title: Global LexA1 binding sites assessment in Leptospira interrogans serivar Copenhageni using ChIP-seq

city: Sao Paulo

first: Paulo

last: Lee Ho

state: SP

address: 1500 Vital Brazil

department: Centro de Biotecnologia

country: Brazil

institute: Instituto Butantan

summary: The pathogen L. interrogans serovar Copenhageni can be shed in the urine of carrier mammals, and infect humans after weeks on water or mud. This wide range of possible niches implies the bacterium can be exposed to several different genotoxic stresses during its lifecycle.  We assessed the impact of DNA damage in this leptospire, integrating high throughput data from ChIP-seq and DNA microarrays to determine the role of the SOS regulator LexA1. We observed 24 LexA1 binding sites located throughout the chromosome 1 and one in chromosome 2. Analyses of LexA1 ChIP-seq peak sequences revealed the SOS box is an imperfect asymmetric palindrome of 16bp, CTAA[A/T/G]CANNTG[T/A]TTAG. DNA damage caused significant changes of several aspects of bacterial physiology, decreasing expression of genes involved in energy metabolism and translation, in addition to genes related to virulence and motility. On the other hand, post replicative and recombination repair, but not the canonical DNA repair genes, were up regulated. The most striking feature of this response was the massive up-regulation of two prophages. Our findings point to an expression profile shift from cell growth and virulence to mutagenesis and recombination, emphasizing the fundamental role of DNA damage response as a highway for adaptation and evolution.

sample_organism: Leptospira interrogans serovar Copenhageni

overall_design: Two pairs of samples were used: two "total" samples from lysates from exponential growing cells, crosslinked with 2% final concentration of formaldehyde and the corresponding immunoprecipitated sample. One lysate was crosslinked for 40min, and the other for 60min. The immunoprecipitation was carried with anti-LexA1 mice sera in 1:100 final concentration, and protein G Sepharose resin. The DNA from total and immunoprecipitated samples were isolated, size-selected for 200-400bp and sequenced by HiSeq. Aligment of reads to the reference genome was performed by Bowtie2 and peak-calling with CisGenome, using the total samples as background.

first: Luciane

last: Schons-Fonseca

first: Josefa

middle: B

last: da silva

first: Juliana

last: Milanez

first: Janet

middle: L

last: Smith

first: Helder

last: Nakaya

first: Alan

last: Grossman

last: Ho

first: Renata

last: da Costa


title: roX ChIRP-seq in four Drosophila species

status: Public on Jan 25 2016

city: Stanford

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

country: USA

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We identified orthologs of the roX lncRNAs across diverse Drosophilid species, and then mapped the genomic binding sites of roX1 and roX2 in four Drosophila species (D. melanogaster, D. willistoni, D. virilis, and D. busckii) using ChIRP-seq (chromatin isolation by RNA Purification and sequencing), thus revealing the interplay of the evolution of roX1 and roX2 and their genomic binding sites.

sample_organism:
Drosophila melanogaster
Drosophila virilis
Drosophila willistoni
Drosophila busckii

overall_design: We found roX1 and roX2 orthologs in D. willistoni, D. virilis, and D.busckii and designed antisense biotinylated 20-mer ChIRP oligos against each RNA target. The ChIRP oligo pools were then divided into Even (E) or Odd (O) pools for independent ChIRP experiments for each RNA target. In each species, chromatin was prepared directly from larval tissue; the RNA target was recovered using the indicated ChIRP oligo pools. Input DNA was sampled from the prepared chromatin. DNA from each ChIRP-seq experiment was purified, prepared into libraries, and sequenced as described. Each sample was then mapped to the respective Drosophila genome; each even-odd pair was then merged and peaks were called using MACS2.

first: Jeffrey

middle: J

last: Quinn

first: Qiangfeng

middle: C

last: Zhang

first: Howard

middle: Y

last: Chang


title: MicroRNAs 24 and 27 suppress allergic inflammation and target a network of regulators of T helper-2 cell-associated cytokine production

status: Public on Jan 22 2016

city: San Francisco

first: Heather

middle: H

last: Pua

address: 513 Parnassus Ave, HSE-201, Box 0997

institute: UCSF

type: Expression profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are important regulators of cell fate decisions in immune responses. They act by coordinate repression of multiple target genes, a property that we exploited to uncover regulatory networks that govern T helper-2 (Th2) cells. A functional screen of individual miRNAs in primary T cells uncovered multiple miRNAs that inhibited  Th2 cell differentiation. Among these were miR-24 and miR-27, miRNAs coexpressed from two genomic clusters, which each functioned independently to limit interleukin-4 (IL-4) production. Mice lacking both clusters in T cells displayed increased Th2 cell responses and tissue pathology in a mouse model of asthma. Gene expression and pathway analyses placed miR-27 upstream of genes known to regulate Th2 cells. They also identified targets not previously associated with Th2 cell biology which regulated IL-4 production in unbiased functional testing. Thus, elucidating the biological function and target repertoire of miR-24 and miR-27 reveals regulators of Th2 cell biology.

overall_design: Gene expression analysis of miRNA-deficient mouse CD4+ T cells transfected with miRNA mimics twice over a 5 day in vitro culture in the presence of low amounts of exogenous IL-4 (10U/ml). Cells transfected with either miR-23, miR-24 or miR-27 were compared to cells transfected with a control mimic.  Data are from at least biologic triplicates.

first: Karl

middle: M

last: Ansel


title: Δ9-tetrahydrocannabinol  (Δ9-THC) promotes neuroimmune-modulatory microRNA profile in striatum of simian immunodeficiency virus (SIV)-infected macaques.

city: New Orleans

first: Liz

last: Simon

state: Louisiana

address: 1901 Perdido Street

department: Physiology

institute: Louisiana State University Health Sciences Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Cannabinoid administration before and after simian immunodeficiency virus (SIV)-inoculation ameliorated disease progression and decreased inflammation in male rhesus macaques. Δ9-tetrahydrocannabinol (Δ9-THC) did not increase viral load in brain tissue or produce additive neuropsychological impairment in SIV-infected macaques. To determine if the neuroimmunomodulation of Δ9-THC involved differential microRNA (miR) expression, miR expression in the striatum of uninfected macaques receiving vehicle (VEH) or Δ9-THC (THC) and SIV-infected macaques administered either vehicle (VEH/SIV) or Δ9-THC (THC/SIV) was profiled using next generation deep sequencing.

overall_design: Brains were removed, flash frozen on dry ice, and RNA was harvested using Norgen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit was used with 500 ng of total RNA for the construction of sequencing libraries.

first: Keijing

last: Song

first: Curtis

middle: V

last: Stouwe

first: Andrew

last: Hollenbach

first: Angela

last: Amedee

first: Mahesh

last: Mohan

first: Peter

last: Winsauer

first: Patricia

last: Molina


title: Genome-wide profiling of the DNA methylation landscape at base-pair resolution in human neurological disorders (Bisulfite-Seq)

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

type: Methylation profiling by high throughput sequencing

summary: Whole genome bisulphite sequencing of 4 human neurological disorders.

overall_design: Sequencing of bisulfite converted DNA of brain samples from patient suffering from Down’s syndrome, Dementia of Lewy bodies or Alzheimer's and Parkinson's disease.

first: Holger

last: Heyn


title: Identification of Novel and Differentially Expressed MicroRNAs in Goat Enzootic Nasal Adenocarcinoma

city: Yaan

first: Yan

middle: Qi

last: gui

address: Xin kang road no.48

department: College of Veterinary Medicine

country: China

institute: Sichuan Agricultural University

summary: Enzootic nasal adenocarcinoma (ENA), an epithelial tumor induced in goats and sheep by enzootic nasal tumor virus (ENTV), is a chronic, progressive, contact sexually transmitted disease. This study aimed to identify novel and differentially expressed miRNAs in the tumor and para-carcinoma nasal tissues of Nanjiang yellow goats with ENA. Small RNA Illumina high-throughput sequencing was used to construct a goat nasal miRNA library; 406 known miRNAs and 29 novel miRNAs were identified. A total of 116 miRNAs were significantly differentially expressed in para-carcinoma nasal tissues and ENA (54 downregulated; 60 upregulated; 2 only expressed in control group); Target gene prediction and functional analysis revealed that 6176 non-redundancy target genes, 1792 significant GO and 97 significant KEGG pathway for 121 miRNAs (116 significant expression miRNAs and 5 star sequence) were predicted. GO and KEGG pathway analysis revealed the majority of target genes in ENA are involved in cell proliferation, signal transduction and other processes associated with cancer. This is the first large-scale identification of miRNAs in Capra hircus ENA and provides a theoretical basis for investigating the complicated miRNA-mediated regulatory networks involved in the pathogenesis and progression of ENA.

overall_design: miRNA expression profiles of goat nose tissues between enzootic nasal adenocarcinoma and para-carcinoma nasal tissues were generated by deep sequencing using Illumina Hiseq 2500

first: Ye

last: Ni

first: Wang

last: Bin

middle: Q

last: Gui


title: RNA-seq analysis reveals MAPKKK family members related to drought tolerance in maize

city: Beijing

first: Xu

middle: Zhao

last: Gao

state: Beijing

address: The Summer Palace Road No. 5

department: College of Biological Sciences

institute: Peking University

summary: The mitogen-activated protein kinase (MAPK) cascade is an evolutionarily conserved signal transduction pathway that is involved in plant development and stress responses. As the first component of this phosphorelay cascade, mitogen-activated protein kinase kinase kinases (MAPKKKs) act as adaptors linking upstream signaling steps to the core MAPK cascade to promote the appropriate cellular responses; however, the functions of MAPKKKs in maize are unclear. Here, we identified 71 MAPKKK genes, of which 14 were novel, based on a computational analysis of the maize (Zea mays L.) genome. Using an RNA-seq analysis in the leaf, stem and root of maize under well-watered and drought-stress conditions, we identified 5,866 differentially expressed genes (DEGs), including 8 MAPKKK genes responsive to drought stress. Many of the DEGs were enriched in processes such as drought stress, abiotic stimulus, oxidation-reduction, and metabolic processes.  The other way round, DEGs involved in processes such as oxidation, photosynthesis, and starch, proline, ethylene, and salicylic acid metabolism were clearly co-expressed with the MAPKKK genes. Furthermore, a quantitative real-time PCR (qRT-PCR) analysis was performed to assess the relative expression levels of MAPKKKs. Correlation analysis revealed that there was a significant correlation between expression levels of two MAPKKKs and relative biomass responsive to drought in 8 inbred lines. Our results indicate that MAPKKKs may have important regulatory functions in drought tolerance in maize.

overall_design: Totally six samples, two treatments and three organs

first: Ya

last: Liu

first: Miaoyi

last: Zhou

first: Zhaoxu

first: Wen

last: Ren

first: Hang

last: He

first: Jiuran

last: Zhao


title: Genome-scale profiling of the DNA methylation landscape in human neurological disorders

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

overall_design: Refer to individual Series


title: Cancer Immunosurveillance by Innate Lymphoid Cells and Innate-like T Cells

status: Public on Jan 21 2016

city: New York

first: Saida

last: Dadi

state: NY

address: 1275 York Ave

department: Immunology

institute: MSKCC

summary: Malignancy can be suppressed by the immune system in a process termed immunosurveillance.  However, to what extent immunosurveillance occurs in spontaneous cancers and the composition of participating cell types remain obscure.  Here we show that cell transformation triggers a tissue-resident lymphocyte response in oncogene-induced murine cancer models.  Non-circulating cytotoxic lymphocytes, derived from innate, TCRαβ and TCRγδ lineages, expand in early tumors.  Characterized by high expression of NK1.1, CD49a and CD103, these cells share a gene expression signature distinct from those of conventional NK cells, T cells and invariant NKT cells.  Generation of these lymphocytes is dependent on the cytokine IL-15, but not the transcription factor Nfil3 that is required for the differentiation of tumor-infiltrating NK cells; and IL-15, but not Nfil3, deficiency results in accelerated tumor growth.  These findings reveal a novel tumor-elicited cancer immunosurveillance mechanism that engages unconventional type 1-like innate lymphoid cells and type 1 innate-like T cells.

overall_design: Total 11 samples were analyzed. 2 replicates per sample.

first: Sagar

last: Chhangawala


title: Gene expression profiling and mutation analysis of B cell lymphomas arising in mice expressing NIK and BCL6 transgenes

status: Public on Jan 23 2016

city: Boston

first: Baochun

last: Zhang

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: In this study, by RNA sequencing we generated the gene expression profile (GEP) of each mouse lymphoma. By comparing the GEP of a lymphoma to that of normal B cells at physiological differentiation stages, we classified the lymphomas to either ABC- or GCB-type of DLBCL. Analysis of RNA sequencing data also led to identification of various mutations in these lymphomas.

overall_design: In this experiment, 12 lymphoma samples, 6 reference samples (two resting B cell controls, two activated B cell controls (ABC) and two germinal center B cell controls (GCB))

first: Klaus

last: Rajewsky

first: Dinis

last: Calado

first: Wei

last: Chen


title: E2F1 transcription factor knockdown effect on gene expression in LNCaP-abl cells

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

summary: Our computational approach identified E2F1 as a potential collaborator of EZH2 in androgen-independent prostate cancer. This experiment is to designed to validate the crosstalking of E2F1 and EZH2 pathways. We showed that majority of the EZH2-induced genes in androgen-independent prostate tumor cells are in downstream of E2F1, providing insight into the EZH2-E2F1 collaborative regulatory pathway.

overall_design: We performed RNA-seq experiments to compare the gene expression profles before and after E2F1 siRNA silencing

first: Housheng

first: Han

last: Xu

first: Myles

last: Brown

first: X

middle: S


title: The LSM1-7 Complex Differentially Regulates Arabidopsis Tolerance to Abiotic Stress Conditions by Promoting Selective mRNA Decapping

city: Madrid

first: Carlos

last: Perea-Resa

address: Ramiro de Maeztu,9

institute: CIB-CSIC

summary: We report the role of LSM1-7 complex in the Arabidopsis tolerance to abiotic stresses. LSM1-7 controls gene expression reprogramming at the post-transcriptional level by promoting the decapping of mRNA. This function is selectively achieve over selected stress-induced transcripts depending on stress nature.

overall_design: Comparison of transcriptomes from Col-0 and lsm1a lsm1b plants exposed to low temperatures, drought or high salt conditions

first: Cristian

last: Carrasco-López

first: Rafael

last: Catalá

first: Veronika

last: Turečková

first: Ondrej

last: Novak

first: Weiping

first: Leslie

middle: E

last: Sieburth

first: Jose

last: Jiménez-Gómez

first: Julio

last: Salinas


title: Nonsense-Mediated Decay restricts lncRNAs levels in yeast unless blocked by double-stranded RNA structure

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Antisense long non-coding (aslnc)RNAs represent a substantial part of eukaryotic transcriptomes that are, in yeast, controlled by the Xrn1 exonuclease. Nonsense-Mediated Decay (NMD) destabilizes the Xrn1-sensitive aslncRNAs (XUT), but what determines their sensitivity remains unclear. We report that 3’ single-stranded (3’-ss) extension mediates XUTs degradation by NMD, assisted by the Mtr4 and Dbp2 helicases. Single-gene investigation, genome-wide RNA analyses and double-stranded (ds)RNA mapping revealed that 3'-ss extensions discriminate the NMD-targeted XUTs from stable lncRNAs. Ribosome profiling showed that XUT are translated locking them for NMD activity. Interestingly, mutants of the Mtr4 and Dbp2 helicases accumulated XUTs, suggesting that dsRNA unwinding is a critical step for degradation. Indeed, expression of anti-complementary transcripts protects cryptic intergenic lncRNAs from NMD. Our results indicate that aslncRNAs form dsRNA that are only translated and targeted to NMD if dissociated by Mtr4 and Dbp2. We propose that NMD buffers genome expression by discarding pervasive regulatory transcripts.

overall_design:
Strand-specific transcriptome analysis of biological replicates (1) of WT and xrn1-delta cells of the S288C, W303 and SK1 (n & 2n) genetic background of S. cerevisiae; (2) of WT, dcp2-7 and upf1-delta cells; (3) of WT, xrn1-delta and dcp2-7 cells upon treatment of total RNA with Terminator 5'-Phosphate-Dependent Exonuclease.
This record also contains CAGE-Seq analysis in wild-type and decapping-deficient cells of the budding yeast S. cerevisiae.

first: Marc

last: Descrimes

first: Nicolas

last: Vogt

first: Anne-Sophie

last: Dallongeville

first: Daniel

last: Gautheret

first: Antonin

last: Morillon


title: Newly constructed network models of different WNT signaling cascades applied to breast cancer expression data

city: Göttingen

first: Tim

last: Beissbarth

address: Humboldtallee 32

department: Medical Statistics

country: Germany

institute: University Medical Center Göttingen

summary:
RNA-Seq profiling of MCF-7 and MDA-MB-231.
We profiled RNA expression in the estrogen-receptor-positive (ER+) MCF-7 and the triple-negative MDA-MB-231 breast cancer cells.
The objective was to find genes differentially expressed between these cell lines as potential drivers of invasiveness of the triple-negative MDA-MB-231.
We further utilized the identified differential genes to validate expression-responsive module of non-canonical Wnt signaling pathway.

overall_design: 2 biological replicates of MCF-7 and 3 biological replicates of MDA-MB-231

first: Michaela

last: Bayerlová

first: Florian

last: Klemm

first: Kerstin

last: Menk

first: Annalen

last: Bleckmann


title: Quantitative Analysis of mRNA expression in calvaria tissue from control and Med23-/-  vs. wild type and Runx2+/- mice through Next Generation Sequencing

city: Shanghai

first: Gang

last: Wang

address: 320 Yueyang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

summary: We sequenced mRNA from 12 single newborn mouse calvaria tissues ( from 3 control and 3 Med23-/- cKO mice from a litter; 3 wildtype and 3 Runx2+/- mice from another litter) to investigate the correlation between Med23 and Runx2 in terms of affect on the mRNA level by their deficiencies. We find there is a positiove correlation in gobal gene expression affected by defiencies of the two genes.

overall_design: Examination of mRNA levels in individual newborn murine calvaria.

first: Zhen

last: Liu

first: Yichi

last: Xu

first: Xiao

last: Yao


title: Investigating gene expression changes upon ageing in chm mutants

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

summary: We report here mRNA-seq data of adult male Drosophila head tissues. We compare two different ages: young and midlife as well as chm/chameau (CG5229) heterozygous mutants.

overall_design: Comparison of ageing effect (young vs. midlife) in wild-type and mutant.

first: Shahaf

last: Peleg

first: Catherine

last: Regnard


title: H2A.Z.1 mono-ubiquitylation antagonizes BRD2 to maintain poised chromatin in ESCs

city: Cambridge

first: Laurie

middle: A

last: Boyer

address: 77 Massachusetts Avenue

department: Biology

institute: Massachusetts Institute of Technology

summary: Histone variant H2A.Z occupies the promoters of active and poised, bivalent genes in ESCs to regulate developmental programs, yet how it contributes to these contrasting states is poorly understood. Here, we investigate the function of H2A.Z.1 mono-ubiquitylation (H2A.Z.1ub) by mutation of the PRC1 target residues (H2A.Z.1K3R3). We show that H2A.Z.1K3R3 is properly incorporated at target promoters in murine ESCs (mESCs), however, loss of mono-ubiquitylation leads to de-repression of bivalent genes, loss of Polycomb binding, and to faulty lineage commitment. Using quantitative proteomics, we find that tandem bromodomain proteins, including the BET family member Brd2, are enriched in H2A.Z.1 chromatin. We further show that Brd2 is gained at de-repressed promoters in H2A.Z.1K3R3 mESCs whereas Brd2 inhibition restores gene silencing at these sites. Together, our study reveals an antagonistic relationship between H2A.Z.1ub and Brd2 to regulate the transcriptional balance at bivalent genes to enable proper execution of developmental programs.

overall_design: ChIP-Seq analysis of BET proteins, Brd2 and Brd4, in wild type mESCs and mESCs harboring H2A.Z or H2A.Z.K3R3 (3 C-terminal lysines mutated to arginines) tagged with YFP, in the presence of a knockdown hairpin targeting the endogenous H2A.Z transcript.

first: Lauren

last: Surface

first: Paul

last: Fields


title: The MYC-MIZ1 interaction defines tumor identity

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary: Medulloblastoma (MB) is the most common malignant brain tumor. MB is a cerebellar tumor that occurs mostly in children between the ages of 3-7 years but also in adults. Human MBs are classified into four subgroups: Wingless (WNT), Sonic Hedgehog (SHH), Group 3 (G3) and G4, each of which with distinct molecular signatures. SHH MBs with MYCN amplification and TP53 mutations and G3 MBs characterized by C-MYC (MYC) overexpression in ~17% of cases from gene amplification with stem like properties, are the most aggressive and least curable with current therapeutic regimen.   Using an orthotopic transplant approach, we found that enforced expression of MYCN in cerebellar granule neural progenitors (CGNPs) from 5-7 days old Trp53-null mice induced SHH MBs after transfer in the cortices or cerebella of naive recipient mice. In contrast, overexpression of MYC induced G3 MBs. Because MYCN and MYC bind to the same E-box DNA sequences, we hypothesized that the difference between MYC and MYCN-induced gene expression and tumor identity might be due to their interaction with different partners in CGNPs.   In this study, we investigated the role of the Myc interacting zinc finger protein 1 (MIZ1). We found that MIZ1 binds with higher affinity to MYC than to MYCN and that MIZ1 and MYC co-occupy thousands of promoters in G3 MB.  Remarkably, enforced expression of a MYC mutant (MYCV394D) that no longer binds to MIZ1 in Trp53-null CGNPs or expression of wild type MYC in CGNPs that lack functional Miz1 resulted in massive changes of the resulting tumor’s transcriptional program. Tumors differed from both SHH and G3 medulloblastoma and had a later time of onset compared to MYC-driven G3 medulloblastoma.  Our data demonstrate that interaction of MYC with MIZ1 is required for the development of G3 medulloblastoma.

overall_design: ChIP-Seq experiments for Miz1, c-Myc and NMyc  from murine medulloblastoma material. Either sorted tumor cells (Miz1 and c-Myc) or spheres from tumor cells (Miz1 and NMyc) were used. Input-samples were sequenced as controls. RNA-Seq from G3 medulloblastomas after restoration of Atoh1 expression.

first: BaoHan

middle: T

last: Vo

first: Elmar

last: Wolf

first: Daisuke

last: Kawauchi

first: Anneli

last: Gebhardt

first: Jerold

last: Rehg

first: Susanne

last: Walz

first: David

last: Finkelstein

first: Brian

last: Murphy

first: Yong

last: Youn

first: Young-Goo

last: Han

first: Martine

middle: F

last: Roussel


title: DNA methylation dynamics during cotton ovule and fiber development [Bisulfite-Seq]

city: Austin

first: Qingxin

last: Song

state: Texas

address: 3517 North Hills Drive Apt C207

institute: UT austin

summary: DNA methylation is essential for plant and animal development. In plants, methylation occurs at CG, CHG, and CHH (H = A, C or T) sites. CHH methylation is established by the small RNA-directed DNA methylation (RdDM) pathway. Cotton is an allotetraploid consisting of two progenitor genomes, and each cotton fiber is a rapidly-elongating cell from the ovule epidermis. Here we show that inhibiting DNA methylation impairs fiber development. Genome-wide bisulfite -, mRNA-, and small RNA-sequencing analyses reveal that CHH hypermethyaltion through RdDM in euchromatin is associated with expression changes of nearby genes in ovules. The ovule-derived fiber cells not only maintain euchromatic CHH hypermethylation, but also generate additional heterochromatic CHH hypermethylation independent of RdDM. Moreover, CHG and CHH methylation in promoter and transcribed regions contribute to the expression bias of homoeologous genes in the allotetraploid cotton. This epigenetic and expression dynamics of developmental regulation could provide a molecular basis for natural selection and domestication of plants and animals.

overall_design: Libraries for MethylC-seq with two replicates, small RNA-seq with three replicates and mRNA-seq with two replicates were constructed using leaves, ovules at 0 DPA and 14 DPA, fibers at 14 DPA of Gossypium hirsutum cv. TM-1. These libraries were sequenced using Hiseq 2500.

first: Xueying

last: Guan

first: Z. Jeffrey

last: Chen


title: DNA methylation dynamics during cotton ovule and fiber development [ncRNA-Seq]


title: DNA methylation dynamics during cotton ovule and fiber development [RNA-Seq]


title: Dynamic Roles for Small RNAs and DNA Methylation during Ovule and Fiber Development in Allotetraploid Cotton

summary: DNA methylation is essential for plant and animal development. In plants, methylation occurs at CG, CHG, and CHH (H = A, C or T) sites via distinct pathways. Cotton is an allotetraploid consisting of two progenitor genomes. Each cotton fiber is a rapidly-elongating cell derived from the ovule epidermis, but the molecular basis for this developmental transition is unknown. Here we analyzed methylome, transcriptome, and small RNAome and revealed distinct changes in CHH methylation during ovule and fiber development. In ovules, CHH hypermethylation in promoters correlated positively with siRNAs, inducing RNA-dependent DNA methylation (RdDM), and up-regulation of ovule-preferred genes. In fibers, the ovule-derived cells generated additional heterochromatic CHH hypermethylation independent of RdDM, which repressed transposable elements (TEs) and nearby genes including fiber-related genes. Furthermore, CHG and CHH methylation in genic regions contributed to homoeolog expression bias in ovules and fibers. Inhibiting DNA methylation using 5-aza-2'-deoxycytidine in cultured ovules has reduced fiber cell number and length, suggesting a potential role for DNA methylation in fiber development. Thus, RdDM-dependent methylation in promoters and RdDM-independent methylation in TEs and nearby genes could act as a double-lock feedback mechanism to mediate gene and TE expression, potentiating the transition from epidermal to fiber cells during ovule and seed development.

overall_design: Gossypium hirsutum acc. TM-1 grew in the greenhouse at The University of Texas at Austin. Leaves and bolls (0 and 14 DPA) were harvested with three biological replications. Ovules and fibers were carefully dissected from cotton bolls at 14 DPA and immediately frozen in liquid nitrogen for RNA and DNA preparation.


title: RNA-seq analysis reveals genetic response and tolerance mechanisms to ozone exposure in soybean

city: Charlotte

first: Adam

middle: Michael

last: Whaley

state: NC

address: 9201 University City Blvd

department: Bioinformatics and Genomics

institute: UNCC

summary: Oxidative stress caused by ground level ozone is a major contributor to yield loss in a number of important crop plants.  Soybean (Glycine max) is especially ozone sensitive, and research into its response to oxidative stress is limited.  To better understand the genetic response in soybean to oxidative stress, an RNA-seq analysis of two soybean cultivars was performed comparing an ozone intolerant cultivar and an ozone resistant cultivar after being exposed to ozone.  A cursory analysis of the transcriptome data revealed differences between cultivars in the expression levels of genes previously implicated in oxidative stress responses, indicating unique cultivar-specific responses.  An examination of the timing of gene responses over the course of ozone exposure showed expression of cuticle wax genes in the intolerant line over all sampled time points, whereas the tolerant line only expressed this pathway in the first time point.  The ozone tolerant cultivar has a thicker leaf structure and we believe this lends a passive benefit to the plant which the intolerant cultivar is attempting to supplement via cuticle wax synthesis.  These results suggest that differences in genetic responses work in concert with physiological differences to explain differences in ozone tolerance between soybean cultivars.

overall_design: 16 total samples.  8 control, 8 at high ozone, 4 time points (30 minute increments starting 5 hours after introduction of ozone) .  Replicates were pooled at extraction.

first: Sajedeh

last: Safari

first: Jaime

last: Sheridan

first: Kent

last: Burkey

first: Amy

last: Burton

first: Jessica

last: Schlueter


title: Impacts of high ATP supply from chloroplasts and mitochondria on the leaf metabolism of Arabidopsis thaliana

city: Hong Kong

first: Anna

last: Liu

state: Hong Kong

address: Pokfulam Road

department: CS

country: Hong Kong

institute: HKU

summary: Arabidopsis thaliana ecotypes Columbia (overexpression line) was used in this study. After sterilization, the seeds were placed on Murashige and Skoog medium supplemented with 2% (w/v) sucrose for 10 days and then the seedling were transferred to soil under 16 hours light (22°C) / 8 hours dark (18°C) period in growth chamber at a light intensity of 120?150 µmol m-2 s-1. 20-day-old Arabidopsis leaves without bolting were immediately frozen in liquid nitrogen for RNA and protein and metabolites extraction. Leaves were harvested at three different time points: t = 0 hr (end of night), t = 1 hr (one hour after light turn on) and t = 8 hr (eight hours after light turn on), respectively.

overall_design: Total RNA was extracted from leaves at all three time points and DNA contamination was removed by DNase I (RNeasy Plant Mini Kit, Qiagen, Hong Kong).Ribosomal RNAs were removed from the total RNA by the Ribo-Zero rRNA removal kit for plant leaf (Epicentre, USA) before cDNA library construction. The libraries were sequenced using Illumina HiSeqTM2000. After removal of low quality reads, clean reads from three different RNA-seq samples (3 times points, t = 0, 1, 8) were aligned to Arabidopsis genome. No biological replication carried out in this experiment.

first: Chao

last: Liang

first: Yuzhe

last: Sun

first: Shifeng

last: Cheng

first: Boon-Leong

last: Lim


title: Ammopiptanthus mongolicus leaf gene expression under drought and cold stress

first: Luyang

last: Zhao

address: 28 Fuxing Road, HaiDian District

department: Department of Gynecology and Obstetrics

institute: People’s Liberation Army (PLA) Medical School, Chinese PLA General Hospital

summary: To undersand the machanism underlying the drought and cold srress tolerance of Ammopiptanthus mongolicus,we investigate the gene expression profile of Ammopiptanthus mongolicus leaves under drought stress(1hours,24hours,72hours) and low temperature (1hours,72hours ).

overall_design: Mesophyll mRNA profiles of  wild type (WT) Ammopiptanthus mongolicus leaf (normal,drought stress,cold stress)  were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Yijun

last: Zhou

first: Fei

last: Gao


title: Transcriptome profiling of sterile daf-2; mes-1 double vs. mes-1 single mutants

status: Public on Jan 20 2016

city: Santa Cruz

first: Andrew

middle: Kekupa'a

last: Knutson

address: 1156 High St

department: MCD Biology

institute: University of California, Santa Cruz

summary: The germ lineage is considered to be immortal.  In the quest to extend lifespan, a possible strategy is to drive germline traits in somatic cells, to try to confer some of the germ lineage’s immortality on the somatic body.  Notably, a study in C. elegans suggested that expression of germline genes in the somatic cells of long-lived daf-2 mutants confers some of daf-2’s longevity.  Specifically, mRNAs encoding components of C. elegans germ granules (P granules) were up-regulated in daf-2 mutant worms, and knock-down of individual P-granule and other germline genes in daf-2 young adults modestly reduced their lifespan.  We investigated the contribution of a germline program to daf-2’s long lifespan, and also tested if other mutants known to express germline genes in their somatic cells are long-lived.  Our key findings are:  1) We could not detect P-granule proteins in the somatic cells of daf-2 mutants by immunostaining or by expression of a P-granule transgene.  2) Whole-genome transcript profiling of animals lacking a germline revealed that germline transcripts are not up-regulated in the soma of daf-2 worms compared to the soma of control worms.  3) Simultaneous removal of multiple P-granule proteins or the entire germline program from daf-2 worms did not reduce their lifespan.  4) Several mutants that robustly express a broad spectrum of germline genes in their somatic cells are not long-lived.  Taken together, our findings argue against the hypothesis that acquisition of a germ cell program in somatic cells increases lifespan and contributes to daf-2’s longevity.

overall_design: Transcriptome profiles of 3 replicates of sterile daf-2; mes-1 double mutants (experimental) and 3 replicates of sterile mes-1 single mutants (control) grown at 24°C

middle: K

first: Andreas

last: Rechtsteiner

first: Susan

last: Strome


title: PTBP1 excludes UPF1 to protect long 3'UTRs from nonsense-mediated mRNA decay

city: Bethesda

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

institute: NIH

summary: RNA-seq analysis of human 293 Tet-off cells depleted of PTBP1 and UPF1 alone and in tandem with specific siRNAs.

overall_design: siRNA-based depletion of PTBP1, UPF1, and PTBP1/UPF1 together, with a validated non-silencing siRNA as a control.

first: Zhiyun

last: Ge

first: Bao-Lin

last: Quek

first: Karen

middle: L

last: Beemon

first: J

middle: R

last: Hogg


title: RNA profiling of p16ink4a-expressing pancreatic beta-cells

city: Jerusalem

first: Ittai

last: Ben-Porath

address: Ein-Kerem

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University Faculty of Medicine

summary: Transcriptome of beta-cells isolated from mice expressing p16ink4a and GFP transgenes  and of control β-cells isolated from mice expressing only the GFP transgene

overall_design: RNAseq of murine beta-cells sorted based on GFP expression from three Ins-rtTA/tet-GFP/tet-p16ink4a mice and two control Ins-rtTA/tet-GFP mice following 10 days tet-mediated induction.

first: Aharon

last: Helman

first: Agnes

last: Klochendler

first: Yuval

last: Dor


title: A Streamlined Tethered Chromosome Conformation Capture Protocol

city: Stanford

first: Idan

last: Gabdank

state: California

address: 3165 Porter Drive

department: Genetics

institute: Stanford

summary:
Background: Identification of locus-locus contacts at the chromatin level provides a valuable foundation for understanding of nuclear architecture and function and a valuable tool for inferring long-range linkage relationships. As one approach to this, chromatin conformation capture-based techniques allow creation of genome spatial organization maps.  While such approaches have been available for some time, methodological advances will be of considerable use in minimizing both time and input material required for successful application.
Results: Here we report a modified tethered conformation capture protocol that utilizes a series of rapid and efficient molecular manipulations. We applied the method to Caenorhabditis elegans, obtaining chromatin interaction maps that provide a sequence-anchored delineation of salient aspects of Caenorhabditis elegans chromosome structure, demonstrating a high level of consistency in overall chromosome organization between biological samples collected under different conditions. In addition to the application of the method to defining nuclear architecture, we found the resulting chromatin interaction maps to be of sufficient resolution and sensitivity to enable detection of large-scale structural variants such as inversions or translocations.
Conclusion: Our streamlined protocol provides an accelerated, robust, and broadly applicable means of generating chromatin spatial organization maps and detecting genome rearrangements without a need for cellular or chromatin fractionation.

overall_design: Application of modified version of TCC protocl using different C. elegans strains (N2 and glp-1)  in L1, and adult life stages.

first: Sreejith

last: Ramakrishnan

first: Anne

last: Villeneuve

middle: Z

last: Fire


title: H2A.Z.1 mono-ubiquitylation antagonizes BRD2 to maintain poised chromatin in ESCs [ChIP-seq]

first: Laurie

last: Boyer

overall_design: ChIP-Seq analysis on mouse embryonic stem cells harboring H2A.Z or H2A.Z.K3R3 (3 C-terminal lysines mutated to arginines) tagged with YFP, in the presence of a knockdown hairpin targeting the endogenous H2A.Z transcript.

first: Lauren

last: Surface

first: Paul

last: Fields


title: H2A.Z.1 mono-ubiquitylation antagonizes BRD2 to maintain poised chromatin in ESCs [RNA-seq]

overall_design: RNA-Seq analysis on mouse embryonic stem cells harboring H2A.Z or H2A.Z.K3R3 (3 C-terminal lysines mutated to arginines) tagged with YFP, in the presence of a knockdown hairpin targeting the endogenous H2A.Z transcript.


title: A broad RNA virus survey reveals dependence on host miRNAs and specific sequestration modulating the cellular transcriptome

city: Copenhagen N

first: Troels

middle: K H

last: Scheel

state: Copenhagen

address: Blegdamsvej 3

department: Institute for Immunology and Microbiology

country: Denmark

institute: University of Copenhagen

summary: Small non-coding RNAs have emerged as key players in modulation of viral infection. A unique example is the critical dependence of hepatitis C virus (HCV) on the liver-specific microRNA (miRNA), miR-122, which has surfaced as therapeutic target. Here, we used crosslinking immunoprecipitation (CLIP) of the Argonaute (AGO) protein to characterize strengths and specificities of miRNA interactions across 15 viral genomes. Intriguingly, replication of pestiviruses, which are major threats to milk and meat industry, critically depends on cellular miR-17 and let-7 interactions with the viral 3’UTR. Like HCV, miRNA binding enhanced translation and prevented viral RNA degradation. On the cellular transcriptome, pestiviral miR-17 sequestration in vitro and ex vivo conferred reduced AGO binding and functional mRNA de-repression for miR-17 targets. These findings generalize the concept of RNA virus dependence on cellular miRNAs, highlight such interactions as therapeutic targets, and connect functional regulation of the transcriptome in primary cells to miRNA sequestration.

sample_organism:
Homo sapiens
Bos taurus

platform_organism:
Homo sapiens
Bos taurus

overall_design: Several subseries of analyses were performed. For each sample, subseries to which it belongs are indicated. In the “Virus AGO-CLIP” subseries, AGO-CLIP was performed on cells infected with virus as indicated. Processed reads were aligned to the host genome (hg18 or BosTau7) and to the respective viral genome. The primary data of interest from this subseries concerns AGO binding to viral RNA, and is given as processed data file “Table S1”. In the “Virus AGO-CLIP: BVDV vs. Mock” subseries, AGO-CLIP was performed on four replicates each of BVDV and mock infected MDBK cells. CLIP reads aligned to BosTau7 were clustered, and differential analysis was performed on binding to each cluster. In addition, differential analysis of AGO bound miRNAs was performed. The associated data is given as processed data file “Table S3 and S4”. In the “AGO-CLIP: tinyLNA-17 vs. Mock” AGO-CLIP was performed on four replicates each of tinyLNA-17 and mock treated MDBK cells. CLIP reads aligned to BosTau7 were clustered, and differential analysis was performed on binding to each cluster. The associated data is given as processed data file “Table S5”. In the “RNA-seq: BVDV vs. Mock” subseries, mRNA-seq was performed on two replicates each of MDBK cells infected with different biotypes of BVDV or with miR-17 seed site mutant BVDV. The latter (incl. mock controls) were trans-complemented with the corresponding mutated miR-17. Differential gene expression analysis was performed between selected conditions. The associated data is given as processed data file “Table S6”.

first: Joseph

last: Luna

first: Matthias

last: Liniger

first: Eiko

last: Nishiuchi

first: Kathryn

last: Rozen-Gagnon

first: Amir

last: Shlomai

first: Gaël

last: Auray

first: Markus

last: Gerber

first: John

last: Fak

first: Irene

last: Keller

first: Rémy

last: Bruggmann

first: Robert

middle: B

last: Darnell

first: Nicolas

last: Ruggli

first: Charles

last: Rice


title: Genome-wide profiling of inflammatory cistrome reveals AP-1/c-Jun as a key regulator of TNFalpha-mediated triple-negative breast cancer progression [ChIP-seq]

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

summary: Triple-negative breast cancer (TNBC) represents a highly aggressive form of breast cancer with limited treatment options. Proinflammatory cytokines such as TNF can facilitate tumor progression and metastasis. However, our knowledge of the molecular mechanisms underlying TNBC progression mediated by inflammation is still limited. Here, we define the AP-1 transcription factor c-Jun cistrome, which is comprised of 13800 binding sites responsive to TNFalpha-induced signaling in TNBC cells. In addition, we show that c-Jun regulates nearly a third of the TNFalpha-elicited transcriptome. Expression of the c-Jun-regulated pro-invasion gene program is strongly associated with clinical outcomes in TNBCs. Mechanistically; we demonstrate that c-Jun drives TNFalpha-mediated TNBC tumorigenicity by transcriptional regulation of Ninj1. As exemplified by the c-Jun bound CXC chemokine genes clustered on chromosome 4, we demonstrate that NF-kB might be a pioneer factor and is required for the regulation of TNFalpha-inducible inflammatory genes, whereas c-Jun has little effect. Together, our results uncover AP-1 as an important determinant for inflammation-induced cancer progression, rather than inflammatory response.

overall_design: BT549 cells were serum-starved overnight and then treated with or without TNFalpha for 3 hours.

first: Yichun

last: Qiao

first: Philip

last: Jonsson

first: Chunyan

last: Zhao

first: Indranil

last: Sinha


title: Insights into function and regulation of microRNAs by decoding degradation dynamics [serum]

city: Milan

first: Heiko

last: Muller

address: Via Adamello 16

country: Italy

institute: Italian Institute of Technology

summary: The regulation of the miRNA pool is one of the critical events in the definition of cell identity and behavior both in steady-state condition as well during cell transitions. While mechanisms controlling biogenesis have received much attention, little is known about how miRNA are turned over, due to the lack of proper approaches to analyze miRNA decay without globally perturbing gene transcription or miRNA biogenesis. To overcome such limitations we developed a “pulse-chase” approach for the analysis of miRNA degradation dynamics at genome-wide scale in unperturbed mammalian cells. MiRNA half-lives appeared heterogeneous: while many species were very stable (T1/2 >24h, ‘slow’ miRNAs), some others are quickly turned over (T1/2 =4-14h ‘fast’ miRNAs). ‘Fast’ species comprises passenger miRNAs, as expected, and a consistent number (25/129) of guide miRNAs. These miRNAs are associated to high Target:miRNA stoichiometric ratios, particularly evident considering targets with extensive complementarity, and are enriched for 3’-end modifications (tailing and trimming), implying that target abundance and enzymatic activities are in place and mediates miRNA degradation. By integrating decay rates with biosynthetic parameters, we could model the abundance and regulation of miRNAs as a function of transcription and degradation rates and highlight how different decays could affect the magnitude and the kinetics of miRNA regulation. These findings were recapitulated in a specific biological process, namely the regulation of miRNAs by serum stimulation of quiescent fibroblast, pointing out how multiple regulatory mechanisms (synthesis, decay, target abundance and miRNA modification) concomitantly control miRNA functions.

overall_design: miRNA dynamic regulation in quiescent fibroblasts upon serum stimulation. Two independent biological experiments were performed over 9 time-points

first: Matteo

middle: J

last: Marzi

first: Francesco

last: Nicassio


title: Genome-wide profiling of inflammatory cistrome reveals AP-1/c-Jun as a key regulator of TNFalpha-mediated triple-negative breast cancer progression.

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

overall_design: Refer to individual Series


title: Genome-wide map of SET1A occupancy in mouse ES cells

first: Jiemin

last: Wong

address: 500 Dongchuan Road

institute: Institute of Biomedical Sciences and School of Life Sciences, East China Normal University

summary: To identify SET1A genome-wide occupancy and further unveil its role in transcriptional regulation in mouse ES cells, we carried out chromatin immunoprecipitation followed by high sequencing (ChIP-seq).We established a stable ES cell line expressing 2X Flag tagged SET1A and performed ChIP with anti-Flag M2 beads, followed by deep sequencing. We found that the SET1A peaks show an outstanding enrichment in promoter region. Importantly, these SET1A binding loci revealed a clear co-localization with OCT4, and high H3K4me3 level, which is consistent with its interaction with OCT4 and intrinsic H3K4 methylase activity.

overall_design: Examination of SET1A genome-wide occupancy in mouse ESCs.

first: Lan

last: Fang


title: Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination

first: Anna

last: Liu

summary: Arabidopsis thaliana ecotypes Columbia (Col-0) (wild type: WT) was used in this study. After sterilization, the seeds were placed on Murashige and Skoog medium supplemented with 2% (w/v) sucrose for 10 days and then the seedling were transferred to soil under 16 hours light (22°C) / 8 hours dark (18°C) period in growth chamber at a light intensity of 120?150 µmol m-2 s-1. 20-day-old Arabidopsis leaves without bolting were immediately frozen in liquid nitrogen for RNA and protein and metabolites extraction. Leaves were harvested at three different time points: t = 0 hr (end of night), t = 1 hr (one hour after light turn on) and t = 8 hr (eight hours after light turn on), respectively.

overall_design: Total RNA was extracted from leaves at all three time points and DNA contamination was removed by DNase I (RNeasy Plant Mini Kit, Qiagen, Hong Kong).Ribosomal RNAs were removed from the total RNA by the Ribo-Zero rRNA removal kit for plant leaf (Epicentre, USA) before cDNA library construction. The libraries were sequenced using Illumina HiSeqTM2000. After removal of low quality reads, clean reads from three different RNA-seq samples (WT 3 times points, t = 0, 1, 8) were aligned to Arabidopsis genome. No biological replication carried out in this experiment.

first: Chao

last: Liang

first: Yuzhe

last: Sun

first: Shifeng

last: Cheng

first: Boon-Leong

last: Lim


title: Genome-wide characterization of maize small RNA loci and their regulation in the required to maintain repression6-1 (rmr6-1) mutant and long-term abiotic stresses

city: State College

first: Michael

last: Axtell

state: PA

address: University Park

department: Department of Biology

institute: Penn State University

summary: Endogenous small RNAs (sRNAs) contribute to gene regulation and genome homeostasis but their activities and functions are incompletely known. The maize genome has a high number of transposable elements (TEs; almost 85%), some of which spawn abundant sRNAs. We performed sRNA and total RNA sequencing from control and abiotically stressed B73 wild-type (wt) plants and rmr6-1 mutants. RMR6 encodes the largest subunit of the RNA polymerase IV (Pol IV) complex, and is responsible for accumulation of most 24 nucleotide (nt) small interfering RNA (siRNAs). We identified novel MIRNA loci and verified miR399 target conservation in maize. RMR6-dependent 23-24 nt siRNA loci were specifically enriched in the upstream region of the most highly expressed genes. Most genes mis-regulated in rmr6-1 did not show a significant correlation with loss of flanking siRNAs, but we identified one gene supporting existing models of direct gene regulation by TE-derived siRNAs. Long-term drought correlated with changes of miRNA and sRNA accumulation, in particular inducing down-regulation of a set of sRNA loci in the wt leaf.

overall_design: sRNA profile of maize leaf and shoot apical meristematic area, of wt and rmr6-1 mutant plants grown under 1) control conditions 2) salt stress 3) drought stress 4) salt+drought stress. Each condition was replicated two/three times, after 10 days of treatment and after 7 days of recovery.

first: Alice

last: Lunardon

first: Cristian

last: Forestan

first: Silvia

last: Farinati

first: Serena

last: Varotto


title: Insights into function and regulation of microRNAs by decoding degradation dynamics [4SU]

overall_design: To obtain a global picture of miRNA decays, we performed high-throughput sequencing analysis (Illumina) of labeled miRNAs along the “pulse and chase” experiment. A total of 21 libraries were produced, using 4SU RNA isolated from 7 time points and 3 independent biological replicas. We additionally sequenced i) total RNA from growing cells (not labeled without extraction – UNT), ii) total RNA pulsed with 4SU (labeled without extraction – 4SU); and iii) 4SU RNA from non-labeled cells (not labeled with extraction, negative control – NEG).


title: iPSC RNA-seq upon CRISPRn or CRISPRi manipulation

status: Public on Jan 19 2016

city: San Francsico

first: Max

last: Horlbeck

address: 1700 4th Street

department: Cellular and Molecular Pharmacology

institute: UCSF

summary: Assess the on- and off-target effects of dox-inducible CRISPR/Cas9 and CRISPRi constructs in a human iPS cell line.

overall_design: Transcript quantification of 3 cell lines, each plus or minus doxycycline and with or without specific single guide RNAs (sgRNAs), with 2 biological replicates each.

first: Mohammad

last: Mandegar

first: Nathaniel

last: Huebsch

first: Ekaterina

last: Balandina

first: Edward

last: Shin

first: Annie

last: Truong

middle: P

last: Olvera

first: Amanda

middle: H

last: Chan

first: Yuichiro

last: Miyaoka

first: Kristin

last: Holmes

first: C

middle: I

last: Spencer

first: Luke

middle: M

last: Judge

first: David

last: Gordon

first: Tilde

middle: V

last: Eskildsen

first: Jacqueline

last: Villalta

last: Gilbert

first: Nevan

last: Krogan

first: Soren

last: Sheikh

first: Jonathan

last: Weissman

first: Lei

last: Qi

first: Po-Lin

last: So

first: Bruce

last: Conklin


title: Insights into function and regulation of microRNAs by decoding degradation dynamics

first: Heiko

last: Muller


title: RNA-seq analysis of dickkopf-3 knockout and C57Bl/6 mice kidneys 7 days after unilateral ureteral obstruction

city: München

first: Carsten

last: Jäckel

address: Schillerstr 42

department: Klinische Biochemie

institute: Klinikum der Universität München, Klinische Biochemie

summary: Renal tubular atrophy and interstitial fibrosis are common hallmarks of etiologically different progressive chronic kidney diseases (CKD) that eventually result in organ failure. We identify Dickkopf-3 (Dkk3) as a stress-induced, tubular epithelia-derived mediator of kidney fibrosis. Genetic as well as antibody-mediated abrogation of Dkk3 led to reduced tubular atrophy and decreased interstitial matrix accumulation in two mouse models of renal fibrosis. This was accompanied by an amplified, anti-fibrogenic, inflammatory response within the injured kidney. Mechanistically, Dkk3 deficiency led to diminished canonical Wnt/β-catenin signaling in stressed tubular epithelial cells. To identify global changes in gene expression due to the lack of Dkk3, whole-transcriptome sequencing (mRNA-seq) was performed on RNA isolated from kidneys of Wt and Dkk3-/- mice 7 days after UUO.

overall_design: Kidneys of Dkk3-/- and C57Bl/6 mice were harvested 7 days after UUO. Total RNA was isolated and each Sample was prepared as a 10-plex, which was sequenced on three lanes. HiSeq 2000 50bp SR run was used.

first: Giuseppina

last: Federico

first: Thomas

last: Hielscher

first: Daniel

last: Mathow


title: RNA-Seq analysis, transcriptome assembly and gene expression profile analysis for Zea may ssp. mexicana L. under cold and drought stress

city: Hobart

first: Xiang

last: LU

state: TAS

address: Private Bag 98

department: Tasmania of Institute Agriculture

country: Australia

institute: University of Tasmania

summary:
Purpose: The goals of this study are studies the response of annual Zea mays ssp. mexicana L. under cold and drought stress
Methods: The seedlings of zea may ssp. mexicana L. were generated by Illumina HiSeq2500 deep-sequencing. In order to generate a global overview of Zea mexicana transcriptome data, 3 of complement DNA (cDNA) libraries were prepared from RNA isolated from root, stem, and leave mixed tissues of Zea Mexicana from Control (24℃), Cold (4℃) and Drought (PEG2000, 20%) treatments and each teatment has two repetitions. The sequence reads that passed quality filters were merged and de novo to generate all transcripts set by Trinity with default parameter, which will be treated as reference genome. The number of paired-reads of each sample were mapped to reference genome by Bowtie software v1.1.1 and the number of mapped reads were calculated by RSEM. qRT-PCR validation was performed using BIO-RAD CFX96 sequence detection system and SYBR Green assays.
Results: Using RNA-Seq technology with the Trinity assembled method, we generated a seedling plant transcriptome at a sequencing size of 51.78Gb of Zea mays ssp. mexicana L. from pooled RNA samples which included control (CK), cold (4℃) and drought (PEG2000, 20%) stressed plant samples. A total of 414,232,462 high quality clean reads were used to conduct de novo assembly and annotation of genes without reference genome information. All of these reads were assembled into 251,145 transcripts (N50 = 1,269 bp) and 184,280 unigenes (N50 = 923 bp). A total of 3,504 up-regulated and 1,220 down-regulated genes were detected under cold stress and 532 up-regulated and 82 down-regulated genes were detected under drought stress. A Venn diagram indicated that 208 genes were affected by both cold and drought stresses. 3 cold stress pathways and 5 drought related pathways showed significant KEGG pathways. Functional enrichment analyses identified many common or specific biological processes and gene sets in response to drought and cold stresses. The ABA dependent pathway, trehalose synthetic pathway and CBF6 gene of ICE1-CBF pathway may play important roles in the DEGs co-up-regulated by both stresses of Zea mays ssp. mexicana L.

Conclusions: We analyzed transcriptome data and gene expression profile information from seedlings of Zea mays ssp. mexicana L. under cold and drought stresses. Together these data provides the most comprehensive sequence study available for Zea mays ssp. mexicana L. and provides some important functional genes and molecular mechanism information for improving the quality characteristic of maize in the future.

overall_design: Zea may ssp. mexicana L. "8493" variety mRNA profiles of 13-day seedlings were generated by deep sequencing, in triplicate and 2 repetition using Illumina HiSeq2500 deep-sequencing platform.

last: Lu

first: Xuan

last: Zhou

first: Yu

last: Cao

first: Meixue

last: McNeil

first: Chengwei

last: Yang


title: Antisense transcription of retro transposable elements in Drosophila: The origin of endogenous small interfering RNA precursors

status: Public on Jan 26 2016

city: St. Louis

first: Mindy

last: Steiniger

address: 1 University Blvd.

institute: University of Missouri-St. Louis

summary: Unrestricted movement of mobile genetic elements could cause pre-mature lethality in Drosophila melanogaster. Specifically, retro transposons can disrupt genomic integrity through insertions, deletions and chromosomal rearrangements. Therefore, eukaryotes have developed defense mechanisms to silence these elements. In Drosophila, endogenous small interfering (endo-siRNAs) repress retro transposon mobility in somatic cells. The generation of endo-siRNAs requires Dicer-2 processing of double-stranded RNA precursors, yet the origins of this precursor are unknown. Here we show that retro transposons in Dmel-2 cells produce sense and antisense transcripts and identify bonafide transcription start sites for these RNAs. We determine that retro transposon antisense transcripts are less polyadenylated than sense transcripts. RNA-seq and small RNA-seq upon Dicer-2 depletion showed global decrease in endo-siRNAs mapping to retro transposons and increased expression of both S and AS retro transposon transcripts. These data support a model in which double-stranded RNA precursors are derived from convergent transcription and retained in the nucleus. Dicer-2 processes these precursors into endo-siRNAs that silence both sense and antisense retro transposon transcripts. Reduction of sense retro transposon transcripts potentially lowers element specific protein levels required for movement. This mechanism preserves genomic integrity and is especially important for Drosophila fitness because mobile genetic elements are highly active.

overall_design: This submission includes 12 raw data files. Two samples (LacZ control and Dcr-2 RNAi-depleted) are represented by three technical triplicate raw data files. RNA-seq and small RNA-seq data are provided for each sample.

first: J

last: Russo

first: A

last: Harrington

first: M


title: Diverse fates of uracilated HIV DNA during infection of myeloid lineage cells

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

summary: Using novel methods for mapping U/A base pairs in HIV DNA, we find that HIV proviruses within infected monocytes and macrophages contain high levels of U/A base pairs arising from the high levels of dUTP present during reverse transcription in these cells. Although U/A pairs retain the coding information of T/A pairs, they are the substrate for the nuclear uracil base excision repair (UBER) machinery that effectively degrades most of the uracilated viral DNA at the pre-integration stage of infection. Uracilated proviruses that successfully integrate either retain the uracils, undergo U/A T/A repair, or experience catastrophic mutagenesis induced by cytokine stimulated error-prone repair. Uracil is abundant in proviruses isolated from genomic DNA of short-lived blood monocytes, but not T cells, of HIV infected blood donors who show complete drug suppression plasma virus. This suggests that monocytes are recently infected by coming into contact with persistent virus producing cells in one or more tissue reservoirs.

overall_design: Data for HIV lockdown of Illumina libraries of MDM cells post viral infection with and without UDG treatment.


title: H2A.Z.1 mono-ubiquitylation antagonizes BRD2 to maintain poised chromatin in ESCs

city: Cambridge

first: Laurie

middle: A

last: Boyer

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology


title: RNA-seq of 9 tissues from an adult male C57BL/6 mouse

city: South San Francisco

first: Melanie

last: Huntley

address: 1 DNA Way

institute: Genentech

summary: RNA-editing is a tightly regulated, and essential cellular process for a properly functioning brain. Dysfunction of A-to-I RNA editing can have catastrophic effects, particularly in the central nervous system. Thus, understanding how the process of RNA-editing is regulated has important implications for human health. However, at present, very little is known about the regulation of editing across tissues, and individuals. Here we present an analysis of RNA-editing patterns from 9 different tissues harvested from a single mouse. For comparison, we also analyzed data for 5 of these tissues harvested from 15 additional animals. We  find that tissue specificity of editing largely reflects differential expression of substrate transcripts across tissues. We identified a surprising enrichment of editing in intronic regions of brain transcripts, that could account for previously reported higher levels of editing in brain. There exists a small but remarkable amount of editing which is tissue-specific, despite comparable expression levels of the edit site across multiple tissues. Expression levels of editing enzymes and their isoforms can explain some, but not all of this variation. Together, these data suggest a complex regulation of the RNA-editing process beyond transcript expression levels.

overall_design:
Tissues include: brain, heart, kidney, liver, lung, skin, spleen, testis, thymus
mRNA profiles of 9 tissues from an 8 week old, male C57BL/6 mouse were generated by deep sequencing using Illumina HiSeq.


title: Gene expression profile in Ronin (Thap11) conditional knock out retina through RNA-sequencing

city: Houston

first: Ross

middle: A.

last: Poché

address: One Baylor Plaza Room T424, Mail Stop 335

department: Department of Molecular Physiology and Biophysics

institute: Baylor College of Medicine

summary: Conditional knockout of the transcription factor Ronin (Thap11) in retinal progenitor cells (RPCs) results in a profound failure cell proliferation resulting in a hypoplastic adult retina that also suffers from photoreceptor degeneration. The goal of this study was to determine which genes are deregulated in response to loss of Ronin transcription factor activity in the developing retina. We generated Ronin flox/flox (Control) and Chx10-Cre::GFP+/tg; Ronin flox/flox (CKO) mice, in which Ronin loss occurs specifically within RPCs, and performed RNA-Seq analysis of embryonic day E14.5 (E14.5) retinae. Three independent pools of control and Ronin CKO retinae were collected consisting of a minimum of 10 retinae per pool and total RNA was extracted followed by polyA selection, fractionation (200-500 nucleotide range) and generation of cDNA. The resulting DNA was then used for standard Illumina adaptor ligation and sequencing. This experiment revealed decreased expression of a large group of mitochondrial genes including components of the electron transport chain (ETC), which have been recently implicated as direct regulators of the cell cycle.

overall_design: Retinal mRNA profiles of embryonic day 14.5 (E14.5) Control (Ronin flox/flox) and Ronin CKO (Chx10-Cre::GFP+/tg; Ronin flox/flox) mice were generated by deep sequencing, in triplicate using Illumina HiSeq2500

first: Min

last: Zhang


title: Ronin transcriptional target genes in the developing mouse retina


title: The Epigenomic Landscape of Prokaryotes

city: Berkeley

first: Matthew

middle: James

last: Blow

address: 1 Cyclotron Road

department: Genomics Division

institute: Lawrence Berkeley National Laboratory

summary: DNA methylation is an important regulator of genome function in the eukaryotes, but it is currently unclear if the same is true in prokaryotes. While regulatory functions have been demonstrated for a small number of bacteria, there have been no large-scale studies of prokaryotic methylomes and the full repertoire of targets and biological functions of DNA methylation remains unclear. Here we applied single-molecule, real-time sequencing to directly study the methylomes of 232 phylogenetically diverse prokaryotes.  Collectively, we identified 834 methylated motifs, enabling the specific annotation of 415 DNA methyltransferases (MTases), and adding substantially to existing databases of MTase specificities. While the majority of MTases function as components of restriction-modification systems, 139 MTases have no cognate restriction enzyme in the genome, suggesting some other functional role. Several of these ‘orphan’ MTases are conserved across species and exhibit patterns of DNA methylation consistent with known regulatory MTases. Based on these patterns of methylation, we identify candidate novel regulators of gene expression in several phyla of bacteria, and candidate regulators of DNA replication in Haloarchaea.  Together these data substantially advance our knowledge of DNA restriction-modification systems, and hint at a wider role for methylation in prokaryotic genome regulation.

sample_organism: Salmonella enterica subsp. arizonae serovar 62:z4,z23:-

sample_organism: Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150

sample_organism: Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088

sample_organism: Dinoroseobacter shibae DFL 12 = DSM 16493

sample_organism: Staphylococcus aureus subsp. aureus USA300_TCH1516

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

sample_organism: Thermanaerovibrio acidaminovorans DSM 6589

sample_organism: Sediminispirochaeta smaragdinae DSM 11293

sample_organism: Zymomonas mobilis subsp. pomaceae ATCC 29192

sample_organism: Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7

sample_organism: Geopsychrobacter electrodiphilus DSM 16401

sample_organism: Solidesulfovibrio cf. magneticus IFRC170

overall_design: Single-molecule, real-time sequencing of DNA modifications across 232 diverse prokaryotic genomes.

first: Richard

last: Roberts


title: A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha

city: Vienna

first: Philipp

last: Rescheneder

address: Dr. Bohr Gasse 9

country: Austria

institute: MFPL


title: A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha [gene expression]

summary: Lamins are components of the peripheral nuclear lamina and interact with heterochromatic genomic regions, termed lamina-associated domains (LADs). In contrast to lamin B1, lamin A/C also localizes throughout the nucleus, where it associates with the chromatin-binding protein lamina-associated polypeptide (LAP) 2alpha. Here we show lamin A/C also interacts with euchromatin, as determined by chromatin immunoprecipitation analyses of eu- and heterochromatin-enriched samples. By way of contrast, lamin B1 was only found associated with heterochromatin. Euchromatic regions occupied by lamin A/C overlap with those bound by LAP2alpha, the depletion of which shifts binding of lamin A/C towards more heterochromatic regions. These alterations in lamin A/C chromatin interaction affect epigenetic histone marks in euchromatin without significantly affecting gene expression, while loss of lamin A/C in heterochromatic regions increased gene expression. Our data show a novel role of nucleoplasmic lamin A/C and LAP2alpha in regulating euchromatin.

overall_design: Examination of LaminA, LaminB and Lap2a DNA binding in Lap2alpha +/+ and Lap2a -/- cells and according changes in Histone modifications and gene expression

first: Kevin

last: Gesson

first: Michael

last: Skoruppa

first: Arndt

last: von Haeseler

first: Thomas

last: Dechat

first: Roland

last: Foisner


title: Genome-wide occupancy profiling of Ronin (Thap11) in retinal development

summary: Conditional knockout of the transcription factor Ronin (Thap11) in retinal progenitor cells (RPCs) results in a profound failure cell proliferation resulting in a hypoplastic adult retina that also suffers from photoreceptor degeneration.  The goal of this study was to determine the genes that are transcriptionally regulated by Ronin during retinogenesis. P0 wild type retinae (CD-1 background) were pooled (>10 each) in ice-cold 1X PBS and immediately processed for chromatin extraction, fragmentation and immunoprecipitation using custom antibodies against Ronin G4275 (Dejosez et al., 2010), G4275 preimmune serum or normal rabbit IgG (Santa Cruz, sc-2027). The immunoprecipitated DNA fragments were then sequenced using the Ion Torrent PGM system.

overall_design: Examination of Ronin binding sites throughout the postnatal day 0 (P0) retinal genome.


title: Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

summary: Polycomb Group Proteins (PcGs) is critical in defining the epigenetic blueprint for animal and plant development. In plants, loss of different PcGs display both common and unique phenotypic defects, yet little is known about how these are established. Here, based on quantitative comparison of epigenomics data from mutants of key PcG components in Arabidopsis seedlings, we found that the PcG partners of CURLY LEAF (CLF), one of the major plant H3K27 trimethyltransferases, determines its selectivity in repressing gene loci involved in distinct developmental programs. The non-redundant role of CLF in determining flower development is specifically associated with HETEROCHROMATIN PROTEIN1 (LHP1). This context dependent effect of CLF corresponds well with tissue-biased target gene expression, and importantly, to differential co-occupancy of transcription factors, such as MADS box and B3-domain transcription factors. These results provide valuable insight as to the dynamic interplay between different PcGs and their collaborative control of plant development.

overall_design: To compare the effect of different PcGs on epigenetic structure from the genome-wide scale, we used chromatin immunoprecipitation followed by high-throughtput sequencing (ChIP-seq) to characterize the genome-wide binding profile of H3K27me3 in Col, clf-29, tfl2-2, atbmi1a/b and atring1a/b; To investigate the functional consequence of the distinct H3K27me3 profile controlled by different combinations of PcGs, we characterized the transcriptome change in PcG mutants, including Col, clf-29, tfl2-2, lhp1-6, atbmi1a/b, atring1a/b, and clf29swn21.

first: Yijing

first: Lin

last: Xu


title: BPTF is required for c-MYC-induced remodelling of target chromatin and transcriptional activation [RNA-Seq]

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

institute: Spanish National Cancer Research Centre (CNIO)

summary: The c-MYC oncogene is a key transcription factor deregulated in most human tumors. Histone marks associated with transcriptionally active genes in euchromatic islands define the set of high-affinity c-MYC targets. The mechanisms involved in their recognition by c-MYC are not known but likely involve chromatin-remodelling and chromatin-modifying complexes. Here, we show that c-MYC interacts with BPTF, a core subunit of the NURF complex that binds active chromatin. BPTF is required for the activation of the full c-MYC transcriptional programme in fibroblasts. BPTF knockdown leads to a decrease in c-MYC recruitment to DNA and to changes in chromatin accessibility. Using BPTF-null MEFs we show that BPTF is necessary for c-MYC-driven proliferation, G1-S progression, and replication stress, but not for c-MYC-driven apoptosis. Consistently, BPTF is required for the proliferation of cells driven by c-MYC, such as Burkitt lymphoma, and its expression in human cancer lines correlates with the activation of c-MYC gene signatures. Our findings point to the c-MYC-BPTF axis as a potential therapeutic target in cancer.

overall_design: To assess whether BPTF is required for the transcriptional activity of c-MYC, human foreskin fibroblasts (HFF) were stably transduced with the chimeric MYC-ER cDNA (HFF MYC-ER) and infected with lentiviruses coding for either control (shNt) or BPTF-targeting shRNAs. Cells were serum-starved for 2 days to achieve quiescence and then treated with 4-hydroxytamoxifen (4-OHT)

first: Laia

last: Richart

last: Carrillode Santa Pau

first: Víctor

last: Sánchez-Arévalo Lobo

first: F

middle: X

last: Real


title: Single cell differences in matrix gene expression do not predict matrix deposition

status: Public on Jan 18 2016

city: Philadelphia

first: Arjun

last: Raj

address: 210 S 33rd St

department: Bioengineering

institute: University of Pennsylvania

summary: We performed RNA sequencing on several clones of bovine mesenchymal stem cells from the same donor.

overall_design: Bulk mRNA sequencing in 17 different clones from the same donor and a heterogeneous population from the same donor.

first: Allison

last: Cote

first: Claire

last: McLeod

first: Megan

last: Farrell

first: Patrick

middle: D

last: McClanahan

first: Margaret

middle: C

last: Dunagin

first: Robert

last: Mauck


title: BPTF is required for c-MYC-induced remodelling of target chromatin and transcriptional activation [ChIP-Seq]


title: Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis (PAGODA)

city: Boston

first: Jean

last: Fan

address: 10 Shattuck St 336B

department: Department of Biomedical Informatics

institute: Harvard University

summary:
The extent of transcriptional diversity in mouse NPCs is likely to be influenced by a variety of unexamined factors that include programmed cell death, genomic mosaicism as well as a variety of “environmental” influences such as changes in exposure to signaling lipids. We therefore used scRNA-seq to assess a cohort of cortical NPCs from an embryonic mouse.
We demonstrate that PAGODA (Pathway And Geneset OverDispersion Analysis) effectively recovers the known neuroanatomical and functional organization of NPCs, identifying multiple aspects of transcriptional heterogeneity within the developing mouse cortex that are difficult to discern by the existing heterogeneity analysis approaches.

overall_design: Examination of mouse NPC transcriptional heterogeneity via single cell RNA-seq

first: Peter

last: Kharchenko


title: Parallel quantitative CRISPR interference in yeast identifies chemical-genetic interactions and new rules for guide RNA design

city: Palo Alto

first: Ulrich

last: Schlecht

address: 3165 Porter Drive

institute: Stanford University

summary:
Background: The CRISPR/Cas9 toolbox has recently been expanded to include approaches for modulating gene expression. To successfully build on this work, and apply it for answering biological questions, it is important to establish it in a broad range of circumstances. Genome-scale CRISPR interference (CRISPRi) has been used in human cells lines, however the rules for designing effective guide RNAs (gRNAs) in different organisms are not well known. We sought to determine rules that determine gRNA effectiveness at transcriptional repression in Saccharomyces cerevisiae.

Results: We created an inducible single plasmid CRISPRi system for gene repression in yeast, and used it to analyze fitness effects of gRNAs under 18 small molecule treatments. Our approach correctly identified previously-described chemical-genetic interactions, as well as a new mechanism of suppressing fluconazole toxicity by repression of the ERG25 gene. Assessment of multiple target loci across treatments allowed us to determine generalizable features associated with gRNA efficacy.  Guides that target regions with low nucleosome occupancy and high chromatin accessibility were clearly more effective. We also found the best region to target gRNAs was between the transcription start site (TSS) and 200bp upstream of the TSS. Finally, unlike nuclease-proficient Cas9 in human cells, point mutations were tolerated equally well by truncated (18 nt specificity sequence) and full length (20 nt) gRNAs, however, 18 nt gRNAs were generally less potent than full length gRNAs.

Conclusions: Our results establish a powerful functional genomics screening method, provide rules for designing effective gRNAs for gene repression, and show that 18 nt and 20 nt gRNAs exhibit similar tolerance to mismatches in the target sequence. These findings will enable effective library design and genome-wide screening in many genetic backgrounds.

overall_design: An expression construct was created for inducible CRISPRi in yeast. Key features include ORFs expressing dCas9-Mxi1 and the tetracycline repressor (TetR), as well as a tetracycline inducible gRNA locus containing the RPR1 promoter with a TetO site, a NotI site for cloning new gRNA specificity sequences, and the constant part of the gRNA. When yeast containing this plasmid are grown in the absence of anhydrotetracycline (ATc) TetR binds the gRNA promoter and prevents PolIII from binding and transcribing the gRNA.  This in turn prevents dCas9-Mxi1 from binding the target site. In the presence of ATc, TetR dissociates and gRNA is expressed, allowing dCas9-Mxi1 to bind its target locus, and repress gene expression. gRNA libraries were cloned into this construct and transformed into yeast to create pools. Experiments were conducted in which yeast pools were grown in inducing (+ATc) and non-inducing conditions (-ATc) in the presence of different drugs. After multiple generations of growth in these conditions, yeast plasmids were minipreped and the gRNA locus was PCRed and sequenced via MiSeq. Counts of each gRNA were compared in different conditions.

first: Justin

last: Smith

first: Sundari

last: Suresh

first: Manhong

last: Wu

first: Gary

last: Peltz

first: Ronald

middle: W

last: Davis

first: Lars

last: Steinmetz

first: Leopold

last: Parts


title: BPTF is required for c-MYC-induced remodelling of target chromatin and transcriptional activation

first: Enrique

last: Carrillo de Santa Pau

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

overall_design: Refer to individual Series


title: Thymic T-cell progenitor development is supported by membrane bound Kit ligand provided by a combined vascular endothelial and epithelial niche.

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

summary: Gene expression analysis of purified  KitL-tomato+  and  KitL-tomato- thymic vascular endothelial cells, cortical and medullary thymic epithelial cells from 5 weeks old male kitL-tomato reporter mice

overall_design: Differentially expressed genes analysis of thymic stromal cells

first: M

last: Buono

first: S

last: Thongjuea

first: A

last: Giustacchini

middle: E

last: Jacobsen


title: Gene expression changes during overexpression of bacterial small RNA, DicF

status: Public on Jan 16 2016

city: Urbana

first: Carin

middle: K.

last: Vanderpool

state: Illinois

address: 601 S. Goodwin Avenue, C226

department: Microbiology

institute: University of Illinois at Urbana-Champaign

summary: Hundreds of small RNAs (sRNAs) have been identified in diverse bacterial species, and while the functions of most remain unknown, some regulate key processes, particularly stress responses. The sRNA DicF was identified over twenty-five years ago as an inhibitor of cell division, but since then has remained uncharacterized. DicF is 53 nucleotides and is encoded on a prophage (Qin) in the genomes of many Escherichia coli strains. Here, we performed RNA-Seq analyses of an E. coli strain with chromosomal deletion of dicF and overexpressing either empty plasmid or dicF from a plasmid.  Systems analysis using computational methods identified additional mRNA targets of DicF: xylR and pykA mRNAs, encoding the xylose uptake and catabolism regulator and pyruvate kinase, respectively. We have further validated these target genes experimentally.

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

overall_design: RNA-Seq analyses was performed on E. coli strains overexpressing either the vector control or the small RNA DicF.

first: Divya

last: Balasubramanian

first: Preethi

middle: T

last: Ragunathan

middle: K


title: Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer [ChIP-seq]

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

institute: IRCCS San Raffaele Scientific Institute

summary: The histological grade of carcinomas describes the ability of tumor cells to organize differentiated epithelial structures and has prognostic impact. Molecular control of differentiation in normal and cancer cells relies on lineage-determining transcription factors (TFs) that activate the repertoire of cis-regulatory elements controlling cell type-specific transcriptional outputs. TF recruitment to cognate genomic DNA binding sites results in the deposition of histone marks characteristic of enhancers and other cis-regulatory elements. Here we integrated transcriptomics and genome-wide analysis of chromatin marks in human pancreatic ductal adenocarcinoma (PDAC) cells of different grade to identify first, and then experimentally validate the sequence-specific TFs controlling grade-specific gene expression. We identified a core set of TFs with a pervasive binding to the enhancer repertoire characteristic of differentiated PDACs and controlling different modules of the epithelial gene expression program. Defining the regulatory networks that control the maintenance of epithelial differentiation of PDAC cells will help determine the molecular basis of PDAC heterogeneity and progression.

overall_design: Chromatin from human pancreatic ductal adenocarcinoma cell lines was immunoprecipitated with different antibodies for histone modifications and transcription factors and subjected to multiparallel sequencing. Experiments were carried out in unmodified cells and genome edited clonal CFPAC1 cells.

first: Giuseppe

last: Diaferia

first: Gioacchino

last: Natoli


title: Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer.


title: Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer [RNA-seq]

overall_design: Poly(A) fraction of the total RNA from human pancreatic ductal adenocarcinoma cell lines was extracted and subjected to by multiparallel sequencing. Experiments were carried out in unmodified cells in duplicate, genome edited clonal CFPAC1 cells (2 KLF5-deleted CRISPR-Cas9 clones, 3 ELF3-deleted CRISPR-Cas9 clones and 2 wt clones) and CFPAC1 cells ectopically expressing ZEB1 or empty vector control (in duplicate).


title: A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha [ChIP-Seq]

first: Philipp

last: Rescheneder

summary: Lamins are components of the peripheral nuclear lamina and interact with heterochromatic genomic regions, termed lamina-associated domains (LADs). In contrast to Lamin B11, lamin A/C also localizes throughout the nucleus, where it associates with the chromatin-binding protein lamina-associated polypeptide (LAP) 2alpha. Here we show lamin A/C also interacts with euchromatin, as determined by chromatin immunoprecipitation analyses of eu- and heterochromatin-enriched samples. By way of contrast, Lamin B11 was only found associated with heterochromatin. Euchromatic regions occupied by lamin A/C overlap with those bound by LAP2alpha, the depletion of which shifts binding of lamin A/C towards more heterochromatic regions. These alterations in lamin A/C chromatin interaction affect epigenetic histone marks in euchromatin without significantly affecting gene expression, while loss of lamin A/C in heterochromatic regions increased gene expression. Our data show a novel role of nucleoplasmic lamin A/C and LAP2alpha in regulating euchromatin.

overall_design: Examination of Lamin A/C, Lamin B1 and Lap2a DNA binding in Lap2alpha +/+ and Lap2a -/- cells and according changes in Histone modifications and gene expression

first: Kevin

last: Gesson

first: Michael

middle: P

last: Skoruppa

first: Arndt

last: von Haeseler

first: Thomas

last: Dechat

first: Roland

last: Foisner


title: Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines

city: San Francisco

first: Kathleen

last: Giacomini

state: CA

address: 1550 4th St, Mission Bay, RH 581

institute: University of California, San Francisco

summary: Variation in the expression level and activity of genes involved in drug disposition and action (“pharmacogenes”) can affect drug response and toxicity, especially when in tissues of pharmacological importance.  Previous studies have relied primarily on microarrays to understand gene expression differences, or have focused on a single tissue or small number of samples. The goal of this study was to use RNA-seq to determine the expression levels and alternative splicing of 389 PGRN pharmacogenes across four tissues (liver, kidney, heart and adipose) and lymphoblastoid cell lines (LCLs), which are used widely in pharmacogenomics studies. Analysis of RNA-seq data from different individuals across the 5 tissues (N = 139 samples) revealed substantial variation in both expression levels and splicing across samples and tissue types. This in-depth exploration also revealed 183 splicing events in pharmacogenes that were previously not annotated.  Overall, this study serves as a rich resource for the research community to inform biomarker and drug discovery and use.

overall_design: mRNA profile of 389 genes in 24 liver, 20 kidney (cortex), 25 heart (left ventricle), 25 adipose (subcutaneous) samples, and 45 lymphoblastoid cell lines (LCLs). The raw data for the LCL Samples will be available through dbGap under phs000481.

first: Steven

last: Brenner

last: Scherer


title: A novel role for ASCL1 in the regulation of mesendoderm formation via HDAC-dependent antagonism of VegT function

city: Beijing

first: Li

last: Gao

address: Qinghuayuan  Street

department: School of Life Sciences

institute: Tsinghua University

summary: Maternally expressed proteins function in vertebrates to establish the major body axes of the embryo, and to establish a pre-pattern that sets the stage for later acting zygotic signals. This pre-pattern drives the propensity of Xenopus animal cap cells to adopt neural fates under various experimental conditions. Previous studies found that the maternally expressed transcription factor, encoded by the Xenopus achaete-scute like gene ascl1, is enriched at the animal pole. Asc1l is a bHLH protein involved in neural development, but its maternal function has not been studied. In this study, we have performed a series of gain and loss of function experiments on maternal ascl1, and present three novel findings. First, Ascl1 is a repressor of mesendoderm induced by VegT, but not of Nodal induced mesendoderm. Secondly, a previously uncharacterized N-terminal domain of Ascl1 interacts with HDAC1 to inhibit mesendoderm gene expression. This N-terminal domain is dispensable for its neurogenic function, indicating that Ascl1 has acts by different mechanisms at different times. Ascl1-mediated repression of mesendoderm genes was dependent on HDAC activity and accompanied by histone deacetylation in the promoter regions of VegT targets. Finally, maternal Ascl1 is required for animal cap cells to retain their competence to adopt neural fates. These results establish maternal Asc1l as a key factor in establishing the pre-pattern of the early embryo, acting in opposition to VegT and biasing the animal pole to adopt neural fates. The data presented here significantly extend our understanding of early embryonic pattern formation.

overall_design: Examination of genes expression in control (cMO) and Ascl1 MO knockdown (AMOs) embryos by deep sequencing.

first: Xin

last: Ma

first: Qinghua

last: Tao


title: The RNA binding protein IGF2BP3 promotes hematopoietic progenitor cell proliferation by targeting leukemogenic pathways

city: Santa Cruz

first: Jonathan

middle: Michael

last: Howard

address: 1154 High Street

department: Molecular, Cell, and Developmental Biology

institute: University of California-Santa Cruz

summary: The goal of this study was to determine IGF2BP3 RNA targets in human B-cell Acute Lymphocitic Leukemia cell models.

overall_design: Included are iCLIP-seq libraries for IGF2BP3 from RS4;11 and REH B-ALL cell samples and RNA-seq data sets from control and IGF2BP3 knockdown RS4;11 B-ALL cell lines

first: Jayanth

last: Palanichamy

first: Tiffany

last: MTran

first: Jeremy

middle: R

last: Sanford

first: Dinesh

middle: S

last: Rao


title: Diarrhea in lymphocytic colitis: ERK1/2-dependent ENaC dysregulation and claudin-4-, -5- and -8-related barrier defects

city: Berlin

first: Michal

middle: Ruth

last: Schweiger

address: Ihnestrasse 63-73

department: Lehrach

institute: Max Planck Institute For Molecular Genetics

summary:
Background: Lymphocytic colitis (LC) causes watery diarrhea. This study aimed to identify the inherent pathomechanisms of epithelial transport and barrier dysfunction and regulatory inputs.
Methods: 8 (4 LC samples and 4 unrelated control samples) biopsies of fresh sigmoid colon were analysed by paired end sequencing (Illumina High Seq 2500)
Conclusions: ENaC-mediated Na+ malabsorption via ERK1/2 and epithelial barrier dysfunction from tight junction downregulation through claudin-4, -5, and -8 are mechanisms causing malabsorptive and leak flux diarrhea in LC resulting from the key effector cytokines TNFa and INFg.

overall_design: Sigmoid colon mRNA profiles from 8 unrelated individuals (4 with LC, 4 as control) were generated using paired end sequencing with Illumina High Seq 2500

first: Christian

last: Barmeyer

first: Irene

last: Erko

first: Anja

last: Fromm

last: Bojarski

first: Svenja

last: Ploeger

first: Jan

middle: F

last: Richter

first: Christoph

last: Loddenkemper

first: Petra

last: Dames

first: Martin

last: Kerick

first: Britta

last: Siegmund

first: Jörg-Dieter

last: Schulzke


title: Transcriptomic Analysis of Petunia hybrida in Response to Salt Stress Using High Throughput RNA Sequencing

status: Public on Jan 15 2016

city: Ithaca

first: Neil

middle: Scott

last: Mattson

address: 134A Plant Sci Bldg

department: School of Integrative Plant Science

institute: Cornell University

summary: Salinity and drought stress are the primary cause of crop losses worldwide. In sodic saline soils sodium chloride (NaCl) disrupts normal plant growth and development. The complex interactions of plant systems with abiotic stress have made RNA sequencing a more holistic and appealing approach to study transcriptome level responses in a single cell and/or tissue. In this work, we determined the Petunia transcriptome response to NaCl stress by sequencing leaf samples and assembling 196 million Illumina reads with Trinity software. Using our reference transcriptome we identified more than 7,000 genes that were differentially expressed within 24 h of acute NaCl stress. The proposed transcriptome can also be used as an excellent tool for biological and bioinformatics in the absence of an available Petunia genome and it is available at the SOL Genomics Network (SGN) http://solgenomics.net. Genes related to regulation of reactive oxygen species, transport, and signal transductions as well as novel and undescribed transcripts were among those differentially expressed in response to salt stress. The candidate genes identified in this study can be applied as markers for breeding or to genetically engineer plants to enhance salt tolerance. Gene Ontology analyses indicated that most of the NaCl damage happened at 24 h inducing genotoxicity, affecting transport and organelles due to the high concentration of Na+ ions. Finally, we report a modification to the library preparation protocol whereby cDNA samples were bar-coded with non-HPLC purified primers, without affecting the quality and quantity of the RNA-seq data. The methodological improvement presented here could substantially reduce the cost of sample preparation for future high-throughput RNA sequencing experiments

overall_design: Control group received the Hoagland's solution with no added NaCl, the salt treatment group received Hoagland's solution amended with 150 mM NaCl.

first: Gonzalo

middle: H

last: Villarino


title: RNA-Seq-mediated transcriptome analysis of Staphylococcus aureus Newman wild-type, walKD119A, walKV149A and DHBP-treated wild-type strains

city: Chicago

first: Guan-Zheng

last: Luo

state: IL

address: 929 E 57th St

department: Chemistry

institute: UChicago

summary: We reported the RNA-Seq results of  Staphylococcus aureus Newman wild-type, walKD119A, walKV149A and DHBP-treated wild-type strains. We found that mutations of the potential signal transduction residues of WalK attenuate the activity of walKR two-component system, whereas DHBP supplementation activates this two-component system.

sample_organism: Staphylococcus aureus subsp. aureus str. Newman

overall_design: Examination of transcriptome changes in the mutant and drug-treatment strains.

first: He

last: Chuan

first: Ji

last: Quanjiang

first: Deng

last: Xin


title: The LRF/ZBTB7A transcription factor is a BCL11A-independent repressor of fetal hemoglobin

first: Peter

last: Kharchenko

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

summary: Hemoglobinopathies, including sickle cell disease and _-thalassemia, are global public health concerns. Induction of fetal-type hemoglobin (HbF) is a promising means to treat these disorders; however, precisely how HbF expression is silenced in adult erythroid cells is not fully understood. Here, we show that the LRF/ZBTB7A transcription factor is a potent repressor of HbF production. LRF inactivation derepresses embryonic/fetal _-globin expression in mouse and human adult erythroid cells. We employed genome-wide analysis of the transcriptome, chromatin accessibility and LRF occupancy sites, and demonstrate that LRF occupies the _-globin loci and maintains nucleosome density necessary for _-globin silencing. LRF confers its repressive activity through a unique NuRD repressor complex independent of BCL11A. Strikingly, human erythroid lines lacking both LRF and BCL11A exhibited almost a complete switch in expression from adult- to fetal-type globin, suggesting that these two factors cumulatively represent the near entirety of _-globin repressive activity in adult erythroid cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq, LRF ChIP-seq and ATAC-seq assays were used to investigtae LRF binding, effect of LRF depletion on transcription and chromatin landscape in mouse and human cells.

first: Takahiro

last: Maeda

middle: V


title: The genome of the seagrass Zostera marina

city: Kiel

first: Till

last: Bayer

address: Düsternbrookerweg 20

department: Marine Ecology

institute: GEOMAR Helmholtz Centre for Ocean Research

summary: This dataset contains the transcriptome sequence of Zostera marina as produced by Illumina sequencing. Four tissues were sequenced, female flower in late and early stages of development, the male flower, the root and leaf tissue.

overall_design: Full transcriptome sequencing of four tissues, including female flower at two time points in development

first: Janina

last: Brakel

first: Yves

last: Van de Peer

first: Thorsten

last: Reusch

first: Jeanine

middle: L

last: Olsen