Advancing Small-Molecule-Based Chemical Biology with Next-Generation Sequencing Technologies

被引：22

作者：

Anandhakumar, Chandran ^{[1
]}

Kizaki, Seiichiro ^{[1
]}

Bando, Toshikazu ^{[1
]}

Pandian, Ganesh N. ^{[2
]}

Sugiyama, Hiroshi ^{[1
,2
]}

机构：

[1] Kyoto Univ, Dept Chem, Grad Sch Sci, Sakyo Ku, Kyoto 6068502, Japan

[2] Kyoto Univ, Inst Integrated Cell Mat Sci ICeMS, Sakyo Ku, Kyoto 6068501, Japan

来源：

CHEMBIOCHEM | 2015年 / 16卷 / 01期

关键词：

aptamers; chemical biology; genomics; next-generation sequencing; small molecules; DNA-BINDING MOLECULES; IN-VITRO SELECTION; GENE-EXPRESSION; CHIP-SEQ; SPATIAL-ORGANIZATION; APTAMER SELECTION; EMERGING CLASS; RNA MOLECULES; GROWTH-FACTOR; HIGH-AFFINITY;

D O I：

10.1002/cbic.201402556

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

Next-generation-sequencing (NGS) technologies enable us to obtain extensive information by deciphering millions of individual DNA sequencing reactions simultaneously. The new DNA-sequencing strategies exceed their precursors in output by many orders of magnitude, resulting in a quantitative increase in valuable sequence information that could be harnessed for qualitative analysis. Sequencing on this scale has facilitated significant advances in diverse disciplines, ranging from the discovery, design, and evaluation of many small molecules and relevant biological mechanisms to maturation of personalized therapies. NGS technologies that have recently become affordable allow us to gain in-depth insight into small-molecule-triggered biological phenomena and empower researchers to develop advanced versions of small molecules. In this review we focus on the overlooked implications of NGS technologies in chemical biology, with a special emphasis on small-molecule development and screening.

引用

页码：20 / 38

页数：19

共 146 条

[1]

Pyrosequencing: History, biochemistry and future [J].

Ahmadian, A ;

Ehn, M ;

Hober, S .

CLINICA CHIMICA ACTA, 2006, 363 (1-2) :83-94

[2]

DREME: motif discovery in transcription factor ChIP-seq data [J].

Bailey, Timothy L. .

BIOINFORMATICS, 2011, 27 (12) :1653-1659

[3]

Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? [J].

Balasubramanian, Shankar ;

Hurley, Laurence H. ;

Neidle, Stephen .

NATURE REVIEWS DRUG DISCOVERY, 2011, 10 (04) :261-275

[4]

G-quadruplex nucleic acids as therapeutic targets [J].

Balasubramanian, Shankar ;

Neidle, Stephen .

CURRENT OPINION IN CHEMICAL BIOLOGY, 2009, 13 (03) :345-353

[5]

Barnes C., 2002, US patent, Patent No. [7,057,026, 7057026]

[6]

The methylome: approaches for global DNA methylation profiling [J].

Beck, Stephan ;

Rakyan, Vardhman K. .

TRENDS IN GENETICS, 2008, 24 (05) :231-237

[7]

Spatial organization of the mammalian genome surveillance machinery in response to DNA strand breaks [J].

Bekker-Jensen, S ;

Lukas, C ;

Kitagawa, R ;

Melander, F ;

Kastan, MB ;

Bartek, J ;

Lukas, J .

JOURNAL OF CELL BIOLOGY, 2006, 173 (02) :195-206

[8]

Accurate whole human genome sequencing using reversible terminator chemistry [J].

Bentley, David R. ;

Balasubramanian, Shankar ;

Swerdlow, Harold P. ;

Smith, Geoffrey P. ;

Milton, John ;

Brown, Clive G. ;

Hall, Kevin P. ;

Evers, Dirk J. ;

Barnes, Colin L. ;

Bignell, Helen R. ;

Boutell, Jonathan M. ;

Bryant, Jason ;

Carter, Richard J. ;

Cheetham, R. Keira ;

Cox, Anthony J. ;

Ellis, Darren J. ;

Flatbush, Michael R. ;

Gormley, Niall A. ;

Humphray, Sean J. ;

Irving, Leslie J. ;

Karbelashvili, Mirian S. ;

Kirk, Scott M. ;

Li, Heng ;

Liu, Xiaohai ;

Maisinger, Klaus S. ;

Murray, Lisa J. ;

Obradovic, Bojan ;

Ost, Tobias ;

Parkinson, Michael L. ;

Pratt, Mark R. ;

Rasolonjatovo, Isabelle M. J. ;

Reed, Mark T. ;

Rigatti, Roberto ;

Rodighiero, Chiara ;

Ross, Mark T. ;

Sabot, Andrea ;

Sankar, Subramanian V. ;

Scally, Aylwyn ;

Schroth, Gary P. ;

Smith, Mark E. ;

Smith, Vincent P. ;

Spiridou, Anastassia ;

Torrance, Peta E. ;

Tzonev, Svilen S. ;

Vermaas, Eric H. ;

Walter, Klaudia ;

Wu, Xiaolin ;

Zhang, Lu ;

Alam, Mohammed D. ;

Anastasi, Carole .

NATURE, 2008, 456 (7218) :53-59

[9]

SELECTION OF SINGLE-STRANDED-DNA MOLECULES THAT BIND AND INHIBIT HUMAN THROMBIN [J].

BOCK, LC ;

GRIFFIN, LC ;

LATHAM, JA ;

VERMAAS, EH ;

TOOLE, JJ .

NATURE, 1992, 355 (6360) :564-566

[10]

Booth MJ, 2014, NAT CHEM, V6, P435, DOI [10.1038/NCHEM.1893, 10.1038/nchem.1893]

← 1 2 3 4 5 6 7 8 9 10 →