TFCheckpoint Transcription Factor checkpoint 2.0

Introduction

Transcription factors (TFs) in TFcheckpoint comprise the following categories:

TFs function in large protein-DNA complexes that govern RNA polymerase activity and thereby regulate the onset and rate of gene transcription. dbTFs guide the protein complexes to specific genomic addresses, thus constituting the primary mechanism that specifies which genes are transcriptionally regulated. The dbTFs serve as adaptors to bring additional coregulators (coTFs) to their binding sites. The dbTF - coTF protein complexes profoundly influence chromatin structure and function via a multitude of mechanisms including nucleosome remodelling, histone modification and DNA modification. Ultimately, these molecular complexes and processes result in gene-specific increase or decrease in frequency and amplitude of the transcription catalysed by RNA polymerases from the pre-initiation complex (PIC) constituted by RNA polymerase itself together with GTFs. For further details see e.g. Kim and Wysocka, 2023.

Access to accurate and genome-scale knowledge concerning these dbTFs and coTFs therefore is of key importance. Multiple resources with knowledge about mammalian transcription factors exist, and an integrated resource with information from these various resources, some of them reflecting prevailing understanding of what constituted a TFs at the time, can be helpful to understand why proteins are or are not yet described as a TF in the literature.