Deep transcriptome sequencing analyses have demonstrated that transcription is substantially more widespread in the testis than any other organ. Germ cells provide the largest contribution to this transcriptome complexity, which stems largely from the promiscuous expression of protein-coding and noncoding genes during meiotic prophase I. Prophase I cells experience robust transcriptional activation during pachynema and produce thousands of genes critical for meiotic and post-meiotic processes. Many of the mRNAs produced by prophase I spermatocytes are stably stored until they are needed during the transcriptionally inert stages of spermiogenesis. Disturbances in gene expression during prophase I can lead to meiotic arrest and spermiogenic failure. Thus, to further understand the transcriptional control of male germ cell differentiation, my thesis research aimed to identify novel regulatory mechanisms of prophase I gene expression. Here, I asked which molecular mechanisms are responsible for directing recruitment of RNA Polymerase II (Pol II) to meiotic chromatin. I hypothesized that promoter-proximal pausing of Pol II is responsible for establishing and maintaining the spatiotemporal control of gene expression during prophase I. To test this hypothesis, I performed the first comprehensive analysis of gene expression and chromatin accessibility for all meiotic prophase I substages: leptonema, zygonema, pachynema, and diplonema. Using a recently developed nuclear run-on method, length-extension chromatin run-on and sequencing (leChRO-seq), I determined the profiles of paused and elongating Pol II in representative mouse prophase I substages. Through genome-wide systematic analyses, I report that pausing is enriched near the promoters of meiotic genes and identify 13 transcription factor families coordinating the profound increase in transcription during pachynema. Furthermore, I provide clear evidence that the testis-specific member of the double bromodomain and extraterminal (BET) protein family BRDT regulates transcription in spermatocytes. My results represent the first stage-resolved maps of nascent transcription and genome architecture during prophase I and provide evidence for novel regulatory mechanisms of meiotic gene expression.