title: Amino acid misincorporation promotes mRNA instability

city: Lexington

first: John

middle: Kyle

last: Friend

state: VA

address: A427 Science Addition, 204 W Washington St

department: Chemistry and Biochemistry

institute: Washington and Lee University

summary: Messenger RNA (mRNA) translation can lead to higher rates of mRNA decay, suggesting a role for the ribosome in mRNA destruction. Furthermore, features of an mRNA, such as codon identities, that are directly probed by the ribosome also correlate with mRNA decay rates. Specifically, many amino acids are encoded by synonymous codons, and some synonymous codons are decoded by more abundant tRNAs leading to more optimal translation and increased mRNA stability. In addition to different translation rates, the presence of individual codons can lead to higher or lower rates of amino acid misincorporation which could potentially lead to protein misfolding if an individual amino acid makes many critical contacts in a structure. Here, we directly test whether amino acid misincorporation affects mRNA stability, taking advantage of an aminoglycoside antibiotic (G418) which promotes higher error rates in the ribosome. We observe that G418 decreases firefly luciferase mRNA stability in an in vitro system, and we similarly observe that G418 reduces mRNA stability in mouse embryonic stem cells (mESCs). G418-sensitive mRNAs are enriched for suboptimal hydrophobic amino acid codons as well as other codons that are known to result in higher rates of amino acid misincorporation. Since protein folding is highly sensitive to the identity of hydrophobic amino acids, these results strongly suggest that defects in protein folding are linked to mRNA decay.

overall_design: Measurement of RNA half-lives in mouse embryonic stem cells treated with different translation inhibitors.

first: Y

last: Durmaz

first: A

last: Shatadal

first: K


title: Transcriptional profiling

status: Public on Mar 01 2022

city: AMSTERDAM

first: Kevin

last: Kos

email: k.kos@nki.nl, k.d.visser@nki.nl

state: NOORD-HOLLAND

address: PLESMANLAAN 121

department: Immunology

country: Netherlands

institute: Netherlands Cancer Institute

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptional profiling of WT Tregs and Tregs sorted from K14cre;Cdh1F/F;Trp53F/F mice bearing 225mm2  mammary tumors from blood, spleen, lungs, TDLNs, tumor and healthy mammary gland [Treg]

summary: We studied the impact of mammary tumorigenesis on Tregs in tumors and distant organs (CD3+CD4+CD25+). Here we generated RNAseq data from sorted Tregs  (CD3+CD4+CD25+) from WT and K14cre;Cdh1F/F;Trp53F/F mice bearing 225mm2  mammary tumors from blood, spleen, lungs, TDLNs, tumor and healthy mammary gland

overall_design: In this study, gene expression profiles of Tregs sorted from K14cre;Cdh1F/F;Trp53F/F mice bearing 225mm2  mammary tumors, or non-tumor bearing WT littermates from blood, spleen, lungs, TDLNs, tumor and healthy mammary gland were analysed by RNAsequencing. Each WT sample is a sorted pool of n=3 WT mice. We generated 3 biological replicates for spleen/lung/blood/tumor/TDLN, and 4 for healthy mammary gland. Samples were grouped according to tissue and tumor status. Comparisons were made between Tregs derived from KEP and WT mice.

first: Muhammad

middle: A

last: Aslam

first: Max

middle: D

last: Wellenstein

first: Wietske

middle: C

last: Pieters

first: Antoinette

last: Weverwijk

first: Kim

last: Vrijland

first: Lisanne

last: Raeven

first: Sergio

last: Quezada

first: Rudy

last: Beyaert

first: Heinz

last: Jacobs

first: Karin

middle: E

last: de Visser


title: Age-associated decline of MondoA drives cellular senescence through impaired autophagy and mitochondrial homeostasis

city: Suita

first: Ryuya

last: Edahiro

country: Japan

institute: Osaka University

summary: Accumulation of senescent cells affects organismal aging and the prevalence of age-associated disease. Emerging evidence suggests that activation of autophagy protects against age-associated diseases and promotes longevity, but the roles and regulatory mechanisms of autophagy in cellular senescence are not well understood. Here we identified the transcription factor, MondoA, as a novel regulator of cellular senescence, autophagy and mitochondrial homeostasis. MondoA protected against cellular senescence by activating autophagy partly through the suppression of an autophagy negative regulator, Rubicon. In addition, we identified peroxiredoxin 3 (Prdx3) as another downstream regulator of MondoA essential for mitochondrial homeostasis and autophagy. Rubicon and Prdx3 worked independently to regulate senescence. Furthermore, we found that MondoA knockout mice had exacerbated senescence during ischemic acute kidney injury (AKI), and a decrease of MondoA in the nucleus was correlated with human aging and ischemic AKI. Our results suggest that retaining MondoA activity protects from senescence and age-associated disease.

overall_design: MondoA or Mlx knockdown treated with or without doxorubicin (DXR) in RPE-1 cells

first: Hitomi

last: Yamamoto-Imoto

first: Shuhei

last: Nakamura

first: Tamotsu

last: Yoshimori


title: RNA sequencing microglia depletion model

city: Zurich

first: Sina-Maria

last: Schalbetter

address: Winterthurerstrasse 260

country: Switzerland

institute: Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse

summary: We developed an experimental model system in mice, in which microglia can be depleted selectively and temporarily from the prefrontal cortex (PFC) during a defined window of adolescence (6 weeks of age). This was achieved using a single, bilateral stereotaxic intra-PFC injection of clodronate disodium salt (CDS), which induces selective apoptosis of microglia. To  ascertain the cellular selectivity of intra-PFC administration of CDS, we conducted next-generation RNA sequencing (RNAseq) of bulk medial PFC tissue from CDS- or phosphate buffered saline (PBS)-injected mice. PFC samples were extracted either during the peak of microglia depletion, that is, 5 days post injection (5 dpi) or in adulthood (12 weeks of age) after full microglia repopulation.

overall_design: Next-generation RNA sequencing of mouse medial prefrontal cortex samples a) in adolescence (6 weeks of age), 5 days after intra-PFC PBS or CDS injection and b) in adulthood (12 weeks of age), 6 weeks after intra-PFC PBS or CDS injection.

first: Sina

middle: M

first: Anina

middle: S

last: von Arx

first: Natalia

last: Cruz-Ochoa

first: Kara

last: Dawson

first: Andranik

last: Ivanov

first: Flavia

last: Mueller

first: Han-Yu

last: Lin

first: René

last: Amport

first: Wiebke

last: Mildenberger

first: Daniele

last: Mattei

first: Dieter

last: Beule

first: Csaba

last: Földy

first: Melanie

last: Greter

first: Tina

last: Notter

first: Urs

last: Meyer


title: USP25 promotes pathological HIF-1-driven metabolic reprogramming and is a therapeutic target in pancreatic cancer

city: London

first: Jessica

last: Nelson

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: Deubiquitylating enzymes (DUBs) play an essential role in targeted protein degradation and represent an emerging therapeutic paradigm in cancer. However, their therapeutic potential in pancreatic ductal adenocarcinoma (PDAC) has not been explored. Here, we developed a DUB discovery pipeline, combining activity-based proteomics with a loss-of-function genetic screen in patient-derived PDAC organoids and murine genetic models. This approach identified USP25 as a master regulator of PDAC growth and maintenance. Genetic and pharmacological USP25 inhibition resulted in potent growth impairment in PDAC organoids, while normal pancreatic organoids were insensitive, and caused dramatic regression of patient-derived xenografts. Mechanistically, USP25 deubiquitinated and stabilised the HIF-1a transcription factor. PDAC is characterised by a severely hypoxic microenvironment, and USP25 depletion abrogated HIF-1a transcriptional activity and impaired glycolysis, inducing PDAC cell death in the tumor hypoxic core. Thus, the USP25/HIF-1a axis is an essential mechanism of metabolic reprogramming and survival in PDAC, which can be therapeutically exploited.

overall_design: Murine PDAC organoids were derived from primary PDAC tumors from KPCY mice (KPCY mice: Pdx1-Cre; LSL-KrasG12D; Trp53flox/flox; Rosa26-LSL-YFP). Organoids were grown as 3D cultures, in Matrix gel with defined stem cell medium. Organoids were transduced with lentiviruses containing shRNAs targeting either Usp25 or the YFP reporter as a control. Post-transduction, organoids recovered for 72hrs and selected with puromycin for 30 hours prior to analysis.

first: Axel

last: Behrens


title: A Rapid Translational Immune Response Program in CD8 Memory T Lymphocytes

first: Gunnar

last: Rätsch

state: -None-

address: Universitatstrasse 6

department: Institute for Machine Learning

institute: ETH Zürich

summary: Abstract: Immune cell activation is a very rapid and concerted cellular response that requires coordination between cellular processes that occur in different compartments and on very different time scales. Here, we use ribosome profiling and deep RNA sequencing to define the acute mRNA translation changes that follow initial signaling events and enable subsequent events of T cell activation and expansion.  Briefly, early events in the activation of antigen experienced CD 8 T cells are insensitive to transcriptional blockade with actinomycin, and instead depend on the translation of pre-existing mRNAs and blocked by cycloheximide. Ribosome profiling identifies ~92 mRNAs that are recruited into ribosomes following CD8 T cell stimulation. These mRNAs typically have structured GC and pyrimidine rich 5’UTRs and they encode key regulators of T cell activation and proliferation such as Notch1, Ifngr1, Il2rb, serine metabolism enzymes Psat1 and Shmt2, and translation factors eEF1a1 and eEF2. The increased production of receptors of IL2 and IFNγ precedes the activation of gene expression and augments cellular signals and T cell activation. Together, we identify the early RNA translation program that acts in a feed-forward manner to enable the rapid and dramatic process of CD8 T cell expansion and activation.

overall_design: mRNA and Ribosome footprints of CD8 memory T cells before and after  two hours after CD3/CD28 stimulation

first: Darin

last: Salloum

first: Natalie

middle: R

last: Davidson

first: Linlin

last: Cao

first: David

last: Kuo

first: Viraj

last: Sanghvi

first: Man

last: Jiang

first: Agnes

last: Viale

last: Raetsch

first: Hans-Guido

last: Wendel


title: Transcriptome analysis of piperonylic acid-treated tomato root and shoot tissues

city: Ghent

first: Willem

last: Desmedt

address: Valentin Vaerwyckweg 1

department: Plants and Crops

country: Belgium

institute: Ghent University

summary: We used mRNA sequencing to study the effects of piperonylic acid treatment on the transcriptome of tomato plants (cv. Moneymaker) to gain insights in the molecular basis of piperonylic acid-induced disease resistance

overall_design: mRNA sequencing of tomato seedlings (harvested 15 days after transplantation, treated with piperonylic acid or a mock treatment 7 and 14 days post transplantation)

last: Kyndt


title: Genome-wide maps in MDA-MB-231 cells treated with or without CPUL119(4.5 μM), CPUL129(1.8 μM), CPUL149(0.9 μM)

city: NANJING

first: yue

last: yang

address: 639 LONGMIAN AVENUE

country: China

institute: china pharmaceutical university

summary: Analysis of MDA-MB-231 cells following  CPUL119, CPUL129, CPUL149 treatment or not. CPUL119, CPUL129, CPUL149 regulates various mRNA expression in MDA-MB-231 cells.Results provide insight into the role of mRNAs-involved mechanisms underlying CPUL119-, CPUL129-, CPUL149-mediated effects on breast cancer stemness.

overall_design: MRNA profiles of MDA-MB-231 cells treated with or without CPUL119, CPUL129, CPUL149 were generated by deep sequencing, in two repeats, using Illumina GAIIx.

first: Lufeng

last: Zheng

first: Tao

last: Xi


title: Targeting Type I arginine methyltransferase PRMT1 promotes the T cell mediated antitumor immune response

city: Collegeville

first: Satyajit

last: Rajapurkar

state: PA

address: 1250S. Collegeville Rd.

country: USA

institute: GlaxoSmithKline LLC

summary: Type I protein arginine methyltransferases (PRMTs) have been implicated in human cancers and a Type I PRMT inhibitor, GSK3368715, has recently entered clinical trials in solid and hematological malignancies. In cancer cell lines, Type I PRMT inhibitors induce an interferon gene signature, amplified responses to interferon and innate immune signaling pathways, and decreased expression of the immunosuppressive cytokine VEGFA. In immunocompetent mouse tumor models, Type I PRMT inhibition increased T cell infiltration, produced durable responses dependent on CD8 T cells and enhanced efficacy of anti-PD1, including a model of T cell exclusion, representing a common mechanism of PD1 resistance in humans. These data suggest Type I PRMT inhibition can potentiate an anti-tumor immunity in refractory settings.

overall_design: Paired end sequenced RNA-seq data from 10 Non-small cell lung cancer cell lines. All cell lines listed here have been sequenced with 2 replicates, containing GSK3368712 (treated) and control (DMSO) samples.

first: Andy

last: Fedoriw


title: Combinatorial targeting of MYC/BCL2 double-hit lymphoma with mitochondrial complex I and BCL2 inhibitors

city: Milan

first: Marco

last: Filipuzzi

address: Via Giuseppe Ripamonti, 435

country: Italy

institute: IEO

summary: Activation of the MYC oncogene is common in B-cell lymphomas, and frequently associated with compensatory events that dampen Myc-induced apoptosis, such as over-expression of anti-apoptotic Bcl2-family proteins. For example, concurrent translocations of MYC and BCL2 in a subset of Diffuse large B-cell lymphoma (DLBCL) lead to the high-grade “double-hit” lymphoma subtype (DHL), characterized by dismal prognosis in the face of current front-line regimens, thus calling for the pursuit of tailored therapeutic strategies. Here, we show that Myc and Bcl2 modulate the sensitivity of B-cells to IACS-010759, a selective inhibitor of mitochondrial respiratory complex I. Myc activation in non-transformed lymphoid precursors suppressed endogenous Bcl2 and sensitized the cells to IACS-010759-induced apoptosis. Treatment with the Bcl2 inhibitor venetoclax also sensitized to IACS-010759, while overexpression of Bcl-2 was protective. IACS-010759 engaged an ATF4-driven Integrated Stress Response (ISR) with dual anti- and pro-apoptotic effects, the latter mediated by the CHOP transcription factor, which contributed to selective killing of Myc-overexpressing cells. In line with the above data, IACS-010759 and venetoclax synergized in killing human DHL cells, and showed strong combinatorial effects in a pre-clinical setting. In a Bcl2-negative Burkitt’s lymphoma cell line, instead, IACS-010759 synergized with the Mcl-1 inhibitor S63845. Altogether, our data point to the combination of IACS-010759 with distinct Bcl2-family inhibitors for therapeutic reactivation of the intrinsic apoptotic pathway in Myc-associated B-cell lymphomas

overall_design: Total RNA profiling of gene expression of  FL5.12 cells expressing MycER, treatment where indicated with IACS-010759 135 nM and/or 4-hydroxytamoxifen 100 nM for the 24 and 72 hours, respectively

first: Giulio

last: Donati


title: RNA-seq analysis the whole transcriptome in MCF7 cells

city: Washington DC

first: huadong

last: Pei

state: District of Columbia

address: 800 22ND ST NW

institute: BioChemistry and Molecular Medicine

summary: Transcriptome analysis of total RNA samples from human MCF7 cell line. And the cells line were knocked down endogenous SRPK2 and overexpressed the SRPK2 WT or SRPK2 O-GlcNAcylation deficient 4A mutation

overall_design: We analyzed MCF7 cell lines after knockdown SRPK2 and overexpressed SRPK2 WT  or  SRPK2 O-GlcNAcylation deficient 4A mutation using Illumina platform.

first: Huadong

first: Wei

last: Tan


title: Role and efficacy of the ironized anti-PD1 inhibitors in antitumor immunity in hepatocellular carcinoma

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: The inherently therapeutic nanomedicine can alter and augment immune response in liver cancer, potentially leading to the development of a new family of combination immunotherapy.

overall_design: BNL-MEA tumor-bearing Balb/c mice treated with vehicle, anti-PD1, and ironized anti-PD1

first: D

middle: L

last: Ou

first: C


title: Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization

city: Vienna

first: Hannah

last: Schmidbaur

address: Althanstraße 14, UZA1

department: Department of Neuroscience and Developmental Biology

country: Austria

institute: University of Vienna

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Coleoid cephalopods (squids, cuttlefish, octopus) have the largest nervous system among invertebrates that together with many lineage-specific morphological traits enables complex behaviors. The genomic basis underlying these innovations remains unknown. Using comparative and functional genomics in the model squid Euprymna scolopes, we reveal the unique genomic, topological, and regulatory organization of cephalopod genomes. We show that cephalopod genomes have been extensively restructured compared to other animals leading to the emergence of hundreds of tightly linked and evolutionary unique gene clusters (microsyntenies). Such novel microsyntenies correspond to topological compartments with a distinct regulatory structure and contribute to complex expression patterns. In particular, we identified a set of microsyntenies associated with cephalopod innovations (MACIs) broadly enriched in cephalopod nervous system expression. We posit that the emergence of MACIs was instrumental to cephalopod nervous system evolution and propose that microsyntenic profiling will be central to understand cephalopod innovations.

overall_design: We are using Hi-C and Atac-seq data of developing Euprymna scolopes embryos to understand if and how genome re-oragization affects regulation in cephalopods

first: Akane

last: Kawaguchi

first: Tereza

last: Gerguri

first: Xiao

last: Fu

first: Oi

middle: P

last: Hoang

first: Bob

last: Zimmermann

first: Elena

last: Ritschard

first: Anton

last: Weissenbacher

first: Jamie

last: Foster

first: Spenver

last: Nyholm

first: Paul

last: Bates

first: Caroline

last: Albertin

first: Elly

last: Tanaka

first: Oleg

last: Simakov


title: Dual functions of NEIL3 in DNA repair and the epithelial-mesenchymal transition

city: Tainan

first: Wenya

last: Huang

address: No.1, University Road

institute: NCKU

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived liver cancer transcriptome profiling (RNA-seq) to quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis.

overall_design: mRNA profiles of Huh7 liver cancer cell lines were generated using the Cufflinks package v2.2.1.

first: Hui-Huang

last: Lai


title: Molecular characterization of bovine embryonic stem cells derived from IVF, cloned, and parthenogenetic embryos

city: Fort Collins

first: Michelle

last: Halstead

state: CO

address: 200 West Lake Street

department: Biomedical Sciences

institute: Colorado State University

summary:
Purpose: Embryonic stem cells (ESC) indefinitely maintain the pluripotent state of the blastocyst epiblast. Stem cells are invaluable for studying development and lineage commitment, and in livestock they constitute a useful tool for genomic improvement and in vitro breeding programs. Although these cells have been recently derived from bovine blastocysts, a detailed characterization of their molecular state is still lacking.
Methods: Here, we compared the transcriptomic and epigenomic profiles of bovine ESC (bESC) obtained from in vitro fertilized (IVF), somatic cell nuclear transfer (SCNT), and parthenogenetic (PAR) embryos.
Results: Bovine ESC were efficiently derived from SCNT and IVF embryos and expressed pluripotency markers while retaining genome stability. Transcriptome analysis revealed that only 46 genes were differentially expressed between IVF- and SCNT-derived bESC, which did not reflect significant deviation in cellular function. Additionally, by interrogating the histone marks H3K4me3, H3K9me3 and H3K27me3 with CUT&Tag, we found that the epigenomes of bESC subtypes were virtually indistinguishable. Minor epigenetic differences were randomly distributed throughout the genome and were not associated with differentially expressed or developmentally important genes. Finally, categorization of genomic regions according to their combined histone mark signal demonstrated that bESC subtypes shared the same epigenomic signatures, especially at promoters.
Conclusions: Overall, we conclude that bESC derived from SCNT and IVF embryos are transcriptomically and epigenetically analogous.

overall_design: Gene expression profiles were determined by 3'-Tag-RNA-seq for three independent male bESC lines derived from IVF blastocysts, three independent male bESC lines derived from SCNT blastocysts, one bESC line derived from PAR blastocysts, male fibroblasts used as nuclear donors for SCNT, and two other fibroblast cell lines (one male, one female). CUT&Tag was used to profile H3K4me3, H3K9me3, and H3K27me3 in the same three independent male bESC lines derived from IVF blastocysts, the same three independent male bESC lines derived from SCNT blastocysts, and the male fibroblasts used as nuclear donors for SCNT. Additionally, IgG was profiled by CUT&Tag in one bESC-IVF replicate, one bESC-SCNT replicate, and fibroblast nuclear donor cells.

first: Halstead

last: Michelle

first: Navarro

last: Micaela

first: Ross

middle: J

last: Pablo


title: Transcriptomic analysis in E9.5 heart tubes identify genes dysregulated in Sox7-null heart tubes

city: Houston

first: sangbae

last: Kim

address: 1 baylor plaza

institute: Baylor College of Medicine

summary: RNA-seq differential gene expression analysis was accomplished in E9.5 pooled(n = approximately 30) microdissected heart tubes from Sox7-null embryos and a wild-type littermates.

overall_design: To identify genes that are differenctially expressed in the developing heart as a result of SOX7 deficiency, we performed bulk RNA-seq on Sox7-null and wild-type heart tubes harvested at E9.5.

first: Daryl

last: Scott

first: Andres

last: Hernandez-Garcia

first: Yumei

last: Li

first: Rui

last: Chen


title: Differential effects of nitrogen addition on soil organic carbon decomposition correlate with changes in microbial C-degradation functional potentials in a Pinus tabulaeformis forest

city: Yangling

first: jingjing

last: li

address: xi nong road 26

institute: Northwest A&F University

summary: Anthropogenic nitrogen (N) deposition may affect soil organic carbon (SOC) decomposition, thus affecting the global terrestrial carbon (C) cycle. However, it remains unclear how the level of N deposition affects SOC decomposition by regulating microbial community composition and function, especially C-cycling functional genes structure. We investigated the effects of short-term N addition on soil microbial C-cycling functional gene composition, SOC-degrading enzyme activities, and CO2 emission in a 5-year field experiment established in an artificial Pinus tabulaeformis forest on the Loess Plateau, China.

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: soil microbial functional gene diversity; 16 samples were collected from an artificial Pinus tabulaeformis forest located in Loess Plateau (China) to which N at four different concentrations was added (0 [N0], 3 [N3], 6 [N6], and 9 [N9] g N m–2 y–1) for 5 years, with 4 replicates in every treatment.

first: Jingjing

first: Guobin

last: Liu


title: Coordination of Circadian Clock in Chilling Stress Response of Rice (Oryza sativa L.)

city: Changsha

first: Xuedan

last: Lu

state: Hunan

address: No. 1 Nongda Road

institute: Hunan Agricultural University

summary: Chilling stress is a major abiotic stress that affects rice growth and development. Rice seedlings are quite sensitive to chilling stress and this harms global rice production. Comprehensive studies of the molecular mechanisms for response to low temperature are of fundamental importance to chilling tolerance improvement. The number of identified cold regulated genes (CORs) in rice is still very small. Circadian clock is an endogenous timer that enables plants to cope with forever changing surroundings including light–dark cycles imposed by the rotation of the planet. Previous studies have demonstrated that the circadian clock regulates stress tolerances in plants show circadian clock regulation of plant stress tolerances. However, little is known about coordination of the circadian clock in rice chilling tolerance. In this study, we investigated rice responses to chilling stress under conditions with natural light-dark cycles. We demonstrated that chilling stress occurring at nighttime significantly decreased chlorophyll content and photosynthesis efficiency in comparison with that occurring at daytime. Transcriptome analysis characterized novel CORs in indica rice, and suggested that circadian clock obviously interferes with cold effects on key genes in chlorophyll (Chl) biosynthesis pathway and photosynthesis-antenna proteins. Expression profiling revealed that chilling stress during different Zeitberger times (ZTs) at nighttime repressed the expression of those genes involved Chl biosynthesis and photosynthesis, whereas stress during ZTs at daytime increases their expression dramatically. Moreover, marker genes OsDREBs for chilling tolerance were regulated differentially by the chilling stress occurring at different ZTs. The phase and amplitude of oscillation curves of core clock component genes such as OsLHY and OsPRR1 are regulated by chilling stress, suggesting the role of chilling stress as an input signal to the rice circadian clock. Our work revealed impacts of circadian clock on chilling responses in rice, and proved that the effects on the fitness costs are varying with the time in a day when the chilling stress occurs.

overall_design: For RNA sampling, 10-day-seedlings were treated with chilling temperature (13°C) for 4 h at different Zeitgeber Time (ZT) (ZT0-ZT36) before harvesting for RNA extraction on the 11th day. For transcriptome analyses, CT12 group seedlings experienced 4 hrs treatment of chilling temperature from ZT8-ZT12, while NT12 group seedlings were kept at 28°C before harvesting at ZT12 as controls. CT24 group seedlings were chilling-treated from ZT20 to ZT24 before being harvested, while NT24 group seedlings were harvested at the same time at normal growth temperature.

first: Junhua

last: Peng

first: Shufeng

last: Song

first: Fan

last: Fan

first: Zhou

last: Yan

first: Gaofeng

last: Jia


title: CD82 is a useful marker to isolate b cell precursors from human iPS-derived cells and plays a role for the maturation of b cells

city: Tokyo

first: Ami

last: Watanabe

address: 1-1-1 yayoi, Bunkyo-ku

department: Institute of Molecular and Cellular Biosciences

institute: University of Tokyo

summary: Gene expression analysis of the differentiation process of iPS cells to pancreatic islet cells has revealed that expression of CD82 defines a subset of iPS cell-derived pancreatic endocrine progenitors (EP).  While some cell surface proteins such as CD142, CD200 and SUSD2 have been reported as markers of pancreatic progenitor (PP) and EP, CD82+ EP cells are distinct from those PP and EP characterized by the previously identified markers. CD82+ cells isolated from EP cells efficiently differentiated into pancreatic endocrine cells, particularly β cells. Also, CD82+ cells isolated from human cadaver pancreases secreted insulin in response to a high glucose concentration. Furthermore, blocking of CD82 expression by siRNA or inhibition of CD82 in EP by monoclonal antibodies suppressed maturation of β cells, indicating that CD82 plays a role for maturation of EP to β cells. In conclusion, this study identified CD82 not only as a useful marker to isolate β cell precursors but also as an important molecule for functional maturation of β cells.

overall_design: To identify the pancreatic endocrine progenitor marker gene, we compared gene expression of endocrine marker gene Ngn3 high expression cell and weak expression cells derived from iPS cells.

first: Anna

last: Tanaka

first: Atushi

last: Miyajima


title: The vascular endothelial thromboxane A2/prostaglandin H2 receptor controls its own activation and impairs angiogenesis via an autocrine cyclooxygenase-2-dependent positive feedback loop.

city: Halle

first: Robert

last: Eckenstaler

address: Kurt-Mothes-Str. 3

department: Institute of Pharmazie

country: Germany

institute: Martin-Luther-University

summary: The thromboxane A2/prostaglandin H2 receptor (TP) plays an eminent role in the pathogenesis of cardiovascular disease and its expression has been reported to increase in the dysfunctional endothelium of cardiovascular high-risk patients. Yet it remains enigmatic in which way the vascular endothelial TP affects angiogenesis. Here we show that increased endothelial TP expression, in the absence of exogenous TP agonists, profoundly inhibits, whereas TP knockdown or endothelial-specific knockout enhance the angiogenic capacity of vascular endothelial cells in vitro and in vivo. Global transcriptome, lipidomic, and functional analyses reveal that the TP induces endothelial cyclooxygenase-2 and downregulates prostacyclin synthase to promote TP ligand release, persistent TP activation, suppression of VEGFR2 expression and inhibition of angiogenesis, effects that are reversed by pharmacological TP inhibition or prostacyclin synthase reconstitution. Further mechanistic analyses reveal that endothelial TP increase cell tension, disturb focal adhesion dynamics and inhibit migration, tube formation and angiogenic sprouting via pathways that enhance endothelial actomyosin contractility. In conclusion, our work uncovers an anti-angiogenic feedback loop by which the TP may disturb angiogenesis and vascular endothelial homeostasis in disease states associated with increased TP expression.

overall_design: Three biological replicates were analyzed for each of three different conditions (overexpression of thromboxane A2 receptor isoforms TPa and TPb compared to control without overexpression of the receptor).

first: Anne

last: Ripperger

first: Ralf

last: Benndorf


title: Hepatic transcriptome of eIF2α heterozygotic mouse

city: Beijing

first: Yilie

last: Liao

address: Zhongguancun Street

institute: Tsinghua University

summary: To examine the relationship between protein synthesis and energy homeostasis, we created the whole body eIF2α haploinsufficient mouse model to establish a constantly reduced translation state.

overall_design: Liver samples of eIF2α heterozygous and control mice.

first: Xia

last: Xiao


title: RNA sequencing results of treatment with BET inhibitor (JQ1) in human diffuse large B-cell lymphoma (DLBCL) cells based on Illumina HiSeq 2500 platform

first: Muh-Hwa

last: Yang

address: No. 155, Sec. 2, Li-Nong Street

institute: National Yang-Ming University

summary: High-throughput RNA sequencing Analysis of human diffuse large B-cell lymphoma (DLBCL) cells treated with BET inhibitor. Our study represents the detailed analysis of the more accurate quantitative and qualitative evaluation of mRNA content within DBLBC cells. Our study represents the detailed analysis of the more accurate quantitative and qualitative evaluation of mRNA content within DLBCL cells.

overall_design: Gene expression profiles in two DLBCL cell lines treated with JQ1 was generated by Illumina RNA sequencing and compared to profiles from DMSO-treated control cells.

first: Y

last: Pan

first: P

middle: H

last: Lin

first: M


title: Hepatic transcriptome of eIF4EBP3 deficient mouse

summary: Previously we observed that when constantly reducing protein synthesis using the whole-body eIF2α haploinsufficient mouse model, the hepatic lipogenesis process would gear down. To figure out whether translation can regulate lipogenesis in a cell-autonomous way, we created the liver-specific eIF4EBP3 deficient mouse by adenovirus-mediated shRNA targeting Eif4ebp3. eIF4EBP3 suppresses translation initiation by sequestering eIF4E. Therefore, by knocking down it, we established a translation hyperactive state in liver.

overall_design: adenovirus-mediated knockdown of Eif4ebp3 and the lacZ control in mouse liver.


title: Next generation seuquencing of 3D breast cancer cell culture in synthetic hydrogels presenting either a collagen mimic or laminin mimic with low and high mechanical properties

city: Newark

first: Shawn

middle: William

last: Polson

state: DE

department: Center for Bioinformatics and Computational Biology

institute: University of Delaware

summary: MDA-MB-231 (ER-) and T47D (ER+)  breast cancer cells were encapsualted in synthetic hydrogels, formed with a multi-arm bioinert polymer poly(ethylene glycol), cell-degradable peptide crosslinks, and receptor-binding pendant peptides, and cultured for 3 days and up to 40 days to assess initial cell responses to different matrix compositions. The synthetic matrices had a Young's modulus (E) ~ 0.6 kPa (low wt%) and # ~ 5 kPa (high wt%), in the range of bone marrow or healthy mammary tissue and lung tissue, respectively, and Biochemcial cues to mimic binding sites found in collagen (GFOGER peptide) or laminin (IKVAV peptide). After 3 days and 40 days in culture, mRNA was collected and RNA-seq performed to compare cell responses between the collagen and laminin mimetic cultures overtime in both low wt% and high wt% matrices.

overall_design: Examination of two different peptide compositions, collagen (GFOGER) and laminin (IKVAV), on two breast cancer cell lines MDA-MB-231 (ER-) and T47D (ER+) cultured in three dimensional PEG hydrogels for 3 days.

first: April

last: Kloxin

first: Elisa

last: Ovadia

middle: W


title: Gene expression profile of hepatocellular carcinomain in Taiwan (subset 2)

first: Chia-Lang

last: Hsu

summary: In this study, we used RNA-seqeuncing to develop gene expression profile of HCC patients in Taiwan.

overall_design: RNAs were extracted from HCC samples and profiled by RNA-seq

first: C

first: D

last: Ou


title: Gene expression profile of hepatocellular carcinomain in Taiwan

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

overall_design: Refer to individual Series


title: Gene expression profile of hepatocellular carcinomain in Taiwan (subset 1)

last: LOu


title: Transcriptome analysis of hematopoietic stem cells treated with transduction enhancers

city: london

first: Alessia

last: Cavazza

state: Greater London

address: 30 guilford street

department: GOS Institute of Child Health

institute: University College London

summary: We systematically tested three GMP-compliant HSPC culture media and eight previously described transduction enhancers (TE) to develop a state-of-the-art clinically applicable protocol. We performed RNA-seq on hematopoietic stem cells treated and non treated with transduction enhancers and found no major differences in the global transcriptional profile.

overall_design: RNA-seq on hematopoietic stem cells tranduced with a lentiviral vector with or without the addition of transduction enhancers


title: Toxicogenomic analysis of the effects of BDE-47/209, TBBPA/S, TCBPA on early neural development, with human embryonic stem cells

city: beijing

first: liang

middle: sheng

last: xian

address: shuangqing road

institute: chinese academy of science

summary: Flame retardants are detected globally in the environment, and pose great risks to human health. The potential effects of these chemicals on the development of nervous system have raise public concerns. In this study, to explore the toxicity profiles of these chemicals in the early developmental stage of human nervous system, we induced neural ectoderm from human embryonic stem cells in the presence of individual or mixture of BDE-47, BDE-209, TBBPA, TBBPS, TCBPA. By analyzing the whole transcriptional changes in the samples treated with 1 μΜ of each chemical, we identified a set of neural development relative biological processes that response to these chemicals. Genes involved in the GO terms relative to neural development were further confirmed by qRT-PCR assay, with samples treated with various concentrations (10 nM, 100 nM, 1 μΜ, 5 μΜ) of these chemicals. We found out that axon guidance and synaptogenesis may be the major target of these chemicals. In addition, these flame retardants may dysregulate the WNT and AHR signaling pathways. BDE-209 showed similar toxicity with BDE-47, whereas TBBPS and TCBPA may not be safe alternatives to TBBPA.

overall_design: Totally have 14 samples with 7 groups, including control, BDE-47 treated group, BDE-209 treated group, TBBPA  treated group, TBBPS  treated group, TCBPA  treated group and the group treated with the mixture of these five chemicals;  each group contrain two replicates.

first: Shengxian

last: Liang

first: Shaojun

first: Francesco

last: Faiola


title: Identification of genes are regulated by AURKA at transcription level

city: DA LIAN

first: Liu

last: Quentin

address: Lvshunkou District, Dalian, Liaoning

institute: DA LIAN MEDIACAL UNIVERSITY

summary: To gain insight into genes regulated by AURKA, AURKA was knocked down (KD) in MDA-MB-231 cells

overall_design: Differential expression analysis of AURKA KD versus mock-transfected MDA-MB-231 cells, in 2 biological replicates

first: Quentin

last: Liu


title: RNA-seq and ChIP-seq in SUM159 triple negative breast cancer cell line

city: montpellier

first: stanislas

last: du manoir

address: 280 rue des apothicaires

country: France

institute: IRCM


title: Probiotic normalization of systemic inflammation in siblings of Type 1 diabetes patients

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary: BACKGROUND.  The incidence of Type 1 Diabetes (T1D) has significantly increased in recent decades and coincides with lifestyle changes that have likely altered the composition of the gut microbiota.  Dysbiosis and gut barrier dysfunction are associated with T1D, and notably, our studies have identified an inflammatory state in T1D families that is consistent microbial antigen exposure.     METHODS.  We conducted a 6-week, single-arm, open-label trial to investigate whether daily multi-strain probiotic (Bifidobacteria, Lactobacillus, and Streptococcus) supplementation could reduce the familial inflammatory state in 25 unaffected siblings of diabetes patients.    RESULTS.  Probiotic supplementation was found safe and well-tolerated; there were no adverse events and participant adherence was 93%.  Bacterial 16S rDNA gene sequencing of stool revealed that community alpha and beta diversity were not altered between the pre- and post-supplement samplings.  LEfSe analyses identified post-supplement enrichment of the family Lachnospiraceae, producers of the anti-inflammatory short chain fatty acid butyrate.  Systemic inflammation was measured by plasma induced transcription and quantified with a gene ontology-based composite inflammatory index (I.I.com).  After supplementation, I.I.com was reduced (p=0.017), and pathway analysis predicted inhibition of IL17A, lipopolysaccharide, NFkB, IL1B, and TNF (Z-score≤-2.0) and activation of IL10RA (Z-score=2.0).  Post-supplement plasma levels of IL12p40, IL-13, IL-15, IL-18, CCL2, CCL24 were reduced (p<0.05), while butyrate levels trended 2.4-fold higher (p=0.06).    CONCLUSION.  There is a substantial need for safe, broadly applicable therapies to reduce T1D susceptibility.  This study indicates that investigations of prebiotic and probiotic strategies are warranted as they may be efficacious either alone or in combination with other therapeutic agents.

overall_design: UPN119 PBMC cells were stimulated with unaffected siblings of diabetes patients' pre VSL3 probiotic supplement or post VSL3 probiotic supplement (n=25) plasma. Gene expression analysis was perfromed in order to evaluate modulation of the inflammatory state associated with T1D susceptibility.

first: Susanne

last: Cabrera

first: Alison

middle: T

last: Coren

first: Shuang

last: Jia

first: Rhonda

last: Geoffrey

first: Jeffrey

last: Woodliff

first: Mark

middle: F

last: Roethle

first: Joanna

last: Kramer

first: Pippa

last: Simpson

first: Samantha

middle: N

last: Atkinson

first: Nita

last: Salzman

first: Yi-Guang

last: Chen


title: ChIP-seq of E4F1 in SUM159 triple negative breast cancer cell line

summary: E4F1 is a ubiquitously expressed zinc-finger protein of the Gli-Kruppel family that was first identified, more than 30 years ago, as a cellular target of the adenoviral oncoprotein E1A13S (Ad type V), required for transcriptional regulation of adenoviral genes. In order to decipher E4F1 cellular target genes, we performed chromatin immunoprecipitation of endogenous E4F1 in SUM159 triple negative breast cancer cell line. Both input and immunoprecipitated DNA of two independant experiments were exhaustively sequenced and mapped on the human genome (hg38). Peak detection has been achieved with the HOMER suite algorithms.

overall_design: Genome-wide mapping of E4F1 binding in human SUM159 cell line

first: Kalil

last: Batnini

first: Stanislas

last: Du Manoir

first: Olivier

last: Kirsh

first: Geneviève

last: Rodier

first: Claude

last: Sardet


title: Transcriptome profiling of MDA-MB-231 cells following the MEL-18 phosphorylation at T334

city: Seoul

first: Gu

last: Kong

address: 17 Haengdang-dong, Seongdong-gu

department: Department of Pathology

country: South Korea

institute: College of Medicine, Hanyang University

summary: RNA-sequencing analysis of MEL-18 WT- or MEL-18 T334A-overexpressing MDA-MB-231 cell lines. MEL-18, a core component of polycomb-repressive complex (PRC)-1, has been known to be phosphorylated at multiple residues in vitro; however, its functional roles in mammalian cells and human cancer remains largely unknown. Here, we examined the effect of MEL-18 phosphorylation at T334 site on polycomb-mediated epigenetic silencing in human breast cancer. Our results demonstrated that the phosphorylation of MEL-18 at T334 alters its genomic distribution and transcriptional activity that reflects functional change of MEL-18 in modulating breast tumour progression.

overall_design: MDA-MB-231 cells stably expressing either MEL-18 wild type (WT) or T334 phosphorylation-deficient mutant form of MEL-18 (MEL-18 T334A) and control cells (CON, empty vector) were cultured in DMEM supplemented with 10% FBS for 48h. Total RNA was isolated from the cultures using Trizol reagent. For each of the 3 conditions, 3 biological replicates were included. In total, 9 RNA-sequencing samples were analyzed; 3 controls, 3 MEL-18 WT, and 3 MEL-18 T334A overexpressing cells.

first: Jeong-Yeon

last: Lee


title: Targeted sequencing of cutaneous squamous cell carcinoma [SCC_NodalMet]

status: Public on Feb 28 2022

city: Omaha

first: Marissa

last: Lobl

state: NE

address: 4014 Leavenworth St.

institute: UNMC

type: Genome variation profiling by high throughput sequencing

summary: We report sequencing of 10 SCC_NodalMet samples from human subjects. Sequencing was done on an oncology targeted gene mutation panel consisting of 76 genes.

overall_design: Case-control study

first: Ashley

last: Wysong


title: lncRNA expression profiles in spermatocyte cell line (GC2) after exposure to triptolide and triptonide

city: Nanchang

first: Xiaoning

last: Zhang

address: 999 Xuefu R.D., Nanchang

institute: Nanchang University

type: Non-coding RNA profiling by high throughput sequencing

summary: Triptolide or triptonide, major bioactive components isolated from the traditional Chinese herb Tripterygium wilfordii Hook f. (TWHF), have been shown to exert various pharmacological effects on systemic autoimmune disease. However, the severe toxicity, especially reproduction toxicity, of triptolide or triptonide prevents wide clinical use for those people with fertility needs. Long noncoding (lnc) RNAs are critical for spermatogenesis, and their dysregulation might lead to male infertility. However, whether they are involved in triptolide or triptonide -induced reproduction toxicity is unknown. Here we found that exposure of spermatocyte cell line (GC2) to triptolide or triptonide led to reduction in cell viability and induced cell apoptosis and autophagy. Then the total RNAs of triptolide or triptonide -treated GC2 cells were used to investigate lncRNA expression profiles by strand-specific RNA sequencing at the transcriptome level to help determine any RNA-related mechanisms in triptolide or triptonide-induced toxicity. Gene ontology and pathway analyses showed that the functions of differentially expressed lncRNA targets and mRNAs were closely linked with many processes involved in spermatogenesis.

overall_design: LncRNA profiles of testis were generated by stranded-specific RNA-seq, using Illumina HiSeq™  X Ten platform with PE150.

first: Suping

last: Xiong


title: search for downstream target genes of HTG3 based on RNA seq data

city: Wuhan

first: Nai

last: Wu

state: Hubei

address: No.1, Shizishan Street, Hongshan District

institute: HZAU

summary: With the threshold of absolute value of log2 (Fold Change) ≥1 and P < 0.05, 4122 and 4100 differentially expressed genes (DEGs) were up-regulated and down-regulated, respectively by HS in ZH11; 4725 genes(H-DEGs) were up or down-regulated in the htg3 mutant under normal or stress conditions; Among the H-DEGs, 1025 and 947 genes were up- and down-regulated, respectively, by HS in ZH11.

overall_design: rice leaf mRNA profiles of 4-leaf stage ZH11 (Zhonghua 11) and htg3 mutant under normal, HS for 0.5h

first: Yilong

last: Yao


title: Hepatic gene expression profiling of mice given high-fat diet added Japanese yam propagule powder

city: Kawasaki

first: Fumika

last: SHINOZAKI

address: 3-25-13 Tonomachi, Kawasaki-ku

institute: Kanagawa Institute of Industrial Science and Technology

summary: We studied the effect of propagule on hepatic transcriptome in mice loaded high-fat for four weeks. Improved genes, which were restored the effects of high-fat loading by simultaneous ingestion with propagule, were picked up using hepatic transcriptome analysis. They mainly belonged to immune system and fat metabolism. High-fat loading induced hepatic inflammation, but simultaneous ingestion with propagule repressed it. As for lipid metabolism, propagule was repressed a rise of cholesterol biosynthesis and catabolism by high-fat loading. As for carbohydrate metabolism, propagule was decreased glycolysis, glycogen synthesis and increased gluconeogenesis. Moreover, amino acids were converted into pyruvate, and then they would be used for gluconeogenesis. In conclusion, propagule will be acted to delay the occurrence of hepatic disease by the suppression of carbohydrate and fat metabolism disorder in high-fat loaded mice.

overall_design:
Mice were acclimated with low-fat diet and divided into three groups: low-fat diet group (LF), 45% high-fat diet group (HF) and 45% HF diet added 5% propagules powder group (HF+P). The mice were fed the experimental diets ad libitum for 4 weeks and then starved for 16 h prior to dissection. Small hepatic pieces were frozen immediately by liquid nitrogen. All samples were extracted total RNA and hybridized on Affymetrix microarrays. LF and HF were compared to evaluate high-fat loading effects. The effects of propagule ingestion were made a comparison between  HF and HF+P.

Please note that the HF group samples were analyzed once with LF samples and re-analyzed with the HF+P group samples.

first: SHINOZAKI

last: Fumika


title: Single-cell RNA sequencing of medial vascular smooth muscle cells of normal aorta from healthy mouse

city: Shijiazhuang

first: Yakun

last: Gao

state: China

address: Department of Biochemistry and Molecular Biology College of Basic Medicine Hebei Medical UniversityNo. 361, Zhongshan Road, Shijiazhuang, Hebei, China

institute: Hebei Medical University

summary: Vascular smooth muscle cell (VSMC) subpopulations relevant to vascular disease and injury repair have been depicted in healthy vessels and atherosclerosis profiles. However, whether VSMC subpopulation associated with vascular homeostasis exists in the healthy artery and how are their nature and fate in vascular remodeling remains elusive. Here, using single-cell RNA-sequencing (scRNA-seq) to detect VSMC functional heterogeneity in an unbiased manner, we showed that VSMC subpopulations in healthy artery presented transcriptome diversity and that there was significant heterogeneity in differentiation state and development within each subpopulation. Notably, we detected an independent subpopulation of VSMCs that highly expressed regulator of G protein signaling 5 (Rgs5), upregulated the genes associated with inhibition of cell proliferation and construction of cytoskeleton compared with the general subpopulation, and mainly enriched in descending aorta. Additionally, the proportion of Rgs5+ VSMCs was markedly decreased or almost disappeared in the vascular tissues of neointimal formation, abdominal aortic aneurysm and atherosclerosis. Specific spatiotemporal characterization of Rgs5+ VSMC subpopulation suggested that this subpopulation was implicated in vascular homeostasis. Together, our analyses identify homeostasis-relevant transcriptional signatures of VSMC subpopulations in healthy artery, which may explain the regional vascular resistance to atherosclerosis at some extent.

overall_design: Detection of VSMC functional heterogeneity in medial cell layer of normal mouse aortic tissue by single-cell RNA sequencing.

first: Ruijuan

last: Guo

first: Xin

last: Xu

first: Xiaofu

last: Huang


title: Gene expression data from the syngeneic mouse endometriosis model

city: Kyoto

first: Shiho

last: Iwasaki

state: Kyoto

address: 14, Nishinosho-monguchi-cho, Kisshoin, Minami-ku

institute: Nippon Shinyaku Co., Ltd.

summary:
Retrograde menstruation is considered a major reason for the development of endometriosis. The syngeneic transplantation mouse model is an endometriosis animal model that is considered to mimic retrograde menstruation. However, it remains poorly understood which genetic signatures of endometriosis are reflected in this model.
Here, we employed an in vivo syngeneic mouse endometriosis model and identified differentially expressed genes (DEGs) between the ectopic and eutopic tissues using microarray analysis.

overall_design: Total RNA was isolated from the mouse ectopic cystic tissue or uterus using an RNeasy Lipid Tissue Mini Kit (Qiagen Inc., Hilden, Germany) (n = 5 animals per group). Purified RNA was labeled by using the GeneChip WT Plus Reagent Kit (Thermo Fisher Scientific, Inc.), then hybridized to a Clariom S Mouse Array (Thermo Fisher Scientific, Inc.).

first: Katsuyuki

last: Kaneda


title: RNA-seq of shE4F1 or shCTRL SUM159 triple negative breast cancer cell line treated or not with Gemcitabine

first: stanislas

last: du manoir

summary: E4F1 is a ubiquitously expressed zinc-finger protein of the Gli-Kruppel family that was first identified, more than 30 years ago, as a cellular target of the adenoviral oncoprotein E1A13S (Ad type V), required for transcriptional regulation of adenoviral genes. In this study we investigated the impact of direct translational target genes on DNA damage response induced by Gemcitabine.   To do so, we performed RNAseq SUM159 triple negative breast cancer cell line. SUM159 was tranfected either with shE4F1 OR shscramble  treated or not with Gemcitabine for 24 hours.

overall_design: mRNA profiles of SUM159  treated or not with Gemcitabine and transfected either with scramble shRNA or shRNA-E4F1 were generated using TruSeq stranded RNA Library Prep Kit (Illumina) followed by sequencing with 50 bp single-end reads on HiSeq 2500.

first: Kalil

last: Batnini

first: Stanislas

last: Du Manoir

first: Olivier

last: Kirsh

first: Geneviève

last: Rodier

first: Claude

last: Sardet


title: Genome-wide binding of phosphorylated MEL-18 protein at T334 in MDA-MB-231 cells

first: Gu

last: Kong

summary: ChIP-seq analysis of MEL-18 WT- or MEL-18 T334A-overexpressing MDA-MB-231 cell lines. MEL-18, a core component of polycomb-repressive complex (PRC)-1, has been known to be phosphorylated at multiple residues in vitro; however, its functional roles in mammalian cells and human cancer remains largely unknown. Here, we examined the effect of MEL-18 phosphorylation at T334 site on polycomb-mediated epigenetic silencing in human breast cancer. Our results demonstrated that the phosphorylation of MEL-18 at T334 alters its genomic distribution and transcriptional activity that reflects functional change of MEL-18 in modulating breast tumour progression.

overall_design: For the comparative analysis of the genomic binding patterns of MEL-18 wild type (MEL-18 WT) and its T334-phosphorylation-deficient mutant form (MEL-18 T334A), lysates from MDA-MB-231 cells stably expressing either FLAG-tagged MEL-18 WT or FLAG-tagged MEL-18 T334A were cross-linked, sonicated, and subjected to immunoprecipitation with anti-FLAG antibody. The ChIPed DNA and input DNA per each group were then sequenced using Hiseq2500 platform (Illumina)

first: Jeong-Yeon

last: Lee


title: Single-cell RNA-seq (10X Genomics Chromium) of LGE, MGE, CGE, and Cortex from mouse embryonic forebrain

city: Bethesda

first: Apratim

last: Mitra

state: MD

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

institute: NICHD

summary: We performed single-cell RNA sequencing to characterize transcriptional heterogeneity of neural progenitors within the ventricular zone and subventricular zone of E12.5 and E14.5 mouse cortex and ganglionic eminences. By using a transgenic mouse line (Nestin-d4-Venus) to enrich for VZ cells, we detect significant transcriptional heterogeneity within VZ and SVZ progenitors, both between forebrain regions and within spatial subdomains of specific GEs.

overall_design: LGE, MGE, CGE, and cortex from E12.5 and E14.5 mouse embryos.

first: D

first: C

last: Rhodes

first: A


title: ALKBH3 CLIP-seq in HeLa cells.

city: Chicago

first: Guan-Zheng

last: Luo

state: IL

address: 929 E 57th St

department: Chemistry

institute: UChicago

summary: The CLIP procedures were conducted using HeLa cells according to the previous study (Liu et al., 2016) with slight modifications. Briefly, 4 plates of HeLa cells in 15 cm dishes were transfected with pPB/ALKBH3 plasmid for 48 h to reach about 90% cell confluency. After washing twice with ice-cold PBS, cells were irradiated twice with 400 mJ/cm2 at 254 nm by Stratalinker on ice. Cells were lysed in high salt lysis buffer (300 mM NaCl, 0.2% NP-40, 20 mM Tris-HCl PH 7.6, 0.5 mM DTT, protease inhibitor cocktail (1 tablet/50 ml), and RNase inhibitor (1:200)) at 4°C for 30 min. Supernatant was collected after centrifuged at 17,000 g at 4°C for 15 min and further treated with 1 U RNase T1 for 15 min at 24 °C. After centrifugation and filtration through 0.22 µM filter, 10% supernatant was collected as input for further sequencing analysis. Anti-Flag M2 beads (Sigma-Aldrich, St. Louis, MO, 80 μl) were washed three times with lysis buffer and incubated with the filtered supernatant at 4°C for 4 hrs. After removing the flow through by magnetic rack, beads and input were further incubated with 10 U RNase T1 exactly for 8 min. Samples were treated with 95 µL commercial PNK buffer and 0.5 U PNK for 15 min at 37 °C. After treatments, final concentration of 100 µM ATP and 1 U PNK were added and incubated at 37 °C for another 30 min. The RNA/protein complexes were eluted by NuPAGE 1 × loading buffer and fractionated by neutral NuPAGE 4–12% bis-tris gel. After cutting the gel, RNAs were recovered by proteinase K digestion in proteinase K buffer, followed by phenol/chloroform extraction using glycogen as carrier.  The RNA fragments were ligated to adapter and established library by NEB small RNA library preparation kit (E7330S).

overall_design: Examination of RNAs bound by ALKBH3 in HeLa cells

first: Hongsheng

last: Wang

first: Guanzheng


title: Transcriptome profiling in an Escherichia coli strain collection

city: Cambridge

first: Pedro

last: Beltrao

address: Wellcome Genome Campus

institute: EMBL-EBI

summary: In order to understand the impact of genetic variants on transcription and ultimately in changes in observed phenotypes we have measured transcript levels in an Escherichia coli strains collection, for which genetic and phenotypic data has also been measured.

overall_design: Each sample has been analysed at least in duplicate. All samples were harvested when cultures reached O.D. of about 0.2 (at 600 nanometers).

first: Marco

last: Galardini

first: Matylda

last: Zeitek

first: Anja

last: Telzerow

first: Dinko

last: Pavlinic

first: Jelena

last: Pistolic

first: Nick

last: Goldman

first: Athanasios

last: Typas


title: Overexpression of AIM2 inhibits metastasis and promotes apoptosis of hepatocellular carcinoma cells

city: changzhou

first: runzi

last: sun

state: Jiangsu

address: 185 juqian street

institute: soochow university

summary: It was shown that the AIM2 expression was decreased in human HCC tissues compared with the adjacent normal tissues, and the OS rate of HCC patients with higher AIM2 expression was significantly higher compared with the ones with lower AIM2 expression, indicating that the expression level of AIM2 was significantly correlated with clinical stage. Besides, the expression of AIM2 was significantly associated with the AFP expression, but not associated with PD-L1, Ki67, or CD34 expression in HCC. Pathology classification in HCC tissues could be used as an independent prognostic predictor for the patients. Overexpression of AIM2 could significantly inhibit cancer cell migration and promote their apoptosis. Furthermore, notch signaling pathway may be involved in the regulation of AIM2 in the cellular network of HCC cells.

overall_design: paired end RNA-seq data of AIM2 over-expressing HCC cell lines and its control

first: Panpan

last: Zheng

first: Jingting

last: Jiang


title: Customised dynamic bioreactor system enables the production of radially aligned 3D diaphragmatic muscle constructs promoting ECM remodelling and inhibiting fibroblasts overgrowth.

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

summary:
The production of skeletal muscle constructs useful for in vivo large defects replacement, such as congenital diaphragmatic hernia (CDH), is still considered a challenge. The standard application of prosthetic material presents strong limitations, like hernia recurrences in a remarkable number of CDH patients. With this work, we developed a tissue engineering approach based on decellularized diaphragmatic muscle and human cells for the generation in vitro of diaphragmatic-like tissues as proof-of-concept of a new option for the surgical treatment of large diaphragm defects. A specific bioreactor for diaphragmatic muscle was achieved to control mechanical stimulation during the construct generation. In vitro tests demonstrated the increased maturation of mechanically stimulated constructs, with the formation of new oriented and aligned muscle fibres. Moreover, after in vivo orthotopic implantation in a CDH mouse model, mechanically stimulated muscles maintained the presence of human cells within myofibers, supporting the idea of a new therapeutic option for this dramatic congenital malformation.
Production of diaphragmatic-like tissues using mouse decellularized extracellular matrix, human cells and mechanical stimulation with bioreactor

overall_design: Gene expression was measured using  Affymetrix platform in 12 diaphragm-like tissues (6 STATIC and 6 DYNAMIC samples)

first: Silvia

last: Bresolin

first: Martina

last: Piccoli


title: C10orf99/GPR15L Regulates Proinflammatory Response of Keratinocytes and Barrier Formation of the Skin

city: Singapore

first: Vipin

last: Narang

address: 8A Biomedical Grove

country: Singapore

institute: Singapore Immunology Network

summary: The epidermis, outermost layer of the skin, forms a barrier and is involved in innate and adaptive immunity in an organism. Keratinocytes participate in all these three protective processes. However, a regulator of keratinocyte protective responses against external dangers and stresses remains elusive. We found that upregulation of the orphan gene 2610528A11Rik was a common factor in the skin of mice with several types of inflammation. In the human epidermis, peptide expression of G protein-coupled receptor 15 ligand (GPR15L), encoded by the human ortholog C10orf99, was highly induced in the lesional skin of patients with atopic dermatitis or psoriasis. C10orf99 gene transfection into normal human epidermal keratinocytes (NHEKs) induced the expression of inflammatory mediators and reduced the expression of barrier-related genes. Gene ontology analyses showed its association with translation, mitogen-activated protein kinase (MAPK), mitochondria, and lipid metabolism. Treatment with GPR15L reduced the expression levels of filaggrin and loricrin in human keratinocyte 3D cultures. Instead, their expression levels in mouse primary cultured keratinocytes did not show significant differences between the wild-type and 2610528A11Rik deficient keratinocytes. Lipopolysaccharide-induced expression of Il1b and Il6 was less in 2610528A11Rik deficient mouse keratinocytes than in wild-type, and imiquimod-induced psoriatic dermatitis was blunted in 2610528A11Rik deficient mice. Furthermore, repetitive subcutaneous injection of GPR15L in mouse ears induced skin inflammation in a dose-dependent manner. These results suggest that C10orf99/GPR15L is a primary inducible regulator that reduces the barrier formation and induces the inflammatory response of keratinocytes.

overall_design: Transcriptomes from Normal Human Epidermal Keratinocytes (NHEK) in untreated, empty vector-transfected, or C10orf99-transfected conditions (3 replicates per condition)

first: Teruki

last: Dainichi

first: Kenji

last: Kabashima


title: Splicing Factor SRSF1 Deficiency in the Liver Triggers NASH-like Pathology via R-Loop Induced DNA Damage and Cell Death

city: Urbana

first: Waqar

last: Arif

address: 506 S. Mathews Avenue

department: Biochemistry

institute: UIUC

summary: Regulation of RNA processing contributes profoundly to tissue development and physiology. Here, we report that serine-arginine-rich splicing factor 1 (SRSF1) is essential for hepatocyte function and survival. Although SRSF1 is mainly known for its many roles in mRNA metabolism, it is also crucial for maintaining genome stability. We show that acute liver damage in the setting of targeted SRSF1 deletion in mice is primarily mediated by the excessive formation of deleterious RNA-DNA hybrids (R-loops), which induce DNA damage. Combining hepatocyte-specific transcriptome, proteome, and RNA binding analyses, we demonstrate that widespread genotoxic stress following SRSF1 depletion results in global inhibition of mRNA transcription and protein synthesis, leading to impaired metabolism and trafficking of lipids. Accumulation of lipids in SRSF1-deficient hepatocytes is quickly followed by necroptotic cell death, inflammation, and fibrosis, resulting in NASH-like liver pathology. This pathogenesis is recapitulated in SRSF1-depleted human liver cancer cells illustrating a conserved and fundamental role for SRSF1 in preserving genome integrity and tissue homeostasis. Thus, our study uncovers how accumulation of detrimental R-loops impedes hepatocellular gene expression, triggering metabolic derangements and liver failure.

overall_design: Hepatocytes were isolated from 1-month-old C57BL/6j (2 replicates) using the two-step collagenase perfusion method. Isolated hepatocytes were crosslinked with 400 mJ/cm2 of 254 nm UV radiation to stabilize RNA binding protein (RBP)-RNA interactions. Subsequent immunoprecipitation of SRSF1-RNA complexes, RNA isolation, library preparation and sequencing were performed using the eCLIP protocol described in the ENCODE project.

first: Steven

last: Blue

first: Brian

middle: A

last: Yee

first: Eric

last: Van Nostrand

first: Gene

last: Yeo

first: Auinash

last: Kalsotra


title: Inflammation of gill epithelia in fish causes increased permeation of polar organic chemicals from OSPW via disruption of tight junctions

city: Saskatoon

first: Markus

last: Hecker

state: Saskatchewan

address: 44 Campus Drive

department: Toxicology

country: Canada

institute: University of Saskatchewan

summary: The epithelial cell layer that lines the fish gill controls the paracellular permeation of chemicals through tight junctions. The integrity of tight junctions can be affected by inflammation, which is likely to impact the branchial bioavailability of chemicals. In this study, we experimentally induced inflammation in the rainbow trout gill cell line RTgill-W1 via exposure to bacterial lipopolysaccharides (LPS). We then co-exposed the cells to extracts of oil sands process-affected water (OSPW), which contain a complex mixture of toxicologically relevant chemicals. Cells exposed to LPS showed a significant reduction in transepithelial electrical resistance (TEER), an indicator of tight junction integrity, after 24 h of exposure. Quantitative RT-PCR analysis determined that the abundance of transcripts of genes coding for tight junction proteins (Claudin 28b and 10e) was significantly decreased in cells exposed to 20, 50, and 100 mg L-1 LPS. Chemical analysis revealed a significant increase in permeation of constituents of OSPW across the gill cell epithelial layer at all studied LPS concentrations. These in vitro findings were confirmed in vivo in rainbow trout fingerlings exposed to both LPS and 10% OSPW for 48 h, which similarly resulted in an increase in chemical uptake relative to fish exposed to OSPW alone. This research demonstrated that inflammation of gill epithelia and the resulting disruption of tight junction integrity could lead to significantly greater uptake of potentially harmful chemicals from the environment, which has important implications for risk assessment.

overall_design: mRNA profiles of Rtgill-W1 cells exposed to L-15 media (reference/control) and 100 mg/L bacterial lipopolysaccharide (LPS; treated) for 4 hours. There were 4 replicates of control/reference and 3 replicates of LPS-treated cells.

first: Ulyana

last: Fuchylo

first: Hattan

last: Alharbi

first: Alper

last: Alcaraz

first: Paul

middle: D

last: Jones

first: John

last: Giesy

last: Brinkmann


title: RNA-seq and miRNA-seq of gastric cancer cell lines after overexpression of FN1 3' UTR

status: Public on Feb 27 2022

city: Shenyang

first: Funan

last: Liu

state: Liaoning

address: Nanjing Street 155

institute: first affiliated hospital of china medical university

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

overall_design: Refer to individual Series


title: Transcellular chaperone signaling is an intercellular stress-response that is distinct from the HSF-1 mediated HSR [WGS]

city: Leeds

first: Patricija

last: van Oosten-Hawle

state: --Select State--

address: Woodhouse Lane

department: Molecular and Cell Biology

institute: UNIVERSITY OF LEEDS

summary: The goal of this Whole Genome Sequencing (WGS) analysis was to identify genes underlying TCS in C. elegans strain expressing the gut-specific hsp-90 hairpin RNAi construct compared to a control strain (strain AM994). To do this we performed a forward genetic screen using the mutagen EMS and screened progeny for reduced TCS-mediated expression of the hsp-70p::mCherry reporter in muscle cells.

overall_design: The forward genetic mutagenesis screen identified four mutants showing reduced hsp-70p::mCherry expression. These mutants were taken forward to a one-step WGS and SNP mapping approach as described in Doitsidou M, Poole RJ, Sarin S, Bigelow H, Hobert O. C. elegans mutant identification with a one-step whole-genome-sequencing and SNP mapping strategy. PLoS One. 2010;5(11):e15435. Published 2010 Nov 8. doi:10.1371/journal.pone.0015435.

first: J

last: Miles

first: P


title: NPM1c hijacks the active trancription in leukemia development [ATAC-Seq]

city: Houston

first: Xiaotian

last: Zhang

state: TX

address: 6431 Fannin St

department: Biochemistry and Molecular Biology

institute: The University of Texas Health Science Center at Houston

summary: Nucleophosmin (NPM1) is a ubiquitously expressed nucleolar protein with a wide range of functions including ribosome biogenesis, mRNA processing, and maintenance of genomic stability1-4. In acute myeloid leukemia (AML), the terminal exon of NPM1 is often mutated (~30% of adult AMLs), resulting in the change of the nucleolar localization signal into a nuclear export signal and a shift of the protein to the cytoplasm (NPM1c)2,3,5. AMLs carrying this mutation have aberrant expression of the HOXA genes, whose overexpression leads to leukemogenic transformation6-8. Recently, it was shown that depletion or re-localization of the NPM1c protein into the nucleus causes downregulation of the HOXA genes, leading to the speculation that NPM1c directly regulates their transcription9-11. Here, we show that NPM1c binds to a subset of active gene promoters marked with high levels of H3K27ac in NPM1c leukemia cell lines and primary leukemia blasts, including well-known leukemia-driving genes such as posterior HOXA, HOXB, and MEIS1/PBX3 genes as well as novel targets IRX5 and NKX2-3. The binding of NPM1c on chromatin sustains active transcription of key target genes by maintaining high local-concentration of transcriptional complexes, including the Super Elongation Complex (SEC) and Menin/MLL1. NPM1c also maintains the active chromatin landscape by inhibiting the activity of histone deacetylases (HDACs). Depletion of NPM1c causes histone deacetylation and the silencing of key leukemic genes, leading to cell differentiation and growth arrest. The export protein XPO1 plays a key role by tethering NPM1c onto chromatin. The combination of XPO1 inhibitors (e.g., Selinexor and Eltanexor) with the Menin inhibitor MI-3454 has a synergistic effect on inducing differentiation in both NPM1-mutated leukemia cell lines and PDX model. Together, these findings reveal the neomorphic function of NPM1c as transactivator for leukemic gene expression and open up potential avenues for therapeutic intervention.

overall_design: Cells treated with DMSO and dTag-13 for 24hrs. Then ATAC-seq was performed to profile the chromatin accesibility change.


title: NPM1c hijacks the active trancription in leukemia development [RNA-Seq]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: OCI-AML3 NPM1c degron2 cell line treated with DMSO, 500nM dTag-13 for 24hrs. OCI-AML3 cell line was treated with DMSO, 25nM Selinexor for 24hrs.  We included the biological duplicates in each treatment group. We also performed the CRISPR/Cas9 knock-in on NPM1ca-GFP in mouse immortalized hematopietic progenitor cell line. We have generated 3 single cell clones from this knock-in, we also include the 2 replicates of HOXB8 immortalized cell lines as control.


summary: As a key protein in the tumor microenvironment, FN1 has been proven to promote cancer in a variety of cancer species. However, in our previous study on gastric cancer, it was found that FN1 protein expression in patient tissues was not significantly correlated with prognosis, and clinical data analysis was only correlated with T stage of gastric cancer. Analysis of the relationship between FN1 mRNA expression level and prognosis by TCGA-STAD database revealed that high FN1 mRNA expression was significantly correlated with poor prognosis. Moreover, many miRNA binding sites were found on FN1 3' UTR by database prediction, so we speculated that FN1 played different functions at mRNA and protein levels, and FN1 3' UTR might function as ceRNA. At present, FN1 3' UTR overexpression has been proved to significantly promote the invasion and metastasis of gastric cancer in vivo and in vitro, and its effect is stronger than FN1 protein. Therefore, in this study, transcriptome sequencing of FN1 3' UTR after overexpression was carried out to further explore its cancer-promoting mechanism.

overall_design: RNA-sequencing of HGC27 cells with and without FN1 3' UTR overexpression, 3 replications.

first: Siwei

last: Pan


title: RNA-Seq to identify NMUR-1-regulated genes in C. elegans defense against pathogen infection

city: Spokane

first: Yiyong

state: WA

address: 412 E Spokane Falls Blvd

institute: Washington State University

summary: To gain molecular insights on how NMUR-1 regulates C. elegans defense against pathogen infection, we used RNA-Seq to profile gene expression in nmur-1(ok1387) animals relative to wild-type animals with or without E. faecalis or S. enterica infection.  We found that NMUR-1 modulates C. elegans transcription activity by regulating the expression of transcription factors, which, in turn, controls the expression of distinct immune genes in response to different pathogens.

overall_design: Five replicates of six groups of RNA samples (nmur-1(ok1387) and wild-type animals with or without exposure to E. faecalis or S. enterica) were sequenced.  Gene expression was compared between groups to identify NMUR-1-regulated genes under uninfection or infection conditions.

first: Phillip

last: Wibisono

first: Jingru

last: Sun


title: NPM1c hijacks the active trancription in leukemia development [


title: NPM1c hijacks the active trancription in leukemia development [ChIP-Seq]

overall_design: Chromatin state (H3K27ac for active enhancer/promoter and H3K27me3 for Polycomb target region) is assayed by using  ChIP-seq with the 500nM dTag-13 treatment at different time points in OCI-AML3 Degron2 cells. Samples were taken at 6hr, 24hr, 4 days after wash-off.


title: Transcellular chaperone signaling is an intercellular stress-response that is distinct from the HSF-1 mediated HSR


title: Dissecting the stem cell compartment in Csnk1a1 haploinsufficiency

city: Aachen

first: Ronghui

last: Li

address: Pauwelsstr. 19

institute: RWTH Aachen

summary: We sorted hematopoietic progenitors from mouse bone marrow previously transplanted with either Csnk1a1 fl/+ or Mx1Cre+ bone marrow and performed scRNAseq. We identified cell populations in a continuum of differentiation from quiescent stem cell to cycling lineage-marker expressing progenitor. Our analysis revealed signaling changes in primitive stem cells with Csnk1a1 haploinsufficiency that result in downregulation of inflammatory NFkB signaling while upregulating Myc and E2f dependent pro-proliferative pathways

overall_design: We used scRNA 3' RNA sequencing product from 10x Genomics to investigate the stem cell compartment in murine models of Csnk1a1 haploinsufficiency

first: Ursula

last: Stalmann

first: Ronghu

last: i Li

first: Ivan

middle: G

last: Costa

first: Rebekka

middle: K

last: Schneider


title: Effects of zinc ions and HrasG12V-activated signaling on gene expression of rat embryonic fibroblasts maintained in serum-free media

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: To identify intracellular events affected by HrasG12V and zinc ion availability, gene expression profiling was performed with Rat-1·RasValA1, a stably transfected cell line where oncogenic mutant HrasG12V is expressed under the control of an IPTG-inducible promoter. Rat-1·RasValA1 cells were treated for 24 h with or without 5 mM IPTG in serum-free DMEM in the presence or absence of ZnCl2 supplementation at 3 microM. Total RNA was purified for gene expression profiling with microarray.

overall_design: In the study presented here assessing the effects of HrasG12V and zinc ions on gene expression profiles, Rat-1·RasValA1 cells, which express HrasG12V in an IPTG-inducible manner, were used. They were maintained in serum-free DMEM and exposed to the following 4 different conditions for 24 h: IPTG(-) ZnCl2(-), IPTG(+) ZnCl2(-), IPTG(-) ZnCl2(+), and IPTG(+) ZnCl2(+). Expression profiles of a total of ~2,000 genes were acquired.

first: Hironori

last: Edamatsu


title: Alternative splicing of EZH2 regulates gene expression in oocytes

city: Wuhan

first: Li-quan

last: Zhou

address: 13 Hangkong road

department: Tongji Medical College

institute: Huazhong University of Science and Technology

summary: We demonstrated the expression of Ezh2 long subtype is important in female reproductive system.

overall_design: We generated Ezh2 exon 3 alternative splicing site point mutation Ezh2Long / Ezh2Short mice, and examined female reproduction.

first: Shi-meng

last: Guo

first: Xing-ping

first: Qing

last: Tian

first: Yi-ran


title: Despite its sequence identity with canonical H4, Drosophila H4r product is enriched at specific chromatin regions

status: Public on Feb 26 2022

city: Szeged

first: Andrea

last: Ábrahám

state: Csongrád

address: Közép fasor 52.

country: Hungary

institute: University of Szeged

summary: A single H4 variant gene (H4r) that is located outside of the histone cluster and gives rise to a polyA tailed messager RNA via replication-independent expression is preserved in Drosophila strains despite that its protein product is identical with canonical H4. In order to reveal information on the possible role of this alternative H4 we epitope tagged endogenous H4r and revealed its genome-wide localization to chromatin at the nucleosomal level. Comparing H4r-localization to the localization of another histone variant H3.3 we found that the genome-wide distribution of H4r is more similar to the histone variant H3.3 than to the canonical histone H3. Our ChIP-seq experiments revealed H4r association with regulatory regions of genes involved in cellular stress response. The data presented here indicate that H4r has a variant histone function.

overall_design: Examination of the genome-wide localization of two epitope-tagged variant histones at nucleosomal level via ChIP-seq.

last: Abraham

first: Imre

middle: M

last: Boros

first: Laszlo

last: Henn

first: Zoltan

last: Villanyi

first: Nora

last: Zsindely

last: Bodai

first: Gabor

last: Nagy

first: Aron

last: Szabo


title: Dynamic Control of Chromatin-associated m6A Methylation Regulates Nascent RNA Biogenesis

city: Boston

first: Emily

last: Kaye

state: MA

address: 45 Shattuck Street

institute: Harvard Medical School

summary: N6-methyladenosine (m6A) regulates various aspects of RNA biology. Although m6A methylation on mRNA has been shown to be co-transcriptionally deposited, a possible regulatory role of m6A on transcription remains poorly understood. Here, we demonstrate that the METTL3/METTL14/WTAP m6A methyltransferase complex (MTC) components are co-localized to many promoters and enhancers and deposit the m6A modification to local chromatin associated transcripts including pre-mRNAs, promoter upstream transcripts (PROMPTs) and enhancer RNAs (eRNAs), suggesting a possible regulatory role for m6A methylation at these transcripts. Indeed, PRO-seq analyses demonstrate that nascent RNAs originating from both promoters and enhancers are significantly decreased in the METTL3 depleted cells. The Integrator complex has been reported to cleave nascent RNAs, which causes transcriptional attenuation. Importantly, simultaneous depletion of METTL3 and INTS11, the endonuclease subunit in the Integrator complex, suppressed the nascent RNA decrease, suggesting an antagonistic relationship between METTL3 and the Integrator complex. Consistently, we found an elevated level of INTS11 at promoters and enhancers upon loss of MTC or the m6A binder HnRNP G. Taken together, our findings suggest that MTC-mediated m6A modification protects nascent RNAs and promotes productive transcription, thus unraveling a novel layer of gene regulation imposed by RNA m6A modification.

overall_design: Precision run-on sequencing (PRO-seq) was performed on 6 samples in Drosophila S2 cells. These samples consist of 3 replicates of control (β-galactosidase targeting dsRNA) and 3 replicates of IntS9 depleted cells.

first: Wenqi

last: Xu

first: Chenxi

last: He

first: Jiahui

last: Li

first: Mandi

last: Mu

first: Geoffrey

last: Nelson

first: Li

last: Dong

first: Jiahua

last: Wang

first: Feizhen

last: Wu

first: Yujiang

last: Shi

first: Karen

last: Adelman

first: Fei

last: Lan

first: Yang

first: Hongjie

last: Shen


title: Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading[RNA-seq]

city: Shenzhen

first: Xuemei

last: Chen

state: Guangdong

address: Nanhai Road 3688

institute: Shenzhen University

summary: MicroRNAs (miRNAs) play crucial roles in gene expression regulation through RNA cleavage or translation repression. Here, we report the identification of an evolutionarily conserved WD40 domain protein as a player in miRNA biogenesis in Arabidopsis thaliana. A mutation in the REDUCTION IN BLEACHED VEIN AREA (RBV) gene encoding a WD40 domain protein led to the suppression of leaf bleaching caused by an artificial miRNA; the mutation also led to a global reduction in the accumulation of endogenous miRNAs. The nuclear protein RBV promotes the transcription of MIR genes into pri-miRNAs by enhancing the occupancy of RNA polymerase II (Pol II) at MIR gene promoters. RBV also promotes the loading of miRNAs into AGO1. In addition, RNA-seq revealed a global splicing defect in the mutant. Thus, this evolutionarily conserved, nuclear WD40 domain protein acts in miRNA biogenesis and RNA splicing.

overall_design: mRNA profiles of 15-d-old Arabidopsis thaliana seedlings with wild type (WT) in columbia background, and ab57  were generated by deep sequencing, in triplicate, using Illumina Hiseq X10.

first: Chao

last: Liang

first: Qiang

last: Cai

first: Shaofang

first: Chenjiang

last: You

first: Chi

first: Lei

last: Gao

first: Dechang

last: Cao

first: Ting

first: Bailong

last: Zhang

first: Beixin

last: Mo


title: Dynamic Control of Chromatin-associated m6A Methylation Regulates Nascent RNAs Stability [MeRIP]

status: Public on Feb 25 2022

city: Shanghai

address: NO. 138, Yi-Xue-Yuan Road

institute: Fudan university

summary: N6-methyladenosine (m6A) has been shown to regulate various aspects of mRNA biology. Although m6A has been shown to be co-transcriptionally deposited in mRNA by the chromatin-bound methyltranferase METTL3, the precise role of METTL3 and the resulting m6A methylation remain incompletely understood. Here, we demonstrate that the nascent RNAs generated from enhancers and promoters are co-transcriptionally and dynamically regulated by the chromatin bound METTL3/14 methyltransferase complex, and the demethylase, ALKBH5. Importantly, nascent RNA m6A is recognized by the reader protein hnRNP G, which prevents access of the RNA endonuclease INTS11 and thus protects nascent RNA from inappropriate degradation. Our study thus reveals an important chromatin function of m6A in stabilizing the enhancer- and promoter-derived nascent RNAs, which function to promote transcription activation.

overall_design: MeRIP of chromatin RNA in siCtrl and siMETTL3 MCF-7 cells.

first: Wenqi

last: Xu

first: Chenxi

last: He


title: Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading [sRNA-seq]

overall_design: small RNA profiles of 15-d-old Arabidopsis thaliana seedlings with amiR-SUL, amiR-SUL ab57, wild type (Columbia background)and ab57 in Col background input and after AGO1 IP  were generated by deep sequencing, in triplicate, using Illumina HiSeq2500 and illumina Nextseq, respectively.

last: Li


title: Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading


title: Dynamic Control of Chromatin-associated m6A Methylation Regulates Nascent RNAs Stability [ChIP-seq]

overall_design: Examination of METTL3/METTL14/WTAP/ALKBH5/hnRNP G binding and histone modifications.


title: Single-cell RNA-sequencing of IL-21-tRFP+ GP66+ splenic CD4+ T cells on days 7 and 14 post LCMV Cl13 infection

city: Chicago

first: Weiguo

last: Cui

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: CD4+ T cell-derived interleukin 21 (IL-21) sustains CD8+ T cell responses during chronic viral infection, but the helper subset that confers this protection remains unclear. Here, we applied scRNA and ATAC-seq approaches to determine the heterogeneity of IL-21+CD4+ T cells during LCMV clone 13 infection.

overall_design: IL-21-tRFP+ GP66-specific CD4+ T cells were FACS-sorted from LCMV Cl13-infected IL-21-tRFP 10Bit reporter mice on days 7 and 14 p.i. (with 2 donor mice per time point) and were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol

first: Ryan

last: Zander


title: CRISPR/Cas9 screen identifies oxidative phosphorylation as essential for cancer cell survival at low extracellular pH

city: Oxford

first: Pawel

last: Swietach

address: Sherrington Building, Parks Road

department: Department of Physiology, Anatomy & Genetics

institute: University of Oxford

summary: Unlike most cell types, many cancer cells survive at low extracellular pH (pHe), a chemical signature of tumors. Genes that facilitate survival under acid stress are therefore potential targets for cancer therapies. We performed a genome-wide CRISPR/Cas9 cell viability screen at physiological and acidic conditions to systematically identify gene knockouts associated with pH-related fitness defects in colorectal cancer cells. Knockouts of genes involved in oxidative phosphorylation (NDUFS1) and iron-sulfur cluster biogenesis (IBA57, NFU1) grew well at physiological pHe, but underwent profound cell death under acidic conditions. We identified several small-molecule inhibitors of mitochondrial metabolism that can kill cancer cells at low pHe only. Xenografts established from NDUFS1-/- cells grew considerably slower than their wild-type controls, but growth could be stimulated with systemic bicarbonate therapy which lessens the tumoral acid stress. These findings raise the possibility of therapeutically targeting mitochondrial metabolism in combination with acid stress as a cancer treatment option.

overall_design: CRISPR screen.  SW480 cells were infected with TKO v3 virus library with a target MOI of 0.3 After puromycin selection, 3 million cells per 15 cm-dish were seeded and were incubated with 32 mL medium (NaHCO3-free DMEM D7777) containing either 22 mM, 5.5 mM or 2.75 mM sodium bicarbonate (equilibrated in 5% CO2 to pHe 7.4, 6.9 and 6.63) supplemented with various concentrations of NaCl to maintain constant osmolarity. The cells were exposed to different pH levels for 11 days. The screen was carried out in duplicate, independent experimental setups.

first: Johanna

last: Michl

first: Yunyi

last: Wang

first: Stefania

last: Monterisis

last: Beveridge

first: Esther

last: Bridges

first: Jana

last: Koth

first: Walter

last: Bodmer


title: Bulk RNA-sequencing of IL-21-tRFP+ CD44+ Th1, Tfh, and memory-like CD4+ T cell subsets on day 14 post LCMV Cl13 infection

overall_design: IL-21-tRFP+ CD44+ CXCR6+ (Th1), CXCR5+ (Tfh), and CXCR6-CXCR5- (memory-like) CD4+ T cells were FACS-sorted from LCMV Cl13-infected IL-21-tRFP 10Bit reporter mice on day 14 p.i. (  5,000 cells per subset from 3 replicate (independent) donor mice were used to prepare RNA-seq libraries, which were prepared using SMART-seq technology (Picelli et al., 2014) and sequenced on an Illumina NextSeq.


title: ATAC-sequencing of  Th1, Tfh, and memory-like splenic CD4+ T cells on day 14 post LCMV Cl13 infection

summary: CD4+ T cell-derived interleukin 21 (IL-21) sustains CD8+ T cell responses during chronic viral infection, but the helper subset that confers this protection remains unclear. Here, we applied scRNA and ATAC-seq approaches to determine the heterogeneity of CD4+ T cells during LCMV clone 13 infection.

overall_design: ATAC-seq was performed according to a published protocol (Buenrostro, Giresi et al. 2013). 50,000 cells of CXCR6+, CXCR5+ and CXCR6-CXCR5- PD-1hi CD4 T cell subsets (per mouse, with n=3 separate mice) were used for library construction. 37 cycles paired-end sequencing was performed on a Nextseq 550 sequencer and about fifty million reads were generated for each sample.


title: Chromatin accessibility changes caused by expression of histone 3.3(K9M) in A375 cells

city: New York

first: Yariv

last: Houvras

state: NY

address: 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: We use ATAC-seq to examine chromatin accessibility changes in A375 cells after expression of mScarlet tagged H3.3(wildtype) vs. H3.3(K9M)

overall_design: FACS was used to sort mScarlet positive cells after transfection with constructs driving expression of H3.3 (wild-type) versus H3.3 (K9M)

first: Raul

last: Martinez-McFaline


title: Mitochondrial respiratory chain dysfunction alters ER sterol sensing and mevalonate pathway activity

city: LAUSANNE

first: Christopher

last: Wall

state: Schweiz

address: RUE SAINT-MARTIN 22

department: EDSV

institute: EPFL

summary: Mitochondrial dysfunction induces a strong adaptive retrograde signaling response, however many of the down-stream effectors remain to be discovered. Here, we studied the shared transcriptional responses to three different mitochondrial respiratory chain inhibitors in human primary skin fibroblasts using QuantSeq 3’RNA-sequencing. We found that mevalonate pathway genes were concurrently downregulated irrespective of the respiratory chain complex affected. Targeted metabolomics demonstrated that impaired mitochondrial respiration at any of the three affected complexes also had functional consequences on the mevalonate pathway, reducing cholesterol precursor metabolites. A deeper study of complex I inhibition showed a reduced activity of ER-bound sterol sensing enzymes through impaired processing of the transcription factor SREBP2 and accelerated degradation of the ER cholesterol sensors SQLE and HMGCR. These adaptations of mevalonate pathway activity neither affected total intracellular cholesterol levels nor the cellular free (non-esterified) cholesterol pool.  Measurement of intracellular cholesterol using the fluorescent cholesterol binding dye filipin revealed that complex I inhibition elevated cholesterol on intracellular compartments. Our study shows that mitochondrial respiratory chain dysfunction elevates intracellular free cholesterol levels and therefore attenuates the expression of mevalonate pathway enzymes, which lowers endogenous cholesterol biosynthesis, disrupting the metabolic output of the mevalonate pathway. Intracellular disturbances in cholesterol homeostasis may alter systemic cholesterol management in diseases associated with declining mitochondrial function.

overall_design: 48 samples, 6 replicates, 4 conditions, 2 timepoints. Control (0.1% DMSO), 100 nM rotenone, 500 nM antimycin A, 1 µM Oligomycin A. Cells treated for 1 or 5 days.

first: Andreas

last: Wiederkehr

first: Jaime

last: Santo-Domingo


title: Metabolic profiling of prostate cancer in skeletal microenvironments identifies G6PD as a key mediator of growth and survival

first: Srinivasa

last: Rao

address: Botnar Research Centre, Institute of Musculoskeletal Sciences, Windmill Road, Headington

department: Nuffield Dept. of Surgical Sciences

summary: The spread of cancer to bone is invariably fatal, with complex crosstalk between tumour cells and the bone microenvironment responsible for driving disease progression. By combining in silico analysis of patient datasets with metabolomic profiling of prostate cancer cells cultured with bone cells, we demonstrate the changing energy requirements of prostate cancer cells in the bone microenvironment, identifying the pentose phosphate pathway (PPP) as elevated in prostate cancer bone metastasis, with increased expression of the PPP rate-limiting enzyme (G6PD) associated with a reduction in progression-free survival. Genetic and pharmacologic manipulation demonstrates that G6PD inhibition reduces prostate cancer growth and migration, associated with changes in cellular redox state and increased chemosensitivity. Genetic blockade of G6PD in vivo results in reduction of tumour growth within bone. In summary, we demonstrate the metabolic plasticity of prostate cancer cells in the bone microenvironment, identifying the PPP and G6PD as metabolic targets for the treatment of prostate cancer bone metastasis.

overall_design: 3 replicates each of scrambled or G6PD shRNA transduced into PC3 cells

first: Jessica

last: Whitburn

first: Claire

last: Edwards


title: Dynamic Control of Chromatin-associated m6A Methylation Regulates Nascent RNAs Stability [ChIP-seq Dm]

first: Yang

last: Shi

overall_design: Examination of METTL3 binding Fly S2 cells.

first: Wenqi

last: Xu

first: Chenxi

last: He

first: Fei

last: Lan

first: Hongjie

last: Shen


title: Transcriptomics reveals pathways involved in myeloid-derived suppressor cell (MDSC) supernatant attenuation of TGF-β1-induced myofibroblastic differentiation of mesenchymal stem cells (MSCs)

first: Yin Celeste

last: Cheuk

address: 180 Fenglin Road, Shanghai,China

institute: Department of Urology, Zhongshan Hospital, Fudan University

summary: Transcriptomic analyses were conducted to discover potential mechanisms of TGF-β1-induced changes in MSCs and the effect of MDSC supernatant treatment.

overall_design: Four groups were included to perform RNA-seq analysis: MSCs without treatment (control), MSCs treated with 5 ng/mL TGF-β1 (TGF-β1), MSCs treated with 5 ng/mL TGF-β1 plus M-MDSC supernatant (TGF-β1 with M-MDSC sup) and MSCs treated with 5 ng/mL TGF-β1 plus G-MDSC supernatant (TGF-β1 with G-MDSC sup).

first: Yin

middle: C

first: Ruiming

last: Rong


title: Dynamic Control of Chromatin-associated m6A Methylation Regulates Nascent RNAs Stability [PRO-seq]

overall_design: Examination of  nascent RNAs in control and METTL3/INTS11 KD MCF-7 cells.


title: Tissue adaptaion of intestinal eosinophils in mice

city: London

first: Nicola

middle: Laura

last: Diny

address: 1 Midland Rd

institute: The Francis Crick Institute

summary: To determine how eosinophils adapt to the intestinal environment, eosinophils were sorted from the bone marrow and small intestine and compared by RNA sequencing. We show here that intestinal eosinophils were specifically adapted to their environment and underwent substantial transcriptomic changes. Intestinal eosinophils upregulated genes relating to the immune response and cell-cell communication, extracellular matrix components and metalloproteases, and the aryl hydrocarbon receptor (AHR), a ligand-activated transcription factor with broad functions in intestinal homeostasis.

overall_design: RNA sequencing of eosinophils from two different tissues, bone marrow and small intestine

first: Brigitta

last: Stockinger

first: Michael

last: Shapiro


title: Dynamic Control of Chromatin-associated m6A Methylation Regulates Nascent RNAs Stability [ChIP-seq Mm]

overall_design: Examination of Mettl3/Mettl14/Wtap/Alkbh5 binding and histone modifications in mouse neural stem cells.


title: Tregs recruited to the omentum and spleen express distinct transcriptomes

city: Birmingham

first: Mingyong

last: Liu

state: AL

address: SHEL 531, 1825 University Blvd

department: Clinical Immunology and Rheumatology

institute: University of Alabama at Birmingham

summary: To test whether Tregs that were newly recruited to tumor-bearing omentum had similar properties to those of adipose resident Tregs, we surgically joined tumor-bearing mice with congenic naive mice, sorted partner-derived Tregs from the omenta and spleens of tumor-bearing (CD45.1+) parabionts on day 14 and performed RNAseq analysis

overall_design: Transcriptomes of Tregs homing to omental tumors and spleen

first: Troy

last: Randall

first: Christopher

last: Scharer


title: Dynamic Control of Chromatin-associated m6A Methylation Regulates Nascent RNAs Stability [ChIP-seq Hs]

overall_design: Examination of METTL3/METTL14/WTAP/ALKBH5/hnRNP G binding and histone modifications in MCF-7 cells and HEK293T cells. Examination of INTS11/DGCR8/EXOSC10/PolII binding and histone modifications in control and METTL3/METTL14/WTAP KD MCF-7 cells.