The expression of transcription factors, such as ETV1, Organoids were passaged using mechanical disruption with a P1000 pipette and re-seeded in fresh growth-factor-reduced Matrigel (Corning). Yang, X. L., KHOSRAVIFAR, R., Chang, H. Y., Baltimore, D. ASYMMETRIC RETRACTION OF GROWTH CONE FILOPODIA FOLLOWING FOCAL INACTIVATION OF CALCINEURIN. View details for DOI 10.1158/0008-5472.CAN-05-3115. A quantitative metric of mRNA-lncRNA decoupling revealed that Dcr and cMyc differentially regulate lncRNAs versus mRNAs in diverse cell types and in vivo. Given the importance of Wnt signaling in the maintenance and repair of skin, liposomal Wnt3a may have widespread application in clinical practice. Instead of continuing through meiotic prophase, the cells attempt an abnormal mitotic-like division and die. In the constellation of genes differentially expressed in AE skin compared to healthy control skin, we have identified several potential susceptibility genes that may play a critical role in the pathological condition of AE. We also found that m6A has important roles for inducible degradation of Socs mRNAs in response to IL-7 signalling in order to reprogram naive T cells for proliferation and differentiation. A comparative gene expression profiling of spondyloarthropathy and rheumatoid arthritis using oligonucleotide based microarrays, CPG stimulation for Gene Expression of unmutated B-CLL, miRNA and mRNA expression profile of CLL cells, Microarray analysis of gene expression differences in prostate specific antigen negative (PSA-ve) cells versus PSA+ve cells in LAPC9 and LNCaP prostate cancer (PCa) cells, Expression profiles of X-ray responsive miRNA in human cells [mRNA data], Expression profiles of X-ray responsive miRNA in human cells, B-cell chronic lymphocytic leukemia side population cells, COLO320 cells: siCDX2 vs. non-targeting control, Gene expression profiling of ElonginA knocked-down Hela cells in the presence of Doxorubicin, A1-2 expression analysis of GR activation, Analysis of Gene expression of human Th17 and Th1 clones. View details for DOI 10.1016/j.cell.2015.03.025. Fifteen percent of genetic variants located within ATAC-peaks affected the accessibility of the corresponding peak (local-ATAC-QTLs). Quantitative assessment of the chromatin state reveals that although ecDNA is packaged into chromatin with intact domain structure, it lacks higher-order compaction that is typical of chromosomes and displays significantly enhanced chromatin accessibility. We highlight new approaches for ascribing lncRNA functions and discuss mammalian dosage compensation as a classic example of an lncRNA network coupled to stem cell differentiation. In this review, we discuss the use of genomic technologies to characterize chromatin structure in vivo, with a focus on data from budding yeast and humans. The interaction of a comprehensive library of RNA mutants with stem-loop-binding protein precisely defined the RNA structural and sequence features that govern affinity. Approaches to differentiating pluripotent stem cells (PSCs) into neurons currently face two major challenges-(i) generated cells are immature, with limited functional properties; and (ii) cultures exhibit heterogeneous neuronal subtypes and maturation stages. Regulation of Her2/neu promoter activity by the ETS transcription factor, ER81 Denis G. Bosc. View details for DOI 10.1038/s41588-018-0263-0, View details for Web of Science ID 000451434400012, View details for DOI 10.1101/cshperspect.a034926, View details for Web of Science ID 000451944700003, View details for DOI 10.1038/s41586-018-0650-9, View details for Web of Science ID 000450960000045. PVT1 undergoes developmentally regulated monoallelic expression, and the PVT1 promoter inhibits MYC expression only from the same chromosome via promoter competition. Paralleling the diversity of genetic and protein activities, pathologic human tissues also exhibit diverse radiographic features. After SNP quality controls, 901,470 SNPs remained for analysis. Finally, the decreased immunogenicity of CD44+ cells was partially reversed by antibody blockade of the programmed death 1 (PD-1) receptor, indicating that the differences in PD-L1 expression between CD44+ and CD44- cells are biologically and clinically relevant.Our findings provide a mechanism by which long-lived CD44+ tumor-initiating cells can selectively evade host immune responses and provide rationale for targeting the PD-1 pathway in the adjuvant therapy setting of SCCHN. By in silico screening, we identified candidate therapeutics that at low concentrations inhibit growth of cancer cells expressing high ZNF217. View details for DOI 10.1158/2159-8290.CD-12-0093, View details for Web of Science ID 000306365800042, View details for PubMedCentralID PMC3546490. Gene expression signatures in miR-29c overexpressed gastric cancer cells. Hence, MYC overexpression can induce ROS and SSBs under some conditions, but generally induces widespread DSBs in vivo and in vitro independent of ROS production. Spitale, R. C., Flynn, R. A., Zhang, Q. C., Crisalli, P., Lee, B., Jung, J., Kuchelmeister, H. Y., Batista, P. J., Torre, E. A., Kool, E. T., Chang, H. Y. Diseases associated with GREM1 include Polyposis Syndrome, Hereditary Mixed, 1 and Hereditary Mixed Polyposis Syndrome.Among its related pathways are Signaling by BMP and Angiogenesis (CST).Gene Ontology (GO) annotations related to this gene include cytokine View details for DOI 10.1016/j.ccr.2009.04.010. The prevention of autoimmunity requires the elimination of self-reactive T cells during their development and maturation. Integrated analysis of 365 microarrays spanning nine tissue types predicted fourteen motifs as major regulators of age-dependent gene expression in human and mouse. Cho, S., Xu, J., Sun, R., Mumbach, M. R., Carter, A. C., Chen, Y., Yost, K. E., Kim, J., He, J., Nevins, S. A., Chin, S., Caldas, C., Liu, S., Horlbec, M. A., Lim, D. A., Weissman, J. S., Curtis, C., Chang, H. Y. ATAC Primer Tool for targeted analysis of accessible chromatin. We conclude that while multiple SHAPE technologies are effective at measuring purified RNAs in vitro, acylimidazole reagents NAI and NAI-N3 give markedly greater signals with lower background than 1M7 for in vivo measurement of the RNA structurome. The six SNPs were interrogated by MassARRAY in a replication group (n=436) with confirmation of rs6975107, an intronic region of KCND2 (potassium voltage-gated channel, Shal-related family member 2) (Pgenotype=0.023). The Daxx apoptotic pathway is sensitive to both Bcl-2 and dominant-negative JNK pathway components and acts cooperatively with the FADD pathway. Skin biopsies from sun-protected inner arm were subjected to 3'-end sequencing for expression quantification, with results verified by quantitative reverse transcriptase-polymerase chain reaction. By gene expression profiling, an imatinib-responsive signature specific to dcSSc was identified (P < 10(-8)). The IP address used for your Internet connection is part of a subnet that has been blocked from access to PubMed Central. We also show that in NPCs, the Xi chromosome lacks active/inactive compartments and topologically associating domains (TADs), except around genes that escape XCI. However, despite the potential importance of long non-coding RNAs to the cancer field, no comprehensive survey of long non-coding RNA expression across various cancers has been reported. Diseases associated with IGFBP7 include Retinal Arterial Macroaneurysm With Supravalvular Pulmonic Stenosis and Diabetic Angiopathy.Among its related pathways are Cellular responses to stimuli and Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Rinn, J. L., Kertesz, M., Wang, J. K., Squazzo, S. L., Xu, X., Brugmann, S. A., Goodnough, L. H., Helms, J. Importantly, single-cell and genome-wide expression analyses showed that fibroblast- and hepatocyte-derived iN cells not only induced a neuronal transcriptional program, but also silenced their donor transcriptome. al. Acts synergistically with FOXN4 to specify the identity of V2b neurons rather than V2a from bipotential p2 progenitors during spinal cord neurogenesis, probably through DLL4-NOTCH signaling activation. A., Chang, H. Y. Gender was the most significant attributable source of variation. 7SK occupies enhancers and super enhancers genome wide in mouse and human cells, and it is required to limit enhancer-RNA initiation and synthesis in a manner distinct from promoter pausing. However, whether the T cell response to checkpoint blockade relies on reinvigoration of pre-existing tumor-infiltrating lymphocytes or on recruitment of novel T cells remains unclear2-4. Center for Personal Dynamic Regulome (2014 - 2024), Member, Stanford Diabetes Research Center (2018 - Present), Member, American Academy of Arts and Sciences (2020), Member, National Academy of Sciences (2020), Investigator, Howard Hughes Medical Institute (2018), NAS Award in Molecular Biology, National Academy of Science (2018), Member, National Academy of Medicine (2017), Outstanding Investigator Award, National Cancer Institute (2016), Paul Marks Prize for Cancer Research, Memorial Sloan Kettering Cancer Institute (2015), Judson Daland Prize, American Philosophical Society (2014), Montagna Lecture, Society for Investigative Dermatology (2012), Salvador E. Luria Lecture, Massachusetts Institute of Technology (2012), Alfred Marchionini Research Prize, Alfred Marchionini Foundation (2011), CE.R.I.E.S. We propose that such a secondary network of self-antigen-expressing stromal cells may help reinforce immune tolerance by preventing the maturation of autoreactive T cells that escape thymic negative selection. The enzyme consists of a protein component with reverse transcriptase activity, encoded by this gene, and an RNA component which serves as a template for the telomere repeat. Taken together, our findings illustrate how disruption in general regulators that compromise nucleolar homeostasis can result in tissue-selective malformations. [provided by RefSeq, Feb 2009]. Alterations in tumour necrosis factor signaling pathways associated with cytotoxicity and resistance to taxanes in tumour cells. Translatome of Jurkat cells: control vs. stress treatment. The ANCR lncRNA is thus required to enforce the undifferentiated cell state within epidermis. N(6)-Methyladenosine (m(6)A) modification is hypothesized to control processes such as RNA degradation, localization, and splicing. RNA structures in human, mouse, fly, yeast and bacterial cells are read out at single-nucleotide resolution, revealing tertiary contacts and RNA-protein interactions. We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. Integrative analysis with global gene expression patterns in wild-type, Sirt6-/-, and double Sirt6-/- RelA-/- cells reveals the epistatic relationships between Sirt6 and RelA in shaping diverse temporal patterns of gene expression. A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation. VIDEO ABSTRACT. These changes were accompanied by a decrease in somatic heterochromatin domains, increased binding of Sox2 to pluripotency-specific targets and activation of associated genes. To explore EC specialization on a global scale, we used DNA microarrays to determine the expression profile of 53 cultured ECs. PRKDC (Protein Kinase, DNA-Activated, Catalytic Subunit) is a Protein Coding gene. miR-204: a novel therapeutic target, Transcriptome analysis of highly metastatic cell line, The Leukemia-associated Mllt10/Af10- Dot1l, dedicated b-catenin coactivators essential for intestinal homeostasis, A six-gene signature predicts survival of patients with localized pancreatic ductal adenocarcinoma. Targeted perturbations of cell cycle or transcription factor signalling evoke stimulus-specific changes in this observed variability. Here we develop a genetically dissectible mouse model of mandibular distraction osteogenesis-which isa process that is used in humans to correct an undersized lower jawthat involves surgically separating the jaw bone, whichelicits new bone growth in the gap. Leukemia cutis may clinically mimic many inflammatory dermatoses. Recently we described SLAMS (stepwise linkage analysis of microarray signatures), a novel method that can prospectively identify genetic regulators of gene expression signatures in cancer. For more information, please contact Joanne Otani, (650) 721 - 2372. View details for DOI 10.1371/journal.pgen.0030089, View details for Web of Science ID 000248349300006, View details for PubMedCentralID PMC1885280. A test for transitive RNAi, extension of the RNAi effect to sequences 5' of the target region that has been observed in Caenorhabditis elegans, was unable to detect this phenomenon in human cells. Z., Chen, X. n., Gil, I. P., Ameen, M. n., Sallam, K. n., Rhee, J. W., Churko, J. M., Chaudhary, R. n., Chour, T. n., Wang, P. J., Snyder, M. P., Chang, H. Y., Karakikes, I. n., Wu, J. C. Functional significance of U2AF1 S34F mutations in lung adenocarcinomas. Our results uncover the multifaceted role of DDX21 in multiple steps of ribosome biogenesis, and provide evidence implicating a mammalian RNA helicase in RNA modification and Pol II elongation control. This protein has no ligand binding domain of its own and therefore cannot bind growth factors. Thus, this lncRNA regulates epigenetic marking of IFN--encoding chromatin, expression of IFN-, and susceptibility to a viral and a bacterial pathogen. Drosophila achaete-scute homolog 1,downregulated in differentiating neuroblastoma cells. Sun, L., Fazal, F. M., Li, P., Broughton, J. P., Lee, B., Tang, L., Huang, W., Kool, E. T., Chang, H. Y., Zhang, Q. C. Enhancer Connectome Nominates Target Genes of Inherited Risk Variants from Inflammatory Skin Disorders. The resulting alteration in gene expression also causes anti-tumorigenic RNAs to bind to and be stabilized by HEXIM1. SDERGs are coordinately repressed in many types of human cancers compared to their normal counterparts, and repression of SDERGs predicts increased risk of cancer progression and death in human breast cancers. SPI1 (Spi-1 Proto-Oncogene) is a Protein Coding gene. This study identified a novel set of candidate skin youthfulness genes demonstrating differences between SY and non-SY group, including pleckstrin homology like domain family A member 1 (PHLDA1) (p = 2.4x10-5), a follicle stem cell marker, and hyaluronan synthase 2-anti-sense 1 (HAS2-AS1) (p = 0.00105), a non-coding RNA that is part of the hyaluronan synthesis pathway. Widely expressed. viral and non-viral vectors), VectorBuilder Virus packaging for HOPX shRNA knockdown vectors (ie. These results highlight regulatory sequences of lncRNA genes as potential disease-associated DNA elements. Discovery of stimulation-responsive immune enhancers with CRISPR activation. The process of cancer metastasis involves a series of sequential and complex steps. Here we introduce Protein-indexed Assay of Transposase Accessible Chromatin with sequencing (Pi-ATAC) that combines single-cell chromatin and proteomic profiling. We develop a resource with which to visualize the interplay of RNA-protein interactions, RNA modifications and RNA structure and predict both direct and indirect reader proteins of RNA modifications. Our data suggest that BMP antagonists may be important constituents of tumor stroma, providing a favorable microenvironment for cancer cell survival and expansion in many cancers. Similarly, human lncRNA HOTAIR can affect PRC2 occupancy on hundreds of genes genome-wide( 3,12,13), but how specificity is achieved is unclear. The Sir2 deacetylase regulates chromatin silencing and lifespan in Saccharomyces cerevisiae. Expression of the TGFbeta-responsive signature was examined in skin biopsies from 17 dSSc, seven limited SSc (lSSc), three morphea patients, and six healthy controls. We are particularly fascinated by HOTAIR, the first known lincRNA that can regulate the chromatin state of genes on distantly located chromosomes. The transcription factor ZNF217 is a candidate oncogene in the amplicon on chromosome 20q13 that occurs in 20% to 30% of primary human breast cancers and that correlates with poor prognosis. These studies shed light on key mechanisms of XCI, such as XIST coating of the X-chromosome, recruitment of DNA, RNA and histone modification enzymes, and compaction and compartmentalization of the inactive X. From transcription to splicing, RNA localization, translation, and decay, RNA is intimately involved in regulating every step of the gene expression program, and is thus essential for health and understanding disease. DOI: http://dx.doi.org/10.7554/eLife.02046.001. Diseases associated with ETV5 include Acoustic Neuroma and Charcot-Marie-Tooth Disease, Axonal, Type 2Dd.Among its related pathways are IL12-mediated signaling events and IL12 signaling mediated by STAT4.Gene Ontology (GO) annotations related to this gene include DNA-binding View details for DOI 10.4161/cc.9.17.13122, View details for Web of Science ID 000281621700004, View details for PubMedCentralID PMC3066151. The importance of these modes of regulation is underscored by the newly recognized roles of long RNAs for proper gene control across all kingdoms of life. Integrating various components of the epigenome from these multiomics measurements allows the interrogation of cellular heterogeneity in addition to the discovery of molecular connectivity maps between the genome and its functional output. The distal-specific gene HOXA13 is continually required to maintain the distal-specific transcriptional program in adult fibroblasts, including expression of WNT5A, a morphogen required for distal development. Aging, Rejuvenation, and Epigenetic Reprogramming: Resetting the Aging Clock. In a recent issue of Science, Wang etal. Impairment of translation initiation is also evident in primary medulloblastomas harboring mutations in DDX3X, further highlighting DDX3's role in this process. 2011), Oligodendrocyte precursor cells(Sundberg M et. SWANSON, S. K., Born, T., ZYDOWSKY, L. D., Cho, H. J., Chang, H. Y., Walsh, C. T., Rusnak, F. Freeman Spogli Institute for International Studies, Institute for Computational and Mathematical Engineering (ICME), Institute for Human-Centered Artificial Intelligence (HAI), Institute for Stem Cell Biology and Regenerative Medicine, Stanford Institute for Economic Policy Research (SIEPR), Stanford Woods Institute for the Environment, Office of VP for University Human Resources, Office of Vice President for Business Affairs and Chief Financial Officer, Maternal & Child Health Research Institute (MCHRI), Directed Reading in Stem Cell Biology and Regenerative Medicine, DOI 10.1146/annurev-biochem-051410-092902, DOI 10.1146/annurev.biochem.78.071107.134639. Effect of Genetic Variant in miR-196a-2 in MCF-7 cells, Gene expression changes in PBMCs from metabolic syndrome patients after acute intake of phenol-rich virgin olive oil, Down-regulation of SFRP1 in a mammary epithelial cell line, Effect of heteronemin on gene expression profiles in chronic myelogenous K562 leukemia cells, miR-17 seed family specific targets in two Hodgkin lymphoma cell lines, Activation of Host Wound Responses in Breast Cancer Microenvironment, Multiomics study to identify virulence factors of Rickettsia prowazekii revealed its adaptive mutation capabilities, Scavenger receptor B2 is a cellular receptor for enterovirus 71, Endometrial gene expression analysis at the time of embryo implantation in women with unexplained infertility, Laughter specific genes and laughter sensitive genes, Human keratinocytes exposed to tungsten carbide and tungsten carbide cobalt nanoparticles and cobalt chloride, Molecular characterization of head and neck cancer cell model genomes, Comparative transcription profiling of peripheral blood mononuclear cells from vasculitis patients, Iodide effect on mRNA expression levels of genes related to immunological function in cultured human thyroid follicles, Detection of Treatment-Induced Changes in Signaling Pathways in GI Stromal Tumors using Transcriptomic Data, Runx1 (Aml1) knockdown in AMkL Meg-01 cells, Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis, The kinase TNIK is an essential activator of Wnt target genes, HER2-positive breast cancer cells resistant to trastuzumab and lapatinib lose reliance upon HER2 and are sensitive to the multitargeted kinase inhibitor sorafenib, BxPC-3 cells: growth in different nutrients, Impact of RNA degradation on gene expression profiling, Human osteoblast treated with chemotherapy-treated bone marrow stromal cell conditioned media, Human osteoblast treated with recombinant TGF-beta, Expression profiles of human osteoblasts directly and indirectly damaged by chemotherapy, Genome-Wide Expression Profiling Deciphers Host Responses Altered during Dengue Shock Syndrome and Reveals the Role of Innate Immunity in Severe Dengue, Effects of dexamethasone on human skeletal muscle and adipose tissue, Control vs. HMEC-1 cells treated with 100ng/ml TNF-alpha for 4h and 24h, Propionibacterium acnes as a frequent inflammatory agent involved in prostate cancer, Identification of LATS transcriptional targets in HeLa cells using whole human genome oligonucleotide micorarray, Genopal: a novel platform for focused microarray analysis, Effects of retinoids on estrogen-receptor-positive and -negative breast carcinoma cells: mRNA profiling, Over-expression of hsa-miR-221 in JSC1 cells and identification of miRNA targets expressed in a panel of B-cell lines, Transcription repression of miR-221 leads to p27 expression in PEL, ChIP-chip from HCT116 cells treated with MMS and LNCaP cells with ATF3, Expression profiles of epicardial and subcutaneous adipose tissue, Genes regulated by high calcium medium in parathyroid tissue explants from patients with primary hyperparathyroidism, Effects of retinoids on estrogen-receptor-positive and -negative breast carcinoma cells: mRNA and miRNA profiling, Chronic Active B Cell Receptor Signaling in Diffuse Large B Cell Lymphoma, Expression consequences of decoy vs scrambled oligonucleotides harboring AAAA[AGT]TT motif in MBA-MD-231 cell line, ELK1 and NFYA knockdown in MBA-MD-231 cell line, Decoy vs Scrambled and siRNA vs Mock Transfected MBA-MD-231 Cell Line, Control of gene expression by the Retinoic acid-related Orphan Receptor alpha in HepG2 human hepatoma cells, Effect of exercise on gene expression profile in unfractionated peripheral blood leukocytes, Human primary subcutaneous preadipocytes: Control vs PBMC co-culture, Dissection of human fibroblast populations by lung regions: genomic differences and functional pathway analysis, Subcutaneous adipose tissue (SAT) gene expression patterns between weight control and regaining weight subjects, BRCA1 Haploinsufficiency Leads to Altered Expression of Genes Involved in Cellular Proliferation and Development, Identification of LY6K target genes in bladder cancer, Gene expression profiles of bladder cancer cell lines, Identification of miR-145 or miR-133a target genes in bladder cancer, Identification of miR-489 or miR-504 target genes in head and neck cancer, Gene expression profile of fresh human acute myeloid leukemia cells exposed ex vivo to AS602868, Effect of valproic acid on hematopoiesis: A functional profiling and cell phenotyping approach, Gene expression profiles of oxaliplatin resistant colorectal cancer and ovarian cancer cell lines, Identification of miR-145 or miR-133a target genes in squamous cell carcinoma, Direct generation of induced pluripotent stem cells from human non-mobilized blood, Bifidobacterium bifidum BF-1 Suppresses Helicobacter pylori-Induced genes in Human Epithelial Cells, A Gene Expression Signature for Chemoradiosensitivity of Colorectal Cancer Cells, Identification of cis- and trans-acting factors involved in the localization of MALAT-1 to nuclear speckles, Whole Blood Cell Gene Expression Profiling in Patients with Coronary Artery Disease from the Cathgen Registry, Whole Blood Cell Gene Expression Profiling in Patients with Coronary Artery Disease from the PREDICT Trial, Whole Blood Cell Gene Expression Profiling in Patients with Coronary Artery Disease (Homo sapiens), Efficacy of anti-TNF biologic agent, infliximab, for RA patients using transcriptome analysis of white blood cells, Gene expression signatures for human iPS cell lines, Mutated KRAS induces overexpression of DUSP4, a MAP-kinase phosphatase, and SMYD3, a histone methyltransferase, in rectal carcinomas. View details for DOI 10.1016/j.cell.2017.05.022. However, how these new genetic subtypes of cancers should be treated is unknown. All Rights Reserved. Gupta, R. A., Shah, N., Wang, K. C., Kim, J., Horlings, H. M., Wong, D. J., Tsai, M., Hung, T., Argani, P., Rinn, J. L., Wang, Y., Brzoska, P., Kong, B., Li, R., West, R. B., van de Vijver, M. J., Sukumar, S., Chang, H. Y. Prevents SRF-dependent transcription either by inhibiting SRF binding to DNA or by recruiting histone deacetylase (HDAC) proteins that prevent transcription by SRF. A., Verhaak, R. G., Hu, M., Furnari, F. B., Chang, H. Y., Ren, B., Bafna, V., Mischel, P. S. Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Rfam classification and This information enabled experimental recapitulation, functional assessment and mechanistic elucidation of the wound signature in breast epithelial cells. In melanoma, we identify HEXIM1, a transcription elongation regulator, as a melanoma tumor suppressor that responds to nucleotide stress. View details for DOI 10.1038/sj.jid.5700636. This website is intended for pathologists and laboratory personnel but not for patients. Consequently, HERVK is transcribed during normal human embryogenesis, beginning with embryonic genome activation at the eight-cell stage, continuing through the emergence of epiblast cells in preimplantation blastocysts, and ceasing during human embryonic stem cell derivation from blastocyst outgrowths. A., Haag, D., Ang, C. E., Tang, Y., Flores, Q., Mall, M., Wapinski, O., Li, M., Ahlenius, H., Rubenstein, J. L., Chang, H. Y., Buylla, A. X-chromosome inactivation (XCI) is a critical epigenetic mechanism for balancing gene dosage between XY males and XX females in eutherian mammals. Diseases associated with HOPX include Choriocarcinoma and Mesenteric Vascular Occlusion. Surprisingly, forced activation of an ESC-like gene expression program in adult epithelial cells can reprogram them into human cancer stem cells and achieve pathologic self-renewal. In addition to membrane delimited organelles, proteins and RNAs can organize themselves into specific domains. Award, Chanel Research and Technology (2010), Early Career Scientist, Howard Hughes Medical Institute (2009-2015), Elected Member, American Society for Clinical Investigation (2009), Senior Scholar Award in Aging, Ellison Medical Foundation (2009), Vilcek Prize for Creative Promise, Vilcek Foundation (2009), New Faculty Award, California Institute for Regenerative Medicine (2008-2013), Research Scholar Award, American Cancer Society (2007-2010), Scholar Award, Damon Runyon Cancer Research Foundation (2006-2008), Clinical Scientist Career Development Award (K08), NIH (2004-2009), Physician-Scientist Career Development Award, Dermatology Foundation (2004), Young Investigator Award, American Academy of Dermatology (2003), Editorial Board, Molecular Cell (2014 - Present), Fellowship: Stanford University Dept of Dermatology (2004) CA, Residency: Stanford University Dermatology Residency (2003) CA, Internship: Santa Clara Valley Medical Center Dept of Medicine (2001) CA, Board Certification: American Board of Dermatology, Dermatology (2004), Medical Education: Harvard Medical School (2000) MA, Cancer > Cutaneous (Dermatologic) Oncology, A Pilot Study of Imatinib Mesylate in Steroid Refractory Chronic Graft Versus Host Disease. (62)EEEE(65) plays a stabilizing role in the formation of a ternary complex between Nef, the MHC-I cytoplasmic domain, and AP-1; Thrombin Stimulation of c-jun mRNA expression showed biphasic responses with two peaks after 1 and 8 hours of exposure. Keratolytic Agents, Small Molecule, Antineoplastic Agents, Endogenous agonist for retinoic acid receptors; inducer of neuronal differentiation, Endogenous retinoic acid receptor agonist, C/ANM_004316.4(ASCL1):c.52C>A (p.Pro18Thr), C/CGCANM_004316.4(ASCL1):c.151CAG[13] (p.Gln62_Ala63insGln), INFRAME_INSERTION,FIVE_PRIME_UTR | INFRAME_DELETION,FIVE_PRIME_UTR, G/TNM_004316.4(ASCL1):c.121G>T (p.Ala41Ser). Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma. The canonical Dgcr8-Dcr-miRNA pathway is required for robust lncRNA transcriptional initiation and elongation. Here, we show that the PVT1 promoter has a tumor-suppressor function that is independent of PVT1 lncRNA. (2017) reveal an additional function of a host-encoded long non-coding RNA (lncRNA) in regulating viral expression by binding a host metabolic enzyme to enhance its catalytic activity. Oncogenes are commonly amplified on particles of extrachromosomal DNA (ecDNA) in cancer1,2, but our understanding of the structure of ecDNA and its effect on gene regulation is limited. Homozygous loss-of-function mutations in AIRE cause autoimmune polyglandular syndrome type 1 (APS 1), which manifests in a classic triad of hypoparathyroidism, adrenal insufficiency, and candidiasis. The protein functions as a transcription co-activator, enhancing the DNA-binding activity of serum response factor, a protein required for the induction of genes by growth and differentiation factors. However, purification of DE in mammals has not been achieved, limiting the molecular "definition" of endoderm, and hindering our understanding of DE development and attempts to produce endoderm from sources such as embryonic stem (ES) cells. RNA structure is important for RNA function and regulation, and there is growing interest in determining the RNA structure of many transcripts. These results are a valuable resource from which multiple future studies may be undertaken to better understand the mechanisms that promote skin youthfulness in humans. Allelic choice at RAMA elements was stable across cell generations and bookmarked through mitosis. Although many expression signatures show promise in predicting patient prognosis or response to therapies, the usefulness of the signatures in understanding the underlying mechanisms of cancer has not been fully exploited. The genes comprising this fibroblast common serum response are coordinately regulated in many human tumors, allowing us to identify tumors with gene expression signatures suggestive of active wounds. The transcriptional memory of Hox genes poses both an opportunity and a challenge for regenerative medicine. Gene expression profile of classical Hodgkin lymphoma according to Epstein-Barr infection status, A murine-ES like state facilitates transgenesis and homologous recombination in human pluripotent stem cells, Identification of genes differentially expressed between control and SMILE siRNA transfected HeLa cells, Transcriptional response to hypoxia of normal and rheumatoid arthritis synovial fibroblasts. Gene expression profiles of MCF7 with with the following NR ligands: estradiol/E2 (ER agonist), AM580 (RARA agonist), CD437 (RARG agonist), ATRA (RARA/RARG agonist), GW0742 (PPARD agonist), R5020 (PGR agonist), and dexamethasone (GR/NR3C1 agonist). Ribonucleic acid (RNA) secondary structure prediction continues to be a significant challenge, in particular when attempting to model sequences with less rigidly defined structures, such as messenger and non-coding RNAs. 9d. Transcription factor that plays a key role in neuronal differentiation: acts as a pioneer transcription factor, accessing closed chromatin to allow other factors to bind and activate neural pathways. The forced loss of Epstein Barr virus from Burkitt's lymphoma cells: uncomplemented cells vs BART miRNA complemented cells. Dynamic gene expression during cellular differentiation is tightly coordinated by transcriptional and post-transcriptional mechanisms. Prior studies mapping RNA occupancy at chromatin have revealed substantial insights (15,16), but only at a single gene locus at a time. View details for DOI 10.1084/jem.20061864, View details for Web of Science ID 000242339700015, View details for PubMedCentralID PMC2118158. Our analysis also identifies many motifs whose target sets are predicted to be regulated by a common microRNA, suggesting a connection between transcriptional and post-transcriptional control processes. Although lincRNAs are expressed in immune cells, their functions in immunity are largely unexplored. Ghosh, R. P., Shi, Q. n., Yang, L. n., Reddick, M. P., Nikitina, T. n., Zhurkin, V. B., Fordyce, P. n., Stasevich, T. J., Chang, H. Y., Greenleaf, W. J., Liphardt, J. T. A Mutation in the Transcription Factor Foxp3 Drives T Helper 2 Effector Function in Regulatory T Cells. The data show that m(6)A-U pairing in the double-stranded context is accompanied by the methylamino group rotating from its energetically preferred syn geometry on the Watson-Crick face to the higher-energy anti conformation, positioning the methyl group in the major groove. The entire experimental protocol takes 5 d to complete, and sequencing and data analysis take an additional 6-8 d. PARS was developed using the yeast genome as proof of principle, but its approach should be applicable to probing RNA structures from different transcriptomes and structural dynamics under diverse solution conditions. A., Sdhof, T. C., Wernig, M. Transcription coactivator and lncRNA duet evoke Hox genes, Gpr124 is essential for blood-brain barrier integrity in central nervous system disease. View details for DOI 10.1016/j.immuni.2015.05.004, View details for Web of Science ID 000354827400007. N6-methyladenosine (m6A) is the most common and abundant messenger RNA modification, modulated by 'writers', 'erasers' and 'readers' of this mark. We apply scATAC-seq to obtain chromatin profiles of more than 200,000 single cells in human blood and basal cell carcinoma. View details for Web of Science ID 000076007100056. Diseases associated with GREM1 include Polyposis Syndrome, Hereditary Mixed, 1 and Hereditary Mixed Polyposis Syndrome.Among its related pathways are Signaling by BMP and Angiogenesis (CST).Gene Ontology (GO) annotations related to this gene include cytokine A. TFAP2C-and p63-Dependent Networks Sequentially Rearrange Chromatin Landscapes to Drive Human Epidermal Lineage Commitment. Ilik, I. Important deviation from the archetype is also observed, usually as a consequence of unique regulatory mechanisms at special genomic loci. The bladder T-IC subpopulation was defined functionally by its enriched ability to induce xenograft tumors in vivo that recapitulated the heterogeneity of the original tumor. My group has substantial experience in epigenetics and RNA biology, including invention of new methods for epigenomic profiling, map RNA occupancy on chromatin, and define RNA structures genome-wide. A unique trivalent chromatin signature in the host cells predicts the permissiveness for Ascl1 pioneering activity among different cell types. Satpathy, A. T., Brown, R. A., Gomulia, E., Briseno, C. G., Mumbach, M. R., Pan, Z., Murphy, K. M., Natkunam, Y., Chang, H. Y., Kim, J. This analysis included two mice whose genotypes were incorrectly assigned. Atypical homeodomain protein which does not bind DNA and is required to modulate cardiac growth and development. Thus, by serving as key intermediates that transmit information from higher order chromosomal looping into chromatin modifications, lincRNAs may organize chromatin domains to coordinate long-range gene activation. The merging of chemistry with genomics is sure to open the door to genome-wide exploration of RNA structure and function. An important paralog of this gene is ASCL2. Many of these genes, including genes with a role in immune responses, lipid homeostasis, and epidermal differentiation, are localized on chromosomal regions previously linked to AE.Through genome-wide expression profiling, we were able to discover a distinct reciprocal expression pattern of induced inflammatory genes and repressed lipid metabolism genes in skin from AE patients. A., Qu, K., Georgiev, P., Chu, C., Akhtar, A., Chang, H. Y. We suggest that a spatial distribution of calcineurin activity within the growth cone can regulate motility and direct outgrowth. We found that a large number of genes of ZNF transcription factors were bound by both KAP1 and H3me3K9 in normal and cancer cells. By probing yeast RNA structures at different temperatures, we obtained relative melting temperatures (Tm) for RNA structures in over 4000 transcripts. Duren, Z., Chen, X., Zamanighomi, M., Zeng, W., Satpathy, A. T., Chang, H. Y., Wang, Y., Wong, W. H. An Activity Switch in Human Telomerase Based on RNA Conformation and Shaped by TCAB1. View details for DOI 10.1083/jcb.201003048, View details for Web of Science ID 000284737200014, View details for PubMedCentralID PMC2983066. 9d). Gene expression analysis of individual hSSCs reveals overall similarity between hSSCs obtained from different sources and partially explains skewed differentiation toward cartilage in fetal and iPSC-derived hSSCs. Here, by integrating ultrastructural imaging, long-range optical mapping and computational analysis of whole-genome sequencing, we demonstrate the structure of circular ecDNA. Diseases associated with THBS2 include Intervertebral Disc Disease and Back Pain.Among its related pathways are Diseases associated with O-glycosylation of proteins and Metabolism of proteins.Gene Ontology (GO) annotations related to this gene include calcium ion binding and heparin binding.An This has enabled the creation of faithful laboratory models of human cancer types, identified specific drugs that can target these cancers, and revealed the hierarchy of transcriptional programs involved in the generation of cancer stem cellsthe cells that continually repopulate a tumor or its metastases. The functional motif reconstructed in a single experiment on our platform uncovers new binding specificities and enriches interpretation of phylogenetic data. Involved in the regulation of neuroendocrine cell development in the glandular stomach (By similarity). The eigenstrat method showed no stratification. Here we show that the deletion of m6A 'writer' protein METTL3 in mouse T cells disrupts T cell homeostasis and differentiation. Consistent with these findings, inhibitors of CDK7 reverse HOXC10-mediated drug resistance in cultured cells. Dcr loss in mouse embryonic stem cells led unexpectedly to decreased levels of hundreds of lncRNAs. Here, we present HiChIRP, a method leveraging bio-orthogonal chemistry and optimized chromosome conformation capture conditions, which enables interrogation of chromatin architecture focused around a specific RNA of interest down to approximately ten copies per cell. The recent discovery of a large number of histone demethylases suggests a central role for these enzymes in regulating histone methylation dynamics. al. B., Hastie, T., Tibshirani, R., Sorlie, T., Dai, H. Y., He, Y. D., Van't Veer, L. J., Bartelink, H., van de Rijn, M., Brown, P. O., van de Vijver, M. J. Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. The generation of defined populations of functionally mature human GABAergic neurons represents an important step toward enabling the study of diseases affecting inhibitory synaptic transmission. Although only 2% of the genome encodes protein, RNA is transcribed from the majority of the genetic sequence, suggesting a massive degree of cellular functionality is programmed in the noncoding genome. How BMDCs are recruited to the tumor and their contribution to the tumor vasculature is poorly understood. To achieve high selectivity within the crowded cellular milieu the cell utilizes scaffolding complexes whose role is to bring molecules in proximity thereby controlling and enhancing intermolecular interactions and signaling events. We found that regions of accessible chromatin (ATAC-peaks) are co-accessible at kilobase and megabase resolution, consistent with the three-dimensional chromatin organization measured by in situ Hi-C in T cells. Disease-causing mutationsthat impair Aire-induced activation also impair the protein'srepressive function, which indicates dual roles for Aire. 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