title: Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: To understand the genetic mechanisms involved in the functional transition of cotyledons from non-photosynthetic storage tissue to metabolically active photosynthetic tissue during soybean seedling development, we constructed seven different RNA-Seq libraries using cotyledons from each developmental stage separately. Analysis of RNA-Seq data from different developmental stages revealed the differential expression of many genes including transcription factors. In this study, we focused on NAC and YABBY transcription factors which showed a conspicuous expression pattern during soybean seedling development. Their expression gradually increases from stage 1 to stage 4 of soybean germinating cotyledons. The highest level of expression was found at stage 4. Then it gradually decreased as the germinating cotyledons develop a mature seedling. We investigated the differential expression of NAC and YABBY regulated genes between stage 3 (before the functional transition) and stage 6 (after the functional transition) using our RNA-Seq data. Based on our RNA-Seq data, we found that 10 genes are up-regulated and 21 genes are down-regulated by NAC transcription factor. Similarly we found that 19 genes are up-regulated and 27 genes are down-regulated by YABBY transcription factor.

overall_design: High-throughput sequencing using Illumina HiSeq 2000 (RNA-Seq) was performed on seven developmental stages of soybean seedlings, with two biological replicates per stage.

first: Md

last: Shamimuzzaman

middle: O


title: RNA Seq analysis of Mefs Isolated from STC1+/+ and STC1-/- mice

status: Public on Jul 29 2014

city: Davis

first: Sanchita

last: Bhatnagar

state: CA

address: 1275 Health Sciences, Tupper Hall 3134

department: Medical Microbiology and Immunology

country: USA

institute: University of California Davis

type: Expression profiling by high throughput sequencing

summary:
Evaluation of X-linked gene expression in MEFs isolated from STC1 wild type and knock out mice
X chromosome inactivation (XCI) is initiated in cis by the Xist RNA, which coats the inactive X chromosome (Xi) from which it is produced.  We performed a large-scale RNA interference screen to identify trans-acting XCI factors (XCIFs) that comprise regulators of cell signaling and transcription. We find that the XCIFs promote Xist expression and/or localization to the Xi. One of the XCIFs, STC1, is a glycoprotein found in both the cytoplasm and nucleus and whose function is poorly understood. A homozygous mouse knockout of STC1 has a defect in XCI but surprisingly is phenotypically normal. We performed transcriptome profiling (RNA-Seq) experiments to determine whether the expression levels of X-encoded genes were elevated in Stc1-/- female MEFs. In these experiments, RNA was prepared from three independent cultures of Stc1+/+ or Stc1-/- female MEFs. RNA samples were processed and amplified followed by deep sequencing. The similarity of X-linked gene expression between Stc1+/+ and Stc1-/- MEFs was statistically significant. The vast majority of autosomal genes were also expressed at comparable levels in Stc1+/+ and Stc1-/- MEFs.

overall_design: Sequenced mRNA isolated from the STC1+/+ or STC1-/- MEFs.

first: Michael

middle: R

last: Green

first: Ling

last: Lin


title: Dynamics of Genomic H3K27me3 Domains and Role of EZH2 during Pancreatic Endocrine Specification

status: Public on Jul 28 2014

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Endoderm cells undergo a sequence of fate choices to generate insulin-secreting β cells. Studies of chromatin transitions during this process have been limited to the pancreatic progenitor stage that can be reconstituted from stem cells in vitro, with a gap in understanding the induction of endocrine cells. To address this, we established conditions for isolating endoderm cells, pancreatic progenitors, and endocrine cells from different staged embryos and performed genome wide analysis of the H3K27me3 mark of the repressive Polycomb complex.  During the transition from endoderm to pancreas progenitors and during the transition from pancreas progenitors to endocrine cells, genes that lose the H3K27me3 mark typically encode transcriptional regulators, whereas genes that acquire the mark typically are involved in cell biology morphogenesis.  Precocious depletion of the EZH2, a H3K27 methylase, at the pancreas progenitor stage enhanced the production of endocrine cells, leading to a later increase in pancreatic beta cells. Similarly, pharmacologic inhibition of EZH2 in embryonic pancreatic tissue explants and human embryonic stem cell cultures led to an increase in endocrine progenitors in vitro.  These findings reveal a repeating target gene pattern in H3K27me3 dynamics and provide a means to modulate β cell development from stem cells.

overall_design: Analyzed five FACS-sorted tissues in early mouse embryo; for each tissue we sequenced H3K27me3 and input; no replicates

first: Cheng-Ran

last: Xu

first: Lin-Chen

last: Li

first: Greg

first: Lei

last: Ying

first: Yu-Wei

last: Zhang

first: Paul

last: Gadue

first: Kenneth

middle: S

last: Zaret


title: RepliSeq of HT-1080 cell line

status: Public on Jul 31 2014

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

summary: Analysis of replication timing by RepliSeq of HT-1080 Human Connective Tissue Fibrosarcoma Cells. HT-1080 subclone +4 cell line as described in “Human gene targeting favors insertions over deletions.”  Russell, D.W., and Hirata, R.K. (2008). Hum Gene Ther 19, 907-914.

overall_design: RepliSeq of HT-1080 cell line was used to determine the impact of DNA replication on targeted adeno-associated virus sites  by mapping replication forks, which revealed a consistent preference for recombination at target loci transcribed towards an incoming fork.

first: Richard

last: Sandstrom

first: Russell

last: David

first: Scott

last: Hansen


title: Nanoscale Chromatin Profiling of Gastric Adenocarcinoma

status: Public on Jul 30 2014

city: Singapore

first: Niantao

last: Deng

state: Singapore

address: Center for Computational Biology, level 6, 8 College Road

country: Singapore

institute: Duke NUS Graduate Medical School

summary: To identify chromatin alterations in primary gastric adenocarcionomas, we performed nano-scale chromatin immunoprecipitation-sequencing (Nano-CHiPseq) of histone modifications in 5 gastric cancers and matched normal tissues, We identified hundreds of somatically-altered promoters (marked by H3K4me3) and enhancers (H3K4me1). The majority of cancer-associated promoters localized to genomic sites lacking previously-annotated transcription start sites (“cryptic promoters”), driving high expression of nearby genes implicated in gastrointestinal cancers, embryonic development, and tissue specification. Our findings demonstrate the feasibility of performing chromatin profiling on solid tumors where tissue is limiting, to identify in non-coding regions regulatory elements, transcriptional patterns and genetic variants associated with cancer. We propose a pervasive role for cryptic promoters in the reactivation of early developmental programs in gastric cancer, and the potential utility of cryptic promoters as biomarkers of malignancy.

overall_design: Five gastric cancer tumor normal pairs are profiling in multiple number of chromatin marks

first: Masafumi

last: Muratani

first: Patrick

last: Tan


title: Transcriptome analysis of Wild Type and Mir-212/132ILN/ILN mouse mammary gland

city: Freiburg

first: Yoko

middle: Fukuda

last: Yuzawa

address: Stübeweg 51

country: Germany

institute: Max-Planck Institute of Immunobiology

summary: Mice deficient for miR-212/132 have been reported to show impaired mammary gland development. However, another miR-212/132-deficient line does not demonstrate any obvious defects in mammary gland organogenesis. The transcriptome analysis in the mammary gland of the previously reported miR-212/132-deficient line by deep RNA-seq revealed significantly deregulated expression of genes flanking Mir-212/132 locus, such as HIC1, implying that the mammary gland phenotype might not be only due to loss of miR-212/132

overall_design: Mammary gland mRNA profiles of Wild Type and Mir-212/132ILN/ILN mice were generated by deep sequencing using Illumina GAIIx.

last: Fukuda-Yuzawa

first: Taro

last: Fukao


title: Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

summary: It remains an open question when and how the first cell fate decision is made in mammals. Using deep single-cell RNA-seq of matched sister blastomeres, we report highly reproducible interblastomere differences among ten 2-cell and five 4-cell mouse embryos. Inter-blastomere gene expression differences dominated between-embryo differences and noises, and were sufficient to cluster sister blastomeres into distinct groups. Dozens of protein-coding genes exhibited reproducible bimodal expression in sister blastomeres (0 vs. 1e3-1e6 of FPKM), which cannot be explained by random fluctuations. The protein expression of one of these bimodal genes, Gadd45a, exhibited clear inter-blastomeric contrasts. We traced some of the bimodal mRNA expressions to embryonic genome activation, and others to blastomere-specific RNA depletion. Inter-blastomere differences created co-expression gene networks that were much stronger and larger than those that can be possibly created by random noises. The highly correlated gene pairs at the 4-cell overlapped with those showing the same directions of differential expression between inner cell mass (ICM) and trophectoderm (TE). These data substantiate the hypothesis of inter-blastomere differences in 2- and 4-cell mouse embryos, and associate these differences with ICM/TE differences.

overall_design: 9 zygotes, 10 2-cell, and 5 4-cell mouse (C57BL/6) embryos were collected and multi-cell embryos were separated into blastomeres. 4 inner cell mass (ICM) and 3 trophectoderm (TE) samples are also extracted from mouse blastocysts. Transcriptome profiles for all samples are obtained via Smart-seq protocol.

first: Xiaoyi

last: Cao

first: Sheng

last: Zhong


title: Ribosome profiling upon glucose starvation in S. cerevisiae

city: La Jolla

first: Brian

middle: Matthew

last: Zid

state: California

address: 9500 Gilman Drive

department: Chemistry and Biochemistry

institute: University of California San Diego

summary: A universal feature of the response to stress and nutrient limitation is transcriptional upregulation of genes encoding proteins important for survival.  Interestingly, under many of these conditions overall protein synthesis levels are reduced, thereby dampening the stress response at the level of protein expression. For example, during glucose starvation in yeast, translation is rapidly and reversibly repressed, yet transcription of many stress- and glucose-repressed genes is increased. Using ribosome profiling and microscopy, we found that this transcriptionally upregulated gene set consists of two classes: (1) one producing mRNAs that are preferentially translated during glucose limitation and are diffusely localized in the cytoplasm – this class includes many heat shock protein mRNAs; and (2) another producing mRNAs that are poorly translated during glucose limitation, have high rates of translation initiation, and are concentrated in foci that co-localize with P bodies and stress granules – this class is enriched for glucose metabolism mRNAs. Remarkably, the information specifying differential localization and translation of these two classes of mRNAs is encoded in the promoter sequence – promoter responsiveness to heat shock factor (Hsf1) specifies diffuse cytoplasmic localization and preferential translation upon glucose starvation, whereas different promoter elements upstream of genes encoding poorly translated glucose metabolism mRNAs direct these mRNAs to RNA granules under glucose starvation. Thus, promoter sequences and transcription factor binding can influence not only mRNA levels, but also subcellular localization of mRNAs and the efficiency with which they are translated, enabling cells to tailor protein production to environmental conditions.

overall_design: Examination of mRNA translation in S. cerevisiae upon glucose starvation.

middle: M

first: Erin

middle: K

last: O'Shea


title: Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration

city: Farmington

first: Jeffrey

last: Chuang

state: CT

address: 263 Farmington Avenue

department: Computational Biology

institute: The Jackson Laboratory for Genomic Medicine

summary: In higher eukaryotes, the large numbers of nuclear-encoded tRNA genes partially ensure the robustness of cytoplasmic protein translation. Here we discover that a loss-of-function in n-Tr20, a member of the nuclear-encoded tRNA Arg UCU family that is expressed specifically in the central nervous systems leads to low but detectable levels of ribosome stalling. In the absence of GTPBP2, a novel binding partner of the ribosome recycling protein Pelota, ribosome stalling increases, leading to widespread neurodegeneration. Our results not only define GTPBP2 as a ribosome rescue factor, but also unmask the disease potential of mutations in nuclear-encoded tRNA genes. In this submission we provide ribosome footprinting data from the cerebella of four strains derived from the C57BL/6J strain with combinations of  n-Tr20 and GTPBP2 mutations.

overall_design:
Examination of ribosome stalling in cerebella from 4 mouse strains derived from the: C57BL/6J (B6J) strain. The nmf205-/- strain has a homozygous mutation in the gene GTPBP2 while the B6J strain has normal GTPBP2. The n-Tr20 J/J strain has a defect in the n-Tr20 tRNA while the n-Tr20 N/N strain has a functional n-Tr20 tRNA. The 4 strains are the 2x2 combinations of these defects and correctly functioning sequences. 2 replicates for each strain.
Please note that only BAM files are included in the records since they form the basis of the study's conclusions.  The raw data ribosomal RNA have been filtered and then unique reads mapping to mm10 were computed using tophat and igenome annotations.

first: Susan

last: Ackerman


title: The effect of transcription factor AtfA on gene expression

city: Callaghan

first: Peter

last: Lewis

address: University Dr

country: Australia

institute: University of Newcastle

summary: We report the effect of the deletion of novel RNA polymerase binding protein AtfA on genome-wide transcription in Acinetobacter baylyi ADP1.

overall_design: Compared the transcription profile of wt vs atfA knockout in Acinetobacter baylyi ADP1 using RNA-seq.

first: Ryan

last: Withers


title: Characterization of Sus scrofa small RNA sequences present in both female and male gonads

status: Public on Jul 27 2014

city: Poznan

first: Aleksandra

middle: Maria

last: Swiercz

address: Piotrowo 2

department: Institute of Computing Science

country: Poland

institute: Poznan University of Technology

type: Non-coding RNA profiling by high throughput sequencing

summary:
We used deep sequencing to characterize 3 families of sRNAs (piRNAs, miRNAs, and tRFs) present in Sus scrofa gonads and focused on the sRNA fraction present in both male and female gonads. Of the sequences detected in the testes, 2.6% of piRNAs, 9% of miRNAs, and 10% of tRFs were also present in the ovaries.
Notably, the majority of the shared piRNAs mapped to the introns of ribosomal RNAs and were derived from clustered loci. In addition, the most abundant miRNAs present in the ovaries and testes are conserved and are involved in many biological processes such as the regulation of homeobox genes, the control of cell proliferation, and carcinogenesis.
Unexpectedly, we detected a novel sRNA type, the tRFs, which are 30–36-nt RNA fragments derived from tRNA molecules, in gonads

overall_design: Determination miRNA, piRNA and tRF expression in swine gonads

first: Dorota

last: Kowalczykiewicz

last: Świercz

first: Luiza

last: Handschuh

first: Katarzyna

last: Wiechetek

first: Marek

last: Figlerowicz

first: Jan

last: Wrzesinski


title: RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer

city: Shanghai

first: Yi

address: 227 South Chongqing Rd.

country: China

institute: SJTU

summary: The translational control of oncoprotein expression is implicated in many cancers. Here we report an eIF4A/DDX2 RNA helicase-dependent mechanism of translational control that contributes to oncogenesis and underlies the anticancer effects of Silvestrol and related compounds. For example, eIF4A promotes T-ALL development in vivo and is required for leukaemia maintenance. Accordingly, inhibition of eIF4A with Silvestrol has powerful therapeutic effects in vitro and in vivo. We use transcriptome-scale ribosome footprinting to identify the hallmarks of eIF4A-dependent transcripts. These include 5'UTR sequences such as the 12-mer guanine quartet (CGG)4 motif that can form RNA G-quadruplex structures. Notably, among the most eIF4A-dependent and Silvestrol-sensitive transcripts are a number of oncogenes, super-enhancer associated transcription factors, and epigenetic regulators. Hence, the 5'UTRs of selected cancer genes harbour a targetable requirement for the eIF4A RNA helicase.

overall_design: Comparison of ribosome-protected RNA for drug treated and DMSO treated KOPT-K1 cell, two replicates of ribosome-protected RNA sequencing and three replicates of RNA-seq.

first: Andrew

middle: L

last: Wolfe

first: Kamini

last: Singh

first: Philipp

last: Drewe

first: Vinagolu

last: Rajasekhar

first: Viraj

last: Sanghvi

first: Konstantinos

middle: J

last: Mavrakis

first: Justine

middle: E

last: Roderick

first: Joni

last: Van der Meulen

first: Jonathan

last: Schatz

first: Christina

last: Rodrigo

first: Man

last: Jiang

first: Chunying

last: Zhao

first: Pieter

last: Rondou

first: Elisa

last: de Stanchina

first: Julie

last: Teruya-Feldstein

first: Michelle

last: Kelliher

first: Frank

last: Speleman

first: John

last: Porco Jr.

first: Jerry

last: Pelletier

first: Gunnar

last: Rätsch

first: Hans-Guido

last: Wendel


title: KRAS and YAP1 converge to regulate EMT and tumor survival

city: Cambridge

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

institute: MIT

summary: Cancer cells that express oncogenic alleles of RAS typically require sustained expression of the mutant allele for survival, but the molecular basis of this oncogene dependency remains incompletely understood. To identify genes that can functionally substitute for oncogenic RAS, we systematically expressed 15,294 open reading frames in a human KRAS-dependent colon cancer cell line engineered to express an inducible KRAS-specific shRNA. We found 147 genes that promoted survival in the setting of KRAS suppression. In this model, the transcriptional co-activator YAP1 rescued cell viability in KRAS-dependent cells upon suppression of KRAS and was required for KRAS-induced cell transformation. Acquired resistance to Kras suppression in a Kras-driven murine lung cancer model also involved increased YAP1 signaling. KRAS and YAP1 converge on the transcription factor FOS and activate a transcriptional program involved in regulating the epithelial-mesenchymal transition (EMT). Together, these findings implicate transcriptional regulation of EMT by YAP1 as a significant component of oncogenic RAS signaling

overall_design: Three biological replicates of primary lung adenocarcinoma cells derived from the Kras Lox-STOP-Lox-G12D;p53flox/flox (KP) mouse lung cancer model into which  a doxycycline-inducible shRNA targeting Kras expressed from the 3’UTR of GFP was introduced (KP-KrasA cells) were analyzed at timepoints (days) D0, D4, and D21.

first: Diane

middle: D

last: Shao

first: Wen

last: Xue

first: Elsa

middle: B

last: Krall

first: Arjun

first: Federica

last: Piccioni

first: Xiaoxing

last: Wang

first: Anna

middle: C

last: Schinzel

first: Sabina

last: Sood

first: Joseph

last: Rosenbluh

first: Jong

middle: W

last: Kim

first: Yaara

last: Zwang

first: Thomas

last: Roberts

first: David

last: Root

first: Tyler

last: Jacks

first: William

last: Hahn


title: Catharanthus Transcriptome and Gene Expression

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary: In this study, we aim to present a global transcriptome analysis of medicinal plant, Catharanthus roseus. We generated about 343 million high-quality reads from three tissues (leaf, root and flower) using Illumina platform. We performed an optimized de novo assembly of the reads and estimated transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses among tissue samples.

overall_design: We collected different tissue samples from the mature plants. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequence data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were used for de novo assembly optimization. The reads were further mapped to the Catharanthus transcripts via CLC Genomics Workbench and differential gene expression analysis was performed using DESeq software.

first: Verma

last: Mohit

first: Ghangal

last: Rajesh

first: Sharma

last: Raghvendra

first: Sinha

last: Alok

first: Jain

last: Mukesh


title: TRIM28 regulates RNA polymerase II promoter proximal pausing and entry into processive elongation

city: RTP

last: Fargo

state: NC

department: HHS

institute: National Institute of Environmental Health Sciences

summary: Analysis of total PolII and Ser2-phosphorylated PolII genomic occupancy in control-transfected (WT) or Trim28-knockdown (Trim28-KD) embryonic stem cells.

overall_design: Embryonic stem cells were transfected with luciferase siRNA (WT) or Trim28 siRNA (Trim28 KD) in duplicate experiments. 48 hrs after transfection, cells were crosslinked with formaldehyde, collected, lysed, and chromatin was fragmented with sonication. Total PolII or Ser2-phosphorylated PolII genomic occupancy in WT or Trim28 KD cells were determined by ChIP-seq.

first: Heeyoun

last: Bunch

first: Xiaofeng

last: Zheng

first: Adam

last: Burkholder

first: Shmulik

last: Motola

first: Simon

middle: T

last: Dillon

first: Christopher

last: Ebmeier

first: Stuart

last: Levine

first: Guang

last: Hu

first: Dylan

last: Taatjes

last: Calderwood


title: Role of TTF-1/NKX2-1, Smad3 and Smad4 on lung cancer cell lines

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

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

overall_design: Refer to individual Series


title: Smad3, Smad4 and TTF-1/NKX2-1 binding sites in H441/A549 lung cancer cell lines

summary: We evaluated the role of TTF-1/NKX2-1 on Smad3 and Smad4 binding in lung cancer cell lines.

overall_design: Smad3 binding sites in A549 cells and Smad3, Smad4, and TTF-1/NKX2-1 binding sites in H441 cells were determined by ChIP-seq.

first: Kazunobu

last: Isogaya

first: Shuichi

last: Tsutsumi

first: Roy-Akira

last: Saito

first: Keiji

last: Miyazawa

first: Hiroyuki

last: Aburatani

first: Kohei

last: Miyazono


title: Trans-generationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing [cuff RNA-seq]

status: Public on Jul 26 2014

city: Pasadena

first: Adrien

last: Le Thomas

state: CA - California

address: 231 South Hudson Avenue

department: Biology and Biological Engineering

institute: California Institute of Technology

summary: Small non-coding RNAs that associate with Piwi proteins, called piRNAs, serve as guides for repression of diverse transposable elements in germ cells of Metazoa. In Drosophila, the genomic regions that give rise to piRNAs, the so-called piRNA clusters, are transcribed to generate long precursor molecules that are processed into mature piRNAs. How genomic regions that give rise to piRNA precursor transcripts are differentiated from the rest of the genome and how these transcripts are specifically channeled into the piRNA biogenesis pathway are not known. We found that trans-generationally inherited piRNAs provide the critical trigger for piRNA production from homologous genomic regions in the next generation by two different mechanisms. First, inherited piRNAs enhance processing of homologous transcripts into mature piRNAs by initiating the ping-pong cycle in the cytoplasm.  Second, inherited piRNAs induce installment of the H3K9me3 mark on genomic piRNA cluster sequences. The HP1 homolog Rhino binds to the H3K9me3 mark through its chromodomain and is enriched over piRNA clusters. Rhino recruits the piRNA biogenesis factor Cutoff to piRNA clusters and is required for efficient transcription of piRNA precursors. We propose that trans-generationally inherited piRNAs act as an epigenetic memory for identification of substrates for piRNA biogenesis on two levels, by inducing a permissive chromatin environment for piRNA precursor synthesis and by enhancing processing of these precursors.

overall_design: total RNA sequencing of RNA from ovaries of cuff+/- or cuff-/- flies

first: Yung-Chia

last: Chen


title: Trans-generationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing [cuff smallRNA]

overall_design: small RNA (19-29nt) sequencing of RNA from ovaries of cuff+/- or cuff-/- flies


title: Trans-generationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing


title: Trans-generationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing [Rhino RNA-seq]

overall_design: total RNA sequencing of RNA from ovaries of shWhite and Rhino knockdown flies

first: Evelyn

last: Stuwe


title: Trans-generationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing [run-on]

overall_design: nuclear run-on in wildtype and Rhino knockdown to investigate the transcriptional activity in Rhino knockdown compared to wildtype


title: Small RNA expression and caste differentiation in the honeybee

city: Stanford

first: Xiangqian

last: Guo

address: 300 Pasteur Dr.

department: Department of Pathology

institute: Stanford University

summary: Honeybees are very important eusocial insects and are involved in the pollination of many plants. Queen bees and worker bees develop from the same fertilized eggs, and are thus genetically identical despite their substantial behavioural and physiological differences. The mechanism governing developmental differences between worker and queen bees has always attracted much interest. While there are several reports on mRNA expression related to caste differentiation, no systematic investigation of small RNAs has thus far been carried out. Results: Using deep sequencing we systematically profiled small RNA expression in 4th-6th day worker larvae and queen larvae (the critical stages at which the fates of workers and queens are determined), and found that 38 miRNAs were differentially expressed between worker and queen larvae. In addition, 639 mature miRNA candidates were identified in our work for the first time, of which, 526 were expressed only in workers (318) or queens (208).  Conclusion: We present the first profile of honeybee small RNAs and explore the mechanism of caste differentiation between worker and queen bees. Caste-specific expression patterns and large discrepancies in small RNA profiles between worker and queen bees indicate that small RNAs may be related to the differential development of worker and queen bee larvae. Results presented here will make a valuable contribution to understanding the caste switch between worker and queen bees.

overall_design: Three healthy 10-frame colonies of ‘Zhenongda No.1’- a high-yielding royal jelly breed of Apis mellifera ligustica , were maintained at the Huajiachi campus of Zhejiang University. In each colony, the queen laid eggs over a period of 24 hours in one empty frame which was subsequently moved to an egg-free super-chamber. After 66 hours (less than 18 hours after hatching), we transferred 150 larvae into queen cups to rear queens in each colony and put the queen cup frames into their corresponding colonies. 40-60 worker larvae and queen larvae were collected from each colony after 4 days (73~90 h after hatching), 5 days (97~114 h after hatching) and 6 days (121~138 h after hatching). The larval samples were collected into 50 ml tubes, immediately frozen in liquid nitrogen and stored at -80C until being used for RNA extraction.   After total RNA was extracted  and quantified , relative equal amounts of total RNAs from each of the three sampling days were pooled into respectively worker and queen samples, and the fraction of small RNAs less than 30nt long was retained and sequenced on the Illumina/Solexa high-throughput platform (HTP).

first: Songkun

last: Su

first: Geir

last: Skogerbø

first: Shenglu

first: Shaowu

last: Zhang

first: Runsheng


title: Trans-generationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing [small RNA-IP]

overall_design:
sequencing of argonaute-bound and total small RNAs from ovaries of different fly crosses: maternal deposition (MD) crosses, in which piRNAs from the P1152 locus are transmitted into the next generation through the mother. No maternak deposition (NMD) crosses, which are reciprocal to the MD crosses. Subsequently, no piRNAs from the P1152 locus are transmitted into the next generation.
The strain P-1152, that carries insertion of P{lArB} construct in telomeric sequences of X chromosome (site 1A) is described in (Roche and Rio 1998). The strain BC69 that has insertion of P{A92} construct at a euchromatic location on chromosome 2L (site 35B10-35C1) is described in (Lemaitre et al. 1993).Both  stocks were a generous gift from S. Ronsseray.


title: Transcriptome sequencing of Pacific oyster Crassostrea gigas

city: Qingdao

first: Fei

last: Xu

address: 7 Nanhai Road

institute: Institute of Oceanology, Chinese Academy of Sciences

summary: Deep sequencing of mRNA from Pacific oyster Crassostrea gigas

overall_design: Competent larvae of Crassostrea gigas were treated with epinephrine solution, and then sampled at different time intervals. For shell damage experiment, shell were broken and then tissues were sampled at different time intervals.

first: Xiaodong

last: Fang

first: Li

last: Li

first: Xiaotong

last: Wang

first: Linlin


title: miRNA of Pacific oyster Crassostrea gigas for different organs and developmental stages

summary: miRNA sequencing of Pacific oyster Crassostrea gigas for different organs and developmental stages.

overall_design: Two RNA pools were created and sequenced by mixing the samples before and after the developmental stage "D shaped larvae". Then ten developmental samples and eleven samples from 7 organs were sequenced.


title: Next Generation Sequencing identifies O2-responsive genes in the human pathogenic fungus Aspergillus fumigatus

status: Public on Jul 25 2014

city: Jena

first: Steffen

last: Priebe

address: Beutenbergstr. 11a

department: Systems Biology / Bioinformatics

institute: Hans-Knöll-Institute (HKI)

summary:
Low oxygen conditions are not only common to natural environments but also occur during tissue invasive growth in the human host. Only few cellular factors have been identified up to now that allow the fungus to efficiently adapt its energy metabolism to the lack of O2. In the present study, we cultivated A. fumigatus in an O2-controlled fermenter and analysed its minute-scale responses to O2 limitation. Transcriptome sequencing revealed a group of genes underlying a rapid and highly dynamic regulation.
As an initial experimental setup, A. fumigatus was cultivated in an O2-controlled fermenter, which allowed minute-scale variations in O2-fluxes largely independent of other secondary effects. Cultures were initially grown at saturated O2 concentrations (100% saturation ≈ 260 µmol l-1) and rapidly shifted to hypoxic growth conditions at an initial O2 saturation of 5% (≈ 13 µmol l-1).

overall_design: Dynamics of low and high O2 responses of A. fumigatus cultivated in an O2-controlled fermenter

first: Falk

last: Hillmann

first: Jörg

last: Linde

first: Axel

last: Brakhage


title: Human somatic cell mutagenesis creates genetically tractable sarcomas

city: Toronto

first: Rama

last: Khokha

address: 101 College St

department: Medical Biophysics

country: Canada

institute: Ontario Cancer Institute

summary: Creating spontaneous yet genetically tractable human tumors from normal cells presents a fundamental challenge. Retroviruses and transposons have been separately used as somatic cell insertional mutagens to identify cancer drivers in model organisms. Here we combined these mutagenic elements to enable cancer gene discovery starting with normal human cells. Lentivirus was used to seed gain- and loss-of-function gene disruption elements which were further deployed by Sleeping Beauty transposons throughout the genome of human bone explant mesenchymal cells. De novo tumors rapidly generated in this context were high-grade sarcomas corresponding to the spectrum of myxofibrosarcoma and undifferentiated pleomorphic sarcoma, aggressive neoplasms with a predilection for older adults. Tumor insertion sites were genome-wide and enriched in regions of recurrent somatic copy number alteration found in multiple cancers, with a bias towards those of sarcomas. Novel driver genes which sustain somatic alterations in cancer patients were pinpointed. We identify the gene HDLBP, which codes for the RNA binding protein vigilin, as a candidate tumor suppressor deleted at 2q37.3 in greater than one in ten tumors across multiple tissues of origin. Hybrid viral-transposon systems will accelerate the functional annotation of cancer genomes by enabling insertional mutagenesis screens in higher eukaryotes that are not amenable to germline transgenesis.

overall_design: Lentivirus was used to seed gain- and loss-of-function gene disruption elements which were further deployed by Sleeping Beauty (SB) transposons throughout the genome of human bone explant mesenchymal cells. Genomic locations of LV (lentiviral backbone) and SB insertion sites were mapped by a pooled strategy utilizing linear amplification mediated PCR (LAM-PCR), followed by Illumina next generation sequencing of the product pool.

first: Sam

last: Molyneux

first: Paul

last: Waterhouse

first: Dawne

last: Sheton

first: Yang

last: Shao

first: Chris

last: Watling

first: Qinglian

last: Tang

first: Issac

last: Harris

first: Brendan

last: Dickson

first: Pirashaanty

last: Tharmapalan

last: Sandve

first: Xiaoyang

first: Swneke

last: Bailey

first: Berman

last: Ha

first: Jay

last: Wunder

first: Zsuzsanna

last: Iszvak

first: Mathieu

last: Lupien

first: Tak

last: Mak


title: MAEL-dependent selective processing of pachytene piRNA precursors and translation of spermiogenic mRNAs

city: Berkeley

first: Nicholas

last: Ingolia

email: ingolia@berkeley.edu, nick@ingolia.org

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: Piwi-interacting small RNAs (piRNAs) of fetal prospermatogonia of mice have been strongly implicated in transposon control. In contrast, little is known about biogenesis and function of abundant piRNAs from adult testes expressed in late spermatocytes and round spermatids. These so-called "pachytene" piRNAs are processed from long non-coding piRNA precursors and have no defined RNA targets in the transcriptome even though their binding partner Piwi, MIWI, is essential for spermiogenesis and fertility. Here we report that 129SvJae mice lacking Maelstrom (MAEL), a conserved piRNA pathway protein, exhibit spermiogenic arrest with defects in acrosome and flagellum formation. Further analysis revealed MAEL association with RNPs containing MIWI, TDRD6, and processed  intermediates of pachytene piRNA precursors of various length. Loss of MAEL causes a 10-fold drop in pachytene piRNA levels but an increase in piRNAs from abundantly expressed mRNAs. These results suggest a MAEL-dependent mechanism for the selective processing of pachytene piRNA precursor into piRNAs. Strikingly, ribosome profiling of Mael-null testes revealed that reduced piRNA production is accompanied by reduced translation of over 800 spermiogenic mRNAs including those encoding acrosome and flagellum proteins. In light of recent reports of piRNA-independent protection of translationally repressed mRNPs by MIWI and piRNA-dependent turnover of MIWI, we propose that pachytene piRNAs function by controlling the availably of MIWI for the translational repression of spermiogenic mRNAs.

overall_design: piRNA sequencing, RNA immunoprecipitation, and expression measurements (RNA-Seq and ribosome profiling) in wild-type and Mael -/- testes

first: Julio

last: Castañeda

first: Godfried

last: van der Heijden

first: Alex

last: Bortvin


title: The role of SPK-1 in alternative splicing regulation in C. elegans

status: Public on Jul 24 2014

city: Haifa

first: Martin

last: Mikl

address: Abba Khoushy 199

department: Department of Human Biology

country: Israel

institute: University of Haifa

summary: The aim of this study was to identify target genes of the SR protein kinase SPK-1. spk-1(RNAi) leads to defects in cell polarity. We were therefore primarily interested in genes who exhibit changes in splicing regulation upon depletion of SPK-1 and could underlie the polarity phenotype of spk-1(RNAi).

overall_design: Transcriptome profiling of control and spk-1(RNAi) worms by RNAseq

first: Carrie

middle: R

last: Cowan


title: HBS1L-MYB intergenic variants modulate fetal hemoglobin via long-range MYB enhancers

city: Oxford

first: Supat

last: Thongjuea

address: Headington

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: The Weatherall Institute of Molecular Medicine

summary: Genetic studies have identified common variants within the HBS1L-MYB intergenic region on chromosome 6q associated with elevated fetal hemoglobin (HbF) levels and other clinically important human erythroid traits. The mechanism by which the non-coding sequence variants affect these traits is still not clear. Here we report that several of the variants affect regulatory elements that are occupied by key erythroid transcription factors within this region. These elements interact with MYB, a critical regulator of erythroid development and HbF levels. We show that several of the variants reduce transcription factor binding, affecting long-range interactions with MYB, and MYB expression levels. We provide here a functional explanation for the genetic association of HBS1L-MYB intergenic polymorphisms with human erythroid traits and HbF levels. Our results further designate MYB as a bona fide target for therapeutic induction of HbF to ameliorate sickle cell and β-thalassemia disease severity.

overall_design: ChIP-Sequencing profiles of the LDB1 and CTCF proteins were generated using primary human erythroid progenitors. 3C-Seq experiments (in duplicate, primary human erythroid progenitors) were performed using the MYB promoter and the -84kb upstream enhancer as viewpoints.

first: Ralph

last: Stadhouders

first: Eric

last: Soler


title: Effect of TTF-1/NKX2-1 expression on TGF-beta induced gene expression in A549 lung cancer cell line.

first: Daizo

last: Koinuma

summary: TTF-1/NKX2-1 was expressed by adenoviral vector and changes in gene expression were determined by RNA-sequencing.

overall_design: A549 cells were infected with Ad-TTF-1 or Ad-LacZ vectors and stimulated with TGF-beta for 24 hours or left untreated. Expression of polyA RNA was determined.

first: Kazunobu

last: Isogaya

first: Shuichi

last: Tsutsumi

first: Roy-Akira

last: Saito

first: Keiji

last: Miyazawa

first: Hiroyuki

last: Aburatani

first: Kohei

last: Miyazono


title: ChIP-exo analysis of the DNA-binding sites of the yeast transcription factor Yfl052w sequenced by Illumina

city: Leuven

first: Ksenia

last: Pougach

address: Gaston Geenslaan 1

department: CMPG

country: Belgium

institute: KU Leuven

summary: We determined DNA-binding sites of the yeast transcription factor Yfl052w by ChIP-exo. Cells were grown in the YP media containing palatinose. Yfl052w was tagged with HA tag and anti-HA antibody was used for the immunoprecipitation.

overall_design: Examination of Yfl052 trancription factor in HA-tagged and wt cells (as a control)

first: Vladimir

last: Benes


title: ChIP-exo analysis of the DNA-binding sites of the yeast transcription factor Yfl052w sequenced by SOLiD


title: Genome wide binding and transcriptome analysis of human FXR in primary human hepatocytes [HTS]

city: Piscataway

first: Le

last: Zhan

state: NJ

address: 170 Frelinghuysen Rd

department: Pharmacology and Toxicology

institute: Rutgers University

summary: We report the genome-wide profiling of FXR binding by ChIP-seq from GW4064 or DMSO treated primary human hepatocytes. We reported altered RNA expression profiles in primary human hepatocypes upon GW4064 treatment compared to DMSO control by RNA-seq. We also reported the altered RNA expression profiles in livers from WT C57BL/6J mice upon GW4064 treatment compared to vehicle control.

overall_design:
Primary human hepatocytes were treated with 5uM GW4064 or DMSO control, 1 hour later, cells were fixed and collected for chromatin isolation. 24 hours post treatment, cells were isolated for RNA isolation.

This submission represents HTS component of study.

first: Grace

last: Guo

first: Yaping

last: Fang


title: Quantitative Analysis by Next Generation Sequencing of LSK (Lin- Sca1+ cKit+) hematopoietic progenitors and splenic B cells (naive and in vitro LPS activated) transcriptomes from Wild Type and Usp3-/- mice

city: Amsterdam

first: Elisabetta

last: Citterio

address: Plesmanlaan 121

department: Molecular Genetics

country: Netherlands

institute: Netherlands Cancer Insitute (NKI-AVL)

summary:
Purpose: the goal of this study is to investigate the consequences of USP3 deletion on gene expression in mouse LSK hematopoietic progenitors and in splenic B cells
Methods: mRNA profiles of 8 weeks-old wild-type (WT) and ubiquitin specific protease 3  knockout (Usp3−/−) mice were generated by deep sequencing, in duplicate, using Illumina Hiseq2000. The sequence reads that passed quality filters were mapped with TopHat and the gene expressions were calculated using HTSeq-count. qRT–PCR validation was performed using SYBR Green assays
Results: We assigned about 8-16 million reads per sample uniquely to a gene of the mouse reference genome (mm9). We identified 23,429 genes in the LSKs, naive B cells and activate B cells of WT and USP3−/− mice using TopHat in combination with HTSeq-count. Comparison of the RNAseq data from LSK with naive or activated B cells show that both the wt and the Usp3-/- LSKs largely exibited a gene expression profile that is specific for wt LSK and distinct from B cells (as supported by statistical significant difference between the transciptional profile of LSK versus naive or activated B cells, p value<0.0001 by Student t test). Comparison of normalized gene expression data for Wt LSKs versus naive B cells of one representative experiment shows Pearson coefficient of r=0.874, and R2=0.763. Distinct LSK-specific expressed genes (such as the MlI receptor and the Kit receptor) and B cells specific genes (such as the MS4A1/CD20 and Spi-B transcription factors) are identified. Expression of a set of 19 genes was assessed by RT-qPCR in three independent LSK mRNA per each genotype. qRT-PCR and the RNA-seq normalized expression data for these genes had a good linear relationship, validating the RNAseq analysis. Comparison of normalized gene expression data for Usp3-/- versus Wt LSK show Pearson coefficient r=0.986; R2=0.9738), naive B cells (Pearson coefficient r=0.987, R2=0.974) and LPS activated B cells (Pearson coefficient r=0.991, R2=0.983). RT-qPCR of a subset of hematopoietic stem cell genes, including Mlp2, ENg, Tek and Fdzl3, show no significant difference beteewn wt and Usp3-/- LSK cells. Less than 100 genes showed differential expression (up or down regulated) between the Wt and Usp3-/- LSK, with a fold change ≥1.5 and p value <0.05.
Conclusions: Our results represent the first detailed analyis of the consequences of USP3 deletion on gene expression in hematopoietic populations such as LSKs progenitors and B cells by genome wide expression profiling in wt and Usp3-/- mice. RNAseq of two freshly isolated biological replicas of sorted LSKs from 8 weeks old Usp3-/- animals showed a very limited number of genes either slighly up or down regulated (<100 out of about 25.000) in Usp3-/- LSKs, none of which are reported to be directly involved in hematopoietic stem cell maintenance or to be linked to premature differentiation. We confirmed that Usp3-/- and wt LSKs express hematopoietic stem cell-specific genes to a similar extent. We conclude that young adult hematopoietic stem and progenitor cells (LSKs) perpetuated a stable gene expression program regardless of the homozygous deletion of USP3.

overall_design: mRNA profiles of 8 weeks-old wild type (WT) and Usp3-/- mice were generated by deep sequencing, in duplicate, using Illumina Hiseq2000. For each experiment  wt n=4, Usp3-/- n=4 mice were analized. FACS sorted cells from from individual animals were pooled and subjected to deep sequencing. Cells were: LSK (Lin- Sca1+ cKit+) from bone marrow, sorted naive B cells from spleens (CD19+) and activated B cells harvested and FACS sorted after 4 days stimulation with lipopolysaccharide (LPS) in culture.

first: Cesare

last: Lancini

first: Gaetano

last: Gargiulo

first: Paul

last: van den Berk

first: Iris

last: de Rink


title: UVB induces a major genome-wide rearrangement of RNA polymerase II at transcribed human genes

city: Rotterdam

first: Akos

last: Gyenis

address: Wytemaweg 80

department: Genetics

institute: ERASMUS MC

summary: Abstract  Background: Faithful transcription of DNA is constantly threatened by different endogenous and environmental genotoxic effects. Transcription coupled repair has been described to quickly remove DNA lesions from the transcribed strand of active genes, permitting rapid resumption of blocked transcription. This repair mechanism has been well characterized in the past using individual target genes. However, the precise mechanism by which RNA polymerase II (Pol II) transcription is affected following UV irradiation during the repair processes genome-wide is not well understood.  Results: We investigated the effect of a non-lethal dose of UVB on global DNA-bound Pol II distribution in human cells. We find that about 90% of the promoters of expressed genes show reduced Pol II occupancy 2-4 hours following UVB irradiation, and that the presence of Pol II is restored to “normal”, or higher, levels 5-6 hours after irradiation. We also identified a smaller set of genes, where the presence of Pol II at the promoter regions does not decrease after UVB irradiation, but often increases throughout the entire transcription units. Interestingly, at promoters, where Pol II promoter clearance occurs, TFIIH but not TBP follows the behavior of Pol II suggesting that at these genes TFIIH may be sequestered for DNA repair upon UVB treatment.  Conclusions: Thus, our study reveals a global negative regulatory mechanism that targets Pol II transcription initiation on the large majority of transcribed genes following sublethal UVB irradiation, and a small subset of genes (including regulators of repair, cell growth and survival), where Pol II escapes this negative regulation.

overall_design: Following genome-wide RNA Polymerase II redistribution over time upon UVB irradiation

first: Ákos

first: David

last: Umlauf

first: Zsuzsanna

last: Ujfaludi

first: Tao

last: Ye

first: Imre

last: Boros

first: Làszlò

last: Tora


title: High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS)

city: Boston

first: Muhammad

last: Ekram

address: 450 Brookline Avenue, DA 740A

department: Medical Oncology

institute: Dana-Farber Cancer Institute

type: Methylation profiling by high throughput sequencing

summary: In vertebrates, DNA methylation-mediated repression of retrotransposons is essential for the maintenance of genomic integrity.  In the current study, we developed a technique termed HT-TREBS (High-Throughput Targeted Repeat Element Bisulfite Sequencing).  This technique is designed to measure the DNA methylation levels of individual loci of any repeat families with next-generation sequencing approaches.  To test the feasibility of HT-TREBS, we analyzed the DNA methylation levels of the IAPLTR family using a set of 12 different genomic DNA isolated from the brain, liver and kidney of 4 one-week-old littermates of the mouse strain C57BL/6N.  This technique has successfully generated the CpG methylation data of 5,233 loci common in all the samples, representing more than 80% of the individual loci of the five targeted subtypes of the IAPLTR family.  According to the results, approximately 5% of the IAPLTR loci have less than 80% average CpG methylation levels with no genomic position preference.  Further analyses of the IAPLTR loci also revealed the presence of extensive DNA methylation variations between different tissues and individuals.  Overall, these data demonstrate the efficiency and robustness of the new technique, HT-TREBS, and also provide new insights regarding the genome-wide DNA methylation patterns of the IAPLTR repeat elements.

overall_design: High-throughput, single-base resolution, singlicate DNA methylation profiles of IAPLTR retrotransposons in the brain, liver , and kidney of four 1-week-old mouse littemates using the developed technique, HT-TREBS.

first: Joomyeong

last: Kim


title: MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma

status: Public on Jul 22 2014

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

summary: We obtained radiographically-localized biopsies during glioma resection surgeries to sample the tumor core and margins from multiple glioma patients. We also procured fresh, non-neoplastic brain tissue specimens from multiple patients having procedures to relieve epilespy symptoms or to place shunts to treat normal pressure hydrocephalus.  We then used RNA-Seq to compare expression patterns between geographically distinct regions of gliomas and computational deconvolution to estimate cell type-specific expression patterns in different disease subtypes.

overall_design: RNA-Seq analysis in 39 contrast-enhancing glioma core samples, 36 non-enhancing FLAIR glioma margin samples, and 17 non-neoplastic brain tissue samples.

last: Canoll


title: ChIP-exo analysis of the DNA-binding sites of the yeast transcription factor Yfl052w

first: Ksenia

last: Pougach

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

overall_design: Refer to individual Series


title: Differential transcript stability measurements in MDA-MB-231 vs. MDA-LM2 cells

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

summary: We performed whole-genome stability measurements for MDA-MB-231 and its highly metastatic derivative MDA-LM2. Our goal was to identify post-transcriptonal regulons that are deregulated en route to higher metastatic capacity.

overall_design: Cells were pulsed with 4-thiouridine for 2 hours and then RNA was extracted at 0, 2, 4, and 7 hr time-points in quadruplicate from each cell line. 4sU labeling followed by RNA-seq was then used to measure the abundance of transcripts in each population. A decay rate was estimated based on the rate at which transcript abundance was reduced at these time-points.

first: H

first: S

last: Zhang

first: CG

last: Buss

first: L

last: Fish

last: Tavazoie

first: SF


title: ChIP-seq and RNA-seq study of human FXR in primary human hepatocytes and microarray analysis of GW4064 versus vehicle treated wild type mouse livers

first: Le

last: Zhan

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition

status: Public on Jul 23 2014

city: Göttingen

first: Carlo

last: Bäjen

address: Am Fassberg 11

department: Molecular Biology

institute: Max Planck Institute for Biophysical Chemistry

summary: Biogenesis of eukaryotic messenger ribonucleoprotein complexes (mRNPs) involves the synthesis, splicing, and 3’-processing of pre-mRNA, and the assembly of mature mRNPs for nuclear export. We mapped 23 mRNP biogenesis factors onto the newly synthesized yeast transcriptome, providing ~10^5-10^6 high-confidence RNA interaction sites per factor.

overall_design: PAR-CLIP data of 23 mRNP biogenesis factors in Saccharomyces cerevisiae

first: Phillipp

last: Torkler


title: Genome-wide mapping of yeast RNA polymerase II termination

city: Baltimore

first: Jeff

last: Corden

state: MD

address: 725 N Wolfe Street

department: Molecular Bio and Gen

institute: JHU

summary: Using a modification of the yeast anchor away and PAR-CLIP protocols, we have mapped the position of Pol II genome-wide in living yeast cells after depletion of components of either the polyadenylation (pA) or non-pA termination complexes. Depletion of Ysh1 from the nucleus does not lead to readthrough transcription. In contrast, depletion of the termination factor Nrd1 leads to widespread runaway elongation of non-pA transcripts. Depletion of Sen1 also leads to readthrough at non-pA terminators but in contrast to Nrd1 this readthrough appears less processive.

overall_design: Examination of PAR-CLIP sequencing data of Pol II after removal of different transcriptional termination factors.

first: Paul

last: Schaughency

first: Jeffry

first: Jonathan

last: Merran


title: Type I IFN responses in rhesus macaques prevent SIV transmission and slow disease progression

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: In acute HIV infection immune activation may provide target cells and drive virus replication, which innate immunity may limit. Thus, the net effects of inflammatory mediators, including type I interferon (IFN-I), are unclear.  Here, we block IFN-I signaling during pathogenic acute SIV infection with an IFN-I receptor antagonist.  Delayed antiviral gene expression, increased SIV reservoir, increased CD4 T cell depletion and accelerated progression to AIDS and death ensue despite decreased T cell activation.  In contrast, IFNα2a treatment initially upregulates antiviral genes and prevents systemic SIV infection after rectal challenge.  Antiviral gene expression normalizes, and infection ensues with fewer transmitted/founder variants.  Continued IFNα2a treatment causes delayed antiviral gene expression, increased SIV reservoir and increased CCR5+ CD4 T cell loss. Thus, the precise timing of antiviral gene expression has a profound impact on disease course.  The benefits of early antiviral activity outweigh the harms of increased immune activation in acute SIV infection.

overall_design: SRA Study accession: SRP034563, BioProject ID:PRJNA231884

first: Netanya

middle: G

last: Sandler

first: Steven

last: Bosinger

first: Jacob

last: Estes

first: Richard

last: Zhu

first: Eli

last: Boritz

first: Doron

last: Levin

first: Sathi

last: Wijeyesinghe

first: Krystelle

middle: N

last: Makamdop

last: del Prete

first: Brenna

last: Hill

first: Nishtha

last: Modi

first: Katherina

last: Timmer

first: Emma

last: Reiss

first: Samuel

last: Darko

first: Eduardo

last: Contijoch

first: John

middle: P

last: Todd

first: Guido

last: Silvestri

first: Martha

last: Nason

first: Brandon

middle: F

last: Keele

first: Srinivas

last: Rao

first: Jerome

last: Langer

first: Jeffrey

last: Lifson

first: Gideon

last: Schreiber

first: Daniel

last: Douek


title: Antifungal drug resistance evoked via RNAi-dependent epimutations

city: Durham

first: Joshua

middle: Aaron

last: Granek

address: Box 3568, 213 Research Drive

department: Department of Biostatistics and Bioinformatics

institute: Duke University School of Medicine

summary: Here we show that the human fungal pathogen Mucor circinelloides develops spontaneous resistance to the antifungal drug FK506 via two distinct mechanisms. One involves Mendelian mutations that confer stable drug resistance and the other via an epigenetic RNA interference (RNAi)-mediated pathway that results in unstable drug resistance. The peptidyl-prolyl isomerase FKBP12 interacts with FK506 to form a complex that inhibits the protein phosphatase calcineurin. In M. circinelloides, inhibition of calcineurin by FK506 blocks the transition to hyphae and enforces yeast growth. Mutations in the fkbA gene encoding FKBP12 or the calcineurin cnbR or cnaA genes confer FK506 resistance, restoring hyphal growth in the presence of this drug. In parallel, RNAi is spontaneously triggered to silence the FKBP12 fkbA gene, giving rise to drug-resistant epimutants. FK506-resistant epimutants readily reverted to the drug-sensitive wild type (WT) phenotype when selection was released by growth without drug. High-throughput small RNA (sRNA) sequencing showed abundant sRNA antisense to fkbA only in the epimutants and not in the WT or revertant strains. Analysis of RNAi mutants revealed components required for the establishment of drug resistant epimutants as well as other factors that constrain or reverse the epimutation pathway. Silencing involves generation of a double stranded RNA trigger intermediate using the fkbA mature mRNA as template. These results uncover a novel epigenetic RNAi-based epimutation mechanism controlling phenotypic plasticity, with possible implications for antimicrobial drug resistance and RNAi regulatory mechanisms in fungi and other eukaryotes.

overall_design: Strand-specific small RNA were sequenced from WT, FK506 resistant epimutants, and FK506 suceptible revertants; there were no replicate samples.

middle: A


title: Small RNAs from four Drosophila melanogaster-subgroup species

city: Stanford

first: Jaaved

last: Mohammed

address: 265 Campus Drive

department: Chemical and Systems Biology

institute: Stanford University

summary: Curration of small RNAs from four melanogaster-subgroup species (Drosophila simulans, Drosophila sechellia, Drosophila erecta, and Drosophila yakuba) for the purpose of non-coding RNA annotation and comparative genomics assessment.

sample_organism:
Drosophila erecta
Drosophila sechellia
Drosophila simulans
Drosophila yakuba

overall_design: Non-replicated small RNA samples from four melanogaster-subgroup species.

first: Alex

middle: S

last: Flynt

first: Eric

last: Lai


title: Differential methylation between mouse embyronic stem cell states

status: Public on Jul 21 2014

city: Pasadena

first: Michael

last: Elowitz

state: Ca

address: 1200 E California Blvd MC 114-96

department: Bioengineering

institute: Caltech

summary: We generated RRBS data between Rex1-high and Rex1-low cells to identify differentially methylated promoters. We observe bimodal methylation levels in both subpopulations, and that Rex1-low cells accumulate increased levels of methylation, frequently as a function of local CpG density

overall_design: We sorted Rex1 high and low cells using a GFP-knockin reporter cell line (kindly provided by Austin Smith), and performed RRBS on the subpopulations

first: Zakary

last: Singer

last: Yong


title: TARBP2 HITS-CLIP

first: Hani

last: Goodarzi

summary: In order to identify TARBP2 binding sites on endogenous RNA, we performed HITS-CLIP on a myc-tagged TARBP2 expressing cell-line (transient transfection)

overall_design: Cells were transfected with tagged TARBP2 vector (Origene) and 48-hr post-transfection, they were subjected to the HITS-CLIP procedure (Licatalosi D, et al. 2008, Nature 456:464-U22)

first: H

first: S

last: Zhang

first: C

last: Buss

first: L

last: Fish

last: Tavazoie


title: DNA-damage induced differentiation of leukemic cells as an anti-cancer barrier

city: Philadelphia

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

department: Pathology

institute: University of Pennsylvania

summary: Here we show that the histone methyltransferase MLL4 (Kmt2d) is required for stem cell activity and an aggressive form of acute myeloid leukemia (AML) harboring the MLL-AF9 oncogene. MLL4 exerts its function by regulating transcriptional programs associated with the anti-oxidant response.

overall_design: The role of Mll4 (Kmt2d) in regulating the transcriptome of primary and transformed hematopoietic stem cells was studied.


title: Comparative phenotypic analysis of the major fungal pathogens Candida parapsilosis and Candida albicans

city: Zürich

first: Markus

last: Schröder

state: Zürich

address: Otto-Stern-Weg 7

department: Biology, Molecular Health Sciences

country: Switzerland

institute: ETH Zürich

summary:
Abstract: Candida parapsilosis and Candida albicans are human fungal pathogens that belong to the CUG clade in the Saccharomycotina. In contrast to C. albicans, relatively little is known about the virulence properties of C. parapsilosis, a pathogen particularly associated with infections of premature neonates. We describe here the construction of  >200 C. parapsilosis strains carrying double allele deletions of transcription factors, protein kinases and species-specific genes.
Two independent deletions were constructed for each target gene. Growth in > 40 conditions was tested, including carbon source, temperature, and the presence of antifungal drugs.  The phenotypes were compared to C. albicans strains with deletions of orthologous transcription factors. We found that many phenotypes are shared between the two species, such as the role of Upc2 as a regulator of azole resistance. Others are unique. For example, Cph2 plays a role in the hypoxic response in C. parapsilosis and not in C. albicans.
We found extensive divergence between the biofilm regulators of the two species. We identified 7 transcription factors and one protein kinase that are required for biofilm development in C. parapsilosis. Only three (Efg1, Bcr1, and Ace2) have similar effects on C. albicans biofilms, whereas Cph2, Czf1, Gzf3 and Ume6 have major roles in C. parapsilosis only.
In addition, two transcription factors (Brg1 and Tec1) with well-characterized roles in biofilm formation in C. albicans do not have the same function in C. parapsilosis. We also compared the transcription profile of C. parapsilosis and C. albicans biofilms. Our analysis suggests the processes shared between the two species are predominantly metabolic.

overall_design: C. parapsilosis mRNA profiles of wild type (WT) at 37 degree celcius in planktonic growth conditions and ace2-/-, cph2-/-, efg1-/-, czf1-/-, ume6-/-, bcr1-/- and WT in biofilm conditions were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: Linda

middle: M

last: Holland

first: Siobhan

last: Turner

first: Heather

last: Taff

first: David

last: Andes

first: Zsuzsanna

last: Grozer

first: Attila

last: Gacser

first: Lauren

last: Ames

first: Ken

last: Haynes

first: Desmond

last: Higgins

first: Geraldine

last: Butler


title: Transcriptome analysis of 'Candidatus Liberibacter solanacearum' in its psyllid vector, Bactericera cockerelli

city: College Station

first: Cecilia

last: Tamborindeguy

address: Heep Center

institute: Texas A&M University

summary: We seqeunced mRNA from the bacterial pathogen 'Candidatus Liberibacter solanacearum" during its association with the psyllid vector Bactericera cockerelli.

overall_design: Total RNA was purified from psyllids,  insect and bacterial rRNAs were depleted. PolyA RNA was purified using Dynabeads. PolyA purified RNA and depleted RNA were sequenced.

first: Freddy

last: Ibanez

first: Julien

last: Levy


title: Transcriptome-Based Analysis of the Pantoea stewartii Quorum-Sensing Regulon and Identification of EsaR Direct Targets

city: Blacksburg

first: Roderick

last: Jensen

address: 970 Washington Street

institute: Virginia Tech

summary:
Introduction: Pantoea stewartii subsp. stewartii is a proteobacterium that causes Stewart’s wilt disease in corn plants. The bacteria form a biofilm
in the xylem of infected plants and produce capsule that blocks water transport, eventually causing wilt. At low cell densities, the quorum-sensing (QS) regulatory protein EsaR is known to directly repress expression of esaR itself as well as the capsular synthesis operon transcription regulator, rcsA, and a 2,5-diketogluconate reductase, dkgA. It simultaneously directly activates expression of genes for a putative small RNA, esaS, the glycerol utilization operon, glpFKX, and another transcriptional regulator, lrhA. At high bacterial cell densities, all of this regulation is relieved when EsaR binds an acylated homoserine lactone signal, which is synthesized constitutively over growth. QS-dependent gene expression is critical for the establishment of disease in the plant.

Objective: However, the identity of the full set of genes controlled by EsaR/QS is unknown. A proteomic approach previously identified around 30 proteins in the QS regulon. In this study, a whole-transcriptome, next-generation sequencing analysis of rRNA-depleted RNA from QS-proficient and -deficient P. stewartii strains was performed to identify additional targets of EsaR.

Result: EsaR-dependent transcriptional regulation of a subset of differentially expressed genes was confirmed by quantitative reverse transcription-PCR (qRT-PCR). Electrophoretic mobility shift assays demonstrated that EsaR directly bound 10 newly identified target promoters. Overall, the QS regulon of P. stewartii orchestrates three major physiological responses: capsule and cell envelope biosynthesis, surface motility and adhesion, and stress response.

overall_design: Comparison of gene expression in two strains of Pantoea stewartii, QS-proficient DC283 ES∆IR (pSVB60) and QS-deficient DC283 ES∆IR (pBBR1MCS-3) to identify those genes that are directly regulated by the master Quorum-sensing regulator, EsaR.

first: Revathy

last: Ramachandran

first: Alison

middle: K

last: Burke

first: Guy

last: Cormier

middle: V

first: Ann

last: Stevens


title: Pharmacologic inhibition of histone demethylation as a therapy for pediatric brainstem glioma [ChIP-seq]

status: Public on Jul 20 2014

first: Rintaro

last: Hashizume

address: 1450 3rd street

department: Neurosurgery

summary: ChIP-Seq analysis of a pediatric human diffuse intrinsic pontine glioma (DIPG) cell line SF8628, harboring the K27M mutation. Goal was to obtain quantitative estimates of K27me3 immunoprecipitation change between vehicle-treated SF8628 cells [dimethyl sulfoxide, (DMSO)] and SF8628 cells incubated with 6 mM GSKJ4 at 24 hours and 72 hours.

overall_design: Three-condition experiment: 72 h GSKJ4-treated cells vs. 24 h GSKJ4-treated cells vs. DMSO-treated cells. Biological replicates: 1 cell line, each with 2 technical replicates per condition.

first: Noemi

last: Andor

first: Yuichiro

last: Ihara

first: Robin

last: Lerner

first: Haiyun

last: Gan

first: Xiaoyue

last: Chen

first: Dong

last: Fang

first: Xi

last: Huang

first: Maxwell

last: Tom

first: Vy

last: Ngo

last: Solomon

first: Sabine

last: Mueller

first: Pamela

last: Paris

first: Zhiguo

last: Zhang

first: Claudia

last: Petritsch

first: Nalin

last: Gupta

first: Todd

last: Waldman

first: C

middle: D

last: James


title: Epigenetic reprogramming in pancreatic acinar cell in the absence of MIST1

city: London

first: Christopher

last: Pin

state: ON

address: 800 Commissioners Road E, 5th floor, Victoria Research labs

department: Pediatrics

institute: Children's Health Research Institute

summary: Epigenetic profile of tissues is reprogrammed under diseased conditions. H3K4Me3 and H3K27Me3 represent active and repressive epigenetic marks, respectively. ChIP-seq is an effective tool to study global protein-DNA interactions. To study global epigenetic differences, we used H3K4Me3 antibody to evaluate its enrichment in pancreatic acinar cells of WT and Mist1-/-  mice followed by next generation sequencing. We found specific hotspots that showed differential enrichment for H3K4Me3 both in WT and Mist1-/-  mice. The data show that pancreatic acinar cells are epigenetically reprogrammed under stressed cellular conditions.

overall_design: Global H3K4Me3 profiling of WT and Mist1-/- pancreatic acinar cells using ChIP-seq.

first: Rashid

last: Mehmood


title: Replication profile from total DNA

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: DNA duplication is intimately connected to setting up post-replicative chromosome structures and events, but molecular details of this coordination are not well understood. A striking example occurs during yeast meiosis, where replication locally influences timing of the DNA double-strand breaks (DSBs) that initiate recombination. We show here that replication-DSB coordination is eliminated by overexpressing Dbf4-dependent Cdc7 kinase (DDK) or removing Tof1 or Csm3, components of the replication fork protection complex (FPC). DDK physically associates with Tof1, and Tof1 is dispensable for replication-DSB coordination if DDK is artificially tethered to replisomes. Furthermore, DDK phosphorylation of the DSB-promoting factor Mer2 is locally coordinated with replication, dependent on Tof1. These findings indicate that DDK recruited by FPC to replisomes phosphorylates chromatin-bound Mer2 in the wake of the replication fork, thus synchronizing replication with an early prerequisite for DSB formation. This may be a general mechanism to ensure spatial and temporal coordination of replication with other chromosomal processes.

overall_design: Forty-eight samples total: 8 time points from WT ARS+, WT ars∆, DDK OP ARS+, DDK OP ars∆,tof1∆ ARS+,tof1∆ ars∆ strains

first: Hajime

last: Murakami

first: Scott

last: Keeney


title: Rec114 ChIP-seq

overall_design: Ninety-six samples total: 12 time points (each time points contains ChIP and input samples) from Rec114-myc ARS+, Rec114-myc ars∆ strains, Rec114-myc tof1∆ARS+ and Rec114-myc tof1∆ ars∆ strains


title: c-Src Modulates Estrogen-Induced Stress and Apoptosis in Estrogen-Deprived Breast Cancer Cells [MCF-7:5C]

status: Public on Jul 18 2014

city: Washington

first: V

middle: Craig

last: Jordan

state: DC

address: 3800 Reservoir Road NW

department: Lombardi Comprehensive Cancer Center

institute: Georgetown University

summary: The emergence of anti-estrogen resistance in breast cancer is an important clinical phenomenon affecting long-term survival in this disease. Identifying factors that convey cell survival in this setting may guide improvements in treatment. Estrogen (E2) can induce apoptosis in breast cancer cells that have been selected for survival after E2 deprivation for long periods (MCF-7:5C cells), but the mechanisms underlying E2-induced stress in this setting have not been elucidated. Here, we report that the c-Src kinase functions as a key adapter protein for the estrogen receptor (ER, ESR1) in its activation of stress responses induced by E2 in MCF-7:5C cells. E2 elevated phosphorylation of c-Src, which was blocked by 4-hydroxytamoxifen (4-OHT), suggesting that E2 activated c-Src through the ER. We found that E2 activated the sensors of the unfolded protein response (UPR), IRE1α (ERN1) and PERK kinase (EIF2AK3), the latter of which phosphorylates eukaryotic translation initiation factor-2α (eIF2α). E2 also dramatically increased reactive oxygen species production and upregulated expression of heme oxygenase HO-1 (HMOX1), an indicator of oxidative stress, along with the central energy sensor kinase AMPK (PRKAA2). Pharmacologic or RNA interference-mediated inhibition of c-Src abolished the phosphorylation of eIF2α and AMPK, blocked E2-induced ROS production, and inhibited E2-induced apoptosis. Together, our results establish that c-Src kinase mediates stresses generated by E2 in long-term E2-deprived cells that trigger apoptosis. This work offers a mechanistic rationale for a new approach in the treatment of endocrine-resistant breast cancer.

overall_design: MCF-7:5C cells were treated with vehicle (0.1% EtOH) as control, E2 (10-9mol/L), 4-OHT (10-6mol/L), E2 (10-9mol/L) plus 4-OHT (10-6mol/L), PP2 (5x10-6mol/L), and E2 (10-9mol/L) plus PP2 (5x10-6mol/L) respectively for 72 hours.

first: Ping

last: Fan

first: Obi

middle: L

last: Griffith

first: Fadeke

last: Agboke

first: Pavana

last: Anur

first: Xiaojun

last: Zou

first: Russell

middle: E

last: McDaniel

first: Karen

last: Creswell

first: Joe

last: Gray

first: Virgil


title: The DNA methylation landscape of human early embryos

city: Hangzhou

first: Hongshan

last: Guo

state: Zhejiang Province

address: No.1369, Wenyixi Road

department: School of Medicine, Zhejiang University

institute: Liangzhu Laboratory

summary: Our data provided a genome-wide DNA methylation landscape of human early development embryos, including human MII oocytes, sperm, zygotes, 2-cell to 8-cell embryos, morula, blastocyst and postimplantation embryos at single base resolution.

overall_design:
In total, 44 samples including biological and technical replicates, from 12 different human embryo development stages were analyzed, including two metaphase II oocytes, two zygotes, three first polar bodies, two second polar bodies, four sperm samples, two 2-cell-stage embryos, two 4-cell-stage embryos, three 8-cell-stage embryos, three morulae, three inner cell masses (ICMs) and three trophectoderms (TEs) seperated from late blastocysts, and three post-implantation embryos.

In addition, 12 different human embryo development stages were analyzed, including metaphase II oocytes, zygotes, first polar bodies, second polar bodies, sperm samples, 2-cell-stage embryos, 4-cell-stage embryos, 8-cell-stage embryos, morulae, inner cell masses (ICMs) and trophectoderms (TEs) seperated from late blastocysts, and post-implantation embryos.

last: Zhu

first: Liying

last: Yan

first: Jie

last: Qiao

first: Fuchou

last: Tang


title: Whole transcriptome sequencing in 274 glioma patients reveals gene fusion profiling and novel candidate fusion genes

city: Beijing

first: Wanlu

last: Ye

state: Beijing

address: Biodynamic Optical Imaging Center

department: Colleage of Life Sciences

institute: Peking University

summary: We detected fusion genes in 274 fresh surgical samples of gliomas using whole transcriptome sequencing. Using this approach we screened a panel of glioma samples and identified a number of activating novel fusion transcripts.

overall_design: Fusion detection in 274 glioma patients

first: Tao

last: Jiang

first: Xiaodong

last: Su

first: Ruiqiang

last: Li


title: Characterization of a bacterial tyrosine kinase in Porphyromonas gingivalis involved in polymicrobial synergy

status: Public on Jul 19 2014

city: Seattle

first: David

middle: A. C.

last: Beck

state: WA

address: Benjamin Hall IRB, Rm 440, UW Box 355014

department: ChemE & eScience Institute

institute: University of Washington

summary: RNA-Seq of wild-type Porphyromonas gingivalis compared to ΔPGN_1524 mutant

overall_design: Illumina based RNA-Seq was used to probe transcriptome differences between wild-type Porphyromonas gingivalis and ΔPGN_1524 mutant

first: Murray

last: Hackett

first: Erik

last: Hendrickson

first: Richard

middle: J

last: Lamont

first: Christopher

last: Wright


title: The regulation of synchronism by abscisic acid-responsive small non-coding RNAs during somatic embryogenesis in larch (Larix leptolepis)

city: beijing

first: junhong

last: zhang

address: Xiangshan Road

institute: Chinese Academy of Forestry

summary:
Small non-coding RNAs (sncRNAs) are emerging as key regulators of embryogenesis. To investigate the roles of sRNAs in regulating synchronism of somatic embryogenesis in Larix leptolepis, we deciphered the endogenous "sRNAome" in synchronous and desynchronous embryos. The 24-nt class sRNAs were overrepresented in both synchronous embryos and desynchronous embryos, accounting for 85.29% and 44.79%. A total of 29 miRNAs were upregulated in synchronous embryos, whereas 59 miRNAs were upregulated in desynchronous embryos. We describe the emerging theme for sncRNAs function: inhibiting the precocious expression, thus regulating the synchronism of somatic embryogenesis.
These findings indicate that larch and possibly other gymnosperms have complex mechanisms of gene regulation involving sRNAs and miRNAs operating transcriptionally and post-transcriptionally during the regulation of synchronism.

overall_design:
One embryogenic cell line of Japanese larch (Larix leptolepis), designated as D878, with a high embryo maturation capacity was used in this study.
Embryogenic callus was induced from immature embryos of Japanese larch on induction medium followed by sub-culture. Calli at the proembryogenic mass III stage were cultured on maturation medium in a dark environment at 25 ± 2°C. Samples were cultured on ABA-plus or ABA-minus maturation medium for 45 days. All samples were snap-frozen in liquid nitrogen, and stored in liquid nitrogen until RNA extraction.

first: Junhong

last: Zhang

first: Liwang

last: Qi


title: Deciphering microRNAs and other small RNAs during the transition of dormant embryo into germinated embryo in larch (Larix leptolepis)

summary:
To investigate the roles of sRNAs in keeping embryo dormancy or germination in Larix leptolepis, we deciphered the endogenous "sRNAome" in dormant and germinated embryos. High-throughput sequencing of the sRNA libraries showed that dormant embryos exhibited a length bias towards 24-nt, while germinated embryos showed a bias towards a 21-nt and/or 22-nt length. Both of proportions for miRNAs to the non-redundant and redundant sRNAs were higher in germinated embryos than those in dormant embryos, while the ratio of unknown sRNAs was higher in dormant embryos than in germinated embryos. The proportion of 21-nt and 22-nt sRNAs increased in germinated embryos, which might attribute to the higher expression level of miRNAs. We identified a total of 160 conserved miRNAs from 39 families, 16 novel miRNAs, and 14 plausible miRNA candidates, of which novel and non-conserved known miRNAs might be the main contributors.
These findings indicate that larch and possibly other gymnosperms have complex mechanisms of gene regulation involving sRNAs and miRNAs operating transcriptionally and post-transcriptionally during embryo dormancy and germination.

overall_design: One embryogenic cell line of Japanese larch (Larix leptolepis), designated as D878, with a high embryo maturation capacity was used in this study. Embryogenic callus were induced from immature embryos of larch on induction medium, followed by sub-culture, and culture on ABA-containing mature medium in a dark environment at 25  2  C. After cultured 45 days in mature medium, embryogenic calli developed into mature somatic embryos. In our study, the samples were harvested at day 57, one sample was collected after mature embryos continued to stay for 12 days on ABA-containing medium, and the other one was harvested after cultured for 12 days on ABA-removing medium. All samples were snap-frozen in liquid nitrogen, and stored in liquid nitrogen until RNA extraction.


title: High-resolution mapping reveals a conserved, widespread, dynamic meiotically regulated mRNA methylation program [Hs]

city: Rehovot

first: Schraga

last: Schwartz

state: Choose a State or Province

address: Herzl 234, Department of Molecular Genetics

institute: WEIZMANN INSTITUTE OF SCIENCE

summary: N6-methyladenosine (m6A) is a common modification of mRNA, with potential roles in fine-tuning the RNA life cycle, but little is known about the pathways regulating this process and its physiological role. Here, we used mass-spectrometry to identify a dense network of proteins physically interacting with METTL3, a core component of the methyltransferase complex, and show that two of them, WTAP and KIAA1429, are required for methylation.  Combining high resolution m6A-Seq with knockdown of WTAP allowed us to define accurate maps, at near single-nucleotide resolution, of sites of mRNA methylation across four dynamic programs in human and mouse, including development, differentiation, reprogramming and immune response. Internal WTAP-dependent methylation sites were largely static across the different surveyed conditions and present in the majority of mRNAs. However, methylations were found at much lower levels within highly expressed mRNAs, and methylation is inversely correlated with mRNA stability, consistent with a role in establishing an overall basal, cell-type invariant, distribution of degradation rates. In addition, we identify thousands of WTAP-independent methylation sites at transcription initiation sites, forming part of the mRNA cap structure. We show that the methylations occur at the first transcribed nucleotide, and find that thousands of transcripts are present in different isoforms differing in the methylation state of the first transcribed nucleotide, a previously unappreciated complexity of the transcriptome. Together, our data sheds new light on the proteomic and transcriptional underpinnings of this epitranscriptomic modification in mammals.

overall_design: Examination of m6A methylation in human Hek293 and A549 cell lines, in human embryonic stem cells (ESCs) undergoing differentiation to neural progenitor cells (NPCs),  in OKMS inducible fibroblasts reprogrammed into iPSC, and upon knockdown of factors using siRNAs or shRNAs.

first: Mumbach

last: Maxwell

first: Eric

last: Lander

first: Aviv

last: Regev


title: Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)

city: Madison

first: Robert

middle: C

last: Landick

state: WI

address: 1550 Linden Dr

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

summary: Efficient microbial conversion of lignocellulosic hydrolysates to biofuels is a key barrier to the economically viable deployment of lignocellulosic biofuels. A chief contributor to this barrier is the impact on microbial processes and energy metabolism of lignocellulose-derived inhibitors, including phenolic carboxylates, phenolic amides (for ammonia-pretreated biomass), phenolic aldehydes, and furfurals. To understand the bacterial pathways induced by inhibitors present in ammonia-pretreated biomass hydrolysates, which are less well studied than acid-pretreated biomass hydrolysates, we developed and exploited synthetic mimics of ammonia-pretreated corn stover hydrolysate (ACSH). To determine regulatory responses to the inhibitors normally present in ACSH, we measured transcript and protein levels in an Escherichia coli ethanologen using RNA-seq and quantitative proteomics during fermentation to ethanol of synthetic hydrolysates containing or lacking the inhibitors. Our study identified four major regulators mediating these responses, the MarA/SoxS/Rob network, AaeR, FrmR, and YqhC. Induction of these regulons was correlated with a reduced rate of ethanol production, buildup of pyruvate, depletion of ATP and NAD(P)H, and an inhibition of xylose conversion. The aromatic aldehyde inhibitor 5‑hydroxymethylfurfural appeared to be reduced to its alcohol form by the ethanologen during fermentation, whereas phenolic acid and amide inhibitors were not metabolized. Together, our findings establish that the major regulatory responses to lignocellulose-derived inhibitors are mediated by transcriptional rather than translational regulators, suggest that energy consumed for inhibitor efflux and detoxification may limit biofuel production, and identify a network of regulators for future synthetic biology efforts.

overall_design: E.coli ethanologen strain GLBRCE1 was grown in 3 media, AFEX corn stover hydrolysate (ACSH), synthetic hydrolysate (SynH) and syntetic hydrolysate with added lignotoxins (SynH_LT).  Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2.  3 biological replicates (independent cultures) were grown in each medium.  RNA samples were obtained at 4 time points, corresponding to exponential (Exp), transitional (Trans), stationary (Stat1) and late stationary (Stat2) growth phases.

middle: H

last: Keating

first: Yaoping

first: Irene

last: Ong

first: Sean

last: McIlwain

first: Eduardo

last: Morales

first: Jeffrey

last: Grass

first: Mary

last: Tremaine

first: William

last: Bothfeld

first: Alan

last: Higbee

first: Arne

last: Ulbrich

first: Allison

last: Balloon

first: Michael

last: Westphall

first: Josh

last: Aldrich

last: Lipton

first: Joonhoon

last: Kim

first: Oleg

last: Moskvin

first: Yury

last: Bukhman

first: Joshua

last: Coon

first: Patricia

last: Kiley

first: Donna

last: Bates


title: Markers of persistent multifunctional memory CD4+ T cells in latent TB infection

city: La Jolla

first: Anna

last: Gerasimova

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

summary: In latent tuberculosis infection (LTBI) spread of the bacteria is contained by a persistent immune response, which includes CD4+ T cells as important contributors. Here we show that TB-specific CD4+ T cells have a characteristic chemokine expression signature (CXCR3+CCR6+CCR4-; Th* cells), and that the overall number of Th* cells is significantly increased in LTBI donors. We have comprehensively characterized the transcriptional signature of Th* cells and find significant differences to conventional Th1, Th17 and Th2 cells, but no major changes between healthy and LTBI donors. Th* cells display linage-specific signatures of both Th1 and Th17 cells, but also have a unique gene expression program including genes associated with susceptibility to TB, enhanced T cell activation, enhanced cell survival, and induction of a cytotoxic program akin to CTL cells. Overall, the gene expression signature of Th* reveals characteristics of cells important in controlling latent infections.

overall_design:
Examination of gene expression in 5 human cell types in healthy and Latent TB infected individuals .

The 'Differentially_expressed_genes.xlsx' contains genes that are differentially expressed in pair-wise comparisons of different cell types and disease groups. The data format/content description is provided in the 'readme.txt'

first: Cecilia

last: Arlehamn

first: Grégory

last: Seumois

first: Bjoern

last: Peters

first: Pandurangan

last: Vijayanand


title: RNA-seq in the broad host range strain Sinorhizobium fredii NGR234 identifies a large set of genes linked to quorum sensing-dependent regulation in the background of a traI and ngrI deletion mutant

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: The α-proteobacterium Sinorhizobium fredii NGR234 has an exceptionally wide host range as it forms nitrogen-fixing nodules with more legumes than any other known microsymbiont. Within its 6.9 Mbp genome it encodes two N-acyl-homoserine-lactone synthase genes (i.e. traI and ngrI) involved in the biosynthesis of two distinct autoinducer I-type molecules. Here we report on the construction of a NGR234-ΔtraI and a NGR234-ΔngrI mutant and the genome wide RNA-seq-based transcriptome analysis in the parent strain and in the two constructed mutants. A high-resolution RNA-seq analysis of early stationary phase cultures in the background of NGR234-ΔtraI suggested that up to 316 genes (4.9% of all predicted genes) were differentially expressed in the mutant vs. the parent strain. Similarly, in the background of NGR234-ΔngrI 466 differentially regulated genes (7.3% of all predicted genes) were identified. A considerable overlap in the gene expression pattern was uncovered between both mutants resulting in a common set of 186 genes which were almost identically regulated. Co-regulated genes that were linked to the ngrI- and the traI-dependent autoinducer regulatory circuits included 53 flagella biosynthesis genes and genes linked to EPS succinoglycan biosynthesis. Among the genes and ORFs that were differentially regulated in NGR234-ΔtraI were those linked to replication of the pNGR234a symbiotic plasmid and cytochrome c-related genes. In the NGR234-ΔngrI mutant biotin and pyrroloquinoline quinone (PQQ) biosynthesis genes were differentially expressed as well as the entire cluster of 21 genes linked to assembly of the NGR234 type three secretion system II (T3SS-II). We also discovered that genes responsible for octopine catabolism in NGR234 are strongly repressed in the presence of high levels of N-acyl-homoserine-lactones (AHLs). Surprisingly, only few truly symbiosis-related genes were identified that appeared to be quorum sensing regulated. Together with nodulation assays, the RNAseq-based findings suggested that QS-dependent gene regulation appears to be of higher relevance during non-symbiotic growth rather than for life within root nodules.

overall_design: In total 12 samples were analyzed (six different treatments with two independent samples), treatment A: NGR234 wild type strain in stationary phase, treatment B: NGR234 traI-mutant strain in stationary phase, treatment C: NGR234 ngrI-mutant strain in stationary phase, treatment D: NGR234 wild type strain in exponential phase, treatment E: NGR234 wild type supplemented with 0.05 µM AHLs in exponential phase, treatment F: NGR234 wild type supplemented with 50 µM AHLs in exponential phase

first: Dagmar

last: Krysciak

first: Mariita

last: Rodriguez Orbegoso

first: Jessica

last: Grote

first: Christian

last: Utpatel

middle: U

first: Lei

last: Li

first: Christel

last: Schmeisser

first: Hari

middle: B

last: Krishnan

first: Wolfgang

middle: R

last: Streit


title: Transcriptomic profiling of HeLa cells infected with Salmonella Typhimurium

summary: We evaluated the transcriptome changes induced by infection with Salmonella (20 hpi, MOI 100).

overall_design: Transcriptmic profiles of HeLa cells infected with Salmonella Typhimurium were generated by deep sequencing, using Illumina HiSeq 2000.

first: Claire

last: Maudet

first: Miguel

last: Mano

first: Ushasree

last: Sunkavalli

first: Malvika

last: Sharan

first: Mauro

last: Giacca

first: Ana

last: Eulalio


title: Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification

first: Robert

last: Landick

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

platform_organism:
Escherichia coli
Escherichia coli K-12

overall_design: Refer to individual Series


title: High-resolution mapping reveals a conserved, widespread, dynamic meiotically regulated mRNA methylation program

first: Schraga

last: Schwartz

first: Mumbach

last: Maxwell

first: Eric

middle: S

last: Lander

first: Aviv

last: Regev


title: Transcriptomic profiling of HeLa cells treated with miR-15a, miR-16, miR-503 and control-miR

first: Konrad

last: Förstner

summary: To have a global picture of the targets of the miR-15 family, we assessed transcriptome changes, by deep-sequencing, of HeLa cells transfected with 3 members of the miR-15 family (miR-15a, miR-16 or miR-503) or a control miRNA (cel-miR-231). We observed a very extensive overlap between the genes down-regulated by these 3 miRNAs, as expected for miRNAs belonging to the same family.

overall_design: transcriptmic profiles of HeLa cells treated miR-15a, miR-16, miR-503 and control-miR  were generated by deep sequencing, using Illumina HiSeq2000.


title: Derivation of endothelial colony forming cells from human pluripotent stem cells

city: New York

first: Olivier

last: Elemento

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

summary: Human induced pluripotent stem (hiPS) cells and human embryonic stem (hES) cells differentiate into cells of the endothelial lineage, but derivation of cells with human umbilical cord blood endothelial colony forming cell (ECFC)-like properties has not been reported. Here we describe a novel serum- and stromal cell-free ECFC differentiation protocol for the derivation of clinically relevant numbers of ECFCs (> 108) from hiPS and hES cells. We identified NRP-1+CD31+ selected cells that displayed a stable endothelial phenotype exhibiting high clonal proliferative potential, extensive replicative capacity, formation of human vessels that inosculated with host vasculature upon transplantation, but lacking in teratoma formation in vivo. We also identified NRP-1-VEGF165-KDR-mediated activation of KDR as a critical mechanism for the emergence and derivation of ECFCs from hiPS and hES cells.  This protocol advances the field by generating highly replicative but stable endothelial cells for use as a potential cell therapy for human clinical disorders.

overall_design: Transcriptome sequencing of undifferentiated day 0 hiPS cells, Day 3 differentiated hiPS-derived mesoderm proginator cells, Day 12 hiPS-derived NRP-1+CD31+ cells, Day 12 H9-hES-derived NRP-1+CD31+ cells and cord blood-derived Endothelial colony forming cells.

first: Nutan

last: Prasain

first: Michael

last: Ginsberg

first: Mervin

last: Yoder


title: Role of microRNAs in the interaction between Salmonella and the host cell


title: Genome-wide translational changes induced by the prion [PSI+]

city: Orsay

last: Namy

address: Rue Gregor Mendel, bat 400

country: France

institute: CNRS, Université Paris-Sud

summary: Prions are infectious proteins that can adopt a structural conformation different from that of the normal protein. This change of conformation is then propagated among other molecules of the same protein. Prions are associated with neurodegenerative diseases in mammals, but are also found in fungi (in the yeast Saccharomyces cerevisiae and the filamentous fungus Podospora anserina), in which they control heritable traits. They are widespread in wild yeast strains, suggesting a biologically important role. [PSI+] is one of the most widely studied yeast prions. It corresponds to an aggregated conformation of the translational release factor, eRF3, which suppresses nonsense codons. [PSI+] modifies cellular fitness, inducing various phenotypes, depending on the genetic background. However, the genes displaying [PSI+]-controlled expression remain largely unknown. We used the recently described ribosome profiling approach to identify genes displaying changes in expression in the presence of [PSI+]. This made it possible to determine the positions of all active ribosomes within the genome, in both [PSI+] and [PSI-] isogenic strains. Comparisons of the translatomes and transcriptomes of the two strains revealed that the primary effect of [PSI+] was to repress genes involved in the stress response. Thus, we provide the first description of the global translational effect of [PSI+] and a new genetic explanation of the phenotypic differences between [PSI-] and [PSI+] strains under stress conditions.

overall_design:
Comparisons of the translatomes and transcriptomes of the two strains.
Comparisons of the translatomes of the two strains : a  [PSI+] strain (two replicates) and a [PSI+] overexpressing SUP35-Cter strain.

first: Agnès

last: Baudin-Baillieu

first: Rachel

last: Legendre

last: Kuchly

first: Isabelle

last: Hatin

first: Stéphane

last: Demais

last: Mestdagh

first: Daniel

last: Gautheret