Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes

[1]  L. Krubitzer,et al.  The subventricular zone is the developmental milestone of a 6-layered neocortex: comparisons in metatherian and eutherian mammals. , 2010, Cerebral cortex.

[2]  T. Nilsen,et al.  Reprogramming of the non-coding transcriptome during brain development , 2010, Journal of biology.

[3]  P. Robson,et al.  Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. , 2010, RNA.

[4]  J. Mattick,et al.  Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation , 2010, BMC Neuroscience.

[5]  C. Ponting,et al.  Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness , 2009, Genome Biology.

[6]  Paulo P. Amaral,et al.  Complex architecture and regulated expression of the Sox2ot locus during vertebrate development. , 2009, RNA.

[7]  P. Rakic.  Evolution of the neocortex: Perspective from developmental biology , 2010 .

[8]  C. Ponting,et al.  Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain , 2009, PLoS genetics.

[9]  S. Auvin,et al.  MEF2C haploinsufficiency caused by either microdeletion of the 5q14.3 region or mutation is responsible for severe mental retardation with stereotypic movements, epilepsy and/or cerebral malformations , 2009, Journal of Medical Genetics.

[10]  Peter A. Meric,et al.  Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse , 2009, PLoS biology.

[11]  C. Ponting,et al.  Evolution and Functions of Long Noncoding RNAs , 2009, Cell.

[12]  Michael F. Lin,et al.  Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals , 2009, Nature.

[13]  Paulo P. Amaral,et al.  Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. , 2008, Genome research.

[14]  Jeffrey D. Zaremba,et al.  Transcription factor MEF2C influences neural stem/progenitor cell differentiation and maturation in vivo , 2008, Proceedings of the National Academy of Sciences.

[15]  Yimin Zou,et al.  Wnt signaling in neural circuit assembly. , 2008, Annual review of neuroscience.

[16]  Paulo P. Amaral,et al.  The Eukaryotic Genome as an RNA Machine , 2008, Science.

[17]  Karla E. Hirokawa,et al.  Lhx2 Selector Activity Specifies Cortical Identity and Suppresses Hippocampal Organizer Fate , 2008, Science.

[18]  S. Sunkin,et al.  Specific expression of long noncoding RNAs in the mouse brain , 2008, Proceedings of the National Academy of Sciences.

[19]  T. Mikkelsen,et al.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.

[20]  M. Takeichi,et al.  The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons , 2007, Journal of Cell Science.

[21]  Ziheng Yang.  PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[22]  Howard Y. Chang,et al.  Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs , 2007, Cell.

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

[24]  Thomas R Gingeras,et al.  Origin of phenotypes: genes and transcripts. , 2007, Genome research.

[25]  T. Gingeras,et al.  Genome-wide transcription and the implications for genomic organization , 2007, Nature Reviews Genetics.

[26]  P. Arlotta,et al.  Neuronal subtype specification in the cerebral cortex , 2007, Nature Reviews Neuroscience.

[27]  Colin N. Dewey,et al.  Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. , 2007, Genome research.

[28]  M. Gerstein,et al.  What is a gene, post-ENCODE? History and updated definition. , 2007, Genome research.

[29]  Piero Carninci,et al.  Constructing the landscape of the mammalian transcriptome , 2007, Journal of Experimental Biology.

[30]  C. Ponting,et al.  Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. , 2007, Genome research.

[31]  Araxi O. Urrutia,et al.  Splicing and the Evolution of Proteins in Mammals , 2007, Nature Reviews Genetics.

[32]  Ivan Ovcharenko,et al.  ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes , 2007, Bioinform..

[33]  Alan M. Moses,et al.  In vivo enhancer analysis of human conserved non-coding sequences , 2006, Nature.

[34]  A. Kriegstein,et al.  Patterns of neural stem and progenitor cell division may underlie evolutionary cortical expansion , 2006, Nature Reviews Neuroscience.

[35]  J. Thierry-Mieg,et al.  AceView: a comprehensive cDNA-supported gene and transcripts annotation , 2006, Genome Biology.

[36]  Robert F. Hevner,et al.  Transcription factors in glutamatergic neurogenesis: Conserved programs in neocortex, cerebellum, and adult hippocampus , 2006, Neuroscience Research.

[37]  Laurent Duret,et al.  The Xist RNA Gene Evolved in Eutherians by Pseudogenization of a Protein-Coding Gene , 2006, Science.

[38]  Brian S. Clark,et al.  The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. , 2006, Genes & development.

[39]  Sin Lam Tan,et al.  Complex Loci in Human and Mouse Genomes , 2006, PLoS genetics.

[40]  Jun Kawai,et al.  Heterotachy in Mammalian Promoter Evolution , 2006, PLoS genetics.

[41]  T. Curran,et al.  BGEM: An In Situ Hybridization Database of Gene Expression in the Embryonic and Adult Mouse Nervous System , 2006, PLoS biology.

[42]  David Haussler,et al.  Identification and Classification of Conserved RNA Secondary Structures in the Human Genome , 2006, PLoS Comput. Biol..

[43]  V. Tarabykin,et al.  Molecular mechanisms of cortical differentiation , 2006, The European journal of neuroscience.

[44]  H. Kennedy,et al.  Comparative aspects of cerebral cortical development , 2006, The European journal of neuroscience.

[45]  Chris P. Ponting,et al.  Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model , 2005, PLoS Comput. Biol..

[46]  D. T. Lee,et al.  SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools , 2006, BMC Bioinformatics.

[47]  C. Disteche,et al.  Evidence for de novo imprinted X-chromosome inactivation independent of meiotic inactivation in mice , 2005, Nature.

[48]  T. Hughes,et al.  A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription , 2005, BMC Genomics.

[49]  D. Haussler,et al.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.

[50]  S. E. Craven,et al.  Identification of Pax2-regulated genes by expression profiling of the mid-hindbrain organizer region , 2005, Development.

[51]  G. Helt,et al.  Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution , 2005, Science.

[52]  Mark Gerstein,et al.  Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery , 2005, Chromosome Research.

[53]  Ewan Birney,et al.  Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags. , 2005, Genome research.

[54]  H. Tabata,et al.  Birth-date dependent alignment of GABAergic neurons occurs in a different pattern from that of non-GABAergic neurons in the developing mouse visual cortex , 2004, Neuroscience Research.

[55]  D. Haussler,et al.  Aligning multiple genomic sequences with the threaded blockset aligner. , 2004, Genome research.

[56]  S. Cawley,et al.  Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. , 2004, Genome research.

[57]  D. Haussler,et al.  Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[58]  E. Birney,et al.  Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs , 2002, Nature.

[59]  J. Squire,et al.  Identification of a novel gene NCRMS on chromosome 12q21 with differential expression between Rhabdomyosarcoma subtypes , 2002, Oncogene.

[60]  D. Barlow,et al.  Quantitative genetics: Turning up the heat on QTL mapping , 2002, Nature Reviews Genetics.

[61]  Mouse Genome Sequencing Consortium.  Initial sequencing and comparative analysis of the mouse genome , 2002, Nature.

[62]  E. Grove,et al.  LIM-homeodomain gene Lhx2 regulates the formation of the cortical hem , 2001, Mechanisms of Development.

[63]  J. Rubenstein,et al.  Pallial and subpallial derivatives in the embryonic chick and mouse telencephalon, traced by the expression of the genes Dlx‐2, Emx‐1, Nkx‐2.1, Pax‐6, and Tbr‐1 , 2000, The Journal of comparative neurology.

[64]  A. Lavdas,et al.  The Medial Ganglionic Eminence Gives Rise to a Population of Early Neurons in the Developing Cerebral Cortex , 1999, The Journal of Neuroscience.

[65]  D. Wilkinson.  In situ hybridization: a practical approach , 1998 .

[66]  Sudhir Kumar,et al.  Continental breakup and the ordinal diversification of birds and mammals , 1996, Nature.

[67]  Acknowledgements , 1992, Experimental Gerontology.

[68]  A. Goffinet,et al.  Neurogenesis in reptilian cortical structures: 3H‐thymidine autoradiographic analysis , 1986, The Journal of comparative neurology.