Characterization of the Arabidopsis Telomerase Negative Regulator: A TE-Containing lncRNA TER2- Defining Its Role in and beyond Telomere Biology

In eukaryotes the ends of chromosomes are constituted by nucleoprotein complexes termed telomeres. Telomeres represses a DNA damage response and, more importantly, facilitate the maintenance of the terminal DNA sequence by telomerase. Telomerase activity can be reconstituted by its two core subunits, the catalytic reverse transcriptase TERT and the telomerase RNA TER. The Shippen lab developed Arabidopsis as a model for telomere studies. Previous work in Shippen lab showed that an alternative copy of telomerase RNA, TER2, serves as a negative regulator of the telomerase in response to DNA damage. In this study I characterized the evolution and function of TER2 and explored its biological significance. TER2 possesses an intron and analysis of sequences from the 1001 genome project showed that the TER2 intron is derived from a transposable element (TE), specifically long terminal repeat (LTR) of a Copia-like retrotransposon. I verified that in most A. thaliana accessions the TER2 TE is intact, while in about 10% of accessions it is missing. The TE within TER2 destabilizes this RNA, enabling the plant to down regulate telomerase activity by modulating TER2 abundance. This RNA stability control mechanism contributes to the accumulation of TER2 after DNA damage, and thus links telomerase regulation directly to the DNA damage response. My results also showed that TER2 is developmentally regulated, but only in accessions that contain the TER2 TE, suggesting the exaptation of the TE endows TER2 with a function in reproductive development. Indeed, plants lacking TER2 have reduced seed production efficiency. In addition, ter2 mutants have lower pollen viability than wild type, though not as low as in tert mutants. These results defined a novel function of TER2 in plant reproduction. My work unexpectedly revealed that TER2 processing and/or stability is influenced by the small RNA processing pathway. In plants lacking Dicer-like2 (DCL2), TER2 abundance increases and the expression profile change during flower development. I further discovered that DCL2 affects TER2 in a post-transcriptional manner. Together, these data uncovered unexpected complexity of TER2 RNA processing and its regulation. Finally, I found that TER1, the canonical TER in A. thaliana, has lessons to teach. Single nucleotide polymorphisms (SNPs) in TER1 telomere templating domain were found. I showed that the SNPs do not change the newly synthesized telomere repeats. This observation provided new insight into the mechanisms of template utilization and how this is evolving. In summary, my research revealed evidence for evolution in two telomerase RNA genes in A. thaliana, and provided several novel insights into lncRNA structure, evolution and metabolism that impact telomerase regulation and benefit plant growth and reproduction