High-throughput multiplex sequencing of miRNA
High-throughput multiplex sequencing of miRNA
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Abstract
Next-Generation Sequencing offers many advantages over other methods of microRNA (miRNA)
expression profiling, such as sample throughput and the capability to discover novel miRNAs. As
the sequencing depth of current sequencing platforms exceeds what is necessary to quantify
miRNAs, multiplexing several samples in one sequencing run offers a significant cost advantage.
Although previous studies have achieved this goal by adding barcodes to miRNA libraries at the
ligation step, this was recently shown to introduce significant bias into the miRNA expression
data. This bias can be avoided, however, by barcoding the miRNA libraries at the PCR step
instead. Here, we describe a user-friendly PCR bar-coding method of preparing multiplexed
microRNA libraries for Illumina-based sequencing. The method also prevents the production of
adapter dimers and can be completed in one day.
Keywords
miRNA; Illumina; Sequencing; library; multiplex; bar code
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INTRODUCTION
MicroRNAs (miRNAs) are approximately 21–23 nucleotide RNAs that control the
expression of most genes. They are involved in many normal cellular processes and their
dysregulation has been implicated in many diseases (Kloosterman & Plasterk, 2006). Thus,
profiling miRNA expression is important for understanding biological processes, as well as
for the development of new diagnostic signatures and therapeutic targets. Next Generations
Sequencing (NGS) is currently the most comprehensive method for profiling miRNA
expression. In addition to avoiding issues with background and non-specific hybridization
found in alternative methods such as miRNA microarrays and qRT-PCR, NGS also allows
for the identification of new miRNAs or other small regulatory RNAs (Creighton, Reid, &
Gunaratne, 2009).
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BASIC PROTOCOL
MULTIPLEX microRNA LIBRARY CONSTRUCTION FOR ILLUMINA SEQUENCING
This procedure describes a method for constructing multiplexed miRNA libraries. A miRNA
library is made (Figure 1) from each RNA sample by 3’ adapter ligation, 5’ RT primer
annealing, 5’ adapter ligation, reverse transcription, and PCR amplification. Although the
forward PCR primer is the same, a different reverse PCR primer with a unique barcode is
used for each RNA sample. The different libraries can then be pooled into a single
sequencing reaction at the end of the library construction. The following instructions are for
the preparation of one sample, so users must scale-up according to the specific number of
samples they are preparing. All incubations are conducted in a thermal cycler.
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MATERIALS
RNase Zap (Ambion, AM9780)
Nuclease-free water (Ambion, AM9937)
10x T4 RNA Ligase 2tr (Enzymatics, L607)
10x T4 RNA Ligase 2tr Buffer (Enzymatics, L607)
100% DMSO (Sigma, D9170)
RNase Inhibitor (Enzymatics, Y924L)
ATP (Enzymatics, N207-10-L)
T4 RNA Ligase 1 (Enzymatics, L605L)
dNTPs (Enzymatics, N205L)
Superscript III First-Strand Synthesis System (Invitrogen, 180080-051)
Phusion High-Fidelity DNA Polymerase (NEB, M0530S)
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PROCEDURE
Ligation of 3’ adenylated adapter—Make sure to clean surfaces and instruments with
RNase Zap and maintain RNase-free conditions throughout the protocol. While as few as
100 ng of total RNA is sufficient, we recommend starting with at least 1 µg of total RNA
(one can also use the equivalent fraction of enriched for small RNAs if desired). We
recommend verifying RNA quality using the Agilent Bioanalyzer RNA nano or pico chip
and using samples of RIN value of 7 or above.
1| Dilute the starting RNA to 200 ng/µL in nuclease-free dH2O, if possible.
2| Set up ligation reaction in a PCR tube.
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Annealing of RT primer—
6| Add the following directly to each reaction on ice:
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The final amount of RT primer must be at equimolar ratio (10 pmoles) with the
starting amount of 3’rApp-adapter (10 pmoles) for each sample.
7| Incubate at 90°C for 30 sec, then 65°C for 5 min, then 4°C for at least 30 sec.
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100mM DTT 1 10 mM
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dH2O 27 To 50 ul total
Reverse Transcribed-miRNAs 10 -
5x HF buffer 10 1x
25 µM BCmiRNA_PCR1 1 0.5 µM
25 µM BCmiRNA_PCR2_BC* 1 0.5 µM
The number of cycles can be varied according to the amount of microRNA present in the
starting sample. In our hands, a total of 12 cycles generally results in the best yield while
limiting unnecessary cycling. We recommend not exceeding 15 cycles as this will increase
non-specific background amplification and reduce optimal yield of the desired products.
Instead, additional starting RNA should be prepared in parallel and combined at the final
stage to increase yield.
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COMMENTARY
BACKGROUND INFORMATION
Most commercially-available kits for NGS have followed the same general method (Thomas
& Ansel, 2010) of preparing miRNA libraries, similar to that used to make a miRNA library
for shotgun sequencing (Lau, Lim, Weinstein, & Bartel, 2001). First, a 3’ adenylated DNA
adapter is ligated to the total pool of miRNAs in the absence of ATP. Using an adenylated
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primers complementary to the 5’ and 3’ adapters. The PCR product is run out by gel
electrophoresis and the appropriate band can be excised. One issue with this approach is that
excess of 5’ adapter can ligates directly to the excess of 3’ adapter, and this adapter dimer
gets PCR amplified to be the predominant product in the library.
We have previously reported that one efficient way of removing this adapter dimer was to
conduct two denaturing PAGE extractions (Alon et al., 2011), but this is quite labor
intensive and time consuming. Other methods have been developed to reduce the formation
of this adapter dimers but with limited success (Kawano et al., 2010). Similarly to others
(NEB product E6120 and Bioscientific product 5132-02), we have noted that pre-annealing
the RT primer in between the 3’ adapter ligation and 5’ adapter ligation steps, as opposed to
doing so at the RT step, works efficiently to reduce adapter dimer. This works by making
the free 3’ adapter double stranded, thus preventing it from ligating to the single-stranded 5’
adapter.
Our protocol includes multiplexing of several miRNA samples in one sequencing reaction
with bar-coded PCR primers. Considering the high sequencing capacity of one lane of a
flow cell on an Illumina machine, multiplexing can significantly reduce the cost of miRNA
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This library design allows for sequencing the miRNA on both the Illumina HiSeq and
GaIIX. Our preferred approach is to conduct a single pass sequencing of ~75 bp where the
miRNA is first sequenced, followed by a short portion of the 3’ adapter and then the bar-
code (as depicted in Figure 1). This is done using the standard Illumina sequencing primer
for genomic libraries (or TruSeq primer), making it convenient to share the same flow cell
with other type of libraries. Optionally, a custom indexing primer can also be used (see
Table 1), but this is usually a more expensive option as one as to cycle the full flow cell to
do so, which is rarely a requirement for most other customer sharing the run.
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ANTICIPATED RESULTS
Our protocol describes the preparation of multiplexed miRNA libraries for NGS. Following
library preparation, bar-coded samples are loaded on a 2% agarose gel (Figure 2), the
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miRNA fraction can then be separated from other RNAs by cutting the gel between 125 bp
and 175 bp. There should be little or no amplified adapter-dimer product (114 bp) visible on
the gel (Figure 3). Following gel extraction, the different bar-coded samples are mixed in
equal proportion and sequenced in one reaction on an Illumina machine (GAII, HiSeq2000).
A standard Illumina sequencing primer can be used to sequence both the miRNA and the
bar-code in one sequencing pass (we recommend using 75 bp sequencing pass) or the bar
code can be sequenced separately with a different custom indexing primer.
TIME CONSIDERATIONS
This protocol can be completed in one day.
Steps 1–5: 1 Hour 30 Minutes
Steps 6–7: 10 Minutes
Steps 8–10: 1 Hour 15 Minutes
Steps 11–12: 45 Minutes
Steps 15–27: 20 Minutes
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Acknowledgments
This work was supported by the Center for Excellence in Genome Sciences grant from the National Human
Genome Research Institute. F.V. is supported by a Canadian Institutes of Health Research and Ragon Institute
Fellowship. J.G.S is supported by grants from the NIH, NHLBI, the SysCODE Consortium (NIH) and the
FondationLeducq. D.T. is supported by the Mazur Fellowship and the NIH Training Grant “Joint Program in Cells,
Molecules, and Organisms.” This work was partially supported by a grant from the United States-Israel Binational
Science Foundation (grant no. 2009290), Jerusalem, Israel.
Literature Cited
Alon S, Vigneault F, Eminaga S, Christodoulou DC, Seidman JG, Church GM, Eisenberg E.
Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome research. 2011; 21(9):
1506–1511. [PubMed: 21750102]
Creighton CJ, Reid JG, Gunaratne PH. Expression profiling of microRNAs by deep sequencing.
Briefings in bioinformatics. 2009; 10(5):490–497. [PubMed: 19332473]
NIH-PA Author Manuscript
Hafner M, Renwick N, Brown M, Mihailoviæ A, Holoch D, Lin C, Pena JTG, et al. RNA-ligase-
dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA
(New York NY). 2011; 17(9):1697–1712.
Kawano M, Kawazu C, Lizio M, Kawaji H, Carninci P, Suzuki H, Hayashizaki Y. Reduction of non-
insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing.
BioTechniques. 2010; 49(4):751–755. [PubMed: 20964636]
Kloosterman WP, Plasterk RHA. The diverse functions of microRNAs in animal development and
disease. Developmental cell. 2006; 11(4):441–450. [PubMed: 17011485]
Lau NC, Lim LP, Weinstein EG, Bartel DP. An abundant class of tiny RNAs with probable regulatory
roles in Caenorhabditis elegans. Science. 2001; 294(5543):858–862. [PubMed: 11679671]
Tarasov V, Jung P, Verdoodt B, Lodygin D, Epanchintsev A, Menssen A, Meister G, et al. Differential
regulation of microRNAs by p53 revealed by massively parallel sequencing: miR-34a is a p53
target that induces apoptosis and G1-arrest. Cell cycle (Georgetown, Tex.). 2007; 6(13):1586–1593.
Thomas MF, Ansel KM. Construction of small RNA cDNA libraries for deep sequencing. Methods in
molecular biology (Clifton, N.J.). 2010; 667:93–111.
Curr Protoc Hum Genet. Author manuscript; available in PMC 2013 June 05.
Vigneault et al. Page 9
Uziel T, Karginov FV, Xie S, Parker JS, Wang Y-D, Gajjar A, He L, et al. The miR-17~92 cluster
collaborates with the Sonic Hedgehog pathway in medulloblastoma. Proceedings of the National
Academy of Sciences of the United States of America. 2009; 106(8):2812–2817. [PubMed:
NIH-PA Author Manuscript
19196975]
Vigneault F, Sismour AM, Church GM. Efficient microRNA capture and bar-coding via enzymatic
oligonucleotide adenylation. Nature methods. 2008; 5(9):777–779. [PubMed: 19160512]
Zhu JY, Pfuhl T, Motsch N, Barth S, Nicholls J, Grässer F, Meister G. Identification of novel Epstein-
Barr virus microRNA genes from nasopharyngeal carcinomas. Journal of virology. 2009; 83(7):
3333–3341. [PubMed: 19144710]
Zhu Q-H, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C. A diverse set of
microRNAs and microRNA-like small RNAs in developing rice grains. Genome research. 2008;
18(9):1456–1465. [PubMed: 18687877]
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Figure 1.
Schematic Illustration of the miRNA library preparation steps. 3’adapter is first ligated to
the total RNA (steps 1–5) followed by RT primer annealing (steps 6–7) and 5’adapter
ligation (steps 8–10 ). The sample is then revere transcribed (steps 11–12) and PCR enriched
using bar-coded primers (steps 13–27) and is then ready for gel extraction of the miRNA
library fraction and QC (steps 28–36). The library is now ready for high-throughput
sequencing using either a single pass or custom indexing sequencing.
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Figure 2.
Final miRNA library analyzed on 2% agarose gel. Following the PCR and clean up steps,
half of the final miRNA is loaded on one lane of a 2% E-gel alongside 100 bp (lane 1) and
25 bp ladders (lane 2). The fraction corresponding to miRNA library to be sequenced was
extracted on a previous gel by cutting between 125 bp and 175 bp (lane 4) as described in
the procedures and also loaded alongside the non-extracted library as a visual reference and
expected recovery yield.
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Figure 3.
Adapter dimer consideration. Agarosegel comparing miRNA library preparation with RT
primer annealing after ligation of both 3’ and 5’ adapter as described previously5 (lane 3)
against miRNA library preparation with RT primer annealing after ligation of 3’ adapter
only, as described here (lane 4). The adapter dimer expected to migrate at 114 bp is shown
against the 100 bp (lane 1) and 25 bp ladder (lane 2). The adapter dimer is caused by ligation
of 5’adapter directly to the excess of 3’adapter without miRNA captured. Our current
protocol prevent the formation of this adapter dimer by annealing the RT primer to any
available 3’adapter, effectively making them double stranded and therefore a poor substrate
for subsequent 5’adapter ligation by T4 RNA Ligase 1.
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Table 1
List of Oligonucleotides:
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BCmiRNA_5'RNA-adapter rUrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrC
BCmiRNA_PCR1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
BCmiRNA_PCR2-BC1 CAAGCAGAAGACGGCATACGAGATCGATGTGCTCCACCGATAAATATTAGCCCGT
BCmiRNA_PCR2-BC2 CAAGCAGAAGACGGCATACGAGATTTAGGCGCTCCACCGATAAATATTAGCCCGT
BCmiRNA_PCR2-BC3 CAAGCAGAAGACGGCATACGAGATTGACCAGCTCCACCGATAAATATTAGCCCGT
BCmiRNA_PCR2-BC4 CAAGCAGAAGACGGCATACGAGATACGGTGGCTCCACCGATAAATATTAGCCCGT
BCmiRNA_PCR2-BC5 CAAGCAGAAGACGGCATACGAGATGCCAATGCTCCACCGATAAATATTAGCCCGT
BCmiRNA_PCR2-BC6 CAAGCAGAAGACGGCATACGAGATCAGATCGCTCCACCGATAAATATTAGCCCGT
BCmiRNA_PCR2-BC7 CAAGCAGAAGACGGCATACGAGATACTTGAGCTCCACCGATAAATATTAGCCCGT
BCmiRNA_PCR2-BC8 CAAGCAGAAGACGGCATACGAGATGATCAGGCTCCACCGATAAATATTAGCCCGT
BCmiRNA_PCR2-BC9 CAAGCAGAAGACGGCATACGAGATTAGCTTGCTCCACCGATAAATATTAGCCCGT
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BCmiRNA_PCR2-BC10 CAAGCAGAAGACGGCATACGAGATGGCTACGCTCCACCGATAAATATTAGCCCGT
BCmiRNA_PCR2-BC11 CAAGCAGAAGACGGCATACGAGATCTTGTAGCTCCACCGATAAATATTAGCCCGT
BCmiRNA_PCR2-BC12 CAAGCAGAAGACGGCATACGAGATATCACGGCTCCACCGATAAATATTAGCCCGT
Notes: All oligonucleotides can be ordered through Integrated DNA Technologies (IDT; http://www.idtdna.com), with HPLC purification. The bar-
codes are designed to be read in a single pass read, but a custom indexing primer can also be used if desired. The adenylated adapter can be ordered
from IDT, or if on a budget, made as previously described (Vigneault, Sismour, & Church, 2008).
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