Capturing the 'ome': the Expanding Molecular Toolbox for RNA and DNA Library Construction

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2018 Mar 8

PMID 29514322

Citations 10

Authors

Morgane Boone

Andries De Koker

Nico Callewaert

Affiliations

Soon will be listed here.

Abstract

All sequencing experiments and most functional genomics screens rely on the generation of libraries to comprehensively capture pools of targeted sequences. In the past decade especially, driven by the progress in the field of massively parallel sequencing, numerous studies have comprehensively assessed the impact of particular manipulations on library complexity and quality, and characterized the activities and specificities of several key enzymes used in library construction. Fortunately, careful protocol design and reagent choice can substantially mitigate many of these biases, and enable reliable representation of sequences in libraries. This review aims to guide the reader through the vast expanse of literature on the subject to promote informed library generation, independent of the application.

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References

Wang K, Koop B, Hood L . A simple method using T4 DNA polymerase to clone polymerase chain reaction products. Biotechniques. 1994; 17(2):236-8. View

Levin J, Yassour M, Adiconis X, Nusbaum C, Thompson D, Friedman N . Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods. 2010; 7(9):709-15. PMC: 3005310. DOI: 10.1038/nmeth.1491. View

Raine A, Manlig E, Wahlberg P, Syvanen A, Nordlund J . SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing. Nucleic Acids Res. 2016; 45(6):e36. PMC: 5389478. DOI: 10.1093/nar/gkw1110. View

Williams R, Peisajovich S, Miller O, Magdassi S, Tawfik D, Griffiths A . Amplification of complex gene libraries by emulsion PCR. Nat Methods. 2006; 3(7):545-50. DOI: 10.1038/nmeth896. View

Arnoldo A, Kittanakom S, Heisler L, Mak A, Shukalyuk A, Torti D . A genome scale overexpression screen to reveal drug activity in human cells. Genome Med. 2014; 6(4):32. PMC: 4062067. DOI: 10.1186/gm549. View

Jayaprakash A, Jabado O, Brown B, Sachidanandam R . Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing. Nucleic Acids Res. 2011; 39(21):e141. PMC: 3241666. DOI: 10.1093/nar/gkr693. View

Gu W, Crawford E, ODonovan B, Wilson M, Chow E, Retallack H . Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Genome Biol. 2016; 17:41. PMC: 4778327. DOI: 10.1186/s13059-016-0904-5. View

Waaijers S, Koorman T, Kerver J, Boxem M . Identification of human protein interaction domains using an ORFeome-based yeast two-hybrid fragment library. J Proteome Res. 2013; 12(7):3181-92. DOI: 10.1021/pr400047p. View

Heather J, Chain B . The sequence of sequencers: The history of sequencing DNA. Genomics. 2015; 107(1):1-8. PMC: 4727787. DOI: 10.1016/j.ygeno.2015.11.003. View

10.

Lan J, Yin Y, Reed E, Moua K, Thomas K, Zhang Q . Impact of three Illumina library construction methods on GC bias and HLA genotype calling. Hum Immunol. 2014; 76(2-3):166-75. PMC: 5089167. DOI: 10.1016/j.humimm.2014.12.016. View

11.

Gohl D, Vangay P, Garbe J, MacLean A, Hauge A, Becker A . Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies. Nat Biotechnol. 2016; 34(9):942-9. DOI: 10.1038/nbt.3601. View

12.

Bhargava V, Ko P, Willems E, Mercola M, Subramaniam S . Quantitative transcriptomics using designed primer-based amplification. Sci Rep. 2013; 3:1740. PMC: 3638165. DOI: 10.1038/srep01740. View

13.

Wood W, Gitschier J, Lasky L, Lawn R . Base composition-independent hybridization in tetramethylammonium chloride: a method for oligonucleotide screening of highly complex gene libraries. Proc Natl Acad Sci U S A. 1985; 82(6):1585-8. PMC: 397316. DOI: 10.1073/pnas.82.6.1585. View

14.

Grothues D, Cantor C, Smith C . PCR amplification of megabase DNA with tagged random primers (T-PCR). Nucleic Acids Res. 1993; 21(5):1321-2. PMC: 309304. DOI: 10.1093/nar/21.5.1321. View

15.

Oyola S, Otto T, Gu Y, Maslen G, Manske M, Campino S . Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics. 2012; 13:1. PMC: 3312816. DOI: 10.1186/1471-2164-13-1. View

16.

Kivioja T, Vaharautio A, Karlsson K, Bonke M, Enge M, Linnarsson S . Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods. 2011; 9(1):72-4. DOI: 10.1038/nmeth.1778. View

17.

Honore B, Madsen P, Leffers H . The tetramethylammonium chloride method for screening of cDNA libraries using highly degenerate oligonucleotides obtained by backtranslation of amino-acid sequences. J Biochem Biophys Methods. 1993; 27(1):39-48. DOI: 10.1016/0165-022x(93)90066-w. View

18.

Shiroguchi K, Jia T, Sims P, Xie X . Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes. Proc Natl Acad Sci U S A. 2012; 109(4):1347-52. PMC: 3268301. DOI: 10.1073/pnas.1118018109. View

19.

Ho C, Wang L, Lima C, Shuman S . Structure and mechanism of RNA ligase. Structure. 2004; 12(2):327-39. DOI: 10.1016/j.str.2004.01.011. View

20.

Chapman A, He Z, Lu S, Yong J, Tan L, Tang F . Single cell transcriptome amplification with MALBAC. PLoS One. 2015; 10(3):e0120889. PMC: 4378937. DOI: 10.1371/journal.pone.0120889. View