Different behavior of chromatin domains encompassing fibroin heavy-chain gene in active, temporarily inactive, and permanently inactive transcriptional states in silk gland nuclei

Dynamic chromatin conformation and accessibility changes mediate the spatial-specific gene regulatory network in Bombyx mori

Silk gland genes of Bombyx mori can have strict spatial expression patterns, which impact their functions and silk quality; however, our understanding of their regulation mechanisms is currently insufficient. To address this, the middle silk gland (MSG) and posterior silk gland (PSG) of the silkworm were investigated. Gene ontology annotation showed that spatially specific expressed genes were involved in the formation of H3k9me and chromatin topology. Chromatin conformation data generated by Hi-C showed that the topologically associated domain boundaries around FibL and Sericin1 genes were significantly different between MSG and PSG. Changes in chromatin conformation led to changes in chromatin activity, which significantly affected the expression of nearby genes in silkworm. Chromatin accessibility regions of MSG and PSG were analyzed using FAIRE-seq, and 1006 transcription factor motifs were identified in open chromatin regions. Furthermore, the spatial-specific expression patterns of silk gland genes were mainly associated with homeobox-contained transcription factors, such as POU-M2, which was specifically bound and relatively highly expressed in the MSG. The regulatory network mediated by POU-M2 regulated most of the spatial-specific expressed genes in MSG, such as ADH1. These results can aid in improving silk performance, optimizing silkworm breeding, and improving the gene spatial regulatory model research for insects.

Histomorphometric and transcriptomic features characterize silk glands' development during the molt to intermolt transition process in silkworm

The molt-intermolt cycle is an essential feature in holometabolous and hemimetabolous insects' development. In the silkworm, silk glands are under dramatic morphological and functional changes with fibroin genes' transcription being repeatedly turned off and on during the molt-intermolt cycles. However, the molecular mechanisms controlling it are still unknown. Here, silk gland's histomorphology and transcriptome analysis were used to characterize changes in its structure and gene expression patterns from molt to intermolt stages. By using section staining and transmission electron microscope, a renewable cell damage was detected in the silk gland at the molt stage, and an increased number of autophagosomes and lysosomes were found in silk gland cells' cytoplasm. Next, by using RNA sequencing, 54,578,413 reads were obtained, of which 85% were mapped to the silkworm reference genome. The expression level analysis of silk protein genes and silk gland transcription factors revealed that fibroin heavy chain, fibroin light chain, P25/fhx, sericin1, sericin3 and Dimm had consistent alteration trends in temporal expression. In addition, differentially expressed genes (DEGs) were identified, and most of the DEGs associated with ecdysone signal transduction, mRNA degradation, protein proteolysis, and autophagy were significantly down-regulated in the transition from molt to intermolt, suggesting that these pathways were activated for the silk gland renewal. These findings provide insights into the molecular mechanisms of silk gland development and silk protein genes transcriptional regulation during the molt to intermolt transition process.

A quicker degradation rate is yielded by a novel kind of transgenic silk fibroin consisting of shortened silk fibroin heavy chains fused with matrix metalloproteinase cleavage sites

Degradation performance of silk fibroin is an important property for its medical applications. Herein we constructed a shortened silk fibroin heavy chain protein fused with a matrix metalloproteinase cleavage site (SSFH-MMP) along with a glutathione S-transferase tag ahead. The digestion assay shows it can be cut by matrix metalloproteinase-2 (MMP-2) at its MMP cleavage site. Furthermore, we introduced the SSFH-MMP into silk fibroin by genetic modification of silkworms in order to increase the degradation rate of the silk fibroin. After acquisition of a race of transgenic silkworms with the coding sequence of the MMP cleavage site in their genomic DNA, we tested some properties of their silk fibroin designated TSF-MMP. The results show that the TSF-MMP has MMP cleavage sites and yields a quicker degradation rate during dilution in MMP-2 enzyme buffer or implantation into tumor tissues compared with that of normal silk fibroin. Moreover, the TSF-MMP is in vitro non-toxic to human bone marrow mesenchymal stem cells (hBM-MSCs) indicating that the TSF-MMP may become a biomaterial with a quicker degradation rate for its medical applications.

A new method for the modification of fibroin heavy chain protein in the transgenic silkworm

We constructed a new plasmid vector for the production of a modified silk fibroin heavy chain protein (H-chain) in the transgenic silkworm. The plasmid (pHC-null) contained the promoter and the 3' region of a gene encoding the H-chain and the coding regions for the N-terminal domain and the C-terminal domain of the H-chain. For the model protein, we cloned a foreign gene that encoded EGFP between the N-terminal domain and the C-terminal domain in pHC-null and generated transgenic silkworms that produced a modified H-chain, HC-EGFP. Transgenic silkworms produced HC-EGFP in the posterior part of silk gland cells, secreted it into the lumen of the gland, and produced a cocoon with HC-EGFP as part of the fibroin proteins. N-terminal sequencing of HC-EGFP localized the signal sequence cleavage site to between positions A((21)) and N((22)). These results indicate that our new plasmid successfully produced the modified H-chain in a transgenic silkworm.

Structure and function of 5'-flanking regions of Bombyx mori fibroin heavy chain gene: identification of a novel transcription enhancing element with a homeodomain protein-binding motif

We studied the promoter activity of a 5'-flanking region from -5000 to +24 (-5000/+24) in Bombyx mori fibroin heavy chain gene (fibH), fibH(-5000/+24). A luciferase reporter vector carrying fibH(-5000/+24) was bombarded to isolated posterior silk glands (PSGs). The PSGs showed a high luciferase activity when transplanted to larvae, indicating its potent promoter activity. Deletion experiments showed the requirement of fibH(-5000/-3844) and fibH(-2211/-542) for the promoter activity. These two regions and fibH(-541/+24) that contained the basal promoter were tandem fused to yield fibH(-5000/-3844:-2211/-542:-541/+24), which was found to retain 88% of the activity of fibH(-5000/+24). Germline transgenic silkworms bearing fibH(-5000/-3844:-2211/-542:-541/+24) as a promoter and enhanced green fluorescent protein (EGFP) gene as a reporter efficiently secreted EGFP in cocoons. The promoter activity of fibH(-2211/-542) was further investigated, because this contained a DNase I-hypersensitive site. The transient expression assay demonstrated that the activity of fibH(-2211/-542) required fibH(-1659/-1590), which contained the homeodomain protein-binding motif. Mutation experiments suggested a critical role of the motif for the promoter activity. Electrophoretic mobility shift assay (EMSA) demonstrated that a nuclear protein of PSGs bound to the motif. We propose fibH(-1659/-1590) as a novel transcription enhancer that plays a key role for the expression by recruiting a homeodomain protein.

Analysis of tissue-specific region in sericin 1 gene promoter of Bombyx mori

The gene encoding sericin 1 (Ser1) of silkworm (Bombyx mori) is specifically expressed in the middle silk gland cells. To identify element involved in this transcription-dependent spatial restriction, truncation of the 5' terminal from the sericin 1 (Ser1) promoter is studied in vivo. A 209bp DNA sequence upstream of the transcriptional start site (-586 to -378) is found to be responsible for promoting tissue-specific transcription. Analysis of this 209bp region by overlapping deletion studies showed that a 25bp region (-500 to -476) suppresses the ectopic expression of the Ser1 promoter. An unknown factor abundant in fat body nuclear extracts is shown to bind to this 25bp fragment. These results suggest that this 25bp region and the unknown factor are necessary for determining the tissue-specificity of the Ser1 promoter.

Loss of posterior silk gland transcription specificity of fibroin light chain promoter due to absence of 41 bp sequence containing possible inhibitor binding sites

The gene encoding fibroin light chain protein (FibL) is specifically expressed in the posterior silk gland of silkworm and repressed in other tissues. The binding sites of several transcription factors involved in the silk gland transcription specificity of fibl promoter have been recognized, including SGFB, PSGF and BMFA. Here we report the leak expression of the enhanced green fluorescent protein (EGFP) reporter gene in tissues other than the posterior silk gland in vivo when under the control of a shortened fibl promoter with deletion of the 5' terminal 41 bp sequence, which is located at -650 nt to -610 nt upstream of the fibl transcription starting site. Assay of silk gland specificity of the promoters was performed by observation of green fluorescence in tissues of silkworm larvae following inter-haemocoelic injection of recombinant Autographa californica multiple nuclear polyhedrosis virus carrying the EGFP reporter gene controlled by different lengths of fibl promoters. Our results indicated that availability of the binding sites of several known factors, including SGFB, PSGF and BMFA, is not sufficient for intact silk gland transcription specificity of fibl promoter, and there are possible inhibitor binding sites in the 41 bp sequence (-650 nt to -610 nt) upstream of the transcription starting site which may be required to repress the activity of fibl promoter in other tissues.

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

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.

Determination of the site of disulfide linkage between heavy and light chains of silk fibroin produced by Bombyx mori

The analysis of fibroin secretion-deficient 'naked-pupa' mutant silkworms has suggested that the disulfide linkage between heavy (H) and light (L) chains of fibroin, produced by the silkworm, Bombyx mori, is essential in its efficient large-scale secretion from the posterior silk gland cells. However, the site of disulfide-linkage between H- and L-chains has not been determined. In this study, cysteine residues involved in the single disulfide linkage between H- and L-chains were identified as the twentieth residue from the carboxyl terminus of H-chain (Cys-c20) and Cys-172 of L-chain by sequencing of genomic clones and peptide analysis. Furthermore, Cys-c4 (fourth residue from the carboxyl terminus) and Cys-c1 at the carboxyl terminus of H-chain were shown to form an intramolecular disulfide bond.

Mouse interleukin-2 receptor alpha gene expression. Delimitation of cis-acting regulatory elements in transgenic mice and by mapping of DNase-I hypersensitive sites

The alpha chain of the interleukin-2 receptor (IL-2R alpha) is a key regulator of lymphocyte proliferation. To analyze the mechanisms controlling its expression in normal cells, we used the 5'-flanking region (base pairs -2539/+93) of the mouse gene to drive chloramphenicol acetyltransferase expression in four transgenic mouse lines. Constitutive transgene activity was restricted to lymphoid organs. In mature T lymphocytes, transgene and endogenous IL-2R alpha gene expression was stimulated by concanavalin A and up-regulated by IL-2 with very similar kinetics. In thymic T cell precursors, IL-1 and IL-2 cooperatively induced transgene and IL-2R alpha gene expression. These results show that regulation of the endogenous IL-2R alpha gene occurs mainly at the transcriptional level. They demonstrate that cis-acting elements in the 5'-flanking region present in the transgene confer correct tissue specificity and inducible expression in mature T cells and their precursors in response to antigen, IL-1, and IL-2. In a complementary approach, we screened the 5' end of the endogenous IL-2R alpha gene for DNase-I hypersensitive sites. We found three lymphocyte specific DNase-I hypersensitive sites. Two, at -0.05 and -5.3 kilobase pairs, are present in resting T cells. A third site appears at -1.35 kilobase pairs in activated T cells. It co-localizes with IL-2-responsive elements identified by transient transfection experiments.