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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 two CTTT motifs separated by all possible distances till 25 bp, across the five chromosomes of Arabidopsis thaliana.
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f0020: Frequency of two CTTT motifs separated by all possible distances till 25 bp, across the five chromosomes of Arabidopsis thaliana.

Mentions: The frequency of AAAGAAAG without any spacer has a maximum occurrence of 12,738 as shown in Table 1 and Fig. 1 As we increase the spacer length, the frequency of occurrences started decreasing. There was a slight increase in frequency for the spacer length 14–17. Statistical analyses (data not shown) indicated them to be non significant as the deviation was essentially within 10–15%. Similar trend was observed for (CTTTnCTTT) as shown in Table 2 and Fig. 2.


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 two CTTT 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

f0020: Frequency of two CTTT motifs separated by all possible distances till 25 bp, across the five chromosomes of Arabidopsis thaliana.
Mentions: The frequency of AAAGAAAG without any spacer has a maximum occurrence of 12,738 as shown in Table 1 and Fig. 1 As we increase the spacer length, the frequency of occurrences started decreasing. There was a slight increase in frequency for the spacer length 14–17. Statistical analyses (data not shown) indicated them to be non significant as the deviation was essentially within 10–15%. Similar trend was observed for (CTTTnCTTT) as shown in Table 2 and Fig. 2.

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.