How transcription circuits explore alternative architectures while maintaining overall circuit output

Abstract

Transcription regulators bind to -regulatory sequences and thereby control the expression of target genes. While transcription regulators and the target genes that they regulate are often deeply conserved across species, the connections between the two change extensively over evolutionary timescales. In this review, we discuss case studies where, despite this extensive evolutionary rewiring, the resulting patterns of gene expression are preserved. We also discuss in silico models that reach the same general conclusions and provide additional insights into how this process occurs. Together, these approaches make a strong case that the preservation of gene expression patterns in the wake of extensive rewiring is a general feature of transcription circuit evolution.

Enhancer and super‐enhancer: Positive regulators in gene transcription

“…RNA polymerase II (RNAPII) is identified as the core factor to initiate and regulate gene expression by coordinating with lots of other factors, including general transcription factors, enhancers, mediators, cohesions, insulators, and silencers accompanying with other epigenetic mechanisms . In the past decades, next generation sequencing (NGS) has been innovated into transcription research . Genome architecture, methylation, acetylation, and other histone modifications have also been brought into the field, which dramatically extended the view of transcription regulation .…”

Transcriptional Circuit Fragility Influences HIV Proviral Fate

“…Both cellular activators and Tat promote proviral transcription in the host and viral phases, respectively, through a complex layer of host factors including general transcription factors, RNA polymerase II (Pol II), co-activators/co-repressors, and chromatin-modifying enzymes, among others (Ott et al, 2011;Van Lint et al, 2013). One key host factor is the positive transcription elongation factor b (the P-TEFb kinase) (Dalal and Johnson, 2017;Wei et al, 1998), which is composed of a cyclin T subunit and the catalytic CDK9 subunit (hereafter referred as CDK9). Both cellular activators and Tat utilize CDK9 to facilitate the transcription elongation program, a critical step in the viral life cycle (Mancebo et al, 1997;Ott et al, 2011;Peterlin and Price, 2006;Zhou et al, 2000).…”

Binding and Regulation of Transcription by Yeast Ste12 Variants To Drive Mating and Invasion Phenotypes

“…Our results add to the emerging argument that transcriptional regulation can be readily rewired, changing the underlying transcriptional circuits in various ways while preserving phenotypic outputs. In evolution, this extensive rewiring can occur even among closely related species, and is facilitated by the rapid gain and loss of short cis-regulatory sequences, or by variation in transcription factors (Dalal and Johnson 2017).…”