ArticlePhilosophical transactions of the Royal Society of London. Series B, Biological sciences2020
Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns.
Article in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 41 citations in OpenAlex.
- Transcriptome of fetal cortex of tree shrew underlying the emergence of outer subventricular zone.Communications biology · 2026Article
- Zinc finger domains bind low-complexity domain polymers.Nature communications · 2025Article
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- Single chromatin fiber profiling and nucleosome position mapping in the human brain.Cell reports methods · 2024Article
- ZNF91 is an endogenous repressor of the molecular phenotype associated with X-linked dystonia-parkinsonism (XDP).Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Four classic "de novo" genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences.Molecular genetics and genomics : MGG · 2024Article
- Epigenome-wide DNA methylation analysis of late-stage mild cognitive impairment.Frontiers in cell and developmental biology · 2024Article
- Structural Evolution of Gene Promoters Driven by Primate-Specific KRAB Zinc Finger Proteins.Genome biology and evolution · 2023Article
- Genetic features and genomic targets of human KRAB-zinc finger proteins.Genome research · 2023Article
- ZFP92, a KRAB domain zinc finger protein enriched in pancreatic islets, binds to B1/Alu SINE transposable elements and regulates retroelements and genes.PLoS genetics · 2023Article
- Zinc in Cognitive Impairment and Aging.Biomolecules · 2022Review
- KRAB zinc finger protein ZNF676 controls the transcriptional influence of LTR12-related endogenous retrovirus sequences.Mobile DNA · 2022Article
- Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans.Mobile DNA · 2021Review
- Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain.Genome research · 2021Article
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- Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics.BMC molecular and cell biology · 2021Article
- Zinc Finger Proteins in Neuro-Related Diseases Progression.Frontiers in neuroscience · 2021Review
- Genomics-Guided Drawing of Molecular and Pathophysiological Components of Malignant Regulatory Signatures Reveals a Pivotal Role in Human Diseases of Stem Cell-Associated Retroviral Sequences and Functionally-Active hESC Enhancers.Frontiers in oncology · 2021Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The large family of KRAB zinc finger (KZNF) genes are transcription factors implicated in recognizing and repressing repetitive sequences such as transposable elements (TEs) in our genome. Through successive waves of retrotransposition-mediated insertions, various classes of TEs have invaded mammalian genomes at multiple timepoints throughout evolution. Even though most of the TE classes in our genome lost the capability to retrotranspose millions of years ago, it remains elusive why the KZNFs that evolved to repress them are still retained in our genome. One hypothesis is that KZNFs become repurposed for other regulatory roles. Here, we find evidence that evolutionary changes in KZNFs provide them not only with the ability to repress TEs, but also to bind to gene promoters independent of TEs. Using KZNF binding site data in conjunction with gene expression values from the Allen Brain Atlas, we show that KZNFs have the ability to regulate gene expression in the human brain in a region-specific manner. Our analysis shows that the expression of KZNFs shows correlation with the expression of their target genes, suggesting that KZNFs have a direct influence on gene expression in the developing human brain. The extent of this regulation and the impact it has on primate brain evolution are still to be determined, but our results imply that KZNFs have become widely integrated into neuronal gene regulatory networks. Our analysis predicts that gene expression networks have been repeatedly innovated throughout primate evolution, continuously gaining new layers of gene regulation mediated by both TEs and KZNFs in our genome. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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