title: Maize and Cercospora zeina transcriptome analysis during gray leaf spot foliar disease

city: Pretoria

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Lynnwood Road

department: Plant and Soil Science

country: South Africa

institute: University of Pretoria

summary: Gray leaf spot (GLS) disease of maize can be caused by either of two sibling fungal species Cercospora zeina or Cercospora zeae-maydis.  These species differ in geographical distribution, for example to date only C. zeina is associated with GLS in African countries, such as South Africa.  Maize inbred line B73, which is susceptible to GLS, was planted in the field, and subjected to natural infection with C. zeina.  Samples were collected from lower leaves with substantial GLS lesions and younger upper leaves of the same plants with very few immature GLS lesions.  The first aim of the experiment was to determine which maize genes are induced in response to C. zeina infection.  The second aim was to identify C. zeina genes expressed in planta during a compatible interaction.  The third aim was to determine whether the C. zeina cercosporin biosynthetic (CTB) genes are expressed in planta.  C. zeina fails to produce cercosporin in vitro in contrast to C. zeae-maydis.  Cercosporin is a phytotoxin that is thought to play a role in pathogenicity of several Cercospora spp., however its role in the pathogenicity strategy of C. zeina is currently under investigation.

sample_organism:
Zea mays
Cercospora zeina

platform_organism:
Zea mays
Cercospora zeina

overall_design: To collect material that reflected a difference between C. zeina infected B73 leaves and control B73 leaf material, samples were collected from two lower GLS infected leaves (second and third leaf internode below ear), and two upper leaves with minimal GLS symptoms (second and third internode above ear), respectively. The two lower leaves from each plant were pooled prior to RNA extraction, and the two upper leaves from each plant were pooled prior to RNA extraction. Upper and lower leaf samples from three maize B73 plants were subjected to RNA sequencing individually. The three maize plants were selected randomly as one plant per row from three rows of ten B73 plants each.

first: Nicholas

last: Olivier

first: Velushka

last: Swart

first: Bridget

last: Crampton

middle: K


title: Exosome-mediated transfer of cardio-protective miRNAs between cardiomyocytes prevents apoptosis induced by hypoxia

status: Public on Jun 14 2017

city: Wen’jiang,Chengu

first: long

middle: ke

last: ren

state: Sichuan

address: Huimin road, 211#

department: 1	Institute of Animal Genetics & Breeding

country: China

institute: sichuan agriculture university

type: Non-coding RNA profiling by high throughput sequencing

summary:
Recent evidence suggests that hypoxia caused by acute myocardial infarction (AMI) can induce evident cardiomyocyte apoptosis. Exosomes, as paracrine signaling mediators by delivering cytosolic components (including miRNA, mRNA, protein), play crucial roles in intercellular communication. However, the systemic regulation of exosome-mediated miRNA delivery and subsequent regulation effect underlying AMI are not well-understood to date. Here, using small RNA-seq, we investigated the miRNAome of H9C2 cells and corresponding paracrine exosmes after hypoxia stress, and identified total of 92 and 62 differentially expressed (DE) miRNAs in cells and exosomes from hypoxia vs. normoxia condition. We found that hypoxia strongly induced the expression of hypoxamiRs in H9C2 cells and altered cardiomyocyte-derived exosomal miRNAome. Functional enrichment analysis revealed extensive roles of DE exosomal miRNAs in HIF-1 signaling pathway and cell apoptosis process, such as TNF signaling pathway, MAPK signaling pathway, mTOR signaling pathway. Furthermore, the gain- and loss-of-function analysis demonstrated the anti-apoptotic effects of hypoxia-induced exosomal miRNAs, i.e. miR-21-5p, miR-378-3p, miR-152-3p, let-7i-5p, and then the luciferase reporter assay confirmed that miR-152-3p and let-7i-5p implemented their anti-apoptotic function by directly targeting Atg12 and Faslg, respectively. In short, this study revealed that hypoxia-exosomes derived from cardiomyocyte, loaded abundant cardio-protective miRNAs, mediate crosstalk among cardiomyocytes and prevent cardiomyocytes apoptosis after hypoxia.
Methods:  we established the anoxia model using H9C2 cells, an immortal cardiac muscle cell line, to imitate hypoxia condition caused by AMI in vitro, and then small RNA-seq were employed to investigate the miRNA transcriptome of H9C2 cells and its exosomes collected from hypoxia and normoxia culture medium.
Results: we identified the miRNAome of H9C2 cells and its exosmes under both hypoxia and normoxia, including 331, 338, 144, 74 unique mature miRNAs from hypoxia-cells, normoxia-cells, hypoxia-exosomes, normoxia-exosomes, respectively. Total of 92 and 62 DE miRNAs were identified from cells and exosomes. Among of which, the DE exosomal miRNAs were mainly involved in HIF-1 signaling pathway and cell apoptosis process, such as TNF signaling pathway, MAPK signaling pathway, mTOR signaling pathway. Interestingly, we found that some DE exosomal miRNAs, including miR-21-5p, miR-378-3p, miR-152-3p, let-7i-5p, have an anti-apoptotic and pro-viability effects in H9C2 cells under hypoxic stress. In addition, Atg12 and Faslg to be respective target of miR-152-3p and let-7i-5p were partly elucidated the anti-apoptosis mechanism of hypoxia-exosomes.
Conclusions:In brief, this study illustrated a potential mechanism that, under hypoxic stress, hypoxia pre-perceived cardiomyocytes can spontaneously secrete the hypoxamiRs enriched exosomes, loaded a large amount of cardio-protective miRNA, which mediate crosstalk among cardiomyocytes and prevent apoptosis to heighten the hypoxia adaptability of cardiomyocytes. In more detail, we first discovered that miR-152-3p and let-7i-5p, enriched in hypoxia-exosomes derived by cardiomyocytes, played an anti-apoptosis role via mitochondrial pathway(intrinsic pathway) and death receptor pathway (extrinsic pathway), respectively.

first: Jinwei

last: Zhang

first: Jideng

last: Ma

first: Keren

last: Long


title: Oxygen tension regulates the miRNA profile and bioactivity of exosomes released from extravillous trophoblast cells – implications for complications of pregnancy

city: Brisbane

first: Dominic

last: Guanzon

state: Queensland

address: Building 71/918 RBWH Herston

department: UQCCR

country: Australia

institute: University of Queensland

summary: Cell-to-cell communication is essential for the spiral artery (SpA) remodeling and required for maternal transfer of nutrient and oxygen to the fetus. Extravillous trophoblast invade the uterine arteries to remodel the SpA during the first 20 weeks of gestation. Interestingly, oxygen tenstion in the uterine environment changes with the progression of pregnancies and damage in the SpA remodelling can lead to preeclampsia and pther pregnancy complications. Recently, our understanding of how cells communicate has undergone a paradigm shift since the recognition of the role of exosomes on intercellular signaling. Here, we investigated whether oxygen tension alters the exosome release and miRNA profile from extravillous trophoblast (EVT), modifying their bioactivity on endothelial cells. Furthermore, we have established the exosomal miRNA profile at early gestation in women who develop pre-eclampsia (PE) and spontaneous preterm birth (SPTB). The effect of  oxygen tension (i.e. 8% and 1% oxygen) on exosome release was quantified using nanocrystals (Qdot®) coupled to CD63 by fluorescence NTA. A real-time, live-cell imaging system (Incucyte™) was used to establish the effect of exosomes on endothelial cells. Plasma samples were obtained at early gestation (<18 weeks) and classified according to pregnancy outcomes. An Illumina TrueSeq Small RNA kit was used to construct a small RNA library from exosomal RNA obtained from EVT and plasma samples. The number of exosomes was significantly hifger in EVT culturedunder 1% compared to 8% oxygen. In total, 741 miRNA were identified in exosomes from EVT. Bioinformatic analysis revealed that these miRNA were associated with cell migration and cytokine production. Interestingly, exosomes isolated from EVT cultured at 8% oxygen increased EC migration, while exosomes from 1% oxygen decrease EC migration. These changes were inversely proportional to TNF-α released from EC. Finally, we have identified a set of uniques miRNA in exosomes from EVT cultured at 1% oxygen and exosomes isolated from maternal at early gestation, who developed PE and SPTB later in pregnancy. We suggest that aberrant exosomal signalling by placental cells is a common aetiological factor in pregnancy complications characterised by incomplete SpA remodeling and is therefore a clinically useful biomarker of pregnancy complications.

overall_design: miRNAs were profiled from exosomes using next generation seqeuencing, utilising the Illumina NextSeq 500 platform

first: Grace

last: Truong

first: Carlos

last: Salomon


title: Dissecting tissue-specific transcriptomic responses from leaf and roots under salt stress in Petunia hybrida Mitchell

city: Ithaca

first: Neil

middle: Scott

last: Mattson

state: NY

address: 134A Plant Sci Bldg

department: School of Integrative Plant Science

country: USA

institute: Cornell University

type: Expression profiling by high throughput sequencing

summary: One of the primary objectives of plant biotechnology is to increase resistance to abiotic stresses, such as salinity. Salinity is a major abiotic stress and increasing crop resistant to salt continues to the present day as a major challenge. Salt stress disturbs cellular environment leading to protein misfolding, affecting normal plant growth and causing agricultural losses worldwide. The advent of state-of-the-art technologies such as high throughput mRNA sequencing (RNA-Seq) has revolutionized whole-transcriptome analysis by allowing, with high precision, to measure changes in gene expression. In this work, we used tissue-specific RNA-Seq to gain insight into the Petunia hybrida transcriptional responses under sodium chloride (NaCl) stress using a controlled hydroponic system. Roots and leaves samples were taken from a continuum of 48 hours of acute 150 mM NaCl. This analysis revealed a set of tissue- and- time point specific differentially expressed genes, such as genes related to transport, signal transduction, ion homeostasis as well as novel and undescribed genes, such as Peaxi162Scf00003g04130  and Peaxi162Scf00589g00323 expressed only in roots under salt stress. In this work, we identified early and late expressed genes in response to salt stress while providing a core of differentially express genes across all time points and tissues, including the trehalose-6-phosphate synthase 1 (TPS1), a glycosyltransferase reported in salt tolerance in other species. To test the function of the novel petunia TPS1 allele, we cloned and showed that TPS1 is a functional plant gene capable of complementing the trehalose biosynthesis pathway in mutants (tps1) yeast. The list of candidate genes to enhance salt tolerance provided in this work constitutes a major effort to better understand the detrimental effects of salinity in petunia with direct implications for other economically important Solanaceous species

overall_design: Assessing the petunia response to salt stress

first: Gonzalo

last: Villarino

middle: S


title: Genetic Dissection of the Spaceflight Transcriptome Responses in Plants: are some responses unnecessary?

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

summary: Experimentation on the International Space Station has reached the stage where repeated and nuanced transcriptome studies are beginning to illuminate the structural and metabolic differences between plants grown in space compared to plants on the Earth. Genes that are important in setting up the spaceflight responses are being identified; their role in spaceflight physiological adaptation are increasingly understood, and the fact that different genotypes adapt differently is recognized. However, the basic question of whether these spaceflight responses are required for survival has yet to be posed, and the fundamental notion that spaceflight responses may be non-adaptive has yet to be explored. Therefore the experiments presented here were designed to ask if portions of the plant spaceflight response can be genetically removed without causing loss of spaceflight survival and without causing increased stress responses. The CARA experiment compared the spaceflight transcriptome responses of two Arabidopsis ecotypes, Col-0 and WS, as well as that of a PhyD mutant of Col-0. When grown with the ambient light of the ISS, phyD displayed a significantly reduced spaceflight transcriptome response compared to Col-0, suggesting that altering the activity of a single gene can actually improve spaceflight adaptation by reducing the transcriptome cost of physiological adaptation. The WS genotype showed and even simpler spaceflight transcriptome response in the ambient light of the ISS, more broadly indicating that the plant genotype can be manipulated to reduce the transcriptome cost of plant physiological adaptation to spaceflight and suggesting that genetic manipulation might further reduce, or perhaps eliminate the metabolic cost of spaceflight adaptation. When plants were germinated and then left in the dark on the ISS, the WS genotype actually mounted a larger transcriptome response than Col-0, suggesting that the in-space light environment affects physiological adaptation, which further implies that manipulating the local habitat can also substantially impact the metabolic cost of spaceflight adaptation.

overall_design: CARA Seed Lines and Planting:   Three seed lines Wild-Type Wassilewskija (Ws), Columbia-0 (Col-0) and Col-0 PhyD (phyD) Mutants were tested for viability, sterility and ability to maintain dormancy before the launch. Tested batches of seeds were planted on phytagel plates as one genotype per plate for gene expression analysis in replicates of three. One set was planted for the flight and one for ground control. The plates were wrapped such that every surface of the plate was covered by two layers of Duvetyn Black-Out cloth (Seattle Fabrics) (Sng et al, 2014). The plates were stored 4° C until launch, and was then launched in a cold-stow bag to maintain the plates at 4° C until integration and activation on the ISS.   On Orbit Operations and harvest:   The dormant plates were activated on station by removing the Black-Out cloth wrapping 12 days after launch. The plates were then placed on a fabric that was mounted in the US Laboratory module on the wall adjoining the MELFI freezer and secured using Velcro. The plants were allowed to grow on orbit for 11 days; some in the ambient light of ISS and some in the dark. The dark-grown plates were first activated by exposing the seeds to light for 4 hours, and then re-wrapped in Black-Out cloth for the duration of the growth period. A corresponding set of seedlings were grown as ground control in KSC.   At 11 days, seedlings were photographed, harvested into KFT containing RNAlater solutions and returned for post-flight analysis. All plates were harvested into KFTs with their counterpart (e.g. Light 1 was harvested with Dark 1). Once the plants were placed in the KFTs, the KFT was actuated with RNAlater to preserve the sample. At 24 hours post-harvest, KFTs were then transferred to MELFI, the -32°C freezer. Following SpaceX-3 splashdown in the Pacific Ocean, the KFTs transferred to the Cold Stowage charter plane at the Long Beach Airport, placed into an insulated shipper with dry ice, and flown to Johnson Space Center (JSC). The KFTs were then transferred via FedEx ground to the Kennedy Space Center. The KFTs were removed from dry ice and transferred to a -80°C freezer on May 22, 2014. The PIs retrieved the plant samples from the KFTs on May 29, 2014 and transferred the samples back to the University of Florida.  The harvested material was used to compare the transcriptomes of each genotype. The patterns of gene expression was compared among genotypes within a treatment (spaceflight or unit gravity) and between treatments (spaceflight versus ground control) for each genotype.

first: Anna-Lisa

last: Paul

first: Natasha

middle: J

last: Sng

first: Agata

last: Zupanska

first: Aparna

last: Krishnamurthy


title: Histone Deacetylase 3 Prepares Brown Adipose Tissue For Acute Thermogenic Challenge

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Histone Deacetylase 3 Prepares Brown Adipose Tissue For Acute Thermogenic Challenge [RNA-Seq]

summary: Brown adipose tissue (BAT) is a thermogenic organ that requires Uncoupling Protein 1 (UCP1) to dissipate chemical energy as heat, to defend core body temperature against hypothermia, and counteract obesity and metabolic diseases1. However, the transcriptional mechanism ensuring BAT thermogenic capacity for survival prior to environmental cold is unknown. Here we show histone deacetylase 3 (HDAC3) is a required transcriptional regulator of BAT enhancers to ensure thermogenic aptitude and survival. Mice with genetic ablation of HDAC3 become severely hypothermic and fail to survive acute cold exposure. UCP1 is nearly absent in BAT lacking HDAC3 and there is marked down-regulation of mitochondrial oxidative phosphorylation (OXPHOS) genes. Remarkably, although HDAC3 canonically functions as a transcriptional corepressor2, HDAC3 functions as a coactivator of the estrogen-related receptor _ (ERR_) in BAT, and loss of HDAC3 leads to robust global down-regulation of ERR±-driven enhancers. HDAC3 coactivation of ERR_ is mediated through deacetylation of PGC-1_ and is required for basal transcription of Ucp1, OXPHOS, and Pgc-1_. Thus, HDAC3 uniquely primes Ucp1 and thermogenic gene transcription to ensure immediate BAT-driven thermogenesis upon acute exposure to dangerously cold temperatures.

overall_design: Wild-type and HDAC3 KO animals of C57BL/6 background were adapted to 29C (thermoneutrality) for RNA-seq. 1ug of RNA was used in the RiboZero treatment followed by library generation through Illumina library kit.

first: Matthew

last: Emmett

first: Kyoung-Jae

last: Won

first: Mitchell

middle: A

last: Lazar


title: Characterization and transplantation of enteric neural crest cells from human induced pluripotent stem cells

city: Guangzhou

first: Weiqiang

last: Li

address: Zhongshan Road 2

institute: Sun Yat-sen university

summary: Here, human pluripotent stem cells (hiPSCs and hESCs) were induced to differentiate to enteric neurons through neural crest specification. We sequenced mRNA samples from enteric neuronal differentiation of human pluripotent stem cells at 4 different stage to generate the gene expression profiles of these cells.

overall_design: 8 samples, including undifferentiated HDF-hiPSCs/H1, freshly isolated p75+/HNK1+ hiPSC-NCSCs and H1-NCSCs, enteric neural crest precursors (hiPSC-ENCPs 1 and hiPSC-ENCPs 2) from hiPSC-NCSCs, and enteric-like neurons (hiPSC-ENs 1 and hiPSC-ENs 2) from hiPSC-NCSCs, were analyzed.

first: Lihua

last: Huang

first: Andy

middle: P

last: Xiang


title: The balance of Influenza A Virus segments is achieved by virus-derived small non-coding RNAs

city: Tarrytown

first: Asiel

middle: Arturo

last: Benitez

state: New York

address: 777 Old Saw Mill River Rd, 92-516A

department: Immunology & Inflammation

institute: Regeneron Pharmaceuticals, Inc

summary: Encoding only ten major proteins, Influenza A virus (IAV) gains access to both the cell and nucleus, replicates its eight genomic segments, then enters the cytoplasm to assemble and egress.  This is achieved through an expansive network of interactions with the host and a coordinated production of viral components.  Here we show that upon infection, primary transcription of the virus results in the accumulation of the splice product, Nuclear Export Protein (NEP), which associates with the viral polymerase leading to the synthesis of segment-specific small viral RNAs (svRNAs).  Here we demonstrate that svRNA biology is responsible for coordinating segment-specific amplification and is predominantly required for amplification of the three larger polymerase segments.  Generation of svRNA ambiguity results in predictable changes in segment-specific vRNA levels and up to a five log attenuation. Together, these data elucidate the molecular function of svRNAs as essential mediators responsible for maintaining a stoichiometric balance between genomic segments and establish these small RNAs as functional components of the virus.

overall_design: Examination of svRNA production in mice

first: Simone

last: Backes

first: Ismarc

last: Reyes

first: David

last: Sachs

first: Benjamin

middle: R

last: tenOever


title: RNA sequencing of Cercospora zeina grown in vitro to annotate gene models

first: Dave

last: Berger

summary: Gray leaf spot (GLS) disease of maize can be caused by either of two sibling fungal species Cercospora zeina or Cercospora zeae-maydis.  These species differ in geographical distribution, for example to date only C. zeina is associated with GLS in Africa.  C. zeae-maydis isolates produce the phytotoxin cercosporin in vitro, whereas C. zeina does not.  C.zeina was grown in different in vitro conditions to determine if the cercosporin biosynthesis genes were expressed.  Furthermore, the choice of a range of different in vitro conditions was aimed at capturing transcript sequences from a broad range of genes to aid in identification of gene models for annotation of the C.zeina genome sequence.

overall_design: Seven separate culture RNA samples were submitted without biological replicates

first: Velushka

last: Swart

first: Nicholas

last: Olivier

first: Bridget

middle: G

last: Crampton

first: Fourie

last: Joubert


title: Effect of digoxin treatment on the gene and alternative splice expression in human pluripotent stem cells- derived mesenchymal stem cells

status: Public on Jun 13 2017

city: Lyon

first: jean-baptiste

last: claude

address: 46, allée d’Italie

country: France

institute: [CNRS/ENS Lyon/UCBL/HCL] Laboratoire de Biologie Moléculaire de la Cellule UMR5239

summary: We report the effect of FDA approved digoxin treatment (50nM for 48h) on the gene expression and alternative splices in control human pluripotent stem cells derived mesenchymal stem cells. Our results demonstrate the effect of digoxin treatment on alternative splice as 258 skipping exons were identified after digoxin treatment. Concerning the gene expression, our results also highlight on the large effect of digoxin treatment on the modulation of gene expression.

overall_design: Gene expression and Alternative splices were examined in three samples of WT human pluripotent stem cells derived mesenchymal stem cells treated or not with 50nM digoxin for 48h.

first: Yves

last: Maury

first: Pauline

last: Poydenot

last: Brinon

first: Lea

last: Lesueur

first: Stéphane

last: Nédelec

first: Sylvain

last: Roquevière

first: Julien

last: Côme

first: Hélène

last: Polvèche

first: Didier

last: Auboeuf

first: Jérome

last: Denis

first: Geneviève

last: Pietu

first: Sandrine

last: Baghdoyan

first: Marc

last: Lechuga

last: Peschanski

first: Cécile

last: Martinat


title: The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: ADAR proteins alter gene expression both via catalyzing adenosine-to-inosine RNA editing and in an editing-independent manner by binding to target RNAs. Loss of ADARs affects neuronal function in all animals studied to date. To identify important neuronal targets in C. elegans, we performed the first unbiased assessment of the effects of ADR-2, the C. elegans editing enzyme, on the neural transcriptome. We identified the neural editome and gene expression changes associated with the loss of adr-2. As C. elegans lacking adr-2 exhibit reduced chemotaxis, our studies focused on targets that regulate this process. We identified an edited mRNA, clec-41, whose expression is dependent on ADR-2. Expressing clec-41 in adr-2 deficient neural cells restored chemotaxis. This study is the first of its kind in the RNA editing field to span from developing novel methodology for tissue-specific target identification to organismal behavior, significantly advancing our understanding of ADAR functions in neural cells.

overall_design: Strand-specific editing sites and differential expression analysis was done on triplicate WT (wildtype) and Adr2- (control) C. elegans neural cells.

first: Sarah

middle: N

last: Deffit

first: Brian

last: Yee

first: Pranathi

last: Vadlamani

first: Emily

middle: C

last: Wheeler

first: Aidan

last: Manning

first: Alain

last: Domissy

first: Michael

last: Washburn

middle: W

first: Heather

last: Hundley


title: Epigenetic analysis reveals the repressive function of MyoD during myogenic differentiation

city: Berlin

first: Silke

last: Sperling

state: Berlin

address: Lindenberger Weg 80

department: Cardiovascular Genetics

country: Germany

institute: Experimental and Clinical Research Center (ECRC), Charité / MDC for Molecular Medicine

summary: We identify a subset of highly expressed genes related to muscle development, which show static H3K4me2 enrichment over the gene body and H3K4me3 enrichment towards the gene body during myogenic differentiation. This study reveals that MyoD significantly binds to this particular subset of genes and further systematic analysis shows the repressive role of MyoD. Interestingly, MyoD binds and down-regulates Patz1 which is important for maintaining pluripotency. These findings might provide a key regulatory mechanism to promote myogenic differentiation.

overall_design: ChIP-seq profile of of two different histone modifications (H3K4me2 and H3K4me3) and a transcription factor MyoD during C2C12 cells differentiation.


title: Differentiation of Inflammation-responsive Astrocytes from Glial Progenitors Generated from Human Induced Pluripotent Stem Cells

status: Public on Jun 15 2017

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary:
The goals of this study are to generate inflammation-sensitive astrocytes from human induced pluripotent stem cells. We examine the transcriptomic inflammatory signature of generated astrocytes following Il1Beta exposure.
Primary human cerebellar astrocytes, human induced pluripotent stem cells (hiPSC)-derived neural precursor cells (NPCs) and hiPSC-derived astrocytes were treated with Il1beta and compared to vehicle treated controls.
Results: hiPSC-derived can be differentiated to astrocytes that are inflammation sensitive.

first: Krishna

last: Vadodaria

first: Fred

last: Gage


title: GRO-seq analysis of MCF7 cells

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

summary: We used GRO-seq to examine RNA transcription rates in MCF7 cells.

overall_design: We measured in duplicates gene transcription rates in MCF7 cells

first: R

last: Agami


title: RNA_seq and Ribo_seq analyses applied to PC9 and H1933 human cancer cell lines

summary: We used RNA-seq and Ribo-seq analyses to examine translation efficiency (TE) in PC9 and H1933 cells

overall_design: We measured expression levels (RNA.seq) and ribosome densities (ribo-seq) in PC9 and H1933 cell lines


title: Histone Deacetylase 3 Prepares Brown Adipose Tissue For Acute Thermogenic Challenge [ChIP-Seq, GRO-Seq]

first: Hee-Woong

last: Lim

overall_design: Interscapular BAT from wild-type and HDAC3 KO animals of C57BL/6 background were adapted to 22C or 29C (thermoneutrality) for ChIP-seq and GRO-seq studies. ChIP-seq studies of HDAC3, ERR- alpha, NCoR, and H3K27ac were performed from individual mice of each genotype and immunoprecipitations were subsequently pooled for sequencing. Nascent transcription changes and eRNAs were measured in WT and HDAC3 KO mice by GRO-seq through pooling 10 interscapular BAT pads from individual mice for nuclei isolation and subsequent nuclear-run on reactions and GRO-seq library construction.

first: Matthew

last: Emmett

first: Jennifer

last: Jager

first: Kyoung-Jae

last: Won

first: Mitchell

last: Lazar


title: An orchestrated intron retention program in meiosis controls timely usage of transcripts during germ cell differentiation (RNA-Seq)

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: Alternative splicing (AS) represents a powerful resource to amplify the coding potential of eukaryotic genomes and to finely tune gene expression during cell differentiation and development. Notably, high-throughput transcriptome analyses identified testis among the tissues displaying the highest proportion of AS events and profiling of whole testis transcriptome during the first wave of mouse spermatogenesis highlighted some AS events that are timely regulated during this process. Thus, AS modulation likely contributes to the fine-tuned regulation of gene expression that occurs during the male germ cell differentiation. In particular, meiotic spermatocytes and post-meiotic spermatids are known to express a highly specific repertoire of protein variants. However, no study has directly investigated whether global splicing-changes occur during the trans-meiotic phases of spermatogenesis to date. Spermatocytes undergo two consecutive meiotic divisions to yield haploid post-meiotic spermatids, which then  differentiate into highly specialized and motile spermatozoa. Herein, to achieve a comprehensive characterization of the splicing changes occurring during trans-meiotic differentiation of male germ cells, we performed high-throughput RNA sequencing (RNA-seq) analyses of polyA+ RNA isolated from highly purified populations of meiotic spermatocytes and post-meiotic spermatids. Our analysis uncovered a robust intron retention (IR) program in meiotic spermatocytes. Intron-retaining genes were strongly enriched in functional categories related to differentiation and properties of the male gamete. We found that meiotic intron-retaining transcripts are long-lived mRNAs, which are preserved in the nucleus until they need to be translated. Thus, our study reveals an unexpected physiological role for IR in ensuring proper and timely control of gene expression during male germ cell differentiation.

overall_design: RNA‐Seq data for purified spermatocytes and spermatids

first: Chiara

last: Naro

first: Ariane

last: Jolly

first: Sara

last: Di Persio

first: Pamela

last: Bielli

first: Niclas

last: Setterblad

first: Antonio

last: Alberdi

first: Elena

last: Vicini

first: Raffaele

last: Geremia

first: Claudio

last: Sette


title: Expression regulation by Pcgf1 in mouse embryonic stem cells

city: Nanjing

first: Wukui

last: Zhao

state: Jiangsu

address: 12 Xuefu Road

department: Model Animal Research Center

institute: Nanjing University

summary: The Polycomb repressive complex 1 (PRC1) is essential for fate decisions of embryonic stem (ES) cells. Emerging evidence suggests that six major variants of PRC1 complex, defined by the mutually exclusive presence of Pcgf subunit, regulate distinct biological processes, yet very little is known about the mechanism by which each version of PRC1 instructs and maintains cell fate. Here, we disrupted the Pcgf1, also known as Nspc1 and one of six Pcgf paralogs, in mouse ES cells by the CRISPR/Cas9 technology. We showed that although these mutant cells were viable and retained normal self-renewal, they displayed severe defects in differentiation in vitro. To gain a better understanding of the role of Pcgf1 in transcriptional control of differentiation, we analysed mRNA profiles from Pcgf1 deficient cells using RNA-seq. In contrast to the canonical role of PRC1 in gene repression, we found that Pcgf1 mainly functioned as a transcriptional activator to drive expression of many genes involved in ectoderm and mesoderm differentiation. Chromatin immunoprecipitation experiments demonstrated that Pcgf1 deletion caused a decrease in Ring1B and its associated H2AK119ub1 mark binding to target genes. Altogether, our results revealed an unexpected function of Pcgf1 in gene activation during ES cell maintenance.

overall_design: Pcgf1 KO, wildtype and Pcgf1KO+ Pcgf1_flag mESCs

first: Yun

last: Yan

first: Jinzhong

last: Qin


title: Multiplexing droplet-based single cell RNA-sequencing using genetic barcodes

city: San Francisco

first: Sasha

last: Targ

state: California

address: 513 Parnassus Ave S-965

institute: UCSF IHG

summary: Here, we introduce an in-silico algorithm demuxlet that harnesses naturally occurring genetic variation in a pool of cells from unrelated individuals to discover the sample identity of each cell and identify droplets containing cells from two different individuals (doublets). These two capabilities enable a simple multiplexing design that increases single cell library construction throughput by experimental design where cells from genetically diverse samples are multiplexed and captured at 2-10x over standard workflows. We further demonstrate the utility of sample multiplexing by characterizing the interindividual variability in cell type-specific responses of ~15k PBMCs to interferon-beta, a potent cytokine. Our computational tool enables sample multiplexing of droplet-based single cell RNA-seq for large-scale studies of population variation and could be extended to other single cell datasets that incorporate natural or synthetic DNA barcodes.

overall_design: HiSeq 2500 data for sequencing of PBMCs from SLE patients and 2 controls. We collected 1M cells each from frozen PBMC samples that were Ficoll isolated and prepared using the 10x Single Cell instrument according to standard protocol. Samples A, B, and C were prepared on the instrument directly following thaw, while samples 2.1 and 2.2 were cultured for 6 hours with (B) or without (A) IFN-beta stimulation prior to loading on the 10x Single Cell instrument.


title: Next Generation Sequencing of Gene expression changes in U2OS osteosarcoma cells with PML silencing

city: Stanford

first: Stephen

middle: B

last: Montgomery

address: 300 Pasteur Dr

department: Pathology

institute: Stanford University

summary: We used next generation sequencing to analyze the gene expression changes in U2OS osteosarcoma cells expressing shRNA targeting the promyelocytic leukemia (PML) gene transcripts

overall_design: cDNA libraries of U2OS cells expressing control shRNA or shRNA targeting PML were generated from one biological replicate

first: Jayme

last: Salsman

first: Kimberly

last: Kurkuba

first: Kevin

last: Smith

first: Graham

last: Dellaire


title: The Arabidopsis Cys2/His2 zinc-finger transcription factor ZAT18 is a positive regulator of plant tolerance to drought stress

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

institute: Huazhong Agricultural University

summary:
Purpose: We aimed to identify ZAT18 target genes and characterize functions of ZAT18 during plant drought tolerance
Methods: A total amount of 3 μg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Index of the Arabidopsis genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of drought stress versus control condition was performed using the DESeq R package (1.18.0).
Results:In total, eight samples with two biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis revealed that 1777 genes were transcriptionally affected by AtZAT18 trasngene or drought treatment. The results showed that overexpression of AtZAT18 modulated expression level changes of 423 and 561genes under control and drought stress conditions, respectively. Drought stress treatment changed expression of 971 genes with 768 up-regulated and 203 down-regulated.

overall_design: In this study, wild type Arabidopsis and two lines of AtZAT18 transgenic plants were grown in moist soil for 7 days. Drought stress was imposed by withholding water for 10 days. The rosette leaves of control and drought treated Col-0 and AtZAT18 transgenic plants were then collected for RAN isolation. AtZAT18 transgenic plant and Col WT were used by deep sequencing, in duplicate

first: Minzhu

last: Yin


title: A single cell transcriptional roadmap for cardiopharyngeal fate diversification [scRNA-seq]

city: New York

first: wei

last: wang

address: 100 washington square east

department: Biology

institute: New York University

summary:
Dynamic gene expression programs determine multipotent cell states and fate choices during development. Multipotent progenitors for cardiomyocytes and branchiomeric head muscles populate the pharyngeal mesoderm of vertebrate embryos, but the mechanisms underlying cardiopharyngeal multipotency and heart vs. head muscle fate choices remain elusive. The tunicate Ciona emerged as a simple chordate model to study cardiopharyngeal development with unprecedented spatio-temporal resolution. We analyzed the transcriptome of single cardiopharyngeal lineage cells isolated at successive time points encompassing the transitions from multipotent progenitors to distinct first and second heart, and pharyngeal muscle precursors. We reconstructed the three cardiopharyngeal developmental trajectories, and characterized gene expression dynamics and regulatory states underlying each fate choice. Experimental perturbations and bulk transcriptome analyses revealed that ongoing FGF/MAPK signaling maintains cardiopharyngeal multipotency and promotes the pharyngeal muscle fate, whereas signal termination permits the deployment of a full pan-cardiac program and heart fate specification. We identified the Dach1/2 homolog as a novel evolutionarily conserved second-heart-field-specific factor and demonstrate, through lineage tracing and CRISPR/Cas9 perturbations,  that it operates downstream of Tbx1/10 to actively suppress the first heart lineage program. This data indicates that the regulatory state of multipotent cardiopharyngeal progenitors determines the first vs. second heart lineage choice, and that Tbx1/10 acts as a bona fide regulator of cardiopharyngeal multi potency.
1823 FACS purified Ciona cardiopharyngeal progenitor cells at successive developmental stages (12, 14, 16, 18, 20 hpfs) have been sequenced in this research, encompassing the developmental spectrum from single multipotent progenitors to diverse fate-restricted progenitor cells.  1796 out of 1823 cells have reads successfully mapped to Ciona genome (i.e only 1796 samples have FPKM data in the *txt processed data files). We adopted multiple quality control criteria to filter out low quality single cell transcriptomes, the contaminating subpopulations and the doublets. Eventually, 848 high-quality cells were retained for further analysis. Based on previously identified cell type specific markers and the well established lineage tree, we identified all five cardiopharyngeal progenitor subtypes (TVC, STVC, ASM, FHP, SHP) and in silico reconstructed three unidirectional trajectories corresponding to the specification of pharyngeal and cardiac fate. Our study enabled us to characterize the global gene expression patterns of heterogeneous cardiopharyngeal progenitors, and interrogate the spatial-temporal dynamics of cardiopharyngeal specification.

overall_design:
Single cell RNA-seq of FACS purified cardiopharyngeal progenitors (Mesp>tagRFP/Handr-r>tagBFP/MyoD905>EGFP) in Ciona Robusta at 12, 14, 16, 18, 20 hours post fertilization (hpf).
Please note that multiple quality control criteria have been applied to filter out low quality single cell transcriptomes, the contaminating subpopulations and the doublets. [1] only single cells that had more than 2,000 and less than 6,000 expressed genes, and genes that were detected in more than 3 cells were retained. [2] Cells with mapping rates less than 30% and total reads more than 2-million were removed. [3] Contaminating non-cardiopharyngeal lineage cells were removed [4] Cells that expressed noticeable degree of both cardiac and ASM markers were considered as doublets and  removed.Eventually, 848 high quality cells were retained for further analysis. However, all samples and their associated raw data files have been included in the records for other researchers who might want to apply their own criteria to pre-process the raw data, although they are not all described in the associated manuscript.

first: Xiang

last: Niu

first: Wei

last: Wang

first: Lionel

last: Christiaen

first: Rahul

last: Satija


title: A single cell transcriptional roadmap for cardiopharyngeal fate diversification

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

overall_design: Refer to individual Series


title: Waterpipe Smoking Induces Epigenetic Changes in the Small Airway Epithelium [RNA-Seq]

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
Waterpipe (also called hookah, shisha, or narghile) smoking is a common form of tobacco use in the Middle East. Its use is becoming more prevalent in Western societies, especially among young adults as an alternative form of tobacco use to traditional cigarettes. While the risk to cigarette smoking is well documented, the risk to waterpipe smoking is not well defined with limited information on its health impact at the epidemiologic, clinical and biologic levels with respect to lung disease. Based on the knowledge that airway epithelial cell DNA methylation is modified in response to cigarette smoke and in cigarette smoking-related lung diseases, we assessed the impact of light-use water-pipe smoking on DNA methylation of the small airway epithelium (SAE) and whether changes in methylation were linked to the transcriptional output of the cells. Small airway epithelium was obtained from 7 nonsmokers and 7 light-use (2.6 ± 1.7 sessions/wk) waterpipe-only smokers. Genome-wide comparison of SAE DNA methylation of waterpipe smokers to nonsmokers identified 727 probesets differentially methylated (fold-change >1.5, p<0.05) representing 673 unique genes. Dominant pathways associated with these epigenetic changes include those linked to G-protein coupled receptor signaling, aryl hydrocarbon receptor signaling and xenobiotic metabolism signaling, all of which have been associated with cigarette smoking and lung disease. Of the genes differentially methylated, 11.3% exhibited a corresponding significant (p<0.05) change in gene expression with enrichment in pathways related to regulation of mRNA translation and protein synthesis (eIF2 signaling and regulation of eIF4 and p70S6K signaling). Overall, these data demonstrate that light-use waterpipe smoking is associated with epigenetic changes and related transcriptional modifications in the SAE, the cell population demonstrating the earliest pathologic abnormalities associated with chronic cigarette smoking.
This study demonstrates that light-use waterpipe smoking in young adults is associated with a broad range of genome-wide DNA methylation-related changes of the SAE impacting a number of genes linked to pathways previously associated with cigarette smoking. Further, many of these methylation-related changes correlate with waterpipe smoking-associated changes in the SAE transcriptome. Together, these data add to the accumulating evidence that waterpipe smoking is harmful, and may lead to lung disease.

overall_design: Small airway epithelium was obtained from 7 nonsmokers and 7 light-use (2.6 ± 1.7 sessions/wk) waterpipe-only smokers. Expression profiling using RNA-Seq.

first: Matthew

last: Walters

first: Jacqueline

last: Salit

first: Jin-Hyun

last: Ju

first: Michelle

last: Staudt

first: Robert

last: Kaner

first: Allison

middle: M

last: Rogalski

first: Teniola

last: Sodeinde

first: Riyaad

last: Rahim

first: Jason

last: Mezey

first: Ahmad

last: Almulla

first: Hisham

last: Sattar

first: Mai

last: Mahmoud

first: Ronald

last: Crystal


title: Waterpipe Smoking Induces Epigenetic Changes in the Small Airway Epithelium

type: Methylation profiling by genome tiling array


title: Characterizing seed weight related genes through transcriptome analyses of wild and cultivated soybeans

city: Nanchang

first: Dong

last: Wang

state: JiangXi

address: Hong Gu Tan New Road, No. 999

institute: Nanchang University

summary: Cultivated soybean has domesticated in China for a long history, and there are several significant phenotypic differences between wild and cultivated soybeans. Seed of cultivar is generally larger than wild soybean, therefore here we comprehensively analyzed transcriptomes of thirteen soybean accessions seeds including seven wild soybeans and six landraces through applying strand-specific RNA sequencing. Differential expressed genes related seed weight were identified, some of them were known to be associated with seed development in Arabidopsis. Noncoding RNAs are known to play important roles in plant development, and we profiled the expression pattern of long noncoding RNA (lncRNA) in cultivated and wild soybean seeds. We have identified 1,251 long intergenic noncoding RNA, 243 intronic RNA and 81 antisense lncRNA, transcriptional levels of a number of lncRNAs were significantly different between cultivated and wild soybeans, suggesting that lncRNA may be involved in soybean seed development.

sample_organism:
Glycine max
Glycine soja

platform_organism:
Glycine max
Glycine soja

overall_design: High-depth paired-end RNA-seq from wild and cultivated soybeans

first: Chao

last: Yu


title: RNA-seq in neutrophils from Juvenile Idiopathic Arthritis

city: Houston

first: Lisha

last: Zhu

state: TX

address: 7000 fannin st

institute: UT Health Science Center at Houston

summary: In this study, we explored transcriptional complexity in human neutrophils from juvenile idiopathis arthritis and healthy control. We obtained differentially expressed genes among 3 ADU (active disease, untreated), 3 ADT (active disease, treated) and 2 HC (healthy control) samples using Cuffdiff2 software.

overall_design: 3 ADU (active disease, untreated), 3 ADT (active disease, treated) and 2 HC (healthy control) samples were carried out RNA-Seq by next-generation sequencing strategy

first: Kaiyu

last: Jiang

first: Tao

last: Liu

first: James

last: Jarvis


title: Erk-dependent Epigenetic Reprogramming Underlies Epithelial to Mesenchymal Transition

city: Mainz

first: Vijay

last: Tiwari

state: Rheinland

institute: Institute of Molecular Biology

summary: The series of events that allows for the conversion of adherent epithelial cells into migratory cells is collectively known as epithelial-mesenchymal transition (EMT). EMT is involved in triggering neural crest migration during development and in the pathogenesis of diseases, such as cancer metastasis. Whereas Erk signalling is known to be essential for EMT, its influence on the epigenetic and transcriptional programme underlying EMT is poorly understood. Here, using a comprehensive genome-wide analysis of H3K27ac mark and gene expression in primary mammary epithelial cells undergoing EMT, we found that Erk signalling is essential for the epigenetic reprogramming underlying hallmark gene expression and phenotypic changes of EMT. We found that the chemical inhibition of Erk signalling during EMT prevents loss and gain of H3K27ac mark at regulatory regions of epithelial and mesenchymal genes, respectively, and results in a transcriptome and epigenome closer to those of epithelial cells. Further computational analyses identified a distinct set of transcription factor motifs enriched at distal regulatory regions that are epigenetically remodelled by Erk signalling. Altogether, our study reveal an Erk-dependent epigenetic remodelling of distal regulatory elements that results in a gene expression programme that is essential for driving EMT.

overall_design: 1) After treatment of NMuMG cells with TGF-beta, three timepoints viz. 0hr, 4hr, 24hr were captured. To inhibit Erk pathway, Erk inhibitor is administered to NMuMG cells 30 min prior to TGF-beta treatment and captured at 4hr and 24hr timepoints.  2) For each timepoint captured, RNAseq and H3K27ac ChIPseq was performed.

first: Mohit

last: Navandar

first: Angela

last: Garding

first: Sanjeeb

last: Sahu

first: Abhijeet

last: Pataskar

first: Sandra

last: Schick


title: Analysis of the effect of two IgH superenhancer deletion on IgH locus transcription

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS


title: RNA-SEQ of mutants B cell for IgH 3'RR and Emu

overall_design: CD43- splenic B-cells from wt, Eµ-deficient or 3'RR deficient mice, non stimulated (NS) or stimulated (S) with 5mg/ml LPS.

first: Y

last: Denizot

first: K

first: P

last: Barbry


title: GRO-seq analysis of BJ cells

first: Ran

last: Elkon

summary: We used GRO-seq to examine RNA transcription rates in human fibroblast BJ cells.

overall_design: We measured in duplicates gene transcription rates in BJ cells

first: R

last: Agami


title: C/EBPβ deficiency reshapes microglial gene expression

city: Barcelona

first: Josep

last: Saura

address: Casanova 143

department: Biomedicina.

country: Spain

institute: Faculty of Medicine. University of Barcelona

summary: CCAAT/enhancer binding protein β (C/EBPβ) is a transcription factor that regulates the expression of important pro-inflammatory genes in microglia. Mice deficient for C/EBPβ show protection against excitotoxic and ischemic CNS damage but the involvement of the various C/EBPβ expressing cell types in this neuroprotective effect is not solved. Since C/EBPβ-deficient microglia show attenuated neurotoxicity in culture we hypothesized that specific C/EBPβ deficiency in microglia could be neuroprotective in vivo. In this study we have tested this hypothesis by generating mice with myeloid C/EBPβ deficiency. Mice with myeloid C/EBPβ deficiency were generated by crossing LysMCre and C/EBPβfl/fl mice . Primary microglial cultures from C/EBPβfl/fl (named here as WT) and LysMCre-C/EBPβfl/fl (named here as KO) mice were treated with lipopolysaccharide ± interferon γ (IFNγ) for 6 h and gene expression was analyzed by RNA sequencing. LysMCre-C/EBPβfl/fl mice showed an efficiency of C/EBPβ deletion of 100% in cultured microglia. Transcriptomic analysis of C/EBPβ-deficient primary microglia revealed C/EBPβ-dependent expression of 1068 genes, significantly enriched in inflammatory and innate immune responses GO terms. This study provides new data that support a central role for C/EBPβ in the biology of activated microglia.

overall_design: LysMCre-C/EBPβfl/fl genotype (12 samples): 4 samples treated with  LPS, 4 with LPS +IFNg, and 4 vehicle. C/EBPβfl/fl genotype  (9 samples): 3 samples treated with  LPS, 3 with LPS +IFNg, and 3 vehicle. Design Case (Treatment LPS or LPS +INF) control (No treatment or vehicle) in LysMCre-C/EBPβfl/fl genotype and in C/EBPβfl/fl genotype

first: Marta

last: Pulido-Salgado

first: Jose

last: Vidal-Taboada


title: RNA_seq and Ribo_seq analyses of control and Nutlin3a-treated MCF7 cells (20 hrs)

summary: We used RNA-seq and Ribo-seq analyses to examine the effect of Nutlin3a (activator of p53) treatment of translation efficiency (TE)

overall_design: We measured expression levels (RNA.seq) and ribosome densities (ribo-seq) in control and Nutlin3a-treated (20 hrs) MCF7 cells


title: Transcriptomic analysis of endometrial tissues following GnRH agonist treatment in a mouse adenomyosis model

city: SHANGHAI

first: SONG

last: GUO

address: RUIJIN 2TH ROAD

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

summary:
Purpose: We sought a transcriptomic analysis of endometrial tissues following GnRH agonist treatment in a mouse model
Methods: The neonatal female mice were randomly divided into three groups: control group, adenomyosis group and GnRH agonist treatment group. The pregnant outcome was observed and compared among the three groups. Besides, endometrial tissues from Day 4 of pregnancy were transcriptomic analysed using bioinformatics approaches.
Results:We found that the litter size was smaller in adenomyosis group than control group (8±0.28vs. 11±0.26; P＜0.05).However, the average live litter size was increased (10±0.28 vs.8±0.28; P＜0.05) after GnRH agonist treatment. Transcriptomic analysis showed that compared with the adenomyosis group, 359 genes were differentially expressed in the GnRH agonist treatment group: 218 were down regulated and 141 were up regulated.Gene function analysis showed that the differentially expressed genes were related to diverse biological processes, including estrogen metabolism, cell cycle, and metabolites biosynthesis.
Conclusions: GnRH agonist can improve the pregnancy outcome of adenomyosis in mouse model. Besides pituitary down regulation effect, other possible mechanisms may play role in GnRH agonist treatment, e.g., regulate cell proliferation cycle. It may be useful for the further understand the the mechanisms of the GnRH agonist in adeomyosis treatment.

overall_design: Transcriptomic analysis of endometrial tissues between GnRH agonist treatment group and non-GnRH agonist treatment group in a mouse adenomyosis model

first: Song

last: Guo

first: Xiaowei

last: Lu

first: Ruihuan

last: Gu

first: Di

last: Zhang

first: Yijuan

last: Sun

first: Yun

last: Feng


title: SmallRNA-SEQ of mutants B cell for IgH 3'RR and Emu

overall_design: CD43- splenic B-cells from wt, Eµ-deficient or 3'RR deficient mice, non stimulated (NS) or stimulated (S) with 5mg/ml LPS in duplicates.


title: Bptf maintains chromatin accessibility and the self-renewal capacity of mammary gland stem cells [RNA-Seq]

city: Cold Spring Harbor

first: Wesley

middle: D.

last: Frey

address: One Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Chromatin remodeling is a key requirement for transcriptional control of cellular differentiation. However, the factors that alter chromatin architecture in mammary stem cells (MaSCs) are poorly understood. Here we show that Bptf, the largest subunit of the NURF chromatin remodeling complex, is essential for MaSC self-renewal and differentiation of epithelial cells in the mammary gland. Bptf depletion arrests cells at a previously undefined stage of epithelial differentiation that is associated with an incapacity to achieve the luminal cell fate. Moreover, genome-wide analysis of DNA accessibility following genetic and chemical inhibition of Bptf, suggests a role for this factor in maintaining the open chromatin landscape of cis-regulatory elements in mammary epithelial cells (MECs). Collectively, our study implicates Bptf in maintaining the unique epigenetic state of MaSCs.

overall_design: FACS-sorted mammary epithelial cells (n=2 per cell type) from Bptf WT and Bptf KO were utilized for RNA purification (Trizol) and preparation of RNA-seq libraries.

middle: D

first: Camila

middle: O

last: Dos Santos


title: RNA-seq analysis of genes regulated by stk in Streptococcus suis serotype 2

first: Chunyan

state: Hubei

address: Shizishan NO.1 Street

department: Huazhong agricultural university

institute: Chunyan Zhang

summary: To reveal the scope of the stk regulation and explore the differences in the regulatory roles of SC-19 and ∆stk, the global gene transcription profiles of the WT and ∆stk  strains were determined by RNA-seq analysis.

overall_design: 2 Samples

first: Rui

last: Zhou

first: Lu

last: Li


title: Impacts of the Hytrosavirus on the Transcriptome of the Housefly, Musca domestica

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: UNIVERSITY OF FLORIDA

summary: Hytrosaviridae family members replicate in the salivary glands (SGs) of their adult dipteran hosts and are transmitted to uninfected hosts via saliva during feeding. Despite inducing similar gross symptoms (SG hypertrophy; SGH), hytrosaviruses (SGHVs) have distinct pathobiologies, including sex-ratio distortions in tsetse flies and refusal of infected housefly females to copulate. Via unknown mechanism(s), SGHV replication in other tissues results in reduced fecundity in tsetse flies and total shutdown of vitellogenesis and sterility in housefly females. We hypothesized that vitellogenesis shutdown is caused by virus-induced modulation of hormonal titers. Here, we used RNA-Seq to investigate virus-induced modulation of host genes/pathways in healthy and virus-infected houseflies, and we validated expression of the most significantly modulated genes (n=23) by RT-qPCR. We also evaluated the levels and activities of hemolymph antimicrobial peptides (AMPs), levels of endogenous sesquiterpenoids, and impacts of exogenous hormones on ovarian development in viremic females. Of the 973 housefly unigenes that were significantly modulated (padj ≤ 0.01; log2FC ≤ or ≥ 2.0 ), 446 and 527 genes were downregulated and upregulated, respectively. While the most downregulated genes were related to reproduction (embryogenesis/oogenesis), the repertoire of upregulated genes was overrepresented by genes related to non-self recognition, ubiquitin-protease system, cytoskeletal traffic, cellular proliferation, development and movement, and snRNA processing. Overall, MdSGHV induced upregulation of components of the siRNA, innate antimicrobial immune, and autophagy pathways. MdSGHV reduced hemolymph sesquiterpenoids and completely shut down egg development in viremic females. However, the hormonal rescue of vitellogenesis did not result in egg production. The mechanism underlying MdSGHV-induced sterility has yet to be resolved.

overall_design: Housefly pupae, obtained from colonies maintained at the USDA Center for Medical, Agricultural and Veterinary Entomology (CMAVE, Gainesville, FL), were placed in rearing cages, provided with deionized , and incubated at 26 °C, a 12:12 h light: dark photoperiod and 40% relative humidity until adult emergence. Experiments were conducted with MdHV03, the Florida type MdSGHV strain collected in 2005.  Both PBS-treated control flies and virus-injected flies were maintained in separate groups in the above-described conditions and provided with food and water ad libitum until used for sample preparation.

first: H

last: Kariithi

first: V-U

last: Lietze

first: Yao

last: Yu

first: Fahong

first: P

last: Teal

first: C

last: Verhoeven

first: Drion

last: Boucias


title: microRNAome of fresh maize

city: Chengdu

first: Yi

last: Luo

address: gongpin road #211

institute: Sichuan Agricultural University

summary: To evaluate the miRNA characteristic in fresh maize, we used small RNA-seq to get microRNAome of fresh maize.In this study, we identified 236 miRNAs sequences, of which 19 miRNAs are aboundantly expressed in fresh maize (normalized reads> 1000 ).

overall_design: Using high-throughput sequencing technology to reveal the microRNAome in fresh maize.

first: Mingzhou


title: Collecting Duct-Specific Inactivation of HNF-1β Leads to Fibrocystic Disease and Impaired Urinary Concentration

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary: Hepatocyte nuclear factor-1β (HNF-1β) is an essential transcription factor that regulates tissue-specific gene expression in the kidney, liver, pancreas and genitourinary tract. In humans, mutations of HNF-1β cause renal cysts and diabetes (RCAD) and congenital anomalies of the kidney and urinary tract (CAKUT). Inactivation of Hnf-1β in tubular epithelial cells throughout the nephron leads to early-onset cyst formation and postnatal lethality. Here, we used Pkhd1/Cre mice to delete Hnf-1β specifically in renal collecting ducts (CD). Hnf-1β mutant mice survived long-term and developed slowly progressive cystic kidney disease, renal fibrosis, and hydronephrosis. Compared with wild-type littermates, Hnf-1β mutant mice had higher urine volume, lower urine osmolality, and higher water intake. Differences were seen at baseline, following 24h water restriction, and following administration of dDAVP. Circulating ADH levels were similar in wild type and mutant mice. Polyuria, polydipsia, and decreased urine osmolality were present prior to the onset of cyst formation and hydronephrosis. These findings indicated that Hnf-1β mutant mice have a primary defect in urinary concentrating ability. Studies using in vitro hypertonicity response experiments identified NR1H4 (FXR), a transcription factor previously shown to regulate water homeostasis, as a novel HNF-1β target. mIMCD3 cells exposed to hypertonic medium robustly upregulated Fxr mRNA levels; this upregulation was lost in Hnf-1β mutant cells. HNF-1β was bound to the Fxr promoter region in vivo, and Fxr mRNA was significantly downregulated in mutant mice. FXR protein localized to CD in wild-type mice and was almost undetectable in the cyst epithelium of mutant mice. These findings highlight a new and critical role for HNF-1β in urinary concentration and hypertonicity by regulating the transcription of FXR in the CD.

overall_design: Cultured cells were treated with two conditions, each in triplicate for a total of twelve RNA-Seq samples

first: Peter

last: Igarashi

first: Karam

last: Aboudehen


title: Incompletely fused carpels ovary development revealed by miRNAs and target genes  analysis in maize. (smallRNA-Seq and degradome-Seq)

city: zhengzhou

first: hongping

last: li

institute: Henan Agricultural University

summary: To identify miRNAs involved in carpels fusion development in maize, four independent small RNA libraries and two degradome libraries from WT and IFC ovaries were constructed at the carpels fusion deficiency just being observed. A total of 162 known miRNAs distributed in 33 faimilies were identified, of which 20 known miRNAs were differentially expressed. In addition, 19 novel miRNAs were shown difference in expression levels between IFC and WT ovaries. By degradome analysis, totals of 113 and 78 target genes were predicted for known and novel miRNAs, respectively. 24 (60%) target genes of the differentially expressed known miRNAs coded for transcription factors, among which target genes encoding auxin response factors (ARF), TB1-CYC-PCFs (TCP), APETALA2 (AP2), growth regulating factor (GRF), MYB, NAC and NF-YA were classified as Class I. These target genes showed opposite expression patterns with their corresponding miRNAs according to quantitative real-time PCR results. The results suggested that the incomplete carpels fusion may partly due to the differential expression of these miRNAs and their target genes

overall_design: sample 1: Examination of small RNA in IFC ovaries at the carpels fusion deficiency just emergence; sample 2: Examination of small RNA in WT ovaries on the same ear with IFC ovaries at the same time of the IFC ovaries collecting.

first: Chaohai

first: Hongping


title: The different gene expression profile of knockdown LRP5/6 or knockdown β-catenin in hepG2 cell line through RNA-Seq

city: Shanghai

first: Liu

last: Zhenping

address: 1239 Si Ping Road

institute: Tongji University

summary: LRP5/6 receptor is an important receptor for the activation of β-catenin. Therefore, the downregulation of LRP5/6 can lead to the degradation of β-catenin. We sequenced mRNA from hepG2 cell after knocking down LRP5/6 or β-catenin separately by siRNA for 48hour. The different expression profile of mRNA was studied in two groups.

overall_design: Examination of mRNA levels in hepG2 cell by knocking down LRP5/6 or β-catenin for 48hour using siRNA.

first: Weidong

last: Zhu

first: Shangfeng

last: Liu

first: Luoquan

last: Ao

first: Dan-ni

last: Ren

first: Cizhong

last: Jiang

first: Zhenping


title: Analysis of the transcriptome of Lactococcus garvieae in presence or absence of Staphylococcus aureus and under a low or a high level of aeration by RNA sequencing

city: AURILLAC

first: Pierre

last: DELPECH

state: Auvergne Rhône Alpes

address: 20 côte de Reyne

department: MICA

institute: INRA

summary: Lactococcus garvieae has a biopreservative potential against Staphylococcus aureus through its growth inhibition in dairy products. This inhibition involves the production of hydrogen peroxyde by L. garvieae under a high aeration level but little is known about the underlying metabolism. It has already been suggested that this inhibition involves another effector, still unidentified. In this experiment, we aimed to determine the changes in L. garvieae transcriptome depending on the aeration level or on the presence of S. aureus. The results led us to a better understanding of the relationship between the hydrogen peroxide metabolism and the inhibition of S. aureus and to suggest the involvement of other pathways wich may be related to the other and still unidentified effector.

sample_organism:
Staphylococcus aureus
Lactococcus garvieae

overall_design: Biological triplicates of mRNA samples from four L. garvieae cultures: pure culture under a high aeration level, pure culture under a low aeration level, co-culture with S. aureus under a high aeration level and co-culture with S. aureus under a low aeration level. Total of 12 samples.

last: Delpech

first: Etienne

last: Rifa

first: Sabine

last: Nidelet

first: Emeric

last: Dubois

first: Geneviève

last: Gagne

first: Marie-Christine

last: Montel

first: Céline

last: Delbès

first: Stéphanie

last: Bornes


title: An analysis of the changes in miRNA expression induced by AR, HOXC6 or NKX2-2 overexpression via Next-generation sequencing

first: Mengzhu

last: Xue

address: No.100, Haike Road

institute: Shanghai Advanced Research Institute

summary: The goal of this study is to validate that AR, HOXC6 and NKX2-2 co-regulate the same core set of metastasis associated miRNAs in prostate cancer.

overall_design: AR, HOXC6 or NKX2-2 were stably overexpressed in RWPE1 cells via lentiviral transfection. RNA samples were collected and analyzed by deep sequencing in trilicate.

first: Hongyuan

last: Chang


title: Microbiota promotes systemic T-cell survival through suppression of an apoptotic factor

status: Public on Jun 12 2017

city: Salt Lake City

first: Raymond

last: Soto

state: UT

address: 15 N Medical Drive East EEJMRB Rm.4208

institute: University of Utah

summary: Examining differences in expression profiles of primary CD4+ T cells overexpressing ERDR1.

overall_design: Splenic CD4+ T cells with control MIGR1 or ERDR1 overexpressing MIGR1 mRNA profiles were generated using deep sequencing in triplicate.


title: Plexin B2 and Semaphorin 4C guide T-cell recruitment and function in the germinal center

city: Beijing

first: Hai

last: Qi

state: Beijing

address: Tsinghuayuan Street

department: School of Medicine

institute: Tsinghua University

summary: Follicular T-helper (TFH) cells are essential for germinal center (GC) responses. TFH localization in GCs is controlled by chemo-guidance cues and antigen-specific adhesion. Here we define an antigen-independent, contact-dependent, adhesive guidance system for TFH cells. Unusual for amoeboid cell migration, the system is composed of transmembrane plexin B2 (PlxnB2) molecule that is highly expressed by GC B cells and its transmembrane binding partner semaphorin 4C (Sema4C) that is upregulated on TFH cells. Instead of effectuating repulsion as a ligand, Sema4C serves as the receptor to sense PlxnB2 and bias TFH migration inward at the GC edge to penetrate the GC territory. The absence of PlxnB2 from the GC or Sema4C from TFH cells causes TFH accumulation along the GC border, impairs TFH -B cell interactions and is associated with defective plasma cell production and affinity maturation. Therefore, Sema4C and PlxnB2 regulate GC TFH recruitment and function and optimal antibody responses.

overall_design: Plxnb2+/+ or Plxnb2-/- CFP-expressing MD4 B cells were co-transferred together with OT-II T cells into B6 recipients that were subsequently immunized with HEL-OVA subcutaneously. MD4 cells of the 7-AAD-CD19+IgD-GL7hiFashi GC phenotype were FACS-sorted from pooled draining lymph nodes on day 5. To conduct transcriptomic RNA-seq analyses on these cells, a protocol initially developed for single-cell RNA-seq (Tang et al., 2011) was modified to accommodate 400 sorted cells by doubling reaction volumes with extra buffers until the step for second strand DNA synthesis. Cells were directly sorted into the lysis buffer, and reverse transcription was carried out for individual sorts within 20 minutes after isolation to preserve sample integrity. SE-100 sequencing was conducted for all samples on a HiSeq 2500 sequencer (Illumina) at the Tsinghua. Sequence reads were aligned to the Mus musculus reference genome using TopHat2 and assembled by Cufflinks to calculate the FPKM for each transcript. Genes with an average read number of at least 1 were subjected to differential expression analysis by the DESeq2 software (Bioconductor) with a call threshold set at padj<0.1.

first: Hu

last: Yan

first: Longyan

last: Wu

first: Changming

last: Shih

first: Shiyue

last: Hou

first: Jingwen

last: Shi

first: Tianyang

last: Mao

first: Wenbin

last: Chen

first: Bhavani

last: Melvin

first: Robert

last: Rigby

first: Yingjia

first: Haochen

first: Roland

middle: H

last: Friedel

first: Carola

last: Vinuesa


title: Prostaglandin E2 is required for skeletal muscle stem cell function, augmenting regeneration and strength

city: PHILADELPHIA

first: Arndt

last: Siekmann

state: Pennsylvania

address: 421 Curie Boulevard, 1114 Biomedical Research Building II/III

department: Perelman School of Medicine

institute: UNIVERSITY OF PENNSYLVANIA

summary: To identify the downstream signaling pathways that contribute to expansion of MuSCs by PGE2

overall_design: Muscle stem cells isolated from 2-4 month old mice by alpha7+/CD34+ sorting. Cells were treated in culture for 24 hours with DMSO or prostagland in E2 in biological triplicates. RNA was collected from 5,000-10,000 total cells.

first: Andrew

middle: T

last: Ho

first: Adelaida

last: Palla

first: Nora

last: Yucel

first: Helen

last: Blau


title: SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation [RNA-Seq]

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

summary: Epigenetic regulation of chromatin states is thought to control the self-renewal and differentiation of embryonic stem (ES) cells. However, the roles of repressive histone modifications such as trimethylated histone lysine 20 (H4K20me3) in pluripotency and development are largely unknown. Here, we show that the histone lysine methyltransferase SMYD5 mediates H4K20me3 at heterochromatin regions. Depletion of SMYD5 leads to compromised self-renewal, including dysregulated expression of OCT4 targets, and perturbed differentiation. SMYD5 bound regions are enriched with repetitive DNA elements. Knockdown of SMYD5 results in a global decrease of H4K20me3 levels, a redistribution of heterochromatin constituents including H3K9me3/2, G9a, and HP1α, and de-repression of endogenous retroelements. A loss of SMYD5-dependent silencing of heterochromatin nearby genic regions leads to upregulated expression of lineage-specific genes, thus contributing to the decreased self-renewal and accelerated differentiation of SMYD5-depeleted ES cells. Altogether, these findings implicate a role for SMYD5 in regulating ES cell self-renewal and H4K20me3-marked heterochromatin.

overall_design: RNA-Seq of undifferentiated and differentiated murine shLuc and shSmyd5 ES cells

first: Keji

last: Zhao


title: SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation [ChIP-Seq]

overall_design: ChIP-Seq for H4K20me3, H3K9me3/2, HP1 in murine shLuc and shSmyd5 ES cells, and SMYD5 in ES cells.


title: SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation

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

overall_design: Refer to individual Series


title: Peripheral huntingtin silencing does not ameliorate central signs of disease in the B6.HttQ111/+ mouse model of Huntington’s disease

city: Bellingham

first: Jeffrey

middle: Bryan

last: Carroll

state: WA

address: 188 E College Way, AIC 434/MS 9172

department: Psychology Department

institute: Western Washington University

summary: Huntington’s disease (HD) is an autosomal dominant neurodegenerative disease whose predominant neuropathological signature is the selective loss of medium spiny neurons in the striatum.  Despite this selective neuropathology, the mutant protein (huntingtin) is found in virtually every cell so far studied, and, consequently, phenotypes are observed in a wide range of organ systems both inside and outside the central nervous system.  We, and others, have suggested that peripheral dysfunction could contribute to the rate of progression of striatal phenotypes of HD.  To test this hypothesis, we lowered levels of huntingtin by treating mice with antisense oligonucleotides (ASOs) targeting the murine Huntingtin gene.  To study the relationship between peripheral huntingtin levels and striatal HD phenotypes, we utilized a knock-in model of the human HD mutation (the B6.HttQ111/+ mouse).  We treated mice with ASOs from 2-10 months of age, a time period over which significant HD-relevant signs progressively develop in the brains of HttQ111/+ mice.  Peripheral treatment with ASOs led to persistent reduction of huntingtin protein in peripheral organs, including liver (64% knockdown), brown adipose (66% knockdown), and white adipose tissues (71% knockdown).  This reduction was not associated with alterations in the severity of HD-relevant signs in the striatum of HttQ111/+ mice at the end of the study, including transcriptional dysregulation, the accumulation of neuronal intranuclear inclusions, and behavioral changes such as subtle hypoactivity and reduced exploratory drive.  These results suggest that the amount of peripheral reduction achieved in the current study does not significantly impact the progression of HD-relevant signs in the central nervous system.

overall_design: HttQ111/+ and Htt+/+  mice were given weekly intraperitoneal injections of Htt ASO, control ASO, or saline from 2 to 10 months of age. Striatal mRNA was sequenced from and N of 5-6 per arm (N=35 total).


title: An RNA-Seq transcriptome analysis of rice genes in response to soil-water deficiencies and the identification of OsPhyB-mediating novel regulatory pathway for drought tolerance in root

city: YONGIN-SI

first: ANIL KUMAR

last: NALINI CHANDRAN

address: 1732, Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do

department: Graduate school of Biotechnology

country: South Korea

institute: Kyung Hee University

summary: To improve our understanding of soil moisture stress, we performed RNA-Seq analysis using roots from four-week-old rice seedlings grown in soil that had been subjected o drought conditions for 2 to 3 d. From the upregulated genes, we found a T-DNA insertional mutant of rice phytochrome B (OsPhyB) that negatively regulates plant’s degree of tolerance to water deficiencies through its control of ascorbate peroxidase and catalase mediating ROS processing machinery besides the control of total leaf area and stomatal density as previously reported.

overall_design: Four weeks old rice seedlings were given drought stress for two and three days. Well watered plants of the same growth stage were used as control. Root samples from control and drought treated plants were used for generating paired end RNASeq data.  Total six samples with two biological replicates were used.

first: Yo-Han

last: Yoo

first: Anil

last: Kumar

first: Jong-Chan

last: Park

first: Yun-Shil

last: Gho

first: Sang-Won

last: Lee

first: Ki-Hong

last: Jung


title: Chromatin remodelers CHD9 and BRM are required for dex-regulated expression of block genes in U2OS-GR⍺ cells

city: Los Angeles

first: Brian

middle: Hae Kang

state: CA

address: 1441 Eastlake Avenue, NOR 6316

department: Biochemistry and Molecular Medicine

institute: University of Southern California

summary: The glucocorticoid-activated glucocorticoid receptor (GR) regulates cellular stress pathways by binding to genomic regulatory elements of target genes and recruiting coregulator proteins to remodel chromatin and regulate transcription complex assembly. The coregulator Hydrogen peroxide-inducible clone 5 (Hic-5) is required for glucocorticoid regulation of some genes, but not others, and blocks regulation of a third gene set. Hic-5 inhibits GR binding to blocked genes but not other glucocorticoid-regulated genes. Site-specific blocking of GR binding is due to gene-specific requirements for ATP-dependent chromatin remodeling enzymes. We investigate whether ATPases CHD9 and BRM were required for glucocorticoid-regulated expression of Hic-5 blocked genes.

overall_design: Since Hic-5 inhibits the actions of CHD9 and BRM, we performed double depletion of Hic-5 and CHD9 or Hic-5 and BRM in U2OS-GR⍺ cell using siRNA and examined gene expression changes at 8 hour dexamethasone (dex) or ethanol (etoh, vehicle control) treatment. Single depletion of CHD9, BRM, Hic-5 and control siRNA (siNS) followed by hormone treatment were performed as contrast and control.

first: Michael

last: Stallcup


title: A Ras GTPase associated protein is involved in the phototropic and circadian photobiology responses in fungi

city: Irapuato

first: Alfredo

last: Herrera-Estrella

state: Guanajuato

address: Libramiento Norte Carretera Leon Km 9.6

department: LANGEBIO

country: Mexico

institute: LANGEBIO

summary: Light is an environmental signal perceived by most eukaryotic organisms that can have major impacts on their growth and development. The MadC protein in the fungus Phycomyces blakesleeanus (Mucoromycotina) has been postulated to form part of the photosensory input for phototropism of the fruiting body sporangiophores, but the madC gene has remained unidentified since the 1960s when madC mutants were first isolated. In this study the madC gene was identified by positional cloning.  All madC mutant strains contain loss-of-function point mutations within a gene predicted to encode a GTPase activating protein (GAP) for Ras. The madC gene complements the Saccharomyces cerevisiae Ras-GAP ira1 mutant and the encoded MadC protein interacts with P. blakesleeanus Ras homologs in yeast two-hybrid assays, indicating that MadC is a regulator of Ras signaling. Deletion of the homolog in the filamentous ascomycete Neurospora crassa affects the circadian clock output, yielding a pattern of asexual conidiation similar to a ras-1 mutant that is used in circadian studies in N. crassa. Thus, MadC is unlikely to be a photosensor, yet is a fundamental link in the photoresponses from blue light perceived by the conserved White Collar complex with Ras signaling in two distantly-related filamentous fungal species.

overall_design: Differential expression in response to light from Phycomyces blakesleeanus, comparing the wild-type strain and a mutant strain that is unable to perform phototropism.

first: Silvia

last: Polaino

first: José

last: Villalobos-Escobedo


title: Identification of liver-specific enhancer-promoter activity in the 3’ UTR of the wild-type AAV2 genome

city: Westmead

first: Grant

middle: Joseph

last: Logan

address: 214 Hawkesbury Road

institute: CHildren's Medcial Research institute

summary: We describe and functionally characterize a previously unknown liver-specific enhancer-promoter element in the wild-type AAV2 (wtAAV2) genome lying between the cap stop codon and right-hand inverted terminal repeat (ITR). Remarkably, this element falls within the 163-nucleotide common insertion region of the AAV genome implicated in HCC oncogenesis, thereby providing a mechanistic explanation for the participation of AAV integration events in the development of HCC.

overall_design: In vitro and in vivo assays demonstrate activity of the enhancer-promoter element in murine and human hepatocytes. An in vitro assessment of wtAAV2 infection demonstrates transcription from the negative strand of the AAV genome.


title: Genomic response to environment affects tomato fruit organoleptic performance

city: Portici

first: Daniela

last: D'Esposito

address: Via Università 100

department: Department of Agriculture

country: Italy

institute: University of Naples Federico II

summary: The environment has a profound influence on the tomato fruit organoleptic quality. The extent of which depends from a well-regulated and dynamic interplay among genes, metabolites and sensorial attributes. A systems biology approach, could be useful for elucidating complex interacting mechanisms regulating the plasticity of sensorial  quality properties.   In order to investigate the transcriptomic and metabolomic environmentally challenged remodeling and to evaluate organoleptic consequences of such variation, three tomato (Solanumlycopersisum) genotypes, Heinz 1706, San Marzano and Vesuviano were grown in two different localities. The metabolome and transcriptome analysis revealed common as well as genotype specific challenged pathways, the dynamic of which are in turn regulated by genome organization and gene diversity. When combined with sensorial data, through a network analysis, interesting aspects of fruit quality fine regulation were revealed: first, duplicated genes and different genes/isoforms and transcription factors have a dominant role in shaping environment response; second the lost or gained interactions and/or the changing position of a node is crucial for phenotypic expression of a given trait; third, sensorial traits as sweetness, turgidity and are much responsive to environment. The fundamental role of cell wall metabolism in tuning all the quality attributes was also highlighted.   Tomato genotypes, although activate the same fruit related quality processes, follow different transcriptomic, metabolomic and sensorial trajectories depending of their own genetic makeup.

overall_design: Examination of 3 different tomato varieties, Heinz, San Marzano and Vesuviano, in 2 Campania locations.

first: Francesca

last: Ferriello

first: Alessandra

last: Dal Molin

first: Gianfranco

last: Diretto

first: Adriana

last: Sacco

first: Andrea

last: Minio

first: Amalia

last: Barone

first: Rossella

last: Di Monaco

first: Silvana

last: Cavella

first: Luca

last: Tardella

first: Giovanni

last: Giuliano

first: Massimo

last: Delledonne

first: Luigi

last: Frusciante

first: Maria

last: Ercolano


title: Small RNA sequencing at early and late differentiation stages of regeneration of the human airway mucociliary epithelium

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: The aim of these two datasets was to compare the abundance of canonical miRNA and isomiR sequence in  human airway epithelial cells at   early and late differentiation stages

overall_design: Human airway epithelial cells  (HAECs) isolated from nasal turbinates of one donor were cultured on collagen-coated permeable filters in an air-liquid interface (Ali). Total RNAs were extracted from undifferentiated (Ali day 4, ALI4) and fully-differentiated stages (Ali day 31, Ali31) of human airway mucociliary epithelium.

first: O

last: Mercey

first: B

last: Marcet

first: K

first: P

last: Barbry


title: Dynamic expression changes in the transcriptome of the prefrontal cortex after repeated exposure to cocaine in mice

first: Mei

last: Zhao

address: 16 Lincui Road, Chaoyang District, Beijing 100101, China

summary: In the current study, we performed transcriptome profiling of the mouse PFC to determine the dynamic changes in the Prefrontal cortex (PFC)after repeated cocaine treatment. In the current study, we observed dynamic changes in the transcriptome profiling of the PFC of repeated-cocaine treated mice, and found that distinct pathways were involved in the acute, sub-acute, and chronic stages of cocaine withdrawal. The main findings of our results include: 1) energy metabolism and protein metabolism pathways showed gradual or fluctuant decrease after cocaine withdrawal; 2) ERK pathway showed persistent changes after cocaine withdrawal; 3) plasticity related pathways, such as long-term potentiation, the regulation of the actin cytoskeleton, and the axon guidance pathway, showed a fluctuant increase after cocaine withdrawal. Our results suggest that maladaptive neural plasticity associated with psychostimulant dependence may be an ongoing degenerative process with dynamic changes in the gene network at different stages of withdrawal.

overall_design: The bilateral PFC was excised from each animal at either 2 h, 24 h, or 7 days after the final injection of cocaine. To account for inter-animal variations, we obtained 2 biological replicates for each treatment group, with each replicate representing the PFCs pooled from 5 animals. Pair-end 75-nt sequencing was performed using the Illumina HiSeq2000.

first: Mingzhen

last: Li

first: Peng

last: Xu

first: Yanhua

first: Huangjing

last: Teng

first: Weiping

last: Tian


title: Transcriptome analysis of microglia in a mouse model of Rett Syndrome: differential expression of genes associated with microglia/macrophage activation and cellular stress

city: New Haven

first: Dejian

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale School of Medicine

summary: Rett Syndrome (RTT) is a severe, neurodevelopmental disorder primarily affecting girls, characterized by progressive loss of cognitive, social and motor skills after a relatively brief period of typical development. It is usually due to de novo loss of function mutations in the X-linked gene, MeCP2, which codes for the gene expression and chromatin regulator, methyl-CpG binding protein 2. Although the behavioral phenotype appears to be primarily due to neuronal Mecp2 deficiency in mice, other cell types, including astrocytes and oligodendrocytes also appear to play a role in some aspects of the RTT phenotype. In addition, microglia may also play a role. However, the effect of Mecp2 deficiency in microglia on RTT pathogenesis is controversial. In the current study we applied whole transcriptome analysis using RNA-seq to gain insight into molecular pathways in microglia that might be dysregulated during the transition, in female mice heterozygous for an Mecp2 null allele, from the pre-phenotypic (5 weeks) to phenotypic phase (24 weeks). There was a significant overlap in differentially expressed genes (DEGs) with genes that are activated or inhibited when macrophages and microglia are stimulated towards the M1 and M2 activation states. However, the M1 and M2 associated genes were different in the 5 and 24 week samples. In addition, a substantial decrease in the expression of 9 members of the heat shock protein (HSP) family was found in the 5 week samples, but not at 24 weeks. The findings suggest that microglia from pre-phenotypic and phenotypic female mice are activated in a manner different from controls, and that pre-phenotypic female mice have alterations in their capacity to response to heat stress and other stressors that function through the HSP pathway.

overall_design: RNA-seq of WT and knockout mice at week 5 and week 24 stages (3 biological replicates at each combination of genotype and stage)

first: Ryan

last: Mokhtari

first: Erika

last: Pedrosa

first: Rayna

last: Birnbaum

first: Deyou

last: Zheng

first: Herbert

last: Lachman


title: Patient iPSC-Derived Neurons for Disease Modeling of Frontotemporal Dementia with Mutation in CHMP2B

city: Copenhagen

first: Yu

last: Zhang

address: Grønnegårdsvej 7

country: Denmark

institute: University of Copenhagen

summary: In order to obtain an overview of gene expression changes in CHMP2B-dependent frontotemporal dementia (FTD3), RNA sequencing analyses were performed in FTD3 patient neurons compared to their gene-corrected isogenic controls.

overall_design: Examination of 7 samples in totoal, including 3 samples of FTD3 paitent iPSC-derived neurons, 3 samples of corresponded isogenic controls and 1 sample of age-matched independent healthy control.

first: Kristine

last: Freude


title: RNA association patterns of Salmonella cold shock proteins direct discovery of essential virulence function of CspC and CspE

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: The functions of many bacterial RNA-binding proteins remain obscure due to a lack of knowledge of their cellular ligands. While well-studied cold-shock protein A (CspA) family members are induced and function at low temperature, other are highly expressed in infection-relevant conditions. Here, RNA ligand profiling of all CspA-family members linked CspC and CspE with Salmonella virulence pathways. Phenotypic assays in vitro demonstrated a crucial role for these proteins in membrane stress, motility, and biofilm formation. Moreover, deletion of cspC and cspE fully attenuates Salmonella in systemic mouse infection. Our results highlight RNA-binding proteins as regulators of pathogenicity and potential targets of antimicrobial therapy.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: RIP-seq of bacterial cold-shock proteins; in vitro RNA-seq; RNA-seq in cell culture

first: Charlotte

last: Michaux


title: H3 ubiquitination by NEDD4 regulates H3 acetylation and

city: New York

first: Xian

address: 580 main st apt 138

institute: MSKCC

summary: genome wide occupancy related to H3 ubiquitination at K23/36/37

overall_design: FK2 antibody occupancy comparing WT and H3 K23/36/37R restored Hep3B cells

first: Hui-Kuan

last: Lin


title: The Transcription Factor T-bet Limits Amplification of Type I IFN Transcriptome and Circuitry in T Helper 1 Cells

city: Bethesda

first: Fred

middle: P.

last: Davis

state: MD

address: 9000 Rockville Pike

department: NIAMS

institute: NIH

summary: Host defense requires the specification of CD4+ helper T (Th) cells into distinct fates including Th1 cells that preferentially produce interferon γ(IFN-γ  ).IFN-γ  , a member of a large family of anti-pathogenic and anti-tumor IFNs, induces T-bet, a lineage defining transcription factor for Th1 cells, which in turn supports IFN-γ   production in a feed-forward manner. Herein, we show a cell intrinsic role of T- bet to influence how T cells perceive their secreted product in the environment. In the absence of T-bet, IFN-γ   aberrantly induces a type I IFN transcriptomic program. T-bet preferentially represses genes and pathways ordinarily activated by type I IFNs to ensure that its transcriptional response does not evoke an aberrant amplification of type I IFN signaling circuitry otherwise triggered by its own product.

overall_design: Integrated analysis of epigenome and transcriptome data from activated T helper cells cultured under either IFN-γ  or IFN-β stimulation

first: S

last: Iwata

first: Y

last: Mikami

first: H

last: Sun

last: Brooks

first: D

last: Jankovic

first: K

last: Hirahara

first: A

last: Onodera

middle: Y

last: Shih

first: T

last: Kawabe

last: Jiang

last: Nakayama

last: Sher

first: J

middle: J

last: O'Shea

first: F

middle: P

last: Kanno


title: Targeted next generation sequencing of 589 genes identifies complementary responses in t-helper-like T regulatory cells

city: London

first: Reuben

last: McGregor

address: Great Maze Pond

country: United Kingdom

institute: Kings College London

summary: Regulatory T-cells (Tregs) play a pivotal role in maintaining peripheral immunological tolerance, by preventing autoimmunity and chronic inflammation. However, they can also play a parallel role in the promotion of antitumor responses. Tregs can be classified as T helper (Th)-like Tregs that phenotypically resemble Th1/Th2/Th17/TH1-TH17 lineages based upon the expression of specific chemokine receptors and transcription factors. The distribution of these Treg subsets can provide mechanistic insights into disease processes, therefore we sought to characterise their immune transcriptome. Targeted RNA sequencing revealed that circulating Th2-like Tregs displayed higher viability and activation as well as suggesting specific disease pathways associated to sifferent T reg subtypes.

overall_design: 2x105 FACS-sorted Th-like Tregs (TH1, TH2, TH17 abnd TH1-TH17) from 3 donors were activated with CD3/CD28 beads (ratio 1:4) for 72h. Cells were lysed in Trizol and RNA was isolated. RNA sequencing was performed using The Human Inflammation & Immunity Transcriptome RNA targeted panel (Qiagen). Samples were sequenced with Illumina MiSeq using MiSeq Reagent Kit v3 (150-cycle).

first: Estefania

middle: N

last: Lamperti


title: DLX3 binding sites in Supabasal Keratinocytes

first: Hong-wei

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary: DLX3 is a homeodomain transcription factor involved in epidermal differentiation.  Here we investigated the distribution of DLX3 DNA binding sites in suprabasal differentiating keratinocytes using ChIP-seq.

overall_design: Suprabasal keratinocytes were isolated from neonatal mice epidermis by Percoll gradient and used for ChIP-seq analysis using anti-DLX3 and anti-H3K4me3 antibodies.

first: Meghan

last: Kellett

first: Paul

middle: W

last: Bible

first: Gustavo

last: Gutierrez-Cruz

first: Stephen

middle: R

first: Hong-Wei

first: Maria

middle: I

last: Morasso


title: Che-1 sustains hypoxic response of colorectal cancer cells by affecting Hif-1α stabilization

city: Rome

first: Matteo

last: Pallocca

address: Via Fermo Ognibene

institute: Italian National Cancer Institute "Regina Elena"

summary:
Solid tumors are less oxygenated than normal tissues, and for this reason the cancer cells have developed several molecular mechanisms of adaptation to hypoxic environment. Moreover, his poor oxygenation is a major indicator of an adverse prognosis and leads resistance to standard anticancer treatment. Previous reports from this laboratory showed an involvement of Che-1/AATF (Che-1) in cancer cell survival under stress conditions, and on the basis of these observations, we hypothesized that Che-1 might have a role in the response of cancer cells to hypoxia.
Methods: The human colon adenocarcinoma cell line HCT116 depleted or not for Che-1 by siRNA, was subjected to normoxic and hypoxic conditions to perform studies about the role of this protein in metabolic adaptation and cell proliferation. The expression of Che-1 under normoxia or hypoxia was detected using western blot assays; cell metabolism was assessed by NMR spectroscopy and functional assays. Further molecular studies were performed by RNA seq, qRT-PCR and ChIP analysis.
Results: In this paper we report that Che-1 expression is required for the adaptation of the cells to hypoxia, playing and important role in metabolic modulation. Indeed, Che-1 depletion impacted on glycolysis by altering the expression of several genes involved in the response to hypoxia by modulating the levels of HIF-1alpha.
Conclusions: These data demonstrate a novel player in the regulation of a HIF1alpha in response to hypoxia. We found that the transcriptional down-regulation of a members of E3 ubiquitin ligase family SIAH2 by Che-1, produces a failure in the degradation by the hydroxylase PHD3 with a decrease in HIF-1alpha levels during hypoxia.

overall_design: The human colon adenocarcinoma cell line HCT116 depleted or not for Che-1 by siRNA was profiled for mRNA high-troughput sequencing (RNA-seq)

first: Bruno

last: Tiziana

first: Pallocca

last: Matteo

first: Fanciulli

last: Maurizio