Thousands of Cis-Regulatory Sequence Combinations Are Shared by Arabidopsis and Poplar

Ding, Jun; Hu, Haiyan; Li, Xiaoman

doi:10.1104/pp.111.186080

Cited by 26 publications

(25 citation statements)

References 75 publications

(105 reference statements)

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“…Additional DNase-seq read dips often presented in individual regions (Figure 8), suggesting binding of additional regulatory proteins to the same region. This agrees with a recent report that the regulation of Arabidopsis genes is often controlled by cis-regulatory modules that contain multiple transcription factor binding sites (Ding et al, 2012).…”

Section: Dh Sites Revealed Protein Binding Footprints Associated Withsupporting

confidence: 82%

Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis

et al. 2012

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Gene expression and regulation in eukaryotes is controlled by orchestrated binding of regulatory proteins, including both activators and repressors, to promoters and other cis-regulatory DNA elements. An increasing number of plant genomes have been sequenced; however, a similar effort to the ENCODE project, which aimed to identify all functional elements in the human genome, has yet to be initiated in plants. Here we report genome-wide high-resolution mapping of DNase I hypersensitive (DH) sites in the model plant Arabidopsis thaliana. We identified 38,290 and 41,193 DH sites in leaf and flower tissues, respectively. The DH sites were depleted of bulk nucleosomes and were tightly associated with RNA polymerase II binding sites. Approximately 90% of the binding sites of two well-characterized MADS domain transcription factors, APETALA1 and SEPALLATA3, were covered by the DH sites. We demonstrate that protein binding footprints within a specific genomic region can be revealed using the DH site data sets in combination with known or putative protein binding motifs and gene expression data sets. Thus, genome-wide DH site mapping will be an important tool for systematic identification of all cis-regulatory DNA elements in plants.

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Section: Dh Sites Revealed Protein Binding Footprints Associated Withsupporting

confidence: 82%

Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis

et al. 2012

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“…Except for enhancers, ULEs could potentially represent part of conserved cis-regulatory modules (CRMs), where one or more transcription factors bind to regulate the expression of neighbor genes. About 18,500 CRMs located upstream of genes are shared by Arabidopsis and poplar (Ding et al 2012). Merely one (ULE6) out of 13 intergenic ULEs tested is part of a such a CRM.…”

Section: Ules From Plants and Animals Have Similar Characteristicsmentioning

confidence: 99%

Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes

Kritsas¹,

Wuest

Hupalo

et al. 2012

Genome Res.

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Ultraconserved elements (UCEs), stretches of DNA that are identical between distantly related species, are enigmatic genomic features whose function is not well understood. First identified and characterized in mammals, UCEs have been proposed to play important roles in gene regulation, RNA processing, and maintaining genome integrity. However, because all of these functions can tolerate some sequence variation, their ultraconserved and ultraselected nature is not explained. We investigated whether there are highly conserved DNA elements without genic function in distantly related plant genomes. We compared the genomes of Arabidopsis thaliana and Vitis vinifera; species that diverged~115 million years ago (Mya). We identified 36 highly conserved elements with at least 85% similarity that are longer than 55 bp. Interestingly, these elements exhibit properties similar to mammalian UCEs, such that we named them UCE-like elements (ULEs). ULEs are located in intergenic or intronic regions and are depleted from segmental duplications. Like UCEs, ULEs are under strong purifying selection, suggesting a functional role for these elements. As their mammalian counterparts, ULEs show a sharp drop of A+T content at their borders and are enriched close to genes encoding transcription factors and genes involved in development, the latter showing preferential expression in undifferentiated tissues. By comparing the genomes of Brachypodium distachyon and Oryza sativa, species that diverged~50 Mya, we identified a different set of ULEs with similar properties in monocots. The identification of ULEs in plant genomes offers new opportunities to study their possible roles in genome function, integrity, and regulation.

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“…In high eukaryotes, multiple TFs often coordinately regulate their target genes by binding to their respective CREs that co-occur in the short regions of a few hundred base pairs (Yuh et al, 1998;Blanchette et al, 2006;Ding et al, 2012). Many co-occurring CREs in plants have also been identified by experimental studies.…”

Section: The Predicted Motif Combinations Are Consistent With Experimmentioning

confidence: 99%

Systematic Prediction of cis-Regulatory Elements in the Chlamydomonas reinhardtii Genome Using Comparative Genomics

Ding

2012

Plant Physiology

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Chlamydomonas reinhardtii is one of the most important microalgae model organisms and has been widely studied toward the understanding of chloroplast functions and various cellular processes. Further exploitation of C. reinhardtii as a model system to elucidate various molecular mechanisms and pathways requires systematic study of gene regulation. However, there is a general lack of genome-scale gene regulation study, such as global cis-regulatory element (CRE) identification, in C. reinhardtii. Recently, large-scale genomic data in microalgae species have become available, which enable the development of efficient computational methods to systematically identify CREs and characterize their roles in microalgae gene regulation. Here, we performed in silico CRE identification at the whole genome level in C. reinhardtii using a comparative genomics-based method. We predicted a large number of CREs in C. reinhardtii that are consistent with experimentally verified CREs. We also discovered that a large percentage of these CREs form combinations and have the potential to work together for coordinated gene regulation in C. reinhardtii. Multiple lines of evidence from literature, gene transcriptional profiles, and gene annotation resources support our prediction. The predicted CREs will serve, to our knowledge, as the first large-scale collection of CREs in C. reinhardtii to facilitate further experimental study of microalgae gene regulation. The accompanying software tool and the predictions in C. reinhardtii are also made available through a Web-accessible database (http://hulab.ucf.edu/research/projects/Microalgae/sdcre/motifcomb.html).

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Thousands of Cis-Regulatory Sequence Combinations Are Shared by Arabidopsis and Poplar

Cited by 26 publications

References 75 publications

Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis

Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis

Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes

Systematic Prediction of cis-Regulatory Elements in the Chlamydomonas reinhardtii Genome Using Comparative Genomics

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