The Core Promoter Is a Regulatory Hub for Developmental Gene Expression

Abstract

The development of multicellular organisms and the uniqueness of each cell are achieved by distinct transcriptional programs. Multiple processes that regulate gene expression converge at the core promoter region, an 80 bp region that directs accurate transcription initiation by RNA polymerase II (Pol II). In recent years, it has become apparent that the core promoter region is not a passive DNA component, but rather an active regulatory module of transcriptional programs. Distinct core promoter compositions were demonstrated to result in different transcriptional outputs. In this mini-review, we focus on the role of the core promoter, particularly its downstream region, as the regulatory hub for developmental genes. The downstream core promoter element (DPE) was implicated in the control of evolutionarily conserved developmental gene regulatory networks (GRNs) governing body plan in both the anterior-posterior and dorsal-ventral axes. Notably, the composition of the basal transcription machinery is not universal, but rather promoter-dependent, highlighting the importance of specialized transcription complexes and their core promoter target sequences as key hubs that drive embryonic development, differentiation and morphogenesis across metazoan species. The extent of transcriptional activation by a specific enhancer is dependent on its compatibility with the relevant core promoter. The core promoter content also regulates transcription burst size. Overall, while for many years it was thought that the specificity of gene expression is primarily determined by enhancers, it is now clear that the core promoter region comprises an important regulatory module in the intricate networks of developmental gene expression.

Transcriptional Regulation and Protein Localization of Zip10, Zip13 and Zip14 Transporters of Freshwater Teleost Yellow Catfish Pelteobagrus fulvidraco Following Zn Exposure in a Heterologous HEK293T Model

“…Similarly, in our study, 2278 bp, 1917 bp, and 1989 bp zip10 , zip13 and zip 14 promoters of P. fulvidraco were cloned. The earlier studies suggested that the core promoters of genes played central roles in initiating the transcriptions [ 51 , 52 ]. In our study, we predicted one GC-box (SP1), one CCAAT-box (NF-Y), and one TATA-box in the core region of the zip10 promoter.…”

Antennapedia: The complexity of a master developmental transcription factor

“…These promoters have unique features that allow selective regulation during development. According to the current classification of eukaryotic promoters (reviewed in Ngoc et al, 2019;Sloutskin et al, 2021), P1 is a dispersed promoter with four non-canonical TSS, while P2 is a focused promoter with a DPE box (Juven-Gershon et al, 2008), a motif recognized by the basal transcription machinery factor TFIID subunits, TAF6 and TAF9 (Burke & Kadonaga, 1996. This complex gene structure and expression have an effect on the production and dosage of different Antennapedia isoforms.…”

The Power of Gene Technologies: 1001 Ways to Create a Cell Model

“…A promoter is a DNA sequence that controls gene expression; it contains binding sites for transcription factors and RNA polymerases [ 19 ]. The number and spectrum of transcription factors involved and the position of their binding sites relative to the transcription start site (TSS) determine the frequency of binding of the transcription complex and, therefore, the efficiency of gene expression that corresponds to such a characteristic of the promoter as “promoter strength” [ 19 , 20 , 21 ]. The versatility or tissue-specificity of a promoter (the ability to provide gene expression in a wide range of cells or in a certain type of them) is ensured by the presence of binding sites for versatile or tissue-specific transcription factors, respectively [ 19 , 20 , 21 ].…”

“…The number and spectrum of transcription factors involved and the position of their binding sites relative to the transcription start site (TSS) determine the frequency of binding of the transcription complex and, therefore, the efficiency of gene expression that corresponds to such a characteristic of the promoter as “promoter strength” [ 19 , 20 , 21 ]. The versatility or tissue-specificity of a promoter (the ability to provide gene expression in a wide range of cells or in a certain type of them) is ensured by the presence of binding sites for versatile or tissue-specific transcription factors, respectively [ 19 , 20 , 21 ]. A constitutively active promoter contains binding sites for transcription factors that are permanently active in a certain cell type, which ensures constant gene expression.…”

“…The main disadvantage includes the lack of flexibility and the high basal level of gene expression during regular cellular activity. Expression of most genes is tightly regulated depending on the cell type, differentiation status and cell cycle phase [ 21 , 27 ]. All this cannot be reproduced by forced expression of a gene under the control of a strong constitutive promoter.…”