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The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes.

This overview of the ENCODE project outlines the data accumulated so far, revealing that 80% of the human genome now has at least one biochemical function assigned to it; the newly identified functional elements should aid the interpretation of results of genome-wide association studies, as many correspond to sites of association with human disease.

Luan et al. find that CTCF shapes the transcriptional landscape in part by suppressing the initiation of upstream antisense transcription at hundreds of divergent gene promoters.

Extensive genomic analyses of the chromatin architecture in acute myeloid leukaemia reveals several characteristics, including subtype-specific distal enhancers and silencers, that may represent new anticancer therapeutic targets.

As part of the mouse ENCODE project, genome-wide transcription factor (TF) occupancy repertoires and co-association patterns in mice and humans are studied; many aspects are conserved but the extent to which orthologous DNA segments are bound by TFs in mice and humans varies both among TFs and genomic location, and TF-occupied sequences whose occupancy is conserved tend to be pleiotropic and enriched for single nucleotide variants with known regulatory potential.

The next step after sequencing a genome is to figure out how the cell actually uses it as an instruction manual. A large international consortium has examined 1% of the genome for what part is transcribed, where proteins are bound, what the chromatin structure looks like, and how the sequence compares to that of other organisms.

Yin Yang 1 (YY1) aids in the formation of enhancer–promoter (E–P) loops independently of cohesin. YY1 maintains a subset of E–P interactions in interphase and establishes an overlapping yet distinct set after mitotic exit.

Condensin-depleted mitotic chromosomes compartmentalize and form contacts among regulatory elements despite lacking transcription and most chromatin-associated factors. Heterochromatin protein 1 (HP1) proteins are surprisingly dispensable for compartmentalizing constitutive heterochromatin.

CRISPR–Cas9-mediated insertion of a naturally occurring benign mutation in blood cell progenitors from patients with sickle cell disease increases fetal hemoglobin expression to levels sufficient to ameliorate the pathological morphology observed in erythrocytes differentiated from these cells.

Analysis of the dynamics of chromosome reorganization after exit from mitosis reveals the distinct but mutually influential forces that drive chromatin reconfiguration.

HIC2 regulates the fetal-to-adult hemoglobin switch. It inactivates an enhancer of the BCL11A gene, a fetal globin repressor, by reducing chromatin accessibility and displacing the transcription factor GATA1.

Insertion of a tissue-invariant chromatin domain boundary into 16 ectopic loci leads to various structural phenotypes, which depend on local chromatin features, CTCF binding and transcriptional status.

Comparisons among experimental results with large amounts of data can be more precise and meaningful when done across multiple different conditions simultaneously. Koch et al. introduce a method, called CLIMB, that does this, and captures interpretable and biologically meaningful information.

Higher-order chromatin structure is temporarily disrupted during mitosis. Here the authors show that loss of the architectural factor CTCF results in failure to form structural loops and leads to inappropriate cis-regulatory contacts and alterations of compartmental interactions after mitosis. Furthermore, they show global 3D architecture is set up without transcription, but that transcription contributes to proper gene domain formation.

The authors present an integrative framework for identifying structural variants (SVs) in cancer that applies optical mapping, Hi-C, and whole-genome sequencing. They find SVs affecting distal regulatory sequences, DNA replication, and three-dimensional chromatin structure.

Two methods are used to identify cis-regulatory sequences by looking at their function.

NFIA and NFIX directly repress the expression of fetal-type β-globin-like genes HBG1 and HBG2 in adult erythroid cells, and also do it indirectly through the upregulation of BCL11A.

A comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin structure, the methylome and 3D genome organization in the zebrafish (Danio rerio) enables identification of species-specific and evolutionarily conserved regulatory features, and provides a foundation for modelling studies on human disease and development.

An ABEmax-based screen identifies regulatory noncoding nucleotides in four loci that control erythroid fetal hemoglobin (HbF) expression. Targeting a repressor element raises HbF levels in cells from patients with sickle cell disease.

RNA expression is quantified at a tissue level in seventeen mouse tissues across embryonic development, and at the single-cell level in the developing limb.

What is the best way to identify regulatory DNA sequences such as enhancers, promoters, insulators and silencers? A new study shows that specific binding by a coactivator protein identifies enhancers that are invisible to common detection methods based on evolutionary constraint.

The Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types; these data were compared with those from human to confirm substantial conservation in the newly annotated potential functional sequences and to reveal pronounced divergence of other sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization.

Several approaches exist for identifyingcis-regulatory modules, which are the regions in the genome that regulate gene expression. The authors describe these strategies and assess how they perform (either alone or in combination) and how they can be improved.

Single nucleotide variants (SNVs) can affect chromatin occupancy by transcription factors (TF). Here the authors mine naturally occurring SNVs to probe cis elements and define contextual sequences that govern in vivo transcription factor chromatin occupancy and chromatin accessibility.

The authors summarize the history of the ENCODE Project, the achievements of ENCODE 1 and ENCODE 2, and how the new data generated and analysed in ENCODE 3 complement the previous phases.

Platypuses are monotremes and combine aspects of both reptilian and mammalian behaviour. An international consortium reports the genome sequence and analysis of Ornithorhynchus anatinus and as expected, parts of the genome look more like mammals, whereas other parts more like reptiles or even chickens.

George Patrinos and colleagues report the first implementation of the microattribution approach to systematically document genetic variation associated with a disease, applied here to hemoglobinopathies and thalassemias. They developed a series of connected locus-specific databases that document genotype and phenotype information for genetic variation in 37 globin and erythroid protein genes in individuals with globin disorders, with reciprocal attribution to data contributors.

The evolution of genes is influenced by regional variation in mutation rates (RViMR). Chromatin organization affects RViMR, although the correlation between chromatin state and mutation types and rates is complex. This Review describes recent research on RViMR and chromatin organization, and the emerging findings from investigations of both germline and somatic mutations.

A study of DNA replication timing in mouse and human cells reveals that replication domains (domains of the genome which replicate at the same time) share a correlation with topologically associating domains; these results reconcile cell-type-specific sub-nuclear compartmentalization with developmentally stable chromosome domains and offer a unified model for large scale chromosome structure and function.

Until now, fully sequenced human genomes of the indigenous hunter-gatherer peoples of southern Africa have been limited to recently diverged populations. The complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and of a Bantu from southern Africa are now presented. The extent of whole-genome and exome diversity is characterized; the observed genomic differences may help to pinpoint genetic adaptations to an agricultural lifestyle.