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RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription

Philipp KapranovAffymetrix Laboratory, Affymetrix, Inc., 3420 Central Expressway, Santa Clara, CA, 95051, USAJill ChengLeipzig UniversitySujit DikeUniversity of Leipzig, Department of Computer Science, Leipzig, GermanyDavid A. NixInstitute for Theoretical Chemistry, University of Vienna, AustriaRadharani DuttaguptaLeipzig UniversityAarron WillinghamInstitute for Theoretical Chemistry, University of Vienna, AustriaPeter F. StadlerFraunhofer Institute for Cell Therapy and Immunology, Leipzig, GermanyJana HertelAffymetrix Laboratory, Affymetrix, Inc., 3420 Central Expressway, Santa Clara, CA, 95051, USAJörg HackermüllerAffymetrix Laboratory, Affymetrix, Inc., 3420 Central Expressway, Santa Clara, CA, 95051, USAIvo L. HofackerLeipzig UniversityIan BellInstitute for Theoretical Chemistry, University of Vienna, AustriaEvelyn J. CheungAffymetrix Laboratory, Affymetrix, Inc., 3420 Central Expressway, Santa Clara, CA, 95051, USAJörg DrenkowUniversity of Leipzig, Department of Computer Science, Leipzig, GermanyErica DumaisFraunhofer Institute for Cell Therapy and Immunology, Leipzig, GermanySandeep PatelFraunhofer Institute for Cell Therapy and Immunology, Leipzig, GermanyGregg HeltInstitute for Theoretical Chemistry, University of Vienna, AustriaMadhavan GaneshFraunhofer Institute for Cell Therapy and Immunology, Leipzig, GermanySrinka GhoshFraunhofer Institute for Cell Therapy and Immunology, Leipzig, GermanyAntonio PiccolboniAffymetrix Laboratory, Affymetrix, Inc., 3420 Central Expressway, Santa Clara, CA, 95051, USAVictor SementchenkoLeipzig UniversityHari TammanaFraunhofer Institute for Cell Therapy and Immunology, Leipzig, GermanyT GingerasAffymetrix Laboratory, Affymetrix, Inc., 3420 Central Expressway, Santa Clara, CA, 95051, USA

2007en

ABI

Annotatsiya

Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated and has reduced protein-coding potential. The genomic origins and the associations of human nuclear and cytosolic polyadenylated RNAs longer than 200 nucleotides (nt) and whole-cell RNAs less than 200 nt were investigated in this genome-wide study. Subcellular addresses for nucleotides present in detected RNAs were assigned, and their potential processing into short RNAs was investigated. Taken together, these observations suggest a novel role for some unannotated RNAs as primary transcripts for the production of short RNAs. Three potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes. These data support a highly interleaved organization of the human transcriptome.

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DOI: 10.1126/science.1138341

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