Transcription of eukaryotic protein-coding genes requires transfer of RNA polymerase II (Pol II) through nucleosomes. Nucleosomes are inherent barriers of transcription, and Pol II stalls at multiple locations within a nucleosome. Nucleosome core particle (NCP) consists of 145–147 base pairs of DNA wrapped around a histone protein octamer. Transcription elongation factors accompany Pol II to facilitate efficient transcription. They enable polymerase progression through NCPs and ensure re-establishment of chromatin after polymerase passage. The mechanisms underlying these processes, however, remain puzzling and poorly understood. Our aim is to present molecular details underlying Spt6 (histone chaperone and transcription factor) binding events. In our study we are revealing this long-standing open question by identifying elements of Spt6 that mediates interactions between Pol II and nucleosome. Cryo-electron microscopy, X-ray and Small Angle X-ray Scattering (SAXS) are used to study the macromolecular complex. Our findings provide a fundamental mechanistic insight into the functional specialization of Spt6 and have implications for the understanding of crosstalk between RNAP II and chromosomes.