Thursday, June 17, 2010
miR-33 in Cholesterol Control
With the well-established link between serum cholesterol levels and cardiovascular disease and the availability of effective cholesterol-lowering drugs, cholesterol screening has rapidly become a routine part of health care. Yet, much remains to be learned about how cholesterol levels are regulated at the cellular level (see the Perspective by Brown et al.). Now, Najafi-Shoushtari et al. (p. 1566, published online 13 May) and Rayner et al. (p. 1570, published online 13 May) have discovered a new molecular player in cholesterol control—a small noncoding RNA that, intriguingly, is embedded within the genes coding for sterol regulatory element-binding proteins (SREBPs), transcription factors already known to regulate cholesterol levels. This microRNA, called miR-33, represses expression of the adenosine triphosphate–binding cassette transporter A1, a protein that regulates synthesis of high-density lipoprotein (HDL, or "good" cholesterol) and that helps to remove "bad" cholesterol from the blood. Reducing the levels of miR-33 in mice boosted serum HDL levels, suggesting that manipulation of this regulatory circuit might be therapeutically useful.
Close, But Not Too Close
MicroRNAs (miRNAs) in plants are generally highly complementary to their target RNAs, yet, in most animal miRNAs, only the 
8-nucleotide "seeds" sequence bases pair fully with the target, with few base pairs between the remainder of the miRNA and target. Plant miRNAs are methylated at their 3' ends, whereas animals' miRNAs are not. Ameres et al. (p. 1534; see the Perspective by Pasquinelli) noticed that, in fruit flies, miRNAs engineered to have high complementarity to target RNAs were present at reduced levels. These miRNAs were trimmed and uridylated at their 3' ends, features involved in RNA degradation. Fly small interfering RNAs, all of which are methylated at their 3' ends, were unaffected, unless the methylating enzyme, Hen1, was mutated. Thus, 3'-methylation may prevent complementarity-driven remodeling and degradation of small RNAs.
8-nucleotide "seeds" sequence bases pair fully with the target, with few base pairs between the remainder of the miRNA and target. Plant miRNAs are methylated at their 3' ends, whereas animals' miRNAs are not. Ameres et al. (p. 1534; see the Perspective by Pasquinelli) noticed that, in fruit flies, miRNAs engineered to have high complementarity to target RNAs were present at reduced levels. These miRNAs were trimmed and uridylated at their 3' ends, features involved in RNA degradation. Fly small interfering RNAs, all of which are methylated at their 3' ends, were unaffected, unless the methylating enzyme, Hen1, was mutated. Thus, 3'-methylation may prevent complementarity-driven remodeling and degradation of small RNAs.
Saturday, April 17, 2010
Thursday, August 28, 2008
LRT in bioinformatics papers
Take a look at the the LRT and empirical P-value calculation in following examples:
Familial combined hyperlipidemia is associated with upstream transcription factor 1 (USF1) - Nature Genetics: "Thus, gene-dropping is done under the null hypothesis of linkage equilibrium and no linkage. To calculate an empirical P value, gene-dropping is carried out multiple times. Here, at least 50,000 simulations were carried out for each analysis. The likelihood ratio test statistic (LRT) from each gene-dropping iteration is compared to the LRT for the observed data. The empirical P value is the proportion of iterations in which the gene-dropping LRT equaled or exceeded the observed LRT. In general, the obtained empirical P values of gene-dropping are more conservative than asymptotic P values for small sample sizes."
http://www.smd.qmul.ac.uk/statgen/dcurtis/lc/gctests.html
The asymptotic p value is 0.00027, as reported in the output from scanassoc. The empirical p value is calculated as (r+1)/(N+1), where N is the number of permutations performed and r is the number of permuted datasets which by chance produce a higher for the LRT statistic than does the real dataset. In order to test whether the p value was really as low as 0.00027 one would want to do 9999 or more permutations. In fact, rungc incorporates a feature called "sequential Monte Carlo testing". This means that a target can be set for the number of permuted datasets to reach the value produced by the real dataset and if this target is reached then the simulation procedure can be terminated early.
Familial combined hyperlipidemia is associated with upstream transcription factor 1 (USF1) - Nature Genetics: "Thus, gene-dropping is done under the null hypothesis of linkage equilibrium and no linkage. To calculate an empirical P value, gene-dropping is carried out multiple times. Here, at least 50,000 simulations were carried out for each analysis. The likelihood ratio test statistic (LRT) from each gene-dropping iteration is compared to the LRT for the observed data. The empirical P value is the proportion of iterations in which the gene-dropping LRT equaled or exceeded the observed LRT. In general, the obtained empirical P values of gene-dropping are more conservative than asymptotic P values for small sample sizes."
http://www.smd.qmul.ac.uk/statgen/dcurtis/lc/gctests.html
The asymptotic p value is 0.00027, as reported in the output from scanassoc. The empirical p value is calculated as (r+1)/(N+1), where N is the number of permutations performed and r is the number of permuted datasets which by chance produce a higher for the LRT statistic than does the real dataset. In order to test whether the p value was really as low as 0.00027 one would want to do 9999 or more permutations. In fact, rungc incorporates a feature called "sequential Monte Carlo testing". This means that a target can be set for the number of permuted datasets to reach the value produced by the real dataset and if this target is reached then the simulation procedure can be terminated early.
Friday, April 25, 2008
Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets.
Just a test~
Combining Flock (for blog post and RSS reader) and Connotea, you can get notice for the latest added reference and write blog after reading it, which is very COOL!!
Combining Flock (for blog post and RSS reader) and Connotea, you can get notice for the latest added reference and write blog after reading it, which is very COOL!!
Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets.
Genomics 91 (5), 467-75 (May 2008)
Blogged with the Flock Browser
Wednesday, October 10, 2007
MiRNA learning note (1)
MicroRNA-143 and -145 in colon cancer. [DNA Cell Biol. 2007]
MicroRNAs (miRNAs) are endogenous, small non-coding RNAs (20-22 nucleotides) that negatively regulate gene expression at the translational level by base pairing to the 3' untranslated region of target messenger RNAs.
"It is predicted that 30% of protein-encoding genes are regulated by miRNAs."
Principles of microRNA regulation of a human cellular signaling network : Article : Molecular Systems Biology: "By analyzing the interactions between miRNAs and a human cellular signaling network, we found that miRNAs predominantly target positive regulatory motifs, highly connected scaffolds and most downstream network components such as signaling transcription factors, but less frequently target negative regulatory motifs, common components of basic cellular machines and most upstream network components such as ligands."
Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos -- Yu et al. 35 (1): 152 -- Nucle: "We found that the expression levels of miRNA targets are lower in all mouse and Drosophila tissues than in the embryos. We also found miRNAs more preferentially target ubiquitously expressed genes than tissue-specifically expressed genes. These results support the current suggestion that miRNAs are likely to be largely involved in embryo development and maintaining of tissue identity."
NB: This kind of expression survey at different ontogenetic stages is very important, because it covers a blind spot in analyses that depend on functional categories. For example GO analyses include categories for "development", but as Yu and colleagues point out, many genes change in expression during development that are not part of the "developmental" categories. (from John Hawks's weblog)
Identification of specific sequence motifs in the ...[Comput Biol Chem. 2007] - PubMed Result: "The significantly reduced frequency of occurrence of all 20 motifs in the regions 2000 bp upstream of 23,570 human RefSeq genes demonstrated that these motifs were specific to the upstream miRNA sequences. The most frequently observed motif M1 (GTGCTTMTAGTGCAG), with a MEME E-value of 3.8e-57 was distributed within 500 bp upstream of stem-loop sequences and was also miRNA-specific."
Regulatory circuit of human microRNA biogenesis. [PLoS Comput Biol. 2007] - PubMed Result: "Newly identified regulatory motifs occur frequently and in multiple copies upstream of miRNAs. The motifs are highly enriched in G and C nucleotides, in comparison with the nucleotide composition of miRNA upstream sequences. Although the motifs were predicted using sequences that are upstream of miRNAs, we find that 99% of the top-predicted motifs preferentially occur within the first 500 nucleotides upstream of the transcription start sites of protein-coding genes; the observed preference in location underscores the validity and importance of the motifs identified in this study. Our study also raises the possibility that a considerable number of well-characterized, disease-associated transcription factors (TFs) of protein-coding genes contribute to the abnormal miRNA expression in diseases such as cancer."
"Further analysis of predicted miRNA-protein interactions lead us to hypothesize that TFs that include c-Myb, NF-Y, Sp-1, MTF-1, and AP-2alpha are master-regulators of miRNA expression."
Spatial regulation of microRNA gene expression in the Drosophila embryo: "we investigate the possibility that localized expression is mediated by tissue-specific enhancers, comparable to those seen for protein-coding genes."
mir-309–6 polycistron (8-miR) : An 800-bp 5′ enhancer was identified that recapitulates this complex pattern when attached to a RNA polymerase II core promoter fused to a lacZ-reporter gene.
mir-1 gene: a mesoderm-specific enhancer located ≈5 kb 5′ of the miR-1 transcription unit.
Evidence is presented that the 8-miR enhancer is regulated by the localized Huckebein repressor, whereas miR-1 is activated by Dorsal and Twist. These results provide evidence that restricted activities of the 8-miR and miR-1 miRNAs are mediated by classical tissue-specific enhancers.
MicroRNAs (miRNAs) are endogenous, small non-coding RNAs (20-22 nucleotides) that negatively regulate gene expression at the translational level by base pairing to the 3' untranslated region of target messenger RNAs.
"It is predicted that 30% of protein-encoding genes are regulated by miRNAs."
Principles of microRNA regulation of a human cellular signaling network : Article : Molecular Systems Biology: "By analyzing the interactions between miRNAs and a human cellular signaling network, we found that miRNAs predominantly target positive regulatory motifs, highly connected scaffolds and most downstream network components such as signaling transcription factors, but less frequently target negative regulatory motifs, common components of basic cellular machines and most upstream network components such as ligands."
Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos -- Yu et al. 35 (1): 152 -- Nucle: "We found that the expression levels of miRNA targets are lower in all mouse and Drosophila tissues than in the embryos. We also found miRNAs more preferentially target ubiquitously expressed genes than tissue-specifically expressed genes. These results support the current suggestion that miRNAs are likely to be largely involved in embryo development and maintaining of tissue identity."
NB: This kind of expression survey at different ontogenetic stages is very important, because it covers a blind spot in analyses that depend on functional categories. For example GO analyses include categories for "development", but as Yu and colleagues point out, many genes change in expression during development that are not part of the "developmental" categories. (from John Hawks's weblog)
Identification of specific sequence motifs in the ...[Comput Biol Chem. 2007] - PubMed Result: "The significantly reduced frequency of occurrence of all 20 motifs in the regions 2000 bp upstream of 23,570 human RefSeq genes demonstrated that these motifs were specific to the upstream miRNA sequences. The most frequently observed motif M1 (GTGCTTMTAGTGCAG), with a MEME E-value of 3.8e-57 was distributed within 500 bp upstream of stem-loop sequences and was also miRNA-specific."
Regulatory circuit of human microRNA biogenesis. [PLoS Comput Biol. 2007] - PubMed Result: "Newly identified regulatory motifs occur frequently and in multiple copies upstream of miRNAs. The motifs are highly enriched in G and C nucleotides, in comparison with the nucleotide composition of miRNA upstream sequences. Although the motifs were predicted using sequences that are upstream of miRNAs, we find that 99% of the top-predicted motifs preferentially occur within the first 500 nucleotides upstream of the transcription start sites of protein-coding genes; the observed preference in location underscores the validity and importance of the motifs identified in this study. Our study also raises the possibility that a considerable number of well-characterized, disease-associated transcription factors (TFs) of protein-coding genes contribute to the abnormal miRNA expression in diseases such as cancer."
"Further analysis of predicted miRNA-protein interactions lead us to hypothesize that TFs that include c-Myb, NF-Y, Sp-1, MTF-1, and AP-2alpha are master-regulators of miRNA expression."
Spatial regulation of microRNA gene expression in the Drosophila embryo: "we investigate the possibility that localized expression is mediated by tissue-specific enhancers, comparable to those seen for protein-coding genes."
mir-309–6 polycistron (8-miR) : An 800-bp 5′ enhancer was identified that recapitulates this complex pattern when attached to a RNA polymerase II core promoter fused to a lacZ-reporter gene.
mir-1 gene: a mesoderm-specific enhancer located ≈5 kb 5′ of the miR-1 transcription unit.
Evidence is presented that the 8-miR enhancer is regulated by the localized Huckebein repressor, whereas miR-1 is activated by Dorsal and Twist. These results provide evidence that restricted activities of the 8-miR and miR-1 miRNAs are mediated by classical tissue-specific enhancers.
Monday, October 8, 2007
Purifying Selection Maintains Highly Conserved Noncoding Sequences in Drosophila -- Casillas et al. 24 (10): 2222 -- Molecular Biology and Evolution
Purifying Selection Maintains Highly Conserved Noncoding Sequences in Drosophila -- Casillas et al. 24 (10): 2222 -- Molecular Biology and Evolution: "We find that point mutations in intronic and intergenic CNSs exhibit a significant reduction in levels of divergence relative to levels of polymorphism, as well as a significant excess of rare derived alleles, compared with either the nonconserved spacer regions between CNSs or with 4-fold silent sites in coding regions"
TOADD: more about the methods.
//Long time, no reading~
TOADD: more about the methods.
//Long time, no reading~
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