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

Genome folding through loop extrusion by SMC complexes

(2021) Iain F. Davidson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

(2021) Jaime A Castro-Mondragon et al.   NUCLEIC ACIDS RESEARCH

Promising Advances in LINC01116 Related to Cancer

(2021) Yating Xu et al.   Frontiers in Cell and Developmental Biology

Theranostic combinatorial drug-loaded coated cubosomes for enhanced targeting and efficacy against cancer cells

(2020) Leilei Zhang et al.   Cell Death & Disease

HOX gene cluster (de)regulation in brain: from neurodevelopment to malignant glial tumours

(2020) Céline S. Gonçalves et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Visualizing and interpreting cancer genomics data via the Xena platform

(2020) Mary J. Goldman et al.   NATURE BIOTECHNOLOGY

Dynamics of the 4D genome during in vivo lineage specification and differentiation

(2020) A. Marieke Oudelaar et al.   Nature Communications

Enhancer RNAs are an important regulatory layer of the epigenome

(2020) Vittorio Sartorelli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy

(2020) Charles P. Couturier et al.   Nature Communications

Glioblastoma-Derived Extracellular Vesicles Facilitate Transformation of Astrocytes via Reprogramming Oncogenic Metabolism

(2020) Ailiang Zeng et al.   iScience

TGF-β1 modulates temozolomide resistance in glioblastoma via altered microRNA processing and elevated MGMT

(2020) Er Nie et al.   NEURO-ONCOLOGY

Knockdown of lncRNA HOXD-AS1 suppresses proliferation, migration and invasion and enhances cisplatin sensitivity of glioma cells by sponging miR-204

(2019) Hui Zhou et al.   BIOMEDICINE & PHARMACOTHERAPY

A novel lncRNA‐LINC01116 regulates Tumorigenesis of Glioma by targeting VEGFA

(2019) Jingliang Ye et al.   INTERNATIONAL JOURNAL OF CANCER

An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma

(2019) Cyril Neftel et al.   CELL

Two major mechanisms of chromosome organization

(2019) Leonid A Mirny et al.   CURRENT OPINION IN CELL BIOLOGY

High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma

(2019) Michael J. Johnston et al.   GENOME RESEARCH

The role of 3D genome organization in development and cell differentiation

(2019) Hui Zheng et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Redistribution of EZH 2 promotes malignant phenotypes by rewiring developmental programmes

(2019) Thomas Mortimer et al.   EMBO REPORTS

Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF

(2019) Anders S. Hansen et al.   MOLECULAR CELL

RNA Interactions Are Essential for CTCF-Mediated Genome Organization

(2019) Ricardo Saldaña-Meyer et al.   MOLECULAR CELL

The generation of a protocadherin cell-surface recognition code for neural circuit assembly

(2019) Daniele Canzio et al.   CURRENT OPINION IN NEUROBIOLOGY

Enhancer transcription: what, where, when, and why?

(2018) Nathaniel D. Tippens et al.   GENES & DEVELOPMENT

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

(2018) Olga Mikhaylichenko et al.   GENES & DEVELOPMENT

HOXD-AS1/miR-130a sponge regulates glioma development by targeting E2F8

(2018) Yinan Chen et al.   INTERNATIONAL JOURNAL OF CANCER

Chromatin organization by an interplay of loop extrusion and compartmental segregation

(2018) Johannes Nuebler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human glioblastoma arises from subventricular zone cells with low-level driver mutations

(2018) Joo Ho Lee et al.   NATURE

Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation

(2018) Sergi Cuartero et al.   NATURE IMMUNOLOGY

Long noncoding RNA HOXD-AS2 regulates cell cycle to promote glioma progression

(2018) Yingjiao Qi et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Similarities and differences in the regulation of HoxD genes during chick and mouse limb development

(2018) Nayuta Yakushiji-Kaminatsui et al.   PLOS BIOLOGY

TheHoxDcluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes

(2017) Eddie Rodríguez-Carballo et al.   GENES & DEVELOPMENT

Genome Editing Reveals Glioblastoma Addiction to MicroRNA-10b

(2017) Rachid El Fatimy et al.   MOLECULAR THERAPY

The novel long non-coding RNA TALNEC2, regulates tumor cell growth and the stemness and radiation response of glioma stem cells

(2017) Shlomit Brodie et al.   Oncotarget

Rapid Reprogramming of Primary Human Astrocytes into Potent Tumor-Initiating Cells with Defined Genetic Factors

(2016) F. Li et al.   CANCER RESEARCH

Ablation of miR-10b Suppresses Oncogene-Induced Mammary Tumorigenesis and Metastasis and Reactivates Tumor-Suppressive Pathways

(2016) Jongchan Kim et al.   CANCER RESEARCH

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

(2016) Michele Ceccarelli et al.   CELL

Therapeutic potential of targeting microRNA-10b in established intracranial glioblastoma: first steps toward the clinic

(2016) N. M. Teplyuk et al.   EMBO Molecular Medicine

Local regulation of gene expression by lncRNA promoters, transcription and splicing

(2016) Jesse M. Engreitz et al.   NATURE

Single-cell profiling reveals that eRNA accumulation at enhancer–promoter loops is not required to sustain transcription

(2016) Samir Rahman et al.   NUCLEIC ACIDS RESEARCH

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

FourCSeq: analysis of 4C sequencing data

(2015) Felix A. Klein et al.   BIOINFORMATICS

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

(2014) Iain Williamson et al.   GENES & DEVELOPMENT

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

(2014) David A. Orlando et al.   Cell Reports

eRNAs reach the heart of transcription

(2013) Carlos A Melo et al.   CELL RESEARCH

Oncogenic effects of miR-10b in glioblastoma stem cells

(2013) Fadila Guessous et al.   JOURNAL OF NEURO-ONCOLOGY

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data

(2013) Supat Thongjuea et al.   NUCLEIC ACIDS RESEARCH

Glioblastoma-Initiating Cells: Relationship with Neural Stem Cells and the Micro-Environment

(2013) Nicolas Goffart et al.   Cancers

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Diagnostic and therapeutic avenues for glioblastoma: no longer a dead end?

(2012) Shota Tanaka et al.   Nature Reviews Clinical Oncology

Dedifferentiation of Neurons and Astrocytes by Oncogenes Can Induce Gliomas in Mice

(2012) D. Friedmann-Morvinski et al.   SCIENCE

Human Glioma Growth Is Controlled by MicroRNA-10b

(2011) G. Gabriely et al.   CANCER RESEARCH

Mosaic Analysis with Double Markers Reveals Tumor Cell of Origin in Glioma

(2011) Chong Liu et al.   CELL

Advances in malignant glioma drug discovery

(2011) David A Reardon et al.   Expert Opinion on Drug Discovery

Functional analysis of HOXD9 in human gliomas and glioma cancer stem cells

(2011) Masanao Tabuse et al.   Molecular Cancer

Maintenance of primary tumor phenotype and genotype in glioblastoma stem cells

(2011) H. Wakimoto et al.   NEURO-ONCOLOGY

Exciting New Advances in Neuro-Oncology: The Avenue to a Cure for Malignant Glioma

(2010) E. G. Van Meir et al.   CA-A CANCER JOURNAL FOR CLINICIANS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Malignant Astrocytomas Originate from Neural Stem/Progenitor Cells in a Somatic Tumor Suppressor Mouse Model

(2009) Sheila Alcantara Llaguno et al.   CANCER CELL

Human Glioblastoma-Derived Cancer Stem Cells: Establishment of Invasive Glioma Models and Treatment with Oncolytic Herpes Simplex Virus Vectors

(2009) H. Wakimoto et al.   CANCER RESEARCH

Oncogenic EGFR signaling cooperates with loss of tumor suppressor gene functions in gliomagenesis

(2009) Haihao Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pten Haploinsufficiency Accelerates Formation of High-Grade Astrocytomas

(2008) C.-H. Kwon et al.   CANCER RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY