title: Computational challenges, tools, and resources for analyzing co- and post-transcriptional events in high throughput.
abstract: Co- and post-transcriptional regulation of gene expression is complex and multifaceted, spanning the complete RNA lifecycle from genesis to decay. High-throughput profiling of the constituent events and processes is achieved through a range of technologies that continue to expand and evolve. Fully leveraging the resulting data is nontrivial, and requires the use of computational methods and tools carefully crafted for specific data sources and often intended to probe particular biological processes. Drawing upon databases of information pre-compiled by other researchers can further elevate analyses. Within this review, we describe the major co- and post-transcriptional events in the RNA lifecycle that are amenable to high-throughput profiling. We place specific emphasis on the analysis of the resulting data, in particular the computational tools and resources available, as well as looking toward future challenges that remain to be addressed.
authors.affiliation: Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
authors.forename: Emad
authors.initials: E
authors.lastname: Bahrami-Samani
authors.forename: Dat T
authors.initials: DT
authors.lastname: Vo
authors.forename: Patricia Rosa
authors.initials: PR
authors.lastname: de Araujo
authors.forename: Christine
authors.initials: C
authors.lastname: Vogel
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Smith
authors.forename: Luiz O F
authors.initials: LO
authors.lastname: Penalva
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Uren
mesh_terms: D017398:Alternative Splicing; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D014176:Protein Biosynthesis; D012313:RNA / Q000096:biosynthesis / Q000737:chemistry* / Q000378:metabolism; D020871:RNA Stability; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism / Q000502:physiology; D013379:Substrate Specificity
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA