Telomeric transcriptome from Chironomus riparius (Diptera), a species with noncanonical telomeres

Abstract

Although there are alternative telomere structures, most telomeres contain DNA arrays of short repeats (6-26 bp) maintained by telomerase. Like other diptera, Chironomus riparius has noncanonical telomeres and three subfamilies, TsA, TsB and TsC, of longer sequences (176 bp) are found at their chromosomal ends. Reverse transcription PCR was used to show that different RNAs are transcribed from these sequences. Only one strand from TsA sequences seems to render a noncoding RNA (named CriTER-A); transcripts from both TsB strands were found (CriTER-B and αCriTER-B) but no TsC transcripts were detected. Interestingly, these sequences showed a differential transcriptional response upon heat shock, and they were also differentially affected by inhibitors of RNA polymerase II and RNA polymerase III. A computer search for transcription factor binding sites revealed putative regulatory cis-elements within the transcribed sequence, reinforcing the experimental evidence which suggests that the telomeric repeat might function as a promoter. This work describes the telomeric transcriptome of an insect with non-telomerase telomeres, confirming the evolutionary conservation of telomere transcription. Our data reveal differences in the regulation of telomeric transcripts between control and stressful environmental conditions, supporting the idea that telomeric RNAs could have a relevant role in cellular metabolism in insect cells.

Telomere structure in insects: A review

“…Taken together with the absence of the (TTAGG) n motif in the examined species of Mecoptera and Siphonaptera, these data suggest an apparent loss of this repeat in a common ancestor of all Antliophora (Biessmann & Mason, ; Frydrychová et al, ; Pardue, Danilevskaya, Traverse, & Lowenhaupt, ). Alternatively, in all studied members of the suborder Nematocera (=lower Diptera) that belong to the genera Chironomus Meigen, 1803 (Chironomidae) and Anopheles Meigen, 1818 (Culicidae), long complex terminal tandem repeats (LCTTR) were found (Biessmann, Kobeski, Walter, Kasravi, & Roth, ; Carmona et al, ; Lopez, Nielsen, & Edström, ; Martínez Guitarte, de la Fuente, & Morcillo, ; Nielsen & Edström, ; Rosén & Edström, , ; Rosén et al, ; Roth et al, ; Saiga & Edström, ; Zhang, Kamnert, López, Cohn, & Edström, ). For example, Chironomus tentans Fabricius, 1805 has 350‐bp repeats at its telomeres (Rosén & Edström, ).…”

“…Alternatively, in all studied members of the suborder Nematocera (=lower Diptera) that belong to the genera Chironomus Meigen, 1803 (Chironomidae) and Anopheles Meigen, 1818 (Culicidae), long complex terminal tandem repeats (LCTTR) were found (Biessmann, Kobeski, Walter, Kasravi, & Roth, 1998;Carmona et al, 1985;Lopez, Nielsen, & Edström, 1996;Martínez Guitarte, de la Fuente, & Morcillo, 2014;Nielsen & Edström, 1993;Rosén & Edström, 2000Roth et al, 1997;Saiga & Edström, 1985;Zhang, Kamnert, López, Cohn, & Edström, 1994). For example, Chironomus tentans Fabricius, 1805 has 350bp repeats at its telomeres (Rosén & Edström, 2000).…”

Conservation of gene architecture and domains amidst sequence divergence in thehsrωlncRNA gene across theDrosophilagenus: Anin silicoanalysis

“…The preset search for the ultra-conserved omega intron splice junctions also failed to identify a definitive hsrω orthologue in these taxa (data not presented). However, presence of tandem repeats and sequence divergence at one of the heat shock induced Balbiani rings in different species of Chironomus (Botella, et al, 1991;Martinez-Guitarte, et al, 2008;Martínez Guitarte and Morcillo, 2014) and the binding of Hsp83 at such a puff site following heat shock (Morcillo, et al, 1993) suggests that a functional equivalent of the hsrω locus may exist in other dipteran species as well. Interestingly, one of the heat shock puffs in the mediterranean fruit fly Ceratitis capitata has been reported (Semeshin, et al, 1995) to harbor giant electron dense ribonucleoprotein (RNP) granules, similar to the omega speckles seen at the hsrω locus and in nucleoplasm (Dangli, et al, 1983;Prasanth, et al, 2000).…”

CriTER-A: A Novel Temperature-Dependent Noncoding RNA Switch in the Telomeric Transcriptome of Chironomus riparius

“…Additionally, three different ncRNAs were identified in C. riparius that are transcribed from these telomeric sequences: the CriTER-A ( Chironomus riparius TElomeric RNA from TsA), the CriTER-B ( Chironomus riparius TElomeric RNA from TsB), and the antisense transcripts produced from a complementary strand of TsB, the so-called αCriTER-B [ 24 ]. Further analyses showed that, under environmentally stressful conditions, such as heat shock, levels of CriTER-A increased up to four-fold whereas CriTER-B and αCriTER-B levels rose slightly.…”

“…Further analyses showed that, under environmentally stressful conditions, such as heat shock, levels of CriTER-A increased up to four-fold whereas CriTER-B and αCriTER-B levels rose slightly. Moreover, the level of CriTER-A is much lower when compared with those of CriTER-B and αCriTER-B under normal growing conditions [ 24 ]. Experimental and in silico studies revealed the existence of not only common but also specific transcription factor binding sites in TsA and TsB [ 24 , 25 ].…”