Core promoter-specific gene regulation: TATA box selectivity and Initiator-dependent bi-directionality of serum response factor-activated transcription

Abstract

Gene-specific activation by enhancers involves their communication with the basal RNA polymerase II transcription machinery at the core promoter. Core promoters are diverse and may contain a variety of sequence elements such as the TATA box, the Initiator (INR), and the downstream promoter element (DPE) recognized, respectively, by the TATA-binding protein (TBP) and TBP-associated factors of the TFIID complex. Core promoter elements contribute to the gene selectivity of enhancers, and INR/DPE-specific enhancers and activators have been identified. Here, we identify a TATA box-selective activating sequence upstream of the human β-actin (ACTB) gene that mediates serum response factor (SRF)-induced transcription from TATA-dependent but not INR-dependent promoters and requires the TATA-binding/bending activity of TBP, which is otherwise dispensable for transcription from a TATA-less promoter. The SRF-dependent ACTB sequence is stereospecific on TATA promoters but activates in an orientation-independent manner a composite TATA/INR-containing promoter. More generally, we show that SRF-regulated genes of the actin/cytoskeleton/contractile family tend to have a TATA box. These results suggest distinct TATA-dependent and INR-dependent mechanisms of TFIID-mediated transcription in mammalian cells that are compatible with only certain stereospecific combinations of activators, and that a TBP-TATA binding mechanism is important for SRF activation of the actin/cytoskeleton-related gene family.

EED, a member of the polycomb group, is required for nephron differentiation and the maintenance of nephron progenitor cells

“…3B). The physiological basis for the differential expression of tdTomato from this transgene is unknown, but might relate to SRF/MRTF-binding sites in the chick ACTB promoter within the CAG construct and the differential activity of these actin levelsensitive transcription factors (Knöll, 2010;Xu et al, 2016) in various cell types of the developing kidney. RNA sequencing (RNA-seq) was used to define these populations obtained from control and Eed mutant mice by FACS (Table S1, Fig.…”

DeePromoter: Robust Promoter Predictor Using Deep Learning

“…In human case, 24% of genes have promoter regions containing TATA-box (Yang et al, 2007). In eukaryotes, TATA-box is located at ~25 bp upstream of the TSS (Xu et al, 2016). It is able to define the direction of transcription and also indicates the DNA strand to be read.…”

Cloning and promoter analysis of palladin 90-kDa, 140-kDa, and 200-kDa isoforms involved in skeletal muscle cell maturation

“…MEF2 site is essential for the amplification of Mef2c involved in skeletal muscle development [22]. Additionally, analysis of the promoters of the actin-related group of serum response factor (SRF) with scaffolding or contractile functions has indicated that approximately 43% of the involved genes in the mouse contains TATA box sequences within the core promoter region [23]. In a cascade regulation process induced by the cytokine transforming growth factor beta (TGF-β), E2A immunoglobulin enhancer-binding factors E12 and E47 regulate palladin cytoskeletal protein [24].…”