Chromosome-naïve global networks of initiators of hybrid assembly pathways of endogenous multiprotein complexes

Mechanisms governing initiation steps of the assembly of endogenous multi-protein complexes (EMC) remain incompletely understood. Here, multiple lines of observations are reported describing the function-aligned initiation sequence of hybrid assembly pathways (HAP) of EMC. HAP concept postulates the creation of cell type-specific intracellular pools of hetero- and homodimers as the first step of chain reactions of protein-protein interactions (PPI) of EMC assemblies. To elucidate the molecular anatomy of HAP, qualitative and quantitative characteristics of protein binding to regulatory loci within defined sets of genomic regulatory elements (GRE) were investigated for a total of 200,393 distinct genomic sequences, including 49,667 sequences representing control sets of genomic loci as well as 150,726 GRE of different evolutionary origins. The consensus set of HAP actions consists of: a) Initiation on genomic DNA of the formation of metastable hetero- and homodimers of EMCs’ protein constituents; b) Release of dimers from DNA templates for delivery to the EMC assembly compartments; c) Assembly of defined EMC by sequential on demand addition to preformed dimers serving as attractors of EMC-specific monomers’ ensembles. Chromosome-naïve DNA scaffolds facilitating creation of intracellular dimer pools engage global networks of ~ 700 transcription factors (TFs), 534 of which manifest patterns of significantly enriched expression in 1358 brain regions. HAP initiators appear to operate within nucleosome-depleted islands of transposable elements (TE) – derived sequences within heterochromatin. PPI assembly lines of EMCs seem to operate in 2 concurrent modes: TF-TF PPI cascade and PPI HUB protein cascade. Regardless of the number of DNA-bound TFs initiating the PPI cascades (ranging from one to 716 TFs), both modes of operations reached the equilibrium at the PPI constituents saturation levels of ~ 245 proteins for TF-TF PPI modes and of ~ 351 proteins for PPI HUB protein modes. Distinct panels of DNA-bound initiator TFs and proteins of PPI cascade ensembles are enriched in either defined sets of neuroanatomical structures (TF-TF PPI mode) or among structural-functional constituents of synapses (PPI HUB proteins mode). Notably, the bifurcated cascades are biologically congruent: TF–TF constituents map to transcriptional signatures of hundreds of brain regions, whereas HUB constituents map to synaptogenesis and synaptic structures, suggesting a unified genomic logic coordinating region identity and connectivity. Evidence-supported examples of default operations of PPI-guided assemblies of hetero- and homodimers of Yamanaka factors, neurogenesis constituents, and protein components of postsynaptic density of excitatory and inhibitory synaptogenesis are reported. Altogether, this contribution reports the foundational set of observations for further experimental and theoretical explorations of TE-seeded genomic codes for initiators of PPI chain reactions of protein dimerization creating pools of attractors to guide and accelerate the EMC assemblies. Collectively, these findings support a Protein-Limited Bifurcated Assembly (PLBA) model, in which millions of TE–encoded DNA templates provide a non-limiting initiation layer while protein availability constrains the real-time bifurcation of PPI cascades into TF–TF pathways associated with brain-region identity and TF–HUB pathways associated with synaptic assembly.