Developmental expression of non-coding RNAs in Chlamydia trachomatis during normal and persistent growth

Chlamydia trachomatis is an obligate intracellular bacterium that exhibits a unique biphasic developmental cycle that can be disrupted by growth in the presence of IFN-γ and β-lactams, giving rise to an abnormal growth state termed persistence. Here we have examined the expression of a family of non-coding RNAs (ncRNAs) that are differentially expressed during the developmental cycle and the induction of persistence and reactivation. ncRNAs were initially identified using an intergenic tiling microarray and were confirmed by northern blotting. ncRNAs were mapped, characterized and compared with the previously described chlamydial ncRNAs. The 5'- and 3'-ends of the ncRNAs were determined using an RNA circularization procedure. Promoter predictions indicated that all ncRNAs were expressed from σ(66) promoters and eight ncRNAs contained non-templated 3'-poly-A or poly-AG additions. Expression of ncRNAs was studied by northern blotting during (i) the normal developmental cycle, (ii) IFN-γ-induced persistence and (iii) carbenicillin-induced persistence. Differential temporal expression during the developmental cycle was seen for all ncRNAs and distinct differences in expression were seen during IFN-γ and carbenicillin-induced persistence and reactivation. A heterologous co-expression system was used to demonstrate that one of the identified ncRNAs regulated the expression of FtsI by inducing degradation of ftsI mRNA.     

Coordinated expression of ncRNAs and HOX mRNAs in the human HOXA locus

In the human HOXA locus a number of ncRNAs are transcribed from the intergenic regions in the opposite direction to HOXA mRNAs. We observed that the genomic organization of genes for the ncRNAs and HOXA proteins is highly conserved between human and mouse. We examined the expression profiles of these ncRNAs and HOXA mRNAs in various human tissues. The expression patterns of ncRNAs in human tissues coincide with those of the adjacent HOXA mRNAs that are collinearly expressed along the anteroposterior axis. This coordinated expression was observed even in transformed tumors and cancer cell lines, suggesting that the expression of ncRNAs is prerequisite for the regulated expression of HOXA genes. HIT18844 ncRNA transcribed from the most upstream position of the HOXA cluster possesses an ultra-conserved short stretch which potentially forms an evolutionarily conserved secondary structure. Our data suggest a critical role for ncRNAs in the regulation of HOXA gene expression.     

Generation of a neuro-specific microarray reveals novel differentially expressed noncoding RNAs in mouse models for neurodegenerative diseases

We have generated a novel, neuro-specific ncRNA microarray, covering 1472 ncRNA species, to investigate their expression in different mouse models for central nervous system diseases. Thereby, we analyzed ncRNA expression in two mouse models with impaired calcium channel activity, implicated in Epilepsy or Parkinson''s disease, respectively, as well as in a mouse model mimicking pathophysiological aspects of Alzheimer''s disease. We identified well over a hundred differentially expressed ncRNAs, either from known classes of ncRNAs, such as miRNAs or snoRNAs or which represented entirely novel ncRNA species. Several differentially expressed ncRNAs in the calcium channel mouse models were assigned as miRNAs and target genes involved in calcium signaling, thus suggesting feedback regulation of miRNAs by calcium signaling. In the Alzheimer mouse model, we identified two snoRNAs, whose expression was deregulated prior to amyloid plaque formation. Interestingly, the presence of snoRNAs could be detected in cerebral spine fluid samples in humans, thus potentially serving as early diagnostic markers for Alzheimer''s disease. In addition to known ncRNAs species, we also identified 63 differentially expressed, entirely novel ncRNA candidates, located in intronic or intergenic regions of the mouse genome, genomic locations, which previously have been shown to harbor the majority of functional ncRNAs.