Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions inDrosophila

Abstract

According to recent models, as yet poorly studied architectural proteins appear to be required for local regulation of enhancer–promoter interactions, as well as for global chromosome organization. Transcription factors ZIPIC, Pita and Zw5 belong to the class of chromatin insulator proteins and preferentially bind to promoters near the TSS and extensively colocalize with cohesin and condensin complexes. ZIPIC, Pita and Zw5 are structurally similar in containing the N-terminal zinc finger-associated domain (ZAD) and different numbers of C2H2-type zinc fingers at the C-terminus. Here we have shown that the ZAD domains of ZIPIC, Pita and Zw5 form homodimers. In Drosophila transgenic lines, these proteins are able to support long-distance interaction between GAL4 activator and the reporter gene promoter. However, no functional interaction between binding sites for different proteins has been revealed, suggesting that such interactions are highly specific. ZIPIC facilitates long-distance stimulation of the reporter gene by GAL4 activator in yeast model system. Many of the genomic binding sites of ZIPIC, Pita and Zw5 are located at the boundaries of topologically associated domains (TADs). Thus, ZAD-containing zinc-finger proteins can be attributed to the class of architectural proteins.

Three-Dimensional Genome Organization and Function in Drosophila

“…Recent studies suggest that the DNA binding proteins CTCF, Dwg, Pita, and ZIPIC can homodimerize. This may also contribute to interactions between insulator elements (Bonchuk et al 2015; Zolotarev et al 2016). The Cp190 and Mod(mdg4) proteins, themselves, are biochemically and functionally different.…”

Architectural protein Pita cooperates with dCTCF in organization of functional boundaries in Bithorax complex

“…Previous genome-wide ChIP experiments with samples from embryos and S2 tissue culture cells identified several Pita-bound regions in BX-C with a high confidence Zolotarev et al, 2016a). These Pita-bound regions coincide with known functional elements in BX-C, including the Fub-2, Fub, Mcp and Fab-7 boundaries, and the Abd-B [AB-E] and [AB-C] promoter regions ( Fig.…”

“…Although only one architectural DNA-binding protein, CTCF, has been as yet identified in mammals (Ali et al, 2016;Ghirlando and Felsenfeld, 2016;Merkenschlager and Nora, 2016), ongoing studies suggest that Drosophila probably has many architectural proteins Zolotarev et al, 2016a). This discrepancy likely reflects the relatively simple methods and assays that are available for studying boundaries/insulators in flies that are not readily feasible in higher eukaryotes.…”

Computer methods of analysis of chromosome contacts in the cell nucleus based on sequencing technology data

“…Продолжаются работы по исследованию хромосомной упаковки, определению дистальных взаимодействий хроматина в модельных организмах [34].…”

“…Применения методов http://mirnylab.bitbucket.org/hiclib/index.html [32] Juicer и Juicebox Компьютерные решения для визуализации контактов по данным Hi-C. http://aidenlab.org/juicer/ [33] анализа трёхмерной структуры генома открывают новые области в биотехнологии, требуя также развития специализированных программ [34].…”