title: Brassinosteroids modulate meristem fate and differentiation of unique inflorescence morphology in Setaria viridis

city: St. Louis

first: Andrea

middle: L

last: Eveland

state: MO

address: 975 N. Warson Road

institute: Donald Danforth Plant Science Center

summary: RNA-seq was performed to profile the transcriptomes of inflorescence primordia hand-dissected from the bristleless1-1 (bsl1-1)mutant in Setaria viridis compared to wild-type controls sampled under the same conditions. Bsl1 encodes a rate limiting enzyme in BR biosynthesis, which is the ortholog of D11 from rice. Mutants are characterized by a homeotic conversion of sterile bristles to spikelets in the inflorescence.

overall_design: Inflorescence primordia were hand-dissected from bsl1 mutant and wild-type control Setaria plants at 15 Days After Sowing (DAS). Plants were grown together in a controlled growth chamber. Inflorescence primordia were pooled (~10 representative primordia per pool) into biological replicates (3 for wild-type and 2 for mutant).  Transcriptomes were sequenced and compared for differentially expressed genes.

first: Jiani

last: Yang


title: Astrocyte-specific and region-specific transcriptomes in control and EAE mice

status: Public on Dec 23 2017

city: Los Angeles

first: Yuichiro

last: Itoh

state: California

address: 635 Charles E. Young Drive South

department: Neurology

country: USA

institute: UCLA

type: Expression profiling by high throughput sequencing

summary: Changes in gene expression that occur across the entire central nervous system (CNS) during disease do not take into account variability from one CNS region to another and can be confounded by alterations in cellular composition during disease. Multiple sclerosis (MS) is characterized by cell proliferation, migration and damage in various cell types in different CNS regions and causes disabilities related to distinct neurological pathways, such as walking, vision and cognition. Here, a cell-specific and region-specific transcriptomic approach was used to determine changes in gene expression in astrocytes derived from spinal cord, cerebellum, cerebral cortex, and hippocampus in the preclinical MS model, chronic experimental autoimmune encephalomyelitis (EAE). RNA sequencing and bioinformatics analysis showed that changes in gene expression pathways in astrocytes differed between neuroanatomic regions. Further, while astrocytes from spinal cord showed increased expression of immune pathway genes during EAE, cholesterol biosynthesis pathway genes were decreased. Translating these findings from the preclinical model to humans, optic nerve from EAE and optic chiasm from MS each showed a significant decrease in cholesterol biosynthesis pathways. Finally, a treatment targeting cholesterol homeostasis in astrocytes was protective in EAE, suggesting a novel neuroprotective strategy for MS. Using a cell-specific and region-specific gene expression approach can provide therapeutically relevant insights into mechanisms underlying specific disabilities in complex multifocal neurological diseases.

overall_design: The mice expressing HA-tagged ribosomal protein RPL22 in astrocytes were generated by crossing RiboTag mice with GFAP-Cre mice, and EAE was induced at age 8-12 week mice were injected with myelin oligodendrocyte glycoprotein (MOG) amino acids 35–55. Astrocyte specific RNA was isolated as the co-immunoprecipitation with anti-HA antibody from EAE (n=5) and age/gender matched control (n=4) mice.

first: Noriko

first: Alessia

last: Tassoni

first: Emily

last: Ren

first: Max

last: Kaito

first: Ai

last: Ohno

first: Yan

last: Ao

first: Hadley

last: Johnsonbaugh

first: Josh

last: Burda

first: Michael

middle: V

last: Sofroniew

first: Rhonda

middle: R

last: Voskuhl


title: Developmental differences between neonatal and adult human erythropoiesis

status: Public on Dec 28 2017

city: New York

first: John

last: Hale

state: NY

address: 310 East 67th Street

institute: New York Blood Center

summary: Studies of human erythropoiesis have relied, for the most part, on the in vitro differentiation of hematopoietic stem and progenitor cells (HSPC) from different sources. Here, we report that despite the common core erythroid program that exists between cord blood- and peripheral blood-HSPC induced towards erythroid differentiation in vitro, significant functional differences exist. We undertook a comparative analysis of human erythropoiesis using these two different sources of HSPC and differentiated them in vitro. We observed that cells derived from cord blood proliferate 4.5 times more than cells derived from peripheral blood. However, these cells present a delay in their differentiation pattern due to increased quantities of progenitors, notably CFU-E. Using our method of immunophenotyping for the study of erythroid progenitors, we document the presence and maintenance of a specific population in peripheral blood-derived erythroid progenitors. This population, defined as IL3R-GPA-CD34+CD36+, has the ability to form both BFU-E and CFU-E colonies in colony-forming assays, reflecting a higher potential. To further understand the differences between cord blood- and peripheral blood- HSPC, we sorted all stages of erythropoiesis from both sources and compared their transcriptome. We document differences at the CD34, BFU-E, poly- and orthochromatic stages. Among the genes presenting the highest differences in expression, many are involved in the regulation of the cell cycle and autophagy. Altogether, our studies provide a qualitative and quantitative comparative analysis of human erythropoiesis and highlight functional differences, critical to our understanding of the impact of the developmental origin of HSPCs on erythroid differentiation.

overall_design: RNA was extracted from FACS-sorted cells at 8 distinct stages of erythropoiesis, derived from CB- and PB-CD34+ cells. cDNA libraries were prepared using the Illumina TruSeq kit and sequenced on the Illumina HiSeq 2500 (Epigenomics Core of Weill Cornell Medical College, New York). This sequencing strategy produced ~15-80 million 50bp single end reads per sample. For each distinct stage of erythropoiesis, 3 biological replicates were obtained from independently cultured and sorted samples from different donations. Quality control of reads was performed and low-quality reads removed. Reads were aligned to the hg19 reference genome using HISAT2. Raw read counts were extracted from the aligned reads using the featureCounts program. Differential expression analysis was done at each stage comparing the two original sources of CD34+ cells using the DESeq2 bioconductor package. Using gene expression data from each stage, the subset of genes differentially expressed as a function of HSPC source was clustered using divisive hierarchical clustering and split into 10 clusters. Gene ontology enrichment analysis of the biological process gene sets was then performed on each cluster using the cluster Profiler R package with the gene background of all genes expressed across all stages in both sources.

first: Hongxia

last: Yan

middle: P

first: Julie

last: Jaffray

first: Jie

last: Li

first: Yaomei

last: Wang

first: Yumin

last: Huang

first: Xiuli

last: An

first: Christopher

last: Hillyer

first: Sandrina

last: Kinet

first: Naomi

last: Taylor

first: Mohandas

last: Narla

first: Anupama

first: Lionel

last: Blanc


title: c-MYC drives a subset of high-risk pediatric neuroblastomas and is activated through mechanisms including enhancer hijacking and focal enhancer amplification [RNA-seq]

status: Public on Dec 22 2017

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Childhood neuroblastoma is known for MYCN gene amplification, and here we show that in a separate subset of cases MYC-itself is activated due to enhancer hijacking from chromosomal translocations or duplications, thus defining a unique subset of high-risk disease.

overall_design: RNA-seq in zebrafish overexpressing human c-Myc or n-Myc

first: Mark

middle: W

last: Zimmerman

first: Yu

last: Liu

first: Shuning

last: He

first: Adam

middle: D

last: Durbin

first: Brian

middle: J

last: Abraham

first: Nina

last: Weichert-Leahey

first: Shizhen

last: Zhu

first: Li

last: Zhaodong

first: Beisi

last: Xu

first: Xiaoling

last: Zhang

first: Jinghui

first: A

middle: T

last: Look


title: Human optic chiasm from healthy controls and multiple sclerosis patients

first: Yuichiro

last: Itoh

overall_design: Five MS patients (average age = 57.6 years) and five age-matched healthy controls (average age = 56.2 years) fresh frozen autopsy optic chiasm tissue samples were obtained from Human Brain and Spinal Fluid Research Center in Los Angeles.

first: Noriko

first: Alessia

last: Tassoni

first: Emily

last: Ren

first: Max

last: Kaito

first: Ai

last: Ohno

first: Yan

last: Ao

first: Hadley

last: Johnsonbaugh

first: Josh

last: Burda

first: Michael

last: Sofroniew

first: Rhonda

last: Voskuhl


title: The Escherichia coli nucleoid is shaped around replication and transcription [GCC]

status: Public on Dec 25 2017

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

summary: The Escherichia coli nucleoid is confined within a rod shaped cell many times smaller than the outstretched chromosome. While extensive compaction is necessary for this process, the chromosome must at the same time remain accessible to essential cellular processes such as replication and transcription. Currently, the individual contributions of cellular confinement, chromosome topology, replication and transcription on nucleoid organization are not well understood. Here we synchronize E. coli cells in stationary phase, where replication has ceased, each cell contains only one copy of the chromosome, and transcription is minimal. We then release the cells and capture chromosome contacts and transcription immediately following release and through-out one cell cycle. Polymer models of confined and topologically constrained circular polymers revealed that cellular confinement and topology do not contribute extensively to the organization of the E. coli nucleoid. Rather, local nucleoid structure is established concurrent with replication, and higher order organization is formed by the replication dependant clustering of linearly distant SeqA bound sites and cell cycle specific gene transcription.

overall_design: There are six proximity ligation (GCC) samples, two biological replicates at t=0, at t=1 and t=2 hours following release of E. coli cells from the stationary phase.

first: Rachel

last: Bowden

middle: M


title: Uhrf1 is indispensable for normal limb growth by regulating chondrocyte differentiation

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

summary: Chondrocyte differentiation is regulated at a transcriptional level and by various hormonal stimuli. Since chondrocyte differentiation is important for normal skeletal growth, inadequate amounts of differentiation can lead to pathological conditions such as osteoarthritis. Transcriptional regulation can be tightly orchestrated by epigenetic regulators. Among these, ubiquitin-like with PHD and RING finger domains 1 (Uhrf1) is reported to have diverse epigenetic functions, including regulation of DNA methylation. However, the physiological functions of Uhrf1 in skeletal tissues remain unclear. Here we show that limb mesenchymal cell-specific Uhrf1 conditional knockout mice (Uhrf1ΔLimb/ΔLimb) exhibit shortened long bones that have morphological deformities due to impaired chondrocyte differentiation and proliferation. RNA-seq performed on primary cultured chondrocytes obtained from control and Uhrf1ΔLimb/ΔLimb mice revealed that expression levels of proliferative chondrocyte marker genes were downregulated, whereas hypertrophic chondrocyte marker genes were upregulated. In addition, gene ontology analyses and Gene Set Enrichment Analysis (GSEA) suggested that limb growth retardation due to compromised chondrocyte differentiation might be caused by increased activity of the focal adhesion signaling pathway. These results indicated that Uhrf1 has a crucial role in normal skeletal maturation by coordinating transcriptional regulatory networks during chondrocyte differentiation.

overall_design: mRNA profiles of primary chondrocytes obtained from 3-day old Control and Uhrf1 cKO mice were generated by deep sequencing, in triplicate, using Illumina Miseq. Sequence data were mapped on the mouse genome (mm10) using Tophat and analyzed by Cufflinks.

first: Michiko

last: Yamashita


title: ADP-ribose derived Nuclear ATP is Required for Chromatin Remodeling and Hormonal Gene Regulation

city: Barcelona

first: Miguel

last: Beato

address: Aiguader 88

country: Spain

institute: CRG

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Key nuclear processes in eukaryotes including DNA replication or repair and gene regulation require extensive chromatin remodeling catalyzed by energy consuming enzymes. How the energetic demands of such processes are ensured in response to rapid stimuli remains unclear. We have analyzed this question in the context of the massive gene regulation changes induced by progestins in breast cancer cells and found that ATP is generated in the cell nucleus via the hydrolysis of poly-ADP-ribose to ADP-ribose. Nuclear ATP synthesis requires the combined enzymatic activities of PARP1, PARG and NUDIX5/NUDT5. Although initiated via mitochondrial derived ATP, the nuclear source of ATP is essential for hormone induced chromatin remodeling, gene regulation and cell proliferation and may also participate in DNA repair. This novel pathway reveals exciting avenues of research for drug development.

overall_design: 1) Hormonal gene regulation requires synthesis of PAR and its degradation to ADPribose by PARG. 2) ADP-ribose is converted to ATP in the cell nuclei by hormone-activated NUDIX5/NUDT5. 3) Blocking nuclear ATP formation precludes hormone-induced chromatin remodeling, gene regulation and cell proliferation.

first: Roni

middle: H

last: Wright

first: Antonios

last: Lioutas

first: Francois

last: LeDily

first: Daniel

last: Soronellas

first: Andy

last: Pohl

first: Jaume

last: Bonet

middle: S

last: Nacht

first: Sara

last: Samino

first: Guillermo

last: Vicent

last: Wierer

first: Miriam

last: Trabado

first: Carlo

last: Carolis

first: Oscar

last: Yanes

first: Baldo

last: Oliva


title: N6-methyladenosine (m6A) sequencing of messenger RNAs in acute myeloid leukemia (AML) cells with and without knockdown of METTL14 [m6A-seq]

status: Public on Dec 29 2017

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: To dissect the mechanism underlying the oncogenic function of METTL14 in AML, we performed m6A RNA immunoprecipitation and deep sequencing for mRNA isolated from MM6 and NB4 cells with and without knockdown of METTL14

overall_design:
We lentivirally transduced pLKO.1-based lentiviral shRNAs targeting METTL14 (i.e., shM14-#1 and shM14-#2) or scramble shRNA (i.e., shNS) into human MM6 and NB4 AML cells. After selected with puromycin (0.5 µg/mL) for two passages, cells were collected for genome-wide m6A-sequencing (m6A-Seq) assays. The m6A-seq procedure was performed according to Dominissini’s protocol (Dominissini D., et al. Nature 2012; 485: 201-206) with some modifications. Polyadenylated RNA was extracted using the Dynabeads mRNA DIRECT kit (ThermoFisher). RNA fragmentation was performed by sonication at 10 ng/µl in 100 µl RNase-free water using Bioruptor Pico (Diagenode) with 30s on/30s off for 30 cycles.
M6A antibody (Synaptic Systems, 202003) was applied for m6A pull down. Library was constructed by TruSeq Stranded mRNA Library Prep Kit (Illumina) and sequenced on Illumina HiSeq 2000.

first: Lei

last: Dong

first: Hengyou

last: Weng

first: Huilin

last: Huang

first: Boxuan

last: Zhao

first: Chuan

last: He


title: Genome-wide maps of histone H3K9/K14 acetylation state in HeLa cells control (Mock) or silenced for Gb3 globoside synthase (Gb3S_KD) or silenced for the epigenetic modulator AUTS2 (AUTS2_KD)

city: Naples

first: Giovanni

last: D'Angelo

address: Via Pietro Castellino, 111

country: Italy

institute: Institute of Protein Biochemistry-National Research Council

summary:
Glycosphingolipid metabolism is reprogrammed during neural development with a switch from globo to ganglio-series glycosphingolipids production. We discovered that globo-series glycosphingolipids repress the epigenetic regulator of neuronal genes expression AUTS2. AUTS2 in turn, binds and activates the promoter of the first and rate limiting ganglioside producing enzyme GM3 synthase, thus fostering the synthesis of gangliosides. By this mechanism the globo-AUTS2 axis controls glycosphingolipid reprogramming and neural genes expression during neural differentiation, which involves this circuit in neurodevelopment and its defects in neuropathology.
We report Gb3 globoside suppresses the expression of the epigenetic modulator AUTS2. The silencing of Gb3 synthase in HeLa cells induces the thepletion of Gb3 globoside, consequentially promoting AUTS2 expression. AUTS2 in turn, binds and activates the promoter of the target genes promoting local histone hyperacetylation and gene expression. Thus, the globo-series glycosphingolipids, by counteracting the expression of AUTS2, decrease histone acetylation at neuronal gene promoters repressing their transcription in HeLa cells.

overall_design: HeLa cells were silenced for 72 hours with 120pmol of specific siRNA. Chromatin immunoprecipitation was performed with antibody anti-acetyl H3K9/K14 (Millipore 06-599). Immunoprecipitated chromatin was purifyed and analyzed by next-generation sequencing.

first: Domenico

last: Russo

first: Mario

last: Guarracino

first: Ilaria

last: Granata


title: Degree of Tissue Differentiation Dictates Susceptibility to BRAF-driven Colorectal Cancer

status: Public on Dec 26 2017

city: Piscataway

first: Michael

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

summary: In murine models, we find that oncogenic BRAF paradoxically suppresses stem cell renewal and instead promotes differentiation and senescence. This corresponds to inefficient tumor formation in oncogenic BRAF mouse models of colon cancer. By reducing levels of differentiation in the gut via genetic manipulation of either of two distinct differentiation-promoting factors (Smad4 or Cdx2), stem cell activity is restored in BRAFV600E intestines, and the oncogenic capacity of mutant BRAF is amplified. In human patients, we observe that reduced levels of differentiation in normal tissue is associated with increased susceptibility to serrated colon tumors. Together, these findings help resolve the conditions necessary for BRAF-driven colon cancer initiation.

overall_design: RNAs were extracted from crypt jejunal epithelia of the indicated genotypes (BRAF-V600Ef/+;Villin-CreER(T2), Smad4f/f BRAF-V600Ef/+;Villin-CreER(T2)  and Cdx2f/f BRAF-V600Ef/+Villin-CreER(T2)) one day following 4 consecutive days of tamoxifen injection. Uninjected mice served as control. After flushing the freshly harvested jejunum with cold PBS, the epithelia was dissociated from underlying mesenchyme by incubating with 3 mM EDTA/PBS at 4°C as described previously (Perekatt, 2014), and filtered through 70 micron filter to isolate the crypts. The crypts were washed with PBS, and pelleted to remove excess PBS prior to addition of TRIzol for RNA extraction according to manufacturer’s protocols.

first: Kevin

last: Tong

last: Pellon-Cardenas

first: Veerin

last: Sirihorachai

first: Warder

last: Bailey

first: Kothari

last: Om

first: Perekatt

last: Ansu

first: Fokas

last: Emily

first: Fullem

last: Robert

first: Zhou

last: Anbo

first: Thackray

last: Joshua

first: Tran

last: Hiep

first: Zhang

last: Lianjing

first: Xing

last: Jinchuan


title: A protective function of IL-22BP in acute liver injury

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

summary: Acute liver injury is a critical life-threatening event. Common causes are infections, intoxication, and ischemic conditions. The cytokine Interleukin 22 (IL-22) has been implicated in this process. However, the role of IL-22 during acute liver damage is controversial, since both protective and pathogenic properties have been reported. IL-22 binding protein (IL-22BP, IL-22Ra2), a soluble endogenous inhibitor of IL-22, is able to regulate IL-22 activity, and thus might explain some of the controversial findings. Since the role of IL-22BP in liver injury is unknown, we used Il22bp deficient mice and mouse models for acute liver damage to address this point. We found that Il22bp deficient mice were more susceptible to ischemia- and acetaminophen- induced liver damage. Deficiency of Il22bp caused increased hepatic damage and delayed liver regeneration. Using an unbiased approach, we found that IL-22, if uncontrolled in Il22bp deficient mice, induced Cxcl10 expression by hepatocytes, thereby recruiting inflammatory CD11b+Ly6C+ monocytes into the liver upon liver damage. Accordingly, neutralization of Cxcl10 reversed the increased disease susceptibility of Il22bp deficient mice. In conclusion, our data suggest dual functions of IL-22 in acute liver damage, and highlight the need to control IL-22 activity via IL-22BP.

overall_design: RNA sequencing of RNA isolated from liver tissue from mice that underwent liver reperfusion treatment (IR) or sham surgery, in triplicate for three genotypes (Wt, Il22-/- and Il22bp-/-).

first: Dörte

last: Kleinschmidt

first: Anastasios

last: Giannou

first: Jan

last: Kempski

first: Francis

last: Huber

first: Thomas

last: Ernst

first: Mustafa

last: Shiri

first: Claudia

last: Wegscheid

first: Elena

last: Tasika

first: Peter

last: Hübener

first: Tobias

last: Fuchs

first: Hannelore

last: Lotter

first: Gisa

last: Tiegs

first: Ansgar

last: Lohse

first: Jonathan

last: Axelrod

first: Eithan

last: Galun

first: Richard

last: Flavell

first: Nicola

last: Gagliani

first: Samuel


title: Opposing functions of H2BK120 ubiquitylation and H3K79 methylation in the regulation of pluripotency

first: Alexandros

last: Strikoudis

address: 550 First Avenue, Smilow 1303

department: Pathology

institute: NYU Medical Center

summary: Phf5a regulates transcription elongation in mouse embryonic stem cells (ESCs), through regulation of the Paf1 complex. In this study we assayed for genome-wide localization of H2BK120-ub in mouse ESCs under conditions of shControl and shPhf5a knockdown. These results revealed that downregualtion of Phf5a results in the increase of the elongation mark H2BK120-ub from the gene bodies of pluripotency genes in ESC.

overall_design: Ten million cells were treated with micrococcal nuclease to generate mono-nucleosomes and chromatin was precipitated using 10 micrograms of antibody against H2Bk120-ub, clone 56 (Millipore, 05-1312).


title: The cohesin complex prevents Myc-induced replication stress

city: Milan

first: Marco

middle: J.

last: Morelli

address: via Adamello 16

department: Center for Genomic Science of IIT@SEMM

institute: Istituto Italiano di Tecnologia

summary: The cohesin complex is mutated in cancer and in a number of rare familiar syndromes collectively known as Cohesinopathies. In the latter case, cohesin deficiencies have been linked to transcriptional alterations affecting Myc and its target genes. Here, we set out to understand to what extent the role of cohesins in controlling cell cycle is dependent on Myc expression and activity. Inactivation of the cohesin complex by silencing the RAD21 subunit led to cell cycle arrest due to both transcriptional impairment of Myc target genes and alterations of replication forks, which were fewer and preferentially unidirectional. Ectopic activation of Myc in RAD21 depleted cells, fully rescued transcription and promoted S-phase entry but failed to sustain S-phase progression thus leading to a strong replicative stress response, which was associated to a robust DNA damage response, DNA damage checkpoint activation and synthetic lethality. Thus, the cohesin complex is dispensable for Myc dependent transcription but essential to prevent Myc induced replicative stress. This suggests the presence of a topological checkpoint orchestrated by cohesins that by regulating Myc level prevents S-phase entry and replicative stress in cohesion compromised cells.

overall_design: RNAseq samples of U2OS -MycER cells (in the presence or absence of OHT) and transfected with non-targeting siRNA or siRNA against RAD21 after 24 and 48 hours of transfection/treatment

first: Sara

last: Rohban

first: Stefano

last: Campaner


title: Temporal Transcriptomic and Proteomic Landscapes of Deteriorating Pancreatic Islets in Type 2 Diabetic Rats

city: Beijing

first: Wen

last: Zhong

address: Datun Road

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Progressive reductions in β-cell mass and function comprise the core of the pathogenesis mechanism leading to type 2 diabetes (T2D). To understand the molecular events in this process, we quantified the temporal transcriptome and proteome of pancreatic islets from Goto-Kakizaki (GK) rats at different stages of diabetes. Integrated omics analysis allowed us to unravel the chronological order of T2D-related molecular events during GK islet deterioration. Two major events occur early in the disease, specifically, a reduction in β-cell mass caused by defective neogenesis and senescence-related low proliferation, and metabolic shift caused by mitochondrial dysfunction. Furthermore, our data revealed the evolution of compensation failure in GK islets and two distinct stages of islet inflammation: priming and amplification. Our study offers a valuable resource for the diabetes research community and will facilitate further studies aimed at protecting β-cell mass and function.

overall_design: We performed a time-course large-scale transcriptome of pancreatic islets in GK male rats vs control, age-matched WST male rats at five time points (week 4, 6, 8, 16 and 24) using MAPS method

first: Junjie

last: Hou

first: Zonghong

last: Li

first: Qiang

last: Hao

first: Dongyu

last: Zhao

first: Pingyong

last: Xu

first: Yifa

last: Zhou

first: You

last: Wang

first: Tao


title: Comparison of Kras;Rank+/+ and Kras;Rankfl/fl mouse primary pneumocytes treated with Rankl ex vivo

city: Vienna

first: Shuan

last: Rao

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

summary: The transcriptional profile of Kras;Rank +/+ and Kras;Rank fl/fl mouse primary pneumocytes were determined by mRNA sequencing and uncovered differences in their molecular signatures including genes involved in cell-cell junction, mitosis, mitochondrial homeostasis, TCA cycle and respiratory electron transport

overall_design: Transcriptome comparison of primary pneumocytes purified from Kras;Rank+/+ and Kras;Rankfl/fl mice treated with Rankl ex vivo

first: S

first: J

last: Penninger


title: Profiling of Human milk cell and lipid microRNAs from healthy and during naturally occurring infection breastfeeding mothers

city: Crawley

first: Mohammed

last: Alsaweed

state: WA

address: 35 stirling hwy

department: Biochemistry

country: Australia

institute: UWA

type: Non-coding RNA profiling by high throughput sequencing

summary: Human milk is highly recommended for infant during the first six month of life by World Healthy Organisation (WHO). Human milk is not only rich in macro-nutritional components, but also rich in cells and molecules. MicroRNAs are small non-coding RNAs, which enriched in human milk. These molecules are vital in enormous biological and cellular functions including immune system and in response to infections. By using deep sequencing method, 770,374,554 raw reads were generated from all samples (n=26). Then, filter analysis was done to remove 81,091,772 (10.5%), and 689,282,782 clean reads (89.5%) were considered as clean reads, which was retained for the subsequent bioinformatics analysis. Annotation and matching reads to miRBase revealed1780 mature known microRNAs identified in human milk cells and lipids derived from healthy, cold and other infection types mothers. In particular, 1680 known microRNAs were determined in infected mothers (n=14), while 1,606 known microRNAs in healthy mothers (n=12). Of these known microRNAs, 453 microRNAs were differentially expressed (p<0.05) between healthy and infected samples. The majority of the highly expressed miRNAs in all samples, in particular top 20 microRNAs, were also differentially expressed between healthy and infections. Further, 592 novel mature microRNA sequences were predicted, with only 65,878 total reads. Amongst the total reads of the novel microRNAs, top 20 novel miRNAs were found to contributed in 73.3% (total reads 48,295) of the total reads (65,878).

overall_design: Human milk samples were collected from 11 mothers in healthy (n=6) and in infection (n7) conditions. Human milk samples were fractionated to obtain cell and lipid fractions. Total RNA and miRNA were extracted and quantified from cell and lipid fractions. Next generation sequencing using illumina HiSeq 2000 was used to profile microRNAs in 26 samples, where 13 cells and 13 lipids. Filtered (clean) reads were aligned to the latest version of miRBase 21.0. Also, mirdeep software was used to predict novel miRNAs.  DESeq and Linear mixed effect models and ANOVA were used to compare miRNA expression levels between samples and conditions

first: Foteini

last: Kakulas

first: Donna

last: Geddes

first: Mezyndra

last: Badsha


title: Genome-wide distribution of transcription-coupled nucleotide excision repair and RNA polymerase II in DRB-treated XP-C cells after UV damage

status: Public on Dec 21 2017

city: Taichung

first: Yi-Ying

last: Chiou

address: No.145, Xingda Rd., South Dist.

department: Graduate Institute of Biochemistry

country: Taiwan

institute: National Chung Hsing University

summary: The fate of RNAPII in the course of the transcription-coupled repair pathway is unclear.  To address this problem we have used methods to control transcription, so as to initiate a discrete ‘wave’ of elongation complexes.  We also used methods to identify where elongation complexes and transcription-repair coupling events are located in genes throughout the genome.

overall_design: XP-C cells which is deficient in the global repair were treated with different DRB regimens. After UV irradiation, XR-seq and mNET were performed to analyze the repair and the localization of elongating RNA polymerase II

first: YI-YING

last: CHIOU

first: Jinchun

last: Hu


title: Hyperactive mTOR and MNK1 phosphorylation of eIF4E confer tamoxifen resistance and estrogen independence through selective mRNA translation reprogramming

first: Robert

last: Schneider

address: 550 First Ave, MSB 238

department: Microbiology

institute: NYU School of Medicine

summary: Tamoxifen resistant translational reprogramming is shown to be mediated by increased expression of eIF4E and its increased availability by hyperactive mTOR, and to require phosphorylation of eIF4E at Ser209 by increased MNK activity.

overall_design: Polysome profiling examining eIF4E knock-down in tamoxifen resistant breast cancer cells (MCF7)

first: Phillip

last: Geter

first: Amanda

last: Ernlund


title: The miRNA profiling of different adult stage in  Moniezia expansa

status: Public on Dec 31 2017

first: Yiru

last: Liu

address: Chaoqian

department: R&D

institute: Beijing Honor Tech Co Ltd

summary: By sequencing, 227 M.expansa miRNAs were identified, of which 162 were new discovered microRNAs in tapeworm. In addition, we found 64 miRNAs (including 28 known miRNAs and 36 new miRNAs) corresponding to 45 potential targeted genes. These genes were related to cell development, reproductive conversion and apoptosis.

overall_design: Examine miRNA profiling of four different adult stage in  Moniezia expansa

first: Xinwen

last: Bo


title: Next Generation Sequencing Facilitates Quantitative Analysis of subcutaneous tumors untreated and treated with doxycycline for 4h to activate shST18

first: Marco

last: Morelli

summary: We report the transcriptome profiling (RNAseq) in hepatoblast-derived tumors, without (untreated) or with ST18 knockdown (4h Doxy) (three independent samples for each condition). We find that ST18 knockdown in hepatoblast-derived tumors affects inflammation-associated genes.

overall_design: Tumors mRNA profiles of untreated or with 4h Doxy (ST18 knockdown) mice were generated by deep sequencing, in triplicate, using Illumina.


title: Binding of High Mobility Group A proteins to the mammalian genome occurs as a function of AT-content

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

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

overall_design: Refer to individual Series


title: Binding of High Mobility Group A proteins to the mammalian genome occurs as a function of AT-content [RNA-Seq]

summary: High mobility group (HMG) proteins are of similar size as histones with HMGA1 and HMGA2 being particularly abundant in replicating normal tissues and in cancerous cells. While numerous roles for HMGA proteins have been proposed we lack a comprehensive description of their genomic location as a function of chromatin, DNA sequence and functional domains. Here we report such a characterization of HMGA proteins in mouse embryonic stem cells in which we introduce biotin-tagged constructs of wild-type and DNA binding domain mutants. Comparative analysis of their genome-wide distribution reveals pervasive binding, a feature that critically depends on a functional DNA binding domain and which is shared by both HMGA proteins. Assessment of the underlying queues instructive for this binding modality identifies AT richness as the major criteria for local binding. Additionally, we show that other chromatin states such as those linked to cis-regulatory regions have little impact on HMGA binding both in stem and differentiated cells. As a consequence HMGA proteins are found most enriched at regions of higher AT density such as constitutively heterochromatic regions but are absent from enhancers and promoters arguing for a limited role in regulating individual genes. In line with this model we show that genetic deletion of HMGA proteins in stem cells causes limited transcriptional effects and that binding is conserved in neuronal progenitors.

overall_design: RNA-seq was performed in WT, Hmga1 KO and Hmga1/2 add-back mouse embryonic stem cells.

first: Daniele

middle: F

last: Colombo

first: Lukas

last: Burger

first: Tuncay

last: Baubec

last: Schübeler


title: Gene expression profiles of SIRT6-deficient pancreatic beta cells from Ngn3-Cre Sirt6 f/f and MIP1-CreERT Sirt6 f/f mice

city: Philadelphia

first: KUNHUA

last: QIN

email: qink@chop.edu, kunhua.qin@gmail.com

state: PA

address: 3615 Civic Center Blvd, 315H

institute: Children's Hospital of Philadelphia

summary:
Purpose: The complete understanding of how genetic and epigenetic components control beta cell differentiation and function is key to the discovery of novel therapeutic approaches to prevent beta cell dysfunction and failure in the progression of type 2 diabetes. Our goal was to elucidate the role of histone deacetylase SIRT6 in beta-cell development and homeostasis.
Methods: The Sirt6 endocrine progenitor cell conditional knockout (EKO) and beta-cell-specific knockout (BKO) mice were generated using the Cre-loxP system. Mice were assayed for islet morphology, glucose tolerance, glucose-stimulated insulin secretion, and susceptibility to streptozotocin. Transcriptional regulatory functions of SIRT6 in primary islets were evaluated by RNA-seq analysis. RT-qPCR and immunoblot were used to verify and investigate the gene expression changes. Chromatin occupancies of SIRT6, H3K9Ac, H3K56Ac, and active RNA Polymerase II were evaluated by chromatin immunoprecipitation.
Results: Deletion of Sirt6 in pancreatic endocrine progenitor cells did not affect endocrine morphology, beta cell mass, or insulin production, but did result in glucose intolerance and defective glucose-stimulated insulin secretion in mice. Conditional deletion of Sirt6 in adult beta cells reproduced the insulin secretion defect. Loss of Sirt6 resulted in aberrant upregulation of TXNIP. SIRT6 deficiency led to increased accumulations of H3K9Ac, H3K56Ac, and active RNA polymerase II at the promoter region of Txnip. SIRT6-deficient beta cells exhibited a time-dependent increase of H3K9Ac, H3K56Ac, and TXNIP levels. Furthermore, beta-cell-specific SIRT6 deficient mice showed increased sensitivity to streptozotocin.
Conclusions: Our results reveal that SIRT6 suppresses Txnip expression in beta-cells via deacetylation of histone H3 and plays a critical role in maintaining beta-cell function and viability. Agents that preserve SIRT6 activity may be beneficial for preventing the progression of type 2 diabetes.

overall_design: Profiles of pancreatic beta cells gene expression from 2-week post tamoxifen MIP1-CreERT Sirt6 f/f and 2-month-old Ngn3-Cre Sirt6 f/f male mice were generated by RNA-sequencing with duplicate using Illumina HiSeq 2000 and 3000. Samples from MIP-CreERT Sirt6 f/+, MIP-CreERT Sirt6 +/+, and Ngn3-Cre Sirt6 +/+, which did not show phenotype, were used as controls for BKO and EKO models, respectively, in the differential gene expression analysis.

first: Kunhua

last: Qin

first: Pei

last: Wang


title: Histone 2B-GFP Label-Retaining Prostate Luminal Cells Possess Progenitor Cell Properties and Are Intrinsically Resistant to Castration

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

institute: Hunan University

summary: Identification of defined cell populations with stem/progenitor properties is key for our understanding of prostate development and tumorigenesis. Prior studies have provided strong evidence of the existence of prostate luminal progenitors, but their identity and functional properties remains unknown. Using an unbiased novel bigenic mouse model to specifically earmark, prospectively isolate, and functionally characterize the quiescent stem-like cells, we identify a label-retaining cell (LRC) population in the mouse prostate luminal cell layer as candidate luminal progenitors. Through comprehensive molecular and biological characterizations, we show that these luminal LRCs exhibit relative dormancy with significant enrichment in the mouse proximal prostate, display bipotent potential in both in vitro organoid formation and the in vivo prostate regeneration assay, express a stem/progenitor gene signature with resemblance to aggressive prostate cancer. Importantly, these luminal LRCs maintain a lower level of Ar expression, are androgen-independent, and resist castration in vivo. Furthermore, analysis of phenotypic markers by immunefluorescent staining reveals heterogeneity within luminal progenitor cell pool. Collectively, our studies establish luminal LRCs as progenitors that may serve as a cellular origin for castration resistant prostate cancer.

overall_design: Mouse total RNA profiles of a pair of normal mouse prostate label-retaining cells (LRCs) and non-LRCs freshly purified from luminal epithelial cell population by deep RNA-seq.

first: Yue

last: Lu

first: Dean

middle: G

last: Tang


title: Genomic and proteomic resolution of heterochromatin and its restriction of alternate fate genes

first: Gregory

last: Donahue

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania


title: Gene expression changes in human melanoma cell lines compared to primary melanocytes

city: Madrid

first: Metehan

last: Cifdaloz

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology Program

institute: CNIO

summary: Gene expression changes in 3 human melanoma cell lines were compared to freshly isolated normal primary melanocytes

overall_design: Three biological replicates for each melanoma cell line and primary melanocytes were labeled and run Illumina HiSeq2500. The transcriptome of melanocytes was compared to cell line SK-Mel-28, SK-Mel-147 or UACC-62.

first: M

first: O

last: Graña

last: Soengas


title: Time course effects of a latent carcinogen in mice

city: RTP

first: Susan

last: Hester

state: NC

address: 109 TW Alexander Dr

institute: US EPA

summary: Early-life environmental factors can increase later-life susceptibility to cancer. Short-term exposure to dichloroacetic acid (DCA), a trace drinking water contaminant with distinctive metabolic effects, increased liver cancer in mice 84 weeks after exposure was stopped. Here we evaluated time course dynamics for key events related to this latent effect. This study followed a stop-exposure design in which 28-day-old male B6C3F1 mice were given the following treatments in drinking water for up to 93 weeks: deionized water (dH20, control); 3.5 g/l DCA continuously; or 3.5 g/l DCA for 4, 10, 26, or 52 weeks followed by dH20. Effects were evaluated at eight interim time points. A short-term biomarker study was used to evaluate DCA effects at 6, 15, and 30 days. Liver tumor incidence was higher in all DCA treatment groups, including carcinomas in 82% of mice previously treated with DCA for only 4 weeks. Direct effects of DCA in the short-term study included decreased liver cell proliferation and marked mRNA changes related to mitochrondrial dysfunction and altered cell metabolism. All observed short-term effects of DCA were reversible. Prior DCA treatment did not alter liver cell proliferation, apoptosis, necrosis, or DNA sequence variants with age. Key intermediate events resulting from early-life DCA exposure do not fit classical cytotoxic, mitogenic, or genotoxic modes of action for carcinogenesis, suggesting a novel epigenetic mechanism related to metabolic disruption.

overall_design: Compare liver trancriptomic profiles from male mice following six day exposure to 0, 1.0, 2.0, and 3.5 g/L DCA (n=6 per dose group) using Illumina Hi-seq.

first: Leah

middle: C

last: Wehmas

first: Anthony

middle: B

last: Deangelo

first: Brian

middle: N

last: Chorley

first: Gleta

last: Carswell

first: Greg

last: Olson

first: Michael

last: George

first: Julia

last: Carter

first: Sandra

last: Eldridge

first: Anna

last: Fisher

first: Beena

last: Vallanat

first: Charles

last: Wood


title: Genomic and proteomic resolution of heterochromatin and its restriction of alternate fate genes (RNA-seq)

summary: Heterochromatic regions in mammalian cells suppress recombination, silence transcription, and are crucial for maintaining cell differentiation. Genomic and biochemical characterization of heterochromatin has relied on the associated histone modifications H3K9me3 and H3K27me3, yet these marks are also found in euchromatic regions that permit transcription. We employed a biophysical method to isolate sonication resistant heterochromatin from human somatic cells, mapped its genomic organization compared to histone modifications, and used proteomics to reveal an extensive number of heterochromatin-bound proteins. We discriminate subtypes of H3K9me3- and H3K27me3-marked domains, in sonication-resistant heterochromatin versus euchromatin, and we present a resource of hundreds of proteins that preferentially bind heterochromatin, a set enriched for RNA-binding proteins and proteins that oppose iPS reprogramming. The sonication-resistant heterochromatin landscape includes repressed genes for alternative lineages that are resistant to activation by introduced transcription factors. Depletion of identified heterochromatin-associated proteins reduces this barrier, rendering alternative-lineage genes more competent for transcriptional activation.

overall_design: This study was designed to assess the role of human SUV39H1 and RBMX/RBMXL1 in impeding the activation of heterochromatic genes by transcription factors. RNA-seq was performed in human BJ foreskin fibroblasts treated with siRNAs in two main experimental protocols: cells expressing the hepatic transcription factors FOXA3/HNF1A/HNF4A ("hepatic TF" protocol) and cells expressing no ectopic transcription factors ("no TF" protocol). There are a total of 12 RNA-seq samples: two experimental protocols, three siRNAs per protocol, and two biological replicates per siRNA/protocol. The three siRNAs are: non-targeting control siRNA, siRNA against SUV39H1, and siRNA co-targeting RBMX and RBMX/L1

first: Justin

last: Becker

first: R

middle: L

last: McCarthy

first: Simone

last: Sidoli

first: Kelsey

middle: E

last: Kaeding

first: Zhiying

last: He

first: Shu

last: Lin

first: Benjamin

last: Garcia

first: Kenneth

last: Zaret


title: Binding of High Mobility Group A proteins to the mammalian genome occurs as a function of AT-content [ChIP-Seq]

first: Dirk

last: Schuebeler

overall_design: ChIP-seq of biotin-tagged HMGA1 and HMGA2 was performed in WT and Hmga1/Hmga2 add-back stem cells as well as in WT neuronal progenitors. The same enrichment strategy was adopted for experiments with GFP and HMGA1-2 DNA-binding domain mutants.

first: Daniele

last: Colombo

first: Lukas

last: Burger

first: Tuncay

last: Baubec

last: Schubeler


title: Identification of heat stress-responsive rice microRNAs and their target genes by high-throughput sequencing and degradome analysis

city: hangzhou, Lin an

first: jinsheng

last: yu

address: 88 huan cheng Rd.

institute: Zhejiang A&F University

summary: In this study, we identified a set of heat stress-responsive miRNAs and verified their targets through degradome sequencing. Nine libraries (triplicate for 0 h, 12 h and 24 h heat treatment) were constructed and sequenced. Four hundred and nineteen conserved miRNAs and 77 novel miRNAs were identified, of which, 40 conserved and two novel miRNAs were expressed differentially. Quantitative PCR of three selected miRNAs and their targets confirmed that these loci were responsive to heat stress. A total of 1364 target transcripts were identified for 114 conserved miRNA and a total of 65 were identified for 22 novel miRNA families. Gene function and pathway analyses showed that these genes probably play vital roles in rice heat stress tolerance.

overall_design:
The plant material used in this study was HT54, an Indica breeding line with heat tolerance possibly inherited from its parental variety Guang-Lu-Ai No 4. Previous study have shown that HT54 seedlings could tolerate high temperature up to 48 °C for 79 h.
For miRNA library, three-leaf stage rice seedlings were treated by heat shock at 45°C for 0, 12 or 24 h, and triplicate for each data point, thus nine libraries were constructed. For degradome library, one library was constructed at each time point.
One miRNA library for each time point was found to be unsuitable for analysis and are not included in this submission.

first: Jinsheng

last: Yu

first: Jumin

last: Tu


title: CUGBP1 RNA immunoprecipitation and sequencing (RIP-seq) in SK-Mel-103 and UACC-62 melanoma cell lines

first: Metehan

last: Cifdaloz

summary: Identification of the mRNAs bound by CUGBP1 in melanoma cells

overall_design: RIP-seq analysis of the mRNAs bound by CUGBP1 in SK-Mel-103 and UACC-62 melanoma cell lines. Pulldowns performed by CUGBP1 antibody are compared to input signals (used as reference). Experiments were performed in biological in duplicates for UACC-62.

first: M

first: O

last: Graña

last: Soengas


title: Epidermal Wnt signaling regulates transcriptome heterogeneity and proliferative fate in neighboring cells

city: London

first: Arsham

last: Ghahramani

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: We performed single-cell mRNA-Seq on wild-type mouse keratinocytes co-cultured with keratinocytes in which beta-catenin was activated. We identified seven distinct cell states in cultures that had not been exposed to the beta-catenin stimulus. Using temporal single-cell analysis we reconstruct the cell fate changes induced by neighbor Wnt activation. Gene expression heterogeneity was reduced in neighboring cells and this effect was most dramatic for protein synthesis associated genes. The changes in gene expression were accompanied by a shift from a quiescent to a more proliferative stem cell state. By integrating imaging and reconstructed sequential gene expression changes during the state transition we identified transcription factors, including Smad4 and Bcl3, that were responsible for effecting the transition in a contact-dependent manner. Our data indicate that non cell autonomous Wnt/beta-catenin signaling decreases transcriptional heterogeneity and further our understanding of how epidermal Wnt signaling orchestrates regeneration and self-renewal.

overall_design: Comparison of cells exposed to Wnt activated neighbors versus unactivated.

first: Fiona

last: Watt

first: Nicholas

last: Luscombe


title: RNA-seq in acute myeloid leukemia (AML) cells with and without knockdown of METTL14

first: Jianjun

last: Chen

institute: Beckman Research Institute of City of Hope

summary: To dissect the mechanism underlying the oncogenic function of METTL14 in AML, we performed deep sequencing for mRNA isolated from MM6 and NB4 cells with and without knockdown of METTL14

overall_design: We lentivirally transduced pLKO.1-based lentiviral shRNA targeting METTL14 (i.e., shM14-#2) or scramble shRNA (i.e., shNS) into human MM6 and NB4 AML cells. After selected with puromycin (0.5 µg/mL) for two passages, cells were collected and RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA). PolyA RNA was subsequently purified from100 ng total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module. NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA) was used for library preparation. Each group was sequenced in duplicate by Illumine Hiseq 1000 with single end 50-bp read length.

first: Lei

last: Dong

first: Hengyou

last: Weng

first: Huilin

last: Huang


title: Genomic and proteomic resolution of heterochromatin and its restriction of alternate fate genes (ChIP-seq)

first: Gregory

last: Donahue

overall_design: This study was designed to map the organization of sonication resistant heterochromatin in the human genome. Crosslinked, sonicated chromatin from human BJ fibroblasts was fractionated using sucrose gradients, to yield a Euchromatin fraction (fraction #2, containing highly sonicated fragments) and a Sonication-Resistant Heterochromatin fraction (fractions #10-17, containing larger, sonication-resistant fragments). In parallel, we performed H3K9me3-directed chromatin immunoprecipitation (ChIP), as well as H3K9me3-directed IPs performed from the Euchromatin fraction and from the Sonication-Resistant Heterochromatin fraction. Corresponding samples for both gradient analysis and ChIP were also sequenced. Purified DNAs containing larger DNA fragments were sonicated (after protein removal) to produce shorter fragments for library preparation. In total there are 7 sample types (5 purified chromatin samples and 2 types of input), with 2 biological replicates for each.

first: Justin

last: Becker

first: R

last: McCarthy

first: Simone

last: Sidoli

first: Greg

first: Kelsey

last: Kaeding

first: Zhiying

last: He

first: Shu

last: Lin

first: Benjamin

middle: A

last: Garcia

first: Kenneth

last: Zaret


title: ChIP-seq analysis of HN1L protein in SUM159 triple-negative breast cancer cells

status: Public on Dec 20 2017

city: Houston

first: Jenny

last: Chang

state: TX

address: 6670 Bertner Ave.

department: Houston Methodist Cancer Center

institute: Houston Methodist Hospital

summary:
Purpose: The goal of this study is to identify the role of HN1L protein as a transcription factor or co-factor in regulating TNBC cells.
Methods: Due to the unavailability of a ChIP-grade HN1L antibody, we overexpressed FLAG-tagged HN1L in SUM159 cells and performed ChIP using anti-FLAG antibodies. ChIP DNA was prepared into libraries and sequenced by the Epigenomics Core of Weill Cornell Medical College using SR50 lane.
Results: ChIP-Seq analysis began with mapping the sequenced reads to the genome. We utilized the Burrows-Wheeler Aligner (BWA) MEM algorithm to align the sequence reads against the human genome GRCh37/hg19 Assembly.  We next used the Hypergoemetric Optimization of Motif Enrichment (HOMER) suite of tools to find and annotate peaks, and identify enriched motifs. HN1L showed 2,249 binding peaks from 10k bp upstream to 5k bp downstream of transcription start site (TSS).
Conclusions: among the binding peaks 35 genes overlapped with a previously published BCSC gene signature, 10 genes overlapped with the HN1L knockdown gene signature and 8 genes are well established CSC transcription factors. When applying overlapped genes in the STRING10 pathway analysis database , a protein interaction network centered with STAT3 was obtained.  STAT3 and FGFR2 peaks were validated by qPCR.  Model-based Analysis of ChIP-Seq (MACS) was then used to confirm the peaks found by Hypergeometric Optimization of Motif EnRichment (HOMER) . Besides the binding peaks found in HOMER, another peak was called by MACS within LEPR , and was also validated by qPCR . These findings indicate that HN1L may act as a transcription factor through binding to enhancer regions of STAT3 and other STAT3 regulators.

overall_design: Gene profile directly bound and transcriptionly regulated by HN1L protein were generated by Illumina HiSeq2000 system with each library sequenced in a 50 bases single-read run.

first: Yi

last: Liu

first: Dong

last: Choi

first: Steve

last: Benz

first: Amanda

last: Polley


title: Triple vectors expand AAV transfer capacity in the retina

city: Pozzuoli

first: Margherita

last: Mutarelli

address: Via Campi Flegrei 34

department: ISASI

institute: CNR

summary: Maddalena et al. showed that the limited DNA transfer capacity (~4.7kb) of adeno associated viral (AAV) vectors can be expanded up to 14kb with triple AAV vectors for the efficient expression of the therapeutic CDH23 (10.1kb) and ALMS1 (12.5kb) genes.

overall_design: cells infected with triple AAV vectors carrying 2 different transgenes in 3 biological replicates; RNA extracted from WT cells was used as control .

first: A

last: Maddalena

first: P

last: Tornabene

last: Manfredi

first: M

first: D

last: Cacchiarelli

last: Auricchio


title: Microglia isolated from juvenile offspring of dams with allergic asthma exhibit methylation and transcriptional alterations to autism risk genes [WGBS]

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

country: Canada

institute: University of British Columbia

type: Methylation profiling by high throughput sequencing

summary: Asthma is one of the most common chronic diseases among pregnant women, and symptoms often worsen during pregnancy. Dysregulation in immune responses during pregnancy, such as those that develop with chronic allergic asthma, increase the risk of a having a child with an Autism Spectrum Disorder (ASD).  We recently developed a mouse model of maternal allergic asthma (MAA) that induces alterations in behavioral outcomes of the offspring including changes in sociability, repetitive and perseverative behaviors. Pregnancy is also a time when epigenetic changes help a static genome adapt to the maternal environment, and consequently activation of the maternal immune system may alter the regulation of gene expression in the developing fetal brain.  Perinatal exposure to maternal asthma alters DNA methylation of immune-related genes in human infants, suggesting that maternal asthma has long-lasting effects on the offspring’s’ immune function.  Here we used the genome-wide approaches of whole genome bisulfite sequencing to examine DNA methylation combined with RNA sequencing to examine gene expression in acutely isolated microglia from juvenile MAA offspring.  Differential analysis revealed significant alterations in the epigenome of microglia from MAA compared to PBS treated control offspring and identified genes involved in controlling microglial sensitivity to the environment and shaping both synaptic and long-range neuronal connections in the developing brain.  Genes with altered methylation and expression in MAA juvenile microglia significantly overlapped with those identified in adult cortex from offspring of a different maternal immune activation (polyIC) autism model and with a curated list of autism risk genes in human, supporting a role for microglia in the pathogenesis of ASD.

overall_design: Whole genome bisulfte sequencing was performed on acutely isolated microglia from female C57BL6/J mice whose mother's had either received maternal immune activation (gestational day9,12, and 17) or PBS treatment. 4 MAA and 4 PBS biological replicates

middle: V

first: Janine

last: LaSalle


title: Arabinose Induced Catabolite Repression as Mechanism for Pentose Hierarchy Control in Clostridium acetobutylicum ATCC 824

city: Adelphi

first: Matthew

last: Perisin

state: MD

address: 2800 Powder Mill Rd

department: Biotechnology Branch

institute: US Army Research Laboratory

summary: Background: Bacterial fermentation of carbohydrates from sustainable lignocellulosic biomass into biofuels by the anaerobic bacterium Clostridium acetobutylicum is a promising alternative energy source to fossil fuels. Understanding the complex metabolic pathways it employs and how they are regulated will contribute to improved biofuel production. Recently, it has been demonstrated that xylose is not appreciably fermented in the presence of arabinose, suggesting a hierarchy of pentose utilization in this organism. Our goal is to uncover if transcriptional regulation contributes to this hierarchy. Results: Growth and sugar consumption rates showed that arabinose, like glucose, actively represses xylose utilization in cultures fermenting xylose. RNA-Seq revealed there was a large overlap in differentially regulated genes after addition of arabinose or glucose, suggesting a common mechanism of regulation. A putative ORF was identified that may be important for transcriptional regulation in response to the nutritional state of the cells. Conclusions: Decreased xylose consumption, increased acetate production, and transcription of the phosphoketolase gene (CA_C1343) revealed a transition of pentose catabolism from the pentose phosphate pathway to the phosphoketolase pathway after addition of arabinose. Together, these results substantiate the claim that arabinose is utilized preferentially over xylose in C. acetobutylicum. Furthermore, they demonstrate that this phenomenon is modulated in part at the transcriptional level, and they provide valuable insight into potential mechanisms for altering pentose utilization to modulate fermentation products for biofuel production.

overall_design: Clostridium acetobutylicum ATCC 824 was grown in CGM with 0.5% xylose. Then either arabinose (0.25%), glucose (0.25%), xylose (0.25%), or water were added and samples were taken at 0, 15, 30, and 60 min to monitor the transcriptional response via RNA-seq

middle: D

last: Servinsky

first: Rebecca

last: Renberg

first: Elliot

last: Gerlach

first: Sanchao

first: Christian

last: Sund


title: H3B-8800, a novel oral splicing modulator, induces lethality in spliceosome mutant cancers [Nalm-6]

city: Cambridge

first: Silvia

last: Buonamici

address: 300 Technology Square #5

institute: H3 Biomedicine

summary: Genomic analyses of cancer have identified recurrent point mutations in the RNA splicing factors SF3B1, U2AF1, and SRSF2 that confer an alteration of function. Although cells bearing these mutations are preferentially dependent on wild-type (WT) spliceosome function, clinical means to therapeutically target the spliceosome do not currently exist. Here, we describe an orally available modulator of the SF3b complex, H3B-8800, which potently and selectively kills spliceosome-mutant epithelial and hematologic malignancies. The effects of H3B-8800 are entirely selective for the Sf3b complex, as evidenced by the identification of drug-resistant cells bearing mutations in Sf3b components. Although H3B-8800 modulates RNA splicing mediated by WT or cancer-associated SF3B1 mutants, its preferential effects on spliceosome-mutant cells is due to preferred retention of short, GC-rich introns, which are enriched in genes encoding a substantial number of spliceosome components. These data demonstrate the therapeutic potential of splicing modulation in spliceosome-mutant cancers.

overall_design: 9 samples, including SF3B1 mutant isogenic Nalm-6 cell lines with and without 13nM treatment with H3B-8800 or 15nM treatment with E7107

first: Michael

last: Seiler


title: Adult-specific trimethylation of histone H3 lysine 4 is prone to dynamic changes with aging in C. elegans somatic cells

city: Ithaca

first: Siu

middle: Sylvia

last: Lee

address: 520 Campus road

institute: Cornell University

summary: In this study, we profiled genome-wide pattern of tri-methylation of lysine 4 on histone H3 (H3K4me3) in the somatic cells of young and old C. elegans to investigate the changes of H3K4me3 during aging. In addition, we profiled H3K4me3 pattern in developmental stage L3. We found that H3K4me3 pattern in L3 is largely maintained in adults and the age-dynamic H3K4me3 are mainly adult stage specific. We profiled gene expression in young and old C. elegans somatic cells with ribo-RNAseq. The changes of H3K4me3 and RNA abundance are positively correlated.

overall_design: We performed genome-wide mapping of histone H3 and H3K4me3 in larval stage L3,  young adult (D2A) and old adult (D12A) C.elegans somatic cells by ChIP-seq.  ribo-RNAseq was performed in young (D2A) and old (D12A) somatic cells to identify RNA expression changes during aging from D2A to D12A.

first: Mintie

last: Pu


title: Transcriptome analysis of normal human lung fibroblasts (NHLFs) following TBX4 knockdown.

city: Tokyo

first: Akira

last: Saito

address: 7-31-, Hongo, Bunkyo

institute: Tokyo University

summary: TBX4 is a transcription factor unique to lung fibroblasts and is associated with super-enhancer. RNA-sequencing analysis on NHLFs following TBX4 knockdown revealed a broad array of genes possibly regulated by TBX4.

overall_design: NHLFs were transfected with siRNAs for TBX4, and RNA-sequencing was performed using Illumina HiSeq.

first: Masafumi

last: Horie

first: Naoya

last: Miyashita

first: Takahide

last: Nagase


title: Identification of a specific 13-miRNA expression signature during follicle activation in Zebrafish

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

summary:
Purpose: We aimed to investigate important miRNA events and to define specific miRNA expression signature underlying the follicle activation of zebrafish.
Methods: By using small and regular RNA-sequencing, we performed transcriptomic analyses of PG (primary growth stage I; inactive) and PV (pre-vitellogenic stage II; activated) follicles to decipher important miRNA and gene events underlying follicle activation of zebrafish. We identified differentially expressed miRNAs for subsequent qPCR validation and miRNA::target gene prediction. Interaction of candidate miRNA:: target gene pairs were further validated by luciferase reporter assay. Global gene networks involved during PG-to-PV transition were also assessed by Gene Ontology as well as KEGG pathway analyses.
Results and Conclusion: Our expression results indicated that PG follicles can be well differentiated from PV follicles by simply using a specific 13-miRNA expression signature (let-7a, -7b, -7c-5p, -7d-5p, -7h, -7i; miR-21, -23a, -27c-3p, -107a-3p, -125b-5p, -145-3p, -202-5p). Besides, we validated interactions of let-7i::atg4a, miR-202-5p::c23h20orf24 and miR-144::ybx1 by luciferase reporter assay.
Purpose: we aimed to investigate important miRNA events and to define specific miRNA expression signature underlying the follicle activation of zebrafish

overall_design: To identify differentially expressed miRNAs and its potential downstream targets during follicle activation of zebrafish, we carried out transcriptomic profiling by both small and regular RNA-sequencing. By intersecting gene lists of the online predicted targets and RNA-seq derived differentially expressed transcripts with a reciprocal expression pattern of miRNAs, we shortlisted 6 pairs of miRNA::target gene for validation using luciferase reporter assay.

first: Wing-Lei

last: Wong

first: Ming-an

first: Chirag

last: Parsania

first: Shaolong

last: Zhou

first: Sheng

last: Yu

first: Silin

last: Zhong

first: Wei

last: Ge


title: RNA-seq to identify P-body associated mRNAs upon glucose starvation, Na+ and Ca2+ stresses

first: Anne

last: Spang

institute: Biozentrum, University of Basel

summary: To examine mRNA species sequestered by P-bodies upon different stress conditions, we employed a modified crosslinking immunoprecipitation (cCLAP) technique to purify P-body associated mRNAs and analyzed by RNA-Seq. To compare, we also performed total RNA-Seq under the same stress conditions.

overall_design: five biological independent replicates for P-body associated RNA-Seq, each consists of four conditions (control, glucose starvation, Na+and Ca2+) and three biological independent replicates for total RNA-Seq, each consists of four conditions (control, glucose starvation, Na+and Ca2+).

first: Congwei

last: Wang

first: Fabian

last: Schmich

first: Sumana

last: Srivatsa


title: Tau-P301L sorted cell types

city: South San Francisco

first: Brad

last: Friedman

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary:
Mice of indicated sexes and genotypes were perfused and their brains dissected and dissociated. Cells were fixed, immunolabeled and FACS sorted. RNA was extracted from neuron, astrocyte, and microglial cell populations. Typical RIN=4-5 for neurons, 6-8 for astrocytes, and 5-7 for microglia. Typical RNA yields ~100ng for neurons, ~20ng for microglia, and ~10ng for astrocytes.
cDNA was generated from up to 25 ng of total RNA using Nugen’s RNA-Seq method for low-input RNA samples, Ovation RNA-Seq System V2 (NuGEN). (Per manufacturers instructions, total RNA was neither depleted of rRNA nor polyA-selected.) 1 μg of sheared cDNA was taken into further processing, starting at end repair step, using Illumina’s TruSeq RNA Sample Preparation Kit v2 (Illumina).
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0010699

overall_design: Cd11b+ myeloid cells were sorted from 11-12 month old Tau-P301L transgenic mice or non-transgenic littermates.

first: Karpagam

last: Srinivasan

first: David

last: Hansen

first: Seung-Hye

last: Lee

first: Gai

last: Ayalon


title: Tau-P301S sorted cell types

overall_design: Cd11b+ myeloid cells were sorted from 6 month old male Tau-P301S transgenic mice or non-transgenic littermates.


title: Single-cell replication profiling reveals stochastic regulation of the mammalian replication-timing program [WGA]

status: Public on Dec 19 2017

city: Tallahassee

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

summary: This study demonstrates the stochastic nature of DNA replication-timing regulation by measures genome-wide replication timing in single-cells

overall_design:
Measuring replication timing in single-cells using copy number variation in haploid cells and diploid hybrid cells that allow homologue specific read parsing.

The processed data for this series can be found on the record GSE102074.

first: Vishnu

last: Dileep


title: Galactic cosmic radiation induces stable epigenome alterations relevant to human lung cancer

city: Atlanta

first: Elizabeth

last: Kennedy

state: GA

address: 615 Michael Street, Suite 301

department: Human Genetics

institute: Emory University

type: Methylation profiling by genome tiling array

summary:
Human deep space and planetary travel is limited by uncertainties regarding the health risks associated with exposure to galactic cosmic radiation (GCR), and in particular the high linear energy transfer (LET), heavy ion component. Here we assessed the impact of two high-LET ions 56Fe and 28Si, and low-LET X rays on genome-wide methylation patterns in human bronchial epithelial cells. We found that all three radiation types induced rapid and stable changes in DNA methylation but at distinct subsets of CpG sites affecting different chromatin compartments. The 56Fe ions induced mostly hypermethylation, and primarily affected sites in open chromatin regions including enhancers, promoters and edges (“shores”) of CpG islands. The 28Si ion-exposure had mixed effects, inducing both hyper and hypomethylation and affecting sites in more repressed heterochromatic environments, whereas X rays induced mostly hypomethylation, primarily at sites in gene bodies and intergenic regions. Significantly, the methylation status of 56Fe ion irradiation sensitive sites, but not those affected by X ray or 28Si ions, could discriminate tumor from normal tissue for human lung adenocarcinomas and squamous cell carcinomas. Thus, high LET radiation exposure leaves a lasting imprint on the epigenome, and affects sites relevant to human lung cancer. The 56Fe ion signature may prove useful in monitoring the cumulative biological impact and associated cancer risks encountered by astronauts in deep space.
Genome wide DNA methylation profiling of normal human bronchial epithelial cells irradiated with varying doses of 28Si-ion radiation ( 300 MeV/u at 0, 0.3, 1.0 Gy) , 56Fe-ion radiation (600 MeV/u at 0, 0.1, 0.3, 1.0 Gy) or X rays (320 kV at 0, 1.0 Gy). Triplicate control and irradiated samples were incubated and sampled at 4 timepoints between 2 and 62 days. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across >485,000 CpGs from collected samples. Samples include: 56Fe ions, 4 doses x 4 time points x 3 replicates (4 removed in QC) = 44 samples; 28Si ions = 3 doses x 4 time points x 3 replicates = 36 samples; X ray, 2 doses x 4 time points x 3 replicates (2 removed in QC)= 22 samples.

overall_design: Bisulphite converted DNA from the 102 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip

first: E

first: D

middle: R

last: Powell

first: Z

last: Li

first: J

last: Bell

first: B

last: Barwick

first: H

last: Feng

first: M

last: McCrary

last: Dwivedi

last: Kowalski

first: W

last: Dynan

first: K

last: Conneely

first: P

last: Vertino


title: Single-cell replication profiling reveals stochastic regulation of the mammalian replication-timing program

middle: M

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

overall_design: Refer to individual Series


title: Epigenetic memory of obesity predisposes to colorectal cancer

city: Research Triangle Park

first: Paul

last: Wade

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

summary: Colorectal cancer (CRC) is the third most common cancer worldwide. Obesity is a major risk factor with long-lasting effects on the predisposition to CRC even after weight loss; however, the mechanistic underpinnings remain poorly understood. Using a diet-induced obesity mouse model, we profiled cell-intrinsic alterations in colonic epithelium from young and aged obese mice compared with their age-matched controls, to gain insights into the progression of obesity-associated dysregulations in colonic cellular states. Cellular metabolic reprogramming occurred at early stage, boosting the number and function of stem/stem-like cells; while cell-intrinsic rewiring of signal transduction networks happened at later stage, promoting growth factor-independent proliferation. Strikingly, colonic DNA methylome was pre-programmed by obesity at young age priming for a tumor-prone gene signature after aging. Furthermore, obesity-related changes were substantially preserved after weight loss, potentially contributing to long-term predisposition to CRC. These findings broadened our perspectives on how obesity shapes the predisposition to CRC.

overall_design: Ribo-zero RNA-Seq was performed in colonic epithelium from mice on three different dietary regimens as follows: 1) low-fat diet for 43 weeks; 2) high-fat diet for 43 weeks; 3) high-fat diet for an initial 15 weeks then switched to low-fat diet for another 28 weeks.

first: Ruifang

first: Sara

last: Grimm


title: H3B-8800, a novel oral splicing modulator, induces lethality in spliceosome mutant cancers

first: Silvia

last: Buonamici


title: Differential expression analysis of a hyperthermophilic archeaon Thermococcus paralvinellae upon hydrogen stress

city: Amherst

first: Begum

middle: D.

last: Topcuoglu

address: 336 North Pleasant St., Apt:3B

institute: University of Massachusetts

summary:
Purpose: Compare the transcriptomes of T. paralvinellae using RNA-Seq gene expression analyses to understand the physiology of this organism when it is grown on different carbon sources, under optimal and hydrogen stress conditions.

Methods: T. paralvinellae was grown in triplicate at with either 0.5% maltose or 0.5% tryptone to investigate its catabolic pathways when grown on a sugar and peptides, respectively. It was also grown on 1% formate to determine the effect of formate on cell growth, metabolite production, and gene expression.  It was also grown separately on maltose or tryptone media as before, except with hydrogen in the media to examine the effects of hydrogen inhibition. The cells remaining in the 2-liter bioreactor were concentrated by centrifugation. The resulting cell pellets were resuspended in TRIzol (Invitrogen) and total RNA was extracted using a Direct-zol RNA extraction kit (Zymo). RNA quantity was determined with Qubit fluorometry. RNA integrity was checked by a bioanalyzer and a Nanodrop spectrometer. Genewiz sequencing facilities performed rRNA removal, library construction, multiplexing and sequence the RNA with HiSeq2500, 2×100 Paired-End. We aligned the RNAseq reads to T. paralvinellae genome (STAR) and assigned aligned sequence reads to genomic features (featureCounts). We then quantified transcriptome and reported pairwise significant genes that are differentially expressed by DESeq available under Bioconductor (www.bioconductor.org) on Galaxy platform and in R.

Results: Sequencing depths ranged from 29,974,378 to 45,240,342 sequences, with a mean of 38,990,002 and a median of 38,951,352 reads per sample. Of 2,138 genes annotated in the T. paralvinellae genome, 2084 transcripts were detected by RNA-Seq.Of the 2084 genes detected by transcriptomics, hydrogen stress caused only 48 genes to be differentially regulated (log2FC > 1, P < 0.05) with maltose and tryptone carbon sources. These included mostly genes associated with formate-dependent metabolism and transporters. The upregulated genes upon growth under H2 stress conditions indicate intrinsic formate production via formate hydrogen lyase and format secretion.

overall_design: mRNA profiles of T. paralvinellae grown on 5 different conditions in triplicates were generated by Illumina RNAseq

first: Cem

last: Meydan


title: Single-cell replication profiling reveals stochastic regulation of the mammalian replication-timing program [SEQXE]

first: David

last: Gilbert

summary: This study demonstrates the stochastic nature of DNA replication-timing regulation by measuring genome-wide replication timing in single-cells

overall_design: Measuring replication timing in single-cells using copy number variation in haploid cells and diploid hybrid cells that allow homologue specific read parsing.

first: Vishnu

last: Dileep


title: Time-dependent regulation of cellular programming of monocytes by NCOR2 [RNASeq_TK]

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Whole transcriptome profiling (RNA-Seq) of a time kinetics experiment containing human monocyte-derived cells, which were activated with IL4 either directly at the start of the culture, or at different hours after an initial activation with GMCSF alone. Cells being activated solely with GMCSF were added as controls

overall_design: CD14+ monocytes were FACS-sorted from blood of human healthy donors and later activated in vitro with either GMCSF alone for 72 hours to obtain Mo-GMCSF[IL4 (0h)] cells as controls, with the combination of GMCSF and IL4 for 72 hours or 144 hours to obtain Mo-GMCSF[IL4 (0-72h)] or Mo-GMCSF[IL4 (0-144h)] cells, respectively, or with first GMCSF and then with the combination of GMCSF and IL4 for different durations. For the latter, monocytes were first activated with GMCSF for either 12, 24, 48 or 72 hours, and then with GMCSF plus IL4 until a total activation time of 144 hours. This resulted in Mo-GMCSF[IL4 (12-144h)], Mo-GMCSF[IL4 (24-144h)] , Mo-GMCSF[IL4 (48-144h)]  and Mo-GMCSF[IL4 (72-144h)] cells, respectively.

first: Jil

last: Sander

first: Susanne

last: Schmidt

first: Branko

last: Cirovic

first: Naomi

last: McGovern

first: Olympia

last: Papantonopoulou

first: Anna-Lena

last: Hardt

first: Anna

last: Aschenbrenner

first: Christopf

last: Kreer

first: Thomas

last: Quast

first: Alex

last: Xu

first: Lisa

last: Schmidleithner

first: Heidi

last: Theis

first: Lan

last: Do

first: Mario

last: Lauterbach

first: Jonas

last: Schulte-Schrepping

first: Patrick

last: Günther

first: Jia

last: Xue

first: Kevin

last: Baßler

last: Ulas

first: Kathrin

last: Klee

first: Stefanie

last: Herresthal

first: Wolfgang

last: Krebs

first: Bianca

last: Martin

first: Eicke

last: Latz

first: Kristian

last: Händler

first: Michael

last: Kraut

first: Waldemar

last: Kolanus

first: Marc

last: Beyer

first: Christine

last: Falk

first: Sven

last: Burgdorf

first: Nicholas

last: Melosh

first: Florent

last: Ginhoux

first: Evan

last: Newell

first: Andreas

last: Schlitzer


title: Time-dependent regulation of cellular programming of monocytes by NCOR2 [RNASeq_KD]

first: Joachim

last: Schultze

summary: Whole transcriptome profiling (RNA-Seq) was performed on human Mo-GMCSF[IL4 (0-72h)] cells with either NCOR2 being knocked down or corresponding WT cells

overall_design: CD14+ monocytes were FACS-sorted from blood of human healthy donors and later activated in vitro with the combination of GMCSF and IL4 for 72h to obtain Mo-GMCSF[IL4 (0-72h)] cells. During the last 24 hours of activation, either siRNAs targeting NCOR2 or scrambled RNAs were added to obtain NCOR2 knock down cells and corresponding WT cells, respectively

first: Jil

last: Sander

first: Susanne

last: Schmidt

first: Branko

last: Cirovic

first: Naomi

last: McGovern

first: Olympia

last: Papantonopoulou

first: Anna-Lena

last: Hardt

first: Anna

last: Aschenbrenner

first: Christopf

last: Kreer

first: Thomas

last: Quast

first: Alex

last: Xu

first: Lisa

last: Schmidleithner

first: Heidi

last: Theis

first: Lan

last: Do

first: Mario

last: Lauterbach

first: Jonas

last: Schulte-Schrepping

first: Patrick

last: Günther

first: Jia

last: Xue

last: Baßler


title: Time-dependent regulation of cellular programming of monocytes by NCOR2

first: Joachim

last: Schultze


title: Intrinsic Immunity Shapes Viral Resistance of Stem Cells

city: Cleveland

first: Xianfang

last: Wu

state: Ohio

address: 9500 Euclid Avenue/NE20, Office NE2-308, Office NE2-308

department: Infection Biology

institute: Cleveland Clinic

summary: Numerous studies have demonstrated that stem cells are more resistant to virus infection than their differentiated progenies; however, the nature of this differential virus resistance remains a mystery. Here we analyzed gene expression in both mammalian stem cells and cells at various stages of differentiation. We found that stem cells intrinsically express a subset of interferon stimulated genes (ISGs) and that this property is conserved across species. We show that ISG expression is truly intrinsic, as stem cells are refractory to interferon (IFN). Further, ISG expression varies in a cell type-specific manner and decreases as cells differentiate. We show that once cell differentiate they become IFN-responsive and a broad spectrum of ISGs are then induced by canonical IFN signaling. Importantly, we also show that intrinsically expressed ISGs protect stem cells from virus infection. Finally, we performed in vivo experiments to show that protecting stem cells from virus infection is critical because stem cells are needed to regenerate tissues damaged by virus infection. Our findings have important implications for understanding both stem cell biology and the evolution of innate immunity.

overall_design: mRNA profiles for hESC-derived cells and primary cells were generated by deep sequencing, in duplicate or triplicate, using IlluminaHiSeq 2000.

first: Charles

last: Rice


title: Gene expression profiles of Id3lo and Id3hi regulatory T cells

city: Freiburg

first: Kristina

last: Schachtrup

address: Breisacher Str. 117

department: Center for Chronic Immunodeficiency

institute: University Medical Center Freiburg

summary: RNA-Sequencing approach to investigate differences in gene expression of Id3lo and Id3hi regulatory T cells.

overall_design: Mouse regulatory T cells (Treg; CD4+CD25+CD45RBlo)  from spleen of Id3GFP/+ mice were FACS sorting into Id3lo and Id3hi Treg cells based on GFP expression (Id3lo: GFPlo; Id3hi: GFPhi).  RNA-sequencing was performed on cells isolated from 4 individual mice.

first: Katharina

last: Rauch

first: Mikael

last: Sigvardsson


title: Comparing gene expression in iPSC derived RPE from control and AMD donors

city: Newcastle upon Tyne

first: Dean

middle: Mark

last: Hallam

state: Tyne and Wear

address: International Centre for Life

department: Institute of Genetic Medicine

institute: Newcastle University

summary: iPSC-RPE cells derived from a patient with AMD, whom harboured the Y402H mutation were compared to healthy donor RPE cells.

overall_design: RPE cells cultured for 6 months on hanging inserts were dissociated with TryPLE, cells were centrifuged at high speed for 3 minutes, TryPLE solution was aspirated. The cell pellet was then re-suspended in PBS. Cells were centrifuged a second time, PBS was removed and cell pellets were snap frozen on dry ice and stored at -80c until use

first: Majlinda

last: Lako


title: High density mapping of 3' extremities of 5.8S rRNA maturation precursors in Arabidopsis exosome mutants

status: Public on Dec 18 2017

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

department: IBMP

country: France

institute: CNRS

summary: The Arabidopsis core exosome (Exo9) has a phosphorolytic activity due to the RRP41 subunit. The goal of this experiment was to determine the role of this intrinsic activity of Exo9 on the maturation of the 5.8S rRNA in Arabidopsis.

overall_design: We complemented the rrp41 null mutant by expressing either a wild type RRP41 transgene (RRP41WT) or transgenes encoding catalytic inactive versions (RRP41Pi- and RRP41Pi-Cat-). High density mapping of 5.8S rRNA precursors and mature 5.8S rRNA was performed using 3’ RACE-seq. 3’ RACE-seq is an IIlumina-based sequencing strategy designed to map 3’ extremities (Sikorska et al. 2017). Mapping of 5.8S rRNA precursors was performed in rrp41 complemented lines and in several exosome mutants.

first: Natalia

last: Sikorska

first: Heike

last: Lange

first: Hélène

last: Zuber


title: H3B-8800, a novel oral splicing modulator, induces lethality in spliceosome mutant cancers [K562]

first: Silvia

last: Buonamici

state: MA

summary: Genomic analyses of cancer have identified recurrent point mutations in the RNA splicing factors SF3B1, U2AF1, and SRSF2 that confer an alteration of function. Although cells bearing these mutations are preferentially dependent on wild-type (WT) spliceosome function, clinical means to therapeutically target the spliceosome do not currently exist. Here, we describe an orally available modulator of the SF3b complex, H3B-8800, which potently and selectively kills spliceosome-mutant epithelial and hematologic malignancies. The effects of H3B-8800 are entirely selective for the Sf3b complex, as evidenced by the identification of drug-resistant cells bearing mutations in Sf3b components. Although H3B-8800 modulates RNA splicing mediated by WT or cancer-associated SF3B1 mutants, its preferential effects on spliceosome-mutant cells is due to preferred retention of short, GC-rich introns, which are enriched in genes encoding a substantial number of spliceosome components. These data demonstrate the therapeutic potential of splicing modulation in spliceosome-mutant cancers.

overall_design: 12 samples, including both SF3B1 WT and mutant isogenic K562 cell lines with and without 13nM treatment with H3B-8800, in triplicate

first: Michael

last: Seiler


title: Transcriptome-based analysis of developing dorsal and ventral hippocampus

status: Public on Dec 17 2017

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: We report the differentiation of dorsal and ventral hippocampus in developing rats by performing and analyzing transcriptome profiling.

overall_design: We isolated dorsal and ventral hippocampus at three developmental ages (P14, P28 and P45) of SD rats for total RNA preparation and subsequent RNA-seq.  Total 6 samples, each with duplicates were performed.

first: Eunsil

last: Cho

first: A-Ram

last: Lee

first: Jong-Hwan

first: Mirang

first: Mikyoung

last: Park


title: Small RNAs from Cuscuta campestris parasitizing Arabidopsis thaliana

city: University Park

middle: J

last: Axtell

address: 280 Mueller Lab

institute: Pennsylvania State University

summary: Dodders (Cuscuta spp.) are obligate parasitic plants that obtain water and nutrients from the stems of host plants via specialized feeding structures called haustoria. Dodder haustoria facilitate bi-directional movement of viruses, proteins, and mRNAs between host and parasite, but the functional effects of these movements are not clear. Here we show that C. campestris haustoria accumulate high levels of many novel microRNAs (miRNAs) while parasitizing Arabidopsis thaliana hosts. Many of these miRNAs are 22 nts long, a usually rare size of plant miRNA associated with amplification of target silencing through secondary small interfering RNA (siRNA) production. Several A. thaliana mRNAs are targeted by C. campestris 22 nt miRNAs during parasitism, resulting in high levels of secondary siRNA production. The targeted mRNAs function in hormone perception, pathogen-defense signaling, phloem function, and stem-cell identity. Homologs of these target mRNAs from diverse plants also have high-confidence complementary sites to C. campestris miRNAs, suggesting that homologous mRNAs are targeted by C. campestris across its very broad host range. These data show that C. campestris miRNAs act as trans-species regulators of host gene expression, and suggest that they may act as virulence factors during parasitism.

sample_organism:
Arabidopsis thaliana
Cuscuta pentagona

platform_organism:
Arabidopsis thaliana
Cuscuta pentagona

overall_design: Two biological replicates each for host-stem (HS), parasite stem (PS), and the host-parasite interface (I)


title: Transcriptional changes during naturally-acquired ZIKA Virus infection render dendritic cells highly conducive to viral replication

first: Xu

last: Yu

state: Massachusetts

address: 400 Technology sqr

institute: Ragon Institute of MGH, MIT and Harvard

summary: Although dendritic cells (DCs) are among the human cell population best equipped for cell-intrinsic antiviral immune defense, they seem highly susceptible to infection with Zika Virus (ZIKV). Using highly-purified mDC isolated from individuals with naturally-acquired acute infection, we here show that ZIKV induces profound perturbations of transcriptional signatures relative to uninfected patients. Interestingly, we noted a remarkable downregulation of antiviral Interferon-stimulated genes and innate immune sensors, suggesting that ZIKV can actively suppress Interferon-dependent immune responses. In contrast, several host factors known to support ZIKV infection were strongly upregulated during natural ZIKV infection; these transcripts included AXL, the main entry receptor for ZIKV, SOCS3, a negative regulator of ISG expression, and IDO-1, a recognized inducer of regulatory T cell responses. Thus, during in vivo infection, ZIKV can transform the transcriptome of dendritic cells in favor of the virus to render these cells highly conducive to ZIKV infection.

overall_design: Examination of transcriptional changes in myeloid dendritic cells between ZIKV-infected patients and healthy donors

first: Xiaoming

last: Sun

first: Stephane

last: Hua

first: Ouyang

last: Zhengyu

first: HsiaoRong

last: Chen

first: Kevin

last: Einkauf

first: Samantha

last: Tse

first: Eric

middle: S

last: Rosenberg

first: Mathias

last: Lichterfeld


title: High density mapping of 3' extremities of rRNA exosome substrates in Arabidopsis exosome mutants

first: Dominique

last: Gagliardi


title: High density mapping of 3' extremities of rRNA maturation by-products in Arabidopsis exosome mutants

summary: The Arabidopsis core exosome (Exo9) has a phosphorolytic activity due to the RRP41 subunit. The goal of this experiment was to determine the role of this intrinsic activity of Exo9 on the degradation of rRNA maturation by-products in Arabidopsis.

overall_design: We complemented the rrp41 null mutant by expressing either a wild type RRP41 transgene (RRP41WT) or transgenes encoding catalytic inactive versions (RRP41Pi- and RRP41Pi-Cat-). High density mapping of intermediates of degradation of the 5’ External Transcribed Spacer (5’ETS), a rRNA maturation by-product, was performed using 3’ RACE-seq. 3’ RACE-seq is an IIlumina-based sequencing strategy designed to map 3’ extremities (Sikorska et al. 2017). Mapping of 5’ external transcribed spacer (ETS) intermediates was performed in rrp41 complemented lines and in several exosome mutants.

first: Natalia

last: Sikorska

first: Heike

last: Lange

first: Hélène

last: Zuber


title: Epigenetic memory of obesity in mouse colonic epithelium

first: Paul

last: Wade

summary: Colorectal cancer is the third most common cancer. Obesity is a major risk factor with long-lasting effects on the predisposition to colorectal cancer; however, the mechanistic underpinnings remain poorly understood. To explore epigenetic mechanisms involved, we performed whole-genome bisulfite sequencing and RNA-Seq in colonic epithelium from control mice, obese mice, and formerly obese mice. We found that obesity-induced DNA methylation changes reprogrammed the transcriptome leading to a metabolic switch favoring long chain fatty acid oxidation, which is essential to colonic stem cell functions and colon tumorigenesis. Remarkably, persistent changes were observed after weight loss mainly at metabolic and cancer-related genes, underlying the long-term predisposition to colorectal cancer. In summary, we provide the epigenetic and metabolic basis of the link between obesity and colorectal cancer.

overall_design: Whole-genome bisulfite sequencing, bisulfite PCR deep sequencing, and RNA-Seq were performed in colonic epithelium from mice on three different dietary regimens as follows: 1) low-fat diet for 20 weeks; 2) high-fat diet for 20 weeks; 3) high-fat diet for an initial 15 weeks then switched to low-fat diet for another 5 weeks.

first: Ruifang

last: Li

first: Sara

last: Grimm


title: Effector CD8 T cells dedifferentiate into long-lived memory cells

status: Public on Dec 16 2017

city: memphis

first: yiping

last: fan

state: tn

address: 262 Danny Thomas Place

institute: st jude children's hospital

summary: DNA methyltransferase 3a regulates CD8 T cell memory differentiation

overall_design: Transgenic P14 CD8 T cells were harvested from naïve P14 TCR transgenic mice and 2K P14 cells were adoptively transferred intravenously to congenically distinct C57BL/6 mice one day before acute LCMV infection. Effector P14 CD8 T cells were FACS-purified from spleens of acutely infected mice on days 4.5 and 8 post-infection for whole genome bisulfite sequencing analysis (WGBS), and naïve antigen-specific cells obtained from transgenic P14 mice were used as an antigen-specific naïve control for WGBS. Dnmt3a conditional knockout mice were generated by breeding previously characterized floxed Dnmt3a mice with mice that contain a granzyme b driven recombinase transgene. Dnmt3a cKO and WT C57BL/6 mice mice were acutely infected with LCMV Armstrong strain and gp33-specific CD8 T cells were FACS-purified from spleens of acutely infected mice on day 8 post-infection.

first: Ben

last: Youngblood

first: J

last: Hale

first: Haydn

middle: T

last: Kissick

first: Eunseon

last: Ahn

first: Xiaojin

last: Xu

first: Andreas

last: Wieland

first: Koichi

last: Araki

first: Erin

last: West

first: Hazem

last: Ghoneim

first: Yiping

last: Fan

first: Pranay

last: Dogra

first: Carl

middle: W

last: Davis

first: Bogumila

last: Konieczny

first: Rustom

last: Antia

first: Xiaodong

last: Cheng

first: Rafi

last: Ahmed


title: Gene Expression in Cx3cr1-GFP+ Cells in PS2APP Alzheimer's Disease mice

first: Brad

last: Friedman

state: CA

summary:
This project defines the microglial gene expression profile in a transgenic mouse model of Alzheimer's, compared to non-transgenic age-matched controls, at a time when amyloid pathology and microgliosis are rampant. Microglia were sorted live from one hemisphere of cerebral cortex, using GFP expressed from Cx3cr1 locus (mice have one intact copy of Cx3cr1). RNA was isolated from sorted microglia using RNeasy mini. Two groups, PS2APP and non-transgenic, with 9 mice/group, aged 14-15 months.
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0006715

overall_design: Gene expression in Cx3cr1::GFP+ sorted cells from cortex of wildtype or PS2APP at 14-15 months of age.

first: Karpagam

last: Srinivasan

first: David

last: Hansen


title: Single-cell replication profiling reveals stochastic regulation of the mammalian replication-timing program [population]

last: Gilbert

summary: This study demonstrates the stochastic nature of DNA replication-timing regulation by measures genome-wide replication timing in single-cells

first: Vishnu

last: Dileep


title: Measurement of transcription factor binding in cyanobacteria grown under simluated natural light conditions [ChIP-Seq]

city: Cambridge

first: Joseph

middle: Robert

last: Piechura

address: 52 Oxford Street

department: FAS Center for Systems Biology

institute: Harvard University

summary: We used ChIP sequencing to measure genome-wide binding of transcription factors in the cyanobacterium Synechococcus elongatus PCC 7942 grown under dynamic light regimes that mimic the rapid changes in light intensity that accompany changes in shading. Our analysis reveals that rapid changes in light intensity modulate the binding of RNA polymerase (RNAP) upstream of genes in a way that correlates with changes in downstream gene expression, suggesting that changes in transcriptional regulation control light-responsive gene expression changes. Also, binding of the circadian clock-controlled transcription factor RpaA and the light-responsive transcription factor RpaB change upstream of genes in a manner correlating with RNAP enrichment and downstream gene expression. This suggests that changes in RpaA and RpaB binding upstream of genes regulate the light-responsive expression of genes in cyanobacteria.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Cyanobacteria were grown under either a High Light pulse or Shade pulse condition and binding of RNAP, RpaA, and RpaB was measured before and after the change in light intensity using ChIP sequencing

first: Kapil

last: Amarnath

middle: K

last: O'Shea


title: Unbiased quantification of immunoglobulin diversity at the DNA level with VDJ-seq

first: Felix

last: Krueger

address: Granta Park

institute: Altos Labs

summary: For high-throughput sequencing and quantification of immunoglobulin repertoires, most methodologies utilise RNA. However, output varies enormously between recombined genes due to different promoter strengths and differential activation of lymphocyte subsets, precluding quantitation of recombinants on a per cell basis. To date, DNA-based approaches have used V gene primer cocktails, with substantial inherent biases. Here we describe VDJ-seq, which accurately quantitates immunoglobulin diversity at the DNA level in an unbiased manner. This is accomplished with a single primer extension step using biotinylated J gene primers. By addition of unique molecular identifiers (UMI) before primer extension, we reliably remove duplicate sequences and correct for sequencing and PCR errors. Furthermore, VDJ-seq captures productive and non-productive VDJ and DJ recombination events on a per cell basis. Library preparation takes 3 days, with 2 days of sequencing, and 1 day of data processing and analysis.

overall_design: A range of starting material concentrations 500ng-5µg and examining different combination of DNA polymerases

first: Peter

last: Chovanec

first: Anne

last: Corcoran