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Rfam 12.0: updates to the RNA families database.

Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD - Nucleic Acids Res. (2014)

Bottom Line: We describe the upgrade of our search pipeline to use Infernal 1.1 and demonstrate its improved homology detection ability by comparison with the previous version.The new pipeline is easier for users to apply to their own data sets, and we illustrate its ability to annotate RNAs in genomic and metagenomic data sets of various sizes.Rfam has been expanded to include 260 new families, including the well-studied large subunit ribosomal RNA family, and for the first time includes information on short sequence- and structure-based RNA motifs present within families.

View Article: PubMed Central - PubMed

Affiliation: HHMI Janelia Farm Research Campus, Ashburn, VA, USA.

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Screenshot of the secondary structure representation for the RsmY RNA family (RF00195) with the annotation for the CsrA binding motif (RM00005) overlaid. Positions in red indicate that all the seed sequences at that position are found to contain the motif while other colours represent fewer sequences having matches at that position. The CsrA protein is a homo-dimeric, RNA binding protein. Each CsrA binds a specific RNA motif that is characterized by a short hairpin that hosts a GGA subsequence, these motifs generally occur in pairs. The CsrA-binding sRNAs, like RsmY, generally sequester excess copies of CsrA which would otherwise bind mRNAs and inhibit translation (23). Therefore, the expression of these sRNAs is a rapid way of altering expression levels for a potentially large network of proteins (24).
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Figure 3: Screenshot of the secondary structure representation for the RsmY RNA family (RF00195) with the annotation for the CsrA binding motif (RM00005) overlaid. Positions in red indicate that all the seed sequences at that position are found to contain the motif while other colours represent fewer sequences having matches at that position. The CsrA protein is a homo-dimeric, RNA binding protein. Each CsrA binds a specific RNA motif that is characterized by a short hairpin that hosts a GGA subsequence, these motifs generally occur in pairs. The CsrA-binding sRNAs, like RsmY, generally sequester excess copies of CsrA which would otherwise bind mRNAs and inhibit translation (23). Therefore, the expression of these sRNAs is a rapid way of altering expression levels for a potentially large network of proteins (24).

Mentions: On the Rfam website, information for each motif can be accessed via individual motif pages. These contain tabs for a Wikipedia article, seed alignments, structures, family matches, references and a curation tab. The page for the Terminator1 motif (RM00022) is shown in Figure 2 as an example. In addition to this, a tab has been added to each family page, displaying the motifs, if any, that match the family. Motif annotations for a family can be visualized by overlaying motif matches on the secondary structure image for the family. For each position of the secondary structure image, the fraction of seed sequences that match a selected motif is calculated and is represented on the structure image using a rainbow scale. Figure 3 gives an example, showing the secondary structure for the RsmY family (RF00195) overlaid with CsrA binding motif (RM00005) annotation. The interaction of RsmY with the RNA binding protein CsrA via this motif is part of a post-transcriptional regulatory network in gammaproteobacteria (23,24).


Rfam 12.0: updates to the RNA families database.

Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD - Nucleic Acids Res. (2014)

Screenshot of the secondary structure representation for the RsmY RNA family (RF00195) with the annotation for the CsrA binding motif (RM00005) overlaid. Positions in red indicate that all the seed sequences at that position are found to contain the motif while other colours represent fewer sequences having matches at that position. The CsrA protein is a homo-dimeric, RNA binding protein. Each CsrA binds a specific RNA motif that is characterized by a short hairpin that hosts a GGA subsequence, these motifs generally occur in pairs. The CsrA-binding sRNAs, like RsmY, generally sequester excess copies of CsrA which would otherwise bind mRNAs and inhibit translation (23). Therefore, the expression of these sRNAs is a rapid way of altering expression levels for a potentially large network of proteins (24).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383904&req=5

Figure 3: Screenshot of the secondary structure representation for the RsmY RNA family (RF00195) with the annotation for the CsrA binding motif (RM00005) overlaid. Positions in red indicate that all the seed sequences at that position are found to contain the motif while other colours represent fewer sequences having matches at that position. The CsrA protein is a homo-dimeric, RNA binding protein. Each CsrA binds a specific RNA motif that is characterized by a short hairpin that hosts a GGA subsequence, these motifs generally occur in pairs. The CsrA-binding sRNAs, like RsmY, generally sequester excess copies of CsrA which would otherwise bind mRNAs and inhibit translation (23). Therefore, the expression of these sRNAs is a rapid way of altering expression levels for a potentially large network of proteins (24).
Mentions: On the Rfam website, information for each motif can be accessed via individual motif pages. These contain tabs for a Wikipedia article, seed alignments, structures, family matches, references and a curation tab. The page for the Terminator1 motif (RM00022) is shown in Figure 2 as an example. In addition to this, a tab has been added to each family page, displaying the motifs, if any, that match the family. Motif annotations for a family can be visualized by overlaying motif matches on the secondary structure image for the family. For each position of the secondary structure image, the fraction of seed sequences that match a selected motif is calculated and is represented on the structure image using a rainbow scale. Figure 3 gives an example, showing the secondary structure for the RsmY family (RF00195) overlaid with CsrA binding motif (RM00005) annotation. The interaction of RsmY with the RNA binding protein CsrA via this motif is part of a post-transcriptional regulatory network in gammaproteobacteria (23,24).

Bottom Line: We describe the upgrade of our search pipeline to use Infernal 1.1 and demonstrate its improved homology detection ability by comparison with the previous version.The new pipeline is easier for users to apply to their own data sets, and we illustrate its ability to annotate RNAs in genomic and metagenomic data sets of various sizes.Rfam has been expanded to include 260 new families, including the well-studied large subunit ribosomal RNA family, and for the first time includes information on short sequence- and structure-based RNA motifs present within families.

View Article: PubMed Central - PubMed

Affiliation: HHMI Janelia Farm Research Campus, Ashburn, VA, USA.

Show MeSH