Literature DB >> 29130153

From Reductionism to Holism: Toward a More Complete View of Development Through Genome Engineering.

Rebecca K Delker1, Richard S Mann2.   

Abstract

Paradigm shifts in science are often coupled to technological advances. New techniques offer new roads of discovery; but, more than this, they shape the way scientists approach questions. Developmental biology exemplifies this idea both in its past and present. The rise of molecular biology and genetics in the late twentieth century shifted the focus from the anatomical to the molecular, nudging the underlying philosophy from holism to reductionism. Developmental biology is currently experiencing yet another transformation triggered by '-omics' technology and propelled forward by CRISPR genome engineering (GE). Together, these technologies are helping to reawaken a holistic approach to development. Herein, we focus on CRISPR GE and its potential to reveal principles of development at the level of the genome, the epigenome, and the cell. Within each stage we illustrate how GE can move past pure reductionism and embrace holism, ultimately delivering a more complete view of development.

Entities:  

Keywords:  CRISPR; Conrad H. Waddington; Development; Epigenome; Genome; Genome engineering; Holism; Reductionism

Mesh:

Year:  2017        PMID: 29130153      PMCID: PMC6935049          DOI: 10.1007/978-3-319-63904-8_3

Source DB:  PubMed          Journal:  Adv Exp Med Biol        ISSN: 0065-2598            Impact factor:   2.622


  170 in total

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Authors:  W T ASTBURY
Journal:  Nature       Date:  1961-06-17       Impact factor: 49.962

Review 2.  High-throughput screens in mammalian cells using the CRISPR-Cas9 system.

Authors:  Jingyu Peng; Yuexin Zhou; Shiyou Zhu; Wensheng Wei
Journal:  FEBS J       Date:  2015-03-16       Impact factor: 5.542

3.  Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9.

Authors:  Gozde Korkmaz; Rui Lopes; Alejandro P Ugalde; Ekaterina Nevedomskaya; Ruiqi Han; Ksenia Myacheva; Wilbert Zwart; Ran Elkon; Reuven Agami
Journal:  Nat Biotechnol       Date:  2016-01-11       Impact factor: 54.908

Review 4.  A mechanistic link between gene regulation and genome architecture in mammalian development.

Authors:  Giancarlo Bonora; Kathrin Plath; Matthew Denholtz
Journal:  Curr Opin Genet Dev       Date:  2014-07-05       Impact factor: 5.578

5.  3D imaging of Sox2 enhancer clusters in embryonic stem cells.

Authors:  Zhe Liu; Wesley R Legant; Bi-Chang Chen; Li Li; Jonathan B Grimm; Luke D Lavis; Eric Betzig; Robert Tjian
Journal:  Elife       Date:  2014-12-24       Impact factor: 8.140

6.  Versatile protein tagging in cells with split fluorescent protein.

Authors:  Daichi Kamiyama; Sayaka Sekine; Benjamin Barsi-Rhyne; Jeffrey Hu; Baohui Chen; Luke A Gilbert; Hiroaki Ishikawa; Manuel D Leonetti; Wallace F Marshall; Jonathan S Weissman; Bo Huang
Journal:  Nat Commun       Date:  2016-03-18       Impact factor: 14.919

7.  Simultaneous live imaging of the transcription and nuclear position of specific genes.

Authors:  Hiroshi Ochiai; Takeshi Sugawara; Takashi Yamamoto
Journal:  Nucleic Acids Res       Date:  2015-06-19       Impact factor: 16.971

8.  CRISPR RNA-guided activation of endogenous human genes.

Authors:  Morgan L Maeder; Samantha J Linder; Vincent M Cascio; Yanfang Fu; Quan H Ho; J Keith Joung
Journal:  Nat Methods       Date:  2013-07-25       Impact factor: 28.547

9.  RNA-guided gene activation by CRISPR-Cas9-based transcription factors.

Authors:  Pablo Perez-Pinera; D Dewran Kocak; Christopher M Vockley; Andrew F Adler; Ami M Kabadi; Lauren R Polstein; Pratiksha I Thakore; Katherine A Glass; David G Ousterout; Kam W Leong; Farshid Guilak; Gregory E Crawford; Timothy E Reddy; Charles A Gersbach
Journal:  Nat Methods       Date:  2013-07-25       Impact factor: 28.547

10.  Integration and exchange of split dCas9 domains for transcriptional controls in mammalian cells.

Authors:  Dacheng Ma; Shuguang Peng; Zhen Xie
Journal:  Nat Commun       Date:  2016-10-03       Impact factor: 14.919

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  3 in total

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Authors:  Roumen Voutev; Richard S Mann
Journal:  G3 (Bethesda)       Date:  2018-05-04       Impact factor: 3.154

Review 2.  Great future or greedy venture: Precision medicine needs philosophy.

Authors:  Fei Jiao; Ruoyu Guo; Jacques S Beckmann; Zhonghai Yan; Yun Yang; Jinxia Hu; Xin Wang; Shuyang Xie
Journal:  Health Sci Rep       Date:  2021-09-14

Review 3.  Epigenetic Studies of Chinese Herbal Medicine: Pleiotropic Role of DNA Methylation.

Authors:  Wenqian Guo; Han Ma; Chong-Zhi Wang; Jin-Yi Wan; Haiqiang Yao; Chun-Su Yuan
Journal:  Front Pharmacol       Date:  2021-12-07       Impact factor: 5.810

  3 in total

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