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| NONCODE Classification |
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The
present or traditional classification of noncoding RNAs is more representative of the historical process by which the ncRNAs were discovered than by an integrated effort to create a uniform classification system. The more than 100 terms used in the literature to denote various groups of noncoding RNAs is therefore a jumble of unconnected concepts based on various and highly divergent criteria, such as cellular location (e.g. small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), small cytoplasmic RNAs (scRNAs), etc), cellular function (e.g. package RNAs (pRNAs), guide RNAs (gRNAs), or their sedimentation coefficient (4.5S RNA, 6S RNA etc). Furthermore, because of this lack of integration, one type of ncRNA often appears under several names or in more than one category.
In NONCODE we have concentrated our classification effort on the process in which a given ncRNA takes part, along with its function in this process. This has given rise to a classification system of at present 26 process function classes (pfclasses). However, even though the pfclass in most cases will cover the most interesting and useful aspect of an ncRNA, we have also subdivided the ncRNAs according to other criteria, as described below.
1. Process function class
The process function class (pfclass) of an ncRNA is based on the cellular process in which it takes part in(e.g DNA duplication, RNA replication, protein translation etc). In addition, a second term and third term specifying a sub-process or the specific function of the ncRNA, may be added to the term describing the main process. For example, the snRNA U1 will be assigned to the pfclass RNA processing_splicing, and Rnase P RNAs to the pfclass RNA processing_cleavage. Each ncRNA is assigned to one or more of 26 pfclasses
2. Molecular mechanism
The molecular mechanism attempt to describe what is the actual mode of action of an ncRNA. We identify five main types of molecular mechanisms:
- Watson-Crick homology (basepair), in which the sequence homology of the ncRNA to another cellular nucleic acid sequence is the main functional component of the ncRNA.
- Structural complementary (structureresemble) denotes that it is the secondary structure of the ncRNA that is responsible for the binding (or complementary) to another cellular component (e.g. a protein).
- Spatial blocking (block) implies that by its action, the ncRNA physically block the action of another cellular component (e.g. RNA polymerase transcription)
- Catalysis (catalyst), implying that the ncRNA acts as a ribozyme.
- Epimodification (epimodify) relates to the process (particularly in imprinting) where an RNA covers parts of a chromosome, thus leading to an epigenetic change.
3. Cellular location
The cellular location describes where in a cell the ncRNA predominantly acts, or is most prominently present. ncRNAs residing in viruses/viroids or their genomes have also been included.
4. Cellular role
The cellular role of an ncRNA (when known) has thus far only two denotations, either constituent or regulatory. The former refers to ncRNAs that are present in most cells at most times and under most condition (corresponds closely to the term "housekeeping" used for proteins), whereas the latter refers to ncRNAs that takes part in a process that is to a certain time, cell stage, cell type or tissue etc.
5. Specificity
A number of ncRNAs have certain features in common other than those covered by the criteria listed above. We have therefore also subdivided a subset of specific ncRNAs according to the information of whether they were disease related, transcribed from repeats or imprinted domains, stress induced or repressed, or specific to species, sex, tissue, or developmental stage.
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Any Problem Please Contact: lcn@ict.ac.cn
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