title: NOTCH1 gene amplification promotes expansion of Cancer Associated Fibroblast populations in human skin

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

summary: Cancer associated fibroblasts (CAFs) represent a key component of the tumor microenvironment. Possible genomic alterations in these cells remain a point of contention. The skin is constantly exposed to clastogenic insults, such as UVA light that can target directly the stromal compartment, therefore representing a relevant model to study. Here we report that CAFs from skin Squamous Cell Carcinoma (SCC) lesions display chromosomal alterations, with heterogeneous levels of NOTCH1 gene amplification that also occur, to a lesser extent, in dermal fibroblasts of apparently unaffected skin. The fraction of the latter cells harboring NOTCH1 gene amplification is expanded by chronic UVA exposure, which induces a DNA damage response (DDR) to which CAFs are resistant. The selective advantage conferred by NOTCH1 gene amplification and over-expression can be explained by NOTCH1 ability to block DDR-mediated growth arrest through competitive suppression of ATM-FOXO3a association and downstream signaling cascade. These findings are of translational significance as, in an orthotopic model of skin SCC, genetic or pharmacological inhibition of NOTCH1 activity suppresses cancer / stromal cells expansion. Thus, NOTCH1 amplification and increased expression contribute to CAFs evolution and are an attractive target for preventing cancer / stromal cell expansion.

overall_design: Three independent CAF strains, at the 2nd passage after tumor dissociation, were analyzed by Comparative Genomic Hybridization (CGH).

first: Giulia

last: Bottoni

first: Atul

last: Katarkar

first: Andrea

last: Clocchiatti

first: Sandro

last: Goruppi

first: Pino

last: Bordignon

first: Francesca

last: Lazzaroni

first: Ilaria

last: Gregnanin

first: Victor

last: Neel

first: Gian

last: Dotto


title: FBXO11 is a candidate tumor suppressor in the leukemic transformation of myelodysplastic syndrome

status: Public on Aug 24 2020

city: Chicago

first: John

last: Crispino

address: 300 Superior St

country: USA

institute: Northwestern University

type: Expression profiling by high throughput sequencing

summary: This experiment is assocaited with a publication defining a tumor supressor role of FBXO11 in the transformation of MDS. We observe decreased expression of FBXO11 is associated with transformation to secondary AML.

overall_design:
This experiment was designed to determine the genes regulated by FBXO11. We compared 4 cell populations.
1. MDS-Cas9 (parent MDS-L cells expressing Cas9 - effectively a control),
2. MDSL-Cas9-FBXO11KO (MDS-L cells with Cas9 and FBXO11 sgRNA - effectively FBXO11 knockout),
3. MDSL-Cas9-FBXO11KOv1OE (FBXO11 knockout cells with overexpression of FBXO11 isoform 1 cDNA),
and 4. MDSL-Cas9-FBXO11KOv4OE (FBXO11 knockout cells with overexpression of FBXO11 isoform 4 cDNA)

first: Christian

last: Marinaccio

first: Michael

middle: S

last: Schieber


title: Three Rules Explain Transgenerational Small RNA Inheritance in C. elegans

city: Tel-Aviv

first: Leah

last: Houri-Ze'evi

address: Haim Levanon

department: Neurobiology

country: Israel

institute: Tel-Aviv University

type: Non-coding RNA profiling by high throughput sequencing

summary: Life experiences trigger transgenerational small RNA-based responses in C. elegans nematodes1. Dedicated machinery ensures that heritable effects would re-set, typically after a few generations2,3. Here we show that isogenic individuals differ dramatically in the persistence of transgenerational responses. By examining lineages composed of >20,000 worms we reveal 3 inheritance rules: (1) Once a response is initiated, each isogenic mother stochastically assumes an “inheritance state”, establishing a commitment that determines the fate of the inheritance. (2) The response that each mother transfers is uniform in each generation of her descendants. (3) The likelihood that an RNAi response would transmit to the progeny increases the more generations the response lasts, according to a “hot hand” principle. Mechanistically, the different parental “inheritance states” correspond to global changes in the expression levels of endogenous small RNAs, immune response genes, and targets of the conserved transcription factor HSF-1. We show that these rules predict the descendants’ developmental rate and resistance to stress.

overall_design: Four mCherry-expressing worms were allowed to lay eggs in separate plates (one worm per plate) for 8 hours. The eggs were allowed to hatch and grew until they reached adulthood. Each group of progenies (isogenic sisters) was then washed with M9 buffer into a 1.5ml Eppendorf tube, followed by 3-4 M9 washes, in order to remove any residual bacteria. Each group was then examined in COPASTM Biosort (Union Biometrica) and sorted to get the top and bottom 25% of mCherry expressing worms in each group. TRIzol® (Life Technologies) was then added to each sorted tube, and the tubes were immediately transferred to -80°C until RNA extraction procedure.

first: Oded

last: Rechavi


title: RNA sequence of preeclampsia and healthy control placentas

city: Jinan

first: Jin

last: Wang

state: China

address: No.2,  Jianguo xiaojing road, Jinan City, Shandong Province, PR China

country: China

institute: Jinan Maternal and Child Health Care Hospital

summary: Preeclampsia (PE) is a multi-system disorder that is primarily characterised by new-onset hypertension accompanied by proteinuria during gestation. This disease affects 3-5% of all pregnancies and is one of the leading causes of maternal and perinatal morbidity and mortality. In this work, placental samples were collected from PE and control patients. RNA-seq was performed to identify differences in gene expression. Significantly differentially expressed genes between the PE and control samples included 68 up-regulated and 52 down-regulated genes. This study may provide further insight in the mechanisms of PE and function as preventive, predictive and therapeutic measures.

overall_design: mRNA profile of placental samples of preeclampsia (n=4) and control patients (n=4), and each group were generated by Illumina Hiseq 4000.

first: Hua

last: Jin


title: Integrated analysis of the transcriptome-wide m6A methylome in preeclampsia and healthy control placentas

summary: N6-methyladenosine (m6A) is the most prevalent modification in eukaryotic mRNA and potential regulatory functions of m6A have been shown by mapping the RNA m6A modification landscape. M6A modification in active gene regulation manifests itself as altered methylation profiles. However, the profiling of m6A modification and its potential role in preeclampsia (PE) has not yet been studied. In this work, placental samples were collected from PE and control patients. MeRIP-seq was performed to identify differences in m6A methylatio. Altered peaks of m6A-modified transcripts were primarily associated with nitrogen compound metabolic process, positive regulation of vascular-associated smooth muscle cell migration, and endoplasmic reticulum organisation. The m6A hyper-methylated genes of Wnt/β-catenin signalling pathway, mTOR signalling pathway, and several cancer-related pathways may contribute to PE. Our data provide novel information regarding m6A modification alterations in PE and help our understanding of the pathogenesis of PE.

overall_design: RNA m6A modification landscape of placental samples of preeclampsia (n=4) and control patients (n=4), were generated by Illumina Hiseq 4000.


title: Role of TGF-β signaling in hypoxia-induced alternative splicing in breast cancer cells

city: Bhopal

first: Sanjeev

last: Shukla

state: Madhya Prades

address: Bhopal Bypass Road, Bhauri Bhopal 462 066 Madhya Pradesh, INDIA

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Bhopal

summary:
Analysis of transcriptome post hypoxia and TGF-β treatment in breast cancer
In order to explore the role of TGF-β signaling in mediating the alternative splicing program in breast cancer, we profiled the pre-mRNA splicing and mRNA gene expression upon hypoxia and TGF-β treatment using Human Transcriptome Array 2.0.

overall_design: Breast cancer cell lines MCF7 and HCC1806 were cultured in 1% O2 for giving hypoxia treatment. For TGF-β induction, cells were treated with 10 ng/ml of TGF-β ligand. Post harvest, samples were analysed on Human Transcriptome Array 2.0 platform. Raw files generated were processed using Transcriptome Analysis Console tool.

first: Neha

last: Ahuja

first: Cheemala

last: Ashok

first: Subhashis

last: Natua

first: Deepak

last: Pant

first: Anna

last: Cherian

first: Madhura

middle: R

last: Pandkar

first: Pooja

last: Yadav

first: Vishnu

last: Narayanan

first: Jharna

last: Mishra

last: Samaiya


title: High-throughput capture of cis-rearrangement and trans-rearrangement sequence [LAM-HTGTS]

city: Paris

first: Ludovic

last: Deriano

address: 25-28 Rue du Docteur Roux

department: Immunology

country: France

institute: Institut Pasteur

summary: Cell cycle is a major determinant of DNA double-strand break (DSB) repair pathway choice with homologous recombination (HR) that is most active in S phase cells and non-homologous end-joining (NHEJ) that dominates in G1 phase cells. A third less well-defined mechanism, 'alternative end-joining', has been shown to promote error-prone repair in NHEJ- or HR-deficient cells. Here, we have used a physiologic system of NHEJ-mediated genomic rearrangements induced by the site-specific RAG1/2 endonuclease in G1 cells to investigate the fate of unrepaired G1 DSBs upon entry into the cell cycle. We show that, in the absence of XRCC4, alternative end-joining rescues RAG-induced DSB repair and promotes chromosome translocations upon G1 cell cycle exit.

overall_design:
We performed linear amplification-mediated high-throughput genome-wide sequencing (LAM-HTGTS) on mouse v-Abl/Bcl2  immortalized pro-B cell lines which included genotypes WT, Xrcc4-/-, p53-/- and Xrcc4-/- p53-/-. Igk-J4 primer was used as bait to capture cis-rearrangement sequence within Igk loci and trans-rearrangement sequence with whole genome-wide. The captured of cis- and trans-rearrangement sequences with Igk-J4 were analyzed and compared among cycling cells, v-Abl kinase inhibitor treated and released cells.

*Please note that each wig processed data was generated from all replicates together and is linked to the corresponding rep1 sample records.

first: Wei

last: Yu

first: Chloé

last: Lescale


title: High-throughput sequencing of RAG induced re-arrangements

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

overall_design: Refer to individual Series


title: Igk locus capture-based target enrichment  sequencing

overall_design: Coding and signal sequences of 140 mouse Igk V and 5 Igk J segments were downloaded from MGI database. 280 bps windows flanking recombination signal site (RSSs) of Igk V and J segments, including coding and signal sequences, were used to design Agilent SureSelect customized probes (Agilent Technologies). A total of 2348 120-mer probes (1168 for signal ends; 1180 for coding ends) were designed for Igk locus capture. SureSelectXT Target Enrichment System kit (Agilent Technologies) was used to prepare Igk locus capture sequencing libraries.


title: RNA-seq analysis after Ssrp1 knockout or Usp7 depletion in embryonic stem cells

status: Public on Aug 23 2020

city: Tainjin

first: Weiyu

last: Zhang

address: No.38 Tongyan Road, Jinnan District

institute: Nankai University

summary: Endogenous retrovirus MERVL is specifically expressed in a minority of embryonic stem cells. To determine the restrain mechanism of MERVL, we knocked out Ssrp1 and analyzed the effect on the expression of transposable elements and coding genes. Ssrp1 further interacts with ubiquitin specific protease Usp7. We knocked down usp7 and analyzed the effect on the expression of MERVL. It turns out the deletion of ssrp1 or usp7 would lead to upregulation of MERVL. This study extends our understandings of the machanism by novel factors regulates MERVL.

overall_design: We knocked out Ssrp1 in E14 by CRISPR/Cas9 System. And we knocked down Usp7 in E14 by shRNA. We performed RNA-seq analysis in order to exam the transcriptome after Ssrp1 KO or Usp7 knockdown.

first: Xinyi

last: Lu

first: Fuquan

last: Chen


title: ChIP-seq analysis of Ssrp1 and Usp7 in mESCs

type: Genome binding/occupancy profiling by high throughput sequencing

summary: FACT was discovered to be a repressor of transcription in mES cells. In addition, the murine endogenous retrovirus were repressed by various mechanisms. Hence, we examined the possibility for Ssrp1 as a repressor of MT2/MERVL.

overall_design: We performed CHIP-seq analysis in order to identifiy the binding sites of Ssrp1 in wild-type mESCs and perform enrichment analysis of Usp7 after Ssrp1 knockout.


title: Evolution of the histone variant H2A.W reconstituted in fission yeast

city: Tübingen

first: Michael

last: Borg

address: Max Planck Ring 5

department: Algal Development & Evolution

country: Germany

institute: Max Planck Insititue for Biology


title: Urinary phosphate-containing nanoparticle contributes to inflammation and kidney injury in salt-sensitive hypertension

status: Public on Aug 22 2020

city: Itabashi

first: Shigeru

last: Shibata

state: Tokyo

department: Division of Nephrology, Department of Internal Medicine

country: Japan

institute: Teikyo University School of Medicine

summary: Although disturbed phosphate metabolism frequently accompanies chronic kidney disease, it is unclear whether it contributes to the progression of renal dysfunction. Here, we show that urinary phosphate-containing nanoparticles promote kidney injury in salt-sensitive hypertension. Remarkably, four weeks of high salt loading resulted in a 2.5-fold increase in urinary phosphate excretion in Dahl salt-sensitive rats on a normal phosphorus diet. Inhibition of intestinal phosphate absorption using sucroferric oxyhydroxide (SF) in this model suppressed phosphaturia, attenuating glomerulosclerosis and tubulointerstitial injury without significantly affecting serum phosphate, blood pressure, or urinary sodium levels. In the kidney, macrophage infiltration and inflammatory cytokine induction were ameliorated by SF. Additionally, macrophage infiltration but not myofibril hypertrophy was alleviated in the heart. In vitro, phosphate loading to proximal tubule cells significantly increased inflammatory cytokine Ccl2, which was abolished by the removal of phosphate-containing nanoparticles but not by the knockdown of phosphate transporter Slc34a1. Finally, transcriptome analysis revealed a potential role of complement C1q in renal inflammation associated with disturbed phosphate metabolism. These data demonstrate that increased phosphaturia promotes inflammation and renal injury from an early stage of salt-sensitive hypertension, and suggest the need for interventions against subclinical phosphate accumulation to improve the prognosis of hypertensive kidney disease.

overall_design: Global gene expression in the kidneys of Dahl-S rats receiving 2.5%SF was compared with that of Dahl-S rats

first: Qin

last: Wang


title: scRNAseq analysis of mouse  L4  whole dorsal root ganglions with and without sciatic nerve crush injury

city: Athens

first: Oshri

last: Avraham

state: GA

address: 120 Cedar St

department: Cellular Biology

institute: University of Georgia

summary: Peripheral sensory neurons with cell body in dorsal root ganglia (DRG) switch to a regenerative state after nerve injury to enable axon regeneration and functional recovery. Studies of nerve injury responses in sensory neurons have revealed signaling and transcriptional mechanisms that increase their intrinsic regenerative capacity. However, the extent to which satellite glial cells (SGC), which completely surround the neuronal soma contribute to these responses remains unexplored. Using single cell RNA-seq, we defined the transcriptional profile of SGC in naïve and injured conditions and identified Fabp7, also known as BLBP, as a novel marker of SGC. We report that nerve injury elicits gene expression changes in SGC, which are mostly related to lipid metabolism, specifically fatty acid synthesis and the peroxisome proliferator-activated receptor (PPAR) signaling. Conditional deletion of Fatty acid synthase (Fasn), the key enzyme in de novo fatty acid synthesis, specifically in SGC, impairs axon regeneration. Treatment with fenofibrate, a PPARa agonist, rescues the impaired regeneration, suggesting that PPRAa, which belongs to a family of lipid regulated transcription factors, functions downstream of fatty acid synthesis in SGC to promote axon regeneration. These results unravel fatty acid synthesis in SGC as a fundamental novel mechanism mediating axon regeneration in mature peripheral nerves.

overall_design: We have applied the high-throughput single-cell mRNA sequencing technique, using the Chromium Single Cell Gene Expression Solution (10x Genomics) to mouse L4 DRG in naïve and injured conditions (3 days post sciatic nerve crush injury), 2 biological replicates for each sample.

first: Valeria

last: Cavalli


title: Effect of SWELL1 (LRRC8a) gene deletion on gene expression in differentiated myotubes

city: Iowa City

first: Chad

last: Grueter

state: Iowa

address: 285 Newton Rd, 4332 PBDB, 285 Newton Rd

institute: University of Iowa

summary: Maintenance of skeletal muscle is beneficial in obesity and Type 2 diabetes. Mechanical stimulation can regulate skeletal muscle differentiation, growth and metabolism, however the molecular mechanosensor remains unknown. Here, we show that SWELL1 (LRRC8a) functionally encodes a swell-activated anion channel that regulates PI3K-AKT, ERK1/2, mTOR signaling, muscle differentiation, myoblast fusion, cellular oxygen consumption, and glycolysis in skeletal muscle cells. SWELL1 over-expression in SWELL1 KO myotubes boosts PI3K-AKT-mTOR signaling to supra-normal levels and fully rescues myotube formation. Skeletal muscle targeted SWELL1 KO mice have smaller myofibers, generate less force ex vivo, and exhibit reduced exercise endurance, associated with increased adiposity under basal conditions, and glucose intolerance and insulin resistance when raised on a high-fat diet, compared to WT mice. These results reveal that the SWELL1-LRRC8 complex regulates insulin-PI3K-AKT-mTOR signaling in skeletal muscle to influence skeletal muscle differentiation in vitro and skeletal myofiber size, muscle function, adiposity and systemic metabolism in vivo.

overall_design:
We used RNA-Sequencing to quantify the changes in global mRNA expression in wild-type as compared to SWELL1 (LRRC8a) knock out differentiated myotubes.
We generated isogenic wild-type (WT) and SWELL1 (LRRC8a) KO myoblast cell lines from mouse C2C12 myoblast cell. CRISPR/Cas9 was used to knockout the LRRC8a gene in the parental C2C12 cell line. These cell lines were grown in culture and RNA was extracted for sequencing under basal culture conditions. RNA was sequenced on an Illumina Hi-Seq at the University of Iowa Core Facility.

first: Rajan

last: Sah

middle: E


title: Gamma-secretase inhibition does not affect gene expression in squamous cell carcinoma cells that do not express Notch1

city: Boston

first: Julia

middle: M

last: Rogers

state: Massachusetts

address: 45 Shattuck Street

department: BCMP

institute: Harvard Medical School

summary: As part of a larger study on the role of Notch1 activation in squamous cell carcinoma (SCC), these control data sets were generated to study the effect of gamma-secretase inhibition on SCC cells that do not express Notch1. We found that no genes are significantly changed in response to gamma-secretase inhibition.

overall_design: IC8 squamous cell carcinoma cells were grown in the presence or absence of gamma secretase inhibitor for 24 hours. Two replicates of each condition were performed.

first: Stephen

middle: C

last: Blacklow

first: Jon

last: Aster


title: Mouse immune cells response Interleukin-33 (IL-33) [nanostring]

status: Public on Aug 21 2020

city: Calgary

last: Robbins

state: Alberta

address: 3330 Hospital Drive N.W.

department: Oncology

country: Canada

institute: University of Calgary

summary:
To validate the modulation of inflammatory genes by ectopic IL-33, we performed Gene expression analysis using the nCounter Mouse v2 Inflammation Panel.
This result validated a significant increase in a number of anti-inflammatory cytokines in the IL-33+ xenografts that were absent in the DNLS xenografts

overall_design: we performed mouse inflammation gene expression analysis in mice bearing intracranial U87 tumors overexpressing IL-33 (N=4) or transfected with pcDNA vector control (N=3) or U87 tumors overexpressing IL-33 DNLS (N=4)

first: Donna

middle: L

last: Senger

first: Astrid

last: DeBoeck

first: BoYoung

last: Ahn


title: Strand-specific RNA-seq analysis after Ssrp1 knockout in embryonic stem cells

last: Zhang

summary: Endogenous retrovirus MERVL is specifically expressed in a minority of embryonic stem cells. To determine the restrain mechanism of MERVL, we knocked out Ssrp1 and analyzed the effect on the expression of transposable elements and coding genes.

overall_design: We knocked out Ssrp1 in E14 by CRISPR/Cas9 System. We performed strand-specific RNA-seq analysis in order to exam the transcriptome after Ssrp1 KO.


title: Single cell profiling of cerebral immune cells in the Interleukin-33 (IL-33) driven tumor microenvironment

summary: IL33 is a dual function cytokine which acts as a major orchestrator of the brain tumor microenvironment that contributes to tumorigenesis. We found that IL33 is expressed in a large subset of human glioma patient specimens and murine glioma models and that its expression is directly associated with the increased presence of tumor associated macrophages/monocytes/microglia. We analyzed the differences in the IL-33+ and IL-33- innate immune microenvironments at a single cell resolution and found substantial differences in the immune populations present and gene expression changes which may contribute to the increased tumoirgenicity of IL-33+ tumors.

overall_design: We preformed single cell RNA sequencing on immune cells in mice bearing intracranial human glioma U87 tumors overexpressing IL-33 (N=3) or transfected with pcDNA vector control (N=3).

first: Charlotte

last: D'Mello

first: Shyam

middle: V

last: Menon


title: AlphaBeta: Computational inference of  epimutation rates and spectra from  high-throughput DNA methylation data in plants

first: Robert

middle: J

last: Schmitz

address: B416 Davison Life Sciences

department: Genetics

type: Methylation profiling by high throughput sequencing

summary: Heritable changes in cytosine methylation can arise stochastically in plant genomes  independently of DNA sequence alterations. These so-called ‘spontaneous epimutations’ appear to be abyproduct of imperfect DNA methylation maintenance during mitotic or meitotic cell divisions. Accurate estimates of the rate and spectrum of these stochastic events are necessary to be able to quantify how epimutational processes shape methylome diversity in the context of plant evolution, development and aging.

overall_design: We created two lineages of mutation accumluation lines for Col-0 that were propagated by single seed descent growth for the indicated number of generations (G#). No replicates are possible in the designed experiment, although independent lineages do serve as a form of replication.


title: Cerebral immune cells in the Interleukin-33 (IL-33) driven tumor microenvironment

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Glioma cells response Interleukin-33 (IL-33) [microarray]

summary:
Determination of the molecular mechanism of IL33 on glioma cells
Since IL-33 is known to associate with chromatin and regulate transcriptional activity  and that nuclear expression of IL-33 increases glioma progression, we determined Nuclear IL-33 regulates the expression and secretion of inflammatory cytokines in glioma cells. Using these parameters 340 genes were induced by the ectopic expression of IL-33 and an additional 377 genes were downregulated. Gene ontology terms over-represented in the genes induced by IL-33 include three major clusters that associate with cytokine activity and inflammation

overall_design: We performed global gene expression analysis on 3 independent IL-33-ectopically-expressing glioma cell clones as compared to control (empty vector) cells.


title: A Point Mutation in the RNA Recognition Motif of CSTF2 Associated with Intellectual Disability in Humans Causes Defects in 3′ End Processing [RNA-seq]

status: Public on Aug 20 2020

city: Lubbock

first: Petar

last: Grozdanov

state: Texas

address: 3601 4th Street

department: Cell Biology and Biochemistry

institute: Texas Tech University Health Sciences Center

summary: CSTF2 encodes an RNA-binding protein that is essential for mRNA cleavage and polyadenylation (C/P). No disease-associated mutations have been described for this gene. Here, we report a mutation in the RNA recognition motif (RRM) of CSTF2 that changes an aspartic acid at position 50 to alanine (p.D50A), resulting in intellectual disability in male patients. In mice, this mutation was sufficient to alter polyadenylation sites in over 1,300 genes critical for brain development. Using a reporter gene assay, we demonstrated that C/P efficiency of CSTF2D50A was lower than wild type. To account for this, we determined that p.D50A changed locations of amino acid side chains altering RNA binding sites in the RRM. The changes modified the electrostatic potential of the RRM leading to a greater affinity for RNA. These results highlight the significance of 3' end mRNA processing in expression of genes important for brain plasticity and neuronal development.

overall_design: Total brain RNA from three wild type and five Cstf2 mutant mice at 50 days were subjected to RNA-seq using the Illumina protocol

middle: N

first: Clinton

last: MacDonald


title: A Point Mutation in the RNA Recognition Motif of CSTF2 Associated with Intellectual Disability in Humans Causes Defects in 3′ End Processing [3'prime-seq]

overall_design:
Total brain RNA from three wild type and five Cstf2 mutant mice at 50 days were subjected to RNA-seq using the Illumina protocol

Please note the column headers in the processed data files represent:
*_pA1 (polyadenylation site 1): the proximal cleavage and polyadenylation site, which is closer to the transcription start site in a gene.
*_pA2 (polyadenylation site 2):the distal cleavage and polyadenylation site, which is further to the transcription start site in a gene.
*_exon3 (3' most exon): the most distal cleavage and polyadenylation site in the 3' most exon.
*_UPS (upstream exon): the proximal cleavage and polyadenylation site, which is in an upstream (closer to the transcription start site) exon of the 3' most exon.
Use of one (exon3) or the other (UPS) cleavage and polyadenylation site often produces mRNAs that differ in their ORFs specifically in the carboxy-end of the protein.


title: Integrated Analysis of Small RNA, Transcriptome, and Degradome Sequencing Reveals the Water-Deficit and Heat Stress Response Network in Durum Wheat

city: Urrbrae

first: Haipei

last: Liu

state: South Australia

address: PMB1 Waite Building, School AFW

country: Australia

institute: The University of Adelaide

summary: Water-deficit and heat stress negatively impact crop production. Mechanisms underlying the response of durum wheat to such stresses are not well understood. With the new durum wheat genome assembly, we conducted the first multi-omics analysis with next-generation sequencing, providing a comprehensive description of the durum wheat small RNAome (sRNAome), mRNA transcriptome, and degradome. Single and combined water-deficit and heat stress were applied to stress-tolerant and -sensitive Australian genotypes to study their response at multiple time-points during reproduction. Analysis of 120 sRNA libraries identified 523 microRNAs (miRNAs), of which 55 were novel. Differentially expressed miRNAs (DEMs) were identified that had significantly altered expression subject to stress type, genotype, and time-point. Transcriptome sequencing identified 49,436 genes, with differentially expressed genes (DEGs) linked to processes associated with hormone homeostasis, photosynthesis, and signaling. With the first durum wheat degradome report, over 100,000 transcript target sites were characterized, and new miRNA-mRNA regulatory pairs were discovered. Integrated omics analysis identified key miRNA-mRNA modules (particularly, novel pairs of miRNAs and transcription factors) with antagonistic regulatory patterns subject to different stresses. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes)   enrichment analysis revealed significant roles in plant growth and stress adaptation. Our research provides novel and fundamental knowledge, at the whole-genome level, for transcriptional and post-transcriptional stress regulation in durum wheat.

overall_design: Analysis of small RNA transcriptome in 120 samples (2 genotypes × 4 treatments × 5 time-points × 3 biological replicates); Analysis of mRNA transcriptome in eight libraries (2 genotypes × 4 treatments × 1 time-point × 1 pool of 3 biological replicates); Analysis of mRNA degradome in eight libraries (2 genotypes × 4 treatments × 1 time-point × 1 pool of 3 biological replicates)

first: Amanda

last: Able

first: Jason

middle: A


title: Transcriptomic profiling in 3-month-old P23H Retinitis Pigmentosa mouse retinas

city: Irvine

first: Henri

last: Leinonen

state: California

address: 829 Health Sciences Rd

department: Ophthalmology

institute: University of California, Irvine

summary: Neuronal plasticity of the inner retina has been observed in response to photoreceptor degeneration. Typically, this phenomenon has been considered maladaptive and may preclude vision restoration in the blind. However, several recent studies utilizing triggered photoreceptor ablation have shown adaptive responses in bipolar cell dendrites expected to support normal vision. Whether such homeostatic plasticity occurs during progressive photoreceptor degenerative disease to help maintain normal visual behavior is unknown. We addressed these issues in an established mouse model of Retinitis Pigmentosa caused by the P23H mutation in rhodopsin. We show robust modulation of the retinal transcriptomic network reminiscent of the neurodevelopmental state as well as potentiation of rod – rod bipolar cell signaling following rod photoreceptor degeneration. Additionally, we found highly sensitive night vision in P23H mice even when more than half of the rod photoreceptors were lost. The results implicate retinal adaptation leading to persistent visual function during photoreceptor degenerative disease.

overall_design: Bulk retina mRNA profiling in heterozygous P23H rhodopsin mutated mice (n=4) and their wild-type littermates (n=3) at postnatal day 90

first: Frans

last: Vinberg


title: A Point Mutation in the RNA Recognition Motif of CSTF2 Associated with Intellectual Disability in Humans Causes Defects in 3′ End Processing

overall_design: Refer to individual Series


title: Transcriptomic analysis of PBMC, CD4 memory and CD8 memory T cells in Alzheimer's disease patients and age-matched controls

status: Public on Aug 19 2020

city: San Diego

first: Rekha

last: Dhanwani

state: CA

address: 9420 Athena Circle

institute: La Jolla Institure for Immunology

summary: Alzheimer’s disease (AD), a chronic multifactorial and complex neurodegenerative disorder is a leading cause of dementia. Recently, neuroinflammation has been hypothesized as a contributing factor to AD pathogenesis. The role of adaptive immune responses against neuronal antigens, which can either confer protection or induce damage in AD, has not been fully characterized. Here, we measured T cell responses to several potential antigens of neural origin including amyloid precursor protein (APP), amyloid beta (Ab), tau, a-synuclein, and transactive response DNA binding protein (TDP-43) in patients with AD and age-matched healthy controls (HC). Antigen-specific T cell reactivity was detected for all tested antigens, and response to tau-derived epitopes was particularly strong, but no significant differences between individuals with AD and age-matched HC were identified. Additionally, further characterization did not reveal any differences in the expression of genes between AD patients and HC. These observations have not identified a key role of neuronal antigen-specific T cell responses in AD.

overall_design:
PBMCs (HC n=28 and AD n=27), CD4 memory (HC n=28 and AD n=27) and CD8 memory (HC n=30 and AD n=26) T cells from AD and HC subjects were sorted and RNA was extracted.

**The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns.**

last: Dhawani

first: Alessandro

last: Sette

first: Cecilia

last: Lindestam Arlehamn


title: Next Generation Sequencing Facilitates Quantitative Analysis of control and MILIP Knockdown by siRNA in A549 human lung cancer cell line

city: Callaghan

first: Yuchen

last: Feng

state: NSW

address: Life science building, University Drive

institute: The university of Newcastle

summary: Enriched p53 signalling after MILIP knockdown was validated by RNA-seq; A c-myc reponsive lncRNA MILIP is commonly upregulated in diverse cancer types. RNA-seq  analysis of A549 cells following MILIP knockdown revealed that p53 signalling was the mostly enriched gene pathway, suggesting c-Myc may inactivate p53 through MILIP in cancer.

overall_design: For RNA-seq analysis of MILIP siRNA versus control siRNA, the A549 cells were transfected with siRNAs for 48 hours before harvesting.

first: Lei

last: Jin

first: Xu

middle: D


title: Genome-wide variation and transcriptional changes in diverse developmental processes underly the rapid evolution of seasonality

city: Dunedin

first: Eddy

last: Dowle

address: 270 Gt King St

department: Department of Anatomy

country: New Zealand

institute: University of Otago

summary: Here, we present the results of an integrative study that leverages naturally segregating variation and a recent, adaptive divergence event affecting seasonal timing to identify developmental mechanisms underlying diapause progression in a tephritid fly, Rhagoletis pomonella. Also called the apple maggot fly, R. pomonella is native to North America, where it infests fruits of native Crataegus (hawthorn) species throughout its range. Derived populations of the fly infest apples (Malus domesticus), and thus have evolved in the last ~250 years since apples were introduced. Many molecular studies in conjunction with mark-recapture experiments document that the populations, or host races, remain genetically distinct despite ongoing gene flow, making R. pomonella a textbook example of incipient speciation with gene flow and host associated divergence. Strong natural selection on two primary traits, host finding behavior and seasonal timing, maintain genetic divergence. Both populations (hereafter apple and haw flies) have one generation per year, with a functionally obligate pupal diapause, overwintering in the soil. Adults must emerge coincident with host fruit availability, typically a period of only a few weeks, in order to successfully oviposit into fruits. Apple flies have evolved an earlier (~3 week) emergence timing to synchronize with apples, which fruit about 3 weeks earlier than hawthorn at a typical, sympatric site in the Midwest (e.g., Michigan or Illinois, USA). We combined RNA sequencing (RNAseq), phenotyping of emergence timing and brain morphology, and whole genome pooled resequencing (Poolseq) to infer mechanisms underlying segregating variation for diapause phenology in each Rhagoletic pomonella host race, and the evolved difference in phenology between host races.

overall_design: Infested apple and hawthorn fruits were collected from Urbana, IL in the late summer and fall of 2014. Infested fruit were returned to the laboratory at the University of Florida, emerging larvae were collected and held at ~24C 14:10 LD for 10 days to complete pupation and enter diapause, then pupae were transferred to 3.5C at 95% Relative Humidity (RH). At monthly intervals from 2 to 6 months we dissected out the Central Nervous System (CNS), homogenized pools of 10 CNS, and extracted RNA (5 samples per time point per host). RNA sequencing libraries were prepared using Illumina’s tru-seq stranded mRNA kit and sequenced using 100bp single end Illumina HiSeq 2500. Cleaned reads were mapped to the R. zephyria genome using STAR, and read counts were generated using RSEM.

first: Edwina

first: Thomas

last: Powell

first: Peter

last: Meyers

first: McCall

middle: B

last: Calvert

first: K

middle: O

last: Walden

first: Hugh

last: Robertson

first: Stewart

middle: H

last: Berlocher

first: Jeffrey

last: Feder

first: Daniel

last: Hahn

first: Gregory

last: Ragland


title: Somatic Mutational Landscape of Wild Populus trichocarpa tree [ncRNA-seq]

first: Robert

last: Schmitz

summary: This research uses terminal branches from a wild poplar tree to track somatic genetic, epigenetic, and transcriptional changes. Using a multi-omics approach, we aim to identify and describe mutations which arise during the lifetime of a long-lived perennial plant.

overall_design: Eight terminal branches from either side of a split Populus trichocarpa tree (4 branches each side)

first: Brigitte

middle: T

last: Hofmeister


title: A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa

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


title: A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa [Bisulfite-Seq]

overall_design: Eight terminal branches from either side of a split wild Populus trichocarpa tree (4 branches each side)


title: A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa [RNA-Seq]


title: A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa [ATAC-Seq]

first: Zefu

last: Lu


title: Transcriptome analysis of mouse hearts infected with Trypanosoma cruzi: Differential modulation of gene expression by two strains

city: Belo Horizonte

first: Gloria Regina

last: Franco

state: Minas Gerais

address: Av. Pres. Antônio Carlos, 6627

department: Bioquimica e Imunologia

country: Brazil

institute: Universidade Federal de Minas Gerais

summary:
Purpose:  One important challenge in the field of Chagas disease research is to determine the main factors leading to the establishment of the parasite in some organs in the chronic stage, mainly the heart and/or digestive system. Our group previously showed that distinct strains of T. cruzi (JG and Col1.7G2) presented differential tissue distribution in the chronic stage in double-infected BALB/c mice. To investigate changes in the host triggered by the two distinct T. cruzi strains, we assessed the gene expression profile of BALB/c mouse hearts infected with either JG, Col1.7G2 or an equivalent mixture of both parasites during the initial phase of infection.

Results: We demonstrate a clear distinction in host gene expression modulation by both parasites. Col1.7G2 strongly activated Th1-polarized immune response genes, whereas JG showed minor immune response activation. Moreover, JG strongly impaired the expression of genes for ribosomal proteins and mitochondrial proteins related to the electron transport chain and the citric acid cycle. Interestingly, evaluation of gene expression in mice inoculated with the mixture of parasites showed expression profiles for both up- and downregulated genes, indicating the coexistence of both parasite strains in the heart during the acute phase.

Conclusions: We suggest that different strains of T. cruzi may be distinguished by their efficiency in activating the immune system, modulating host energy and reactive oxygen species production and impairing protein synthesis during early infection, which may be decisive in defining parasite persistence in specific organs.

overall_design: Processed mice heart from infected and non-infected with T. cruzi.

first: Tiago

last: Castro

first: Maria Cecilia

last: Canesso

first: Mariana

last: Boroni

first: Daniela

middle: F

last: Chame

last: Souza

first: Nayara

last: Toledo

first: Sergio

last: Pena

first: Carlos

last: Machado

first: Egler

last: Chiari

first: Andrea

last: Macedo

first: Gloria


title: Role of Gdpd3 in chronic myelogenous leukemia stem cells

status: Public on Aug 18 2020

city: Hiroshima

first: Kazuhito

last: Naka

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Research Institute for Radiation Biology and Medicine

institute: Hiroshima University

summary: We examined gene expression profiling in long-term chronic myelogenous leukemia (CML) stem cells isolated from Gdpd3+/+ and Gdpd3-/- CML mouse model by RNA sequence.

overall_design: RNA sequence was performed in triplicate RNA samples extracted from Gdpd3+/+ tet-CML-affected mice (22 males, 12 females) and Gdpd3-/- tet-CML-affected mice (5 male, 5 females).

first: Seong

last: Kim

first: Kyung

last: Yang


title: PAR-CLIP Semliki Forest virus capsid protein

status: Public on Aug 17 2020

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

summary: Using photoactivatable ribonucleoside crosslinking and biotinylated Cp retrieval, multiple binding sites on viral gRNA where identified.

overall_design: Vero-BirA cells were infected with SFV-Cp-mAVI for 1.5 h and treated with biotin and photoactivatable ribonucleoside 4-thiouridine (4SU). Cp-mAVI-biotin was retrieved form Total cellular lysates, purified Cellular Nucleocapsids (NC) and from purified Viral NC with Streptavidin beads, and crosslinked RNAs where further processed using the standard PAR-CLIP protocol

first: Rebecca

last: Brown

first: Dimitrios

middle: G

last: Anastasakis

first: Margaret

last: Kielian


title: Spatiotemporal resolved leaf angle establishment improves rice grain yield via controlling population density [miRNA-seq]

city: Wuhan

first: Chang

last: Liu

address: Shizishan Street

institute: Huazhong Agricultural University

summary: Leaf angle is mainly determined by the lamina joint (LJ), and contributes to ideal crop architecture for high yield. Here, we dissected five successive stages with distinct cytological features of LJs spanning organogenesis to leaf angle formation, and obtained the underlying stage-specific mRNAs and small RNAs, which well explained the cytological dynamics during LJ organogenesis and leaf angle plasticity. Combining the gene coexpression correlation with high-throughput promoter analysis, we identified a set of transcription factors determining the stage- and/or cytological structure-specific profiles. The functional studies of these TFs demonstrated that cytological dynamics determined leaf angle, and the knockout rice of these TFs with erect leaves significantly enhanced yield by maintaining the proper tiller number under dense planting. This work revealed the high-resolution mechanisms how the cytological dynamics of LJ determined the leaf erectness, and served as a valuable resource to remodel rice architecture for high yield via controlling population density.

overall_design: Small RNA profiles of rice lamina joint(LJ) and blade from the first complete leaf at 5 stage spanning organogenesis to leaf angle formation

first: Rona

last: Wang

first: Shiyong

last: Sun

first: Xuelu


title: Determination of dynamic changes in chromatin accessibility during cellular reprogramming [RNA-seq]

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: Understanding the heterogeneity of cellular reprogramming process at intermediate stages.

overall_design: Bulk mRNA-Seq libraries at D8 reprogramming cells which are sorted using CD13 and CD201 surface markers.

first: Q

last: Xing

first: C

last: EL Farram

first: H

last: Li

first: Y

last: Loh


title: Spatiotemporal resolved leaf angle establishment improves rice grain yield via controlling population density


title: METTL4 catalyzes m6Am methylation in U2 snRNA to regulate pre-mRNA splicing

city: Shenzhen

first: Wee Siong Sho

last: Goh

state: Guangdong

address: Shenzhen Bay Laboratory, No. 5, Kelian Road, Goh Lab, A1819, Guangming District

department: Institute of Molecular Physiology

institute: Shenzhen Bay Laboratory

summary: N6-methylation of 2’-O-methyladenosine (Am) in RNA occurs in eukaryotic cells to generate N6,2’-O-dimethyladenosine (m6Am). Identification of the methyltransferase responsible for m6Am catalysis has accelerated studies on the function of m6Am in RNA processing. While m6Am is generally found in the first transcribed nucleotide of mRNAs, the modification is also found internally within U2 snRNA. However, the writer required for catalyzing internal m6Am formation had remained elusive. By sequencing transcriptome-wide RNA methylation at single-base-resolution, we identified human METTL4 as the writer that directly methylates Am at U2 snRNA position 30 into m6Am. We found that METTL4 localizes to the nucleus and its conserved methyltransferase catalytic site is required for U2 snRNA methylation. By sequencing human cells with overexpressed Mettl4, we determined METTL4’s in vivo target RNA motif specificity. In the absence of Mettl4 in human cells, U2 snRNA lacks m6Am thereby affecting a subset of splicing events that exhibit specific features such as overall 3’ splice-site weakness with certain motif positions more affected than others. This study establishes that METTL4 methylation of U2 snRNA regulates splicing of specific pre-mRNA transcripts.

overall_design: UV crosslinking, immunoprecipitation and exonuclease treatment with anti-6mA antibodies was used to map m6A/m6Am in transcriptome-wide at single-base-resolution. RNA-seq was also performed using Scriptseq v2.

first: Wee

middle: S


title: Loss of Lysine-Specific Demethylase 1 (LSD1) Drives Aberrant Heterochromatin Formation in Neurospora crassa

city: Eugene

first: Eric

middle: U

last: Selker

state: OR

address: 1229 University of Oregon; 1318 Franklin Blvd.

department: Biology, Institute of Molecular Biology

institute: University of Oregon

summary: Both H3K9me3 and DNA methylation are subject to spreading mechanisms to effectively cover incipient chromatin across heterochromatin domains. Boundary elements and associated limiting factors are necessary to prevent heterochromatin from spreading into neighboring, gene-rich heterochromatin. LSD1 was identified to be one such factor, given previous studies in other models and high conservation throughout eukaryotes. This study identifies the LSD complex in Neurospora and characterizes the heterochromatin spreading defect in Neurospora crassa ∆lsd1 strains. We found ∆lsd1 strains to possess variable extents of excessive heterochromatin spreading, and that this is dependent on the presence of DNA methylation, unlike at canonical heterochromatin domains where loss of DNA methylation has no effect on the presence of other heterochromatin marks (H3K9me3 and HP1-binding). Our findings provide insight of LSD1 function in heterochromatin regulation.

overall_design:
Bisulfite-seq: We analyzed 5mC distribution in asexually propagated ∆lsd1 Neurospora strains, as determined by bisulfite treatment followed by whole genome sequencing.
ChIP-seq: We analyzed H3K4me3 in WT and ∆lsd1 strains as well as H3K9me3 in ∆lsd1;∆hda-1 and lsd1 cat null strains by chromatin immunoprecipitation. Strains were grown, crosslinked, lysed, modified nucleosomes were immunopurified, and associated DNA was sequenced.
RNA-seq: We analyzed gene expression changes in ∆lsd1 Neurospora crassa strains by poly-A+ mRNA-sequencing performed in duplicate. A wild type strain (N3752) serves as the reference strain (deposited in GSE82222: GSM2186738 and GSM2186742).

first: William

middle: K

last: Storck

first: Vincent

last: Bicocca

first: Shinji

last: Honda

first: Tereza

last: Ormsby


title: Bone morphogenetic protein 7 promotes resistance to immunotherapy

city: Dallas

first: Maria

last: Freitas-Cortez

address: 6000 Harry Hines Blvd

institute: UT Southwestern

summary: We previously generated a syngeneic preclinical model of NSCLC (p53R172HΔg/+KrasLA1/+) with acquired resistance to anti-PD1. In the current study, we investigated methylation differences in specific genomic regions comparing anti-PD1-resistant tumors (344SQR) with their parental-tumor counterparts (344SQP).

overall_design: DNA was isolated from 344SQP and 344SQR tumors treated with anti-PD1 for Reduced representation bisulfite sequencing (RRBS) analysis.

last: Cortez

first: Yue

last: Lu

first: Marcos

last: Estecio


title: Determination of dynamic changes in chromatin accessibility during cellular reprogramming [scRNA-seq 10x]

summary: Understanding the heterogeneity of cellular reprogramming process at a single-cell high resolution level.

overall_design: 10X Genomics Single-Cell mRNA-Seq libraries of cells undergoing cellular reprogramming at different time-points.

first: Qiaorui

last: EL Farran

first: G

last: Gautam

first: Hu

first: Yuin-Han


title: Spatiotemporal resolved leaf angle establishment improves rice grain yield via controlling population density [mRNA]

first: Chang

last: Liu

overall_design: mRNA profiles of rice lamina joint(LJ) and blade from the first complete leaf at 5 stage spanning organogenesis to leaf angle formation

first: Rona

last: Wang

first: Shiyong

last: Sun

first: Xuelu


title: Determination of dynamic changes in chromatin accessibility during cellular reprogramming [ChIP-seq]

first: Chadi

last: El Farran

overall_design: ChIP-Seq of FRA1 and TEAD4 in cells undergoing cellular reprogramming.

first: Q

middle: R

last: Xing

first: C

first: T

last: Warrier

first: Y

last: Chuah

first: H

last: Li


title: RNA-seq of WT liver with DEX, Zn and untreated controls

status: Public on Aug 15 2020

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: The cytokine TNF drives inflammatory diseases, e.g. Crohn disease. In a mouse model of TNF-induced systemic inflammatory response syndrome (SIRS), severe impact on intestinal epithelial cells (IECs) is observed. Zinc confers complete protection in this model. We found that zinc no longer protects in animals which lack glucocorticoids (GCs), or express mutant versions of their receptor GR in IECs, nor in mice which lack gut microbiota. RNA-seq studies in IECs showed that zinc caused reduction of expression of constitutive (STAT1-induced) interferon-stimulated response (ISRE) genes and Interferon Regulatory Factor (IRF) genes. Since some of these genes are involved in TNF-induced cell death in intestinal crypt Paneth cells, and since zinc has direct effects on the composition of the gut microbiota (such as several Staphylococcus species) and on TNF-induced Paneth cell death, we postulate a new zinc-related anti-inflammatory mechanism. Zinc modulates the gut microbiota, causing less induction of ISRE/IRF genes in crypt cells, less TNF-induced necroptosis in Paneth cells and less fatal evasion of gut bacteria into the system.

overall_design: Examination of changes in gene expresion in liver of mice after treatment with DEX, Zinc or DEX+Zinc and a control group  a total of 12 samples was sequenced in 4 conditions with 3 (biological) replicates/condition

first: Jolien

last: Souffriau

first: Tineke

last: Vanderhaeghen

first: Charlotte

last: Wallaeys

first: Kelly

last: Van Looveren

first: Lindsy

last: Aelbrecht

first: Sylviane

last: Dewaele

last: Vandewalle

first: Evy

last: Goossens

first: Serge

last: Verbanck

first: Filip

last: Boyen

first: Melanie

last: Eggermont

first: Lindsey

last: De Commer

first: Riet

last: De Rycke

first: Michiel

last: De Bruyne

first: Raul

last: Tito

first: Marlies

last: Ballegeer

first: Sofie

last: Vandevyver

first: Tiago

last: Velho

first: Luis

last: Moita

first: Tino

last: Hochepied

first: Karolien

last: De Bosscher

first: Jeroen

last: Raes

last: Van Immerseel

first: Rudi

last: Beyaert

first: Claude

last: Libert


title: Determination of dynamic changes in chromatin accessibility during cellular reprogramming [scRNA-seq]

first: Chadi

last: El Farran

overall_design: Single-Cell mRNA-Seq libraries of BDD2-C8-trated cells undergoing cellular reprogramming at day 8.

first: Q

last: Xing

first: C

last: EL Farran

middle: X

last: Toh

first: H

last: Li

first: Y

last: Loh


title: Structural basis for substrate recognition and chemical inhibition of oncogenic MAGE ubiquitin ligases

first: Lei

address: University of California, Irvine

summary: Testis-restricted melanoma antigen (MAGE) proteins are frequently hijacked in cancer and play a critical role in tumorigenesis. MAGEs assemble with E3 ubiquitin ligases and function as substrate adaptors that direct the ubiquitination of novel targets, including key tumor suppressors.  However, how MAGEs recognize their targets is unknown and has impeded development of MAGE-directed therapeutics. Here, we report the structural basis for substrate recognition by MAGE ubiquitin ligases. Biochemical analysis of the degron motif recognized by MAGE-A11 and the crystal structure of MAGE-A11 bound to the PCF11 substrate uncovered a conserved substrate binding cleft (SBC) in MAGEs. Mutation of the SBC disrupted substrate recognition by MAGEs and blocked MAGE-A11 oncogenic activity. A chemical screen for inhibitors of MAGE-A11:substrate interaction identified 4-aminoquniolines as potent inhibitors of MAGE-A11 that show selective cytotoxicity. These findings provide important insights into the large family of MAGE ubiquitin ligases and identify approaches for development of cancer-specific therapeutics.

overall_design: Examination of alternative polyadenylation and gene expression upon MAGEA11 wild-type or SBC mutant expression in DAOY cells.

first: SeungWook

last: Yang

first: Wei

first: Patrick

last: Potts


title: Determination of dynamic changes in chromatin accessibilty during cellular reprogramming [scATAC]

overall_design: 480 Single-Cell ATAC-Seq libraries of cells undergoing cellular reprogramming at different time-points.


title: Interferon-λ enhances the differentiation of naïve B-cells into plasmablasts via mTORC1 pathway

status: Public on Aug 14 2020

city: Clayton

first: Ferdinando

last: Bonfiglio

address: Rainforest Walk

institute: Monash University

summary: Type III interferon (IFN-λ) is known to be a potential immune modulator, but the mechanisms behind its immune-modulatory functions and its impact on plasmablast differentiation in humans, remain unknown. Human B-cells and their subtypes directly respond to IFN-λ. We performed B-cell transcriptome profiling to investigate the immune-modulatory role of IFN-λ in B-cells. We found that IFN-λ induced gene expression in B cells is steady, prolonged and importantly cell type-specific. Further, IFN-λ enhances the mTORC1 (mammalian/mechanistic target 34 of rapamycin complex 1) pathway in the B-cell receptor-activated B-cells (BCR/anti-IgM). The engagement of mTORC1 by BCR and IFN-lambda induces the cell cycle progress in B-cells. Subsequently, IFN-λ boosts the differentiation of naïve B-cells into plasmablast upon activation and the cells gain effector functions such as cytokine release (IL-6, IL-10) and antibody production. Our study shows how IFN-λ systematically boosts the differentiation of naïve B-cells into plasmablasts by enhancing the mTORC1 pathway and cell cycle progression in activated B-cells, which is a previously unknown immune modulatory role of IFN-λ.

overall_design: mRNA profiles of isolated B cells stimulated with IFN-lambda (4 donors) or IgM (6 donors) or with a combination of IgM and IFN lambda (6 donors). Unstimulated B-cells from 5 donors were used as control.

first: Mohammedyaseen

last: Syedbasha

first: Janina

last: Linnik

first: Claudia

last: Stuehler

first: Daniel

last: Wuethrich

first: Adrian

last: Egli


title: Transcriptome of Tribolium castaneum selection lines (control-, drought-, heat-, heat/drought-adapted) under different climatic conditions

city: Zurich

first: Frederic

middle: Francois

last: Guillaume

address: Winterthurerstrasse 190

department: Evolutionary Biology and Environmental Studies

country: Switzerland

institute: University of Zurich

summary: We studied plastic and evolutionary responses in gene expression of Tribolium castaneum after beetles’ exposure to new environments that differed from ancestral control conditions in temperature, humidity or both. Using experimental evolution with ten replicated lines per condition, we were able to demonstrate adaptation (higher offspring number compared to control lines) after 20 generations. We measured whole-transcriptome gene expression with RNA-seq to infer evolutionary and plastic changes. We found more evidence for changes in mean expression (shift in the intercept of reaction norms) in adapted lines than for changes in plasticity (shifts in slopes). Plasticity was mainly preserved in selected lines and was responsible for a large part of the phenotypic divergence in expression between ancestral and new conditions. However, we found that genes with the largest evolutionary changes in expression also evolved reduced plasticity and often showed expression levels closer to the ancestral stage. Results obtained in the three different conditions were similar, suggesting that restoration of ancestral expression levels during adaptation is a general evolutionary pattern. With a larger sample in the most stressful condition, we were able to detect a positive correlation between proportion of genes with reversion of the ancestral plastic response and mean fitness per selection line.

overall_design: We used the Tribolium castaneum Cro1 strain collected from a wild population in 2010 and adapted to lab standard conditions (33°C, 70% relative humidity) for more than 20 generations. Beetles were kept in 24h darkness on organic wheat flour mixed with 10% organic baker's yeast. We sterilized flour and yeast by heating them for 12h at 80°C before use. To test for adaptation to new environmental conditions we used replicate lines and exposed them to three treatments and Control conditions. The conditions in the treatments were: Dry : 33°C and 30% relative humidity; Hot : 37°C and 70% r. h.; Hot-Dry: 37°C and 30% r. h. To generate replicate lines, we used 120 individuals (60 females and 60 males in the pupal stage from our Cro1 stock population) and placed them into a vial containing 80g medium. After seven to ten days, in which the pupae became adults, mated and laid eggs, adult beetles were removed by sieving the medium. We waited until the next generation (eggs/larvae in the medium) had reached the pupal stage and again collected 120 pupae per line to establish the next generation. Selection lines could adapt to treatment conditions for 20 generations. Before testing for adaptation, all lines stayed for one generation in control condition. Sequenced individuals were transferred to the respective condition in the egg stage and developed completely in treatment conditions. We sequenced adult reproducing females from different replicate lines under different conditions (seven Control-lines, four Dry-lines, five Hot-lines, seven Hot-Dry lines). For each selection line we used individuals from control conditions as well as individuals from treatment conditions to infer evolutionary changes (difference between Control- and Dry/Hot/Hot-Dry lines within the same condition) and plastic changes (difference between individuals from the same selection line under control and treatment conditions).

first: Eva

middle: L

last: Koch

first: Frédéric


title: Determination of dynamic changes in chromatin accessibility during cellular reprogramming [10X D8 CD13]

first: Chadi

overall_design: 10X Genomics Single-Cell mRNA-Seq libraries of cells undergoing cellular reprogramming at D8 and sorted using CD13 antibody.

first: Q

first: P

last: Gautam

last: Chuah


title: RNA-seq of control shRNA and BHLHE40 shRNA HeLa-S3 cells

city: guangzhou

first: gongcheng

last: Hu

state: guangdong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: In this study, we investigated gene expression profile in HeLa-S3 cells transfected with control shRNA and BHLHE40 shRNA.

overall_design: Gene expression profiling in HeLa-S3 cells transfected with control shRNA and BHLHE40 shRNA. Each experiment was performed in 2 biological replicates.

first: Kaimeng

last: Huang

first: Gongcheng


title: Determination of dynamic changes in chromatin accessibility during cellular reprogramming [scRNA]

last: El Farran

overall_design: 480 Single-Cell mRNA-Seq libraries of cells undergoing cellular reprogramming at different time-points.

last: Xing

first: C

last: EL Farran

last: Toh

first: H

first: Y


title: CTCF HiChIP experiments in cells treatd with control shRNA or BHLHE40 shRNA

summary: In this study, we investigated CTCF mediated chromatin interactions by HiChIP experiment in control shRNA and BHLHE40-depleted HeLa-S3 cells.

overall_design: CTCF HiChIP experiments were performed in control shRNA or  BHLHE40-depleted HeLa-S3 cells.


title: Genome-wide maps of CTCF and BHLHe40 binding in HeLa-S3 cells

summary: In this study, we investigated CTCF and BHLHE40 binding in HeLa-S3 cells transfected with control shRNA and specific shRNA.

overall_design: Examination of factor binding sites in HeLa-S3 cells transfected with control shRNA and specific shRNA.

first: Yawei

last: Song


title: The C. elegans SET-2 histone methyltransferase maintains germline fate by preventing progressive transcriptomic deregulation across generations

city: Santa Cruz

first: Susan

last: Strome

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

summary: Chromatin factors contribute to germline maintenance by preserving a germline-appropriate transcriptional program. In the absence of the conserved histone H3 Lys4 (H3K4) methyltransferase SET-2, C. elegans germ cells progressively lose their identity over generations, leading to sterility. How this transgenerational loss of fertility results from the absence of SET-2 is unknown. Here we performed expression profiling across generations on germlines from mutant animals lacking SET-2 activity. We found that gene deregulation occurred in 2 steps: a priming step in early generations progressing to loss of fertility in later generations. By performing Within-Class Analysis (WCA), a derivative of Principal Component Analysis, we identified transcriptional signatures associated with SET-2 inactivation, both at the priming step and later on during loss of fertility. Further analysis showed that repression of germline genes, derepression of somatic programs, and X-chromosome desilencing through interference with PRC2-dependent repression, are priming events driving loss of germline identity in the absence of SET-2. Decreasing expression of identified priming genes, including the C/EBP homologue cebp-1 and TGF-b pathway components, was sufficient to delay the onset of sterility, suggesting that they individually contribute to the loss of germ cell fate. Altogether, our findings illustrate how the loss of a chromatin regulator at one generation can progressively deregulate multiple transcriptional and signaling programs, ultimately leading to loss of appropriate cell fate.

overall_design: Transcriptome profiles of 3 independent lineages of set-2(bn129) gonads. Each lineage contains fertile F2 set-2 gonads, fertile F4 set-2 gonads, and sterile F4 set-2 gonads. Three replicates of set-2/qC1 gonads serves as a control.

first: Valérie

middle: J

last: Robert

first: Andrew

last: Knutson

first: Andreas

last: Rechtsteiner

first: Gaël

last: Yvert

first: Francesca

last: Palladino


title: Copy Number of an Integron-Encoded Antibiotic Resistance Locus Regulates a Virulence and Opacity Switch in Acinetobacter baumannii AB5075

status: Public on Aug 13 2020

city: Atlanta

first: Gregory

last: Tharp

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: We describe a novel genetic mechanism  in which tandem amplification of a plasmid-borne integron regulates virulence, opacity variation, and global gene expression by altering levels of a putative small RNA (sRNA) in Acinetobacter baumannii AB5075.  Copy number of this amplified locus correlated with the rate of switching between virulent opaque (VIR-O) and avirulent translucent (AV-T) cells.  We found that prototypical VIR-O colonies, which exhibit high levels of switching and visible sectoring with AV-T cells by 24 h of growth, encode two copies of this locus.  However, a subset of opaque colonies that did not form AV-T sectors within 24 h were found to encode only one copy.  The colonies with decreased sectoring to AV-T were designated low-switching opaque (LSO) variants, and were found to exhibit a three-log decrease in switching relative to the VIR-O.  Overexpression studies revealed that the element regulating switching was localized to the 5’ end of the aadB gene within the amplified locus.  Northern blotting indicated that a sRNA of approximately 300 nt is encoded in this region, and is likely responsible for regulating switching to AV-T.  Copy number of the ~300 nt sRNA was also found to affect virulence, as the LSO variant exhibited decreased virulence during murine lung infections. Global transcriptional profiling revealed that over 100 genes were differentially expressed between VIR-O and LSO variants, suggesting that the ~300 nt sRNA may act as a global regulator.  Several virulence genes exhibited decreased expression in LSO cells, potentially explaining their decreased virulence.

overall_design: A. baumannii cultures representative of the LSO and VIR-O (control) subpopulations were grown to an OD of 0.5 in LB medium.  Gene expression was measured via RNA-sequencing for three biological replicates per sample.

first: Sarah

middle: E

last: Anderson

first: Chui

middle: Y

last: Chin

first: David

last: Weiss

first: Philip

middle: N

last: Rather


title: Genome-wide maps of  NFKB1/p50 binding dynamics

city: Chicago

first: Bakhtiar

last: Yamini

address: 900 E 57th St

department: Department of Surgery

institute: University of Chicago

summary: We report the application of ChIP-Seq for high-throughput profiling of NFKB1/p50 binding dynamics. The binding profiles were performed under three conditions/models.   We first examine the p50 binding in HEK293T cells during G1 and S phase. HEK293T cells were synchronized with double thymidine block method. Before and after release to S phase, ChIP was performed, and chromatin immunoprecipitated DNA was converted to libraries for sequencing with HiSeq 4000. We find that these NFKB1/p50 binding peaks in G1 phase dramatically reduced at S phase.   Then, we further examine the p50 binding in HEK293T/TopBP1 cells in response to tamoxifen treatment. These cells have stable expression of TopBP1 activation domain fusion with estrogen receptor. After treatment, chromatin immunoprecipitated DNA was converted to libraries for sequencing with HiSeq 4000. We find that these NFKB1/p50 binding peaks in vehicle control sample dramatically reduced after tamoxifen treatment.   Final, we compare the genome wide binding behavior of wild type p50 and mutant p50 2KR (K354R and K356R). HEK293T cells was transfected with plasmids expression HA-tagged wild type or mutation p50. Chromatin immunoprecipitated DNA was converted to libraries for sequencing with HiSeq 4000. We find that both wild type and p50 2KR mutant share similar binding profile.  However, in general, p50 mutant has less binding affinity to NFKB binding sites.   This study provides a preliminary but solid basis to our understanding of NFKB1/p50 binding dynamics.

overall_design: ChIp-Seq experiments were performed with specific antibodies under designed condtions, and library from HEK293T input was used for background correction.

first: Longtao

last: Wu


title: Deglycosylated azithromycin targets transgelin to enhance intestinal smooth muscle function

status: Public on Aug 12 2020

city: Tianjin

first: Cheng

last: Yang

address: No. 38 Tongyan road

institute: Nankai Universtiy

summary: Human intestinal smooth muscle cells (HISMCs) were collected from Deg-AZM-treated (20 μM, 24h) and control groups. Cells were incubated with Trizol (1 mL) at room temperature for 15 min. Microarray gene expression profiling was performed. R studio analysis tool was used to detect differentially expressed genes (DEGs) with |logFC| ≥ 2 as the cut-off criterion. The differentially expressed genes (DEGs) in the Deg-AZM-treated and control groups were enriched through GO analysis by using the GSEA software.

overall_design: The differentially expressed genes of HISMCs cells treated with DEG-AZM were analyzed


title: Upregulated Vav2 signaling promotes regenerative proliferation in squamous cell carcinoma

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

summary:
Stem cell-like regenerative proliferation and undifferentiation cause poor prognosis in squamous cell carcinoma (SCC). Despite this, the signaling events driving to those traits remain ill-characterized.
We report here that VAV2, an enzyme involved in RHO GTPase activation, becomes frequently upregulated in cutaneous and head-and-neck SCC, where it orchestrates a stem cell-like regenerative state.

overall_design: Dorsal skin of 6-8 week old WT (n = 3) and Vav2Onc (n = 3) mice

first: L

first: Mauricio

last: Menacho-Márquez

first: Salvatore

last: Fabbiano

first: Sonia

last: Rodríguez-Fdez

first: Javier

last: Robles-Valero

first: Gloria

last: Pascual

first: Juana

middle: M

last: García-Pedrero

first: Antonio

last: Abad

first: María

middle: C

last: García-Macías

first: Nazareno

last: González

first: Pablo

last: Menna

first: Miguel

middle: A

last: Pavón

first: Rogelio

last: González-Sarmiento

first: Jesús

last: Paramio

first: Juan

middle: P

last: Rodríguez-Tapia

first: Salvador

last: Benitah

first: Xosé

last: Bustelo


title: A Deep Learning Approach For Programmable RNA Switches

city: Boston

first: Alexander

last: Garruss

state: MA

address: 77 Avenue Louis Pasteur, Rm 238

institute: Harvard Medical School

summary: Engineered RNA elements are programmable tools capable of detecting small molecules, proteins, and nucleic acids. Predicting the behavior of these tools remains a challenge, a situation that could be addressed through enhanced pattern recognition from deep learning. Thus, we investigate Deep Neural Networks (DNN) to predict toehold switch function as a canonical riboswitch model in synthetic biology. To facilitate DNN training, we synthesized and characterized in vivo a dataset of 91,534 toehold switches spanning 23 viral genomes and 906 human transcription factors. DNNs trained on nucleotide sequences outperformed (R2=0.43-0.70) previous state-of-the-art thermodynamic and kinetic models (R2=0.04-0.15) and allowed for human-understandable attention-visualizations (VIS4Map) to identify success and failure modes. This deep learning approach constitutes a major step forward in engineering and understanding of RNA synthetic biology.

overall_design: Identification of RNA toehold switches that respond with high dynamic range to a cognate trigger sequence

first: Nico

last: Angenent-Mari

first: Luis

last: Soenksen

first: George

last: Church

first: James

last: Collins


title: Insulin-like growth factors alter the transcriptional identity of Th17 cells

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

summary: Th17s treated with insulin-like growth factors express higher levels of genes associated with activation, Th17 identity, peripheral maturation and effector function, while control Th17s are relatively enriched for genes associated with Treg identity and function.

overall_design: Sorted naive CD4+ T cells from Ifn-γ/Thy1.1 IL-17a/hCD2 Foxp3/GFP reporter mice were stimulated in Th17 conditions with or without 30ng/mL desIgf1. RNA was isolated from hCD2+ cells after 5 days.

first: Daniel

last: DiToro

first: Steven

last: Witte

first: Robin

last: Hatton

first: Casey

last: Weaver


title: “Reprogram enablement” as an assay for identifying pivotal early oncogenic pathways by their ability to allow neoplastic cells to reacquire a normal epiblast-emulating state: evidence from human thyroid cancer

city: Cleveland

first: Ryan

middle: C.

last: Gimple

state: OH

address: 10900 EUCLID AVENUE

institute: CASE WESTERN RESERVE UNIVERSITY

summary: One approach to understanding how tissue-specific cancers emerge is to determine the requirements for “reprograming” such neoplastic cells back to their developmentally-normal primordial premalignant epiblast-like pluripotent state and then scrutinizing their spontaneous reconversion to a neoplasm, perhaps rendering salient the earliest pivotal oncogenic pathway(s) (before other aberrations accumulate in the adult tumor). For the prototypical malignancy anaplastic thyroid carcinoma (ATC), we found that tonic RAS reduction was obligatory for reprogramming cancer cells to a normal epiblast-emulating cells, confirmed by changes in their transcriptomic and epigenetic profiles, loss of neoplastic behavior, and ability to derive normal somatic cells from their “epiblast organoids”. Without such suppression, ATCs re-emerged from the clones. Hence, for ATC, RAS inhibition was its “reprogram enablement” (RE) factor. Each cancer likely has its own RE factor; identifying it may illuminate premalignant risk markers, better classifications, therapeutic targets, and tissue- specification of a previously pluripotent, now neoplastic, cell.

overall_design:
5 samples were processed using RNAsequencing.
5 samples were processed using DNA methylation sequencing.

first: YANJUN

last: KONG

first: Rachael

last: McVicar

first: Andrew

last: Hodges

first: Jun

last: Yin

first: Weiwei

last: Zhan

first: Yang

last: Liu

first: Evan

last: Snyder


title: Genome Wide Effect of Tetracycline, Doxycycline and 4-epidoxycycline on gene expression in Saccharomyces cerevisiae

status: Public on Aug 11 2020

city: Middletown

first: Joseph

last: Coolon

state: CT

address: 52 Lawn Avenue

department: Biology

institute: Wesleyan University

summary: Investigating  Saccharomyces cerevisiae genome-wide gene expression response to tetracycline family chemicals.

overall_design: Saccharomyces cerevisiae were exposed to Tetracycline, Doxycycline or 4-epidoxycycline and gene expression responses were identified.

first: Guadalupe

last: Sanchez

first: Samuel

last: Linde

middle: D


title: Gene expression of human hepatocytes isolated from chimeric mice with humanized liver

status: Public on Aug 07 2020

city: Higashi-Hiroshima

first: Chise

last: Tateno

state: HIROSHIMA

address: 3-4-1, Kagamiyama

department: Dept of Reseach & Development

institute: PhoenixBio Co., Ltd

summary:
Chimeric mice with humanized livers are considered a useful animal model for predicting human drug metabolism and toxicity. In this study, the characteristics of fresh h-hepatocytes (cFHHs, PXB-cells®) isolated from chimeric mice (PXB-mice®) were evaluated in vitro to confirm their utility for drug development. The cFHHs cultured at high density (2.13 × 10^5 cells/cm2) displayed stable production of human albumin and cytochrome P450 (CYP) 3A activities for at least 21 days. The mRNA expression levels of 10 of 13 CYPs, UDP-glucuronosyltransferase (UGP), and transporters were maintained at >10% of the levels of freshly isolated cFHHs after 21 days. From 7-days cultured cFHHs at high density, many bile canaliculi were observed between cFHHs, and the accumulation of multidrug resistance-associated protein (MRP2) and bile salt export pump (BSEP) substrates in these bile canaliculi was clearly inhibited by cyclosporin A.
We used microarrays to elucidate global gene expressions underlying this higher hepatic functions of high density cultured cFHHs (PXB-cells). Microarray analysis revealed that high density cultured cFHHs maintained high expressions of some transcription factors (HNF4α, PXR, and FXR) perhaps involved in the high CYP, UGT and transporter gene expressions of cFHHs.

overall_design: To identify genes related with the characterization of the cFHHs, we carried out microarray analysis using Affymetrix technolgy with total RNA extracted from high density (2.13 × 10^5 cells/cm2) cultured cFHHs, low density (0.53 x 105 cells/cm2) cultured cFHHs (Day 7) and cFHHs without culture (Day 0) as a reference group.

first: Yuha

last: Kojima


title: RNA sequencing of WT, TP53KO and onco-RNF43/TP53KO human colon organoid lines.

status: Public on Aug 10 2020

city: Utrecht

first: Madelon

last: Maurice

state: Utrecht

address: Heidelberglaan 100

department: Cell Biology

country: Netherlands

institute: UMC Utrecht

summary: RNA sequencing of WT, TP53KO and onco-RNF43/TP53KO human colon organoid lines grown in full medium (high Wnt/Rspo (20%)) or medium without Wnt3a-low Rspo (0.2%).

overall_design: RNA sequencing was performed using human colon organoids grown in full medium or medium w/o Wnt3a-0.2% Rspo for 48h, in triplicate (rep1-3).

first: Maureen

last: Spit

first: Nicola

last: Fenderico

first: Ingrid

last: Jordens

first: Rik

middle: H

last: Lindeboom

first: Michiel

last: Vermeulen


title: Epigenomic profiling of H3K9me3 in the absence and presence of Periphilin variants

city: Lund

first: Christopher

last: Douse

address: Sölvegatan 17

department: Medicine

country: Sweden

institute: Lund University

summary: Targeted epigenomic profiling method CUT&RUN was used to examine PPHLN-regulated H3K9me3 deposition on chromatin.

overall_design: H3K9me3 in Hela cells expressing PPHLN variants.


title: STAT5 is a pioneer factor for BATF-mediated plasticity at the Il9 locus [ATAC-Seq]

city: Indianapolis

first: Mark

last: Kaplan

state: IN

address: 635 Barnhill Dr. MS 420

department: Microbiology and Immunology

country: USA

institute: Indiana University

summary: BATF requires the STAT5 signal to mediate plasticity at the Il9 locus.

overall_design: Chromatin accessibility in Th2,Th9 and Th17 cells

first: Yongyao

last: Fu


title: b-catenin Signaling Dynamics Regulate Cell Fate in Differentiating Neural Stem Cells

status: Public on Aug 08 2020

city: Philadelphia

first: Lukasz

last: Bugaj

state: PA

address: 390 Towne Building, 220 S. 33rd St

department: Bioengineering

institute: University of Pennsylvania

summary: Stem cells undergo differentiation in complex and dynamic environments wherein instructive signals fluctuate on various timescales. Thus, cells must be equipped to properly respond to the timing of signals, for example to distinguish sustained signaling from transient noise. However, how stem cells respond to dynamic variations in differentiation cues is not well characterized. Here, we use optogenetic activation of b-catenin signaling to probe the dynamic responses of differentiating adult neural stem cells (NSCs).  We discover that while elevated, sustained b-catenin activation sequentially promotes proliferation and differentiation, transient b-catenin induces apoptosis. Genetic perturbations revealed that the neurogenic/apoptotic fate-switch was mediated through cell cycle regulation by Growth Arrest and DNA Damage 45 gamma (Gadd45g). Our results thus reveal a role for b-catenin dynamics in NSC fate decisions and may suggest a novel role for signal timing to minimize cell fate errors, analogous to kinetic proofreading of stem cell differentiation.

overall_design: RNA profiles of adult rat neural stem cells subjected to Wnt/b-catenin stimulation over 3-5 days.  Stimulation was achieved using either CHIR99021 (3 mM), Wnt 3a (100 ng/mL), or optogenetics (optoWnt).  Stimulation was applied for one day and was subsequently withdrawn for days 2 and 3. Control conditions include cells that received no stimulation, or cells that received constant stimulation over 3-5 days.

first: Alyssa

middle: B

last: Rosenbloom

first: Marcin

last: Tarczyński

first: Nora

last: Lam

first: Ravi

middle: S

last: Kane

first: David

middle: V

last: Schaffer


title: STAT5 promotes accessibility and is required for BATF-mediated plasticity at the Il9 locus

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

overall_design: Refer to individual Series


title: Effect of HectD3 overexpression on gene expression in neonatal rat cardiomyocytes

status: Public on Aug 06 2020

city: Kiel

first: Ashraf

middle: Yusuf

last: Rangrez

address: Arnold-Heller Str. 3 (Haus 6)

institute: University Medical Center Kiel

summary: The present study focuses on the identification of the gene expression profile of neonatal rat cardiomyocytes (NRVCMs) after overexpressing HectD3, an E3 ligase, through Illumina RNA-sequencing.

overall_design: Illumina RNA-sequencing and subsequent bioinformatics analysis was performed commercially from Arraystar Inc. (Rockville, USA) on Illumina Hiseq 4000 platform. Briefly, mRNA expression profile was determined using RNA isolated from either control (LacZ overexpressing) or HectD3 overexpressing cardiomyocytes for 72 h using Illumina Hiseq 4000 platform. Each study group consisted four biological replicates. The generated RNA-seq data was exploited bioinformatically to compare mRNA profiles of individual samples as well as grouped samples to identify significantly deregulated candidates.

last: Yusuf Rangrez

first: Ankush

last: Borlepawar

first: Anushka

last: Deshpande

first: Norbert

last: Frey


title: STAT5 is a pioneer factor for BATF-mediated plasticity at the Il9 locus [ChIP-Seq]

overall_design: BATF binding in Th9 and Th17 cells.


title: Epigenomic profiling of TASOR in Hela cells using CUT&RUN and CUT&Tag

status: Public on Aug 05 2020

summary: Targeted epigenomic profiling methods CUT&RUN and CUT&Tag were used to examine TASOR genome binding and TASOR-regulated H3K9me3 deposition on chromatin.

overall_design: TASOR binding and H3K9me3 deposition in Hela cells.


title: RNA-Sequencing of salt-stressed watermelon seedlings

city: Uvalde

first: Vijay

last: Joshi

state: Texas

address: 1619 Garner Field Road

department: Department of Horticultural Sciences

institute: Texas A&M AgriLife Research

summary: Purpose: The goals of this study are to compare differentially expressed transcripts in seedlings of watermelon during salt stress using transcriptome profiling (RNA-seq)

overall_design: Methods: Leaf samples for RNA Seq analysis were collected from three independent plants at 7 hours after initiation of salt stress from control (CT2_1, CT2_2, CT2_3) and salt-stressed plants (TT2_1, TT2_2, TT2_3) were flash-frozen in liquid nitrogen for further analysis. Results: The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina Hiseq platform, and 150 bp paired-end reads were generated. Raw reads of fastq format were processed to obtain clean reads by removing the adapter, reads containing ploy-N, and low quality reads from raw data. At the same time, Q20, Q30, and GC content, the clean data were calculated. Watermelon reference genome (cultivar Charleston Gray) and gene model annotation files were downloaded from CuGenDB (http://cucurbitgenomics.org/). Index of the reference genome was built using Bowtie v2.2.3, and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. : HTSeq v0.6.1 was used to count the reads mapped to each gene. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from mapped read by featureCounts. Differential expression analysis of control and drought stressed conditions (three biological replicates per tissue per treatment) was performed using the DESeq R package (1.18.0) (Anders and Huber, 2010). Genes with P-value < 0.05 found by DESeq were assigned as differentially expressed.


title: scRNA-seq of mouse colon after THC administration

city: Columbia

first: William

middle: James

last: Becker

state: South Carolina

address: 6439 Garners Ferry Rd.

department: Pathology, Microbiology, and Immunology

institute: University of South Carolina School of Medicine

summary: We studied the effects of delta-9-tetrhydrocannabinol (THC) on mouse colon cells, 24 hours after a single administration of THC (10mg/kg) or Vehicle (VEH) control.

overall_design: 2 samples were analyzed from WT mice. The WV is the vehicle control, and the WT is the experimental group that received THC.

first: Prakash

last: Nagarkatti

first: Mitzi


title: Authentication of Hippuristanol-eIF4A1 Target Engagement Facilitates Identification of eIF4A1 Helicase Dependencies within 5’ Leader Regions

city: Montreal

first: Jerry

last: Pelletier

state: Quebec

address: McIntyre Medical Sciences Building 3655 promenade Sir-William-Osler

department: Biochemistry

institute: McGill university

summary: Hippuristanol (Hipp) is a natural product that selectively inhibits protein synthesis by targeting eukaryotic initiation factor (eIF) 4A, a DEAD-box RNA helicase required for ribosome recruitmentt o mRNA templates. Using a CRISPR/Cas9-based variomics screen, we identify functional eIF4A1 Hipp-resistant alleles, which in turn allow us to link the translation-inhibitory and cytotoxic properties of Hipp to eIF4A1 target-engagement. Genome-wide translational profiling in the absence or presence of Hipp (~EC50) were undertaken and our validation studies provided insight into structure-activity relationships of eIF4A-dependent mRNAs.

overall_design: Ribosome Profiling and RNA-Sequencing of DMSO and Hippuristanol treated HAP1 cells.

first: Jutta

last: Steinberger

first: Leo

last: Shen

first: Stephen

last: Kiniry

first: Sai

middle: K

last: Naineni

first: Regina

last: Cencic

first: Mehdi

last: Amiri

first: Sarah

last: Aboushawareb

first: Jennifer

last: Chu

first: Rayelle

middle: I

last: Maïga

first: Brahm

last: Yachnin

first: Francis

last: Robert

first: Nahum

last: Sonenberg

first: Pavel

last: Baranov


title: Metabolic and transcriptome responses of RNAi-mediated AMPKα knockdown in Tribolium castaneum

status: Public on Aug 04 2020

city: Yangzhou

first: Heng

last: Jiang

state: Jiangsu

address: 88 University South Road

institute: Yangzhou University

summary: Background: The AMP-activated protein kinase (AMPK) is an intracellular fuel sensor for lipid and glucose metabolism. In addition to the short-term regulation of metabolic enzymes by phosphorylation, AMPK may also exert long-term effects on the transcription of downstream genes through the regulation of transcription factors and coactivators. In this study, RNA interference (RNAi) was conducted to investigate the effects of knockdown of TcAMPKα on lipid and carbohydrate metabolism in the red flour beetle, Tribolium castaneum, and the transcriptome profiles of dsTcAMPKα-injected and dsEGFP-injected beetles under normal conditions were compared by RNA-sequencing.  Results: RNAi-mediated suppression of TcAMPKα increased whole-body triglyceride (TG) level and the ratio between glucose and trehalose, as was confirmed by in vivo treatment with the AMPK-activating compound, 5-Aminoimidazole-4-carboxamide1-β-D-ribofuranoside (AICAR). A total of 1184 differentially expressed genes (DEGs) were identified between dsTcAMPKα-injected and dsEGFP-injected beetles. These include genes involved in lipid and carbohydrate metabolism as well as insulin/insulin-like growth factor signaling (IIS). Real-time quantitative polymerase chain reaction analysis confirmed the differential expression of selected genes. Interestingly, metabolism-related transcription factors such as sterol regulatory element-binding protein 1 (SREBP1) and carbohydrate response element-binding protein (ChREBP) were also significantly upregulated in dsTcAMPKα-injected beetles.  Conclusions: AMPK plays a critical role in the regulation of beetle metabolism. The findings of DEGs involved in lipid and carbohydrate metabolism provide valuable insight into the role of AMPK signaling in the transcriptional regulation of insect metabolism.

overall_design: Total mRNA profiles of 20-day old dsEGFP-injected and dsTcAMPKα-injected larvae were generated by transcriptome sequencing under normal conditions with three replicates.

last: Zhang

first: Caihong

last: Ji

first: Xiangkun

last: Meng

first: Kun

last: Qian

first: Yang

last: Zheng

first: Jianjun

last: Wang


title: Single-cell RNA sequencing of Cd45+ adventitial cells from mice at steady state or treated with AngiotensinII

city: Munich

first: Dena

last: Esfandyari

state: Bavaria

address: Haus 607, Biedersteiner Str. 29, IPT

department: Institute of Pharmacology and Toxicology

institute: Technical University of Munich

summary: Here we show, that arterial macrophages derive predominantly from YS EMPs, which give rise to a transcriptionally distinct cluster of macrophages with mainly homeostatic and anti-inflammatory properties in steady state as well as in response to AngII inflammation. In adult mice, these EMP-derived macrophages persist for long periods of time, but decreas in absolute numbers in senescence without compensation by BM-derived progenitors. EMP-derived macrophages expressed high levels of homeostatic genes such as Lyve-1, which links them to physiological functions in arteries.

overall_design: Examination of adventitial immune cells in RankCreRosa26eYFP in two conditions (steady state and AnII-induced inflammation)

first: Tobias

last: Weinberger

first: Stefan

last: Engelhardt

first: Christian

last: Schulz


title: The Transcriptomic Signature of Tigecycline in Acinetobacter baumannii

status: Public on Aug 03 2020

city: North Ryde

first: Liping

last: Li

state: Now South Walse

address: 14 Eastern Road

department: Department of Molecular Sciences

institute: Macquarie University

summary:
Tigecycline, a protein translation inhibitor, is a treatment of last resort for infections caused by the opportunistic multidrug resistant human pathogen Acinetobacter baumannii. However, strains resistant to tigecycline were reported not long after its clinical introduction. Translation inhibitor antibiotics perturb ribosome function and induce the reduction of (p)ppGpp, an alarmone involved in the stringent response that negatively modulates ribosome production. Through RNA sequencing, this study revealed a significant reduction in the transcription of genes in citric acid cycle and cell
respiration, suggesting tigecycline inhibits or slows down bacterial growth. Our results indicated that the drug-induced reduction of (p)ppGpp level promoted the production but diminished the degradation of ribosomes, which mitigates the translational inhibition effect by tigecycline. The reduction of (p)ppGpp also led to a decrease of transcription coupled nucleotide excision repair which likely increases the chances of development
of tigecycline resistant mutants. Increased expression of genes linked to horizontal gene transfer were also observed. The most upregulated gene, rtcB, involving in RNA repair, is either a direct tigecycline stress response or is in response to the transcription de-repression of a toxin-antitoxin system. The most down-regulated genes encode two b-lactamases, which is a possible by-product of tigecycline-induced reduction in transcription of genes associated with peptidoglycan biogenesis. This transcriptomics study provides a global genetic view of why A. baumannii is able to rapidly develop
tigecycline resistance.

overall_design: The transcriptomes of tigecycline-treated and non-treated of an A. baumannii strain (global clonal lineage I) were compared. The cells were grown to exponential phase, then the culture was splited into two, one with tigecycline treatment at 1/2 MIC and the other without. After this, the cultures were further grew for 30 minutes at 37 degree with shaking, and then the total RNA was extracted. Three biological replicates were prepared, which resulted into 6 total RNA samples.

first: Karl

last: Hassan

first: Sasha

middle: G

last: Tetu

first: Varsha

last: Naidu

first: Alaska

last: Pokhrel

first: Amy

last: Cain

first: Ian

middle: T

last: Paulsen


title: Modelling of H3K4me3 histone modification data identifies signalling molecules that improve cell maintenance and conversion

city: Singapore

first: Uma Sangumathi

last: Kamaraj

state: singapore

address: 8 college road

department: CVMD

institute: Duke NUS

summary: RNA-seq data from H9 ESC, primary astrocyte and at different time-points (day 7, 14 and 21) during astrocyte differentiation and at conditions with control Matrigel and all ligands predicted by EpiMogrify.

overall_design: Total RNAs were isolated and processed from 27 samples (H9 ESC, primary astrocytes and cells from day 7, 14 and 21 during astrocyte differentiation)

first: Uma

first: Joseph

last: Chen

first: Khairunnisa

last: Katwadi

first: Lusy

last: Handoko

first: Jose

last: Polo

first: Enrico

last: Petretto

first: Owen

middle: J

last: Rackham


title: The precursor of PI(3,4,5)P3 alleviates aging by activating daf-18(Pten) and independent of daf-16

city: Shanghai

first: Xian

last: Xia

address: Yueyang Street

institute: PICB, CAS

summary: Aging is characterized by the loss of homeostasis and the general decline of physiological functions, accompanied by various degenerative diseases and higher rates of mortality. Anti-aging targeted small molecule screens have been carried outperformed many times, however, few have focused on endogenous metabolic intermediates—metabolites. Here, using C. elegans lifespan assays, we conducted a worm metabolite screen and identified an conserved metabolite through eEukaryotes-conserved metabolite, myo-inositol (MI), to extend lifespan, increase mobility and reduce fat content. Genetic analysis of enzymes in MI metabolic pathway suggestsed that MI alleviates aging through its derivative PI(4,5)P2. MI and PI(4,5)P2 are precursors of PI(3,4,5)P3, which is negatively related to longevity. However, the mechanism study shows itslongevity effects could be fully blocked by a null-allele mutation of the tumor suppressor gene, daf-18 (homologous to mouse Pten), areand was independent of its classical pathway downstream elements, akt or daf-16., but  Instead, we found MI effects on aging were dependent on its downstream mitophagy regulator pink-1. MI’s anti-aging effect is was also conserved in mouse model, implicatingindicating a conserved mechanism in mammals that may extend to human.

sample_organism:
Caenorhabditis elegans
Mus musculus

platform_organism:
Caenorhabditis elegans
Mus musculus

overall_design: Myo-inositol (MI) was used in both worm and mouse.   For worm experiment, 50mM MI was used from adult day 1. Two strains were used in worm experiment, N2 and daf-18-null-allele (ok480). Sample on N2 without any treatment on adult day 4 was also collected. All the other samples were collected on adult day 10.  For mouse experiment, female C57BL/6J mice were treated with 580 mg MI per kg bodyweight by gavage, twice per week, from 9 months of age to 12 months. Muscle tissue were used for RNA extraction and sequencing. 3-month-old mice were also used as young control samples. All the other samples were collected in 12-month-old mice.

first: Dawei

last: Shi

first: Aoyuan

last: Cui

first: Jing-Dong

last: Han


title: Genome-wide profilings of EDM2-mediated effects on H3K9me2 and transcripts in Arabidopsis thaliana

city: Riverside

first: Xueqing

middle: Maggie

last: Lu

state: CA

address: 3401 Watkins Drive, Genomics, Room 2126

institute: University of California, Riverside

summary: EDM2 is a PHD finger-containing histone binding protein in Arabidopsis thaliana (Arabidopsis) that affects levels of the transposon silencing mark H3K9me2. Here we report on genome-wide profiling by ChIP-seq and RNA-seq of EDM2-mediated effects on H3K9me2 and rRNA-depleted transcripts, respectively. EDM2 affects H3K9me2 and/or transcript levels at hundreds transposons and over 3000 gene loci including 60 NLR genes. In addition, EDM2 also binds to several NLR genes and transposons.

overall_design: H3K9me2 ChIP-seq and rRNA depletion expression profiling in edm2 and wild-type (WT) Col-0; EDM2 binding site identificaion by HA-tagged ChIP-seq for E2pro:HA-E2c line and Col-0

first: Yan

last: Lai

middle: M

first: Karine

last: Le Roche

first: Thomas

last: Eulgem


title: Single cell RNA-seq of mouse NK cells in the blood and the brain after intracerebral hemorrhage

city: Tianjin

first: Qiang

last: Liu

state: Tianjin

address: No.154 Anshan Road, Heping District

department: Neurology

institute: Tianjin Medical University General Hospital

summary: We used single cell RNA-seq technology to find the phenotype and function alteration of NK in C57BL/6 mice after ICH.

overall_design: Single cell suspension was prepared from pooled mouse blood and brain tissues at 12 h after ICH induced by autologous blood injection or sham-operations.

first: Zhiguo

last: Yao