title: Human telomerase RNA processing and quality control

city: Kansas City

first: Peter

last: Baumann

state: MO

institute: Stowers Institute for Medical Research

summary: Primary telomerase RNA transcripts are processed into shorter mature forms that assemble into a complex with the catalytic subunit and provide the template for telomerase activity.  In diverse fungi telomerase RNA 3’ end processing involves a single cleavage reaction by the spliceosome akin to the first step of splicing.  Longer forms of human telomerase RNA (hTR) have been reported, but how the mature form of precisely 451 nucleotides is generated is still unknown.  We now show that the splicing inhibitor isoginkgetin causes accumulation of long hTR transcripts, but find no evidence for a direct role for splicing in hTR processing.  Instead, isoginkgetin mimics the effects of inhibiting the RNA exosome.  Depletion of exosome components and accessory factors reveals functions for the cap binding complex (CBC) and the nuclear exosome targeting (NEXT) complex in hTR turnover.  Whereas longer transcripts are predominantly degraded, shorter precursor RNAs are oligo-adenylated by TRF4-2 and either processed by poly (A) specific ribonuclease (PARN) or degraded by the exosome.  Our results reveal that hTR biogenesis involves a kinetic competition between RNA processing and quality control pathways and suggest new treatment options for dyskeratosis congenita caused by mutations in RNA processing factors.

overall_design: We cloned and sequenced 3’ ends by RLM-RACE coupled with high-throughput sequencing to gain further insights into hTR processing.

first: Chi-Kang

last: Tseng

first: Hui-Fang

last: Wang

first: Allison

last: Burns

first: Morgan

last: Schroeder

first: Martina

last: Gaspari


title: Transcriptional heterogeneity and lineage commitment in myeloid progenitors

status: Public on Nov 25 2015

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


state: Missouri

address: 1000 E 50th Street

country: USA

institute: HHMI/Stowers Institute

summary: RNA sequencing of HeLa cells treated with siRNA against the RNA exosome components hRRP40, hRRP6, hDIS3, and hRRP6/hDIS3 or the splicing inhibitors Isoginkgetin and spliceostatin A, respectively.

overall_design: Stranded, ribo-depleted RNA seq profiles of HeLa cells treated with exosome targeting siRNAs or splicing inhibitors using Illumina HiSeq. All experiments were carried out in triplicate starting with independent cell cultures

first: Chi

middle: K

last: Tang

first: Hui

middle: F

middle: M

middle: R


title: The acute cold response of brown adipose tissue analyzed by RNA-seq

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: We applied RNA sequencing (RNA-seq) to map the global changes in gene expression of interscapular brown adipose tissue (iBAT) of mice subjected to acute cold exposure for 3 days. Here we find extensive changes in the iBAT transcriptome in response to cold with a prominent induction of genes associated to lipid-related metabolic processes.

overall_design: RNA-seq of poly-A enriched RNA isolated from brown adipose tissue of 5 mice housed at room temperature (22°C) and 5 mice exposed to cold (4°C) for 3 days.

first: Ann-Britt

last: Marcher

first: Susanne

last: Mandrup


title: Brain-specific transcriptome analysis in MECP2 transgenic monkeys

city: Shanghai

first: Zilong

last: Qiu

address: No.320, Rd. Yueyang

country: China

institute: Chinese Academic of Science

summary: We have performed gene expression profiling of the MECP2 transgenic monkey, taking advantage of recently completed genome sequencing for the cynomolgus monkey. We found interesting changes in the pattern of alternative splicing of many genes, including genes coding synaptic proteins (e.g., neurexin-3 and Shank-3) and metabolism-related proteins, as compared to the wild-type monkey. This study provides important information for understanding the impact of disease-related gene on brain development.

overall_design: Examination of transcriptome in brain tissues of wild-type and MECP2 transgenic monkeys.

first: Qiang

last: Sun


title: Transcriptional heterogeneity and lineage commitment in myeloid progenitors [single cell RNA-seq]

summary: Within the bone marrow, hematopoietic stem cells differentiate and give rise to diverse blood cell types and functions. Currently, hematopoietic progenitors are defined using surface markers combined with functional assays that are not directly linked with the in vivo potential or gene regulatory mechanisms. Here we comprehensively identify myeloid progenitor subpopulations by transcriptional sorting of single cells from the bone marrow. We describe multiple progenitor subgroups showing unexpected transcriptional priming towards seven differentiation fates, but no progenitors with a mixed state. Transcriptional differentiation is correlated with combinations of known and previously undefined transcription factors, suggesting the process is tightly regulated. Histone maps and knockout assays are consistent with the transcriptional states while traditional transplantation experiments are only partially overlapping myeloid transcriptional priming. Our analyses uncover the function of the underlying regulatory mechanisms for several sub groups and establishes a general framework for dissecting hematopoiesis.

overall_design:
Bone marrow Lin- cKit+ Sca1- myeloid progenitors mRNA profiles from single cells were generated by deep sequencing of thousands of single cells, sequenced in several batches in an Illumina NextSeq

Please note that [1] raw data files were processed as single-ended file since second read (mate) files contain only cell/molecule barcodes and therefore, not provided. This information was appended to the fastq entry header [2] The 'experimental_design.txt' file explains the correspondence of each single cell (WXXXX) in the 'umitab.txt' to a sample (ABXXXX).

first: Amos

last: Tanay

first: Franziska

last: Paul

first: Ya’ara

last: Arkin

first: Amir

last: Giladi


title: Transcriptome profiling of various organs at different developmental stages in rice (paired-end)

city: New York

first: Huan

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

summary: To identificate long noncoding RNAs in rice, we profiled transcriptome of various organs at different developmental stages using nondirectional paired-end RNA-seq based on poly(A) selection.

overall_design: Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds.

first: Hui-Wen

last: Wu

first: Jian

last: Ye

first: Jun

last: Liu

first: Nam-Hai

last: Chua


title: The Nucleosome Landscape of P. falciparum Reveals Chromatin Architecture and Dynamics of Regulatory Sequences

city: Nijmegen

first: Richard

middle: Csaba

last: Bartfai

address: Geert Groteplein 26-26

department: Department of Molecular Biology

country: Netherlands

institute: Radboud University

summary: In eukaryotes, the chromatin architecture has a pivotal role in regulating all DNA-related processes. For P. falciparum, the causative agent of human malaria, the nucleosome landscape of the extremely AT-rich intergenic regulatory regions is largely unexplored. With the aid of a highly controlled MNase-seq procedure we reveal how positioning of nucleosomes provides a structural and regulatory framework to the transcriptional unit. We observe strong positioning of nucleosomes around splice sites that could aid co-transcriptional splicing events. In addition, nucleosome depleted regions are apparent hallmarks of transcription start sites (TSSs) and may support pre-initiation complex assembly. Moreover, we reveal nucleosome occupancy dynamics on strong TSSs during intraerythrocytic development, which correlate with gene expression changes and we observe a characteristic nucleosome architecture of functional - but not inert - TGCATGCA DNA motifs. Collectively, these findings highlight the regulatory capacity of the nucleosome landscape of this deadly human pathogen.

overall_design:
Mnase-seq during the intra-erythrocytic asexual cycle of Plasmodium falciparum var2csa-panned 3D7 parasites for 8 time-points, every 5 hours starting from 5 hours post invasion until 40 hours post-invasion (T5-T40). Cycle length of these parasites is ~43 hours, synchronicity window is ~ 8 hours. T40 has 2 technical replicates (independent digestions; T40A, T40B). Additionally, pellet control sample (T15), histone H4-ChIP control (T40A) and sonicated and amplified genomic DNA. Chromatin was digested using a combined MNase + exonuclease III treatment. Libraries were prepared according to a Plasmodium-optimized library preparation procedure including KAPA polymerase-mediated PCR amplification.
Strand-specific RNA-seq for expression quantification during the intra-erythrocytic asexual cycle of Plasmodium falciparum var2csa-panned 3D7 parasites for 8 time-points every 5 hours starting from 5 hours post invasion invasion until 40 hours post-invasion (T5-T40). Cycle length of these parasites is ~43 hours, synchronicity window is ~ 8 hours.  These samples are originating from the exact same batch of parasites as are the MNase-Seq libraries. Libraries were prepared according to a Plasmodium-optimized library preparation procedure including KAPA polymerase-mediated PCR amplification.

first: Philip

last: Kensche

first: Wieteke

middle: A

last: Hoeijmakers

first: Maaike

last: Bras

first: Lia

last: Chappell

first: Matthew

last: Berriman

first: Richárd

last: Bártfai


title: Transcriptome profiling of noncoding RNAs in maize (single-end)

last: Wang

summary: To identificate long noncoding RNAs in maize, we profiled transcriptome of shoots and roots using stranded single-end RNA-seq based on poly(A) selection.

overall_design: Transcriptom profiling in maize shoots and roots.


title: Transcriptome profiling of noncoding RNAs in maize (paired-end)

summary: To identificate long noncoding RNAs in maize, we profiled transcriptome of shoots and roots using non-directional paired-end RNA-seq based on poly(A) selection.


title: Genome-wide maps of chromatin changes uppon contextual fear conditioning in mice (meDIP-seq)

status: Public on Nov 24 2015

city: Gottingen

first: Ramon

last: Oliveira Vidal

address: Grisebachstraße 5

department: Bioinformatics

country: Germany

institute: DZNE

type: Methylation profiling by high throughput sequencing

summary: The ability to form memories is a prerequisite for an organism’s behavioural adaptation to environmental changes. At the molecular level, the acquisition and maintenance of memory requires changes in chromatin modifications. In an effort to unravel the epigenetic network underlying both short- and long-term memory, we examined chromatin modification changes in two distinct mouse brain regions, two cell-types, and three time-points before and after contextual learning. Here we show that histone modifications predominantly change during memory acquisition and correlate surprisingly little with changes in gene expression. While long-lasting changes are almost exclusive to neurons, learning-related histone modification and DNA methylation changes occur also in non-neuronal cell types, suggesting a functional role for non-neuronal cells in epigenetic learning. Finally, our data provides evidence for a molecular framework of memory acquisition and maintenance, wherein DNA methylation could alter the expression and splicing of genes involved in functional plasticity and synaptic wiring.

overall_design: We examined chromatin modification changes in two distinct mouse brain regions (CA1 and ACC), two cell-types (neurons, non-neurons), and three time-points before and after contextual learning (naive, 1h, 4w).

first: Rashi

last: Halder

first: Magali

last: Hennion

middle: O

last: Vidal

first: Orr

last: Shomroni

first: Raza-Ur

last: Rahman

first: Ashish

last: Rajput

first: Tonatiuh

last: Pena Centeno

first: Frauke

last: van Bebber

first: Vincenzo

last: Capece

first: Julio

middle: C

last: Garcia Vizcaino

first: Anna-Lena

last: Schuetz

first: Susanne

last: Burkhardt

first: Eva

last: Benito

first: Magdalena

last: Navarro Sala

first: Sanaz

last: Bahari Javan

first: Christian

last: Haass

first: Bettina

last: Schmid

first: Andre

last: Fischer

first: Stefan

last: Bonn


title: Genome-wide maps of chromatin changes uppon contextual fear conditioning in mice (RNA-seq)

first: Ramon

last: Oliveira Vidal

first: Rashi

last: Halder

first: Magali

last: Hennion

last: Vidal


title: Genome-wide maps of chromatin changes uppon contextual fear conditioning in mice


title: The effect of Heterogeneous Transcription Start Sites (TSS) on the Translatome: Implications for the Mammalian Cellular Phenotype.

city: Geneva

first: Joseph

last: Curran

address: 1 rue Michel Servet

department: Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva Medical School

summary: Sequencing of total RNA and polysomal RNA of two cell lines, MCF7 (tumoral) and MCF10A (non-tumoral)

overall_design: Polysomal and total RNA was prepared from biological triplicates from the two cell lines.  For each biological triplicate sub-confluent cell monolyers were lysed to produce cytoplasmic extracts. Half of each extract was fractionated on a sucrose gradient and the polysomal fraction recovered. Polysomal-associated RNA was recovered by Trizol extraction. From the second half of each sample total cyoplasmic RNA was recovered (Trizol extraction).

first: Francois-Xavier

last: Dieudonné

first: Patrick

middle: B

last: O’Connor

first: Pascale

last: Gubler-Jaquier

first: Haleh

last: Yasrebi

first: Beatrice

last: Conne

first: Sergey

last: Nikolaev

first: Stylianos

last: Antonarakis

first: Pavel

middle: V

last: Baranov


title: microRNA expression in primary human muscle cells treated with 1,25(OH)2D3 or vehicle

city: Rochester

first: Xuewei

last: Wang

address: 200 1st street

institute: Mayo Clinic

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the effects of 1,25(OH)2D3 treatment on the microRNA expression in human muscle cells

overall_design: Primary cultures of human muscle cells were treated with 1,25(OH)2D3 or vehicle for 48 hours.

first: Rajiv

last: Kumar


title: Genome-wide maps of chromatin changes uppon contextual fear conditioning in mice (ChIP-seq)

first: Orr

last: Shomroni

first: Raza-Ur

last: Rahman

first: Ashish

last: Rajput

first: Tonatiuh

last: Pena Centeno

first: Frauke

last: van Bebber

first: Vincenzo

last: Capece

first: Julio

last: Garcia Vizcaino

first: Anna-Lena

last: Schuetz

first: Susanne

last: Burkhardt

first: Eva

last: Benito

first: Magdalena

last: Navarro Sala

first: Sanaz

last: Bahari Javan

first: Christian

last: Haass

first: Bettina

last: Schmid

last: Fischer


title: Aspergillus fumigatus in blood reveals a "just wait and see" resting stage behavior

city: Valencia

first: Sonia

last: Tarazona

address: Eduardo Primo de Yúfera

country: Spain

institute: Centro de Investigación Príncipe Felipe

summary:
Objective: We analyzed changes in A. fumigatus gene expression profile at various stages of an in vitro model of aspergillosis to study the adaptation of A. fumigatus to the blood environment.
Results: Most of virulence factors described to be involved in aspergillosis were not activated during the blood phase. We found three active processes to be activated in the later phase that may help to the adaptation: Iron homeostasis, a partial secondary metabolite cluster and the formation of detoxification enzymes.
Conclusions: We propose that A. fumigatus is unable to grow in blood and it requires a metabolic change that allows the organism to shut down all uptake and energy-consume mechanisms, resulting in a resting mycelial stage.

overall_design: We performed gene expression profile by sequencing mRNA of A. fumigatus that were growm under two conditions, Minimal Medium (M) and human blood (B), and at different times: before placing the fungus in the final medium (pre), at 30' and at 180', with 2 biological replicates per condition.

first: Henriette

last: Irmer

first: Christoph

last: Sasse

first: Patrick

last: Olbermann

first: Sven

last: Krappmann

first: Ana

last: Conesa

first: Gerhard

middle: H

last: Braus


title: RNA expression in primary huamn muscle cells treated with 1,25(OH)2D3 or vehicle

first: Xuewei

last: Wang

summary: We report the effects of 1,25(OH)2D3 treatment on the mRNA expression in human muscle cells

first: Rajiv

last: Kumar


title: Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci

city: Manchester

first: Paul

last: Martin

state: Greater Manchester

address: Oxford Road

department: Centre for Genetics and Genomics Versus Arthritis

country: United Kingdom

institute: Univeristy of Manchester

summary: Genome-wide association studies have been tremendously successful in identifying genetic variants associated with complex diseases. The majority of association signals are intergenic and evidence is accumulating that a high proportion of signals lie in enhancer regions.We use Capture Hi-C to investigate, for the first time, the interactions between associated variants for four autoimmune diseases and their functional targets in B- and T-cell lines. Here we report numerous looping interactions and provide evidence that only a minority of interactions are common to both B- and T-cell lines, suggesting interactions may be highly cell-type specific; some disease-associated SNPs do not interact with the nearest gene but with more compelling candidate genes (for example, FOXO1, AZI2) often situated several megabases away; and finally, regions associated with different autoimmune diseases interact with each other and the same promoter suggesting common autoimmune gene targets (for example, PTPRC, DEXI and ZFP36L1).

overall_design: Capture Hi-C was carried out to characterise the interactions of confirmed susceptibility loci for four autoimmune diseases: rheumatoid arthritis (RA), type 1 diabetes (T1D), psoriatic arthritis (PsA) and juvenile idiopathic arthritis (JIA) with the aim of linking associated variants with disease-causing genes. We have tested the interactions in two complementary experiments: the first, Region Capture, targets regions associated with disease; the second, Promoter Capture, provides independent validation through capturing all known promoters within 500kb of lead associated disease SNPs. All experiments were performed in human T-cell (Jurkat) and B-cell (GM12878) lines in duplicate.

first: Amanda

last: McGovern

first: Gisela

last: Orozco

first: Kate

last: Duffus

first: Annie

last: Yarwood

first: Anne

last: Barton

first: Jane

last: Worthington

first: Steve

last: Eyre


title: Group 3 innate lymphoid cells continuously require the transcription factor GATA3 after commitment

status: Public on Nov 23 2015

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: GATA3 is indispensable for the development of all IL-7Rα-expressing innate lymphoid cells (ILCs) and maintenance of type 1 ILCs (ILC1s) and type 2 ILCs (ILC2s). However, the importance of low GATA3 expression in type 3 ILCs (ILC3s) is still elusive. Here, we report that GATA3 regulates homeostasis of ILC3s by controlling IL-7Rα expression. In addition, GATA3 is critical for the development of NKp46+ ILC3 subset partially through regulating the balance between T-bet and RORγt. Genome-wide analyses indicate that while GATA3 positively regulates CCR6+ and NKp46+ ILC3 subset-specific genes in respective lineages, it negatively regulates CCR6+ ILC3-specific genes in NKp46+ ILC3s. Furthermore, GATA3 regulates IL-22 production in both CCR6+ and NKp46+ ILC3s. Thus, low GATA3 expression is critical for the development and function of ILC3 subsets.

overall_design: To identify GATA3 regulated genes in total ILC3s with RNA-Seq; To identify unique genes expressed by CCR6+ ILC3 or NKp46+ ILC3 and GATA3 regulated genes within these two ILC3 subsets with RNA-Seq; To identify GATA3 direct binding sites in ILC3s, ILC2s and Th2 cells with ChIP-Seq.

first: Chao

last: Zhong

first: Kairong

last: Cui

last: Wilhelm

first: Kairui

last: Mao

first: Yasmine

last: Belkaid

first: Keji

last: Zhao

first: Jinfang

last: Zhu


title: Genome-wide ChIP-seq  analysis of Pou3f1 during mouse pluripotent stem cell neural fate commitment

city: Guangzhou

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

department: Guangzhou Institutes of Biomedicine and Health

institute: Chinese Academy of Sciences

summary: Appropriate neural initiation of the pluripotent stem cells in the early embryos is critical for the development of the central nervous system. This process is regulated by the coordination of extrinsic signals and intrinsic programs. However, how the coordination is achieved to ensure proper neural fate commitment is largely unknown. Here, taking advantage of genome-wide ChIP-sequencing (ChIP-seq) and RNA-sequencing (RNA-seq) analyses, we demonstrate that the transcriptional factor Pou3f1 is an upstream activator of neural-promoting genes, and it is able to repress neural-inhibitory signals as well. Further studies revealed that Pou3f1 could directly bind  neural lineage genes like Sox2 and downstream targets of neural inhibition signaling such as BMP and Wnt. Our results thus identify Pou3f1 as a critical dual-regulator of the intrinsic transcription factors and the extrinsic cellular signals during neural fate commitment.

overall_design: ChIP-seq assay was ultilized to characterize the targets of Pou3f1 on ESC differentiation day 2.

first: Lu

last: Song

last: Sun


title: Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples

city: Bethesda

state: MD

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

summary: DNase I hypersensitive sites (DHSs) provide important information on the presence of transcriptional regulatory elements and the state of chromatin in mammalian cells1, 2, 3. Conventional DNase sequencing (DNase-seq) for genome-wide DHSs profiling is limited by the requirement of millions of cells4, 5. Here we report an ultrasensitive strategy, called single-cell DNase sequencing (scDNase-seq) for detection of genome-wide DHSs in single cells. We show that DHS patterns at the single-cell level are highly reproducible among individual cells. Among different single cells, highly expressed gene promoters and enhancers associated with multiple active histone modifications display constitutive DHS whereas chromatin regions with fewer histone modifications exhibit high variation of DHS. Furthermore, the single-cell DHSs predict enhancers that regulate cell-specific gene expression programs and the cell-to-cell variations of DHS are predictive of gene expression. Finally, we apply scDNase-seq to pools of tumour cells and pools of normal cells, dissected from formalin-fixed paraffin-embedded tissue slides from patients with thyroid cancer, and detect thousands of tumour-specific DHSs. Many of these DHSs are associated with promoters and enhancers critically involved in cancer development. Analysis of the DHS sequences uncovers one mutation (chr18: 52417839G>C) in the tumour cells of a patient with follicular thyroid carcinoma, which affects the binding of the tumour suppressor protein p53 and correlates with decreased expression of its target gene TXNL1. In conclusion, scDNase-seq can reliably detect DHSs in single cells, greatly extending the range of applications of DHS analysis both for basic and for translational research, and may provide critical information for personalized medicine.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Exploring the landscape of chromatin accessibility in single cells and clinical samples

first: Wenfei

last: Jin

first: Qingsong

last: Tang

first: Mimi

last: Wan

first: Yi

last: Zhang

first: Gang

last: Ren

first: Bing

last: Ni

first: Jeffrey

last: Sklar

first: Teresa

last: Przytycka

first: Richard

last: Childs

first: David

last: Levens


title: Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat.

city: Clayton

first: Nicholas

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

summary: DNA methylation is a complex epigenetic marker that can be analysed using a wide variety of methods. Interpretation and visualisation of DNA methylation data can mask complexity in terms of methylation status at each CpG site, cellular heterogeneity of samples and allelic DNA methylation patterns within a given DNA strand. Bisulfite sequencing is considered the gold standard, however visualisation of massively parallel sequencing results remains a significant challenge. We created a program called Methpat that facilitates visualisation and interpretation of bisulfite sequencing data generated by massively parallel sequencing. To demonstrate this, we performed multiplex PCR that targeted 48 regions of interest across 95 human samples. The regions selected included known gene promoters associated with cancer, repetitive elements, known imprinted regions and mitochondrial genomic sequences. We interrogated a range of samples including human cell lines, primary tumours and primary tissue samples. Methpat generates two forms of output: a tab delimited text file for each sample that summarises DNA methylation patterns and their read counts for each amplicon and a HTML file that summarises this data visually. Methpat can be used with publicly available whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) datasets with sufficient read depths. Using Methpat, complex DNA methylation data derived from massively parallel sequencing can be summarised and visualised for biological interpretation. By accounting for allelic DNA methylation states and their abundance in a sample, Methpat can unmask the complexity of DNA methylation and reveal further biological insight in existing datasets.

overall_design: Multiplex bisulfite PCR and Next Generation sequencing of primary human samples and breast cancer cell lines.


title: Identification of genes in longissimus dorsi muscle differentially expressed between Wannanhua and Yorkshire pigs using RNA sequencing

status: Public on Nov 30 2015

city: hefei

first: xiaojin

last: li

state: anhui

address: nongkenan road no. 40

department: Institute of Animal husbandry and veterinary medicine

institute: Anhui academy of agricultural sciences

summary: Western commercial pig breeds have been intensively selected, resulting in a sizeable, rapid, and efficient accretion of muscle but a reduction in meat quality. When compared with Western commercial pig breeds, Chinese indigenous pig breeds exhibited slower growth rates and reduced lean meat content but superior perceived meat quality. To study the factors that determine meat quality, we examined piglets of one Western commercial breed (Yorkshire) and one Chinese indigenous breed (Wannanhua) and sequenced the longissimus dorsi muscle using RNA-sequencing (RNA-seq). We analyzed their transcriptomes, focusing on identifying candidate genes that may influence porcine muscle growth, meat quality and adipose deposition. Gene ontology functional enrichment and pathway enrichment analyses identified differentially expressed genes primarily associated with glycolytic metabolism, biological processes of muscle development and signaling pathways related to fatty acid metabolism, growth and carcass traits. This finding suggests that the differentially expressed genes may play important roles in determining meat quality traits. Quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) confirmed the differential expression of twelve selected differentially expressed genes. This study identified a number of novel candidate genes for porcine meat quality and carcass traits that merit further investigation to elucidate the molecular mechanisms responsible for muscle growth and fat deposition.

overall_design: Examined piglets of Yorkshire pig and Wannanhua pig and sequenced the longissimus dorsi muscle using RNA-sequencing .

first: Chong-Long

last: Wang

first: Xiao-Jin

last: Li


title: Influenza A virus preferentially snatches non-coding RNA caps

city: Riverside

first: Weifeng

last: Gu

state: California

address: 900 University Ave

department: Molecular, Cell and Systems Biology

institute: University of California at Riverside

summary: Influenza A virus (IAV) lacks the enzyme for adding 5’ caps to its RNAs, and thus snatches the 5’ ends of host capped RNAs to prime transcription. Neither the preference of the host RNA sequences snatched, nor the effect of “cap-snatching” on host processes has been completely defined. Previous studies of influenza cap-snatching used poly(A)-selected RNA from infected cells or relied solely on annotated host protein-coding genes to define host mRNAs selected by the virus. To examine the substrate-product relationship between all host RNAs, including non-coding RNAs, and viral RNAs, we used an unbiased approach to identify the host and viral capped RNAs from IAV-infected cells. We demonstrate that IAV predominantly snatches caps from non-coding host RNAs, particularly U1 and U2 small nuclear RNAs (snRNAs). Because snRNAs regulate host mRNA processing, cap-snatching of snRNAs may constitute a means by which IAV hijacks host cell metabolism.

overall_design: examine caps snatched by influenza virus A

first: Glen

last: Gallagher

first: Weiwei

last: Dai

first: Ping

last: Liu

first: Ruidong

first: Melanie

middle: I

last: Trombly

first: Don

last: Gammon

first: Craig

last: Mello

first: Jennifer

middle: P

first: Robert

middle: W

last: Finberg


title: Transcriptome profiling of various organs at different developmental stages in rice (single-end)

first: Huan

summary: To identificate long noncoding RNAs in rice, we profiled transcriptome of various organs at different developmental stages using stranded single-end RNA-seq based on poly(A) selection.

first: Hui-Wen

last: Wu

first: Jian

last: Ye

first: Jun

first: Nam-Hai

last: Chua


title: Transcriptional profiling of wild type Neurospora crassa cells treated with novel antifungal agents

city: Berkeley

first: António Pedro

last: Gonçalves

address: 341A Koshland Hall

department: Plant and Microbial Biology

institute: University of California, Berkeley

summary:
Purpose: Evaluate the transcriptional profile of Neurospora crassa cells treated with a group of novel antifungal compounds
Methods: Conidial suspensions were obtained and 1 x 106 cells/ml incubated in minimal medium for 6 hours (26ºC, 140 rpm, constant light) followed by the addition of the indicated compound (or DMSO) and growth for 1 more hour. Cells were harvested using 0.45 μm filters and immediately frozen in liquid nitrogen. Total RNA was isolated by the Trizol-Phenol-Chloroform method. After digestion of 25 μg RNA with TURBO DNAse (Life Technologies), mRNA was purified using Dynabeads oligo(dT) magnetic beads (Life Technologies). The mRNA was chemically fragmented using the Ambion RNA fragmentation kit (Life Technologies). First and second strand cDNA synthesis was achieved using appropriate kits (Life Technologies). The illumina TruSeq kit was employed to generate the cDNA libraries with indexing adapters essentially following the manufacturer’s protocol. After purification of the libraries with AMPure XP beads (Roche), the quality of the libraries was analysed in a Agilent 2100 Bioanalyzer. The cDNA libraries were sequenced in a illumina HiSeq2000 and single reads of 50 bp were obtained. Sequencing data was handled essentially with Tophat, Cufflinks and Cuffdiff. Expression levels are presented as Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
Results: XP13 promoted a particularly active transcriptional response. Functional enrichment analysis of the genes with altered expression revealed novel pathways that are affected by these compounds.
Conclusions: These compounds are active in Neurospora crassa and we anticipate that this and future studies will ascertain their potential as antifungal agents.

overall_design: The transcriptional profile of Neurospora crassa wild type cells exposed with a group of novel compounds with antifungal activity was analysed using illumina HiSeq2000 and single reads of 50 bp.

first: A


title: Differential gene expression analysis in adult rotation-resistant (RR) and wild-type (WT) western corn rootworm digestive tracts

city: Champaign

first: Chia-Ching

last: Chu

state: IL

address: 1910 Griffith Drive

institute: University of Illinois at Urbana Champaign

summary: The western corn rootworm (WCR, Diabrotica virgifera virgifera LeConte) is an important pest of corn (Zea mays) in the US. Annual crop rotation between corn and soybean (Glycine max) disrupts the corn-dependent WCR lifecycle and was widely adopted to manage WCR. However, this strategy selected for a rotation-resistant (RR) variant with reduced ovipositional fidelity to cornfields. Previous studies indicated that RR-WCR adults exhibit greater tolerance of soybean tissue diet, different gut physiology, and host-microbe interactions compared to wild-types (WT). To identify genetic mechanisms underlying these phenotypic changes, a de novo assembly of the WCR adult gut transcriptome was constructed and used for RNA-sequencing analyses on RNA libraries from different WCR phenotypes (RR and WT) fed with corn or soybean diets. Differential gene expression analyses and network-based methods were used to identify gene modules transcriptionally correlated with the RR phenotype. Gene ontology enrichment analyses on these modules were then conducted to understand their potential functions and biological importance.

overall_design: Differential gene expression analyses on RNA libraries from adult guts of different WCR phenotypes (rotation-resistant and wild-type) fed with corn or soybean diets

first: Manfredo

last: Seufferheld

first: Joseph

last: Spencer

first: Jorge

last: Zavala

first: Matías

last: Curzi


title: Deep bisulfite amplicon sequencing and visualisation reveal diverse and heterogeneous DNA methylation patterns.

first: Nicholas

last: Wong

summary: DNA methylation at a gene promoter region has the potential to regulate gene transcription. Their patterns are often complex with the region showing multiple allelic patterns in a sample. This complexity is commonly obscured when DNA methylation data is summarised as an average percentage value for each CpG site (or aggregated across CpG sites). The methylation state at adjacent CpG sites is therefore lost when data is summarised this way. Methylation patterns can only be characterised by clonal analysis. Deep sequencing provides the ability to investigate clonal DNA methylation patterns in unprecedented detail and scale, enabling the proper characterisation of the heterogeneity of methylation patterns. However, the sheer amount of sequencing data requires new synoptic approaches to visualise the distribution of allelic patterns. We have developed an analysis and visualisation software tool "Methpat", that extracts and displays clonal DNA methylation patterns from massively parallel sequencing data aligned using Bismark. We have performed multiplex bisulfite amplicon sequencing on a range of CpG island targets across a panel of human cell lines and primary tissues. Using Methpat, we demonstrate clonal diversity of epialleles analysed at specific gene promoter regions. We also describe the existence of DNA methylation within the mitochondrial genome.

overall_design: Multiplex bisulfite PCR and Next Generation sequencing of 35 samples


title: Combinatorial Regulation Mediated by Biochemically Distinct Forms of SWI/SNF [ChIP-Seq]

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

summary: The precise makeup of chromatin remodeling complexes is important for determining cell type and cell function. The SWI/SNF chromatin remodeling complex is made up of multiple subunits that can be filled by mutually exclusive proteins. Inclusion or exclusion of these proteins has profound functional consequences, yet we currently understand little about the direct functional relationship between these biochemically distinct forms of remodeling complexes. Here we combine chromatin immunoprecipitation, transcriptome analysis, and transcription factor binding information from the ENCODE project to determine the functional relationship between three biochemically distinct forms of SWI/SNF. We find widespread overlap in transcriptional regulation and the genomic binding of the three ARID (AT-Rich Interacting Domain) subunits of SWI/SNF. Despite the numerous similarities in their transcriptional regulation and the co-factors bound with each ARID we identify several novel interaction modalities. Previous work has found examples of competition or subunit switching at individual loci, and we find this functional relationship is widespread, and in these cases gene expression changes following loss of one ARID depend on the function of another ARID. We also identify a previously unknown cooperative interaction between ARID1B and ARID2 in the repression of a large number of genes. Together these data help untangle the complicated combinatorial relationships between a highly heterogenous chromatin remodeling family.

overall_design:
We performed ChIP for 4 subunits of SWI/SNF (Arid1a, Arid1b, Arid2, Snf5) and 2 replicates of each, as well as Input. HepG2 cells were fixed in 0.3% formaldehyde for 30 minutes at 4 degrees C, then washed and cell pellets were stored at -80 until immunoprecipitation. Nuclei were released using Dounce homogenizer and layered over a sucrose cushion. Chromatin was then prepared by digesting with micrococcal nuclease for 15 minutes at 37 degrees. Chromatin equivalent to 2x10^7 cells was used in each IP with the antibodies listed.

All scripts used in the data analysis are available at: http://github.com/jraab/raab_swisnf_2015/

first: Terry

last: Magnuson


title: ETS Family Transcriptional Regulators Drive Chromatin Dynamics and Malignancy in Squamous Cell Carcinomas (RNA-Seq I)

status: Public on Nov 22 2015

first: Hanseul

last: Yang

state: NY

institute: Rockefeller University

summary: After characterizing super-enhancer-associated chromatin dynamics accompanied by malignant progression of skin stem cells, we show that ETS family members auto-regulate themselves and a cohort of cancer-associated super-enhancer transcription factors which together are essential for tumor maintenance.

overall_design: Mouse skin squamouse cell carcinoma (SCC) tumor-initiating stem cells (SCC-SC), hair follicle stem cells (HF-SC) and epidermal stem cells (Epi-SC) were FACS-prufied for RNA-sequencing.

first: Elaine

last: Fuchs


title: ETS Family Transcriptional Regulators Drive Chromatin Dynamics and Malignancy in Squamous Cell Carcinomas (RNA-Seq II)

overall_design: Epidermal basal stem cells from ETS2(T72D) super-activated epidermis and normal epidermis were FACS-prufied for RNA-sequencing.


title: The Zinc Finger Transcription Factor SlZFP2 Negatively Regulates Abscisic Acid Biosynthesis and Fruit Ripening in Tomato

city: Shanghai

first: Han

last: Xiao

address: 300 Fenglin Rd

department: National Key Laboratory of Plant Molecular Genetics

institute: Shanghai Institutes for Biological Sciences

summary: Abscisic acid (ABA) regulates plant development and adaptation to environmental conditions. The ABA biosynthesis pathway in plants has been thoroughly elucidated; however, very few transcription factors directly regulating the expression of ABA biosynthetic genes have been identified. Here we show that the tomato (Solanum lycopersicum) zinc finger transcription factor SlZFP2, which is mainly expressed in developing fruits and axillary buds, negatively regulates ABA biosynthesis. Overexpression of SlZFP2 resulted in multiple phenotypic changes, including more branches, early flowering, delayed fruit ripening, lighter seeds and faster seed germination, whereas gene silencing by RNA interference (RNAi) caused poor fruit set and inhibited seed germination. Gene expression analysis showed that SlZFP2 represses ABA biosynthesis mainly through downregulation of the ABA biosynthetic genes SITIENS (SIT), FLACCA (FLC) and aldehyde oxidase SlAO1. SlZFP2 delays the onset of ripening through suppression of the ripening regulator COLORLESS NON-RIPENING (CNR). Using bacterial one hybrid screening and a selected amplification and binding assay we identified the (A/T)(G/C)TT repeat as the core binding sequence of SlZFP2. We further identified a large number of tomato genes containing putative SlZFP2 binding sites in their promoter regions. Chromatin immunoprecipitation and electrophoretic mobility shift assays demonstrated that SIT, FLC and SlAO1 are direct targets of SlZFP2 through binding to their promoter regions. We propose that SlZFP2 represents a novel negative regulator for fine tuning ABA biosynthesis during fruit development and provides a potentially valuable tool for dissecting the role of ABA in fruit ripening.To gain further insight on transcriptome changes regulated by SlZFP2, we sequenced a representative SlZFP2 RNAi line in LA1589 background and its nontransgenic sibling (WT) on a Miseq platform.

overall_design: The RNAi line 207 showed defected fruit set and ABA biosynthesis were chosen for profiling gene expression via RNA sequencing. Its nontransgenic sibling was served as controls. Three biological replicates were conducted.

first: Lin

last: Weng


title: Dynamics of TRIM33 binding in macrophages and effects of TRIM33 deletion on chromatin state during activation of primary macrophages.

city: Fontenay aux roses

first: federica

last: ferri

address: 18 route du panorama

country: France

institute: cea

summary: To get insight into TRIM33 functions, TRIM33 ChIP-seq was carried out in murine macrophage cell line (RAW) and in bone marrow-derived macrophages (BMDM). The results showed that, in addition to its role in hematopoietic differentiation, TRIM33 may modulate PU.1 transcriptional activity during macrophage development and/or activation.To characterize the role of TRIM33 in macrophages, we bred TRIM33fl/fl mice with Lyz-Cre mice where the Cre recombinase gene is under the regulatory sequences of the Lyz gene that is expressed only in mature myeloid cells. Bone marrow cells from  LyzCre/Trim33+/+ mice and LyzCre/Trim33flox/flox mice were differentiated in macrophages and treated during 0h, 4h, 12h and 24h with LPS. Using ChIP-seq, we provide a link between TRIM33 binding and H3K4me3 spreading on inflammatory genes in macrophages.

overall_design: Chromatin immunoprecipitations of TRIM33 and H3K4Me3 followed by multiparallel sequencing performed in murine bone marrow-derived macrophages (BMDM).

first: F

last: Ferri

first: P

last: Romeo


title: 3D Chromosome Regulatory Landscape of Human Pluripotent Cells [ChIAPET]

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The control of cell identity is orchestrated by transcriptional and chromatin regulators in the context of specific chromosome structures. With the recent isolation of human naive embryonic stem cells (ESCs) representative of the ground state of pluripotency, it is possible to deduce this regulatory landscape in one of the earliest stages of human development. Here we generate cohesin ChIA-PET chromatin interaction data in naive and primed human ESCs and use it to reconstruct and compare the 3D regulatory landscapes of these two stages of early human development. The results reveal shared and stage-specific regulatory landscapes of topological domains and their subdomains, which consist of CTCF-CTCF/cohesin loops and enhancer-promoter/cohesin loops. The enhancer-promoter loop data reveal that genes with key roles in pluripotency are nearly always regulated by one or more super-enhancers, and show that these genes tend to occur in insulated neighborhoods. Our results reveal the key features of the 3D regulatory landscape of early human cells that form the foundation for embryonic development.

overall_design: ChIA_PET data against SMC1 from naive and primed human embroynic stem cells.

first: Xiong

last: Ji


title: ETS Family Transcriptional Regulators Drive Chromatin Dynamics and Malignancy in Squamous Cell Carcinomas (ChIP-Seq II)

city: New York

address: 1230 York Avenue

overall_design: Control and ETS2(T72D) super-activated epidermal basal stem cells were FACS-purified for ChIP-sequencing.


title: Transcriptomes of Aspergillus fumigatus Z5 induced by different carbon sources

city: Nanjing

first: youzhi

last: miao

state: JiangSu

address: No.1 WeiGang, XuanWu, NanJing, JiangSu province, China

department: College of Resources & Environmental Science

institute: Nanjing Agricultural University, Nanjing, China

summary: Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural material on earth. It consists of complex carbohydrates and aromatic polymers found in plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was isolated from compost heaps and showed highly efficient plant biomass-degradation capability.Genome analysis revealed an impressive array of genes encoding cellulases, hemicellulases, and pectinases involved in lignocellulosic biomass degradation. We sequenced the transcriptomes of Aspergillus fumigatus Z5 induced by sucrose, xylan, cellulose and rice straw, respectively. There were 444, 1711 and 1386 significantly differently (q-value ≤ 0.0001 and |log2 of the ratio of the RPM values| ≥ 2) expressed genes in xylan, cellulose and rice straw,respectively, relative to sucrose control.

overall_design: After incubation at 45 ℃, 145rpm for 20 hours with sucrose as the carbon source, mycelia were induced for 16 hours using xylan, cellulose and rice straw, respectively. Transcriptome induced by sucrose was used as the control when comparing the differences between other three transcriptomes (induced by xylan, cellulose and rice straw, respectively).

first: Youzhi

last: Miao

first: Ruifu

last: Zhang


title: 3D Chromosome Regulatory Landscape of Human Pluripotent Cells [ChIP-Seq]

overall_design: ChIP-seq data from naive and primed human embroynic stem cells.


title: Genome-wide profilings of IFN-stimulated murine splenic B cells by ATAC-Seq.

status: Public on Nov 21 2015

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: We report the IFN-induced dynamics in murine splenic B cells. Male C57BL/6 mice were injected subcutaneously with 10,000U IFNa and spleens were removed at 90min. B cells were negatively isolated using magnetic beads and profiled for the chromatin configuration by ATAC-seq.

overall_design: Profilings of chromatin configuration by ATAC-seq (0 and 90min, biological duplicate for each).

first: Sara

last: Mostafavi

first: Hideyuki

last: Yoshida

first: Devapregasan

last: Moodley

first: Liang

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: ETS Family Transcriptional Regulators Drive Chromatin Dynamics and Malignancy in Squamous Cell Carcinomas (ChIP-Seq I)

first: Hanseul

last: Yang

overall_design: Mouse skin squamouse cell carcinoma (SCC) tumor-initiating stem cells (SCs) were FACS-purified for ChIP-sequencing.

first: Elaine

last: Fuchs


title: mRNA and miRNA expression in primary human muscle cells treated with 1,25(OH)2D3 or vehicle

city: Rochester

first: Xuewei

last: Wang

address: 200 1st street

institute: Mayo Clinic

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

overall_design: Refer to individual Series


title: Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging

city: Manchester

first: Shona

middle: Hiedi

last: Wood

address: Oxford road

institute: University of Manchester

summary: Using RNA-seq, 39 cerebral cortex RNA samples were sequenced. The study design was as follows:  Ad libitum fed rats at 6 months (n=3, 6 individuals pooled), 12 months (n=3, 6 individuals pooled) and 28 months (n=3, 6 individuals pooled). Calorie restricted rats at  6 months (n=3, 6 individuals pooled), 12 months (n=3, 6 individuals pooled) and 28 months (n=3, 6 individuals pooled). Rats fed alpha lipoic acid as a supplement to ad libitum at 12 months (n=3, 6 individuals pooled) and 28 months (n=3, 6 individuals pooled). Diet switching groups, where diet was changes at 12 months; 28 month ad libitum switched to calorie restriction (n=3, 6 individuals pooled), 28 month calorie restriction switched to ad libitum (n=3, 6 individuals pooled), 28 month ad libitum plus lipoic acid switched to calorie restriction (n=3, 6 individuals pooled), 28 month calorie restriction switched to ad libitum plus lipoic acid (n=3, 6 individuals pooled).

overall_design: Transcriptional profiling of the ageing cerebral cortex at 6, 12 and 28 months and the effect of diet on age and longevity, using carlorie restriction and alpha lipoic acid supplementation

first: Sipko

last: Van Dam

first: Thomas

last: Craig

first: Michael

last: Keane

first: Robi

last: Tacutu

first: Amy

last: O’Toole

first: Brian

middle: J

last: Merry

first: João

last: de Magalhães


title: Genome-wide profilings of IFN-stimulated murine splenic B cells by ChIP-seq.

first: CBDM

last: Lab

summary: We report the IFN-induced dynamics in murine splenic B cells. Male C57BL/6 mice were injected subcutaneously with 10,000U IFNa and spleens were removed at designated time. B cells were negatively isolated using magnetic beads and profiled for the binding of PolII and Stat2 by ChIP-seq analysis.

overall_design: Profilings by PolII ChIP-seq over the time course (0, 0.5, 1, 2, 4, 8, 24 and 48hrs, single replicate for each), Stat2 ChIP-seq (0 and 90min, biological duplicate for each).

first: Sara


title: Ribosomal profiling of CRISPR edited and parental CHL-1 cell line

city: Stanford

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

summary: Ribosomal stress was evaluated in melanoma cell line CHL-1 after CRISPR editing genomic locus containing SNORD50A/B

overall_design: We have used CRISPR genome editing tool to KD snoRNAs SNORD50A/B from CHL-1 genome and assessed ribosomal binding genome-wide using ribosome profiling

first: Zurab

last: Siprashvili

first: Ross

last: Flockhart

first: Dan

last: Webster

first: Paul

last: Khavari


title: Transcriptomes of 35000HP, ΔcpxA, ΔcpxR mutant strains of Haemophilus ducreyi in mid-log, transition, and stationary phase

city: Indianapolis

first: Dharanesh

last: Gangaiah

state: Indiana

address: 635 Barnhill drive, MS 420

department: Department of Microbiology and Immunology

institute: Indiana University School of Medicine

summary: To better understand the role of H. ducreyi CpxRA in controlling virulence determinants, here we defined genes potentially regulated by CpxRA by using RNA-Seq. Activation of CpxR by deletion of cpxA repressed nearly 70% of its targets, including seven established virulence determinants. Inactivation of CpxR by deletion of cpxR differentially regulated few genes and increased the expression of one virulence determinant. We identified a CpxR binding motif that was enriched in downregulated but not upregulated targets. These data reinforce the hypothesis that CpxA phosphatase activity plays a critical role in controlling H. ducreyi virulence in vivo. Characterization of the downregulated genes may offer new insights into pathogenesis.

overall_design: RNA of Haemophilus ducreyi wildtype, cpxA and cpxR mutants were collected at mid-log, transition, and stationary phases of growth, in quadruplicate.

first: Stanley

last: Spinola


title: Tcf7 biology in mouse beta-cells

city: Worcester

first: Yu

last: Liu

address: AS5-1018, 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School

summary: We set out to identify differences in the transcriptome influenced by knockout of the transcription factor T-cell factor 7 (Tcf7) in mouse islets. Furthermore, we wanted to determine if metabolic stress (age,diet) influences these changes. Therefore, we compared the islet transcriptome from WT and Tcf7-/- mice both at a young age (8 weeks old) fed a low fat (10%) diet, versus WT and Tcf7-/- mice at an old age (20 weeks old) on a high-fat (45%) diet.

overall_design: Tcf7-/- mice and littermate wildtype mice were compared. Mice were placed on either a low-fat (10%) or high-fat (45%) diet at weeks of age. For the low fat group, islets from 8 week old mice were isolated and total RNA was extracted with Trizol. For the high fat group, islets from 20 week old mice were isolated and total RNA was extracted with Trizol.

first: Jonathan

last: Campbell

first: Jeffrey

middle: L

last: Wrana

first: Daniel

last: Druck


title: Knockdown of Polyhomeotic in Drosophila Kc cells

status: Public on Nov 20 2015

first: Xiaowei

last: Zhuang

address: 12 Oxford St

department: Chemistry and Chemical Biology

institute: Harvard University

summary: In this experiment, we used RNAi targeting both copies of the gene polyhomeotic (ph-p and ph-d) to knockdown expression of this factor in Drosophila Kc167 cells.  We observed substantial changes to the structure of genomic loci bound by Polycomb-group proteins as assayed by single-molecule based super-resolution imaging with STORM.  We also observed a substantial de-repression of many genes which reside in Polycomb-bound domains, as assayed with RNA-seq.

overall_design: mRNA profiles from Drosophila Kc167 cells with and without knockdown the genes ph-p and ph-d were examined in duplicate.

first: Alistair

last: Boettiger


title: Genome wide binding of ATF4 and CEBPG bZIP transcription factors in MEFs under amino acid deprived (AAD) conditions

status: Public on Nov 19 2015

city: Frederick

first: Peter

last: Johnson

address: 1050 Boyles Street

department: Mouse Cancer Genetics Program

institute: NCI-Frederick

summary:
The integrated stress response (ISR) controls cellular adaptations to nutrient deprivation, redox imbalances and ER stress. ISR genes are upregulated in stressed cells, primarily by the bZIP transcription factor ATF4 through its recruitment to cis-regulatory C/EBP:ATF response elements (CAREs) together with a dimeric partner of uncertain identity. Here we show that C/EBPγ:ATF4 heterodimers, but not C/EBPβ:ATF4 dimers, are the predominant CARE binding species in stressed cells. C/EBPγ and ATF4 associate with genomic CAREs in a mutually-dependent manner and co-regulate many ISR genes. By contrast, the C/EBP family members C/EBPβ and CHOP were largely dispensable for induction of stress genes.
Cebpg−/− MEFs proliferate poorly and exhibit oxidative stress due to reduced glutathione levels and impaired expression of several glutathione biosynthesis pathway genes. Cebpg−/− mice (C57BL/6 background) display reduced body size and microphthalmia, similar to ATF4-null animals. In addition, C/EBPγ-deficient newborns die from atelectasis and respiratory failure which can be mitigated by in utero exposure to the anti-oxidant, N-acetyl-cysteine. Cebpg−/− mice on a mixed strain background show improved viability but, upon aging, develop significantly fewer malignant solid tumors compared to WT animals. Our findings identify C/EBPγ as a novel anti-oxidant regulator and an obligatory ATF4 partner that controls redox homeostasis in normal and cancerous cells.

overall_design: Evaluation of genomic binding of 2 bZIP transcription factors under amino acid deprivation conditions in mouse embryonic fibroblasts

first: Christopher

last: Huggins


title: Identification of global regulators of T-helper cell lineage specification (RNA-Seq)

city: Turku

first: Kartiek

last: Kanduri

address: Tykistokatu 6

country: Finland

institute: Turku Centre for Biotechnology

summary: The aim of the dataset was to identify genome-wide regulators of gene expression in early differentiation of human cord blood derived CD4+ T cells cultured under Th1 (Act+IL12) and Th2 (Act+IL4) polarizing conditions.

overall_design: Total RNA from naive CD4+ T cells was compared to total RNA from cells cultured in the following three conditions: activating (antiCD3+antiCD28)+antiIL4+antiIFNG; activating (antiCD3+antiCD28)+IL12+antiIL4; activating (antiCD3+antiCD28) +IL4+antiIFNG. Samples from 3 biological replicates were analysed.

first: Subhash

last: Tripathi

first: Antti

last: Larjo

first: Henrik

last: Mannerström

first: Ubaid

last: Ullah

first: Riikka

last: Lund

first: David

last: Hawkins

first: Bing

last: Ren

first: Harri

last: Lähdesmäki

first: Riitta

last: Lahesmaa


title: Identification of global regulators of T-helper cell lineage specification


title: ETS Family Transcriptional Regulators Drive Chromatin Dynamics and Malignancy in Squamous Cell Carcinomas

first: Hanseul

last: Yang


title: ATF4 governs functional expansion of hematopoietic stem cells partially via Angptl3 in the fetal liver microenvironment

city: Beijing

first: dan

last: liu

address: NO.1 Beichen West Road, Chaoyang District, Beijing

institute: Beijing Institute of Genomics, Chinese Academy of Sciences


title: The conformation of yeast chromosome III is mating type-dependent and controlled by the recombination enhancer

first: Bryan

last: Lajoie

address: 368 Plantation St.

institute: UMMS

summary: Yeast chromosome III contains the mating type loci that provide a paradigm for long-range interactions between distant loci.  Yeast switch mating type by gene conversion between the MAT locus and either of two silent loci (HML or HMR) on opposite ends of the chromosome.  This long-range process is mating type-specific so that MATa cells choose HML as template, while MATα cells use HMR.  The Recombination Enhancer (RE), located on the left arm regulates this process.  One long-standing hypothesis is that switching is guided by mating type-specific, and possibly RE-dependent three-dimensional folding of chromosome III.  Here we used Hi-C, 5C, and live cell imaging to characterize the conformation of chromosome III in both mating types in non-switching strains.  We discovered a mating type-specific difference in the folding of the left arm: in MATa cells the left arm is located closely to the centromere-proximal portion of the chromosome as well as to MAT, whereas it is more extended away in MATα cells.  Deletion analysis showed that a 1 kb subregion within the RE, which is not necessary during switching, abolished mating type-dependent chromosome folding.  In this mutant the conformation of chromosome III is the same in both mating types, but distinct from the wild type MATa or MATα conformations, indicating that the RE induces conformational changes in both mating types.  The RE is therefore a composite element with one subregion essential for selecting the appropriate donor during switching, and a separate region involved in modulating chromosome conformation prior to switching.

overall_design: This submission contain 2 biological replicates of Hi-C experiments done in MATa and MATalpha cells in Saccharamycese cerevisiae.  It also contains 3 biological replicates of 13 5C experiments in various mutants in MATa and MATalpha cells.

first: Jon-Matthew

last: Belton

first: Sylvain

last: Audibert

last: Cantaloube

first: Imen

last: Lassadi

first: Isabelle

last: Goiffon

first: Davide

last: Baù

first: Marc

last: Marti-Renom

first: Kerstin

last: Bystricky

first: Job

last: Dekker


title: Spontaneous pancreatitis caused by tissue-specific gene ablation of Hhex in mice

city: Philadelphia

first: Mark

middle: Jakob

last: Ferreira

state: PA

address: 3400 Civic Center Blvd Bldg 421

institute: University of Pennsylvania School of Medicine

summary:
Background & Aims: Perturbations in pancreatic ductal bicarbonate secretion often result in chronic pancreatitis. Although the physiological mechanism of ductal secretion is known, its transcriptional control is not well characterized. Here, we investigate the role of the transcription factor Hematopoietically-expressed homeobox protein (Hhex) in pancreatic secretion and pancreatitis.
Methods: We derived mice with pancreas-specific, Cre-mediated Hhex gene ablation to determine the requirement of Hhex in the pancreatic duct in early life and in adult stages. Histological and immunostaining analyses were used to detect the presence of pathology. Pancreatic primary ductal cells (PDCs) were isolated to discover differentially expressed transcripts upon acute Hhex ablation.
Results: Hhex protein was detected throughout the embryonic and adult ductal trees. Ablation of Hhex in pancreatic progenitors resulted in postnatal ductal ectasia associated with acinar-to-ductal metaplasia, a progressive phenotype that ultimately resulted in chronic pancreatitis. Hhex ablation in adult mice, however, did not cause any detectable pathology. Ductal ectasia did not result from perturbations in primary cilia, but was consistent with the effects of primary ductal hypertension. RNA-seq analysis of Hhex-ablated PDCs indicated the G-protein coupled receptor Natriuretic peptide receptor 3, implicated in paracrine signaling, was upregulated 4.70-fold.
Conclusions: Although Hhex is dispensable for adult pancreatic function, ablation of Hhex in pancreatic progenitors results in profound pancreatitis that is consistent with primary ductal hypertension. Our data highlight the critical role of paracrine signaling in maintaining ductal homeostasis, especially in early life, and support ductal hypersecretion as a novel etiology of pediatric chronic pancreatitis.

overall_design: Pancreatic primary ductal cells (PDCs) were isolated from uninduced adult HhexL/L;Sox9CreERT2 (n=2) and littermate control HhexL/L (n=2) mice. PDCs were treated with 500nM 4-hydroxytamoxifen in vitro for 4 days, and then RNA was collected for transcriptome analysis.

first: Klaus

last: Kaestner


title: Characterization of macrophage - cancer cell crosstalk in estrogen receptor positive and triple-negative breast cancer

first: Maija

last: Hollmén

address: Tykistökatu 6A 4th floor

institute: University of Turku

summary: We performed whole transcriptome sequencing of human monocytes that were co-cultured with estrogen receptor positive (ER+) or triple-negative (TNBC) breast cancer cell lines and studied the biological responses related to the differential gene activation in both cell types to understand how different cancer cells educate host cells to support tumor growth

overall_design: To characterize the differences in macrophage activation under the influence of either ER+ or TNBC breast cancer cells, we cultured freshly isolated human peripheral monocytes with two breast cancer cell lines (T47D, ER+ and MDA-MB-231, TNBC) in an in vitro transwell co-culture assay. The transwell setting allowed us to investigate the effect of soluble mediators on macrophage activation since direct cell contact of these cells was inhibited by a (PET) membrane (pore size 0.4 μm).

first: Michael

last: Detmar


title: ATF4 governs functional expansion of hematopoietic stem cells partially via Angptl3 in the fetal liver microenvironment (RNA-Seq)

summary: In this study, we demonstrated that deletion of the activating transcription factor 4 (ATF4) resulted in severely impaired HSC expansion in the fetal liver at E12.5 and E15.5. In contrast, generation of the first HSC population in the aorta-gonad-mesonephros region at E11.5 was not significantly affected. Furthermore, the HSC-supporting ability of both endothelial and stromal cells in fetal liver was significantly compromised in the absence of ATF4. Gene profiling using RNA-seq revealed down-regulated expression of a panel of cytokines in ATF4-/- stromal cells, including angiopoietin-like protein 3 (Angptl3) and vascular endothelial growth factor-A (VEGFA).

overall_design: To investigate the molecular pathways of ATF4 in the stromal cells and LSK cells in the fetal liver.

first: Tao

last: Cheng

first: Bing

last: Liu

first: Yunze

last: Zhao

first: Jie

last: Zhou

first: Dan

first: Fang

last: Dong

first: Hui

first: Weili

last: Wang


title: EWS and FUS Bind a Subset of Transcribed Genes Encoding Proteins Enriched in RNA Regulatory Functions

city: aarhus

first: Yonglun

last: Luo

address: Wilhelm Meyers Allé 4

institute: Aarhus University

summary: Background  FUS (TLS) and EWS (EWSR1) belong to the FET-protein family of RNA and DNA binding proteins. FUS and EWS are structurally and functionally related and participate in transcriptional regulation and RNA splicing. FUS and EWS are identified in translocation generated cancer fusion proteins and involved in the human neurological diseases amyotrophic lateral sclerosis and fronto-temporal lobar degeneration.   Results  To determine the gene regulatory functions of FUS and EWS at the level of chromatin, we have performed Chromatin Immunoprecipitation followed by Next Generation Sequencing (ChIP-Seq). Our results show that FUS and EWS bind to a subset of actively transcribed genes, that binding often is in the 3’ end of genes, and that binding overlaps with RNA polymerase II. Functional examinations of selected target genes verified that FUS and EWS can regulation expression. Gene Ontology (GO) analyses showed that FUS and EWS target genes preferentially encode proteins involved in regulatory processes at the RNA level.  Conclusions  The presented results yield new insights into gene interactions of EWS and FUS and have identified a set of FUS and EWS target genes involved in pathways at the RNA regulatory level with potential to mediate normal and disease-associated functions of the FUS and EWS proteins.

overall_design: To identify the DNA binding profile of FUS, EWS and TAF15 by ChIPseq. Controls: use antibody against H3K9 and input

first: Jenny

last: Blechingberg

first: Ana

last: Fernandes

first: Shengting

last: Li

first: Tue

last: Fryland

first: Anders

middle: D

last: Børglum

first: Lars

last: Bolund

last: Nielsen


title: RpoE-dependent transcriptomes of Haemophilus ducreyi

first: Dharanesh

last: Gangaiah

summary: To potentially understand how H. ducreyi responds to membrane stress, here we defined RpoE-dependent genes using RNA-Seq.  We identified 180 RpoE-dependent genes, of which 98% were upregulated; a major set of these genes encodes homologues of envelope maintenance and repair factors. We also identified and validated a putative RpoE promoter consensus sequence, which was enriched in the majority of RpoE-dependent targets. Comparison of RpoE-dependent genes to those controlled by CpxR showed that each transcription factor regulated a distinct set of genes. Given that RpoE activated a large number of genes encoding envelope maintenance and repair factors and CpxRA represses genes encoding envelope-localized proteins, these data suggest that RpoE and CpxRA appear to play distinct yet complementary roles in regulating envelope homeostasis in H. ducreyi.

overall_design: RNA of Haemophilus ducreyi 35000HP wild-type strain containing a rpoE inducible plasmid and wild-type strain containing a control plasmid were collected at 0 minutes, 5 minutes, and 10 minutes after induction in quadruplicate.

first: Stanley

middle: M

last: Spinola


title: Genome-wide analysis of histone methylations, m5CpG, and SETDB1 binding in ESCs, MSCs, preadipocytes, and adipocytes.

city: Akita

first: Yoshihiro

last: Matsumura

state: Akita

address: Hondo 1-1-1

department: Biochemistry and Metabolic Science

country: Japan

institute: Akita University Graduate School of Medicine

summary: Bivalent H3K4me3 and H3K27me3 chromatin domains in embryonic stem cells keep active developmental regulatory genes expressed at very low levels and poised for activation. Here, we show an alternative and previously unknown bivalent modified histone signature in lineage-committed mesenchymal stem cells and preadipocytes that pairs H3K4me3 with H3K9me3 to maintain adipogenic master regulatory genes (Cebpa and Pparg) expressed at low levels yet poised for activation when differentiation is required. We show lineage-specific gene-body DNA methylation recruits H3K9 methyltransferase SETDB1 which methylates H3K9 immediately downstream of transcription start sites marked with H3K4me3 to establish the bivalent domain. At the Cebpa locus, this prevents transcription factor C/EBPβ binding, histone acetylation, and further H3K4me3 deposition and is associated with pausing of RNA polymerase II, which limits Cebpa gene expression and adipogenesis.

overall_design: H3K4me3, H3K27me3, H3K9me3, SETDB1, MBD1, and Pol II ChIP-seq. m5CpG pull-down using recombinant MBD domain of MBD1 followed by next-generation sequencing.


title: Regulation of mRNA Levels by Suicidal Introns that Induce Nuclear Decay

city: Edinburgh

first: Sander

last: Granneman

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

department: Centre for Synthetic and Systems Biology

institute: University of Edinburgh

summary: In eukaryotic cells, inefficient splicing is surprisingly common and leads to degradation of transcripts with retained introns. How pre-mRNAs are committed to nuclear decay is unknown. Here we uncover a mechanism by which intronic transcripts are targeted for nuclear degradation in fission yeast. Surprisingly, sequence elements within “suicidal” introns co-transcriptionally recruit the exosome adaptor Mmi1 not only to degrade unspliced precursor, but also to downregulate levels of the resulting mRNA. Under conditions permissive for fast splicing, Mmi1 is no longer recruited and negative expression regulation is relieved. This mechanism negatively regulates levels of the RNA-helicase DDX5/Dbp2 to ensure cell survival in response to stress. We propose that suicidal introns are maintained because they facilitate regulation of gene expression. We identify multiple novel Mmi1 targets including mRNAs, non-coding RNAs, and sn/snoRNAs. We suggest a general role in RNA regulation for Mmi1 beyond degradation of meiotic transcripts.

overall_design: Two biological replicates of CRAC experiments (Control and Mmi1-HTP). Six RNAseq datasets in total: three biological replicates of wt and delta Mmi1 strain.

first: Lidia

last: Vasilljeva


title: Transcript abundance in A-T-derived iPSC: Comparing isogenic cells to unrelated individual

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Induced pluripotent stem cells (iPSC) were prepared from multiple subjects with Ataxia-telangiectasia (A-T).  iPSC were prepared from activated T-cells using commercial Sendai virus to deliver reprogramming factors.  ATM protein-expressing and non-expressing cultures would found in multiple sub-lines (sub-lines are generated from distinct founder colonies of cells) from a single subject (Q3).  Genetic analysis determined that all sub-lines originated from the same subject and were likely the product of spontaneous reversion by gene correction.  To compare gene expression profiles, three iPSC samples were assayed: (1) A reverted ATM+/- subline from subject Q3, (2) An ATM-/- subline from subject Q3, and (3) An iPSC line from an unrelated ATM-/- subject, Q1.  Analysis reveals that the majority of significantly-different genes between the unrelated ATM-/- line (Q1SA) and the reverted ATM+/- line (Q3SC) was due to genetic variation between individuals.  A more focused set of contrasting genes could be identified between the isogenic Q3-derived lines (Q3SA, ATM-/-, vs. Q3SC, ATM+/-).  The 206 transcripts that are significantly different point to a differential regulation of p53-associated pathways.

overall_design: Total cellular RNA was prepared from each iPSC culture.  Different passage numbers or sister cultures were used as replicates (n=2).


title: An aspartyl protease defines a novel pathway for export of Toxoplasma proteins into the host cell

city: Parkville

first: Alexandra

last: Garnham

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute of Medical Research

summary: Toxoplasma gondii is an obligate intracellular Apicomplexan parasite capable of invading and surviving within nucleated cells in most warm-blooded animals. This remarkable task is achieved through the delivery of effector proteins from the parasite into the parasitophorous vacuole and host cell cytosol that rewire host cellular pathways, facilitating parasite evasion of the immune system. Here, we have identified a novel export pathway in Toxoplasma that involves cleavage of effector proteins by the Golgi-resident aspartyl protease 5 (ASP5) prior to translocation into the host cell. We demonstrate that ASP5 cleaves a highly constrained amino acid motif that has some similarity to the PEXEL motif of Plasmodium parasites. We show that ASP5 can mature effectors at both the N- and C-terminal ends of proteins and is also required for the trafficking of proteins without this motif. Furthermore, we show that ASP5 controls establishment of the nanotubular network and is required for the efficient recruitment of host mitochondria to the parasitophorous vacuole membrane. Global assessment of host gene expression following infection reveals that ASP5-dependent pathways influence thousands of the transcriptional changes that Toxoplasma imparts on its host cell. This work characterizes the first identified machinery required for export of Toxoplasma effectors into the infected host cell.

overall_design: Three groups of human foreskin fibroblasts are compared. Each group has 3 replicates giving a total of 9 samples. The first group of samples are infected with wild type (GRA16HA) Toxoplasma gondii, the second group with Asp5 knock-out Toxoplasma gondii, and the final group remain uninfected. All fibroblasts are generated from one donor sample.

first: Michael

last: Coffey

first: Christopher

last: Tonkin


title: Silencio/CG9754 connects the Piwi-piRNA complex to the cellular heterochromatin machinery

city: Vienna

first: Grzegorz

last: Sienski

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

summary: The  repression  of  transposable  elements  in  eukaryotes  often involves  their transcriptional silencing via targeted chromatin modifications. In animal gonads, nuclear Argonaute proteins of the PIWI-clade complexed with small guide RNAs (piRNAs) serve as sequence specificity determinants in this process. How binding of nuclear  PIWI-piRNA  complexes  to  nascent  transcripts  orchestrates heterochromatin formation and transcriptional silencing is unknown. Here, we characterize CG9754/Silencio as an essential piRNA pathway factor that is required for  Piwi-mediated  transcriptional  silencing  in Drosophila.  Ectopic  targeting  of Silencio to RNA or DNA is sufficient to elicit silencing independent of Piwi and known  piRNA pathway  factors.   Instead,  Silencio  requires  the  H3K9  methyl-transferase  Eggless/SetDB1  for  its  silencing  ability.  In  agreement  with  this, SetDB1 but  not  Su(var)3-9 is  required  for  Piwi-mediated  transcriptional silencing genome-wide. Due to its interaction with the target-engaged Piwi-piRNA complex we suggest that Silencio acts as linker between the sequence specificity factor Piwi and the cellular heterochromatin machinery.

overall_design: Impact of depletion of CG9754/Silencio, HP1a, SetDB1, Su(var)3-9, G9a on transcription and the H3K9m3 patterns in ovarian somatic cells (OSC)

first: Julius

last: Brennecke


title: Transcriptional elongation requires DNA break-induced signaling

city: Daegu

first: Heeyoun

last: Bunch

address: 80 Daehak-ro, Kyungpook National University, Agriculture and Life Sciences Building #1, Room 207

department: Applied Biosciences

country: South Korea

institute: Kyungpook National University

summary: We have previously shown that RNA polymerase II (Pol II) pause release and transcriptional elongation involve phosphorylation of the factor TRIM28 by the DNA damage response (DDR) kinases ATM and DNA-PK. Here, we report a significant role for DNA breaks and DDR signaling in the mechanisms of transcriptional elongation in stimulus-inducible genes in humans. Our data show the enrichment of TRIM28 and γH2AX on serum-induced genes and the important function of DNA-PK for Pol II pause release and transcriptional activation-coupled DDR signaling on these genes. γH2AX accumulation decreases when P-TEFb is inhibited, confirming that DDR signaling results from transcriptional elongation. In addition, transcriptional elongation-coupled DDR signaling involves topoisomerase II because inhibiting this enzyme interferes with Pol II pause release and γH2AX accumulation. Our findings propose that DDR signaling is required for effective Pol II pause release and transcriptional elongation through a novel mechanism involving TRIM28, DNA-PK, and topoisomerase II

overall_design: 44 samples in total.  IP targets were gammaH2ax, s2-pol-II, pol-II, pTRIM28, and DNA-pk.  Experimental conditions included DMSO treatment (control), pTEFb, topoII-i, dnapk-i.  Matched non-specific IP samples used for control in peak calling.

first: Brian

last: Lawney

first: Yu-Fen

last: Lin

first: Aroumougame

last: Asaithamby

first: Ayesha

last: Murshid

first: Yaoyu

middle: E

last: Wang

first: Benjamin

last: Chen

first: Stuart

middle: K

last: Calderwood


title: Short and Long RNA sequencing of human mature erythrocytes

city: Durham

first: Jen-Tsan

middle: Ashley

last: Chi

state: North Carolina

address: 101 Science Drive

department: MGM

institute: Duke University

summary: We employed high-throughput sequencing of both short (~18-24nt) and long (>200nt) RNAs in human erythrocytes. We obtained blood from five healthy individuals for the short (small) RNA-seq library preparations and blood from three individuals for the long RNA-seq library preparations. We identified an abundant, diverse population of RNAs. Both polyadenylated and nonpolyadenlated long RNAs were identified. Additionally, known and novel microRNAs were identified in the short RNA dataset using the probabalistic modeling algorithm miRDeep. These RNAs lend insight into erythrocyte biology and provide utility as potential biomarkers. To determine both shared and unique aspects of the erythrocyte long RNA transcriptome, we compared this transcriptome with that of the PBMC and CD34+ erythroid progenitor transcriptomes.

overall_design: Sequencing of RNAs from mature erythrocytes of healthy individuals

first: Jennifer

middle: F

last: Doss

first: David

last: Corcoran

first: Dereje

last: Jima


title: Circadian and light-driven regulation of rod dark adaptation

city: St. Louis

first: Joseph

middle: C

last: Corbo

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine

summary: The sensation of light is initiated in photoreceptor cells by the photoisomerization of a chromophore molecule from 11-cis to all-trans retinal. Continuous visual perception requires recycling of the spent chromophore back to the 11-cis form through the visual cycle, a series of reactions in the retinal pigmented epithelium (RPE). Light-driven chromophore consumption by photoreceptors is greater in daytime compared to night time, suggesting that correspondingly higher activity of the visual cycle may be required. On the other hand, as rod photoreceptors are saturated in bright light, the continuous turnover of their chromophore through the visual cycle during daytime would unnecessarily utilize precious energy and produce toxic byproducts. Here, we sought to determine whether the recycling of chromophore and the dark adaptation of rods is regulated by the circadian clock and light exposure. We demonstrate that in melatonin-proficient C3H/f+/+ mice, rod dark adaptation is slower during the day or after light exposure. This surprising daytime downregulation of the RPE visual cycle was further demonstrated by gene analysis, which revealed light-driven reduction in the expression of Rpe65, which encodes a key enzyme of the RPE visual cycle. In contrast, rods in melatonin-deficient strains (C57BL6/J and 129/Sv) were not affected by this daily visual cycle modulation. Our results demonstrate that the circadian clock and light exposure regulate the recycling of chromophore in the RPE visual cycle. This daily modulation of rod dark adaptation is mediated by melatonin and could potentially protect the retina from light-induced damage during the day.

overall_design: mRNA-seq of murine eyes (lens removed) in objective day (OD) vs. subjective day (SD) conditions (2 biological replicates per condition). Each biological replicate consisted of 4 eyes (from 1 female and 1 male).

first: Yunlu

last: Xue

first: Susan

middle: Q

last: Shen

first: Vladimir

last: Kefalov


title: Transcriptomic analysis of the Novel Middle East Respiratory Syndrome Coronavirus (African green monkey, Vero E6 cells)

city: Baltimore

middle: A

last: Rasko

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

summary: We will use the EMC/2012 strain of the novel beta Coronavirus called Middle East Respiratory Syndrome Coronavirus (MERS-CoV). It was initially passaged on Vero E6 cells in Saudi Arabia before being sequenced at the Erasmus Medical College in Rotterdam, Netherlands by Dr Ron Fouchier. We propose to perform a time course of infection of hCoV-EMC on MRC5 cells (Human Lung origin) and Vero cells (African Green Monkey Kidney cells). Both cell lines readily grow and replicate the virus. Importantly these cell lines show signs of Cytopathic effect (CPE), such as cell rounding and release from the petri dish that coincide with time points high virus replication demonstrating the effects of virus replication on the cells. Transcriptomic analysis will be performed after infection with MERS-CoV and SARS-CoV (Urbani strain) to compare the host gene induction that occurs during infection.

overall_design: MRC5 and Vero E6 cells will be infected at an MOI of 0.1 and 3 and RNA harvested from cells at 24 and 48 post infection. RNA will be processed for library creation and sequenced on an Illumina Hiseq. Sequencing reads will be analyzed and compared across the time course and between each virus to identify common response pathways induced during infection as well as unique pathways specific to each virus.

first: Matthew

last: Frieman

first: Chris

last: Coleman

first: Sean

last: Daugherty

first: Kent

last: Shefchek

first: Naomi

last: Sengamalay

first: Luke

last: Tallon

first: Lisa

last: Sadzewicz

first: Claire

last: Fraser


title: Global changes in Mycoplasma gallisepticum Phase-Variable Lipoprotein Gene vlhA Expression during in vivo infection of the natural chicken host

status: Public on Nov 18 2015

city: Storrs

first: Edan

last: Tulman

state: CT

address: 61 North Eagleville Rd

institute: University of Connecticut

summary: The goals of this study were to assess the vlhA gene expression of M. gallisepticum at various time over the course of early infection in the chicken host, and in in-vitro culture before innoculation and after recovery

overall_design: Assessment of vlhA gene expression from broth grown input cultures (n=1), M. gallisepticum collected directly from the trachea over 7 days (n=5 per day), and M. gallisepticum recovered and passaged in-vitro 5 or 10 times (n=2 per passage)

first: Katherine

last: Pflaum

middle: R

first: Steven

last: Geary


title: TRIM33 switches off Ifnb1 transcription during the late phase of macrophage activation

city: Fontenay aux Roses

first: Germain

last: Rousselet

address: 18 route du Panorama

department: Cellular and Molecular Radiobiology (IRCM)

institute: CEA

summary: Despite its importance during viral or bacterial infections, transcriptional regulation of the interferon-b gene (Ifnb1) in activated macrophages is only partially understood. Here we report that TRIM33 deficiency results in high-sustained expression of Ifnb1 at late stages of toll-like receptor-mediated activation in macrophages but not in fibroblasts. In macrophages, TRIM33 is recruited by PU.1 to a conserved region, Ifnb1 Control Element (ICE), located 15kb upstream of the Ifnb1 transcription start site. ICE constitutively interacts with Ifnb1 through a TRIM33-independent chromatin loop. At late phases of lipopolysaccharide activation of macrophages, TRIM33 is bound to ICE, regulates Ifnb1 enhanceosome loading, controls Ifnb1 chromatin structure, and represses Ifnb1 gene transcription by preventing recruitment of CBP/p300. These results characterize a previously unknown mechanism of macrophage-specific regulation of Ifnb1 transcription whereby TRIM33 is critical for Ifnb1 gene transcription shut down.

overall_design: 3c-seq analysis of 4 samples (WT or Trim33-/- BMDM, 0 or 24 hrs LPS treatment) with 2 differents viewpoints (ICE and Ifnb1)

first: Paul-Henri

last: Romeo


title: Phenotypic heterogeneity affects Stenotrophomonas maltophilia K279a colony morphotypes and β-lactamase expression

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: Stenotrophomonas maltophilia K279a diverges into subpopulations with distinct but reversible phenotypes of small and big colonies when challenged with ampicillin. This observation is consistent with the formation of long cell chains during exponential growth phase and the occurrence of mainly coccoid– or rod-shaped cells in liquid media. Further, scanning electron micrographs of SMK279a revealed that cells formed gigantic outer membrane vesicles in response to β-lactam treatment. RNA-seq analysis of small vs. big colonies unveiled that cells regulate at least seven genes differentially among colony morphotypes. Among those were the blaL1 and blaL2 genes the most strongly regulated ones with an eleven- and six-fold increased transcription, respectively. Further studies with promoter fusions of blaL1 and blaL2 genes implied that expression of both genes is also subject to high levels of phenotypic heterogeneous expression on a single cell level. Additional RNA-seq analysis of this homogenously versus heterogeneously blaL2  expressing cells identified comE homologue as differentially expressed, in which by the expression of extra copies of comE in S. maltophilia K279a reduced the level of those cells that were in a blaL2-ON model to 1% or lower. Together with genome-wide sequence analysis of cells from the different colony morphotypes, the data presented here suggests that phenotypic heterogeneity in S. maltophilia K279a is a result of non-genetic variations within isogenic populations and also polymorphisms in this strain do not influence β-lactamase resistance phenotype.

overall_design: In total 10 samples were analyzed (5 different conditions with two independent samples), condition K279a small colonies: S. maltophilia K279a small colonies from LB agar plates grown on ampicillin for 48 h, condition K279a big colonies:  S. maltophilia K279a big colonies from LB agar plates grown on ampicillin for 48 h, condition K279a without ampicillin: S. maltophilia K279a colonies from LB agar plates grown without ampicillin for 48 h as a control, condition K279a liquid culture 27 h: S. maltophilia K279a grown in liquid medium for 27 h,  condition K279a liquid culture 32 h: S. maltophilia K279a grown in liquid medium for 32 h

first: Ebrahim

last: Mama

first: Dagmar

last: Krysciak

first: Ines

last: Krohn-Molt

first: Uwe

last: Mamat

first: Christel

last: Vollstedt

middle: U

first: Ulrich

last: Schaible

first: Thomas

last: Kohl

first: Stefan

last: Nieman

first: Wolfgang

last: Streit


title: Alternative polyadenylation in the anti-bacterial immune response of zebrafish

status: Public on Nov 17 2015

first: Guangrui

last: Huang

address: 11 Beisanhuandong Road, Chaoyang District

institute: Beijing University of Chinese Medicine

summary: We profiled the variation in tandem 3’ UTRs in pathogen-challenged zebrafish and identified hundreds of APA genes with approximately 10% being immune genes. The detected APA immune genes were enriched in Toll-like receptor signaling, apoptosis and JAK-STAT signaling pathways. A greater number of microRNA target sites and AU-rich elements were found in the extended 3’UTR regions than in the common 3’ UTR regions of these APA genes. Further analysis suggested that microRNA and AU-rich element mediated post-transcriptional regulation plays an important role in modulating the expression of APA genes.

overall_design: Poly(A) site profiles of zebrafish spleen in anti-bacterial immune response were generated by SAPAS stragedy using Illumina GAIIx. PRJNA298967

first: Anlong

last: Xu


title: Effects of transcription elongation rate and Xrn2 exonuclease activity on RNA polymerase  II termination suggest widespread kinetic competition

city: Aurora

first: David

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

summary: Transcription termination was analyzed by anti RNA pol II ChIP-seq in isogenic human HEK293 cell lines that inducibly express a-amanitin resistant mutants of the RNA polymerase II large subunit with slow and fast elongation rates and in lines that inducbily over-express WT or an active site mutant of the RNA exonuclease "torpedo" Xrn2.

overall_design: Transcription termination zones were mapped by anti-pol II ChIP-seq under conditions where transcription elongation rate was increased or decreased by point mutations in the large subunit of the enzyme. Termination was also assayed under conditions where Xrn2 exonuclease activity was inhibited by over-expression of an active site mutant (D235A).

first: Hyunmin

last: Kim


title: Effect of CHKA knockdown on C4-2 cell transcriptome

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: Analysis of C4-2 Prostate cancer cell line after 72 hours of knockdown. CHKA is overexpressed in a number of solid tumours, including prostate cancer. Results provide insight into the molecular mechanisms of CHKA in prostate carcinogenesis.

overall_design: This experiment was designed to understand the regulation of transcriptome by Choline kinase alpha (CHKA) which is an important enzyme in Kennedy pathway. In order to achieve this, the endogenous protein was knocked down using siRNA pool that targets the CHKA mRNA.

first: Mohammad

last: Asim

first: Charlie

last: Massie

first: Suraj

last: Menon


title: RNA-seq analysis of Arabidopsis thaliana wild-type roots and type-A arr3,4,5,6,7,8,9,15 mutant roots non-infected and infected with Heterodera schachtii nematodes

city: Chapel Hill

first: Carly

middle: Michelle

last: Shanks

state: NC

address: Genome Sciences Building, Room 4163

department: Biology

institute: UNC Chapel Hill

summary: Plant-parasitic cyst nematodes induce the formation of hypermetabolic feeding sites, termed syncytia, as their sole source of nutrients. The formation of the syncytium is orchestrated by the nematode in part by modulation of phytohormone responses, including cytokinin. In response to infection by the nematode H. schachtii, cytokinin signaling is transiently induced at the site of infection and in the developing syncytium. Arabidopsis lines with reduced cytokinin sensitivity show reduced susceptibility to nematode infection, indicating that cytokinin signaling is required for optimal nematode development. Furthermore, lines with increased cytokinin sensitivity also exhibit reduced nematode susceptibility. To ascertain why cytokinin hypersensitivity reduces nematode parasitism, we examined the transcriptomes in wild-type and a cytokinin-hypersensitive type-A arr Arabidopsis mutant in response to H. schachtii infection. Genes involved in the response to biotic stress and defense response were elevated in the type-A arr mutant in the absence of nematodes and were hyper-induced following H. schachtii infection, which suggests that the Arabidopsis type-A arr mutants impede nematode development because they are primed to respond to pathogen infection. These results suggest that cytokinin signaling is required for optimal H. schachtii parasitism of Arabidopsis, but that elevated cytokinin signaling triggers a heightened immune response to nematode infection.

overall_design: Wild-type Col-0 and type-A arr3,4,5,6,7,8,9,15 octuple mutant Arabidopsis thaliana roots were infected with Heterodera schachti nematodes and whole root tissue was collected at 4 days post infection (dpi) and 10 dpi, along with the corresponding control roots that were not infected with nematodes. We had tissue for collected for 4 experimental groups at 4 dpi and 10 dpi, wild-type non-infected, wild-type infeced, octuple mutant non-infected and octuple mutant infected. Tissue was collected for 3 biological replicates. Therefore we had 12 samples at 4dpi and 12 samples at 10 dpi making a total of 24 samples that we used for sequencing.


title: Human cortical transcriptome informs brain imaging

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: We carried out RNA-sequencing (RNA-seq) of adult human postmortem neocortical brain tissue, and then correlated those expression values with the fMRI signal in each brain region

overall_design: Ten cortical regions were included in the analysis: pre-motor cortex - PMV (BA6), dorsolateral prefrontal cortex – DLPFC (BA9), middle temporal gyrus – pMTG (BA21), superior temporal gyrus – pSTG (BA22), angular gyrus  - AG (BA39), supramarginal gyrus  - SMG (BA40), pars opercularis  - POP (BA44), pars triangularis  - PTr (BA45), middle frontal gyrus – MFG (BA46) and pars orbitalis  - POrB (BA47). For each brain region, three or more samples from left adult brain hemispheres were collected (ages range from 33 to 49) and only males were included to avoid the effect of sex

first: Guang

middle: Z

last: Wang

first: T

middle: G

last: Belgard

first: Deng

last: Mao

first: Leslie

last: Chen

first: Stefano

last: Berto

first: Todd

last: Preuss

first: Hanzhang

last: Lu

first: Daniel

middle: H

last: Geschwind


title: Gene expression profiling of zebrafish embryos at 1 hour post injection of PAMPs

city: Leiden

first: shuxin

last: yang

address: Einsteinweg 55

institute: Leiden University

summary: We use the zebrafish embryo model to study the transcriptome responses to flagellin and Pam3CSK4. Therefore, we injected these PAMPs into the caudal vein at the 27 hours post fertilization and took samples at 1 hour post injection.

overall_design: This deep sequence study was designed to determine the gene expression profile by  Pam3CSK4 and flagellin injection. RNA was isolated from embryos at 1 hour post injection. Wildtypes and tlr2- and tlr5a- morphants zebrafish embryos were micro-injected into the caudal vein with 1ng of Pam3CSK4, 0,1 ng flagellin , or water as a control at 27 hours post fertilization.  After injections embryos were transferred into fresh egg water and incubated at 28°C. At 1 hour post injection triplicates of 10 to 15  embryos per condition were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

first: S

last: Yang

first: R

last: Marín-Juez

first: HP

last: Spaink


title: Combined ultra-low input mRNA and whole-genome sequencing from human embryonic stem cells

city: Berlin

first: Florian

last: Mertes

address: Ihnestraße 63-73

institute: Max Planck Institute for Molecular Genetics

summary: Next Generation Sequencing has proven to be an exceptionally powerful tool in the field of genomics and transcriptomics. With recent development it is nowadays possible to analyze ultra-low input sample material down to single cells. Nevertheless investigating such sample material still limits the analysis to either the genome or transcriptome, hence a combined analysis of both types of nucleic acids from the same sample material is still in demand.We developed a protocol which enables the combined analysis of the genome as well as the transcriptome by Next Generation Sequencing from ultra-low input samples. The protocol was evaluated by sequencing sub-colony structures from human embryonic stem cells containing 150 to 200 cells. The method can be adapted to any available sequencing system (e.g. Illumina, SOLiD, 454, etc.).To our knowledge, this is the first report where sub-colonies of human embryonic stem cells have been analyzed both at the genomic as well as transcriptome level. The method of this proof of concept study may find useful practical applications for cases where only a limited number of cells are available, e.g. for tissues samples from biopsies, circulating tumor cells and cells from early embryonic development. The results we present demonstrate that a combined analysis of genomic DNA and messenger RNA from ultra low input samples is feasible and can readily be applied to other cellular systems with limited material available.

overall_design: sequencing analysis of ultra-low amounts of RNA (in duplicate) and DNA from the same sample

first: Wasco

last: Wruck