The Fire Ant Social Chromosome Exerts a Major Influence on Genome Regulation Article Swipe
Beryl M. Jones
,
Alex H Waugh
,
Michael A. Catto
,
Sasha Kay
,
Karl M. Glastad
,
Michael A. D. Goodisman
,
Sarah D. Kocher
,
Brendan G. Hunt
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1093/molbev/msaf112
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1093/molbev/msaf112
Supergenes underlying complex trait polymorphisms ensure that sets of coadapted alleles remain genetically linked. Despite their prevalence in nature, the mechanisms of supergene effects on genome regulation are poorly understood. In the fire ant Solenopsis invicta, a supergene containing over 500 individual genes influences trait variation in multiple castes to collectively underpin a colony level social polymorphism. Here, we present results of an integrative investigation of supergene effects on gene regulation. We present analyses of ATAC-seq data to investigate variation in chromatin accessibility by supergene genotype and STARR-seq data to characterize enhancer activity by supergene haplotype. Integration with gene co-expression analyses, newly mapped intact transposable elements (TEs), and previously identified copy number variants (CNVs) collectively reveals widespread effects of the supergene on chromatin structure, gene transcription, and regulatory element activity, with a genome-wide bias for open chromatin and increased expression in the presence of the derived supergene haplotype, particularly in regions that harbor intact TEs. Integrated consideration of CNVs and regulatory element divergence suggests each evolved in concert to shape the expression of supergene encoded factors, including several transcription factors that may directly contribute to the trans-regulatory footprint of a heteromorphic social chromosome. Overall, we show how genome structure in the form of a supergene has wide-reaching effects on gene regulation and gene expression.
Related Topics
Concepts
Biology
Supergene (geology)
Genetics
Chromatin
Enhancer
Gene
Genome
Haplotype
Regulation of gene expression
Transposable element
Evolutionary biology
Allele
Transcription factor
Ecology
Mineral
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/molbev/msaf112
- https://academic.oup.com/mbe/advance-article-pdf/doi/10.1093/molbev/msaf112/63328647/msaf112.pdf
- OA Status
- gold
- Cited By
- 1
- References
- 83
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4410706647
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4410706647Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1093/molbev/msaf112Digital Object Identifier
- Title
-
The Fire Ant Social Chromosome Exerts a Major Influence on Genome RegulationWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2025Year of publication
- Publication date
-
2025-05-23Full publication date if available
- Authors
-
Beryl M. Jones, Alex H Waugh, Michael A. Catto, Sasha Kay, Karl M. Glastad, Michael A. D. Goodisman, Sarah D. Kocher, Brendan G. HuntList of authors in order
- Landing page
-
https://doi.org/10.1093/molbev/msaf112Publisher landing page
- PDF URL
-
https://academic.oup.com/mbe/advance-article-pdf/doi/10.1093/molbev/msaf112/63328647/msaf112.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://academic.oup.com/mbe/advance-article-pdf/doi/10.1093/molbev/msaf112/63328647/msaf112.pdfDirect OA link when available
- Concepts
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Biology, Supergene (geology), Genetics, Chromatin, Enhancer, Gene, Genome, Haplotype, Regulation of gene expression, Transposable element, Evolutionary biology, Allele, Transcription factor, Ecology, MineralTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
1Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 1Per-year citation counts (last 5 years)
- References (count)
-
83Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.invicta, | 36 |
| abstract_inverted_index.multiple | 48 |
| abstract_inverted_index.presence | 143 |
| abstract_inverted_index.suggests | 164 |
| abstract_inverted_index.underpin | 52 |
| abstract_inverted_index.variants | 113 |
| abstract_inverted_index.STARR-seq | 88 |
| abstract_inverted_index.activity, | 130 |
| abstract_inverted_index.analyses, | 101 |
| abstract_inverted_index.chromatin | 82, 123, 137 |
| abstract_inverted_index.coadapted | 10 |
| abstract_inverted_index.footprint | 188 |
| abstract_inverted_index.including | 177 |
| abstract_inverted_index.increased | 139 |
| abstract_inverted_index.structure | 199 |
| abstract_inverted_index.supergene | 23, 38, 67, 85, 95, 121, 147, 174, 205 |
| abstract_inverted_index.variation | 46, 80 |
| abstract_inverted_index.Integrated | 156 |
| abstract_inverted_index.Solenopsis | 35 |
| abstract_inverted_index.Supergenes | 1 |
| abstract_inverted_index.containing | 39 |
| abstract_inverted_index.contribute | 184 |
| abstract_inverted_index.divergence | 163 |
| abstract_inverted_index.expression | 140, 172 |
| abstract_inverted_index.haplotype, | 148 |
| abstract_inverted_index.haplotype. | 96 |
| abstract_inverted_index.identified | 110 |
| abstract_inverted_index.individual | 42 |
| abstract_inverted_index.influences | 44 |
| abstract_inverted_index.mechanisms | 21 |
| abstract_inverted_index.prevalence | 17 |
| abstract_inverted_index.previously | 109 |
| abstract_inverted_index.regulation | 27, 211 |
| abstract_inverted_index.regulatory | 128, 161 |
| abstract_inverted_index.structure, | 124 |
| abstract_inverted_index.underlying | 2 |
| abstract_inverted_index.widespread | 117 |
| abstract_inverted_index.Integration | 97 |
| abstract_inverted_index.chromosome. | 193 |
| abstract_inverted_index.expression. | 214 |
| abstract_inverted_index.genetically | 13 |
| abstract_inverted_index.genome-wide | 133 |
| abstract_inverted_index.integrative | 64 |
| abstract_inverted_index.investigate | 79 |
| abstract_inverted_index.regulation. | 71 |
| abstract_inverted_index.understood. | 30 |
| abstract_inverted_index.characterize | 91 |
| abstract_inverted_index.collectively | 51, 115 |
| abstract_inverted_index.particularly | 149 |
| abstract_inverted_index.transposable | 105 |
| abstract_inverted_index.accessibility | 83 |
| abstract_inverted_index.co-expression | 100 |
| abstract_inverted_index.consideration | 157 |
| abstract_inverted_index.heteromorphic | 191 |
| abstract_inverted_index.investigation | 65 |
| abstract_inverted_index.polymorphism. | 57 |
| abstract_inverted_index.polymorphisms | 5 |
| abstract_inverted_index.transcription | 179 |
| abstract_inverted_index.wide-reaching | 207 |
| abstract_inverted_index.transcription, | 126 |
| abstract_inverted_index.trans-regulatory | 187 |
| cited_by_percentile_year.max | 95 |
| cited_by_percentile_year.min | 91 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 8 |
| citation_normalized_percentile.value | 0.89521612 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |