Access Type

Open Access Dissertation

Date of Award

January 2015

Degree Type


Degree Name



Molecular Biology and Genetics

First Advisor

Stephen A. Krawetz


Sperm possess several layers of information that are delivered to the oocyte alongside the paternal DNA. Examples of potential sperm borne molecular cues of probable use to the embryo include RNAs and local and global chromatin structure. To identify candidate sperm RNAs that likely reach the oocyte cytoplasm following fertilization patterns of transcript compartmentalization in the mature gamete were identified. Though all sperm RNAs exhibited a preferential peripheral enrichment, a subset of RNAs were identified in which this trend was reduced. These RNAs are thought to be embedded with perinuclear theca and are correlated with late spermatogenic transcription. Malat1, a well-known nuclear non-coding RNAs, was relatively abundant within the intra-nuclear compartment of the gamete although enriched within the sperm extra-nuclear compartment. If these transcript are localized to the condensed sperm nucleus Maltat1 may contribute to the retention of somatic-like chromatin structures following nuclear remodeling. Histone-bound regions which persist in mature sperm are of interest as they may be informative of past spermatogenic and future embryonic genomic regulation. Genome wide nucleosome mapping in mature mouse sperm was complimented with a nuclease foot printing approach to identify sites of factor retention throughout the paternal gamete. Applying this analysis to a transgenic mouse model harboring the human protamine locus, highlighted the potential regulatory impact of the chromatin environment at the local and domain level. Consideration of these results within the context of the endogenous mouse protamine locus identified a candidate transcriptional regulatory mechanism. Factors predicted to be bound in mature sperm were correlated with genomic elements utilized in the testis and the very early embryo. This included Ctcf, which was significantly enriched within the boundary regions of topologically associated domains and the promoter regions of genes expressed in the zygote. These patterns were not observed in human or bull sperm. It is suggested that delivery of the paternal genome in association with regulatory factors may reflect the accelerated preimplantation development of the murine embryo. Sites of Ctcf retention in mature sperm were considered within a novel model of spermatogenic nuclear remodeling.