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Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain.

Ponjavic J, Oliver PL, Lunter G, Ponting CP - PLoS Genet. (2009)

Bottom Line: Of this set, those expressed in the brain are more frequently conserved and are significantly enriched with predicted RNA secondary structures.Furthermore, brain-expressed long ncRNAs are preferentially located adjacent to protein-coding genes that are (1) also expressed in the brain and (2) involved in transcriptional regulation or in nervous system development.We provide the full set of constrained long ncRNAs as an important experimental resource and present, for the first time, substantive and predictive criteria for prioritising long ncRNA and mRNA transcript pairs when investigating their biological functions and contributions to development and disease.

View Article: PubMed Central - PubMed

Affiliation: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.

ABSTRACT
Besides protein-coding mRNAs, eukaryotic transcriptomes include many long non-protein-coding RNAs (ncRNAs) of unknown function that are transcribed away from protein-coding loci. Here, we have identified 659 intergenic long ncRNAs whose genomic sequences individually exhibit evolutionary constraint, a hallmark of functionality. Of this set, those expressed in the brain are more frequently conserved and are significantly enriched with predicted RNA secondary structures. Furthermore, brain-expressed long ncRNAs are preferentially located adjacent to protein-coding genes that are (1) also expressed in the brain and (2) involved in transcriptional regulation or in nervous system development. This led us to the hypothesis that spatiotemporal co-expression of ncRNAs and nearby protein-coding genes represents a general phenomenon, a prediction that was confirmed subsequently by in situ hybridisation in developing and adult mouse brain. We provide the full set of constrained long ncRNAs as an important experimental resource and present, for the first time, substantive and predictive criteria for prioritising long ncRNA and mRNA transcript pairs when investigating their biological functions and contributions to development and disease.

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Developmental neuronal expression patterns of Slitrk1, Vangl2, and Rbms1 overlap with those from ncRNAs transcribed from adjacent genomic sequence.Brightfield images of in situ hybridization from adjacent wild-type sections are shown. (A) Slitrk1 and the ncRNA AK049627 (derived from an E12 spinal cord cDNA library) are expressed throughout mid/late embryonic development, with the specific co-expression in the brain and spinal column. (B) A similar pattern of co-expression in the CNS is observed for Vangl2 and the adjacent ncRNA AK082938 (derived from an E12 spinal cord library). (C) AK149041 (isolated from a P2 sympathetic ganglion library) was expressed with the adjacent Rbms1 gene at low levels in all major regions of the post-natal and adult brain (data not shown), although high levels of co-expression are observed in the developing Purkinje cell layer in the cerebellum from P12 to adulthood; higher magnification of the adult cerebellum shows that expression of both transcripts occurs in individual Purkinje cell bodies. The sense strand probe from the corresponding protein-coding gene is also shown. (A, B, C) Scale bars represent 2 mm in all cases. No expression information regarding any of these ncRNAs is currently available from the Allen Brain Atlas [23]. (D) The genomic landscape for each protein-coding (light blue) and non-coding (red) transcript pair is shown. Experimental evidence for transcription in the form of CAGE tag clusters (TC) (orange) [1],[18] and EST (green) data are also represented (as modified from the FANTOM3 Mouse Genomic Element Viewer (http://fantom32p.gsc.riken.jp/gev-f3/gbrowse/mm5): only unique transcripts and ESTs are shown). The size of a TC reflects the number of CAGE tags that are mapped to this region. A TC and its surrounding genomic sequence together can be considered a core promoter. It is evident that all three ncRNAs have further experimental support from ESTs (including those that are unspliced) and/or CAGE TCs (also listed in Table S4). AK082938 and AK149041 ncRNA transcripts are overlapped by ESTs and CAGE TCs that are derived from brain-associated tissues from adult and developing mice, whereas AK049627 has EST support from brain-associated tissues from developing mice.
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pgen-1000617-g005: Developmental neuronal expression patterns of Slitrk1, Vangl2, and Rbms1 overlap with those from ncRNAs transcribed from adjacent genomic sequence.Brightfield images of in situ hybridization from adjacent wild-type sections are shown. (A) Slitrk1 and the ncRNA AK049627 (derived from an E12 spinal cord cDNA library) are expressed throughout mid/late embryonic development, with the specific co-expression in the brain and spinal column. (B) A similar pattern of co-expression in the CNS is observed for Vangl2 and the adjacent ncRNA AK082938 (derived from an E12 spinal cord library). (C) AK149041 (isolated from a P2 sympathetic ganglion library) was expressed with the adjacent Rbms1 gene at low levels in all major regions of the post-natal and adult brain (data not shown), although high levels of co-expression are observed in the developing Purkinje cell layer in the cerebellum from P12 to adulthood; higher magnification of the adult cerebellum shows that expression of both transcripts occurs in individual Purkinje cell bodies. The sense strand probe from the corresponding protein-coding gene is also shown. (A, B, C) Scale bars represent 2 mm in all cases. No expression information regarding any of these ncRNAs is currently available from the Allen Brain Atlas [23]. (D) The genomic landscape for each protein-coding (light blue) and non-coding (red) transcript pair is shown. Experimental evidence for transcription in the form of CAGE tag clusters (TC) (orange) [1],[18] and EST (green) data are also represented (as modified from the FANTOM3 Mouse Genomic Element Viewer (http://fantom32p.gsc.riken.jp/gev-f3/gbrowse/mm5): only unique transcripts and ESTs are shown). The size of a TC reflects the number of CAGE tags that are mapped to this region. A TC and its surrounding genomic sequence together can be considered a core promoter. It is evident that all three ncRNAs have further experimental support from ESTs (including those that are unspliced) and/or CAGE TCs (also listed in Table S4). AK082938 and AK149041 ncRNA transcripts are overlapped by ESTs and CAGE TCs that are derived from brain-associated tissues from adult and developing mice, whereas AK049627 has EST support from brain-associated tissues from developing mice.

Mentions: Constrained long ncRNA loci thus exhibit preferences to be transcribed on the same strand as adjacent protein-coding genes that are expressed in similar tissues and that often function as transcription regulators. To test this model experimentally by in situ hybridisation, we selected 6 pairs of ncRNA and mRNA, transcribed from adjacent genomic loci, whose ncRNA transcripts were identified originally from embryonic or neonatal mouse brain libraries. These pairs were chosen essentially at random, except that they were required to be transcribed in the same orientation in order to test experimentally for read-through transcripts between coding and non-coding loci (see below). Experimental evidence for independent promoters for individual ncRNAs and genes was provided by CAGE tags (Figure 5). Note that because these experiments investigated expression at developmental time-points, relevant data from the Allen Brain Atlas are not available.


Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain.

Ponjavic J, Oliver PL, Lunter G, Ponting CP - PLoS Genet. (2009)

Developmental neuronal expression patterns of Slitrk1, Vangl2, and Rbms1 overlap with those from ncRNAs transcribed from adjacent genomic sequence.Brightfield images of in situ hybridization from adjacent wild-type sections are shown. (A) Slitrk1 and the ncRNA AK049627 (derived from an E12 spinal cord cDNA library) are expressed throughout mid/late embryonic development, with the specific co-expression in the brain and spinal column. (B) A similar pattern of co-expression in the CNS is observed for Vangl2 and the adjacent ncRNA AK082938 (derived from an E12 spinal cord library). (C) AK149041 (isolated from a P2 sympathetic ganglion library) was expressed with the adjacent Rbms1 gene at low levels in all major regions of the post-natal and adult brain (data not shown), although high levels of co-expression are observed in the developing Purkinje cell layer in the cerebellum from P12 to adulthood; higher magnification of the adult cerebellum shows that expression of both transcripts occurs in individual Purkinje cell bodies. The sense strand probe from the corresponding protein-coding gene is also shown. (A, B, C) Scale bars represent 2 mm in all cases. No expression information regarding any of these ncRNAs is currently available from the Allen Brain Atlas [23]. (D) The genomic landscape for each protein-coding (light blue) and non-coding (red) transcript pair is shown. Experimental evidence for transcription in the form of CAGE tag clusters (TC) (orange) [1],[18] and EST (green) data are also represented (as modified from the FANTOM3 Mouse Genomic Element Viewer (http://fantom32p.gsc.riken.jp/gev-f3/gbrowse/mm5): only unique transcripts and ESTs are shown). The size of a TC reflects the number of CAGE tags that are mapped to this region. A TC and its surrounding genomic sequence together can be considered a core promoter. It is evident that all three ncRNAs have further experimental support from ESTs (including those that are unspliced) and/or CAGE TCs (also listed in Table S4). AK082938 and AK149041 ncRNA transcripts are overlapped by ESTs and CAGE TCs that are derived from brain-associated tissues from adult and developing mice, whereas AK049627 has EST support from brain-associated tissues from developing mice.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2722021&req=5

pgen-1000617-g005: Developmental neuronal expression patterns of Slitrk1, Vangl2, and Rbms1 overlap with those from ncRNAs transcribed from adjacent genomic sequence.Brightfield images of in situ hybridization from adjacent wild-type sections are shown. (A) Slitrk1 and the ncRNA AK049627 (derived from an E12 spinal cord cDNA library) are expressed throughout mid/late embryonic development, with the specific co-expression in the brain and spinal column. (B) A similar pattern of co-expression in the CNS is observed for Vangl2 and the adjacent ncRNA AK082938 (derived from an E12 spinal cord library). (C) AK149041 (isolated from a P2 sympathetic ganglion library) was expressed with the adjacent Rbms1 gene at low levels in all major regions of the post-natal and adult brain (data not shown), although high levels of co-expression are observed in the developing Purkinje cell layer in the cerebellum from P12 to adulthood; higher magnification of the adult cerebellum shows that expression of both transcripts occurs in individual Purkinje cell bodies. The sense strand probe from the corresponding protein-coding gene is also shown. (A, B, C) Scale bars represent 2 mm in all cases. No expression information regarding any of these ncRNAs is currently available from the Allen Brain Atlas [23]. (D) The genomic landscape for each protein-coding (light blue) and non-coding (red) transcript pair is shown. Experimental evidence for transcription in the form of CAGE tag clusters (TC) (orange) [1],[18] and EST (green) data are also represented (as modified from the FANTOM3 Mouse Genomic Element Viewer (http://fantom32p.gsc.riken.jp/gev-f3/gbrowse/mm5): only unique transcripts and ESTs are shown). The size of a TC reflects the number of CAGE tags that are mapped to this region. A TC and its surrounding genomic sequence together can be considered a core promoter. It is evident that all three ncRNAs have further experimental support from ESTs (including those that are unspliced) and/or CAGE TCs (also listed in Table S4). AK082938 and AK149041 ncRNA transcripts are overlapped by ESTs and CAGE TCs that are derived from brain-associated tissues from adult and developing mice, whereas AK049627 has EST support from brain-associated tissues from developing mice.
Mentions: Constrained long ncRNA loci thus exhibit preferences to be transcribed on the same strand as adjacent protein-coding genes that are expressed in similar tissues and that often function as transcription regulators. To test this model experimentally by in situ hybridisation, we selected 6 pairs of ncRNA and mRNA, transcribed from adjacent genomic loci, whose ncRNA transcripts were identified originally from embryonic or neonatal mouse brain libraries. These pairs were chosen essentially at random, except that they were required to be transcribed in the same orientation in order to test experimentally for read-through transcripts between coding and non-coding loci (see below). Experimental evidence for independent promoters for individual ncRNAs and genes was provided by CAGE tags (Figure 5). Note that because these experiments investigated expression at developmental time-points, relevant data from the Allen Brain Atlas are not available.

Bottom Line: Of this set, those expressed in the brain are more frequently conserved and are significantly enriched with predicted RNA secondary structures.Furthermore, brain-expressed long ncRNAs are preferentially located adjacent to protein-coding genes that are (1) also expressed in the brain and (2) involved in transcriptional regulation or in nervous system development.We provide the full set of constrained long ncRNAs as an important experimental resource and present, for the first time, substantive and predictive criteria for prioritising long ncRNA and mRNA transcript pairs when investigating their biological functions and contributions to development and disease.

View Article: PubMed Central - PubMed

Affiliation: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.

ABSTRACT
Besides protein-coding mRNAs, eukaryotic transcriptomes include many long non-protein-coding RNAs (ncRNAs) of unknown function that are transcribed away from protein-coding loci. Here, we have identified 659 intergenic long ncRNAs whose genomic sequences individually exhibit evolutionary constraint, a hallmark of functionality. Of this set, those expressed in the brain are more frequently conserved and are significantly enriched with predicted RNA secondary structures. Furthermore, brain-expressed long ncRNAs are preferentially located adjacent to protein-coding genes that are (1) also expressed in the brain and (2) involved in transcriptional regulation or in nervous system development. This led us to the hypothesis that spatiotemporal co-expression of ncRNAs and nearby protein-coding genes represents a general phenomenon, a prediction that was confirmed subsequently by in situ hybridisation in developing and adult mouse brain. We provide the full set of constrained long ncRNAs as an important experimental resource and present, for the first time, substantive and predictive criteria for prioritising long ncRNA and mRNA transcript pairs when investigating their biological functions and contributions to development and disease.

Show MeSH
Related in: MedlinePlus