ArticleAmerican journal of human genetics2018
Evolutionary Rewiring of Human Regulatory Networks by Waves of Genome Expansion.
Article in American journal of human genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 45 citations in OpenAlex.
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- Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks.Genome research · 2025Article
- The trait-specific timing of accelerated genomic change in the human lineage.Cell genomics · 2025Article
- Genetic effects of sequence-conserved enhancer-like elements on human complex traits.Genome biology · 2024Article
- The genetic architecture and evolution of the human skeletal form.Science (New York, N.Y.) · 2023Article
- The genetic architecture of the human skeletal form.bioRxiv : the preprint server for biology · 2023Article
- Function and Constraint in Enhancer Sequences with Multiple Evolutionary Origins.Genome biology and evolution · 2022Article
- Young transposable elements rewired gene regulatory networks in human and chimpanzee hippocampal intermediate progenitors.Development (Cambridge, England) · 2022Article
- Three topological features of regulatory networks control life-essential and specialized subsystems.Scientific reports · 2021Article
- Transposable elements shape the evolution of mammalian development.Nature reviews. Genetics · 2021Review
- Leveraging auxiliary data from arbitrary distributions to boost GWAS discovery with Flexible cFDR.PLoS genetics · 2021Article
- Retrotransposons as Drivers of Mammalian Brain Evolution.Life (Basel, Switzerland) · 2021Review
- Role of Transposable Elements in Gene Regulation in the Human Genome.Life (Basel, Switzerland) · 2021Review
- Transposable elements as a potent source of diversePhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Review
- Formation of human long intergenic non-coding RNA genes, pseudogenes, and protein genes: Ancestral sequences are key players.PloS one · 2020Article
- Article
- Disease Heritability Enrichment of Regulatory Elements Is Concentrated in Elements with Ancient Sequence Age and Conserved Function across Species.American journal of human genetics · 2019Article
- An integrated chromatin accessibility and transcriptome landscape of human pre-implantation embryos.Nature communications · 2019Article
- Systematic discovery of conservation states for single-nucleotide annotation of the human genome.Communications biology · 2019Article
- Novel Bioinformatics Approach Identifies Transcriptional Profiles of Lineage-Specific Transposable Elements at Distinct Loci in the Human Dorsolateral Prefrontal Cortex.Molecular biology and evolution · 2018Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome expansion is believed to be an important driver of the evolution of gene regulation. To investigate the role of a newly arising sequence in rewiring regulatory networks, we estimated the age of each region of the human genome by applying maximum parsimony to genome-wide alignments with 100 vertebrates. We then studied the age distribution of several types of functional regions, with a focus on regulatory elements. The age distribution of regulatory elements reveals the extensive use of newly formed genomic sequence in the evolution of regulatory interactions. Many transcription factors have expanded their repertoire of targets through waves of genomic expansions that can be traced to specific evolutionary times. Repeated elements contributed a major part of such expansion: many classes of such elements are enriched in binding sites of one or a few specific transcription factors, whose binding sites are localized in specific portions of the element and characterized by distinctive motif words. These features suggest that the binding sites were available as soon as the new sequence entered the genome, rather than being created later by accumulation of point mutations. By comparing the age of regulatory regions to the evolutionary shift in expression of nearby genes, we show that rewiring through genome expansion played an important role in shaping human regulatory networks.
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