Saturation mutagenesis1,2 – coupled to an appropriate biological assay – represents a fundamental means of achieving a high-resolution understanding of regulatory3 and protein-coding4 nucleic acid sequences of interest. However, mutagenized sequences introduced in trans on episomes or via random or “safe-harbor” integration fail to capture the native context of the endogenous chromosomal locus5. This shortcoming markedly limits the interpretability of the resulting measurements of mutational impact. Here, we couple CRISPR/Cas9 RNA-guided cleavage6 with multiplex homology-directed repair (HDR) using a complex library of donor templates to demonstrate saturation editing of genomic regions. In exon 18 of BRCA1, we replace a six base-pair (bp) genomic region with all possible hexamers, or the full exon with all possible single nucleotide variants (SNVs), and measure strong effects on transcript abundance attributable to nonsense-mediated decay and exonic splicing elements. We similarly perform saturation genome editing of a well-conserved coding region of an essential gene, DBR1, and measure relative effects on growth that correlate with functional impact. Measurement of the functional consequences of large numbers of mutations with saturation genome editing will potentially facilitate high-resolution functional dissection of both cis-regulatory elements and trans-acting factors, as well as the interpretation of variants of uncertain significance observed in clinical sequencing.

Massively parallel reporter assays (MPRAs) functionally screen thousands of sequences for regulatory activity in parallel. To date, there has been no systematic comparison of differences in MPRA design. Here, we screen a library of 2,440 candidate liver enhancers and controls for regulatory activity in HepG2 cells using nine different MPRA designs. We identify subtle but significant differences that correlate with epigenetic and sequence-level features, as well as differences in dynamic range and reproducibility. We also validate en masse that enhancer activity is robustly independent of orientation, at least for our library and designs. Finally, with a new method, we assemble and test the same enhancers as 192-mers, 354-mers, and 678-mers, and observe surprisingly large differences. This work provides a framework for the experimental design of high-throughput reporter assays, suggesting that the extended sequence context of tested elements, and to a lesser degree the precise assay, influence MPRA results.

While the cost of DNA sequencing has dropped by five orders of magnitude in the past decade, DNA synthesis remains expensive for many applications. Although DNA microarrays have decreased the cost of oligonucleotide synthesis, the use of array-synthesized oligos in practice is limited by short synthesis lengths, high synthesis error rates, low yield and the challenges of assembling long constructs from complex pools. Toward addressing these issues, we developed a protocol for multiplex pairwise assembly of oligos from array-synthesized oligonucleotide pools. To evaluate the method, we attempted to assemble up to 2271 targets ranging in length from 192–252 bases using pairs of array-synthesized oligos. Within sets of complexity ranging from 131–250 targets, we observed error-free assemblies for 90.5% of all targets. When all 2271 targets were assembled in one reaction, we observed error-free constructs for 70.6%. While the assembly method intrinsically increased accuracy to a small degree, we further increased accuracy by using a high throughput ‘Dial-Out PCR’ protocol, which combines Illumina sequencing with an in-house set of unique PCR tags to selectively amplify perfect assemblies from complex synthetic pools. This approach has broad applicability to DNA assembly and high-throughput functional screens.

To date, genome-wide association studies have implicated at least 35 loci in osteoarthritis but, due to linkage disequilibrium, the specific variants underlying these associations and the mechanisms by which they contribute to disease risk have yet to be pinpointed. Here, we functionally test 1,605 single nucleotide variants associated with osteoarthritis for regulatory activity using a massively parallel reporter assay. We identify six single nucleotide polymorphisms (SNPs) with differential regulatory activity between the major and minor alleles. We show that the most significant SNP, rs4730222, exhibits differential nuclear protein binding in electrophoretic mobility shift assays and drives increased expression of an alternative isoform of HBP1 in a heterozygote chondrosarcoma cell line, in a CRISPR-edited osteosarcoma cell line, and in chondrocytes derived from osteoarthritis patients. This study provides a framework for prioritization of GWAS variants and highlights a role of HBP1 and Wnt signaling in osteoarthritis pathogenesis.

BackgroundEnhancers play an important role in morphological evolution and speciation by controlling the spatiotemporal expression of genes. Previous efforts to understand the evolution of enhancers in primates have typically studied many enhancers at low resolution, or single enhancers at high resolution. Although comparative genomic studies reveal large-scale turnover of enhancers, a specific understanding of the molecular steps by which mammalian or primate enhancers evolve remains elusive.ResultsWe identified candidate hominoid-specific liver enhancers from H3K27ac ChIP-seq data. After locating orthologs in 11 primates spanning around 40 million years, we synthesized all orthologs as well as computational reconstructions of 9 ancestral sequences for 348 active tiles of 233 putative enhancers. We concurrently tested all sequences for regulatory activity with STARR-seq in HepG2 cells. We observe groups of enhancer tiles with coherent trajectories, most of which can be potentially explained by a single gain or loss-of-activity event per tile. We quantify the correlation between the number of mutations along a branch and the magnitude of change in functional activity. Finally, we identify 84 mutations that correlate with functional changes; these are enriched for cytosine deamination events within CpGs.ConclusionsWe characterized the evolutionary-functional trajectories of hundreds of liver enhancers throughout the primate phylogeny. We observe subsets of regulatory sequences that appear to have gained or lost activity. We use these data to quantify the relationship between sequence and functional divergence, and to identify CpG deamination as a potentially important force in driving changes in enhancer activity during primate evolution.Electronic supplementary materialThe online version of this article (10.1186/s13059-018-1473-6) contains supplementary material, which is available to authorized users.

Massively parallel reporter assays (MPRAs) functionally screen thousands of sequences for regulatory activity in parallel. Although MPRAs have been applied to address diverse questions in gene regulation, there has been no systematic comparison of how differences in experimental design influence findings. Here, we screen a library of 2,440 sequences, representing candidate liver enhancers and controls, in HepG2 cells for regulatory activity using nine different approaches (including conventional episomal, STARR-seq, and lentiviral MPRA designs). We identify subtle but significant differences in the resulting measurements that correlate with epigenetic and sequence-level features. We also test this library in both orientations with respect to the promoter, validating en masse that enhancer activity is robustly independent of orientation.Finally, we develop and apply a novel method to assemble and functionally test libraries of the same putative enhancers as 192-mers, 354-mers, and 678-mers, and observe surprisingly large differences in functional activity. This work provides a framework for the experimental design of high-throughput reporter assays, suggesting that the extended sequence context of tested elements, and to a lesser degree the precise assay, influence MPRA results.

17To date, genome-wide association studies have implicated at least 35 loci in osteoarthritis, but 18 due to linkage disequilibrium, we have yet to pinpoint the specific variants that underlie these 19 associations, nor the mechanisms by which they contribute to disease risk. Here we functionally 20 tested 1,605 single nucleotide variants associated with osteoarthritis for regulatory activity using 21 a massively parallel reporter assay. We identified six single nucleotide polymorphisms (SNPs) 22 with differential regulatory activity between the major and minor alleles. We show that our most 23 significant hit, rs4730222, drives increased expression of an alternative isoform of HBP1 in a 24 heterozygote chondrosarcoma cell line, a CRISPR-edited osteosarcoma cell line, and in 25 chondrocytes derived from osteoarthritis patients. 27Main text 28 29 Genome-wide association studies (GWAS) have successfully implicated thousands of genetic 30 loci in common human diseases. Most of the underlying signal is believed to derive from 31 variation in non-coding regulatory sequences. However, because of linkage disequilibrium (LD), 32 it has been extraordinarily challenging for the field to identify the variants that causally underlie 33 each association. 35Over the past decade, we and others developed massively parallel reporter assays (MPRAs) to 36 increase the throughput at which regulatory sequences can be tested for functional potential [1][2][3][4] . 37An MPRA involves cloning thousands of candidate regulatory sequences to a single reporter was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/379727 doi: bioRxiv preprint first posted online Jul. 30, 2018; 3 scoring quintile includes 240 genomic regions, 67 of which overlap putative enhancers from at 81 least one dataset. In contrast, the least active quintile includes 239 genomic regions, only 37 of 82 which overlap putative enhancers from at least one dataset (1.8-fold difference, chi-square 83 p=9.7e-4). Altogether, these enrichments demonstrate that at least a subset of the 1,605 genomic 84 regions tested here correspond to enhancers in OA-relevant tissues. All activity scores are 85 included in Table S2. 87We next sought to ask whether any alleles are differentially active, focusing on the 752 SNPs for 88 which we successfully measured activity scores for both alleles (Table S3). Overall, activity 89 scores for two alleles of a given SNP were highly correlated, with an overall Spearman 90 correlation of 0.96 (Fig. 1G). This was reassuring, given that each pair of alleles was separately 91 synthesized and cloned, and therefore at non-identical abundances in the STARR-seq library. 92After correcting for multiple testing with Benjamini-Hochberg (BH) at a 5% FDR, we identified 936 SNPs whose alleles ...

The strong influence of various anions upon the hydrogenation of 2-phenyl-1-butene, catalyzed by chiral rhodium catalysts was investigated. Both sulfonates and halides exert large increases in the enantioselectivity when [Rh[(-)-bdpp](NBD)]ClO4 (bdpp = 2,4-bis(diphenylphosphino)pentane, NBD = 2,5-norbornadiene) is used as the catalyst precursor at high pressures (70 atm) of dihydrogen in nonpolar solvents. A dihydride mechanism similar to that for Wilkinson's catalyst [RhCl(PPh3)3] was shown to be operating at both high- and low-pressure conditions through a combination of catalytic studies, 31P, 1H and parahydrogen-induced polarization (PHIP) NMR experiments. With sulfonate and in neat methanol, however, a mechanistic switch takes place from a dihydride route (dihydrogen addition before olefin binding) at high pressure to an unsaturate route (olefin binding before dihydrogen addition) at low pressures (<30 atm). Olefin isomerization is inhibited by halide addition, but occurs with sulfonate and in neat methanol through what is most likely a pi-allyl mechanism. A detailed understanding of the effects of addition of these anions is crucial for development of new classes of catalysts capable of efficient enantioselective reduction of prochiral olefins lacking a secondary polar binding group.