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This paper studies cooperative resource allocation schemes for the inter-cell interference control in multi-cell orthogonal frequency division multiple access (OFDMA) systems. For the purpose of exposition, the downlink transmission in a simplified three-cell system is examined. It is assumed that all cells simultaneously access the same frequency band using OFDMA, which corresponds to a universal frequency reuse in cellular systems. Unlike the conventional approach that treats subcarriers as separate dimensions for user scheduling and power allocation in OFDMA, the paper exploits the interference alignment (IA) technique to formulate a new cooperative resource allocation scheme for multi-cell OFDMA by incorporating the frequency-domain precoding over parallel subcarriers. The joint optimization of frequency-domain precoders via IA, subcarrier user selection and power allocation for all cells is then investigated to maximize the system sum-throughput. Numerical results for a symmetric channel setup reveal that the IA-based scheme achieves notable throughput gains over the traditional scheme without frequency-domain precoding only when the inter-cell interference link has a comparable strength as the direct signal link, and the direct-link signal-to-noise ratio (SNR) is sufficiently high. Motivated by this observation, two hybrid schemes are proposed to exploit the benefits of both traditional and IA-based schemes, for practical cellular systems with heterogenous channel conditions.