Cell differentiation is fundamental to multi-cellular life because a single unspecialized zygote must give rise to all specialized cell types in the body. Cell fate specification requires the coordinated regulation of different genes across developmental time. How genes are regulated during cell differentiation is a longstanding question in biology. Gametogenesis in budding yeast is a cell differentiation program where a diploid cell gives rise to four haploid gametes and is a tractable model to understand gene regulation during development. Multiple studies in various vertebrate systems suggest that a significant fraction of genes are expressed as different transcript isoforms arising from alternative transcription start sites, or overlap with non-coding RNAs (ncRNAs) of unknown function. Here, I investigated how transcript isoforms or overlapping ncRNAs regulate gene expression during budding yeast gametogenesis. First, I showed that the kinetochore gene NDC80 is repressed by transcription of a 5’ extended mRNA isoform from an alternative promoter during early gametogenesis. This repressive mechanism required the co-transcriptional deposition of histone modifications and the stabilization of nucleosomes at the canonical NDC80 promoter. NDC80 repression could also be rapidly reversed to allow cells to re-enter mitosis if they were no longer starved. Next, I showed how a genome-wide approach called transcript end sequencing (TE-seq) could distinguish the ends of overlapping transcripts. TE-seq analysis showed over a thousand meiotic upstream transcripts or isoforms upregulated at specific stages of gametogenesis. Upstream overlapping transcription was associated with different regulatory outcomes on coding genes, and did not always repress them. TE-seq also identified examples of gene regulation which depended on different chromatin remodellers. Finally, most meiotic upstream alternative transcripts were rapidly repressed upon return to growth, similar to the NDC80 example. These results provide a basis for understanding how mRNA isoforms and ncRNAs contribute to local gene regulation during development in eukaryotes.