Mechanisms of Binding Specificity among bHLH Transcription Factors

Abstract

The transcriptome of every cell is orchestrated by the complex network of interaction between transcription factors (TFs) and their binding sites on DNA. Disruption of this network can result in many forms of organism malfunction but also can be the substrate of positive natural selection. However, understanding the specific determinants of each of these individual TF-DNA interactions is a challenging task as it requires integrating the multiple possible mechanisms by which a given TF ends up interacting with a specific genomic region. These mechanisms include DNA motif preferences, which can be determined by nucleotide sequence but also by DNA’s shape; post-translational modifications of the TF, such as phosphorylation; and dimerization partners and co-factors, which can mediate multiple forms of direct or indirect cooperative binding. Binding can also be affected by epigenetic modifications of putative target regions, including DNA methylation and nucleosome occupancy. In this review, we describe how all these mechanisms have a role and crosstalk in one specific family of TFs, the basic helix-loop-helix (bHLH), with a very conserved DNA binding domain and a similar DNA preferred motif, the E-box. Here, we compile and discuss a rich catalog of strategies used by bHLH to acquire TF-specific genome-wide landscapes of binding sites.

False-Positive IRESes from Hoxa9 and other genes resulting from errors in mammalian 5’ UTR annotations

“…However, mutating Hoxa9 E-boxes had a stronger effect (Figure 4), suggesting other bHLH transcription factors may also promote expression from these binding sites. Along those lines, other Hoxa reporters were not affected by USF1 / USF2 depletion, suggesting they may instead be regulated by other bHLH factors that recognize the same core motif (CACGTG) (33, 36). Notably, public mouse ChIP-seq data show USF1 , USF2 , MYC , MAX, TFE3 , ARNTL , BHLHE40 , and BHLHE41 bind to Hoxa gene E-boxes (Figure S7) (38–42, 44–51, 59–66).…”

“…Specifically, these were sensitive to mutations in the nucleotides underlined “GA CACGUGA C”, and similar sequences can be found in other putative Hoxa gene IRESes (4). Using FIMO (23) to search for transcription factor binding sites, we found the equivalent DNA sequence (CACGTG) matches the E-box motif recognized by bHLH transcription factors MYC / MAX (24) and USF1 / USF2 (25, 26). Recent work showed USF2 binds upstream of human Hoxa9 , and that co-depletion of USF1 and USF2 decreases Hoxa9 expression in human tissue culture cells (27)(Figure 3A).…”

MIRA: Joint regulatory modeling of multimodal expression and chromatin accessibility in single cells

“…6c and f, Extended Data Table 6). Ascl1 and Neurod1 belong to separate subgroups of basic helixloop-helix transcription factors 39 ; and Neurod1 promotes differentiation of induced pluripotent stem cells into excitatory neurons, while Ascl1 specifies inhibitory neurons 37 .…”

Key transcription factors influence the epigenetic landscape to regulate retinal cell differentiation

“…Many of these factors are co-expressed in the tRPCs, and some of them continue to be expressed in the differentiated neurons. Although these bHLH factors belong to distinct classes and have some sequence preferences for the E box motif, their binding specificities are significantly redundant [105][106][107][108] . Thus, the molecular basis for the cell lineage specificities of individual bHLH factors is not known.…”