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The evolution and expression of the snaR family of small non-coding RNAs.

Parrott AM, Tsai M, Batchu P, Ryan K, Ozer HL, Tian B, Mathews MB - Nucleic Acids Res. (2010)

Bottom Line: We recently identified the snaR family of small non-coding RNAs that associate in vivo with the nuclear factor 90 (NF90/ILF3) protein.The major human species, snaR-A, is an RNA polymerase III transcript with restricted tissue distribution and orthologs in chimpanzee but not rhesus macaque or mouse.We infer that snaR evolved from the left monomer of the primate-specific Alu SINE family via ASR and CAS in conjunction with major primate speciation events, and suggest that snaRs participate in tissue- and species-specific regulation of cell growth and translation.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, New Jersey Medical School, UMDNJ, Newark, New Jersey, USA.

ABSTRACT
We recently identified the snaR family of small non-coding RNAs that associate in vivo with the nuclear factor 90 (NF90/ILF3) protein. The major human species, snaR-A, is an RNA polymerase III transcript with restricted tissue distribution and orthologs in chimpanzee but not rhesus macaque or mouse. We report their expression in human tissues and their evolution in primates. snaR genes are exclusively in African Great Apes and some are unique to humans. Two novel families of snaR-related genetic elements were found in primates: CAS (catarrhine ancestor of snaR), limited to Old World Monkeys and apes; and ASR (Alu/snaR-related), present in all monkeys and apes. ASR and CAS appear to have spread by retrotransposition, whereas most snaR genes have spread by segmental duplication. snaR-A and snaR-G2 are differentially expressed in discrete regions of the human brain and other tissues, notably including testis. snaR-A is up-regulated in transformed and immortalized human cells, and is stably bound to ribosomes in HeLa cells. We infer that snaR evolved from the left monomer of the primate-specific Alu SINE family via ASR and CAS in conjunction with major primate speciation events, and suggest that snaRs participate in tissue- and species-specific regulation of cell growth and translation.

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Species distribution of snaR genes. (A) Ethidium-stained agarose gel of bonobo (Pp), chimpanzee (Pt), gorilla (Gg), human 293 cell (Hs) and orangutan (Pa) genomic DNA after PCR amplification with primers specific for snaR flanking sequence. Note that the orangutan PCR fragment has slower migration because it is longer, and formed a weaker band because of a mismatch between the forward primer and the genomic sequence. (B) Clustal-W alignment of selected PCR clones: human (H3iii), gorilla (G1iii), bonobo (B1), chimpanzee (C1) and orangutan (O5iii) (Supplementary Data S1). snaR loci are bracketed; nucleotide heterogeneity is highlighted in gray and unique bases in black. Asterisks denote identity in all 5 Great Ape species; dots denote identity in the African Great Apes (orangutan excepted). Putative Pol III B-box is boxed. PCR priming sites are denoted by arrows.
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Figure 2: Species distribution of snaR genes. (A) Ethidium-stained agarose gel of bonobo (Pp), chimpanzee (Pt), gorilla (Gg), human 293 cell (Hs) and orangutan (Pa) genomic DNA after PCR amplification with primers specific for snaR flanking sequence. Note that the orangutan PCR fragment has slower migration because it is longer, and formed a weaker band because of a mismatch between the forward primer and the genomic sequence. (B) Clustal-W alignment of selected PCR clones: human (H3iii), gorilla (G1iii), bonobo (B1), chimpanzee (C1) and orangutan (O5iii) (Supplementary Data S1). snaR loci are bracketed; nucleotide heterogeneity is highlighted in gray and unique bases in black. Asterisks denote identity in all 5 Great Ape species; dots denote identity in the African Great Apes (orangutan excepted). Putative Pol III B-box is boxed. PCR priming sites are denoted by arrows.

Mentions: The snaR genes were identified in two members of the Hominini tribe (human and chimpanzee) but not in rhesus macaque or mouse (8). To establish the distribution of these genes more broadly within the Great Ape family (Hominidae), we conducted PCR analysis on genomic DNA of human, bonobo, common chimpanzee, Western gorilla and Sumatran orangutan, using primers against flanking sequences that are highly conserved for most human and chimpanzee snaR genes (8). PCR products of the expected size (∼320 bp in humans) were generated from the genomes of all five hominids (Figure 2A). Clones were sequenced (Supplementary Data S1) and classified into the various snaR subsets (Table 1).Figure 2.


The evolution and expression of the snaR family of small non-coding RNAs.

Parrott AM, Tsai M, Batchu P, Ryan K, Ozer HL, Tian B, Mathews MB - Nucleic Acids Res. (2010)

Species distribution of snaR genes. (A) Ethidium-stained agarose gel of bonobo (Pp), chimpanzee (Pt), gorilla (Gg), human 293 cell (Hs) and orangutan (Pa) genomic DNA after PCR amplification with primers specific for snaR flanking sequence. Note that the orangutan PCR fragment has slower migration because it is longer, and formed a weaker band because of a mismatch between the forward primer and the genomic sequence. (B) Clustal-W alignment of selected PCR clones: human (H3iii), gorilla (G1iii), bonobo (B1), chimpanzee (C1) and orangutan (O5iii) (Supplementary Data S1). snaR loci are bracketed; nucleotide heterogeneity is highlighted in gray and unique bases in black. Asterisks denote identity in all 5 Great Ape species; dots denote identity in the African Great Apes (orangutan excepted). Putative Pol III B-box is boxed. PCR priming sites are denoted by arrows.
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Figure 2: Species distribution of snaR genes. (A) Ethidium-stained agarose gel of bonobo (Pp), chimpanzee (Pt), gorilla (Gg), human 293 cell (Hs) and orangutan (Pa) genomic DNA after PCR amplification with primers specific for snaR flanking sequence. Note that the orangutan PCR fragment has slower migration because it is longer, and formed a weaker band because of a mismatch between the forward primer and the genomic sequence. (B) Clustal-W alignment of selected PCR clones: human (H3iii), gorilla (G1iii), bonobo (B1), chimpanzee (C1) and orangutan (O5iii) (Supplementary Data S1). snaR loci are bracketed; nucleotide heterogeneity is highlighted in gray and unique bases in black. Asterisks denote identity in all 5 Great Ape species; dots denote identity in the African Great Apes (orangutan excepted). Putative Pol III B-box is boxed. PCR priming sites are denoted by arrows.
Mentions: The snaR genes were identified in two members of the Hominini tribe (human and chimpanzee) but not in rhesus macaque or mouse (8). To establish the distribution of these genes more broadly within the Great Ape family (Hominidae), we conducted PCR analysis on genomic DNA of human, bonobo, common chimpanzee, Western gorilla and Sumatran orangutan, using primers against flanking sequences that are highly conserved for most human and chimpanzee snaR genes (8). PCR products of the expected size (∼320 bp in humans) were generated from the genomes of all five hominids (Figure 2A). Clones were sequenced (Supplementary Data S1) and classified into the various snaR subsets (Table 1).Figure 2.

Bottom Line: We recently identified the snaR family of small non-coding RNAs that associate in vivo with the nuclear factor 90 (NF90/ILF3) protein.The major human species, snaR-A, is an RNA polymerase III transcript with restricted tissue distribution and orthologs in chimpanzee but not rhesus macaque or mouse.We infer that snaR evolved from the left monomer of the primate-specific Alu SINE family via ASR and CAS in conjunction with major primate speciation events, and suggest that snaRs participate in tissue- and species-specific regulation of cell growth and translation.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, New Jersey Medical School, UMDNJ, Newark, New Jersey, USA.

ABSTRACT
We recently identified the snaR family of small non-coding RNAs that associate in vivo with the nuclear factor 90 (NF90/ILF3) protein. The major human species, snaR-A, is an RNA polymerase III transcript with restricted tissue distribution and orthologs in chimpanzee but not rhesus macaque or mouse. We report their expression in human tissues and their evolution in primates. snaR genes are exclusively in African Great Apes and some are unique to humans. Two novel families of snaR-related genetic elements were found in primates: CAS (catarrhine ancestor of snaR), limited to Old World Monkeys and apes; and ASR (Alu/snaR-related), present in all monkeys and apes. ASR and CAS appear to have spread by retrotransposition, whereas most snaR genes have spread by segmental duplication. snaR-A and snaR-G2 are differentially expressed in discrete regions of the human brain and other tissues, notably including testis. snaR-A is up-regulated in transformed and immortalized human cells, and is stably bound to ribosomes in HeLa cells. We infer that snaR evolved from the left monomer of the primate-specific Alu SINE family via ASR and CAS in conjunction with major primate speciation events, and suggest that snaRs participate in tissue- and species-specific regulation of cell growth and translation.

Show MeSH
Related in: MedlinePlus