Lens development depends on a pair of highly conserved Sox21 regulatory elements

► Conserved non-coding elements (CNEs) linked to Sox21 contain two lens enhancers. ► Removal of these enhancers from a reporter BAC abolishes lens expression. ► Morpholino knockdown of zebrafish sox21b leads to defects in lens development. ► Conserved putative Sox binding sites are vital for enhancer activity in lens and CNS. ► CNEs are crucial for normal development and contain overlapping embryonic enhancers.