Open Access Open Badges Research article

Functional genomics of HMGN3a and SMARCAL1 in early mammalian embryogenesis

Alper Uzun1, Nelida Rodriguez-Osorio23, Abdullah Kaya4, Hongfeng Wang2, John J Parrish4, Valentin A Ilyin1* and Erdogan Memili2*

Author Affiliations

1 Department of Biology, Northeastern University, Boston, MA, USA

2 Department of Animal and Dairy Science, Mississippi State University, Mississippi State, MS, USA

3 Grupo Centauro Universidad de Antioquia, Medellín, Antioquía, Colombia

4 Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, USA

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BMC Genomics 2009, 10:183  doi:10.1186/1471-2164-10-183

Published: 24 April 2009



Embryonic genome activation (EGA) is a critical event for the preimplantation embryo, which is manifested by changes in chromatin structure, transcriptional machinery, expression of embryonic genes, and degradation of maternal transcripts. The objectives of this study were to determine transcript abundance of HMGN3a and SMARCAL1 in mature bovine oocytes and early bovine embryos, to perform comparative functional genomics analysis of these genes across mammals.


New annotations of both HMGN3a and SMARCAL1 were submitted to the Bovine Genome Annotation Submission Database at Careful analysis of the bovine SMARCAL1 consensus gene set for this protein (GLEAN_20241) showed that the NCBI protein contains sequencing errors, and that the actual bovine protein has a high degree of homology to the human protein. Our results showed that there was a high degree of structural conservation of HMGN3a and SMARCAL1 in the mammalian species studied. HMGN3a transcripts were present at similar levels in bovine matured oocytes and 2–4-cell embryos but at higher levels in 8–16-cell embryos, morulae and blastocysts. On the other hand, transcript levels of SMARCAL1 decreased throughout preimplantation development.


The high levels of structural conservation of these proteins highlight the importance of chromatin remodeling in the regulation of gene expression, particularly during early mammalian embryonic development. The greater similarities of human and bovine HMGN3a and SMARCAL1 proteins may suggest the cow as a valuable model to study chromatin remodeling at the onset of mammalian development. Understanding the roles of chromatin remodeling proteins during embryonic development emphasizes the importance of epigenetics and could shed light on the underlying mechanisms of early mammalian development.