Abstract
ABSTRACTGene regulation by enhancers is important for precise temporal and spatial gene expression. Enhancers can drive gene expression regardless of their location, orientation or distance from the promoter. Changes in chromatin conformation and chromatin looping occur to bring the promoter and enhancers into close proximity. αA-crystallin ranks among one of the most abundantly expressed genes and proteins in the mammalian lens. The αA-crystallin locus is characterized by a 16 kb chromatin domain marked by two distal enhancers, 5′ DCR1 and 3′ DCR3. Here we used chromatin conformation capture (3C) analysis and transgenic approaches to analyze temporal control of the mouse αA-crystallin gene. We find that DCR1 is necessary, but not sufficient alone to drive expression at E10.5 in the mouse lens pit. Chromatin looping revealed interaction between the promoter and the region 3′ to DCR1, identifying a novel enhancer region in the αA-crystallin locus. We determined that this novel enhancer region, DCR1S, recapitulates the temporal control by DCR1. Acting as shadow enhancers, DCR1 and DCR1S are able to control expression in the lens vesicle at E11.5. It remains to be elucidated however, which region of the αA-crystallin locus is responsible for expression in the lens pit at E10.5.
Highlights
Precise regulation of gene transcription during tissue development lays the foundation for cellular identity, with levels of gene expression varying greatly between cell types as well as developmental time points (Regev et al, 2017)
Exogenous expression of EGFP driven by a 15 kb αA-crystallin locus (Fig. 2A), allowed for recapitulation of the endogenous αA-crystallin expression (Wolf et al, 2008), with expression beginning in the lens pit at E10.5 (Fig. 2C–F)
Even when the entire locus is present, the absence of DCR1 delayed the expression of EGFP (Fig. 2G–J), with no EGFP expression being seen at E10.5 in the lens pit (Fig. 2G)
Summary
Precise regulation of gene transcription during tissue development lays the foundation for cellular identity, with levels of gene expression varying greatly between cell types as well as developmental time points (Regev et al, 2017). Important regulatory elements for tissueand developmental-specific transcription are the enhancers: cisregulatory elements comprised of clustered arrays of transcription factor binding sites (see Barolo and Posakony, 2002; Catarino and Stark, 2018; Long et al, 2016). These ‘classical’ enhancers can drive transcription regardless of their location, orientation or distance from the gene promoter (reviewed in Schaffner, 2015). Received 2 July 2018; Accepted 15 October 2018 becoming a routine process by way of genome-wide chromatin profiling methods to identify ‘open’ chromatin regions as well as enhancer associated histone marks (Andrey and Mundlos, 2017), elucidation of the precise cell-specificity and temporal/spatial activities of individual candidate enhancers requires experimentation
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