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A major challenge in the application of the CRISPR-Cas13d system is to accurately predict its guide-dependent on-target and off-target effect. Here, we perform CRISPR-Cas13d proliferation screens and design a deep learning model, named DeepCas13, to predict the on-target activity from guide sequences and secondary structures. DeepCas13 outperforms existing methods to predict the efficiency of guides targeting both protein-coding and non-coding RNAs. Guides targeting non-essential genes display off-target viability effects, which are closely related to their on-target efficiencies. Choosing proper negative control guides during normalization mitigates the associated false positives in proliferation screens. We apply DeepCas13 to the guides targeting lncRNAs, and identify lncRNAs that affect cell viability and proliferation in multiple cell lines. The higher prediction accuracy of DeepCas13 over existing methods is extensively confirmed via a secondary CRISPR-Cas13d screen and quantitative RT-PCR experiments. DeepCas13 is freely accessible via http://deepcas13.weililab.org.

High-order chromatin organization plays a central role in regulating spatial-temporal gene expression by facilitating or constraining the interactions between cis-regulatory elements (cREs). cREs are often the accessible DNA sequences and can be identified at genome-wide scale with assays such as ATAC-seq, DHS-seq, and FAIRE-seq. However, it remains technically challenging to comprehensively identify the long-range interactions that occur between cREs, especially using low-input cells and in a cost effective manner. Here, we report HiCAR, Hi gh-throughput C hromosome conformation capture on A ccessible DNA with m R NA-seq co-assay, which enables simultaneous mapping of chromatin accessibility and cRE anchored chromatin contacts. Notably, using the same input material, HiCAR also yields high-quality transcriptome data that represents the functional outputs of chromatin accessibility and interaction. Unlike immunoprecipitation-based methods such as HiChIP, PLAC-seq, and ChIA-PET, HiCAR does not require target-specific antibodies and thus can capture cis-regulatory contacts anchored on the accessible DNA regions associated with multiple epigenetic modifications and transcription factor binding. We compared HiCAR to another technology designed to capture interactions between accessible chromatin regions, called Trac-looping, and found that HiCAR yielded much more informative long-range cis- reads at similar sequencing depth, and requires far fewer cells as input. We applied HiCAR to H1 human embryonic stem cells (hESC) and identified 46,792 open-chromatin anchored loops at 5Kb resolution. Interestingly, we found that the poised cREs form extensive and significant chromatin interactions comparable to the active cREs. We further showed that the spatial interactive activity of cREs do not correlate with their transcriptional activity, enhancer activity, and chromatin accessibility. Additionally, we identified 2,096 super interactive regulatory (SINTER) loci showing abnormally high levels of chromatin interactivity and associated with unique epigenetic features. In summary, HiCAR is a robust, sensitive, and cost effective multi-omics coassay that can be used to study chromatin structure and function as well as gene expression.

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