title: The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene regulatory networks

status: Public on Jul 25 2016

city: Winnipeg

first: Kelly

last: Duke

address: 410 Buller Bldg, 100 Chancellors Circle

institute: University of Manitoba

summary:
Background: The biological control agent Pseudomonas chlororaphis PA23 is effective at protecting Brassica napus (canola) from the necrotrophic fungus Sclerotinia sclerotiorum via direct antagonism. Despite the growing importance of biocontrol bacteria in plant protection from fungal pathogens, little is known about how the host plant responds to bacterial priming on the leaf surface or about changes in gene activity genome-wide in the presence and absence of S. sclerotiorum.
Results: PA23 priming of mature canola plants reduced the number of lesion forming petals by 90%. Global RNA sequencing of the host pathogen interface showed a reduction in the number of genes uniquely upregulated in response to S. sclerotiorum by 16-fold when pretreated with PA23. Upstream defense-related gene patterns suggest MAMP-triggered immunity via surface receptors detecting PA23 flagellin and peptidoglycans. Although systemic acquired resistance was induced in all treatment groups, a response centered around a glycerol-3-phosphate (G3P)-mediated pathway was exclusively observed in plants treated with PA23 alone. Activation of these defense mechanisms by PA23 involved mild reactive oxygen species production as well as pronounced thylakoid membrane structures and plastoglobule formation in leaf chloroplasts.
Conclusion: Further to the direct antibiosis that it exhibits towards the pathogen S. sclerotiorum, PA23 primes defense responses in the plant through the induction of unique local and systemic defense regulatory networks. This study has shed light on the potential effects of biocontrol agents applied to the plant phyllosphere. Understanding these interactions will aid in the development of biocontrol systems as a viable alternative to chemical pesticides in the protection of important crop systems.

overall_design: Mature canola leaf tissue treated with combinations of PA23 or S. sclerotiorum ascospores (3 treatment groups) was compared to a water treated control (all treatments done in triplicate).

first: Michael

last: Becker

first: Ian

last: Girard

first: Jenna

middle: L

last: Millar

first: Mark

middle: F

last: Belmonte

first: W

last: Fernando

first: Teresa

last: de Kievit


title: A Pro-Asthmatic IL-4 Receptor Allele Promotes Airway Inflammation by Programming TH17 Cell-Like Regulatory T cells

city: Los Angeles

first: Matteo

last: Pellegrini

state: CA

address: 610 Charles Young Drive East

country: USA

institute: UCLA

type: Expression profiling by high throughput sequencing

summary: Mechanisms by which regulatory T (Treg) cells fail to control inflammation in asthma remain poorly understood. We show that a severe asthma-associated polymorphism in the interleukin-4 receptor alpha chain (IL-4Rα-R576) biases induced Treg (iTreg) cells towards a T helper 17 (TH17) cell fate. This skewing reflects the recruitment by IL-4Rα-R576 of the adaptor protein growth factor receptor-bound protein 2 (GRB2), which drives IL-17 expression by an extracellular signal-regulated kinase-, IL-6- and STAT3-dependent mechanism.  We showed that the IL-4Rα-R576 mutation elicits TH17 airway responses in vivo, in a house dust mite (HDM)- or ovalbumin (OVA)-driven model of airway inflammation in the mice carry the IL-4Rα-R576 mutation (Il4raR576 mice).  Treg cell-specific deletion of genes encoding IL-6Rα or the master TH17 cell regulator Retinoid-related Orphan Receptor γt (RORγt), but not IL-4 and IL-13, protected mice against exacerbated airway inflammation induced by IL-4Rα--576.  Analysis of lung tissue Treg cells revealed that the expression of IL-17 and the TH17 cell-associated chemokine receptor CCR6 was largely overlapping and highly enriched in Treg and conventional T (Tconv) cells of allergen-treated Il4raR576 mice.  To further characterize the subset of IL-17 producing Foxp3+ Treg in the lung of OVA-treated mice we utilized CCR6 as a marker of Treg cells committed towards the TH17 cell lineage to examine their functional, epigenetic and transcriptional profiles. CCR6+Foxp3EGFP+ Treg cells isolated from OVA-sensitized and challenged Il4raR576 mice, by FACS (Fluorescence Activated Cell Sorting) exhibited decreased methylation of the Foxp3 CNS2 locus comparing to CCR6–Foxp3EGFP+ Treg cells from same animals, indicative of decreased stability. They also exhibited profoundly decreased suppressive function as compared to CCR6– WT and CCR6– Il4raR576 counterparts. Transcriptional profiling of CCR6+Foxp3EGFP+ Treg cells revealed increased relative expression in CCR6+ Il4raR576 Treg cells of genes associated with a TH17 cell signature, including Rorc, Ccr6, Il23r, Il17a, Il17f, Il1r1, Nr1d1, Cstl, and Ahr comparing to CCR6–Foxp3EGFP+ Treg cells from same animals.

overall_design: Three CCR6+Foxp3EGFP+ Il4raR576 replicates and four CCR6–Foxp3EGFP+ Il4raR576 Treg replicates (controls) were sampled

first: A

middle: H

last: Massoud

first: Louis-Marie

last: Charbonnier

first: D

last: Lopez

first: M

last: Phipatanakul

first: T

last: Chatila


title: Transcriptomic analysis of regulatory gene expression profiles by NF-YCs, and RGL2 under paclobutrazol (PAC) condition

city: Guangzhou

first: Xu

last: Liu

state: Guangdong

address: No.723, Xingke Road, Tianhe District

department: South China Botanical Garden

country: China

institute: Chinese Academy of Sciences

summary: To understand how the NF-YC-RGL2 complex functions in repressing seed germination, a genome-wide transcriptomic analysis was carried out using germinating seeds of rgl2, nf-ycT and the wild-type (Col) grown on the medium containing 5 µM PAC and Col grown on mock treatment. Basing on the criteria of 1.5-fold cutoff for the genes with 5% false discovery rate, we first identified the differentially expressed genes in Col_PAC vs Col_mock, nf-ycT_PAC vs Col_PAC, and rgl2_PAC vs Col_PAC subsets, which are referred to as PAC-, NF-YC-, and RGL2-regulated genes.These data reveal that NF-YCs and RGL2 co-target a set of common genes in response to phytohormone signals, strongly supporting the role of NF-YC-RGL2 in seed germination regulation.

overall_design: Digital gene expression tag profiles of wild type (Col), nf-ycT mutant, and rgl2 mutant germinating seed for 12 h after stratification were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Xingliang

last: Hou


title: Homeostatic skin contains two different subsets of resident macrophages with distinct origin and gene profile.

status: Public on Jul 26 2016

city: Madrid

first: Francisco

last: Sanchez-Madrid

address: Diego de Leon 62

country: Spain

institute: Hospital Universitario de la Princesa

summary: We have found the existence of two independent populations contributing to the skin-resident macrophage pool based on their different origin. We have analyzed their gene profile by deep-sequencing (RNA-Seq). Analysis of RNA-Seq data revealed a differential expression signature between both subsets of skin macrophages for 744 of 17741 genes compiled (198 of them showing similar normalized expression levels across replicates). We have further characterized their specialized functions related to their different gene profiles.

overall_design: Examination of gene profile of 2 different macrophage subsets coexisting in skin under steady state.

last: Sánchez-Madrid

first: Olga

last: Barreiro


title: Integration of developmental and nutritional cues determines timing of female flower opening in cucumber

city: Shanghai

first: Renyi

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

summary: The timing of flower opening is essential for pollination and thus seed production. Despite flower opening has been a long lasting topic for plant biologists, the underling molecular mechansim remains elusive. Here we used a unique cucumber line ‘6457’ that spontaneously produces super ovary with delayed corolla opening as material, and explored the physiological, cytological, nutritional and transcriptomic reasons for the delayed corolla opening in super ovary. Our data showed that cell division and cell expansion persisited for a longer period of time in the super ovary, especially during the green yellow bud stage and yellow bud stage. Similarly, RNA-seq analyses showed that RNA and protein synthesis related genes were upregulated during these two stages, which may account for the decreased nitrogen and phosphrate content in the super ovary. Further, activation of transcription factors were delayed in the green yellow bud stage, while signalling kinases related genes were upregulated in the yellow bud stage in the super ovary. Photosynthesis related genes were also significantly activated in the super ovary, which corresponds to the increased soluble suble content. Phytohoromones such as cytokinins and gibberllins were elevated in the super ovary. Consistently, cytokinins and gibberllins related genes showed significantly enhanced expression. Therefore, both developmental and nutritional factors regulate the timing of female flower opening in cucumber, and provide a valuable foundation for dissecting the underling regulatory pathways of flower opening in planta.

overall_design: The normal ovary blooms at 4-5 days after labeling (when the ovary is visible) (DAL), with the majority blooms at 5 DAL, while the anthesis of super ovary occurs at 8-9 DALs, with most super ovaries blooms at 9 DAL.In the normal ovary, corolla at 1 DAL (N1), 3 DAL (N3), 4 DAL (N4), and 5 DAL (N5) is the typical stage for green bud, green yellow bud, yellow bud, and flowering, respectively, whereas in the super ovary, corolla at 1 DAL (S1) is the green bud, corolla at 3, 4 and 5 DAL (S3, S4, S5) is the green yellow bud, corolla at 7 and 8 DAL (S7, S8) is the yellow bud, and corolla at 9 DAL (S9) is the typical flowering stage.Transcriptome profiling of 11 stages include N1,N3,N4,N5,S1,S3,S4,S5,S7,S8 and S9 were performed, and each stage had 3 biological replicates.

first: Chengzhen

last: Sun

first: Wensheng

last: Zhao

first: Yanqiang

last: Li

first: Xiaofei

last: Song

first: Man

last: Lu

first: Xiaoli

first: Liying

last: Yan

first: Xiaolan

last: Zhang


title: RNA-seq analysis of TALEN-mediated LATS2 knockout HeLa-S3 cells

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: Chromatin modifying activities for construction of appropriate epigenetic landscapes by polycomb repressive complex 2 (PRC2) play an essential role in development and tumorigenesis. However, the spatiotemporal mechanisms by which PRC2 achieves diverse epigenomes for specific tissue or cellular contexts remain poorly understood. Here, we discovered that LATS2 knockout causes dysregulation of PRC2 and subsequent transcriptome changes for differentiation in both mouse and human cells. LATS2 depletion dependent dysregulation of PRC2 also effects H3K4me3 and forms negative feedback loop for maintenance of PRC2. Further analyses reveal that LATS2 on chromatin binds to EZH2 and LATS2 has ability to phosphorylate PRC2 in vitro. These LATS2 dependent H3K27me3 targets are highly induced during neurogenesis, and statistical analysis of glioblastoma multiforme reveals that LATS2-high cases show more dedifferentiated transcriptome and poor prognosis with silencing of H3K27me3 targets. These observations suggest that LATS2-mediated epigenome coordination is pivotal for development and disease, including cancer.

overall_design: mRNA of wild type (WT) and LATS2 KO HeLa-S3 cells were subjected to deep sequencing  profiling using Illumina HiSeq 2500

first: Shota

last: Nakamura

last: Motooka

first: Kosuke

last: Torigata


title: RNA-Seq and N6-Adenosine (m6A) Methylation profiling in Arabidopsis thaliana wild-type and fip37-4 LEC1:FIP37

city: Singapore

first: Hao

last: Yu

address: Science Drive 4

country: Singapore

institute: National University of Singapore

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

overall_design: Refer to individual Series


title: Profiling of N6-Adenosine (m6A) Methylation in Arabidopsis thaliana wild-type and fip37-4 LEC1:FIP37

summary: N6-methyladenosine (m6A) represents the most prevalent internal modification on messenger RNA, and requires a multicomponent m6A methyltransferase complex in mammals. How their plant counterparts determine the global m6A modification landscape and its molecular link to plant development remain elusive. Here we show that FKBP12 INTERACTING PROTEIN 37 KD (FIP37) is a core component of the m6A methyltransferase complex, which underlies control of shoot stem cell fate in Arabidopsis. The mutants lacking FIP37 exhibit massive overproliferation of shoot meristems and a transcriptome-wide loss of m6A RNA modifications. We further demonstrate that FIP37 mediates m6A RNA modification on key shoot meristem genes inversely correlated with their mRNA stability, thus confining their transcript levels to prevent shoot meristem overproliferation. Our results suggest an indispensable role of FIP37 in mediating m6A mRNA modification, which is required for maintaining the shoot meristem as a renewable source for continuously producing all aerial organs in plants.

overall_design: m6A-seq in Arabidopsis thaliana (Col-0) wild-type and  fip37-4 LEC1:FIP37, two replicates for each sample

first: Lisha

last: Shen

first: Zhe

last: Liang

first: Xiaofeng

last: Gu

first: Ying

last: Chen

first: Zhiwei

middle: N

last: Teo

first: Weiling

middle: M

last: Cai

first: Peter

middle: C

last: Dedon

first: Lu

last: Liu


title: Analyses of genes regulated by the N-terminal photolyase homology region (CNT1/PHR) of CRY1 by RNA-seq

first: Sheng-Bo

last: He

address: 800 Rd Dongchuan

institute: Shanghai Jiao Tong University

summary:
Total RNA was extracted from samples including 35S::CNT1-NLS-YFP;cry1 and 35S::CNT1-G283E-NLS-YFP;cry1 seedlings grown in continuous blue light and subjected to high throughput sequencing.
Previous studies reported that the C-terminal domain of CRY1 regulates hypocotyl elongation and blue light-regulated genes. This study reveals that CNT1 overexpression also regulates blue light-regulated genes, supporting the role of CNT1 in hypocotyl elongation at transcriptomic level.

overall_design: mRNA from blue light-grown CNT1 or CNT1 variant (G283E) overexpressors was sequenced to analyze the genes regulated by CNT1.

first: Hong-Quan

last: Yang


title: An ABA response regulator unique to basal land plants required for the acquisition of desiccation tolerance

city: Leeds

first: Andrew

last: Cuming

address: Faculty of Biological Sciences

department: Centre for Plant Sciences

country: United Kingdom

institute: University of Leeds

summary:
Purpose: The plant hormone abscisic acid (ABA) coordinates responses leading to desiccation tolerance in all land plants. RNA-seq was employed to obtain differential expression data in response to ABA, dehydration and mannitol treatments in wild-type tissue. This was compared against the targeted gene knockout line PpanrKO. The ANR gene encodes a novel ABA regulator identified from ABA non-responsive (anr) mutant screens.
Methods: RNA-seq on the Illumina HiSeq platform and mapping to the V3.0 genome and transcriptome assemblies using tophat2 enabled gene abundance data to be generated for differential gene expression analysis with edgeR in the Trinity package.
Results: We observe a coordinated up-regulation of ca. 900 genes, with extensive overlaps between hormone and stress treatments as well as ca. 900 down-regulated genes. Of the up-regulated genes, those encoding LEA proteins, membrane channel proteins and transporters and oxidative-stress-associated genes comprised a significant fraction while those encoding growth-associated cell wall enzymes (e.g. expansins) and components of secondary metabolism (notably enzymes in the phenylpropanoid pathway) were prominent in the down-regulated genes. The ANR gene, a modular MAP3 kinase comprising an N-terminal PAS domain, a central EDR domain and a C-terminal MAPKKK-like domain unique to basal plant lineages, is found to play a central role in these responses with mutants failing to accumulate the wide spectrum of dehydration tolerance-associated gene products characteristic of the wild-type response and do not acquire ABA-dependent desiccation tolerance.
Conclusions: Our study adds considerable data to the stress responses in bryophytes helping understand the mechanisms behind vegetative dehydration tolerance; an important trait for crop species. We also confirmed the vital role that PpANR plays in these responses in the moss Physcomitrella patens likely representing an ancestral mechanism for ABA-mediated dehydration tolerance vital in the conquest of land.

overall_design: RNA from 3 biological replicas was bulked per library. 8 libraries were generated from two genotypes, wild-type and PpanrkO, which included 3 treatments and a control sample for each.

first: A

first: Y

last: Kamisugi

first: S

last: Stevenson


title: An epigenetic mark of polycomb response elements implemented by Trx/MLL/COMPASS

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In Drosophila, Polycomb Response Elements (PREs) are identified as genomic sequences allowing the maintenance of transcriptional repression in the absence of the initiating signal. Although PREs in Drosophila are well characterized, the existence of mammalian PRE-like elements remains debated.  Accumulating evidence supports a model in which CpG islands function to recruit Polycomb-Group complexes (PcG), however, it is not evident which subclasses of CpG islands serve as PREs. Trithorax (Trx), which is required for positive regulation of gene expression in Drosophila, is known to co-bind Drosophila PREs where it is thought to antagonize polycomb-dependent silencing of nearby genes.  Here, we demonstrate the existence of Trx-dependent H3K4 dimethylation loci that specifically mark Drosophila PREs and are required for the maintenance of expression of the nearby genes. Similarly, in human cells, we find ~ 3000 MLL1 (human Trx homologue)-dependent H3K4 dimethylation loci, which correlate strongly with CpG island density. In the absence of MLL1 and H3K4 dimethylation at these loci, there is an increase in H3K27 trimethylation levels, suggesting these sites can recruit Polycomb Repressive Complex 2 (PRC2). By inhibiting PRC2-dependent silencing in the absence of MLL1, we establish that a balance exists between MLL1 and PRC2, and their respective capacity to maintain or repress transcription. Thus, by investigating a conserved function between Trx and MLL1, we provide rules for the identification of CpG island subclasses serving as PRE-like sequences within the human genome.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: To examine changes in histone-modification profiles and gene expression after depletion of Trx in Drosophila S2 cells, and MLL1 in human HCT116 cells. We also treated MLL1-NULL HCT116 cells with GSK126 (5uM) for 4 days and measured changes in gene expression.

first: Ryan

middle: A

last: Rickels

first: Clayton

middle: K

last: Collings


title: Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Embryonic Stem Cells (ChIP-seq)

status: Public on Aug 02 2016

last: King

address: Gonda Bldg Rm. 6554, P.O.Box 957088

department: Human Genetics

summary: In this study, we mapped modification of lysine 4 and lysine 27 of histone H3 genome-wide in a series of mouse embryonic stem cells (mESCs) varying in DNA methylation levels based on knock-out and reconstitution of DNA methyltransferases (DNMTs). We extend previous studies showing cross-talk between DNA methylation and histone modifications by examining a breadth of histone modifications, causal relationships, and direct effects. Our data shows a causal regulation of H3K27me3 at gene promoters as well as H3K27ac and H3K27me3 at tissue-specific enhancers. We also identify isoform differences between DNMT family members. This study provides a comprehensive resource for the study of the complex interplay between DNA methylation and histone modification landscape.

overall_design: Histone ChIP-seq of H3K4me3, H3K27me3, H3K4me1, and H3K27ac were performed on wild-type, Dnmt triple knock-out (Dnmt1/3a/3b; TKO), Dnmt double knock-out (Dnmt3a/3b; DKO), and respective reconstitution mouse embryonic stem cell lines

middle: D

first: Guoping

last: Fan


title: LATS2 regulates repressive epigenetic integrity via regulation of Polycomb repressive complex 2

first: Daisuke

last: Okuzaki

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: A global view on the role of SMAD4 gene in porcine follicular granulosa cells by RNA-Seq

city: Nanjing

first: lifan

last: zhang

state: Jiangsu

address: No.6 Tongwei road

department: College of Animal Science and Technology

institute: Nanjing agricultural university

summary: Sma- and Mad-related protein 4 (SMAD4) is closely associated with the development of ovarian follicular. However, current knowledge of the genome-wide view on the role of SMAD4 gene in mammalian follicular granulosa cells (GCs) is still largely unknown. In the present study, RNA-Seq was performed to investigate the effects of SMAD4 knockdown by RNA interference (SMAD4-siRNA) in porcine follicular GCs. A total of 1025 differentially expressed genes (DEGs), including 530 upregulated genes and 495 downregulated genes, were identified in SMAD4-siRNA treated GCs compared with that treated with NC-siRNA. Furthermore, functional enrichment analysis indicated that upregulated DEGs in SMAD4-siRNA treated cells were mainly enriched in cell-cycle related processes, interferon signaling pathway, and immune system process, while downregulated DEGs were mainly involved in extracellular matrix organization/disassembly, pathogenesis, and cell adhesion. In particular, cell cycle and TGF-β signaling pathway were discovered as the canonical pathways changed under the SMAD4 silencing. Taken together, our data reveals SMAD4 knockdown alters the expression of numerous genes involved in key biological processes of the development of follicular GCs and provides a novel global clue of the role of SMAD4 gene in porcine follicular GCs.

overall_design: mRNA profiles of NC-siRNA treated and SMAD4-siRNA treated porcine GCs were generated by RNA sequencing using Ion Torren Proton

first: Lifan

last: Zhang

first: Qifa

last: Li


title: HP1BP3, a chromatin retention factor for co-transcriptional microRNA processing (ChIP-Seq)

status: Public on Jul 24 2016

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Identification and characterization of HP1BP3 (a human histone H1 homologue) as a novel chromatin retention factor essential for the co-transcriptional processing of pri-miRNA.

overall_design: We generated BAC transgenic cells at 80% confluency (~1x107) were cross-linked with 1% formaldehyde for 10 minutes at 37°C, and quenched with 125 mM glycine at room temperature for 5 minutes. The fixed cells were washed twice with cold PBS, scraped, and transferred into 1 ml PBS containing protease inhibitors (Roche). After centrifugation at 700 g for 4 minutes at 4°C, the cell pellets were resuspended in 100 μl ChIP lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl [pH 8.1] with protease inhibitors) and sonicated at 4°C with a Bioruptor (Diagenode) (30 seconds ON and 30 seconds OFF at highest power for 15 minutes). The sheared chromatin with a fragment length of ~200 – 600 bp) was centrifuged at 20,000 g for 15 minutes at 4°C). 100 μl of the supernatant was used for ChIP or as input. A 1:10 dilution of the solubilized chromatin in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl 16.7 mM Tris-HCl [pH 8.1]) was incubated at 4°C overnight with 6 μg/ml of a goat anti-GFP (raised against His-tagged full-length eGFP and affinity-purified with GST-tagged full-length eGFP). Immunoprecipitation was carried out by incubating with 40 μl pre-cleared Protein G Sepharose beads (Amersham Bioscience) for 1 hour at 4°C, followed by five washes for 10 minutes with 1ml of the following buffers: Buffer I: 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.1], 150 mM NaCl; Buffer II: 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.1], 500 mM NaCl; Buffer III: 0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl [pH 8.1]; twice with TE buffer [pH 8.0]. Elution from the beads was performed twice with 100 μl ChIP elution buffer (1% SDS, 0.1 M NaHCO3) at room temperature (RT) for 15 minutes. Protein-DNA complexes were de-crosslinked by heating at 65°C in 192 mM NaCl for 16 hours. DNA fragments were purified using QiaQuick PCR Purification kit (QIAGEN) and eluted into 30 μl H2O according to the manufacturer’s protocol after treatment with RNase A and Proteinase K.

first: Haoming

first: Rahul

last: Kollipara

first: Qinghua


title: Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing

city: Pasadena

first: Chun-Kan

last: Chen

address: 1200 E California Blvd

institute: California Institute of Technology

summary: Xist orchestrates X chromosome inactivation, a process that entails chromosome-wide silencing and remodeling of the 3-dimensional structure of the X chromosome. Yet, it remains unclear whether these changes in nuclear structure are mediated by Xist and whether they are required for silencing. Here we show that Xist directly interacts with the Lamin B Receptor (LBR), an integral component of the nuclear lamina, and that this interaction is required for Xist-mediated silencing. We show that this interaction recruits the inactive X to the nuclear lamina and by doing so enables Xist to spread to actively transcribed genes across the X. Our results demonstrate that lamina recruitment changes the accessibility of DNA thereby enabling Xist, and its silencing proteins, to spread across the X to silence transcription.

overall_design: We examined the genomic localization of the Xist lncRNA using RNA Antisense Purification (RAP) in male mouse ES cells where the endogenous Xist promoter is replaced by a tet-inducible one (pSM33) containing 1) wild-type Xist (WT), 2) LBR binding site deletion Xist (dLBS), 3) dLBS-Xist rescued with LMNB1 (LMNB1Res), 4) LBR CRISPRi knock down (LBRKD), or 5) SHARP CRISPRi knock down (SHARPKD). A-repeat deletion Xist (dA) was obtained from Engreitz et al. (2013) (GSE46918).


title: MicroRNA expression in chicken cecum following Campylobacter jejuni infection

city: Tian'an

first: XIANYAO

last: LI

address: No. 61  Daizong Street,

department: Department of Animal Science

institute: Shandong Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: SPF leghorn chickens were infected with C. jejuni. The cecum were collected at 8h post infection for total RNA isolation. The significantly expressed microRNAs between infected and non-infected chickens were identified through Solexa sequencing technology.

overall_design: Two libraries were made from each group, in total, four libraries were used for Solexa sequencing.

first: Xiaoyi

last: Liu

first: Xianyao


title: Conversion of Human Gastric Epithelial Cells to Multipotent Endodermal Progenitors using Defined Small Molecules [DNA methylation]

city: Beijing

first: Jinhua

last: Qin

address: Taiping Road

institute: Beijing Institute of Transfusion

type: Methylation profiling by high throughput sequencing

summary: Endodermal stem/progenitor cells have diverse potential applications in research and regenerative medicine, so a readily available source could have widespread uses. Here we describe derivation of human induced endodermal progenitor cells (hiEndoPCs) from gastrointestinal epithelial cells using a cocktail of defined small molecules along with support from tissue-specific mesenchymal feeders. The hiEndoPCs show clonal expansion in culture and give rise to hepatocytes, pancreatic endocrine cells, and intestinal epithelial cells when treated with defined soluble molecules directing differentiation. The hiEndoPC-derived hepatocytes are able to rescue liver failure in Fah-/-Rag2-/- mice after transplantation, and, unlike hESCs, transplanted hiEndoPCs do not give rise to teratomas. Since human gastric epithelial cells are readily available from donors of many ages, this conversion strategy can generate clonally expandable cell populations with a variety of potential applications, including personalized drug screening and therapeutic strategies for liver failure and diabetes.

overall_design: Gastric epithelial cells (GECs) were isolated from human stomach. Human induced endodermal progenitor cells (hiEndoPCs) were reprogrammed from GECs by small molecules. The hiMEP-Heps were differentiated from hiEndoPCs under hepatic differentiation protocol. Fetal-Heps were isolated from aborted fetal liver. We used RNA sequencing and DNA methylation analysis to detail the global gene expression profile of GECs, hiEndoPCs, hiEndoPC-Heps and Fetal-Heps to delineate the difference of these cells.

first: Shuyong

last: Wang

first: Wencheng

first: Yunfang

first: Xuetao

last: Pei


title: Beauveria bassiana SNF 1 (BbSNF1) regulating genes involved in conidiation

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

institute: Zhejiang University

summary: Gene BbSNF1 playes an essential role in mediating metabolism and cell development during conidation, a determinant to the biocontrol  potential of entomopathogenic fungi.  The genome-wide exprssion analysis involved in fungal conidiation was analyzed by using high throughput sequencing (RNA-Seq). Our transcriptional profiles revealed that numerous differentially expressed genes (DEGs), of which involved in metabolism, cell transport and cell rescue, were significantly involved in deveopment of fungal conida.  .

overall_design: Total RNA obtained from BbSNF1 disruption mutant were compared to that of wild type strain (WT) grown on SDA plates (Glucose 4%, Peptone 1%, and Yeast extract 1% plus 1.5% Agar).

first: Sheng-Hua

first: Ming-Guang

last: Feng


title: HP1BP3, a chromatin retention factor for co-transcriptional microRNA processing (miRNA-Seq)

overall_design: Compare global miRNA expression profile between control sample and sample depleted of HP1BP3


title: The Nrd1-like protein Seb1 coordinates co-transcriptional 3’ end processing and polyadenylation site selection

status: Public on Jul 22 2016

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

institute: University of Edinburgh

summary: Termination of RNAPII transcription is associated with RNA 3’ end formation. For coding genes, termination is initiated by the cleavage/polyadenylation machinery. In contrast, a majority of noncoding transcription events in S. cerevisiae do not rely on RNA cleavage for termination, but instead terminate via a pathway that requires the Nrd1-Nab3-Sen1 (NNS) complex. Here we show that the S. pombe ortholog of Nrd1, Seb1, does not function in NNS-like termination, but promotes polyadenylation site selection of coding and noncoding genes. We found that Seb1 associates with 3’ end processing factors, is enriched at the 3’ end of genes, and binds RNA motifs downstream of cleavage sites. Importantly, a deficiency in Seb1 resulted in widespread changes in 3’ UTR length as a consequence of increased alternative polyadenylation. Given that Seb1 levels affected the recruitment of conserved 3’ end processing factors, our findings indicate that the conserved RNA-binding protein Seb1 co-transcriptionally controls alternative polyadenylation.

overall_design: Two biological replicates of Seb1 and Control (parental strain) CRAC experiments

first: Francois

last: Bachand


title: BET Bromodomain inhibition promotes neurogenesis while inhibiting gliogenesis in neural progenitor cells

first: Guofeng

last: Meng

address: Jinke 3528

institute: Shanghai University of Traditional Chinese Medicine

summary: Neural stem cells (NSCs) and progenitor cells (NPCs) are increasingly appreciated to hold great promise for regenerative medicine to treat CNS injuries and neurodegenerative diseases. However, evidence for effective stimulation of neuronal production from endogenous or transplanted NPCs for cell replacement with small molecules remains limited. To identify novel chemical entities/targets for neurogenesis, we had established a NPC phenotypic screen assay and validated it using known small-molecule neurogenesis inducers. Through screening small molecule libraries with annotated targets, we identified BET bromodomain inhibition as a novel mechanism for enhancing neurogenesis. BET bromodomain proteins, Brd2, Brd3, and Brd4 were found to be downregulated in NPCs upon differentiation, while their levels remain unaltered in proliferating NPCs. Consistent with the pharmacological study using bromodomain selective inhibitor (+)-JQ-1,  knockdown of each BET protein resulted in an increase in the number of neurons with simultaneous reduction in both astrocytes and oligodendrocytes. Gene expression profiling analysis demonstrated that BET bromodomain inhibition induced a broad but specific transcription program enhancing directed differentiation of NPCs into neurons  while suppressing cell cycle progression and gliogenesis. Together, these results highlight a crucial role of BET proteins as promising epigenetic regulators in NPC development and suggest a therapeutic potential of BET inhibitors in treating CNS injury and neurodegenerative diseases.

overall_design: NPCs were treated with (+)-JQ-1 or inactive enantiomer (-)-JQ-1 at 0.2 μM or 0.5 μM for 12 and 24 hrs in differentiation medium. The experiments were carried out in  3 independent preparations of NPCs (triplicates)

first: JingJun

first: Jing

last: Ma


title: HP1BP3, a chromatin retention factor for co-transcriptional microRNA processing

first: Ralf


title: Conversion of Human Gastric Epithelial Cells to Multipotent Endodermal Progenitors using Defined Small Molecules [gene expression]

overall_design: Gastric epithelial cells (GECs) were isolated from human stomach. Human induced endodermal progenitor cells (hiEndoPCs) were reprogrammed from GECs by small molecules. The hiEndoPC-Heps were differentiated from hiEndoPCs under hepatic differentiation protocol. Fetal-Heps were isolated from aborted fetal liver. Definitve endoderm (DE), primitive gut tube (PGT), and posterior foregut (PFG) were endodermal stem cells derived form human enbryonic stem cells (hESCs).We used RNA sequencing and DNA methylation analysis to detail the global gene expression profile of GECs, hiEndoPCs, hiEndoPC-Heps, Fetal-Heps, DE, PGT and PFG to delineate the difference of these cells.


title: A Highly Sensitive and Unbiased Approach for Elucidating Antibody Repertoires

city: Boston

first: Jiazhi

last: Hu

state: MA

address: 300 Longwood Ave

department: PCMM

institute: Children's Hospital Boston

summary: Developing B lymphocytes undergo V(D)J recombination to assemble germline V, D, and J gene segments into exons that encode the antigen-binding variable region of immunoglobulin (Ig) heavy (H) and light (L) chains.  IgH and IgL chains associate to form the B cell receptor (BCR), which upon antigen binding activates B cells to secrete BCR as an antibody.  Each of the huge number of clonally independent B cells expresses a unique set of IgH and IgL variable regions.  Ability of V(D)J recombination to generate vast primary B cell repertoires results from combinatorial assortment of large numbers of different V, D, and J segments, coupled with diversification of the junctions between them to generate the complementary determining region 3 (CDR3) for antigen contact.  Approaches to evaluate in depth the content of primary antibody repertoires and, ultimately, to study how they are further molded by secondary mutation and affinity maturation processes are of great importance to the B cell development, vaccine, and antibody fields.  We now describe an unbiased, sensitive, and readily accessible assay, referred to as HTGTS repertoire sequencing (HTGTS-Rep-seq), to quantify antibody repertoires.  HTGTS-Rep-seq quantitatively identifies the vast majority of IgH and IgL V(D)J exons, including their unique CDR3 sequences, from progenitor and mature mouse B lineage cells via the use of specific J primers.  HTGTS-Rep-seq also accurately quantifies DJH intermediates and V(D)J exons in either productive or non-productive configurations.  HTGTS-Rep-seq should be useful for studies of human samples, including clonal B-cell expansions and also for following antibody affinity maturation processes.

overall_design: We employed high-throughput genome-wide translocation sequencing adapted repertoire sequencing (HTGTS-Rep-seq) to study antibody repertoires. For HTGTS-Rep-seq libraries, we utilize bait coding ends of J segments to identify, in unbiased fashion, mouse IgH DJH repertoires [processed tlx files] along with both productive and non-productive IgH V(D)J repertoires from both pro-B and peripheral B cells [processed xls files of samples 1-18, 21-51].  Similarly, we also identify mouse productive and non-productive Igk repertoires from peripheral B cells [processed xls files of samples 19,20,52-57].

first: Frederick

middle: W

last: Alt

first: Sherry

middle: G

last: Lin

first: Zhaoqing

last: Ba

first: Zhou

last: Du


title: Histone H2B ubiquitylation represses gametogenesis by opposing RSC-Dependent chromatin remodeling at the ste11 master regulator locus

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

institute: CNIC

summary:
Chromatin modifications play a pivotal role in cell fate decision. In fission yeast, the ste11 gene encodes the master regulator initiating the switch from vegetative growth to gametogenesis when cells starve. The methylation of H3K4 by Set1-COMPASS and consequent promoter nucleosome deacetylation was shown to repress ste11 induction and cell differentiation but the regulatory steps remain poorly understood.
A genetic screen highlighted H2B ubiquitylation and the RSC remodeling complex as activators of ste11 expression. Mechanistic analyses revealed more complex, opposite roles of H2B-ub1 at the promoter where it represses expression, and over the transcribed region where it sustains transcription of ste11. By promoting H3K4 methylation at the promoter, H2B-ub1 initiates the deacetylation process, which decreases chromatin remodeling by RSC. Upon induction, this process is reversed and efficient NDR formation leads to high expression.
Therefore, H2B-ub1 represses gametogenesis by opposing the recruitment of RSC at the promoter of the master regulator ste11 gene.

overall_design: Samples from mononucleosomal DNA from S. pombe strains h-972 and h-972 rsc1::kanR were sequenced (Illumina NextSeq 500 platform) using the pair-end read protocol

first: Philippe

last: Materne

last: Vázquez

first: Mar

last: Sánchez

first: Carlo

last: Yague-Sanz

first: Jayamani

last: Anandhakumar

first: Valerie

last: Migeot

first: Francisco

last: Antequera

first: Damien

last: Hermand


title: ChIP-Seq for Pbx1 in the mouse E12.5 ventral midbrain

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: Investigations into the roles for Pbx1 and its transcriptional network in dopaminergic neuron development and Parkinson's Disease

overall_design: One sample each for Pbx1, IgG, and input

first: J

last: Villaescusa

first: Ernest

last: Arenas


title: A Primary Role of TET Proteins in Establishment and Maintenance of De Novo Bivalency at CpG Islands of Developmental Genes

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

institute: Institutes of Biomedical Sciences Fudan University

summary: TET protein-catalyzed 5mC oxidation not only creates novel DNA modifications such as 5hmC, but also initiates active or passive DNA demethylation. However, the TETs’ function in crosstalk with specific histone modifications is largely elusive. Here, we show that TET2-mediated DNA demethylation plays a primary role in the de novo establishment and maintenance of H3K4me3/H3K27me3 bivalent domain underlying the methylated DNA CpG islands (CGIs). Overexpression of wild type (WT) but not catalytic inactive mutant (Mut) TET2 in TET-low-expressing cells results in increase of 5hmC level and accompanying DNA demethylation at a subset of CGIs. Importantly, this is sufficient to create de novo bivalent domains at these loci. Genome-wide analysis reveals that these de novo synthesized bivalent domains are largely associated with a subset of key developmental gene promoters, which are often located within CpG islands that are previously hyper-methylated and silenced. On the other hand, depletion of Tet1 and Tet2 in mouse ES cells results in an apparent loss of H3K27me3 at bivalent domains, which are located within CGIs and associated with a particular set of key developmental gene promoters. Collectively, these data suggest that TET proteins have a primary role in charge of regulating the crosstalk between two key epigenetic mechanisms, DNA methylation and histone methylation (H3K4me3 and H3K27me3), particularly at a subset of CpG islands associated with developmental genes.

overall_design: We examined H3K4me3,H3K27me3,5mC and 5hmC in 293T and mES cell types,using Illumina Hiseq2500.

first: Lingchun

last: Kong

last: Lv


title: ChIP-Seq and RNA-Seq of mouse E12.5

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

overall_design: Refer to individual Series


title: Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: The diversity of small RNA-directed DNA methylation (RdDM) mechanisms have been underestimated due to the nearly complete transcriptional silencing of transposable elements (TEs) in the wild-type reference strains of Arabidopsis thaliana. In plants mutant for the SWI/SNF histone remodeler DDM1, TEs are globally activated due to loss of genome wide heterochromatin condensation. Transcriptionally activated TEs go through additional non-canonical forms of RdDM that are dependent on RNA Polymerase II expression. However, the global targets of the non-canonical RdDM pathway have not been explored. In an attempt to identify and contrast the targets of canonical and expression-dependent non-canonical RdDM, we performed MethylC-seq of genome-wide DNA methylation patterns from several RdDM mutants in either the TE-silent or the TE-active (ddm1) contexts.

overall_design: Arabidopsis wildtype and twenty RdDM pathway mutants

first: R

last: Slotkin


title: Whole transcriptome target sequencing: profiling  gene expression and alternative polyadenylation with one pipeline.

city: Pullman

first: Zhihua

last: Jiang

state: WA

address: Veterinary and Biomedical Research Building, Room 151

department: Animal Science

institute: Washington State University

summary: We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method can simultaneously profile gene expression and alternative polyadenylation.

overall_design: A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay.  The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method.  Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method.  Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq.  Therefore, this submission involved a total of 26 libraries.

first: Xiang

last: Zhou

first: Rui

last: Li

first: Jennifer

last: Michal

first: Richard

last: Harland


title: Regulation of PERK-eIF2α Signaling by Tuberous Sclerosis Complex-1 Controls Homeostasis and Survival of Myelinating Oligodendrocytes

city: Cincinnati

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

summary:
Tuberous sclerosis complex (TSC), an autosomal dominant disorder caused by mutations in either TSC1 or TSC2, exhibits white matter abnormalities including CNS myelin deficits. however, underlying  mechanisms are not fully understood. Here we find that, unexpectedly, constitutive activation of mTOR signaling caused by Tsc1 deletion in the oligodendrocyte lineage
results in severe myelination defects and oligodendrocyte cell death. Expression profiling analysis reveals that Tsc1 ablation induces prominent endoplasmic reticulum (ER) stress responses through the PERK‐eIF2α dependent signaling axis and activates Fas-JNK apoptotic pathways. Our studies suggest that TSC1-mTOR signaling acts as an important checkpoint for maintaining oligodendrocyte homeostasis.

overall_design: Gene expression profiling of optic nerve from P12 control and Tsc1cKO mice

first: Minqing

first: Lei

last: Liu


title: Distinct gene expression profile of Xanthomonas retroflexus engaged in synergistic multispecies biofilm formation

city: Lyngby

first: Lea Benedicte

middle: Skov

last: Hansen

address: Kemitorvet 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: Technical University of Denmark

summary: It is well known that bacteria often exist in naturally formed multispecies biofilms. Within these biofilms, interspecies interactions seem to play an important role in ecological processes. Little is known about the effects of interspecies interactions on gene expression in these multispecies biofilms. This study presents a comparative gene expression analysis of the Xanthomonas retroflexus transcriptome when grown in a single-species biofilm and in dual- and four-species consortia with Stenotrophomonas rhizophila, Microbacterium oxydans and Paenibacillus amylolyticus. The results revealed complex interdependent interaction patterns in the multispecies biofilms. Many of the regulated functions are related to interactions with the external environment and suggest a high phenotypic plasticity in response to coexistence with other species. Furthermore, the changed expression of genes involved in aromatic and branched chain amino acid biosynthesis suggests nutrient cross feeding as an contribution factor for the observed synergistic biofilm production when these four species coexists in a biofilm.

sample_organism:
Paenibacillus amylolyticus
Microbacterium oxydans
Stenotrophomonas rhizophila
Xanthomonas retroflexus

overall_design:
X. retroflexus was cultivated in three replicates of single-species biofilm and combined with S. rhizophila, M. oxydans and P. amylolyticus in dual-species biofilms with three respective replicates. At last, we combined all four species in a multispecies biofilm with five replicates and conducted a RNA seq based comparative gene expression study utilizing the Illumina sequencing technology.
Please note that the 'prodigal_all_new.txt' contains gene  names (which are listed in the matrix_sum.txt) and their position in the genomes, which are included in the file 'all_contigs_500.fasta'.

first: Lea

middle: B

first: Dawei

last: Ren

first: Mette

last: Burmølle

first: Søren

last: Sørensen


title: Numerical and Spatial Patterning of Yeast Meiotic DNA Breaks by Tel1

city: New York

first: Neeman

last: Mohibullah

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: MSKCC

summary: The Spo11-generated double-strand breaks (DSBs) that initiate meiotic recombination are dangerous lesions that can disrupt genome integrity, so meiotic cells regulate their number, timing, and distribution. Here, we use Spo11-oligonucleotide complexes, a byproduct of DSB formation, to examine the contribution of the DNA damage-responsive kinase Tel1 (ortholog of mammalian ATM) to this regulation in Saccharomyces cerevisiae. A tel1Δ mutant had globally increased amounts of Spo11-oligonucleotide complexes and altered Spo11-oligonucleotide lengths, consistent with conserved roles for Tel1 in control of DSB number and processing. A kinase-dead tel1 mutation also increased Spo11-oligonucleotide levels, but mutating known Tel1 phosphotargets on Hop1 and Rec114 did not. Deep sequencing of Spo11 oligonucleotides from tel1Δ mutants demonstrated that Tel1 shapes the nonrandom DSB distribution in ways that are distinct but partially overlapping with previously described contributions of the recombination regulator Zip3. Finally, we uncover a context-dependent role for Tel1 in hotspot competition, in which an artificial DSB hotspot inhibits nearby hotspots. Evidence for Tel1-dependent competition involving strong natural hotspots is also provided.

overall_design: Eighteen samples total: The first 14 are two biological replicate Spo11-oligo maps from each of the following: wild type and tel1 each collected at 4, 5, and 6 hours after meiotic induction; the next 4 are one biological replicate Spo11-oligo map from each of the following: wild type and tel1 bearing an artificial hotspot insertion either on Chr III or on Chr IX.

first: Scott

last: Keeney


title: FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function

city: Atlanta

first: Jindan

last: Yu

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

summary: FOXA1 is a FKHD family protein that translates epigenetic signatures at target enhancers to lineage-specific transcription and differentiation. Through genome-wide location analyses, here we show that FOXA1 expression and occupancy are, in turn, required for the maintenance of this epigenetic signature, namely DNA hypomethylation and histone 3 lysine 4 methylation. Mechanistically, this involves TET1, a 5-methylcytosine dioxygenase. We found that FOXA1 induces TET1 expression via direct binding at its cis-regulatory elements. Further, FOXA1 physically interacts with the TET1 protein through its CXXC domain. TET1 thus co-occupies FOXA1-dependent enhancers and mediates local DNA demethylation and concomitant histone 3 lysine 4 methylation, further potentiating FOXA1 recruitment. FOXA1 binding events were markedly reduced following TET1 depletion. Together, our results support that FOXA1 is not only a reader, but also a writer, of the epigenetic signatures at lineage-specific enhancers and that TET1 and FOXA1 form a feed-forward regulatory loop for enhancer activation.

overall_design: ChIP-Seq examination of FOXA1 binding sites in LNCaP cell, and epigenetic markers (5mC, 5hmC, H3K4me2) profiling upon TET1 depletion

first: Yeqing

last: Yang

first: Jonathan

last: Zhao


title: RNA-Seq of mouse E12.5 brain regions

first: Sten

last: Linnarsson

overall_design: Three samples each from dorsal midbrain, forebrain, hindbrain, Alar plate, and ventral midbrain

first: J

last: Villaescusa

first: Ernest

last: Arenas


title: Conversion of Human Gastric Epithelial Cells to Multipotent Endodermal Progenitors using Defined Small Molecules

first: Jinhua

last: Qin


title: Loss of NAD homeostasis leads to progressive and reversible degeneration of skeletal muscle

city: Philadelphia

first: Ian

last: Silverman

state: Pennsylvania

address: 433 South University Ave, Room 104

department: Biology

institute: University of Pennsylvania

summary: NAD is an obligate co-factor for the catabolism of metabolic fuels in all cell types. However, the availability of NAD in several tissues can become limited during genotoxic stress and the course of natural aging. The point at which NAD restriction imposes functional limitations on tissue physiology remains unknown. We examined this question in murine skeletal muscle by specifically depleting Nampt, an essential enzyme in the NAD salvage pathway. Knockout mice exhibited a dramatic 85% decline in intramuscular NAD content, accompanied by fiber degeneration and progressive loss of both muscle strength and treadmill endurance. Administration of the NAD precursor nicotinamide riboside rapidly ameliorated functional deficits and restored muscle mass, despite having only a modest effect on the intramuscular NAD pool. Additionally, lifelong overexpression of Nampt preserved muscle NAD levels and exercise capacity in aged mice, supporting a critical role for tissue-autonomous NAD homeostasis in maintaining muscle mass and function.

overall_design: Messenger RNA was isolated from quadriceps muscle of mice from three different age groups and three different genotypes. Wildtype mice were aged 4, 7, and 24 months. Mice deficient for Nampt in skeletal muscle (mNKO) were aged 7 months. Mice overexpressing Nampt in skeletal muscle were aged 4 and 24 months.

first: David

last: Fredrick

first: Sager

last: Gosai

first: Brian

last: Gregory

first: Joseph

last: Baur


title: Grasses suppress shoot-borne roots to conserve water during drought

city: Stanford

first: Jose

middle: Ramon

last: Dinneny

state: United States

address: 260 Panama St

department: Plant Biology

institute: Carnegie Institution for Science, Department of Plant Biology

summary: Setaria viridis, the wild ancestor of millet, exhibits strong repression of crown root growth in drought. We compare  in gene expression in the S. viridis crown between drought vs watered treatments.

overall_design: RNA from Lower region (crown) or Upper region (stem) of watered (W) or drought (D) treated Setaria plants were harvested at 6 or 9 days after sowing; there are 8 samples per biological repeat, 3 biological repeats.


title: Transcriptomic changes associated with DNA pol epsilon deficiency

city: evry

first: remi

last: bounon

state: essonne

address: 2 avenue Gaston Crémieux

department: BAP

country: France

institute: INRA

summary:
What is the impact of DNA pol epsilon deficiency on gene expression as well as on the expression of ncRNA, gene silencing etc.?
Plantlets were grown in vitro on half strength MS for 9 days and used for total RNA extraction.

overall_design: mRNA seq on wild-type Col0, two DPB2oe mutants overexpress and one abo4-1 mutant knock out.

first: Raynaud

last: Cécile

first: Sandrine

last: Balzergue

first: Rémi

last: Bounon

first: Véronique

last: Brunaud

first: Etienne

last: Delannoy

first: Marie-Laure

last: Martin-Magniette


title: CELF2 CLIP-seq in human JSL1 T cells

first: Kristen

last: Lynch

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

summary: In this study, CLIP-seq was used to identify sites of CELF2-mRNA interactions in JSL1 T cells.

overall_design: (SRA study SRP059226, BioProject accession PRJNA285907)

middle: S

last: Cole


title: Comparing the targets of distinct RNA Directed DNA Methylation mechanisms in Arabidopsis thaliana

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

summary: The diversity of small RNA-directed DNA methylation (RdDM) mechanisms have been underestimated due to the nearly complete transcriptional silencing of transposable elements (TEs) in the wt Col ecotype of Arabidopsis thaliana. In plants mutant for the SWI/SNF2 histone remodeler DDM1, TEs are globally activated due to loss of genome wide heterochromatin condensation. Activated TEs go through additional non-canonical forms of RdDM. However, the global targets of the non-canonical RdDM pathway are unidentified. In an attempt to identify and contrast the targets of canonical and non-canonical RdDM, we sequenced small RNAs from several RdDM mutants in either the TE-silent or the TE-active (ddm1) contexts.

overall_design:
Examination of unopened flower bud small RNAs from wild type and various single or double mutant combinations, many of which have biological replicates.
Small RNA sequences from wt Col, controls and other mutants shown in the study are available at GSE41755 and GSE57191.

first: K

last: Panda

first: R


title: Genome-wide analysis of RARβ transcriptional targets in mouse striatum links retinoic acid signaling with Huntington’s disease and other neurodegenerative disorders

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

institute: IGBMC (CNRS/INSERM/UDS)

summary: The active vitamin A derivative retinoic acid (RA) is an important regulator of adult brain functions. How these regulations are achieved is poorly known, partly due to the paucity of information on RA molecular targets. The striatum, the region involved in control of motor, cognitive and affective functions, may be particularly prone to such regulation as it displays the highest levels of RA and its receptors (RARs). We report the first genome-wide analysis of RAR-binding sites in the brain. Using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), as well as transcriptomic analysis of RARβ-null mutant mice, we identified genomic transcriptional targets of RARβ in the striatum. Our data point to a strong contribution of RARβ in controlling neurotransmission, energy metabolism, and transcription, with a particular involvement of G-protein, cAMP and calcium signaling. Quantitative PCR analysis of striatal subregions revealed a higher sensitivity of ventral structures (nucleus accumbens) to lack of RARβ signaling. There is a high overlap of transcriptional targets of RARβ and genes affected in expression in Huntington’s disease (HD), and we observed a decrease of RARβ expression in the striatum of R6/2 transgenic mice, a murine model of HD. A large number of genes bearing RARβ binding sites have also been implicated in Alzheimer’s and Parkinson’s diseases, raising the possibility that compromised RA signaling in striatum may be a mechanistic link explaining the similar affective and cognitive symptoms of these diseases. Globally, our data point to a possibility of a neuroprotective function of RARβ in the striatum.

overall_design: Genome-wide mapping of RARβ and H3K4me3 binding sites in mouse caudate putamen

first: Anna

last: Niewiadomska-Cimicka

last: Ye

first: Wojciech

last: Krezel


title: Genome-wide microRNA expression induced by TNF

first: Baohong

last: Zhao

address: 535 E70th ST

institute: Hospital for Special Surgery

summary: We sequenced microRNAs from bone marrow derived macrophages derived from the control (WT) and RBP-J conditional knockout mice (RBP-J KO; Rbpjf/f; LysM Cre).

overall_design: Examination of differential microRNA expression levels induced by TNF as well as regulated by RBP-J in bone marrow derived macrophages.


title: Hfq regulated genes in Pseudomonas chlororaphis 30-84

city: Vernon Hills

first: DONGPING

last: WANG

address: 777 Forest Edge Dr

department: Amlan

institute: OilDri Corporation of America

summary: Pseudomonas chlororaphis strain 30-84 is an effective biological control agent against take-all disease of wheat.  In this study, we conducted an RNA-seq analysis by comparing the wild type strain with a Hfe deficient mutant. RNA-seq analysis identified over 900 genes differentially regulated by Hfq.

sample_organism: Pseudomonas chlororaphis subsp. aureofaciens 30-84

overall_design: A total of 4 samples were analyzed in AB medium + 2% casamino acids, Pseudomonas chlororaphis wild type strain (2 replicates);  Pseudomonas chlororaphis ZN mutant (2 replicates).

first: Dongping

last: Wang

first: Elizabeth

last: Pierson


title: Identification of miRNAs from Glehnia littoralis by high-throughput sequencing and their response to salt stress

status: Public on Jul 21 2016

city: Nanjing

first: Xiwu

last: Qi

address: No 1, Qianhuhoucun

institute: Institute of Botany, Jiangsu Province and Chinese Academy of Sciences

summary: Glehnia littoralis is a perennial herb growing on the sandy beaches. In this study, high-throughput sequencing of small RNA was performed to identify miRNAs and their response to salt stress in G. littoralis. As a result, 37 conserved miRNAs belonging to 13 families and 37 novel miRNAs were identified. Among the 74 miRNAs, the expression levels of miR-156b*, miR-171, miR-171*, and miR-319 were downregulated and that of miR-399a, miR-399a*, miR-399b, miR-399b*, novel-9 and novel-14* were upregulated under salt stress. Target prediction of salt-responsive miRNAs indicated that these miRNAs exerted a role by regulating specific stress-responsive genes, such as SPLs. However, a lot of target genes of salt-responsive miRNAs were uncharacterized, which implied that there might be some new miRNA-mediated reguatory of salt response in G. littoralis.

overall_design: Small RNA profiles of G. littoralis under control (CK), salt stress (SS) and  (RS)

first: Yifeng

last: Zhou

first: Sheng

last: Qiang


title: HOS1 versus hos1 mRNA sequencing

city: Harpenden

first: Dana

middle: Reid

last: MacGregor

state: Hertfordshire

address: Rothamsted Research

department: Biointeractions and Crop Protection

institute: Rothamsted Research

summary:
Sequencing of mRNA extracted from 14 day old Columbia and hos1-3 seedlings grown at 22°C 12:12 light dark
Cold acclimation has been shown to be attenuated by the degradation of the INDUCER OF CBF EXPRESSION1 protein by the E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES1 (HOS1). However, recent work has suggested that HOS1 may have a wider range of roles in plants than previously appreciated. Here, we show that hos1 mutants are affected in circadian clock function, exhibiting a long-period phenotype in a wide range of temperature and light environments. We demonstrate that hos1 mutants accumulate polyadenylated mRNA in the nucleus and that the circadian defect in hos1 is shared by multiple mutants with aberrant mRNA export, but not in a mutant attenuated in nucleo-cytoplasmic transport of microRNAs. As revealed by RNA sequencing, hos1 exhibits gross changes to the transcriptome with genes in multiple functional categories being affected. In addition, we show that hos1 and other previously described mutants with altered mRNA export affect cold signaling in a similar manner. Our data support a model in which altered mRNA export is important for the manifestation of hos1 circadian clock defects and suggest that HOS1 may indirectly affect cold signaling through disruption of the circadian clock [PMID: 24254125]

overall_design: Col and hos1-3 seeds were surface sterilized and stratified at 4°C for 2 to 4 d on Murashige and Skoog (MS) agar (Melford) and 0.9% agar (Sigma-Aldrich) with no Suc added to the media, grown for 14 days at 22°C in 12:12 light dark, and harvested at dawn into liquid nitrogen. Total RNA was extracted using standard protocols. Five micrograms of total RNA was submitted to sequencing using standard protocols for Illumina TruSeq (version 3) technologies.

middle: R

first: Steven

last: Penfield

first: Konrad

last: Paszkiewicz


title: A glimpse of natural selection of long-lived T cell clones in healthy life

city: Chongqing

first: Qingzhu

last: Jia

address: Xinqiao

department: Department of Onoclogy

institute: XinQiao Hospital

summary: We designed a lineage tracing method to label a wave of T cells produced in the thymus of young. TCR repertoire analysis revealed that the lineage-tracked CD4 memory-like T cells and T regulatory cells exhibited age-dependent enrichment of shared clonotypes, indicating that antigen matched T regulatory cells are involved in maintaining the tolerant status of long-lived T cell clones.  Furthermore, these shared clonotypes were found across different mice maintained in the same housing condition mice.

overall_design: Examination of antigen-specificity of aging-tracking T-cell subtype.

first: Yuan

last: Zhuang

first: Ying

last: Wan


title: Identification of Tissue-Specific Protein-Coding and Noncoding Transcripts across 14 Human Tissues Using RNA-seq

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

institute: Fudan University

summary: Many diseases and adverse drug reactions exhibit tissue specificity. To better understand the tissue-specific expression characteristics of transcripts in different human tissues, we deeply sequenced RNA samples from 14 different human tissues. After filtering many lowly expressed transcripts, 24,729 protein-coding transcripts and 1,653 noncoding transcripts were identified. By analyzing highly expressed tissue-specific protein-coding transcripts (TSCTs) and noncoding transcripts (TSNTs), we found that testis expressed the highest numbers of TSCTs and TSNTs. Brain, monocytes, ovary, and heart expressed more TSCTs than the rest tissues, whereas brain, placenta, heart, and monocytes expressed more TSNTs than other tissues. Co-expression network constructed based on the TSCTs and TSNTs showed that each hub TSNT was co-expressed with several TSCTs, allowing functional annotation of TSNTs. Important biological processes and KEGG pathways highly related to the specific functions or diseases of each tissue were enriched with the corresponding TSCTs. These TSCTs and TSNTs may participate in the tissue-specific physiological or pathological processes. Our study provided a unique data set and systematic analysis of expression characteristics and functions of both TSCTs and TSNTs based on 14 distinct human tissues, and could facilitate future investigation of the mechanisms behind tissue-specific diseases and adverse drug reactions.

overall_design: Identification of Tissue-Specific Transcripts across 14 Human Tissues Using RNA-seq

first: Jinhang

last: Zhu


title: Determination of the RNA linked to the paraspeckle in the GH4C1 cell line

city: Marseille

first: Anne-Marie

last: François-Bellan

address: 27 Bd Jean Moulin

department: Facute de Medecine

institute: CNRS-AMU

summary: The goal of this study was to determine the identity of the RNA linked to the paraspeckles in the rat GH4C1 cell line.

overall_design: GH4C1 cell were fixed with 1% paraformaldehyde in PBS. Then nuclei were purified, lysed and sonicated. RNA pull-down was performed using two antisense DNA biotinylated oligonucleotide probes that target the lncRNA Neat1. Streptavidin-magnetic beads were added to hybridization reaction and complexes were captured by magnets. RNA was isolated using NucleoSpin®RNA XS (Macherey-Nagel).

first: Manon

last: Torres

first: Denis

last: Becquet

first: Marie-Pierre

last: Blanchard

first: Severine

last: Guillen

first: Benedicte

last: Boyer

first: Mathias

last: Moreno

first: Jean-Louis

last: Franc


title: Nudt3 is a mRNA Decapping Enzyme That Modulates Cell Migration

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: The Dcp2 and Nudt16 Nudix hydrolases, are mRNA decapping enzymes that preferentially modulate stability of a subset of mRNAs.  Here we report Nudt3 is a third Nudix protein that possess mRNA decapping activity in cells and is a modulator of cell migration in MCF-7 breast cancer cells.  Genome-wide analysis of Nudt3 compromised cells identified increases in mRNAs involved in cell motility including integrin β6, lipocalin-2 and fibronectin.  The increase in mRNA levels was dependent on Nudt3 decapping activity where integrin β6 and lipocalin-2 were modulated directly through mRNA stability, while fibronectin was indirectly controlled.  Moreover, increased cell migration observed in Nudt3 depleted cells was mediated through the extracellular integrin β6 and fibronectin protein nexus.  We conclude, Nudt3 is an mRNA decapping enzyme that orchestrates expression of a subset of mRNAs to modulate cell migration and further substantiates the existence of multiple decapping enzymes functioning in distinct cellular pathways in mammals.

overall_design: Stably transformed MCF-7 cell lines constitutively expressing either a short hairpin RNA (shRNA) directed against Nudt3 (Nudt3KD) or a non-targeted control shRNA (ConKD) were used, with three replicate cultures used per group (n=3).

first: Ewa

last: Grudzien-Nogalska

first: Xinfu

last: Jiao

first: Megerditch

last: Kiledjian

middle: P


title: Deciphering H3K4me3 Broad Domains Associated With Gene Regulatory Networks and Conserved Epigenomic Landscapes in the Human Brain [RNA-Seq]

first: Aslihan

last: Dincer

address: 1470 Madison Ave, 9th Floor Room 202

institute: Icahn School of Medicine at Mount Sinai

summary: Trimethylated histone H3-lysine 4 is primarily distributed in the form of sharp peaks, extending in neuronal chromatin on average only across 500-1500 base pairs mostly in close proximity to annotated transcription start sites. To explore whether H3K4me3 peaks could also extend across much broader domains, we undertook a detailed analysis of broadest domain cell-type specific H3K4me3 peaks in ChIP-seq datasets from sorted neuronal and non-neuronal nuclei in human, non-human primate and mouse prefrontal cortex (PFC), and blood for comparison.

overall_design: We collected separately cortical gray (GM) and subcortical white matter (WM) from 6 adult human subjects without neurological disease and extracted total RNA processed by the RNA-Seq approach.


title: Transcriptomic Analysis of Differentially Expressed Genes during Larval Development of Rapana Venosa by Digital Gene Expression Profiling

city: Qingdao

first: Hao

last: Song

state: Shandong

address: 7 Nanhai Road

institute: Institute of Oceanology,Chinese Academy of Sciences

summary: In present study, digital gene expression (DGE) profiling was performed to obtain a general picture of the transcriptomic implicated in the early development of R. venosa. Eighteen DGE libraries at six developmental stages of R. venosa were constructed, sequenced by IIIumina HiSeq 2500 platform.

overall_design: RNA from six developmental stages of R. venosa  was sequenced using Illumina Hi-seq 2500. Each stage have three replicates

first: Tao

last: Zhang


title: Deciphering H3K4me3 Broad Domains Associated With Gene Regulatory Networks and Conserved Epigenomic Landscapes in the Human Brain [ChIP-Seq]

summary: Trimethylated histone H3-lysine 4 is primarily distributed in the form of sharp peaks, extending in neuronal chromatin on average only across 500-1500 base pairs mostly in close proximity to annotated transcription start sites. To explore whether H3K4me3 peaks could also extend across much broader domains, we undertook a detailed analysis of broadest domain cell-type specific H3K4me3 peaks in ChIP-seq datasets from sorted neuronal and non-neuronal nuclei in human, non-human primate and mouse prefrontal cortex (PFC), and blood for comparison. In this GEO submission, we list six newly generated  ChIP-seq data sets.

overall_design: FACS sorted Neuronal (NeuN+) nuclei and non-neuronal (NeuN-) nuclei collected from prefrontal cortex (PFC) and processed by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq). In addition we collected nucleated blood cells from 3 control subjects. These are additional subjects unrelated to brain cohort.


title: Schistosoma-pulmonary hypertension sorted macrophage gene expression

city: Aurora

first: Brian

last: Graham

state: CO

department: Medicine

institute: University of Colorado Denver

summary: Alveolar and tissue macrophages were sorted from Schistosoma-exposed and unexposed mice.

overall_design: The mice were C57Bl6/J background. Schistosoma mansoni exposure was intraperitoneal sensitization and intravenous challenge with purified eggs (see Kumar et al. Am J Respir Crit Care Med. 2015;192(8):998-1008. doi: 10.1164/rccm.201410-1820OC. PMID: 26192556). Samples were pooled from N=5 animals per group. Cell sorting was performed on day 3 after IV challenge. Alveolar macrophages were identified as CD45+F4/80+CD11c+SiglecF+. Tissue macrophages were identified as CD45+F4/80+CD11b+SSClow. The RNA library was prepared using a Kappa Stranded mRNA-Seq kit. RNA sequencing was performed on an Ion Proton platform. Expression analysis was performed using Tophat-Bowtie-Cufflinks with Galaxy online.

first: Rahul

last: Kumar


title: Deciphering H3K4me3 Broad Domains Associated With Gene Regulatory Networks and Conserved Epigenomic Landscapes in the Human Brain

summary:
ChIP-seq and RNA-seq datasets newly generated for this manuscript are included in the SubSeries listed below. For previously published datasets, see accession no. GSE21172 and additional links provided in references 16, 18, 20.

For references 16, 18:
https://zlab.umassmed.edu/zlab/publications/ShulhaPLOSGen2013.html
https://zlab.umassmed.edu/zlab/publications/ShulhaAGP2011.html

For reference 20, sequences are accessible through:
http://www.umassmed.edu/zlab/publications/

overall_design: Refer to individual Series


title: Spliced synthetic genes as internal controls in RNA sequencing experiments.

city: Darlinghurst

first: Simon

middle: Andrew

last: Hardwick

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

summary: RNA sequencing (RNA-seq) can be used to assemble spliced isoforms, quantify expressed genes and provide a global profile of the transcriptome. However, the size and diversity of the transcriptome, the wide dynamic range in gene expression and inherent technical biases confound RNA-seq analysis. We have developed a set of spike-in RNA standards, termed ‘sequins’ (sequencing spike-ins), that represent full-length spliced mRNA isoforms. Sequins have an entirely artificial sequence with no homology to natural reference genomes, but align to gene loci encoded on an artificial in silico chromosome. The combination of multiple sequins across a range of concentrations emulates alternative splicing and differential gene expression, and provides scaling factors for normalization between samples. We demonstrate the use of sequins in RNA-seq experiments to measure sample-specific biases and determine the limits of reliable transcript assembly and quantification in accompanying human RNA samples. In addition, we have designed a complementary set of sequins that represent fusion genes arising from rearrangements of the in silico chromosome to aid in cancer diagnosis. RNA sequins provide a qualitative and quantitative reference with which to navigate the complexity of the human transcriptome.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Detailed transcriptomic analysis of two human cell lines with synthetic RNA spike-ins ('sequins'). Sequins were initially combined at equimolar concentrations (a "flat" mix) and sequenced neat (i.e. without any natural RNA added). We then prepared two staggered mixtures (Mix A & B) and sequenced them neat. Mix A was then spiked into total RNA extracted from K562 cells, while Mix B was spiked into total RNA extracted from GM12878 cells. Finally, we prepared a staggered mixture of fusion sequins and sequenced it neat.

first: Tim

last: Mercer


title: Cell-autonomous function of LSH ATPase in de novo DNA methylation

city: Edinburgh

first: Alastair

middle: Robert

last: Kerr

state: Midlothian

address: 2.21 Michael Swann Building, Kings Buildings, Mayfield Road

department: Wellcome Centre for Cell Biology

institute: University of Edinburgh

summary:
Purpose: We aimed to determine whether the expression of either wild-type or catalytically inactive LSH, carrying a single point mutation in its ATP binding site (K237Q), could restore the levels and patterns of DNA methylation in Lsh-/-  mouse embryonic fibroblasts (MEFs).
Methods: Lsh-/- MEFs were transduced with lentiviral particles carrying empty pMSCV vector, pMSCV-LSH-3xFLAG and pMSCV-LSH K/Q-3xFLAG, respectively. Clonal cell lines were generated and tested for LSH expression. Two independent cell lines expressing wild-type LSH and two expressing LSH K/Q were used for further analyses and comparison with wild-type MEFs and Lsh-/- MEFs carrying the empty vector. Genomic DNA was purified from all six cell lines and methylated DNA immunoprecipitation (MeDIP) was performed as described in Weber et al., 2007, Nat Genetics. MeDIP libraries were generated and sequenced on Illumina HiSeq 2000 instrument.
Results and conclusions: Our experiments demonstrate that the expression of wild-type LSH, but not the catalytically inactive LSH K/Q, in Lsh-/- MEFs leads to reestablishment of DNA methylation at repetitive sequences and unique developmentally regulated loci in a cell-autonomous manner.

overall_design: Analyses of DNA methylation upon expression of either wild-type or catalytically-inactive LSH in Lsh-/- mouse embryonic fibroblasts.

first: Ausma

last: Termanis

first: Irina

last: Stancheva


title: Modeling the Neuropathology of Tuberous Sclerosis with Human Stem Cells Reveals a Role for Inflammation and Angiogenic Growth Factors [Cell Model]

city: Basel

first: Jitao David

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

summary: Tuberous sclerosis complex (TSC) is a rare genetic disease characterized by mTOR hyperfunction induced benign tumor growths in multiple organs and neurological symptoms. Because the molecular pathology is highly complex and the etiology poorly understood we employed a defined human neuronal model with a single mTOR activating mutation to dissect the disease-relevant molecular responses driving the neuropathology. TSC2 deficient neural stem cells showed severely reduced neuronal functional maturation and characteristics of astrogliosis instead. Accordingly, transcriptome analysis uncovered an inflammatory response and increased metabolic activity, while ribosome profiling revealed excessive translation of ribosomal transcripts and higher synthesis rates of angiogenic growth factors. Treatment with mTOR inhibitors corrected translational alterations but not transcriptional dysfunction. These results extend our understanding of the molecular pathophysiology of TSC brain lesions, and suggest phenotype-tailored pharmacological treatment strategies.

overall_design: Two TSC+/- cell lines and two TSC-/- cell lines were independently generated from wild-type human embryonic stem cells by genome editting with zinc finger nucleases. Two cell lines were handled in the same way but without any known human gene editted and they are used as negative controls. Two independent biological replicates of each of the six cell lines are profiled with ribosome profiling technique.

first: Nils

last: Grabole

first: Jitao

first: Stefan

last: Aigner

first: Nadine

last: Ruderisch

first: Veronica

last: Costa

first: Felix

middle: C

last: Weber

first: Michel

last: Theron

first: Nikolaos

last: Berntenis

first: Olivia

last: Spleiss

first: Martin

last: Ebeling

first: Gene

last: Yeo

first: Ravi

last: Jagasia

first: Anna

last: Kiialainen


title: EZH2 and BCL6 cooperate to assemble CBX8-BCOR Polycomb complex to repress bivalent promoters, mediate germinal center formation and promote lymphomagenesis

status: Public on Jul 20 2016

city: New York

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

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


title: High-throughput sequencing reveals key genes and immune homeostatic pathways activated in myeloid dendritic cells by Porphyromonas gingivalis 381 and its fimbrial mutants

city: Augusta

first: Pachiappan

last: Arjunan

state: Georgia

address: 1120 15th ST, Laney walker Blvd,

department: Anatomy, Unit on Retinal Vascular Neurobiology, BMB

institute: NUS, NIH, GRU

summary:
Periodontitis affects 47.1% of adult population in the U.S. Porphyromonas gingivalis is an opportunistic oral pathogen that colonizes the oral mucosa, invades myeloid dendritic cells and accesses the bloodstream, brain, placenta and other organs in human with periodontitis. Periodontitis also sustains a chronic long-term pro-inflammatory immune disorder, potentially contributing to other systemic conditions such as cardiovascular disease, type 2 diabetes mellitus, adverse pregnancy outcomes, and osteoporosis. However, the role of P. gingivalis minor and major fimbriae in DC-SIGN-TLR2 crosstalk during traverses from oral mucosa to these distant sites and its influence on survival of P. gingivalis within DCs and its immune-mechanism involve at molecular/transcriptome level has not been examined. In this study to address the role of fimbriae we utilized defined bacterial mutants that solely express minor fimbriae (Mfa1+Pg), major fimbriae (FimA+Pg) or are deficient in both fimbriae (MFB) and compared with un-infected control.
P. gingivalis strains were maintained anaerobically (10% H2, 10% CO2, and 80% N2) in a Forma Scientific anaerobic system glove box model 1025/1029 at 37°C in Difco anaerobe broth MIC. Mutant strains were maintained using erythromycin (5 μg/ml) for mutant Mfa1+Pg, tetracycline (2 μg/ml) for mutant FimA+Pg and both erythromycin and tetracycline for double fimbriae mutant MFB. Bacterial suspensions were washed five times in PBS and re-suspended for spectrophotometer reading at OD 660 nm of 0.11, which previously determined to be equal to 5 x 107 CFU. For bacterial CFSE staining, the suspension were washed (3 times) and re-suspended in 5 μM of CFSE in PBS. The bacteria were incubated for 30 min at 37°C in the dark. MoDCs were pulsed with Pg381, Mfa1+Pg, FimA+Pg and MFB at 10 MOI and incubated with the MoDCs for 12 hours and each experimental condition was performed in triplicate.

overall_design: To facilitate our understanding on host immunity and defense mechanism of this pathogen, here we used the Illumina High-throughput RNA-seq transcriptome profiling to investigate the myeloid dendritic cells response to oral Amphibiont (1. Pg381, 2. Mfa1+Pg, 3. FimA+Pg, 4. MFB and 5. Un-infected control group).

first: Ahmed

last: El-Awady

first: Christopher

last: Cutler


title: Distinct Function for ASCL1 and NEUROD1 in Pulmonary Neuroendocrine Tumors (RNA-seq)

city: Dallas

first: Jane

middle: E

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

department: Neuroscience

institute: UT Southwestern Medical Center

summary: Small cell lung carcinoma (SCLC) and large cell neuroendocrine carcinoma (LCNEC) are high-grade pulmonary neuroendocrine tumors. The neural basic helix-loop-helix (bHLH) transcription factors ASCL1 and NEUROD1 have been shown to play crucial roles in promoting the malignant behavior and survival of human SCLC cell lines. In this study, we find ASCL1 and NEUROD1 identify distinct neuroendocrine tumors, bind distinct genomic loci, and regulate mostly distinct genes. ASCL1 and NEUROD1 are often bound in super-enhancers that are associated with highly expressed genes in their respective SCLC cell lines suggesting different cell lineage of origin for these tumors. ASCL1 targets oncogenic genes such as MYCL1, RET, and NFIB, while NEUROD1 targets the oncogenic gene MYC. Although ASCL1 and NEUROD1 regulate different genes, many of these gene targets commonly contribute to neuroendocrine and cell migration function. ASCL1 in particular also regulates genes in the NOTCH pathway and genes important in cell-cycle dynamics. Finally, we demonstrate ASCL1 but not NEUROD1 is required for SCLC and LCNEC tumor formation in current in vivo genetic mouse models of pulmonary neuroendocrine tumors

overall_design: RNA-seq analysis performed on two ASCL1high and two NEUROD1high human SCLC cell lines to identify gene expression patterns in these cells. Also, we performed RNA-seq in mouse neuroendocrine lung tumors obtained from Trp53;Rb1;Rbl2 triple knockout model mice treated with Adeno-CMVCRE intratracheally.

first: Mark

last: Borromeo

first: Trisha

last: Savage

first: Rahul

last: Kollipara

first: Min

last: He

first: Alexander

last: Augustyn

first: Jihan

last: Osborne

first: Luc

last: Girard

first: John

last: Minna

first: Adi

middle: F

last: Gazdar

first: Melanie

middle: H

last: Cobb


title: Synergistic model of chromatin predicts Dnase-I accessibility

city: Cambridge

first: David

last: Gifford

state: MA

address: 32 Vassar St

institute: MIT

summary: Enhancers and promoters commonly occur in accessible chromatin characterized by depleted nucleosome contact; however, it is unclear how chromatin accessibility is governed. We show that a logic of cis-acting DNA sequence features can predict the majority of chromatin accessibility at high spatial resolution. We develop a new type of high-dimensional machine learning model, the Cooperative Chromatin Model (CCM), that is capable of predicting a large fraction of genome-widepromoters chromatin accessibility at basepair-resolution in a range of human and mouse cell types from DNA sequence alone. We confirm that a CCM accurately predicts chromatin accessibility, even of a vast array of synthetic DNA sequences, with a novel CrispR-based method of highly efficient site-specific DNA library integration. CCMs are directly interpretable and reveal that a logic based on local, non-specific cooperation, largely among pioneer TFs, is sufficient to predict a large fraction of cellular chromatin accessibility in a wide variety of cell types.

overall_design: Dnase-seq on human and mouse cells as well as massively parallel report assay (MPRA) validation using CRISPR editing of native genomic loci.

first: Tatsunori

last: Hashimoto

first: Richard

middle: I

last: Sherwood


title: Retrotransposon derepression leads to activation of the unfolded protein response and apoptosis in pro B cells

city: Planegg-Martinsried

first: Gunnar

last: Schotta

address: Grosshaderner Strasse 9

department: Biomedical Center

country: Germany

institute: LMU Munich

summary: The establishment of distinct transcription programs during development is controlled by transcription factor networks acting in specific chromatin environments. The H3K9me3-specific histone methyltransferase Setdb1 impacts on transcriptional regulation by repressing both developmental genes and retrotransposons. How impaired retrotransposon silencing may lead to developmental phenotypes is currently unclear. Here we show that loss of Setdb1 in pro-B cells completely abrogates B cell development. In pro-B cells, Setdb1 is dispensable for silencing of lineage-inappropriate developmental genes. Instead, we detect strong derepression of endogenous Murine Leukemia Virus (MLV) copies. Production of MLV proteins leads to activation of the unfolded protein response pathway and apoptosis. Thus, our data demonstrate that B cell development critically depends on the proper repression of retrotransposon sequences through Setdb1.

overall_design: Transcriptomic and chromatin analysis of control and Setdb1-deficient pro-B cells

first: Anja

last: Ebert


title: The Nuclear Receptor Rev-erb alpha Regulates Adipose Tissue-Specific FGF21 Signaling (ChIP-seq, eWAT)

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: The goal of this study is to identify the cistrome of the transcriptional repressor Rev-erb alpha in epididymal white adipose tissue. Performing Rev-erb alpha ChIP-seq on epididymal white adipose tissue from wildtype mice at 5PM when Rev-erb alpha protein level peaks in wild type (WT) mice, we were able to globally determine the genomic regions undergoing Rev-erb alpha-dependent de-repression.

overall_design: Examination of Rev-erb alpha binding in epididymal white adipose tissue.

first: Jennifer

last: Jager

first: Fenfen

last: Wang

first: Bin

last: Fang

last: Steger

first: Kyoung-Jae

last: Won

first: Mitchell

middle: A

last: Lazar


title: EZH2 and BCL6 cooperate to assemble CBX8-BCOR Polycomb complex to repress bivalent promoters, mediate germinal center formation and promote lymphomagenesis [RNA-seq]

first: Matt

last: Teater

summary: EZH2 mediates the humoral immune response and drives lymphomagenesis through de novo formation of bivalent chromatin domains and critical germinal center (GC) B cell promoters.  We show that such formation is dependent on the presense of BCL6 and the presence of non-canonical PRC1-BCOR complex.  We observe that BCL6 and EZH2 cooperate to accelerate diffuse large B cell lymphoma (DLBCL) development and combinatorial targeting of these repressors results in enhanced anti-lymphoma activity in vitro, in vivo, and in primary human DLBCLs.

overall_design: DLBCL cell lines treated with BCL6 inhibitor 79-6.1085

first: Wendy

last: Béguelin

first: Olivier

last: Elemento

first: Ari

middle: M

last: Melnick


title: Subsets of visceral adipose tissue nuclei with discrete levels of 5-hydroxymethylcytosine

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: We explored the hypothesis that adipose tissue contains epigenetically distinct subpopulations of adipocytes that are differentially potentiated to record cellular memories of their environment. Adipocytes are large, fragile, and technically difficult to efficiently isolate and fractionate. We developed fluorescence nuclear cytometry (FNC) and fluorescence activated nuclear sorting (FANS) of cellular nuclei from Sus scrofa visceral adipose tissue (SsVAT) using the levels of the pan-adipocyte protein, peroxisome proliferator-activated receptor gamma-2 (PPARg2) to distinguish PPARg2-Positive nuclei from PPARg2-Neg (negative) leukocyte, endothelial, and adipocyte progenitor cell nuclei. PPARg2-Postive VAT nuclei showed 2- to 50-fold higher levels of transcripts encoding most of the chromatin-remodeling factors assayed regulating the methylation of histones and DNA cytosine (e.g., DNMT1, DNMT3A, TET2, TET3, KMT2C, SETDB1, PAXP1, ARID1A, KMT2C, JMJD6, CARM1/PRMT4, PRMT5). PPARg2-Positive nuclei have a large decondensed chromatin structure. TAB-seq demonstrated 5´-hydroxymethylcytosine (5hmC) levels were remarkably dynamic in the gene body of PPARg2-Positive nuclei, dropping 3.8-fold from the highest quintile of expressed genes to the lowest.

overall_design: Sus scrofa VAT (SsVAT) nuclei were isolated from SsVAT. SsVAT nuclei were stained with PPARg2 and sorted with fluorescence activated nuclear sorting (FANS) into PPARg2-High, PPARg2-Med (Medium), PPARg2-Low, and PPARg2-Neg (Negative) four populations.TAB-seq data on 5-hydroxymehtylcytosine (Yu, M. et al. 2012. Cell 149, 1368-1380) was collected from genomic DNA isolated from PPARg2-High, PPARg2-Med+Low (pooled PPARg2-Med and PPARg2-Low), and PPARg2-Neg SsVAT nuclei.


title: Base J represses genes at the end of polycistronic gene clusters in Leishmania major by promoting RNAP II termination [RNA-seq]

summary: Base J and H3.V promote RNA Polymerase (RNAP) II termination within polycistronic gene clusters in the kinetoplastid species Trypanosoma brucei. Although base J has been shown to promote RNAP II termination in the related kinetoplastid species Leishmania major and Leishmania tarentolae, the role of H3.V was unclear. The effect of acute J loss on mRNA transcript abundance was also unknown. We find here that H3.V does not promote transcription termination in Leishmania major, but loss of H3.V does reduce J levels. The J loss in H3.V knockout cells is not enough to result in a termination defect, which we show is due to a threshold level of J that is sufficient to promote termination. Loss of J beyond that threshold results in termination defects. Further, the decreased J in H3.V knockout cells allowed greater reduction of J by dimethyloxalylglycine (DMOG), which inhibits J synthesis, compared to wild type cells treated with DMOG, and resulted in stronger defects in RNAP II termination and cell growth. By mRNA-seq we see largely upregulation of genes near the ends of gene clusters following J loss, indicating that J represses genes near termination sites. These findings reveal a conserved role of J in promoting termination prior to the end of polycistronic gene clusters in kinetoplastid parasites and suggest that the essential nature of J is related to its role in repressing genes by promoting termination.

overall_design: The role of base J and H3.V in promoting RNA Polymerase II transcription termination was assessed by small RNA-seq, mRNA-seq, and strand-specific RT-PCR. Wild type cells were compared to H3.V knockout cells and to WT and H3.V knockout cells treated with dimethyloxalylglycine (DMOG) to reduce base J.

last: Sabatini

middle: L

last: Reynolds

first: Laura

last: Cliffe

first: Nicolai

last: Siegel

first: Britta

last: Anderson

first: Stephen

last: Beverley

first: Brigitte

middle: T

last: Hofmeister


title: EZH2 and BCL6 cooperate to assemble CBX8-BCOR Polycomb complex to repress bivalent promoters, mediate germinal center formation and promote lymphomagenesis [ChIP-seq]

summary: The EZH2 histone methyltransferase mediates the humoral immune response and drives lymphomagenesis through de novo formation of bivalent chromatin domains at critical germinal center (GC) B cell promoters. Herein we show that the actions EZH2 in driving GC formation and lymphoma precursor lesions are dependent on the presence of the BCL6 transcriptional repressor, both of which are in turn dependent on the presence of non-canonical PRC1-BCOR complex. BCL6-BCOR complexes assemble preferentially at bivalent promoters in an H3K27me3-dependent manner. We observe specific induction of the CBX8 chromodomain protein in GC B cells. CBX8 binds to H3K27me3 at bivalent promoters and is required for stable association of BCOR complex and its histone modifications. CBX8 loss of function in B cells phenocopies loss of EZH2 and H3K27me3. Moreover, oncogenic BCL6 and EZH2 cooperate to accelerate diffuse large B cell lymphoma (DLBCL) development and combinatorial targeting of these repressors results in enhanced anti-lymphoma activity in vitro, in vivo and in primary human DLBCLs.

overall_design: KDM2B ChIP-sequencing of OCI-Ly1 cells

last: Beguelin


title: Small molecule proteostasis regulators that reprogram the ER to reduce extracellular protein aggregation

city: La Jolla

first: Katja

last: Lamia

state: California

address: 10550 North Torrey Pines Road

institute: The Scripps Research Institute

summary: Imbalances in endoplasmic reticulum (ER) proteostasis are associated with etiologically-diverse degenerative diseases linked to excessive extracellular protein misfolding and aggregation. Reprogramming of the ER proteostasis environment through genetic activation of the Unfolded Protein Response (UPR)-associated transcription factor ATF6 attenuates secretion and extracellular aggregation of amyloidogenic proteins. Here, we employed a screening approach that included complementary arm-specific UPR reporters and medium-throughput transcriptional profiling to identify non-toxic small molecules that phenocopy the ATF6-mediated reprogramming of the ER proteostasis environment. Comprehensive transcriptome analysis was employed to validate the capacity of three prioritized compounds to remodel the ER proteostasis environment, and to assess the prefential activation of ATF6 transcriptional targets relative to targets of the IRE1/XBP1s and PERK arms of the UPR.

overall_design: HEK293T-Rex and HEK293-DAX cells were treated for 6 hr with vehicle (DMSO), 1 µM Tg, 10 mM TMP (in HEK293DAX), or 10 µM 132, 147 or 263 in biological triplicate at 37 ̊C

first: Lars

last: Plate

first: Christina

middle: B

last: Cooley

first: Evan

last: Powers

first: Luke

last: Wiseman

first: Jeffery

middle: W

last: Kelly


title: RNA 5'end sequencing in polysome profiling fractions

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

summary: It has been shown that in mammalian cells alternative transcription initiation is extensively regulated during development and across cell-types, which confers dynamic transcript 5’UTR repertoire. However it is underexplored how the heterogeneity of 5’UTR isoforms would affect the downstream steps for protein expression, such as translation. To this end, we globally compared the translational profile of distinct mRNA TSS isoforms in mouse fibroblast cells, by combining deep-sequencing based mRNA 5’ends profiling and polysome fractionation. We demonstrated the extensive translation regulation conferred by TSS heterogeneity.

overall_design: 5'end sequencing in seven polysome fractions, in two replicates, using Illumina Hiseq2000

first: Jingyi

last: Hou

first: Wei

last: Chen