title: Functional genomics of HMGN3a and SMARCAL1 in early mammalian embryogenesis.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  New annotations of both HMGN3a and SMARCAL1 were submitted to the Bovine Genome Annotation Submission Database at BovineGenome.org. 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Biology, Northeastern University, Boston, MA, USA. uzun.a@neu.edu
authors.forename: Alper
authors.initials: A
authors.lastname: Uzun
authors.forename: Nelida
authors.initials: N
authors.lastname: Rodriguez-Osorio
authors.forename: Abdullah
authors.initials: A
authors.lastname: Kaya
authors.forename: Hongfeng
authors.initials: H
authors.lastname: Wang
authors.forename: John J
authors.initials: JJ
authors.lastname: Parrish
authors.forename: Valentin A
authors.initials: VA
authors.lastname: Ilyin
authors.forename: Erdogan
authors.initials: E
authors.lastname: Memili
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001755:Blastocyst / Q000502:physiology; D002417:Cattle / Q000196:embryology; D002478:Cells, Cultured; D042002:Chromatin Assembly and Disassembly; D017124:Conserved Sequence; D004265:DNA Helicases / Q000235:genetics*; D047108:Embryonic Development / Q000235:genetics*; D018507:Gene Expression Regulation, Developmental; D023281:Genomics; D024001:HMGN Proteins / Q000235:genetics*; D006801:Humans; D008957:Models, Genetic; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009865:Oocytes / Q000502:physiology; D010802:Phylogeny; D017433:Protein Structure, Secondary; D012333:RNA, Messenger / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D024001:HMGN Proteins; D012333:RNA, Messenger; D004265:DNA Helicases