ArticleBMC genomics2009
Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it, 29 citations in OpenAlex.
- Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis.Functional & integrative genomics · 2020Pooled it
- Single-Base Resolution Map of Evolutionary Constraints and Annotation of Conserved Elements across Major Grass Genomes.Genome biology and evolution · 2018Article
- Predictive Models of Spatial Transcriptional Response to High Salinity.Plant physiology · 2017Article
- RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response.Frontiers in plant science · 2017Article
- Redundant ERF-VII Transcription Factors Bind to an Evolutionarily Conserved cis-Motif to Regulate Hypoxia-Responsive Gene Expression in Arabidopsis.The Plant cell · 2016Article
- Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining.Rice (New York, N.Y.) · 2015Article
- Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice.Frontiers in plant science · 2015Article
- Systematic prediction of cis-regulatory elements in the Chlamydomonas reinhardtii genome using comparative genomics.Plant physiology · 2012Article
- Screening of tissue-specific genes and promoters in tomato by comparing genome wide expression profiles of Arabidopsis orthologues.Molecules and cells · 2012Article
- Colinearity and similar expression pattern of rice DREB1s reveal their functional conservation in the cold-responsive pathway.PloS one · 2012Article
- Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes.Genome biology and evolution · 2012Article
- Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes.Nucleic acids research · 2011Article
- Coordinated activation of cellulose and repression of lignin biosynthesis pathways in rice.Plant physiology · 2011Article
- A comparative genome-wide study of ncRNAs in trypanosomatids.BMC genomics · 2010Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe spatiotemporal regulation of gene expression largely depends on the presence and absence of cis-regulatory sites in the promoter. In the economically highly important grass family, our knowledge of transcription factor binding sites and transcriptional networks is still very limited. With the completion of the sorghum genome and the available rice genome sequence, comparative promoter analyses now allow genome-scale detection of conserved cis-elements.
resultsIn this study, we identified thousands of phylogenetic footprints conserved between orthologous rice and sorghum upstream regions that are supported by co-expression information derived from three different rice expression data sets. In a complementary approach, cis-motifs were discovered by their highly conserved co-occurrence in syntenic promoter pairs. Sequence conservation and matches to known plant motifs support our findings. Expression similarities of gene pairs positively correlate with the number of motifs that are shared by gene pairs and corroborate the importance of similar promoter architectures for concerted regulation. This strongly suggests that these motifs function in the regulation of transcript levels in rice and, presumably also in sorghum.
conclusionOur work provides the first large-scale collection of cis-elements for rice and sorghum and can serve as a paradigm for cis-element analysis through comparative genomics in grasses in general.
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