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The ENCODE Consortium’s efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to investigate cis-regulatory mechanisms. The ENCODE4 Functional Characterization Centers conducted 108 screens in human cell lines, comprising >540,000 perturbations across 24.85 megabases of the genome. Using 332 functionally confirmed CRE–gene links in K562 cells, we established guidelines for screening endogenous noncoding elements with CRISPR interference (CRISPRi), including accurate detection of CREs that exhibit variable, often low, transcriptional effects. Benchmarking five screen analysis tools, we find that CASA produces the most conservative CRE calls and is robust to artifacts of low-specificity single guide RNAs. We uncover a subtle DNA strand bias for CRISPRi in transcribed regions with implications for screen design and analysis. Together, we provide an accessible data resource, predesigned single guide RNAs for targeting 3,275,697 ENCODE SCREEN candidate CREs with CRISPRi and screening guidelines to accelerate functional characterization of the noncoding genome. 

Silicon photonics is an emerging technology which, enabling nanoscale manipulation of light on chips, impacts areas as diverse as communications, computing, and sensing. Wavelength division multiplexing is commonly used to maximize throughput over a single optical channel by modulating multiple data streams on different wavelengths concurrently. Traditionally, wavelength (de)multiplexers are implemented as monolithic devices, separate from the grating coupler, used to couple light into the chip. This paper describes the design and measurement of a grating coupler demultiplexer—a single device which combines both light coupling and demultiplexing capabilities. The device was designed by means of a custom inverse design algorithm which leverages boundary integral Maxwell solvers of extremely rapid convergence as the mesh is refined. To the best of our knowledge, the fabricated device enjoys the lowest insertion loss reported for grating demultiplexers, small size, high splitting ratio, and low coupling-efficiency imbalance between ports, while meeting the fabricability constraints of a standard UV lithography process.