Description

In eukaryotic organisms, gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs (mRNAs) have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins (RBPs) play a major role in regulating multiple mRNAs in order to facilitate gene expression patterns.

These tracks can elucidate RNA processing by identifying RNA molecules that interact with specific RBPs. They were developed using assays that first purify mRNA-RBP complexes and then separate the complexes to identify the target mRNAs bound to specific RBPs. The mRNAs can be identified by methods including sequencing, microarrays, and SAGE.

The tracks in this supertrack contain two forms of information: genes whose transcripts were bound by the given RBP (such as SUNY RIP GeneSt) and approximate location of the RBP binding site in the mRNA sequence (such SUNY RIP Tiling and SUNY RIP-seq).

Please note:

RIP input tracks (both array and sequencing based) were created for use in downstream informatic analysis to produce RBP specific RIP tracks. Low abundance RNA that is undetectable in the input samples may be proportionally enriched to the point of detection in the RIPs. This may be confusing to some users expecting to see RIP as a subset of input. Users seeking information on total RNA should examine the "expression" RNA-seq tracks produced by other ENCODE groups.

Display Conventions and Configuration

These tracks are multi-view composite tracks that contains multiple data types (views). Each view within each track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages.

Credits

These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions, to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks.

References

Baroni TE, Chittur SV, George AD, Tenenbaum SA. Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling. Methods Mol Biol. 2008;419:93-108.

George AD, Tenenbaum SA. MicroRNA modulation of RNA-binding protein regulatory elements. RNA Biol. 2006 Apr;3(2):57-9.

Keene JD, Tenenbaum SA. Eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell. 2002 Jun;9(6):1161-7.

Penalva LO, Tenenbaum SA, Keene JD. Gene expression analysis of messenger RNP complexes. Methods Mol Biol. 2004;257:125-34.

Tenenbaum SA, Lager PJ, Carson CC, Keene JD. Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods. 2002 Feb;26(2):191-8.

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here.