Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

Iengar, Prathima; Joshi, N. V.

doi:10.1186/1471-2164-10-18

Cited by 23 publications

(21 citation statements)

References 39 publications

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“…An additional complication to identifying cis- regulatory elements is that C. parvum UTRs are largely undefined. Apicomplexan cis- regulatory elements have traditionally been identified by looking in the 1-2 kb of sequence directly upstream of coding regions, or until a gene is encountered on either strand [18,22,53]; however, there is some evidence that in highly compacted eukaryotic genomes, such as that of C. parvum , transcripts overlap, and UTRs are not necessarily limited to intergenic spaces [54]. The extent of occurrences of overlapping transcripts in C. parvum has not been quantified.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide upstream motif analysis of Cryptosporidium parvum genes clustered by expression profile

2013

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BackgroundThere are very few molecular genetic tools available to study the apicomplexan parasite Cryptosporidium parvum. The organism is not amenable to continuous in vitro cultivation or transfection, and purification of intracellular developmental stages in sufficient numbers for most downstream molecular applications is difficult and expensive since animal hosts are required. As such, very little is known about gene regulation in C. parvum.ResultsWe have clustered whole-genome gene expression profiles generated from a previous study of seven post-infection time points of 3,281 genes to identify genes that show similar expression patterns throughout the first 72 hours of in vitro epithelial cell culture. We used the algorithms MEME, AlignACE and FIRE to identify conserved, overrepresented DNA motifs in the upstream promoter region of genes with similar expression profiles. The most overrepresented motifs were E2F (5′-TGGCGCCA-3′); G-box (5′-G.GGGG-3′); a well-documented ApiAP2 binding motif (5′-TGCAT-3′), and an unknown motif (5′-[A/C] AACTA-3′). We generated a recombinant C. parvum DNA-binding protein domain from a putative ApiAP2 transcription factor [CryptoDB: cgd8_810] and determined its binding specificity using protein-binding microarrays. We demonstrate that cgd8_810 can putatively bind the overrepresented G-box motif, implicating this ApiAP2 in the regulation of many gene clusters.ConclusionSeveral DNA motifs were identified in the upstream sequences of gene clusters that might serve as potential cis-regulatory elements. These motifs, in concert with protein DNA binding site data, establish for the first time the beginnings of a global C. parvum gene regulatory map that will contribute to our understanding of the development of this zoonotic parasite.

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Section: Discussionmentioning

confidence: 99%

Genome-wide upstream motif analysis of Cryptosporidium parvum genes clustered by expression profile

2013

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“…Although unique motifs are not expected for every set of co-expressed genes, 8 to identify the motifs that are present in majority of genes (over represented), a thorough scan was made. Interestingly, more than half of the analyzed rice and Arabidopsis sequences have showed the presence of five and six over represented motifs, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…6,7 In silico methods can predict TFBMs in a wide range of upstream regions of target genes with less effort, time, and cost, making functional analysis of the TFBMs simpler and more efficient. In eukaryotes, transcription related regulatory motifs were repeated many times in the upstream regions 8 and these over represented motifs were correlated with transcriptional activity. 9 However, identification of over represented "true" motifs in eukaryotic genome is still a challenge because of shorter motif size (usually 4-20 bp) in a large genome, 10,11 high degeneracy of nucleotides in the motif sequence (up to 50%), 12 and their wide spread presence over long distance, ie distal parts of the promoter.…”

Section: Methodsmentioning

confidence: 99%

“…Although the motifs identified by all three bioinformatic tools had higher significance, motifs returned by at least two programs were only considered as strong motifs. 8 The selected strong motifs were checked with TFBM databases viz., PLACE (Plant cis-acting regulatory DNA elements) (http://www.dna.affrc.go.jp/PLACE/ signalscan.html) 19 plant CARE (http://bioinformatics.psb. ugent.be/webtools/plantcare/html/), 20 and literatures for further information about these motifs.…”

Section: Methodsmentioning

confidence: 99%

“…33,34 It was reported that different combinations of less numbers of motifs regulate gene expression in many organisms rather than a large variety of TFBMs. 8,35 Expression of many genes in a cell rely on the combinatorial control of several TFs 36,37 and in order to understand those cellular processes better, motif combinations also have to be analyzed along with novel motif identification. Occurrence of motif network in promoters of late embryogenesis abundant genes in rice and their use in finding the co-expressed/complementary genes by analyzing their motifs pattern was demonstrated efficiently.…”

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confidence: 99%

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Genome-wide Identification and Characterization of Transcription Factor Binding Motifs of NBS-LRR Genes in Rice and Arabidopsis

Ramkumar¹,

Madhav²,

Biswal³

et al. 2014

Journal of Genomes and Exomes

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Nucleotide binding site leucine rich repeat (NBS-LRR) gene encoding proteins are the major biotic stress resistance genes of rice and Arabidopsis thaliana. Upstream sequences of 206 entire NBS-LRR genes of Arabidopsis and 120 genes of rice were analyzed with three highly reliable motif prediction tools for enhanced accuracy of prediction and characterization of potential transcription factor binding motifs (TFBMs). A total of 36 and 30 novel, strong TFBMs were discovered from NBS-LRR genes of rice and A. thaliana, respectively. All the motifs identified in these sequences were analyzed for their positional conservation and the possible motif network associations were also identified. Further, the probability of the presence of motifs in these NBS-LRR genes were validated and statistically tested. Although Arabidopsis NBS-LRR sequences showed 76.3% similarity with rice sequences at motif level, the analysis revealed that rice sequences have many unique TFBMs and are more evolved in gene expression mechanisms. The study also provided a list of novel candidate motifs for these genes, which will be a good resource for experimental validation. A novel strategy of prediction of gene expression based on motif arrangement was also demonstrated in this study. The findings of this study, such as the motifs' positional conservation, architecture, etc. offered new biological insights into the role of TFBMs in the regulation of resistance genes.

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Gene regulation

Scherf

Malmquist

Martins

et al. 2016

Advances in Malaria Research

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Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

Cited by 23 publications

References 39 publications

Genome-wide upstream motif analysis of Cryptosporidium parvum genes clustered by expression profile

Genome-wide upstream motif analysis of Cryptosporidium parvum genes clustered by expression profile

Genome-wide Identification and Characterization of Transcription Factor Binding Motifs of NBS-LRR Genes in Rice and Arabidopsis

Gene regulation

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