CLIP Identifies Nova-Regulated RNA Networks in the Brain

By Jernej Ule, K. Jensen, M. Ruggiu, Aldo Mele, A. Ule, R. Darnell. Science, 2003

1,177 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/1daf3e84451a99eebf5d9828c79d311c309a9d93

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Citations in the corpus

Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP (2010, methodology): “For comparison to conventional and high-throughput sequencing CLIP (Licatalosi et al., 2008; Ule et al., 2003), we also sequenced cDNA libraries prepared from UV 254 nm crosslinking.”
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions (2013, background): “Ultraviolet cross-linking and immunoprecipitation (CLIP) was first developed to identify specific Nova RNA–protein complexes in mouse brain tissue (30).”
Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes (2011, background): “…longer—tightly packed ribosome pairs protect 58–62 nt of mRNA (Wolin and Walter, 1988), and 48S preinitiation complexes are reported to protect 50 nt or 70 nt under different conditions (Lazarowitz and Robertson, 1977; Pisarev et al., 2008; Ule et al., 2003; Chi et al., 2009; Lunde et al., 2007).”
Function of alternative splicing. (2005, neutral): “NOVA-1 target genes are highly related in function.”
Integrative regulatory mapping indicates that the RNA-binding protein HuR (ELAVL1) couples pre-mRNA processing and mRNA stability (2011, methodology): “A number of subsequent methods utilizing crosslinking followed by immunoprecipitation have addressed this deficiency to varying degrees (Ule et al., 2003; König et al., 2010; Hafner et al., 2010).”
Dido3-dependent SFPQ recruitment maintains efficiency in mammalian alternative splicing (2019, methodology): “Altered SFPQ binding to GAS2L1 RNA was confirmed by CLIP and RT-PCR (42).”
Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43 (2011, background): “Moreover, cross-linking, immunoprecipitation and high-throughput sequencing (CLIP-seq or HITS-CLIP) experiments have found that a single RNA-binding protein can have previously unrecognized roles in RNA processing and affect many alternatively spliced transcript”
Alternative splicing: new insights from global analyses. (2006, result): “These results corroborated earlier findings by the same authors demonstrating that transcripts bound by Nova splicing factors in vivo also tend to be predominately associated with these neuronal functions (Ule et al., 2003).”