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Here, the authors develop a high-throughput assay to measure the jumping potential of thousands of transposons in parallel.

Nadav Ahituv, Nicola Illing, Jeff Wall and colleagues sequence the genome of the bat Miniopterus natalensis and perform RNA-seq and ChIP-seq (H3K27ac and H3K27me3) analyses on its developing forelimb and hindlimb autopods at sequential embryonic stages. Their analyses identify genomic regions that may contribute to bat wing formation.

Nadav Ahituv and colleagues use a massively parallel reporter assay to test 4,970 synthetic regulatory element sequences, containing patterns of 12 known liver transcription factor binding sites, in mice and in HepG2 cells. They systematically test the impact of binding site copy number, spacing, combination and order on gene expression.

MPRAs and in vivo transgenic mouse assays are two potentially complementary ways to assay the impact of noncoding variants. Here, authors find a strong and specific correlation between the assays in neural cells. Mouse assays also reveal pleiotropic effects not observed in MPRA.

Adipose manipulation transplantation can reduce tumor growth and proliferation in vitro and in mouse models.

Scalable CRISPRa screening of cis-regulatory elements in non-cancer cell lines has proved challenging. Here, the authors describe a scalable, CRISPR activation screening framework to identify regulatory element-gene pairs in diverse cell types including cancer cells and neurons.

Lentivirus-based reporter assays for 680,000 regulatory sequences from three cell lines coupled to machine-learning models lead to insights into the grammar of cis-regulatory elements.

Interpreting genetic variation in the noncoding genome remains challenging, with functional effects difficult to predict. Here, the authors perform saturation mutagenesis combined with massively parallel reporter assays for 20 disease-associated regulatory elements, quantifying the effects of over 30,000 variants.

The authors show that the deletion of ultraconserved TAD boundaries affects gene expression and phenotype, highlighting TAD evolution’s function. Human-specific TAD boundaries reveal a role in brain development and disease.

Frugivory evolved multiple times in mammals, including bats. Here, the authors use integrative single-cell sequencing on fruit and insect bat kidneys and pancreases and identify cell population, gene expression and regulatory differences associated with frugivory that also relate to diabetes.

Acheiropodia is associated with homozygous deletions in the LMBR1 gene around ZRS, an enhancer regulating SHH during limb development, but how these deletions lead to this phenotype is unknown. Here the authors use whole-genome sequencing, ChIP-seq, 4C-seq and DNA FISH to show that alterations in CTCF motifs are responsible via altered enhancer–promoter interactions.

Gene regulatory grammar remains difficult to decipher, hindering our ability to link genotype to phenotype. Here they use massively parallel reporter assays to test over 200,000 synthetic sequences, finding that transcription factor binding site order and orientation have a major effect on gene regulatory activity.

How gene regulatory elements regulate gene expression during cellular differentiation remains largely unknown. Here the authors use perturbation-based massively parallel reporter assays at early time points of neural differentiation to systematically characterize how regulatory elements and motifs within them guide different transcriptional patterns.

Inoue et al. use genetic and epigenetic tools to map active gene regulatory elements in leptin-responsive neurons in the mouse hypothalamus. These regulatory elements overlap with several obesity-associated GWAS SNPs.

cis-Regulation therapy (CRT) — modifying the activity of gene-regulatory elements — is emerging as a potential approach to treat genetic diseases. Here, Matharu and Ahituv assess emerging CRT technologies and present proof-of-concept studies in cell and animal models. Key factors to be considered for the translation of CRT into the clinic are discussed.

Massively parallel reporter assays (MPRAs) enable high-throughput assessments of regulatory elements in single experiments. This work compares nine MPRA designs and reports how differences in reporter assays influence the results of MPRAs.

Two groups describe approaches for synthesizing and assaying the function of thousands of variants of mammalian DNA regulatory elements. Melnikov et al. use their results to engineer short optimized regulatory elements in human cells, whereas Patwardhan et al. study enhancers hundreds of bases long in mice.

Here, the authors review the complex gene regulatory mechanisms that underlie limb development and that determine forelimb versus hindlimb identity. They explain how the modification of these regulatory elements leads to morphological evolution, acquired regeneration capacity or limb malformations in diverse species, including humans.

A class of conserved regions in the tetrapod genome is derived from a SINE retroposon family that was active as much as 400 million years ago, and has retained recent activity in the coelacanth.

Massively parallel reporter assays identify 165 functional variants associated with skin pigmentation in ethnically diverse Africans. Functional characterization of eight variants demonstrates their impact in regulating melanin levels and validates CYB561A3 as a novel gene involved in melanogenesis and pigmentation.

After the production of double-stranded breaks in mammalian cells, ATM drives the formation of the D compartment, which regulates DNA damage-responsive genes, through the clustering of damaged topologically associating domains, with a mechanism that is consistent with polymer–polymer phase separation.

Girls are tenfold more likely than boys to require surgical treatment for idiopathic scoliosis, a common paediatric skeletal disorder. Here, Sharma et al. identify the first sexually dimorphic idiopathic scoliosis risk locus, and demonstrate that it may play a role in the regulation of spinal cells.

A subset of oestrogen-sensitive neurons integrate melanocortin and oestrogen signalling to rebalance energy allocation in female mice leading to reduced sedentary behaviour and decreasing obesity in oestrogen-depleted female mice

Analysis of chromatin state at a single-cell level in samples of developing human forebrain demonstrate both cell-type-specific and region-specific changes during neurogenesis.

Human–chimpanzee tetraploid fusions serve as a model to study gene expression differences between these species, allowing for separation of cis- from trans-regulatory effects and analysis of unique craniofacial morphologies.

Inguinal hernia has high lifetime prevalence, especially in men. This genome-wide association study identifies 4 loci to be associated with inguinal hernia, and shows expression of nearby genes in mouse connective tissues.

This protocol describes a lentivirus-based massively parallel reporter assay (lentiMPRA) for quantitative assessment of the activity of gene regulatory elements and an accompanying Nextflow-based computational pipeline for analysis.

A premature stop codon in the DMRT3 gene has a major effect on the pattern of locomotion in horses, and the Dmrt3 transcription factor is critical in the development of a coordinated locomotor network in mice, suggesting that it has an important role in configuring the spinal circuits that control stride.

A chromatin interaction analysis with paired-end tagging (ChIA-PET) approach is used to delineate chromatin interactions mediated by RNA polymerase II in several different stem-cell populations; putative long-range promoter–enhancer interactions are inferred, indicating that linear juxtaposition does not necessarily guide enhancer target selection and prevalent cell-specific enhancer usage.

The Impact of Genomic Variation on Function Consortium is combining single-cell mapping, genomic perturbations and predictive modelling to investigate relationships between human genomic variation, genome function and phenotypes and will provide an open resource to the community.