Inducible Protein Degradation to Understand Genome Architecture

Abstract

We review exciting recent advances in protein degradation, with a focus on chromatin structure. In our analysis of the literature, we highlight studies of kinetic control of protein stability for cohesin, condensin, ATP-dependent chromatin remodeling, and pioneer transcription factors. With new connections emerging between chromatin remodeling and genome structure, we anticipate exciting developments at the intersection of these topics to be revealed in the coming years. Moreover, we pay special attention to the 20-year anniversary of PROTACs, with an overview of E3 ligase/target pairings and central questions that might lead to the next generation of PROTACs with an expanded scope and generality. While steady-state experimental measurements with constitutive genome editing are impactful, we highlight complementary approaches for rapid kinetic protein degradation to uncover early targeting functions and to understand the central determinants of genome structure–function relationships.

Functional Epigenomics: Pioneering Changes in Chromatin Structure

“…The elusive relationship between RNA transcription and genome conformation has been a major focus in recent literature. 1 Of note, a study from Hsieh et al 5 uses integrated chromatin structural sequencing and imaging to uncover a large degree of independence between the major players of mammalian chromatin structure (cohesin, CTCF, WAPL) and RNA expression. Combining the nucleosome sensitivity of MNase and the in situ components of Hi-C (Micro-C), the authors find that rapid inducible depletion of cohesin complexes only affects a small fraction of the exome.…”

“…The elusive relationship between RNA transcription and genome conformation has been a major focus in recent literature . Of note, a study from Hsieh et al uses integrated chromatin structural sequencing and imaging to uncover a large degree of independence between the major players of mammalian chromatin structure (cohesin, CTCF, WAPL) and RNA expression.…”

“…Recent studies have provided mechanistic and conceptual connections among the functions of pioneer transcription factors, ATP-dependent chromatin remodelers, molecular motors, and genome structure. We previously provided our perspective on key points of epigenetic interactivity at different scales of genome organization, with a focus on rapid kinetically controlled experiments . Now, we are especially interested in newly published studies that address the spectrum between canonical transcription factors (TFs), which bind only accessible chromatin regions, and pioneering transcription factors (PFs), which can invade closed chromatin to destabilize nucleosomes.…”

Chromatin structure in cancer

“…Recent evidence indicates that chromatin domains can be targeted by clinical [ 11 ] or pre-clinical [ 9 , 29 ] chemotherapeutic strategies. New insights into the regulatory roles of topoisomerases have revealed the potential of the clinical molecule etoposide to covalently disrupt chromatin domains [ 11 ].…”

EBF1 is continuously required for stabilizing local chromatin accessibility in pro-B cells

“…The recent analysis aimed at elucidating the dynamics of SWI/SNF function by inducible protein degradation or pharmacological inhibition showed that the loss of SWI/SNF activity results in a rapid closure of active chromatin ( 20 , 21 ). To address the question of whether or not the maintenance of stable chromatin accessibility also requires a continuous function of pioneer TFs, we adopted the degradation TAG (dTAG) system for inducible degradation of EBF1, tagged with FK506-binding protein (FKBP) ( 22 – 24 ). Here, we report that EBF1 is required for continuous BRG1 recruitment and maintenance of open chromatin regions.…”