title: Whole genome RNA sequencing analysis to measure the effect of Ehmt2 (G9a, Bat8) deficiencies in somite-staged mouse embryos

first: Piroska

last: Szabó

summary: The experiment was designed to interpret transcription changes in embryos that are developmentally delayed due to different genetically induced deficiencies in the Ehmt2 gene encoding the H3K9 methyltransferase EHMT2. The deficiencies included zygotic homozygosity, maternal mutation, and parental (maternal, paternal, and biparental) haploinsufficiencies, and their respective controls. The age of the embryos was between 8.5 and 9.5 dpc to allow collecting somite-stage matched embryos and detect transcriptome changes shortly before the death of homozygous mutant embryos at 10.5 dpc. Analyzing the  homozygous mutants in a novel four-way comparison we distinguished differentially expressed genes (DEGs) that are direct effects of the mutation from those that correspond to embryo development. We separated the developmental DEGs that occur regardless of EHMT2 between the 6-and 12-somite stages, and then identified those developmental DEGs that uniquely change in either the normal or the mutant development. Ehmt2 zygotic and maternal mutant embryos display an increased variance, suggesting that EHMT2 is responsible for narrowing the transcriptional noise after gastrulation. Some transposable element classes correlate with genotype, but others correlate with developmental stage. EHMT2 is required for suppressing long noncoding transcripts that initiate in transposable elements predominantly of the ERVK-class. The ERVK promoters of noncanonical imprinted genes in the embryo require EHMT2 for biallelic silencing and DNA methylation. The transcriptome of delayed parental haploinsufficient wild type embryos is normal, consistent with their good survival prospects. Our four-way comparison approach is generally applicable to functional dissection of essential transcriptional regulators during development.

overall_design: We performed allele-specific and RNA strain-specific RNA-seq analysis of total RNA samples isolated from individual, 8.5-9.5 dpc somite stage-matched embryos carrying different deficiencies of Ehmt2. The genotypes and parental genotypes regarding the Ehmt2 mutant allele varied to allow detecting robust or subtle RNA changes due to the specific deficiencies in EHMT2 function. Maternal mutant, maternal haploinsufficient, paternal haploinsufficient and control embryos were collected at the 6-somite stage. Zygotic homozygous and wild type embryos were collected at the 6-somite and 12-somite stage to allow measuring transcriptomic differences in the progression of development. Reciprocal mouse crosses between the 129S1 and JF1/Ms mouse strains were used to generate the embryos to allow distingushing the parental alleles. Four replicate embryos (2 males and 2 females) were collected for RNAseq analysis from each condition above. Additionally, two of the rarely found maternal-zygotic mutant female embryos were included. Total RNA was deep sequenced to allow detecting non-coding RNAs.

first: Zeng

last: Tie-Bo

first: Pierce

last: Nicholas

first: Szabó

last: Piroska


title: Role of the major determinant of polar flagellation FlhG in the endoflagella-containing spirochete Leptospira

status: Public on Oct 31 2021

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

type: Expression profiling by high throughput sequencing

summary: To better understand the mechanisms underlying the motility phenotype observed in the flhG mutant, we used RNA-Seq to compare the transcriptomes of wild-type L. biflexa with that of the flhG  and hfq-like mutants under ideal culture conditions at mid-log phase.

overall_design: RNA prepared from exponential-phase cultures of L. biflexa in triplicates

first: Mathieu

last: Picardeau

first: Lenka

last: Fule

first: Odile

last: Sismeiro

first: Hugo

last: Varet


title: Sex‐specific accelerated decay in time/activity‐dependent plasticity and associative memory in an animal model of Alzheimer's disease

status: Public on Oct 30 2021

city: Singapore

first: Jessica

middle: R

last: Gaunt

address: 11 Mandalay Road

department: LKC Medicine

country: Singapore

institute: Nanyang Technological University

summary: In a series of slice electrophysiology experiments, we demonstrated that female APPSwe-Psen1dE9 Alzheimer's disease model mice show greater impairments in hippocampal synaptic plasticity than male mice of the same age and genotype. Female APP/PS1 mice also showed greater impairments in behavioural associative memory, higher amyloid plaque burden and increased microglial activation in the hippocampus than males at age 4-5 months. We thus profiled hippocampal mRNA from these mice to investigate the underlying molecular mechanisms. Compared to wild-type mice of the same sex, we found that female APP/PS1 mice showed a greater upregulation of microglial and inflammatory genes than males. Moreover, downregulation of genes associated with memory and plasticity was observed uniquely in female APP/PS1 mice. These data provide insight into the potential mechanisms of the greater prevalence and faster progression of AD in females.

overall_design: Sex differences in the hippocampal transcriptome of APPSwe-Psen1dE9 Alzheimer's disease model mice

first: Sheeja

last: Navakkode

first: Toh

middle: H

last: Ch'ng

first: Sreedharan

last: Sajikumar


title: Single-cell RNA-seq analysis reveals two specific endothelial cells promote fracture healing

status: Public on Nov 01 2021

city: shanghai

first: Renkai

last: Wang

address: 168 Changhai Road,

country: China

institute: changhai hospital

summary: Recent studies have identified a bone vessel subtype of CD31hi endomucinhi (CD31hiEMCNhi) endothelium that positively promotes bone formation. However, it remains unknown how CD31hiEMCNhi endothelium participate in the healing of fractures. Here we find that CD31hiEMCNhi endothelial cells increase significantly during fracture healing by single-cell profiling. Furthermore, CD31hiEMCNhi endothelial cells can balance membrane and cartilage osteogenesis in this progress. Moreover, two different types of CD31hiEMCNhi endothelial cells were found in this progress, One of these endothelial cells tends to deliver molecules that induce mesenchymal stem cells differentiate into osteoblast. The other one tends to deliver inflammatory factors associated with osteoclasts. Thus, our study indicates that two specific endothelial cells promote fracture healing and may represent a potential treatment for promoting fracture healing.

overall_design: scRNA profiles of fracture at different stage(control group, third day, 7th day, 14th day)

first: Hao

last: Tang


title: A dual role of human tRNA methyltransferase hTrmt13 in regulating translation and transcription [RNA-seq]

status: Public on Oct 29 2021

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hosipital

summary: Since numerous RNAs and RBPs prevalently localize to active chromatin regions, many RNA binding proteins (RBPs) may be potential transcriptional regulators. RBPs are generally thought to regulate transcription via noncoding RNAs. Here, we describe a distinct, dual mechanism of transcriptional regulation by the previously uncharacterized tRNA-modifying enzyme, hTrmt13. On one hand, hTrmt13 acts in the cytoplasm to catalyze 2'-O-methylation of tRNAs, thus regulating translation in a manner depending on its tRNA-modification activity. On the other hand, nucleus-localized hTrmt13 directly binds DNA as a transcriptional co-activator of key epithelial mesenchymal transition factors, thereby promoting cell migration independent of tRNA-modification activity. These dual functions of hTrmt13 are mutually exclusive, as it can bind either DNA or tRNA through its CHHC zinc finger domain. Finally, we find that hTrmt13 expression is tightly associated with poor prognosis and survival in diverse cancer patients. Our discovery of the noncatalytic roles of an RNA modifying enzyme provides a new perspective for understanding epitranscriptomic regulation.

overall_design: RNA-seq (Control and Knockdown) and CHIP-seq to identify hTrmt13 transcription target genes. All Samples have 2 replicates. CLIP-seq to identify it's tRNA binding targets

last: Li

first: Rujuan

last: Liu


title: Dynamic O-GlcNAcylation of eIF3a controls translation reinitiation during integrated stress response

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

summary: In eukaryotic cells, many mRNAs possess upstream open reading frames (uORFs) in addition to the main coding region. After uORF translation, the ribosome could either recycle at the stop codon or resume scanning for downstream start codons in a process known as reinitiation. Accumulating evidence suggests that some initiation factors, including eIF3, linger on the early elongating ribosome, forming an eIF3-80S complex. Very little is known how the eIF3 is carried along with the 80S during elongation and its implications in subsequent translation reinitiation. Here we report that eIF3a undergoes dynamic O-GlcNAc modification in response to nutrient starvation. Stress-induced de-O-GlcNAcylation promotes eIF3 retention on the elongating ribosome and facilitates reinitiation at downstream start codons. Eliminating the modification site from eIF3a via genome editing induces ATF4 reinitiation under the nutrient rich condition. Our findings illustrate a mechanism in balancing ribosome recycling and reinitiation, thereby linking integrated stress response and translational reprogramming.

overall_design: Ribo-seq and eIF3-seq of WT and OTG knockout MEF cells with or without starvation, and with or without ThiametG treatment.

first: Xin

middle: E

last: Shu

first: Shu-Bing

last: Qian


title: A dual role of human tRNA methyltransferase hTrmt13 in regulating translation and transcription [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing


title: A dual role of human tRNA methyltransferase hTrmt13 in regulating translation and transcription

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

overall_design: Refer to individual Series


title: A transcriptome study of a non-shedding fruit Elaeis oleifera palm

status: Public on Oct 28 2021

city: Montpellier

first: Timothy

middle: John

last: TRANBARGER

address: 911 avenue agropolis BP 64501

department: Ecology, Biodiversity and Functioning of Continental Ecosystems (ECOBIO)

institute: Institut de Recherche pour le Développement

summary: A comparative transcriptome analysis was performed to compare the fruit AZs of the non-shedding E. oleifera variant and from an individual of the same progeny that sheds its ripe fruit normally. The study provides evidence for widespread perturbation to gene expression in the AZ of the non-shedding variant, compared to the normal fruit-shedding control, and allows insight into abscission related functions.

overall_design: We used an RNA-Seq approach to determine globally the expression of genes affected in the variant compared with that of an E. oleifera individual that normally sheds its fruit.

middle: J

last: Tranbarger

first: Fabienne

last: Morcillo


title: A dual role of human tRNA methyltransferase hTrmt13 in regulating translation and transcription [CLIP-seq]


title: Cellular heterogeneity of circulating CD4+CD8+ double positive T cells characterized by single-cell RNA sequencing

status: Public on Oct 27 2021

city: Seoul

first: Jaeil

last: Lee

address: 103 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

summary: We subdivided circulating CD4+CD8+ double positive T cells, which are known to be related to various disease environments, into several subtypes through single-cell RNA sequencing, and compared gene signatures according to CD4 and CD8 protein expression levels using CD4 and CD8 antibody derived tags (feature barcode).

overall_design: Heterogeneous subsets of circulating CD4+CD8+ double positive T cells were analyzed by scRNA-seq after labeling CD4 and CD8 feature barcodes, characterized their characteristic with CD4, CD8 coreceptor expresion levels.

first: Jae

middle: I

first: Sung

middle: M

last: Choi


title: MINCR: a Long non-coding RNA shared between cancer and neurodegeneration

status: Public on Oct 26 2021

city: Pavia

first: Maria

last: Garofalo

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

summary: Investigating MINCR potential mechanisms of action and its implications in cancer and neurodegeneration in relation to its expression levels in SH-SY5Y cells through RNA-seq approach.

overall_design: Whole transcriptome analysis of SH-SY5Y neuronal cells carrying overexpression (SH-MINCR+) (n=4) and down-regulation (SH-siMINCR) (n=4) of MINCR compared to wild type cells (SH-MOCK) (n=4).

first: Cecilia

last: Pandini

first: Federica

last: Rey

last: Garau

first: Susanna

last: Zucca

first: Daisy

last: Sproviero

first: Matteo

last: Bordoni

first: Giulia

last: Berzero

first: Annalisa

last: Davin

first: Tino

last: Poloni

first: Orietta

last: Pansarasa

first: Stephana

last: Carelli

first: Stella

last: Gagliardi

first: Cristina

last: Cereda


title: RNAseq of Colletotrichum orbiculare on Nicotiana benthamiana

city: Yokohama

first: Pamela

last: Gan

state: Kanagawa

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

department: RIKEN Plant Sciences

country: Japan

institute: RIKEN

summary: Time course of C. orbiculare infection of the host plant, N. benthamiana, and comparison to in vitro grown tissue (conidia and in vitro grown hyphae) to identify genes that  contribute to the infection process by transcript expression profile.

overall_design: Transcript expression profiles of C. orbiculare at 1, 3 and 7 days post inoculation (dpi) of N. benthamiana as well as conidia and in vitro grown hyphae

first: Gan

last: Pamela


title: Valine tRNA biogenesis and bioavailability regulates mitochondrial complex I levels in acute leukemia [CRISPR screen]

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

country: Germany

institute: Helmholtz Centre for Infection Research

summary: We report the effects of gene knockout via CRISPR/Cas9 system targeting either the whole genome or specifically genes involved in tRNA biogenesis in T cell acute lymphoblastic leukemia cell lines under normal versus valine limited media.

overall_design: Examination of CRISPR/Cas9 sgRNA "brunello" library (targeting the whole genome) or a tRNA-gene specific library in T-ALL cell lines in normal or differential valine conditions.

first: Palaniraja

last: Thandapani

first: Iannis

last: Aifantis


title: Valine tRNA biogenesis and bioavailability regulates mitochondrial complex I levels in acute leukemia [RNAseq]

summary: We report the effects on gene expression on dietary modulation of valine in an in vivo model of T cell acute lymphoblastic leukemia

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of changes in the RNA transcripts following either NOTCH1-inhibition in human cell line or dietary modulation of valine in an in vivo model of T cell acute lymphoblastic leukemia.


title: Valine tRNA biogenesis and bioavailability regulates mitochondrial complex I levels in acute leukemia [Ribo-Seq]

summary: We report the effects on gene expression at the translational level on dietary modulation of valine in in vivo model of T cell acute lymphoblastic leukemia

overall_design: Examination of changes in the ribosome occupancy as a measure of translational effeciency following dietary modulation of valine in in vivo model of T cell acute lymphoblastic leukemia


title: Valine tRNA biogenesis and bioavailability regulates mitochondrial complex I levels in acute leukemia [tRNAseq]

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the effects on changes in tRNA expression in T cell acute lymphoblastic leukemia relative to CD4 T cells.

overall_design: Examination of changes in the tRNA gene expression levels in human primary and cell-line T cell acute lymphoblastic leukemia.


title: Untimely TGFβ responses in COVID-19 limit antiviral functions of NK cells

status: Public on Oct 25 2021

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary:
Single cell transcriptomes of flow cytometry-sorted peripheral blood NK cells from COVID-19 patients and healthy controls.
Single cell transcriptomes of peripheral blood NK cells from healthy donors stimulated with IL-12 and IL-15 +/- TGF-beta.

overall_design:
RNA Sequencing of flow cytometry-sorted peripheral blood NK cells (live CD3-CD14-CD19-CD45+CD56+ lymphocytes) from blood samples longitudinally obtained from 13 severe COVID-19 patients, 11 ambulant COVID-19 patients and 5 healthy controls.
For in vitro stimulation, sorted NK cells from healthy donors were cultured in RPMI containing rh-IL12 and rh-IL15 with or without additional rh-TGF-beta.
The 10X Genomics platform with the Single Cell 5’ Library & Gel Bead Kit was used for single cell RNA sequencing.

first: Marta

last: Ferreira-Gomes

first: Caroline

last: Tizian

first: Mario

last: Witkowski

first: Gitta

middle: A

last: Heinz

first: Frederik

last: Heinrich

first: Mir-Farzin

last: Mashreghi


title: Dual RNAseq analysis of the interaction between the plant pathogen Pythium myriotylum and the mycoparasite Pythium oligandrum

city: Nanjing

first: Paul

last: Daly

state: Jiangsu

address: 50 Zhongling St

institute: Jiangsu Academy of Agricultural Sciences

summary: Biological control is a promising approach to control diseases caused by Pythium species. Unusually for a single genus, the Pythium genus also includes species that can antagonise Pythium plant pathogens, such as Pythium oligandrum. These Pythium plant pathogens are commonly found in the soil such as the broad host-range pathogen Pythium myriotylum and cause various diseases of important crops. While P. oligandrum genes expressed in the interaction with oomycete plant pathogens have been identified previously, the transcriptional response of an oomycete plant pathogen to P. oligandrum has not been investigated. An isolate of P. oligandrum, GAQ1, recovered from soil could antagonise P. myriotylum in a plate-based confrontation assay. The P. oligandrum isolate had a strong disease control effect on soft-rot of ginger caused by P. myriotylum. We investigated the transcriptional interaction between P. myriotylum and P. oligandrum. As part of the transcriptional response of P. myriotylum to the presence of P. oligandrum, putative effector genes such as a sub-set of Kazal-type protease inhibitors were strongly upregulated. P. myriotylum cellulases and elicitin-like putative effectors were also upregulated. In P. oligandrum, cellulases, peroxidases, proteases and NLP effectors were upregulated. The transcriptional response of P. myriotylum suggests clear features of a counter-attacking strategy that may contribute to the variable success and durability of biological attempts to control diseases caused by Pythium species. Whether aspects of this counter-attack could inhibit aspects of this virulence of P. myriotylum is another interesting aspect for future studies.

sample_organism:
Pythium oligandrum
Pythium myriotylum

platform_organism:
Pythium oligandrum
Pythium myriotylum

overall_design: Nine RNA samples in total were analyzed  from three conditions (self-confrontation of P. oligandum, P. myriotylum, and  the cross-species confrontation) in triplicate.

first: Siqiao

last: Chen

first: Jingjing

last: Li

first: Taiqiang

last: Xue

first: Taha

last: Sheikh

first: Qimeng

last: Zhang

first: Jinfeng

first: Sheng

last: Deng

first: Dongmei

last: Zhou

first: Lihui

last: Wei


title: Temporal transitions in post-mitotic neurons throughout the C. elegans nervous system [ChIP-seq]

city: Birmingham

first: HaoSheng

last: Sun

state: AL

address: 1918 University Blvd, MCLM 916

department: Cell, Developmental and Integrative Biology

institute: University of Alabama at Birmingham

summary: The nervous system of animals is functional at early postembryonic stages but undergoes extensive anatomical and functional changes throughout postembryonic development to eventually form a fully mature nervous system at adulthood. The molecular changes in post-mitotic neurons across post-embryonic development and the genetic programs that control these temporal transitions are not well understood. Using the model organism C. elegans, we comprehensively characterized the distinct functional states (locomotor behavior) and corresponding distinct molecular states (transcriptome) of the post-mitotic nervous system across temporal transitions from early post-embryonic periods to adulthood. We observed pervasive changes in gene expression, many of which controlled by the conserved heterochronic miRNA lin-4/mir-125 and its target, the transcription factor lin-14. The functional relevance of these molecular, lin-4/lin-14 controlled transitions are exemplified by a novel neuropeptide, nlp-45, which confers temporally controlled anti-exploratory activities. Our studies provide new insights into a perhaps generalizable regulatory mechanism that alters neuron-type specific gene batteries to modulate distinct behaviors states, and also provides a rich atlas of post-embryonic molecular changes to uncover additional regulatory mechanisms.

overall_design: LIN-14 ChIP in L1 and L2 worms.

first: Oliver

last: Hobert


title: Hematopoiesis under telomeric attrition at the single-cell resolution

status: Public on Oct 23 2021

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: The molecular mechanisms that drive hematopoietic stem cell (HSC) functional decline under conditions of stress are not completely understood. Here, in light of the recent advances in single-cell technologies, we sought to redefine the transcriptional and epigenetic landscape of mouse and human hematopoietic stem cells (HSCs) under telomeric stress, as that induced by pathogenic germline mutations in telomerase complex genes. These analyses revealed that telomere attrition maintains HSCs in a state of persistent metabolic activation and differentiation towards the megakaryocytic lineage through the cell-intrinsic upregulation of interferon (IFN) signaling response, which directly comprises HSCs’ self-renewal capabilities and eventually leads to their exhaustion. Telomerase reactivation completely restored HSC transcriptional homeostasis at the single-cell level, overcame enhanced megakaryocytic differentiation and significantly ameliorated HSCs’ repopulation capacity in the setting of competitive transplantation, suggesting that HSCs can repristinate their function upon telomere damage resolution. This study challenges the long-standing hypothesis that telomere attrition limits the proliferative potential of HSCs by inducing apoptosis or senescence and suggests that early intervention targeting the IFN axis could prevent bone marrow failure syndromes in patients with pathogenic mutations affecting telomere maintenance.

overall_design: To understand how telomeric attrition affects the function of hematopoietic stem cells (HSCs) and leads to degenerative defects in bone marrow (BM) by scRNA-seq

first: Natthakan

last: Thongon

first: Andrea

last: Santoni

first: Matteo

last: Pellegrini

first: Simona

last: Colla


title: Valine tRNA biogenesis and bioavailability regulates mitochondrial complex I levels in acute leukemia

first: Andreas

last: Kloetgen


title: A novel human fetal model of infant ALL reveals a link between MLL-AF4, PAF1 and increased H3K79me2/3

city: Oxford

first: Siobhan

last: Rice

address: Room 320, WIMM, JR Hospital/Headley Way

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine


title: Temporal transitions in post-mitotic neurons throughout the C. elegans nervous system

overall_design: Immunoprecipitation of neuronal nuclei, at 4 post-embryonic stages: 3 larval stages (L1, L2, and L4) and one adult (A) stage in control animals as well as in heterochronic mutants (lin-4 null, lin-14 gain of function, and lin-28 gain of function)


title: Leukemia antigen specific TCR transgenic CD8+ T cell TCRTg101 RNA seq

status: Public on Oct 22 2021

city: Chicago

first: Xiufen

last: Chen

state: IL

address: 900 E 57th Street KCBD 6230A

institute: The University of Chicago

summary:
Purpose: To identify potential underlying molecular programs associated with the observed dysfunctional TCRTg101 phenotype, RNA sequencing (seq) was performed on TCRTg101 isolated from livers of leukemia-bearing mice at several time points following their adoptive transfer (days 6-7, 13-14, and 167-18), andas well as on TCRTg101 isolated from control (leukemia-free)  analysis
Methods: TCRTg101 in livers and spleens of leukemia-bearing mice were isolated at various time points following adoptive transfer (day 0, day 6-7, day 13-14, day 16-18) by FACS and were re-suspended in Trizol (Life Technologies). TCRTg101 RNA was isolated via chloroform extraction. Low input RNA sequencing was performed in the University of Chicago Genomic. Genes with fewer than 10 reads in at least 6 samples were filtered out, resulting in a dataset of 11,164 genes. Differential gene expression analysis was performed on raw aligned read counts using DESeq2 (Love et al., 2014), with batch effects accounted for in the design formula. Genes were considered to be differentially expressed if they had an adjusted p-value < 0.05 using a Benjamini-Hochberg test (FDR). Counts per gene were regular log (rlog)-transformed, and batch effects were removed using the removeBatchEffect function from limma (Ritchie et al., 2015) for principal component analysis (PCA), sample clustering based on Euclidean distance, and heatmaps depicting z-scores of gene expression. rlog-transformed, batch-corrected counts were also used for weighted gene correlation network analysis (WGCNA) (Langfelder and Horvath, 2008) while additionally filtering out the 50% of genes with the lowest variance to reduce noise, resulting in a set of 5,582 genes. Adjacency was determined using a signed analysis and a soft thresholding power of 14, which was determined by scale-free fit index (Zhang and Horvath, 2005). 12 clusters of genes were initially identified, 2 of which contained a combined 4,269 genes (76.5% of the dataset), and roughly corresponded to genes whose expression increased or decreased over the experimental time course. Of the other 10 clusters, 2 were identified as containing genes which were transiently upregulated or downregulated. These two clusters contained 448 genes, combined. The remaining 865 genes were assigned to eight different clusters, which appeared to be the result of high variance within sample groups, either due to low overall gene expression or low outlier values. No conclusions were drawn regarding these clusters due to uncertainty in the data. Core Facility on the Illumina HiSeq 2500 platform in two batches. Reads were mapped onto the University of California Santa Cruz mouse genome using kallisto (Bray et al., 2016)
Results: In total, 4,075 genes were found to be significantly differentially expressed across all pairwise comparisons
Conclusion:Dysfunctional TCRTg101 acquire a transcriptional program canonically associated with T cell exhaustion

overall_design: RNA-seq

first: Brendan

last: MacNabb


title: Pharmacological activation of the Integrated Stress Response triggers a transcriptional program centered on ribosome biogenesis and function in honey bees

city: New York

first: Jonathan

middle: W.

last: Snow

state: New York

address: 3009 Broadway

department: Biology

institute: Barnard College

summary: Seeking to further characterize the effect of Halofuginone in honey bees and to better understand cellular stress pathways in this species more generally, we used RNAseq to identify novel changes in gene expression after its ingestion and observed a striking induction of genes involved in ribosome biogenesis, translation, tRNA synthesis, and ribosome-associated quality control (RQC). Feeding bees cycloheximide (CHX) to halt ribosome translocation also induced all tested target genes, suggesting that this gene expression program could be induced by ribosome stalling in addition to tRNA-synthetase inhibition. Only a subset of these ribosome biogenesis genes are upregulated by UPR induction, suggesting that the ISR induces overlapping but distinct responses depending on the mode of activation and cross-talk with other cellular signaling pathways.

overall_design: Six samples: 3 from honey bees fed Halofuginone, and 3 from honey bees fed DMSO (control).

middle: W

first: Melissa

last: Flores

first: Nora

last: McNamara-Bordewick


title: mRNA-seq to test effect of PYK2 inhibitor (defactinib) on LPS induced gene expression in WT and IRF5-/- BMDMs

first: Irina

last: Udalova

state: Oxfordshire

address: The Kennedy Institute of Rheumatology, Roosevelt Drive, Headington

department: NDORMS

institute: Kennedy Institute

summary: To investigate the specificity of Defactinib on IRF5 target genes we compare LPS-induced transcriptomes in WT and IRF5 KO BMDMs treated with either Defactinib or vehicle. Macrophage transcriptomic signature under PYK2 inhibition phenocopied IRF5 deficiency

overall_design: unstimulated (DMSO treated)  and LPS stimulated (DMSO or Defactinib treated) BMDMs from WT  or IRF5-/- mice. 3 biological replicates per condition

first: Hannah

last: Almuttaqi

first: Tariq

last: Khoyratty


title: HIF-dependent NFATC1 Activation Upregulates ITGA5 and PLAUR in Intestinal Epithelium in Inflammatory Bowel Disease

status: Public on Oct 21 2021

city: Moscow

first: Stepan

last: Nersisyan

address: Vavilova str 7

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

summary: Intestinal epithelial cells exist in physiological hypoxia, leading to hypoxia-inducible factor (HIF) activation and supporting barrier function and cell metabolism of the intestinal epithelium. In contrast, pathological hypoxia is a common feature of some disorders, including inflammatory bowel disease (IBD). This work was aimed at studying HIF-associated changes in the intestinal epithelium in IBD. In the first step, a list of genes responding to chemical activation of hypoxia was obtained in an in vitro intestinal cell model with RNA sequencing. Cobalt (II) chloride and oxyquinoline treatment of both undifferentiated and differentiated Caco-2 cells activate the HIF-signaling pathway according to gene set enrichment analysis. The core gene set responding to chemical hypoxia stimulation in the intestinal model included 115 upregulated and 69 downregulated genes. Of this set, protein product was detected for 32 genes, and fold changes in proteome and RNA sequencing significantly correlate. Analysis of publicly available RNA sequencing set of the intestinal epithelial cells of patients with IBD confirmed HIF-1 signaling pathway activation in sigmoid colon of patients with ulcerative colitis and terminal ileum of patients with Crohn’s disease. Of the core gene set from the gut hypoxia model, expression activation of ITGA5 and PLAUR genes encoding integrin α5 and urokinase-type plasminogen activator receptor (uPAR) was detected in IBD specimens. The interaction of these molecules can activate cell migration and regenerative processes in the epithelium. Transcription factor analysis with the previously developed miRGTF tool revealed the possible role of HIF1A and NFATC1 in the regulation of ITGA5 and PLAUR gene expression.

overall_design: RNA sequencing was performed for undifferentiated Caco-2 cells treated with Cobalt (II) chloride and oxyquinoline.

first: Evgeny

last: Knyazev


title: A novel human fetal model of infant ALL reveals a link between MLL-AF4, PAF1 and increased H3K79me2/3 [RNA-seq]

summary: Acute Lymphoblastic Leukemia (ALL) caused by chromosomal translocation involving the Mixed Lineage Leukemia (MLL) gene remains a poor prognosis disease, especially in infants. The most common MLL-rearrangement in infant ALL (iALL), MLL-AF4, originates in utero where the properties of fetal target cells likely provide a permissive landscape for transformation. We describe the first faithful MLL-AF4 iALL model derived by CRISPR-Cas9 genome editing of primary human fetal liver (FL) cells. Using this model, we demonstrate that H3K79me2/3 is increased during transformation as a direct consequence of MLL-AF4 binding, but correlates weakly with changes in gene expression. DOT1L, the only known H3K79 methyltransferase, does not form part of the MLL-AF4 complex. Instead, we identify PAF1 as a key protein recruited by the MLL-AF4 complex, which in turn can recruit DOT1L. These results explain the previously unclear link between MLL-AF4 binding and increased H3K79me2/3, and introduce an iALL-specific model for future drug studies.

first: Thomas

last: Jackson

first: Natalina

last: Elliott

first: Anindita

last: Roy

last: Milne


title: Transcriptomic analysis of wild-type and mutant strains of Bacillus subtilis 168

city: Wuhan

first: Zhuoran

last: Jiang

state: Hubei

address: Bayi Road

department: College of Chemistry and Molecular Sciences

institute: Wuhan University

summary: The transcriptional profiling and global gene expression analysis revealed a higher globally gene expression level in BS-F91L or BS-Q150W strains with enhanced N6-methyladenosine deaminase activity. The differentially expressed genes categorized by GO, KEGG and COG analysis, highlighted the crucial roles of Bsu06560 in regulating N6-methyladenosine metabolism and further influenced a myriad of biological processes in multiple layers, including transcription, translation, metabolites regulations, and cellular signal transduction.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Transcriptomic analysis of 2 Bsu06560 mutant strains of  Bacillus subtilis 168. Wild-type strain of Bacillus subtilis 168 were referance samples. All samples were tested in triplicate.

first: Xiang

last: Zhou

first: Heng

last: Song


title: Pbx1 expression is required for myeloproliferative neoplasm onset and maintenance

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

institute: IRCCS Istituto Giannina Gaslini

summary: Pre B cell leukemia homeobox 1 (Pbx1) regulates the balance between self-renewal and differentiation of hematopoietic stem cells, and maintains proto-oncogenic transcriptional pathways implicated in several tumors. Its aberrant expression was found in a subset of myeloproliferative neoplasms (MPN) patients bearing the JAK2V617F mutation. To investigate if Pbx1 contributes to MPN, and to explore its potential as therapeutic target, we generated a new mouse strain, that we called JP, by crossing a known JAK2V617F inducible knock-in MPN model with a Pbx1 conditional-ko. In JP mice we can simultaneously activate the human JAK2 mutation and delete Pbx1. Typical MPN features, such as thrombocytemia and granulocytosis, did not develop in the absence of Pbx1. Erythrocytosis, initially displayed by JP mice, gradually resolved over time. Moreover, splenic myeloid metaplasia and in vitro cytokine independent growth were rescued by Pbx1 inactivation. Through RNA-Sequencing we analyzed molecular pathways downstream of Pbx1 and involved in MPN maintenance in stem and progenitor cells. The aberrant transcriptome in the MPN model compared to wild-type was rescued by the absence of Pbx1.  Our results demonstrate that inhibition of the Pbx1-driven transcriptional program is beneficial in MPN. Modulation of Pbx1 activity by direct targeting or by targeting its downstream mediators might thus represent a novel therapeutic approach.

overall_design: mRNA profiles from LKS sorted from the BM of pIpC-treated JAK2-cKI, JP and WT control mice (3-4 biological replicates/group)

first: Sharon

last: Muggeo

first: Laura

last: Crisafulli

first: Elena

last: Fontana

first: Marta

last: Ubezio

first: Emanuela

last: Morenghi

first: Federico

middle: S

last: Colombo

first: Erica

last: Travaglino

first: Stefano

last: Mantero

first: Rosita

last: Rigoni

first: Clelia

last: Peano

last: Vezzoni

first: Matteo

last: Della Porta

first: Anna

last: Villa

first: Francesca

last: Ficara


title: A novel human fetal liver-derived model reveals that MLL-AF4 drives fetal gene expression programs in infant ALL [ChIP-seq]

first: Siobhan

last: Rice

summary: Although 90% of children with acute lymphoblastic leukemia (ALL) are now cured, the prognosis of infant-ALL (diagnosis within the first year of life) remains dismal. Infant-ALL is usually caused by a single genetic hit that arises in utero: rearrangement of the MLL/KMT2A gene (MLL-r). This is sufficient to give rise to a uniquely aggressive and treatment-refractory leukemia compared to older children with the same MLL-r. The reasons for disparate outcomes in patients of different ages with identical molecular drivers are unknown. This paper addresses the hypothesis that fetal-specific gene expression programs co-operate with MLL-AF4 to initiate and maintain infant-ALL.  Using direct comparison of fetal and adult HSC and progenitor transcriptomes we identify fetal-specific gene expression programs in primary human cells. We show that MLL-AF4-driven infant-ALL, but not MLL-AF4 childhood-ALL, displays expression of fetal-specific genes. In a direct test of this observation, we find that CRISPR-Cas9 gene editing of primary human fetal liver cells (to produce a t(4;11)/MLL-AF4 translocation) replicates the clinical features of infant-ALL and drives infant-ALL-specific and fetal-specific gene expression programs. These data strongly support the hypothesis that fetal-specific gene expression programs co-operate with MLL-AF4 to initiate and maintain the distinct biology of infant ALL.

overall_design: ChIP-seq

first: Thomas

last: Jackson

first: Nicholas

middle: T

last: Crump

first: Anindita

last: Roy

last: Milne


title: Genome-wide quantitative functional enhancer map of mESCs, in the pluripotent state and after induced differentiation

middle: V

last: Glaser

address: Ihnestraße 63-73

department: Computational Molecular Biology

institute: Max Planck Institute for Molecular Genetics

summary: Precise spatiotemporally regulated gene expression is pivotal for cell homeostasis, cell differentiation and during development. Gene expression networks are tightly regulated by transcription factors (TF) and their targeted regulatory genomic elements (enhancers), which are known to correlate with specific histone modifications. However, the ultimate prerequisites, which determine functionally active enhancers, remain unclear.   To elucidate the regulatory landscape of murine ESCs, a massively parallel reporter assay, based on STARR-seq (Self-Transcribing Active Regulatory Region sequencing), assessing genomic fragments prepared from accessible chromatin, (FAIRE-STARR-seq) has been applied. Thus, a genome-wide quantitative map of functional mESC enhancers in naive state and after retinoic acid (RA)-induced differentiation was generated.   To investigate sequence features associated with RA-mediated inducibility of enhancers bound by retinoic acid receptor alpha (RARα), the main receptor for RA, genomic binding sites of RARα have been determined.

overall_design: mESCs, in the pluripotent state or after induced differentiation, were assessed for genome-wide changes enhancer activity by FAIRE-STARR-seq. Additionally, RARα genomic binding sites after RA-induced differentiation were identified by ChIP-seq.

first: Alisa

last: Fuchs

first: Ho-Ryun

last: Chung

first: Sebastiaan

last: Meijsing


title: Functional screen of Inflammatory bowel disease genes reveals key epithelial functions: Illumina Whole Genome Dataset

status: Public on Oct 20 2021

city: Montréal

first: John

middle: D

last: Rioux

state: QC

address: 5000 Bélanger St.

department: Research Center

country: Canada

institute: Montreal Heart Institute

summary:
Background: Genetic studies have been tremendously successful in identifying genomic regions associated with a wide variety of phenotypes, although the success of these studies in identifying causal genes, their variants, and their functional impacts have been more limited.
Methods: We identified 145 genes from IBD-associated genomic loci having endogenous expression within the intestinal epithelial cell compartment.  We evaluated the impact of lentiviral transfer of the open reading frame (ORF) of these IBD genes into the HT-29 intestinal epithelial cell line via transcriptomic analyses.  Comparing the genes whose expression was modulated by each ORF, as well as the functions enriched within these gene lists, identified ORFs with shared impacts and their putative disease-relevant biological functions.
Results: Analysis of the transcriptomic data for cell lines expressing the ORFs for known causal genes such as HNF4a, IFIH1 and SMAD3 identified functions consistent with what is known for these genes.  These analyses also identified two major clusters of genes with shared impact on the transcriptome:  Cluster 1 contained the known IBD causal genes IFIH1, SBNO2, NFKB1 and NOD2, as well as genes from other IBD loci (ZFP36L1, IRF1, GIGYF1, OTUD3, AIRE and PITX1), whereas Cluster 2 contained the known causal gene KSR1 and implicated DUSP16 from another IBD locus. Our analyses of these clusters highlighted how multiple IBD gene candidates impact on epithelial structure and function, including the protection of the mucosa from intestinal microbiota.
Conclusions: This functional screen, based on expressing IBD genes within an appropriate cellular context, in this instance intestinal epithelial cells, resulted in changes to the cell’s transcriptome that are relevant to their endogenous biological function(s). This not only helped in identifying likely causal genes within genetic loci but also provided insight into their biological functions.  Furthermore, this work has highlighted the central role of intestinal epithelial cells in IBD pathophysiology.

overall_design: This dataset includes 426 samples for 145 ORFs, mostly in independently transducted triplicates. Empty vector controls are also included.

first: Jessy

middle: C

last: Ntunzwenimana

first: Gabrielle

last: Boucher

first: Jean

last: Paquette

first: Hugues

last: Gosselin

first: Azadeh

last: Alikashani

first: Nicolas

last: Morin

first: Claudine

last: Beauchamp

first: Louise

last: Thauvette

first: Marie-Ève

last: Rivard

first: Frédérique

last: Dupuis

first: Sonia

last: Deschenes

first: Sylvain

last: Foisy

first: Frédéric

last: Latour

first: Geneviève

last: Lavallée

first: Mark

last: Daly

first: Ramnik

last: Xavier

first: Guy

last: Charron

first: Philippe

last: Goyette


title: Relaxed 3D genome conformation facilitates the pluripotent to totipotent-like state transition in embryonic stem cells [Hi-C]

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

summary: The 3D genome organization is crucial for gene regulation. Although recent studies have revealed a uniquely relaxed genome conformation in totipotent early blastomeres of both fertilized and cloned embryos, how weakened higher-order chromatin structure is functionally linked to totipotency acquisition remains elusive. Using low-input Hi-C, ATAC-seq, and ChIP-seq, we systematically examined the dynamics of 3D genome and epigenome during pluripotent to totipotent-like state transition in mouse embryonic stem cells (ESCs). The spontaneously converted 2-cell-embryo-like cells (2CLCs) exhibited more relaxed chromatin architecture compared to ESCs, including global weakening of both enhancer-promoter interactions and TAD insulation. While the former correlated with inactivation of ESC enhancers and down-regulation of pluripotent genes, the latter might facilitate contacts between the putative new enhancers arising in 2CLCs and neighboring 2C genes. Importantly, disruption of chromatin organization by depleting CTCF or the cohesin complex promoted the ESC to 2CLC transition. Our results thus establish a critical role of 3D genome organization in totipotency acquisition.

overall_design: ESC and 2C-like cells are performed high-throughput sequencing.

first: Jiali

last: Yu

first: Yezhang

last: Zhu


title: Relaxed 3D genome conformation facilitates the pluripotent to totipotent-like state transition in embryonic stem cells [ATAC-seq, ChIP-seq, RNA-seq, CUT&Tag]


title: A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

city: Seattle

first: Hongkui

last: Zeng

state: WA

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

summary: The isocortex and hippocampal formation (HPF) in the mammalian brain play critical roles in perception, cognition, emotion and learning. We profiled ~1.3 million cells covering the entire adult mouse isocortex and HPF and derived a transcriptomic celltype taxonomy which includes many new glutamatergic and GABAergic neuron types. Contrary to the traditional view of HPF as having a simpler cellular organization, we discover a complete set of glutamatergic types in HPF homologous to all major subclasses found in the six-layered isocortex, suggesting that HPF and isocortex share a common circuit organization. We also identify large-scale continuous and graded variation of cell types along isocortical depth, across isocortical sheet and in multiple dimensions in hippocampus and subiculum. Overall, our study establishes a molecular architecture of mammalian isocortex and hippocampal formation and begins to shed light on its underlying relationship with the development, evolution, connectivity and function of these two brain structures.

overall_design: Single cell RNA-seq using the 10x genomics and Smart-seq v4 methods. Cells were isolated from mouse cortex and hippocampal formation. The dataset includes 175 10x genomics libraries containing ~1.2 million cells and 73.363 Smart-seq v4 cells.

first: Zizhen

last: Yao

first: Cindy

last: van Velthoven

first: Thuc

middle: N

last: Nguyen

first: Jeff

last: Goldy

first: Adriana

last: Sedeno-Cortes

first: Fahimeh

last: Baftizadeh

first: Darren

last: Bertagnolli

first: Tamara

last: Casper

first: Megan

last: Chiang

first: Kirsten

last: Crichton

first: Song-Lin

last: Ding

first: Olivia

last: Fong

first: Emma

last: Garren

first: Alexandra

last: Glandon

first: Nathan

last: Gouwens

first: James

last: Gray

first: Lucas

last: Graybuck

first: Michael

last: Hawrylycz

first: Daniel

last: Hirschstein

first: Matthew

last: Kroll

first: Kanan

last: Lathia

first: Changkyu

last: Lee

first: Boaz

last: Levi

first: Delissa

last: McMillen

first: Stephanie

last: Mok

first: Thanh

last: Pham

first: Qingzhong

last: Ren

first: Christine

last: Rimorin

first: Nadiya

last: Shapovalova

first: Josef

last: Sulc

first: Susan

last: Sunkin

last: Tieu

first: Amy

last: Torkelson

first: Herman

last: Tung

first: Katelyn

last: Ward

first: Nick

last: Dee

first: Kimberly

last: Smith

first: Bosiljka

last: Tasic


title: Relaxed 3D genome conformation facilitates the pluripotent to totipotent-like state transition in embryonic stem cells

first: Li

last: Shen

overall_design: Refer to individual Series


title: Cilia locally synthesize proteins to sustain their ultrastructure and functions

status: Public on Oct 19 2021

city: Boston

first: Jiehui

last: Chen

state: MA

address: 320 Longwood Ave

institute: Boston Children’s Hospital

summary: Cilia are microtubule-based hair-like organelles propelling locomotion and extracellular liquid flow or sensing environmental stimuli. As cilia are diffusion barrier-gated subcellular compartments, their protein components are thought to come from the cell body through intraflagellar transport or diffusion. Here we show that cilia locally synthesize proteins to maintain their ultrastructure and functions. Multicilia of mouse ependymal cells were abundant in ribosomal proteins, translation initiation factors, and RNA, including 18S rRNA and tubulin mRNA. The cilia actively generated nascent peptides, including those of tubulin. FMRP, an RNA-binding component of messenger ribonucleoprotein granules critical for local translation, was concentrated in ciliary central lumen. Its depletion by RNAi impaired ciliary nascent peptide production and induced multicilia degeneration. Expression of exogenous FMRP, but not an isoform tethered to mitochondria, rescued the degeneration defects. Therefore, local translation defects in cilia might contribute to the pathology of ciliopathies and other diseases such as Fragile X syndrome.

overall_design: Purified ciliary mRNA profiles of ctrl-i and Fmr-i1 by deep sequencing with two biological replicates.

first: Kai

last: Hao


title: NogoA-expressing astrocytes limit peripheral macrophage infiltration after ischemic brain injury in primates

status: Public on Oct 18 2021

city: New Haven

first: Nenad

last: Sestan

address: 333 Cedar Street, SHM C-316C

department: Neuroscience

institute: Yale University School of Medicine

summary: Reactive astrocytes play critical roles after brain injury, but their precise function is not well defined, particularly in humans and nonhuman primates (NHPs). Here, we utilized single nuclei transcriptomics to characterize astrocytes after ischemic stroke in the primary visual cortex (V1) of the marmoset monkey. We observed nearly complete segregation between stroke and control astrocyte clusters. Screening the top 30 differentially expressed genes to identify candidates that might limit stroke recovery, we discovered that RTN4A/ NogoA, a neurite-outgrowth inhibitory protein previously associated specifically with oligodendrocytes but not astrocytes, was expressed in a majority of reactive astrocytes. Robust NogoA upregulation on reactive astrocytes following stroke was confirmed in both the marmoset and human brain, whereas rodents exhibited only a marginal change in NogoA expression following stroke. Further, in vivo and in vitro studies determined that NogoA mediated an anti-inflammatory response which likely contributes to limiting deeper infiltration of peripheral macrophages into the surviving parenchyma during the subacute post-stroke period. These findings are directly relevant to the development of NogoA-targeting therapies designed for clinical use shortly after ischemic stroke. In addition, our data have uncovered the complexity of astrocyte responses in primates, which highlights the importance of preclinical model selection for discovery research designed to identify novel therapeutics for brain injury.

overall_design: Adult marmosets (n=3) received unilateral injections of endothelin-1 (ET-1) to the primary visual cortex (V1), with grey matter tissues encompassing all cortical layers of operculum collected 7 days later. Non-lesioned adult marmoset (n=3) V1 was used as control.

first: Anthony

middle: G

last: Boghdadi

first: Joshua

last: Spurrier

first: Leon

last: Teo

first: Mingfeng

last: Li

first: Mario

last: Skarica

first: Benjamin

last: Cao

first: William

last: Kwan

first: Tobias

last: Merson

first: Susie

middle: K

last: Nilsson

first: Stephen

last: Strittmatter

first: James

last: Bourne


title: Transcriptomes of the developing larval ovaries of Drosophila melanogaster during terminal filament formation

city: Cambridge

first: Shreeharsha

last: Tarikere

state: Massachusetts

address: 16 Divinity Avenue, Biolabs

department: Organismic and Evolutionary Biology

institute: Harvard University

summary: Insect ovaries are made up of tubular egg producing subunits called ovarioles, whose number largely determines the number of eggs that can be potentially laid. Ovariole number is directly determined by the number of cellular structures called terminal filaments, which are stacks of cells that assemble in the larval ovary. Elucidating the developmental and regulatory mechanisms of terminal filament formation is thus key to understanding the regulation of insect reproduction through ovariole number regulation. We systematically measured mRNA expression of all cells in the Drosophila larval ovary at the beginning, middle and end of terminal filament formation using RNA-seq. We also separated somatic and germ line cells during these stages and assessed their tissue-specific gene expression during larval ovary development.

overall_design: We extracted RNA from the whole ovaries of Drosophila melanogaster larvae at three stages - the beginning, middle and end of terminal filament formation. The three larval developmental stages were assigned as follows- early (72 hours After Egg Laying, h (AEL)), middle (96h AEL) and late (120h AEL) stages. In a subsequent experiment we used Fluorescence Activated Cell Sorting (FACS) to separate GFP-expressing somatic (bab Gal4>GFP) or germ line (nos Gal4>GFP) tissues of the three stages of larval ovaries. Total RNA was isolated from the three stages of whole ovaries and the two tissue types. Three biological replicates of cDNA libraries were prepared for each sample from Poly-A enriched-RNA using Takara PrepX kit. These cDNA libraries were sequenced using a single end 50bp protocol in an Illumina HiSeq 2500 sequencer. Sequences obtained were checked for quality and replicates with 10 million or more reads were considered for downstream differential expression analysis.

first: Guillem

last: Ylla

first: Cassandra

last: Extavour


title: Impact of AZA on myeloid leukemia cells

status: Public on Oct 16 2021

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: To understand the transcriptional changes of myeloid leukemia cells when exposed to Aza we used different AML cell lines and exposed them to AZA for multiple time periods.

overall_design: The AML cell lines were cultured and exposed to the indicated concentration of AZA for the indicated time points. RNA was isolated from the AML cells at the end of the culture period. RNA was processed for RNA seq analysis.

first: Melanie

last: Boerries

first: Cornelius

last: Miething

first: Desiree

last: Redhaber

first: Nadia

last: Khawanky


title: Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors

city: La Jolla

first: Maike

last: Sander

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

summary: FOXA pioneer transcription factors (TFs) associate with primed enhancers in endodermal organ precursors. Using a human stem cell model of pancreas differentiation, we here discover that only a subset of pancreatic enhancers is FOXA-primed, whereas the majority is unprimed and engages FOXA upon lineage induction. Primed enhancers are enriched for signal-dependent TF motifs and harbor abundant and strong FOXA motifs. Unprimed enhancers harbor fewer, more degenerate FOXA motifs, and FOXA recruitment to unprimed but not primed enhancers requires pancreatic TFs. Strengthening FOXA motifs at an unprimed enhancer near NKX6.1 renders FOXA recruitment pancreatic TF-independent, induces priming, and broadens the NKX6.1 expression domain. We make analogous observations about FOXA binding during hepatic and lung development. Our findings suggest a dual role for FOXA in endodermal organ development: First, FOXA facilitate signal-dependent lineage initiation via enhancer priming, and second, FOXA enforce organ cell type-specific gene expression via indirect recruitment by lineage-specific TFs.

overall_design: Anaysis of gene expression patterns by RNA-Seq, chromatin accessability by ATAC-Seq, and TF binding sites and histone marker distribution through ChIP-Seq performed within hESC-based models of endoderm differentiation. Effects of genetic deletion of FOXA1 and FOXA2 TFs on each aspect are examined in the context of pancreas induction.

first: R

last: Geusz

first: M


title: Functional screen of Inflammatory bowel disease genes reveals key epithelial functions: Agilent Targeted Dataset

first: John

last: Rioux

overall_design:
This dataset includes 426 samples for 145 ORFs, mostly in independently transducted triplicates. Empty vector used as controls are also included.

iGenoMed Consortium

first: Jessy

last: Ntunzwenimana

first: Gabrielle

last: Boucher

first: Jean

last: Paquette

first: Hugues

last: Gosselin

first: Azadeh

last: Alikashani

first: Nicolas

last: Morin

first: Claudine

last: Beauchamp

first: Louise

last: Thauvette

first: Marie-Ève

last: Rivard

first: Frédérique

last: Dupuis

first: Sonia

last: Deschenes

first: Sylvain

last: Foisy

first: Frédéric

last: Latour

first: Geneviève

last: Lavallée

first: Mark

last: Daly

first: Ramnik

last: Xavier

first: Guy

last: Charron

first: Philippe

last: Goyette


title: Identification of pharmacologic inhibitors and activators of IL-4-induced macrophage polarization [THP-1 RNA-seq]

city: Charlestown

first: Alexander

last: Marneros

address: 13th Street

department: Department of Dermatology, Cutaneous Biology Research Center

institute: Massachusetts General Hospital, Harvard Medical School

summary: Macrophages polarize towards different subpopulations with distinct and partly antagonistic functions in various diseases. IFNγ/LPS-polarized M1-type macrophages can have antiangiogenic activity, whereas IL-4-induced M2-type macrophages can be proangiogenic and profibrotic. Therapeutic strategies to inhibit M2-type polarization while promoting M1-type polarization could serve to inhibit pathological angiogenesis and fibrosis. Here, by combining global quantitative time-course proteomics and phosphoproteomics with a small-molecule inhibitor screen we identify signaling events that promote specifically IL-4-induced and not IFNγ/LPS-induced macrophage polarization and found that the MEK inhibitor trametinib and the HDAC inhibitor panobinostat potently prevent M2-type macrophage polarization without inhibiting M1-type polarization. In contrast, selective B-Raf inhibition promotes M2-type polarization. Trametinib and panobinostat also blocked M2-type macrophage polarization and concomitantly angiogenesis and fibrosis in models of wound healing and neovascular age-related macular degeneration in vivo. Thus, these pharmacologic inhibitors could be utilized therapeutically to selectively block IL4-induced macrophage polarization and reduce pathologic angiogenesis and fibrosis.

overall_design: THP-1 cell M1-type and M2-type polarizations

first: Lizh

last: i He

first: Alaxander


title: Identification of pharmacologic inhibitors and activators of IL-4-induced macrophage polarization [PBMC RNA-seq]

overall_design: PBMC cell M1-type and M2-type polarizations

first: Lizhi

last: He


title: RNA-sequencing Analysis (RNA-seq)，Genome-wide Maps of Chromatin State (ChIP-seq) and Assay for Transposase Accessible Chromatin with High-throughput Sequencing (ATAC-seq) in BMDMs or Raw 264.7 cell lines.

city: Shang Hai

first: Pan

last: Jia

state: — Please Select —

address: No.320.Yueyang Road,Shanghai

institute: Shanghai Institute of Nutrition and Health Chinese Academy of Science

summary: For RNA-seq,mRNA profiles of Bone marrow derived macrophages(BMDMs) of wild-type(WT) and Zmynd8 knockout(Zmynd8 cKO),p65 KO + p65,p65 KO + K122R in Raw264.7 cells,Zmynd8 KO + Zmynd8,Zmynd8 KO + D/E-A in Raw264.7 cells were generated from GUANGZHOU RIBOBIO,using Illumina Hiseq.The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays.For ChIP-seq,BMDMs or Raw264.7 cells (about 1x107 cells) were fixed with 1% methanol-free formaldehyde at room temperature for 10 min, followed by quenching with 125mM glycine,and chromatin immunoprecipitated DNA was send to Novogene,using Nova-PE150.The FASTQ data were mapped to the mouse genome (mm10) using Bowtie, and significant enrichments were identified by MACS2.0 using Broad Peak mode with p-value ≤1*10 -5, FDR ≤ 0.01 as a cutoff to call peaks from the aligned results.For ATAC-seq,BMDMs were send to Shanghai Da Che Biotechnology Company,and the FASTQ data were mapped to the mouse genome (mm10) using Bowtie, and significant enrichments were identified by MACS2.0  using Broad Peak mode with p-value ≤1*10 -5, FDR ≤ 0.01 as a cutoff to call peaks from the aligned results.

overall_design: mRNA profiles of Bone marrow derived macrophages(BMDMs) of wild-type(WT) and Zmynd8 knockout(Zmynd8 cKO),p65 KO + p65,p65 KO + K122R in Raw264.7 cells,Zmynd8 KO +Zmynd8,Zmynd8 KO + D/E-A in Raw264.7 cells .For ChIP-seq,examination of ZMYND8 ,LSD1,H3K4me1 binding peaks in BMDMs,and ZMYND8 binding peaks in p65 KO,p65 KO + p65,p65 KO +K122R Raw264.7 cells ,Zmynd8 KO,Zmynd8 KO + Zmynd8,Zmynd8 KO + D/E-A Raw264.7 cells.

first: Xiang

last: Li

first: Xuelei

last: Wang

first: Wei

last: Lv


title: scAAVengr, a transcriptome-based pipeline for quantitative ranking of engineered AAVs with single-cell resolution

city: Pittsburgh

first: Leah

last: Byrne

state: PA

address: 3501 Fifth Avenue

department: Ophthalmology

institute: University of Pittsburgh

summary: Adeno-associated virus (AAV)-mediated gene therapies are rapidly advancing to the clinic, and AAV engineering has resulted in vectors with increased ability to deliver therapeutic genes. Although the choice of vector is critical, quantitative comparison of AAVs, especially in large animals, remains challenging. Here, we developed an efficient single-cell AAV engineering pipeline (scAAVengr) to simultaneously quantify and rank efficiency of competing AAV vectors across all cell types in the same animal. To demonstrate proof-of-concept for the scAAVengr workflow, we quantified – with cell-type resolution – the abilities of naturally occurring and newly engineered AAVs to mediate gene expression in primate retina following intravitreal injection. A top performing variant identified using this pipeline, K912, was used to deliver SaCas9 and edit the rhodopsin gene in macaque retina, resulting in editing efficiency similar to infection rates detected by the scAAVengr workflow. scAAVengr was then used to identify top-performing AAV variants in mouse brain, heart and liver following systemic injection. These results validate scAAVengr as a powerful method for development of AAV vectors.

sample_organism:
Callithrix jacchus
Macaca fascicularis
Mus musculus

overall_design: Single cell RNA analysis of 36 samples, including 2 replicates of each of the marmoset 1 retinal regions.

first: Byrne

last: Leah

first: Öztürk

last: Bilge

first: Johnson

last: Molly


title: Identification of pharmacologic inhibitors and activators of IL-4-induced macrophage polarization in PBMC and THP-1 cells

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


title: Exercise prevents fatty liver by modifying the compensatory response of mitochondrial metabolism to excess substrate availability

status: Public on Oct 15 2021

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: Exercise training is a potent treatment of NAFLD and hepatic insulin resistance. Here we provide molecular information about the hepatic mitochondrial metabolism in mice when chronic overnutrition (high-energy diet (HED) for 6 weeks) is combined with exercise training. Training reduced the hepatic triacylglycerol content, fasting insulin, and reversed glucose intolerance. Training modified the hepatic mitochondrial proteome with a decrease in enzymes related to pyruvate metabolism and entry of acetyl-CoA into the TCA cycle. Transcriptome data revealed down-regulation of glucose oxidation and lipogenesis. The mitochondrial respiratory capacity of trained HED-fed mice is increased despite reduced content of complex I. Training decreased diacylglycerol species and JNK phosphorylation, both of which can induce insulin resistance. Increased mitochondrial mass and oxidative capacity of the trained muscle further unburdens the liver from substrate overload. Together, when high fat and carbohydrate intake in mice is accompanied by exercise, the decline of mitochondrial function and insulin resistance can be prevented by modification of mitochondrial acetyl-CoA metabolism.

overall_design: We performed gene expression microarray analysis of liver from mice treated with high-energy diet or control diet combined with exercise training

first: Miriam

last: Hoene

first: Lisa

last: Kappler

first: Laxmikanth

last: Kollipara

first: Chunxiu

last: Hu

first: Martin

last: Irmler

first: Daniel

last: Bleher

first: Christoph

last: Hoffmann

last: Hrabě de Angelis

first: Hans-Ulrich

last: Häring

first: Andreas

last: Birkenfeld

last: Peter

first: Albert

last: Sickmann

first: Guowang

last: Xu

first: Rainer

last: Lehmann

first: Cora

last: Weigert


title: RNA-seq analysis of gene expression regulated by LSD1 in CD8+ TILs

first: Wanqiang

last: Sheng

state: Zhejiang

department: Department of Immunology

institute: Zhejiang University School of Medicine

summary: T cell dysfunction is a hallmark of many cancers. Features of dysfunctional T cells and mechanisms leading to T cell dysfunction remain incompletely understood. Significant chromatin changes happen when T cells become dysfunctional, implicating a critical role of epigenetic regulators in such process. Here we study the role of LSD1 in regulating T cell function in cancer and perform a RNA-seq analysis of gene expression program controlled by LSD1.

overall_design: MC38 tumors were implanted to Cd4-Cre+Lsd1f/f mice and littermate control for 14 days. Tumors were harvested and tumor-infiltrating lymphocytes were enriched, then subjected to CD8+ T cells isolation by microbeads and positive selection. Afterwards, CD8+CD44+PD1+ cells were sorted by FACS. Total RNA was extracted and subjected to ribo-RNA depletion, before used for making library. The prepared libraries were sequenced at 75bp from both ends.

first: Mingfeng

last: Li

first: Nenad

last: Sestan

first: Yang

last: Shi


title: Next Generation Sequencing Facilitates Quantitative Analysis of mRNA expression of STAT3 deficiency skin

city: Yokohama

first: Kosuke

last: Miyauchi

state: Kanagawa

address: 1-7-22 Suehiro-sho

institute: RIKEN Center for Integrative Medical Sciences

summary: Dominant-negative mutations of signal transducer and activator of transcription 3 (STAT3) signaling which controls epithelial proliferation in various tissues, leads to atopic dermatitis (AD) in hyper IgE syndrome (HIES). We found that the STAT3 signaling in keratinocytes is required to maintain skin homeostasis through this transcriptome analysis.

overall_design: Ear skin of  skin specific-Stat3 sufficient or deficient mice were taken and analyzed the transcriptome using Illumina HiSeq1500.

first: Masato

last: Kubo


title: ERK, differentially regulated by costimulation molecules, represses Zfp831, a critical regulator in T follicular helper cell differentiation

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University


title: Phase Separation by the NUP98-HOXA9 Fusion Oncoprotein Drives an Oncogenic Phenotype in Hematopoietic Cells

status: Public on Oct 13 2021

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

summary: RNA-seq of mouse hematopoietic stem and progenitor cells expressing NUP98-HOXA9 (NHX9) show upregulation of HOX and other NUP98 fusion target genes, but expression changes are dampened or lost with the introduction of mutations in NUP98's FG repeats or HOXA9's DNA binding domain

overall_design: RNA-seq of mouse hematopoietic stem and progenitor cells expressing NUP98-HOXA9 (NHX9) and mutants after 1 week of growth in methylcellulose containing myeloid and erythroid growth factors

first: Nicole

last: Michmerhuizen

first: Charles

last: Mullighan


title: Identification of pharmacologic inhibitors and activators of IL-4-induced macrophage polarization [PBMC ChIP-seq]

first: Alexander

last: Marneros

overall_design: PBMC ChIP-seq

first: Lizhi

last: He

first: Alaxander


title: Identification of pharmacologic inhibitors and activators of IL-4-induced macrophage polarization [THP-1 ChIP-seq]


title: Bone marrow sinusoidal endothelium controls terminal erythroid differentiation and reticulocyte maturation

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg


title: Analysis of EMCN+ bone marrow cells in Stab2-iCreF3tg/wt Ctnnb1(Ex3)fl/wt mice

summary: Endothelial-derived Wnt/Ctnnb1-signaling is an important angiocrine regulator. Ctnnb1 gain-of-function (GOF) in sinusoidal endothelial cells was generated via Stab2-iCreF3tg/wt Ctnnb1(Ex3)fl/wt mice to analyze the effects of endothelial β-catenin signaling on bone marrow function. We used microarrays to detail the global programme of gene expression in bone marrow EMCN+ cells with β-catenin (Ctnnb1) gain-of-function compared to Wildtype.

overall_design: Stab2-iCreF3tg/wt Ctnnb1(Ex3)fl/wt and Ctnnb1(Ex3)fl/wt (Stab2-iCreF3 neg) mice were sacrificed at the age of three months, lower limb bones were flushed, digested with 0.7mg/ml of collagenase A (Sigma Aldrich).  EMCN+ cells were extracted using EMCN antibody coated magnetic beads.  Thereafter, RNA was isolated and prepared for microarray analysis.

first: Victor

last: Olsavszky

first: Joschka

last: Heil

first: Philipp

last: Reiners-Koch


title: Dynamic changes in tRNA modifications and abundance during T-cell activation [RNA/Ribo-seq]

city: Rehovot

first: Roni

last: Rak

address: Herzl 229

department: Animal Science

country: Israel

institute: Agriculture Research Organization

summary: The tRNA pool determines the efficiency, throughput, and accuracy of translation. Previous studies have identified dynamic changes in the tRNA supply and mRNA demand during cancerous proliferation. Yet, dynamic changes may occur also during physiologically normal proliferation, and these are less characterized. We examined the tRNA and mRNA pools of T-cells during their vigorous proliferation and differentiation upon triggering of the T cell antigen receptor. We observe a global signature of switch in demand for codon at the early proliferation phase of the response, accompanied by corresponding changes in tRNA expression levels. In the later phase, upon differentiation of the T cells, the response of the tRNA pool is relaxed back to basal level, potentially restraining excessive proliferation. Sequencing of tRNAs allowed us to also evaluate their diverse base-modifications. We found that two types of tRNA modifications, Wybutosine and ms2t6A, are reduced dramatically during T-cell activation. These modifications occur in the anti-codon loops of two tRNAs that decode “slippery codons”, that are prone to ribosomal frameshifting. Attenuation of these frameshift-protective modifications is expected to increase proteome-wide frameshifting during T-cell proliferation. Indeed, human cell lines deleted of a Wybutosine writer showed increased ribosomal frameshifting, as detected with a reporter that consists of a critical frameshifting site taken from the HIV gag-pol slippery codon motif. These results may explain HIV’s specificity to proliferating T-Cells since it requires ribosomal frameshift exactly on this codon for infection. The changes in tRNA expression and modifications uncover a new layer of translation regulation during T-cell proliferation and exposes a potential trade-off between cellular growth and translation fidelity.

overall_design: tRNA-sequencing of naïve and in-vitro activated T-cells

first: Michal

last: Polonskey

first: Inbal

last: Eizenberg

first: Yufeng

last: Mo

first: Yuriko

last: Sakaguchi

first: Orel

last: Mizrachi

first: Orna

last: Dahan

first: Noam

last: Stern-Ginossar

first: Tsutomu

last: Suzuki

first: Nir

last: Friedman

first: Yitzhak

last: Pilpel


title: Dynamic changes in tRNA modifications and abundance during T-cell activation [tRNA-seq]


title: Dynamic changes in tRNA modifications and abundance during T-cell activation [MARS-seq]


title: Next Generation Sequencing Facilitates Quantitative Analysis of Stat3f/f K5cre Skin Keratinocytes Transcriptomes

status: Public on Oct 12 2021

first: Kosuke

last: Miyauchi

summary: Atopic dermatitis (AD) is the most common inflammatory skin disease. Stat3 mutation is a major cause of hyper IgE syndrome (HIES), which consistently represent AD like eczematous dermatitis. Based on multi-dimensional transcriptome analysis in pre- and post-flares skin, dermatitis phenotype was controlled by sequential two steps of Stat3 deficiency and environmental pathogenic stimuli. The Stat3 deficiency determined the barrier integrity that lowered threshold of inflammation, but this step was not sufficient to form pathogenicity. Transcriptome data indicated that emergence of dermatitis phenotype need to trigger robust activation of NFB pathway and TH2 cells. Continuous colonization of Staphylococcus aureus was an environmental stimulus to lower the activation threshold of TH2 inflammation in the skin.

overall_design: Kinetical transcriptome analysis in cultured skin keratinocyte and ear skin of specific Stat3 deficient mice

first: Kouske

first: Masato

last: Kubo


title: Analysis of terminal erythroid progenitor populations PIII and PIV in Stab2-iCreF3tg/wt Ctnnb1(Ex3)fl/wt mice

first: Carolina

last: Delatorre

summary: Stab2-iCreF3tg/wt Ctnnb1(Ex3)fl/wt become anemic by the age of three months. We utilzed this model to investigated effects of niche Wnt-Signaling alterations on the terminal erythroid progenitor populations PIII (polychromatic erythroblasts) and PIV (orthochromatic erythroblasts and reticulocytes) by microarray transcriptome analysis.

overall_design: Stab2-iCreF3tg/wt Ctnnb1(Ex3)fl/wt and Ctnnb1(Ex3)fl/wt (Stab2-iCreF3 neg) mice were sacrificed at the age of five months, lower limb bones were flushed and immediately stained for FACS sorting. PIII was defined as SinglecellsLiveCD19negCD3negCD4negCD8negCD11bnegGr1negNk1.1negTer119posCD71posCD44midFSCmid , PIV was defined as SinglecellsLiveCD19negCD3negCD4negCD8negCD11bnegGr1negNk1.1negTer119posCD71posCD44lowFSClow. Cells were lysed directly after sorting and stored at -80°C for 7 days. Thereafter, RNA was isolated and prepared for microarrays.

last: De La Torre


title: The transcriptome sequencing of Chrysin treated Scc9 Extracellular vesicles

city: Changchun

first: Dongxu

last: Wang

state: Jilin

address: Xi'an Road #5333

department: Laboratory Animal Center, College of Animal Science

institute: Jilin University

summary: EVs-Chrysin(Chrysin-treated SCC9) were isolated from SCC9 cells that were treated with chrysin. To improve the therapeutic effect, AuNPs were carried by EVs-Chrysin (Au-EVs). Compared to BGC823 and HCC-LM3 cells, the uptake of Au-EVs were specific in SCC9 cells. Moreover, Au-EVs combined with NIR enhanced cell apoptosis in TSCC cells. To confirm the role of miRNAs in cell apoptosis, the differentially expressed miRNAs between EVs-Con and EVs-Chrysin were screened by RNA-seq.

overall_design: RNA-seq screen differentially expressed miRNAs between EVs-Con and EVs-Chrysin.

first: Zhijing

last: Yang

first: Weiwei

last: Liu


title: EZH2 inhibition confers PIK3CA-driven lung tumors enhanced sensitivity to PI3K inhibition

city: Lexington

first: Fan

last: Chen

state: Kentucky

address: 1095 V.A. Drive, HSRB 461

department: Toxicology and Cancer Biology

institute: University of Kentucky

summary: The purpose of this research is to study the mechanism of the synergistic effect combining EZH2 inhibition and PI3K inhibition. In this study, we observed that the PIK3CA-mutant or amplified lung cancer cells were more sensitive to EZH2 inhibition. PIK3CA E545K, the most common mutation in lung cancer, harbored a modest transformation capacity along with p53 loss in lung epithelial cells, and developed adenocarcinoma autochthonously. EZH2 inhibitor synergized with PI3K inhibitor in human cancer cells in vitro and worked together efficiently in vivo. Mechanistically, EZH2 inhibition cooperated with PI3K inhibition to produce a more potent suppression of phospho-AKT downstream of PI3K.

overall_design: RNA-sequencing profiles of normal human lung epithelial cells (BEAS-2B) with empty vector, p53 R175H mutation, p53 R175H mutation+PIK3CA E545K and p53 R175H mutation+KRAS G12V were analyzed to study the molecular mechanisms of how PIK3CA E545K mutation induced malignant transformation and why PIK3CA mutated cells were more sensitive to EZH2 inhibition.

first: Jinpeng

first: Chi

first: Christine

middle: F

last: Brainson


title: Therapeutic landscape of targeting epigenetically reprogrammed vascular adaptome in the fibrotic liver of multiple species

city: New York

first: Bi-Sen

last: Ding

state: NY

address: York Avenue

institute: Weill Cornell

summary: Targeting pro-fibrotic epigenetic crosstalk in the liver circulatory ecosystem reduces liver fibrosis in multiple species

sample_organism:
Homo sapiens
Sus scrofa

platform_organism:
Homo sapiens
Sus scrofa

overall_design: 1 ctrl,ill(hc) and treated(hma) pig liver NPC sample

first: Bisen


title: The histone chaperone FACT facilitates heterochromatin spreading through regulation of histone turnover and H3K9 methylation states

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

summary: Heterochromatin formation requires several steps involving: nucleation followed by spreading of large, silent domains and its faithful re-establishment and maintenance after each replication cycle. The essential histone chaperone FACT has been implicated in heterochromatin silencing, however, little is known about the specificity of FACT in this process. Here, by applying single cell assays, ChIP and genetics, we show that FACT mutants have defects in the spreading of heterochromatin at subtelomeres and mating type locus in fission yeast. Further, we demonstrate that the transition of H3K9me2 to me3 is impaired in the FACT mutant and we link the spreading function of FACT to its role in histone turnover suppression. We also identify Epe1 as a specific factor that counteracts heterochromatin spreading defects in the FACT mutants. Together, our studies identify FACT as a first histone chaperone that promotes heterochromatin spreading and add to the current models on histone turnover in propagation of epigenetic marks.

overall_design: ChIP-seq experiments in wild type and pob3∆ mutant fission yeast.

first: Magdalena

last: Murawska

first: Andreas

last: Ladurner


title: RNA Sequencing and Ribosome profiling of GIR2 and PUB1 knockout yeast strains.

status: Public on Oct 11 2021

city: Moscow

first: Sergey

middle: E.

last: Dmitriev

address: Leninskie Gory, 1

institute: Lomonosov Moscow State University

summary: We present ribosome profiling and RNA-Seq data for the wild type BY4742 S. cerevisiae strain, and strains with the complete individual deletions of the GIR2 and PUB1 genes.

overall_design: Yeast cells of 3 different S. cerevisiae strains, namely: wt, gir2Δ, pub1Δ were maintained in YPD media. The libraries were sequenced, resulting in 14 RNA-Seq and 12 Ribo-Seq data sets.

first: Artyom

last: Egorov

first: Desislava

last: Makeeva

first: Nadezhda

middle: E

last: Makarova

first: Olga

last: Mitkevich

first: Alexander

last: Alexandrov

first: Ivan

last: Kulakovskiy


title: A comparative analysis of gene and protein expression throughout a full 28-day retinal regeneration time-course in adult zebrafish

city: Detroit

first: Ashley

middle: Catherine

last: Kramer

state: Michigan

address: 540 E Canfield St

department: Ophthalmology, Visual and Anatomical Sciences

institute: Wayne State University School of Medicine

summary: Following photoreceptors ablation by intense light exposure, adult zebrafish are capable of complete regeneration due to the ability of their Müller glia (MG) to re-enter the cell cycle, creating progenitors that differentiate into new photoreceptors. The majority of previous reports on retinal regeneration focused on the first few days of the regenerative response, which include MG cell-cycle re-entry and progenitor cell proliferation. With this study, we analyzed the full 28-day time-course of regeneration by pairing a detailed morphological/immunological analysis with RNA-seq transcriptional profiling at 8 key time points during retinal regeneration. We observed several novel findings. First, we provide evidence for two separate peaks of MG gliosis, with the secondary gliotic peak occurring after MG cell-cycle re-entry. Second, we highlight a distinct transcriptional shift between 5- and 10-days post lesion that highlights the transition from progenitor proliferation to differentiation into new photoreceptors. Third, we show distinctly different patterns of transcriptional recovery of the photoreceptor opsins at 28 days post lesion. Finally, using differential gene expression analysis, we revealed that the established functional recovery of the retina at 28 days post lesion does not, in fact, return to an undamaged transcriptional state, potentially redefining what the field considers complete regeneration. Together, to our knowledge, this work represents the first histological and transcriptomic map of a 28-day time-course of retinal regeneration in adult zebrafish.

overall_design: 3'mRNA sequencing of single adult zebrafish retinas harvested at 7 different time-points post intense light lesion, along with dark adapted and non-dark adapted undamaged controls (n=6).

first: Katherine

last: Gurdziel

first: Ryan

last: Thummel


title: Self-organization of human dorsal-ventral forebrain structures by light induced SHH

first: Riccardo

last: De Santis

address: 1230 York Ave

institute: The Rockefeller univeristy

summary: We report the use of a light stimulus to geometrically confine SHH expression in neuralizing hESCs. This led to the self-organization of mediolateral neural patterns. scRNA-seq analysis established that these structures represent the dorsal-ventral forebrain, at the end of the first month of development. Here, we show that morphogen light-stimulation is a scalable tool that induces self-organizing centers.

overall_design: scRNA-seq using 10X genomics platform of light induced SHH structures in hESC during differentiation. Two replica at day 14.


title: RNA-seq of nulliparus Robo1+/+ and Robo1-/- luminal progenitors

city: Santa Cruz

first: Lindsay

last: Hinck

state: CA

address: 831 California St

institute: University of California, Santa Cruz

summary: The goal of the study was to compare gene expression of Robo1+/+ and Robo1-/- luminal progenitors.  Total RNAs were then extracted from FACS purified luminal progenitor cells, harvested from Robo1+/+ or Robo1-/- mice (n=3 per genotype, two animals per n) using TRIreagent LS (Sigma, T3934). Poly(A)+ RNA sequencing libraries were made from each sample using the TruSeq RNA library preparation kit v.1 (Illumina). Illumina RNA PolyA library preparation guide. A total of 6 libraries were created by PCR amplification with Illumina barcoding primers using kit recommended conditions and quantified using a Bioanalyzer DNA 1000 kit (Agilent).

overall_design: Total RNAs were isolated from FACS purified luminal progenitors, and sequenced on a HiSeq 2000 Sequencing system (Illumina).

first: Jonathan

last: Howard

first: Gwyndolen

last: Harburg

first: Sol

last: Katzman

first: Jeremy

last: Sanford


title: Stepwise chromatin loading of MCM hexamers toward onset of DNA replication

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

summary: MCM dynamics under conditions of G1 arrest in hTERT-RPE1 cells.

overall_design: Examination of MCM3 localization with or without siRNA treatment in hTERT-RPE1 cells

first: Yoko

last: Hayashi-Takanaka

first: Yuichiro

last: Hayashi

first: Yasuhiro

last: Hirano

first: Atsuko

last: Miyawaki-Kuwakado

first: Tokuko

last: Haraguchi

first: Hiroshi

last: Kimura

first: Yasushi

last: Hiraoka


title: Tbx1 regulates a cardiopharyngeal mesodermal niche in forming the heart and branchiomeric muscles [scRNA-Seq 3]

status: Public on Oct 10 2021

city: Bronx

first: Hiroko

last: Nomaru

address: 1300 Morris Park ave

department: Genetics

institute: Albert Einstein College of Medicine

summary: The heart and branchiomeric muscles are formed from the cardiopharyngeal mesoderm (CPM) during mammalian embryogenesis. The molecular mechanisms for lineage progression in the CPM in mammals remain elusive. Here, we have used single cell RNA-seq and lineage analysis and identified a cardiopharyngeal niche containing multilineage primed cells termed multilineage progenitors (MLPs), which is maintained throughout maturation of the pharyngeal apparatus. We found that MLP function is dependent on Tbx1, encoding a T-box transcription factor and the gene for 22q11.2 deletion syndrome. TBX1 positively regulates novel MLP enriched genes such as Aplnr and Nrg1, as well as known CPM genes related to both BrM and cardiac muscle cell development. Further, loss of Tbx1 results in ectopic expression of neuronal and other non-mesodermal specification genes such as Bdnf and Pax8, respectively, indicating that normal developmental regulation is disrupted. Integration of the multi-omic data generated a TBX1 gene regulatory network, including Isl1, Pitx2, Foxc2, Six1/2 and Tcf21, that regulates CPM lineage progression from MLPs. Our finding suggests that TBX1 is a one of the key regulators in MLP to maintain CPM property and promote differentiation toward both BrM and cardiac muscle cells.

overall_design: Tbx1 gene expresses in pharyngeal apparatus. To capture all the Tbx1 expressing cells and their derivatives, sorted GFP positive cell from Tbx1-Cre/+;GFPflox/+ and Tbx1-Cre/flox;GFPflox/+ embryos at E8.5 and E9.5 embryos were used for scRNA-seq analysis.

first: Bernice

last: Morrow

first: Deyou

last: Zheng

first: Yang

last: Liu


title: Tbx1 regulates a cardiopharyngeal mesodermal niche in forming the heart and branchiomeric muscles [scRNA-Seq 1]

summary: The heart and branchiomeric muscles are formed from the cardiopharyngeal mesoderm (CPM) during mammalian embryogenesis.  The molecular mechanisms for lineage progression in the CPM in mammals remain elusive.  Here, we have used single cell RNA-seq and lineage analysis and identified a cardiopharyngeal niche containing multilineage primed cells termed multilineage progenitors (MLPs), which is maintained throughout maturation of the pharyngeal apparatus.  We found that MLP function is dependent on Tbx1, encoding a T-box transcription factor and the gene for 22q11.2 deletion syndrome.  TBX1 positively regulates novel MLP enriched genes such as Aplnr and Nrg1, as well as known CPM genes related to both BrM and cardiac muscle cell development.  Further, loss of Tbx1 results in ectopic expression of neuronal and other non-mesodermal specification genes such as Bdnf and Pax8, respectively, indicating that normal developmental regulation is disrupted.  Integration of the multi-omic data generated a TBX1 gene regulatory network, including Isl1, Pitx2, Foxc2, Six1/2 and Tcf21, that regulates CPM lineage progression from MLPs. Our finding suggests that TBX1 is a one of the key regulators in MLP to maintain CPM property and promote differentiation toward both BrM and cardiac muscle cells.

overall_design: Mesp1 gene expresses in early cardiac mesodermal cells. To capture mesodermal cell lineages,  sorted GFP positive cell from Mesp1-Cre/+;GFPflox/+ embryos at E8.0 to E10.5 embryos were used for scRNA-seq analysis.


title: daf-16/FOXO blocks adult cell fate in Caenorhabditis elegans dauer larvae via lin-41/TRIM71

status: Public on Oct 09 2021

city: Baltimore

first: Margaret

middle: R

last: Starostik

state: MD

address: 3400 Charles Street

department: Department of Biology

institute: Johns Hopkins University

summary: Many tissue-specific stem cells maintain the ability to produce multiple cell types during long periods of non-division, or quiescence. FOXO transcription factors promote quiescence and stem cell maintenance, but the mechanisms by which FOXO proteins promote multipotency during quiescence are still emerging. The single FOXO ortholog in C. elegans, daf-16, promotes entry into a quiescent and stress-resistant larval stage called dauer in response to adverse environmental cues. During dauer, stem and progenitor cells maintain or re-establish multipotency to allow normal development to resume after dauer. We find that during dauer, daf-16/FOXO prevents epidermal stem cells (seam cells) from prematurely adopting differentiated, adult characteristics. In particular, dauer larvae that lack daf-16 misexpress collagens that are normally adult-enriched. Using col-19p::gfp as an adult cell fate marker, we find that all major daf-16 isoforms contribute to opposing col-19p::gfp expression during dauer. By contrast, daf-16(0) larvae that undergo non-dauer development do not misexpress col-19p::gfp. Adult cell fate and the timing of col-19p::gfp expression are regulated by the heterochronic gene network, including lin-41 and lin-29.  lin-41 encodes an RNA-binding protein orthologous to LIN41/TRIM71 in mammals, and lin-29 encodes a conserved zinc finger transcription factor. In non-dauer development lin-41 opposes adult cell fate by inhibiting the translation of lin-29, which directly activates col-19 transcription and promotes adult cell fate. We find that during dauer, lin-41 blocks col-19p::gfp expression, but surprisingly, lin-29 is not required in this context. Additionally, daf-16 promotes the expression of lin-41 in dauer larvae. The col-19p::gfp misexpression phenotype observed in dauer larvae with reduced daf-16 requires the downregulation of lin-41, but does not require lin-29. Taken together, this work demonstrates a novel role for daf-16/FOXO as a heterochronic gene that promotes expression of lin-41/TRIM71 to contribute to multipotent cell fate in a quiescent stem cell model.

overall_design: mRNA-seq profiles in VT2317 daf-16(mgDf50); daf-7(e1372) and control CB1372 daf-7(e1372) dauer larvae.

first: Matthew

middle: J

last: Wirick

first: Allison

last: Cale

first: Isaac

last: Smith

first: Amelia

last: Alessi

first: Liberta

last: Cuko

first: Kyal

last: Lalk

first: Mikayla

last: Schmidt

first: Benjamin

last: Olson

first: Payton

last: Salomon

first: Alexis

last: Santos

first: Axel

last: Schmitter

first: Himani

last: Galagali

first: Kevin

last: Ranke

last: Wolbert

first: Macy

last: Knoblock

first: John

last: Kim

first: Xantha

last: Karp


title: RNA Sequencing and Ribosome profiling of TMA46, STM1 and YGR054W knockout yeast strains

status: Public on Oct 08 2021

first: Sergey

last: Dmitriev

summary: We present ribosome profiling and RNA-Seq data for the wild type BY4742 S. cerevisiae strain, and strains with the complete individual deletions of the TMA46, STM1 and YGR054W genes.

overall_design: Yeast cells of 4 different S. cerevisiae strains, namely: wt, tma46Δ, eif2aΔ, stm1Δ were maintained in YPD media. The libraries were sequenced, resulting in 16 RNA-Seq and 16 Ribo-Seq data sets.

first: Artyom

middle: A

last: Egorov

first: Desislava

last: Makeeva

first: Nadezhda

last: Makarova

first: Olga

last: Mitkevich

first: Alexander

middle: I

last: Alexandrov

first: Ivan

last: Kulakovskiy


title: Effect of GW2580 treatment on primary microglia transcriptome

city: Urbana

first: Katiria

last: Soto Diaz

state: IL

address: 1201 W Gregory Dr

institute: University of Illinois at Urbana-Champaign

summary: The objective of this study was to assess transcriptomic changes to microglia as a result of treatment with the CSF1R angonist GW2580   in healthy mice.

overall_design: To determine how GW2580 affects microglia function, C57BL/6J mice were orally gavaged with vehicle or GW2580 (80mg/kg/d) for 8 days. Microglia were isolated by percoll gradient and then magnetically isolated with a CD11b+ positive selection kit to determine transcriptomic changes.

first: Andrew

last: Steelman

last: Soto-Diaz

first: Mario

last: Vallati-Riboni

first: Allison

last: Louie

first: Daniel

last: McKim

first: H

last: Gaskins

first: Rodney


title: A molecular framework for control of oriented cell division in the Arabidopsis embryo

status: Public on Oct 05 2021

city: Wageningen

first: Dolf

last: Weijers

address: Stippeneng 4

department: Biochemistry

country: Netherlands

institute: Wageningen University

summary:
Premitotic control of cell division orientation is critical for plant development, as cell walls prevent extensive cell remodelling or migration. Whilst many divisions are proliferative and add cells to existing tissues, some divisions are formative, and generate new tissue layers or growth axes. Such formative divisions are often asymmetric in nature, producing daughters with different fates. We have previously shown that in the Arabidopsis thaliana embryo, developmental asymmetry is correlated with geometric asymmetry, creating daughter cells of unequal volume. Such divisions are generated by division planes that deviate from a default “minimal surface area” rule. Inhibition of auxin response leads to reversal to this default, yet the mechanisms underlying division plane choice in the embryo have been unclear. Here we show that auxin-dependent division plane control involves alterations in cell geometry, but not in cell polarity or nuclear position. Through transcriptome profiling, we find that auxin regulates genes controlling cell wall and cytoskeleton properties. We confirm the involvement of microtubule (MT)-binding proteins in embryo division control. Topology of both MT and Actin cytoskeleton depend on auxin response, and genetically controlled MT or Actin depolymerization in embryos leads to disruption of asymmetric divisions, including reversion to the default. Our work shows how auxin-dependent control of MT- and Actin cytoskeleton properties interacts with cell geometry to generate asymmetric divisions during the earliest steps in plant development.
Transcriptional profiling of Col-0 vs bdl 8-cell Arabidopsis embryos

overall_design: Three replicates of Col-0 and bdl mutant 8-cell embryos were used for transcriptome profiling


title: Mutations in CHMP2B Causes Impaired Autophagy and Distorted Energy Metabolism cumulating in Reactive Astrocyte Phenotypes

status: Public on Oct 04 2021

city: Frederiksberg

first: Kristine

middle: Karla

last: Freude

address: Groennegardsvej

country: Denmark

institute: University Copenhagen

summary: CHMP2B mutant astrocytes revealed an accumulation of autophagosomes, which trigger the observed astrocyte reactivity leading to increased cytokine release, altered mitochondria dynamics and metabolic changes.

overall_design: In order to investigate the astrocyte specific impact of mutated CHMP2B we differentiated human induced pluripotent stem cells (hiPSCs) from FTD3 patients and their CRISPR/Cas9 gene edited isogenic controls.

first: Abinaya

last: Chandrasekaran


title: Transcriptional response of human enteroids/colonoids on transwells to infection

status: Public on Oct 01 2021

city: Houston

first: Noah

last: Shroyer

state: Texas

address: One Baylor Plaza, Room N710

department: Medicine Section of Gastroenterology and Hepatology

institute: Baylor College of Medicine

summary: The goal of this study was to evaluate the transcriptional response of human enteroids/colonoids on transwells to infections (bacterial and rotavirus). Enteroids/colonoids lines C103, C109, D103, D109, I103, I109, J2 and J11 were plated on transwells coated with Matrigel, differentiated, and inoculated (rotavirus (Ito), bacteria or mock) for 6 or 24 hours. Subsequently, total RNA was isolated and paired-end sequencing was performed.

overall_design: Enteroid/colonoid mRNA profiles from 48 samples (no technical replicates) were generated by paired-end sequencing.

first: Sue

last: Crawford

first: Sarah

last: Blutt

first: Zachary

last: Criss

first: Mary

last: Estes


title: Tbx1 binding site in whole mouse embryo at E9.5 from in vivo ChIP-seq

first: Hiroko

last: Nomaru

summary: We generated Avidin tag inserted at 3' end of Tbx1 using CRISPR/Cas9 genomic engineering and crossed them with BirA mice from the Jackson laboratory. After established double homozygous mouse colony, total twenty embryos at E9.5 were collected for each samples. After extraction of nucleus, Tbx1 binding regions were captured with Dynabeads™ MyOne™ Streptavidin T1.

overall_design: Tbx1 is T-box transcription factor which expresses in pharyngeal apparatus in mouse embryo. To capture Tbx1 binding site in vivo,  nucleus from Tbx1-Avi;BirA double homozygous embryos at E9.5  were collected for ChIP-assay with streptavidin beads

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