Using genetic (yeast two-hybrid system) and biochemical (coprecipitation of proteins from cellular lysates) approaches, we have performed a whole-genome wide search for interacting partners of variants of the hRPB11 subunit of human RNA polymerase II that we have previously described (hRPB11bα, hRPB11cα, hRPB11bβ, hRPB11cβ) in fetal brain and the Jurkat cell line libraries. In consequence, the main spectra of the protein partners of these human-specific isoforms of the RNA polymerase II subunit hRPB11 (POLR2J) were defined. Functional characteristics of the uncovered protein partners of the hRPB11bα and hRPB11cα isoforms clearly indicate that these isoforms, like the major subunit hRPB11a, are components of distinct transcription complexes that not only participate in transcription of specific DNA matrices, but are also involved in the later stages of mRNA biogenesis. The common subunit of RNA polymerases I?III hRPB6 (POLR2F) and basal component of the exon-exon junction complex Y14 (RBM8A) were found among the protein partners of the isoforms hRPB11bβ and hRPB11cβ, together with a number of proteins involved in biogenesis of microRNAs, including a novel, previously undescribed variant of the microRNA processing nuclease DROSHA. These data indicate the existence of a special coordination between processes of transcription and RNA interference in the nuclei of human cells. © 2013 Pleiades Publishing, Ltd.