species, highlighting their fundamental role and placing them at the top of the
regulatory hierarchy. Conversely, since the discovery of miRNAs, the progress on
the roles of miRNAs as critical regulators of transcriptome has gained momentum
defining various abiotic responses. This is in part owing to the fact that most of the
targets of miRNAs are TFs themselves. Thus, many TF and miRNA regulatory
modules have emerged as key nodes in the plant abiotic stress networks that can be
categorized into two genetic sub-networks: one where miRNA controls the posttranscriptional regulation of its target TF mRNAs directly by transcript cleavage or
by translational repression and second where the TF drives the miRNA gene
transcription. Several studies form the basis for the first sub-network through
utilizing the NGS and degradome technologies. However, only a few have been
functionally validated in-planta for stress tolerance. Some such examples where
miRNAs regulate various TF families include miR159:MYB, miR169:NF-YA,
miR396:WRKY, miR164:NAC, miR395:GRF, and miR156:SPL. These modules
have been validated by different wet lab experiments for their specific roles in
drought tolerance, heat tolerance, nutrient homeostasis, salinity, and cold tolerance
by analyzing transgenic plants with miRNA overexpression, target overexpression,
resistant targets that bypass miRNA cleavage and miRNA target-mimics that sponge
up the mature miRNA. Several of these miRNA:TF modules exhibit similar expression in different stress conditions which suggest that they are part of a canonical
response that is required to counter stress. However, there are some modules that
show contrasting regulation in response to different stress regimens suggesting a
possible functional diversification of mature miRNAs to target novel forms or these
miRNA genes have acquired new regulatory regions in their promoters that respond
to different stresses by recruiting stress-specific TFs. In nature, plants always
encounter a combination of different stress. Therefore, it is important to study the
miRNA-TF sub-networks in combination of multiple stress conditions to not only
understand their mechanism of action but also to be able to identify modules that
would give broad-spectrum tolerance.
One hurdle that needs attention is how specific are these miRNA:TF modules?
This question stems from the fact that a single miRNA can functionally regulate
several targets at a time depending upon tissue and stress regimens. This requires
specific and sophisticated strategies to modulate miRNA and target levels in-planta
followed by careful phenotyping and assessing stress response. It is also the need of
the hour to revisit, compile, and reanalyze the previously published large amount of
next-generation sequence data on different tissues and molecular levels and uncover
novel aspects about not just for the TF:miRNA but also about plant stress regulatory
networks. Still, very few reports are available in literature on the TFs as upstream
regulator of miRNA transcription. Thus, continued inputs are required for the
experimental mapping of transcriptional networks using various methods like chromatin immunoprecipitation (ChIP) and yeast one hybrid (Y1H) assays. Regulatory
interactions of TFs and miRNAs determine the expression of specific genes in a
spatio-temporal manner that in turn governs the implementation of particular cellular
or developmental processes. Current research focuses majorly on the networks
operating at tissue or organ level, however to get detailed and significant insights
8 Orchestration of MicroRNAs and Transcription Factors in the Regulation of Plant. . .
267
regulatory hierarchy. Conversely, since the discovery of miRNAs, the progress on
the roles of miRNAs as critical regulators of transcriptome has gained momentum
defining various abiotic responses. This is in part owing to the fact that most of the
targets of miRNAs are TFs themselves. Thus, many TF and miRNA regulatory
modules have emerged as key nodes in the plant abiotic stress networks that can be
categorized into two genetic sub-networks: one where miRNA controls the posttranscriptional regulation of its target TF mRNAs directly by transcript cleavage or
by translational repression and second where the TF drives the miRNA gene
transcription. Several studies form the basis for the first sub-network through
utilizing the NGS and degradome technologies. However, only a few have been
functionally validated in-planta for stress tolerance. Some such examples where
miRNAs regulate various TF families include miR159:MYB, miR169:NF-YA,
miR396:WRKY, miR164:NAC, miR395:GRF, and miR156:SPL. These modules
have been validated by different wet lab experiments for their specific roles in
drought tolerance, heat tolerance, nutrient homeostasis, salinity, and cold tolerance
by analyzing transgenic plants with miRNA overexpression, target overexpression,
resistant targets that bypass miRNA cleavage and miRNA target-mimics that sponge
up the mature miRNA. Several of these miRNA:TF modules exhibit similar expression in different stress conditions which suggest that they are part of a canonical
response that is required to counter stress. However, there are some modules that
show contrasting regulation in response to different stress regimens suggesting a
possible functional diversification of mature miRNAs to target novel forms or these
miRNA genes have acquired new regulatory regions in their promoters that respond
to different stresses by recruiting stress-specific TFs. In nature, plants always
encounter a combination of different stress. Therefore, it is important to study the
miRNA-TF sub-networks in combination of multiple stress conditions to not only
understand their mechanism of action but also to be able to identify modules that
would give broad-spectrum tolerance.
One hurdle that needs attention is how specific are these miRNA:TF modules?
This question stems from the fact that a single miRNA can functionally regulate
several targets at a time depending upon tissue and stress regimens. This requires
specific and sophisticated strategies to modulate miRNA and target levels in-planta
followed by careful phenotyping and assessing stress response. It is also the need of
the hour to revisit, compile, and reanalyze the previously published large amount of
next-generation sequence data on different tissues and molecular levels and uncover
novel aspects about not just for the TF:miRNA but also about plant stress regulatory
networks. Still, very few reports are available in literature on the TFs as upstream
regulator of miRNA transcription. Thus, continued inputs are required for the
experimental mapping of transcriptional networks using various methods like chromatin immunoprecipitation (ChIP) and yeast one hybrid (Y1H) assays. Regulatory
interactions of TFs and miRNAs determine the expression of specific genes in a
spatio-temporal manner that in turn governs the implementation of particular cellular
or developmental processes. Current research focuses majorly on the networks
operating at tissue or organ level, however to get detailed and significant insights
8 Orchestration of MicroRNAs and Transcription Factors in the Regulation of Plant. . .
267