Evidence map›Paper›PMID 29735996›Full record

ArticleNature methods2018

C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2.

Xin D Gao, Li-Chun Tu, Aamir Mir, Tomás Rodriguez, Yuehe Ding, John Leszyk, Job Dekker, Scott A Shaffer, Lihua Julie Zhu, Scot A Wolfe and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature methods, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.

0numbers the graph read from it
0cells of the map it votes in
106citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

106 citing papers in PubMed.

  1. Article
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  7. Article
  8. A unified photosensitizer platform forbioRxiv : the preprint server for biology · 2026
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  12. Article
  13. Review
  14. Review
  15. Article
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  17. Methods for the Investigation of Protein-Ligands Interactions.Advances in experimental medicine and biology · 2026
    Review
  18. Article
  19. Review
  20. Article

46 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Xin D GaoRNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.
Li-Chun TuRNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.
Aamir MirRNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.
Tomás RodriguezRNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.
Yuehe DingRNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.
John LeszykProteomics and Mass Spectrometry Facility, University of Massachusetts Medical School, Worcester, MA, USA.
Job DekkerDepartment of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
Scott A ShafferProteomics and Mass Spectrometry Facility, University of Massachusetts Medical School, Worcester, MA, USA.
Lihua Julie ZhuDepartment of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.
Scot A WolfeDepartment of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
Erik J SontheimerRNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA. erik.sontheimer@umassmed.edu.

Funding

Center for 3D Structure and Physics of the GenomeU54DK107980 · NIDDK · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI DEKKER, JOB, MIRNY, LEONID A · 2015 to 2019
$14.9M
Deciphering real-time dynamics of the human genome organization in response to DNA damage and gene expressionK99GM126810 · NIGMS · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI TU, LI-CHUN · 2017 to 2018
$128k
NIDDK NIH HHS U54 DK107980NIGMS NIH HHS K99 GM126810
6 · The paper itself

Abstract

Mapping proteomic composition at distinct genomic loci in living cells has been a long-standing challenge. Here we report that dCas9-APEX2 biotinylation at genomic elements by restricted spatial tagging (C-BERST) allows the rapid, unbiased mapping of proteomes near defined genomic loci, as demonstrated for telomeres and centromeres. C-BERST enables the high-throughput identification of proteins associated with specific sequences, thereby facilitating annotation of these factors and their roles.

Indexed as

Cell Line, TumorChromosome MappingCRISPR-Associated Protein 9DNA-(Apurinic or Apyrimidinic Site) LyaseEndonucleasesGene Expression RegulationGenomeGenomicsHumansMultifunctional EnzymesProtein EngineeringProteomeProteomicsAPEX2 protein, humanCRISPR-Associated Protein 9DNA-(Apurinic or Apyrimidinic Site) LyaseEndonucleasesMultifunctional EnzymesProteome

Identifiers

PMID29735996
PMCPMC6202229

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.