title: Human DDX6 regulates translation and decay of inefficiently translated mRNAs

city: Schlieren

first: Ramona

last: Weber

address: Wagistrasse 12

department: Institute for Regenerative Medicine

institute: University of Zurich

summary: Recent findings indicate that the translation elongation rate influences mRNA stability. One of the factors that has been implicated in this link between mRNA decay and translation speed is the yeast DEAD-box helicase Dhh1p. Here, we demonstrate that the human ortholog of Dhh1p, DDX6, triggers deadenylation-dependent decay of inefficiently translated mRNAs in human cells. DDX6 interacts with the ribosome through the Phe-Asp-Phe (FDF) motif in its RecA2 domain. Furthermore, RecA2-mediated interactions and ATPase activity are both required for DDX6 to destabilize inefficiently translated mRNAs. Using ribosome profiling and RNA sequencing, we identified two classes of endogenous mRNAs that are regulated in a DDX6-dependent manner. The identified targets are either translationally regulated or regulated at the steady-state-level and either exhibit signatures of poor overall translation or of locally reduced ribosome translocation rates. Transferring the identified sequence stretches into a reporter mRNA caused translation- and DDX6-dependent degradation of the reporter mRNA. In summary, these results identify DDX6 as a crucial regulator of mRNA translation and decay triggered by slow ribosome movement and provide insights into the mechanism by which DDX6 destabilizes inefficiently translated mRNAs.

overall_design: Two cell types with two biological replicates analysed using RNA-Seq and Ribo-Seq

first: Chung-Te

last: Chang


title: sciMET-cap: High-throughput single-cell methylation analysis with a reduced sequencing burden

status: Public on Dec 19 2023

city: Portland

first: Andrew

last: Adey

state: OR

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

department: MMG

country: USA

institute: Oregon Health & Science University

summary: DNA methylation is a key component of the mammalian epigenome, playing a regulatory role in development, disease, and other processes. Robust, high-throughput single-cell DNA methylation assays are now possible (sciMET); however, the genome-wide nature of DNA methylation results in a high sequencing burden per cell. Here, we leverage target enrichment with sciMET to capture sufficient information per cell for cell type assignment using substantially fewer sequence reads (sciMET-cap). Sufficient off-target coverage further enables the production of near-complete methylomes for individual cell types. We characterize sciMET-cap on human PBMCs and brain (middle frontal gyrus).

overall_design: Crypreserved commercially-obtained PBMCs were used for all data included in this data deposition


title: Oryza sativa ssp. japonica (Kitaake) stressed by cold stress (5°C, 24 h) targeted to leaves (C-L), roots (C-R) or the whole plant (C), and exposed to previous acclimation (15°C, 12 h)

status: Public on Jan 01 2024

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: The experiment tested organ-specific responses of rice (Oryza sativa ssp. japonica) to cold stress with a special focus on phytohormonal regulation. Cold stress (5°C, 24 h) was applies on the whole plants, leaves or roots. The results showed distinct responses when cold stress was applied on leaves, relating to photosynthesis and sugar synthesis as well as specific changes in phytohormones. On the other hand, stress applied to roots was more similar to the stress on the whole plant indicating roots to be more important in cold stress responses. Acclimation by mild temperature (15°C, 12 h) highlighted changes which are connected even with lower temperature exposure or which are characteristic for untreated organs. Recovery (3 d) indicated ability of plants to restore growth which correlated between individual phytohormones and plant growth. The article connect transcriptome, hormonome, proteome and sugar analyses of rice cold-stress responses.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from roots of Oryza sativa seedlings grown 13 days in hydroponics, treated for 24 h by cold stress (5°C, 24 h) targeted to leaves, roots or the whole plant. Some plants were pre-treated by acclimation (15°C, 12 h). Some samples were collected after 3-day recovery under control conditions. Three independent biological replicates were collected.

first: Jana

last: Jarosova

first: Sylva

last: Prerostova


title: A single-cell transcriptomic analysis of the mouse hippocampus after voluntary exercise

status: Public on Dec 31 2023

city: Göttingen

first: André

last: Fischer

state: Niedersachsen

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

country: Germany

institute: Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE)

summary: Exercise has been recognized as a beneficial factor for cognitive health, particularly in relation to the hippocampus, a vital brain region responsible for learning and memory. Previous research has demonstrated that exercise-mediated improvement of learning and memory in humans and rodents correlates with increased adult neurogenesis and processes related to enhanced synaptic plasticity. Nevertheless, the underlying molecular mechanisms are not fully understood. With the aim to further elucidate these mechanisms we provide a comprehensive dataset of the mouse hippocampal transcriptome at the single-cell level after four weeks of voluntary wheel-running. Our analysis provides a number of interesting observations. For example, the results suggest that exercise affects adult neurogenesis by accelerating the maturation of a subpopulation of Prdm16-expressing neurons. Moreover, we uncover the existence of an intricate crosstalk among multiple vital signaling pathways such as NF-κB, Wnt/β-catenin, Notch, retinoic acid (RA) pathways altered upon exercise in a specific cluster of excitatory neurons within the Cornu Ammonis (CA) region of the hippocampus. In conclusion, our study provides an important dataset and sheds further light on the molecular changes induced by exercise in the hippocampus. These findings have implications for developing targeted interventions aimed at optimizing cognitive health and preventing age-related cognitive decline.

overall_design: 8 WT adult mice were divided into 2 equally sized groups - runners that had free and voluntary access to running wheels in their cages (the ‘exercise’ group), and sedentary mice that had similar wheels in their cages that were however blocked (the ‘control’ group). This voluntary exercise paradigm lasted 4 weeks, after which whole hippocampal nuclei were isolated from all mice for snRNA-seq analysis.

first: Aditi

last: Methi

first: Rezaul

last: Islam

first: Lalit

last: Kaurani

first: Sadman

last: Sakib

first: Dennis

middle: M

last: Krüger

first: Susanne

last: Burkhardt

first: David

last: Liebetanz


title: Engrailed-1 Promotes Pancreatic Cancer Metastasis

city: Davis

first: Chang-il

last: Hwang

state: CA

address: One Shields Ave

department: Microbiology and Molecular Genetics

institute: University of California Davis

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Engrailed-1 Promotes Pancreatic Cancer Metastasis [RNA-Seq]

summary: Engrailed-1 (EN1) is a critical homeodomain transcription factor (TF) required for neuronal survival, and EN1 expression has been shown to promote aggressive forms of triple negative breast cancer. Here, we report that EN1 is aberrantly expressed in a subset of pancreatic ductal adenocarcinoma (PDA) patients with poor outcomes. EN1 predominantly repressed its target genes through direct binding to gene enhancers and promoters, implicating a role in the cellular response to the stimulation of mesenchymal cell properties. Gain- and loss-of-function experiments demonstrated that EN1 promoted PDA transformation and metastasis in vitro and in vivo. Our findings nominate the targeting of EN1 and downstream pathways in aggressive PDA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mM3P and mM15 organoids and its EN1 knockdown derivatives (shScr, shEn1#1, and shEn1#2).

first: Jihao

last: Xu

middle: A

last: Tuveson


title: Engrailed-1 Promotes Pancreatic Cancer Metastasis [CUT&RUN]

overall_design: Comparative analysis of cleavage under targets and release using nuclease-sequencing (CUT&RUN-seq) for EN1 genmic targets and the histone modifications H3K4me3, H3K27ac, and H3K27me3 in mT3-2D, mT4-2D, mT5-2D, and mT8-2D cells.


title: A natural small molecule alleviates liver fibrosis by targeting apolipoprotein L2

status: Public on Dec 17 2023

city: Guangzhou

first: lu

last: gan

state: Guangdong

address: 132 Outer Ring East Road, Panyu District

country: China

institute: School of Pharmaceutical Sciences, Sun Yat-sen University

summary: Liver fibrosis is an urgent clinical problem without effective treatment. Herein, we conduct a high-content screening on a natural “privileged” diterpenoid library to identify a potent anti-liver fibrosis lead DP. Leveraging photoaffinity labeling approach, apolipoprotein L2 (APOL2), an ER-rich protein, is identified as the direct target of DP. APOL2 is mainly expressed in activated hepatic stellate cells (HSCs) and could activate HSCs to synthesize ECM proteins. It can be induced by TGF-b1 and be antagonized by DP. Mechanistically, upon TGF-b1 stimulation, APOL2 binds ER Ca2+ pump SERCA2 to trigger ER stress, elevating its downstream PERK-HES1 axis to promote liver fibrosis, mildly dependent on the canonical TGF-b/Smad signaling. As a result, ablation of APOL2 significantly alleviates TGF-b1-stimulated HSCs activation, and abolishes anti-fibrosis effect of DP. Our findings not only define APOL2 as a novel therapeutic target for liver fibrosis, but also highlight DP as a promising lead for treatment of this symptom.

overall_design: LX-2 cells mRNA profiles of treatment with DMSO, TGF-b1, and TGF-b1 + 10 μM DP for 48 h.

first: Sheng

last: Yin

first: Jianping

last: Guo

first: Lu

last: Gan


title: Analysis of monocyte-derived dendritic cell transcriptome upon HIV-1 challenge and effect of MDA5 knockdown

status: Public on Dec 14 2023

city: Worcester

first: Ozkan

last: Aydemir

state: Massachusetts

address: 366 Plantation Street, Paul J. DiMare Center  N4-1085

institute: UMass Medical School

summary: The purpose of this study is to characterize the changes in global transcriptome of monocyte-derived dendritic cells (MDDCs) upon HIV-1 challenge, and examine the effect of MDA5 knockdown on MDDC transcriptome in the presence and absence of HIV-1 challenge. For this study, human CD14+ monocytes were enriched from peripheral blood mononuclear cells (PBMCs) and transduced with lentivectors encoding  puromycin acetyltransferase and a short hairpin RNA (shRNA) targeting either control luciferase (Luc) or MDA5. Immediately following challenge with the knockdown vector, monocytes were placed in culture with IL-4 and GM-CSF to promote differentiation into MDDCs. Three days after transduction, puromycin was added to the medium to select for cells that had been transduced. On day seven, the resulting immature MDDCs were either challenged with a single-cycle HIV-1 vector or left untreated for 48 hours. RNA isolated from these samples was used to generate poly(A)-selected RNA-seq libraries. Analyses of these samples revealed that HIV-1 challenge in MDDCs induces a robust type-1 interferon response, whereas MDA5 suppression significantly limits this innate immune response to HIV-1.

overall_design: mRNA profiles of MDDCs, isolated from 3 different donors, that are transduced with shRNA lentivectors targeting either luciferase or MDA5, and subsequently either challenged with HIV-1 for 48 hours or left uninfected. RNA-seq libraries were generated via poly(A)-enrichment.

first: Mehmet

last: Hakan Guney


title: Transcriptional analysis of neonatal mouse cortex following morphine exposure

status: Public on Dec 15 2023

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: We developed a mouse model of NOWS that includes gestational and post-natal morphine exposure that encompasses the developmental equivalent of all three human trimesters of gestation. This exposure paradigm causes delayed developmental milestones and acute withdrawal phenotypes reminiscent of those observed in infants.

overall_design: RNA was isolated from mouse cortex from male and female pups. We performed bulk RNA sequencing in the right hemisphere, generating male and female-specific datasets for morphine or saline, in each of the three exposure protocols, six hours after birth for the PND1 cohort and six hours after the last morphine injection for the PND15 and 3-trimester cohorts. Importantly, the number of animals per group was similar (N=5-7 animals), and the quality controls, library construction and sequence parameters were also identical across all groups.

first: Amy

last: Dunn

first: Chiso

last: Nwokafor

first: Shivon

last: Robinson

first: Angie

middle: V

last: Ramirez-Jimenez

first: B

middle: W

last: Hamilton

first: Emilie

middle: L

last: Castranio

first: Jean-Vianney

last: Haure-Mirande

first: Julie

last: Blendy

first: Michelle

middle: E

last: Ehrlich


title: Defective Integrator activity shapes the transcriptome of patients with multiple sclerosis: mouse model

status: Public on Dec 12 2023

city: Paris Cedex 05

first: Christian

last: MUCHARDT

address: Sciences Sorbonne Université Campus Pierre et Marie Curie 7-9, Quai Saint Bernard - Bât A, 2ème étage

department: UMR8256 – Biological Adaptation and Ageing

country: France

institute: CNRS

summary: While the role of the immune system in multiple sclerosis (MS) is widely acknowledged, our comprehension of the transcriptional foundations of this prevalent neurological disorder remains largely incomplete. Here, we conducted high-depth RNA sequencing on monocytes from a cohort of patients with MS to explore rare RNA species associated with the disease. In a subset of the patients, a markedly altered transcriptome was observed, coinciding with a decreased expression of the epigenetic silencer HP1α/CBX5. These patients also exhibited diminished expression of multiple genes encoding subunits of the Integrator complex. Alongside, there were clear indications of decreased Integrator activity, including impaired U snRNA and enhancer-RNA maturation/degradation and dysregulated RNA polymerase II (RNAPII) pause-release. Inactivation of Cbx5 in the mouse recapitulated the defects in Integrator activity and resulted in hypersensitivity to Experimental Autoimmune Encephalomyelitis (EAE). While these data implied an unexpected function for HP1α in regulating RNAPII pause-release, they also showed that the dysregulation of numerous genes in MS patients could be attributed to either the biased distribution of transcription toward the 5' end of genes or the heightened elongation and stability of enhancer RNAs. An impaired Integrator activity, which has been hinted at by mutations within Integrator subunits previously linked to an increased risk of MS, provides a well-defined mechanistic understanding of the transcriptional anomalies associated with the disease, while introducing new criteria to categorize MS patients.

overall_design: C57BL/6N-Atm1Brd Cbx5tm1a(EUCOMM)Wtsi/WtsiOrl strain inactivated for Cbx5 was received from the EUCOMM Consortium. Either control mice or Cbx5 KO mice were included or not in an experimental autoimmune encephalomyelitis (EAE) protocol, as indicated. For each mouse, CD4+ T cells were purified from spleenocytes using the Miltenyi kit 130-104-454. Total RNA was extracted by Trizol LS (Thermo Fisher Scientific, ref. 10296028), according to the manufacturer's protocol. Total RNA library preparation and sequencing were performed by Novogene Co., Ltd, as a lncRNA sequencing service, including lncRNA directional library preparation with rRNA depletion (Ribo-Zero Magnetic Kit), quantitation, pooling and Paired End 150 sequencing (30G raw data) on Illumina HiSeq 2500 platform.

first: Yevhenia

last: POROZHAN

first: Eric

last: BATSCHE

first: Mickaël

last: COSTALLAT


title: RNA polymerase stalling-derived genome instability underlies ribosomal antibiotic efficacy and resistance evolution

status: Public on Dec 24 2023

city: Shanghai

first: Tianmin

last: Wang

address: Huaxia Middle Road, 393

department: School of Life Science and Technology

institute: ShanghaiTech University

summary: In bacteria, the precise coordination of DNA replication, transcription and translation is mediated by dynamic interactions among the corresponding macromolecular machineries, playing a pivotal role in maintaining cellular homeostasis. Here we showed that such coordination could be hijacked by ribosome antibiotics to trigger secondary damage predominantly contributing to their efficacy, via a yet overlooked reverse-central-dogma pathway. Through the utilization of a self-establishing transcription dynamics profiling method, complemented by genetic and biochemical approaches, we unveil that the disruption of transcription-translation coupling leads to premature stalling of RNA polymerase (RNAP) at genome scale, subsequently triggering extensive genomic instability. Moreover, a distinct subpopulation exhibits hyperactivation of the SOS response, facilitating an inducible evolutionary path towards genetic resistance characterized by a unique mutation spectrum. Our findings reveal the emergence of secondary drug damage resulting from network disorder, and establish a framework to understand antibiotic efficacy and induced mutagenesis from a systems biology perspective.

overall_design: To investigate the secondary effect of gentamicin treatment, which is transcription elongation chaos and mutagensis, we performed RNA-seq and 3' -end-seq to profile transcription dynamics and genome re-sequencing to identify mutations.

first: Yayun

last: Zheng

first: Ruochen

last: Chai


title: Inhibition of PARP11 inactivates tumor-infiltrating regulatory T cells and improves the efficacy of immunotherapies.

status: Public on Dec 07 2023

city: Philadelphia

first: Raghavendra

last: Basavaraja

address: 380 south, University ave

department: Biomedical Sceinces

institute: Univeristy of Pennsylvania

summary: Tumor-infiltrating regulatory T cells (TI-Tregs) elicit immunosuppressive effects in the tumor microenviroment (TME) leading to accelerated tumor growth and resistance to immunotherapies against solid tumors. Here we demonstrate that Poly-(ADP-ribose)-polymerase-11 (PARP11) acts as an essential regulator of TI-Tregs regulatory and protumorigenic activities. Expression of PARP11 correlated with TI-Treg infiltration and poor responses to immune checkpoint blockade (ICB) in human cancer patients. PARP11 was induced in the TI-Treg cells by tumor-derived factors including adenosine and prostaglandin E2. Knockout of PARP11 in the cells of the TME or treatment of tumor-bearing mice with selective PARP11 inhibitor ITK7 inactivated TI-Treg cells and reinvigorated anti-tumor immune responses. Accordingly, ITK7 decelerated tumor growth and significantly increased the efficacy of anti-tumor immunotherapies including ICB and adoptive transfer of CAR T cells. These results characterize PARP11 as a key driver of TI-Treg activities and a major regulator of immunosuppressive TME and argue for targeting PARP11 to augment anti-cancer immunotherapies.

overall_design: This study aimed to elucidate the impact of ITK7 on the transcriptomic profile of  tumor microenvironment in C57BL/6J mice. After confirming MC38 tumors, mice were treated with either a control vehicle (DMSO) or ITK7. Post-treatment, tumors were harvested for RNA extraction and subsequent bulk RNA sequencing analysis, comparing the transcriptomic changes between the DMSO and ITK7 treatment groups.

first: Daniel

middle: P

last: Beiting

first: Subin

last: George

first: Serge

middle: Y

last: Fuchs


title: Autism-associated transcriptional regulators target shared loci proximal to brain-expressed genes

status: Public on Dec 04 2023

city: San Francisco

first: Kenneth

last: Lim

department: Psychiatry

institute: UCSF

summary: Many autism spectrum disorder (ASD)-associated genes act as transcriptional regulators (TRs). ChIP-seq was used to identify the regulatory targets of ARID1B, BCL11A, FOXP1, TBR1, and TCF7L2, ASD-associated TRs in the developing human and mouse cortex. These TRs shared substantial overlap in the binding sites, especially within open chromatin. The overlap within a promoter region, 1-2,000bp upstream of transcription start site, was highly predictive of brain expressed genes. This signature was observed at 96 out of 102 ASD-associated genes. In vitro CRISPRi against ARID1B and TBR1 delineated downstream convergent biology in mouse cortical cultures. After eight days, NeuN+ and CALB+ cells were decreased, GFAP+ cells were increased, and transcriptomic signatures correlated with the postmortem brain samples from individuals with ASD. We suggest functional convergence across five ASD-associated TRs leads to shared neurodevelopmental outcomes of haploinsufficient disruption.

overall_design: ChIP-seq was used to identify the regulatory targets of ARID1B, BCL11A, FOXP1, TBR1, and TCF7L2 in the developing mouse cortex.

first: Siavash

last: Fazel Darbandi

first: Joon-Yong

last: An

first: Nicholas

middle: F

last: Page

first: Lindsay

last: Liang

first: Athena

middle: R

last: Ypsilanti

first: Eirene

last: Markenscoff-Papadimitriou

first: Matthew

last: State

first: Alex

last: Nord

first: Stephan

middle: J

last: Sanders

first: John

last: Rubenstein


title: Single-cell transcriptome analysis reveals distinct cell populations in dorsal root ganglia and their potential roles in diabetic peripheral neuropathy

status: Public on Nov 23 2023

city: Wuhan

first: Guojun

last: Guo

state: Hubei

address: 1277# Jiefang Avenue

department: Hand Surgery

institute: Union Hospital of Tongji medical college, Huazhong University of Science & Technology

summary: Diabetic peripheral neuropathy (DPN) is the most common form of neuropathy, and have considerable morbidity, which occurs in approximately 50% of diabetic patients. Here, we performed scRNA-seq technology using 10× Genomics sequencing on DRG tissues isolated from control and DPN rats, to identify the cell type composition of DRG, and to reveal the roles of different cell types in mediating DPN.

overall_design: One sample from bilateral L3-6 DRG tissues of five DPN rats, and one sample from bilateral L3-6 DRG tissues of five normal SD rats.

first: Zhenbing

last: Chen


title: Med12 ablation promotes anti-tumor function by enhancing tumor intrinsic immunogenicity in Pancreatic ductal adenocarcinoma [CUT&Tag]

status: Public on Nov 30 2023

first: JIng

last: Xue

address: No.1630 dongfang road, pudong new district, Shanghai

institute: Renji Hospital, School of Medicine,Shanghai Jiaotong University

summary: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers with limited treatment options, including checkpoint blockade (ICB) immunotherapy. Epigenetic dysregulation is a defining feature of tumorigenesis and contributes to immune escape. However, little is known about whether and how epigenetic regulators evade immune surveillance in PDAC. Here, we identified Med12, a subunit of RNA polymerase II, as a mediator of immune escape in PDAC with in vivo CRISPR-Cas9 Screening. In murine PDAC models, Med12 loss effectively promoted infiltration and cytotoxicity of CD8+ T cells and NK cells，thereby sensitized to ICB and led to a marked extension of survival. Mechanistically, Med12 loss derepressed endogenous retroelements via impairing H3K9me3 and increasing H3K27Ac modification, triggering cytosolic RNA-sensing and DNA-sensing pathways as well as the type I interferon pathways. Moreover, Med12 depletion induced H3K27Ac gain in the Med12-binding domains, further enhanced the interferon-related genes transcription. Our results demonstrated the role of Med12 in suppressing tumor-intrinsic immunogenicity, thus provided a potential target or marker for immunotherapy of PDAC.

overall_design: To investigate the function of Med12 regulating tumor instrinsic immunogenicity, wo conducted Med12 KO and WT cell lines. Then, we performed CUT&Tag sequencing to analyse how Med12 regulates retroelements inhibition. Markers are :MED12,SETDB1,H3K9me3,H3K27ac,H3K27me3.

first: Yingying

last: Tang

first: Jing


title: Med12 ablation promotes anti-tumor function by enhancing tumor intrinsic immunogenicity in Pancreatic ductal adenocarcinoma [human RNA-seq]

overall_design: To investigate the function of Med12 regulating tumor instrinsic immunogenicity, wo conducted Med12 KO and WT cell lines. Then, we performed RNA sequencing to analyse gene expression profile of Med12 KO and WT cells.


title: Natural variation in yeast reveals multiple paths for acquiring higher stress resistance

status: Public on Nov 21 2023

city: Fayetteville

first: Jeffrey

middle: A.

last: Lewis

state: AR

address: 850 W. Dickson St.

department: Biological Sciences

institute: University of Arkansas

summary: Organisms frequently experience environmental stresses that occur in predictable patterns and combinations. For wild Saccharomyces cerevisiae yeast growing in natural environments, cells may experience high osmotic stress when they first enter broken fruit, followed by high ethanol levels during fermentation, and then finally high levels of oxidative stress resulting from respiration of ethanol. Yeast have adapted to these patterns by evolving sophisticated “cross protection” mechanisms, where mild ‘primary’ doses of one stress can enhance tolerance to severe doses of a different ‘secondary’ stress. For example, in many yeast strains, mild osmotic or mild ethanol stresses cross protect against severe oxidative stress, which likely reflects an anticipatory response important for high fitness in nature. During the course of genetic mapping studies to understand the mechanisms underlying natural variation in ethanol-induced cross protection against H2O2, we found that a key H2O2 scavenging enzyme, cytosolic catalase T (Ctt1p), was absolutely essential for cross protection in a wild oak strain, suggesting the absence of compensatory mechanisms for acquired H2O2 resistance under that condition. In this study, we found surprising heterogeneity across diverse yeast strains in whether CTT1 function was fully necessary for acquired H2O2 resistance. Some strains exhibited partial dispensability of CTT1 when ethanol and/or salt were used as mild stressors, suggesting that compensatory peroxidases may play a role in acquired stress resistance in certain genetic backgrounds. We leveraged global transcriptional responses to ethanol and salt stresses in strains with different levels of CTT1 dispensability, allowing us to identify possible regulators of these alternative peroxidases and acquired stress resistance in general. Ultimately, this study highlights how superficially similar traits can have different underlying molecular foundations and provides a framework for understanding the diversity and regulation of stress defense mechanisms.

overall_design: We performed RNA-seq on different Saccharomyces cerevisiae strains (DBY8268, M1, M22, Y10, YJM1129, YJM308, YPS163, YPS606) responding to either ethanol or salt (NaCl) stress. We also compared the expression of wild-type YPS606 to different YPS606 transcription factor mutants (msn2/4∆, skn7∆, yap1∆).

first: Amanda

middle: N

last: Scholes

first: Stephanie

last: Hood

first: Cader

last: Locke

first: Tara

last: Stuecker


title: ONECUT2 Activates Diverse Resistance Drivers of Androgen Receptor-Independent Heterogeneity in Prostate Cancer (CUT&RUN-seq)

city: Los Angeles

first: Qian

last: Yang

address: 8700 Beverly Blvd

department: Department of Surgery

institute: CEDARS SINAI MEDICAL CENTER

summary: Androgen receptor- (AR-) indifference is a mechanism of resistance to hormonal therapy in prostate cancer (PC). Here we demonstrate that the HOX/CUT transcription factor ONECUT2 (OC2) directly activates resistance through multiple drivers associated with adenocarcinoma, stem-like and neuroendocrine (NE) variants. OC2 regulates gene expression by promoter binding, enhancement of chromatin accessibility, and formation of novel super-enhancers. Pharmacologic inhibition of OC2 suppresses lineage plasticity reprogramming induced by the AR signaling inhibitor enzalutamide. These results demonstrate that OC2 activation promotes a range of drug resistance mechanisms associated with treatment-emergent lineage variation in PC.

overall_design: Compare the TF binding (OC2, AR, GR) and histone markers (H3K27Ac, H3K4me3, H3K27me3) of CUT&RUN-seq data in LNCaP Vector Control vs. OC2 overexpression cells. Compare the FOXA1 binding change in LNCaP cells after 7 days of vehicle control, enzalutamide treatment (10uM), and combination treatment (Enzalutamide (10uM) + OC2 inhibitor (10uM))

first: Chen

last: Qian

first: Mirja

last: Rotinen

first: Rongrong

last: Huang

first: Hyoyoung

last: Kim

first: Brad

last: Gallent

first: Yiwu

last: Yan

first: Radu

last: Cadaneanu

first: Baohui

last: Zhang

first: Salma

last: Kaochar

first: Stephen

last: Freedland

first: Edwin

last: Posadas

first: Leigh

last: Ellis

first: Dolores

last: Di Vizio

first: Colm

last: Morrissey

first: Peter

last: Nelson

first: Lauren

last: Brady

first: Ramachandran

last: Murali

first: Moray

last: Campbell

first: Wei

first: Beatrice

last: Knudsen

first: Elahe

last: Mostaghel

first: Huihui

last: Ye

first: Isla

last: Garraway

first: Sungyong

last: You

first: Michael

last: Freeman


title: ONECUT2 Activates Diverse Resistance Drivers of Androgen Receptor-Independent Heterogeneity in Prostate Cancer (ATAC-seq)

first: Qian

last: Yang

overall_design: Compare the chromatin accessibility changes after the overexpression OC2 gene in LNCaP cells.  Compare the chromatin accessibility changes after 7 days of vehicle control, enzalutamide treatment (10uM), and combination treatment (Enzalutamide (10uM) + OC2 inhibitor (10uM)).

first: Chen

last: Qian

first: Mirja

last: Rotinen

first: Rongrong

last: Huang

first: Hyoyoung

last: Kim

first: Brad

last: Gallent

first: Yiwu

last: Yan

first: Radu

last: Cadaneanu

first: Baohui

last: Zhang

first: Salma


title: ONECUT2 Activates Diverse Resistance Drivers of Androgen Receptor-Independent Heterogeneity in Prostate Cancer


title: Med12 ablation promotes anti-tumor function by enhancing tumor intrinsic immunogenicity in Pancreatic ductal adenocarcinoma

first: JIng

last: Xue


title: RNA-seq analysis after ASCL1 overexpression in GI-MEN cells [Part 1]

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

summary: RNA-seq analysis was performed in a Neuroblastoma cell line (GI-MEN) to analyze gene expression changes after ASCL1 overexpression.

overall_design: Lentiviral transduction was carried out in GI-MEN cells to overexpress ASCL1 on day 3.  Total RNA was harvested 3 days after ASCL1 overexpression and RNA-seq analysis was performed.

first: Wang

last: Lu

first: Tze

middle: K

first: Takaomi

last: Sanda


title: Cut & Run-seq analysis for transcription factors overexpression in GI-MEN cells

summary: Cut & Run analysis was performed in an neuroblastoma cell line to analyze DNA bindings of ASCL1-tag-HA in GI-MEN ASCL1-tag-HA cells and GI-MEN ASCL1-tag-HA+4TFs cells; analyze DNA bindings of MYCN, PHOX2B and H3K27ac in, GI-MEN 4TFs cells, and GI-MEN ASCL1-tag-HA+4TFs cells.

overall_design: CUT&RUN was performed using an EpiCypher kit (SKU: 14-1048). Approximately 0.5 million cells were used for each reaction. Antibody targeting the transcription factor or histone modification of interest as well as IgG were used. DNA was purified for library construction using an Illumina sequencing library kit. Illumina HiSeq sequencing of ~10 M paired-end 150-bp reads was performed at Genewiz.


title: RNA-seq analysis after transcription factors overexpression in GI-MEN cells [Part 2]

summary: RNA-seq analysis was performed in a Neuroblastoma cell line (GI-MEN) to analyze gene expression changes after ASCL1 ot other TFs overexpression.

overall_design: Lentiviral shRNA transduction was carried out in GI-MEN cells to overexpress ASCL1. Retrovirus were used to overexpress PHOX2B, ISL1, MYCN and LMO1.  Total RNA was harvested after ASCL1 or other TFs overexpression and RNA-seq analysis was performed.


title: H3K27ac HiChIP analysis in  GI-MEN DOX-ASCL1 cells

summary: H3K27ac HiChIP analysis was performed in  GI-MEN DOX-ASCL1 cells to analyze active chromatin-chromatin interactions in  GI-MEN DOX-ASCL1 cells.

overall_design: Cells were crosslinked with formaldehyde for 10 min.  DNA was enriched by chromatin-immunoprecipitation (ChIP), tagmented with Tn5 and analyzed by DNBseq.  HiChIP was performed using an antibody against H3K27ac Antibody  (ab4729).


title: AP2XII-1 and AP2XI-2 Suppress Schizogony Gene Expression in Toxoplasma gondii

status: Public on Dec 10 2023

city: Nanning

first: Dandan

last: Hu

state: China

address: Daxue East Rd #100, College of Animal Science and Techenology, Guangxi University.

institute: Guangxi University

summary: Toxoplasma gondii is a medically and veterinary important intracellular parasite that undergoes distinct developmental transitions in its intermediate and definitive hosts. The switch between stages of T. gondii is meticulously regulated by a variety of factors. Previous studies have explored the role of the microrchidia (MORC) protein complex as a transcriptional suppressor of sexual commitment. By utilizing immunoprecipitation and mass spectrometry, constituents of this protein complex have been identified, including MORC, Histone Deacetylase 3 (HDAC3), and several ApiApiAP2 transcription factors. Conditional knockout of MORC or inhibition of HDAC3 results in upregulation of a set of genes associated with schizogony and sexual stages in T. gondii tachyzoites. Here, our focus extends to three primary ApiAP2s: ApiAP2XII-1, ApiAP2XI-2, and ApiAP2V-2, demonstrating their significant impact on the fitness of asexual tachyzoites and their target genes. Notably, the targeted disruption of ApiAP2XII-1 and ApiAP2XI-2 resulted in a more profound alteration in merozoite-specific genes targeted by the MORC/HDAC3 complex compared to ApiAP2V-2. Additionally, considerable overlap was observed in downstream gene profiles between ApiAP2XII-1 and ApiAP2XI-2, with ApiAP2XII-1 specifically binding to a subset of ApiAP2 transcription factors, including ApiAP2XI-2. These findings reveal an intricate cascade of ApiAP2 regulatory networks involved in T. gondii schizogony development, orchestrated by ApiAP2XII-1 and ApiAP2XI-2. This study provides valuable insights into the transcriptional regulation of T. gondii growth and development, shedding light on the intricate life cycle of this parasitic pathogen.

overall_design: Transgenic parasite strains cultured in Vero cells were treated with either 500 μM IAA or vehicle for 12 h. Total RNAs from T. gondii tachyzoites were then extracted using the M5 Total RNA Extraction Reagent (Mei5 Biotechnology Co., Ltd, Beijing) according to the manufacturer’s protocol. Each treatment consisted of three biological replicates. The purity, concentration and integrity of RNAs were tested using the NanoPhotometer® (IMPLEN, CA, USA), the Qubit® RNA Assay Kit in the Qubit® 2.0 Fluorometer (Life Technologies, CA, USA) and the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively. Only qualified samples were used for library preparation. Illumina sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s recommendations. Sequencing was performed using the Illumina Novaseq 6000 platform from Shanghai Personal Biotechnology Co., Ltd. to generate 150 bp paired-end reads. The original sequencing data can be found in the Sequence Read Archive database under the accession number PRJNA1009254. RNA-seq reads were uploaded to the BMKCloud (www.biocloud.net) platform for analysis based on the reference genome of Toxoplasma Type II ME49 strain (ToxoDB-57). Briefly, Paired-end clean reads were aligned to the reference genome using Hisat242. Read counts for each gene were calculated using the sorted bam files using StringTie43. Differentially expressed genes (DEGs) between treated and untreated parasites were calculated by edgeR44. Gene ontology enrichment analysis was performed in ToxoDB. Gene expression with a fold change >2 or < -2 and FDR < 0.05 was defined as significantly differentially expressed. TPM (Transcripts per kilobase million) was calculated for each gene and used for clustered heatmap drawing. The transgenic strains were inoculated in 25 cm2 cell culture flasks and washed after 4 h to remove non-invasive parasites. Transgenic strains (1 x 105) were harvested after 12 h of incubation with or without IAA (500 μM). Library construction was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, Nanjing, China) according to the manufacturer's instructions. Briefly, fresh tachyzoites were bound to activated concanavalin A beads (10 ml/sample) and incubated for 10 min at room temperature. The mixture was resuspended and incubated with primary antibody (1:50, mice anti-HA) at 4°C overnight. After several washes, the parasites were incubated with secondary antibody (1:100, goat anti-mouse IgG) for 1 h at room temperature. The parasites were then resuspended with 300 ml of pA-Tn5 buffer (0.04 mM) and incubated for 1 h at room temperature on a rotator. Tagmentation was stopped by proteinase K treatment and DNA extraction was performed using DNA extract beads (Vazyme, Jiangsu, China)45. Illumina sequencing libraries were generated by PCR amplification with specific adaptors according to the manufacturer’s recommendations (TruePrep Index Kit V4 for Illumina, Vazyme, Nanjing, China). Cut-Tag libraries were sequenced using the Illumina Novaseq 6000 platform (Shanghai Personal Biotechnology Co., Ltd). The paired-end reads were filtered and then aligned to the T. gondii reference genome using Bowtie246 (v.2.1.0). The resulting sam files were transformed into bam files. PCR duplicates were removed from the sorted bam files using Sambamba47. The filtered reads were then employed to identify Cut-Tag peaks using MACS248. The overlapped peaks in two biological replicates were identified by the Irreproducibility Discovery Rate (IDR)49. The final peaks were annotated against the latest T. gondii data in ToxoDB. The sorted and filtered bam files of Cut-Tag peaks and RNA-seq reads were normalized to RPKM with a resolution of 10 bp (bin size) and transformed into bigwig files for direct visualization in IGV (Integrative Genomics Viewer)50. All raw and processed files can be accessed on the Gene Expression Omnibus (GEO).

first: Yucong

last: Jiang

first: Yuehong

last: Shi

first: Yingying

first: Xingju

last: Song


title: Nuclear Pyruvate Dehydrogenase Complex regulates EIN2-directed Histone Acetylation and Transcriptional Regulation in the Ethylene Response. [RNA-Seq]

status: Public on Dec 01 2023

city: Austin

first: Zhengyao

last: Shao

state: TX

address: 2506 Speedway, NMS 5.324

department: MBS

institute: University of Texas at Austin

summary: Next-generation sequencing (NGS) has been used to study the differential gene expression in Arabidopsis etiolated seedlings under air and ethylene treatment. The goal of this study is to investigate how pyruvate dehydrogenase complex is  involved in transcriptional regulation in response to ethylene.

overall_design: Three-day-old etiolated Arabidopsis seedling mRNA profiles of pdc mutants were generated by sequencing, in 2 replications, using Illumina HiSeq 2000

first: Hong

last: Qiao


title: ASCL1 a pioneer factor that induces subtype switching and characterizes adrenergic neuroblastoma

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

overall_design: Refer to individual Series


title: Nuclear Pyruvate Dehydrogenase Complex regulates EIN2-directed Histone Acetylation and Transcriptional Regulation in the Ethylene Response.


title: Translation in Bacillus subtilis is spatially and temporally coordinated during sporulation

status: Public on Dec 06 2023

city: Warsaw

first: Agata

middle: L.

last: Starosta

address: Pawińskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

summary:
The transcriptional control of sporulation in Bacillus subtilis is reasonably well understood, but its translational control is underexplored. Here, we use RNA-seq, ribosome profiling and fluorescence microscopy to study the translational dynamics of B. subtilis sporulation. We identify two events of translation silencing and describe spatiotemporal changes in subcellular localization of ribosomes during sporulation. We investigate the potential regulatory role of ribosomes during sporulation using a strain lacking zinc-independent paralogs of three zinc-dependent ribosomal proteins (L31, L33 and S14). The mutant strain exhibits delayed sporulation, reduced germination efficiency, dysregulated translation of metabolic and sporulation-related genes, and disruptions in translation silencing, particularly in late sporulation.

This SuperSeries is composed of the SubSeries listed below.

first: Olga

last: Iwańska

first: Przemysław

last: Latoch

first: Natalia

last: Kopik

first: Mariia

last: Kovalenko

first: Małgorzata

last: Lichocka

first: Remigiusz

last: Serwa


title: ATAC-seq analysis for GI-MEN DOX-ASCL1 cells and GI-MEN DOX-ASCL1-4TFs cells.

first: Tze King

summary: ATAC-seq analysis was performed in an neuroblastoma cell line to analyze chromatin opening of Gi-MEN cells under four different conditions.

overall_design: Cells were freshly collected to perform ATAC assay.  DNA was analyzed by Illumina Hiseq 4000.

first: Wang


title: Transcriptome profiling of hos2-deleted mutant under glycerol-based growth in Saccharomyces cerevisiae

status: Public on Nov 19 2023

city: Taipei

first: Wei-Han

last: Lin

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: To investigate the function of the histone deacetylase Hos2 under the glycerol-based growth condition in S. cerevisiae, we analyzed the gene expression profiles by RNA-Seq and performed comparative analyses between the wild-type and hos2-deleted strains.

overall_design: We performed gene expression profiling analysis using data from RNA-Seq of the wild-type and hos2-deleted strains under the YPGly condition. Three biological repeats for each strain.

first: Jun-Yi

last: Leu


title: Identification of a novel, tunable interface in the S.pombe HP1 protein, Swi6, that underpins epigenetic inheritance.

status: Public on Nov 27 2023

city: Waltham

first: Melissa

last: Seman

address: 415 South St

institute: Brandeis University

summary: HP1 proteins bind dynamically to H3K9 methylation and are essential for establishing and maintaining transcriptionally silent epigenetic states, known as heterochromatin. HP1 proteins can dimerize, forming a binding interface that interacts with and recruits diverse chromatin-associated factors. HP1 proteins rapidly evolve through sequence changes and gene duplications, but the extent of variation required to achieve functional specialization is unknown. To investigate how changes in amino acid sequence impact epigenetic inheritance, we performed a targeted mutagenesis screen of the dimerization and protein interaction domain of the S.pombe HP1 homolog Swi6. We discovered that substitutions mapping to an auxiliary motif in Swi6 outside the dimerization interface can lead to complete functional divergence. Specifically, we identified point mutations at a single amino acid residue that resulted in either persistent gain or loss of function in epigenetic inheritance without affecting heterochromatin establishment. These substitutions increase Swi6 chromatin occupancy in vivo and alter Swi6-protein interactions that selectively affect H3K9me inheritance. Based on our findings, we propose that relatively minor changes in Swi6 amino acid composition can lead to profound changes in epigenetic inheritance, underscoring the remarkable plasticity associated with HP1 proteins and their ability to evolve new functions.

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) for H3K9me2 and H3K9me3


title: ONECUT2 Activates Diverse Resistance Drivers of Androgen Receptor-Independent Heterogeneity in Prostate Cancer (RNA-seq)

first: Qian

last: Yang

overall_design: Compare the transcriptome changes after the overexpression OC2 gene in LNCaP and LAPC4 cells.Compare the transcriptome changes after the knockdown of OC2 gene in LNCaP cells. Compare the transcriptome changes after 7 days of vehicle control, enzalutamide treatment (10uM), and combination treatment (Enzalutamide (10uM) + OC2 inhibitor (10uM)).

first: Chen

last: Qian

first: Mirja

last: Rotinen

first: Rongrong

last: Huang

first: Hyoyoung

last: Kim

first: Brad

last: Gallent

first: Yiwu

last: Yan

first: Radu

last: Cadaneanu

first: Baohui

last: Zhang

first: Salma

last: Kaochar

first: Stephen

last: Freedland

first: Edwin

last: Posadas

first: Leigh

last: Ellis

first: Dolores

last: Di Vizio

first: Colm

last: Morrissey

first: Peter

last: Nelson

first: Lauren

last: Brady

first: Ramachandran

last: Murali

first: Moray

last: Campbell

first: Wei

first: Beatrice

last: Knudsen

first: Elahe

last: Mostaghel

first: Huihui

last: Ye

first: Isla

last: Garraway

first: Sungyong

last: You

first: Michael

last: Freeman


title: Med12 ablation promotes anti-tumor function by enhancing tumor intrinsic immunogenicity in Pancreatic ductal adenocarcinoma [mouse RNA-seq]

first: JIng

last: Xue

first: Yingying

last: Tang

first: Jing


title: Nuclear Pyruvate Dehydrogenase Complex regulates EIN2-directed Histone Acetylation and Transcriptional Regulation in the Ethylene Response.[ChIP-Seq]

first: Zhengyao

last: Shao

summary: Next-generation sequencing (NGS) has been used to study the histone acetylation  in Arabidopsis etiolated seedlings under air and ethylene treatment. The goal of this study is to investigate how pyruvate dehydrogenase complex is  involved in histone acetylation changes  in response to ethylene.

overall_design: Three-day-old etiolated Arabidopsis seedling genome histone acetylation profiling by high throughput sequencing of pdc mutants were generated by sequencing, in 2 replications, using Illumina HiSeq 2000

first: Hong

last: Qiao


title: shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production [DU-145 cells]

status: Public on Nov 17 2023

city: Moscow

first: Anton

last: Zhiyanov

address: 20 Myasnitskaya ulitsa

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

type: Non-coding RNA profiling by high throughput sequencing

summary: miRNA overexpression strategy based on RNA Polymerase (Pol) III mediated expression of short hairpin RNA (shRNA) coding particular miRNA is widely used for miRNA functional studies. For some miRNAs, e.g., encoded in the genome as a part of a polycistronic miRNA cluster, it is most likely the only way for their individual stable overexpression. Here we have revealed that extra \texttt{U} residues (up to five) added Pol III at the 3$'$-end of the transcribed shRNA associated with a shift in the Dicer cleavage position of the shRNA. This results in the undesirable formation of 5$'$-end miRNA isoforms (5$'$-isomiRs), which have a significantly altered seed region compared to the initially encoded canonical hsa-miR-93-5p. The predominant expression of 5$'$-isomiRs without three or four first nucleotides instead of the canonical isoform could be disclosed based on miRNA-Seq analysis. Moreover, mRNA sequencing data showed that the 5$'$-isomiRs of hsa-miR-93-5p presumably regulate their own mRNA targets. Thus, omitting miRNA-Seq analysis may lead to erroneous conclusions regarding revealed mRNA targets and possible molecular mechanisms in which studied miRNA is involved.

overall_design:
DU-145 (prostate cancer) cell line was transduced by lentiviral particles coding one of the three types of shRNA to achieve stable overexpression of hsa-miR-93-5p.
All shRNA constructs contained the sequence of the canonical hsa-miR-93-5p and differed in their loop sequence only (5'-CUACCUGCACGAACAGCACUUUG-3' -- upper stem; 5'-CUCGAG-3', 5'-UUCAAGAGA-3', 5'-UUCUAAAA-3' -- stem loops; 3'-...UUGAUGGACGUGCUUGUCGUGAAAC-5' -- lower stem).
To comprehensively understand the overexpressed isoforms of hsa-miR-93-5p and their impact on the cellular transcriptome profile, we conducted sequencing of both miRNAs (3 repeats for the control, 3 repeats for the first loop and 2 repeats for other ones) and mRNAs (3 repeats for control and all loops).

first: Diana

last: Maltseva

first: Ivan

last: Kirillov

first: Daria

last: Averinskaya

first: Roman

last: Suvorov

last: Gubani

first: Anna

last: Kudriaeva

first: Alexey

last: Belogurov

first: Alexander

last: Tonevitsky


title: ChIP-seq analysis for H3K27ac in GI-MEN DOX-ASCL1 cells and for ASCL1-HA in GI-MEN DOX-ASCL1-tag-HA cells.

first: Tze King

last: Tan

summary: ChIP-seq analysis was performed in an neuroblastoma cell line to analyze DNA bindings of H3K27ac in GI-MEN DOX-ASCL1 cells and ASCL1-HA in GI-MEN DOX-ASCL1-tag-HA cells.

overall_design: Cells were crosslinked with formaldehyde for 10 min.  DNA was enriched by chromatin-immunoprecipitation (ChIP) and analyzed by Illumina Hiseq 4000.  A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment.  ChIP was performed using an antibody against H3K27ac (ab4729, abcam) or HA (Cat#3724, Cell Signalling Technology) Antibody.

first: Wang

last: Lu

first: Tze

first: Takaomi

last: Sanda


title: Classifying pathogenic variants in amyloid beta using intramolecular genetic interaction profiling

status: Public on Nov 15 2023

city: Barcelona

first: Mireia

last: Seuma

state: Barcelona

address: Carrer de Baldiri Reixac, 10, 12

country: Spain

institute: Institute for Bioengineering of Catalonia

summary: Changes in the amino acid sequences of proteins cause thousands of human genetic diseases. However, only a subset of variants in any protein is typically pathogenic, with variants having a diversity of molecular consequences. Determining which of the thousands of possible variants in any protein have similar molecular effects is very challenging, but crucial for identifying pathogenic variants, determining disease mechanisms, understanding clinical phenotypic variation, and developing targeted therapeutics. Here we present a general method to classify variants by their molecular effects that we term intramolecular genetic interaction profiling. The approach relies on the principle that variants with similar molecular consequences have similar genetic interactions with other variants in the same protein. These intramolecular genetic interactions are straightforward to quantify for any protein with a selectable function. We apply intramolecular genetic interaction profiling to amyloid beta, the protein that aggregates in Alzheimer’s disease (AD) and is mutated in familial AD (fAD). Genetic interactions identify two classes of gain-of-function variants, with all known familial Alzheimer’s disease variants having very similar genetic interaction profiles, consistent with a common gain-of-function mechanism leading to pathology.  We believe that intramolecular genetic interaction profiling is a powerful approach for classifying variants in disease genes that will empower rare variant association studies and the discovery of disease mechanisms.

overall_design: Systematic measurement of the amyloid nucleation of mutations at the C-terminus of Amyloid beta (amino acid residues 28-42), labelled as 'fingerprint' mutations; in combination with mutations at the N-terminus of Amyloid beta (amino acid residues 1-27), labelled as 'query' mutations. The selection experiment to quantify amyloid nucleation was performed in 3 biological replicates, each of them with one input sample (before selection) and one output sample (after selection).

first: Ben

last: Lehner

first: Benedetta

last: Bolognesi


title: Toll-like receptor agonist CBLB502 protects against radiation-induced intestine injury in mice

status: Public on Nov 10 2023

city: Beijing

first: wang

last: qiong

address: 27 Taiping Road

institute: Beijing Institute of Radiation Medicine

summary: Radiation-induced intestinal injury is one of the most common complications of abdominal and pelvic radiotherapy. Severe intestinal injury caused by ionizing radiation (IR) has a high mortality rate, which is a worldwide problem requiring urgent attention. IR can cause intestinal tissue damage, inflammatory cell infiltration and pro-inflammatory cytokine release. However, methods to protect against radiation-induced intestinal injury are limited. CBLB502, a Toll-like receptor 5 (TLR5) agonist from Salmonella flagellin, has radioprotective effects on various tissues and organs. In order to further explore the molecular mechanism of IR-induced intestinal injury and the mechanism of protective effect of CBLB502 on IR-induced intestinal injury, mice were given CBLB502 and irradiated with different doses at different times. The survival rate, body weight, hemogram and histopathology of the mice were analyzed. The results showed that CBLB502 before IR can reduce intestinal injury induced by IR. RNA-seq analysis showed that different doses and different time of IR induced different damage mechanisms to promote gene regulation patterns. In addition, CBLB502 exerts its protective effect on IR-induced intestinal injury mainly through biological processes such as immune response. Notably, CBLB502 protected against intestinal injury only after IR, and might play a protective role by reversing the regulation of IR-induced genes. Therefore, this paper basically describes the mechanism of IR-induced intestinal injury and the potential molecular protective mechanism of CBLB502, which provides a basis for further research on functional genes and molecular mechanisms that mediate protection against IR-induced injury in the future.

overall_design: C57BL/6 male mice (6-8 weeks old) were maintained in SFP room under light:dark = 1:1. They were randomly divided into 7 groups: irradiated with 6Gy and sampled at 6h (6Gy6h), 15Gy6h, 15Gy24h, 15Gy3d, treated with radioprotectant CBLB502, pretreated with CBLB502 at 0.5h before 15Gy (15Gy+CBLB502), PBS used as control for CBLB502 (PBS only), 10 mice in each group. Animals were irradiated with 60Co γ-rays radiation source at the Beijing Institute of Radiation Medicine at a dose rate of 72R/min.

first: Qiong

last: Wang

first: Changhui

last: Ge

first: Xiaofei

last: Zheng


title: Pathogenic role of alarmin IL-33 in a mouse model of SARS-CoV-2 infection

status: Public on Nov 13 2023

city: Galveston

first: Lynn

last: Soong

address: 301 University Blvd

department: Microbiology and Immunology

institute: University of Texas Medical Branch

summary: Male WT C57BL/6j mice (stock #000664, age 8-10 wks) and IL-33 knockout (KO) mice (B6 background) were anesthetized via isoflurane, followed by the intranasal infection with mouse adapted SARS-CoV-2 CMA3p20 (5×10^5 PFU). Mock mice were administrated with identical volumes of cell culture medium. Lungs were perfused with cold PBS and were harvested at days 2 and 4 post-infection. Lung RNA was isolated by Qiagen RNeasy Kits, followed by the Poly (A) RNA sequencing. We then performed differential expression analysis, meta-analysis, and gene set enrichment anaylsis using data obtained by RNA-seq of mock, IL-33 KO, and WT SARS-CoV-2-infected mice.

overall_design: RNA isolated from lungs of SARS-CoV-2-infected mice was and analyzed using RNAseq.

first: Yuejin

last: Liang


title: Single-cell transcriptional mapping of the developing human brainstem

status: Public on Oct 31 2023

city: XiaMen

first: chao

last: tu

state: FuJian

address: JiMei street,668

department: Center for precision medicine

institute: HuaQiao university

summary: The anatomical relationship of the brainstem is complex, which is the center of respiratory circulation in the human body. We used single cell RNA sequencing (scRNA-seq) to analyze the cellular molecular diversity of the fetal brainstem.

overall_design: Fetal brainstem tissue from 9 to 12 weeks was isolated and analyzed using scRNAseq.

first: Chao

last: Tu

first: Tao

last: Sun


title: ASCL1 induces neurogenesis in human Muller glia

status: Public on Oct 30 2023

city: Seattle

first: Thomas

last: Reh

state: Washington

address: 1959 NE Pacific Street, UW School of Medicine, Seattle, WA 98195

department: Department of Neurobiology and Biophysics

institute: University of Washington

summary: In mammals, loss of retinal cells due to disease or trauma is an irreversible process which can lead to blindness. Interestingly, regeneration of retinal neurons is a well-established process in some non-mammalian vertebrates and is driven by the Muller glia (MG), which are able to re-enter the cell cycle and reprogram into neurogenic progenitors upon retinal injury or disease. Progress has been made to restore this mechanism in mammals to promote retinal regeneration: MG can be stimulated to generate new neurons in vivo in the adult mouse retina after the over-expression of the pro-neural transcription factor Ascl1. In this study, we applied the same strategy to reprogram human MG derived from fetal retina and retinal organoids into neurons. Combining scRNA-seq, scATAC-seq, Immunofluorescence, and electrophysiology we demonstrate that human MG can be reprogrammed into neurogenic cells in vitro.

overall_design: To study the development of the Muller glial cell over time in the human retina, fetal retinal tissues from a D59 and D76 samples were processed with the Multiome kit (snRNA-seq and snATAC-seq). For the D76 sample, the central part of the retina was isolated from the periphery and samples were further processed individually. We also include in this submission scRNA-seq data from the over expression of ASCL1 in human fetal Muller glia cultures. For the reprogramming paradigme we used Muller glia in vitro cultures derived from Retinal organoids and Retinospheres were generated. Cultures were then infected with a lentivirus driving the expression of the pro-neural transcription factor ASCL1 prior to processing with the 10x genomics platform.

first: Juliette

last: Wohlschegel

first: Connor

last: Finkbeiner

first: Dawn

last: Hoffer

first: Faith

last: Kierney

first: Aric

last: Prieve

first: Isabel

last: Ortuno-Lizaran

first: Alexandria

middle: D

last: Murry

first: Alex

last: Haugan

first: Fred

last: Rieke

first: Sam

last: Golden


title: Single-nucleus transcriptomics of epicardial adipose tissue from female pigs reveals effects of exercise training on resident innate and adaptive immune cells

status: Public on Nov 05 2023

city: College Station

first: James

last: Cai

address: 4458 TAMU

department: Veterinary Intergrative Biosciences

institute: Texas A&M University

summary: Coronary artery disease (CAD) is a leading cause of death in women. Although exercise mitigates CAD, the mechanisms by which exercise impacts epicardial adipose tissue (EAT) are unknown. We hypothesized that exercise promotes an anti-inflammatory microenvironment in EAT from female pigs. Female Yucatan pigs (n=7) were assigned to sedentary (SED) or exercise (EX) treatments and coronary arteries were occluded (O vs N) with an ameroid to mimic CAD. EAT was collected for bulk and single-nucleus  transcriptomic sequencing (snRNA-seq). Clustering analysis revealed nine cell types in EAT with the fibroblast and macrophage populations predominantly from O-EX EAT and the T cell population predominantly from the N-EX EAT. Exercise upregulated G-protein coupled receptor, S100 family, and FAK pathways and downregulated the coagulation pathway. Exercise caused increased interaction between immune cells and endothelial and mesenchymal cells in the insulin-like growth factor pathway and between endothelial cells and other cell types except B cells in the platelet endothelial cell adhesion molecule pathway 1. Coronary occlusion impacted the largest number of genes in T and endothelial cells. Genes related to fatty acid metabolism were the most highly upregulated in non-immune cells from O-EX EAT. Sub-clustering of endothelial cells revealed that N-EX EAT separated from other treatments. In conclusion, exercise training increased interaction amongst immune and mesenchymal and endothelial cells in female EAT. Exercise was minimally effective at reversing alterations in gene expression in endothelial and mesenchymal cells in EAT surrounding occluded coronary arteries. These findings lay the foundation for future work focused on the impact of exercise on cell types in EAT from women.

overall_design: Animals were divided into two exercise (sedentary vs exercised) and two coronary artery (non-occluded and occluded) treatment groups. Surgeries were performed to place an ameroid constrictor (2.5-3.5 mm) around the proximal left circumflex artery. The ameroid constrictor progressively narrowed the artery and induced an inflammatory response resulting in total obstruction occurring at approximately two-three weeks post-operatively. Pigs recovered for eight weeks before the exercise training experimental regimen was initiated and maintained for 14 weeks. Speed and duration of the exercise training sessions were progressively increased so that during the last three weeks of training, animals ran at 4-5.5 mph for 60 minutes and at 6 mph for 5-15 minutes. Sedentary pigs maintained normal activity in their pens throughout the experimental protocol.

first: Irshad

last: Ahmad

first: Shreyan

last: Gupta

first: Patricia

last: Faulkner

first: Destiny

last: Mullens

first: Micah

last: Thomas

first: Sharanee

last: Sytha

first: Ivan

last: Ivanov

first: Cristine

last: Heaps

first: Annie

last: Newell-Fugate


title: Independent compartmentalization of functional, metabolic, and transcriptional maturation of hiPSC-derived cardiomyocytes

status: Public on Oct 14 2023

city: Chicago

first: Paul

middle: W.

last: Burridge

state: IL

address: 320 East Superior Street

institute: Northwestern University

summary: To investigate transcriptional changes on three different cell lines cultured in 8 different maturation media formulations compared to maintanence media

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 19c3, 25c3, and GW132c2B cell lines cultured in RBAI, complete maturation media with galactose (MMc), complete maturation media with glucose (MMc-glu) complete maturation media with no fatty acids (MMc-no FA), complete maturation media with no fatty acids or BSA (MMc-CD), simple maturation media with galactose (MMs), simple maturation media with glucose (MMs-glu), simple maturation media with no fatty acids (MMs-no FA), simple maturation media with no fatty acids or BSA (MMs-CD), with one independent biological replicates (derived from different passages) for each sample.

first: K

last: AFetterman

first: Malorie

last: Blancard


title: Subcellular refinement of RNA binding protein target interactions with colocalization CLIP [CLIP-seq]

status: Public on Oct 25 2023

city: Cleveland

first: Soon Yeul

last: Yi

state: OH

address: CWRU Wood Research Building W127A, 2109 Adelbert Rd,

department: Biochemistry

institute: Case Western Reserve University

summary: RNA binding proteins (RBPs) are essential for RNA metabolism and have profound impacts in both health and disease. The subcellular organization of RBP interaction networks with target RNAs remains largely unexplored. Here, we develop colocalization CLIP, a method that combines CrossLinking and ImmunoPrecipitation (CLIP) with proximity labeling, to explore in-depth the subcellular RNA interactions of the well-studied RNA-binding protein HuR. Using this method, we uncover HuR's dynamic and location-specific interactions with RNA, revealing alterations in sequence preferences and interactions in the nucleus, cytosol, or stress granule compartments. We uncover HuR's unique binding preferences within stress granules during arsenite stress, illuminating intricate interactions that conventional methodologies cannot capture. Overall, coCLIP provides a powerful method for revealing RBP:RNA interactions based on localization, and lays the foundation for an advanced understanding of RBP models that incorporate subcellular location as a critical determinant of their functions.

overall_design: To investigate nuclear/cytoplasm/stress granule-specific binding behaviors of HuR, three different cell lines expressing ascorbate peroxidase protein in the respective compartments were generated. Then, proximity labeling of the local proteome was performed by treating the cells with hydrogen peroxide and biotin phenol. Following proximity labeling, UV crosslinking and immunoprecipitation for HuR followed by high-throughput sequencing (CLIP-Seq) were performed in the three cell lines. HuR CLIP-Seq was performed on cytoplasm and nuclear fraction as comparison groups.

first: Joseph

middle: M

last: Luna

first: Soon


title: O-GlcNAcylation promotes Palbociclib resistance in breast cancer by regulating MITF nuclear translocation

status: Public on Oct 10 2023

city: WASHINGTON

first: Wenge

last: Zhu

state: DC

address: 800 22ND ST NW, Room 8480, Science & Engineering Hall

department: Biochemistry and Molecular Medicine

institute: George Washington University


title: Detection of CD133+ cell circular RNA in sepsis patients and normal individuals

status: Public on Oct 09 2023

city: Guangzhou

first: Weixin

last: Guo

address: No. 106, Zhongshan 2nd Road

institute: Guangdong Provincial People’s Hospital

summary:
Analysis of differential expression of cyclic RNA in CD133 cells between sepsis patients and normal individuals
Analysis of differential expression of cyclic RNA in CD133 cells between sepsis patients and normal individuals

overall_design: The experiment was divided into a sepsis group and a control group, with a total of 9 male sepsis patients and 9 normal males aged between 65 and 90 years old. Blood samples were taken within 24 hours of diagnosis of sepsis, with each group consisting of 3 males, and each group had 3 replicates.


title: Sex-specific resilience of neocortex to food restriction

city: Edinburgh

first: Emily

last: Osterweil

state: Scotland

address: Hugh Robson Building, 15 George Square

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

summary: Mammals have evolved sex-specific adaptations to reduce energy usage in times of food scarcity. These adaptations are well described for peripheral tissue, though much less is known about how the energy-expensive brain adapts to food restriction, and how such adaptations differ across the sexes. Here, we examined how food restriction impacts energy usage and function in the primary visual cortex (V1) of adult male and female mice. Molecular analysis and RNA sequencing revealed that food restriction modulated canonical, energy-regulating pathways including oxidative phosphorylation, AMP-activated protein kinase (AMPK) and mammalian target of rapamycin (mTOR) signalling, significantly in males but not in females V1. Moreover, we found that in contrast to males, food restriction in females non-significantly affected V1 ATP usage and visual coding precision (assessed by orientation selectivity). Decreased serum leptin is necessary for triggering energy-saving changes in male mouse V1 during food restriction. Consistent with this result, we found a significant decrease of serum leptin in food-restricted males but no significant change in food-restricted females. Collectively, our findings demonstrate that cortical function and energy usage in female mice are more resilient to food restriction than in males. The neocortex, therefore, contributes to sex-specific, energy-saving adaptations in response to metabolic challenge.

overall_design: Primary visual cortex (V1) tissue was collected from adult male and female mice(7-9 weeks of age) that had either access to ad libitum food or were food restricted for 2-3 weeks to 85% of their baseline bodyweight prior to experimentation.  Mice were briefly anesthetized and decapitated and tissue snap-frozen. RNA isolation was performed and integrity confirmed (RIN>7) and samples were sent to Oxford genomics Centre for sequencing using Illumina NovaSeq6000

first: Zahid

last: Padamsey

first: Danai

last: Katsanevaki

last: Maeso

first: Manuela

last: Rizzi

first: Nathalie

last: Rochefort


title: Subcellular refinement of RNA binding protein target interactions with colocalization CLIP [RNA-seq]

overall_design: To investigate transcriptome changes in APEX2 engineered cell lines during cellular stress, we performed standard RNA-Seq experiments for three different engineered cell lines (APEX-NLS, APEX-NES, APEX-G3BP1 expressing Huh-7.5 cells) in mock and sodium arsenite stress conditions.


title: O-GlcNAcylation promotes Palbociclib resistance in breast cancer by regulating MITF nuclear translocation [ChIP-seq]

summary: Cyclin-dependent kinases 4 and 6 (CDK4/6) are essential drivers of the cell cycle and are also critical for the initiation and  progression of diverse malignancies. Pharmacological inhibitors targeting CDK4/6 have demonstrated significant activity against various tumor types such as breast cancer. However, resistance to CDK4/6 inhibitors (CDK4/6i) (such as palbociclib) remains an immense obstacle in clinical and the underlying mechanisms have not been fully understood.  Using quantitative high-throughput combinational screen (qHTCS) and genomic sequencing, we report that the Microphthalmia-associated transcription factor (MITF), was significantly elevated in palbociclib-resistance cells. Inhibition of MITF can enhance the therapeutic efficacy of Palbociclib and surmount Palbociclib resistance both in vitro and in vivo. Mechanistically, we found that O-GlcNAc transferase (OGT) modifies MITF with O-GlcNAcylation at Serine 49 (Ser49) within its nuclear localization signal (NLS), thereby promoting MITF binding to importin α/ β and facilitating its nuclear transportation, which is crucial in regulating senescence. Significantly, clinical studies also confirm that MITF was elevated in palbociclib-resistance patients. Collectively, these results reveal a previously unrecognized mechanism by which MITF-mediated palbociclib resistance, and provide valuable insights for the development of innovative therapeutic strategies in future clinical contexts.

overall_design: Chromatin immunoprecipitated DNA-sequencing (ChIP) for MITF in MCF-7 Wild type (WT) and MCF-7 Palbociclib resistance (PR) cell lines

first: Yi

last: Zhang


title: Single-nucleus sequencing reveals enriched expression of genetic risk factors in Extratelencephalic Neurons sensitive to degeneration in ALS

status: Public on Oct 01 2023

city: Cambridge

first: Francesco

last: Limone

address: 7 divinity avenue, Bauer Laboratory 008

institute: harvard university

summary: Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder characterised by a progressive loss of motor function. The eponymous spinal sclerosis observed at autopsy is the result of the degeneration of extratelencephalic neurons, Betz cells (ETNs, Cortico-Spinal Motor Neuron). It remains unclear why this neuronal subtype is selectively affected. To understand the unique molecular properties that sensitise these cells to ALS, we performed RNA sequencing of 79,169 single nuclei from cortices of patients and controls. In unaffected individuals, we found that expression of ALS risk genes was significantly enriched in THY1+-ETNs and not in other cell types. In patients, these genetic risk factors, as well as genes involved in protein homeostasis and stress responses, were significantly induced in a wide collection of ETNs, but not in neurons with more superficial identities. Examination of oligodendroglial and microglial nuclei revealed patient-specific changes that were at least in part a response to alterations in neurons: downregulation of myelinating genes in oligodendrocytes and upregulation of a reactive state connected to endo-lysosomal pathways in microglia. Our findings suggest that the selective vulnerability of extratelencephalic neurons is partly connected to their intrinsic molecular properties sensitising them to genetics and mechanisms of degeneration.

overall_design:
Pooled "villages" of lower induced Motor Neurons differentiated from human stem-cells (ALS or control) were analyzed using scRNAseq

>>>Raw data are not available due to patient privacy concerns<<<

first: Daniel

middle: A

last: Mordes

first: Alexander

last: Couto

first: Brian

last: Joseph

first: Jana

last: Mitchell

first: Martine

last: Therrien

first: Sulagna

last: Dia Ghosh

last: Meyer

first: Yingying

first: Melissa

last: Goldman

first: Laura

last: Bortolin

first: Inma

last: Cobos

first: Irena

last: Kadiu

first: Steven

last: McCarroll

first: Beth

last: Stevens

first: Olli

last: Pietiläinen

first: Aaron

last: Burberry

first: Kevin

last: Eggan


title: Distinct transcriptional profiles of maternal and fetal placental macrophages at term are associated with gravidity

status: Public on Oct 02 2023

city: San Francisco

first: Stephanie

last: Gaw

address: 513 Parnassus Avenue, Health Sciences East 1622

department: Obstetrics, Gynecology and Reproductive Sciences

institute: University of California, San Francisco

summary: Maternal intervillous monocytes (MIMs) and fetal Hofbauer cells (HBCs) are myeloid-derived immune cells at the maternal-fetal interface. Little is known regarding the molecular phenotypes and roles of these distinct monocyte/macrophage populations. Here, we used RNA sequencing to investigate the transcriptional profiles of MIMs and HBCs in six normal term pregnancies. Our analyses revealed distinct transcriptomes of MIMs and HBCs. Genes involved in differentiation and cell organization pathways were more highly expressed in MIMs vs. HBCs. In contrast, HBCs had higher expression of genes involved in inflammatory responses and cell surface receptor signaling. Maternal gravidity influenced monocyte programming, as expression of pro-inflammatory molecules was significantly higher in MIMs from multigravidas compared to primigravidas. In HBCs, multigravidas displayed enrichment of gene pathways involved in cell-cell signaling and differentiation. In summary, our results demonstrated that MIMs and HBCs have highly divergent transcriptional signatures, reflecting their distinct origins, locations, functions, and roles in inflammatory responses. Our data further suggested that maternal gravidity influences the gene signatures of MIMs and HBCs, potentially modulating the interplay between tolerance and trained immunity. The phenomenon of reproductive immune memory may play a novel role in the differential susceptibility of primigravidas to pregnancy complications.

overall_design:
We isolated paired maternal intervillous monocytes and fetal hofbauer cells from term human placenta (n=6) and conducted RNA-sequencing.
First, we compared the transcirptional profiles of maternal intervillous monocytes and fetal Hofbauer cells.
Second, we investigated the impact of maternal gravidity by comparing primigravida vs. multigravida in each cell type.

first: Nida

last: Ozarslan

first: Joshua

last: Robinson

first: Sirirak

last: Buarpung

first: M

last: Kim

first: Megan

last: Ansbro

first: Jason

last: Akram

first: Dennis

last: Montoya

first: Moses

last: Kamya

first: Abel

last: Kakuru

first: Grant

last: Dorsey

first: Philip

last: Rosenthal

first: Genhong

last: Cheng

first: Margaret

last: Feeney

first: Susan

last: Fisher


title: Evolutionary adaptation of the chromodomain of the HP1 protein Rhino allows th eintegration of heterochromatin and DNA sequence signals [ChIP-seq]

status: Public on Oct 03 2023

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

summary: Members of the diverse heterochromatin protein 1 (HP1) family of proteins play crucial roles in heterochromatin formation and maintenance. Despite the similar affinities of their chromodomains for di- and tri-methylated histone H3 lysine 9 (H3K9me2/3), different HP1 proteins exhibit distinct chromatin binding patterns, presumably due to their interactions with various specificity factors. Here, we elucidate the molecular basis of the protein-protein interaction between the HP1 protein Rhino, a critical factor of the Drosophila piRNA pathway, and Kipferl, a DNA sequence-specific C2H2 zinc finger protein and Rhino guidance factor. Through phylogenetic analyses, structure prediction, and in vivo genetics, we identify a single amino acid change within Rhino’s chromodomain, G31D, that does not affect H3K9me2/3 binding but abolishes the specific interaction between Rhino and Kipferl. Flies carrying the rhinoG31D mutation phenocopy kipferl mutant flies, with Rhino redistributing from piRNA clusters to satellite repeats, causing pronounced changes in the ovarian piRNA profile of rhinoG31D flies. Thus, Rhino’s chromodomain serves as a dual-specificity module, facilitating interactions with both a histone mark and a DNA-binding protein.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MTD-Gal4 knock-downs of control, rhino and CG2678.

first: Lisa

last: Baumgartner

first: Jonathan

last: Ipsaro

first: Ulrich

last: Hohmann

first: Alexander

last: Schleiffer

first: Peter

last: Duchek

first: Julius

last: Brennecke


title: Evolutionary adaptation of the chromodomain of the HP1 protein Rhino allows th eintegration of heterochromatin and DNA sequence signals

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

overall_design: Refer to individual Series


title: TrxA-mediated regulation of protein synthesis contributes to the maintenance of carbon and nitrogen balance in cyanobacteria.

status: Public on Sep 24 2023

city: Sevilla

first: Manuel Jesús

last: Mallén-Ponce

state: Sevilla

address: Americo Vespucio 49

department: IBVF

institute: CSIC-US

summary: Thioredoxins play an essential role in regulating enzyme activity upon response to environmental changes, especially in photosynthetic organisms. These are crucial for the regulation of metabolism in cyanobacteria, but the key central processes redox-regulated remain to be determined. Physiological, metabolic and transcriptomic characterization of a conditional mutant of the essential trxA gene in Synechocystis (STXA2) revealed that reduced TrxA levels alter cell morphology and enter in a dormant-like state. TrxA depletion in the STXA2 strain inhibited protein synthesis and led to changes in amino acid pools and nitrogen/carbon reserve polymers, accompanied by oxidation of the Elongation Factor EF-Tu. Transcriptomic analysis of TrxA depletion in STXA2 showed a robust transcriptional response. Genes that responded negatively were grouped in a large cluster and were directly related to photosynthesis, ATP synthesis and CO2 fixation, while genes that responded positively were grouped in different clusters and related to respiratory electron transport, carotenoids synthesis, amino acid metabolism and protein degradation, among others. Regulation of cyanobacterial metabolism is complex and fine-tuned, our results link TrxA to the switch from anabolic to maintenance metabolism in cyanobacteria, regulating carbon and nitrogen balance.

overall_design: To investigate a possible function of TrxA in central cellular processes, we established a mutant strain (STXA2) in which the trxA gene has been knocked down

first: Manuel J

first: María José

last: Huertas

first: Francisco J

last: Florencio Bellido


title: Distinct spectrum of ciliopathic diseases results from de novoTUBB4B variants through differential effects on organelle-specific microtubules

status: Public on Sep 27 2023

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh, The Institute of Genetics and Cancer

summary: We establish a necessary and non-redundant function for TUBB4B in building centrioles and axonemes of multiciliated cells placing ciliopathies more broadly into human tubulinopathies.

overall_design: RNA-seq data of primary cultured nasal epithelial cells from biopsies of controls and patients carrying p.P259L and pP358S variants of TUBB4B

first: Patricia

last: Yeyati


title: Integrative epigenomic and transcriptomic anlaysis of odontogenic differentiation of dental pulp stem cells [RNA-seq]

status: Public on Sep 29 2023

city: Okayama

first: Shigeki

last: Suzuki

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Operative Dentistry

country: Japan

institute: Okayama University

summary: Chromatin accessibility is key epigenomic regulatory mechanisms of transcription. Herein, to profile open chromatin maps and transcriptional feature associated with odontogenic tropism of dental pulp stem cells (DPSCs), we conducted integrative analysis of epigenomic alteration and transcriptome changes during odontogenic differentiation of DPSCs. DPSCs were long-term cultured in odontogenic induction medium to evaluate differentiation abilities. ATAC-seq and RNA-seq samples were collected before and after the 9-day culture. One of the day 9 specific-super-enhancer was constructed in ALPL (Alkaline Phosphatase, Biomineralization Associated) intragenic region in which all the day 9-specific open chromatin peaks were included and BMP-mediated Smad binding element are specifically accumulated.  These results suggest that the specific local chromatin regions were selectively opened and, particularly, super-enhancers were constructed, which was able to guide differentiative transcriptional factors such as Smad1/4 to their target gene loci in differentiating DPSCs; hence, epigenetic modifications such as histone deacetylase (HDACs) inhibitor application have therapeutic potential for DPSCs-induced dentin/pulp regeneration.

overall_design: RNA-seq and ATAC-seq samples collected before and aftehr the differentiation. Sonicated DNA fragments were used as input in ATAC-seq analysis.


title: Robust reprogramming of glia into neurons by inhibition of Notch signaling and NFI factors in adult mammalian retina.

status: Public on Nov 03 2023

city: Ann Arbor

first: Thanh

last: Hoang

state: MI

address: 1000 Wall St, Brehm Building , Room 7426

department: Ophthalmology

institute: University of Michigan

summary: scRNA-Seq was performed on  adult control and Rbpj-deleted mouse retinas to profile changes in gene expression.

overall_design: scRNA-seq were prepared on dissociated retinal cells using the 10X Genomics Chromium Single Cell 3’ Reagents Kit v3.1 (10X Genomics, Pleasanton, CA). Libraries were constructed following the manufacturer’s instructions. Sequencing data were processed through the Cell Ranger 7.0.1 pipeline (10X Genomics) using default parameters.

first: Nguyet

last: Le

first: Seth

last: Blackshaw


title: Integrative epigenomic and transcriptomic anlaysis of odontogenic differentiation of dental pulp stem cells [ATAC-seq]


title: RIP-seq of RNA associated in vivo with the PNPase and PNPaseD493A proteins, performed in Bacillus subtilis 9407

status: Public on Sep 20 2023

first: Xiaofei

last: Gu

address: NO 2 Yuanmingyuan West Road , Haidian District, Beijing

institute: China Agricultural University

summary: PNPase is the primary RNA turnover enzyme in Bacillus subtilis and plays a crucial role in regulating gene expression. To investigate the life activities that PNPase participated in Bacillus subtilis 9407, RNA immunoprecipitation-sequencing (RIP-seq) analysis was performed to pinpoint the direct RNA targets of PNPase using  6×his-tagged PNPase  (PNPase group) and PNPaseD493A (D493A group) constructs that were driven by the IPTG-induced Pgrac promoter.

overall_design: The wild-type pnpA CDS with a 6×His tag was integrated into the plasmid pHT01, which contains the IPTG-induced Pgrac promoter, to create a pHT01 derivative vector pXF11. Similarly, the pnpA D493A CDS with a 6×His tag containing the active site D493A mutation was also integrated into pHT01 to obtain another pHT01 derivative vector pXF15. Subsequently, the PNPase deletion strain (∆pnpA: GXF1006) was transformed with pXF11 and pXF15 by electroporationto obtain strain GXF2015 (expressing active PNPase protein) and GXF2023 (expressing inactive PNPase D493A protein), respectively. GXF2015 and GXF2023 were grown to the exponential growth phase in the presence of 0.1 mM IPTG induction. The 10% lysis sample was stored and labeled as "Input". 80% of the sample was used in immunoprecipitation reactions with anti-6×His antibody (Abcam) and referred to as "IP", while the remaining 10% was incubated with rabbit IgG (Cell Signaling Technology) as a negative control, named "IgG". RNA Immunoprecipitation (RIP) was conducted using EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Sigma-Aldrich) and 6×his monoclonal rabbit antibodies (Abcam), following the manufacturer's instructions. The target RNAs of "Input" and "IP" samples were extracted using TRIzol reagent (Invitrogen). The stranded RNA sequencing library was constructed using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Seqhealth) following the manufacturer's instruction. The library products corresponding to 200-500 bps were enriched, quantified, and finally sequenced using the PE150 model on a Novaseq 6000 sequencer (Illumina).

first: Qi

last: Wang

first: Yu

last: Zhao

first: Qingchao

last: Zeng

first: Xiangliu

last: Liang


title: Single-cell nascent RNA sequencing using click-chemistry unveils coordinated transcription

status: Public on Sep 15 2023

first: Dig

middle: B

last: Mahat

email: mahat@mit.edu, dbm222@cornell.edu

state: MA

address: Koch Institute, MIT, 500 Main St, Building 76, #417

department: Koch Institute for Integrative Cancer Research

institute: Massachusetts Institute of Technology

summary: Transcription is the primary regulatory step in gene expression coordinating the coding and non-coding genomic regions across space and time. Divergent initiation of transcription from promoters and enhancers produces stable RNAs from genes and unstable RNAs from enhancers. Nascent RNA capture and sequencing assays simultaneously measure gene and enhancer activity from cell populations. However, the lack of single-cell resolved view of active transcription has left fundamental questions in gene regulation unanswered. In this study, we present scGRO-seq - a single-cell nascent RNA sequencing assay using copper-catalyzed azide-alkyne cycloaddition - unveiling the coordinated regulation of dynamic transcription throughout the genome. scGRO-seq demonstrates the episodic nature of transcription and provides estimates of burst size and frequency by directly quantifying transcribing RNA polymerases. It reveals the co-transcription of functionally related genes and leverages the transcription of replication-dependent non-polyadenylated histone genes to elucidate cell-cycle dynamics. The single-nucleotide spatiotemporal resolution of scGRO-seq characterizes networks of enhancers and genes and indicates the bursting of transcription at super-enhancers before the activation of burst from associated genes. Our method offers insights into the dynamic nature of transcription, functional architecture of the genome, and serves as a powerful tool to investigate the role of the non-coding genome in gene regulation.

overall_design: Nascent RNA in mouse embryonic stem cells were labelled with propargyl (click-chemistry compatible moiety) via nuclear run-on reaction. Individual intact nuclei after labelling were placed in 96-well plate and nascent RNA was conjugated to single-stranded DNA containing single-cell barcode by copper-catalyzed azide-alkyne cycloaddition. Single-cell barcoded nascent RNA from wells of a 96-well plate were pooled and NGS library was prepared and sequenced.

first: Nathaniel

last: Tippens

first: Jorge

last: Martin-Rufino

first: Sean

last: Waterton

first: Jiayu

last: Fu

first: Sarah

last: Blatt

first: Phillip

last: Sharp


title: Transcriptomic analysis of differentially expressed genes in the Winnie mouse model of chronic colitis

status: Public on Oct 08 2023

city: Werribee

first: Ramya

middle: Sindhoora

last: Ephraim

state: VIC

address: 235 Hoppers Ln

country: Australia

institute: Victoria University

summary: The Winnie mouse, carrying a missense mutation in the Muc2 gene, is a model for chronic colitis closely resembling the pathological changes of human IBD. Herein, transcriptomic analyses of the differentially expressed genes in the distal colon of Winnie mice with mild colitis and Winnie-Prolapse mice with severe colitis are compared to control C57BL/6 mice. Gene ontology analysis and KEGG pathway analysis demonstrated the upregulation of genes in immune and inflammation-related pathways, metabolic pathways, cancer-related pathways, and neurological processes. Further research into these pathways and individual genes may lead to the identification of new targets for the treatment of IBD. The overexpression of oncogenes, in particular, may serve as an indicator of inflammation progressing to cancer.

overall_design: To investigate different pathways involved in the up and down-regulated genes from Winnies (spontaneous IBD model), highly inflamed Winnie-Prolapse mouse models, closely resembling human IBD, to discover novel therapeutics as well as give insights into the paths of inflammation that might lead to cancer.

last: Fraser

first: Jeannie

last: Devereaux

first: Lauren

last: Sahakian

first: Rhian

last: Stavely

first: Majid

last: Davidson

first: Jack

last: Feehan

first: Kulmira

last: Nurgali

first: Vasso

last: Apostolopoulos


title: SPAG7 deletion causes intrauterine growth restriction, resulting in adulthood obesity and metabolic dysfunction

status: Public on Nov 01 2023

first: Mary

last: Piper

state: Massachusetts

address: 1 Portland St

institute: Pfizer Inc

summary: From a forward mutagenetic screen to discover mutations associated with obesity, we identified mutations in the spag7 gene linked to metabolic dysfunction in mice. Here we show that SPAG7 KO mice are born smaller and develop obesity and glucose intolerance in adulthood. This obesity does not stem from hyperphagia, but a decrease in energy expenditure. The KO animals also display reduced exercise tolerance and muscle function due to impaired mitochondrial function. Furthermore, SPAG7-deficiency in developing embryos leads to intrauterine growth restriction, brought on by placental insufficiency, likely due to abnormal development of the placental junctional zone. This insufficiency leads to loss of SPAG7-deficient fetuses in utero and reduced birth weights of those that survive. We hypothesize that a “thrifty phenotype” is ingrained in SPAG7 KO animals during development that leads to adult obesity. Collectively, these results indicate that SPAG7 is essential for embryonic development and energy homeostasis later in life.

overall_design:
To investigate the role of SPAG7 in skeletal muscle function, gastrocnemius muscle was isolated from WT and SPAG-deficient male and female mice.
28-week-old WT and SPAG7 KO animals were sacrificed and gastrocnemius muscle was snap-frozen in liquid nitrogen, before preparation for RNAseq
We then performed gene expression profiling analysis using data obtained from bulk RNAseq.

first: Stephen

last: Flaherty


title: Integrative epigenomic and transcriptomic anlaysis of odontogenic differentiation of dental pulp stem cells

first: Shigeki

last: Suzuki


title: Evolutionary adaptation of the chromodomain of the HP1 protein Rhino allows th eintegration of heterochromatin and DNA sequence signals [RNA-seq]

first: Dominik

last: Handler

first: Lisa

last: Baumgartner

first: Jonathan

last: Ipsaro

first: Ulrich

last: Hohmann

first: Alexander

last: Schleiffer

first: Peter

last: Duchek

first: Julius

last: Brennecke


title: SHP2 as a Primordial Epigenetic Enzyme Expunges Histone H3 pTyr-54 to Amend Androgen Receptor Homeostasis

status: Public on Sep 28 2023

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

summary: Mutations that decrease activity of the tyrosine phosphatase, SHP2 (encoded by PTPN11), causes Noonan syndrome with multiple lentigines or NSML (also called LEOPARD syndrome), while the gain-of-function mutations promotes several malignancies. Precisely how a spectrum of maladies ranging from developmental disorders to cancer are regulated by varying a solitary phosphatase activity is not clearly understood. We uncovered that SHP2 is a distinct class of an epigenetic enzyme; upon phosphorylation by the kinase ACK1/TNK2, pSHP2 was escorted by androgen receptor (AR) to chromatin, erasing hitherto unidentified pY54-H3 (phosphorylation of histones H3 at Tyr54) epigenetic marks to trigger a transcriptional program of AR and its target genes. The SANT domain of NCOR was identified as the epigenetic reader for pY54-H3 marks. NSML patients, SHP2 knock-in mice (which develops NSML), as well as ACK1 knockout mice presented dramatic increase in pY54-H3, leading to loss of AR transcriptome. In contrast, prostate tumors with high pSHP2 and pACK1 activity exhibited progressive downregulation of pY54-H3 levels and higher AR expression that correlated with disease severity. Overall, pSHP2/pY54-H3 signaling acts as a sentinel of AR homeostasis, explaining not only growth retardation, genital abnormalities and infertility among NSML patients, but also significant AR upregulation promoting tumor growth in prostate cancer patients.

overall_design: Chromatin was isolated from (R)-9b and SHP099 inhibitor (0.5 µM, 18h) treated LNCaP cells and ChIP was performed using pY54-H3 antibody, followed by sequencing. In addition, prostates lysates were prepared from ACK1 knockout mouse, wild type mouse, mouse treated with (R)-9b and SHP099 inhibitor. The prostate lysates were subjected to ChIP with pY54-H3 antibody, followed by sequencing

first: Nupam

last: Mahajan


title: GTPBP8 is essential for mitoribosome formation in human mitochondria

status: Public on Sep 13 2023

city: STOCKHOLM

first: Miriam

last: Cipullo

address: Solnavägen 9

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: Mitochondrial gene expression relies on mitoribosomes to translate mitochondrial mRNAs. The biogenesis of mitoribosomes is an intricate process involving multiple assembly factors. Among these factors, GTP-binding proteins (GTPBPs) play crucial roles. In bacterial systems, numerous GTPBPs are required for ribosome subunit maturation, with EngB being a GTPBP involved in the ribosomal large subunit assembly. In this study, we focused on exploring the function of GTPBP8, the human homolog of EngB. We found that ablation of GTPBP8 leads to the inhibition of mitochondrial translation, resulting in significant impairment of oxidative phosphorylation. In the absence of GTPBP8, numerous mitoribosomal proteins from both subunits become destabilized, indicating GTPBP8's involvement in synchronized subunit assembly. Furthermore, structural analysis of mitoribosomes from GTPBP8 knock-out cells showed the accumulation of mitoribosomal large subunit assembly intermediates that are incapable of forming functional monosomes. Our study highlights the crucial role of GTPBP8 as a component of the mitochondrial gene expression machinery involved in mitoribosome biogenesis.

overall_design: The mitochondrial translation was investigated by mitochondrial ribosome profiling (mitoRiboSeq) in two HEK293 cell lines: HEK293 wildtype, GTPBP8 knockout 1

first: Genís

middle: V

last: Gesé

first: Shreekara

last: Gopalakrishna

first: Annika

last: Krueger

first: Petra

last: Páleníková

first: Dmitrii

last: Shiriaev

first: Yong

last: Liu

first: Jelena

last: Misic

first: Yu

last: Cai

first: Minh

last: Nguyen

first: Abubakar

last: Abdelbagi

first: Xinping

first: Michal

last: Minczuk

first: Ilian

last: Attanasov

first: Martin

last: Hällberg

first: Joanna

last: Rorbach


title: Lung tumor-infiltrating Treg have divergent transcriptional profiles and function linked to checkpoint blockade response

status: Public on Sep 11 2023

city: Baltimore

first: Kellie

last: Smith

state: MD

address: 1650 Orleans Street

institute: Johns Hopkins University