title: The onset of whole-body regeneration in Botryllus schlosseri: morphological and molecular characterization

city: Villefranche-sur-mer

first: Stefano

last: Tiozzo

address: 181 chemin du Lazaret

institute: CNRS - IMEV

summary: Colonial tunicates are the only chordates that regularly regenerate a fully functional whole body as part of their asexual life cycle, starting from specific epithelia and/or mesenchymal cells. In addition, in some species, whole-body regeneration (WBR) can also be triggered by extensive injuries, which deplete most of their tissues and organs and leave behind only small fragments of their body. In this study we characterized the onset of WBR in Botryllus schlosseri, one colonial tunicate long used as a laboratory model. We first analyzed the transcriptomic response to a WBR-triggering injury. Then, through morphological characterization, in vivo observations via time-lapse, vital dyes, and cell transplant assays, we started to reconstruct the dynamics of the cells triggering regeneration, highlighting an interplay between mesenchymal and epithelial cells. The dynamics described here suggest that WBR in B. schlosseri is initiated by extravascular tissue fragments derived from the injured individuals rather than particular populations of blood-borne cells, as has been described in closely related species. The morphological and molecular datasets here reported provide the background for future mechanistic studies of the WBR ontogenesis in B. schlosseri and allow to compare it with other regenerative processes occurring in other tunicate species and possibly independently evolved.

overall_design: Transcriptomic profile of whole-body regeneration of Botryllus schlosseri at 0, 6, 18 and 24 hours post-injury

first: Alexandre

last: Alié

first: Lorenzo

last: Ricci


title: IL-11 is elevated and drives the profibrotic phenotype transition of orbital fibroblasts in thyroid-associated ophthalmopathy [RNA-seq]

status: Public on Jan 28 2022

city: Guangzhou

first: Pengsen

last: Wu

address: NO. 54, Xianlie Road (South), Yuexiu District

country: China

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

type: Expression profiling by high throughput sequencing

summary: Orbital fibrosis is a hallmark of tissue remodeling in thyroid-associated ophthalmopathy (TAO). Previous studies have shown that interleukin (IL)-11 plays a pivotal profibrotic role in various inflammatory and autoimmune diseases. However, the expression pattern of IL-11 in patients with TAO and whether IL-11 is mechanistically linked with pathological fibrosis remains unknown. In this study, we investigated IL-11 levels in the serum and orbital connective tissue of patients with TAO, and evaluated the correlation of these levels with the patient’s clinical activity score. We also evaluated the expression pattern of IL-11Rα in orbital connective tissue. Furthermore, we elucidated the regulatory factors, profibrotic function, and downstream signaling pathways for IL-11 in TAO using in vitro studies. Serum and orbital connective tissues IL-11 levels were increased in patients with TAO, as compared with healthy controls. In addition, both levels were positively correlated with disease activity. Single-cell RNA sequencing of orbital connective tissue indicated that IL-11Rα was dominantly expressed in orbital fibroblasts (OFs). RNA sequencing of paired unstimulated and transforming growth factor (TGF)-β1-stimulated samples demonstrated that upregulation of IL-11 expression defined the dominant transcriptional response. IL-11 signaling was also confirmed to be downstream of TGF-β1 and IL-1β. Therefore, we deduced that IL-11 protein is secreted in an autocrine loop in TAO. We also indicated that IL-11 mediated the profibrotic phenotype switch by detecting the expression of myofibroblast differentiation markers, including α-smooth muscle actin and collagen type I α1, which could be abrogated by an anti-IL-11 neutralizing antibody. Furthermore, we revealed that extracellular regulated protein kinase may be a crucial factor in the pro-fibrotic, translationally specific signaling activity of IL-11. These data demonstrate that IL-11 plays a crucial role in orbital fibroblast phenotype switching and may be a potential therapeutic target candidate for the treatment of TAO.

overall_design: mRNA profiles of paired unstimulated and TGFβ1 stimulated orbital fibroblasts.

first: Bingying

last: Lin

first: Siyu

last: Huang

first: Jie

last: Meng

first: Fan

last: Zhang

first: Min

last: Zhou

first: Xiangqing

last: Hei

first: Yu

last: Ke

first: Huasheng

last: Yang

first: Danping


title: IL-11 is elevated and drives the profibrotic phenotype transition of orbital fibroblasts in thyroid-associated ophthalmopathy.

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

overall_design: Refer to individual Series


title: Increased phosphocreatine/creatine ratio in white adipocytes promotes inflammation

status: Public on Jan 27 2022

city: Huddinge

first: hui

last: Gao

address: Novum

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

summary: The mechanisms promoting disturbed white adipocyte function in obesity remain largely unclear. Herein, we integrate white adipose tissue (WAT) metabolomic and transcriptomic data from clinical cohorts and find that the WAT phosphocreatine/creatine ratio is increased and creatine kinase-B expression and activity is decreased in the obese state. . In human in vitro and murine in vivo models, we demonstrate that decreased phosphocreatine metabolism in white adipocytes alters AMPK activity via effects on ATP/ADP levels, independently of WAT beigeing. This disturbance promotes a pro-inflammatory profile characterized, in part, by increased CCL2 production. These data suggest that the phosphocreatine/creatine system links cellular energy shuttling with pro-inflammatory responses in human and murine white adipocytes. Our findings provide unexpected perspectives on the mechanisms driving WAT inflammation in obesity and may present avenues to target adipocyte dysfunction.

overall_design: Short interfering oligonucleotides (siRNAs) were introduced by electroporation to human in vitro differentiated hADSCs at day eight of differentiation. 3 replicates for siCKB and sicontrol group, respectively.   Total RNA was extracted for microarray analysis.

first: Salwan

last: Maqdasy

first: Hui


title: A novel regulatory mechanism of U2 spliceosome proteostasis that controls the transcriptome and therapy response in cancer [RNAseq_CUTLL1_E7107_NMDi]

status: Public on Jan 31 2022

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

country: USA

institute: New York University, NYU Langone Medical Center

summary: Aberrant splicing is an important cause of cancer, and the production of noncanonical, cancer-specific, mRNA transcripts associate with transformation. Studies have focused on characterizing the effect of spliceosome mutations on disease progression. Here, we have uncovered a novel mode of regulation of the U2 complex component SF3B1 in leukemia via lysosomal degradation. Elevated levels of SF3B1 protein control splicing and active transcription via direct interaction with the general transcriptional machinery and are critical for leukemia growth due to the control of cell cycle and DNA damage response-related transcripts, such as the serine/threonine kinase CHEK2. We further exploited these findings to show that clinically-used SF3B1 inhibitors synergize with transcriptional inhibitors, CHEK2 inhibitors and chemotherapy drugs to block leukemia growth. Our study provides the proof-of-principle for post-translational regulation of the splicing machinery via the lysosome and associated splicing-dependent and -independent roles of the U2 complex in cancer, that can be exploited for therapeutic purposes.

overall_design: Whole RNA was extracted from 1-5 million T-ALL (lines) cells using the Total RNA Mini Kit (Bio-Rad) according to the manufacturer’s protocol. Poly-A+ (magnetic oligodT-containing beads (Illumina)) or Ribominus RNA was used for library preparation. cDNA preparation and unstranded library construction was performed using the TruSeq RNA Sample Preparation Kit. Libraries were sequenced on the NextSeq 500/550 using 76bp paired-end read method. Differential gene expression analysis was performed for each matched treatment vs control pairs, separately in each biological or technical replicate in CUTLL1 cell line. Five types of comparisons were tested: (a) Control vs SF3B1 knockdown CUTLL1 cells with shSF3B1.1, (b) Control vs SF3B1 knockdown CUTLL1 cells with shSF3B1.2, (c) Control vs E7107 treated CUTLL1 cells (24hr), (d)  Control vs E7107 treated CUTLL1 cells (15 and 30 min), (e) Control vs E7107 and/or NMDi treated CUTLL1 cells. Analysis was performed using edgeR package.

first: Cuijuan

last: Han

first: Yalu

first: Adam

last: Lorch

first: Panagiotis

last: Ntziachristos


title: A novel regulatory mechanism of U2 spliceosome proteostasis that controls the transcriptome and therapy response in cancer [RNAseq_CUTLL1_shSF3B1.1]


title: A novel regulatory mechanism of U2 spliceosome proteostasis that controls the transcriptome and therapy response in cancer [RNAseq_CUTLL1_E7107_24hr]


title: The Identification and Functional Analysis of CircRNAs in Endometrial Receptivity of Mice with Polycystic Ovary Syndrome

status: Public on Jan 29 2022

city: Soochow

first: Zi

middle: wei

last: Zhao

state: Jiangsu

address: Pinghai Road

department: Reproductive Medicine Center

institute: the First Affiliated Hospital of Soochow University

summary: The disorders of endometrial receptivity and ovulatory dysfunction are both important causes of infertility of patients with Polycystic Ovary Syndrome (PCOS). The study aimed to investigate the expression profile and functional analysis of circRNAs in the endometrial receptivity of mice with PCOS. Twenty-four 4-week-old female C57BL/6 mice were randomly divided into two groups (PCOS group and Normal control group, n=12) and PCOS group was subcutaneously with DHEA 6mg/kg for 20 days. The circRNA expression profile in the endometrium tissue of two groups on the 4th day of gestation was screened by gene chip technique.

overall_design: In this experiment, 24 female mice were randomly divided into two groups of 12, including PCOS group (P) and NC group (N). The PCOS group mice were subcutaneously injected with DHEA (6mg·100g-1·day-1) dissolved in the sterile soybean oil solution (0.2ml) for 20 consecutive days.The NC group were subcutaneously injected with sterile soybean oil (0.2ml) for 20 consecutive days.On the 21 day, the mice from each group were mated with fertile males of the same strain to induce pregnancy at five in the afternoon.On Day 4 of pregnancy, the mice were killed by the cervical dislocation to collect endometrial samples by squeezing. One sample set is mixed by the same endometrial samples of 3 mice.

middle: W

first: Da

last: Li

last: Wang

first: Li

last: Xu

middle: J

last: Weng

first: Yan

middle: P

last: Pan

first: Cai

last: Mao

first: Wei

middle: Q


title: Evaluating the mode of Antifungal action of Heat-Stable Antifungal Factor (HSAF) in Neurospora crassa

city: Fuzhou

first: Lina

last: Qin

address: No.8 Xuefu South Road, Shangjie, Minhou

department: College of Life Sciences

institute: Fujian normal university

summary: Heat-stable antifungal factor (HSAF) isolated from Lysobacter enzymogenes has shown a broad-spectrum of antifungal activities. However, little is known about its mode of action. In this study, we used the model filamentous fungus Neurospora crassa to investigate the antifungal mechanism of HSAF. We first used HSAF to treat N. crassa strain for different time points. Spore germination, growth phenotype and differential gene expression analysis were conducted by utilizing global transcriptional profiling combined with genetic and physiological analyses. Our data showed that HSAF could significantly inhibit the germination and aerial hyphae growth of N.crassa. RNA-seq analysis showed a group of genes associated with cell wall formation and remodeling were highly activated. Screening of N. crassa gene deletion mutants combined with scanning electron microscopic observation revealed 3 fungal cell wall integrity related genes played important role in the interaction between N. crassa and L. enzymogens. In addition, WGCNA analysis, accompany with confocal microscopy observation revealed that HSAF could trigger autophagy mediated degradation and eventually result in cell death in N. crassa. The findings of this work provided new insights into the interactions between the predatory Lysobacter and its fungal prey.

overall_design: Transcriptome of Neurospora crassa mycelia after treatment with 40 μM HSAF for different time points (0, 5, 30 and 60min).

first: Xiaodong

last: Liu


title: Engineered human meniscus in modeling sex differences of knee osteoarthritis in vitro

status: Public on Jan 26 2022

city: Edmonton

first: Zhiyao

last: Ma

state: Alberta

country: Canada

institute: University of Alberta

summary: This study aimed to evaluate the effects of mechanical loading and unloading via CHP and SMG, respectively, on the   OA-related profile changes of engineered meniscus tissues and explore biological sex-related differences

overall_design: Tissue-engineered menisci were made from female and male meniscus fibrochondrocytes (MFCs) under static conditions of normal gravity in chondrogenic media and subjected to SMG and CHP culture. Constructs were assayed via histology,  immunofluorescence, GAG/DNA assays, RNA sequencing, and testing of mechanical properties.

first: David

first: Melanie

last: Kunze

first: Aillette

last: Mulet-Sierra

first: Lindsey

last: Westover

first: Adetola

middle: B

last: Adesida


title: Synergistic anti-tumor effect of combining selective CDK7 and BRD4 inhibition in MYCN-amplified neuroblastoma

city: Memphis

first: Brian

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

summary: Cyclin-dependent kinases (CDKs) that have critical roles in RNA polymerase II (Pol II)-mediated gene transcription are emerging as therapeutic targets in cancer. We have previously shown that THZ1, a covalent inhibitor of CDKs7/12/13, leads to cytotoxicity in MYCN-amplified neuroblastoma through the downregulation of super-enhancer-associated transcriptional upregulation. We sought to dissect the mechanisms of cytotoxicity in NB cells and to identify additional targets that could be inhibited together with CDK7 in combination therapy.

overall_design: RNA-Seq in human neuroblastoma cells treated with CDK7 inhibitor (YKL-5-124), BRD4 inhibitor (JQ1) or both. DMSO treated cells were used as control.

first: Yang

last: Gao

first: Marina

last: Volegova

first: Nicole

last: Nasholm

first: Sanjukta

last: Das

first: Nicholas

last: Kwiatkowski

first: Tinghu

last: Zhang

first: Nathanael

middle: S

last: Gray

first: Clay

last: Gustafson

first: Malgorzata

last: Krajewska

first: Rani

middle: E

last: George


title: MicroRNA-seq of cell lines expressing pri-miR-9 paralog constructs II

city: Frederick

first: Xavier

last: Bofill-De Ros

state: MD

address: 1050 Boyles St., blg 560

department: RNA Biology Laboratory

institute: National Cancer Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNA (miRNA) biogenesis begins with Drosha cleavage, the fidelity of which is critical for downstream processing and mature miRNA target specificity. To understand how pri-miRNA sequence and structure influence Drosha cleavage, we studied the processing of pri-miR-9-1 sequence variants, which encode the same mature miRNA but differ in the surrounding scaffold. We show that, in addition to previously known features, the overall structural flexibility of pri-miRNA impacts Drosha cleavage fidelity. Internal loops and nearby G·U wobble pairs on the pri-miRNA stem induce the use of non-canonical cleavage sites by Drosha, resulting in 5’ isomiR production. Here, we report the the miRNA-seq data of HEK293T cell lines transfected with different pri-miR-9 constructs.

overall_design: Briefly, HEK293 cells were transfected with several wild-type and chimeric pri-miR-9 constructs. Transfections were performed using PolyJet™ DNA Transfection Reagent (SignaGen) according to the manufacturer's instructions. 48 hours after transfection total RNA was obtained using a chloroform-isopropanol extraction. 5µg of total RNA was ligated with RNA 3’ adaptor using T4 RNA Ligase 2 - truncated (NEB), in the presence of RNase Inhibitor (NEB). RNA 5’ adaptor was ligated using T4 RNA Ligase 1 - high concentration (NEB) and 10 mM ATP. Ligated small RNAs were reverse transcribed using SuperScript® IV Reverse Transcriptase (Thermo-Fisher). Small RNA library cDNA was amplified and indexed using Phusion® High-Fidelity DNA polymerase (NEB). Constructs were purified in a 6% (w/v) native acrylamide gel based on the expected product size and purified by ethanol precipitation. Libraries quality was assessed by using Qubit dsDNA HS Assay Kit (ThermoFisher) and Agilent High Sensitivity DNA kit (Agilent). Libraries were pulled together, denaturalized and prepared at a final concentration of 12pM and run on MiSeq Reagent Kit v3 (Illumina) according to the manufacturer specifications.  Fastq files were analyzed using a Python-based custom software, QuagmiR (https://cgc.sbgenomics.com/public/apps#nikola_tesic/quagmir/quagmir-1-0/) designed for the optimal mapping and analysis of isomiRs.

first: Shuo

last: Gu


title: Direct regulation of shikimate, early phenylpropanoid and stilbenoid pathways by Subgroup 2 R2R3-MYBs in grapevine

city: Paterna

first: José Tomás

last: Matus

state: Valencia

address: Carrer del Catedràtic Agustín Escardino Benlloch

country: Spain

institute: Institute for Integrative Systems Biology

summary: V. vinifera cv. ‘Shiraz’ leaves from 10-week old plants were transformed via Agrobacterium-mediated infiltration with MYB15 (35S::VviMYB15) or an empty vector control. Samples were subsequently collected at five different time points (8h, 24h, 48h, 72h and 96h) in separate replicate pools (L1 and L2) consisting of three leaves from independent plants per time-point (n=2 biological replicates). Microarray analysis, using the Affymetrix V. vinifera Grape Array (A-AFFY-78), was carried out on extracted leaf RNA from three of the time points described for both control and MYB15 infiltrated samples.

overall_design: Across each time point, the two different pools of each condition (MYB15 vector and empty vector) were used as biological replicates.

first: Jochen

last: Bogs

first: Janine

last: Höll

first: Patrick

last: Mer

first: Luis

last: Orduña

first: José

last: Tomás Matus


title: scRNAseq analysis comparing  primary CD4+ T cells in resting memory state or stimulated with anti-CD3/anti-CD28 states and the effect of loss of ADAP1

city: Dallas

first: Ivan

last: D'Orso

state: TX

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

summary: By comparing the differenital gene expression of resting memory CD4+ cell and their transition to stimulated states, we are able to interrogate the effects that loss of ADAP1 has on T cell activation. Comparison between DEG of Ctrl cells (resting to stimulated) vs ADAP1 CRISPR cells (resting to stimulated) yielded 515 overlapping DEG (397 upregulated and 118 downregulated). Out of which, 364 of the 397 overlapping upregulated genes induced to significantly lower levels in ADAP1CRISPR cells compared to the level of fold change induction in Ctrl cells.

overall_design: Primary  CD4+ T cells of WT (Ctrl) or cells subjected to ADAP1 CRISPR/Cas9 (KD) were left resting or stimulated with anti-CD3/anti-CD28 for 4 hrs

first: Nora-Guadalupe

last: Ramirez

first: Jeon

last: Lee


title: An epigenomic shift in amygdala marks the transition to maternal behaviors in alloparenting virgin female mice

city: Seattle

first: Christopher

middle: H

last: Seward

state: WA

address: Stubbs Lab, Rm 404, 720 Broadway

institute: Pacific Northwest Research Institute

type: Genome binding/occupancy profiling by genome tiling array

summary: In many species, adults care for young offspring that are not their own, a phenomenon called alloparenting.  However, most nonparental adults must be sensitized by repeated or extended exposure to pups before robustly displaying of parental-like behaviors.  To capture neurogenomic events underlying the transition to active parental caring behaviors, we analyzed brain gene expression and chromatin profiles of virgin female mice co-housed with mothers during pregnancy and after birth.  After an initial display of antagonistic behaviors and a surge of defense-related gene expression, we observed a dramatic shift in the chromatin landscape specifically in amygdala of the pup-exposed virgin females, accompanied by a dampening of defense-related gene expression.  This epigenetic shift coincided with hypothalamic expression of the oxytocin gene and the emergence of behaviors and gene expression patterns classically associated with maternal care. The results outline a neurogenomic program associated with dramatic behavioral changes and suggest molecular networks relevant to human postpartum mental health.

overall_design: RNA-Seq was performed on 53 individual mouse brain samples, with 4-5 biological replicates per condition and ChIP-Seq was performed on 25 samples, with 2 biological replicate pools of 3 animals per condition.  ChIP-seq input samples were generated by skipping immunoprecipitation and sequencing background DNA.

first: Michael

middle: C

last: Saul

first: Joseph

middle: M

last: Troy

first: Payam

last: Dibaeinia

first: Huimin

first: Saurabh

last: Sinha

first: Lisa

last: Stubbs


title: QKI regulated splicing required for cell polarity

status: Public on Jan 25 2022

city: montreal

first: Stephane

last: Richard

address: 3999 chemin de la cote sainte catherine

institute: McGill University

summary: the RNA binding protein QKI is a post-transcriptional regulator of polarity proteins in muscle stem cells

overall_design: Primary muscle stem cells were isolated from wildtype and QKI knockout mice and bulk RNA was isolated for sequencing on the Illumina platform

first: Claudia

last: Dominici


title: Transcriptome sequencing of Brassica of Wild Type

city: Wuhan

first: Bin

middle: jie

last: Gu

address: No. 152 Luoyu Road

institute: Hubei Key Laboratory of Genetic Regulation and Integrative Biology

summary:
Purpose:  We conducted an evolutionary-based genome-wide analysis of the MYB-CC gene family in Brassica species.
Methods: B. napus (accession Zhongshuang11) was kindly provided by the Oilcrops Research Institute, Chinese Academy of Agricultural Sciences. The seeds were disinfected in 70% ethanol for 1 min, washed with ddH2O three to four times, placed on a petri dish lined with two layers of filter paper, and then germinated at 24oC in growth chamber. After three days, the germinated seedlings were transferred to MS medium containing 0.3% agar and 3% sucrose at pH 5.7. The seedlings grew at 24oC under a long-day light cycle (16 h light/8 h dark) and a relative humidity of 65%. Then the two-week-old plants were cultured in 1 mM and 1 μM Pi liquid medium for 24 h, respectively. Rapeseed seedlings’ shoots and roots were collected and frozen in liquid nitrogen. The RNA-seq analysis was carried out by Biomarker (Beijing). A total of 16 RNA samples were sequenced using the Illumina HiSeq 2,000 platform (Illumina, USA).
Results: The position of the MYB-CC genes was investigated according to the B. napus database (http://www.genoscope.cns.fr), the B. oleracea genome database (http://www.ocri-genomics.org), and the Brassica database (BRAD, http://brassicadb.org), respectively. MapInspect software was used to locate the MYB-CC genes. The gene duplication was defined as: a coverage region between two sequences of more than 70% with more than 85% similarity in the coverage region (Zhou et al., 2004; Yang et al., 2008). Additionally, the ka (non-synonymous mutation rate) and ks (synonymous mutation rate) values of the repeating gene pairs were calculated using DnaSp software.
Conclusions:This study comprehensively evaluated the identification, classification, expression and evolution analyses of MYB-CC gene family of Brassica species. A total of 30, 34, and 55 MYB-CC genes were identified in B. rapa, B. oleracea, and B. napus, respectively. All of the MYB-CC genes were divided into nine groups in the phylogenetic tree. Members of the same group have similar gene structures and conserved motifs, indicating that they could be conserved during evolution. In Brassica, WGT and allotetraploidy were vital for the expansion of MYB-CC genes.

first: Bin-Jie

first: Yi-Kai

last: Tong


title: Transcriptomic and genomic studies classify NKL54 as a histone deacetylase inhibitor with indirect influences on MEF2-dependent transcription (RNA-Seq)

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

country: Italy

institute: Università degli Studi di Udine

summary: In leiomyosarcoma class IIa HDACs bind MEF2 and convert these transcription factors into repressors to sustain proliferation. Theoretically, disruption of this complex should reverse the transformed phenotype. NKL54, a PAOA (pimeloylanilide o-aminoanilide) derivative, binds a hydrophobic groove of MEF2, that is used as a docking site by class IIa HDACs. However, NKL54 could also act as an HDAC inhibitor (HDACI). Therefore, it is not clear which activity is predominant. Here, we show that NKL54 and similar compounds are unable to release MEF2 from binding to class IIa HDACs. Comparative transcriptomic analysis classifies these compounds as strongly related to SAHA/vorinostat. Low expressed genes are upregulated by HDACI, while abundant genes are repressed. This transcriptional resetting correlates with a reorganization of H3K27 acetylation around the TSS.  Among the upregulated genes there are several BH3-only family members, thus explaining the induction of apoptosis. Moreover, NKL54 triggers the upregulation of MEF2 and the downregulation of class IIa HDACs. NKL54 also increases the binding of MEF2D to promoters of genes that are upregulated after treatment. In summary, although NKL54 cannot relieve MEF2 from binding to class IIa HDACs binding, it supports MEF2-dependent transcription through several actions, including potentiation of chromatin binding.

overall_design: Examination of the transcriptome of SK-UT-1 Leiomyosarcomas cells treated for 6 and 24h with different HDACIs.

first: Martina

last: Minisini

first: Eros

last: Di Giorgio

first: Emanuela

last: Kerschbamer

first: Christian

middle: X

last: Weichenberger

first: Claudio

last: Brancolini


title: The chromatin organization of a chlorarachniophyte nucleomorph genome

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Nucleomoprhs are remnants of secondary endosymbiotic events between two eukaryote cells wherein the endosymbiont has retained its eukaryotic nucleus. Nucleomoprhs have evolved at least twice independently, in chlorarachniophytes and cryptophytes, yet they have converged on a remarkably similar genomic architecture, characterized by the most extreme compression and minituarization among all known eukaryotes. Previous computational studies have suggested that nucleomorph chromatin likely exhibits a number of divergent features. In this work, we provide the first maps of open chromatin, active transcription, and three-dimensional genome architecture in the nucleomorph of the chlorarachniophyte Bigelowiella natans

overall_design: Hi-C, KAS-Seq, ATAC-Seq

middle: K

first: Xinyi

last: Chen

first: Tong

last: Wu

first: Chuan

last: He

first: Arthur

middle: R

last: Grossman

first: Anshul

last: Kundaje

first: William

last: Greenleaf


title: The effect of the brood and the queen on early gene expression in bumble bee workers' brains

status: Public on Feb 13 2022

city: University Park

first: Etya

last: Amsalem

state: PA

address: 202 Huck Life Sciences Building

institute: The Pennsylvania State University

summary: We used RNA-se to compare gene expression patterns in workers of the bumble bee Bombus impatiens in response to the queen, the brood, both or none.

overall_design: Pairs of newly emerged bumble bee workers were assigned to four treatments and kept for three days with the queen (CQ), young brood (CB), the queen and young brood (CBQ), or alone (C). RNA was isolated from brain tissue and six replicates per treatment were sequenced on three Illumina NextSeq 550 High Output, 75 nt single read sequencing, runs.

first: Priscila

last: Santos

first: David

last: Galbraith

first: Jesse

last: Starkey


title: IL-11 is elevated and drives the profibrotic phenotype transition of orbital fibroblasts in thyroid-associated ophthalmopathy [scRNA-seq]

first: Pengsen

summary: Orbital fibrosis is a hallmark of tissue remodeling in thyroid-associated ophthalmopathy (TAO). Previous studies have shown that interleukin (IL)-11 plays a pivotal profibrotic role in various inflammatory and autoimmune diseases. However, the expression pattern of IL-11 in patients with TAO and whether IL-11 is mechanistically linked with pathological fibrosis remains unknown. In this study, we investigated IL-11 levels in the serum and orbital connective tissue of patients with TAO, and evaluated the correlation of these levels with the patient’s clinical activity score. We also evaluated the expression pattern of IL-11Rα in orbital connective tissue. Furthermore, we elucidated the regulatory factors, profibrotic function, and downstream signaling pathways for IL-11 in TAO using in vitro studies. Serum and orbital connective tissues IL-11 levels were increased in patients with TAO, as compared with healthy controls. In addition, both levels were positively correlated with disease activity. Single-cell RNA sequencing of orbital connective tissue indicated that IL-11Rα was dominantly expressed in orbital fibroblasts (OFs). RNA sequencing of paired unstimulated and transforming growth factor (TGF)-β1-stimulated samples demonstrated that upregulation of IL-11 expression defined the dominant transcriptional response. IL-11 signaling was also confirmed to be downstream of TGF-β1 and IL-1β. Therefore, we deduced that IL-11 protein is secreted in an autocrine loop in TAO. We also indicated that IL-11 mediated the profibrotic phenotype switch by detecting the expression of myofibroblast differentiation markers, including α-smooth muscle actin and collagen type I α1, which could be abrogated by an anti-IL-11 neutralizing antibody. Furthermore, we revealed that extracellular regulated protein kinase may be a crucial factor in the pro-fibrotic, translationally specific signaling activity of IL-11. These data demonstrate that IL-11 plays a crucial role in orbital fibroblast phenotype switching and may be a potential therapeutic target candidate for the treatment of TAO.

overall_design: Single cell sequencing profiles of orbital adipose tissue from one patient with TAO and one healthy control patient.

first: Bingying

last: Lin

first: Siyu

last: Huang

first: Jie

last: Meng

first: Fan

last: Zhang

first: Min

last: Zhou

first: Xiangqing

last: Hei

first: Yu

last: Ke

first: Huasheng

last: Yang

first: Danping


title: Loss of Liver X Receptor alters the transcriptional landscape

first: Lara

last: Bideyan

address: 5323 Harry Hines Blvd., MC: 9077 Y6.314

department: Internal Medicine

institute: UT Southwestern

summary: The nuclear receptors LXRa and LXRb play a crucial role in regulating hepatic lipid metabolism. Many genes induced in response to pharmacologic LXR agonism in mouse liver have been defined; however, the transcriptional consequences of loss of LXR binding to its genomic targets are not well characterized. Here we addressed how deletion of both LXRa and LXRb from mouse liver (LXRDKO) affects the transcriptional regulatory landscape by integrating changes in LXR/RXR binding, chromatin accessibility, and gene expression. Many genes involved in fatty acid metabolism have reduced expression and chromatin accessibility at their intergenic and intronic regions in LXRDKO livers. Genes that were upregulated in LXRDKO livers have increased chromatin accessibility in their promoter regions and are enriched for those with functions not linked to lipid metabolism. We further showed that loss of LXR binding in liver reduces the activity of a broad set of hepatic transcription factors, inferred through motif accessibility. In contrast, accessibility at promoter NFY motifs is strongly increased in the absence of LXR. Surprisingly, we define small set of direct target genes for ligand-dependent LXR repression. These genes with LXR binding sites show increased expression in LXRDKO liver and reduced expression in response to LXR agonist treatment. In summary, while our results support the established roles for LXRs as ligand-dependent activators of genes linked to lipid metabolism, the binding of LXR/RXR heterodimers to the hepatic genome has broad effects on the transcriptional landscape that extend beyond its canonical function as an activator of lipid metabolic genes.

overall_design: RNA-Seq and ATAC-Seq of LXRa-/- LXRb-/- double knockout mice compared to control (n=2).

first: Peter

last: Tontonoz


title: CG and CHG Methylation Contribute to the Transcriptional Control of OsPRR37-output Genes in Rice

city: Chongqing

first: Chuan

last: Liu

address: Chongwen Road

institute: Chongqing University of Posts and Telecommunications

type: Methylation profiling by high throughput sequencing

summary: Plant circadian clock coordinates endogenous transcriptional rhythms with diurnal changes of environmental cues. OsPRR37, a negative component in the rice circadian clock, reportedly regulates transcriptome rhythms, and agronomically important traits. However, the underlying regulatory mechanisms of OsPRR37-output genes remain largely unknown. In this study, whole genome bisulfite sequencing and high-throughput RNA sequencing were applied to verify the role of DNA methylation in the transcriptional control of OsPRR37-output genes. We found that the overexpression of OsPRR37 suppressed rice growth and altered cytosine methylations in CG and CHG sequence contexts in but not the CHH context (H represents A, T, or C). In total, 35 overlapping genes were identified, and 25 of them showed negative correlation between the methylation level and gene expression. The promoter of the hexokinase gene OsHXK1 was hypomethylated at both CG and CHG sites, and the expression of OsHXK1 was significantly increased. Meanwhile, the leaf starch content was consistently lower in OsPRR37 overexpression lines than in the recipient parent Guangluai 4. Further analysis with published data of time-course transcriptomes revealed that most overlapping genes showed peak expression phases from dusk to dawn. The genes involved in DNA methylation, methylation maintenance, and DNA demethylation were found to be actively expressed around dusk. A DNA glycosylase, namely ROS1A/DNG702, was probably the upstream candidate that demethylated the promoter of OsHXK1. Taken together, our results revealed that CG and CHG methylation contribute to the transcriptional regulation of OsPRR37-output genes, and hypomethylation of OsHXK1 leads to decreased starch content and reduced plant growth in rice.

overall_design: Identification of methylated OsPRR37-output genes using Whole Genome Bisulfite Sequencing and high-throughput RNA sequencing data


title: Single cell transcriptomics of PBMCs during severe COVID-19

city: St Louis

first: Ashley

last: Steed

state: Missouri

address: 660 South Euclid Ave

institute: Washington University In St Louis

summary: Single-cell RNA-seq analysis of PBMCs during COVID-19

overall_design: PBMCs were isolated at the stated days into COVID-19 study enrollment and hospitalizaiton for single-cell RNA sequencing


title: AMPK activator O304 protects against kidney aging through promoting energy metabolism and autophagy

city: Guangzhou

first: Mingsheng

last: Zhu

address: 1838 North Guangzhou Avenue

institute: Nanfang hospital

summary: Energy homeostasis plays a key role in retarding aging, and mitochondria are responsible for energy production.AMPK plays a central role in maintaining energy homeostasis and mitochondrial homeostasis, and commands autophagy, a clearing and recycling process to maintain cellular homeostasis. However, the effect of AMPK activators on kidney aging has not been fully elucidated. We testified the effects of O304, a novel direct AMPK activator, in naturally aging mice model and D-galactose (D-gal)-treated renal tubular cell culture. We identified that O304 perfectly protects against cellular senescence and aged-related fibrosis in kidneys. Also, O304 restored energy metabolism, promoted autophagy, and preserved mitochondrial homeostasis. Transcriptomic sequencing also proved that O304 induced fatty acid metabolism, mitochondrial biogenesis and ATP process, and downregulated cell aging, DNA damage response and collagen organization. All these results suggest that O304 has a strong potential to retard aged kidney injury through regulating AMPK-induced multiple pathways.

overall_design: naturally aging mice model and Human proximal tubular epithelial cells (HKC-8)


title: Spacer prioritization in CRISPR-Cas9 immunity is enabled by the leader RNA

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

summary: RIP-seq analysis to identify SpyCas9 and LrhCas9 bound RNAs using co-immunoprecipitation and sequencing.

sample_organism:
Escherichia coli
Lacticaseibacillus rhamnosus

overall_design: SpyCas9, tracrRNA, and CRIPSR array encoding loci of S. pyogenes SF370 were cloned into a low copy plasmid. DNA encoding 3XFLAG tag was inserted upstream of the stop codon of the SpyCas9 gene. Mutations were introduced into the leader region through Q5 mutagenesis. The resulting plasmids were transferred into a E. coli  BW25113 strain with the endogenous CRISPR system removed. Co-immunoprecipitations were conducted to extract the SpyCas9 bound RNA for RIP-seq using the untagged SpyCas9 as control. For Lactobacillus rhamnosus, the plasmid harboring the LrhCas9 encoding locus and 3XFLAG tag was transferred into Lactobacillus rhamnosus and used for Co-immunoprecipitation and extraction of RNA for RIP-seq. The wild type Lactobacillus rhamnosus was used as control. R1 and R2 represent two biological replicates from coIP experiments used for RIP-seq.

first: Chunyu

last: Liao

first: Sahil

last: Sharma

first: Sarah

middle: L

last: Svensson

first: Anuja

last: Kibe

first: Zasha

last: Weinberg

first: Omer

last: Alkhnbashi

first: Thorsten

last: Bischler

first: Rolf

last: Backofen

first: Neva

last: Caliskan

first: Cynthia

first: Chase

last: Beisel


title: Cell death genetic signature in histotripsy treated canine Osteosarcoma cells

status: Public on Jan 24 2022

city: Blacksburg

first: Joanne

last: Tuohy

state: Virginia

address: 205 Duck Pond Dr

department: Small Animal Clinical Sciences

institute: Virginia Maryland College of Veterinary Medicine

summary: The objectives of the current study were to ablate three canine OS cells in-vitro with the novel focused ultrasound technique histotripsy.  The cell death gene signature associated with histotripsy treatment was then evaluated 24 hours post histotripsy ablation.

overall_design: 3 canine osteosarcoma cell lines (Abrams, D17, and D418) were analyzed under 3 different conditions, untreated, sham treated, and histotripsy treated. This resulted in the analysis of 9 different samples which were analyzed in one single experiment. The gene GAPDH was used as the housekeeping/reference gene and gene expression patterns for the sham and histotripsy treated cells are reported relative to gene expression in untreated cells.

first: Alayna

middle: N

last: Hay

first: Riley

last: Amore

first: Jessica

last: Gannon

first: Lauren

last: Ruger

first: Eli

last: Vlaisavljevich


title: RNA-seq data from two metronidazole resistant and one revertant line derived from Giardia intestinalis line WB

city: Uppsala

first: Feifei

last: Xu

address: Husargatan 3

institute: Uppsala University

summary: In this study we compare the baseline transcriptomic changes two resistant lines show without drug in the media compared to both the line they are derived from as well as a revertant.

overall_design: RNA from all lines grown in TYDK without added drug was extracted to find whether the lines are primed for being metrondiazole resistance by constant changes in expression levels or if they change expression levels only in presence of the drug metronidazole.

first: Sascha

last: Krakovka


title: Next Generation Sequencing Facilitates Quantitative Analysis of N. crassa Wild Type, stk-17ko and stk-17com Transcriptomes treated with or without ketoconazole

city: Beijing

first: Chengcheng

last: Hu

address: NO.1 Beichen West Road

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: STK-17, a kinase that responses to azoles transcriptionally, is required for azole resistance. By analyzing and comparing the transcriptomes from samples of N. crassa Wild Type, stk-17ko and stk-17com strain treated with or without ketoconazole, the biological processes that would be affected by stk-17 deletion was revealled.

overall_design: Total mRNA profiles of wild type (WT), stk-17ko and stk-17com strain treated with or without 1 μg/mL ketoconazole for 12 h.

first: Mi

last: Zhou

first: Xianhe

last: Cao

first: Wei

last: Xue

first: Zhenying

last: Zhang

first: Shaojie

last: Li

first: Xianyun

last: Sun


title: Next Generation Sequencing of Saline and Methamphetamine-treated Mouse Hippocampus Transcriptomes

city: Kunming

first: Juehua

last: Yu

address: Xicang Rd

institute: Kunming Medical University

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived hippocampus transcriptome profiling (RNA-seq) in mouse to evaluate alterations in hippocampus with methamphetamine administrations.

overall_design: Methods: Hippocampus mRNA profiles of Control and Methamphetamine-treated mice were generated by deep sequencing, in triplicate, using Illumina Sequencing Platform.

first: Fengrong

last: Chen


title: Neuradapt: Structural Optimization and Transcriptomic Analysis

city: Moscow

first: Sergey

last: Nikulin

address: 7, Vavilova st.

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

summary: A newly developed “branched tail” oxyquinoline, neuradapt, and its variants are an order of magnitude more effective HIF prolyl hydroxylase (HIF PHD) inhibitors than roxadustat and vadadustat in HIF1 ODD-luc reporter assay. Structure-activity relationships and computer modeling for the oxyquinoline inhibitors point to the plausible engagement of the pyridine ring nitrogen in interaction with Asp254 residue inside the active site pocket. 2-Methyl-substituted variant of neuradapt was found active in the reporter assay and equally effective in pretreatment paradigm of oxygen glucose deprivation model in neuroblastoma cell line. Microtranscriptomic analysis of the signaling pathways induced by two neuradapt variants in comparison with roxadustat and dimethyl oxalyl glycine shows extreme potency of novel inhibitors working at low micromolar concentrations. Neuradapt and its 2-methyl analog exert the same activation of glycolytic and other HIF-triggered pathways, but result in distinct effects on pathways linked to alternative substrates of HIF PHD1/3 such as p53, NfkB, ATF4, etc. This finding can be interpreted as the specificity of the 2-methyl-substituted variant for HIF PHD2.

overall_design: Total RNA was prepared from SH-SY5Y cells treated with 2 variants of neuradapt (compounds 5704-0720 and 4896-3249), roxadustat (FG-4592) and dimethyl oxalylglycine (DMOG) as well as from control SH-SY5Y cells and the cells after hypoxia.

first: Andrey

last: Poloznikov

first: Dmitry

last: Hushpulian

first: Anna

last: Khristichenko

last: Ossipyants

first: Vladimir

last: Tishkov

first: Irina

last: Gazaryan


title: Crosstalk between CRISPR-Cas9 and the human transcriptome

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: CRISPR-Cas9 expression independent of its cognate synthetic guide RNA (gRNA) causes widespread genomic DNA damage in human cells. To investigate whether Cas9 can interact with endogenous human RNA transcripts independent of its guide, we perform eCLIP (enhanced CLIP) of Cas9 in human cells and find that Cas9 reproducibly interacts with hundreds of endogenous human RNA transcripts. This association can be partially explained by a model built on gRNA secondary structure and sequence. Critically, transcriptome-wide Cas9 binding sites do not appear to correlate with published genome-wide Cas9 DNA binding or cut-site loci under gRNA co-expression. However, even under gRNA co-expression low-affinity Cas9-human RNA interactions (which we term CRISPR crosstalk) do correlate with published elevated transcriptome-wide RNA editing. Our findings do not support the hypothesis that human RNAs can broadly guide Cas9 to bind and cleave human genomic DNA, but they illustrate a clear cellular RNA impact likely inherent to CRISPR-Cas systems.

overall_design: Crosslinking and immunoprecipitation of dSpCas9 with bound RNA and sequencing from 2 bioreplicates with V5 and FLAG antibodies, with 2 controls (size-matched input; empty vector IP).

first: Aaron

middle: A

last: Smargon

first: Assael

last: Madrigal

first: Kevin

middle: D

last: Dong

first: Brian

last: Yee

first: Jasmine

last: Mueller

middle: W


title: Chromatin state of mTEClo/int in the RipmOVAxOTII mTEC/Tcell crosstalk mouse model

city: Nantes

first: Matthieu

last: Giraud

address: 30 bd Jean Monnet

department: CRTI

country: France

institute: INSERM _ Université de Nantes

summary: mTEC/Tcell crosstalk drives epigenetic programs conditioning immunological tolerance

overall_design: Nano-ChIP-seq on H3K4me3 and H3K27me3 was performed as previously described (Adli and Bernstein, 2011) on 5*10^4 purified mTEClo/int (EpCAM+ UEA-1+ Ly51lo CD80lo/int) from individual WT, RipmOVAxOTII and OTII mice. ChIP-seq libraries were prepared with the TruSeq ChIP Sample Preparation Kit (Illumina) and 2x75-bp paired-end reads were sequenced on an Illumina HiSeq 2000 machine.

first: Magali

last: Irla


title: Glucocorticoid inducton of DDIT4 transcription

city: Research Triangle Park

first: Jackson

middle: Andrew

last: Hoffman

state: North Carolina

address: 111 TW Alexander Dr, Building 101 Room C432

department: DIR

institute: NIEHS

summary: The hormone stimulated Glucocorticoid Receptor (GR) modulates transcription by interacting with thousands of enhancers and GR binding sites (GBSs) throughout the genome. Here, we examined the effects of GR binding on enhancer dynamics and interrogated the contributions of individual GBSs to the hormone response. Hormone treatment resulted in genome-wide reorganization of the enhancer landscape in breast cancer cells. Upstream of the DDIT4 oncogene, GR bound to four sites constituting a hormone-dependent super enhancer. Three GBSs were required as hormone-dependent enhancers that differentially promoted histone acetylation and transcription frequency and burst size. Conversely, the fourth site suppressed transcription and hormone treatment alleviated this suppression. GR binding within the super enhancer promoted a loop-switching mechanism that allowed interaction of the DDIT4 TSS with the active GBSs. The unique functions of each GR binding site contributed to hormone-induced transcriptional heterogeneity and demonstrate the potential for targeted modulation of oncogene expression.

overall_design: ChIP-seq and 4C-seq in A1-2 human breast cancer cells

last: Trotter

first: Christopher

last: Day

first: James

last: Ward

first: Kaoru

last: Inoue

first: Joseph

last: Rodriguez

first: Trevor

last: Archer


title: An HNF1A truncation associated with maturity-onset diabetes of the young impairs pancreatic progenitor differentiation by antagonising HNF1B function

city: London

first: Rocio

last: Sancho

state: London

address: Great Maze Pond, Guy's hospital

department: Centre for Stem Cells and Regenerative Medicine

country: United Kingdom

institute: KCL

summary:
Purpose: The goal of this study is to conduct and compare NGS-derived transcriptome profiling (RNA-seq) of progenitor lines derived from 3 HNF1A-WT and 3 HNF1A-CRISPR (with p291fsinsC mutation) human induced pluripotent stem cell lines.
Methods: mRNA profiles of WT/CRISPR pancreatic progenitor cells obtained after in-vitro differentiation for 14 days were generated by deep sequencing using Illumina HiSeq 2000 sequencer. The raw RNA-sequencing read files were processed using the research computing facility at King’s College London, Rosalind (https://rosalind.kcl.ac.uk). RNA-sequencing reads were trimmed from adapters using Trimmomatic/0.39 (Bolger et al., 2014) and quality control was done using FASTQC/0.11.8 (Andrews, 2010). Reads were mapped to a concatenated genome sequence of human GRCh38/hg38 using STAR/2.4.2 (Dobin and Gingeras, 2015). Transcript abundance was measured using featureCount in Subread package (Liao et al., 2013).
Results: The DESeq2 package (Love et al., 2014) was used to identify differentially expressed genes. We found 919 significantly regulated genes (271 upregulated, 648 downregulated), with 16 HNF1B targets and 19 HNF1A specific targets within the significantly dysregulated genes when comparing HNF1A-CRISPR versus HNF1A-WT groups.
Conclusions: HNF1A and HNF1B gene targets are disturbed by the p291fsinsC mutation engineered in the CRISPR-Cas9 lines.

overall_design: 3 samples from HNF1A-WT lines and 3 samples from three HNF1A-CRISPR clones

first: Ana-Maria

last: Cujba


title: mTEClo/int RNAseq profiling in three mouse models of impaired mTEC/Tcell crosstalk

summary: mTEC/Tcell crosstalk drives transcriptional and epigenetic programs conditioning immunological tolerance

overall_design: Total RNA was isolated with miRNeasy Micro Kit (Qiagen) from mTEClo/int cells (EpCAM+ UEA-1+ Ly51lo CD80lo/int) from individual mice of three different mouse models in which the mTEC/Tcell crosstalk is impaired: CIITA-KO [CIIta(III+IV)-/-]  vs WT ; K14xCIITAKO vs WT and RipmOVAxOTII vs OTII. The extracted RNA was used to generate transcriptome libraries using the SMART-Seq-v4-Ultra Low Input RNA Kit (Clontech) combined to the Nextera library preparation kit (Illumina) following the manufacturer's protocols. Single-end (75 bp) sequencing was performed using the Illumina NextSeq 500 machine.


title: Transcriptomic and genomic studies classify NKL54 as a histone deacetylase inhibitor with indirect influences on MEF2-dependent transcription

first: Emiliano

last: Dalla

address: Piazzale Kolbe 4

institute: Università degli Studi di Udine

summary:
Purpose: Define the chromatin remodelling induced by second generation HDACIs
Outcome:  We demonstrate that NKL54 treatment increased the number of H3K27ac peaks and caused a slight redistribution of H3K27ac peaks in promotorial regions. The hyperacetylation effect is evident in poorly acetylated loci, while hyperacetylated TSS turned out to be paradoxically deacetylated by NKL54 treatment. NKL54 caused a reduction in the binding of HDAC4 and HDAC9, especially at the intergenic regions. Instead, their binding to promoters was conserved. In contrast, NKL54 caused a dramatic increase in MEF2D binding to several genomic regions and especially to promoters. These new NKL54-enhanced MEF2D-chromatin interactions are often located at new genomic regions, whereas 40% of MEF2D peaks in untreated cells are conserved in NKL54-treated cells. Importantly, in these new regions, MEF2D is frequently recruited in the absence of HDAC4 or of HDAC9.

overall_design: Examination of the H3K27ac histone modifications and of MEF2D, HDAC4 and HDAC9 binding in SK-UT-1 Leiomyosarcomas cells (DMSO and NKL54 treated, 14h 5 µM).

first: C

last: Brancolini

first: M

last: Minisini

first: E

last: Di Giorgio


title: Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N(6)-Carboxymethyllysine

status: Public on Jan 23 2022

city: Freiburg im Breisgau

first: Omar

last: Mossad

address: Breisacher str 64

department: Institute of Neuropathology

institute: University Hospital Freiburg

summary: We found that the microbiota influenced critical characteristics linked with aging.

overall_design: We compared microglia from young adult and aged mice housed under germ-free and specific-pathogen-free conditions. Moreover, we examined the impact of CML treatment on young adult mice.

first: Bérénice

last: Batut

first: Thomas

last: Blank


title: Localization of wildtype Ioc4 in wildtype and set2 yeast strains. Localization of Ioc4 mutants (dPWWP, 2KE, dINS) in wildtype yeast strains.

city: Martinsried-Planegg

first: Michaela

last: Smolle

address: Grosshaderner Street 9

department: Physiological Chemistry

institute: University of Munich

type: Genome variation profiling by genome tiling array

summary: ChIP-chip assays to assess the localization of FLAG-tagged, wildtype and mutant Ioc4 in yeast.

overall_design: Two color experiment. WT Ioc4 in WT and set2 cells. Mutant Ioc4 (dPWWP, 2KE, dINS) in WT cells. Biological replicates=3 per IP per cell type.

first: Madelaine

last: Gogol


title: Induction of osteogenesis by bone-targeted Notch activation

city: Münster

first: Kai

last: Kruse

state: North Rhine-Westphalia

address: Roentgenstr. 20

department: Bioinformatics Core Facility

institute: Max Planck Institute for Molecular Biomedicine

summary: Declining bone mass is associated with aging and osteoporosis, a disease characterized by progressive weakening of the skeleton and increased fracture incidence. Growth and lifelong homeostasis of bone involve interactions between different cell types including vascular cells and mesenchymal stromal cells (MSCs). As these interactions involve Notch signaling, we have explored whether treatment with secreted Notch ligand proteins can enhance osteogenesis in adult mice. We show that a bone-targeting, high affinity version of the ligand Delta-like 4 (termed Dll4(E12)) induces bone formation without causing adverse effects in other organs, which are known to rely on intact Notch signaling interactions. Single cell analysis of stromal cells indicates that Dll4(E12)  primarily acts via bone marrow MSCs and has comparably minor effects on osteoblast lineage cells, endothelial cells or chondrocytes. Based on this example, we propose that bone-targeted fusion proteins might be therapeutically useful and can avoid detrimental effects caused by systemic administration.

overall_design: Bone marrow stromal single cell RNA sequencing of 11-week old wild type (WT) and Dll4(E12) treated mice

first: Ralf

last: Adams

first: Cong

last: Xu

first: Hyun-Woo

last: Jeong

first: Emma

last: Watson

first: Susanne

first: Martin

last: Stehling

first: Qi

last: Chen

first: Katsuhiro

last: Kato

first: Van-Vuong

last: Dinh

first: Frank

last: Berkenfeld

first: Seyed Javad

last: Rasouli

first: Rui

last: Fan

first: Ivan

last: Bedzhov

first: Mara

last: Pitulescu


title: RNA sequencing for HUVECs treated with si-FLRT2

status: Public on Jan 22 2022

city: Tokyo

first: Yoshiaki

last: Kubota

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Anatomy

country: Japan

institute: Keio University School of Medicine

summary: RNA sequencing for HUVECs treated with si-control or si-FLRT2

overall_design: mRNA profiles of HUVECs. Four experiments for each group (si-cont and si-FLRT2).


title: Transcriptome profiling of bone marrow LSK cells in control and dopamine receptors knockout mice

city: Muenster

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

summary: We performed RNA sequencing analyses of adult mouse bone marrow lineage-negative, Sca-1-positive, and c-kit-positive (LSK) multipotent progenitor cells in wildtype and Drd2 Drd3 double knockout mice

overall_design: Adult LSK cells from control and Drd2 Drd3 double knockout mice were sorted by FACS. FACS sorted LSK cells were directly collected in RLT lysis buffer and processed for RNA-Seq.

first: Yang

last: Liu


title: Annorade mRNA Sequencing Qualified the Transcriptome Analysis of Fresh and Warmed Tissue of Hepatocellular Carcinoma

status: Public on Jan 21 2022

city: Shanghai

first: Bo

last: Zhai

address: No.160, Pujian Road

department: Interventional Oncology

institute: Shanghai Jiao Tong University, School of Medicine, Affiliated Renji Hospital

summary:
Purpose: The aim of this study was to create a patient-derived slice model by combining cryopreservation technique with precision-cut slice culture method and explore its effectivity of predicting anti-cancer drug sensitivity in vitro.
Methods: We prepared 0.3 mm thick tissue slices by a microtome and maintain its cell viability by cryopreservation technique. Slices were cultured individually in the presence or absence of regorafenib (REG) for 72 hours. Alterations in morphology and gene expression were assessed by histological and genetic analysis. Overall viability was also analyzed in tissue slices by CCK-8 quantification assay and fluorescent staining. Tissue morphology and cell viability could be evaluated to quantify drug effects.
Results: Histological and genetic analysis showed that no significant alterations in morphology and gene expression were induced by vitrification‑based cryopreservation. The viability of warmed HCC tissues was up to 90% of the fresh tissues. The viability and proliferation could be retained for at least four days in filter culture system. The positive drug responses in precision-cut slice culture in vitro were evaluated by tissue morphology and cell viability.
Conclusion: In summary, the successful application of precision-cut HCC slice culture combining cryopreservation technique in a systematic drug screen demonstrates the feasibility and utility of slice culture method for drug response.

overall_design: Fresh and warmed tissue of hepatocellular carcinoma is analysed and fresh group is control group.

first: Yuan

last: Zhang

first: Zhen-yu

last: Wang

first: Hong-shu

last: Jing

first: Hong-dan

first: He-xin

last: Yan

first: Jian-xia


title: SAPCD2 promotes neuroblastoma progression by altering the subcellular distribution of E2F7

city: Suzhou

first: Zimu

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: We report a previously unrecognized role of SAPCD2 in E2F signaling pathway in neuroblastoma. To explore SAPCD2-dependent gene regulation, RNA-seq analysis was conducted and the differently expressed genes were revealed in the SAPCD2-knockdown SK-N-BE(2) cells in comparison to control group. We find that SAPCD2 contributes to E2F7 mislocalization and decreases the level of nuclear E2F7 in NB cells, thus restraining the inhibitory effect of nuclear E2F7 on E2F signaling pathway. SAPCD2 knockdown limits the overactivation of E2F signaling in NB cells, affects the expression of genes involved in cell cycle and chromosome stability, and thereby blocking tumor progression.

overall_design: mRNA profiles of SK-N-BE(2) cells transfected with scramble shRNA (sh-Scb) or sh-SAPCD2 were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Jian

last: Pan


title: Transcriptome profiling of ALK-rearranged lung cancer cells upon STAT3 inhibition.

city: Niigata

first: Naohiro

last: Yanagimura

address: 1–757 Asahimachi-dori, Chuo-ku

department: Respiratory Medicine and Infectious Diseases

institute: Niigata University

summary: DNA microarray analysis of ALK-rearranged lung cancer cells (H3122) comparing control untreated cells with cells treated by YHO-1701 (STAT3 inhibitor) for 24h.

overall_design: Two-condition experiment, Control vs. YHO-1701 (STAT3 inhibitor) treated cells. One replicate per array.

last: Yangimura

first: Shinji

last: Takeuchi


title: Sulforaphane Reduces Obesity by Reversing Leptin Resistance

city: Nashville

first: Masoud

last: Ghamari-Langroudi

address: 8435 MRB #IV, 2215 Garland ave

institute: Vanderbilt University

summary:
Introduction: The ascending prevalence of obesity in recent decades is commonly associated with soaring rates of morbidity and mortality resulting in increased health care costs and decreased quality of life. A systemic state of stress characterized by low grade inflammation and pathologic formation of reactive oxygen species (ROS) usually manifest in obesity. The transcription factor nuclear factor (erythroid-derived 2)-like 2 (NRF2) is the master regulator of the redox homeostasis and plays a critical role in the resolution of inflammation. Our results indicate that the natural isothiocyanate and potent NRF2 activator sulforaphane reverses the diet-induced obesity in rodents and implicate involvement of leptin receptor singling in this effect.
Purpose: Here, we investigate molecular pathways underlying the effects of sulforaphane in reversing diet-induced obesity and interrogate potential pathways that link NRF2 with leptin receptor signaling by conducting whole transcriptome analysis in 6 metabolically active tissues from the diet-induced obese mice that were treated with SFN.
Methods: Male 12-week-old C57/BJ wild type mice were fed with high fat diet for 16-20 weeks. Around 28 weeks of age, mice were treated with daily ip injections of either SFN (5 mg/kg) or vehicle for one week. We probed the whole transcriptome in several metabolic tissues including the hypothalamus, liver, brown adipose tissue (BAT), epididymal white adipose tissue (eWAT), inguinal white adipose tissue (iWAT), and skeletal muscle following peripheral SFN administration. Total RNA samples from each tissue were prepared with Trizol. Whole transcriptome were conducted by using Novogene sequencing platform NovaSeq 6000 PE150. The following bioinformatics analysis have been conducted. 1. Data Quality Control: filtering reads containing adapter or with low quality. 2. Statistics Analysis of Data Production and Quality. 3. Mapping Reads to Reference Genome. 4. Gene Expression Quantification. 5. Correlation analysis (For biological replicates only). 6. Differential Expression Analysis (two or more groups of samples). 7. GO Enrichment Analysis of Differentially Expressed Genes (DEGs) (two or more groups of samples). 8. KEGG Pathway Enrichment Analysis of Differentially Expressed Genes (DEGs) (two or more groups of samples). 9. GSEA Enrichment Analysis of Expressed Genes (two or more groups of samples). 10. Protein Protein Interaction Analysis. 11. Reactome Pathway Enrichment Analysis of Differentially Expressed Genes (DEGs) (two or more groups of samples and only for mouse samples). 12. Oncogene Functional Annotation analysis of Differentially Expressed Genes (DEGs) (two or more groups of samples and only for mouse sample).
Results: RNAseq results indicated a significant upregulation of the NRF2 target gene HMOX1 only in the skeletal muscle. We also conducted an enrichment analysis to identify potential transcription factors for the significantly upregulated genes. NRF2 was identified as the most significant transcription factor only for the skeletal muscle gene set, providing further support for the skeletal muscle being a primary target tissue of SFN action. We thus conducted a KEGG and GO pathway analysis, and identified ribosome biogenesis, proteasome pathway, and the RNA transport as the significantly upregulated pathways in the SFN-treated muscle samples. In addition to HMOX1, the RNA seq results indicate upregulation of other genes involved in oxidative stress response capacity in SFN treated mice in the skeletal muscle. GCLM (glutamate-cysteine ligase), the first rate-limiting enzyme of glutathione synthesis, SRXN1 (Sulfiredoxin), an oxidoreductase that reduces cysteine-sulfinate, and GSR (glutathione-disulfide reductase), a central antioxidant enzyme, which reduces oxidized glutathione disulfide (GSSG) to the sulfhydryl form glutathione (GSH), and TXNRD1 (thioredoxin reductase 1) which reduces thioredoxins are all upregulated in the skeletal muscle of the SFN-treated DIO animals.
Conclusions: Here, we show that the natural isothiocyanate and potent NRF2 activator sulforaphane reverses diet-induced obesity through an NRF2-dependent mechanism that requires a functional leptin receptor signaling and hyperleptinemia. Transcriptional profiling of six major metabolically relevant tissues highlights that sulforaphane suppresses fatty acid synthesis while promoting ribosome biogenesis, reducing ROS accumulation and resolving inflammation, therefore representing a unique transcriptional program that leads to protection from obesity. Our findings argue for clinical evaluation of sulforaphane for weight loss and obesity-associated metabolic disorders.

overall_design: Transcriptome profiles in 6 metabolically active tissues of sulforaphane-treated diet-induced obese 28-week-old wild type (WT) mice.

first: Işın

last: Çakır

first: Pauline

last: Lining Pan

first: Colleen

last: Hadley

first: Abdulrahman

last: El-Gamal

first: Amina

last: Fadel

first: Dina

last: Elsayegh

first: Nasser

last: Rizk


title: Stage Specific Non-coding RNA Expression Patterns During in vitro Human B Cell Differentiation into Antibody Secreting Plasma Cells

city: ROCHESTER

first: Diane

last: Jelinek

state: MN

address: 200 1st St SW

institute: Mayo Clinic

summary: The differentiation of activated B cells into antibody secreting plasma cells (PCs) is governed by a strict regulatory network that results in expression of specific transcriptomes along the continuum.  In vitro models resulting in PCs that are phenotypically identical to the in vivo state permit investigation of molecules, transcripts, pathways, and metabolomes not previously identified in the differentiation process.  We used an in vitro system and RNA-seq to identify protein-coding and non-coding RNA (ncRNA) transcripts expressed in human resting and activated B cells, and PCs.  Analysis of immunoglobulin (Ig) transcripts showed that the repertoire was not skewed, and that memory B cells preferentially expanded and differentiated into PCs. Of interest, we identified more than 980 differentially expressed ncRNA transcripts displaying stage-specific patterns of increased or decreased expression across differentiation some of which are known to target transcription, proliferation, cytoskeletal, autophagy and proteasome pathways.  Interestingly, ncRNAs located within Ig loci may be targeting both Ig and non-Ig related transcripts.  ncRNAs associated with B cell malignancies were also identified in this model.  Taken together, this system provides a platform to study the detailed role of specific ncRNAs in B cell differentiation and altered expression of those ncRNAs involved in B cell malignancies.

overall_design: Transcriptome profiles from 3 human B cell differentiation experiments.   RNA-seq was performed from resting cells (Day 0), Plasmablasts (Day 4) and in vitro Plasma Cells (IVPCs, Day 10).

first: Renee

last: Tschumper

first: Dominique

middle: B

last: Hoeliznger

first: Denise

last: Walters

first: Jaime

middle: I

last: Davila

first: Collin

last: Osborne

middle: F


title: A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer (liver cancer cell lines)

first: Chen

last: Yang

address: Xietu Road

institute: Shanghai Cancer Institute

summary: We first treated liver cancer cells with vehicle or HHT for 6 hours. Then, RNA sequencing was conducted to quantify the mRNA expression level of vehicle-treated or HHT-treated liver cancer cells.  HHT-induced expression changes were obtained based on the resultant data.

overall_design: Examination of the transcriptome changes of liver cancer cells treated with homoharringtonine (HHT)


city: New York

first: Ekta

last: Khurana

address: 1305 York Ave

institute: Weill Cornell Medicine

summary: Chromatin accessibility profiling analsis was performed in 22 human prostate cancer organoid, 6 Xenografts and 7 cell lines

overall_design:
ATAC-Seq of MSK-PCa series of Patient Derived Organoids and Xenografts, and prostate cell lines

Please note that the processed data includes 5 samples (MSKEF1/PARCB1/PARCB3/PARCB6/PARCB8) from another study GSE118207:
GSM3320999: prostate: MSKCC-EF1 ATAC-seq
GSM3320990: prostate: PARCB1 ATAC-seq
GSM3320991: prostate: PARCB3 ATAC-seq
GSM3320992: prostate: PARCB6 ATAC-seq
GSM3320993: prostate: PARCB8 ATAC-seq
and the consensus peak set was generated using those samples.

last: Kharuna

first: Yu

last: Chen


title: Two zinc finger proteins with functions in m6A writing interact with HAKAI

city: Loughborough

first: Nathan

last: Archer

state: East Midlands

address: Sutton Bonington

department: School of Veterinary Medicine and Sciences

institute: University of Nottingham

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

overall_design: Refer to individual Series


title: Expression data from neuroblastoma cells treated with GSK-J4 or KTP-330

first: Zimu

last: Zhang

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

summary: Neuroblastoma (NB) is a common pediatric malignancy tumor with poor outcome. Recent studies show that GSK-J4, an inhibitor of lysine 27 of histone 3 (H3K27) demethylases, and KTP-330, a clinically available inhibitor of XPO1 protein, are promising anti-cancer agents. However, their molecular mechanisms  in neuroblastoma are still unclear. In this study, we used microarrays to analyze the global change in gene expression as a result of GSK-J4 or KTP-330 treatment in the human neuroblastoma cell line SH-SY5Y.

overall_design: We treated SH-SY5Y cells with the GSK-J4 (0.5 uM) or KTP-330 (0.5 uM) for 24 h and then extracted the global RNA. We subjected the RNA to Arraystar Human LncRNA microarray V4.

first: Zhi-Heng

last: Li

first: Jian

last: Pan


title: Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors

city: Charlottesville

first: Roza

middle: Kamila

last: Przanowska

department: Biomedical Engineering

institute: University of Virginia


title: Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors [ChIRP-seq]

summary: Many lncRNAs have been discovered using transcriptomic data, however, it is unclear what fraction of lncRNAs is functional and what structural properties affect their phenotype. MUNC lncRNA (also known as DRReRNA) acts as an enhancer RNA for the Myod1 gene in cis and stimulates the expression of other promyogenic genes in trans by recruiting the cohesin complex. Here, experimental probing of the RNA structure revealed that MUNC contains multiple structural domains not detected by prediction algorithms in the absence of experimental information. We show that these specific and structurally distinct domains are required for induction of promyogenic genes, for binding genomic sites and gene expression regulation, and for binding the cohesin complex. Myod1 induction and cohesin interaction comprise only a subset of MUNC phenotype. Our study reveals unexpectedly complex, structure-driven functions for the MUNC lncRNA and emphasizes the importance of experimentally determined structures for understanding structure-function relationships in lncRNAs.

overall_design: MUNC ChIRP-seq with lacZ as negative control; control C2C12 cells; differentiation conditions; 2 biological replicates each

first: Magdalena

last: Cichewicz

first: Anindya

last: Dutta


title: Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors [RNA-seq]

overall_design: RNA-seq on 18 samples; control C2C12 cells, MUNC spliced overexpressing cells, and MUNC genomic overexpressing cells; proliferation and differentiation conditions; 3 biological replicates each

first: Piotr

last: Przanowski

first: Michael

last: Guertin


title: Gene expression of human embryonic stem cells during endoderm differentiation

city: WuHan

first: chenchao

last: yan

state: Hubei Province

address: Donghu Road, No. 115

institute: WuHan university

summary: Using a well-established human definitive endoderm differentiation system, we can analyze the gene expression dynamic of human embryonic stem cells (hESCs) during endoderm differentiation. Samples from hESCs, D2 cells and definitive endoderm cells (DE) were collected for deep sequencing with two replicates for each sample. Differentially expressed genes analysis showed that endodermal genes were induced during endoderm differentiation.

overall_design: We performed RNA-seq for human embryonic stem cells (hESCs), endoderm cells induced from hESCs for 2 days (D2) and definitive endoderm cells (DE) in duplicate.

first: Jing

last: Lv

first: Wei

last: Jiang


title: H3K4me3 ChIP_Seq in mouse decidua

status: Public on Jan 20 2022

city: Xiamen

first: Wenbo

last: Deng

state: Fujian

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University

summary: To detect the direct target genes of H3K4me3 in decidual stromal cells, decidual stromal cells are collected and subjected to ChIP-Seq. After aligned to mouse mm10 by STAR, peaks are called by MACS2. We found that H3K4me3 was significantly enriched at the transcription start site (TSS) of expressed genes (RPKM>1). A direct comparison of Menin and H3K4me3 ChIP-seq peaks at gene promoters showed a significantly strong positive correlation (R2=0.5888291). The promoters of 6,800 genes bound by Menin (92% of all genes with promoter bound by Menin) were also H3K4me3 modified.

overall_design: Chromatin immunoprecipitation (ChIP) was modified and performed according to the previous described standard protocol. Decidual tissue wetted with PBS quickly cut into small pieces with an iris scissor. The pieces should not be bigger than 0.5 cm3. Snipped tissue was fixed with 1% formaldehyde (CST) for 10 mins at RT (for H3K4me3 ChIP), or fixed with disuccinimidyl glutarate (DSG, Santa Cruz, 2 mM) for 30 mins at RT, washed twice with PBS and then double fixed with 1% formaldehyde for another 10 mins at RT (for Menin ChIP). Fixation was stopped by adding glycine (0.125 M). Tissue homogenate obtained by using Dounce Tissue Grinder was filtered through a 200 μm cell strainer to remove connective tissue. Fixed cells were lysed by Lysis Buffer 1 (50 mM HEPES pH 7.5, 1 mM EDTA, 140 mM NaCl, 0.5% NP-40, 10% glycerol, 0.25% Triton X-100) and Lysis Buffer 2 (10 mM Tris-HCl pH8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and Lysis Buffer 3 (10 mM Tris-HCl pH8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Sodium Deoxycholate, 0.1% N-lauroylsarcosine). All lysis buffers should be supplemented with protease inhibitors cocktail (Roche) before use. Chromatin DNA was sheared to 300-500 bp average in size by using a BioRuptor sonicator (Diagenode). Solubilized chromatin was was centrifuged to remove debris and incubated overnight at 4°C with antibody against Menin (Bethyl, 10 μg) and H3K4me3 (Abcam, 1 μg) bound to 20 μl protein A magnetic beads (Invitrogen). After washing and elution, the protein-DNA complex was reversed by heating at 65°C overnight. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen). Immunoprecipitated and input DNA were quantified using Qubit 4.0 fluorometer. ChIP-seq libraries were prepared by using the KAPA DNA Hyper Prep Kit (KK8502) following the manufacturer’s instruction and sequenced with an Illumina Nova PE150. For ChIP-qPCR, chromatin was sheared by sonication until the average length of 500-1000 bp.


title: Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors [SHAPE-MaP]

overall_design: SHAPE-MaP on RNA from C2C12 cells overexpressing MUNC variants for a total 16 samples (8 DMSO, 85NIA): Cell-free SHAPE of 2 MUNC spliced replicates, MUNC genomic, CH1 deletion, and CH4 deletion; In-cell SHAPE of 2 replicates of MUNC spliced and 1 replicate of MUNC genomic

first: Chase

last: Weidmann

first: Patrick

last: Irving

first: Kevin

last: Weeks


title: Bulk RNA-seq of mice covering the whole lifespan (2 days to 904 days) from four tissues

status: Public on Feb 02 2022

city: Ankara

first: Mehmet

last: Somel

address: Dumlupınar Bulvarı No:1

department: Biology

country: Turkey

institute: Middle East Technical University

summary: Gene expression changes during ageing were shown to oppose developmental trajectories; a reversal pattern previously linked to cellular identity loss. Generating cortex, lung, liver and muscle tissue transcriptomes of 16 mice of different ages, covering development and ageing periods, we found that expression reversals were widespread but tissue-specific. Consistent with this result, we observed an inter-tissue divergence during development and convergence during ageing (DiCo), further confirmed in independent mouse and human datasets. The genes displaying DiCo pattern were enriched among tissue-specific genes that tended to lose developmental expression levels during ageing. Finally, analysing publicly available single-cell transcriptome data, we studied the contribution of cellular composition and cell-autonomous changes to the convergence in ageing. Our results, for the first time, suggest inter-tissue convergence during ageing is widespread and associated with the loss of specialisation at the tissue and possibly also at the cellular level.

overall_design: Age-series mRNA expression profiles from 4 tissues (cerebral cortex, lung, liver, skeletal muscle) of 16 mice, covering postnatal development (2 days - 61 days) and ageing (93 days – 904 days) periods.

first: Hamit

last: Izgi

first: DingDing

last: Han

first: Ulas

last: Isildak

first: Shuyun

last: Huang

first: Ece

last: Kocabiyik

first: Philipp

last: Khaitovich

first: Handan

last: Donertas


title: Menin and H3K4me3 ChIP_Seq in mouse decidua

summary: To detect the direct target genes of Menin and H3K4me3 in decidual stromal cells, decidual stromal cells are collected and subjected to ChIP-Seq. After aligned to mouse mm10 by STAR, peaks are called by MACS2. We found that Menin and H3K4me3 was significantly enriched at the transcription start site (TSS) of expressed genes (RPKM>1). A direct comparison of Menin and H3K4me3 ChIP-seq peaks at gene promoters showed a significantly strong positive correlation (R2=0.5888291). The promoters of 6,800 genes bound by Menin (92% of all genes with promoter bound by Menin) were also H3K4me3 modified.


title: Gene expression in D8 WT and Menin KO uteri

summary: Differential expression genes were normalized to fragments per kilobase of exon model per million mapped reads (RPKM) using EdgeR package in R with the criteria of fold change significantly greater than 1.5 and P<0.05. Gene ontology (GO) enrichment analysis of the DEGs was analyzed by using DAVID (the Database for Annotation, Visualization and Integrated Discovery, https://david.ncifcrf.gov). GO terms with corrected p <0.05 were considered significantly enriched. Gene Set Enrichment Analysis (GSEA) was performed to determine whether a defined set of genes shows statistically significant, consistent differences between Men1f/f and littermates Men1d/d decidual tissues.

overall_design: Total RNAs from D8 uteri were extracted by TRIzol and purified by poly-A before subjected to RNA-Seq. The expression of level of each gene is normalized to RPKM.


title: RNA-seq and Ribo-seq of Ythdc2KO and Ythdc2-WLA mutants

first: Yuhki

last: Saito

state: NY

address: 1230 York avenue

institute: The Rockefeller University

summary: We sequenced RNA from testis of Ythdc2 mutant and wild type mice to compare gene expression level, and translation efficiency.

overall_design: mRNA abundance and translation efficiency profiles by deep sequencing using Illumina Hiseq2500.

first: Devanshi

last: Jain


title: A MicroRNA Next-Generation-Sequencing Discovery Assay (miND) For Genome-Scale and Absolute Quantitation of Circulating MicroRNA Biomarkers

city: Wien

first: Andreas

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

summary: The plasma levels of tissue-specific microRNAs can be used as prognostic and diagnostic biomarkers for chronic and acute diseases. Thereby, the combination of diverse miRNAs into biomarker signatures using multivariate statistics seems especially powerful in view to tissue and condition specific miRNA shedding into the plasma.  Although Next-Generation Sequencing (NGS) technology enables to analyse circulating microRNAs on a genome-scale level, it suffers from potential biases (e.g. adapter ligation bias) and lacks absolute transcript quantitation. In order to develop a robust NGS discovery assay for genome-scale quantitation of circulating microRNAs we first evaluated the sensitivity, repeatability and ligation bias of four commercially available small RNA library preparation protocols. The protocol from RealSeq Biosciences was selected based on its performance and usability, and coupled with a novel panel of exogenous small RNA spike-in controls to enable absolute quantitation and ensure comparability of data across independent NGS experiments. The established MicroRNA Next-Generation-Sequencing Discovery Assay (miND) was validated for its relative accuracy, precision, analytical measurement range and sequencing bias and was considered fit-for-purpose for microRNA biomarker discovery. Summarized, all these criteria were met and thus our analytical platform is considered fit-for-purpose for microRNA biomarker discovery from plasma, serum, cerebrospinal fluid (CSF), synovial fluid (SF), or extracellular vesicles (EV) extracted from cell culture medium in the setting of any diagnostic, prognostic or patient stratification need.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: A comprehensive comparison of four commersially available small RNA sequencing protocols followed by the assay development and validation for the MicroRNA Next-Generation Discovery Assay (miND)

first: Kseniya

last: Khamina

first: Susanna

last: Skalicky

first: Moritz

last: Weigl

first: Marianne

last: Pultar

first: Teresa

last: Krammer

first: Catharine

last: Fournier

first: Amy

last: Schofield

first: Carolin

last: Otto

first: Aaron

middle: T

last: Smith

first: Nina

last: Buchtele

first: Christian

last: Schoergenhofer

first: Bernd

last: Jilma

first: Bernhard

middle: J

last: Frank

first: Jochen

middle: G

last: Hofstaetter

first: Regina

last: Grillari

first: Johannes

first: Klemens

last: Ruprecht

first: Christopher

middle: E

last: Goldring

first: Hubert

last: Rehrauer

first: Warren

last: Glaab

first: Matthias

last: Hackl


title: Effects of DNA topoisomerase inhibitor acriflavine on endothelial gene expression and chromatin accessibility (ATAC-Seq)

status: Public on Jan 19 2022

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: RNA-Seq of human endothelial cells treated with ACF revealed massive changes on gene expression. These were non-randomly and strongly conserved to murine lung endothelial cells potentially due to DNA topoisomerase inhibition rather than HIF inhibition. Surprisingly, in contrast to protein-coding genes, RNA-Seq yielded that an exceeding number of lncRNAs is upregulated, e.g. FENDRR, H19, HIF1α-AS1 and FLJ31356, whereas BOLA3-AS1 and MEG3 were strongly downregulated. ATAC-Seq demonstrated that ACF leads to strong changes on chromatin accessibility on lncRNA promoters.

overall_design: Examination of acriflavine treatment in mouse lung endothelial cells and HUVECs.

first: Sandra

last: Seredinski

first: Ralf

middle: P

last: Brandes

middle: S

last: Leisegang


title: Rapid factor depletion highlights intricacies of nucleoplasmic RNA degradation

city: Aarhus C

first: Torben

middle: Heick

last: Jensen

address: C. F. Møller Alle 3

country: Denmark

institute: Aarhus University

summary: Turnover of nucleoplasmic transcripts by the mammalian multi-subunit RNA exosome is mediated by two adaptors: the Nuclear EXosome Targeting (NEXT) complex and the Poly(A) tail eXosome Targeting (PAXT) connection. Functional analyses of NEXT and PAXT have largely utilized long-term factor depletion strategies, facilitating the appearance of indirect phenotypes. Here, we rapidly deplete NEXT, PAXT and core exosome components, uncovering the direct consequences of their acute losses. Generally, proteome changes are sparse and largely dominated by co-depletion of other exosome and adaptor subunits, reflecting possible subcomplex compositions. While parallel high-resolution 3 end sequencing of newly synthesized RNA confirms previously established factor specificities, it concomitantly demonstrates an inflation of long-term depletion datasets by secondary effects. Most strikingly, a general intron degradation phenotype, observed in long-term NEXT depletion samples, is undetectable upon short-term depletion, which instead emphasizes NEXT targeting of snoRNA-hosting introns. Further analysis of these introns uncovers an unusual mode of core exosome-independent RNA decay. Our study highlights the accumulation of RNAs as an indirect result of long-term decay factor depletion, which we speculate is, at least partly, due to the exhaustion of alternative RNA decay pathways.

overall_design: RNA 3'end seq of early (10min 4sU labelled) pA+ and pA+ + pA- RNA 3' ends after rapid depletion of exosome core- (EXOSC3) and co-factors (ZCCHC8, ZFC3H1) in OsTIR1-expressing HeLa cells.

first: Maria

last: Gockert

first: Manfred

last: Schmid

first: Lis

last: Jakobsen

first: Marvin

last: Jens

first: Jens

last: Andersen

middle: H


title: Transcriptome profile of the host antiviral response to Chikungunya virus infection in human monocyte-derived macrophages (MDMs)

city: Botucatu

first: Geysson Javier

middle: Fernandez

last: Garcia

state: Sao Paulo

address: Departamento morfologia IBB UNESPRubiao Junior

country: Brazil

institute: UNESP

summary: Chikungunya virus (CHIKV) infection is characterized by alterations in gene expression profile on host cells that consequently lead to an immune response. Here, we used RNA sequencing to analyze the mRNA expression profile in human monocyte-derived macrophages (MDMs) infected with a Colombian clinical isolate of CHIKV at 6 and 24 hpi.  analyze the mRNA expression profile in the human monocyte-derived macrophages infected at 6 and 24 hrs with a Colombian clinical isolate of Chikungunya virus.

overall_design: Human peripheral blood mononuclear cells (PBMCs) from blood samples of 4 healthy donors mixed with 2% EDTA, were isolated through density gradient with Lymphoprep. Monocytes were obtained from total PBMCs by adherence to the plastic and differentiation to macrophages was allowed to occur for 6 days in RPMI-1640 medium supplemented with 10% (v/v) FBS, 4 mM L-glutamine, 0.3% (v/v) NaCO3, and 1% (v/v) antibiotic-antimycotic solution 100X (complete medium), at 37 °C and 5% CO2, without growth factors. CHIKV infection of human MDMs was performed at MOI 5 in serum-free RPMI-1640 medium. Samples were incubated at 37°C for 1.5 h. An hour and a half after infection, the cells were washed with PBS 1X to remove the unbound virus and fresh complete medium was added and incubated at 37°C with 5% CO2. RNA was collected from uninfected MDMs and CHIKV-infected MDMs at 6 and 24 hpi.

first: Geysson

last: Fernandez

first: Silvio

last: Urcuqui-Inchima


title: Genome-wide identification of transcriptional targets for H4K12la in total brain cells and microglia of WT and 5XFAD mice

city: Beijing

first: Lin

last: He

address: Xueyuan Road 38

institute: Peking University

summary: In this study, we found that H4K12la level is elevated in plaque-adjacent microglia of 5XFAD mice. To further explore the potential functional significance of H4K12la in AD, we performed genome-wide cleavage under targets and tagmentation (CUT&Tag) analysis to identify candidate genes regulated by H4K12la in total brain cells and microglia. Following CUT&Tag, H4K12la-associated DNAs were amplified using non-biased conditions, labeled, and sequenced with Illumina NovaSeq 150PE.

overall_design: Examination of transcriptional targets for H4K12la in total brain cells and microglia of WT and 5XFAD mice.

first: Rui-yuan

last: Pan

first: Xinhua

last: Liu


title: Roles of close homologues SigB and SigD in heat and bright light acclimation of the cyanobacterium Synechocystis sp. PCC 6803

city: Turku

first: Taina

last: Tyystjärvi

address: Itäinen pitkäkatu 4

country: Finland

institute: University of Turku

summary: Acclimation of cyanobacterium Synechocystis sp. PCC6803 to suboptimal conditions is largely dependent on adjustments of gene expression, which is highly controlled by the σ factor subunits of RNA polymerase (RNAP). The SigB and SigD σ factors are close homologues. Here we show that sigB and sigD genes are both induced in bright light and high temperature stresses. Comparison of transcriptomes of the control strain (CS), ΔsigB, ΔsigD, ΔsigBCE (SigD is an only functional group 2 σ factor), and ΔsigCDE (SigD is an only functional group 2 σ factor) strains in standard, bright light and high temperature conditions revealed that the SigB and SigD factors regulate different set of genes, and that SigB and SigD regulons are highly dependent on stress conditions. The SigB regulon is bigger than the SigD regulon at high temperature, whereas in bright light the SigD regulon is bigger the SigB regulon. Furthermore, our results show that favoring the SigB or SigD factor by deleting other group 2 σ factors do not lead to superior acclimation to bright light or high temperature conditions, indicating that all group 2 σ factors play roles in acclimation processes.

overall_design: The 30-ml cell cultures (Synechocystis sp. PCC 6803 were grown in standard condition to OD730 ~ 1, cells were collected from the standard conditions, or treated for 1h at the PPFD of 750 μmol photons m-2 s-1 or 1h at 42 °C maintaining the other condition same as in the standard conditions. 15-ml of cell suspension was pour to pre-frozen centrifugation tube, and cell pellet was collected by centrifugation at 7000 g for 5min at 4 °C. Three independent experiments were performed at each conditions.

first: Satu

last: Koskinen

first: Juha

last: Kurkela


title: Loss of Slc38a4 imprinting is a major cause of mouse SCNT placenta hyperplasia at late gestation

city: Boston

first: Wenhao

last: Zhang

state: MA

address: Warren Alpert Bldg, Rm 160, 200 Longwood Ave

department: Genetics

institute: Harvard Medical School

summary: Placenta hyperplasia is commonly observed in cloned animals and is believed to impede the proper development of cloned embryos. However, the mechanism underlying this phenomenon is largely unknown. Here we show that placenta hyperplasia of cloned mouse embryos occurs in both middle and late gestation. Interestingly, restoring paternal-specific expression of an amino acid transporter Slc38a4, which loses maternal H3K27me3-dependent imprinting and becomes bi-allelically expressed in cloned placentae, rescued the overgrowth of cloned placentae at late gestation. Molecular analyses reveal that loss of Slc38a4 imprinting leads to over activation of the mechanistic target of rapamycin complex 1 (mTORC1) signaling pathway in cloned placentae, which is likely due to the increased amino acids transportation by SLC38A4. Collectively, our study not only reveals loss of Slc38a4 imprinting is responsible for overgrowth of cloned placentae at late gestation, but also suggests the underlying mechanism involves increased amino acid transportation and over activation of mTORC1.

overall_design: We conducted RNA sequencing in in vitro fertilized (IVF), wild type SCNT and Slc38a4 maternal knockout SCNT placenta at E14.5 and E19.5

first: Zhenfei

last: Xie

first: Yi


title: YTHDC2 CLIP

first: Yuhki

last: Saito

summary: Mouse testes samples from P8, P10, adult, and Ythdc2-WLA homozygous mutant mice were subjected to CLIP assays to generate YTHDC2-RNA interaction maps.

overall_design: Tissues were UV-irradiated and subjected to YTHDC2 CLIP with anti-YTHDC2 antibodies (ab220160 from Abcam and 27779-1-AP from Proteintech) . Detailed desription in accompanying paper.

first: Devanshi

last: Jain


title: Dynamic regulation of stress-responsive non-genomic CTCF complexes [ChIP-seq]

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: The nuclear protein CCCTC-binding factor (CTCF) has diverse roles in chromatin architecture and gene regulation. Functionally, CTCF associates with thousands of genomic sites and interacts with proteins, such as cohesin, or non-coding RNAs to facilitate specific transcriptional programming. In this study, we examined CTCF during the cellular stress response in human primary cells using immune-blotting, quantitative real time-PCR, chromatin immunoprecipitation-sequence analysis, mass spectrometry, RNA immunoprecipitation-sequence analysis, and Airyscan confocal microscopy. Unexpectedly, we found that CTCF is exquisitely sensitive to diverse forms of stress in normal patient-derived human mammary epithelial cells (HMECs). In HMECs, the majority of CTCF protein forms non-genomic complexes that localize to Serine/arginine-rich splicing factor (SC-35)-containing nuclear speckles, exclusive of its canonical association with chromatin. Upon stress, non-genomic CTCF protein is rapidly downregulated by changes in protein stability, resulting in loss of CTCF from SC-35 nuclear speckles and changes in CTCF-RNA interactions. CTCF complexes that associate with genomic DNA are resistant to stress-induced degradation and CTCF-DNA binding is largely unchanged. Restoration of cellular CTCF protein abundance and re-localization to nuclear speckles can be achieved by inhibition of proteasome-mediated degradation. Surprisingly, we observed the same characteristics of the stress response during neuronal differentiation of human pluripotent stem cells (hPSC). CTCF forms stress-sensitive complexes that localize to SC-35 nuclear speckles during a specific stage of neuronal commitment/development but not in differentiated neurons. We speculate that these non-canonical CTCF complexes serve a largely non-genomic role in RNA processing, potentially to maintain cells in a particular differentiation state, that is dynamically regulated by environmental signals.  The non-canonical, stress-regulated activity of CTCF is uncoupled in persistently stressed, epigenetically re-programmed “variant” HMECs and certain cancer cell lines. These results reveal new insights into CTCF function in cell differentiation and the stress-response with implications for oxidative damage-induced cancer initiation and neuro-degenerative diseases.

overall_design: ChIP-Seq

first: Bettina

last: Lehman

first: Fernando

last: Lopez-Diaz

first: Thom

last: Santisakultarm

first: Lingjing

last: Fang

first: Maxim

middle: N

last: Shokhirev

first: Kenneth

last: Diffenderfer

first: Uri

last: Manor

first: Beverly

middle: M

last: Emerson


title: Quantification of transcriptome levels in mouse spermatogonia TET1 overexpression group and control cells by RNA-seq

status: Public on Jan 17 2022

city: Hefei

first: Lingling

last: Liu

state: Anhui

address: Anhui Medical University, No.81 Meishan Road, Shushan District, Hefei, Anhui, China

summary: By analyzing the sequencing results of RNA-seq, we found that TET1 maintains self-renewal of mouse spermatogonia and promotes cellular transcription and enhances cellular activity, and we identified key differential genes that are specifically affected by TET1 and the mechanism of interaction between these key differential genes, providing a scientific basis for studying spermatogenesis, revealing the causes of spermatogenic disorders, and elucidated the mechanisms, which may contribute to the understanding of male reproductive disorders.

overall_design: GC-1 mRNA profiles of control (MYC) and overexpression group (MYC-TET1) mouse spermatogonia at 24h and 36h

first: Liming

last: Zheng


title: Dynamic regulation of stress-responsive non-genomic CTCF complexes

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

overall_design: Refer to individual Series


title: YTHDC2 CLIP and RNA-seq and Ribo-seq of Ythdc2KO and Ythdc2-WLA mutants


title: Dynamic regulation of stress-responsive non-genomic CTCF complexes [RIP-seq]

overall_design: RIP-Seq


title: Transcriptome profiling of renal glomeruli from Parva-fl/fl*hNPHS2Cre and WT mice

city: Freiburg

first: Manuel

last: Rogg

state: Baden Wuerttemberg

address: Breisacher Straße 115a

department: Institute of Surgical Pathology

institute: University Medical Center Freiburg

summary: Podocyte specific knockout mice for Parva (Parva-fl/fl*hNPHS2Cre) were generated. Transcriptome profiling (RNA-Seq) and differential gene expression analysis of isolated renal glomeruli from KO and WT mice was performed. Parva KO mice showed transcriptional changes associated with podocyte and glomerular disease.

overall_design: mRNA analysis of renal glomeruli from 3 Parva KO (Parva-fl/fl*hNPHS2Cre) and 3 WT mice.

first: Christoph

last: Schell