title: Expression profile comparison between paired tumor- and normal tissue-associated MSCs from lung carcinoma patients

status: Public on Mar 31 2018

city: LAUSANNE

first: Mathieu

last: Quinodoz

state: Vaud

address: Rue du Bugnon 27

department: DBC

country: Switzerland

institute: Université de Lausanne

summary:
Lung cancer is a highly malignant tumor and the majority of cancer-related deaths are due to metastasis. The tumor microenvironment (TME) plays a fundamental role in the metastatic spread of tumor cells. Among other stromal cells, mesenchymal stem cells (MSCs) are known to be present within the TME and to be involved in cancer progression. However the majority of previous studies have been performed on bone marrow-derived MSCs. To investigate the role of the TME on the pulmonary MSC phenotype, we compared the expression profile of paired MSCs isolated from lung tumor (T-) and normal adjacent tissues (N-) from lung carcinoma patients.
We used microarray data to find differentially expressed genes between N- and T-MSCs and identified several genes associated with poor prognosis that are more highly expressed in T- than in N-MSCs and potentially involved in the MSC promotion of lung cancer metastasis.

overall_design: MSCs were isolated from paired lung tumor (T-) and normal tissues (N-) from 9 patients diagnosed with lung carcinoma and characterized for surface expression markers and differentiation potential. RNA was extracted at culture passage 5 or 6 from fresh MSCs (frozen in DMSO-FBS10%) to be sure to have pure MSC cell culture representative of the pathophysiological characteristics of the primary samples. Paired N- and T-MSC expression profiles were analyzed using Affymetrix microarrays. We sought to identify differentially expressed genes between N- and T-MSCs to gain insight into the mechanisms whereby the stroma promotes lung cancer metastasis.

first: Giulia

last: Fregni

first: Emely

last: Möller


title: Regional preferences of DNA methylation changes in response to X-ray-irradiation

city: Munich

first: Benjamin

last: Becker

address: Neuherbergstr. 11

department: Genomics II

country: Germany

institute: Bundeswehr Institute for Radiobiology

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Exploring the link between ER stress and autophagy in Arabidopsis

city: Ames

first: Stephen

last: Howell

state: Iowa

address: 1035A Roy J. Carver Co-Laboratory 1111 WOI Road

department: Department of Genetics, Development and Cell Biology

country: USA

institute: Plant Sciences Institute

type: Expression profiling by high throughput sequencing

summary: Autophagy is a conserved process in eukaryotes that contributes to cell survival in response to stress. Previously, we found that ER stress induces autophagy in a manner dependent upon IRE1b, an ER membrane-associated factor involved in the splicing of bZIP60 mRNA. IRE1 is a dual protein kinase and ribonuclease, and here we studied the involvement of the protein kinase catalytic domain, nucleotide binding and RNase domains of IRE1b in activating autophagy.  Autophagy was assessed by quantifying the numbers of autophagosomes in transgenic Arabidopsis seedlings bearing mutations in the various IRE1b domains. The results showed that nucleotide binding and RNase activity of IRE1b are required for ER stress-mediated autophagy.  The RNase activity is involved in IRE1b’s mRNA splicing function, but its principal splicing target, bZIP60, is not involved in IRE1b’s activation of autophagy. We therefore considered other roles for IRE1b in the activation of autophagy.  Clustering of ER localized IRE1b-YFP was observed when seedlings were subjected to ER stress, and so we investigated whether IRE1b clustering induced autophagy. However, the RNase knockout mutation in IRE1b still undergoes clustering, suggesting that IRE1b clustering does not induce autophagy. In response to ER stress, the RNase of IRE1 has been found to engage in another activity called Regulated Ire1-Dependent Decay of Messenger RNA (RIDD), which is the promiscuous degradation of other mRNA in response to ER stress.  By analyzing the RNA-seq data, 12 RIDD target genes were picked up for testing their role in inhibiting autophagy, and glucosidase 21 and peroxidase 14 are proved to be degraded to support the induction of autophagy by ER stress.

overall_design: We examined gene expression by RNA-seq in Arabidopsis wide-type and mutant ire1b and double mutant ire1a/ire1b treated with DMSO (as the control) or with 5μg/mL TM

first: Yan

last: Bao

first: Xiang

last: Yu

first: Brian

last: Gregory

first: Diane

last: Bassham


title: Gene expression altered by csi-miR156a overexpression in citrus callus

city: Wuhan

first: Jianmei

last: Long

state: Hubei

address: shizishan street NO.1

country: China

institute: Huazhong Agricultural University

summary: To investigate the global gene expression change caused by csi-miR156a overexpression which enhanced soamtic embryogenesis in citrus, we cpmpared  gene expression profiles of trangenic and wild type callus prior to and at the stage of soamtic embryos presence (40 and 60 days after somatic embryos induction, referref to 40 and 60 DAI, respectively). A total of  3020 and 1452 differentially expressed genes were found between trangenic and wild type at 40 and 60 DAI, respectively. Our result indicated that csi-miR156a overexpression could cause large-scale gene expression alteration.

overall_design: Two lines of citrus callus overexpressing csi-miR156a were compared with two  that from wild type at 40 and 60 DAI, respectively.

first: Wenwu

last: Guo


title: MicroRNA expression profiles predict the response to PegIFNα-2a treatment of Chronic Hepatitis B

city: ChongQing

first: YanLin

last: Yang

state: ChongQing

address: 29 Gaotanyan Main Street, Shapingba District, Chongqing, China

department: Institute for Infectious Diseases

institute: The First Affiliated Hospital, Third Military Medicale University

summary:
The differential expression profiles of PBMCs microRNA pretreatment between the HBsAg loss group and the non-HBsAg loss group were constructed by using the miRCURYTM LNA Array (v.19.0)(Exiqon),  the results were validated by qRT-PCR,all the expresison levels of selected microRNAs were consistent with the microarray results.
The receiver operating characteristic curve was performed to estimate the predictive value of the selected miRNAs,indicated that microRNAs may be potential predictive biomarkers for PegIFN response.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In the present study,identification cohort (n=20) and confirmation cohort (n=46) were conducted, the differential expression profiles of miRNAs were screened in the identification cohort by RNA microarray,composed of 10 HBsAg loss and 10 non HBsAg loss patients.qRT-PCR was used to validated the results of the microarray.The receriver operating characteristic curve and GO/Pathway analyses were preformed to evaluate their predictive values for PegIFN response.

first: Qing

last: Mao

first: Ming

last: Liu

first: Yi

last: Wu


title: Expression alternations in liraglutide treated rats cardiac muscle

status: Public on Mar 30 2018

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

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

platform_organism:
Rattus norvegicus
synthetic construct


title: Regional preferences of DNA methylation changes in response to X-ray-irradiation [Agilent-069114 array]

summary:
In this study we screened for changes of DNA methylation in response to X-irradiation in the lymphoblastoid cell line GM12878 and the primary lung fibroblast cell line IMR90.
We employed methylated DNA-Immunoprecipitation in combination with genome wide and region specific DNA microarrays to identify preferences of radiation induced changes of methylation with respect to genomic and epigenomic characteristics.

overall_design: Multiple samples from two different cell lines were tested at different time points after X-ray irradiation (0 Gy and 0.5 Gy), respectively.

middle: V

first: Reinhard

last: Ullmann


title: Gene expression changes in Fbxw11 variants overexpressed in L1210 cell line

status: Public on Mar 29 2018

city: Tianjin

first: Guo Guang

last: Zheng

state: Tianjin

address: Blood Hospital,288 Nanjing Road,Heping District

department: Institute of Hematology & Blood Hospital

institute: Chinese Academy of Medical Science& Peking Union  Medical College

summary: We compared the transcriptomic changes in L1210 cells when Fbxw11 variants were overexpressed. In order to study the function of Fbxw11 in L1210 cells.

overall_design: Single-color experiment using Agilent Mouse GE 8x60K Microarray Cat.# G4858A-028005.

first: Lina

last: Wang

first: Guoguang


title: Regional preferences of DNA methylation changes in response to X-ray-irradiation [Agilent-021850 array]

first: Benjamin

overall_design: Multiple samples from two different cell lines were tested at different time points after X-ray irradiation with administered doses ranging from 0 to 4Gy, respectively.


title: Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch

city: Boston

first: Stuart

last: Orkin

state: MA

address: 1 Blackfan Circle

department: Hematology and Oncology

institute: Boston Children's Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Fetal hemoglobin (HbF) level is genetically controlled and modifies severity of adult hemoglobin (HbA) disorders. Common genetic variation affects expression of BCL11A, a critical regulator of HbF silencing. Current models suggest that BCL11A acts at a distance from the gamma-globin genes via long-distance chromosomal interactions. Here we use a functional cellular assay and protein-binding microarray to establish a requirement for a zinc-finger cluster of BCL11A for globin repression, and identify a preferred DNA recognition sequence (TGACCA). The motif is present in embryonic and fetal-expressed globin promoters, and duplicated in gamma-globin promoters, yet only the distal motif is mutated in alleles of individuals with hereditary persistence of hemoglobin. Using CUT&RUN to map protein binding sites, we detected BCL11A occupancy preferentially at the distal motif, and validated its absence in HbF-expressing, promoter-edited erythroid cells. Taken together, our findings reveal that direct gamma-globin gene promoter repression by BCL11A underlies hemoglobin switching.

overall_design:
To assess DNA binding of BCL11A, CUT&RUN experiments with BCL11A as antibody were performed on HUDEP-2 and CD34+ differentiated cells at various differentiation days. Various pA-MNase digestion times, and controls (IgG, knockout) were included. CUT&RUN was also assessed on CRISPR promoter edited cells where the gamma-globin promoter was modified.

ATAC-seq experiments were performed in HUDEP-2 cells, single clone edited cells, bulk edited cells to assess their chromatin accessibility.  ChIP-seq experiments were also performed in HUDEP-2 cells.

last: Zhu

first: Victoria

last: Hargreaves


title: N6-methyladenosine modification  in lytic viral gene expression during Kaposi's sarcoma-associated herpesvirus infection [MeRIP-seq]

city: Berkeley

first: Britt

last: Glaunsinger

state: CA

address: 1951 Oxford Street

department: Plant and Microbial Biology

institute: UC Berkeley

type: Methylation profiling by high throughput sequencing

summary: Methylation at the N6 position of adenosine (m6A) is a highly prevalent reversible modification within eukaryotic mRNAs that has been linked to many stages of RNA processing and fate. Recent studies suggest that m6A deposition and proteins involved in the m6A pathway play a diverse set of roles in either restricting or modulating the lifecycles of select viruses. Here, we report that m6A levels are significantly increased in cells infected with the oncogenic human DNA virus Kaposi’s sarcoma-associated herpesvirus (KSHV). Transcriptome-wide m6A-sequencing of the KSHV-positive renal carcinoma cell line iSLK.219 during lytic reactivation revealed the presence of m6A across multiple kinetic classes of viral transcripts, and a concomitant decrease in m6A levels across much of the host transcriptome.

overall_design:
iSLK.219 cells that were either uninduced (latent virus), or induced for five days with doxycycline to allow KSHV lytic replication.  2 separate biological replicates for the uninduced and induced samples were used per treatment condition.

Plase note that each processed data file derived from the corresponding input and m6A IP conditions is lined to each IP sample records.

first: Charles

last: Hesser

first: John

last: Karijolich

first: Dan

last: Dominissini

first: Chuan

last: He


title: Gene expression alternations in liraglutide treated rats cardiac muscle

status: Public on Mar 28 2018

summary: Diabetic rats changes gene exprssion in liraglutide treated rats cardiac muscle

overall_design: We performed microarray analyses of liraglutide treated rats cardiac muscle

first: Xinhua

last: Xiao

first: Jia

last: Li

first: Miao

last: Yu

first: Fan

last: Ping

first: Zhixin

first: Cuijuan

last: Qi

first: Tong

first: Xiaojing


title: Gene expression profiles of PBMCs in healthy subjects (CTRL) and patients with Metabolic Syndrome (MS)  - PART 1 - Genes

city: Bari

first: Antonio

last: Moschetta

address: Via Orazio Flacco, 65

country: Italy

institute: IRCCS Ospedale Oncologico di Bari

summary: The aim of the present study was to investigate the whole-genome gene and miRNA profiles in MS. Results provide the information of changes in the PBMCs transcriptome in subjects with MS.

overall_design: RNA obtained from PBMCs of the CTRL subjects and MS patients. Comparisons: CTRL vs. MS.

first: Simona

last: D'Amore

first: Andria

last: D'Orazio


title: Gene expression profiles of PBMCs in healthy subjects (CTRL) and patients with Metabolic Syndrome (MS)  - PART 2 - miRNAs

summary: The aim of the present study was to investigate the whole-genome gene and miRNA profiles in MS. Results provide the information of changes in the PBMCs mirnome in subjects with MS.


title: Comprehensive analysis of area-specific and time-dependent changes in gene expression in the motor cortex of macaque monkeys during recovery from spinal cord injury

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

country: Japan

institute: Toyohashi University of Technology

summary: The present study aimed to assess the molecular bases of cortical compensatory mechanisms following spinal cord injury in primates. To accomplish this, comprehensive changes in gene expression were investigated in the bilateral primary motor cortex (M1), dorsal premotor cortex (PMd), and ventral premotor cortex (PMv) after a unilateral lesion of the lateral corticospinal tract (l-CST). At 2 weeks after the lesion, a large number of genes exhibited altered expression levels in the contralesional M1, which is directly linked to the lesioned l-CST. Gene ontology and network analyses indicated that these changes in gene expression are involved in the atrophy and plasticity changes observed in neurons. Orchestrated gene expression changes were present when behavioral recovery was attained 3 months after the lesion, particularly among the bilateral premotor areas, and a large number of these genes are involved in plasticity. Moreover, several genes abundantly expressed in M1 of intact monkeys were upregulated in both the PMd and PMv after the l-CST lesion. These area-specific and time-dependent changes in gene expression may underlie the molecular mechanisms of functional recovery following a lesion of the l-CST.

overall_design:
Brain tissue samples were obtained from 9 young adolescent rhesus monkeys (Macaca mulatta), 3-4 years old, and categorized into the following groups: intact monkeys (n = 3), monkeys perfused at 2 weeks after lesioning of the l-CST (n = 3), and monkeys perfused at 3 months (n = 3) after lesioning of the l-CST. The animal use protocol was approved by the National Institutes of Natural Sciences, and adequate measures were taken to minimize any pain and discomfort in accordance with the National Institute of Health Guide for the Care and Use of Laboratory Animals (NIH publication no. 80?23). The l-CST lesion was established as described previously (Sasaki S et al. 2004; Nishimura Y et al. 2007). First, the animals were anesthetized using ketamine hydrochloride (10 mg/kg, intramuscular [i.m.]) and xylazine (1 mg/kg, i.m.), and anesthesia was maintained using sodium pentobarbital (20 mg/kg, intravenous [i.v.]). The border between the C4 and C5 spinal segments was exposed by laminectomy of the C3 and C4 vertebrae, and a transverse opening was made in the dura. The l-CST lesion was made under a surgical microscope in three steps. First, a small opening was made in the pia mater at the lateral convexity of the spinal cord, and a horizontal strip was made in a mediolateral direction relative to the lateral funiculus by inserting a minute L-shape hook that could not be inserted more than 5 mm deep, which corresponds to the distance from the lateral convexity of the spinal cord to the midline. Second, using watchmaker's forceps, the dorsal part of the lateral funiculus was ventrally transected from the dorsal root entry zone to the level of the horizontal strip lesioned in Step 1. Third, the lesion was extended ventrally using the watchmaker?s forceps at the most lateral part of the lateral funiculus. Finally, the opening of the dura mater was closed, and the skin and back muscles were sutured using either nylon or silk.
Hand movement performances prior to and after the lesion were evaluated daily using a small-object retrieval task in which the monkeys had to reach, grasp, and retrieve a small piece of sweet potato (7 × 7 × 7 mm in size) through a narrow vertical slit using their index finger and thumb. The food piece was placed at the center of the vertical slit, which was at shoulder height for each monkey at a sagittal distance of 15 cm. The monkeys were trained intensively every day to retrieve these small food pieces, sometimes using manual assistance of the movements, as described previously (Sugiyama Y et al. 2013).
Following the completion of the behavioral tests, the monkeys were perfused with 500-1000 ml ice cold saline containing heparin sodium (1000 units/ml, Novo Heparin, Leo Pharmaceutical Products; Ballerup, Denmark) through the ascending aorta within 15 min of an overdose injection of pentobarbital sodium (50 mg/kg, intraperitoneal [i.p.], Somnopentyl, Kyoritsu Shoji; Tokyo, Japan). The abovementioned six neocortical areas (bilateral M1, PMd, and PMv) were determined using sulcal landmarks. A total of 50?150 mg of tissue from each area was dissected and frozen immediately in liquid nitrogen. The forelimb region of M1, which is located around the superior genu of the central sulcus (Higo N et al. 2007; Murata Y et al. 2015), was obtained for the present analysis. The PMd and PMv were obtained from the caudal bank of the upper and lower limbs of the arcuate sulcus and their convex regions rostral to M1, respectively.

first: Noriyuki

last: Higo

first: Akira

last: Sato

first: Tatsuya

last: Yamamoto

first: Takao

last: Oishi

first: Yukio

last: Nishimura

first: Yumi

last: Murata

first: Hirotaka

last: Onoe

first: Tadashi

last: Isa


title: Role of histone demethylase Kdm6a in pancreatic cancer (MoGene-2_0)

status: Public on Apr 01 2018

city: Washington

first: Alexandros

last: Tzatsos

state: DC

address: 800 22nd St NW SEH 8850

department: GW Cancer Center

institute: George Washington University

summary:
Transcriptional profile of murine Kdm6a null pancreatic cancer cell lines
Loss-of-function mutations of KDM6A, an X chromosome encoded histone H3K27 demethylase, are frequent in a broad spectrum of epithelial and hematopoietic malignancies and contribute to oncogenesis with so far poorly characterized mechanisms. Pancreas specific ablation of Kdm6a in mice accelerated Kras-driven cell transformation and compromised survival in a gender specific manner. Female knockout animals were particularly vulnerable and developed aggressive squamous and quasi-mesenchymal tumors with metastatic potential, as opposed to males which developed adenocarcinomas and exhibited a better prognosis. Integration of gene expression studies coupled to ChIP-seq profiling of chromatin modifications demonstrated that loss of Kdm6a caused genome-wide remodeling of bivalent promoters and rewiring of enhancer chromatin to repress endodermal fate by activating c-MYC and TP63 dependent transcriptional programs favoring squamous and quasi-mesenchymal differentiation.

overall_design: Male and female wild-type and Kdm6a null cell lines were established from murine pancreata in the context of Kras. Gene expression profile using the Affymetrix platform was performed to identify differentially expressed genes.

first: Yan

last: Kai


title: Low-input and multiplexed microfluidic assay reveals epigenomic variation across cerebellum and prefrontal cortex

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

summary: There has been an extensive effort underway to profile epigenetic features at the genome-wide scale using primary ex vivo tissues. Cell-type specificity of epigenomes calls for enrichment to obtain a homogenous cell population from a small quantity of tissues. Thus technologies that permit both ultralow input and high throughput are desired for profiling an array of histone marks. Here we demonstrate a simple microfluidic technology, SurfaceChIP-seq, for profiling genome-wide histone modifications using as few as 30 cells per assay and with up to 8 assays running in parallel. We applied the technology to study epigenomic landscapes in neurons and glia in prefrontal cortex and cerebellum of mouse brain. The data revealed extensive epigenomic difference in the two regions on important functional elements such as promoters and enhancers.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We examined genome-wide H3K4me3 and H3K27me3 profiles in GM12878 cell line (using 30 to 10k cells per assay) using SurfaceChIP-seq. They include data generated by 4-channel (4C) and 8-channel (8C) devices and also devices produced using (3-Aminopropyl) triethoxysilane /Glutaraldehyde/Protein A (AGP) linker.  We also profiled H3K4me3, H3K27ac and H3K27me3 marks in neurons (NeuN+) and glia (NeuN-) from mouse cerebellum and prefronal cortex (using 100 or 1k nuclei per assay) using SufaceChIP-seq. We generated RNA-seq data on neurons and glia from mouse prefronal cortex and cerebellum. Finally, we also included SurfaceChIP-seq and RNA-seq data obtained using the homogenate of mouse prefrontal cortex and cerebellum (referred to as "mix" in their file names). Three mice (M1, M2 and M3) were used in the study.

first: Sai

last: Ma


title: ERα Dependent Alterations in the Epigenetic Landscape of the Mouse Uterus Following Neonatal Estrogen Exposure [ChIP-Seq]

status: Public on Mar 27 2018

city: RTP

first: Wendy

last: Jefferson

state: NC

address: 105 T. W. Alexander Drive

institute: NIEHS

summary: Abstract. Very little is known regarding how hormonal exposures impact the epigenetic landscape of developing tissues in the context of a whole organism, in contrast to the impact on cultured cells. Here we took a global approach to understanding how neonatal exposure to the xenoestrogen, diethylstilbestrol (DES), alters the uterine epigenome. RNA-seq and ChIP-seq (H3K4me3, H3K27me3, H3K27ac and H3K4me1) were performed on DES-treated and control uteri. The most striking finding was differential association of H3K27ac and H3K4me1 at typical and super-enhancer regions of 79% of altered genes. These peaks overlapped with previously reported estrogen receptor a (ERα) ChIP-seq peaks. Conditional uterine deletion of ERα (Esr1cKO) conferred protection of 88% of altered genes. H3K27ac ChIP-seq on Esr1cKO samples showed that 72% of protected genes had a differential H3K27ac enhancer. These data suggest that DES regulates gene expression in the neonatal mouse uterus by H3K27ac association at ERα binding sites near estrogen-regulated genes.

overall_design: Mice were treated neonatally with DES (1 mg/kg) on days 1-5 and uteri collected on PND5, 4 hrs after the last treatment. Uteri were pooled (4-6 per sample). For H3K27me3 and H3K4me3 ChIP seq there is one sample deposited here. For H3K27ac and H3K4me1 ChIP seq there are two biological replicates for each condition.

middle: N

first: H

last: Karimi Kinyamu

first: Tianyuan

last: Wang

first: Elizabeth

last: Padilla-Banks

first: Alisa

middle: A

last: Suen

first: Carmen

middle: J

last: Williams


title: Gene expression profiles of PBMCs in healthy subjects (CTRL) and patients with Metabolic Syndrome (MS)

first: Antonio

last: Moschetta


title: ERα Dependent Alterations in the Epigenetic Landscape of the Mouse Uterus Following Neonatal Estrogen Exposure [RNA-Seq]

overall_design: Mice were treated neonatally with DES (1 mg/kg) on days 1-5 and uteri collected on PND5, 4 hrs after the last treatment. Each sample is from a single uterus. There are 4 control samples and 4 DES treated samples


title: ERα Dependent Alterations in the Epigenetic Landscape of the Mouse Uterus Following Neonatal Estrogen Exposure


title: DNA methylation profiling by MBD-Seq in the mouse seminal vesicles (SVs) and uterus (U) following neonatal DES exposure

first: Yin

last: Li

address: 111 TW alexander Drive

summary: DES is a synthetic estrogen that is associated with adverse effects on reproductive organs. Our group has employed estrogen receptor (ER) α knockout (αERKO) mice to gain insight into the contribution of ER α in DES-induced toxicity following neonatal exposure

overall_design: Mice were neonatally exposed to DES. SVs were collected at weeks 5 and 10, and uteri were collected at week 10. DNA methylation profiling was performed using MBDcapture Seq.


title: Genome-wide transcriptome in the mouse seminal vesicles (SVs) and uterus (U) following neonatal DES exposure [RNA-seq]

summary: DES is a synthetic estrogen that is associated with adverse effects on reproductive organs. Our group has employed estrogen receptor (ER) α knockout (αERKO) mice to gain insight into the contribution of ER a in DES-induced toxicity following neonatal exposure.

overall_design: Mice were neonatally exposed to DES. The SVs or uterus were collected at week 10. Genome-wide transcriptome was performed by RNA-Seq.


title: Profiling of cytosine DNA-methylation in the Arabidopsis CAF-1 mutant fas2

status: Public on Mar 26 2018

city: Uppsala

first: Minerva

middle: Susana

last: Trejo Arellano

state: Uppsala

address: Almas Allé 5

department: Plant Biology

country: Sweden

institute: SLU

summary: Chromatin Assembly Factor CAF-1 is a histone chaperone involved in nucleosome formation after replication. Here, cytosine DNA-methylation was profiled by bisulphite DNA sequencing in Arabidopsis wild type and the fas2 CAF-1 mutant. To test for transgenerational changes in DNA methylation, fas2 mutants of generation 1 and 6 were compared.

overall_design: Characterisation of the transgenerational methylation changes in fas2-4 mutants using genome-wide bisulfite sequencing. The transgenerational effect was assessed by bisulphite sequencing the first homozygous generation segregated from a selfed heterozygous fas2-4 parental plant and the 6th selfed generation. Col-0 accession was used as a reference. The DNA was sequenced in 100 bp pair-end mode. To increase coverage, mates were mapped as independent single end reads: R1 as directional and R2 in a non-directional.

first: Iva

last: Mozgova

first: Thomas

last: Wildhaber

middle: S

last: Trejo-Arellano

first: Jiri

last: Fajkus

first: Pawel

last: Roszack

first: Claudia

last: Köhler

first: Lars

last: Hennig


title: Gene expression and DNA methylation profiling in the seminal vesicles (SVs) from neonatal DES-treated mice

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

overall_design: Refer to individual Series


title: OCEAN-C: mapping hubs of open chromatin interactions across the genome reveals gene regulatory networks

status: Public on Mar 25 2018

first: lumeng

last: Jia

address: Yiheyuan road

institute: Peking university

summary: We develop a method called open chromatin enrichment and network Hi-C (OCEAN-C) for antibody-independent mapping of global open chromatin interactions. By integrating FAIRE-seq and Hi-C, OCEAN-C detects open chromatin interactions enriched by active cis-regulatory elements. We identify more than 10,000 hubs of open chromatin interactions (HOCIs) in human cells, which are mainly active promoters and enhancers bound by many DNA-binding proteins and form interaction networks crucial for gene transcription. In addition to identifying large-scale topological structures including topologically associated domains and A/B compartments, OCEAN-C can detect HOCI-mediated chromatin interactions that are strongly associated with gene expression, super-enhancers and broad H3K4me3 domains.

overall_design: Analysis of open chromatin interactions and gene regulatory networks in 3 different cell types.

first: Tingting

first: Lumeng


title: PtWOX11 Promote de novo Shoot Regeneration by Involving a Two- Step Mechanism in Poplar

city: Fuzhou

first: Bobin

last: Liu

address: No.15 Shangxiadian Road, Cangshan District

institute: Fujian Agriculture and Forestry University

summary: De novo shoot regeneration is an essential step for massive propagation and genetic engineering of elite germplasm in forestry. Poplar that is a fast growth tree species have a very important ecologically and economically role around the world, especially in China. In this study, we found that PtWOX11 that is a homologue of AtWOX11 not only involved de novo root formation but also promote de novo shoot regeneration in poplar. We demonstrated that PtWOX11 can enhance callus regeneration competence and shoot regeneration during two-step de novo shoot regeneration. Furthermore, by using RNA-seq and qPCR, we uncovered that during callus induction stage PtWOX11 activates PtPLTs expression to promote callus formation and regeneration competence, and promote PtCUC2/3, PtWUSa and PtSTM transcription to fulfil shoot organogenesis during shoot regeneration stage. Overall, our data indicated that PtWOX11 play a new function and transcriptional regulation mechanism on de novo shoot regeneration in poplar.

overall_design: RNA-seq of leaf, callus on CIM8, SIM4 and SIM8

first: Lianfeng

last: Gu

first: Jin

last: Zhang

first: Mengzhu

last: Lu

first: Yoshito

last: Oka


title: ChIP-Seq analysis of transcription factors CREB and C/EBP beta in vasopressin-responsive mouse renal collecting duct mpkCCD cells

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

summary: Vasopressin, a peptide hormone, controls renal water excretion, largely through regulation of water channel aquaporin-2 (AQP2) in the renal collecting duct. There are two regulatory mechanisms of AQP2: 1) short-term regulation by membrane trafficking of AQP2; and 2) long-term regulation involving vasopressin-induced changes of protein abundance of AQP2 through regulation of gene transcription and protein half-life. Vasopressin binds a G protein-coupled receptor (V2R) activating a cyclic AMP/protein kinase A (PKA) signaling pathway. Sequentially, after activation of cAMP/PKA signaling, many of transcription factors involve gene transcription process. cAMP-response element binding protein (CREB) and cAMP-responsive transcription factor C/EBP beta are potential candidates for vaopressin-mediated regulation of Aqp2 gene transcription proviously reported. In the present study, genome-wide binding sites for two b-ZIP transcription factors CREB and C/EBP beta were identified in vasopressin-responsive mouse collecting duct mpkCCD cells using ChIP-Seq.

overall_design: To identify binding sites of transcription factors CREB and C/EBP beta in cultured mouse collecting duct mpkCCD cells, we carried out ChIP-seq for genome-wide distribution of CREB (n=4) and C/EBP beta (n=2). Observations were made both after 30 minutes treatment with the vasopressin analog dDAVP or vehicle.

first: Jae Wook

last: Lee

first: Mark

last: Knepper


title: NFAT3-regulated genes in human aortic smooth muscle cells (ASMC)

city: Chuo

first: Osamu

last: Kaminuma

state: Yamanashi

address: 1110 Shimokato

institute: University of Yamanashi

summary: NFAT family transcription factors play crucial roles in immunological and other biological activities. Since we found that NFAT3 was highly expressed in ASMC, the target genes of NFAT3 in ASMC were investigated.

overall_design: Four samples, NFAT3-expressing vector- vs. control vector-transfected cells, NFAT3-specific RNAi oligo- vs. control oligo-transfected cells

first: Yasumasa

last: Nishito

first: Noriko

last: Kitamura


title: Identification of sex-specific DNA methylation changes driven by specific chemicals in cord blood in a Faroese birth cohort

city: Little Rock

first: Yuetkin

last: Leung

state: AR

address: 323 Jack Stephens Dr

department: Pharmacology and Toxicology

institute: University of Arkansas for Medical Sciences

summary:
Genome wide DNA methylation profiling of cord blood in Faroe Island cohort. The Illumina Infinium 450k Human DNA methylation Beadchip  was used to obtain DNA methylation profiles across approximately 485,000 CpGs in cord blood samples.
Background: Faroe islanders consume marine foods contaminated with methylmercury (MeHg), polychlorinated biphenyls (PCBs), and other toxicants associated with chronic disease risks. Differential DNA methylation at specific CpG sites in cord blood may serve as a surrogate biomarker of health impacts from chemical exposures.
Objective: We aimed to identify key environmental chemicals in cord blood associated with DNA methylation changes in a population with elevated exposure to chemical mixtures.
Method: We studied 72 participants of a Faroese birth cohort recruited between 1986 and 1987 and followed until adulthood. The cord blood DNA methylome was profiled using Infinium Methylation 450K BeadChips. We determined the associations of CpG site changes with concentrations of MeHg, major PCBs, other organochlorine compounds, (hexachlorobenzene [HCB], p,p’-dichlorodiphenyldichloroethylene [p,p’-DDE] and p,p’-dichlorodiphenyltrichloroethane) and perfluoroalkyl substances.
Results: In a combined sex analysis, among the 16 chemicals studied, PCB congener 105 (CB-105) exposure was associated with the majority of differentially methylated CpG sites (214 out of a total of 250). In female-only-analysis, only 73 CB-105 associated CpG sites were detected, 44 of which were mapped to genes in the ELAV1-associated cancer network. In males-only, methylation changes were seen for perfluorooctane sulfonate, HCB, and p,p’-DDE in 10,598; 1,238; and 1,473 CpG sites, respectively, 15% of which were enriched in cytobands of the X chromosome associated with neurological disorders.
Conclusion: In this multiple-pollutant and genome-wide study, we identified key epigenetic toxicants. The significant enrichment of specific X-chromosome sites in males implies potentially sex-specific epigenome responses to prenatal chemical exposures.

overall_design: Bisulphite converted DNA from the 72 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip (samples 2, 3, 4, 6, 12, 13, 15, 17, 18,  24, 30, 32, 33, 34, 40, 42, 43, 44, 46, 68 and 71 were removed from the final analysis due to poor quality).

first: Yuet-Kin

first: Shuk-Mei

last: Ho

first: Philippe

last: Grandjean


title: 10X genomics analysis of adult and larval habenula from the gng8-GFP transgenic line

status: Public on Mar 23 2018

city: Cambridge

first: Shristi

last: Pandey

address: 16 Divinity Ave

department: Molecular and Cellular Biology

institute: Harvard University

summary: The identification of cell types and marker genes is critical for dissecting neural development and function, but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single-cell RNA-seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula, a conserved forebrain hub involved in pain processing and learning. Single-cell transcriptomes of ~13000 habenular cells (>4x coverage) identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly, despite brain growth and functional maturation, cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions.

overall_design: For larval dataset, multiple gng8-GFP labeled zebrafish brains were dissociated and habenular cells FAC sorted into PBS+1%BSA and immediately loaded into 10X chromium for cell capture. For adult dataset, 5-6 habenulae were cleanly dissected out, dissociated, filtered in PBS+BSA and immediately captured in droplets with 10x platform. Both libraries were then constructed using standard instrutions of the 10x plaform.


title: The striatal kinase DCLK3 produces neuroprotection against mutant huntingtin

status: Public on Mar 22 2018

city: Corbeil-Essonnes

first: MARGOT

last: JARRIGE

address: 28, Rue Henri Desbruères

country: France

institute: I-Stem/INSERM U861

summary:
The neurobiological functions of a number of kinases expressed in the brain are unknown.  Here, we report new findings on DCLK3 (Doublecortin-like kinase 3) which is preferentially expressed in neurons in the striatum and dentate gyrus. Its function has never been investigated. DCLK3 expression is markedly reduced in Huntington's disease. Recent data obtained in studies related to cancer suggest DCLK3 could have anti-apoptotic effect. Thus, we hypothesized that early loss of DCLK3 in Huntington's disease may render striatal neurons more susceptible to mutant huntingtin (mHtt). We discovered that DCLK3 silencing in the striatum of mice exacerbated the toxicity of an N-terminal fragment of mHtt. Conversely, overexpression of DCLK3 reduced neurodegeneration produced by mHtt. DCLK3 also produced beneficial effects on motor symptoms in a knock-in mouse model of Huntington's disease. Using different mutants of DCLK3, we found that the kinase activity of the protein plays a key role in neuroprotection. To investigate the potential mechanisms underlying DCLK3 effects, we studied the transcriptional changes produced by the kinase domain in human striatal neurons in culture.  Results show that DCLK3 regulates in a kinase-dependent manner the expression of many genes involved in transcription regulation and nucleosome/chromatin remodeling. Consistent with this, histological evaluation showed DCLK3 is present in the nucleus of striatal neurons and, protein-protein interaction experiments suggested that the kinase domain interacts with zinc finger proteins, including TADA3, a core component of SAGA complex. Our novel findings suggest that the presence of DCLK3 in striatal neurons may play a key role in transcription regulation and chromatin remodeling in these brain cells, and show that reduced expression of the kinase in Huntington’s disease could render the striatum highly vulnerable to neurodegeneration.
Examination of DCLK3 as neuroprotector against mutant huntingtin in vivo and in vitro models.

overall_design: Examination of DCLK3 as neuroprotector against mutant huntingtin in vitro experiments.

first: Emmanuel

last: Brouillet

first: Laurie

last: Galvan

first: Laetitia

last: Francelle

first: Marie-Claude

last: Gaillard

first: Lucie

last: de Longprez

first: Maria-Angeles

last: Carrillo-de Sauvage

first: Géraldine

last: Liot

first: Karine

last: Cambon

first: Lev

last: Stimmer

first: Sophie

last: Luccantoni

first: Julien

last: Flament

last: Valette

first: Michel

last: de Chaldée

first: Gwenaelle

last: Auregan

first: Martine

last: Guillermier

first: Charlène

last: Joséphine

first: Fanny

last: Petit

first: Caroline

last: Jan

first: Margot

last: Jarrige

first: Noëlle

last: Dufour

first: Jean-Marc

last: Elalouf

first: Gilles

last: Bonvento

first: Sandrine

last: Humbert

first: Frédéric

last: Saudou

last: Hantray

last: Merienne

first: Alexis-Pierre

last: Bemelmans

first: Anselme

middle: L

last: Perrier

first: Nicole

last: Déglon


title: RNA-seq analysis of gene expression profile in Uhrf1 WT and KO germinal center B cells

city: Nanjing

first: Xiaoming

last: Wang

address: 101 Longmian Road

institute: Nanjing Medical University

summary: The goals of this study are to compare gene expression profiles of Uhrf1 WT and KO germinal center B cells and reveal the underlying mechanisms by which Uhrf1 regulates germinal center B cell responses. We found that upon Uhrf1 depeletion in germinal center B cells, most of the differentially expressed genes were upreguated.

overall_design: The germinal center B cell specific Uhrf1-deficient mice and WT control mice were immunized and 10e6 germinal center B cells were FACS sorted for RNA extraction. Library were then generated with illumina protocol and subject to NGS and bioinformatic analysis.

first: Chao

last: Chen


title: HIV-1 infection of human monocyte-derived dendritic cells with and without the integrase inhibitor, Raltegravir (gene expression).

city: Seattle

first: Jarrod

last: Johnson

state: Washington

address: 307 Westlake Ave, Suite 500

institute: Center for Infectious Disease Research

summary: Myeloid dendritic cells (DCs) have the innate capacity to sense pathogens and orchestrate immune responses. However, DCs do not mount efficient immune responses to HIV-1, due to potent restriction at the level of reverse transcription. Here, we uncover that when reverse transcription is allowed to proceed, DCs detect HIV-1 in distinct phases, before and after integration. Blocking integration suppressed, but did not abolish, activation of the transcription factor, IRF3, interferon responses, and DC maturation. The cytoplasmic DNA sensor, cGAS, and the E3 ligase, TRIM5, were both required for these responses. Consistent with two stages of innate activation, HIV-1 altered host chromatin accessibility before and after integration. Our studies support the hypothesis that HIV-1 replication increases the amount of material available for sensing and that cGAS signaling can be tuned by discrete inflammatory inputs to drive DC maturation.

overall_design: DCs were derived from the peripheral blood from two deidentified human donors and infected with a single-cycle HIV-1 reporter virus (HIV-GFP) in the presence of Vpx, with and without Raltegravir. RNA expression was measured at 0, 8, 16, 20, 24, 28, 32, and 40 hours after infection.

first: Lynn

middle: M

last: Amon

first: Alan

last: Aderem


title: HIV-1 infection of human monocyte-derived dendritic cells with and without the integrase inhibitor, Raltegravir


title: Targeted in situ genome-wide profiling with high efficiency for low cell numbers

status: Public on Mar 21 2018

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is an epigenomic profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. As only the targeted fragments enter into solution, and the vast majority of DNA is left behind, CUT&RUN has exceptionally low background levels. CUT&RUN outperforms the most widely- used Chromatin Immunoprecipitation (ChIP) protocols in resolution, signal-to-noise, and depth of sequencing required. In contrast to ChIP, CUT&RUN is free of solubility and DNA accessibility artifacts and has been used to profile insoluble chromatin and to detect long-range 3D contacts without cross-linking. Here we present an improved CUT&RUN protocol that does not require isolation of nuclei and provides high-quality data starting with only 100 cells for a histone modification and 1000 cells for a transcription factor. From cells to purified DNA CUT&RUN requires less than a day at the lab bench and requires no special skills.

overall_design: We used Cleavage under targets and Release using nuclease (Cut-and-Run), a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing.

first: Peter

last: Skene

first: Steven


title: HIV-1 infection of human monocyte-derived dendritic cells with and without the integrase inhibitor, Raltegravir (ATAC-Seq).

overall_design: DCs were derived from the peripheral blood from three deidentified human donors and infected with a single-cycle HIV-1 reporter virus (HIV-GFP) in the presence of Vpx, with and without Raltegravir.  At 0, 16, 32, and 48 hours after infection, live cells were sorted and then prepped for an Assay for Transposase-Accessible Chromatin with high-throughput Sequencing (ATAC-Seq).


title: LPS stimulated murine RAW264.7 cells, incubated with DMSO carrier or mycolactone

city: GULDFORD

first: RACHEL

last: SIMMONDS

state: Surrey

address: FHMS UNIVERSITY OF SURREY, STAG HILL CAMPUS

country: United Kingdom

institute: University of Surrey

summary: Translational profiling of RAW264.7 cells stimulated with LPS in the presence and absence of 125ng/ml mycolactone: polysomal and subpolysomal RNA isolated by sucrose gradient centrifugation to determine the effect of mycolactone on translation during a proinflammatory response

overall_design: Subpolysomal vs polysomal RNA under 2 conditions: control and mycolactone treated. Biological replicates: 3 replicates control, 3 replicates treated, with dyeswap

first: Rachel

middle: E

last: Simmonds

first: Belinda

last: Hall

first: Joy

last: Ogbechi

first: Thomas

last: Sbarrato

first: Anne

last: Willis


title: Transcriptome profile analysis reveals the regulation mechanism of floral sex differentiation in Jatropha curcas L.

city: Beijing

first: Wenkai

last: Hui

state: Beijing

address: Qinghua East Street

institute: Beingjing Forestry University

summary: Our results showed that hundreds of differentially expressed genes (DEGs) were detected in floral sex initiation period, but thousands of DEGs were involved in stamens and ovules development process. Moreover, the DEGs were mainly showed up-regulation in male floral initiation, but mainly down-regulation in female floral initiation. Male floral initiation was associated with the flavonoid biosynthesis pathway while female floral initiation was related to the phytohormone signal transduction pathway. In addition, the floral organ identity genes played important roles in floral sex differentiation process and displayed a general conservation of the ABCDE model in J. curcas.

overall_design: Five different samples during floral sex differentiation stages

first: Xiaoyang


title: Comprehensive comparative analysis of 5’ end RNA sequencing methods

first: Joshua

last: Levin

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

summary: RNA-Seq is an effective method to study the transcriptome, but specialized methods are required to identify 5’ ends of transcripts. Several published strategies exist for this specific purpose, but their relative merits have not been systematically analyzed. Here, we directly compare the performance of six such methods – testing five with cellular RNA as well as a novel spike-in RNA assay that helps address interpretation challenges that arise from uncertainties in annotation or RNA processing. Using a single human RNA sample, we constructed and sequenced 18 libraries with these methods and one standard, control RNA-Seq library. We find that the CAGE method performed best for mRNA and that most of its unannotated peaks are supported by evidence from other genomic methods. We then applied CAGE to eight brain-related samples and revealed sample-specific transcription start site (TSS) usage as well as a transcriptome-wide shift in TSS usage between fetal and adult brain.

overall_design: Examination of 19 different RNA-Seq libraries starting from total RNA from 5 distinct 5' end methods; also 1 control RNA-Seq library

middle: Z

first: Xian

last: Adiconis

first: Adam

last: Haber

first: Sean

middle: K

last: Simmons


title: Lifelong calorie restriction and markers of colonic health in aging mice

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Diminishment of colonic health is associated with various age-related pathologies. Calorie restriction (CR) is an efficient strategy to increase healthy lifespan, although underlying mechanisms are not fully elucidated. Here we report the effects of lifelong CR on markers of colonic health in aging mice. We show that 30% energy reduction, as compared to a control (C) and moderate-fat (MF) diet, is associated with attenuated immune-related gene expression and lower levels of bile acids in the colon. Pronounced shifts in microbiota composition, together with lowered plasma levels of interleukin 6, in mice exposed to CR are in line with these findings. Furthermore, expression of genes involved in lipid metabolism was higher upon CR as compared to C and MF, pointing towards efficient regulation of energy metabolism. Switching from CR to an ad libitum MF diet at old age revealed remarkable phenotypic plasticity, although expression of a small subset of genes remained CR-associated. This research demonstrates that CR beneficially affects markers of colonic health in aging mice and as such may attenuate the progressive age-related decline in health.

overall_design: Male C57BL/6J mice were randomized to different dietary regimens starting at the age of 9 weeks. Mice were lifelong fed either a semi-synthetic control diet consisting of 10E% of fat (C), a CR diet without malnutrition (30% energy reduction compared to the C diet) or a moderate-fat (MF) diet consisting of 25E% of fat. All diets, except the CR diet, were fed ad libitum. A subgroup of mice on CR was switched to the MF diet at the age of 24 months until sacrifice at 28 months. Upon sacrifice at 6 or 28 months of age, colonic scrapings were collected and RNA was isolated for microarray analyses.

first: Dieuwertje

last: Kok

first: Fenni

last: Rusli

first: Benthe

last: van der Lugt

first: Carolien

last: Lute

first: Luca

last: Laghi

first: Stefano

last: Salvioli

first: Gianfranco

last: Picone

first: Claudio

last: Franceschi

first: Hauke

last: Smidt

first: Jacques

last: Vervoort

first: Ellen

last: Kampman

first: Michael

last: Müller

first: Wilma

last: Steegenga


title: Gene expression analysis upon mtDNA depletion [microarray]

first: Janine

last: Santos

address: 111 TW Alexander drive

department: GISBL

summary: The goal of the study was to understand whether mitochondrial-driven epigenetic changes regulate gene expression. Mitochondrial metabolism has been implicated in epigenetics but the extent to which this impacts gene expression is unclear. Here we show that loss of mitochondrial DNA (mtDNA) results in locus-specific alterations in histone acetylation, DNA methylation and expression of a subset of genes. Most of these changes are rescued by restoring mitochondrial electron transport in a way that maintains the oxidative tricarboxylic acid cycle, but not reactive oxygen species or ATP production, or by modulating the mitochondrial pool of acetyl-CoA. Changes in acetyl-CoA and histone acetylation precede overt mitochondrial dysfunction and significant changes in gene expression and DNA methylation. This suggests that acetyl-CoA levels signal mitochondrial status to the nucleus. Differentially expressed genes with altered histone marks or DNA methylation regulate amino acid degradation, which likely compensates for the changes in acetyl-CoA and one carbon metabolism. These have the potential to further affect methylation reactions, redox control and nucleotide levels. These results illustrate the extent to which mitochondria impact cell physiology through epigenetic remodeling.

overall_design: We analyzed HEK293 cells in which mtDNA was depleted by doxycycline addition to the medium to turn a dominant negative mitochondrial DNA polymerase (DN-POLG). Samples were analyzed at days 0, 3, 6 and 9 for a total of 4 samples. Each time point was done in three indepedent biological replicates. Time point 0 was used as controls with samples being un-induced.  To determine the TCA cycles effects, HEK293 DN-POLG overexpressing AOX/NDI1 were also included at days 0 and 9, with 3 biological replicates to each Gene expression was also evaluated in 143B cells in which mtDNA was chronically depleted based on ethidium bromide treatment. Samples include 3 independent biological replicates of controls (rho+) and 3 of mtDNA depleted (rho0).

first: Oswaldo

last: Lozoya

first: Inmaculada

last: Martinez-Reyes

first: Tianyuan

last: Wang

first: Dagoberto

last: Grenet

first: Taylor

last: Wolfgang

first: Pierre

last: Bushel

first: Jianying

last: Li

first: Gonzalo

last: Riadi

first: Douglas

last: Ganini da Silva

first: Richard

middle: P

last: Woychik

middle: H


title: The histone methyltransferase G9a is required for silencing of helper lineage genes in CD8+ T cells

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: During a binary cell fate decision, a progeny silences the gene expression program associated with the alternative fate. Helper versus cytotoxic lineage decision in the thymus has been studied as a model for gene silencing of alternative lineage genes, including Cd4. While RUNX3 is required for the initiation of Cd4 silencing, it remains unknown how silenced states of Cd4 and other helper lineage genes are maintained. We show that the histone methyltransferase G9a is necessary for heritable silencing of Cd4 and other helper lineage genes in CD8 T cells. Despite normal Cd4 downregulation during the development, G9a-deficient CD8 T cells fail to maintain silencing of helper lineage genes when they repeatedly divide under non-inflammatory conditions. However, Cd4 depression is prevented during division driven by elevated TCR signaling and an inflammatory cytokine signaling. These results reveal the requirement for G9a in silencing of helper lineage genes in CD8 T cells and also suggest that CD8 T cells employ an alternative mechanism to maintain their cellular identity during immune responses.

overall_design:
RNA-sequencing on CD4+CD8+ G9a KO, CD4–CD8+ G9a KO, and CD4–CD8+ G9a WT T cells after 4 weeks of proliferation in a lymphopenic environment.
ChIP-sequencing on H3K9me3 IP'ed from Ehmt2+/+ and Ehmt2-/- CD8+ T cells cultured in vitro with antibodies to CD3 and CD28

first: Daniel

last: Verbaro


title: Gene expression analysis upon mtDNA depletion [RNA-seq]

institute: NIEHS

overall_design: We analyzed HEK293 cells in which mtDNA was depleted by doxycycline addition to the medium to turn a dominant negative mitochondrial DNA polymerase (DN-POLG). Samples were analyzed at days 0, 3, 6 and 9 for a total of 4 samples. Each time point was done in three indepedent biological replicates. Time point 0 was used as controls with samples being un-induced.


title: Gene expression analysis upon mtDNA depletion [ChIP-seq]

overall_design: We analyzed HEK293 cells in which mtDNA was depleted by doxycycline addition to the medium to turn a dominant negative mitochondrial DNA polymerase (DN-POLG). Samples were analyzed at days 0, 3, 6 and 9 for a total of 4 samples. Each time point was done in 2 indepedent biological replicates. Time point 0 was used as controls with samples being un-induced.  To determine the TCA cycles effects, HEK293 DN-POLG overexpressing AOX/NDI1 were also included at days 0, 3, 6 and 9 with 2 biological replicates each.


title: Mitochondrial retrograde signaling in mammals is mediated by the transcriptional cofactor GPS2 via direct mitochondria-to-nucleus translocation [RNA-seq]

city: Boston

first: Valentina

last: Perissi

address: 72 E. Concord St

institute: Boston University

summary: As most of the mitochondrial proteome is encoded in the nucleus, mitochondrial functions critically depend on nuclear gene expression and bidirectional mito-nuclear communication. However, mitochondria-to-nucleus communication pathways are incompletely understood. Here, we identify G-Protein Pathway Suppressor 2 (GPS2) as a mediator of mitochondrial retrograde signaling and a key transcriptional activator of nuclear-encoded mitochondrial genes in mammals. GPS2 regulated translocation from mitochondria to nucleus is essential for the transcriptional activation of the nuclear stress response to mitochondrial depolarization and for supporting basal mitochondrial biogenesis in differentiating adipocytes and in brown adipose tissue from mice. In the nucleus, GPS2 recruitment to target gene promoters regulates histone H3K9 demethylation and RNA Polymerase II (POL2) activation through inhibition of Ubc13-mediated ubiquitination. These findings, together, reveal an unexpected layer of regulation of mitochondrial gene transcription, uncover a novel direct mitochondria-nuclear communication pathway and indicate that GPS2 retrograde signaling is a key component of the mitochondrial stress response in mammals.

overall_design: The changes in the gene expression profiles were investigated by RNA-seq, GRO-seq, and ChIP-seq, after the knock-down of GPS2 .

first: Maria

middle: D

last: Cardamone

first: Bogdan

last: Tanasa


title: Mitochondrial retrograde signaling in mammals is mediated by the transcriptional cofactor GPS2 via direct mitochondria-to-nucleus translocation [ChIP-seq]


title: Mitochondrial retrograde signaling in mammals is mediated by the transcriptional cofactor GPS2 via direct mitochondria-to-nucleus translocation


title: Comprehensive identification and spatial mapping of habenular neuronal types using single cell RNAseq

first: Shristi

last: Pandey

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

overall_design: Refer to individual Series


title: Gene expression analysis upon mtDNA depletion

first: Janine

last: Santos


title: Nabiximols treatment in Multiple Sclerosis patients

status: Public on Mar 19 2018

city: Milan

first: Melissa

last: Sorosina

address: via Olgettina 58

department: INSPE

institute: IRCCS San Raffaele Hospital

summary: The aim of the study is to explore the transcriptional changes induced by 4 weeks of Nabiximols treatment in whole blood of multiple sclerosis patients.

overall_design: Total RNA from whole blood was collected from 33 patients affected by multiple sclerosis using the PaxGene System (PreAnalytix). Sample collection was performed at baseline and after 4 weeks of treatment with Nabiximols.

first: Ferdinando

last: Clarelli

first: Filippo

last: Martinelli Boneschi


title: Effects of 21 days of bedrest on human skeletal muscle gene expression

status: Public on Mar 16 2018

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

institute: Karolinska Institutet

summary:
The present study concerns the effects of 21 days of sustained recumbence (bedrest) on skeletal muscle gene expression.
14 male subjects participated in normoxic bedrest (NBR) with muscle unloading, for 21 days, this is a substudy of tha PlanHab-study which apart from normoxic bedrest also involved hyboxic bedrest and hypoxic ambulation  Throughout both bedrest interventions, each subject remained in a horizontal position at all times. He was allowed one pillow for the head and to occasionally lean on an elbow while eating or being transferred to a gurney. Muscular exercise was prohibited. During the HAMB confinement, each subject was allowed to move freely within the hypoxic area. To mimic a normal level of physical activity subjects performed 30 minutes of low-to-moderate-intensity exercise twice daily.    Muscle samples from Vastus lateralis.

overall_design: Biospy material sufficient for anlaysis was available for 12x2 observations


title: Adjuvant associated peripheral-blood mRNA profiles and kinetics induced by the adjuvanted recombinant-protein candidate tuberculosis vaccine M72/AS01 in BCG-vaccinated adults

city: Rixensart

first: Laurane

last: De Mot

address: Rue de l'Institut 89

country: Belgium

institute: GSK Vaccines

summary: Systems biology has the potential to identify gene signatures associated with vaccine immunogenicity or protective efficacy. The main objective of our study was to identify optimal post-vaccination time points for evaluating blood RNA-expression profiles in recipients of the candidate tuberculosis vaccine M72/AS01. In this phase II open-label study (NCT01669096), healthy Bacillus Calmette-Guérin (BCG)-primed, HIV-negative adults were administered two doses (30-days apart) of M72/AS01. Blood samples were collected pre-dose 1, pre-dose 2 and 1, 7, 10, 14, 17 and 30 days post-dose 2. RNA expression in blood and peripheral-blood mononuclear cells (PBMCs) was quantified using microarray technology. The data analysis used as a reference, a PBMC-gene signature that was associated with the protective efficacy of a similarly adjuvanted candidate malaria vaccine. Peripheral-blood CD4+ T-cell reactivity, serum interferon-gamma (IFNG) concentrations and safety were also assessed. Twenty subjects completed the study and 18 subjects received two doses. The observed safety profile was similar to previous trials. Serum IFNG responses and M72-specific CD4+ T cell responses to vaccination were detected as expected, based on previous trial experience. PBMC and whole-blood RNA-expression data at day 14 post-dose 2 relative to pre-vaccination and whole-blood RNA-expression data at 7, 10, and 17 days  post-dose 2 relative to pre-vaccination could be used to classify vaccine recipients into gene-signature positive or gene-signature negative groups. In conclusion, whole blood sampled from the 7, 10, 14, or 17  day post-vaccination time points, in addition to pre-vaccination, could be selected to assess potentially clinically relevant responses to M72/AS01 using transcriptome analysis.

overall_design: There are 50 WB (whole blood) samples and 114 PBMC (pheripheral blood mononuclear cells) samples from 18 distinct human subjects, at various time points during vaccination schedule: subjects are injected with M72/AS01E tuberculosis vaccine candidate at D0 and D30, whole blood samples are collected at D0, D30, D31, D37, D40, D44 and D47 and PBMC samples are collected at D0, D31, D44. There is no replicate, control or reference sample.

first: Robert

last: van den Berg

first: Geert

last: Leroux-Roels

first: Viviane

last: Bechtold

first: Frédéric

last: Clement

first: Margherita

last: Coccia

first: Erik

last: Jongert

first: Thomas

middle: G

last: Evans

first: Paul

last: Gillard

first: Robbert

last: van der Most


title: Bacterial translocation is required for pre-leukemic myeloproliferation in Tet2 deficient mice

status: Public on Mar 15 2018

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

summary: Ten-Eleven-translocation (Tet2) encodes an epigenetic modifier enzyme and is mutated somatically during age-associated clonal hematopoiesis of indeterminate potential (CHIP) as well as in myeloid malignancies 1-7. Tet2 deficiency leads to increased hematopoietic stem cell (HSC) renewal in human 7 and mouse 8. However, the development of myeloproliferation and myeloid malignancies occurs at late age, and only occasionally in humans 2,6,7,9 and in 50-75% of Tet2 deficient animals 8,10,11, suggesting that undefined triggers are required for pre-leukemic myeloid expansion. Our studies reveal that Tet2 deficient mice can exhibit high levels of plasma IL-6, systemic dissemination of indigenous gut bacteria and increased intestinal permeability that correlate with the development of a pre-leukemic myeloproliferative phenotype. Increased intestinal permeability was linked to a large number of transcriptional changes in the jejunum, especially among genes involved in defense response to bacterium and intestinal barrier function. Strikingly, antibiotic treatment reduced plasma IL-6 levels and both, prevented early myeloid expansion and reversed the pre-leukemic myeloproliferative phenotype in Tet2-/- mice. In summary, we show that Tet2 deficiency promotes intestinal bacterial translocation and subsequent systemic inflammation, and that gut-derived microbial signals are required for the development of pre-leukemic myeloproliferation in a Tet2-deficient host. Our studies suggest that controlling bacterial translocation and bacteria-associated systemic inflammation could decrease the risk of myeloid malignancies significantly in individuals with somatic Tet2 mutations.

overall_design: Expression profiles in intestinal tissues from WT and TET2KO mice, before and after ABX treatment

first: Marlies

last: Meisel

first: Reinhard

last: Hinterleitner

first: Manuel

last: Buscarlet

first: Li

last: Chen

first: Joseph

middle: F

last: Pierre

first: Romain

last: Bouziat

first: Jordan

last: Ernest

first: Daina

last: Ringus

first: Benjamin

last: McDonald

first: Vu

last: Dinh

first: Matthew

last: Zurenski

first: Mark

middle: W

last: Musch

first: Glaucia

last: Furtado

first: Sergio

last: Lira

first: Eugene

middle: B

last: Chang

first: Lucy

last: Godley

first: Lambert

last: Busque

first: Luis

last: Barreiro

first: Bana

last: Jabri


title: Gene expression analysis upon mtDNA depletion [methylation]

city: RTP

first: Janine

last: Santos

overall_design: We analyzed HEK293 cells in which mtDNA was depleted by doxycycline addition to the medium to turn a dominant negative mitochondrial DNA polymerase (DN-POLG). Samples were analyzed at days 0, 3, 6 and 9 for a total of 4 samples. Each time point was done in three indepedent biological replicates. Time point 0 was used as controls with samples being un-induced.  To determine the TCA cycles effects, HEK293 DN-POLG overexpressing AOX/NDI1 were also included at days 0 and 9, with 3 biological replicates to each time point.  Nuclear DNA methylation was also evaluated in 143B cells in which mtDNA was chronically depleted based on ethidium bromide treatment. Samples include 3 independent biological replicates of controls (rho+) and 3 of mtDNA depleted (rho0).

first: Oswaldo

last: Lozoya

first: Inmaculada

last: Martinez-Reyes

first: Tianyuan

last: Wang

first: Dagoberto

last: Grenet

first: Taylor

last: Wolfgang

first: Pierre

last: Bushel

first: Jianying

last: Li

first: Gonzalo

last: Riadi

first: Douglas

last: Ganini da Silva

first: Richard

last: Woychik


title: The microRNA-200 family mediates hair follicle development through coordinated regulation of cell adhesion and polarity

city: Boulder

first: Jaimee

last: Hoefert

state: CO

address: 347 UCB

department: MCDB

institute: University of Colorado Boulder

summary: The microRNA-200 family is highly expressed in epithelial cells and frequently lost in metastatic cancer. Although the tumor-suppressing roles of this family are well documented and directly linked to the inhibition of mesenchymal genes, their targets and functions in normal epithelial tissues remain unclear. Furthermore, how the two sub-families of the five-microRNA family distinguished by a single nucleotide within the seed region regulate their targets is unclear. Here we show that the microRNA-200 family governs hair morphogenesis and fine-tunes stem cell specification by regulating cell adhesion, polarity and signaling pathways. By directly ligating microRNAs to their targeted mRNA regions, we identify numerous targets involved in the regulation of actin cytoskeleton, focal adhesion, cell cycle and Hippo/Yap signaling in a miRNA:mRNA pair-specific manner. The two sub-families bind to largely distinct target sites although many genes are regulated by both sub-families for a greater degree of regulation. Using inducible and knockout mouse models, we show that the microRNA-200 family enhances cell adhesion, inhibits migration and reduces cell division, contributing to precise stem cell specification. Our findings demonstrate that combinatorial targeting of many genes is critical for microRNA functions and provide new insights into microRNA-200s’ functions in normal epithelial tissues.

overall_design: Total RNA extracted from hair germ (HG) and interfollicular epidermis (IFE) from pTRE2-200bcl/K14rtTA (Tg) and control (ctrl) animals at P0.5.

first: Rui

last: Yi


title: Distinct distribution of H3K27me3 and DNA methylation stabilizes the segregation of extraembryonic and embryonic lineages

city: Shanghai City

first: Naihe

last: Jing

address: Yueyang Road 320

institute: shanghai institute of biochemistry and cell biology

summary: One of the most important topic in mammalian embryogenesis is cell lineage segregation. Briefly, one totipotent zygote will develop into inner cell mass (ICM) and trophectoderm (TE) at blastocyst stage, then the ICM will finally develop into multiple somatic cell lineages and TE will majorly become the placenta tissue which supports and protects the development of the embryo proper. Multiple extrinsic and intrinsic regulatory pathways are involved in facilitating the appropriate development of the embryo. Epigenetic reprogramming is one of the most pervasive events during mouse embryo development(Li, 2002). Recent studies had implied that distinct features for the establishment of DNA methylation(Monk et al., 1987) and histone modifications especially H3K27me3(Liu et al., 2016) during mouse early embryo development. The re-establishment of DNA methylation in early mouse embryos starts at blastocyst stage (about embryonic day 3.5, E3.5) and peaks around the gastrulation stage, while the re-establishment of H3K27me3 exhibits a great level of dynamics and gradually increased CpG preference during pre-implantation embryo development(Liu et al., 2016). However, the underlying epigenetic mechanism concerning the lineage segregation and developmental competence restriction between the pluripotent embryo proper and the supporting extraembryonic tissues especially extraembryonic ectoderm (ExE) remains largely unknown. Surprisingly, no significant difference exists for the distribution of H3K27me3 and DNA methylation between ICM and TE in the preimplantation embryos. Therefore, it is of great importance for unveiling the interplays between H3K27me3 and DNA methylation involving in the restriction of developmental competence between embryonic cells and extraembryonic cells in post-implantation embryos.

overall_design:
To obtain a comprehensive epigenetic mechanism of mouse embryo development and the corresponding lineage development process, we have dissected mouse gastrula from pre-steak stage (E6.5) to late streak stage (E7.5) into extra-embryonic (ExE) and embryonic parts, and embryonic parts of E7.0 and E7.5 embryos will be further divided into sub-regions (anterior (A), posterior (P), anterior mesoderm (AM)) due to the emergence of embryo asymmetry.

Please note that each '*repMerge.fc.signal.bw' processed data was generated from two *IP-K27me3 replicate samples together and is linked to the corresponding *rep2 sample records.

first: Xianfa

last: Yang

first: Boqiang

last: Hu

first: Yu

last: Hou

first: Yunbo

last: Qiao

first: Fuchou

last: Tang


title: The cis-regulatory dynamics of embryonic development at single cell resolution

city: Tucson

first: Darren

middle: A.

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

institute: University of Arizona

summary: Single cell measurements of gene expression are providing new insights into lineage commitment, yet the regulatory changes underlying individual cell trajectories remain elusive. Here, we profiled chromatin accessibility in over 20,000 single nuclei across multiple stages of Drosophila embryogenesis. Our data reveal heterogeneity in the regulatory landscape prior to gastrulation that reflects anatomical position, a feature that aligns with future cell fate. During mid embryogenesis, tissue granularity emerges such that cell types can be inferred by their chromatin accessibility, while maintaining a signature of their germ layer of origin. We identify over 30,000 distal elements with tissue-specific accessibility. Using transgenic embryos, we tested the germ layer specificity of a subset of predicted enhancers, achieving near-perfect accuracy. Overall, these data demonstrate the power of shotgun single cell profiling of embryos to resolve dynamic changes in open chromatin during development, and to uncover the cis-regulatory programs of germ layers and cell types.

overall_design: sci-ATAC-seq data was collected on whole Drosophila embryos collected from 3 time points - 2 to 4 hours after egg laying (AEL), 6 to 8 hours AEL, and 10 to 12 hours AEL). In total, we collected data on 23,086 individual cells. Custom scripts for processing data are available at https://github.com/shendurelab/fly-atac.  This series includes bulk DNAse-seq samples from wildtype, elav+, or Mef2+ 6-8 hr embryonic nuclei.

first: James

last: Reddington

first: David

last: Garfield

first: Riza

last: Daza

first: Delasa

last: Aghamirzaie

first: Raquel

last: Marco-Ferreres

first: Hannah

last: Pliner

first: Lena

last: Christiansen

first: Xiaojie

last: Qiu

first: Frank

last: Steemers

first: Cole

last: Trapnell

first: Jay

last: Shendure

first: Eileen

last: Furlong


title: Expression data from WT and Ezh2-deficient macrophages non-treated (NT) or stimulated for 2 h with LPS

city: Shanghai

first: Xingli

last: Zhang

address: yueyang road 320

institute: Institute of Health Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences

summary: we conducted gene expression profile analysis by using WT and Ezh2-deficient bone marrow-derived macrophages.Gene ontology (GO) analysis revealed the most prominent biological processes altered in macrophages upon LPS stimulation were associated with immune system process.

overall_design: Genome-wide expression profiling of WT and Ezh2-deficient macrophages non-treated (NT) or stimulated for 2 h with LPS were generated by RNA-sequencing analysis

first: Yichuan

last: Xiao


title: EZH2 occupancy profiling by high throughput sequencing from  macrophages non-treated (NT) or stimulated with LPS

summary: To identify the potential genes that regulated by Ezh2, we immunoprecipitated chromatin from macrophages stimulated with or without LPS, and analyzed the precipitated DNA with deep sequencing (CHIP-Seq).

overall_design: To examine EZH2 modification in macrophages,the chromatin of  macrophages non-treated (NT) or stimulated for 2 h with LPS was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against EZH2 ( Active Motif 39901).


title: Bifidobacterium breve UCC2003 employs multiple transcriptional regulators in a series of glycan-induced positive feedback loops to regulate HMO metabolism

status: Public on Mar 14 2018

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

summary: Regulation of carbohydrate metabolism in Bifidobacterium breve has been studied in detail for a variety of both plant and human-derived glycans, particularly in the model strain UCC2003. We have recently comprehensively elucidated the precise metabolic pathways by which the human milk oligosaccharide (HMO) components LNT, LNnT and LNB are utilized by B. breve UCC2003. However, no work has been carried out to date in identifying and understanding the regulatory mechanisms that control transcription of the genetic loci involved in these metabolic pathways. In the current study, we identified and characterized several transcriptional regulators involved in controlling the expression of HMO loci, and the regulatory sequences of each locus required for these regulatory mechanisms. A series of positive feedback loops inducing the expression of each locus, with the function of each regulator itself dependent on the presence of the specific monosaccharide metabolite released by the breakdown of the glycan targeted by the individual locus controlled by each respective regulator. Furthermore, we dissect the regulatory regions of each affected gene, and identify the key features within them.

overall_design: DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003 were designed by and obtained from Agilent Technologies (Palo Alto, Ca., USA). Methods for cell disruption, RNA isolation, RNA quality control, complementary DNA synthesis and labeling were performed as described previously (van Hijum et al., 2005). Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described (Garcia De La Nava et al., 2003). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long et al., 2001). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.

first: Kieran

last: James


title: The Arabidopsis transcription factor TCP5 during petal and inflorescence development

first: Sam

middle: Wijnand

last: van Es

address: Droevendaalsesteeg

department: Plant Developmental Systems

institute: Wageningen University and Research

summary: RNA-sequencing performed on petals and inflorescence of Arabidopsis plants. The study provides insight into the role of the TCP5 transcription factor and its molecular mechanism underlying petal growth, using knock-out, overexpression and induction lines on which RNA-sequencing was performed.

overall_design: Analysis of differential gene expression using petals from TCP5 overexpression and knockout lines, as well as inflorescences of an inducible TCP5 mutant.

first: Richard

last: Immink

first: Gerco

middle: C

last: Angenent


title: T cell activation in skin explants from patients with psoriasis and controls

city: besancon

first: irène

last: gallais sérézal

address: boulevard stalingrad

institute: CHU Besançon

summary: We have worked on skin explants and activated T cells locally with a CD3 antibody, whole biopsies were activated, then epidermal and dermal RNA was sequenced. Sequencing was performed by BGI (Hong Kong) as well as the group analysis.

overall_design: Examination of skin tissue responses to local T cell activation (acd3) compared to isotype at the RNA level. Samples include biopsies from healthy controls and patients with psoriasis treated with Ustekinumab or untreated lesional psoriasis. All biopsy samples were treated either with acd3 or with isotype as indicated.

first: Irène

last: Gallais Sérézal

first: Liv

last: Eidsmo


title: A multi-omic analysis reveals a regulatory role of CD180 during the response of macrophages to Borrelia burgdorferi

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE


title: Epigenome analysis reveals novel aspects of ILC2 activation and supports a pathogenic role in asthma

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

institute: Erasmus Medical Center

summary: Recent studies have shown that group 2 innate lymphoid cells (ILC2s) can drive eosinophilic airway inflammation in mouse models of asthma. Moreover, elevated ILC2 counts and/or activity have been reported in asthmatics, together suggesting that ILC2s play an important role in asthma pathophysiology. However, many aspects of ILC2 biology are not fully understood, including the mechanisms underlying ILC2 activation, the tissue-specific functions of ILC2s during inflammation (e.g. lung versus draining lymph node) and what drives ILC2 plasticity. Importantly, it is unknown whether human (epi)genetic variation associated with asthma susceptibility and persistence can be coupled to ILC2s. We address these questions in our manuscript by studying the epigenome of murine ILC2s obtained from Gata3-reporter mice with eosinophilic airway inflammation as well as human ILC2s obtained from peripheral blood and activated in vitro.

overall_design: biological replicate (n=2-4) RNA-Seq and ChIPmentation experiments including negative controls

first: Rudi

last: Hendriks


title: Expression data from renal cortexes of diabetic rats

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
Angiotensin II is a key factor driving diabetic nephroparthy via ist AT1R. The role of ist AT2R in diabetic nephropathy is less known, however assumed to be renoprotective
We used microarray data to study the effect of transgenic renal AT2R overexpression on the renal expression profile at early stages of diabetes

overall_design: In transgenic rats overexpressing the AT2R and wildtype rats diabetes was induced  by streptozotocin injection. Kidneys were harvested 28 days therafter for RNA isolation. Nondiabetic transgenic and wildtype rats served as controls.

first: Sigrid

last: Hoffmann

first: Tamara

last: Micakovic


title: Next Generation Sequencing Facilitates Quantitative Analysis of  Transcriptomes of neural stem/progenitor cells (NS/PCs) in control and prenatal valproic acid (VPA) exposed mice with or without voluntary exercise

city: Ikoma

first: Taito

last: Matsuda

institute: Nara Institute of Science and Technology

summary:
Purpose: The goals of this study are to investigate the effect of prenatal VPA exposure on transcriptome profile of NS/PCs during development, and the effect of exercise on transcriptome profile of adult NS/PCs in prenatal VPA exposed mice.
Methods: NS/PCs mRNA profiles of embryonic day15 (E15), postnatal day5 (P5) and 12-week-old (12w) contol mice and E15, P5, 12w with or without voluntary exercise  prenatal VPA exposed mice were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with a method: TopHat/Bowtie2 followed by Cufflinks.NS/PCs were isolated from forebrain (E15), hippocampal dentate gyrus (P5 and 12w) of Nestin-EGFP mice.
Results: Hierarchial clustering using eighteen samples (E15 Ctrl, E15 VPA, P5 Ctrl, P5 VPA, 12w Ctrl, 12w VPA, three samples each) identified three distinct clusters composed of NS/PCs derived from each developmental stage. Gene set enrichment analysis using transcriptome of E15 Ctrl and E15 VPA revealed a significant increase in the expression of neuron differentiation- and nervous system development-related genes in VPA compared with Ctrl. Gene ontology analysis of biological processes using differentially expressed genesin 12w VPA compared with 12w Ctrl revealed that expression levels of cell-migration-associated genes were altered. Voluntary running mostly amended both positively and negativly distorted gene expression in the 12w VPA compared with 12w Ctrl NS/PCs. The altered expression of cell migration-related genes was largely normalized by voluntary running.

overall_design: NS/PCs mRNA profiles of E15, P5 and 12w old control and prenatal VPA exposed mice were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500. In addition, NS/PCs mRNA profiles of 12w prenatal VPA mice with voluntary exercise was generated by deep sequencing, in triplicate, using Illumina Hiseq 2500.

first: T

first: A

last: Sakai

first: K

last: Nakashima


title: A multi-omic analysis reveals a regulatory role of CD180 during the response of macrophages to Borrelia burgdorferi [microarray]

summary: Macrophages are cells of the innate immune system with the ability to phagocytose and induce a global pattern of responses that depend on several signalling pathways. We have determined the biosignature of murine bone marrow-derived macrophages and human blood monocytes using transcriptomics and proteomics approaches. We identified a common pattern of genes transcriptionally regulated that overall indicate that the response to B. burgdorferi involves the interaction of spirochetal antigens with several inflammatory pathways corresponding to primary (triggered by pattern recognition receptors) and secondary (induced by proinflammatory cytokines) responses. We also show that the Toll-like receptor family member, CD180 is downregulated by the stimulation of macrophages, but not monocytes, with the spirochete. Silencing Cd180 results in increased phagocytosis while tempering the production of the proinflammatory cytokine, TNF. Cd180-silenced cells produced increased levels of Itgam and surface CD11b, suggesting that the regulation of CD180 by the spirochete initiates a cascade that increases the CR3-mediated phagocytosis of the bacterium while repressing the consequent inflammatory response.

overall_design: Genome-wide changes in gene expression of normal human monocytes stimulated with Borrelia burgdorferi or left unstimulated were generated by microarray gene expression arrays.

first: Juan

last: Anguita

last: Lavín


title: Macrophage/microglial Ezh2 facilitates autoimmune inflammation through inhibition of Socs3

first: Xingli

last: Zhang

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

overall_design: Refer to individual Series


title: Allele-specific expression in a family quartet with autism reveals mono-to-biallelic switch and novel transcriptional processes

city: Taipei

first: Hsien-Sung

last: Huang

address: Rm: 1547, 15th Floor, No.1, Sec.1, Ren-ai Rd.

country: Taiwan

institute: National Taiwan University

summary: Autism spectrum disorder (ASD) is a highly prevalent neurodevelopmental disorder, and the exact causal mechanism is unknown. Dysregulated allele-specific expression (ASE) has been identified in persons with ASD; however, a comprehensive analysis of ASE has not been conducted in a family quartet with ASD. To fill this gap, we analyzed ASE using genomic DNA from parent and offspring and RNA from offspring’s postmortem prefrontal cortex (PFC); one of the two offspring had been diagnosed with ASD. DNA- and RNA-sequencing revealed distinct ASE patterns from both offspring PFC. However only the PFC of the offspring with ASD exhibited a mono-to-biallelic switch for LRP2BP and ZNF407. We also identified novel RNA-editing and monoallelically-expressed genes and miRNAs. Our results demonstrate the prevalence of ASE in human PFC and ASE abnormalities in the PFC of a person with ASD. Taken together, these findings may provide mechanistic insights into the pathogenesis of ASD.

overall_design: We performed RNA-Seq on prefrontal cortex from subjects without and with autism and DNA-Seq on their and their parents' genomic DNA


title: DNA microarray analysis of Jmjd1a and/or Jmjd1b knockout embryonic stem cells

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: Histone H3 lysine 9 (H3K9) methylation is an epigenetic mark of transcriptionally repressed chromatin. During mammalian development, H3K9 methylation levels seem to be spatiotemporally regulated by the opposing activities of methyltransferases and demethylases to govern correct gene expression. However, the combination(s) of H3K9 methyltransferase(s) and demethylase(s) that contribute to this regulation and the genes regulated by them remain unclear. Herein, we demonstrate the essential roles of H3K9 demethylases Jmjd1a and Jmjd1b in the embryogenesis and viability control of embryonic stem (ES) cells. Mouse embryos lacking Jmjd1a/Jmjd1b died after implantation. Depletion of Jmjd1a/Jmjd1b in mouse ES cells induced rapid cell death accompanied with a massive increase in H3K9 methylation. Jmjd1a/Jmjd1b depletion induced an increase in H3K9 methylation in the gene-rich regions of the chromosomes, indicating that Jmjd1a/Jmjd1b removes H3K9 methylation marks in the euchromatin. Importantly, the additional disruption of the H3K9 methyltransferase G9a in a Jmjd1a/Jmjd1b-deficient background rescued not only the H3K9 hypermethylation phenotype but also the cell death phenotype. We also found that Jmjd1a/Jmjd1b removes H3K9 methylation marks deposited by G9a in the Oct4 and Ccnd1 loci to activate transcription. In conclusion, Jmjd1a/Jmjd1b ensures ES cell viability by antagonizing G9a-mediated H3K9 hypermethylation in the gene-rich euchromatin.

overall_design: Jmjd1b-conditional targeting vector was constructed using the BAC recombineering technique and introduced into the Jmjd1bΔ/+ ES cell line 2b-11. Homologous recombination was confirmed by Southern blot analysis with the aforementioned probe. The homologous recombinant ES cell line YY90 (genotype: Jmjd1bΔ/2lox2FRT) was used for further evaluation. The Jmjd1b-deficient ES cell lines, D23.6 and D4.1 (genotype: Jmjd1bΔ/1lox2FRT), were established from a pool of YY90 cells infected with Cre-expressing recombinant adenoviruses. Jmjd1b conditional targeting vector was introduced into the Jmjd1a-deficient ES line 31-1 (Inagaki et al. 2009, Genes Cells 14: 991-1001). The expression plasmid for MerCreMer was then introduced into the recombinant ES cell lines #117 and #131 (genotype: Jmjd1aΔ/Δ; Jmjd1b2lox1FRT/2lox2FRT).

first: Shunsuke

last: Kuroki

first: Ryo

last: Maeda

first: Naoki

last: Okashita

first: Mika

last: Akiyoshi

first: Yutaro

last: Yamaguchi

first: Satsuki

last: Kitano

first: Hitoshi

last: Miyachi

first: Ryuichiro

last: Nakato

first: Kenji

last: Ichiyanagi

first: Katsuhiko

last: Shirahige

first: Hiroshi

last: Kimura

first: Yoichi

last: Shinkai

first: Makoto

last: Tachibana


title: Effect of CBL0137 on nascent transcription in HT1080 cells [RNA-seq]

status: Public on Mar 13 2018

city: Buffalo

first: Katerina

last: Gurova

state: NY

address: Elm and Carlton Str

department: Cell Stress Biology

institute: Roswell Park Cancer Institute

summary:
Small molecule curaxin CBL0137 has broad anti-cancer activity in different preclinical models. It interferes with histone-DNA interactions via binding to DNA without causing DNA damage. It resposents first in class "chromatin damaging" agent without genotoxic properties. Its effect on the transcription in human tumor cells was evaluated.
DNA-targeting small molecules are widely used for anticancer therapy based on their ability to induce cell death, presumably via DNA damage. DNA in the eukaryotic cell is packed into chromatin, a highly-ordered complex of DNA, histones, and non-histone proteins. These agents perturb chromatin organization. However, the mechanisms, consequences, and impact of the alterations of chromatin structure in relation to their anti-cancer activity is unclear because it is difficult to separate DNA damage and    chromatin damage    in cells. We recently demonstrated that curaxins, small molecules with broad anticancer activity, bind DNA without causing detectable DNA damage by interfering with histone/DNA interactions and destabilizing the nucleosome. Chromatin unfolding caused by curaxins is sensed by histone chaperone FACT. FACT binds unfolded nucleosomes, which leads to    chromatin trapping    or c-trapping. In this study, we investigated whether other DNA-targeting small molecules disturb chromatin and cause c-trapping. We found that only compounds directly binding DNA induce    chromatin damage    and c-trapping. Chromatin damage may occur in the absence of DNA damage and is dependent on the mechanism of compound binding to DNA and its ability to bind chromatinized DNA in cells. We show that FACT is sensitive to a plethora of nucleosomes perturbations induced by DNA-binding small molecules, including displacement of the linker histone, eviction of core histones, and accumulation of negative supercoiling. Most importantly, the cytotoxicity of DNA-binding small molecules correlates with their ability to cause    chromatin damage   , but not DNA damage.

overall_design: HT1080 cells were treated with CBL0137 for 1 hour at 1uM. EU was added for the last 15 minutes. Newly synthesized RNA was isolated using Click-iT™ Nascent RNA Capture Kit (Invitrogen, cat#C10365) according to manufacturer instruction.


title: Primary osteoporosis is not reflected by disease-specific DNA methylation or accelerated epigenetic age in blood

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

summary: Osteoporosis is an age-related metabolic bone disease. Hence, osteoporotic patients might suffer from molecular features of accelerated aging, which is generally reflected by specific age-associated DNA methylation (DNAm) changes. In this study, we analyzed genome wide DNAm profiles of peripheral blood from patients with manifest primary osteoporosis and non-osteoporotic controls. Statistical analysis did not reveal any individual CG dinucleotides (CpG sites) with significant aberrant DNAm in osteoporosis. Subsequently, we analyzed if age-associated DNAm patterns are increased in OP. Using three independent age-predictors we did not find any evidence for accelerated epigenetic age in blood of osteoporotic patients. Taken together, osteoporosis is not reflected by characteristic DNAm patterns of peripheral blood that might be used as biomarker for the disease. The prevalence of osteoporosis is age-associated – but it is not associated with premature epigenetic aging in peripheral blood.

overall_design: Illumina Infinium 450k Human Methylation Beadchip analysis of whole peripheral blood from primary osteoporotic patients and control individuals.

first: Eduardo

last: Fernandez-Rebollo

first: Monika

last: Eipel

first: Lothar

last: Seefried

first: Per

last: Hofmann

first: Klaus

last: Strathmann

first: Franz

last: Jakob


title: Cardiac gene expression in chromograninA and catestatin knockout mice

city: La Jolla

first: Nick

last: Webster

state: CA

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

summary: Investigation of whole genome gene expression in left ventricular tissue from hearts of wild-type, chromogranin A knockout,  and catestatin knockout mice

overall_design: A 12x135K array study using total RNA from hearts of mixed 129svJ/C57BL/6 (50:50) mice

first: Sushil

last: Mahata

first: Nicholas


title: Metastasis in triple-negative breast cancer

city: Melbourne

first: Andrew

last: Pattison

state: Vic

address: Wellington Rd

country: Australia

institute: Monash University


title: Effect of DNA bindng small molecules on SSRP1 genomic distribution

summary:
Small molecules directly binding DNA in cells destabilized chromatin what is "sensed" by histone chaperone FACT. FACT binds regions with destabilized chromatin via "c-trapping".
DNA-targeting small molecules are widely used for anticancer therapy based on their ability to induce cell death, presumably via DNA damage. DNA in the eukaryotic cell is packed into chromatin, a highly-ordered complex of DNA, histones, and non-histone proteins. These agents perturb chromatin organization. However, the mechanisms, consequences, and impact of the alterations of chromatin structure in relation to their anti-cancer activity is unclear because it is difficult to separate DNA damage and    chromatin damage    in cells. We recently demonstrated that curaxins, small molecules with broad anticancer activity, bind DNA without causing detectable DNA damage by interfering with histone/DNA interactions and destabilizing the nucleosome. Chromatin unfolding caused by curaxins is sensed by histone chaperone FACT. FACT binds unfolded nucleosomes, which leads to    chromatin trapping    or c-trapping. In this study, we investigated whether other DNA-targeting small molecules disturb chromatin and cause c-trapping. We found that only compounds directly binding DNA induce    chromatin damage    and c-trapping. Chromatin damage may occur in the absence of DNA damage and is dependent on the mechanism of compound binding to DNA and its ability to bind chromatinized DNA in cells. We show that FACT is sensitive to a plethora of nucleosomes perturbations induced by DNA-binding small molecules, including displacement of the linker histone, eviction of core histones, and accumulation of negative supercoiling. Most importantly, the cytotoxicity of DNA-binding small molecules correlates with their ability to cause chromatin damage, but not DNA damage.

overall_design: HT1080 cells were treated with 3uM of CBL0137, 0.3uM of CBL0100 or 3uM of aclacinomycin A for 1.5 hours

first: Jianmin

last: Wang