Table 1.

High-throughput sequencing strategies relevant to investigation of microRNA post-transcriptional function

Sequencing strategy	Feature analysed	Applications	Reference(s)
mRNA-Seq	Poly(A) RNA expression	Identification of mRNAs committed to degradation or upregulation with respect to miRNA expression.	Nagalakshmi et al. (136).
Small RNA-Seq	Small RNA expression	High-throughput, global quantification of mature miRNA.	Lu et al. (137); Hafner et al. (138).
Ribosome profiling (Ribo-Seq)	Active mRNA translation	Nucleotide resolution of actively translated mRNAs. May be integrated with mRNA expression to elucidate miRNA targets selectively regulated at the level of translation, particularly in the context of synaptic miRNA function.	Ingolia et al. (54).
Poly(A) tail sequencing (PAT-Seq)	mRNA poly(A) tail length mRNA 3′UTR usage	Resolves changes in mRNA poly(A) tail length which may be correlated with miRNA-induced 5′ to 3′ degradation. Additionally provides high-resolution analysis of alternate 3′ UTR sequences, which modifies abundance of miRNA binding sites.	Harrison et al. (139).
Cap analysis gene expression sequencing (CAGE-Seq)	mRNA 5′ extremity	Identification of miRNA binding sites housed within the mRNA 5′ UTR, which may have functional relevance for translational regulation.	Shiraki et al. (140); Takahashi et al., 2012 (141).
RNA immunoprecipitation sequencing (RIP-Seq)	Protein-associated RNA	May be utilized to identify mRNAs complexed with proteins known to associate with microRNA and regulate mRNA stability/translation (e.g. Ago2, FMRP, MOV10)	Keene et al. (142).
Cross-linking, ligation and sequencing of hybrids (CLASH-Seq)	mRNA-microRNA interactions	Direct quantitative analysis of mRNA-microRNA pairings.	Helwak et al. (143).
Mammalian native elongating transcript sequencing (mNET-Seq)	Nascent transcription	Integration with mRNA expression data for dissection of mRNAs subjected to upregulation via transcriptional activity and mRNAs upregulated through release from miRNA repression.	Nojima et al. (144).
Parallel analysis of RNA ends (PARE-Seq)	Degrading RNA	Identification of microRNA targets subjected to degradation.	German et al. (145).
m6A-methylated RNA sequencing (m6A-Seq)	m6A RNA methylation	Transcriptomic profiling of mRNA m6A methylation events, thought to have functional relevance for post-transcriptional miRNA regulation of mRNA.	Meyer et al. (146).
Circular RNA-Seq (Circ-Seq)	Expression of circular, RNAse R resistant RNA	Analysis and identification of circRNA with potential to function as microRNA sponges.	Memczak et al. (92); Nair et al. (147).