Extensive polycistronism and antisense transcription in the mammalian Hox clusters
The Hox clusters play a crucial role in body patterning during animal development. They encode both Hox transcription factor and micro-RNA genes that are activated in a precise temporal and spatial sequence that follows their chromosomal order. These remarkable collinear properties confer functional...
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| Veröffentlicht in: | PloS one 2007-04, Vol.2 (4), p.e356-e356 |
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| description | The Hox clusters play a crucial role in body patterning during animal development. They encode both Hox transcription factor and micro-RNA genes that are activated in a precise temporal and spatial sequence that follows their chromosomal order. These remarkable collinear properties confer functional unit status for Hox clusters. We developed the TranscriptView platform to establish high resolution transcriptional profiling and report here that transcription in the Hox clusters is far more complex than previously described in both human and mouse. Unannotated transcripts can represent up to 60% of the total transcriptional output of a cluster. In particular, we identified 14 non-coding Transcriptional Units antisense to Hox genes, 10 of which (70%) have a detectable mouse homolog. Most of these Transcriptional Units in both human and mouse present conserved sizeable sequences (>40 bp) overlapping Hox transcripts, suggesting that these Hox antisense transcripts are functional. Hox clusters also display at least seven polycistronic clusters, i.e., different genes being co-transcribed on long isoforms (up to 30 kb). This work provides a reevaluated framework for understanding Hox gene function and dys-function. Such extensive transcriptions may provide a structural explanation for Hox clustering. |
| doi_str_mv | 10.1371/journal.pone.0000356 |
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They encode both Hox transcription factor and micro-RNA genes that are activated in a precise temporal and spatial sequence that follows their chromosomal order. These remarkable collinear properties confer functional unit status for Hox clusters. We developed the TranscriptView platform to establish high resolution transcriptional profiling and report here that transcription in the Hox clusters is far more complex than previously described in both human and mouse. Unannotated transcripts can represent up to 60% of the total transcriptional output of a cluster. In particular, we identified 14 non-coding Transcriptional Units antisense to Hox genes, 10 of which (70%) have a detectable mouse homolog. Most of these Transcriptional Units in both human and mouse present conserved sizeable sequences (>40 bp) overlapping Hox transcripts, suggesting that these Hox antisense transcripts are functional. Hox clusters also display at least seven polycistronic clusters, i.e., different genes being co-transcribed on long isoforms (up to 30 kb). This work provides a reevaluated framework for understanding Hox gene function and dys-function. Such extensive transcriptions may provide a structural explanation for Hox clustering.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0000356</identifier><identifier>PMID: 17406680</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Annotations ; Antisense Elements (Genetics) ; Antisense RNA ; Biology ; Biomarkers ; Chromosomes ; Clustering ; Clusters ; Developmental Biology ; Developmental Biology/Developmental Evolution ; Developmental Biology/Developmental Molecular Mechanisms ; DNA Transposable Elements ; Exons ; Gene expression ; Gene Expression Profiling ; Genes ; Genes, Homeobox ; Genetic aspects ; Genomes ; Genomics ; Homology ; HOX gene ; Isoforms ; Laboratories ; Mammals ; Mathematics ; MicroRNAs ; Multigene Family ; Nucleotide sequence ; Pattern formation ; Proteins ; Ribonucleic acid ; RNA ; Software ; Transcription (Genetics) ; Transcription, Genetic ; Trends</subject><ispartof>PloS one, 2007-04, Vol.2 (4), p.e356-e356</ispartof><rights>COPYRIGHT 2007 Public Library of Science</rights><rights>2007 Mainguy et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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They encode both Hox transcription factor and micro-RNA genes that are activated in a precise temporal and spatial sequence that follows their chromosomal order. These remarkable collinear properties confer functional unit status for Hox clusters. We developed the TranscriptView platform to establish high resolution transcriptional profiling and report here that transcription in the Hox clusters is far more complex than previously described in both human and mouse. Unannotated transcripts can represent up to 60% of the total transcriptional output of a cluster. In particular, we identified 14 non-coding Transcriptional Units antisense to Hox genes, 10 of which (70%) have a detectable mouse homolog. Most of these Transcriptional Units in both human and mouse present conserved sizeable sequences (>40 bp) overlapping Hox transcripts, suggesting that these Hox antisense transcripts are functional. 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Such extensive transcriptions may provide a structural explanation for Hox clustering.</description><subject>Annotations</subject><subject>Antisense Elements (Genetics)</subject><subject>Antisense RNA</subject><subject>Biology</subject><subject>Biomarkers</subject><subject>Chromosomes</subject><subject>Clustering</subject><subject>Clusters</subject><subject>Developmental Biology</subject><subject>Developmental Biology/Developmental Evolution</subject><subject>Developmental Biology/Developmental Molecular Mechanisms</subject><subject>DNA Transposable Elements</subject><subject>Exons</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Genes</subject><subject>Genes, Homeobox</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Homology</subject><subject>HOX 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They encode both Hox transcription factor and micro-RNA genes that are activated in a precise temporal and spatial sequence that follows their chromosomal order. These remarkable collinear properties confer functional unit status for Hox clusters. We developed the TranscriptView platform to establish high resolution transcriptional profiling and report here that transcription in the Hox clusters is far more complex than previously described in both human and mouse. Unannotated transcripts can represent up to 60% of the total transcriptional output of a cluster. In particular, we identified 14 non-coding Transcriptional Units antisense to Hox genes, 10 of which (70%) have a detectable mouse homolog. Most of these Transcriptional Units in both human and mouse present conserved sizeable sequences (>40 bp) overlapping Hox transcripts, suggesting that these Hox antisense transcripts are functional. Hox clusters also display at least seven polycistronic clusters, i.e., different genes being co-transcribed on long isoforms (up to 30 kb). This work provides a reevaluated framework for understanding Hox gene function and dys-function. Such extensive transcriptions may provide a structural explanation for Hox clustering.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>17406680</pmid><doi>10.1371/journal.pone.0000356</doi><tpages>e356</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Annotations Antisense Elements (Genetics) Antisense RNA Biology Biomarkers Chromosomes Clustering Clusters Developmental Biology Developmental Biology/Developmental Evolution Developmental Biology/Developmental Molecular Mechanisms DNA Transposable Elements Exons Gene expression Gene Expression Profiling Genes Genes, Homeobox Genetic aspects Genomes Genomics Homology HOX gene Isoforms Laboratories Mammals Mathematics MicroRNAs Multigene Family Nucleotide sequence Pattern formation Proteins Ribonucleic acid RNA Software Transcription (Genetics) Transcription, Genetic Trends |
| title | Extensive polycistronism and antisense transcription in the mammalian Hox clusters |
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