title: ChIP-seq in MEG3+ and MEG3- hIPSCs

summary: In this experiment we sought to identify region with differential PRC2, JARID2, and H3K27me3 occupancy in human induced pluripotent stem cell lines with silenced or expressed MEG3 locus to indirectly determine the effect of this ncRNA on PRC2 function.

overall_design: 8 hIPSC lines, 5 MEG3+ and 3 MEG3-; ChIP-seq for EZH2, JARID2, and H3K27me3. Some done in replicates.

first: Syuzo

last: Kaneko

first: Danny

last: Reinberg


title: ChIP-seq in MRC5 hIPSCs overexpressing MEG3 RNA.

status: Public on Dec 25 2013

city: Philadelphia

first: Roberto

last: Bonasio

state: PA

address: 3400 Civic Center Blvd - SCTR 9-111

department: Cell and Developmental Biology

country: USA

institute: University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This experiment was designed to detect differences in PRC2 occupancy in a human induced pluripotent cell line (MRC5) naturally deficient in MEG3 RNA after lentiviral overexpression of MEG3.

overall_design: MRC5 were transduced with lentiviruses for the overexpression of MEG3 lncRNA or GFP as a control. ChIP-seq was performed with EZH2 and JARID2 antibodies.


title: Regulation of inflorescence architecture by inter-tissue-layer ligand-receptor communication between endodermis and phloem

status: Public on Mar 28 2012

city: Austin

first: Keiko

middle: U

last: Torii

address: 2506 SPEEDWAY

institute: University of Texas at Austin

summary: Inflorescence architecture of Arabidopsis thaliana is regulated by ER-EPFL4/6 signaling module. To analyze the genes governed by this module, the transcriptional profiles of er-2 (allelic to er-106) mutant and epfl4 epfl6 double mutant were investigeted.

overall_design: 9 samples are included in this study. Three biological replicates of 33 d post germination inflorescence tips of er-2  (allelic to er-106, Lease et al., 2001) and epfl4 epfl6 were compared with wild type (Col-0) sample for changes in gene expression.

first: Naoyuki

last: Uchida

first: Jin-Suk

last: Lee

first: Robin

middle: J

last: Horst

first: Hung-Hsueh

last: Lai

first: Ryoko

last: Kajita

first: Tatsuo

last: Kakimoto

first: Masao

last: Tasaka


title: SFMBT1 Functions with LSD1 to Regulate Expression of Canonical Histone Genes and Chromatin-Related Factors

status: Public on Mar 26 2013

type: Expression profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: The C-Terminal Domain of RNA Polymerase II is Modified by Site-Specific Methylation

status: Public on Apr 01 2011

summary: The Carboxy-terminal domain (CTD) of RNA Polymerase II (RNAPII) in mammals undergoes extensive post-translational modification, which is essential for transcriptional initiation and elongation. Here, we show that the CTD of RNAPII is methylated at a single arginine (R1810) by the transcriptional co-activator CARM1. Although methylation at R1810 is present on the hyper-phosphorylated form of RNAPII in vivo, Ser-2 or Ser-5 phosphorylation inhibit CARM1 activity towards this site in vitro, suggesting that methylation occurs before transcription initiation. Mutation of R1810 results in the mis-expression of a variety of snRNAs and snoRNAs, an effect that is also observed in Carm1-/- MEFs.  These results demonstrate that CTD methylation facilitates the expression of select RNAs, perhaps serving to discriminate the RNAPII-associated machinery recruited to distinct gene types.

overall_design: To address the function of RNAPII methylation, we generated Raji cell lines expressing an RNA Polymerase II resistant to α-amanitin and carrying either wild-type R1810 or an arginine to alanine substitution at that same residue, abolishing R1810 methylation of the CTD. In cells cultured in α-amanitin, the α-amanitin-resistant mutants fully replaced the functions of endogenous RNAPII, allowing us to study if gene-expression is affected by the absence of R1810me

first: Robert

last: Sims


title: Molecular profiling of stomatal lineage cell states

status: Public on Nov 08 2011

summary: We initiated a study to investigate the transcriptional profiles associated with cell states of the stomatal lineage. A stem-cell like precursor of stomata, a meristemoid. reiterates asymmetric divisions and renews itself before differentiating into guard cells. The transient and asynchronous nature of the meristemoid has made it difficult to study its molecular characteristics. Through combinatorial use of genetic resources that either arrest or constitutively drive stomatal cell-state progressions due to loss- or gain-of-function mutations in the key transcription factor genes, SPEECHLESS, MUTE, and SCRM, we obtained seedlings highly enriched in pavement cells, meristemoids, or stomata. Here we present transcriptome and genome-wide trends in gene regulation associated with each cell state and identify molecular signatures associated with meristemoids.

overall_design: 12 samples are included in this study. Three biological replicates of 5-dag seedlings of speechless, scrm-D and scrm-D;mute were compared wild type seedlings for changes in gene expression.

first: Lynn

last: Pillitteri

first: Kylee

middle: M

last: Peterson


title: SFMBT1 Functions with LSD1 to Regulate Expression of Canonical Histone Genes and Chromatin-Related Factors [RNA-Seq]

summary: SFMBT1 is a poorly characterized mammalian MBT domain-containing protein homologous to Drosophila SFMBT, a Polycomb group protein involved in epigenetic regulation of gene expression. Here, we show that SFMBT1 regulates transcription in somatic cells and during spermatogenesis through the formation of a stable complex with LSD1 and CoREST.  When bound to its gene targets, SFMBT1 recruits its associated proteins and causes chromatin compaction and transcriptional repression.  SFMBT1, LSD1, and CoREST share a large fraction of target genes including those encoding replication-dependent histones.  Simultaneous occupancy of histone genes by SFMBT1, LSD1, and CoREST is regulated during the cell cycle and correlates with the loss of RNA polymerase II at these promoters during G2, M, and G1. The interplay between the repressive SFMBT1–LSD1–CoREST complex and RNA polymerase II contributes to the timely transcriptional regulation of histone genes in human cells. SFMBT1, LSD1, and CoREST also form a stable complex in germ cells and their chromatin binding activity is regulated during spermatogenesis.

overall_design: RNA-seq in HeLaS3 cells ctrl compared to triple knockdown for SFMBT1, CoREST, and LSD1

first: Jin

last: Zhang


title: SFMBT1 Functions with LSD1 to Regulate Expression of Canonical Histone Genes and Chromatin-Related Factors [ChIP-Seq]

overall_design: ChIP-seq in HeLaS3 at different phases of the cell cycle and primary germ cells at different stages of spermatogenesis using antibodies against endogenous proteins


title: EZH2-RNA interactions in embryonic stem cells

status: Public on Oct 19 2013


title: PCGF Homologs and RYBP Define Functionally Distinct PRC1 Family Complexes

status: Public on Feb 09 2012

summary: The heterogeneous nature of mammalian PRC1 complexes has hindered our understanding of their biological functions. Here, we present a comprehensive proteomic and genomic analysis that uncovered six major groups of PRC1 complexes each containing a distinct PCGF subunit, a RING1A/B ubiquitin ligase, and a unique set of associated polypeptides. These PRC1 complexes differ in their genomic localization and only a small subset co-localize with H3K27me3. Further biochemical dissection revealed that the six PCGF–RING1A/B combinations form multiple complexes through association with RYBP or its homolog YAF2, which prevents the incorporation of other canonical PRC1 subunits such as CBX, PHC and SCM. Although both RYBP/YAF2- and CBX/PHC/SCM-containing complexes compact chromatin, only RYBP stimulates the activity of RING1B toward H2AK119ub1, suggesting a central role in PRC1 function. Knockdown of RYBP in ES cells compromised their ability to form embryoid bodies, likely because of defects in cell proliferation and maintenance of H2AK119ub1 level.

overall_design: ChIP-seq experiments of different PRC1 components were performed either on HA-tagged transgenic stable 293T-REx lines or on endogenous subunits using specific antibodies.

first: Zhonghua

last: Gao


title: Long-term exposure to low-concentrations of Cr(VI) induce DNA damage and disrupt the transcriptional response to benzo[a]pyrene

status: Public on Aug 07 2013

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: Living organisms are exposed on a daily basis to widespread mixtures of toxic compounds. Mixtures pose a major problem in the assessment of health effects because they often generate substance-specific effects that cannot be attributed to a single mechanism.  Two compounds often found together in the environment are the heavy metal chromium and the polycyclic aromatic hydrocarbon benzo[a]pyrene (B[a]P).  We have examined how long-term exposure to a low concentration of Cr(VI) affects the transcriptional response to B[a]P, a second toxicant with an unrelated mechanism of action.   Growth of mouse hepatoma cells for 20 passages in medium with 0.1 or 0.5 uM Cr(VI) increases DNA damage and apoptosis and decreases clonogenic ability.  These cells also show transcriptome changes indicative of increased expression of DNA damage response and repair genes.  In them, B[a]P activates cancer progression pathways, unlike cells never exposed to Cr(VI), where B[a]P activates mostly xenobiotic metabolism pathways.  Cells grown in Cr(VI) for 20 passages and then cultured for an additional 5 passages in the absence of Cr(VI) recover from some but not all the chromium effects.  They show B[a]P-dependent transcriptome changes strongly weighted towards xenobiotic metabolism, similar to those in B[a]P-treated cells that had no previous Cr(VI) exposure, but retain a high level of Cr(VI)-induced DNA damage and silence the expression of DNA damage and cancer progression genes. We conclude that the combined effect of these two toxicants appears to be neither synergistic nor cumulative, generating a toxic/adaptive condition that cannot be predicted from the effect of each toxicant alone.

overall_design: Mouse Hepa-1 cells treated with Cr, Bap, Cr+Bap and untreated were profiled using RNAseq in duplicates.

first: Jerald

middle: L

last: Ovesen

first: Yunxia

last: Fan

first: Jing

last: Chen

first: Alvaro

last: Puga


title: Transcript abundance patterns in Kawasaki disease patients IVIG-resistance

status: Public on Oct 17 2009

city: Tarrytown

first: Wen

last: Fury

state: NY

address: 777 Old Saw Mill River Road

department: Molecular Profiling

institute: Regeneron Pharmaceuticals, Inc.

summary: We compared the abundance of gene transcripts of whole blood RNA between IVIG-resistant and –responsive KD patients to identify biomarkers that might differentiate between these two groups and to generate new targets for therapies in IVIG-resistant KD patients.

overall_design: 48 whole blood samples from 9 healthy age-appropriate controls, 8 IVIG non-responding and 12 IVIG-responding patients at acute and convalescent stages

first: Adriana

middle: H

last: Tremoulet

first: Virginia

middle: E

last: Watson

first: Brookie

middle: A

last: Best

first: Chisato

last: Shimizu

first: Jennifer

last: Hamilton

first: John

middle: T

last: Kanegaye

first: Yi

last: Wei

first: Chiayi

last: Kao

first: Scott

last: Mellis

first: Calvin

last: Lin

first: Jane

middle: C

last: Burns


title: PAR-CLIP for HA-tagged EZH2 in mouse embryonic stem cells

first: Roberto

last: Bonasio

summary: This experiment was designed to indentify RNAs making direct contact with  EZH2 in mouse embryonic stem cells

overall_design: E14 with an integrated transgene encoding HA-EZH2 were pulsed with 4-SU, irradiated with UV, and subjected to HA immunoprecipitation.

first: Syuzo

last: Kaneko

first: Danny

last: Reinberg


title: ChIP-seq for PRC2 components and H3K27me3 in E14 mouse embryonic stem cells

summary: This experiment sought to determine the chromatin structure and PRC2 occupancy at the promoters of all genes in mouse ESCs

overall_design: ChIP-seq for EZH2, SUZ12, and H3K27me3 were performed on WT E14 cells in 2 biological replicates each. In addition H3K27me3 ChIP-seq was also performed on a clone of E14 cells expressing a tagged version of EZH2, which for the purpose of this study was used as replicate #3.


title: Cyclin-dependent kinase 6 is a chromatin-bound cofactor for nuclear factor kappaB-dependent gene expression [Agilent]

status: Public on Dec 31 2013

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

summary: Given the intimate link between inflammation and dysregulated cell proliferation in cancer we investigated cytokine-triggered gene expression in different cell cycle stages. High density microarray analysis revealed that G1 release primes and cooperates with the cytokine-driven gene response. This effect is transmitted through CDK6 which shares the ability to regulate expression of inflammatory genes with its functional homologue CDK4. CDK6 contributes to the regulation of inflammatory gene expression by physical and functional cooperation with the NF-κB subunit p65 in the nucleus. ChIPSeq experiments showed a tight co-recruitment of CDK6 and p65 to enhancers and promoters of many transcriptionally active NF-κB target genes. While CDK6 recruitment to distinct chromatin regions of inflammatory target genes had no effect on histone modifications, it was essential for proper loading of NF-κB p65 to its cognate binding sites and for the function of p65 coactivators such as TRIP6. Furthermore, cytokine-inducible nuclear translocation and chromatin association of CDK6 depends on the kinase activity of TAK1 and p38. These results have widespread biological implications, as aberrant CDK6 expression or activation that is frequently observed in human tumors cooperates with NF-κB to shape the cytokine- and chemokine-repertoire in chronic inflammation and cancer.

overall_design: Four sets of experiments were performed in total (Exp1-4). Within each of these sets biological duplicates (Rep1-2) were included and analyzed. HeLa control cells or cells with established shRNA-mediated knockdown of CDK4 or CDK6 were analyzed. Cells were subjected to cell cycle arrest or were released from the arrested state for 6h. Cells were treated for 30 minutes with Interleukin-1-alpha at the arrested state or after release or were left untreated.

first: Katja

last: Handschick

first: Knut

last: Beuerlein

first: Liane

last: Jurida

first: Helmut

last: Mueller

first: Johanna

last: Soelch

first: Axel

last: Weber

first: Oliver

last: Dittrich-Breiholz

first: Heike

last: Schneider

first: Maren

last: Scharfe

first: Michael

last: Jarek

first: Julia

last: Stellzig

first: Lienhard

last: Schmitz

last: Kracht


title: Cyclin-dependent kinase 6 is a chromatin-bound cofactor for nuclear factor kappaB-dependent gene expression [ChIP-Seq]

summary: Given the intimate link between inflammation and dysregulated cell proliferation in cancer we investigated cytokine-triggered gene expression in different cell cycle stages. Transcriptome analysis revealed that G1 release through CDK6 and CDK4 primes and cooperates with the cytokine-driven gene response. CDK6 physically and functionally interacts with the NF-κB subunit p65 in the nucleus and is found at enhancers and promoters of many transcriptionally active NF-κB target genes. CDK6 recruitment to distinct chromatin regions of inflammatory genes was essential for proper loading of p65 to its cognate binding sites and for the function of p65 coactivators such as TRIP6. Furthermore, cytokine-inducible nuclear translocation and chromatin association of CDK6 depends on the kinase activity of TAK1 and p38. These results have widespread biological implications, as aberrant CDK6 expression or activation that is frequently observed in human tumors cooperates with NF-κB to shape the cytokine- and chemokine-repertoire in chronic inflammation and cancer.

overall_design: 10 samples, five different antibodies for ChIP, no replicates, unstimulated cells as controls


title: RNA seq in two lines of E14 mouse embryonic stem cells

last: Bonasio

summary: This experiment was designed to obtain the polyA+ transcriptome in E14 ESCs

overall_design: PolyA+ RNA was extracted and purified  from two separate clones of E14, which were treated as biological replicate


title: PAR-CLIP for JARID2 in mouse embryonic stem cells

summary: This experiment was designed to identify RNAs making direct contact with JARID2 in mouse embryonic stem cells

overall_design: E14 cells were pulsed with 4-SU, irradiated with UV, and subjected to JARID2 immunoprecipitation.

last: Kaneko


title: SIRT3 functions in the nucleus in the control of stress-related gene expression.

status: Public on Oct 16 2012

summary: SIRT3 is a member of the Sir2 family of NAD+-dependent protein deacetylases that promotes longevity in many organisms. The processed, short form of SIRT3 is a well-established mitochondrial protein whose deacetylase activity regulates various metabolic processes. However, the presence of full-length (FL) SIRT3 in the nucleus and its functional importance remains controversial. Our previous studies demonstrated that nuclear FL-SIRT3 functions as a histone deacetylase and is transcriptionally repressive when artificially recruited to a reporter gene. Here, we report that nuclear FL-SIRT3 is subjected to rapid degradation upon cellular stress, including oxidative stress and UV-irradiation, whereas the mitochondrial, processed form is unaffected. FL-SIRT3 degradation is mediated by the ubiquitin-proteasome pathway, at least partially through the E3 activity of SKP2. Finally, we show by chromatin immunoprecipitation that some target genes of nuclear SIRT3 are derepressed upon the degradation of SIRT3 caused by stress stimuli. Thus, SIRT3 exhibits a previously unappreciated role in the nucleus modulating the expression of some stress-related and nuclear-encoded mitochondrial genes.

overall_design: ChIP-seq with a SIRT3 antibody in untreated, UV-irradiated, and stable SIRT3 knockdown (KD) U2OS cells

first: Toshinori

last: Iwahara

last: Reinberg