Regulation of cancer epigenomes with a histone-binding synthetic transcription factor

Editing the epigenome: technologies for programmable transcription and epigenetic modulation

(2016) Pratiksha I Thakore et al.   NATURE METHODS

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Genomic loss of EZH2 leads to epigenetic modifications and overexpression of the HOX gene clusters in myelodysplastic syndrome

(2016) Feng Xu et al.   Oncotarget

Hypermethylation of the tumor-suppressor cell adhesion molecule 1 in human papillomavirus-transformed cervical carcinoma cells

(2015) HYUN JU WOO et al.   INTERNATIONAL JOURNAL OF ONCOLOGY

Polycomb Group (PcG) Proteins and Human Cancers: Multifaceted Functions and Therapeutic Implications

(2015) Wei Wang et al.   MEDICINAL RESEARCH REVIEWS

Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains

(2015) Junwei Shi et al.   NATURE BIOTECHNOLOGY

Chromatin regulation at the frontier of synthetic biology

(2015) Albert J. Keung et al.   NATURE REVIEWS GENETICS

miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database

(2015) Chih-Hung Chou et al.   NUCLEIC ACIDS RESEARCH

Zinc finger transcription factor CASZ1 interacts with histones, DNA repair proteins and recruits NuRD complex to regulate gene transcription

(2015) Zhihui Liu et al.   Oncotarget

Targeting activating mutations of EZH2 leads to potent cell growth inhibition in human melanoma by derepression of tumor suppressor genes

(2015) Jessamy C. Tiffen et al.   Oncotarget

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Interferon regulatory factor 8 functions as a tumor suppressor in renal cell carcinoma and its promoter methylation is associated with patient poor prognosis

(2014) Qian Zhang et al.   CANCER LETTERS

Poised chromatin in the mammalian germ line

(2014) B. J. Lesch et al.   DEVELOPMENT

Genome-wide characterization of the routes to pluripotency

(2014) Samer M. I. Hussein et al.   NATURE

Direct activation of human and mouse Oct4 genes using engineered TALE and Cas9 transcription factors

(2014) Jiabiao Hu et al.   NUCLEIC ACIDS RESEARCH

Regulation and Role of EZH2 in Cancer

(2014) Hirohito Yamaguchi et al.   Cancer Research and Treatment

Finding the active genes in deep RNA-seq gene expression studies

(2013) Traver Hart et al.   BMC GENOMICS

In Vivo RNAi Screen for BMI1 Targets Identifies TGF-β/BMP-ER Stress Pathways as Key Regulators of Neural- and Malignant Glioma-Stem Cell Homeostasis

(2013) Gaetano Gargiulo et al.   CANCER CELL

CASZ1 inhibits cell cycle progression in neuroblastoma by restoring pRb activity

(2013) Zhihui Liu et al.   CELL CYCLE

Expression of Polycomb Targets Predicts Breast Cancer Prognosis

(2013) A. Jene-Sanz et al.   MOLECULAR AND CELLULAR BIOLOGY

Tunable and Multifunctional Eukaryotic Transcription Factors Based on CRISPR/Cas

(2013) Fahim Farzadfard et al.   ACS Synthetic Biology

Characterization of Critical Domains within the Tumor Suppressor CASZ1 Required for Transcriptional Regulation and Growth Suppression

(2012) R. A. Virden et al.   MOLECULAR AND CELLULAR BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Chromatin H3K27me3/H3K4me3 histone marks define gene sets in high-grade serous ovarian cancer that distinguish malignant, tumour-sustaining and chemo-resistant ovarian tumour cells

(2012) N Chapman-Rothe et al.   ONCOGENE

Liposome-based DNA carriers may induce cellular stress response and change gene expression pattern in transfected cells

(2011) Anna Fiszer-Kierzkowska et al.   BMC MOLECULAR BIOLOGY

EZH2 Mediates Epigenetic Silencing of Neuroblastoma Suppressor Genes CASZ1, CLU, RUNX3, and NGFR

(2011) C. Wang et al.   CANCER RESEARCH

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Developing Histone Deacetylase Inhibitors as Anti-Cancer Therapeutics

(2011) B. Venugopal et al.   CURRENT MEDICINAL CHEMISTRY

Structure and functions of powerful transactivators: VP16, MyoD and FoxA

(2011) Hiroyuki Hirai et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Synthetic Reversal of Epigenetic Silencing

(2011) Karmella A. Haynes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

Structure and VP16 binding of the Mediator Med25 activator interaction domain

(2011) Erika Vojnic et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters

(2011) Frederic Koch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity

(2011) Matthew D. Young et al.   NUCLEIC ACIDS RESEARCH

Recognition and Specificity Determinants of the Human Cbx Chromodomains

(2010) Lilia Kaustov et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Ring1B Compacts Chromatin Structure and Represses Gene Expression Independent of Histone Ubiquitination

(2010) Ragnhild Eskeland et al.   MOLECULAR CELL

The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation

(2010) Sohail Malik et al.   NATURE REVIEWS GENETICS

Polycomb Target Genes Are Silenced in Multiple Myeloma

(2010) Antonia Kalushkova et al.   PLoS One

Epigenetics in cancer

(2009) S. Sharma et al.   CARCINOGENESIS

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS

Repression of E-cadherin by the polycomb group protein EZH2 in cancer

(2008) Q Cao et al.   ONCOGENE

Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains

(2008) Manching Ku et al.   PLoS Genetics