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PMID: 15489326 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

1274 full-open reading frames of transcripts expressed in the developing mouse nervous system.

Genome research ·Vol. 14 ·No. 10B ·2004-10-00 ·Pages 2053-63

Bonaldo MF, Bair TB, Scheetz TE, Snir E, Akabogu I, Bair JL, Berger B, Crouch K, Davis A, Eyestone ME, Keppel C, Kucaba TA, Lebeck M, Lin JL, de Melo AI, Rehmann J, Reiter RS, Schaefer K, Smith C, Tack D, Trout K, Sheffield VC, Lin JJ, Casavant TL, Soares MB

Abstract

As part of the trans-National Institutes of Health (NIH) Mouse Brain Molecular Anatomy Project (BMAP), and in close coordination with the NIH Mammalian Gene Collection Program (MGC), we initiated a large-scale project to clone, identify, and sequence the complete open reading frame (ORF) of transcripts expressed in the developing mouse nervous system. Here we report the analysis of the ORF sequence of 1274 cDNAs, obtained from 47 full-length-enriched cDNA libraries, constructed by using a novel approach, herein described. cDNA libraries were derived from size-fractionated cytoplasmic mRNA isolated from brain and eye tissues obtained at several embryonic stages and postnatal days. Altogether, including the full-ORF MGC sequences derived from these libraries by the MGC sequencing team, NIH_BMAP full-ORF sequences correspond to approximately 20% of all transcripts currently represented in mouse MGC. We show that NIH_BMAP clones comprise 68% of mouse MGC cDNAs > or =5 kb, and 54% of those > or =4 kb, as of March 15, 2004. Importantly, we identified transcripts, among the 1274 full-ORF sequences, that are exclusively or predominantly expressed in brain and eye tissues, many of which encode yet uncharacterized proteins.

MeSH Terms
Animals Brain/anatomy & histology,embryology,metabolism DNA, Complementary Eye/anatomy & histology,embryology,metabolism Female Gene Expression Profiling Gene Expression Regulation, Developmental/physiology Gene Library Genome Mice Mice, Inbred C57BL Nerve Tissue Proteins/classification,genetics Open Reading Frames/genetics Pregnancy RNA, Messenger/genetics,metabolism
Chemicals
DNA, Complementary Nerve Tissue Proteins RNA, Messenger
Authors & Affiliations
25 authors, click to expand affiliations / ORCID
Bonaldo Maria F
Department of Pediatrics, The University of Iowa, Iowa City, Iowa 52242, USA.
Bair Thomas B
Scheetz Todd E
Snir Einat
Akabogu Ike
Bair Jennifer L
Berger Brian
Crouch Keith
Davis Aja
Eyestone Mari E
Keppel Catherine
Kucaba Tamara A
Lebeck Mark
Lin Jenny L
de Melo Anna I R
Rehmann Joshua
Reiter Rebecca S
Schaefer Kelly
Smith Christina
Tack Dylan
Trout Kurtis
Sheffield Val C
Lin Jim J-C
Casavant Thomas L
Soares Marcelo B
References (36)
36 references, click to expand
  1. High-throughput plasmid DNA purification for 3 cents per sample.
    Nucleic Acids Res. 1999 Dec 15;27(24):e37 PMID: 10572189
  2. High-efficiency full-length cDNA cloning.
    Methods Enzymol. 1999;303:19-44 PMID: 10349636
  3. Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes.
    Genome Res. 2000 Oct;10(10):1617-30 PMID: 11042159
  4. Identification of a human brain-specific gene, calneuron 1, a new member of the calmodulin superfamily.
    Mol Genet Metab. 2001 Apr;72(4):343-50 PMID: 11286509
  5. Cloning full-length, cap-trapper-selected cDNAs by using the single-strand linker ligation method.
    Biotechniques. 2001 Jun;30(6):1250-4 PMID: 11414214
  6. Construction of full-length-enriched cDNA libraries. The oligo-capping method.
    Methods Mol Biol. 2001;175:143-53 PMID: 11462832
  7. Construction of long-transcript enriched cDNA libraries from submicrogram amounts of total RNAs by a universal PCR amplification method.
    Genome Res. 2001 Sep;11(9):1553-8 PMID: 11544199
  8. Balanced-size and long-size cloning of full-length, cap-trapped cDNAs into vectors of the novel lambda-FLC family allows enhanced gene discovery rate and functional analysis.
    Genomics. 2001 Sep;77(1-2):79-90 PMID: 11543636
  9. Mutations in LGI1 cause autosomal-dominant partial epilepsy with auditory features.
    Nat Genet. 2002 Mar;30(3):335-41 PMID: 11810107
  10. BLAT--the BLAST-like alignment tool.
    Genome Res. 2002 Apr;12(4):656-64 PMID: 11932250
  11. Extra-long first-strand cDNA synthesis.
    Biotechniques. 2002 May;32(5):984-5 PMID: 12019793
  12. The LGI1 gene involved in lateral temporal lobe epilepsy belongs to a new subfamily of leucine-rich repeat proteins.
    FEBS Lett. 2002 May 22;519(1-3):71-6 PMID: 12023020
  13. Highly conserved mouse and human brain sulfotransferases: molecular cloning, expression, and functional characterization.
    Gene. 2002 Feb 20;285(1-2):39-47 PMID: 12039030
  14. Pooled library tissue tags for EST-based gene discovery.
    Bioinformatics. 2002 Sep;18(9):1162-6 PMID: 12217907
  15. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
    Nature. 2002 Dec 5;420(6915):563-73 PMID: 12466851
  16. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.
    Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903 PMID: 12477932
  17. The UCSC Genome Browser Database.
    Nucleic Acids Res. 2003 Jan 1;31(1):51-4 PMID: 12519945
  18. Construction of a full-length enriched and a 5'-end enriched cDNA library using the oligo-capping method.
    Methods Mol Biol. 2003;221:73-91 PMID: 12703735
  19. Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.
    Genome Res. 2003 Jun;13(6B):1273-89 PMID: 12819125
  20. Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts.
    Biotechniques. 2003 Sep;35(3):510-6, 518 PMID: 14513556
  21. Complete sequencing and characterization of 21,243 full-length human cDNAs.
    Nat Genet. 2004 Jan;36(1):40-5 PMID: 14702039
  22. Transcription maps of polyoma virus-specific RNA: analysis by two-dimensional nuclease S1 gel mapping.
    Methods Enzymol. 1980;65(1):718-49 PMID: 6154876
  23. Molecular cloning and chromosomal localization of one of the human glutamate receptor genes.
    Proc Natl Acad Sci U S A. 1991 Sep 1;88(17):7557-61 PMID: 1652753
  24. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides.
    Gene. 1994 Jan 28;138(1-2):171-4 PMID: 8125298
  25. Cloning provides evidence for a family of inward rectifier and G-protein coupled K+ channels in the brain.
    FEBS Lett. 1994 Oct 10;353(1):37-42 PMID: 7926018
  26. Cloning and expression of SEZ-6, a brain-specific and seizure-related cDNA.
    Brain Res Mol Brain Res. 1995 Feb;28(2):201-10 PMID: 7723619
  27. The neuron-specific kinesin superfamily protein KIF1A is a unique monomeric motor for anterograde axonal transport of synaptic vesicle precursors.
    Cell. 1995 Jun 2;81(5):769-80 PMID: 7539720
  28. T-brain-1: a homolog of Brachyury whose expression defines molecularly distinct domains within the cerebral cortex.
    Neuron. 1995 Jul;15(1):63-78 PMID: 7619531
  29. Normalization and subtraction: two approaches to facilitate gene discovery.
    Genome Res. 1996 Sep;6(9):791-806 PMID: 8889548
  30. Localization of a novel human RNA-editing deaminase (hRED2 or ADARB2) to chromosome 10p15.
    Hum Genet. 1997 Sep;100(3-4):398-400 PMID: 9272162
  31. Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library.
    Gene. 1997 Oct 24;200(1-2):149-56 PMID: 9373149
  32. Base-calling of automated sequencer traces using phred. I. Accuracy assessment.
    Genome Res. 1998 Mar;8(3):175-85 PMID: 9521921
  33. Consed: a graphical tool for sequence finishing.
    Genome Res. 1998 Mar;8(3):195-202 PMID: 9521923
  34. Expression of PACAP, and PACAP type 1 (PAC1) receptor mRNA during development of the mouse embryo.
    Brain Res Dev Brain Res. 1998 Aug 8;109(2):245-53 PMID: 9729410
  35. Characterization of two novel protocadherins (PCDH8 and PCDH9) localized on human chromosome 13 and mouse chromosome 14.
    Genomics. 1998 Oct 1;53(1):81-9 PMID: 9787079
  36. Cbln3, a novel member of the precerebellin family that binds specifically to Cbln1.
    J Neurosci. 2000 Sep 1;20(17):6333-9 PMID: 10964938
Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.2601304
Published
2004-10-00
Pages
2053-63
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC528920
Subset
IM
Grants
NHGRI NIH HHS · F32 HG002881 · United States
NIMH NIH HHS · N01MH12006 · United States
NHGRI NIH HHS · 1F32HG002881-01A1 · United States
External Links
PubMed source DOI: 10.1101/gr.2601304 PMC Full Text View journal details
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