Title

Pervasive and CpG-dependent promoter-like characteristics of transcribed enhancers.

Document Type

Article

Publication Date

6-4-2020

Keywords

JGM, CpG Islands, Enhancer Elements, Genetic, Gene Expression Regulation, Histone Code, Humans, Organ Specificity, Promoter Regions, Genetic, TATA Box, Transcription Factors, Transcription Initiation, Genetic, Transcription, Genetic

JAX Source

Nucleic Acids Res 2020 Jun 4; 48(10):5306-5317

Volume

48

Issue

10

First Page

5306

Last Page

5317

ISSN

1362-4962

PMID

32338759

DOI

https://doi.org/10.1093/nar/gkaa223

Abstract

The temporal and spatial expression of genes is controlled by promoters and enhancers. Findings obtained over the last decade that not only promoters but also enhancers are characterized by bidirectional, divergent transcription have challenged the traditional notion that promoters and enhancers represent distinct classes of regulatory elements. Over half of human promoters are associated with CpG islands (CGIs), relatively CpG-rich stretches of generally several hundred nucleotides that are often associated with housekeeping genes. Only about 6% of transcribed enhancers defined by CAGE-tag analysis are associated with CGIs. Here, we present an analysis of enhancer and promoter characteristics and relate them to the presence or absence of CGIs. We show that transcribed enhancers share a number of CGI-dependent characteristics with promoters, including statistically significant local overrepresentation of core promoter elements. CGI-associated enhancers are longer, display higher directionality of transcription, greater expression, a lesser degree of tissue specificity, and a higher frequency of transcription-factor binding events than non-CGI-associated enhancers. Genes putatively regulated by CGI-associated enhancers are enriched for transcription regulator activity. Our findings show that CGI-associated transcribed enhancers display a series of characteristics related to sequence, expression and function that distinguish them from enhancers not associated with CGIs.

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