Biology subjects

Mantovani, R.

Publications and source records attributed to Mantovani, R..

2 recordsLinked to original sources

bioRxiv2026

Cooperative reading of DECA-CCAAT composite element by the TALE/NF-Y/Sp2 transcription factors

To understand how genes are regulated it is important to assess the molecular basis of TFs cooperation in promoter and enhancer regulatory elements. Compelling genetic, genomic and biochemical data in mammals and zebrafish point at DECA-CCAAT composite elements as important for regulation of gene expression in development. DECA is recognized by the homeodomain (HD) heterodimeric TALE TFs (PBX/PREP), CCAAT by the NF-Y trimer. Both are evolutionarily conserved in eukaryotes, including plants. Sp2, a member of the Sp/KLF family, potentiates association of TALE and NF-Y on DNA. We applied AlphaFold to infer the structural basis of the hexameric complex with DNA. The resulting models position TALE and NF-Y on the respective sites, predicting the complex arrangement of the MEINOX/PBC heterodimerization module of the TALE TFs and the sequence-specific DNA contacts of the HDs to DECA. The complex is tied by the Sp2 N-terminus, which contacts the TALE dimer through the -helical SP-box and the NF-Y trimer through a novel short linear motif (YA-SLiM). A flexible linker separates the anchor points, consistent with the constrained stereo-alignment of the DECA-CCAAT motif. The models are confirmed by assembly of the recombinant NF-Y/TALE/Sp2 in complex with DNA in vitro. Mutagenesis confirms the importance of the SP-box and YA-SLiM for cooperativity. Rationalising available genomic and biochemical data, the structural models depict a novel mode of cooperative binding on DNA, providing important clues as to how TFs potentially function beyond DECA-CCAAT in different eukaryotic contexts.

molecular biology↗

bioRxiv2026

A recently evolved TAF8 isoform arising from an Alu insertion increases TFIID assembly complexity in the human lineage

Despite its centrality in regulating RNA polymerase II transcription in all eukaryotes, the TFIID general transcription factor exhibits several layers of variability across different tissues and developmental stages, representing an underexplored hub of evolutionary innovation. Here, we describe a novel short isoform of TAF8 (TAF8s) - a TFIID scaffold subunit - which evolved from the use of an intronic polyadenylation site (iPAS) in the human lineage. Comparative genomics analyses show that the emergence of TAF8s expression in the human lineage coincides with minute DNA changes in the iPAS at the edge of a FLAM-C Alu element that inserted into intron 5 in the common ancestor of anthropoid primates (Simiiformes). The human-specific TAF8s isoform lacks nearly half of the canonical coding sequence, is widely expressed across human tissues, and constitutes a substantial fraction of the TAF8 transcript pool. TAF8s is translated into a truncated protein isoform that lacks the nuclear-localization signal and localises in the cytoplasm. TAF8s interacts with its histone-fold partner TAF10 and other core TFIID subunits, while entirely losing its interactions with TAF2, thus giving rise to alternative TFIID sub-complexes in human cells. Our study suggests that the TFIID complex underwent a recent diversification through a stepwise evolutionary acquisition of complexity in the TAF8 locus in the human lineage, leading to the expression of a novel truncated pan-isoform that might work as a modulator of TFIID assembly. We discuss the ramifications of our findings in TFIID complex diversification, its evolvability, and the genetics of TAF-related congenital disorders.

molecular biology↗