Transcriptional regulation and its misregulation in disease

Abstract

The gene expression programs that establish and maintain specific cell states in humans are controlled by thousands of transcription factors, cofactors, and chromatin regulators. Misregulation of these gene expression programs can cause a broad range of diseases. Here, we review recent advances in our understanding of transcriptional regulation and discuss how these have provided new insights into transcriptional misregulation in disease.

Figure 1

Transcriptional regulation A. Formation of a pre-initiation complex. Transcription factors bind to specific DNA elements (enhancers) and to coactivators, which bind to RNA polymerase II, which in turn binds to general transcription factors at the transcription start site (arrow). The DNA loop formed between the enhancer and the start site is stabilized by cofactors such as the Mediator complex and cohesin. B. Initiation and pausing by RNA polymerase II. RNA polymerase II begins transcription from the initiation site, but pause control factors cause it to stall some tens of base pairs downstream. C. Pause release and elongation. Various transcription factors and cofactors recruit elongation factors, including P-TEFb, which phosphorylates the pause release factors and polymerase, allowing elongation to proceed. D. Chromatin structure is regulated by ATP-dependent remodeling complexes that can mobilize the nucleosome, allowing regulators and the transcription apparatus increased access to DNA sequences. E. Transcriptional activity is influenced by proteins that modify and bind the histone components of nucleosomes. Some proteins add modifications (writers), some remove modifications (erasers) and others bind via these modifications (readers). The modifications include acetylation (Ac), methylation (Me), phosphorylation (P), sumoylation (Su) and ubiquitination (Ub). F. Histone modifications occur in characteristic patterns associated with different transcriptional activities. As an example, the characteristic patterns observed at actively transcribed genes are shown for histone H3 lysine 27 acetylation (H3K27Ac), histone H3 lysine 4 trimethylation (H3K4me3), histone H3 lysine 79 dimethylation (H3K79me2) and histone H3 lysine 36 trimethylation (H3K36me3).

Figure 2

Master transcriptional regulators and reprogramming factors Transcription factors that have dominant roles in the control of specific cell states and that are capable of reprogramming cell states when ectopically expressed in various cell types (Buganim et al., 2012; Davis et al., 1987; Huang et al., 2011; Ieda et al., 2010; Kajimura et al., 2009; Marro et al., 2011; Pang et al., 2011; Sekiya and Suzuki, 2011; Takahashi and Yamanaka, 2006; Vierbuchen et al., 2010; Xie et al., 2004; Zhou et al., 2008).

Figure 3

Features of master transcription factors of ES cells that likely extend to other cell types A. Master transcription factors are expressed at high levels relative to other transcription factors (30,000 – 300,000 molecules/cell). B. Master transcription factors dominate control of the gene expression program by forming enhancers that are associated with most active ESC genes. C. Master transcription factors positively regulate transcription of cell type-specifying genes and, together with Polycomb group proteins, negatively regulate the expression of genes that specify other cell types. D. Master transcription factors (circles) positively regulate their own genes (boxes), forming interconnected autoregulatory loops.

Figure 4

Global alterations in gene expression programs through transcription elongation. Top panel: Transcriptional amplification of the gene expression program. The transcription factor c-Myc stimulates increased elongation of most actively transcribed genes, producing increased levels of transcripts for most genes in the gene expression program of the cell. Middle panel: Expanded pause release extends the gene expression program. In some cells, RNA polymerase will initiate transcription at some genes but fails to transition to elongation. AIRE stimulates pause release for many of these initiated genes, thus producing transcripts for many genes that are normally expressed only in peripheral tissues. Bottom panel: Specific pause release. Some elongation factors stimulate pause release at specific sets of genes that are important for a particular cell’s function.