Genomics and Applied Biology 2018, Vol.9, No.10, 62-71
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researchers found the insertion mutation of a lncRNA, XLOC_057324, in the rice mutation database. Mutations at
the lncRNA insertion site resulted in a significant decrease in isoforms content of such lncRNA, leading to
phenotypic changes. Researchers planted the lncRNA mutant and wild type of ZH11 rice at the same time, and
found that the mutant rice bloomed earlier than the wild type, but the ears of the mutant rice were not significantly
as full as the wild type. The findings of this study fully proved that lncRNA (XLOC_057324) was involved in the
regulation of rice spike growth and development and was closely related to sexual reproduction of rice.
Latest researches have indicated that lncRNA also plays an important regulatory role in the growth and
development of soybeans. In a study on lncRNA in soybean, researchers found that lncRNA could be involved in
stress response, signal transduction and development process through co-expression analysis of protein-coding
genes and lncRNA. In addition, the researchers also observed the expression of lncRNA in centromere regions,
especially in active meristems, suggesting that lncRNA might be involved in the regulation of cell division.
4 Related Databases and Its Classification of LncRNA
4.1 LncRNA databases
With the wide spreading of lncRNA researches, a number of different organizations and academic research
institutes have established lncRNA databases in order to facilitate relevant researches and academic exchanges
(Amaral et al., 2011). The data of these databases are from a wide range of sources, of which some are from
published literature or directly from experiments, and are classified according to different species or different
research objects (Table 1).
Table 1 Classification of lncRNA databases
Database name
Characteristics
Website
Noncode
Established by Institute of Computing, Chinese Academy of Sciences, it is by far
the most complete database of non-coding RNA (Liu, 2004). When using this
database, there is a place that needs to be paid special attention. Since this
database uses a set of lncRNA naming system specified by itself, if the general
naming system is used to search in this database, the desired lncRNA cannot be
found. Here is a way to find the lncRNA we want in this database. Blast function
is provided in this database. If the user has the nucleic acid sequence of lncRNA,
the corresponding number of lncRNA in this database can be found according to
blast results, so as to further find the annotation information that the user wants.
lncRNADisease
The database collects more than 160 disease-related lncRNA and provides
annotations of disease-related lncRNA reported in literature (Chen et al., 2012).
It is worth mentioning that this database provides the function of browsing
lncRNA annotation information on the website, which makes it much easier for
us to annotate lncRNA.
ncrnadisease
CHIPBase
This database is significantly rich in content, so you can find a lot of lncRNA
comments here. This database also provides the loci that bind lncRNA and
expression map to transcription factors identified by RNA-seq (Yang et al.,
2013).
cn/chipbase/
lncRNAdb
The database collects eukaryotes lncRNA information that has been reported in
the literature. Each entry in the database contains reference information about
RNA, the expression of lncRNA, subcellular localization and conservative,
functional evidence and other relevant information. We can use the lncRNAdb
database to continuously proofread the literature related to lncRNA and other
genomic elements (Amaral et al., 2011).
/
4.2 LncRNA classification
There are many classification methods for lncRNA. lncRNA can be divided into the following categories
according to the relative positions of lncRNA in the genomes and exons (Figure 3). Sense lncRNA refers to
lncRNA that overlaps with one or more exons of the protein-coding gene of the chain in the same position.
