While the successes of transformers across many domains are indisputable, accurate understanding of the learning mechanics is still largely lacking. Their capabilities have been probed on benchmarks which include a variety of structured and reasoning tasks---but mathematical understanding is lagging substantially behind. Recent lines of work have begun studying representational aspects of this question: that is, the size/depth/complexity of attention-based networks to perform certain tasks. However, there is no guarantee the learning dynamics will converge to the constructions proposed. In our paper, we provide fine-grained mechanistic understanding of how transformers learn ``semantic structure'', understood as capturing co-occurrence structure of words. Precisely, we show, through a combination of mathematical analysis and experiments on Wikipedia data and synthetic data modeled by Latent Dirichlet Allocation (LDA), that the embedding layer and the self-attention layer encode the topical structure. In the former case, this manifests as higher average inner product of embeddings between same-topic words. In the latter, it manifests as higher average pairwise attention between same-topic words. The mathematical results involve several assumptions to make the analysis tractable, which we verify on data, and might be of independent interest as well.