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The EMC effect in deuterium and helium-3 is studied using a convolution formalism that allows isolating the impact of high-momentum nucleons in short-ranged correlated (SRC) pairs. We assume that the modification of the structure function of bound nucleons is given by a universal (i.e. nucleus independent) function of their virtuality, and find that the effect of such modifications is dominated by nucleons in SRC pairs. This SRC-dominance of nucleon modifications is observed despite the fact that the bulk of the nuclear inelastic scattering cross-section comes from interacting with low-momentum nucleons. These findings are found to be robust to model details including nucleon modification function parametrization, free nucleon structure function and treatment of nucleon motion effects. While existing data cannot discriminate between such model details, we present predictions for measured, but not yet published, tritium EMC effect and tagged nucleon structure functions in deuterium that are sensitive to the neutron structure functions and bound nucleon modification functions.