Functional and mechanistic diversity of distal transcription enhancers

By M. Bulger, Mark Groudine. Cell, 2011

1,117 citations recorded by the source corpus.

Biological differences among metazoans, and between cell types in a given organism, arise in large part due to differences in gene expression patterns. The sequencing of multiple metazoan genomes, coupled with recent advances in genome-wide analysis of histone modifications and transcription factor binding, has revealed that among regulatory DNA sequences, gene-distal enhancers appear to exhibit the greatest diversity and cell-type specificity. Moreover, such elements are emerging as important targets for mutations that can give rise to disease and to genetic variability that underlies evolutionary change. Studies of long-range interactions between distal genomic sequences in the nucleus indicate that enhancers are often important determinants of nuclear organization, contributing to a general model for enhancer function that involves direct enhancer-promoter contact. In a number of systems, however, mechanisms for enhancer function are emerging that do not fit solely within such a model, suggesting that enhancers as a class of DNA regulatory element may be functionally and mechanistically diverse.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1964050c9f956e60755cc12706c013d65d5b2b63

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes (2013, positive): “Much of the transcriptional control of mammalian development is due to the diverse activity of transcription factor-bound enhancers that control cell type-specific patterns of gene expression (Bulger and Groudine, 2011; Hawrylycz et al., 2012; Maston et al., 2006).”
Transcriptional Amplification in Tumor Cells with Elevated c-Myc (2012, positive): “Furthermore, enhancers loop into proximity of core promoters at active genes (Bulger and Groudine, 2011; Göndör and Ohlsson, 2009; Kagey et al., 2010; Ong and Corces, 2011) and this proximity may facilitate binding of c-Myc to nearby enhancer elements once binding to sites in core promoters is satur”
Non-coding RNAs in Development and Disease: Background, Mechanisms, and Therapeutic Approaches. (2016, background): “Enhancer elements can activate genes independently of their genomic distance, orientation, and location (34, 210).”
PEDLA: predicting enhancers with a deep learning-based algorithmic framework (2016, neutral): “(4) H3K27ac peaks with significant enrichment of H3K4me3 within a 2 kb window centred on the peak were also removed.”
Functional Importance of eRNAs for Estrogen-dependent Transcriptional Activation Events (2013, methodology): “In addition, for each interaction, we define supplementary parameters, such as (1) fold enrichment over Poisson’s l, and (2) a fold enrichment over background (where the background represents the average intensity of the ligations between the probes on the neighbouring restriction sites).”
Systematic mapping of functional enhancer-promoter connections with CRISPR interference (2016, positive): “Studies of individual regulatory elements have revealed principles of their function, such as the ability of enhancers to recruit activating transcription factors, modify chromatin state, and physically interact with target genes (1, 2).”
Transcriptional Addiction in Cancer (2017, neutral): “…cooperatively to enhancer DNA elements and recruit coactivators and the transcription apparatus (Banerji et al., 1981; Benoist and Chambon, 1981; Bulger and Groudine, 2011; Gruss et al., 1981; Jolma et al., 2015; Lelli et al., 2012; Levine et al., 2014; Malik and Roeder, 2010; Ong and Corces,…”
Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence (2011, background): “Promoters and enhancers are the best understood types of CRE”
CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function (2015, neutral): “Genome-wide studies of mammalian genomes have shown that there are far more enhancers than promoters and that spatiotemporal gene expression is regulated through one or more promoters and multiple enhancers (Bulger and Groudine, 2011; ENCODE Project Consortium, 2012; Zhang et al., 2004).”
Modification of enhancer chromatin: what, how and why? (2013, background): “…play a central role in driving cell-type-specific gene expression and are capable of activating transcription of their target genes at great distances, ranging from several to hundreds, in rare cases even thousands, of kilobases (reviewed in Bulger and Groudine, 2011; Ong and Corces, 2011, 2012).”
YY1 Is a Structural Regulator of Enhancer-Promoter Loops (2017, positive): “Graphical abstract INTRODUCTION Cell-type-specific gene expression programs in humans are generally controlled by gene regulatory elements called enhancers (Buecker and Wysocka, 2012; Bulger and Groudine, 2011; Levine et al., 2014; Ong and Corces, 2011; Ren and Yue, 2015).”