PROMoterBINDING

Promoter binding refers to the interaction of RNA polymerase and transcription factors with promoter regions of DNA to initiate transcription. It is a key step in gene expression that precedes RNA synthesis. In bacteria, the RNA polymerase holoenzyme binds promoter sequences with the help of a sigma factor, recognizing conserved elements typically located about 35 and 10 bases upstream of the transcription start site. In eukaryotes, promoter binding involves a set of general transcription factors that assemble at the core promoter, often including a TATA box, initiator, or other core elements, and recruit RNA polymerase II to form a pre-initiation complex. Chromatin structure and histone modifications regulate promoter accessibility in higher organisms.

Binding is governed by DNA sequence specificity and protein–DNA interactions, with affinity modulated by regulatory proteins that activate or repress binding. In bacteria, activators and repressors influence sigma factor binding or promoter opening; in eukaryotes, transcription factors, coactivators, and chromatin remodelers alter chromatin to permit or inhibit promoter binding and RNA polymerase II recruitment. Promoter binding is often coupled to promoter melting/opening and initiation of RNA synthesis.

Regulation and significance: Proper promoter binding ensures correct spatial and temporal gene expression. Alterations in promoter sequence, transcription factor levels, or chromatin state can change binding dynamics and downstream transcription, contributing to development, adaptation, or disease.

Methods to study promoter binding include chromatin immunoprecipitation followed by sequencing (ChIP-seq) to map promoter-bound proteins in vivo, electrophoretic mobility shift assays (EMSA) for DNA–protein interactions in vitro, DNase I footprinting, promoter-reporter assays, and genome-wide assays that measure occupancy and transcription output.