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

Dynamics of nuclear matrix attachment regions during 5th instar posterior silk gland development in Bombyx mori

Background

Chromatin architecture is critical for gene expression during development. Matrix attachment regions (MARs) control and regulate chromatin dynamics. The position of MARs in the genome determines the expression of genes in the organism. In this study, we set out to elucidate how MARs temporally regulate the expression of the fibroin heavy chain (FIBH) gene during development. We addressed this by identifying MARs and studying their distribution and differentiation, in the posterior silk glands of Bombyx mori during 5th instar development.

Results

Of the MARs identified on three different days, 7.15% MARs were common to all 3 days, whereas, 1.41, 19.27 and 52.47% MARs were unique to day 1, day 5, and day 7, respectively highlighting the dynamic nature of the matrix associated DNA. The average chromatin loop length based on the chromosome wise distribution of MARs and the distances between these MAR regions decreased from day 1 (253.91 kb) to day 5 (73.54 kb) to day 7 (39.19 kb). Further significant changes in the MARs in the vicinity of the FIBH gene were found during different days of 5^th instar development which implied their role in the regulation and expression of the FIBH gene.

Conclusions

The presence of MARs in the flanking regions of genes found to exhibit differential expression during 5^th instar development indicates their possible role in the regulation of their expression. This reiterates the importance of MARs in the genomic functioning as regulators of the molecular mechanisms in the nucleus. This is the first study that takes into account the tissue specific genome-wide MAR association and the potential role of these MARs in developmentally regulated gene expression. The current study lays a foundation to understand the genome wide regulation of chromatin during development.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08446-3.

Bioactive three-dimensional silk composite in vitro tumoroid model for high throughput screening of anticancer drugs

HYPOTHESIS

Modeling three-dimensional (3D) in vitro culture systems recapitulating spatiotemporal characteristics of native tumor-mass has shown tremendous potential as a pre-clinical tool for drug screening. However, their applications in clinical settings are still limited due to inappropriate recapitulation of tumor topography, culture instability, and poor durability of niche support.

EXPERIMENTS

Here, we have fabricated a bio-active silk composite scaffold assimilating tunable silk from Bombyx mori and - arginine-glycine-aspartate (RGD) rich silk from Antheraea assama to provide a better 3D-matrix for breast (MCF 7) and liver (HepG2) tumoroids. Cellular mechanisms underlying physiological adaptations in 3D constructs and subsequent drug responses were compared with conventional monolayer and multicellular spheroid culture.

FINDINGS

Silk composite matrix assists prolonged growth and high metabolic activity (Cytochrome P450 reductase) in breast and liver 3D-tumoroids. Enhanced stemness expression (Cell surface adhesion receptor; CD44, Aldehyde dehydrogenase 1) and epithelial-mesenchymal-transition markers (E-cadherin, Vimentin) at transcript and protein levels demonstrate that bio-active matrix-assisted 3D environment augmenting metastatic potential in tumoroids. Together, enhanced secretion of Transforming growth factor β (TGFβ), anchorage-independency, and colony-forming potential of cells in the 3D-tumoroids further corroborates the aggressive behavior of cells. Moreover, the multilayered 3D-tumoroids exhibit decreased sensitivity to some known anticancer drugs (Doxorubicin and Paclitaxel). In conclusion, the bio-active silk composite matrix offers an advantage in developing robust and sustainable 3D tumoroids for a high-throughput drug screening platform.

Enhanced expression of EGFP gene in CHSE-214 cells by an ARS element from mud loach (Misgurnus mizolepis)

The origins of replication are associated with nuclear matrices or are found in close proximity to matrix attachment regions (MARs). In this report, fish MARs were cloned into an autonomously replicating sequence (ARS) cloning vector and were screened for ARS elements in Saccharomyces cerevisiae. Sixteen clones were isolated that were able to grow on the selective plates. In particular, an ARS905 that shows high efficiency among them was selected for this study. Southern hybridization indicated the autonomous replication of the transformation vector containing the ARS905 element. DNA sequences analysis showed that the ARS905 contained two ARS consensus sequences as well as MAR motifs, such as AT tracts, ORI patterns, and ATC tracts. In vitro matrix binding analysis, major matrix binding activity and ARS function coincided in a subfragment of the ARS905. To analyze the effects of ARS905 on expression of a reporter gene, an ARS905(E1158) with ARS activity was inserted into pBaEGFP(+) containing mud loach beta-actin promoter, EGFP as a reporter gene, and SV40 poly(A) signal. The pBaEGFP(+)-ARS905(E1158) was transfected into a fish cell line, CHSE-214. The intensity of EGFP transfected cells was a 7-fold of the control at 11days post-transfection. These results indicate that ARS905 enhances the expression of the EGFP gene and that it should be as a component of expression vectors in further fish biotechnological studies.

The Acrolepiopsis assectella silk cocoon: kairomonal function and chemical characterisation

Two soluble sericin-like polypeptides, B1 and B2, from leek moth (Acrolepiopsis assectella) cocoons trigger host-acceptance behaviour in the parasitoid, Diadromus pulchellus (Proc. Roy. Soc. London B 269 (2002) 1879). We found that these polypeptides were particularly cysteine-rich and lost their ability to trigger host-acceptance behaviour after being denatured and purified. This suggests that inter-disulphide bonds and the secondary structure of B1 and B2 are important for their biological activity. We also isolated six insoluble polypeptides (or polypeptides of low solubility) from A. assectella cocoons. At least four of these polypeptides triggered host-acceptance behaviour. The strongest responses were observed with P22, a light-chain fibroin or a seroin-peptide, and P100, a sericin-like polypeptide that is probably more strongly associated with the silk core than are B1 and B2. In conclusion, several polypeptides from different parts of the A. assectella silk-cocoon (the insoluble core and coating of the silk thread) are able to elicit host-acceptance behaviour in D. pulchellus females. These polypeptides belong to different silk protein families and are used as kairomones by this specialist parasitoid.