreased expression of genes encoding electron transport chain subunits and other metabolic proteins, associated with reduced histone acetylation which may be contributing to mitochondrial dysfunction. AR ChIP-sequencing results indicate that this is not a direct transcriptional effect of mutant AR on mitochondrial gene expression. Furthermore, we found decreased acetyl-CoA, and pyruvate supplementation to correct this deficiency improved mitochondrial function and SBMA motor neuron viability. We propose that epigenetic dysregulation of metabolic genes contributes to reduced mitochondrial ATP production. Our results show a molecular link between altered epigenetic regulation and mitochondrial metabolism that contributes to neurodegeneration.

overall_design: Paired-end ChIP-Seq was performed on 8 human iPSC derived Motor Neuron (iMN) samples. Of these samples, four represented Wild Type condition cultured from two different donors, one represented AR KO condition cultured from one donor, and three represented SBMA condition cultured from three different donors.

first: Naemeh

last: Pourshafie

first: Ester

last: Masati

first: Eric

last: Bunker

first: Alec

last: Nickolls

first: Parisorn

last: Thepmankorn

first: Tyler

last: Ekins

first: Christopher

last: Grunseich

first: Kenneth

middle: H

last: Fischbeck


title: Caskin2-induced changes in endothelial cell gene expression

city: Durham

last: Kontos

address: 180A CARL Bldg, 213 Research Dr

department: Cardiology

institute: Duke University

summary: Caskin2 is a previously uncharacterized gene encoding a predicted scaffolding protein that we have found is highly expressed in vascular endothelial cells. We used microarray to identify genes that are differentially expressed in the setting of Caskin2 overexpression to test the hypothesis that Caskin2 expression induces a quiescent gene expression profile in cultured endothelial cells.

overall_design: Human umbilical vein endothelial cells (HUVECs) were infected with adenovirus encoding human Caskin2 variant 1 or GFP (n=3 technical replicates per treatment group) and allowed to recover in growth medium. RNA was extracted and hybridized on Affymetrix human transcriptome microarrays. Robust multi-array (RMA) normalization was performed using the Partek Genomics Suite 6.5.

first: Sarah

middle: B

last: Mueller


title: A non-pharmacological approach in the gut triggers distal metabolic rewiring capable of ameliorating diet-induced metabolic dysfunction

city: irvine

first: Siwei

last: Chen

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

summary: Here we show that Libramed has remarkable, beneficial effects on daily metabolism of an animal model of diet-induced obesity. We decipher the molecular and genomic signatures by which Libramed exerts its effects, and link them to the modifications in the composition of the gut microbiota observed upon its administration. Finally, we describe the mechanism by which such effects are obtained, highlighting the fact that the amelioration of metabolic dysfunction observed upon Libramed administration is profound and of systemic nature, despite being originated by sequestering, therefore non-pharmacological events elicited in the gut lumen.

overall_design: 8-week-old, male C57BL/6 mice were fed a high-fat diet (HFD) and treated with Libramed or vehicle. Liver was harvested at the two circadian time points ZT0 and ZT12 (n=3). Total RNA was extracted and used for RNA-seq.

first: Carolina

last: Greco

first: Stefano

last: Garretto

first: Emilie

last: Montellier

first: Yu

last: Liu

first: Pierre

last: Baldi

first: Paolo

last: Sassone-Corsi

first: Jacopo

last: Lucci


title: Expression profiling of microRNA in mouse eye, lung and testicle tissue

city: Beijing

first: Jiangcheng

last: Shi

address: 38 Xueyuan Road

country: China

institute: Peking University

type: Non-coding RNA profiling by high throughput sequencing

summary: microRNA profile in mouse eye, lung and testicle tissue

overall_design: In the study presented here, we used  three left entities and three right entities of eyes, lungs, and testicles from normal mice and identified the genome-wide expression level of microRNAs.

first: Qinghua

last: Cui

first: Jichun

last: Yang


title: Human primary fetal lung fibroblasts (HFL-1) undergoing replicative senescence

city: Athens

first: Niki

last: Chondrogianni

address: 48 Vassileos Constantinou Ave.

department: Institute of Chemical Biology

country: Greece

institute: National Hellenic Research Foundation

summary: We profiled the global gene expression of human primary fetal lung fibroblasts (HFL-1) at different stages while they were undergoing replicative senescence

overall_design: We maintained human primary fetal lung fibroblasts (HFL-1) in culture from a young stage until they reached a senescent stage after 50 replication cycles. The cells were collected at three different time points while undergoing RS. In the first young stage the cells were replicating every 24 hours, in the second middle-aged stage the cells were replicating every 7 days and in the third stage the cells have not replicated for 14 days.

first: Ilona

last: Binenbaum

first: Maria

last: Lefaki

first: Aristotelis

last: Chatziioannou


title: Mechanism of Mitochondrial Dysfunction in Spinal and Bulbar Muscular Atrophy

first: Kory

last: Johnson


title: Gut microbiome communication with the bone marrow regulates intestinal inflammation and susceptibility to amebiasis.

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

summary: We discovered that colonization of the gut with the human bile acid 7'-dehydroxylating bacteria Clostridia scindens provided immunity to the parasite E. histolytica in a murine model, increased granulocyte monocyte progenitors, and that adoptive marrow transplant from C. scindens colonized mice into naive mice could recapitualte this protection.

overall_design: RNA-seq in granulocyte monocyte progenitors

first: Stacey

middle: L

last: Burgess

first: William

middle: A

last: Petri


title: Identification of SHOT1/MTERF18 binding sites on the mitochondrial genome of Arabidopsis thaliana

status: Public on Aug 09 2020

city: Amherst

first: Minsoo

last: Kim

state: MA

address: 240 Thatcher Rd. N340B

department: BMB

institute: University of Massachusetts Amherst

summary: To identify possible mitochondrial DNA binding targets of SHOT1/MTERF18 (AT3G60400), C-terminal GFP fusion constructs under either a constitutive 35S promoter (35S::SHOT1-GFP) or the SHOT1 native promoter (SHOT1p::SHOT1-GFP) were made. The transgenes were introduced into the shot1-2 mutant background (Kim et al., 2012, Plant Cell) and verified to be functional based on recovery of shot1 from growth defects. As a control, a transgenic line harboring mitochondria-targeted GFP (Mito-GFP) under the 35S promoter was used. All enriched peaks in SHOT1-GFP samples are located upstream of different tRNA genes: trnS, trnM, trnG and trnF

overall_design: Immunoprecipitation of SHOT1-GFP (using GFP-Trap (ChromoTek)) crosslinked to DNA from isolated mitochondria of Mito-GFP (control), 35S::SHOT1-GFP (MK30) and SHOT1p::SHOT1-GFP (MK108) plants

first: Elizabeth

last: Vierling


title: Cell type identity determines transcriptomic immune responses in Arabidopsis thaliana roots

city: Coventry

first: Patrick

last: Schafer

address: Gibbet Hill Road

department: Life Sciences

country: United Kingdom

institute: University of Warwick

summary: Root pathogens are a major thread in global crop production and protection strategies are required to sustainably enhance the efficiency of root immunity. Our understanding of root immunity is still limited in comparison to the knowledge gained for the regulation of immune response in leaves. In an effort to reveal the organisation of root immunity in roots, we undertook a cell type-specific transcriptome analysis to identify gene networks in epidermis, cortex and pericycle cells of Arabidopsis roots upon treatment with two immunity elicitors, bacterial microbe-associated molecular pattern flagellin and the endogenous damage-associated molecular pattern Pep1. Our analyses revealed that both elicitors induced cell type-specific immunity gene networks. Interestingly, both elicitors did not alter cell identity determining gene networks. Using sophisticated paired motif promoter analyses, we identified key transcription factor pairs involved in the regulation of cell type-specific immunity networks. In addition, our data show that cell identity networks are liaised with cell immunity networks to activate cell type-specific immune response according to the functional capabilities of each cell type.

overall_design:
The response of epidermis, cortex and pericycle cells, isolated using Fluorescence Activated Cell Sorting (FACS) was analysed 2 hours after treatment with 1uM flg22 or 1uM Pep1 or H2O in Arabidopsis thaliana Col0 roots; genotypes carried GFP reporters marking either epidermis, cortex or pericycle root cells.
Gene expression was analysed using RNAseq, aligned to the TAIR10 genome.

first: Charlotte

last: Rich-Griffin

first: Ruth

last: Eichmann

first: Marco

middle: U

last: Reitz

first: Sophie

last: Hermann

first: Karl-Heinz

last: Kogel

first: Eddi

last: Esteban

first: Sascha

last: Ott

last: Schäfer


title: A role for alternative splicing in circadian control of insulin secretion and glucose homeostasis

city: La Jolla

first: Mark

last: Perelis

email: mperelis@ucsd.edu, perelis@gmail.com

address: Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Dr., Room 3805/Yeo Lab

institute: University of California San Diego

summary: We report the discovery of circadian clock-controlled alterantive pre-mRNA splicing in pancreatic beta cells and its role in insulin secretion. We performed RNA-sequencing in CRISPR-CAS9 edited Clock and Bmal1 knockout BetaTC6 cells and used differential mRNA expression and splicing analysis to identify and validate transcriptional and alternative splicing targets of the circadian clock regulating insulin secretion.

overall_design: We have profiled the transcriptomes of wild type and Bmal1 knockout pancreatic beta cells by RNA-seq and performed ChIP-seq and eCLIP-seq to map the DNA and RNA binding positions of the RNA binding protein THRAP3 in these cells.


title: Mechanism of Mitochondrial Dysfunction in Spinal and Bulbar Muscular Atrophy [ChIP-seq]

overall_design: Single-end ChIP-Seq was performed on 12 human iPSC derived Motor Neuron (iMN) samples. Of these samples, four represented Wild Type condition cultured from one donor, three represented AR KO condition cultured from one donor, and five represented SBMA condition cultured from one donor.

first: Naemeh

last: Pourshafie

first: Ester

last: Masati

first: Eric

last: Bunker

first: Alec

last: Nickolls

first: Parisorn

last: Thepmankorn

first: Tyler

last: Ekins

first: Christopher

last: Grunseich

first: Kenneth

last: Fischbeck


title: Differential gene expression of lymphocytes stimulated with rhinovirus species A and C in asthmatic and non-asthmatic children

city: Nedlands

first: Anya

last: Jones

state: Western Australia

address: Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute, The University of Western Australia

summary:
Background: Evidence suggests that immune responses to rhinovirus A and C are altered in asthmatic children and rhinovirus species induce different types of antibody responses.

Objective: To ascertain and compare the T-cell memory response induced by RV-A and RV-C in asthmatic and non-asthmatic children.

Methods: Peripheral blood mononuclear cells from children who previously suffered asthma exacerbation (asthmatics) and non-asthmatic controls were stimulated in vitro with peptide formulations to induce representative species-specific responses to RV-A and RV-C.  Expression of genes was measured by RNA-seq and differentially expressed genes were further analysed to identify enriched pathways and upstream regulators.

Results: Responses to RV-A showed markedly higher upregulation of IFNG and the IFNG responsive genes CXCL9, 10 and 11 and STAT1 compared to RV-C. There was no reciprocal upregulation of Th2 cytokine genes or the Th2 chemokine genes CCL11, CCL17 and CCL22. RV-C but not RV-A induced high upregulation of CCL24 (eotaxin-2) in both non-asthmatic and asthmatic responses. Upstream regulator analysis showed both RV-A and, although to a diminished extent, RV-C  induced predominant Th1 and inflammatory cytokine expression. The responses of asthmatics compared to non-asthmatics was diminished to both RV-A and RV-C while retaining the pattern for gene expression and upstream regulators characteristic of each species and there was no upregulation of Th2-type responses. All groups showed activation of the IL-17A pathway.

Conclusions: RV-C induced memory cells with a lower IFNG type response than RV-A without Th2 upregulation. Asthmatics had lower recall responses than non-asthmatics while largely retaining the same gene activation profile for each species.

first: Denise

last: Anderson

first: Cibele

middle: M

last: Gaido

first: Kim

middle: W

last: Carter

first: Ingrid

last: Laing

first: Anthony

last: Bosco

first: Wayne

last: Thomas

first: Belinda

middle: J

last: Hales


title: Exon array analysis of N2A cells after knocking down FUS

city: Nagoya

first: Akio

last: Masuda

state: Aichi

address: 65 tsurumai-cho, Showa-ku

country: Japan

institute: Nagoya University Graduate School of Medicine

summary:
To analyze the role of Fus, Ewsr1, and Taf15 in alternative RNA processing, we performed exon array analysis in N2A cells using exon arrays.
N2A cells were transfected with siRNA using Lipofectamine RNAiMAX (Life Technologies) according to the manufacturer’s instructions.

overall_design: We analyzed total RNA of N2A cells transfected with siRNA against mouse Fus, combination of Fus, Ewsr1 and Taf15, or control. RNA was harvested 48 hours after transfection.

first: Takaaki

last: Okamoto

first: Kinji

last: Ohno


title: DNA microarray analysis of blood before and after ingesting carotenoid-rich vegitable beverage for 8 weeks, a randomized and double-blinded controlled clinical trial

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: Metabolic syndrome, whose main diagnostic component is obesity, is a risk factor for lifestyle-related diseases, type 2 diabetes, and cardiovascular disease. Diet is known to affect the prevalence of metabolic syndrome. However, the effect of diet on metabolic syndrome in Japanese subjects has not been thoroughly explored. In the present study, we investigated the effect of carotenoid-rich vegetables, particularly lycopene- and lutein-rich vegetables, on the metabolic syndrome in obese Japanese men. We conducted an 8-week long randomized, double-blinded, controlled clinical trial in which, 28 middle-aged (40 ≤ age < 65) Japanese men with high body mass index (BMI ≥ 25) were randomized into four dietary groups: high lycopene + high lutein (HLyHLu), high lycopene + low lutein (HLyLLu), low lycopene + high lutein (LLyHLu), and low lycopene + low lutein (LLyLLu). Our results showed that daily beverage-intake increased the plasma levels of carotenoids without adverse effects, and the visceral fat level was significantly decreased in all the groups. The waist circumference was significantly decreased only in the HLyLLu group, whereas the CoQ10 oxidation rate was decreased in all the groups. The gene expression profiles of whole blood samples before and after ingestion differed only in the LLyLLu group, indicating the effect of carotenoids on gene expression profile. In conclusion, our results suggest that dietary uptake of carotenoids increases their concentration in blood, and reduces the intra-abdominal visceral fat.

overall_design: This study was a randomized, double-blind controlled (RCT) study, 8 weeks in duration from May 14th, 2014 to June 11th, 2014. The study protocol was approved by the Ethics Committee of Kyoto Prefectural University of Medicine (approved number: ERB-C-111), and all subjects provided informed consent. The eligibility of each subject was evaluated based on full review of their clinical history and physical examination, as well as on full blood count and serum chemistry. Selected eligible subjects were of middle age (40 ≤ age < 65), with high BMI (BMI ≥ 25) and were expected to be free from any medications. Subjects who had participated in other clinical trial within the last 3 months before the beginning of this study were excluded.    After successful screening, 28 subjects out of 50 candidates, were enrolled in this study. Eligible subjects were randomly assigned and equally distributed to receive one of four interventions: (A) TCH-722 carrot and TCL-499 kale pastes (high lycopene + high lutein or HLyHLu group); (B) TCH-722 carrot and ‘Shibuki’ cabbage pastes (high lycopene + low lutein or HLyLLu group); (C) ’Kinbi’ carrot and TCL-499 kale pastes (low lycopene + high lutein or LLyHLu group); (D) ‘Kinbi’ carrot and cabbage pastes (low lycopene + low lutein or LLyLLu group). During the 8-week intervention phase, each subject received once daily, before breakfast, an identical beverage containing 400 g of the testing pastes (Figure 2). The experimental conditions were registered with the University Hospital Medical Information Network (UMIN) Center (www.umin.ac.jp) and the UMIN Clinical Trials Registry (UMIN-CTR) Identifier is UMIN000014482.   Twenty-eight subjects were randomly assigned to four groups and consumed the test beverage for 8 weeks. After randomization, 2 men of HLyLLu group withdrew from the study, one because of hospitalization after a traffic injury and the other because of residence relocation. From LLyLLu group, 2 men were also excluded from the analysis, one because the received serum sample was inadequate and the other because of pharmacological treatment commencement for a non-related with this study issue. One sample from LLyHLu group was not used for DNA microarray analysis due to its markedly low integrity of total RNA. Thus, a total of 46 samples (23 participants) was analyzed.

first: Tomohisa

last: Takagi

first: Ryotaro

last: Hayashi

first: Shinji

last: Okada

first: Rumiko

last: Miyashita

first: Mayumi

last: Yamada

first: Yoichi

last: Mihara

first: Katsura

last: Mizushima

first: Mayuko

last: Morita

first: Kazuhiko

last: Uchiyama

first: Akihiro

last: Hino

last: Naito

first: Yoshito

last: Itoh


title: Mechanism of Mitochondrial Dysfunction in Spinal and Bulbar Muscular Atrophy [RNA-seq]

first: Kory

last: Johnson

overall_design: Paired-end stranded RNA-Seq was performed on a total of 11 human iPSC derived Motor Neuron (iMN) samples for a target depth of 100M read pairs per sample. Of these samples, four represented Wild Type condition cultured from two different donors, three represented Androgen Receptor (AR) Knock-Out (KO) condition cultured from one donor, and four represented Spinal and Bulbar Muscular Atrophy (SBMA) condition cultured from three different donors.

first: Naemeh

last: Pourshafie

first: Ester

last: Masati

first: Eric

last: Bunker

first: Alec

last: Nickolls

first: Parisorn

last: Thepmankorn

last: R Johnson

first: Tyler

last: Ekins

first: Christopher

last: Grunseich

first: Kenneth

last: Fischbeck


title: Molecular features of the measles virus viral fusion complex that favor infection and spread in the brain

status: Public on Aug 08 2020

city: Seattle

first: Nicole

middle: A P

last: Lieberman

state: WA

address: 850 Republican St S130

department: Laboratory Medicine

institute: University of Washington


title: Molecular features of the measles virus viral fusion complex that favor infection and spread in the brain [human]

summary: A measles virus (MeV) isolate bearing a single amino acid change in the fusion protein (F) -- L454W -- was identified in two patients who died of MeV central nervous system (CNS) infection. We analyzed whether this mutation confers an advantage over wild type virus in the CNS, thereby contributing to disease in these patients. Using murine ex vivo organotypic brain cultures and human induced pluripotent stem cell-derived brain organoids, we show that specific CNS adaptive mutations in F result in augmented spread of virus ex vivo and that this is associated with an enhanced innate immune response. The spread of virus in brain organoids is blocked by an inhibitory peptide that targets F, confirming that dissemination in the brain tissue is attributable to F. A single mutation in MeV F thus alters the fusion complex to render the virus more neuropathogenic, allowing it to propagate in the face of the innate immune response.

overall_design:
RNAseq of human brain organoids following infection with WT or fusion protein mutant  measles virus, or no infection
Note from submitter: Please note that raw fastq files have not been included for the human data; the consent of the donors of cells that made the iPSC lines used does not explicitly cover sharing of genomic data, therefore our IRB will not allow us to upload sequence data.

first: Cyrille

last: Mathieu

first: Alexander

last: Greninger

first: Matteo

last: Porotto


title: Single-cell transcriptomic analysis of mammary tumors reveals distinct patterns of hierarchical and subtype heterogeneity

city: Cincinnati

first: Xiaoting

last: Zhu

state: OH

address: 3333 burnet avenue,MLC7024

institute: Cincinnati Children's Hospital Medical Center

summary: Breast cancer stem cells (BCSCs) contribute to intra-tumoral heterogeneity and therapeutic resistance. However, the binary concept of universal BCSCs co-existing with bulk tumor cells is over-simplified. Through single-cell RNA-sequencing, we found that Neu, PyMT and BRCA1-null mammary tumors each corresponded to a spectrum of minimally overlapping cell differentiation states without a universal BCSC population. Instead, our analyses revealed that these tumors contained distinct lineage-specific tumor propagating cells (TPCs) and this is reflective of the self-sustaining capabilities of lineage-specific stem/progenitor cells in the mammary epithelial hierarchy. By understanding the respective tumor hierarchies, we were able to identify CD14 as a TPC marker in the Neu tumor. Additionally, single-cell breast cancer subtype stratification revealed the co-existence of multiple breast cancer subtypes within tumors. Collectively, our findings emphasize the need to account for lineage-specific TPCs and the hierarchical composition within breast tumors, as these heterogenous sub-populations can have differential therapeutic susceptibilities.

overall_design: We compared the gene expression profile at single-cell level of four breast tumor models in mice.

first: Syn

middle: K

last: Yeo

first: Long

last: Lu

first: Jun-Lin

last: Guan


title: Transcriptome profiles of pancreatic macrophage following AP injury

city: Shanghai

first: jinghua

last: wu

state: Shanghai

address: 160 Pujian Rd, Shanghai 200127,China

department: Stem Cell Research Center

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

summary: Upon injury, immune cells undergo dynamic changes in population size, differentiation state and function in response to maintain organismal integrity. Myeloid cells, mostly macrophages have been shown to act as positive regulators of development, tissue homoeostasis, inflammation，especially in inducing resolution after inflammation, remodeling and repair. Here we report what specific role macrophages play in every precisely dynamical period after injury in vivo. We first confirmed that M2-like macrophages from recruited monocytes accumulate during AP recovery(RAP). By macrophage depletion in different time points, before or after ADM phase, we elucidate distinct roles of macrophage in different stages of AP recovery. To further understanding the phenotype and function of macrophage during AP recovery, pancreatic macrophages were isolated in all precisely indicated time points for RNA-seq analysis. By analyzing RNA-seq result, we verify PI3K-AKT activation in macrophage aids in resolving inflammation in ADM phase and IL4RA deficiency impairs M2-like macrophages and AP recovery. Finally, we further investigated PGE2’s role in regulating M2 macrophage polarization and we found PGE2 augments IL4Ra signaling to enhance M2 activation of macrophage.

overall_design: Briefly, acute pancreatitis (AP) was induced using caerulein. Mice were fasted one night before injection, after that mice were given 10 hourly i.p. injections of saline as control or 100 mg/kg caerulein, and harvested immediately on d1, d3, d5, d7 post the first injection.We named mock as d0. Pancreas leukocytes were enriched by CD45.2 magnetic beads and sorted by FACSAriaⅡto get pure macrophages (CD45+CD11b+F4/80+). RNA was isolated to conduct RNA-seq. Each sample has 1 repeat, but was pooled from more than 3 mice.

first: Jing

last: Xue


title: Gene expression study of Calotropis procera to identify and analyze the genes expressed in different  tissues in normal conditions.

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: In this study, we used customized oligo-array in symbiotic association with the RNA-SEQ tool. Sequences generated previously in our lab through RNA-SEQ were validated on Agilent microarray platform. Gene expression in different tissues of Calotropis plant was studied. Whole plant was considered as control in this study and leaf, stem and root specific genes were mined out in reference to whole plant. Specific genes in a tissue, common genes in all the tissues as well as highly abundant genes were identified from the dataset.

overall_design: Agilent Custom Plant Gene Expression  4X180K Array (AMADID: 076611) designed by Dr. Vineeta Tripathi with the help of Genotypic Technology Private Limited, Bangalore

first: Vineeta

last: Tripathi

first: Tushar

last: Pandey

first: Akansha


title: Molecular features of the measles virus viral fusion complex that favor infection and spread in the brain [mouse]

overall_design: RNAseq of mouse organotypic brain cultures following infection with WT or F-L454W measles virus, or no infection


title: Human pancreatic islets methylation array

city: Bruxelles

first: Jean-Valery

last: Turatsinze

address: Route de Lennik 808 CP618

department: Faculté de Medecine

country: Belgium

institute: Université Libre de Bruxelles

type: Methylation profiling by genome tiling array

summary: Circulating cell-free unmethylated DNA fragments arising from the human INS gene have been proposed as biomarkers of β-cell death for the presymptomatic detection of diabetes. However, given the variability of CpG methylation in the INS gene in different cell types, this gene alone may not yield sufficiently specific information to unambiguously report β-cell damage. We employed an unbiased approach using data from a human DNA methylation gene array to identify the CHTOP gene as a candidate biomarker whose CpGs show a greater frequency of unmethylation in human islets. When tested across an array of non-islet human tissues by digital PCR, both INS and CHTOP contain unmethylated CpG sites in several of these tissues, but in a non-overlapping pattern: INS showed a slightly higher frequency of unmethylation in adipose tissue, whereas CHTOP appeared to be unmethylated in pancreas, brain, and skeletal muscle. Notably, INS and CHTOP genes are both unmethylated in human β and α cells, suggesting that each species at best would represent markers of islet cell death in general, and together might distinguish death arising from islets vs. other tissues. To validate unmethylated CHTOP as a biomarker for islet cell damage, we used digital PCR to measure cell-free circulating DNA in human populations. Compared to healthy controls, we observed that levels of differentially methylated CHTOP and INS were higher in youth with new onset type 1 diabetes and in healthy youth who have first-degree relatives with T1D. When tested in youth across a spectrum of metabolic dysfunction, increased levels of unmethylated INS and CHTOP were observed in obese individuals compared to lean controls. Together, these data suggest that simultaneous measurement of both circulating differentially methylated INS and CHTOP is likely to detect islet death in T1D, and raise new questions about β-cell health in populations at risk for both T1D and T2D. Importantly, our data support the use of multiple parameters to increase the accuracy of biomarkers of β-cell health in youth with diabetes.

overall_design: Bisulphite-converted DNA from 64 samples of human pancreatic islets were hybridised to the Illumina Infinium 450K Human Methylation BeadChip.

first: Farooq

last: Syed

first: Sarah

last: Tersey

first: Jean

middle: V

first: Jamie

last: Felton

first: Jennifer

last: Nelson

first: Emily

last: Sims

first: Mathieu

last: Defrance

first: Francois

last: Fuks

first: Miriam

last: Cnop

first: Marco

last: Bugliani

first: Piero

last: Marchetti

first: Anette

middle: G

last: Ziegler

first: Ezio

last: Bonifacio

first: Bobbie

last: Webb-Robertson

first: Carmella

last: Evans-Molina

first: Decio

last: Eizirik

first: Kieren

last: Mather

first: Silva

last: Arslanian

first: Raghavendra

last: Mirmira


title: Genome-wide transcriptome analysis of human iPSC-derived cortical interneurons under inflammation conditions

status: Public on Aug 12 2020

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

summary: We report changes in gene expression in cortical interneurons under inflammation conditions by genome-wide transcriptome analysis.

overall_design: RNA sequencing analysis (bulk) of healthy control interneurons and schizophrenia interneurons. Four independent iPS lines per group (total 8 iPSC lines) with three independent differentiations

first: Sangmi

last: Chung


title: RNA-seq analysis of PRMT5 targeted  genes in  Tu212 cells

city: Meizhou

last: Wang

address: Meisong Road

institute: Jiaying University

summary: RNA-sequencing was performed to identify the possible underlying signaling pathway of PRMT5 overexpressing in Tu212 cells. Cells were treated with pEZ-PRMT5 or pEZ-Vector.

overall_design: Examination of  PRMT5 overexpression mediated signaling pathway in Tu212 cells

first: Xuekui

last: Liu


title: PRMT1-Mdm4-p53 pathway controls epicardial invasion and cell fate transition

status: Public on Aug 18 2020

city: New Orleans

first: Olan

last: Jackson-Weaver

state: Louisiana

address: 1430 Tulane Ave, Department of Surgery

department: Surgery

institute: Tulane University

summary: Epicardial cells are progenitors giving rise to the majority of cardiac fibroblasts, coronary smooth muscle cells, and pericytes during cardiac development, and critically modulating heart morphogenesis and coronary development. An integral phase of epicardial cell fate transition is epithelial-to-mesenchymal transition (EMT), which confers motility and facilitates cell fate transition. We identify a pathway involving protein arginine methyltransferase 1 (PRMT1) and its downstream p53 signaling that drives epicardial EMT and invasion. We show that PRMT1 determines the half-life of p53 through regulating alternative splicing of Mdm4, which is a key controller of p53 degradation. Loss of PRMT1 promotes the expression of Mdm4 short form, which inhibits p53 degradation. Accumulation of p53 subsequently enhances Slug degradation and blocks epicardial EMT. We further demonstrated that the PRMT1-Mdm4-p53 pathway drives epicardial cell fate transition into cardiac fibroblasts, coronary smooth muscle cells and pericytes in vivo, and modulates ventricular morphogenesis and coronary vessel formation. Together, our results establish critical functions of the PRMT1-Mdm4-p53 pathway in epicardial EMT, invasion and cell fate transition.

overall_design: 8 groups analyzed, 2 biological replicates per group. Total of 16 samples.

first: Jiang

last: Qian

first: Yongchao

last: Gou

first: Jian

last: Wu

first: Hua

last: Shen

first: Yibu

last: Chen

first: Meng

last: Li

first: Henry

last: Sucov

last: Xu


title: Inhibition of O-GlcNAc transferase renders prostate cancer cells dependent on CDK9

city: Belfast

first: Rebecca

middle: Elizabeth

last: Steele

address: 97 Lisburn Road

department: CCRCB

institute: Queen's University Belfast

summary: O-GlcNAc transferase (OGT) is a nutrient-sensitive glycosyltransferase that is overexpressed in prostate cancer, the most common cancer in males. We recently developed specific and potent inhibitor targeting this enzyme, and here we report a synthetic lethality screen using this compound. Our screen identified pan-cyclin-dependent kinase (CDK) inhibitor AT7519 as lethal in combination with OGT inhibition. Follow-up chemical and genetic approaches identified CDK9 as the major target for synthetic lethality with OGT inhibition in prostate cancer cells. OGT expression is regulated through retention of the fourth intron in the gene and CDK9 inhibition blunted this regulatory mechanism. CDK9 phosphorylates carboxy-terminal domain (CTD) of RNA Polymerase II (RNA Pol II) to promote transcription elongation. We showed that OGT inhibition augments effects of CDK9 inhibitors on CTD phosphorylation and general transcription. Finally, the combined inhibition of both OGT and CDK9 blocked growth of organoids derived from metastatic prostate cancer patients but had minimal effects on normal prostate spheroids. We report a novel synthetic lethal interaction between inhibitors of OGT and CDK9 that specifically kills prostate cancer cells but not normal cells. Our study highlights the potential of combining OGT inhibitors with other treatments to exploit cancer specific vulnerabilities.

overall_design: mRNA profiles of LNCaP cells treated with control, OGT inhibitor (40μM OSMI-2), CDK inhibitor (0.5μM AT7519) and Combination treatment (0.5μM AT7519 + 40μM OSMI-2), for 4 hours prior to harvesting.

first: Harri

last: Itkonen

first: Ninu

last: Poulose

first: Sara

last: Martin

first: Zebulon

last: Levine

first: Damien

middle: Y

last: Duveau

first: Ryan

last: Carelli

first: Reema

last: Singh

first: Alfonso

last: Urbanucci

first: Massimo

last: Loda

first: Criag

last: Thomas

first: Ian

last: Mills

first: Suzanne

last: Walker


title: ATAC-Seq of RSV infected small airway epithelial cells

city: Madison

first: Allan

last: Brasier

state: WI

address: 715 Highland

department: ICTR

institute: university of Wissconsin

summary: We sought to identify transcriptionally active open chromatin domains in highly differentiated lower airway epithelial cells using transposase cleavage -next generation sequencing (ATAC-Seq).

overall_design: ATAC-seq was performed in two biological replicates per treatment.


title: Erk1/2 mediated negative feedback regulation is essential for postnatal intestinal development and homeostasis

first: Jiwei

last: Chen

address: 500 Dongchuan Rd.

institute: East China Normal University

summary:
Objective: Homeostasis of intestinal stem cells (ISCs) is maintained by external niche signals and complicated intrinsic signaling networks. Mitogen-activated protein kinase (MAPK) cascades play pivotal roles in stem cell self-renewal and differentiation, but the functions and underlying molecular mechanisms are not fully understood.
Design: We performed studies with mice deletion of Erk1/2 genes in intestinal epithelial cells at embryonic stages or a control mice. Intestinal tissues were collected and analyzed by histology, gene expression profiling, immunohistochemistry, immunfluorescence, western blotting and organoid culture. Organoids were treated with specific inhibitors for Ras or Akt activity. Mice were treated by intraperitoneal injection of rapamycin to inhibit mTOR signaling.
Results: We found that deletion of Erk1/2 genes resulted in an unexpected increase in cell proliferation and migration, expansion of ISCs and formation of polyp-like structures, leading to postnatal death. Deficiency of epithelial Erk1/2 strongly impaired secretory cell differentiation and enterocyte maturation with aberrant Wnt signaling activation. Erk1/2 depletion resulted in loss of feedback regulation leading to Ras/Raf cascade activation. Ras then transactivated Akt activity to stimulate mTOR and phosphorylate β-catenin on Ser552. Suppression of Ras or Akt activity through specific inhibitors significantly repressed Akt downstream signaling and restored cell proliferation and differentiation phenotypes ex vivo. Moreover, inhibition of mTOR signaling by rapamycin partially rescued Erk1/2 depletion-induced intestinal defects and significantly prolonged mutant mouse life span.
Conclusions Our study demonstrates an unexplored critical role of ERK/MAPK pathway negative feedback regulation of Akt/mTOR in intestine development and homeostasis, suggesting a complicated regulatory network in ISC function.

overall_design: Small intestine mRNA profiles of 14-day old wild type (WT) and Erk1/2 -/- mice were generated by deep sequencing, in triplicate, using HiSeq 2000.

first: Dali

last: Li

first: Gaigai

last: Wei


title: NuRD subunit CHD4 regulates super-enhancer accessibility in Rhabdomyosarcoma and represents a general tumor dependency

city: Bethesda

first: Javed

last: Khan

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

summary: ATP-dependent chromatin remodelers modulate gene expression by regulating genome accessibility and can contribute to tumorigenesis. In fusion-positive rhabdomyosarcoma (FP-RMS), we have previously identified the chromatin remodeler and NuRD subunit CHD4 as an essential gene for tumor survival. Here, we demonstrate that the FP-RMS vulnerability to CHD4 goes beyond its function as a NuRD member. Mechanistically, CHD4 interacts with BRD4 and co-localizes with the tumor driver and fusion protein PAX3-FOXO1 at super-enhancers where it generates a chromatin architecture permissive for the binding of the fusion protein. This allows the positioning of RNA polymerase 2 at promoters and the expression of the oncogenic program of PAX3-FOXO1. Additionally, analysis of genome-wide cancer dependency databases identifies CHD4 amongst the NuRD subunits as general novel cancer vulnerability. Our findings describe, for the first time, CHD4 as a regulator of super-enhancer-mediated gene expression and establish this chromatin remodeler as an unexpected broad tumor susceptibility.

overall_design: ChIP assays were performed using the iDeal ChIP-seq kit for Transcription Factors (Diagenode), and were performed once per target per cell line per condition.

first: Berkley

middle: E

last: Gryder

first: Xinyu

last: Wen


title: Polycomb represses a gene network controlling puberty via modulation of histone demethylase Kdm6b expression

city: Beaverton

first: Hollis

last: Wright

state: OR

address: 505 NW 185th Avenue

department: DIvision of Neuroscience

institute: ONPRC/OHSU

summary: We report gene expression profiles in the medial basal hypothalami of 28-day-old female rats infected with a lentivirus construct that overexpresses EED and matched controls infected with a GFP-expression construct.

overall_design: Expression analysis between perturbed (overexpressing EED) and control animals.

first: Carlos

last: Toro

middle: F

last: Alywin

first: Sergio

last: Ojeda

first: Alejandro

last: Lomniczi


title: Rate of transcription elongation and sequence-specific pausing by RNA polymerase I directly influence ribosomal RNA processing

city: Birmingham

first: David

last: Schneider

state: AL

address: Kaul Human Genetics Bldg, Rm 442, 720 20th St South

institute: University of Alabama at Birmingham

summary: We report altered pause profiles and sensitivity to nucleotide composition in the rpa190-f1205h RNA polymerase I mutant in vivo and in vitro

overall_design: WT and rpa190-f1205h RNA polymerase I NET-seq in s. cerevisiae

first: Krysta

last: Engel


title: circRNA Expression Profile in prostate cancer

status: Public on Aug 07 2020

city: Gaozhou

first: Zhi-Hai

last: Deng

state: Guangdong

address: 89 Xiguan road

department: Urology

institute: Gaozhou People's Hospital

summary: One matched prostate cancer and normal tissues were used for microarray.

overall_design: circRNA expression profile in 1 pair of prostate cancer tissue and adjacent non-neoplastic tissue by circRNA integrated microarrays


title: Gene expression profiling of Dermal Papilla cells isolated from wild type (WT) and Fgfr1/Fgfr2 double mutant mice during anagen (at P14 and P16) was performed by RNA-seq analysis

city: Safed

last: Enshell-Seijffers

address: 8 Henrietta Szold

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar Ilan University

summary: Gene expression analysis revealed that the DP transcriptome is  altered in the Fgfr1/Fgfr2 double mutant. At P14 the expression of 188 genes was significantly altered. At P16 the expression of 1082 genes were significantly altered.

overall_design: 3 samples for wt and 3 samples for Fgfr1/Fgfr2 double mutant were used for each time point (P14 and P16)

first: Sarina

last: Harshuk-Shabso


title: Identification and Characterization of Cellular Heterogeneity within the Developing Renal Interstitium

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

summary: Kidney formation requires the coordinated growth of multiple cell types including the collecting ducts, nephrons, vasculature and interstitium. We show that during development, the interstitium is a highly heterogeneous, patterned population of cells that occupies distinct positions correlated to the adjacent parenchyma. Our analysis indicates that the heterogeneity is not a mere reflection of different stages in a linear developmental trajectory but instead represents several novel differentiated cell states. Further, we find that beta-catenin has a cell autonomous role in the development of a medullary subset of the interstitium and that this non-autonomously affects the development of the adjacent epithelia.

overall_design: We performed single cell RNA sequencing on Foxd1-positive cells purified by fluorescence activated cell sorting (FACS) from Foxd1Cre;Rosa-Tomato E18.5  mouse kidneys.

first: Alicia

middle: R

last: England


title: Genome and Transcriptome Sequencing of Novel Pseudomonas sp. NLX-4 Strain Involved in Bio-restoration of Over Exploited Mining Sites

city: Jiangsu

first: Jinchi

last: Zhang

state: Nanjing,

address: Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China

department: Co-innovation Center for Sustainable Forestry in Southern China

institute: Nanjing Forestry University

summary: Relentless mining operations have destroyed our environment significantly. Soil inhabiting microbes play a significant role in ecological restoration of these areas. Microbial weathering processes like chemical dissolution of rocks significantly promotes the soil properties and enhances the rock to soil ratio respectively. Earlier studies have reported that bacteria exhibit efficient rock-dissolution abilities by releasing organic acids and other chemical elements from the silicate rocks. However, rock-dissolving mechanisms of the bacterium remain to be unclear till date. Thus, we have performed rock-dissolution experiments followed by genome and transcriptome sequencing of novel Pseudomonas sp.NLX-4 strain to explore the efficiency of microbe-mediated habitat restoration and its molecular mechanisms underlying this biological process. Results obtained from initial rock dissolution experiments revealed that Pseudomonas sp. NLX-4 strain efficiently accelerates the dissolution of silicate rocks by secreting amino acids, exopolysaccharides, and organic acids with elevated concentrations of potassium, silicon and aluminium elements. The rock dissolution experiments of NLX-4 strain exhibited an initial increase in particle diameter variation values between 0-15 days and decline after 15 days-time respectively. The 6,771,445-base pair NLX-4 genome exhibited 63.21 GC percentage respectively with a total of 6041 protein coding genes. Genome wide annotations of NLX-4 strain exhibits 5045-COG, 3996-GO, 5342-InterPro, 4386-KEGG proteins respectively Transcriptome analysis of NLX-4 cultured with/without silicate rocks resulted in 539 (288-up and 251-down) differentially expressed genes (DEGs). Fifteen DEGs encoding for siderophore transport, EPS and amino acids synthesis, organic acids metabolism, and bacterial resistance to adverse environmental conditions were highly up-regulated by cultured with silicate rocks. This study has not only provided a new strategy for the ecological restoration of rock mining areas, but also enriched the applicable bacterial and genetic resources.

overall_design: We have performed genome-wide transcriptome analysis of rock-dissolving Pseudomonas sp NLX4 strain to understand and reveal the molecular mechanisms employed NLX4 strain for dissolution of rock samples. We have designed our experiment with a total of 6 samples with three replicates each  treatment (NLX-4 strain was cultured with rock sample 5.0 g L-1 using fermentation medium at 30℃ with 180 rpm for 15 days) and control (NLX-4 cultured in fermentation medium added with 0.3 g L-1 KCl).

first: Yanwen

last: Wu

first: Ayyappa

last: Kameshwar

first: Bo

first: Feifei

last: Chen

first: Wensheng

last: Qin

first: Miaojing

last: Meng


title: Linking Key Steps of MicroRNA Biogenesis by TREX-2 and the Nuclear Pore Complex in Arabidopsis

first: Chenjiang

last: You

address: 2005 Songhu Rd

institute: Fudan University

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

overall_design: Refer to individual Series


title: Linking Key Steps of MicroRNA Biogenesis by TREX-2 and the Nuclear Pore Complex in Arabidopsis [mRNA-Seq]

summary: Unlike in metazoans, the stepwise biogenesis of microRNAs (miRNAs) occurs within the nucleus in plants. Whether or how the major steps in miRNA biogenesis are coordinated is largely unknown. Here, we show that the plant TREX-2 complex promotes multiple steps in miRNA biogenesis, including transcription, processing and nuclear export. Core subunits of TREX-2, THP1 and SAC3A, interact and co-localize with RNA Polymerase II to promote the transcription of MIR genes in the nucleoplasm. TREX-2 interacts with the microprocessor component SERRATE and promotes the formation of Dicing bodies in the nucleoplasm. THP1 also interacts and co-localizes with a nucleoporin protein NUP1 at the nuclear envelope. NUP1 and THP1 promote the nuclear export of miRNAs and AGO1. These results suggest that TREX-2 coordinates the transcription, processing and export steps in miRNA biogenesis to ensure efficient miRNA production.

overall_design: Examination mRNAs in thp1-5 and sac3 mutants

first: Bailong

first: Xuemei


title: Next-generation sequencing facilitates quantitative analysis of microRNAs under TOR inhibitors treatment in potato

city: Chongqing

first: Kexuan

address: 174 Shazheng ST, Shapingba

institute: Chongqing University

summary: MiRNA plays an important role in post-transcriptional gene regulation in plants. Whether TOR is involved in post-transcriptional gene regulation remains unclear in potato and other plants. In this study, we conducted the high-throughput sequencing of genome-wide miRNAs in the potato seedlings for profiling their expression patterns and identifying TOR related miRNAs in potato.

overall_design: MiRNA profiles of potato seedlings under TOR inhibitors treatment.

first: Huan

last: Yin

first: Fangjie

last: Xiong

first: Li

last: Feng

first: Fengping

last: Zhuo

first: Pan

last: Dong

first: Maozhi

last: Ren


title: Linking Key Steps of MicroRNA Biogenesis by TREX-2 and the Nuclear Pore Complex in Arabidopsis [miRNA-Seq]

overall_design: Examination small RNAs in thp1-5 and nup1-cs line


title: Transcriptomics of Human Liver Ischemia and Reperfusion Injury

city: Los Angeles

first: Richard

middle: Sungho

last: Ahn

state: CA

address: 611 Charles E. Young Drive East, UCLA, Boyer Hall, 510C

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California Los Angeles

summary: For orthotopic liver transplants, ischemia-reperfusion injury (IRI) is known to compromise allograft survival. To better understand the transcriptomics of immune responses underlying liver transplant IRI, RNA-seq was performed on liver biopsies from 23 IRI+ and 17 IRI- patients, both pre-transplant and post-transplant. Genes that are differentially expressed in IRI+ samples, along with the pathways enriched for by those genes, were identified.

overall_design: Needle-core liver biopsies from liver transplant recipients were obtained at 2 timepoints: pre-transplantation (n = 40) and post-transplantation (n = 40). Of the 40 samples at each timepoint, 23 were IRI+ and 17 were IRI-. All samples were sequenced on the Illumina HiSeq3000 platform.

first: Rebecca

last: Sosa


title: Transcriptome changes in mouse retina after conditional knockout of UXT

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

summary: Ubiquitously expressed transcript (UXT), a small chaperone-like protein, is widely expressed in diverse human and mouse tissues and is more abundant in retina and kidney. Here, we investigated changes after  conditional knockout of UXT in mouse retina at  molecular, morphological and functional aspects.

overall_design: Total RNA in mouse retina after conditional knockout of UXT was isolated and sequenced by deep sequencing using the Hi-Seq (Illumina) platform at Beijing Novel Bioinformatics Co., Ltd. (https://en.novogene.com/).

first: Mingyu

last: Pan


title: Dissecting transcriptome complexity in chronic myeloid leukemia using TIF-Seq2

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

summary: Eukaryotic transcriptomes are complex involving thousands of overlapping transcripts. The interleaved nature of the transcriptome complicates its annotation, limits our ability to identify regulatory regions and, in some cases, can lead to misinterpretation of gene expression. Long-read technologies promise to solve this problem, however short-read approaches have still better throughput and quality. To bridge this gap, we have developed an optimized method, TIF-Seq2, able to sequence simultaneously the 5’ and 3’ end of individual mRNA molecules at single-nucleotide resolution. We investigate the transcriptome of a well-characterized human cell line (K562) and identify thousands of new transcript isoforms. By focusing on mRNAs challenging to investigate with RNA-Seq, we accurately define boundaries of low expressed intergenic and read-through transcripts. We validate those novel features in cell lines and in chronic myeloid leukaemia patients. Our results demonstrate that TIF-Seq2 improves the annotation of complex genomes facilitating the assignment of promoters to genes and the identification of transcriptionally fused proteins.

overall_design: We performed an optimised TIF-seq2 method to determine the co-occurrence of transcription start sites and poly(A) sites in human cell line K562, together with 3'T-fill sequencing approach (PMID: 23295673) to define the PAS in the same cell line. In order to validate selected isoforms discovered by TIF-Seq2, we performed targeted long-read sequencing on the Pacific Biosciences platform.

first: Jingwen

last: Wang

first: Bingnan

last: Li

first: Sueli

last: Marques


title: Robust partitioning of microRNA targets from downstream regulatory changes [Ribo-seq]

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotech Bldg

department: Molecular Biology and Genetics

institute: Cornell University

summary: MicroRNA’s function is defined by the targets it regulates. Despite miRNAs’ crucial role in various cellular processes and disease states, the identification of their targets remains challenging. Existing methods suffer from high false-positive rates and are inadequate in differentiating direct targets from downstream regulatory changes. Here, we introduce a simple approach involving combined analysis of RNA-seq and Precise RunOn-seq (PRO-seq) (CARP) to effectively measure post-transcriptional regulation. We apply this approach to seven different miRNAs and robustly distinguish their direct targets from downstream changes. We validate the efficacy of our approach using argonaute-CLIP-seq. We show using CARP and ribosome-profiling analyses that accelerated mRNA decay is the major mode of target regulation by miRNAs. Additionally, our comparative analyses reveal that CARP aids in discovery of complex regulatory mechanisms and in capturing false-negatives of existing approaches. Furthermore, post-transcriptional changes measured using CARP uncover miRNA-dependent regulation of coding sites. Lastly, we demonstrate that PRO-seq provides mechanistic explanation of indirect targeting, unraveling miRNA regulatory networks. Finally, we believe that CARP is particularly suitable to study in vivo functions of miRNAs in primary cells.

overall_design: Ribosome profiling of HEK293 cells with and without specific miRNAs by high-throughput sequencing, in duplicate, using Illumina NextSeq500

first: Ravi

last: Patel


title: Robust partitioning of microRNA targets from downstream regulatory changes [miRNA-seq]

summary: The biological impact of microRNAs is determined by their targets, and robustly identifying direct miRNA targets remains challenging. Existing methods suffer from high false-positive rates and are unable to effectively differentiate direct miRNA targets from downstream regulatory changes. Here, we present a simple approach to deconvolute post-transcriptional and transcriptional changes using PRO-seq with RNA-seq. In combination, these methods allow us to systematically profile the regulatory impact of a miRNA. We refer to this approach as CARP: Combined Analysis of RNA-seq and PRO-seq. We apply CARP to multiple miRNAs and show that it robustly distinguishes direct targets from downstream changes, while greatly reducing false positives. We validate our approach using Argonaute eCLIP-seq and ribosome profiling, demonstrating that CARP defines a comprehensive repertoire of targets. We identify miRNA-specific activity of target sites within the coding region. CARP facilitates the dissection of complex changes in gene regulatory networks triggered by miRNAs and identification of transcription factors that underlie downstream regulatory changes. Given the robustness of the approach, CARP is particularly suitable for dissecting miRNA regulatory networks in vivo.

overall_design: MicroRNA profiling of HEK293 cells with and without specific miRNAs by high-throughput sequencing using Illumina NextSeq500.


title: Genome-wide R-loop analysis defines unique roles for DDX5, XRN2, and PRMT5 in DNA/RNA hybrid resolution

city: Montreal

first: Stéphane

last: Richard

state: Quebec

address: 3755 Côte-Ste-Catherine Road

department: Departments of Oncology and Medicine

country: Canada

institute: Lady Davis Institute - JGH, McGill University

summary: DDX5, XRN2, and PRMT5 have been shown to resolve DNA/RNA hybrids (R-loops) at RNA polymerase II transcription termination sites at few genomic loci. Herein, we perform genome-wide R-loop mapping using classical DNA/RNA immunoprecipitation and high-throughput sequencing (DRIP-seq) of loci regulated by DDX5, XRN2, and PRMT5. We observed hundreds to thousands of R-loop gains and losses at transcribed loci in DDX5-, XRN2-, and PRMT5-deficient U2OS cells. R-loop gains were characteristic of highly transcribed genes located at gene-rich regions, whereas R-loop losses were observed in low-density gene areas. DDX5, XRN2, and PRMT5 shared many R-loop gain loci at transcription termination sites, consistent with their coordinated role in RNA polymerase II transcription termination. DDX5-depleted cells had unique R-loop gain peaks near the transcription start site that did not overlap with those of siXRN2 and siPRMT5 cells, suggesting a role for DDX5 in transcription initiation independent of XRN2 and PRMT5. Moreover, we observed that the accumulated R-loops at certain loci in siDDX5, siXRN2, and siPRMT5 cells near the transcription start site of genes led to antisense intergenic transcription. Our findings define unique and shared roles of DDX5, XRN2, and PRMT5 in DNA/RNA hybrid regulation.

overall_design: DNA-RNA immunoprecipitation (DRIP-seq) and RNA-seq were performed on control as well as DDX5, PRMT5 and XRN2 knockdown treated U2OS cell lines.

first: Oscar

middle: D

last: Villarreal

first: Sofiane

last: Mersaoui

first: Zhenbao

last: Yu

first: Jean-Yves

last: Masson


title: Robust partitioning of microRNA targets from downstream regulatory changes [AGO-eCLIP-seq]

overall_design: AGO-eCLIP analyses of HEK293 cells with and without specific miRNAs by high-throughput sequencing, in duplicate, using Illumina NextSeq500.


title: miRNA profiling of biliary intraepithelial neoplasia reveals step-wise tumorigenesis in cholangiocarcinoma

city: Heidelberg

first: Stephanie

last: Roessler

address: Im Neuenheimer Feld 224

country: Germany

institute: Heidelberg University Hospital

summary: Biliary intraepithelial neoplasia (BilIN) is a common precursor lesion of distal cholangiocarcinoma (dCCA). However, the sequence leading from a single epithelial layer in normal biliary epithelia to intraepithelial precursor lesions and finally to the invasive tumor is poorly understood. Here, we aimed to elucidate key miRNAs involved in this stepwise process and to identify their possible mRNA target genes in distal cholangiocarcinogenesis. As basis of our study, we conducted Laser Capture Microdissection of FFPE tissue sections of 12 patients with distal cholangiocarcinoma. For each patient, we isolated three matched sample sets, including non-neoplastic biliary epithelia, high grade BilIN (grade 3), and invasive dCCA, thereby representing different stages of distal cholangiocarcinogenesis. This resulted in a total of 36 samples. Total RNA was extracted and the expression of ~800 miRNAs was assessed using the Nanostring® technology. Significantly deregulated miRNAs were validated by quantitative RT-PCR. Target genes were identified using miRWalk2.0 and validated by qRT-PCR and Western blot.

overall_design: Tissue sections of 12 patients with distal cholangiocarcinoma were included in this study. For each patient, we isolated three matched sample sets, including non-neoplastic biliary epithelia, high grade BilIN, and invasive dCCA, thereby representing different stages of distal cholangiocarcinogenesis. This resulted in a total of 36 samples.


title: The Neocortical Progenitor Specification Program Is  Established through Combined Modulation of SHH and FGF Signaling

city: San Francisco

first: Samuel

last: Pleasure

address: 675 Nelson Rising Lane

institute: UCSF

summary: Identification of gene expression changes in cortex-specific Sufu knockout mice

overall_design: mRNA profiles of the E12.5 Emx1-cre/+;Sufu-fl/fl (Sufu-cKO) and control (Sufu-fl/fl or Sufu-fl/+) murine dorsal forebrain

first: Odessa

last: Yabut


title: Foxp3+ regulatory T cells mediate glucocorticoid-induced treatment via a miR342-dependent metabolic programming

city: Cleveland

first: BOOKI

last: MIN

state: Ohio

address: 9500 Euclid Avenue

department: INFLAMMATION AND IMMUNITY

institute: Lerner Research Institute, Cleveland Clinic Foundation

summary: Glucocorticoids (GC) are the mainstay treatment option for acute and chronic inflammatory conditions including autoimmune and allergic diseases. Despite the broad usage of GC in managing inflammatory conditions, the mechanisms by which GC exerts its immune modulatory functions remain poorly understood. Here, utilizing murine autoimmune and allergic inflammation models we report that Foxp3+ regulatory T (Treg) cells are the primary target cells of GC necessary for its anti-inflammatory functions. Dexamethasone (Dex) administered in the absence of Tregs was unable to inhibit inflammatory responses, and adoptive Treg cell transfer restored the control. Glucocorticoid receptor (GR) expression in Treg cells was essential, suggesting a direct involvement of Treg cells. Genome-wide RNA sequencing analysis uncovered a unique Dex-induced gene signature in Treg cells. miRNA-342-3p was induced by Dex treatment only in inducible Treg cells, and mTORC2 protein, Rictor, expression was directly controlled by miRNA-342. Modulation of miRNA-342 expression level directly controlled Treg cell suppressive functions by altering metabolic profiles. Collectively, our results uncover for the first time a novel pathway by which GC interferes with inflammatory responses via miR-342-dependent metabolic control in Treg cells.

overall_design: Three samples for each group. Vehicle-treated samples were used as control for the comparison.

first: Dongkyun

last: Kim

first: Quang

middle: T

last: Nguyen

first: Juyeon

last: Lee

first: Sung

middle: H

first: Allison

last: Janocha

first: Sohee

first: Hongnga

last: Le

first: Nina

last: Dvorina

first: Kelly

last: Weiss

first: Kewal

last: Asosingh

first: Serpil

middle: C

last: Erzurum

first: William

last: Baldwin III

first: Mark

last: Cameron

first: Ju

middle: S

first: Booki

last: Min


title: Gene expression profiling of E1A;HrasG12V mouse embryonic fibroblasts grown under physiological (5%) oxygen conditions, with wild-type p53 or p53 null

city: Stanford

first: Liz

last: Valente

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

summary: To investigate how pleiotropic the impact of p53 loss is on cellular function, generated isogenic, polyclonal wild-type (sgNTC) and p53-null (sgp53) E1A;HrasG12V mouse embryonic fibroblast cell lines using CRISPR/Cas9. Here we show gene expression analysis on p53 wild-type (sgNTC) and p53null (sgp53) E1A;HrasG12V MEFs grown under physiological oxygen conditions (5% oxygen).

overall_design: Examination of gene expression in p53 wild-type and p53-null E1A;HrasG12V MEFs, grown in physiological oxygen (5% oxygen)

first: Laura

last: Attardi


title: Robust partitioning of microRNA targets from downstream regulatory changes [RNA-seq]

first: Andrew

last: Grimson

overall_design: Gene expression profiling of HEK293 cells with and without specific miRNAs by high-throughput sequencing, in duplicate or triplicate, using Illumina NextSeq500.

first: Ravi

last: Patel

middle: W


title: Robust partitioning of microRNA targets from downstream regulatory changes [PRO-seq]

overall_design: Gene expression profiling of HEK293 cells with and without specific miRNAs by high-throughput sequencing, in duplicate or triplicate, using Illumina NextSeq500


title: Robust partitioning of microRNA targets from downstream regulatory changes

overall_design: Refer to individual Series


title: RNA nucleation by MSL2 induces selective compartmentalization of the X chromosome

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

summary:
Confinement of the X chromosome into a territory for dosage compensation (DC) is a prime example of subnuclear compartmentalization for transcription regulation at the megabase scale. In D. melanogaster, two sex-specific non-coding (nc) RNAs roX1 and roX2 are transcribed from the X chromosome. They associate with the Male-specific lethal (MSL) complex, which by acetylating histone H4 lysine 16 (H4K16ac) confers approximately 2-fold upregulated expression of male X-linked genes. Current models explain X-over-autosome specificity based on the MSL2 subunit recognizing cis-regulatory DNA high-affinity sites (HAS). However, HAS motifs are also found on autosomes, indicating that additional factors have evolved to confer stable association of the MSL complex with the X.
Here, we show that the low-complexity C-terminal domain (CTD) of MSL2 renders its recruitment to the X chromosome sensitive to roX ncRNAs. roX-MSL2-CTD form a stably condensated state, and functional analyses in Drosophila and mammalian cells reveal the critical importance of their interplay for DC in vivo. Replacing the CTD of mammalian MSL2 with that from Drosophila and expressing roX in cis is sufficient to nucleate ectopic DC in mammalian cells. Thus, the condensating nature of roX-MSL2CTD is the primary determinant for specific compartmentalization of the X in Drosophila.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus


title: Proteomic and transcriptomic analyses indicate metabolic changes and reduced defense responses in mycorrhizal roots of Oeceoclades maculata (Orchidaceae) collected in nature

city: Belém

first: RAFAEL

middle: BORGES

last: VALADARES

state: PA

address: Travessa Dom PEDRO 1, 575 Apto1303

country: Brazil

institute: Instituto Tecnologico Vale

summary: Orchids form an endomycorrhizal association with fungal symbionts mainly belonging to Basidiomycetes. The molecular events taking place in orchid mycorrhiza are poorly understood, although the cellular changes necessary to accommodate the fungus and to control nutrient exchange between the symbionts imply a modulation of gene expression. In this study, we used proteomic and transcriptomic approaches to identify changes in the steady-state levels of proteins and transcripts in roots of the green terrestrial orchid Oeceoclades maculata. When mycorrhizal and non-mycorrhizal roots from the same individuals of O. maculata were compared, 94 proteins showed differential accumulation using the label-free protein quantitation approach, 86 using isobaric tagging (iTRAQ) and 60 using 2D-differential electrophoresis. After de novo assembly of transcriptomic data, 11,179 plant transcripts were found to be differentially expressed and 2175 were successfully annotated. The annotated plant transcripts allowed the identification of up- and down-regulated metabolic pathways in mycorrhizal roots, as compared to non-mycorrhizal roots. Overall, proteomics and transcriptomics revealed in mycorrhizal roots increased levels of transcription factors and nutrient transporters, as well as ethylene-related proteins. The expression pattern of proteins and transcripts involved in plant defense responses suggest that plant defense is reduced in mycorrhizal roots. These results expand our current knowledge towards a better understanding of the orchid mycorrhizal symbiosis in adult plants under natural conditions.

overall_design: Mycorrhizal roots from three adult plants were compared to non-mycorrhizal roots from other three plants. (3 biological replicates per condition).

first: Rafael

last: Valadares

first: Silvia

last: Perotto


title: Systems biological assessment of immunity to severe and mild COVID-19 infections

first: Madeleine

last: Scott

address: 729 Lagunita Dr

institute: Stanford

summary: CITE-seq of 7 patients with COVID-19 and 5 healthy controls

overall_design: Single cell blood CITE-seq

first: Prabhu

last: Arunachalam

first: Florian

last: Wimmers


title: HA-TFE3 bound regions in HK-2 HA-TFE3-inducible cells

city: Kumamoto

first: Masaya

last: Baba

state: Kumamoto

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

institute: Kumamoto University

summary: TFE3 is a bHLH-ZIP transcription factor, which nuclear localization is regulated by a tumor suppressor FLCN. In order to analyze TFE3 occupancy in whole genome, we have generated and utilized a HK-2 HA-TFE3-inducible cell line which express HA-tagged TFE3 in a doxycycline-dependent manner. HA-TFE3 bound regions were determined by ChIPSeq.

overall_design: We performed ChIP-seq analysis in duplicate with an antibody against HA-tag on a HK-2 HA-TFE3-inducible cell line.

first: Yorifumi

last: Satou

first: Yoshiaki

last: Kubota


title: Outcomes of MSL complex mutations on X chromosome dosage compensation by RNA-Seq

summary:
Confinement of the X chromosome into a territory for dosage compensation (DC) is a prime example of subnuclear compartmentalization for transcription regulation at the megabase scale. In D. melanogaster, two sex-specific non-coding (nc) RNAs roX1 and roX2 are transcribed from the X chromosome. They associate with the Male-specific lethal (MSL) complex, which by acetylating histone H4 lysine 16 (H4K16ac) confers approximately 2-fold upregulated expression of male X-linked genes. Current models explain X-over-autosome specificity based on the MSL2 subunit recognizing cis-regulatory DNA high-affinity sites (HAS). However, HAS motifs are also found on autosomes, indicating that additional factors have evolved to confer stable association of the MSL complex with the X.
Here, we show that the low-complexity C-terminal domain (CTD) of MSL2 renders its recruitment to the X chromosome sensitive to roX ncRNAs. roX-MSL2-CTD form a stably condensated state, and functional analyses in Drosophila and mammalian cells reveal the critical importance of their interplay for DC in vivo. Replacing the CTD of mammalian MSL2 with that from Drosophila and expressing roX in cis is sufficient to nucleate ectopic DC in mammalian cells. Thus, the condensating nature of roX-MSL2CTD is the primary determinant for specific compartmentalization of the X in Drosophila.

overall_design: RNA-seq experiments were conducted from dissected male wing imaginal discs. Homozygous mutants of the msl-2.227, roX1.SMC17A roX2.∆, mle.9 and msl-1.L60 alleles were compared with heterozygous CyO-GFP controls.

first: Claudia

middle: I

last: Valsecchi

first: Giuseppe

last: Semplicio


title: Outcomes of MSL2 domain-swap mutation in mouse embryonic stem cells

overall_design: 5 cell lines were analyzed by RNA-seq in 3-4 replicates; Control Cell lines MF (parental) were compared with Msl2 knock-out (D12) or knock-in cell lines (D11, F4, G2)


title: Studies on bleomycin-induced lung fibrosis in mice

city: Waco

first: Sudhiranjan

last: Gupta

state: TX

address: One Bear Place

department: Biology

institute: Baylor University

summary: We perfomed a microRNA microarray on to assess differentially expressed miRNAs in bleomycin-induced lung fibrosis in mice. To induce pulmonary fibrosis, belomycine (Sigma-Aldrich, St Louis, MO) was dissolved and  administred intratracheally at a dose of 1.5U/kg body weight. Control animals received saline only.  21 days post bleomycin treatment, mice were sacrificed and lung tissue were collected for RNA extraction   and microRNA microarray.

overall_design: C57Bl6 mice were treated with either 1.5U/kg bw bleomycin (N=3) or saline (n=3) and after 21 days, lung tissue were dissected out and RNAs were extracted and miRNA array was performed.


title: Outcomes of MSL complex mutations on X chromosome dosage compensation by ChIP

overall_design: ChIP-seq profiles of H4K16ac and FLAG-tagged MSL2-transgenes in Drosophila melanogaster. Separated male and female third instar larva.


title: THE ACTIN-BINDING MOESIN PROTEIN IS REQUIRED FOR HEAT SHOCK GENE EXPRESSION IN DROSOPHILA

status: Public on Aug 06 2020

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: The cytoskeletal actin-binding ERM (ezrin, radixin and moesin) proteins play essential role in modulating numerous signal transduction events in the cytoplasm by crosslinking actin  filaments with plasma membrane proteins. The nuclear localization of ERMs has been also  reported and the involvement of the single Drosophila ERM protein in nuclear mRNA export  was recently described. However, because the cytoskeletal activity of ERMs is essential in the  cell, and the exact mechanism of their nuclear transport is still unknown, the biological  significance of the presence of ERM proteins in the nucleus has not been yet determined. Here  we present the first attempt to reveal the in vivo relevance of the nuclear localization of the  cytoskeletal ERM protein, Drosophila Moesin. With the help of a nuclear export signal (NES)  we decreased the amount of Moesin in the nuclei of the animal. As a result, we observed various  developmental defects, demonstrating for the first time the importance of ERM function in the  cell nucleus. Transcriptome analysis of the mutant flies revealed, that the lack of nuclear Moe  function leads to expression change of about 700 genes, among them a group of heat shock  genes. This result together with additional findings demonstrates that in Drosophila, the  expression of protein chaperons requires the nuclear functions of Moesin.

overall_design: RNA seq of ovaries of moe[NES] flies. 3 replicates for each group.

first: Tomas

last: Venit

first: Nizar

last: Drou

first: Peter

last: Vilmos

first: Csaba

last: Bajusz


title: Transcriptome analysis of partially degraded and fragmented RNA samples from PAO1

city: Guangzhou

first: Jianhe

last: Wang

state: guangdong

address: wushan road

institute: Integrative Microbiology Research Centre, South China Agricultural University

summary: In order to determine the effect of ALA on geneexpression, P. aeruginosa PAO1 was incubated with and without 30 μM ALA under T3SS-inducing conditions (calcium depletion by addition of NTA to growth medium), followed by RNA extraction and microarray analysis.

first: Chao


title: Identification of open chromatin regions in three different tissues of Oikopleura dioica

city: Bergen

first: Pavla

last: Navratilova

address: Thorm hlensgt. 55

department: Sars International Centre for Marine Molecular Biology

country: Norway

institute: University of Bergen

summary: ATAC-seq was used to locate putative enhancer regions in the early development (tailbud stage), developing male and female gonads of the marine chrodate Oikopleura dioica.

overall_design: Assay for transposase-accessible chromatin sequencing (ATAC-seq)

first: Gunnar

last: Schulze


title: IFNγ treatment restores TAP-dependent presentation competence of PD-L1 sensitive PDAC cells

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

institute: University of Ulm

summary: For immunotherapy, there is an urgent need to restore presentation-competence of cancer cells with defects in MHC-I processing/presentation. We identified two tumor-specific antigens expressed in the ER of pancreatic ductal adenocarcinoma cells (PDACCs) that induced effector CD8 T cells either independent (Cripto-1-Kb/Cr16-24) or dependent (gp70-Kb/p15E) on TAP-mediated antigen processing/presentation by DNA immunization. In systematic analyses, we showed that transplantation into syngeneic C57BL/6J mice or IFNγ-treatment in vitro upregulated MHC-I but also co-inhibitory PD-L1 molecules on PDACCs. IFNγ-treated PDACCs efficiently formed solid tumors in transplanted C57BL/6J and PD-L1-/- but were rejected in PD-1-/- mice. PDACCs induced a prophylactic immunity against tumor transplants in C57BL/6J mice when irradiated at day 2-3 post IFNγ-treatment, thereby silencing the tumor-initiated immune-suppressive PD-L1/PD-1-signaling axis. Immune-protection correlated with a significant enhanced induction of CD8 T cells against the TAP- but not the TAP-dependent antigen/epitope.

overall_design: RNA from PDAC cell lines, derived from  KrasG12D/+, Trp53fl/fl, p48cre/+ mice on a C57BL/6J background (3 male, 2 female) was used. Cells were treated with IFNγ (20 ng/ml, 16 h) or left untreated prior to RNA extraction. Agilent Mouse Gene Expression Microarrays 4x44Kv2 were used.

first: Reinhold

last: Schirmbeck

first: Katja

last: Stifter


title: Indirect co-cultivation of HepG2 with differentiated THP-1 cells induces AHR signalling and release of pro-inflammatory cytokines.

city: Berlin

first: Florian

last: Padberg

address: Max-Dohrn-Strasse 8-10

department: Chemicals and Product Safety

institute: German Federal Institute for Risk Assessment (BfR)

summary: HepG2 and THP-1 cells, the latter differentiated by phorbol 12-myristate 13-acetate (PMA), were co-cultured and characterized for typical liver-specific functions, such as xenobiotic detoxification, lipid and cholesterol metabolism. Furthermore, liver injury-associated pathways, such as inflammation, were studied. In general, the co-cultivation of these cells produced a pro-inflammatory system, as indicated by increased levels of cytokines (IL-8, TGF-α, IL-6, GM-CSF, G-CSF, TGF-β, and hFGF) in the respective supernatant. Increased expression levels of target genes of the aryl hydrocarbon receptor (AHR), e.g., CYP1A1, CYP1A2 and CYP1B1, were detected, accompanied by the increased enzyme activity of CYP1A1. Moreover, transcriptome analyses indicated a significant upregulation of cholesterol biosynthesis, which could be reduced to baseline levels by lovastatin. In contrast, total de novo lipid synthesis was reduced in co-cultured HepG2 cells. Key events of the adverse outcome pathway (AOP) for fibrosis were activated by the co-cultivation, however, no increase in the concentration of extracellular collagen was detected. This indicates, that AOP should be used with care. In summary, the indirect co-culture of HepG2/THP 1 cells results in an increased release of pro-inflammatory cytokines, an activation of the AHR pathway and an increased enzymatic CYP1A activity.

overall_design: Characterisation of HepG2 cells under influence of PMA-differentiated THP-1 cells using the Affymetrix Human Clariom S. Array data was processed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany). Five biological replicates were performed for each condition.

first: Henrik

last: Hering

first: Andreas

last: Luch

first: Sebastian

last: Zellmer


title: Metabolic Regulations by ceRNA under Grass-fed and Grain-fed regimens in Angus Beef Cattle [RNA-Seq]

city: Yangling

first: Cunling

last: Jia

state: Shaanxi

address: Xinong road 22#

department: Animal science

institute: Northwest A&F University

summary: To clarify the mechnism that  grass-fed and grain-fed regimens inducing the different characteristics of Wyu Angus cattle, we used high-throughput sequencing and metabolomics analysis to explore differentially expressed genes , differentially expressed miRNAs and lnRNAs,  meanwhile constructed importantly regulatory networks.

overall_design: Liver sample of Wyu Angus cattle from grass-fed and grain-fed regimens were  sequenced with each group 2 individuals.

first: Jiuzhou

last: Song

last: Song’lab


title: THE FUSED LEAVES1-ADHERENT1 REGULATORY MODULE IS REQUIRED FOR MAIZE CUTICLE DEVELOPMENT AND ORGAN SEPARATION

city: Piscataway

first: Andrea

last: Gallavotti

state: NJ

address: 190 Frelinghysen Rd.

department: Waksman Institute of Microbiology

institute: Rutgers University

summary: RNA-seq was performed on 3-4mm WT and fdl1 mutant maize coleoptile tips

overall_design: wild type vs mutant; 3 replicates each

first: Chen

last: Zongliang

first: Gallavotti

last: Andrea


title: Ribosome profiling of NIH-3T3 cells infected with MCMV

city: Würzburg

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

institute: Julius-Maximilians-Universität Würzburg

summary: NIH-3T3 cells were infected with wildtype MCMV at a multiplicity of infection (MOI) of 10. Ribosome profiling was performed at the indicated times of infection as described in Rutkowski et al., Nature Communications 2015.

overall_design: Ribosome profiling was performed at 0 and 48 h post infection. Two biological replicates were analysed.

first: Lars

last: Dölken


title: Targets of Hnf4alpha during conversion from mouse embryonic fibroblasts (MEFs) to hepatocyte-like (iHep) cells.

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

summary: We have found three specific combinations of two transcription factors, comprising Hnf4alpha plus Foxa1, Foxa2 or Foxa3, could convert mouse embryonic fibroblasts (MEFs) into cells that closely resemble hepatocytes in vitro. Then we used ChIP-seq to explore the targets of Hnf4alpha during conversion event from MEFs to iHep cells.

overall_design: Using an anti-Hnf4alpha antibody we performed ChIP-Seq for iHep_4a1 cells (Foxa1/Hnf4alpha), iHep_4a2 cells (Foxa2/Hnf4alpha), iHep_4a3 cells (Foxa3/Hnf4alpha).

first: Yasuyuki

last: Ohkawa

first: Masao

last: Nagasaki

first: Kenichi

last: Horisawa

first: Kazuko

last: Ueno


title: Foxa and Hnf4alpha targets during conversion from mouse embryonic fibroblasts (MEFs) to hepatocyte-like (iHep) cells and hepatocytes (Hep).

summary: We have found three specific combinations of two transcription factors, comprising Hnf4alpha plus Foxa1, Foxa2 or Foxa3, could convert mouse embryonic fibroblasts (MEFs) into cells that closely resemble hepatocytes in vitro. Then we used ChIP-seq to explore the targets of Foxa and Hnf4alpha during conversion event to iHep cells.  Besides we performed for hepatocytes.

overall_design: Using anti-Foxa antibodies and an anti-Hnf4alpha antibodies we performed ChIP-Seq for iHep_4a1 cells (Foxa1/Hnf4alpha), iHep_4a2 cells (Foxa2/Hnf4alpha), iHep_4a3 cells (Foxa3/Hnf4alpha), 3 cells 48 hours after injection (48hr_4a1, 48hr_4a2, 48hr_4a3) and hepatocytes (Hep).


title: Molecular interactions at the bovine embryo–endometrial epithelium interface

city: Wilrijk

first: Veerle

last: Van Hoeck

state: Antwerp

address: Campus Drie Eiken, Universiteitsplein 1

department: Department of Veterinary Sciences

institute: University of Antwerp

summary: We aimed to interrogate the embryo–maternal interface for embryo-induced changes in the global transcriptome of bovine endometrial epithelial cells (bEECs). In vitro-produced day-5.5 morulae were cultured in juxtacrine apposition (Contact+) with bEECs, or in transwells (Contact⎼), for 48 h. A group of bEECs cultured in the absence of embryos (Control bEEC) was also included. After co-culture, bEECs were recovered for transcriptome analysis.

overall_design: Bovine endometrial epithelial cells (bEECs) were co-cultured in juxtacrine (Contact+) or non-juxtacrine (Contact-) apposition with in vitro-derived morulae for 48 h. bEECs transcriptomes were sequenced (NGS) on the BGISEQ-500 platform.

first: Mariana

last: Sponchiado

first: Waleed

last: Marei

first: Gerrit

last: Beemster

first: Peter

last: Bols

first: Mario

last: Binelli

first: Jo

middle: L

last: Leroy


title: Targets of transduced Foxa and Hnf4alpha proteins in mouse embryonic fibroblasts (MEFs).

summary: We have found three specific combinations of two transcription factors, comprising Hnf4alpha plus Foxa1, Foxa2 or Foxa3, could convert mouse embryonic fibroblasts (MEFs) into cells that closely resemble hepatocytes in vitro. Then we used ChIP-seq to explore the targets of the transduced Foxa and Hnf4alpha proteins in MEFs.

overall_design: Using anti-Foxa antibodies and an anti-Hnf4alpha antibody we performed ChIP-Seq for MEFs.


title: Targets of DNA binding, N-terminal, or C-terminal domain swapped mutant forms fo Foxa proteins in induced hepatocyte-like (iHep) cells.

summary: We have found that three specific combinations of two transcription factors, comprising Hnf4alpha plus Foxa1, Foxa2 or Foxa3, could convert mouse embryonic fibroblasts (MEFs) into cells that closely resemble hepatocytes in vitro, and DNA binding, N-terminal, and C-terminal domains (DBD, NTD, and CTD, respectively) of Foxa proteins are swappable in the direct reprogramming of the iHep cells. Then we used ChIP-seq to explore the targets of the domain swapped mutant forms of Foxa proteins during conversion event to iHep cells.

overall_design: Using anti-Foxa antibodies we performed ChIP-Seq for iHep cells which were induced by forced transduction of Hnf4alpha and domain swapped mutant forms of Foxa proteins.


title: Novel circRNA_103758-miRNA-19b-3p-CIT axis is associated with proliferation and migration of bladder cancer via RhoA-ROCK signaling pathway

status: Public on Aug 05 2020

city: Harbin

first: Yang

last: Yang

state: Heilongjiang

address: No. 23 Youzheng Street

institute: Harbin Medcial University

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

overall_design: Refer to individual Series


title: Foxa and Hnf4alpha targets during conversion from mouse embryonic fibroblasts (MEFs) to hepatocyte-like (iHep) cells

summary: We have found three specific combinations of two transcription factors, comprising Hnf4alpha plus Foxa1, Foxa2 or Foxa3, could convert mouse embryonic fibroblasts (MEFs) into cells that closely resemble hepatocytes in vitro. Then we used ChIP-seq to explore the targets of Foxa and Hnf4alpha during conversion event to iHep cells.

overall_design: Using anti-Foxa antibodies and an anti-Hnf4alpha antibody we performed ChIP-Seq for iHep_4a1 cells (Foxa1/Hnf4alpha), iHep_4a2 cells (Foxa2/Hnf4alpha), iHep_4a3 cells (Foxa3/Hnf4alpha), 3 cells 48 hours after injection (48hr_4a1, 48hr_4a2, 48hr_4a3). Also, using an anti-Ty1-tag antibody we performed ChIP-Seq for 48hr_4a3_del2 cells (Foxa3 del2 mutant fused with Ty1-tag/Hnf4alpha).


title: Transcriptome analysis of the induced hepatocyte-like (iHep) cells

summary: We have found three specific combinations of two transcription factors, comprising Hnf4alpha plus Foxa1, Foxa2 or Foxa3, could convert mouse embryonic fibroblasts (MEFs) into cells that closely resemble hepatocytes in vitro. Then we used RNA-seq to explore the conversion event to the iHep cells.

overall_design: RNA-Seq for 6 iHep_4a1 cells (Foxa1/Hnf4alpha), 4 iHep_4a2 cells (Foxa2/Hnf4alpha), 6 iHep_4a3 cells (Foxa3/Hnf4alpha), 6 cells 48 hours after transfection (48hr_4a1, 48hr_4a2, 48hr_4a3), 2 iMEFs transduced with Foxa3 del2 mutant/Hnf4alpha, 2 MEFs, and 2 hepatocytes (Hep).


title: RNA Sequencing facilitates quantitative analysis of differently expressed genes with GA or SKN treatment in rheumatoid fibroblast-like synoviocytes

city: guangzhou

first: cuicui

last: wang

address: 1 Pan Fu Road

department: rheumatology

institute: Guangzhou First People’s Hospital, The Second Affiliated Hospital of South China University of Technology

summary: To explore downstream gene expression profile of PKM2,we evaluated the transcriptome of GA- or SKN-treated RA FLSs compared to untreated control using RNA sequencing analysis. The data were analyzed for differential expression with a nominal P<0.05. GA Treatment induced downregulation of 46 genes and upregulation of 58 genes compared to DMSO treatment. SKN treatment resulted in downregulation of 14 genes and upregulation of 27 genes compared to DMSO treatment.A Venn diagram showed the overlap of the significantly expressed genes between GA and SKN treatment. We found that in the overlap of both GA and SKN treatment, STAT5A and ARHGAP11A were significantly downregulated, and THAP6 and AHRR were significantly upregulated.

overall_design: First, to detect differently expressed genes (P<0.05) by RNA sequencing in GA- (G+T) or SKN-treated (S+T) vs. DMSO-treated (D+T) RA FLSs from three different patients; second, to analyze the number of shared and distinct GA- or SKN-treated genes.

first: Cuicui

last: Wang

first: Youjun

last: Xiao

first: Minxi

last: Lao


title: Novel circRNA_103758-miRNA-19b-3p-CIT axis is associated with proliferation and migration of bladder cancer via RhoA-ROCK signaling pathway [RNA-seq]

summary:
Purpose:The purpose of this study is to investigate the potential mechanisms that triggering the onset of bladder cancer and to screen differential expressed genes.
Methods: We screened differentially expressed genes with the data obtained from RNA-seq on Bladder carcinoma samples and matched normal samples. Functional annotation analysis and protein-protein interaction (PPI) network were performed to investigate the potential key pathways and genes that play significant roles in BCa. Furthermore, the ceRNA network was established and the Gene Set Enrichment Analysis (GSEA) was executed to dig key circRNAs.
Results: Following the identification of differentially expressed genes, functional annotation analysis was conducted, suggesting that differentially expressed mRNAs (DEMs) were mainly involved in cell cycle related pathways. The top 11 genes with the highest degree were extracted from PPI network. The predicted regulatory relationships among the differentially expressed genes were found and the ceRNA network was established. Finally, GSEA was conducted on the circRNAs and the key biological pathways were identified.
Conclusion: Our study is the pioneering research to analyze the pathogenesis of BCa with integrated informatics and we have identified several hub genes, which reveals that the generation of BCa is closely related to cell cycle.

overall_design: Pericardial RNA profiles of four test and four control samples were generated by deep sequencing, using Illumina HiSeq 4000.

first: Zan

last: Liu

first: Zhe

first: Shunyao

last: Xia

first: Dasen

last: Lin

first: Bang

first: Youcheng

last: Xiu


title: PRDM15 mutation prevents forebrain development through an Otx2 pathway

city: Toronto

first: Landry

last: Nfonsam

state: Ontario

address: 686 Bay Street

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

summary: Acquiring correct brain anatomy and function requires extensive morphogenesis and patterning, which is regulated by a complex gradient of transcription factors. Members of the PR domain containing (PRDM) chromatin-modulating family of transcriptional regulators function in neuronal specification and brain patterning. Little is known about the function of PRDM15, even though it is predicted to have a role in the development of the central nervous system, and lies in the Down syndrome trisomy region of HSA21 and MMU16. Here, we show that PRDM15 is required for forebrain development and repression of hindbrain gene expression. The phenotype of Prdm15 mutants mimics that of Otx2 loss. Using RNA sequencing, we found that a PRDM15 dependent molecular pathway, which includes many homeodomain factors that pattern the forebrain, including OTX2 and PAX6, is disrupted in Prdm15 mutants. Consistent with the role of OTX2 as a master regulator of forebrain development, which represses rostral expansion of the hindbrain to maintain the brain rostro-caudal axis, conditionally inactivating PRDM15 in the forebrain also truncates the forebrain and disrupts the brain rostro-caudal axis. PRDM15 co-expresses with OTX2 in cells of the primordial anterior forebrain, a region where OTX2 is known to function, and PRDM15 binds to the Otx2 promoter, suggesting it may directly impact Otx2 expression. These findings place PRDM15 in the forebrain transcriptional hierarchy for the first time, revealing that PRDM15 is a candidate for pathogenesis in Down syndrome or other neurodevelopmental disorders.

overall_design: Six samples were analyzed, including replicates of two for wildtype (Prdm15tm1a+/+), Heterozygote (Prdm15tm1a+/-), and Mutant (Prdm15tm1a-/-)

first: Stephanie

last: Almeida

first: Travis

last: Brooke-Bisschop

first: Monica

last: Justice