Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits

Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals

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Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data

(2018) Quan H Nguyen et al.   GigaScience

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA

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Regulation of disease-associated gene expression in the 3D genome

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Functional Mutations Form at CTCF-Cohesin Binding Sites in Melanoma Due to Uneven Nucleotide Excision Repair across the Motif

(2016) Rebecca C. Poulos et al.   Cell Reports

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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

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Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

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CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

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Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

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Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

(2015) Matthew T Maurano et al.   NATURE GENETICS

Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance

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The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

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Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

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Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

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Genome-Wide H3K4me3 Analysis in Angus Cattle with Divergent Tenderness

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Enhancer loops appear stable during development and are associated with paused polymerase

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Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle

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Motif-based analysis of large nucleotide data sets using MEME-ChIP

(2014) Wenxiu Ma et al.   Nature Protocols

CTCF: an architectural protein bridging genome topology and function

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

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Insulator function and topological domain border strength scale with architectural protein occupancy

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Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

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Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

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

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A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

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(2012) Jesse R. Dixon et al.   NATURE

Widespread Site-Dependent Buffering of Human Regulatory Polymorphism

(2012) Matthew T. Maurano et al.   PLoS Genetics

Dissecting the regulatory architecture of gene expression QTLs

(2012) Daniel J Gaffney et al.   GENOME BIOLOGY

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(2011) Charles E. Grant et al.   BIOINFORMATICS

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

(2011) Eitan Yaffe et al.   NATURE GENETICS

Genome-wide association and genomic selection in animal breedingThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

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Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster

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An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

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

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