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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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Subcellular localization of snaR-A. (A) Total RNA isolated from 293T, 293 and HeLa S3 cell nuclear and cytoplasmic extracts was examined for snaR-A by northern blotting (top panel). Extracts were immunoblotted for PARP (middle panel) and α-tubulin (bottom panel). Asterisk denotes a possible snaR-A conformer band. (B) Northern blot of 293 cell and testis total RNA, probed for snaR-A. (C) Co-sedimentation of snaR-A with ribosomes. HeLa cell extract was fractionated in a sucrose gradient and analyzed by northern blotting for snaR-A (top panel) and 5S rRNA (middle panel), and by immunoblotting for NF90 (bottom panel). The percentage of snaR-A in three regions of the gradient was determined by phosphorimager quantitation of the blot. Blot is duplicated from (32) with permission. (D) Extract of HeLa cells incubated with puromycin was analyzed as in C.
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Figure 6: Subcellular localization of snaR-A. (A) Total RNA isolated from 293T, 293 and HeLa S3 cell nuclear and cytoplasmic extracts was examined for snaR-A by northern blotting (top panel). Extracts were immunoblotted for PARP (middle panel) and α-tubulin (bottom panel). Asterisk denotes a possible snaR-A conformer band. (B) Northern blot of 293 cell and testis total RNA, probed for snaR-A. (C) Co-sedimentation of snaR-A with ribosomes. HeLa cell extract was fractionated in a sucrose gradient and analyzed by northern blotting for snaR-A (top panel) and 5S rRNA (middle panel), and by immunoblotting for NF90 (bottom panel). The percentage of snaR-A in three regions of the gradient was determined by phosphorimager quantitation of the blot. Blot is duplicated from (32) with permission. (D) Extract of HeLa cells incubated with puromycin was analyzed as in C.

Mentions: To approach their function, we examined the subcellular distribution of snaR-A. Fractionation of 293, 293T and HeLa cells revealed snaR-A to be predominantly cytoplasmic (Figure 6A, upper panel). Efficient cellular fractionation was confirmed by immunoblotting for the compartment specific proteins PARP and α-tubulin (Figure 6A, middle and lower panels). As reported earlier (32), snaR-A gel mobility is greatly affected by polyacrylamide density: in high percentage denaturing gels it resolves into several bands, with the major band migrating slower than 5S rRNA. Cytoplasmic forms of snaR-A displayed faster migration than the predominant nuclear form (Figure 6A, upper panel), indicating that the RNA is processed or adopts a different structure in the cytoplasm. snaR-A isolated from testis displayed a similar migration pattern to that in 293 cells, suggesting that snaR-A is predominantly cytoplasmic in this tissue (Figure 6B).Figure 6.


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)

Subcellular localization of snaR-A. (A) Total RNA isolated from 293T, 293 and HeLa S3 cell nuclear and cytoplasmic extracts was examined for snaR-A by northern blotting (top panel). Extracts were immunoblotted for PARP (middle panel) and α-tubulin (bottom panel). Asterisk denotes a possible snaR-A conformer band. (B) Northern blot of 293 cell and testis total RNA, probed for snaR-A. (C) Co-sedimentation of snaR-A with ribosomes. HeLa cell extract was fractionated in a sucrose gradient and analyzed by northern blotting for snaR-A (top panel) and 5S rRNA (middle panel), and by immunoblotting for NF90 (bottom panel). The percentage of snaR-A in three regions of the gradient was determined by phosphorimager quantitation of the blot. Blot is duplicated from (32) with permission. (D) Extract of HeLa cells incubated with puromycin was analyzed as in C.
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Related In: Results  -  Collection

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Figure 6: Subcellular localization of snaR-A. (A) Total RNA isolated from 293T, 293 and HeLa S3 cell nuclear and cytoplasmic extracts was examined for snaR-A by northern blotting (top panel). Extracts were immunoblotted for PARP (middle panel) and α-tubulin (bottom panel). Asterisk denotes a possible snaR-A conformer band. (B) Northern blot of 293 cell and testis total RNA, probed for snaR-A. (C) Co-sedimentation of snaR-A with ribosomes. HeLa cell extract was fractionated in a sucrose gradient and analyzed by northern blotting for snaR-A (top panel) and 5S rRNA (middle panel), and by immunoblotting for NF90 (bottom panel). The percentage of snaR-A in three regions of the gradient was determined by phosphorimager quantitation of the blot. Blot is duplicated from (32) with permission. (D) Extract of HeLa cells incubated with puromycin was analyzed as in C.
Mentions: To approach their function, we examined the subcellular distribution of snaR-A. Fractionation of 293, 293T and HeLa cells revealed snaR-A to be predominantly cytoplasmic (Figure 6A, upper panel). Efficient cellular fractionation was confirmed by immunoblotting for the compartment specific proteins PARP and α-tubulin (Figure 6A, middle and lower panels). As reported earlier (32), snaR-A gel mobility is greatly affected by polyacrylamide density: in high percentage denaturing gels it resolves into several bands, with the major band migrating slower than 5S rRNA. Cytoplasmic forms of snaR-A displayed faster migration than the predominant nuclear form (Figure 6A, upper panel), indicating that the RNA is processed or adopts a different structure in the cytoplasm. snaR-A isolated from testis displayed a similar migration pattern to that in 293 cells, suggesting that snaR-A is predominantly cytoplasmic in this tissue (Figure 6B).Figure 6.

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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Related in: MedlinePlus