title: Transcriptome profiling of mkk3-1 and mpk7_ko3  seeds in Arabidopsis thaliana

city: Shenzhen

first: Xi

last: Chen

address: No.97in Buxin road, Dapeng district, Shenzhen

institute: Chinese Academy of Agricultural Sciences

summary: Seeds establish dormancy to delay germination until the arrival of a favorable growing season. In this study, we identify a fate switch comprised of the MKK3–MPK7 kinase cascade and the ethylene response factor ERF4 that is responsible for the seed state transition from dormancy to germination. We show that dormancy-breaking factors activate the MKK3–MPK7 module, which affects the expression of some α-EXPANSIN (EXPA) genes to control seed dormancy. Furthermore, we identify a direct downstream substrate of this module, ERF4, which suppresses the expression of these EXPAs by directly binding to the GCC boxes in their exon regions. The activated MKK3–MPK7 module phosphorylates ERF4, leading to its rapid degradation and thereby releasing its inhibitory effect on the expression of these EXPAs. Collectively, our work identifies a signaling chain consisting of protein phosphorylation, degradation, and gene transcription, by which the germination promoters within the embryo sense and are activated by germination signals from ambient conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for dry and imbibed seeds of wildtype Col-0 and mutant mkk3-1 and mpk7_ko3.

first: Qiujia

last: Li

first: Yong

last: Xiang


title: Transcription Elongation Factor ChIP-Seq in A.thaliana

status: Public on Aug 23 2023

city: Regensburg

first: Simon

last: Obermeyer

address: Universitätsstraße 31

country: Germany

institute: University Regensburg

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin Immunoprecipitation was performed with antibodies directed against several native Arabidopsis elongation factors in order to map the genomic positions.

overall_design: In conjunction with Chromatin Immunoprecipitation against S2 and S5 phosphorylations of the RNAPII-CTD the interplay between those factors with the actively transcribing RNAPII was studied.


title: Epigallocatechin gallate delays age-related cataract development via the RASSF2/AKT pathway

city: mudanjiang

first: shanshan

last: hu

address: Mudanjiang City, Heilongjiang Province

country: China

institute: Hongqi Hospital Affiliated to Mudanjiang Medical College

type: Expression profiling by high throughput sequencing

summary: Based on the transcriptional data of mice, analyze the important role and regulation mechanism of EGCG target gene RASSF2 in age correlation cataracts.

overall_design: We divided the mice into the young control group, the old control group and the old treatment group, and the anterior lens capsule tissue was taken for transcriptome sequencing. The total number of samples was 9, and there were duplicate samples.

first: Shanhe

last: Liu

first: Dongmei

last: Su

first: Xu

last: Ma

first: Shanshan

last: Hu


title: Lactobacillus from the Altered Schaedler Flora maintain IFNγ homeostasis to promote behavioral stress resilience.

status: Public on Aug 22 2023

city: Charlottesville

first: Alban

last: Gaultier

state: VA

address: 409 Lane Rd

country: USA

institute: University of Virginia

summary: The gut microbiome consists of trillions of bacteria, fungi, and viruses that inhabit the digestive tract. These communities are sensitive to disruption from environmental exposures ranging from diet changes to illness. Disruption of the community of lactic acid producing bacteria, Lactobaccillacea, has been well documented in mood disorders and stress exposure. In fact, oral supplement with many Lactobacillus species can ameliorate these effects, preventing depression- and anxiety-like behavior.  Here, we utilize a gnotobiotic mouse colonized with the Altered Schaedler Flora to remove the two native species of Lactobaccillacea. Using this novel microbial community, we found that the Lactobacillus species themselves, and not the disrupted microbial communities are protective from environmental stressors. Further, we determine that Lactobaccillacea are maintaining homeostatic IFNγ levels which are mediating these behavioral and circuit level responses. By utilizing the Altered Schaedler Flora, we have gained new insight into how probiotics influence behavior and provide novel methods to study potential therapies to treat mood disorders.

overall_design: Microbiome comparative analysis via 16S sequencing of feces of C57Bl6J mice.

first: Andrea

middle: R

last: Merchak

first: Samuel

last: Wachamo

first: Lucille

middle: C

last: Brown

first: Alisha

last: Thakur

first: Brett

last: Moreau

first: Ryan

middle: M

first: Courtney

last: Rivet-Noor

first: Tula

last: Raghavan


title: The timing of transcription of RpoS-dependent genes varies across multiple stresses

city: Claremont

first: Daniel

last: Stoebel

state: CA

address: 301 Platt Blvd

department: Biology

institute: Harvey Mudd College

summary: The alternative sigma factor RpoS regulates transcription of many genes in Escherichia coli in response to many different stresses. The rate of change of RpoS levels in response to stress, and the consequences of that change for the temporal patterns of expression of RpoS-regulated genes has not been described. We measured the temporal pattern of RpoS levels in response to the entry to stationary phase, high osmolarity, or low temperature. We found that RpoS levels peaked 50 minutes after osmolarity increased, but took 240 minutes to peak in response to lowered temperature. We quantified the transcriptome across these stresses using RNA-seq. Stresses differed in the number of differentially expressed genes, with 1379 DE genes were identified in in stationary phase, 633 in high osmolarity, and 302 in cold shock. We attempted to fit sigmoid or double sigmoid models to each individual differentially expressed genes in each stress, and fit 47 to 62% of all DE genes, depending on the stress. During the entry into stationary phase, genes whose expression rose earlier tended to be those that had been found to respond most strongly to low levels of RpoS.The timing of individual genes expression was not correlated across stresses. Taken together, our results demonstrate E. coli activates RpoS with different timing in response to different stresses, which in turn generates a unique pattern of timing of the transcription response in each stress.

overall_design: RNA-seq for E. coli K-12 (both wt and ∆rpoS) at time points during the transition from exponenital to stationary phase, and following shift to high osmolarity and low temperature

first: Josephine

last: Adams

first: Johnson

last: Hoang

first: Emily

last: Petroni


title: Delineation of two multi-invasion-induced rearrangement pathways that differently affect genome stability

city: Fort Collins

first: Ruth

last: Watson

state: CO

address: 1385 Center Ave

department: ERHS

institute: Colorado State University

type: Genome variation profiling by genome tiling array

summary: Punctuated bursts of structural genomic variations (SVs) have been described in various organisms, but their etiology remains incompletely understood. Homologous recombination (HR) is a template-guided mechanism of repair of DNA double-strand breaks and stalled or collapsed replication forks. We recently identified a DNA break amplification and genome rearrangement pathway originating from the endonucleolytic processing of a multi-invasion (MI) DNA joint molecule formed during HR. Genome-wide sequencing approaches confirmed that multi-invasioninduced rearrangement (MIR) frequently leads to several repeat-mediated SVs and aneuploidies. Using molecular and genetic analysis, and a novel, highly sensitive proximity ligation-based assay for chromosomal rearrangement quantification, we further delineate two MIR sub-pathways. MIR1 is a universal pathway occurring in any sequence context, which generates secondary breaks and frequently leads to additional SVs. MIR2 occurs only if recombining donors exhibit substantial homology, and results in sequence insertion without additional break or SV. The most detrimental MIR1 pathway occurs late on a subset of persisting DNA joint molecules in a PCNA/Polδ- independent manner, unlike recombinational DNA synthesis. This work provides a refined mechanistic understanding of these HR-based SV formation pathways and shows that complex repeat-mediated SVs can occur without displacement DNA synthesis. Sequence signatures for inferring MIR1 from long-read data are proposed.

overall_design: 24 Lys+ recombinant strains were analyzed by array CGH on two separate arrays, with no replicates. Each Lys+ recombinant strain was hybridized with its repective parent strain (Lys-) as the reference (exception: YAP550-10 was hybridized with YAP500 parent).

first: Diedre

last: Reitz

first: Yasmina

last: Djeghmoum

middle: A

first: Pallavi

last: Rajput

first: Juan

middle: L

last: Argueso

first: Wolf-Dietrich

last: Heyer

first: Aurèle

last: Piazza


city: Lyon

first: Aurele

address: 46 Allee d'Italie

country: France

institute: ENS Lyon

summary: Punctuated bursts of structural genomic variations (SVs) have been described in various organisms, but their etiology remains incompletely understood. Homologous recombination (HR) is a template-guided mechanism of repair of DNA double-strand breaks and stalled or collapsed replication forks. We recently identified a DNA break amplification and genome rearrangement pathway originating from the endonucleolytic processing of a multi-invasion (MI) DNA joint molecule formed during HR. Genome-wide sequencing approaches confirmed that multi-invasion-induced rearrangement (MIR) frequently leads to several repeat-mediated SVs and aneuploidies. Using molecular and genetic analysis, and a novel, highly sensitive proximity ligation-based assay for chromosomal rearrangement quantification, we further delineate two MIR sub-pathways. MIR1 is a universal pathway occurring in any sequence context, which generates secondary breaks and frequently leads to additional SVs. MIR2 occurs only if recombining donors exhibit substantial homology, and results in sequence insertion without additional break or SV. The most detrimental MIR1 pathway occurs late on a subset of persisting DNA joint molecules in a PCNA/Pold-independent manner, unlike recombinational DNA synthesis. This work provides a refined mechanistic understanding of these HR-based SV formation pathways and shows that complex repeat-mediated SVs can occur without displacement DNA synthesis. Sequence signatures for inferring MIR1 from long-read data are proposed.

overall_design: DNA from APY85 and APY89 parental strains (Lys-) and of APY85 and APY89 Lys+ recombinants obtained following DSB formation on chr. V was isolated, sequenced and/or analyzed by aCGH to identify structural variants and copy number variations.


title: Prolonged STAT1 activation in neurons drives a pathological transcriptional response

city: Durham

first: Shane

middle: Mitchell

last: O'Neil

state: NC

address: 701 W Main St

department: Neuroscience

institute: Duke University

summary:
To investigate the effects of pathological IFN-γ stimulation on neurons in the context of subsequent activation, we established cell cultures of primary mouse neurons receiving pathological priming or no priming.
We then performed RNA-Seq on these cells after vehicle, physiological, and pathological IFN-γ restimulation.

overall_design: Cultured primary mouse neurons were sequenced after treatment. Cells from each mouse were separated into six wells and each well given a different treatment. Each well was sequenced on two lanes and the data combined.

first: Danielle

middle: N

last: Clark

first: Li

last: Xu

first: Justin

middle: T

last: Steppe

last: Savage

first: Kavya

last: Raghunathan

first: Anthony

middle: J

last: Filiano


title: Human Pluripotent stem cells-derived Inner ear organoids recapitulate otic development in vitro

city: 8091 Zurich

first: Marta

last: Roccio

address: Frauenklinikstrasse 24

department: Department Otolaryngology, Head and Neck Surgery

country: Switzerland

institute: University Hospital Zurich,

summary: The molecular characterization of early stages of human inner ear development is limited by the difficulty in accessing samples at early gestational stages. Some aspects of inner ear morphogenesis can be recapitulated using pluripotent stem cell directed differentiation in inner ear organoids (IEOs). Once validated and benchmarked, these models could provide a unique tool to complement and refine our understanding of human otic differentiation and could be used to model developmental defects.Here we provide a first characterization of early human embryonic otocyst development and compare the primary tissue to the iPSC-derived inner ear cell types. Multiplex immunostaining and single cell RNA sequencing were used to characterize human iPSC-derived IEOs at 3 key developmental steps, providing a new and unique signature of in vitro derived otic- placode, epithelium, neuroblasts and sensory epithelia. The expression and localization of key markers were further evaluated in human embryos. We show that the otic placode derived in vitro (day 8-12) matches marker expression of Carnegie Stage (CS) 11 embryos, and subsequently (day 20-40) gives rise to otic epithelia and neuroblasts comparable to the CS13 embryonic stage. Differentiation of sensory epithelia, including supporting cells and hair cells, starts in vitro at day 50-60 of culture. The maturity of these cells is equivalent to vestibular sensory epithelia at week 10 or cochlear tissue at week 12 of development, prior to functional onset. Taken together these data indicates that the current state of the art protocol enables the specification of bona fide otic tissue, supporting further application of IEOs to model inner ear biology and disease

overall_design:
We have analyzed by transcriptional profiling 3 steps of otic development in inner ear organoids obtained through directed differentiation of iPSC in 3D culture.
1: day 8 of culture: otic placode stage;
2: day 26 of culture: otic vesicle stage;
3: day 60 of culture: sensory epithelia development.
Cells collected at day 8 were obtained from 200 unsorted organoids. This provides an overview of the efficiency of otic placode induction. In addition to otic placode, other tissues co-develop including: epidermis, mesenchyme, neural crest and neural epithelium. A small percentage of placode neurons is also detected.
Cells collected at day 26 were obtained from 100 organoids. After trituration cells were SORTED using EPCAM/CD326 antibody staining. Only the EPCAM+ fraction was processed for scRNAseq. This enable to identify the otic epithelium (OP) as well as otic neuroblasts (ONB) derived from delamination from the former. In addition, EPCAM+ epidermis can also be identified. Small populations of mesenchyme and neural epithelia cells are purified and identified.
Cells harvested at day 60 were obtained from 2 independent experiment.
EXP1: 48 organoids (unselected) were collected and  SORTED using EPCAM/CD326 antibody staining.
EXP2: 8 organoids (selected based on visual assessment of GFP positive vesicles) were collected and  SORTED using EPCAM/CD326 antibody staining.
In both cases the EPCAM+ pool were sequenced.
Beside otic epithelium (OEP) and Epidermis (EP), other co-developed tissues (mesenchyme and neural epilelia etc) were identified.
The same 3 stages of otic development are characterized in parallel by immunostaining and compared to human tissue and the equivalent stage of differentiation. This study a fits comparison of inner ear organoid differentiation from human pluripotent stem cells and human primary tissue.

first: Sara

last: Alonso Jimenez

first: Hubert

last: Rehrauer


title: BMAL1 Modulates Senescence Programming via AP-1 (WT RNA-seq)

city: Rochester

first: Sarah

middle: Katherine

last: Jachim

state: MN

address: 222 3rd Ave SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

summary:
Cellular senescence and circadian dysregulation are biological hallmarks of aging. Whether they are interdependent has not been thoroughly studied. We hypothesize that BMAL1, a pioneer transcription factor and master regulator of the molecular circadian clock, plays a role in the senescence program.
In this study, we show that BMAL1 in is uniquely localized to genomic motifs associated with AP-1 in senescent cells and contributes to AP-1 transcriptional control of the senescence program.

overall_design: Triplicate samples of control and senescent primary mouse fibroblasts were collected for RNA-seq 12 hours post-synchronization with dexamethasone.

first: Aditya

middle: V

last: Bhagwate

first: Nagaswaroop

middle: K

last: Nagaraj


title: BMAL1 Modulates Senescence Programming via AP-1 (BMAL1-ChIP-seq)

overall_design: Triplicate samples of control and senescent primary mouse fibroblasts were collected for BMAL1-ChIP-seq 12 hours post-synchronization with dexamethasone.

first: Jian

last: Zhong

first: Tamas

last: Ordog

first: Jeong-Heon

last: Lee


title: The ubiquitin conjugase Rad6 mediates ribosome pausing during oxidative stress

city: Bethesda

first: Nicholas

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

summary: Oxidative stress causes K63-linked ubiquitination of ribosomes by the E2 ubiquitin conjugase, Rad6. How Rad6-mediated ubiquitination of ribosomes affects translation, however, is unclear. We therefore performed Ribo-seq and Disome-seq in Saccharomyces cerevisiae, and found that oxidative stress caused ribosome pausing at specific amino acid motifs, and this also led to ribosome collisions. However, these redox pausing signatures were lost in the absence of Rad6 but did not depend on the ribosome-associated quality control (RQC) pathway. We also found that Rad6 is needed to inhibit overall translation in response to oxidative stress and its deletion leads to increased expression of antioxidant genes. Finally, we observed that the lack of Rad6 leads to changes during translation initiation that affect activation of the integrated stress response (ISR) pathway. Our results provide a high-resolution picture of the gene expression changes during oxidative stress and unravel an additional stress response pathway affecting translation elongation.

overall_design: Gene expression and ribosome pausing analysis of wild-type cells or cells with mutants of HEL2 or RAD6  -/+  hydrogen peroxide by using Ribo-seq, Disome-seq and RNA-seq. Biological replicates are indicated when available. Strain backgrounds SUB280 and S288C are utilized.

first: Sezen

last: Meydan


title: BMAL1 Modulates Senescence Programming via AP-1.

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

overall_design: Refer to individual Series


title: The Swi-Snf chromatin remodeling complex mediates gene activation through metabolic control [ChIP-seq II]

city: Kansas City

first: Andrew

middle: Joseph

last: Price

state: MO

address: 1000 E. 50th Street

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: In eukaryotes, ATP-dependent chromatin remodelers regulate gene expression in response to nutritional and metabolic stimuli. The Swi-Snf complex is one such remodeler that has been implicated in disease, where loss of Swi-Snf function leads to dysregulated gene transcription. However, altered transcription of metabolic genes may have consequences for entire pathways that remain poorly understood. In this study, we use genetic and molecular approaches to uncover a role for Swi-Snf as a critical regulator of metabolism. We find that Δsnf mutants are cysteine-deficient, despite growth in nutrient-rich media. This cysteine deficiency causes widespread perturbations in sulfur metabolic gene transcription. This includes global alteration and redistribution of the transcription factor Met4 which senses cysteine deficiency and also has roles in heavy metal stress response and cell cycle progression. Additionally, we show that in its role as a metabolic regulator, Swi-Snf is a critical determinant of survival following oxidative stress. Our findings show how a chromatin remodeler can have a significant impact on a whole metabolic pathway by directly regulating an important gene subset and demonstrate an emerging role for chromatin remodeling complexes as key determinants of metabolic control.

overall_design: Met4 was conditionally depleted in wt and snf2 mutant strains by the anchor away method and RNA polymerase II (Rpb1 subunit) occupancy was monitored by ChIP

first: Michael

last: Church

first: Hua

last: Li

first: Jerry

last: Workman


title: An iPSC-based model of Progressive Pseudorheumatoid Arthropathy of Childhood identifies transcriptional changes in patient-iPSC-specific cartilage tissues

status: Public on Aug 24 2023

city: Boston

first: April

last: Craft

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: Bulk RNA-seq is used to study transcriptomic differences between WISP3-deficient and WISP3-sufficient articular cartilage derived from hPSCs in vitro

overall_design:
Transcriptomic profiling of in vitro  chondrocyte populations

Please note: Raw data are not available for the PPAC iPSC samples due to patient privacy concerns.

first: Chaochang

first: Mireia

last: Alemany Ribes

first: Rosanne

last: Raftery

first: Uzochi

last: Nwoko

first: Matthew

last: Warman


title: Whole transcriptome sequencing of E. coli BW25113 wt and nudC knockout strains

city: Vilnius

first: Kotryna

last: Kvederaviciute

address: Sauletekio av. 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

summary: In the present study we performed total RNA sequencing of E. coli BW25113 wt and nudC knockout strains. RNA-seq analysis revealed that the inactivation of nudC gene in bacteria shows alteration of level of sRNA and protein-coding transcripts mainly associated with bacterial chemotaxis and flagellar assembly pathways.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for E. coli BW25113 wt and nudC KO strains.

first: Giedrius

last: Vilkaitis

first: Milda

last: Mickutė

last: Kvederavičiūtė


title: 5’-NAD-RNA identification in E. coli BW25113 wt, nudC and csdA knockouts

summary: In the present study we applied NAD captureSeq to charecterize the 5'-NAD-RNA profile of E. coli BW25113 wt strain as well as nudC and csdA knockouts. The data obtained showed that both knockouts resulted in an increased number of identified 5’-NAD-RNA species, thus suggesting that CsdA might add a potentially new layer of control on NAD-epitranscriptomic landscape.

overall_design: 5'-NAD-RNA identification in E. coli BW25113 wt, nudC KO and csdA KO strains. 3 Biological replicates for ADRPC+ and 2 biological replicates for ADRPC- libraries.


title: Simultaneous inhibition of SIRT3 and cholesterol homeostasis targets AML stem cells by perturbing fatty acid β-oxidation and inducing lipotoxicity

city: Toronto

first: Soheil

last: Jahangiri

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

summary: To invesetigate the transcriptional changes as a result of SIRT3 perturbation in leukemic stem cells and AML blasts

overall_design: Leukemic stem cells and blasts enriched from patient samples were treated with inhibitor or control and collected for RNA sequencing.

first: Cristiana

last: O’Brien

first: Tianyi

last: Ling

first: Jacob

last: Berman

first: Rachel

last: Culp-Hill

first: Julie

last: Reisz

first: Vincent

last: Rondeau

first: Jonathan

last: St-Germain

first: Vinitha

last: Macwan

first: Audrey

last: Astori

first: Andy

last: Zeng

first: Jun

middle: Y

last: Hong

first: Meng

first: Min

last: Yang

first: Sadhan

last: Jana

first: Fabia

last: Gamboni

first: Emily

last: Tsao

first: Weiti

last: Liu

first: John

middle: E

last: Dick

first: Hening

last: Lin

first: Ari

last: Melnick

first: Anastasia

last: Tikhonova

first: Andrea

last: Arruda

first: Mark

middle: D

last: Minden

first: Brian

last: Raught

first: Angelo

last: D'Alessandro

first: Courtney

last: Jones


title: NFIB Is a Pioneer Factor for DNA Replication by Acting as a Genome Organizer [Repli-seq]

city: Beijing

first: Yongjie

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology

summary: Genome-wide DNA replication profiles of U2OS cells without or with NFIB depletion.

overall_design: U2OS cells treated with control siRNAs or siRNAs against NFIB were synchronized at G1/S transition by thymidine and aphidicolin double treatments. Cells were cultured with 20 μM of EdU for 10 min after release into S phase by washing out aphidicolin for 0, 4, and 6 h, respectively.The cells were collected and lysed for repli-seq.

first: Wenting

last: Zhang


title: NFIB Is a Pioneer Factor for DNA Replication by Acting as a Genome Organizer [H3K9me3 CUT&Tag]

summary: Genome-wide profiling of histone H3K9me3 of G1 or S phase U2OS cells without or with NFIB depletion.

overall_design: U2OS cells treated with control siRNAs or siRNAs against NFIB were synchronized at G1/S transition by double-thymidine block. These cells were released for 0 (G1 phase) or 4 h (S phase) respectively. About 100,000 cells were obtained for H3K9me3 CUT&Tag.


title: Interplay between bacterial RNA 5'-termini deNADding protein NudC and DEAD-box RNA helicase CsdA in stress-responses

first: Kotryna

last: Kvederaviciute


title: NFIB Is a Pioneer Factor for DNA Replication by Acting as a Genome Organizer [H3K4me3 CUT&Tag]

summary: Genome-wide profiling of histone H3K4me3 of G1 or S phase U2OS cells without or with NFIB depletion.

overall_design: U2OS cells treated with control siRNAs or siRNAs against NFIB were synchronized at G1/S transition by double-thymidine block. These cells were released for 0 (G1 phase) or 4 h (S phase) respectively. About 100,000 cells were obtained for H3K4me3 CUT&Tag.


title: A new antibiotic from an uncultured bacterium binds to an immutable target

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

summary: Antimicrobial resistance is a leading mortality factor worldwide. Here we report the discovery of clovibactin, a new antibiotic, isolated from uncultured soil bacteria. Clovibactin efficiently kills drug-resistant Gram-positivebacterial pathogens without detectable resistance. Using biochemical assays,solid-state NMR, and atomic force microscopy, we dissect its mode of action. Clovibactin blocks cell wall synthesis by targeting pyrophosphate of multiple essential peptidoglycan precursors (C55PP, Lipid II, LipidWTA). Clovibactin uses anunusual hydrophobic interface to tightly wrap aroundpyrophosphate, butbypasses the variable structural elements of precursors, accounting for the lack of resistance. Selective and efficient target binding is achieved by the sequestration of precursors into supramolecular fibrils that only form on bacterial membranes that contain lipid-anchored pyrophosphate groups.Uncultured bacteria offer a rich reservoir of antibiotics with new mechanisms of action that could replenish the antimicrobial discovery pipeline.

overall_design: Gene expression of an untreated bacteria (with 6 biological replicates) compared with two different antibiotics treatment (3 biological replicates each)

first: Stefania

last: de Benedetti

first: Theresa

last: Harbig

first: Tanja

last: Schneider


title: NFIB Is a Pioneer Factor for DNA Replication by Acting as a Genome Organizer [ATAC-seq II]

summary: Chromatin accessibility of G1 or S phase of U2OS cells without or with NFIB depletion were profiled using transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to identify potential regulatory elements.

overall_design: U2OS cells treated with control siRNAs or siRNAs against NFIB were synchronized at G1/S transition by double-thymidine block. These cells were released for 0 (G1 phase) or 4 h (S phase) respectively. About 50,000 cells were obtained for ATAC-seq libraries.


title: scRNAseq of spleen and atherosclerotic plaques from young and aged healthy and young and aged atherosclerotic mice

city: Birmingham

first: Daniel

last: Tyrrell

state: AL

address: 901 19th Street South

department: Pathology

institute: University of Alabama at Birmingham

summary: T cells change substantially with age and are involved in atherosclerosis. Aging is the strongest clinical risk factor for atherosclerosis so we profiled T cells in young and aged mice prior to atherosclerosis (healthy) and in young and aged atherosclerotic mice (diseased).

overall_design: Spleens from 3-month or 18-month and atherosclerotic plaques from 5-month and 21-month female C57BL/6 mice were rendered into single cell suspension, enriched for CD3+ cells and sequenced.

last: Goldstein


title: NFIB Is a Pioneer Factor for DNA Replication by Acting as a Genome Organizer [NS-seq]

last: Liu

summary: Nascent strand sequencing (NS-seq) in U2OS cells without or with NFIB depletion to identify de facto activated replication origins.

overall_design: U2OS cells were infected with lentiviruses carrying control shRNA or NFIB shRNA. RNA-primed nascent DNA at replication origins (0.5-2.0 kb in length) were purified and subsequently sequenced using the Illumina platform.


title: The Swi-Snf chromatin remodeling complex mediates gene activation through metabolic control [RNA-Seq II]

first: Andrew

last: Price

overall_design: RNA seq and ChIP seq in snf2, snf5 mutants and wild type cells in YPD and YPD supplemented with 3 mM cysteine

first: Michael

last: Church

first: Hua

last: Li

first: Jerry

last: Workman


title: NFIB Is a Pioneer Factor for DNA Replication by Acting as a Genome Organizer [Micro-C]

summary: Micro-C performed on U2OS cells without or with NFIB depletion at G1/S phase and S phase to investigate the effect of NFIB on higher-order chromatin structure during DNA replication.

overall_design: U2OS cells without or with NFIB depletion at G1/S phase and S phase were synchronized at G1/S boundary by double-thymidine block and followed by release for 4 h to allow cells entering S phase, respectively. Micro-C experiments of those cells in each treatment were biologically repeated twice.


title: NFIB Is a Pioneer Factor for DNA Replication by Acting as a Genome Organizer [ATAC-seq]

summary: Chromatin accessibility of G1 phase of U2OS cells without or with NFIB depletion were profiled using transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to identify potential regulatory elements.

overall_design: U2OS cells without or with NFIB depletion were fractionated into G0, G1, S, and G2/M phases by FACS in the presence of Hoechst 33342 and Pyronin Y. Only G1 phase cells were collected. ATAC-seq experiments of G1 phase cells were biologically repeated twice.


title: The Swi-Snf chromatin remodeling complex mediates gene activation through metabolic control [RNA-seq I]

address: 1000 E 50th Street

overall_design: RNA seq in snf2, snf5 mutants and wild type cells in YPD and YPD supplemented with 3 mM cysteine


title: The Swi-Snf chromatin remodeling complex mediates gene activation through metabolic control [ChIP-seq]

overall_design: ChIP seq in snf2, snf5 mutants and wild type cells in YPD and YPD supplemented with 3 mM cysteine


title: A Pan-Cancer Single Cell Panorama of Natural Killer Cells

first: Fei

last: Tang

state: Beijing

address: Haidian District, Beijing Summer Palace Road No. 5

department: BIOPIC

institute: Peking University

summary: Natural killer (NK) cells play indispensable roles in innate immune responses against tumor progression, but their phenotypic and functional diversities in the tumor microenvironment (TME) remain unclear. Here, we performed integrated analyses on the single-cell RNA sequencing (scRNA-seq) data for NK cells across multiple cancer types. Our study provides new insights into NK cell–based cancer immunity and highlights the potential clinical utilities of NK cell subsets as therapeutic targets.

overall_design:
We generated scRNA-seq data from 47 cancer patients to investigate tumor-infiltrating NK cells across multiple cancer types, including tumor and normal tissue. The raw sequencing data were provided at China Genomic Sequence Archive (GSA): HRA000321.
NOTE FROM SUBMITTER: The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA: HRA000321 (https://ngdc.cncb.ac.cn/search/?dbId=hra&q=HRA000321).

first: Jinhu

first: Linnan

last: Zhu

first: Dongfang

last: Wang

first: Zemin


title: NFIB Is a Pioneer Factor for DNA Replication by Acting as a Genome Organizer [WGS]

first: Yongjie

summary: Whole genome sequencing (WGS) of MCF-10A cells without or with NFIB overexpression cultured at 30 or 75 days and 5-fluoracil-resistant or oxaliplatin-resistant MCF-10A cells with NFIB overexpression cultured at 75 days to investigate whether the oncogenic potential of NFIB is linked to its function in replication initiation.

overall_design: MCF-10A clones stably overexpressing NFIB via lentivirally delivered NFIB expression vector. These clones were further cultured 30 or 75 days and NFIB overexpression MCF-10A cells under the treatment of oxaliplatin or 5-fluoracil at 75 days being subjected to whole genome sequencing.


title: RNA-seq analysis of bulk Human and single-cell Musashi2-CreER-MycT58A; R26-LSL-tdTomato Mouse Pancreas ASCP, PDAC, and ACC Tumors

status: Public on Aug 21 2023

city: La Jolla

first: Nirakar

last: Rajbhandari

state: Ca

address: 2880 Torrey Pines Scenic Dr

institute: University of California San Diego

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: The histone demethylase 7A regulates immediate early genes in neurons [RNA-seq]

city: Shanghai

first: Yifan

address: 130 Dong An Road

institute: Fudan University

summary: There are multiple post-translational modifications on amino acid residues at the N-terminus of histones that affect the structure of chromatin and alter the transcription of genes, thereby regulating a variety of biological processes. Lysine demethylase 7A (KDM7A) mainly removes histone modifications such as H3K9me1/2 and H3K27me1/2. Current research on KDM7A has focused on tumors, metabolism and development, while research on the function of the mammalian nervous system is still lacking. The functions and mechanisms of KDM7A in the regulation of neuronal cell differentiation and cell activity in the nervous system were investigated. Our study found that KDM7A regulates H3K9me2 and H3K27me2 but also affects other inhibitory or active histones, such as H3K9me3 and H3K27ac, thereby disturbing the transcription of some immediate early genes (IEGs) and consequently affecting the differentiation and activity of neuronal cells. IEGs are important for neuron cell proliferation, differentiation, formation of dendrites and neural circuit-related proteins, which are involved in maintaining the normal function of the nervous system. Imbalances in IEG expression have been found in some neurological disorders, such as depression and schizophrenia. Moreover, the changes in various histone modifications in neurodegenerative diseases and brain injury have recently received increasing attention. Therefore, our study provides a basis for revealing the epigenetic regulatory mechanisms of neurological disorders.

overall_design: To investigate the  function of KDM7A in the regulation of N2a differentiation, we established N2a cell lines in which  Kdm7a has been knocked down by shRNA.

first: Qin

last: Hong


title: Therapy-induced senescence contributes to the efficacy of abemaciclib in patients with dedifferentiated liposarcoma

city: New York

last: Koff

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

summary: Current research on CDK4/6 inhibitors (CDK4/6i) in the pre-clinical and clinical spaces are largely concerned with gaining a deeper understanding of how these drugs delay tumor growth, and how to prevent cancer cell resistance.  By coordinating a first-in-kind phase II clinical trial of the CDK4/6i abemaciclib for patients with progressive dedifferentiated liposarcoma (DDLS) with cellular studies to identify the molecular basis of geroconversion, we have defined how therapy induced senescence contributes to disease management.  Thirty patients with progressing DDLS enrolled in the clinical trial and were treated with 200mg abemaciclib twice daily.  The median progression free survival was 33 weeks at the time of the data lock, with 23 of 30 progression-free at 12 weeks (76.7%, two-sided 95% CI 57.7% - 90.1%).  ANGPTL4 is a necessary late regulator of geroconversion, the pathway from reversible cell cycle exit to a stably arrested inflammation-provoking senescent cell, in liposarcoma cell lines treated with CDK4/6i.  Using ANGPTL4 and CDKN2A expression, we were able to identify patients in which abemaciclib induced tumor cell senescence. We were then able to correlate this with outcomes. Senesence correlated with increased leukocyte infiltration, primarily CD4-positive cells, within a month of therapy, and possibly with an improved initial response to abemaciclib.  However, those individuals with both senescence and increased TILs were also more likely to acquire resistance after six months of therapy.  This suggests that combining senolytics with abemaciclib in a subset of patients may improve the durability of patient responses to this class of compounds.

overall_design: Two to three independent biological replicates of genetically engineered LS8817 cells were made to arrest in quiescence following doxyxyline and palbociclib treatment and  released from this arrest to progress synchronously into senesecence.  Samples were obtained over the next 28 days, RNA prepared, and correlated to the appearance of different phenotypes associated with senescence.

first: Mary

last: Klein


title: The histone demethylase 7A regulates immediate early genes in neurons [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for KDM7A  in N2a cells and histone modifications H3K9me2  in shCtrl or shKdm7a N2a cells.

first: Bo

last: Wen


title: Bulk RNA-seq analysis of Human ASCP and ACC Pancreas Tumors

summary: Identifying the cells from which cancers arise, and the paths they take towards malignancy is critical for understanding the molecular basis of tumor initiation and progression. To determine whether stem and progenitor cells can serve as cells of origin for cancer, we created a new Msi2-CreERT2 knock-in strain. When crossed to a conditional CAG-LSL-MycT58A model, Msi2-CreERT2 mice developed multiple pancreatic cancer subtypes: pancreatic ductal adenocarcinoma (PDAC), adenosquamous carcinoma of the pancreas (ASCP), acinar cell carcinoma (ACC), and rare anaplastic tumors. Combining single-cell genomics with computational analysis of developmental states and lineage trajectories, we demonstrate that oncogenic MYC preferentially triggers the transformation of the most immature subset of Msi2+ cells, leading to the rise of a common pool of pre-cancer cells with multi-lineage properties. These pre-cancer cells subsequently diverge to distinct pancreatic cancer subtypes by activation of distinct transcriptional programs and large-scale genomic changes. Importantly, the enforced expression of specific molecular signals can redirect cells toward specific subtypes. This study shows that multiple pancreatic cancer subtypes can arise from a common pool of Msi2+ cells and provides a powerful framework to understand and control the programs that shape divergent fates in pancreatic cancer.

overall_design: Human pancreatic tumors were characterized by flow cytometry and then processed with bulk RNA-seq to determine the transcriptional differences of each subtype of disease and compare effects on transcriptome to this paper's novel mouse model

last: Hamilton

first: Tannishtha

last: Reya


title: The histone demethylase 7A regulates immediate early genes in neurons [CUT & Tag]

overall_design: CUT&Tag for  histone modifications H3K27me2, H3K27me3, H3K9me3, H3K27ac and H3K4me3 in shCtrl or shKdm7a N2a cells.


title: Glutathione dynamics is a potential diagnostic and therapeutic trait determining the neoadjuvant chemotherapy response to bladder cancer

city: Seoul

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

department: Department of Biomedical Sciences

country: South Korea

institute: University of Ulsan College of Medicine

summary: Radical cystectomy with preoperative cisplatin-based neoadjuvant chemotherapy (NAC) is a current standard care for muscle-invasive bladder cancers (MIBCs). However, the response rate remains relatively low, and current clinico-pathologic and molecular classifications are inadequate to prospectively stratify MBIC patients regarding the NAC response. Here, we showed that dysregulation in glutathione (GSH) pathway is fundamental for the NAC resistance of MBICs. Comprehensive analysis of transcriptome profiles from four independent cohorts revealed that GSH metabolism and immune response genes were significantly enriched in NAC resistant and sensitive MIBC tumors, respectively. A machine learning based tumor/stroma classifier was applied for high-throughput digitalized immunohistochemistry analysis, identifying GSH dynamic proteins including glutaminase-1 (GLS1) were associated with the NAC resistance and unfavorable clinical characteristics. Consistently, GSH dynamics was activated in cisplatin resistant human MIBC cells, stimulating their proliferation, stemness features, and invasion. Combination treatment of GSH dynamics modulators and cisplatin significantly suppressed tumor growth in an orthotopic xenograft animal model. Our results demonstrate the prognostic and therapeutic values of GSH dynamic mediators in determining the clinical features and response to NAC of patients with MIBCs.

overall_design: This ASAN cohort included 105 MIBC (cT2-4aN0M0) patients who underwent TUR and NAC at least 3 cycles were retrospectively collected. The ASAN cohort was classified into two groups showing marked contrast in NAC response: NAC response (R) patients with the absence of residual invasive tumor and NAC nonresponse (NR) patients with large residual MIBC (4.9 ± 2.5 cm) in the radical/partial cystectomy specimens. To investigate a tumor specific molecular nature determining NAC response, we performed laser capture microdissection (LCMD) of tumors from the formalin-fixed and paraffin-embedded (FFPE) TURBT specimens of 39 patients (N=18 in NR group and N=21 in R group) from ASAN cohort and then compared their genome-wide transcriptome profiles.

first: YongHwan

last: Kim

first: Hyein

last: Ju

first: Seung-Yeon

last: Yoo

first: Jinahn

last: Jeong

first: Gowun

first: Dong-Myung

last: Shin

first: Yong

last: Cho

first: Jae

last: Lee

first: Bumsik


title: MATR3 is an endogenous inhibitor of DUX4 in FSHD muscular dystrophy

city: Milan

first: Anna Sofia

last: Tascini

address: Via Olgettina, 60

department: Center for Omics Science

country: Italy

institute: IRCCS, Ospedale San Raffaele

summary: We identified MATR3 as the first direct endogenous inhibitor of DUX4. We found that MATR3 directly binds to DUX4 DNA-binding domain and blocks DUX4-mediated gene expression. As a result, MATR3 administration rescues cell viability and myogenic differentiation of FSHD muscle cells, while it does not affect healthy muscle cells. Notably, we characterized a short MATR3 fragment that is necessary and sufficient to directly block DUX4-induced toxicity to the same extent of the full-length protein.

overall_design: Examination of the transcriptomic differences due to MATR3 overexpression in muscle cells from FSHD muscular dystrophy patients.

first: Valeria

last: Runfola

first: Davide

last: Gabellini


title: DNA methylation analysis of malignant and normal uveal melanocytes reveals novel molecular features of uveal melanoma

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

institute: institut curie

type: Methylation profiling by high throughput sequencing

summary: In order to address epigenetic regulation, NM and UM models were analyzed through OxBS sequencing pipeline (Cambridge Epigenetics). Whole genome DNA methylation analysis was carried out with a Cambridge Epigenetics kit (TrueMethyl kit) that corresponds to an oxidative bisulfite reaction, to identify and analyze only 5-methylcytosine (5-mC). This modification of bisulfite sequencing was found to be more robust in our samples, particularly for the normal melanocytes, most probably due to the abundance of melanin

overall_design: Normal choroidal melanocytes, fresh sorted UM cells from MP41 and MP46 models were analyzed in simplicate

first: David

last: Gentien

first: Cecile

last: Reyes

first: Aurelie

last: Teissandier

first: Deborah

last: Bourchis


title: The fruit fly acetyltransferase chameau promotes starvation resilience at the expense of longevity

city: Berlin

first: Anuroop

middle: Venkateswaran

last: Venkatasubramani

state: Berlin

address: Robert-Rössle-Straße 10

institute: MDC-Berlin

summary: Proteins involved in cellular metabolism and molecular regulation can extend lifespan in various organisms in the laboratory. However, any improvement in aging would only provide an evolutionary benefit if the organisms were able to survive under non-ideal conditions. We have previously shown that Drosophila melanogaster carrying a loss of function allele of the acetyltransferase chameau (chm) has an increased healthy life span when fed ad libitum. Here, we show that loss of chm and a reduction of its activity result in a substantial reduction of weight and a decrease in starvation resistance. This phenotype is caused by a failure to properly regulate the genes and proteins required for energy storage and expenditure. The previously observed increase in survival time thus comes with the inability to prepare for and cope with nutrient stress. As the ability survive in environments with restricted food availability is likely a stronger evolutionary driver than the ability to live a long life, chm is still present in the organism’s genome despite its apparent negative effect on lifespan.

overall_design: Anuroop V Venkatasubramani

first: Axel

last: Imhof


title: Transcriptomic profiling of MGT#1-mVenus-reporter harboring A549 and H1944 cells upon stimulation with GSK126 and TGF-β1.

status: Public on Aug 20 2023

first: Gaetano

last: Gargiulo

institute: Max-Delbrück-Centrum für Molekulare Medizin

summary: Investigation of gene expression profiles of MGT#1-mVenus-reporter harboring A549 and H1944 lung cancer cell lines upon PRC2 inhibition (GSK126) and activation of TGF-β1 pathway (TGF-β1).

overall_design: MGT#1-mVenus harboring A549 and H1944 cells were treated with GSK126 (5 μM) or TGF-β1 (5 ng/ml) for 11 days, sorted by FACS for MGT#1-mVenus high and low expression alongside naïve controls, and subjected to whole transcriptome profiling.

first: Michela

last: Serresi

first: Yuliia

last: Dramaretksa

first: Lifei

last: Li


title: The Swi-Snf chromatin remodeling complex mediates gene activation through metabolic control.

first: Andrew

last: Price


title: NFIB facilitates replication licensing by acting as a genome organizer

first: Yongjie

last: Liu


title: DNA topology analysis reveals stable compartments and TADs in malignant and normal uveal melanocytes as novel molecular features of uveal melanoma

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

summary: To elucidate if regulation of gene expression could be linked to chromatin organization and DNA folding, we investigated the chromatin structure and DNA topology of two uveal melanoma models.

overall_design: The HiC dataset was composed of  several biological replicates of Uveal Melanoma models:  MP41 and MP46

first: Joshua

last: Watterfall


title: Astrovirus replication is dependent on induction of double membrane vesicles through a PI3K-dependent, LC3-independent pathway

city: Memphis

first: Stacey

last: Schultz-Cherry

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: The cellular response to astrovirus infection is not well defined. We used single cell RNA sequencing (scRNA-seq) to determine cellular response to astrovirus early or late in infection.

overall_design: Caco-2 cells were infected with HAstV-1 or mock control and collected at 4, 8, and 24-hpi for scRNA-seq analysis

first: Shaoyuan

last: Tan

first: Theresa

last: Bub

first: Ana

last: Vazquez-Pagan

first: Tim

last: Flerlage


title: Epigenomic analysis of regulatory evolution in mole rats

city: London

first: Diego

last: Villar

address: 4 Newark Street, Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

summary: Changes in gene regulation have long been though to underlie most phenotypic differences between species. Subterranean rodents, and in particular the naked mole-rat (NMR), have attracted substantial attention due to their proposed phenotypic adaptations, which include hypoxia tolerance, metabolic changes and cancer resistance. However, it is largely unknown what regulatory changes may associate with these phenotypic traits, and whether these are unique to the NMR, the mole-rat clade or also present in other mammals. Here, we undertook a comparative genomics approach to identify genome-wide promoter and enhancer regions harbouring epigenomic hallmarks of regulatory activity, in heart and liver from two mole-rat species (NMR and DMR) and two rodent outgroups.  To identify promoters and enhancers displaying robust shifts in regulatory activity in the mole-rat clade, we adapted and applied a phylogenetic modeling approach to quantitatively compare epigenomic signals at orthologous locations, while accounting for phylogenetic distance and inter-species variation. This method identified thousands of orthologous promoter and enhancer regions with increased activity in ancestral or single-species mole-rat branches, as well as hundreds of promoters and enhancers with reduced activity in mole-rats versus other rodents. These elements underlie both shared tissue-specific changes in gene regulation associated with mole-rat evolution, which include metabolic and functional adaptations in heart and liver. Moreover, by comparing mole-rat specific changes in promoters and enhancers between ancestral and single-species branches, our data revealed a number of candidate pathways with stepwise regulatory changes during mole-rat evolution. Lastly, we analysed the genomic properties of non-alignable promoters and enhancers in mole-rats, and report (i) their overlap with specific repetitive elements and transcription factor binding sites; and (ii) their association with metabolic gene functions.  On the whole, these comparative analyses reveal mole-rat specific epigenomic changes across orthologous and non-mappable promoters and enhancers - which inform previously reported mole-rat adaptations from a gene regulation perspective.

sample_organism:
Mus musculus
Cavia porcellus
Heterocephalus glaber
Fukomys damarensis

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) for histone postranslational modifications H3K27ac, H3K4me3 and H3K4me1 in liver and heart tissues from naked mole-rat, damaraland mole-rat, guinea pig and mouse (with three to six biological replicates)

first: Elise

last: Parey

last: Fernandez-Aroca

first: Stephanie

last: Frost

first: Camille

last: Berthelot


title: Gene expression analysis of malignant and normal uveal melanocytes reveals novel molecular features of uveal melanoma

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: As a starting point of our integrative analysis, we performed a gene expression analysis to compare the transcriptome of UM models to normal choroidal melanocytes..

overall_design: The RNAseq dataset was composed of five normal melanocytes cell lines (NM) including a technical replicate, four MP41 biological replicates and three MP46 biological replicates

first: David

last: Gentien

first: Ariane

last: Jolly


title: RNA sequencing of SARS-CoV and SARS-CoV-2 N proteins expressing cell lines

city: Changchun

first: Yinghua

last: Zhao

address: Dongminzhu street 519

institute: 1st hosptal of Jinli University

summary: SARS-CoV and SARS-CoV-2, the causative agents of severe acute respiratory syndrome (SARS) and coronavirus disease 2019 (COVID-19), are genetically related positive-sense RNA viruses that may cause similar pathophysiology. Despite host could activate interferon responses upon coronaviral infection to suppress virus replication, both SARS-CoV and SARS-CoV-2 have evolved strategies to inhibit interferon response. Here, we constructed SARS-CoV and SARS-CoV-2 N proteins expressing cell lines (HEK293T-N and HEK293T-2N) and performed RNA sequencing analysis, showing that both SARS-CoV-2 and SARS-CoV N proteins could inhibit expression of early growth response gene 1 (EGR1) to suppress interferon response. Moreover, EGR1 could degrade N proteins of SARS-CoV and SARS-CoV-2 in a lysosome-dependent manner, and inhibit viral replication of SARS-CoV-2. Our findings revealed the important role of EGR1 in host innate immune response against SARS-CoV and SARS-CoV-2, which would contribute to understanding the pathogenesis of human coronaviruses and development of antiviral therapies. In addition, we demonstrated that both N proteins could upregulate expression of nervous development-related genes, which may be associated with the neurological symptoms of COVID-19 and SARS patients.

overall_design: We constructed the Flag-tagged SARS-CoV and SARS-CoV-2 N proteins (N and 2N) stably-expressing HEK293T cell lines, Flag-tagged GFP stably-expressing HEK293T cell line was used as a control. The cell lines were transfected with or without poly (I:C). At 24 hours post transfection, cells were collected for RNA sequencing at Majorbio (http://www.majorbio.com/).

first: Quan


title: Fibroblast growth factor 21 ameliorates cholestatic liver injury via a hepatic FGFR4-JNK pathway

status: Public on Aug 19 2023

city: wenzhou

first: chuanren

last: zhou

address: chashan road

institute: wenzhou meidical university

summary: Cholestasis is characterized by hepatic accumulation of cytotoxic bile acids (BAs), which often subsequentlyleads to liver injury, inflammation, fibrosis, and ultimately liver cirrhosis. Fibroblast growth factor 21 (FGF21) is a liver secreted hormone with pleiotropic effects on the homeostasis of glucose, lipid, and energy metabolism. However, whether hepatic FGF21 plays a role in cholestatic liver injury remains elusive. We found that serum and hepatic FGF21 levels were significantly increased in response to cholestatic liver injury. Hepatocyte-specific deletion of Fgf21 exacerbated hepatic accumulation of BAs, further accentuating liver injury. Consistently, administration of rFGF21 ameliorated cholestatic liver injury in α-naphthylisothiocyanate (ANIT)-treated and Mdr2 deficiency mice. Mechanically, FGF21 activated a hepatic FGFR4-JNK signaling pathway to decrease Cyp7a1 expression, thereby reducing hepatic BAs pool. Our study demonstrates that hepatic FGF21 functions as an adaptive stress-responsive signal to downregulate BA biosynthesis, thereby ameliorating cholestatic liver injury, and FGF21 analogs may represent a candidate therapy for cholestatic liver diseases.

overall_design: Eight-week-old male Mdr2-/- mice treated with vehicle or rFGF21 (1.0 mg/kg) for 4 hours and then collect liver tissues.


title: Comparison of gene expression profiles of Atg7 or Keap1 knockout mouse livers

city: Sendai

first: Keiko

last: Taguchi

state: Miyagi

address: 2-1 Seiryo-machi, Aoba

department: Tohoku Medical Megabank Organization

country: Japan

institute: Tohoku University

summary: Total RNA from mouse whole livers was extracted.

overall_design: Gene expression was measured in livers at the age of 6-8 weeks.

first: Masayuki

last: Yamamoto


title: Rapid Attenuation of B-Cell and Interferon Gamma Associated Chemokines in Clinical Responders to Janus Kinase Inhibition with Upadacitinib in Hidradenitis Suppurativa II.

status: Public on Aug 18 2023

city: Liverpool

first: John

last: Frew

address: Elizabeth St

department: Dermatology

country: Australia

institute: Liverpool Hospital

summary: Serum Proteomic Analysis of patients with Pyoderma Gangrenosum Treated with Tildrakizumab 200mg q4weekly for 12 weeks

overall_design: Retrospective Cohort Study

first: J

middle: W


title: Comparative analysis of Cd61 high and Cd61 low populations of HSCs in M.musculus C97/Bl6 mice.

city: Groningen

first: Leonid

last: Bystrykh

email: l.bystrykh@umcg.nl, l.bystrykh@rug.nl

address: Ant.Deusinglaan 1

department: ERIBA

country: Netherlands

institute: UMCG

summary: Aging leads to a decline in function of hematopoietic stem cells (HSCs) and increases susceptibility to hematological disease. We found CD61 to be highly expressed in aged HSCs. Here we investigate the role of CD61 in identifying distinct subpopulations of aged HSCs and assess how expression of CD61 affects stem cell function. We show that HSCs with high expression of CD61 are functionality superior and retain self-renewal capacity in serial transplantations. A population of aged HSCs with highest CD61 expression is functionally comparable to young HSCs.  These CD61High HSCs display a notably higher quiescence compared to their CD61Low counterparts. We also show that CD61High and CD61Low HSCs are transcriptomically distinct populations within aged HSCs.  Collectively, our research identifies CD61 as a key player in maintaining stem cell quiescence during aging, ensuring the preservation of their functional integrity and potential. Moreover, CD61 emerges as a marker to prospectively isolate a superior, highly dormant population of young and aged HSCs, making it a valuable tool both in fundamental and clinical research.

overall_design:
22-24 month Old male mice were used for the isolation of the hematopoietic stem cells (LT-HSCs). The LT-HSCs were sorted for the following markers: Lin-, Sca1+, cKit+, CD48-, CD150+. Each pool of LT-HSC was divided on LT-HSCs CD61High and 3 samples CD61Low as follows: LT-HSC CD61High : top 10% of LT-HSC,  LT-HSC CD61Low : bottom 10% of LT-HSC population. In both cases 5,000 LT-HSC cells were sorted into 5uL of RLT Plus buffer.
RNA isolation using RNeasy Plus Micro Kit (Quiagen) cDNA conversion was done using SMART-Seq v4 Ultra low input RNA kit for sequencing (TAKARA Bio, 4ng total RNA was used).
Kit used for library preparation: Nextera XT DNA Library Prep, preparation was performed according to the protocol. 1ng of amplified cDNA was used and the remaining volume was supplemented with EB buffer. A 0.6x bead cleanup was performed. Samples were eluted in 14μl EB. Tagmentation was used for primer attachment

first: Natalia

last: Skinder


title: Comparative analysis of gene expression between whole and upper epidermis of humans

city: Yokohama

first: Umi

last: Tahara

state: Kanagawa

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

institute: RIKEN Center for Integrative Medical Sciences

summary: Microarray analysis was performed to analyze genes expressed in whole epidermis and upper epidermis (SG1 and SG2 cells) isolated from healthy human skins.

overall_design: Whole epidermal sheets were separated from dermis by dispase treatment, and upper epidermal sheets containing SG1/2 cells were separated from lower epidermis using exfoliative toxin-A.

first: Toru

last: Atsugi


title: Gene expression profile at single cell level of mouse ear epidermis

summary: Single-cell RNA-seq analysis was performed to analyze genes expressed in epidermal cells isolated from ear skin of adult mice.

overall_design: Epidermal cells of the C57BL/6N mice were isolated from ear skin and analyzed using scRNAseq.

first: Tommy

last: Terooatea


title: Sustained increases in cardiomyocyte protein O-GlcNAc levels leads to cardiac hypertrophy and reduced mitochondrial function without systolic contractile impairment

city: Birmingham

first: Chae-Myeong

last: Ha

state: Alabama

institute: University of Alabama at Birmingham

summary:
Lifestyle and metabolic diseases influence the severity and pathogenesis of cardiovascular disease (CVD) through numerous mechanisms, including regulation via post-translational modifications (PTM). A specific PTM, the addition of O-linked β-N acetylglucosamine (O-GlcNAcylation), has been implicated in both physiological and pathological mechanisms. The current study aimed to test the hypothesis that protein O-GlcNAcylation contributes to cardiac adaptations, and its progression to pathophysiology when sustained in cardiomyocytes.
Using an inducible cardiomyocyte-specific dominant-negative O-GlcNAcase (dnOGAh) overexpression transgenic mouse model, we induced dnOGA in 8-10-weeks-old mouse hearts. We examined the effects of 2-weeks (2wk) and 24-weeks (24wk) dnOGA overexpression, which progressed to a 1.8-fold increase in protein O-GlcNAcylation. 2wk increases in protein O-GlcNAc levels did not alter heart weight or function; however, 24wk increases in protein O-GlcNAcylation led to cardiac hypertrophy, reduced mitochondrial function, fibrosis, and diastolic dysfunction. Interestingly, systolic function was maintained in 24wk dnOGA overexpression, despite several changes in gene expression associated with CVD. Specifically, mRNA-seq analysis revealed several gene signatures, including reduction of mitochondrial oxidative phosphorylation, fatty acid and glucose metabolism pathways, and antioxidant response pathways at 24wk. In contrast, cardiac fibrosis pathway genes were induced at 24wk after dnOGA overexpression. Changes in mitochondrial function after 24wk induction were independent of changes in mitochondrial DNA copy number.
This study indicates that moderate protein O-GlcNAcylation leads to a differential response with an initial reduction of metabolic pathways (2wk phase), which leads to cardiac remodeling (24wk phase) including cardiac hypertrophy, decreased oxidative phosphorylation pathways, and increased cardiac structural changes. This study shows that sustained exposure of elevated protein O-GlcNAcylation in cardiomyocytes alters gene expression and supports a switch to pathophysiological mechanisms of O-GlcNAcylation in adaptive versus maladaptive changes.

overall_design: Comparative gene expression analysis of RNA-seq data from left ventricle tissue using Control, cardiac specific overexpressed dominant negative OGA for 2wk induction and 24 week induction.

first: Sayan

last: Bakshi

first: Luke

last: Potter

first: Adam

middle: R

last: Wende


title: SRSF2 is required for mRNA splicing and spermatogenesis [LACE-seq]

city: Beijing

first: Wenlong

last: Lei

state: 北京

address: 北京市朝阳区北辰西路1号院5号

institute: 中国科学院

summary: Serine/arginine-rich splicing factor 2 (SRSF2), also known as SC35, is a member of a SRs protein family, which plays significant roles in numerous fundamental biological activities. However, the roles and underlying mechanisms of SRSF2 remain largely unclear during spermatogenesis. Here, we report that SRSF2 is involved in alternative splicing and that male germ cell-specific deletion of Srsf2 by Stra8-GFPCre causes absolute infertility and defective spermatogenesis. Further analyses revealed that deletion of Srsf2 in the male germ cells had harmful influences on the differentiation of spermatogonia and meiosis initiation. Mechanistically, by combining RNA-seq data with LACE-seq data, we showed that spermatogenesis, meiotic cell cycle, male gamete generation, reproductive development, and male sex differentiation were involved in the SRSF2 regulatory networks. Furthermore, SRSF2 affects expression and AS of Stra8, Stag3 and Atr in a direct manner, which were critical factors during spermatogenesis. Taken together, our results demonstrate that SRSF2 has important functions in spermatogenesis and male fertility by regulating alternative splicing.

overall_design: We performed LACE-seq  by using wildtype testes at P10 to profile SRSF2-binding sites in testes.

first: Wen-Long

first: Zongchang

last: Du

first: Ruibao

last: Su


title: SRSF2 is required for mRNA splicing and spermatogenesis.

address: 北京市朝阳区北辰西路1号院5号

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

overall_design: Refer to individual Series


title: SRSF2 is required for mRNA splicing and spermatogenesis [RNA-seq]

address: 北京市朝阳区北辰西路1号院5号

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Srsf2WT and Srsf2cKO mice testes at P10


title: Hepatocyte FBXW7-dependent activity of nutrient-sensing nuclear receptors controls systemic energy homeostasis and NASH progression

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

institute: McGill University


title: Red vs white skins of Vitis vinifera cv. ‘Bequignol Noir’

status: Public on Aug 17 2023

city: Potsdam

first: Christian

last: Kappel

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

summary: Transcriptome analysis of red vs white berry skin parts of variegated Vitis vinfera ‘Bequignol Noir’ berries.

overall_design: Two color micoarrays. Two seasons.

first: Thilia

last: Ferrier

first: José

last: Mutus

first: François

last: Barrieu


title: The effect of larval diet on the fecundity-longevity relationship and age-related gene expression in Drosophila melanogaster

city: Norwich

first: David

middle: C.

last: Prince

address: Norwich Research Park

institute: University of East Anglia

summary: Our two main aims were 1) to isolate age-related changes in gene expression in females of the solitary insect, Drosophila melanogaster; and 2) to determine whether experimentally changing the shape of the fecundity-longevity relationship (by changing larvae diet) caused changes in age-related gene expression in these females. To address these aims we extracted RNA from three key tissues (fat body, head and ovary) from females at two time points (10% and 60% mortality phases). Each of these females had experienced one of two treatments: medium-quality larval diet (M) treatment (resulting in a positive fecundity-longevity relationship) and high-quality larval diet (H) treatment (resulting in a negative fecundity-longevity relationship).

overall_design: We used mRNA-seq to identify the RNA profiles in three tissue types (fat body, head and ovary) in two time points (after 10% cohort death (RNA-1) and 60% cohort death (RNA-2)) for two treatments (medium-quality larval diet (M) and high-quality larval diet (H)), with three biological replicates per tissue/time point/treatment combination.

middle: H

last: Collins

middle: C

first: Jenny

last: Donelan

first: Tracey

last: Chapman

first: Andrew

middle: F

last: Bourke


title: Changing expression profiles of circular RNA reveal the key regulators and interaction networks of competing endogenous RNA in neurogenic bladder after suprasacral spinal cord injured

first: Jimeng

last: Ruan

address: No. 45 Changchun Street, Xuanwu District

institute: Xuanwu Hospital Capital Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: Neurogenic bladder (NB) after suprasacral spinal cord injury (SSCI) is an interstitial disease with structural remodeling of bladder tissue and matrix over-deposition. Circular RNAs (circRNAs), which have extensive post-transcriptional regulatory functions, widely participate in the pathogenesis of fibrotic diseases and may be promising new biomarkers and potential therapeutic targets. However, the expression profiles and possible roles of circRNAs in bladder fibrosis and NB after SSCI still remain elusive.  Methods: Spinal cord transection at the T10–T11 level was used to construct the NB after SSCI model in rats. The bladders were collected in rats without (sham) and with (SSCI 1-3 groups) NB status. Morphological observation was performed to detect the severity of bladder fibrosis. The expression profiles of mRNAs and circRNAs were detected by transcriptome high-through-put sequencing. The dynamic changes of differentially expressed mRNAs (DEMs) and circRNAs (DECs) in different time periods of SSCI were further analyzed. Moreover, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were performed to investigate the potential functions. In addition, the co-expression network (circRNA–miRNA–mRNA) was constructed to understand the internal regulating relationships of these DEMs and DECs. The top ten common expressed DECs in each NB stage were subjected to Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) to verify their expression.  Results: Bladder weight, smooth muscle cells hypertrophy, and extracellular matrix gradually increased over time after SSCI. Compared with the normal control (NC) group, 3255 DEMs and 1339 DECs, 3449 DEMs and 1324 DECs, 884 DEMs and 1151 DECs were detected in the SSCI 1-3 groups, respectively. Specifically, circRNA3621, circRNA5775, circRNA3111, and circRNA0586 were significant DECs common to SSCI 1–3 compared with NC group. Moreover, GO enrichment suggested that “inflammatory response”, “inflammatory response” and “chronic inflammatory response” were the key events in NB progression. The KEGG pathway related to “Chemokine signaling pathway”, “IL-17 signaling pathway”, and “TGF-beta signaling pathway” were enriched, implying potential roles in regulatory process.   Conclusion: This study provides a systematic perspective on the potential functions of these DEMs and DECs during bladder fibrosis process and NB after SSCI, and could help pave the way for effective therapeutics for this devastating and complex disease.

overall_design: Twenty female Wistar rats were randomly divided into suprasacral spinal cord injured (SCI) 1–3 and normal control (NC) groups. The spinal cord was completely transected at the T9–T10 level to establish the SCI model. Bladder tissues were collected on days 7, 14, and 28 after the operation. The expression profiles of circRNAs were detected by high-through-put sequencing. Differentially expressed circRNAs (DECs) were chosen for qRT-PCR verification to validate the RNA sequencing results. The results revealed the expression profiles and possible roles of circRNAs in neurogenic bladder of SCI.

first: Xin

last: Cui

first: Zhenhua

last: Shang

first: Tongwen

last: Ou


title: CXCR6 orchestrates brain CD8+ T cell residency and limits mouse Alzheimer’s disease pathology [scRNA-seq4]

first: Hongbo

last: Chi

department: Immunology

institute: St Jude Children's Research Hospital

summary: Our study reveals a previously unappreciated role for microenvironment-specific, inter-cellular crosstalk between CD8+ T cells and microglia in delaying neurodegenerative disease development

overall_design: We used scRNA-seq to profile CD45+ cells from the brain parenchyma of 5xFAD and 5xFAD;B2m-/- mice

first: Hao

last: Shi

first: Yu

last: Sun


title: Using human pluripotent stem cells to dissect the molecular basis of human pharyngeal endoderm development [scRNA_RA_titration]

city: Worcester

first: René

last: Maehr

state: MA

address: 368 Plantation St

department: Program in Molecular Medicine/Diabetes Center of Excellence

institute: UMass Medical School

summary: Developmental defects affecting the pharynx and derived tissues can be found in a variety of syndromes, including DiGeorge, 22q11 deletion, CHARGE and Otofaciocervical syndromes. The associated malformations and dysfunctions of pharynx-derived tissues precipitate phenotypes ranging from malformed features and endocrine disorders to severe immunodeficiency, some of which are associated with high morbidity or elaborate treatment and health care costs. While some of the developmental defects have been linked to mutations or single-nucleotide polymorphisms in transcription factors (TFs) or cis-regulatory elements (CREs), the origin of most pharynx-specific birth defects remain poorly understood and the underlying genetic causes as well as epigenetic context remain elusive. Unfortunately, restricted human tissue access, and discordance of genetic factor requirement and phenotypic penetrance of disease associated human mutations when modeled in mice, has prohibited detailed insights on the molecular basis of mentioned human diseases. Human pluripotent stem cells (hPSCs) could in principle allow for detailed a genetically tractable model to decipher the molecular logic of normal and impaired pharynx development. To unlock hPSC for investigation of pharyngeal malformations and ensuing syndromes, we have developed a differentiation protocol to generate human pharyngeal endoderm in vitro. We have applied multi-omic approaches to characterize the molecular logic of cell fate transitions and developed models of gene regulatory network activities.

overall_design: Single cell transcriptomic data and analysis of 2 replicates profiled using 10X on anterior foregut endoderm of the directed differentiation protocol described in the study in the presence of 4 hashtagged retinoic acid concentrations (no RA, 100nM, 1uM, and 10uM) which were added at DE

first: Nicola

middle: A

last: Kearns

first: Macrina

last: Lobo

first: Ryan

middle: M

last: Genga

middle: G

last: Abramowitz

first: Mohan

last: Parsi

first: Jiang

last: Min

first: Eric

last: Kernfeld

first: Jack

last: Huey

first: Jamie

last: Kady

first: Erica

last: Hennessy

first: Michael

last: Brehm

last: Ziller


title: Hepatocyte FBXW7-dependent activity of nutrient-sensing nuclear receptors controls systemic energy homeostasis and NASH progression [RNA-Seq]

first: Vincent

last: Giguère

summary: Nonalcoholic steatohepatitis (NASH) is epidemiologically associated with obesity and diabetes and can lead to liver cirrhosis and hepatocellular carcinoma if left untreated. The intricate signaling pathways that orchestrate hepatocyte energy metabolism and cellular stress, intrahepatic cell crosstalk, as well as interplay between peripheral tissues remain elusive and are crucial for the development of anti-NASH therapies. Herein, we reveal E3 ligase FBXW7 as a key factor regulating hepatic catabolism, stress responses, systemic energy homeostasis, and NASH pathogenesis, with attenuated FBXW7 expression as a feature of advanced NASH. Multiomics analysis and pharmacological intervention showed that loss of FBXW7 function in hepatocytes disrupts a metabolic transcriptional axis conjointly controlled by the nutrient-sensing nuclear receptors ERRα and PPARα, resulting in suppression of fatty acid oxidation, elevated ER stress, apoptosis, immune infiltration, fibrogenesis, and ultimately NASH progression. These results provide the foundation for developing alternative strategies co-targeting ERRα and PPARα for the treatment of NASH.

overall_design: RNA-seq analysis of livers (n=4) isolated from WT and ERRa KO mice on a C57BL/6N genetic background fed either a chow or high-fat diet (HFD) for 15 weeks initiated from 6 weeks of age.

first: Catherine

last: Dufour

first: Wafa

last: B'Chir

first: Hui

last: Xia

last: Giguere


summary: Nonalcoholic steatohepatitis (NASH) is epidemiologically associated with obesity and diabetes and can lead to liver cirrhosis and hepatocellular carcinoma if left untreated. The intricate signaling pathways that orchestrate hepatocyte energy metabolism and cellular stress, intrahepatic cell crosstalk, as well as interplay between peripheral tissues remain elusive and are crucial for the development of anti-NASH therapies. Herein, we reveal E3 ligase FBXW7 as a key factor regulating hepatic catabolism, stress responses, systemic energy homeostasis, and NASH pathogenesis, with attenuated FBXW7 expression as a feature of advanced NASH. Multiomics analysis and pharmacological intervention showed that loss of FBXW7 function in hepatocytes disrupts a metabolic transcriptional axis conjointly controlled by the nutrient-sensing nuclear receptors ERRa and PPARa, resulting in suppression of fatty acid oxidation, elevated ER stress, apoptosis, immune infiltration, fibrogenesis, and ultimately NASH progression. These results provide the foundation for developing alternative strategies co-targeting ERRa and PPARa for the treatment of NASH.

overall_design: ChIP-seq analysis of livers isolated from 24 h-fasted flox (control) and liver-specific Fbxw7 KO (Fbxw7 LKO) on a C57BL/6J genetic background.

first: Charlotte

last: Scholtes


title: Using human pluripotent stem cells to dissect the molecular basis of human pharyngeal endoderm development [RNA-seq]

last: Maehr

overall_design: Gene expression profiling analysis of RNA-seq data from a directed differentiation protocol of human embryonic stem cells (hESCs) toward pharyngeal foregut endoderm (hPFE). 4 timepoints are profiled : hESC, definitive endoderm (hDE), anterior foregut endoderm (hAFE) and hPFE with 2 replicates each

last: Kearns

last: Lobo

middle: J


title: Regulators of mitonuclear balance link mitochondrial metabolism to mtDNA expression

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

institute: Université de Sherbrooke

summary: Mitochondrial oxidative phosphorylation (OXPHOS) complexes are assembled from proteins encoded by both nuclear and mitochondrial DNA. These dual-origin enzymes pose a complex gene regulatory challenge for cells requiring coordinated gene expression across organelles. To identify genes involved in dual-origin protein complex synthesis, we performed fluorescence-activated cell-sorting-based genome-wide screens analysing mutant cells with unbalanced levels of mitochondrial- and nuclear-encoded subunits of Complex IV. We identified genes involved in OXPHOS biogenesis, including two uncharacterized genes: PREPL and NME6. We found that PREPL specifically impacts Complex IV biogenesis by acting at the intersection of mitochondrial lipid metabolism and protein synthesis, whereas NME6, an uncharacterized nucleoside diphosphate kinase, controls OXPHOS biogenesis through multiple mechanisms reliant on its NDPK domain. Firstly, NME6 forms a complex with RCC1L, which together perform nucleoside diphosphate kinase activity to maintain local mitochondrial pyrimidine triphosphate levels essential for mitochondrial RNA abundance. Secondly, NME6 modulates the activity of mitoribosome regulatory complexes, altering mitoribosome assembly and mitochondrial RNA pseudouridylation. Taken together, we propose that NME6 acts as a link between compartmentalized mitochondrial metabolites and mitochondrial gene expression.

overall_design: Direct RNA nanopore sequencing for analysis of mitochondrial transcriptome

first: Nicholas

last: Kramer

first: Gyan

last: Prakash

first: R

middle: S

last: Isaac

first: Iliana

last: Soto

first: Boryana

last: Petrova

first: Hope

last: Merens

first: Naama

last: Kanarek

first: L

last: Churchman


title: Using human pluripotent stem cells to dissect the molecular basis of human pharyngeal endoderm development [scRNA-Seq]

first: René

overall_design: Single cell transcriptomic data and analysis from a directed differentiation protocol of human embryonic stem cells (hESCs) toward pharyngeal foregut endoderm (hPFE). 4 timepoints are profiled : hESC (3 replicates), definitive endoderm (hDE) (2 replicates), anterior foregut endoderm (hAFE) (2 replicates) and hPFE (1 replicate )

first: Nicola

first: Macrina

first: Ryan

last: Genga

last: Abramowitz

first: Mohan

last: Parsi

first: Jiang

last: Min

first: Eric

last: Kernfeld

first: Jack

last: Huey

first: Jamie

last: Kady

last: Brehm

last: Ziller


title: Using human pluripotent stem cells to dissect the molecular basis of human pharyngeal endoderm development [ATAC-seq]

last: Maehr

overall_design: Chromatin accessibility profiling analysis of ATAC-seq data from a directed differentiation protocol of human embryonic stem cells (hESCs) toward pharyngeal foregut endoderm (hPFE). 4 timepoints are profiled : hESC (2 replicates), definitive endoderm (hDE) (2 replicates), anterior foregut endoderm (hAFE) (2 replicates) and hPFE (1 replicate )

last: Kearns

last: Lobo

first: Michael


title: Using human pluripotent stem cells to dissect the molecular basis of human pharyngeal endoderm development II


city: Boston

first: Nicholas

last: Kramer

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Mitochondrial oxidative phosphorylation (OXPHOS) complexes are assembled from proteins encoded by both nuclear and mitochondrial DNA. These dual-origin enzymes pose a complex gene regulatory challenge for cells requiring coordinated gene expression across organelles. To identify genes involved in dual-origin protein complex synthesis, we performed FACS-based genome-wide screens analyzing mutant cells with unbalanced levels of mitochondrial- and nuclear-encoded subunits of Complex IV. We identified novel genes involved in OXPHOS biogenesis, including two uncharacterized genes: PREPL and NME6. We found that PREPL specifically impacts Complex IV biogenesis by acting at the intersection of mitochondrial lipid metabolism and protein synthesis, while NME6, an uncharacterized nucleoside diphosphate kinase (NDPK), controls OXPHOS biogenesis through multiple mechanisms reliant on its NDPK domain. First, NME6 forms a complex with RCC1L, which together perform NDPK activity to maintain local mitochondrial pyrimidine triphosphate levels essential for mitochondrial RNA abundance. Second, NME6 modulates the activity of mitoribosome regulatory complexes, altering mitoribosome assembly and mitochondrial RNA pseudouridylation. Taken together, we propose that NME6 acts as a link between compartmentalized mitochondrial metabolites and mitochondrial gene expression.

overall_design: Ribosome profiling and total RNA-sequencing in control and NME6 KO K562 cells

first: Gyan

last: Prakash

last: Isaac

first: Karine

last: Choquet

last: Soto


overall_design: CMC-sequencing to detect pseudouridine modifications in mitochondrial RNA from NME6 and RPUSD4 mutant cells

first: Iliana

first: Boryana

last: Petrova

last: Kanarek

last: Churchman


title: Asymmetric distribution of H3K9me3 at replicating DNA strands silences L1 retrotransposons during S phase

city: New York

first: Zhiguo

last: Zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

summary: In higher eukaryotes, repetitive DNA sequences are transcriptionally silenced through histone H3 lysine 9 tri-methylation (H3K9me3). A loss of silencing of these elements leads to genome instability and human diseases, including cancer and aging1-3. While the role of H3K9me3 in the establishment and maintenance of heterochromatin and repression of DNA repeats has been extensively studied4-6, the pattern and mechanism underlying the partitioning of H3K9me3 at replicating DNA strands were unknown. Here, we report that H3K9me3 is preferentially transferred onto the leading strands of replication forks, which occurs predominantly at Long Interspersed Nuclear Element (LINE) retrotransposons that are theoretically transcribed at the head-on direction with replication fork movement. In contrast, all other modified forms of histones tested are distributed in a nearly symmetric manner at the leading and lagging strands. Mechanistically, the Human Silencing Hub (HUSH) complex interacts with the leading strand DNA polymerase Pol ε, and contributes to the asymmetric segregation of H3K9me3 during chromatin replication. Cells deficient for Pol ε (POLE3 and POLE4), the HUSH complex (MPP8 and TASOR), or cells expressing a MPP8 mutant defective of H3K9me3 binding, or TASOR mutants with reduced interaction with Pol ε, show compromised H3K9me3 asymmetry and increased LINE expression. These results reveal an unexpected mechanism whereby the HUSH complex functions with Pol ε to promote asymmetric H3K9me3 distribution at LINEs to suppress their expression during S phase.

overall_design: The CUT&TAG, CUT&RUN, and eSPAN experiments were conducted in WT, MCM2-2A, POLE3KO, POLE4KO,MPP8KO,TASORKO,POLE3MPP8KO,SETDB1KD, G9aKO, GLPKO, SUV39h1KO, etc mES cells, activated mouse B cells and HeLa cells. The histone markers performed by CUT&TAG and eSPAN methods in mES cells , activated mouse B cells and HeLa cells included H3K9me3, H3K9me2, H3K27me3 ,H4K20me3, H4K20me2 etc. For the regulation of gene expression, we performed GRO-seq experiments in WT, MCM2-2A mutant, POLE3 KO and POLE4 KO mES cells.

first: Zhiming

last: Li

first: Shoufu

last: Duan

first: Xu

last: Hua

first: Xiaowei

last: Xu

first: Yinglu

first: Hui

last: Zhou


title: Using human pluripotent stem cells to dissect the molecular basis of human pharyngeal endoderm development [ChIP-seq]

first: René

last: Maehr

overall_design: Histone mark analysis of ChIP-seq data from a directed differentiation protocol of human embryonic stem cells (hESCs) toward pharyngeal foregut endoderm (hPFE). 4 timepoints and 3 marks are profiled as follows: hESC H3K4me2 (2 replicates), hESC H3K27ac (2 replicates), hESC H3K27me3 (2 replicates), definitive endoderm (hDE)  hDE H3K4me2 (2 replicates), hDE H3K27ac (2 replicates), hDE H3K27me3 (2 replicates), anterior foregut endoderm (hAFE)  hAFE H3K4me2 (1 replicate), hAFE H3K27ac (2 replicates), hAFE H3K27me3 (1 replicate), and hPFE H3K4me2 (1 replicate), hPFE H3K27ac (2 replicates), hPFE H3K27me3 (2 replicates). Additionally, control samples were processed as follows: hESC (2 replicates), hDE (2 replicates), hAFE (2 replicates), hPFE (2 replicates)

first: Nicola

first: Macrina

first: Ryan

last: Genga

last: Abramowitz

first: Mohan

last: Parsi

first: Jiang

last: Min

last: Kernfeld

last: Huey

last: Kady

last: Brehm

last: Ziller


title: CXCR6 orchestrates brain CD8+ T cell residency and limits mouse Alzheimer’s disease pathology [scRNA-seq2]

city: Memphis

first: Hongbo

last: Chi

address: 262 Danny Thomas Place

overall_design: We used scRNA-seq and scTCR-seq to profile CD45+ cells from the brain parenchyma and meninges of 5xFADTg and NonTg mice

first: Hao

last: Shi

first: Yu

last: Sun

first: Isabel

last: Risch


title: CXCR6 orchestrates brain CD8+ T cell residency and limits mouse Alzheimer’s disease pathology [microarray]

overall_design: We used microarrays to compare the global transcription profiles of  brain microglia from 5XFAD and 5XFAD B2m KO mice

first: Wei

last: Su


title: CXCR6 orchestrates brain CD8+ T cell residency and limits mouse Alzheimer’s disease pathology [scRNA-seq1]

overall_design: We used scRNA-seq and scTCR-seq to profile CD45+ cells from the brain parenchyma of 5xFAD and 5xFAD;Cxcr6-/- mice


title: Role of ZmCCT in drought tolerance of maize by transcriptome and DAP-seq experiments

status: Public on Aug 16 2023

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

summary: Abiotic stressors are widespread in plants and can affect their growth, productivity, and quality. Previously, the maize transcription factor ZmCCT was been proved to be involved in the photoperiod response, delayed flowering and quantitative resistance to Gibberella stalk rot. In this study, we demonstrate that ZmCCT can regulate plant drought stress. ZmCCT physically interacted with ZmFra a 1, ZmWIPF2, and ZmAux/IAA8, which localised to the cytomembrane, cytoplasm, and nucleus, respectively, both in vitro and in vivo in a yeast two-hybrid screen in response to abiotic stress. Notably, ZmCCT recruits ZmWIPF2 to the nucleus, which has strong E3 self-ubiquitination activity dependent on its RING-H2 finger domain in vitro. When treated with higher indole-3-acetic acid (IAA)/abscisic acid (ABA) ratios, the height and root length of Y331-ΔTE increased, and this resulted in an increase in auxin and ABA tolerance. In vivo, ZmCCT promoted IAA biosynthesis in ZmCCT-overexpressed Arabidopsis. RNA-seq and DAP-seq analyses showed that ZmCCT can regulate the expression of ZmRD17, ZmAFP3, ZmPP2C and ZmARR16 under drought stress. Our finding provides a detailed overview of the molecular mechanism controlling ZmCCT functions and highlights that it HAS multiple roles in promoting stress tolerance.

overall_design: For maize RNA-seq analysis, pooled leaf tissues from three maize seedlings at three-leaf stage were collected from Y331-ΔTE (control, stalk rot-resistant) and Y331 (TE insertion caused non-functional ZmCCT) and plants before or after drought stress to conduct the RNA-seq analysis. Three biological replicates of RNA-seq were included for each condition. Further more, ZmAux/IAA8, a interacting partner of ZmCCT, was fused to Halotag and conducted DAP-seq (DNA Affinity Purification sequencing) to identify its target regions in maize genome. Two biological replicates of IP samples and one replicate of input samples were included for DAP-seq experiment.

first: Zhaoheng

first: Jiayue

last: Qu

first: Min

last: Lu

first: Weixiang

last: Wang


title: Replating of Human Pluripotent Stem Cell Derived Cardiomyocytes Induces a Shift in Myosin Heavy Chain Expression and Changes in Contractile Function

city: Hannover

first: Joachim

middle: D.

last: Meissner

address: Carl-Neuberg-Str. 1

department: Molecular and Cellular Physiology

institute: Hannover Medical School

summary: Human embryonic stem cell-derived cardiomyocytes (hESC-CMs) and human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) grown for 35 days on laminin-coated coverslips, a stiff matrix, were enzymatically dissociated, replated on laminin-coated coverslips and grown for further 2 days. Gene expression was compared with controls grown for 37 days on laminin-coated coverslips. Total RNA was isolated and gene expression was analyzed by RNA-sequencing (RNA-seq) on an Illumina NextSeq 550 sequencer using a High Output Flowcell for single reads (20024906; Illumina). Gene enrichment analysis based on RNA-Seq data of hESC-CMs replated for 2 days as compared with 37 days old controls was performed by using the comprehensive gene set enrichment analysis tool Enrichr for pathway analysis with KEGG Pathways 2019 Human, as well as for Gene Ontology (GO) analysis with GO Cellular Component 2018, GO Molecular Function 2018, and GO Biological Process 2018. Gene enrichment was also analyzed by Ingenuity Pathway analysis (IPA, Qiagen), especially Canonical Pathways analysis. Gene enrichment analysis revealed changes in the gene expression profile, especially of mechanosensation/-transduction-related genes and pathways in replated hESC-CMs.

overall_design: Gene enrichment analysis based on RNA-Seq data from hESC-CMs replated on day 35 and cultivated for 2 more days versus hES-CMs cultivated for 37 days

first: Theresia

last: Kraft

first: Felix

last: Osten


title: NFIB Is a Pioneer Factor for DNA Replication by Acting as a Genome Organizer [CUT&TAG]

first: Yongjie

last: Liu

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology

summary: Genome-wide binding profile of NFIB and ORC1 in G1 phase of U2OS cells without or with NFIB depletion were profiled using cleavage under targets and tagmentation sequencing (CUT&Tag-seq).

overall_design: CUT&Tag-seq librarys of NFIB- or ORC1- associated chromatin were immunoprecipitated in G1 phase of U2OS cells without or with NFIB depletion.

first: Wenting


title: RNA Sequencing of Semitendinosus Skeletal Muscle from Intrauterine Growth Restricted and Normally-Grown Near Term Sheep Fetuses and 30 day old Lambs

city: Tucson

first: Sean

last: Limesand

state: AZ

address: 4101 N Campbell Ave

department: Animal & Comparative Biomedical Sciences

institute: University of Ariziona

summary: The study objective was to determine differentially expressed mRNA transcripts in skeletal muscle from fetal sheep and 30 day old lambs to determine persistent gene changes following placental insufficiency-induced intrauterine growth restriction.

overall_design: Semitendinosus muscle was isolated for high-throughput sequencing from 30 day old lambs and sheep fetuses with placental insufficiency-induced IUGR and controls. IUGR and control lambs were nourished the same with milk replacer to eliminate variables from maternal milk production.

first: S


title: BMAL1 Modulates Senescence Programming via AP-1 (WT and Bmal1 KO RNA-seq)

city: Rochester

first: Sarah

middle: Katherine

last: Jachim

state: MN

address: 222 3rd Ave SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

summary:
Cellular senescence and circadian dysregulation are biological hallmarks of aging. Whether they are interdependent has not been thoroughly studied. We hypothesize that BMAL1, a pioneer transcription factor and master regulator of the molecular circadian clock, plays a role in the senescence program.
In this study, we show that BMAL1 in is uniquely localized to genomic motifs associated with AP-1 in senescent cells and contributes to AP-1 transcriptional control of the senescence program.

overall_design: Triplicate samples of control and senescent primary mouse fibroblasts, from WT C57BL/6 mice and Bmal1 -/- mice were collected for RNA-seq 12 hours post-synchronization with dexamethasone.

first: Zain

last: Alvi


title: MLL-AF4 cooperates with PAF1 and FACT to drive high density enhancer interactions in leukemia [ChIP-seq]

city: London

first: Nick

last: Crump

address: Du Cane Road

department: Dept of Immunology and Inflammation

institute: Imperial College London

summary: Aberrant enhancer activation is a key mechanism driving oncogene expression in many cancers. While much is known about the regulation of larger chromosome domains in eukaryotes, the details of enhancer-promoter interactions remain poorly understood. Recent work suggests co-activators like BRD4 and Mediator have little impact on enhancer-promoter interactions. In leukemias controlled by the MLL-AF4 fusion protein, we use the ultra-high resolution technique Micro-Capture-C (MCC) to show that MLL-AF4 binding promotes broad, high-density regions of enhancer-promoter interactions at a subset of key targets. These enhancers are enriched for transcription elongation factors like PAF1C and FACT and loss of these factors abolishes enhancer-promoter contact. This work not only provides an additional model for how MLL-AF4 is able to drive high levels of transcription at key genes in leukemia, but also suggests a more general model linking enhancer-promoter crosstalk and transcription elongation.

overall_design: ChIP-seq

first: Nicholas

middle: T

first: Alastair

middle: L

last: Smith

first: Thomas

last: Milne


title: Genome wide analysis of binding regions for MYC, MYCN and various histone modifications using Cut&Run

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

summary: Cut&Run analysis was performed in RPMI-8402 cells to analyze binding regions of MYC, MYCN and various histone modifications in normal culture conditions

overall_design: RPMI-8402 cells were incubated with antibodies specific to MYC(CST, #5605), MYCN(CST, #84406), H3K4me3 (Epicypher, 13-0041), H3K27ac (Abcam, ab4729), H3K4me1 (Abcam, ab176877) or control IgG (CST, #2729) overnight and subsequently with CUTANA pA/G-Mnase to release cleaved chromatin fragments. Chromtain fragments were then purified utilizing with DNA purification kit. Libraries were generated using a NEBNext Ultra II DNA library prep kit and sequencing was performed on Illumina NovaSeq at GENEWIZ Azenta Life Sciences Co. Ltd.

first: Shi

first: Tze

middle: K

first: Takaomi

last: Sanda