BACKGROUND: Over 10,000 long intergenic non-coding RNAs (lincRNAs) have been 
identified in the human genome. Some have been well characterized and known to 
participate in various stages of gene regulation. In the post-transcriptional 
process, another class of well-known small non-coding RNA, or microRNA (miRNA), 
is very active in inhibiting mRNA. Though similar features between mRNA and 
lincRNA have been revealed in several recent studies, and a few isolated 
miRNA-lincRNA relationships have been observed. Despite these advances, the 
comprehensive miRNA regulation pattern of lincRNA has not been clarified.
METHODS: In this study, we investigated the possible interaction between the two 
classes of non-coding RNAs. Instead of using the existing long non-coding 
database, we employed an ab initio method to annotate lincRNAs expressed in a 
group of normal breast tissues and breast tumors.
RESULTS: Approximately 90 lincRNAs show strong reverse expression correlation 
with miRNAs, which have at least one predicted target site presented. These 
target sites are statistically more conserved than their neighboring genetic 
regions and other predicted target sites. Several miRNAs that target to these 
lincRNAs are known to play an essential role in breast cancer.
CONCLUSION: Similar to inhibiting mRNAs, miRNAs show potential in promoting the 
degeneration of lincRNAs. Breast-cancer-related miRNAs may influence their 
target lincRNAs resulting in differential expression in normal and malignant 
breast tissues. This implies the miRNA regulation of lincRNAs may be involved in 
the regulatory process in tumor cells.