title: The histone variant H3.3 G34W substitution in giant cell tumor of the bone link chromatin and RNA processing

first: Jinyeong

last: Lim

overall_design: We performed gene expression microarray on 29 samples, of which 27 were GCTB and 2 were control cell lines (mesenchymal stem cell line KM1234 and the hFOB1.19 osteoblast cell line). Collectively, 19 samples were H3.3G34W and 10 were H3.3WT. The samples were run on a HumanHT-12 v4 Expression BeadChip (Illumina).

first: Joo

middle: H

last: Park

first: Annika

last: Baude

first: Youngran

last: Yoo

first: Yeonkyu

last: Lee

first: Christopher

last: Schmidt

first: Jong

middle: B

first: Jörg

last: Fellenberg

first: Josef

last: Zustin

first: Florian

last: Haller

first: Hyun

last: Kang

first: Yoon

first: Christoph

last: Plass

first: Anders

middle: M

last: Lindroth


title: Gene expression analysis of human liver progenitor-like cells in culture

status: Public on Oct 17 2017

city: shanghai

first: yan

last: hexin

address: No. 1630 East Road

country: China

institute: Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine

type: Expression profiling by high throughput sequencing

summary: To compare the global expression profiles among primary human hepatocytes and liver progenitor-like cells with or without in vitro differentiation.

overall_design: Human liver progenitor-like cells were derived from 3 donor and cultured in the transition and expansion medium for 4 days, 10 days, passage 5 and passage 10 or in the differentiation medium for 8 days. Primary hepatocytes were isolated using a two-step collagenase perfusion technique.

first: Yan

last: Xin

first: Fu

middle: G

last: Bo


title: Base-resolution mapping reveals distinct classes of N1-methyladenosine methylome in nuclear- and mitochondrial-encoded transcripts

status: Public on Oct 18 2017

city: Hangzhou

first: Xushen

last: Xiong

state: Zhejiang

address: Wenyi Road West

department: Medical Center

institute: Zhejiang University

type: Non-coding RNA profiling by high throughput sequencing

summary: Gene expression can be post-transcriptionally regulated via dynamic and reversible RNA modifications. N1-methyladenosine (m1A) is a recently identified mRNA modification; however, little is known about its precise location, regulation and function. Here, we develop a single-nucleotide resolution m1A profiling method, based on m1A-induced misincorporation during reverse transcription, and report distinct classes of m1A methylome in the human transcriptome. m1A in the 5’-untranslated region, particularly those located exactly at the first nucleotide of mRNA transcripts, associates with increased translation efficiency. A different subset of m1A sites exhibit a GUUCRA tRNA-like motif, are evenly distributed in the transcriptome and are dependent on the methyltransferase complex TRMT6/61A. Additionally, we show for the first time that m1A is prevalent in the mitochondrial-encoded transcripts. Manipulation of m1A level via TRMT61B, a mitochondria-localizing m1A methyltransferase, demonstrates that m1A in mitochondrial mRNA interferes with translation. Collectively, our approaches reveal distinct classes of m1A methylome and provide a resource for functional studies of m1A-mediated epitranscriptomic regulation.

overall_design:
We developed a method named "m1A-MAP" to detect m1A in both the nuclear-encoded and mitochondrial encoded  transcriptome in a single-base resolution. We first tested several available RTases (including AMV, SuperScript II, SuperScript III and TGIRT) under different conditions for their performance on capturing m1A-induced reverse transcription signature (RT1-RT10). Then we applied our methods to detect m1A sites in the human transcriptome (m1A_input_TGIRT,m1A_IP_TGIRT, m1A_IP_demethylase_TGIRT, two replicates for each sample) . We also perform m1A seq for RNA fractions below 200nt in TRMT6/61 KD cells to evaluate the substrat specifity of m1A sites in tRNA (Mock and TRMT6_61A). Lastly, we investigated the correlation between m1A-mRNAs and their translation efficiency by performing ribosome profiling (HEK293T_RNA-seq and HEK293_Ribo-seq).
Please note that these data were produced from the X-ten sequencing platform, and the output raw data were pair-end. However, due to the particularity of our library construction (a random barcode of 10 nt were included in our 3' end cDNA adapter, which cannot be precisely located in Read 1), data of Read 1 were discarded and only the data of Read 2 were used in our analysis and, therefore, submitted as single-end files.

first: Xiaoyu

last: Li

first: Kun

last: Wang

first: Meiling

last: Zhang

first: Chengqi

last: Yi


title: Genome-wide map of BrdU incorporation, SMC3 and SMC3(ac) binding in HeLa cells in early S phase

city: Vienna

first: Heinz

last: Ekker

address: Dr. Bohrgasse 3

country: Austria

institute: VBCF

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Differential acetylation of SMC3 relative to BrdU as a function of ESCO2 motif PBMA deletion and depletion of ESCO1

overall_design: SMC3 and SMC(ac) chromatin-immunoprecipitation and BrdU DNA-immunoprecipitation were performed from cells synchronized in G1/S by double thymidine arrest and 1-hour release in S phase.

first: Miroslav

middle: P

last: Ivanov

first: Jan-Michael

last: Peters


title: MafB enhances oncogenic Notch signaling in T-ALL [Microarray]

city: Philadelphia

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

department: Pathology

country: USA

institute: University of Pennsylvania

summary:
Notch dependent gene expression in T6E cell line
Transcription profiles of Notch signaling active, inactive and recovered were compared

overall_design: Expression profiling on a set of RNAs obtained from T6E T-ALL cells in which Notch signaling is inhibited (gamma-secretase inhibitor (GSI)-treated), is unchanged (DMSO-treated cells) or recovered after being inhibited (GSI treatment was washed out).

first: Yumi

last: Ohtani


title: CACUL1 reciprocally regulates SIRT1 and LSD1 to repress PPARγ and inhibit adipogenesis

city: Seoul

first: Ui-Hyun

last: Park

address: 209 Neungdong-ro Gwangjin-gu

department: Division of Integrative Bioscience and Biotechnology

country: South Korea

institute: Sejong Univ.

summary: Peroxisome proliferator-activated receptor γ (PPARγ) is the master regulator of adipocyte differentiation and is closely linked to the development of obesity. Despite a large progress on the transcriptional network of PPARγ, the epigenetic regulation associated with histone modification remains elusive. Here, we found that CDK2-associated cullin 1 (CACUL1), identified as a novel SIRT1 interacting protein, directly binds to PPARγ through the CoRNR box 2 and represses the transcription activity and adipogenic potential of PPARγ. Upon CACUL1 depletion, less SIRT1 and more LSD1 was recruited to the PPARγ-responsive gene promoter, leading to the increased histone H3K9 acetylation and decreased H3K9 methylation for PPARγ activation during adipogenesis of 3T3-L1 cells. These findings were reversed upon fasting or resveratrol treatment. Further, gene expression profiling using RNA-seq supported the repressive role of CACUL1 in PPARγ activation and fat accumulation. Finally, we confirmed the CACUL1 function in human adipose-derived stem cells. Overall, our data suggest that    CACUL1 tightly regulates PPARγ signaling through the mutual opposition between SIRT1 and LSD1, providing additional insight into its use for anti-obesity treatment.

overall_design: mRNA profiles of 3T3-L1 cells, which are stably expressing Flag-emtpy, Flag-CACUL1, sh-Luciferase or sh-CACUL1, were generated by RNA-seq after adipogenesis for 8 days

first: Min-Jun

last: Jang


title: The Circadian Clock Gene Bmal1 Controls Thyroid Hormone-Mediated Spectral Identity and Cone Photoreceptor Function

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: Here we reveal a novel role for the circadian clock gene Bmal1 and Period2 in regulating the spatial organization of the cone opsins. Deletion of Bmal1 and Per2 have opposing effects on S-opsin expression and patterning of the cone photoreceptors is disrupted in cone specific knockouts of these genes. Using ChIP analysis we show that BMAL1 directly binds to the promoter region of the thyroid activating enzyme type II deiodinase (Dio2).

overall_design: 3 WT vs 3 Bmal1 CKO mice were compared

first: Onkar

last: Sawant

first: Sujata

last: Rao


title: Histone H3 threonine 11 phosphorylation is catalyzed directly by the meiosis-specific kinase Mek1 and provides a molecular readout of Mek1 activity in vivo

city: Suita

first: Masaru

last: Ito

state: Osaka

address: Yamadaoka 3-2

country: Japan

institute: Osaka University

summary: Saccharomyces cerevisiae Mek1 is a CHK2/Rad53-family kinase that regulates meiotic recombination and progression upon its activation in response to DNA double-strand breaks (DSBs). The full catalog of direct Mek1 phosphorylation targets remains unknown. Here, we show that phosphorylation of histone H3 on threonine 11 (H3 T11ph) is induced by meiotic DSBs in S. cerevisiae and Schizosaccharomyces pombe. Molecular genetic experiments in S. cerevisiae confirmed that Mek1 is required for H3 T11ph and revealed that phosphorylation is rapidly reversed when Mek1 kinase is no longer active. Reconstituting histone phosphorylation in vitro with recombinant proteins demonstrated that Mek1 directly catalyzes H3 T11 phosphorylation. Mutating H3 T11 to nonphosphorylatable residues conferred no detectable meiotic defects, indicating that H3 T11ph is dispensable for Mek1 functions in controlling recombination. However, H3 T11ph provides an excellent marker of ongoing Mek1 kinase activity in vivo. Anti-H3 T11ph chromatin immunoprecipitation followed by deep sequencing demonstrated that H3 T11ph was highly enriched at presumed sites of attachment of chromatin to chromosome axes, gave a more modest signal along chromatin loops, and was present at still lower levels immediately adjacent to DSB hotspots. These localization patterns closely tracked the distribution of Red1 and Hop1, axis proteins required for Mek1 activation. These findings provide insight into the spatial disposition of Mek1 kinase activity and the higher order organization of recombining meiotic chromosomes.

overall_design:
ChIP-seq analysis of Red1 on budding yeast meiotic chromosomes
Distribution of Red1 at 3h after meiotic induction

first: Ryan

last: Kniewel

first: Hajime

last: Murakami

first: Yan

last: Liu

first: Kunihiro

last: Ohta

first: Nancy

last: Hollingsworth

first: Scott

last: Keeney


title: m6A and YTHDF1, YTHDF2, YTHDF3 mapping of IAV RNA with PAR-CLIP and pA-m6A-seq

city: Durham

first: Bryan

last: Cullen

state: NC

address: 213 Research Drive

department: Molecular Genetics & Microbiology

institute: Duke University

overall_design: In this GEO submission we include the PAR-CLIP data sets for IAV-PR8 in 293T cells, and pA-m6A-seq in 293T cells

first: David

last: Courtney


title: Critical role for very-long chain sphingolipids in invariant natural killer T cell development and homeostasis

status: Public on Oct 15 2017

city: Rehovot

first: Ester

last: Feldmesser

state: Rehovot

address: POB 25

department: Life Science Core Facilities

country: Israel

institute: Weizmann Institute

summary: The role of sphingolipids (SLs) in the immune system has come under increasing scrutiny recently due to the emerging contributions that these important membrane components play in regulating a variety of immunological processes. The acyl chain length of SLs appears particularly critical in determining SL function. Here we show a role for very-long acyl chain SLs (VLC-SLs) in invariant natural killer T (iNKT) cell maturation in the thymus and homeostasis in the liver. Ceramide synthase 2 (CerS2) null mice, which lack VLC-SLs, were susceptible to a hepatotropic strain of lymphocytic choriomeningitis virus, which is due to a reduction in the number of iNKT cells. Bone marrow chimera experiments indicated that hematopoietic-derived VLC-SLs are essential for maturation of iNKT cells in the thymus, whereas parenchymal-derived VLC-SLs are crucial for iNKT cell survival and maintenance in the liver. Our findings suggest a critical role for VLC-SL in iNKT cell physiology.

overall_design: Liver mRNA profiles of 3-4 month old wild type (WT), WT iNKT cell transfered and CerS2-/-mice, infected or not with LCMV were generated by deep sequencing. Several replicateswere included and pocessed using the MARS-seq protocol  (Jaitin et al. 2014 Science.343:776-9) and sequencing in the Illumina NextSeq 500 instrument

first: Ashish

last: Saroha

first: Yael

last: Pewzner-Jung

first: Natalia

middle: S

last: Ferreira

first: Piyus

last: Sharma

first: Youenn

last: Jouan

first: Samuel

last: Kelly

first: Alfred

last: Merrill Jr

first: François

last: Trottein

first: Christophe

last: Paget

first: Karl

last: Lang

first: Anthony

last: Futerman


title: CONTROL OF GROWTH AND GUT MATURATION BY HoxD GENES AND THE ASSOCIATED LncRNA Haglr

city: Geneva

first: Jozsef

last: Zakany

state: Geneva

address: 30, quai Ernest Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

summary: In this work we have analyzed the transcriptomic profiles of E9 mouse embryos. We show that Hoxd1 and Haglr transcripts are absent after targeted deletion of the CpG: 114 island.

overall_design: RNA-seq analysis of trunk from the anterior limit of the forelimb bud to the tailbud, aiming to exclude all extra-embryonic, head, cervical and heart  tissues. Individuals 443 (wt) and 445 (Del(CpG114) homozygous), were siblings from the same dam, while biological replicates 456 (wt) and 455 (Del(CpG114) homozygous) were siblings from another dam.

first: Anamaria

last: Necsulea

first: Denis

last: Duboule


title: CDK8 Mediator kinase drives colon cancer hepatic metastasis by regulating gene expression of the matrix metalloproteinase network [Illumina]

status: Public on Oct 16 2017

city: Columbia

first: Mengqian

last: Chen

state: SC

address: CLS710, 715 Sumter Street

department: College of Pharmacy

institute: University of South Carolina

summary: CDK8 Mediator kinase is amplified and overexpressed in colon cancers; elevated CDK8 expression is associated with shorter patient survival. Nevertheless, CDK8 kinase inhibitors do not generally suppress colon cancer growth. We addressed this paradox by investigating the effects of CDK8 knockdown or a CDK8 kinase inhibitor on tumor growth at primary and metastatic sites. CDK8 knockdown or inhibition had no significant effect on primary tumors but suppressed the growth of hepatic metastases in murine and human colon cancer models. The effect of CDK8 inhibition on liver metastasis is mediated by upregulation of matrix metalloproteinase (MMP) inhibitor TIMP3 and downregulation of several MMPs.

overall_design: Transcriptomic comparison between CT26-pLKO.1 and CT26-shCDK8 cells were performed using Illumina MouseWG-6 v2.0 microarrays by the Hollings Cancer Center Genomics Shared Resource facility at Medical University of South Carolina.

first: Jiaxin

last: Liang

first: Igor

last: Roninson


title: MafB enhances oncogenic Notch signaling in T-ALL

first: Robert

last: Faryabi

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

overall_design: Refer to individual Series


title: IgG immunocomplexes sensitize human monocytes for  inflammatory hyperactivity via transcriptomic and epigenetic reprogramming in Rheumatoid Arthritis

city: Suzhou

first: Xiao-Ming

last: Gao

address: 199 Ren’ai Road

department: Institute of Biology and Medical Sciences, School of Biology and Basic Medical Sciences,

institute: Soochow University

summary: Prevalence of circulating immunocomplexes (ICs) strongly correlates with rheumatoid arthritis (RA) in humans. Deposits of IgG-ICs are abundant in affected joints of patients, yet molecular mechanisms for the pathogenic roles of such ICs are not fully understood. In this study, we present evidence that IgG-ICs precipitated from RA sera sensitized human monocytes for a long lasting inflammatory functional state, characterized by a strong TNF-a response to cellular proteins representing damage associated molecular patterns and microbe-derived pathogen-associated molecular patterns. Importantly, plate-coated human IgG (a mimic of deposited IC without Ag restriction) exhibited a similarly robust ability of monocyte sensitization in vitro. The plate-coated human IgG–induced functional programming is accompanied by transcriptomic and epigenetic modification of various inflammatory cytokines and negative regulator genes. Moreover,  macrophages freshly isolated from synovia of patients with RA, but not sera-negative arthropathy, displayed a signature gene expression profile highly similar to that of IC-sensitized human monocytes, indicative of historical priming events by IgG-ICs in vivo. Thus, the ability of IgG-ICs to drive sustainable functional sensitization/reprogramming of monocytes and macrophages toward inflammation may render them key players in the of RA.

overall_design: H3K4me3 ChIP-Seq (4 samples) and RNA-Seq (12 samples)

first: Qiao

last: Zhong

first: Fang-Yuan

last: Gong

first: Zheng

first: Sheng-Hao

last: Hua

first: Ke-Qin

last: Zeng


title: Identification of candidate genes associated with breast muscle of broilers exposed to atmospheric ammonia using RNA sequencing

status: Public on Oct 14 2017

city: Beijing

first: Bao

last: Yi

address: No.2 Yuanmingyuan West Road

department: Institute of Animal Sciences

institute: Chinese Academy of Agricultural Sciences

summary: Abstract: Ammonia is one of the most prominent air pollutants in poultry houses. High levels of ammonia have adverse effects on respiratory health, growth performance, meat production of broilers, and breast meat growth and yield are critical important in the broiler industry. To date, studies focus on the negative relationship of ammonia exposure and breast muscle tissue are still very limited, and the underlying molecular mechanisms remain poorly understood. In this study, high concentrations of atmospheric ammonia were found to lower slaughter rate and broiler breast meat yield significantly (P < 0.05). To explore the candidate genes that ammonia regulates breast meat yield of broilers, high throughout RNA-Seq was used to compare the transcriptome of breast muscle with different ammonia exposure (50 ppm vs 3 ppm). In total, 129 differentially expressed genes (DEGs) were identified (P-value < 0.05; fold-change ≥ 2), among which 87 genes were significantly down-regulated and 42 were up-regulated. Bioinformatics analysis suggested that DEGs (such as PDK4, ACSL1, GLUL, FBXO32) were involved in fatty acid degradation/metabolism, nitrogen metabolism, PPAR signaling and adipocytokine signaling pathways. Functional annotation showed that DEGs were mainly enriched in reactive oxygen species metabolic process and muscle contraction. It can be concluded that decreased meat yield was due to the DEGs participating in above biological processes and pathways. This study provides novel insights into transcriptional differences in breast meat between high- and low-ammonia exposed broiler chickens.

overall_design: Breast muscle mRNA profiles of 42-day old Arbor Acres male broilers exposed to  50 ppm (treatment) concentrations of atmospheric ammonia were generated by RNA sequencing, in triplicate, using Illumina HiSeq2000.

first: Liang


title: Cohesin loss eliminates all loop domains [ChIP-Seq]

status: Public on Oct 13 2017

city: Houston

first: Suhas

last: Rao

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: The human genome folds to create thousands of intervals, called “contact domains,” that exhibit enhanced contact frequency within themselves. “Loop domains” form because of tethering between two loci – almost always bound by CTCF and cohesin – lying on the same chromosome. “Compartment domains” form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loss of loop domains does not lead to widespread ectopic gene activation, but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes, and affecting the regulation of nearby genes. We then restore cohesin and monitor the re-formation of each loop. Although re-formation rates vary greatly, many megabase-sized loops recovered in under an hour, consistent with a model where loop extrusion is rapid.

overall_design: we use in situ Hi-C, ChIP-Seq and PRO-Seq to probe nuclear architecture, the epigenome and transcription during cohesin loss and recovery

first: Erez

middle: L

last: Aiden


title: Heritable DNA methylation marks associated with susceptibility to breast cancer

city: Melbourne

first: Jihoon

middle: Eric

last: Joo

state: Vic

address: 305 Grattan Street

department: Clinical Pathology

country: Australia

institute: University of Melbourne

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA Methylation analysis of 210 affected and unaffected individuals from 25 Australian families with multiple cases of breast cancer without carrying a mutation at breast cancer susceptibility genes. Genome-wide methylation was assessed using the Infinium HumanMethylation450K platform.

overall_design: Genomic DNA from 210 whole blood samples was bisulfite converted and hybridised to the Infinium HumanMethylation450K (Illumina)

middle: E

first: James

last: Dowty

first: Roger

last: Milne

first: Ming

last: Wong

first: Pierre-Antoine

last: Dugue

first: Dallas

last: English

first: John

last: Hopper

first: David

last: Goldgar

first: Graham

last: Giles

first: Melissa

middle: C

last: Southey


title: CDK8 Mediator kinase drives colon cancer hepatic metastasis by regulating gene expression of the matrix metalloproteinase network

first: Mengqian

last: Chen


title: ATAC-seq analyses during spermatogenesis

city: Cincinnati

first: So

last: Maezawa

address: 3333 Burnet Ave.

department: Reproductive Sciences

institute: Cincinnati Children's Hospital Medical Center

summary: To determine the dynamics of open chromatin at a genomic resolution during spermatogenesis, we performed ATAC-seq and detected genomic regions of accessible chromatin by Tn5 transposase during spermatogenesis. We analyzed four representative stages of spermatogenesis: Thy1+ undifferentiated spermatogonia, which contains spermatogonial stem cells and progenitor cells; c-Kit+ differentiating spermatogonia from P7 testes; purified pachytene spermatocytes (PS) undergoing meiosis; and postmeiotic round spermatids (RS) from adult testes

overall_design: ATAC-seq analyses using purified spematogenic cells from wild-type mice and Scml2 knockout mice

first: Artem

last: Barski

first: Satoshi

last: Namekawa


title: MafB enhances oncogenic Notch signaling in T-ALL [ChIP-Seq]

first: Robert

last: Faryabi

summary: MafB effect on H3K27ac in T6E cell line

overall_design: histone acetylation mark H3K27Ac in T6E cells transduced with scrambled shRNA or MafB shRNA were compared

first: Jelena

last: Petrovic


title: Differential expression CTX positive and CTX negative Vibrio cholerae O139 strains

status: Public on Oct 12 2017

city: bhubaneswar

first: Durg

middle: Vijai

last: Singh

state: odisha

address: nalco square

department: infectious biology division

country: India

institute: institute of life sciences

summary: To gain an insight into the changes between CTX-positive and -negative strain, apart from the CTX phage deletion, we carried out microarray analysis and whole genome sequencing of both strains

overall_design: Organism : Vibrio cholerae, Agilent's V.cholerae GXP Expression  8x15k Array (AMADID: 022386) desined by Genotypic Technology, Bangalore

first: Moon

last: Das

middle: V


title: Genomic instability induced by furfural-treated in S. cerevisiae [whole genome]

first: Daoqiong

last: Zheng

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

type:
Genome variation profiling by array
Genome variation profiling by SNP array

summary: Furfural is a key inhibitor in S. cerevisiae fermentation causing serious economic loss. To understand the toxic mechanisms of furfural-induced genomic instability and phenotypic evolution, we mapped chromosomal alterations in 21 furfural-treated yeast strains by whole genome SNP microarrays at a resolution about 1kb.

overall_design: Using whole genome SNP microarrays, we analyzed genomic alterations in 21 yeast strains treated with 2% furfural for 2h repeated for 18 generations to accumulate genomic alterations. For each generation, after furfural treatment, cells were streaked on YPDA plates and cultured at 30 degree for 2 days to form single colony for the next round furfural treatment.

first: Lei

last: Qi

first: Ke

last: Zhang

first: Dao-Qiong


title: Genomic instability induced by furfural-treated in S. cerevisiae [sectored colonies]

summary:
Furfural is a key inhibitor in S. cerevisiae fermentation causing serious economic loss. To disclose of the recombinational DNA lesions induced by furfural, we analyzed 19 JSC25-derived sectored colonies using chromosome IV SNP-specific microarrays.

The parent diploid S. cerevisiae strain JSC25 (constructed by crossing two haploid strains isogenic W303-1A and YJM789) was homologous for ade2-1 alleles. One copy of gene SUP4-o, an ochre-suppressing tRNA, was inserted at the end of right arm of chromosome IV.  Under normal conditions, the colony color of JSC25 is pink. A crossover event occurred on the right arm of chromosome IV at the first cell cycle would result in a white/red sectored colony on solid plate.

overall_design: By SNP microarrays specific for chromosome 4, we analyzed 19 sectored colonies induced by furfural to uncover the details of furfural-induced reciprocal crossover.


title: Genomic instability induced by furfural-treated in S. cerevisiae


title: Expression data from APA+ and APA- progenitors and SSEA5+ human pluripotent stem cells

city: Neuherberg

first: Dmitry

last: Shaposhnikov

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Center Munich

summary:
Human embryonic stem cells (hESC) can be differentiated into progenitors resembling trophoblast upon exposure to BMP4. Putative trophpblast progenitors express APA cell surface marker
Using FACS sorting and microarray we analysed the gene expression of APA-positive trophoblast progenitors, APA-negative progenitors and SSEA5-positive undifferentiated hESC and identified genes that contribute to the trophoblast fate

overall_design: Undifferentiated hESC and hESC treated with BMP4 for 2.5 days (cell line H9) were FACS-sorted to isolate APA+, APA- and SSEA5+ cell populations. Sorted cells were subjected to RNA isolation and microarray protocol. The experiment was conducted using 3 independent differentiation experiments

first: Christian

last: Krendl


title: Gene expression signatures for combined ATO and CDDP treatment (Ato-C) in CML cell lines

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

summary: To investigate the effect of Ato-C on gene expression, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to suppress the cell proliferation of Ph+ CML cell lines.  K562, KU-812 and MEG-A2 cells were treated with ATO, CDDP or Ato-C for 24 h in vitro.

overall_design: K562, KU0812 and MEG-A cells were treated with ATO, CDDP or Ato-C for 24 h in vitro.

first: Md

last: Wahiduzzaman


title: Computational guideline for small RNA profiling in virus-infected plants

city: Murcia

first: Livia

last: Donaire

state: Murcia

address: Campus de Espinardo

department: Plant Pathology

country: Spain

institute: Centro de Edafología y Biología Aplicada del Segura

summary: We describe a series of computational pipelines for the in silico analysis of small RNAs (sRNA) produced in response to viral infections in plants. Our workflow is primarily focused on the analysis of sRNA populations derived from known or previously undescribed viruses infecting host plants. Furthermore, we provide an additional pipeline to examine host-specific endogenous sRNAs activated or specifically expressed during viral infections in plants. We present some key points for a successful and cost-efficient processing of next generation sequencing sRNA libraries, from purification of high quality RNA to guidance for library preparation and sequencing strategies. We report a series of free available tools and programs as well as in-house Perl scripts to perform in-house sRNA-seq data mining. A multi-step analysis pipeline is extensively detailed so previous bioinformatic background is not required, but experience with basic Unix commands is desirable.

overall_design: sRNAseq from Arabidopsis leaves non-infected and infected with Tobacco rattle virus (TRV)

first: Cesar

last: Llave


title: Response to the combination of farnesyltransferase inhibitors and gamma-secretase inhibitors in glioblastoma stem cells

status: Public on Oct 11 2017

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

summary: Notch-targeted gamma-secretase inhibitors (GSIs) exhibited limited efficacy in glioblastoma patients. We identified that farnesyltransferase inhibitors (FTIs) increased sensitivity to GSIs in glioblastoma stem cells. To interrogate the mechanisms mediating the interaction between these two classes of compounds, we studied the impact on gene expression profiles by the combination of tipifarnib (FTI) and RO4929097 (GSI). We found that this combination treatment significantly suppressed genes implicated cell cycle progression. Real-time PCR validated the activities of tipifarnib to modulate expression of cell cycle regulators. We also showed that RO4929097 sensitized glioblastoma stem cells to compounds targeting some of these cell cycle regulators, such as AURKB and CDK4/6. These results suggest that regulation of cell cycle progression partially mediates the ability of FTIs to sensitize glioblastoma stem cells to GSIs.

overall_design: Short-term cultures of CD133+ cells were derived and enriched from three glioblastoma xenograft lines and treated with 100 nM tipifarnib plus 100 nM RO4929097 for expression profiling assays.

first: Jialiang

last: Wang


title: The CBF1/L3MBTL3 axis promotes the repression of Notch signaling by the histone demethylase KDM1A

city: Ann Arbor

first: Jean-Francois

middle: Michel

last: Rual

state: Mi

address: 109 Zina Pitcher Place

institute: University of Michigan

summary: We performed ChIP-seq experiments to investigate on a genome-wide scale the co-localization of CBF1 (also known as RBPJ or CSL) and L3MBTL3 on chromatin in the MDA-MB-231 cell line. Analysis of the CBF1 and L3MBTL3 ChIP-seq experiments in the MDA-MB-231 cell line revealed a substantial and significant genome-wide co-localization on chromatin, in agreement with our hypothesis that CBF1 contributes to the recruitment of L3MBTL3 to chromatin.

overall_design: ChIP-seq experiments to investigate the co-localization of CBF1 and L3MBTL3 on chromatin in the MDA-MB-231 cell line.

first: Tao

last: Xu

first: Jean-François


title: RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of human mesenchymal stem cells differentiation from human embryonic stem cells and adult bone marrow mesenchymal stem cells

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

summary:
Purpose: The goals of this study are to identify the process and the key transcription factors and signaling pathways governing differentiation through comparing the transcriptome profilings in hESC samples collected from day 0 to day 7 after mesenchymal stem cells differentiation with human adult bone marrow MSCs.
Methods: mRNA profiles of human adult bone marrow MSCs and hESC samples collected from day 0 to day 7 after mesenchymal stem cells differentiation were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Conclusions: Our study represents the first detailed analysis of mesenchymal stem cells transcriptomes from human embryonic stem cells, generated by RNA-seq technology. We provide a framework for comparative investigations of expression profiles and help illustrate the key signaling and transcription factors during hESCs differentiation towards MSCs.

overall_design: 7 samples

first: Leisheng


title: A 17-molecule set as a predictor of complete response to neoadjuvant chemotherapy with docetaxel, cisplatin, and 5-fluorouracil in esophageal cancer

city: Yufu

first: Hajime

last: Fujishima

state: Oita

address: 1-1 Idaigaoka Hasama-machi

department: Gastroenterological and Pediatric Surgery

institute: Oita University Faculty of Medicine

summary: Background  Recently, neoadjuvant chemotherapy with docetaxel/cisplatin/5-fluorouracil (NAC-DCF) was identified as a novel strong regimen with a high rate of pathological complete response (pCR) in advanced esophageal cancer in Japan. Predicting pCR will contribute to the therapeutic strategy and the prevention of surgical invasion. However, a predictor of pCR after NAC-DCF has not yet been developed. The aim of this study was to identify a novel predictor of pCR in locally advanced esophageal cancer treated with NAC-DCF.  Patients and Methods   A total of 32 patients who received NAC-DCF followed by esophagectomy between June 2013 and March 2016 were enrolled in this study. We divided the patients into the following 2 groups: pCR group (9 cases) and non-pCR group (23 cases), and compared gene expressions between these groups using DNA microarray data and KeyMolnet. Subsequently, a validation study of candidate molecular expression was performed in 7 additional cases.  Results   Seventeen molecules, including transcription factor E2F, T-cell-specific transcription factor, Src (known as “proto-oncogene tyrosine-protein kinase of sarcoma”), interferon regulatory factor 1, thymidylate synthase, cyclin B, cyclin-dependent kinase (CDK) 4, CDK, caspase-1, vitamin D receptor, histone deacetylase, MAPK/ERK kinase, bcl-2-associated X protein, runt-related transcription factor 1, PR domain zinc finger protein 1, platelet-derived growth factor receptor, and interleukin 1, were identified as candidate molecules. The molecules were mainly associated with pathways, such as transcriptional regulation by SMAD, RB/E2F, and STAT. The validation study indicated that 12 of the 17 molecules (71%) matched the trends of molecular expression.  Conclusions   A 17-molecule set that predicts pCR after NAC-DCF for locally advanced esophageal cancer was identified.

overall_design: The aim of this study was to identify the predictors of pCR after NAC-DCF for locally advanced esophageal cancer. We investigated gene expressions in clinical esophageal cancer samples and performed comparisons between pCR cases and non-pCR cases using DNA microarray data and KeyMolnet (KM Data; www.km-data.jp). Esophageal cancer tissue samples were collected at biopsy during endoscopic examination before the administration of the first course of chemotherapy. The biopsy specimen was collected from an elevated part at the proximal side of the tumor in a unified manner. The specimens were frozen and preserved in a freezer maintained at −80℃. The pathological response was evaluated according to the Japanese Classification of Esophageal Cancer 11th edition as follows: grade 0, no recognizable cytological or histological therapeutic effect; grade 1a, viable cancer cells account for two-thirds or more of the tumor tissue; grade 1b, viable cancer cells account for between one-third and two-thirds of the tumor tissue; grade 2, viable cancer cells account for less than one-third of the tumor tissue; grade 3, no viable cancer cells are apparent (pCR). Patients were divided into 2 groups (pCR and non-pCR) according to the pathological response. We analyzed these data using 39 cases. The samples of RNA 1, 4, 7, 10, 12, 17, 24, 29, 35, and 43 were pCR group. The samples of RNA 3, 5, 6, 8, 9, 11, 14, 15, 16, 18, 19, 20, 21, 22, 25, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 41, and 42 were non-pCR group.

first: Shoichi

last: Fumoto

first: Tomotaka

last: Shibata

first: Kohei

last: Nishiki

first: Yoshiyuki

last: Tsukamoto

first: Tsuyoshi

last: Etoh

first: Masatsugu

last: Moriyama

first: Norio

last: Shiraishi

first: Masafumi

last: Inomata


title: Transcriptomic analysis of gibberellic acid and paclobutrazol treated rice seedlings under submergence

city: Hangzhou

first: Haiyan

last: Lin

state: Zhejiang

address: No 28, Rice Road, Fuyang Dist

institute: China National Rice Research Insititution

summary: Analysis of the impact of plant growth regulators on submergence tolerance of rice at gene expression level. The hypothesis tested in the present study was that the submergence-tolerance was improved by foliar application of paclobutrazol under sumergence stress conditions.

overall_design: Total RNA obtained from leaves of rice treated by plant growth regulators subjected to 4 days in submergence condition compared to un-plant growth regulators treatment.

first: Jing

last: Xiang

first: Jian

last: Zhang


title: Streptomyces tsukubaensis: transcriptomic response to tacrolimus repressing carbon sources

city: León

first: Antonio

last: Rodríguez-García

address: Avenida Real 1

institute: INBIOTEC

summary: In this work, we identified glucose and glycerol as tacrolimus repressing carbon sources in the important species Streptomyces tsukubaensis. A genome-wide analysis of the transcriptomic response to glucose and glycerol additions was performed using microarray technology. The transcriptional time series obtained allowed us to compare the transcriptomic profiling of S. tsukubaensis growing under tacrolimus producing and non-producing conditions. The analysis revealed important and different metabolic changes after the additions and a lack of transcriptional activation of the fkb cluster. In addition, we detected important differences in the transcriptional response to glucose between S. tsukubaensis and the model species Streptomyces coelicolor. A number of genes encoding key players of morphological and biochemical differentiation were strongly and permanently downregulated by the carbon sources. Finally, we identified several genes showing transcriptional profiles highly correlated to that of the tacrolimus biosynthetic pathway regulator FkbN that might be potential candidates for the improvement of tacrolimus production

overall_design: The transcriptomic experiment is composed of 54 samples from three time series named glucose, glycerol and maltose. Streptomyces tsukubaensis spores (10e9) were inoculated into 0.5-L flasks containing 100 mL of MGm-2.5 medium (PMID 22990582) and cultivated at 28 ºC, 220 rpm. Samples for RNA extraction were taken from flask cultures at 70 h, immediately before carbon source addition; then, glucose, glycerol or maltose were added and more samples were taken at 70.7 h, 72 h, 76 h, 80 h, 89 h, 92 h, 100 h, 124 h and 148 h. The final concentrations of glucose and glycerol were established at the same molarity (0.22 M; 2 % w/v and 4 % w/v for glucose and glycerol, respectively). The final concentration of maltose was  0.11 M (3 % w/v) in order to equalize the number of glucose molecules available after maltose incorporation. Each time series is composed of 2 biological replicates for 8 the first timepoints (70 h - 100 h) and 1 biological replicate for the rest of the culture time; i.e., only one culture was sampled at 124 h and 148 h. In summary, (8 timepoints × 2 replicates × 3 carbon sources) = 48 samples; (2 timepoints × 1 replicates × 3 carbon sources) = 6 samples; 48 + 6 = 54 samples in total.

first: María

last: Ordóñez-Robles

first: Fernando

last: Santos-Beneit

first: Silvia

last: Albillos

first: Paloma

last: Liras

first: Juan

middle: F

last: Martín


title: Epigenome analysis of whole blood samples in Chinese children

city: Shanghai

first: Lei

last: Shi

address: No. 1665 Kongjiang Road

institute: Xinhua Hospital, Shanghai Jiao Tong University School of Medicine

summary:
Methylome-wide DNA methylation profiling of whole blood samples in health children to find age-associated  methylation sites. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA
methylation profiles across approximately 485,000 CpGs in 48 samples. Samples included 29 boys and 19girls.

overall_design: Bisulphite converted DNA from the 48 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2

first: Zhimin

last: Wang


title: LncRNA/mRNA expression  in SKOV3/SKOV3_DDP/IOSE80

city: harbin

first: Gao

last: Ce

state: Heilongjiang

address: 哈尔滨市南岗区学府路246号

institute: The Second Affiliated Hospital of Harbin Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: To determine the lncRNA and mRNA expression profile in SKOV3/SKOV3_DDP/IOSE80, we uesed lncRNA microArray analysis form Arraystar to examine the expression of lncRNAs and mRNAs in SKOV3/SKOV3_DDP/IOSE80.

overall_design: we use three experimental groups: SKOV3/SKOV3_DDP/IOSE80, then perform lncRNAs chips by Arraystar Human lncRNAs chip (Arraystar)

first: Ce

last: Gao

first: Di

last: Zhao


title: Comparison of the transcriptomes of mESCs, E14.5 dental Sox2+ cell and P30 dental Sox2+ cells

city: Montpellier

first: Frederic

last: Michon

address: 80, rue Augustin Fliche

department: Institute for Neurosciences of Montpellier

country: France

institute: Inserm

summary: We compared the transcriptome of the Sox2+ cells in forming incisor (E14.5) to the Sox2+ cells in renewing incisor (P30), using the MTA Affymetrix array. We used mouse embryonic stem cells (mESCs) as naïve cell reference.

overall_design: Three biological replicates were used for each of the samples (mESCs, E14.5 Sox2+ dental cells and P30 Sox2+ dental cells). The mESCs were purchased. For the Sox2+ cells, each sample was composed of cells from multiple individuals (embryos or postnatal mice); embryonic incisors and postnatal labial cervical loops were dissected out from Sox2-GFP+ mice, digested into a single cell suspension and Sox2-GFP+ alive cells (AAD-) were collected using fluorescence-activated flow cytometry.

first: Maria

last: Sanz-Navarro


title: LaminB and H3K9me2 ChIP-seq During Mouse Cardiogenesis

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Progenitor cells require coordinated expression of lineage-specific programs, and the nuclear lamina has emerged as an important scaffold for organizing chromatin in many cell types. These ChIP-seq experiments accompany a study focused on defining nuclear organization changes during cardiac development. Specifically, these experiments map the binding sites of LaminB (a key nuclear lamina protein) and H3K9me2 (a histone modification enriched at the nuclear periphery) in mouse ESCs and ESC-derived cardiac myocytes. The observations of these experiments, within the context of the study, indicate that changes in the organization of key genes and cell-type specific genes occurs during cardiogenesis.

overall_design: A total of 18 samples are included for the ChIP-seq experiments. These include: (2) biological replicate samples of ESC LaminB ChIP-seq; (2) biological replicate samples of CM LaminB ChIP-seq; (2) biological replicate samples of ESC H3K9me2 ChIP-seq; (2) biological replicate samples of CM H3K9me2 ChIP-seq; (1) ESC Input; (1) CM Input; (2) biological replicate samples of uninduced (minus tamoxifen) CMV-creERT Hdac3f/f LB1 ChIP-seq; (2) biological replicate samples of uninduced (minus tamoxifen) CMV-creERT Hdac3f/f H3K9me2 ChIP-seq; (1) CMV-creERT Hdac3f/f Input; (2) biological replicate samples of induced (plus tamoxifen) CMV-creERT Hdac3f/f LB1 ChIP-seq; (1) induced (plus tamoxifen) CMV-creERT Hdac3f/f Input;

first: Andrey

last: Poleshko

first: Mudit

last: Gupta

first: Parisha

last: Shah

first: Apoorva

last: Babu

first: Lauren

middle: J

last: Manderfield

first: Jamie

last: Ifkovits

first: Damelys

last: Calderon

first: Haig

last: Aghajanian

first: Javier

last: Sierra-Pagan

first: Zheng

last: Sun

first: Qiaohong

first: Li

last: Li

first: Nicole

last: Dubois

first: Edward

last: Morrisey

first: Mitchell

middle: A

last: Lazar

first: Cheryl

last: Smith

first: Jonathan

last: Epstein

first: Rajan

last: Jain


title: Epithelial vimentin plays a functional role in mammary gland development

city: Turku

first: Emilia

last: Peuhu

address: Medisiina D5, Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of turku

summary: Primary mammary gland basal epithelial cells from adult vimentin knockout mice and their littermate controls

overall_design: mRNA seq data from 2 wt and 4 vimentin knockout mouse mammary gland basal epithelial cell samples

first: Reetta

last: Virtakoivu

first: Johanna

last: Ivaska


title: Molecular analyses of prostate tumors for diagnosis of malignancy on Fine-Needle Aspiration biopsies

first: qianllin

last: xia

address: 2901 Caolang Road, Jinshan District

institute: Shanghai Public Health Clinical Center, Fudan University

summary: Prostate cancer (PCa) is a common cancer and remains the second leading cause of cancer-associated mortality in men. To investigate the involvement of differentially expressing genes in PCa with deregulated pathways to allow earlier diagnosis of the disease, transcriptomic analyses of differential expression genes in Fine-Needle Aspiration (FNA) biopsies were for discrimination of PCa from benign prostatic hyperplasia (BPH). The RNA samples were extracted from four PCa biopsy samples and four BPH biopsy controls for microarray profiling and performed in Affymetrix Human U133 Plus 2 arrays for gene expression profiling analysis. Microarray data were analyzed using GeneSpring GX 10 (Agilent).On average, we detected expression of 47,000 transcripts.Under the criteria fold change > 2 or < 0.5, we obtained 1819 differential expressed genes(DEGs).Hierarchy cluster analysis also indicated that the 8 samples were distributed into two clusters, 4 PCa samples in one cluster and 4 BPH samples in another cluster.Then,qRT-PCR validation of the DEGs in PCa tissue and prostate cancer cells.The results revealed that grouping was reasonable and the data can be directly applied to further analysis.

overall_design: Examination of Prostate cancer (PCa) from benign prostatic hyperplasia (BPH) from n Fine-Needle Aspiration (FNA) biopsies

first: Menglin

last: Shan

first: Qianlin

last: Xia


title: microRNAs and their targets engage in apple-Valsa mali interaction

city: Yangling

first: Hao

last: Feng

state: Shaanxi

address: Taicheng Road 3#

department: State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection

institute: Northwest A&F University

summary: miRNAs were important regulators involving in plant-pathogen interactions. However, their roles in apple response to Valsa canker pathogen (Valsa mali, Vm) infection were poorly understood. In this study, we constructed two miRNA libraries using the bark tissues of apple twig (Malus domestica Borkh “Fuji”) inoculated with Vm (IVm) and PDA medium (control, BMd). Among the all miRNAs, 23 miRNAs were specifically isolated in BMd and 39 miRNAs were specifically isolated in IVm. Compared with BMd, the expression of 294 miRNAs decreased, and 172 miRNAs increased in IVm, respectively. We also identified the target genes of these miRNAs using degradome sequencing technology. In total, 353 differentially expressed miRNAs during the pathogen infection were detected to target 1 077 unigenes with 2 251 cleavage sites. Based on GO and KEGG analysis, the genes were found to be mainly related to transcription regulation and signal transduction. We further selected 17 miRNAs and 22 corresponding target genes to detect the expression profiles during pathogen infection. The results indicate that most of them are involved in apple twig-Vm interaction. What’s more, miRNAs and their corresponding target genes seem to regulate the apple twig-Vm interaction by forming many complicated regulation networks. It is worth that a conserved miRNAs mdm-miR482b, which was down regulated in IVm compared with BMd, has 14 potential target genes, and most of them were disease resistance related genes. More important, the feedback regulation of sRNA pathway in apple twig was much more complex and critical in the interaction between apple bark tissue and V. mali. The results provide insights into the crucial functions of miRNAs in the woody plant, apple tree-Vm interaction.

overall_design: miRNAs were isolated using high-throughput sequence analysis and their corresponding target genes were identified using degradome sequencing technology.

first: Ming

last: Xu

first: Xiang

last: Zheng

first: Tongyi

last: Zhu

first: Xiaoning

last: Gao

first: Lili

last: Huang


title: Brd4 and CEBPB binding profiles with or without BET inhibitor JQ1 in human leukemia OCI-AML3 cells

city: Stanford

first: Min

state: CA

address: 265 Campus Drive

department: Internal Medicine

institute: Stanford Cancer Institute

summary: Brd4 is the best characterized member of the bromo- and extra-terminal (BET) domain family of proteins and has been widely studied in tumor-associated transcriptional programs. Here we show that activation of Brd4 is associated with the presence of autophagy in NPMc+ and MLL AML cells. Brd4 binds to the promoters of Atg 3, 7 and CEBPb, and expression of these genes is markedly reduced by inhibitors of Brd4, as well as by Brd4-shRNA and CEBPb depletion. Inhibitors of Brd4 also dramatically suppress the transcription of Keap1, thereby increasing the expression of anti-oxidant genes through the Nrf2 pathway. We conclude that Brd4 plays a significant role in autophagy activation through the direct transcriptional regulation of genes essential for autophagy, as well as through the Keap1-Nrf2 axis in NPMc+ and MLL-fusion AML cells.

overall_design: Chromatin immunoprecipitation of Brd4 and CEBPB followed by high-throughput sequencing (ChIP-seq) in human NPMc+ leukemia OCI-AML3 cells in the presence or absence of BET inhibitor JQ1.

first: Beverly

last: Mitchell


title: Role of the glial glutamate exchanger xCT in ventral hippocampus in resilience to stress

city: New York

first: Carla

last: Nasca

state: NY

address: 1 Park Avenue

institute: NYU Grossman School of Medicine

summary: We demonstrate that stress differentially regulates glutamate homeostasis in the dorsal and ventral hippocampus and established a previously unknown role for the glial marker xCT in the homeostatic regulation of the ventral dentate gyrus (vDG) in stress resilience and antidepressant responses. We provide RNAseq roadmap for the stress-sensitive vDG and show that the transcription factor REST binds to xCT promoter in co-occupancy with the epigenetic marker H3K27acet, to negatively regulate xCT expression. Reduced xCT was also observed in a genetic mouse model of inherent susceptibility to depression. Pharmacologically modulating histone acetylation with next-generation therapeutics, such as acetyl-N-cysteine (NAC) or acetyl-L-carnitine (LAC), rapidly increased xCT reduction and activated a network that included mGlu2 receptors to prime an enhanced glutamate homeostasis that promoted stress resilience and antidepressant-like responses. Moreover, pharmacological xCT blockage counteracted NAC prophylactic effects. Anatomical (vDG) and cell-type specific (GFAP+) virus-overexpression mimicked the effects of pharmacological treatments in increasing stress resilience. These findings establish xCT as critical regulator of the glutamate system in a network with mGlu2 receptors. These studies also point to a role of histone acetylation as mediator of stress resilience.

overall_design: Ventral dentate gyrus RNA from 3 biological replicates per group (Not-stressed Controls or Ctrl and Chronic Restrained Stress or CRS, all male mice) was used for library prep (TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat) and sequenced on Illumina HiSeq2500 at the Genomic Core facility at The Rockefeller University. Each sample was provided with a unique adapter and all samples were put in the same pool and run in multiple lanes to control for lane effects with a sequencing depth of about 30M (100bp, single end).

first: Benedetta

last: Bigio

first: Danielle

last: Zelli

first: Paolo

last: de Angelis

first: Timothy

last: Lau

first: Masahiro

last: Okamoto

first: Hideaki

last: Soya

first: Jason

last: Ni

first: Lars

last: Brictha

first: Paul

last: Greengard

first: Rachael

last: Neve

first: Francis

last: Lee

first: Bruce

last: McEwen


title: Transcriptome analysis of Pseudomonas aeruginosa PAO1 Response to L-Ala, L-Asn and L-Asp

city: LOWELL

first: GUOQING

last: LI

state: MA

address: 220 Pawtucket St

institute: University of Massachusetts Lowell

summary: P. aeruginosa possesses the ability to utilize a wild range of compounds as the sole source of carbon and nitrogen, including proteogenic amino acids. In particular, utilization of L-Asp and L-Asn is insensitive to carbon catabolite repression as strong growth retains in the cbrAB mutants devoid of the essential regulators for the activation of most catabolic genes. Transcriptome analysis and functional characterization were conducted to identify genes that participate in the catabolism, uptake, and regulation of these two amino acids. Through gene knockout and growth phenotype analysis, degradation of L-Asn to L-Asp was shown to be mediated by two asparaginases AsnA and AsnB, whereas only AnsB is required for the deamidation of D-Asn to D-Asp. While D-Asp is a dead-end product, conversion of L-Asp to fumurate is catalyzed by an aspartase AspA as further evidenced by enzyme kinetics. The results from the measurements of promoter-lacZ expression in vivo and mobility shift assays in vitro demonstrated that the asnR and aspR genes encode two transcriptional regulators in response to L-Asn and L-Asp, respectively, for the induction of the ansPA operon and the aspA gene.  In addition, exogenous L-Glu also cause induction of the aspA gene, most likely due to its conversion to L-Asp by the aspartate transaminase AspC. Expression of several transporters were also found inducible by L-Asn and/or L-Asp, including AatJQMP for acid amino acids, DctA and DctPQM for C4-dicarboxylates, and PA5530 for C5-dicarboxylates. In summary, a complete pathway and regulation for L-Asn and L-Asp catabolism was established in this study. Cross induction of three transport systems for dicarboxylic acids may provide a physiological explanation for the insensitivity of L-Asn and L-Asp utilization to carbon catabolite repression.

overall_design: We conducted four independent microarray experiments in the presence (experimental) of L-Ala, L-Asn or L-Asp. P. aeruginosa PAO1 was grown aerobically in minimal medium P with 300 rpm shaking at 37°C, in the presence of 20mM Pyruvate with the addition of L-Ala, L-Asn or L-Asp at 20 mM.

first: Guoqing

last: Li

first: Chung-Dar

last: Lu


title: CD5−NK1.1+ γδ T cells that develop in a Bcl11b-independent manner participate in early protection against infection

city: Fukuoka

first: Yasunobu

last: Yoshikai

address: 3-1-1 Maidashi Higashi-ku

department: Division of Host Defense

institute: Medical Institute of Bioregulation, Kyushu University

summary: We recently found that a unique subset of innate-like γδ T cells develop from the DN2a-stage of the fetal thymus independent of the zinc-finger transcription factor B-cell leukemia/lymphoma 11b (Bcl11b). Herein we characterized these Bcl11b-independent γδ T cells in the periphery as CD5−NK1.1+ and Granzyme B+, and show that they are capable of producing interferon (IFN)-γ upon T cell receptor stimulation without Ca2+ influx. In wild-type mice, these cells were sparse in lymphoid tissues but abundant in non-lymphoid tissues such as the liver. Bcl11b-independent CD5−NK1.1+ γδ T cells appeared and contributed to early protection before Bcl11b-dependent CD5+NK1.1− γδT cells following Listeria monocytogenes infection, recapitulating their appearance during thymic development.

overall_design: We analyzed global gene expression by comparing the transcriptome profiles of whole γδ T cells from CreRag1;Bcl11b flox/flox  (flox/flox) mice, in which more than 99% were CD5−NK1.1+, prototypical Bcl11b-independent γδ T cells (CD5−NK1.1+ γδ T cells) and a prototypical Bcl11b-dependent γδ T cell subset (CD5+NK1.1− γδ  T cells) sorted from the liver of WT mice.

first: Shinya

last: Hatano

first: Tesshin

last: Murakami

first: Naoto

last: Noguchi

first: Hisakata

last: Yamada


title: Expression data of E12.5 Slc39a8 knockout (KO) embryo heart and wild type (WT) control

status: Public on Oct 10 2017

first: Wen

last: Lin

state: PA - Pennsylvania

address: 11-167, SCTR, 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Slc39a8 KO mouse embryo hearts exhibit ventricle noncompaction phenotype which becomes evident at E12.5. The goal of this experiment is to identify genes that are differentially expressed between Slc39a8 KO and WT, which may be underlying the phenotype.

overall_design: Whole heart was isolated from E12.5 mouse embryo, RNA was extracted and microarray was performed. N=4

first: Deqiang

first: Jonathan

last: Epstein

first: Daniel

last: Rader


title: Quantitative Transcriptome Analysis of T cells stimulated with STING ligands

city: Yokohama

first: Takayuki

last: Imanishi

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN Center for Integrative Medical Sciences (IMS)

summary: STING plays a key role in detecting cytosolic DNA and induces type I interferon responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. In this study, we show that costimulation of T cells via TCR and STING ligand induce  type I  IFN responses like innate immune cells.

overall_design: Naïve CD4+ T cells were stimulated with anti-CD3/28 in the presence or absence of STING ligand and analyzed the transcriptome using Illumina HiSeq1500.

first: Takashi

last: Saito


title: RNAseq on WT and Meteor KO Embryonic Stem Cells and day3 differentiated cells

city: Lausanne

last: Maric

state: Vaud

address: Rue du Bugnon 27

department: Coeur-vaisseaux

institute: CHUV

summary: We have demonstrated that Meteor KO cells are associated with a global transcriptional reprogramming associated to a block of Mesendoderm specification. Meteor KO cells loses their developmental competence for Mesendoderm specification in pluripotency and are redirected to a neuroectoderm fate.

overall_design: RNA profile on WT and Meteor KO Embryonic Stem Cells and day3 differentiated cells

first: Michael

last: Alexanian

first: Stephen

last: Jenkinson

first: Marco

last: Mina

first: Clayton

last: Friedman

first: Ching-Chia

last: Ting

first: Rudi

last: Micheletti

first: Isabelle

last: Plaisance

first: Mohamed

last: Nemir

first: Damien

last: Maison

first: Jasmin

last: Kernen

first: Iole

last: Pezzuto

first: Dominic

last: Villeneuve

first: Frédéric

last: Burdet

first: Mark

last: Ibberson

last: Leib

first: Nathan

last: Palpant

first: Nouria

last: Hernandez

first: Samir

last: Ounzain

first: Thierry

last: Pedrazzini


title: Potential forensic application of DNA methylation profiling for identical twin identification

city: daejeon

first: Jonglyul

last: Park

address: 52, Eoeun-dong, Yuseong-gu

department: Medical genomics

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Genome wide DNA methylation profiling of 12 paired monozygotic twin samples. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in 12 paired monozygotic twin samples.

overall_design: Bisulphite converted DNA from the 24 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Jong-Lyul

first: Yong-Sung

last: Kim

first: Seon-Young


title: Expression data of human CD4+CD45RA+CCR7+ Naïve T cells

city: London

first: Prashant

last: Hiwarkar

address: 30 Guildford street

country: United Kingdom

institute: Institute of Child health, UCL

summary:
T-cell replete cord blood transplantation results in a rapid thymus-independent T-cell reconstitution which  is strikingly CD4+ biased compared to the well-established observation of CD8+ T-cell biased expansion after T-cell replete bone marrow transplant.
We used microarrays to detail the distinct gene expression profile underlying rapid CD4+ T cell expansion following T-cell replete cord blood transplantation and identified distinct up-regulated pathways during this process.

overall_design: Twenty-four total samples were analyzed. Naive CD4+ T cells were selected from normal donor cord blood, normal donor peripheral blood and, from recipients of cord blood and bone marrow graft two months after stem cell transplantation. RNA was extracted from naive CD4+ T cells and hybridized on Affymetrix microarrays. Biological replicates of samples from normal donor cord blood (n=3) and normal donor peripheral blood (n=3) were compared in 3 separate experiments. The third experiment compared cord blood and peripheral blood samples from the same donors, thus allowing a paired analysis. In the same experiment, we also performed biological replicates of reconstituting naïve CD4+ T cells at two months after cord blood transplantation (n=3) and bone marrow transplantation (n=3).

first: Paul

last: Veys


title: Activation of the p53 transcriptional program sensitizes cancer cells to Cdk7 inhibitors

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Cdk7, the CDK-activating kinase and transcription factor IIH component, is a target of inhibitors that kill cancer cells by exploiting tumor-specific transcriptional dependencies. However, whereas selective inhibition of analog-sensitive (AS) Cdk7 in colon cancer derived cells arrests division and disrupts transcription, it does not by itself trigger apoptosis efficiently. Here we show that p53 activation by 5-fluorouracil or nutlin-3 synergizes with a reversible Cdk7as inhibitor to induce cell death. Synthetic lethality was recapitulated with covalent inhibitors of wild-type Cdk7, THZ1 or the more selective YKL-1-116. The effects were allele-specific; a CDK7as mutation conferred both sensitivity to bulky adenine analogs and resistance to covalent inhibitors. Non-transformed colon epithelial cells were resistant to these combinations, as were cancer-derived cells with p53-inactivating mutations. Apoptosis was dependent on death receptor DR5, a p53 transcriptional target whose expression was refractory to Cdk7 inhibition. Therefore, p53 activation induces transcriptional dependency to sensitize cancer cells to Cdk7 inhibition.

overall_design: RNAseq in colorectal cancer cell line HCT116 in the presence or absence of CDK7 and p53 inhibitors

first: Sampada

last: Kalan

first: Ramon

last: Amat

first: Miriam

middle: M

last: Shachter

first: Nicholas

last: Kwiatkowski

first: Brian

last: Abraham

first: Yanke

last: Liang

first: Tinghu

last: Zhang

first: Calla

first: Stéphane

last: Larochelle

first: Nathanael

last: Gray

first: Robert

last: Fisher


title: RNAseq of Burkholderia pseudomallei TctR mutant, a regulator of type VI secretion

status: Public on Oct 09 2017

city: Rockville

first: Liliana

last: Losada

state: MD

address: 9704 Medical Center Dr

institute: JCVI

summary: We report the transcriptome of Burkholderia pseudomallei type VI secretion regulator TctR mutant grown in rich media compared to wild type.  The RNA-seq studies confirmed the role of TctR as a negative regulator of T6SS-2, a positive regulator of T6SS-6 and suggest a potential role in regulation of the T6SS-3 and T6SS-4 gene clusters.

overall_design: To identify genes regulated by TctR, wild type and tctR mutant cells were grown in LB to log phase and the transcriptomes were compared between strains.

first: April

last: Shae

first: David

last: DeShazer


title: miRNA expression microarrays in GM-CSF or GM-CSF+IL6-induced mouse MDSC

city: tianjin

first: Yunhuan

last: Gao

address: Wei Jin Road No. 94

department: School of Medicine

institute: Nankai University

summary: Myeloid-derived suppressor cells (MDSCs) have emerged as major regulators of immune responses in cancer and other pathological conditions. Multiple factors including cytokines, transcription factors  and multiple signaling pathways are involved in MDSC differentiation. Cytokines such as granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin(IL-6) etc could in vitro mediate development of MDSCs.IL-6 with GM-CSF mediated MDSC not only had stronger suppressive function but also the dynamics of their suppressive function was different from GM-CSF alone mediated MDSCs.To found a new regulatory factor (s) in tumor and inflammatory environments, we compared GM-CSF and IL-6 mediated MDSCs with GM-CSF alone mediated MDSCs using lncRNA microarray, miRNA microarrays and protein-coding mRNA microarrays.

overall_design: Inflammatory factors associated MDSCs were generated by cultivating bone marrow cells of C57BL/6 mice in petri dishes for 4 days in the presence of 5% FBS medium containing GM-CSF (40 ng/ml) only, GM-CSF (40 ng/ml) plus IL-6 (40 ng/ml) using different processing group for each experiment.

first: Shiyue

last: Mei

first: Rongcun

last: Yang


title: mRNA and long noncoding RNA expression microarrays in GM-CSF or GM-CSF+IL6-induced mouse MDSC

summary: Myeloid-derived suppressor cells (MDSCs) have emerged as major regulators of immune responses in cancer and other pathological conditions. Multiple factors including cytokines, transcription factors  and multiple signaling pathways are involved in MDSC differentiation. Cytokines such as granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin(IL-6) etc could in vitro mediate development of MDSCs.IL-6 with GM-CSF mediated MDSC not only had stronger suppressive function but also the dynamics of their suppressive function was different from GM-CSF alone mediated MDSCs.To found a new regulatory factor (s) in tumor and inflammatory environments, we compared GM-CSF and IL-6 mediated MDSCs with GM-CSF alone mediated MDSCs using lncRNA microarray and protein-coding mRNA microarrays.


title: Downregulation of p53 drives autophagy during human trophoblast differentiation

city: Graz

first: Andreas

last: Prokesch

state: Styria

address: Harrachgasse 21/7

department: Institute of Cell Biology, Histology, and Embryology

institute: Medical University Graz

summary: A functional placental barrier is crucial for the supply of the embryo or foetus throughout pregnancy. It is formed by the syncytiotrophoblast, which develops via fusion of cytotrophoblast cells. How this “differentiation-by-fusion” is regulated is only partially understood. Here we analysed transcriptome changes during in vitro cytotrophoblast fusion. Pathway analyses yielded the tumor suppressor p53 as upstream negative regulator and indicated an upregulation of autophagy-related genes. We further showed that, during differentiation, p53 is downregulated on the mRNA and protein levels, while the autophagy marker LC3B-II (lipidated LC3B) is increased. In first-trimester placentae, we find reciprocal expression patterns of p53 and LC3B, with p53 expression primarily in cytotrophoblasts and predominant LC3B expression in the apical side of the syncytiotrophoblast layer. Furthermore, in the syncytiotrophoblast, we could show increased autophagic flux, which is alleviated by ectopically overexpression of p53. This was also shown in placental explants treated with a pharmacological p53 activator. On the contrary, in a fusion-deficient trophoblast cell line we could not see an interdependency of p53 and LC3B lipidation. In summary our data suggests, that the downregulation of p53 during syncytialization is a prerequisite for the activation of autophagy in the placental barrier.

overall_design: Trophoblast cell line BeWo was used as in vitro model to study global transcriptome changes in villous trophoblast differentiation. For this purpose BeWo cells were cultured for 48h in presence of forskolin, a compound well described to induce syncytiotrophoblast formation. Control cells were treated with solvent for 48 hours (DMSO). Each group comprised three replicates.

first: Martin

last: Gauster

first: Sabine

last: Maninger

first: Monika

last: Siwetz

first: Urlsula

last: Hiden

first: Gernot

last: Desoye

first: Florian

last: Herse


title: Erasure of Tet-oxidized 5-methylcytosine by a SRAP nuclease

city: Los Angeles

first: Douglas

middle: Edmund

last: Feldman

address: 2011 Zonal Avenue

department: Pathology

institute: USC Keck School of Medicine

type: Methylation profiling by high throughput sequencing

summary: Enzymatic oxidation of 5-methylcytosine (5mC) in DNA by the Tet (Ten-eleven translocation) family of dioxygenases reprograms genome function during pre-implantation development and in primordial germ cells. Tet-oxidized derivatives of 5mC such as 5-hydroxymethylcytosine (5hmC) act as transient intermediates in DNA demethylation or serve as stable epigenetic marks, yet how these alternate fates are specified at individual CpGs is not understood. Here, we report that the Sos-response associated peptidase (SRAP) domain-containing protein Srap1, the mammalian orthologue of an ancient protein superfamily operonically associated with the DNA damage response in bacteria and bacteriophage, binds directly and selectively to Tet-oxidized forms of 5mC in DNA and catalyses turnover of these bases to unmodified cytosine by an autopeptidase cleavage-coupled endonuclease. Biallelic inactivation of Srap1 in mouse embryonic stem (ES) cells results in the global accumulation of Tet-oxidized 5mC derivatives, with ectopic 5hmC in promoters of highly expressed genes, across gene bodies and within enhancer elements. Srap1 deficiency causes partially penetrant lethality in late blastocysts prior to uterine implantation, while surviving midgestation embryos exhibit aberrant patterns of DNA methylation associated with altered gene expression, including hypermethylation in regions closely linked to ectopic 5hmC detected earlier in development. Thus, highly specific removal of 5hmC and its oxidized derivatives by Srap1 sustains genome-wide DNA methylation homeostasis. These findings establish a function for a previously unknown structural class of DNA base modification-specific eraser enzymes that combine the catalytic properties of an autopeptidase with endonuclease activation, and position Srap1 as a key determinant of 5mC demethylation trajectories during mammalian embryonic development.

overall_design: Analysis of Srap1 distribution by ChIP-seq and 5mC/5hmC/5fC/5caC distribution by DIP-seq in wild-type and Srap1 knockout (KO) mouse ES cells.  RNA-seq profiling in wild-type and Srap1 KO mouse ES cells. RRBS analysis of E9.5 wild-type and Srap1 KO embryos.

first: Soo-mi

last: Kweon

first: Bing

last: Zhu

first: Yibu

last: Chen

first: L

last: Aravind

first: Shuang-Yong

last: Xu


title: No reliable gene expression biomarkers of current or impending neurocognitive impairment in peripheral blood monocytes of persons living with HIV

status: Public on Oct 07 2017

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South

department: Human Genetics

institute: University of California, Los Angeles

summary: Analysis of HIV-associated neurocognitive disorder (HAND) in peripheral monocytes at the gene expression level. The hypothesis tested in the present study was that monocyte gene expression would be predictive of HAND. Results provide  information of the associations between monocytes and global neurocognitive function.

overall_design: Total RNA obtained from monocytes purified from the blood of HIV+ and HIV- subjects with neurocognitive profiling.

first: Andrew

last: Levine


title: Role of ERb in neural differentiation of mouse embryonic stem cells

city: Huddinge

first: Ivan

last: Nalvarte

address: Hälsovägen 7

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

summary:
Global gene expression profile of midbrain neural differentiation of mESCs from WT and ERb knockout mice, with or without the selective ERb agonist LY3201 (0.5 nM).
Estrogen receptor beta (ERβ) is highly expressed in the fetal brain and is essential for proper corticogenesis during development. Nevertheless, the transcriptional signatures regulated by ERβ during defined neural differentiation stages have not been investigated. In the present study we used mouse embryonic stem cells (mESCs) from wildtype (WT) and ERβ knockout (BERKO) mice to derive neural precursor cells (NPCs) and further differentiated these towards defined midbrain neural fates. This allowed us to systematically investigate transcriptionally active determinants during stages of midbrain neurogenesis. We found that ERβ is important during early neural development in regulating proliferation and maintaining the stem cell pool of neuroepithelial and midbrain stem cells. Detailed gene profiling analysis revealed that loss of ERβ perturbs normal neurogenesis by affecting the expression of factors involved in cell adhesion, axon guidance, and signaling of Notch, Wnt, glutamate- and GABA receptors. Among these we identified several factors that are crucial for dopaminergic neuron development and maintenance, as well as the promotion of oligodendrocyte differentiation. We also demonstrate that these effects are largely independent of ligand activated ERβ. Our data identifies ERβ as an important component in midbrain neurogenesis, where its disruption results in premature depletion of the neural stem cell pool in favor of oligodendrogliogenesis.

overall_design: WT and ERb knockout (BERKO) mESCs were differentiated to neural precursor cells (NPCs), midbrain neural precurosors (mDPCs) and mature midbrain neurons (MNs). Two biological replicates from all stages were used (except fo runtreated BERKO MNs which had three biological replicates), in total 29 samples. mESCs: 2 WT, 2 BERKO; NPCs: 2 WT, 2 WT+LY3201, 2 BERKO, 2 BERKO+LY3201; mDPCs: 2 WT, 2 WT+LY3201, 2 BERKO, 2 BERKO+LY3201; MNs: 2 WT, 2 WT+LY3201, 3 BERKO, 2 BERKO+LY3201. The analysis was performed using Affymetrix Mouse Clariom D (MTA 1.0) array.

first: Mukesh

middle: K

last: Varshney

first: José

last: Inzunza

first: Diana

last: Lupu

first: Vaidheeswaran

last: Ganapathy

first: Per

last: Antonson

first: Joëlle

last: Rüegg

first: Margaret

last: Warner

first: Jan-Åke

last: Gustafsson


title: RNA-Seq Profiling of Pharmacological Activation of PXR and CAR Mice

city: Seattle

first: Julia

middle: Yue

last: Cui

state: WA

address: 4225 Rossevelt Way Ne

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: This study aimed to quantify and compare the mRNA abundance of major xenobiotic processing genes in liver following activation of PXR and CAR using RNA-Seq

overall_design: mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.

middle: Y

first: Joseph

last: Dempsey


title: AR-independent prostate cancer is sustained through FGF signaling

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Androgen receptor (AR) signaling is a distinctive feature of prostate cancer (PC) and represents the major therapeutic target for the treatment of metastatic disease. Though highly effective, AR antagonism has the potential to generate tumors that bypass a functional requirement for AR activity. We show here that a phenotypic shift has occurred in metastatic PCs with the emer-gence of a double-negative AR-null neuroendocrine-null phenotype that is notable for MAPK and FGF pathway activity. To identify mechanisms capable of sustaining PC survival, we gener-ated a model system designated AR program-independent prostate cancer (APIPC) which re-sists AR-targeted therapeutics, lacks neuroendocrine features, expresses high levels of FGF8 and the ID1 oncogene, and activates MAPK signaling. Pharmacological blockade of MAPK or FGF signaling inhibited APIPC tumor growth, supporting FGF/MAPK as a therapeutic avenue for treating AR-null PC.

overall_design: RNA sequencing of human prostate tumor cell lines using the Illumina TruSeq Library prep and sequenced on Illumina HiSeq 2500.

first: Eric

middle: G

last: Bluemn

first: Colm

last: Morrissey

first: Roger

first: Jared

last: Lucas

first: Susana

last: Hernandez-Lopez

first: Robin

last: Tharakan

first: Daniella

last: Bianchi-Frias

first: Alexandra

last: Corella

first: Yu

last: Yang

first: Michael

last: Nyquist

first: Elahe

last: Mostaghel

first: Xiaotun

last: Zhang

first: Eva

last: Corey

first: Lisha

last: Brown

first: Holly

last: Nguyen

first: Kenneth

last: Pienta

last: Ittmann

first: Larry

last: True

first: David

last: Wise

first: Paul

middle: S

last: Rennie

first: Robert

last: Vessella

first: Peter

last: Nelson


title: mRNA-seq comparison of N2 and tps1;tps2 double mutants with and without trehalose supplementation

city: Eugene

first: Amy

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

summary: Wild-type (N2) and tps1;tps2 double mutant embryos were resuspended at 1 embryo/uL in S-basal with or without 50mM trehalose. Samples were collected after 24 hours after bleach as L1 larvae

overall_design: 4 biological replicates were sequenced for each of four conditions: N2 in S-basal, tps-1;tps-2 in S-basal, N2 in 50mM trehalose, and tps-1;tps-2 in 50mM trehalose

first: A

first: J

middle: D

last: Hibshman

first: R

last: Chitrakar

first: L

middle: R

last: Baugh


title: CDK9-dependent RNA polymerase II pausing controls transcription initiation

city: Göttingen

first: Björn

last: Schwalb

address: Fassberg 11

institute: MPI

summary: Gene transcription can be activated by decreasing the duration of RNA polymerase II pausing in the promoter-proximal region, but how this is achieved remains unclear. Here we use a ‘multi-omics’ approach to show that the duration of polymerase pausing generally limits the frequency of transcription initiation in human cells (‘pause-initiation limit’). We further engineer a human cell line to allow for specific and rapid inhibition of the P-TEFb kinase CDK9, which is implicated in polymerase pause release. We show that CDK9 activity decreases the pause duration but also increases the initiation frequency. This shows that CDK9 stimulates release of paused polymerase and activates transcription by increasing the number of transcribing polymerases and thus the amount of mRNA synthesized per time. CDK9 activity is also associated with long-range chromatin interactions, suggesting that enhancers can influence the pause-initiation limit to regulate transcription.

overall_design: We performed mNET-seq reactions including empigen BB detergent treatment during immunoprecipitation in two biological replicates of human Raji B lymphocyte (CDK9as) cells treated for 15 min with DMSO (control) or 5 µM 1-NA-PP1 (CDK9as inhibitor). We performed TT-seq reactions including RNA spike-ins in two biological replicates of human Raji B lymphocyte (wild type, or CDK9as) cells treated for 15 min with DMSO (control) or 5 µM 1-NA-PP1 (CDK9as inhibitor), including 5 minutes of 4sU labeling. Raji B lymphocyte (CDK9as) cells were engineered using the CRISPR/Cas9 system and contain a homozygous mutation (F103A) at the CDK9 gene loci.

first: Saskia

last: Gressel

first: Tim

last: Decker

first: Weihua

last: Qin

first: Heinrich

last: Leonhardt

first: Dirk

last: Eick

first: Patrick

last: Cramer


title: Integrated Transcriptomic and Epigenomic Comparison of Human Induced Pluripotent Stem Cells Generated from Various Reprogramming Methods

city: Stanford

first: Jared

last: Churko

address: 265 Campus Dr G1105 SIM1

department: Radiology

institute: Stanford

summary: Within the last decade, multiple reprogramming methods have been developed to generate human induced pluripotent stem cells (hiPSCs) which closely resemble human embryonic stem cells (hESCs). This has led to studies which assess how similar hiPSCs are to hESCs, by evaluating the differences in gene expression, epigenetic marks, and differentiation potential. However, these studies were all performed using hiPSCs acquired from different laboratories, passage numbers, culturing conditions, genetic backgrounds, and reprogramming methods which may contribute to the reported differences. In this study, we reprogrammed the same primary fibroblast population with six different reprogramming methods (episomal vectors, mRNA, microRNA/mRNA transfections (microRNA), minicircle vectors, lentivirus, and Sendai virus) and performed high-throughput sequencing on the hiPSCs with standardized cell culturing conditions and passage number. RNA-sequencing on all of our lines determined that clones derived from the same reprogramming method clustered together, which may indicate the reprogramming method could influence the resulting gene expression profile of the hiPSCs. In comparison to hESCs, a significant proportion of differentially expressed and spliced genes could be attributed to polycomb repressive complex (PRC) targets and the activity of HDAC2, SOX2, NANOG, LEF1, TCF3, and c-MYC transcription factors. Differences in epigenetic signatures (H3K4me3, H3K27me3, and HDAC2 ChIP-seq profiles) also corresponded to the activity of these factors.  In addition, some hiPSC lines displayed a more similar PRC transcriptome profile to that of hESCs, and these lines also produced a higher percentage of cardiac troponin-T positive cells after cardiomyocyte differentiations were performed in parallel.  Collectively, differential PRC activity contributes to the differences between hESCs and hiPSCs and likely impacts the differentiation potential of hiPSCs.

overall_design: We profiled hESCs and hiPSCs by RNA-seq and ChIP-seq for H3K27me3 and H3K4me3 marks. In addtion, we performed ChIP-seq for HDAC2 in hiPSCs and hESCs.


title: Architectural alterations of the fission yeast genome across the cell cycle

first: Hideki

last: Tanizawa

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

summary:
Eukaryotic genomes are highly ordered through various mechanisms, including topologically associating domain (TAD) organization. We employed an in situ Hi-C approach to follow the 3D organization of the fission yeast genome during the cell cycle. We demonstrate that during mitosis, large domains of 300 kb–1 Mb are formed by condensin. This mitotic domain
organization does not suddenly dissolve, but gradually diminishes until the next mitosis. By contrast, small domains of 30–40 kb that are formed by cohesin are relatively stable across the cell cycle. Condensin and cohesin mediate long- and short-range contacts, respectively, by bridging their binding sites, thereby forming the large and small domains. These domains are inversely regulated during the cell cycle but assemble independently. Our study describes the chromosomal oscillation between the formation and decay phases of the large and small domains, and we predict that the condensin-mediated domains serve as chromosomal compaction units.

overall_design: Hi-C experiment of 20,30,40,50,60,70,80,120min and cut3, cut14, rad21, cut14 & cut3 double mutant and wild type cell. RNA-seq experiment of wild type, cut14, cut3 mutant.

first: Ken-ichi

last: Noma


title: Single stranded DNA formation during S phase in orc4Y232C yeast cells

status: Public on Oct 06 2017

first: Joseph

last: Sanchez

state: Washington

address: Foege Building S-250, 3720 15th Ave NE

department: Molecular and Cellular Biology

summary: A form of dwarfism known as Meier-Gorlin syndrome (MGS) is caused by recessive mutations in one of six different genes (ORC1, ORC4, ORC6, CDC6, CDT1, and MCM5).  These genes encode components of the pre-replication complex, which assembles at origins of replication prior to S phase.  Also, variants in two additional replication initiation genes have joined the list of causative mutations for MGS (Geminin and CDC45).  The identity of the causative MGS genetic variants strongly suggests that some aspect of replication is amiss in MGS patients; however, little evidence has been obtained regarding what aspect of chromosome replication is faulty.  Since the site of one of the missense mutations in the human ORC4 alleles is conserved between humans and yeast, we sought to determine in what way this single amino acid change affects the process of chromosome replication, by introducing the comparable mutation into yeast (orc4Y232C).  To examine early replication dynamics on a genome-wide scale in orc4Y232C cells, we utilized an assay that was previously developed in our lab.  This assay uses microarray hybridization to measure the levels of single stranded DNA exposed at replication forks.  While we do not fully understand the molecular processes that give rise to peaks of different amplitudes—e.g., number of cells that have activated a particular origin vs. amount of ssDNA revealed at different forks—the results from different replicates of the experiment are highly reproducible.  We find that origins that are known to fire early and are efficient produce the peaks of greatest magnitude, while later firing and less efficient origins produce smaller or no peaks in this assay.  The characteristic time and/or efficiency of origin firing within the S phase is altered for at least 15% of the 300 yeast origins.  Among the origins with delayed/reduced origin firing are normally early-firing origins adjacent to centromeres.

overall_design: To investigate the dynamics of ssDNA formation on a genomic scale, we harvested cells at discrete times after releasing them from late G1 phase arrest with alpha factor into a synchronous S phase in the presence of 200 mM HU. Chromosomal DNA isolated from these S phase samples and an alpha factor arrested G1 control sample were differentially labeled with Cy-conjugated deoxyribonucleotides by random priming and synthesis without denaturation of the DNA, followed by co-hybridization to a microarray. Because the labeling was done without denaturation of the template DNA, single-stranded regions of the genome should preferentially act as templates for dye incorporation. Comparison of experimental (S phase) and control (G1 phase) samples from the microarray hybridization revealed regions of the genome that became single-stranded in S phase. The calculated total percentages of ssDNA in the samples were then used to normalize the raw ratio of ssDNA (S/G1) (raw data) to generate the normalized ratio of ssDNA (S/G1) (raw normalized data). The normalized relative ratio of ssDNA was then smoothed over a 22 kb window (smoothed data) via loess smoothing.  Peaks of S-phase specific ssDNA accumulation mark locations of active origins.

middle: C

first: M

last: Raghuraman

first: Bonita

last: Brewer


title: Expression data from Imiquimod-induced psoriasis mouse model

city: Ibaraki

first: Yayoi

last: Natsume-Kitatani

state: Osaka

address: 7-6-8 Asagi Saito

institute: National Institutes of Biomedical Innovation, Health and Nutrition

summary: Psoriasis is a chronic inflammatory skin disorder that is predominantly characterized by sharply demarcated chronic erythematous plaques. Although its etiological mechanisms are largely unknown, recent evidence suggests that the topical application of imiquimod (IMQ) cream causes psoriasis-like skin inflammation in humans and mice. Skin examined 4 hours after IMQ cream treatment. Results provide insight into the role of each knockout mice phenotype in the response to IMQ-induced psoriasis model.

overall_design: WT, Card14−/−, Tlr7−/−, Tlr9−/−, and Tlr7−/−Tlr9−/− mice were treated with or without a topical dose of 62.5 mg of Beselna cream containing 5% Imiquimod (Mochida Pharmaceutical Co., Ltd). Total RNA was isolated from control and IMQ-treated (4 h) whole-ear skin using TRIzol reagent (Invitrogen) and purified using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Equal aliquots of total RNA from six to eight mice were pooled (total, 10ug), and treated with DNase with the RNase-Free DNase Set (Qiagen). RNA quality and quantity were determined with a Bioanalyzer 2100 (Agilent Technologies). In brief, 200 ng of total RNA was labeled with Cy3 using the SurePrint G3 Mouse Gene Expression v2 8x60K Microarray Kit (Agilent) at the DNA-chip Development Center for Infectious Diseases (University of Osaka). After background subtraction, quartile normalization was performed with the limma package in R (R Development Core Team [2011]).

first: Mayuri

last: Tanaka

first: Ken

last: Ishii


title: Complex immune evasion strategies in classical Hodgkin lymphoma

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary: The cellular microenvironment in classical Hodgkin lymphoma (cHL) is dominated by a mixed infiltrate of inflammatory cells with typically only about 1% Hodgkin and Reed/Sternberg (HRS) tumor cells. T cells are usually the largest population of cells in the cHL microenvironment, encompassing T helper (Th) cells, regulatory T (Treg) cells and cytotoxic T cells. Th and Treg cells presumably provide essential survival signals for HRS cells. Treg cells are also involved in rescuing HRS cells from anti-tumor immune responses. An understanding of the immune evasion strategies of HRS cells is not only highly relevant for a characterization of the pathophysiology of cHL, but also clinically, given the current treatment approaches targeting checkpoint inhibitors. Here, we characterized the cHL-specific CD4+ T cell infiltrate regarding its role in immune evasion. Global gene expression analysis of CD4+ Th and Treg cells isolated from cHL lymph nodes and reactive tonsils revealed that Treg cell signatures were enriched in CD4+ Th cells of cHL. Hence, HRS cells may induce a Treg differentiation in Th cells, which was supported by in vitro studies with Th cells and cHL cell lines. Furthermore, we found indication for immune-suppressive purinergic signaling and a role of the inhibitory receptor-ligand pairs BTLA-HVEM and CD200R-CD200 in promoting immune evasion. Taken together, this study reveals that the immune evasion strategies in cHL are even more complex and multifaceted than previously recognized.

overall_design: Human CD4+ T helper (CD127+ CD25-) cells and Treg (CD127- CD25+) cells from tonsils were compared with these populations from Hodgkin lymphoma samples.

first: Frederik

last: Wein


title: Role of N-α-acetyltransferase 10 Protein in DNA Methylation and Genomic Imprinting

status: Public on Oct 05 2017

city: Taipei

first: Li-Jung

last: Juan

address: 128 Academia Road, Section 2, Nankang

department: Genomic Research Center

country: Taiwan

institute: Academia Sinica

summary: Genomic imprinting is an allelic gene expression phenomenon primarily controlled by allele-specific DNA methylation at the imprinting control region (ICR), of which the underlying mechanism remains largely unclear. Mammalian N-α-acetyltransferase 10 protein (Naa10p) catalyzes N-α-acetylation of nascent proteins. Mutation of human Naa10p is linked to severe developmental delays. Here we report that Naa10-null mice display partial embryonic lethality, growth retardation, brain disorder and maternaleffect lethality, phenotypes commonly observed in defective genomic imprinting. Genome-wide analyses further revealed global DNA hypomethylation and enriched dysregulation of imprinted genes in Naa10p-knockout embryos and ES cells. Mechanistically, Naa10p facilitates the binding of DNA methyltransferase 1 (Dnmt1) to DNA substrates and recruits Dnmt1 to ICRs of the imprinted allele during S phase. Moreover, the clinical lethal Ogden syndrome-associated mutation of Naa10p disrupts its binding to H19-ICR and Dnmt1 recruitment. Our study thus links Naa10p mutationassociated human disease to defective DNA methylation and genomic imprinting.

overall_design: Examination of Naa10p binding sites in WT mouse embryonic stem (ES) cells using Naa10-KO ES cells as control

first: Chen-Cheng

last: Lee


title: Genomic profiles of oxidative stress-induced renal cell carcinomas developed in Mutyh deficient mice

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

institute: Nagoya University

type: Genome variation profiling by genome tiling array

summary: Intraperitoneal administration of ferric nitrilotriacetate initiates Fenton reaction in the renal proximal tubules in rodents that ultimately leads to a high incidence of renal cell carcinoma (RCC) after repeated treatment. We performed high-resolution microarray comparative genomic hybridization to identify characteristics in the genomic profiles of oxidative stress-induced RCCs and simultaneously developed malignant lymphomas in the mice. The results highlighted a substantial difference in the predisposition to chromosomal changes between animal species.

overall_design: The carcinogenesis protocol was performed for two groups of wild type mice and Mutyh deficient mice. Genomes of 4 renal cell carcinomas and 5 malignant lymphomas from the treated groups were profiled on Agilent 180K mouse genome CGH microarrays. Three spontaneous malignant lymphomas from the untreated control groups were also analyzed with the same Agilent CGH microarrays.

first: Guang-Hua

last: Li

last: Akatsuka


title: Integrator orchestrates RAS/ERK1/2 signaling transcriptional programs

status: Public on Oct 08 2017

city: Miami

first: Jingyin

last: Yue

state: FL

address: 1501 NW 10th Ave

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

summary: We investigated the occupancy of RNA PolII and INTS11 during the stimulation of EGF and compared with drug treated condition using inhibitors against MAPK pathway and Integrator. Additionally, we examined transcription by sequencing the chromatin-bound fraction of RNA.

overall_design: We employed several cel lines in our experiment, including HELA, KRAS mutant lung cancer cell line A549 and BRAF mutatant melanoma cell line A375.  The conditons we  checked including EGF stimulation, MAPK pathway inhibition using BRAF, MEK or ERK inhibitiors, targeting INTS11 with RNAi or integrator inhibitor.  We used RNA sequencing to measure the expression profile and CHIP sequencing to detect INTS11 and RNA PolII recruitment on chromatin.

first: Fan

last: Lai

first: Chiara

last: Pastori

first: Anda

last: Zhang

first: Felipe

last: Beckedorff

first: Ramin

last: Shiekhattar


title: ARPE-19 adriamycin gene expression II

city: Hangzhou

first: Yuchen

last: Lin

address: 866 Yuhangtang Road

institute: Zhejiang University School of Medicine

summary: This study compared the gene expression change of ARPE-19 cells before and after adriamycin treatment

overall_design: ARPE-19 cells were treated with 1 μM, 2 μM, 4 μM adriamycin for 24 h compared with control


title: Growth differentiation factor 15 (GDF15) promotes human rhinovirus infection and inflammation

city: Denver

first: Brian

last: OConnor

state: Colorado

address: 1400 Jackson St

department: Center for Genes, Environment and Health

institute: National Jewish Health

summary: Analysis of normal human tracheobronchial epithelial cells treated with or without recombinant human GDF15 for two hours. Results provide insights of the genome-wide transcriptional regulation by Smad1 associated with GDF15 in human airway epithelium.

overall_design: Normal human tracheobronchial epithelial cells at passage 2 were seeded onto collagen-coated 60 mm tissue culture dishes (4 x105 cells) in bronchial epithelial cell growth medium (BEGM) with SingleQuots™ supplements (Lonza, Walkersville, MD) at 37°C, 5% CO2. At 80-90% confluence, cells were treated with 0.1% BSA-HCl (control) or 25 ng/ml of recombinant human GDF15 (rhGDF15, R&D Systems, Minneapolis, MN) for 2 h.

middle: P

first: Laura

last: Harmacek

first: Qun

last: Wu

first: Sonia

last: Leach