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In this paper, we investigate the TCP throughput performance enhancement for cognitive radio networks (CRNs) through lower-layer configurations. There is an interaction between TCP and the lower-layer operations. The TCP sending rate at the transport layer determines the packet arrival rate of the lower-layer buffer, and meanwhile it is influenced by the average round trip time and packet loss rate, which are determined by the lower-layer mechanisms and configurations. Therefore, an iteration process is employed to investigate the TCP throughput under given channel condition and lower-layer configurations. For each iteration, queueing analysis is done to derive the packet loss rate and average delay on wireless link, which are then used to calculated the TCP throughput. Through derivations and numerical evaluations, the impacts of lower-layer parameters, primary user (PU) activities and channel conditions on the TCP throughput are discussed. Moreover, the way how these factors influence the TCP throughput is tracked. By using the proposed analytical method, TCP throughput enhancement can be achieved through appropriately setting lower-layer configurations.