[440 @GencodeGenes] #Pseudogenes transcribed in breast…carcinoma show subtype-specific expression & ceRNA potential http://www.biomedcentral.com/1471-2164/16/113
http://www.sciencemag.org/content/early/2009/12/10/science.1181421
Published Online December 10 2009
Science DOI: 10.1126/science.1181421
REPORT
Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila
Sergei Nechaev1,
David C. Fargo2,
Gilberto dos Santos1,
Liwen Liu3,
Yuan Gao4 and
Karen Adelman1,*
Landscape of lncRNAs in the human #transcriptome
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3192.html Derived from RNAseq read assembly; not much overlap w/ @GencodeGenes
Matthew K Iyer,
Yashar S Niknafs,
Rohit Malik,
Udit Singhal,
Anirban Sahu,
Yasuyuki Hosono,
Terrence R Barrette,
John R Prensner,
Joseph R Evans,
Shuang Zhao,
Anton Poliakov,
Xuhong Cao,
Saravana M Dhanasekaran,
Yi-Mi Wu,
Dan R Robinson,
David G Beer,
Felix Y Feng,
Hariharan K Iyer
& Arul M Chinnaiyan
Nature Genetics (2015) doi:10.1038/ng.3192Received 20 June 2014 Accepted 18 December 2014
QT:{{”
We identify an lncRNA pseudogene, Lethe (named after the mythological river of forgetfulness, for its role in negative feedback), which is expressed in response to proinflammatory cytokines TNFα and IL-1β, and the anti-inflammatory agent, dexamthasone, but is not responsive to microbial components, and is primarily found on the chromatin. Lethe is regulated by RelA, independent of pseudogene family members and proximal genes. Additionally, Lethe is dramatically downregulated in aged spleen. Finally, Lethe binds directly to RelA to inhibit NF-κB DNA binding activity. These findings suggest that Lethe may function as a novel negative regulator of NF-κB, to help fine tune the inflammatory response.
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A mammalian #pseudogene #lncRNA at the interface of inflammation… Lethe may down-regulate NF-kB via binding to RelA
http://elifesciences.org/content/2/e00762
No use of Gencode pgenes !
recent publication from the Donnelly group comparing using GENCODE or Refeq annotation when predicting variants effects.
Choice of transcripts and software has a large effect on variant annotation
Genome Medicine 2014, 6:26 doi:10.1186/gm543