title: Kmt5a Controls Hepatic Metabolic Pathways by Facilitating RNA Pol II Release from Promoter-Proximal Regions

city: Vassilika Vouton, Herakleion

first: Iannis

last: Talianidis

state: Crete

address: 100 N. Plastira Str

department: Institute of Molecular Biology and Biotechnology

country: Greece

institute: Foundation for Research and Technology - Hellas

summary: H4K20 monomethylation maintains genome integrity by regulating proper mitotic condensation, DNA damage response and replication licensing. Here we show that in non-dividing hepatic cells H4K20Me1 is specifically enriched in the gene bodies of active genes and dynamically regulated by the antagonistic action of PR-Set7 methylase and Phf8 demethylase. In liver-specific PR-Set7-deficient mice, reduced H4K20Me1 levels primarily affected RNAPII release from promoter-proximal regions. Glucose and fatty acid metabolic genes were highly sensitive to impaired RNAPII release. Downregulation of glycolytic genes resulted in an energy starvation condition partially compensated by AMPK activation and increased mitochondrial activity. This metabolic reprogramming generated a normoglycemic, but highly sensitized state, which upon different metabolic stress conditions, quickly aggravated into a senescent phenotype initiated by ROS overproduction and oxidative DNA damage. The results illustrate how defects in the general process of RNAPII transition into elongation phase can trigger specific metabolic changes, which lead to genome instability.

overall_design: PR-Set7 (other name Set8; Setd8) knockout mice (other name Set8; Setd8) were generated by crossing PR-SET7loxp mice carrying floxed exon 7 allele of PR-SET7 (Oda et al., 2009) with Alb-Cre mice (Yakar et al., 1999) in mixed F1 background. Mice (WT = Wild type; Set8-KO = Setd8-KO; PR-SET7-KO) were sacrificed at 45 days postnatal age. Livers from these mice were used for ChIP-seq and RNA-seq approaches. For Global Run-On sequencing newly synthesized RNA GRO-EU-seq, mice were treated with xxx mg /g bodyweight Ethydyl-Uridine (EU) before sacrifice. For the GRO-Br-seq experiments nuclei were prepared from the livers and treated with Br-UTP for 3 minutes.

first: Kostas

last: Nikolaou

first: Panagiotis

last: Moulos

first: Vangelis

last: Harokopos

first: George

last: Chalepakis


title: genome-wide analysis of replication timing by repli-chip and repli-seq

status: Public on Jul 28 2017

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

country: USA

institute: Florida State University

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: RNA-seq in HT-29 colorectal cancer cells after F. nucleatum treatment

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

country: China

institute: Renji Hospital

type: Expression profiling by high throughput sequencing

summary: To elucidate whether F. nucleatum plays a role in colorectal cancer tumorigenesis,  RNA-seq analysis was performed to compare the gene expression profiles of F. nucleatum treated HT-29 cell line or not.

overall_design: RNA-seq was performed in HT-29 colorectal cancer cells after  F. nucleatum treatment

first: Jie

last: Hong


title: The RhoJ-BAD Signaling Network: An Achilles Heel for BRAF Mutant Melanomas

status: Public on Jul 26 2017

city: Irvine

first: Anand

last: Ganesan

state: CA

address: 836 Health Science Rd

department: Dermatology

institute: University of California, Irvine

summary: Genes and pathways that allow cells to cope with oncogene-induced stress represent selective cancer therapeutic targets that remain largely undiscovered. In this study, we identify a RhoJ signaling pathway that is a selective therapeutic target for BRAF mutant cells. RhoJ deletion in BRAF mutant melanocytes modulates the expression of the pro-apoptotic protein BAD as well as genes involved in cellular metabolism, impairing nevus formation, cellular transformation, and metastasis. Short-term treatment of nascent melanoma tumors with PAK inhibitors that block RhoJ signaling halts the growth of BRAF mutant melanoma tumors in vivo and induces apoptosis in melanoma cells in vitro via a BAD-dependent mechanism. As up to 50% of BRAF mutant human melanomas express high levels of RhoJ, these studies nominate the RhoJ-BAD signaling network as a therapeutic vulnerability for fledgling BRAF mutant human tumors.

overall_design: 5 Braf CA/+; Pten fl/+; Cre +; RhoJ +/+ melanoma tumors from mice were compared to 5 Braf CA/+; Pten fl/+; Cre +; RhoJ -/- melanoma tumors. Standard RNA isolation progocols were used.

first: Rolando

last: Ruiz


title: The role of FAM46C in myeloma cells [sequencing]

city: Rochester

first: Xuewei

last: Wang

address: 200 1st street

institute: Mayo Clinic

summary: FAM46C is one of the most recurrently mutated genes in multiple myeloma (MM), however its role in disease pathogenesis is not determined. Here we demonstrate that wild type (WT) FAM46C overexpression induces substantial cytotoxicity in MM cells. In contrast, FAM46C mutations found in MM patients abrogate this cytotoxicity indicating a MM survival advantage conferred by the FAM46C mutant phenotype. WT FAM46C overexpression downregulated IRF4, CEBPB, MYC and upregulated immunoglobulin (Ig) light chain and HSPA5/BIP. Furthermore, pathway analysis suggests that enforced FAM46C expression activates the unfolded protein response (UPR) pathway and induces mitochondrial dysfunction. In contrast, endogenous CRISPR FAM46C depletion enhanced MM cell growth and notably decreasing Ig light chain and BIP expression, activating of ERK and anti-apoptotic signaling and conferring relative resistance to dexamethasone and lenalidomide treatment. The genes altered in FAM46C depleted cells are enriched for signaling pathways regulating estrogen, glucocorticoid, B cell receptor signaling and ATM signaling. Together these results implicate FAM46C in myeloma cell growth and survival. FAM46C mutation contributes to myeloma pathogenesis and disease progression by perturbation in plasma cell differentiation and endoplasmic reticulum homeostasis.

overall_design: Two myeloma cell lines (MM1.S and KMS11) were infected with lentivirus harboring either vector (pCDH or vec) or FAM46C-expressing cassette. At day 3 after infection, cells were harvested for mRNA sequencing analysis. A total of 8 samples were analyzed, including replicates of two controls (vector) and FAM46C overexpression from each cell line.

first: Yuan

middle: X

last: Zhu

first: Chang

last: Shi

first: Esteban

last: Braggio

first: A

middle: K

last: Stewart


title: Divergent mechanisms of EZH1 regulation of heart development and regeneration

city: Chicago

first: Yong

last: Peng

state: IL

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

type: Genome binding/occupancy profiling by high throughput sequencing


title: RNA Missplicing in Fuchs Endothelial Corneal Dystrophy

first: Xiaojia

last: Tang

state: MN

address: 200 1st ST SW

summary: RNA-Seq splicing data from the corneal endothelia of FECD patients and controls reveal hundreds of differential alternative splicing events. These include events previously characterized in the context of myotonic dystrophy type 1 and epithelial-to-mesenchymal transition, as well as splicing changes in genes related to proposed mechanisms of FECD pathogenesis

overall_design: RNA-Seq was used to compare corneal endothelial specimens from subjects with Fuchs endothelial corneal dystrophy and control subjects

first: Keith

middle: H

last: Baratz

first: Eric

middle: D

last: Wieben


title: Ribosome profiling and RNA sequencing of U2OS cells overexpressing myc

status: Public on Jul 27 2017

city: Amsterdam

first: Koos

last: Rooijers

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

summary: Ribosome profiling and RNA sequencing was performed on U2OS cells, either control or overexpressing myc.

overall_design: 2 biological replicates of each condition.

first: Fabricio

last: Loayza-Puch

first: Jelle

last: Zijlstra

first: Joachim

middle: F

last: Oude Vrielink

first: Rui

last: Lopes

first: Alejandro

middle: P

last: Ugalde

first: Axel

last: Bex

first: Reuven

last: Agami


title: Deletion of the celA gene in Aspergillus nidulans triggers overexpression of secondary metabolite biosynthetic genes

city: Hautcharage

first: Gea

last: Guerriero

state: Luxembourg

address: 5, rue Bommel, Z.A.E. Robert Steichen, L-4940

department: Environmental Research and Innovation Department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology (LIST)

summary: The cell wall is a structure involved in important stages of fungal growth and morphogenesis. Several studies in the literature have shown how perturbations at the cell wall-level trigger dramatic effects on growth (e.g. Horiuchi, 2009). Despite the importance of fungal cell walls and despite the great advances made in the field, there are still missing pieces in our understanding of cell wall dynamics in filamentous fungi. Some cell wall biosynthetic genes, for example, are still uncharacterized (for a detailed inventory of Aspergillus nidulans cell wall-related genes, see de Groot et al., 2009). The chief polysaccharides in the cell wall of the model organism A. nidulans are β-glucans (β-1,3-, β-(1,3;1,4)- and β-1,6-glucans), chitin and α-1,3-glucans. While much is known about the chitin and α-1,3-glucan biosynthetic genes in A. nidulans (Horiuchi et al., 1999; Fujiwara et al., 2000; Ichinomiya et al., 2002 and 2005; Takeshita et al., 2006; Yoshimi et al., 2013), no characterization is yet available for the celA gene (ANIA_08444) encoding a putative mixed-linkage glucan synthase (de Groot et al., 2009). Recently, a study on A. fumigatus has characterized Tft1, an enzyme shown to be responsible for the production of β-(1,3;1,4)-glucans in this organism (Samar et al., 2015). Deletion of Tft1 causes no obvious phenotype in A. fumigatus and a modest increase in virulence. To characterize the role of β-(1,3;1,4)-glucans in the growth and development of filamentous fungi, we here sought to provide transcriptomics data of an A. nidulans strain showing reduced expression of the gene encoding the putative mixed linkage glucan synthase celA.

overall_design: RNA-Seq analysis of the control (SAA.111) and downregulated celA- strains of Aspergillus nidulans. Each condition consists of 3 biological replicates.

first: Lucia

last: Silvestrini

first: Sylvain

last: Legay

first: Frank

last: Maixner

first: Jean-Francois

last: Hausman

first: Joseph

last: Strauss


title: In vivo Monitoring of Transcriptional Dynamics After Lower-Limb Muscle Injury Enables Quantitative Classification of Healing

city: Lexington

first: Darrell

middle: Orlyn

last: Ricke

state: MA

address: 244 Wood Street

department: Group 48 Bioengineering Systems & Technology

institute: MIT Lincoln Laboratory

summary: Traumatic lower-limb musculoskeletal injuries are pervasive amongst athletes and the military and typically an individual returns to activity prior to fully healing, increasing a predisposition for additional injuries and chronic pain. Monitoring healing progression after a musculoskeletal injury typically involves different types of imaging but these approaches suffer from several disadvantages. Isolating and profiling transcripts from the injured site would abrogate these shortcomings and provide enumerative insights into the regenerative potential of an individual’s muscle after injury. In this study, a traumatic injury was administered to a mouse model and healing progression was examined from 3 hours to 1 month using high-throughput RNA-Sequencing (RNA-Seq). Comprehensive dissection of the genome-wide datasets revealed the injured site to be a dynamic, heterogeneous environment composed of multiple cell types and thousands of genes undergoing significant expression changes in highly regulated networks. Four independent approaches were used to determine the set of genes, isoforms, and genetic pathways most characteristic of different time points post-injury and two novel approaches were developed to classify injured tissues at different time points. These results highlight the possibility to quantitatively track healing progression in situ via transcript profiling using high- throughput sequencing.

overall_design: RNA-Seq time couse of muscle injury healing with controls

middle: O

first: Carlos

last: Aguilar


title: Divergent mechanisms of EZH1 regulation of heart development and regeneration [RNA-Seq]

first: Yong

last: Peng

summary: RNA-seq for DKO, E1KO, E2KO and WT E12.5 heart revealed that EZH1 and EZH2 play a partially redundant role to trimethylate histone H3 at Lys 27 (H3K27me3). Through EZH1, H3K27me3 and H3K27ac ChIP-seq and RNA-seq for P13 EZH1 and GFP overexpressing heart (AAVEzh1 and AAVGFP respectively) suffered MI at P10, we surprisingly found that EZH1 can active the expression of regenerating relevant genes by directly binding to the promoter of targeted genes and through a mechanism independent of H3K27me3 deposition. Together, we unravel a requirement but divergent mechanisms of EZH1 in heart development and regeneration

overall_design: For early embryonic state, RNA-seq was performed on DKO, E1KO, E2KO and WT E12.5 heart ventricular. For the MI heart, RNA-seq was performed on EZH1 and GFP overexpressing heart apex below the ligation site, the heart was injected with AAV9 expressing Ezh1 or GFP respectively. As for the sham control, RNA-seq was also performed on the heart apex part

first: Shanshan

last: Ai

first: Xianhong

last: Yu

first: Yumei

last: Li

first: Yanzhu

last: Yue

first: Chen

first: Aibin

last: He


title: RNA-seq of regenerating blastema cells in Drosophila melanogaster

status: Public on Jul 25 2017

city: URBANA

first: Sumbul

middle: J

last: Khan

address: 601 S. Goodwin Ave, CLSL C615

department: Cell and Development Biology

institute: University of Illinois at Urbana-Champaign

summary: We have carried out eukaryotic whole-genome Illumina RNA-seq of regenerating blastema cells and control undamaged wing imaginal disc cells to identify the differentially expressed genes during regeneration.

overall_design: Ablated sample vs. Control, 3 biological replicates for each

first: Rachel

last: Smith-Bolton


title: Adult Cardiac Stem Cells are Multipotent and Robustly Myogenic: c-kit Expression is Necessary but not Sufficient for their Identification

city: Catanzaro

first: Daniele

last: Torella

address: Viale Europa

department: Medical and Surgical Sciences

country: Italy

institute: Magna Graecia University

summary: Multipotent adult resident cardiac stem cells (CSCs) originally were identified by the expression of c-kit, the stem cell factor receptor. However, in the adult myocardium c-kit alone distinguish CSCs from other c-kit-expressing cardiac cells because the adult heart contains a heterogeneous mixture of c-kitpos cells, mainly composed of mast and endothelial/progenitor cells. This heterogeneity of cardiac c-kitpos cells has not been considered in recent c-kit-expressing cell fate mapping publications, which have equated the contribution of the whole heterogeneous c-kitpos population to cardiomyocyte generation in adulthood, which is minimal, to that of the CSCs, a result at odds with previous publications. To shed light on this issue, we have assessed the identity, abundancy and myogenic potential of true multipotent CSCs within the total c-kitpos cardiac cell cohort. Blood lineage-committed c-kitpos cells were removed by CD45 negative sorting to obtain a CD45negc-kitpos cell population (<10% of the total c-kitpos cells), which is enriched for cells that express c-kit at low levels and possess all properties of multipotent stem/progenitor cells in vitro. These characteristics are absent from the c-kitneg and the lineage-committed c-kitpos cardiac cells. Single Linnegc-kitpos cell-derived CSC clones, representing 1-2% of total c-kitpos cells, when instructed by TGF-b/Wnt molecules, acquire full transcriptome expression, sarcomere organization,  spontaneous contraction and electrophysiological properties of differentiated cardiomyocytes. Significantly, clonogenic CSCs have a potent cardio-regenerative/repair capacity in vivo after acute  myocardial infarction. CSC myogenic regenerative capacity is dependent on cardiomyocyte commitment through activation of the SMAD2 pathway. Such regeneration was not apparent when freshly-isolated total c-kitpos cardiac cells were administered. In conclusion, only a very small  fraction of cardiac c-kitpos cells (~1-2%) have the characteristics of multipotent CSCs but these  exhibit robust myogenic properties.

overall_design:
RNA-seq data from CSCs, iCMs, neonatal (neoCMs) and adult cardiac myocytes (aCMs) (triplicated) have been analysed and compared. Also, mRNA was collected from clonogenic undifferentiated rat CSCs, beating colonies of CSC-derived iCMs, freshly isolated cardiomyocytes obtained from the hearts of 1-2 post-natal day and from 12 week-old Wistar rats.

Please note that the datasets of CSC1,2 and 3 are from a biological triplicate of the same cardiac stem cell clone. In particular, the dataset of the sample entitled CSC1 has also been used in a different experiment with the title of cCSC4. This dataset was compared with three datasets respectively from three different cardiac stem cell clones (cCSC1, 2, and 3) for clonal identity analysis.

first: Carla

last: Vicinanza

first: Iolanda

last: Aquila

first: Mariangela

last: Scalise

first: Francesca

last: Cristiano

first: Fabiola

last: Marino

first: Annalaura

first: Pierangelo

last: Veltri

first: Bernardo

last: Nadal-Ginard

first: Georgina

last: Ellison-Hughes


title: The LncRNA NEAT1 Nests RNA Binding Proteins and the Microprocessor to Globally Enhance Pri-miRNA Processing

city: La Jolla

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNA biogenesis is known to be modulated by a variety of RNA binding proteins (RBPs), but in most cases, individual RBPs appear to influence the processing of a small number of selective targets.  We herein report binding of the NONO/PSF heterodimer to hundreds of expressed pri-miRNAs in HeLa cells to globally enhance pri-miRNA processing by the Drosha/DGCR8 Microprocessor.  As NONO/PSF are key components of paraspeckles organized by the lncRNA NEAT1, we find that NEAT1 also has profound effects on global pri-miRNA processing.  Mechanistic dissection reveals that NEAT1 broadly interacts with NONO/PSF as well as many other RBPs, and that multiple RNA segments in NEAT1, including a “pseudo pri-miRNA” near its 3’ end, help attract the Microprocessor.  These findings suggest a bird nest model for a large lncRNA to orchestrate efficient processing of an entire class of small RNAs in the nucleus.we used small RNA-seq to identify miRNA level in response to secific knockdowns relative to siGFP treatment control

overall_design: We profiled the miRNAs expression levels under conditions including siGFP(control), siNEAT1, siNEAT1_V2, siNONO, siPSF and siPSPC1 through small RNA-seq respectively.  And we also examined the in vivo interactions between NONO/PSF and RNA through CLIP-seq.

first: Li

last: Jiang

first: Changwei

last: Shao

first: Yu

last: Zhou


title: CHD1 loss sensitizes prostate cancer to DNA damaging therapy by promoting error-prone double-strand break repair

city: Beijing

first: Weilong

last: Guo

address: Intergrated Science Building

institute: Peking University

summary:
BACKGROUND:
Deletion of the chromatin remodeler CHD1 is a common genomic alteration found in human prostate cancers (PCas). CHD1 loss represents a distinct PCa subtype characterized by SPOP mutation and higher genomic instability [1-3]. However, the role of CHD1 in PCa development in vivo and its clinical utility remain unclear.
DESIGN:
To study the role of CHD1 in PCa development and its loss in clinical management, we generated a genetically engineered mouse model with prostate-specific deletion of murine Chd1 as well as isogenic CHD1 WT and homozygous deleted human benign and PCa lines. We also developed patient-derived organoid cultures and screened patients with metastatic PCa for CHD1 loss.
RESULTS:
We demonstrate that CHD1 loss sensitizes cells to DNA damage and causes a synthetic lethal response to DNA damaging therapy in vivo, ex vivo and in a patient with metastatic PCa. Mechanistically, CHD1 loss leads to decreased error-free homologous recombination (HR) repair, which is compensated by increased error-prone non-homologous end joining (NHEJ) repair for DNA double-strand break (DSB) repair.
CONCLUSIONS:
Our study provides the first in vivo and in patient evidence supporting the role of CHD1 in DSB repair and in response to DNA damaging therapy. We uncover mechanistic insights that CHD1 modulates the choice between HR and NHEJ and suggest that CHD1 loss may contribute to genomic instability seen in this subset of PCa patients.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In total, 11 murine samples and 9 human samples were analyzed. For each genotype, there are 3 to 6 replicates.

first: TR

last: Shenoy

first: G

last: Boysen

first: MY

last: Wang

first: QZ

last: Xu

first: W

first: FM

last: Koh

first: C

first: LZ

last: Zhang

first: Y

first: V

last: Gil

first: S

last: Aziz

first: Daniel

last: Nava Rodrigues

first: R

last: Christova

first: DN

last: Rodrigues

first: M

last: Crespo

first: P

last: Resign

first: N

last: Tunariu

last: Riisnaes

first: Z

last: Zafeiriohu

last: Flohr

last: Yuan

first: E

last: Knight

first: A

last: Swain

last: Ramalho-Santos

first: DY

first: J

last: de Bono

first: H

last: Wu


title: Transgenerational inheritance of mitochondrial stress adaptation in C. elegans

first: Yong

last: Peng

summary: Using Caenorhabditis elegans to investigate environmental cues-induced mitochondrial dysfunction, we found that exposure to electron transport chain (ETC) inhibitors at the parental generation initiates the transmission of heritable information to descendants and make descendants stress-adaptive. This mitochondrial stress adaptation phenotype can persist for at least three generations. Animals lacking histone H3K4me3 chromatin modifiers, or the methyltransferase of N6-methyldeoxyadenosine (6mA), lose the ability to initiate stress adaptation in progeny. H3K4me3 plays a role upstream of 6mA, while both mark promoter regions of mitochondrial unfolded protein response (UPR mt ) genes and activate the UPR mt pathway to alleviate mitochondrial damage.

overall_design: Profile H3K4me3 occupancy in whole body from L3-L4 mix C. elegans, worms were treated with antimycin A (AA) or not treated (NT).

first: Chengchuan

last: Ma

first: Rong

last: Niu

first: Li-Wa

last: Shao

first: Ye

last: Wang

first: Guifang

last: Jia

first: Aibin

last: He

first: Chuan

first: Ying

last: Liu


title: Mechanisms of transcription factor-mediated direct reprogramming of mouse embryonic stem cells to trophoblast stem-like cells

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway NMS 4.246

department: Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology

institute: University of Texas at Austin

summary: Direct reprogramming can be achieved by forced expression of transcription factors (TFs). Yet how such TFs mediate repression of initial cell-type-specific genes while activating target cell-type-specific genes is unclear. Here, we achieve embryonic stem (ES) to trophoblast stem (TS)-like cell reprogramming by introducing individual TS-specific “CAG” factors (Cdx2, Arid3a, Gata3). We interrogated their chromosomal target occupancies, modulation of global transcriptome and chromatin accessibility at the initial stage of reprograming. Our findings uncovered a sequential, two-step mechanism of cellular reprogramming in which repression of exiting ES pluripotency is followed by activated conversion to TS cells by CAG factors.

overall_design: TS-like cells were generated from ES cells using CAG factors, followed by deep sequencing, using Illumina


title: Bmp signaling maintains a mesoderm progenitor cell state in the mouse tailbud

city: Montreal

first: Maxime

last: Bouchard

state: Québec

address: 1160 Pine Avenue West, Rm 408

department: Biochemistry

country: Canada

institute: McGill University

summary: Caudal somites are generated from a pool of progenitor cells located in the tailbud region. These progenitor cells form the presomitic mesoderm that gradually differentiates into somites under the action of the segmentation clock. The signals responsible for tailbud mesoderm progenitor pool maintenance during axial elongation are still elusive. Here, we show that Bmp signaling is sufficient to activate the entire mesoderm progenitor gene signature in primary cultures of caudal mesoderm cells. Bmp signaling acts through the key regulatory genes Brachyury (T) and Nkx1-2 and contributes to the activation of several other regulators of the mesoderm progenitor gene network. In the absence of Bmp signaling, tailbud mesoderm progenitor cells acquire aberrant gene expression signatures of the heart, blood, muscle and skeletal embryonic lineages. Treatment of embryos with the Bmp inhibitor Noggin confirmed the requirement for Bmp signaling for normal Brachyury expression and the prevention of abnormal lineage marker activation. Together, these results identify Bmp signaling as a non-cell autonomous signal necessary for mesoderm progenitor cell homeostasis.

overall_design: Examination of the effect of growth factors on specification of primary mesoderm progenitor cells isolated from embryonic mice

first: Maxwell

middle: E

last: Shafer


title: Orphan box C/D snoRNAs guide rRNA base acetylations in yeast

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

summary: Box C/D snoRNAs snR4 and snR45, whose role was unknown, guide 18S rRNA acetylations by Kre33 in yeast. UV-crosslinking (CRAC) was used to determine binding sites of Kre33 on RNA.

overall_design: Duplicate data-sets of cDNA reads of RNAs UV-crosslinked to Kre33-HTP in vivo using the CRAC protocol. Cells were in mid-log phase when irradiated, immediately collected by filtration and frozen

first: Rob

last: van Nues


title: Integrative analysis of DNA methylation and expression during EPC differentiation_MeDIP-Seq

city: Daejeon

first: Yukyung

last: Jun

address: 245 Daehak-ro, Yuseong-gu

department: Center for Supercomputing Applications

country: South Korea

institute: Korea Institute of Science and Technology Information

type: Methylation profiling by high throughput sequencing

summary: Analysis of DNA methylation and gene expression changes during regulated endothelial progenitor cells (EPCs) to outgrowth endothelial cells (OECs). Results provide information of DNA methylation and gene expression pattern during cord-blood derived EPCs differentiation. Taken together, we discovered specific set of genes regulated by hyper- and hypo-methylation during differentiation.

overall_design: mRNA and MeDIP seq using total RNA and genomic DNA isolated from cord blood-derived EPCs and OECs.

first: YoonJeong

last: Jeong

first: Young-Guen

last: Kwon

first: Sanghyuk

last: Lee


title: Exploration of bovine milk exosomal microRNAs during Streptococcus uberis induced mastitis

city: beltsvill

first: jiajie

last: sun

state: MD

address: 10300 BALTIMORE AVENUE

department: Agriculture research sevice

institute: U.S. department of agriculture

summary: Milk is an indispensable source of infant nutrition in all mammals, made up of complex constituents needed for infant nourishment and immunity. Comparison of miRNA profiles between infected and non-infected/control Holstein cattle could provide important information on the differences in composition of milk at the level of miRNA, if any, and broaden our perspective and understanding of the effect of pathology on cellular compositions and functions. In the present study we therefore analyzed the expression profiles of bovine milk exosomal miRNAs during S. uberis infection and identified 328 known miRNAs and 82 high-confidence miRNA candidates by deep sequencing. The top 10 miRNAs in both control and infected replicates accounted for approximately 80% of total counts, which were predicted to target 605 genes using two computational approaches. In addition, 15 significantly differentially expressed miRNAs were identified between control and infected replicates during S. uberis infection, and a total of 1,852 unique genes were predicted to be targeted by these miRNAs. Ingenuity Canonical Pathways and Diseases and Biological Function analyses using IPA indicated that the identified miRNAs targets mainly enriched in regulating the innate and adaptive immune responses in newborns, as well as infant growth and development. The characterization of these miRNAs could contribute to a better understanding of the molecular mechanisms involved in lactation physiology and milk imparted immune function in the dairy cattle.

overall_design: Three exosomal small RNA libraries were constructed from S. uberis  infected bovine breast milk at 2 days post-infection (dpi), and correspondingly three libraries from bovine milk prior to infection were used as controls. They were named control (1, 2 and 3) and infection (1, 2 and 3), respectively.

first: JIAJIE

last: SUN

first: Tad

middle: S

last: Sonstegard

first: Kshama

last: Aswath


title: RNA sequencing analysis of the Lewis versus Brown Norway rat, with or without Toxoplasma gondii infection

status: Public on Jul 24 2017

city: Urbana

first: William

middle: Harold

last: Witola

state: Illinois

address: 2001 South Lincoln Avenue

department: Pathobiology

summary: Rats vary in their susceptibilities to Toxoplasma gondii infection depending on the rat strain. Compared to the T. gondii-susceptible Brown Norway (BN) rat, the Lewis (LEW) rat is extremely resistant to T. gondii. Thus, these two rat strains are ideal models for elucidating host mechanisms that are important for host resistance to T. gondii infection. Therefore, in an attempt to unravel molecular factors directing the protective early innate immune responses in the LEW rat, we performed RNA sequencing analysis of the LEW versus BN rat, with or without T. gondii infection.

overall_design: Total RNA was obtained from fresh peritoneal cells of LEW and BN rats (with or without T. gondii infection), 24 hours post-infection. RNA libraries were generated using the Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). The libraries were quantitated by fluorometry (Qubit), and their quality determined using a Bioanalyzer. The libraries were then diluted and quantified by qPCR. Sequencing of the RNA libraries was done using a HiSeq SBS sequencing kit version 4 and a HiSeq2500 system (Illumina). Residual adapter content and low quality bases on the generated sequences were trimmed using Trimmomatic (version 0.33), while the bcl2fastq v2.17.1.14 Conversion Software (Illumina) was used to generate and demultiplex Fastq files from the sequence data. ASCII offset of 33 known as Sanger scores were used to determine the quality scores line in fastq files. Feature Counts in the Sub-read (version 1.5.0) package were used to derive gene counts, while gene annotations, including gene ontology terms, were downloaded from Ensembl Release 84 for Rnor_6.0, and ToxoDB.org Release 28 for T. gondii GT1. Samtools (v. 1.3) idxstats tool was used to determine the number of reads mapping to each rat chromosome and to the T. gondii genome. By ANOVA, using a false discovery rate (FDR) of 0.05, genes’ expression patterns related to the four experimental groups (T. gondii-infected and uninfected LEW and BN rat groups; n = 4 per group) were generated with reads ranging from 13.1 – 18.3 million per sample that aligned uniquely within 32,662 rat genes and 8,637 T. gondii genes.

first: Chi Yong

first: Xuejin

last: Zhang


title: Integrative analysis of DNA methylation and expression during EPC differentiation_mRNA-Seq


title: Multi-cellular Transcriptional Profiling Reveals an Epigenetic Barrier to Adult Heart Regeneration [RNA-Seq]

city: Melbourne

first: Mark

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

summary: Background - The inability of the adult mammalian heart to regenerate following injury represents a major barrier in cardiovascular medicine. In contrast, the neonatal mammalian heart retains a transient capacity for regeneration, which is lost shortly after birth. Defining the molecular mechanisms that govern regenerative capacity in the neonatal period remains a central goal in cardiac biology. Here, we construct a transcriptional atlas of multiple cardiac cell populations, which enables comparative analyses of the regenerative (neonatal) versus non-regenerative (adult) state for the first time.  Methods - Cardiomyocytes, fibroblasts, leukocytes and endothelial cells from infarcted and non-infarcted neonatal (P1) and adult (P56) hearts were isolated by enzymatic dissociation and FACS. RNA sequencing (RNA-seq) was performed on these cell populations to generate a transcriptomic atlas of the major cardiac cell populations during cardiac development, repair and regeneration. In addition, we surveyed the epigenetic landscape of cardiomyocytes during post-natal maturation by performing deep sequencing of accessible chromatin regions using the Assay for Transposase-Accessible Chromatin (ATAC-seq) from purified cardiomyocyte nuclei (P1, P14 and P56).  Results - Profiling of cardiomyocyte and non-myocyte transcriptional programs uncovered several injury responsive genes across regenerative and non-regenerative time points. However, the majority of transcriptional changes in all cardiac cell types resulted from developmental maturation from neonatal stages to adulthood rather than activation of a distinct regeneration-specific gene program. Furthermore, adult leukocytes and fibroblasts reverted to a neonatal state and re-activated a neonatal proliferative network following infarction. In contrast, cardiomyocytes failed to re-activate the neonatal proliferative network following infarction, which was associated with loss of chromatin accessibility around cell cycle genes during post-natal maturation.  Conclusions – This work provides a comprehensive transcriptional resource of multiple cardiac cell populations during cardiac development, repair and regeneration. Our findings define a transcriptional program underpinning the neonatal regenerative state and identifies an epigenetic barrier to re-induction of the regenerative program in adult cardiomyocytes.

overall_design: Examination of RNA expression in developing cardiomyocytes isolated at P1 (day 1), P14 (day 14) and P56 (day 56 since birth) in biological triplicate

first: Choon

middle: B

last: Sim

first: Gregory

middle: A

last: Quaife-Ryan

first: Antony

last: Kaspi

first: Haloom

last: Rafehi

first: Mirana

last: Ramialison

first: Assam

last: El-Osta

first: James

last: Hudson

first: Enzo

middle: R

last: Porrello


title: Multi-cellular Transcriptional Profiling Reveals an Epigenetic Barrier to Adult Heart Regeneration

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

overall_design: Refer to individual Series


title: Application of next generation sequencing approaches to assess effects of PDE12 knockout on the mitochondrial transcriptome

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

institute: University of Cambridge

summary:
Approach 1, RNAseq: Knockout of the mitochondrial poly(A) specific exoribonuclease PDE12 led to a severe defect in mitochondrial translation. We aimed to assess the effects of the absence of PDE12 on the differential expression or aberrant accumulation of mitochondrial mRNA transcripts or anti-sense RNAs.  We performed RNA-seq of mitochondrial-enriched RNA from PDE12+/+ and PDE12-/- cell lines, in triplicate using Illumina MiSeq following library generation using TruSeq Stranded Total RNA library prep kit. Knockout of PDE12 did not indicate changes to the steady-state levels of mitochondrial mRNAs nor to accumulation of aberrant non-coding transcripts which would explain the strong mitochondrial translation defect observed in PDE12-/- cells
Approach 2, MPAT-Seq: We aimed to assess the nature of 3' extensions to mitochondrial tRNAs. Mitochondrial poly(A) tail length (MPAT) assay was performed using total RNA from PDE12+/+ and PDE12-/- cells with either endogenous or overexpressed levels of mtPAP, or PDE12-/- expressing either wildtype or E351A catalytic mutant PDE12. In this assay 3' DNA adaptor (LIGN) were ligated to the 3' ends of total RNA followed by reverse transcription using anti-LIGN primer. Transcript specific PCRs were generated for each mt-tRNA and pooled for each cell line. Illumina sequencing libraries were prepared via A tailing and ligation of TruSeq adapters from a TruSeq LT kit and sequenced using Illumina MiSeq. This analysis confirmed extensions present on the 3' ends of various mitochondrial tRNAs were adenylate in nature. Different mitochondrial tRNAs were affected by spurious adenylation to varying degrees.

overall_design: Examination of effect of PDE12 knockout to mitochondrial transcriptome

first: Sarah

last: Pearce


title: An HDAC3-PROX1 Corepressor Module Acts on HNF4α to Control Hepatic Triglycerides

city: Boston

first: Manashree

last: Damle

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary: The histone deacetylase HDAC3 is a critical mediator of hepatic lipid metabolism, and liver-specific deletion of HDAC3 leads to fatty liver. To elucidate the underlying mechanism we developed a method of cross-linking followed by mass spectrometry to define a high-confidence HDAC3 interactome in vivo that includes the canonical NCoR/HDAC3 complex as well as Prospero-related homeobox 1 protein (PROX1). HDAC3 and PROX1 co-localize extensively on the mouse liver genome, and are co-recruited by Hepatocyte Nuclear Factor 4α (HNF4α). The HDAC3-PROX1 module controls the expression of a gene program regulating lipid homeostasis, and hepatic-specific ablation of either component increases triglyceride content in liver. These findings underscore the importance of specific combinations of transcription factors and coregulators in the fine tuning of organismal metabolism.

overall_design: Biological replicates were uploaded in separated files and indicated in the file names.

first: Sean

last: Armour

first: Jarrett

last: Remsberg

first: Simone

last: Sidoli

first: Wesley

middle: Y

last: Ho

first: Zhenghui

last: Li

first: Benjamin

last: Garcia

first: Mitchell

last: Lazar


title: Multi-cellular Transcriptional Profiling Reveals an Epigenetic Barrier to Adult Heart Regeneration [ATAC-Seq]

first: Mark

last: Ziemann

overall_design: Examination of chromatin accessibility in developing cardiomyocytes isolated at P1 (day 1), P14 (day 14) and P56 (day 56 since birth) in biological triplicate

first: Choon

last: Sim

first: Gregory

last: Quaife-Ryan


title: Genome-wide map of H4K8ac in Plasmodium falciparum

city: Singapore

first: Zbynek

last: Bozdech

state: Select if applicable

department: Molecular Genetics&Cell Biology

country: Singapore

institute: Nanyang Technological University

summary: P. falciparum H4K8ac ChIP-seq

overall_design: ChIP-seq was performed at 3 stages across the intra-erythrocytic cycle of P. falciparum

first: Archana

last: Gupta

first: Lei

last: Zhu


title: Integrative analysis of DNA methylation and expression during EPC differentiation

first: Yukyung

last: Jun


title: Transcriptome analysis to investigate the oncogenic TGF-β-Smad-Snail signaling pathway

city: Seoul

first: Simon

middle: Weonsang

last: Ro

address: Yonsei-ro 50-1

department: Institute of Gastroenterology

institute: Yonsei University College of Medicine

summary: Our study shows that TGF-β signaling promotes tumorigenesis in the  liver through upregulation of its target gene, Snail. We explored gene expression changes in tumors following TGF-β inhibition, and tumors ectopically expressing Snail with the TGF-β inhibition. RNA samples were harvested from tumors expressing Smad7 (S7HP tumors), firefly luciferase (LHP tumors), and Smad7 plus Snail (S7HP+Snail), respectively. Differentially expressed genes were investigated in LHP and S7HP+Snail tumors, compared with S7HP tumors.

overall_design: mRNA profiles of LHP, S7HP, and S7HP+Snail tumors were generated, in triplicate, by RNA-sequencing

first: Hyuk

last: Moon

first: Kyung

last: Cho

middle: W


title: Neural circuit-specialized astrocytes: genomic, proteomic, morphological and functional evidence

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: The Khakh laboratory used Aldh1l1-Cre/ERT2 transgenic mouse line crossed with RiboTag mice to sequence actively translated mRNAs and compare striatal and hippocampal astrocyte transcriptomes from adults.

overall_design: Whole striata and hippocampii were extracted from 4 adult (P63) male and female Aldh1l1-Cre/ERT2 x Ribotag mice. After homogenization, RNA was purified from (i) cleared lysate as the input and control, and (ii) astrocyte-specific ribosome-associated RNA precipitated via a hemagglutinin (HA) tag.

first: Hua

last: Chai

first: Blanca

last: Diaz-Castro

first: Eiji

last: Shigetomi

first: Emma

last: Monte

first: Pradeep

last: Rajendran

first: Thomas

middle: M

last: Vondriska

first: Whitaker

last: Cohn

first: Julian

last: Whitelegge

first: Baljit

last: Khakh


title: Multicellular Transcriptional Analysis of Mammalian Heart Regeneration

city: Brisbane

first: James

last: Hudson

state: QLD

address: 300 Herston Rd

institute: QIMR Berghofer Medical Research Institute

summary: The inability of the adult mammalian heart to regenerate following injury represents a major barrier in cardiovascular medicine. In contrast, the neonatal mammalian heart retains a transient capacity for regeneration, which is lost shortly after birth. Defining the molecular mechanisms that govern regenerative capacity in the neonatal period remains a central goal in cardiac biology. Here, we construct a transcriptional atlas of multiple cardiac cell populations, which enables comparative analyses of the regenerative (neonatal) versus non-regenerative (adult) state for the first time. This work provides a comprehensive transcriptional resource of multiple cardiac cell populations during cardiac development, repair and regeneration. Our findings define a transcriptional program underpinning the neonatal regenerative state and identifies an epigenetic barrier to re-induction of the regenerative program in adult cardiomyocytes.

overall_design: Cardiomyocytes, fibroblasts, leukocytes and endothelial cells from infarcted and non-infarcted neonatal (P1) and adult (P56)  hearts were isolated by enzymatic dissociation and FACS. RNA sequencing (RNA-seq) was performed on these cell populations to generate a transcriptomic atlas of the major cardiac cell populations during cardiac development, repair and regeneration. In addition, we surveyed the epigenetic landscape of cardiomyocytes during post-natal maturation by performing deep sequencing of accessible chromatin regions using the Assay for Transposase-Accessible Chromatin (ATAC-seq) from purified cardiomyocyte nuclei (P1, P14 and P56).

first: Gregory

last: Quaife-Ryan

first: Enzo

last: Porrello


title: Stable Inheritance of Spontaneous Epialleles in Arabidopsis thaliana

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: This research uses consecutive generations of two independent mutation accumulation (MA) lines in model organism A. thaliana to understand transgenerational stability of epialleles via self-fertilization. With whole-genome bisulfite sequencing, regions of instability were identified and quantified. The vast majority of the methylated genome is stably inherited to offspring and the identified unstable regions do not change frequently between generations. Additionally, an epigenetic cross of two MA lines was created to understand inheritance patterns of epialleles via outcrossing in the absence of genetic variation. Whole-genome bisulfite sequencing was used to predict epigenotype of the offspring without single nucleotide polymorphisms. In regions of differential methylation between the parents, about half of regions show predictable inheritance.

overall_design: Eight and ten nearly consequetive generations from Arabidopsis thaliana mutation accumulation lines; genetic cross of two individuals from different MA lines, parents, twenty F2s, individuals of two generations of single-seed decent from the parents

first: Brigitte

middle: T

last: Hofmeister


title: Transcriptome analysis of Escherichia coli under deoxynivalenol and nivalenol conditions

status: Public on Jul 23 2017

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

institute: Pusan National University

summary: We constructed E. coli transcriptome under deoxynivalenol (DON) and nivalenol (NIV) condition from Fusarium spp. To identify differentially expressed genes in mycotoxin condition, we compared mycotoxin (DON and NIV) transcriptome to acetonitrile (ACN) transcriptome as the solvent of myxotoxin. As a result, 435-929 transcripts were identified from all conditions, respectively.

overall_design: Two deoxynivalenol (0.2 ppm and 2 ppm), two nivalenol (0.2 ppm and 2 ppm) and one acetonitrile (control) RNA-seq data in E. coli

first: Jungkwan

last: Lee

first: Young-Su

last: Seo


title: Next Generation Sequencing Analysis of Wild Type and fl3 Transcriptomes in 10DAP(day after pollination) endosperm

status: Public on Jul 22 2017

city: Shanghai

first: Jie-chen

last: Wang

address: 300 Fenglin Road

institute: SIPPE, CAS

summary: Maize floury3 (fl3) is a classic semi-dominant mutant that shows severe defects in the endosperm but appears normal in the plant.The goals of this study are to compare WT to fl3 transcriptomes in 10DAP(day after pollination) endosperm by Next Generation Sequencing.

overall_design: 10 DAF endosperm of WT and fl3 were used to compare the gene expression, and three independent biological replicates for each material.

first: Qi

last: Li

first: Yongrui

last: Wu


title: RNA-sequencing of Mbd3-null and control haematopoietic stem cell and lymphoid progenitor cell populations

first: Stephen

middle: John

last: Loughran

address: Wellcome Trust/MRC building, Addenbrooke's Hospital

department: Haematology

summary: To determine the role of Mbd3/NuRD in lymphopoiesis, gene expression in purified populations of Mbd3-deleted and control lymphoid progenitor cells was analysed using RNA-seq.

overall_design: Mbd3-deficient and control lymphoid progenitors were isolated from mouse bone marrow by flow cytometry, including haematopoietic stem cells (HSCs), lymphoid-primed multipotent progenitors (LMPPs), all-lymphoid progenitors (ALPs) and B cell-biased lymphoid progenitors (BLPs). RNA-seq was performed on 100 HSCs or 150 cells from the other populuations, using the previously described smartseq2 protocol for RNA-seq of small numbers of cells (Picelli et al. (2014) Nature protocols 9:171).


title: DNA methyltransferase 3b regulates articular cartilage homeostasis by altering chondrocyte metabolism

city: SAINT LOUIS

first: Daofeng

state: MO

address: 4515 McKinley Avenue

institute: Washington University in St. Louis

summary: Osteoarthritis (OA) is the most common form of arthritis worldwide. It is a complex disease affecting the whole joint but is generally characterized by progressive degradation of articular cartilage. Recent genome-wide association screens have implicated distinct DNA methylation signatures in OA patients. We show that the de novo DNA methyltransferase (Dnmt) 3b, but not Dnmt3a, is present in healthy murine and human articular chondrocytes and expression decreases in OA mouse models and in chondrocytes from human OA patients. Targeted deletion of Dnmt3b in murine articular chondrocytes results in an early onset and progressive post-natal OA-like pathology. RNA-seq and MethylC-seq analyses of Dnmt3b loss-of-function chondrocytes shows that cellular metabolic processes are affected. Specifically, TCA metabolites and mitochondrial respiration are elevated. Importantly, a chondroprotective effect was found following Dnmt3b gain-of-function in murine articular chondrocytes in vitro and in vivo. This study shows that Dnmt3b plays a significant role in regulating post-natal articular cartilage homeostasis. Cellular pathways regulated by Dnmt3b in chondrocytes may provide novel targets for therapeutic approaches to treat OA.

overall_design: RNA-seq and whole-genome bisulfite sequencing (WGBS) of DNMT3b knockout and control samples in mouse.

first: Jie

last: Shen

first: Cuicui

first: Jason

last: Meyer

first: John

last: Ashton Ting Wang

first: Audrey

last: McAlinden

first: Regis

last: O'Keefe


title: SPOP mutation confers intrinsic BET inhibitor resistance in prostate cancer (BRD4_JQ1_RNA-seq)

city: San Antonio

first: Zhenqing

last: Ye

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

summary: Bromodomain and extraterminal domain (BET) protein inhibitors are emerging as promising therapeutics of cancers including prostate cancer.  The E3 ubiquitin ligase adaptor protein speckle-type POZ protein (SPOP) is implicated in human prostate cancers due to its frequent mutation.  Here we demonstrate that SPOP binds to the BET proteins BRD2, BRD3 and BRD4.  Wild-type SPOP, but not prostate cancer-associated mutants, promotes polyubiquitination and proteasome degradation of BET proteins by recognizing a common degron motif.  BET protein levels are highly elevated in SPOP-mutated prostate cancers in patients.  Expression of cancer-derived SPOP mutants upregulates cholesterol biosynthesis genes and confers resistance to the BET inhibitor in cultured prostate cancer cells and tumors in mice, and this effect can be overcome by the AKT inhibitor.  Our findings reveal BET proteins as proteolytic targets of SPOP and identify deregulated cholesterol biosynthesis as a downstream event of SPOP mutation-mediated tumorigenesis and therapy resistance in prostate cancer.

overall_design: Examination of RNA expression in  SPOP wt and mutation stable cell lines with JQ1 treatment.

first: Yu

last: Zhao

first: Wang

last: Dejie

last: Liguo

first: Huang

last: Haojie


title: MEF2C restrains microglial responses to inflammatory stimuli and is reduced upon IFN-I in brain aging

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: RNA-Seq data of micoglia  isolated from brains of indicated mouse types.

overall_design: Microglia were collected from perfused brains of mice based on FACS markers CD11b+ CD45int to lysis buffer

first: Aleksandra

last: Deczkowska

first: Orit

last: Matcovitch-Natan

first: Eyal

last: David


title: Medial Ganglionic Eminence and Cortical Organoids Model Human Brain Development and Interneuron Migration [RNA-seq]

status: Public on Jul 21 2017

city: New Haven

first: Yangfei

last: Xiang

state: CT

address: 10 Amistad St. Room 214J

institute: Yale University

summary: Organoid techniques provide unique platforms to model brain development and neurological disorders. While organoids recapitulating corticogenesis were established, a system modeling human medial ganglionic eminence (MGE) development, a critical ventral brain domain producing cortical interneurons and related lineages, remains to be developed. Here, we describe a system to generate MGE or cortex-specific organoids from human pluripotent stem cells. These organoids recapitulate the developments of MGE and cortex domains respectively. Population and single-cell transcriptomic profiling revealed transcriptional dynamics and lineage productions during MGE and cortical organoids development. Chromatin accessibility landscapes were found to be involved in this process. Furthermore, MGE and cortical organoids generated physiologically functional neurons and neuronal networks. Finally, we applied fusion organoids as a model to investigate human interneuron migration. Together, our study provides a new platform for generating domain-specific brain organoids, for modeling human interneuron migration, and offers deeper insight into molecular dynamics during human brain development.

overall_design: mRNA profiles of hMGEOs and hCOs were generated by deep sequencing

first: Yoshiaki

last: Tanaka

first: Benjamin

last: Patterson

first: In-Hyun

last: Park


title: UHRF2 regulates local 5-methylcytosine and suppresses spontaneous seizures [RNA-seq]

city: Hangzhou

first: Lin-Yu

last: Lu

state: Zhejiang

address: 268 Kaixuan Road, North Central Building, Room 536

institute: Zhejiang University

summary: 5-methylcytosine (5mC) regulates multiple cellular processes and is faithfully maintained following DNA replication. Ubiquitin-like PHD and ring finger domain-containing protein 1 (UHRF1) plays an important role in the maintenance of 5mC levels. Interestingly, UHRF1 has a paralog UHRF2 that has similar sequence and domain architecture, but the biological function of UHRF2 is not clear. Here, we have generated Uhrf2 knockout mice and characterized the role of UHRF2 in vivo. Uhrf2 knockout mice are viable, but the adult mice develop frequent spontaneous seizures and display abnormal electrical activities in brain. To explore possible mechanism beyond these phenomenon, we utilized high-throughput sequencing to identify global expression changes in Uhrf2 knockout mice brains. In addition, we explored genome-wide 5mc profiles in these samples to examine if UHRF2 regulates 5mc levels in specific genome loci.

overall_design: Examination of global gene expressions in brains of wild type and Uhrf2 knockout mice by RNA-seq.

first: Lin

first: Xiaochun

last: Yu


title: Reprogramming of human stem cells towards a rejuvenated and transformation-resisting state by recoding a single nucleotide

city: Beijing

first: Jingyi

last: Li

address: Yiheyuan Road, No.5, Haidian District

institute: Peking University

summary: Premature senescence-associated functional decay and neoplastic transformation of transplanted human stem cells or their derivatives represent two major roadblocks for regenerative medicine. Cellular senescence acts as a major mechanism antagonizing neoplastic transformation, and stem cells evading senescence are prone to oncogenic transformation. So far it is unknown whether there is any genetic code, rewriting of which can simultaneously brake cellular senescence and oncogenic transformation programs. Here, we identify a single nucleotide in human genome(target on the transcription factor NRF2) as a candidate code, switch of which blocks both senescence and transformation pathways. Genetic modification stabilizes the wild type human mesenchymal stem cells (hMSCs) at a “sustainably younger” state. More importantly, the same genetic manipulation endows hMSCs with the ability of counteracting oncogenic transformation. Our study thus provides the first proof-of-concept of genetic enhancement of human stem cells, a strategy holding potential to generate superior and safer stem cell materials for cell replacement therapy.

overall_design: RNA-seq of MSCs-NRF2 +/+_EP, MSCs-NRF2 AG/AG_EP, MSCs-NRF2 +/+_LP, MSCs-NRF2 AG/AG_LP, TMSCs-NRF2 +/+ and TMSCs-NRF2 AG/AG.

first: Xiaomeng

last: Liu

first: Jiping

last: Yang

first: Guanghui

first: Fuchou

last: Tang


title: Medial Ganglionic Eminence and Cortical Organoids Model Human Brain Development and Interneuron Migration [ATAC-seq]

overall_design: Chromatin organization profiles of hMGEOs and hCOs were generated by deep sequencing


title: Nonmuscle myosin IIB regulates epicardial integrity and epicardium-derived mesenchymal cell maturation

city: Bethesda

first: Yanqin

state: Maryland

address: 10 Center Dr.

institute: NIH

summary: Nonmuscle myosin IIB (NMIIB; heavy chain encoded by MYH10) is essential for cardiac myocyte cytokinesis. The role of NMIIB in other cardiac cells is not known. Here, we show that NMIIB is required in epicardial formation and functions to support myocardial proliferation and coronary vessel development. Ablation of NMIIB in epicardial cells results in disruption of epicardial integrity with a loss of E-cadherin at cell-cell junctions and a focal detachment of epicardial cells from the myocardium. NMIIB-knockout and blebbistatin-treated epicardial explants demonstrate impaired mesenchymal cell maturation during epicardial epithelial-mesenchymal transition. This is manifested by an impaired invasion of collagen gels by the epicardium-derived mesenchymal cells and the reorganization of the cytoskeletal structure. Although there is a marked decrease in the expression of mesenchymal genes, there is no change in Snail (also known as Snai1) or E-cadherin expression. Studies from epicardium-specific NMIIB-knockout mice confirm the importance of NMIIB for epicardial integrity and epicardial functions in promoting cardiac myocyte proliferation and coronary vessel formation during heart development. Our findings provide a novel mechanism linking epicardial formation and epicardial function to the activity of the cytoplasmic motor protein NMIIB.

overall_design: Total RNA is prepared from 8 explants each with or without treatmnet with 20mM blebbistatin.

first: Xuefei

last: Ma

first: Yoshi

last: Wakabayashi

first: Robert

last: Adelstein


title: Cell-mediated cytotoxicity (CMC) in European sea bass leucocytes

status: Public on Jul 20 2017

city: MURCIA

first: ALBERTO

last: CUESTA

state: MURCIA

address: CAMPUS UNIVERSITARIO ESPINARDO, FACULTAD BIOLOGIA

department: CELL BIOLOGY AND HISTOLOGY

country: Spain

institute: UNIVERSITY OF MURCIA

summary: Sea bass leucocytes were incubated with mock- or NNV-infected DLB-1 cell line and the cell-mediated cytotoxic activity determined

overall_design: We examine the transcriptomic profile of leucocytes under cell-mediated cytotoxicity

first: A

last: Cuesta

last: Esteve-Codina

first: J

last: Gómez-Garrido


title: TRANSCRIPTIONAL RESPONSES OF ECOLOGICALLY DIVERSE DROSOPHILA SPECIES TO LARVAL DIETS DIFFERING IN RELATIVE SUGAR AND PROTEIN RATIOS

city: Irapuato

first: NESTOR

middle: OCTAVIO

last: NAZARIO-YEPIZ

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera León

country: Mexico

institute: LANGEBIO-CINVESTAV Irapuato

summary: We utilized three ecologically diverse Drosophila species to explore the influence of ecological adaptation on transcriptomic responses to isocaloric diets differing in their relative proportions of protein to sugar. Drosophila melanogaster, a cosmopolitan species that breeds in decaying fruit, exemplifies individuals long exposed to a Western diet higher in sugar, while the natural diet of the cactophilic D. mojavensis, is much lower in carbohydrates. Drosophila arizonae, the sister species of D. mojavensis, is largely cactophilic, but also utilizes rotting fruits that are higher in sugars than cacti. We exposed third instar larvae for 24 hours to diets either (1) high in protein relative to sugar, (2) diets with equal amounts of protein and sugar, and (3) diets low in protein but high in sugar. As we predicted, based upon earlier interspecific studies of development and metabolism, the most extreme differences in gene expression under different dietary conditions were found in D. mojavensis followed by D. arizonae. No differential expression among diets was observed for D. melanogaster, a species that survives well under all three conditions, with little impact on its metabolism. We suggest that these three species together provide a model to examine individual and population differences in vulnerability to lifestyle-associated health problems such as metabolic syndrome and diabetes.

sample_organism:
Drosophila melanogaster
Drosophila mojavensis
Drosophila arizonae

overall_design: Examination of transcriptional responses on 3 species of Drosophila exposed to 3 diets differing in sugar-protein index.

first: Nestor

last: Nazario-Yepiz

first: Mariana

last: Loustalot-Laclette

first: Javier

last: Carpinteyro-Ponce

first: Cei

last: Abreu-Goodger

first: Therese

last: Markow


title: Transcriptomic analysis of wild-type and lin-22 mutants in C.elegans

city: London

first: Michalis

last: Barkoulas

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

summary: We used RNA-seq to identify gene expression changes associated with lin-22 mutations affecting seam cell pattering in C. elegans

overall_design: Total RNA was extracted from synchronised C. elegans L3 larvae

first: Dimitrios

last: Katsanos

first: Sneha

middle: L

last: Koneru


title: p53 Regulates Enhancer Accessibility and Activity in Response to DNA Damage

city: Kansas City

first: Scott

last: Younger

address: 2401 Gillham Road

institute: Children's Mercy Kansas City

summary: The tumor suppressor p53 is a well-characterized transcription factor that can bind gene promoters and regulate target gene transcription in response to DNA damage.  Recent studies, however, have revealed that p53 binding events occur predominantly within regulatory enhancer elements.  The effect of p53 binding on enhancer function has not been systematically evaluated.  Here, we perform a genome-scale analysis of enhancer activity from p53-bound sequences using a series of massively parallel reporter assays (MPRAs) coupled with the assay for transpose-accessible chromatin (ATAC-Seq).  We find that the majority of p53 bound sequences examined are potent regulators of enhancer activity during the DNA damage response.  Enhancer regulation requires the presence of the p53 consensus sequence and results in significant induction of target gene transcription.  Surprisingly, our analyses revealed that most p53-bound enhancers are located within regions of inaccessible chromatin.  Many of these enhancers display significantly increased accessibility in response to DNA damage suggesting that p53 regulates their activity, in part, by altering local chromatin environments.  The recognition and activation of inaccessible enhancers may contribute to the ability of the p53 network to function across the diverse chromatin landscapes of different cell and tissue types.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: MPRA (massively parallel reporter assay) and ATAC-Seq (assay for transpose-accessible chromatin) screening enhancer activity from p53 binding sites in cultured human fibroblasts.

first: John

last: Rinn


title: Induced pluripotent stem cell-derived primitive macrophages as a cellular platform to model tissue-resident macrophage differentiation and function

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

institute: Singapore Immunology Network

summary: Specialized tissue macrophages arise during embryogenesis from yolk-sac (YS) progenitors that migrate into developing tissues and terminally differentiate in situ. Until recently, it has been impossible to isolate or derive sufficient numbers of YS-derived macrophages for further study, but data now suggest that induced pluripotent stem cells (iPSCs) can be driven to undergo a process reminiscent of YS-hematopoiesis in vitro. We asked whether iPSC-derived primitive macrophages (iMac) can terminally differentiate into specialized macrophages using growth factors and organ-specific cues. Co-culturing murine iMac with iPSC-derived neurons promoted differentiation into microglia-like cells in vitro. Furthermore, murine iMac differentiated in vivo into microglia following injection into the brain, and functional alveolar macrophages after engraftment in the lung.

overall_design: 24 samples, 12 iMac/iMicro, 12 BM-Mac/BM-Micro. Macrophages were analysed at 4 time points (day 0, 3, 6, 12), with 3 independent replicates for each time point. Non-cocultured samples from the same batch (Day 0 iMac/BM-Mac) were used as controls for the experiment.

first: Kazuyuki

last: Takata

first: Tatsuya

last: Kozaki

first: Christopher

middle: Z

first: Masayuki

last: Otsuka

first: Florent

last: Ginhoux


title: Histone H3G34R mutation causes replicative stress, defective homologous recombination and genomic instability in Fission Yeast

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Recurrent somatic mutations of H3F3A in aggressive pediatric high-grade gliomas generate K27M or G34R mutant histone H3.3.  H3.3-G34R mutants are common in tumors additionally mutant for p53 and ATRX, an H3.3-specific chromatin remodeler. To gain insight into the role of H3-G34R, we generated fission yeast that express only the mutant histone H3. H3-G34R specifically reduces H3K36 tri-methylation and H3K36 acetylation, but minimally affects transcriptional control. H3-G34R mutants exhibit genomic instability and increased replicative stress including slowed replication fork restart although DNA replication checkpoints are functional. H3-G34R mutants are defective for DNA damage repair by homologous recombination (HR), and on damage have altered HR protein dynamics suggestive that H3-G34R slows resolution of HR-mediated repair.  In summary our analysis of H3-G34R mutant fission yeast provides mechanistic insight into how G34R mutation may promote genomic instability in glioma.

overall_design: H3.3 mutations in fission yeast are explored through a panel of 3 H3 WT samples, 3 G34R mutants and 3 Set2D mutants

first: Rajesh

middle: K

last: Yadav

first: Carolyn

last: Jablonowski

first: Satish

last: Kallappagoudar

first: Alfonso

middle: G

last: Fernandez

first: Brandon

last: Lowe

first: Ryan

last: Henry

first: Kevin

last: Barnum

first: Alison

last: Pidoux

first: Yin-Ming

last: Kuo

first: Matthew

last: O’Connell

first: Andrew

last: Andrews

first: Robin

middle: C

last: Allshire

first: Janet

middle: F

last: Partridge


title: An arrayed CRISPR library for individual, combinatorial and multiplexed gene knockout I

city: Cambridge

first: Nicolas

last: Erard

address: Robinson Way

institute: CRUK Cambridge Institute

summary: We have combined a machine-learning approach with other strategies to optimize the efficiency of sgRNAs for CRISPR screens and have constructed a genome-wide, sequence-verified, arrayed CRISPR library.  This incorporates expression strategies to facilitate multiplexed or combinatorial screening.  By conducting parallel loss-of-function screens, we compare our approach to existing sgRNA design and expression strategies.

overall_design: High throughput sequencing was performed to identify representation of sgRNA pairs in depletion screens at the initial (T0) or final (T6) timepoints.

first: Simon

last: Knott

first: Gregory

last: Hannon


title: An arrayed CRISPR library for individual, combinatorial and multiplexed gene knockout III

overall_design: High throughput sequencing was performed to identify CRISPR/Cas9 induced genomic scars at olfactory receptor loci.


title: An arrayed CRISPR library for individual, combinatorial and multiplexed gene knockout

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

overall_design: Refer to individual Series


title: An arrayed CRISPR library for individual, combinatorial and multiplexed gene knockout II

overall_design: High throughput sequencing was performed to identify the sgRNA representation  in depletion screens at the initial (T0) or final (T6) timepoints, with 3 biological replicates per screen. We compared 5 different sgRNA libraries, with around 200 sgRNAs per library.


title: Chromatin structures in pre-selection DP thymocytes  of WT and Bcl11b hypomorphic mutant

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

summary: T-cell receptor (TCR) signals play a critical role in guiding selected thymocytes to distinct lineages by activating genes for transcription factors, such as ThPOK and Runx3, for the helper- or cytotoxic-lineage, respectively. Here we show that Bcl11b, known as an early T-lineage commitment factor, is essential for proper expression of ThPOK and Runx3. Loss of Bcl11b resulted in premature and random expression of these specification factors, leading to lineage scrambling that was disconnected from TCR restriction by MHC. Early Thpok repression by Bcl11b is independent of its known transcriptional silencer, but requires the C-terminal zinc-finger of Bcl11b. Collectively, our findings shed new light on the role of Bcl11b in priming lineage-specifying genes to integrate TCR signals into a subsequent developmental program that dissects effector lineages.

overall_design: Sequencing of ATAC-seq from pre-selection DP thymocytes.

first: Ichiro

last: Taniuchi

first: Satoshi

last: Kojo

first: Ye

last: Liu

first: Akiko

last: Minoda


title: Medial Ganglionic Eminence and Cortical Organoids Model Human Brain Development and Interneuron Migration [RNA-seq2]

first: Yangfei

last: Xiang

overall_design: mRNA profiles of hMGEOs and hCOs with single-cell level were generated by deep sequencing

first: Yoshiaki

last: Tanaka

first: Benjamin

last: Patterson

first: In-Hyun

last: Park


title: Genome-wide maps of Bcl11b bound regions in thymocytes

overall_design: Sequencing of Bcl11b ChIP-seq from thymocytes.


title: Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle

city: Paris

first: Vittore

middle: Ferdinando

last: Scolari

address: 28, rue du Dr. Roux

department: Genomics and Genetics & C3BI

country: France

institute: Institut Pasteur

summary: The duplication and segregation of chromosomes involve the dynamic re-organization of their internal structure by conserved architectural proteins, such as structural maintenance of chromosomes complexes (i.e., cohesin and condensin). Although the roles of these factors is actively investigated, a genome-wide view of chromosome dynamic architecture at both small and large-scales during cell division remains elusive. Here we report the first comprehensive 4D analysis of the Saccharomyces cerevisiae genome higher-order organization during the cell cycle, and investigate the roles of SMC in the observed structural transitions. During replication, cohesion establishment promotes long-range intra-chromosomal contacts and correlates with the individualization of chromosomes, which culminates at metaphase. Mitotic chromosomes are then abruptly reorganized in anaphase by mechanical forces exerted by the mitotic spindle. The formation of a condensin-dependent loop, that bridges the centromere cluster with the rDNA loci, suggests that condensin-mediated forces may also directly facilitate segregation. This work provides a comprehensive overview of chromosome dynamics during the cell cycle of a unicellular eukaryote that recapitulates and unveils new features of highly conserved stages of the cell division.

overall_design: Chromosome organization investigation through Hi-C

first: Luciana

last: Lazar-Stefanita

first: Guillaume

last: Mercy

first: Heloise

last: Muller

first: Thomas

last: Guerin

first: Agnes

last: Thierry

first: Julien

last: Mozziconacci

first: Romain

last: Koszul


title: Genome-wide Analysis Reveals Extensive Changes in LncRNAs during Skeletal Muscle Development in Hu sheep

city: Nanjing

first: Caifang

last: Ren

state: Jiangsu

address: 1 Weigang

institute: Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University

summary: To explore functional lncRNAs during sheep muscle growth, we systematically investigated lncRNAs using strand-specific Ribo-Zero RNA Sequencing at three key developmental stages of Hu sheep (110-day fetus, 5-day-old lamb and 2-year-old adult)

overall_design: LncRNA profiles of  Hu sheep were generated by deep sequencing, three longissimus dorsi muscle samples for each developmental stage, including 110-day fetus, 5-day-old lamb and 2-year-old adult, using Illumina.

first: Yanli

last: Zhang


title: Bcl11b hypomorphic mutant thymocytes

first: Takaho

last: Endo


title: Transcriptome analysis of Bcl11b mutant CD4+CD8+ thymocytes

summary: Comparison of transcriptome  between wild type, CD4 cre conditional knock-out and Bcl11b mutant mice.

overall_design: Five replicates from wt newborn thymus, three replicates mutant new born thymus and four replicate of Bcl11bfl/fl: Cd4-Cre mice.

first: Ichiro

last: Taniuchi

first: Kiyokazu

last: Kakugawa

middle: A


title: comparative analysis of DNA methylation of soybean

city: nanjing

first: yanwei

last: li

state: jiangsu

address: No. 1 Weigang Street, Xuanwu Region, Nanjing City

department: College of Agriculture

institute: Nanjing Agricultural University

summary: In this study, comparative genome-wide DNA methylation profiles of the soybean CMS line NJCMS5A and its maintainer NJCMS5B were completed by whole-genome bisulfite sequencing. The results showed that 3,527 differentially methylated regions (DMRs) and 485 differentially methylated genes (DMGs), including 353 high-credible methylated genes, 56 methylated genes coding unknown protein and 76 novel methylated genes with no known function were identified. Finally, 14 key DMGs were identified as potentially related to CMS in soybean.

first: Yanwei

last: Li

first: Xianlong

last: Ding

first: Xuan

last: Wang

first: Tingting

last: He

first: Hao

first: Longshu

last: Yang

first: Tanliu

first: Linfeng

last: Chen

first: Junyi

last: Gai

first: Shouping


title: RNA-seq on dual-FACS sorted Drosophila Intestinal stem cell and Enteroblast, and effect of SPEN loss of function on gene expression

first: Maheva

last: Andriatsilavo

address: 11-13 rue Pierre et Marie Curie

department: Génétique et biologie du développement / Institut Curie / UMR 3215 CNRS / U934 Inserm

institute: Institut Curie

summary: Precise regulation of stem cell self-renewal and differentiation properties is essential for tissue homeostasis. Using the adult Drosophila intestine to study molecular mechanisms controlling stem cell properties, we identify the gene split-ends (spen) in a genetic screen as a novel regulator of intestinal stem cell fate. Spen family genes encode conserved RNA recognition motif-containing proteins that are reported to have roles in RNA splicing and transcriptional regulation. We demonstrate that spen loss of function in intestinal stem cells results in an abnormal increase in the number of stem cell-like cells and that Spen acts to control early commitment events of the stem cells. Using two-color cell sorting of stem cells and their daughters, we characterize spen-dependent changes in RNA abundance and exon usage, and find potential key regulators downstream of spen. Our work identifies spen as an important regulator of adult stem cells in the Drosophila intestine, provides new insight to Spen-family protein functions, and may also shed light on Spen’s mode of action in other developmental contexts.

overall_design: Three biological replicates were sequenced per each 4 conditions

first: Allison

middle: J

last: Bardin


title: Molecular Analysis of Sink Limited Soybeans

city: West Lafayette

first: Karen

last: Hudson

state: IN

address: 915 West State Street

department: Crop Production and Pest Control

institute: USDA-ARS

summary: Soybean plants that do not produce a sink, such as depodded or male sterile plants, exhibit physiological and morphological changes during the reproductive stages, including increased levels of nitrogen and starch in the leaves and a delayed senescence. To identify transcriptional changes that occur in leaves of sink-limited plants, we used RNAseq to compare gene expression levels in trifoliate leaves from depodded and ms6 male sterile plants and control plants. In sink-limited tissues, we observed a deferral of the expression of senescence-associated genes and a continued high expression of genes associated with the maturity phase of leaf development. We identified GO-terms associated with growth and development and storage protein in sink limited tissues. We also identified that the bHLH. ARFs, and SBP transcription factors were expressed in sink limited tissues while the senescing control leaves expressed WRKY and NAC transcription factors.  We identified genes that were not expressed during normal leaf development but highly expressed in sink-limited plants, including the D4 “non-yellowing” gene.  These changes highlighted several metabolic pathways that were involved in distinct modes of resource parttioning in the “stay green” leaves.

overall_design: Timecourse gene expression analysis of sink-limited soybean leaves. Gene expression was profiled from R2 growth stage (flowering) until the onset of leaf seenscence, and contrasted between mechanically and genetically sink-limited soybeans.

first: Anne

middle: V

last: Brown


title: Integrative genomics identifies the molecular basis of resistance to Azacytidine therapy in Myelodysplastic Syndromes

city: Sydney

first: Ashwin

last: Unnikrishnan

state: NSW

address: Room 217, Level 2, Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales

department: Lowy Cancer Research Centre

institute: University of New South Wales

summary: RNA-seq of bone marrow CD34+ cells of myelodysplastic syndrome (MDS) and chronic myelomonocytic leukemia (CMML) patients to identify at the molecular pathways involved in primary resistance to AZA therapy.

overall_design: RNA-seq of bone marrow CD34+ cells of MDS and CMML patients at pre-treatment and after 6 cycles of AZA treatment to identify at the molecular pathways involved in resistance to AZA therapy.

first: John

middle: E

last: Pimanda


title: Gene and retrotransposon expression analysis in the F1 hybrid background of B6 and MSM for WT, Pld6 KO, and Dnmt3l KO male germ cells

city: Fukuoka

first: Kota

last: Inoue

address: 3-1-1 Maidashi, Higashiku

department: Medical Institute of Bioregulation

institute: Kyushu University

summary: mRNA sequencing analysis of FACS-purified leptotene/zygotene (L/Z) spermatocytes

overall_design: Compare transcriptomes of WT, Pld6 KO, and Dnmt3l KO germ cells in the F1 hybrid background of B6 and MSM to study these mutations affecting gene expression due to nearby retrotransposons.

first: Kenji

last: Ichiyanagi


title: Small RNA sequencing analysis for male germ cells during spermatogenesis

summary: Small RNAs in FACS-purified spermatogonia, spermatocytes (L/Z and P/D) and round spermatids were sequenced to study piRNA populations.


title: Whole-genome DNA methylation analysis  for purified WT, Pld6 KO, and Dnmt3l KO spermatogonia

summary: DNA methylomes were obtained to analyze methylation levels of retrotransposons as welll as the genome-wide methylation levels.

overall_design: Bisulfite shotgun sequencing libraries were prepared by the PBAT method, and sequenced by HiSeq2500


title: The effect of the Pld6 and Dnmt3l mutations on DNA methylation and expression of retrotransposons in mouse male germ cells

summary: Mammalian genomes harbor millions of retrotransposon copies, some of which are transpositionally active. In mouse prospermatogonia, PIWI-interacting small RNAs called piRNAs combat retrotransposon activity. The piRNA system guides de novo DNA methylation at retrotransposon promoters, but it remains unclear whether DNA methylation is involved in retrotransposon silencing in prospermatogonia. We performed a genome-wide study of DNA methylation and RNA abundance for retrotransposons in developing mouse male germ cells, using Pld6/Mitopld and Dnmt3l knockout (KO) mice deficient in piRNA biogenesis and de novo DNA methylation, respectively. The Dnmt3l mutation greatly reduced DNA methylation at most retrotransposons but its effect on their RNA abundance was low in prospermatogonia. In the Pld6 mutants, only few retrotransposons exhibited reduced DNA methylation but many were more upregulated at the RNA level than in the Dnmt3l mutants. Moreover, the retrotransposon upregulation by the Pld6 mutation was observed even in the Dnmt3l KO background. Thus, in prospermatogonia, post-transcriptional RNA digestion by the piRNA system plays a more important role in retrotransposon regulation than transcriptional silencing by DNA methylation. However, their relative importance was changed in meiotic spermatocytes where hypomethylation of retrotransposons increased their expression by up to 100-fold in both mutants. Interestingly, retrotransposon activation disrupted the transcriptome integrity because intergenic and intronic retrotransposon sequences, in particular, the antisense promoter of LINE-1, drive expression of nearby genes.

overall_design: To study the effect of the Pld6 and Dnmt3l mutations on retrotransposon regulation, we determined the DNA methylation levels in the mutant spermatogonia and the RNA expression levels of retrotransposons in the mutant testes at P0 (containing prospermatogonia) and mutant leptotene/zygotene spermatocytes using bowtie2 (both are available as supplementary tables in the original article).  We also determined genome-wide DNA methylation map (using bismark) and the levels of gene expression (using Tophat and Cuffdiff), which are available as processed files here.  We also analyzed small RNAs in spermatogonia, spermatocytes and round spermatids to analyze the population of piRNAs in these cells.


title: Gene and  retrotransposon expression analysis for WT, Pld6 KO, and Dnmt3l KO male germ cells during spermatogenesis

summary: mRNA sequencing analysis of P0 testes and FACS-purified leptotene/zygotene (L/Z) spermatocytes

overall_design: Compare transcriptomes of WT, Pld6 KO, and Dnmt3l KO germ cells to study the effects of these mutations affecting piRNA biogenesis and DNA methylation, respectively.


title: 3' RNA-seq of ADAR hypomorph flies grown in different temperatures

city: Waltham

first: Sebastian

last: Kadener

state: MA

address: 415 South Street

institute: Brandeis University

summary: In order to test whether ADAR is responsible for mediating part of the transcriptional response to temperature changes in fly we determined the gene expression profile of fly heads from control and ADAR Hypomorph flies at 18 and 29°C by 3’ RNA-seq.

overall_design: ADAR hypomorph flies and the control flies were grown in 18C (3 replicas each) or in 29C (3 replicas each) and harvested 3-6 days after eclosion .


title: ChIP-seq analysis of MCF10A cells exressing active mutant YAP-5SA

status: Public on Jul 19 2017

city: daejeon

first: wonyul

last: jang

state: State...

address: yuseong-gu, daehakro

institute: KAIST (Korea Advanced Institute of Science and Technology)

summary: To understand the direct target genes YAP transcription co-activator invovled with in gonome-wide levels, next generation sequencing was conducted in Flag-YAP-5SA overexpressing MCF10A cells using Flag (sigma) antibody.

overall_design: Genomic profiles bound by YAP was generated in MCF10A expressing Flag-YAP-5SA using Illumina's Hi-Seq

first: Wonyul

last: Jang

first: Tackhoon

last: Kim


title: A histone mimic within DNA Ligase 1 links DNA replication and DNA remethylation: a revised model for the maintenance of DNA methylation by UHRF (RRBS)

first: Pierre-Antoine

last: Defossez

address: 35 rue Hélène Brion

department: UMR7216 "Epigenetics and Cell Fate"

institute: CNRS-Université Paris Diderot - Sorbonne Paris Cité

summary: DNA methylation is an essential epigenetic mark in mammals, and its pattern has to be re-established after each round of DNA replication. The protein UHRF1 is known to be necessary for this process, but its mode of action is unclear. Using proteomics, we havefound that a replication factor, DNA Ligase 1 (LIG1), is a direct interactor of UHRF1. The interaction is mediated bythe Tudor domain of UHRF1 and an H3K9-like histone mimic within LIG1. This mimic ismethylated on a conserved lysine by the enzymes G9a and GLP, and outcompetes H3K9me3 for UHRF1 binding. Lastly, the interaction with LIG1 promotes the recruitment of UHRF1 to sites of DNA replication and is required for DNA methylation maintenance. These results clarify UHRF1 activity, identify a new non-histone target of G9a and GLP, and provide the first example of a histone mimic that coordinates DNA replication and DNA remethylation

overall_design: Reduced representation bisulfite sequencing (RRBS) experiments performed in mouse embryonic stem cells ES-E14, WT,  Np95 -/-, and CRISPR mutant clones for Ligase1

first: Laure

last: Ferry

first: Olivier

last: Kirsh


title: Analysis of gene expression and of H3.3 distribution and abundance in a ATRX loss-of-function line

city: Aubière

first: Céline

last: Duc

address: 10 Avenue Blaise Pascal

institute: CNRS

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

overall_design: Refer to individual Series


title: In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

institute: University of Groningen

summary: Defining the in vivo folding pathway of cellular RNAs is essential to understand how they reach their final native conformation. We here introduce a novel method, named Structural Probing of Elongating Transcripts (SPET-seq), that permits single-base resolution analysis of transcription intermediates’ secondary structures on a transcriptome-wide scale, enabling base-resolution analysis of the RNA folding events. Our results suggest that cotranscriptional RNA folding in vivo is a mixture of cooperative folding events, in which local RNA secondary structure elements are formed as they get transcribed, and non-cooperative events, in which 5΄-halves of long-range helices get sequestered into transient non-native interactions until their 3΄ counterparts have been transcribed. Together our work provides the first transcriptome-scale overview of RNA cotranscriptional folding in a living organism.

overall_design: Transcritome-wide mapping of nascent RNA secondary structures in Escherichia coli

first: Edoardo

last: Morandi

first: Francesca

last: Anselmi

first: Lisa

last: Simon

first: Giulia

last: Basile

first: Salvatore

last: Oliviero


title: Analysis of eH3.3 occupancy in a ATRX loss-of-function line [ChIP-seq]

summary: Analysis of H3.3 position and abundance in the presence and absence of a functionnal ATRX protein: we wanted to analyse how the absence of the  Arabidopsis putative ATRX chaperone would impact the abundance and the distribution of H3.3 variant at a genome-wide level.

overall_design: 2 replicates for WT, 2 replicates for mutant, Input control: in vitro grown 2.5 week-old seedlings were harvested and formaldehyde fixed. ChIP was performed according to Veluchamy et al., 2016 [PMID: 27410265] with Anti-FLAG® M2 Magnetic beads (Sigma)

first: Celine

first: Aline

last: Probst


title: Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide

status: Public on Jul 18 2017

city: New York

first: Spiro

last: Pantazatos

state: New York

address: 1051 Riverside Dr.

department: Psychiatry

institute: Columbia University

summary: Brain gene expression profiling studies of suicide and depression using oligonucleotide microarrays have often failed to distinguish these two phenotypes. Moreover, next generation sequencing approaches are more accurate in quantifying gene expression and can detect alternative splicing. Using RNA-seq, we examined whole-exome gene and exon expression in non-psychiatric controls (CON, N=29), DSM-IV major depressive disorder suicides (MDD-S, N=21) and MDD non-suicides (MDD, N=9) in the dorsal lateral prefrontal cortex (Brodmann Area 9) of sudden death medication-free individuals post mortem. Using small RNA-seq, we also examined miRNA expression (nine samples per group). DeSeq2 identified 35 genes differentially expressed between groups and surviving adjustment for false discovery rate (adjusted P<0.1). In depression, altered genes include humanin-like-8 (MTRNRL8), interleukin-8 (IL8), and serpin peptidase inhibitor, clade H (SERPINH1) and chemokine ligand 4 (CCL4), while exploratory gene ontology (GO) analyses revealed lower expression of immune-related pathways such as chemokine receptor activity, chemotaxis and cytokine biosynthesis, and angiogenesis and vascular development in (adjusted P<0.1). Hypothesis-driven GO analysis suggests lower expression of genes involved in oligodendrocyte differentiation, regulation of glutamatergic neurotransmission, and oxytocin receptor expression in both suicide and depression, and provisional evidence for altered DNA-dependent ATPase expression in suicide only. DEXSEq analysis identified differential exon usage in ATPase, class II, type 9B (adjusted P<0.1) in depression. Differences in miRNA expression or structural gene variants were not detected. Results lend further support for models in which deficits in microglial, endothelial (blood-brain barrier), ATPase activity and astrocytic cell functions contribute to MDD and suicide, and identify putative pathways and mechanisms for further study in these disorder

overall_design: We examined whole-exome gene and exon expression in non-psychiatric controls (CON, N=29), DSM-IV major depressive disorder suicides (MDD-S, N=21) and MDD non-suicides (MDD, N=9) in the dorsal lateral prefrontal cortex (Brodmann Area 9) of sudden death medication-free individuals post mortem. Using small RNA-seq, we also examined miRNA expression (nine samples per group).

middle: P

first: Victoria

last: Arango

first: J

last: Mann


title: Expression profiling of the retina of pde6c, a zebrafish model of retinal degeneration

city: San Diego

first: Nadejda

last: Beliakova-bethell

state: CA

address: 9500 Gilman Dr, La Jolla

institute: University of California San Diego

summary: Retinal degeneration often affects the whole retina even though the disease-causing gene is specifically expressed in the light-sensitive photoreceptors. These retinal defects can potentially be determined by gene-expression profiling of the whole retina. In this study, we measured the gene-expression profile of retinas microdissected from a zebrafish pde6cw59 (pde6c) mutant. Its retinas display not only photoreceptor degeneration but also issues in other cell types starting from 4 days postfertilization (dpf). To capture these initial changes, we subjected pde6c and wild-type (WT) retinas at 5 dpf to RNA sequencing (RNA-Seq) on the Illumina HiSeq 2000 platform. The sequencing analyses indicate that the RNA-Seq dataset was of high quality. We also validated the RNA-Seq results by Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) of seven phototransduction genes. We found that the fold changes of these genes measured by RT-qPCR highly correlated to those measured by RNA-Seq. Therefore, our RNA-Seq dataset likely captures the molecular changes in the whole pde6c retina. This dataset will facilitate the characterization of the molecular defects in the pde6c retina at the initial stage of retinal degeneration

overall_design: 3 samples of pde6c mutant and 3 samples of wild type animals are analyzed.

first: Liyun

last: Zhang

first: Xinlian

first: Gaonan

first: Chi

last: Pang

first: Yuk

last: Leung

first: Mingzhi

first: Wenxuan

last: Zhong


title: Dihydropyrimidine-thiones and clioquinol synergize to target b-amyloid cellular pathologies through a metal-dependent mechanism

first: Dan

last: Tardiff

state: Massachusetts

address: 790 Memorial Drive

institute: Yumanity Therapeutics

summary: DHPM-thiones rescue Ab-mediated toxicity in a metal-dependent manner that strongly synergizes with clioquinol, a known metal-binding and cytoprotective compound. RNA-seq experiments reveal a modest, yet specific effect on metal-responsive genes that do not change with the inactive control compound.

overall_design: Treatment of biological replicates with DMSO, 0.8 uM clioquinol, or 20 uM 10{3,3,1} (DHPM-thione) for ~6 hours prior to harvesting of cells and isolation of total RNA.

first: Daniel

first: Lauren

last: Brown

first: Xiaohui

last: Yan

first: Richard

last: Trilles

first: Nathan

last: Jui

first: M

middle: I

last: Barrasa

first: Kim

last: Caldwell

first: Guy

first: Scott

last: Schaus

first: Susan

last: Lindquist


title: Isogenic mice exhibit sexually-dimorphic DNA methylation patterns across multiple tissues

city: Darlinghurst

first: Paul

last: Young

address: 405 Liverpool Street

institute: Victor Chang Cardiac Research Institute

summary: Our findings suggest that gender is underwritten in the epigenome in a tissue-specific manner. Gender-specific epigenetic states are likely to have important implications for understanding sexually dimorphic phenotypes in health and disease.

overall_design: Methylation profiling male vs female by RRBS of 3 mouse tissues. 6 x 6 liver samples, 3 x 3 brain, 3 x 3 heart.

first: Helen

last: McCormick

first: suzy

last: Hur

first: Jennifer

last: Cropley

first: Keith

last: Booher

first: Hunter

last: Cheung

first: Eleni

last: Giannolatou

first: Catherine

last: Suter


title: Krox20 hindbrain regulation involves multiple modes of cooperation between cis-acting elements [4C-seq]

first: Pascale

last: Gilardi-Hebenstreit

address: 46 Rue d'Ulm

department: IBENS - UMR ENS - CNRS 8197 - INSERM 1024

institute: Institut de Biologie de l'Ecole Normale Superieure

summary: Many genes harbour multiple transcriptional enhancers that act concomitantly to achieve robust and precise spatial-temporal expression. In vertebrates, however, the mechanisms underlying cooperation between cis-acting elements are poorly documented. The mouse gene Krox20 encodes a transcription factor required for the specification of two segments (rhombomeres) of the developing hindbrain. In rhombomere 3, Krox20 is subject to positive feedback, governed by enhancer A, which is directly bound by the KROX20 protein, whereas another element, C, distant from 70 kb, was supposed to be only required for initiation of expression. Here, using both enhancer knock-outs and investigations of chromatin organisation, we show that element C possesses a dual activity: besides its classical enhancer function, it is also permanently required in cis to potentiate element A autoregulatory activity, by increasing its chromatin accessibility. This work uncovers a novel, asymmetrical, long-range mode of cooperation between cis-acting elements that might be essential to avoid promiscuous activation of positive autoregulatory elements.

overall_design: Circular Chromosome Conformation Capture (4C-seq) samples from mouse embryonic samples at different time points and anatomical positions. Data based on 23 biological samples.

first: Elodie

last: Thierion

first: Johan

last: Le Men

first: Samuel

last: Collombet

first: Céline

last: Hernandez

first: Fanny

last: Coulpier

first: Morgane

last: Thomas-Chollier

first: Daan

last: Noordermeer

first: Patrick

last: Charnay


title: Host plant driven transcriptome plasticity in the salivary glands of the cabbage looper (Trichoplusia ni)

city: University Park

first: David

middle: Asher

last: Galbraith

state: Pennsylvania

address: 19a Chemical Ecology Lab

institute: Penn State University

summary: We report on the transcriptome differences in the salivary glands of cabbage looper larvae fed on different diets

overall_design: cabbage looper larvae were reared on cabbage, tomato, and artificial diet. Transcriptome of salivary glands were characterized and compared

first: Loren

last: Rivera Vega

first: Christina

middle: M

last: Grozinger

first: Gary

middle: W

last: Felton


title: Krox20 hindbrain regulation involves multiple modes of cooperation between cis-acting elements [ATAC-seq]

overall_design: Chromatin accessibility assessed by ATAC-seq from mouse embryonic samples at different time points and anatomical positions.


title: Krox20 hindbrain regulation involves multiple modes of cooperation between cis-acting elements [ChIP-Seq]

overall_design: Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) samples from mouse embryonic samples at different time points and anatomical positions. Data based on 24 biological samples.


title: Krox20 hindbrain regulation involves multiple modes of cooperation between cis-acting elements