RNA velocity-current challenges and future perspectives

被引：128

作者：

Bergen, Volker ^{[1
,2
]}

Soldatov, Ruslan A. ^{[3
]}

Kharchenko, Peter, V ^{[3
]}

Theis, Fabian J. ^{[1
,2
]}

机构：

[1] Helmholtz Ctr Munich, Inst Computat Biol, Munich, Germany

[2] Tech Univ Munich, Dept Math, Munich, Germany

[3] Harvard Med Sch, Dept Biomed Informat, Boston, MA 02115 USA

来源：

MOLECULAR SYSTEMS BIOLOGY | 2021年 / 17卷 / 08期

关键词：

challenges; dynamics; limitations; perspectives; RNA velocity; SINGLE-CELL; GENE-EXPRESSION;

D O I：

10.15252/msb.202110282

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

RNA velocity has enabled the recovery of directed dynamic information from single-cell transcriptomics by connecting measurements to the underlying kinetics of gene expression. This approach has opened up new ways of studying cellular dynamics. Here, we review the current state of RNA velocity modeling approaches, discuss various examples illustrating limitations and potential pitfalls, and provide guidance on how the ensuing challenges may be addressed. We then outline future directions on how to generalize the concept of RNA velocity to a wider variety of biological systems and modalities.

引用

页数：9

共 24 条

[1] Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation [J].

Barile, Melania ;

Imaz-Rosshandler, Ivan ;

Inzani, Isabella ;

Ghazanfar, Shila ;

Nichols, Jennifer ;

Marioni, John C. ;

Guibentif, Carolina ;

Gottgens, Berthold .

GENOME BIOLOGY, 2021, 22 (01)

[2] Sequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategies [J].

Battich, Nico ;

Beumer, Joep ;

de Barbanson, Buys ;

Krenning, Lenno ;

Baron, Chloe S. ;

Tanenbaum, Marvin E. ;

Clevers, Hans ;

van Oudenaarden, Alexander .

SCIENCE, 2020, 367 (6482) :1151-+

[3] Control of Transcript Variability in Single Mammalian Cells [J].

Battich, Nico ;

Stoeger, Thomas ;

Pelkmans, Lucas .

CELL, 2015, 163 (07) :1596-1610

[4] Generalizing RNA velocity to transient cell states through dynamical modeling [J].

Bergen, Volker ;

Lange, Marius ;

Peidli, Stefan ;

Wolf, F. Alexander ;

Theis, Fabian J. .

NATURE BIOTECHNOLOGY, 2020, 38 (12) :1408-1414

[5] Sci-fate characterizes the dynamics of gene expression in single cells [J].

Cao, Junyue ;

Zhou, Wei ;

Steemers, Frank ;

Trapnell, Cole ;

Shendure, Jay .

NATURE BIOTECHNOLOGY, 2020, 38 (08) :980-+

[6] scSLAM-seq reveals core features of transcription dynamics in single cells [J].

Erhard, Florian ;

Baptista, Marisa A. P. ;

Krammer, Tobias ;

Hennig, Thomas ;

Lange, Marius ;

Arampatzi, Panagiota ;

Juerges, Christopher S. ;

Theis, Fabian J. ;

Saliba, Antoine-Emmanuel ;

Doelken, Lars .

NATURE, 2019, 571 (7765) :419-+

[7] Diffusion pseudotime robustly reconstructs lineage branching [J].

Haghverdi, Laleh ;

Buettner, Maren ;

Wolf, F. Alexander ;

Buettner, Florian ;

Theis, Fabian J. .

NATURE METHODS, 2016, 13 (10) :845-+

[8] A Comparison of Deterministic and Stochastic Modeling Approaches for Biochemical Reaction Systems: On Fixed Points, Means, and Modes [J].

Hahl, Sayuri K. ;

Kremling, Andreas .

FRONTIERS IN GENETICS, 2016, 7

[9] RNA velocity of single cells [J].

La Manno, Gioele ;

Soldatov, Ruslan ;

Zeisel, Amit ;

Braun, Emelie ;

Hochgerner, Hannah ;

Petukhov, Viktor ;

Lidschreiber, Katja ;

Kastriti, Maria E. ;

Lonnerberg, Peter ;

Furlan, Alessandro ;

Fan, Jean ;

Borm, Lars E. ;

Liu, Zehua ;

van Bruggen, David ;

Guo, Jimin ;

He, Xiaoling ;

Barker, Roger ;

Sundstrom, Erik ;

Castelo-Branco, Goncalo ;

Cramer, Patrick ;

Adameyko, Igor ;

Linnarsson, Sten ;

Kharchenko, Peter V. .

NATURE, 2018, 560 (7719) :494-+

[10]

Lange M., 2020, PREPRINT BIORXIV, DOI [10.1101/2020.10.19.345983, DOI 10.1101/2020.10.19.345983]

← 1 2 3 →