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Background  The avian eggshell membranes surround the egg white and provide a structural foundation for calcification of the eggshell which is essential for avian reproduction; moreover, it is also a natural biomaterial with many potential industrial and biomedical applications. Due to the insoluble and stable nature of the eggshell membrane fibres, their formation and protein constituents remain poorly characterized. The purpose of this study was to identify genes encoding eggshell membrane proteins, particularly those responsible for its structural features, by analyzing the transcriptome of the white isthmus segment of the oviduct, which is the specialized region responsible for the fabrication of the membrane fibres.    Results  The Del-Mar 14 K chicken microarray was used to investigate up-regulated expression of transcripts in the white isthmus (WI) compared with the adjacent magnum (Ma) and uterine (Ut) segments of the hen oviduct. Analysis revealed 135 clones hybridizing to over-expressed transcripts (WI/Ma + WI/Ut), and corresponding to 107 NCBI annotated non-redundant  Gallus gallus  gene IDs. This combined analysis revealed that the structural proteins highly over-expressed in the white isthmus include collagen X ( COL10A1 ), fibrillin-1 ( FBN1 ) and cysteine rich eggshell membrane protein ( CREMP ). These results validate previous proteomics studies which have identified collagen X (α-1) and CREMP in soluble eggshell extracts. Genes encoding collagen-processing enzymes such as lysyl oxidase homologs 1, 2 and 3 ( LOXL1, LOXL2 and LOXL3),  prolyl 4 hydroxylase subunit α-2 and beta polypeptide ( P4HA2  and  P4HB)  as well as peptidyl-prolyl cis-trans isomerase C ( PPIC ) were also over-expressed. Additionally, genes encoding proteins known to regulate disulfide cross-linking, including sulfhydryl oxidase ( QSOX1 ) and thioredoxin ( TXN ), were identified which suggests that coordinated up-regulation of genes in the white isthmus is associated with eggshell membrane fibre formation.    Conclusions  The present study has identified genes associated with the processing of collagen, other structural proteins, and disulfide-mediated cross-linking during eggshell membrane formation in the white isthmus. Identification of these genes will provide new insight into eggshell membrane structure and mechanisms of formation that will assist in the development of selection strategies to improve eggshell quality and food safety of the table egg.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-2013-3) contains supplementary material, which is available to authorized users.

Identifying specific proteins involved in eggshell membrane formation using gene expression analysis and bioinformatics