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.
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Noncoding RNA Regulation of Dormant States in Evolutionarily Diverse Animals
Dormancy is evolutionarily widespread and can take many forms, including diapause, dauer formation, estiva- tion, and hibernation. Each type of dormancy is characterized by distinct features; but accumulating evidence suggests that each is regulated by some common processes, often referred to as a common “toolkit” of regulatory mechanisms, that likely include noncoding RNAs that regulate gene expression. Non- coding RNAs, especially microRNAs, are well-known regula- tors of biological processes associated with numerous dormancy- related processes, including cell cycle progression, cell growth and proliferation, developmental timing, metabolism, and en- vironmental stress tolerance. This review provides a summary of our current understanding of noncoding RNAs and their in- volvement in regulating dormancy.
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- Award ID(s):
- 1755318
- PAR ID:
- 10560600
- Publisher / Repository:
- University of Chicago Press
- Date Published:
- Journal Name:
- The Biological Bulletin
- Volume:
- 237
- Issue:
- 2
- ISSN:
- 0006-3185
- Page Range / eLocation ID:
- 192 to 209
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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