The article analyzes the processes of interaction between social institutions of academic science and higher education in contemporary Russia. The author used the method of case study, and the object of analysis are scientific and educational communities of regional scientific centers of Siberian Branch RAS (Krasnoyarsk, Irkutsk, Tomsk, Novosibirsk). The main determining factor in the current conditions became a reform of the university education system and academic research institutions. In the context of the reform, when the main indicator of the success of the university is now its high positions in university rankings (Program «5-100», etc.), clearly marked an urgent need to accelerate the strengthening of the scientific potential of leading (federal and national research) universities. The universal way to satisfy it, as a rule, is the intensification of cooperation with academic institutions. The author concludes that it results in the phenomenon of forced integration, understood as a forceful incorporation of the academic research institutions into the leading universities, to boost the scientific potential of the latter. The author is critical of this trend, offering to find and use other, softer methods and forms of mutually beneficial integration.