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Cited by 259Genomics and Chromatin DynamicsCRISPR and Genetic EngineeringChromatin Remodeling and Cancer

A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells

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Diao, Yarui, Fang, Rongxin, Li, Bin, Meng, Zhipeng, Yu, Juntao, Qiu, Yunjiang, Lin, Kimberly C, Huang, Hui +6 more·2017·Nature Methods
DOI 10.1038/nmeth.4264PMC PMC5490986
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Abstract

Millions of cis-regulatory elements are predicted to be present in the human genome, but direct evidence for their biological function is scarce. Here we report a high-throughput method, cis-regulatory element scan by tiling-deletion and sequencing (CREST-seq), for the unbiased discovery and functional assessment of cis-regulatory sequences in the genome. We used it to interrogate the 2-Mb POU5F1 locus in human embryonic stem cells, and identified 45 cis-regulatory elements. A majority of these elements have active chromatin marks, DNase hypersensitivity, and occupancy by multiple transcription factors, which confirms the utility of chromatin signatures in cis-element mapping. Notably, 17 of them are previously annotated promoters of functionally unrelated genes, and like typical enhancers, they form extensive spatial contacts with the POU5F1 promoter. These results point to the commonality of enhancer-like promoters in the human genome.

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  • A shared limitation of single-gene screens is that phenotyping is restricted to one or a few genes per experiment.

    “A shared limitation of single-gene screens, whether by CRISPR, CRISPRi, or CRISPRa, is that the phenotyping is restricted to one or a few genes per experiment, e.g. by engineering a reporter to the target gene133,201,203,208, by labelling mRNA products with fluorescence in situ hybridization (FISH)209, or by focusing on drug-responsive202,204, antibody-detectable92, or proliferation-related105,200”

    From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [203]

  • Certain promoters, termed epromoters, can also function as enhancers.

    “Finally, evidence from multiple sources including reporter assays [169, 175, 239, 240], CRISPR [240–242], chromatin mapping [243, 244] and population genetics analysis [207, 245] suggests that certain promoters, termed ‘epromoters’, can also function as enhancers (reviewed in [246]).”

    From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [242]

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Cited by

Sorted by citations

Authors
Diao, Y., Fang, R., Li, B., Meng, Z., Yu, J., Qiu, Y., Lin, K. C., Huang, H., Liu, T., Marina, R. J., Jung, I., Shen, Y., Guan, K.-L., & Ren, B.
Affiliations
  • Ludwig Cancer Research (US)
  • University of California San Diego (US)
  • University of Science and Technology of China (CN)
  • Korea Advanced Institute of Science and Technology (KR)
  • University of California, San Francisco (US)
Corresponding author
Ren, Bing
ORCID
Venue
Nature Methods
Publisher
Springer Science and Business Media LLC
Published
2017-04-17
Volume
14
Issue
6
Pages
629-635
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
DOI
10.1038/nmeth.4264
PMC
PMC5490986
OpenAlex
W2606434976
Cited by
259
References
14
Citations by year
2026: 14 · 2025: 17 · 2024: 16 · 2023: 25 · 2022: 27 · 2021: 36 · 2020: 41 · 2019: 43 · 2018: 26 · 2017: 13
FWCI
14.53
Type
journal article
Language
en
Open access
Licence
www.springer.com/tdm (tdm)
Locations
  • Nature Methods (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
Funders
  • National Human Genome Research Institute (U54HG006997, R01HG008135, UM1HG009402)
  • National Institute of General Medical Sciences (P50GM085764, T32GM007752)
  • National Institute of Diabetes and Digestive and Kidney Diseases (U01DK105541)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Keywords
cis-regulatory elements, CRISPR/Cas9 genome editing, distal enhancers, human embryonic stem cells, chromatin accessibility, DNase hypersensitivity, transcription factor occupancy, enhancer-promoter interactions, functional genomic screens
MeSH terms
Algorithms, Cells, Cultured, Chromosome Mapping, Gene Expression Regulation, Genetic Testing, Humans, Regulatory Sequences, Nucleic Acid, Sequence Analysis, DNA, Embryonic Stem Cells, Single-Cell Analysis, High-Throughput Nucleotide Sequencing

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