Project description:To understand widespread differences in the DNA methylation patterns of Conyza canadensis leaf samples from its native and non-native ranges. Using Whole Genome Bisulfite Sequencing, we found average read coverages in high mapped reads across native and non-native samples of Conyza canadensis. Using R bioconductor package, we found enrichment score of methylated sites in both native and non-native samples. while analyzing CG, CHG and CHH methylation, we found relatively low CG and CHG methylation across transcriptional units in natives over non-natives. However, differentially methylated regions were found to be 53% hypomethylated and 41% hypermethylated in non-natives on genic regions.
Project description:Native and non-targeted metabolomics with E.coli CutA and cell extracts of E.coli and Synechococcus elongatus PCC 7942. Cell extraction with 20% or 80% MeOH.
Project description:The NDH1 complex fulfils numerous tasks in the cyanobacterial cell such as respiration, cyclic electron flow, and inorganic carbon concentration. Despite the immense progress in our understanding of structure/function relation of the cyanobacterial NDH1 complex, the subunits catalysing the NAD(P)H docking and oxidation are still missing. The gene sml0013 of Synechocystis 6803 encodes for a small protein of unknown function for that homologs exist in all completely known cyanobacterial genomes. The protein exhibits weak similarities to the NDF6 protein, which was reported from Arabidopsis chloroplasts as a NDH subunit (Ishikawa et al. 2008). A sml0013 inactivation mutant of Synechocystis 6803 was generated and characterized. It showed only weak differences regarding growth and pigmentation at various culture conditions; most remarkably it exhibited a glucose-sensitive phenotype in the light. The genome-wide expression pattern of the Δsml0013::Km mutant was almost identical to wild type when grown under high CO2 conditions as well as after shifts to low CO2 conditions. However, measurements of the photosystem I redox kinetic in cells of the Δsml0013::Km mutant revealed differences to wild type such as a decreased capability of cyclic electron flow as well as of utilization of electrons from catabolic processes. These results suggest that the Sml0013 protein (named NdhP) represent a novel subunit of the cyanobacterial NDH1 complex mediating its coupling to the respiratory or photosynthetic electron flow.
Project description:We report the transcriptomic analyses of a tropical coralliomrpharian, Ricordea yuma, following the establishment of symbiosis with either native symbiont or non-native symbiont. We examined the expression profiles, and results showed distinct metabolic consequences for the cnidarian host when they host different symbionts.
Project description:G-quadruplexes (G4s) are noncanonical DNA secondary structures formed through the self-association of guanines. They are distributed genome-widely and participate in multiple biological processes including gene transcription, and quadruplex-targeted ligands serve as potential therapeutic agents for DNA-targeted therapies. However, the roles of G-quadruplexes in transcriptional regulation remains elusive. Here, we establish a sensitive G4-CUT&Tag method for genome-wide profiling of native G-quadruplexes with high resolution and specificity. We find that native G-quadruplex signals are cell-type specific and are associated with transcriptional regulatory elements with active epigenetic modifications. Promoter-proximal RNA polymerase II pausing promotes native G-quadruplex formation, oppositely, G-quadruplex stabilization by quadruplex-targeted ligands globally reduces RNA polymerase II occupancy at gene promoters as well as nascent RNA synthesis. Moreover, G-quadruplex stabilization modulates chromatin states and impedes transcription initiation via inhibiting the loading of general transcription factors to promoters.Together, these studies reveal a reciprocal regulation between native G-quadruplex dynamics and gene transcription in the genome, which will deepen our knowledge of G-quadruplex biology towards considering therapeutically targeting G-quadruplexes in human diseases.