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Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition.

Deb A, Kundu S - PLoS ONE (2015)

Bottom Line: Our analysis includes a wide spectrum of biologically important results.We couple the network approach with experimental results of plant gene regulation and defense mechanisms and find evidences of auto and cross regulation among TF families, cross-talk among multiple hormone signaling pathways, similarities and dissimilarities in regulatory combinatorics between different tissues, etc.It can be further applied to unravel the tissue and/or condition specific combinatorial gene regulation in other eukaryotic systems with the availability of annotated genomic sequences and suitable experimental data.

View Article: PubMed Central - PubMed

Affiliation: Department of Biophysics Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, West Bengal, India.

ABSTRACT
Combinations of cis-regulatory elements (CREs) present at the promoters facilitate the binding of several transcription factors (TFs), thereby altering the consequent gene expressions. Due to the eminent complexity of the regulatory mechanism, the combinatorics of CRE-mediated transcriptional regulation has been elusive. In this work, we have developed a new methodology that quantifies the co-occurrence tendencies of CREs present in a set of promoter sequences; these co-occurrence scores are filtered in three consecutive steps to test their statistical significance; and the significantly co-occurring CRE pairs are presented as networks. These networks of co-occurring CREs are further transformed to derive higher order of regulatory combinatorics. We have further applied this methodology on the differentially up-regulated gene-sets of rice tissues under fungal (Magnaporthe) infected conditions to demonstrate how it helps to understand the CRE-mediated combinatorial gene regulation. Our analysis includes a wide spectrum of biologically important results. The CRE pairs having a strong tendency to co-occur often exhibit very similar joint distribution patterns at the promoters of rice. We couple the network approach with experimental results of plant gene regulation and defense mechanisms and find evidences of auto and cross regulation among TF families, cross-talk among multiple hormone signaling pathways, similarities and dissimilarities in regulatory combinatorics between different tissues, etc. Our analyses have pointed a highly distributed nature of the combinatorial gene regulation facilitating an efficient alteration in response to fungal attack. All together, our proposed methodology could be an important approach in understanding the combinatorial gene regulation. It can be further applied to unravel the tissue and/or condition specific combinatorial gene regulation in other eukaryotic systems with the availability of annotated genomic sequences and suitable experimental data.

No MeSH data available.


Related in: MedlinePlus

Diagrammatic representation of a pair of CREs (E1, E2) in a set of promoters (prom1, prom2, … prom6).Out of these 6 promoters, 3 contain both the CREs (so, CpromE1E2 = 3), 2 contain the first CRE, E1 exclusive to E2 (CpromE1¬E2 = 2) and the remaining one contains the second CRE, E2 exclusive to E1 (CpromE2¬E1 = 1). Similarly, in the first category of promoters E1 has occurred 13 times and E2 has occurred 11 times (hence, CE1E1E2 = 13 and CE2E1E2 = 11). The number of occurrences of E1 exclusive to E2 is 5 (CE1E1¬E2 = 5) and the number of occurrences of E2 exclusive to E1 is 2 (CE1E2¬E1 = 2). In this case the estimated COR value is 1.77.
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pone.0137295.g002: Diagrammatic representation of a pair of CREs (E1, E2) in a set of promoters (prom1, prom2, … prom6).Out of these 6 promoters, 3 contain both the CREs (so, CpromE1E2 = 3), 2 contain the first CRE, E1 exclusive to E2 (CpromE1¬E2 = 2) and the remaining one contains the second CRE, E2 exclusive to E1 (CpromE2¬E1 = 1). Similarly, in the first category of promoters E1 has occurred 13 times and E2 has occurred 11 times (hence, CE1E1E2 = 13 and CE2E1E2 = 11). The number of occurrences of E1 exclusive to E2 is 5 (CE1E1¬E2 = 5) and the number of occurrences of E2 exclusive to E1 is 2 (CE1E2¬E1 = 2). In this case the estimated COR value is 1.77.

Mentions: The numerator of the above equation (Eq 1) represents the frequency of joint occurrence of a CRE pair (E1 and E2) and the denominator represents the frequencies of exclusive occurrences of these two CREs. Therefore, COR value > 1 indicates higher tendency of co-occurrence of two CREs, whereas, COR value < 1 means there is a poor co-occurrence tendency. We did not count the occurrences at overlapping sites of the two CREs to restrict the co-occurrence bias emerging from the overlap (i.e CE1E1E2 and CE2E1E2 were not incremented when their occurrences found at overlapping sites) [16]. We present Fig 2 as an example of the COR value calculation. For further details see S1 Text.


Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition.

Deb A, Kundu S - PLoS ONE (2015)

Diagrammatic representation of a pair of CREs (E1, E2) in a set of promoters (prom1, prom2, … prom6).Out of these 6 promoters, 3 contain both the CREs (so, CpromE1E2 = 3), 2 contain the first CRE, E1 exclusive to E2 (CpromE1¬E2 = 2) and the remaining one contains the second CRE, E2 exclusive to E1 (CpromE2¬E1 = 1). Similarly, in the first category of promoters E1 has occurred 13 times and E2 has occurred 11 times (hence, CE1E1E2 = 13 and CE2E1E2 = 11). The number of occurrences of E1 exclusive to E2 is 5 (CE1E1¬E2 = 5) and the number of occurrences of E2 exclusive to E1 is 2 (CE1E2¬E1 = 2). In this case the estimated COR value is 1.77.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4556519&req=5

pone.0137295.g002: Diagrammatic representation of a pair of CREs (E1, E2) in a set of promoters (prom1, prom2, … prom6).Out of these 6 promoters, 3 contain both the CREs (so, CpromE1E2 = 3), 2 contain the first CRE, E1 exclusive to E2 (CpromE1¬E2 = 2) and the remaining one contains the second CRE, E2 exclusive to E1 (CpromE2¬E1 = 1). Similarly, in the first category of promoters E1 has occurred 13 times and E2 has occurred 11 times (hence, CE1E1E2 = 13 and CE2E1E2 = 11). The number of occurrences of E1 exclusive to E2 is 5 (CE1E1¬E2 = 5) and the number of occurrences of E2 exclusive to E1 is 2 (CE1E2¬E1 = 2). In this case the estimated COR value is 1.77.
Mentions: The numerator of the above equation (Eq 1) represents the frequency of joint occurrence of a CRE pair (E1 and E2) and the denominator represents the frequencies of exclusive occurrences of these two CREs. Therefore, COR value > 1 indicates higher tendency of co-occurrence of two CREs, whereas, COR value < 1 means there is a poor co-occurrence tendency. We did not count the occurrences at overlapping sites of the two CREs to restrict the co-occurrence bias emerging from the overlap (i.e CE1E1E2 and CE2E1E2 were not incremented when their occurrences found at overlapping sites) [16]. We present Fig 2 as an example of the COR value calculation. For further details see S1 Text.

Bottom Line: Our analysis includes a wide spectrum of biologically important results.We couple the network approach with experimental results of plant gene regulation and defense mechanisms and find evidences of auto and cross regulation among TF families, cross-talk among multiple hormone signaling pathways, similarities and dissimilarities in regulatory combinatorics between different tissues, etc.It can be further applied to unravel the tissue and/or condition specific combinatorial gene regulation in other eukaryotic systems with the availability of annotated genomic sequences and suitable experimental data.

View Article: PubMed Central - PubMed

Affiliation: Department of Biophysics Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, West Bengal, India.

ABSTRACT
Combinations of cis-regulatory elements (CREs) present at the promoters facilitate the binding of several transcription factors (TFs), thereby altering the consequent gene expressions. Due to the eminent complexity of the regulatory mechanism, the combinatorics of CRE-mediated transcriptional regulation has been elusive. In this work, we have developed a new methodology that quantifies the co-occurrence tendencies of CREs present in a set of promoter sequences; these co-occurrence scores are filtered in three consecutive steps to test their statistical significance; and the significantly co-occurring CRE pairs are presented as networks. These networks of co-occurring CREs are further transformed to derive higher order of regulatory combinatorics. We have further applied this methodology on the differentially up-regulated gene-sets of rice tissues under fungal (Magnaporthe) infected conditions to demonstrate how it helps to understand the CRE-mediated combinatorial gene regulation. Our analysis includes a wide spectrum of biologically important results. The CRE pairs having a strong tendency to co-occur often exhibit very similar joint distribution patterns at the promoters of rice. We couple the network approach with experimental results of plant gene regulation and defense mechanisms and find evidences of auto and cross regulation among TF families, cross-talk among multiple hormone signaling pathways, similarities and dissimilarities in regulatory combinatorics between different tissues, etc. Our analyses have pointed a highly distributed nature of the combinatorial gene regulation facilitating an efficient alteration in response to fungal attack. All together, our proposed methodology could be an important approach in understanding the combinatorial gene regulation. It can be further applied to unravel the tissue and/or condition specific combinatorial gene regulation in other eukaryotic systems with the availability of annotated genomic sequences and suitable experimental data.

No MeSH data available.


Related in: MedlinePlus