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Genome wide analysis of Arabidopsis thaliana reveals high frequency of AAAGN7CTTT motif.

Mehrotra R, Jain V, Shekhar C, Mehrotra S - Meta Gene (2014)

Bottom Line: These motifs have been over represented in many promoters.Similar analyses was done with AAAG-CTTT motifs.We report unusual high frequency of AAAGN7CTTT in Arabidopsis thaliana genome.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan 333031, India ; Okinawa Institute of Science and Technology, Onna son, Okinawa, Japan.

ABSTRACT
Sequence specific elements in DNA regulate transcription by recruiting transcription factors. The Dof proteins are a large family of transcription factors that share a single highly conserved zinc finger. The core to which Dof proteins bind has a consensus AAAG or ACTTTA sequence. These motifs have been over represented in many promoters. We performed a genome wide analysis of AAAG repeat elements increasing the spacer length from 0 to 25. Similar analyses was done with AAAG-CTTT motifs. We report unusual high frequency of AAAGN7CTTT in Arabidopsis thaliana genome. We also conclude that there is a preference for A/G nucleotides in spacer sequence between two AAAG repeats.

No MeSH data available.


Frequency of CTTT and AAAG motifs separated by all possible distances till 25 bp, across the five chromosomes of Arabidopsis thaliana.
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f0025: Frequency of CTTT and AAAG motifs separated by all possible distances till 25 bp, across the five chromosomes of Arabidopsis thaliana.

Mentions: A very interesting observation was made when we looked for combination of AAAG and CTTT sequences. An unexpected high frequency was observed for AAAGn7CTTT. The frequency of occurrence was observed as 14,977 which is more than two times the predecessor whose frequency is 7177 as shown in Table 3 and Fig. 3. However, when we change the orientation to CTTTn7 AAAG this tendency was not observed as shown in Table 4. The other implication of this is that transcriptional factor binding is direction specific. Not all AAAG motifs in plant promoters are targets of the Dof domain proteins. However, since an AAAG and a CTTT motif separated by a distance of 7 bp is present in an exceptionally high frequency, we think it is highly likely that this sequence combination may have a functional significance yet to be discovered.


Genome wide analysis of Arabidopsis thaliana reveals high frequency of AAAGN7CTTT motif.

Mehrotra R, Jain V, Shekhar C, Mehrotra S - Meta Gene (2014)

Frequency of CTTT and AAAG motifs separated by all possible distances till 25 bp, across the five chromosomes of Arabidopsis thaliana.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4288566&req=5

f0025: Frequency of CTTT and AAAG motifs separated by all possible distances till 25 bp, across the five chromosomes of Arabidopsis thaliana.
Mentions: A very interesting observation was made when we looked for combination of AAAG and CTTT sequences. An unexpected high frequency was observed for AAAGn7CTTT. The frequency of occurrence was observed as 14,977 which is more than two times the predecessor whose frequency is 7177 as shown in Table 3 and Fig. 3. However, when we change the orientation to CTTTn7 AAAG this tendency was not observed as shown in Table 4. The other implication of this is that transcriptional factor binding is direction specific. Not all AAAG motifs in plant promoters are targets of the Dof domain proteins. However, since an AAAG and a CTTT motif separated by a distance of 7 bp is present in an exceptionally high frequency, we think it is highly likely that this sequence combination may have a functional significance yet to be discovered.

Bottom Line: These motifs have been over represented in many promoters.Similar analyses was done with AAAG-CTTT motifs.We report unusual high frequency of AAAGN7CTTT in Arabidopsis thaliana genome.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan 333031, India ; Okinawa Institute of Science and Technology, Onna son, Okinawa, Japan.

ABSTRACT
Sequence specific elements in DNA regulate transcription by recruiting transcription factors. The Dof proteins are a large family of transcription factors that share a single highly conserved zinc finger. The core to which Dof proteins bind has a consensus AAAG or ACTTTA sequence. These motifs have been over represented in many promoters. We performed a genome wide analysis of AAAG repeat elements increasing the spacer length from 0 to 25. Similar analyses was done with AAAG-CTTT motifs. We report unusual high frequency of AAAGN7CTTT in Arabidopsis thaliana genome. We also conclude that there is a preference for A/G nucleotides in spacer sequence between two AAAG repeats.

No MeSH data available.