Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans
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Like Father, Like Mother, Like Child: Transcriptional regulation is mediated by chromatin structure, which may affect the binding of transcription factors, but the extent of how individual-to-individual genetic variation affects such regulation is not well understood. Kasowski et al. (p. 232 , published online 18 March) investigated the binding of two transcription factors across the genomes of human individuals and one chimpanzee. Transcription factor binding was associated with genomic features such as nucleotide variation, insertions and deletions, and copy number variation. Thus, genomic sequence variation affects transcription factor binding and may explain expression difference among individuals. McDaniell et al. (p. 235 , published online 18 March) provide a genome-wide catalog of variation in chromatin and transcription factor binding in two parent-child trios of European and African ancestry. Up to 10% of active chromatin binding sites were specific to a set of individuals and were often inherited. Furthermore, variation in active chromatin sites showed heritable allele-specific correlation with variation in gene expression.
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An analysis of chromatin accessibility and CTCF binding in parents and children from families of different ancestry found many bound sites unique to each ancestry, with differential binding mainly explained by genetic variation.
“For example, analysis of chromatin accessibility and 'CCCTC-binding factor' (CTCF) DNA binding in parents and children from families with different ancestry found a substantial percentage of bound sites that were unique to each ancestry, with differential binding being explained mainly by genetic variation 56 .”
From Advances in epigenetics link genetics to the environment and disease (2019) · cites this paper as [56]
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- Authors
- McDaniell, R., Lee, B.-K., Song, L., Liu, Z., Boyle, A. P., Erdos, M. R., Scott, L. J., Morken, M. A., Kucera, K. S., Battenhouse, A., Keefe, D., Collins, F. S., Willard, H. F., Lieb, J. D., Furey, T. S., Crawford, G. E., Iyer, V. R., & Birney, E.
- Affiliations
- The University of Texas at Austin (US)
- Duke University (US)
- National Human Genome Research Institute (US)
- University of Michigan (US)
- European Bioinformatics Institute (GB)
- University of North Carolina at Chapel Hill (US)
- Corresponding author
- Liu, Zheng
- Crawford, Gregory E.
- Iyer, Vishwanath R.
- Birney, Ewan
- ORCID
- Venue
- Science
- Published
- 2010-04-09
- Volume
- 328
- Issue
- 5975
- Pages
- 235-239
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC2929018
- OpenAlex
- W2091303550
- Cited by
- 308
- References
- 17
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 6 · 2023: 8 · 2022: 9 · 2021: 18 · 2020: 2 · 2019: 9 · 2018: 13 · 2017: 16 · 2016: 23 · 2015: 24 · 2014: 28 · 2013: 37 · 2012: 46
- FWCI
- 19.30
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Funders
- National Institutes of Health (5u54hg004563-04)
- National Human Genome Research Institute (U54‑HG004563, Z01HG000024)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- chromatin signatures, transcription factor binding, heritability, copy number variation, indels, nucleotide variation, gene expression variation, parent-child trios, chimpanzee genome, transcriptional regulation
- MeSH terms
- CCCTC-Binding Factor, Alleles, Binding Sites, Cell Line, Chromatin, Chromosomes, Human, Deoxyribonuclease I, Female, Gene Expression Regulation, Humans, Male, Nuclear Family, Protein Binding, Repressor Proteins, Transcription Factors, Genetic Variation, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Chromosomes, Human, X, Black People, White People, Chromatin Immunoprecipitation, X Chromosome Inactivation, Regulatory Elements, Transcriptional
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