Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression

Mihailovich, Marija; Militti, Cristina; Gabaldón, Toni; Gebauer, Fátima

doi:10.1002/bies.200900122

Cited by 145 publications

(119 citation statements)

References 84 publications

Supporting

Mentioning

114

Contrasting

Order By: Relevance

“…Importantly, most (68%) of all the Lingulodinium DNA-binding domains fall into the class of cold-shock domains. However, because these domains also bind mRNA, and are better known for their role in posttranscriptional regulation in eukaryotes (17), we conclude that Lingulodinium shows a marked underrepresentation in the types of proteins and protein domains involved in regulating transcription.…”

Section: Resultsmentioning

confidence: 82%

“…Little is known about the regulation of gene expression in dinoflagellates, but this observation suggests that transcriptional control may not be used as extensively as in other organisms. Interestingly, the most abundant DNA-binding domain, the cold-shock domain, is also associated with posttranscriptional regulation in eukaryotes (17) and thus may not function as a DNA-binding protein at all in Lingulodinium. The idea that dinoflagellates favor regulation of gene expression at a posttranscriptional level agrees with studies on circadian regulation of protein synthesis showing extensive translation control (24,25).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic

Beauchemin

Roy

Daoust

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Dinoflagellates are an important component of the marine biota, but a large genome with high–copy number (up to 5,000) tandem gene arrays has made genomic sequencing problematic. More importantly, little is known about the expression and conservation of these unusual gene arrays. We assembled de novo a gene catalog of 74,655 contigs for the dinoflagellate Lingulodinium polyedrum from RNA-Seq (Illumina) reads. The catalog contains 93% of a Lingulodinium EST dataset deposited in GenBank and 94% of the enzymes in 16 primary metabolic KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, indicating it is a good representation of the transcriptome. Analysis of the catalog shows a marked underrepresentation of DNA-binding proteins and DNA-binding domains compared with other algae. Despite this, we found no evidence to support the proposal of polycistronic transcription, including a marked underrepresentation of sequences corresponding to the intergenic spacers of two tandem array genes. We also have used RNA-Seq to assess the degree of sequence conservation in tandem array genes and found their transcripts to be highly conserved. Interestingly, some of the sequences in the catalog have only bacterial homologs and are potential candidates for horizontal gene transfer. These presumably were transferred as single-copy genes, and because they are now all GC-rich, any derived from AT-rich contexts must have experienced extensive mutation. Our study not only has provided the most complete dinoflagellate gene catalog known to date, it has also exploited RNA-Seq to address fundamental issues in basic transcription mechanisms and sequence conservation in these algae.

show abstract

Section: Resultsmentioning

confidence: 82%

Section: Discussionmentioning

confidence: 99%

Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic

Beauchemin

Roy

Daoust

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…64 This technique identifies phages producing a single polypeptide, and it could not have been used for NF-Y, as all three of its subunits are required for DNA binding. YB-1 was shown to be a protein with a known nucleic acid-binding domain, termed CSD (cold-shock domain), which is highly conserved in eukaryotes and prokaryotes ( Figure 1 and Mihailovich et al 65 ). Intriguingly, two cloning manuscripts published in the same period were at odds with the interpretation that YB-1 was a classic sequence-specific TF: (i) YB-1 was identified in screenings of expression libraries with a completely unrelated oligo, the W box, also from the DRa promoter, but sharing no sequence similarity to Y/CCAAT; 66 these authors first provided evidence that YB-1 binds well to single-stranded (ssDNA) and, surprisingly, to abasic DNA.…”

Section: Y and Ccaat: Two Names One Entitymentioning

confidence: 99%

Targeting the Y/CCAAT box in cancer: YB-1 (YBX1) or NF-Y?

Dolfini

Mantovani

2013

Cell Death Differ

View full text Add to dashboard Cite

The Y box is an important sequence motif found in promoters and enhancers containing a CCAAT box -one of the few elements enriched in promoters of large sets of genes overexpressed in cancer. The search for the transcription factor(s) acting on it led to the biochemical purification of the nuclear factor Y (NF-Y) heterotrimer, and to the cloning -through the screening of expression libraries -of Y box-binding protein 1 (YB-1), an oncogene, overexpressed in aggressive tumors and associated with drug resistance. These two factors have been associated with Y/CCAAT-dependent activation of numerous growth-related genes, notably multidrug resistance protein 1. We review two decades of data indicating that NF-Y ultimately acts on Y/CCAAT in cancer cells, a notion recently confirmed by genome-wide data. Other features of YB-1, such as post-transcriptional control of mRNA biology, render it important in cancer biology.

show abstract

“…An example of coordinated regulation is provided by the protein Upstream of N-ras (UNR), a conserved RBP involved in the regulation of mRNA stability and translation (Mihailovich et al 2010). In Drosophila, UNR contributes to opposite, sex-specific outcomes in X-chromosome dosage compensation via differential binding to RNA.…”

Section: Introductionmentioning

confidence: 99%

Widespread generation of alternative UTRs contributes to sex-specific RNA binding by UNR

Mihailovich

Wurth

Zambelli

et al. 2011

RNA

Self Cite

View full text Add to dashboard Cite

Upstream of N-ras (UNR) is a conserved RNA-binding protein that regulates mRNA translation and stability by binding to sites generally located in untranslated regions (UTRs). In Drosophila, sex-specific binding of UNR to msl2 mRNA and the noncoding RNA roX is believed to play key roles in the control of X-chromosome dosage compensation in both sexes. To investigate broader sex-specific functions of UNR, we have identified its RNA targets in adult male and female flies by high-throughput RNA binding and transcriptome analysis. Here we show that UNR binds to a large set of protein-coding transcripts and to a smaller set of noncoding RNAs in a sex-specific fashion. The analyses also reveal a strong correlation between sex-specific binding of UNR and sex-specific differential expression of UTRs in target genes. Validation experiments indicate that UNR indeed recognizes sex-specifically processed transcripts. These results suggest that UNR exploits the transcript diversity generated by alternative processing and alternative promoter usage to bind and regulate target genes in a sex-specific manner.

show abstract

Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression

Cited by 145 publications

References 84 publications

Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic

Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic

Targeting the Y/CCAAT box in cancer: YB-1 (YBX1) or NF-Y?

Widespread generation of alternative UTRs contributes to sex-specific RNA binding by UNR

Contact Info

Product

Resources

About