title: Lsd1 is an essential regulator of the chromatin and transcriptional landscapes during the maternal-to-zygotic

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

summary: How the parental genomes of the very specialized sperm and oocyte cells are remodelled upon fertilization to confer totipotency has remained a tantalizing open questions. Indeed, in the case of mammals, the parental genomes undergo dramatic reprogramming upon fertilization, including differential dynamics of histone post-translational modifications. The roles of histone modifying enzymes in this process, which are maternally provided, are only just starting to emerge. Here, we explore the function of the oocyte inherited pool of Lsd1/Kdm1a, which encodes a histone H3K4 and K9 demethylase, during early mouse development. Maternal deficiency of Lsd1/Kdm1a results in developmental arrest by the two-cell stage, associated with dramatic and stepwise alterations in H3K9 and H3K4 methylation patterns depending on its demethylase activity. At the transcriptional level, two major changes occur. On one hand, switch from maternal-to-zygotic program fails to be induced. On the other hand, LINE-1 retrotransposons are not properly silenced, along with evidences for increased LINE-1 activity. We propose that Lsd1/Kdm1a is involved in the correct establishment of epigenetic information harboured by histones and is involved in the initiation of new pattern of genome expression driving early mouse development and preserving genome integrity

overall_design: RNA-seq of invidual mouse oocytes

first: K

last: Ancelin

first: I

last: Vassilev

first: C

last: Chen

first: E

last: Heard


title: CIPHER: An extensive and flexible processing platform for next-generation sequencing data and de-novo enhancer discovery

status: Public on Nov 16 2016

city: Dallas

first: Ivan

last: D'Orso

state: TX

address: 5323 Harry Hines

department: Microbiology

country: USA

institute: UT Southwestern Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report a unified tool that can be used to process a broad range of sequencing datasets and it's use in identifying transcriptional enhancers

overall_design: Identification and analysis of transcriptional enhancers in two different chromatin states

first: Carlos

last: Guzman


title: Anti-obesity effect of radix Angelica sinensis and candidate causative genes in transcriptome analyses of adipose tissues in high-fat diet-induced mice

status: Public on Nov 15 2016

city: Chengdu

first: Tao

last: Zhong

state: Sichuan

address: No. 211 Huimin Road, Wenjiang District

country: China

institute: Sichuan Agricultural University

type: Expression profiling by high throughput sequencing

summary: We have previously reported that radix Angelica sinensis (RAS) suppressed body weight and altered FTO expression in mice with high fat diet (HFD)-induced obesity. In the present study we performed RNA sequencing-mediated transcriptome analysis to elucidate the molecular mechanisms underlying the anti-obesogenic effects of RAS in mice. The results revealed that 36 differentially-expressed genes (DEGs) were identified between the RAS supplementation group (DH) and control group (HC). These 36 DEGs were clustered into 297 functional gene ontology (GO) categories, among which several GO annotations and signaling pathways were associated with lipid homeostasis. Six out of the 36 DEGs were identified to be involved in lipid metabolism, with the APOA2 gene a potential anti-obesogenic influence. The expression pattern revealed by RNA-Seq was identical to the results of quantitative real-time PCR (qPCR). Therefore, RAS supplementation in HFD-induced obese mice was associated with an anti-obesogenic global transcriptomic response. This study provides insight into potential applications of RAS in obesity therapy.

overall_design: Examination ofdifferentially-expressed genes in 2 groups.

first: Lili

last: Niu


title: RNA-Seq gene profiling comparison from human cDC subsets and pre-cDC subsets

city: Sao Paulo

first: Israel

middle: Tojal da

last: Silva

state: SP

address: Tagua, 440

country: Brazil

institute: HOSPITAL A C CAMARGO

summary: The goal of this study is to compare the gene profiling of human blood BDCA-1+ cDCs, blood BDCA-3+ cDCs, CB CD172a-pre-cDCs and CB CB172a+ pre-cDCs.  RNA from sorted populations was extracted and column-purified using the Arcturus PicoPure RNA Isolation kit (Applied Biosystems). Genomic DNA was removed by on-column digest with DNAse I (Qiagen), according to the PicoPure RNA Isolation kit manual. RNA libraries were prepared using the SMARTer Ultra Low Input RNA for Sequencing kit (Clontech Laboratories) followed with Nextera XT DNA Library Prep kit (Illumina).  Libraries were sequenced by 75-bp single-end reading on a NextSeq 500 sequencer (Illumina). Our results show that CD172a+ and CD172a- pre-cDCs represent developmentally discrete populations that differentially express lineage-restricted transcription factors. Moreover CD172a- pre-cDCs cluster with BDCA-3hi cDCs and CD172a+ pre-cDCs with BDCA-1+ cDCs.

overall_design: RNA from sorted cord blood pre-cDC subsets (150-400 cells) and peripheral blood cDC subsets (2000-10000 cells). Done in quadruplicate.

first: Gaelle

last: Breton

last: Tojal da Silva

first: Renan

last: Valieris


title: Dynamics of Human and Viral RNA Methylation during ZIKA Virus Infection

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

summary: Human infection with the flavivirus ZIKA (ZIKV) causes severe neurological, immunological, and developmental defects. Despite recent progress, the mechanisms by which ZIKV infection alters host transcriptional and translational programs remains unclear. Here, we report that ZIKV infection has profound effects on the topology and function of N6-adenosine methylation (m6A) of both viral and human RNAs. m6A and 2′-O-methylated nucleosides are abundant in ZIKV genomic RNA, and m6A-seq identified 12 m6A peaks spanning the full length of ZIKV RNA. m6A abundance in ZIKV RNA is controlled by the host methyltransferases METTL3 and METTL14 and the demethylase ALKBH5. Profiling of the m6A methylome of host mRNAs revealed that ZIKV infection alters the location of m6A in mRNAs, the methylation motifs, and the target genes modified by the methyltransferases. Our results identify a new mechanism by which ZIKV interacts with and alters the function of the host cell.

sample_organism:
Homo sapiens
Zika virus

platform_organism:
Homo sapiens
Zika virus

overall_design: m6A-seq of virus genomic RNA and mRNA from human cells infected with virus.

first: Boxuan

middle: S

last: Zhao

first: Chuan

last: He


title: Auxin production in the endosperm drives seed coat development in Arabidopsis

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

type: Expression profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Regulatory T cells exhibit distinct features in human breast cancer

city: New York

first: Catherine

last: Konopacki

state: NY

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary: The goal of this study is to compare transcriptional profiles of regulatory T cells and conventional CD4 T cells in human breast cancer to regulatory T cells and conventional CD4 T cells in normal breast parenchyma and in peripheral blood.

overall_design: RNA sequencing of 2 different cell types in 3 different tissues

first: George

last: Plitas

first: Kenmin

last: Wu

first: Paula

last: Bos

first: Monica

last: Morrow

first: Ekaterina

middle: V

last: Putintseva

first: Dmitriy

middle: M

last: Chudakov

first: Alexander

middle: Y

last: Rudensky


title: A cost-effective RNA sequencing protocol for large-scale gene expression studies

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

summary: We present a simple RNA sequencing protocol with substantially reduced costs.

overall_design: This protocol uses as little as 10 ng of total RNA, allows multiplex sequencing of up to 96 samples per lane, and is strand specific. H1p16 (3 replicates) and H1p43 (3 replicates) are sequenced by Illumina TruSeq. Lane1 - Lane 4 are sequenced by LM-Seq (Hou, Zhonggang, et al. 2015). Lane 1 - Lane 4 samples are multiplexed by 95, 48, 24 and 6 samples per lane, respectively.

first: Zhonggang

last: Hou

first: Scott

last: Swanson

first: Angela

last: Elwell

first: Bao

middle: K

last: Nguyen

first: Jennifer

last: Bolin

first: Ron

last: Stewart

first: James

middle: A

last: Thomson


title: DNA methylation is required for chromatin binding by Mbd2 and Mbd3 in ES cells (ChIP-Seq)

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

summary: Cytosine methylation on DNA is an important epigenetic and regulatory mark. Chromatin remodeling complexes containing methyl-CpG binding domain (MBD) proteins modulate chromatin structure and transcription at methylated loci. Two MBD proteins, Mbd2 and Mbd3, are mutually exclusive members of the NuRD chromatin remodeling complex, and have been shown to bind methylated or hydroxymethylated DNA, respectively. However, a recent study called both results into question, showing that chromatin binding by these proteins is partially (Mbd2) or completely (Mbd3) independent of DNA methylation/hydroxymethylation. Here we re-analyze these data and observe discrepancies with both conclusions. Furthermore, we describe multiple new datasets that demonstrate the dependence of endogenous Mbd2 and Mbd3 on DNA methylation. Interestingly, we find that Mbd2 and Mbd3 are also dependent on one another for binding, likely due to the fact that both are required for normal levels of DNA methylation/hydroxymethylation. These findings describe a regulatory loop controlling the DNA methylation machinery and its readers.

overall_design: Examine Mbd2 and Mbd3 occupancy (ChIP-seq) in ES cells

first: Kurtis

middle: N

last: McCannell

first: Jun

last: Yu

first: Ly-Sha

last: Ee

first: Lihua

last: Zhu

first: Oliver

last: Rando

first: Thomas

middle: G

last: Fazzio


title: A Druggable TCF4- and BRD4-dependent Transcriptional Network Sustains Malignancy in Blastic Plasmacytoid Dendritic Cell Neoplasm (ATAC-Seq)

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive and largely incurable hematologic malignancy originating from plasmacytoid dendritic cells (pDCs). Using RNA interference screening, we identified the E-box transcription factor TCF4 as a master regulator of the BPDCN oncogenic program. TCF4 served as a faithful diagnostic marker of BPDCN, and its downregulation caused the loss of the BPDCN-specific expression program and apoptosis. High-throughput drug screening revealed that bromodomain and extra-terminal domain inhibitors (BETi's) induce BPDCN apoptosis, which was attributable to disruption of the TCF4-dependent transcriptional network and loss of BPDCN-specific super-enhancers. BETi's retarded the growth of BPDCN xenografts, supporting their clinical evaluation in this recalcitrant malignancy.

overall_design: We performed ATAC-Seq to measure chromatin accessibility in normal pDCs (n=2) and primary BPDCN (n=1), together with BPDCN cell lines (Cal-1 and Gen2.2) (n=2), AML cell lines (HL-60 and MOLM-14) (n=2) and conventional myeloid DCs (n=2) as specificity controls.


title: Expression data of agl62/- and wild-type seeds at 30 hrs after pollination

first: Juan

last: Santos-González

summary: We generated deep sequencing data of total RNA isolated from seeds of homozygous agl62 mutants plants at 30 hrs after pollination.

overall_design: agl62 and wild-type plants were emasculated 1-2 days prior to anthesis, hand-pollinated and seeds were harvested 30 h after pollination. Three biological replicates were generated per sample.

first: Pawel

last: Roszak

first: Claudia

last: Köhler


title: Mapping of Long-Range Chromatin Interactions using Proximity Ligation Assisted ChIP-seq

city: La Jolla

first: Rongxin

last: Fang

state: CA

institute: Ludwig Institute for Cancer Research

summary: We report Proximity Ligation Assisted ChIP-sequencing (PLAC-seq), a method for comprehensive detection of long-range interactions associated with proteins of interest. PLAC-seq requires up to 500-fold less starting material compared to ChIA-PET and using experimentally determined input as control precisely reveals protein associated interaction upto single-element resolution. Application of PLAC-seq to mouse embryonic stem cells revealed a comprehensive map of regulatory interactions.

overall_design:
PLAC-seq experiments against H3k4me3 (2M cells), Pol2 (5M cells), H3k27ac (0.5M, 2.5M cells) and in situ Hi-C experiment in mouse embryonic stem cell (F123)

PLAC-Seq data can be visualized at 3D Genome Browser (3dgenome.org)

first: Miao

first: Bing

last: Ren


title: Single-cell RNA-seq reveals heterogeneity within human pre-cDCs

city: NEW YORK

first: Thiago

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

summary: Here, we use a microfluidics-based approach to prepare single-cell RNA-Seq libraries from 164 primary human conventional dendritic cells (cDCs) as well as cord blood (452) and blood (341) pre-cDCs. We examined heterogeneity between individual cells to document potential subpopulations within human cDCs and pre-cDCs.

overall_design:
RNA seq libraries from 957 single cells were prepared using the SMART-Seq 2 protocol (Picelli et al., 2013)
341 Blood pre-cDC (Blood pre-cDC_S* data columns in the expMatrix.txt)
452 CB pre-cDC (CB pre-cDC_S* data columns in the expMatrix.txt)
87 CD141+ cDC (blood_bdca3_S* data columns in the expMatrix.txt)
77 CD1c+ cDC (blood_bdca1_S* data columns in the expMatrix.txt)

first: Rahul

last: Satija


title: A Druggable TCF4- and BRD4-dependent Transcriptional Network Sustains Malignancy in Blastic Plasmacytoid Dendritic Cell Neoplasm (RNA-Seq)

overall_design: We performed RNA sequencing (RNA-Seq) on the 6 FFPE BPDCN biopsies for which the FFPE RNA was not excessively degraded. Because only one PHN and none of the primary AML cases passed the RNA QC for library generation, we embedded BPDCN cell lines (Cal-1 and Gen2.2) and AML cell lines (HL-60, MOLM-14 and SKM-1) in paraffin blocks after formalin fixation, and used the FFPE RNA-Seq from these cell lines as a compare/contrast control.


title: Epigenetic regulation of the transcriptional program in memory and terminally differentiated CD8+ T cells

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

type: Methylation profiling by genome tiling array


title: Epigenetic regulation of the transcriptional program in memory and terminally differentiated CD8+ T cells [HCAFIS_03_ChIPseq]

summary: Epigenetic mechanisms play a critical role during differentiation of T cells by contributing to the formation of stable and heritable transcriptional patterns. To further study the mechanisms of memory maintenance in CD8+ T cells, we performed genome-wide analysis of DNA methylation, histone marking (H3K9Ac and H3K9me3) and gene expression profiles in naive, effector memory (EM) and terminally differentiated memory (TEMRA) cells. Our results indicate that DNA demethylation and histone acetylation are coordinated to generate the transcriptional program associated with memory cells. Conversely, EM and TEMRA cells share a very similar epigenetic landscape. Nonetheless, the TEMRA transcriptional program predicts an innate immunity phenotype associated with genes never reported in these cells, including several mediators of NK cell activation (VAV3 and LYN) and a large array of NK receptors (KIR2DL3, KIR2DL4, KIR2DL1, KIR3DL1, KIR2DS5, etc.). In addition, we identified up to 161 genes that encode transcriptional regulators, some of unknown function in CD8+ T cells, that were differentially expressed in the course of differentiation. Overall, these results provide new insights into the regulatory networks involved in memory CD8+ T cell maintenance and T cell terminal differentiation.

overall_design: Genome-wide changes in H3K9Ac and H3k9me3 in human CD8+ T cell subsets isolated from peripheral blood

first: Ramón

last: Rodriguez

first: Carlos

last: Lopez Larrea

first: José

last: Luis Lavín


title: Gene expression profile of regenerated CD8αα T cells and CD8αβ T cells from LMP2 T-iPSCs

city: Kyoto

first: Takuya

last: Maeda

state: Kyoto

address: 53 Kawahara-cho Shogoin Sakyo-ku

department: Department of Immunology

country: Japan

institute: Institute for Frontier Medical Science, Kyoto University

summary: Whereas cytotoxic T lymphocytes (CTLs) represent the most promising therapeutic avenue in cancer immunotherapy, adaptive transfer of antigen-specific CTLs has faced difficulty in efficient expansion of CTLs from patients in ex vivo culture. To solve this issue, several groups have proposed that the induced pluripotent stem cell (iPSC) technology can be applied for the expansion of antigen-specific CTLs: when iPSCs are produced from antigen-specific CTLs and CTLs are induced from these iPSCs, all regenerated CTLs express the same TCR as original CTLs. However, in these previous studies, one critical issue remains to be solved. With current methods, the regenerated CTLs are mostly of the CD8αα+ innate type and have less antigen-specific cytotoxic activity than primary CTLs. Here we report that, by stimulating purified iPSC-derived CD4/CD8 double positive (DP) cells with anti-CD3 antibody, T cells expressing CD8αβ were generated and they had cytotoxic activity comparable to primary CTLs.

overall_design: mRNA profiles of regenerated CD8αα T cells and CD8αβ T cells from LMP2 T-iPSCs and CD8αα T cells, CD8αβ T cells and γδ T cells from peripheral blood were generated by deep sequencing, in triplicate, using Illumina HiSeq 3000/HiSeq 4000.

first: Keisuke

last: Kataoka

first: Hiroshi

last: Kawamoto


title: Nucleoporin-mediated regulation of cell identity genes

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: The organization of the genome in the three-dimensional space of the nucleus is coupled with cell type-specific gene expression. However, how nuclear architecture influences transcription that governs cell identity remains unknown. Here, we show that Nuclear Pore Complex (NPC) components Nup93 and Nup153 bind super-enhancers (SE), regulatory structures that drive the expression of key genes that specify cell identity. We found that nucleoporin-associated SEs localize preferentially to the nuclear periphery, and absence of Nup153 and Nup93 results in dramatic transcriptional changes of SE-associated genes. Our results reveal a crucial role of NPC components in the regulation of cell type specifying genes and highlight nuclear architecture as a regulatory layer of genome functions in cell fate.

overall_design: DamID-Seq of Nup153 and Nup93 in human U2OS, DamID-Seq of Nup153 in IMR90 cells, RNA-seq of control and knocked-down populations in U2OS and IMR90 cells, ChIP-Seq of histone modifications in U2OS and IMR90 cells and DNAseI-Seq of U2OS cells.

first: Arkaitz

last: Ibarra

first: Martin

middle: W

last: Hetzer


title: Synergistically acting agonists and antagonists of G protein–coupled receptors prevent photoreceptor cell degeneration

first: Matthew

last: Brooks

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Photoreceptor degeneration is the central event leading to visual impairment or blindness in most retinal diseases. However, the discovery of safe and effective therapeutic strategies conferring photoreceptor protection remains challenging. A systems pharmacology approach, synergistically targeting distinct cellular pathways could provide an effective strategy for evaluating, preventing or treating retinal dystrophies. Here this concept was investigated using a mouse model of light-induced retinal degeneration. We show that a combination of FDA-approved drugs acting on different G protein-coupled receptors in a synergistic manner could protect retinas against light-induced degeneration when each drug in the combination treatment was administered at a sub-therapeutic dose. Furthermore, transcriptome analyses demonstrated that such combined treatments also preserved patterns of retinal gene expression more characteristic of the normal retina than did single therapies at higher doses. The current study thus supports a new systems pharmacology approach that may extend to other complex neurodegenerative disorders in addition to retinal diseases.

overall_design:
Male and female Abca4-/-Rdh8-/- at the age of 4- to 6-weeks were used for the current study. All mice were housed and maintained in a 12 h light (≤10 lux)/12 h dark cyclic environment in the Animal Resource Center at the School of Medicine, Case Western Reserve University (CWRU). Bright light-induced retinal damage was generated by exposing Abca4-/-Rdh8-/- mice to white light delivered at 10,000 lux (150 W spiral lamp, Commercial Electric) for 30 min. All indicated treatments were administered by intraperitoneal injection 30 min prior to bright light exposure and retinas collected one day later. Single compounds and their tested doses were: 2-Bromo-α-ergocryptine methanesulfonate salt (BRM), metoprolol tartrate (MTP), tamsulosin (TAM), and doxazosin (DOX). Combined treatments were: BRM, MTP and TAM (BMT), or MTP, DOX, and BRM (MDB).

Processed data files (linked as series supplementary files):
DE_combined.txt; Significant differential expression results from the combined pretreatment experiment.
DE_mono.txt; Significant differential expression results from the mono pretreatment experiment.
eXpress_counts_combined.txt; Quantitation output from eXpress of effective counts from the combined pretreatment experiment.
eXpress_counts_mono.txt; Quantitation output from eXpress of effective counts from the mono pretreatment experiment.
eXpress_fpkm_combined.txt; Quantitation output from eXpress of fpkm values from the combined pretreatment experiment.
eXpress_fpkm_mono.txt; Quantitation output from eXpress of fpkm values from the mono pretreatment experiment.
normalized_fpkm_combined.txt; TMM normalized fpkm values from the combined pretreatment experiment.
normalized_fpkm_mono.txt; TMM normalized fpkm values from the mono pretreatment experiment.

first: Yu

last: Chen

first: Grazyna

last: Palczewska

first: Songqi

last: Gao

first: Hui

last: Jin

first: Zhiqian

last: Dong

first: Linn

last: Gieser

first: Philip

middle: D

last: Kiser

first: Timothy

last: Kern

first: Anand

last: Swaroop

first: Krzysztof

last: Palczewski


title: Transcriptome perturbations within NIH3T3 cell lines expressing rhodopsin and its retinitis pigmentosa mutant and implication for drug screening

summary: Mammalian cells are commonly employed to identify active compounds that could affect progression of many human diseases including retinitis pigmentosa. Here, using transcriptome analysis to compare NIH3T3 cells expressing rod opsin with the disease-causing a single point P23H mutation, we differentiated between genes affected by heterologous opsin expression and those influenced by the P23H opsin mutant gain- or loss-of-function. Surprisingly, heterologous expression of normal opsin causes changes in 783 out of 16888 protein coding transcripts more than 1 fragments per kilobase of transcript per million mapped reads (FPKM) in NIH3T3 cells despite that opsin is exogenous to this cell. The perturbed genes are involved in cell adhesion, morphology and migration and encode extracellular matrix proteins, growth factors, cytoskeleton proteins, glycoproteins or metalloproteases. Not fully overlapping 347 differentially expressed genes were affected when the P23H mutant opsin was expressed. Transcriptome perturbation by individual drug candidates also revealed that different active compounds can target distinct molecular pathways that result in a similar phenotype selected by a cell-based high throughput screen. This transcriptome approach is capable of detecting minute changes in the transcriptome and can be a key to therapeutic success of a candidate drug to restore the normal gene expression landscape in affected tissue.

overall_design: Five cell assay conditions were arranged: 1) NIH3T3(GFP) cells were treated with 0.05% DMSO, labeled as WT; 2) NIH3T3(WT-opsin/GFP) cells were treated with 0.05% DMSO, labeled as OPSIN; 3) NIH3T3(P23H-opsin/GFP) cells were treated with 0.05% DMSO, labeled as P23H; 4) NIH3T3(P23H-opsin/GFP) cells were treated with 5 µM of compound 1 (an isoquinoline-2(3H)-hexanamide), labeled as T1; 5) NIH3T3(P23H-opsin/GFP) cells were treated with 10 µM of compound 2 (4-(5-chlorothiophen-2-yl)furan-2(5H)-one), labeled as T2. Each treatment condition was repeated in three 50 mm dishes as biological replicates. The medium was aspirated, and cells were washed with PBS after 24 h of each treatment before being lysed. Cells were lysed with TRIzol and total RNA was extracted from each sample according to the TRIzol reagent manual.  High quality total RNA was subjected to sequencing library construction using 100 ng of total RNA as input. Transcript libraries were made with TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA). The 100 base paired-end sequenced samples were run on 2 lanes of a HiSeq 2500. Fastq files were generated from reads passing chastity filter.

first: Yuanyuan


title: Pluripotent Reprogramming of Human AML Resets Leukemic Behavior and Models Therapeutic Targeting of Subclones [RNA-seq]

status: Public on Nov 14 2016

city: Stanford

first: Andrew

last: Gentles

address: 1201 Welch Road

institute: Stanford University

summary: Understanding the contribution of abnormal genetic and epigenetic programs to acute myeloid leukemia (AML) is necessary for the integrated design of targeted therapies. To investigate this, we determined the effect of epigenetic reprogramming on leukemic behavior by generating induced pluripotent stem cells (iPSCs) from AML patient samples harboring MLL rearrangements. AML-derived iPSCs (AML-iPSCs) retained leukemic mutations, but reset leukemic DNA methylation/gene expression patterns and lacked leukemic potential. However, when differentiated into hematopoietic cells, AML-iPSCs reacquired the ability to give rise to leukemia in vivo and reestablished leukemic methylation/gene expression patterns, including an aberrant MLL signature, indicating that epigenetic reprogramming was insufficient to eliminate leukemic behavior. In one case, we identified distinct AML-iPSC KRAS mutant and wildtype subclones that demonstrated differential growth properties and therapeutic susceptibilities, predicting KRAS wildtype clonal relapse due to increased cytarabine resistance. Increased cytarabine resistance was further observed in a cohort of KRAS wildtype MLL-rearranged AML samples, demonstrating the utility of AML-iPSCs in predicting subclonal relapse and facilitating clonal targeting in AML.

overall_design: RNA seq profiling of normal and leukemic differentiated and iPSC populations

first: Mark

last: Chao


title: DNA methylation is required for chromatin binding by Mbd2 and Mbd3 in ES cells (ChIP-Seq, meDIP-seq and hmDIP-seq)

first: Sarah

last: Hainer

type: Methylation profiling by high throughput sequencing

overall_design: Examine Mbd2 and Mbd3 occupancy (ChIP-seq) and DNA methylation/hydroxymethylation (meDIP-seq/hmDIP-seq) in ES cells

first: Kurtis

last: McCannell

first: Jun

last: Yu

first: Ly-Sha

last: Ee

first: Lihua

last: Zhu

first: Oliver

last: Rando

first: Thomas

last: Fazzio


title: Analysis of the RDR6-dependent small RNA profile in ein5 ski2 in Arabidopsis

city: West Lafayette

first: Damon

last: Lisch

state: IN

address: 915 West State Street

institute: Purdue University

type: Non-coding RNA profiling by high throughput sequencing

summary: Post-transcriptional gene silence (PTGS) is employed in plants to shut down transgenes, invading viral genes and a certain group of endogenous genes. Meanwhile, it is not clear how the risk of expansive PTGS from endogenous genes featured by transitive siRNA production is minimized. Here we demonstrate two essential components of the SKI complex in cytoplasmic 3’-5’ mRNA decay pathway, SKI2 and SKI3, function as negative regulators of transgene PTGS in Arabidopsis. The ski2 mutants manifested severe synthetic phenotypes with a 5’-3’ exoribonuclease mutant, ein5, which were substantially suppressed by the PTGS mutants, rdr6 and ago1. RDR6 is essential for the altered gene expression in ein5 ski2 on a transcriptome-wide scale. mRNA-seq approach was used to investigate the physiological relevance veiled by the myriad developmental phenotypes in Col-0 (C), ein5-1 (e), ski2-3 (s), ein5-1 ski2-3 (es), rdr6-11 (r) and rdr6-11 ein5-1 ski2-3 (res). A number of endogenous genes, including many miRNA target genes, manifest transitive 21-22 nt siRNA production and compromised gene expression in ein5 ski2 in an RDR6-dependent manner. Taken together, our study brings to light a dual-safeguard system in preventing the expansive siRNA production by the 5’-3’ and 3’-5’ cytoplasmic mRNA decay pathways.

overall_design: Examination of small RNA profiles in 4 genotypes.

first: Hongwei

last: Guo

first: Xinyan

last: Zhang


title: A druggable TCF4- and BRD4-dependent transcriptional network sustains malignancy in blastic plasmacytoid dendritic cell neoplasm (ChIP-Seq)

first: Louis

last: Staudt

summary: We combined loss-of-function RNA interference screening and a high-throughput drug toxicity screening to define novel therapeutic targets in blastic plasmacytoid dendritic cell neoplasm (BPDCN), an aggressive hematologic malignancy for which no curative therapy exists. The E-box transcription factor TCF4 emerged as the master transcriptional regulator of the BPDCN oncogenic program, a finding that can be exploited for the accurate molecular diagnosis of BPDCN. Genetic interference with the TCF4-dependent network induced a rewiring of BPDCN gene expression, resulting in apoptosis. Treatment of BPDCN lines with bromodomain and extra-terminal domain inhibitors (BETi's) down regulated TCF4 and its target gene network, inducing apoptosis both in vitro and retarding growth of BPDCN xenografts in vivo, supporting the clinical evaluation of BETi's in this lethal cancer.

overall_design: We performed chromatin immunoprecipitation coupled to NGS (ChIP-Seq) to identify genomic binding sites for TCF4 in both cell lines, using an anti- TCF4 rabbit monoclonal antibody that we developed for this purpose. We performed BRD4 and RNA Pol2 ChIP-Seq before and after JQ1 treatment, in both the Cal-1 and Gen2.2 BPDCN lines.


title: DNA methylation is required for chromatin binding by Mbd2 and Mbd3 in ES cells

overall_design: Refer to individual Series


title: The ω Subunit Governs RNA Polymerase Stability and Transcriptional Specificity in Staphylococcus aureus

city: Tampa

first: Andy

last: Weiss

state: Florida

address: 4202 East Fowler Avenue, ISA2015

department: Department of Cell Biology, Microbiology and Molecular Biology

institute: University of South Florida

summary: Staphylococcus aureus is a major human pathogen that causes infection in a wide variety of sites within the human body. Its ability to adapt to the human host, and to produce a successful infection, requires precise orchestration of gene expression. While DNA-dependent RNA polymerase (RNAP) is generally well characterized, the role of several small accessory subunits within the complex has yet to be fully explored. This is particularly true for the omega (ω or RpoZ) subunit, which has been extensively studied in Gram-negative bacteria, but largely neglected in Gram-positive counterparts. In Escherichia coli, it has been shown that ppGpp binding, and thus control of the stringent response, is facilitated by ω. Interestingly, key residues that facilitate ppGpp binding by ω are not conserved in S. aureus, and consequently, survival under starvation conditions is unaffected by rpoZ deletion. Further to this, ω-lacking strains of S. aureus display structural changes in the RNAP complex, which result from increased degradation and misfolding of the β’ subunit, alterations in δ and σ-factor abundance, and a general dissociation of RNAP in the absence of ω. Through RNAseq analysis we detected a variety of transcriptional changes in rpoZ-deficient strains, presumably as a response to the negative effects of ω-depletion on the transcription machinery. These transcriptional changes translated to an impaired ability of ΔrpoZ mutant strains to resist stress, and to fully form a biofilm. Collectively, our data underlines, for the first time, the importance of ω for RNAP stability, function and cellular physiology in S. aureus.

overall_design: Two Samples

first: Brittney

last: Moore

first: Miguel

middle: H

last: Tremblay

first: Dale

last: Chaput

first: Astrid

last: Kremer

first: Lindsey

last: Shaw


title: A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space

city: Boulder

first: Luis

last: Zea

state: Colorado

address: 429 UCB ECAE 1B02

institute: University of Colorado Boulder

summary: Bacterial behavior has been observed to change during spaceflight. Higher final cell counts, enhanced biofilm formation, increased virulence, and reduced susceptibility to antibiotics have been reported to occur for cells cultured in space . Most of these phenomena are theorized as being an indirect effect of an altered extracellular environment, where the carbon source uptake is inhibited and excreted acidic byproducts buildup around the cell due to the lack of gravity-driven transport forces. However, to date neither spaceflight results, ground-based studies, physical measurement techniques nor computational approaches have provided sufficient evidence needed to confirm this model. Gene expression data from the Antibiotic Effectiveness in Space (AES-1) experiment, however, have now allowed us to look into the biomolecular processes behind these observations and showed a systematic activation of glucose starvation and acid resistance genes. These results corroborate the reduced mass transport model proposed to govern bacterial responses to spaceflight. Furthermore, the gene expression data suggests that metabolism was stimulated in space, which could play a role in causing the observed increase in bacterial cell concentrations in microgravity. Similarly, the decrease in extracellular pH may also be involved with the reported increase in virulence in space.

overall_design: E. coli ATTC 4157 was cultured and challenged with Gentamicin Sulfate (between 0 and 150 ug/mL) on board the International Space Station while maintaining matched ground (1g) controls (every tested condition consisted of four replicates). BioServe's spaceflight hardware, Fluid Processing Apparatus (FPA) and Group Activation Packs (GAP) were used for flight and ground samples. The FPA contains four chambers, the first one was loaded with 2.75 mL of Growth Medium (Medium E), the second with 0.50 mL inoculum (E. coli at a concentration that would yield and experiment start cc of 1.2e6 cell/mL), the third with 0.25 mL of antibiotic, and the fourth with 2.10 mL of fixative (RNA Later II). Post-flight analyses included cell concentration and differential gene expression.

first: Nripesh

last: Prasad

first: Shawn

last: Levy

last: Stodieck

first: Angela

last: Jones

first: Shristi

last: Shrestha

first: David

last: Klaus


title: The SigB regulon of Staphylococcus aureus

summary: Global expression analysis comparing gene expression of wild-type and sigB mutant in the SH1000 background

overall_design: Two Samples, WT and sigB


title: DNMT3A R882 mutations promote anthacyline resistance through impaired DNA-damage sensing [Bisulfite-Seq]

first: Barbara

last: Spitzer

address: 411 E 67th St

summary: Although the majority of acute myeloid leukemia (AML) patients initially respond to chemotherapy, most of them subsequently relapse due to persistent, chemoresistant disease.  However, the mechanistic basis by which AML cells persist during chemotherapy has not been fully delineated.  Recurrent somatic mutations in the DNA methyltransferase 3A gene (DNMT3A), most frequently at arginine 882 (DNMT3Amut), are commonly observed in AML patients, and are also detected in elderly subjects with clonal hematopoiesis in the absence of leukemic transformation.  DNMT3Amut AML patients have an inferior outcome when treated with standard dose daunorubicin-based induction chemotherapy, suggesting that DNMT3Amut AML cells can persist following chemotherapy and drive relapse.  DNMT3Amut cells show impaired nucleosome eviction and chromatin remodeling in response to DNA damage in the setting of anthracycline exposure.  This defect leads to an inability to sense and repair DNA damage, which results in the accumulation of single-stranded DNA breaks and increased mutagenesis. Our studies identify a critical role for DNMT3A R882 mutations in driving AML chemoresistance, and highlight the importance of chromatin remodeling in the response to cytotoxic chemotherapy.

overall_design: We have generated a novel genetic mouse model conditionally expressing mutant Dnmt3a from an endogenous locus and examined transcriptomes from FACS-sorted LSK populations from Dnmt3a+/+ (wt_Mx+), Dnmt3a+/m (cKI_Mx+), and Dnmt3a+/- (cKI_Cre-) animals at 6 months of age

first: Olga

last: Guryanova

first: Francine

middle: E

last: Garrett-Bakelman

first: Caroline

last: Sheridan

first: Yaseswini

last: Neelamraju

first: Ross

middle: L

last: Levine


title: A microRNA-mRNA Expression Network during Oral Siphon Regeneration in Ciona [mRNA]

city: Santa Barbara

first: William

last: Smith

address: Biological Sciences II

department: MCDB

institute: UCSB

summary: Among the Chordates tunicates demonstrate the highest capacity for regeneration, ranging from full-body regeneration in colonial ascidians to appendage regeneration in solitary ascidians. Here we present a parallel study of mRNA and microRNA expression at three stages of oral siphon regeneration in the solitary ascidian Ciona robusta (a.k.a., Ciona intestinalis), and the derived network of their interactions. In the process of identifying 248 mRNAs and 15 microRNAs as differentially expressed (DE) across the course of regeneration, we also identified 57 novel microRNAs, several of which are among the most highly DE. Analysis functional categories identified transcripts related to stress responses and apoptosis enriched at the wound healing stage, various signaling pathways including Wnt and TGF-β enriched during early regrowth, and negative regulation of extracellular remodeling proteases as enriched in late stage regeneration. Additionally, comprehensive 3’-UTR binding site prediction and probability of conserved targeting for all C. robusta microRNAs (including those identified here) was calculated using TargetScanS. A microRNA-target network was subsequently constructed by calculating Pearson correlation coefficients for all predicted microRNA-mRNA target pairs expressed during regeneration. Network based clustering associated one or more microRNAs and their targets into 22 non-overlapping groups. Functional analysis of mRNA targets in each network cluster showed that enrichment of stress response, signaling pathway and extracellular remodeling categories associated with specific stages could also be associated with specific microRNAs. Finally, predicted targets of the miR-9 network cluster suggest a role in regulating differentiation and proliferative state of neural progenitors through regulation of the cytoskeleton and cell cycle. This work represents a significant advance in the prediction of microRNA effects on appendage regeneration and provides a foundation for investigating evolutionary conservation of microRNAs during regeneration in chordates.

overall_design: mRNA profiles of Ciona robusta oral siphons before and during regeneration

first: Elijah

last: Spina

first: Elmer

middle: B

last: Guzman

first: Hongjun

last: Zhou

first: Kenneth

middle: S

last: Kosik


title: A microRNA-mRNA Expression Network during Oral Siphon Regeneration in Ciona [microRNA]

middle: C

overall_design: microRNA profiles of Ciona robusta oral siphons during regeneration


title: A microRNA-mRNA Expression Network during Oral Siphon Regeneration in Ciona

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


title: Nucleosome occupancy as a novel chromatin parameter for replication origin functions

city: Seattle

first: Laura

last: Lee

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: This study defines nucleosome occupancy as a novel parameter for regulating origin activities. Nucleosome occupancy at origins was assessed using histone H3 ChIP-seq during G1 and G2M. Origin activity was determined using BrdU ChIP-seq.

first: Jairo

last: Rodriguez

first: Bryony

last: Lynch

first: Toshio

last: Tsukiyama


title: Endogenous small RNAs from Arabidopsis thaliana wild-type, dcl4 mutant and dcl4 mutant expressing nuclear or cytoplasmic DCL4

city: Zürich

first: Alexis

last: Sarazin

address: Universitätstrasse 2

country: Switzerland

institute: ETH

summary: Parallel RNA silencing pathways regulate gene expression in plants, either by transcriptional gene silencing via RNA-dependent DNA methylation (RdDM), or by post-transcriptional silencing targeting mRNAs. Both pathways rely on distinct Dicer-like proteins to cleave double-stranded RNA into small-interfering RNAs. Experiments to determine the subcellular localization of Dicer-like proteins in Arabidopsis revealed that DCL4 is predominantly expressed as a transcriptional start site isoform that encodes a cytoplasmic protein. A second, longer DCL4 transcript isoform encodes a nuclear-localization signal and its expression is repressed by DNA methylation. Consequently this isoform is induced when promoter methylation decreases due to infection with a bacterial pathogen or during silique development. Nuclear DCL4 produces unique populations of small RNAs, called DCL4NLS isoform-dependent siRNAs (disiRNAs), which function via a post-transcriptional silencing effector, but whose precursors are generated by the RdDM pathway. Arabidopsis cells can thus respond to genome methylation changes by modulating DCL4 localization, which in turn recruits PTGS factors to reinforce RNA silencing.

overall_design: 4 samples examined: wild type, dcl4 mutant and dcl4 mutant expressing nuclear or cytosplasmic DCL4

first: Nathan

last: Pumplin

first: Pauline

last: Jullien

first: Nicolas

last: Bologna

first: Stefan

last: Oberlin

first: Olivier

last: Voinnet


title: Capturing the biology of mild versus severe disease in a pluripotent stem cell-based model of Familial Dysautonomia

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: Familial Dysautonomia is a genetic disease, however patietns with the same genotype present with mild or severe forms of the disease. We used the pluripotent stem cell technology to capture the differences in disease severity in vitro during neurodevelopment as well as during maintanance of the cells, showing developmental and degenerative phenotypes. RNA seq. analysis of the groups confirmed those diffferences.

overall_design: Analysis of RNA from PSC-derived neural crest cells from severe FD, mild FD and healthy patients

first: Nadja

last: Zeltner

first: Lorenz

last: Studer


title: RNA Sequencing Data in differentiating mouse embryonic stem cells

city: Ann Arbor

first: Vesa

middle: Matti

last: Kaartinen

state: MI

address: 1011 N. University

department: BMS

institute: University of Michigan

summary: ES cell lines were established from mouse embryos, which were homozygous for the Trim33-flox allele and carried the UbcCreERT2 transgene. Cells were cultured without feeder cells in the presence of LIF and 2i. Embryoid bodies (EBs) were generated using the ATCC protocol on low attachment dishes under differentiating conditions. EBs were induced with Tamoxifen at day 4 and harvested at day 7.

overall_design: Investigate differentially expressed genes in control and Trim33-deficient embryoid bodies derived from mouse embryonic stem cells

middle: M

first: Sudha

last: Rajderkar


title: The transcriptome and chromatin accessbility landscape of mammalian germline

city: Hangzhou

first: Hongshan

last: Guo

state: Zhejiang Province

address: No.1369, Wenyixi Road

department: School of Medicine, Zhejiang University

institute: Liangzhu Laboratory

summary: We first isolate the PGCs from the Oct4-Gfp knock-in mice, and KIT-positive PGCs from the post-implantation human fetus. Then we use the Nome-seq (Nucleosome Occupancy and Methylome Sequencing), using a in vitro GpC methyltransferase (M.CviPI) and next generation sequencing to generate the endogenous DNA methylation information and chromatin accessibility of the same DNA molecules in these mammalian germ cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Together, we isolated the E6.5 epiblast, E11.5 PGC, E13.5 PGC, E16.5 PGC and their surrounding somatic cells from mouse embryos, and week5 heart, week7 PGC, week11 PGC,  week12 PGC, week17 PGC and week26 PGC, and also their gonadal somatic cells from human fetus.

first: Boqiang

last: Hu

first: Liying

last: Yan

first: Jun

last: Yong

first: Jie

last: Qiao

first: Fuchou

last: Tang


title: Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes

city: Paris

first: Yuvia

middle: Alheli

last: Perez Rico

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Super-enhancers (SEs) are key transcriptional drivers of cellular, developmental and disease states in mammals, yet the conservational and regulatory features of these enhancer elements in non-mammalian vertebrates are unknown. To define SEs in zebrafish and enable sequence and functional comparisons to mouse and human SEs, we used genome-wide histone H3 lysine 27 acetylation (H3K27ac) occupancy as a primary SE delineator. Our study determined the set of SEs in pluripotent state cells and adult zebrafish tissues and revealed both similarities and differences between zebrafish and mammalian SEs. Although the total number of SEs was proportional to the genome size, the genomic distribution of zebrafish SEs differed from that of the mammalian SEs. Despite the evolutionary distance separating zebrafish and mammals and the low overall SE sequence conservation, ~42% of zebrafish SEs from all cells and tissues analyzed were associated with orthologs that also were associated with SEs in mouse and human. Compared to their non-associated counterparts, higher sequence conservation was revealed for those SEs that have maintained orthologous vertebrate gene associations. Functional dissection of two of these SEs identified conserved sequence elements and tissue-specific expression patterns, while chromatin accessibility analyses predicted transcription factors governing the function of pluripotent state zebrafish SEs. Our zebrafish enhancer characterizations and comparative studies show the extent of SE usage and their conservation across vertebrates, permitting future gene regulatory studies in several tissues.

overall_design: H3K27ac profiles of zebrafish adult brain, heart, intestine and testis generated by deep sequencing.

last: Pérez-Rico

first: Alena

last: Shkumatava


title: RNAseq of Arabidopsis thaliana Col-0 inflorescences

first: Alexis

last: Sarazin

summary: Paired-end Illumina RNA sequencing of Arabidopsis thaliana Col-0 inflorescences

overall_design: mRNA profil of Arabidopsis Col-0 WT inflorescences were generated by paired-end deep sequencing, in replicate using Illumina HiSeq 2000

first: Nathan

last: Pumplin

first: Pauline

last: Jullien

last: Bologna


title: Digitalis-like compounds facilitate redifferentiation of non-medullary thyroid cancer through intracellular Ca2+, cFOS and autophagy dependent pathways

city: Nijmegen

first: Theo

last: Plantinga

address: Geert Grooteplein Zuid 10

department: Department of Pathology

country: Netherlands

institute: Radboud University Medical Center

summary: About 20-30% of patients with metastatic non-medullary thyroid cancer (TC) have persistent or recurrent disease resulting from tumor dedifferentiation. Tumor redifferentiation to restore sensitivity to radioactive iodine therapy is considered a promising strategy to overcome RAI resistance. Autophagy has emerged as an important mechanism in cancer dedifferentiation. Here, we demonstrate the therapeutic potential of autophagy activation for redifferentiation in thyroid cancer cell lines. Five, all digitalis-like compounds, restored hNIS expression and iodine uptake in TC cell lines. Upregulation of hNIS was mediated by intracellular Ca2+ and cFOS activation. Cell proliferation was inhibited by downregulating Akt1 and by induction of autophagy and p21-dependent cell cycle arrest. All together, digitalis-like compounds could represent a promising treatment modality for patients with dedifferentiated TC.

overall_design: Non-medullary TC cell lines were treated with digitalis-like compounds for 24, 48 and 72 hours. RNA was isolated and prepared for RNA sequencing by Illumina HiSeq 2000.

first: Tesselaar

last: Marika

first: Crezee

last: Thomas

first: Plantinga

last: Theo


title: Endothelin signaling activates neural crest gene expression via a MEF2C-dependent positive-feedback transcriptional mechanism

city: San Francisco

first: Jianxin

address: 555 Mission Bay Blvd South

institute: CVRI

summary: Endothelin signaling is one of the essential signaling pathways that control vertebrate development. Dysregulated Endothelin signaling plays an important role in the pathogenesis of human diseases such as Hirschsprung’s disease, pulmonary hypertension and cancer. However, the downstream transcriptional program and transcriptional factors of Endothelin signaling have been incompletely understood. Here, we used RNA-sequencing to identify the genes regulated by Endothelin signaling in the neural crest, where Endothelin signaling functions primarily during development. We further demonstrate that Endothelin induces gene expression through the de-repression of the MADS Box transcription factor MEF2C. Moreover, in the Mef2c gene locus, we identified an Endothelin responsive cis-regulatory element which functions as a central component of an Endothelin-MEF2C positive feedback transcriptional mechanism that regulates downstream gene expression.

overall_design: We performed RNA-sequencing experiment on genetically labeled Neural crest cells that treated with Endothelin-1 (or PBS) in the presence or absence of Mef2c. Specifically, we characterized Endothelin-1 regulated genes by comparing gene expression profile in Endothelin-1 treated wild type (sample 4-6) neural crest cells and PBS treated wild type (sample1-3) neural crest cells (gene list 1). We also characterized all Mef2c dependent genes in our Endothelin-1 induction experiment by comparing gene expression profile in Endothelin-1 treated wild type (sample 4-6) neural crest cells and Endothelin-1 treated Mef2c neural crest conditional knockout (sample7-9) neural crest cells (gene list 2). We identify Mef2c-dependent, Endothelin-1 regulated genes by overlapping gene list 1 to gene list 2.

first: Brian

last: Black


title: DNMT3A R882 mutations promote anthacyline resistance through impaired DNA-damage sensing [RNA-Seq]

city: New York

first: Barbara

last: Spitzer

first: Olga

middle: A

last: Guryanova

first: Ross

last: Levine


title: DNMT3A R882 mutations promote anthacyline resistance through impaired DNA-damage sensing [ChIP-Seq]

overall_design: We have generated a novel genetic mouse model conditionally expressing mutant Dnmt3a from an endogenous locus and examined binding of wild-type and mutant Dnmt3a to DNA in mouse embryonic fibroblasts (MEF) derived from Dnmt3a(+/+), Dnmt3a(+/-), and Dnmt3a(-/m) animals

first: Richard

middle: P

last: Koche


title: DNMT3A R882 mutations promote anthacyline resistance through impaired DNA-damage sensing


title: Comparison of gene expression of memory B cells subpopulations

status: Public on Nov 13 2016

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

summary: We investigated the ability of monoclonal B cells to restore primary and secondary antibody responses in adoptive immune-deficient hosts. Priming induced B cell activation and expansion, AID expression, antibody production and the generation of IgM+IgG- and IgM-IgG+ antigen-experienced B-cell subsets that persisted in the lymphopenic environment by cell division. Using RNA sequencing, we compared the gene expression profil of memory B cells subpopulations and activated B cells. These data showed a clear discrimination of naïve and activated/memory cells while indicating only minor differences between both subsets of memory cells.

overall_design: mRNA profiles of B cell subtypes (activated, memory IgM+, memory IgG+) were generated by deep sequencing, in triplicate, using Illumina

first: Marie

last: Anson

first: François

last: Huetz

first: Antonio

last: Freitas


title: Bach2-Batf interactions control Th2-type immune responses by regulating the IL-4 amplification loop

city: Toon-shi

first: Makoto

last: Kuwahara

state: Ehime

address: Shitsukawa

institute: Graduate School of Medicine, Ehime University

summary: Although Bach2 plays an important role in regulating the Th2-type immune response, the underlying molecular mechanisms remain unclear.  We herein demonstrate that Bach2 associates with Batf and binds to the regulatory regions of the Th2 cytokine gene loci.  The Bach2-Batf complex antagonizes the recruitment of the Batf-Irf4 complex to AP-1 motifs and suppresses Th2 cytokine production.  Furthermore, we found that Bach2 regulates the Batf and Batf3 expressions via two distinct pathways.  First, Bach2 suppresses the maintenance of the Batf and Batf3 expression through the inhibition of IL-4 production.  Second, the Bach2-Batf complex directly binds to the Batf and Batf3 gene loci and reduces transcription by interfering with the Batf-Irf4 complex.  These findings suggest that IL-4 and Batf form a positive feedback amplification loop to induce Th2 cell differentiation and the subsequent Th2-type immune response, and Bach2-Batf interactions are required to prevent an excessive Th2 response.

overall_design:
Global patterns of H3K27ac level at the Th2 cytokine gene loci in the WT and Bach2-deficient naïve cells cultured under neutral or Th2 conditions (ChIP-seq analysis).

Global patterns of Bach2 binding at the Th2 cytokine gene loci in the WT and Bach2-deficient naïve cells cultured under neutral conditions (ChIP-seq analysis).

Gene expression in Bach2 WT-Th (Bach2 WT-Th (-)), Bach2 KO-Th (Bach2 KO-Th (-)), restimulated Bach2 WT-Th (Bach2 WT Th (+)) and re-stimulated Bach2 KO-Th (Bach2 KO Th (+)).


title: Bach2 inhibits Th2-type immune responses by regulating glutamine metabolism [ChIP-seq]

summary: It is becoming clear that the acquisition of T cell functions is closely linked to the reprogramming of the metabolic pathway.  However, the impact of metabolic changes on the differentiation of helper T cell subsets remains unclear.  We herein demonstrate a critical role of glutamine metabolism in regulating type 2-immune response.  Bach2, a transcriptional repressor, binds to an AP-1 motif, and suppresses Th2 cell differentiation and glutaminolysis.  Glutaminase 2, which controls glutamine metabolism, was identified as a Bach2 target gene.  The pharmacological inhibition of glutamine metabolism normalized allergic lung inflammation that developed spontaneously in T-cell specific Bach2-deficient mice.  These findings reveal the importance of the Bach2-dependent modulation of glutamine metabolism in regulating Th2 cell differentiation and Th2 cell- mediated inflammation.

overall_design: Examination of transcriptional factor Bach2 binding and histone modefications in Bach2 WT and KO CD4 T cells

first: Masakatsu

last: Yamashita


title: Cistromic and gene expression analyses associated with HDAC3, SCAP and SREBP1c in mouse livers

city: Boston

first: Manashree

last: Damle

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary: HDAC3 is a repressor of lipogenic gene expression whereas nuclear SREBP1c is a potent activiator that is controlled by SCAP. Since these factors share many lipogenic gene targets, we sought to determine their molecular crosstalk by ChIP-sequencing. We also tested whether ectopic expression of nSREBP1c interferes with HDAC3 binding near lipognic genes. To faciliate these pulldowns, we ectoipcally expressed HA-tagged nSREBP1c in mouse livers in vivo using AAV8 viruses and the thyroxine-binding globulin promoter for hepatocyte-specifc expression. ChIP-sequencing identified over 7,000 HA-nSREBP1c binding sites, almost 50% of which were in the same vicinity as HDAC3 peaks. However, ectopic expression of nSREBP1c did not disrupt HDAC3 binding indicating that these factors indepedently bind near lipogenic genes and are regulated by distinct regulatory pathways. Gene expression changes in livers of HDAC3 liver specific knockout (LKO), SCAP LKO, and double LKO mice are provided.

overall_design: C57Bl/6 mice were injected with adeno-associated virus serotype 8 (AAV8) viruses expressing either GFP (control), HA-nSREBP1c, or Cre. Anti-HDAC3 or anti-HA antibodies were used for ChIP. For inputs, mouse livers lacking HDAC3 were used for HDAC3 ChIPs, and mouse livers expressing GFP were used for HA ChIPs. For gene expression, mice injected with AAV8:GFP were used as controls and indicated floxed mice were injected with AAV8:Cre.

first: Romeo

last: Papazyan


title: Identification of differentially expressed genes between adult males and adult females of the two-spotted spider mite (Tetranychus urticae)

status: Public on Nov 12 2016

city: Salt Lake City

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

summary: Sex-specific differences in gene expression underlie differences in morphology, behavior, and reproduction. To date, little is known about sex-specific differences in gene expression in spider mites, even though males and females differ markedly in morphology and behavior. In this study, we describe the complement of sex-specific gene expression differences between males and females of the two-spotted spider mite (Tetranychus urticae), an important generalist herbivore that is a significant crop pest. Gene expression differences were detected from analyses of mRNA-seq data collected with the Illumina method (eight samples in total consisting of four biological replicates each for males and females).

overall_design: mRNA profiles consisting of four biological replicates each for male and female spider mites (Tetranychus urticae, strain London), eight samples total, were generated with RNA collected from adults grown on bean plants.

first: Robert

last: Greenhalgh

first: Wannes

last: Dermauw

first: Sabina

last: Badja

first: Thomas

last: Van Leeuwen


title: Illumina Solexa Digital Gene Expression Sequencing Facilitates Quantitative Analysis of Wild Type (Kasa-1) and OsMYB103L overexpression transgenic rice plant (Y103-1). Transcriptomes

city: Beijing

first: lili

last: hao

address: Beichen west road

institute: BIG

summary: Overexpression of OsMYB103L leads to leaf rolling in transgenic rice plants. To explore the possible molecular mechanism of OsMYB103L’s effects on rice leaf development, we examined the expression profiles of OsMYB103L overexpression transgenic rice plants and wild type leaf blades using Digital Gene Expression (DGE) profiling analysis.

overall_design: OsMYB103L overexpression line (Y103-1) and Wild Type (Kasa-1) plants were used for Digital Gene Expression (DGE) profiling analysis.

first: Chunhua

last: Yang

first: Dayong

last: Li

first: Xue

last: Liu

first: Chengjun

last: Ji

first: Lili

last: Hao

first: Xianfeng

last: Zhao

first: Xiaobing

first: Caiyan

last: Chen

first: Zhukuan

last: Cheng

first: Lihuang

last: Zhu


title: RNA-seq analysis upon ARID1B overexpression

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: We transduced either an empty vector or ARID1B cDNA in IMR90 cells. Cells were selected with puromycin and 6 days after the infection we collected the RNA. ARID1B is a member of the SWI/SNF chromatin-remodeling complex. Our previous experiments showed that knockdown of ARID1B allows cells to bypass cellular senescence. By performing RNA-seq we have shown that ARID1B expression can induce a set of genes involved in the senescence response.

overall_design: 2 samples examined: IMR90 cells expressing an empty vector and IMR90 cells expressing ARID1B cDNA

first: Luca

last: Tordella

first: Jesus

last: Gil


title: Core binding factor (CBF) is required for Epstein-Barr virus EBNA3 proteins to regulate target gene expression

first: Martin

last: Allday

state: London

address: Norfolk Place

institute: Imperial College London

summary: ChIP-seq performed on lymphoblastoid cell lines (LCLs), expressing epitope-tagged EBNA3A, EBNA3B or EBNA3C from EBV-recombinants, revealed important principles of EBNA3 binding to chromatin. When combined with global chromatin looping data, EBNA3-bound loci were found to have a singular character, each directly associating with either EBNA3-repressed or EBNA3-activated genes, but not with both. EBNA3A and EBNA3C showed significant association with repressed and activated genes. Significant direct association for EBNA3B loci could only be shown with EBNA3B-repressed genes. A comparison of EBNA3 binding sites with known transcription factor binding sites in LCL GM12878 revealed substantial co-localization of EBNA3s with RUNX3 – a protein induced by EBV during B cell transformation. The beta-subunit of core binding factor (CBFβ), that heterodimerizes with RUNX3, could co-immunoprecipitate robustly EBNA3B and EBNA3C, but only weakly EBNA3A. Depletion of either RUNX3 or CBFβ with lentivirus-delivered shRNA impaired epitope-tagged EBNA3B and EBNA3C binding at multiple regulated gene loci, indicating a requirement for CBF heterodimers in EBNA3 recruitment during target-gene regulation. ShRNA-mediated depletion of CBFβ in an EBNA3C-conditional LCL confirmed the role of CBF in the regulation of EBNA3C-induced and -repressed genes. These results reveal an important role for RUNX3/CBF during B cell transformation and EBV latency that was hitherto unexplored.

overall_design: Each EBNA3 was tagged individually in recombinant viruses and ChIP-seq was performed to determine global localization of each EBNA3.

first: Kostas

last: Paschos


title: Correlation of the expression of the key enzymes and the yield of the lipid

city: xiamen

first: yang

last: zhang

address: Daxue Road No. 178, Siming District

institute: Third Institute of Oceanography, State Oceanic Administration

summary: Characterization of the expression of the key enzymes during the growth of Chlorella minutissima UTEX2341

first: Jin


title: A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis

city: Cold Spring Harbor

first: Simon

middle: Robert Vincent

last: Knott

state: NY

address: 1 Bungtown Rd

department: Biology

institute: Cold Spring Harbor Laboratory

summary: Cancer metastasis requires that primary tumour cells evolve the capacity to intravasate into the lymphatic system or vasculature, and extravasate into and colonize secondary sites1. Others have demonstrated that individual cells within complex populations show heterogeneity in their capacity to form secondary lesions2   5. Here we develop a polyclonal mouse model of breast tumour heterogeneity, and show that distinct clones within a mixed population display specialization, for example, dominating the primary tumour, contributing to metastatic populations, or showing tropism for entering the lymphatic or vasculature systems. We correlate these stable properties to distinct gene expression profiles. Those clones that efficiently enter the vasculature express two secreted proteins, Serpine2 and Slpi, which were necessary and sufficient to program these cells for vascular mimicry. Our data indicate that these proteins not only drive the formation of extravascular networks but also ensure their perfusion by acting as anticoagulants. We propose that vascular mimicry drives the ability of some breast tumour cells to contribute to distant metastases while simultaneously satisfying a critical need of the primary tumour to be fed by the vasculature. Enforced expression of SERPINE2 and SLPI in human breast cancer cell lines also programmed them for vascular mimicry, and SERPINE2 and SLPI were overexpressed preferentially in human patients that had lung-metastatic relapse. Thus, these two secreted proteins, and the phenotype they promote, may be broadly relevant as drivers of metastatic progression in human cancer.

overall_design: RNAseq of Individual 4T1 Clonal Populations_10samples

first: Elvin

last: Wagenblast

first: Mar

last: Soto

first: Sara

last: Gutierrez-Angel

first: Christina

last: Hartl

first: Annika

last: Gable

first: Ashley

middle: R

last: Maceli

first: Nicolas

last: Erard

first: Alissa

last: Williams

first: Sun

middle: Y

last: Kim

first: Steffen

last: Dickopf

first: J

last: Harrell

first: Andrew

last: Smith

first: Charles

last: Perou

first: John

last: Wilkinson

first: Gregory

middle: J

last: Hannon


title: Genome-wide binding profile of the AhR transcription factor in keratinocytes

city: Sendai

first: Eri

last: Kobayashi

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

summary: Atopic dermatitis is increasing worldwide, correlating with air pollutions. Various organic components of pollutants activate transcription factor AhR (aryl-hydrocarbon receptor). We have established AhR-CA mice, whose keratinocytes express constitutive-active AhR, and these mice developed atopic dermatitis-like frequent scratching and allergic inflammation. In this study we performed ChIP-seq analyses and identified keratinocyte-specific AhR target genes, including inflammatory cytokines Tslp and IL33, and neurotrophic factor Artemin. While AhR-CA mice exhibited epidermal hyperinnervation and alloknesis leading to hypersensitivity to pruritus, blockade of Artemin alleviated these phenotypes. AhR-CA mice showed scratching-induced barrier insufficiency and enhanced sensitization to epicutaneously-applied antigens, recapitulating human atopic dermatitis. Consistently, AhR activation and Artemin expression was detected in the epidermis of atopic dermatitis patients and keratinocytes exposed to air pollutants. Thus, AhR in keratinocytes senses the environmental stimuli and responds to them through moderating inflammation. We propose a mechanism in which air pollution induces atopic dermatitis through AhR activation.

overall_design: Three individual samplings of primary keratinocytes obtained from neonatal mice transduced with HA-tagged constitutive active form of AhR. ChIP-seq was performed using antibody to HA.

first: Takanori

last: Hidaka

first: Eisaku

last: Ogawa

last: H. Kobayashi

first: Takafumi

last: Suzuki

first: Ryo

last: Funayama

first: Takeshi

last: Nagashima

first: Taku

last: Fujimura

first: Setsuya

last: Aiba

first: Keiko

last: Nakayama

first: Ryuhei

last: Okuyama

first: Masayuki

last: Yamamoto


title: DNA methylation status of Individual 4T1 Clonal Populations

first: Simon

last: Knott

summary: The methylation profiles of 6 cell lines derived from single clones of the 4T1 cell lines were assessed based on genomewide methylation levels The the promoters of genes that were overexpressed in intravasating clones were found had lower methylation levels for those clones relative to the others.

overall_design:
Clone_Methylation
1) 23 clonal lines were established using single cell FACs sorting from the 4T1 mammary cancer cell line.
2) After establishing the lines the clones were assesed (in a pooled setting) for their capacity to intravasate the vascular system.
3) DNA methylation profilling was carried out on a genomewide scale on two intravasting clones and four non-intravasating clones.
4) The methylation levels of the gene promoters and hypomethylated regions of the intravasating clones were then compared with the same regions of non-intravasating clones.


title: Loss of EGFR-DDEF1 signaling in metastatic and unresectable hepatoblastoma

status: Public on Nov 11 2016

city: Rockville

first: Brandon

middle: W

last: Higgs

state: Maryland

address: 2273 Research Blvd Suite 220

institute: Immunocore, Ltd

summary: We report that the application of PE sequencing of mRNA in hepatoblastoma patient biopsies effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

overall_design: Comparison of normal liver and hepatoblastoma tissue.


title: Long RNA Seq on Sham Adult Mouse Heart

city: Lausanne

first: Frederic

last: Burdet

address: Quartier Sorge - Batiment Amphipole

institute: Swiss Institute of Bioinformatics

summary: Enhancers are the key information processing units within the cardiac gene regulatory network. We have demonstrated that cardiac enhancers generate non-coding RNAs. RNA sequencing demonstrates that some of these transcripts are polyadenylated, multi-exonic long non-coding RNAs.

overall_design: 1 conditions, 4 biological replicates per condition

first: Samir

last: Ounzain

first: Rudi

last: Micheletti

first: Mark

last: Ibberson

first: Mohamed

last: Nemir

first: Alexandre

last: Sarre

first: Michael

last: Alexanian

first: Mathew

last: Blow

first: Dalit

last: May

first: Rory

last: Johnson

first: Len

last: Pennacchio

first: Thierry

last: Pedrazzini


title: Genetic and Epigenetic Landscapes of Laterally Spreading Tumors of the Colorectum

city: Sydney

first: Jason

last: Wong

state: NSW

address: Level 2, Lowy Cancer Research Centre, University of New South Wales

country: Australia

institute: UNIVERSITY OF NEW SOUTH WALES

summary: Laterally spreading tumors (LSTs) are colorectal adenomas that develop into extremely large lesions but rarely become malignant. Elucidating their molecular profiles, and how these contrast with colorectal cancer (CRC), offers the opportunity to understand their biology and how they are able to grow to such large lesions without progressing to cancer. Profiling of 11 LSTs with multiple genome-wide approaches showed mutation rates comparable with microsatellite stable CRCs at 2.4 versus 2.6 mutations per megabase respectively, however copy number alterations are infrequent (averaging 1.5 per LST). Only 28.5% of genes with promoter CpG island hypermethylation showed >2-fold downregulation of expression in LST tissue relative to paired normal mucosa. Integration of genetic and epigenetic data identified driver genes not previously implicated in colorectal neoplasia (ANO5, MED12L, EPB41L4A, RGMB, SLITRK1, NRXN1, ANK2), including genes targeted by both genetic and epigenetic alterations. Alterations to pathways commonly mutated in CRCs, namely the p53, PI3K and TGFb pathways, are rare. Instead LST-altered genes converge on axonal guidance, Wnt and actin cytoskeleton signalling. Non-granular morphology, which is associated with an elevated risk of cancer, correlates with low frequencies of epigenetic inactivation and KRAS mutations and the hyperactivation of CXCR4 signalling. These data show that mutation load is a poor predictor of invasive potential and that genomic structural aberrations or alterations in key pathways is important in progression to cancer. By integrating genetic, epigenetic and transcriptional data this study identifies novel genes important in early colorectal neoplasia.

overall_design: DNA methylation and gene expression analyses of 11 laterally spreading tumors and paired normal colorectal mucosa

first: Luke

last: Hesson


title: The tumor suppressor FLCN mediates an alternate mTOR pathway to regulate browning of adipose tissue

city: Philadelphia

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: differential display between WT and FLCN KO

overall_design: Global gene expression pattern of ingWAT from wildtype and FLCN adipKO animals

first: Shogo

last: Wada

first: Zoltan

last: Arany


title: Modulation of nonsense-mediated decay by rapamycin

city: Santa Cruz

first: Andrew

last: Wallace

state: CA

address: University of California, Santa Cruz Molecular, Cell & Developmental Biology Sinsheimer Labs 1156 High Street

department: Molecular, Cell and Developmental Biology

institute: University of California, Santa Cruz

summary: Rapamycin is a naturally occurring macrolide whose target is at the core of nutrient and stress regulation in a wide range of species. Despite well-established roles as an inhibitor of cap-dependent mRNA translation, relatively little is known about its effects on other modes of RNA processing. Here, we characterize the landscape of rapamycin-induced post-transcriptional gene regulation. Transcriptome analysis of rapamycin-treated cells revealed genome-wide changes in alternative mRNA splicing and pronounced changes in NMD-sensitive isoforms. We demonstrate that despite well-documented attenuation of cap-dependent mRNA translation, rapamycin can augment NMD of certain transcripts. Rapamycin-treatment significantly reduces the levels of both endogenous and exogenous PTC-containing mRNA isoforms and its effects are dose-, UPF1- and 4EBP-dependent manner. The PTC-containing SRSF6 transcript exhibits a shorter half-life upon rapamycin-treatment as compared to the non-PTC isoform. Rapamycin-treatment also caused depletion of PTC-containing mRNA isoforms from polyribosomes, underscoring the functional relationship between translation and NMD. Enhanced NMD activity also correlates with an enrichment of the nuclear Cap Binding Complex (CBC) in rapamycin-treated cells. Our data demonstrate that rapamycin modulates global RNA homeostasis by NMD.

overall_design: We performed cytoplasmic RNA-seq of HEK 293 T cells stimulated with rapamycin, emetine or control, in triplicates.

first: Rocio

middle: T

last: Martinez-Nunez

first: Jeremy

last: Sanford


title: POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in Arabidopsis

city: Madison

first: Xuehua

last: Zhong

state: WI

address: 330 N. Orchard St.

department: Epigenetics

institute: Wisconsin Institute for Discovery

summary: Functional analysis of HDA9 in Arabidopsis

overall_design:
HDA9 binding sites were investigated by ChIP sequencing,
Transcriptome analysis of hda9 were performed in hda9 mutant in both young (YL) and early senescence (ES) leaves.
Transcriptome analysis of pwr were performed in pwr mutant in early senescence (ES) leaves.
H3K27ac ChIP-seq were performed with mixture of mature and early senescence leaves.

first: Xiangsong

last: Chen

first: Li

last: Lu


title: HSF1 ChIP-seq: Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

summary: An important distinction is frequently made between constitutively expressed housekeeping genes versus regulated genes. Although generally characterized by different DNA elements, chromatin architecture and cofactors, it is not known to what degree promoter classes strictly follow regulatability rules and which molecular mechanisms dictate such differences. We show that SAGA-dominated/TATA-box promoters are more responsive to changes in the amount of activator, even compared to TFIID/TATA-like promoters that depend on the same activator Hsf1. Regulatability is therefore an inherent property of promoter class. Further analyses show that SAGA/TATA-box promoters are more dynamic because TBP recruitment through SAGA is susceptible to removal by Mot1. In addition, the nucleosome configuration upon activator depletion shifts on SAGA/TATA-box promoters and seems less amenable to preinitiation complex formation. The results explain the fundamental difference between housekeeping and regulatable genes, revealing an additional facet of combinatorial control: an activator can elicit a different response dependent on core promoter class.

overall_design: Hsf1 binding was determined under standard laboratory growth conditions using ChIP-seq. Hsf1 was depleted from the nucleus using the anchor away technique and subsequently changes in nucleosome positioning were investigated using Mnase-seq, with different concentrations of Mnase.

first: Wim

last: de Jonge

first: Eoghan

last: O'Duibhir

first: Philip

last: Lijnzaad

first: Dik

last: van Leenen

first: Patrick

last: Kemmeren

first: Frank

last: Holstege


title: Macrophage ontogeny underlies differences in tumor-specific education in brain malignancies

status: Public on Nov 10 2016

first: Robert

last: Bowman

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania School of Medicine

summary: Recent efforts have uncovered immense transcriptional and ontogenetic diversity among tissue-resident macrophages, each with their own transcriptional profile endowing the cell with its tissue-specific functions. However, it is currently unknown whether the origins of different macrophage populations may affect their roles in malignancy. Given potential artifacts associated with irradiation-based lineage tracing, it remains unclear if bone marrow-derived macrophages (BMDM) are even present in tumors of the brain, a tissue where there is no homeostatic involvement of peripherally-derived myeloid cells. Here, we employed multiple models of murine brain malignancy and genetic lineage tracing models to demonstrate that BMDM are indeed abundant in primary and metastatic brain tumors. Transcriptional profiling of tumor-associated BMDM and resident microglia showed that these cells acquire substantially different gene expression profiles. Our data suggest that transcriptional networks in each cell population are associated with tumor-mediated education, yet are also influenced by chromatin landscapes established before tumor initiation. Furthermore, we demonstrate that microglia specifically repress Itga4 (CD49D), enabling its utility as a discriminatory marker between brain-resident microglia and peripherally-derived macrophages in both primary and metastatic disease in mouse and human.

overall_design: Tumor associated microglia and macrophages were isolated from mouse glioma tumors.  Samples are provided as matched microglia and macrophages from 3 tumors.

first: Johanna

last: Joyce


title: HSF1 and MOT1-expression and binding: Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

type: Genome binding/occupancy profiling by array

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

overall_design: Refer to individual Series


title: A novel L-arabinose-responsive regulator found in the rice-blast fungus Pyricularia oryzae (Magnaporthe oryzae)

first: miaomiao

last: Zhou

address: Uppsalalaan 8

department: fungal physiology

institute: centre of fungal biodiversity, Utrecht, KNAW

summary: In this study we identified the L-arabinose-responsive regulator of Pyricularia oryzae that regulates L-arabinose release and catabolism. Previously we identified the Zn2Cys6 transcription factor (TF) AraR that has this role in the Trichocomaceae family (Eurotiales), but is absent in other fungi. Candidate Zn2Cys6 TF genes were selected according to their transcript profiles on L-arabinose. Deletion mutants of these genes were screened for their growth phenotype on L-arabinose. One mutant, named Δara1, was further analyzed. Our analysis demonstrated that Ara1 from P. oryzae is the functional homolog of AraR from A. niger, while sequence analysis did not reveal significant homology between them.

overall_design: Putative P. oryzae L-arabinose responsive regulators were selected by  the comparison of RNAseq data of P. oryzae wild type strain grown for 2 hours on D-fructose and a time-course (2, 4 and 8 h) on L-arabinose.

first: Miaomiao

first: Sylvia

last: Klaubauf

first: Marc-Henri

last: Lebrun

first: Ronald

last: de Vries

first: Evy

last: Battaglia


title: Differential gene expressions in the hypertensive heart using Angiotensin II infusion model

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary: Differential gene expressions were constructed through expression profiling of a total of 22,556 genes in the hypertensive heart during the early and lately phase of Angiotensin II infusion, then 1019 or 647 significant differential genes were filtered based on the criteria (p<0.05 and fold change >2 or 1.5), respectively.

overall_design: In the study presented here, the mice were infused Angiotensin II for 0, 7, 28 days (n=2). The hearts were collected and performed transcriptome analysis by RNA-sequencing. Compared to control, 1019 or 537 significant differentially expressed genes (filtering criteria p<0.05, fold change >2.0 for 7 days; fold change >1.5 for 28 days) were identified 7-days or 28 days post-Ang II infusion.

first: Yulin

last: Li

first: Wanshi

last: Cai


title: Genome-wide mapping of autonomous promoter activity in human cells

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

summary: Previous methods to systematically characterize sequence-intrinsic activity of promoters have been limited by relatively low throughput and the length of sequences that could be tested.  Here we present Survey of Regulatory Elements (SuRE), a method to assay more than 10^8 DNA fragments, each 0.2-2kb in size, for their ability to drive transcription autonomously. In SuRE, a plasmid library is constructed of random genomic fragments upstream of a 20bp barcode and decoded by paired-end sequencing. This library is then transfected into cells and transcribed barcodes are quantified in the RNA by high throughput sequencing. When applied to the human genome, we achieved a 55-fold genome coverage, allowing us to map autonomous promoter activity genome-wide. By computational modeling we delineated subregions within promoters that are relevant for their activity. For instance, we show that antisense promoter transcription is generally dependent on the sense core promoter sequences, and that most enhancers and several families of repetitive elements act as autonomous transcription initiation sites.

overall_design:
SuRE-seq assays in K562 cell-line; 1 experiment using library SuRE23 covering the entire K562 genome, with 2 biological replicates (with 4 and 2 PCR replicates resp.); 1 experiment using a library derived from
9 BACs covering in total 1.3Mb of the genome (SuRE BAC library), including hemin treated and control samples, with 1 biological replicate (each with 2 PCR replicates).

first: Joris

last: van Arensbergen

first: Ludo

last: Pagie

first: Vincent

middle: D

last: FitzPatrick

first: Harmen

last: Bussemaker

first: Marcel

last: de Haas


title: The SPOP-containing Complex Functions as an E3 Ligase for SETD2 to Regulate Gene-Specific H3K36me3-Coupled Alternative Splicing

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

summary: H3K36me3 has been reported to associate with active gene expression, and SETD2 is the mainly methyltransferase for H3K36me3. We identified SPOP which is a CUL3 family protein as a E3 ligase for SETD2. Genome wide analysis by using ChIPSeq and RNASeq demonstrate that SPOP specificly eliminate H3K36me3 modification at target genes and resulted in alternative splicing of those target genes.

overall_design: RNA-Seq was perfomed in negative control(NC), siSPOP, siSEDT2, and SPOP/SETD2 double knock down cell lines. For alternative splicing events analysis illumina HiSeq4000 platform was used for sequencing with 150 paired end mode and sequencing reads range from 67 million to 90 million. H3K36me3 ChIP-Seq was performed in NC, siSPOP, siSETD2, SPOP and SETD2 double knock down cell lines. ChIP-Seq libraries were sequenced by HiSeq 2500 platform with single end 50bp mode.

first: Kun

last: Zhu

first: Xiang

last: Wang

first: Lin-gao

last: Ju


title: The dynamic landscape of fission yeast meiosis alternative-splice isoforms

city: Pittsburgh

first: Zheng

last: Kuang

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

summary: Alternative splicing increases the diversity of transcriptomes and proteomes in metazoans. The extent to which alternative splicing is active and functional in unicellular organisms is less understood. Here we exploit a single-molecule long-read sequencing technique and develop a computational tool, SpliceHunter, to characterize the transcriptome in the meiosis of fission yeast. We reveal 17017 alternative splicing events in 19741 novel isoforms at different stages of meiosis, including antisense and read-through transcripts. Intron retention is the major type of alternative splicing, followed by “alternate intron in exon”. 887 novel transcription units are detected; 60 of the predicted proteins show homology in other species and form theoretical stable structures. We compare the dynamics of novel isoforms based on the number of supporting full-length reads with those of annotated isoforms and explore the translational capacity and quality of novel isoforms. The evaluation of these factors indicates that the majority of novel isoforms are unlikely to be both condition-specific and translatable but the possibility of functional novel isoforms is not excluded. Together, this study highlights the diversity and dynamics at the isoform level in the sexual development of fission yeast.

overall_design: 2 replicates of 6 time points total RNA for pacbio sequencing

first: Jef

last: Boeke

first: Stefan

last: Canzar


title: Single cell transcriptomics defines human islet cell signatures and reveals cell-type-specific expression changes in type 2 diabetes [bulk]

status: Public on Nov 09 2016

city: Farmington

first: Michael

last: Stitzel

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary:
Blood glucose levels are tightly controlled by the coordinated action of at least five cell types constituting pancreatic islets. Changes in the proportion and/or function of these cells are associated with genetic and molecular pathophysiology of monogenic, type 1, and type 2 diabetes (T2D). Cellular heterogeneity impedes precise understanding of the molecular components of each islet cell type that govern islet dysfunction, particularly the less abundant delta and gamma/pancreatic polypeptide (PP) cells. Here, we report single cell transcriptomes for 617 islet cells after profiling ~1000 cells from non-diabetic (ND) and T2D human organ donors. Analyses of non-diabetic single cell transcriptomes identified distinct alpha, beta, delta, and PP/gamma cell-type signatures. Genes linked to rare and common forms of islet dysfunction and diabetes were expressed in the delta and PP/gamma cell types. Moreover, this study revealed that delta cells specifically express receptors that receive and coordinate systemic cues from the leptin, ghrelin, and dopamine signaling pathways implicating them as integrators of central and peripheral metabolic signals into the pancreatic islet. Finally, single cell transcriptome profiling revealed genes differentially regulated between T2D and ND alpha, beta, and delta cells that were undetectable in paired whole islet analyses. This study thus identifies fundamental cell type-specific features of pancreatic islet (dys)function and provides a critical resource for comprehensive understanding of islet biology and diabetes pathogenesis.

Grant ID: Award No. W81XWH-16-1-0130
Grant title: Peer Reviewed Medical Research Program
Funding Source: Assistant Secretary of Defense for Health Affairs
Affiliation: Jackson Laboratory for Genomic Medicine, Farmington, CT
Name: Michael Stitzel

overall_design: RNA-seq profiles of 24 human pancreatic islet/other bulk cell samples obtained from non-diabetic and type 2 diabetic cadaveric organ donors.

first: Nathan

last: Lawlor

first: Joshy

last: George

first: Mohan

last: Bolisetty

first: Romy

last: Kursawe

first: Lili

last: Sun

first: V

last: Sivakamasundari

first: Ina

last: Kycia

first: Paul

last: Robson

middle: L


title: Single cell transcriptomics defines human islet cell signatures and reveals cell-type-specific expression changes in type 2 diabetes [single cell]

overall_design: RNA-seq profiles of 638 human pancreatic islet/other single cells obtained from 5 non-diabetic and 3 type 2 diabetic cadaveric organ donors.


title: Sox2 is the determining oncogenic switch in promoting lung squamous cell carcinoma from different cells-of-origin

first: Anton

last: Berns

state: Amsterdam

address: Plesmanlann 121

department: Division of Molecular Genetics

institute: NKI

summary: Squamous cell carcinoma (SCC) of lung is a devastating malignancy with no effective  treatments, due to its complex genomic profile. Therefore, pre-clinical models  mimicking its salient features are urgently needed. Here we describe mouse models  bearing various combinations of genetic lesions predominantly found in human SCC.  We show that Sox2 but not Fgfr1 overexpression in tracheobronchial basal cells  combined with Cdkn2ab and Pten loss results in SCC closely resembling the human  counterpart. Interestingly, Sox2;Pten;Cdkn2ab mice develop SCC with a more  peripheral location when Club or Alveolar type 2 (AT2) cells are targeted. Our model  highlights the essential role of Sox2 in promoting a squamous cell fate from different  cells-of-origin and represents an invaluable tool for the developing better intervention  strategies.

overall_design: After RNA extraction and Bioanalyzer analysis, we processed samples with high quality RNA profiles using Illumina Hiseq2500.

first: Giustina

last: Ferone

first: Ji-Ying

last: Song

first: Kate

last: Sutherland

first: Rajith

last: Bhaskaran

first: Jan-Paul

last: Lambooij

first: Natalie

last: Proost

first: Gaetano

last: Gargiulo


title: REST regulation of gene networks in adult neural stem cells

city: Dallas

first: Jenny

last: Hsieh

state: Texas

address: 6001 Forest Park Road, NA6.514AA

institute: UT Southwestern Medical Center


title: Genome-wide sequencing of REST binding (ChIP-seq) in adult hippocampal neural stem cells in vitro a.k.a. HCN cells in quiescent (iQNP) and proliferative (TAP) conditions

summary: We report the high-throughput profiling of REST binding in mammalian adult hippocampal stem cells in culture (HCN cells). By obtaining 33 to 38 million single-end reads of sequence from chromatin immunoprecipitated DNA, we generated genome-wide REST binding state of HCN cells in induced quiescent (iQNP) and proliferating (TAP) conditions. Thereafter, we annotated the peaks to genomic regions and associated genes. We find that with +/-10kb of transcription start site of genes, REST efficiently binds neuronal genes and represses them in HCN cells in both iQNP and TAP conditions. Moreover, only in the iQNP REST also binds non-neuronal genes like DNA replication genes. This study reveals that in addition to its well known function as a neuronal repressor in non-neuronal tissue, REST can also play other diverse roles in non-neuronal tissues.

overall_design: Examination of REST binding in two growth conditions

first: Shradha

last: Mukherjee


title: Genome wide transcriptome analysis (RNA-seq) of adult hippocampal neural stem cells in vitro a.k.a. HCN cells in quiescent and proliferative conditions in non-electroporated or electroporated with control empty vector or REST knock-down shRNA vector

summary: We report the high-throughput transcriptome profiling of induced quiescent (iQNP) and proliferative (TAP) conditions in mammalian adult hippocampal stem cells in culture (HCN cells). By obtaining 145 to 78 million pair-end reads of sequence from isolated RNA from HCN cells in iQNP and TAP conditions. Thereafter, we intersected this gene expression data with REST bound ChIP-seq peaks within +/-10kb of transcription start site of genes also from HCN cells in iQNP and TAP conditions. We find that with +/-10kb of transcription start site of genes, REST efficiently binds neuronal genes and represses them in HCN cells in both iQNP and TAP conditions. Moreover, only in the iQNP REST also binds non-neuronal genes like DNA replication genes. We also report the high-throughput transcriptome profiling of iQNP and TAP condition HCN cells electroporated with a control empty vector or REST knock-down shRNA vector. By obtaining 145 to 78 million pair-end reads of sequence from isolated RNA from HCN cells in electroporated control empty vector or REST knock-down vector in iQNP and TAP conditions. In REST knockdown in iQNP and TAP conditions we found that predominantly non-neuronal genes and neuronal genes were derepressed. This study reveals that in addition to its well known function as a neuronal repressor in non-neuronal tissue, REST can also play other diverse roles in non-neuronal tissues.

overall_design: Examination of global gene expression or transcriptome in two growth conditions in non-electroporated or with electroporation of a control empty vector or REST knock-down shRNA vector


title: Chromatin environment, transcriptional regulation and splicing distinguish lncRNAs and mRNAs [NucFrac]

city: Cambridge

first: MARTA

last: MELE

address: 7 divinity avenue

department: Harvard Stem Cells and Regenerative Biology

institute: Harvard University

summary: While long noncoding RNAs (lncRNAs) and mRNAs share similar biogenesis pathways, these two transcript classes differ in many regards. LncRNAs are less conserved, less abundant, and more tissue specific than mRNAs, implying that our understanding of lncRNA transcriptional regulation is incomplete. Here, we perform an in depth characterization of numerous factors contributing to this regulation. We find that lncRNA promoters contain fewer transcription factor binding sites than do those of mRNAs, with some notable exceptions. Surprisingly, we find that H3K9me3 –typically associated with transcriptional repression–is enriched at active lncRNA loci. However, the most discriminant differences between lncRNAs and mRNAs involve splicing: only half of lncRNAs are efficiently spliced, which can be partially attributed to defects in lncRNA splicing signals and diminished U2AF65 binding. These attributes are conserved between humans and mice. Finally, we find that certain transcriptional properties are enriched in known, functionally characterized lncRNAs, demonstrating that our multidimensional analysis might discern lncRNAs that are likely to be functional

overall_design: Examination of RNA abundance for cytosolic and nuclear fractions in mouse ES cells. Two replicates each.

first: Marta

last: Mele

first: David

last: Sheqner

first: John

last: Rinn


title: small RNA-seq from gastroesophageal sphincter (ENCSR998CRC)

status: Public on Nov 08 2016

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's esophagogastric junction tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Chromatin environment, transcriptional regulation and splicing distinguish lncRNAs and mRNAs [Stability]

overall_design: Examination of RNA abundance in two cell lines (K562 and Hues9) and 5 time points after actinomycin D treatment. Three replicates per time point and cell type.

first: Chiara

last: Gerhardinger


title: Chromatin environment, transcriptional regulation and splicing distinguish lncRNAs and mRNAs