title: Transcriptome analysis of Listeria monocytogenes infected bone marrow derived macrophages with or without DEAD-box helicase DDX3X

city: Vienna

first: Daniel

last: Szappanos

address: Dr Bohr Gasse 9

department: Department of Microbiology, Immunobiology and Genetics

country: Austria

institute: MFPL

summary: Bone marrow derived macrophages were infected with Listeria monocytogenes for 4 hours. We investigated differently expressed genes in the absence of DDX3X upon infection and also in steady state conditions.

overall_design: Investigation of gene expression in wt and Ddx3x deficient bone marrow derived macrophages in response to Listeria monocytogenes infection.

first: Thomas

last: Perlot

last: Decker


title: Molecular basis of fast and slow growing individuals of the mussel Mytilus galloprovincialis

status: Public on Oct 10 2018

city: Leioa

last: Prieto

address: Barrio Sarriena s/n

country: Spain

institute: University of the Basque Country

summary: Endogenously determined inter-individual differences in growth rate of bivalve molluscs have been widely analyzed at different organizational levels. Most studies have focused on the characterization of the physiological differences between fast (F) and slow (S) growing individuals. Although several genes have been described to be up regulated on fast growing individuals, the molecular basis underlying the mechanisms at the origin of growth variation is still poorly understood. In the present study we reared mussel spat of the species Mytilus galloprovincialis under diets below the pseudofaeces threshold (BP) and above the pseudofaeces threshold (AP). After 3 months, F and S mussels on each condition were selected, so that 4 experimental groups were obtained: FBP, SBP, FAP and SAP. We hypothesized that nurturing conditions during their growing period would modify the molecular basis of growth rate differences. However, results of feeding experiments showed that F mussels displayed higher clearance and ingestion rates and higher efficiencies of food selection prior to ingestion, as well as higher gill surface areas, irrespective of the rearing nutritional environment. To decipher molecular mechanism at the origin of growth variation, gills of the 4 mussel groups were dissected, and used for transcriptome analysis with a custom Agilent single channel microarray. Gene expression analysis revealed i) a low number (12) of genes differentially expressed associated to maintenance condition differences and ii) 117 genes differentially expressed when comparing fast and slow growing mussels (FBP + FAP vs. SBP + SAP). We further investigated this comparison: GO terms and KEGG pathway association of the differentially expressed genes allowed us to analyze the functions involved on the differentially expressed encoding. Transcriptomic differences between F and S mussels were mainly based on the up-regulation of response to stimulus, growth and cell activity Biological Process GO terms. Regarding the KEGG terms, carbohydrate metabolism and Krebs cycle were found to be up-regulated in F mussels whereas biosynthetic processes were up-regulated in S mussels. Among the differentially expressed genes that are annotated, the following ones were found to be up regulated in F mussels: i) Mucin, related to mucus secretion, known to be crucial in food acquisition and pre-ingestive selection processes in bivalves, ii) genes related to growth such as Myostatin or Insulin-like growth factor, iii) genes involved in feeding activity, such as Fibrocystin or Dynein and iv) genes involved in the energetic metabolism; Citrate synthase.  S mussels mainly over-expressed genes related to immune system and defence (Leucine-rich repeat-containing protein, Metalloendopeptidase, Small heat shock protein 24, Multidrug resistance,…).The present results suggest that differences in feeding activity and in the allocation of metabolic energy between growth groups could account for the differences in growth rate in spat of Mytilus galloprovincialis. In accordance with their higher feeding rates and growth, fast growing mussels were found to mainly over-express genes involved in the development and maintenance of such activities, however, slow growing mussels needed to expend energy in immune and defence processes to ensure survival at the expense of growth rate.

overall_design: The gene expression, in gill tissue, was measured in 16 samples, representing 4 different experimental groups of the mussel Mytilus galloprovincialis. Thus, 4 samples per experimental groups were analyzed. Each sample was a pool of 5 individuals.

first: Pablo

last: Markaide

first: Iñaki

last: Urrutxurtu

first: Enrique

last: Navarro

first: Sebastien

last: Artigaud

first: Elodie

last: Fleury

first: Irrintzi

last: Ibarrola

first: Miren

middle: B

last: Urrutia


title: Layers of regulation on cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae

city: Hanover

first: Christina

middle: M

last: Kelliher

state: NH

address: 7400 Hinman

department: Molecular & Systems Biology

country: USA

institute: Geisel School of Medicine at Dartmouth

type: Expression profiling by high throughput sequencing

summary: Transcript profiling from a population of cell-cycle-arrested B-type cyclin mutant budding yeast. We compared transcript to protein expression levels in mutant cells.

overall_design:
One time course experiment, 30 degrees Celsius, rich media (YEPD) shift from YEPGalactose
Please note that the 'Scerevisiae_wildtype_re-normalized_GSE80474.txt' contains the wild type sample data from the published records (GSE80474; GSM2128020-GSM2128069). The raw data is available from the GSE80474 records and the re-analyzed data matrix is linked to the current records.

first: Matthew

middle: W

last: Foster

first: Francis

middle: C

last: Motta

first: Anastasia

last: Deckard

first: Erik

middle: J

last: Soderblom

first: M

middle: A

last: Moseley

first: Steven

last: Haase


title: Transcriptome analysis reveals the genetic foundation for starch and lipid accumulation dynamics in Neochloris oleoabundans

status: Public on Oct 11 2018

city: Qingdao

first: Yanhai

last: Gong

address: No.189 Songling Road

department: single cell center

country: China

institute: qibebt, cas

summary: The oleaginous green microalga Neochloris oleoabundans accumulates both starch and lipids to high levels under stress conditions such as nitrogen starvation. In order to steer the metabolism towards starch or lipids only, it is important to understand the mechanisms behind it. In this study physiological changes and gene expression upon nitrogen starvation were analysed in controlled flat-panel photobioreactors over both short- and long-term time-scales. Starch accumulation is transient and occurs rapidly within 24 hrs upon starvation, while lipid accumulation lasts longer and reaches a maximum after 4 days. The major fraction of accumulated lipids is composed of de novo synthesized neutral lipids - triacylglycerides (TAG) - and is characterized by a decreased composition of the polyunsaturated fatty acids (PUFAs) C18:3 and C16:3 and an increased composition of the mono-unsaturated and saturated fatty acids C18:1/C16:1 and C18:0/C16:0, respectively. RNA-sequencing revealed that genes related to starch biosynthesis and degradation show different temporal expression dynamics compared to those of lipid biosynthesis. An immediate rapid increase in starch synthesis gene expression is followed by an increase in starch degradation and decrease in starch synthesis gene expression. In contrast, increased gene expression for fatty acid and TAG synthesis is initiated later and occurs more gradually. Expression of several fatty acid desaturase (FAD) genes was decreased upon starvation, which corresponds to the observed changes to higher levels of mono-unsaturated and saturated fatty acids. Moreover, several homologs of transcription regulators that were implicated in controlling starch and lipid metabolism in other microalgae showed differential gene expression and might be key regulators of starch and lipid metabolism in N. oleoabundans as well. Promising candidates for future metabolic engineering are a DYRKP homolog that in Chlamydomonas acts as a negative regulator of carbon storage and photosynthetic efficiency under N-starvation, and two bZIP-type regulators that have been implicated to control several steps in microalgal TAG synthesis. Our data for the first time show the temporal dynamics of storage compound accumulation and transcriptional changes on a short- and long-term time-scale during nitrogen starvation in N. oleoabundans, and increases insight into the genetic foundation for starch and lipid metabolism in this microalga. This information and the identified target genes can now be used for metabolic engineering strategies towards tailored N. oleoabundans strains for industrial applications with increased lipid production and altered fatty acid composition.

overall_design: Nine time points, three replicates.

first: Mark

middle: H

last: Sturme

first: Josue

last: Heinrich

first: Anne

last: Klok

first: Gerrit

last: Eggink

first: Dongmei

last: Wang

first: Jian

last: Xu

first: Rene

last: Wijffels


title: Vitamin C Promotes Apoptosis in Breast Cancer Cells by Increasing TRAIL Expression

city: Provo

first: David

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

summary: In this study we show that ascorbate (vitamin C) shifts the transcriptome of MDA-MB-231 cells and increases apoptosis.

overall_design: Examination of transcriptome in vitamin C treated  or control MDA-MB-231 cells

first: Gaofeng

first: Sushmita

last: Mustafi


title: Extensive structural differences of closely related 3’ mRNA isoforms: links to Pab1 binding and mRNA stability

city: Boston

first: Zarmik

last: Moqtaderi

state: MA

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

summary: Alternative polyadenylation generates numerous 3' mRNA isoforms per gene; regulation of this process is critical in development and impaired in cancer. Individual isoforms from the same gene can vary greatly in biological properties such as translational efficiency, localization, and half-life. Even closely related isoforms - including those differing by a single nt - can have different biological properties, but the underlying mechanisms are unknown. Here we show that many highly similar yeast isoforms unexpectedly exhibit extensive structural variation and differential Pab1 binding, and that these physical properties serve as a good predictor of relative isoform stability. We developed DREADS, a dimethyl sulphate (DMS)-based technique, to obtain the first transcriptome-scale structural description of individual 3' mRNA isoforms in vivo. Strikingly, near-identical yeast mRNA isoforms arising from the same gene can possess dramatically different DMS modification profiles over hundreds of nt upstream of the poly(A) tail. DREADS analyses of the same mRNAs refolded in vitro or in different species indicate that structural differences in vivo are often due to trans- acting factors. CLIP-READS, a technique we developed to measure isoform-specific binding, reveals that differences in Poly(A) binding protein (Pab1) binding to 3' ends correlate with the extent of structural variation for closely-spaced isoforms. A pattern encompassing single-strandedness near the 3' terminus, double-stranded character of the poly(A) tail, and low Pab1 binding is significantly associated with mRNA stability. Sequences responsible for isoform-specific structures, differential Pab1 binding, and mRNA stability are evolutionarily conserved, and are indicative of biological function.

sample_organism:
Saccharomyces cerevisiae
Debaryomyces hansenii
Kluyveromyces lactis

overall_design: In vivo DREADS and SHREADS: Two independent biological replicates (A and B) each of a DMS or NAI treated sample and corresponding untreated control.  For the first DMS samples and controls, two technical replicates (1 and 2) of the library preparation were performed for each biological replicate, and two sequencing runs were performed to increase sequencing depth.  For the NAI samples and controls, two biological replicates were perfromed, and two sequencing runs were performed to increase sequencing depth.  For the SOD1 randomization experiment, two biological replicates were performed for both DMS-treated and control samples.  In vitro refolded DREADS: Two independent biological replicates A and B, each with a DMS-treated sample and an untreated control.  CLIP-READS: Two independent biological replicates of the triple-Myc-tagged Pab1 strain, and one with the triple-V5-tagged Pab1 strain), each with IP and input control.  Cross-species experiment:  Two independent biological replicates each of D. hansenii, K. lactis, and YAC-containing S. cerevisiae strains JYAC2 and JYAC7.

first: Joseph

middle: V

last: Geisberg

first: Kevin

last: Struhl


title: Identification of lineage-specific transcription factors setting the active distal regulatory landscape that drives astrogliogenesis

city: Mainz

first: Abhijeet

last: Pataskar

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The gene regulatory mechanisms that steer neural stem cells towards astrocytes during brain development are largely unknown. Here we set out to comprehensively identify transcription factors that drive the developmental trajectory of astrogliogenesis from mouse embryonic stem cells. To attain this we performed a genomewide analysis of gene expression and epigenetic signature hallmarks of primed and active enhancers through the distinct stages of astrogliogenesis. We revealed distal regulatory elements that become activated in a stage-specific manner which confer the transcriptional program underlying generation and maturation of astrocytes. By searching for lineage-specific transcription factors functioning at these elements, we identified ATF3 and NFIA as drivers of differentiation of neural precursor cells to astrocytes, while RUNX2 promotes their maturation. These transcription factors are crucial for switching the chromatin state of these elements from primed to active, thereby driving the gene expression program underlying astrocyte differentiation and maturation.Method: RNA was extracted from embryonic stem cells (ES) differentiated into neural progenitor cells (aNPC) and subsequently differentiated for 1 day into early astrocytes (eA) and further progressively for 5 and 21 days into mature astrocytes  (lA_1 and lA_2). These samples are further subjected for RNA-sequencing to reveal the genome wide changes at transcriptional level at each stage. aNPC, eA and lA_1 (further called as lA) were subjected for H3K27ac and H3K4me1 ChIP and sequenced genome wide (ChIP-seq) to reveal the active and primed enhancers regions during astrogliogenesis, respectively. In quest to identify the TF required for early and late astrogliogeneis, we depleted Nfia (SiNfia) and Atf3 (siAtf3) in eA and Stat3 (siStat3), Prdm9 (siPrdm9) and Runx2 (siRunx2) at lA by using siRNAs and perfomed H3K27ac ChIP and sequence them.  We also extracted RNA after depletion (only after siNfia, siAtf3 and siRunx2) and perform the RNA-seq.

overall_design:
RNA was extracted from embryonic stem cells (ES) differentiated into neural progenitor cells (aNPC) and subsequently differentiated for 1 day into early astrocytes (eA) and further progressively for 5 and 21 days into mature astrocytes  (lA_1 and lA_2). These samples are further subjected for RNA-sequencing to reveal the genome wide changes at transcriptional level at each stage. aNPC, eA and lA_1 (further called as lA) were subjected for H3K27ac and H3K4me1 ChIP and sequenced genome wide (ChIP-seq) to reveal the active and primed enhancers regions during astrogliogenesis, respectively. In quest to identify the TF required for early and late astrogliogeneis, we depleted Nfia (SiNfia) and Atf3 (siAtf3) in eA and Stat3 (siStat3), Prdm9 (siPrdm9) and Runx2 (siRunx2) at lA by using siRNAs and perfomed H3K27ac ChIP and sequence them.  We also extracted RNA after depletion (only after siNfia, siAtf3 and siRunx2) and perform the RNA-seq.
RNA-seq in ES, aNPC, eA, lA_1 and lA_2. H3K27ac and H3K4me1 ChIP-seq in aNPC, eA and lA.  H3K27ac ChIP-seq in siControl_eA, siNfia_eA, siAtf3_eA, siControl_lA, siStat3_lA, siPrdm9_lA and siRunx2_lA.

first: Neha

last: Tiwari


title: Genome-nuclear lamina interactions regulate progenitor cell behavior during cardiac development

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

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

overall_design: Refer to individual Series


title: RNA-seq analysis of livers of C57BL/6 mice upon antagomiR-122 and CL316243 treatment

city: Jerusalem 9112001

first: chofit

last: chai

address: Ein Karem

department: gene therapy

country: Israel

institute: hadassah

summary: Purpose: miR-122 plays a role in lipid metabolism in the liver. The goal of this study is to search for additional metabolic pathways in which miR-122 is involved. Methods: mice were administered with antagomiR-122 (to inhibit miR-122) or antagomiR-control together with CL316243 (β 3-adrenergic receptor agonist, which causes TG hydrolysis to FFAs). Liver mRNAS were generated from 4 mice in each group by deep sequencing using Illumina Nextseq 500 System. The sequence reads that passed quality filters were analyzed with TopHat followed by Cufflinks. The Ingenuity IPA and GeneAnalytics analysis were performed to untangle the biological processes involving the differentially expressed genes. Results: Cufflink algorithm revealed that 182 genes were differentially expressed in the mice livers. According to IPA analysis, the circadian rhythm pathway and adipogenesis were significantly disrupted. Conclutions: Inhibition of miR-122 Activates Several Metabolic Pathways Which Regulate Hepatic Triglycerides Synthesis and Storage

overall_design: C57BL/6 mice were administered with antagomiR-122 or antagomiR-control together with CL316243 (β 3-adrenergic receptor agonist, which causes TG hydrolysis to FFAs). Livers mRNA were generated from 4 mice in each group by deep sequencing using Illumina Nextseq 500 System.


title: MicroRNA expression profile of pigeon milk exosomes

status: Public on Oct 16 2018

city: Chengdu

first: Yao

last: Ma

state: Sichuan

address: Huiming road #211

institute: Sichuan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study,we found that the highly expressed miRNAs appear to assist the biosynthesis and metabolism of PM. Notably, immune and growth-related miRNAs in PM distributed in the early stage of lactation, having the similar expression with mammals. Therefore, we hypothesized the maternally secreted miRNAs may be another factor protect the infant from infections and play developmental functions integral to the infant.

overall_design: we investigated miRNA expression profiles from pigeon milk exosomes across five stage (1d1,1d2,1d3,5d,10d,15d,20d)by using high-throughput sequencing technology.

first: Siyuan

last: Feng


title: Regulation of kidney field specification by transcriptional regulation of microRNAs

city: Pittsburgh

first: Neil

middle: A.

last: Hukriede

department: Developmental Biology

institute: University of Pittsburgh

summary: The transcriptional events driving specification of the kidney field have been well characterized.  However, it remains unknown how the initial field size is established, patterned, and proportioned.  Lhx1 is a transcription factor expressed in the kidney anlage and is required for specification of the kidney field, but few Lhx1 interacting cofactors or downstream targets have been identified.  By tandem-affinity purification, we isolated Furry (FRY), a multifunctional protein that acts as a transcriptional co-repressor of microRNAs.  We found that Xenopus embryos depleted of fry exhibit loss of the kidney field, phenocopying the lhx1 depleted animals.  In addition, we demonstrated a synergism between Fry and Lhx1, identified candidate microRNAs regulated by the protein pair, and show at least two microRNA clusters influence specification of the kidney field.  Therefore, our data shows that a tissue-specific transcription factor, Lhx1, can interact with a broadly expressed microRNA repressor, Fry, to establish the kidney field.

overall_design: miRNA Deep sequencing of 3 Xenopus laevis samples

first: M

last: Cirio


title: Integration of genome-wide analysis to characterize long noncoding RNAs in diverse immune cell types of the stage IV melanoma patients

city: Baltimore

first: Yuji

last: Zhang

state: MD

address: 660 W. Redwood Street

institute: University of Maryland

summary: We investigated the expression profiles in the CD4+, CD8, and CD14+ peripheral blood cells (PBLs) of the stage IV melanoma patients and the healthy donors.

overall_design: Examination of long noncoding RNA in the CD4+, CD8, and CD14+ peripheral blood cells (PBLs) of the stage IV melanoma patients and the healthy donors.

first: Larry

middle: R

last: Pease


title: Regulation of gene expression change in autism by microRNA [miRNA-seq]

city: Shanghai

first: Xiling

last: Liu

address: 320 Yue Yang Road

institute: Partner Institute for Computational Biology

summary: To identify the regulation of gene expression change in autism, we sequenced small RNAs in autism and control samples using miRNA-seq. We found a significant enrichment of binding sites in the 3'UTR regions of one cluster of genes with expression change in autism. Furthermore, expression of 18 miRNAs showing significant binding site enrichment in this cluster, correlated significantly with the expression of their predicted targets.

overall_design: Identify the microRNA expression change in autism and compare them with the expression change of their targets

first: Xi

last: Jiang


title: RNA-seq of LCMV GP33-specific CD8 TCR transgenic cells (P14) primed at the onset versus in the midst of persistent LCMV-Clone 13 viral infection

status: Public on Oct 09 2018

city: Toronto

first: David

middle: G

last: Brooks

state: Ontario

address: 610 University Avenue

department: Research

country: Canada

institute: Princess Margaret Cancer Centre

summary: Altered CD8 T cell differentiation and functional exhaustion prevent control of chronic virus infection and cancer. Yet, how fate commitment and exhaustion are determined and dynamically modulated throughout persistent infection are unclear. We compared the activation and differentiation of LCMV GP33-specific CD8 TCR transgenic cells (P14) primed at the onset versus in the midst of established persistent LCMV-Clone 13 viral infection. LCMV GP33-specific CD8 TCR transgenic (P14) cells were injected into naïve mice immediately infected with LCMV-Cl13 (Early priming) or into mice that had been infected 21 days earlier with LCMV-Cl13 (Late Priming). Sixty hours post-priming P14 cells were sorted from mice and subjected to RNA seq. We show early primed cells very rapidly exhibit a transcriptional profile of robust activation, effector differentiation and dysfunction, while late primed cells have increased expression of genes involved in memory differentiation and maintenance.

overall_design: 3 early prime, 3 late prime and 3 naïve P14 T cell samples were analyzed.


title: Immune stimuli shape the small non-coding transcriptome of extracellular vesicles released by dendritic cells

status: Public on Oct 19 2018

city: Utrecht

first: Esther

last: Nolte-'t Hoen

address: Yalelaan 2

department: Biochemistry & Cell Biology

country: Netherlands

institute: Utrecht University

summary:
PURPOSE: The molecular composition of extracellular vesicles (EV) is regulated by cellular activation and differentiation stimuli, thereby  affecting their signaling function to target cells. While activation-associated changes in EV-derived microRNAs (miRNA) have been intensively studied, it is unknown whether cell stimulation affects other classes of small non-coding RNA in EV.
METHODS: RNA isolated from primary immune cells that were made tolerogenic with VitD3, activated by LPS, or left untreated (control), and RNA isolated from EV purified from the supernatant of these dendritic cells were analyzed by RNA seq (n = 3 biological replicates)
RESULTS: Prominent changes were found in the miRNA, snoRNA and Y-RNA content of EV from differentially stimulated dendritic cells, whereas tRNA and snRNA levels were much less affected. Comparing changes in EV-RNA with changes in the corresponding cells, we found that EV-RNA levels only partly reflected changes in cellular RNA.
CONCLUSIONS: Our results implicate that the EV-transcriptome not necessarily predicts RNA levels in EV-producing cells. The acquired knowledge can guide discovery and understanding of non-coding RNA types beyond miRNAs as functional entities in EV and as EV-RNA-based biomarkers.

overall_design: SmallRNA isolated from n = 3 biological replicates of cells (3 conditions: LPS, VitD3, control) and corresponding EV (3 conditions: LPS, VitD3, control). Libraries were prepared with NebNext smallRNA kit for Illumina, 150 bp paired end reads on Illumina HiSeq 4000 sequencer

first: Tom

last: Driedonks


title: Manganese (II) Activates cGAS-STING pathway

city: Rockville

first: Yukun

last: Guan

address: 5625 Fishers Lane, Room 2S-30

institute: NIAAA

summary: We show that Manganese (II) is a potent type I-IFN inducing agonist, stimulating cells into an anti-viral state in the absence of infection. Mechanically, Mn2+ treatment led to a profound cGAS-STING-dependent innate immune activation, conferring cells or mice viral resistance.

overall_design: THP1 cells were treated with Mn2+, VACV, IFNβ or empty media (control). RNA was extracted and sequenced.

first: Zhengfan


title: Partial loss of psychiatric risk gene Mir137 in mice causes repetitive behavior and impairs sociability and learning via increased Pde10a

city: Atlanta

first: Ying

last: Cheng

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University

summary: Genetic analyses have linked microRNA-137 (MIR137) to neuropsychiatric disorders, including schizophrenia and autism spectrum disorder. miR-137 plays important roles in neurogenesis and neuronal maturation, but the impact of miR-137 loss-of-function in vivo remains unclear. Here we show the complete loss of miR-137 in the mouse germline (gKO) or nervous system (cKO) leads to postnatal lethality, while heterozygous gKO and cKO mice remain viable. Partial loss of miR-137 in heterozygous cKO mice results in dysregulated synaptic plasticity, repetitive behavior, and impaired learning and social behavior. Transcriptomic and proteomic analyses revealed that the miR-137 mRNA target, phosphodiesterase 10a (Pde10a), is elevated in heterozygous knockout mice. Treatment with the Pde10a inhibitor papaverine or knockdown of Pde10a ameliorates the deficits observed in the heterozygous cKO mice. Collectively, our results suggest that MIR137 plays essential roles in postnatal neurodevelopment and that dysregulation of miR-137 potentially contributes to neuropsychiatric disorders in humans.

overall_design: Systematically investigate the role of miR-137 in neurodevelopment by using miR-137 knockout mice

first: Peng

last: Jin


title: Active ribosome profiling  from mouse brains with RiboLace

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

summary:
We developed RiboLace, a novel method based on a new puromycin-containing molecule, for the isolation of active ribosomes by means of an antibody-free and tag-free pull-down approach. RiboLace is fast, it works with very low input material and can be easily and rapidly used to enhance Ribo-Seq, obtaining  a global snapshot on active ribosome footprints at single nucleotide resolution from  eukaryotic in vitro and in vivo systems.
Keywords: ribosome profiling, translation, RiboLace, Ribo-Seq, active translation

overall_design: We performed active ribosome profiling with RiboLace in brain extracts from a mouse (Smn+/-; SMN2tg/0). Experiments were performed in biological duplicate.

first: Massimiliano

last: Clamer

first: Paola

last: Bernabò

first: Fabio

last: Lauria

first: Ewout

last: Groen

first: Alessandro

last: Quattrone

first: Thomas

last: Gillingwater

first: Gabriella

last: Viero


title: Next Generation Sequencing of p53 KO and Utx/p53 DKO Hematopoietic Stem Cells Transcriptomes

status: Public on Oct 08 2018

first: Liting

last: Zheng

address: 320 Yueyang Road

institute: Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences

summary: Hematopoitic stem cells from Utx/p53 DKO mice showed increased self-renewal potential and predisposition of differentiation to myeloid lineage compared with those from p53 KO mice. To figure out what mechanism leads to the increased self-renewal, we compared the transcriptional profiles using RNA-sequencing of FACS sorted LSK (Lin-Ckit+Sca1+) cells, which contains the hematopoietic stem cells.

overall_design:
Examination of differential genes expression in 2 genotipic hematopoitic stem cells
LSK cells were sorted directly into TRIzol (Invitrogen),then column-purified with Direct-zol RNA MiniPrep Kit (Zymo research). 50ng total RNA was used for preparation of cDNA sequencing library. Sample libraries were pooled for 100bp double read sequencing on Illumina HiSeq2500 resulting in 50 million reads per sample.

first: Charli

middle: D

last: Chen

first: Longyong

last: Xu


title: Transcriptome of zebrafish neurohypophyseal astroglia (pituicytes)

status: Public on Oct 07 2018

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

institute: Weizmann Institute of Science

summary: The hypothalamo-neurohypophyseal system (HNS) is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine-vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections, endothelial blood vessels and astroglial-like cells, termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro-vascular interface, which allows the release of neurohormones from the brain to the periphery. However, the molecular blueprint of pituicytes-specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature.

overall_design: mRNA profiles of hypophyseal b-Ala-Lys-Ne positive (pituicytes) and b-Ala-Lys-Ne negative (non-pituicytes) were generated by next-generation sequencing, in 5 biological replicates, using Illumina HiSeq 2500 v4 instrument

first: Savani

last: Anbalagan

first: Gil

last: Levkowitz


title: Widespread cytoplasmic polyadenylation programs asymmetry in the germline and early embryo

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

summary: The PAT-seq approach was utilised to determine the gene expression, poly(A)-site and polyadenylation state of the transcriptome of  C. elegans of wildtype (N2), gld-2(q497) and cpb-3(bt17) strains. A series of deadenylases were aditionally depleted by RNAi in the gld-2 background to determine the identity of the initiating deadenylase.  RNAi was performed by bacterial feeding, using the E. Coli HT115 (DE3) strain carrying pL4440-based feeding vectors. These vectors contained individual open reading frames (ORFs) for the five deadenylases, and the pCB19 control used in this study. The RNAi constructs used were pCB19, parn-1, panl-2, ccr-4, parn-2, ccf-1. The pCB19 control contains fragment of a Arabidopsis thaliana gene that shares no homology with any C. elegans gene. All RNAi vectors were sequenced to confirm the correct target sequence prior to use. For all experiments, worms were synchronised by bleaching and harvested at 60(N2) or 65(gld-2(q497) hours post L1 stage and either imaged directly or snap-frozen with liquid nitrogen and stored at -80C until RNA/DNA/protein extraction could be performed. gld-2(q497) heterozygotes mutants were maintaned over the hT2[qIs48] I;III balancer chromosome and homozygote gld-2(q497) progeny were analysed

overall_design: Analysis of poly(A) dynamics in early C. elegans embryos responding to depletion of specific RNA binding proteins and adenylation state regulators

first: Peter

last: Boag

first: Paul

middle: F

last: Harrison


title: Global Transcriptome and Gene Regulatory Network of MAPK Signaling Pathway in Trichoderma reesei During Sugarcane Bagasse Degradation

city: Campinas

first: Gabriela

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

summary: The filamentous fungus Trichoderma reesei is a saprophyte involved with polysaccharides cell wall depolymerization, being the most important industrial source of cellulases, which have been used for bioethanol production. The regulation of cellulase expression is controlled at the transcriptional level and in a carbon source-dependent manner. However, the signaling pathways and mechanisms involved in regulating the expression of these enzymes in T. reesei are still poorly understood. In this study, we demonstrate through transcriptional analysis by RNA-Seq the main changes in gene expression that occur in functional mutants for two genes of the MAPK, tmk1 and tmk2. The results obtained allowed us to identify that these proteins in T. reesei regulate independent processes, but sometimes might regulate the same process through different mechanisms of action, being responsible for modulating gene expression in this organism. Regarding to Δtmk2 strain, it was demonstrated that growth in sugarcane bagasse and glucose modulates the expression of genes involved with chromatin remodeling, metabolism of carbohydrates and cell signaling genes such as GPCR, calcium signaling and phospholipases. On the other hand, deletion of MAPK TMK1 promotes more discrete changes in the transcriptional profile and the main changes are related to the decrease in the expression of the major genes for cellulases and xylanases, repressing the expression of transporters belonging to the MFS family, transporters of amino acids and ions such as Ca2+ and Mg2+. Our results revealed that the MAPK signaling pathway in T. reesei regulates many important processes that allow the fungus to promote the recognition, transport and metabolism of different carbon sources during the process of cell wall degradation. Therefore, the clustering of these data will contribute to the construction of a global model for the events that occur during the degradation of lignocellulose in T. reesei, which will lead to the development of more efficient strains in the plant biomass degradation.

overall_design: T. reesei (QM6a and mutant strains ) were grown in Mandels-Andreotti medium, supplemented with 2% of glucose for 48 hours. The cultures were incubated on an orbital shaker (200 rpm) at 30°C for 48 hours using glucose as carbon source. For the sugarcane bagasse induction,  the strains were grown in Mandels-Andreotti medium, supplemented with 1% of glycerol for 24 hours. Then, the mycelia was collected and transfered to Mandels-Andreotti medium supplemented with 1% of sugarcane bagasse. The cultures were incubated on an orbital shaker (200 rpm) at 30°C for 48 hours using sugarcane bagasse as carbon source.  All experiments were performed in three biological replicates. The resultant mycelia were collected by filtration, frozen and stored at -80°C until RNA extraction. After growth, total RNA was isolated from the mycelia using TRIzol® reagent. RNA-seq experiments were performed by Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE)  using the platform Illumina/HiSeq2500.

first: Renato

last: de Paula

first: Amanda

last: Antoniêto

first: Cláudia

last: Carraro

first: Nalu

middle: T

last: Peres

first: Nilce

last: Martinez-Rossi

first: Rafael

last: Silva-Rocha

first: Roberto

middle: N

last: Silva


title: RNA sequencing of murine Nup98-Phf23-driven pro-B1 ALL

city: Frederick

first: Jack

address: SAIC-Frederick Miller Dr

institute: NIH

summary: B-1 and B-2 lymphocytes are derived from distinct developmental pathways, and represent layered arms of the innate and adaptive immune systems, respectively. In contrast to the majority of murine B- cell malignancies, which stain positive with the B220 antibody, we discovered a novel form of B-cell leukemia in NUP98-PHF23 (NP23) transgenic mice. The immunophenotype (Lin- B220 - CD19+ AA4.1+) was identical to B-1 progenitor cells, and VH gene usage was skewed toward 3’ V regions, similar to murine fetal liver B-cells. We performed RNA sequencing and determined that the expression profile of these leukemias was most similar to fetal liver pro B fraction BC, a known source of B-1 B cells, further supporting a B-1 progenitor origin of these leukemias. The NP23 B-1 progenitor ALLs acquired spontaneous mutations in both Bcor and Jak pathway (Jak1/2/3 and Stat5a) genes, supporting a hypothesis that mutations in three critical pathways (stem cell self-renewal, B-cell differentiation, and cytokine signaling) collaborate to induce B-cell precursor (BCP) ALL. Finally, the Tslp cytokine is required for murine B- 1 development, and chromosomal rearrangements resulting in overexpression of the TSLP receptor (CRLF2) are present in some high risk BCP ALL patients (referred to as CRLF2r ALL). Gene expression profiles of NP23 pro-B1 ALL were more similar to CRLF2r ALL than non-CRLF2r ALL, and analysis of VH gene usage from CRLF2r ALL patients demonstrated preferential usage of VH regions used by human B-1 B-cells, leading to the suggestion that this subset of BCP ALL patients have a malignancy of B-1, rather than B-2 B-cell origin.

overall_design: RNA was extracted from seven NP23 pro-B1,  two E2A-PBX pre-B2, and three Eμ-RET pre-B2 ALL samples, and purified wild-type fetal liver Ter119-AA4.1+CD19+B220+ cells pooled from E15.5-16 embryos.  Cells were purified using fluorescence activated cell sorting (FACS) at the NCI FACS core facility using an Aria Violet-Cli FACS sorter. RNA samples were prepared using TRIzol reagent (Invitrogen) following the manufacturer’s recommended protocol.  Samples were evaluated using Fragment Analyzer and NanoDrop.  Indexed cDNA sequencing libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit, and bar-coded with individual tags, following the manufactures recommendations. Library preparation was performed using a 96-well plate method. The libraries were quantified using Qubit fluoroscopy and the NGS kit for Fragment Analyzer. Any failed results from the fragment analyzer were repeated using 2100 Bioanalyzer. Indexed libraries were prepared as equimolar pools and run on HiSeq4000 (2x150 paired end runs) to generate 40 million paired-end reads per sample library.

last: Aplan

first: Liat

last: Goldberg


title: Spliceosome specifically associates with RNA polymerase II CTD Ser5-P isoform to promote co-transcriptional splicing

status: Public on Oct 06 2018

city: Lisboa

first: Kenny

last: Rebelo

address: Av. Professor Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

summary: Co-transcriptional splicing of introns is a defining feature of eukaryotic gene expression. We show that the mammalian spliceosome specifically associates with the S5P CTD isoform of RNA polymerase II (Pol II) as it elongates across spliced exons of protein coding genes, both in human Hela and murine lymphoid cell lines. Immuno-precipitation of MNase digested chromatin with phospho CTD specific antibodies reveals that components of the active spliceosome (both snRNA and proteins) form a specific complex with S5P CTD Pol II. Furthermore a dominant splicing intermediate formed by cleavage at intron 5’ss results in the tethering of upstream exons to this complex at all spliced exons. These are invariably connected to upstream spliced constitutive and less frequently to alternative exons. Finally S5P CTD Pol II accumulates over spliced exons but not adjacent introns. We propose that mammalian splicing employs a rapid, co-transcriptional splicing mechanism based on CTD phosphorylation transitions.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of co-transcritional splicing kinetics using nascent RNA-sequence, mNET-seq

first: Takayuki

last: Nojima

first: Tomás

last: Gomes

first: Ana Rita

last: Grosso

first: Nicholas

last: Proudfoot

first: Maria

last: Carmo-Fonseca


title: Single cell profilng of hCS derived from hiPSC cultured in feeder-free conditions

status: Public on Oct 05 2018

city: Menlo Park

first: Christina

last: Fan

state: CALIFORNIA

address: 4040, Campbell Ave

institute: BD Biosciences

summary: Single cell gene expression profilling of hCS derived from iPSC at day 105 of differentiation

overall_design: 3 samples of hiPSC cultures, each derived from a donor

first: Sergiu

last: Pasca


title: RUNX1 and the endothelial origin of blood

city: Philadelphia

first: Long

last: Gao

address: 4002 Colket Translational Research Building (CTRB) 3501 Civic Center Boulevard

institute: The Children’s Hospital of Philadelphia

summary: The transcription factor RUNX1 is required in the embryo for formation of the adult hematopoietic system. Here we describe the seminal findings that led to the discovery of RUNX1 and of its critical role in blood cell formation in the embryo from hemogenic endothelium. We also present RNA-Seq data demonstrating that hemogenic endothelial cells in different anatomic sites, which produce hematopoietic progenitors with dissimilar differentiation potentials, are molecularly distinct. Hemogenic endothelial cells and non-hemogenic endothelial cells in the yolk sac are more closely related to each other than either are to hemogenic or non-hemogenic endothelial cells in the major arteries. Thus, a major driver of the different lineage potentials of the committed erythro-myeloid progenitors that emerge in the yolk sac, versus hematopoietic stem cells that originate in the major arteries, is likely to be the distinct molecular properties of the hemogenic endothelial cells from which they are derived. We use bioinformatics analyses to predict signaling pathways active in arterial hemogenic endothelium, several of which are functionally validated pathways including Notch, Wnt, and Hedgehog. We also use a novel bioinformatics approach to assemble transcriptional regulatory networks and predict transcription factors that may be specifically involved in hematopoietic cell formation from arterial hemogenic endothelium, which is the origin of the adult hematopoietic system.

overall_design: 16 samples were analyzed and each has two replicates.

first: Joanna

last: Tober

first: Peng

first: Qin

last: Zhu

first: Changya

last: Chen

first: Kai

last: Tan

first: Nancy

last: Speck


title: Multi-Omic Molecular Profiling of Lung Cancer Risk in Chronic Obstructive Pulmonary Disease

city: Minneapolis

first: Chris

last: Wendt

state: MN

address: 420 Delaware St SE

department: Medicine

institute: University of Minnesota

summary: Chronic obstructive pulmonary disease (COPD) is a known risk factor for developing lung cancer suggesting that the COPD stroma contains factors supporting tumorigenesis. Since cancer initiation is complex we used a multi-omic approach to identify gene expression patterns that distinguish COPD stroma in patients with or without lung cancer. We obtained lung tissue from patients with COPD and lung cancer (tumor and adjacent non-malignant tissue) and those with COPD without lung cancer for proteomic and mRNA (cytoplasmic and polyribosomal) profiling.  We used the joint and individual variation explained (JIVE) method to integrate and analysis across the three datasets.  JIVE identified eight latent patterns that robustly distinguished and separated the three groups of tissue samples. Predictive variables that associated with the tumor, compared to adjacent stroma, were mainly represented in the transcriptomic data, whereas, predictive variables associated with adjacent tissue compared to controls was represented at the translatomic level. Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis revealed extracellular matrix (ECM) and PI3K-Akt signaling pathways as important signals in the pre-malignant stroma. COPD stroma adjacent to lung cancer is unique and differs from non-malignant COPD tissue and is distinguished by the extracellular matrix and PI3K-Akt signaling pathways.

overall_design: Polysome-profiling of lung tumor, adjacent non-cancerous lung stroma tissue samples from the same patient compared to patients without lung cancer across a range of forced expiratory volume in one second (FEV1)

first: Brian

last: Sandri


title: Intestinal microbiome adjusts the innate immune setpoint during colonization through negative regulation of MyD88

city: Leiden

first: Bjorn

middle: Erik Vind

last: Koch

address: Einsteinweg 55

department: Institute of Biology

institute: Leiden University

summary: Host pathways mediating changes in immune states elicited by intestinal microbial colonization are incompletely characterized. Here we describe alterations of the host immune state induced by colonization of germ-free zebrafish larvae with an intestinal microbial community or single bacterial species. We show that microbiota-induced changes in intestinal leukocyte subsets and whole-body host gene expression are dependent on the innate immune adaptor gene myd88. Similar patterns of gene expression are elicited by colonization with conventional microbiome, as well as mono-colonization with two different zebrafish commensal bacterial strains. By studying loss-of-function myd88 mutants, we find that colonization suppresses Myd88 at the mRNA level. Tlr2 is essential for microbiota-induced effects on myd88 transcription and intestinal immune cell composition.

overall_design: Zebrafish embryos were sterilized to generate germ-free groups. Transcriptomic responses in germ-free embryos were  were assessed relative to colonized embryos, either colonized by complex and in characterized microbial communities (Conventionalozation) or by specefic single commensal bacterial species (monoassociation, Exiguobacterium/Chryseobacterium)

first: Bjørn

middle: E

first: Jens

last: Stougaard

first: Herman

middle: P

last: Spaink

first: Shuxin

last: Yang

first: Gerda

last: Lamers


title: Heat Shock in C. elegans Induces Downstream of Gene Transcription and Accumulation of Double-Stranded RNA

city: boulder

first: marko

last: melnick

state: CO

address: 1725 pleasant st

department: Integrative Physiology

institute: University of Colorado at Boulder

summary: We observed that heat shock of Caenorhabditis elegans leads to the formation of nuclear double-stranded RNA (dsRNA) foci, detectable with a dsRNA-specific monoclonal antibody. These foci significantly overlap with nuclear HSF-1 granules. To investigate the molecular mechanism(s) underlying dsRNA foci formation, we used RNA-seq to globally characterize total RNA and immunoprecipitated dsRNA from control and heat-shocked worms.  We find antisense transcripts are generally increased after heat shock, and a subset of both sense and antisense transcripts enriched in the dsRNA pool by heat shock overlap with dsRNA transcripts enriched by deletion of tdp-1, which encodes the C. elegans ortholog of TDP-43. Interestingly, transcripts involved in translation are over-represented in the dsRNAs induced by either heat shock or deletion of tdp-1. Also enriched in the dsRNA transcripts are sequences downstream of annotated genes (DoGs), which we globally quantified with a new algorithm.  To validate these observations, we used fluorescence in situ hypridization (FISH) to confirm both antisense and downstream of gene transcription for eif-3.B, one of the affected loci we identified.

overall_design: Total of 11 samples:  1 N2 heat shock input RNA input sample with 2 N2 heat shock J2 immunoprecipated samples. The following samples were re-analyzed from GSE61581.  3 tdp1 J2 immunoprecipitated samples and tdp1 total RNA input with 3 N2 J2 immunoprecipitated controls (with N2 input).

first: Marko

last: Melnick

first: Patrick

last: Gonzales

first: Joseph

last: Cabral

first: Mary

last: Allen

first: Robin

last: Dowell

first: Christopher

last: Link


title: Unliganded Progesterone Receptor Governs Estrogen Receptor Gene Expression by Regulating DNA Methylation in Breast Cancer Cells

status: Public on Oct 04 2018

city: Barcelona

first: François

last: Le Dily

address: Dr. Aiguader, 88

institute: CRG-Centre for Genomic Regulation

type: Methylation profiling by high throughput sequencing

summary: How breast cancers respond to endocrine therapy strongly depends on the expression of the estrogen and progesterone receptors (ER and PR, respectively), with doublenegative ER-/PR- breast cancers having worse clinical outcome than ER+/PR+ breast cancers. Although much is known about ERα gene (ESR1) regulation after hormonal stimulation, how it is regulated in the absence of hormones is not fully understood. We used ER+/PR+ positive breast cancer cells to investigate the role of PR in ESR1 gene regulation in the absence of hormones. We show that PR binds to the low-methylated ESR1 promoter and maintains both gene expression and the DNA methylation profile of the ESR1 locus in hormone-deprived breast cancer cells. Depletion of PR reduces ESR1 expression, with a concomitant increase in gene promoter methylation. The high amount of DNA methylation in the ESR1 promoter of PR-depleted cells persists after the stable re-expression of PR and inhibits PR binding to this genomic region. Consequently, the rescue of PR expression in PR-depleted cells is insufficient to restore ESR1 expression. Consistent with these data, DNA methylation impedes PR binding to consensus progesterone responsive elements in vitro. These findings help us understand the complex crosstalk between PR and ER, and suggest that the analysis of DNA methylation of ESR1 promoter in breast cancer cells can help to design the appropriate targeted therapies for different types of breast cancer patients.

overall_design: DNA methylation analysis in hormone-deprived T47D breast cancer cells

first: Gaetano

last: Verde

first: Lara

middle: I

last: De Llobet

first: Roni

last: Wright

first: Javier

last: Quilez

first: Sandra

last: Peiró

first: Miguel

last: Beato


title: Fate-restricted retinal progenitor cells adopt a molecular profile and spatial position distinct from multipotent progenitor cells

status: Public on Oct 03 2018

city: New York

first: Mark

middle: Monroe

last: Emerson

state: NY

address: 160 Convent Ave

department: Biology

institute: The City College of New York

summary: Here we report a transcriptomic analysis of fate-restricted progenitor cells biased to produce cone photoreceptors and horizontal cells, marked by the THRB cis-regulatory element ThrbCRM1. Comparison to a control population enriched in multipotent progenitor cells identified several genes considered to be pan-progenitor, such as VSX2, LHX2, and PAX6, as downregulated in these fate-restricted retinal progenitor cells

overall_design: Comparison of two FACS-sorted chick retinal progenitor cell populations after electroporation of reporter plasmids and 20hr culture.

first: Diego

last: Buenaventura

first: Miruna

last: Ghinia-Tegla

middle: M


title: Transcriptomic basis for  reinforcement of elm anti-herbivore defense mediated by insect egg deposition

city: Berlin

first: Monika

last: Hilker

address: Haderslebener Str. 9

institute: Freie Universität Berlin

summary: In this study we applied RNA-sequencing to a set of larvae-challenged elm trees that had either been untreated before or been exposed to prior egg deposition by elm leaf beetles. This dataset allowed us to characterize the global transcriptional response of egg-primed and non-primed elm trees at different time points after the priming stimulus itself and after the onset of larval feeding.

overall_design: At time point 0 of the experiment, elm leaves were treated with simulated egg deposition (compare Austel et al. 2015, Plant, Cell & Environment). Leaf material was harvested at 1hr, 6hrs and 24hrs after simulated egg-deposition (priming stimulus) from treated (P) and control samples (C) in triplicates. These samples are refered to as priming set (2 treatments P, C x 3 time points x 3 replicates = 18 samples). To obtain leaf tissue with larval feeding damage (triggering stimulus), neonate larvae were placed 7 days after the onset of the experiment onto plants with or without prior simulated egg deposition. Seven days match the egg incubation time until larvae would hatch. For the triggering set, leaf samples were taken in triplicates at 1hr, 6hrs and 24hrs after larval feeding from leaves with or without prior simulated egg-deposition in a full factorial design (i.e. control [CC], primed [PC], triggered [CT] and primed+triggered [PT ]) The triggering set is thus comprised of 36 samples in total (4 treatments x 3time points x 3 replicates).

first: Simone

last: Altmann

first: José

last: Muino

first: Ronny

last: Brandt

first: Axel

last: Himmelbach

first: Lothar

last: Altschmied


title: RNA-seq - Combining developmental and perturbation-seq uncovers transcriptional modules orchestrating neuronal remodeling

status: Public on Oct 02 2018

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

summary:
Developmental neuronal remodeling is an evolutionarily conserved mechanism required for accurate wiring of mature nervous systems.
Despite its fundamental role in neurodevelopment and proposed contribution to various neuropsychiatric disorders, the mechanisms instructing remodeling are only partially known.
Here, we uncover the fine temporal transcriptional landscape of a stereotypic remodeling event - that of the Drosophila mushroom body γ neurons.
To enrich and complement this developmental expression atlas, we also sequenced developing γ neurons perturbed for three key transcription factors known to regulate pruning.
Together, these datasets allowed us to construct the developmental and temporal framework of transcriptional modules that together drive remodeling.
Moreover, we identified 10 DNA binding proteins that are involved in various aspects of remodeling, and describe their hierarchical relationships.
Overall, this study provides the first broad and detailed molecular insight into the complex regulatory dynamics of developmental neuronal remodeling.

overall_design: Transcriptional profiling of drosophila γ neurons during development and when perturbed by EcR-DN, E75 RNAi or Sox14 RNAi. Other adult neurons and astrocyte-like cells also sequenced.

first: Oren

last: Schuldiner

first: Idan

last: Alyagor

first: Hadas

last: Keren-Shaul

first: Eyal

last: David

first: Neta

last: Marmor-Kollet


title: Pathogen size alters C-type lectin receptor signaling in dendritic cells to influence CD4 T cell differentiation

city: Los Angeles

first: vineela

last: gangalapudi

address: 8723 Alden drive

department: Biomedical sciences

institute: Cedars- sinai Medical center

summary: A key mechanism to eliminate pathogens from the body is the physical internalization (phagocytosis) and degradation of microbes by specialized cells of the immune system including neutrophils, macrophages, and dendritic cells. Phagocytosis not only eliminates potentially harmful pathogens, but also provides information about the “type” of microbe encountered, and helps to orchestrate an appropriate adaptive immune response. Certain pathogens, including filamentous fungi and parasite worms (helminths), exceed the size limit for phagocytosis. In this study we show that when dendritic cells encounter pathogens that are too large to internalize, or when phagocytosis of small microbes is blocked, dendritic cells adopt an activation profile that allows them to orchestrate an adaptive immune response commonly associated with tissue repair and anti-helminth immunity.

overall_design: Examination of mice bone marrow derived dendritic cell behavior with different physical forms of C.albicans

first: David

last: Underhill

first: Matthew

middle: L

last: Wheeler

first: Marissa

middle: J

last: Paterson

first: Andrea

last: Wolf

last: Gargus

first: Jie

last: Tang

first: Vineela

last: Gangalapudi


title: Microglial repopulation rewires and rejuvenates the aged brain

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

country: United Kingdom

institute: UCL

summary: Changes in microglial form and function contribute to age-related cognitive impairment. Developing methods to target microglia is critical to understand and prevent the adverse effects of aging. Using a specific colony-stimulating factor 1 receptor (CSF1R) inhibitor, our lab has shown that the majority of microglia can be eliminated from the CNS (Elmore et al., 2014). Withdrawal of the CSF1R inhibitor, stimulates brain-wide repopulation with new cells, that express microglial markers (Elmore et al., 2014; Elmore et al., 2015). The impact of these newly repopulated cells on the aged brain has not been explored, but will provide useful insight into the role of microglia in aging. In addition, the therapeutic potential of replacing “primed” or “senescent” microglia in the aged brain with new cells is of great interest. Therefore, our goal was to fully characterize the gene expression profiles of the aged control vs. aged repopulated brains in comparison to young controls.

overall_design: mRNA from C57BL/6 male mouse whole-brain homogenates were analyzed. A total of 9 samples, including three from young control (~5 months of age at sacrifice), three from aged control (~24 months of age at sacrifice), and three from aged repopulated (microglia were eliminated for 2 weeks using a CSF1R inhibitor, then the inhibitor was removed, and new microglia were allowed to repopulate the entire brain for 4 weeks prior to sacrifice, ~24 months of age at sacrifice) mice.

first: Monica

last: Elmore

first: Kim

last: Green


title: Wipi1 is a Genetic Hub that Mediates Right Ventricular Failure

first: Christoph

middle: Daniel

last: Rau

state: United States

address: 675 Charles E Young Drive S

institute: UCLA

summary: Right ventricular dysfunction (RVD) independently predicts worse outcomes in both heart failure (HF) and pulmonary hypertension (PH), irrespective of their etiologies. Yet no evidence-based therapies exist for RVD and progression towards RV failure (RVF) can occur in spite of optimal medical treatment of HF or PH. This disparity reflects our insufficient understanding of the molecular pathophysiology of RVF. To identify molecular mechanisms that may uniquely underlie RVF, we investigated the cardiac ventricular transcriptome of advanced HF patients, with and without RVF. Using weighted gene co-expression network and module-phenotype analyses, we identified a 279-member gene module that correlated significantly and specifically with RVF. Within this module, WIPI1 served as a genetic hub, HSPB6, SNAP47, and MAP4 as drivers, and PRDX5 as a repressor of RVF. We subsequently confirmed the ventricular specificity and temporal relationship of Wipi1, Hspb6, and Map4 transcript expression changes in murine models of pressure overload induced RV failure versus LV failure and subsequently uncovered differential dysregulation of autophagy in the failing RV versus the failing LV, namely a shift towards excessive non-canonical, Beclin1-independent, Wipi1/LC3II-mediated autophagy in RVF. In vitro siRNA silencing of Wipi1 partially protected isolated neonatal rat ventricular cardiac myocytes against aldosterone-induced failing phenotype. Moreover, silencing Wipi1 blunted mitochondrial superoxide production and limited non-canonical autophagy in this in vitro RVF model. Our findings suggest that Wipi1 regulates mitochondrial oxidative signaling and autophagy in cardiac myocytes. Inhibition of Wipi1 may hold promise as a therapeutic target for RVF.

overall_design: Examination of RNAseq results from Left and Right Ventricles of 15 individuals, 5 control, 5 left-sided Heart Failure, 5 bi-ventricular Heart Failure

first: Emily

last: Tsai


title: Metabolic flexibility enables positive selection of mtDNA in Drosophila (RNA-seq)

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: The study used two Drosophila melanogaster fly lines, Alstonville and Dahomey, which have mitochondrial DNA variants but otherwise similar genomes. Female third instar larvae from both lines were fed on two diets, one with a 1:2 protein:carbohydrate ratio and the other with a 1:16 ratio. RNA was extracted and profiled by RNA-seq. Samples were sequenced on an Illumina Hiseq 2000 sequencer at the Ramaciotti Centre for Genomics, Sydney, Australia to produce 100bp paired end reads. At least 80 million read pairs were generated per sample.

overall_design: Four independent replicates were obtained for each mitotype-diet combination.


title: Physiological trade-off and transcriptome reprogramming are involved in acclimation to salinity gradient in diatoms

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

summary: In estuaries and coastal areas, salinity regimes vary with river discharge, seawater evaporation, morphology of the coastal waterways, and dynamics of marine water mixing. Therefore, microalgae have to respond to salinity variations at various time scales, from daily to annual cycling. They might also adapt to physical alteration that might induce loss of connectivity and enclosure of water bodies. Here we integrate physiological-based assays, morphological plasticity with functional genomics approach to examine the regulatory change that occur during the acclimation to salinity in an estuary diatom, Thalassiosira weissflogii. We found that this diatom respond to salinity (i.e. 21, 28 and 35 psu) with minute adjustments of its physiology (i.e., carbon and silicon metabolisms, pigments concentration and photosynthetic parameters). In contrast after short- (~ 5 generations) or long-term (~ 700 generations) culture at the different salinity we found a large transcriptome reprogramming. With most of the genes being down-regulated in long-term, and only a few genes in common between short and long term experiments.

overall_design: Comparison of transcriptome of Thalassiosira Weissflogii in 3 salinity concentrations with adapted and non-adapted strains

first: Adrien

last: Bussard

first: Erwan

last: Corre

first: Cédric

last: Hubas

first: Evelyne

last: Duvernois-Berthet

first: Gildas

last: Le Corguille

first: Laurent

last: Jourdren

first: Fanny

last: Coulpier

first: Pascal

last: Claquin

last: Lopez


title: Truncated O-glycan connection to Cancer: Depletion of O-glycosyltransferase C1GALT1 leads to early PDAC onset and metastasis

city: Omaha

first: Surinder Kumar

last: Batra

state: Nebraska

address: 42nd and Emile

department: Biochemistry and Molecular Biology

institute: University of Nebraska Medical Center

summary: Aberrant expression of truncated O-glycan structures, such as Tn and STn, is frequently observed in pancreatic ductal adenocarcinoma (PDAC). The focus of our study is to investigate the functional role of truncated O-glycans in PDAC progression and metastasis. Our study revealed that kmockout of C1GALT1 leads to increased expression of truncated glycans and accelerates PDAC progression and metastasis.

overall_design: We performed the CRISPR/Cas9 knockout of C1GALT1 in human T3M4 PDAC cells followed by whole transcriptome analysis using RNA sequencing.

first: Surinder

first: Seema

last: Chugh


title: Metformin reduces air pollution-induced thrombosis

city: Chicago

first: Alexander

middle: V

last: Misharin

state: IL

address: 240 E Huron

department: Pulmonary and Critical Care

institute: Northwestern University

summary: As our results suggested that metformin acts to limit mitochondrial ROS and calcium-mediated activation of IL-6, we reasoned it would likely affect other processes in alveolar macrophages triggered by exposure to particulate matter (PM). Therefore, we treated mice with metformin in the drinking water for 24 hours before we instilled PM intratracheally. We then flow-sorted alveolar macrophages from whole lung homogenates 24 hours later for transcriptomic analysis (RNA-Seq).

overall_design: 3-4 biological replicates per group were used.

first: Saul

last: Soberanes

first: Alexandra

middle: C

last: McQuattie-Pimentel

first: Gokhan

last: Mutlu

first: G

middle: S

last: Budigner


title: Comparison of PPWD1 knockdown in HEK293T cells compared to scrambled shRNA control

status: Public on Oct 01 2018

first: Tara

last: Davis

institute: Drexel University College of Medicine

summary:
HEK293T cells transduced with shRNA from MISSION library TRCN0000000165 using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, Jenna Marinock, and Jennifer Ayoub performed primary experimental contributions to cell lines, RNA/cDNA preparation, and validation, all Drexel University College of Medicine, Philadelphia, PA. Hetty Rodriguez and John Tobias performed Bioanalyzer and microarray expreriments, and initial data processing. Affiliation: Molecular Profiling Facility and Genomic Analysis Core Bioinformatics Group, University of Pennsylvania, Philadelphia, PA.
Human PPWD1 is a cyclophilin, an enzyme that interconverts cis and trans isomers of proline. The PPWD1 gene, in addition to the cyclophilin domain, encodes for an N-terminal WD40 domain. PPWD1 associates with the human spliceosome, the complex and dynamic machinery that removes intronic sequence from pre-messenger RNA (pre-mRNA). Nothing is known about the function of PPWD1 in regulation of nuclear events. To further understand the function of PPWD1, we knocked down PPWD1 in human cells. We characterized a set of alternative splicing and transcriptional events that are PPWD1-responsive. We used these splicing and transcriptional bioassays to show that PPWD1-responsive events are largely specific, even within the cyclophilin family.

overall_design: 3 replicates of PPWD1 knockdown cell lines (HEK293T cells, stably integrated, selected using puro, MISSION shRNA (TRCN0000000165, 5'-CCGGGCTTAGGACTTGCTGAATATACTCGAGTATATTCAGCAAGTCCTAAGCTTTTT-3'). 3 replicates of SCR control cells lines (HEK293T cells, stably integrated, selected using puro, sequence 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′). total RNA purified from ~1 million cells, cDNA converted using random hexamer primers, quantity measured using NanoDrop, quality quantified using BioAnaylzer. Affymatrix HTA2.0 array

first: S

middle: R

last: Jackson

first: Beth

last: Adams

first: Anh

last: Trinh

first: Jenna

last: Marinock

first: Jennifer

last: Ayoub

first: Hetty

last: Rodriguez

first: John

last: Tobias


title: Comparison of PPIL3 knockdown in HEK293T cells compared to scrambled shRNA control

summary:
HEK293T cells transduced with shRNA from MISSION library TRCN0000000185 using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, Jonathan Amora, Peter Naranjo, Gueil Wong-Shing, and Nii Martey performed primary experimental contributions to cell lines, RNA/cDNA preparation, and validation, all Drexel University College of Medicine, Philadelphia, PA. Hetty Rodriguez and John Tobias performed Bioanalyzer and microarray expreriments, and initial data processing. Affiliation: Molecular Profiling Facility and Genomic Analysis Core Bioinformatics Group, University of Pennsylvania, Philadelphia, PA.
Human PPIL3 is a cyclophilin, an enzyme that interconverts cis and trans isomers of proline. PPIL3 associates with the human spliceosome, the complex and dynamic machinery that removes intronic sequence from pre-messenger RNA (pre-mRNA). Nothing is known about the function of PPIL3 in the nucleus. To understand the function of PPIL3, we knocked down PPIL3 in human cells. We characterized a set of alternative splicing and transcriptional events that are PPIL3-responsive. We used these splicing and transcriptional bioassays to show that PPIL3-responsive events are largely specific, even within the cyclophilin family.

overall_design: 3 replicates of PPIL3 knockdown cell lines (HEK293T cells, stably integrated, selected using puro, MISSION shRNA (TRCN0000000185, 5'-CCGGTCTCAGTTCTTCATCACCTATCTCGAGATAGGTGATGAAGAACTGAGATTTTT-3'). 3 replicates of SCR control cells lines (HEK293T cells, stably integrated, selected using puro, sequence 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′). total RNA purified from ~1 million cells, cDNA converted using random hexamer primers, quantity measured using NanoDrop, quality quantified using BioAnaylzer). Affymatrix HTA2.0 array

first: S.

first: Jonathan

last: Amora

first: Peter

last: Naranjo

first: Gueil

last: Wong-Shing

first: Nii

last: Martey


title: Comparison of PPIL2 knockdown in HEK293T cells compared to scrambled shRNA control

summary:
HEK293T cells transduced with shRNA from MISSION library TRCN0000230475 using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, Tracey Yenailtus, Jessica Kopenhaver, Angie Giang, and Alyson Hurlock performed primary experimental contributions to cell lines, RNA/cDNA preparation, and validation, all Drexel University College of Medicine, Philadelphia, PA. Hetty Rodriguez and John Tobias performed Bioanalyzer and microarray expreriments, and initial data processing. Affiliation: Molecular Profiling Facility and Genomic Analysis Core Bioinformatics Group, University of Pennsylvania, Philadelphia, PA.
Human PPIL2 is a cyclophilin, an enzyme that interconverts cis and trans isomers of proline. The PPIL2 gene, in addition to the cyclophilin domain, encodes for an N-terminal U-box motif. PPIL2 associates with the human spliceosome, the complex and dynamic machinery that removes intronic sequence from pre-messenger RNA (pre-mRNA). Nothing is known about the function of PPIL2 in regulation of alternative splicing, although it has been shown to modulate transcription of a handful of targets, albeit indirectly. To further understand the function of PPIL2, we knocked down PPIL2 in human cells. We characterized a set of alternative splicing and transcriptional events that are PPIL2-responsive. We used these splicing and transcriptional bioassays to show that PPIL2-responsive events are largely specific, even within the cyclophilin family.

overall_design: 3 replicates of PPIL2 knockdown cell lines (HEK293T cells, stably integrated, selected using puro, MISSION shRNA (TRCN0000230475, 5'-CCGGTCCACTGAGGGCACGATTTAACTCGAGTTAAATCGTGCCCTCAGTGGATTTTTG-3'). 3 replicates of SCR control cells lines (HEK293T cells, stably integrated, selected using puro, sequence 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′). total RNA purified from ~1 million cells, cDNA converted using random hexamer primers, quantity measured using NanoDrop, quality quantified using BioAnaylzer. Affymatrix HTA2.0 array

first: Tracey

last: Yenilaitus

first: Jessica

last: Kopenhaver

first: Alyson

last: Hurlock

first: Angie

last: Giang


title: Structural characterization of ribosome variants

city: Baltimore

first: Boris

last: Zinshteyn

state: Maryland

address: 725 N Wolfe St, PCTB 714

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: DMS probing of E coli ribosomes

overall_design: Purified ribosomes are probed with DMS to identify structural differences

first: Chad

last: Kurylo

first: Matthew

last: Parks

first: Manuel

middle: F

last: Juette

first: Jordana

last: Thibado

first: Justin

last: Morse

first: Rachel

last: Green

first: C

last: Vincent

first: Scott

last: Blanchard


title: Comparison of CWC27 knockdown in HEK293T cells compared to scrambled shRNA control

first: Tara

last: Davis

state: PA

summary:
HEK293T cells transduced with shRNA from MISSION library TRCN0000000139 using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Sequence is 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′. Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, Peter Naranjo, and Angie Giang performed primary experimental contributions to cell lines, RNA/cDNA preparation, and validation of results, all Drexel University College of Medicine, Philadelphia, PA 19102. Hetty Rodriguez and John Tobias performed Bioanalyzer and microarray expreriments, and initial data processing. Affiliation: Molecular Profiling Facility and Genomic Analysis Core Bioinformatics Group, University of Pennsylvania.
Human CWC27 (aliases: NY-CO-10, Serologically Defined Colon Cancer Antigen 10 or SDCCAG-10) is a cyclophilin, an enzyme that interconverts cis and trans isomers of proline. The CWC27 gene, in addition to the cyclophilin domain, encodes for two low complexity regions and a coiled coil region. CWC27 associates with the human spliceosome, the complex and dynamic machinery that removes intronic sequence from pre-messenger RNA (pre-mRNA). Nothing is known about the function of CWC27 in the nucleus. To understand the function of CWC27, we knocked down CWC27 in human cells. We characterized a set of alternative splicing and transcriptional events that are CWC27-responsive. We used these splicing and transcriptional bioassays to show that CWC27-responsive events are largely specific, even within the cyclophilin family.

overall_design: 3 replicates of CWC27 knockdown cell lines (HEK293T cells, stably integrated, selected using puro, MISSION shRNA TRCN0000000139: 5'-CCGGACGGGAACTCTTAGCAGCAAACTCGAGTTTGCTGCTAAGAGTTCCCGTTTTTT-3'). 3 replicates of SCR control cell lines (HEK293T cells, stably integrated, selected using puro, sequence 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′). total RNA purified from ~1 million cells, cDNA converted using random hexamer primers, quantity measured using NanoDrop, quality quantified using BioAnaylzer. Affymatrix HTA2.0 array

first: S

last: Jackson

first: Beth

last: Adams

first: Anh

last: Trinh

first: Hetty

last: Rodriguez

first: John

last: Tobias


title: Comparison of PPIG knockdown in HEK293T cells compared to scrambled shRNA control

summary:
HEK293T cells transduced with shRNA from MISSION library TRCN0000049326 using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh performed primary experimental contributions to cell lines, RNA/cDNA preparation, and validations, all Drexel University College of Medicine, Philadelphia, PA. Hetty Rodriguez and John Tobias performed Bioanalyzer and microarray expreriments, and initial data processing. Affiliation: Molecular Profiling Facility and Genomic Analysis Core Bioinformatics Group, University of Pennsylvania, Philadelphia, PA.
Human PPIG (alias: SR-Cyp, CARS) is a cyclophilin, an enzyme that interconverts cis and trans isomers of proline. The PPIG gene, in addition to the cyclophilin domain, encodes for a multiple C-terminal SR motifs. PPIG associates with the human spliceosome, the complex and dynamic machinery that removes intronic sequence from pre-messenger RNA (pre-mRNA). Nothing is known about the function of PPIG in regulation of alternative splicing. To understand the function of PPIG, we knocked down PPIG in human cells. We characterized a set of alternative splicing and transcriptional events that are PPIG-responsive. We used these splicing and transcriptional bioassays to show that PPIG-responsive events are largely specific, even within the cyclophilin family.

overall_design: 3 replicates of PPIG knockdown cell lines (HEK293T cells, stably integrated, selected using puro, MISSION shRNA (TRCN0000049326, 5'-CCGGGCAGTCTGATTCTAAAGGAAACTCGAGTTTCCTTTAGAATCAGACTGCTTTTTG-3'). 3 replicates of SCR control cells lines (HEK293T cells, stably integrated, selected using puro, sequence 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′). total RNA purified from ~1 million cells, cDNA converted using random hexamer primers, quantity measured using NanoDrop, quality quantified using BioAnaylzer). Affymatrix HTA2.0 array

first: S.


title: Genome-wide fork-collapse sites in MEF and MDA-MB-231 from ATR inhibition

first: Nishita

last: Shastri

state: Pennsylvania

address: 421 Curie Boulevard

department: Cancer Biology

institute: University of Pennsylvania

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

overall_design: Refer to individual Series


title: Deletion of the FlbA-regulated transcription factor msnB of Aspergillus niger affects protein secretion

city: Utrecht

first: Wieke

last: Teertstra

address: Padualaan 8

department: Science, Biology

institute: Utrecht University

summary: Colonies of Aspergillus niger secrete proteins throughout the colony except for the sporulating zone. Strains in which the sporulation gene flbA is deleted do not reproduce asexually and secrete proteins throughout the mycelium. Moreover, ΔflbA hyphae lyse and have thinner cell walls. This pleiotropic phenotype is associated with differential expression of 36 transcription factor genes, of which msnB was inactivated in this study. Whole genome expression analysis of wild-type and ΔmsnB colonies showed differential expression of genes encoding secreted proteins, genes involved in the oxidoreductive balance, and in (secondary) metabolism. Biomass formation, sporulation, and the secretome in the medium were not affected in strain ΔmsnB. In contrast, ΔmsnB secreted more protein when compared to wild type. Taken together, msnB affects protein secretion and is a potential lead for improving A. niger as a cell factory.

overall_design: mRNA profiles from ΔrpnR and the control strain MA234.1 were generated by Illumina Hiseq using duplicate samples from liquid shaken cultures.

first: David

last: Aerts

first: Robin

middle: A

last: Ohm

first: Han

last: Wösten


title: Landscape of H3K4me3 in human CD19 cells

city: Duarte

first: Amy

last: Leung

address: 1500 E. Duarte Rd

department: Diabetes/Cancer

institute: Beckman Research Institute, City of Hope

summary: Chromatin immunoprecipiation of H3K4me3 of isolated B cells from healthy human donors and LCLs and RNA-sequencing of extracted RNAs

overall_design: Analysis of H3K4me3 enriched sites across B cells from healthy human donors and LCLs and Gene expression analysis

first: Dustin

last: Schones


title: Comprehensive profiling of mRNA m6A methylome revealed by m6A-seq in porcine adipose and muscle tissues

first: zhike

last: lu

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

summary: Using Jinhua and Landrace pigs as fat and lean models, we present a comprehensive transcriptome-wide m6A profiling in adipose and muscle tissues from these two pig breeds.The results show m6A is widely spread and highly conserved in pig mRNA. m6A occurs in the conserved sequence motif of GGACU and exhibits a unique topology in pig. m6A peak enrichment correlates positively with gene expression, and transcripts with m6A at 5’UTR or CDS are correlated with gene activation than those at 3’UTR. Common m6A peaks in both layer of backfat from Landrace (L-LB) and Jinhua (J-LB) pigs are involved in lipid metabolism, while common m6A peaks in both longissimus dorsi muscle from Landrace (L-LDM) and Jinhua (J-LDM) mapped to muscle development, suggesting m6A-containing genes are involved in many biological processes especially related to tissue-specific functions.

overall_design: m6A-seq of mRNA from Jinhua LB (J-LB), Jinhua LDM (J-LDM), Landrace LB (L-LB) and Landrace LDM (L-LDM) tissue.

first: Xinxia

last: Wang

first: Yizhen


title: Genome-wide fork-collapse sites in MEFs from ATR inhibition

summary: Transient obstruction of DNA polymerase progression activates the ATR checkpoint kinase, which suppresses fork breakage, strand resection, and RPA accumulation. Herein, we use RPA ChIP-Seq to identify replication-problematic loci (RPLs) across the mammalian genome from ATR inhibition.

overall_design: Examination of RPA-enriched sites in mouse embryonic fibroblasts arising from low-dose aphidicolin treatment or TIMELESS supression and ATR inhibition. Two replicates of each condition are included (except for ATRi+APH,18h, which has 3 replicates), totaling 21 samples. This includes DMSO-treated controls. Samples were deep sequenced through Illumina HiSeq.

first: Yu-Chen

last: Tsai

first: Eric

last: Brown


title: Spermatid-specific linker histone HILS1 is a poor condenser of DNA and chromatin, and preferentially associates with LINE L1 elements

city: Bangalore

first: Manchanahalli

middle: Rangaswamy

last: Satyanarayana Rao

state: Karnataka

address: Jakkur, Bengaluru, Karnataka

department: Molecular Biology and Genetics Unit (MBGU)

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)

summary:
Background: Eleven linker histone subtypes are reported in mammals. Linker histones establish and maintain higher order chromatin structure. HILS1 is a spermatid-specific linker histone and its expression overlaps with the chromatin reorganization process during spermiogenesis; however, role of HILS1 in chromatin restructuring is largely unknown.
Method: Genome-wide occupancy of the rat HILS1 protein was studied by ChIP-sequencing of pulldown DNA isolated from nuclei of 50-60 days old rat testis, using anti HILS1 antibody.
Conclusion: Present study revealed that HILS1 is preferentially associated Line L1 elements in rat spermatids.

overall_design: Nuclei of elongating/condensing spermatids cell types of the Rat (Rattus norvegicus) testicular cells were used for this purpose. Two runs were made with two different samples having two replicates each with a control for the ChIP used in each run. Illumina HiSeq 1000 sequencing platform was used with 101nt read length and paired end read type.

first: Narayan

last: Mishra

first: V

last: Shalini

first: Nikhil

last: Gupta

first: Krittika

last: Ghosh

first: Neeraj

last: Suthar

first: Utsa

last: Bhaduri

first: M

last: Rao


title: Comparison of PPIL1 knockdown in HEK293T cells compared to scrambled shRNA control

city: Philadelphia

first: Tara

last: Davis

summary:
HEK293T cells transduced with shRNA from MISSION library TRCN0000420470 using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, Jenna Marinock, Peter Naranjo, NIcholas Fox, and Gueil Wong-Shing performed primary experimental contributions to cell lines, RNA/cDNA preparation, and validation, all Drexel University College of Medicine, Philadelphia, PA. Hetty Rodriguez and John Tobias performed Bioanalyzer and microarray expreriments, and initial data processing. Affiliation: Molecular Profiling Facility and Genomic Analysis Core Bioinformatics Group, University of Pennsylvania, Philadelphia, PA.
Human PPIL1 is a cyclophilin, an enzyme that interconverts cis and trans isomers of proline. PPIL1 associates with the human spliceosome, the complex and dynamic machinery that removes intronic sequence from pre-messenger RNA (pre-mRNA). Nothing is known about the function of PPIL1 in regulating transcription or alternative splicing events. To understand the nuclear function of PPIL1, we knocked down PPIL1 in human cells. We characterized a set of alternative splicing and transcriptional events that are PPIL1-responsive. We used these splicing and transcriptional bioassays to show that PPIL1-responsive events are largely specific, even within the cyclophilin family.

overall_design: 3 replicates of PPIL1 knockdown cell lines (HEK293T cells, stably integrated, selected using puro, MISSION shRNA (TRCN0000420470, 5'-CCGGTACTACACATGAACCATAATGCTCGAGCATTATGGTTCATGTGTAGTATTTTTTG-3'). 3 replicates of SCR control cells lines (HEK293T cells, stably integrated, selected using puro, sequence 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′). total RNA purified from ~1 million cells, cDNA converted using random hexamer primers, quantity measured using NanoDrop, quality quantified using BioAnaylzer). Affymatrix HTA2.0 array

first: S

last: Jackson

first: Beth

last: Adams

first: Anh

last: Trinh

first: Jenna

last: Marinock

first: Gueil

last: Wong-Shing

first: Peter

last: Naranjo

first: Nicholas

last: Fox

first: Hetty

last: Rodriguez

first: John

last: Tobias


title: The abundantly expressed microRNA locus miR-144/451 regulates only about 100 target mRNAs during erythroid development [miRNA-seq]

city: Memphis

first: Lance

last: Palmer

state: TN

address: 262 Danny Thomas Place

department: Computational Biology

institute: St. Jude Children's Research Hospital

summary: MicroRNAs inhibit gene expression by recruiting the RNA-induced silencing complex (RISC) to mRNAs in a process termed RNA interference (RNAi). While it is generally accepted that RNAi modulates gene expression pervasively, the number of mRNAs bound and repressed by miRNAs in vivo in individual cell types remains unknown, with estimates ranging from a few hundred genes to many thousands. We examined microRNA activities in primary cells by combining genetic loss of function with RNA-sequencing, quantitative proteomics and High-Throughput Sequencing of RNA isolated by Crosslinking Immunoprecipitation (HITS-CLIP), focusing on miR-144/451, the most highly expressed microRNA locus during red blood cell (RBC) formation. We show that Argonaute (Ago) protein binds over one thousand different mRNAs in a miR-144/451-dependent manner, accounting for one third of all Ago-bound mRNAs. However, only about 100 mRNAs are stabilized in RBC precursors after ablation of the miR-144/451 locus. Thus, Ago-miRNA complexes destabilize only a small subset of bound mRNAs, probably no more than a few hundred in erythroblasts under physiological conditions. Our integrated approach identified more than 50 new miR-144/451 target mRNAs, including Cox10, which facilitates assembly of the mitochondrial cytochrome c oxidase (COX) electron transport complex. Loss of miR-144/451 resulted in increased Cox10 expression, accumulation of the COX complex, and increased mitochondrial membrane potential with no change in mitochondrial mass. Thus, miR-144/451 represses mitochondrial respiration during erythropoiesis by inhibiting Cox10.

overall_design: HITS-CLIP analysis of 3 WT mice fetal livers vs 3 miR-144/451 KO mice fetal livers

first: Vikram

last: Paralkar

first: Peng

last: Xu

first: Christophe

last: Lechauve

first: Guowei

last: Zhao

first: Yu

last: Yao

first: Jing

last: Luan

first: Anastasios

last: Vourekas

middle: D

last: Scheutz

first: Zissimos

last: Mourelatos

first: Gang

last: Wu

first: Mitchell

last: Weiss


title: KDM5B links cellular transcriptome heterogeneity to therapy resistance (Exome-Seq)

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: The KDM5B histone H3 lysine 4 (H3K4) demethylase has been implicated in therapy resistance in multiple cancer types including breast cancer, but the underlying mechanism is poorly defined. Here we show that inhibition of KDM5B activity increases sensitivity to anti-estrogens by modulating estrogen-receptor (ER) signaling. Conversely, acquired resistance to KDM5 inhibitors leads to gain of ER chromatin binding and estrogen-independent growth. Sequencing of barcoded cell populations and mathematical modeling demonstrate selection for pre-existent genetically distinct endocrine-resistant cells, while resistance to KDM5 inhibitors is a switch to an acquired epigenetic state. Rare resistant cells can already be detected by single cell RNA-seq prior to treatment. Inhibition of KDM5B in luminal ER+ cells increases H3K4me3 broad domains at promoters and decreases cellular transcriptional heterogeneity. Higher transcriptome heterogeneity is associated with higher KDM5B levels and poor prognosis in ER+ luminal breast tumors.

overall_design: Exome-seq of parental and multiple resistant breast cancer cell lines

first: Kunihiko

last: Hinohara

first: Hua-Jun

first: Franziska

last: Michor


title: Tissue specific transcriptional profiling of the consequences of 16p11.2 deletion and duplication in Mouse

first: Ashok

last: Ragavendran

address: 185 Cambridge St

department: Center for Human Genetic Research

institute: Massachusetts General Hospital

summary:
16p11.2 microdeletion/microduplication syndrome is one of the common genetic causes of autism spectrum disorder, although it is not wholly penetrant with a wide range of phenotypic manifestations. We have previously explored the transcriptional consequences of the copy number variant (CNV) in cortical tissue of mouse models of the CNV within the syntenic 7qF3 region (Blumenthal et al 2014).  We found that the strongest effects were from genes within the region itself, with no evidence for dosage compensation for any gene. Importantly, we found that global transcriptional effects due to the CNV were associated with multiple hypotheses for ASD pathogenesis, at the level of individual genes, networks and functional enrichments.
To delineate tissue-specificity effects of the CNV, we embarked on exploration of the transcriptional landscape across multiple tissues for all mice from our earlier study. Specifically to disentangle brain-specific effects from others, we chose two additional brain tissues, namely Cerebellum and Striatum, as well as three other non-neuronal tissues, namely Liver, White Fat and Brown Fat.  We present strand-specific RNAseq data for these five tissues in addition to the data for the Cortical tissue from our previous publication.
Preliminary analyses of the data suggest that there are strong tissue-specific consequences of the CNV, with the effect being strongest in the Cortical tissue relative to other tissues, and observe low overlaps in differentially expressed genes across tissue. Furthermore, we see that the genes within the CNV region behave in a strong-tissue specific manner, with differences being more pronounced among the neuronal and non-neuronal tissues, relative to within tissue classes. Interestingly, we see that in non-neuronal tissues dosage compensation occurs for a handful of genes, when expressed. Finally, we see that genes within the CNV region  show the  strongest effects relative to the overall transcriptome in neuronal tissues and these effects are ameliorated in non-neuronal tissues.

overall_design: Transcriptomic profiles for mRNa were generated for 16 mice across 3 genotypes for 6 tissues, 3 from brain ( Cortex, Cerebellum and Striatum) and 3 non-brain tissues (Liver, White Fat and Brown Fat) using paired-end illumina sequencing

first: Michael

middle: E

last: Talkowski


title: Comparison of PPIE knockdown in HEK293T cells compared to scrambled shRNA control

first: Tara

last: Davis

summary:
HEK293T cells transduced with shRNA from MISSION library TRCN0000049368 using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, and Jennifer Ayoub performed primary experimental contributions to cell lines, RNA/cDNA preparation, and validation, all Drexel University College of Medicine, Philadelphia, PA. Hetty Rodriguez and John Tobias performed Bioanalyzer and microarray expreriments, and initial data processing. Affiliation: Molecular Profiling Facility and Genomic Analysis Core Bioinformatics Group, University of Pennsylvania, Philadelphia, PA.
Human PPIE is a cyclophilin, an enzyme that interconverts cis and trans isomers of proline. The PPIE gene, in addition to the cyclophilin domain, encodes for an N-terminal RRM. PPIE associates with the human spliceosome, the complex and dynamic machinery that removes intronic sequence from pre-messenger RNA (pre-mRNA). Nothing is known about the function of PPIE in regulation of alternative splicing, although it has been shown to modulate chromatin modification. To further understand the function of PPIE, we knocked down PPIE in human cells. We characterized a set of alternative splicing and transcriptional events that are PPIE-responsive. We used these splicing and transcriptional bioassays to show that PPIE-responsive events are largely specific, even within the cyclophilin family.

overall_design: 3 replicates of PPIE knockdown cell lines (HEK293T cells, stably integrated, selected using puro, MISSION shRNA (TRCN0000049368, 5'-CCGGGCAGCTATCGACAACATGAATCTCGAGATTCATGTTGTCGATAGCTGCTTTTTG-3'). 3 replicates of SCR control cells lines (HEK293T cells, stably integrated, selected using puro, sequence 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′). total RNA purified from ~1 million cells, cDNA converted using random hexamer primers, quantity measured using NanoDrop, quality quantified using BioAnaylzer. Affymatrix HTA2.0 array

first: S

last: Jackson

first: Beth

last: Adams

first: Anh

last: Trinh

first: Jennifer

last: Ayoub

first: Hetty

last: Rodriguez

first: John

last: Tobias


title: The Estrogen Receptor α (ERα) has stage- and cell type-specific roles in the mammary epithelium with distinct requirements for activation function-1 and -2

city: Lausanne

first: George

last: Sflomos

address: SV 2815, Batiment SV, Station 19

department: ISREC

country: Switzerland

institute: EPFL

summary: We provide evidence that luminal responder cells express low level ERα required for cell expansion during ductal growth but growth inhibitor during pregnancy.

overall_design: Intraductally engrafted WT.GFP+ or ERα-/-.GFP+ cells from contralateral glands of the pregnant NSG hosts by FACS sorting for GFP and analysed global gene expression of 3 independent samples by RNA sequencing.

first: Stéphanie

last: Cagnet

first: Dalya

last: Ataca

first: Sonia

last: Schuepbach-Mallepell

first: Patrick

last: Aouad

first: Henry

last: Hugues

first: Andrée

last: Krust

first: Ayyakkannu

last: Ayyannan

first: Valentina

last: Scabia

first: Cathrin

last: Brisken


title: Transcriptomic Analysis for Differentially Expressed Genes in Ovarian Follicle Activation and Puberty Onset in the Zebrafish

first: Bo

last: Zhu

address: 1 Blackfan Circle

department: Biology of Vascular Program

institute: Boston Children's Hospital

summary: Puberty is a special transition period in sexual maturation, and it has been extensively studied in vertebrates in the past decades. In mammals, the initiation of puberty involves activation of numerous genes; however, there have been few comprehensive reports in small model teleosts such as the zebrafish. In the zebrafish, the onset of puberty in females is marked by the appearance of the first wave of pre-vitellogenic (PV) follicles in the ovary during sexual maturation.  Using transcriptomics and real-time qPCR, this study was undertaken to investigate temporal gene expression differences between the primary growth (PG) follicles and pre-vitellogenic (PV) follicles, with particular emphasis on oocyte and follicular cell specific genes as well as several closely associated signaling pathways. Our results showed that totally 1082 genes were significantly upregulated and 530 evidently downregulated during the PG-PV transition, and among them were some well recognized biomarkers such as cyp19a1a, fshr, inha and inhbaa and some novel genes like notch3, amh, gadd45ga and lpl.  Further gene ontology analysis showed that egg coat formation and steroid hormone mediated signaling pathway might be critical for follicle activation from PG to PV stage. In addition, KEGG identified several signaling pathways that might play pivotal roles in early folliculogenesis, including phosphatidylinositol signaling system, glycolsaminoglycan biosynthesis, RNA transport, and p53 signaling pathways. Overall, this study reported a comprehensive analysis for biomarker genes and potential pathways involved in PG-PV transition or follicle activation, which also marks female puberty onset in the zebrafish when occurring for the first time in sexual maturation.

overall_design: Examination of gene expression patterns in 2 different stage follicles (PG and PV follicles)

first: Lakhansing

last: Pardeshi

first: Yingying

last: Chen

first: Wei

last: Ge


title: Ppef2 controls the survival and function of CD8+ dendritic cells

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: Expression analyses of Ppef2 by qPCR and other assays were performed and Ppef2+/+ and Ppef2-/- mice were analyzed for the biological function of Ppef2 in dendritic cells (DCs)

overall_design: Analysis of dendritic cell surface marker, gene expression, differentiation and function

first: Markus

last: Zwick

first: Thomas

last: Ulas

first: Yi-Li

last: Cho

first: Christine

last: Ried

first: Veit

last: Buchholz

last: Brocker