Comment[ArrayExpressAccession] E-MTAB-1936 MAGE-TAB Version 1.1 Investigation Title Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects Comment[Submitted Name] Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects Experiment Description Comprehensive sequencing of human cancers has identified recurrent mutations in genes encoding chromatin regulatory proteins. For clear cell renal cell carcinoma (ccRCC), three of the five commonly mutated genes encode the chromatin regulators PBRM1, SETD2, and BAP1. How these mutations alter the chromatin landscape and transcriptional program in ccRCC or other cancers is not understood. Here, we identified alterations in chromatin organization and transcript profiles associated with mutations in chromatin regulators in a large cohort of primary human kidney tumors. By associating variation in chromatin organization with mutations in SETD2, which encodes the enzyme responsible for H3K36 trimethylation, we found that changes in chromatin accessibility occurred primarily within actively transcribed genes. This increase in chromatin accessibility was linked with widespread alterations in RNA processing, including intron retention and aberrant splicing, affecting approximately 25% of all expressed genes. Further, decreased nucleosome occupancy proximal to misspliced exons was observed in tumors lacking H3K36me3. These results directly link mutations in SETD2 to chromatin accessibility changes and RNA processing defects in cancer. Detecting the functional consequences of specific mutations in chromatin regulatory proteins in primary human samples could ultimately inform the therapeutic application of an emerging class of chromatin-targeted compounds. Additional file: MutationAnnotation.txt- contains sample ID, location of variant on hg19, reference allele, alternate allele, reference depth, alternate depth, frequency, confidence score, gene symbol, mutation type, mutation location (transcript ID and exon number, if applicable), and amino acid change. Experimental Design genotype design in_vivo_design FAIRE-Seq co-expression_design disease state design Comment[AEExperimentType] ChIP-seq genotyping by high throughput sequencing RNA-seq of coding RNA RNA-seq of non coding RNA Comment[AEExperimentDisplayName] Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects Experimental Factor Name genotype immunoprecipitate disease Experimental Factor Type genotype immunoprecipitate disease Quality Control Type biological replicate Quality Control Term Source REF EFO Public Release Date 2013-10-17 Person Last Name Simon Davis Person First Name Jeremy Ian Person Mid Initials M J Person Email jmsimon@email.unc.edu ian_davis@med.unc.edu Person Phone +1 919-966-4340 +1 919-966-4340 Person Address 450 West Drive LCCC 21-241, Chapel Hill, NC 27599 450 West Drive LCCC 21-241, Chapel Hill, NC 27599 Person Affiliation University of North Carolina - Chapel Hill University of North Carolina - Chapel Hill Person Roles submitter investigator PubMed ID Publication Author List Jeremy M. Simon, Kathryn E. Hacker, Darshan Singh, A. Rose Brannon, Joel S. Parker, Matthew Weiser, Thai H. Ho, Pei-Fen Kuan, Eric Jonasch, Terrence S. Furey, Jan F. Prins, Jason D. Lieb, W. Kimryn Rathmell, and Ian J. Davis Publication Title Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects Publication Status Protocol Name P-MTAB-35212 P-MTAB-35213 P-MTAB-35214 P-MTAB-35215 P-MTAB-35216 P-MTAB-35217 P-MTAB-35218 Protocol Type growth protocol nucleic acid extraction protocol nucleic acid library construction protocol nucleic acid sequencing protocol nucleic acid sequencing protocol high throughput sequence alignment protocol normalization data transformation protocol Protocol Description Tumors and normal kidney stored at -80C. FAIRE was performed as described in Simon et al 2012, Nature Protocols. RNA-seq was performed on riboMinus-extracted RNA. Libraries were prepared using manufacturer's recommendations with TruSeq adapters or Illumina adapters. Illumina GAIIx or HiSeq 2000, single-end reads 36 or 50bp in length. Illumina GAIIx or HiSeq 2000, single-end reads 36 or 50bp in length. Reads were aligned to the reference human genome (hg19) using Bowtie or TopHat, where appropriate. For FAIRE-seq data, the number of aligned reads at each nucleotide in the genome was summarized into a bigWig signal track. For ChIP-seq experiments, regions of significant enrichment relative to input control were identified using ZINBA; broader domains were defined by merging two or more significant regions within 5kb using Galaxy. Protocol Term Source REF EFO EFO EFO EFO EFO EFO EFO Protocol Hardware Illumina Genome Analyzer IIx Illumina HiSeq 2000 Term Source Name EFO Term Source File http://www.ebi.ac.uk/efo Comment[SecondaryAccession] ERP004043 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/ERR351345-ERR351445 Comment[AdditionalFile:TXT] MutationAnnotation.txt SDRF File E-MTAB-1936.sdrf.txt