Chemical Decorations of "MARs" Residents in Orchestrating Eukaryotic Gene Regulation

Abstract

Genome organization plays a crucial role in gene regulation, orchestrating multiple cellular functions. A meshwork of proteins constituting a three-dimensional (3D) matrix helps in maintaining the genomic architecture. Sequences of DNA that are involved in tethering the chromatin to the matrix are called scaffold/matrix attachment regions (S/MARs), and the proteins that bind to these sequences and mediate tethering are termed S/MAR-binding proteins (S/MARBPs). The regulation of S/MARBPs is important for cellular functions and is altered under different conditions. Limited information is available presently to understand the structure-function relationship conclusively. Although all S/MARBPs bind to DNA, their context- and tissue-specific regulatory roles cannot be justified solely based on the available information on their structures. Conformational changes in a protein lead to changes in protein-protein interactions (PPIs) that essentially would regulate functional outcomes. A well-studied form of protein regulation is post-translational modification (PTM). It involves disulfide bond formation, cleavage of precursor proteins, and addition or removal of low-molecular-weight groups, leading to modifications like phosphorylation, methylation, SUMOylation, acetylation, PARylation, and ubiquitination. These chemical modifications lead to varied functional outcomes by mechanisms like modifying DNA-protein interactions and PPIs, altering protein function, stability, and crosstalk with other PTMs regulating subcellular localizations. S/MARBPs are reported to be regulated by PTMs, thereby contributing to gene regulation. In this review, we discuss the current understanding, scope, disease implications, and future perspectives of the diverse PTMs regulating functions of S/MARBPs.

Keywords: S/MAR-binding protein; chromatin 3D architecture; disease; gene regulation; post-translation modification (PTM).

Figure 1

Distinct chromosomal territories showing scaffold/matrix attachment region binding proteins (S/MARBPs) that mediate chromatin attachment and with matrix can be regulated by post-translational modifications, leading to various outcomes.

Figure 2

I-TASSER web server was used to predict the structural models for the following proteins: (A) CTCF, (B) SATB1, (C) SMAR1, (D) HMG1, (E) Ku70, (F) PARP1, (G) MeCP2, and (H) nucleolin. The best model out of the top five predicted models for each has been shown.

Figure 3

TopMatch tool was used to perform a pair-wise structural alignment between the PDB structures: (A) alignment between 1JJR (C-terminal DNA-binding domain of human Ku70) vs. 2KRR (RBD 1,2 domains of human nucleolin), 1JJR vs. 3TUO (N-terminal domain of human SATB1), 1JJR vs. 5YEH (CTCF ZFs4-8-eCBS), 2KRR vs. 3TUO, 2KRR vs. 5YEH, 2O49 (N-terminal CUT domain of SATB1 bound to S/MAR DNA) vs. 6OGK (MeCP2 methyl-binding domain in complex with DNA), 3D0A (Human MUT p53 R249S with second site suppressor mutation H168R, core domain in complex with DNA) vs. 3TUO, 3D0A vs. 5YEH, 3TUO vs. 5YEH, 5T00 (Human CTCF ZnF3-7 in complex with methylated DNA) vs. 1QK9 (MeCP2 DNA-binding domain in complex with methylated DNA), 5T00 vs. 6OGK, 5T00 vs. 6OGJ (MeCP2 methyl-binding domain in complex with DNA), 6OGJ vs. 1UB1 (S/MAR-binding domain of chicken MeCP2), and 6OGK vs. 1UB1. (B) Details of the sequence length aligned and the corresponding scores.

Figure 4

D²P² tool was used to assess the intrinsically disordered regions (IDRs) in the following S/MARBPs: CTCF, SATB1, SMAR1, PARP1, MeCP2, nucleolin, HMG1, and Ku70. It uses the following tools for prediction of disordered regions: PONDR VL-XT, PONDR VSL2b, PrDOS, Espritz, PV2, IUPred, and ANCHOR. The pastel-colored blocks (disorder predictions) are aligned and stacked against the polypeptide chain in black. The SCOP (structural classification of proteins) domains are represented by the brightly colored rounded blocks. The agreement level across the different predictors is displayed by color intensity in aligned bar and stacked below the predictions. The yellow blocks having zigzag infills represent the ANCHOR-binding region predictions along with PTM sites predicted by PhosphoSitePlus.

Figure 5

InteractiVenn was used to construct the Venn diagrams to understand similarity of protein–protein interactions (PPIs) between different combinations of S/MARBPs: (A) HMG1, DNAPK, MeCP2, SATB1, and PARP1; (B) BANP (SMAR1), CTCF, PARP1, and SATB1; (C) BANP, CTCF, and Ku70; and (D) SATB1 and SATB2. The numerical values represent the number of interacting partners.

Figure 6

Examples showing importance of PTMs in regulating S/MARBP functions.

Figure 7

Identification of link between S/MARBP PTM code and disease predisposition.