Although silencer cCREs are enriched within CA-TF and TF cCRE classes, these groups also contain regulatory elements with distinct and previously underappreciated functions. One prominent example is cCREs bound by the transcription factors MAFF and MAFK. While a substantial fraction of MAFF/MAFK-bound elements lack detectable chromatin accessibility across most biosamples, integrative analysis of functional activity, chromatin state, gene expression, and evolutionary conservation reveals that these elements often behave as latent, stimulus-responsive enhancers rather than silencers. These findings motivated the formal inclusion of TF cCREs in the Registry and highlight the importance of anchoring regulatory annotation beyond open chromatin alone.
Frequently Asked Questions
Not all MAFF/MAFK-bound cCREs reside in inaccessible chromatin. A substantial subset is classified as enhancer cCREs and shows active chromatin signatures and regulatory activity in well-profiled cell types such as K562 and HepG2. This enables direct comparison of MAFF/MAFK-associated enhancers to other enhancers within the same cellular contexts, as well as comparison of their activity across cell types.
These analyses show that MAFF/MAFK-associated enhancers exhibit distinct activity patterns across biosamples, differ in transcription factor binding profiles, and are linked to genes enriched for developmental and stimulus-responsive processes. Together, the coexistence of active enhancers in some contexts and latent or inaccessible elements in others provides strong evidence that MAFF/MAFK mark a dynamic class of enhancers whose regulatory activity depends on cell type and cell state.
Analyses of genes proximal to MAFF/MAFK+ cCREs show strong enrichment for developmental and morphogenetic processes, including organ development, neural differentiation, signal transduction, and pathways such as Wnt and TGF-β signaling. These functional categories are characteristic of regulatory programs that are activated transiently during development or in response to environmental or cellular cues, rather than constitutively active across cell types.
Consistent with this interpretation, MAFF/MAFK+ enhancer cCREs exhibit active chromatin signatures in a restricted set of biosamples, including myeloid-derived primary cells, fibroblasts, and select tumor or stress-associated contexts, while remaining inactive in most other cell types. A subset of MAFF/MAFK+ TF cCREs lacking active chromatin marks is instead linked to sensory perception pathways, such as olfaction, suggesting activity in specialized cell types or developmental states not yet represented in the Registry. Together, these results support a model in which MAFF/MAFK mark latent, context-dependent enhancers that become active only in specific developmental, environmental, or cell-state conditions.
Many MAFF/MAFK-associated enhancers lack detectable chromatin accessibility across most surveyed biosamples and therefore would not be captured by annotations anchored solely on DNase hypersensitivity. By incorporating TF-cluster–based anchors into the Registry, we identify regulatory elements that are bound by transcription factors but remain inaccessible under baseline conditions. These results emphasize that regulatory activity depends not only on cell type but also on cell state, with some enhancers poised for activation in response to stress or external stimuli rather than constitutively active.
Although MAFF and MAFK have been described as transcriptional repressors in specific contexts by previous reports, our analyses show that cCREs bound by these factors do not exhibit intrinsic silencer activity when tested in STARR-seq or inferred from nearby gene expression. This distinction is important: transcription factor–mediated repression can depend on co-factors, chromatin context, or higher-order regulatory mechanisms that are not captured by sequence-centric reporter assays. Thus, MAFF and MAFK may still function as repressors in vivo, even when the underlying cCRE sequence does not independently encode silencer activity as measured by our assays.
Many MAFF/MAFK-associated enhancers lack detectable chromatin accessibility across most surveyed biosamples and therefore would not be captured by annotations anchored solely on DNase hypersensitivity. By incorporating TF-cluster–based anchors into the Registry, we identify regulatory elements that are bound by transcription factors but remain inaccessible under baseline conditions. These results emphasize that regulatory activity depends not only on cell type but also on cell state, with some enhancers poised for activation in response to stress or external stimuli rather than constitutively active.