Genomics: Protein fossils live on as RNA

Pseudogenes constitute many of the non-coding DNA sequences that make up large parts of genomes. Once considered merely protein fossils, it now emerges that some of them have active regulatory roles.

[1]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[2]  E. Devor Primate microRNAs miR-220 and miR-492 lie within processed pseudogenes. , 2006, The Journal of heredity.

[3]  James C. Carrington,et al.  Specialization and evolution of endogenous small RNA pathways , 2007, Nature Reviews Genetics.

[4]  Manolis Kellis,et al.  Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila , 2007, Cell.

[5]  M. Gerstein,et al.  Comparative analysis of processed pseudogenes in the mouse and human genomes. , 2004, Trends in genetics : TIG.

[6]  D. Petrov,et al.  High intrinsic rate of DNA loss in Drosophila , 1996, Nature.

[7]  Taishin Kin,et al.  Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells , 2008, Nature.

[8]  Sudha Balla,et al.  Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster , 2008, Nature Structural &Molecular Biology.

[9]  F. Ayala,et al.  Positive and Negative Selection in the β-Esterase Gene Cluster of the Drosophila melanogaster Subgroup , 2006, Journal of Molecular Evolution.

[10]  Gi-Ho Sung,et al.  Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana , 2004, Nature Genetics.

[11]  Oliver H. Tam,et al.  Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes , 2008, Nature.

[12]  Y. Sakaki,et al.  Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes , 2008, Nature.

[13]  Atsushi Yoshiki,et al.  An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene , 2003, Nature.

[14]  D. Bartel,et al.  The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs , 2008, Nature.

[15]  Mark Gerstein,et al.  Identification of pseudogenes in the Drosophila melanogaster genome. , 2003, Nucleic acids research.

[16]  P. Zamore,et al.  Small silencing RNAs , 2007, Current Biology.

[17]  Philipp Kapranov,et al.  Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. , 2007, Genome research.

[18]  M. O'Shea,et al.  Neuronal Expression of Neural Nitric Oxide Synthase (nNOS) Protein Is Suppressed by an Antisense RNA Transcribed from an NOS Pseudogene , 1999, The Journal of Neuroscience.

[19]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[20]  Z. Weng,et al.  Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells , 2008, Science.

[21]  N. Perrimon,et al.  An endogenous small interfering RNA pathway in Drosophila , 2008, Nature.