MEME SUITE: tools for motif discovery and searching

Bailey, Timothy L.; Bodén, Mikael; Buske, Fabian A.; Frith, Martin C.; Grant, Charles E.; Clementi, Luca; Ren, Jingyuan; Li, Wilfred W.; Noble, William Stafford

doi:10.1093/nar/gkp335

Cited by 8,527 publications

(7,530 citation statements)

References 16 publications

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“…Using MEME (Bailey, et al, 2009), we took 100 bp sequences centered at the ARBS peaks to identify potential ARE motifs. Three motifs are consistently found in high frequency across different parameter settings with an incidence of 622, 1,085 and 971 for motif 1, 2 and 3 respectively (Fig.…”

Section: Resultsmentioning

confidence: 99%

Putative Prostate Cancer Risk SNP in an Androgen Receptor‐Binding Site of the Melanophilin Gene Illustrates Enrichment of Risk SNPs in Androgen Receptor Target Sites

Narisu

Schlick

et al. 2015

Human Mutation

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Genome-wide association studies have identified genomic loci, whose single nucleotide polymorphisms (SNPs) predispose to prostate cancer (PCa). However, the mechanisms of most of these variants are largely unknown. We integrated chromatin-IP coupled sequencing and microarray expression profiling in TMPRSS2-ERG gene rearrangement positive DUCaP cells with the GWAS PCa risk SNPs catalog to identify disease susceptibility SNPs localized within functional androgen receptor binding sites (ARBSs). Among the 48 GWAS index risk SNPs and 3,917 linked SNPs, 80 were found located in ARBSs. Of these, rs11891426:T>G in an intron of the melanophilin gene (MLPH), was within a novel putative auxiliary AR binding motif, which is enriched in the neighborhood of canonical androgen responsive elements. T→G exchange attenuated the transcriptional activity of the ARBS in an AR reporter gene assay. The expression of melanophilin in primary prostate tumors was significantly lower in those with the G compared to the T allele and correlated significantly with AR protein. Higher melanophilin level in prostate tissue of patients with a favourable PCa risk profile points out a tumor suppressive effect. These results unravel a hidden link between AR and a functional putative PCa risk SNP, whose allele alteration affects androgen regulation of its host gene MLPH.

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Section: Resultsmentioning

confidence: 99%

Putative Prostate Cancer Risk SNP in an Androgen Receptor‐Binding Site of the Melanophilin Gene Illustrates Enrichment of Risk SNPs in Androgen Receptor Target Sites

Narisu

Schlick

et al. 2015

Human Mutation

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“…CpG island and promoter definitions were downloaded from the UCSC browser. Enriched motifs were identified by MEME-ChIP 41 .…”

Section: Methodsmentioning

confidence: 99%

Polycomb-like proteins link the PRC2 complex to CpG islands

Liefke

Jiang

et al. 2017

Nature

254

323

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The Polycomb repressive complex 2 (PRC2) mainly mediates transcriptional repression1,2 and plays essential roles in various biological processes including the maintenance of cell identity and proper differentiation. Polycomb-like proteins (PCLs), including PHF1, MTF2 and PHF19, are PRC2 associated factors that form sub-complexes with PRC2 core components3, and have been proposed to modulate PRC2’s enzymatic activity or its recruitment to specific genomic loci4–13. Mammalian PRC2 binding sites are enriched in CG content, which correlate with CpG islands that display a low level of DNA methylation14. However, the mechanism of PRC2 recruitment to CpG islands is not fully understood. In this study, we solved the crystal structures of the N-terminal domains of PHF1 and MTF2 with bound CpG-containing DNAs in the presence of H3K36me3-containing histone peptides. We found that the extended homologous (EH) regions of both proteins fold into a winged-helix structure, which specifically binds to the unmethylated CpG motif but in a manner completely different from the canonical winged-helix motif-DNA recognition. We further showed that the PCL EH domains are required for efficient recruitment of PRC2 to CpG island-containing promoters in mouse embryonic cells. Our research provides the first direct evidence demonstrating that PCLs are critical for PRC2 recruitment to CpG islands, thereby further clarifying their roles in transcriptional regulation in vivo.

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“…6 and performed using systemPipeR (https://github.com/tgirke/systemPipeR). The MEME online tool 36 was used to search strand-specific 5′ leader sequences for enriched consensuses compared to whole genome 5′ leader sequences with default parameters. Density plot was presented using IGB 37 .…”

Section: Methodsmentioning

confidence: 99%

“…The nucleotide resolution of the coverage around start and stop codons was performed using the 15 th nucleotide of 30-nt reads of RF, similar as reported previously 10, 38 . Whole transcriptome R-motif search was performed using FIMO tool in the MEME suite 36 . LUC/RLUC ratio was first tested for normal distribution using the Shapiro-Wilk test.…”

Section: Methodsmentioning

confidence: 99%

Global translational reprogramming is a fundamental layer of immune regulation in plants

Greene

Yoo

et al. 2017

Nature

197

212

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In the absence of specialized immune cells, the need for plants to reprogram transcription to transition from growth-related activities to defence is well understood1, 2. However, little is known about translational changes that occur during immune induction. Using ribosome footprinting (RF), we performed global translatome profiling on Arabidopsis exposed to the microbe-associated molecular pattern (MAMP) elf18. We found that during this pattern-triggered immunity (PTI), translation was tightly regulated and poorly correlated with transcription. Identification of genes with altered translational efficiency (TE) led to the discovery of novel regulators of this immune response. Further investigation of these genes showed that mRNA sequence features are major determinants of the observed TE changes. In the 5′ leader sequences of transcripts with increased TE, we found a highly enriched mRNA consensus sequence, R-motif, consisting of mostly purines. We showed that R-motif regulates translation in response to PTI induction through interaction with poly(A)-binding proteins. Therefore, this study provides not only strong evidence, but also a molecular mechanism for global translational reprogramming during PTI in plants.

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MEME SUITE: tools for motif discovery and searching

Cited by 8,527 publications

References 16 publications

Putative Prostate Cancer Risk SNP in an Androgen Receptor‐Binding Site of the Melanophilin Gene Illustrates Enrichment of Risk SNPs in Androgen Receptor Target Sites

Putative Prostate Cancer Risk SNP in an Androgen Receptor‐Binding Site of the Melanophilin Gene Illustrates Enrichment of Risk SNPs in Androgen Receptor Target Sites

Polycomb-like proteins link the PRC2 complex to CpG islands

Global translational reprogramming is a fundamental layer of immune regulation in plants

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