RNAi

RNAi Curation Mission Summary

The term "RNAi" stands for "RNA-interference" and refers to the targeted silencing of gene expression of a "target gene" via introduction of double stranded RNA (dsRNA) containing high degrees of sequence identity to the "target gene". In C. elegans, sequences of dsRNA may be introduced into the worm by a variety of different methods including direct micro-injection, soaking of worms in solution containing dsRNA, feeding worms bacteria that express dsRNA from a plasmid, and transgenic expression (within the worm) of dsRNA. For efficient and specific knockdown of gene expression, the dsRNA must have a minimum sequence identity with the target gene sequence. Any phenotype(s) resulting from the RNAi-mediated knockdown of a particular gene is thought to directly reflect the phenotype of a loss-of-function mutation in that gene, hence providing evidence as to the gene's biological function.

The goal of RNAi curation is to associate RNAi-mediated phenotypes with the target genes knocked down in RNAi experiments, as found in the literature pertaining to C. elegans and related species.

RNAi Data Model

This is the RNAi data model as of WormBase Release WS222:

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// ?RNAi class
//
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?RNAi   Evidence #Evidence
        History_name UNIQUE ?Text
        Homol Homol_homol ?Homol_data XREF RNAi_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
        Sequence_info   DNA_text Text UNIQUE Text //stores actual probe sequence for automated mapping
						  // 1st Text is DNA, 2nd is probe name
                       Sequence ?Sequence XREF RNAi  //links to a real Sequence object used in the experiment 
                                                     // such as yk clone; not UNIQUE anymore
                       PCR_product ?PCR_product XREF RNAi // links to a PCR_product object used in 
                                                          // the experiment; not UNIQUE anymore
       Uniquely_mapped  //boolean; if present, signifies that ?RNAi object has a unique sequence 
                        // which maps to a single place in the genome
       Experiment      Laboratory ?Laboratory
                       Author ?Author
                       Date UNIQUE DateType
                       Strain UNIQUE ?Strain
                       Genotype UNIQUE ?Text   //used when no Strain object exists
                       Treatment UNIQUE ?Text
                       Life_stage UNIQUE ?Life_stage
                       Temperature UNIQUE Int
                       Delivered_by UNIQUE Bacterial_feeding      //RL [010327]
                                           Injection              //RL [010327]
                                           Soaking                //RL [010327]
                                           Transgene_expression   //RL [010327]
       Inhibits        Predicted_gene ?CDS XREF RNAi_result #Evidence // "gene" parent (unreliable)
                       Gene ?Gene   XREF RNAi_result #Evidence           //RL [010327]
                       Transcript ?Transcript XREF RNAi_result #Evidence // [021126 krb]
                       Pseudogene ?Pseudogene XREF RNAi_result #Evidence // [030801 krb]
       Supporting_data Movie ?Movie XREF RNAi    // Lincoln, krb [010807]
                       Picture ?Picture XREF RNAi
       DB_info    Database ?Database ?Database_field ?Accession_number //to link out to Phenobank ar2 02-DEC-05 //removed UNIQUE as reqs multiple connections
       Species UNIQUE ?Species
       Gene_regulation ?Gene_regulation XREF RNAi  // this tag is used when an RNAi experiment describes gene regulation ar2 29-MAR-06 for igor
       Interaction ?Interaction
       Reference UNIQUE ?Paper XREF RNAi //[070215 ar2] made reference unique so Paper sort of equates to a Study class for Will S
       Phenotype ?Phenotype XREF RNAi #Phenotype_info
       Phenotype_not_observed ?Phenotype XREF Not_in_RNAi #Phenotype_info //added by Wen to separate Not phenotype from real phenotypes
       Expr_profile ?Expr_profile XREF RNAi_result // connection added during build [030106 krb]
       Remark ?Text #Evidence
       Method UNIQUE ?Method

RNAi Curation Standard Operating Procedure (SOP)

In order to ensure consistency of RNAi curation across curators and WormBase releases, a set of standard procedures for RNAi curation are outlined below. The descriptions of these procedures include use of the two main methods for generating *.ace files for release submission: (1) the web-based CGI form for one-at-a-time RNAi object generation and (2) the batch form submission method.

Minimum Requirements for an RNAi Object

Regardless of which curation method you (the curator) choose, there are a set of minimum requirements in order to generate a complete RNAi experiment object:

1) A reference (WBPaperID)

2) A curator name

3) The sequence of the dsRNA used in the experiment to knockdown gene expression

4) A phenotype (observed or not_observed)

Without any one of these four basic pieces of information, the scripts that generate the *.ace file will fail, returning an error.

Two Methods of Curation: Web CGI & Batch Form

Web-based CGI

The web-based RNAi curation form can be found at:

http://elbrus.caltech.edu/cgi-bin/igor/rnaitools/rnai_curation

The first page of the web form looks like this:

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This page requests information about the paper (e.g. WBPaperID), laboratory (usually senior/corresponding author; for a list of all labs two-letter codes look here: http://www.wormbase.org/db/misc/laboratory?name=*;class=laboratory), date of publication (accepted date), and a curator name.