Browsing by Subject "Chromatin Immunoprecipitation"
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Item Open Access Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma.(PLoS One, 2014) Wortham, Matthew; Guo, Changcun; Zhang, Monica; Song, Lingyun; Lee, Bum-Kyu; Iyer, Vishwanath R; Furey, Terrence S; Crawford, Gregory E; Yan, Hai; He, YipingDespite an emerging understanding of the genetic alterations giving rise to various tumors, the mechanisms whereby most oncogenes are overexpressed remain unclear. Here we have utilized an integrated approach of genomewide regulatory element mapping via DNase-seq followed by conventional reporter assays and transcription factor binding site discovery to characterize the transcriptional regulation of the medulloblastoma oncogene Orthodenticle Homeobox 2 (OTX2). Through these studies we have revealed that OTX2 is differentially regulated in medulloblastoma at the level of chromatin accessibility, which is in part mediated by DNA methylation. In cell lines exhibiting chromatin accessibility of OTX2 regulatory regions, we found that autoregulation maintains OTX2 expression. Comparison of medulloblastoma regulatory elements with those of the developing brain reveals that these tumors engage a developmental regulatory program to drive OTX2 transcription. Finally, we have identified a transcriptional regulatory element mediating retinoid-induced OTX2 repression in these tumors. This work characterizes for the first time the mechanisms of OTX2 overexpression in medulloblastoma. Furthermore, this study establishes proof of principle for applying ENCODE datasets towards the characterization of upstream trans-acting factors mediating expression of individual genes.Item Open Access Co-regulation of nuclear respiratory factor-1 by NFkappaB and CREB links LPS-induced inflammation to mitochondrial biogenesis.(J Cell Sci, 2010-08-01) Suliman, Hagir B; Sweeney, Timothy E; Withers, Crystal M; Piantadosi, Claude AThe nuclear respiratory factor-1 (NRF1) gene is activated by lipopolysaccharide (LPS), which might reflect TLR4-mediated mitigation of cellular inflammatory damage via initiation of mitochondrial biogenesis. To test this hypothesis, we examined NRF1 promoter regulation by NFκB, and identified interspecies-conserved κB-responsive promoter and intronic elements in the NRF1 locus. In mice, activation of Nrf1 and its downstream target, Tfam, by Escherichia coli was contingent on NFκB, and in LPS-treated hepatocytes, NFκB served as an NRF1 enhancer element in conjunction with NFκB promoter binding. Unexpectedly, optimal NRF1 promoter activity after LPS also required binding by the energy-state-dependent transcription factor CREB. EMSA and ChIP assays confirmed p65 and CREB binding to the NRF1 promoter and p65 binding to intron 1. Functionality for both transcription factors was validated by gene-knockdown studies. LPS regulation of NRF1 led to mtDNA-encoded gene expression and expansion of mtDNA copy number. In cells expressing plasmid constructs containing the NRF-1 promoter and GFP, LPS-dependent reporter activity was abolished by cis-acting κB-element mutations, and nuclear accumulation of NFκB and CREB demonstrated dependence on mitochondrial H(2)O(2). These findings indicate that TLR4-dependent NFκB and CREB activation co-regulate the NRF1 promoter with NFκB intronic enhancement and redox-regulated nuclear translocation, leading to downstream target-gene expression, and identify NRF-1 as an early-phase component of the host antibacterial defenses.Item Open Access Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.(Nucleic Acids Res, 2014-10-29) Yardımcı, Galip Gürkan; Frank, Christopher L; Crawford, Gregory E; Ohler, UweDNaseI footprinting is an established assay for identifying transcription factor (TF)-DNA interactions with single base pair resolution. High-throughput DNase-seq assays have recently been used to detect in vivo DNase footprints across the genome. Multiple computational approaches have been developed to identify DNase-seq footprints as predictors of TF binding. However, recent studies have pointed to a substantial cleavage bias of DNase and its negative impact on predictive performance of footprinting. To assess the potential for using DNase-seq to identify individual binding sites, we performed DNase-seq on deproteinized genomic DNA and determined sequence cleavage bias. This allowed us to build bias corrected and TF-specific footprint models. The predictive performance of these models demonstrated that predicted footprints corresponded to high-confidence TF-DNA interactions. DNase-seq footprints were absent under a fraction of ChIP-seq peaks, which we show to be indicative of weaker binding, indirect TF-DNA interactions or possible ChIP artifacts. The modeling approach was also able to detect variation in the consensus motifs that TFs bind to. Finally, cell type specific footprints were detected within DNase hypersensitive sites that are present in multiple cell types, further supporting that footprints can identify changes in TF binding that are not detectable using other strategies.Item Open Access Expression in aneuploid Drosophila S2 cells.(PLoS Biol, 2010-02-23) Zhang, Yu; Malone, John H; Powell, Sara K; Periwal, Vipul; Spana, Eric; Macalpine, David M; Oliver, BrianExtensive departures from balanced gene dose in aneuploids are highly deleterious. However, we know very little about the relationship between gene copy number and expression in aneuploid cells. We determined copy number and transcript abundance (expression) genome-wide in Drosophila S2 cells by DNA-Seq and RNA-Seq. We found that S2 cells are aneuploid for >43 Mb of the genome, primarily in the range of one to five copies, and show a male genotype ( approximately two X chromosomes and four sets of autosomes, or 2X;4A). Both X chromosomes and autosomes showed expression dosage compensation. X chromosome expression was elevated in a fixed-fold manner regardless of actual gene dose. In engineering terms, the system "anticipates" the perturbation caused by X dose, rather than responding to an error caused by the perturbation. This feed-forward regulation resulted in precise dosage compensation only when X dose was half of the autosome dose. Insufficient compensation occurred at lower X chromosome dose and excessive expression occurred at higher doses. RNAi knockdown of the Male Specific Lethal complex abolished feed-forward regulation. Both autosome and X chromosome genes show Male Specific Lethal-independent compensation that fits a first order dose-response curve. Our data indicate that expression dosage compensation dampens the effect of altered DNA copy number genome-wide. For the X chromosome, compensation includes fixed and dose-dependent components.Item Open Access Fluorescent Detection of Chromatin using Functionalized Magnetic Beads on a Digital Microfluidic Device(2022) Bigdeli, YaasEpigenetics is the study of inheritable mechanisms and factors that regulate gene expression. Although the underlying genetic sequence is the same in every cell, it is the epigenome that controls the expression of these genes and accounts for differences in phenotype. Epigenetic controls have clinical ramifications from cancer to autoimmune disorders to psychiatric pathologies. The main tool to study epigenetics is chromatin immunoprecipitation (ChIP), which probes the relationship between the underlying DNA and its structural histone proteins. Standard benchtop ChIP has five major drawbacks: (1) it requires a large input volume of cells, (2) it is very time consuming, work intensive, and low throughput, (3) it suffers from poor chromatin yield and sensitivity, (4) ChIP antibodies can be non-specific, vary by batch, and have low sensitivity, (5) and ChIP performs bulk tissue analysis which loses the granularity necessary to detect cell-to-cell variations. Digital microfluidic biochips (DMFBs) have proven successful at utilizing small volumes of reagents and samples to perform high throughput analyses using a variety of assaying techniques, making them an ideal platform for ChIP adaptation. Droplet manipulation using electrowetting-on-dielectric, in conjunction with magnetic bead control using magnetic field gradients generated by a current running through a wire on the device, provide all the necessary functionality to successfully run ChIP more efficiently on a DMFB. Translation of the benchtop ChIP protocol onto a DMFB addresses the issues facing epigenetic study workflow. The smaller volumes reduce reaction time, decrease reagent and sample use, and increase sensitivity and granularity towards single-cell resolution. Automation makes ChIP less labor consuming. DMFB platforms can be expanded for parallel operation and multiplexing thus increasing throughput. Finally, streamlining all the steps of ChIP onto one device greatly reduces sample loss, thereby expanding the type of studies possible. Herein, specifically modified nucleosomes and human chromatin were detected in a new semi-quantitative fluorescent immunoassay on a DMFB. Furthermore, chromatin was immunoprecipitated using a new targeted biotinylated technique. Successful chromatin capture and detection is a powerful tool for ChIP protocol development. This approach provides a rapid method to screen for antibody specificity and sensitivity as well as a confirmatory check point in the overall ChIP protocol to ensure that the target analyte has been isolated prior to any downstream analyses. Finally, a new modified ‘pull-through’ DMFB design was introduced to enhance the capture and detection of analyte-bound magnetic beads. The contributions from the studies described in this dissertation have provided the first steps towards ChIP implementation on a DMFB: 1) Developed new fluorescent confirmatory chromatin and nucleosome immunoprecipitation assays.
2) Demonstrated that the immunoprecipitation assays were detectible on-chip without any complex downstream analyses nor specialized fluoroscopy instrumentation.
3) Demonstrated that the immunoprecipitation assays performed at higher sensitivity than traditional benchtop ChIP.
4) Developed a single-channel pixel intensity measurement system for semi-quantitative analysis of chromatin and post-translationally modified nucleosomes directly on-chip.
5) Designed a new DMFB for improved capture of magnetic beads with twice the measured signal intensity using a new pull-through droplet scan method with on-chip embedded magnetic controls.
Item Open Access Genome-wide direct target analysis reveals a role for SHORT-ROOT in root vascular patterning through cytokinin homeostasis.(Plant Physiol, 2011-11) Cui, Hongchang; Hao, Yueling; Kovtun, Mikhail; Stolc, Viktor; Deng, Xing-Wang; Sakakibara, Hitoshi; Kojima, MikikoSHORT-ROOT (SHR) is a key regulator of root growth and development in Arabidopsis (Arabidopsis thaliana). Made in the stele, the SHR protein moves into an adjacent cell layer, where it specifies endodermal cell fate; it is also essential for apical meristem maintenance, ground tissue patterning, vascular differentiation, and lateral root formation. Much has been learned about the mechanism by which SHR controls radial patterning, but how it regulates other aspects of root morphogenesis is still unclear. To dissect the SHR developmental pathway, we have determined the genome-wide locations of SHR direct targets using a chromatin immunoprecipitation followed by microarray analysis method. K-means clustering analysis not only identified additional quiescent center-specific SHR targets but also revealed a direct role for SHR in gene regulation in the pericycle and xylem. Using cell type-specific markers, we showed that in shr, the phloem and the phloem-associated pericycle expanded, whereas the xylem and xylem-associated pericycle diminished. Interestingly, we found that cytokinin level was elevated in shr and that exogenous cytokinin conferred a shr-like vascular patterning phenotype in wild-type root. By chromatin immunoprecipitation-polymerase chain reaction and reverse transcription-polymerase chain reaction assays, we showed that SHR regulates cytokinin homeostasis by directly controlling the transcription of cytokinin oxidase 3, a cytokinin catabolism enzyme preferentially expressed in the stele. Finally, overexpression of a cytokinin oxidase in shr alleviated its vascular patterning defect. On the basis of these results, we suggest that one mechanism by which SHR controls vascular patterning is the regulation of cytokinin homeostasis.Item Open Access GREAT improves functional interpretation of cis-regulatory regions.(Nature biotechnology, 2010-05-02) McLean, Cory Y; Bristor, Dave; Hiller, Michael; Clarke, Shoa L; Schaar, Bruce T; Lowe, Craig B; Wenger, Aaron M; Bejerano, GillWe developed the Genomic Regions Enrichment of Annotations Tool (GREAT) to analyze the functional significance of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. GREAT incorporates annotations from 20 ontologies and is available as a web application. Applying GREAT to data sets from chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) of multiple transcription-associated factors, including SRF, NRSF, GABP, Stat3 and p300 in different developmental contexts, we recover many functions of these factors that are missed by existing gene-based tools, and we generate testable hypotheses. The utility of GREAT is not limited to ChIP-seq, as it could also be applied to open chromatin, localized epigenomic markers and similar functional data sets, as well as comparative genomics sets.Item Open Access Loss of tumor suppressor IGFBP4 drives epigenetic reprogramming in hepatic carcinogenesis.(Nucleic acids research, 2018-09) Lee, Ying-Ying; Mok, Myth Ts; Kang, Wei; Yang, Weiqin; Tang, Wenshu; Wu, Feng; Xu, Liangliang; Yan, Mingfei; Yu, Zhuo; Lee, Sau-Dan; Tong, Joanna HM; Cheung, Yue-Sun; Lai, Paul BS; Yu, Dae-Yeul; Wang, Qianben; Wong, Grace LH; Chan, Andrew M; Yip, Kevin Y; To, Ka-Fai; Cheng, Alfred SLGenomic sequencing of hepatocellular carcinoma (HCC) uncovers a paucity of actionable mutations, underscoring the necessity to exploit epigenetic vulnerabilities for therapeutics. In HCC, EZH2-mediated H3K27me3 represents a major oncogenic chromatin modification, but how it modulates the therapeutic vulnerability of signaling pathways remains unknown. Here, we show EZH2 acts antagonistically to AKT signaling in maintaining H3K27 methylome through epigenetic silencing of IGFBP4. ChIP-seq revealed enrichment of Ezh2/H3K27me3 at silenced loci in HBx-transgenic mouse-derived HCCs, including Igfbp4 whose down-regulation significantly correlated with EZH2 overexpression and poor survivals of HCC patients. Functional characterizations demonstrated potent growth- and invasion-suppressive functions of IGFBP4, which was associated with transcriptomic alterations leading to deregulation of multiple signaling pathways. Mechanistically, IGFBP4 stimulated AKT/EZH2 phosphorylation to abrogate H3K27me3-mediated silencing, forming a reciprocal feedback loop that suppressed core transcription factor networks (FOXA1/HNF1A/HNF4A/KLF9/NR1H4) for normal liver homeostasis. Consequently, the in vivo tumorigenicity of IGFBP4-silenced HCC cells was vulnerable to pharmacological inhibition of EZH2, but not AKT. Our study unveils chromatin regulation of a novel liver tumor suppressor IGFBP4, which constitutes an AKT-EZH2 reciprocal loop in driving H3K27me3-mediated epigenetic reprogramming. Defining the aberrant chromatin landscape of HCC sheds light into the mechanistic basis of effective EZH2-targeted inhibition.Item Open Access Pol II docking and pausing at growth and stress genes in C. elegans.(Cell Rep, 2014-02-13) Maxwell, Colin S; Kruesi, William S; Core, Leighton J; Kurhanewicz, Nicole; Waters, Colin T; Lewarch, Caitlin L; Antoshechkin, Igor; Lis, John T; Meyer, Barbara J; Baugh, L RyanFluctuations in nutrient availability profoundly impact gene expression. Previous work revealed postrecruitment regulation of RNA polymerase II (Pol II) during starvation and recovery in Caenorhabditis elegans, suggesting that promoter-proximal pausing promotes rapid response to feeding. To test this hypothesis, we measured Pol II elongation genome wide by two complementary approaches and analyzed elongation in conjunction with Pol II binding and expression. We confirmed bona fide pausing during starvation and also discovered Pol II docking. Pausing occurs at active stress-response genes that become downregulated in response to feeding. In contrast, "docked" Pol II accumulates without initiating upstream of inactive growth genes that become rapidly upregulated upon feeding. Beyond differences in function and expression, these two sets of genes have different core promoter motifs, suggesting alternative transcriptional machinery. Our work suggests that growth and stress genes are both regulated postrecruitment during starvation but at initiation and elongation, respectively, coordinating gene expression with nutrient availability.Item Open Access PPAR-δ is repressed in Huntington's disease, is required for normal neuronal function and can be targeted therapeutically.(Nat Med, 2016-01) Dickey, Audrey S; Pineda, Victor V; Tsunemi, Taiji; Liu, Patrick P; Miranda, Helen C; Gilmore-Hall, Stephen K; Lomas, Nicole; Sampat, Kunal R; Buttgereit, Anne; Torres, Mark-Joseph Manalang; Flores, April L; Arreola, Martin; Arbez, Nicolas; Akimov, Sergey S; Gaasterland, Terry; Lazarowski, Eduardo R; Ross, Christopher A; Yeo, Gene W; Sopher, Bryce L; Magnuson, Gavin K; Pinkerton, Anthony B; Masliah, Eliezer; La Spada, Albert RHuntington's disease (HD) is a progressive neurodegenerative disorder caused by a CAG trinucleotide repeat expansion in the huntingtin (HTT) gene, which encodes a polyglutamine tract in the HTT protein. We found that peroxisome proliferator-activated receptor delta (PPAR-δ) interacts with HTT and that mutant HTT represses PPAR-δ-mediated transactivation. Increased PPAR-δ transactivation ameliorated mitochondrial dysfunction and improved cell survival of neurons from mouse models of HD. Expression of dominant-negative PPAR-δ in the central nervous system of mice was sufficient to induce motor dysfunction, neurodegeneration, mitochondrial abnormalities and transcriptional alterations that recapitulated HD-like phenotypes. Expression of dominant-negative PPAR-δ specifically in the striatum of medium spiny neurons in mice yielded HD-like motor phenotypes, accompanied by striatal neuron loss. In mouse models of HD, pharmacologic activation of PPAR-δ using the agonist KD3010 improved motor function, reduced neurodegeneration and increased survival. PPAR-δ activation also reduced HTT-induced neurotoxicity in vitro and in medium spiny-like neurons generated from stem cells derived from individuals with HD, indicating that PPAR-δ activation may be beneficial in HD and related disorders.Item Open Access RNA-Seq and ChIP-Seq reveal SQSTM1/p62 as a key mediator of JunB suppression of NF-κB-dependent inflammation.(J Invest Dermatol, 2015-04) Zhang, Xiaoling; Jin, Jane Y; Wu, Joseph; Qin, Xiaoxia; Streilein, Robert; Hall, Russell P; Zhang, Jennifer YMice with epidermal deletion of JunB transcription factor displayed a psoriasis-like inflammation. The relevance of these findings to humans and the mechanisms mediating JunB function are not fully understood. Here we demonstrate that impaired JunB function via gene silencing or overexpression of a dominant negative mutant increased human keratinocyte cell proliferation but decreased cell barrier function. RNA-seq revealed over 500 genes affected by JunB loss of function, which included the upregulation of an array of proinflammatory molecules relevant to psoriasis. Among these were tumor necrosis factor α (TNFα), CCL2, CXCL10, IL6R, and SQSTM1, an adaptor protein involved in nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation. Chromatin immunoprecipitation (ChIP)-Seq and gene reporter analyses showed that JunB directly suppressed SQSTM1 by binding to a consensus AP-1 cis element located around 2 kb upstream of SQSTM1-transcription start site. Similar to JunB loss of function, SQSTM1-overexpression induced TNFα, CCL2, and CXCL10. Conversely, NF-κB inhibition genetically with a mutant IκBα or pharmacologically with pyrrolidine dithiocarbamate (PDTC) prevented cytokine, but not IL6R, induction by JunB deficiency. Taken together, our findings indicate that JunB controls epidermal growth, barrier formation, and proinflammatory responses through direct and indirect mechanisms, pinpointing SQSTM1 as a key mediator of JunB suppression of NF-κB-dependent inflammation.