The epigenetic landscape ofAlurepeats delineates the structural and functional genomic architecture of colon cancer cells

DNA methylation variation of human-specific Alu repeats

(2016) Arundhati Bakshi et al.   Epigenetics

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations

(2016) Phillippa C. Taberlay et al.   GENOME RESEARCH

A knowledgebase of the human Alu repetitive elements

(2016) Izaskun Mallona et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Epigenetic modulators, modifiers and mediators in cancer aetiology and progression

(2016) Andrew P. Feinberg et al.   NATURE REVIEWS GENETICS

Aluretrotransposons promote differentiation of human carcinoma cells through the aryl hydrocarbon receptor

(2016) Antonio Morales-Hernández et al.   NUCLEIC ACIDS RESEARCH

Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells

(2016) Sabine Klawitter et al.   Nature Communications

Quantification of Unmethylated Alu (QUAlu): a tool to assess global hypomethylation in routine clinical samples

(2016) Raquel Buj et al.   Oncotarget

MIEN1 is tightly regulated by SINE Alu methylation in its promoter

(2016) Smrithi Rajendiran et al.   Oncotarget

Placental Hypomethylation Is More Pronounced in Genomic Loci Devoid of Retroelements

(2016) Aniruddha Chatterjee et al.   G3-Genes Genomes Genetics

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

(2016) Zhuoya Gu et al.   Protein & Cell

The role of Alu elements in the cis-regulation of RNA processing

(2015) Chammiran Daniel et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites

(2015) Fiorella C. Grandi et al.   GENOME RESEARCH

The role of DNA methylation in directing the functional organization of the cancer epigenome

(2015) Fides D. Lay et al.   GENOME RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

Competition between DNA methylation and transcription factors determines binding of NRF1

(2015) Silvia Domcke et al.   NATURE

Cell-of-origin chromatin organization shapes the mutational landscape of cancer

(2015) Paz Polak et al.   NATURE

A-to-I editing of coding and non-coding RNAs by ADARs

(2015) Kazuko Nishikura   NATURE REVIEWS MOLECULAR CELL BIOLOGY

IntergenicAluexonisation facilitates the evolution of tissue-specific transcript ends

(2015) Mojca Tajnik et al.   NUCLEIC ACIDS RESEARCH

Intermediate DNA methylation is a conserved signature of genome regulation

(2015) GiNell Elliott et al.   Nature Communications

SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation

(2015) Dhaval Varshney et al.   Nature Communications

Role of DNA Methylation in Modulating Transcription Factor Occupancy

(2015) Matthew T. Maurano et al.   Cell Reports

Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs

(2015) Kenji Ichiyanagi   GENES & GENETIC SYSTEMS

Effects of cytosine methylation on transcription factor binding sites

(2014) Yulia A Medvedeva et al.   BMC GENOMICS

Architectural proteins: regulators of 3D genome organization in cell fate

(2014) Elena Gómez-Díaz et al.   TRENDS IN CELL BIOLOGY

CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer

(2014) Christopher J. Kemp et al.   Cell Reports

Evolution of Alu Elements toward Enhancers

(2014) Ming Su et al.   Cell Reports

Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors

(2014) Winston Timp et al.   Genome Medicine

Long range epigenetic silencing is a trans-species mechanism that results in cancer specific deregulation by overriding the chromatin domains of normal cells

(2013) Marta Forn et al.   Molecular Oncology

DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape

(2013) Mingchao Xie et al.   NATURE GENETICS

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Mining cancer methylomes: prospects and challenges

(2013) Clare Stirzaker et al.   TRENDS IN GENETICS

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Regional Activation of the Cancer Genome by Long-Range Epigenetic Remodeling

(2012) Saul A. Bert et al.   CANCER CELL

Widespread plasticity in CTCF occupancy linked to DNA methylation

(2012) H. Wang et al.   GENOME RESEARCH

Epigenetic Nucleosomes: Alu Sequences and CG as Nucleosome Positioning Element

(2012) F. Salih et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Latent Regulatory Potential of Human-Specific Repetitive Elements

(2012) Michelle C. Ward et al.   MOLECULAR CELL

Chromatin organization is a major influence on regional mutation rates in human cancer cells

(2012) Benjamin Schuster-Böckler et al.   NATURE

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Evaluation of single CpG sites as proxies of CpG island methylation states at the genome scale

(2012) Víctor Barrera et al.   NUCLEIC ACIDS RESEARCH

Alu expression in human cell lines and their retrotranspositional potential

(2012) Andrew J Oler et al.   Mobile DNA

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

(2011) Feng Cui et al.   Biology Direct

Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates

(2011) Antoine Molaro et al.   CELL

Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome

(2011) Juan Sandoval et al.   Epigenetics

Global methylation profiles in DNA from different blood cell types

(2011) Hui-Chen Wu et al.   Epigenetics

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

(2011) G. C. Hon et al.   GENOME RESEARCH

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

(2011) Benjamin P Berman et al.   NATURE GENETICS

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

Genome-wide approaches for cancer gene discovery

(2011) Paul M. Lizardi et al.   TRENDS IN BIOTECHNOLOGY

Replication Timing: A Fingerprint for Cell Identity and Pluripotency

(2011) Tyrone Ryba et al.   PLoS Computational Biology

Alu elements: know the SINEs

(2011) Prescott Deininger   GENOME BIOLOGY

Sensitive measurement of unmethylated repeat DNA sequences by end-specific PCR

(2010) Keith Rand et al.   BIOTECHNIQUES

Methylation status of individual CpG sites within Alu elements in the human genome and Alu hypomethylation in gastric carcinomas

(2010) Shengyan Xiang et al.   BMC CANCER

Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types

(2010) T. Ryba et al.   GENOME RESEARCH

Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns

(2010) J. R. Edwards et al.   GENOME RESEARCH

Alu and Satα hypomethylation in Helicobacter pylori-infected gastric mucosae

(2010) Takeichi Yoshida et al.   INTERNATIONAL JOURNAL OF CANCER

Methods for DNA methylation analysis and applications in colon cancer

(2010) Mireia Jordà et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Taking the measure of the methylome

(2010) Stephan Beck   NATURE BIOTECHNOLOGY

Quantitative comparison of genome-wide DNA methylation mapping technologies

(2010) Christoph Bock et al.   NATURE BIOTECHNOLOGY

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity

(2010) Marcel W. Coolen et al.   NATURE CELL BIOLOGY

Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution

(2010) Hongcang Gu et al.   NATURE METHODS

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Distinctive patterns of age-dependent hypomethylation in interspersed repetitive sequences

(2010) Pornrutsami Jintaridth et al.   PHYSIOLOGICAL GENOMICS

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

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

(2009) Akiko Doi et al.   NATURE GENETICS

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

(2009) Rafael A Irizarry et al.   NATURE GENETICS

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum

(2009) Hehuang Xie et al.   NUCLEIC ACIDS RESEARCH

Chromatin remodeling at Alu repeats by epigenetic treatment activates silenced microRNA-512-5p with downregulation of Mcl-1 in human gastric cancer cells

(2009) Y Saito et al.   ONCOGENE

DNA hypomethylation in cancer cells

(2009) Melanie Ehrlich   Epigenomics

Evolutionary rate heterogeneity of Alu repeats upstream of the APOA5 gene: do they regulate APOA5 expression?

(2008) Edward A. Ruiz-Narváez et al.   JOURNAL OF HUMAN GENETICS

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE

DNA methylation landscapes: provocative insights from epigenomics

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

Epigenetics in Cancer

(2008) Manel Esteller   NEW ENGLAND JOURNAL OF MEDICINE

Bivalent domains enforce transcriptional memory of DNA methylated genes in cancer cells

(2008) J. Rodriguez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA