title: Clock controlled and cold induced CDF6 alters growth and development to changing temperatures

city: Riverside

first: Dawn

last: Nagel

address: 3401 Watkins Avenue (Batchelor Hall Rm 1123)

department: Botany and Plant Sciences

institute: University of Califonia, Riverside

summary: The circadian clock represents a critical regulatory network, which allows plants to anticipate environmental changes as inputs and promote plant survival by regulating various physiological outputs. Here, we examine the function of the clock-regulated transcription factor, CYCLING DOF FACTOR 6 (CDF6), during cold stress in Arabidopsis thaliana. We found that the clock gates CDF6 transcript accumulation in the vasculature during cold stress. CDF6 mis-expression results in an altered flowering phenotype during both ambient and cold stress. A genome-wide transcriptome analysis links CDF6 to genes associated with flowering and seed germination during cold and ambient temperatures, respectively. Analysis of key floral regulators indicates that CDF6 alters flowering during cold stress by repressing photoperiodic flowering components, FLOWERING LOCUS T (FT), CONSTANS (CO), and BROTHER OF FT (BFT). Gene ontology enrichment further suggests that CDF6 regulates circadian and developmental associated genes. These results provide insight into how the clock-controlled CDF6 modulates plant development during moderate cold stress.

overall_design: Measured transciptome changes in Columbia-0 (WT), cdf6, and SUC2::CDF6 under ambient (22°C) and 1-hr cold (10°C) temperature on 11-day-old seedlings entrained in diurnal light for 8 days before transfer to constant light for two days. Three replicates were sampled for all genotypes and conditions at ZT0.

first: Emily

last: Blair

first: Greg

last: Goralogia

first: Matthew

last: Lincoln

first: Takato

last: Imaizumi


title: Hi-C in MGE, CGE, LGE and cortical regions from mouse embryonic forebrain

status: Public on Jul 01 2022

city: Bethesda

first: Timothy

last: Petros

state: Maryland

address: 35 Convent Drive, Bg 35 Room 3B-1002

country: USA

institute: NICHD

summary: While comparative genetic analysis has been performed between distinct regions of the embryonic forebrain, a comprehensive characterization of differential epigenomic organization has not been performed. We collected single-cell chromatin accessibility profiles from four distinct neurogenic regions of the embryonic mouse forebrain using single nuclei ATAC-Seq (snATAC-Seq). We identified thousands of differentially accessible peaks, many restricted to distinct progenitor cell types or brain regions. We integrated snATAC-Seq and single cell transcriptome data to characterize changes of chromatin accessibility at enhancers and promoters that were tightly coupled to transcript abundance. Multi-modal integration of histone modifications (CUT&Tag and CUT&RUN), promoter-enhancer interactions (Capture-C) and high-order chromatin structure (Hi-C) extended these initial observations. This dataset reveals a diverse chromatin landscape with region-specific regulatory mechanisms and genomic interactions in distinct neurogenic regions of the embryonic mouse brain and represents an extensive public resource of a ‘ground truth’ epigenomic landscape at this critical stage of neurogenesis.

overall_design: MGE, CGE, LGE and cortical regions from E12.5 mouse embryos

first: Christopher

middle: T

last: Rhodes

first: Pedro

last: Rocha


title: Capture-C in MGE, CGE, LGE and cortical regions from mouse embryonic forebrain

overall_design: MGE, CGE, LGE, cortex, and liver from E12.5 mouse (C57BL/6J) embryos


title: CUT&Tag (H3K27me3) in MGE, CGE, LGE and cortical regions from mouse (C57BL/6J) embryonic forebrain

type: Genome binding/occupancy profiling by high throughput sequencing


title: In vitro generation of brain regulatory T cells by co-culturing with astrocytes

city: Fukuoka

first: Minako

last: Ito

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

country: Japan

institute: Kyushu University

type: Expression profiling by high throughput sequencing

summary: We developed a culture method that confers brain Treg characteristics in vitro. Naive Tregs from the spleen were activated and efficiently amplified by T-cell receptor (TCR) stimulation in the presence of primary astrocytes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Treg cells from spleen (SP-Treg) and brain with ischemic stroke (Isckemia-Treg) and in vitro culture (iB-Treg(A), iB-Treg(B), iB-Treg(C)).

first: Shinichi

last: Yamamoto

first: Ako

last: Matsui

first: Masaki

last: Ohyagi

first: Chie

last: Kikutake

first: Yoshihiro

last: Harada

first: Mana

last: Iizuka-Koga

first: Mikita

last: Suyama

first: Akihiko

last: Yoshimura


title: CUT&RUN (H3K27Ac3) in MGE, CGE, LGE and cortical regions from mouse embryonic forebrain


title: CUT&Tag (H3K4me3) in MGE, CGE, LGE and cortical regions from mouse (C57BL/6J)  embryonic forebrain


title: Regulation of retina microexons by SRRM3, SRRM4 and MSI1 in human cell lines

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

summary: To investigate the role of MSI1, SRRM3 and SRRM4 as a regulator of retina microexons (RetMICs) in vitro in humans, we have ectopically expressed these genes in HEK293 cells and performed RNA-seq.

overall_design: For each gene and a control empty vector, we generated stable HEK293 cells lines inducible by Doxycycline.

first: M

last: Ciampi

first: S

last: Head

first: L

last: Serrano


title: A single-cell based precision medicine approach using glioblastoma patient specific models

city: Seattle

first: James

middle: H.

last: Park

state: WA

address: 1736 Belmont ave, Apt 105

institute: Institute for Systems Biology

summary: Glioblastoma (GBM) is a heterogeneous tumor made up of cell states that evolve over time. Here, we modeled tumor evolutionary trajectories during standard-of-care treatment using multi-omic single-cell analysis of a primary tumor sample, corresponding mouse xenografts subjected to standard of care therapy, and recurrent tumor at autopsy. We mined the multi-omic data with single cell SYstems Genetics Network AnaLysis (scSYGNAL) to identify a network of 52 regulators that mediate treatment-induced shifts in xenograft tumor-cell states that were also reflected in recurrence. By integrating scSYGNAL-derived regulatory network information with transcription factor accessibility deviations derived from single-cell ATAC-seq data, we developed consensus networks that modulate cell state transitions across subpopulations of primary and recurrent tumor cells. Finally, by matching targeted therapies to active regulatory networks underlying tumor evolutionary trajectories, we provide a framework for applying single-cell-based precision medicine approaches in a concurrent, adjuvant, or recurrent setting.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell RNA-sequencing of primary GBM tumor and recurrent GBM tumor (Samples 1 and 3). Additional single-cell RNA-sequencing was performed on PDX samples post 24hrs and 72hrs treated with fractionated radiotherapy and temozolomide and corresponding untreated control samples (Sample 2).

first: Abdullah

middle: H

last: Feroze

first: Samuel

middle: N

last: Emerson

first: Anca

middle: B

last: Mihalas

first: C

middle: D

last: Keene

first: Patrick

middle: J

last: Cimino

first: Adrian

middle: L

last: Garcia de Lomana

first: Kavya

last: Kannan

first: Wei-Ju

last: Wu

first: Serdar

last: Turkarslan

first: Nitin

middle: S

last: Baliga

first: Anoop

middle: P

last: Patel


title: Regulation of retina microexons by srrm3 in zebrafish and by SRRM3, SRRM4 and MSI1 in human cell lines

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

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: Refer to individual Series


title: Regulation of retina microexons by srrm3 in zebrafish

summary: To investigate the role of srrm3 as a regulator of retina microexons (RetMICs) we have sequenced adult retina from WT animals, and enucleated eyes from 5 dpf larvae WT and KO for srrm3.

overall_design: 24 hpf heads were collected from WT AB fish. Larvae at 48 hpf, 60 hpf and 72 hpf were collected, genotyped using fin clip, and RNA extracted from enucleated eyes from srrm3 KO and WT siblings.


title: LCMV-Armstrong infection

city: La Jolla

first: Ananda

last: Goldrath

state: CA

address: 9500 Gilman Dr

institute: UCSD


title: Single cell RNA-seq of CD4+ T cell subsets during LCMV-Armstrong infection

summary: CD4+ memory T cells play a pivatol role in mediating long-term immunity and therefore are an important target in vaccine development. Multiple functionally distinct helper CD4+ T cell subsets can arise in response to a single invading pathogen, complicating the identification of rare memory CD4+ T cells. Here we found that expression of Id3, an inhibitor of E protein transcription factors, identified a population of cells within both the CD4+ Tfh and Th1 helper lineages that exhibited memory potential in response to secondary infection. Notably, a subset of Th1 memory cells expressing Id3 exhibited enhanced expansion upon response to pathogen, generating both Th1 and Tfh secondary effector cell populations, and displayed enrichment of key molecules associated with memory potential when compared to Id3lo Th1 cells. Thus, Id3 expression serves as an important marker of multipotent memory CD4+ T cells.

overall_design: 3 samples, 2 replicates each, single cell rna-seq was performed on SMARTA T cells at D7, D21, and D44 of LCMV-Arm infection

first: T

middle: Z

last: Deng

first: A

middle: W


title: RNA-seq of CD4+ Helper T cell subsets (Th1 and Tfh) during LCMV-Armstrong infection

overall_design: 7 Samples, 2-5 replicates each, Naïve SMARTA CD4+ T cells or Day 7, 21, 41 Th1 and Tfh subsets


title: Fine-tuned KDM1A alternative splicing regulates human cardiomyogenesis through an enzymatic-independent mechanism

city: Jeddah

first: Antonio

last: Adamo

state: Not in US

address: 4700 KAUST, Thuwal

department: Biological and Environmental Science and Engineering Division, BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology, KAUST

summary: Background: The histone demethylase KDM1A is a multi-faceted regulator of critical developmental processes, including mesodermal and cardiac tube formation during mice gastrulation. The fine-tuning of KDM1A splicing has been linked to regulating the transcriptional program of excitable cells such as neurons. However, it is unknown whether modulating the expression of KDM1A isoforms is crucial for the specification and maintenance of cell identity of other cell types sensitive to electrical cues such as the cardiomyocytes.  Objective: We investigated the role of ubKDM1A and KDM1A+2a ubiquitous splice variants during cardiomyogenesis and evaluated their impact on the regulation of cardiac differentiation in vitro. Methods and Results: We discovered a temporal modulation of ubKDM1A and KDM1A+2a isoform levels during human and mouse fetal cardiac development. Therefore, we generated human embryonic stem cells (hESCs) exclusively devoid of one or both isoforms and assessed their potential to derive cardiomyocytes. KDM1A depletion severely impaired cardiac differentiation. Conversely, KDM1A+2a-/- hESCs give rise to functional cardiomyocytes, displaying increased beating amplitude and frequency compared to wild-type cells. Transcriptomic profiling revealed that KDM1A-/- cardiomyocytes fail to activate an effective cardiac transcriptional program, while the depletion of KDM1A+2a enhances the expression of key cardiogenic markers. Notably, the impaired cardiac differentiation of KDM1A-/- cells can be rescued by re-expressing ubKDM1A or catalytically deficient ubKDM1A-K661A, but not by KDM1A+2a or KDM1A+2a-K661A. These data demonstrate a divergent role of the two KDM1A isoforms that is independent of their enzymatic activity. Through an exhaustive biochemical and genome-wide binding characterization, we excluded that the opposite ubKDM1A- and KDM1A+2a-mediated regulation of cardiac differentiation resides into differential substrate specificity, H3K4 demethylation efficiency, core-partners binding affinity, or alternative genome binding profiles. Conclusions: Our findings suggest the existence of a divergent scaffolding role of KDM1A splice variants during hESC differentiation into cardiomyocytes.

overall_design:
Bulk RNA-SEQ of KDM1A Knockout or KDM1A+2a knockout hESC and hESC-derived cardiomyocytes. Bulk RNA-SEQ of KDM1A Knockout hESC rescued with either KDM1A+2a or ubKDM1A splice varinats. For each genotype and differentiation stage two clones have been generated. Six to four independent RNA-Seq libraries have been processed.
ChIP-Seq experiments performed at different stages (Day 0=hESC stage; Day 2=mesodermal cells; Day 4 = cardiac precursors; Day 18-20 = cardiomyocytes) of WT hESC differentiation into cardiomyocytes. ChIP-Seq experiments of hESC-derived cardiomyocytes of KDM1A KO cells rescued with either KDM1A+2a or ubKDM1A isoforms. The differentiation into cardiomyocytes has been performed using the The PSC Cardiomyocyte Differentiation Kit (Thermo Fisher Scientific) according to manufacturer' instructions.  For each differentiation stage two independent ChiP-Seq experiments have been performed, with the exception of Day 4 (n=1) and the rescue for KDM1A+2a (n=1).

first: Veronica

last: Astro

first: Roberta

last: Pennucci

first: Jonathan

last: Caroli

first: Alfonso

last: Saera-Vila

first: Kelly

last: Cardona-Londoño

first: Chiara

last: Forastieri

first: Elisabetta

last: Fiacco

first: Gustavo

last: Ramirez-Calderon

first: Fatima

last: Maksoud

first: Maryam

last: Alowaysi

first: Elisa

last: Sogne

first: Andrea

last: Falqui

first: Federico

last: Gonzàlez

first: Nuria

last: Montserrat

first: Elena

last: Battaglioli

last: Mattevi


title: Bromodomain targeting overcomes treatment resistance in distinct molecular subtypes of melanoma

city: San Francisoc

first: Mehdi

last: Nosrati

state: California

address: 475 Brannan, Suite 220

department: Research Institute

institute: California Pacific Medical Center

overall_design: NSG mice bearing tumors from the MM-300 PDX line were treated with vehicle or the combination of bromosporine + cobimetinib (bromo+cobi). RNA was extracted from subcutaneous tumors to perform next generation sequencing to identify differentially expressed genes between the vehicle  and drug treatment groups. RNA Seq was performed from tumors of 3 mice each for vehicle vs. treatment group.

first: Altaf

middle: A

last: Dar

first: Mohammed

last: Kashani-Sabet


title: RNA-seq of memory CD4+ Helper T cell subsets (Th1 and Tfh) during LCMV-Armstrong infection

first: Ananda

last: Goldrath

overall_design: 4 Samples, 3 replicates each, Day 30 Th1 and Tfh subsets

first: T

last: Deng

first: A


title: STUB1 is an intracellular checkpoint for interferon gamma sensing

status: Public on Jun 30 2022

city: Singapore

first: Simon

last: Ng

address: 8 Biomedical Grove

country: Singapore

institute: MSD

summary: Immune checkpoint blockade (ICB) leads to durable and complete tumour regression in some patients but in others gives temporary, partial or no response. Accordingly, significant efforts are underway to identify tumour-intrinsic mechanisms underlying ICB resistance. Results from a published CRISPR screen in a mouse model suggested that targeting STUB1, an E3 ligase involved in protein homeostasis, may overcome ICB resistance but the molecular basis of this effect remains unclear. Herein, we report an under-appreciated role of STUB1 to dampen the interferon gamma (IFNg) response. Genetic deletion of STUB1 increased IFNGR1 abundance on the cell surface and thus enhanced the downstream IFNg response as showed by multiple approaches including Western blotting, flow cytometry, qPCR, phospho-STAT1 assay, immunopeptidomics, proteomics, and gene expression profiling. Human prostate and breast cancer cells with STUB1 deletion were also susceptible to cytokine-induced growth inhibition. Furthermore, blockade of STUB1 protein function recapitulated the STUB1-null phenotypes. Despite these encouraging in vitro data and positive implications from clinical datasets, we did not observe in vivo benefits of inactivating Stub1 in mouse syngeneic tumour models – with or without combination with anti-PD-1 therapy. However, our findings elucidate STUB1 as a barrier to IFNg sensing, prompting further investigations to assess if broader inactivation of human STUB1 in both tumors and immune cells could overcome ICB resistance.

overall_design: CRISPR-engineered B16-F10 cells (gControl, gStub1 #1, and gStub1 #2), either untreated or treated with 0.03 ng/ml IFNg for 6 h or 24 h

first: Brian

last: Henry

first: Anthony

last: Partridge


title: 2-Ethylhexyl Diphenyl Phosphate  (CAS No. 1241-94-7): 5-Day Rat Gavage Toxicogenomic Study

city: Durham

first: Scott

last: Auerbach

state: North Carolina

address: 111 TW Alexander Drive

institute: Division of the National Toxicology Program at NIEHS

summary: 2-Ethylhexyl Diphenyl Phosphate (EHDP) is an organophosphate flame retardant currently on the market and used as a replacement for phased-out polybrominated diphenyl ethers. Toxicity information on this class of chemicals is inadequate. Herein, the NTP use short-term, in vivo transcriptomic studies to inform potential points of departure for EHDP.

overall_design:
The National Toxicity Program (NTP) conducted a transcriptomic study on EHDP, in male Harlan Sprague Dawley rats. EHDP was dissolved in corn oil. Exposure was once daily for 4 days by oral gavage. EHDP (>99%) was tested at six doses (0, 61, 123, 245, 489, and 979 mg/kg body weight). On Day 5, animals were sacrificed, standard toxicological measures assessed, and the liver taken for gene expression studies using Affymetrix microarrays.
contributor: National Toxicology Program


title: CHIP-seq analysis of cetuximab-resistant cells in oral cancer

city: Chiba

first: Tomoaki

last: Saito

address: 1-8-1 Inohana, Chuo-ku

department: Oral Science

institute: Chiba University

summary: We conducted chromatin immunoprecipitation for H3K27ac and BRD4, followed by sequencing (ChIP-seq) to investigate super-enhancer (SE) for drug-resistant using cetuximab-resistant cells and control cells. SE analysis revealed that several unique SE-associated genes in cetuximab-resistant cells were identified.

overall_design: To investigate the reaction at the genome level in cetuximab-resistant cells, control cells and cetuximab-resistant cells were sent to Active Motif for ChIP-Seq.

first: N

last: Tanaka

last: Seki

first: K

last: Uzawa


title: tert-Butylphenyl Diphenyl Phosphate  (CAS No. 56803-37-3): 5-Day Rat Gavage Toxicogenomic Study

summary: tert-Butylphenyl Diphenyl Phosphate (BPDP) is an organophosphate flame retardant currently on the market and used as a replacement for phased-out polybrominated diphenyl ethers. Toxicity information on this class of chemicals is inadequate. Herein, the NTP use short-term, in vivo transcriptomic studies to inform potential points of departure for BPDP.

overall_design:
The National Toxicity Program (NTP) conducted a transcriptomic study on BPDP, in male Harlan Sprague Dawley rats. BPDP was dissolved in corn oil. Exposure was once daily for 4 days by oral gavage. BPDP (>99%) was tested at six doses (0, 65, 129, 258, 516, and 1033 mg/kg body weight). On Day 5, animals were sacrificed, standard toxicological measures assessed, and the liver taken for gene expression studies using Affymetrix microarrays.
contributor: National Toxicology Program


title: Tricresyl Phosphate (CAS No. 1330-78-5): 5-Day Rat Gavage Toxicogenomic Study

summary: Tricresyl Phosphate (TCP) is an organophosphate flame retardant currently on the market and used as a replacement for phased-out polybrominated diphenyl ethers. Toxicity information on this class of chemicals is inadequate. Herein, the NTP use short-term, in vivo transcriptomic studies to inform potential points of departure for TCP.

overall_design:
The National Toxicity Program (NTP) conducted a transcriptomic study on TCP, in male Harlan Sprague Dawley rats. TCP was dissolved in corn oil. Exposure was once daily for 4 days by oral gavage. TCP (>99%) was tested at six doses (0, 62, 125, 249,  497, and 995 mg/kg body weight). On Day 5, animals were sacrificed, standard toxicological measures assessed, and the liver taken for gene expression studies using Affymetrix microarrays.
contributor: National Toxicology Program


title: Isopropylated Phenol Phosphate (CAS No. 68937-41-7): 5-Day Rat Gavage Toxicogenomic Study

summary: Isopropylated Phenol Phosphate (IPP) is an organophosphate flame retardant currently on the market and used as a replacement for phased-out polybrominated diphenyl ethers. Toxicity information on this class of chemicals is inadequate. Herein, the NTP use short-term, in vivo transcriptomic studies to inform potential points of departure for IPP.

overall_design:
The National Toxicity Program (NTP) conducted a transcriptomic study on IPP, in male Harlan Sprague Dawley rats. IPP was dissolved in corn oil. Exposure was once daily for 4 days by oral gavage. IPP (>99%) was tested at five doses (0, 77, 153, 306,  and 611 mg/kg body weight). On Day 5, animals were sacrificed, standard toxicological measures assessed, and the liver taken for gene expression studies using Affymetrix microarrays.
contributor: National Toxicology Program


title: Differentially expressed genes in B-1b compared to B-1a

city: Charlottesville

first: Tanyaporn

last: Pattarabanjird

state: Virginia

address: 345 Crispell Dr. MR6

department: Carter Immunology Center

institute: University of Virginia

summary: B-1b cells are known to produce higher IgM level compared to B-1a cells. This study aims to identify differentially expressed genes and pathways that might enrich in B-1b cells and contribute to higher IgM production.

overall_design: Sort-purified B-1a (n = 3) and B-1b (n = 3) from murine peritoneal cavity, extracted RNA from these cells, and performed RNA sequencing

first: Coleen

last: McNamara

first: Prasad

last: Srikakulapu


title: Isodecyl Diphenyl Phosphate (CAS No. 29761-21-5): 5-Day Rat Gavage Toxicogenomic Study

summary: Isodecyl Diphenyl Phosphate (IDDP) is an organophosphate flame retardant currently on the market and used as a replacement for phased-out polybrominated diphenyl ethers. Toxicity information on this class of chemicals is inadequate. Herein, the NTP use short-term, in vivo transcriptomic studies to inform potential points of departure for IDDP.

overall_design:
The National Toxicity Program (NTP) conducted a transcriptomic study on IDDP, in male Harlan Sprague Dawley rats. IDDP was dissolved in corn oil. Exposure was once daily for 4 days by oral gavage. IDDP (>99%) was tested at six doses (0, 66, 132, 264, 527, and 1054 mg/kg body weight). On Day 5, animals were sacrificed, standard toxicological measures assessed, and the liver taken for gene expression studies using Affymetrix microarrays.
contributor: National Toxicology Program


title: RankL induced mice BMM  treated with or without dimethyl itaconate for 24h

city: PALO ALTO

first: yuting

last: wang

address: 265 campus drive, lokey stem cell research building, RM-G3105-SIM1

institute: Stanford University

summary: RankL induced mice BMM  following dimethyl itaconate treatment for 24h

overall_design: BMMs isolated from 8-week-old male C57BL/6 mice were cultured with a-MEM in the absence of FBS for  12 h, then changed to complete media supplied with RANKL (100 ng/mL) and DI (20mM) or vehicle for 24 hours. Cells for RNA-sequencing were lysed with Trizol Reagent and submitted to Shanghai Biotechnology Corporation for the following process. Briefly, total RNA was extracted and checked for a RIN number to inspect RNA integrity. Qualified total RNA was further purified by RNAClean XP and RNase-Free DNase Set. The libraries were prepared with VAHTS mRNA-seq v2 Library Prep Kit for Illumina. The libraries were then sequenced with pair-end protocol, average raw bases data was 6Gb.

first: Yuting

last: Wang

first: Liming

last: Zhao


title: Pancreas agenesis mutations disrupt a lead enhancer controlling a developmental enhancer cluster

city: BArcelona

first: Irene

last: Miguel-Escalada

address: Dr Aiguader 88

institute: CRG


title: An inhaled therapeutic targeting a   conserved RNA structure in SARS-CoV-2

city: Berkeley

first: Chi

last: Zhu

state: CA California

address: Morgan Hall, Rm238

department: Department of Nutritional Sciences & Toxicology

institute: University of California, Berkeley

summary: The Covid-19 pandemic is exacting an increasing toll worldwide, with new SARS-CoV-2 variants emerging that exhibit higher infectivity rates and which may partially evade vaccine and antibody immunity. Rapid deployment of non-invasive therapeutic avenues capable of preventing infection by all SARS-CoV-2 variants could complement current vaccination efforts and help turn the tide on the Covid-19 pandemic. Here, we describe a novel therapeutic strategy targeting the SARS-CoV-2 RNA using locked nucleic acid antisense oligonucleotides (LNA ASOs). We identified an LNA ASO binding to the 5’ leader sequence of SARS-CoV-2 ORF1a/b and which disrupts a highly conserved stem-loop structure, with nanomolar efficacy in preventing viral replication in human cells. Daily intranasal administration of this LNA ASO in the K18-hACE2 humanized Covid-19 mouse model potently (98-99%) suppressed viral replication in the lungs of infected mice, revealing strong prophylactic and treatment effects. We found that the LNA ASO is highly efficacious in countering all SARS-CoV-2 variants of concern (VOC) tested in vitro and in vivo, including B.1.427 (CA), B.1.1.7 (UK), and B.1.351 (SA) variants. LNA ASOs are chemically stable and can be flexibly modified to target different viral RNA sequences. Hence, virus-targeting LNA ASOs represent a promising therapeutic approach to reduce the transmission of SARS-CoV-2, especially in areas where vaccine distribution is a challenge, and it may be stockpiled for future coronavirus pandemics.

overall_design:
Evaluate the viral repressive effect of LNA ASO in SARS-CoV-2-infected K18-hACE2 mice at day 4 post-infection
Evaluate the immune-stimulatory effect of LNA ASO in lung of wild-type mice

first: Fei

last: Ji

first: Ruslan

middle: I

last: Sadreyev

first: Anders

middle: M

last: Näär


title: The Effect of Decitabine and ATRA on the Methylome in the AML cell line U-937

city: Heidelberg

first: Benedikt

last: Brors

address: Im Neuenheimer Feld 280

department: Div. Applied Bioinformatics

country: Germany

institute: German Cancer Research Center (DKFZ)

type: Methylation profiling by genome tiling array

summary: The combination of the demethylating agent Decitabine (DAC) and the retinoic acid ATRA has shown potent antileukemic action both in vitro and in vivo. The likely synergistic mechanism of action remains unknown. Both DAC and retinoid acids are known to affect methylation. DAC inhibits DNA-methyltransferases by covalent bonding, thereby causing demethylation after several replication cycles (Stresemann and Lyko, 2008). Depending on gene and entity, both demethylation (Das et al., 2010; Di Croce et al., 2002) as well as hypermethylation (Das et al., 2010) have been induced by treatment with retinoids. Therefore, a synergistic mechanism of action regarding the methylome to explain the combinatorial strong antileukemic effect of DAC+ATRA was investigated.

overall_design: A total of 24 samples was analzyed. These consisted of 3 treament modes (DAC, ATRA, DAC+ATRA) and an untreated control analyzed at 72 and 120 hours in technical triplicates.

first: Ruth

last: Meier

first: Ralitsa

last: Langova


title: Genome-wide functional perturbation of human microsatellite repeats using engineered zinc finger transcription factors

city: Charlestown

first: Keith

last: Joung

state: MA

institute: MGH

overall_design:
RNA-seq, H3K27Ac ChIP-seq data of MSCs and Ewing Sarcoma and non-Ewing sarcoma cells treated with EWS-ZFA or KRAB-ZFA
Two biological replicates for each samples were prepared.

first: Y

middle: E

last: Tak


title: Club cells employ regeneration mechanisms during lung tumorigenesis

first: Reka

last: Toth

institute: DKFZ

summary: Lung adenocarcinoma (LUAD) is one of the deadliest malignancies worldwide. Dynamic lineage changes within the lung epithelium and the high plasticity of these epithelial cells confound the correct identification of the cell-of-origin of LUAD. Here, we combined lineage-tracing mouse models with an autochthonous cell type-independent LUAD model in order to discover the cellular origin of ALK-translocated LUAD. We identified Club and AT2 cells as the cells-of-origin of LUAD. Moreover, we uncovered epigenetic imprints in the tumours originating from Club or AT2 cells by whole-genome bisulfite sequencing. Single-cell transcriptomes of Club cells at different stages of tumour development identified two trajectories of Club cell evolution. On both routes, tumours lose their Club cell identity and gain an AT2-like phenotype. Together, this study highlights the role of Club cells in LUAD initiation and unveils key mechanisms conferring LUAD heterogeneity.

overall_design: 2 normal control samples, 4 samples with induced tumor and 1 tumor samples. The 4 induced tumour samples are from 2 and 4 weeks after the induction

first: Yuanyuan

last: Chen

first: Sara

last: Chocarro

first: Dieter

last: Weichenhan

first: Joschka

last: Hey

first: Pavlo

last: Lutsik

first: Stefan

last: Sawall

first: Gergios

last: Stathopoulos

first: Christoph

last: Plass

first: Sotillo

last: Rocio


title: RNA sequencing and integrative analysis reveal pathways and hub genes associated with TGFβ1 stimulation on prostatic stromal cells (PrSCs)

status: Public on Jun 29 2022

city: Beijing

first: Hao

last: Ping

state: China

address: Department of Urology, Beijing Tongren Hospital, Capital Medical University, No1. Dongjiaomingxiang street, Dongcheng District, Beijing, 100730, China.

country: China

summary:
To examine the effect of TGFβ1 on prostatic stromal cells, we firstly isolated primary prostatic stromal cells from five benign prostatic hyperplasia sample.
Then RNA sequencing and bioinformatics analysis were used to reveal important pathways and hub genes associated with TGFβ1 stimulation on PrSCs.

overall_design: Comparative analysis of RNA-seq data for primary prostatic stromal cells with and without TGFβ1 stimulation

first: Peng

last: Xiang


title: Hepatic senescence is associated with clinical progression of NAFLD/NASH: Role of BMP4 and its antagonist Gremlin1 (Hepatocytes)

city: Stockholm

first: Xiangyu

last: Li

address: Tomtebodavägen 23, Solna

department: Science for life laboratory

country: Sweden

institute: KTH-Royal Institute of Technology

summary: We performed RNA sequencing of IHH cells incubated with GREM1 in order to identify novel genes and their associated biological pathways.

overall_design: Comparative gene expression profiling analysis of RNS-seq data for control and GREM1-treated IHH cells.

first: Ulf

last: Smith

first: Ritesh

middle: K

last: Baboota


first: Irene

last: Miguel-Escalada

summary: Single cell RNA-Seq and ATAC-Seq in mouse E10.5 multipotent pancreatic progenitors (MPCs) and single cell ATAC-Seq of mouse E13.5 pancreas.

overall_design: scRNA-Seq  and scATAC-Seq profiles (10X Genomics) of a pool of Ptf1a+/+ and Ptf1aenh/enh MPCs manually dissected from E10.5 mouse embryos (between 5-9 embryos/dataset) and scATAC-Seq dataset of E13.5 pancreas from a pool of Ptf1a+/+ and Ptf1aenh/enh embryos (n=6 embryos/dataset).

first: Anamaria

last: Elek

first: Jorge

last: Ferrer


first: Reka

last: Toth

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


summary: Genome-wide maps of H3K27ac, Mediator and PTF1A binding in stage-4 human multipotent pancreatic progenitor cells

overall_design: ChIP-Seq datasets (n=2) of H3K27ac, Mediator  and PTF1A binding from in vitro derived human PTF1A+/+ and PTF1AenhΔ/enhΔ MPCs.

first: Diego

last: Balboa


title: Long non-coding RNA Tug1 modulates mitochondrial and myogenic responses to exercise in skeletal muscle

city: Parkville

first: Adam

middle: James

last: Trewin

state: Victoria

address: Royal Pde

department: Anatomy and Physiology

country: Australia

institute: University of Melbourne

summary: Mitochondrial adaptations play a central role in the beneficial effects of exercise, particularly in metabolically active tissues such as skeletal muscle. Despite this, the molecular regulators of mitochondrial adaptive responses have not yet been fully elucidated. The long non-coding RNA (lncRNA) taurine-upregulated gene 1 (TUG1) interacts with the master transcriptional regulator of mitochondrial biogenesis, peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α). In skeletal muscle of young healthy humans (n=14), we observed that TUG1 gene expression was elevated following an acute bout of continuous, moderate intensity cycling exercise and this positively correlated with PPARGC1A gene expression. Therefore, we hypothesised that TUG1 may modulate skeletal muscle mitochondrial responses to exercise. Knockdown (KD) of Tug1 in differentiating mouse myotubes resulted in altered mitochondrial morphology and impaired mitochondrial respiratory function, which was accompanied by greater myosin heavy chain slow isoform protein expression, despite lower Ppargc1a gene and MFN2 protein expression. Tug1 KD prevented the induction of Ppargc1a expression from a Ca2+ mediated stimulus (caffeine) yet the response to an AMPK agonist (AICAR ) was unaffected. RNA-sequencing revealed that Tug1 KD affected genes relating to mitochondrial Ca2+ transport and downstream targets of PGC-1α. Finally, in response to electrical pulse stimulation (EPS), an in vitro model of exercise in myotubes, there were ~300 genes whose upregulation in response to EPS was either blunted or augmented by Tug1 KD, including regulators of muscle differentiation and myogenesis. These data demonstrate that the lncRNA Tug1 is a novel regulator of skeletal muscle transcriptional responses to exercise and myogenesis.

overall_design: RNA profiles of myotubes (mouse C2C12) with or without Tug1 knockdown under three conditions: unstimulated (rest), immediately after and 3 hours after 3 hours of electrical pulse stimulation.

first: Jessica

last: Silver

first: Hayley

middle: T

last: Dillon

first: Paul

last: Della Gatta

first: Lewan

last: Parker

first: Danielle

last: Hiam

first: Yin Peng

last: Lee

first: Mark

last: Richardson

first: Glenn

last: Wadley

first: Séverine

last: Lamon


title: Hepatic senescence is associated with clinical progression of NAFLD/NASH: Role of BMP4 and its antagonist Gremlin1 (Visceral adipose cells)

first: Xiangyu

last: Li

summary: To understand the role of adipose tissue senescence in NAFLD/NASH,  RNA sequencing was performed in the visceral adipose tissue of NAFLD and NASH pateints.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for visceral adipose tissue of NAFLD and NASH patients

first: Ulf

last: Smith


overall_design: Tumor and normal bulk samples from lineage tracing models: 5 normal and 4 tumor from the CCSP+ lineage, 4 controls and 2 tumors from the HOPX+ lineage, 6 controls and 4 tumors from the SPC+ lineage

first: Yuanyuan

last: Chen

first: Sara

last: Chocarro

first: Dieter

last: Weichenhan

first: Joschka

last: Hey

first: Pavlo

last: Lutsik

first: Stefan

last: Sawall

first: Gergios

last: Stathopoulos

first: Christoph

last: Plass

first: Sotillo

last: Rocio


title: RNA sequencing of wild-type and mutant KRAS human lung cancer cell lines with of without FASN inhibition.

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

summary: The goal of this study is to compare the RNA-seq derived transcriptome of mutant KRAS and wild-type KRAS lung cancer cell lines under fatty acid synthase (FASN) inhibition. We extracted total RNA with TRIzol from cells treated with 0.2 μM TVB-3664 (FASN inhibitor) or 0.2% DMSO for 4 days. One µg of total DNAse-treated RNA was used for library. cDNA was ligated to adapters and PCR amplified. Before being normalized and pooled, samples were quantified by Qubit then run on the Illumina NextSeq 500. Reads were aligned to the human hg38 reference genome. Only uniquely mapped reads were retained for further analyses. Gencode annotation for human (version v37) was used as reference alignment annotation and downstream quantification. Gene level expression was calculated using featureCount (v2.0.1) using intersection-strict mode by exon. Counts were calculated based on protein-coding genes from the annotation file. Low expressed genes were filtered using a per time-point approach with RPKM >= 0.5 in all samples in one or the other group.

overall_design: We extracted total RNA from 2 mutant KRAS (H460 and A549) and 2 wild-type KRAS (H522 and H661) human lung cancer cell lines treated with 0.2 μM TVB-3664 or 0.2% DMSO for 4 days

first: Cristina

last: Andreani

first: Caterina

last: Bartolacci

first: Pier

last: Scaglioni


title: Exosomal miRNA profiling of saliva-derived exosomes

status: Public on Jun 28 2022

city: Ulm

first: Linda

last: Hofmann

state: Deutschland

address: Frauensteige 14a, Haus 18

institute: University of Ulm

summary: Exosomes were isolared from saliva od healthy individuals and head and neck cancer (HNSCC) patients.miRNA profiling of saliva-derived exosomes was perfomred using nCounter SPRINT system. Samples were grouped according to Healthy and Tumor based on their saliva-derived exosomal miRNA profile.

overall_design: Comparison between saliva-derived exosomal miRNA profiles between healthy individuals (n=7) and head and neck cancer patients (n=14).

first: Valentin

last: Medyany

first: Marie-Nicole

last: Theodoraki


title: Polysome-CAGE of TCL1-driven chronic lymphocytic leukemia revealed induction of multiple N-terminally altered epigenetic regulators and a translation stress signature

city: Rehovot

first: Ariel

last: Ogran

address: 234 Herzl Street

department: Bimolecular Sciences

country: Israel

institute: Weizmann Institute of Science

summary: The transformation of normal to malignant cells is accompanied by substantial changes in gene expression programs through diverse mechanisms. Here we examined the changes in the landscape of transcription start sites (TSSs) and alternative promoter (AP) usage and their impact on the translatome in TCL1-driven chronic lymphocytic leukemia (CLL). Our findings revealed a marked elevation of APs in CLL cells from Eµ-Tcl1 transgenic mice, which are particularly enriched with intragenic promoters that generate N-terminally truncated or modified proteins. Intragenic promoter activation is mediated by (i) loss of function of ‘closed chromatin’ epigenetic regulators due to the generation of inactive N-terminally modified isoforms or reduced expression; (ii) upregulation of transcription factors, including c-Myc, targeting the intragenic promoters and associated enhancers. Exogenous expression of Tcl1 in MEFs is sufficient to induce intragenic promoters of epigenetic regulators and promote c-Myc expression. We further found a dramatic translation downregulation of transcripts bearing CNY cap-proximal tri-nucleotides, reminiscent of cells undergoing metabolic stress. These findings uncovered the role of Tcl1 oncogenic function in altering promoter usage and mRNA translation in leukemogenesis.

overall_design: CAGE-seq of total RNA extracted from splenic CD19+ B cells of two Eu-Tcl1 transgenic mice and two WT mice. CAGE-seq of three main polysome profiling fractions (Free, Light, and Heavy polysomes) extracted from splenic CD19+ B cells of two transgenic Eu-Tcl1 mice. Raw (SRA deposited) fastq files of ‘Light’ and ‘Heavy’ polysomes fractions of Eu-Tcl1 mice, were merged to form one BAM file (per Eu-TCl1 mice) representing all translated fractions, deposited here as BIGWIG files of Polysomes fractions (e.g., ‘Polysomes_fraction_Eu-Tcl_mouse_1.CTSS.plus.bw’).

first: Tal

last: Havkin-Solomon

first: Shirley

last: Becker-Herman

first: Keren

last: David

first: Idit

last: Shachar

first: Rivka

last: Dikstein


title: Real-time quantitative analysis of genes related to human innate & adaptive immune responses in neuroendocrine liver metastasis.

city: London

first: Elena

last: Palma

state: -- US/Canada Only --

address: 111 Coldharbour Lane

country: United Kingdom

institute: The Roger Williams Institute of Hepatology

summary:
The immunological profile of patient-derived Precision Cut Tissue Slices (PCTS) obtained from neuroendocrine liver metastasis (LM-NEN=liver metastasis of neuroendocrine neoplasm) (n=3), cholangio carcinoma (CCA) (n=1) and  tumour-free liver tissue (n=4) was analysed and the expression of 84 genes involved in innate and adaptive immune response was assessed.
PCTS were kept in culture at 37C for 2 hours (recovery step) in a sealed chamber filled with carbogen under constant shaking prior to collection. Upon collection tissue slices were preserved in AllProtect Tissue Reagent (Qiagen) and stored at -80C until processing. RNA was isolated with Allprep Mini Kit (Qiagen) according to manifacturer's instructions. cDNA was synthesized with RT2 First Strand Kit (Qiagen) and analysed with Innate and Adaptive Immune Responses RT2 Profiler PCR Array (Qiagen) with RT2 SYBR® Green qPCR Mastermix (Qiagen). qPCR array for Human Innate & Adaptive Immune Responses (Qiagen 330231 PAHS-052ZA, full list of genes available online) was run on ABI 7500 Real-Time PCR System with an initial denaturation step at 95°C for 10 minutes followed by 40 cycles of denaturation at 95°C for 15 seconds and annealing/extension at 60°C for 60 seconds. More information about the histology of the slices used in this analysis can be found in the original manuscipt Doornebal et al.

overall_design: Liver tumour tissue slices from 3 patients with neuroendocrine liver metastasis and 1 with cholangio carcinoma were used as test samples. Tumour-free liver tissue slices were used as controls.

first: Ewald

last: Doornebal


title: Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases

city: princeton

first: Ang

last: Li

state: NJ

address: Washington Road

department: chemistry

institute: princeton university


title: NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization

city: Bethesda

first: Elissa

last: Lei

state: Montgomery

address: 9000 rockville pike

institute: NIDDK

summary: Chromatin insulators are DNA-protein complexes that can prevent the spread of repressive chromatin and block communication between enhancers and promoters to regulate gene expression. In Drosophila, the gypsy chromatin insulator complex consists of three core proteins: CP190, Su(Hw), and Mod(mdg4)67.2. These factors concentrate at nuclear foci termed insulator bodies, and their normal localization is correlated with proper insulator function. Here, we identified NURF301/E(bx), a nucleosome remodeling factor, as a novel regulator of gypsy insulator body localization through a high-throughput RNAi imaging screen. NURF301 promotes gypsy-dependent insulator barrier activity and physically interacts with gypsy insulator proteins. Using ChIP-seq, we found that NURF301 co-localizes with insulator proteins genome-wide, and NURF301 promotes chromatin association of Su(Hw) and CP190 at gypsy insulator binding sites. These effects correlate with NURF301-dependent nucleosome repositioning. At the same time, CP190 and Su(Hw) are also required for recruitment of NURF301 to chromatin. Finally, Oligopaint FISH combined with immunofluorescence revealed that NURF301 promotes 3D contact between insulator bodies and gypsy binding site DNA, and NURF301 is required for proper nuclear positioning of gypsy binding sites. Our data provide new insights into how a nucleosome remodeling factor and insulator proteins cooperatively contribute to nuclear organization.

overall_design: Here, we examined of overlapping of NURF301 with insulator proteins Su(Hw), CP190, and Mod(mdg4) genome-wide in Kc167 embryonic cell lines. We also found that gypsy insulator proteins and nucleosome remodeler--NURF301 are cooperatively required to bind to chromatin.

first: Shue

last: Chen


title: Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases [II]

summary: We adapted the Aldehyde reactive probe (ARP; O-(biotinylcarbazoylmethyl) hydroxylamine) pulldown method to map ALKBH1 dependent targets in a transcriptome-wide manner.

overall_design: Fragmented total RNA extracted from WT and ALKBH1 knock out cells was first incubated with ARP and then enriched by streptavidin pulldown. RNA were subject to Iclip library construction and high throughput sequencing.

first: Ralph

last: Kleiner


title: ATAC-seq analysis to examine global accessibilty of chromatin in limb bud cells

city: Minneapolis

first: Daniel

last: Garry

state: MN

address: 2231 6th Street SE, 4th Floor

department: Lillehei Heart Institute

institute: University of Minnesota

summary: The study compares two cell populations one where Etv2 is expressed and other lacks Etv2 expression. The cells from wild-type E9.5 hindlimbs , cells from Shh-EGFP E10.5 anterior hindlimbs , EGFP+ cells from Shh-EGFP E10.5 posterior hindlimbs, and EYFP+ cells from Etv2-EYFP transgenic E10.5 hindlimbs and forelimbs were collected and processed

overall_design: Limb bud tissues were digested in 200 ml of TripLE (ThermoFisher 12605010) at 37°C in two cycles of 5 min incubation followed by trituration. Cells were cooled on ice for 5 min between incubations. Digestion was stopped with 1ml of medium with 10% fetal calf serum that was filtered through a 50 mm mesh filter (Partec). Cells were collected by centrifugation and stained with staining medium containing 0.2 mg each of CD31-APC, Tie2-APC, CD45-APC and 0.5 mg anti CD16/CD32, and EYFP positive, APC negative live cells were sorted on FACSAria (BD). Cells from EYFP negative embryos were used as a negative control for FACS sorting.

first: Wuming

last: Gong

first: Naoko

last: Koyano-Nakagawa

first: Yasuhiko

last: Kawakami

first: Nikita

last: Dsouza


title: Single base-pair resolution analysis of DNA binding motif with MoMotif reveals an oncogenic function of CTCF zinc-finger 1 mutation.

city: Montreal

first: Michael

last: Witcher

state: Quebec

address: 3755 Chem. de la Côte-Sainte-Catherine

department: Experimental Medicine

country: Canada

institute: McGill University


title: Single base-pair resolution analysis of binding motif with diffMotif uncovers the oncogenic impact of CTCF mutations in breast cancer  [RNA-Seq]

summary: Most cancer associated CTCF mutations are involved in the recognition of CTCF core binding motif. Interestingly, mutations of the currently uncharacterized ZF1 of CTCF are practically exclusive to breast cancer, where they are associated with increased metastatic ability and therapeutic resistance. Although unnecessary to bind the core-binding motif, it is still unknown if the ZF1 of CTCF promotes binding to an altered CTCF motif. Further, classical motif analysis tools are powerless to identify minute changes in core binding motif. Therefore, the biological and epigenetic mechanism of action of CTCF ZF1 mutations is still unexplored. In order to explain the impact of CTCF ZF1M in breast models, we developed a new tool, diffMotif, that allows the identification, at the single base-pair resolution, of extension or alteration of core binding motif. Using diffMotif, we identified an extension of CTCF core binding motif, necessitating a functional ZF1 to bind appropriately. Using a combination of ChIP-Seq and RNA-Seq, we discover that the inability to bind the extended motif led to altered gene expression driving increased invasive ability and drug metabolism, mimicking the harmful oncogenic phenotypes observed clinically. Our study demonstrates the oncologic relevance of the characterisation of mutation induced altered DNA binding ability, by diffMotif.

overall_design: Examination of mRNA expression and CTCF binding changes in the context of CTCF ZF1 mutations

first: Benjamin

last: Lebeau

first: Kaiqiong

last: Zhao

first: Celia

last: Greenwood


title: The HDAC7-TET2 epigenetic axis is essential during early B lymphocyte development

city: Barcelona

first: Maria

last: Vila-Casadesús

state: Barcelona

address: Carrer del Dr. Aiguader, 88

summary: B lymphopoiesis is the result of several cell lineage choices and differentiation steps whose perturbation leads to B cell malignancies. Cellular transitions for B cell generation have been associated with gene activation and silencing by networks of B cell specific transcription factors (TFs) and dynamic changes in DNA methylation. How gene repression is established and which lineage-specific transcriptional repressors are involved during B cell lymphopoiesis are still not totally understood. Here, by using our in vivo experimental approach, we have found that HDAC7 represses Tet2 enzyme in pro-B cells. In fact, HDAC7 deficient pro-B cells show a significant increase in the percentage of global 5-hydroxymethylation. To prove the role of HDAC7 in 5-hydroxymethylation, we have performed a genome-wide experimental approach. hMeDIP-sequencing experiments reveal an increase in the enrichment of this epigenetic modification at many loci related to lineage inappropriate genes. Our results corroborate that HDAC7 is an essential transcriptional regulator during early B cell development that silences lineage or functionally inappropriate genes and unveil an unexpected role of a class IIa HDAC in controlling DNA methylation

overall_design: Study of hydroxymethylation genomic distribution in murine progenitor B cells depending on the presence of the protein HDAC7


title: Splice Factor Polypyrimidine tract-binding protein 1 (Ptbp1) Primes Endothelial Inflammation in Atherogenic Disturbed Flow Conditions [CRISPR]

status: Public on Jun 27 2022

city: Farmington

first: Patrick

last: Murphy

state: CT

address: 263 Farmington Ave

department: Center for Vascular Biology

institute: University of Connecticut Health Center

summary: Analysis of effects of Ptbp1 deletion on RNA splicing and expression in aortic endothelial cells

overall_design: A mouse aortic endothelial cell line with CRISPR deletion (single cell clone) of Ptbp1, and then rescue with human PTBP1 cDNA was analyzed before and after TNF treatment.

first: Jessica

last: Hensel


title: Splice Factor Polypyrimidine tract-binding protein 1 (Ptbp1) Primes Endothelial Inflammation in Atherogenic Disturbed Flow Conditions


title: HLA-B*46 associates with rapid HIV disease progression in  Asian cohorts and prominent differences in NK cell phenotype

city: Silver Spring

first: Rasmi

last: Thomas

state: MD

address: 503 Robert Grant Avenue

department: MHRP

institute: Walter Reed Army Institute of Research

summary: In an unbiased transcriptomic screen we observed reduced NK cell activation phenotypes in HLA-B*46 positive people with HIV. These findings show that contemporaneous treated cohorts can be used to analyze host genetic effects in HIV disease, and support a role for NK cells in HIV control revealed by unique properties of the recombinant HLA-B*46 allele which is frequent only in Asia.

overall_design: Gene expression profiles of immune cell subtypes at different timepoints in the course of HIV-1 infection

first: S

last: Shangguan

first: A

last: Geretz

first: P

last: Ehrenberg

first: R

last: Clifford


title: Splice Factor Polypyrimidine tract-binding protein 1 (Ptbp1) Primes Endothelial Inflammation in Atherogenic Disturbed Flow Conditions [Ptbp1]

overall_design: Primary mouse aortic endothelial cells from Ptbp1 EC-KO (Cdh5-CreERT2; Ptbp1 ff) mice were analyzed after <1 week in culture and treatment (or not) with TNF.


title: Single base-pair resolution analysis of binding motif with diffMotif uncovers the oncogenic impact of CTCF mutations in breast cancer  [ChIP-Seq]


title: Genome-wide analysis of CqCrRLK1Ls and CqRALFs in Chenopodium quinoa

city: Shanghai

first: Chao

last: Li

address: No. 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

summary: Quinoa (Chenopodium quinoa) is a highly nutritious crop showing a remarkable tolerance to multiple abiotic stresses. The Catharanthus roseus RLK1-like kinase (CrRLK1L) family is involved in multiple processes during plant growth and stress responses. However, little is known about the members of the CqCrRLK1L subfamily and their biological functions. In this study, up to 26 CqCrRLK1L members were identified in quinoa genome. To systematically investigate their tissue-specific expression pattern and gene expression profiles in response to abiotic stresses, different quinoa samples including leaf, pistil, stamen, root, and leaf treated with NaCl were harvested for transcrioptome analysis with three biological replicates for each sample. Finally,we mapped about 30 million sequence reads per sample to the quinoa genome (NL-6) and combining the four different tissues (leaf, pistil, stamen, and root), totally 40382 genes were detected, accounting for 69% of total genes in quinoa. The expression of most CqCrRLK1Ls genes were detected in all four kind of tissues, and they showed tissue-specific expression pattern. In salt-treated leaves, we observe that about 6-thosands genes changed their expression, with log2FoldChange < -1 or >1 and p value <0.05. And four CqCrRLK1L genes largely altered their transcript levels, implying that these genes are involved in the regulation of salt stress response in quinoa. The present study provides a base for future research on elucidating the varied biological functions of CqCrRLK1Ls and their contributions to stress responses.

overall_design: mRNA profiles of quinoa samples, including stamens and pistills of newly open flowers, roots of 3 days seedlings, leaves of 14 days plants exposure to 400 mM NaCl for 8 hours and the untreated controls.

first: Chunzhao

first: Wei

last: Jiang


title: Maternal Smchd1 regulates Hox gene expression and patterning in the mouse embryo [ESC RRBS]

first: Natalia

last: Benetti

address: 1G Royal Parade

institute: WEHI

summary: Parents transmit genetic and epigenetic information to their offspring. Maternal effect genes regulate the offspring epigenome to ensure normal development. Here we report that the epigenetic regulator SMCHD1 has a maternal effect on Hox gene expression and skeletal patterning. Maternal SMCHD1, present in the oocyte and preimplantation embryo, prevents precocious activation of Hox genes post-implantation. Without maternal SMCHD1, highly penetrant posterior homeotic transformations occur in the embryo. Hox genes are decorated with Polycomb marks H2AK119ub and H3K27me3 from the oocyte throughout early embryonic development; however, loss of maternal SMCHD1 does not deplete these marks. Therefore, we propose maternal SMCHD1 acts downstream of Polycomb marks to establish a chromatin state necessary for persistent epigenetic silencing and appropriate Hox gene expression later in the developing embryo. This is a striking role for maternal SMCHD1 in long-lived epigenetic effects impacting offspring phenotype.

overall_design: Our overall design it to compare between Smchd1 control and Smchd1 maternally deleted samples. We have performed reduced representation bisulfite sequqencing (RRBS) in a differentiation timecourse in 2 replicate mESC of each genotype at 2 timepoints comparing the Smchd1 maternally deleted to the control, at the matched timepoint.

first: Marnie

last: Blewitt


title: Maternal Smchd1 regulates Hox gene expression and patterning in the mouse embryo [RNAseq tailbud]

summary: RNAseq from somite-matched tailbud tissue from E8-8.5 embryo tailbuds at the 6-11 somite developmental stages

overall_design: Our overall design is to compare between Smchd1 control and Smchd1 maternally deleted samples. We have performed RNA-seq in 37 tailbud samples from E8-8.5 mouse embryos, with 6 to 11 somites each.  In all cases we compare the Smchd1 maternally deleted to the control, at the matched somite number.


title: The HDAC7-TET2 epigenetic axis is essential during early B lymphocyte development [ATAC-seq]

city: Badalona

first: Maribel

last: Parra

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

department: Lymphocyte Development and Disease

institute: Josep Carreras Leukaemia Research Institute

summary:
The establishment of proper epigenomic landscape is essential during B lymphocyte development in order to acquire a correct B cell identity at each cellular differentiation stage. We previously identified HDAC7 as a critical regulator of early B cell development. Its absence indeed led to the aberrant activation of inappropriate lineage genes, a reduction of proliferation and an increase in cell apoptosis. More recently, we have demonstrated that HDAC7 loss in infant pro-B-ALL associates with poor prognosis. Here we shed light into the HDAC7-mediated molecular mechanisms during early B cell development. HDAC7 deficiency drives not only the expression of inappropriate lineage genes, but also global chromatin de-condensation and deregulation of epigenetic regulators of DNA methylation and potential damaging elements. Specifically, HDAC7 absence induces the expression of TET2, which promotes DNA 5-hydroxymethylation and aberrant gene activation. HDAC7 deficiency also results in the uncontrolled expression of microRNAs and non-coding elements such as LINE-1 transposable elements. These findings are relevant for the mechanistic explanation of why HDAC7 is affected in multiple B-related hematological malignancies.
Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) was performed in murine pro-B and pre-B lymphocytes.

overall_design: Cells were extracted from bone marrow (femur and tibia of both hind legs) of Hdac7+/- and Hdac7fl/- mice. Cells were stained and sorted as pro-B cells (IgM-,CD19+,B220+, CD43+) and pre-B cells (IgM-,CD19+,B220+, CD43-). Fresh whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina). DNA libraries were prepared as described in Buenrostro et al., 2015 and were sequenced using HiSeqX 150+150PE platform from Magrogene Inc. Two duplicates per condition were processed.

first: Alba

last: Azagra

first: Ainara

last: Meler

first: Oriol

last: de Barrios

first: Laureano

last: Tomás-Daza

first: Olga

last: Collazo

first: Beatriz

last: Monterde

first: Mireia

last: Obiols

first: Llorenç

last: Rovirosa

last: Vila-Casadesus

first: Mónica

last: Cabrera-Pasadas

first: Mar

last: Gusi-Vives

first: Thomas

last: Graf

first: Ignacio

last: Varela

first: José

last: Sardina

first: Biola

last: Javierre


summary: Correct B cell identity at each stage of cellular differentiation during B lymphocyte development is critically dependent on a tightly controlled epigenomic landscape. We previously identified HDAC7 as an essential regulator of early B cell development and its absence leads to a drastic block at the pro-B to pre-B cell transition. More recently, we demonstrated that HDAC7 loss in pro-B-ALL in infants associates with a worse prognosis. Here we delineate the molecular mechanisms by which HDAC7 modulates early B cell development. We find that HDAC7 deficiency drives global chromatin de-condensation, histone marks deposition and deregulates other epigenetic regulators and mobile elements. Specifically, the absence of HDAC7 induces TET2 expression, which promotes DNA 5-hydroxymethylation and chromatin de-condensation. HDAC7 deficiency also results in the aberrant expression of microRNAs and LINE-1 transposable elements. These findings shed light on the mechanisms by which HDAC7 loss or misregulation may lead to B cell–based hematological malignancies.

overall_design: Cells were extracted from bone marrow (femur and tibia of both hind legs) of Hdac7+/- and Hdac7fl/- mice.  Cell were stained and sorted as pro-B cells: IgM-,CD19+,B220+, CD43+; pre-B cells: IgM-,CD19+,B220+, CD43+. Total RNA was extracted from HDAC7 deficient and control pro-B and pre-B cells in the Genomics facility of Institute for Research in Biomedicine (IRB) in Barcelona. Samples were quantified and subjected to quality control using a Bioanalyzer apparatus (IRB, Barcelona). Samples were processed at BGI Genomics Service, in China.Two duplicates for condition were processed.

first: Maria

last: Vila-Casadesús


title: Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases [I]

first: Ang

last: Li

summary: We adapted the iCLIP method to map ALKBH1L modification sites in a transcriptome-wide manner by treating the cells with 5-EC.

overall_design: Flp-In T-Rex 293 cells expressing 3xFlag-ALKBH1 were treated with 5-EC, ALKBH1-RNA were extracted and subject for Iclip library preparation.

first: A

last: Arguello

first: Ralph

last: Kleiner


title: RNA-Seq in senescent cells with restored levels of TRF2

city: Nice

first: Melanie

last: Pousse

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

country: France

institute: IRCAN

summary: Cellular senescence is accompanied by profound changes in telomere and heterochromatin structure that contribute to ageing. Telomere shortening is a key driver of replicative senescence that activate DNA damage response signaling ending on a p53-dependent downregulation of the shelterin subunit TRF2. Restoring the levels of TRF2 in pre-senescent cells leads to delay entry into senescent and restoration of constitutive heterochromatin structure and damage. Here we set to determine whether the restoration of TRF2 levels change the senescent program by doing RNA-sequencing of senescent cells transduced with a TRF2-expressing lentivirus or an empty lentivirus control.

overall_design: RNA-Seq performed on senescent MRC-5 cells expressing a TRF2 lentivirus vector or control.

first: Aaron

last: Mendez-Bermudez

first: Eric

last: Gilson


title: The interdependency between MiDAC complex and MLL3/4 complexes

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

summary: Enhancers play a pivotal role in gene transcriptional regulation in response to developmental cues. Active enhancers are marked by H3K4me1/2 and H3K27ac, while poised enhancers are marked by H3K27me3 instead of H3K27ac in addition to H3K4me1/2. How these histone modifications and/or other histone modification(s) at enhancers are regulated remains not fully understood. Through immunoprecipitation followed by mass spectrometry of UTX, a specific subunit of the enhancer associated COMPASS complex: MLL3/4, we identified DNTTIP1 and ELMSAN1, which are scaffolds of the mitotic deacetylase complex (MiDAC), as new UTX interactors. Our biochemistry data shows that UTX-ELMSAN1 is the interface between MiDAC and MLL3/4 complexes. The loss of MiDAC causes genome wide increase of H4K20ac, suggesting H4K20ac is a MiDAC substrate in vivo. H4K20ac is genome-wide co-localized with H3K4me1/2, H3K27ac, UTX, and MLL4, suggesting it is located at active enhancers. Genome-wide increased occupancy of UTX and MLL4 is observed at Dnttip1 knockout mES cells, which means under normal conditions MiDAC may repress MLL3/4-UTX’s genomic localization. However, we observe an increase of H3K4me2 but not H3K4me1 at those UTX & MLL4 increased loci. In MLL3/4 double knockout mES cells, Dnttip1 is reduced genome-wide, which however does not lead to a genome-wide increase of H4K20ac, but a genome-wide loss of it. At either H4K20ac or Dnttip1 reduction loci, we observe an increase of H3K27me3, suggesting the formation of repressed chromatin state which may suppress the increase of H4K20ac at Dnttip1 reduced loci. Our study for the first time reveals the functional intersection between MiDAC and MLL3/4 complexes.

overall_design: Study the functional intersection between MiDAC and MLL3/4 complexes.

first: Xiaokang

last: Wang

first: Beisi

last: Xu

first: Hans-Martin

last: Herz


title: The HDAC7-TET2 epigenetic axis is essential during early B lymphocyte development [ChIP-seq]

first: Maribel

last: Parra

summary:
The establishment of proper epigenomic landscape is essential during B lymphocyte development in order to acquire a correct B cell identity at each cellular differentiation stage. We previously identified HDAC7 as a critical regulator of early B cell development. Its absence indeed led to the aberrant activation of inappropriate lineage genes, a reduction of proliferation and an increase in cell apoptosis. More recently, we have demonstrated that HDAC7 loss in infant pro-B-ALL associates with poor prognosis. Here we shed light into the HDAC7-mediated molecular mechanisms during early B cell development. HDAC7 deficiency drives not only the expression of inappropriate lineage genes, but also global chromatin de-condensation and deregulation of epigenetic regulators of DNA methylation and potential damaging elements. Specifically, HDAC7 absence induces the expression of TET2, which promotes DNA 5-hydroxymethylation and aberrant gene activation. HDAC7 deficiency also results in the uncontrolled expression of microRNAs and non-coding elements such as LINE-1 transposable elements. These findings are relevant for the mechanistic explanation of why HDAC7 is affected in multiple B-related hematological malignancies.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K27ac and H3K27me3 in murine pro-B lymphocytes.

overall_design: Cells were extracted from bone marrow (femur and tibia of both hind legs) of Hdac7+/- and Hdac7fl/- mice. Cells were stained and sorted as pro-B cells (IgM-,CD19+,B220+, CD43+). Pro-B lymphocytes from HDAC7 deficient and control mice were fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer. DNA sequencing libraries were prepared using the TRUESEQ ChIP kit (Illumina). Libraries were sequenced using HiSeqX 150+150PE platform from Magrogene Inc.Two duplicates per condition were processed.

first: Alba

last: Azagra

first: Ainara

last: Meler

first: Oriol

last: de Barrios

first: Laureano

last: Tomás-Daza

first: Olga

last: Collazo

first: Beatriz

last: Monterde

first: Mireia

last: Obiols

first: Llorenç

last: Rovirosa

last: Vila-Casadesus

first: Mónica

last: Cabrera-Pasadas


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

overall_design: Refer to individual Series


title: Maternal Smchd1 regulates Hox gene expression and patterning in the mouse embryo [RNAseq mESC reciprocal cross]

first: Natalia

last: Benetti

summary:
Parents transmit genetic and epigenetic information to their offspring. Maternal effect genes regulate the offspring epigenome to ensure normal development. Here we report that the epigenetic regulator SMCHD1 has a maternal effect on Hox gene expression and skeletal patterning. Maternal SMCHD1, present in the oocyte and preimplantation embryo, prevents precocious activation of Hox genes post-implantation. Without maternal SMCHD1, highly penetrant posterior homeotic transformations occur in the embryo. Hox genes are decorated with Polycomb marks H2AK119ub and H3K27me3 from the oocyte throughout early embryonic development; however, loss of maternal SMCHD1 does not deplete these marks. Therefore, we propose maternal SMCHD1 acts downstream of Polycomb marks to establish a chromatin state necessary for persistent epigenetic silencing and appropriate Hox gene expression later in the developing embryo. This is a striking role for maternal SMCHD1 in long-lived epigenetic effects impacting offspring phenotype.
Our overall design it to compare between Smchd1 control and Smchd1 heterozygous samples. We have performed RNA-seq in a differentiation timecourse in 3 replicate mESC of each genotype with 4 timepoints, comparing the Smchd1 heterozygous to the control, at the matched timepoint.

overall_design: Natalia,Benetti

first: Marnie

last: Blewitt


title: Neuroblastoma-associated mutations in Drosophila Alk peturb neuronal differentiation and promote neuronal survival.

city: Göteborg

first: Vimala

last: Anthonydhason

address: Medicinaregatan 9 a-b

department: Institute of Biomedicine

institute: University of Gothenburg

summary: Activating mutations in the Anaplastic Lymphoma Kinase (ALK) receptor tyrosine kinase (RTK) are found in pediatric neuroblastoma, where they are often associated with poor prognosis. To study the effects of ALK-activating mutations in a genetically controllable system we employed CRIPSR/Cas9 to incorporate orthologues of the oncogenic human driver mutations ALKF1174 and ALKY1278S in the Drosophila Alk locus. AlkF1251 and AlkY1355S mutant Drosophila exhibit phenotypes similar to that previously associated with enhanced Alk signaling. Unexpectedly, both mutant alleles are still dependent on the presence of Jeb ligand for activation, as neither can rescue mutants of the Alk ligand Jeb. However, both Alk mutant third instar brains display hyperplasia, represented by increased numbers of Alk-positive neuronal populations. Despite this hyperplasic phenotype within the central brain area, no brain tumors were observed in mutant animals. Further investigation indicated that larval brain hyperplasia in Alk mutants was not caused by significantly increased rates of proliferation, but rather by decreased levels of apoptosis in the larval brain. Using single cell RNA sequencing (scRNAseq) analysis, we identify maintained neuronal fate change during the temporal fate specification of in the mushroom body lineages, with AlkY1355S mutants displaying precocious a’b’ neuron identity. These findings shed important light on the role of Alk in perturbation of neurodevelopmental processes and highlight the potential of activating Alk mutations to promote survival in neuronal lineages

overall_design: To investigate the effect of the AlkY1355S mutation from Drosophila melanogaser third instar larval brains of control (w1118) and AlkY1355S alleles using single cell RNA sequencing (scRNAseq), employing 10X genomics.

first: Ruth

last: Palmer

first: Kathrin

last: Pfeifer

first: Badrul

last: Arefin

first: Mendoza

last: Garcia Patricia


title: Transcriptome analysis reveals key gene expression changes in blue catfish sperm in response to cryopreservation

status: Public on Jun 26 2022

city: Auburn University

first: Xu

last: Wang

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

summary: Cryopreservation of blue catfish sperm can cause variable embryo hatch rates, which is the limiting factor for hybrid catfish breeding. In this study, we investigated gene expression changes caused by cryopreservation using transcriptome profiles of fresh sperm samples and cryopreserved sperm from the same set of blue catfish.

overall_design: Profile of transcriptome-wide gene expression changes in cryopreserved sperm samples (n=3) compared to fresh sperm samples (n=3).

first: Ian

last: Butts


title: Transcriptome dynamics in developing larynx, trachea, and esophagus

status: Public on Jun 25 2022

city: Madison

first: Christina

last: Kendziorski

state: WI

address: 425, Henry Mall (2122 UWBC)

institute: UW-Madison

summary: The larynx, trachea, and esophagus share origin and proximity during embryonic development, with clinical and experimental evidence supporting the existence of neurophysiological, structural, and functional interdependencies before birth.  This investigation provides the first comprehensive transcriptional profiling of all three organs during embryonic organogenesis, where differential gene expression gradually assembles the identity and complexity of these proximal organs from a shared origin in the anterior foregut.  Through the application of bulk RNA sequencing and gene network analysis of differentially expressed genes (DEGs), both within and across developing embryonic mouse larynx, esophagus, and trachea, we identified co-expressed modules of genes enriched for key biological processes.  Organ-specific temporal patterns of gene activity corresponding to gene modules within and across shared tissues during embryonic development (E10.5-E18.5) are described, and the laryngeal transcriptome during vocal fold development and maturation from birth to adult is characterized in the context of laryngeal organogenesis.  The findings of this study provide new insights into interrelated gene sets governing organogenesis of this tripartite organ system within the aerodigestive tract, with relevance to multiple families of disorders defined by cardiocraniofacial syndromes.

overall_design: Wild type FVB/N mice males and females were mated, when vaginal plugs were found noon of that day was designated as embryonic day (E) 0.5. For RNA-Seq, pregnant females were sacrificed at E10.5, E11.5, E13.5, E15.5, E18.5, mouse larynges, trachea and esophagus were dissected, tissues were pooled together from 10 animals at E10.5, E11.5, E13.5, E18.5 time points, and 20 animals at the E15.5 timepoint. Approximately ~1-3 mm pieces of tissue were excised separately from the LPh/larynx (E10.5-Adult), esophagus (E10.5-E18.5) dorsoposterior to the larynx, and trachea (E10.5-E18.5) ventroposterior to the larynx with two medial biological replicates used at each timepoint. Tissue was collected anteriorly at the level of the LPh (E10.5 and E11.5) and vocal folds (E13.5 to adult) for the larynx and immediately posterior to the larynx in the case of both the esophagus and trachea. Additional timepoints for postnatal stage 0 (P0) and adult (6-8 weeks) larynx were included in the “within tissue” laryngeal analysis, where bulk tissue was collected at the level of the bilateral vocal folds. All tissues were micro-dissected in an RNase-free environment and immersed in RNAlater (Qiagen, Valencia, CA) at 4°C overnight, and then transferred to 80°C for long term storage prior to RNA extraction.

first: Kristy

last: Wendt

first: Jared

last: Brown

first: Vidisha

last: Mohad

first: Vlasta

last: Lungova

first: Susan

last: Thibeault


title: PRC1-mediated epigenetic programming is required to generate the ovarian reserve

city: Davis

first: Satoshi

last: Namekawa

state: CA

address: One Shields Avenue

institute: UC Davis

summary: The ovarian reserve defines the female reproductive lifespan, which in humans spans decades due to robust maintenance of meiotic arrest in oocytes residing in primordial follicles. Epigenetic reprogramming, including DNA demethylation, accompanies meiotic entry, but the chromatin changes that underpin the generation and preservation of ovarian reserves are poorly defined. We report that the Polycomb Repressive Complex 1 (PRC1) establishes repressive chromatin states in perinatal mouse oocytes that directly suppress the gene expression program of meiotic prophase-I and thereby enable the transition to dictyate arrest. PRC1 dysfuction causes depletion of the ovarian reserve and leads to premature ovarian failure. Our study demonstrates a fundamental role for PRC1-mediated gene silencing in female reproductive lifespan, and reveals a critical window of epigenetic programming required to establish ovarian reserve.

overall_design: RNA-seq analysis using PRC1ctrl and PRC1cKO P1 or P5 non-growing oocytes; Cut&Run analysis using PRC1ctrl and PRC1cKO P1 non-growing oocytes or wildtype (stella-GFP) P1 non-growing oocytes

first: Mengwen

last: Hu

middle: H


title: Components of the autonomous flowering pathway form a complex that suppresses FLC transcription by regulating multiple histone modifications

city: Beijing

first: Xin-Jian

last: He

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

institute: National Institute of Biological Sciences


title: MafB maintains β-cell identity under MafA-deficient condition

status: Public on Jun 24 2022

city: Tsukuba

first: Akihiro

last: Kuno

state: Ibaraki

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary: The transcription factor MafB plays an essential role in β-cell differentiation during the embryonic stage in rodents. Although MafB disappears from β-cells after birth, it has been reported that MafB can be evoked in β-cells and is involved in insulin+ β-cell number and islet architecture maintenance in adult mice under diabetic conditions. However, the underlying mechanism by which MafB protects β-cells remains unknown. To elucidate this, we performed RNA sequencing using an inducible diabetes model (A0BΔpanc mice) that we previously generated. We found that the deletion of Mafb can induce β-cell dedifferentiation, characterized by the upregulation of dedifferentiation markers, Slc5a10 and Cck, and several β-cell-disallowed genes; and the downregulation of mature β-cell markers, Slc2a2 and Ucn3. However, there is no re-expression of well-known progenitor cell markers, Foxo1 and Neurog3. Furtherly, the appearance of ALDH1A3+ cell and disappearance of UCN3+ cell also verify the β-cell de-differentiation state. Together, our results suggest that MafB can maintain β-cell identity under certain pathological conditions in adult mice, providing novel insight into the role of MafB in β-cell identity maintenance.

overall_design: Pancreatic islets mRNA profiles of 10-week-old wild type (WT), MafA-/-;MafB flox/flox (A0B2) and MafA-/-;MafB flox/flox;Pdx1-CreERTM (A0BΔpanc) mice

first: Satoru

last: Takahashi

first: Deng

last: Zhaobin


title: Components of the autonomous flowering pathway form a complex that suppresses FLC transcription by regulating multiple histone modifications [ChIP-seq]

summary: The autonomous flowering pathway promotes flowering in rapid-flowering accessions of Arabidopsis thaliana by reducing the expression of the key flowering repressor gene FLC. Although previous studies identified several autonomous pathway components, little is known about how these components cooperate in the regulation of flowering time. Here, we identified an autonomous pathway complex (APC) composed of three known autonomous pathway components (FLD, LD, and SDG26) and three previously uncharacterized components (EFL2, EFL4, and APRF1). Loss-of-function mutations of all of these components result in increased FLC expression and delayed flowering. The late-flowering phenotype is independent of photoperiod and can be overcome by vernalization, supporting the inference that the complex regulates flowering time specifically through the autonomous pathway. Our ChIP-seq analyses indicated that the APC components are required for the suppression of the histone modifications (H3Ac, H3K4me3, and H3K36me3) associated with the activation of gene expression and for the promotion of the histone modification (H3K27me3) associated with the repression of gene expression at FLC. We also found that the C-terminal coiled-coil domain of SDG26 binds to DNA in vitro and that the DNA-binding ability mediates the association of SDG26 with FLC chromatin in vivo. These results reveal the molecular basis of the autonomous pathway.

overall_design: The enrichment of histone modifications, including H3Ac, H3K4me2, H3K4me3, H3K36me3, and H3K27me3, on chromatin was detected by ChIP-seq assays.


title: Age-related alterations in macrophage distribution and function impair cutaneous wound healing

city: SINGAPORE

first: Chin Yan

last: Lim

address: 8A Biomedical Grove, Immunos, #06-06,

institute: A*STAR Skin Research Labs

summary: Ageing-related delays in wound healing are well-documented in both human and animal models. However, the mechanisms underlying this impairment in healing progression are not fully understood. In this study, we characterised ageing-associated changes to the structure and function of the skin in young and aged mice and investigated the cellular differences that impacted the progression of wound healing. Full-thickness wounds created on the dorsum of C57BL/6J young and aged mice were excised on Day 0, Day 3 and Day 7 post-wounding for analysis by immunohistochemistry, flow cytometry, RNA sequencing. Our data revealed that macrophages were significantly reduced in aged wounds in comparison to young. Functional transcriptomic analyses showed that macrophages from aged wounds exhibited significantly reduced expression of cell cycle, DNA replication, and repair pathway genes. Furthermore, we uncovered an elevated pro-inflammatory gene expression program in the aged macrophages linked to poor inflammation resolution and excessive tissue damage observed in aged wounds. Altogether, our work provides insights into how poorly healing aged wounds are phenotypically defined by the presence of macrophages with reduced proliferative capacity and an exacerbated inflammatory response, both of which are pathways that can be targeted to improve healing in the elderly.

overall_design: mRNA profiles of wound macrophages sorted from young and aged female wild type mice 3 days post-wounding

first: Chin

middle: Y

first: Christabel

last: Dube

first: Kimberly

last: Mace


title: RNA-seq analysis of human spinal ligaments

city: HONGO, BUNKYO-KU

first: Taku

last: Saito

state: TOKYO

department: Orthopaedic Surgery, Faculty of Medicine

institute: The University of Tokyo

summary: Ectopic endochondral ossification in the tendon/ligament is caused by repetitive mechanical overload or inflammation. Tendon stem/progenitor cells (TSPCs) contribute to tissue repair and lubrication by producing proteoglycan 4 (Prg4). However, the mechanisms of ectopic ossification and association of TSPCs are not yet known. Here, we investigated the characteristics of Prg4-positive (+) cells and identified that R-spondin 2 (RSPO2), a WNT activator, is specifically expressed in a distinct Prg4+ TSPC cluster. The Rspo2+ cluster was characterized as mostly undifferentiated, and RSPO2 overexpression suppressed ectopic ossification in a mouse Achilles tendon puncture model via chondrogenic differentiation suppression. RSPO2 expression levels in patients with ossification of the posterior longitudinal ligament were lower than those in spondylosis patients, and RSPO2 protein suppressed chondrogenic differentiation of human ligament cells. RSPO2 was induced by inflammatory stimulation and mechanical loading via nuclear factor-kappa B (NF-κB). Rspo2+ cells may contribute to tendon/ligament homeostasis by suppressing chondrogenic differentiation.

overall_design: We compared yellow ligaments from cervical ossification of posterior longitudinal ligament (OPLL) and cervical spondylotic myelopathy (CSM) patients.

first: Naohiro

last: Tachibana


title: Global analyses of mRNA expression in human sensory neurons reveals eIF5A as a conserved target for inflammatory pain

first: Zachary

last: Campbell

address: 1111 Highland Avenue

department: Anesthesiology

institute: University of Wisconsin - Madison

summary: Nociceptors are a type of sensory neurons that is integral to most forms of pain. Targeted disruption of nociceptor sensitization affords unique opportunities to prevent pain. An emerging model for nociceptors are sensory neurons derived from human stem cells. Here, we subjected five groups to high-throughput sequencing: human induced pluripotent stem cells (hiPSCs) prior to differentiation, mature hiPSC-derived sensory neurons, mature co-cultures containing hiPSC-derived astrocytes and sensory neurons, mouse DRG tissues, and mouse DRG cultures. Co-culture of nociceptors and astrocytes promotes expression of transcripts enriched in DRG tissues. Comparisons of the hiPSC models to tissue samples reveals that many key genes linked to pain are present. Marker genes indicative of a range of neuronal subtypes present in the DRG were detected in mature hiPSCs. Intriguingly, translation factors were maintained at consistently high expression levels across species and culture systems.  As a proof of concept for the utility of this resource, we validated expression of eukaryotic initiation factor 5A (eIF5A) in DRG tissues and hiPSC samples. eIF5A is subject to a unique post-translational hypusine modification required for its activity. Inhibition of hypusine biosynthesis prevented hyperalgesic priming by inflammatory mediators in vivo. One of two hypusine inhibitors diminished hiPSC activity in vitro. Collectively, our results illuminate the transcriptomes of hiPSC sensory neuron models. We provide a proof of concept for this resource through our investigation of eIF5A. Our findings reveal hypusine as a potential target for inflammation associated pain in males.

overall_design: RNA-sequencing of mouse DRG cultures and tissues. RNA sequencing of immature, mature monoculture and mature astrocyte co-culture hiPSCs.

first: Rebecca

last: Chase

first: June

middle: B

last: de la Peña

first: Patrick

middle: R

last: Smith

first: Jennifer

last: Lawson

first: Tzu-Fang

last: Lou

first: Alexander

last: Stanowick

first: Bryan

last: Black


title: Components of the autonomous flowering pathway form a complex that suppresses FLC transcription by regulating multiple histone modifications [RNA-seq]

first: Xin-Jian

last: He

overall_design: Examination of the mRNA expression of wild type and four mutants grown under long day condition.


title: scRNA-seq of Achilles tendons from Prg4-CreERT2;R26-tdTomato ATP mice

overall_design: Prg4-CreERT2;R26-tdTomato mice were sacrificed one week after induction of ectopic ossification.


title: Developmental cell death of cortical projection neurons is controlled by a Bcl11a/Bcl6-dependent pathway I

city: Ulm

first: Christoph

last: Wiegreffe

address: Albert-Einstein-Allee 11

institute: Ulm University

summary: Developmental neuron death plays a pivotal role in refining organization and wiring during neocortex formation. Aberrant regulation of this process results in neurodevelopmental disorders including impaired learning and memory. Underlying molecular pathways are incompletely determined. Loss of Bcl11a in cortical projection neurons induces pronounced cell death in upper-layer cortical projection neurons during postnatal corticogenesis. We used this genetic model to explore genetic mechanisms by which developmental neuron death is controlled. Unexpectedly, we found Bcl6, previously shown to be involved in transition of cortical neurons from progenitor to postmitotic differentiation state to provide a major check point regulating neuron survival during late cortical development. We show that Bcl11a is a direct transcriptional regulator of Bcl6. Deletion of Bcl6 exerts death of cortical projection neurons. In turn, reintroduction of Bcl6 into Bcl11a mutants prevents induction of cell death in these neurons. Together, our data identify a novel Bcl11a/Bcl6-dependent molecular pathway in regulation of developmental cell death during corticogenesis.

overall_design: Neocortical layers II-IV were laser-microdissected from four control (Bcl11a flox/+;Emx1 IRESCre/+) and four Bcl11a mutant (Bcl11a flox/flox;Emx1 IRESCre/+) pups at P2. Total RNA was isolated using the RNeasy Micro Plus Kit (Qiagen). The isolated RNA was checked for purity and integrity using Nanodrop spectrophotometer and TapeStation (Agilent), respectively. Transcriptome analysis was performed using GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) and BRB-ArrayTools developed by Dr. Richard Simon and BRB-ArrayTools Development Team (http://linus.nci.nih.gov/BRB-ArrayTools.html).

first: Tobias

last: Wahl

first: Natalie

last: Joos

first: Jerome

last: Bonnefont

first: Pentao

last: Liu

first: Stefan

last: Britsch


title: Developmental cell death of cortical projection neurons is controlled by a Bcl11a/Bcl6-dependent pathway II

overall_design: Neocortical layers II-IV were laser-microdissected from four control (Bcl6 flox/flox;Nex +/+) and four Bcl6 mutant (Bcl6 flox/flox;Nex Cre/+) pups at P5. Total RNA was isolated using the RNeasy Micro Plus Kit (Qiagen). The isolated RNA was checked for purity and integrity using Nanodrop spectrophotometer and TapeStation (Agilent), respectively. Transcriptome analysis was performed using GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) and BRB-ArrayTools developed by Dr. Richard Simon and BRB-ArrayTools Development Team (http://linus.nci.nih.gov/BRB-ArrayTools.html).


title: Synaptotagmin 2 is ectopically overexpressed in a widely used CaMK2a-Cre mouse line

city: Kunigami-gun

first: Mohieldin

last: Youssef

state: Okinawa

address: 1919-1 Tancha

department: Cell Signal Unit

institute: Okinawa Institute of Science and Technology


title: Synaptotagmin 2 is ectopically overexpressed in a widely used CaMK2a-Cre mouse line [CamiCre dataset]

summary: The Cre-loxP system is one of the most powerful and commonly used techniques in neurogenetics, as well as in broad biomedical studies. The CaMKIIa-Cre mouse line, one of the earliest established Cre driver lines, has resulted in over 800 papers to date. While Cre driver lines are well characterized for Cre expression patterns, many are not well characterized for phenotypes. Here, we demonstrate that the second most widely used CaMKIIa-Cre line, Tg(Camk2a-cre)2Gsc (or CamiCre), shows significant overexpression of synaptotagmin 2, the most efficient Ca2+ sensor for fast synchronous neurotransmitter release, in Cre+/- hippocampus compared to wild-type littermates. Moreover, upregulation of immediate early genes, such as Arc and Fos, and genes presumably derived from bacterial artificial chromosome transgene, such as Slc6a7 were also observed in the Cre+/- hippocampus. These unexpected results suggest difficulties in interpreting results from studies using the CamiCre line and raise awareness of potential pitfalls in the use of Cre driver lines in general.

overall_design: HIppocampal RNA profiles of 9-week-old wild type (WT) and Tg(Camk2a-cre)2Gsc (CamiCre) Cre+/- mice

first: Ken

last: Matsuura

first: Haytham

last: Mohamed

first: Tadashi

last: Yamamoto


title: PrrA modulates Mycobacterium tuberculosis response to nitric oxide

status: Public on Jun 23 2022

city: Boston

first: Shumin

last: Tan

state: MA

address: 150 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

summary: The purpose of this study was to understand the impact of prrA overexpression on global M. tuberculosis transcriptional response to nitric oxide.

overall_design: Mtb strain CDC1551 harboring a tetracycline inducible prrA-FLAG construct was grown in aerated conditions to mid-log phase (OD600 ~0.6), and treated with either ethanol (EtOH) as a carrier control or 200 ng/ml anhydrotetracycline (ATC) for 2 hours. Bacteria were subcultured to an OD600 = 0.3 in filter-capped  T-75 flasks laid flat, in 12 ml 7H9, pH 7 media ± 100 µM DETA NONOate (an NO donor), with continued presence of EtOH or ATC as appropriate. Exposure to DETA NONOate was for 4 hours in a humidified, 37°C, 5% CO2 incubator before RNA was extracted. RNA was prepared by removing the rRNA and library prepping with a TruSeq Stranded kit (Illumina) before high-throughput sequencing with an Illumina HiSeq 2500 (High Output v4) (100 bp single end reads, one lane). Two biological samples per condition were sequenced.

first: David

last: Giacalone


title: PrrA modulation of Mycobacterium tuberculosis response to acidic pH and high chloride levels is critically regulated by serine/threonine protein kinases

summary: The purpose of this study was to understand how prevention of serine/threonine protein kinase (STPK) phosphorylation of PrrA impacts PrrA modulation of M. tuberculosis transcriptional response to acidic pH and high chloride levels.

overall_design: Mtb strain CDC1551 with a deletion of the native copy of prrA, and harboring a prrA-FLAG-DAS4 (wild type prrA allele - prrA-DUC/∆prrA) or prrA-T6A-FLAG-DAS4 (T6A STPK-phosphoablative prrA allele - prrA-T6A-DUC/∆prrA) construct was grown to an OD600 of ~0.6 in standing, filter-capped  T-75 flasks. Bacteria were then subcultured to an OD600 = 0.3 in standing, filter-capped  T-25 flasks in 7H9, pH 7 media ± 250 mM NaCl, or 7H9, pH 5.7 media ± 250 mM NaCl. Exposure to the different media conditions was for 4 hours in a humidified, 37°C, 5% CO2 incubator before RNA was extracted. RNA was prepared by removing the rRNA and library prepping with a TruSeq Stranded kit (Illumina) before high-throughput sequencing with an Illumina HiSeq 2500 (High Output v4) (100 bp single end reads, one lane). Two biological samples per condition were sequenced.


title: Analysis of time series gene expression and DNA methylation reveals the molecular features of myocardial infarction progression (RNA-Seq)

first: Han

last: Yuru

state: Shanghai

address: 279 Zhouzhu Rd. Pudong New District, Shanghai

institute: Shanghai University of Medicine and Health Sciences

summary: Myocardial infarction (MI) is one of the deadliest diseases in the world, and the changes at the molecular level after MI and the DNA methylation features are not clear. Understanding the molecular characteristics of the early stages of MI is of significance for the treatment of the disease. In this study, RNA-seq and MeDIP-seq were performed on heart tissue from mouse models at multiple time points (0 h, 10 min,1 h, 6 h, 24 h and 72 h) to explore genetic and epigenetic features that influence MI progression. Analysis based on a single point in time, the number of differentially expressed genes (DEGs)and differentially methylated regions (DMRs)increased with the time of myocardial infarction, using 0 h as a control group. Moreover, within 10 minutes of MI onset, the cells are mainly in immune response, and as the duration of MI increases, apoptosis begins to occur. Analysis based on time series data, the expression of 1012 genes was specifically downregulated, and these genes were associated with energy metabolism. The expression of 5806 genes was specifically upregulated, and these genes were associated with immune regulation, inflammation and apoptosis. 14 transcription factors were identified in the genes involved in apoptosis and inflammation, which may be potential drug targets. Analysis based on MeDIP-seq combined with RNA-seq methodology, focused on methylation at the promoter region. GO revealed that the downregulated genes with hypermethylation at 72 h were enriched in biological processes such as cardiac muscle contraction. In addition, the upregulated genes with hypomethylation at 72 h were enriched in biological processes, such as cell-cell adhesion, regulation of the apoptotic signalling pathway and regulation of angiogenesis. Among these genes, the Tnni3 gene was also present in the downregulated model. Hypermethylation of Tnni3 at 72 hours after MI may be an important cause of exacerbation of MI.

overall_design: Eighteen 12-week-old male C57BL/6JR mice were included in the experiment. The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (50 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately. The mice in the control group received the same operation, sutured through the inferior artery, but not ligated. Complete anaesthesia of mice with 1-3% isoflurane after specific time of MI, followed by euthanasia by cervical dislocation. Total RNA was isolated from myocardial region of infarcted left ventricle.

first: Yanfei

last: Li


title: PHF20 Activates Autophagy Genes through Enhancer Activation via H3K36me2 Binding Activity [RNA-seq]

city: Seoul

first: Se Won

last: Park

state: Gwanak-Gu

address: Gwanak-ro 1, Gwanak-gu, Seoul, Seoul Nat'l Univ Bldg504 Rm607

country: South Korea

institute: Seoul national university

summary: Autophagy is a catabolic pathway that maintains cellular homeostasis under various stress conditions, including nutrient-deprived conditions. To elevate autophagic flux to a sufficient level under stress conditions, transcriptional activation of autophagy genes occurs to replenish autophagy components. Here, using combination of RNA-seq, ATAC-seq and ChIP-seq, we demonstrated found that plant homeodomain finger protein 20 (Phf20PHF20), which is an epigenetic reader possessing methyl binding activity, plays a key role in controlling the expression of autophagy genes. PHF20 activates autophagy genes through enhancer activation via H3K36me2 binding activity as an epigenetic reader and that our findings emphasize the importance of nuclear regulation of autophagy.

overall_design: mRNA-seq, ATAC-seq and ChIP-seq experiments under normal and 24hrs of glucose starvation condition in WT and Phf20-/- MEFs

first: Se

first: Daechan

first: Sung

last: Baek


title: PHF20 Activates Autophagy Genes through Enhancer Activation via H3K36me2 Binding Activity [ChIP-seq]


title: PHF20 Activates Autophagy Genes through Enhancer Activation via H3K36me2 Binding Activity [ATAC-seq]