Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells.

By Ryan D. Morin, Michael D. O’Connor, Malachi Griffith, F. Kuchenbauer, Allen D. Delaney, A. Prabhu, Yongjun Zhao, H. McDonald, Thomas Zeng, M. Hirst and 2 more. Genome Research, 2008

1,160 citations recorded by the source corpus.

MicroRNAs (miRNAs) are emerging as important, albeit poorly characterized, regulators of biological processes. Key to further elucidation of their roles is the generation of more complete lists of their numbers and expression changes in different cell states. Here, we report a new method for surveying the expression of small RNAs, including microRNAs, using Illumina sequencing technology. We also present a set of methods for annotating sequences deriving from known miRNAs, identifying variability in mature miRNA sequences, and identifying sequences belonging to previously unidentified miRNA genes. Application of this approach to RNA from human embryonic stem cells obtained before and after their differentiation into embryoid bodies revealed the sequences and expression levels of 334 known plus 104 novel miRNA genes. One hundred seventy-one known and 23 novel microRNA sequences exhibited significant expression differences between these two developmental states. Owing to the increased number of sequence reads, these libraries represent the deepest miRNA sampling to date, spanning nearly six orders of magnitude of expression. The predicted targets of those miRNAs enriched in either sample shared common features. Included among the high-ranked predicted gene targets are those implicated in differentiation, cell cycle control, programmed cell death, and transcriptional regulation.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/03d298f8231ed2b6548ff774803ab84e71edea88

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Citations in the corpus

Genetic variation in microRNA networks: the implications for cancer research (2010, positive): “Before their official annotation as 'isomiRs' by Morin et al”
Metazoan MicroRNAs (2018, background): “The exception is the MIR1306 gene (Friedlander et al., 2008; Morin et al., 2008), which was subsequently shown to be a negative-control element that overlaps the DGCR8 coding sequence (Han et al., 2009).”
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology (2008, methodology): “We present here an efficient application for use with chromatin-immunoprecipitation (ChIP-Seq) experimental data that includes novel functionality for identifying areas of gene enrichment and transcription factor binding site locations, as well as for estimating DNA fragment size distributions in…”
Evolution of microRNA diversity and regulation in animals (2011, background): “Mature miRNAs that are produced from the same hairpin but that differ in their termini are called isomiR”
MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells. (2009, positive): “More than 100 miRNAs are differentially expressed in human embryonic stem cells (hESCs) and the differentiated embryoid bodies (EBs) (Morin et al., 2008), but the genes targeted by most of these miRNAs are unknown.”
Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells (2008, methodology): “Effects on miRNA regulation were measured globally using quantitative sequencing of short RNAs (18–30 nucleotides) in these cells (Morin et al., 2008).”
Expression profiling of microRNAs by deep sequencing (2009, neutral): “DICER processing that has been typically reported for mature miRNAs [12], 3-base overhang on the 50-end and a 6-base overhang on the 30-end are allowed.”
MicroRNAs: key regulators of stem cells (2009, methodology): “In support of this, a recent miRNA sequencing effort using the Solexa sequencing technology ( Box 2 ) discovered several miRNAs in human ES cells that overlapped with those detected in mouse ES cells, and also with those that are differentially expressed between self-renewing and differentiating dau”
Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. (2008, background): “Deletion of Dicer in mouse ES cells (mESCs) results in severe proliferation and differentiation defects (Kanellopoulou et al. 2005; Murchison et al. 2005).”
Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA. (2008, background): “It has been reported that some miRNAs show sequence variations at the 30 ends, many of which have untemplated U additions (1 to 2 nt) (Landgraf et al., 2007; Morin et al., 2008; Seitz et al., 2008).”
Applications of next-generation sequencing technologies in functional genomics. (2008, methodology): “Our laboratory has recently used the Illumina technology to sequence small RNA libraries from human embryonic stem cells before and after their differentiation into embryonic bodies [30].”
Predicting effective microRNA target sites in mammalian mRNAs (2015, background): “In contrast, the seed backbone is pre-organized to favor A-form pairing, with bases of nucleotides 2–5 accessible to nucleate pairing ( Nakanishi et al., 2012 ; Schirle and MacRae, 2012 ).”