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Widespread antisense transcription in Escherichia coli.

Dornenburg JE, Devita AM, Palumbo MJ, Wade JT - MBio (2010)

Bottom Line: The vast majority of annotated transcripts in bacteria are mRNAs.Here we identify ~1,000 antisense transcripts in the model bacterium Escherichia coli.We propose that these transcripts are generated by promiscuous transcription initiation within genes and that many of them regulate expression of the overlapping gene.

View Article: PubMed Central - PubMed

Affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA.

ABSTRACT
The vast majority of annotated transcripts in bacteria are mRNAs. Here we identify ~1,000 antisense transcripts in the model bacterium Escherichia coli. We propose that these transcripts are generated by promiscuous transcription initiation within genes and that many of them regulate expression of the overlapping gene.

No MeSH data available.


Related in: MedlinePlus

(A) Distribution of nucleotides at the transcription start site (+1) and positions upstream for transcripts with published start sites. Equivalent distributions are shown for 1,000 random intragenic sequences (B) and the 1,005 putative aRNAs identified in this work (C).
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f1: (A) Distribution of nucleotides at the transcription start site (+1) and positions upstream for transcripts with published start sites. Equivalent distributions are shown for 1,000 random intragenic sequences (B) and the 1,005 putative aRNAs identified in this work (C).

Mentions: The housekeeping σ factor σ70 binds a bipartite DNA sequence at E. coli promoters during transcription initiation. The downstream recognition site, the −10 hexamer, has the consensus sequence TATAAT and is typically positioned 7 or 8 bp upstream of the transcription start site (21). For the set of 471 published transcription start sites (19), the −10 hexamers match the consensus, on average, 3.28 times out of 6 (−10 match score) (base distribution shown in Fig. 1A). In contrast, 1,000 randomly selected sequences antisense to genes match the consensus only 2.00 times out of 6 (control match score) (base distribution shown in Fig. 1B). This difference is highly significant (Mann-Whitney U test, P of 8.9e−70). Furthermore, 46% of the RNAs with published start sites initiate with “A,” significantly more than expected by chance (P < 1e−22) (Fig. 1A and B). The −10 hexamer sequences for the 1,005 putative aRNAs identified in this work have a −10 match score of 3.27, significantly higher than the control match score (Mann-Whitney U test, P of 8.8e−102) (base distribution shown in Fig. 1C). This holds true even for the 141 aRNA 5′ ends that were sequenced only once (score of 3.12; Mann-Whitney U test, P of 2.8e−21). The −10 match score for the 1,005 aRNAs is not significantly different from that for the set of published start sites (Mann-Whitney U test, P = 0.49). Moreover, 48% of the putative aRNAs initiate with “A,” significantly more than expected by chance (P < 1e−50) (Fig. 1B and C) but not significantly different from the set of published start sites (Fisher’s exact test, P of 0.40) (Fig. 1A and C). Thus, the promoters and transcription start sites of the 1,005 putative aRNAs have DNA sequence properties that are indistinguishable from those of characterized transcripts.


Widespread antisense transcription in Escherichia coli.

Dornenburg JE, Devita AM, Palumbo MJ, Wade JT - MBio (2010)

(A) Distribution of nucleotides at the transcription start site (+1) and positions upstream for transcripts with published start sites. Equivalent distributions are shown for 1,000 random intragenic sequences (B) and the 1,005 putative aRNAs identified in this work (C).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2912661&req=5

f1: (A) Distribution of nucleotides at the transcription start site (+1) and positions upstream for transcripts with published start sites. Equivalent distributions are shown for 1,000 random intragenic sequences (B) and the 1,005 putative aRNAs identified in this work (C).
Mentions: The housekeeping σ factor σ70 binds a bipartite DNA sequence at E. coli promoters during transcription initiation. The downstream recognition site, the −10 hexamer, has the consensus sequence TATAAT and is typically positioned 7 or 8 bp upstream of the transcription start site (21). For the set of 471 published transcription start sites (19), the −10 hexamers match the consensus, on average, 3.28 times out of 6 (−10 match score) (base distribution shown in Fig. 1A). In contrast, 1,000 randomly selected sequences antisense to genes match the consensus only 2.00 times out of 6 (control match score) (base distribution shown in Fig. 1B). This difference is highly significant (Mann-Whitney U test, P of 8.9e−70). Furthermore, 46% of the RNAs with published start sites initiate with “A,” significantly more than expected by chance (P < 1e−22) (Fig. 1A and B). The −10 hexamer sequences for the 1,005 putative aRNAs identified in this work have a −10 match score of 3.27, significantly higher than the control match score (Mann-Whitney U test, P of 8.8e−102) (base distribution shown in Fig. 1C). This holds true even for the 141 aRNA 5′ ends that were sequenced only once (score of 3.12; Mann-Whitney U test, P of 2.8e−21). The −10 match score for the 1,005 aRNAs is not significantly different from that for the set of published start sites (Mann-Whitney U test, P = 0.49). Moreover, 48% of the putative aRNAs initiate with “A,” significantly more than expected by chance (P < 1e−50) (Fig. 1B and C) but not significantly different from the set of published start sites (Fisher’s exact test, P of 0.40) (Fig. 1A and C). Thus, the promoters and transcription start sites of the 1,005 putative aRNAs have DNA sequence properties that are indistinguishable from those of characterized transcripts.

Bottom Line: The vast majority of annotated transcripts in bacteria are mRNAs.Here we identify ~1,000 antisense transcripts in the model bacterium Escherichia coli.We propose that these transcripts are generated by promiscuous transcription initiation within genes and that many of them regulate expression of the overlapping gene.

View Article: PubMed Central - PubMed

Affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA.

ABSTRACT
The vast majority of annotated transcripts in bacteria are mRNAs. Here we identify ~1,000 antisense transcripts in the model bacterium Escherichia coli. We propose that these transcripts are generated by promiscuous transcription initiation within genes and that many of them regulate expression of the overlapping gene.

No MeSH data available.


Related in: MedlinePlus