CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana

Lavrekha, Viktoriya V.; Levitsky, Victor G.; Tsukanov, Anton V.; Bogomolov, Anton; Grigorovich, D. A.; Omelyanchuk, N. A.; Ubogoeva, Elena V.; Zemlyanskaya, Elena V.; Миронова, В. В.

doi:10.3389/fpls.2022.942710

Cited by 4 publications

(6 citation statements)

References 45 publications

(86 reference statements)

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“…Two highly asymmetric homotypic CEs in the promoter of IAA5 gene support effective regulation of the IAA5 gene under the action of ARF5. Further, the same trend to the asymmetry within homotypic CEs we confirmed for the entire dataset of DAP-seq peaks for ARF5 TF [4,39]. Whereas the specific pattern of spacer length distribution in homotypic CEs for ARF5 (Figure 3A) was noted previously [4,37], the asymmetry of motifs conservation within these homotypic CEs has not been identified yet (Figure 3B).…”

Section: Discussionsupporting

confidence: 84%

“…To derive a proper ARF5 motif we took in analysis the entire dataset of ARF5 peaks from DAPseq (see Section 4.1, [4,39]), and applied de novo motif search [40]. Figure 2A depicts the logo of this motif for the direct and reverse strands.…”

Section: Definition and Examples Of Asymmetry In The Conservation Of ...mentioning

confidence: 99%

“…In this section, we check the abundance of homotypic asymmrtric CEs in the entire DAP-seq dataset of ARF5 peaks [4,39]. We have updated the source code of MCOT [26] and its web interface WebMCOT [32] to test asymmetry within homotypic CEs as described above (Figure 1C).…”

Section: Analysis Of a Whole Dataset: Example Of Significant Asymmetr...mentioning

confidence: 99%

“…ChIP-seq datasets were processed in GTRD by the MACS2 peak caller [58]. Raw DAP-seq data were also processed with this peak caller [39]. We used full-sized peaks for all benchmark collections.…”

Section: Benchmark Collections Of Chip-seq and Dap-seq Data Their Pre...mentioning

confidence: 99%

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Asymmetry of Motifs Conservation within Homotypic Composite Elements Differentiates DNA-Binding Domains of Target Transcription Factors in ChIP-Seq Data

Levitsky,

Raditsa,

Tsukanov

et al. 2023

Preprint

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(1) Background: Transcription factors (TFs) are main regulators of eukaryotic gene expression. The cooperative binding of at least two TFs to genomic DNA is the widespread mechanism of transcription regulation. Massive analysis of co-occurrence of overrepresented pairs of motifs (composite elements, CEs) for different target TFs studied in ChIP-seq experiments can clarify the mechanisms of TF cooperation. (2) Methods: We focused on homotypic CEs representing the same motif models and considered only CEs with spacers. We improved the capability of the Motifs Co-Occurrence Tool (MCOT) to predict asymmetric homotypic CEs in which one of par-ticipating motifs has higher conservation than the other. We categorized the target TFs from the data of M. musculus ChIP-seq and A. thaliana ChIP-seq/DAP-seq according to the structure of DNA-binding domains (DBDs) into classes. (3) Results: For all TF classes the predominance of asymmetric CEs over both symmetric and those with no enrichment in both directions was re-vealed. Target TFs from classes Basic helix-loop-helix factors (bHLH) and Basic leucine zipper factors (bZIP) showed the highest fractions of datasets with asymmetric CEs. We showed that pioneer TFs, despite their DBD types, have a higher significance of asymmetry within homotyp-ic CEs compared to other TFs. (4) Conclusion: Asymmetry within homotypic CEs is a promising new feature decrypting the mechanisms of gene transcription regulation.

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Section: Discussionsupporting

confidence: 84%

Section: Definition and Examples Of Asymmetry In The Conservation Of ...mentioning

confidence: 99%

Section: Analysis Of a Whole Dataset: Example Of Significant Asymmetr...mentioning

confidence: 99%

Section: Benchmark Collections Of Chip-seq and Dap-seq Data Their Pre...mentioning

confidence: 99%

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Asymmetry of Motifs Conservation within Homotypic Composite Elements Differentiates DNA-Binding Domains of Target Transcription Factors in ChIP-Seq Data

Levitsky,

Raditsa,

Tsukanov

et al. 2023

Preprint

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“…The cis-element enrichment analysis was performed using the CisCross web service (https://plamorph.sysbio.ru/ciscross/). The analysis aimed to predict upstream regulators, and the following parameters were employed: promoter length, 1500 bp; background, ARAPORT11; DAP-seq collection, Plant Cistrome, CisCross MACS2; multiple comparisons, Benjamini-Hochberg; adjusted p-value threshold, 0.001 [19,20].…”

Section: Cis-regulatory Element Enrichment On Promoters Of Prgsmentioning

confidence: 99%

Modulation of early gene expression responses to water deprivation stress by the E3 ubiquitin ligase ATL80: implications for retrograde signaling interplay

Méndez-Gómez,

Sierra-Cacho,

Jiménez-Morales

et al. 2024

BMC Plant Biol

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Background Primary response genes play a pivotal role in translating short-lived stress signals into sustained adaptive responses. In this study, we investigated the involvement of ATL80, an E3 ubiquitin ligase, in the dynamics of gene expression following water deprivation stress. We observed that ATL80 is rapidly activated within minutes of water deprivation stress perception, reaching peak expression around 60 min before gradually declining. ATL80, despite its post-translational regulation role, emerged as a key player in modulating early gene expression responses to water deprivation stress. Results The impact of ATL80 on gene expression was assessed using a time-course microarray analysis (0, 15, 30, 60, and 120 min), revealing a burst of differentially expressed genes, many of which were associated with various stress responses. In addition, the diversity of early modulation of gene expression in response to water deprivation stress was significantly abolished in the atl80 mutant compared to wild-type plants. A subset of 73 genes that exhibited a similar expression pattern to ATL80 was identified. Among them, several are linked to stress responses, including ERF/AP2 and WRKY transcription factors, calcium signaling genes, MAP kinases, and signaling peptides. Promoter analysis predicts enrichment of binding sites for CAMTA1 and CAMTA5, which are known regulators of rapid stress responses. Furthermore, we have identified a group of differentially expressed ERF/AP2 transcription factors, proteins associated with folding and refolding, as well as pinpointed core module genes which are known to play roles in retrograde signaling pathways that cross-referenced with the early ATL80 transcriptome. Conclusions Based on these findings, we propose that ATL80 may target one or more components within the retrograde signaling pathways for degradation. In essence, ATL80 serves as a bridge connecting these signaling pathways and effectively functions as an alarm signal.

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To bind or not to bind: how AUXIN RESPONSE FACTORs select their target genes

Rienstra

Hernández-García

Weijers

2023

Journal of Experimental Botany

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Most plant growth and development processes are regulated one way or another by auxin. The best-studied mechanism by which auxin exerts its regulatory effects is through the nuclear auxin pathway (NAP). In this pathway, AUXIN RESPONSE FACTORs (ARFs) are the transcription factors that ultimately determine which genes become auxin-regulated by binding to specific DNA sequences. ARFs have primarily been studied in Arabidopsis thaliana, but recent studies in other species have revealed family-wide DNA-binding specificities for different ARFs and the minimal functional system of the NAP system, consisting in a duo of competing ARFs of the A and B classes. In this review, we provide an overview of key aspects of ARF DNA-binding such as auxin response elements (TGTCNN) and tandem repeat motifs, and consider how structural biology and in vitro studies help us understand ARF DNA preferences. We also highlight some recent aspects related to the regulation of ARF levels inside a cell, which may alter the DNA-binding profile of ARFs in different tissues. We finally emphasize on the need to study minimal NAP systems to understand fundamental aspects of ARF function, the need to characterize algal ARFs to understand how ARFs evolved, how cutting-edge techniques can increase our understanding of ARFs, and which remaining questions can only be answered by structural biology.

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CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana

Cited by 4 publications

References 45 publications

Asymmetry of Motifs Conservation within Homotypic Composite Elements Differentiates DNA-Binding Domains of Target Transcription Factors in ChIP-Seq Data

Asymmetry of Motifs Conservation within Homotypic Composite Elements Differentiates DNA-Binding Domains of Target Transcription Factors in ChIP-Seq Data

Modulation of early gene expression responses to water deprivation stress by the E3 ubiquitin ligase ATL80: implications for retrograde signaling interplay

To bind or not to bind: how AUXIN RESPONSE FACTORs select their target genes

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