Molecular recording: transcriptional data collection into the genome.

CRISPR-Cas Systems DNA / genetics Genome / genetics Genomics Data Collection Gene Editing

Journal

Current opinion in biotechnology
ISSN: 1879-0429
Titre abrégé: Curr Opin Biotechnol
Pays: England
ID NLM: 9100492

Informations de publication

Date de publication:
02 2023
Historique:
received: 31 05 2022
revised: 08 11 2022
accepted: 14 11 2022
pmc-release: 01 02 2024
pubmed: 9 12 2022
medline: 8 2 2023
entrez: 8 12 2022
Statut: ppublish

Résumé

Advances in regenerative medicine depend upon understanding the complex transcriptional choreography that guides cellular development. Transcriptional molecular recorders, tools that record different transcriptional events into the genome of cells, hold promise to elucidate both the intensity and timing of transcriptional activity at single-cell resolution without requiring destructive multitime point assays. These technologies are dependent on DNA writers, which translate transcriptional signals into stable genomic mutations that encode the duration, intensity, and order of transcriptional events. In this review, we highlight recent progress toward more informative and multiplexable transcriptional recording through the use of three different types of DNA writing - recombineering, Cas1-Cas2 acquisition, and prime editing - and the architecture of the genomic data generated.

Identifiants

DOI: 10.1016/j.copbio.2022.102855 PMID: 36481341 PMC: PMC10547096
pubmed: 36481341
pii: S0958-1669(22)00189-6
doi: 10.1016/j.copbio.2022.102855
pmc: PMC10547096
mid: NIHMS1932549
pii:
doi:

Substances chimiques

DNA 9007-49-2

Types de publication

Journal Article Review Research Support, Non-U.S. Gov't Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

102855

Subventions

Organisme : NIGMS NIH HHS
ID : DP2 GM140917
Pays : United States

Informations de copyright

Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Références

Curr Opin Chem Biol. 2019 Oct;52:54-62
pubmed: 31200335
Nat Chem Biol. 2014 Dec;10(12):1020-7
pubmed: 25306443
Nature. 2017 Jan 5;541(7635):107-111
pubmed: 27869821
CRISPR J. 2022 Feb;5(1):31-39
pubmed: 35076284
Protein Cell. 2021 Nov;12(11):899-902
pubmed: 34403072
Nature. 2018 Oct;562(7727):380-385
pubmed: 30283135
Science. 2013 May 3;340(6132):599-603
pubmed: 23539178
Nat Biotechnol. 2021 Mar;39(3):320-325
pubmed: 33077959
Science. 2014 Nov 14;346(6211):1256272
pubmed: 25395541
Nat Commun. 2014 Oct 14;5:4729
pubmed: 25311543
Science. 2012 Aug 10;337(6095):746-9
pubmed: 22879516
Nat Chem Biol. 2022 Feb;18(2):199-206
pubmed: 34949838
Nucleic Acids Res. 2017 Jan 9;45(1):367-381
pubmed: 27899566
Nature. 2022 Aug;608(7921):217-225
pubmed: 35896746
Nat Methods. 2021 Jul;18(7):723-732
pubmed: 34155396
Science. 2016 Jul 22;353(6297):aad8559
pubmed: 27463678
Science. 2022 May 13;376(6594):eabm6038
pubmed: 35549411
Nature. 2022 Aug;608(7921):98-107
pubmed: 35794474
Nat Biotechnol. 2023 May;41(5):631-639
pubmed: 36593408
Nat Commun. 2020 Jan 7;11(1):95
pubmed: 31911609
Nat Biotechnol. 2013 May;31(5):448-52
pubmed: 23396014
Cell. 2018 Oct 4;175(2):544-557.e16
pubmed: 30245013
Nat Protoc. 2020 Feb;15(2):513-539
pubmed: 31925399
Science. 2016 Feb 26;351(6276):aad4234
pubmed: 26917774
Mol Cell. 2016 Jun 16;62(6):824-833
pubmed: 27211867
Sci Transl Med. 2015 May 27;7(289):289ra83
pubmed: 26019219
Nat Struct Mol Biol. 2014 Jun;21(6):528-34
pubmed: 24793649
Mol Syst Biol. 2016 May 17;12(5):869
pubmed: 27193783
Science. 2018 Apr 13;360(6385):
pubmed: 29449507
Nat Rev Neurosci. 2013 Nov;14(11):755-69
pubmed: 24105342
Nat Biotechnol. 2023 May;41(5):640-651
pubmed: 36593405
Nature. 2019 Dec;576(7785):149-157
pubmed: 31634902
Nat Biotechnol. 2017 May;35(5):453-462
pubmed: 28346402
Science. 2016 Sep 9;353(6304):
pubmed: 27540006
Nat Chem Biol. 2022 Jul;18(7):742-750
pubmed: 35637351
Nat Rev Genet. 2017 Apr;18(4):230-244
pubmed: 28111472
Nature. 2017 Jul 20;547(7663):345-349
pubmed: 28700573
Nat Chem Biol. 2021 Mar;17(3):246-253
pubmed: 33432236
Nat Chem Biol. 2021 Jun;17(6):739-747
pubmed: 33753928
Curr Opin Biomed Eng. 2017 Dec;4:143-151
pubmed: 29915814
Nat Methods. 2014 Dec;11(12):1261-6
pubmed: 25344638
Nucleic Acids Res. 2012 Jul;40(12):5569-76
pubmed: 22402487
Development. 2019 Jun 27;146(12):
pubmed: 31249005
Science. 2017 Dec 15;358(6369):1457-1461
pubmed: 29170279
Science. 2016 Jul 29;353(6298):aaf1175
pubmed: 27284167

Auteurs

Sierra K Lear (SK)

Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA; Graduate Program in Bioengineering, University of California, San Francisco and Berkeley, CA, USA.

Seth L Shipman (SL)

Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA. Electronic address: seth.shipman@gladstone.ucsf.edu.

Articles similaires

Comparative genomic analysis and characterization of novel high-quality draft genomes from the coal metagenome.

Arunmozhi Bharathi Achudhan, Lilly M Saleena
1.00
Coal Metagenome Phylogeny Bacteria Genome, Bacterial

Generation of isogenic models of Angelman syndrome and Prader-Willi syndrome in CRISPR/Cas9-engineered human embryonic stem cells.

Rachel B Gilmore, Dea Gorka, Christopher E Stoddard et al.
1.00
Prader-Willi Syndrome Humans Angelman Syndrome CRISPR-Cas Systems Human Embryonic Stem Cells

From cactus to crop: genomic insights of a beneficial and non-pathogenic Curtobacterium flaccumfaciens strain and the evolution of its pathosystem.

Dilson Fagundes Ribeiro, Jéssica Pereira de Matos, Lorrana Cachuite Mendes Rocha et al.
1.00
Genome, Bacterial Virulence Phylogeny Genomics Plant Diseases

Prediction of strain level phage-host interactions across the Escherichia genus using only genomic information.

Baptiste Gaborieau, Hugo Vaysset, Florian Tesson et al.
1.00
Host Specificity Bacteriophages Genomics Algorithms Escherichia coli

Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Épigenèse génétique › Extinction de l'expression des gènes › Systèmes CRISPR-Cas › Molecular recording: transcriptional data...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › Molecular recording: transcriptional data...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Molecular recording: transcriptional data...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › Molecular recording: transcriptional data...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Collecte de données › Molecular recording: transcriptional data...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Génie génétique › Édition de gène › Molecular recording: transcriptional data...