Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome

Aluelements: at the crossroads between disease and evolution: Figure 1

(2015) Jernej Ule   BIOCHEMICAL SOCIETY TRANSACTIONS

Genome organization and long-range regulation of gene expression by enhancers

(2013) Andrea Smallwood et al.   CURRENT OPINION IN CELL BIOLOGY

Evolutionary rate of human tissue-specific genes are related with transposable element insertions

(2013) Ping Jin et al.   GENETICA

Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome

(2013) Yulan Lu et al.   NUCLEIC ACIDS RESEARCH

Transposable elements as genetic regulatory substrates in early development

(2013) Wesley D. Gifford et al.   TRENDS IN CELL BIOLOGY

Alu repeat-induced deletions in chronic granulomatous disease: a cause not only for p67-phox, but also for p47-phox deficiency

(2012) Stefan Winkler et al.   ANNALS OF HEMATOLOGY

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

The novel MER transposon-derived miRNAs in human genome

(2012) Kung Ahn et al.   GENE

A decade of 3C technologies: insights into nuclear organization

(2012) E. de Wit et al.   GENES & DEVELOPMENT

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Impact of Alu repeats on the evolution of human p53 binding sites

(2011) Feng Cui et al.   Biology Direct

Epigenetic regulation of transposable element derived human gene promoters

(2011) Ahsan Huda et al.   GENE

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

Genomic Analysis Reveals a Novel Nuclear Factor-κB (NF-κB)-binding Site in Alu-repetitive Elements

(2011) Athina Antonaki et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

(2011) Vincent J Lynch et al.   NATURE GENETICS

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

(2011) Eitan Yaffe et al.   NATURE GENETICS

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Evolution of microRNA diversity and regulation in animals

(2011) Eugene Berezikov   NATURE REVIEWS GENETICS

Enhancers in embryonic stem cells are enriched for transposable elements and genetic variations associated with cancers

(2011) Li Teng et al.   NUCLEIC ACIDS RESEARCH

Interaction of hnRNPA1/A2 and DAZAP1 with an Alu-Derived Intronic Splicing Enhancer Regulates ATM Aberrant Splicing

(2011) Tibor Pastor et al.   PLoS One

Intronic L1 Retrotransposons and Nested Genes Cause Transcriptional Interference by Inducing Intron Retention, Exonization and Cryptic Polyadenylation

(2011) Kristel Kaer et al.   PLoS One

Widespread establishment and regulatory impact of Alu exons in human genes

(2011) S. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species

(2010) D. Xie et al.   GENOME RESEARCH

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

(2010) Ragnhild Eskeland et al.   MOLECULAR CELL

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Epigenomic analysis of Alu repeats in human ependymomas

(2010) H. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

(2010) Guoliang Li et al.   GENOME BIOLOGY

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS

Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues

(2008) Lan Lin et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY