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Keywords {🔍}

regions, race, transcripts, genome, pubmed, article, rna, human, products, google, scholar, transcription, antisense, analysis, sequencing, cas, gene, sequences, cdna, transcribed, encode, tars, figure, transcript, additional, genes, splice, reverse, protein, sequence, pcr, consensus, data, previously, file, exons, total, primers, detected, central, strand, expression, tiling, shown, region, science, usa, transcriptome, produced, coding,

Topics {✒️}

large-scale rt-pcr recovery long-read high-throughput sequencing large-scale rt-pcr analysis real-time pcr quantification real-time quantitative pcr high-density tiling arrays 1186/gb-2006-7-s1-s4 article number r3 /sis/rtpcr/upl/adc article download pdf gov/sage/anatomicviewer] perocchi specific cell/tissue types genome-wide mutant collections central nervous system database similarity search cell type specific developmental biology department sense-antisense transcription phenomena create single-stranded cdna full-length cdna clones sequencing full-length cdna article published online jia qian wu strand-specific microarray produced authors’ original file tiling array experiments tiling array studies make 5'-race-ready cdna privacy choices/manage cookies specific cell types open reading frames additional data files cooper sj genome tiling arrays nested universal primer genomic tiling arrays comprehensive search full size image intergenic regions distal sage adaptor ligation mol cell endocrinol tiling microarray analysis synapsin iii gene encode pilot project entire pcr reaction consensus splice sites consensus splice site signal intensity data antisense transcription occurs purported antisense transcription

Questions {❓}

• How much of the human genome produces transcripts that are present in the mRNA population?
• Vanhee-Brossollet C, Vaquero C: Do natural antisense transcripts make sense in eukaryotes?

Schema {🗺️}

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         description:Recent studies of the mammalian transcriptome have revealed a large number of additional transcribed regions and extraordinary complexity in transcript diversity. However, there is still much uncertainty regarding precisely what portion of the genome is transcribed, the exact structures of these novel transcripts, and the levels of the transcripts produced. We have interrogated the transcribed loci in 420 selected ENCyclopedia Of DNA Elements (ENCODE) regions using rapid amplification of cDNA ends (RACE) sequencing. We analyzed annotated known gene regions, but primarily we focused on novel transcriptionally active regions (TARs), which were previously identified by high-density oligonucleotide tiling arrays and on random regions that were not believed to be transcribed. We found RACE sequencing to be very sensitive and were able to detect low levels of transcripts in specific cell types that were not detectable by microarrays. We also observed many instances of sense-antisense transcripts; further analysis suggests that many of the antisense transcripts (but not all) may be artifacts generated from the reverse transcription reaction. Our results show that the majority of the novel TARs analyzed (60%) are connected to other novel TARs or known exons. Of previously unannotated random regions, 17% were shown to produce overlapping transcripts. Furthermore, it is estimated that 9% of the novel transcripts encode proteins. We conclude that RACE sequencing is an efficient, sensitive, and highly accurate method for characterization of the transcriptome of specific cell/tissue types. Using this method, it appears that much of the genome is represented in polyA+ RNA. Moreover, a fraction of the novel RNAs can encode protein and are likely to be functional.
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      headline:Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome
      description:Recent studies of the mammalian transcriptome have revealed a large number of additional transcribed regions and extraordinary complexity in transcript diversity. However, there is still much uncertainty regarding precisely what portion of the genome is transcribed, the exact structures of these novel transcripts, and the levels of the transcripts produced. We have interrogated the transcribed loci in 420 selected ENCyclopedia Of DNA Elements (ENCODE) regions using rapid amplification of cDNA ends (RACE) sequencing. We analyzed annotated known gene regions, but primarily we focused on novel transcriptionally active regions (TARs), which were previously identified by high-density oligonucleotide tiling arrays and on random regions that were not believed to be transcribed. We found RACE sequencing to be very sensitive and were able to detect low levels of transcripts in specific cell types that were not detectable by microarrays. We also observed many instances of sense-antisense transcripts; further analysis suggests that many of the antisense transcripts (but not all) may be artifacts generated from the reverse transcription reaction. Our results show that the majority of the novel TARs analyzed (60%) are connected to other novel TARs or known exons. Of previously unannotated random regions, 17% were shown to produce overlapping transcripts. Furthermore, it is estimated that 9% of the novel transcripts encode proteins. We conclude that RACE sequencing is an efficient, sensitive, and highly accurate method for characterization of the transcriptome of specific cell/tissue types. Using this method, it appears that much of the genome is represented in polyA+ RNA. Moreover, a fraction of the novel RNAs can encode protein and are likely to be functional.
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      dateModified:2008-01-03T00:00:00Z
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         Antisense Transcript
         Tiling Array
         Antisense Transcription
         Encode Region
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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