Evidence map›Paper›PMID 26512062›Full record

ArticleHuman molecular genetics2016

Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation.

Isabel Mendizabal, Soojin V Yi

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Human molecular genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.

0numbers the graph read from it
0cells of the map it votes in
34citing papers in PubMed
2.3field-weighted citation impact, top 12% of its field
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

34 citing papers in PubMed, 55 citations in OpenAlex.

  1. Germline hypomethylation shapes dynamic CpG reservoirs in ape genomes.bioRxiv : the preprint server for biology · 2026
    Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. The important role of miR-1-3p in cancers.Journal of translational medicine · 2023
    Review
  8. Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Review
  14. Article
  15. Article
  16. Article
  17. Review
  18. Article
  19. Article
  20. Review
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

2 authors at 2 institutions in 2 countries.

Isabel MendizabalSchool of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA and Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain.
Soojin V YiSchool of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA and soojinyi@gatech.edu.
Georgia Institute of Technology · USUniversity of the Basque Country · ES

Funding

Human Specific Brain DNA Methylation and Neuropsychiatric DiseasesR01MH103517 · NIMH · GEORGIA INSTITUTE OF TECHNOLOGY · PI JORDAN, IRVING KING, PREUSS, TODD M · 2015 to 2019
$3.5M
Resource development for a new model of social threat responseR21MH102677 · NIMH · EMORY UNIVERSITY · PI MANEY, DONNA L, YI, SOOJIN · 2014 to 2015
$430k
NIMH NIH HHS 1R01MH102677-01A1NIMH NIH HHS 1R01MH103517-01A1NIMH NIH HHS R01 MH103517NIMH NIH HHS R21MH102677
6 · The paper itself

Abstract

CpG islands (CGIs) are one of the most widely studied regulatory features of the human genome, with critical roles in development and disease. Despite such significance and the original epigenetic definition, currently used CGI sets are typically predicted from DNA sequence characteristics. Although CGIs are deeply implicated in practical analyses of DNA methylation, recent studies have shown that such computational annotations suffer from inaccuracies. Here we used whole-genome bisulfite sequencing from 10 diverse human tissues to identify a comprehensive, experimentally obtained, single-base resolution CGI catalog. In addition to the unparalleled annotation precision, our method is free from potential bias due to arbitrary sequence features or probe affinity differences. In addition to clarifying substantial false positives in the widely used University of California Santa Cruz (UCSC) annotations, our study identifies numerous novel epigenetic loci. In particular, we reveal significant impact of transposable elements on the epigenetic regulatory landscape of the human genome and demonstrate ubiquitous presence of transcription initiation at CGIs, including alternative promoters in gene bodies and non-coding RNAs in intergenic regions. Moreover, coordinated DNA methylation and chromatin modifications mark tissue-specific enhancers at novel CGIs. Enrichment of specific transcription factor binding from ChIP-seq supports mechanistic roles of CGIs on the regulation of tissue-specific transcription. The new CGI catalog provides a comprehensive and integrated list of genomic hotspots of epigenetic regulation.

Indexed as

CpG IslandsEpigenesis, GeneticSequence Analysis, DNAChromatinHumansMolecular Sequence AnnotationOrgan SpecificityPromoter Regions, GeneticSulfitesTranscription FactorsChromatinhydrogen sulfiteSulfitesTranscription Factors

Identifiers

PMID26512062
PMCPMC4690492
OpenAlexW2209288790

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.