title: Chromatin interactions involving super-enhancers associate with specific expression patterns of target genes

city: Singapore

first: Melissa

middle: Jane

last: Fullwood

address: 14 Medical Drive, #12-01

department: School of Biological Sciences

institute: Nanyang Technological University

summary: Super-enhancers may regulate target genes through chromatin looping. We connected super-enhancers in the K562 chronic myelogenous leukemia cell line with chromatin interactions identified from Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) data. Gene expression at proximal elements that are connected with distal super-enhancers showed significantly higher cell-type specificity than at proximal elements connected with other elements or not involved in interaction. 4C and Episwitch analysis of chromatin interactions showed that certain chromatin interactions are cell-specific, but others are more general. While super-enhancers upstream of c-MYC at the MYC-335 element can be found in other cancers, only super-enhancers downstream of c-MYC can be found in K562. 4C analysis of the c-MYC promoter revealed no chromatin interactions that are directed upstream of c-MYC, but only downstream of c-MYC, in the PVT1 long non-coding RNA gene. Cell-specific usage of super-enhancers could explain why the MYC-335 element that is associated with many solid cancers such as colorectal cancer and breast cancer, but not with leukemia. Surprisingly, we found that a chromatin interaction between c-MYC and a c-MYC super-enhancer is lost in chronic myelogenous leukemia patient blood as compared with blood from individuals without the disease through Oxford Biodynamics’ Episwitch analysis. These results provide evidence for fine-tuning of expression patterns, such as cell-specific regulation of target genes by distal super-enhancers through chromatin interactions and an association between chromatin interactions and disease, and highlight that super-enhancers are more complex than previously described.

overall_design: Examination of several chromatin interactions involving super-enhancers using 4C-Seq and Episwitch (TM)

first: Hong

last: Tan

first: Fan

last: Cao


title: RNA-Seq data for KRAS wild-type(WT) and two mutant forms G12V and Q61H over-expressed samples with green fluorescent protein control samples using human mammary epithelial cells

status: Public on May 01 2017

city: Salt Lake City

first: Mumtahena

last: Rahman

state: UT

address: 20 South 2030 East, Rm 420

department: Biomedical Informatics

country: USA

institute: University of Utah

type: Expression profiling by high throughput sequencing

summary: The goal was to capture the transcriptional activity due to over-expression of KRAS gene. Over-expressions were validated using Western Blots. Illumina RNA-Seq technology was used to capture the downstream transcriptional activity. Reads were 101 base pairs long and single ended. An R open source package “Rsubread” was used to align and quantify the read using UCSC hg19 annotation. The integer-based gene counts were later normalized in TPM .

overall_design: Profiles of gene expression were generated in cells derived from breast and used to generate a gene-expression signatures.

first: L

middle: K

last: Jackson

first: M

first: S

last: MacNeil

first: A

middle: H

last: Bild


title: Acetyl-CoA metabolism by ACSS2 regulates neuronal histone acetylation and long-term memory

city: Philadelphia

first: Shelley

middle: L.

last: Berger

state: Pennsylvania

address: 3400 CIVIC CENTER BLVD

department: Cell and Developmental Biology

institute: University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: degradome sequence data

city: Beijing

first: Zhixi

last: Tian

address: No.1 Building, No.1 West Beichen Road,Chaoyang District

country: China

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: To identity the targets of miRNAs, we bundled 12 samples from different developing satages into four mixture samples. These samples were used to cosntruct degradome libraries and preform degradome sequencing on Illumina Hi-seq 2000 analyzer. More than 44.98 millions clean reads were obtained and 33.52 million reads were mapped to the soybean cDNA. The mapped reads were used to identity miRNA targets by CleaveLand4 pipeline.

overall_design:
4 degradome mixed samples, no replicates, but every degradome data consists of two parts data.

Please note that every degradome sample has two processed and two raw data files. To have enough data, additional sequencing was performed from each sample library.  And each sample raw data was processed separately (tissue_name*degradome.txt) and also combined (all_degradome*.txt).


title: Deciphering Pancreatic Islet β Cell and α Cell Maturation Pathways and Characteristic Features at the Single-Cell Level

status: Public on May 02 2017

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

summary: Pancreatic β and α cells play essential roles in maintaining glucose homeostasis. However, the mechanisms by which these distinct cell populations are generated, expand, and mature during pancreas development remain unclear. In this study, we addressed this critical question by performing a single-cell transcriptomic analysis of mouse β and α cells sorted from fetal to adult stages. We discovered that β and α cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times. However, the quiescent and proliferative cells in both the β lineage and α lineage are synchronous in their maturation states. The heterogeneity of juvenile β cells reflects distinct cell-cycling phases, origins, and maturation states, whereas adult β cells are relatively homogeneous at the transcriptomic level. These analyses provide not only a high-resolution roadmap for islet lineage development but also insights into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both β and α cells.

overall_design:
The overall goal of this study was to define the roadmaps for pancreatic β- and α-cell development. Specifically, we performed single-cell RNA-seq at various developmental stages of E17.5, P0, P3, P9, P15, P18 and P60 of β- and α- cells (except P3), as well as endocrine progenitor cells at P0, which were fluorescence-activated cell sorting (FACS) sorted from Insulin-RFP, Gcg-Cre; Rosa-RFP or Ngn3-GFP mouse strains, respectively. To develop a workflow to decipher the maturation process through bulk-cell transcriptomic analysis, we performed RNA-seq using 3-5 × 10^4 sorted cells at various developmental time points as we have done in the single-cell study.
The background strains of our mouse samples are:
Ngn3-GFP mice: mixed background of C57BL/6 and C3H
Ins1-RFP mice: mixed background of C57BL/6 and C3H
Gcg-Cre, Rosa-RFP mice: mixed background of C57BL/6, CBA/J and C3H.

first: Yu-Wei

last: Zhang

first: Wei-Lin

last: Qiu

first: Ye

last: Feng


title: Acetyl-CoA metabolism by ACSS2 regulates neuronal histone acetylation and long-term memory [ChIP-seq]

summary: Metabolic production of acetyl-CoA has been linked to histone acetylation and gene regulation, however the mechanisms are largely unknown. We show that the metabolic enzyme acetyl-CoA synthetase 2 (ACSS2) is a critical and directchum regulator of histone acetylation in neurons and of long-term mammalian memory. We observe increased nuclear ACSS2 in differentiating neurons in vitro. Genome-wide, ACSS2 binding corresponds with increased histone acetylation and gene expression of key neuronal genes. These data indicate that ACSS2 functions as a chromatin-bound co-activator to increase local concentrations of acetyl-CoA and to locally promote histone acetylation for transcription of neuron-specific genes. Remarkably, in vivo attenuation of hippocampal ACSS2 expression in adult mice impairs long-term spatial memory, a cognitive process reliant on histone acetylation. ACSS2 reduction in hippocampus also leads to a defect in upregulation of key neuronal genes involved in memory. These results reveal a unique connection between cellular metabolism and neural plasticity, and establish a link between generation of acetyl-CoA and neuronal chromatin regulation.

overall_design: Genome-wide examination of histone H3 and H4 acetylation, as well as ACSS2 binding, in undifferentiated CAD cells and differentiated CAD neurons; background adjusted by H3 ChIP or Input.

first: Philipp

last: Mews

first: Adam

middle: M

last: Drake

first: Vincent

last: Luczak

first: Ted

last: Abel

middle: L


title: Transcriptome Analysis of Immunity- and Reproduction-related Differential Gene Expression in Parasitized Locusta migratoria

city: Hangzhou

first: Xiaojun

last: Liu

state: Zhejiang

address: No 16, Xuelin Street

department: College of Life and Environmental Sciences

institute: Hangzhou Normal University

summary: The transcriptome and DGE analysis of the fat body and ovary of L. migratoria based on the Illumina short-read sequencing technology and De novo assembly. Research on the trade-offs between immunity and reproduction is contributing significantly to the understanding of the fitness of organisms in nature.

overall_design: The cDNA libraries for the mixed tissue samples of the fat body and ovary collected from the Sephadex group, the bacterial parasite group, and the dipteran parasite group at 4 hours and 6 days post-treatment were made for the DGE analysis. Every experimental treatment sample had one DGE-seq and one parallel replication.

first: Bin

last: Tang

first: Shigui

last: Wang


title: Acetyl-CoA metabolism by ACSS2 regulates neuronal histone acetylation and long-term memory [RNA-seq]

summary: Metabolic production of acetyl-CoA has been linked to histone acetylation and gene regulation, however the mechanisms are largely unknown. We show that the metabolic enzyme acetyl-CoA synthetase 2 (ACSS2) is a critical and direct regulator of histone acetylation in neurons and of long-term mammalian memory. We observe increased nuclear ACSS2 in differentiating neurons in vitro. Genome-wide, ACSS2 binding corresponds with increased histone acetylation and gene expression of key neuronal genes. These data indicate that ACSS2 functions as a chromatin-bound co-activator to increase local concentrations of acetyl-CoA and to locally promote histone acetylation for transcription of neuron-specific genes. Remarkably, in vivo attenuation of hippocampal ACSS2 expression in adult mice impairs long-term spatial memory, a cognitive process reliant on histone acetylation. ACSS2 reduction in hippocampus also leads to a defect in upregulation of key neuronal genes involved in memory. These results reveal a unique connection between cellular metabolism and neural plasticity, and establish a link between generation of acetyl-CoA and neuronal chromatin regulation.

overall_design: Global survey of gene expression in CAD cells and differentiated CAD neurons following lentiviral knockdown of ACSS2 or ATP citrate lyase (ACL) (and control = scramble hairpin); survey of hippocampal gene expression changes associated with retrieval of fear memory, after ACSS2-AAV knockdown or in EGFP-AAV control (comparison of 0h vs. 1h post-memory retrieval).


title: Microtubule-associated CLASP balances brassinosteroid signaling through negative feedback to sustain plant cell proliferation

city: Winnipeg

first: Mark

last: Belmonte

state: Manitoba

address: 50 Sifton Rd

department: Biological Sciences

country: Canada

institute: University of Manitoba

summary: The capacity for sustained cell division is a critical determinant of plant meristem development, and ultimately, organ size. This capacity is diminished in mutants lacking the microtubule-associated protein CLASP, and when brassinosteroid signaling is increased. Here, we discovered that CLASP is both targeted by and promotes activity of the brassinosteroid pathway in Arabidopsis root apical meristems. We show that enhanced brassinosteroid signalling reduces CLASP transcript and protein levels, and dramatically shifts microtubule organization to promote exit from the cell division cycle. Notably, CLASP sustains brassinosteroid signalling by fostering retrieval of endocytosed BRI1 receptors to the plasma membrane through the tethering of SNX1 vesicles to microtubules. clasp-1 null mutants have fewer BRI1 receptors, and impaired BR-mediated transcriptional activity and responses. Global transcript profiling confirmed the collapse of cell cycle activity in clasp-1 and revealed hormone crosstalk. Together, these findings reveal an unprecedented form of negative feedback that supports meristem homeostasis.

overall_design: mRNA profiling of response of clasp-1 mutant and wild type root tips to epibrassinolide

first: Geoffrey

middle: O

last: Wasteneys

middle: F


title: Genome-wide RNA-seq analysis during carbon catabolite repression in Trichoderma reesei reveals a multilevel control of cellulase production and action

city: Campinas

first: Gabriela

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

summary: The ascomycete Trichoderma reesei is one of the most well studied cellulolytic fungi and widely used in the biotechnology industry, as in the production of second-generation bioethanol. Carbon catabolite repression (CCR) mechanism adopted by T. reesei is mediated by the transcription factor CRE1 and consists in the repression of genes related to the production of cellulase when a readily available carbon source is present in the medium. Using RNA sequencing this study aims to contribute to understanding of CCR during growth in cellulose and glucose, by comparing the mutant strain of T. reesei Δcre1 with its parental, QM9414.

overall_design:
T. reesei (QM9414 and Δcre1) was grown in Mandels-Andreotti medium, supplemented with 1% of cellulose or 2% of glucose. The cultures were incubated on an orbital shaker (200 rpm) at 28°C for 24, 48 and 72 hours using cellulose as carbon source and for 24 and 48 hours with glucose as the carbon source. All experiments were performed in three biological replicates. The resultant mycelia were collected by filtration, frozen and stored at -80°C until RNA extraction. After growth, total RNA was isolated from the mycelia using TRIzol® reagent. RNA-seq experiments were performed by LGC Genomics GmbH (Berlin/Germany) using the platform Illumina/HiSeq2000.
The samples from the parental strain QM9114 were previously submitted in GSE53629.

first: Amanda

last: Campos Antoniêto

first: Lílian

last: dos Santos Castro

first: Rafael

last: Silva-Rocha

first: Roberto

last: do Nascimento Silva


title: RNA sequencing of striatum tissue from naive Csnk1e knockout mice and wild-type mice

status: Public on Apr 30 2017

city: Boston

first: Lisa

last: Goldberg

state: Massachusetts

address: 72 E Concord St, R604

institute: Boston University School of Medicine

overall_design: For this study, 3mm punches from both striatal hemispheres were collected and pooled from 16 mice (8 Csnk1e knockouts, 8 wild-type controls), and RNA was extracted and prepared for cDNA library preparation using the Illumina TruSeq (oligo-dT; 50bp single-end reads). Samples 1-13,and 15-17 were run in four lanes total, with all samples run in L001, and L002 on one flow cell and L001_2 and L002_2 on a second flowcell. Raw samples provided are labeled with the "CB-" prefix, followed by the sample number and the lane that it was run in is described at the tail end as "_L00#" with # being either lane 1 or 2 and _2 denoting lanes on the second flow cell.]

first: Camron

middle: D

last: Bryant

first: W

middle: E

last: Johnson


title: Modulation of the inflammatory response by dematiaceous fungal morphotypes and its impact on inflammatory response chronicity

city: Brasília

first: Taina

last: Raiol

state: DF

address: Av. L3 Norte, Campus Universitário Darcy Ribeiro

department: Fiocruz Brasília (GEREB)

institute: Oswaldo Cruz Foundation - Fiocruz

summary:
Purpose: A common theme across multiple fungal pathogens is their ability to impair the establishment of a protective immune response. Although early inflammation is beneficial in containing the infection, an uncontrolled inflammatory response is detrimental and may eventually oppose disease eradication. Chromoblastomycosis (CBM), a cutaneous and subcutaneous mycosis, caused by dematiaceous fungi, is capable of inducing a chronic inflammatory response. This work was performed in order to understand how fungal cells were able to induce intense inflammatory response in the host.
Methods:Peritoneal macrophages (PM) were infected for 6h with F. pedrosoi conidia or muriform cells and then lysed so that total RNA was extracted with the RNeasy kit (Qiagen). Paired-end cDNA reads (100bp) were generated using the HiSeq 2000 Sequencing system (Illumina) located at the Scripps DNA Sequencing Facility (California, USA). Quality check of the paired-end reads was performed using FASTQC, and clipping and trimming was done using CUTADAPT and PRINSEQ softwares, respectively. The filtered reads were aligned to the mouse genome downloaded from the Ensembl database using open source TopHat 2.0.9. The aligned files were ordered and indexed using Samtools followed by read count using HTSeq-count. Statistical analysis was done using the R environment for statistical computing. Gene model quantification were performed using the Bioconductor package EdgeR.
Results: High throughput RNA sequencing analysis (RNA-Seq) showed a strong up-regulation of genes related to fungal recognition, cell migration, inflammation, apoptosis and phagocytosis in macrophages exposed in vitro to Fonsecaea pedrosoi muriform cells, but not F. pedrosoi conidia. This is the main fungal form responsible for the intense inflammatory pattern observed in CBM, clarifying the chronic inflammatory reaction observed in most patients.
Conclusions: Our findings reveal two different fungal-host interaction strategies according to fungal form, highlighting fungal dimorphism as an important key in understanding the bipolar nature of inflammatory response in fungal infections

overall_design: Comparison of differentially expressed genes in peritoneal macrophages infected with F. pedrosoi conidia or muriform cells.

first: Isaque

last: Siqueira

first: Raffael

middle: J

last: de Castro

first: Luiza

middle: C

last: Leonhardt

first: Márcio

middle: S

last: Jerônimo

first: Tainá

first: Christiane

last: Nishibe

first: Nalvo

last: Almeida

first: Aldo

last: Tavares

first: Christian

last: Hoffman

first: Anamélia

last: Bocca


title: The CCAAT-Binding Complex Controls Mitochondrial Activity and Iron Homeostasis in Candida glabrata

city: Paris

first: Antonin

last: Thiébaut

address: 7-9 quai Saint Bernard, building C, floor 3, room C321B

country: France

institute: Sorbonne Université

summary: We conducted a network-based analysis of the Hap5 transcription factor belonging to the CCAAT-Binding Complex in Candida glabrata.

overall_design: We performed ChIPseq experiments using myc-tagged versions of Hap5 factor.

first: Thierry

last: Delaveau

first: Médine

last: Benchouaia

first: Julia

last: Boeri

first: Mathilde

last: Garcia

first: Gaëlle

last: Lelandais

first: Frédéric

last: Devaux


title: Transcriptome analysis of wild type, ar21 and i4g1 mutants in developing seeds

city: Wuhan

first: Qiang

last: Li

state: Saskatchewan

address: #1 Shizishan Street

institute: Huazhong Agricultural University

summary: To explore transcriptional regulations between lipid metabolism and eIFiso4G1, we performed RNAseq analysisin ar21 an i4g1 single mutants.

overall_design: Total RNA were extracted from wild type, ar21 and i4g1 mutants seeds at 13 days after flowering (DAF) with two biological replicates for each line.

first: Jitao

last: Zou


title: BCL11B AND COMBINATORIAL RESOLUTION OF CELL FATE IN THE T-CELL GENE REGULATORY NETWORK

city: Irvine

first: Weihua

last: Zeng

state: CA

address: 2300E Bio Sci III

department: Dev & Cell Biology

institute: UCIrvine

summary: We report the RNA-seq results from mouse T-cell precursors in different developmental stages including DN1, DN2a, DN2b, DN3 and DP in order to study the gene regulation network in T cell development.  Some of the samples also have certain kind of perturbations, such as Bcl11b knockout and the treatment of Notch signaling pathway inhibitor GSI, in order to study the roles of these factors in T cell development.

overall_design: Examine the transcriptome of 47 mouse T-cell precursor samples from five developmental stages (DN1, DN2a, DN2b, DN3 and DP).  Among them, 19 have Bcl11b knockout and 4 have GSI treatment.

first: Jingli

middle: A

last: Zhang

first: Long

first: Ali

last: Mortazavi

first: Ellen

middle: V

last: Rothenberg


title: Roles of activating transcription factor 4 in the murine response to asparaginase in liver.

city: New Brunswick

first: William

middle: J.

last: Belden

state: NJ

address: 59 Dudley Rd

department: Animal Sciences

institute: Rutgers, The State University of New Jersey

summary: In liver, the anti-leukemic agent asparaginase (ASNase) increases phosphorylation of eukaryotic initiation factor 2 by general control nonderepressible 2 (GCN2) kinase. This event promotes gene-specific translation of activating transcription factor 4 (ATF4) which alters gene expression in response to amino acid depletion. The objective of this study was to investigate the role of GCN2 versus ATF4 in controlling the global transcriptome to ASNase in liver. We compared global gene expression patterns in livers from wildtype,Gcn2-/-, andAtf4-/-mice (all on C57BL/6J background) treated with ASNase or phosphate buffered saline (PBS) excipient. These analyses revealed that ATF4 controls a hepatic gene expression profile that partially overlaps with GCN2 both basally and following amino acid depletion by ASNase.

overall_design: RNA-seq from liver of female and male mice treated with 8 daily intraperitoneal  injections of asparaginase (3 international units per gram body weight) or equivolume excipient (phosphate buffered saline) in intact mice (WT), or mice with a homozygous deletion of Gcn2 (Gcn2-/-), or mice with a homozygous deletion of Atf4 (Atf4-/-).  All mice were 8-12 weeks old and on the C57BL/6J genetic background for at least 8 generations. Three mice were used for each genotype and treatment  (Total = 18 samples).

first: Tracy

middle: G

last: Anthony


title: The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci (RNA-Seq)

status: Public on Apr 28 2017

city: Shanghai

first: Heng

address: 3888 Chenhua Rd, Gate 3

department: Shanghai Center for Plant Stress Biology

institute: Chinese Academy of Sciences

summary:
Background: The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in noncoding RNA-directed DNA methylation in Arabidopsis thaliana.
Results: Through forward genetic screens we identified PKL, a gene required for developmental regulation in plants, as a factor promoting transcriptional silencing at the transgenic RD29A promoter. Mutation of PKL results in DNA methylation changes at more than half of the loci that are targeted by RNA-directed DNA methylation (RdDM). A small number of transposable elements and genes had reduced DNA methylation correlated with derepression in the pkl mutant, though for the majority, decreases in DNA methylation are not sufficient to cause release of silencing. The changes in DNA methylation in the pkl mutant are positively correlated with changes in 24-nt siRNA levels. In addition, PKL is required for the accumulation of Pol V-dependent transcripts and for the positioning of Pol V-stabilized nucleosomes at several tested loci, indicating that RNA polymerase V-related functions are impaired in the pkl mutant.
Conclusions: PKL is required for transcriptional silencing and has significant effects on RdDM in plants. The changes in DNA methylation in the pkl mutant are correlated with changes in the noncoding RNAs produced by Pol IV and Pol V. We propose that at RdDM target regions, PKL may be required to create a chromatin environment that influences noncoding RNA production, DNA methylation and transcriptional silencing.

overall_design: BS-seq, mRNA-seq, and sRNA-seq in 2-week-old seedlings of WT, nrpd1-3, nrpe1-11 and pkl-1; mRNA-seq and sRNA-seq were performed with 3 biological replicates

first: Rong

last: Yang

first: Zhimin

last: Zheng

first: Huan

last: Huang

first: Daisuke

last: Miki

first: Jian-Kang

last: Zhu


title: Transcription factor Interplay between LEAFY and APETALA1/ CAULIFLOWER during Floral Initiation

city: Dublin

first: Pat

last: Ryan

address: College Green

country: Ireland

institute: TCD

summary: The transcription factors LEAFY (LFY) and APETALA1 (AP1), together with the AP1 paralog CAULIFLOWER (CAL), control the onset of flower development in a partially redundant manner. This redundancy is thought to be mediated, at least in part, through the regulation of a shared set of target genes. However, whether these genes are independently or cooperatively regulated by LFY and AP1/CAL, is currently unknown. To better understand the regulatory relationship between LFY and AP1/CAL during floral initiation, we monitored the activity of LFY in the absence of AP1/CAL function. We found that the regulation of several known LFY target genes is unaffected by AP1/CAL perturbation, while others appear to require AP1/CAL activity. Furthermore, we obtained evidence that LFY and AP1/CAL control the expression of some genes in an antagonistic manner. Notably, these include key regulators of floral initiation such TERMINAL FLOWER1 (TFL1), which had been previously reported to be directly repressed by both LFY and AP1. We show here that TFL1 expression is suppressed by AP1 but promoted by LFY. We further demonstrate that LFY has an inhibitory effect on flower formation in the absence of AP1/CAL activity. We propose that LFY and AP1/CAL may act as part of an incoherent feed-forward loop to control the establishment of a stable developmental program for the formation of flowers.

overall_design: Two ChIP-Seq datasets performed in Arabidopsis lines expressing a LFY-GR construct. The first ChIP uses a LFY specific polyclonal AB generated by the authors. The second is an input control with no exposure to the LFY specific AB.

first: Kevin

last: Goslin

first: Beibei

first: Antonio

last: Serrano-MIslata

first: Liina

last: Rae

first: Patrick

middle: T

first: Kamila

last: Kwasniewska

first: Bennett

last: Thomson

first: Diarmuid

last: Ó'Maoiléidigh

first: Francisco

last: Madueño

first: Frank

last: Wellmer

first: Emmanuelle

last: Graciet


title: Epigenetic identity in AML is mostly dependent on disruption of non-promoter regulatory elements and reveals potentially antagonistic effects of mutations in epigenetic modifiers

city: New York

first: Jacob

middle: Lowell

last: Glass

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

type: Methylation profiling by high throughput sequencing


title: Transcriptome sequencing identify a recurrent CRYL1-IFT88 chimeric transcript in hepatocellular carcinoma

city: Fuzhou

first: Yi

state: Fujian Province

address: 134 Dong Street

department: Department of Pathology

institute: Fujian Provincial Hospital

summary: We performed transcriptome sequencing for hepatocellular carcinoma (HCC) and adjacent non-tumorous tissues to investigate the molecular basis of HCC. Nine HCC patients were recruited and differentially expressed genes (DEGs) were identified. Candidate fusion transcripts were also identified. Further RT-PCR and Sanger sequencing experiments were performed to validate potential recurrent fusion transcripts in other 54 pairs of tumor and adjacent non-tumor samples. A total of 1943 DEGs were detected, including 690 up-regulated and 1253 down-regulated genes, and enriched in ten pathways, especially cell cycle, DNA replication, p53 and complement and coagulation cascades. Seven candidate fusion genes were detected and CRYL1-IFT88 was successfully validated in the discovery sequencing sample and another 5 tumor samples with the recurrent rate of about 9.52% (6/63). The full length of CRYL1-IFT88 was obtained by 3' and 5' RACE. The function of the fusion transcript is closed to CRYL1 because it contained most of domain of CRYL1. According to the bioinformatics analysis, IFT88, reported as a tumor suppressor, might be seriously depressed in the tumor cell with this fusion because the transcript structure of IFT88 was totally changed. The function depression of IFT88 caused by gene fusion CRYL1-IFT88 might be associated with tumorigenesis or development of HCC.

overall_design: RNA-Seq for tumor and adjacent non-tumorous tissues from nine hepatocellular carcinoma (HCC) patients.

first: Yangyang

last: Deng


title: Genome-wide transcriptional and epigenomic map of primary and metastatic Sonic Hedgehog subgroup medulloblastomas

city: Sioux Falls

first: Haotian

last: Zhao

state: SD

address: 2301 E. 60th St. North

department: Children's Health Research Center

institute: Sanford Research

summary: We report findings that illuminate a dynamic metastasis pathway in the common pediatric brain tumor medulloblastoma.

overall_design: We examined binding states of H3K27ac and ATOH1 in primary and metastatic medulloblastoma driven by ATOH1 in collaboration with aberrant Sonic Hedgehog (SHH) signaling.

first: Erliang

last: Zeng


title: Cytotoxic Vibrio T3SS1 Rewires Host Gene Expression to Subvert Cell Death Signaling and Activate Cell Survival Networks

city: Dallas

first: Nicole

middle: Janell

last: De Nisco

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UTSW Medical Center

summary:
Abstract: The type three secretion system 1 (T3SS1) of the marine bacterium, Vibrio parahaemolyticus, orchestrates a host cell death comprised of distinct stages defined by the action of specific effectors. To understand how the host responds to the T3SS1, we analyzed gene expression changes over time in infected primary fibroblasts by RNA-seq. The host cell’s transcriptional response was rapid, robust and temporally distinct. Despite the lethal action of the T3SS1 effectors, network analysis indicated that the integrated host transcriptional response to T3SS1 effectors activated cell survival and repressed cell death networks, suggesting that T3SS1 masks its cytotoxicity to the host cell. Pathway analysis revealed that signaling through several pathways, including MAPK pathways, was specifically altered by T3SS1. Overall, this temporal analysis of T3SS1-mediated subversion of host cell signaling revealed cytoprotective pathways that are likely hijacked by many bacterial pathogens to ensure survival.
Methods: We employed genome-wide transcriptional profiling methods (RNA-seq) to measure changes in gene expression over time in response to infection with POR4:T3SS1- or POR3:T3SS1+. Time points were collected 45, 60, 75 and 90 minutes post-infection. In total, libraries from 27 samples (triplicates of uninfected, POR3/4 at t=45, 60, 75, and 90 minutes) were sequenced and mapped to the human genome. EdgeR was used for differential expression analysis using statistical cutoffs of of false discovery rate (FDR) ≤0.01, log2counts-per-million (log2CPM) ≥0 and fold change (FC) cutoffs of -1.5≥ FC ≥1.5

overall_design: Overall 27 samples were analyzed. Each of the 9 conditions was performed in triplicate. There are two sets of reference groups. Group one is unifected cells collected at the end of the time course. Group 2 are cells infected with a non-cytoxic V. para strain (POR4), which does not express a functional T3SS1 and samples of these were collected at each time point indicated.

first: Kim

last: Orth

first: Chao

last: Xing

first: Mohammed

last: Kanchwala


title: The regulatory network of OsNAC6 targets drought-related genes orchestrating rice drought tolerance

status: Public on Apr 29 2017

city: Pyeongchang

first: Pil Joong

last: Chung

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

country: South Korea

institute: Seoul National University

summary: OsNAC6 is a stress responsive NAC transcription factor in rice known as a regulator for the transcriptional networks of the drought tolerance mechanisms. However, little is known about the associated molecular mechanisms for drought tolerance. Here, we identified OsNAC6-mediated root structural adaptation such as increased root number and root diameter that was sufficient to confer drought tolerance. Multiyear (5 years) drought field tests clearly demonstrated that OsNAC6 overexpression in roots produced higher grain yield under drought conditions. Genome-wide analyses revealed that OsNAC6 directly up-regulated 13 genes. Taken together, OsNAC6 is a valuable candidate for genetic engineering of drought-tolerant high-yielding crops.

overall_design: ChIPseq using roots of NT and RCc3::6xmyc-OsNAC6 plants

first: Pil

first: Ju-Kon

last: Kim


title: Chromochloris zofingiensis response to high light

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

summary: RNA-Seq of Chromochloris zofingiensis following the transition from medium light to high light.

overall_design:
Cultures of Chromochloris zofingiensis were grown diurnally (16 h light, 8 h dark) in 100 μmol photons m^−2 s^−1 medium light (ML).
At t = 0, cultures were transferred to 400 μmol photons m^−2 s^−1 high light (HL). Samples were collected in quadruplicate at 0, 0.5, 1, 3, 6, and 12 h for ML cultures and at 0.5, 1, 3, 6, and 12 h for HL cultures.
All samples were collected during the 16hr daylight period.

first: Melissa

last: Roth

first: Shawn

last: Cokus

first: Andreas

last: Walter

first: David

last: Lopez

first: Erika

last: Erickson

first: Benjamin

last: Endelman

first: Daniel

last: Westcott

first: Carolyn

last: Larabell

first: Sabeeha

last: Merchant

first: Matteo

last: Pellegrini

first: Krishna

middle: K

last: Niyogi


title: Achilles is a circadian clock controlled gene that regulates innate immune function in Drosophila

city: St. Louis

first: Jiajia

last: Li

state: Missouri

address: 435 Research Building, One University Boulevard

department: Biology

institute: University of Missouri-St. Louis

summary: RNAseq transcriptional profiling of Drosophila heads from Achilles RNAi or control animals

overall_design: Achilles RNAi and control flies; males and females; 5-8 heads per sample, 3-4 bilogical replicates each.

first: Michael

last: Hughes

first: Joseph

last: Logsdon

first: Lisa

last: Rois

first: Maria

last: Scuderi

first: Edith

last: Fejer

first: Diana

last: Gamba

last: Michalski

first: Natalie

last: Hartmann


title: C/EBPalpha regulated microRNA expression profiling in inducible K562-C/EBPalpha-ER cells

city: Leipzig

first: Gerhard

last: Behre

address: Johannisallee 32a

department: Hematology and Oncology

country: Germany

institute: University of Leipzig

type: Non-coding RNA profiling by high throughput sequencing

summary: C/EBPalpha is an important myeloid transcription factor that is inactivated in approximately 50% of acute myeloid leukemia cases. We were interested in microRNAs that are regulated by C/EBPalpha during myeloid differentiation.

overall_design: We induced K562-C/EBPalpha-ER cells for 6 hours with 5µM ß-estradiol or ethanol as control. NGS was performed out of 3 independent experiments.

first: Alexander

last: Wurm


title: Transcriptional profiling of hair follicle stem cells in the presence and absence of Regulatory T-cells

city: San Francisco

first: Niwa

last: Ali

address: 513 Parnassus Avenue HSW1201b

department: Dermatology

institute: UCSF

summary:
Purpose: The goals of this study were to identify Pathways that Tregs utilize in the skin to maintain tissue homesostasis in the context of hair follcile cycling.
Methods: Hair follicle stem cells (HFSCs), in the presence and absence of Tregs, were induced into cycle through a model of depilation induced anagen. HFSCs were then purified by cell sorting at day 4 post depilation based on cell surface marker expression (CD45 negative, MHC Class II negative, Sca-1 negative, EpCAM negative, CD34 Positive, Integrin alpha6 High) to generate mRNA transcription profiles.
Results: Transcriptional profiling revealed a significant reduction in proliferation/differentiation associated genes expressed in HFSCs isolated from Treg depleted mice
Conclusion: Our study represents the first detailed analysis of Treg modulation of tissue stem cell behaviour

overall_design: mRNA profiles of HFSC isolated from 7-10 week old WT and Foxp3-DTR mice at 4 days post depilation of dorsal skin.

last: Rosenblum


title: Molecular phenotyping of multiple mouse strains under metabolic challenge uncovers Elovl2 as a novel regulator of glucose-induced insulin secretion

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: Defective insulin secretion by pancreatic β cells underlies the development of type 2 diabetes (T2D). High fat diet-fed mice are commonly used to study diabetes progression, but studies are usually limited to a single strain, such as C57Bl/6J. Here, we use a systems biology approach to integrate large phenotypic and islet transcriptomic data sets from six commonly used strains fed a high fat or regular chow diet to identify genes associated with glucose intolerance and insulin secretion. One of these genes is Elovl2, encoding very long chain fatty acid elongase 2. ELOVL2 is responsible for the synthesis of the polyunsaturated fatty acid, docosahexaenoic acid (DHA). We show that DHA rescues glucose-induced insulin secretion and cytosolic Ca2+ influx impaired by glucolipotoxicity, and that Elovl2 over-expression is able to restore the insulin secretion defect under these conditions. We propose that increased endogenous DHA levels resulting from Elovl2 up-regulation counteracts the insulin secretion defect associated with glucolipotoxicity. Although we focus our experimental validation on Elovl2, the comprehensive data set and integrative network model we used to identify this candidate gene represents an important novel resource to dissect the molecular aetiology of β cell failure in murine models.

overall_design: 6 mouse strains, 4 time points, 2 diets

first: Lara

last: Bellini

first: Céline

last: Cruciani-Guglielmacci

first: Jessica

last: Denom

first: Neïké

last: Fernandez

first: Priscilla

last: Normandie-Levi

first: Nadim

last: Kassis

first: Tracy

last: Gorman

first: David

middle: M

last: Smith

first: Anna

last: Marley

first: Robin

last: Liechti

first: Leonore

last: Wigger

first: Frédéric

last: Burdet

first: Anne-Laure

last: Lefèvre

first: Isabelle

last: Werlhe

first: Ingo

last: Uphues

first: Tobias

last: Hildebrandt

first: Werner

last: Rust

first: Catherine

last: Bernard

first: Alain

last: Ktorza

first: Ioannis

last: Xenarios

first: Alice

last: Marmugi

last: Leclerc

first: Guy

last: Rutter

first: Hervé

last: Le Stunff

first: Christophe

last: Magnan

first: Bernard

last: Thorens


title: Regulatory and evolutionary footprints of messenger RNA secondary structure in primate transcriptomes

city: Wilmington

first: Qi

last: Zheng

state: DE

address: 1701 Rockland Road

institute: Nemours Children's Health

summary: Messenger RNA secondary structure is critical to all aspects of post-transcriptional regulation. However, the global regulatory and evolutionary significance of mRNA secondary structure remains largely illusive. Here, we describe a transcriptome-wide analysis of RNA secondary structure in humans and two non-human primates, based on a high-throughput, nuclease-mediated, structure mapping approach. Using this methodology, we uncover global patterns of mRNA secondary structure, which we find to be conserved through primate evolution. We provide evidence for secondary structure-based regulatory pathways, which impact on gene expression through associations with translational machinery and RNA-binding proteins, including components of the microprocessor complex. Our results lend support to an unexpected, conserved mechanism by which highly structured regions of mRNAs serve as processing sites for small RNAs, resulting in subsequent turnover.

sample_organism:
Macaca fascicularis
Macaca mulatta
Homo sapiens

overall_design: Global mRNA secondary structure analysis in primate transcriptomes using high-throughput, nuclease-mediated, structure mappinng approaches of dsRNA-seq and ssRNA-seq, also with polyA+ mRNA-seq, smRNA-seq (small RNA), and genome-wide mapping of uncapped and cleaved transcripts (GMUCT); these NGS-seq experiments were carried out in three primate brains as well as three different cell lines, both in in vitro and in vivo.

first: Ian

last: Silverman

first: Fan

last: Li

first: Matthew

middle: R

last: Willmann

first: Nathan

last: Berkowitz

first: Allison

middle: L

last: Richards

first: Brian

last: Gregory


title: EBF2-regulated epigenome in brown adipose tissue [ChIP-Seq]

status: Public on Apr 27 2017

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: EBF2 activates the expression of brown fat-selective genes in adipocytes, but whether EBF2 regulates these genes via direct binding was unknown. To address this question, we analyzed the genome-wide binding profile of EBF2 in BAT using chromatin immunoprecipitation followed by deep sequencing (ChIP-seq). To determine if EBF2 is required for the activity of lineage-specific enhancers, we examined the levels of PPARγ, RNA Polymerase II (Pol II), and H3K27ac at brown fat-specific genes in wildtype (WT) and Ebf2 KO BAT.

overall_design: Brown adipose tissues were collected from Ebf2 knockout and wildtype mice and ChIP-seq was performed for EBF2, PolII, PPARy, and H3K27ac.

first: Suzanne

middle: N

last: Shapira

first: Sona

last: Rajakumari

first: Alexander

middle: P

last: Sakers

first: Jeff

last: Ishibashi

last: Harms

first: Kyoung-Jae

last: Won

first: Patrick

last: Seale


title: Genome-wide analysis of DNA hydroxymethylation and methylation during epstein-barr virus infection.

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

summary: Extensive DNA methylation in promoter regions is observed in gastric cancer with Epstein-barr virus (EBV) infection and EBV infection is the cause to induce this extensive hypermethylaiton phenotype in gastric epithelial cells. From transcriptome analysis, we found that TET2, one of the demethylase enzymes, was downregulated by EBV infection in gastric epithelial cell line MKN7. TET2 was overexpressed in a gastric epithelial cell line, GES1, to see its function and the hydroxymethylation, a byproduct of DNA demethylation, acquired genes by TET2 overexpression and methylation acquired genes by EBV infection were significantly overlapped. These suggested that hydroxymethylation by TET2 could function to keep unmethylated status of genes before EBV infection, and TET2 depression could contribute to methylation acquisition of these target genes after EBV infection.

overall_design:
Hydroxymethylation analysis in TET2 over expressed cell line, and methylation and transcriptome analysis in EBV infected cell lines.
Examination of 2 different histone modifications in 2 cell types.

first: Atsushi

last: Kaneda

first: Hiroe

last: Namba-Fukuyo


title: Ebf2 Knockout Brown Adipose Tissue

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

overall_design: Refer to individual Series


title: Transcriptional profiling of Regulatory T-cells isolated from adult skin and skin draining lymph nodes (SDLNs)

first: Niwa

last: Ali

summary:
Purpose: The goals of this study were to identify preferential gene expression signatures that are unique to telogen skin resident Tregs relative to peripheral Tregs
Methods: Tregs from telogen skin and SDLNs were purified by cell sorting (using the Treg GFP reporter mouse line Foxp3-DTR/GFP) to generate mRNA transcription profiles.
Results: Transcriptional profiling revealed a unique Skin treg signature relative to SDLN Tregs
Conclusion: Our study represents the first detailed analysis of the skin Treg transcriptome.

overall_design: mRNA profiles of skin and SDLN Tregs isolated from 6 week old Foxp3-DTR/GFP mice.

first: Tiffany

last: Scharschmidt

first: Michael

middle: D

last: Rosenblum


title: Ebf2 Knockout Brown Adipose Tissue [RNA-Seq]

summary: The helix-loop-helix transcription factor Early B-Cell Factor 2 (EBF2) is required for the differentiation and function of brown and beige adipocytes. The presumptive BAT in Ebf2 knockout (KO) animals has a white-fat like morphology and molecular profile. We examined the transcriptome of WT and Ebf2 KO BAT by high-throughput sequencing.

overall_design: Two control replicates (wildtype mice) and two experimental replicates (Ebf2 KO mice) were analyzed

first: Matthew

middle: J


title: Piwi is required during Drosophila embryogenesis to license dual-strand piRNA clusters for transposon repression in adult ovaries

city: MONTPELLIER

first: SEVERINE

last: CHAMBEYRON

address: 141, rue de la Cardonille

department: Institute of Human Genetics

institute: CNRS


title: Identification of differentially methylated regions between the GDDH13 and GDDH18 apple genotypes at two developmental stages

city: Beaucouzé

first: Jean-Marc

last: Celton

address: 42 rue Georges Morel

institute: INRA-IRHS

summary: The main objective of this analysis was to sequence the epigenome of two apple (Malus domestica) doubled haploid 'Golden Delicious' fruits (GDDH13 and GDDH18). Our secondary objective was to identify differentially methylated regions between DNA purified from the GDDH13 genotype and the GDDH18 genotypes at two developmental stages.

overall_design: Six samples have been analyzed. The six samples were collected from pools of young fruits. After DNA purification,  Bisulfite treatment was applied to determine the cytosine methylation status. Illumina reads of the three libraries were generated using an Illumina Hiseq instrument. Differencialy methylated regions were computed according to Hagmann et al. 2015.

first: Nicolas

last: Daccord

first: Etienne

last: Bucher


title: Epigenetic identity in AML is mostly dependent on disruption of non-promoter regulatory elements and reveals potentially antagonistic effects of mutations in epigenetic modifiers [mouse]

first: Jacob

last: Glass

summary: Aberrant DNA methylation of gene promoters is a hallmark of AML. To define more precisely how cytosine methylation is redistributed in AML, we performed base-pair resolution methylome sequencing in 119 patients. We find that leukemic DNA methylation patterning is tightly linked to somatic mutations and primarily driven by regulatory elements outside of promoters and by CpG shores as opposed to CpG islands. Active enhancers displayed much stronger focal differential methylation than promoters and were generally aberrantly hypomethylated except in IDH2 mutant and CEBPA silenced AMLs. AMLs with dominant hypermethylation feature greater epigenetic disruption of promoters. Those with dominant hypomethylation, such as DNMT3A mutated AMLs, display greater disruption of distal and intronic regions. IDH mutant AMLs manifest profound hypermethylation whereas DNMT3A mutant AMLs manifest profound hypomethylation of a different set of CpGs.  In striking contrast, AMLs with co-occurring IDH1 and DNMT3A mutations exhibited epigenetic antagonism in which most CpGs affected by either mutation alone were no longer affected in the double mutant cases.

sample_organism:
Homo sapiens
Mus musculus

overall_design: Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) was performed on Idh2, Dnmt3a, and Idh2/Dnmt3a mutant mice. Idh2 mouse profiling is detailed in PMID: 28193779 and deposited here (LSK controls are deposited under GSE57114). Dnmt3a mutant and LSK control mouse profiling is detailed in PMID: 26710888 and deposited under GSE86827 with a set of LSK controls under GEO series GSE74165

first: Francine

middle: E

last: Garrett-Bakelman

first: Olga

last: Guryanova

first: Robert

last: Bowman

first: Shira

last: Redlich

first: Andrew

last: Intlekofer

first: Cem

last: Meydan

first: Mame

last: Fall

first: Alicia

last: Alonso

first: Craig

middle: B

last: Thompson

first: Ross

last: Levine

first: Ruud

last: Delwel

first: Ari

last: Melnick

first: Maria

last: Figueroa


title: ENPP1 Mutation Causes Recessive Cole Disease by Altering Melanogenesis

city: Singapore

first: Bruno

last: Reversade

state: Singapore

address: #05-40 Immunos Building, 8A Biomedical Grove,, Institute of Medical Biology/ Bruno Reversade laboratory, 138648, Singapore

country: Singapore

institute: Institute of Medical Biology/A*STAR, Singapore

summary:
Propose: We used next-generation RNA sequencing (RNA-seq) to characterize the transcriptional changes  in primary human melanocytes during recessive Cole disease. Our patient carried missense mutation in the ENPP1 gene (c.358T>C; p.C120R). RNA-seq was performed using mRNA extracted from primary hypo- and hyper-pigmented melanocytes isolated from  affected patient  and melanocytes from his healthy heterozygous sibling  and an aged- and ethnicity-matched control.
Results: A pairwise fold-change comparison was performed and genes were computationally filtered using a cutoff of more than 2 fold change and P<0.01. We first compared hyper-pigmented melanocytes to each control individually and  then overlapped the results to obtain a list of 1041 up-regulated and 692 down-regulated genes. The same analysis was done for hypo-pigmented melanocytes to found that 535 genes were up-regulated and 520 were down-regulated. Finally, to obtain a profile of the overall differential gene expression, down-regulated genes in hyper and hypo-pigmented cells were overlapped to identify 143 genes that were down-regulated in patient melanocytes compared to controls regardless of pigmentation status. Similar analysis was performed to obtain the list of 172 up-regulated genes. We selected 36 deregulated genes, most of which were associated with melanocyte development and pigmentation signaling pathways, and validated 32 of them by Q-PCR, indicating that our RNA-Seq data was accurate and reliable.
Conclusion: Our study represents the first analysis of hypo- and hyper-pigmented primary melanocytes isolated from affected patient  versus healthy controls in recessive Cole disese pathology.

overall_design: mRNA profiles of hyper- and hypo-pigmented mutant melanocytes, heterozygous and wild type melanocytes were sequenced in triplicate on the Hiseq 2500 High output 100PE

first: Marwa

last: Chourabi

first: Liang

last: Dai

first: Mei

middle: S

last: Liew

first: Pui

last: Wong

first: Simon

last: Denil

first: Kim

last: Robinson

first: Shawn

last: Lim

first: Carine

last: Bonnard


title: Piwi is required during Drosophila embryogenesis to license dual-strand piRNA clusters for transposon repression in adult ovaries [ChIP-seq]

first: SEVERINE

last: CHAMBEYRON

summary: Most piRNAs in the Drosophila female germline are transcribed from heterochromatic regions called dual-strand piRNA clusters. Histone 3 lysine 9 trimethylation (H3K9me3) is required for licensing piRNA production by these clusters. However, it is unclear when and how they acquire this permissive heterochromatic state. Although it has been suggested that piRNA cluster licensing is Piwi-independent, here we show that transient Piwi depletion in Drosophila embryos, using a refined knock-down system, results in H3K9me3 decrease at piRNA clusters. This is accompanied by aberrant maturation of piRNA precursor transcripts, accumulation of transposable element transcripts and female sterility. Conversely, Piwi knock-down at later developmental stages does not disturb piRNA cluster licensing, as previously reported. These results indicate that the identity of piRNA clusters is epigenetically acquired in a Piwi-dependent manner during a limited embryonic development window, which is reminiscent of the widespread genome reprogramming occurring during early mammalian zygotic development.

overall_design: 3 independate biological triplicates of Chip H3K9me3 input and IP were performed for each of the 2 genotypes (piwi-embKD and white_embKD).

first: Abdou

last: Akkouche

last: Mugat

first: Bridlin

last: Barckmann

first: Carolina

last: Varela-Chavez

first: Blaise

last: Li

first: Raoul

last: Raffel

first: Alain

last: Pélisson

first: Séverine

last: Chambeyron


title: Piwi is required during Drosophila embryogenesis to license dual-strand piRNA clusters for transposon repression in adult ovaries [smallRNA-seq]

overall_design: Study of small regulatory RNA populations in D. melanogaster ovaries in 3 types of libraries: 1) Transient embryonic temperature-dependent depletion of piwi (at 28°, 2 replicates), 2) Transient embryonic temperature-dependent depletion of white (at 28°, 2 replicates) and 3) Same genotype as type 1, but temperature-dependent depletion not activated (at 18° all along the development, 1 replicate).

first: Bruno


title: Identification of extensive cellular diversity and maturation of active neuronal networks in long-term cultures of human brain organoids

city: Cambridge

first: Paola

last: Arlotta

state: MA

address: 7 Divinity Avenue

department: Stem Cell & Regenerative Biology

institute: Harvard University

summary: We analyzed  gene expression in  over  80,000  individual  cells  isolated  from  31  human  whole-brain  organoids  that  has developed  for  3-6  months.  We  find  that  organoids  can  generate a  broad  diversity  of  cells, which  we  show  are  related  to  known  endogenous  classes, including  subpopulations  of neurons and progenitors of the cerebral cortex

overall_design: Single cell Droplet sequencing of human cerebral organoid

first: Giorgia

last: Quadrato

first: Tuan

last: Nguyen

first: Evan

middle: Z

last: Macosko

first: John

last: Sherwood

first: Daniel

last: Berger

first: Natalie

last: Maria

first: Jorg

last: Scholvin

first: Melissa

last: Goldman

first: Justin

last: Kinney

first: Ed

last: Boyden

first: Jeff

last: Lichtman

first: Ziv

last: Williams

first: Steven

middle: A

last: McCarroll


title: mRNA expression levels in splenic human mononuclear cells of mock- and HIV-1-infected humanized mice

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

institute: The Institute of Medical Science, The University of Tokyo

summary: Through RNA sequencing and gene ontology analyses, we report that immune activation is elicited in the spleen of 4 HIV-1-infected humanized mice when compared to 4 mock-infected humanized mice.

overall_design: mRNA expression profiles in the splenic human mononuclear cells of HIV-1-infected humanized mice at 6 weeks post-infection (n=4) and mock-infected humanized mice (n=4) were generated by RNA sequencing. RNA was extracted using QIAamp RNA Blood Mini kit (Qiagen). RNA sequencing was conducted in Medical & Biological Laboratories, co (Nagoya, Japan).

first: Yusuke

last: Nakano

first: Shinji

last: Nakaoka

first: Yoshio

last: Koyanagi


title: An ES cell–specific NuRD complex functions through interaction with Wdr5

city: Worcester

first: Thomas

last: Fazzio

state: Massachusetts

address: 364 Plantation Street

institute: University of Massachusetts Medical School

summary: The Nucleosome Remodeling and Deacetylase (NuRD) complex is a chromatin regulatory complex that functions as a transcriptional co-repressor in metazoans. The NuRD subunit Mbd3 is essential for targeting and assembly of a functional NuRD complex as well as embryonic stem cell (ESC) pluripotency. Three Mbd3 isoforms (Mbd3a, Mbd3b, and Mbd3c) are expressed in mouse. Here, we find that the Mbd3c isoform contains a unique 50–amino acid N-terminal region that is necessary for Mbd3c to specifically interact with the histone H3 binding protein Wdr5. Domain analyses of Wdr5 reveal that the Wdr5 H3K4/MLL binding pocket is required for interaction with Mbd3c. We find that while Mbd3c KO ESCs differentiate normally, Mbd3c is redundant with the Mbd3a and Mbd3b isoforms in regulation of gene expression and ESC pluripotency, with the unique Mbd3c N-terminus required for this redundancy. Together, our data characterize a novel NuRD complex variant that functions specifically in ESCs

overall_design: Gene expression profiles generated by RNA-seq of Mbd3 isoform mutant mouse embryonic stem cells

first: Ly-sha

last: Ee

first: Kurtis

last: McCannell

first: Yang

last: Tang

first: Nancy

last: Fernandes

first: William

last: Hardy

first: Michael

last: Green

first: Feixia

last: Chu

middle: G


title: Piwi is required during Drosophila embryogenesis to license dual-strand piRNA clusters for transposon repression in adult ovaries [RNA-seq]

first: SEVERINE

last: CHAMBEYRON

overall_design: Ribo-Zero ribosomal depletion total RNA profil of D. melanogaster ovaries in 2 experimental conditions : control (white-embKD) and piwi-embKD. 2 independant biological replicates for each condition were performed.

first: Abdou

last: Akkouche

first: Bruno

last: Mugat

first: Bridlin

last: Barckmann

first: Carolina

last: Varela-Chavez

first: Blaise

last: Li

first: Raoul

last: Raffel

first: Alain

last: Pélisson

first: Séverine

last: Chambeyron


title: Differential gene expression of endosphere and soil Bacillus mycoides isolate in response to root exudates using RNA sequencing

status: Public on Apr 26 2017

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary: In general, the endosphere isolate EC18 showed more numbers of genes significantly altered in the presence of root exudates than the soil isolate SB8 . Some of the altered genes in the two strains showed overlap. Some of these genes were previously reported to be involved in microbe-plant interactions, such as organic substance metabolism, oxidation reduction, transmembrane transportation and a subset with putative or unknown function. It was also found some genes showed opposite trend among the two strains.

overall_design: Two strains, two conditions.

first: Yanglei

last: Yi

last: de Jong

first: Oscar

last: Kuipers


title: Alternative poly(A) in Alzheimer's disase

city: New York

first: Shahar

last: Barbash

address: 1230 York Ave

institute: The Rockefeller University

summary: Alternative polyadenylation (APA) contributes to post-transcriptional regulation, but its role in Alzheimer’s disease (AD) is largely unknown. Using high-resolution SQUARE multiple 3’ primer-based sequencing, we discovered massive APA differences in temporal gyrus tissues from demented AD patients compared to either healthy controls or non-demented donors with AD neuropathology (NDWP). Advanced statistics, microfluidics RT-PCR and protein measurements validated known and novel APA-modified 3’-intact transcripts. Moreover, APA modifications, more than total transcript counts, distinguished AD patients from both controls and NDWP donors and identified cell type-characteristic, cognition-associated and neuropathology-related changes. AD-enhanced APA variants included known therapeutic targets of brain, vascular and autoimmune disorders, predicting co-involvement of these target genes in AD progression; AD/NDWP increases in 3’-intact proteinopathy-related hnRNP mRNAs were inversely associated with protein decreases, whereas NDWP-potentiated cognition was accompanied by distinct ATP and mitochondrial variants. APA variations thus provide a novel resource of unique value for both basic and translational neuroscience researchers.

overall_design: Examination of poly adenylation sites in brain tissues of Alzheimer's disease patients, non-demented with Alzheimer's disease like pathology and non-demented without Alzheimer's disease like pathology.

first: Hermona

last: Soreq

first: Alexander

last: Seitz


title: Nucleosome Repositioning During Differentiation of a Human Myeloid Leukemia Cell Line

city: Colchester

first: Vladimir

last: Teif

address: Wivenhoe Park

department: School of Life Sciences

country: United Kingdom

institute: University of Essex

summary: Cell differentiation is associated with changes in chromatin organization and gene expression. In this study, we examine chromatin structure following differentiation of the human myeloid leukemia cell line (HL-60/S4) into granulocytes with retinoic acid (RA) or into macrophage with phorbol ester (TPA). We performed ChIP-seq of histone H3 and its modifications, analyzing changes in nucleosome occupancy, nucleosome repeat length, eu-/heterochromatin redistribution and properties of epichromatin (surface chromatin adjacent to the nuclear envelope). Nucleosome positions changed genome-wide, exhibiting a specific class of alterations involving nucleosome loss in extended (~1kb) regions, pronounced in enhancers and promoters.  Genes that lost nucleosomes at their promoters showed a tendency to be upregulated. On the other hand, nucleosome gain was not systematic at functional elements and did not show simple effects on transcript levels. The average genome-wide nucleosome repeat length (NRL) did not change significantly with differentiation.  However, we detected an approximate 10 bp NRL decrease around the hematopoietic transcription factor (TF) PU.1 and the architectural protein CTCF, suggesting an effect on NRL proximal to TF binding sites. Nucleosome occupancy changed in regions associated with H3K4me3 in differentiated cells, compared to untreated HL-60/S4 cells. Epichromatin regions, largely unaffected by cell differentiation, revealed an increased GC content and high nucleosome density compared to surrounding chromatin. Epichromatin showed depletion of major (permissive and repressive) histone modifications and revealed enrichment with PML body-associated genes. In general, chromatin changes during HL-60/S4 differentiation appeared to be more localized, compared to changes among diverse cell types studied elsewhere, suggesting that the cell lineage differentiation of HL-60/S4 cells involves less drastic nucleosome repositioning.

overall_design: In this study, we examine chromatin structure following differentiation of the human myeloid leukemia cell line (HL-60/S4) into granulocytes with retinoic acid (RA) or into macrophage with phorbol ester (TPA). We performed ChIP-seq of histone H3 and its modifications.

first: Jan-Philipp

last: Mallm

first: Tanvi

last: Sharma

first: David

last: Welch

first: Karsten

last: Rippe

first: Jörg

last: Langowski

first: Roland

last: Eils

first: Ada

last: Olins

first: Donald


title: Response in the NGF withdrawal model

city: South San Francisco

first: Kevin

last: Huang

address: 1 DNA Way

department: Bioinformatics

institute: Genentech

summary:
RNA was purified from DRG neurons grown for 4 days in culture.

The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0011148

overall_design: RNA sequencing from primary DRG neurons grown for 4 days in vitro and deprived of NGF for 4.5 h in the presence of DMSO, DLKi 400 nM or ISRIB 400 nM. NGF with DMSO was used as control.


title: Lineage specific differentiation is influenced by state of human pluripotency [RNA-seq]

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

summary: Human pluripotent stem cells (hPSCs) have been reported in naïve and primed states. However, the ability of human PSCs to generate mature cell types is the only imperative property for translational utility. Here, we reveal that the naïve state enhances self-renewal capacity while restricting lineage differentiation in vitro to neural default fate. Gene expression analyses indicate expression of multiple lineage associated transcripts in naïve hPSCs and thus failed to predict biased functional differentiation.  Naïve hPSCs can be converted to primed allowing recovery of multilineage differentiation over long serial passage or immediately through suppression of OCT4 but not NANOG. To this end, we identified chemical inhibitors of OCT4 expression that acutely restore naïve hPSC differentiation. Our study identifies unique cell fate features and critical restrictions in human pluripotent states, and provides an approach to overcome these barriers that harness both efficient naïve hPSC growth whilst maintaining in vitro differentiation capacities essential for hPSC applications.

overall_design: hPSC lines were transduced with shRNA lentiviruses in order to assess the effects of reducing NANOG and OCT4 gene expression on differention in the naïve state.  shRNA expressing cells were sorted and then total RNA was extracted in order to perform transcriptome profiling by RNA-seq. Each experimental condition involves 2 technical replicates of 2 biological replicates (2 tech X 2 biol = 4 reads).

first: Jong

middle: H

last: Lee


title: RNA-Seq of ILC2p WT

city: Melbourne

first: Cyril

last: Seillet

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

summary: We have generated RNA-seq of ILC2 progenitors form WT bone marrow mice.

overall_design: Sorted ILC2p from 8 week-old mice were analysed in RNA-seq. Each replicate is a pool of 8 mice.

first: Aaron

last: Lum

first: Gordon

last: Smyth


title: Single cell gene expression in Dlxi1/2b::eGFP+ cells before and after migration, 4 weeks

city: Palo Alto

first: Wu

last: Wei

address: 3165 Porter Dr.

institute: Stanford Genome Technology Center

summary: We report the expression of selected genes associated with cortical, striatal and olfactory interneurons in hSS-derived Dlxi1/2::eGFP cells before (in hSS) and after migration (in hCS). By fusing hiPSC-derived fusions that were separately patterned to generate either human subpallial spheroids (hSS) or human cortical spheroids (hCS) we are able to model human interneuron migration in vitro. The aim of this experiment is to examine the gene expression of hSS-derived Dlxi1/2::eGFP cells before and after migration.

overall_design: Examination of 88 cells Dlxi1/2::eGFP cells in hSS (not migrated) and 93 Dlxi1/2::eGFP cells in hCS (migrated).

first: Saiful

last: Islam


title: A third generation therapeutic vaccine for human visceral leishmaniasis and post kala azar dermal leishmaniasis: first-in-human trial of ChAd63-KH

city: York

first: Paul

last: Kaye

address: Wentworth way

institute: University of York

summary: Whole  blood transcriptomic profiling indicated that CHAd63-KH induced innate immune responses  characterized by an interferon signature and the presence of activated dendritic cells.

overall_design: Whole transcriptome using paired RNA samples with a high dose of the vaccine, pre vaccination and 24 hour post vaccination, and a subsequent experiment showing RNAseq from a low dose of the vaccine pre vaccination, 2hours post, 24 hours post and 14 days post vaccination.

first: Mohamed

last: Osman

first: Anoop

last: Mistry

last: Keding

first: Rhian

last: Gabe

first: Elizabeth

last: Cook

first: Sarah

last: Forrester

first: Rebecca

last: Wiggins

first: Stefania

last: Di Marco

first: Stefano

last: Colloca

first: Loredana

last: Siani

first: Riccardo

last: Cortese

first: T

last: Aebischer

first: Charles

last: Lacey


title: Single cell gene expression in Dlxi1/2b::eGFP+ cells before and after migration

overall_design: Examination of Dlxi1/2::eGFP cells in hSS (not migrated) and Dlxi1/2::eGFP cells in hCS (migrated).


title: Dynamic rewiring of promoter-anchored chromatin loops during adipocyte differentiation

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Interactions between transcriptional promoters and their distal regulatory elements play an important role in transcriptional regulation; however, the extent to which these interactions are subject to rapid modulations in response to signals is unknown. Here, we use promoter capture Hi-C to demonstrate a rapid reorganization of promoter anchored  chromatin loops within four hours after induction of differentiation of 3T3-L1 preadipocytes. This reorganization is tightly coupled to dynamic changes in target gene expression. The formation of promoter-enhancer loops is tightly linked to the activation of poised (histone H3 lysine 4 mono- and dimethylated) enhancers, as evidenced by the acquisition of histone H3 lysine 27 acetylation and the binding of MED1, SMC1 and P300 proteins to these regions. Intriguingly, formation of loops connecting activated enhancers and promoters is also associated with extensive recruitment of corepressors such as NCoR and HDACs, indicating that this class of coregulators may play a previously unrecognized role during enhancer activation.

overall_design: We performed Hi-C and promoter capture Hi-C (PCHi-C) to investigate the dynamics of the 3D chromatin structure during adipocyte differentiation. We used mRNA-seq to identify changes in gene expression and ChIP-seq to map the chromatin binding of transcriptional regulators and epigenomic marks.

first: Siersbaek

last: Rasmus

first: Jesper

last: Madsen

first: Javierre

last: Biola

first: Ronni

last: Nielsen

first: Emilie

last: K. Bagge

first: Jonathan

last: Cairns

first: Steven

last: Wingett

first: Sofie

last: Traynor

first: Mikhail

last: Spivakov

first: Peter

last: Fraser


title: Single cell gene expression in Dlxi1/2b::eGFP+ cells before and after migration, 2 weeks

first: Wu

last: Wei

overall_design: Examination of 123 cells Dlxi1/2::eGFP cells in hSS (not migrated) and 106 Dlxi1/2::eGFP cells in hCS (migrated).

first: Saiful

last: Islam


title: CHD1 in yeast is recruited by transcription elongation factors and maintains H3K4me3/H3K36me3 domains at actively transcribed and spliced genes [RNA-seq]

city: Austin

first: Vishy

last: Iyer

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary: We report quantitative transcriptome data in WT and CHD1 mutant.

overall_design: RNA-seq in wild-type and CHD1 mutant.

first: Yaelim

last: Lee

first: Vishwanath


title: Lineage specific differentiation is influenced by state of human pluripotency

first: Mickie

last: Bhatia

type: Methylation profiling by genome tiling array

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

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: A Reciprocal Regulatory Loop Between TAZ/YAP and G protein Gαs Regulates Schwann Cell Proliferation and Differentiation

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

summary: Schwann cell (SC) myelination in the peripheral nervous system is essential for motor function, and uncontrolled SC proliferation occurs in cancer. Here, we show that a dual direct role for Hippo effectors TAZ and YAP in regulation of SC proliferation and myelination through modulating G protein expression and interacting with SOX10, respectively. Developmentally-regulated mutagenesis indicates that TAZ/YAP are critical for SC proliferation yet also required for their differentiation and myelination. Genome-wide occupancy mapping and transcriptome profiling reveal that nuclear TAZ and YAP promote SC proliferation by activating cell cycle regulators, while targeting critical differentiation regulators in cooperation with SOX10 for myelination. We further identified that TAZ targets and represses Gnas, encoding Gαs-protein, which opposes TAZ/YAP activities to decelerate proliferation. Gnas deletion expands SC precursor pools and blocks myelination in the sciatic nerve.  Thus, our study revealed that the Hippo/TAZ/YAP and Gαs-protein feedback circuit functions as a fulcrum balancing SC proliferation and differentiation, providing insights into molecular programming of SC lineage progression and homeostasis.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: 3 Control Samples and 3 Mutant

first: Yaqi

last: Deng

first: Lai

last: Wu

first: Shujun

last: Bai

first: Qing


title: CHD1 in yeast is recruited by transcription elongation factors and maintains H3K4me3/H3K36me3 domains at actively transcribed and spliced genes [ChIP-seq]

summary: We report genome-wide Chd1 occupancy in WT and in ten elongation factor mutants, and genome-wide H3K4me3/H3K36me3 profiles in WT and CHD1 mutant.

overall_design: ChIP-seq for Chd1 in wild-type and in ten elongation factor mutants. ChIP-seq for H3K4me3/H3K36me3 in wild-type and CHD1 mutant.


title: Biphasic metabolism and host interaction of a chlamydial symbiont

city: Vienna

first: Lena

last: König

address: Althanstrasse 14

country: Austria

institute: University of Vienna

summary: Chlamydiae are obligate intracellular bacteria comprising well-known human pathogens and ubiquitous symbionts of protists, which are characterized by a unique developmental cycle. Here we comprehensively analyzed gene expression dynamics of Protochlamydia amoebophila during infection of its Acanthamoeba host by RNA sequencing. This revealed a highly dynamic transcriptional landscape, where major transcriptional shifts are conserved among chlamydial symbionts and pathogens. Our data served to propose a time-resolved model for type III protein secretion during the developmental cycle, and we provide evidence for a biphasic metabolism of P. amoebophila during infection, which involves energy parasitism and amino acids as carbon source during initial stages and a post-replicative switch to endogenous glucose-based ATP production. This fits well with major transcriptional changes in the amoeba host, where upregulation of complex sugar breakdown precedes the P. amoebophila metabolic switch. The biphasic chlamydial metabolism represents a unique adaptation to exploit eukaryotic host cells, which likely contributed to the evolutionary success of this group of microbes.

sample_organism:
Acanthamoeba castellanii
Candidatus Protochlamydia amoebophila

overall_design: RNA-seq of endosymbionts of amoebae at 3 different time points during infection (2, 48, 96 hours post infection) and the extracellular stage; in triplicates; each of the 12 samples was sequenced on a single lane using an Illumina HiSeq2000 system

first: Alexander

last: Siegl

first: Thomas

last: Penz

first: Susanne

last: Haider

first: Cecilia

last: Wentrup

first: Julia

last: Polzin

first: Evelyne

last: Mann

first: Stephan

last: Schmitz-Esser

first: Daryl

last: Domman

first: Matthias

last: Horn


title: A heterochromatin-dependent transcription machinery drives piRNA expression

city: Aarhus

first: Peter

last: Andersen

state: Denmark

address: Universitetsbyen 83

department: MBG

institute: Aarhus University

summary: Nuclear small RNA pathways safeguard genome integrity by establishing transcription-repressing heterochromatin at transposable elements. This inevitably also targets the transposon-rich source loci of the small RNAs themselves. How small RNA source loci are efficiently transcribed while transposon promoters are potently silenced, is not understood. Here, we show that transcription of Drosophila piRNA clusters—major small RNA source loci in the animal germline—is enforced through formation of the RNA Polymerase II pre-initiation complex within repressive heterochromatin. This is accomplished through the TFIIA-L paralog Moonshiner, which is recruited to piRNA clusters via the Heterochromatin Protein-1 variant Rhino. Moonshiner triggers transcription initiation within piRNA clusters by recruiting the TATA box-binding protein (TBP)-related factor TRF2, a conserved animal TFIID core variant. Our work reveals that transcription of heterochromatic small RNA source loci relies on direct recruitment of the core transcriptional machinery to DNA via histone marks rather than sequence motifs, a concept that we argue is a recurring theme in evolution.

overall_design: This study characterizes a transcriptional pathway that drive expression of small RNA precursors from heterochromatin

last: Refsing Andersen

first: Laszlo

last: Tirian

first: Milica

last: Vunjak

first: Julius

last: Brennecke


title: Environmental Enrichment Induces Pericyte and IgA-Dependent Wound Repair and Lifespan Extension in a Colon Tumor Model (RNAseq)

city: Salt Lake City

first: Melinda

middle: L.

last: Angus-Hill

state: UT

address: 2000 Circle of Hope

department: Medicine

institute: University of Utah

summary: Environmental enrichment (EE) replicates mind-body therapy by providing complex housing to laboratory animals to improve their activity levels, behavior and social interactions. Using a Tcf4Het/+ ApcMin/+-mediated model of colon tumorigenesis, we found that EE vastly improved the survival of tumor-bearing animals, with differential effect on tumor load in male compared to female animals. Analysis of Tcf4Het/+ ApcMin/+ males showed drastically reduced expression of circulating inflammatory cytokines and induced nuclear hormone receptor signaling, both of which are common in the wound repair process. Interestingly, EE provoked tumor wound repair resolution through revascularization, plasma cell recruitment and IgA secretion, replacement of glandular tumor structures with pericytes in a process reminiscent of scarring, and normalization of microbiota. These EE-dependent changes likely underlie the profound improvement in survival of colon-tumor-bearing Tcf4Het/+ ApcMin/+ males. Our studies highlight the exciting promise of EE in the design of future therapeutic strategies for colon cancer patients.

overall_design: Four samples from EE and NE (non-enriched controls) were analyzed


title: The identification and functional annotation of RNA structures conserved in vertebrates

city: Copenhagen N

first: Niels

last: Tommerup

state: Copenhagen

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine (ICMM)

institute: Wilhelm Johannsen Centre for Functional Genome Research

summary: We report the genome-wide screen of the vertebrate genomes for conserved RNA structures (CRSs) by CMfinder [Yao et al. Bioinformatics 2006] and predict around 515k human genomic regions that harbor such structures. For a customized CaptureSeq experiment 125k probes of 60bp length were synthesized for both strands. These probes target 77k CRS regions, which were selected by largest CRS prediction score (pscores), more than 3 substitutions to their closest genomic paralog, and conservation in human and mouse.

overall_design: Expression analysis by customized CaptureSeq

first: Stefan

last: Seemann

first: Aashiq

last: Mirza

first: Claus

last: Hansen

last: Bang-Berthelsen

first: Christian

last: Garde

first: Mikkel

last: Christensen-Dalsgaard

first: Elfar

last: Torarinsson

first: Zizhen

last: Yao

first: Christopher

last: Workman

first: Flemming

last: Pociot

first: Henrik

last: Nielsen

first: Walter

last: Ruzzo

first: Jan

last: Gorodkin


title: CHD1 in yeast is recruited by transcription elongation factors and maintains H3K4me3/H3K36me3 domains at actively transcribed and spliced genes

first: Vishy

last: Iyer

summary:
Chd1 is a conserved ATP-dependent chromatin remodeler that maintains the nucleosomal structure of chromatin, but the determinants of its specificity and its impact on gene expression are not well defined. To identify the determinants of Chd1 binding specificity in the yeast genome, we investigated Chd1 occupancy in mutants of several candidate factors. We found that several components of the PAF1 transcription elongation complex contribute to Chd1 recruitment to highly transcribed genes, and identified Spt4 as a factor that appears to negatively modulate Chd1 binding to chromatin. We discovered that CHD1 loss alters H3K4me3 and H3K36me3 patterns throughout the yeast genome. Interestingly, the aberrant histone H3 methylation patterns were predominantly observed within 1 kb from the transcription start site, where both histone H3 methylation marks co-occur. A reciprocal change between the two marks was obvious in the absence of Chd1, suggesting a role for CHD1 in establishing or maintaining the boundaries of these largely mutually exclusive histone marks. Strikingly, intron-containing genes were most susceptible to CHD1 loss, and exhibited a high degree of histone H3 methylation changes. Intron retention was significantly lower in the absence of CHD1, suggesting that CHD1 function as a chromatin remodeler could indirectly affect RNA splicing.

This SuperSeries is composed of the SubSeries listed below.


title: The inhibitory effect of TIAM1 on TAZ transcriptional activity [ChIP-seq]

city: Manchester

first: Zoi

last: Diamantopoulou

address: Wilmslow road, Withington

department: Cell Signalling

institute: CRUK MI

summary: The T lymphoma invasion and metastasis inducing protein 1 (TIAM1) is a guanine nucleotide exchange factor (GEF) that activates the small GTPase RAC1 and regulates a plethora of functions such as cell proliferation, migration, apoptosis and polarity. Recently, we demonstrated that TIAM1 shuttles between the cytoplasm and nucleus. Nuclear TIAM1 has an inhibitory role on TAZ transcriptional activity by impairing the interaction of TAZ with TEAD. To further demonstrate the inhibitory role of TIAM1 on TAZ we performed ChIP-Seq analysis to determine the enrichment of TAZ to chromatin of parental or CRISPR-mediated TIAM1 knockout SW480 cells.

overall_design: ChIP-seq qnalysis of TAZ on parental or CRISPR-mediated TIAM1 knockout SW480 cells.

first: Muhammad

last: Fadlullah

first: Angeliki

last: Malliri


title: Environmental Enrichment Induces Pericyte and IgA-Dependent Wound Repair and Lifespan Extension in a Colon Tumor Model

first: Melinda

last: Angus-Hill

sample_organism:
Mus musculus
mouse gut metagenome

platform_organism:
Mus musculus
mouse gut metagenome


title: Single cell profiling of hCS and hSS derived from human iPSC

city: Menlo Park

first: Christina

last: Fan

state: CALIFORNIA

address: 4040, Campbell Ave

institute: BD Biosciences

summary: Single gene expression proifiling of dissociated hiPSC-derived 3D cultures of the pallium and subpallium at day 105 of differentiation (n= 11,838 cells; BDTM Resolve system), revealing the various cell types and heterogenity within cell types in the cultured organoids

overall_design: 2 samples: hCS and hSS

first: Sergiu

last: Pasca


title: The inhibitory effect of TIAM1 on TAZ transcriptional activity and TIAM1 differentially expressed genes


title: List of TIAM1 differentially expressed genes in SW620 cells [RNA-seq]

summary: The T lymphoma invasion and metastasis inducing protein 1 (TIAM1) is a guanine nucleotide exchange factor (GEF) that activates the small GTPase RAC1 and regulates a plethora of functions such as cell proliferation, migration, apoptosis and polarity. Recently, we demonstrated that TIAM1 shuttles between the cytoplasm and nucleus. To determine the nuclear role of TIAM1, we performed RNA-seq on SW620 cells transfected either with a specific pre-validated siRNA for TIAM1 (siTIAM1) or a negative control siRNA (siNT) and generated a list of TIAM1 differentially expressed genes. GSEA revealed significant enrichment among TIAM1-regulated genes for YAP-associated molecular signature. To investigate the interplay of TIAM1 with YAP/TAZ we used RNA-seq, generated a list of YAP/TAZ differentially expressed genes from SW620 cells transfected either with specific siRNAs for YAP/TAZ or a negative control siRNA and compared it with the siTIAM1 RNA-seq dataset. Interestingly, we found that 50% of the TAZ/YAP regulated genes were also TIAM1 dependent.

overall_design: mRNA profiles of control, TIAM1 or YAP/TAZ knockdown SW620 cells were generated from three independent experiments using RNA-seq


title: Non-overlapping control of transcriptome by Promoter and Super-Enhancer-Associated Dependencies

city: Boston

first: Nikhil

middle: C

last: Munshi

address: 450 Brookline Avenue

department: Hematologic Oncology

institute: Dana-Farber Cancer Institute

summary: The relationship between promoter proximal transcription factor-associated gene expression and super-enhancer-driven transcriptional programs are not well-defined. Some level of their distinct genomic occupancy may suggest a mechanism with specific target gene control. We explored the transcriptional and functional interrelationship between E2F transcription factors and BET transcriptional co-activators in multiple myeloma. Global chromatin analysis reveals distinct regulatory axes for E2F and BETs, with E2F predominantly localized to active gene promoters of growth/proliferation genes and BETs disproportionately at enhancer- regulated tissue specific genes. Depletion of E2F selectively down-regulates its regulatory axis and is generally synergistic with BET inhibition. In vivo, combined inhibition of BETs and E2F strongly reduces tumor growth, implicating E2F as a myeloma dependency that is potently leveraged with BET inhibition.

overall_design: ChIP-Seq in U266 and MM1.S multiple myeloma cell lines

first: Mariateresa

last: Fulciniti

first: Charles

middle: Y

last: Lin


title: Adipose tissue from β-3 agonist-treated mice

status: Public on Apr 25 2017

city: Durham

first: Rana

middle: K

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

summary: We previously established the transcription factor Zfp423 is critical for maintaining white adipocyte identity through suppression of the thermogenic gene program. The loss of Zfp423 in mature adipocytes triggers the rapid conversion of energy-storing white adipocytes into thermogenic beige adipocytes in subcutaneous WAT. In contrast to subcutaneous WAT, visceral WAT is relatively resistant to browning. However, visceral adipocytes lacing Zfp423 are capable of inducing the thermogenic gene program upon β-3 adrenergic stimulus. Here, we generated mice lacking Zfp423 in visceral adipose by breeding transgenic mice expressing Cre recombinase under the control of the Wilms Tumor 1 locus (Wt1-Cre) to animals carrying the floxed Zfp423 alleles (Zfp423loxP/loxP) (“Vis-KO” mice). Inactivation of Zfp423 in visceral WAT gives rise to thermogenic adipocytes that share properties of subcutaneous beige adipocytes and classic brown adipocytes.

overall_design: In order to address whether deletion of Zfp423 in visceral adipose converts the white visceral adipocytes into bona fide subcutaneous beige adipocytes, we obtained and compared global gene expression profiles of adipose depots from control and Vis-KO animals through RNA sequencing. We treated the mice with vehicle (PBS) or β-3 adrenergic agonism (1 mg/kg CL316,243) daily for 3 days at thermoneutrality (30°C). RNA-sequencing was performed on mRNA libraries prepared from brown, gonadal, and inguinal adipose tissues from control mice (Cre negative), as well as from gonadal adipose tissue of Vis-KO animals

first: Chelsea

last: Hepler


title: The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status

city: La Jolla

first: Julie

middle: Ann

last: Law

state: CA

address: 10010 North Torrey Pines Rd

department: PLANT MOLECULAR AND CELLULAR BIOLOGY LABORATORY

institute: The Salk Institute for Biological Studies

summary: DNA methylation is a chromatin modification that is associated with gene silencing in eukaryotic organisms. Although pathways controlling the establishment, maintenance and removal of DNA methylation have been identified, relatively little is understood about how DNA methylation influences gene expression. Using complementary genetic and biochemical approaches we identified a protein complex that antagonizes the transcriptional gene silencing of two LUCIFERASE (LUC) reporters in a manner that requires DNA methylation. At its core, this complex contains LOW IN LUCIFERASE EXPRESSION (LIL), an α-crystallin domain protein, and METHYL-CpG-BINDING DOMAIN 7 (MBD7), a protein previously associated with DNA methylation. At the LUC reporters, loss of MBD7 or LIL resulted in decreased LUC expression concomitant with modest, but reproducible increases in DNA methylation that can be phenocopied by DNA demethylase mutants. These findings are consistent with other reports and reveal a genetic connection between MBD7, LIL and DNA demethylation. However, we found that the hyper-methylation and gene expression phenotypes at a LUC reporter can be genetically uncoupled, demonstrating that changes in DNA methylation alone are not sufficient to silence LUC expression, and suggesting a role for the MBD7-LIL complex downstream of DNA methylation. Consistent with this hypothesis, our more extensive analysis of DNA methylation in mbd7 and lil mutants revealed only a small number of hyper-methylated loci genome wide. Furthermore, these loci displayed minimal overlap with demethylase targets, suggesting that, in general, the DNA demethylation machinery does not function in a manner dependent on the MBD7-LIL complex. Taken together, our findings place the MBD7-LIL complex amongst a small number of factors that regulate gene expression without causing significant changes in DNA methylation. This complex, however, is unique in that it functions to suppress, rather than enforce the silencing effects of DNA methylation, enabling gene expression of several transgene reporters despite high levels of promoter methylation.

overall_design:
A total 23 bisufite libraries (samples 1-23) were sequenced  in several sets as detailed in Table S4, each set with its own controls including three replicates in the lil-1 background.  In addition, traditional bisulfite sequencing (conversion, cloning, and sanger based sequencing) was conducted on 9 samples (24-32) and for these experiments the percent methylation at each cystosine was tabulated and is presented in wiggle format files.

Please note that [1] Ler_r6_Cat3.C*wig files contain no methylated reads mapping to the transgene as they are negative control samples.
[2] For the samples 19 and 23, the DMRs relative to both the Wt control and the mutant background that was complemented were called to study complementation of a genetic defect.  In all the other cases the only comparison was to the Wt control (i.e. one comparison per mutant).
[3] The traditional bisulfite sequencing samples (samples 24-32) have their raw data available only in FASTA format (generated by 'ABI 3730XL DNA Analyzer'), and thus their raw data were not provided. Please contact the submitter for the sequence data.

first: Dongming

last: Li

first: Ana-Marie

last: Palanca

first: So

last: Won

first: Lei

last: Gao

first: Ying

last: Feng

first: Ajay

last: Vashisht

first: Li

last: Liu

first: Yuanyuan

last: Zhao

first: Xigang

first: Xiuyun

last: Wu

first: Shaofang

first: Brandon

last: Le

first: Yun

last: Kim

first: Guodong

last: Yang

first: Shengben

first: Jinyuan

first: James

last: Wohlschlegel

first: Hongwei

last: Guo

first: Beixin

last: Mo

first: Xuemei

last: Chen


title: Pax7 remodels the chromatin landscape in skeletal muscle stem cells

city: New York

first: Karin

last: Lilja

state: New York

address: 522 First Avenue, Smilow Research Building, 1106

department: Cancer Institute

institute: New York University School of Medicine

summary: The mechanisms by which Pax7 promotes skeletal muscle stem (satellite) cell identity are not yet understood. We have taken advantage of pluripotent stem cells wherein the induced expression of Pax7 robustly initiates the muscle program and enables the generation of muscle precursors that repopulate the satellite cell compartment upon transplantation. Pax7 binding was excluded from H3K27 tri-methylated regions, suggesting that recruitment of this factor is circumscribed by chromatin state. Further, Pax7 binding provoked localized chromatin remodeling, including the acquisition of enhancer-associated histone marks and induction of chromatin accessibility. Conversely, removal of Pax7 led to rapid reversal of these features on a subset of enhancers. Another cohort of Pax7 binding sites exhibited a durably accessible and remodeled chromatin state after Pax7 removal, and persistent enhancer accessibility was associated with subsequent binding by muscle regulatory factors. Our studies provide new insights into Pax7 and the epigenetic landscape of skeletal muscle stem cells.

overall_design: Examining the role of Pax7 in myogenesis and the chromatin context of Pax7-bound regions. (1) RNA-seq in the presence and absence of doxycyline (dox, inducing Pax7-expression) through the inducible iPax7-cell system (2) ChIP-seq of Pax7, H3K27Ac, H3K4me1, H3K4me3, and H3K27me3 in the presence and absence of dox in iPax7 myogenic progenitors (3) ATAC-seq  of satellite cells, myogenic progenitors, myoblasts

first: Brian

last: Dynlacht


title: Differential gene expression pattern of mouse livers transfected with dual oncogenes (day-3 post-injection data set)

first: Jijun

address: Rm1220 Bay-C, Biomedical Research Facility II, 9500 Gilman Drive

department: Pathology

institute: UC San Diego

summary: To understand global gene expression patterns of mouse livers upon dual-oncogene transfection, RNA sequencing and analysis were conducted on liver samples from Shp2F/F or Shp2∆H (Shp2F/F:Alb-cre) mice hydrodynamically injected with the combination of Met/β-Catenin or Met/PIK3CA .

overall_design: 18 mice from 6 experimental groups (n=3 for each group) were included in the experiment. Group1: Age-matched untreated Shp2F/F control mice; Group2: Age-matched Shp2ΔH mice; Group3: Met/β-Catenin hydrodynamically injected Shp2F/F mice;  Group4: Met/β-Catenin hydrodynamically injected Shp2ΔH mice; Group5: Met/PIK3CA hydrodynamically injected Shp2F/F mice; Group6: Met/PIK3CA hydrodynamically injected Shp2ΔH mice. Total RNA was extracted on day3 post-injection from liver of each mouse.

first: Yanjie

last: Li

first: Gen-Sheng


title: β-catenin deficiency in hepatocytes promotes liver tumorigenesis driven by oncogenic β-Catenin and c-Met in mice

first: Min

last: Zong

state: California

address: 9500 Giman Dr.

institute: UCSD

summary: To understand differential gene expression globally with/without hepatocyte β-catenin knockout on liver cancer mouse model, RNA-seq analysis were examined using hydrodynamic β-catenin and c-Met induced β-catenin∆H (β-cateninF/F:Alb-cre) and WT mice.

overall_design: Total RNA extracts from liver on 2-month-old mice, 3 days and 7 weeks after β-catenin and c-Met injection of β-catenin KO and WT mice, Group 1: 2-month-old mice (n=3); Group 2: 2-month-old β-catenin KO mice (n=3); Group 3: 3 days after β-catenin and c-Met injection of  WT mice (n=3); Group 4: 3 days after β-catenin and c-Met injection of β-catenin KO mice (n=3); Group 5: 7 weeks after β-catenin and c-Met injection of  WT mice (n=3); Group 6: 7 weeks after β-catenin and c-Met injection of β-catenin KO mice (n=3).


title: Crizotinib v. DMSO in SW480 cells

first: Giulio

last: Superti-Furga

state: Wien

address: Lazarettgasse 14, AKH BT25.3

institute: CeMM

summary: SW480 cells were treated with 2uM crizotinib for 72h (versus DMSO)

overall_design: Examination of differential up- or down-regulated genes after crizotinib treatment


title: BAF60 binding sites and their role in Modulating DNA accessibility in Arabidopsis thaliana

city: Thuwal

first: Alaguraj

last: Veluchamy

address: Thuwal

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: SWI/SNF protein BAF60 mediates seedling growth

overall_design: Examination of BAF60 binding sites by ChIP-seq. ATAC-seq, MNase-seq and FAIRE-seq were also performed on wildtype seedlings.

first: Teddy

last: Jégu

first: Charley

last: Rizzi-Paillet

first: Anais

last: Lhomme

first: Emeline

last: Coleno

first: Serge

last: Vicaire

first: Stephanie

last: Legras

first: Bernard

last: Jost

first: Martin

last: Rougee

first: Fredy

last: Barneche

first: Catherine

last: Bergounioux

first: Cécile

last: Raynaud

first: Moussa

last: Benhamed