title: BCDIN3D RNA methyltransferase stimulates Aldolase C expression and glycolysis through let-7 microRNA in breast cancer cells

city: Austin

first: Blerta

last: Xhemalce

state: Texas

address: 2500 Speedway

institute: University of Texas at Austin

summary: BCDIN3D is an RNA modifying enzyme that methylates specific precursor microRNAs and tRNAHis. In addition to breast cancer, BCDIN3D may also be linked to metabolism, as its gene locus is associated with obesity and T2D. In order to uncover metabolic pathways regulated by BCDIN3D in cancer, we performed an unbiased analysis of the metabolome, transcriptome, and proteome of breast cancer cells depleted for BCDIN3D. Intersection of these analyses showed that BCDIN3D-depleted cells have increased levels of Fructose 1,6 Bisphosphate (F1,6-BP), the last six-carbon glycolytic intermediate accompanied by reduced glycolytic capacity.

overall_design: We performed combined RNA-Seq, miRNA-seq, and ribosome profiling in shBCDIN3D MDA-MB-231 breast cancer cells

first: Calder

middle: W

last: Reinsborough

first: Hélène

last: Ipas

first: Nathan

last: Abell

first: Ellen

last: Gouws

first: J

last: Williams

first: Marvin

last: Mercado

first: Carla

last: Ven Den Berg

last: Xhemalçe


title: Impact of LXR activation on alternatively activated human macrophages

status: Public on Apr 14 2021

city: Frankfurt

first: Ryan

middle: G

last: Snodgrass

address: Theodor-Stern-Kai 7, building 74

department: Institute of Biochemistry I

country: Germany

institute: Goethe-University Frankfurt

type: Expression profiling by high throughput sequencing

summary: To investigate how LXR activation potentiates expression of Th2 cytokine-dependent genes in primary human macrophages, we pulsed macrophages with synthetic LXR ligand T0901317 then polarized cells to alternatively activated macrophages with IL-4 or IL-13.

overall_design: Human monocytes derived from three individual donors were differentiated into naïve macrophages with RPMI 1640 medium containing 5% AB-positive human serum for 7 days. Naive macrophages were pulsed with T0901317 (1 µM) for 3 hours, then media was aspirated and cells were polarized to alternatively activated macrophages with IL-4 (5 ng/ml) or IL-13 (10 ng/ml) for 24 hours.

first: Bernhard

last: Brüne


title: Noncanonical post-transcriptional feedback between microRNA and messenger RNA enables bistability and governs robust cell fate decisions

city: Taipei

first: Jun-An

last: Chen

address: 128 Academia Road, Section 2

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: Positive feedback driven by transcriptional regulation has long been considered a key mechanism underlying cell lineage segregation during embryogenesis. Using the developing spinal cord as a paradigm, we found that canonical, transcription-driven feedback cannot explain robust lineage segregation of motor neuron subtypes marked by two cardinal factors, Hoxa5 and Hoxc8. We propose a feedback mechanism involving elementary microRNA-mRNA reaction circuits that differ from known feedback loop-like structures. Strikingly, we show that a wide range of biologically-plausible post-transcriptional regulatory parameters are sufficient to generate bistable switches, a hallmark of positive feedback. Through mathematical analysis, we explain intuitively the hidden source of this feedback. Using embryonic stem cell differentiation and mouse genetics, we corroborate that microRNA-mRNA circuits govern tissue boundaries and hysteresis upon motor neuron differentiation with respect to transient morphogen signals. Our findings reveal a previously underappreciated feedback mechanism that may have widespread functions in cell fate decisions and tissue patterning.

overall_design: Single cell RNA seq of e12.5 mouse spinal motor neurons at cervical segment (C2-T1). Motor neurons were labeled in GFP and sorted via FACS, pooled and loaded onto 10x  Genomics Single Cell 3’ Chip as a single sample.

first: E

middle: S

last: Liau

middle: A


title: Reprogramming the spleen into a functioning “liver” in vivo II

status: Public on Apr 17 2021

city: Nanjing

first: Chunyan

last: Liu

address: 163 Xianlin Avenue

country: China

institute: Nanjing University

summary: We restored liver function in the spleen by direct reprogramming splenic fibroblasts in situ and thereby transformed the spleen into a “liver” with sufficient physiological functions within a living animal.

overall_design: The Gene Expression profiling of PBS-treated spleens (PBS) vs SiO2-remodelled spleens (SiO2), PBS as control; primary mouse SiO2-remodelled spleen fibroblasts (MF) vs hepatocyte-like cells (iHep) vs primary hepatocytes (PH), MF as control; SiO2-treated spleens (SiO2) vs SiO2-3TF-3C-treated spleen (hepatized spleens) vs normal liver tissues, SiO2 as control.Five cell/spleen samples were pooled according to individual groups.

first: Lei

last: Dong

first: Chunming

last: Wang

first: Junfeng

last: Zhang


title: Control of RNA polymerase II promoter-proximal pausing by DNA supercoiling [ChIP-seq]

city: Madrid

first: Felipe

last: Cortés Ledesma

state: Madrid

address: Melchor Fernández Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

type: Genome binding/occupancy profiling by high throughput sequencing

summary: During transcription, DNA supercoiling generated by the advance of RNA polymerase II (Pol II) is resolved by DNA topoisomerases, enzymes that bind chromatin and produce transient breaks to relax DNA. Recently, this idea of mere facilitators of transcription progression is changing, as topoisomerases are being assigned new functions in regulating the expression of specific genes. In fact, mammalian type II topoisomerases, both the [Symbol] (TOP2A) and [Symbol] (TOP2B) paralogs, are enriched at promoter regions, where they have been proposed to trigger transcription through the generation of DNA double-strand breaks (DSBs). However, this is difficult to reconcile with the intrinsic catalytic properties of TOP2 and the high risk of genome instability that continuous production and repair of DSBs implies. Here, we show that TOP2A enforces promoter-proximal pausing of Pol II by removing transcription-associated negative DNA supercoiling. Interestingly, this topological balance and its disruption is essential for the transcriptional control of Immediate Early Genes (IEGs) and their typical bursting behaviour in response to stimulus. We therefore uncover a novel layer of transcriptional regulation that relies on canonical functions of TOP2A that are independent of aberrant DSB formation, providing a topological framework for the control of promoter-proximal pausing and the tight regulation of IEGs.

overall_design: A total of 5 ChIP-seq experiments on human RPE cells were generated: ChIP-seq on POL2 (vehicle treatment, 3 replicates), ChIP-seq on POL2 (no treatment, 3 replicates), ChIP-seq on POL2 (30 min merbarone treatment, 3 replicates), ChIP-seq on POL2 (1 h merbarone treatment, 2 replicates) and ChIP-seq on TOP2A (no treatment, 2 replicates). Additionally, 3 IgG samples were generated (untreated, vehicle treatment and merbarone treatment).

first: Andrés

last: Herrero-Ruiz

first: Pedro

middle: M

last: Martínez-García

first: José

last: Terrón-Bautista

first: Silvia

last: Jimeno-González

last: Cortés-Ledesma


status: Public on Apr 13 2021

city: hangzhou

first: xiao

middle: chen

last: wen

address: desheng_road NO.298

institute: Zhejiang Academy of Agricultural Sciences

summary: Dermatophytosis is a common and relevant zoonotic disease of public health concern, Various antifungal compounds, including clotrimazole, terbinafine, and ketoconazole have been reported for the treatment of dermatophytosis,In the present study,Transcriptome profile of T. mentagrophytes exposed to different drugs was performed in order to find the important drug antifungal active point.

overall_design: Thirty three samples were examined including SDA control group and other reagent treatment groups. Each group has three repeat samples

first: Xiao

last: Chenwen

first: Bao

last: Guolian


title: Neonatal rat ventricular  cardiomyocytes Cells: Control vs. hypertrophic cardiomyocytes induced by isoproterenol

city: Shenyang

first: Ai

address: Nanjing Bei Street

institute: the first hospital of China Medical University

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

summary: the expression characteristics of lncRNAs among hypertrophic cardiomyocytes induced by isoproterenol in rat ventricular myocytes from newborn Sprague-Dawley rats.

overall_design: Two-condition experiment, normal cardiomyocytes  vs. hyeprtrophic cardiomyocytes. Biological replicates: 3 control replicates, 3 transfected replicates.

first: Zhao

last: Li

first: Qun

last: Ma

first: Lin

middle: L

last: Miao


title: Expression data of control, doxorubicin and/or Y27632 treated HeLa cells

city: Ankara

first: Ceren

last: Sucularli

address: Sihhiye

country: Turkey

institute: Hacettepe University

summary:
In the treatment of cancer with chemotherapeutics, it has been observed that a significant amount of cancer cells turn into senescent cells. These senescent cells secrete several factors in their microenvironment called SASP. Therefore, recently, to develop the senolytic and/or senomorphic drugs, targeting the senescent cells gains importance as a new strategy for preventing the damage that senescent cancer cells cause. In the current work, we evaluated whether Rho/Rho kinase pathway has a potential to be used as a target pathway for the development of senolytic and/or senomorphic drugs, in doxorubicin-induced senescent cancer cell lines.
We performed a whole-genome microarray analysis to determine how the expressions of SASP factors change in senescent cells and whether ROCK inhibition also causes changes in the expression of these factors.

overall_design: HeLa cells were incubated for 6 days without treatment (group K, n=3), or treated with 300 nM doxorubicin for 72 h and then incubated for 72 hours without treatment (group D, n=3), or treated with 300 nM doxorubicin for 72 h and then treated with 10μM Y27632 ( a Rho kinase inhibitor) for 72h (group D+Ys, n=3), or pretreated with 10μM Y27632 ( a Rho kinase inhibitor, 30 min) and treated with 300 nM doxorubicin for 72 h, and then incubated for 72 hours without treatment (group D+Y, n=3),or incubated for 72 h without treatment and then treated with 10μM Y27632 ( a Rho kinase inhibitor) for 72 h (group Y, n=3). Human Gene 1.0 ST Array chips were used for gene expression analyses. The cell intensity, CEL, files were analyzed using Affymetrix Expression Console Software 1.4.1.46 at gene level with RMA (Robust Multiarray Average) normalization algorithm. Differentially expressed genes were identified using BRB-ArrayTools version 4.6.0.

first: Yaprak

middle: D

last: SIMAY DEMIR

first: Aysun

last: OZDEMIR

last: SUCULARLI

first: Mustafa

last: ARK


title: mRNA from Ionizing radiation treatment of chondrocyte-like cells derived from human induced pluripotent stem cells: gene and microRNA expression profile and high-throughput screening of secreted cytokines, chemokines, and growth factors

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

summary: Human induced pluripotent stem cells (hiPSCs) possess the ability to differentiate into chondrocytes and produce cartilaginous matrix without the need to biopsy healthy cartilage. However, this strategy is not without risk given that those transplanted cells can be subjected to IR during Head and Neck (H&N) (re-)treatment. The main aim of this study was to investigate the gene expression profile. The differentiated hiPSC into chondrocyte were irradiated in accordance with conventional therapy, hypofractionation and hyperfractionation protocols (1, 2, 3 Gy) intended for larynx region. Then, to fulfill  objective we performed following high-throughput analysis: gene expression profile based on microarrays. Our findings allowed for the selection of crucial biological processes activated in hiPSC-derived chondrocytes after IR such as: “apoptotic process”, “cellular response to DNA damage stimulus” and “regulation of programmed cell death”. Moreover, we observed decrease of expression of genes involved in e.g. cell cycle and cell division. Microarray data were confirmed by RT-qPCR technique. We have proved that IR have a great impact on DDR mechanisms of hiPSCs differentiated towards chondrogenic lineage.

overall_design: To irradiate the chondrocyte-like cells the specially modified and redesigned the Alderson Radiation Therapy phantom (ART) was used to obtain similar condition to those in patient’s larynx region treatment. Eppendorf tube with the one million of chondrocyte-like cells was used to irradiate the cells and was delineated as the quasi-Gross tumor volume (GTV), defining 1 cm geometrical margins around GTV to create the quasi-Clinical Target Volume (CTV) was done. Total RNA from hiPSCs after chondrogenic differentiation were purified with miRNeasy Kit and RNeasy MinElute according to the manufacturer’s instructions (217004, Quiagen, Hilden, Germany).

first: Ewelina

last: Stelcer

first: Katarzyna

last: Kulcenty


title: ATAC-seq of uncultured CD112high and CD112low long-term(LT) human hematopoietic stem cells (HSC) from umbilical cord blood

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

summary: We performed ATAC-sequencing to elucidate the chromatin accessibility that underlie the differential in vitro priming and regeneration phenotypes of CD112high and CD112low LT-HSC. Therefore, we prospectively isolated these subpopulations from 3 independent human umbilical cord blood pools and subjected to ATAC-sequencing directly. We show that distinct subsets of human LT-HSC respond differently to regeneration-mediated stress and that INKA1 governs these distinct stemness states where CD112low  LT-HSC are marked by an alternative state of quiescence with high INKA1 and low H4K16ac preserving self-renewal and regenerative capacity upon successive rounds of regeneration-mediated stress.

overall_design:
chromatin accessibility in 2-3 pools of human cord blood sorted by flow cytometry into  CD112high and CD112low LT-HSC subpopulations.
*** Submitter states that raw data is available on the EGA ***

first: Kerstin

last: Kaufmann

first: Alex


title: A Prognostic Gene Expression Signature for Oropharyngeal Squamous Cell Carcinoma

city: Chicago

first: Xiaowei

last: Wang

state: IL

address: 909 S Wolcott Ave, Rm 5137

country: USA

institute: University of Illinois at Chicago

summary:
Background: Robust prognostic stratification of patients with oropharyngeal squamous cell carcinoma (OPSCC) is important for developing individualized treatment plans. This study was conducted to develop and validate a clinically feasible prognostic classifier based on transcriptome-wide gene expression profiles.
Methods: Tumor tissues were collected from 208 OPSCC patients treated at Washington University in St. Louis and 115 OPSCC patients treated at Vanderbilt University, used for model training and validation, respectively. OPSCC patients (n = 70) from the TCGA cohort were also included for independent validation. Based on RNA-seq profiling data, Cox proportional hazards regression analysis was performed to identify genes associated with disease outcomes. Then, Lasso-penalized multivariate survival models were constructed to identify biomarker genes for developing a prognostic gene signature.
Findings: A 60-gene signature was identified by RNA-seq profiling analysis. Computed risk score of the gene signature was significantly predictive of 5-year overall survival of the training cohort (Hazard ratio (HR) 28.32, P = 4.3E-41). Subgroup analysis stratified by HPV status revealed that the signature was prognostic in HPV-positive OPSCC patients (HR 30.55, P = 7.0E-37) and was independent of clinical features. Importantly, the gene signature was validated in two independent patient cohorts, including the TCGA cohort (HR 3.94, P = 0.0018) and the Vanderbilt cohort (HR 8.50, P = 5.7E-09) for overall survival.
Conclusions: The prognostic gene signature is a robust tool for risk stratification of OPSCC patients. The signature remains prognostic among HPV-positive OPSCC patients.

overall_design: RNA-seq profiling analysis of oropharyngeal cancer cases treated at Washington University in St. Louis and Vanderbilt University

first: Xinyi

last: Liu

first: Ping


title: microRNA from Ionizing radiation treatment of chondrocyte-like cells derived from human induced pluripotent stem cells: gene and microRNA expression profile and high-throughput screening of secreted cytokines, chemokines, and growth factors

summary: Human induced pluripotent stem cells (hiPSCs) possess the ability to differentiate into chondrocytes and produce cartilaginous matrix without the need to biopsy healthy cartilage. However, this strategy is not without risk given that those transplanted cells can be subjected to IR during Head and Neck (H&N) (re-)treatment. The main aim of this study was to investigate the microRNA expression profile after ionizing radiation (IR) treatment of chondrocyte-like cells differentiated from hiPSCs. The differentiated hiPSC into chondrocyte were irradiated in accordance with conventional therapy, hypofractionation and hyperfractionation protocols (1, 2, 3 Gy) intended for larynx region. Then, to fulfill specific objective we performed following high-throughput analysis: gene expression profile based on microarrays. Our findings allowed for the selection of crucial biological processes activated in hiPSC-derived chondrocytes after IR. Moreover, we observed decrease of expression of genes involved in e.g. cell cycle and cell division. Next, we have selected crucial microRNAs which are responsible for controlling genes of aforementioned biological processes. Microarray data were confirmed by RT-qPCR technique. We have proved that IR have a great impact on DDR mechanisms of hiPSCs differentiated towards chondrogenic lineage.

overall_design: To irradiate the chondrocyte-like cells the specially modified and redesigned the Alderson Radiation Therapy phantom (ART) was used to obtain similar condition to those in patient’s larynx region treatment. Eppendorf tube with the one million of chondrocyte-like cells was used to irradiate the cells and was delineated as the quasi-Gross tumor volume (GTV), defining 1 cm geometrical margins around GTV to create the quasi-Clinical Target Volume (CTV) was done. The miRNA-enriched fraction from hiPSCs after chondrogenic differentiation were purified with miRNeasy Kit and RNeasy MinElute according to the manufacturer’s instructions (217004, Quiagen, Hilden, Germany).


title: Multi-omics effect of  5-(4′-Hydroxyphenyl)-γ-valerolactone metabolites

city: Kannapolis

first: Dragan

last: Milenkovic

state: NC

address: 600 Laureate Way

department: Department of Food Bioprocessing & Nutrition Sciences

institute: North Carolina State University

summary:
Integrated multi-omic analyses of the genomic modifications by 5-(4′-Hydroxyphenyl)-γ-valerolactone metabolites in TNFalpha-stimulated primary human brain microvascular endothelial cells.
We exposed human brain microvascular endothelial cells to mixture of 2 metabolites of 5-(4′-Hydroxyphenyl)-γ-valerolactone after they have been exposed to TNF. Total RNA has been extracted and expression of mRNA, miRNas, snoRNAs and lncRNAs has been obtained using microarrays.

overall_design: Primary human microvascular cells were acquired from Lonza. The cells, at the passage 5, were exposed to TNF for 4 hours, or without TNF for negative control. Following the TNF traitement, the cells were exposed to the mixture of gut metabolites for 20h. The metabolites were 5-(4′-Hydroxyphenyl)-γ-valerolactone-3′-sulfate (γVL3′G) and 5-(4′-Hydroxyphenyl)-γ-valerolactone-3′-O-glucuronide (γVL3′S)

first: Saivageethi

last: Nuthikattu


title: Sequencing of chronic myeloid leukemia (CML) cell lines upon upregulation or downregulation of G0/G1 switch gene (G0S2)

city: El Paso

first: Anna

last: Eiring

state: TX

address: 5001 El Paso Drive, MSB1 Room 2112, MSC 32002

department: Molecular and Translational Medicine

institute: Texas Tech University Health Sciences Center at El Paso

summary: Current treatment for CML involves tyrosine kinase inhibitors (TKIs), which turned it into a managable disease. In a transcriptional profile of TKI-resistant versus newly diagnosed CML patient samples, G0S2 was shown to be profoundly downregulated.

overall_design: CML cell line (K562) was lentivirally transduced (shNT, shG0S2, pLVX G0S2, shATGL) and selected in the presence of puromycin. Resulting cells were treated with doxycycline (0.1 ug/ml, 72 h) to induce vector expression.

first: Mayra

last: Gonzalez


title: LOSS OF NEURONAL TET2 ENHANCES HIPPOCAMPAL-DEPENDENT COGNITIVE FUNCTION

city: San Francisco

first: Karishma

middle: Joanne Bhatia

last: Pratt

state: CA

address: 513 Parnassus Ave, Med. Sci. Bldg S1364

department: Anatomy

institute: UCSF

type: Methylation profiling by high throughput sequencing

summary: Chromatin methylation has emerged as a critical modulator of neuronal plasticity and cognitive function. Notwithstanding, the role of enzymes that demethylate DNA remain to be fully explored. Here we report that loss of ten eleven translocation methylcytosine dioxygenase 2 (Tet2), which catalyzes oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), in adult neurons enhances cognitive function. In the adult mouse hippocampus, we detected an enrichment of Tet2 in neurons. Abrogation of neuronal Tet2 in vitro altered synaptic-plasticity related gene expression. We observed that loss of Tet2 in mature glutamatergic neurons in adult mice resulted in differential hydroxymethylation on genes involved in synaptic transmission in the hippocampus. Correspondingly, RNA sequencing identified changes in both long-term potentiation pathways and immune-related genes linked to synaptic plasticity. Functionally, loss of neuronal Tet2 improved performance on hippocampal-dependent spatial and associative memory tasks. Ultimately, this work identifies neuronal Tet2 as a molecular target to enhance cognitive function.

overall_design: hMeDIP sequencing of hippocampal neuronal nuclei isolated from CamKIIaCreERT2;Tet2fl/fl mice vs WT Tet2fl/fl.

middle: J

first: Jeremy

last: Shea

first: Saul

last: Villeda


title: Temporarily epigenetic repression in Bergmann glia regulates the migration of Granule cells

city: Xiamen

first: shaoxuan

last: chen

state: Fujian Province

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District

institute: xiamen university

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

overall_design: Refer to individual Series


title: The Dystonia Gene THAP1 Controls DNA Double Strand Break Repair Choice [ChIP-Seq]

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

summary: The Shieldin complex, consisting of SHLD1, SHLD2, SHLD3 and REV7, shields double strand DNA breaks (DSBs) from nucleolytic resection. The end-protecting activity of Shieldin promotes productive non-homologous end joining (NHEJ) in G1 but can threaten genome integrity during S-phase by blocking homologous recombination (HR). Curiously, the penultimate Shieldin component, SHLD1 is one of the least abundant mammalian proteins. Here, we report that the transcription factors THAP1, YY1 and HCF1 bind directly to the SHLD1 promoter, where they cooperatively maintain the low basal expression of SHLD1. Functionally, this transcriptional network ensures that SHLD1 protein levels are kept in check to enable a proper balance between end protection and end resection during physiological DSB repair. In the context of BRCA1 deficiency, loss of THAP1 dependent SHLD1 expression confers cross resistance to PARP inhibitor and cisplatin, and shorter progression free survival in ovarian cancer patients. In contrast, loss of THAP1 in BRCA2 deficient cells increases genome instability and correlates with improved responses to chemotherapy. Pathogenic THAP1 mutations are causatively linked to adult-onset torsion dystonia type 6 (DYT6) movement disorder, but the critical disease targets are unknown. We further demonstrate that murine models of Thap1-associated dystonia show reduced Shld1 expression concomitant with elevated levels of unresolved DNA damage in the brain. In summary, our study provides the first example of a transcriptional network that directly controls DSB repair choice and reveals a previously unsuspected link between DNA damage and dystonia.

overall_design: ChIP-seq data to study THAP1 direct target genes in MEFs

first: Kenta

last: Shinoda

first: Dali

last: Zong

first: Elsa

last: Callen

first: Lavinia

middle: C

last: Dumitrache

first: Frida

last: Belinky

first: Nancy

last: Wong

first: Momoko

last: Ishikawa

first: Andre

last: Stanlie

first: Michelle

middle: E

last: Ehrlich

first: Peter

last: McKinnon

first: André

last: Nussenzweig


title: The Dystonia Gene THAP1 Controls DNA Double Strand Break Repair Choice [Nascent RNA-seq]

institute: Center for Excellence in Molecular Cell Science

overall_design: Nascent RNA-seq data to study gene expression profiles of Thap1-/- MEFs


title: Transcriptome-wide analysis of epitranscriptome and translational efficiency associated with heterosis in maize

city: Beijing

first: Yan

last: He

state: Beijing

address: 2 Yuanmingyuan West Road

department: Plant Genetics and Breeding

institute: China Agricultural University

summary: Heterosis, also known as hybrid vigor, has been extensively utilized to increase productivity in crop, yet the underlying molecular mechanisms remain largely elusive. Recent studies have reported that in addition to mRNA transcription, epigenetic variations in DNA methylation, small RNAs and histone modifications also contribute to heterosis. However, the operative mode of post-transcriptional regulation on gene expression such as RNA m6A methylation and translational efficiency in heterosis has never been explored. In this study, we generated transcriptome-wide profiles of mRNA abundance, m6A methylation, and translational efficiency from the maize (Zea mays) F1 hybrid B73×Mo17 and its two parental lines B73 and Mo17 to ascertain contributions of each regulatory layer to heterosis at the seedling stage. We documented that although the global abundance and the distribution configuration of m6A maintained unchanged, a greater number of genes have gained m6A modification in hybrid compared to parent lines. m6A modification and translational efficiency exhibited greater variations between hybrid and parents as compared with observed variation of mRNA abundance. In hybrid, the vast majority of genes with m6A modification exhibited non-additive expression pattern, the percentage of which was exceedingly higher than that of differential genes at mRNA abundance and translation efficiency levels. Non-additive genes involved in different biological processes were hierarchically coordinated by discrete combinations of three regulatory layers. These findings suggest that transcriptional and post-transcriptional regulations on gene expression adopt divergent approaches to participate in the formation of heterosis in hybrid. Overall, the integrated multi-omics analysis provides a valuable portfolio for interpreting transcriptional and post-transcriptional regulation on gene expression in maize hybrid, and pave new avenues for exploring molecular mechanisms underlying hybrid vigor.

overall_design: m6A-seq, RNA-seq and polysome profiling of 14-day-old F1 hybrid B73×Mo17 and its two parental inbred lines B73 and Mo17 were constructed to ascertain contributions of each regulatory layer to heterosis at the seedling stage in maize.


title: The Dystonia Gene THAP1 Controls DNA Double Strand Break Repair Choice [CRISPR-Cas9 screen]

overall_design: Whole-genome CRISPR-Cas9 screens to search for genes whose mutation confer PARP inhibitor resistance in BRCA1-deficient cells


title: GUIDE-Seq analysis of the designed gRNAs (SG1, SG2, SG3, SG4, SG7 and SG8)

first: Oscar

last: Quintana Bustamante

state: Spain

address: Av Complutense 40

institute: CIEMAT/CIBERER/IIS-FJD

summary: Off-target (OT) analysis of different guide RNAs targeting PKLR gene. GUIDE-Seq analyses were done in HEK293 cells stably expressing Cas9 transfected with gRNA complexes, generated using Alt-R® CRISPR-Cas9 crRNA XT and Alt-R®CRISPR-Cas9 tracrRNA, and transfected with a dsODN tag

overall_design: OT analysis of different guide RNAs targeting PKLR gene by GUIDE-Seq

first: Rolf

last: Turk


title: ADAMTS13 deficiency promotes platelet accumulation in pyrrolizidine alkaloids-induced liver injury

city: shanghai

first: ronggui

last: hu

state: China

address: Shanghai Institute of Biochemistry and Cell Biology

summary: RNA-seq was employed to detect hepatic differential expression genes between pyrrolizidine alkaloids-induced  liver injury mice and the untreated ones.

overall_design: Hepatic mRNA profiles of control group and pyrrolizidine alkaloids-induced liver injury mice

first: Hong

last: Gao

first: Xiaoqing

last: Zeng


title: Analysis of ChIP-Seq data identifies BfmR and CzcR regulons

first: Ke

last: Fan

address: No.646, Songtao Road

institute: Shanghai Institute of Materia Medica


title: High-throughput RNA sequencing analysis of mouse pre-pro-B cells and pro-B cells from wild type and Lactoferrin knockout mouse

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

summary:
Purpose: The goal of this study is using  RNA sequencing analysis to evaluate the role lactoferrin in the early development of B cells in mouse
Methods: The pre-pro-B cells and pro-B cells were isolated from the wild type and lactoferrin knockout mice (n=3 for each group) by flow cytometry. Then the cell RNA was sequenced by the NovaSeq 6000 high-throughput sequencing service (Jingneng, Shanghai, China). Data were extracted and normalized according to the manufacturer’s standard protocol.
Results: Log-fold changes of up- or down-regulated mRNAs between the control and experiment group were selected with a significance threshold of p<0.05.
Conclusions: Our study describes the mRNA changes of pre-pro-B and pro-B cells from wild type and lactoferrin knockout mice

overall_design: The pre-pro-B and pro-B cells were isolated from the wild type and lactoferrin mice, and cellular RNA was used for RNA-sequencing to show the gene expression profile change induced by lactoferrin deﬁciency

first: Lingyu

last: We


title: Analysis of ChIP-Seq data identifies CzcR regulon

summary:
Purpose:To identify the direct targets and regulatory mechanism of CzcR in Pseudomonas aeruginosa, we performed chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (Seq).
Methods: In the experiment, chromatin bound CzcR was crosslinked, sheared, bound to antibody, nonspecific proteins and nucleic acids removed, purified and sequenced. The sequencing data were obtained from several independent ChIP samples and then located on the p. aeruginosa genome. The MACS (Model-based Analysis for ChIP-Seq) software was used to call peak for sequence reads.
Results: We identified 108 enriched loci (p-value≤1e-5; fold enrichment>1) containing CzcR binding peak in the P. aeruginosa genome. In accordance with the previous studies, oprD, phzA1 promoters were significantly enriched compared to input DNA (80, 76-fold, respectively).

overall_design: Examination of 3 samples of pseudomonas aeruginosa

first: Lefu

last: Lan


title: Comparative Transcriptome Profiling of mRNA and lncRNA of Ovaries in High and Low Egg Production Performance in Domestic Pigeons (Columba livia)

city: Hangzhou

first: Haiguang

last: Mao

state: Zhejiang

address: Yuhangtang Road 866

institute: Zhejiang University

summary: To evaluate the lncRNAs and mRNAs in ovaries associated with egg production performance  in domestic pigeons, high-throughput RNA sequencing of ovaries between high and low egg production performance groups were performed and analyzed in this study.

overall_design: Three samples of ovarian tissue with high egg  production performance and three samples of ovarian tissue with low egg  production performance

first: Mao

last: Haiguang

first: Yin

last: Zhaozheng

first: Xu

last: Xiuli


title: Analysis of ChIP-Seq data identifies BfmR regulon

summary:
Purpose:To identify the direct targets and regulatory mechanism of BfmR in Pseudomonas aeruginosa, we performed chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (Seq).
Methods: In the experiment, chromatin bound BfmR was crosslinked, sheared, bound to antibody, nonspecific proteins and nucleic acids removed, purified and sequenced. The sequencing data were obtained from several independent ChIP samples and then located on the p. aeruginosa genome. The MACS (Model-based Analysis for ChIP-Seq) software was used to call peak for sequence reads.
Results: We identified 141 enriched loci (p-value≤1e-5; fold enrichment>3) containing BfmR binding peak in the P. aeruginosa genome. In accordance with the previous studies, bfmR, PA4103 promoters were significantly enriched compared to input DNA (49, 60-fold, respectively), had the highest degree of enrichment in all peaks.

overall_design: Examination of 9 samples of pseudomonas aeruginosa


title: RNA-seq analysis reveals differential expression profile between periostin knockout and wild-type mice

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

summary: Chondrocyte transcriptome of periostin knockout and wild-type mice showed that 4 genes (Tm4sf1, Evx2, Sscaml1, and GDf10) are statistically significant with FDR <= 0.05. 1247 genes have unadjusted p-values less than 0.05, but only 12 of those have log 2 fold-changes >= |2|. The GO biological process results do show statistically significant up-regulation of cell adhesion, cell signaling, angiogenesis, and differentiation in the KO samples.

overall_design: Chondrocytes were isolated by enzymatic digestion from mouse joints at the age of 21 days. After 2 days of cultures, RNA was extracted and subjected to RNA-seq to determine the gene expression differences between periostin knockout mice and wild-type B6/129 mice.

first: Weili

last: Zhang

first: Xin

last: Duan

first: Lei

last: Cai

first: Eric

last: Tycksen

first: Muhammad

last: Farooq Rai


title: Transcriptome analysis of human aortic endothelial cells (HAECs) with KLF11 knockdown

city: Ann Arbor

first: Guizhen

last: Zhao

state: MI

address: 2800 Plymouth Rd

department: Cardiovascular Center

institute: University of Michigan

summary: HAECs were infected with Ad-shlacZ (10MOI) or Ad-shKLF11 (10MOI) for 48 hours and harvest for RNA-sequencing

overall_design: HAECs mRNA profiles of Ad-shlacZ (3 replicates) or Ad-shKLF11 (3 replicates) infection were generated by RNA-sequencing

first: Jifeng

first: Y

last: Chen


title: Genome-wide Identification and Analysis of Long non-coding RNAs Involved in Fatty acid Biosynthesis in Young Soybean pods

city: Changchun City

first: Dan

last: Yao

address: No.2888 Xincheng street, Changchun City, Jilin Province

institute: country College of Life Sciences, Jilin Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Here, the low-linolenic acid mutant “MT72” and the wild-type control “JN18” were used as materials. The lncRNAs in young pods at 30 and 40 days (d) after flowering were systematically identified and analyzed using transcriptome sequencing technology combined with bioinformatics tools. A total of 39,324 lncRNAs and 561 differentially expressed lncRNAs were identified. A lncRNAs-miRNAs- protein-coding genes (mRNAs) network was constructed, and 46 lncRNAs, 46 miRNAs and 137 mRNAs were found to be correlated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of 12 targeted mRNAs in the competing endogenous RNA network showed that these lncRNAs may be involved in the biological processes of fatty acid transport, lipid synthesis and cell division. Finally, the expression levels of differentially expressed lncRNAs, miRNAs and mRNAs were verified using qRT-PCR. The expression patterns of most genes were consistent with the sequencing results. In conclusion, new information was provided for the study of fatty acid synthesis by lncRNAs in young soybean pods.

overall_design: Studies on low linolenic acid mutants “MT72” and wild-type “JN18” at 30d and 40d after flowering of soybean

first: Bohan


title: Tristetraprolin expression by keratinocytes protects against skin carcinogenesis

city: Gosselies

first: Stanislas

last: Goriely

address: Rue Adrienne Bolland 8

country: Belgium

institute: Université Libre de Bruxelles

summary: Cancer is caused primarily by somatic mutations of proto-oncogenes, leading to deregulation of gene regulatory circuits in key growth, apoptosis or DNA repair pathways. Multiple genes associated with the initiation and development of tumors are also regulated at the level of mRNA decay, through the recruitment of RNA binding proteins to AU-rich elements (AREs) located in their 3’-untranslated regions. One of these ARE-binding proteins, tristetraprolin (TTP, encoded by Zfp36) is consistently dysregulated in many human malignancies. Herein, using regulated overexpression or conditional ablation in the context of chemical cutaneous carcinogenesis, we show that TTP represents a critical regulator of skin tumorigenesis. We provide evidence that TTP controls both tumor-associated inflammation and key oncogenic pathways in malignant epidermal cells. We identify Areg as a direct target of TTP in keratinocytes, and show that EGFR signaling contributes to exacerbated tumor formation. We conclude that TTP expression by epidermal cells plays a major role in the control of early steps leading to tumorigenesis.

overall_design: 18 mouse samples: 3 cell types (Mock/Treated/Tumoral keratinocytes) x 2 conditions (Zfp36 ΔK14/Zfp36 fl/fl) x 3 replicates

first: Assiya

last: Assabban

first: Ingrid

last: Dubois-Vedrenne

first: Laurye

last: Van Maele

first: Rosalba

last: Salcedo

first: Deborah

last: Stumpo

first: Lecong

last: Zhou

first: Abdulkader

last: Azouz

first: Bérengère

last: de Toeuf

first: Gaëlle

last: Lapouge

first: Caroline

last: La

first: Maxime

last: Melchior

first: Muriel

last: Nguyen

first: Séverine

last: Thomas

first: Wu

last: Fan

first: Wenqian

last: Hu

first: Cédric

last: Blanpain

first: Giorgio

last: Trinchieri

first: Cyril

last: Gueydan

first: Perry

last: Blackshear


title: Inhibition of a pathologic RBM39/MLL1 epigenomic regulatory complex with a dominant-negative peptides disrupts cancer cell transcription, proliferation and survival

city: Houston

first: Yao

last: Yu

address: 1155 Pressler

institute: UT MD Anderson Cancer Center

summary: We report high-throughput profiling of RBM39 and MLL1 chromatin occupancy; H3K4me3 marks in T47D Control, T47D RBM39 KD and PME cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of RBM39, MLL1 and H3K4me3 in T47D and PME cells. We found that more than 4500 regions were cofound by RBM39 and MLL1.

overall_design: Examination of RBM39 and MLL1 chromatin occupancy in T47D cells.


title: Single cell RNA transcriptome analysis of Epicardial Derived Cells in the Desmoplakin haplo-insufficient Arrhythmogenic Cardiomyopathy mouse

first: Lukas

last: Simon

address: 1 Baylor Plaza

department: THINC

institute: Baylor College of Medicine

summary: To delineate the role of the epicardium, the initial site of presentation of the ACM phenotype, the Dsp gene, encoding desmosome protein desmoplakin (DSP) was conditionally deleted in the mouse epicardial cells under the transcriptional regulation of Wilms tumor 1 (Wt1) locus.  Single cell RNA sequencing (scRNA-Seq) of ~ 40,000 tagged epicardial-derived cells (EDCs), isolated using the dual reporter R26mT/mG mice, showed an increased number of EDCs expressing unique molecular identifiers of fibroblasts as well as a unique subset of epicardial-derived fibroblasts expressing pro-fibrotic genes in the Wt1-Cre: R26mT/mG: Dsp mice. Analysis of pseudo-bulk RNA-Seq data identified ~ 800 differentially expressed genes (DEGs), which were predominantly involved in epithelial-mesenchymal transition (EMT). The DEGs were the targets of TGFB1 among other trophic/mitotic factors, whose activation was verified by immunohistochemistry and quantification of transcript levels of selected TGBF1 pathway genes. Retro-mapping of the DEGs to the cell clusters, identified by scRNA-Seq, denoted epicardial-derived fibroblasts and to a lesser extent the epithelial cells as the main sources of paracrine factors in the myocardium of Wt1-Cre: R26mT/mG: Dsp mice.

overall_design: Integrative analysis of epicardial derived single-cell RNA-seq in the Desmoplakin haplo-insufficient Arrhythmogenic Cardiomyopathy mouse model.

first: Ping

last: Yuan

first: Ali

last: Marian


title: Ionizing radiation treatment of chondrocyte-like cells derived from human induced pluripotent stem cells: gene and microRNA expression profile

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

institute: Poznan University of Medical Science

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Detection of Chemotherapy-Resistant Pancreatic Cancer Using a Glycan Biomarker

city: Grand Rapids

first: Ian

last: Beddows

address: 333 Bostwick Ave NE

institute: Van Andel Institute

summary: A subset of pancreatic ductal adenocarcinomas (PDACs) is highly resistant to systemic chemotherapy, but no markers are available in clinical settings to identify this subset. We found that chemotherapy-resistant PDACs, but not chemotherapy-sensitive PDACs, express a glycan biomarker called sTRA. We confirmed the use of this marker to identify treatment-resistant PDAC in multiple systems: sets of 24 cell lines, 27 organoids, and isogenic cell lines; gene-expression signatures in primary tumors; tissue microarrays containing primary tumors; and blood plasma from cohorts of human subjects. These findings establish the use of tissue or plasma assays to identify the PDACs that are resistant to chemotherapy, which could improve the precision of systemic treatments and facilitate biomarker-guided trials targeting resistant PDAC.

overall_design: 27 pancreatic cancer cell lines with differing glycan status: sTRA positive (n=11), None (n=10), CA199 (n=3), and both sTRA & CA199 (n=3)

first: Brian

middle: B

last: Haab

first: ChongFeng

last: Gao


title: Inhibition of a pathologic RBM39/MLL1 epigenomic regulatory complex with a dominant-negative peptides disrupts cancer cell transcription, proliferation and survival.


title: Hypoxia induced cholecystokinin gene expression in 3D engineered muscle.

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: At high altitude, hypoxic atmosphere decreases the oxygen partial pressure (pO2) in the body, inducing several metabolic changes in tissues and cells. Furthermore, it exerts potent anorectic effects, thus causing energy deficit. Two decades ago, a marked increase in the level of resting plasma cholecystokinin (CCK) was observed at Mt. Kanchenjunga basecamp (BC) located at 5,100 m above the sea level, compared to sea-level control values. Interestingly, acute exercise also raises plasma CCK and exerts potent anorectic effects under normoxic conditions. However, the molecular mechanism underlying these effects has not yet been established.   We employed acute electrical pulse stimulation (EPS), followed by a microarray analysis, to discover novel myokines in 3D engineered muscle. Acute EPS efficiently affects the contractile function, inducing a decline of the contractile force. Surprisingly, microarray analysis revealed an EPS-induced activation of the cholecystokinin receptor (CCKR)-mediated signaling. Furthermore, Cck was constitutively expressed in 3D engineered muscle, and was upregulated by hypoxic conditions. Notably, a hypoxia responsive element (HRE) was detected in the Cck promoter of mice and humans.   Our results suggested that, under hypoxic conditions, Hif-1a binding to HRE transactivated Cck expression in mice and humans. Furthermore, the plasma CCK elevation after acute exercise or at high altitude might be partly attributed to myogenic cells.

overall_design: Microarray analysis was carried out in 3D engineered muscles at 0 min and 5 h after a 30-min acute EPS, and 3D engineered muscle with no acute EPS was adopted as the negative control (EPS-).

first: Tomohiro

last: Nakamura


title: Genome-wide chromatin occupancy of RBM39 and MLL1 in T47D cells

summary: We report high-throughput profiling of RBM39 and MLL1 chromatin occupancy in T47D cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of RBM39 and MLL1 in T47D cells. We found that more than 4500 regions were cofound by RBm39 and MLL1.


title: Next Generation Sequencing Facilitates Quantitative Analysis of RBM39 knockdown Transcriptomes in T47D cells

summary: Methods: Total RNA was prepared from control and RBM39 siRNAs transfected in T47D cells and subsequently used for deep sequencing, in duplicates.

overall_design: Control and RBM39 siRNAs transfected in T47D cell


title: Comparison between MCF7-IKKe overexpressing cells and MCF7 control cells

city: Mexico City

first: Jorge

last: Melendez-Zajgla

address: Periferico Sur 4809 Col. Arenal Tepepan

country: Mexico

institute: Instituto Nacional de Medicina Genomica

summary: Analysis of differentially expressed genes in MCF7 cancer cells transiently transfected with an expression vector containing the ORF of IKKe and as a control, cells were transfected with a vector containing the ORF of Lacz.

overall_design: Two groups were analyzed in triplicate each. The first group consisted on MCF7 transfected with an expression vector that overexpresses IKK and the other group was MCF7 cells transfected with a vector containing the ORF of Lacz

first: Karla

last: Vazquez

last: Melendez


title: Isolation and characterization of hESC-derived heart field-specific cardiomyocytes unravels new insights into their transcriptional and electrophysiological profiles

city: Los Angeles

first: Reza

last: Ardehali

address: 675 Charles E Young dr

department: Cardiology

institute: UCLA

summary: We prospectively isolate and characterize first and second heart field- and nodal-like cardiomyocytes using a double reporter line from human embryonic stem cells

overall_design: We performed RNA sequencing of  hESC derived CMs at various timepoints, and scRNA seq on Day 20 hESC derived CMs and human fetal heart at 10 weeks of gestation.

first: Arash

last: Pezhouman

first: James

last: Engel

first: Ngoc

last: Nguyen

first: Rhys

middle: P

last: Skelton

first: W

last: Gilmore

first: Rong

last: Qiao

first: Debashis

last: Sahoo

first: Peng

last: Zhao

first: David

last: Elliott

first: Ardehali

last: Reza


title: Pseudocell Tracer - a method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination

status: Public on Apr 12 2021

city: Chicago

first: Aly

middle: Azeem

last: Khan

address: 6045 S. Kenwood Ave.

institute: University of Chicago

summary: Single cell RNA sequencing (scRNAseq) can be used to infer a temporal ordering of cellular states. Current methods for the inference of cellular trajectories rely on unbiased dimensionality reduction techniques. However, such biologically agnostic ordering can prove difficult for modeling complex developmental or differentiation processes. The cellular heterogeneity of dynamic biological compartments can result in sparse sampling of key intermediate cell states. To overcome these limitations, we develop a supervised machine learning framework, called Pseudocell Tracer, which infers trajectories in pseudospace rather than in pseudotime. The method uses a supervised encoder, trained with adjacent biological information, to project scRNAseq data into a low-dimensional manifold that maps the transcriptional states a cell can occupy. Then a generative adversarial network (GAN) is used to simulate pesudocells at regular intervals along a virtual cell-state axis. We demonstrate the utility of Pseudocell Tracer by modeling B cells undergoing immunoglobulin class switch recombination (CSR) during a prototypic antigen-induced antibody response. Our results revealed an ordering of key transcription factors regulating CSR to the IgG1 isotype, including the concomitant expression of Nfkb1 and Stat6 prior to the upregulation of Bach2 expression. Furthermore, the expression dynamics of genes encoding cytokine receptors suggest a poised IL-4 signaling state that preceeds CSR to the IgG1 isotype.

overall_design: Live NP+B220+ splenocytes from C57Bl6/J mice on day 14 post-NP-KLH iummunization were FACS-purified. Single-cell suspensions of FACS-purified cells were loaded onto the 10X Genomics Chromium Controller. Library construction was performed using the Chromium Single Cell 5’ Library Construction Kit followed by sequencing, 30,000 reads per cell on a NovaSeq6000.

first: Derek

last: Reiman

first: Godhev

middle: K

last: Manakkat Vijay

first: Harinder

last: Singh


title: Study on the Effect of Astragalus Polysaccharides in the Prevention and Treatment of Nonalcoholic Fatty Liver

first: Xuyun

last: He

address: Cailun Road 1200

institute: Shanghai University of Traditional Chinese Medicine

summary: On the basis of the clear role of Astraglus polysaccharides (APS) in the prevention of obesity and non-alcoholic fatty liver (NAFLD) induced by high-fat diet, the potential effector genes of APS are screened by means of transcriptional techniques.

overall_design: 24 male C57bl/6J mice were randomly divided into 3 groups including control group (Con), high-fat-diet group (HFD) and high-fat-diet with APS treatment group (APS). All animals were fed with corresponding diet for consecutive 12 weeks during which their body weight was measured weekly. According to the results of liver HE staining and TG detection, 3 liver samples of each group were detected by transcriptional techniques.

first: Houkai

last: Li


title: The effect of SEAP1 on the accumulation of miRNAs and mRNAs

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

summary: SE-Associated Protein 1 (SEAP1), is a conserved protein in eukaryotes. Its orthologs, SART3 and PRP24 from metazoans and yeast play essential roles in splicing. Here, we report that SE-Associated Protein 1 (SEAP1), is required for miRNA biogenesis in Aradopsis. Lack of SEAP1 causes embryo lethality and knockdown of SEAP1 by an artificial miRNA (amiRSEAP1) causes pleiotropic growth defects and reduction in miRNA accumulation, accompanied with increased levels of target transcripts. SEAP1 associates with the RNase III enzyme Dicer-like 1(DCL1) complex, which processes primary miRNA transcripts (pri-miRNAs) into miRNAs, and seems to promote the interaction of the DCL1 complexes with pri-miRNAs. SEAP1 is also required for pri-miRNA accumulation. However, it does not affect the transcription of pri-miRNAs, suggesting it may indirectly or directly stabilize pri-miRNAs. SEAP1 also affects the spicing of pri-mRNAs. These results suggest that SEPA1 promotes miRNA biogenesis by positively modulating pri-miRNA splicing, processing and stability. We also find that intron retention in amiRSEAP1 is altered at global levels, linking SEAP1 to spicing. Collectively, our results uncover the function of SEAP1 in plants.

overall_design: To exam the effect of artifical miRNA targeting to SEAP1 on the accumation of miRNAs by RNA Sequencing Non-coding RNA Deep Sequencing

first: Mu

first: Bin

last: Yu


title: Transcript profile analysis suggests marker genes to distinguish between Phase 0 and Phase 1 responses of Arabidopsis to salt stress

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Most physiological and molecular mechanisms of salinity stress are researched based on salt shock conditions. However, salt shock doesn’t occur in agricultural practice or natural ecosystem. In the fields, salts accumulate gradually through high salt or sodium irrigation water and poor managements that allow ground water to rise to soil surface. Therefore, it is more reasonable to research salinity stress in a mild way (stepwise salt addition). The objective of this study is to select marker genes to differentiate between salt shock (Phase 0) and salt stress (Phase 1). Three replicates were used for all RNA-Seq experiments conducted on control, Phase 0 and Phase 1 samples in Arabidopsis thaliana. Phase 0 samples (rosette leaves) were harvested 1 hour later from 105 mM NaCl salt shock treatment; Phase 1 samples (rosette leaves) were harvested 2 days later after reaching 90 mM NaCl by a stepwise addition (15 mM NaCl per day).

first: Wenting

first: Sven

last: Schubert


title: RNA sequencing identifies sub-clinical hepatic response to stocking density

city: Albemarle

first: Chandler

last: Keck

address: 1510 Melchor rd

institute: NC State University

summary: We report the hepatic response of broiler chickens to an increase in stocking density. Here we compare gene expression profiles of liver cells via RNA-seq of broiler chicken raised under a high stocking density to broiler chickens raised under a lower stocking density with the objective of this study being to identify biomarkers of stress before the clinical and economic impacts are observed. We found that increasing stocking density seems to have a unique impact on hepatic gene expression prior to eliciting common clinical signs associated with stress. The cellular functions that are most affected appear to be those involved in steroidogenesis and cell movement/migration as identified by RNA-seq analysis of the liver transcriptome. These results could provide a baseline of information that future research to identify genes or molecules that could aid in the detection of negative effects of stressors such as stocking density prior to negative clinical and economic signs presenting themselves.

overall_design: Hepatic gene expression profiles via RNAseq of broilers raised under a stocking density of 24.4kg/m2 (5 lbs/ft2 (treatment A)) and 39.1kg/m2 (8 lbs/ft2 (treatment D))

first: Christopher

last: Ashwell


title: Integrated mRNA and miRNA expression profile analyses reveal the potential roles of miRNA–mRNA pairs in skin color variation between wild-type and yellow mutant rainbow trout

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

summary: As an important cold-water economic fish species, rainbow trout (Oncorhynchus mykiss) exhibits several intra-specific variation in skin pigmentation that can give rise to distinctive phenotypes, and wild-type rainbow trout with black skin (WR) and yellow mutant rainbow trout with yellow skin (YR) are the major two types in the farms, whose distinct skin colors make them suitable model for elucidating the skin pigmentation process. Skin color as a key indicator for selection in rainbow trout farming as well as has a strong visual impact on the consumer when rainbow trout are marketed. Previously, extensive studies have been conducted on skin color in rainbow trout, including the observation of skin spots and the expression analysis of some important pigment genes. However, up to date, no studies have systematically examined the molecular regulation mechanism of skin color difference between WR and YR through a high throughput method. Therefore, the aim of this study was to reveal the molecular regulation mechanism of skin color difference between these two strains at the mRNA and miRNA transcriptome level, and candidate genes, miRNAs and miRNA-mRNA pairs that may be responsible for rainbow trout albinism were obtained.

overall_design: This study simultaneously analysis mRNA and miRNA expression profiles and construct miRNA-mRNA regulatory networks to identify key miRNA-mRNA pairs that may participate in skin color formation of WR and YR.

first: Jinqiang

last: Huang

first: Shenji

last: Wu


title: SLC36A1-mTORC1 signaling drives acquired resistance to CDK4/6 inhibitors

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

summary: The CDK4/6 kinase is dysregulated in melanoma highlighting a potential therapeutic benefit.  Indeed, such CDK4/6 inhibitors are being evaluated in trials for melanoma and additional cancers. While beneficial, resistance to therapy is a concern and the molecular mechanisms of such resistance remain undefined. Here, we demonstrate that reactivation of mTORC1 signaling through increased expression of the amino acid transporter, SLC36A1, drives resistance to CDK4/6 inhibitors. Increased expression of SLC36A1 reflects two distinct mechanisms; 1) Rb loss which drives SLC36A1 via reduced suppression of E2f; 2) FXR1 overexpression which promotes SLC36A1 translation and subsequently mTORC1. Finally, we demonstrate that a combination of a CDK4/6 inhibitor with an mTORC1 inhibitor has increased therapeutic efficacy in vivo providing an important avenue for improved therapeutic intervention in aggressive melanoma.

overall_design:
Palbociclib (PD) resistant cells (PDR) were generated from 1205Lu cells via sustained treatment with 1uM PD and kept in PD-containing medium. Parental cells were cultured in parallel in standard growth media.
Cells were seeded (without drugs) in standard culture media and treated with 1uM PD for 24hours or 8 days

first: Akihiro

last: Yoshida

first: Yiwen

last: Bu

first: Shuo

last: Qie

first: John

last: Wrangle

first: E

middle: R

last: Camp

last: Hazard

first: Renée

last: de Leeuw

first: Karen

last: Knudsen

first: J

last: Diehl


title: Single cell RNAseq coupled with TCR repertoire analysis of thymocytes in thymus autonomy and turnover

city: Oeiras

first: Vera

last: Martins

address: Rua da Quinta Grande, 6

country: Portugal

institute: Instituto Gulbenkian de Ciência

summary: Wild type thymi were transplanted into wild recipients (turnover) or Rag2-/-gc-/- mice (autonomy) and, after 28 days of transplant, thymocytes (double negative 3 and 4, immature CD8 single positive and CD4 CD8 double positive) were sorted and single cell RNAseq and TCR repertoire analysis performed

overall_design: Single cell analysis of the transcriptome and VDJ rearrangements of thymocytes in autonomy or turnover conditions.

first: Rafael

last: Paiva


title: Genome-wide Programmable Transcriptional Memory by CRISPR-based Epigenome Editing

city: Dallas

first: Jin

last: Chen

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: General approaches for heritably altering gene expression would enable many discovery and therapeutic efforts. Here, we present CRISPRoff— a programmable epigenetic memory writer consisting of a single dead Cas9 fusion protein that establishes DNA methylation and repressive histone modifications. Transient CRISPRoff expression initiates highly specific DNA methylation and gene repression that is maintained through cell division and differentiation of stem cells to neurons. Pairing CRISPRoff with genome-wide screens and analysis of chromatin marks enabled us to explore the rules for heritable silencing. We identify sgRNAs capable of silencing the large majority of genes including those lacking canonical CpG islands (CGIs) and reveal a wide targeting window extending beyond annotated CGIs. Our finding that targeted DNA methylation outside of CGIs leads to memorized gene silencing expands the canonical model of methylation-based silencing and broadly enables diverse applications including genome-wide screens, multiplexed cell engineering, enhancer silencing, and mechanistic exploration of epigenetic inheritance.

overall_design: RNA-seq, ChIP-seq, and Whole Genome Bisulfite Sequencing samples to characterize CRISPRoff knockdown efficiency and offtargets.

first: James

last: Nuñez

first: Greg

last: Pommier

middle: Z

last: Cogan

first: Joseph

last: Replogle

first: Carmen

last: Adriaens

first: Gokul

middle: N

last: Ramadoss

first: Quanming

last: Shi

first: King

last: Hung

first: Avi

last: Samelson

first: Angela

last: Pogson

middle: Y

last: Kim

first: Amanda

last: Chung

first: Manuel

last: Leonetti

first: Howard

last: Chang

first: Martin

last: Kampmann

first: Brad

last: Bernstein

first: Volker

last: Hovestadt

first: Luke

last: Gilbert

first: Jonathan

last: Weissman


title: Single cell RNA sequencing data in CD11chiMHChiSIRPa+ Peyer's patch cells

city: Jeonju-si, Jeollabuk-do,

first: Saehae

address: 567 Baekje-daero, Deokjin-gu,

department: Molecular biology

country: South Korea

institute: Jeonbuk National University

summary: We report the single celll RNA sequencing data of CD11chiMHChiSIRPa+ Peyer's patch cells

overall_design: mRNA profiles in CD11chiMHChiSIRPa+ cells derived from BALB/c Peyer's patch

first: Sae-Hae

first: Yong-Suk

last: Jang


title: Gene Expression in Wild Type and TTP Delta ARE Knock-in Mice using RNA-seq

city: Durham

first: Perry

last: Blackshear

address: 111 T W Alexander Drive

institute: NIH/NIEHS

summary:
Purpose: The goals of this study are to compare NGS-derived skin transcriptome profiling (RNA-seq) in wild type mice with TTP delta ARE knock-in mutants.
Methods: Skin mRNA profiles of approximately 27 week old wild-type (WT) and TTP delta ARE knock-in mice were generated by deep sequencing, with five biological replicates, using Illumina sequencers.  The skin RNA samples were prepared from skin biopsies from treated but not papillomatous skin from mice treated with a standard DMBA-TPA protocol for 20 weeks.  The sequence reads that passed quality filters were mapped to mm10 with STAR Aligner followed by featureCounts and DESeq2 anlysis.
Results:  We observed 1144 statistically differentially expressed genes (232 and 912 up- and down-regulated genes in TTP delta ARE mice, respectively, with fold changes >2 and FDR<0.05.
Conclusions:  Regulated overexpression of TTP by a stablizing deletion in the 3'UTR of its mRNA causes many changes in gene expression in mice subjected to a standard skin papilloma protocol.

overall_design: Skin mRNA profiles of wild type (WT) and knockin (KI) mice were generated by deep sequencing, in quintuplicate.

first: Assyia

last: Assabban

first: Ingrid

last: Dubois-Vedrenne

first: Laurye

last: Van Maele

first: Rosalba

last: Salcedo

first: Brittany

last: Snyder

first: Lecong

last: Zhou

first: Abdulkader

last: Azouz

first: Bérengère

last: de Toeuf

first: Gaëlle

last: Lapouge

first: Caroline

last: La

first: Maxime

last: Melchior

first: Muriel

last: Nguyen

first: Séverine

last: Thomas

first: Wu

middle: S

last: Fan

first: Wenqian

last: Hu

first: Cédric

last: Blanpain

first: Giorgio

last: Trinchieri

first: Cyril

last: Gueydan

first: Stanislas

last: Goriely


title: Bulk RNAseq analysis of CD4 CD8 double negative 3 (DN3) and CD4 CD8 double positive (DP) thymocytes in thymus autonomy and turnover

first: Vera

last: Martins

summary: Wild type thymi were transplanted into wild recipients (turnover) or Rag2-/-gc-/- mice (autonomy) and, after 28 days of transplant, DN3 and DP thymocytes were sorted and their transcriptomes analyzed.

overall_design: Analysis of the transcriptome of DN3 and DP thymocytes in autonomy or turnover conditions.

first: Rafael

middle: A

last: Paiva


title: Negative Elongation Factor (NELF) regulation of muscle progenitor expansion assessed via Precision Run-On Sequencing (PRO-seq)

city: Boston

first: Karen

last: Adelman

state: MA

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

summary: Assessment of promoter-proximal RNA polymerase II pausing in wild type and NELF-B KO (muscle stem cell-specific deletion) myoblasts

overall_design: PRO-seq: 2 biological replicates each for WT and NELF-B KO; RNA-seq: 2 biological replicates each for WT and NELF-B KO

first: Daniel

last: Robinson

first: Seth

last: Goldman

first: Geoffrey

middle: M

last: Nelson

first: F

last: Dilworth


title: Transcriptional reprogramming in transgenic Arabidopsis plants expressing C4G2A and a cas-1 mutant upon activation of plant immunity.

city: Shanghai

first: Xing

last: Fu

address: 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences

summary: Transcriptional overlap between transgenic Arabidopsis plants expressing C4G2A from the Tomato yellow leaf curl virus (TYLCV) and a cas-1 mutant upon activation of plant immunity by treatment with the bacterial peptide elicitor flg22 (1 µM, 12 h).

overall_design: RNA-seq data were obtained from ten-day-old Arabidopsis seedlings grown on ½ MS agar plates under long-day conditions prior to transfer to ½ MS liquid for elicitation with the bacterial peptide elicitor flg22 (1 µM, 12 h). UR: up-regulated; DR: down-regulated. Comparisons are made with treated control (wild-type) plants.

first: Laura

last: Medina-Puche

first: Rosa

last: Lozano-Duran*


title: Gene expression data from mouse brain endothelial cells after SAH

city: Toronto

first: Michael

last: Tso

state: ON

address: 30 Bond St.

department: Neurosurgery

institute: University of Toronto

summary: SAH pathophysiology includes blood-brain barrier (BBB) disruption. Gene expression changes at the endothelial cell level may provide insight into BBB pathophysiology. We used microarray gene expression data comparing freshly isolated brain endothelial cells isolated from Sham or SAH mice.

overall_design: 4 sham mice (burr hole and no blood injection) vs. 4 SAH mice (burr hole and 80 microL prechiasmatic blood injection); mouse brain CD45-CD31+ endothelial cells isolated at the 24h time-point after SAH/sham induction using magnetic-beads with immediate RNA extraction; RNA amplified with Ovation Pico WTA System V2 and then hybridized to Affymetrix Mouse Gene 2.0 ST Arrays; intensities normalized using robust multi-array average (RMA) algorithm.

first: Robert

middle: L

last: Macdonald


title: Overexpression of CYGB led to differential gene expression in HCT116 cells (RNA-seq)

city: Ningbo

first: YANG

last: XI

address: Fenghua Road

department: School of medicine

institute: Ningbo University

summary: The goal of this study was to define the cohort of genes whose expression is regulated by CYGB function in colorectal cancer. Towards this goal, HCT116 cells stably expressing CYGB (HCT-CYGB) were established. In addition, a control cells (HCT-MOCK) was generated by transfection with empty vector. Subsequently, total RNA was isolated and then performed transcriptome RNA sequence.

overall_design: We had two groups: (1) HCT-MOCK and (2) HCT-CYGB. Each group had 3 biological replicates.

first: Xi

last: Yang

first: Ye

last: Shazhou

first: Xu

last: Mingjun


title: The C5a signaling triggers functional intracellular signaling in C5aR+ LysoDCs

first: Saehae

last: Kim

summary: C5a–C5aR signaling results in an intracellular calcium influx through activation of the coupled G-protein, which triggers ROS generation in APCs. To investigate the effect of C5a–C5aR signaling on cell function, we analyzed the gene expression profile of rC5a-treated C5aR+ LysoDCs.

overall_design: PP cells were prepared by collagenase D (Roche)/DNase I buffer and after removing dead cells using a dead cell removal kit, CD11c+ cells were enriched using anti-mouse CD11c microbeads. Sorted C5aR+ LysoDCs were stimulated with recombinant C5a protein (100 nM) for 3 hours. Total RNA was prepared using an RNeasy PLUS Micro kit according to the manufacturer’s protocols (Qiagen).

first: Sae-Hae

first: Yong-Suk

last: Jang


title: C5aR+ lysozyme-expressing dendritic cells (LysoDCs) comprise a unique cell population in the Peyer’s patch (PP) subepithelial dome (SED).

summary:
CD11chi cells can be subdivided into six different cell subsets:plasmacytoid DCs (pDCs), CD8a+ DCs, CD11b+ DCs, double-negative (DN) DCs, LysoDCs, and LysoMacs. Among these, LysoDC (CD4–) and LysoMacs (CD4+) are classified as CD11chiMHC class II+BST2intSIRPαhi lysozyme+ cells, depending on whether they express CD4. Here, we determine that C5aR expressed in LysoDC and LysoMacs.
We used microarrays to determine the lineage of C5aR+ LysoDC and C5aR- LysoDC.

overall_design: PP cells were prepared by collagenase D (Roche)/DNase I buffer and after removing dead cells using a dead cell removal kit, CD11c+ cells were enriched using anti-mouse CD11c microbeads. C5aR+ LysoDC, C5aR- LysoDC, and LysoMac were sorted using FACSAria III and total RNA was prepared using an RNeasy PLUS Micro kit.


title: Cell-type-specific profiling of defects in translation and neurogenesis in a human iPSC model of fragile X syndrome

city: Atlanta

first: Feiran

last: Zhang

state: GA

address: 615 Michael St NE

department: Human Genetics

institute: Emory University

summary: Transcriptional silencing of the FMR1 gene in fragile X syndrome (FXS) leads to loss of the RNA-binding protein, FMRP. In addition to its well-established role of regulating protein synthesis, emerging evidence suggests that FMRP acts to coordinate proliferation and differentiation during early neural development. However, whether translational control by FMRP drives critical cellular events of fate specification and developmental transitions in the developing human brain remains unknown. Here, we have designed a high-throughput, in vitro assay that allows for the simultaneous quantification of protein synthesis and proliferation within defined neural subpopulations. Using iPSC-derived neural progenitor cells and organoids to model human cortical neurogenesis in FXS, we show that abnormal protein synthesis during early development alters cellular decisions to favor proliferative over neurogenic cell fates.

overall_design: Gene expression analyses were performed on mRNA samples isolated from iPSC-derived 3D cerebral organoids of control and FXS patients

first: Peng

last: Jin

first: J

last: Taliaferro


title: Establishment of bovine expanded potential stem cells

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

summary: Embryonic stem cells (ESCs) and induced pluripotent stem cells have the potential to differentiate to all cell types of an adult individual and are useful for studying development and for translational research. However, extrapolation of mouse and human ESC knowledge to deriving stable ESC lines of domestic ungulates and large livestock species has been challenging. In contrast to ESCs that are usually established from the blastocyst, mouse expanded potential stem cells (EPSCs) are derived from four-cell and eightcell embryos. We have recently used the EPSC approach and established stem cells from porcine and human preimplantation embryos. EPSCs are molecularly similar across species and have broader developmental potential to generate embryonic and extraembryonic cell lineages. We further explore the EPSC technology for mammalian species refractory to the standard ESC approaches and report here the successful establishment of bovine EPSCs (bEPSCs) from preimplantation embryos of both wild-type and somatic cell nuclear transfer. bEPSCs express high levels of pluripotency genes, propagate robustly in feeder-free culture, and are genetically stable in long-term culture. bEPSCs have enriched transcriptomic features of early preimplantation embryos and differentiate in vitro to cells of the three somatic germ layers and, in chimeras, contribute to both the embryonic (fetal) and extraembryonic cell lineages. Importantly, precise gene editing is efficiently achieved in bEPSCs, and genetically modified bEPSCs can be used as donors in somatic cell nuclear transfer. bEPSCs therefore hold the potential to substantially advance biotechnology and agriculture.

overall_design: Firstly, bovine EPSC medium was established and optimized by bovine induced pluripotent stem cells (biPSCs) reprogramming. Then, bovine ESCs were obtained in EPSCM. Characterization assay were carried out and proved the expanded potency of bovine pluripotent stem cells, and all these cells were called bovine EPSCs.

first: Lixia

last: Zhao

first: Xuefei

last: Gao

first: Zixin

last: Wang

first: Gaoping

first: Jie

last: Ren

first: Jia

first: Jian

last: Wu

first: Baojiang

first: Yanglin

last: Chen

first: Wei

last: Sun

first: Yunxia

last: Li

last: Su

first: Yulin

last: Ding

first: Yuan

first: Moning

last: Liu

first: Xiaochun

last: Bai

first: Liangzhong

first: Guifang

last: Cao

first: Fuchou

last: Tang

first: Siqin

last: Bao

first: Pentao

first: Xihe


title: Evolution of biofilm formation in Candida

city: Irapuato

first: Eugenio

last: Mancera

state: Guanajuato

address: Km. 9.6 Libramiento Norte Carretera Irapuato-Leon

department: Ingenieria Genetica

institute: Cinvestav

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

sample_organism:
Candida albicans
Candida parapsilosis
Candida tropicalis
Candida dubliniensis
Candida albicans x Candida dubliniensis

overall_design: Refer to individual Series


title: Molecular tracking devices quantify antigen distribution and archiving in the lymph node.

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

summary:
Live, attenuated vaccines generate humoral and cellular immune memory, increasing the duration of protective immune memory. We previously found that antigens derived from vaccination or viral infection persist beyond infection clearance via acquisition and retention (“archiving”) in lymphatic endothelial cells (LECs). Archived antigen maintains an effector-like pool of antigen-specific memory T cells, enhancing clearance of subsequent infections. Technical limitations of fluorescent labeling have precluded a complete picture of antigen archiving across cell types in lymph tissue. We developed a “molecular tracking device” to follow the distribution, acquisition, and retention of antigen in the lymph node. We immunized mice with an antigen conjugated to a nuclease-resistant DNA tag and used single-cell mRNA sequencing to quantify its abundance across major cell types in the lymph node two weeks later, validating its acquisition by migratory dendritic cells and durable retention by LECs and unexpected stromal cell types. Variable antigen levels in LECs enabled the identification and validation of caveolar endocytosis as a mechanism of antigen acquisition. Molecular tracking devices enable new approaches to study dynamic tis-sue dissemination at cellular resolution in vivo.

We developed a 'molecular tracking device' to follow the distribution, acquisition, and retention of antigen across cell types in the lymph node. We immunized mice with an antigen conjugated to a nuclease-resistant DNA tag and used single-cell mRNA sequencing to quantify its abundance in immune and stromal cell types two weeks later, validating its retention by LECs and transfer to migratory dendritic cells and defining new reservoirs of archived antigen in stromal cells. Molecular tracking devices broadly enable new approaches to study molecular dissemination and retention in live animals.

overall_design: Single-cell mRNA sequencing libraries and matching antigen-tracking libraries generated from the 10X Genomics system.


title: Strigolactones and auxin cooperate to regulate lateral root development in response to nitrate

status: Public on Apr 11 2021

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

country: Italy

institute: University of Bologna

summary: In maize, nitrate regulates root development thanks to the coordinated action of many players. In this study, the involvement of SLs and auxin as putative downstream components of the nitrate regulation of lateral root development was investigated. To this aim, the endogenous SL content of maize root in response to nitrate availability was assessed by means of LC-MS/MS and measurements of lateral root density in the presence of analogues or inhibitors of auxin and strigolactones were performed. Furthermore, un untargeted RNA-seq based approach was used to better characterize the participation of auxin and strigolacotones to the transcriptional signature of maize root response to nitrate.   Our results suggested that N deprivation toughly induces zealactone and carlactonoic acid biosynthesis in maize root, to a higher extent if compared to P-deprived roots. Moreover, data on lateral root density led to hypothesise the existence of both auxin-dependent and auxin-independent effects of nitrate on LR development. In addition, the inhibition of SL biosynthesis seems to participate to the auxin-dependent induction of LR, but the involvement of further downstream unknown components cannot be ruled out.

overall_design: Illumina RNA-Seq analysis of maize roots collected from seedlings grown for 24 h in nutrient solution supplied with NO3-, TIS108 and NO3- plus PCIB compared to negative controls grown in a N-deprived nutrient solution. 3 days old maize B73 inbreed seedlings were treated for 24 h prior to roots collection and RNA extraction.  3 biological replicates per condition were produced, each composed by 4-8 plants.

first: Laura

last: Ravazzolo

first: Stéphanie

last: Boutet-Mercey

first: François

last: Perreau

first: Serena

last: Varotto

first: Benedetto

last: Ruperti

first: Silvia

last: Quaggiotti


title: Dicalcium silicate promotes osteogenic differentiation and bone defect healing via circ_1983–miR-6931–Gas7 interaction

city: guangzhou

first: Xingyang

last: Li

state: Guangdong

address: 195, dongfengxi road

department: Department of Temporomandibular Joint Surgery

institute: Affiliated Stomatology Hospital of Guangzhou Medical University

summary:
Background: Dicalcium cilicate (C2S) is a potent biomaterial for bone regeneration application. Circular RNA (circRNAs) plays crucial role in osteogenic differentiation of mesenchymal stem cells (MSCs) and bone defect healing. In this study, we aim to elucidate the differential expression of circ_RNAs and mRNAs in C2S-treated MSCs, the role of circ_1983 in C2S-mediated bone regeneration, and its mechanism.
Methods: The effect of C2S on osteogenic differentiation of mice bone marrow-derived MSCs (BMSCs) and rat cranial bone defect healing were analyzed. Differential expression of circ-RNAs and mRNAs in C2S-treated BMSCs were profiled by RNA-sequencing. The interaction between circ_1983 and miR-6931 was confirmed by pull-down and dual luciferase reporter assays. ceRNA function of circ_1983 via sponging miR-6931 and targeting Gas7 mRNA expression in BMSCs was analyzed by miRanda (http://www.microrna.org/microrna/). Role of circ_1983 in C2S-induced osteogenic differentiation of BMSCs was analyzed by shRNA-mediated knockdown of circ_1983.
Results: C2S enhanced osteogenic differentiation of BMSCs and bone defect healing. CircRNAs (total 1384) and mRNAs (total 1725) were differentially upregulated in C2S-treated BMSCs. Upregulated circRNAs and ceRNA-interaction networks were associated with osteogenesis-related signaling pathways, i.e. MAPK, PI3K-Akt.    RNA-sequencing and qRT-PCR results confirmed upregulation of circ_1983 in C2S-tretaed BMSCs. Circ_1983 showed ceRNA effect by sponging miR-6931 and overexpressing Gas mRNA that enhanced Runx2 expression and promoted osteogenic differentiation of BMSCs. Knockdown of circ_1983 inhibited the C2S-induced osteogenic differentiation of BMSCs.
Interpretation: C2S-induced circ_1983 upregulation in BMSCs sponges miR-6931 and targets Gas7 gene to enhance Runx2 expression thereby promotes osteogenic differentiation and bone regeneration.

overall_design: circRNA profiles of BMSCs inducted by C2S were generated by deep sequencing, using Illumina GAIIx.

first: Wenchao

last: Zhong


title: Conserved and unique features of the SAGA complex in plants

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences


title: Conserved and unique features of the SAGA complex in plants [ChIP-seq]

summary: The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex is an evolutionarily conserved, multifunctional co-activator complex, which has a critical role in histone acetylation, gene expression, and various developmental processes in eukaryotes. However, little is known about the composition and function of the SAGA complex in plants. Here, we found that the SAGA complex in Arabidopsis thaliana contains not only conserved subunits and but also four plant-specific subunits, including three homologous subunits, SCS1, SCS2A, and SCS2B (SCS1/2A/2B), and a TAF-like subunit, TAFL. We also found that a series of SAGA subunits are shared in yeast and/or metazoans but are absent in Arabidopsis. Mutations in the unique SAGA subunits SCS1/2A/2B lead to defective phenotypes similar to those caused by mutations in the conserved SAGA subunits HAG1 and ADA2B; these defective phenotypes include delayed juvenile-to-adult phase transition, late flowering, and increased trichome density. SCS1/2A/2B function in the SAGA complex to promote the transcription of development-related genes by facilitating histone H3 acetylation. The results suggest that, compared to SAGA complexes in other eukaryotes, the SAGA complex in plants has evolved unique features that are necessary for normal growth and development.

overall_design: Examination of H3K9Ac levels in wild type and three mutants.

first: Xin-Jian


title: RNA-sequencing and function analysis of adult gonad tissue identify potential key transcription factors in Macrobrachium resenbergii with sex determination

city: Hangzhou

first: Jindong

last: Ren

address: No.198, Shiqiao Road

institute: Zhejiang Academy of Agricultural Sciences

summary: M. rosenbergii is a classical aquatic organism with sex-reversed phenomenon by gene-expressed regulation. Reversal of gonad development in M. rosenbergii received great attention but the role of transcription factors for gonadal maintenance and sex determination in adult shrimps remain unclearly. In this study, we sequencing the transcriptomes for the adult testis, ovary and androgenic gland by third-generation sequencing plus second-generation sequencing, and 21,345 were identified. In total, 9,199 differentially expressed genes (DEGs) were identified in pairwise comparison where 2,990 DEGs were upregulated expression in testis than other tissues, and 5,775 DEGs were upregulated expression in ovary, and 2,244 DEGs were upregulated expression in androgenic. There are 272 differentially expressed transcription factors (DETs) in total. The upregulated DETs in one of the testis, ovary and androgenic glands compared to the others were 107, 152 and 13 respectively. The GO and KEGG of DETs analysis suggested that MAPK signaling pathway and transcriptional misregulation pathway have key function in testis, the thyroid hormone signaling pathway and neuroactive ligand-receptor interaction play a important role in ovary. We determined the existence of networks containing significant DETs related to sex determination in the adult goands of M. rosenbergii. The key DETs are Piwi (only expression in testis and ovary) and Argonaute 2 (only expression in ovary) might be involved with the regulation of ovary development.

overall_design: Three gonad mRNA profiles of adult male and female M.rosenbergii

first: Bao

last: Lou

first: Baolong

last: Niu


title: The glucocorticoid receptor coordinates myofiber-selective transcriptional networks

status: Public on Apr 10 2021

city: Cambridge

first: Scott

last: Jelinsky

address: 610 Main Street

department: Inflammation and Immunology

institute: Pfizer

summary: Muscle fibers have the capacity to modulate their size in response to hormones, including  glucocorticoids. Their effects are mediated by the ubiquitously expressed glucocorticoid  receptor (GR). However, GR-mediated transcriptional regulation in skeletal muscle at  physiological glucocorticoid levels remains elusive. Our study reveals an increased expression  of numerous anabolic factors in GR-deficient myofibers, and a reduced expression of antianabolic  factors, leading to fiber hypertrophy. Genome-wide analyses demonstrate that myofiber  GR controls broad gene networks by binding to glucocorticoid response elements (GREs) at  enhancers. Moreover, we provide topological and molecular insights into the chromatin  landscape of GR-controlled genes in myofibers. We demonstrate that cooperative binding of GR  with the transcription factors Myod1 and Foxf2 in enhancer regions, in collaboration with Nrf1  at promoters, plays a key role in the negative regulation of muscle mass. Thus, these results  open new perspectives to counteract muscle weakness in various diseases.

overall_design: Gene expression profiling was performed on total RNA isolated from control and GR(i)skm-/- gastrocnemius muscles

first: Daniel

last: Metzger


title: Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit

first: James

last: Locke

address: Bateman street

country: United Kingdom

institute: SLCU

summary: Genetically identical individuals in bacterial populations can display significant phenotypic variability. This variability can be functional, for example by allowing a fraction of stress prepared cells to survive an otherwise lethal stress. The optimal fraction of stress prepared cells depends on environmental conditions. However, how bacterial populations modulate their level of phenotypic variability remains unclear. Here we show that the alternative sigma factor σV circuit in B. subtilis generates functional phenotypic variability that can be tuned by stress level, environmental history, and genetic perturbations. Using single-cell time-lapse microscopy and microfluidics, we find the fraction of cells that immediately activate σV under lysozyme stress depends on stress level and on a transcriptional memory of previous stress. Iteration between model and experiment reveals that this tunability can be explained by the autoregulatory feedback structure of the sigV operon. As predicted by the model, genetic perturbations to the operon also modulate the response variability. The conserved sigma-anti-sigma autoregulation motif is thus a simple mechanism for bacterial populations to modulate their heterogeneity based on their environment.

overall_design: A mutant (JLB154: PY79 ppsb::PtrpE-mCh (PhleoR) sacA::PsigV-YFP (CmR) ytvA::neo haG::erm  sigV::tet) and a WT (JLB130: PY79 ppsb::PtrpE-mCh (PhleoR) sacA::PsigV-YFP (CmR) ytvA::neo haG::erm ) line were analysed in absence or presence of lysosyme treatment (1 µg/ml lysozyme for 30min). We performed 2 biological replicates.

first: Christian

last: Schwall

first: Torkel

last: Loman

first: Bruno

last: Martins

first: Sandra

last: Cortijo

first: Casandra

last: Villava

first: Vassili

last: Kusmartsev

first: Toby

last: Livesey

first: Teresa

last: Saez


title: Polysome-profiling of IL4 or INFG polarized BMDMs

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

summary: BMDMs from naïve female FVB mice were used to generate BMDMs which were polarized for 4 hours using either INFG or IL4. These were subjected to polysome-profiling.

overall_design: Polarized BMDMs were generated and their translatomes and transcriptomes were compared using polysome-profiling


title: The long noncoding RNA SNHG1 promotes carboplatin resistance retinoblastoma

city: harbin

first: shoubin

last: sun

address: baojian road 157

institute: harbin medical university

summary: carboplatin resistance retinoblastoma cell lines (Weri-RB1/CRP) transfect SNHG1-specific shSNHG1 to knockdown SNHG1 and analysis differential gene in Weri-RB1/CRP

overall_design: Weri-RB1/CRP-shSNHG1#1 and Weri-RB1/CRP-shSNHG1#2 were designed to knockdown SNHG1 in Weri-RB1/CRP.Weri-RB1/CRP-shNC was control.

first: sun

last: shoubin


title: Conserved and unique features of the SAGA complex in plants [RNA-seq]

first: xinjian

last: He

overall_design: Examination of the mRNA expression of wild type and three mutants in Arabidopsis.

first: Xin-Jian


title: Significance of zinc on skin molecular signatures in Atlantic salmon with Winter ulcer disease

status: Public on Apr 09 2021

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Vaccinated seawater adapted Atlantic salmon (average weight ~340 g) fed with variable levels of zinc were infected with Moritella viscosa at VESO Vikan. Early responses in skin to infection were investigated 4 days post challenge. Effect of chronic ulceration was investigated 35 days post challenge.

overall_design: Skin biopsies were excised from the left side of each fish in the area posterior of the dorsal fin and above the lateral line, and in addition sampled at the wound site. Skin layer dissection was performed to split samples into epidermis and dermis.

last: Karlsen

first: Elisabeth

last: Ytteborg

first: Gerrit

last: Timmerhaus


title: Chromatin Immunoprecipitation analysis of mouse hippocampal neuron HT22 cells

city: Guangzhou

first: Boyu

last: Yuan

address: 24 Dongsha Street

institute: Zhongkai University of Agriculture and Engineering

summary: We used H4K5bu and H4K5ac antibodies to specifically enrich mouse hippocampal neuronal cells (HT22) before and after BHBA administration. We found that the acetylation and butylation of histone H4K5 play a key role in the neuroprotection of BHBA.

overall_design: Examination of 2 different histone modifications in HT22 cells.

first: Mingming

last: Liu

first: Xinxin

last: Jin


title: Genomic and transcriptomic profiling expands precision cancer medicine: the WINTHER trial (Lung patients)

city: Villejuif

first: Shai

last: Magidi

address: rue Guy Moquet

country: France

institute: WIN Consortium

summary: Transcriptomic profiling of metastatic NSCLC cancer patients from tumor tissue and organ-matched normal tissue as reference which were taken as part of the WINTHER clinical trial. The organ-matched normal tissues were used in order to eliminate host gene expression variability while discarding most genetic variability between individuals. The goal was to trial was to navigate patients to therapy on the basis of fresh biopsy-derived DNA sequencing or RNA expression

overall_design: Dual biopsies experiment - Tumor tissue vs. organ-matched normal tissue from the same individuals. 32 lung samples and 32 matched normal samples were collected as part of the WINTHER trial

first: Jordi

last: Rodon

first: Jean-Charles

last: Soria

first: Raanan

last: Berger

first: Wilson

middle: H

last: Miller

first: Eitan

last: Rubin

first: Aleksandra

last: Kugel

first: Apostolia

last: Tsimberidou

first: Pierre

last: Saintigny

first: Aliza

last: Ackerstein

first: Irene

last: Brana

first: Yohann

last: Loriot

first: Mohammad

last: Afshar

first: Vincent

first: Fanny

last: Wunder

first: Catherine

last: Bresson

first: Jean-Francois

last: Martini

first: Jacques

last: Raynaud

first: John

last: Mendelsohn

first: Gerald

last: Batist

first: Amir

last: Onn

first: Josep

last: Tabernero

first: Richard

last: Schilsky

first: Vladimir

last: Lazar

first: J

last: Lee

first: Razelle

last: Kurzrock


title: Skin responses in Atlantic salmon post-smolts during exposure to Tenacibaculum finnmarkense

first: Aleksei

last: Krasnov

summary: Tenacibaculum finnmarkense is a novel Gram-negative, aerobic bacterial strain causing skin ulcers in Atlantic salmon. This is an emerging pathogen, which may cause serious problems to aquaculture. The study was designed to compare the life stages (smolt and posmolt) and to assess effects of environment (fresh and brackis water) on the course of disease and salmon responses to the pathogen.

overall_design: The experiment was conducted at ILAB Bergen, Norway. The facility includes two units. Fish kept in the holding unit in fresh or brackish water is referred to as holding controls. Smolts and postsmolts were moved to the challenge unit and full-strength seawater (34 ppt) was applied 24 hours prior to the challenge with Tenacibaculum finnmarkense strain HFJT. Groups from the challenge unit are referred to as control and infected. To follow the development of the challenged skin, samples were taken three days post challenge. Ventral skin samples for microarray analysis were selected based on ulcer scoring. For each sample, RNA from epidermis and dermis was isolated separately. Total RNA was extracted using the automated Biomek 4000 (Beckman Coulter).

first: Christian

last: Karlsen

first: Marte

last: Fredriksen

first: Lene

last: Sveen

first: Gerrit

last: Timmerhaus

first: Sverre

last: Småge


title: DNA methylation analysis of three distinct human odontogenic stem cells

first: Tingting

last: Ai

address: 56# Lingyuan West Road

institute: Sun Yat-sen University School and Hospital of Stomatology

summary: Using the HumanMethylation450 Beadchip, whole genomes of human dental pulp stem cells (DPSCs), periodontal ligament stem cells (PDLSCs), and dental follicle progenitor cells (DFPCs) were compared.The DNA methylation profiles were obtained across approximately 485,512 CpGs in human odontogenic stem cells samples.  Samples included DPSCs, DFPCs and PDLSCs from each 4 (12 in total) human individuals.

overall_design: Bisulphite converted DNA from the 4 samples in each stem cell group (12 samples in total) were hybridised to the Illumina Infinium HumanMethylation450 Beadchip


title: plasma circRNA-expression profiles in children with pulmonary hypertension secondary to congenital heart disease

city: Nanning

first: Danyan

last: Su

address: 22, Shuangyong Road

institute: The First Affiliated Hospital of Guangxi Medical University

summary: Pulmonary arterial hypertension (PAH) is a common and serious complication of left-to-right shunt congenital heart disease (CHD).Some studies have provided evidence indicating that various circRNAs are abnormally expressed in pulmonary hypertension. However, the diagnostic value and biological functions of circRNAs in PAH remain largely elusive. To study the potential roles of circRNAs in PAH, we performed microarray analysis to identify circRNAs differentially expressed between pediatric patients with PAH due to CHD and control subjects.

overall_design: We enrolled eight patients in the microarray study with CHD combined with PAH (the PAH group) and another five patients with CHD who did not have PAH (the control group). Blood was taken from the femoral vein by cardiac catheterization. The blood samples were then centrifuged at 1000 × g for 15 min to completely remove the cellular components. The plasma samples were then stored at -80°C until total RNA were isolated. The total RNA of each sample was quantified using a NanoDrop ND-1000 instrument. Sample preparation and microarray hybridization were performed using an Arraystar Human circRNA Array (8× 15K).

first: Yanyun

last: Huang

first: Yusheng

last: Pang


title: RNA-Seq of M1 activated ErbB4-null and WT bone-marrow macrophages.

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

summary: We tested the hypothesis that NRG4/ErbB4 signaling regulates cytokine production in macrophages. Loss of ErbB4 in bone-marrow derived macrophages results in elevated pro-inflammatory cytokine production. These results demonstrate a feedback mechanism by which growth factor signaling can limit immune cells activity.

overall_design: Gene expression profiling from M1 activated bone-marrow macrophages from 6 LysMCre/ErbB4-floxxed (KO) and 6 littermate ErbB4-floxxed (WT) controls. Samples are pair-matched with 1 KO and 1 WT from separate litters.

first: Michael

last: Schumacher

first: Mark

last: Frey