CLT-seq as a universal homopolymer-sequencing concept reveals poly(A) tail-tuned ncRNA regulation
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ABSTRACT:
PROVIDER: PRJNA835141 | ENA |
REPOSITORIES: ENA
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Project description:To more understand the poly(A) tail-tuned regulation in eukaryotic cells, we describe central limit theorem (CLT)-managed RNA-seq (CLT-seq) as a universal homopolymer-sequencing concept that features unbiased RNA-seq and facilitates accurate homopolymer base-calling. We then performed transcriptome-wide poly(A)-tail profiling analysis using data obtained from oligo(dT)-primed RNA-seq of HEK293T and A549 cell lines.
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As amniote vertebrates, lizards are the most closely related organisms to humans capable of appendage regeneration. Lizards can autotomize, or release their tails as a means of predator evasion, and subsequently regenerate a functional replacement. Green anoles (Anolis carolinensis) can regenerate their tails through a process that involves differential expression of hundreds of genes, which has previously been analyzed by transcriptomic and microRNA analysis. To investigate protein expression in regenerating tissue, we performed whole proteomic analysis of regenerating tail tip and base. This is the first proteomic data set available for the green anole lizard. We identified 976 proteins only in the regenerating tail base, 796 only in the tail tip, and 874 in both tip and base. For 90% of these proteins in these tissues, we were able to assign a clear orthology to gene models in either the Ensembl or NCBI databases. For 20 proteins in the tail base (2.5%), 7 proteins in the tail tip (0.9%), and 7 proteins in both regions (0.8%), the gene model in Ensembl and NCBI matched an uncharacterized protein, confirming that these predictions are present in the proteome. Ontology and pathways analysis of proteins expressed in the regenerating tail base identified categories including actin filament-based process, ncRNA metabolism, regulation of phosphatase activity, small GTPase mediated signal transduction, and cellular component organization or biogenesis. Analysis of proteins expressed in the tail tip identified categories including regulation of organelle organization, regulation of protein localization, ubiquitin-dependent protein catabolism, small GTPase mediated signal transduction, morphogenesis of epithelium, and regulation of biological quality. These proteomic findings confirm pathways and gene families activated in tail regeneration in the green anole as well as identify uncharacterized proteins whose role in regrowth remains to be revealed.
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