Structural variation in the 3D genome

M Spielmann, DG Lupiáñez, S Mundlos - Nature Reviews Genetics, 2018 - nature.com
Structural and quantitative chromosomal rearrangements, collectively referred to as
structural variation (SV), contribute to a large extent to the genetic diversity of the human …

Evolution to the rescue: using comparative genomics to understand long non-coding RNAs

I Ulitsky - Nature Reviews Genetics, 2016 - nature.com
Long non-coding RNAs (lncRNAs) have emerged in recent years as major players in a
multitude of pathways across species, but it remains challenging to understand which of …

Developmental dynamics of lncRNAs across mammalian organs and species

I Sarropoulos, R Marin, M Cardoso-Moreira… - Nature, 2019 - nature.com
Although many long noncoding RNAs (lncRNAs) have been identified in human and other
mammalian genomes, there has been limited systematic functional characterization of these …

Sequence determinants of human gene regulatory elements

B Sahu, T Hartonen, P Pihlajamaa, B Wei, K Dave… - Nature Genetics, 2022 - nature.com
DNA can determine where and when genes are expressed, but the full set of sequence
determinants that control gene expression is unknown. Here, we measured the …

Formation of new chromatin domains determines pathogenicity of genomic duplications

M Franke, DM Ibrahim, G Andrey, W Schwarzer… - Nature, 2016 - nature.com
Chromosome conformation capture methods have identified subchromosomal structures of
higher-order chromatin interactions called topologically associated domains (TADs) that are …

Transcriptional enhancers: from properties to genome-wide predictions

D Shlyueva, G Stampfel, A Stark - Nature Reviews Genetics, 2014 - nature.com
Cellular development, morphology and function are governed by precise patterns of gene
expression. These are established by the coordinated action of genomic regulatory …

Transcription factors: from enhancer binding to developmental control

F Spitz, EEM Furlong - Nature reviews genetics, 2012 - nature.com
Developmental progression is driven by specific spatiotemporal domains of gene
expression, which give rise to stereotypically patterned embryos even in the presence of …

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

EP Nora, BR Lajoie, EG Schulz, L Giorgetti, I Okamoto… - Nature, 2012 - nature.com
In eukaryotes transcriptional regulation often involves multiple long-range elements and is
influenced by the genomic environment. A prime example of this concerns the mouse X …

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

PHL Krijger, W De Laat - Nature reviews Molecular cell biology, 2016 - nature.com
Genetic variation associated with disease often appears in non-coding parts of the genome.
Understanding the mechanisms by which this phenomenon leads to disease is necessary to …

Functional dissection of the Sox9Kcnj2 locus identifies nonessential and instructive roles of TAD architecture

A Despang, R Schöpflin, M Franke, S Ali, I Jerković… - Nature …, 2019 - nature.com
The genome is organized in three-dimensional units called topologically associating
domains (TADs), through a process dependent on the cooperative action of cohesin and the …