Anthony A et al. (2007) BMC Genomics "Association of the matrix attachment region recognition signature with coding regions in Caenorhabditis elegans."

Anthony A, Blaxter M

[BMC Genomics, 2007]

ABSTRACT: BACKGROUND: Matrix attachment regions (MAR) are the sites on genomic DNA that interact with the nuclear matrix. There is increasing evidence for the involvement of MAR in regulation of gene expression. The unsuitability of experimental detection of MAR for genome-wide analyses has led to the development of computational methods of detecting MAR. The MAR recognition signature (MRS) has been reported to be associated with a significant fraction of MAR in C. elegans and has also been found in MAR from a wide range of other eukaryotes. However the effectiveness of the MRS in specifically and sensitively identifying MAR remains unresolved. RESULTS: Using custom software, we have mapped the occurrence of MRS across the entire C. elegans genome. We find that MRS have a distinctive chromosomal distribution, in which they appear more frequently in the gene-rich chromosome centres than in arms. Comparison to distributions of MRS estimated from chromosomal sequences randomised using mono-, di- tri- and tetra-nucleotide frequency patterns showed that, while MRS are less common in real sequence than would be expected from nucleotide content alone, they are more frequent than would be predicted from short-range nucleotide structure. In comparison to the rest of the genome, MRS frequency was elevated in 5'' and 3'' UTRs, and striking peaks of average MRS frequency flanked C. elegans coding sequence (CDS). Genes associated with MRS were significantly enriched for receptor activity annotations, but not for expression level or other features. CONCLUSION: Through a genome-wide analysis of the distribution of MRS in C. elegans we have shown that they have a distinctive distribution, particularly in relation to genes. Due to their association with untranslated regions, it is possible that MRS could have a post-transcriptional role in the control of gene expression. A role for MRS in nuclear scaffold attachment is not supported by these analyses.

Li L et al. (2017) PLoS One "RNA-seq-based analysis of drug-resistant Salmonella enterica serovar Typhimurium selected in vivo and in vitro."

Li L, Zhao X, Yang Y, Wang L, Wang Y, Zeng M, Dai X

[PLoS One, 2017]

The aim of this study was to characterize the mechanism of fluoroquinolone (FQ) resistance in Salmonella Typhimurium. We established the Caenorhabditis elegans-Salmonella Typhimurium model to select for ciprofloxacin resistance in Salmonella Typhimurium colonizing C. elegans, generating the resistant strains TN4. Gradient doses of ciprofloxacin were used to generate the resistant strain TW4 in vitro. RNA sequencing was used to establish the whole-transcriptome profile of three strains of Salmonella Typhimurium. The gene expression patterns of resistant strains TN4 and TW4 differed from those of the parental strain. In TN4, 2,277 genes were differentially expressed (1,833 upregulated and 444 downregulated) relative to the parental strain, and in TW4, 3,464 genes were differentially expressed (3,433 upregulated and 31 downregulated). Among these differentially expressed genes, 28 were associated with drug resistance and 26 were associated with the two-component systems in the two resistant strains. Seven different pathways were significantly sffected in two strains. Efflux pump overexpression was identified as one of the main mechanisms underlying FQ resistance in the two resistant strains. TW4 differentially expressed more efflux pump genes than TN4 and most of these genes were more strongly expressed than in TN4. However, expression of the efflux pump repressor gene and the mar operon was downregulated in TN4 but not in TW4. Two-component systems are also important in drug resistance. Our findings provide an important basis for further studies of the complex network that regulate FQ resistance in Salmonella.