etv1 transcription factor
Leads to constitutive phosphorylation of the receptor tyrosine kinase and activation of downstream pathways cell proliferation and survival Although CsA is a competitive inhibitor of PPIase activity, it can complex with enzymatically inactive cyclophilins and inhibit the phosphatase activity of calcineurin. Long non-coding RNAs (lncRNAs) are a diverse class of RNAs that engage in numerous biological processes across every branch of life. Here we show that a 3.7-kilobase lncRNA, terminal differentiation-induced ncRNA (TINCR), controls human epidermal differentiation by a post-transcriptional mechanism. Finally, transcription factor binding analysis suggests that lncRNAs are directly regulating cardiac gene expression during development.-We provide a systematic analysis of lncRNA control of heart development that gives clues to the roles that specific lncRNAs play in fetal and adult hearts. EDEM1 associates with lifespan in animal models, although not humans. This locus was defined by crosses between SJL/J and B10.S mice and contains several candidate genes, including NeST. RNA-protein interactions are central to biological regulation. Xu, J., Nuno, K., Litzenburger, U. M., Qi, Y., Corces, M. R., Majeti, R., Chang, H. Y. RNA structure maps across mammalian cellular compartments. Further, we speculate on additional, yet undiscovered roles that ncRNAs may be playing as molecular scaffolds. Spatial organization of cellular differentiation may be achieved by unique specification of each cell type; alternatively, organization may arise by cells interpreting their position along a coordinate system. Mechanistically, CAF-1 suppression led to a more accessible chromatin structure at enhancer elements early during reprogramming. Hotair inactivation causes H3K4me3 gain and, to a lesser extent, H3K27me3 loss at target genes. View details for DOI 10.1016/j.sbi.2016.01.007, View details for Web of Science ID 000372681200019, View details for PubMedCentralID PMC4785074. At the molecular level, we demonstrate that impaired rRNA synthesis elicits a DNA damage response, and that rDNA damage results in tissue-selective and dosage-dependent effects on craniofacial development. Simultaneous measurement of cell lineage and cell fates is a longstanding goal in biomedicine. The process of cancer metastasis involves a series of sequential and complex steps. Thus, G1 arrest is not always dependent on Rb family members, which illustrates the robustness of cell cycle regulatory networks during differentiation and allows for the identification of candidate pathways to inhibit the expansion of cancer cells with mutations in the Rb pathway. 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. We introduce GenomeSpace (http://www.genomespace.org), a cloud-based, cooperative community resource that currently supports the streamlined interaction of 20 bioinformatics tools and data resources. Free for academic non-profit institutions.Other users need a Commercial license, The protein encoded by this gene is a homeodomain protein that lacks certain conserved residues required for DNA binding. These findings suggest that expression of pseudogenes lncRNAs are actively regulated and constitute functional regulators of inflammatory signaling. The HOX family of homeodomain transcription factors is implicated in specifying site-specific transcriptional programs. HOPX (HOP Homeobox) is a Protein Coding gene. This gene is overexpressed in Skin (13.0), Oral epithelium (11.8), Esophagus (6.6), and Heart (6.6). Comparison of SHAPE reagents for mapping RNA structures inside living cells. Here, we report the isolation of a self-renewing and multipotent human skeletal stem cell (hSSC) that generates progenitors of bone, cartilage, and stroma, but not fat. Long noncoding RNAs (lncRNAs) are an important class of pervasive genes involved in a variety of biological functions. Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells. Increasing negative torsional stress in DNA enhances Satb1 binding and Satb1 stabilizes base unpairing regions against melting by molecular machines. Our integrated approach provides a unique framework for identifying regulatory genes and functional gene sets underlying pancreas development and associated diseases such as diabetes mellitus. 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. Initiation of apopotosis requires the conversion of procaspases to mature caspases. These findings suggest potentially widespread roles for promoter lncRNAs in cell-growth control. Along with genetic and biochemical studies of resident chromatin proteins and their modifying enzymes, mapping of chromatin structure in vivo is one of the main pillars in our understanding of how chromatin relates to cellular processes. In the nucleolus, DDX21 occupies the transcribed rDNA locus, directly contacts both rRNA and snoRNAs, and promotes rRNA transcription, processing and modification. We apply PARS to profile the secondary structure of the messenger RNAs (mRNAs) of the budding yeast Saccharomyces cerevisiae and obtain structural profiles for over 3,000 distinct transcripts. The functional motif reconstructed in a single experiment on our platform uncovers new binding specificities and enriches interpretation of phylogenetic data. HHS Vulnerability Disclosure, Help SChLAP-1, a long non-coding RNA, antagonizes the SWI/SNF complex and coordinates aggressive prostate cancer. Using the known structures of a wide range of mRNAs and noncoding RNAs as benchmarks, we demonstrate that SeqFold outperforms or matches existing approaches in accuracy and is more robust to noise in experimental data. gene expression, shRNA knockdown, CRISPR), VectorBuilder Viral vectors for HOPX (ie. SCENIC enables simultaneous regulatory network inference and robust cell clustering from single-cell RNA-seq data. Here we reveal the RNA structuromes in three compartments, chromatin, nucleoplasm and cytoplasm, in human and mouse cells. Chromosomal looping brings HOTTIP into close proximity to its target genes. A core cancer progression signature was distilled using the increased signaling specificity of downstream oncogene effectors and subjected to network modeling. Facilitating the proximity of CED-3 zymogen molecules was found to induce caspase activation and cell death. Genomic analysis of Treg cells by RNA-sequencing, Foxp3 chromatin immunoprecipitation followed byhigh-throughput DNA sequencing (ChIP-sequencing), and H3K27ac-HiChIP revealed a specific de-repression of the Th2 transcriptional program leading to the generation of Th2-like Treg cells that were unable to suppress extrinsic Th2 cells. View details for DOI 10.1016/j.ceb.2012.12.001, View details for Web of Science ID 000317886100008, View details for PubMedCentralID PMC3633454. Iterative module network analysis nominated and prioritized transcriptional regulators, including diabetes risk genes. We identified several CRISPRa-responsive elements with chromatin features of stimulus-responsive enhancers, including an IL2RA enhancer that harbours an autoimmunity risk variant. This work should accelerate our understanding of mechanisms regulating DE development in mice and humans, and guide further use of ES cells for tissue replacement. (and/or Entrez Gene and/or Ensembl if different), Santa Cruz Biotechnology (SCBT) Antibodies for HOPX, Taconic Biosciences Mouse Models for HOPX, Santa Cruz Biotechnology (SCBT) CRISPR for HOPX, Santa Cruz Biotechnology (SCBT) siRNA for HOPX, SVs/CNVs around HOPX on UCSC Golden Path with GeneCards custom tracks (. A variety of physiological cues, such as adhesion molecules and neurotransmitters, increases intracellular calcium, and artificial manipulations of growth cone calcium levels affect growth cone morphology and neurite outgrowth. Human tumors consist of heterogeneous populations of cells with distinct marker expression and functional properties. To address these challenges, we report HTChIP, an automated microfluidic-based platform for performing high-throughput ChIP screening measurements of 16 different targets simultaneously, with potential for further scale-up. Small RNA-seq and gene expression analysis reveal a miRNA profile of cancer-susceptibility in ATM deficient human mammary epithelial cells, Expression correlates of the full-length androgen receptor and its splicing variants, Gene expression profile in HHUA treated with telmisartan, Expression profiling shows differential functions and provides potential new diagnostic biomarkers for colorectal serrated adenocarcinoma, Comparison of host cell gene expression in cowpox, monkeypox or vaccinia virus infected cells reveals virus-specific regulation of immune response genes, Rotating wall vessel (RWV) grown A549s compared to monolayer grown A549s, Examination of the role of peptidylarginine deiminase 2 (PAD2) in gene expression in MCF-7 breast cancer cells, Differentiating factors of cumulus cells related to quality of the human oocyte [CadoretPart1], Differentiating factors of cumulus cells related to quality of the human oocyte [CadoretPart3], Differentiating factors of cumulus cells related to quality of the human oocyte [CadoretPart2], Gene expression profile in HHUA treated with scytonemin, EpCAM knock-down in FaDu head and neck carcinoma cells, Differentiating factors of cumulus cells related to quality of the human oocyte, HepG2 treated with Polycyclic Aromatic Hydrocarbons (PAHs), Tumor-derived Tissue Factor Activates Coagulation and Enhances Thrombosis in a Mouse Xenograft Model of Human Pancreatic Cancer, Epidermolysis bullosa associated cutaneous SCC fibroblast expression profiling, Differential metabolic effects of insulin detemir versus NPH in patients with type 2 diabetes, Gene expression of the pigmented and non-pigmented epithelia of the ciliary body of human healthy eyes. Understanding these technologies, including their advantages and caveats, and developing them in the future will be essential to progress from description to comprehension of the myriad roles of lncRNAs. DNA methylation regulates lineage-specifying genes in the human vascular system. Inappropriate activation of genes can give rise to birth defects, premature aging, or cancer, among many other diseases. Targeted deletion of Pten in mouse embryonic fibroblasts (MEFs) endowed cells with greater potential to overcome G1 arrest than wild-type MEFs and led to the elevated expression of cyclin D2, which was suppressed by the introduction of PTEN. We further defined a pathway involving GSK3beta and beta-catenin/TCF in PTEN-mediated suppression of cyclin D2 transcription. (and/or Entrez Gene and/or Ensembl if different), Santa Cruz Biotechnology (SCBT) Antibodies for ASCL1, Boster Bio Recombinant Proteins for ASCL1, Santa Cruz Biotechnology (SCBT) CRISPR for ASCL1, Santa Cruz Biotechnology (SCBT) siRNA for ASCL1, SVs/CNVs around ASCL1 on UCSC Golden Path with GeneCards custom tracks (. Telomerase is a ribonucleoprotein polymerase that maintains telomere ends by addition of the telomere repeat TTAGGG. not provided, Benign: Bioinformatic analysis did not detect either nonhuman transcripts to support a viral etiology of SS or recurrently expressed gene fusions, but it did identify 21 SC-associated annotated long noncoding RNAs (lncRNAs). p38 mapmapk Custom zebrafish/c. Here we apply 3'-end sequencing for expression quantification ("3-seq") to discover the gene expression program associated with human photoaging and intrinsic skin aging (collectively termed "skin aging"), and the impact of broadband light (BBL) treatment. By further characterizing RAPs, we discover the presence of ufmylation, a metazoan-specific post-translational modification (PTM), on ribosomes and define its direct substrates. Aire exerted this repressive influence within minutes after recruitment to chromatin and restrained the amplitude of active transcription. Diseases associated with ID2 include Retinoblastoma and Ewing Sarcoma.Among its related pathways are Signaling by NTRKs and Nuclear Events (kinase and transcription factor activation).Gene Ontology (GO) annotations related to this gene include protein dimerization activity and transmembrane Furthermore, the dominant-negative effect of the G228W variant was exerted through recruitment of WT Aire away from active sites of transcription in the nucleus of medullary thymic epithelial cells in vivo. lentivirus, AAV, adenovirus), Custom and pre-made DNA vectors for HOPX (ie. View details for Web of Science ID 000250045000036, View details for Web of Science ID 000247902800016. The ANCR lncRNA is thus required to enforce the undifferentiated cell state within epidermis. 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. This method, Chromatin Isolation by RNA Purification (ChIRP) (Figure 1), is based on affinity capture of target lncRNA:chromatin complex by tiling antisense-oligos, which then generates a map of genomic binding sites at a resolution of several hundred bases with high sensitivity and low background. Here we show that oligomerization of pro-caspases is sufficient to induce proteolytic generation of mature caspase subunits and activation of their cell death activity. The proteins W121A (Liu, J., Chen, C.-M., & Walsh, C.T., 1991a, Biochemistry 30, 2306-2310), H54Q, R55A, F60A, Q111A, F113A, and H126Q were assayed for cis-trans peptidyl-prolyl isomerase (PPIase) activity, their ability to bind the immunosuppressive drug cyclosporin A (CsA), and protein phosphatase 2B (calcineurin) inhibition in the presence of CsA. PRKDC (Protein Kinase, DNA-Activated, Catalytic Subunit) is a Protein Coding gene. DINO was required for p53-dependent gene expression, cell cycle arrest and apoptosis in response to DNA damage, and DINO expression was sufficient to activate damage signaling and cell cycle arrest in the absence of DNA damage. An Integrated Cell Purification and Genomics Strategy Reveals Multiple Regulators of Pancreas Development. Here we review emerging RNA-centric methods to interrogate the intrinsic structure of lncRNAs as well as their genomic localization and biochemical partners. Koh, A. S., Miller, E. L., Buenrostro, J. D., Moskowitz, D. M., Wang, J., Greenleaf, W. J., Chang, H. Y., Crabtree, G. R. m(6)A mRNA methylation sustains Treg suppressive functions. Chen, L., Roake, C. M., Freund, A., Batista, P. J., Tian, S., Yin, Y. In a recent issue of Science, Wang etal. Custom zebrafish/c. ASCL1 (Achaete-Scute Family BHLH Transcription Factor 1) is a Protein Coding gene. An Activity Switch in Human Telomerase Based on RNA Conformation and Shaped by TCAB1. During female mammalian development, XCI is triggered by upregulation of the non-coding Xist RNA from one of the two X chromosomes. Recent advances have enabled transcriptome-wide maps of RNA secondary structure, called 'RNA structuromes'. Brunner, A. L., Beck, A. H., Edris, B., Sweeney, R. T., Zhu, S. X., Li, R., Montgomery, K., Varma, S., Gilks, T., Guo, X., Foley, J. W., Witten, D. M., Giacomini, C. P., Flynn, R. A., Pollack, J. R., Tibshirani, R., Chang, H. Y., van de Rijn, M., West, R. B. Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions. View details for DOI 10.1371/journal.pgen.0020119. The fact that HOTAIR drives chromatin reprogramming genome-wide suggests that long-range regulation by lncRNAs may be a widespread mechanism. The protein activates transcription by binding to the E box (5'-CANNTG-3'). The overall survival at 15 years for patients with tumours in groups 1, 2 and 3 are 79%, 59% and 27%, respectively. Long noncoding RNAs (lncRNAs) are important regulators of cell fate, yet little is known about mechanisms controlling lncRNA expression. We now appreciate that the genome is pervasively transcribed to give rise to thousands of lincRNAs, which are likely to play key roles in the gene regulation of diverse biological states and disease. A., Swetter, S. A., Marinkovich, M. P. Gene expression signature of fibroblast serum response predicts human cancer progression: Similarities between tumors and wounds. Several new analytic strategies have now been developed to improve the interpretation of microarray data. View details for DOI 10.1016/j.stem.2008.02.009. 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. Prevents SRF-dependent transcription either by inhibiting SRF binding to DNA or by recruiting histone deacetylase (HDAC) proteins that prevent transcription by SRF. 2010), Lateral Ganglionic Eminence progenitors(Ma L et. Using a mouse hybrid F1 system, we found that monoallelic DNA accessibility across autosomes was pervasive, developmentally programmed and composed of several patterns. Open chromatin regions are correlated with active regulatory elements in development and are dysregulated in diseases. Simsek, D., Tiu, G. C., Flynn, R. A., Byeon, G. W., Leppek, K., Xu, A. F., Chang, H. Y., Barna, M. Generation of pure GABAergic neurons by transcription factor programming. 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. al. Specific signatures of RNA Tm demarcated the polarity of mRNA open reading frames and highlighted numerous candidate regulatory RNA motifs in 3' untranslated regions. OIP5-AS1 specifies p53-driven POX transcription regulated by TRPC6 in glioma. With the recent discovery of thousands of novel human RNA molecules by high-throughput RNA sequencing, efficient methods to uncover RNA-protein interactions are urgently required. This gene encodes a member of the epidermal growth factor (EGF) receptor family of receptor tyrosine kinases. The chromatin accessibility landscape of primary human cancers. View details for Web of Science ID 000257643400003, View details for PubMedCentralID PMC2492733. Chang, A. S., Atzmon, G., Bergman, A., Chang, H. Y., Barzilai, N. Active chromatin and noncoding RNAs: an intimate relationship, Chromatin Isolation by RNA Purification (ChIRP), Suppression of progenitor differentiation requires the long noncoding RNA ANCR. Pi-ATAC reveals a casual link between transcription factor abundance and DNA motif access, and deconvolute cell types and states in the tumor microenvironment in vivo. The recent discovery of H3K27me3 demethylases suggests that H3K27me3 may dynamically regulate gene expression, but this potential role in mammalian tissue homeostasis remains uncharacterized. Studies in mice suggest that this protein may interact with serum response factor (SRF) and modulate SRF-dependent cardiac-specific gene expression and cardiac development. View details for DOI 10.1016/j.ejca.2008.07.015, View details for Web of Science ID 000261020800031, View details for PubMedCentralID PMC3756930. ZBTB46 is a zinc finger and BTB domain-containing transcription factor, which is expressed by dendritic cells and committed dendritic cell precursors, but not by plasmacytoid dendritic cells, monocytes, macrophages, or other immune cell populations. Conversely, loss of HOTAIR can inhibit cancer invasiveness, particularly in cells that possess excessive PRC2 activity. Here we test these models by analyzing the genome-wide gene expression profiles of primary fibroblast populations from 43 unique anatomical sites spanning the human body. This gene was present in the common ancestor of animals. IGFBP7 (Insulin Like Growth Factor Binding Protein 7) is a Protein Coding gene. Rinn, J. L., Wang, J. K., Liu, H., Montgomery, K., van de Rijn, M., Chang, H. Y. SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin. View details for DOI 10.1016/j.molcel.2013.07.001, View details for Web of Science ID 000322424200005. Biochemical validation of newly identified interactions between TP53-Stau1 and HRAS-CNBP using reciprocal pull-down experiments, both in vitro and in vivo, demonstrates the utility of this approach to study uncharacterized RNA-protein interactions. We show that in human breast cancers, activation of a poor-prognosis "wound signature" is strongly associated with induction of both a mitochondria gene module and a proteasome gene module. Diseases associated with OLFM4 include Pancreatic Cancer and Atrophy Of Prostate.Among its related pathways are Innate Immune System and Adhesion.Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and cadherin binding.An important paralog of this Gene expression profiling of normal prostates and prostate cancer metastases, DNA methylation alterations exhibit striking intra-individual stability and inter-individual heterogeneity across metastatic dissemination, Gene Expression Profiling of Human Pediatric Astrocytomas, Gene expression signatures in anti-FGFR2IIIc monoclonal antibody-treated human colorectal cancer cells. View details for DOI 10.1186/s13059-016-0933-0. After adequate treatment (excision with free margins and radiotherapy), young age and incompletely excised extensive intraductal component are predictors for local recurrence, but many local recurrences can still not be predicted. Hey2, the human homologue of the zebrafish gene gridlock, was selectively expressed in arterial ECs and induced the expression of several arterial-specific genes. hSSCs undergo local expansion in response to acute skeletal injury. Here we demonstrate that DNA hypomethylation at long terminal repeat elements representing the most recent genomic integrations, together with transactivation by OCT4 (also known as POU5F1), synergistically facilitate HERVK expression. The principal cells of stromal tissue are called fibroblasts, a catch-all designation that belies their diversity. View details for DOI 10.1182/blood-2012-04-423061. Ransom, R. C., Carter, A. C., Salhotra, A., Leavitt, T., Marecic, O., Murphy, M. P., Lopez, M. L., Wei, Y., Marshall, C. D., Shen, E. Z., Jones, R., Sharir, A., Klein, O. D., Chan, C. F., Wan, D. C., Chang, H. Y., Longaker, M. T. Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment. Studies in model organisms suggest that aged cells can be functionally rejuvenated, but whether this concept applies to human skin is unclear. 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. A., Chang, H. Y., Corn, J. E., Marson, A. Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations. DOI: http://dx.doi.org/10.7554/eLife.02046.001. Here we show that FADD, which couples Fas to pro-caspase-8, and, Daxx, which couples Fas to the Jun N-terminal kinase pathway, bind independently to the Fas death domain. Here we show a critical role for specific recognition of histone H3 trimethylated at lysine 4 (H3K4me3) by the ING4 PHD finger in mediating ING4 gene expression and tumor suppressor functions. RAMA elements in neural progenitor cells were biallelically accessible in embryonic stem cells but premarked with bivalent histone modifications; one allele was silenced during differentiation. By probing yeast RNA structures at different temperatures, we obtained relative melting temperatures (Tm) for RNA structures in over 4000 transcripts. Cell death activity can be restored by oligomerization of pro-caspase-8 protease domains by two heterologous inducible oligomerization systems. 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. The BAF (SWI/SNF) complex is essential for development, and has been demonstrated to remodel reconstituted chromatin in vitro and to control the accessibility of a few individual regions in vivo. Here we present a novel biochemical approach, in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE), which enables the first global view, to our knowledge, of RNA secondary structures in living cells for all four bases. Genome conformation is central to gene control but challenging to interrogate. Comparison of native deproteinized RNA isolated from cells versus refolded purified RNA suggests that the majority of the RSS information is encoded within RNA sequence. We made a series of discoveries that introduced the important and pervasive roles of long noncoding RNAs in biological regulation. Biological response to 2.5 Gy of X-rays in 3-dimensional skin model, Epi-200. 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). 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 A unique trivalent chromatin signature in the host cells predicts the permissiveness for Ascl1 pioneering activity among different cell types. Schoppmann SF, Jesch B, Friedrich J, Jomrich G, Maroske F, Birner P. Phosphorylation of signal transducer and activator of transcription 3 (STAT3) correlates with Her-2 status, carbonic anhydrase 9 expression and prognosis in esophageal cancer. 7SK physically interacts with the BAF chromatin-remodeling complex, recruits BAF to enhancers and inhibits enhancer transcription by modulating chromatin structure. 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. Chang, H. Y., Takei, K., SYDOR, A. M., Born, T., Rusnak, F., Jay, D. G. ACTIVATION OF CLN1 AND CLN2 G(1) CYCLIN GENE-EXPRESSION BY BCK2, ACTIVE-SITE MUTANTS OF HUMAN CYCLOPHILIN-A SEPARATE PEPTIDYL-PROLYL ISOMERASE ACTIVITY FROM CYCLOSPORINE-A BINDING AND CALCINEURIN INHIBITION. Diseases associated with SFRP2 include Colorectal Cancer and Esophageal Basaloid Squamous Cell Carcinoma.Among its related pathways are ncRNAs involved in Wnt signaling in hepatocellular carcinoma and Signaling by WNT.Gene Ontology (GO) annotations related to this gene include View details for DOI 10.1084/jem.20061864, View details for Web of Science ID 000242339700015, View details for PubMedCentralID PMC2118158. We further found that GREMLIN 1 is expressed by stromal cells in many carcinomas but not in the corresponding normal tissue counterparts that we examined. View details for Web of Science ID 000289035600128, View details for Web of Science ID 000289035600373. Federal government websites often end in .gov or .mil. This gene is overexpressed in Skin - Sun Exposed (Lower leg) (x10.0), Skin - Not Sun Exposed (Suprapubic) (x9.1), and Esophagus - Mucosa (x5.5). lentivirus, AAV, adenovirus), Validated shRNA from LipExoGen - Guaranteed knockdown for any gene - 10 days or less, Custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling, VectorBuilder Custom and pre-made DNA vectors for HOPX (ie. Here, we show that CSN5 isopeptidase activity is essential for breast epithelial transformation and progression. View details for DOI 10.1016/j.immuni.2015.05.004, View details for Web of Science ID 000354827400007. Here, we tested the requirement for the retinoblastoma (Rb) protein and its family members p107 and p130 in G0/G1 arrest and differentiation in mammalian cells. This allows complex gene programs observed in human cancers to be easily recapitulated in the laboratory as models for drug development. View details for DOI 10.1067/mjd.2003.233, View details for Web of Science ID 000184135000021. Transcription factor-induced activation of cardiac gene expression in human c-kit+ cardiac progenitor cells has been reported. A., Farnham, P. J., Segal, E., Chang, H. Y. Decoding global gene expression programs in liver cancer by noninvasive imaging. In the subgroup of lymph node positive patients, the combination signature outperforms the 70-gene signature in multivariate analysis. View details for DOI 10.1016/S0076-6879(06)20010-7. A., Qu, K., Georgiev, P., Chu, C., Akhtar, A., Chang, H. Y. 9)." Here we show that SS and SD activate distinct early transcriptional responses genome-wide that converge on a late symmetric transcriptional program. An abnormality of the sensory perception of sound. We review the evidence linking lncRNAs to diverse human diseases and highlight fundamental concepts in lncRNA biology that still need to be clarified to provide a robust framework for lncRNA genetics. Here we repurpose a high-throughput sequencing instrument to quantitatively measure binding and dissociation of a fluorescently labeled protein to >10(7) RNA targets generated on a flow cell surface by in situ transcription and intermolecular tethering of RNA to DNA. Tsai, M., Manor, O., Wan, Y., Mosammaparast, N., Wang, J. K., Lan, F., Shi, Y., Segal, E., Chang, H. Y. Tumor suppression by the histone demethylase UTX, Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. not specified, Likely Benign: Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element. In epidermis, ANCR loss abolished the normal exclusion of differentiation from the progenitor-containing compartment. al. Clin Exp Metastasis. Multiple alternatively spliced transcript variants have been identified for this gene. Consistently, RNA interference inhibition of UTX led to increased H3K27me3 levels at some HOX gene promoters. Complementation in ESCs shows that WDR5 F266A mutant is unable to accumulate on chromatin, and is defective in gene activation, maintenance of histone H3 lysine 4 trimethylation, and ESC self renewal. At telomeric chromatin, SIRT6 deacetylates H3K9 and is required for the stable association of WRN, the factor that is mutated in Werner syndrome. Zarnegar, B. J., Flynn, R. A., Shen, Y., Do, B. T., Chang, H. Y., Khavari, P. A. Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human beta Cell Function. Grow, E. J., Flynn, R. A., Chavez, S. L., Bayless, N. L., Wossidlo, M., Wesche, D. J., Martin, L., Ware, C. B., Blish, C. A., Chang, H. Y., Pera, R. A., Wysocka, J. Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells, Long Noncoding RNA in Hematopoiesis and Immunity, Systematic Discovery of Xist RNA Binding Proteins. We identify a dominant role for hypoxia, marked by HIF1alpha protein, in the tumor microvenvironment for shaping the regulome in a subset of epithelial tumor cells. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and sequence-specific DNA binding. 1. Diseases associated with NEUROD1 include Maturity-Onset Diabetes Of The Young, Type 6 and Type 2 Diabetes Mellitus.Among its related pathways are Regulation of beta-cell development and Nervous system development.Gene Ontology (GO) annotations related to this gene include The expression of promoter-associated lncRNAs in adult and fetal heart also appears to be related to these epigenetic states. DOI:http://dx.doi.org/10.7554/eLife.00762.001. NeST RNA was found to bind WDR5, a component of the histone H3 lysine 4 methyltransferase complex, and to alter histone 3 methylation at the IFN- locus. This provides a comprehensive RSS map of human coding and non-coding RNAs. Stem cell regulation and hierarchical organization ofhuman skeletal progenitors remain largely unexplored. Chang, H. Y., Ridky, T. W., Kimball, A. RNA has the unique ability to base-pair with itself and other nucleic acids to form complex structures. A fundamental feature of the architecture and functional design of vertebrate animals is a stroma, composed of extracellular matrix and mesenchymal cells, which provides a structural scaffold and conduit for blood and lymphatic vessels, nerves, and leukocytes. View details for DOI 10.1073/pnas.0409462102. Profiling of RWPE cells stably over-expressing ETV1: GSE7702: Comparison of the prostate cancer cell line LNCaP and its androgen insensitive derivative C4-2B: GSE7900: Gene expression in undifferentiated human ES cells - Agilent X-chromosome inactivation (XCI) is a critical epigenetic mechanism for balancing gene dosage between XY males and XX females in eutherian mammals. official website and that any information you provide is encrypted IGFBP7 (Insulin Like Growth Factor Binding Protein 7) is a Protein Coding gene. LncRNAs can also serve as modular scaffolds to recruit the assembly of multiple protein complexes. lentivirus, AAV, adenovirus), Browse OriGene Inhibitory RNA Products For HOPX, VectorBuilder shRNA knockdown vectors for HOPX (ie. Integrated analysis of 365 microarrays spanning nine tissue types predicted fourteen motifs as major regulators of age-dependent gene expression in human and mouse. In turn, lncRNAs may become targets for therapeutic intervention or new tools for biotechnology. Thus, numerous lncRNAs may be modulated as a class in development and disease, notably where Dcr and cMyc act. We find variation consistent with lineage bias toward different developmental branches in multipotent cell types. Using chromatin and transcriptional profiling, we show that these stem-cell populations gain activity within the focal adhesion kinase (FAK) signalling pathway, and that inhibiting FAK abolishes new bone formation. 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. Discovery of stimulation-responsive immune enhancers with CRISPR activation (vol 549, pg 111, 2017). 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 (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. Chan, C. F., Gulati, G. S., Sinha, R., Tompkins, J., Lopez, M., Carter, A. C., Ransom, R. C., Reinisch, A., Wearda, T., Murphy, M., Brewer, R. E., Koepke, L. S., Marecic, O., Manjunath, A., Seo, E., Leavitt, T., Lu, W., Allison Nguyen, Conley, S. D., Salhotra, A., Ambrosi, T. H., Borrelli, M. R., Siebel, T., Chan, K., Schallmoser, K., Seita, J., Sahoo, D., Goodnough, H., Bishop, J., Gardner, M., Majeti, R., Wan, D. C., Goodman, S., Weissman, I. L., Chang, H. Y., Longaker, M. T. Expression of the transcription factor ZBTB46 distinguishes human histiocytic disorders of classical dendritic cell origin. Adler, A. S., Sinha, S., Kawahara, T. L., Zhang, J. Y., Segal, E., Chang, H. Y. Analysis of stable enhancers identified a new, essential role for a constitutively expressed, lineage-restricted ETS-family transcription factor, EHF, in epidermal differentiation. Chang, H. Y., Chi, J. T., Dudoit, S., Bondre, C., van de Rijn, M., Botstein, D., Brown, P. O. Proteases for cell suicide: Functions and regulation of caspases, Dissecting Fas signaling with an altered-specificity death-domain mutant: Requirement of FADD binding for apoptosis but not Jun N-terminal kinase activation, Activation of apoptosis signal regulating kinase 1 (ASK1) by the adapter protein Daxx. National Library of Medicine We demonstrate a crucial role for Xist and the DXZ4-containing boundary in shaping Xi chromosome structure using allele-specific genome-wide chromosome conformation capture (Hi-C) analysis, an assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) and RNA sequencing. This ability of TKO cells to arrest in G0/G1 is associated with the repression of key E2F target genes. An anomaly of the musculoskeletal system, which consists of the bones of the skeleton, muscles, cartilage, tendons, ligaments, joints, and other connective tissue. In this Letter, analysis of steady-state regulatory T (Treg) cell percentages from Il2ra enhancer deletion (EDEL) and wild-type (WT) mice revealed no differences between them (Extended Data Fig. Yamaguchi et al. Using EMBLEM, we define the genetic and epigenomic clonal evolution of hematopoietic stem cells and their progenies in patients with acute myeloid leukemia. Large intervening non-coding RNAs (lincRNAs) are pervasively transcribed in the genome yet their potential involvement in human disease is not well understood. View details for DOI 10.1158/0008-5472.CAN-10-2483, View details for DOI 10.1016/j.stem.2010.11.018. In addition, we stated in the Methods that we observed consistent immunophenotypes of EDEL mice across three founders, but in fact, we observed consistent phenotypes in mice from two founders. Here, we summarize recent studies on XCI, highlight the critical contributions of new technologies and propose a unifying model for XIST function in XCI where modular domains serve as the structural and functional units in both lncRNA-protein complexes and DNA-protein complexes in chromatin.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'. Mediators in Crohns disease influence the gene expression profiles of mesenchymal progenitor cells differentiated into the osteoblastic lineage. Adler, A. S., Lin, M. H., Horlings, H., Nuyten, D. S., Van de Vijver, M. J., Chang, H. Y. Microarray analysis of stem cells and differentiation, Predicting a local recurrence after breast-conserving therapy by gene expression profiling. View details for DOI 10.1016/j.cell.2015.03.025. The results provide a plethora of candidate genes that may mediate DKK1's inhibitory effects on melanocyte function. In particular, genome-wide microarray analysis of differently aged individual organisms or tissues has been used to track the global expression changes that occur during normal aging. lncRNAs have been proposed to modulate gene expression and nuclear architecture, but their physiological functions are still largely unclear. knockout, knockin, CRISPRa, CRISPRi), Virus packaging for HOPX CRISPR vectors (ie. Burkitt Lymphoma Pathogenesis and Therapeutic Targets from Structural and Functional Genomics, Transcriptional profiling of Lung H1299-BRG1 inducible cells, Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor-suppressor in hepatocellular carcinoma (expression), Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor-suppressor in hepatocellular carcinoma, Gene expression analysis of U251 human glioblastoma cell line, CD98 marks a subpopulation of head and neck squamous cell carcinoma cells with stem cell properties, Control shRNA- vs. obscurin shRNA-expressing MCF10A cells, Gene expression and ChIP-chip analysis of U251 human glioblastoma cell line, Gene expression and ChIP-seq analyses of mesenchymal stem cells, osteoblasts and the U2OS osteosarcoma cell line, Microarray analysis of gene expression differences in prostate specific antigen negative (PSA-ve) cells versus PSA+ve cells in human prostate cancer (HPCa) samples, sRSM1 synthetic decoy vs. scrambled transfections in MDA-MB-231 cells, Whole-genome decay rate measurements in MDA-MB-231 cells transfected with HNRPA2B1 siRNAs versus controls, siRNA-mediated HNRPA2B1 knock-down in MDA-MB-231 cells, Systematic Discovery of Structural Elements Governing Mammalian mRNA Stability, The PSA-/lo prostate cancer cells harbor self-renewing long-term tumor-propagating cells that resist castration, Identifying microRNA-mRNA regulatory networks in colorectal cancer by a combination of expression profile and bioinformatics analysis, Small RNA-seq and gene expression analysis reveal a miRNA profile of cancer-susceptibility in ATM deficient human mammary epithelial cells (mRNA). In all inhibition assays with [32P]casein or [Ser(32P)15]RII, the concentration of calcineurin required for measurable phosphatase activity is such that these complexes behave as tight-binding inhibitors of calcineurin, and steady-state kinetics cannot be used to assess inhibition patterns or Ki values. Instead, the TINCR-STAU1 complex seems to mediate stabilization of differentiation mRNAs, such as KRT80. Promoter-bound DDX21 facilitates the release of the positive transcription elongation factor b (P-TEFb) from the 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes. In addition, lack of IRBP expression solely in the thymus, even in the presence of aire expression, is sufficient to trigger spontaneous eye-specific autoimmunity. View details for DOI 10.1101/gad.182121.111, View details for Web of Science ID 000300626800004, View details for PubMedCentralID PMC3289881. 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. The long term goal of my laboratory is to decipher the regulatory information in the human genome for disease diagnosis and therapy. Thus, how one genome encodes thousands of patterns in space and time is of central importance to biology and medicine. Using genetically engineered mice, we found that Rai1 preferentially occupies DNA regions near active promoters and promotes the expression of a group of genes involved in circuit assembly and neuronal communication. Ash2L is a core component of the MLL family histone methyltransferases and has an important role in regulating the methylation of histone H3 on lysine 4. Diseases associated with ASCL1 include Congenital Central Hypoventilation Syndrome and Central Hypoventilation Syndrome, Congenital, 1. Analysis of scATAC-seq profiles from serial tumor biopsies before and after programmed cell death protein 1 blockade identifies chromatin regulators of therapy-responsive T cell subsets and reveals a shared regulatory program that governs intratumoral CD8+ T cell exhaustion and CD4+ T follicular helper cell development. Consistently, TFAP2C, but not p63, is sufficient to initiate surface ectoderm differentiation, and TFAP2C-initiated progenitor cells are capable of maturing into functional keratinocytes. Here we survey variation and dynamics of active regulatory elements genome-wide using longitudinal samples from human individuals. Living cells are treated with the icSHAPE chemical NAI-N3 followed by selective chemical enrichment of NAI-N3-modified RNA, which provides an improved signal-to-noise ratio compared with similar methods leveraging deep sequencing. Here we performed paired single-cell RNA and T cell receptor sequencing on 79,046 cells from site-matched tumors from patients with basal or squamous cell carcinoma before and after anti-PD-1 therapy. Martin, L., Meier, M., Lyons, S. M., Sit, R. V., Marzluff, W. F., Quake, S. R., Chang, H. Y. In addition, various system-wide interventions in old animals can reverse features of aging. The exosome complex recognizes unpaired bases during heat shock to degrade these RNAs, coupling intrinsic structural stabilities to gene regulation. Whyte, J. L., Smith, A. An organizing principle of the diverse cell types in multicellular organisms is their anatomic location. View details for Web of Science ID 000247077500025. THBS2 (Thrombospondin 2) is a Protein Coding gene. al. Although most remain functionally uncharacterized biological "dark matter," lncRNAs have garnered considerable attention for their diverse roles in human biology, including developmental programs and tumor suppressor gene networks. View details for DOI 10.1073/pnas.1805681115, View details for Web of Science ID 000439574700050. View details for DOI 10.1371/journal.pgen.0030089, View details for Web of Science ID 000248349300006, View details for PubMedCentralID PMC1885280. Dynamic gene expression during cellular differentiation is tightly coordinated by transcriptional and post-transcriptional mechanisms. Some genomic regions harbor multiple, regularly spaced Satb1 binding motifs (typical separation ~1 turn of the DNA helix) characterized by highly cooperative binding. View details for DOI 10.1016/j.molcel.2012.08.008. From chromatin to analyzable PCR results only takes one day using HTChIP, as compared to several days up to one week for conventional protocols. . The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. View details for DOI 10.1016/j.molcel.2016.03.013. View details for DOI 10.1073/pnas.162488599. Eukaryotic genomes are packaged into a nucleoprotein complex known as chromatin, which affects most processes that occur on DNA. Here, we apply H3K27ac HiChIP high-resolution contact maps, generated from primary human T-cell subsets (CD4+ Naive, TH17, and Treg), to 21 dermatologic conditions associated with single nucleotide polymorphisms (SNPs) from 106 genome-wide association studies (GWAS). These findings indicate that lincRNAs have active roles in modulating the cancer epigenome and may be important targets for cancer diagnosis and therapy. Sneddon, J. knockout, knockin, CRISPRa, CRISPRi), VectorBuilder Virus packaging for HOPX CRISPR vectors (ie. Arda, H. E., Li, L., Tsai, J., Torre, E. A., Rosli, Y., Peiris, H., Spitale, R. C., Dai, C., Gu, X., Qu, K., Wang, P., Wang, J., Grompe, M., Scharfmann, R., Snyder, M. S., Bottino, R., Powers, A. C., Chang, H. Y., Kim, S. K. Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. After SNP quality controls, 901,470 SNPs remained for analysis. We performed a genome-scale chromatin immunoprecipitation (ChIP)-chip comparison of two modifications (trimethylation of lysine 9 [H3me3K9] and trimethylation of lysine 27 [H3me3K27]) of histone H3 in Ntera2 testicular carcinoma cells and in three different anatomical sources of primary human fibroblasts. Wan, Y., Qu, K., Zhang, Q. C., Flynn, R. A., Manor, O., Ouyang, Z., Zhang, J., Spitale, R. C., Snyder, M. P., Segal, E., Chang, H. Y. Here, we reveal a hierarchical mechanism in the direct conversion of fibroblasts into induced neuronal (iN) cells mediated by the transcription factors Ascl1, Brn2, and Myt1l. Noncoding RNAs (ncRNAs) function with associated proteins to effect complex structural and regulatoryoutcomes. 2011), Oligodendrocyte progenitor cells(Najm FJ et. Existing methods to study proteins associated with a given RNA are laborious and require substantial amounts of cell-derived starting material. UTX removes H3K27me3 and maintains expression of several RB-binding proteins, enabling cell cycle arrest. Stanford is currently not accepting patients for this trial. We used tiled CRISPR activation (CRISPRa) to synthetically recruit a transcriptional activator to sites across large genomic regions (more than 100 kilobases) surrounding two key autoimmunity risk loci, CD69 and IL2RA. The members of one of these complementation groups have mutations in the BCK2 gene. However, it does bind tightly to other ligand-bound EGF receptor family members to form a heterodimer, stabilizing ligand binding and enhancing kinase-mediated activation of The Omni-ATAC protocol enables the interrogation of personal regulomes in tissue context and translational studies. Microarrays have revolutionized molecular biology and enabled biologists to perform global analysis on the expression of tens of thousands of genes simultaneously. We show that immunologic gene sets are the most significantly altered in skin youthfulness (with the most significant gene set p = 2.4x10-5), suggesting the immune system plays an important role in skin youthfulness, a finding that has not previously been recognized. The ability to tether two distinct complexes enables RNA-mediated assembly of PRC2 and LSD1 and coordinates targeting of PRC2 and LSD1 to chromatin for coupled histone H3 lysine 27 methylation and lysine 4 demethylation. In March 2017, dupilumab was approved for use in the treatment of atopic dermatitis (eczema). Little is known about the functional domain architecture of long noncoding RNAs (lncRNAs) because of a relative paucity of suitable methods to analyze RNA function at a domain level. Several serum deprivation early response genes (SDERGs), including the putative tumor suppressor genes SALL2 and MXI1, are required for cessation of DNA synthesis in response to SD and induction of additional SD genes. Our work shows that disease risk variants related to pancreas are significantly enriched in these regulatory regions and reveals previously unrecognized links between endocrine and exocrine pancreas in diabetes risk. We found that HOXC10 is overexpressed in primary carcinomas of the breast, and even more significantly in distant metastasis arising after failed chemotherapy. Wong, D. J., Liu, H., Ridky, T. W., Cassarino, D., Segal, E., Chang, H. Y. In addition, our benchmark indicates that general structure prediction algorithms (e.g. Protein tissue co-expression partners and Interferon- (IFN) treatment preferentially induced even further PD-L1 expression on CD44+ cells and was associated with enhanced IFN receptor expression and phosphorylation of STAT1. It also can predict the progression of a subset of recurring non-muscle-invasive cancers. lentivirus, AAV, adenovirus, MMLV, MSCV, baculovirus), VectorBuilder Custom and pre-made pooled libraries (ie. RAI1 encodes a nuclear protein but little is known about itsmolecular function or the cell types responsible for SMS symptoms. Lee, J. n., Termglinchan, V. n., Diecke, S. n., Itzhaki, I. n., Lam, C. K., Garg, P. n., Lau, E. n., Greenhaw, M. n., Seeger, T. n., Wu, H. n., Zhang, J. As new lncRNAs are being discovered at a rapid pace, the molecular mechanisms of lncRNAs are likely to be enriched and diversified. 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. View details for DOI 10.1016/j.cels.2015.06.003, View details for Web of Science ID 000209925400012, View details for PubMedCentralID PMC4522940. An emerging class of enhancer-like lncRNAs may link chromosome structure to chromatin state and establish active chromatin domains. Essential for the generation of olfactory and autonomic neurons. The cytotopic structuromes substantially expand RNA structural information and enable detailed investigation of the central role of RNA structure in linking transcription, translation and RNA decay. In the past, transcriptomes have largely been parsed by primary sequences and expression levels, but it is now becoming feasible to annotate and compare transcriptomes based on RNA structure. We found that in each of the cell types the two modifications were differentially enriched at the promoters of the two largest classes of transcription factors. Furthermore, factors that interact with lncRNAs in this process are not well characterized.-Utilizing RNA sequencing, we systematically define the contrasting lncRNA expression patterns between fetal and adult heart. Chisholm, K. M., Wan, Y., Li, R., Montgomery, K. D., Chang, H. Y., West, R. B. Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated lncRNAs and novel transcripts. The MALAT-1 noncoding RNA Regulates Cell Mobility by Modulating Gene Expressions, Heterogeneity of Response to Chemotherapy and Recurrence-free Survival in Neoadjuvant Breast Cancer: Results from the I-SPY 1 TRIAL, Identification of genes differentially expressed between control and EHF siRNA transfected HCT116 cells, Fungal allergen extracts-induced gene expression in airway epithelial cells (NCI-H292), Systematic Bias in Genomic Classification Due to Contaminating Normal Tissue in Breast Tumor Samples, Inflammatory activation of airway epithelial cells by pyocyanin. 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