The 62-kb upstream region of Bombyx mori fibroin heavy chain gene is clustered of repetitive elements and candidate matrix association regions

• Published in: Gene Vol. 312; pp. 189 - 195
• Main Authors: Zhou, Cong-Zhao, Confalonieri, Fabrice, Esnault, Catherine, Zivanovic, Yvan, Jacquet, Michel, Janin, Joel, Perasso, Roland, Li, Zhen-Gang, Duguet, Michel
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 17.07.2003
• Subjects: 5' Flanking Region - genetics; Animals; Base Composition; Binding Sites - genetics; Bombyx - genetics; Bombyx mori; exons; fibroins; Fibroins - genetics; Fibroins - metabolism; introns; Matrix association region(s) (MARs) recognition signatures; Matrix association region(s) (MARs)-finder; Matrix association regions (MARs); Nuclear matrix; Nuclear Matrix - metabolism; repetitive sequences; Repetitive Sequences, Nucleic Acid - genetics; Silkworm; Fib-L, fibroin light chain; Matrix association region(s) (MARs) recognition signatures; kb, kilobase; MDa, megaDaltion; LINE(s):, long interspersed repetitive elements(s); PSG, posterior silkgland; bp, base pair(s); MRS, MAR recognition signature; Matrix association regions (MARs); kDa, kiloDalton; Fib-H, fibroin heavy chain; GCG, Genetics Computer Group; ORI, origin of replication; EST(s), expressed sequence tag(s); Matrix association region(s) (MARs)-finder; ORF(s), open reading frame(s); MSG, middle silkgland; BAC, bacterial artificial chromosome; MAR(s), matrix association region(s); Nuclear matrix; Silkworm; SINE(s), short interspersed repetitive element(s)
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/S0378-1119(03)00616-4

We sequenced an 80 kb DNA region containing the complete sequence of the silkworm Bombyx mori fibroin gene and its flanking, especially the upstream, regions (−62 kb). About 30% of the 62 kb upstream region is composed of repetitive elements including short interspersed elements Bm1, long interspersed elements L1Bm and mariner-like elements Bmmar1 which are widespread over the silkworm genome. This 62 kb region is also enriched of commonly considered matrix association region (MAR) motifs. A total of 25 individual MAR recognition signatures (MRSs) were identified, with 24 at the upstream and one at the downstream region. Combining two newly developed MAR prediction programs (MAR-finder and Chrclass), ten candidate MARs were predicted, with five containing MRS and seven related to the repetitive elements. The wide distribution of nested repetitive elements, candidate MARs, DNase I hypersensitive sites and other potential regulatory factors recognition sites indicates this region is probably a unique huge cis-acting element contributing to the regulation of the spatial and temporal specificity and efficiency of fibroin gene expression.