Transcription in Living Cells: Molecular Mechanisms of Bursting

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106

A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116

Differential expression analysis for sequence count data

Anders, S., & Huber, W. (2010) · Genome Biology · doi:10.1186/gb-2010-11-10-r106 · Cited by 15,581

Topological domains in mammalian genomes identified by analysis of chromatin interactions

Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829

Spatial partitioning of the regulatory landscape of the X-inactivation centre

Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

Lupiáñez, D. G., Kraft, K., Heinrich, V., Krawitz, P., Brancati, F., Klopocki, E., Horn, D., Kayserili, H., Opitz, J. M., Laxova, R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.004 · Cited by 2,132

Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution

Chen, B., Legant, W. R., Wang, K., Shao, L., Milkie, D. E., Davidson, M. W., Janetopoulos, C., Wu, X., Hammer, J. A., Liu, Z. J., et al. (2014) · Science · doi:10.1126/science.1257998 · Cited by 1,947

Cohesin Loss Eliminates All Loop Domains

Rao, S. S. P., Huang, S.-C., Glenn St Hilaire, B., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K.-R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.026 · Cited by 1,883

Supercoiling of the DNA template during transcription.

Liu, L. F., & Wang, J. C. (1987) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.84.20.7024 · Cited by 1,877

An oestrogen-receptor-α-bound human chromatin interactome

Fullwood, M. J., Liu, M. H., Pan, Y. F., Liu, J., Han, X., Mohamed, Y. B., Orlov, Y. L., Velkov, S., Ho, A., Poh, H. M., et al. (2009) · Nature · doi:10.1038/nature08497 · Cited by 1,752

The Interplay Between Postbiotics and Colorectal Cancer

Parameshwar, K., Kumar, C. K. A., Mohanalakshmi, S., Pathak, N., & Kalra, M. (2025) · Cancer drug discovery and develogment/Cancer drug discovery and development · doi:10.1007/978-3-031-86065-2_10

Single-cell Analysis of Attenuation-Driven Transcription Reveals New Principles of Bacterial Gene RegulationPreprint

Moradian, S., Ali, N., Jagadeesan, R., Behrends, V., Ribeiro, A. S., & Engl, C. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.06.680652

Inferring the burst dynamics of coupled self-feedback gene expression circuits based on single-cell data

Wang, J., Yin, Y., Cao, W., Qiu, H., & Zhang, B. (2025) · Physical review. E · doi:10.1103/4nt8-xgs6

Ubiquitous and Brain Cell-Type-Specific Promoters and Enhancers in Lentiviral Vectors

Matsuzaki, Y., Konno, A., & Hirai, H. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4807-0_7

Stochastic Gene Expression under Sequestration: Noise Reduction and Emergent DistributionsPreprint

Morozova, O., Oravcová, I., Zabaikina, I., Bokes, P., & Singh, A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.24.690157

Additional file 2 of Differentiation is accompanied by a progressive loss in transcriptional memory

Fourneaux, C., Racine, L., Koering, C., Dussurgey, S., Vallin, E., Moussy, A., Parmentier, R., Brunard, F., Stockholm, D., Modolo, L., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25389952

Additional file 8 of CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos

Huang, Y., Gao, B.-Q., Meng, Q., Yang, L.-Z., Ma, X.-K., Wu, H., Pan, Y.-H., Yang, L., Li, D., & Chen, L.-L. (2023) · Figshare · doi:10.6084/m9.figshare.22605988

Additional file 8 of Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network

Hunt, G., Vaid, R., Pirogov, S., Pfab, A., Ziegenhain, C., Sandberg, R., Reimegård, J., & Mannervik, M. (2024) · Figshare · doi:10.6084/m9.figshare.26658871

Additional file 3 of Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network

Hunt, G., Vaid, R., Pirogov, S., Pfab, A., Ziegenhain, C., Sandberg, R., Reimegård, J., & Mannervik, M. (2024) · Figshare · doi:10.6084/m9.figshare.26658856

Additional file 6 of Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network

Hunt, G., Vaid, R., Pirogov, S., Pfab, A., Ziegenhain, C., Sandberg, R., Reimegård, J., & Mannervik, M. (2024) · Figshare · doi:10.6084/m9.figshare.26658865

Additional file 1 of CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos

Huang, Y., Gao, B.-Q., Meng, Q., Yang, L.-Z., Ma, X.-K., Wu, H., Pan, Y.-H., Yang, L., Li, D., & Chen, L.-L. (2023) · Figshare · doi:10.6084/m9.figshare.22605964

Additional file 1 of Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network

Hunt, G., Vaid, R., Pirogov, S., Pfab, A., Ziegenhain, C., Sandberg, R., Reimegård, J., & Mannervik, M. (2024) · Figshare · doi:10.6084/m9.figshare.24934273

Additional file 2 of Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network

Hunt, G., Vaid, R., Pirogov, S., Pfab, A., Ziegenhain, C., Sandberg, R., Reimegård, J., & Mannervik, M. (2024) · Figshare · doi:10.6084/m9.figshare.24934634

Additional file 1 of Differentiation is accompanied by a progressive loss in transcriptional memory

Fourneaux, C., Racine, L., Koering, C., Dussurgey, S., Vallin, E., Moussy, A., Parmentier, R., Brunard, F., Stockholm, D., Modolo, L., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25389433

Additional file 7 of Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network

Hunt, G., Vaid, R., Pirogov, S., Pfab, A., Ziegenhain, C., Sandberg, R., Reimegård, J., & Mannervik, M. (2024) · Figshare · doi:10.6084/m9.figshare.26658868

Additional file 7 of CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos

Huang, Y., Gao, B.-Q., Meng, Q., Yang, L.-Z., Ma, X.-K., Wu, H., Pan, Y.-H., Yang, L., Li, D., & Chen, L.-L. (2023) · Figshare · doi:10.6084/m9.figshare.22605985

Additional file 4 of Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network

Hunt, G., Vaid, R., Pirogov, S., Pfab, A., Ziegenhain, C., Sandberg, R., Reimegård, J., & Mannervik, M. (2024) · Figshare · doi:10.6084/m9.figshare.26658859

Additional file 5 of Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network

Hunt, G., Vaid, R., Pirogov, S., Pfab, A., Ziegenhain, C., Sandberg, R., Reimegård, J., & Mannervik, M. (2024) · Figshare · doi:10.6084/m9.figshare.26658862

Discrete Modeling of Bursty Gene Expression in Single Cells and Growing Populations

Poljovka, J., Zabaikina, I., Bokes, P., & Singh, A. (2025) · IEEE Conference on Decision and Control (CDC) · doi:10.1109/cdc57313.2025.11312242

Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damagePreprint

Huang, Z., Luo, S., Wang, Z., Zhang, Z., Jiang, B., Nie, Q. H., & Zhang, J. (2026) · eLife · doi:10.7554/elife.100623.3

Mid-infrared light nonthermally produces anti-aging effects through cellular efficiency enhancement in living organismsPreprint

Shao, C., Peng, D., Zhao, Y., Shu, Y., Zhuang, S., Huang, Q., & Song, B. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.08.704722

Minute-scale coupling of chromatin marks and transcriptional burstsPreprint

Gao, X., Ko, C., Dong, Y., Fujii, T., Uchino, S., Kobayashi, Y., Harada, A., Ohishi, H., Ohkawa, Y., Kimurâ, H., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.08.704500 · Cited by 1

Rôle des partenaires de CTIP2 dans la latence post-intégrative du VIH-1 : importance de la voie SUMO

Assche, J. V. (2022) · theses.fr (ABES) · doi:10.70675/3cb6a549ze973z487dz98f4z6fbf5991098c

Mécanismes transcriptionnels et épigénétiques dans la régulation de l'expression du locus IgH murin au cours du développement des lymphocytes B

Oudinet, C. (2020) · theses.fr (ABES) · doi:10.70675/23318135zf12bz4a65z8f19z52bd3936b280

How do transcription and chromosomal context interfere with an efficient replication origin ?

Mandelbrojt, J. (2024) · doi:10.70675/c1242b9czb7daz44cez9f1cz64b284d42197

Mathematical modeling of gene expression in space and time

Douaihy, M. (2023) · theses.fr (ABES) · doi:10.70675/67c74725z37e4z4098zbc54z7723d45af5f9

Protocol for measuring endocrine-disruptive effects on transcriptional bursting using single-molecule imaging in human breast cancer cells

Yaşar, P., Day, C. R., & Rodriguez, J. (2026) · STAR Protocols · doi:10.1016/j.xpro.2026.104821

Premature transcription termination modulates stochastic gene expression in bacteria

Moradian, S., Ali, N., Jagadeesan, R., Behrends, V., Ribeiro, A. S., & Engl, C. (2026) · Science Advances · doi:10.1126/sciadv.aed0831

Transcriptional Bursting in Pluripotent Stem Cells

Lin, R., Liu, Y., & Wu, Q. (2026) · Biology · doi:10.3390/biology15120951

Transcription elongation mechanisms that control gene expression in erythropoiesis

Mukherjee, K., & Bieker, J. J. (2026) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2026.06.004

Invariant nonequilibrium dynamics in gene regulation optimize information flow

Zoller, B., Bénichou, A., Gregor, T., & Tkačik, G. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2524855123

Transcription factor clusters enhance gene expression in vivo without modulating bursting dynamics

Cadar, E., Birnie, A., Marsman, R., Grond, R., & Bothma, J. P. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.09.011

Quantitative Model of Transcriptional Noise Regulation by mRNA Condensates

Lanitis, A., & Kolomeisky, A. B. (2026) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.6c02757

A Journey with Enrico Gratton: Orbiting Around Bright Ideas and Fluorescent Molecules

Levi, V., Diaz, M. C., Lareu, A. V., & Presman, D. M. (2026) · Springer series on fluorescence · doi:10.1007/4243_2026_63

Mechanisms of transcription control by distal enhancers from single-gene nanoscopy

Cheng, L., De, C., Li, J., Korff, R., & Pertsinidis, A. (2026) · Cell · doi:10.1016/j.cell.2026.09.028 · Cited by 33

Visualizing transcription: key to understanding gene expression dynamics

Brouwer, I., & Lenstra, T. L. (2019) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2019.05.031 · Cited by 73

What makes genes burst

Sood, V., & Misteli, T. (2025) · Trends in Cell Biology · doi:10.1016/j.tcb.2025.08.004 · Cited by 5

Regulatory Mechanisms for Transcriptional Bursting Revealed by an Event-Based Model

Wu, R., Zhou, B., Wang, W., & Liu, F. (2023) · Research · doi:10.34133/research.0253 · Cited by 8

What Is a Transcriptional Burst?

Tunnacliffe, E., & Chubb, J. R. (2020) · Trends in Genetics · doi:10.1016/j.tig.2020.01.003 · Cited by 223

Unwinding transcriptional bursting

Lokody, I. B. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3800