title: Bcl2l10 induces metabolic alterations in ovarian cancer cells by regulating the TCA cycle enzymes SDHD and IDH1

city: Sungnam-Si

first: Su-Yeon

last: Lee

address: Pangyo-Ro 335

department: Department of Biomedical Science

institute: CHA University

summary: The aim of this study was to identify possible downstream target genes and investigate the underlying mechanisms of action of Bcl2l10 in ovarian cancer cells. We performed RNA sequencing (RNA-Seq) and obtained a list of differentially expressed genes (DEGs) in Bcl2l10-suppressed SKOV3 and A2780 cells. RNA-Seq data showed that DEGs after Bcl2l10 knockdown are involved in transcriptional regulation and energy metabolism in ovarian cancer cells. The RNA-Seq data were validated by quantitative real-time PCR (qRT-PCR) and western blot analysis, and the levels of metabolites after Bcl2l10 knockdown were measured by ELISA. KEGG enrichment analysis showed that the commonly downregulated genes in SKOV3 and A2780 cells after Bcl2l10 knockdown were significantly enriched in metabolic pathways. The analysis of the DEGs identified from the RNA-Seq and validated by qRT-PCR revealed that succinate dehydrogenase complex subunit D (SDHD) and isocitrate dehydrogenase 1 (IDH1), which are key enzymes of the TCA cycle that regulate oncometabolite production, are potential downstream targets of Bcl2l10. We further found that Bcl2l10 knockdown induced the accumulation of succinate and isocitrate through the downregulation of SDHD and IDH1.

overall_design: Identification of differentially expressed genes after Bcl2l10 knockdown in SKOV3 and A2780 cells

first: Jinie

last: Kwon

first: Kyung-Ah


title: A two-gene signature for diagnosis of tuberculosis in persons with advanced HIV

status: Public on Feb 02 2021

city: Salvador

first: Artur

middle: Trancoso Lopo

last: Queiroz

address: Rua Waldemar Falcão, 121

country: Brazil

institute: Instituto Gonçalo Moniz

type: Expression profiling by high throughput sequencing

summary:
Background: Tuberculosis (TB) among persons living with HIV (PLWH) poses diagnostic challenges. Although several transcriptional signatures have recently been identified as promising tool for TB diagnosis, data are limited in persons with advanced HIV.
Methodology: Reads were aligned to the human transcriptome (GRCh38 version 100), comprising both mRNA and ncRNA, with Salmon v1.2.0. A Random Forest algorithm with “leave-one-out” cross-validation was applied in the variance stabilizing transformation gene expression. The identified biomarkers were compared to previous TB transcriptional signatures using the Area Under the Curve (AUC).
Results:  Functional analysis indicated that common upregulated pathways in TB/HIV patients were associated with Toll-like receptor cascades and neutrophil degranulation. A machine learning decision tree algorithm identified the expression values from RAB20 and INSL3 as most informative for classifying TB status in PLWH. Only these two genes were able to correctly classify all samples.

overall_design: 25 samples were used from HIV-infected subjects and HIV-infected and TB-infected subjects.


title: Rodents as models of human sarcopenia: a comparative analysis reveals conserved modulators of aging-dependent muscle loss

status: Public on Jan 30 2021

city: Basel

first: Anastasiya

last: Boersch

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

summary:
Aims: Sarcopenia is the degenerative loss of skeletal muscle mass and function at high age, which affects 5-13% of people aged 60-70 years. Although a number of factors have been linked to sarcopenia, it remains unclear what determines its emergence in some but not all individuals and there are no medical treatments available. Mice and rats are widely used as model organisms to identify factors predisposing to sarcopenia, but the extent to which age-related molecular changes in wild-type mice and rats recapitulate those occurring in humans is not known. The aim of this project was to define a conserved set of regulators of aging-related reduction in muscle function that could be targeted by future therapies.
Methods: We comparatively analyzed phenotypic parameters as well as the transcriptomes of the Gastrocnemius muscle from mice, rats and humans of a wide range of ages. We further inferred computationally the transcription regulators that likely underlie the molecular changes associated with aging-related loss in muscle functionality.
Results: The analysis showed that the biological age of rodents that muscle mass is a better indicator of muscle functionality than the chronological age. Investigating the molecular changes associated with the aging-related loss of muscle mass, we discovered changes in gene expression that are shared between the studied species at the level of molecular pathways rather than at the level of individual genes. Beyond the known involvement of inflammation and mitochondrial function in aging, we found that the transcription regulators SPIB, ESRRB and YY1/YY2 consistently underlie aging-related molecular changes across the studied species.
Conclusions: Rodents recapitulate well the molecular changes observed in human sarcopenia, but the conservation is stronger at the molecular pathway level than at the level of individual genes. Phenotypic parameters such as the muscle mass should be taken into account in stratifying samples for analyzing aging-related processes, as the chronological age is a poorer indicator of organ functionality. The shared regulators of aging-related muscle loss that we identified here can be studied further in rodent models of sarcopenia toward defining new targets for therapy in humans.

overall_design: Gastrocnemius muscle mRNA profiles of 8, 18, 22, 24, 26 and 28 months old wild type mice were generated by next-generation sequencing.

first: Daniel

middle: J

last: Ham

last: Börsch

first: Mihaela

last: Zavolan

first: Markus

middle: A

last: Rüegg


title: Arabidopsis Mitochondrial Transcription Termination Factor mTERF2 Promotes Splicing of Group IIB Introns

status: Public on Jan 29 2021

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

country: Germany

institute: Ludwig-Maximilians-Universität München

summary: Members of the mitochondrial transcription termination factor (mTERF) family regulate gene expression in chloroplasts and/or mitochondria at different steps. Here, we investigated the molecular function of chloroplast-localized mTERF2 in Arabidopsis thaliana. Loss-of-function mterf2 mutants are embryo lethal. Thus, artificial microRNA-mediated mterf2 knockdown plants were generated. In amiR-mterf2 mutants, plant development is perturbed and chlorophyll content reduced. A defect in photosynthesis is accompanied by reduced levels of photosystem subunits, although corresponding messenger RNA levels are unaffected. RNA immunoprecipitation followed by RNA sequencing (RIP-Seq) experiments combined with whole-genome RNA-Seq, RNA gel-blot and quantitative RT-PCR analyses revealed the requirement of mTERF2 for splicing of the group IIB introns of ycf3 (intron 1) and rps12.

overall_design: Examination of differential gene expression in the Arabdidopsis thaliana artificial micro RNA generated mterf2 knock-down mutant compared to wild type in three replicates


title: iCLIP-seq, RNA-seq and MACE-seq studies in P19 cells

status: Public on Jan 28 2021

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

department: Institute for Cell Biology and Neuroscience

institute: Goethe University Frankfurt

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

overall_design: Refer to individual Series


title: MACE-seq of P19 cells after knockdown of Srsf3 and Srsf7

summary: Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3’ untranslated regions (3’UTRs). APA regulates stage- and tissue-specific gene expression by affecting the stability, subcellular localization and translation rate of transcripts. We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, connect APA with mRNA export. The mechanism underlying APA regulation by SRSF3 and SRSF7 remained, however, unknown. Here, we combined iCLIP, RNA-Seq and 3’-end sequencing to find that both proteins bind upstream of proximal PASs (pPASs), yet they exert opposite effects on 3’UTR length. We show that SRSF7 enhances pPAS usage in a concentration-dependent but splicing-independent manner by recruiting the cleavage factor FIP1, thereby generating short 3’UTRs. Protein domains unique to SRSF7, which are absent from SRSF3, and hypo-phosphorylation contribute to FIP1 recruitment. In contrast, SRSF3 promotes distal PAS (dPAS) usage and hence long 3’UTRs by maintaining high levels of cleavage factor Im (CFIm) via alternative splicing. Upon reduced expression of SRSF3, CFIm levels strongly decrease and 3’UTRs are globally shortened. In SRSF3-regulated transcripts, CFIm and FIP1 bind upstream of dPASs and promote their usage. Surprisingly, both factors are also recruited to pPASs under conditions where their usage is blocked, suggesting the formation of inactive cleavage complexes. Thus, we identify SRSF3 as a novel regulator of CFIm activity, provide evidence that CFIm inhibits pPAS usage and show that small differences in the domain architecture of SR proteins confer opposite effects on PAS selection.

overall_design:
P19 cells were depleted of SRSF3 or SRSF7 using esiRNAs.
2 biological replicates each were subjected to MACE-seq.


title: The Breast Cancer Susceptibility Gene TOX3 Promotes Estrogen Synthesis: An RNA-sequencing and Network Study

status: Public on Feb 04 2021

city: Jinan

first: Yuanyuan

last: Man

state: Shandong

address: No.157, Jingliuweiwu Road

department: Center for Reproductive Medicine

country: China

institute: Shandong University

summary: We aimed to explore the effect of the breast cancer susceptibility gene TOX3 on estrogen synthesis from the perspective of estrogen production, in an attempt to link abnormalities in hormone production with the development of breast cancer. After overexpression of TOX3, several crucial key genes and pathways that contribute to estrogen production were upregulated. Forced expression of TOX3 also promotes proliferation and inhibits apoptosis of granulosa cells. These findings discuss the possible impact of susceptibility genes and steroid hormones on breast cancer from the perspective of extra-mammary tissues such as those in the ovary, thus providing new insights for early prevention and treatment of breast cancer.

overall_design: KGN mRNA profiles of TOX3 overexpression and control group


title: RNA-seq of P19 cells after knockdown of Srsf3, Srsf7 and Cpsf6 and after differentiation into neuronal cells

overall_design:
P19 cells were either depleted of SRSF3, SRSF7 and CPSF6 using esiRNAs or differentiated into neuronal cells using retinoic acid.
2-3 biological replicates each were subjected to RNA-seq.


title: Effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 N. Fifth Street

department: Integrated Cancer genomics division

country: USA

institute: Translational Genomics Research Institute

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by genome tiling array


title: Transcriptome-wide mapping of RNA:protein interactions of CPSF5 and FIP1 in P19 cells by iCLIP

overall_design:
We used P19 cells that express GFP-tagged CPSF5 and FIP1 at physiological levels and compared their binding pattern on distal, proximal and single PAS. For this we performed iCLIP using anti-GFP antibodies.
For each GFP-tagged SRSF7 protein,  2-3 biological replicates were subjected to the iCLIP procedure with UV-crosslinking at 254 nm. For IPs either an anti-GFP antibody was used or an anti-SRSF7 antibody.


title: Diversified transcriptional responses of myeloid and glial cells in spinal cord injury shaped by HDAC3 activity

status: Public on Jan 27 2021

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: The innate immunity influences neural repair after spinal cord injury (SCI). Here, we combined myeloid-specific nuclear transcriptomics and single-cell RNA-sequencing to uncover a common core but also temporally distinct gene programs in injury-activated microglia and macrophages (IAM). Intriguingly, we detected a wide range of microglial activation states even in healthy spinal cord; upon injury, reactive microglia and infiltrated macrophages progressively acquired an overall reparative, yet highly diversified gene expression profile, while maintaining their distinct transcriptional identities. Microglia and macrophages each comprise four distinct transcriptional subtypes with specialized tasks. Notably, IAM and disease-associated microglia (DAM) shared similar gene signatures, with a predominant enrichment in infiltrating macrophages and only a small subset of reactive microglia that specialized in phagocytosis, autophagy, and TyroBP network activity. We also identified an immediate response microglial subtype that may serve as source population for microglial transformation, and a highly proliferative subtype that is controlled by the epigenetic regulator HDAC3. Together, our data unveiled diversification of myeloid and other glial cell types and an extensive influence of HDAC3, which may be exploited to enhance neural repair.

overall_design: Studying single cells collected from HDAC3i and Vehicle treated spinal cord 5 days post injury in mice

first: Shalaka

last: Wahane

first: Xianxiao

last: Zhou

first: Xiang

first: Bin

last: Zhang

first: Roland

middle: H

last: Friedel

first: Hongyan

last: Zou


title: Diagnostic performance of transcriptomic signatures for the evaluation of suspected tuberculosis in routine clinical practice

status: Public on Jan 26 2021

city: London

first: Long

last: Hoang

address: Dovehouse Street

department: Genomic Medicine

country: United Kingdom

institute: Imperial College London

summary: Background: Blood transcriptomic signatures for diagnosis of tuberculosis (TB) have shown promise in case-control studies but their diagnostic accuracy has not been prospectively validated in adults presenting with the full clinical spectrum of suspected TB, including extra-pulmonary TB, and its associated differential diagnoses with concomitant latent TB infection.  Methods: Our study was nested within a prospective multi-center cohort study in secondary care in England. Patients had whole-blood taken for microarray to measure abundance of 47,275 transcripts and interferon-gamma release assays (IGRAs) at clinical presentation with suspected TB and were followed up for 6-12 months’ to determine final diagnoses based on pre-defined diagnostic criteria. The diagnostic accuracy of published transcriptomic signatures and a novel cohort-derived signature were assessed to generate area under the receiver-operating characteristic curves (AUC), sensitivities and specificities.

overall_design: Three millilitres  of whole blood were collected into each of two Tempus tubes (Applied  Biosystems/Ambion) by trained research staff following a standard phlebotomy protocol. Blood was vigorously mixed immediately following collection and stored at -80°C before RNA extraction. For each patient, the contents of one tube were used for analysis and the other tube was retained in case of assay failure. RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion), as per the manufacturer’s instructions. 250 g of isolated total RNA was globin-reduced using the GLOBINclear 96-well format kit (Applied Biosystems/Ambion) according to the manufacturer’s instructions. Total and globin-reduced RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA yield was assessed using a NanoDrop8000 spectrophotometer (NanoDrop Products, Thermo Fisher Scientific). High-quality (>6.5 RIN) whole blood RNA was successfully obtained and processed by microarray in all cases. Biotinylated, amplified antisense complementary RNA (cRNA) targets were prepared from 200-250 ng of globin-reduced RNA using the Illumina CustomPrep RNA amplification kit (Applied Biosystems/Ambion). For each sample, seven hundred and fifty nanograms of labelled cRNA were hybridised overnight to Illumina Human HT12 V4 BeadChip arrays (Illumina), which contained greater than 47,000 probes. The arrays were washed, blocked, stained and scanned on an Illumina iScan, as per the manufacturer’s instructions. GenomeStudio (Illumina) was used to perform quality control and generate signal intensity values.

middle: T

first: Pooja

last: Jain

first: Mica

last: Tolosa-Wright

first: Timesh

middle: D

last: Pillay

first: Yemisi

last: Takwoingi

first: Alice

last: Halliday

first: Joanthan

last: Deeks

first: Peter

last: Beverley

first: Onn

middle: M

last: Kon

first: Ajit

last: Lalvani


title: ELF3 activated by a super-enhancer and an autoregulatory feedback loop is required for high level HLA-C expression on extravillous trophoblasts

city: Cambridge

first: Qin

last: Li

email: qin_li@harvard.edu, qinli9566@gmail.com

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology Department

institute: Harvard University

summary: HLA-C arose during evolution of pregnancy in the Great Apes 10-15 million years ago. It has a dual function on placental extravillous trophoblasts (EVT) as it contributes to both tolerance and immunity at the maternal-fetal interface. The mode of its regulation is of considerable interest in connection with the biology of pregnancy and pregnancy abnormalities. First trimester primary EVT in which HLA-C is highly expressed, as well as JEG3, an EVT model cell lines, were employed. Single cell RNA-seq data and quantitative PCR identified high expression of the transcription factor ELF3 in those cells. ChIP-PCR confirmed that both ELF3 and MED1 bound to the proximal HLA-C promoter region.  However, binding of RFX5 to this region was absent or severely reduced and the adjacent HLA-B locus remained closed. Expression of HLA-C was inhibited by ELF3 siRNAs and by wrenchnolol treatment. Wrenchnolol is a cell-permeable synthetic organic molecule that mimics ELF3 and is relatively specific for binding to ELF3’s coactivator, MED23, as our data also showed in JEG3. Moreover, the ELF3 gene is regulated by a super-enhancer that spans more than 5 Mb, identified by ATAC-seq, as well as by its sensitivity to (+)-JQ1 (inhibitor of BRD4). ELF3 bound to its own promoter, thus creating an autoregulatory feedback loop that establishes expression of ELF3 and HLA-C in trophoblasts. Wrenchnolol blocked binding of MED23 to ELF3, thus disrupting the positive feedback loop that drives ELF3 expression, with down regulation of HLA-C expression as a consequence.

overall_design: To assess the chromatin accessibility of somatic cell lines and trophoblast model cell lines, ATAC-seq was applied to cell line BJ fibroblasts, Hela, JEG3, BeWo and Jar.


title: Non-target site herbicide resistance is conferred by two distinct mechanisms in blackgrass (Alopecurus myosuroides)

city: Newcastle upon Tyne

first: Robert

last: Edwards

address: Agriculture Building, Newcastle University, King's Rd

department: School of  Natural and Environmental Sciences

institute: Newcastle University

summary: Identification of the mechanisms that led to two different subtypes of multiple herbicide resistance in blackgrass using RNA-Seq data.

overall_design: Five biological replicates for each population each one of them including 5 plants (7-days old seedlings). One sensitive population (Rothamsted), one population resistant to fenoxaprop-p-ethyl  (Fenoxaprop population, FOX) and one population with multiple herbicide resistance to a group (ACCases and pendimethalin herbicides; Pendimethalin population, PEN)

first: Sara

last: Franco Ortega


title: DNA methylation-linked chromatin accessibility affects genomic architecture in Arabidopsis

status: Public on Jan 25 2021

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: DNA methylation is one of the most widely distributed epigenetic marks that has a profound impact on developmental regulation, yet its influence on chromatin accessibility and 3D genome architecture is not well explored in plants. Here, we present genome-wide chromatin accessibility profiles of 18 Arabidopsis mutants that are deficient in CG, CHG or CHH DNA methylation. We find that chromatin inaccessibility at heterochromatin regions are maintained by DNA methylation in all three contexts. Many regions maintain their chromatin inaccessibility when DNA methylation is lost in only one or two contexts but we found the most increase in accessibility at sites that shown DNA methylation reduction in all contexts, suggesting an interplay between CG and non-CG methylation and chromatin accessibility. In addition, we observed that an increase in chromatin accessibility is accompanied with chromatin decompaction of many transposable elements, which leads to heterochromatin decompaction and an enhancement of long-range chromosomal interactions in the 3D genome architecture. Together, these results provide a valuable resource for chromatin compaction analyses and uncover a pivotal role for DNA methylation in the maintenance of heterochromatin inaccessibility in Arabidopsis.

overall_design: Compare chromatin accessibility of Arabidopsis DNA methylation diffecient mutants

first: Zhong

last: Zhenhui


title: The Alteration of M6A-tagged Transcript Profiles in The Retina of Rats After Traumatic Optic Neuropathy

city: Shanghai

first: Xiaolin

last: Qu

address: No.415, Fengyang Road

department: Department of neurosurgery

institute: Changzheng Hospital affliated to Naval Medical University

summary: Messager RNA (mRNA) can be modified in a variety of ways, among which the modification of N6-methyladenosine (m6A) is one of the most common ones. Recent studies have found that the m6A modification in mRNA could functionally regulate the splicing, localization, translation and stability of mRNA, which might be closely related to multiple diseases. However, the roles of m6A modification in traumatic optic neuropathy (TON) are unknown. Herein, we detected the expression of m6A-related genes via quantitative real-time PCR (qRT-PCR) and performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) as well as RNA-sequencing to analyze the alteration profiles of m6A modification after TON. The results showed that the expression of m6A-related genes (METTL3, WTAP, FTO and ALKBH5) were all upregulated after TON. In all, 2810 m6A peaks were differentially upregulated and 689 m6A peaks were downregulated. In addition, the hypermethylated and hypomethylated profiles of mRNA transcripts were also identified. To sum up, our study revealed the differentially expressed m6A modification in the early stage of TON, which may provide novel insights into the mechanism and treatment of TON.

overall_design:
RNA-seq:
Twelve hours after operation, rats were anesthetized with pentobarbital sodium and were transcardially perfused with 20 ml of 4°C PBS. The retinal tissues were rapidly dissected and stored in liquid nitrogen. According to the manufacturer’s protocol, total RNAs from the retina of each rat were isolated using TRIzol reagent (Invitrogen). Three replicates were conducted for sham-operated and TON model group. To attain 60 μg of total RNA, retinal samples from 4 rats were integrated into one centrifuge Tubes. The concentration and quality of total RNAs were assessed using NanoDrop ND-1000(Thermo Fisher Scientiﬁc). The integrity of RNA was evaluated by denaturing agarose gel electrophoresis. The extraction of mRNA was conducted using NEBNext rRNA Depletion Kit (New England Biolabs, Hertfordshire, UK) following the manufacturer’s protocol. Bioanalyzer 2100 system (Agilent Technologies, CA, USA) was used for quality control and quantification of the RNA libraries, and Illumina Hiseq4000 platforms (Illumina, CA, USA) was used for double-ended sequencing of RNA.
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4)  (Kechin et al., 2017). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified (Trapnell et al., 2010).
MeRIP-seq, data analysis and bioinformatics
At 12h after operation, rats were anesthetized with pentobarbital sodium and were transcardially perfused with 20 ml of 4°C PBS. The retina was then rapidly dissected and stored in liquid nitrogen. Total RNAs from the retinal tissue of each rat were isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. In this study, three biological replicates were conducted in sham-operated and TON model group, retinal tissue samples from 4 rats were combined into one sample to attain 60 μg of total RNA. mRNA extraction was performed using NEBNext rRNA Depletion Kit (New England Biolabs) following the manufacturer’s protocol. Briefly, m6A RNA immunoprecipitation was performed with the GenSeqTM m6A RNA IP Kit (GenSeq Inc., shanghai, China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs). The quality control (QC) of the libraries was evaluated using BioAnalyzer 2100 system (Agilent Technologies). Library sequencing was performed on an Illumina Hiseq4000 platforms under 150bp pair-ended resolution.
Cutadapt software (V1.9.3) was used to remove low quality reads and obtain clean reads (Kechin et al., 2017). The clean reads from all samples were then aligned to Ensembl reference genome by HISAT2 software (v2.0.4) (Kim et al., 2015). Model-based Analysis of ChIP-Seq(MACS) software (v1.4.2) was used to identify methylated genes in each sample (Zhang et al., 2008). DiffReps software was used for identification of differential methylated genes (Shen et al., 2013). The differentially methylated peaks (fold changes ≥ 2.0 and p < 0.05) between sham-operated group and TON model group were analyzed by exomePeak and annotated accordingly by the latest Ensembl database. Gene ontology (GO) database (www.geneontology.org)and the latest Kyoto Encyclopedia of Genes and Genomes (KEGG) database (www.genome.jp/kegg)were used to perform GO analysis and pathway enrichment analysis on differentially methylated mRNA genes.
Statistical analyses
Data are expressed as mean ± standard deviation (SD). Statistical analyses were conducted using  GraphPad Prism Version 8.3 software (GraphPad Software LLC, CA, USA). Student’s t-test (paired) was used for comparing the statistical significance between two groups. For each analysis, P< 0.05 was considered as statistically significant and marked with *.

first: Qu

last: Xiaolin

first: Zhu

last: Kaixin

first: Li

last: Zhenxing

first: Zhang

last: Danfeng

first: Hou

last: Lijun


title: DNMTs Play an Important Role in Maintaining the Pluripotency of Leukemia Inhibitory Factor Dependent Embryonic Stem Cells

city: Guangzhou

first: Lin

address: Shatai South Road

department: Pathophysiology

institute: Southern Medical University

type: Methylation profiling by high throughput sequencing

summary: Naïve pluripotency can be maintained in 2i/LIF supplements, which primarily affect canonical WNT, FGF/ERK, and JAK/STAT3 signaling. However, whether one of these tripartite supplements alone is sufficient to maintain naïve self-renewal remain unclear. Here we show that LIF alone medium is sufficient for adaptation of 2i/L-ESCs to ESCs with hypermethylated state (L-ESCs). Global transcriptomic analysis show that L-ESCs are close to 2i/L-ESCs and in a stable state between naïve and primed pluripotency. Notably, our results demonstrate that DNA methyltransferases (DNMTs) play an important role for LIF-dependent mouse ESCs adaptation and self-renew. LIF-dependent ESCs adaptation efficiency is significantly increased in serum treatment and reduced in Dnmt3a or Dnmt3l knockout ESCs. Importantly, unlike epiblast stem cells, L-ESCs contribute to somatic tissues and germ cells in chimaeras. L-ESCs cultured in such a simple conditions in this study would provide a more conducive platform to clarify the molecular mechanism of ESCs in vitro culture.

overall_design: Replicate DNA methylation-seq datasets from mouse L-ESCs maintained in different stem cells culture conditions.

first: Baojiang

last: Wu

first: Junpeng

last: Gao


title: HOXB13, HOXA11 and HOXA11-AS transcriptome regulation in prostate cancer cells

status: Public on Jan 24 2021

city: Tokyo

first: Aya

last: Misawa

address: 1-1-5 Sendagi Bunkyo-ku

department: Medicine

country: Japan

institute: Nippon Medical School

summary:
Long noncoding RNAs (lncRNAs) are emerging as critical regulators of gene expression, playing fundamental roles in cancer development.
We analyzed changes in transcriptome profiling in prostate cancer PC-3 cells transfected with siRNAs targeting lncRNA HOXA11-AS, its upstream regulator HOXB13 and its opposite strand protein coding gene HOXA11.

overall_design: PC-3 cells were transfected for 24h or 48 h with 20 uM siRNAs targeting HOXB13, HOXA11-AS or HOXA11. siRNAs targeting two different sequences were combined for more efficient gene silencing and downstream effects. Total RNA was extracted with NucleoSpin Plus (MHN) and sent for microarray analysis.

first: Toshihiro

last: Takizawa

first: Yukihiro

last: Kondo

first: Hiroyuki

last: Takei


title: Profiling of exosomal miRNAs during maturation of 3T3-L1 adipocytes

city: Tsukuba

first: Koichi

last: Ojima

address: 2 Ikenodai

institute: Institute of Livestock and Grassland Science, NARO

summary: We profiled miRNAs in 3T3-L1 adipocyte-secreted exosomes and our microarray analysis revealed that more than 300 exosomal miRNAs were detected during adipocyte differentiation.

overall_design: Total RNA was isolated from exosome fractions which were released from differentiating 3T3-L1 adipocytes at 4 different maturing stages.


title: Effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes [ATAC-seq]

first: Nicholas

last: Banovich

summary: The predominant outcome of cardiovascular disease (CVD) is myocardial infarction (MI), where cardiomyocytes are deprived of oxygen. To study inter-individual differences in cardiomyocytes’ response to hypoxia, we established an in vitro model of induced pluripotent stem cell-derived cardiomyocytes from 15 individuals. We characterized gene expression levels, chromatin accessibility, and methylation profiles in these cardiomyocytes in four culturing conditions that correspond to normoxia (10% O2), hypoxia (1% O2) and short or long-term re-oxygenation (back to 10% O2). In our population sample, 2,113 genes change their expression following hypoxia and short- or long-term re-oxygenation. Using available genotypes from all individuals, we identified 1,573 genes with a cis eQTL in at least one of the four culturing conditions. Taking into account the incomplete power to identify eQTLs in any given condition, we also identified 367 dynamic eQTLs, which are classified as eQTLs in at least one, but not in all conditions. A subset of dynamic eQTLs, which are detected only following hypoxia, have not been previously annotated as eQTLs even in much larger collections of heart tissues. We did not detect differences in DNA methylation, or chromatin accessibility as the cells transitioned between normoxia and hypoxia, but we observed a change in chromatin accessibility in 831 genomic regions upon re-oxygenation. Differentially accessible regions are enriched for features of active regulatory regions, SINE elements, and E2F4 transcription factor binding sites . Finally, we found that genes associated with dynamic eQTLs are also associated with complex traits and disease. Our data thus demonstrate how unique genetic effects on gene expression, which are likely relevant for disease, can be uncovered under conditions of stress.

overall_design: We collected ATAC-seq data from iPSC-derived cardiomyocytes under normoxia, hypoxia and at two re-oxygenation timepoints in 14 human individuals.

first: Michelle

middle: C

last: Ward

middle: E


title: Effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes [methylation]

overall_design: We collected DNA methylation data from iPSC-derived cardiomyocytes under normoxia, hypoxia and at two re-oxygenation timepoints in 13 human individuals. Three individuals were replicated three times.


title: Effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes [RNA-seq]

overall_design: We collected RNA-seq data from iPSC-derived cardiomyocytes under normoxia, hypoxia and at two re-oxygenation timepoints in 15 human individuals. Three individuals were replicated three times.


title: Comparative transcriptomics: finding candidate genes responsible for kale domestication

city: East Lansing

first: Chad

middle: E.

last: Niederhuth

state: M

address: 612 Wilson Road

department: Plant Biology

institute: Michigan State University

summary: Morphotypes of Brassica oleracea are the result of a dynamic interaction between the genes that regulate the transition between vegetative and reproductive stages and those that regulate leaf morphology and plant architecture. In kales ornate leaf patterns, flowering delaying and nutrient quality are some of the characters were potentially selected by humans during domestication. Understanding candidate genes responsible for kale domestication is of importance to ultimately improve crop production. We aim to identify candidate genes that are responsible for kale leaf shape diversity and the evolution of domestic kale. Here we look at the global pattern of expressed genes during one single phase of development in kale, cabbage and TO1000 to gain an understanding of the genome-wide differences among some of the vegetative B. oleracea phenotypes. We identified gene expression patterns that are shared among the phenotypes and estimate the contribution of morphotype-specific gene expression patterns that set each of them apart. Differentially expressed developmental genes that regulate the vegetative to reproductive transition were abundant and present in all comparisons.

overall_design: Three replicates each of Kale and TO1000. Two replicates of Cabbage.

first: Tatiana

last: Arias

first: J

last: Pires

first: Paula

last: McSteen


title: Deciphering the state of immune silence in fatal COVID-19 patients

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Since the beginning of the SARS-CoV-2 pandemic, COVID-19 has appeared as a unique disease with unconventional tissue and systemic immune features. While COVID-19 severe forms share clinical and laboratory aspects with various pathologies such as hemophagocytic lymphohistiocytosis, sepsis or cytokine release syndrome, their exact nature remains unknown. This is severely impeding the ability to treat patients facing severe stages of the disease. To this aim, we performed an in-depth, single-cell RNA-seq analysis of more than 150.000 immune cells isolated from matched blood samples and broncho-alveolar lavage fluids of COVID-19 patients and healthy controls, and integrated it with clinical, immunological and functional ex vivo data. We unveiled an immune signature of disease severity that correlated with the accumulation of naïve lymphoid cells in the lung and an expansion and activation of myeloid cells in the periphery. Moreover, we demonstrated that myeloid-driven immune suppression is a hallmark of COVID-19 evolution and arginase 1 expression is significantly associated with monocyte immune regulatory features. Noteworthy, we found monocyte and neutro-phil immune suppression loss associated with fatal clinical outcome in severe patients. Additionally, our analysis discovered that the strongest association of the patients clinical outcome and immune phenotype is the lung T cell response. We found that patients with a robust CXCR6+ effector memory T cell response have better outcomes. This result is line with the rs11385942 COVID-19 risk allele, which is in proximity to the CXCR6 gene and suggest effector memory T cell are a primary feature in COVID-19 patients. By systemically quantifying the viral landscape in the lung of severe patients, we indeed identified Herpes-Simplex-Virus 1 (HSV-1) as a potential opportunistic virus in COVID-19 patients. Lastly, we observed an unexpectedly high SARS-CoV-2 viral load in an immuno-compromised patient, allowing us to study the SARS-CoV-2 in-vivo life cycle. The development of my-eloid dysfunctions and the impairment of lymphoid arm establish a condition of immune paralysis that supports secondary bacteria and virus infection and can progress to “immune silence” in patients facing death.

overall_design: Cells from blood or bronchoalveloar lavage samples from COVID-19 patients or healthy donors were sequenced using the Chromium 10X scRNA-seq technology (NextGEM Single Cell 3′ GEM, Library& Gel Bead kit v3.1 )

first: Pierre

last: Bost

first: Francesco

last: De Sanctis

first: Stefania

last: Canè

first: Stefano

last: Ugel

first: Katia

last: Donadello

first: Monica

last: Castellucci

first: David

last: Eyal

first: Alessandra

last: Fiore

first: Cristina

last: Anselmi

first: Roza

last: Barouni

first: Rosalinda

last: Trovato

first: Simone

last: Caligola

first: Alessia

last: Lamolinara

first: Manuelle

last: Iezzi

first: Federica

last: Facciotti

first: Anna

middle: R

last: Mazzariol

first: Divide

last: Gibellini

first: Pasquale

last: De Nardo

first: Evelina

last: Tacconelli

first: Leonardo

last: Gottin

first: Enrico

last: Polati

first: Benno

last: Schwikowski

first: Vicenzo

last: Bronte


title: Identification of Natural Antisense Transcripts in Mouse Brain and Their Association with Autism Spectrum Disorder Risk Genes

first: Roland

last: Schmucki

address: Grenzacherstrase

institute: F. Hoffmann - La Roche AG

summary: We performed strand-specific, deep RNA sequencing to profile expression of sense and antisense reads with a focus on 100 ASD-related genes in medial prefrontal cortex (mPFC) and striatum across mouse development (P7, P14 and P56). Using de novo transcriptome assembly, we generated a comprehensive long non-coding RNA (lncRNA) transcriptome. We conducted BLAST analyses to compare the resultant transcripts with the human genome and identified transcripts with high sequence similarity and coverage.

overall_design: Strand specific deep RNA sequencing of medial prefrontal cortex (mPFC) and striatum across mouse development.

first: Baran

last: Koç

first: Benjamin

last: Hall

first: Geoffrey

last: Fucile

first: Nicolas

last: Giroud

first: Tobias

last: Bergauer


title: Unique Patterns of H3K4me3 and H3K27me3 in 2-Cell-like Embryonic Stem Cells (ESCs)

status: Public on Jan 23 2021

first: Yanping

last: zhang

address: Siping Road 1239

institute: Tongji University

summary: A small subgroup of embryonic stem cells (ESCs) exhibit molecular features similar to those of 2-cell (2C) embryos. These so-called 2C-like cells display highly relaxed chromatin architecture and expanded developmental potential. However, it remains elusive whether 2C-like cells and 2-cell embryos share similar epigenetic features. Here, we map the genome-wide profiles of histone H3K4me3 and H3K27me3 in 2C-like cells. We integrated transcriptome and epigenome data to conduct a detailed comparison of 2-cell embryos and 2C-like cells. We found that the majority of genes in 2C-like cells inherit their histone status from ESCs. Among the genes showing a switch in their histone methylation status during 2C-like transitions, only a small number acquire a 2-cell-embryo epigenetic signatures. In contrast, broad H3K4me3 domains display extensive loss in 2C-like cells. Most of differentially expressed genes display decreased H3K4me3 and H3K27me3 levels in 2C-like cells whereas de novo H3K4me3 deposition is closely linked with the expression levels of upregulated 2C-embryo-specific genes. Taken together, our study reveals the unique epigenetic profiles of 2C-like cells, facilitating the further exploration of totipotency in the future.

overall_design: Embryo stem cells histone profiles and 2 cell like ESCs were generated by deep sequencing.

last: Zhang

first: Yixin

last: Huang


title: aCGH analysis of liver tumors generated in C57BL/6J mice with a liver specific loss of Trp53-/-

status: Public on Jan 22 2021

city: Ulm

first: André

last: Lechel

address: Albert-Einstein-Allee 23

department: Department of Internal Medicine I

institute: University hospital Ulm

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: aCGH analysis of liver tumors generated in C57BL/6J mice with a liver specific loss of Trp53-/- [Agilent-024427]

type: Genome variation profiling by high throughput sequencing

summary:
Background and aims: P53 limits the self-renewal of stem cells from various tissue. A Loss of p53 in combination with other oncogenic events results in aberrant self-renewal and transformation of progenitor cells. Here, we investigated whether a loss of p53 as a single genetic lesion is sufficient to induce liver tumor formation.
Methods: AlfpCre mice were crossed with Trp53 conditional knockout mice to achieve a liver-specific loss of Trp53.
Results: The liver-specific loss of Trp53 results in liver tumor formation. A high percentage of the tumors showed a mixed differentiation of hepatocellular carcinoma and intrahepatic cholangiocarcinoma.
Conclusion: The liver-specific deletion of Trp53 is sufficient to induce liver tumor formation.

overall_design: Liver tumors from 4 invidual Trp53-/- mice were analyzed, pooled spleen DNA from 3 sex matched littermates were used as controls


title: Sca1+ macrophages activate hematopoietic stem/progenitor cells upon bone marrow stress. [scRNA-Seq]

status: Public on Jan 20 2021

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Although hematopoietic stem and progenitor cells (HSPCs) become activated in the cell-cycle status after chemotherapy to supply hematopoietic loss, the detailed mechanisms of activation remain unknown. Here we show that Sca1+ macrophages play a key role for bone marrow (BM) recovery through granulocyte-macrophage colony-stimulating factor (GM-CSF) secretion. By analyzing gene expression profiles of HSPCs lodged in 5-fluolouracil (5-FU)-treated mice, we found GM-CSF as a key proliferative signal. Sca1+ macrophages in BM after 5-FU treatment expressed high levels of GM-CSF. GM-CSF-knockout mice treated with 5-FU were lethal because of severe BM suppression. Up-regulation of Csf2 in Sca1+ macrophages by 5-FU was suppressed in MyD88-knockout mice, suggesting that TLR signaling via damage-associated molecular patterns caused by cell death is critical for up-regulation of Csf2. In 5-FU treated BM, majority of Sca1+ macrophages and transplanted HSPCs locate perivascular areas. These findings together indicate that Sca1+ macrophages induce HSPCs to proliferate through GM-CSF signaling in the stressed BM environments.

overall_design: Sca1+ cells were sorted from 5-FU treated BMMNCs and targeted single-cell RNA-seq analysis was conducted (4424 single cells).

first: Takao

last: Sudo

last: Motooka

first: Masaru

last: Ishii


title: Divergence in alternative polyadenylation between humans and chimpanzees contributes to gene regulatory differences between species

city: Chicago

first: Yoav

last: GiladLi

state: IL

address: 920 e 58th St

department: Section of Genetic Medicine

institute: University of Chicago

summary: Differences in gene regulation contribute to phenotypic differences between humans and other primates. While co-transcriptional gene regulatory mechanisms such as alternative polyadenylation (APA) can help explain how variation in gene regulation manifests, such mechanisms remain understudied. We measured polyadenylation site (PAS) usage in a panel of 6 human and 6 chimpanzee lymphoblastoid cell lines (LCLs). While APA is largely conserved between humans and chimpanzees, genes with divergent APA patterns are enriched among differentially expressed and differentially translated genes. Differential usage of 3’ UTR and intronic PAS are both significantly correlated with differential mRNA expression effect sizes but in opposite directions. For many genes, there is one PAS dominant, meaning it is used much more often than others. The dominant PAS for these gene is overwhelmingly shared between species, however, differences in dominant PAS are enriched for genes with expression differences. Finally, through post-translational mechanisms, we believe APA contributes to genes differentially expressed at the protein level but not in mRNA. As this is the first primate comparative study of APA, our study establishes APA as a key mechanism underlying the genetic regulation of gene and protein expression levels in primates.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: We measured polyadenylation site (PAS) usage in a panel of 6 human and 6 chimpanzee lymphoblastoid cell lines (LCLs). We collected 3' Seq on total and nuclear mRNA using the Lexogen Rev Quant Seq protocol. We collected RNA sequencing on the total mRNA using the Illumina TruSeq kit.

first: Briana

last: Mittleman

first: Sebastian

last: Pott

first: Shane

last: Warland

first: Kenneth

last: Barr

first: Claudia

last: Cuevas

last: Gilad


title: Gene expression profiling of Hif1α defective hearts in E12.5 mice

status: Public on Jan 21 2021

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: Hypoxia is an important environmental cue in heart development. Despite of extensive characterization of gain and loss of function models, there is disagreement about the impact of HIF1 signaling elimination during cardiac development. Here, we used new conditional knock out models of Hif1α in Nkx2.5 cardiac progenitors and cardiomyocytes to assess the morphological and functional consequences of HIF1α loss in the developing heart. By combining histology, electron microscopy and high-throughput genomics and proteomics, we found that deletion of Hif1α leads to impaired embryonic glycolysis without influencing cardiomyocyte proliferation and results in an increased mitochondrial number, activation of a transient amino acid response and temporal upregulation of HIF2α and ATF4 by E12.5. Hif1α mutants display normal expression of genes and proteins involved in fatty acid oxidation and do not show any sign of cardiac dysfunction in the adulthood. Our results demonstrate that cardiac HIF1 signaling is dispensable for heart development and reveal the metabolic flexibility of the embryonic myocardium, opening the potential application of alternative energy sources as therapeutic interventions during ischemic events.

overall_design: RNA was isolated from individual E12.5 embryonic hearts after removal of the atria and valvular region. KOs and control littermates were matched by somite count and a total number of 2 KOs and 2 controls from the same litter. For RNA extraction QIAzol Lysis Reagent (Qiagen; CA; USA) and the miRNeasy Mini Kit (Qiagen; CA; USA). RNA was quantified and its purity checked with a NanoDrop ND-1000 spectophotometer (Thermo Scientific; MA; USA). RNA integrity was verified with an Agilent 2100 Bioanalyzer (Agilent Technologies; CA; USA). Index-tagged cDNA libraries were constructed from 500 ng of total RNA using the TruSeq RNA Sample Preparation v2 Kit (Illumina; CA; USA). Libraries were quantified by Quant-iT™ dsDNA HS assay in a Q-bit fluorometer (Life Technologies; CA; USA). Average library size and size distribution were determined by DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using 10mM Tris-HCl, pH8.5 containing 0.1% Tween 20 and then applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and sequencing-by-synthesis. Single reads of length 75bp were generated with the TruSeq SBS Kit v5 (Illumina; CA; USA) on the Genome Analyzer IIx platform, following the standard RNA sequencing protocol. Reads were further processed using the CASAVA package (Illumina; CA; USA) to split reads according to adapter indexes and produce fastq files.

first: Ivan

last: Menendez-Montes

first: Beatriz

last: Escobar

first: Teresa

last: Albendea-Gomez

last: Palacios

first: Elena

last: Bonzon

first: Jose

middle: L

last: Izquierdo-Garcia

first: Ana

middle: V

last: Alonso

first: Alessia

last: Ferrarini

first: Luis

last: Jimenez-Borreguero

first: Jesus

last: Ruiz-Cabello

last: Vázquez

first: Silvia

last: Martin-Puig


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and LATS1/2 double knockout MCF-7 cells Transcriptome

city: La Jolla

first: Shenghong

last: Ma

state: CA

address: 2880 TORREY PINES SCENIC DR, Sanford Consortium

institute: UCSD

summary: We report the transcriptional difference of LATS1/2 gene knock out MCF-7 cells with wild type control using RNA-seq technology.

overall_design: mRNA profiles of wild type and LATS1/2 knock out MCF-7 cells

first: Feng

last: Yang


title: Long non-coding RNA lnc_3712 impedes nuclear reprogramming via repressing Kdm5b

status: Public on Jan 19 2021

city: Nanjing

first: Mingtian

last: Deng

state: Jiangsu

address: Weigang No.1

department: College of Animal Science and Technology

institute: Nanjing Agricultural University

summary: Effects were investigated to improve the nuclear reprogramming efficiency by modulating the epigenetic modifications. Long non-coding RNAs (lncRNAs) are involved in shaping chromosome conformation and regulation of preimplantation development. However, the role of lncRNA during nuclear reprogramming remains largely unknown. In the present study, we performed RNA sequencing and identified 687 differentially expressed lncRNAs as candidate key molecules involved in nuclear reprogramming in goat.

overall_design: We performed RNA-seq to identify differencially expressed lncRNAs during embryonic genome activation in goat SCNT embryos, and performed RNA-seq to assess the effect of lnc_3712 knockdown on SCNT reprogramming in goat

first: Yongjie

last: Wan

first: Baobao

last: Chen

last: Wang


title: Sca1+ macrophages activate hematopoietic stem/progenitor cells upon bone marrow stress.

first: Daisuke

last: Okuzaki


title: Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML

city: Worcester

first: Anne-Laure

last: Valton

address: 368 Plantation St

institute: University of Massachusetts Medical School

summary: The cohesin complex plays an essential role in chromosome maintenance and transcriptional regulation. Recurrent somatic mutations in the cohesin complex are frequent genetic drivers in cancer including myelodysplatic syndromes (MDS) and acute myeloid leukemia (AML). Here, using genetic dependency screens of STAG2-mutant AML, we identified DNA damage repair and replication as genetic dependencies in cohesin-mutant cells. We demonstrated increased levels of DNA damage and sensitivity of cohesin-mutant cells to PARP inhibition. We developed a mouse model of MDS in which Stag2 mutations arise as clonal secondary lesions in the background of clonal hematopoiesis driven by Tet2 mutations, and demonstrated selective depletion of cohesin-mutant cells with PARP inhibition in vivo. Finally, we demonstrated a shift from STAG2- to STAG1-containing cohesin complexes in cohesin-mutant cells, which is associated with longer DNA loop extrusion, more intermixing of chromatin compartments, and increased interaction with PARP and RPA proteins. Our findings inform the biology and therapeutic opportunities for cohesin-mutant malignancies.

overall_design: Hi-C was performed in a set of STAG2-wild type (2 clones) and knockout AML cell line (2 clones). We observed a global weakening of compartmentalization (A and B compartments), a decrease in TAD boundary insulation and an increase in the loop size in the STAG2 knockout cells.

first: Zuzana

last: Tothova

first: Rebecca

last: Gorelov

first: Mounica

last: Vallurupalli

first: John

last: Krill-Burger

first: Amie

last: Holmes

first: Catherine

last: Landers

first: J

last: Haydu

first: Edyta

last: Malolepsza

first: Christina

last: Hartigan

first: Melanie

last: Donahue

first: Katerina

last: Popova

first: Sebastian

last: Koochaki

first: Sergey

last: Venev

first: Jeanne

last: Rivera

first: Edwin

first: Kasper

last: Lage

first: Monica

last: Schenone

first: Alan

last: D'Andrea

first: Steven

last: Carr

first: Elizabeth

last: Morgan

first: Job

last: Dekker

first: Benjamin

last: Ebert


title: Nuclear enriched RNA-Seq data of cerebellar granular cells with efnA5-FC versus control-FC treatment

city: Aachen

first: Daniel

last: Pensold

state: Nordrhein-Westfalen

address: Worringerweg 3

department: Institute for Biology II

institute: RWTH Aachen

type: Non-coding RNA profiling by high throughput sequencing

summary: The Eph receptor tyrosine kinases and their respective ephrin-ligands are an important family of membrane receptors, being involved in developmental processes such as proliferation, migration, and in the formation of brain cancer such as glioma. Intracellular signaling pathways, which are activated by Eph receptor signaling, are well characterized. In contrast, it is unknown so far whether ephrins modulate the expression of lncRNAs, which would enable the transduction of environmental stimuli into our genome through a great gene regulatory spectrum. Applying a combination of functional in vitro assays, RNA sequencing, and qPCR analysis, we found that the proliferation and migration promoting stimulation of mouse cerebellar granule cells (CB) with ephrinA5 diminishes the expression of the cancer-related lncRNA Snhg15. Computational analysis identified triple-helix-mediated DNA-binding sites of Snhg15 in promoters of genes found up-regulated upon ephrinA5 stimulation and known to be involved in tumorigenic processes. Our findings propose a crucial role of Snhg15 downstream of ephrinA5-induced signaling in regulating gene transcription in the nucleus. These findings could be potentially relevant for the regulation of tumorigenic processes in the context of glioma. (published in Pensold et al., 2021, The Expression of the Cancer-Associated lncRNA Snhg15 Is Modulated by EphrinA5-Induced Signaling. IJMS, 22, 1332, https://doi.org/10.3390/ijms22031332)

overall_design: 6 Samples in total; 3 samples per condition (control-FC treated and efnA5-FC treated), nuclear enriched RNA was isolated and total RNA-Seq after ribosomal depletion was performed

first: Julia

last: Gehrmann

first: Ivan

middle: G

last: Costa

first: Geraldine

last: Zimmer-Bensch


title: Sca1+ macrophages activate hematopoietic stem/progenitor cells upon bone marrow stress. [RNA-Seq]

first: Daisuke

last: Okuzaki

overall_design: Lin- Sca1+ c-Kit+ (LSK) cells from CAG-EGFP mice were transplanted into steady-state control or 5-FU treated WT mice. Conditioning by 5-FU (200mg/kg) was performed 2 days before transplantation. Twenty-four hours after transplantation, EGFP+ cells in recipient BM were sorted from 2 groups and conducted RNA-seq analyses.

first: Takao

last: Sudo

last: Motooka

first: Masaru

last: Ishii


title: Expression data of tumor and non-tumor liver tissues from Peruvian patients with hepatocellular carcinoma (HCC)

status: Public on Jan 31 2021

city: Toulouse

first: Juan Pablo

last: Cerapio

address: Av 2 Hubert Curien

country: France

institute: CRCT

summary:
A large fraction of HCC in Peru arises in younger, non-cirrhotic patients. Transcriptomic analysis of the HCC and non-tumor liver (NTL) tissues highlights a divergent gene expression profile that coincides with Amerind haplogrouping. This metagene is also associated with a peculiar molecular signature that does not conform with the current molecular classifications of HCCs.
We used microarrays to compare gene expression between tumors and non-tumor counter parts in order to identify genes and ontologies that are differentially expressed.

overall_design: HCC patients were treated by anatomic liver resection. Non-tumor liver tissues were obtained from tumor-free margins of resected surgical pieces. Total RNA was extracted from flash-frozen samples for hybridization on Affymetrix microarrays.

first: Juan

middle: P

first: Pascal

last: Pineau


title: Genome-wide expression analysis of PTI and ETI responses in wild type and PRR-deficient Arabidopsis plants

status: Public on Jan 18 2021

first: Minhang

last: Yuan

address: Fenglin

department: Shanghai Institute of Plant Physiology and Ecology

institute: Chinese Academy of Sciences

summary:
Purpose: The goal of this study is to demonstrate the global expression profile of Arabidopsis wild type and PRR mutant plants in response to PTI- and ETI-eliciting strains of Pseudomonas syringae pv tomato (Pst) bacterium.
Methods: Four-week-old Arabidopsis plant leaves were infiltrated with sterile water (Mock) or different Pst strains and harvested at 3h or 6h after infiltration for RNA extraction and deep sequencing by Illumina. Raw data were cleaned up and trimmed and reads were mapped to Arabidopsis genome. Gene expression levels were calculated using the TPM method (Transcripts per Kb of exon model per Million mapped reads).
Results and Conclusions: This study showed that Pst DC3000 D36E and D36E(avrRpt2) strains both induced significant gene expression changes (with changes of more than 3000 and 7000 genes respectively) in Col-0 plant, and D36E(avrRpt2) strain induced stronger expression changes globally. Furthermore, many genes are differentially regulated in the PRR mutant plants in response to D36E inoculation compared with wild type plant; however, D36E(avrRpt2) inoculation induced very similar expression patterns in two genotypes, suggesting that ETI can largely restore PTI-associated gene expression in the PRR mutant plant. In addition, we also found that ETI can largely induce the expression levels of many key PTI signaling components.

overall_design: Investigation of genome-wide expression profiles of Arabidopsis wildtype and PRR mutants in response to PTI- and ETI-inducing bacterial strains.

first: Xiu-Fang

last: Xin


title: Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development [Capture Hi-C]

city: Memphis

first: Yong

last: Cheng

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Childrens Research Hospital

summary: The ubiquitously expressed transcription factor CTCF maintains higher-order chromatin structure in multiple cell types and species through well-established common mechanisms. Here we define a new role for CTCF in tissue-specific gene regulation revealed by serial examinations of genome-wide CTCF occupancy during red blood cell (RBC) differentiation of human CD34+ hematopoietic stem/progenitor cells (HSPCs). We identified 1753 dynamic, erythroid developmental stage-specific CTCF chromatin occupancy sites that occur through both direct DNA binding and indirectly via interactions with lineage-specific transcription factors. These dynamic sites display features of transcriptional enhancers, function as hubs of cis-regulatory elements (CREs) interactome, and are enriched for single nucleotide polymorphisms (SNPs) associated with RBC traits. Precise deletion of CTCF binding motifs from those dynamically bound sites alternated local CRE-interactions and disrupted erythropoiesis.  Our study highlights novel, lineage-specific functions for CTCF and provides new insights into how genetic variation regulates erythropoiesis

overall_design: Capture-C libraries were constructed on HUDEP2 and mutant cells with or without 3-day maturation

first: Qian

last: Qi

first: Li

first: Yanghua

last: He


title: m6A modification in effector CD4+ T cells [m6A-miCLIP-seq]

city: Beijing

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

summary: GP61-primed effector CD4+ T cells were isolated from Ctrl or Mettl3-deficient SMARTA mice. Total RNAs were extracted with TRIzol reagent, and mRNAs were then isolated with Dynabeads® mRNA purification kit, followed by stardard m6A-miCLIP-SMARTer-seq with some modifications. Raw sequencing reads were aligned to the mouse genome (mm10) with BWA, and then m6A sites were determined.

overall_design: Ctrl or Mettl3fl/flCd4-Cre SMARTA mice were primed with LCMV GP61 peptide , and 16-18 h later, CD62LloCD44hiCD4+ T cells were sorted and subjected to m6A-miCLIP-SMARTer-seq.

first: Yingpeng

last: Yao


title: Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development [HiChIP]

overall_design:
HiChIP libraries were constructed on HUDEP2 and mutant cells after 3-day maturation.
HiChIP libraries were constructed on human erythroblasts.


title: DNA methylation analysis in dermal fibroblasts from African ancestry patients with systemic sclerosis

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

institute: Medical University of South Carolina

summary: Background.  The etiology and reasons underlying the ethnic disparities in systemic sclerosis (SSc) remain unknown. African-Americans (AA) are disproportionally affected by SSc, yet dramatically underrepresented in research. The role of DNA methylation in disease risk remains unclear. This analysis was conducted to comprehensive identify differentially methylated loci associated with SSc in AA.  Methods.  Genomic DNA was isolated from cultured dermal fibroblasts isolated from 15 AA SSc cases and 15 AA controls. All patients met the 2013 ACR/EULAR classification criteria for SSc, most (93%) presenting with diffuse cutaneous SSc. DNA methylation patterns were profiled through reduced representation bisulfite sequencing (RRBS). Alignment and methylation calling were performed using Bismarck v0.16.3 and the GRCh37/hg19 reference genome. Data was filtered, normalized, and analyzed with RnBeads v1.6.1. Differential methylation analysis was conducted on CpG, promoter, gene and system level.   Results.  We generated DNA methylation data for over 5 million CpGs in each sample and between 10x to 40x coverage in CpGs sites. Using the Combined Score approach implemented in RnBeads, a total of 9 CpG islands, 17 genes and 11 promoters showed significant differential methylation levels between cases and controls at the gene-level. The top differentially methylated genes constitute mostly non-coding RNA genes (42%), followed by pseudogenes (27%), then protein coding genes (19%). Enrichment analysis revealed that both hypo- and hypermethylated genes and their promoter regions were enriched for cell differentiation and immune-related gene ontology terms (hypermethylated regions: mesenchymal cell transition and differentiation; hypomethylated regions: type I IFN signaling).  Conclusion.  The observed DNA methylation differences between cases and controls support a modest role for DNA methylation differences in mediating susceptibility to SSc in AA. Instead of protein-coding, most differentially methylated genes comprise non-coding RNA genes, supporting a larger contribution of dysregulated regulatory elements to disease. While previous DNA methylation profiling analyses in European-Americans reported an enrichment of extracellular matrix and focal adhesion genes, our data supports a potentially stronger immune-driven etiology in AA.

overall_design: Reduced representation bisulfite sequencing (RRBS) was performed in cultured dermal fibroblasts isolated from 15 African ancestry patients with systemic sclerosis and 15 African ancestry controls.

first: Deanna

middle: B

last: Frost

first: E

middle: S

last: Hazard

first: Willian

last: da Silveira

first: Paula

last: Ramos


title: Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development [ATAC-seq]

overall_design: ATACseq libraries constructed on human CD34+ HSPC and erythroblasts


title: The HIF-1α antisense long non-coding RNA drives a positive feedback loop of HIF-1α mediated transactivation and glycolysis

city: Guangzhou

first: Fang

last: Zheng

address: 107 Yanjiang West Road

institute: Sun Yat-Sen Memorial Hospital

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

summary: Hypoxia-inducible factor-1 (HIF-1) is a master regulator of glucose metabolism in cancer cells. Here, we demonstrate that a HIF-1α anti-sense lncRNA, HIFAL, is essential for maintaining and enhancing HIF-1α-mediated transactivation and glycolysis. Mechanistically, HIFAL recruits PHD3 to PKM2 to induce its prolyl hydroxylation and introduces the PKM2/PHD3 complex into the nucleus via binding with hnRNPF to enhance HIF-1α transactivation. Reciprocally, HIF-1α induces HIFAL transcription, which forms a positive feed-forward loop to maintain the transactivation activity of HIF-1α. Clinically, high HIFAL expression is associated with aggressive breast cancer phenotype and poor patient outcome. Furthermore, HIFAL overexpression promotes tumor growth in vivo, while targeting both HIFAL and HIF-1α significantly rescues their effect on cancer growth. Overall, our results indicate a critical regulatory role of HIFAL in HIF-1α-driven transactivation and glycolysis, identifying HIFAL as a therapeutic target for cancer treatment.

overall_design: Breast cancer cell lines 76N and MBA-MD-231 under normoxia (20%) or hypoxia (0.6%) conditions and 4 pairs of breast cancer and adjacent normal tissues.

first: Jia-ning

last: Chen


title: Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development

overall_design: Refer to individual Series


title: Spatially mapped single-cell chromatin accessibility

status: Public on Jan 15 2021

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

summary: sciMAP-ATAC as a technology to produce single-cell ATAC-seq data with cells mapped to spatially-defined regions.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell ATAC-seq data including sci-ATAC-seq and sciMAP-ATAC-seq.

first: Casey

last: Thornton


title: Dynamic CTCF occupancy during differentiation rewires cis-regulatory module interactions essential for development [ChIP-seq]

overall_design: ChIP libraries constructed on human CD34+ HSPC, erythroblasts, differetiated HUDEP2 and mutant cell line,


title: Vitamin E deficiency disrupts gene expression networks during zebrafish development

city: Corvallis

first: Maret

last: Traber

address: 2900 SW Campus Way

department: Linus Pauling Institute

institute: Oregon State University

summary: Vitamin E (VitE) is essential for vertebrate embryogenesis, but the mechanisms involved remain unknown. To study embryonic development, we fed zebrafish adults (>45 days) either VitE sufficient (E+) or deficient (E–) diets for >80 days, then the fish were spawned to generate E+ and E– embryos. To evaluate the transcriptional basis of the metabolic and phenotypic outcomes, E+ and E– embryos at 12-, 18- and 24 hours post-fertilization (hpf) were subjected to gene expression profiling by RNASeq. Hierarchical clustering, over representation analyses and gene set enrichment analyses were performed with differentially expressed genes. E– embryos experienced overall disruption to gene expression associated with gene transcription, metabolism, intracellular signaling and the formation of embryonic structures. Thus, the apparently moderate changes in lipid peroxidation and metabolic alterations due to VitE deficiency result in major genetic and transcriptional dysregulation as early as 12 hpf, leading to metabolic dysfunction and ultimately lethal outcomes.

overall_design: RNA extracted from whole zebrafish embryos with (E+) and without (E–) Vitamin E at 12, 18 and 24 hours post-fertilization

first: Brian

last: Head

first: Robyn

last: Tanguay


title: The transcriptome, histone modification and chromatin organization of kidney tubule cells

status: Public on Feb 02 2021

first: Jingping

last: Yang

address: 22 Hankou Road

department: Medical School

institute: Nanjing University

summary: To understand the transcription regulation in kidney tubule cells, we captured histone modifications by ChIP and chromatin interaction profile by HiChIP with H3K27ac. We establish a transcription network by integrating the epigenetic map and transcription output.

overall_design: Kidney tubule cell culture HK2 were subjected to ChIP-seq, RNA-seq and HiChIP.

first: Duan

last: Aiping

first: Yang

last: Jingping


title: m6A methyltransferase METTL3 regulates Tfh cell differentiation

first: Shuyang

last: Yu

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


title: Platinoid drugs augment immunotherapy via histone acetylation of MHCI machinery genes [TRAMP]

status: Public on Feb 01 2021

city: Houston

first: Shabnam

last: Shalapour

state: TX

address: 1881 East Road

department: Cancer Biology

institute: MD Anderson Cancer Center

summary: Here we show that low dose Oxali, and to a lesser extent other platinoids, can uniquely activate the transcriptional program that controls MHCI antigen processing and presentation. Activation of this program correlates with induction of histone acetylation and enhanced chromatin accessibility. Oxaliplatin also induces NF-kB dependent IFNg receptor 2 (IFNgR2) thereby augmenting the tumor response to exogenous IFNg produced by reinvigorated effector CD8+ T cells.

overall_design: RNA were isolated after 24h treatment of prostate cancer cell lines Myc-Cap and TRAMP-C2 with Oxaliplatin and Cisplatin at 2uM or 20uM dosages.

first: Michael

last: Karin


title: Kinome-wide RNAi screen uncovers role of Ballchen in maintenance of gene activation by trithorax group in Drosophila

status: Public on Jan 29 2021

city: Lahore

first: Muhammad

last: Tariq

state: Punjab

address: DHA, Lahore Cantt.

department: Biology

country: Pakistan

institute: Lahore University of Management Sciences

summary: We report an ex vivo kinome-wide RNAi screen in Drosophila aimed to identify cell signaling genes that facilitate trxG to counteract PcG mediated repression. From the list of trxG candidates, Ballchen (BALL), a histone kinase, known to phosphorylate histone H2A at threonine 119 (H2AT119p), was characterized as a trxG regulator. BALL co-localizes with Trithorax on chromatin and depletion of BALL results in increased H2AK118 ubiquitination, a histone mark central to PcG mediated gene silencing. Moreover, analysis of genome-wide binding profile of BALL shows an overlap with 85% known binding sites of TRX across the genome. Both BALL and TRX are highly enriched at actively transcribed genes, which also correlate with presence of H3K4me3 and H3K27ac. We propose that BALL mediated signal positively contributes to the maintenance of gene activation by trxG by counteracting the repressive effect of PcG.

overall_design: To examine the genome-wide binding profile of BALL in Drosophila S2 cells.

first: M

last: Khan

first: J

last: Akhtar

first: A

last: Shaukat

first: Z

last: Umer

first: N

last: Shaheen

last: Munir


title: Expression data from testes fragment of 7-week-old W/Wv mouse testes

city: Yayoi, Bunkyo-ku

first: Yoshiakira

last: Kanai

state: Tokyo

institute: The University of Tokyo

summary:
In the terminal end of the seminiferous tubules adjacent to rete testis (RT), there are valve-like structures called Sertoli valve (SV) epithelia. SV epithelia are constitutively missing  most spermatogenesis activity partially through high GDNF expression, leading to the SV-specific enrichment of undifferentiated spermatogonia.
We used microarrays to elucidate the molecular characterization in the SV epithelia.

overall_design: RT, SV and convoluted seminiferous epithelia (ST) samples were obtained from 7-week-old W/Wv mouse testes. 20 testes were used for 1 analysis and 3 biological replicates of each region were analyzed.


title: The transcriptional profiles of severe COVID-19

city: Hangzhou

first: Qiong

last: Zhang

address: 866 YuHangTang Rd, Medical Research Building A212, ZiJinGang Campus, Zhejiang University

institute: Zhejiang University

summary: The study aims at investigating the specifical transcriptional signatures of severe COVID-19

overall_design: We applied microarray analysis of the whole genome transcriptome to peripheral blood mononuclear cells (PBMCs) taken from severe and mild COVID-19 patients as well as healthy controls.

first: Hongyan

last: Diao


title: Hepatic RNA sequence in male mice offspring conceived by in-vitro Fertilization and Frozen-thawed Embryo Transfer

city: Shanghai

first: Ningxin

last: Qin

address: 910, Hengshan Road

institute: The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China

summary: Our study reported an increased risk of metabolic disorders in in-vitro Fertilization and Frozen-thawed Embryo Transfer (IVF-FET) conceived offspring compared with those born after IVF-ET.  To explore the underlying mechanisms of the aberrant metabolism in male offspring conceived by IVF and FET compared with natural conceived (NC), we performed the RNA-sequencing of livers from three groups.  We performed GSEA analysis. The results suggested more severe alterations in the expression of genes involved in insulin resistance pathway in the FET-chow group than that in the IVF-chow group.

overall_design: Hepatic mRNA profile of 20-weeks-old mice conceived by NC, IVF-ET and IVF-FET. 3 samples from NC group, 3 samples from IVF-ET group and 3 samples from IVF-FET group.

first: Kexin

last: Zou

first: Hefeng

last: Huang


title: Regulation of Tfh differentiation by Mettl3 [RNA-seq]

summary: T follicular helper (Tfh) cells are a specialized subset of CD4 T cells that are essential for most antibody productions and humoral responses. It is well characterized that transcriptional network exerts indispensable roles in Tfh cell differentiation. However, how post-transcriptional regulation controls Tfh biology has largely remained unclear. Multiple mice models were used here by a series of experimental approaches to illustrate m6A methyltransferase Mettl3 programs Tfh cell differentiation at post-transcriptional layer.

overall_design: Ctrl and Mettl3-null Tfh cells (3 samples per group) or Th1 cells (2 samples per group) were sorted at day 8 after LCMV Armstrong infection. Then the total RNAs were extracted and subjected to RNA sequencing.

first: Yingpeng

last: Yao


title: Overview of the HERV-loci differentially expressed in SKOV3WT ovarian carcinoma cells treated with the HDACis romidepsin and vorinostat

city: Herne

first: David

last: Diaz-Carballo

state: NRW

address: Düngelstr. 33

department: Medical clinic of hematology & oncology

institute: Marienhospital Herne, Clinic of Ruhr University Bochum

summary: To check the acetylation levels at the positions harbouring HERV-loci and assess their variation after the treatment with HDACis (Vorinostat, romidepsin), the univocal genomic coordinates of about 3280 HERV-loci have been compared with the position of the H3AcK9 peaks identified by ChIP-seq analysis. The first analysis confirmed that HDACis are able to modulate the acetylation of repetitive elements, including HERV sequences. Subsequently, we considered only the differential peaks (diffpeaks), i.e. the peaks showing significant variation after the treatment with vorinostat and/or romidepsin. Interestingly, even if more than half of HERV-loci co-localised with acetylation peaks after HDACi treatment, only a minority of them (0.9 to 1.9%) co-localised with diffpeaks, showing mostly a reduction in their acetylation levels. Diffpeaks co-localised HERV-loci could be classified into 24 HERV groups and included the ERV-V2 locus. We focused then on the 11 HERV-loci which co-localised with diffpeaks showing an increase in acetylation levels, hence indicating an increased transcriptional activation after HDACi treatment. Remarkably, diffpeaks corresponding to the ERV-V2 locus were identified in all samples and were the most significantly upregulated in both vorinostat and romidepsin treatment. This was in part confirmed by ChIP-qPCR in different OC cells. Beside ERV-V2, only the HML8 sequence at locus 2q11,2 showed increased acetylation levels in all treated samples, independent from the HDACis used, but having lower statistical significance. The analysis revealed that the treatment with HDACis did not only account for the significant increase of ERV-V2 acetylation, but also led to the shift and concentration of acetylation peaks at the 5’ region of the HERV provirus. This observation allows us to hypothesize that HDACi treatment could not only increase ERV-V2 transcriptional activation, but also modify its pattern of expression, and eventually leading to alternative splicing.

overall_design:
SKOV3 wt cells were treated with HDACis romidepsin and vorinostat. After 24 h chromatin immunoprecipitation was performed. The harvested DNA was ChIP sequenced and analyzed.
*** Submitter declares raw data are unavailable.

last: Díaz-Carballo

first: Sahitya

last: Saka

first: Ali

last: Haydar Acikelli

first: Ekaterina

last: Homp

first: Julia

last: Erwes

first: Rebecca

last: Demmig

first: Jacqueline

last: Klein

first: Katrin

last: Schröer

first: Sascha

last: Malak

first: Flevy

last: D?Souza

first: Adrien

last: Noa-Bolaño

first: Saskia

last: Menze

first: Emilio

last: Pano

first: Swetlana

last: Andrioff

first: Nicole

last: Grandi

first: Enzo

last: Tramontano

first: Dirk

last: Strumberg


title: A Dietary Oxysterol, 7-Ketocholesterol, Accelerated Hepatic Lipid Accumulation and Infiltration of Macrophages in Obese Mice

city: Suita

first: Daisuke

last: Okuzaki

address: Yamadaoka 3-1

institute: Osaka univ.

summary: Non-alcoholic fatty liver disease is strongly associated with obese and type 2 diabetes.  It has been reported that an oxidized cholesterol, 7-ketocholesterol (7KC) might cause inflammatory response in macrophages and plasma 7KC concentration were higher in patients with cardiovascular diseases or diabetes.  Therefore, we have decided to test whether small amount of 7KC in diet might induce hepatic steatosis and inflammation in two types of obese models.  We found that addition of 0.01% 7KC either in chow diet (CD, regular chow diet with 1% cholesterol) or western type diet (WD, high fat diet with 1% cholesterol) accelerated hepatic neutral lipid accumulation by Oil Red O staining.  Importantly, by lipid extraction analysis, it has been recognized that triglyceride rather than cholesterol species was significantly accumulated in CD+7KC compared to CD as well as in WD+7KC compared to WD.  Immunostaining revealed that macrophages infiltration was increased in CD+7KC compared to CD and also in WD+7KC compared to WD.  These phenotypes were accompanied by inducing inflammatory response and downregulating fatty acid oxidation.  Furthermore, RNA sequence analysis demonstrated that 7KC reduced expression of genes which related to autophagy process.  Levels of LC3-II protein were decreased in WD+7KC compared to WD.  Similarly, we have confirmed the effect of 7KC on acceleration of steatohepatitis in db/db mice model.   Collectively, our study has demonstrated that small amount of dietary 7KC contributed to accelerate hepatic steatosis and inflammation in obese mice models.

overall_design: We compared hepatic gene expression in ob/ob mice fed normal chow diet or high fat diet with or without 7-KC for 4 weeks.

first: Jiuyang

last: Chang

first: Masahiro

last: Koseki


title: A hexokinase isoenzyme switch in human liver cancer cells promotes lipogenesis and enhances innate immunity

city: Lyon

first: Olivier

last: Diaz

address: Avenue Tony Garnier

department: Centre International de Recherche en Infectiologie (CIRI)

institute: INSERM U1111 – CNRS UMR5308 Université Lyon 1, ENS de LyonINSERM U1111 – CNRS UMR5308 Université Lyon 1, ENS de Lyon

summary: HK2 is expressed in the hepatocellular carcinoma cell line Huh7 while GCK is expressed in the normal hepatocyte. In order to analyze the functional consequences of the expression of one or other of the hexokinases (HK2 or GCK) we have invalidated the expression of HK2 and induced the expression of GCK in Huh7 cells. We analyzed transcriptome of both cell line

overall_design: triplicates extracions were analyzed for each cell line

first: Laure

last: Perrin-Cocon

first: Pierre-Olivier

last: Vidalain

first: Clémence

last: Jacquemin

first: Anne

last: Aublin-Gex

first: Patrice

last: André

first: Vincent

last: Lotteau


title: Comparison of gene expression in hippocampus among three strains (SAMP8, SAMR1 and JF1) of mice

status: Public on Jan 14 2021

city: Toyama City

first: Masaharu

last: Isobe

address: 3190 Gofuku

department: Faculty of Engineering

institute: Uniersity of Toyama

summary: We identified Searpina3n from SAMP8 strain plays a role as pathogenic chaperon by prolonging the oligomeric state of Amyloid beta 42 peptide. SAMP8 Serpina3n has 2 unique SNPs compared JF1 and SAMR1 strains of mice. Furthermore, the expression level of Searpina3n in SAMP8 is higher than other strains.

overall_design:
Expression profile of hippocampus mRNA from three strains of mice at 5 months of age
Male (n=1) and female (n=2) mice from each strain

first: Maruf

last: Akbor

first: Nobuyuki

last: Kurosawa


title: Knockout of zebrafish colony-stimulating factor 1 receptor by CRISPR/Cas9 affects metabolism and locomotion capacity

city: Tianjin

first: Yue

last: Shang

address: Tianjin Key Laboratory of Tumor Microenvironment and Neurovascular Regulation, Department of Pathology, Nankai University School of Medicine, Tianjin 300071, China

institute: Nankai University

summary:
Purpose: Colony-stimulating factor 1 receptor (CSF1R), a tyrosine kinase receptor, is a key regulator in the proliferation, differentiation, migration and colonization of macrophage lineage cells. Under pathological conditions, CSF1R was not only involved in the pathogenesis of immune disorders and hematopoietic diseases, but also closely related to tissue damage and tumor growth and metastasis. Therefore, comprehensive understanding of CSF1R function is of great significance.
Methods: In this study, a csf1ra−/− zebrafish mutant line was generated using clustered regularly interspaced short palindromic repeats (CRISPR)-associated 9 (CRISPR/Cas9) technology.
Results:The csf1ra−/− larvae were lack of the yellow cast on the head and over the flank, while the adult mutants had poorly formed stripes. The RNA-sequence analysis revealed that genes related to bile acid secretion, fat digestion and absorption and pancreatic secretion were differentially expressed in csf1ra−/− mutants, leading to the fatty change in the liver. Besides, genes related to locomotion were also significantly changed with more active movement in csf1ra−/− larvae and adults.
Conclusions: Overall, our data reveal that csf1ra participates the metabolic process and behavior. This study provides new insight into the functions of csf1ra gene during the development in zebrafish.

overall_design: Embryo mRNA of 3 days post fertilization (dpf)  wild type (WT) and csf1ra-/-zebrafish

first: Yuhao

last: Li

first: Jianlin

last: Cui

first: Huiling

last: Meng


title: Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection

city: Cold Spring Harbor

first: Zachary

last: Lippman

address: 1 Bungtown Rd

department: Plant Biology

institute: Cold Spring Harbor Laboratory

summary: Divergence of gene function is a hallmark of evolution, but assessing functional divergence over deep time is not trivial. The few alleles available for cross-species studies often fail to expose the entire functional spectrum of genes, potentially obscuring deeply conserved pleiotropic roles. Here, we explore the functional divergence of WUSCHEL HOMEOBOX9 (WOX9), suggested to have species-specific roles in embryo and inflorescence development. Using a cis-regulatory editing drive system, we generated a comprehensive allelic series in tomato, which revealed hidden pleiotropic roles for WOX9. Analysis of accessible chromatin and conserved cis-regulatory sequences identified the regions responsible for this pleiotropic activity, the functions of which were conserved in groundcherry, a tomato relative. Mimicking these alleles in arabidopsis, distantly related to tomato and groundcherry, revealed new inflorescence phenotypes, exposing a deeply conserved pleiotropy. We suggest that targeted cis-regulatory mutations can uncover conserved gene functions and reduce undesirable effects in crop improvement.

overall_design: Six replicate of ATAC-seq data from anantha inflorescences (meristematic enriched tissue) were generated using  Illumina MiSeq


title: Transcriptome Profiling of SW480 and SW620 tumors from zebrafish xenografts

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

overall_design: Refer to individual Series


title: Bulk Transcriptome Profiling of SW480 and SW620 tumors from zebrafish xenografts

summary: Buk transcriptome profiling of SW480 and SW620 tumors dissected from zebrafish xenografts at 2dpi.

overall_design: SW480 and SW620 tumors were dissected from zebrafish xenografts at 2dpi, a timepoint that corresponds to the timing when clearance is actively taking place. A pool of ~30 tumors from at least 3 independent experiments were collected for RNA extraction.

first: Vanda

last: Povoa

first: Caria

last: Rebelo de Almeida

first: Mariana

last: Maia-Gil

first: Micaela

last: Domingues

first: Mayra

last: Martinez-Lopez

first: Miguel

last: de Ameida Fuzeta

first: Carlos

last: Silva

first: Isabel

last: Campo

first: Daniel

last: Sobral

first: Rita

last: Fior


title: Single-cell Transcriptome Profiling of SW480 tumors from zebrafish xenografts

summary: Single-cell transcriptome profiling of SW480 tumors dissected from zebrafish xenografts at 1dpi and 4dpi.

overall_design: SW480 parental cells (GFP transfected) were injected in zebrafish and then dissected tumors at 2 time-points for single cell RNAseq: 1dpi (where all clones should be present) and at 4dpi (where only the clones that escape clearance are present). A pool of ~100 tumors were collected in a mixture. Dissociated single cells were sorted by fluorescence-activated cell sorting (FACS) into 384 well plates for scRNAseq SORT-seq, 3 plates for the first time-point and 2 plates for the second.


title: A versatile platform for locus-scale genome rewriting and verification

city: New York

first: Mathew

last: Maurano

state: NY

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU Langone Health

summary: Sequencing data supporting the Big-IN method for targeted delivery of large DNA constructs to mammalian cells.

sample_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design: WGS and Capture-seq data from cell lines engineered to harbor landing pads (LPs) at the HPRT1 locus in human ESCs and two different loci in mouse ESCs, and various payloads subsequently delivered to these LPs.

first: Ran

last: Brosh

first: Jon

last: Laurent

first: Raquel

last: Ordoñez

first: Emily

last: Huang

first: Megan

last: Hogan

first: Angela

last: Hitchcock

first: Leslie

last: Mitchell

first: Sudarshan

last: Pinglay

first: John

last: Cadley

first: Raven

last: Luther

first: Jef

last: Boeke

first: Matthew


title: An Intrinsic Disordered Region Mediated Confinement State Contributes to Dynamics and Function of Transcription Factors

city: Bethesda

first: Thomas

last: Johnson

state: Maryland

address: 41 Medlars Dr. Room B307

department: CCR

institute: National Cancer Institute

summary: In this study we used single-molecule tracking and machine-learning based classification to directly measure the nuclear mobility of the glucocorticoid receptor (GR) in live cells. We revealed two distinct and dynamic sub-diffusive populations. One accounts for specific binding to chromatin, while the other represents a confinement state that requires an intrinsically disordered region (IDR), consistent with liquid-liquid condensate subdomains. Further analysis showed that the dwell times of both subpopulations follow a power-law distribution, consistent with a broad distribution of affinities on the GR cistrome and interactome. Altogether, our data link IDRs with a confinement state that is functionally distinct from specific chromatin binding and modulates the transcriptional output by increasing the local concentration of TFs at specific sites.

overall_design: Genome-wide occupancy profiling of GR ChIP-seq from mouse mammary adenocarcinoma cell lines (3617) knock-out of endogenous GR (3617-KOGR) and stably integrated with GFP-tagged GR mutants, in biological duplicates, using Illumina NextSeq 500. GRwt binding data from the 3617-KOGR cells was used as comparison standard for GR (GSE108634).

first: David

last: Garcia

first: Diego

last: Presman

first: Gregory

last: Fettweis

first: Kaustubh

last: Wagh

first: Lorenzo

last: Rinaldi

first: Diana

last: Stavreva

first: Ville

last: Paakinaho

first: Rikke

last: Jensen

first: Susanne

last: Mandrup

first: Arpita

last: Upadhyaya

first: Gordon

last: Hager


title: Shiga toxin remodels the intestinal epithelial transcriptional response to Enterohemorrhagic Escherichia coli

city: Boston

middle: K

last: Waldor

state: MA

address: 181 Longwood Avenue

department: Microbiology

institute: Harvard Medical School

summary: Enterohemorrhagic Escherichia coli (EHEC) is a food-borne pathogen that causes diarrheal disease and the potentially lethal hemolytic uremic syndrome. Here, we used an infant rabbit model of EHEC infection that recapitulates many aspects of human intestinal disease to comprehensively assess the host colonic epithelial and lamina propria cell transcriptional responses to EHEC infection. Furthermore, comparisons of colonic pathology and intestinal transcriptomic profiles in animals infected with EHEC strains containing or lacking Shiga toxins (∆∆stx) were carried out to investigate how these potent toxins shape the host response to the pathogen. We found that Stx is required for severe, multi-focal hemorrhage and extensive apoptosis in the colon. RNA-sequencing revealed that EHEC infection elicits a robust innate immune response in the colonic epithelium that is dramatically shaped by Stx. Over 1400 genes were differentially expressed in animals infected with WT versus ∆∆stx EHEC strains. Several pathways linked to innate immune responses were dependent on Stx. Upregulated genes in the presence of toxin included cytokines IL23a and CXCL8, as well as F3, the gene encoding the coagulation initiator Tissue Factor. RNA FISH revealed that these elevated transcripts were found almost exclusively in epithelial cells, suggesting that Stx remodels the transcriptional profile of the epithelium. Collectively, these findings reveal that Stx potently modulates the innate immune response to EHEC in the intestine, and suggest that Stx drives the response to infection towards type 3 immunity.

overall_design: We performed RNAseq on colon epithelial cells and lamina propria cells derived from 3 infant rabbits orogastrically inoculated with wild-type enterohemorrhagic E. coli O157:H (WT), an isogenic mutant in which shiga toxins are deleted (∆∆stx), or PBS (mock) to identify differentially expressed genes during infection.

first: Alyson

last: Warr

first: Carole

middle: J

last: Kuehl


title: Leukemia-associated ZMYND11-MBTD1 chimera induces leukemogenesis by hijacking TIP60 acetyltransferase and a PWWP-mediated chromatin association mechanism

city: Chapel Hill

first: Gang (Greg)

last: Wang

state: NC

address: 450 West Drive, Lineberger Cancer Center

institute: UNC-Chapel Hill

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


title: Leukemia-associated ZMYND11-MBTD1 chimera induces leukemogenesis by hijacking TIP60 acetyltransferase and a PWWP-mediated chromatin association mechanism (ChIP-seq)

summary: The recurring t(10;17)(p15;q21) chromosomal translocation as detected in a subset of human acute myeloid leukemia (AML) patients produces an aberrant fusion gene ZMYND11-MBTD1 (ZM), the biological consequence of which, however, remains elusive. Here we show that ZM chimera confers primary murine hematopoietic stem/progenitor cells (HSPCs) an indefinite self-renewal capability ex vivo and causes AML in vivo. Genomics analyses revealed that ZM directly binds to and maintains high expression of pro-leukemic transcription factor (TF) genes such as Hox, Meis1, Myc, Myb, and Sox4. Mechanistically, ZM interacts with and recruits the Tip60 acetyltransferase complex, both of which occupy promoter-proximal genomic regions that are enriched with histone acetylation and devoid of H3K27me3. Furthermore, systematic mutagenesis of ZM revealed an essential requirement of Tip60 association and an H3K36me3-binding PWWP domain for leukemic transformation and proto-oncogene activation. Finally, inhibitor of histone acetylation-‘reading’ bromodomain proteins is efficacious in treating ZM-induced AML. Collectively, this study demonstrated the AML-causing effect of ZM chimera with relevant animal models, examined into its gene-regulatory functions and protein interactome, and reports a promising mechanism-based therapeutic strategy.

overall_design: Mapping genome-wide binding sites of ZMYND1-MBTD1 (tagged with either 3XHA-3FLAG or GFP), Tip60 (tagged with GFP) and Brd4 in ZM-transformed murine AML cells. Genome-wide analysis of different histone modifications including H3K36me3, H3K27me3, H3K27ac, H4ac in ZM-transformed murine AML cells.

first: Jie

last: Li

first: Greg


title: Effect of PPAR-delta on murine microglia gene expression during experimental autoimmune encephalomyelitis

status: Public on Jan 13 2021

city: Toronto

first: Shannon

last: Dunn

state: ON

address: 30 Bond Street, Office Location: 209 Victoria Street, 5th floor, 516

department: Keenan Research Centre for Biomedical Research

country: Canada

institute: St. Michael's Hospital

summary: Mice were generated that had a tamoxifen-inducible Cre recombinase transgene under the control of the CX3CR1 promoter. These mice were crossed with mice that had a floxed PPAR-delta allele.  EAE was induced in these mice and controls that just had the floxed allele at 30 days after tamoxifen treatment. Mice were euthanized (N=9/genotype) for isolation of microglia at 2-3 days after the onset of EAE, a time when clinical scores were equivalent between the groups. Spinal cords were pooled (N=3/sample) for microglia isolation and sorting. Microglia were isolated from spinal cords by collagenase digestion, percoll gradient and FACS sorting using CD45 and CD11b antibodies resulting in N=3 spinal cords resulting in N=3 pooled samples/group. RNA was isolated from sorted microglia using the PicoPure™ RNA Isolation Kit (Thermo Fisher Scientific). RNA quality was evaluated using the 2100 Bioanalyzer (Agilent) and N=2 samples per group with RIN numbers > 7 were submitted for sequencing and analysis at the UHN Bioinformatics and HPC Core, Princess Margaret Cancer Centre.

overall_design: Two samples are microglia from CX3CR1-CreERT PPARdelta floxed mice and two samples are from PPARdelta floxed mice. All mice had EAE for 2-3 days at the time of microglia isolation.


title: Leukemia-associated ZMYND11-MBTD1 chimera induces leukemogenesis by hijacking TIP60 acetyltransferase and a PWWP-mediated chromatin association mechanism (RNA-seq)

overall_design: Transcriptome profiling of murine HSPC culture 2-weeks post-transduction of ZMYND11-MBTD1 (ZM; short-term culture), as well as the established murine AML cells that were stably transformed (cultured for >6-8 weeks) by either ZM (long-term culture), Hoxa9 plus Meis1a (A9M) or MLL-AF9; Transcriptome profiling of the empty vector (EV)-transduced murine HSPC culture was performed 2 weeks post-transduction.


title: Ovarian tissue of third generation PCOS-like mice versus control animals

city: Illkirch

first: Damien

last: PLASSARD

address: 1 rue Laurent Fries

institute: IGBMC


title: Methylome profile of ovarian tissue of third generation PCOS-like mice versus control animals

summary: The aim of this study is to investigate possible differences in methylated regions between ovarian tissue of third generation PCOS-like (PAMH F3) mice versus control animals (CNTR)

overall_design: There are 2 groups (CNTR and PAMH) in triplicate and quadruplicates respectively, two inputs and two IgG.

first: Paolo

last: Giacobini