Promoter and enhancer RNAs regulate chromatin reorganization and activation of miR-10b/HOXD locus, and neoplastic transformation in glioma.

[1]  L. Mirny,et al.  Transcription shapes 3D chromatin organization by interacting with loop extrusion , 2022, bioRxiv.

[2]  L. Mirny,et al.  Dynamics of CTCF and cohesin mediated chromatin looping revealed by live-cell imaging , 2021, bioRxiv.

[3]  Rafael Riudavets Puig,et al.  JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles , 2021, Nucleic Acids Res..

[4]  Yuting He,et al.  Promising Advances in LINC01116 Related to Cancer , 2021, Frontiers in Cell and Developmental Biology.

[5]  J. Peters,et al.  Genome folding through loop extrusion by SMC complexes , 2021, Nature Reviews Molecular Cell Biology.

[6]  Jing Li,et al.  Effects of signaling pathway inhibitors on hematopoietic stem cells , 2020, Molecular medicine reports.

[7]  Yingyi Wang,et al.  TGF-β1 modulates temozolomide resistance in glioblastoma via altered microRNA processing and elevated MGMT , 2020, Neuro-oncology.

[8]  Anna M. Krichevsky,et al.  Glioblastoma-Derived Extracellular Vesicles Facilitate Transformation of Astrocytes via Reprogramming Oncogenic Metabolism , 2020, iScience.

[9]  Kevin Petrecca,et al.  Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy , 2020, Nature Communications.

[10]  V. Sartorelli,et al.  Enhancer RNAs are an important regulatory layer of the epigenome , 2020, Nature Structural & Molecular Biology.

[11]  Daniel Hidalgo,et al.  Dynamics of the 4D genome during in vivo lineage specification and differentiation , 2020, Nature Communications.

[12]  Brian Craft,et al.  Visualizing and interpreting cancer genomics data via the Xena platform , 2020, Nature Biotechnology.

[13]  P. Arnaud,et al.  HOX gene cluster (de)regulation in brain: from neurodevelopment to malignant glial tumours , 2020, Cellular and Molecular Life Sciences.

[14]  Shiqing Huang,et al.  A putative competing endogenous RNA network in cisplatin-resistant lung adenocarcinoma cells identifying potentially rewarding research targets , 2020, Oncology letters.

[15]  D. Tian,et al.  Theranostic combinatorial drug-loaded coated cubosomes for enhanced targeting and efficacy against cancer cells , 2020, Cell Death & Disease.

[16]  T. Maniatis,et al.  The generation of a protocadherin cell-surface recognition code for neural circuit assembly , 2019, Current Opinion in Neurobiology.

[17]  D. Reinberg,et al.  RNA Interactions Are Essential for CTCF-Mediated Genome Organization. , 2019, Molecular cell.

[18]  S. Brandner,et al.  Redistribution of EZH2 promotes malignant phenotypes by rewiring developmental programmes , 2019, EMBO reports.

[19]  Mariella G. Filbin,et al.  An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma , 2019, Cell.

[20]  R. Tjian,et al.  Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF. , 2019, Molecular cell.

[21]  Wei Xie,et al.  The role of 3D genome organization in development and cell differentiation , 2019, Nature Reviews Molecular Cell Biology.

[22]  L. Mirny,et al.  Two major mechanisms of chromosome organization. , 2019, Current opinion in cell biology.

[23]  Li Yang,et al.  Knockdown of lncRNA HOXD-AS1 suppresses proliferation, migration and invasion and enhances cisplatin sensitivity of glioma cells by sponging miR-204. , 2019, Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie.

[24]  Junjun Cheng,et al.  LncRNA linc01116 prometes glioma cell migration and invasion by modulation of radixin targeted by miR-31. , 2019, International journal of clinical and experimental pathology.

[25]  Xiaozhong Peng,et al.  Long noncoding RNA HOXD‐AS2 regulates cell cycle to promote glioma progression , 2018, Journal of cellular biochemistry.

[26]  Leonardo Beccari,et al.  Similarities and differences in the regulation of HoxD genes during chick and mouse limb development , 2018, PLoS biology.

[27]  Richard A. Moore,et al.  High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma , 2018, bioRxiv.

[28]  E. Petretto,et al.  Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation , 2018, Nature Immunology.

[29]  Ji-Yong Um,et al.  Human glioblastoma arises from subventricular zone cells with low-level driver mutations , 2018, Nature.

[30]  Jian Chen,et al.  HOXD‐AS1/miR‐130a sponge regulates glioma development by targeting E2F8 , 2018, International journal of cancer.

[31]  J. Lis,et al.  Enhancer transcription: what, where, when, and why? , 2018, Genes & development.

[32]  I. Schor,et al.  The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription , 2018, Genes & development.

[33]  Leonardo Beccari,et al.  The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes , 2017, bioRxiv.

[34]  L. Mirny,et al.  Chromatin organization by an interplay of loop extrusion and compartmental segregation , 2017, Proceedings of the National Academy of Sciences.

[35]  S. Kalkanis,et al.  The novel long non-coding RNA TALNEC2, regulates tumor cell growth and the stemness and radiation response of glioma stem cells , 2017, Oncotarget.

[36]  Ting Wang,et al.  The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions , 2017, Genome Biology.

[37]  Anna M. Krichevsky,et al.  Genome Editing Reveals Glioblastoma Addiction to MicroRNA-10b. , 2017, Molecular therapy : the journal of the American Society of Gene Therapy.

[38]  Matthew R. Krause,et al.  Single-cell profiling reveals that eRNA accumulation at enhancer–promoter loops is not required to sustain transcription , 2016, Nucleic acids research.

[39]  Li Ma,et al.  Ablation of miR-10b Suppresses Oncogene-Induced Mammary Tumorigenesis and Metastasis and Reactivates Tumor-Suppressive Pathways. , 2016, Cancer research.

[40]  E. Lander,et al.  Local regulation of gene expression by lncRNA promoters, transcription and splicing , 2016, Nature.

[41]  D. Bigner,et al.  Rapid Reprogramming of Primary Human Astrocytes into Potent Tumor-Initiating Cells with Defined Genetic Factors. , 2016, Cancer research.

[42]  Fidel Ramírez,et al.  deepTools2: a next generation web server for deep-sequencing data analysis , 2016, Nucleic Acids Res..

[43]  E. Chiocca,et al.  Therapeutic potential of targeting microRNA‐10b in established intracranial glioblastoma: first steps toward the clinic , 2016, EMBO molecular medicine.

[44]  Steven J. M. Jones,et al.  Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma , 2016, Cell.

[45]  Shawn M. Gillespie,et al.  Insulator dysfunction and oncogene activation in IDH mutant gliomas , 2015, Nature.

[46]  Felix A. Klein,et al.  FourCSeq: analysis of 4C sequencing data , 2015, bioRxiv.

[47]  Robert S Illingworth,et al.  Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization , 2014, Genes & development.

[48]  David A. Orlando,et al.  Quantitative ChIP-Seq normalization reveals global modulation of the epigenome. , 2014, Cell reports.

[49]  Shawn M. Gillespie,et al.  Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma , 2014, Science.

[50]  T. Meehan,et al.  An atlas of active enhancers across human cell types and tissues , 2014, Nature.

[51]  Bernard Rogister,et al.  Glioblastoma-Initiating Cells: Relationship with Neural Stem Cells and the Micro-Environment , 2013, Cancers.

[52]  R. Agami,et al.  eRNAs reach the heart of transcription , 2013, Cell Research.

[53]  C. Glass,et al.  Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation , 2013, Nature.

[54]  Boris Lenhard,et al.  r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data , 2013, Nucleic acids research.

[55]  R. Shiekhattar,et al.  Activating RNAs associate with Mediator to enhance chromatin architecture and transcription , 2013, Nature.

[56]  D. Schiff,et al.  Oncogenic effects of miR-10b in glioblastoma stem cells , 2013, Journal of Neuro-Oncology.

[57]  Eric A Bushong,et al.  Dedifferentiation of Neurons and Astrocytes by Oncogenes Can Induce Gliomas in Mice , 2012, Science.

[58]  L. Mirny,et al.  Iterative Correction of Hi-C Data Reveals Hallmarks of Chromosome Organization , 2012, Nature Methods.

[59]  Kevin W Eliceiri,et al.  NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.

[60]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[61]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[62]  Stephen Yip,et al.  Maintenance of primary tumor phenotype and genotype in glioblastoma stem cells. , 2012, Neuro-oncology.

[63]  I. Ellis,et al.  Differential oestrogen receptor binding is associated with clinical outcome in breast cancer , 2011, Nature.

[64]  L. Luo,et al.  Mosaic Analysis with Double Markers Reveals Tumor Cell of Origin in Glioma , 2011, Cell.

[65]  A. Brandes,et al.  Advances in malignant glioma drug discovery , 2011, Expert opinion on drug discovery.

[66]  H. Okano,et al.  Functional analysis of HOXD9 in human gliomas and glioma cancer stem cells , 2011, Molecular Cancer.

[67]  Ming Yi,et al.  Human glioma growth is controlled by microRNA-10b. , 2011, Cancer research.

[68]  Erwin G. Van Meir,et al.  Exciting New Advances in Neuro‐Oncology: The Avenue to a Cure for Malignant Glioma , 2010, CA: a cancer journal for clinicians.

[69]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[70]  H. Wakimoto,et al.  Human glioblastoma-derived cancer stem cells: establishment of invasive glioma models and treatment with oncolytic herpes simplex virus vectors. , 2009, Cancer research.

[71]  D. Housman,et al.  Oncogenic EGFR signaling cooperates with loss of tumor suppressor gene functions in gliomagenesis , 2009, Proceedings of the National Academy of Sciences.

[72]  Arturo Alvarez-Buylla,et al.  Malignant astrocytomas originate from neural stem/progenitor cells in a somatic tumor suppressor mouse model. , 2009, Cancer cell.

[73]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[74]  R. Mason,et al.  Pten haploinsufficiency accelerates formation of high-grade astrocytomas. , 2008, Cancer research.

[75]  R. Weinberg,et al.  Tumour invasion and metastasis initiated by microRNA-10b in breast cancer , 2007, Nature.

[76]  Dawen Zhao,et al.  Early inactivation of p53 tumor suppressor gene cooperating with NF1 loss induces malignant astrocytoma. , 2005, Cancer cell.

[77]  K. Aldape,et al.  Formation of intracranial tumors by genetically modified human astrocytes defines four pathways critical in the development of human anaplastic astrocytoma. , 2001, Cancer research.

[78]  R. McLendon,et al.  A genetically tractable model of human glioma formation. , 2001, Cancer research.

[79]  A. Merlo,et al.  Frequent Co‐Alterations of TP53, p16/CDKN2A, p14ARF, PTEN Tumor Suppressor Genes in Human Glioma Cell Lines. , 1999, Brain pathology.

[80]  Shuhan Sun,et al.  A novel lncRNA‐LINC01116 regulates tumorigenesis of glioma by targeting VEGFA , 2019, International journal of cancer.

[81]  Z. Medarova,et al.  The fundamental role of miR-10b in metastatic cancer. , 2018, American journal of cancer research.

[82]  Peter J. Park,et al.  HiGlass: Web-based visual comparison and exploration of genome interaction maps , 2017 .

[83]  D. Noordermeer,et al.  Determination of High-Resolution 3D Chromatin Organization Using Circular Chromosome Conformation Capture (4C-seq). , 2016, Methods in molecular biology.

[84]  H. E. Johansson,et al.  Simultaneous detection of nuclear and cytoplasmic RNA variants utilizing Stellaris® RNA fluorescence in situ hybridization in adherent cells. , 2014, Methods in molecular biology.

[85]  D. Louis,et al.  Diagnostic and therapeutic avenues for glioblastoma: no longer a dead end? , 2013, Nature Reviews Clinical Oncology.