ChIP-Hub provides an integrative platform for exploring plant regulome

Fu, Liang-Yu; Zhu, Tao; Zhou, Xinkai; Yu, Rongrong; He, Zhaohui; Zhang, Peijing; Wu, Zhigui; Chen, Ming; Kaufmann, Kerstin; Chen, Dijun

doi:10.1038/s41467-022-30770-1

Cited by 46 publications

(50 citation statements)

References 98 publications

(69 reference statements)

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“…On the other hand, many web database platforms were also developed to explore the functional information from multi-omics data, including CARMO, OmicsAnalyst, MapMan4, KBCommons, and Plant regulomics ( Wang et al, 2015 ; Schwacke et al, 2019 ; Ran et al, 2020 ; Zeng et al, 2020 ; Zhou et al, 2021 ). Lately, an integrative platform in the ENCODE standards, ChIP-Hub, has provided rich resources from the regulome and epigenome data in plants ( Fu et al, 2022 ). Moreover, the integration of regulome and genetic variations leads CRISPR-cereal to promote precise gene editing for wheat, rice, and maize ( He et al, 2021 ).…”

Section: Integrative Methodologies and Databasesmentioning

confidence: 99%

Integration of multi-omics technologies for crop improvement: Status and prospects

Zhang

Zhang²,

Yu³

et al. 2022

Front. Bioinform.

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With the rapid development of next-generation sequencing (NGS), multi-omics techniques have been emerging as effective approaches for crop improvement. Here, we focus mainly on addressing the current status and future perspectives toward omics-related technologies and bioinformatic resources with potential applications in crop breeding. Using a large amount of omics-level data from the functional genome, transcriptome, proteome, epigenome, metabolome, and microbiome, clarifying the interaction between gene and phenotype formation will become possible. The integration of multi-omics datasets with pan-omics platforms and systems biology could predict the complex traits of crops and elucidate the regulatory networks for genetic improvement. Different scales of trait predictions and decision-making models will facilitate crop breeding more intelligent. Potential challenges that integrate the multi-omics data with studies of gene function and their network to efficiently select desirable agronomic traits are discussed by proposing some cutting-edge breeding strategies for crop improvement. Multi-omics-integrated approaches together with other artificial intelligence techniques will contribute to broadening and deepening our knowledge of crop precision breeding, resulting in speeding up the breeding process.

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Section: Integrative Methodologies and Databasesmentioning

confidence: 99%

Integration of multi-omics technologies for crop improvement: Status and prospects

Zhang

Zhang²,

Yu³

et al. 2022

Front. Bioinform.

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“…6 Some recent studies ( da Silveira Falavigna et al, 2021 ; Lai et al, 2021a , b ) applied the MACS2 tool for DAP-seq data processing for several TFs in Arabidopsis. The benchmark DAP-seq collection ( O’Malley et al, 2016 ) was also re-processed with MACS2 in the ReMap and ChIP-Hub databases ( Fu et al, 2022 ; Hammal et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2022

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Having DNA-binding profiles for a sufficient number of genome-encoded transcription factors (TFs) opens up the perspectives for systematic evaluation of the upstream regulators for the gene lists. Plant Cistrome database, a large collection of TF binding profiles detected using the DAP-seq method, made it possible for Arabidopsis. Here we re-processed raw DAP-seq data with MACS2, the most popular peak caller that leads among other ones according to quality metrics. In the benchmarking study, we confirmed that the improved collection of TF binding profiles supported a more precise gene list enrichment procedure, and resulted in a more relevant ranking of potential upstream regulators. Moreover, we consistently recovered the TF binding profiles that were missing in the previous collection of DAP-seq peak sets. We developed the CisCross web service (https://plamorph.sysbio.ru/ciscross/) that gives more flexibility in the analysis of potential upstream TF regulators for Arabidopsis thaliana genes.

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“…Transcripts per million for each biological replicate and time-point from Kivivirta et al ., 2020 were generously shared with us by Dr. Annette Becker and Clemens Rössner (Justus-Liebig Universität Giessen, Germany). ChIP-Seq peaks were visualized using online software at ChIP-Hub (https://biobigdata.nju.edu.cn/ChIPHub/) (Fu et al ., 2022). Seq-DAP-seq sequences were downloaded from the genome browser (https://genome.ucsc.edu/s/ArnaudStigliani/MADS) (Lai et al ., 2020).…”

Section: Methodsmentioning

confidence: 99%

AGAMOUS mediates timing of guard cell formation during gynoecium development

Brazel

Fattorini

McCarthy

et al. 2023

Preprint

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In Arabidopsis thaliana, stomata are composed of two guard cells that control the aperture of a central pore to facilitate gas exchange between the plant and its environment, which is particularly important during photosynthesis. Although leaves are the primary photosynthetic organs of higher plants, floral organs are also photosynthetically active. In the Brassicaceae, evidence suggests that silique photosynthesis is important for optimal seed oil content. A group of transcription factors containing MADS DNA binding domains is necessary and sufficient to confer floral organ identity. Elegant models, such as the ABCE model of flower development and the floral quartet model, have been instrumental in describing the molecular mechanisms by which these floral organ identity proteins govern flower development. However, we lack a complete understanding of how the floral organ identity genes interact with the underlying leaf development program. Here, we show that the MADS domain transcription factor AGAMOUS (AG) represses stomatal development on the gynoecial valves, so that maturation of stomatal complexes coincides with fertilization. We present evidence that this regulation by AG is mediated by direct transcriptional repression of the master regulator of the stomatal lineage, MUTE, and that this interaction is conserved among the Brassicaceae. This work extends on our understanding of the mechanisms underlying floral organ formation and provides a framework to decipher the mechanisms that control floral organ photosynthesis.

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ChIP-Hub provides an integrative platform for exploring plant regulome

Cited by 46 publications

References 98 publications

Integration of multi-omics technologies for crop improvement: Status and prospects

Integration of multi-omics technologies for crop improvement: Status and prospects

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

AGAMOUS mediates timing of guard cell formation during gynoecium development

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