1. Watson School of Biological Sciences,
2. Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
3. Affymetrix, Inc. Santa Clara, California 95051, USA.
4. Present address: Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 5 East 98th Street, New York, New York 10029, USA.
5. These authors contributed equally to this work.
6. Lists of participants and their affiliations appear at the end of the paper.

Correspondence to: Correspondence and requests for materials should be addressed to G.J.H. (Email: hannon@cshl.edu) or T.R.G. (Email: gingeras@cshl.edu).

The transcriptomes of eukaryotic cells are incredibly complex. Individual non-coding RNAs dwarf the number of protein-coding genes, and include classes that are well understood as well as classes for which the nature, extent and functional roles are obscure¹. Deep sequencing of small RNAs (<200 nucleotides) from human HeLa and HepG2 cells revealed a remarkable breadth of species. These arose both from within annotated genes and from unannotated intergenic regions. Overall, small RNAs tended to align with CAGE (cap-analysis of gene expression) tags², which mark the 5' ends of capped, long RNA transcripts. Many small RNAs, including the previously described promoter-associated small RNAs³, appeared to possess cap structures. Members of an extensive class of both small RNAs and CAGE tags were distributed across internal exons of annotated protein coding and non-coding genes, sometimes crossing exon–exon junctions. Here we show that processing of mature mRNAs through an as yet unknown mechanism may generate complex populations of both long and short RNAs whose apparently capped 5' ends coincide. Supplying synthetic promoter-associated small RNAs corresponding to the c-MYC transcriptional start site reduced MYC messenger RNA abundance. The studies presented here expand the catalogue of cellular small RNAs and demonstrate a biological impact for at least one class of non-canonical small RNAs.

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