Cargando…

Transcriptional activity and strain-specific history of mouse pseudogenes

Pseudogenes are ideal markers of genome remodelling. In turn, the mouse is an ideal platform for studying them, particularly with the recent availability of strain-sequencing and transcriptional data. Here, combining both manual curation and automatic pipelines, we present a genome-wide annotation o...

Descripción completa

Detalles Bibliográficos
Autores principales:	Sisu, Cristina, Muir, Paul, Frankish, Adam, Fiddes, Ian, Diekhans, Mark, Thybert, David, Odom, Duncan T., Flicek, Paul, Keane, Thomas M., Hubbard, Tim, Harrow, Jennifer, Gerstein, Mark
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Nature Publishing Group UK 2020
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7392758/ https://www.ncbi.nlm.nih.gov/pubmed/32728065 http://dx.doi.org/10.1038/s41467-020-17157-w

Ejemplares similares

The GENCODE pseudogene resource
por: Pei, Baikang, et al.
Publicado: (2012)

Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates
por: Zhang, Zhengdong D, et al.
Publicado: (2010)

Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals
por: Wong, Emily S., et al.
Publicado: (2015)

Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation
por: Karro, John E., et al.
Publicado: (2007)

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System
por: Leigh-Brown, Sarah, et al.
Publicado: (2015)

Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes
por: Balasubramanian, Suganthi, et al.
Publicado: (2009)

Sixteen diverse laboratory mouse reference genomes define strain specific haplotypes and novel functional loci
por: Lilue, Jingtao, et al.
Publicado: (2018)

Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals
por: Stefflova, Klara, et al.
Publicado: (2013)

Chromosome assembly of large and complex genomes using multiple references
por: Kolmogorov, Mikhail, et al.
Publicado: (2018)

A computational approach for identifying pseudogenes in the ENCODE regions
por: Zheng, Deyou, et al.
Publicado: (2006)

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution
por: Wong, Emily S., et al.
Publicado: (2017)

Pseudofam: the pseudogene families database
por: Lam, Hugo Y. K., et al.
Publicado: (2009)

Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes
por: Liu, Yang, et al.
Publicado: (2004)

Using semantic web rules to reason on an ontology of pseudogenes
por: Holford, Matthew E., et al.
Publicado: (2010)

Small RNAs Originated from Pseudogenes: cis- or trans-Acting?
por: Guo, Xingyi, et al.
Publicado: (2009)

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression
por: Goncalves, Angela, et al.
Publicado: (2012)

Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability
por: Harrison, Paul M., et al.
Publicado: (2005)

Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity
por: Liu, Yuen-Jong, et al.
Publicado: (2009)

Segmental duplications in the human genome reveal details of pseudogene formation
por: Khurana, Ekta, et al.
Publicado: (2010)

Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes
por: Ezkurdia, Iakes, et al.
Publicado: (2014)

The human ABC transporter pseudogene family: Evidence for transcription and gene-pseudogene interference
por: Piehler, Armin P, et al.
Publicado: (2008)

Defining the human reference protein-coding gene set
por: Balasubramanian, Suganthi, et al.
Publicado: (2010)

Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat
por: Martín-Gálvez, David, et al.
Publicado: (2017)

Pseudogenes as an alternative source of natural antisense transcripts
por: Muro, Enrique M, et al.
Publicado: (2010)

Pseudogenes
por: Tutar, Yusuf
Publicado: (2012)

Progress, Challenges, and Surprises in Annotating the Human Genome
por: Zerbino, Daniel R., et al.
Publicado: (2020)

Functional signatures of evolutionarily young CTCF binding sites
por: Azazi, Dhoyazan, et al.
Publicado: (2020)

Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi
por: Holt, Kathryn E, et al.
Publicado: (2009)

The importance of identifying alternative splicing in vertebrate genome annotation
por: Frankish, Adam, et al.
Publicado: (2012)

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene
por: Gonzàlez-Porta, Mar, et al.
Publicado: (2013)

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
por: Thybert, David, et al.
Publicado: (2018)

Implications of high level pseudogene transcription in Mycobacterium leprae
por: Williams, Diana L, et al.
Publicado: (2009)

Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data
por: Rensch, Thomas, et al.
Publicado: (2016)

Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes
por: Schwalie, Petra C, et al.
Publicado: (2013)

Assessment of transcript reconstruction methods for RNA-seq
por: Steijger, Tamara, et al.
Publicado: (2013)

Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression
por: Berthelot, Camille, et al.
Publicado: (2017)

Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
por: Fiddes, Ian T., et al.
Publicado: (2018)

Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells
por: Tunstall, Tate, et al.
Publicado: (2018)

Functional transcriptomics in the post-ENCODE era
por: Mudge, Jonathan M., et al.
Publicado: (2013)

GENCODE reference annotation for the human and mouse genomes
por: Frankish, Adam, et al.
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_98umsoh0khjjasfpihkoothgha