title: Comprehensive nucleosome mapping of the human genome in cancer progression

city: Rochester

first: Brooke

last: Druliner

state: MN

address: 200 First St. SW

institute: Mayo Clinic

summary: Altered chromatin structure is a hallmark of cancer, and inappropriate regulation of chromatin structure may represent the origin of transformation. Several important studies have mapped human nucleosome distributions genome wide, but the genome-wide role of chromatin structure in cancer progression has not been addressed. We developed a MNase-Sequence Capture method, mTSS-seq, to map genome-wide nucleosome distribution in primary human lung and colon adenocarcinoma tissue. Here, we confirm that nucleosome redistribution is an early, widespread event in lung (LAC) and colon (CRC) adenocarcinoma. These altered nucleosome architectures are consistent between LAC and CRC patient samples indicating that they may serve as important early adenocarcinoma markers.  We demonstrate that the nucleosome alterations are driven by the underlying DNA sequence and potentiate transcription factor binding. We conclude that DNA-directed nucleosome redistributions are widespread early in cancer progression. We have proposed an entirely new hierarchical model for chromatin-mediated genome regulation.

overall_design:
Nucleosome distribution mapping in primary patient tissue at all transcription start sites in the human genome

Please note that two processed data files '4137N_ALLcombined.bed' and '4137T_ALLcombined.bed' (linked as Series supplementary file) are processed bed files combined from three 4137N_*_hiseq samples (total 6 raw data files) and three 4137T_*_hiseq samples (total 6 raw data files), respectively.

first: Jonathan

middle: H

last: Dennis


title: Identification and characterization of circular RNAs as a new class of putative biomarkers in human blood

status: Public on Oct 26 2015

city: Berlin

first: Nikolaus

last: Rajewsky

address: Robert Rössle Str 10 (H. 87)

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

type: Expression profiling by high throughput sequencing

summary: Covalently closed circular RNA molecules (circRNAs) have recently emerged as a class of RNA isoforms with widespread and tissue specific expression across animals, oftentimes independent of the corresponding linear mRNAs. circRNAs are remarkably stable and sometimes highly expressed molecules. Here, we sequenced RNA in human peripheral whole blood to determine the potential of circRNAs as biomarkers in an easily accessible body fluid. We report the reproducible detection of thousands of circRNAs. Importantly, we observed that hundreds of circRNAs are much higher expressed than corresponding linear mRNAs. Thus, circRNA expression in human blood reveals and quantifies the activity of hundreds of coding genes not accessible by classical mRNA specific assays. Our findings suggest that circRNAs could be used as biomarker molecules in standard clinical blood samples.

overall_design: Sequencing of blood RNA from five healthy individuals (biological replicates) plus technical replicate of one sample and detection of circRNAs.

first: Sebastian

last: Memczak

first: Panagiotis

last: Papavasileiou

first: Oliver

last: Peters


title: P300 ChIP-Seq analysis of PC3 cells treated with MnTE-2-PyP or not 24 hours prior to irradiation of 20 Gy.

status: Public on Oct 27 2015

city: Denver

first: Brian

middle: Patrick

last: OConnor

state: Colorado

address: 1400 Jackson St

department: Center for Genes, Environment and Health

country: USA

institute: National Jewish Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In order to identify how MnTE-2-PyP affects p300 association to chromatin genome-wide, we performed a p300 chromatin Immunoprecipitation assay followed by Next Generation Sequencing on PC3 cells treated with or without MnTE-2-PyP one hour post-irradiation (Figure 3A). Based on the called peaks near genes, we predicted that HIF-1βand CREB transcription factors were associating DNA less in the presence of MnTE-2-PyP.

overall_design: DNA was ChIP-Fixed from Pc3 cells treated with 20 Gy radiation and with and without T2E drug. There are 2 biological replicates of PC3 untreated cells and 3 biological replicates of PC3 cells treated with MnTE-2-PyP. There are two corresponding input samples for the biological replicates.

middle: P

first: Laura

middle: D

last: Harmacek


title: m6A in 5’ untranslated regions promotes cap-independent translation of mRNA

city: D

first: Kate

last: Meyer

state: NC

address: 307 Research Drive Box 3711

department: Biochemistry

institute: Duke University School of Medicine

summary: N6-methyladenosine (m6A) is a widespread internal RNA modification whose function is poorly understood. Here we report that m6A residues within the 5'UTR promote a novel form of cap-independent translation which is mediated through an interaction between m6A residues and the translation initiation factor, eIF3. We performed m6A profiling in cells subjected to heat shock stress and observed increased 5'UTR methylation after heat shock. For these studies, we used single-nucleotide resolution m6A mapping (miCLIP), which enables the detection of m6A residues separately from m6Am residues. Thus,  the goal of these experiments was to identify m6A residues which are increased in the 5'UTR after heat shock stress.

overall_design: Two replicates of eIF3a PAR-iCLIP in HEK293T cells. m6A profiling in HEK and HepG2 cells after heat shock.

first: Deepak

last: Patil

first: Samie

middle: R

last: Jaffrey


title: Transcriptome analysis of ATRX and DAXX knockout mouse ESC

city: Dallas

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

overall_design:
PolyA+ RNA-Seq was performed on wildtype, ATRX and DAXX knockout cells derived by CRISPR targeting (Sadic et. al, EMBO Rep, 16(7), p836-850, 2015, DOI: 10.15252/embr.201439937).
Cells (isogenic, male)

middle: A

first: Simon

middle: J

last: Elsasser

first: C

last: Allis


title: Identifying Glioblastoma Gene Networks Based on Hypergeometric Test Analysis

city: Miami

first: Nagi

last: Ayad

state: Florida

address: 1095 NW 14th Terrace, LPLC, R48

department: Psychiatry and Behavioral Sciences

institute: University of Miami

summary: Patient specific therapy is emerging as an important possibility for many cancer patients.  However, to identify such therapies it is essential to determine the genomic and transcriptional alterations present in one tumor relative to control samples. This presents a challenge since use of a single sample precludes many standard statistical analysis techniques.  We reasoned that one means of addressing this issue is by comparing transcriptional changes in one tumor with those observed in a large cohort of patients analyzed by The Cancer Genome Atlas (TCGA).  To test this directly, we devised a bioinformatics pipeline to identify differentially expressed genes in tumors resected from patients suffering from the most common malignant adult brain tumor, glioblastoma (GBM).  We performed RNA sequencing on tumors from individual GBM patients and filtered the results through the TCGA database in order to identify possible gene networks that are overrepresented in GBM samples relative to controls.  Importantly, we demonstrate that hypergeometric-based analysis of gene pairs identifies gene networks that validate experimentally.  These studies identify a putative workflow for uncovering differentially expressed patient specific genes and gene networks for GBM and other cancers.

overall_design: RNAseq on 2 gliosblastoma samples and 2 epileptic samples

first: Vasileios

last: Stathias

first: Chiara

last: Pastori

first: Tess

middle: Z

last: Griffin

first: Ricardo

last: Komotar

first: Jennifer

last: Clarke

first: Ming

last: Zhang

middle: G


title: FOXM1 Cistrome Predicts Breast Cancer Metastatic Outcome Better Than FOXM1 Expression Levels or Tumor Proliferation Index

city: Novato

first: Christina

last: Yau

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute of Age Research

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

overall_design: Refer to individual Series


title: A MYC-driven change in mitochondrial dynamics limits stem cell properties of mammary epithelial cells (RNA-seq)

status: Public on Oct 28 2015

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary: In several developmental lineages, an increase in expression of the MYC proto-oncogene drives the transition from quiescent stem cells to transit amplifying cells. The mechanism by which MYC restricts self-renewal of adult stem cells is unknown. Here, we show that MYC activates a stereotypic transcriptional program of genes involved in protein translation and mitochondrial biogenesis in mammary epithelial cells and indirectly inhibits the YAP/TAZ co-activators that are essential for mammary stem cell self-renewal. We identify a phospholipase of the mitochondrial outer membrane, PLD6, as the mediator of MYC activity. PLD6 mediates a change in the mitochondrial fusion/fission balance that promotes nuclear export of YAP/TAZ in a LATS- and RHO-independent manner. Mouse models and human pathological data confirm that MYC suppresses YAP/TAZ activity in mammary tumors. PLD6 is also required for glutaminolysis, arguing that MYC-dependent changes in mitochondrial dynamics balance cellular energy metabolism with the self-renewal potential of adult stem cells.

overall_design: RNA-Seq Experiments in 2 different primary breast epithelial cell lines (HMLE, which were sorted according to CD44/CD24 surface markers & unsorted IMEC). Both cell lines expressed a doxycycline-inducible version of MYC. For the HMLE cell line DGE analysis was performed for the uninduced (EtOH) situation, comparing CD44high vs CD44 low and for the induced situation Dox vs. EtOH for the CD44high population. For the IMEC cell line DGE was performed by comparing Dox-treated populations expressing either Dox-inducible MYC or a vector control which allows to filter out potential effects due to doxycycline treatment.

first: Björn

last: von Eyss

last: Jaenicke

first: Roderik

middle: M

last: Kortlever

first: Nadine

last: Royla

first: Katrin

middle: E

last: Wiese

first: Sebastian

last: Letschert

first: Markus

last: Sauer

first: Andreas

last: Rosenwald

first: Gerard

middle: I

last: Evan

first: Stefan

last: Kempa


title: FOXM1 Cistrome Predicts Breast Cancer Metastatic Outcome Better Than FOXM1 Expression Levels or Tumor Proliferation Index [RNA-Seq]

summary: FOXM1 is a key transcription factor regulating cell cycle progression, DNA damage response, and a host of other hallmark cancer features, but the role of the FOXM1 cistrome in driving estrogen receptor-positive (ER+) vs. ER- breast cancer clinical outcomes remains undefined.

overall_design: Chromatin immunoprecipitation sequencing (ChIP-Seq) coupled with RNA sequencing (RNA-Seq) analyses was used to identify FOXM1 target genes in breast cancer cells (MCF-7) where FOXM1 expression was either induced by cell proliferation or repressed by p53 upregulation.

first: Laurence

last: Meyer

first: Stephen

last: Benz

first: Charles

last: Vaske

first: Gary

last: Scott

first: Brian

last: Egan

first: Paul

last: Labhart

first: Nader

last: Pourmand

first: Christopher

middle: C


title: Mitotic Transcriptional Clearance of Actively Engaged Pol II Through Transcriptional Elongation Control

status: Public on Oct 30 2015

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: Chromatin is highly condensed and transcriptionally repressed during mitosis. Although it is established that some general transcription factors are inactivated by phosphorylation at mitosis, many details of mitotic transcriptional repression and its underlying mechanisms are largely unknown. Here, we provide evidence that as cells enter mitosis, genes with transcriptionally engaged RNA Polymerase II (Pol II) can continue transcription until the end of the gene to clear Pol II from mitotic chromatin. Using ChIP-Seq, we find that the transcriptional reinitiation process is globally impaired in early mitosis (prophase/prometaphase), with loss of TFIIB occupancy and nucleosome-free regions at promoters. Pretreatment of nocodazole-arrested mitotic cells with the P-TEFb inhibitor flavopiridol prevents the release of promoter-proximal engaged Pol II. Global nascent RNA sequencing and RNA fluorescence in situ hybridization (FISH) of individual genes demonstrate the existence of transcriptionally engaged Pol II in early mitosis. Chemical and mutational inhibition of P-TEFb in mitosis leads to delays in the progression of cell division. Together, our study reveals a novel mechanism for mitotic transcriptional repression whereby transcriptionally engaged Pol II can progress into productive elongation and finish transcription to allow proper cellular division.

overall_design: ChIP-Seq of Pol II of different forms, TFIIB, H3K4me3 in human HeLa cells at different cell cycle stages. ChIP-Seq of Pol II in HeLa mitotic cells with or without CDK9 inhibitor flavopiridol pretreatment. Nascent RNA-seq in asynchronous and arrested mitotic cells.

first: Kaiwei

last: Liang

first: Ashley

last: Woodfin


title: Gene expression of baseline biopsies from etrolizumab-treated ulcerative colitis (UC) patients

city: South San Francisco

first: Mark

last: McCreary

state: California

address: 1 DNA Way, MS 93

department: Bioinformatics

institute: Genentech

summary: RNA sequencing was performed on RNA isolated from baseline biopsies from UC patients enrolled in the Phase II EUCALYPTUS study of etrolizumab. Gene expression differences were identified in a subset of anti-TNF naïve patients that achieved clinical remission at 10 weeks in response to etrolizumab.

overall_design: Baseline colonic biopsies from UC patients treated with etrolizumab were sequenced by the Illumina HiSeq 2000 Sequencing System.

first: Mary

last: Keir

first: Gaik

middle: W

last: Tew

first: Jason

last: Hackney

first: Deena

last: Gibbons

last: Lamb

first: Diana

last: Luca

first: Jackson

last: Egen

first: Lauri

last: Diehl

first: Jeff

last: Eastham Anderson

first: Severine

last: Vermeire

first: John

last: Mansfield

last: Feagan

first: Julian

last: Panes

first: Daniel

last: Baumgart

last: Schreiber

first: Iris

last: Dotan

first: William

last: Sandborn

last: Kirby

first: Peter

last: Irving

first: Gert

last: De Hertogh

last: Van Assche

last: Rutgeerts

first: Sharon

last: O’Byrne

first: Adrian

last: Hayday


title: FOXM1 Cistrome Predicts Breast Cancer Metastatic Outcome Better Than FOXM1 Expression Levels or Tumor Proliferation Index [ChIP-Seq]

first: Christina

last: Yau

first: Laurence

last: Meyer

first: Stephen

last: Benz

first: Charles

last: Vaske

first: Gary

last: Scott

first: Brian

last: Egan

first: Paul

last: Labhart

first: Nader

last: Pourmand

first: Christopher


title: ChIP-seq of H3K27ac in lung cancer, endometrial carcinoma and head and neck squamous cell carcinoma cells.

city: Salt Lake City

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

institute: University of Utah

summary: Using H3K27ac ChIP-seq profile to map active enhancers in lung cancer, endometrial carcinoma and head and neck squamous cell carcinoma cells

overall_design: ChIP-seq of H3K27ac was done in lung adenocarcinoma cell lines (NCI-H358 and NCI-H2009), squamous cell lung carcinoma cell lines (HCC95), endometrial carcinoma cell lines (Ishikawa) and head and neck squamous cell lines (BICR-31)

first: Hideo

last: Watanabe


title: Comprehensive analysis of microRNA expression in regionalized human neural progenitor cells reveals microRNA-10 as a caudalizing factor

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

summary: MicroRNAs (miRNAs) have been implicated in regulating multiple processes during brain development in various species. However, the function of miRNAs in human brain development remains largely unexplored. Here, we provide a comprehensive analysis of miRNA expression of regionalized neural progenitor cells derived from human embryonic stem cells and human fetal brain. We found mir-92b-3p and mir-130b-5p to be specifically associated with neural progenitors and several miRNAs that display both age-specific and region-specific expression patterns. Among these miRNAs, we identified miR-10 to be specifically expressed in the human hindbrain and spinal cord, while absent from rostral regions. We found that miR-10 regulates a large number of genes enriched for functions including transcription, actin cytoskeleton and ephrin receptor signaling. When overexpressed, miR-10 influences caudalization of human neural progenitors cells. Together, these data confirms a role for miRNAs in establishing different human neural progenitor populations. This data set also provides a comprehensive resource for future studies investigating the functional role of different miRNAs in human brain development.

overall_design: Human embryonic stem cells (hESCs) were transduced with lentiviral vectors expressing either miR10a-GFP or miR10b-GFP. The expression of the vectors is Tet-regulated and they will only be expressed in the presence of Doxycycline. In order to detect direct targets of the miR10a and miR10b, we differentiated the trasduced hESCs for 14 days, and added doxycycline to only half of the groups - resulting in groups that are overexpressing miR10a or miR10b and some groups that are not overexpressing these miRNAs.

first: Marie

last: Jönsson

first: Jenny

last: Nelander Wahlestedt

first: Malin

last: Åkerblom

first: Agnete

last: Kirkeby

first: Josephine

last: Malmevik

middle: L

last: Brattås

first: Johan

last: Jakobsson

last: Parmar


title: FOXP1 orchestration of ASD-relevant signaling pathways.

first: Genevieve

last: Konopka

address: 5323 Harry Hines Blvd.

department: Neuroscience

summary: Mutations in the gene encoding the transcription factor forkhead box P1 or FOXP1 occur in patients with neurodevelopmental disorders, including autism. However, the function of FOXP1 in the brain remains mostly unknown. Here, we identify the gene expression program regulated by FoxP1 in both human neural cells and mouse brain and demonstrate a conserved role for FOXP1 transcriptional regulation of autism and Fragile X Mental Retardation Protein (FMRP) mediated pathways. Coexpression networks support a role for Foxp1 in neuronal activity, and we show that Foxp1 is necessary for neuronal excitability. Using a Foxp1 mouse model, we observe defects in ultrasonic vocalizations. This behavioral phenotype is reflected at the genomic level as striatal Foxp1-regulated overlap with genes known to be important in rodent vocalizations. These data support an integral role for FOXP1 in regulating signaling pathways vulnerable in developmental disorders and the specific regulation of pathways important for vocal communication.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We carried out RNA-sequencing (RNA-seq) and ChIP-sequencing of human neural progenitors cells. We carried out RNA-sequencing (RNA-seq) of mouse striatal tissue, mouse hippocampal tissue and mouse cortical tissue. For the RNA-seq, four indipendent replicates were used for the neural progenitor cells and mouse tissues. For the Chip-seq, a single neural progenitor cell line was used.

first: Daniel

last: Araujo

first: Ashley

last: Anderson

first: Stefano

last: Berto

first: Matt

last: Harper

first: Wesley

last: Runnels

first: Hung-Chung

last: Huang


title: Active chromatin and transcription play a key role in chromosome partitioning into topologiсally associating domains

city: Skolkovo

first: Ekaterina

last: Khrameeva

state: Moscow region

address: Novaya St., 100

country: Russia

institute: Skolkovo Institute of Science and Technology

summary: Recent advances enabled by Hi-C technique have unraveled principles of chromosomal folding, which were since linked to many genomic processes. In particular, Hi-C revealed that chromosomes of animals are organized into Topologically Associating Domains (TADs), evolutionary conserved compact chromatin domains that influence gene expression. However, mechanisms that underlie partitioning of the genome into TADs remain poorly understood. To explore principals of TAD folding in Drosophila melanogaster, we performed Hi-C and PolyA+ RNA-seq in four cell lines of various origins (S2, Kc167, DmBG3-c2, and OSC). Contrary to previous studies, we find that regions between TADs (i.e. the inter-TADs and TAD boundaries) in Drosophila are only weakly enriched with the insulator protein dCTCF, while another insulator protein Su(Hw) is preferentially present within TADs. However, Drosophila inter-TADs harbor active chromatin and constitutively transcribed (housekeeping) genes. Accordingly, we find that binding of insulator proteins dCTCF and Su(Hw) predict TAD boundaries much worse than the active chromatin marks (in the minimal case, H3K4me3 and total RNA) do. Moreover, inter-TADs correspond to decompacted interbands of polytene chromosomes, whereas TADs mostly correspond to densely packed bands. Collectively, our results suggest that TADs are condensed chromatin domains depleted in active chromatin marks, separated by regions of active chromatin that cannot be organized into compact structures, possibly due to high levels of histone acetylation. Finally, we test this hypothesis by polymer simulations, and find that TAD partitioning can be explained by different modes of inter-nucleosomal interactions for active and inactive chromatin.

overall_design: Hi-C experiments, PolyA+ RNA profiling and mapping of chromosomal rearrangements in four Drosophila melanogaster cell lines.

first: Sergey

middle: V

last: Ulianov


title: Genes expression in case of PEV caused by chromosomal rearrangement

status: Public on Oct 25 2015

city: Moscow

last: Lavrov

address: Kurchatov sq. 2

department: DMBC

institute: IMG

summary: Heterochromatic position effect variegation (PEV) is the epigenetic disruption of genes expression near the new-formed eu-heterochromatic border. We characterized the inversion In(2)A4, demonstrating cis-acting PEV as well as trans-inactivation of the reporter transgenes on the opposite normal chromosome in combination with the inversion. Euchromatic breakpoint of In(2)A4 inversion was localized at 105 bp region (chr2L:21182214-21182318) of the second exon of the Mcm10 gene, the heterochromatic breakpoint is located at the block of dodecasatellite in 2L pericentromeric heterochromatin. In order to check the effects of heterochromatin on neighbor euchromatic genes and estimate the distance of inactivation spreading, we performed RNA-seq analysis of genes expression in larvae and adults females of genotypes A12/A12 (control) and In(2)A4/In(2)A4. Cis-influence of heterochromatin in the inversion causes not only repression, but also activation of genes, and the effects of heterochromatin are different at different developmental stages. Cis-actions affect only a few genes located near the heterochromatin

overall_design: Comparison of genes expression in wild type and demonstrating PEV larvae and adults in two repeats each

first: Alexey

middle: S

last: Shatskikh


title: Enhancers

first: Xiaoyang

last: Zhang


title: RNA sequencing of Bifidobacterium bifidum SC555 in response to various substrates

city: Davis

first: Danielle

last: Lemay

address: 451 Health Sciences Dr

department: Genome Center

institute: University of California Davis

summary: The purpose of this project was to determine the whole transcriptome response of Bifidobacterium bifidum SC555 to pooled and individual human milk oligosaccharides (HMO) relative to lactose

overall_design: Bacterial isolates grown on lactose, pooled human milk oligosaccharides (HMO), lacto-N-tetraose (LNT), lacto-N-neotetraose (LNnT), 2’fucosyllactose (2’FL), 3-fucosyllactose (3FL), 6’sialyllactose (6’SL) and porcine mucin (MUC). RNA was extracted and sequenced, in duplicate, on an Illumina HiSeq. Early, mid, and late timepoints in response to pooled HMO were additionally sequenced in duplicate.

first: David

last: Mills

last: Garrido


title: Aneuploidy-induced cellular stresses limit autophagic degradation.

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: An unbalanced karyotype, a condition known as aneuploidy, has a profound impact on cellular physiology and is a hallmark of cancer. Determining how aneuploidy affects cells is thus critical to understanding tumorigenesis. Here we show that aneuploidy interferes with the degradation of autophagosomes within lysosomes. Mis-folded proteins that accumulate in aneuploid cells due to aneuploidy-induced proteomic changes overwhelm the lysosome with cargo, leading to the observed lysosomal degradation defects. Importantly, aneuploid cells respond to lysosomal saturation. They activate a lysosomal stress pathway that specifically increases the expression of genes needed for autophagy-mediated protein degradation. Our results reveal lysosomal saturation as a universal feature of the aneuploid state that must be overcome during tumorigenesis.

overall_design:
RPE-1 cells either untreated or treated with one of Reversine, Bafilomycin A1 or MG132, each condition was done in triplicate.
D14-*_Control: untreated control
D14-*_Rev: cells treated with 0.5uM Reversine for 24hrs and harvested 48hrs later
D14-*_Baf: cells treated with 0.1uM BafA1 for 6hrs
D14-*_Mg: cells treated with 1uM MG132 for 24 hrs

last: Santaguida

first: Eliza

last: Vazile

first: Eileen

last: White

first: Angelika

last: Amon


title: Expression of ATHB17 in Maize Increases Ear Weight at Silking

city: Saint Louis

first: Jim

last: Morrell

state: Missouri

address: 800 North Lindbergh Blvd

department: Biotechnology

institute: Monsanto Co.

summary: Transformation of the Arabidopsis ATHB17 gene into maize results in the expression of a truncated protein (smaller by 113 amino acids) that functions as a dominant-negative regulator that can modify activity of endogenous maize HD-Zip II transcription factors.  This RNASeq experiment indicates that the observed effects of ATHB17d113 on the maize ear inflorescence and ear transcriptome are very small. Expression of ATHB17delta113 protein in maize leads to changes in ear growth resulting in increased ear size at early reproductive stages and, potentially increased sink size.

overall_design: Two ATHB17delta113 expressing events (Event 1 and Event 2) were compared to control plants (herein referred to as WT) in the context of Monsanto Elite Maize hybrid line NN6306.  Three bioreps of both Ear inflorescence and Ear tissues were sampled for the WT and each of the two transgenic events.

first: Abha

last: Khandelwal

first: James

first: Deepak

last: Purushotham

first: Mingya

first: Rico

last: Caldo

first: Kim

last: Beazley

first: Elena

last: Rice

first: Paul

last: Loida


title: 3’ and 5’ end modifications in plant microRNA post biogenesis: evidences from NGS of small RNAs [Arabidopsis thaliana]

status: Public on Oct 24 2015

city: New Delhi

first: Dinesh

last: Gupta

state: Delhi

address: Aruna Asaf Ali Marg

department: Structural and Computational Biology

country: India

institute: ICGEB

type: Non-coding RNA profiling by high throughput sequencing

summary:
Backgropund:In a major paradigm shift in the last decade, the knowledge about a whole class of non-coding RNAs known as miRNAs has emerged, which have proved these to be important regulators of a wide range of cellular processes by the way of modulation of gene expression. It is reported that some of these miRNAs are modified by addition or deletion of nucleotides at their ends, after biogenesis. However, the biogenesis and functions of these modifications are not well studied in eukaryotes, especially in plants. In this study, we examined the miRNA modifications in different tissues of the various plants, namely rice, tomato and Arabidopsis and identified some common features of such modifications.
Results:We have analyzed different aspects of miRNA modifications in plants. To achieve this end, we developed a PERL script to find the modifications in the sequences using small RNA deep sequencing data. The modification occurs in both mature and passenger (star) strands, as well as at both the 5' and 3' ends of miRNAs. Interestingly, we found a position-specific nucleotide biased modification, as evident by increased number of modification at the 5' end with the presence of Cytosine (nucleotide 'C') at the 3’end of the miRNA sequence. The level of modifications is not strictly dependent on the abundance of miRNA. Our study showed that the modification events are independent of plant species, tissue and physiological conditions. Our analysis also indicates that the RNAi enzyme, namely, the RNA dependent RNA polymerase 6 (RDR6) may not have any role in Arabidopsis miRNA modifications. Some of these modified miRNAs are bound to AGO1, suggesting their possible roles in biological processes.
Conclusions:This is a first report that reveals that 5' nucleotide additions are preferred for mature miRNA sequences with 3’ terminal ‘C’ nucleotide. Our analysis also indicates that the miRNAs modifications involving addition of nucleotides to the 5’ or 3’ end are independent of RDR6 activity and are not restricted by plant species, physiological conditions and tissue types. The results also indicate that such modifications might be important for biological processes.

overall_design: small RNA profiles of wild type and RDR6 (-) of Arabidopsis plants were generated using deep sequencing data.

first: Nial

last: Gursanscky

first: Bernard

last: Carroll

first: Shradha

last: Saraf


title: Genome-wide profiling of small RNAs in sorghum under abiotic stresses

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

country: China

institute: Shanghai Center for Plant Stress Biology

summary: To identify novel miRNA and NAT-siRNAs that are associated with abiotic stresses in sorghum, we generated small RNA sequences from sorghum seedlings that grew under control and under dought, salt, and cold stress treatments.

overall_design: sequencing of small RNAs in sorghum under control, drought, salt, and cold stress conditions.

first: Zhigang

last: Wu

first: Lei

last: Gao

first: Blanca

last: Barrera-Figueroa

first: Jian-kang

last: Zhu


title: 3' and 5' end modifications in plant microRNA post biogenesis: evidences from NGS of small RNAs

sample_organism:
Arabidopsis thaliana
Solanum lycopersicum
Oryza sativa


title: Systematic discovery of cap-independent translation sequences in human and viral genomes

status: Public on Oct 23 2015

first: Shira

last: Weingarten-Gabbay

address: 75 Ames St

institute: The Broad Institute

summary: To investigate gene specificity at the level of translation in both the human genome and viruses, we devised a high-throughput bicistronic assay to quantify cap-independent translation. We uncovered thousands of novel cap-independent translation sequences, and we provide insights on the landscape of translational regulation in both humans and viruses. We find extensive translational elements in the 3′ untranslated region of human transcripts and the polyprotein region of uncapped RNA viruses. Through the characterization of regulatory elements underlying cap-independent translation activity, we identify potential mechanisms of secondary structure, short sequence motif,and base pairing with the 18S ribosomal RNA (rRNA). Furthermore, we systematically map the 18S rRNA regions for which reverse complementarity enhances translation. Thus, we make available insights into the mechanisms of translational control in humans and viruses.

overall_design: high-throughput bicistronic assay for obtaining cap-independent translation measurements of 55,000 fully designed sequences in parallel using fluorescence-activated cell sorting and high-throughput DNA sequencing (FACS-seq).

first: Shani

last: Elias-Kirma

first: Ronit

last: Nir

first: Alexey

last: Gritsenko

first: Noam

last: Stern-Ginossar

first: Zohar

last: Yakhini

first: Adina

last: Weinberger

first: Eran

last: Segal


title: RNA-seq following enhancer repression

first: Xiaoyang

last: Zhang

summary: Using RNA-seq to identify genes regulated by dCas9-KRAB mediated enhancer repression in NCI-H2009 lung adenocarcinoma cells

overall_design: NCI-H2009 cells were first transfected with dCas9-KRAB fusion and subsequently transfected with no guide RNA (Empty), a guide RNA that has no target in the human genome (Dummy), and two separate guide RNAs (e3 #1 and e3 #2) recognizing the enhancer region of our study.

first: Joshua

last: Francis


title: 3’ and 5’ end modifications in plant microRNA post biogenesis: evidences from NGS of small RNAs [Oryza sativa]

first: Dinesh

last: Gupta

overall_design: Total 14 samples were analyzed, each in a pair of control and heat stress.

first: Sunil

middle: K

last: Mukherjee

first: Neeti

last: sanan-Mishra


title: E12.5 distal forelimb embryonnic transcriptome

city: Lausanne

first: Marion

last: LELEU

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

country: Switzerland

institute: EPFL

summary: Analysis of gene expression in the distal forelimbs

overall_design: RNA-Seq polyA on transcripts extracted from the dissection of three pairs of embryonnic forelimbs at E12.5

first: Pierre

last: Fabre

first: Denis

last: Duboule


title: Positional proteomics reveals differences in N-terminal proteoform stability

city: Gent

first: Petra

last: Van Damme

address: Albert Baertsoenkaai 3

country: Belgium

institute: VIB

summary: To understand the impact of alternative translation initiation on a proteome, we performed the first study on protein turnover using positional proteomics and ribosome profiling to distinguish between N-terminal proteoforms of individual genes. Overall, we monitored the stability of 1,941 human N-terminal proteoforms, including 147 N-terminal proteoform pairs that originate from alternative translation initiation, alternative splicing or incomplete processing of the initiator methionine.

overall_design: Ribosome profiling of lactimidomycin and cycloheximide treated human Jurkat T-lymphocytes

first: Daria

last: Gawron

first: Elvis

last: Ndah

first: Kris

last: Gevaert


title: Gene expression signatures of transgenic and wild-type tobaccos under normal or salt-stress conditions

city: Lanzhou

first: Yulan

last: Shi

address: Donggang road 320#

institute: Cold and Arid Regions Environmental and Engineering Research Institution

summary: To understand the effect of salt stress on CbFAD3 transgenic and wild-type tobaccos, we have employed whole genome microarray expression profiling of transgenic and wild-type plants under normal or salt-stress conditons, respectively. We also found the founction of CbFAD3 gene on tobaccos through comparing these data.

overall_design: Gene expression of tobacco leaves under normal conditions was measured using two-week-old seedlings grown at 25C under 16 h light/8 h dark. Salt stress-induced gene expression in tobacco leaves was measured at 6 hours after treatment with 200 mM NaCl. Leaves from five independent plants of each sample were collected for each hybridization.


title: Identification of a novel Aire-regulating cis-regulatory element using H3K27ac ChIP-seq

city: San Francisco

first: Mark

middle: S.

last: Anderson

address: 513 Parnassus Ave., Box 0540

department: Diabetes Center

institute: UCSF

summary: Thymic central tolerance is essential to preventing autoimmunity. In medullary thymic epithelial cells (mTECs), the Autoimmune regulator (Aire) gene plays an essential role in this process by driving the expression of a diverse set of tissue-specific antigens (TSAs), which are presented and help tolerize self-reactive thymocytes. Interestingly, Aire has a highly tissue-restricted pattern of expression, with only mTECs and peripheral extrathymic Aire-expressing cells (eTACs) known to express detectable levels in adults. Despite this high level of tissue specificity, the cis-regulatory elements that control Aire expression have remained obscure. We used sequence conservation analysis and ChIP-seq against the enhancer-associated histone mark H3K27ac to identify a candidate Aire cis-regulatory element. There is enrichment of H3K27ac near this element, ACNS1, in mTECs and the element also has characteristics of being  NF-κB-responsive. Finally, we find that this element is essential for Aire expression in vivo and necessary to prevent spontaneous autoimmunity, reflecting the importance of this regulatory DNA element in promoting immune tolerance.

overall_design: Two experimental groups (GFP neg mTECs and GFP pos mTECs), each with three samples, and one control sample (D10 Th2 cells).

first: Taylor

middle: N

last: LaFlam

first: Gregory

last: Seumois

first: Corey

last: Miller

first: Wint

last: Lwin

first: Kayla

last: Fasano

first: Michael

last: Waterfield

first: Jason

last: Greenbaum

first: Irina

last: Proekt

first: Pandurangan

last: Vijayanand


title: T Cell Deficiency in Spinal Cord Injury: Altered Locomotor Recovery and Whole-Genome Transcriptional Analysis

city: Minneapolis

first: Ann

middle: Margaret

last: Parr

address: 2001 6th St SE

department: Department of Neurosurgery

institute: University of Minnesota

summary: T cells undergo autoimmunization following spinal cord injury (SCI) and play both protective and destructive roles during the recovery process. T-cell deficient athymic nude (AN) rats recover better than immunocompetent Sprague-Dawley (SD) rats following spinal cord transection. In the present study, we evaluated locomotor recovery in SD and AN rats following moderate spinal cord contusion. To explain variable locomotor outcome, we assessed whole-genome expression using RNA sequencing, in the acute (1 week post-injury) and chronic (8 weeks post-injury) phases of recovery. AN rats demonstrated greater locomotor function than SD rats only at 1 week post-injury, coinciding with peak T cell infiltration in immunocompetent rats. Genetic markers for T cells and helper T cells were acutely enriched in SD rats, while AN rats expressed genes for Th2 cells, cytotoxic T cells, NK cells, mast cells, IL-1a, and IL-6 at higher levels. Acute enrichment of cell death-related genes suggested that SD rats undergo secondary tissue damage from T cells. Additionally, SD rats exhibited increased acute expression of voltage-gated potassium (Kv) channel-related genes. However, AN rats demonstrated greater chronic expression of cell death-associated genes and less expression of axon-related genes. We put forth a model in which T cells facilitate early tissue damage, demyelination, and Kv channel dysregulation in SD rats following contusion SCI. However, compensatory features of the immune response in AN rats cause delayed tissue death and limit long-term recovery. T cell inhibition combined with other neuroprotective treatment may thus be a promising therapeutic avenue.

overall_design: 2x2 model with 4 groups and 12 total samples. 2 rat strains (athymic nude [AN] and Sprague-Dawley [SD]) and 2 time points (1 week post-injury [acute] and 8 weeks post-injury [chronic]). 3 samples per group, for a total of 12 samples. No technical replicates were performed. Acute SD group = rats 618, 619, and 620. Chronic SD group = rats 605, 606, and 608. Acute AN group = rats 714, 715, and 717. Chronic AN group = rats 707, 712, and 713.

first: David

last: Satzer

first: Catherine

first: Jacob

last: Maxon

first: Joseph

last: Voth

first: Christina

last: DiBartolomeo

first: Rebecca

last: Mahoney

first: James

middle: R

last: Dutton

first: Walter

last: Low


title: The influence of the estrous cycle on sex differences in the rat adult medial prefrontal cortex transcriptome

city: Tallahassee

first: Mohamed

last: Kabbaj

address: 1115 W Call St

department: Biomedical Sciences

institute: Florida State University

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

overall_design: Refer to individual Series


title: Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

city: Houston

first: Suhas

last: Rao

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: We recently used in situ Hi-C to create kilobase-resolution 3D maps of mammalian genomes. Here, we combine these with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that the observed contact domains are inconsistent with the equilibrium state for an ordinary condensed polymer. Combining Hi-C data and novel mathematical theorems, we show that contact domains are also not consistent with a fractal globule. Instead, we use physical simulations to study two models of genome folding. In one, intermonomer attraction during polymer condensation leads to formation of an anisotropic "tension globule." In the other, CTCF and cohesin act together to extrude loops during interphase. Both models are consistent with the observed contact domains and with the observation that contact domains tend to form inside loops. However, the extrusion model explains a far wider array of observations, such as why loops tend not to overlap and why the CTCF-binding motifs at pairs of loop anchors lie in the convergent orientation. Finally, we perform 13 genome-editing experiments examining the effect of altering CTCF-binding sites on chromatin folding. The convergent rule correctly predicts the affected loop in every case. Moreover, the extrusion model accurately predicts in silico the 3D maps resulting from each experiment using only the location of CTCF-binding sites in the WT. Thus, we show that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair.

overall_design: in situ Hi-C and HYbrid Capture Hi-C (Hi-C2) were used to probe the three-dimensional structure of the genome in two different human cell types before and after genome editing.

first: Adrian

last: Sanborn

first: Erez

last: Aiden


title: The influence of the estrous cycle on sex differences in the rat adult medial prefrontal cortex transcriptome [ChIP-Seq]

summary: Hormonal fluctuations throughout the ovarian cycle contribute to females’ higher vulnerability to anxiety disorders when compared to males. Notably, such sex differences are controlled by regulation of genes in the medial prefrontal cortex (mPFC) including the transcription factor early growth response 1 (Egr1) in rats, which highlights a control of anxiety-like behaviors by sexually-biased gene expression. We therefore undertook a large-scale characterization of sex differences and their interaction with the estrous cycle in the adult mPFC transcriptome and report that proestrus and diestrus females (with high and low ovarian hormones levels, respectively) exhibited a partly-opposed sexually-biased transcriptome. Surprisingly, the extent of regulations within females vastly exceeded sex differences, and support a multi-level reorganization of synaptic function across the estrous cycle. Furthermore, genome-wide analysis of Egr1 binding highlighted its role in controlling the synapse-related genes varying within females, and the sex- and estrous cycle-dependent transcriptomic reorganization in the rat mPFC.

overall_design: Early growth response 1 (Egr1) binding profiling in the adult rat medial prefrontal cortex of males, proestrus females, and diestrus females. A total of 9 animals were used, corresponding to 3 Males, 2 proestrus females, and 4 diestrus females.

first: Florian

last: Duclot


title: 3’ and 5’ end modifications in plant microRNA post biogenesis: evidences from NGS of small RNAs [Solanum lycopersicum]

first: Dinesh

last: Gupta

overall_design: small RNA profiles of Healthy and ToLCV infected tomato leaves were generated by deep sequencing using Illumina GAII.

first: Sunil

last: Mukherjee

first: Neeti

last: sanan-Mishra

first: Shradha

last: Saraf


title: Next Generation Sequencing identifies Cdh11 and Mrc1 as novel translational biomarkers of kidney fibrosis

city: Boston

first: John

last: Hutchinson

state: Massachusetts

address: 201 Wachusett Street

institute: Diamond Age Data Science

summary: Chronic kidney disease (CKD) is the gradual, asymptomatic loss of kidney function and current tests only identify it when significant loss has already happened. Using RNA sequencing in a mouse model of folic acid (FA) induced nephropathy, here we report the identification of 10 genes that track kidney fibrosis development, the common pathological finding in CKD patients. The gene expression of all 10 candidates was confirmed to be significantly high (~ 10-150 fold) in three well-established and mechanistically distinct mouse models of kidney fibrosis. Protein expression was also high in the FA model as well as patients with biopsy-proven kidney fibrosis. The specificity of these 10 candidates for kidney fibrosis was demonstrated by showing a very modest (~ 2-5 fold) increase in the mouse models of acute kidney injury as well as following liver fibrosis in mice and humans. Using targeted selected reaction monitoring mass spectrometry (SRM-MS) we found that 3 out of 10, cadherin 11 (CDH11), mannose receptor C1 (MRC1), phospholipid transfer protein (PLTP), are detectable in human urine. Furthermore, the levels of CDH11 and MRC1 are able to distinguish patients with chronic kidney disease from healthy individuals (n = 78, p<0.01). In summary, we report the identification of CDH11 and MRC1 as novel non-invasive biomarkers of CKD.

overall_design: mRNA sequencing of mouse kidney before and at various time points (1,2,3,7 & 14 days) after intraperitoneal treatment with folic acid.

first: Florin

last: Craciun

first: Vishal

last: Vaidya


title: AEBP2’s roles in cell migration and Polycomb Repressive Complex 2 (PRC2)

city: Baton Rouge

first: Joomyeong

last: Kim

state: LA

address: 202 Life Sciences Bldg

department: Biological Sciences

institute: Louisiana State University

summary: Aebp2 encodes a zinc finger protein that is associated with the Polycomb Repressive Complex 2 (PRC2). The alternative promoters and protein isoforms of Aebp2 have been characterized in this study. Aebp2 is controlled through three alternative promoters, deriving three different transcripts which encode the embryonic (32 kDa) and somatic (52 kDa) forms. Chromatin ImmunoPrecipitation (ChIP) experiments revealed that AEBP2 binds to its own promoter as well as the promoters of Jarid2 and Snai2. While the embryonic form acts as a transcriptional repressor for Snai2, the somatic form functions as a transcriptional activator for Jarid2, Aebp2 and Snai2. Cell migration assays suggest that the Aebp2 somatic form can enhance cell migration. This is consistent with the functional association of Aebp2 with migratory neural crest cells. Overall, the two protein isoforms of AEBP2 may have opposite functions for the PcG target genes, and may play significant roles in cell migration during development.

overall_design: 6 Aebp2 Thymus ChIP samples were combined for 2 rounds of Ion torrent sequencing

first: Hana

first: Muhammad

middle: B

last: Ekram

first: Arundhati

last: Bakshi


title: The influence of the estrous cycle on sex differences in the rat adult medial prefrontal cortex transcriptome [RNA-Seq]

overall_design: mRNA profiling of 2-3 month-old males and females Sprague-Dawley rats in either Proestrus or Diestrus. A total of 11 samples were analyzed, corresponding to 4 males, 3 proestrus females, and 4 diestrus females.


title: Differences in murine miR-150-/- CD8+ T cells

status: Public on Oct 22 2015

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

summary: MicroRNAs are a major class of gene regulators in mammals.  While numerous aspects of the immune systems are controlled by miRNAs, their precise role in the CD8+ T cell response remains unclear.  In this report, we show that miR-150 is the most abundant miRNA expressed in CD8+ T cells and its expression is required for proper effector cell differentiation in response to acute and chronic pathogens.  In the absence of miR-150, CD8+ T cells failed to both undergo robust expansion and differentiate into short-lived terminal effector cells. The lack of miR-150 also altered the effector CD8+ T cell transcriptome such that, despite activation, genes associated with naïve or memory cells were highly expressed.  The deletion of miR-150 also reduced killing efficiency of CD8+ T cells.  These results uncover a cell-intrinsic role for miR-150 in the regulation of CD8+ T cell effector fate and function.

overall_design: mRNA and small RNAs were sequenced each from 2 biological replicates of wild-type and miR-150 KO CD8+ T cells

first: Erin

last: Wissink


title: Barx2 and Pax7 have antagonistic functions in regulation of Wnt signaling and satellite cell differentiation

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary: The canonical Wnt signaling pathway is critical for myogenesis and can induce muscle progenitors to switch from proliferation to differentiation; how Wnt signals integrate with muscle specific regulatory factors in this process is poorly understood. We previously demonstrated that the Barx2 homeobox protein promotes differentiation in cooperation with the muscle regulatory factor (MRF) MyoD. Pax7, another important muscle homeobox factor represses differentiation. We now identify Barx2,MyoD,and Pax7 as novel components of the Wnt effector complex, providing a new molecular pathway for regulation of muscle progenitor differentiation. Canonical Wnt signaling induces Barx2 expression in muscle progenitors and perturbation of Barx2 leads to misregulation of Wnt target genes. Barx2 activates two endogenous Wnt target promoters as well as the Wnt reporter gene TOPflash, the latter synergistically with MyoD. Moreover, Barx2 interacts with the core Wnt effectors β-catenin and TCF, is recruited to TCF/LEF sites, and promotes recruitment of β-catenin. In contrast, Pax7 represses the Wnt reporter gene and antagonizes the activating effect of Barx2. Pax7 also binds β-catenin suggesting that Barx2 and Pax7 may compete for interaction with the core Wnt effector complex. Overall, the data show for the first time that Barx2, Pax7, and MRFs can act as direct transcriptional effectors of Wnt signals in myoblasts and that Barx2 and Wnt signaling participate in a regulatory loop. We propose that antagonism between Barx2 and Pax7 in regulation of Wnt signaling may help mediate the switch from myoblast proliferation to differentiation.

overall_design: RNA-Seq analyses was used to characterize gene expression in primary myoblasts from wild-type and Barx2 knockout mice.

first: Robyn

last: Meech


title: Transcriptome response to 4h IL-1b stimulation of primary chondrocytes

status: Public on Oct 21 2015

city: Bath

first: Mark

middle: Andrew

last: Lindsay

address: Claverton Down

department: Pharmacy and Pharmacology

country: United Kingdom

institute: University of Bath

summary: Using RNA sequencing (Illumina Hi-Seq 2000 sequencer) we report the transcriptome profile of primary human chondrocytes isolated from patients with hip osteoarthritis (OA), and the transcriptome response of these cells to 4h stimulation with IL-1β (1ng/ml).  In total, 983 long non-coding RNAs (lncRNAs) were identified, which included 642 intergenic lncRNAs (lincRNAs), 124 antisense and pseudogenes.  Less than 4% of the identified lncRNAs overlapped with putative eRNAs regions, and visual inspection showed that they were uni-directional and multi-exonic.  Upon  IL-1β stimulation 499 protein-coding genes were differentially expressed, and 158 lncRNAs were differentially expressed, including 92 lincRNAs, 13 antisense and 18 psudogenes.  This study demonstrates that IL-1β induces a rapid and widespread change in the transcriptome of the primary human OA chondrocyte.

overall_design: RNA sequencing analysis of primary human chondrocytes isolated from n=3 patients with hip osteoarthritis, with and without 4h IL-1b (1ng/ml) stimulation

first: Simon

last: Jones

middle: A


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Jmjd6-/- Thymic stromal Transcriptomes

city: Fukuoka

first: Toyoshi

last: Yanagihara

state: Fukuoka

address: Maidashi, Higashi-ku

department: Immunobiology and neuroscience

country: Japan

institute: Medical institute of bioregulation, Kyushu University

summary:
The goals of this study are to comprehensively identify genes controlled by Jmjd6 in the thymic stroma, and to identify a novel alternative splicing mechanism.

Methods: Samples were WT and Jmjd6-/- fetal thymus organ culture with (2 samples for each category) or without (1 sample for each category) RANKL stimulation for 4 days under 2-DG. One µg of total RNA was used for library construction with TruSeq RNA Sample Prep Kit v2. THe ligated products were amplified using 8 cycles of PCR to generate RNA-seq library. Library integrity was verified by Bioanalyzer DNA1000 assay. Sequencing was performed in 101-bp paired-end mode using an Illumina HiSeq.Technical duplicate has done.

Results: A total of 177,060,020 reads were obtained for 6 samples. Filtered reads were mapped to the UCSC mm10 using the TopHat program(v2.0.10) with the default parameters. The Cufflinks program (v2.1.1) was then used to assemble 22,448 transcripts and to calculate the fragments per kilobase of exon per million mapped fragments(FPKM) values, which are normalized measurement of gene expression levels(= genes-FPKM file).To identify differentially expressed genes, the ratio of the maximum FPKM to the minimum FPKM was compared among 6 samples. When the ratio was more than 3, the gene was regarded as being significantly altered in expression level. We added 0.1 to the FPKM value to avoid division by zero. This led us to identify 3212 genes with differential expression. Among these, the expression levels of 2536 genes were significantly associated with the RANKL treatment or Jmjd6 expression ( P value <0.05). Analysis for intron retention was performed as follows. According to the current gene annotation ("known genes" in UCSC mm10), there are 188,208 introns in total. As intron retention events should be observed in the genes with relatively high expression, we only focused on the genes with the maximum FPKM value more than 10 at least in one of the six samples. As a result, we obtained 84,708 introns. The reads mapped to these intronic regions were counted by the intersectBed program in the BEDTools utilities with -c option, and the counts are converted into the FPKM values for each intron (intronic FPKM). There are 1051 introns with intronic FPKM more than 10 in at last on of the six samples, and the degree of intron retention was calculated by dividing intronic FPKM value by conventional FPKM value for each gene (intron-FPKM file).

first: Yoshinori

last: Fukui


title: ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Chromatin endogenous cleavage (ChEC) uses fusion of a protein of interest to micrococcal nuclease (MNase) to target calcium-dependent cleavage to specific genomic loci in vivo. Here we report the combination of ChEC with high-throughput sequencing (ChEC-seq) to map budding yeast transcription factor (TF) binding. Temporal analysis of ChEC-seq data reveals two classes of sites for TFs, one displaying rapid cleavage at sites with robust consensus motifs and the second showing slow cleavage at largely unique sites with low-scoring motifs. Sites with high-scoring motifs also display asymmetric cleavage, indicating that ChEC-seq provides information on the directionality of TF-DNA interactions. Strikingly, similar DNA shape patterns are observed regardless of motif strength, indicating that the kinetics of ChEC-seq discriminates DNA recognition through sequence and/or shape. We propose that time-resolved ChEC-seq detects both high-affinity interactions of TFs with consensus motifs and sites preferentially sampled by TFs during diffusion and sliding.

overall_design: We adapted ChEC to a genome-wide sequencing readout (ChEC-seq) to map the genome-wide distributions of the budding yeast transcription factors Abf1, Rap1 and Reb1 without the limitations associated with ChIP-based methods.

first: Gabriel

middle: E

last: Zentner

first: Sivakanthan

last: Kasinathan

first: Steven


title: RNA expression in wild-type and Nipped-B heterozygous mutant Drosophila third instar imaginal wing discs

city: Saint Louis

first: Dale

last: Dorsett

state: MO

address: 1100 South Grand Boulevard

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

summary: RNA expression in wild-type and Nipped-B heterozygous mutant wing discs was quantified by RNA-seq and compared

overall_design: Examination of RNA expression in matched wild-type and mutant Drosophila wing discs


title: Next generation sequencing identifies polyadenylated species of hTR

city: Sherbrooke

first: Michelle

last: Scott

state: Quebec

address: 3201 Jean Mignault

department: Biochemistry

country: Canada

institute: University of Sherbrooke

summary: The paired-end next-generation sequencing of all hTR versions of less than 200 nucleotides in length was used to analyze the 3’ end distribution of hTR associated to Flag-tagged versions of PABPN1, hTERT and Dyskerin. In total, we obtained 2,716,342, 3,152,013, and 3,077,395 hTR-specific reads for the PABPN1, hTERT, and Dyskerin purifications, respectively. We found that the majority of polyadenylated telomerase RNA recovered in the PABPN1, hTERT, and Dyskerin purifications had poly(A) tails starting immediately after the annotated hTR 3’ end. However, a greater proportion of poly(A) tails were found on genome-encoded 3’-extentions in the PABPN1-bound fraction compared to the population of hTR that was copurified with hTERT and DKC1: 15.5% for PABPN1, 6.9% for hTERT, and 6.5% for Dyskerin. Notably, the population of polyadenylated telomerase RNA recovered with PABPN1 was significantly different in terms of poly(A) tail length compared to polyadenylated hTR retrieved in the hTERT- and Dyskerin-bound fractions (P-value=5.551e-16, Kolmogorov-Smirnov test), showing a tendency toward longer poly(A) tails in the PABPN1-bound fraction. The enrichment of telomerase RNA with long poly(A) tails in the PABPN1-bound fraction is consistent with a role of PABPN1 in a maturation pathway that depends on hTR 3’ end polyadenylation. Moreover, our results indicate that a fraction of hTERT and Dyskerin are associated with polyadenylated versions of hTR.

overall_design: Total RNA was immunoprecipitated with FLAG-PABPN1, FLAG-hTERT, and FLAG-DKC1 by the RNA-Immunoprecipitate (RIP) method as previously described. The RNA Ligase-Mediated Rapid Amplification of cDNA End (RLM-RACE) approach was applied to prepare RNA libraries. Briefly, Co-IPed RNAs were ligated with a linker-3 oligo (IDT) followed by a reverse transcription reaction. Three consecutive PCR reactions were performed with specific primers containing unique barcodes for each RNA sample to amplify RNA libraries, which were analyzed by Illumina MiSeq technology.

first: Francois

last: Bachand


title: Opposite Imp/Syp temporal gradients govern birth time-dependent neuronal fates

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

summary: Generating diverse neurons involves spatially distinct neural stem cells that show age dependent developmental fates. Drosophila neuroblasts produce long, diverse yet stereotyped series of distinct neurons, called lineages. We searched for novel temporal factors that could pattern such extended lineages by RNA-sequencing of specific neuroblasts at various developmental times. We found that two RNA-binding proteins, Imp and Syp, display opposing high-to-low and low-to-high temporal gradients with distinct dynamics in specific lineages. Manipulating Imp/Syp levels in mushroom body neuroblasts revealed opposing roles in the specification of early and late temporal fates, primarily via regulation of Chinmo translation. This study implicates the opposing Imp/Syp gradients as temporal morphogens that encode stem cell age and govern birth time-dependent offspring cell fate through post-transcriptional regulation of temporal dentity genes.

overall_design: Examination of 2 different cell types under 4 different time points

first: Tzumin

last: Lee

first: Zhiyong

last: Liu

first: Ching-Po

last: Yang


title: Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences

city: Seattle, WA 98195

first: Alexander

last: Rosenberg

address: 4000 15th Ave NE

department: Electrical Engineering

institute: University of Washington

summary: Most human transcripts are alternatively spliced, and many disease-causing mutations affect RNA splicing. Towards better modeling the sequence determinants of alternative splicing, we measured the splicing patterns of nearly 2 million (M) synthetic mini-genes, which include degenerate subsequences totaling to nearly 100M bases of variation. The massive size of these training data allowed us to improve upon current models of splicing as well as to gain new mechanistic insights. Our results show that a vast majority of hexamer sequence motifs measurably influence splice site selection when positioned within alternative exons, with multiple motifs acting additively rather than cooperatively. Intriguingly, motifs that enhance (suppress) exon inclusion in alternative 5’ splicing also enhance (suppress) exon inclusion in alternative 3’ or cassette exon splicing, suggesting a universal mechanism for alternative exon recognition.  Finally, our empirically trained models are highly predictive of the effects of naturally occurring variants on alternative splicing in vivo.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: HEK293 cells were transfected with two alternatively spliced plasmid libraries. Spliced reads were sequenced to determine isoform counts for each library sequence.

first: Rupali

middle: P

last: Patwardhan

first: Jay

last: Shendure

first: Georg

last: Seelig


title: Genome-wide maps of Cic binding sites in intestinal stem cells (ISCs) & Entroblasts (EBs) and transcriptome profiling of Cic depleted progenitor cells (ISCs & Ebs).

city: Palo Alto

first: Roel

last: Nusse

address: 265 Campus Drive

department: Developmental biology

institute: Stanford University, School of Medicine

summary:
Purpose: Cic is a transcription factor regulating intestinal stem cell (ISC) proliferation as downstream effector of EGFR signaling pathway. ISC-specific mRNA expression profiling and DNA binding mapping using DamID were performed to identify potential target of Cic.
Methods: Total RNA was isolated from GFP+ FACS sorted cells and sent for sequencing after amplification.
Conclusions: We identified potential target genes of Cic, which is differetially expressed in Cic depleted ISCs and also associated Cic binding peaks.

overall_design: 4 biological replicates were performed for RNA-Seq, and 2 biological replicates were performed for Cic DamID-Seq and Cic DamID-Seq after infection.

first: Yinhua

last: Jin

first: Bruce

last: Edgar


title: Gene expression profile of hepatic lincRNAs in male mouse liver using nuclear RNA-Seq

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: Gene expression in adult male mouse liver was assayed by nuclear RNA-seq, as part of a study of hepatic lincRNAs.

overall_design: Three independent pools, comprised of nuclear RNA isolated from 4 individual male livers per pool, were prepared and used for RNA-seq.

first: Nicholas

middle: J

last: Lodato

first: Tisha

last: Melia


title: Gene expression profile of adult male mouse liver using total liver RNA-seq and nuclear liver RNA-Seq

summary: Gene expression in male mouse liver was assayed by RNA-seq, as part of a study to study cellular compartmentalization of hepatic lincRNAs.

overall_design: Pools comprised of total or nuclear liver RNA isolated from individual male mice killed at either 11 AM or 2 PM were prepared and used for RNA-seq (paired-end 100 seq reads).


title: Gene expression profile of intact and hypophysectomized adult male and female mouse liver

summary: Gene expression in intact and hypophysectomized adult mouse liver was assayed by RNA-seq analysis of total liver RNA, as part of a study of growth hormone regulation of hepatic lincRNAs.

overall_design: Eight independent pools: two intact males, two intact females, two hypophysectomized males and two hypophysectomized females, comprised of total RNA isolated from 3-5 individual livers / pool, were prepared and used for unstranded RNA-seq.

first: Jeanette

last: Connerney


title: Gene expression profile of hepatic lincRNAs in female mouse liver using nuclear RNA-Seq

summary: Gene expression in adult female mouse liver was assayed by nuclear RNA-seq, as part of a study of hepatic lincRNAs.

overall_design: Three independent pools, comprised of nuclear RNA isolated from 4 individual livers per pool, were prepared and used for unstranded RNA-seq.


title: Survey of methylomes of two beetles, Nicrophorus vespilloides and Tribolium castaneum

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

type: Methylation profiling by high throughput sequencing

summary: The presence of DNA methylation in beetles (Coleoptera) has only been investigated with bisulfite sequencing of Tribolium castaneum, which produced no evidence of DNA methylation. Here, we used whole genome bisulfite sequencing to assay if DNA methylation was present in another beetle, Nicrophorus vespilloides. We used T. castaneum as a negative control.

sample_organism:
Tribolium castaneum
Nicrophorus vespilloides

overall_design: MethylC-seq of Nicrophorus vespilloides and Tribolium castaneum larva.


title: Response of liver-expressed genes (including lincRNAs) to continuous growth hormone (GH) infusion

summary: Gene expression in livers of adult male mice subjected to continuous GH infusion using Alzet osmotic minipumps for 1, 4 or 7 days was assayed by RNA-seq, as part of a study of growth hormone regulation of hepatic lincRNAs (PMID:26459762) and protein-coding genes (PMID:28694329).

overall_design: RNA isolated from livers obtained from untreated male mice, or from male mice subjected to continuous GH tratment for 1, 4 or 7 days were prepared and used for unstranded RNA-seq.

first: Dana

last: Lau-Corona

last: Suvorov


title: Genome-wide profiling of small RNAs in maize under abiotic stresses

city: Shanghai

first: Renyi

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

summary: To identify novel miRNA and NAT-siRNAs that are associated with abiotic stresses in maize, we generated small RNA sequences from maize seedlings that grew under control and under dought, salt, and cold stress treatments.

overall_design: Sequencing of small RNAs in maize under control, drought, salt, and cold stress conditions.

first: Zhigang

last: Wu

first: Lei

last: Gao

first: Blanca

last: Barrera-Figueroa

first: Jian-kang

last: Zhu


title: Identification of sex-specific hepatic lincRNAs using nuclear RNA-Seq

summary: Gene expression in adult male and female mouse liver was analyzed based on nuclear RNA-seq, as part of a study on hepatic lincRNAs.

overall_design: Nuclear liver RNA was prepared from 6 individual male and 6 individual female mice. Pools comprised of RNA isolated from 6 individual male or female livers (1 pool of 6 biological replicates for each sex) were then prepared and used for strand-specific RNA-seq.

first: Pengying

last: Hao


title: Gene expression in endometrium and corpus luteum of Holstein cows selected for high and low fertility

status: Public on Oct 20 2015

city: Dunsany

first: Paul

last: Cormican

state: Meath

address: Grange

country: Ireland

institute: Teagasc

summary: Our hypothesis was that genes differentially expressed in the endometrium and corpus luteum on day 13 of the estrous cycle between cows with either good or poor genetic merit for fertility would be enriched for genetic variants associated with fertility. We combined a unique genetic model of fertility (cattle which have been selected for high and low fertility and show substantial difference in fertility), with gene expression data from these cattle, and genome-wide association study (GWAS) results in ~20,000 cattle, to identify quantitative trait loci (QTL) regions and sequence variants associated with genetic variation in fertility.

overall_design: 26 samples total; 8 Fert+ (high fertility) endometrium, 6 Fert- (low fertility) endometrium; 7 Fert+ corpus luteum, 5 Fert- corpus luteum; Fert+ Fert- differential gene expression analysis

first: Stephen

middle: G

last: Moore

first: Jennie

last: Pryce

first: Ben

last: Hayes

first: Amanda

last: Chamberlain

first: Kath

last: Kemper

first: Donagh

last: Berry

first: Matthew

last: McCabe

first: Pat

last: Lonergan

first: Trudee

last: Fair

last: Butler


title: The Msi Family of RNA-Binding Proteins Function Redundantly as Intestinal Oncoproteins

city: Philadelphia

first: Christopher

last: Lengner

state: PA

address: 3800 Spruce Street, Room 390EA

institute: University of Pennsylvania

summary: Members of the Msi family of RNA-binding proteins have recently emerged as potent oncoproteins in a range of malignancies. MSI2 is highly expressed in hematopoietic cancers, where it is required for disease maintenance. In contrast to the hematopoietic system, colorectal cancers can express both Msi family members, MSI1 and MSI2. Here, we demonstrate that, in the intestinal epithelium, Msi1 and Msi2 have analogous oncogenic effects. Further, comparison of Msi1/2-induced gene expression programs and transcriptome-wide analyses of Msi1/2-RNA-binding targets reveal significant functional overlap, including induction of the PDK-Akt-mTORC1 axis. Ultimately, we demonstrate that concomitant loss of function of both MSI family members is sufficient to abrogate the growth of human colorectal cancer cells, and Msi gene deletion inhibits tumorigenesis in several mouse models of intestinal cancer. Our findings demonstrate that MSI1 and MSI2 act as functionally redundant oncoproteins required for the ontogeny of intestinal cancers.

overall_design: 2 wild-type, 2 transgenic samples

first: Zhengquan

last: Yu

first: Ning

last: Li

first: Fan

first: Brian

middle: D

last: Gregory

first: Chris


title: Expression and transcriptional regulation dynamics of hepatic lincRNAs

first: David

last: Waxman

summary: Gene expression in adult male and female mouse liver was assayed by RNA-seq, as part of a study on hepatic lincRNAs.

overall_design: Total liver RNA was prepared from 12 individual male and 12 individual female mice. Four independent pools, comprised of RNA isolated from 6 individual male or female livers (2 pooled biological replicates for each sex) were then prepared and used for RNA-seq.

first: Tara

last: Conforto

first: Dana

last: Lau-Corona

first: Tisha

last: Melia


title: Epigenome Editing by CRISPR/Cas9 Repressors for Silencing of Distal Regulatory Elements

status: Public on Oct 19 2015

city: Durham

first: Charles

last: Gersbach

state: NC

address: 101 Science Dr

department: Biomedical Engineering

institute: Duke University

summary: Epigenome editing with the CRISPR/Cas9 platform is a promising technology to modulate gene expression to direct cell phenotype and to dissect the causal epigenetic mechanisms that direct gene regulation.  Fusions of the nuclease-inactive dCas9 to the KRAB repressor domain (dCas9-KRAB) can effectively silence target gene expression.  We targeted dCas9-KRAB to the HS2 enhancer, a distal regulatory element that orchestrates the expression of multiple globin genes. Genome-wide analyses demonstrated that localization of dCas9-KRAB to HS2 specifically induced H3K9 tri-methylation (H3K9me3) at that enhancer and reduced the chromatin accessibility of both the enhancer and its promoter targets.  Targeted epigenetic modification of HS2 silenced the expression of multiple globin genes, with minimal off-target changes in gene expression. These results demonstrate that repression mediated by dCas9-KRAB is sufficiently specific to disrupt the activity of individual enhancers via local modification of the epigenome. This approach enables precise modulation of epigenetic function without modifying the underlying genome sequence.

overall_design: K562 cells were transduced with in triplicate lentivirus encoding dCas9-KRAB with gRNA targeted to the HS2 globin enhancer.  Cells transduced with dCas9-KRAB without gRNA or dCas9 with gRNA targeted to the HS2 globin enhancer were included as controls.  RNA-seq was used to identify differential expression at on-target and off-target sites.

first: Pratiksha

middle: I

last: Thakore

first: Anthony

middle: M

last: D'Ippolito

first: Lingyun

last: Song

first: Alexias

last: Safi

first: Nishkala

middle: S

last: Shivakumar

first: Ami

last: Kabadi

first: Gregory

last: Crawford

first: Timothy

last: Reddy


title: Molecular function of Lhx1 in early mouse development

city: Oxford

first: Arne

middle: Wyndham

last: Mould

state: Oxfordshire

address: Warneford Hospital

department: Psychiatry

institute: Oxford University

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

overall_design: Refer to individual Series


title: Genome-wide maps of chromatin state in HSC, Pro B and mature B cells

city: Basel

first: Mohamed-Amin

last: choukrallah

address: Maulbeerstrasse 66

department: Epigenetic

institute: FMI

summary: We have used a genome-wide ChIP-sequencing approach to define and investigate the dynamics of the cis-regulatory landscape in three developmental stages of the murine hematopoietic system. To this end, we have compared the profiles of H3K4me3, H3K4me1, H3K27ac, H3K27me3 and H3K9me2 in HSCs, committed pro-B and splenic mature B cells. We find the enhancer repertoire to be dynamically reshaped during hematopoiesis progression, surprisingly only a small fraction of primed enhancers in HSCs or committed progenitors become activated in subsequent stages. In turn, the majority of active enhancers in terminally differentiated cells are not primed in earlier stages. We also found that The heterochromatin mark H3K9me2 covers large domains that remain largerly invariant across the three stages and are depleted in both active chromatin marks and the Polycomb related mark H3K27me3.

overall_design: Investigating enhancer dynamics in 3 different stages of B cell development

last: Choukrallah

first: Shuang

first: Antonius

last: Rolink

first: Lukas

last: Burger

first: Patrick

last: Matthias


title: Long non-coding RNA profiling of human lymphoid progenitors reveals transcriptional divergence of B cell and T cell lineages

city: Los Angeles

first: Gay

middle: Miriam

last: Crooks

state: California

address: 610 Charles E. Young Drive, East

department: Pathology & Laboratory Med

institute: University of California Los Angeles

summary: To elucidate the transcriptional ‘landscape’ that regulates human lymphoid commitment during postnatal life, we used RNA sequencing to assemble the long non-coding transcriptome across human bone marrow and thymic progenitor cells spanning the earliest stages of B lymphoid and T lymphoid specification. Over 3,000 genes encoding previously unknown long non-coding RNA (lncRNAs) were revealed through the analysis of these rare populations. Lymphoid commitment was characterized by lncRNA expression patterns that were highly stage specific and were more lineage specific than those of protein-coding genes. Protein-coding genes co-expressed with neighboring lncRNA genes showed enrichment for ontologies related to lymphoid differentiation. The exquisite cell-type specificity of global lncRNA expression patterns independently revealed new developmental relationships among the earliest progenitor cells in the human bone marrow and thymus.

overall_design: We performed RNA-Seq of 10 distinct cell types isolated by fluorescence activated cell sorting (FACS). From BM, we isolated CD34+CD38neglinneg cells, a population highly enriched for HSC, as well as three lymphoid progenitor populations; LMPP (CD34+CD45RA+CD38+CD10neg CD62Lhilinneg), CLP (CD34+CD38+CD10+CD45RA+linneg ) and fully B cell committed progenitors (BCP, CD34+CD38+CD19+). From thymus we isolated three CD34+ subsets; Thy1 (CD34+CD7neg CD1aneg CD4negCD8neg), Thy2 (CD34+CD7+CD1aneg CD4negCD8neg), and Thy 3 (CD34+CD7+CD1a+CD4negCD8neg), as well as fully T cell committed populations CD4+CD8+ (Thy 4), CD3+CD4+CD8neg (Thy5) and CD3+CD4neg CD8+ (Thy6).

first: David

last: Casero

first: Salemiz

last: Sandoval

first: Christopher

last: Seet

first: Jessica

last: Scholes

first: Yuhua

last: Zhu

first: Vi

middle: L

last: Ha

first: Chintan

last: Parekh


title: Changes in relative transcript amounts caused by ∆tprA, ∆phrA, double ∆tprA ∆phrA mutation or the addition of PhrA peptide in Streptococcus pneumoniae

city: Bloomington

first: Ho-Ching

middle: Tiffany

last: Tsui

state: IN

address: 1001 E. Third St.

department: Biology

institute: Indiana University

summary: Lantibiotics are highly modified peptides that are part of the bacteriocin family of antimicrobial peptides. We have identified a Phr peptide quorum sensing system (TprA/PhrA) that controls the expression of a lantibiotic gene cluster in the Gram-positive human pathogen, Streptococcus pneumoniae. We have characterized the basic mechanism for a Phr peptide signaling system in S. pneumoniae D39 and found that it induces expression of the lantibiotic genes when pneumococcal cells are at high density in the presence of galactose, a main sugar of the human nasopharynx, a highly competitive microbial environment. In this study we used RNA-seq analysis to examine the changes in relative transcript amounts caused by ∆tprA and ∆phrA mutations or the addition of the 10-residue synthetic PhrA peptide. These analyses reveal that PhrA peptide addition induces the transcription of a cluster of lantibiotic gene that appear to process and provide immunity to a lantibiotic peptide. In addition, TprA, a transcriptional factor regulated by a Phr peptide, autoregulates its own transcription.

overall_design: RNA samples were prepared from a wild-type strain, a wild-type strain treated with PhrA peptide, and three mutant strains. Three independent biological replicates of RNA were prepared for each strain or condition. cDNA libraries were sequenced and the sequencing results were used as the data base for differential expression analysis.

first: Sharon

last: Hoover

first: Dhriti

last: Sinha

first: Kurt

last: Zimmer

first: Doug

last: Rusch

first: Malcolm

last: Winkler

first: Beth

last: Lazazzera


title: RNA-Seq analysis of mouse liver lincRNAs

city: Boston

last: Waxman

state: MA


city: Cambridge

first: Mudit

last: Chaand

address: 35 Cambridgepark Drive

institute: Syros Pharmaceuticals

overall_design: K562 cells were transduced with in triplicate lentivirus encoding dCas9-KRAB with gRNA targeted to the HS2 globin enhancer.  Cells transduced with dCas9-KRAB without gRNA or dCas9 with gRNA targeted to the HS2 globin enhancer were included as controls.  RNA-seq was used to identify differential expression at on-target and off-target sites. ChIP-seq was used to identify dCas9-KRAB occupancy and H3K9me3 changes, and DNase-seq was used to identify changes in chromatin accessibility.

first: Pratiksha

last: Thakore

first: Anthony

last: D'Ippolito

first: Lingyun

last: Song

first: Alexias

last: Safi

first: Nishkala

last: Shivakumar

first: Ami

last: Kabadi

first: Gregory

last: Crawford

first: Timothy

last: Reddy

first: Charles

last: Gersbach


title: Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function

city: Potsdam

first: Alexander

last: Bartholomaeus

address: Telegrafenberg C

department: Department 3 Geochemie

institute: Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences

summary: Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation.

overall_design: Structural probing of the total RNA of E.coli under normal conditions

first: Cristian

last: Del Campo

last: Bartholomäus

first: Ivan

last: Fedyunin

first: Zoya

last: Ignatova


title: Paf1 complex factors, Leo1 and Paf1, promote local histone turnover to modulate chromatin states in fission yeast [ChIP-exo]

status: Public on Oct 18 2015

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

institute: Karolinska Inst

summary: Maintenance of open and repressed chromatin states is crucial for regulation of gene expression. To study the genes involved in maintaining chromatin states we generated a random mutant library using the Hermes transposon mutagenesis system in fission yeast Schizosacchromyces pombe. The silencing of reporter genes inserted in the euchromatic region adjacent to the heterochromatic mating type locus was monitored. We identified Leo1-Paf1, a subcomplex of the RNA Polymerase II Associated Factor 1 Complex (Paf1C), required to prevent spreading of heterochromatin into euchromatin. Through high-resolution genome-wide ChIP (ChIP-exo) we mapped the heterochromatin mark H3K9me2 in leo1∆ cells. Loss of Leo1-Paf1 led to increased heterochromatin stability at several facultative heterochromatin loci. The RNAi machinery is the major pathway for heterochromatin formation in S. pombe. However, small RNA sequencing showed that heterochromatin assembly in leo1∆ cells was RNAi-independent. By examining histone turnover rate in leo1∆ cells, we showed that deletion of Leo1 decreased nucleosome turnover, which led to heterochromatin spreading. Our data revealed that Leo1-Paf1 promotes chromatin state fluctuations by enhancing histone turnover.

overall_design: H3K9me2 ChIP experiments performed on wild-type and leo1::kan strains.  Two-replicates each.

first: Laia

last: Sadeghi

first: Punit

last: Prasad

first: Amikam

last: Cohen

first: J

last: Svensson


title: RNA-Seq of rice endosperm under high temperature

city: hangzhou

first: ying

last: zhu

address: 198, Shiqiao Rd

institute: Zhejiang Academy of Agricultural Sciences

summary: High temperature during the grain-filling stage causes deleterious effects on storage material accumulation and grain quality. But it is still unclear how high temperature affects storage materials accumulation. In this study, we systemically analyzed the expression pattern of rice genes under high temperture during the grain-filling stage.

overall_design: Five days after pollination rice plants were then transferred to either a 35°C /28°C or 28°C / 22°C artificial climate room for high temperature or control treatment. endosprem were sampled 5d after treatment.

first: Y

last: Zhu

first: H

last: Xu


title: Genetic predisposition to neuroblastoma mediated by a single nucleotide polymorphism within a LMO1 oncogene super-enhancer element

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: A previous genome-wide association study identified common polymorphisms at the LMO1 gene locus that are highly associated with neuroblastoma susceptibility in children and oncogenic addiction to LMO1 in the tumor cells1. Here we sought to discover the causal DNA variant at this locus and the mechanism by which it leads to neuroblastoma tumorigenesis. We first imputed all possible genotypes across the LMO1 locus and then mapped highly associated single nucleotide polymorphism (SNPs) to areas of chromatin accessibility, evolutionary conservation, and transcription factor binding sites. SNP rs2168101 G>T was the most highly associated variant (combined P=7.47x10-29, Odds Ratio 0.65, 95% CI: 0.60-0.70) and resided in a super-enhancer defined by extensive acetylation of histone H3 lysine 27 within the first intron of LMO1. The ancestral G allele that is associated with tumor formation resides in a conserved GATA transcription factor binding motif. We show that the newly evolved protective TATA allele is associated with decreased total LMO1 expression (P=0.028) in neuroblastoma primary tumors and ablates GATA3 binding (P=0.007). We demonstrate monoallelic LMO1 expression from the G-containing strand in tumors heterozygous for this SNP as demonstrated both by RNA sequencing (P<0.0001) and reporter assays (P=0.002). These findings show that a recently evolved polymorphism within a super-enhancer element in the first intron of LMO1 influences neuroblastoma susceptibility through differential GATA transcription factor binding and direct modulation of LMO1 expression in cis, and this leads to an oncogenic dependency in tumor cells.

overall_design: ChIP-Seq for H3K27ac and GATA3 in neuroblastoma cell lines

first: Andrew

middle: C

last: Wood

first: Derek

last: Oldridge

first: Ian

last: Crimmins

first: Robyn

last: Sussman

first: Cynthia

last: Winter

first: Lee

last: McDaniel

first: Shizhen

first: Nina

last: Weichert

first: Adam

last: Durbin

first: Brian

last: Abraham

first: Lars

last: Anders

first: Lifeng

last: Tian

first: Jun

last: Wei

first: Javed

last: Khan

first: Kelli

last: Bramlett

first: Nazneen

last: Rahman

first: Mario

last: Capasso

first: Hakon

last: Hakonarson

first: Sharon

last: Diskin

first: A

last: Look

first: John

last: Maris


title: A spinal opsin controls early neural activity and drives a behavioral light response

city: Berkeley

first: Ehud

last: Isacoff

state: CA

address: 279 Life Sciences Addition

department: MCB

institute: UC Berkeley

summary:
Purpose: using RNA-seq as a screening tool to determine candidate genes of interest within a genetically defined neural subpopulation in the zebrafish embryonic spinal cord.
Results: The early embryonic spinal cord displays patterns of spontaneous activity that generate the earliest motor behavior in the zebrafish. We show the behavior and the neural activity to be inhibited by environmental levels of light. Since at these young ages the fish is blind, and since restricted illumination patterns on the trunk of the fish can elicit a photo-response, we hypothesized that the photo-inhibition is an intrinsic property of the active central pattern generator network within the spinal cord. We FACS-isolated cells from this network as well as those from a panneuronal population and sequenced mRNAs. Through differential expression analysis we identified vertebrate ancient long opsin a as a candidate and then further validated its function in the circuit through knockdown and rescue experiments.

overall_design: RNA sequencing of 2 FACS purified neural populations from zebrafish spinal cord.

first: Drew

last: Friedmann

last: Hoagland

first: Shai

last: Berlin

middle: Y


title: Cyp27c1 red-shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2

status: Public on Oct 17 2015

city: Saint Louis

first: Jennifer

last: Enright

address: 660 S. Euclid, Box 8118

institute: Washington University School of Medicine

summary: The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2, resulting in red-shifted spectral sensitivity of the visual system.  We conducted next-generation sequencing of mRNA derived from the retinal pigment epithelium (RPE) of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone, so we profiled the RPE from TH- and vehicle-treated zebrafish (n=3). The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina, but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE (n=3). Using this approach, we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets, and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production.

sample_organism:
Danio rerio
Aquarana catesbeiana

platform_organism:
Danio rerio
Aquarana catesbeiana

overall_design: Differential gene expression analysis in TH-treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE, conducted in triplicate

first: Joseph

last: Corbo


title: Transcriptome Analysis Identifies Linc-Yy1, A Novel Functional LincRNA During Myogenesis

status: Public on Oct 16 2015

city: Shenzhen

first: Kun

last: Sun

address: Rm B505, No. 9 Duxue Road, Nanshan District

department: Cancer Research

institute: Shenzhen Bay Laboratory

summary: Little is known how lincRNAs are involved in skeletal myogenesis. Here we describe the discovery of a novel lincRNA, Linc-YY1 from the promoter of transcription factor (TF) Yin Yang 1 (YY1) gene. We demonstrate that Linc-YY1 is dynamically regulated during myogenesis in vitro and in vivo. Gain or loss of function of Linc-YY1 in C2C12 myoblast cells or satellite cells alters myogenic differentiation and in injured muscles impacts the course of regeneration. Further studies suggest LincYY1 may interact with YY1 through its middle domain to evict YY1

overall_design: 9 ChIP-seq and 4 RNA-seq experiments performed

first: Huating

last: Wang

first: Hao

first: Liang

last: Zhou

first: Yu

last: Zhao


title: Molecular function of Lhx1 in early mouse development (ChIP-Seq)

first: Arne

last: Mould

summary: ChIP-seq using anti-Lhx1 antibody to map genomic binding of Lhx1 in stably transfected P19 mouse embryonic carcinoma cells

overall_design: ChIP-seq for two independent SF-Lhx1-cmER expressing P19 embryonic carcinoma cell clones and the parent P19 cell line.  These samples have paired input samples.

first: I

last: Costello

first: S

last: Nowotschin

first: X

last: Hadjantonakis

first: E

last: Bikoff

last: Robertson


title: Paf1 complex factors, Leo1 and Paf1, promote local histone turnover to modulate chromatin states in fission yeast [ncRNA-Seq]

first: Karl

last: Ekwall

overall_design: RNA-Seq experiments performed in wild-type, ago1::kan, rrp6::kan, htb1-K119R:kan, and leo1::kan strains. Two-replicates each.

first: Laia

last: Sadeghi

first: Punit

last: Prasad

first: Amikam

last: Cohen

first: J

last: Svensson


title: Single cell expression profiles of the earliest cardiac precursor cells

city: London

first: Kenta

last: Yashiro

address: Charterhouse Square

department: Willaim Harvey research Institute

institute: Barts and The London School of Medicine and Dentistry, Queen Mary University of London

summary: The character of the earliest cardiac precursor cells remains largely unknown. To elucidate this further, we constructed single cell cDNAs from the mouse embryonic cardiac precurcsor cells of the early allantoic bud stage and the early headfold stage, and subjected them to deep sequencing.

overall_design: The most anterior part of the embryos where cardiac precursor cells exist was digested by trypsin to separate into single cells. After a cell was transferred into a reaction tube, single cell cDNAs were constructed as PCR amplicons. cDNAs of cardiac precursor cells were identified by PCR of marker genes.


title: Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish

city: Singapore

first: Vivek

last: Tanavde

state: Singapore

address: 30 Biopolis Street, #07-01, Matrix

department: Genome and Gene Expression Data Analysis Division

country: Singapore

institute: Bioinformatics Institute, A*STAR, Singapore

summary: The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish, substantially less microRNAs have been discovered in zebrafish compared to human (Release 19). It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain, gut, liver, ovary, testis, eye, heart and embryo of zebrafish.  In brain, gut and liver sequencing was done in male and female separately. Majority of the sequenced reads (16-62%) mapped to known miRNAs, with the exception of ovary (5.7%) and testis (7.8%). Using the miRNA discovery tool (miRDeep2), we discovered novel miRNAs from the un-annotated reads that ranged from 7.6 to 23.0%, with exceptions of ovary (51.4%) and testis (55.2%). The prediction tool identified a total of 459 novel pre-miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated (22) and sex associated (34) miRNAs, respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further, we have discovered 459 novel pre-miRNAs (~30% seed homology to human miRNA) as  a genomic resource which can facilitate further investigations to understand miRNA-mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs.

overall_design: Known miRNA profiling, novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish (in triplicate) was carried out using the Illumina HiSeq 2000 platform.

first: Candida

last: Vaz

first: Choon

middle: W

last: Wee

first: Gek

last: Lee

first: Philip

last: Ingham

first: Sinnakaruppan

last: Mathavan


title: B cell survival and development is dependent on the coordination of NFkappaB family members RelB and cRel

first: Alexander

last: Hoffmann

address: 570 Boyer Hall

department: MIMG

institute: UCLA

summary: Identify genes which are induced in wild type, crel ko, and relbcrle dbko B cells under  BAFF stimulation, and find the differential expressed genes which are distinct from wildtype controls.

overall_design: RNA-seq analysis of wild type, crelko, relbcrel dbko follicular B cells stimulated with BAFF ligand for 6 hours and wildtype only for 27 hours

first: Jonathan

last: Almaden

first: Harry

last: Birnbaum

first: Jeremy

last: Davis-Turak