Abstract
The mammalian genome is depleted in CG dinucleotides, except at protected regions where they cluster as CpG islands (CGIs). CGIs are gene regulatory hubs and serve as transcription initiation sites and are as expected, associated with gene promoters. Advances in genomic annotations demonstrate that a quarter of CGIs are found within genes. Such intragenic regions are repressive environments, so it is surprising that CGIs reside here and even more surprising that some resist repression and are transcriptionally active within a gene. Hence, intragenic CGI positioning within genes is not arbitrary and is instead, selected for. As a wealth of recent studies demonstrate, intragenic CGIs are embedded within genes and consequently, influence ‘host’ gene mRNA isoform length and expand transcriptome diversity.
Highlights
Gene regulation is a prerequisite of life, the seemingly simple decision of whether to express a gene or not is present in most organisms
These findings demonstrate that a transcriptionally active iCGI can influence alternative polyadenylation and highlight the ways in which iCGIs can shape the transcriptome
Counterparts (Illingworth et al, 2010; Auclair et al, 2014), implying that regulation of iCGIs is crucial for tissue specific programming
Summary
Department of Medical and Molecular Genetics, King’s College London, Guy’s Hospital, London, United Kingdom Edited by: Robert Feil, UMR5535 Institut de Génétique Moléculaire de Montpellier (IGMM), France Reviewed by: Maxim Van Cleef Greenberg, UMR7592 Institut Jacques Monod (IJM), France Specialty section: This article was submitted to Developmental Epigenetics, a section of the journal
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