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Enhancer-driven genomic recording of transcriptional activity in multiplex (ENGRAM) is used for multiplex recording of the cell-type-specific activities of dozens to hundreds of cis-regulatory elements with high fidelity, sensitivity and reproducibility.

Single-cell quantitative expression reporters enable high-sensitivity quantitative characterization of cis-regulatory elements at the single-cell level in multicellular systems.

Patwardhan et al. describe a high-throughput approach for analyzing at single-nucleotide resolution the DNA regulatory sequences that control gene expression. Characterizing these sequences in a massively parallel manner will be useful for deciphering the regulatory logic of the cell and for synthetic biology.

Gene synthesis is currently limited by the need to use error-prone oligonucleotide building blocks. Dial-out PCR overcomes the sequence verification bottleneck by using unique sequence tags and massively parallel sequencing to identify and selectively retrieve error-free DNA molecules of interest from complex mixtures.

The topologies of, and spatial relationships between, chromosomes are important but poorly understood. Here, a high-throughput method is used to study intra- and inter-chromosomal interactions in Saccharomyces cerevisiae. A map of the haploid genome is generated at kilobase resolution, and is used to construct a three-dimensional model of the yeast genome. The findings provide a glimpse of the interface between the form and function of a eukaryotic genome.

Jay Shendure and colleagues report exome sequencing of ten individuals with Kabuki syndrome. They identify mutations in MLL2, encoding a Trithorax-group histone methyltransferase, as causal for this rare autosomal dominant malformation disorder.

Short sequence reads are grouped based on the long genomic fragments from which they derive, enabling efficient local assembly of the long fragments and therefore accurate de novo genome assembly and metagenome sequencing.

Paired prime editing is used to precisely delete genomic sequences up to 10 kb.

A DNA memory device, DNA Typewriter, uses sequential prime editing to record the order of multiple cellular events.

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.

Michael Bamshad, Jay Shendure and colleagues report the first application of exome resequencing to identify the cause of a mendelian disorder. They sequenced the exomes of four individuals with Miller syndrome in three independent families and identify mutations in DHODH, a key enzyme in the pyrimidine de novo biosynthesis pathway, as causal for the disorder.

Targeted DNase Hi-C uses DNase I instead of restriction enzymes for chromatin fragmentation and improves the resolution of chromatin interaction maps.

Hamazaki, Yang et al. report that an early pulse of retinoic acid robustly induces human gastruloids with a neural tube, segmented somites and more advanced cell types than conventional gastruloids.

Haplotype-resolved whole-genome sequencing of the HeLa CCL-2 strain shows that HeLa is relatively stable in terms of point variation; integration of several data sets reveals strong, haplotype-specific activation of the proto-oncogene MYC by the human papilloma virus type 18 genome, and enables the relationship between gene dosage and expression to be examined.

Although DNA sequencing costs have fallen dramatically, they are still too high for whole genome sequencing to be used to routinely identify rare and novel variants in large cohorts. The targeted capture and massively parallel sequencing of the exomes of 12 humans is now reported. Freeman–Sheldon syndrome is used as a proof-of-concept that candidate genes for monogenic disorders can be identified by exome sequencing of a small number of unrelated, affected individuals.

Exome sequencing on a large cohort of parent–child trios with sporadic autism spectrum disorders shows that de novo point mutations are mainly paternal in origin and positively correlate with paternal age, and identifies a highly interconnected network formed from the products of the most severe mutations.

Evan Eichler, Jay Shendure and colleagues sequenced the exomes of 20 sporadic cases of autism spectrum disorder and their unaffected parents. They identified potentially causative de novo mutations in four cases, including a frameshift in FOXP1, a splice-site mutation in GRIN2B and missense variants in SCN1A and LAMC3.