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Poly A- transcripts expressed in HeLa cells.

Wu Q, Kim YC, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu CI, Wang SM - PLoS ONE (2008)

Bottom Line: Most of the poly A- 3' ESTs do not match known transcript sequences; they have a similar distribution pattern in the genome as the poly A+ and bimorphic 3' ESTs, and their mapped intergenic regions are evolutionarily conserved.Experiments confirmed the authenticity of the detected poly A- transcripts.The abundance of the poly A- transcripts highlights the need for comprehensive identification of these transcripts for decoding the transcriptome, annotating the genome and studying biological relevance of the poly A- transcripts.

View Article: PubMed Central - PubMed

Affiliation: Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America.

ABSTRACT

Background: Transcripts expressed in eukaryotes are classified as poly A+ transcripts or poly A- transcripts based on the presence or absence of the 3' poly A tail. Most transcripts identified so far are poly A+ transcripts, whereas the poly A- transcripts remain largely unknown.

Methodology/principal findings: We developed the TRD (Total RNA Detection) system for transcript identification. The system detects the transcripts through the following steps: 1) depleting the abundant ribosomal and small-size transcripts; 2) synthesizing cDNA without regard to the status of the 3' poly A tail; 3) applying the 454 sequencing technology for massive 3' EST collection from the cDNA; and 4) determining the genome origins of the detected transcripts by mapping the sequences to the human genome reference sequences. Using this system, we characterized the cytoplasmic transcripts from HeLa cells. Of the 13,467 distinct 3' ESTs analyzed, 24% are poly A-, 36% are poly A+, and 40% are bimorphic with poly A+ features but without the 3' poly A tail. Most of the poly A- 3' ESTs do not match known transcript sequences; they have a similar distribution pattern in the genome as the poly A+ and bimorphic 3' ESTs, and their mapped intergenic regions are evolutionarily conserved. Experiments confirmed the authenticity of the detected poly A- transcripts.

Conclusion/significance: Our study provides the first large-scale sequence evidence for the presence of poly A- transcripts in eukaryotes. The abundance of the poly A- transcripts highlights the need for comprehensive identification of these transcripts for decoding the transcriptome, annotating the genome and studying biological relevance of the poly A- transcripts.

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Example of histone 3′ EST distribution.Fifteen 3′ ESTs that map to the full-length histone 1H2AB cDNA sequences (NM_003513) are clustered proximal to the 3′ end of the full-length sequence. See Table 3, Table S3 and Figure S1 for the distribution of other histone 3′ ESTs.
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pone-0002803-g002: Example of histone 3′ EST distribution.Fifteen 3′ ESTs that map to the full-length histone 1H2AB cDNA sequences (NM_003513) are clustered proximal to the 3′ end of the full-length sequence. See Table 3, Table S3 and Figure S1 for the distribution of other histone 3′ ESTs.

Mentions: Histone transcripts are the only known polymerase II-generated poly A- transcripts with sequence information [12], [15], [20]. A total of 315 distinct 3′ ESTs from 46 histone genes was detected in this study. Comparison of the 3′ ends of the detected histone 3′ ESTs to the full-length histone transcript sequences shows that 80% of the 3′ ESTs matched proximal to the 3′ end of their corresponding full-length sequences (Table 3, Figure 2, Figure S1, Table S3). The pattern of the 3′ end distribution of these histone sequences closely resembles that observed in a recent histone study [21]. The high-degree of intact 3′ ends of the detected histone transcripts provides an internal control for the authenticity of the poly A- transcripts detected in this study.


Poly A- transcripts expressed in HeLa cells.

Wu Q, Kim YC, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu CI, Wang SM - PLoS ONE (2008)

Example of histone 3′ EST distribution.Fifteen 3′ ESTs that map to the full-length histone 1H2AB cDNA sequences (NM_003513) are clustered proximal to the 3′ end of the full-length sequence. See Table 3, Table S3 and Figure S1 for the distribution of other histone 3′ ESTs.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2481391&req=5

pone-0002803-g002: Example of histone 3′ EST distribution.Fifteen 3′ ESTs that map to the full-length histone 1H2AB cDNA sequences (NM_003513) are clustered proximal to the 3′ end of the full-length sequence. See Table 3, Table S3 and Figure S1 for the distribution of other histone 3′ ESTs.
Mentions: Histone transcripts are the only known polymerase II-generated poly A- transcripts with sequence information [12], [15], [20]. A total of 315 distinct 3′ ESTs from 46 histone genes was detected in this study. Comparison of the 3′ ends of the detected histone 3′ ESTs to the full-length histone transcript sequences shows that 80% of the 3′ ESTs matched proximal to the 3′ end of their corresponding full-length sequences (Table 3, Figure 2, Figure S1, Table S3). The pattern of the 3′ end distribution of these histone sequences closely resembles that observed in a recent histone study [21]. The high-degree of intact 3′ ends of the detected histone transcripts provides an internal control for the authenticity of the poly A- transcripts detected in this study.

Bottom Line: Most of the poly A- 3' ESTs do not match known transcript sequences; they have a similar distribution pattern in the genome as the poly A+ and bimorphic 3' ESTs, and their mapped intergenic regions are evolutionarily conserved.Experiments confirmed the authenticity of the detected poly A- transcripts.The abundance of the poly A- transcripts highlights the need for comprehensive identification of these transcripts for decoding the transcriptome, annotating the genome and studying biological relevance of the poly A- transcripts.

View Article: PubMed Central - PubMed

Affiliation: Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America.

ABSTRACT

Background: Transcripts expressed in eukaryotes are classified as poly A+ transcripts or poly A- transcripts based on the presence or absence of the 3' poly A tail. Most transcripts identified so far are poly A+ transcripts, whereas the poly A- transcripts remain largely unknown.

Methodology/principal findings: We developed the TRD (Total RNA Detection) system for transcript identification. The system detects the transcripts through the following steps: 1) depleting the abundant ribosomal and small-size transcripts; 2) synthesizing cDNA without regard to the status of the 3' poly A tail; 3) applying the 454 sequencing technology for massive 3' EST collection from the cDNA; and 4) determining the genome origins of the detected transcripts by mapping the sequences to the human genome reference sequences. Using this system, we characterized the cytoplasmic transcripts from HeLa cells. Of the 13,467 distinct 3' ESTs analyzed, 24% are poly A-, 36% are poly A+, and 40% are bimorphic with poly A+ features but without the 3' poly A tail. Most of the poly A- 3' ESTs do not match known transcript sequences; they have a similar distribution pattern in the genome as the poly A+ and bimorphic 3' ESTs, and their mapped intergenic regions are evolutionarily conserved. Experiments confirmed the authenticity of the detected poly A- transcripts.

Conclusion/significance: Our study provides the first large-scale sequence evidence for the presence of poly A- transcripts in eukaryotes. The abundance of the poly A- transcripts highlights the need for comprehensive identification of these transcripts for decoding the transcriptome, annotating the genome and studying biological relevance of the poly A- transcripts.

Show MeSH
Related in: MedlinePlus