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Genome-wide annotation of small RNAs expressed in HeLa and HepG2 cells

ABSTRACT: We report an applicaton of small RNA sequencing using high throughput next generation sequencing to identify the small RNA content of cell lines. By sequencing over 30 million reads we could identify a new class of small RNAs previousy observed with tiling arrays and mapping to promoter regions of coding genes. We also identified a large number of small RNAs corresponding to internal exons of coding genes. By using different enzymatic treatments and immunoprecipitation experiments, we have determined that both the promoter associated small RNAs as well as ones within the body of the genes bear 5' cap structures.

ORGANISM(S): Homo sapiens

PROVIDER: GSE14362 | GEO | 2009/01/26

SECONDARY ACCESSION(S): PRJNA111397

REPOSITORIES: GEO

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Genome-wide annotation of small RNAs expressed in HeLa and HepG2 cells

Project description:We report an applicaton of small RNA sequencing using high throughput next generation sequencing to identify the small RNA content of cell lines. By sequencing over 30 million reads we could identify a new class of small RNAs previousy observed with tiling arrays and mapping to promoter regions of coding genes. We also identified a large number of small RNAs corresponding to internal exons of coding genes. By using different enzymatic treatments and immunoprecipitation experiments, we have determined that both the promoter associated small RNAs as well as ones within the body of the genes bear 5' cap structures. Examination of the expression of small RNAs (<200nt).

2009-01-26 | E-GEOD-14362 | biostudies-arrayexpress

Influenza A virus preferentially snatches non-coding RNA caps

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The 3' exonuclease TOE1 selectively processes snRNAs through recognition of Sm complex assembly and 5’ cap trimethylation [global seq]

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The 3' exonuclease TOE1 selectively processes snRNAs through recognition of Sm complex assembly and 5’ cap trimethylation [gene specific seq]

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Hypermethylated capped selenoprotein mRNAs in mammals

Project description:Mammalian mRNAs are generated by complex and coordinated biogenesis pathways and acquire 5'-end m7G caps that play fundamental roles in processing and translation. Here we show that several selenoprotein mRNAs are not recognized efficiently by translation initiation factor eIF4E because they bear a hypermethylated cap. This cap modification is acquired via a 5M-bM-^@M-^Yend maturation pathway similar to that of the small nucle(ol)ar RNAs (sn- and snoRNAs). Our findings also establish that the trimethylguanosine synthase 1 (Tgs1) interacts with selenoprotein mRNAs for cap hypermethylation and that assembly chaperones and core proteins devoted to sn- and snoRNP maturation contribute to recruiting Tgs1 to selenoprotein mRNPs. We further demonstrate that the hypermethylated-capped selenoprotein mRNAs localize to the cytoplasm, are associated with polysomes and thus translated. Moreover, we found that the activity of Tgs1, but not of eIF4E, is required for the synthesis of the GPx1 selenoprotein in vivo. In total 7 samples; 3 control IP (HeLa 1,2 & 9), 2 TGS1-SF IP(C2 & C2b) and 2 TGS1-LF IP(C7 & C7b)

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