Description

This track is produced as part of the ENCODE Project. This track displays transcriptional fragments associated with RNA binding proteins in different cell lines, using RIP-Chip (Ribonomic) profiling on Affymetrix GeneChip ENCODE 2.0R Tiling Arrays. The RBP Assoc RNA view shows the genomic location of transcripts associated with the array probes. Data for this track was produced as part of the Encyclopedia of DNA Elements (ENCODE) Project.

In eukaryotic organisms, gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins play a major role in regulating multiple mRNAs in order to facilitate gene expression patterns. These tracks show the associated mRNAs that co-precipitate with the targeted RNA-binding proteins using RIP-Chip profiling.

Display Conventions and Configuration

This track is a multi-view composite track. For each view there are multiple subtracks that display individually in the browser. The subtracks within this track correspond to different antibodies/target proteins tested in different cell lines. This track is initially released with a single view:

RBP Assoc RNA

The RBP Assoc RNA view shows the genomic extent of the transcriptional segments associated with the Affymetrix Tiling Array probes.

Methods

RBP-mRNA complexes were purified from cells grown according to the approved ENCODE cell culture protocols . The associated transcriptional fragments were identified using Affymetrix GeneChip ENCODE 2.0R Tiling Arrays. Arrays were analyzed using Affymetrix Tiling Analysis Software (TAS) version 1.1.

Total Input and T7Tag (negative control) tracks were each developed by single sample analysis of their respective triplicate sets with quantile normalization and linear scaling applied. Probe signals were calculated using the Hodges-Lehmann estimator with a bandwidth of 100 bases. Resulting signal files were examined to develop percentiles. Interval analysis was performed using a minimum cut-off equal to the 95th percentile signal score, a minimum run of 21 (3 * platform resolution) and max gap of 63 (9 * platform resolution).

Treatment RIP tracks (e.g., ELAVL1, PABC1) were developed by two sample analysis with T7Tag used as the control. Quantile normalization and scaling was applied to these sample groups individually. Probe signals were calculated with the Hodges-Lehmann estimator using signal log (log2) ratios and a bandwidth of 100 bases. Resulting signal files were examined to develop percentiles. Interval analysis was performed using a minimum cut-off equal to the 95th percentile signal ratio score, a minimum run of 21 (3 * platform resolution) and max gap of 63 (9 * platform resolution).

For additional RIP methods detail, see Tenenbaum et al. 2002; Baroni et al. 2008; Penalva et al. 2004, below.

Verification

All experiments (including controls) performed in and analyzed as triplicates.

Credits

These data were produced and analyzed by a collaboration between the Tenenbaum lab at the University at Albany-SUNY, College of Nanoscale Science and Engineering, the Luiz Penalva group at the Greehey Children's Cancer Research Institute, University of Texas Health Science Center and the Microarray Core Facility at the Center for Functional Genomics, Rensselaer, NY .

Contact: STenenbaum@uamail. albany. edu

References

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.

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.

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

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

George AD, Tenenbaum SA. MicroRNA modulation of RNA-binding protein regulatory elements. RNA Biol. 2006;3(2):57-9. Epub 2006 Apr 1.

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, above. The full data release policy for ENCODE is available here.