Literature DB >> 24091454

Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics.

Carlos A Aguilar1, Harold G Craighead.   

Abstract

Deoxyribonucleic acid (DNA) is the blueprint on which life is based and transmitted, but the way in which chromatin - a dynamic complex of nucleic acids and proteins - is packaged and behaves in the cellular nucleus has only begun to be investigated. Epigenetic modifications sit 'on top of' the genome and affect how DNA is compacted into chromatin and transcribed into ribonucleic acid (RNA). The packaging and modifications around the genome have been shown to exert significant influence on cellular behaviour and, in turn, human development and disease. However, conventional techniques for studying epigenetic or conformational modifications of chromosomes have inherent limitations and, therefore, new methods based on micro- and nanoscale devices have been sought. Here, we review the development of these devices and explore their use in the study of DNA modifications, chromatin modifications and higher-order chromatin structures.

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Year:  2013        PMID: 24091454      PMCID: PMC4072028          DOI: 10.1038/nnano.2013.195

Source DB:  PubMed          Journal:  Nat Nanotechnol        ISSN: 1748-3387            Impact factor:   39.213


  124 in total

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Journal:  Nat Struct Biol       Date:  2001-07

2.  Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules.

Authors:  Stephen Winters-Hilt; Wenonah Vercoutere; Veronica S DeGuzman; David Deamer; Mark Akeson; David Haussler
Journal:  Biophys J       Date:  2003-02       Impact factor: 4.033

3.  Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions.

Authors:  Zhihu Zhao; Gholamreza Tavoosidana; Mikael Sjölinder; Anita Göndör; Piero Mariano; Sha Wang; Chandrasekhar Kanduri; Magda Lezcano; Kuljeet Singh Sandhu; Umashankar Singh; Vinod Pant; Vijay Tiwari; Sreenivasulu Kurukuti; Rolf Ohlsson
Journal:  Nat Genet       Date:  2006-10-08       Impact factor: 38.330

4.  Single-molecule analysis of DNA-protein complexes using nanopores.

Authors:  Breton Hornblower; Amy Coombs; Richard D Whitaker; Anatoly Kolomeisky; Stephen J Picone; Amit Meller; Mark Akeson
Journal:  Nat Methods       Date:  2007-03-04       Impact factor: 28.547

5.  Crystal structure of the nucleosome core particle at 2.8 A resolution.

Authors:  K Luger; A W Mäder; R K Richmond; D F Sargent; T J Richmond
Journal:  Nature       Date:  1997-09-18       Impact factor: 49.962

6.  High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states.

Authors:  Ronnie Blecher-Gonen; Zohar Barnett-Itzhaki; Diego Jaitin; Daniela Amann-Zalcenstein; David Lara-Astiaso; Ido Amit
Journal:  Nat Protoc       Date:  2013-02-21       Impact factor: 13.491

7.  Isolation and characterization of circulating tumor cells from patients with localized and metastatic prostate cancer.

Authors:  Shannon L Stott; Richard J Lee; Sunitha Nagrath; Min Yu; David T Miyamoto; Lindsey Ulkus; Elizabeth J Inserra; Matthew Ulman; Simeon Springer; Zev Nakamura; Alessandra L Moore; Dina I Tsukrov; Maria E Kempner; Douglas M Dahl; Chin-Lee Wu; A John Iafrate; Matthew R Smith; Ronald G Tompkins; Lecia V Sequist; Mehmet Toner; Daniel A Haber; Shyamala Maheswaran
Journal:  Sci Transl Med       Date:  2010-03-31       Impact factor: 17.956

8.  Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells.

Authors:  Patrick J Murphy; Benjamin R Cipriany; Christopher B Wallin; Chan Yang Ju; Kylan Szeto; James A Hagarman; Jaime J Benitez; Harold G Craighead; Paul D Soloway
Journal:  Proc Natl Acad Sci U S A       Date:  2013-04-22       Impact factor: 11.205

9.  Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition.

Authors:  Mari-Liis Visnapuu; Eric C Greene
Journal:  Nat Struct Mol Biol       Date:  2009-09-06       Impact factor: 15.369

10.  Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution.

Authors:  Hongcang Gu; Christoph Bock; Tarjei S Mikkelsen; Natalie Jäger; Zachary D Smith; Eleni Tomazou; Andreas Gnirke; Eric S Lander; Alexander Meissner
Journal:  Nat Methods       Date:  2010-01-10       Impact factor: 28.547

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  17 in total

1.  Electrophoretic stretching and imaging of single native chromatin fibers in nanoslits.

Authors:  Jia-Wei Yeh; Kylan Szeto
Journal:  Biomicrofluidics       Date:  2017-07-25       Impact factor: 2.800

2.  Translational Opportunities for Microfluidic Technologies to Enable Precision Epigenomics.

Authors:  Yi Xu; Steven R Doonan; Tamas Ordog; Ryan C Bailey
Journal:  Anal Chem       Date:  2020-06-04       Impact factor: 6.986

3.  Fracture fabrication of a multi-scale channel device that efficiently captures and linearizes DNA from dilute solutions.

Authors:  Byoung Choul Kim; Priyan Weerappuli; M D Thouless; Shuichi Takayama
Journal:  Lab Chip       Date:  2015-03-07       Impact factor: 6.799

4.  Internal Motion of Chromatin Fibers Is Governed by Dynamics of Uncompressed Linker Strands.

Authors:  Rajib Basak; William Rosencrans; Indresh Yadav; Peiyan Yan; Nikolay V Berezhnoy; Qinming Chen; Jeroen A van Kan; Lars Nordenskiöld; Anatoly Zinchenko; Johan R C van der Maarel
Journal:  Biophys J       Date:  2020-10-27       Impact factor: 4.033

Review 5.  Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices.

Authors:  Sanjay M Prakadan; Alex K Shalek; David A Weitz
Journal:  Nat Rev Genet       Date:  2017-04-10       Impact factor: 53.242

6.  Toward single-molecule optical mapping of the epigenome.

Authors:  Michal Levy-Sakin; Assaf Grunwald; Soohong Kim; Natalie R Gassman; Anna Gottfried; Josh Antelman; Younggyu Kim; Sam O Ho; Robin Samuel; Xavier Michalet; Ron R Lin; Thomas Dertinger; Andrew S Kim; Sangyoon Chung; Ryan A Colyer; Elmar Weinhold; Shimon Weiss; Yuval Ebenstein
Journal:  ACS Nano       Date:  2013-12-20       Impact factor: 15.881

Review 7.  Single molecule and single cell epigenomics.

Authors:  Byung-Ryool Hyun; John L McElwee; Paul D Soloway
Journal:  Methods       Date:  2014-09-07       Impact factor: 3.608

Review 8.  Analysis of single nucleic acid molecules in micro- and nano-fluidics.

Authors:  Sarah M Friedrich; Helena C Zec; Tza-Huei Wang
Journal:  Lab Chip       Date:  2016-03-07       Impact factor: 6.799

9.  Fracture-based micro- and nanofabrication for biological applications.

Authors:  Byoung Choul Kim; Christopher Moraes; Jiexi Huang; M D Thouless; Shuichi Takayama
Journal:  Biomater Sci       Date:  2014-03-01       Impact factor: 6.843

10.  Direct Analysis of Gene Synthesis Reactions Using Solid-State Nanopores.

Authors:  Spencer Carson; Scott T Wick; Peter A Carr; Meni Wanunu; Carlos A Aguilar
Journal:  ACS Nano       Date:  2015-11-20       Impact factor: 15.881

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