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

Interactions and screening in gated bilayer graphene nanoribbons

The effects of Coulomb interactions on the electronic properties of bilayer graphene nanoribbons (BGNs) covered by a gate electrode are studied theoretically. The electron density distribution and the potential profile are calculated self-consistently within the Hartree approximation. A comparison to their single-particle counterparts reveals the effects of interactions and screening. Due to the finite width of the nanoribbon in combination with electronic repulsion, the gate-induced electrons tend to accumulate along the BGN edges where the potential assumes a sharp triangular shape. This has a profound effect on the energy gap between electron and hole bands, which depends nonmonotonously on the gate voltage and collapses at intermediate electric fields. We interpret this behavior in terms of interaction-induced warping of the energy dispersion.Comment: 6 pages, 4 figure

Edge disorder induced Anderson localization and conduction gap in graphene nanoribbons

We study the effect of the edge disorder on the conductance of the graphene nanoribbons (GNRs). We find that only very modest edge disorder is sufficient to induce the conduction energy gap in the otherwise metallic GNRs and to lift any difference in the conductance between nanoribbons of different edge geometry. We relate the formation of the conduction gap to the pronounced edge disorder induced Anderson-type localization which leads to the strongly enhanced density of states at the edges, formation of surface-like states and to blocking of conductive paths through the ribbons

Impurity and edge roughness scattering in armchair graphene nanoribbons: Boltzmann approach

The conductivity of armchair graphene nanoribbons in the presence of short-range impurities and edge roughness is studied theoretically using the Boltzmann transport equation for quasi-one-dimensional systems. As the number of occupied subbands increases, the conductivity due to short-range impurities converges towards the two-dimensional case. Calculations of the magnetoconductivity confirm the edge-roughness-induced dips at cyclotron radii close to the ribbon width suggested by the recent quantum simulations

Geometric magnetoconductance dips by edge roughness in graphene nanoribbons

The magnetoconductance of graphene nanoribbons with rough zigzag and armchair edges is studied by numerical simulations. nanoribbons with sufficiently small bulk disorder show a pronounced magnetoconductance minimum at cyclotron radii close to the ribbon width, in close analogy to the wire peak observed in conventional semiconductor quantum wires. In zigzag nanoribbons, this feature becomes visible only above a threshold amplitude of the edge roughness, as a consequence of the reduced current density close to the edges

Electronic properties of quantum dots formed by magnetic double barriers in quantum wires

The transport through a quantum wire exposed to two magnetic spikes in series is modeled. We demonstrate that quantum dots can be formed this way which couple to the leads via magnetic barriers. Conceptually, all quantum dot states are accessible by transport experiments. The simulations show Breit-Wigner resonances in the closed regime, while Fano resonances appear as soon as one open transmission channel is present. The system allows to tune the dot's confinement potential from sub-parabolic to superparabolic by experimentally accessible parameters.Comment: 5 pages, 5 figure