Limits...
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

Positional distribution (exclusive/single vs joint occurrence) of CRE pairs.(A) The frequencies of occurrence (single and joint) of two CREs (DOFCOREZM and GT1CONSENSUS) with significantly high COR value (1.92) is presented. The positional distribution patterns of the two CREs are very similar (R = 0.95) where they occur together. Moreover, there is a distinct difference in between frequencies of single and joint occurrences of CREs. The joint occurrence frequencies are about 3 times higher than their corresponding single occurrence frequencies, which indicates the tendency of co-occurrence. (B) Positional distribution of DOFCOREZM and GCCCORE exhibit completely different scenario, in which the distribution pattern of single and joint occurrences of each CRE have no difference rather the frequencies of single occurrence are more favored over joint occurrences. As a result, this CRE pair exhibits weak COR value (0.80) and highly dissimilar positional distribution pattern (R = −0.94) of joint occurrences.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4556519&req=5

pone.0137295.g005: Positional distribution (exclusive/single vs joint occurrence) of CRE pairs.(A) The frequencies of occurrence (single and joint) of two CREs (DOFCOREZM and GT1CONSENSUS) with significantly high COR value (1.92) is presented. The positional distribution patterns of the two CREs are very similar (R = 0.95) where they occur together. Moreover, there is a distinct difference in between frequencies of single and joint occurrences of CREs. The joint occurrence frequencies are about 3 times higher than their corresponding single occurrence frequencies, which indicates the tendency of co-occurrence. (B) Positional distribution of DOFCOREZM and GCCCORE exhibit completely different scenario, in which the distribution pattern of single and joint occurrences of each CRE have no difference rather the frequencies of single occurrence are more favored over joint occurrences. As a result, this CRE pair exhibits weak COR value (0.80) and highly dissimilar positional distribution pattern (R = −0.94) of joint occurrences.

Mentions: The positional distribution of CREs at promoter region remained one of the important factors to estimate their complex association [52]. Highly similar distribution patterns between the joint occurrences of CREs (e.g., DOFCOREZM and GT1CONSENSUS; r = 0.95) were associated with their elevated COR values (COR = 1.92) (Fig 5). Consequently, dissimilar joint distribution patterns of pairs of CREs (e.g., DOFCOREZM and GCCCORE; r = −0.94) were associated with low COR values (COR = 0.8). In our study, a pair of CREs (GT1CONSENSUS and GATABOX) simultaneously exhibited strong co-occurrence tendency (COR = 1.51) and highly similar positional distribution pattern (r = 0.94) of their joint occurrences. Earlier, experimental results confirmed a cooperative relationship existing between GT1CONSENSUS and GATABOX [53, 54]. In cellular system, combinatorial control may occur either by the combinatorial logic of CREs [6] or by cooperative interactions of TFs [55]. The COR value and the distribution patterns of joint occurrences of two CREs at the promoter regions are likely being the indicators of both the co-regulatory phenomena.


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

Deb A, Kundu S - PLoS ONE (2015)

Positional distribution (exclusive/single vs joint occurrence) of CRE pairs.(A) The frequencies of occurrence (single and joint) of two CREs (DOFCOREZM and GT1CONSENSUS) with significantly high COR value (1.92) is presented. The positional distribution patterns of the two CREs are very similar (R = 0.95) where they occur together. Moreover, there is a distinct difference in between frequencies of single and joint occurrences of CREs. The joint occurrence frequencies are about 3 times higher than their corresponding single occurrence frequencies, which indicates the tendency of co-occurrence. (B) Positional distribution of DOFCOREZM and GCCCORE exhibit completely different scenario, in which the distribution pattern of single and joint occurrences of each CRE have no difference rather the frequencies of single occurrence are more favored over joint occurrences. As a result, this CRE pair exhibits weak COR value (0.80) and highly dissimilar positional distribution pattern (R = −0.94) of joint occurrences.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0137295.g005: Positional distribution (exclusive/single vs joint occurrence) of CRE pairs.(A) The frequencies of occurrence (single and joint) of two CREs (DOFCOREZM and GT1CONSENSUS) with significantly high COR value (1.92) is presented. The positional distribution patterns of the two CREs are very similar (R = 0.95) where they occur together. Moreover, there is a distinct difference in between frequencies of single and joint occurrences of CREs. The joint occurrence frequencies are about 3 times higher than their corresponding single occurrence frequencies, which indicates the tendency of co-occurrence. (B) Positional distribution of DOFCOREZM and GCCCORE exhibit completely different scenario, in which the distribution pattern of single and joint occurrences of each CRE have no difference rather the frequencies of single occurrence are more favored over joint occurrences. As a result, this CRE pair exhibits weak COR value (0.80) and highly dissimilar positional distribution pattern (R = −0.94) of joint occurrences.
Mentions: The positional distribution of CREs at promoter region remained one of the important factors to estimate their complex association [52]. Highly similar distribution patterns between the joint occurrences of CREs (e.g., DOFCOREZM and GT1CONSENSUS; r = 0.95) were associated with their elevated COR values (COR = 1.92) (Fig 5). Consequently, dissimilar joint distribution patterns of pairs of CREs (e.g., DOFCOREZM and GCCCORE; r = −0.94) were associated with low COR values (COR = 0.8). In our study, a pair of CREs (GT1CONSENSUS and GATABOX) simultaneously exhibited strong co-occurrence tendency (COR = 1.51) and highly similar positional distribution pattern (r = 0.94) of their joint occurrences. Earlier, experimental results confirmed a cooperative relationship existing between GT1CONSENSUS and GATABOX [53, 54]. In cellular system, combinatorial control may occur either by the combinatorial logic of CREs [6] or by cooperative interactions of TFs [55]. The COR value and the distribution patterns of joint occurrences of two CREs at the promoter regions are likely being the indicators of both the co-regulatory phenomena.

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