title: Genome-wide maps of gV sPLA2 binding sites in Raw 264.7 cells

city: Chuo

first: Daisuke

last: Fujioka

state: Yamanashi

address: 1110 Shimokato

institute: University of Yamanashi

summary: We have searched genome-wide binding sites of mouse group V secretory phospholipase A2 (gV sPLA2) in Raw 264.7 cells. Since we previously had technical problems in immunoblotting analysis and immunoprecipitation of the gV sPLA2 protein due in part to unavailability of a specific antibody against mouse gV sPLA2 and other issues, we used a monoclonal antibody against the Myc-tag to analyze gV sPLA2 knockdown (KD) RAW 264.7 cells with re-constitutive expression of Myc-tagged gV sPLA2 or Myc-tagged gV sPLA2-H48Q, lacking catalytic activity, as well as gV sPLA2 KD RAW 264.7 cells transfected with empty vector. Among the significant peaks, the region corresponding to -375 ~ +6 from the transcriptional start site of the Pgk1 (phosphoglycerate kinase 1) gene was the strongest binding peak in the nucleus of both gV sPLA2 KD cells expressing Myc-tagged gV sPLA2 and gV sPLA2 KD cells expressing Myc-tagged gV sPLA2-H48Q. Meanwhile, the Pgk1 gene was not identified as a significant peak in the nucleus of gV sPLA2 KD cells transfected with empty vector.

overall_design: Examination of binding sites of gV sPLA2 protein in Raw 264.7 cell line.

first: Kiyotaka

last: Kugiyama


title: Identification of IL-6/Jak/STAT3 axis as a specific communicator between gastric cancer-associated fibroblast and gastric cancer cells

status: Public on Mar 26 2021

city: Suwon

first: Hoon

last: Hur

address: 164 Worldcup-ro, Yeongtong-gu

department: Department of Surgery

country: South Korea

institute: Ajou University School of Medicine

type: Expression profiling by high throughput sequencing

summary: To identify CAF-specific secreted molecules, we performed transcriptome analysis to compare gene expression patterns between paired NAFs and CAFs isolated from one GC patient.

overall_design: RNA-seq of Gastric normal associated-fibroblasts cells and Gastric cancer associated-fibroblasts cells from the same patient.

first: In-hye

last: Ham


title: Genome-wide profiling of expression of human glomeruli and tubules

city: Nanjing

first: Jingping

last: Yang

state: Jiangsu

address: 22 Hankou Road

department: Medical School

country: China

institute: Nanjing University

summary: Glomeruli and tubules are two key components in adult kidney cortex, and are important for kidney function. In order to understand the transcriptional regulation of kidney glomeruli and tubules, we generated genome wide transcription profiles with laser isolated glomeruli and tubules. Human Transcriptome 2.0 GeneChips (HTA2.0) were used to examine global gene expression.

overall_design: Five samples of glomeruli or tubules were laser isolated from kidney speciments. RNAs were extracted and prepared for labeling and hybridization on HTA2.0 chips. Data were then normalized and quantified through Affymetrix Transcriptome analysis console (TAC).

first: Jinsong

last: Shi

first: Song

last: Jiang


title: Neuronal Enhancers are Hotspots for DNA Single-Strand Break Repair [SAR-seq]

status: Public on Mar 25 2021

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

summary: Defects in DNA repair frequently lead to neurodevelopmental and neurodegenerative diseases, underscoring the particular importance of DNA repair in long-lived post-mitotic neurons. The cellular genome is subjected to a constant barrage of endogenous DNA damage, but surprisingly little is known about the identity of the lesion(s) that accumulate in neurons and whether they accrue throughout the genome or at specific loci. Here, we show that post-mitotic neurons accumulate unexpectedly high levels of DNA single-strand breakage at specific sites within the genome. Genome-wide mapping reveals that these single-strand breaks (SSBs) are located within enhancers at or near to CpG dinucleotides and sites of DNA demethylation, and are repaired by PARP1 and XRCC1-dependent mechanisms. Notably, deficiencies in XRCC1-dependent short-patch repair elevate the extent of DNA repair synthesis at neuronal enhancers, whereas deficiencies in long-patch repair reduce synthesis, suggesting that the high steady-state level of SSB repair in neuronal enhancers is sustained by both short-patch and long-patch processes. These data provide the first evidence of site- and cell type-specific SSB repair, revealing unexpected levels of localized and continuous DNA single-strand breakage in neurons. In addition, these data suggest an explanation for the neurodegenerative phenotypes that occur in patients with defective SSB repair.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We developed synthesis-associated with repair sequencing (SAR) to detect DNA repair in postmotitic neuron cells. Combined with ChIP-seqs, SEAL-seq, END-seq and HiC, we were able to study the DNA damage and its repair mechansim in neurons.

first: Sarah

middle: E

last: Hill

first: William

middle: J

last: Nathan

first: Jacob

last: Paiano

first: Elsa

last: Callen

first: Dongpeng

last: Wang

first: Kenta

last: Shinoda

first: Niek

last: van Wietmarschen

first: Jennifer

middle: M

last: Colón-Mercado

first: Dali

last: Zong

first: Raffaella

last: de Pace

first: Han-Yu

last: Shih

first: Steve

last: Coon

first: Maia

last: Parsadanian

first: Raphael

last: Pavani

first: Hana

last: Hanzlikova

first: Solji

last: Park

first: Seol

middle: K

last: Jung

first: Peter

last: McHugh

first: Andres

last: Canela

first: Chongyi

last: Chen

first: Rafael

last: Casellas

first: Keith

middle: W

last: Caldecott

first: Michael

last: Ward

first: André

last: Nussenzweig


title: Neuronal Enhancers are Hotspots for DNA Single-Strand Break Repair [SEAL]

first: Wei

last: Wu

institute: Center for Excellence in Molecular Cell Science

type: Methylation profiling by high throughput sequencing

first: Sarah

last: Hill

first: William

last: Nathan

first: Jacob

last: Paiano

first: Elsa

last: Callen

first: Dongpeng

last: Wang

first: Kenta

last: Shinoda

first: Niek

last: van Wietmarschen

first: Jennifer

last: Colón-Mercado


title: Diabetes induces macrophage dysfunction through cytoplasmic dsDNA/AIM2 associated pyroptosis

city: Chengdu

first: Lulingxiao

last: Nie

state: Sichuan

address: Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, 3rd Section S Renmin Road

institute: Sichuan University

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

summary: Diabetes is emerging as a severe global health problem that threatens health and increases socio-economic burden. Periodontal impairment is one of its well-recognized complication. The destruction of the periodontal defense barrier makes it easier for periodontal pathogens to invade in, triggering a greater inflammatory response, and causing secondary impairment. Macrophages are the major immune cells in periodontium, forming the frontier line of local innate immune barrier. Here, we explored the periodontal impairments and functional changes of macrophages under the diabetic and aging condition. Besides, we further explored the molecular mechanism of how the hyperglycemia and aging contributes to this pathogenesis. To test this, we used young and aged mice to build diabetic mice, and metformin treatment was applied to a group of them. We demonstrated that under hyperglycemia condition, macrophage functions, such as inflammatory cytokines secretion, phagocytosis, chemotaxis, and immune response were disturbed. Simultaneously, this condition elevated the local senescent cell burden and induced secretion of senescence-associated secretory phenotype (SASP). Meanwhile, we found that expressions of GSDMD and caspase-1 were upregulated in diabetic conditions, suggesting that the local senescent burden and systemic proinflammatory state during diabetes were accompanied by the initiation of pyroptosis. Furthermore, we found that the changes in aged condition were similar to those in diabetes, suggesting a hyperglycemia-induced pre-aging state. In addition, we show that metformin treatment alleviated and remarkably reversed these functional abnormalities. Our data demonstrated that diabetes initiated macrophage pyroptosis, which further triggered macrophage function impairments and gingival destructions.  This pathogenesis could be reversed by metformin.

overall_design: Examination of mRNA expression of normal, hyperglucose-treated, and metformin, hyperglucose-treated BMDM

first: Qi

first: Lullingxiao


title: Neuronal Enhancers are Hotspots for DNA Single-Strand Break Repair [END-seq]

first: Dali

last: Zong

first: Raffaella

last: de Pace

first: Han-Yu

last: Shih

first: Steve

last: Coon

first: Maia

last: Parsadanian

first: Raphael

last: Pavani

first: Hana

last: Hanzlikova

first: Solji

last: Park

first: Seol

last: Jung

first: Peter

last: McHugh

first: Andres

first: Chongyi


title: Neuronal Enhancers are Hotspots for DNA Single-Strand Break Repair [RNA-seq]

first: Wei

last: Wu

first: Sarah

last: Hill

first: William

last: Nathan

first: Jacob

last: Paiano

first: Elsa

first: Dongpeng

first: Kenta

first: Niek

last: Canela

last: Chen

first: Rafael

last: Casellas

first: Keith

last: Caldecott

first: Michael

last: Ward

first: André

last: Nussenzweig


title: Neuronal Enhancers are Hotspots for DNA Single-Strand Break Repair [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

last: Callen

last: Wang

last: Shinoda

last: van Wietmarschen

first: Jennifer

last: Colón-Mercado

first: Dali

last: Zong

first: Raffaella

last: de Pace

first: Han-Yu

last: Shih

first: Steve

last: Coon

first: Maia

first: Raphael

first: Hana

first: Solji


title: Neuronal Enhancers are Hotspots for DNA Single-Strand Break Repair [HiC]

first: Wei

last: Wu

first: Sarah

last: Hill

first: William

last: Nathan

first: Jacob

first: Elsa

last: Parsadanian

last: Pavani

last: Hanzlikova

last: Park

first: Seol

last: Jung

first: Peter

last: McHugh

first: Andres

first: Chongyi


title: NORAD-induced phase separation of PUMILIO proteins is required for genome maintenance

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

country: USA

institute: UT Southwestern Medical Center

summary: Long noncoding RNAs (lncRNAs) can regulate the activity of interacting RNA binding proteins (RBPs), but how lncRNAs efficiently compete against other transcripts to bind and regulate RBP activity is poorly understood. This problem is exemplified by NORAD, a lncRNA that maintains genomic stability by inhibiting PUMILIO (PUM) proteins. Here we show that NORAD is able to out-compete other PUM-binding transcripts by nucleating the formation of phase-separated PUM condensates, termed NP bodies. Dual mechanisms of PUM recruitment, involving multivalent PUM-NORAD and PUM-PUM interactions, enable NORAD to sequester a super-stoichiometric amount of PUM in these condensates. Accordingly, synthetic RNAs that induce PUM phase separation rescue genome instability in NORAD-deficient cells. These results illuminate mechanisms of RBP regulation by RNA-driven phase separation and uncover an essential role for this process in genome maintenance.

overall_design: Total RNA was isolated from biological triplicates of each cell line using the miRNeasy Mini RNA isolation kit (QIAGEN). Library preparation and next generation sequencing were performed by DNA Link using NEB Next Small RNA Library Prep for Illumina (New England BioLabs).

first: Mahmoud

last: Elguindy

middle: T


title: TNF is a homeostatic regulator of distinct epigenetically primed human osteoclast precursors

city: Glasgow

first: John

middle: Joseph

last: Cole

address: University Avenue

country: United Kingdom

institute: University of Glasgow

summary: Balanced osteoclast differentiation is crucial in maintaining skeleton health through life. Receptor activator of nuclear factor kappa-Β (RANK) is indispensable for OCs normal development in vivo and for the in vitro fusion of circulating progenitor cells into OCs. Many cytokines enhance RANK and RANK-ligand (RANK-L)-mediated differentiation of myeloid cells into OCs. In particular, tumor necrosis factor (TNF) is recognized as a potent activator and is associated with in vivo bone destruction in the context of OC dysregulation in inflammatory arthritis.  Paradoxically, infiltration of monocytes into TNF rich inflammatory sites does not lead to a preponderance of osteoclasts but rather macrophages. Recent in vivo murine studies have shown how circulating myeloid precursors play a crucial role in post-natal OC differentiation and skeletal health. However, little is known about such pathways in humans. Herein we demonstrate that, unexpectedly TNF can act as a critical homeostatic regulator of human CD14+ monocyte differentiation into osteoclast by inhibiting osteoclastogenesis to favour macrophage development. In contrast, a distinct, previously unidentified human CD11c+ myeloid pre-osteoclast population is exempt from this negative regulation. In healthy humans, to control cell fate and specifically overcome OC differentiation, TNF drives epigenetic modification of the RANK promoter via a TNFR1-IKK-dependent pathway. In contrast in rheumatoid arthritis, patient-derived monocytes exhibit an altered epigenetic state that results in dysregulated TNF-mediated osteoclast homeostasis providing a pathologic consequence of failure of this pathway.

overall_design: Examination of H3K4me3 in human monocytes from patients with and without rheumatoid arthritis

first: Cecilia

last: Ansalone

first: Carl

last: Goodyear


title: DNA affinity purification sequencing (DAP-seq) data of LEAFY (LFY)

city: Grenoble

first: Jérémy

last: LUCAS

address: 17 avenue des Martyrs

country: France

institute: CNRS

summary: In this study, we use DNA affinity purification sequencing to identiy genome-wide binding of LFY transcription factor, a master regulator of flower development in Arabidopsis. We generated two sets of data, one using genomic DNA from plant tissue, thus retain DNA methylation, as probe for DNA affinity purification (DAP-seq dataset), and the other using PCR amplified genomic DNA (without DNA methylation; AmpDAP-seq dataset).

first: Xuelei

last: Lai

first: Romain

last: Blanc-Mathieu

first: Arnaud

last: Stigliani

first: François

last: Parcy

last: Lucas

first: Chloe

last: Zubieta


title: Genomic analysis of chromatin conformation and DNA damage distribution in ovarian cancer cell lines derived following acquired resistance to chemotherapy [Exo-Seq]

status: Public on Mar 27 2021

city: London

first: Ed

last: Curry

address: Hammersmith Hospital, Du Cane Road

institute: Imperial College London

summary: Changes in chromatin organization are associated with resistance to anti-cancer drugs, such as platinum-based chemotherapy used as the primary treatment of ovarian cancer. We have examined the genomic distribution of chromatin accessibility changes, and relationship to gene expression changes, occurring during acquisition of resistance in vivo of high grade serous ovarian cancer (HGSOC) patients and whether this associates with genomic DNA damage distribution. Using matched chemo-sensitive and chemo-resistant ovarian cell lines isolated from HGSOC patients before and following acquisition of clinical resistance to platinum-based chemotherapy, we have examined the relationship between chromatin accessibility by ATAC-seq, platinum-DNA adduct distribution by Pt-Exo-seq and gene expression by RNA-seq. We have correlated chromatin changes between the lines at gene promoters, CpG islands, enhancer sequences and other genomic regions with changes in gene expression and platinum-DNA adduct distribution. We observe chromatin conformation differences following acquisition of platinum-resistance, with the HGSOC resistant lines clustering together, separately from their respective sensitive counterparts. Resistant lines show altered chromatin accessibility at intergenic regions, but less so at gene promoters. Super-enhancers, as defined by clusters of cis-regulatory elements, at these intergenic regions show chromatin changes that are associated with altered expression of linked genes, with enrichment for genes involved in the Fanconi anemia/BRCA DNA damage response pathway. Genome-wide distribution of platinum adducts associates with the chromatin changes and distinguish sensitive from resistant lines. Regions incurring fewer platinum-adducts showed a significant reduction in accessibility the resistant HGSOC cell line PEO4 compared to the sensitive PEO1 counterpart. Surprisingly, regions showing increased damage in PEO4 had an even greater reduction in accessibility. In the resistant line, we observe fewer adducts around gene promoters and more adducts at intergenic regions. In cell lines derived from patients following acquisition of clinical resistance to platinum-based chemotherapy, chromatin changes at super-enhancers correlate with gene expression changes in DNA repair pathways known to influence platinum sensitivity. Although cisplatin is a relatively non-specific DNA damaging agent, there are consistent differences in distribution of adducts between the matched sensitive and resistant ovarian cell lines, which is independent of the overall level of adducts formed.

overall_design: Genetic, epigenetic and transcriptional profiling of ovarian cancer cells following cisplatinum treatment [Exo-seq]

first: Robert

last: Brown

last: Gallon

first: Erick

last: Loomis

first: James

last: Flanagan


title: The architecture of the SARS-CoV-2 RNA genome inside virion

city: Beijing

first: Yuanchao

last: Xue

address: Datun Road #15

department: Institute of Biophysics

institute: Chinese Academy of Sciences

summary: The coronavirus disease 2019 caused by SARS-CoV-2 has led to an unprecedented health crisis. However, to date, the architecture of the viral RNA genomes inside virions have not been observed because the interiors of viral particles are not visible, even using sophisticated Cryo-electron microscopy and tomography methods. Here, we devised a virion applicable RNA in situ conformation sequencing (RIC-seq) technology, named vRIC-seq, for probing viral RNA structures in intact virions. Using vRIC-seq, we successfully generated an RNA 3D interaction map for SARS-CoV-2 and observed many topologically isolated RNA domains. Based on the map, we reconstructed the whole genome structure of SARS-CoV-2, which revealed a fascinating “unentangled globule” conformation of this RNA genome. Our secondary structure model not only faithfully captured known RNA structural elements but also identified many previously unknown long-range duplexes and higher-order junctions with apparent biological impacts. Importantly, our structural model also enabled rapid screening of potent small interfering RNAs to target vulnerable regions of the SARS-CoV-2 RNA genome to against its infections in Vero cells. Thus, beyond illustrating an innovative method for characterizing the viral RNA structures present in intact virions of potentially any RNA virus and showing how this data can be quickly exploited to develop antiviral treatments, our work offers the first empirical-data-based look at how the SARS-CoV-2 RNA genome is organized inside virions.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: We first developed an virus-suitable iteration of RIC-seq technology, termed vRIC-seq. Using vRIC-seq, we probed—at the whole-genome scale—the structure of the SARS-CoV-2 RNA genome in intact virions and reconstructed a model of the surprisingly compact yet unentangled SARS-CoV-2 genome structure. Beyond confirming known functional structures from previous studies of related betacoronaviruses, our comparative analyses of multiple SARS-CoV-2 strains helped identify conserved, apparently functionally impactful structural features in the SARS-CoV-2 RNA genome. Importantly, we uncovered several highly accessible regions, and demonstrate the therapeutic utility of our vRIC-seq data and genome-scale structural model with infectivity assays showing how targeted viral RNA cleavage can be achieved using small interfering RNAs. Thus, beyond offering the first look at the SARS-CoV-2 RNA genome as it is organized within virions, our study introduces a genome structure profiling method suitable for any RNA virus and illustrates how empirical-data-driven genome models can be harnessed to develop potent therapeutic technologies which target structurally vulnerable genome regions.

first: Changchang

last: Cao

first: Zhaokui

last: Cai

first: Xia

last: Xiao


title: Principles of Signalling Pathway Modulation for Enhancing Human Naïve Pluripotency Induction [RNA-seq]

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: Isolating human MEK/ERK signalling independent pluripotent stem cells (PSCs) with characteristics of naive pluripotency while maintaining differentiation competence and genetic integrity, remains challenging. Here we engineer reporter systems that allow screening for conditions that induce molecular and functional features of human naive pluripotency. Synergistic inhibition of WNT-ßCATENIN, PKC and SRC signalling enables induction of teratoma competent naïve human PSCs, with capacity to differentiate into trophoblast stem cells (TSC) and extraembryonic endodermal (XEN) cells in vitro. Divergent signalling and transcriptional requirements for boosting naïve pluripotency were found between mouse and human. P53 depletion in human naïve PSCs endows them with competitiveness to better contribute to mouse-human cross-species chimeric embryos upon priming. Finally, MEK/ERK inhibition can be substituted with inhibition for NOTCH/RBPj, which allows inducing alternative human naïve-like PSCs with diminished risk for deleterious global DNA hypomethylation. Our findings set a framework for defining the signalling foundations of human naïve pluripotency.

overall_design: Human pluropotent cells (PSCs) maintained in naïve conditions (Enhanced-NHSM), are compared to conventional/primed human PSCs, from various cell lines

first: Tom

last: Shani

first: Jonathan

last: Bayrel

first: Muneef

last: Ayash

first: Jacob

last: Hanna


title: Principles of Signalling Pathway Modulation for Enhancing Human Naïve Pluripotency Induction [WGBS]


title: Survey of GPCR gene expression in apterous-GAL4/+ Drosophila wing discs

status: Public on Mar 24 2021

city: Montreal

first: David

last: Hipfner

state: QC

address: 110, ave des Pins O

country: Canada

institute: IRCM

summary: In order to identify which of the 116 G protein-coupled receptors are expressed in late third instar wing discs, we carried out RNAseq analysis of apterous-GAL4/+ wing discs, which served as the genetic background for most of our followup studies

overall_design: RNA was isolated from 100-120 dissected wing discs from wandering third instar larvae of the genotype w;apGAL4/+. Triplicate RNA samples were anlyzed by RNAseq.


title: Maintenance DNA methylation in pre-meiotic germ cells regulates meiotic prophase by facilitating homologous chromosome pairing

city: Yokohama-shi

first: Jafar

last: Sharif

state: Kanagawa-ken

address: 1-7-22 Suehiuro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

summary: During spermatogenesis, mammalian spermatogonia undergo mitotic division, to maintain stem cell pool via self-renewal and generate differentiating progenitor cells for entry into meiotic prophase. During the perinatal stage, de novo DNA methylation occurring in pro-spermatogonia plays a key role to complete meiotic prophase and initiate meiotic division. In contrast, the role of the maintenance DNA methylation pathway for regulation of meiotic prophase, or meiotic division, in the adult is not well understood. Here, by using conditional mutants for Np95 (nuclear protein 95 kDa, also known as Uhrf1) or Dnmt1 [DNA (cytosine-5)-methyltransferase 1], two proteins that are essential for maintenance DNA methylation, we reveal that both NP95 and DNMT1 are co-expressed in spermatogonia and that these factors are necessary for meiosis in male germ cells. We found that Np95- or Dnmt1-deficient spermatocytes exhibited spermatogenic defects involving synaptic failure during meiotic prophase. In addition, assembly of pericentric heterochromatin clusters in early meiotic prophase, a phenomenon that is required for subsequent pairing of homologous chromosomes, is disrupted in Np95-deficient as well as Dnmt1-deficient spermatocytes. Based on these observations, we propose that DNA methylation established in pre-meiotic spermatogonia regulates synapsis of homologous chromosomes, and in turn quality control of male germ cells. Maintenance DNA methylation, therefore, plays a role to ensure faithful transmission of both genetic and epigenetic information to offspring.

overall_design: Examination of mRNA expression pattern of control or Np95 knocked out spermatocytes

first: Yuki

last: Takada

first: Haruhiko

last: Koseki

first: Kazuyuki

last: Ohbo


title: Principles of Signalling Pathway Modulation for Enhancing Human Naïve Pluripotency Induction [ChIP-seq]

overall_design: ChIP-seq of the following proteins: H3K27ac, KLF17, KLF4, NANOG, OCT4, SOX2 and TFAP2C, measured in human pluropotent cells (PSCs) maintained in naïve conditions (Enhanced-NHSM), or in conventional/primed human PSCs, Measured on various cell lines.


title: Principles of Signalling Pathway Modulation for Enhancing Human Naïve Pluripotency Induction [ATAC-Seq]

first: Awni

last: Mousa


title: Brd4 modulates diet-induced obesity via PPARγ-dependent Gdf3 expression in adipose tissue macrophages

city: fuzhou city

first: guo

last: Li

state: fujian province

address: shangjie road

institute: Fujian medical university

summary: Macrophage-mediated inflammatory response has been implicated in the pathogenesis of obesity and insulin resistance. Brd4 has emerged as a key regulator in the innate immune response. However, the role of Brd4 in obesity-associated inflammation and insulin resistance remains uncharacterized. Here, we demonstrated that myeloid-lineage specific Brd4 knockout (Brd4-CKO) mice were protected from high-fat-diet (HFD)-induced obesity with less fat accumulation, higher energy expenditure, and increased lipolysis in adipose tissue. Brd4-CKO mice also displayed reduced local and systemic inflammation with improved insulin sensitivity upon HFD. RNA-sequencing of adipose tissue macrophages (ATMs) from HFD-fed wide-type and Brd4-CKO mice revealed that expression of antilipolytic factor Gdf3 was significantly decreased in ATMs of Brd4-CKO mice. We also found that Brd4 bound to the promoter and enhancers of Gdf3 to facilitate PPARγ-dependent Gdf3 expression in macrophages. Furthermore, Brd4-mediated expression of Gdf3 acted as a paracrine signal targeting adipocytes to suppress the expression of lipases and the associated lipolysis in cultured cells and mice. Controlling the expression of Gdf3 in ATMs could be one of the mechanisms by which Brd4 modulates lipid metabolism and diet-induced obesity. This study suggests that Brd4 could be a potential therapeutic target for obesity and insulin resistance.

overall_design: Gene expression of adipose tisssue macrophages from Brd4-CKO mice was compared to wile type mice.

first: Xiangming

last: Hu

first: Xingchen

last: Dong

first: Guo

first: Jinjing

last: Chen

first: Xiaoxin

last: He

first: Hao

last: Sun

first: Dong-Hyun

last: Kim

first: Jongsook

last: Kemper

first: Lin-Feng


title: Patient-derived glioblastoma stem cells transcriptome regulation by CD109

city: Helsinki

first: Vadim

last: Le Joncour

state: Uusimaa

address: Haartmaninkatu 8

department: Research Programs Unit

country: Finland

institute: University of Helsinki

summary: Glioma stem cells (GSCs) drive propagation and therapeutic resistance of glioblastomas, the most aggressive diffuse brain tumor. However, the molecular mechanisms that maintain the stemness and promote therapy resistance remain poorly understood. Here we study CD109 – STAT3 axis as crucial for the maintenance of stemness and tumorigenicity of GSCs and as a mediator of chemoresistance. Mechanistically, CD109 physically interacts with glycoprotein 130 (GP130) to promote activation of the IL-6/STAT3 pathway in GSCs. Genetic depletion of CD109 abolished the stemness and self-renewal of GSCs and impaired tumorigenicity. Loss of stemness was accompanied with a phenotypic shift of GSCs to more differentiated astrocytic-like cells. Importantly, genetic or pharmacologic targeting of CD109 – STAT3 axis sensitized the GSCs to chemotherapy suggesting that targeting CD109 – STAT3 axis has potential to overcome therapy resistance in glioblastoma.

overall_design: Profiling of patient-derived glioblastoma stem cells according to the phenotypic subtypes identified by Neftel et al., 2019 (PMID 31327527) and investigation of the impact of CD109 silencing on the phenotypic states of Mesenchymal and Neuronal Precursor cells.

first: Pirjo

last: Laakkonen

first: Pauliina

last: Filppu

first: Jayendrakishore

last: Ramanathan

first: Juho

last: Väänänen

first: Martyn

last: James


title: scRNAseq of FACS-isolated microglia from spinal cords of Optn KO mice

city: Boston

first: Lauren

last: Mifflin

state: MA

address: 260 Longwood Ave

department: Department of Cell Biology

institute: Harvard Medical School

summary: CD11b+ CX3CR1+ CD45-Int microglia were FACSorted from Optn KO mice and single cell RNA sequenced using the SmartSeq2 protocol.

overall_design: SmartSeq2 single cell RNA sequencing

first: Chengyu

last: Zou

first: Junying

last: Yuan


title: scRNAseq from spinal cords

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

overall_design: Refer to individual Series


title: scRNAseq from spinal cords of SOD1-G93A and WT mice

summary: We prepared spinal cords from SOD1-G93A and WT mice treated with vehicle or the RIPK1 inhibitor Nec-1s, which were single cell RNA sequenced using the DropSeq protocol.

overall_design: DropSeq single cell RNA sequencing

first: Mifflin

last: Lauren

first: Zou

last: Chengyu

first: Yuan

last: Junying


title: Impact of maternal age and in vitro maturation on the transcriptome of denuded human oocytes

city: Barcelona

first: Paula

last: Nieto

state: Spain

address: Barcelona Science Park, Carrer de Baldiri Reixac, 4, tower I, 08028 Barcelona

department: CNAG

country: Spain

institute: CNAG

summary: While the oocytes’ transcriptome is predominantly determined by maturation stage, transcripts related to specific pathways such as chromosome segregation, mitochondria and RNA processing are affected by age after in vitro maturation of denuded oocytes.

overall_design: 75 oocytes

first: Silvia

last: Llonch

first: Bernhard

last: Payer

first: Montserrat

last: Barragan

first: Filippo

last: Zambelli

first: Rita

last: Vassena

first: Holger

last: Heyn


title: Identification of the Regulatory Network of Autophagy and Novel Autophagic Genes in Normal Spermatogenesis and Male Infertility via Single-Cell Transcriptome Analysis

city: Guangzhou

first: Xinyan

last: Yang

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

department: Developmental Biology

institute: Southern Medical University

summary: Autophagy has been implicated to be involved in spermatogenesis and dysfunction of autophagy can lead to male infertility. However, sophisticated transcriptional signatures of autophagic genes in spermatogenesis and its significance remain uncharacterized. Here, we explore the transcriptional profiling of autophagy-related genes across human spermatogenesis in donors with normal fertility and nonobstructive azoospermia (NOA) patient using single-cell RNA sequencing (scRNA-seq) analysis. Core component gene sets in each step of autophagy exhibit stage-specific expression pattern in human spermatogenesis, which is further confirmed by immunostaining; in this context, we further uncover a unique stage-specific enrichment of a cohort autophagy-related genes. Human-to-mouse comparison analysis reveals that this stage-specific expression pattern of autophagy-related genes is highly conserved in mammals and dysregulation of this pattern is associated with human male infertility. Moreover, we discover several stage-specific autophagic genes, which have not been identified to regulate spermatogenesis before. Among these candidate genes, Cst3, an actively expressed autophagic gene in spermatogonia and early spermatocytes, is involved in the regulation of SSC maintenance and subsequent male germ cell development. Downregulation of Cst3 increases the autophagy activity in mouse SSCs, which exerts its roles by regulating the expression of SSC core factors such as Oct4, Id1 and Nanos3. Collectively, our study provides novel insights into the global transcriptional signatures of autophagy-related genes and confirms the role of proper autophagy activity in SSC maintenance and normal spermatogenesis, opening new avenues for further investigation of the correlation between autophagy and spermatogenesis as well as male infertility.

overall_design:
Here we performed scRNA sequencing for 432 individual human testicular cells including spermatogonia, spermatocytes, spermatids, and testicular somatic cells (soma) from donors with nonobstructive azoospermia
Note from submitter: Due to the Regulations of the People's Republic of China on the Management of Human Genetic Resources, raw data related to humans needs to be uploaded to the National Genomics Data Center, China National Center for Bioinformation (CNCB-NGDC), so we cannot upload raw data to NCBI.
The GSA number accession is HRA000317.

first: Xiaoyang

last: Zhao

first: Mei

last: Wang

first: Gang

last: Chang

first: Caihong

last: Zheng

first: Jiexiang


title: Global miRNA dosage control of embryonic germ layer specification

first: Xuehui

last: Lv

address: No.5 Yiheyuan Road, Haidian district, Beijing, 100871, China

institute: Peking University

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) have essential functions during embryonic development, and their dysregulation causes cancer. Altered global miRNA abundance is found in different tissues and tumours, which implies that precise control of miRNA dosage is important[134], but the underlying mechanism(s) of this control remain unknown. The protein complex Microprocessor, which comprises one DROSHA and two DGCR8 proteins, is essential for miRNA biogenesis. Here we identify a developmentally regulated miRNA dosage control mechanism that involves alternative transcription initiation (ATI) of DGCR8. ATI occurs downstream of a stem-loop in DGCR8 mRNA to bypass an autoregulatory feedback loop during mouse embryonic stem cell (mES cell) differentiation. Deletion of the stem-loop causes imbalanced DGCR8:DROSHA protein stoichiometry that drives irreversible Microprocessor aggregation, reduced primary miRNA processing, decreased mature miRNA abundance, and widespread de-repression of lipid metabolic mRNA targets. Although global miRNA dosage control is not essential for mES cells to exit from pluripotency, its dysregulation alters lipid metabolic pathways and interferes with embryonic development by disrupting germ layer specification in vitro and in vivo. This miRNA dosage control mechanism is conserved in humans. Our results identify a promoter switch that balances Microprocessor autoregulation and aggregation to precisely control global miRNA dosage and govern stem cell fate decisions during early embryonic development.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
WT mESCs and ΔSL1 mESCs were used for EB, neural, EpiLC differentiation. PolyA(+) RNA-seq were performed from the samples at different time points. Small RNA-seq were performed from Neural differentiation samples.Both RNA-seq and small RNA-seq were performed form  WT, ΔSL1 mESCs and several human cancer cell lines.
WT mESCs treated with DMSO or 20uM GW9662 were used for EB differentiation. PolyA(+) RNA-seq were performed from the samples at different time points.

first: Yingzi

last: Cui

last: Lyu

first: Peng

last: Du

first: Gregory

last: RI


title: Neuronal Enhancers are Hotspots for DNA Single-Strand Break Repair [ChIP-seq]

first: Wei

last: Wu

summary: Defects in DNA repair frequently lead to neurodevelopmental and neurodegenerative diseases, underscoring the particular importance of DNA repair in long-lived post-mitotic neurons. The cellular genome is subjected to a constant barrage of endogenous DNA damage, but surprisingly little is known about the identity of the lesion(s) that accumulate in neurons and whether they accrue throughout the genome or at specific loci. Here, we show that post-mitotic neurons accumulate unexpectedly high levels of DNA single-strand breakage at specific sites within the genome. Genome-wide mapping reveals that these single-strand breaks (SSBs) are located within enhancers at or near to CpG dinucleotides and sites of DNA demethylation, and are repaired by PARP1 and XRCC1-dependent mechanisms. Notably, deficiencies in XRCC1-dependent short-patch repair elevate the extent of DNA repair synthesis at neuronal enhancers, whereas deficiencies in long-patch repair reduce synthesis, suggesting that the high steady-state level of SSB repair in neuronal enhancers is sustained by both short-patch and long-patch processes. These data provide the first evidence of site- and cell type-specific SSB repair, revealing unexpected levels of localized and continuous DNA single-strand breakage in neurons. In addition, these data suggest an explanation for the neurodegenerative phenotypes that occur in patients with defective SSB repair.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We developed synthesis-associated with repair sequencing (SAR) to detect DNA repair in postmotitic neuron cells. Combined with ChIP-seqs, SEAL-seq, END-seq and HiC, we were able to study the DNA damage and its repair mechansim in neurons.

first: Sarah

last: Hill

first: William

last: Nathan

first: Jacob

last: Paiano

first: Elsa

last: Callen

first: Dongpeng

first: Kenta

last: Shinoda

first: Niek

last: van Wietmarschen

first: Jennifer

last: Colón-Mercado

first: Dali

last: Zong

first: Raffaella

last: de Pace

first: Han-Yu

last: Shih

first: Steve

last: Coon

first: Maia

last: Parsadanian

first: Raphael

last: Pavani

first: Hana

last: Hanzlikova

first: Solji

last: Park

first: Seol

last: Jung

first: Peter

last: McHugh

first: Andres

last: Canela

first: Chongyi

last: Chen

first: Rafael

last: Casellas

first: Keith

last: Caldecott

first: Michael

last: Ward

first: André

last: Nussenzweig


title: Paired-end small RNA sequencing reveals a possible overestimation in isomiR sequence repertoire previously reported from conventional single read data analysis

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

summary: Next generation sequencing has allowed the discovery of miRNA isoforms, termed isomiRs. Some isomiRs are derived from imprecise processing of pre-miRNA precursors, leading to length variants. Additional variability is introduced by non-templated addition of bases at the ends or editing of internal bases, resulting in base differences relative to the template DNA sequence. We hypothesized that some component of the isomiR variation reported so far could be due to systematic technical noise. We have developed the XICRA pipeline to analyze small RNA sequencing data at the miRNA,. We exploited its ability to use single or merged reads to compare miRNA isomiR results derived from paired-end (PE) reads with those from single reads (SR) to address whether detectable sequence differences relative to canonical miRNAs found in isomiRs are true biological variations or the result of errors in sequencing. We have detected non-negligible systematic differences between single and PE data which primarily affect putative internally edited isomiRs, and at a much smaller frequency terminal length changing isomiRs. This is relevant for the identification of true isomiRs in small RNA sequencing datasets. . We conclude that potential artifacts derived from sequencing errors and/or data processing could result in an overestimation of abundance and diversity of miRNA isoforms. Efforts in annotating the isomiRnome should take this into account.

overall_design: This is an mRNA sequencing study which addressed the effect of paired end sequencing versus single read sequencing on miRNA and isomir expression profiling by next generation sequencing. A total of 28 serum derived total RNA samples were proifiled in the study derived form fourteen male and fourteen of female individuals. The small RNA fraction was sequenced using Illumina technology generating reads from both ends of the library. Differential expression was assessed by comparing normalized sequencing read count levels between the two genders. We focused on the differences in the results derived from using single reads versus joined read pairs.

first: Jose Francisco

last: Sanchez Herrero

first: Raquel

last: Pluvinet

first: Antonio Jesus

last: Luna De Haro


title: Atlas of chromatin accessibility and translatome of tomato and rice root tip cell types

city: Davis

first: Siobhan

last: Brady

state: CA

address: 451 Health Sciences Dr

department: Genome Center and Plant Biology

institute: University of California Davis

summary: Plant species have evolved specialized cell types and regulatory programs. To understand this diversity, we profiled tomato cell type translatomes and chromatin accessibility. While cell type expression signatures are diverse, some genes exhibit robust cell type expression across time and environments. Using xylem differentiation as a model, newly described, repurposed and conserved genes illustrate this spatial variation. Data integration into regulatory networks demonstrates the function of molecularly uncharacterized cell types. Analyses of rice, tomato and Arabidopsis tissues suggest that root meristems are more conserved, while other cell types/tissues exhibit species-specific genes and processes. Several transcriptional properties observed in animals were also observed in plants and suggest cross-kingdom higher-order organizational properties. These data serve as a community resource, paving the way for engineering resilient crops.

sample_organism:
Solanum lycopersicum
Oryza sativa Japonica Group

overall_design: Examination of cell type-specific ATAC and TRAP seq profiles in tomato and rice roots. Tomato plate-based experiments (the nuclear and translating ribosome affinity purification experiments) were conducted with four independent replicates of each of the 12 lines, with T1 seed stocks (and T2 as needed). Tomato pot-based experiments were conducted with four independent replicates of the meristematic cortex and cortex lines and each root tissue was dissected for the lateral roots and the adventitious (hypocotyl-derived) roots. Following filtering steps only four samples were included, one lateral and one adventitious root sample of the meristematic cortex and cortex lines. Tomato field-based experiment was performed with six independent replicates of the meristematic cortex, endodermis, meristematic zone and 35S lines. Following filtering steps, one replicate was removed from the endodermis and one from the meristematic cortex. Rice plate-based experiments were conducted with three independent replicates of the endodermis, vasculature and 35S lines, with T1 seed stocks (and T2 as needed), except for the meristematic cortex for which two independent replicates of two lines were used. Arabidopsis plate-based experiments were done with two independent replicates of the meristematic cortex, endodermis, vasculature and 35S lines as described in Mustroph et al., 2009.

first: Kaisa

last: Kajala

first: G

middle: A

last: Mason

first: Alex

last: Canto-Pastor

first: Lidor

last: Shaar-Moshe

first: Mona

last: Gouran

first: Concepcion

last: Manzano

first: Sharon

last: Gray

first: Dorota

last: Kawa

first: Andrew

last: Yao

first: Donnelly

last: West

first: Mauricio

last: Reynoso

first: Germain

last: Pauluzzi

first: Neelima

last: Sinha

first: Julia

last: Bailey-Serres


title: Apc-mutants act as supercompetitors in intestinal tumour initiation

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

summary: Almost all colorectal cancers (CRC) present with mutations in the Apc gene, leading to unrestrained Wnt activation and the initiation of tumour development. We previously reported the competitive benefit of Apc-mutant intestinal stem cells (ISCs) within the crypt, however, the mechanism by which they  outcompete their wild type (WT) neighbours remained elusive. Here, we studied the effect of Apc-mutants using an in vitro culture system of WT (Lgr5-CreErt2) and Apc-/- (Lgr5-CreErt2;Apcfl/fl) organoids . The expression patterns of WT and Apc-/- organoids revealed significant upregulation in specific secreted Wnt antagonists Notum, Wif1 and Dkk2. Furthermore, we studied the effect of the secreted antagonist by treating WT organoids with either WT or Apc-/- conditioned medium (CM) for 48 hours and observed a significant decrease in stem cell markers and an increase in goblet cell markers. We report that Apc-mutants act as bona fide supercompetitors by secreting Wnt antagonists that result in active differentiation of WT ISCs.

overall_design: Intestinal organoids of Apc-mutant (Day2 n=3, Day 4 n=3); wild-type (Day 2 n=3, Day 4 n=3); Apc-mutant treated with Apc-mutant conditioned medium (Day 2 n=3); wild-type treated with Apc-mutant conditioned medium (Day 2 n=3)

middle: P

first: Sanne

last: van Neerven

first: Louis

last: Vermeulen


title: Gene expression changes in K562 upon USP7 inhibition

city: Groningen

first: JJ

last: Schuringa

address: Hanzeplein 1

department: Experimental Hematology

country: Netherlands

institute: UMCG

summary: K562 cells were grown in the presence of DMSO or the USP7 inhibitor FT671 (10 uM, 48h) after which RNA was isolated for transcriptome analyses.

overall_design:
Cells were treated with DMSO or FT671 (10 uM, 48h) in triplicate.
Cells were treated with DMSO or FT671 (10 uM) for 24h. ChIP was performed on sonicated chromatin for the histone marks H2AK119ub, H3K4me3, H3K36me3 and H3K27me3.

first: Jan


title: OsNF-YB1 acts in the regulation of RGB1 on grain development and starch accumulation through activation of OsYUC11-mediated auxin biosynthesis in rice endosperm cells

status: Public on Mar 23 2021

city: Yangzhou

first: Dongping

last: Zhang

address: 12 East Wenhui Avenue

institute: Yangzhou University

summary: To investigate how RGB1 regulates the grain development and starch biosynthesis, the expression profiles of genes in caryopsis of WYJ8 and RGB1Ri-5 line at 5 and 10 DAF were analyzed, using the RNA-seq assay. Approximately 3216 and 3363 genes that were up- or down-regulated, respectively, in RGB1Ri-5 as compared with WYJ8, were identified at 5 DAF. The numbers of up-regulated expressed genes (DEGs) at 10 DAF decreased to 2832 and those of down-regulated DEGs increased to 3398, respectively

overall_design: mRNA profiles of 5 and 10 DAF grains of wild type (WYJ8) and RGB1 RNAi line (RGB1Ri-5 )

first: Zhang

last: Dongping

last: Minyan

first: Liang

last: Jiansheng


title: Expression data from ECRSwNP, non-ECRSwNP and control (miRNA)

city: nanchang

first: Jieqing

last: Yu

state: Jiangxi Province

address: No. 17, Yongwaizheng street

institute: The First Affiliated Hospital of Nanchang University

summary:
Primarily on the basis of the absence or presence of nasal polyps (NPs)Chronic Rhinosinusitis(CRS) is often classified as CRS with nasal polyps (CRSwNP) and CRS without nasal polyps (CRSsNP). CRSwNP remains a signifificant public health problem with a considerable socioeconomic burden. The previous research reported that the pathophysiology of CRSwNP is a complex multifactorial disease. There have been many studies on its etiology, but its pathogenesis remains unclear. Dysregulated expression of miRNAs has been shown in psoriasis, rheumatoid arthritis, pulmonary fibrosis, and allergic asthma. CircRNA is also involved in the inflammatory diseases, such as in  rheumatoid arthritis, septic acute kidney injury, myocardial ischemia/reperfusion injury, epsis-induced liver damage and so on. Especially, the function of miRNA is research hotspots, including in CRSwNP. While, the study on circRNA in CRSwNP is still unknown. Additionally, according to the different percentage of eosinophil, CRSwNP was further divided into eosinophilic CRSwNP (ECRSwNP) and non-ECRSwNP. However, little is known about the functions of circRNAs and miRNAs in CRSwNP. The study is aimed to investigate the expression of circular RNA (circRNA) and microRNA (miRNAs) in CRSwNP and control group, to conform whether these molecules are related with the occurrence and development of  CRSwNP.
We aimed to compare the microarray expression profile of miRNAs and circRNAs in nasal polyps of CRSwNP and normal nasal mucosa from control subjects.

overall_design: 9 nasal mucosas were collected , including 3 ECRSwNP, 3 non-ECRSwNP and 3 control, for genomic microarray analysis of circRNA and microRNA expression. All tissue samples were from patients who were undergoing functional endoscopic sinus surgery in our department

first: Xue

last: Kang


title: Expression data from ECRSwNP, non-ECRSwNP and control (CircRNA)


title: Comparison of gene expression in the cervix of wild-type and WAPL Tg mice

city: Tokyo

first: Katsuyoshi

last: Kumagai

institute: Tokyo Medical University

summary: We searched for a group of genes correlated with WAPL.

overall_design: Search for gene clusters correlated with WAPL


title: Blocking ABA-signaling and ABA-treatment; ABA treatment dependence on VND transcription factors

city: Uppsala

first: Frauke

last: Augstein

address: Almas Allé 5

department: IOB

country: Sweden

institute: Uppsala University


title: Expression data from peripheral blood mononuclear cells（PBMCs) in newly diagnosed type 2 diabetes

city: Zhenjiang

first: shihe

last: shao

state: Jiangsu Province

address: 301 Xuefu Road

institute: School of Medicine, Jiangsu University

summary:
Type 2 diabetes mellitus is mainly affected by genetic and environmental factors, and long noncoding RNAs (lncRNAs) have been shown to be correlated with diabetes.LncRNA is expected to be a target for the treatment and prediction of type 2 diabetes.
We used microarrays to detail the lncRNAs and mRNAs expression in type 2 diabetes patients and healthy controls and obtained differentially expressed genes. and then the differentially expressed genes were further studied.

overall_design: Total RNA was extracted from peripheral blood mononuclear cells from diabetic and nondiabetic subjects .Four cases of T2DM and controls RNA samples were selected for chip analysis (OEBiotech, Shanghai, China).

first: Shihe

last: Shao

first: Yangguang

last: Du


title: Effect of blocking ABA-signaling in different tissues on transcriptomic changes induced by ABA-treatment

summary: ABA-signaling in disitinct root tissues is important for xylem phenotypes observed both under mock and ABA-treatment. We performed RNA-sequencing on Arabidopsis plants in which ABA-signalling is specifically blocked in the endodermis (J0571), the xylem (J1721) or the procambium (Q0990) to investigate the underlying transcriptomic changes.

overall_design: Transcriptomic changes in 1cm roots of 5 day old Arabidopsis plants upon treatment with 1µM ABA/ mock for 8h. Plants used in this experiments are in the F1 generation from the cross of the UAS::abi1-1 line with different enhancer trap lines: UAS::abi1-1xC24 (wt), UAS::abi1-1xJ1721, UAS::abi1-1xJ0571, UAS:abi1-1xQ0990

first: Prashanth

last: Ramachandran

first: Annelie

last: Carlsbecker


title: Human fetal immunity and microbial priming during early development

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN), A*STAR

summary: Here we report the 16S rRNA sequencing results of human fetal tissues, to identify bacterial genera present in developing fetus.

overall_design: Human fetal organs are collected and the tissues are used to amplify 16S rRNA

first: Archita

last: Mishra

first: Ghee

last: Lai

first: Leong

last: Yao

first: Thet

last: Aung

first: Noam

last: Shental

first: Aviva

last: Rotter-Maskowitz

first: Edwin

last: Shepherdson

first: Gurmit

last: Singh

first: Rhea

last: Pai

first: Adhika

last: Shanti

first: Regina

last: Wong

first: Andrea

last: Lee

first: Costerwell

last: Khyriem

first: Charles

last: Dutertre

first: Svetoslav

last: Chakarov

first: K

middle: G

last: Srinivasan

first: Nurhidaya

last: Shadan

first: Xiao-Meng

first: Shabnam

last: Khalilnezhad

first: Fabien

last: Cottier

first: Alrina

last: Tan

first: Gillian

last: Low

first: Phyllis

last: Chen

first: Yiping

last: Fan

first: Pei

last: Hor

first: Avery

first: Mahesh

last: Choolani

first: David

last: Vermijlen

first: Ankur

last: Sharma

first: Garold

last: Fuks

first: Ravid

last: Straussman

first: Norman

last: Pavelka

first: Benoit

last: Malleret

first: Naomi

last: McGovern

first: Salvatore

last: Albani

first: Jerry

last: Chan


title: Transcriptomic changes upon ABA treatment dependent on VND transcription factors

first: Frauke

last: Augstein

summary: Distinct transcriptomic changes upon ABA treatment are dependent on different VND transcription factors. We performed RNA-sequencing on mock and ABA-treated Arabidopsis plants to investigate the impact of VND1/2/3 and VND7 on gene expression changes upon ABA treatment.

overall_design: Transcriptomic changes in 1cm roots of 5 day old Arabidopsis plants upon treatment with 1µM ABA/ mock for 8h. Genotypes used in this experiment: Col-0 (wt), vnd1 vnd2 vnd3 triple mutant and vnd7 mutant

first: Prashanth

last: Ramachandran

first: Annelie

last: Carlsbecker


title: RNA sequencing of Arabidopsis mature seed and germination stages

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

institute: INRAE / IRHS

summary: We analysed transcriptome changes in Arabidopsis Col-0 and ros1-4 mutant seeds (3 stages corresponding mature (mat), germination II (II) and germination IV (IV)

overall_design: Three replicates of at least 100 seeds at three developemental stages with same growing conditions

first: Jaiana

last: Malabarba


title: scRNAseq of CD45 enriched cells from spinal cords of Optn floxed and KO mice

first: Lauren

last: Mifflin

summary: We prepared spinal cords from Optn floxed and KO mice treated with vehicle or the RIPK1 inhibitor Nec-1s, which were enriched for CD45+ cells and single cell RNA sequenced using the inDrop protocol.

overall_design: inDrop single cell RNA sequencing

first: Chengyu

last: Zou

first: Junying

last: Yuan


title: RNA sequencing of Arabidopsis seed developmental stages at different degrees of heat stress

summary: We analyzed transcriptome changes in Arabidopsis between seed development (3 stages corresponding Heart (H), Bent (B) and mature (MS) embryo stages) at three growing conditions (23, 25 and 27°C)

overall_design: Three replicates of at least 50 seeds at three developemental stages and different growing conditions


title: Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes

city: Chicago

first: Feng

last: Yue

state: IL

address: 303 E Chicago Ave. Simpson Querrey 7-518

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: Recent efforts have shown that structural variations (SVs) can disrupt three-dimensional genome organization and induce enhancer hijacking, yet no computational tools exist to identify such events from chromatin interaction data. Here, we develop NeoLoopFinder, a computational framework to identify the chromatin interactions induced by SVs, including interchromosomal translocations, large deletions and inversions. Our framework can automatically resolve complex SVs, reconstruct local Hi-C maps surrounding the breakpoints, normalize copy number variation and allele effects and predict chromatin loops induced by SVs. We applied NeoLoopFinder in Hi-C data from 50 cancer cell lines and primary tumors and identified tens of recurrent genes associated with enhancer hijacking. To experimentally validate NeoLoopFinder, we deleted the hijacked enhancers in prostate adenocarcinoma cells using CRISPR–Cas9, which significantly reduced expression of the target oncogene. In summary, NeoLoopFinder enables identification of critical oncogenic regulatory elements that can potentially reveal therapeutic targets.

overall_design:
In situ Hi-C was used to probe the chromatin interaction changes after deleting the hijacked enhancers in LNCaP cells.
4C-Seq was used to probe the chromatin interaction anchored at MYC gene in SKNMC cells

first: Xiaotao

last: Wang

first: Jie

last: Xu

first: Baozhen

last: Zhang

first: Ye

last: Hou

first: Fan

last: Song

first: Huijue

last: Lyu


title: Nonpeptidergic MrgprD-expressing neurons maintain cutaneous homeostasis via glutamate-mediated mast cell suppression

city: Pittsburgh

first: Daniel

middle: H

last: Kaplan

state: PA

address: 200 Lothrop Street

institute: University of Pittsburgh

summary: Cutaneous mast cells (MC) mediate numerous skin inflammatory processes and have anatomical and functional associations with sensory afferent neurons.  We found that Langerhans cell (LC)-deficient mice have reduced numbers of MrgprD-expressing epidermal nerve endings and manifest enhanced irritant dermatitis due to exaggerated MC degranulation.  Ablation of LC or MrgprD-expressing neurons increased expression of a MC gene module including the activating receptor, Mrgprb2, resulting in increased MC degranulation and cutaneous inflammation in multiple models.  β-alanine agonism of MrgprD-expressing neurons reduced expression of MC module genes and suppressed MC responses.  MrgprD-expressing neurons released glutamate which was increased by MrgprD agonism and decreased in LC-deficient mice.  Inhibiting glutamate release or glutamate receptor binding yielded hyperresponsive MC and a genomic state similar to that in mice lacking MrgprD-expressing neurons.  These data demonstrate that MrgprD-expressing neurons suppress MC hyperresponsiveness and skin inflammation via glutamate release thereby revealing an unexpected neuro-immune mechanism maintaining cutaneous immune homeostasis.

overall_design: For whole skin tissue RNAseq, mRNA was isolated from whole ear of DT treated MrgprdDTR mice, DT treated control MrgprdCre mice and WT mice treated with 50 mM β-ala or vehicle. For purified mast cell RNAseq, mRNA was extracted from sorted mast cells of DT treated MrgprdDTR and control MrgprdCre mice, or from peritoneal-derived mast cells cultured with 4 mM glutamate or 50 uM glutamate receptor anatognist NS102.

first: Shiqun

first: Virendra

last: Chaudhri


title: The ribosome collision sensor Hel2 functions as preventive quality control in the secretory pathway

first: Yoshitaka

last: Matsuo

address: 4-6-1, Shirokanedai, Minato-Ku

department: IMSUT

institute: The University of Tokyo,

summary: The ribosome collision due to translational stalling is recognized as a problematic event in translation by E3 ubiquitin ligase Hel2, leading to the non-canonical subunit dissociation followed by targeting of the faulty nascent peptides for degradation. Although Hel2-mediated quality control greatly contributes to maintaining cellular protein homeostasis, its physiological role in dealing with endogenous substrates remains unclear. Here we present a genome-wide analysis, based on selective ribosome profiling, to survey the endogenous substrates for Hel2. This reveals that Hel2 preferentially binds to the pre-engaged secretory ribosome-nascent-chain complexes (RNCs), which is translating upstream of targeting signals. Notably, Hel2 recruitment into secretory RNCs is elevated in the SRP-deficient condition; furthermore, the mitochondrial defects caused by insufficient SRP are enhanced by hel2 deletion, together with the mistargeting of secretory proteins into mitochondria. Collectively, our findings provide novel insights into the risk management in the secretory pathway for maintaining the cellular protein homeostasis.

overall_design: 2 replicates in 12 different treatment

first: Toshifumi

last: Inada


title: Type I interferon response in human HTBE and A549 cells

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: RNA-seq was used to profile gene expression changes in human tracheobronchial epithelial (HTBE) and A549 cells following type I interferon treatment.

overall_design: Transcriptomic comparison of type I interferon treatment against mock in HTBE and A549 cells.

first: Ariel

last: Rodriguez-Frandsen

first: Laura

last: Martin-Sancho

first: Sumit

last: Chanda


title: A Phase-Separated Nuclear GBPL Circuit Controls Immunity in Plants

city: West Haven

first: John

middle: David

last: MacMicking

state: CT

address: 850 West Campus Dr.

department: Microbial pathogenesis and immunobiology

institute: Yale University

summary: Liquid-liquid phase separation (LLPS) has emerged as a central paradigm for understanding how membrane-less organelles compartmentalize diverse cellular activities in eukaryotes. Here, we identified a new superfamily of plant Guanylate Binding Protein-Like GTPases (GBPLs) that assemble LLPS-driven condensates within the nucleus to protect against infection and autoimmunity. In Arabidopsis thaliana, two family members - GBPL1 and GBPL3 - undergo phase transition behavior to control transcriptional responses as part of an allosteric switch triggered by exposure to biotic stress. GBPL1, a pseudoGTPase, sequesters catalytically-active GBPL3 under basal conditions but is displaced by LLPS when GBPL3 enters the nucleus following immune cues to drive formation of unique membrane-less organelles termed GDACs (GBPL Defense-Activated Condensates) that we visualized by in situ cryo-electron tomography. Within these mesoscale GDAC structures, native GBPL3 directly bound defense gene promoters and recruited specific transcriptional coactivators of the Mediator complex plus RNA Pol II machinery to massively reprogram host gene expression for disease resistance. Together, our study identifies a new GBPL circuit that reinforces the biological importance of phase-separated condensates, in this case, as indispensable players in plant defense.

overall_design: RNA-seq analysis of WT, gbpl1-1, gbpl3-5, and GBPL3-OX arabidopsis seedlings. Four genotypes each contain 2 biological replicates resulting in a total of 8 samples.

first: Shuai

last: Huang

first: Shiwei

last: Zhu

first: Pradeep

last: Kumar

middle: D


title: Genome-wide distribution of Ash2L and H3K4me3 in mouse embryonic stem cell line E14

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

summary: The H3K4me3 levels on Ash2L binding sites are compared with the presence or absence of the co-binding of Dpy30

overall_design: Cut & Run profiling of HA-tag and H3K4me3 in E14 cell line stably expressing HA-Ash2L

first: Yali

last: Dou


title: MrgprD-expressing neurons maintain cutaneous mast cell homeostasis

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

summary: This study shows that croton oil has a specific inflammatory signature involving altered expression of cytokines that is quantitatively altered by long-term LC ablation.

overall_design: transcriptomes of whole ear tissue obtained 6 hours following application of vehicle or croton oil from LCDTA (long-term LC ablation) or LCDTR 3 days after DT administration (short-term LC ablation)


title: Purkinje neurons with loss of STIM1 exhibit age-dependent changes in gene expression and synaptic components

status: Public on Mar 22 2021

city: Bangalore

first: Gaiti

last: Hasan

state: Karnataka

address: GKVK Campus, Bellary Road

department: Laboratory of Intracellular calcium signaling

country: India

institute: National Centre for Biological Sciences

summary: The Stromal interaction molecule 1 (STIM1) is an ER-Ca2+ sensor and an essential component of ER-Ca2+ store operated Ca2+entry (SOCE). Loss of STIM1 affects metabotropic Glutamate Receptor 1 (mGluR1) mediated synaptic transmission, neuronal Ca2+ homeostasis and intrinsic plasticity in Purkinje Neurons (PNs). Long-term changes of intracellular Ca2+ signaling in PNs lead to neurodegenerative conditions, as evident in individuals with mutations of the ER-Ca2+ channel, the Inositol, 1,4,5-triphosphate receptor (IP3R). Moreover, Changes in gene expression upon reduced SOCE in non-excitable immune cells, the developing mouse brain, Drosophila pupal neurons  and human neural precursor cells have been reported. Gene expression profiles of mature differentiated neurons with loss of STIM1/nSOC have not been published to date. The study evaluated the differential gene expression in STIM1 knockout purkinje neurons compared to wild type purkinje neurons from 1 year old mice. Analysis of gene expression profiles demonstrated that STIM1 dependent Ca2+ homeostasis and signaling helps to maintain the expression of multiple key components of synaptic architecture and function in ageing animals. Our findings are significant in the context of finding new therapeutic means of alleviating the neurodegenerative changes associated with human SCAs.

overall_design: RNA isolated from the microdissected purkinje neuronal layer and molecular layer followed by RNA sequencing using Illumina Hiseq 2500 platform. Three biological replicates each of wild type and  STIM1 knockout purkinje neurons of 1 year old mice was used for the experiment.

first: Sreeja Kumari

last: Dhanya


title: Ectopic targeting of CG DNA methylation in Arabidopsis with the bacterial SssI methyltransferase.

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

summary: Targeting of epigenetic marks like DNA methylation to specific loci to manipulate gene expression is important in both basic research and in crop plant engineering. However, the extent to which targeted DNA methylation can be heritable is unknown. Here, we show that targeting the CG-specific methyltransferase M.SssI (SssI) from Spiroplasma sp. strain MQ1 with an artificial zinc finger (ZF) protein can establish heritable CG methylation and silencing of the targeted loci in Arabidopsis. This occurs even in the absence of a functional RNA-directed DNA methylation pathway, which is usually required for de novo methylation. In addition to the locus-specific targeted CG methylation, we observed widespread ectopic CG methylation throughout the genome that was highly heritable over generations, even in the absence of the effector transgene. A comparison with other epigenetic features showed that this ectopic methylation occurred preferentially at less open chromatin regions that were lacking in positive epigenetic histone marks. Although ectopic CG methylation was highly enriched over gene body regions, it showed little effect on transcription of these genes. However, we observed a mild but significant reduction in the histone variant H2A.Z and H3K27me3 over genes with ectopic CG methylation. These results outline general principals of the interaction of CG methylation with other epigenomic features that should help guide future efforts to engineer epigenomes.

overall_design: This dataset contains 9 BSPCR-seq, 32 WGBS, 35 RNA-seq, 30 ChIP-seq and 3 ATAC-seq data.

first: Javier

last: Gallego-Bartolome


title: Polysaccharide-based scaffolds for in situ hydrogelation: Use for next generation of bioartificial cardiac tissues

city: Hannover

first: Monika

last: Szepes

address: Carl-Neuberg Str. 1

department: Department of Cardiac, Thoracic, Transplantation and Vascular Surgery

country: Germany

institute: Hannover Medical School

summary: In search for Matrigel substitutes, which is composed of proteins and glycans from mouse sarcoma, we disclose new dextran-derived functionalised hydrogels of different molecular weight suited as matrices in bioartificial cardiac tissue (BCT) cultivation. Moreover, the biopeptide RGD was coupled to the dextran polysaccharide backbone in order to modulate the bioactivity of the new matrices. Dextrans in combination with human collagen I, supported cardiac tissue formation with induced pluripotent stem cell-derived cardiomyocytes and fibroblasts. The strength and frequency of the formed heart muscles were monitored over time in a bioreactor. It was shown that covalently in situ cross linked dextrans are promising matrix systems for tissue formation in the field of regenerative medicine.

overall_design: The transcriptome of two bioartificial cardiac tissue (BCT) groups with induced pluripotent stem cell-derived cardiomyocytes (iPSC-CM), prepared using human collagen I (hColI) and functionalised dextrane (Dex) with or without RGD (Dex-RGD), was compared to the differentiated CM source and undifferentiated iPSCs.

first: Samhita

last: Banerjee

first: Nick

last: Dibbert

first: Julio

middle: C

last: Rios Camacho

first: Andreas

last: Kirschning

first: Ina

last: Gruh

first: Gerald

last: Dräger


title: Transcriptional profiling of mouse germinal center B cells (B220+, GL7+, CD95+) isolated from GC-specific (Cg1-Cre) DAF-TM transgenic or control mice

city: New York

first: David

last: Dominguez-Sola

state: NY

address: One Gustave L. Levy Place, Box 1044A

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Germinal centers (GCs) support diversification and affinity maturation of antibody repertoires through iterative cycles of T-cell-dependent positive selection, B cell clonal expansion and antigen-receptor hypermutation.  Positive selection is critical for efficient affinity maturation and depends on only partially understood signaling processes. We show that BCL6-dependent physiological repression of decay accelerating factor (DAF/CD55) on GC B cells is critical for effective positive selection and affinity maturation during GC responses. Absence of DAF on GC B cells lifts restraint on local complement activation, yielding autocrine C3a/C5a-receptor signaling that is indispensable for CD40-dependent mTOR pathway activation during positive selection. Genetic disruption of this pathway causes premature GC collapse and impairs affinity maturation. These results identify previously undiscerned targets to therapeutically manipulate protective and potentially injurious humoral immune responses.

overall_design: Cg1-cre(+/-) or Cg1-cre(+/-);R26-DAF-TM(fl/fl) mice were immunized intraperitoneally with sheep red blood cells. Splenic germinal center B cells were sorted 10 days later for gene expression analysis.

first: Mark

last: Roberto

first: Yuan

last: Hu


title: Differential expression analyses in endothelial cells from APP/Psen1 mouse model

city: Sevilla

first: María Isabel

middle: Álvarez

last: Vergara

state: Sevilla

address: C/Manuel Siurot, sn

institute: Instituto de Biomedicina de Sevilla

summary:
Endothelial cells were isolated by flow cytometry using a specific marker (CD31) and their global gene expression profile was analyzed. CD11b marker was contraselected. This data were used to study molecular mechanisms implicated in endothelial cells from App/Psen1 mouse model.
In this dataset, we include the expression data obtained in endothelial cells from APP/Psen1   (18 month-old) mouse model using a specific marker for this cell type (CD31+). Functional enrichment analyses were carried out through GSEA, where we have included specific categories potentially involved with blood vessel formation.

overall_design: 6 Total samples were analyzed with 3 biological replicates in each condition (App/Psen1 and control mice). We generated the following comparison: App/Psen1 vs Control. Data were normalized by using rma algorithm (robust multiarray average) and the normalized matrix that we obtained with this analyses was used such input in the GSEA tool.

first: Maria

middle: I

last: Alvarez-Vergara

first: Alicia

last: Rosales-Nieves

first: Clara

last: Ortega-de San Luis

first: Rosana

last: March-Diaz

first: Guiomar

last: Rodriguez-Perinan

first: Jose

middle: L

last: Trillo-Contreras

first: Antonio

last: Heras-Garvín

first: Pedro

last: Gómez-Gálvez

first: Pablo

last: Vicente-Munuera

first: Rocío

last: González-Martínez

first: Raquel

last: del Toro

first: Eloisa

last: Herrera

first: Luis

last: Escudero

last: Villadiego

first: Miriam

last: Echevarría

last: Vitorica

first: Alberto

last: Pascual


title: Transcriptome Analyses of Myometrium from Fibroid Patients Reveals Phenotypic Differences Compared to Non-diseased Myometrium

status: Public on Mar 21 2021

city: Grand Rapids

last: Teixeira

state: MI

address: 400 Monroe Ave NW

department: Ob/Gyn

institute: Michigan State University

summary: Uterine fibroid tissues are often compared to their matched myometrium in an effort to understand their pathophysiology, but it is not clear whether the myometria of uterine fibroid patients represent truly non-disease control tissues. We analyzed the transcriptomes of myometrial samples from non-fibroid patients (M) and from matched myometrial (MF) and fibroid (F) samples to determine whether there is a phenotypic difference between fibroid and non-fibroid myometria. Multidimensional scaling plots revealed that M samples clustered separately from both MF and F samples.  A total of 1,169 differentially expressed genes (DEGs) (false discovery rate < 0.05) were observed in the MF comparison with M. Overrepresented Gene Ontology terms showed a high concordance of upregulated gene sets in MF compared to M, particularly extracellular matrix and structure organization. Gene set enrichment analyses showed that the leading-edge genes from the TGFβ signaling and inflammatory response gene sets were significantly enriched in MF. Overall comparison of the three tissues by three-dimensional principal component analyses showed that M, MF, and F samples clustered separately from each other and that a total of 732 DEGs from F vs M were not found in the F vs MF, which are likely understudied in the pathogenesis of uterine fibroids. These results suggest that the transcriptome of MF tissues are different from non-diseased myometrial tissues. Many dysregulated genes were not included in the F vs MF DEGs and may contain key genes for future investigations suggesting that fibroid studies should consider using not only matched myometrium but also non-diseased myometrium as the control.

overall_design: RNA-seq results for 6 myometrial samples from non-fibroid patients (control), 6 fibroid samples and 6 matched myometrialsamples from the same patient

first: Emmanuel

middle: N

last: Paul

first: Gregory

last: Burns

first: Tyler

middle: J

last: Carpenter

first: Joshua

last: Grey

first: Asgerally

last: Fazleabas


title: Decreased GLUT2 expression and defective glucose uptake in MODY3 human iPSC-Derived beta cells

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

institute: IMCB, A*STAR

summary: Purpose: To investigate the impact of HNF1A mutation on the development of pancreatic endocrine progenitors using differentiated control and MODY3-hiPSCs  Methods: ChIP-Seq was performed on pancreatic endocrine progenitors obtained on day 20 of the directed differentiation of control hPSCs (1 clone from H9 and 3 clones from iAgB-hiPSC) and hiPSCs from MODY3 patients (3 clones from P2. Peak calling analyses were carried out. qRT-PCR validation was also performed using SYBR Green assays.  Results: ChIP-Seq analysis revealed that numerous HNF1A target genes were downregulated in MODY3-hiPSC-derived pancreatic endocrine progenitors. Altered expression of a number of genes were further confirmed with qRT-PCR.  Conclusions: The H126D mutation in HNF1A does not affect the expression levels of HNF1A. However, this mutation affects the DNA binding capability of the transcription factor, thereby resulting in deficiency in the gene expression of proteins that are essential to maintain normal human beta-cell function for insulin secretion.

overall_design: ChIP-Seq was performed on pancreatic endocrine progenitors obtained on day 20 of the directed differentiation of hPSC of controls (1 clone from H9 and 3 clones from iAgB-hiPSCs) hiPSCs from MODY3 patients (3 clones from iP002).

first: Blaise

middle: S

last: Low

first: Chang

last: Lim

middle: K


title: Decreased GLUT2 expression and defective glucose uptake in MODY3 human iPSC-derived beta cells

summary: To evaluate the impact of HNF1A+/H126D mutation on pancreatic beta cell biology, we performed RNA-Seq analyses on the day 20 endocrine progenitor cells which maximally expressed HNF1A. Principal component analysis (PCA) plot showed distinct clustering of WT cells separate from the mutant cells, indicating that the HNF1A+/H126D mutation has an impact on global transcript profiles in the cells. A volcano plot demonstrated that there were 1724 genes downregulated and only 583 genes upregulated in mutant cells as compared to WT cells. Gene ontology (GO) analysis revealed that the genes that were downregulated in mutant cells were largely involved in biological processes such as localization, transport and secretion and molecular functions such as protein binding and transporter activity.

overall_design: RNA-Seq was performed on pancreatic endocrine progenitors obtained on day 20 of the directed differentiation of hiPSCs from MODY3 patients (3 clones from P1, 3 clones from P2) and wild-type genotype (1 clone from H9 and 1 clone from iAG).

first: B

first: C

first: A


title: Regulation of DNA (de)methylation positively impacts seed germination during seed development under heat stress

first: Jerome

last: Verdier

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

overall_design: Refer to individual Series


title: Blood transcriptome and clonal T cell correlates of response and nonresponse to eltrombopag therapy in a cohort of patients with chronic immune thrombocytopenia

city: Palo Alto

first: Haiyu

last: Zhang

address: 300 Pasteur Dr.

institute: Stanford University

summary: We evaluated the longitudinal effect of eltrombopag, a thrombopoietin receptor agonist, on gene expression in heavily pretreated patients with chronic immune thrombocytopenia (ITP) using blood transcriptome analysis on pretreatment, and following 1 week and 1 month of treatment samples. A strong stimulation of 208 eltrombopag-induced genes was identified in responders at 1-week time point. 90% of these genes are present in platelets, with GATA1, THPO, VIPAS39 and TGFB1 as top upstream regulators. Subsequently, despite a continued increase in platelet in responders, the eltrombopag-induced gene expression decreased at 1 month compared with the level at 1-week time point. This novel observation of the longitudinal effect of eltrombopag therapy over time suggests different stages of eltrombopag response. Non-responders did not exhibit eltrombopag-induced gene expression changes. This study provides novel insights into the mechanisms of eltrombopag response and nonresponse.

overall_design:
With informed consent, 17 patients with chronic ITP receiving eltrombopag monotherapy (75 mg daily via oral administration) during the period of blood sample collections were enrolled in this study. The criteria for response assessment are modified from the International Working Group guidelines (Rodeghiero F, 2009, PMID: 19005182). Response (R) in this study includes both complete response (platelet count >100 x 109/L and absence of bleeding) and response (platelet count ranges from 30 to 100 x 109/L, and at least a two-fold increase of the baseline count without bleeding) that defined in the International Working Group guideline. Nonresponse (NR) was defined as platelet count <30 x 109/L or failed to double baseline platelet count within 90 days of treatment, or bleeding. Peripheral blood samples were collected into PAXgene blood RNA tubes at pretreatment (pre), and at 1-week (1wk) and 1-month (1mon) on treatment. Total of 46 samples were included in this blood transcriptome analysis.
Total RNAs were extracted from these blood samples. Human alpha- and beta-globin mRNAs were depleted prior to RNA sequencing library construction. We then performed 3’-end sequencing for expression quantification (3SEQ) analysis on these samples (Beck AH, 2010, PMID: 20098735). 3SEQ is a type of RNA-seq that focuses on quantitative analysis of transcriptome by generating a directional sequencing library targeting 3’UTRs and flanking regions in near upstream of poly-A tail and ensuring that one read is produced and measured per transcript. The sequencing libraries were constructed, and Index associated 36 bp sequences of each sample were generated using Illumina HiSeq 2000 system. Next, 3SEQ data were filtered and mapped to human transcriptome hg19, and read counts for each transcript were generated as previously described (Guo X, 2013, PMID: 24342436).
For identification of differentially expressed genes, we employed significance analysis of microarrays (SAM)-Seq algorithm (SAMseq) for paired analysis between different time points of the same patient group using following cut off criteria: fold change > 2; average transcript per million (TPM) > 0.25; and q-value < 0.05. As we performed globin mRNA reduction procedure before 3SEQ library construction, the expressions of hemoglobin subunit alpha 1 (HBA1), alpha 2 (HBA2), and beta (HBB) were excluded from the SAMseq analysis.

first: Bing

middle: M

first: Xiangqian

last: Guo

first: Robert

middle: B

last: West

first: James

last: Bussel

last: Zehnder


title: Bisulfite sequencing (WGBS) of Arabidopsis seed developmental stages at different degrees of heat stress

summary: We analyzed methylome changes in Arabidopsis between seed development (2 stages corresponding to Bent (B) and mature (MS) embryo stages) at three growing conditions (23, 25 and 27°C)

overall_design: Two replicates of at least 500 seeds at two developemental stages and different growing conditions

first: Jaiana

last: Malabarba


title: Hi-C of fibroblasts and germ cells from wild mice with Rb fusions

city: Cerdanyola del Vallès (Bellaterra)

first: Covadonga

last: Vara

address: Campus UAB

department: Biologia cel·lular, Fisiologia i Immunologia

institute: Universitat Autònoma de Barcelona

summary: Structural data of genome organization in somatic cells (fibroblasts) and germ cells (primary spermatocytes and round spermatids) from wild mice with Rb fusions from the Barcelona Rb System.

overall_design: Spermatogenesis cell populations were isolated by Fluorescence-Activated Cell sorting. Hi-C of isolated populations (primary spermatocytes at lpachynema/diplonema stage and round spermatids) and fibroblasts (by the establishment of a cell line from Rb mice tissue).

first: Andreu

last: Paytuví-Gallart

first: Aurora

last: Ruiz-Herrera


title: Glucocorticoid signaling in pancreatic islets modulates gene regulatory programs and genetic risk of type 2 diabetes

status: Public on Mar 20 2021

first: Paola

last: Benaglio

address: 9500 Gilman Drive #0761

institute: University of California San Diego

summary: Glucocorticoids are key regulators of glucose homeostasis and pancreatic islet function. In this study we used ATAC-seq and RNA-seq to map chromatin accessibility and gene expression from eleven primary human islet samples cultured in vitro with the glucocorticoid dexamethasone at multiple doses and durations. We identified thousands of accessible chromatin sites and genes with significant changes in activity in response to glucocorticoids. Chromatin sites up-regulated in glucocorticoid signaling were prominently enriched for glucocorticoid receptor binding sites and up-regulated genes were enriched for ion transport and lipid metabolism, whereas down-regulated chromatin sites and genes were enriched for inflammatory, stress response and proliferative processes. Genetic variants associated with glucose levels and T2D risk were enriched in glucocorticoid-responsive chromatin sites, including fine-mapped variants at 51 known signals. Among fine-mapped variants in glucocorticoid-responsive chromatin, a likely casual variant at the 2p21 locus had glucocorticoid-dependent allelic effects on beta cell enhancer activity and affected SIX2 and SIX3 expression. Our results provide a comprehensive map of islet regulatory programs in response to glucocorticoids through which we uncover a role for islet glucocorticoid signaling in mediating genetic risk of T2D.

overall_design: Eleven primary human islet samples cultured in vitro with dexamethasone at multiple doses and durations. ATAC-seq and RNA-seq were performed in treated and untreated matched samples to map islet regulatory programs in response to glucocorticoids.

first: Anthony

last: Aylward

first: Mei-Lin

last: Okino

first: Joshua

last: Chiou

first: Elisha

last: Beebe

first: Jose

middle: A

last: Padilla

first: Sharlene

last: Diep

first: Kyle

last: Gaulton


title: RNAseq of Salvia dorisiana plant parts

city: Wageningen

first: Esmer

last: Jongedijk

address: Droevendaalsesteeg 1

department: Plant Sciences

institute: Wageningen University

summary: RNAseq of Salvia dorisiana plant parts

overall_design: RNAseq of Salvia dorisiana plant parts

first: Jules

last: Beekwilder


title: The mode of expression divergence in Drosophila fat body is infection-specific

city: Irvine

first: Zeba

last: Wunderlich

address: 4432 Natural Science II

department: Developmental and Cell Bio

institute: University of California Irvine

summary: Transcription is controlled by the interactions of cis-acting DNA elements with diffusible trans-acting factors. Changes in cis or trans factors can drive expression divergence within and between species, and the relative prevalence of each can reveal the evolutionary path to variation. Previous work delineating the mode of expression divergence in animals has largely used whole body expression measurements in a single condition. Since cis-acting elements often drive expression in a subset of cell types or conditions, these measurements may not capture the complete contribution of cis-acting changes. Here, we quantify the mode of expression divergence in the Drosophila fat body, the primary immune organ, in several conditions. We performed allele-specific expression analysis using two geographically distinct lines of D. melanogaster and their F1 hybrids. We performed separate infections with Gram-negative S. marcescens or Gram-positive E. faecalis bacteria, which trigger the two primary signaling pathways in the Drosophila innate immune response. The mode of expression divergence strongly depends on the condition, with trans-acting effects dominating in response to Gram-positive infection and cis-acting effects dominating in Gram-negative and pre-infection conditions. Expression divergence in several receptor proteins may underlie the infection-specific trans effects. Before infection, when the fat body has a metabolic role, there are many compensatory effects, changes in cis and trans that counteract each other to maintain expression levels. This work demonstrates that within a single tissue, the mode of expression divergence varies between conditions and suggests that these differences reflect the diverse evolutionary histories of host-pathogen interactions.

overall_design: 48 samples analyzed, 4 distinct genotypes with 3 different treatment conditions. Minimum of three bioreplicates per genotype/treatment.

first: Bryan

last: Ramirez-Corona

first: Stephanie

last: Fruth

first: Oluchi

last: ofoegbu


title: A single embryo, single cell time-resolved model for mouse gastrulation

city: Rehovot

first: Markus

last: Mittnenzweig

state: Shfela

address: 234 Herzl St.

institute: Weizmann Institute of Science

summary: Mouse embryonic development is a canonical model system for studying mammalian cell fate acquisition. Recently, single-cell atlases comprehensively charted embryonic transcriptional landscapes, yet inference of the coordinated dynamics of cells over such atlases remains challenging. Here we introduce a temporal model for mouse gastrulation, consisting of data from 153 individually sampled embryos spanning 36 hours of molecular diversification. Using new algorithms and precise timing we infer differentiation flows and lineage specification dynamics over the embryonic transcriptional manifold. Rapid transcriptional bifurcations characterize the commitment of early specialized node and blood cells. However, for most lineages, we observe combinatorial multi-furcation dynamics rather than hierarchical transcriptional transitions. In the mesoderm, dozens of transcription factors combinatorially regulate multi-furcations, as we exemplify using time-matched chimeric embryos of Foxc1/Foxc2 mutants. Our study rejects the notion of differentiation being governed by a series of binary choices, providing an alternative quantitative model for cell fate acquisition.

overall_design: Single cells from 153 WT mouse embryos (E6.5 - E8.25) were sequenced using MARS-seq2.0 which allowed to record each single cell's embryo identity during FACS cell-sorting. Using chimera and tetraploid complementation assays we analyzed the role of Foxc1 and Foxc2 during mesoderm specification. For both assays, we injected Foxc1/2 DKO and control cells into the blastocyst and performed scRNA-seq at ca. E7.5. Fluorescence intensity and embryo identity of each single cell from chimera and tetraploid embryos was recorded during FACS index-sorting.

first: Yoav

last: Mayshar

first: Saifeng

last: Cheng

first: Raz

last: Ben-Yair

first: Ron

last: Hadas

first: Yoach

last: Rais

first: Elad

last: Chomsky

first: Netta

last: Reines

first: Anna

last: Uzonyi

first: Lior

last: Lumerman

first: Aviezer

last: Lifshitz

first: Zohar

last: Mukamel

first: Ayelet-Hashahar

last: Orenbuch

first: Amos

last: Tanay

first: Yonatan

last: Stelzer


title: RNA Sequencing of H1 WT hESCs, H1 QSER1 KO hESCs, H1 TET1 KO hESCs, H1 QSER1/TET1 DKO hESCs, WT Day10 EBs, QSER1 KO Day10 EBs, TET1 KO Day10 EBs, QSER1/TET1 DKO Day10 EBs, WT PP1, QSER1 KO PP1, TET1 KO PP1, and QSER1/TET1 DKO PP1.

status: Public on Mar 19 2021

city: Beijing

first: Heng

last: Pan

address: 49 North Garden Rd., Haidian District

institute: Peking University Third Hospital

summary:
RNA Sequencing of H1 WT hESCs, H1 QSER1 KO hESCs, H1 TET1 KO hESCs, H1 QSER1/TET1 DKO hESCs, WT Day10 embryoid bodies (EBs), QSER1 KO Day10 EBs, TET1 KO Day10 EBs, QSER1/TET1 DKO Day10 EBs, WT pancreatic progenitors (PP1), QSER1 KO PP1, TET1 KO PP1, and QSER1/TET1 DKO PP1.
DNA methylation is essential to mammalian development, and dysregulation can cause serious pathological conditions. Key enzymes responsible for deposition and removal of DNA methylation are known, but how they cooperate to tightly regulate the methylation landscape remains a central question. Utilizing a knockin DNA methylation reporter, we performed a genome-wide CRISPR/Cas screen in human embryonic stem cells to discover DNA methylation regulators. The top screen hit was an uncharacterized gene QSER1, which proved to be a key guardian of bivalent promoters and poised enhancers of developmental genes, especially those residing in DNA methylation valleys (or canyons). We further demonstrate cooperation of QSER1 and TET1 through genetic and biochemical interactions to inhibit DNMT3-mediated de novo methylation and safeguard developmental programs.

overall_design: For RNA Sequencing, total RNA was isolated with the RNeasy Mini Kit (Qiagen, 74136). H1 WT hESCs had n=5 biological replicates. All other conditions had n=3 biological replicates.

first: Pan

last: Heng

first: Dixon

last: Gary


title: Aberrant claudin-6–adhesion signal promotes endometrial cancer progression via estrogen receptor α

city: Fukushima

first: Hideki

last: Chiba

address: 1 Hikarigaoka

institute: Fukushima Medical University

summary: Cell adhesion proteins not only maintain tissue integrity but also possess signaling abilities to organize diverse cellular events in a variety of physiological and pathological processes; however, the underlying mechanism remains obscure. Among cell adhesion molecules, the claudin (CLDN) family often possesses aberrant expression in various cancers, but the biological relevance and molecular basis have not yet been established. Here, we show that high CLDN6 expression accelerates cellular proliferation and migration in human endometrial cancer cells in vitro. Using xenograft model, we also revealed that aberrant CLDN6 expression promotes tumor growth and invasion in endometrial cancer tissues. The second extracellular domain and Y196/200 of CLDN6 were required to recruit and activate Src-family kinases (SFKs) and to stimulate malignant phenotypes. Importantly, we demonstrate that the CLDN6/SFK/PI3K-dependent AKT and SGK (serum- and glucocorticoid-regulated kinase) signalings target Ser518 in the human estrogen receptor α and ligand-independently activate target genes in endometrial cancer cells, resulting in cancer development. CLDN6, at least in part, also regulated gene expression in an ERα-independent manner.

overall_design: RNA-seq analysis was performed using wild-type (WT) and CLDN6-overexpressed Ishikawa cell lines.

first: Manabu

last: Kojima

first: Kotaro

last: Sugimoto

first: Makoto

last: Kobayashi

first: Naoki

last: Ichikawa-Tomikawa

first: Korehito

last: Kashiwagi

first: Takafumi

last: Watanabe

first: Shu

last: Soeda

first: Keiya

last: Fujimori


title: Transcriptome changes in differentiating primary brite adipocytes 24 or 72 hours after knockdown of long noncoding RNA Ctcflos

city: Freising

first: Tobias

last: Fromme

address: Gregor-Mendel-Str. 2

department: Molecular Nutritional Medicine

institute: Technical University of Munich

summary: We analyzed coding and noncoding transcript abundance in primary differentiating brite adipocytes derived from murine inguinal white adipose tissue, 24 hours or 72 hours in response to lncRNA Ctcflos knockdown at day 1 of differentiation

overall_design: We prepared primary preadipocytes from stromal-vascular fraction of murine inguinal white adipose tissue of 129SvEv mice, induced them at sub-confluence for 2 days and differentiated them for 1 day in the presence of rosiglitazone to induce browning. Cells were reverse transfected with lncRNA Ctcflos-targeting or non-targeting control LNA Gapmer Antisense oligonucleotides [50nM] and harvested either 24 hours or 72 hours post transfection. We sequenced total RNA and determined transcript abundance.

first: Andrea

last: Bast-Habersbrunner

first: Yongguo

last: Li

first: Fromme

last: Tobias

first: Martin

last: Klingenspor

first: Petra

last: Schwalie

first: Bart

last: Deplancke


title: comparative transcriptome analysis between original strain FS35 and FK520 high-yield strain OphaCfkbU

city: Tianjin

first: Pan

last: Wang

address: Peiyang Park Campus: No.135 Yaguan Road, Haihe Education Park

institute: Tianjin university

summary: To solve the problem of low FK520 production by Streptomyces hygroscopicus var. ascomyceticus FS35, PHB synthesis gene phaC and PHB decomposition gene fkbU were co-overexpressed in parent strain FS35 to construct recombinant strain OphaCfkbU. Surprisingly, recombinant strain OphaCfkbU accumulated more biomass than parent strain FS35 in whole fermentation. Therefore, to explore the effect of co-overexpression on the strain growth, comparative transcriptome analysis were carried out between parent strain FS35 and recombinant strain OphaCfkbU. Transcriptome data showed that co-overexpression increased the utilization of sugar sources and stimulated the generation of coenzymes, ribosome, acyl carrier proteins and sulfate donors. This study revealed the internal mechanism of the effect of PHB on strain growth, proving a reference for the role of PHB in other microorganisms.

sample_organism: Streptomyces hygroscopicus subsp. ascomyceticus

overall_design: Determination of one sample from strain FS35 and one sample from strain OphaCfkbU at 50 h of fermentation, with the sample from strain FS35 as the control

first: Yue

last: Zhang


title: Antagonistic activities of co-transcriptional regulators within an early developmental window sets quantitative FLC expression

first: Michael

last: Nodine

state: Gelderland

address: Radix West

institute: Wageningen University & Research

summary: Quantitative variation in expression of the Arabidopsis floral repressor FLC influences whether plants overwinter before flowering or have a rapid cycling habit, enabling multiple generations a year. Genetic analysis has identified activators and repressors of FLC expression, but how they interact to set expression level is poorly understood. Here, we show that antagonistic functions of the FLC activator FRIGIDA (FRI), and the repressor FCA, at a specific stage of embryo development, determines FLC expression and flowering. FRI antagonizes an FCA-induced proximal polyadenylation to increase FLC expression and delay flowering. Sector analysis shows that FRI activity during the early heart stage of embryo development maximally delays flowering. Opposing functions of co-transcriptional regulators during an early embryonic developmental window thus set FLC expression levels and determine flowering time.

overall_design: mRNA-seq libraries were constructed for three biological replicates of early heart stage embryos from three genotypes