title: Genome-wide expression profile of the Tet-On HCT116 inducible cell line that express either the human HNF4α2 or HNF4α8 under control of Doxycycline (DOX)

first: joseph

last: dhahbi

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

overall_design: Refer to individual Series


title: HNF4α and TCF4 (TCF7L2) ChIPseq in Tet-On HCT116 inducible cell lines that express either the human HNF4α2 or HNF4α8 under the control of doxycycline (DOX) [ChIP-Seq]

status: Public on Aug 28 2015

city: Elk Grove

middle: M

state: ca

address: 9700 West Taron Drive

department: Medical Education

country: USA

institute: California Northstate University College of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Purpose: Aim of the study is to determine how many of the dysregulated genes in the RNAseq are direct targets of (P1) HNF4α2 and (P2) HNF4α8 and examine HNF4α and TCF4 binding in vivo. We performed ChIPseq on TCF4 in the absense or presence of DOX in the Tet-On inducible HCT116 HNF4α2 and HNF4α8 lines, and ChIPseq for HNF4α (a445 Ab) in the presence of DOX.  Methods: HNF4α2 and HNF4α8 lines were induced with 0.3 μg/mL DOX for 24 hours. Samples were generated by deep sequencing, using the NEXTflex ChIPseq. Result: There were more HNF4α2 peaks than HNF4α8 peaks, with some common peaks bound by HNF4α2 and HNF4α8. Binding patterns were observed between HNF4α and TCF4. Conclusion: HNF4α2 can displace TCF4 better than HNF4α8 on AP-1 bound sites.

overall_design: Tet-On inducible HCT116 cell (HNF4α2 and HNF4α8) lines, treated with (0.3 μg/mL) or without DOX for 24 hours, were 50bp single-end sequenced using Illumina-compatible-NEXTflex ChIP kit (Bioo Scientific).

first: J

last: Dhahbi

first: F

last: Sladek


title: Small RNA deep sequencing identifies viral microRNAs during malignant catarrhal fever induced by alcelaphine herpesvirus 1

status: Public on Aug 27 2015

city: Liege

first: Benjamin

middle: G

last: Dewals

address: Avenue de Cureghem, 10

country: Belgium

institute: University of liege

type: Non-coding RNA profiling by high throughput sequencing

summary: Alcelaphine herpesvirus 1 (AlHV-1) is a γ-herpesvirus (γ-HV) carried asymptomatically by wildebeest. Upon cross-species transmission, AlHV-1 induces an acute and fatal lymphoproliferative disease named malignant catarrhal fever (MCF) in many ruminants, including cattle and the rabbit model. Latency has been shown to be essential for MCF induction. However, the mechanisms causing the activation and proliferation of infected CD8+ T cells are unknown. Many γ-HVs express microRNAs (miRNAs). These small noncoding RNAs can suppress host or viral target genes involved in various pathways and are thought to facilitate viral infection and/or mediate activation and proliferation of infected lymphocytes. AlHV-1 genome has been predicted to encode a large number of miRNAs. However, their precise contribution in viral infection and pathogenesis in vivo remains unknown. Here, we have cloned small RNAs and sequenced 36 potential miRNAs expressed in a lymphoblastoid cell line propagated from a calf infected with AlHV-1 and developing MCF. Among the sequenced candidate miRNAs, 32 were expressed on the reverse strand of the genome in two main clusters. The expression of these 32 viral miRNAs was further validated using Northern blot and qRT-PCR in lymphoid organs of MCF-developing calves or rabbits. To determine the concerted contribution in MCF of 28 viral miRNAs clustered in the non-protein-coding region of the AlHV-1 genome, a recombinant virus was produced. The absence of these 28 miRNAs did not affect viral growth in vitro nor MCF induction in rabbits, demonstrating that AlHV-1 miRNAs clustered in the non-protein-coding genomic region are not essential for MCF induction.

overall_design: Small RNA sequencing from total RNA from AlHV-1-infected bovine lymphoblastoid cell line propagated with interleukin 2

first: Océane

last: Sorel

first: Lee

last: Tuddenham

first: Françoise

last: Myster

first: Leonor

last: Palmeira

first: Pierre

last: Kerkhofs

first: Sébastien

last: Pfeffer

first: Alain

last: Vanderplasschen


title: Whole cell mRNA expression profiling in control and complex I deficient patient fibroblasts incubated with DMSO, AICAR, chloramphenicol, and resveratrol

status: Public on Aug 31 2015

city: Nijmegen

first: Rutger

last: Vogel

state: Gelderland

address: Geert Grooteplein 10

department: Pediatrics

country: Netherlands

institute: Radboud university medical center

type: Expression profiling by high throughput sequencing

summary:
Background: Transcription control of mitochondrial metabolism is essential for cellular function. A better understanding of this process will aid the elucidation of mitochondrial disorders, in particular of the many genetically unsolved cases of oxidative phosphorylation (OXPHOS) deficiency. Yet, to date only few studies have investigated nuclear gene regulation in the context of OXPHOS deficiency. In this study, we combined RNA sequencing of human complex I-deficient patient cells across 32 conditions of perturbed mitochondrial metabolism, with a comprehensive analysis of gene expression patterns, co-expression calculations and transcription factor binding sites.
Results: Our analysis shows that OXPHOS genes have a significantly higher co-expression with each other than with other genes, including mitochondrial genes. We found no evidence for complex-specific mRNA expression regulation in the tested cell types and conditions: subunits of different OXPHOS complexes are similarly (co-)expressed and regulated by a common set of transcription factors. However, we did observe significant differences between the expression of OXPHOS complex subunits compared to assembly factors, suggesting divergent transcription programs. Furthermore, complex I co-expression calculations identified 684 genes with a likely role in OXPHOS biogenesis and function. Analysis of evolutionarily conserved transcription factor binding sites in the promoters of these genes revealed almost all known OXPHOS regulators (including GABP, NRF1/2, SP1, YY1, E-box factors) and a set of six yet uncharacterized candidate transcription factors (ELK1, KLF7, SP4, EHF, ZNF143, and EL2).
Conclusions: OXPHOS genes share an expression program distinct from other mitochondrial genes, indicative of targeted regulation of this mitochondrial sub-process. Within the subset of OXPHOS genes we established a difference in expression between subunits and assembly factors. Most transcription regulators of genes that co-express with complex I are well-established factors for OXPHOS biogenesis. For the remaining six factors we here suggest for the first time a link with transcription regulation in OXPHOS deficiency.

overall_design: RNA-SEQ of whole cell RNA in 2 control and 2 complex I deficient patient fibroblast cell lines treated with 4 compounds in duplicate, resulting in a total of 2x2x4x2=32 samples

middle: O


title: Genome-wide expression profile of the Tet-On HCT116 inducible cell line that express either the human HNF4α2 or HNF4α8 under control of Doxycycline (DOX) [RNAseq]

summary: Purpose: Aim of the study is to identify functional differences between the P1 and P2-HNF4α isoforms. To do this, we generated Tet-On inducible lines that express either the human (P1) HNF4α2 or (P2) HNF4α8 under control of DOX in the HCT116 human colon cancer cells. Methods: HNF4α2 and Parental lines were induced with 0.3 μg/mL DOX, while HNF4α8 line was induced with either 0.1 or 0.3 μg/mL DOX for 24 hours. Samples were generated by deep sequencing, using the Illumina TruSeq RNA. Result: There were common and unique dysregulated genes identified in the HNF4α2 and HNF4α8 lines (+DOX); more upregulated genes than downregulated genes in both the lines. Conclusion: The functional difference between HNF4α2 and HNF4α8 is that the latter tends to upregulate genes involved in proliferation and anti-apoptosis while HNF4α2 upregulates genes involved in growth suppression and cell death.

overall_design: Tet-On inducible HCT116 cell (Parental, HNF4α2, and HNF4α8) lines, treated with (0.0, 0.1, or 0.3 μg/mL) DOX for 24 hours, were 50bp pair-ended sequenced in triplicate using Illumina TruSeq RNA Sample Prep v2 Kit.


title: Cross platform standardization of an experimental pipeline for use in the identification of dysregulated human circulating miRNAs

status: Public on Aug 30 2015

city: Dublin

first: Tim

last: Downing

state: Other

address: DCU

department: Biotechnology

country: Ireland

institute: DCU

summary: In this study we present an experimental pipeline that takes into consideration sample collection, processing, enrichment, and the subsequent comparative analysis of circulating small ribonucleic acids using small RNA sequencing and RT-qPCR. Initially, a panel of miRNAs dysregulated in circulating blood from breast cancer patients compared to healthy women were identified using small RNA sequencing. MiR-320a was identified as the most dysregulated miRNA between the two female cohorts. Total RNA and enriched small RNA populations (<30 bp) isolated from peripheral blood from the same female cohort samples were then tested using a miR-320a RT-qPCR assay. When total RNA was analyzed with this miR-320a RT-qPCR assay, a 2.3-fold decrease in expression levels was observed between blood samples from healthy controls and breast cancer patients. However, upon enrichment for the small RNA population and subsequent analysis of miR-320a using RT-qPCR, its dysregulation in breast cancer patients was more pronounced with an 8.89-fold decrease in miR-320a expression.

overall_design:
miRNAseq with Illumina 2000 of human females n=23 controls and n=14 cases
[Ethics Statement] Written informed consent was received from all participants in the study. Ethical approval was granted by the Clinical Research Ethics Committee, Galway University Hospital.

first: Helena

last: Kelly

first: Nina

middle: L

last: Tuite

first: Terry

middle: J

last: Smith

first: Michael

last: Kerin

first: Róisín

last: Dwyer

first: Eoin

last: Clancy

first: Thomas

last: Barry

first: Kate

last: Reddington


title: A Genome-wide mRNA Screen and Functional Analysis Reveal FOXO3 as a Candidate Gene for Chicken Growth

city: Nanchang

first: Chen

last: Biao

state: Jiang Xi

address: Zhimin main street 1101#

department: College of animal science and technology

country: China

institute: Jiangxi Agricultural University

summary: The objective of this study was to identify candidate genes associated with chicken growth and investigate their potential mechanisms. We used RNA-Seq to study the breast muscle transcriptome in high and low tails of Recessive White Rock (WRRh, WRRl) and Xinghua chickens (XHh, XHl). A total of 60, 23, 153 and 359 differentially expressed genes were detected in WRRh vs. WRRl, XHh vs. XHl, WRRh vs. XHh and WRRl vs. XHl, respectively. GO, KEGG pathway and gene network analyses showed that CEBPB, FBXO32, FOXO3 and MYOD1 played key roles in growth. The functions of FBXO32 and FOXO3 were validated.

overall_design: Examination of mRNA profiles  in  two-tail samples of WRR and XH strains.

first: Xiaomei

last: He

first: Qinghua

last: Nie


title: H3K4me2 and gene expression profiling in control and KMT2D KD murine B220 cells

city: New York

first: Yanwen

last: Jiang

state: NY

institute: Weill Cornell Medical College

summary: Define and compare H3K4me2 enrichment in murine B220 cells transduced with empty vector (ct) or KMT2D-shRNA. Compare gene expression by RNAseq in murine B220 cells transduced with empty vector (ct) or KMT2D-shRNA.

overall_design: Using H3K4me1/2 ChIPseq and RNAseq we profiled murine B220 purified cells from tumors transduced with EV (n=3) or KMT2D-shRNA (n=3).

first: Ana

last: Ortega-Molina

first: Isaac

middle: W

last: Boss

first: Heng

last: Pan

first: Deqing

last: Hu

first: Ali

last: Shilatifard

first: Olivier

last: Elemento

first: Ari

last: Melnick

first: Hans-Guido

last: Wendel


title: Single-cell RNA-seq with Waterfall Reveals Molecular Cascades underlying Adult Hippocampal Neurogenesis

city: Baltimore

first: Jaehoon

last: Shin

state: Maryland

address: 733 N Broadway

institute: Johns Hopkins University

summary: Somatic stem cells contribute to tissue ontogenesis, homeostasis, and regeneration through sequential processes. Systematic molecular analysis of stem cell behavior is challenging because classic approaches cannot resolve cellular heterogeneity or capture developmental dynamics. Here we provide a comprehensive resource of single-cell transcriptomes of adult hippocampal quiescent neural stem cells (qNSCs) and their immediate progeny. We further developed Waterfall, a bioinformatic suite, to statistically quantify singe-cell gene expression along de novo reconstructed continuous developmental trajectory. Our study reveals molecular signatures of qNSCs, characterized by high niche signaling integration and low protein translation capacity. Our analyses further delineate molecular cascades underlying adult qNSC activation and neurogenesis initiation, exemplified by decreased extrinsic signaling capacity, primed translational machinery, and regulatory switches in transcription factors, metabolism, and energy sources. Our study reveals the molecular continuum underlying adult neurogenesis and illustrates how Waterfall can be used for single-cell omics analyses of various continuous biological processes.

overall_design: Single-cell transcriptomes of adult hippocampal quiescent neural stem cells (qNSCs) and their immediate progeny.

first: Hongjun

last: Song


title: The nuclear pore-associated TREX-2 complex employs the Mediator Med31 submodule as a docking site to regulate gene expression

city: Vienna

first: Alwin

last: Koehler

address: Dr.-Bohr-Gasse 3/9

country: Austria

institute: Max F. Perutz Laboratories

summary: Nuclear pore complexes (NPCs) influence gene expression besides their established function in nuclear transport. The TREX-2 complex localizes to the NPC basket and affects gene-NPC interactions, transcription and mRNA export. How TREX-2 regulates the gene expression machinery is unknown. Here, we show that TREX-2 interacts with the Mediator complex, an essential regulator of RNA Polymerase (Pol) II. Structural and biochemical studies identify a conserved region on TREX-2, which directly binds the Mediator Med31/Med7N submodule. TREX-2 regulates assembly of Mediator with its Cdk8 kinase and is required for recruitment and site-specific phosphorylation of Pol II. Transcriptome and phenotypic profiling confirm that TREX-2 and Med31 are functionally interdependent. TREX-2 additionally uses its Mediator-interacting surface to regulate mRNA export suggesting a mechanism for coupling transcription initiation and early steps of mRNA processing at the Mediator level. In sum, we provide insight into how NPC-associated adaptor complexes can access the core transcription machinery.

overall_design: RNAseq was performed from WT, sac3∆, cdk8∆ and Sac3 R288D mutant cells. For each strain triplicates were analyzed. WT strain was sac3∆ transformed with pRS315 SAC3 WT

first: Tobias

last: Schubert

first: Sini

last: Junttila


title: PARP1- and CTCF-mediated interactions between active and repressed chromatin at the lamina promote oscillating transcription

city: Stockholm

first: Anita

last: Göndör

address: Nobels väg 16, KI Solna Campus, Karolinska Institutet, Box 280

department: MTC

country: Sweden

institute: Karolinska Institutet

summary: Transcriptionally active and inactive chromatin domains tend to segregate into separate sub-nuclear compartments to maintain stable expression patterns. However, we have uncovered here an inter-chromosomal network connecting active loci enriched in circadian genes to repressed lamina-associated domains (LADs). The interactome is regulated by PARP1 and its co-factor, CTCF, which not only mediate chromatin fiber interactions, but also promote the recruitment of circadian genes to the lamina. Synchronization of circadian rhythm by serum shock induces oscillations in PARP1-CTCF interactions, which is accompanied by oscillating recruitment of circadian loci to the lamina, followed by the acquisition of repressive H3K9me2 marks and transcriptional attenuation. Furthermore, depletion of H3K9me2/3, inhibition of PARP activity by Olaparib or down-regulation of PARP1 or CTCF expression counteracts both recruitment to the envelope and circadian transcription. PARP1- and CTCF-regulated contacts between circadian loci and the repressive chromatin environment at the lamina thus mediate circadian transcriptional plasticity.

overall_design: ChIP-Seq for H3k9me2 in HCT116 colon cancer cells (2 replicates)

first: Honglei

last: Zhao

first: Emmanouil

last: Sifakis

first: Noriyuki

last: Sumida

first: Lluís

last: Millán-Ariño

first: Barbara

middle: A

last: Scholz

first: Peter

last: Svensson

first: Xingqi

last: Chen

first: Anna

last: Ronnegren

first: Carolina

last: Diettrich Mallet de Lima

first: Farzaneh

last: Shahin Varnoosfaderani

first: Chengxi

last: Shi

first: Olga

last: Loseva

first: Samer

last: Yammine

first: Maria

last: Israelsson

first: Li-Sophie

last: Rathje

first: Balázs

last: Németi

first: Erik

last: Fredlund

first: Thomas

last: Helleday

first: Marta

middle: P

last: Imreh


title: RNA-Seq whole transcriptome analysis of normal human epidermal keratinocytes and cutaneous squamous cell carcinoma cell lines.

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

country: Finland

institute: University of Turku

summary: The incidence of keratinocyte-derived skin cancer, cutaneous squamous cell carcinoma (cSCC) is increasing worldwide making it the second most common metastatic skin cancer. In this project we used SOLiD next generation sequencing to characterize gene expression profiles in normal human epidermal keratinocytes (NHEKs) and cSCC cell lines.

overall_design: Total RNAs from normal human epidermal keratinocytes (NHEKs) (n=4) and cSCC cell lines (n=8) were extracted. The samples were sequenced using SOLiD next generation sequencing.

first: Mehdi

last: Farshchian

first: Risto

last: Ala-aho

first: Veli-Matti

last: Kähäri


title: RNA-seq of human fibroblasts during normal aging and during aging with rotenone perturbation

status: Public on Aug 26 2015

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

summary:
Human fibroblasts at different population doublings were treated with low amounts of rotenone (mild stress) and compared to untreated fibroblasts. Two different cell lines were used (MRC-5, HFF). Illumina sequencing (HiSeq2000) was applied to generate 50bp single-end reads.

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 60 samples: 3 biological replicates for each group: MRC-5 cells at 4 different population doublings (PD) with and without rotenone; HFF cells at 6 different population doublings with and without rotenone

first: Shiva

last: Marthandan

first: Karolin

last: Klement

first: Steffen

last: Priebe

first: Marco

last: Groth

first: Matthias

last: Platzer

first: Peter

last: Hemmerich

first: Stephan

last: Diekmann


title: FYRN and FYRC domains of the histone demethylase, JMJ14, mediated chromatin binding and transgene silencing through a pair of NAC transcription factors

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

summary: JmjC domain containing protein 14 (JMJ14) is an H3K4-specific histone demethylase that plays important roles in RNA-mediated gene silencing and flowering time regulation in Arabidopsis. However, how JMJ14 is recruited to their target genes remains unclear. Here, we show that the C-terminal FYRN and FYRC domains of JMJ14 are required for RNA silencing and flowering time regulation. Chromatin binding of JMJ14 is lost upon deletion of its FYRN and FYRC domains, along with increased H3K4me3. FYRN and FYRC domains interact with a pair of NAC domain containing transcription factors, NAC050 and NAC052. Genome-wide analysis revealed that JMJ14 and NAC050/052 share a set of common target genes with CTTGNNNNNCAAG consensus sequences. Mutations in either NAC052 or NAC050 impair RNA-mediated gene silencing. Thus, our findings demonstrate an important role of FYRN and FYRC in targeting JMJ14 through direct interaction with NAC050/052 transcription factors, which reveals a novel mechanism of recruiting a histone demethylases to its target loci in higher plants.

overall_design: anti-HA ChIP-seq were performed with six samples: Col, NAC050-HA, NAC052-HA, jmj14-1, JMJ14-HA and JMJ14-FYR-HA. Anti-H3K4me3 ChIP were performed with four samples: Col, jmj14-1, JMJ14-HA and JMJ14-FYR-HA. (NAC050-HA indicates PNAC050::NAC050-HA nac050-1, NAC052-HA indicates PNAC052::NAC052-HA nac052-2, JMJ14-HA indicates PJMJ14::JMJ14-HA jmj14-1, JMJ14-FYR-HA indicates PJMJ14::JMJ14-FYR-HA jmj14-1)

first: Shuaibin

last: Zhang

first: Bing

last: Zhou

first: Xiaofeng

last: Cao


title: RUNX1/ETO role's in hematopoietic system

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham


first: Anita

last: Göndör

overall_design:
Examination of intra- and interchromosomal interactions in human embryonic stem cells (HESCs) and derived embryoid bodies (HEBs) generated by 4C-seq, as described in (Zhao et al., 2006), using Illumina Genome Analyzer II and Illumina MiSeq.
Examination of mRNA profiles in HESCs and derived HEBs generated by deep sequencing, in duplicate, using Illumina HiSeq 2500.

first: Honglei

last: Zhao

first: Emmanouil

last: Sifakis

first: Noriyuki

last: Sumida

first: Lluís

last: Millán-Ariño

first: Barbara

last: Scholz

last: Svensson

first: Xingqi

last: Chen

first: Anna

last: Ronnegren

first: Carolina

last: Diettrich Mallet de Lima

first: Farzaneh

last: Shahin Varnoosfaderani

first: Chengxi

last: Shi

first: Olga

last: Loseva

first: Samer

last: Yammine

first: Maria

last: Israelsson

first: Li-Sophie

last: Rathje

first: Balázs

last: Németi

first: Erik

last: Fredlund

first: Thomas

last: Helleday

first: Márta

last: Imreh


title: CGGBP1 inhibits cytosine methylation at repetitive DNA sequences

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

type: Methylation profiling by high throughput sequencing

summary: By depleting CGGBP1 in normal human fibroblasts and by performing genome-wide sequencing (with and without bisulfite conversion) we show that upon CGGBP1 depletion cytosine methylation increases significantly at repeat regions. Using Pacbio sequencing of Alu and LINE-1 repeats amplified genome-wide from bisulfite converted DNA, we further establish the cytosine methylation-inhibitory functions of CGGBP1.

overall_design:
Control shmiR and CGGBP1 shmiR genomic DNA (both with or without sodium bisulfite conversion) used for Illumina sequencing experiments. Further bisulfite converted samples were used as templates to amplify Alu-SINEs and L1-LINEs genome wide and used for PacBio sequencing experiment.
We have sequenced the human genomic DNA (no experimental enrichment, so no modification of BAM files during analyses) and used the BAM files, the  most analyzed files, to calculate the genome composition statistics, such as base composition bias etc. The differences in base composition (C->T drift upon CGGBP1-depletion) changes are our key findings.

first: Prasoon

last: Agarwal


title: Regulation of nucleosome architecture and factor binding revealed by nuclease footprinting of the ESC genome

city: Pittsburgh

first: Sarah

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

summary: Functional interactions between gene regulatory factors and chromatin architecture have been difficult to directly assess. Here, we use micrococcal nuclease (MNase) footprinting to probe the functions of two chromatin remodeling complexes. By simultaneously quantifying alterations in small MNase footprints over the binding sites of 30 regulatory factors in mouse embryonic stem cells (ESCs), we provide evidence that esBAF and Mbd3/NuRD modulate the binding of several regulatory proteins. In addition, we find that nucleosome occupancy is reduced at specific loci in favor of subnucleosomes upon depletion of esBAF, including sites of histone H2A.Z localization. Consistent with these data, we demonstrate that esBAF is required for normal H2A.Z localization in ESCs, suggesting esBAF either stabilizes H2A.Z-containing nucleosomes or promotes subnucleosome to nucleosome conversion by facilitating H2A.Z deposition. Therefore, integrative examination of MNase footprints reveals insights into nucleosome dynamics and functional interactions between chromatin structure and key gene regulatory factors.

overall_design: Examine three read size footprints from MNase-Seq in EGFP KD, Mbd3 KD, and Smarca4 KD mESCs using ChIP-Seq datasets.

last: Fazzio


title: Orientation-Specific Joining of AID-initiated DNA Breaks Promotes Antibody Class Switching

city: Boston

first: Junchao

last: Dong

state: MA

address: 1 Blackfan Circle

department: PCMM

institute: Boston Children's Hospital, Harvard Medical School

summary: During B cell development, RAG endonuclease cleaves immunoglobulin heavy chain (IgH) V, D, and J gene segments and orchestrates their fusion as deletional events that assemble a V(D)J exon in the same transcriptional orientation as adjacent Cμ constant region exons. In mice, six additional sets of constant region exons (CHs) lie 100-200kb downstream in the same transcriptional orientation as V(D)J and Cμ exons. Long repetitive switch (S) regions precede Cμ and downstream CHs. In mature B cells, class switch recombination (CSR) generates different antibody classes by replacing Cμ with a downstream CH. Activation Induced Cytidine Deaminase (AID) initiates CSR by promoting deamination lesions within Sμ and a downstream acceptor S region; these lesions are converted into DNA double strand breaks (DSBs) by general DNA repair factors. Productive CSR must occur in a deletional orientation by joining the upstream end of an Sμ DSB to the downstream end of an acceptor S region DSB. However, the relative frequency of deletional to inversional CSR junctions had not been measured. Thus, whether orientation-specific joining is a programmed mechanistic feature of CSR as it is for V(D)J recombination and, if so, how this is achieved was unknown. To address this question, we adapted high throughput genome wide translocation sequencing (HTGTS) into a highly sensitive DSB end-joining assay and applied it to endogenous AID-initiated S region DSBs. We find that CSR indeed is programmed to occur in a productive deletional orientation and does so via an unprecedented mechanism that involves in cis IgH organizational features in combination with frequent S region DSBs initiated by AID. We further implicate ATM-dependent DSB response (DSBR) factors in enforcing this mechanism and provide a solution to the enigma of why CSR is so reliant on the 53BP1 DSBR factor.

overall_design:
We performed high-throughput genome-wide translocation sequencing (HTGTS) with different B cell genotypes that induces either I-SceI or AID-initiated DSBs as bait to study their joining pattern to AID-initiated S region breaks

Please note that the 'ΔSγ1_2xI/ΔSµ_2xI-3' raw data files were analyzed twice with different reference assemblies to address specific points, and associated with both 'ΔSγ1_2xI_ΔSµ_2xI-3'.txt and Sγ1_2xI_ΔSµ_2xI-3'_trans-Sm.txt processed data files.

As for the reference genome mm9_129_IgHC, it is a custom built generated based on mm9 (Bl6 line based mouse genome) and the partial genome sequence of another mouse line 129sv. It is not currently available in any public database however can be easily obtained either from the authors or self-built using information provided in the associated manuscript.

first: Rohit

last: Panchakshari

first: Frederick

last: Alt


title: Genome-wide analyses for the WOPR regulator osaA and the velvet regulator veA

status: Public on Aug 25 2015

city: Madison

first: Fahad

last: Alkhayyat

state: Wisconsin

address: 1550 linden dr.

department: Bacteriology

institute: UW Madison

summary: Orchestration of cellular growth and development occurs during the life cycle of Aspergillus nidulans. A multi-copy genetic screen intended to unveil novel regulators of development identified the AN6578 locus predicted to encode a protein with the WOPR domain, which is a broadly present fungi-specific DNA-binding motif. Multi-copy of AN6578 disrupted the normal life cycle of the fungus leading to enhanced proliferation of vegetative cells, whereas the deletion resulted in hyper-active sexual fruiting with reduced asexual development (conidiation), thus named as osaA (Orchestrator of Sex and Asex). Further genetic studies indicate that OsaA balances development mainly by repressing sexual development downstream of the velvet regulator VeA. The absence of osaA is sufficient to suppress the veA1 allele leading to the sporulation levels comparable to veA+ wild type (WT). Genome-wide transcriptomic analyses of WT, veA1, and osaA veA1 strains by RNA-Seq further corroborate that OsaA functions in repressing sexual development downstream of VeA. However, OsaA also plays additional roles in controlling development, as the ΔosaA veA1 mutant exhibits precocious and enhanced formation of Hülle cells compared to WT. The OsaA orthologue of Aspergillus flavus is able to complement the osaA null phenotype in A. nidulans, suggesting a conserved role of this group of WOPR domain proteins. In summary, OsaA is an upstream orchestrator of morphological and chemical development in Aspergillus that functions downstream of VeA.

overall_design: Examining the transcriptomic profiles of three Aspergillus nidualns strains: FGSC4, FGSC26, and ΔosaA veA1. Samples were collected at 12 h post developmental induction. Samples were collected in triplictaes.

first: Min

last: Ni

first: Sun-Chang

last: Kim

first: Jae-Hyuk

last: Yu


title: Regulatory T cells Maintain Lung Function Upon Infectious Damage

first: Aaron

last: Arvey

institute: Memorial Sloan-Kettering Cancer Center

summary: RNA-Seq analysis of Treg cell subsets isolated from lungs of Il10GFPFoxp3Thy1.1 mice. Thy1.1+ Treg cells were FACS-sorted into IL-10–IL-18R–, IL-10+IL-18R– and IL10–IL-18R+ populations on day 5 following intranasal infection with 0.5 LD50 PR8-OTI influenza virus.

overall_design: mRNA profiles of each Thy1.1+ Treg cell population (IL-10–IL-18R–, IL-10+IL-18R– and IL10–IL-18R+) from lungs on day 5 following influenza infection from 5 infected mice, sorted into TRIzol LS reagent.

first: Alexander

middle: Y

last: Rudensky

first: Nicholas

last: Arpaia


title: Cell stage dependent transcriptional response to leukaemic oncogene expression

first: Salam

last: Assi

summary: Acute myeloid leukemia (AML) is characterized by a block in myeloid differentiation the stage of which is dependent on the nature of the transforming oncogene and the developmental stage of the oncogenic hit. This is also true for the t(8;21) translocation which gives rise to the RUNX1/ETO fusion protein and initiates the most common form of human AML. To understand the molecular principles governing this differential action, we used the differentiation of mouse embryonic stem cells expressing an inducible RUNX1/ETO protein into blood cells as a traceable model combined with genome-wide analyses of transcription factor binding and gene expression. We found that RUNX1/ETO interferes with both the activating and repressive function of its normal counterpart, RUNX1, at early and late stages of blood cell development. However, the response of the transcriptional network to RUNX1/ETO expression is stage-specific, highlighting the molecular mechanisms determining specific target cell expansion after an oncogenic hit.

overall_design: High throughput sequencing data have been used to study RUNX1/ETO role in hematopoietic system

first: Kakkad

last: Regha

first: Olga

last: Tsoulaki

first: Georges

last: Lacaud

first: Constanze

last: Bonifer


title: RGS9-2-controlled adaptations in the striatum determine the onset of action and eficacy of antidepressants in neuropathic pain states

first: Venetia

last: Zachariou

state: New York

address: 1425 Madison Ave Icahn School of Medicine

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: The striatal protein Regulator of G protein signaling-2 (RGS9-2) plays a key modulatory role in opioid, monoamine and other GPCR responses. Here, we use the murine spared-nerve injury model of neuropathic pain to investigate the mechanism by which RGS9-2 in the nucleus accumbens (NAc), a brain region involved in mood reward and motivation, modulates the actions of tricyclic antidepressants (TCAs). Prevention of RGS9-2 action in the NAc increases the efficacy of the TCA desipramine and dramatically accelerates its onset of action. By controlling the activation of effector molecules by G protein a and bg subunits, RGS9-2 affects several protein interactions, phosphoprotein levels, and the function of the epigenetic modifier histone deacetylase 5 (HDAC5), that are important for TCA responsiveness. Furthermore, information from RNA-seq analysis reveals that RGS9-2 in the NAc affects the expression of many genes known to be involved in nociception, analgesia and antidepressant drug actions. Our findings provide novel information on NAc-specific cellular mechanisms that mediate the actions of TCAs in neuropathic pain states.

overall_design: The RNAseq study was designed in order to reveal the impact of RGS9-2 on gene regulation in the Nucleus Accumbens under neuropathic pain and antidepressant treatment conditions. A total of 18 samples was used, coprising 6 different groups , and each group consisted of three different biological replicates.

first: Vasiliki

last: Mitsi


city: Ann Arobr

first: Manjusha

last: Pande

address: 2800 Plymouth Rd.

department: BRCF

institute: University of Michigan

summary: FoxO transcription factors promote longevity across taxa. How they do so is poorly understood. In the nematode Caenorhabditis elegans, the A- and F-isoforms of the FoxO transcription factor DAF-16 extend life span in the context of reduced DAF-2 insulin-like growth factor receptor (IGFR) signaling. To elucidate the mechanistic basis for DAF-16/FoxO-dependent life span extension, we performed an integrative analysis of isoform-specific daf-16/FoxO mutants. In contrast to previous studies suggesting that DAF-16F plays a more prominent role in life span control than DAF-16A, isoform-specific daf-16/FoxO mutant phenotypes and whole transcriptome profiling revealed a predominant role for DAF-16A over DAF-16F in life span control, stress resistance, and target gene regulation. Integration of these data sets enabled the prioritization of a subset of 92 DAF-16/FoxO target genes for functional interrogation. Among 29 genes tested, two DAF-16A-specific target genes significantly influenced longevity. Our discovery of new longevity genes underscores the efficacy of our integrative strategy while providing a general framework for identifying specific downstream gene regulatory events that contribute substantially to transcription factor functions. As FoxO transcription factors have conserved functions in promoting longevity and may be dysregulated in aging-related diseases, these findings promise to illuminate fundamental principles underlying aging in animals.

overall_design: Whole-transcriptome profiling of daf-16/FoxO isoform-specific deletion mutants in the long-lived daf-2(e1370) background. Included are daf-16 wild-type, daf-16 null mutation, daf-16a/f mutation, two independent daf-16a mutations, and daf-16f mutation. N2 wild-type controls are also included.

first: Albert

middle: T

last: Chen

first: Patrick

last: Hu


title: Regulation of bifurcating B cell trajectories by mutual antagonism between IRF4 and IRF8 (RNA-Seq)

city: Cincinnati

first: Harinder

last: Singh

state: OH

address: 333 Burnet Avenue

department: Immunobiology

institute: CCHMC

summary: Upon antigen recognition B cells undertake a bifurcated response in which some cells rapidly differentiate into plasmablasts while others undergo affinity maturation in germinal centers (GC). We uncover a double negative feedback loop between interferon regulatory factors IRF4 and IRF8, which regulates the initial bifurcation of activated B cells as well as the GC response. IRF8 dampens BCR signaling, facilitates antigen specific interaction with helper T cells, and promotes selection of high affinity clones while antagonizing IRF4 driven plasmablast differentiation. Genomic analysis reveals concentration dependent action of IRF4 and IRF8 in regulating distinctive gene expression programs. Stochastic modeling suggests that the double negative feedback is sufficient to initiate bifurcating B cell developmental trajectories.

overall_design: Naïve B cells were isolated from Irf8+/+ (wild type, WT) mice spleen and activated in vitro with 10μg/ml LPS (Sigma). CD138hi IgMhi (IRF4hi*) cells and CD138lo IgMlo (IRF8hi*) cells were sorted by flow cytometry at 72 hours. Total RNA was prepared by using Rneasy Mini kit (Qiagen) and sequenced with Illumina HiSeq2500. Alignment was performed with Taphat2, and transcript abundance quantification using Cuffdiff function from Cufflinks. GC B cells were sorted from CD19cre/+ Irf8+/+ (Ctrl) or CD19cre/+ Irf8flox/flox (Irf8 cKO) mice on dpi 13 post NP-KLH immunization. Total RNA was prepared by using Rneasy Mini kit (Qiagen) and amplified with with Ovation RNA-Seq System v2 (NuGEN). The data were analyzed by Wardrobe. More details are provided in the manuscript.

first: H

last: Xu

first: V

last: Chaudhri

first: Z

last: Wu

first: K

last: Dienger-Stambaugh


title: A high-throughput screen of inactive X chromosome reactivation identifies the enhancement of DNA demethylation by 5-aza-2’-dC upon inhibition of ribonucleotide reductase-wide

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

institute: UCLA

summary:
Background: DNA methylation is important for maintenance of the silent state of genes on the inactive X chromosome (Xi). Here, we screened for siRNAs and chemicals that reactivate an Xi-linked reporter in the presence of 5-aza-2’-deoxycytidine (5-aza-2’-dC), an inhibitor of DNA methyltransferase 1, at a concentration that, on its own, is not sufficient for Xi-reactivation.
Results: We found that inhibition of ribonucleotide reductase (RNR) induced expression of the reporter. RNR inhibition potentiated the effect of 5-aza-2’-dC by enhancing its DNA incorporation, thereby decreasing genome-wide DNA methylation levels. Since both 5-aza-2’-dC and RNR-inhibitors are used in the treatment of hematological malignancies, we treated myeloid leukemia cell lines with 5-aza-2’-dC and the RNR inhibitor hydroxyurea, and observed synergistic inhibition of cell growth and decreases in genome-wide DNA methylation.
Conclusions: Taken together, our study identifies a drug combination that enhances DNA demethylation by altering nucleotide metabolism. We demonstrate that XCR assays can be used to optimize epigenetic activity of drug combinations.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Reduced representation bisulfite sequencing (MspI,~40-220bp size fraction) of murine and human cells.

first: Alissa

last: Minkovsky

first: Anna

last: Sahakyan

first: Giancarlo

last: Bonora

first: Robert

last: Damoiseaux

first: Elizabeth

last: Dimitrova

first: Liudmilla

last: Rubbi

first: Matteo

last: Pellegrini

first: Caius

last: Radu


title: Meis1 coordinates a network of genes implicated in eye development and microphthalmia

city: Madrid

first: Carlos

last: Torroja

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Bioinformatics Unit

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

summary: Microphthalmos is a rare congenital anomaly characterized by reduced eye size and visual deficits of variable degrees. Sporadic and hereditary microphthalmos has been associated to heterozygous mutations in genes fundamental for eye development. Yet, many cases are idiopathic or await the identification of molecular causes. Here we show that haploinsufficiency of Meis1, a transcription factor with an evolutionary conserved expression in the embryonic trunk, brain and sensory organs, including the eye, causes microphthalmic traits and visual impairment, in adult mice. In the trunk, Meis1 acts as a cofactor for genes of the Hox complex, mostly binding to Hox-Pbx target sequence on the DNA. By combining the analysis of Meis1 loss-of-function and conditional Meis1 functional rescue with ChIPseq and RNAseq approaches, we show that during the development of the optic cup, an Hox-free region, Meis1 binds instead to Hox/Pbx-independent Meis binding site, and coordinates, in a dose-dependent manner, retinal proliferation and differentiation by regulating the expression of components of the Notch signalling pathway. Meis1 also controls the activity of genes responsible for human microphthalmia and eye patterning so that in Meis1-/- embryos, the eye size is reduced and boundaries among the different eye territories are shifted or blurred. We thus propose that Meis1 is at the core of a genetic network implicated in microphthalmia, itself representing an additional candidate for syndromic cases of these ocular malformations.

overall_design: Transcriptomics and Meis1 Occupancy analysis on mouse isolated optic cups and ChIP data for histone methylation marks were obtained from about 100 eyes of E10.5 CD1 embryos.

first: Séverine

last: Marcos

first: Monica

last: González-Lázaro

first: Leonardo

last: Beccari

first: Laura

last: Carramolino

first: María

last: Martín-Bermejo

first: Oana

last: Amarie

first: Daniel

last: Mateos-San Martín

first: Juan

last: Tena

first: Roisin

last: Doohan

first: Oliver

last: Puk

first: Martín

last: Hrabě de Angelis

first: Jochen

last: Graw

first: Jose

last: Gómez-Skarmeta

first: Fernando

last: Casares

first: Miguel

last: Torres

first: Paola

last: Boloventa


title: Postnatal epigenetic development of mouse intestinal stem cells (RNA-seq)

city: Houston

first: Lanlan

last: Shen

address: 1100 Bates Ave.

institute: Baylor College of Medicine

summary: We used RNA sequencing to quantify the gene expression levels in the intestinal stem cells (ISCs) or their progeny during the suckling period of mouse colon development.

overall_design: Lgr5-EGFP mice were used to identify ISC populations in the colons. RNA sequencing was performed using EGFP labeled Lgr5+ ISCs and epithelial cell adhesion molecule (EpCAM) labeled epithelial cells isolated at the beginning and end of the suckling period (postnatal day 0-P0 and P21).


title: Altered interactions between the gut microbiome and colonic mucosa precede polyposis in APCMin/+ mice

status: Public on Aug 24 2015

city: Stony Brook

first: Ellen

last: Li

address: Health Sciences Tower Level 17-080

institute: Stony Brook University

summary: Mutation of the adenomatous polyposis coli (APC gene), an early event in the adenoma-carcinoma sequence, is present in 70-80% of sporadic human colorectal adenomas and carcinomas.  To test the hypothesis that mutation of the APC gene alters microbial interactions with host intestinal mucosa prior to the development of polyposis, culture-independent methods (targeted qPCR assays and Illumina sequencing of the 16S rRNA gene V1V2 hypervariable region) were used to compare the intestinal microbial composition of 30 six-week old C57BL/6 APCMin/+ and 30 congenic wild type (WT) mice.  The results demonstrate that similar to 12-14 week old APCMin/+ mice with intestinal neoplasia, 6 week old APCMin/+ mice with no detectable neoplasia, exhibit an increased relative abundance of Bacteroidetes spp in the colon.  Parallel mouse RNA sequence analysis, conducted on a subset of proximal colonic RNA samples (6 APCMin/+, 6 WT) revealed 130 differentially expressed genes (DEGs, fold change ≥ 2, FDR <0.05). Hierarchical clustering of the DEGs was carried out by using 1-r dissimilarity measurement, where r stands for the Pearson correlation, and Ward minimum variance linkage, in order to reduce the number of input variables.  When the cluster centroids (medians) were included along with APC genotype as input variables, analysis of variance and covariance (ANCOVA) with stepwise variable selection, selected two of seven mouse gene clusters, in addition to APC genotype, as significantly associated (p = 0.011 and p = 0.004) with the increased relative abundance of Bacteroidetes spp.  One of the two clusters includes several downregulated genes encoding immunoglobulin variable regions and non-protein coding RNAs.   These results support the concept that mutation of the APC gene alters colonic-microbial interactions prior to polyposis. It remains to be determined whether interventions directed at ameliorating dysbiosis in APCMin/+mice, such as through probiotics, prebiotics or antibiotics, could reduce tumor formation.

overall_design: Comparing the differential gene expressions in proximal colonic mucosal samples from 6 six-week-old female Apc Min/+ and 6 six-week-old female WT mice

first: Joshua

last: Son

first: Shanawaj

last: Khair

first: Donald

last: Pettet

first: Nengtai

last: Ouyang

first: Xinyu

last: Tian

first: Yuanhao

last: Zhang

first: Wei

last: Zhu

first: Gerardo

last: Mackenzie

first: Charles

middle: E

last: Robertson

first: Diana

last: Ir

middle: N

last: Frank

first: Basil

last: Rigas


title: Regulation of bifurcating B cell trajectories by mutual antagonism between IRF4 and IRF8

first: Harinder

last: Singh

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

overall_design: Refer to individual Series


title: YAP1 exerts its transcriptional control via TEAD-mediated activation of enhancers

city: Illkirch

first: Anais

middle: Flore

last: Bardet

address: 1 rue Laurent Fries

country: France

institute: IGBMC

summary: YAP1 is a major effector of the Hippo pathway and a well-established oncogene. Elevated YAP1 activity due to mutations in Hippo pathway components or YAP1 amplification is observed in several types of human cancers. Here we investigated its genomic binding landscape in YAP1-activated cancer cells, as well as in non-transformed cells. We demonstrate that TEAD transcription factors mediate YAP1 chromatin-binding genome-wide, further explaining their dominant role as primary mediators of YAP1-transcriptional activity. Moreover, we show that YAP1 largely exerts its transcriptional control via distal enhancers that are marked by H3K27 acetylation and that YAP1 is necessary for this chromatin mark at bound enhancers and the activity of the associated genes. This work establishes YAP1-mediated transcriptional regulation at distal enhancers and provides an expanded set of target genes resulting in a fundamental source to study YAP1 function in a normal and cancer setting.

overall_design: Sequencing of ChIP and input samples for YAP1 and TEAD1 transcription factors and H3K27ac histone modification in SF268 glioblastoma cells and for YAP1 transcription factor in NCI-H2052 mesothelioma cells and IMR90 non-transformed lung fibroblast cells.

first: Claudia

last: Stein

first: Anaïs

middle: F

first: Guglielmo

last: Roma

first: Sebastian

last: Bergling

first: Ieuan

last: Clay

first: Alexandra

last: Ruchti

last: Agarinis

first: Tobias

last: Schmelzle

first: Tewis

last: Bouwmeester

first: Dirk

last: Schübeler

first: Andreas

last: Bauer


title: Comparative whole-transcriptomic analysis between normal and AKAP-Lbc-depleted human embryonic stem cells

city: Chuou-ku

first: Masatoshi

last: Ohgushi

state: Kobe

address: 2-2-3 Minatojima-minamimachi,

country: Japan

institute: RIKEN Center for Developmental Biology

summary: Human embryonic stem cells (hESCs) have the unique property of immortality, ability to infinitely self-renew and survive in vitro. In contrast to tumor-deribed cells, their immortality are free from any genomic abberations. Instead, they depend on the AKAP-Lbc/Rho signaling cascade. To understand the downstream way, we performed RNA-seq analyses between normal and AKAP-Lbc-depleted hESCs using the doxycyclin-inducible gene silensing strategy.

overall_design: We use the genetically modified hESCs in which AKAP-13-targeting shRNA is induced by doxycyclin(dox) treatment. To minimize cell loss during treatment, anti-apoptotic factor Bcl-XL is overexpressed. We collected RNA from dox-treated and untreated cells in biological triplicate. We measured gene expression in these 2 sample groups using RNA-seq (illumina HiSeq) .

first: Maki

last: Minaguchi

first: Yoshiki

last: Sasai


title: Optogenetic induction of Brn2 drive neural differentiation

city: San Francisco

first: Matt

last: Thomson

state: CA

address: 600 16th Street

institute: UCSF

summary: We use optical induction of Brn2 to probe mechanisms for gating embryonic stem cell differentiation

overall_design: mRNA-seq time-course following Brn2 induciton


title: The dynamic transcriptional profile of sertoli cells during the progression of spermatogenesis

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

institute: Inserm U1085-Irset

summary: Sertoli cells (SCs), the only somatic cells within seminiferous tubules, associate intimately with developing germ cells. They not only provide physical and nutritional support but also secrete factors essential to the complex developmental processes of germ cell proliferation and differentiation. The SC transcriptome must therefore adapt rapidly during the different stages of spermatogenesis. We report comprehensive genome-wide expression profiles of pure populations of SCs isolated at 5 distinct stages of the first wave of mouse spermatogenesis, using RNA sequencing technology. We were able to reconstruct about 13 901 high-confidence, nonredundant coding and noncoding transcripts, characterized by complex alternative splicing patterns with more than 45% comprising novel isoforms of known genes. Interestingly, roughly one-fifth (2939) of these genes exhibited a dynamic expression profile reflecting the evolving role of SCs during the progression of spermatogenesis, with stage-specific expression of genes involved in biological processes such as cell cycle regulation, metabolism and energy production, retinoic acid synthesis, and blood-testis barrier biogenesis. Finally, regulatory network analysis identified the transcription factors endothelial PAS domain-containing protein 1 (EPAS1/Hif2α), aryl hydrocarbon receptor nuclear translocator (ARNT/Hif1β), and signal transducer and activator of transcription 1 (STAT1) as potential master regulators driving the SC transcriptional program. Our results highlight the plastic transcriptional landscape of SCs during the progression of spermatogenesis and provide valuable resources to better understand SC function and spermatogenesis and its related disorders, such as male infertility.

overall_design: Genome-wide expression profiling analysis using Illumina next-generation sequencing technology

first: Céline

last: Zimmermann

first: Béatrice

last: Conne

first: Christelle

last: Borel

first: Jean-Luc

last: Pitetti

first: Pierre

last: Calvel

first: Isabelle

last: Stévant

first: Bernard

last: Jégou

first: Serge

last: Nef


title: Physical and functional CSL-p53 interactions underlie control of cancer stromal cell evolution [RNA-seq]

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

summary: Senescence of stromal fibroblasts has been linked to establishment of cancer associated fibroblasts (CAF) and aging-associated increase of tumors. However, in clinically occurring carcinomas, density and proliferation of CAFs are frequently increased rather than decreased. We previously showed that genetic deletion or down-modulation of the canonical Notch effector CSL/RBP-Jκ in skin dermal fibroblasts is sufficient for CAF activation with consequent development of multifocal keratinocyte tumors. We now show that CSL deletion or knockdown induces senescence of primary fibroblasts derived from dermis, oral mucosa, breast and lung. CSL functions in these cells as a constitutive direct repressor of multiple senescence- and CAF-effector genes. At the same time, it physically interacts with p53, repressing its activity, and p53 activation provides a failsafe mechanism against compromised CSL function. Concomitant loss of CSL and p53 overcomes fibroblast senescence, enhances expression of CAF effector genes and, in vivo, promotes tumour and stromal cell expansion. Together, the findings support a CAF activation/stromal evolution model under convergent CSL/p53 control.

overall_design: Human Dermal Fibroblasts were transfected with two different siRNA against CSL in parallel with a control siRNA. Total RNA was extracted 3 days post-transfection, followed by RNA-Seq analysis.

first: Maria-Giuseppina

last: Procopio

first: Csaba

last: Laszlo

first: Dania

last: Allabban

first: Pino

last: Bordignon

first: Seung-Hee

last: Jo

first: Ugo

last: Ala

first: Paolo

last: Provero

first: Vic

last: Neel

first: Witek

last: Kilarski

first: Melody

last: Swartz

first: Cathrin

last: Brisken

first: Karine

last: Lefort

first: G

last: Dotto


title: mRNAseq analysis of Nkx2.2, Nkx6.1, and Olig2 overexpression in neural progenitors

first: Yuichi

last: Nishi

address: 1425 San Pablo St.

department: Eli and Edythe Broad-CIRM Center for Regenerative Medicine

institute: University of Southern California

summary: Nkx2.2, Nkx6.1, and Olig2 repressors were overexpressed, singly or in combination, in in vitro-derived mouse neural progenitors to identify thier repression targets

overall_design: Overexpression study to identify genes repressed by Nkx2.2, Nkx6.1, and Olig2 in neural progenitors

first: Andrew

last: McMahon


title: Regulation of bifurcating B cell trajectories by mutual antagonism between IRF4 and IRF8 (ChIP-Seq)

first: Harinder

last: Singh

overall_design: Naïve B cells were isolated from wild type (WT) mice spleen and activated in vitro with 10μg/ml LPS (Sigma). ChIP was performed by using anti-IRF4, -IRF8 antibodies (Santa Cruz Biotech). For massively parallel sequencing, 10-20 μg of chromatin fragments from indicated samples were immunoprecipitated by using anti-IRF-4 and anti-IRF8 antibodies, and DNA libraries were prepared with Illumina Kit. DNA was sequenced by using the Illumina HiSeq2500. Reads were aligned to the mouse genome (mm9) by using Taphat2 and peak calling were performed by homer 2. GC B cells were sorted from WT mice on dpi 13 post NP-KLH immunization. Cells were flash frozen immediately and process by Active Motif for IRF8 ChIP-Seq. Reads were aligned to mm9 by using BAM and peak calling were performed by using MACS. More details are provided in the manuscript.

first: H

last: Xu

first: V

last: Chaudhri

first: Z

last: Wu

first: K

last: Dienger-Stambaugh


title: Nkx2.2, Nkx6.1, Olig2, and Gli3 genomic binding regions and overexpression in neural progenitors


title: Enhancer activation during EGF response

city: Miami

first: Alessandro

last: Gardini

state: FL

address: 1501 NW 10 Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

summary: We investigated the acetylation of H3K27, in normal condition and after stimulation of EGF and before or after the depletion of INTS11. Additionally, we examined transcription by sequencing the chromatin-bound fraction of RNA and by fractionating total RNA into polyadenylated and non-polyadenylated compartement.

overall_design: Comparison of the genome wide profiles of H3K27ac and RNA in HeLa cells

first: Fan

last: Lai

first: Anda

last: Zhang

first: Ramin

last: Shiekhattar


title: Conserved Molecular Program for Root Development in Diverse Plants

city: Ann Arbor

first: John

last: Schiefelbein

state: Michigan

address: 830 North University Avenue

department: Molecular, Cellular, and Developmental Biology

summary: We define genome-wide temporal expression patterns of root development genes in seven vascular plants, enabling a detailed comparative analysis of the molecular development of a single organ across diverse species.

sample_organism:
Cucumis sativus
Arabidopsis thaliana
Glycine max
Solanum lycopersicum
Oryza sativa
Zea mays
Selaginella moellendorffii

overall_design: Measuring mRNA expression of the root development zones in 7 vascular plants.  Each measurement includes 3 biological replicates.

first: Ling

last: Huang


title: Brd4 regulation of activity dependent transcription

city: Philadelphia

first: Erica

last: Korb

state: PENNSYLVANIA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

summary: Inhibition of Brd4 with Jq1 in neurons with or without BDNF stimulation

overall_design: Examination of the effects of Jq1 treatment on primary mouse cortical neurons


title: N-Acetylglucosamine-Induced Cell Death in Candida albicans and Its Implications for Adaptive Mechanisms of Nutrient Sensing in Yeasts

status: Public on Aug 22 2015

city: Beijing

first: Guanghua

address: NO.1 West Beichen Road, Chaoyang District

institute: Institute of Microbiology

summary: Single-celled organisms have different strategies to sense and utilize nutrients in their ever-changing environments. The opportunistic fungal pathogen Candida albicans is a common member of the human microbiota, especially that of the gastrointestinal (GI) tract. An important question concerns how C. albicans gained a competitive advantage over other microbes to become a successful commensal and opportunistic pathogen. Here, we report that C. albicans uses N-acetylglucosamine (GlcNAc), an abundant carbon source present in the GI tract, as a signal for nutrient availability. When placed in water, C. albicans cells normally enter the G0 phase and remain viable for weeks. However, they quickly lose viability when cultured in water containing only GlcNAc. We term this phenomenon GlcNAc-induced cell death (GICD). GlcNAc triggers the upregulation of ribosomalbiogenesis genes, alterations of mitochondrial metabolism, and the accumulation of reactive oxygen species (ROS), followed by rapid cell death via both apoptotic and necrotic mechanisms. Multiple pathways, including the conserved cyclic AMP (cAMP) signaling and GlcNAc catabolic pathways, are involved in GICD. GlcNAc acts as a signaling molecule to regulate multiple cellular programs in a coordinated manner and therefore maximizes the efficiency of nutrient use. This adaptive behavior allows C. albicans’ more efficient colonization of the gut.

overall_design: Expression profiles of Candida alibcans in three different 5 hours) were determined by high throughput sequencing technology.

first: Han

last: Du


title: Study of RFX1 and RFX3 binding sites in the mouse genome

city: Geneva

first: Walter

last: Reith

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

summary: The aim of the study was to identify RFX1 and RFX2 binding sites in mouse pancreatic beta cells.

overall_design: Chromatin immunoprecipitation experiments were performed with the mouse MIN6 beta cell line and antibodies raised against RFX1 and RFX3. Immunoprecipitated DNA was sequenced using the Genome Analyzer II (Illumina). Antibodies were described in       Reith W,   Ucla C,   Barras E,   Gaud A,   Durand B,   Herrero-Sanchez C,   Kobr M,   Mach B    : RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins. Mol Cell Biol 1994;14:1230–1244

first: Aouatef

last: Ait-Lounis

first: Christoph

middle: D

last: Schmid


title: Proteogenomic analysis of psoriasis reveals discordant and concordant changes in mRNA and protein abundance

status: Public on Aug 23 2015

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

summary: Background: Psoriasis is a chronic disease characterized by the development of scaly red skin lesions and possible co-morbid conditions. The psoriasis lesional skin transcriptome has been extensively investigated, but mRNA levels do not necessarily reflect protein abundance.  Methods: Lesional (PP) and uninvolved (PN) skin samples from 14 patients were analyzed using high-throughput complementary DNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS).  Results: We identified 4122 differentially expressed genes (DEGs) along with 748 differentially expressed proteins (DEPs). Global shifts in mRNA were modestly correlated with changes in protein abundance (r = 0.40). We identified similar numbers of increased and decreased DEGs, but 4-fold more increased than decreased DEPs. Ribosomal subunit and translation proteins were elevated within lesions, without a corresponding shift in mRNA expression (RPL3, RPS8, RPL11). We identified 209 differentially expressed genes/proteins (DEGPs) with corresponding trends at the transcriptome and proteomic levels. Most DEGPs were similarly altered in at least one other skin disease. Psoriasis-specific and non-specific DEGPs had distinct cytokine-response patterns, with only the former showing disproportionate induction by IL-17A in cultured keratinocytes.  Conclusions: Our findings reveal global imbalance between the number of increased and decreased proteins in psoriasis lesions, consistent with heightened translation. This effect could not have been discerned from mRNA profiling data alone. We have also identified high-confidence DEGPs and shown that only those most specific to psoriasis are enriched with IL-17A targets.

overall_design: RNA-seq-based comparison between gene expression in psoriasis lesions and uninvolved skin from 14 patients

first: Johann

last: Gudjonsson


title: Deregulation of the Ras-Erk Signaling Axis Modulates the Enhancer Landscape [ChIP-seq]

city: Boston

first: Behnam

last: Nabet

address: 360 Longwood Ave, LC-2100

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: Unrestrained receptor tyrosine kinase (RTK) signaling and epigenetic deregulation are root causes of tumorigenesis. We establish linkage between these processes by demonstrating that aberrant RTK signaling unleashed by oncogenic HRasG12V or loss of negative feedback through Sprouty gene deletion remodels histone modifications associated with active typical and super-enhancers. However, while both lesions disrupt the Ras-Erk axis, the expression programs, enhancer signatures, and transcription factor networks modulated upon HRasG12V-transformation or Sprouty deletion are largely distinct. Oncogenic HRasG12V elevates histone 3 lysine 27 acetylation (H3K27ac) levels at enhancers near the transcription factor Gata4 and the kinase Prkcb, as well as their expression levels. We show that Gata4 is necessary for the aberrant gene expression and H3K27ac marking at enhancers, and Prkcb is required for the oncogenic effects of HRasG12V-driven cells. Taken together, our findings demonstrate that dynamic reprogramming of the cellular enhancer landscape is a major effect of oncogenic RTK signaling.

overall_design: We performed ChIP-seq to assess the  global changes in the histone modifications H3K27ac (AC), H3K4me1 (me1), and H3K4me3 (me3) upon loss of feedback regulation through Sprouty (Spry) deletion, and upon unrestrained signaling driven by oncogenic HRasG12V. ChIP-seq was performed in biological duplicate; replicate2 is indicated in the sample name. Spry124fl/fl (VEC) and Spry124-/- (CRE) MEFs were profiled in three conditions: unsynchronized (U), serum starved (S), and serum starved and FGF treated (F). Spry124fl/fl (VEC) MEFs transduced with empty vector (EV) control or HRasG12V (HRas) were profiled in the unsynchronized state.

first: Jonathan

last: Licht


title: Nkx2.2, Nkx6.1, Olig2, and Gli3 genomic binding regions in neural progenitors [ChIP-Seq]

first: Yuichi

last: Nishi

summary: Nkx2.2, Nkx6.1, and Olig2 are transcriptional repressors regulating somatic motor neuron and interneuron subtypes in neural progenitors. The purpose of this study was to identify their target genes and to elucidate their gene regulatory mechanisms, including their relationship to Sonic Hedgehog/Gli pathway.

overall_design: Nkx2.2, Nkx6.1, Olig2, and Gli3 binding profiles were determined by ChIP-seq in neural progenitors derived in vitro from mouse embryonic stem cells

first: Andrew

last: McMahon


title: Deregulation of the Ras-Erk Signaling Axis Modulates the Enhancer Landscape


title: Bas1 and Ino4 ChIP-seq

status: Public on Aug 21 2015

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: Meiotic recombination is initiated by developmentally programmed DNA double-strand breaks (DSBs). In S. cerevisiae, the vast majority of DSBs occur in the nucleosome-depleted regions at gene promoters, where transcription factors (TFs) bind. It has been proposed that TF binding can stimulate DSB formation nearby by modulating local chromatin structure. However, a prior study in TF bas1 mutant suggested that the role of TF binding in determining break formation is complex. Here, we examined fine-scale DSB distributions in TF mutant (bas1Δ and ino4Δ) strains. In bas1Δ mutants, 239 out of the 2468 hotspots showed reduced DSB activity, whereas 87 hotspots showed increased DSB activity. Similarly, in ino4Δ mutant, 415 out of the 2468 hotspots showed reduced DSB activity, whereas 322 hotspots showed increased DSB activity. We also mapped Bas1 and Ino4 binding sites in meiosis and found that only a small portion of the affected hotspots contained TF binding sites. This indicates that TF can influence DSB distribution both directly and indirectly. Surprisingly, these DSB changes in TF mutants did not correlate with change in chromatin structure and histone H3K4me3 modification, suggesting that the role of TF on DSB distribution cannot be simply explained by affecting local chromatin status.

overall_design: Four samples total: Bas1-Myc (ChIP and input samples), Ino4-Myc (ChIP and input samples)

first: Xuan

last: Zhu

first: Scott

last: Keeney


title: Molecular profiling of activated olfactory neurons identifies odorant receptors for odors in vivo

city: Durham

first: Hiroaki

last: Matsunami

state: NC

address: 264 CARL Building Box 3509 DUMC

department: Department of Molecular Genetics and Microbiology

institute: Duke University Medical Center

summary: We present a high-throughput in vivo method to identify odorant receptors responding to odorants, using phosphorylated ribosome immunoprecipitation of mRNA from olfactory epithelium of odor-stimulated mice followed by RNA-Seq.

overall_design: pS6-IP RNA-Seq in odor stimulated vs control mice olfactory epithelium

first: Yue

last: Jiang


title: Histone 3 lysine 4 trimethylation (H3K4me3) ChIP in bas1 and ino4 mutants

state: NY

overall_design: Twelve samples total: four wild type, four bas1 mutant and four ino4 mutant (each an independent culture has one H3K4me3 ChIP sample and one H3 ChIP sample)


title: Deregulation of the Ras-Erk Signaling Axis Modulates the Enhancer Landscape [RNA-seq]

overall_design: We assessed gene expression changes upon loss of feedback regulation through Sprouty (Spry) deletion, and upon unrestrained signaling driven by mutant oncogenes. RNA-seq was performed in biological triplicate; replicate number is included in the sample name. Spry124fl/fl (VEC) and Spry124-/- (CRE) MEFs were profiled in three conditions: unsynchronized (U), serum starved (S), and serum starved and FGF treated (F). Spry124fl/fl (VEC) MEFs transduced with empty vector (EV) control or the indicated oncogenes (KRasG12V, HRasG12V, and BRafV600E) as well as Spry124-/- (CRE) MEFs transduced with EV control were profiled in the unsynchronized state.


title: Spo11-oligo mapping in bas1 and ino4 mutants

overall_design: Nine samples total: two wild type, four bas1 mutant and three ino4 mutant (each an independent culture)


title: Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells

city: Singapore

first: Arun George

last: Devasia

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary: Embryonic stem cell (ESCs) identity is orchestrated by co-operativity between the transcription factors (TFs) Sox2 and the class V POU-TF, Oct4 at composite Sox/Oct motifs. Neural stem cells (NSCs) lack Oct4 but express Sox2 and class III POU-TFs. This raises the question of how Sox2 interacts with POU-TFs to transcriptionally specify ESCs or NSCs. Here we show that Oct4 alone binds the Sox/Oct motif and the octamer-containing palindromic MORE equally well. Sox2 binding selectively increases the affinity of Oct4 for the Sox/Oct motif. In contrast, Oct6 binds preferentially to the MORE, and is unaffected by Sox2. ChIP-seq in NSCs shows the MORE to be the most enriched motif for class III POU-TFs, with  MORE sub-types apparent, but no Sox/Oct motif enrichment. These results suggest that in NSCs, co-operativity between Sox2 and class III POU-TFs may not occur and that POU-TF driven transcription uses predominantly the MORE cis architecture. Thus, distinct interactions between Sox2 and POU-TF subclasses distinguish pluripotent ESCs from multipotent NSCs, providing molecular insight into how Oct4 alone can convert NSCs to pluripotency.

overall_design: ChIP-seq of four transcription factors (Sox2, Oct6, Brn1, Brn2) in mouse neural stem cell line NS5. ChIP was done once for each transcription factor. Brn1 and Oct6 ChIP were from the same chromatin prep and therefor share the same input conttrol. Sox2 and Brn2 ChIP were done on independent chromatin preps and thus each has its own control. Each ChIP-seq library was sequenced over 2 lanes of an Illumina Genome Analyzer.

first: Tapan

middle: K

last: Mistri

first: Arun

first: Lee

last: Chu

first: Wei

last: Ng

first: Florian

last: Halbritter

first: Douglas

last: Colby

first: Ben

last: Martynoga

first: Simon

last: Tomlinson

first: Ian

last: Chambers

first: Paul

last: Robson

first: Thorsten

last: Wohland


title: Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation

first: Christine

last: Rushlow

address: 100 Washington Sq. E. Room 1001

department: Biology

country: USA

institute: NYU

summary: A central question in biology is how enhancers are made accessible. The Drosophila embryo is a good model system to study this question as the gene regulatory networks regulating early developmental events have been well characterized. Zelda (Zld) is a uniformly distributed transcription factor (TF) integral to these networks, acting prior to and in collaboration with the patterning TFs to regulate target enhancers. Here we test the hypothesis that Zld directs TF binding, examplified by Dorsal (Dl) which patterns the dorsoventral axis,  across the genome by displacing nucleosomes at enhancers. By performing ChIP-seq and MNase-seq experiments on early embryos with or without Zld, we demonstrated that early enhancers are characterized by an intrinsically high nucleosome barrier, which is overcome by Zld, and that without Zld, Dl binding decreases at enhancers and redistributes to open regions devoid of enhancer activity. We propose that enhancers are initially specified across the genome by the binding of Zld, which locally decreases nucleosome occupancy, thereby assisting TFs in accessing their binding motifs and promoting transcriptional activity.

overall_design: Zld, Dl, Pol II ChIP-seq and MNase-seq profiles comparing 2-3h wild-type (wt) and zld- embryos, and MNase-seq profiles comparing 2-4h wt and gd7 embryos, all in 2 replicates

first: Yujia

last: Sun

first: Chung-Yi

last: Nien

first: Kai

last: Chen

first: Hsiao-Yun

last: Liu

first: Jeff

last: Johnston

first: Nina

last: Koenecke

first: Julia

last: Zeitlinger


title: Gene expression differences associated with parental care

status: Public on Aug 20 2015

city: St Andrews,

first: Darren

middle: James

last: Parker

state: Fife

address: Dyers Brae House

department: Centre for Biological Diversity

institute: University of St. Andrews

summary: We examined gene expression differences associated with parental care in the burying beetle Nicrophorus vespilloides

overall_design: 24 samples in 12 conditions control, parenting, postparenting for males and females, caring uni- or bi-parentally

first: Christopher

middle: B

last: Cunningham

first: Craig

last: Walling

first: Clare

last: Stamper

first: Megan

last: Head

first: Eileen

middle: M

last: Roy-Zokan

first: Elizabeth

middle: C

last: McKinney

first: Michael

middle: G

last: Ritchie

first: Allen

last: Moore


title: Tissue-specific laser microdissection of the Brassica napus funiculus improves gene identification and spatial control of biological processes

city: Winnipeg

middle: G.

last: Becker

state: Manitoba

address: 66 Chancellors Circle

department: Biological Sciences

country: Canada

institute: University of Manitoba

summary: Tissue-specific RNA profiling of the Brassica napus funiculus and funicular subcompartments using laser microdissection and RNA-sequencing

overall_design: Funiculi were collected seven days after fertilization, histologically processed, and and embedded in paraffin. Entire funiculus or funiculus subcompartment (vasculature, epidermis, cortex) was collected using laser microdissection. RNA was extracted from laser microdissected tissues. This was used to prepare RNA-sequencing libraries with the Ovation RNA seq V2 cDNA amplificationand Illumina Truseq V2 library preparation kits.

first: Mark

last: Belmonte

first: Ainsley

last: Chan


title: Activation of the Integrated Stress Response by a Jumonji Histone Demethylase Inhibitor Induces Pro-Apoptotic Metabolic Reprogramming in Multiple Myeloma

city: Oxford

first: Laurynas

last: Pliuskys

address: Windmill Rd

department: NDORMS

institute: University of Oxford

summary: Regulation of gene expression by chromatin modification through methylation of histone lysine residues is a dynamic, reversible process that when deregulated is associated with cancer development. In multiple myeloma, combined inhibition of the histone demethylases JARID1B, UTX and JmjD3 by the small molecule GSK-J4 prevents cellular glutamine utilization leading to amino acids deprivation, activates the integrated stress response via GCN2-dependent ATF4 activation, and induces apoptosis.  This response is associated with a profound upregulation of metallothionein genes. Combined with clinical data demonstrating that overexpression of JARID1B is associated with shorter survival in multiple myeloma patients, this study highlights histone demethylases as epigenetic drug targets and places this demethylase inhibitor chemotype as having unique potential relative to established anti-myeloma treatment options.

overall_design: In total there are 7 different samples analyzed and one input control. Treatments are carried out with the demethylase inhibitor (or DMSO as negative control) at 6h and 48h, or with LNA targeting demethylases (or scrambled LNA) at 7 days. A negative control at 0h is included.

first: Edward

last: Hookway

first: Federica

last: Lari

first: Peter

last: Cain

first: Charlotte

last: Pawlyn

first: Michelle

last: Reed

first: Deborah

last: Brotherton

first: Faith

last: Davies

first: Anthony

last: Tumber

first: KaHing

last: Che

first: Ralph

last: Mazitschek

first: Cansu

last: Kucukkose

first: Duygu

last: Koca

first: Ferah

last: Gulacti

first: Fernando

last: Martinez

first: Cyrille

last: Thinnes

first: Radoslav

last: Novak

middle: J

last: Schofield

first: Daniel

last: Korr

first: Cora

last: Mund

first: Dave

last: Wilson

first: Rab

last: Prinjha

first: Claire

last: Edwards

first: Giuseppe

last: Gallone

first: Chris

middle: P

last: Ponting

first: Paul

last: Brennan

last: Bunnage

first: Alison

last: O’Mahony

first: Hinrich

last: Gronemeyer

first: Ulrich

middle: L

last: Günther

first: Morten

last: Lindow

first: Henrik

last: Ørum

first: Susanna

last: Obad

first: Gareth

last: Morgan

first: Nick

last: Athanasou

first: John

last: Christianson

first: Udo

last: Oppermann


title: Regulation of Gene Expression Dynamics during Developmental Transitions by the Ikaros Transcription Factor

city: Los Angeles

first: Teresita

last: Arenzana

state: California

address: 675 Charles E. Young Dr. S., MRL 6-535

department: Microbiology, Immunology, and Molecular Genetics

institute: UCLA

summary: The DNA-binding protein, Ikaros, functions as a potent tumor suppressor and hematopoietic regulator. However, the mechanisms by which Ikaros functions in the nucleus remain largely undefined, due in part to its atypical DNA-binding properties and partnership with the poorly understood Mi-2/NuRD complex. In this study, we extended our analysis of thymocyte development and lymphomagenesis in a mouse strain containing a specific deletion of Ikaros zinc finger 4, which exhibits a select subset of abnormalities observed in Ikaros null mice. By examining thymopoiesis in vivo and in vitro, numerous abnormalities were observed. RNA-sequencing revealed that each developmental stage is characterized by mis-regulation of a limited number of genes, with a strong preference for genes modulated in a stage-specific manner. Strikingly, individual genes and pathways rarely exhibited Ikaros-dependence at all developmental stages. Instead, the most consistent feature of aberrantly expressed genes was a reduced magnitude of expression level change during a developmental transition. These results and others suggest that Ikaros may not be a dedicated and consistent activator or repressor of a defined set of genes. Instead, its primary function may be to support the dynamic range of gene expression changes during developmental transitions via atypical molecular mechanisms that remain undefined.

overall_design: RNA-Seq of T cells at varying developmental stages and T cells expressing activated Notch in WT and Ikzf1-dF4/dF4 mutant backgrounds

first: Stephen

middle: T

last: Smale


title: Genome-wide transcriptomic profiling of ramie (Boehmeria nivea (L.) Gaudich.) in response to cadmium stress

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

summary: Cadmium (Cd)-contamination in soil has been becoming a major environmental problem in China. Ramie, a fiber crop, was frequently proposed to be used as the crop for phytoremediation of Cd-contaminated farmlands. However, high level Cd accumulation can cause a great inhibition of growth in ramie. To understand the potential mechanism for this phenomenon, the ramie genes involved in the Cd stress response were identified using Illumina pair-end sequencing in two Cd-stressed plants (CdS1 and CdS2) and two control plants (CO1 and CO2) in this study. Approximately 48.7, 51.6, 41.2, and 47.1 million clean sequencing reads generated from the libraries of CO1, CO2, CdS1, and CdS2, respectively, were De novo assembled to yield 56,932 non-redundant unigenes. A total of 26,686 (46.9%) genes were annotated for their function. Comparison of gene expression levels between CO and CdS ramie revealed 155 differentially expressed genes (DEGs). Sixteen DEGs was further confirmed their expression difference by real-time quantitative PCR (qRT-PCR). Among these 16 DEGs, 2 genes encoding GA2-oxidase which is a major enzyme for deactivating bioactive gibberellins (GAs) were found with a markedly up-regulated expression, which is possibly responsible for the growth inhibition of Cd-stressed ramie. Pathway enrichment analysis revealed that a pathway (Cutin, suberine and wax biosynthesis) was markedly enriched by DEGs. The discovery of these Cd stress-responsive genes and pathways will be helpful for further understanding the mechanism of Cd-stressed response and improving the ability of Cd stress tolerance in ramie.

overall_design: A total of four samples, two replicates of control plants (CO1 and CO2) and two replicates of cadmium-stressed plants (CdS1 and CdS2) were used for RNA-seq.


title: MicroRNA signatures of Insulin-producing cells differentiated from mesenchymal stem cells

city: BEIJING

first: Weijun

last: Guan

address: NO.2 YUANMINGYUAN WEST STREET

department: Institute of Animal Science

institute: Chinese Academy of Agricultrual Sciences

summary: The expression profile of miRNAs in MSCs and differentiated Insulin-producing cells was examined using RNA-seq technology. The expression of 411 miRNAs was observed, which we classified into three groups according to expression levels in differentiated Insulin-producing cells relative to that in MSCs: group I contained 107 miRNAs with an increased level of expression, group II contained 250 miRNAs that showed no change in expression and group III contained 54 miRNAs with decreased levels of expression.

overall_design: Examination of 2 different expression profile of miRNAs in 2 cell types

first: Chunyu

last: Bai


title: Effect of high fat diet versus low fat diet on histone distribution in sperm of male mice

city: Frederick

first: Scott

last: Durum

state: MD

address: Building 560, Room 31-71

department: CCR

institute: National Cancer Institute

summary: Several studies have described phenotypic changes in offspring of mice exposed to environmental factors including diet, but the effect of diet on sperm chromatin  remains unclear. We used a high fat diet (HFD) induced obesity mouse model, and examined chromatin of paternal spermatozoa. We performed chromatin immunoprecipitation followed by high throughput sequencing using specific H3 antibodies or specific H3K4me1antibodies.

overall_design: Genome-wide maps of H3 and H3K4me1 in spermatozoa of high fat diet and low fat diet male C57BL/6J mice. C57BL/6J males were fed for 10 to 12 weeks a high-fat diet (HFD)( with 60 kcal% fat) or a low-fat diet (LFD)(with 10 kcal% fat). Male mice show increased body weight, elevated blood glucose and impaired glucose tolerance without developing overt diabetes. Spermatozoa (live motile sperm) were isolated from the cauda epididymis. Spermatozoa from five animals were pooled for each experimental group and their biologic replica (HFD4 n=5, LFD5 n=5, HFD7 n=5, LFD8 n=5). Chromatin immunoprecitation (ChIP) assay was performed using anti- H3 antibody or anti- H3K4me1 antibody. ChIP DNA libraries were made using the Illumina ChIP-seq library preparation kit and subjected to Solexa sequencing (Illumina). Reads were aligned to mouse genome build mm9 as reference genome

first: Minoru

last: Terashima

first: Samatha

last: Barbour

first: Jianke

last: Ren

first: Yixing

last: Han

first: Weishi

last: Yu

first: Kathrin

last: Muegge


title: Genome-wide maps of nucleosome positions in purified quiescent S. cerevisiae cells [MNase-Seq]

city: Eugene

first: Jeffrey

last: McKnight

state: OR

address: 1229 University of Oregon, 1318 Franklin Blvd, Rm 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon

summary: Nucleosome positions were determined for purified S. cerevisiae quiescent cells and compared to logarithmically growing cells. By analyzing nucleosome positions and MNase digestion patterns for two separate matched digestion amounts (~80% and ~50% mononucleosomes) we show that global nucleosome stabilization and repositioning occurs at transcription start sites. This repositioning indicates a repressive chromatin architecture that reflects global transcriptional shutoff in quiescent yeast.

overall_design: Two matched MNase digests from two independent prototrophic W303 isolates during log growth (OD600=0.4-0.6) or from purified quiescent cells (pellet in Percoll gradient from 7-day stationay phase cultures) were subject to paired-end sequencing.

first: Joseph

middle: W

last: Boerma

first: Linda

last: Breeden

first: Toshio

last: Tsukiyama


title: Unique microRNAs appear at different times during the course of a delayed-type hypersensitivity reaction in human skin

first: Kemal

middle: Marc

last: Akat

address: 1230 York Avenue

institute: The Rockefeller University

summary: Diphencyprone (DPCP) is a hapten that induces delayed-type hypersensitivity (DTH) reactions.  MicroRNAs (miRNAs) are short non-coding RNAs that negatively regulate gene expression, and have been implicated in various inflammatory skin diseases, but their role in DTH reactions is not well understood.  We generated global miRNA expression profiles (using next-generation sequencing) of DPCP reactions in skin of 7 healthy volunteers at 3, 14, and 120 days after challenge.  Compared to placebo-treated sites, DPCP-challenged skin at 3 days (peak inflammation) had 127 miRNAs significantly deregulated.  At 14 days (during resolution of inflammation), 43 miRNAs were deregulated and, at 120 days (when inflammation had completely resolved), 6 miRNAs were upregulated.  While some miRNAs have been observed in psoriasis or atopic dermatitis, most of the deregulated miRNAs have not yet been studied in the context of skin biology or immunology.  Across the three time points studied, many but not all miRNAs were uniquely expressed.  As various miRNAs may influence T cell activation, this may indicate that the miRNAs exclusively expressed at different time points function to promote or resolve skin inflammation, and therefore may inform on the paradoxical ability of DPCP to treat both autoimmune conditions (alopecia areata) and conditions of ineffective immunity (melanoma).

overall_design: Total RNA isolated from human skin biopsies after either application of topical placebo gel or topical diphencyprone (DPCP) gel at different times post-challenge

first: Nicholas

last: Gulati

first: Marianne

last: Løvendorf

first: John

last: Zibert

first: Neil

last: Renwick

first: Thomas

last: Tuschl

first: James

last: Krueger


title: Strand-Specific RNA Sequencing for wild type and Drpd3 yeast entering quiescence [RNA-seq]

middle: N

summary: Strand-specific RNA sequencing was performed on wild type yeast in log phase, after diauxic shift, and after entry into quiescence with incorporation of external ERCC RNA spike-in controls to account for global changes in RNA abundance.  We find that RNA profiles undergo at least two transitions: 1) From log-to-diauxic shift where stress response genes are induced and translational machinery is massively repressed.  2) From diauxic shift-to-quiescence, where global transcript abundance is repressed 15-fold. The transition from diauxic shift to quiescence was found to require Rpd3, as deletion of Rpd3 prevented the global repression of the transcriptome after the diauxic shift.

overall_design: Strand-specific RNA sequencing was carried out in biological replicate with external controls then transcript abundance was normalized to reflect RNA content per cell.


title: Rpd3 drives transcriptional quiescence

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

overall_design: Refer to individual Series


title: Characterization of H3 density, H3 or H4 acetylation, Rpd3 binding, TFIIB binding, and Rpb3 (pol II) binding in wild type and rpd3 cells as they transition from logarithmic growth to diauxic shift to quiescence [ChIP-Seq]

summary: Binding profiles for H3 and H4ac were determined as cells transition from log growth to quiescence. We found that massive chromatin changes that reflect global transcriptional repression occur after the diauxic shift in an Rpd3-dependent manner.  Binding of Rpd3 is dramatically expanded to reflect binding at thousands of genes after quiescence entry, demonstrating an Rpd3-driven mechanism to change chromatin and repress transcription after entry into quiescence.

overall_design: Chomatin was harvested and fragmented from cells during log growth, after the diauxic shift, and after quiescence entry.  H3 ChIP, H4 hyperacetyl ChIP, H3K23ac ChIP, Rpd3-Myc ChIP, Rpb3 (pol II) ChIP, or TFIIB ChIP was performed to monitor genomic distribution at different times in wild type or rpd3 (H3 or H4ac) strains.


title: An Interaction between RRP6 and SU(VAR)3-9 Targets RRP6 to Heterochromatin and Contributes to Heterochromatin Maintenance in Drosophila melanogaster

city: Stockholm

first: Neus

last: Visa

address: Svante Arrhenius väg 20c

department: Molecular Biosciences, The Wenner-Gren Institute (MBW)

institute: Stockholm University


title: Uptake and function studies of maternal milk-derived miRNAs

status: Public on Aug 19 2015

city: Zurich

first: Alexandra

middle: Chloe

last: Title

state: Zurich

address: Otto-Stern-Weg 7

department: Institute of Molecular Heath Sciences

institute: ETH Zurich

summary: MicroRNAs are important regulators of cell-autonomous gene expression that influences many biological processes. They are also released from cells and are present in virtually all body fluids, including blood, urine, saliva, sweat, and milk. The functional role of extracellular miRNAs is controversial, and irrefutable demonstration of miRNA uptake by cells and canonical miRNA function is still lacking. Here we show that miRNAs are present at high levels in milk of lactating mice. To investigate intestinal uptake of miRNAs in newborn mice, we employed genetic models in which newborn miR-375 and miR-200c KO mice received milk from wildtype foster mothers. Analysis of intestinal epithelium, blood, liver and spleen revealed no evidence for miRNA uptake. miR-375 levels in hepatocytes were at the limit of detection and remained orders of magnitude below the threshold for target gene regulation (between 1000 and 10,000 copies/cell). Furthermore, our study revealed rapid degradation of milk miRNAs in the intestinal fluid. Together, our results indicate a nutritional rather than gene regulatory role of miRNAs in milk of newborn mice.

overall_design: miRNA profiling of WT murine milk clots from day 2, day 8, and day 14 of lactation, with 2 biological replicates per day.

first: Remy

last: Denzler

first: Markus

last: Stoffel


title: Histone Reader BRWD1 Targets and Restricts Recombination to the Igk Locus

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

summary: B lymphopoiesis requires that immunoglobulin genes be accessible to RAG1-RAG2 recombinase. However, the RAG proteins bind widely to open chromatin, which suggests that additional mechanisms must restrict RAG-mediated DNA cleavage. Here we show that developmental downregulation of interleukin 7 (IL-7)-receptor signaling in small pre-B cells induced expression of the bromodomain-family member BRWD1, which was recruited to a specific epigenetic landscape at Igk dictated by pre–BCR-dependent Erk activation. BRWD1 enhanced RAG recruitment, increased gene accessibility and positioned nucleosomes 5′ to each Jκ recombination signal sequence. BRWD1 thus targets recombination to Igk and places recombination within the context of signaling cascades that control B cell development. Our findings represent a paradigm in which,at any particular antigen-receptor locus, specialized mechanisms enforce lineage- and stage-specific recombination.

overall_design: ChIP-seq for 1 transcription factor and 2 histone modifications in flow purified mouse small pre-B cells. ATAC-seq and RNA-seq in WT and Brwd-Mut mouse flow purified small pre-B cells.

first: Malay

last: Mandal

first: Marcus

last: Clark

first: Keith

last: Hamel

first: Azusa

last: Tanaka

first: Grace

last: Teng

first: Jigyasa

middle: H

last: Tuteja

last: Bunker

last: Bahroos

last: Eppig

first: David

last: Schatz


title: An Interaction between RRP6 and SU(VAR)3-9 Targets RRP6 to Heterochromatin and Contributes to Heterochromatin Maintenance in Drosophila melanogaster [ChIP-Seq]

summary: We have investigated the effect of RRP6 depletion on the transcriptome of S2 cells using Affymetrix whole-genome tiling arrays. We have also carried out Illumina ChIP-seq analysis of RRP6 genome occupancy in control S2 cells (GFP-KD) and in cells depleted of SU(VAR)3-9.

overall_design: 8 samples total; 4 RNA-Seq samples (1 RRP6-KD and 1 GFP-KD, 2 biological replicates each); and 4 ChIP-Seq samples (RRP6 IP in GFP-KD and in Su(var)3-9-KD conditions; plus their respective Input samples).

first: Andrea

last: Eberle

first: Antoni

last: Gañez-Zapater

first: Antonio

last: Jordán-Pla

first: Viktoria

last: Hessle

first: Gilad

last: Silberberg

first: Anne

last: von-Euler

first: Rebecca

middle: A

last: Silverstein


title: Effect of cis-2-dodecenoic acid on F. novicida gene expression

city: Manassas

first: Monique

last: van Hoek

state: VA

address: Discovery Hall, George Mason Circle

department: School of Systems Biology and National Center for Biodefense and Infectious Diseases

institute: George Mason University

summary: In many bacteria, the ability to modulate biofilm production relies on specific signaling molecules that are either self-produced or made by neighboring microbes within the ecological niche. We analyzed the potential interspecies signaling effect of the Burkholderia diffusible signal factor (BDSF) on Francisella novicida, a model organism for Francisella tularensis, and demon- strated that BDSF both inhibits the formation and causes the dispersion of Francisella biofilm. Specificity was demonstrated for the cis versus the trans form of BDSF. Using transcriptome sequencing, quantitative reverse transcription-PCR, and activity as- says, we found that BDSF altered the expression of many F. novicida genes, including genes involved in biofilm formation, such as chitinases. Using a chitinase inhibitor, the antibiofilm activity of BDSF was also shown to be chitinase dependent. In addition, BDSF caused an increase in RelA expression and increased levels of (p)ppGpp, leading to decreased biofilm production. These results support our observation that exposure of F. novicida to BDSF causes biofilm dispersal. Furthermore, BDSF upregulated the genes involved in iron acquisition (figABCD), increasing siderophore production. Thus, this study provides the first evidence for a potential role and mechanism of diffusible signal factor (DSF) signaling in the genus Francisella and suggests the possibility of interspecies signaling between Francisella and other bacteria. Overall, this study suggests that in response to the interspecies DSF signal, F. novicida can alter its gene expression and regulate its biofilm formation.

sample_organism: Francisella tularensis subsp. novicida U112

overall_design: Treatment of F. novicida with cis-2-dodecenoic acid. One treated sample, one untreated control.

first: Scott

last: Dean


title: Herpesvirus saimiri microRNAs Preferentially Target Host Cell-Cycle Regulators

city: Cambridge

first: Yang

middle: Eric

last: Guo

state: MA

address: 455 Main St

institute: Whitehead Institute MIT

summary: In latently-infected marmoset T cells, Herpesvirus saimiri (HVS) expresses six microRNAs (known as miR-HSURs). The viral miR-HSURs are processed from chimeric primary transcripts, each containing a noncoding U-rich RNA (HSUR) and a pre-miRNA hairpin. To uncover functions of miR-HSURs, we identified mRNA targets in infected cells using High-Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation (HITS-CLIP). HITS-CLIP revealed hundreds of robust Argonaute (Ago) binding sites mediated by miR-HSURs in the host genome, but few in the HVS genome. Gene Ontology analysis showed that several pathways regulating the cell cycle are enriched among cellular targets of miR-HSURs. Interestingly, miR-HSUR4-3p represses expression of the p300 transcriptional co-activator by binding the open reading frame of its mRNA. miR-HSUR5-3p directly regulates BiP, an endoplasmic reticulum (ER) localized chaperone facilitating maturation of the Major Histocompatibility Complex I (MHC I) and the antiviral response. miR-HSUR5-3p also robustly downregulates WEE1, a key negative regulator of cell-cycle progression, leading to reduced phosphorylation of its substrate cyclin-dependent kinase (Cdk1). Consistently, inhibition of miR-HSUR5-3p in HVS-infected cells decreases their proliferation. Together, our results shed light on the roles of viral miRNAs in cellular transformation and viral latency.

overall_design: Ago HITS-CLIP analysis and small RNA-Seq in HVS infected marmoset T cells

middle: E

first: Theresa

last: Oei

first: Joan

last: Steitz


title: Aubergine iCLIP and expression

city: MONTPELLIER

first: Simonelig

last: Martine

address: 141, rue de la Cardonille

department: Genetics and Development

institute: Institut de Genetique Humaine - CNRS


title: Genome-wide map of H3K4me3 before and after methionine restriction in HCT116 cells.

status: Public on Aug 17 2015

first: Jason

last: Locasale

address: LSRC C270A

department: Pharmacology and Cancer Biology

institute: Duke University School of Medicine

summary: The goals of this study were to compare the distribution of H3K4me3 before and after methionine restriction to understand how nutrient availability and alterations in methionine metabolism affect the epigenetic state and regulate gene transcription.  To do this we performed ChIP-seq with an H3K4me3 antibody and RNA-seq using PolyA+ mRNA.

overall_design: We compared genome-wide H3K4me3 and mRNA profiles generated by Next Generation Sequencing (NGS) between +Methionine and -Methionine conditions after 24 hours in HCT116

first: Samantha

last: Mentch