We are analyzing https://link.springer.com/article/10.1186/gb-2012-13-9-r51.

Title:
The GENCODE pseudogene resource | Genome Biology
Description:
Background Pseudogenes have long been considered as nonfunctional genomic sequences. However, recent evidence suggests that many of them might have some form of biological activity, and the possibility of functionality has increased interest in their accurate annotation and integration with functional genomics data. Results As part of the GENCODE annotation of the human genome, we present the first genome-wide pseudogene assignment for protein-coding genes, based on both large-scale manual annotation and in silico pipelines. A key aspect of this coupled approach is that it allows us to identify pseudogenes in an unbiased fashion as well as untangle complex events through manual evaluation. We integrate the pseudogene annotations with the extensive ENCODE functional genomics information. In particular, we determine the expression level, transcription-factor and RNA polymerase II binding, and chromatin marks associated with each pseudogene. Based on their distribution, we develop simple statistical models for each type of activity, which we validate with large-scale RT-PCR-Seq experiments. Finally, we compare our pseudogenes with conservation and variation data from primate alignments and the 1000 Genomes project, producing lists of pseudogenes potentially under selection. Conclusions At one extreme, some pseudogenes possess conventional characteristics of functionality; these may represent genes that have recently died. On the other hand, we find interesting patterns of partial activity, which may suggest that dead genes are being resurrected as functioning non-coding RNAs. The activity data of each pseudogene are stored in an associated resource, psiDR, which will be useful for the initial identification of potentially functional pseudogenes.
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Keywords {🔍}

pseudogenes, pseudogene, genome, gene, pubmed, sequence, parent, annotation, transcription, transcribed, human, data, article, active, genes, google, scholar, processed, figure, chromatin, duplicated, activity, number, genomic, functional, proteincoding, cas, sequences, identity, cell, central, manual, upstream, regions, analysis, parents, binding, models, encode, selection, evidence, evolutionary, locus, gencode, gerstein, based, showing, pipelines, annotated, results,

Topics {✒️}

large-scale rt-pcr-seq experiments high-throughput wet-lab experiments large-scale rt-pcr-seq article number r51 comparative genomics search genome-wide high-quality annotation rt-pcr-seq techniques article download pdf wilcoxon rank-sum test enhancer/gene body middle tissue/cell line-specific information encode chip-seq experiments combines rt-pcr amplification protein-coding paralogous loci adjacent protein-coding locus processed pseudogene rp11-409k20 weak/poor biological replicates cristina sisu total rna-seq data analyze rna-seq data paired-end tag sequencing genome-wide pseudogene assignment protein-coding loci derived genome-wide segmentation pattern large-scale manual annotation active chromatin state chromatin state segmentation liu yj locus-specific transcription evidence rt-pcr-seq full size image privacy choices/manage cookies chromatin accessibility data high-throughput sequencing small interfering rna population-scale sequencing retroposed gene copies chip-seq data filled green box neighboring genomic locations gene body middle wet-lab validation genome-wide scale full size table neighboring genomic loci pol2 binding sites rna-based gene duplication rna-seq data rna-interference pathway [19 lacking transcription evidence

Questions {❓}

Balakirev E, Ayala F: Pseudogenes: are they "junk" or functional DNA?
Guo X, Zhang Z, Gerstein MB, Zheng D: Small RNAs originated from pseudogenes: cis- or trans-acting?
Zheng D, Gerstein MB: The ambiguous boundary between genes and pseudogenes: the dead rise up or do they?

Schema {🗺️}

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         Plant Genetics and Genomics
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            name:Center for Biomolecular Science and Engineering University of California
            address:
               name:Center for Biomolecular Science and Engineering University of California, Santa Cruz, USA
               type:PostalAddress
            type:Organization
      name:Alexandre Reymond
      affiliation:
            name:University of Lausanne
            address:
               name:Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
               type:PostalAddress
            type:Organization
      name:Tim J Hubbard
      affiliation:
            name:Welcome Trust Campus
            address:
               name:Wellcome Trust Sanger Institute, Welcome Trust Campus, Hinxton, UK
               type:PostalAddress
            type:Organization
      name:Jennifer Harrow
      affiliation:
            name:Welcome Trust Campus
            address:
               name:Wellcome Trust Sanger Institute, Welcome Trust Campus, Hinxton, UK
               type:PostalAddress
            type:Organization
      name:Mark B Gerstein
      affiliation:
            name:Yale University
            address:
               name:Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
               type:PostalAddress
            type:Organization
            name:Yale University
            address:
               name:Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA
               type:PostalAddress
            type:Organization
            name:Yale University
            address:
               name:Department of Computer Science, Yale University, New Haven, USA
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
      name:Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
      name:Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA
      name:Wellcome Trust Sanger Institute, Welcome Trust Campus, Hinxton, UK
      name:Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
      name:Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
      name:Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
      name:Center for Biomolecular Science and Engineering University of California, Santa Cruz, USA
      name:Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
      name:Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA
      name:Centre for Genomic Regulation (CRG) and UPF, Barcelona, Spain
      name:Center for Biomolecular Science and Engineering University of California, Santa Cruz, USA
      name:Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
      name:Wellcome Trust Sanger Institute, Welcome Trust Campus, Hinxton, UK
      name:Wellcome Trust Sanger Institute, Welcome Trust Campus, Hinxton, UK
      name:Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
      name:Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA
      name:Department of Computer Science, Yale University, New Haven, USA

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