title: Disruption of developmental enhancer and PRC2 function by K27M in childhood glioma

city: Dublin 2

first: Craig

last: Monger

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: Diffuse Intrinsic Pontine Glioma (DIPG) is a universally fatal childhood brain tumour which frequently carries a mutation in genes encoding histone H3. These mutations lead to a lysine-to-methionine (K-to-M) substitution at position 27 (H3K27M) within the histone H3 tail and initiate global shifts in the abundance of Polycomb Repressive Complex 2 (PRC2) mediated H3K27 methylation (me) and P300/CBP mediated acetylation (ac). Acquisition of the H3K27M mutation is the founding genetic event in DIPG tumours, making it likely that these global shifts in H3K27me/ac are instrumental in promoting the early steps toward gliomagenesis. Here, we show that the H3.3K27M oncogene directly disrupts the function of tissue specific gene enhancers and increases Polycomb target gene repression limiting developmental potential of neural stem cells (NSCs). To study the initial functional consequences of H3K27M in glioma, we developed an isogenic human model system. To do this, we modelled the earliest stages of DIPG development by introducing either K27M or wildtype (WT) H3.3 into hindbrain derived NSC cultures. Importantly, this model faithfully recapitulated the global H3K27ac/me dynamics observed in patient samples. Moreover, epitope tagging of the K27M and WT histones allowed us to globally assess the localisation of K27M and WT H3.3. This for the first time facilitated a global analysis of H3.3K27M distribution, as it relates to the WT histone in a biologically relevant context. We found that the presence of the K27M mutation does not alter the localisation of the mutant histone, which is most abundant at enhancer elements with lower levels at gene promoters. Remarkably, the H3.3K27M oncogene limits the developmental potential of NSCs by directly impeding tissue specific enhancer function. Moreover, we found that PRC2 function is primarily altered outside of stably bound Polycomb target sites, with the majority of H3K27me3 lost outside of these regions. Finally, we provide in vivo evidence for sequestration of the PRC2 complex at a subset of Polycomb target promoters. Taken together, these findings provide important new mechanistic insights on the initial steps of DIPG development.

overall_design: RNA-Seq, Chip-RX (H3K27ac, H3K27me3, H3K27me2, H3K4me3 & SUZ12), ATAC-Seq and Chip-Seq (tagged H3.3WT-V5 & H3.3M-V5) of human hindbrain derived neural stem cells expressing wild-type or mutant H3.3.

first: Gerard

last: Brien

first: Raul

last: Bressan

first: Dáire

last: Gannon

first: Orla

last: Deevy

first: Hannah

last: Neikes

first: Darren

last: Fitzpatrick

first: Steven

last: Pollard

first: Adrian

last: Bracken


title: Gene expression changes and DNA damage after ex vivo exposure of peripheral blood cells to variable CT photon spectra

status: Public on Jun 01 2021

city: Munich

first: Hanns Leonhard

last: Kaatsch

address: Neuherbergstraße 11

country: Germany

institute: Bundeswehr Institute of Radiobiology

type: Expression profiling by high throughput sequencing

summary: In this study, we display traceable impact of energetically-varying CT irradiation on gene regulation with common upregulation of five radiation-responsive genes after single-energy (80 kV or 150kV) and dual-energy CT (80kV + 150kV) exposure. Furthermore, no evdidence for an elevated radiobiological effectiveness in respect to transcriptional impact of low energy photons emitted during dual-energy CT was found.

overall_design: Analysis of RNA-Seq changes after single-energy CT- and dual-energy CT-exposure in peripheral human blood cells.

first: Benjamin

middle: V

last: Becker

first: Reinhard

last: Ullmann


title: Mutational synergy during leukemia induction remodels chromatin accessibility, modification and genome topology to alter gene expression

city: Stuttgart

first: Haiyang

last: Yun

address: Auerbachstraße 112

institute: Robert Bosch Center for Tumor Diseases

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Histone H4 lysine 20 mono-methylation directly facilitates chromatin ‘openness’ and promotes transcription of housekeeping genes (ATAC-seq)

status: Public on Jun 04 2021

city: Copenhagen N

first: Mads

last: Lerdrup

address: Blegdamsvej 3C

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: To study the role of Histone H4 lysine 20 mono- and tri-methylation (H4K20me1, H4K20me3) in relationship to chromatin accessibility and gene expression, we report the application of high-throughput profiling of these marks in synchronized and asynchronous Human Osteosarcoma U2OS and asynchronous Mouse Fibroblast (MEF) cells with Set8 knockdown or control siRNA treatment. We find that H4K20me1 contributes to the open chromatin structure at active genes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: siRNA knockdown of the H4K20 methyltransferase Set8 in mouse and humans cells followed by ATAC-seq of synchronized and asynchronously grown cells.

first: Muhammad

last: Shoaib

first: Qinming

last: Chen

first: Xiangyan

last: Shi

first: Nidhi

last: Nair

first: Chinmayi

last: Prasanna

first: Renliang

last: Yang

first: Chuan

middle: F

last: Liu

first: David

last: Walter

first: Klaus

middle: S

last: Frederiksen

first: Peter

last: Svenson

first: Karl

last: Ekwall

first: Lars

last: Nordenskiöld

first: Claus

last: Sørensen


title: Mutational synergy coordinately remodels chromatin accessibility, enhancer landscape and 3-Dimensional DNA topology to alter gene expression during leukemia induction (pCHiC)

summary: Altered transcription is a cardinal feature of acute myeloid leukemia (AML), however, exactly how mutations synergise to remodel the epigenetic landscape and rewire 3-Dimensional (3-D) DNA topology is unknown. We have utilized an allelic series of mice carrying the most common mutations in AML, namely Flt3-ITD and Npm1c. These model different “transition states” (normal: wild-type (WT); pre-malignant: single mutant (SM) with either Flt3-ITD or Npm1c; malignant: double mutant (DM)) during AML induction. We have analyzed hematopoietic stem and progenitor cells (HSPCs) from WT and mutant mice for gene expression (RNA-seq), chromatin activation states (ChIP-seq for H3K4me1, H3K4me3, H3K27ac), chromatin accessibility (ATAC-seq), and promoter-anchored 3-D chromatin interaction (promoter capture HiC, pCHiC) and have integrated these analyses to determine the transcriptional, epigenetic and DNA-topological evolution of AML. These findings allow the identification of long-range cis-regulatory circuits, as well as larger and more detailed gene-regulatory networks, whose importance we demonstrate through perturbation of network members.

overall_design: 3-D chromatin interaction was profiled by performing promoter catpure HiC (pCHiC) in WT and mutant HSPCs, as well as in WT neutrophils. Two biological replicates were performed for each cellular state.

first: Shabana

last: Vohra

first: Brian

middle: J

last: Huntly


title: Neuroinflammatory astrocyte subtypes in the mouse brain [bulk RNA-seq]

status: Public on Jun 03 2021

city: New York

first: Philip

last: Hasel

address: 435 E 30th St

country: USA

institute: NYU Langone Medical Centre

summary: Bulk-seq of FACS purified astrcoytes from saline- and LPS-injected Aldh1l1-GFP mice across time and sex

overall_design: Total RNA was purified from astrocytes from P30-35 Aldh1l1-GFP mice, FACS-puified and RNA collected for bulk-seq and sequenced on a NOVAseq 6000

first: Shane

last: Liddelow


title: Histone H4 lysine 20 mono-methylation directly facilitates chromatin ‘openness’ and promotes transcription of housekeeping genes (ChIP-seq)

first: Mads

last: Lerdrup

summary: To study the role of Histone H4 lysine 20 mono- and tri-methylation (H4K20me1, H4K20me3) in relationship to chromatin accessibility and gene expression, we report the application of high-throughput profiling of these marks in Human Osteosarcoma U2OS and Mouse Fibroblast (MEF) cells with Set8 knockdown or control siRNA treatment. We find that H4K20me1 contributes to the open chromatin structure at active genes.

overall_design: siRNA knockdown of the H4K20 methyltransferase Set8 in mouse and humans cells followed by ChIP-seq of H4K20 methylation.

first: Muhammad

last: Shoaib


title: Hybrid stomach-intestinal chromatin states underlie human Barrett’s metaplasia

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary:
Background & Aims: Tissue metaplasia is uncommon in adults because established cis-element programs resist rewiring. In Barrett’s esophagus, the distal esophageal mucosa acquires predominantly intestinal character, with notable gastric features, and is predisposed to develop invasive cancers. We sought to understand the chromatin underpinnings of Barrett’s metaplasia and why it commonly displays simultaneous gastric and intestinal properties.

Methods: We profiled cis-regulatory elements with active histone modifications in primary human biopsy materials using chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq). Mutations in Barrett’s esophagus were examined in relation to tissue-specific enhancer landscapes using a random-forest machine learning algorithm. We also profiled open chromatin at single-cell resolution in primary Barrett’s biopsy specimens using the assay for transposase-accessible chromatin (ATAC-seq). We used one- and two-color immunohistochemistry to examine protein expression of tissue-restricted genes.

Results: Barrett’s esophagus bears epigenome fingerprints of human stomach and intestinal columnar, but not esophageal squamous, epithelia. Mutational patterns were best explained as arising on the epigenome background of active gastric cis-elements, supporting the view that adjoining stomach epithelium is a likely tissue source. Individual cells in Barrett’s metaplasia co-express gastric and intestinal genes, reflecting concomitant chromatin access at enhancers ordinarily restricted to one or the other epithelium. Protein expression of stomach-specific mucins, CLDN18, and a novel gastric marker, ANXA10, revealed extensive tissue and sub-clonal heterogeneity of dual stomach-intestinal cell states.

Conclusions: These findings reveal mixed and dynamic tissue-restricted chromatin states and phenotypic heterogeneity in Barrett’s esophagus. Pervasive intra-gland variation argues against stem-cell governance of this phenotype.

overall_design:
ChIP-Seq on FFPE human tissue obtained on routine clinical endoscopy

Single Cell ATAC-seq on human Barretts metaplasia biopsy, stomach body biopsy and dudenal biopsy.

first: Harshabad

last: Singh

first: Kyungsik

last: Ha

first: Jason

middle: L

last: Hornick

first: Shariq

last: Madha

first: Paloma

last: Cejas

first: Kunal

last: Jajoo

first: Pratik

first: Paz

last: Polak

first: Hwajin

last: Lee

middle: A


title: The KRAB-ZFP/TRIM28 system exploits transposons to sharpen lineage-specific and activation-induced transcription in human adult T lymphocytes

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL


title: CSF1R inhibition rescues tau pathology and neurodegeneration in an A/T/N model with combined AD pathologies, while preserving plaque associated microglia

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

summary: Alzheimer's disease (AD) is characterized by a sequential progression of amyloid plaques (A), neurofibrillary tangles (T) and neurodegeneration (N), constituting ATN pathology. While microglia are considered key contributors to AD pathogenesis, their contribution in the combined presence of ATN pathologies remains incompletely understood. As sensors of the brain microenvironment, microglial phenotypes and contributions are importantly defined by the pathologies in the brain, indicating the need for their analysis in preclinical models that recapitulate combined ATN pathologies, besides their role in A and T models only. Here, we report a new tau-seed model in which amyloid pathology facilitates bilateral tau propagation associated with brain atrophy, thereby recapitulating robust ATN pathology. Single-cell RNA sequencing revealed that ATN pathology exacerbated microglial activation towards disease-associated microglia (DAM) states, with a significant upregulation of Apoe as compared to amyloid-only models (A). Importantly, Colony-Stimulating Factor 1 Receptor inhibition preferentially eliminated non-plaque-associated versus plaque associated microglia. The preferential depletion of non-plaque-associated microglia significantly attenuated tau pathology and neuronal atrophy, indicating their detrimental role during ATN progression. Together, our data reveal the intricacies of microglial activation and their contributions to pathology in a model that recapitulates the combined ATN pathologies of Alzheimer's disease. Our data may provide a basis for microglia-targeting therapies selectively targeting detrimental microglial populations, while conserving protective populations.

overall_design: Sample of WT mouse whole brain (pool of 4 whole brains) (WT), sample of 5xFAD mouse whole brain (pool of 4 whole brains) (5xFAD), sample of 5xFAD x PS19 and Tau seed injected mouse whole brain (pool of 4 hemispheres ipsilateral of the Tau-seed injection) (5xFAD_T_Ts_Ipsilateral), sample of 5xFAD x PS19 and Tau seed injected mouse whole brain (pool of 4 hemispheres contralateral of the Tau-seed injection) (5xFAD_T_Ts_Contralateral), sample of 5xFAD x PS19 and Tau seed injected mouse whole brains treated with PLX3397 (pool of 2 whole brains) (5xFAD_T_Ts_PLX), sample of 5xFAD x PS19 and Tau seed injected mouse control untreated whole brains (pool of 2 whole brains) (5xFAD_T_Ts_CTRL)

first: Chritica

last: Lodder

first: Isabelle

last: Scheyltjens

first: Ilie

last: Cosmin Stancu

first: Pablo

last: Botella Lucena

first: Manuel

last: Gutiérrez de Ravé

first: Sarah

last: Vanherle

first: Tim

last: Vanmierlo

first: Niels

last: Cremers

first: Hannah

last: Vanrusselt

first: Bert

last: Brône

first: Bernard

last: Hanseeuw

first: Jean-Noël

last: Octave

first: Astrid

last: Bottelbergs

first: Kiavash

last: Movahedi

first: Ilse

last: Dewachter


title: Aurora A kinase Inhibition Reprograms Metabolism dependent on PGC1α to Drive Synthetic Lethality with Fatty Acid Oxidation Inhibition in Glioblastoma

first: Markus

last: Siegelin

state: New York

department: Pathology and Cell Biology

institute: Columbia University


title: Double-stranded RNA in testis

city: Newcastle

first: Andreas

last: Werner

address: Framlington Place

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

summary: We precipitated dsRNA using the monoclonal J2 antibody and deep-sequenced the enriched samples from testis of juvenile dicer knock-out mice, age matched controls and adult animals. The dsRNA transcriptome is significantly less complex in juvenile mice as compared to adult controls and, possibly as a consequence, the knock-out of Dicer had only a minor effect of the total number of transcribed regions associated with dsRNA. The genes that potentially generate dsRNA are significantly expressed in isolated sperm cells with particular enrichment in pachytene spermatocytes.

overall_design: Double-stranded RNA immunopurification using the J2 antibody (Scicons) from mouse testis, including 18 days old mice, age matched dicer knock-out mice and adult controls.

first: John

last: Mattick


title: Impact of Wnt6 knockout in Mtb infected murine BMDM

city: Borstel

first: Sebastian

last: Marwitz

address: Parkallee 3a

department: Histology

institute: Research Center Borstel - Leibniz Lung Center

summary: In view of emerging drug-resistant tuberculosis, host directed therapies are urgently needed to improve treatment outcomes with currently available anti-tuberculosis therapies. One option is to interfere with the formation of lipid-laden “foamy” macrophages in the infected host. Here, we provide evidence that WNT6, a member of the evolutionary conserved WNT signaling pathway, promotes foam cell formation by regulating key lipid metabolic genes including acetyl-CoA carboxylase-2 (ACC2) during pulmonary TB. In addition, we demonstrate that Mycobacterium tuberculosis (Mtb) facilitates its intracellular growth and dissemination in the host by exploiting the WNT6-ACC2 pathway. Using genetic and pharmacological approaches, we show that lack of functional WNT6 or ACC2 significantly reduces intracellular TAG levels, Mtb growth and necrotic cell death of macrophages. In combination with the anti-TB drug isoniazid, pharmacological inhibition of ACC2 improved anti-mycobacterial treatment in vitro and in vivo. Therefore, we propose the WNT6-ACC2 signaling pathway as a promising target for a host-directed therapy to reduce intracellular replication of Mtb by modulating neutral lipid metabolism.

overall_design: 3 wildtype vs 3 knockout mice

first: Julius

last: Brandenburg

first: Norbert

last: Reiling


title: Transthyretin alters cardiac fibroblast structure, function and inflammatory gene expression.

status: Public on Jun 02 2021

city: Chicago

first: Brenda

last: Russell

state: IL

address: 835 S Wolcott Ave

department: Physiology

institute: University Illinois at Chicago

summary: Age-related wild type transthyretin amyloidosis (wtATTR) is characterized by systemic deposition of amyloidogenic fibrils of misfolded transthyretin (TTR) in the connective tissue of many organs. In the heart this leads to cardiac dysfunction, which is a significant cause of age-related heart failure. The hypothesis tested is that TTR affects cardiac fibroblasts in ways that may contribute to fibrosis. When primary cardiac fibroblasts were cultured on TTR-deposited substrates, the F-actin cytoskeleton disorganized, focal adhesion formation decreased, and nuclear shape was flattened. Fibroblasts had faster collective and single cell migration velocities on TTR-deposited substrates. Additionally, fibroblasts cultured on microposts with TTR deposition had reduced attachment and increased proliferation above untreated. Transcriptomic and proteomic analyses of fibroblasts grown on glass covered with TTR showed significant upregulation of inflammatory genes after 48 hours, indicative of progression in TTR-based diseases. Together, results suggest that TTR deposited in tissue extracellular matrix may affect both the structure, function and gene expression of cardiac fibroblasts. As therapies for wtATTR are cost-prohibitive and only slow disease progression, better understanding of cellular maladaptation may elucidate novel therapeutic targets.

overall_design: Three samples of cardiac fibroblasts grown on both untreated (UT) and TTR fibril-containing (TTR) substrates.

first: K

middle: T

last: Dittloff

first: A

last: Iezzi

first: J

middle: X

last: Zhong

first: P

last: Mohindra

first: T

last: Desai

first: B


title: Mutational synergy coordinately remodels chromatin accessibility, enhancer landscape and 3-Dimensional DNA topology to alter gene expression during leukemia induction (ATAC-seq)

first: Haiyang

last: Yun

overall_design: Chromatin accessibility was profiled by performing ATAC-seq in WT and mutant HSPCs, as well as in WT neutrophils. Two biological replicates were performed for each cellular state.

first: Shabana

last: Vohra

first: Brian

last: Huntly


title: Variant PCGF1-PRC1 links PRC2 recruitment with induced transcriptional inactivation at target genes [CUT&Tag]

status: Public on May 31 2021

city: Tsurumi-ku,Yokohama

first: Hiroki

last: Sugishita

state: Kanagawa

address: 1-7-22, Suehiro-cho

department: IMS

country: Japan

institute: RIKEN

summary: Polycomb repressive complexes-1 and -2 (PRC1 and 2), silence developmental genes in spatiotemporally regulated manner during metazoan embryogenesis. How PcG proteins contribute to down-regulation of target genes upon differentiation, however, remains elusive. Here, by differentiating embryonic stem cells into embryoid bodies, we reveal a crucial role of a PCGF1 (Polycomb group RING finger protein 1)-containing variant PRC1 complex (PCGF1-PRC1) to facilitate induced down-regulation of a group of genes. Binding of PCGF1-PRC1 results in down-regulation of transcriptional activity, followed by Histone H2AK119 mono-ubiquitination (H2AK119ub1) and subsequent recruitment of PRC2, to initiate PcG-repressive domain formation. Based on these findings, we propose that PCGF1-PRC1 mediates establishment of PcG-repressive domains at target genes during differentiation.

overall_design: CUT&Tag analysis of mouse ES cell and embryoid body (EB)

first: H

first: N

last: Yakushiji-Kaminatsui

last: Koseki


title: Aurora A kinase Inhibition Reprograms Metabolism dependent on PGC1α to Drive Synthetic Lethality with Fatty Acid Oxidation Inhibition in Glioblastoma [ATAC-Seq]

first: Markus

last: Siegelin

summary: By integration of transcriptome, CHIP-seq, ATAC-seq, proteomic and metabolite screening followed by carbon tracing (U-13C-Glucose, U-13C-Glutamine and U-13C-Palmitic acid) and extracellular flux analysis we provided evidence that genetic (shRNA and CRISPR/Cas9) and pharmacological (Alisertib) AURKA inhibition elicited substantial metabolic reprogramming supported in part by inhibition of MYC targets and concomitant activation of PPARA signaling. While glycolysis was suppressed by AURKA inhibition, we noted a compensatory increase in oxygen consumption rate fueled by enhanced fatty acid oxidation (FAO). Whereas interference with AURKA elicited a suppression of c-Myc, we detected an upregulation of PGC1α, a master regulator of oxidative metabolism, upon AURKA inhibition. Chromatin immunoprecipitation experiments confirmed binding of c-Myc to the promoter region of PGC1α, which is abrogated by AURKA inhibition and in turn unleashed PGC1α expression. To interfere with this oxidative metabolic reprogramming, we combined AURKA inhibitors with inhibitors of FAO (etomoxir) and electron transport chain (gamitrinib) and found substantial synergistic growth inhibition in patient derived xenograft in vitro and extension of overall survival without induction of toxicity in normal tissue.

overall_design: GBM22 cells were exposed with alisertib for 10 days to generate resistance cell line (GBM22AR). Thereafter, cells were harvested and subjected to ATAC-seq kit according to the company instruction.

first: Trang

last: Nguyen


title: Splicing factor SRSF1 is indispensable for regulatory T cell homeostasis and function

first: Takayuki

last: Katsuyama

address: 3 Blackfan Circle, CLS-948

department: Rheumatology and Clinical Immunology

institute: Beth Israel Deaconess Medical Center

summary: Purpose: The goals of this study are to determine the role of the serine/ arginine-rich splicing factor 1 (SRSF1) in regulatory T cells

overall_design: Methods: Total T cells were isolated from spleens of 8-10-week-old WT and T cell Srsf1-KO mice (n=3 each). CD4+CD25+CD127lo natural (n)Treg cells were sorted by flow cytometry. nTregs were stimulated with anti-CD3 (2 μg/ml) and anti-CD28 (2 μg/ml) antibodies and rIL-2 (10 ng/ml) for 72h. Cells were collected, and total RNA was extracted using the RNeasy mini kit (Qiagen) and submitted for RNA sequencing to the Molecular Biology Core Facilities at the Dana-Farber Cancer Institute (DFCI). Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits according to the manufacturer’s protocols. Samples were sequenced on an Illumina NextSeq500 run with single-end 75-bp reads. Data analyses were performed using the VIPER pipeline by the DFCI Core.

first: Vaishali

middle: R

last: Moulton


title: Variant PCGF1-PRC1 links PRC2 recruitment with induced transcriptional inactivation at target genes


title: The KRAB-ZFP/TRIM28 system exploits transposons to sharpen lineage-specific and activation-induced transcription in human adult T lymphocytes [ChIP-seq]

first: Evarist

last: Planet

summary: Transposable elements (TEs) are subjected to early embryonic repression through sequence-specific recruitment of KRAB zinc finger proteins (KRAB-ZFPs), their cofactor TRIM28 and associated chromatin modifiers. This prevents transposition and modulates TE-induced changes of gene expression in embryonic stem cells (ESCs). It leads to DNA methylation, a self-perpetuating modification considered as responsible for the permanent silencing of TEs after this period. Challenging this view, we reveal here that the KRAB/TRIM28 system keeps mediating a highly dynamic control of TEs and TE-mediated transcriptional influences in adult human cells. Using CD4+ T lymphocytes as an experimental model, we first observed that in these cells many TEs are still bound by TRIM28, the recruitment of which is dynamically regulated upon T cell receptor stimulation. Second, we determined that this transition reflects marked changes in the expression patterns of TE-binding KRAB-ZFPs. Finally, we could demonstrate that TRIM28 depletion induces broad transcriptional alterations in T cells, with de-repression notably of TE-based enhancers leading to the illegitimate activation of nearby genes and breaches of lineage-specific transcriptional restrictions. These data contribute to demonstrate that TEs and their KRAB-ZFP/TRIM28 control system are important regulators of gene expression in adult human cells.

overall_design: H3K9me3 and KAP1 ChIP-seq in CD4+ T lymphocytes. Transcriptome profiling of control and KAP1 KD CD4+ T lymphocytes.

first: Flavia

last: Marzetta

first: Julien

last: Duc

first: Didier

last: Trono


title: Aurora A kinase Inhibition Reprograms Metabolism dependent on PGC1α to Drive Synthetic Lethality with Fatty Acid Oxidation Inhibition in Glioblastoma [ChIP-Seq]

overall_design: GBM22 cells were exposed with alisertib for 10 days to generate resistance cell line (GBM22AR). Thereafter, cells were harvested and subjected to CHIP isolation. DNA was subsequently processed for CHIP sequencing.


title: Variant PCGF1-PRC1 links PRC2 recruitment with induced transcriptional inactivation at target genes [RNA-seq]

overall_design: RNA-seq analysis of mouse ES cells and embryoid body (EB)


title: Whole Genome Bisulfite Sequencing Data of Botrytis cinerea

city: Beijing

first: Chang

last: He

address: No.20 Nanxincun, Xiangshan

department: Key Laboratory of Plant Resources

country: China

institute: Institute of Botany, the Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: Analysis of the genome-wide DNA methylation pattern of Botrytis cinerea. Results provide new and important information that DNA methylation is critical for pathogenicity and development of Botrytis cinerea by regulating gene expression.

overall_design: Bisulphite converted DNA from the 12 samples were sequenced by using the HighSeq2000.

first: Zhanquan

last: Zhang


title: CircRNAs full-length sequencing in the human and mouse brain samples using Oxford Nanopore Technology

city: Aarhus N

first: Morten

last: Veno

state: DK

address: Aabogade 15

institute: Omiics ApS

type: Non-coding RNA profiling by high throughput sequencing

summary: We optimized a protocol to enrich, digest and add poly(A) tail to the circular RNAs in order to make them compatible with the Oxfor Nanopore Technology for full-length sequencing

overall_design: Circular RNAs from human cortex and total mouse brain was sequenced

first: Karim

last: Rahimi

last: Venø

first: Daniel

middle: M

last: Dupont

first: Jorgen

last: Kjems


title: Mutational synergy coordinately remodels chromatin accessibility, enhancer landscape and 3-Dimensional DNA topology to alter gene expression during leukemia induction (ChIP-seq)

first: Haiyang

last: Yun

overall_design: Chromatin states were profiled by performing ChIP-seq on histone modifications (including H3K4me1, H3K4me3 and H3K27ac) in WT and mutant HSPCs, as well as in WT neutrophils. Two biological replicates were performed for each cellular state.

first: Shabana

last: Vohra

first: Brian

last: Huntly


title: Single cell RNA sequencing data of T cells co-cultured with tumor cells

city: Amsterdam

first: Anne

middle: Magdalena

last: van der Leun

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: We developed a photosensitive tag (PsT) to label cells that reside in specific areas of interest in (human) primary tissues through specific exposure with violet light, allowing analysis of single cells while preserving their spatial information. As a benchmarking experiment, we used the PsT  to assess transcriptional differences between CD8+ T cells that reside in an area containing tumor cells that do express cognate antigen, or an area of tumor cells that do not express the antigen. Single cell RNA sequencing revealed differential expression of activation markers between CD8+ T cells from antigen-positive or antigen-negative areas, demonstrating the value of the PsT to investigate spatially-induced differences between cells residing in primary tissues.

overall_design:
single cell transcriptional profiles of CD8+  T cells isolated from areas with antigen-positive or antigen-negative tumor cells. Samples contain exposed ("uncapped") and non-exposed ("capped") CD8+ T cells from cocultures in which cells residing in antigen-positive (Ag+) or antigen-negative (Ag-) tumor areas were specifically exposed. Capping status of each cell was defined by flow cytometry and is specificied in "M_metadata_ann.txt" file.

Please note that additional files (containing the code and annotated data objects etc. as described in the readme.txt) have been added on Jun 9, 2021.

first: A

first: T

middle: N

last: Schumacher


title: The KRAB-ZFP/TRIM28 system exploits transposons to sharpen lineage-specific and activation-induced transcription in human adult T lymphocytes [RNA-seq]


title: YBX1 mediates translation of oncogenic transcripts to control cell competition in AML

status: Public on May 28 2021

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

institute: Hannover Medical School

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

overall_design: Refer to individual Series


title: microRNA identification in the Mycoplasma bovis infected mammary gland tissue in Holstein Friesian cattle

status: Public on May 25 2021

city: Erzurum

first: Selçuk

last: Özdemir

address: Atatürk University Faculty of Veterinary Medicine

country: Turkey

institute: Atatürk University

summary: The immune response associated with mastitis caused by Mycoplasma bovis is a very complicated biological process in several type of cells, including immune cells, mammary epithelial cells and, endothelial cells. Thus, revealing of the microRNAs in the Mycoplasma bovis infected mammary gland tissues is particularly important for the immune response mechanism to Mycoplasma bovis. Firstly, mammary gland tissue samples were collected from Holstein cows and screened for Mycoplasma bovis. Then, total RNA was isolated from mycoplasma bovis infected tissues and RNA sequencing was performed. After bioinformatics analysis, GO and KEGG analysis of target genes of identified microRNAs were conducted. Our results revaled that 24 of the known microRNAs were expressed differently and 13 of the novel microRNAs were expressed differently in Mycoplasma bovis positive tissues. The target genes of these microRNAs were found to be associated with especially inflammation pathways. In conclusion, this study demonstrated that identified miRNAs may be involved in the signaling pathways during mastitis case caused by Mycoplasma bovis.

overall_design:
Examination of Mycoplasma bovis infected mamary tissues in cattle.

GRANT INFORMATION: Grant Id: 116O618; Grant title; T  BITAK; The Scientific and Technological Research Council of Turkey


title: Gene expression profiles of breast cancer metastasis according to organ site

city: Barcelona

first: Fara

last: Brasó-Maristany

state: Barcelona

address: C/Casanova 143

country: Spain

institute: Institut d'Investigacions Biomediques August Pi I Sunyer

summary: In advanced breast cancer, biomarker identification and patient selection using a metastatic tumor biopsy is becoming more necessary. However, the biology of metastasis according to the organ site is largely unknown. Here, we evaluated the expression of 771 genes in 184 metastatic samples across 11 organs, including liver, lung, brain and bone, and made the following observations. First, all PAM50 molecular intrinsic subtypes were represented across organs and within immunohistochemistry-based groups. Second, HER2-low disease was identified across all organ sites, including bone, and HER2 expression significantly correlated with ERBB2 expression. Third, the majority of expression variation was explained by intrinsic subtype and not organ of metastasis. Fourth, subtypes and individual subtype-related genes/signatures were significantly associated with overall survival. Fifth, we identified 74 genes whose expression was organ-specific and subtype-independent. Finally, immune profiles were found more expressed in lung compared to brain or liver metastasis. Our results suggest that relevant tumor biology can be captured in metastatic tissues across a variety of organ sites; however, unique biological features according to organ site were also identified and future studies should explore their implications in diagnostic and therapeutic interventions.

overall_design: 184 breast cancer metastasis

first: Aleix

last: Prat


title: YBX1 mediates translation of oncogenic transcripts to control cell competition in AML [RNA-seq polysomes]

summary: RNA-seq followed by digital gene expression analyses we assessed genes that change upon CRISPR-Cas9-mediated knockout of YBX1 in myeloid leukemia cells (MOLM13 cell line).

overall_design: Gene expression in total mRNA and mRNA from purified polysomal fractions was assessed in cells harboring a YBX1-knockout using a pre-validated CRISPR-Cas9 guide-RNAs and a non-targeting guide as control at 14 days after lentiviral transduction.

first: Nicolas

last: Huber


title: Whole blood transciptome analysis in severe Covid-19  patients and healthy donors

status: Public on May 27 2021

city: Créteil

first: cecile

last: lefebvre

address: 51 Avenue du Marechal De Lattre de Tassigny

country: France

institute: INSERM U955_VRI

summary: The identification of COVID-19 patients with high-risk of severe disease is a challenge in routine care. We performed blood RNA-seq gene expression analyses in severe hospitalized patients compared to healthy donors. Supervised and unsupervised analyses revealed a high abundance of CD177, a specific neutrophil activation marker, contributing to the clustering of severe patients. Gene abundance correlated with high serum levels of CD177 in severe patients. These results highlight neutrophil activation as a hallmark of severe disease and CD177 assessment as a reliable prognostic marker for routine care.

overall_design: Analysis of whole-blood gene expression profiles of 44 covid-19 patients and 10 Healthy donnors

first: Yves

last: Lévy

first: Aurélie

last: Wiedemann

first: Boris

middle: P

last: Hejblum

first: Mélany

last: Durand

first: Cécile

last: Lefebvre

first: Mathieu

last: Surénaud

first: Christine

last: Lacabaratz

first: Matthieu

last: Perreau

first: Emile

last: Foucat

first: Marie

last: Déchenaud

first: Pascaline

last: Tisserand

first: Fabiola

last: Blengio

first: Benjamin

last: Hivert

first: Marine

last: Gauthier

first: Minerva

last: Cervantes-Gonzalez

first: Delphine

last: Bachelet

first: Cédric

last: Laouénan

first: Lila

last: Bouadma

first: Jean-François

last: Timsit

first: Yazdan

last: Yazdanpanah

first: Giuseppe

last: Pantaleo

first: Hakim

last: Hocini

first: Rodolphe

last: Thiébaut


title: Neuronal control of maternal provisioning in response to social cues

status: Public on May 19 2021

city: Basel

first: Jadiel

last: Wasson

address: Klingelbergstrasse 50/70

department: Zell Biologie

institute: Biozentrum, University of Basel

summary: Mothers contribute cytoplasmic components to their progeny in a process called maternal provisioning. Provisioning is influenced by the parental environment, but the molecular pathways that transmit environmental cues between generations are not well understood. Here we show that in C. elegans, social cues modulate maternal provisioning to regulate gene silencing in offspring. Intergenerational signal transmission depends on a pheromone-sensing neuron and neuronal FMRFamide (Phe-Met-Arg-Phe)-like peptides. Parental FMRFamide-like peptide signaling dampens oxidative stress resistance and promotes the deposition of mRNAs for translational components in progeny, which in turn reduces gene silencing. This study identifies a new pathway for intergenerational communication that links neuronal responses to maternal provisioning. We suggest that loss of social cues in the parental environment represents an adverse environment that stimulates stress responses across generations.

overall_design: RNA sequencing of early, pre-gastrulation C. elegans embryos from wildtype and flp-21 mutants


title: Variant PCGF1-PRC1 links PRC2 recruitment with induced transcriptional inactivation at target genes [ChIP-seq]

first: Hiroki

last: Sugishita

overall_design: ChIP-seq analysis of mouse ES cell and embryoid body (EB)

first: H

first: S

last: Ito

last: Koseki


title: YBX1 mediates translation of oncogenic transcripts to control cell competition in AML [RNA-seq]

first: Florian

last: Perner

overall_design: Gene expression was assessed in cells harboring a YBX1-knockout using 2 different CRISPR guide-RNAs and a non-targeting guide as control at 7 days after lentiviral transduction.

first: Charlie

last: Hatton


title: Transcriptional profiling of Regulatory T (Treg) cells in obesity

status: Public on May 20 2021

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: We reported transcriptional characterization of vTreg53 TCR transgenic Treg cells from splenic and visceral adipose tissue (VAT) in mice fed with normal chow diet (NCD) or high fat diet (HFD) for different durations. We also reported transcriptional profile of VAT Treg cells stimulated by IFNa in vitro. Through this analysis, we found that the reduction of VAT Treg cells during obesity is driven by increased production of IFNa in VAT.

overall_design: For the HFD dataset, 12-week-old vTreg53 TCR tg mice were fed with NCD or HFD for 2, 4, 8, or 16 weeks. The clonotype+ Tregs from the spleen and VAT of recipient mice were double sorted and processed for RNA-seq. For the in vitro dataset, 8-10-week-old PPARγ-tdT Foxp3-GFP mice were injected with two doses of IL-33 in a week to expand VAT-Treg cells, and PPARγ(tdT)+ VAT-Treg cells were sorted and cultured in the presence of 10ng/ml IL-33, 2000U/ml IL-2, with or without 50ng/ml IFNa for 3 days. Foxp3/GFP+ Treg cells were sorted and processed for RNA-Seq.

first: Chaoran

last: Li

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Interrogation of the Dynamic Properties of Higher-Order Heterochromatin Using CRISPR/dCas9

status: Public on May 26 2021

city: Menlo Park

first: Stephen

last: Shang

state: California

address: 297 Jane Stanford Way

institute: Stanford University

summary: Eukaryotic chromosomes feature large regions of compact, transcriptionally-repressed heterochromatin hallmarked by the presence of Heterochromatin Protein 1 (HP1) family members. HP1 proteins play multi-faceted roles in directly shaping the properties of heterochromatin, and in vivo , HP1 tethering to individual gene promoters leads to epigenetic modifications and gene silencing. However, emergent properties of HP1 at supranucleosomal scales have been difficult to study in cells due to a lack of appropriate tools. Here, we develop CRISPR-Engineered Chromatin Organization (EChO), a novel approach for combining live cell CRISPR-based imaging with inducible and reversible large-scale recruitment of heterochromatin components to native chromatin in human cells. Using CRISPR-EChO, we demonstrate that human HP1α binding across tens of kilobases of genomic DNA leads to formation of novel contacts with other heterochromatin regions and reversibly compacts chromatin from a diffuse to condensed state. The condensed chromatin state exhibits delayed disassembly kinetics and represses transcription across over 600 kilobases. Collectively, these findings support a polymer model of HP1α-mediated chromatin regulation and highlight the utility of CRISPR-EChO in studying and manipulating supranucleosomal chromatin organization in living cells.

overall_design: 3 replicates of ABA-treated and Control DMSO-treated samples.  Paired end fastq files as well as processed bigwig files are uploaded.

first: Tony

last: Gao

first: Mengting

last: Han

first: Haifeng

last: Wang

first: Stanley

last: Qi


title: Transcriptome and oxylipin profiling joint analysis reveals the opposite roles of 9-oxylipins and jasmonic acid in maize resistance to Gibberella stalk rot

status: Public on May 17 2021

city: Nanjing

first: wang

last: yinying

state: Jiangsu

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

department: College of Agriculture

institute: Nanjing Agricultural University

summary: Gibberella stalk rot (GSR) caused by Fusarium graminearum is one of the devastating diseases causing significant losses to maize production worldwide. Although plant oxylipins have been widely reported as potent signals to activate diverse biotic stress responses, the roles of distinct oxylipin pathway branches initiated by either 9- or 13-lipoxygenases (LOXs) in defense against GSR remain unexplored. In this study, the functional analysis showed that disruption of ZmLOX5, a maize 9-LOX gene, resulted in increased susceptibility to GSR. To identify the key genes and metabolites associated with GSR resistance, we profiled transcriptome and oxylipins in the lox5 mutant and near-isogenic wild type. The results showed that JA biosynthetic pathway genes are highly up-regulated, whereas multiple 9-LOX pathway genes down-regulated in lox5-3 mutant in response to F. graminearum infection. Furthermore, oxylipin profiling of the mutant and corresponding wild type, B73, as well as a more resistant line, W438, uncovered significantly higher contents of JA-isoleucine (JA-Ile) and other jasmonates but relatively lower levels of 9-oxylipins in lox5-3 upon infection. By contrast, resistant line W438 and B73 displayed relatively lower levels of JAs, yet considerable increase of 9-oxylipins. Taken together, these results clearly indicated that the signaling pathways of 9-oxylipins and JAs antagonize each other, and that while ZmLOX5-produced 9-oxylipins contribute to resistance, JAs are likely to function as negative regulator in maize defense against GSR.

overall_design: the RNA-seq analysis using B73 and mutant lox5-3 at different time points (0h,12h and 24h) after infection with F. graminearum.

first: Qing

first: Yali

last: Sun

first: Fang

first: Xiquan


title: Characterization of CD44low CD62Llow CD8 T-cell subset

city: Kyoto

first: Kenji

last: Chamoto

state: Kyoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

institute: Graduate School of Medicine, Kyoto University

summary: To characterize CD44low CD62low CD8 T-cell subset (P4), we compared gene expression among four CD8 T-cell subsets. A hierarchical clustering of global gene expression showed that each subset of CD8 T-cells expresses a distinct gene profile. Genes expressed in activated T-cells were highly expressed in P4 cells compared to naive P1 cells.  On the other hand, genes expressed in differentiated T-cells were less expressed in P4 cells compared to either central memory (P2) or effector/memory (P3) cells.  These results indicate that P4 cells are in an activated, but pre-mature state and distinct from more differentiated subsets of CD8 T-cells such as central memory and effector/memory cells.

overall_design: FACS sorted CD8 subset cells from spleens and lymph nodes of PD-1-/- C57BL/6 mice

first: Yuka

last: Nakajima

first: Tasuku

last: Honjo


title: Transient side effects of CRISPR/Cas9-VP160 for gene activation

status: Public on May 21 2021

city: Bronx

first: Andrew

last: Johnston

state: NY

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

summary: Cas9 fused to VP16 repeats have been used in several systems of gene activation. Here we aimed to evaluate the undesirable effects of this system whether in presence or absence of gRNAS targeting a specific gene, CD34.

overall_design: HEK293T cells were transfected with dCas9-VP160 in the presence or absence of 6 gRNAs targeting the promoter of CD34, and two technical replicates of each treatment as well as a control (non-transfected cells) were assayed using dirRNAseq. This was repeated with a second batch of cells.

first: Claudia

last: Simoes-Pires

middle: D

first: John

last: Greally


title: Single-cell profiling reveals transcriptional signatures, novel epithelial cells and cell-cell crosstalk in idiopathic membranous nephropathy patients

status: Public on May 30 2021

city: Changsha

first: Yong

last: Zhong

state: Hunan province

address: 87 Xiangya Road

department: Nephrology

institute: Xiangya Hospital, Central South University

summary: Our understanding of the pathogenesis of idiopathic membranous nephropathy is limited by an incomplete molecular characterization of the cell types in the kidney and interaction between the cells. Besides, the reason for the heterogeneity of these patients as well as the variety of clinical outcomes remains elusive. Therefore, we applied scRNA-seq to kidney biopsies of patients with IMN to identify gene expression at the single-cell level, elucidate cells involved in the progression of IMN, and uncover intercellular interactions.

overall_design: We analyzed kidney samples from 6 patients with IMN and 2 healthy control subjects using single-cell RNA sequencing. We then identified distinct cell clusters through unsupervised clustering analysis of kidney specimens. Identification of the differentially expressed genes (DEGs) and enrichment analysis in different  cells as well as the interaction between cells were also performed. In addition, the differences of gene expression and enrichment pathway in patients with different levels of proteinuria were analyzed.

first: Jie

last: Xu

first: Qiaoling

last: Zhou


title: Transcriptional alterations of P. falciparum 3D7-A heat shock-adapted vs control parasites.

first: Elisabet

last: Tinto-Font

address: c/Rossello 153

department: Malaria

institute: ISGlobal

summary: Periodic fever is the most characteristic clinical feature of human malaria. However, how parasites survive malarial febrile episodes, which often involve temperatures of >40ºC, is not known. To understand the molecular basis of heat shock (HS) resistance in Plasmodium falciparum, we took advantage of previously developed P. falciparum lines adapted to periodic HS (3D7-A-HS) and their non-selected controls maintained in parallel (3D7-A). Their ability to adapt in only a few cycles suggested that the parental parasite population contained a selectable subset of parasites resistant to HS. Transcriptomic analysis of both 3D7-A-HS and 3D7-A was used to study the differences at a transcriptional level that could be related with the HS-resistant phenotype.

overall_design: Timecourse transcriptomic analysis of P. falciparum lines adapted to periodic HS (3D7-A-HS) and their non-selected controls maintained in parallel (3D7-A), from two independent biological replicates.  Parasites were tightly sinchronized to a 5 h age window, and samples collected from each culture at different hours post-invasion (hpi): 8 hpi, 16 hpi, 24 hpi, 32 hpi and 40 hpi. Reference pool samples were collected from 3D7-A cultures at several stages, covering the full asexual blood cycle. Total RNA was harvested using the Trizol method. A comparative genomic hybridization was performed using gDNA from each parasite population. A total number of 24 individual microarrays was used.

first: Bozdech

last: Zybnek

first: Cortés

last: Alfred

first: Rovira-Graells

last: Núria


title: Effect of ZIC3/TEAD2/TEAD4 on Reprogramming of Human Urine Cells

status: Public on May 15 2021

city: 广州

first: yu

last: liu

address: :广州市黄埔区开源大道188号3栋

institute: 生物岛实验室

summary: We performed RNA-seq and ATAC-seq on UCs from healthy humans and human embryonic stem cell line H1. By analyzing the transcriptome expression profile and chromatin accessibility bettween them, we find new transcription factors that can be used for reprogramming to study the mechanism of reprogramming.

overall_design:
RNA-Seq analysis was performed on different groups of cells on the last day of reprogramming (D16) to try to find the specific role of TEAD2\TEAD4.
The cell lines reprogrammed with tead2, tead4 and ZIC3 renamed as UiPSC-TEAD2, UiPSC-TEAD4 and UiPSC-ZIC3. Then we performed RNA-seq sequencing of UiPSC-TEAD2, UiPSC-TEAD4 and UiPSC-ZIC3, UiPSC, H1 and UC of different generations. UiPSC-TEAD2, UiPSC-TEAD4 and UiPSC-ZIC3 were found to have very similar expression profiles to UiPSC, and they are all similar to H1, but are quite different from UC. This study shows that Tead2/Tead4/Zic3 can promote UCs reprogramming.

first: Ping

last: Huang

first: Yu

last: Liu


title: RNA-Seq of Prunus persica to preventive treatment with PpPep1 and PpPep2 endogenous peptides

city: Girona

first: Maria

middle: Pla

last: de Solà-Morales

state: Catalonia

address: Campus Montilivi (EPS-1)

department: Institute for Agricultural and Food Technology

institute: Universitat de Girona

summary: We charactarize the transcriptomic response of Prunus persica to preventive treatment with PpPep1 and PpPep2 endogenous peptides. The most effective dose of each peptide was applied to leaves and we sequenced their transcriptomes after 1, 24 and 48 h using untreated plants as control. mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq2000. Differential expression analysis was performed with  R package DESeq2 version 1.20.0, genes were considered significant with FDR<0.01 and log2FC>1 or log2FC<-1. We identified a total of 2,076 genes exhibiting differential expression upon PpPep1 application and 1,985 for PpPep2, accounting for 8% of the P. persica genes, 6% in response to both peptides. The similarity of PpPep responses was higher shortly after treatment (1 h), with some asynchrony at later stages and some variation in the specific regulated genes, always within the same functional categories. qRT–PCR validation with 19 genes was performed using SYBR Green assays (R 0.92).

overall_design: mRNA profiles of  P. persica pretreated with PpPep1 or PpPep2 after 1, 24 and 48 h, untreated plants as control.

last: Pla

first: Anna

last: Nadal

first: Kristina

last: Gruden

first: Laura

last: Foix

last: Esteve-Codina

first: Maja

last: Zagorščak

first: Živa

last: Ramšak


title: Chromosomal Mcm2-7 distribution and the genome replication program in species from yeast to humans

status: Public on May 18 2021

city: Seattle

first: Eric

middle: Jan

last: Foss

state: WA

address: 1100 Fairview Ave N

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary: The spatio-temporal program of genome replication across eukaryotes is thought to be driven both by the uneven loading of pre-replication complexes (pre-RCs) across the genome at the onset of S-phase, and by differences in the timing of activation of these complexes during S-phase. To determine the degree to which distribution of pre-RC loading alone could account for chromosomal replication patterns, we mapped the binding sites of the Mcm2-7 helicase complex (MCM) in budding yeast, fission yeast, mouse and humans. We observed identical individual MCM double-hexamer (DH) footprints across the species, but notable differences in their distribution. Nonetheless, most fluctuations in replication timing in all four organisms could be accounted for by differences in chromosomal MCM distribution. We conclude that, although certain genomic regions, most notably the inactive X-chromosome, are subject to post-licensing regulation, most differences in replication timing along the chromosome reflect uneven chromosomal distribution of stochastically firing pre-replication complexes.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Homo sapiens
Mus musculus x Mus spretus

overall_design:
MCM helicase genes are tagged with micrococcal nuclease (MNase), arrested in G1, MNase is activated with calcium, DNA is subjected to high throughput sequencing (all 4 organisms); sonicated DNA is isolated from flow-sorted cells from S phase and G1 and subjected to high throughput sequencing (mouse only).
We used the MCM2-Mnase fusion proteins to identify the sites of binding of the MCM replicative helicase in budding yeast, fission, mouse and humans.

first: Smitha

last: Sripathy

first: Tonibelle

last: Gatbonton-Schwager

first: Hyunchang

last: Kwak

first: Adam

middle: H

last: Thiesen

first: Uyen

last: Lao

first: Antonio

last: Bedalov


title: Effect of early-life plane of nutrition on the transcriptional profile  of visceral adipose tissue in heifer calves

status: Public on May 12 2021

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

institute: Teagasc Grange

summary: The aim of this study was to examine changes in the transcriptional profile of visceral adipose tissue in heifer calves offered varying planes of nutrition during the early life period. From approximately 3 weeks of age (19 ± 5 days of age) Angus X Holstein-Friesian heifer calves  were offered either a high (HP, n=15) or moderate (MP, n=15) plane of nutrition to achieve  target growth rates of 1.2 kg/d and 0.5 kg/d, respectively. After 18 weeks of differential feeding all calves were euthanized and visceral adipose tissue samples harvested from each calf. RNA was extracted and subsequently subjected to RNAseq analysis. A total of 1052 genes were identified as significantly differentially expressed between calves on the High plane of nutrition and those on the Moderate plane of nutrition. Biological pathway analysis revealed an enrichement from these genes for processes and pathways including Sirtuin signalling, oxidative phosphorylation and adipogenesis.

overall_design: In total 30 visceral adipose RNA samples were analysed in total. 15 samples were derived from calves fed the High plane of nutrition (HP, n=15) and 15 samples were derived from the claves fed the Moderate plane of nutrition (MP, n=15). Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates during the calf phase. During the subsequent post-weaning phase this group were then offered concentrates ad libitum and hay to appetite. During the calf phase, the Moderate plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 1 kg of concentrates, subsequently receiving 1kg of concentrates and hay to appetite during the post-weaning phase. The calf phase lasted for 8 weeks and was followed by the post-weaning phase which lasted for 11 weeks. All samples were collected at the same time-point (21 weeks of age) all differentially expressed genes reported were up- or down-regulated in HP calves compared to MP calves.

first: Alan

middle: K

last: Kelly

first: David

last: Kenny


title: Deficiency of intellectual disability-related gene Brpf1 attenuated hippocampal excitatory neurotransmission and impaired learning and memory behavior

city: Shanghai

first: Weiwei

last: Xian

address: Dongan Road 131

institute: Fudan University

summary: We hypothesized that mouse Brpf1 plays critical roles in the morphology and function of hippocampal neurons, and its deficiency leads to learning and memory deficits. To test this, we performed immunofluorescence, whole-cell patch clamp, mRNA-Seq on shBrpf1 infected primary cultured hippocampal neurons to study the effect of Brpf1 knockdown on neuronal morphology, electrophysiological characteristics and gene regulation. In addition, we performed stereotactic injection into adult mouse hippocampus to knockdown Brpf1 in vivo and examined the learning and memory ability by Morris Water Maze. We found that mild knockdown of Brpf1 reduced mEPSC frequency of cultured hippocampal neurons, before any significant changes of dendritic morphology showed. We also found that hippocampal knockdown of Brpf1 reduced the learning and memory ability of mice to some extent. Finally, mRNA-Seq analyses showed that genes related to learning, memory, movement and synaptic transmission (such as C1ql1, Gpr17, Htr1d, Glra1, Cxcl10, Grin2a) were dysregulated upon Brpf1 knockdown. Our results showed that Brpf1 mild knockdown attenuated hippocampal excitatory neurotransmission and reduced learning and memory ability, which helps explain the symptoms of patients with BRPF1 mutations.

overall_design: investigate the role of Brpf1 in the development and function of primary cultured hippocampal neurons and hippocampal CA1

first: Jingli

last: Cao

first: Guomin

last: Zhou

first: Linya

last: You


title: Haploinsufficiency of ribosomal genes limits the viability of monosomic human cells by activation of the p53 pathway

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Chromosome loss that results in monosomy has detrimental consequences for human cells, but the underlying molecular mechanisms remain enigmatic. Using p53 deficient monosomic cell lines, we found that chromosome loss impairs proliferation and genomic stability. Transcriptome and proteome analysis revealed a partial compensation of the gene dosage changes that mitigates the effects of chromosome loss. Monosomy triggers global gene expression changes that differ from the effects of trisomy. Strikingly, ribosome biogenesis and translation were commonly downregulated in monosomic cells. Polysome profiling and translation analysis suggest that the defects arise due to haploinsufficiency of ribosomal genes. The ensuing ribosome biogenesis stress triggers the p53 pathway and G1 arrest when TP53 is reintroduced into monosomic cells. Accordingly, impaired ribosome biogenesis and p53 inactivation are associated with monosomy in cancer. Our first systematic study of monosomy in human cells demonstrates that haploinsufficiency of ribosomal genes presents a dominant negative phenotype of monosomy.

overall_design: Transcriptome of human monosomic cell lines

first: Zuzana

last: Storchova

first: Narendra

last: Kumar Chunduri

first: Paul

last: Menges


title: Development and genetics of red coloration in the zebrafish relative Danio albolineatus

city: Charlottesville

first: Delai

last: Huang

state: VA

address: University of Virginia

institute: UVA

summary: Animal pigment patterns play important roles in behavior and, in many species, red coloration serves as an honest signal of individual quality in mate choice. Among Danio fishes, some species develop erythrophores, pigment cells that contain red ketocarotenoids, whereas other species, like zebrafish (D. rerio) only have yellow xanthophores. Here, we use pearl danio (D. albolineatus) to assess the developmental origin of erythrophores and their mechanisms of differentiation. We show that erythrophores in the fin of D. albolineatus share a common progenitor with xanthophores and maintain plasticity in cell fate even after differentiation. We further identify the predominant ketocarotenoids that confer red coloration to erythrophores and use reverse genetics to pinpoint genes required for the differentiation and maintenance of these cells. Our analyses are a first step towards defining the mechanisms underlying the development of erythrophore-mediated red coloration in Danio and reveal striking parallels with the mechanism of red coloration in birds.

overall_design: Identification of differentially expressed genes between proximal erythrophore and distal xanthophore regions

first: Victor

last: Lewis

last: Parichy

first: Andrew

last: Aman

first: Lauren

last: Saunders


title: Transcriptomic analysis of heat shock resistance in Plasmodium falciparum

first: Elisabet

last: Tinto-Font

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

overall_design: Refer to individual Series


title: YBX1 mediates translation of oncogenic transcripts to control cell competition in AML [ChIP-seq]

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

summary: ChIP-seq for the cold shock protein YBX1 in MOLM13 cells.

overall_design: ChIP-seq for YBX1 was performed in MOLM13 cells under steady-state conditions.

first: Charles

last: Hatton


title: The CSF1R-Microglia Axis Has Protective Host-Specific Roles During Neurotropic Picornavirus Infection

status: Public on May 10 2021

city: Salt Lake City

first: Ana Beatriz

last: DePaula-Silva

state: UT

address: 15N Medical Drive East room 2800

department: Pathology

institute: University of Utah

summary:
Goal: Determine the role of microglia in the antiviral response during neurotropic picornavirus infection of C57BL/6J and SJL/J mice and whether absence of microglia would affect CD4 and CD8 T cell functions.
Methods: Brains from C57BL/6J and SJL/J mice treated with PLX5622 (to deplete microlgia) or control diet were harvested at 6 days post TMEV-infection.  CD4+ T cells and CD8+ T cells were obtained using Easy Sep Mouse CD4+ T cell isolation Kit and  Easy Sep Mouse CD8+ T cell isolation Kit (Stemcell). RNA was obtained using RNeasy (QIAGEN) and Illumina TruSeq stranded RNA Kit with Ribo-Zero Gold was then utilized to prepare cDNA library for RNA-seq.
Results: Our results demonstrate strain-specific effects of the CSF1R-microglia axis in the context of neurotropic viral infection as well as inherent differences in microglial antigen presentation and subsequent T cell crosstalk that contribute to susceptibility to neurotropic picornavirus infection.

overall_design: RNA was isolated from CD4 and CD8 T cells obtained from the brains of C57BL/6J (n=20) and SJL/J (n=20) treated with PLX5622 (n=10/mouse strain) or control diet (n=10/mouse strain), at 6 days post TMEV-infection of the CNS.

first: John-Michael

last: Sanchez

first: Ana

middle: B

first: Daniel

last: Doty

first: Tyler

last: Hanak

first: Amanda

last: Truong

first: Jane

middle: E

last: Libbey

first: Robert

last: Fujinami


title: Characterization of the SARS-CoV-2 Host Response in Primary Human Airway Epithelial Cells from Aged Individuals

status: Public on May 29 2021

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

summary: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19), a global pandemic characterized by respiratory illness and an exaggerated immune response. Age (>60 years) is a significant risk factor for developing severe COVID-19. However, the underlying mechanisms of how aging impacts SARS-CoV-2 infection and the host response are largely unknown. Therefore, we performed an in vitro study to characterize the host response to SARS-CoV-2 infection using primary human bronchial epithelial cells from donors >67 years of age differentiated on air-liquid interface culture. We demonstrate that SARS-CoV-2 infection leads to early induction of a proinflammatory response and a delayed interferon response. In addition, we observe changes in genes and pathways associated with cell death and senescence throughout infection. In summary, our study provides important insights into the temporal kinetics of the airway epithelial innate immune response to SARS-CoV-2 in older individuals.

overall_design: mRNA profiling of primary human bronchial epithelial cells (HBECs) from normal, nonsmoker, aged individuals (>67 years old) either uninfected or infected with SARS-CoV-2 as a function of time post-infection (24, 48, 72 and 96 hr)

first: Matthew

middle: S

last: Walters


title: The effect of STAG2 loss in Ewing sarcoma

status: Public on May 14 2021

city: New York

first: Caleb

last: Lareau

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: SMC1a HiChIP was performed for the Ewing sarcoma cell line A673 under two conditions: 1) cells treated with non-targeting CRISPR Cas9 guides or 2) STAG2-targeting CRISPR Cas9 guides. Cells treated for gene editing were clonally selected and confirmed to either express STAG2 (control condition) or have loss of STAG2 expression (STAG2 loss condition). For the control condition, we used the cell clones A673.sgNT-1c4 and the STAG2 knockout clone A673.sgSTAG2-1c6. HiChIP was performed for each clone in duplicate.

overall_design: A 2x2 comparison of differential looping for SMC1 HiChIP in A673 cells +/- STAG2, mutated with Cas9

first: Brian

last: Crompton


title: Methyltransferase-directed orthogonal tagging and sequencing of miRNAs and bacterial small RNAs in probiotic Lactobacillus casei

city: Vilnius

first: Kotryna

last: Kvederaviciute

address: Sauletekio av. 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

sample_organism:
Lacticaseibacillus casei
synthetic construct


title: Gene expression profiles in human duodenal organoid-derived monolayer

city: Suita

first: Tomoki

last: Yamashita

state: Osaka

address: 1-6 Yamadaoka

department: Graduate School of Pharmaceutical Sciences

institute: Osaka University

summary: The human small intestine is the key organ for absorption, metabolism, and excretion of orally administered drugs. To preclinically predict these reactions in drug discovery research, a cell model that can precisely recapitulate the in vivo human intestinal monolayer is desired. Here, we developed a monolayer platform using human biopsy-derived duodenal organoids for application to pharmacokinetic studies. The human duodenal organoid-derived monolayer was prepared by a simple method in 3–8 days. It consisted of polarized absorptive cells and had a barrier function. It showed much higher cytochrome P450 (CYP) 3A4 and carboxylesterase (CES) 2 activities than Caco-2 cells. It also showed efflux activity of P-glycoprotein (P-gp) and inducibility of CYP3A4. Finally, its gene expression profile was closer to the adult human duodenum, compared to the profile of Caco-2 cells. Based on these findings, this monolayer assay system using biopsy-derived human intestinal organoids is likely to be widely adopted.

overall_design: Human adult duodenal biopsies, human duodenal organoids, human duodenal organoid-derived monolayer, and Caco-2 cells were subjected to DNA microarray analysis. Human adult duodenal biopsies were pooled from 5-donor samples (excluding the material used to make the organoids). Human duodenal organoids, the human duodenal organoid-derived monolayer, and Caco-2 cells were pooled from triplicate samples of one independent experiments.

first: Tatsuya

last: Inui

first: Jumpei

last: Yokota

first: Kentaro

last: Kawakami

first: Gaku

last: Morinaga

first: Masahito

last: Takatani

first: Daisuke

last: Hirayama

first: Ryuga

last: Nomoto

first: Kohei

last: Ito

first: Yunhai

last: Cui

first: Stephanie

last: Ruez

first: Kazuo

last: Harada

first: Wataru

last: Kishimoto

first: Hiroshi

last: Nakase

first: Hiroyuki

last: Mizuguchi


title: Aging affects gene expression in CD8 T-cells from mice with or without MC38 tumors

first: Kenji

last: Chamoto

institute: Graduate School of Medicine, Kyoto University

summary: We provide differentially gene expression between young and aged CD8 T-cells from WT or PD-1-/- mice with or without MC38 tumors.

overall_design: CD8 T-cells were isolated from young or aged C57BL/6 mice with either WT or PD-1-/- genotype by CD8a micro beads.  Tumore bearing mice were sacrificed 9 days after MC38 cell inoculation.

first: Yuka

last: Nakajima

first: Tasuku

last: Honjo


title: The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans

city: Riverside

first: Weifeng

last: Gu

address: 900 University Ave

department: Molecular, Cell and Systems Biology

institute: University of California at Riverside

summary: Eukaryotic cells regulate 5’ triphosphorylated (ppp) RNAs to promote cellular functions and to prevent recognition by viral RNA sensors.  For example, the triphosphatase domain of RNA capping enzymes removes the γ phosphate of ppp-RNAs in RNA capping reactions. Members of a related RNA polyphosphotase family including human PIR1 remove both the β and γ phosphates from ppp-RNAs. Here we demonstrate that C. elegans PIR-1, previously identified as a Dicer-interacting protein, dephosphorylates single and double-stranded ppp-RNAs, and is required for the maturation of 26G-RNAs, which regulate thousands of genes during spermatogenesis and embryogenesis. We find that 26G-RNAs are generated in a unique semi-phasing manner in which primary 26G-RNAs are required for generating secondary 26G-RNAs and PIR-1 is required for removing a diphosphate group from each triphosphorylated precursor, which only generates one 26G-RNA. Our findings also implicate PIR-1 in regulating ppp-RNAs in Dicer-independent pathways, supporting PIR-1 as a master phosphatase regulating ppp-RNAs.

overall_design: This study examines how PIR-1, a novel RNA polyphosphatase, regulates small RNA biogenesis in C. elegans. We generated pir-1 mutants and compared the small RNA profiles between the mutants and the WT control using high-throughput sequencing followed by bioinformatics. We also utilized biochemistry to characterize the in vitro activity of PIR-1 in C. elegans.

first: Daniel

last: Chaves

first: Hui

last: Dai

first: Lichao

last: Li

first: James

middle: J

last: Moresco

first: Myung

last: Oh

first: Darryl

last: Conte Jr

first: John

last: Yates III

first: Craig

last: Mello


title: Transcriptome alterations of an in vitro-selected, moderately-resistant, two-row malting barley in response to 3ADON, 15ADON and NIV chemotypes of Fusarium graminearium

status: Public on May 08 2021

city: Brandon

middle: Raymond

last: Tucker

state: MB

address: 2701 Grand Valley Rd.

country: Canada

institute: Agriculture and Agri-Food Canada

summary: Fusarium head blight caused by Fusarium graminearum is a devastating disease of malting barley. Mycotoxins associated with contaminated grain can be transferred from malt to beer and pose a health risk to consumers. In western Canada, F. graminearum has undergone an adaptive shift from 15ADON constituency to dominance by virulent 3ADON-producers, likewise NIV-producers have established in regions of southern United States. Lack of adapted resistance sources with adequate malting quality has promoted the use of alternative breeding methodologies such as in vitro selection. We studied the low-deoxynivalenol characteristic of in vitro selected, two-row malting barley variety ‘Norman’ by RNAseq in contrast to its parental line ‘CDC Kendall’, when infected by 15ADON-, 3ADON- and NIV-producing isolates of F. graminearum. The current study documents higher mycotoxin accumulation by 3ADON isolates, thereby representing increased threat to barley production. At 72-96 hours post infection, significant alterations in transcription patterns were observed in both varieties with pronounced upregulation of the phenylpropanoid pathway and detoxification gene categories (UGT, GST, CyP450 and ABC) particularly in 3ADON treatment. Defense response was multi-tiered, where differential expression in ‘Norman’ associated with antimicrobial peptides (thionin 2.1, defensing, non-specific lipid-transfer protein) and stress-related proteins such as late embryogenesis abundant proteins, heat-shock, desiccation-related and a peroxidase (HvPrx5). Several gene targets identified in ‘Norman’ would be useful in application of breeding varieties with reduced deoxynivalenol content.

overall_design: Adult plants of Norman and CDC Kendall were sprayed with macroconidia (5 x 10^4 spores ml-1) of  Fusarium graminearum (3ADON, 15ADON and NIV chemotypes + mock control). Seed tissue samples were collected at the time-points 72 h and 96h post-inoculation for Norman and CDC Kendall from all Fusarium treated and control plants. Total RNA was prepared and used for the RNA-seq analysis. Three independent biological replicates were sampled.

first: William

middle: G

last: Legge

first: Sujit

last: Maiti

first: Colin

middle: W

last: Hiebert

first: Senay

last: Simek

first: Zehn

last: Yao

first: Wayne

last: Xu

first: Ana

last: Badea

first: W

last: Fernando


title: P. falciparum heat shock response in a PfAP2-HS-defective population compared to its wild type control.

city: Barcelona

first: Elisabet

last: Tinto-Font

institute: ISGlobal

summary: Periodic fever is the most characteristic clinical feature of human malaria. However, how parasites survive malarial febrile episodes, which often involve temperatures of >40ºC, is not known. Plasmodium falciparum cultures adapted to periodic heat shock were used to identify PfAP2-HS as a transcription factor that is essential for survival at febrile temperatures. Transcriptomic analysis was performed to compare the effect of heat shock in parasites presenting the wild type form of PfAP2-HS (10E) and parasites that have defects in this protein, either a premature stop codon mutation (10G) or the deletion of the entire pfap2-hs gene (10E_pfap2-hs). A timecourse analysis including samples taken before, during and after heat shock revealed that the initial phase of the PfAP2-HS-dependent response is largely restricted to hsp70-1 and hsp90.

overall_design: Time-course transcriptomic analysis of 10E, 10G and 10E_pfap2-hs cultures under control (35C) and heat shock conditions (HS, 41.5C for 3 h). Parasites were tightly sinchronized to a 5 h age window and HS was started at 30-35 hpi (33-38 hpi for the 10E_pfap2-hs line that develops more slowly). Samples for transcriptomic analysis were collected before (0 h), during (1.5 h and 3 h) and after HS (2 h post). The reference pool consisted of RNA from 3D7-A cultures, maintained under control conditions, throughout the asexual blood cycle. Total RNA was harvested using the Trizol method. A total number of 21 individual samples were analysed using the microarray design AMADID-084561 (GEO ID: GPL26985).

last: Tintó-Font

first: Lucas

last: Michel-Todó

first: Alfred

last: Cortés


title: Cortical Overgrowth in a Preclinical Forebrain Organoid Model of CNTNAP2-Associated Autism Spectrum Disorder

first: Job

last: de Jong

address: 1051 Riverside Drive

department: Psychiatry

institute: Columbia University

summary: We performed bulk-RNAseq on 8-week-old forebrain organoids grown from 3 patient derived cell lines and 3 control derived cell lines and subsequently of 3 technical replicates of one patient derived line and 3 technical replicates of the CRISPR rescue of this patient derived line

overall_design: Bulk-RNA sequencing experiment

first: J

first: B

first: S

last: Markx


title: Pro-inflammatory Beta Cell Small Extracellular Vesicles Induce Beta Cell Failure Through Activation of the CXCL10/CXCR3 Axis in Diabetes

city: Rochester

first: Naureen

last: Javeed

state: MN

address: 200 First St SW

institute: Mayo Clinic

summary: Coordinated communication among pancreatic islet cells is necessary for the maintenance of glucose homeostasis. In diabetes, chronic exposure to pro-inflammatory cytokines has been shown to perturb β-cell communication and function. Compelling evidence has implicated extracellular vesicles (EVs) in modulating physiological and pathological responses to β-cell stress. We report that pro-inflammatory β-cell small EVs (cytoEV) induce β-cell dysfunction, promote a pro-inflammatory islet transcriptome, and enhance recruitment of CD8+ T-cells and macrophages. Proteomic analysis of cytoEV revealed an enrichment of the chemokine, CXCL10, with surface topological analysis depicting CXCL10 as membrane-bound on cytoEV to facilitate direct binding to CXCR3 receptors on the surface of β-cells. CXCR3 receptor inhibition reduced CXCL10-cytoEV binding and attenuated β-cell dysfunction, inflammatory gene expression, and leukocyte recruitment to islets. Collectively, this work implicates the significant role of pro-inflammatory β-cell derived small EVs in modulating β-cell function, global gene expression, and antigen presentation through activation of the CXCL10/CXCR3 axis.

overall_design: 4 samples total were analyzed. 2 replicates for control (UT) islets vs. 2 replicates for cytoEV treated islets

first: Tracy

last: Her

first: Matthew

middle: R

last: Brown

first: Patrick

last: Vanderboom

first: Kuntol

last: Rakshit

first: Aoife

last: Egan

first: Adrian

last: Vella

first: Ian

last: Lanza

first: Aleksey

middle: V

last: Matveyenko


title: SLFN2 protection of tRNAs from stress-induced cleavage is essential for T cell-mediated immunity

city: Dallas

first: Sara

last: Hildebrand

state: TX

address: 5323 Harry Hines blvd

department: Center for the Genetics of Host Defense

institute: UT Southwestern Medical Center

summary: During T cell mediated immune response, metabolic reprograming is required for energy production to support the following clonal expansion, and leading to increased levels of reactive oxygen species. Proper responses to such oxidative stress in activated T cells have been shown to be extremely important in mediating T cell proliferation. Here we report Schlafen (SLFN) 2, upregulated upon the stimulation of T cell antigen receptor (TCR), directly binds to tRNAs and maintains their integrity against stress-activated cleavage. T-cell specific inactivation of Slfn2 in mice leads to compromised humoral and cellular immune responses in mice. Mechanistically, loss of Slfn2 in activated T cells causes significantly enhanced tRNA fragmentation, stress granule assembly and protein synthesis inhibition, which impairs activation-induced T cell proliferation by failing to upregulate protein synthesis and conferring IL-2 insensitivity. Thus, SLFN2 is a novel trans-acting factor for tRNA integrity and crucial to T cell-mediated immunity.

overall_design: RNAs isolated from each of indicated groups by using miRNA Isolation Kit, were demethylated for subsequent cDNA library preparation using TruSeq Small RNA Library Prep kit. Each cDNA library containing tRNA-derived fragments with index was size-selected on 8% TBE-PAGE gel to isolate cDNAs. Individual purified tRNA-derived framgent libraries were pooled and sequenced by using the NSQ 500/550.

first: Tao

last: Yue


title: A CTP-dependent gating mechanism enables ParB spreading on DNA

status: Public on May 01 2021

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

institute: John Innes Centre

summary: Proper chromosome segregation is essential in all living organisms. The ParA-ParB-parS system is widely employed for chromosome segregation in bacteria. Previously, we showed that Caulobacter crescentus ParB requires cytidine triphosphate to escape the nucleation site parS to spread by sliding to the neighboring DNA. Here, we provide the structural basis for this transition from nucleation to spreading by solving co-crystal structures of a C-terminal domain truncated C. crescentus ParB with parS and with a CTP analog. Nucleating ParB is an open clamp, in which parS is captured at the DNA-binding domain (the DNA-gate). Upon binding CTP, the N-terminal domain (NTD) self-dimerizes to close the NTD-gate of the clamp. The DNA-gate also closes, thus driving parS into a compartment between the DNA-gate and the C-terminal domain. CTP hydrolysis and/or the release of hydrolytic products may re-open the gates. Overall, we suggest a CTP-operated gating mechanism that regulates ParB nucleation and spreading.

sample_organism:
Escherichia coli
Caulobacter vibrioides

platform_organism:
Escherichia coli
Caulobacter vibrioides

overall_design: Chromatin-immunoprecipitation with deep sequencing experiments (ChIP-seq) were performed on exponential-growing Caulobacter crescentus (see the supplementary Materials and Methods for the exact treatment that were applied to each strain).

first: Adam

last: Jalal

first: Ngat

middle: T

last: Tran

first: Clare

last: Stevenson

first: David

middle: M

last: Lawson


title: BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome.

status: Public on May 03 2021

city: Oxford

first: Nadezda

middle: A

last: Fursova

address: South Parks Rd

department: Department of Biochemistry

institute: University of Oxford

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus


title: A photosynthesis operon in the chloroplast genome drives speciation in evening primroses

status: Public on May 11 2021

city: Potsdam

first: Stephan

last: Greiner

state: Branbenburg

address: Max-Planck-Institute of Molecular Plant Physiology

department: Organelle Biology, Biotechnology and Molecular Ecophysiology

institute: MPI for Molecular Plant Physiology

summary: Genetic incompatibility between the cytoplasm and the nucleus is thought to be a major factor in species formation, but mechanistic understanding of this process is poor. In evening primroses (Oenothera spp.), a model plant for organelle genetics and population biology, hybrid offspring regularly display chloroplast-nuclear incompatibility. This usually manifests in bleached plants, more rarely in hybrid sterility. Hence, most of these incompatibilities affect photosynthetic capability, a trait that is under selection in changing environments. Here we show that light-dependent misregulation of the plastid psbB operon, which encodes core subunits of photosystem II and the cytochrome b6f complex, can lead to hybrid incompatibility, and this ultimately drives speciation. This misregulation causes an impaired light acclimation response in incompatible plants. Moreover, as a result of their different chloroplast genotypes, the parental lines differ in photosynthesis performance upon exposure to different light conditions. Significantly, the incompatible chloroplast genome is naturally found in xeric habitats with high light intensities, whereas the compatible one is limited to mesic habitats. Consequently, our data raise the possibility that the hybridization barrier evolved as a result of adaptation to specific climatic conditions.

sample_organism: Oenothera elata subsp. hookeri x Oenothera grandiflora

overall_design: Photosynthesis genes encoded on the chloroplast genome can establish hybridization barriers.

first: Arkadiusz

last: Zupok

first: Danijela

last: Kozula

first: Mark

last: Schöttler

first: Julia

last: Niehörster

first: Frauke

last: Garbsch

first: Karsten

last: Liere

first: Axel

last: Fischer

first: Reimo

last: Zoschke

first: Irina

last: Malinova

first: Ralph

last: Bock


title: Chitinase-3-like-1 Protein Complexes Modulate Macrophage-Mediated Immune Suppression in Glioblastoma

city: Pittsburgh

first: Baoli

last: Hu

state: PA

address: 4401 Penn Ave

department: Neurological Surgery

institute: University of Pittsburgh School of Medicine

summary: Glioblastoma is a highly malignant and incurable brain tumor characterized by intrinsic and adaptive resistance to immunotherapies. However, how glioma cells induce tumor immunosuppression and escape immunosurveillance remains poorly understood. Here, we find upregulation of cancer-intrinsic Chitinase-3-like-1 (CHI3L1) signaling modulating an immunosuppressive microenvironment by reprogramming tumor-associated macrophages (TAMs). Mechanistically, CHI3L1 binding with Galectin-3 (Gal3) selectively promotes TAM migration and infiltration with a protumor M2-like but not an antitumor M1-like phenotype in vitro and in vivo, governed by a transcriptional program of NFκB/CEBPβ in the CHI3L1/Gal3-PI3K/AKT/mTOR axis. Conversely, Galectin-3-binding protein (Gal3BP) negatively regulates this process by competing with Gal3 to bind CHI3L1. Administration of a Gal3BP mimetic peptide in a syngeneic glioblastoma mouse model reverses immune suppression and attenuates tumor progression. These results shed light on the role of CHI3L1 protein complexes in immune evasion by glioblastoma and as a potential immunotherapeutic target for this devastating disease.

overall_design: TAMs mRNA profiles from orthotopic xenograft glioma models in C57BL/6 mice bearing the isogenic line QPP7 with shChi3l1 (Chi3l1 knockdown) and shSC (Control Vector)

first: Apeng

last: Chen

first: Songjian

last: Lu

first: Han

last: Zou


title: Rate of recipient-derived alveolar macrophages development and major histocompatibility complex cross-dressing after lung transplantation in humans

last: Snyder

address: 200 Lothrop Street, BST12

department: Medicine

institute: University of Pittsburgh

summary: Analyzing the kenetics of alveolar macrophage turnover after human lung transplantation and identifying protein and transcriptional differences between donor and recipient-derived alveolar macrophages

overall_design: Bulk RNA sequencing performed from FACS sorted donor and recipient-derived alveolar macrophages derived from the bronchoalveolar lavage of lung transplant recipients, defined as CD45+, Live, lineage negative, CD64+CD206+ cells.


title: Genome-wide ChIP-Seq maps of EZH2 distribution between Wild Type (WT), Actb+/- (HET), and Actb-/- (KO) Mouse Embryonic Fibroblast

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: β-actin is a crucial component of several chromatin remodeling complexes which control chromatin structure and accessibility. The mammalian Brahma-associated factor (BAF) is one such complex that plays essential roles in development and differentiation by regulating the chromatin state of critical genes and opposing the repressive activity of polycomb repressive complexes. While previous work has shown that β-actin loss can lead to extensive changes in gene expression and heterochromatin organization, it is not known if changes in β-actin levels can directly influence chromatin remodeling activities of BAF and polycomb proteins. Here we conduct a comprehensive genomic analysis of β-actin knockout mouse embryonic fibroblasts (MEFs) using ATAC-Seq, HiC-seq, RNA-Seq and ChIP-Seq of various epigenetic marks. We demonstrate that β-actin levels can affect the complex interplay between chromatin remodelers such as BAF/BRG1 and EZH2 in a dosage-dependent manner. Our results show that changes in β-actin levels and associated chromatin remodeling activities can not only impact local chromatin accessibility but also induce reversable changes in 3D genome architecture. Our findings support a novel role for β-actin levels in shaping the chromatin landscape during development and differentiation.

overall_design: ChIP-Seq was performed for 6 samples (3 different genotypes with two biological replicates each)

first: Syed

last: Mahmood

first: Xin

last: Xie

first: Nadine

last: ElSaid

first: Kristin

middle: C

last: Gunsalus


title: Modeling chemotherapy induced neurotoxicity with human induced pluripotent stem cell (iPSC) -derived sensory neurons - RNA-Seq data on transcriptional changes induced by 1µM paclitaxel treatment for 24h

status: Public on Apr 30 2021

city: Berlin

first: Christian

last: Schinke

state: Berlin

address: Charitéplatz 1

institute: Charité Universitätsmedizin Berlin

summary: We report data on transcriptome sequencing analyses of functional iPSC-DSN (maturation >d40) treated with 1 µM paclitaxel for 24h compared to DMSO treatment. RNA-Sequencing analyses revealed 319 significantly differentially (padjusted <0.01) expressed genes out of which 227 were upregulated and 92 downregulated. 84 of the upregulated and 33 of the downregulated changed expression by at least 2 fold. Upregulated genes involve known neuronal injury markers such as the Activation Transcription Factor (ATF3), stress-inducible proteins such as Sestrin-2 (SESN2), apoptosis associated genes such as Caspase 3 (CASP3), the JUN proto-oncogene (JUN) or BCL2-interacting proteins such as BBC3 or Harakiri (HRK). Also, vasoactive substances and pain inducing neuropeptides of the calcitonine gene related peptide family such as CALCB and adrenomedullin (ADM) were found amongst the top 50 differentially regulated genes. Downregulated genes involve pathways of sterol homeostasis, glucose homeostasis and  lipogenesis, e.g., 3-Hydroxy-3-Methylglutaryl-CoA Synthase 1 (HMGCS1), Insulin Induced Gene 1 (INSIG1) or ELOVL Fatty Acid Elongase 6 (ELOVL6). Gene set enrichment analysis outlined significant deregulation of genes involved in cholesterol biosynthesis pathways, PERK regulated genes and genes involved in amino acid transport across the membrane. In summary, there is a significant overlap of the above mentioned genes and gene sets outlined by unbiased global differential transcriptome analyses with pathways known from the literature of neuropathy and neurodegeneration.

overall_design: 3 replicates of iPSC-DSN of the cell line BIHi005-A were treated with DMSO 1/6000 and 2 with with 1 µM paclitaxel.

first: Valeria

last: Fernandez Vallone

first: Andranik

last: Ivanov

first: Yangfan

last: Peng

first: Péter

last: Körtvelyessy

first: Luca

last: Nolte

first: Petra

last: Huehnchen

first: Dieter

last: Beule

first: Harald

last: Stachelscheid

first: Wolfgang

last: Boehmerle

first: Matthias

last: Endres


title: A new identified lncBCAS1-4_1 associated with Vitamin D signaling and EMT in ovarian cancer cells

city: Suzhou

first: Ping

last: Wang

state: Jiangsu

address: No.199 Ren ai Road

department: School of public health

institute: Soochow University

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

summary: Long non-coding RNAs (lncRNAs) has been identified rapidly due to the important role of lncRNAs in many biological processes and human diseases including cancer. Vitamin D compounds are supported to be applied as preventative and therapeutic anticancer agents. However, the expression profile of lncRNAs regulated by 1α,25-dihydroxyvitamin D3 [1α,25(OH)2D3] in ovarian cancer remains to be clarified. In the present study, we identified 244 differentially expression (DE) lncRNAs and 102 DE mRNAs by our microarray data. GO and KEGG pathway analysis indicated that the DE genes were mainly enriched in TGF-β, MAPK, Ras, PI3K-Akt and Hippo signaling pathways, as well as vitamin D-related pathway. We further assessed the potential lncRNAs linking vitamin D signaling with EMT, and lncBCAS1-4_1 was identified. Moreover, we found the most upregulation lncBCAS1-4_1 has 75% transcripts same to CYP24A1, metabolic enzyme of 1α,25(OH)2D3. Finally, we established lncBCAS1-4_1 gain-of-function cell models and demonstrated that knockdown of lncBCAS1-4_1 inhibited proliferation and migration of ovarian cancer cells by regulating EMT-related mRNAs. Furthermore, our results also indicated that high lncBCAS1-4_1 obviously resisted the anti-tumor effect of 1α,25(OH)2D3 by upregulating ZEB1. These data will provide new evidence that lncRNAs are served as a target for the anti-tumor of 1α,25(OH)2D3.

overall_design: Our microarray data to comprehensively explore the profile of lncRNA regulated by 1α,25(OH)2D3 in human ovarian cancer SKOV-3 cells

first: Bingyan

last: Li


title: scRNA sequencing of cells harvested from the tendon injury site after a severe burn/tenotomy injury with and without sciatic neurectomy

first: Chase

middle: Arthur

last: Pagani

state: Texas

address: 6000 Harry Hines Blvd

department: Surgery

institute: The University of Texas Southwestern

summary: scRNA sequencing was performed on cells harvested from the injury site of mice that underwent a burn/tenotomy injury with sciatic neurectomy or sham neurectomy (skin incision) to study the role of nerves in the formation of heterotopic ossification and aberrant stem cell differentiation following traumatic injury.

overall_design: C57B6 mice received pre-operative treatment with 0.06 mg/kg buprenorphine subcutaneously and were anesthetized with 2% isofluorane inhalation. A 10 mm longitudinal skin incision was made along the medial aspect of the left Achilles tendon. The Achilles tendon was separated from surrounding tissue and dissected at it’s midsection. For the sciatic neurectomy, blunt dissection was performed through the biceps femoris to expose the sciatic nerve. The sciatic nerve was transected with reflection and suturing of the proximal nerve stump to the nearby semitendinosus muscle to prevent re-innervation.  As a control, sham nerve injuries consisted of surgical exposure of the sciatic nerve without transection. Incisions were sutured closed with 5-0 Vicryl suture. Tenotomy injury site, consisting of tissue from the Achilles’ tendon insertion at the gastrocnemius to the distal tendon enthesis at the calcaneus and surrounding tissue, excluding bone and skin, was harvested 7 days after injury. Tissue samples were digested for 20 minutes in 750U/ml Type 1 Collagenase and 7U/ml Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37°C under constant agitation of 160rpm. Digestions were subsequently quenched with 2% FBS in PBS and filtered through 40μm sterile strainers. Cells were then washed in 2% FBS in PBS, counted and resuspended at a concentration of 1000-1200 cells/ul. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and only samples with >85% viability were used for scRNA sequencing. Enough reagent was taken to sequence the transcriptome of 5000 cells according to 10x guidelines. 100,000 remaining cells were used for nuclei isolation according to the 10X Nuclei Isolation for Single Cell ATAC Sequencing protocol (available on their website).

first: Simone

last: Marini

first: Amanda

last: Huber

first: Suengyong

last: Lee

first: Aaron

last: James

first: Benjamin

last: Levi


title: De novo transcriptome assembly of Stenocereus queretaroensis suspension cells and DEG nalysis

status: Public on Apr 24 2021

city: Mérida

first: Javier

last: Morales

state: Yucatán

address: Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo

department: Unidad de Bioquímica y Biología Molecular

country: Mexico

institute: Centro de Investigación Científica de Yucatán

summary: We evaluated gene expression of two growth conditions in MS culture medium  for the induction of betalains

overall_design: Two different culture media were used: Sucrose at 3 and 8%. Three replicates of each were made to prepare six libraries for the transcriptome assembly.

first: Jorge

last: Araujo

first: Lizbeth

last: Castro-Concha

first: Ángela

last: Kú

first: Alejandro

last: Pereira

first: Maria

middle: L

last: Miranda-Ham

first: Enrique

last: Castaño


title: A novel transcription factor PunR and Nac are involved in purine and purine nucleoside transporter punC regulation in E. coli

status: Public on Apr 28 2021

city: San Diego

first: Anand

last: Sastry

state: CA

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

summary: Recently, novel analytic methods have divided bacterial transcriptomes into independently modulated sets of genes (iModulons). Functionally annotated iModulons that contain y-genes lead to testable hypotheses to elucidate y-gene function. The inversely correlated expression of a putative transporter gene, ydhC, relative to purine biosynthetic genes, has led to the hypothesis that it encodes a purine-related transporter and revealed a LysR-family regulator, YdhB, with a predicted 23-bp palindromic binding motif. RNA-Seq analysis of a ydhB knockout mutant confirmed the YdhB-dependent activation of ydhC in the presence of adenosine. The deletion of either the ydhC or the ydhB gene led to a substantially decreased growth rate for E. coli in minimal medium with adenosine, inosine, or guanosine as the nitrogen source. Taken together, we provide clear evidence that YdhB activates the expression of the ydhC gene that encodes a novel purine transporter in E. coli. We propose that the genes ydhB and ydhC be re-named as punR and punC, respectively.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design:
The wild type MG1655 strain was grown as a control for the isogenic punR mutant strain.
The cells were grown in M9 glucose medium supplemented with 2.5 mM adenosine and collected at an OD600 of 0.6 and were harvested using the Qiagen RNA-protect bacterial reagent according to the manufacturer’s specifications.

first: Irina

last: Rodionova

first: Hyungyu

last: Lim

first: Bernhard

middle: O

last: Palsson