ArticleGenome biology2009
Transcriptional features of genomic regulatory blocks.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed, 108 citations in OpenAlex.
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- The chromatin, topological and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo.Nature communications · 2021Article
- Topologically Associating Domains and Regulatory Landscapes in Development, Evolution and Disease.Frontiers in cell and developmental biology · 2021Review
- Embryonic tissue differentiation is characterized by transitions in cell cycle dynamic-associated core promoter regulation.Nucleic acids research · 2020Article
- Promoter CpG Density Predicts Downstream Gene Loss-of-Function Intolerance.American journal of human genetics · 2020Article
- Enhancer-gene maps in the human and zebrafish genomes using evolutionary linkage conservation.Nucleic acids research · 2020Article
- Understanding the genetics of neuropsychiatric disorders: the potential role of genomic regulatory blocks.Molecular psychiatry · 2020Review
- A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates.Bioinformatics (Oxford, England) · 2019Article
- Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes.Nature genetics · 2019Article
- The landscape of transcription initiation across latent and lytic KSHV genomes.PLoS pathogens · 2019Article
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- Eukaryotic core promoters and the functional basis of transcription initiation.Nature reviews. Molecular cell biology · 2018Review
- Epigenome-wide association in adipose tissue from the METSIM cohort.Human molecular genetics · 2018Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenomic regulatory blocks (GRBs) are chromosomal regions spanned by highly conserved non-coding elements (HCNEs), most of which serve as regulatory inputs of one target gene in the region. The target genes are most often transcription factors involved in embryonic development and differentiation. GRBs often contain extensive gene deserts, as well as additional 'bystander' genes intertwined with HCNEs but whose expression and function are unrelated to those of the target gene. The tight regulation of target genes, complex arrangement of regulatory inputs, and the differential responsiveness of genes in the region call for the examination of fundamental rules governing transcriptional activity in GRBs. Here we use extensive CAGE tag mapping of transcription start sites across different human tissues and differentiation stages combined with expression data and a number of sequence and epigenetic features to discover these rules and patterns.
resultsWe show evidence that GRB target genes have properties that set them apart from their bystanders as well as other genes in the genome: longer CpG islands, a higher number and wider spacing of alternative transcription start sites, and a distinct composition of transcription factor binding sites in their core/proximal promoters. Target gene expression correlates with the acetylation state of HCNEs in the region. Additionally, target gene promoters have a distinct combination of activating and repressing histone modifications in mouse embryonic stem cell lines.
conclusionsGRB targets are genes with a number of unique features that are the likely cause of their ability to respond to regulatory inputs from very long distances.
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