MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates

Comparison of human, chimpanzee, and macaque brain transcriptomes reveals a significant developmental remodeling in the human prefrontal cortex, potentially shaped by microRNA.

[1]  M. Monden,et al.  Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. , 1999, Nucleic acids research.

[2]  Alkes L. Price,et al.  Single-Tissue and Cross-Tissue Heritability of Gene Expression Via Identity-by-Descent in Related or Unrelated Individuals , 2011, PLoS genetics.

[3]  Anirvan Ghosh,et al.  Transcriptional regulation of vertebrate axon guidance and synapse formation , 2007, Nature Reviews Neuroscience.

[4]  Eugene Berezikov,et al.  Detection of microRNAs in frozen tissue sections by fluorescence in situ hybridization using locked nucleic acid probes and tyramide signal amplification , 2007, Nature Protocols.

[5]  Dave T. Gerrard,et al.  Gene expression divergence recapitulates the developmental hourglass model , 2010, Nature.

[6]  Andrew G. Clark,et al.  Evolutionary changes in cis and trans gene regulation , 2004, Nature.

[7]  Andreas Prlic,et al.  Ensembl 2007 , 2006, Nucleic Acids Res..

[8]  Stijn van Dongen,et al.  miRBase: microRNA sequences, targets and gene nomenclature , 2005, Nucleic Acids Res..

[9]  T. Chu,et al.  Principal Variance Components Analysis: Estimating Batch Effects in Microarray Gene Expression Data , 2009 .

[10]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

[11]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[12]  Julian J. Faraway,et al.  Practical Regression and Anova using R , 2002 .

[13]  S. Pääbo,et al.  A Neutral Model of Transcriptome Evolution , 2004, PLoS biology.

[14]  P. Nelson,et al.  MicroRNAs in CNS injury: Potential roles and therapeutic implications , 2011, BioEssays : news and reviews in molecular, cellular and developmental biology.

[15]  A. Clark,et al.  Regulatory changes underlying expression differences within and between Drosophila species , 2008, Nature Genetics.

[16]  B. Nickel,et al.  Transcriptional neoteny in the human brain , 2009, Proceedings of the National Academy of Sciences.

[17]  B. Derrick,et al.  Cytokine responses to LTP induction in the rat hippocampus: a comparison of in vitro and in vivo techniques. , 2000, Learning & memory.

[18]  Y. Xing,et al.  A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function , 2008, The Journal of Neuroscience.

[19]  Mijna Hadders-Algra,et al.  Ontogeny of the human central nervous system: what is happening when? , 2006, Early human development.

[20]  K. Amunts,et al.  Spatial organization of neurons in the frontal pole sets humans apart from great apes. , 2011, Cerebral cortex.

[21]  Z. Weng,et al.  Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex , 2010, Proceedings of the National Academy of Sciences.

[22]  Andreas Scherer,et al.  Batch Effects and Noise in Microarray Experiments: Sources and Solutions , 2009 .

[23]  Katja Nowick,et al.  Rapid sequence and expression divergence suggest selection for novel function in primate-specific KRAB-ZNF genes. , 2010, Molecular biology and evolution.

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

[25]  Alcino J. Silva,et al.  Calmodulin-Kinases: Modulators of Neuronal Development and Plasticity , 2009, Neuron.

[26]  Naama Barkai,et al.  Evolution of gene sequence and gene expression are not correlated in yeast. , 2008, Trends in genetics : TIG.

[27]  M. Barnes,et al.  Analysis of gene expression in two large schizophrenia cohorts identifies multiple changes associated with nerve terminal function , 2009, Molecular Psychiatry.

[28]  M. King,et al.  Evolution at two levels in humans and chimpanzees. , 1975, Science.

[29]  John Quackenbush,et al.  Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories , 2008, BMC Genomics.

[30]  J. Rilling.  Human and nonhuman primate brains: Are they allometrically scaled versions of the same design? , 2006 .

[31]  Raymond K. Auerbach,et al.  A User's Guide to the Encyclopedia of DNA Elements (ENCODE) , 2011, PLoS biology.

[32]  L. Comai.  Faculty Opinions recommendation of Morphological evolution caused by many subtle-effect substitutions in regulatory DNA. , 2011 .

[33]  S. Pääbo,et al.  Parallel Patterns of Evolution in the Genomes and Transcriptomes of Humans and Chimpanzees , 2005, Science.

[34]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[35]  H. Nijhout,et al.  optix Drives the Repeated Convergent Evolution of Butterfly Wing Pattern Mimicry , 2011, Science.

[36]  Alexander E. Kel,et al.  MATCHTM: a tool for searching transcription factor binding sites in DNA sequences , 2003, Nucleic Acids Res..

[37]  Jean L. Chang,et al.  Initial sequence of the chimpanzee genome and comparison with the human genome , 2005, Nature.

[38]  M. Lachmann,et al.  MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain. , 2010, Genome research.

[39]  G. Kreiman,et al.  Widespread transcription at neuronal activity-regulated enhancers , 2010, Nature.

[40]  Juan M. Vaquerizas,et al.  A census of human transcription factors: function, expression and evolution , 2009, Nature Reviews Genetics.

[41]  M. Long,et al.  Accelerated Recruitment of New Brain Development Genes into the Human Genome , 2011, PLoS biology.

[42]  Terrence S. Furey,et al.  Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain , 2010, Genome biology and evolution.

[43]  S. Pääbo,et al.  Intra- and Interspecific Variation in Primate Gene Expression Patterns , 2002, Science.

[44]  David N. Messina,et al.  Evolutionary and Biomedical Insights from the Rhesus Macaque Genome , 2007, Science.

[45]  J. N. Wood.  Social cognition and the prefrontal cortex. , 2003, Behavioral and cognitive neuroscience reviews.

[46]  Arthur J. Robson,et al.  The emergence of humans: The coevolution of intelligence and longevity with intergenerational transfers , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[47]  S. Pääbo,et al.  Evolution of Neuronal and Endothelial Transcriptomes in Primates , 2010, Genome biology and evolution.

[48]  Edwin Cuppen,et al.  Diversity of microRNAs in human and chimpanzee brain , 2006, Nature Genetics.

[49]  D. Geschwind,et al.  Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis , 2009, Neuron.

[50]  Wenbo Xu,et al.  Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Matthew A. Zapala,et al.  Elevated gene expression levels distinguish human from non-human primate brains , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[52]  Iris Barshack,et al.  MiR‐92b and miR‐9/9* Are Specifically Expressed in Brain Primary Tumors and Can Be Used to Differentiate Primary from Metastatic Brain Tumors , 2008, Brain pathology.

[53]  Yoshihiro Yamanishi,et al.  KEGG for linking genomes to life and the environment , 2007, Nucleic Acids Res..

[54]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[55]  H. Tettelin,et al.  Genome Sequencing and Analysis , 2005 .

[56]  Christian J. Buhay,et al.  Rhesus Macaque Genome Sequencing and Analysis Rhesus Macaque Genome Evolutionary and Biomedical Insights from the , 2010 .

[57]  E. Wingender,et al.  MATCH: A tool for searching transcription factor binding sites in DNA sequences. , 2003, Nucleic acids research.

[58]  Sean B. Carroll,et al.  Genetics and the making of Homo sapiens , 2003, Nature.