title: Dynamic DNA Methylation Regulates Levodopa-Induced Dyskinesia

city: Birmingham

first: David

last: Figge

state: AL

address: 1719 6th Ave. S, CIRC 520

department: Neurology

institute: University of Alabama-Birmingham

summary: Levodopa-induced dyskinesia (LID) is a persistent behavioral sensitization that develops after repeated levodopa (L-DOPA) exposure in Parkinson disease (PD) patients.  we used reduced representation bisulfite sequencing to determine the methylation status of cytosines genome wide at base pair resolution following a parkinsonian-like lesion and LID development. Due to the enrichment of RRBS, we focused our analysis to cytosines in a CpG context and observed extensive locus-specific changes in DNA methylation, including a preponderance of demethylation, in the dorsal striatum following the development of dyskinetic behaviors in our animal model system. Changes in DNA methylation were concentrated in putative regulatory regions of many genes known to be aberrantly transcribed following L-DOPA exposure and enriched for genes relevant to mechanisms of synaptic plasticity. In the areas of the genome exhibiting the highest levels of effect, the magnitudes of change to methylation were strongly correlated with dyskinetic behaviors.

overall_design: Rats were given a unilateral dopaminergic lesion to the left medial forebrain bundle with 6-OHDA to destroy at least 90% of TH positive axons.  Animals were allowed to recover for 3 weeks and then given daily injections of L-DOPA (6 mg/kg) for seven days to establish stable dyskinesia. Animals were sacked 3 hrs following the final L-DOPA injection and the dorsal striatum was immediately dissected and flash frozen. Striatal tissue samples were processed for nucleic acid isolation using the AllPrep DNA/RNA Mini Kit (Qiagen) following the manufacturer's instructions. One μg of gDNA sample was used for library construction. Bisulfite converted DNA libraries were produced and adaptor ligated, and single-end reads were sequenced on an Illumina HiSeq-2500 following library QC. Bisulfite conversion efficiency was greater that 98% for all of the samples and we obtained an average of 68 million reads per library. Quality control on raw reads was performed with FastQC (version 0.10.1, http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc), and adaptor trimming and removal of trimmed reads shorter than 20 bp was performed with Trim Galore (version 0.3.7, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore). Trimmed reads were mapped to the UCSC Rattus norvegicus rn5 genome with the methylation-aware mapper bismark (version 0.13.0). Samtools (version 0.1.19–96b5f2294a) was used to sort SAM files produced by bismark and de-duplicate reads. SAM files were analyzed using MethylKit (version 0.9.2) in R (Akalin et al., 2012). Reads were filtered based on coverage, with a cutoff of at least ten reads per site, and normalized for each samples coverage before analysis. The genome was tiled at 250 bp and regions were counted if they contained at least 2 identified CpGs per tile. Differential methylation was defined as a sliding linear model correct p-value of <0.01 and, for highly dynamic regions, included at least a 5% change.

last: Standaert


title: The Zinc Finger Transcription Factor Sp9 Is Required for the Development of Striatopallidal Projection Neurons

status: Public on Jun 16 2016

city: Shanghai

first: Zhengang

last: Yang

address: 138 Yi Xue Yuan Road

department: Institutes of Brain Science and State Key Laboratory of Medical Neurobiology

country: China

institute: Fudan University

type: Expression profiling by high throughput sequencing

summary:
Purpose: To assess changes in gene expression profiles from the P0 littermate Sp9Flox/Flox control striatum (including SVZ) and conditional mutant striatum of Drd2-Cre; Sp9Flox/Flox mice.
Methods: total RNA was isolated and sequenced from the striatum of the P0 littermate Sp9Flox/Flox control or conditional mutant striatum of Drd2-Cre; Sp9Flox/Flox mice in triplicate using an Illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered changed which demonstrated fold-change>=2, and p value <=0.05. Changed genes were then filtered to reveal Sp9 downstream targets which were altered in vivo due to the loss of Sp9 expression.
Results: 179 genes were significantly increased and 147 genes were significantly decreased in expression level due to the loss of Sp9 expression.

first: Q

last: Zhang

first: Y

first: C

last: Wang

first: Z

last: Xu

last: Liang

first: L

last: An

first: J

last: Li

last: Liu

last: You

first: M

last: He

last: Mao

first: B

last: Chen

last: Xiong

middle: L

last: Rubenstein


title: Transcriptome profiling of Arabian horses blood during training regime

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

summary:
Purpose: Next-generation sequencing (NGS) was used to select genes potentially associated with exercise adaptation in Arabian horses.
Methods: Whole transcriptome profiling of blood was performed for  untrained horses and  horses from which samples were collected during at 3 different periods of training procedure (T1-during intense training period - March, T2- before starts - May and T3 -after flat racing season - October). The muscle transcriptome sequencing was performed for 37 blood samples using Illumina HiScan SQ in 75 single-end cycles. The quantifying transcript abundances was made using the RSEM supported by STAR aligner. The raw reads were aligned to the Equus caballus reference genome. Differentially expressed genes in blood tissue were detected by DESeq2. The RNA-seq results were validated using by qPCR.
Results: The increase of the number of DEGs between subsequent training periods has been observed and the highest amount of DEGs was detected between untrained horses (T0) and horses at the end of the racing season (T3) – 440. The comparison of transcriptome of T2 vs T3 and T0 vs T3 showed a significant advantage of up-regulated genes during long-term exercise (up-regulation of 266 and 389 DEGs in T3 period compared T2 and T0; respectively). Our results showed that the largest number of identified genes encoded transcription factors, nucleic acid binding proteins and G-protein modulators, which mainly were transcriptional  activated at the last training phase (T3) . Moreover, in the T3 period the identified DEGs represented genes coded for cytoskeletal proteins including actin cytoskeletal proteins and kinases. The most abundant exercise-upregulated genes were involved in pathways important in regulating the cell cycle (PI3K-Akt signaling pathway), cell communication (cAMP-dependent pathway), proliferation, differentiation and apoptosis as well as immunity processes (Jak-STAT signaling pathway). We also observed exercise induced expression of genes related in regulation of actin cytoskeleton, gluconeogenesis (FoxO signaling pathway; Insulin signaling pathway), glycerophospholipid metabolism and calcium signaling.
Conclusions: TOur results allow to identify changes in genes expression profile following training schedule in Arabian horses. Based on comparison analysis of blood transcriptomes, several exercise-regulated pathways and genes most affected by exercise were detected. We pinpointed overrepresented molecular pathways and genes essential for exercise adaptive response via maintaining of body homeostasis. The observed transcriptional activation of such gene as LPGAT1, AGPAT5, PIK3CG, GPD2,  FOXN2, FOXO3, ACVR1B and ACVR2A can be a base for further research in order to identify genes potentially associated with race performance in Arabian horses. Such markers will be essential to choice the training type, and could result in differences in racing performance specific to various breeds.

overall_design: The blood  transcriptome sequencing was performed for 37 samples collected form Arabian horses using Illumina HiScan SQ in75 single-end cycles and in 3-4 technical repetitions.repetitions.

first: Katarzyna

last: Ropka-Molik

first: Monika

last: Stefaniuk-Szmukier

last: Żukowski

last: Piórkowska

first: Artur

last: Gurgul

last: Bugno-Poniewierska


title: Retinoic Acid Is Sufficient for the in vitro Induction of Mouse Spermatocytes

city: Beijing

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

summary: To identify RA-regulated genes in mSSCs, we treated mSSCs with vehicle, RA and RA plus CHX. To characterize the induced spermatogenic cells by transcriptome profiling, we cultured mSSCs on pup Sertolic cells supplemented with RA. Induced differentiating spermatogonia and induced spermatocytes were collected after a 3-day- and 6-day-induction, respectively.

overall_design: We carried out RNA-seq analysis of samples after different treatment and samples from different in vitro induction stages.Two biological replicates were included for each sample.

first: Si

last: Wang

first: Xiwen

last: Lin


title: A splicing switch of TEAD4 regulates Hippo-YAP signaling pathway to inhibit tumor proliferation

first: Zefeng

address: 320 Yueyang Road

institute: CAS-MPG Partner Institute for Computational Biology (PICB)

summary: Splicing dysregulations extensively occur in cancers, yet the biological consequences of such alterations are mostly undefined. Here we report that the Hippo-YAP signaling, a key pathway that regulates cell proliferation and organ size, is under control of a new splicing switch. We show that TEAD4, the transcription factor that mediates Hippo-YAP signaling, undergoes alternative splicing facilitated by the tumor suppressor RBM4, producing a truncated isoform, TEAD4-S, which lacks N-terminal DNA-binding domain but maintains YAP-interaction domain. TEAD4-S is located in both nucleus and cytoplasm, acting as a dominant negative isoform to YAP activity. Consistently, TEAD4-S is reduced in cancer cells, and its re-expression suppresses cancer cell proliferation and migration, inhibiting tumor growth in xenograft mouse model.  Furthermore, TEAD4-S is reduced in human cancers, and patients with elevated TEAD4-S levels have improved survival.  Altogether these data reveal a novel RBM4-mediated splicing switch that serves to fine-tune Hippo-YAP pathway.

overall_design: Cell lines stably expressing YAP, YAP/TEAD4-S, YAP/TEAD4-FL, YAP/RBM4 and control vector were created, and the total RNA was purified from the cells using TRIzol reagents.  The polyadenylated RNAs were purified for construction of sequencing library using kapa TruSeq Total RNA Sample Prep kits (UNC High Throughput Sequencing Facility).

first: Yangfan

last: Qi

first: Jing

last: Yu

first: Wei

first: Yang


title: Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus

city: College Station

first: Masako

last: Suzuki

state: TX

address: 498 Olsen Blvd, Norman E. Borlaug Building 202C

department: Nutrition

country: USA

institute: Texas A&M University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: ChIP-seq analysis of Guanylate Cyclase Soluble Subunit Beta-3 (GUCY1B3 or sGCβ1) binding to chromatin DNA

city: washington

first: haijie

last: xiao

state: DC

address: 2300 eye street

department: Biochemistry

institute: george washington University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To identify sGCβ1 binding sites to chromatin DNA, we performed ChIP analysis by using anti-sGCβ1 antibody (Sigma G4405). We have successfully identified 4169 intervals. In this study, sGCβ1 was found to bind to many genes' promoter region.

overall_design: We used U-87 MG (ATCC® HTB-14) glioma cells which overexpress sGCβ1 (generated by us) to perform ChIP assay by using anti-sGCβ1 antibody (Sigma G4405) and genome-wide sGCβ1 binding was determined with sequencing. The ChIP DNA was processed into a standard Illumina ChIP-Seq library and sequence. The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the hg19 genome using the BWA algorithm with default settings. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. Intervals (= Peaks) were determined using the MACS peak finding algorithm.

first: Haijie

last: Xiao

first: Ka

last: Bian


title: Stem cell function and sensitivity to genotoxic stress is controlled by protein translation rates

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Whether protein synthesis and cellular stress response pathways interact to control stem cell functions is currently unknown. Here, we show that skin stem cells synthesise less protein than their immediate progenitors in vivo, even when forced to proliferate in a tumour model. Our analyses reveal that activation of stress response pathways drives both a global reduction of protein synthesis and altered translation of specific mRNAs that together promote stem cell functions and tumourigenesis. Mechanistically we show that inhibition of post-transcriptional cytosine-5 methylation locks stem cells in this distinct translational inhibition programme. Paradoxically, this stress-induced translation inhibition renders stem cells hypersensitive to genotoxic stress, as tumour regeneration after treatment with 5-fluorouracil is blocked. Thus, stem cells must revoke translation inhibition pathways to regenerate a tissue or tumour.

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


title: Comparative dynamic transcriptome analysis (cDTA-seq) and total RNA-seq of ATP-analog sensitive Kin28 budding yeast

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

summary: During transcription initiation, the TFIIH-kinase Kin28/Cdk7 marks RNA polymerase II (Pol II) by phosphorylating the C-terminal domain (CTD) of its largest subunit. Here we describe a structure-guided chemical approach to covalently and specifically inactivate Kin28 kinase activity in vivo. This method of irreversible inactivation recapitulates both the lethal phenotype and the key molecular signatures that result from genetically disrupting Kin28 function in vivo. Inactivating Kin28 impacts promoter release to differing degrees and reveals a “checkpoint” during the transition to productive elongation. While promoter-proximal pausing is not observed in budding yeast, inhibition of Kin28 attenuates elongation-licensing signals, resulting in Pol II accumulation at the +2 nucleosome and reduced transition to productive elongation. Furthermore, upon inhibition, global stabilization of mRNA masks different degrees of reduction in nascent transcription. This study resolves long-standing controversies on the role of Kin28 in transcription and provides a rational approach to irreversibly inhibit other kinases in vivo.

overall_design: Total RNA was collected from wild-type and analog-sensitive Kin28 strains treated with reversible inhibitor 1-NAPP-1, irreversible inhibitor CMK, and solvent control DMSO. Equivalent ratios of S. pombe : S. cerevisiae cells were added to each sample before RNA extraction for normalization of read counts after sequencing. Nascent RNA was purified from total RNA by 4-thiouracil labeling, biotinylation, and streptavidin-pulldown. As a negative control, nascent RNA was also extracted from total RNA from cells that had not been treated with 4-thiouracil.

middle: Z

first: Sandra

middle: C

last: Tseng


title: Transcriptomic analysis of VBNC Escherichia coli O157:H7 induced by HPCD by high-throughput Illumina sequencing technology

status: Public on Jun 19 2016

first: Feng

last: Zhao

address: No. 17 Qinghua East Road, Haidian District

department: College of Food Science and Nutritional Engineering

institute: China Agricultural University

summary: Escherichia coli O157:H7 can cause haemorrhagic colitis and haemolytic uremic syndrome (HUS) in humans. This pathogen has been implicated in large food-borne outbreaks all over the world. By investigating the implicated salted salmon roe, Makino et al. (2000) suggested that E. coli O157:H7 in the viable but nonculturable (VBNC) state should be the culprit of the outbreak in Japan. High pressure CO2 (HPCD), one of the non-thermal pasteurization techniques, is an effective means to inactivate microorganisms. But in the previous study, we have demonstrated for the first time that HPCD could induce E. coli O157:H7 into the VBNC state, which poses a potential health risk to HPCD-treated products. In order to explore the potential formation mechanisms of VBNC E. coli O157:H7 induced by HPCD, the high-throughput Illumina RNA-seq transcriptomic analysis was conducted for E. coli O157:H7 cells treated at 5 MPa and 25 ℃ for 40 min (VBNC cells) and exponential-phase cells (the control). Finally, 97 genes that differentially transcribed between VBNC state and the control were obtained, with 22 genes up-regulated and 75 genes down-regulated in VBNC cells. These differentially expressed genes were classified in a variety of functional categories, including central metabolic processes, gene replication and expression, cell division, general stress response, respiration, membrane biosynthesis and transport and pathogenicity. Based on these differentially expressed genes, we suggest putative formation mechanisms of VBNC cells induced by HPCD. The finding will provide theoretical foundation for restraining the VBNC state formation under HPCD processing.

overall_design: Whole mRNA profiles of Escherichia coli O157:H7 in the VBNC state and the exponential phase were generated using Illumina sequencing technology and differentially expressed genes were anylyzed.

first: Xiaojun

last: Liao


title: Ribosome Profiling of mouse skin squamous tumours

summary: Purpose: Ribosome profiling has revolutionized systems-based analysis and which produces a “global snapshot” of all the ribosomes translationally active in a cell at a particular moment. The goals of this study are to first apply ribosome profiling to in vivo samples for the first time and in particular to stem cells and tumours and second to determine which mRNAs are being actively translated in these particular situations. Although much is known about gene expression regulation, little is known about how protein translation regulation can affect stem cell differentiation and tumour progression. Methods: several replicates of  ribosome and mRNA profiles of wild-type (WT) and NSun2 -/- mouse skin squamous tumours were generated by deep sequencing, using Illumina HiSeq platform. Results: Our analyses reveal that activation of stress response pathways in vivo drives both a global reduction of protein synthesis and altered translation of specific mRNAs that together promote stem cell functions and tumourigenesis.

overall_design: Ribosome profiles of wild-type (WT) and NSun2 -/- mouse skin squamous tumours

last: Blanco


title: Transfer RNA (tRNA) processing and RNA m5C-methylation profiles of mouse skin squamous tumours

summary: Purpose: High-throughput RNA sequencing has accelerated discovery of the complex regulatory roles of small RNAs, such those derived from tRNAs. Also recent advances in high-throughput RNA sequencing has revealed the complex RNA modification landscape and the complex role these nucleosides modifactions have in cell signalling, stem cell biology, development and cancer. The goal of this study is to establish how m5C-tRNA methylation and tRNA-derived small RNAs can affect stem cell fucntion in cancer. Methods: four replicates of  tRNAs and RNA buisulphite sequencing of wild-type (WT) and NSun2 -/- mouse skin squamous tumours were generated by deep sequencing, using Illumina HiSeq platform. Results: Our analyses reveal that inhibition of post-transcriptional cytosine-5 methylation locks stem cells in this distinct translational inhibition programme that results in tumour progression but that also sentizes cancer cells to genotoxic stress.

overall_design: Transfer RNA (tRNA) sequencing and RNA Bisulphite sequencing of wild-type (WT) and NSun2 -/- mouse skin squamous tumours


title: A damage independent role for 53BP1 that impacts break order and Igh architecture during CSR

city: New York

first: Jane

last: Skok

state: NY

address: 550 First Ave, Smillow 307

institute: NYU

summary: During Class Switch Recombination (CSR) B cells replace the Igh Cμ/δ exons with another downstream constant region exon (CH), altering the antibody isotype. CSR occurs through the introduction of AID-mediated double strand break (DSBs) in switch regions and subsequent ligation of broken ends. Here we developed an assay to investigate the dynamics of DSB introduction in individual cells.  We demonstrate that the upstream switch region Sμ is always targeted first during recombination and that the mechanism underlying this control relies on 53BP1. Surprisingly, regulation of break order occurs through residual binding of 53BP1 to chromatin before the introduction of damage and independent of its established role in DNA repair. Using chromosome conformation capture we show that 53BP1 mediates changes in chromatin architecture that affect break order. Finally, our results explain how changes in Igh architecture in the absence of 53BP1 could promote inversional rearrangements that compromise CSR.

overall_design: High Resolution 4C was performed in resting and activated B cells using a bait on the Eμ enhancer

first: Pedro

middle: P

last: Rocha

first: Ramya

last: Raviram

middle: A


title: Profiling of upstream enhancers of SHOX in idiopathic short stature and functional characterization of the cis-regulatory landscape of SHOX

city: Seville

first: Ana

last: Fernandez-Miñan

address: Crta. Utrera, km.1

country: Spain

institute: CABD-CSIC-UPO

summary: SHOX mutations and deletions of the downstream regulatory region have been reported in cases with idiopathic short stature (ISS) and Leri-Weill dyschondrosteosis (LWD). Recently, a deletion and duplication of upstream enhancers have been described in ISS. Here, we aimed to evaluate the contribution of upstream copy number variations (CNVs) to the pathogenesis of ISS, to validate the enhancer role of the upstream enhancers in human cells, and to characterize the chromatin architecture of the cis-regulatory landscape of SHOX. CNV analysis of three upstream conserved non-coding elements (CNEs), CNE-5, CNE-3 and CNE-2, in 501 ISS referrals with no established molecular diagnosis revealed two deletions and one duplication. Enhancer activity of the upstream CNEs was corroborated by luciferase assays in human osteosarcoma U2OS cells. In addition, all three CNEs overlap with reported H3K27ac ChIP-seq marks in human embryonic limb buds. To characterize the chromatin interaction profile of the SHOX region, chromosome conformation capture (4C-seq) was performed in chicken embryo limb buds and in U2OS cells, revealing interactions of the upstream CNEs with the SHOX promoter. Moreover, the 4C-seq interaction maps and H3K27ac marks indicated that the cis-regulatory landscape of SHOX encompasses 1 Mb, suggesting additional cis-regulatory elements controlling SHOX.In conclusion, we showed that upstream CNVs of SHOX are rare in ISS and have incomplete penetrance. Chromatin interaction maps, luciferase assays and H3K27ac marks further support an enhancer function for the upstream CNEs. Finally, we demonstrated that the cis-regulatory landscape of SHOX is larger than previously anticipated potentially harboring novel cis-regulatory elements, which may be involved in the pathogenesis of molecularly unsolved ISS cases..

sample_organism:
Gallus gallus
Homo sapiens

platform_organism:
Gallus gallus
Homo sapiens

overall_design: 4C-seq samples forshox gene promoter in different samples: HH28 chicken limbs and human U2OS cells

first: José

last: Gómez-Skarmeta

last: Fernández-Miñán


title: A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition [CaptureC]

status: Public on Jun 15 2016

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

summary: Capture-C of G1E ER4 cell line in a nocodazole arrest-release experiment anchored at multiple gene promoters to quantify long-range chromatin interactions at the mitosis-G1 transition.

overall_design: Nocodazole arrest-release in G1E ER4 cell line under conditions of 13h estradiol treatment (unless otherwise specified as 'unin', i.e. no estradiol treatment).

first: Chris

last: Hsiung

first: Gerd

last: Blobel


title: ChIP-seq from forebrain (ENCSR041KEJ)

status: Public on Jun 22 2016

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
H3K9me3 ChIP-seq on embryonic 13.5 day mouse forebrain

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


title: A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition


title: Next Generation Sequencing of liver and subcutaneous fat tissues obtained from obese subjects

city: Gothenburg

first: Adil

last: Mardinoglu

state: Gothenburg

address: Kemivägen 10

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

summary: Patients had low calorie diet weight reduction run in prior to the day of surgery. The human liver and subcutaneous fat tissue samples were obtained from 12 obese  subjects undergoing bariatric surgery and then used for the mRNA expression analyses.

overall_design: mRNA profiles of human liver and subcutaneous fat tissue samples were generated by RNA sequencing using Illumina HiSeq 2500.

first: Sunjae

last: Lee

first: Cheng

last: Zhang

first: Björn

last: M. Hallström


title: A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition [Pol2ChIP]

summary: ChIP-seq of total Pol II in G1E ER4 cell line at time points after mitosis.

overall_design: Nocodazole arrest-release in G1E ER4 cell line under conditions of 13h estradiol treatment.


title: ChIP-seq from neural tube (ENCSR044SNE)

summary:
H3K4me3 ChIP-seq on embryonic 15.5 day mouse neural tube

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


title: A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition [Hist]

summary: ChIP-seq of H3K27Ac in the G1E-ER4 cell line in prometaphase (nocodazole block), between anaphase-telophase (nocodazole release 40min), and interphase (asynchronous).


title: Regulation of chromatin structure by Set1 H3K4 methyltransferase and Jhd2 H3K4 demethylase [histone turnover]

city: Salt Lake City

first: Timothy

middle: J

last: Parnell

state: UT

address: 2000 Circle of Hope

institute: Huntsman Cancer Institute

summary: Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic role in transcription and chromatin dynamics remains poorly understood. Here, we investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase and H3K4 demethylase, respectively, in S. cerevisiae. Our data show that Set1 and Jhd2 predominantly co-regulate transcription. We find combined activities of Set1 and Jhd2 via H3K4 methylation contribute to positive or negative transcriptional regulation at shared target genes. Providing mechanistic insights, our data reveal that Set1 and Jhd2 together control nucleosomal occupancy during transcriptional co-regulation. Moreover, we find a remarkable genome-wide co-regulation of nucleosome and chromatin structure by Set1 and Jhd2 at different groups of transcriptionally active or inactive genes and at different regions within yeast genes. Overall, our study prompts a model wherein combined actions of Set1 and Jhd2 via H3K4 methylation−demethylation control chromatin dynamics during various facets of transcriptional regulation.

overall_design: Genome-wide nucleosome maps were generated from three different yeast strains representing no tag control, 8V5-Set1 and Jhd2-12V5. Cells were cross-linked with formaldehyde, spheroplasted, nuclei were isolated and chromatin was prepared using micrococcal nuclease digestion, chromatin immunoprecipitation was performed using an epitope-tag specific antibody, libraries were prepared from ChIP and input DNA, sequenced, and analyzed separately.

first: Saravanan

last: Ramakrishnan

first: Srijana

last: Pokhrel

first: Sowmiya

last: Palani

first: Christian

last: Pflueger

first: Bradley

middle: R

last: Cairns

first: Srividya

last: Bhaskara

first: Mahesh

middle: B

last: Chandrasekharan


title: ERRalpha mediates metabolic adaptations that drive lapatinib resistance in breast cancer (ERRalpha binding profiles in breast cancer cells by ChIP-seq)

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University

summary: Ablation of ERRalpha significantly delays ERBB2-induced mammary tumorigenesis and ERRalpha regulates genes of the ERBB2 amplicon. To further investigate the relationship between ERRalpha activity and RTK signaling, we mapped ERRalpha binding sites in SKBr3 cells upon EGF treatment or heregulin treatment. Inhibition of ERBB2 signaling using the RTK inhibitor lapatinib impacts on ERRalpha stability, while cells resistant to lapatinib treatment exhibit restored ERRalpha expression. We therefore mapped ERRalpha binding sites in parental (sensitive) cells (pSKBr3) as well as in lapatinib-resistant cells (LRSKBr3).

overall_design: ChIP-Seq analysis of ERRalpha binding profile in SKBr3 or BT-474 breast cancer cells.

last: Giguere


title: Regulation of chromatin structure by Set1 H3K4 methyltransferase and Jhd2 H3K4 demethylase [H3K4me ChIP-seq]

sample_organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

overall_design: Genome-wide nucleosome maps were generated from three different yeast strains representing wild type control, Set1G990E hyperactive mutant and jhd2 null mutant. Two independent biological samples were grown for each S. cerevisiae strain. S. cerevisiae cells were mixed with C. glabrata cells at 2:1 ration before chromatin preparation by sonication, chromatin immunoprecipitation was performed using H3K4 methylation specific antibodies, libraries were prepared from ChIP and input DNA, sequenced, and analyzed separately.


title: Regulation of chromatin structure by Set1 H3K4 methyltransferase and Jhd2 H3K4 demethylase [ChIP-seq]

overall_design: Genome-wide nucleosome maps were generated from three different yeast strains representing no tag control, 8V5-Set1 and Jhd2-12V5. Cells were cross-linked with formaldehyde, spheroplasted, nuclei were isolated and chromatin was prepared using micrococcal nuclease digestion , chromatin immunoprecipitation was performed using an epitope-tag specific antibody, libraries were prepared from ChIP and input DNA, sequenced, and analyzed separately.


title: The landscape of accessible chromatin in mammalian pre-implantation embryos (ChIP -Seq)

first: Wei

last: Xie

address: zhongguancun beidajie

institute: Tsinghua University

summary: In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development.

overall_design: Mouse 2-cell embryos were obtained from crosses of C57BL/6N x PWK for ChIP-seq samples.

first: Jingyi

last: Wu

first: Bo

last: Huang

first: He

last: Chen


title: Activation of GCN2 by Ribosome Stalling Links Translation Elongation with Translation Initiation

city: Farmington

first: Jeffrey

last: Chuang

state: CT

address: 263 Farmington Avenue

department: Computational Biology

institute: The Jackson Laboratory for Genomic Medicine

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

overall_design: Refer to individual Series


title: Expression profiling of fission yeast strains: wild-type, erh1∆, and ccr4∆

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

summary: We report gene expression profiling in the fission yeast Schizosaccharomyces pombe. We performed high-throughput sequencing of RNA isolated from wild-type, erh1∆, and ccr4∆ strains. We find that many meiotic gene containing degradation sequence DSR are expressed in vegetative erh1∆, while these meiotic mRNAs do not increase in ccr4∆, indicating that Erh1 and Ccr4 target different set of genes during vegetative growth.

overall_design: RNA sequencing in wild-type, erh1∆ and ccr4∆ strains. Two biological replicates for erh1∆ and ccr4∆, and one sample for wild-type because we already reported wild-type data previously.

first: Tomoyasu

last: Sugiyama

first: Venkata

last: Chalamcharla

first: Gobi

last: Thillainadesan

first: Vanivilasini

last: Balachandran

first: Jothy

last: Dhakshnamoorthy

middle: I


title: Expression profiling and ChIP-chip of Schizosaccharomyces pombe strains wildtype, erh1∆, and ccr4∆

type: Genome binding/occupancy profiling by genome tiling array


title: Image based identification and targeting of cancer stem cells in pancreatic adenocarcinoma (PDAC)

city: La Jolla

first: Roman

last: Sasik

address: 9500 Gilman Dr.

department: Center for Computational Biology and Bioinformatics

institute: UCSD

summary: Purpose: The goals of this study were to identify quantitative gene expression differences between wild type,  Musashi1 null, Msuashi2 null and Musashi1/Musashi2 null MIAPaCa2 pancreatic cancer cells

overall_design: mRNA profiles of MIA PaCa-2 cancer cells were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.

first: Raymond

last: Fox


title: Comparative transcriptomic analysis of human and Drosophila extracellular vesicles reveals extensive conservation

city: Montreal

first: Fabio

middle: Alexis

last: Lefebvre

state: Quebec

address: 110 Ave des Pins

department: RNA biolog

institute: IRCM

summary: Extracellular vesicles (EVs) are membrane-enclosed nanoparticles containing specific repertoires of genetic material. In mammals, EVs can mediate the horizontal transfer of various cargos and signaling molecules, notably miRNA and mRNA species. Whether this form of intercellular communication prevails in other metazoans remains unclear. Here, we report the first parallel comparative morphologic and transcriptomic characterization of EVs from Drosophila and human cellular models. Electronic microscopy revealed that Drosophila, like human cells release exosome-like EVs with diameter ranging from 30 to 200 nm, which contain complex populations of transcripts. RNA-seq identified abundant ribosomal RNA pseudogenes and retrotransposons in human and Drosophila EVs. Vault RNAs and Y RNAs abounded in human samples, whereas small nucleolar RNAs involved in pseudouridylation were most prevalent in Drosophila EVs. Numerous mRNAs were identified, largely consisting of exonic sequences displaying full-length read coverage and enriched for translation and electronic transport chain functions. By analogy with human systems, these extensive similarities suggest that EVs could also enable RNA-mediated intercellular communication in Drosophila.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: We performed RNA-seq on extracellular vesicles purified from of human and Drosophila cell line cultures. S2R+ and D17 Drosophila EVs were analyzed, along with human A431 and HepG2 EVs.  No ribosomal RNA depletion or polyA selection was performed on EV samples. For comparative analyses, we also analyzed total cellular RNA from Drosophila D17 and human HepG2. Ribodepletion was performed on cellular samples.

first: Louis

last: Benoit Bouvrette

first: Lilyanne

last: Perras

first: Alexis

last: Blanchet-Cohen

first: Delphine

last: Garnier

first: Janusz

last: Rak

first: Éric

last: Lécuyer


title: Interleukin-23-induced transcription factor Blimp1 promotes pathogenicity of T helper 17 cells

first: Yuka

last: Kanno

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

summary: Interleukin-23 (IL-23) is a pro-inflammatory cytokine required for the pathogenicity of T  helper 17 (Th17) cells but the molecular mechanisms governing this process remain  unclear. We identified the transcription factor Blimp-1 (Prdm1) as a key IL-23-induced  factor that drove the inflammatory function of Th17 cells. In contrast to thymic deletion  of Blimp-1, which causes T cell development defects and spontaneous autoimmunity,  peripheral deletion of this transcription factor resulted in reduced Th17 activation and  reduced severity of autoimmune encephalomyelitis. Furthermore, genome wide  occupancy and overexpression studies in Th17 cells revealed that Blimp-1 co-localized  with transcription factors RORγt, STAT-3 and p300 at the Il23r, Il17a/f and Csf2  cytokine loci to enhance their expression. Blimp-1 also directly bound to and repressed  cytokine loci Il2 and Bcl6. Taken together, our results demonstrate that Blimp-1 is an  essential transcription factor downstream of IL-23 that acts in concert with RORγt to  activate the Th17 inflammatory program.

overall_design: Genome-wide binding analysis of Blimp1 from in vitro generated T effector and regulatory cells

first: R

last: Jain

first: Y

last: Chen

first: B

last: Joyce

first: G

last: Vahedi

first: K

last: Hirahara

first: W

middle: M

last: Blumenschein

first: S

last: Sukumar

first: C

last: Haines

last: Sadekova

first: T

last: McClanahan

first: M

last: McGeachy

first: J

last: O'Shea

first: D

last: Cua


title: UMI-4C for quantitative and targeted chromosomal contact profiling

city: Rehovot

first: Omer

last: Schwartzman

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

summary: We developed a targeted chromosome conformation capture (4C) approach that uses unique molecular identifiers (UMI) to derive high complexity quantitative chromosome contact profiles with controlled signal to noise ratios. We demonstrate that the method improves the sensitivity and specificity for detection of long-range chromosomal interactions, and that it allows the design of interaction screens with predictable statistical power. UMI-4C robustly quantifies contact intensity changes between cell types and conditions, opening the way toward incorporation of long-range interactions in quantitative models of gene regulation.

overall_design: We constructed UMI-4C profiles of 13 different genomic loci (viewpoints) in five different cell lines, in order to study the 3D chromatin contact maps of these selected loci. The coordinates for these viewpoints are: G1p1 chrX:48646542;  baitG1_3_5kb chrX:48641393; bait_50kb chrX:48595987; bait_165kb chrX:48476525; ANK1 chr8:41654693;  hbb_3HS chr11:5221346; hbb_HBB chr11:5248714; hbb_HBBP1_G1 chr11:5266532;  HBB_HBE chr11:5292159; HBB_HS2 chr11:5301345; HBB_HS3 chr11:5306690; HBB_HS5 chr11:5313539; HBB_HBD chr11:5256597

first: Amos

last: Tanay


title: Methylation interactions in Arabidopsis hybrids require RNA-directed DNA methylation and are influenced by genetic variation

city: Boston

first: Yanqiang

last: Li

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

summary: DNA methylation is a conserved epigenetic mark in plants and many animals. How parental alleles interact in progeny to influence the epigenome is poorly understood. We analyzed the DNA methylomes of Arabidopsis Col and C24 ecotypes, and their hybrid progeny. Hy- brids displayed nonadditive DNA methylation levels, termed meth- ylation interactions, throughout the genome. Approximately 2,500 methylation interactions occurred at regions where parental DNA methylation levels are similar, whereas almost 1,000 were at differ- entially methylated regions in parents. Methylation interactions were characterized by an abundance of 24-nt small interfering RNAs. Furthermore, dysfunction of the RNA-directed DNA methylation pathway abolished methylation interactions but did not affect the increased biomass observed in hybrid progeny. Methylation interac- tions correlated with altered genetic variation within the genome, suggesting that they may play a role in genome evolution.

overall_design: Whole genome bisulfite sequencing and small RNA sequencing of the wild type and nrpd1nrpe1 double mutant background of parent Col ,C24, the hybrid ColXC24 and C24XCol to explore the role of the RdDM pathway in DNA methylation interactions.

first: Qingzhu

last: Zhang

first: Dong

last: Wang

first: Li

last: He

first: Lan

last: Yang

first: Liang

last: Zeng

first: Cheng

last: Zhao

first: Huan

last: Huang

first: Huiming

first: Heng

first: Zhaobo

last: Lang

first: Jian-Kang

last: Zhu


title: Crohn's disease risk variant in GPR65 alters lysosomal function

first: Ramnik

last: Xavier

address: 185 Cambridge Street

institute: Massachusetts General Hospital

summary: Using an siRNA screen we identify a role for GPR65 in the defense against intracellular pathogens. Epithelial cells and macrophages lacking GPR65 exhibited impaired clearance of intracellular bacteria as well as an accumulation of aberrant phagosomes and lysosomes. Transcriptional profiling revealed changes in genes associated with lysosomal function.

overall_design: Bone marrow-derived macrophages from WT or Gpr65-/- mice were harvested for RNA analysis.

first: K

last: Lassen

first: G

last: Goel

first: R


title: Transcriptional regulation by Set1 H3K4 methyltransferase and Jhd2 H3K4 demethylase

first: Timothy

last: Parnell

summary: Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic role in transcription and chromatin dynamics remains poorly understood. Here, we investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase and H3K4 demethylase, respectively, in S. cerevisiae. Our data show that Set1 and Jhd2 predominantly co-regulate transcription. To further understand the role for H3K4 methylation, we overexpressed Flag epitope-tagged SET1-G990E (a dominant hyperactive allele of SET1) in yeast using the constitutive ADH1 promoter (ADH1p). As a control, we also overexpressed Flag epitope-tagged wild type SET1 in yeast. Analysis of gene expression in set1-null, jhd2-null and wild type SET1 or hypeactive SET1-G990E overexpressing mutants together revealed that the transcriptional regulation at a sub-set of genes, inclduing those governing glycogen metabolism and ribosome biogenesis, is highly sensitive to any change (i.e., loss or gain) in H3K4 methylation levels. Overall, we find combined activities of Set1 and Jhd2 via dynamic modulation of H3K4 methylation contribute to positive or negative transcriptional regulation at shared target genes.

overall_design: Gene expression changes were generated from five different yeast strains representing wild type control, set1 null and jhd2 null mutants, and  wild type SET1 or dominant hyperacive SET1-G990E overexpressing mutants. Three independent biological samples were grown for each strain, total RNA was isolated, libraries were prepared, sequenced, and analyzed separately.

first: Saravanan

last: Ramakrishnan

first: Srijana

last: Pokhrel

first: Christian

last: Pflueger

first: Bradley

last: Cairns

first: Srividya

last: Bhaskara

first: Mahesh

last: Chandrasekharan


title: Rocaglamide A converts RNA helicase eIF4A into a sequence-specific translational repressor

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: S205 Bioscience Bldg. 2-1 Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

summary: Rocaglamide A (RocA) typifies a novel class of protein synthesis inhibitors that selectively kill aneuploid tumor cells and repress translation of specific mRNAs. RocA targets eukaryotic initiation factor 4A (eIF4A), the prototypical DEAD-box RNA helicase, and its mRNA selectivity is proposed to reflect highly structured 5′ UTRs that are very dependent on eIF4A-mediated unwinding. Here, we show that secondary structure in 5′ UTRs is only a minor determinant for RocA selectivity and RocA does not repress translation by reducing eIF4A activity. Rather, in vitro and in vivo, RocA clamps eIF4A onto a specific sequence motif even after ATP hydrolysis. This artificially clamped eIF4A blocks 43S scanning, leading to premature, upstream translation initiation and reducing gene expression on transcripts bearing the RocA-eIF4A target sequence. In elucidating the mechanism of this lead anti-cancer compound and explaining its mRNA selectivity, we provide the first example of a drug stabilizing sequence-specific RNA-protein interactions.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design:
Ribosome profiling, mRNA-Seq, RIP-Seq, and Bind-n-Seq
Ribosome profiling for sample 1-5, and 11-15.  Sample1 and 2  are replicates of control of DMSO treatment for sample 3-5, and 11, with RocA and PP242  treatments. Sample 12 and 13 are replicates of control of DMSO treatment for sample 14 and 15 with Hipp treatments.
mRNA-Seq for sample 6-10.  Sample 6 and 7  are replicates of control of DMSO treatment for sample 8-10 with RocA treatments.
RIP-Seq for 16-19. Sample 16 and 17  are replicates of control of DMSO treatment for sample 18-19 with RocA treatments.
Bind-n-Seq for 20-23. Sample 21 is control of DMSO treatment for sample 22-23 with RocA treatments. Sample 20 is a input contol for protein-bound fraction of sample 21.
We stably expressed SBP (streptavidin binding peptide)-tagged eIF4A in HEK 293T-REx cells and purified it via M270 streptavidin beads (life techonologies).

first: Stephen

middle: N

last: Floor

first: Nicholas

middle: T

last: Ingolia


title: Set1 H3K4 methyltransferase and Jhd2 H3K4 demethylase

platform_organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus


title: The landscape of accessible chromatin in mammalian pre-implantation embryos

city: Beijing

first: Wei

last: Xie

summary:
In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development.

This SuperSeries is composed of the SubSeries listed below.


title: Chronological expression data from mouse skeletal muscle stem cells

city: Paris

first: Sonia

last: Alonso-Martin

address: 105 bd de l'Hôpital

department: Development and stem cells

country: France

institute: Myology Research Center U974-INSERM - UPMC-Paris VI - Institut de Myologie

summary: Satellite cells are the primary source of stem cells for skeletal muscle growth and regeneration. Since adult stem cell maintenance involves a fine balance between intrinsic and extrinsic mechanisms, we performed genome-wide chronological expression profiling to identify the transcriptomic changes involved in acquisition of muscle stem cell characteristics.

overall_design:
Muscle samples were isolated from the trunk during development, postnatally and in adult and aged Pax3GFP/+ mice. After digestion, GFP cells were purified via FACS and process for RNA extraction and hybridization on Affymetrix microarrays (Affymetrix Mouse Genome 430 2.0 Arrays).
The different ages selected for sample isolation were E11.5-E12.5-E13.5-E14.5-E15.5-E17.5-P1-P12-1MO-2MO-18MO (E, Embryonic days; P, Postnatal days; MO, age in months), covering embryonic and fetal progenitors and proliferant, quiescent satellite cells. The eleven stages were done in triplicate for E11.5-E12.5-E14.5-E15.5-1MO-2MO-18MO, twice for E13.5, 4 times for P1-P12 and 5 times for E17.5, so 36 samples included in the microarray.

first: Anne

last: Rochat

first: Aurelién

last: de Reyniès

first: Fred

last: Relaix


title: The β-catenin/CBP-antagonist ICG-001 inhibits pediatric glioma tumorigenicity in a Wnt-independent manner

status: Public on Jun 14 2016

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: In pediatric glioma cell lines, treatment with ICG-001 had no inhibitory effect on canonical Wnt-target genes but induced significant up regulation of various known β-catenin target genes in both cell lines and top 20 GO-annotations of down-regulated genes by ICG-001  were associated with biosynthetic and metabolic processes and cell cycle division processes.

overall_design: Pediatric cell lines were treated with ICG-001 or DMSO for 48h

first: Maria

last: Wiese

first: Neele

last: Walther

first: Christof

last: Kramm

last: Salinas-Riester


title: The landscape of accessible chromatin in mammalian pre-implantation embryos (ATAC-Seq)

overall_design: Mouse preimplantation embryos were obtained from crosses of C57BL/6N and DBA/2N. ATAC-seq was performed in these embryos at various stages in preimplantation development.

first: Jingyi

last: Wu

first: Bo

last: Huang

first: He

last: Chen


title: Analyses of blue light (BL) and CRY-regualted genes and genes dependent on auxin receptors by RNA-seq

city: Shanghai

first: Sheng-Bo

last: He

address: 800 Rd Dongchuan

institute: Shanghai Jiao Tong University

summary: Total RNA was extracted from samples including dark-grown WT and tir1 afb123, blue light-grown WT and cry1 cry2 seedlings in continuous conditions for 4.5 days and subjected to high throughput sequencing. Light and auxin co-regulate a variety of developmental processes. This study reveals the molecular basis for light and auxin crosstalk by analyzing gene expression profile under control of both signals.

overall_design: mRNA from dark-grown WT, BL-grown WT, BL-grown BL photoreceptors, and dark-grown auxin receptors was sequenced to analyze the genes regulated by CRY-mediated BL signaling and TIR1/AFBs-mediated auxin signaling.

first: Hong-Quan

last: Yang


title: mRNA cap methylation in pluripotency and differentiation

city: Dundee

first: Victoria

last: Cowling

address: Dow Street

department: School of Life Sciences

country: United Kingdom

institute: University of Dundee

summary: The mRNA cap recruits factors essential for transcript processing and translation initiation.  We report that regulated mRNA cap methylation is a feature of embryonic stem cell (ESC) differentiation.  Expression of the mRNA cap methyltransferase activating subunit, RAM, is elevated in ESCs resulting in high levels of mRNA cap methylation and expression of Oct4 and Sox2 and other pluripotency-associated factors.  During neural differentiation, RAM is suppressed which is required for loss of Oct4 and Sox2 and correct expression of neural markers.

overall_design: Cells were treated with control or RAM siRNA and cytosolic RNA or polysome RNA (actively translated) was sequenced.

first: Olga

last: Suska


title: PI3K/AKT signaling regulates H3K4 methylation in breast cancer

first: Koen

last: Dreijerink

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute


title: Genetic lineage tracing defines myofibroblast origin and function in the injured heart

city: Cincinnati

first: Bruce

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

summary:
Cardiac fibroblasts convert to myofibroblasts with injury to mediate healing after acute myocardial infarction and to mediate long-standing fibrosis with chronic disease.  Myofibroblasts remain a poorly defined cell-type in terms of their origins and functional effects in vivo.
Methods: Here we generate Postn (periostin) gene-targeted mice containing a tamoxifen inducible Cre for cellular lineage tracing analysis. This Postn allele identifies essentially all myofibroblasts within the heart and multiple other tissues.
Results: Lineage tracing with 4 additional Cre-expressing mouse lines shows that periostin-expressing myofibroblasts in the heart derive from tissue-resident fibroblasts of the Tcf21 lineage, but not endothelial, immune/myeloid or smooth muscle cells. Deletion of periostin+ myofibroblasts reduces collagen production and scar formation after myocardial infarction. Periostin-traced myofibroblasts also revert back to a less activated state upon injury resolution.
Conclusions:  Our results define the myofibroblast as a periostin-expressing cell-type necessary for adaptive healing and fibrosis in the heart, which arises from Tcf21+ tissue-resident fibroblasts.

overall_design: Fluidigm C1 whole genome transcriptome analysis of lineage mapped cardiac myofibroblasts

first: Onur

last: Kanisicak

first: Phillip

last: Dexheimer

first: Hadi

last: Khalil

first: Malina

last: Ivey

first: Jason

last: Karch

first: Bryan

last: Maliken

first: Robert

last: Correll

first: Matthew

last: Brody

first: Suh-Chin

last: Lin

first: Michelle

last: Tallquist

first: Jeffery

last: Molkentin


title: Genome-wide KDM5A occupancy after MK2206/DMSO treatment of T47D cells

summary: We perfomed ChIP-seq using KDM5A antibodies in T47D cells after 24 hour treatment with the AKT inhibitor MK2206 or DMSO. We show that the cistrome of the H3K4 demethylase KDM5A is affected by AKT inhibition.

overall_design: Comparison of genome-wide KDM5A binding after AKT inhibition vs vehicle

first: Anna

last: Groner

first: Jennifer

last: Spangle


title: Messenger RNA expression after MK2206/DMSO treatment of T47D cells

summary: We performed RNA-seq in T47D cells after 24 hour treatment with the AKT inhibitor MK2206 or DMSO. We show that a group of transcripts is differentailly expressed after AKT inhibition.

overall_design: Comparison of mRNA levels using RNA-seq after AKT inhibition vs vehicle


title: Reciprocal regulation of cardiac chromatin by the chromatin structural proteins HMGB and CTCF

city: Los Angeles

first: Tom

last: Vondriska

address: 650 Charles E Young Dr, BH553

institute: UCLA

summary: Transcriptome remodeling in heart disease occurs through the coordinated actions of transcription factors, histone modifications and other chromatin features at pathology-associated genes. It remains unknown the extent to which genome-wide chromatin reorganization also contributes to the pathologic gene expression. We examined the roles of two chromatin structural proteins, CTCF (CCCTC-binding factor) and HMGB2 (high mobility group protein B2), in regulating pathologic transcription and chromatin remodeling. Our data demonstrate a reciprocal relationship between HMGB2 and CTCF in controlling aspects of chromatin structure and gene expression. Both proteins regulate each other’s expression as well as transcription in cardiac myocytes: however, only HMGB2 does so in a manner that involves global reprogramming of chromatin accessibility. We demonstrate that the actions of HMGB2 on local chromatin accessibility are conserved across genomic loci, whereas the effects on transcription are loci-dependent and emerge in concert with histone modification and other chromatin features. Lastly, while both proteins share gene targets, HMGB2 and CTCF neither bind these genes simultaneously nor do they physically co-localize in myocyte nuclei. Our study uncovers a previously unknown relationship between these two ubiquitous chromatin proteins and provides a mechanistic explanation for how HMGB2 regulates gene expression and cellular phenotype. Furthermore, we demonstrate direct evidence for hierarchical remodeling of chromatin on a genome-wide scale in the setting of cardiac disease.

overall_design: Examination of a chromatin structural protein, HMGB2 in basal and agonist-treated cells.

first: Haodong

last: Chen


title: Genome-wide H3K4me3 after MK2206/DMSO treatment of T47D cells

first: Koen

last: Dreijerink

summary: We perfomed ChIP-seq using H3K4me3 antibodies in T47D cells after 24 hour treatment with the AKT inhibitor MK2206 or DMSO. We demonstrate that at a selected group of loci H3K4me3 is affected by AKT inhibition.

overall_design: Comparison of genome-wide H3K4me3 binding after AKT inhibition vs vehicle


title: Transcriptome sequencing reveals aberrant alternative splicing in Huntington's disease

first: Yu-Ting

last: Tseng

state: California

address: 650 Charles E. Young Drive South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: University of California, Los Angeles

summary: Huntington’s disease (HD) is an autosomal dominant neurodegenerative disorder caused by a CAG expansion in the gene encoding Huntingtin (HTT). Transcriptome dysregulation is a major feature of HD pathogenesis, as revealed by a large body of work on gene expression profiling of tissues from human HD patients and mouse models. These studies were primarily focused on transcriptional changes affecting steady-state overall gene expression levels using microarray based approaches. A major missing component however has been the study of transcriptome changes at the post-transcriptional level, such as alternative splicing. Alternative splicing is a critical mechanism for expanding regulatory and functional diversity from a limited number of genes, and is particularly complex in the mammalian brain. Here we carried out a deep RNA-seq analysis of 7 human HD brains and 7 controls to systematically discover aberrant alternative splicing events and characterize potential associated splicing factors in HD. We identified 593 differential alternative splicing events between HD and control brains. Using an expanded panel of 54 brain tissues from patients and controls, we also identified 9 splicing factors exhibiting significantly altered expression levels in HD patient brains. Moreover, follow-up molecular analyses of one splicing factor PTBP1 revealed its impact on disease-associated splicing patterns in HD. Collectively, our data provide genomic evidence for widespread splicing dysregulation in HD brains, and suggest the role of aberrant alternative splicing in the pathogenesis of HD

overall_design: RNA-seq analysis of the BA4 motor cortex of 7 control and 7 Huntington's disease patients. 1.5 ug of total RNA was used for RNA-seq library preparation using the TruSeq™ Stranded mRNA LT Sample Prep Kit (Illumina). 100x2 bp paired-end RNA-seq reads were generated on a HiSeq 2000 sequencer.

first: Yi

last: Xing

first: Lan

first: Juw

middle: W

last: Park

first: Beverly

last: Davidson


title: Regulation of chromatin structure by Set1 H3K4 methyltransferase and Jhd2 H3K4 demethylase

first: Timothy

last: Parnell

address: 2000 Circle of Hope

institute: Huntsman Cancer Institute

summary: Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic role in transcription and chromatin dynamics remains poorly understood. Here, we investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase and H3K4 demethylase, respectively, in S. cerevisiae. Our data show that Set1 and Jhd2 predominantly co-regulate transcription. We find combined activities of Set1 and Jhd2 via H3K4 methylation contribute to positive or negative transcriptional regulation at shared target genes. Providing mechanistic insights, our data reveal that Set1 and Jhd2 together control nucleosomal occupancy during transcriptional co-regulation. Moreover, we find a remarkable genome-wide co-regulation of nucleosome and chromatin structure by Set1 and Jhd2 at different groups of transcriptionally active or inactive genes and at different regions within yeast genes. Overall, our study prompts a model wherein combined actions of Set1 and Jhd2 via H3K4 methylation−demethylation control chromatin dynamics during various facets of transcriptional regulation.

overall_design: Genome-wide nucleosome maps were generated from three different yeast strains representing wild type control, set1 null and jhd2 null mutants. Three independent biological samples were grown for each strain, nucleosomes were prepared by micrococcal nuclease digestion, libraries were prepared, mononculeosomal DNA was isolated, sequenced, and analyzed separately.

first: Saravanan

last: Ramakrishnan

first: Srijana

last: Pokhrel

first: Christian

last: Pflueger

first: Bradley

last: Cairns

first: Srividya

last: Bhaskara

first: Mahesh

last: Chandrasekharan


title: Examination of gene expression in cerebellum of mouse strains B6J, B6J-nmf205-/-, B6J-Gcn2-/- and B6J-nmf205-/-;Gcn2-/-.

first: Jeffrey

last: Chuang

address: 263 Farmington Avenue

institute: The Jackson Laboratory for Genomic Medicine

summary: Ribosome stalling during translation has recently been shown to cause neurodegeneration, yet the signaling   pathways triggered by stalled elongation complexes are unknown.  To investigate these pathways we   analyzed the brain of B6J-nmf205-/-   mice in which neuronal elongation complexes are stalled at AGA   codons due to deficiencies in a tRNA  Arg(UCU) tRNA and GTPBP2, a mammalian ribosome rescue factor.   Increased levels of phosphorylation of eIF2α (Ser51) were detected prior to neurodegeneration in these   mice and transcriptome analysis demonstrated activation of ATF4, a key transcription factor in the   integrated stress response (ISR) pathway. Genetic experiments showed that this pathway was activated by the eIF2α kinase, GCN2, in an apparent deacylated tRNA-independent fashion. Further we found that the ISR attenuates neurodegeneration in B6J-nmf205-/-   mice, underscoring the importance of cellular and stress context on the outcome of activation of this pathway.   These results demonstrate the critical interplay between translation elongation and initiation in regulating neuron survival during cellular stress.

overall_design: Examination of gene expression in cerebellum and hippocampus for 4 mice strains derived from C57BL/6J (B6J) strain. Microarray data was performed for 3 week and 5 week old mice in both cerebellum and hippocampus for B6J and B6J-nmf205-/- three replicates each. RNA-Seq data was perform on cerebellum of mice 3 weeks old, three replicates for each genotype: B6J, B6J-nmf205-/-, B6J-Gcn2-/- and B6J-nmf205-/-;Gcn2-/-.

first: Ryuta

last: Ishimura

first: Gabor

last: Nagy

first: Ivan

last: Dotu

middle: H

first: Susan

last: Ackerman


title: miR-126 Orchestrates an Oncogenic Program in B-Cell Precursor Acute Lymphoblastic Leukemia

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

summary: MicroRNA (miRNA)-126 is a known regulator of hematopoietic stem cell quiescence. We engineered murine hematopoiesis to express miRNA-126 across all differentiation stages. Thirty percent of mice developed monoclonal B cell leukemia, which was prevented or regressed when a tetracycline-repressible miRNA-126 cassette was switched off. Regression was accompanied by upregulation of cell-cycle regulators and B cell differentiation genes, and downregulation of oncogenic signaling pathways. Expression of dominant-negative p53 delayed blast clearance upon miRNA-126 switch-off, highlighting the relevance of p53 inhibition in miRNA-126 addiction. Forced miRNA-126 expression in mouse and human progenitors reduced p53 transcriptional activity through regulation of multiple p53-related targets. miRNA-126 is highly expressed in a subset of human B-ALL, and antagonizing miRNA-126 in ALL xenograft models triggered apoptosis and reduced disease burden.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Study 1: Turning off miR-126 expression from an experimental murine B-ALL in vivo;
Study 2: Modulation of miR-126 expression in human cord blood stem and progenitor cell populations in vitro.

first: Francesco

middle: E

last: Boccalatte

first: Silvia

last: Nucera

first: Davide

last: Cittaro

first: Alice

last: Giustacchini

first: Cristiana

last: Fanciullo

first: Tiziana

last: Plati

first: Luigi

last: Naldini

first: Bernhard

last: Gentner


title: Systematic reconstruction of molecular cascades regulating growth plate development using single-cell RNA-seq

first: Haofei

last: Luo

address: Tsinghua Univ. Beijing

institute: Tsinghua university

summary: The growth plate, which comprises sequentially differentiated cell layers, is a critical structure for bone elongation and regeneration. Although several key regulators in growth plate development have been identified using primarily genetic perturbation, the systematic understanding is still limited. Here we used single cell RNA-seq to interrogate gene expression profiles of 217 single cells from growth plates, and developed the bioinfromatics pipeline Sinova to de-novo reconstruct physiological growth plate development in both temporal and spatial high-resolution. Our unsupervised model not only confirmed prior knowledge but also enabled systematic discovery of novel genes, potential signal pathways and surface markers CD9/CD200 to precisely depict the development. Sinova further identified effective transcriptional factor portfolio directing growth plate maturation, which was cross-validated experimentally using an in-vitro EGFP-Col10a screening system. Our case demonstrated systematic reconstructing of molecular cascades of a developmental process from single-cell profiling, and the workflow is readily transferable to other physiological scenarios.

overall_design: 217 single-cell RNA-seq for cell isolated from mouse growth plate at postnatal day7

first: Junxiang

last: LI

first: Rui

last: Wang

first: Jidong

last: Lang

first: Qiong

last: Wu


title: Developmental transcriptomes of the two sexes in Caenorhabditis elegans during sexual maturation

status: Public on Jun 13 2016

city: Bronx

first: Byunghyuk

last: Kim

address: 1300 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

summary: We compare whole-animal RNA-seq transcriptomes for C. elegans males and hermaphrodites from the late L3 larval stage to young adulthood. During this interval, male sexual structures develop, including extensive neurogenesis and synaptogenesis that nearly doubles the size of the nervous system. Previous genome-wide expression studies in C. elegans have usually focused on only one sex – the hermaphrodite, and there are a relatively large number of predicted genes that still remain without meaningful annotation. In the present study, differential expression analysis of the RNA-seq data revealed 1,751 genes expressed at a higher level in the male. By differential expression analysis, unbiased gene correlation analysis, and a guilt-by-association approach, we identified new transcription factors required for differentiation of male genital structures, semen proteins, and candidates for previously-unknown components for synapse function. The results validate the dataset as a rich resource for future gene discovery in C. elegans.

overall_design: To analyze gene expression during sexual maturation in C. elegans, we performed RNA-seq for five samples for each sex ranging at 6 hr intervals from late L3 to young adult stages

first: Scott

last: Emmons


title: ChIP-seq to profile LPS-induced RNA polymerase II transcription in bone marrow-derived macrophages  from WT and Hes1 KO mice

city: New York

first: Yingli

last: Shang

address: 535E 70th Street

institute: Hospital for Special Surgery

summary: We characterized the RNA polymerase II occupancy on gene loci in WT and Hes1 KO  BMDMs under untreated and LPS-stimulated conditions

overall_design: WT and Hes1 KO BMDMs were left untreated or stimulated with LPS  for 1 hour. Pol II ChIP was performed and the DNA products were subject to ChIPseq

first: Maddalena

last: Coppo

first: Yu

last: Qiao

first: Yushan

last: Li


title: The landscape of accessible chromatin in mammalian pre-implantation embryos (RNA-Seq)

first: Wei

last: Xie

address: zhongguancun beidajie

institute: Tsinghua University

summary: In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development.

overall_design: Mouse preimplantation embryos were obtained from crosses of C57BL/6N and DBA/2N. RNA-seq was performed in these embryos at various stages in preimplantation development.

first: Jingyi

first: Bo

last: Huang

first: He

last: Chen


title: DICER controls macrophage polarization and tumor response to immunotherapy

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

summary: Tumor-associated macrophages (TAMs) have immunosuppressive capacity in mouse models of cancer. Here we show that the genetic deletion of the microRNA (miRNA)-processing enzyme DICER in TAMs broadly programs them to a CD11c+MRC1−/low M1-like immunostimulatory phenotype characterized by activated interferon-γ (IFN-γ)/STAT1/IRF signaling. M1-like TAM programming fostered the recruitment of cytotoxic T-cells (CTLs), including tumor-antigen-specific CTLs, inhibited tumor growth, and enhanced the efficacy of PD1 checkpoint blockade. Bioinformatics analysis of TAM transcriptomes identified a limited set of miRNAs putatively involved in TAM programming. Re-expression of Let-7 in Dicer-deficient TAMs was sufficient to partly rescue the M2-like (protumoral) TAM phenotype and abate tumor CTL infiltration. Targeted suppression of DICER activity in TAMs may, therefore, stimulate antitumor immunity and enhance the efficacy of cancer immunotherapy.

overall_design: To explore the role of DICER in the development, activation and immunological functions of TAMs, we crossed homozygous LysM-Cre (Clausen et al., 1999) with Dicerlox/lox (Harfe et al., 2005) mice to obtain mice with myeloid-cell-specific Dicer1 gene deletion (LysM-Cre;Dicer–/–, referred to as D–/–). These mice were then backcrossed to LysM-Cre to obtain the control LysM-Cre; Dicer+/+ mice (referred to as D+/+). Both LysM-Cre and Dicerlox/lox mutations were always homozygous in our experiment. We then inoculated Lewis lung carcinoma (LLC) cells subcutaneously (s.c.) in D–/– and control D+/+ mice. Once the tumors were established, we isolated by fluorescence-activated cell sorting (FACS) tumor-associated macrophages (F4/80+ cells).

first: Michele

last: De Palma


title: Gene expression profiling of sciatic nerves from Zeb2cKO and control mice

first: Richard

last: Lu

address: 3333 Burnet Ave

department: CBDI

summary:
We performed gene expression pofiling of Zeb2cKO and control sciatic nerves and identified significantly changed genes
ZEB2 is also known as SIP1

overall_design: 4 RNA-Seq samples from P7 sciatic nerves of Ctrl and Zeb2 cKO mice (duplicatess, Ctrl and cKO)

first: Natalie

middle: L


title: ChIPseq to profile CDK9 and Hes1 occupancy in bone marrow-derived macrophages from C57BL/6 mice

summary: We characterized the CDK9 and Hes1 occupancy on gene loci in conditions of unstimuated and LPS stimualtion in BMDMs

overall_design: BMDMs were left untreated or stimulated with LPS for 1 hour. CDK9 or Hes1 ChIP was performed and the DNA products were subject to ChIPseq

first: Li

last: Yu

first: Bin

last: Zhang


title: Pin1 is required for sustained B cell proliferation upon oncogenic activation of Myc

first: Marco

middle: J.

last: Morelli

address: via Adamello 16

department: Center for Genomic Science of IIT@SEMM

institute: Istituto Italiano di Tecnologia

summary: The c-myc proto-oncogene is activated by translocation in Burkitt's lymphoma and substitutions in codon 58 stabilize the Myc protein or augment its oncogenic potential. In wild-type Myc, phosphorylation of Ser 62 and Thr 58 provide a landing pad for the peptidyl prolyl-isomerase Pin1, which in turn promotes Ser 62 dephosphorylation and Myc degradation. However, the role of Pin1 in Myc-induced lymphomagenesis remains unknown. We show here that genetic ablation of Pin1 reduces lymphomagenesis in Eµ-myc transgenic mice. In both Pin1-deficient B-cells and MEFs, the proliferative response to Myc was selectively impaired, with no alterations in Myc-induced apoptosis or mitogen-induced cell cycle entry. This proliferative defect wasn't attributable to alterations in either Ser 62 phosphorylation or Myc-regulated transcription, but to the indirect activation of an Arf-p53 dependent cytostatic response. Pin1 silencing in lymphomas retarded disease progression in mice, making Pin1 an attractive therapeutic target in Myc-driven tumors.

overall_design: RNAseq samples of Pin1+/+ control  (n=4), Pin1 -/- control (n=2),  Pin1+/+ Eµ-myc pre-tumoral (n=3), and  Pin1-/-  Eµ-myc pre-tumoral (n=4) B cells.

first: Luana

last: D'Artista

first: Bruno

last: Amati

first: Stefano

last: Campaner


title: The ortholog of DDM1 is mainly required for CHG and CG methylation of heterochromatin and is involved in DRM2-mediated CHH methylation that targets mostly genic regions of the rice genome

city: yichang

first: chao

last: zhou

address: No.8,daxuelu Street

institute: CTGU

summary: OsDDM1 and OsDRM2 display functional specificities that define distinct DNA methylation pathways in the bulk of DNA methylation of the rice genome

overall_design:
Cr_DJ.CG.bw: Cr_DJ CG methylation
Cr_DJ.CHG.bw: Cr_DJ CHG methylation
Cr_DJ.CHH.bw: Cr_DJ CHH methylation
ddm1ab.CG.bw: ddm1a/1b CG methylation
ddm1ab.CHG.bw: ddm1a/1b CHG methylation
ddm1ab.CHH.bw: ddm1a/1b CHH methylation
S706.CG.bw: osdrm2 CG methylation
S706.CHG.bw: osdrm2 CHG methylation
S706.CHH.bw: osdrm2 CHH methylation
H3k9me2_macs_peaks.xls: CrDJ H3K9me2 modification peaks
H3k9me2_macs_treat_afterfiting.wig: CrDJ H3K9me2 modification wig
CrDJ_K27_macs_peaks.xls: CrDJ H3K27me3 modification peaks
CrDJ_K27_macs_treat_afterfiting.wig: CrDJ H3K27me3 modification wig
DJvsddm1a1b_DESeq2_treated_results.xls: CrDJ and osddm1a1b different expression genes
DJvsS706_DEseq2_treated.results.xls: CrDJ and osdrm2 different expression genes
smRNA24nt.gff: CrDJ 24nt smRNA
smRNA24nt.706.gff: osdrm2 24nt smRNA

first: Feng

last: Tan

first: Chao

last: Zhou

first: Qiangwei


status: Public on Jun 12 2016

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Central to the molecular pathogenesis of MLL leukaemia is the abnormal co-optation of members of transcription complexes including disrupter of telomeric silencing 1-like (DOT1L) and bromodomain containing protein 4 (BRD4). Consequently, targeted therapies against DOT1L and BRD4 are currently being evaluated in clinical trials. However, the mechanisms by which BRD4 and DOT1L regulate leukaemogenic transcription programs remain unclear. Using quantitative proteomics, chemoproteomics and biochemical fractionation we find that native BRD4 and DOT1L exist in largely separate protein complexes. Genetic disruption or small molecule inhibition of BRD4 and DOT1L shows marked synergistic activity against MLL-FP leukaemia cell lines, primary human leukaemia cells and murine leukaemia models. Mechanistically, we find a previously unrecognised functional collaboration between DOT1L and BRD4 that is especially important at highly transcribed genes in close proximity to superenhancers. DOT1L via H3K79me2 facilitates the deposition of histone H4 acetylation, which in turn regulates the binding of BRD4 to chromatin. These data provide novel insights into the regulation of transcription and specify a molecular framework for therapeutic intervention in this poor prognostic disease.

overall_design: RNASeq of MV4;11 cell treated with DMSO, I-BET, SGC0946 and combination of I-BET and SGC0946 in duplicate

first: Omer

last: Gilan

first: Enid

last: Lam


title: Critical modulation of hematopoietic lineage fate by Hepatic Leukemia Factor

city: Lund

first: Martin

last: Wahlestedt

address: Klinikgatan 26

department: Divison of Molecular Hematology

institute: Lund University

summary: A gradual restriction in lineage potential of multipotent stem/progenitor cells is a hallmark of adult hematopoiesis, but the underlying molecular events governing these processes remain incompletely understood. Here, we identified robust expression of the leukemia-associated transcription factor Hepatic Leukemia Factor (Hlf) in normal multipotent hematopoietic progenitors, which was rapidly downregulated upon differentiation. Interference with its’ normal downregulation revealed Hlf as a strong negative regulator of lymphoid development, while remaining compatible with myeloid fates. Reciprocally, we observed rapid lymphoid commitment upon reduced Hlf activity. The arising phenotypes resulted from Hlf-binding to active enhancers of myeloid-competent cells, transcriptional induction of myeloid and ablation of lymphoid gene programs, with Hlf induction of Nuclear Factor I C (Nfic) as a functionally relevant target gene. Thereby, our studies establish Hlf as a key regulator of the earliest lineage-commitment events at the transition from multipotency to lineage-restricted progeny, with implications for both normal and malignant hematopoiesis.

overall_design: Gene expression profiling of control or Hlf/Hlf lentivirus infected GMLPs (2 replicates per group) and Hlf inducible GMLPs maintained for 4 days on OP9 stroma in the presence or absence of doxycycline (2 replicates per group)

first: Vasileiosis

last: Ladopoulos

first: Isabel

last: Hidalgo

first: Manuel

last: Sanchez Castillo

first: Rebecca

last: Hannah

first: Petter

last: Säwén

first: Haixia

last: Wan

first: Monika

last: Dudenhöffer-Pfeifer

first: Mattias

last: Magnusson

first: Gudmundur

last: Norddahl

first: Berthold

last: Göttgens

first: David

last: Bryder


title: ChIPSeq of MV4;11 cell treated with SGC0946 for 8 hours and washout


title: ChIPSeq of MV4;11 cell treated with DMSO, I-BET, SGC0946 and combination of I-BET and SGC0946


title: Recurrent alterations of TNFAIP3 (A20) in T-cell large granular lymphocytic leukemia

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary: We identified a novel recurrent genetic lesion in T-LGL. Mutations of the tumour suppressor gene TNFAIP3 causing amino-acid exchanges or protein truncations were seen in 3/39 cases (8%).

overall_design: RNA sequencing (Illumina HiSeq 2500) of 5 index patients with paired tumor and non-tumor samples.

first: Patricia

last: Johansson


title: Functional interdependency of BRD4 and DOT1L in MLL leukaemia

first: Mark

last: Dawson

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

overall_design: Refer to individual Series


title: Drosophila melanogaster Show a Threshold Effect in Response to Radiation

city: Providence

first: Michael

last: Antosh

state: RI

address: Brown University Box 1843

institute: Michael Antosh

summary: We investigate the biological effects of radiation using Drosophila Melanogaster as a model organism, focusing on gene expression and lifespan analysis to determine the effect of different radiation doses. Our results support a threshold effect in response to radiation: no effect on lifespan and no permanent effect on gene expression is seen at doses below 10,000 Roentgens.

overall_design: Adult male Drosophila were irradiated 2 days after eclosion, with one of 6 radiation doses: 10; 1,000; 5,000; 10,000; 20,000 Roentgens. Samples were taken at 3 time points (2, 10 and 20 days post-irradiation).

first: Nicola

last: Neretti


title: RNA sequencing of pancreatic adenocarcinoma tumors yields novel expression patterns associated with long-term survival and reveals a role for *ANGPTL4*

status: Public on Jun 11 2016

city: Huntsville

first: Marie

middle: K

last: Kirby

state: AL

address: 601 Genome Way NE

institute: HudsonAlpha Institute for Biotechnology


title: Identification and Comparative Analysis of Cotton miRNA Target Genes using Degradome Sequencing

city: Anyang

first: Zujun

last: Yin

state: Henan

address: 38 Huanghe Dadao, Anyang 455000, Henan, China

department: Cotton Research Institute

institute: Chinese Academy of Agricultural Sciences

summary: To gain insight into the functions of salt-regulated miRNAs, target genes were identified through degradome sequencing approach. Three cotton RNA libraries were constructed and sequenced under normal consideration, osmotic and ionic stress. A total of 73,988,644 reads represented by 3,254,054 unique reads from the 5’ ends of uncapped and poly-adenylated RNAs were obtained. The PairFinder software was used to identify the sliced targets for the known miRNAs and novel miRNAs. These sequences were further compared with transcriptome sequencing data of G. arboretum and G. raimondii. We obtained the data from (Cotton Genome Project, http://cgp.genomics.org.cn/page/species/index.jsp).Based on degradome sequencing, 31 target genes were identified for 20 cotton miRNA families. The abundance of transcripts was plotted for each transcript. Conserved miRNAs target conserved homologous genes in diverse plant species.

overall_design: Three cDNA libraries were constructed using total RNA obtained from control samples (CK), the 4 h and 5 d salt-treated samples. A total of 74,351,180 sequence reads were obtained from three libraries. After removing the 3p and 5p adapter sequences and filtering out low quality ‘‘n’’ sequences, 864,720, 1,217,757 and 1,171,577 clean reads remained in the CK, 4 h and 5 d samples, respectively.


title: Transcriptome analysis of 100-day fetal skin revealing the differences of skin pigmentation in goats

city: Chongqing

first: Hangxing

last: Ren

address: Rongchang District, Changlong Street 51#

institute: Chongqing Academy of Animal Sciences

summary: We identified the mRNA and long non-coding RNA expression profiles of 100-day fetal skin between the dark and normal (white) skin in two breeds of goats using the deep RNA sequencing method.

overall_design: Case-control. Briefly, the 100-day fetal skin sampled from the normal and hyperpigmentated goats for deep sequencing, in triplicate for each breed, using Illumina

first: Peng

last: Zhou


title: RNA-sequencing of human pancreatic adenocarcinoma cancer tissues

summary: RNA-seq profiling was conducted on clinically-annotated human pancreatic adenocarcinoma cancer tissues

overall_design: We measured the transcriptome in 51 clinically-annotated human pancreatic adenocarcinoma cancer tissues

first: Ryne

middle: C

last: Ramaker

first: James

last: Posey

first: William

last: Grizzle

first: Selwyn

last: Vickers

first: Donald

last: Buchsbaum

first: Sara

last: Cooper

first: Richard

last: Myers


title: RNA sequencing of human pancreatic cancer cell lines

summary: RNA-seq profiling was conducted on human pancreatic cancer cell lines

overall_design: We measured the transcriptome in 14 human pancreatic cancer cell linees

first: Patsy

middle: G

last: Oliver


title: PyMT 4 stages tumor progression microRNA sequencing

status: Public on Jun 10 2016

city: bronx

first: ying

last: cai

state: New York

address: 1300 morris park ave

summary: We sequenced mammary gland samples of MMTV-PyMT mouse from 4 stages (hyperplasia at week 6, adenoma/MIN at week 8, early carcinoma at week 10, and late carcinoma with lung metastasis at week 12) during tumor progression.

overall_design: We sacrificed 3 PyMT (FVB background) mice and 3 FVB control mice at each of the 4 stages, extracted small RNA and performed sequencing.

first: Ruben

last: Nogales-Cadenas

first: Ying

last: Cai

first: Quanwei

last: Zhang

first: Jhih-rong

last: Lin

first: Wen

first: Zhengdong


title: Identification of microRNAs involved in cold stress response in grapevine.

city: Wuhan

first: Xiaoming

last: Sun

state: Hubei

address: Lumo road, No. 1

institute: Wuhan Botanical Garden, Chinese Academy of Sciences

summary: Two small RNA libraries were generated from micropropagated ‘Muscat Hamburg’ (Vitis vinifera) plantlets under normal and low temperatures (4 °C). A total of 163 known miRNAs and 299 putative novel miRNAs were detected from two small RNA libraries by Solexa sequencing. Forty-four cold-inducible miRNAs were identified through differentially expressed miRNAs (DEMs) analysis; among which, 13 belonged to upregulated DEMs while 31 belonged downregulated DEMs. This study indicated that a diverse set of miRNAs in V. vinifera are cold-inducible and may play an important role in cold stress response.

overall_design: Examination of small RNA populations in grapevine under cold treatment and none cold treatment.

first: Shaohua

last: Li

first: Haiping

last: Xin


title: Alteration in microRNA-25 Balance Causes Heart and Kidney Impairment

city: Reno

first: Binghai

last: Zhao

state: helongjiang

address: No.3 Tongxiang Street

department: physiology

institute: Mudanjiang Medical University

summary: Contradictorily, both up- and downregulation of miR-25 can reverse heart failure. Importantly, these findings were based on the same animal model of pressure overloaded transverse aortic constriction (TAC) mice. How can we explain and, if possible, reconcile these two conflicting findings? Heart failure is a multi-step process that involves multiple organs, and we hypothesized that determining whether altering miR-25 alone could induce heart failure should provide a mechanistic basis for miR-25’s action in this process. Here, we show that overexpression of miR-25 in normal mice caused cardiomyocyte fibrosis and apoptosis but no obvious kidney impairment. By contrast, inhibition of miR-25 in normal mice led to hypertension, mild heart dilation, and severe kidney dysfunction. With the expectation that restoring miR-25 might ameliorate kidney injury, we demonstrated that increasing miR-25 reversed proteinuria and kidney fibrosis in diabetic nephropathy. MiR-25 expression in humans is initially decreased at the onset of heart failure but is later increased in end-stage heart failure. RNA sequencing of mouse kidneys with elevated and reduced miR-25 identified distinct alterations of a number of putative miR-25 target mRNAs, including those involved in the Ras signaling pathway, oxidant stress. In summary, differences in miR-25 expression during different stages of heart disease and its distinct roles in the heart and kidney, offer a new perspective for the role of miR-25 function in heart failure, which may begin to resolve this catch-22.

overall_design: Detect the mRNA alteration in wildtype and miR-25 agomir or antagomir treated mice


title: An ectopic network of transcription factors regulated by Hippo signaling drives growth and invasion of a malignant tumor model [larval imaginal discs (eye, wing and leg)]

city: Marseille

first: Delphine

last: Potier

address: 27 boulevard Lei Roure

institute: CRCM

summary: Cancer cells have abnormal gene expression patterns, however, the transcription factors and the architecture of the regulatory network that drive cancer specific gene expression profiles is often not known. Here we studied a model of Ras-driven invasive tumorigenesis in Drosophila larval epithelial tissues and combined in vivo genetic analyses with high-throughput sequencing and computational modeling to decipher the regulatory logic of tumor cells. Surprisingly, we discovered that tumor specific gene expression is driven by a highly interconnected network composed of few transcription factors. These are: Stat, Mef2, the AP-4 homolog Cropped, the nuclear receptor Ftz-f1, the bHLH factors Myc and Taiman, and the AP-1 transcription factors Kayak, ATF-3, Pdp1, and dCEBPG. Many of these transcription factors are ectopically expressed and/or hyperactivated in human tumors. The members of this tumor master regulatory network are predicted to directly regulate the majority of the tumor specific gene expression profile. Similar to networks of master regulators that control organ development and cellular differentiation, there is a predicted high degree of co-regulation of target genes, and these network members are required in multiple eptihelia for tumor growth and invasiveness. We further found that Yki/Sd and bZIP/AP-1 factors, the downstream transcription factors of the Hippo and JNK pathways, initiate cellular reprogramming by activating several transcription factors of this network. Thus, modeling regulatory networks identified an ectopic yet highly ordered network of master regulators that control cancer cell specific gene expression.

overall_design: RNA-seq gene expression profiling across Drosophila 3rd instar larval imaginal discs (eye-antenna, wing and leg) in a hh driven tumor model, perturbations and controls.

first: Mardelle

last: Atkins

first: Lucia

last: Romanelli

first: Jelle

last: Jacobs

first: Jana

last: Mach

first: Fisun

last: Hamaratoglu

first: Stein

last: Aerts

first: Georg

last: Halder


title: Transcriptionally Driven DNA Replication Programme of the Human Parasite Leishmania major

city: Madrid

first: Maria

last: Gomez

address: Nicolas Cabrera, 1

institute: CBMSO(CSIC/UAM)

summary: Faithful inheritance of the large eukaryotic genomes requires the orchestrated activation of multiple DNA replication origins. Although origin activation is mechanistically conserved among eukaryotes, how replication origins are specified and selected for activation in each S-phase seem to differ across the model systems studied. Here we provide a complete analysis of the nucleosomal landscape and replication programme of the human parasite Leishmania major, building on a better evolutionary understanding of replication organization in Eukarya. We found that active transcription is a driving force for the nucleosomal organization of L. major genome, and that both the spatial and the temporal programme of DNA replication can be explained as associated to RNA polymerase kinetics, without the need to invoke specific regulatory mechanisms. This simple scenario likely provides these organisms with the flexibility and robustness to deal with the continuous environmental changes that impose alterations in their genetic programmes during their parasitic life cycle stages. Our findings also suggest that coupling replication initiation to transcription elongation could be an ancient solution used by eukaryotic cells for origin maintenance

overall_design: Replication intitiation sites were defined using two replicates of short nascent strands of increasing sizes (F4 and F5) purified through three rounds of Lambda-exonuclease digestion, and a genomic DNA control (Ctrl). Nucleosome landscape was determined using two replicates of mononucleosomal-DNA derived from MNase-digested chromatin

first: Rodrigo

last: Lombraña

first: Alba

last: Álvarez

first: José Miguel

last: Fernández-Justel

first: Ricardo

last: Almeida

first: César

last: Poza-Carrión

first: Fábia

last: Gomes

first: Arturo

last: Calzada

first: José María

last: Requena

first: María

last: Gómez


title: Photorespiratory stress in catalase deficient plants

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

country: Belgium

institute: Ghent University

summary: Hydrogen peroxide (H2O2) can act as a signaling molecule that influences various aspects of plant growth and development, including stress signaling and cell death. To unravel the molecular mechanisms that regulate the response towards an impact of increased H2O2 levels in plant cells, we focused on the photorespiration-dependent peroxisomal H2O2 production in Arabidopsis thaliana mutants lacking CATALASE2 (CAT2) activity (cat2-2).

overall_design: Unstressed and stressed samples of cat2-2 in triplicate

first: Kerchev

last: Pavel

first: Cezary

last: Waszczak

first: Frank

last: Van Breusegem


title: Arabidopsis GLYCOLATE OXIDASE 1 and 2 display divergent roles under conditions promoting photorespiration

summary: Hydrogen peroxide (H2O2) can act as a signaling molecule that influences various aspects of plant growth and development, including stress signaling and cell death. To unravel the molecular mechanisms that regulate the response towards an impact of increased H2O2 levels in plant cells, we focused on the photorespiration-dependent peroxisomal H2O2 production in Arabidopsis thaliana mutants lacking CATALASE2 (CAT2) activity (cat2-2) and screened for second-site mutations that attenuate the Fv'/Fm' decrease and lesion formation linked to the cat2-2 phenotype. A mutation in GLYCOLATE OXIDASE 1, encoding one of the two photorespiratory isoforms of glycolate oxidase rescued the cell death phenotype of cat2-2 plants under photorespiration-promoting conditions. Interestingly, introduction of gox2 into the cat2 background did not have the same effect and the double cat2 gox2 mutants were as affected as the parental cat2 mutants under conditions promoting photorespiration. Using a series of physiological, biochemical and metabolomic approaches we investigated the differential photorespiratory response of cat2 mutants underlied by the lack of GOX1 and GOX2. These differences are in line with the non-redundant functions of GOX1 and GOX2 which could be observed under enhanced photorespiration.

overall_design: Unstressed and stressed samples of cat2 gox1 and cat2 gox2 double mutants in triplicate