Two novel DXZ4-associated long noncoding RNAs show developmental changes in expression coincident with heterochromatin formation at the human (Homo sapiens) macrosatellite repeat

The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation

(2015) Fan Yang et al.   GENOME BIOLOGY

Array-based assay detects genome-wide 5-mC and 5-hmC in the brains of humans, non-human primates, and mice

(2014) Pankaj Chopra et al.   BMC GENOMICS

In This Issue

(2014)   CELL

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

(2014) Ezgi Hacisuleyman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Small RNA Expression from the Human Macrosatellite DXZ4

(2014) Michael Pohlers et al.   G3-Genes Genomes Genetics

X Chromosome Inactivation and Epigenetic Responses to Cellular Reprogramming

(2013) Derek Lessing et al.   Annual Review of Genomics and Human Genetics

Genome-wide analysis of macrosatellite repeat copy number variation in worldwide populations: evidence for differences and commonalities in size distributions and size restrictions

(2013) Mireille Schaap et al.   BMC GENOMICS

TET enzymatic oxidation of 5-methylcytosine, 5-hydroxymethylcytosine and 5-formylcytosine

(2013) Jean Cadet et al.   MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS

A simple tool to improve pluripotent stem cell differentiation

(2013) Sundari Chetty et al.   NATURE METHODS

RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

(2013) Stephane E. Castel et al.   NATURE REVIEWS GENETICS

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

(2012) Miao Yu et al.   CELL

A Long ncRNA Links Copy Number Variation to a Polycomb/Trithorax Epigenetic Switch in FSHD Muscular Dystrophy

(2012) Daphne S. Cabianca et al.   CELL

New and Xisting regulatory mechanisms of X chromosome inactivation

(2012) Yesu Jeon et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Centromeres Poised En Pointe: CDKs Put a Hold on CENP-A Assembly

(2012) Kaitlin M. Stimpson et al.   DEVELOPMENTAL CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Selective Development of Myogenic Mesenchymal Cells from Human Embryonic and Induced Pluripotent Stem Cells

(2012) Tomonari Awaya et al.   PLoS One

Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

(2012) M. J. Booth et al.   SCIENCE

The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite

(2012) Andrea H Horakova et al.   GENOME BIOLOGY

Formation of novel CENP-A domains on tandem repetitive DNA and across chromosome breakpoints on human chromosome 8q21 neocentromeres

(2011) Dan Hasson et al.   CHROMOSOMA

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation

(2011) Gabriella Ficz et al.   NATURE

5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging

(2011) Keith E Szulwach et al.   NATURE NEUROSCIENCE

YY1 associates with the macrosatellite DXZ4 on the inactive X chromosome and binds with CTCF to a hypomethylated form in some male carcinomas

(2011) Shawn C. Moseley et al.   NUCLEIC ACIDS RESEARCH

Variation in Array Size, Monomer Composition and Expression of the Macrosatellite DXZ4

(2011) Deanna C. Tremblay et al.   PLoS One

Concise Review: Pluripotency and the Transcriptional Inactivation of the Female Mammalian X Chromosome

(2011) Alissa Minkovsky et al.   STEM CELLS

Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells

(2011) Keith E. Szulwach et al.   PLoS Genetics

Characterization of DXZ4 conservation in primates implies important functional roles for CTCF binding, array expression and tandem repeat organization on the X chromosome

(2011) Christine R McLaughlin et al.   GENOME BIOLOGY

5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells

(2011) Hume Stroud et al.   GENOME BIOLOGY

A top-down analysis of Xa- and Xi-territories reveals differences of higher order structure at ≥ 20 Mb genomic length scales

(2011) Kathrin Teller et al.   Nucleus

Expression, tandem repeat copy number variation and stability of four macrosatellite arrays in the human genome

(2010) Deanna C Tremblay et al.   BMC GENOMICS

Enhanced differentiation of human embryonic stem cells to mesenchymal progenitors by inhibition of TGF-β/activin/nodal signaling using SB-431542

(2010) Amer Mahmood et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates

(2010) Daniel Globisch et al.   PLoS One

A Unifying Genetic Model for Facioscapulohumeral Muscular Dystrophy

(2010) R. J. L. F. Lemmers et al.   SCIENCE

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Specific Loss of Histone H3 Lysine 9 Trimethylation and HP1γ/Cohesin Binding at D4Z4 Repeats Is Associated with Facioscapulohumeral Dystrophy (FSHD)

(2009) Weihua Zeng et al.   PLoS Genetics

The D4Z4 Macrosatellite Repeat Acts as a CTCF and A-Type Lamins-Dependent Insulator in Facio-Scapulo-Humeral Dystrophy

(2009) Alexandre Ottaviani et al.   PLoS Genetics

Analysis of the largest tandemly repeated DNA families in the human genome

(2008) Peter E Warburton et al.   BMC GENOMICS

DXZ4 chromatin adopts an opposing conformation to that of the surrounding chromosome and acquires a novel inactive X-specific role involving CTCF and antisense transcripts

(2008) B. P. Chadwick   GENOME RESEARCH