Seeing transcription in real time
Lenstra TL
Nat Rev Mol Cell Biol. 2024 Apr 5; doi: 10.1038/s41580-024-00731-1.
Transcription factor exchange enables prolonged transcriptional bursts
Pomp W, Meeussen JVW, Lenstra TL
Mol Cell. 2024 Mar 21;84(6):1036-1048.e9. doi: https://doi.org/10.1016/j.molcel.2024.01.020.
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Time will tell: comparing timescales to gain insight into transcriptional bursting
Meeussen JVW, Lenstra TL
Trends Genet. 2024 Feb;40(2):160-174. doi: 10.1016/j.tig.2023.11.003.
Measuring Transcription Dynamics of Individual Genes Inside Living Cells
Brouwer I, de Kort MAC, Lenstra TL
Methods Mol Biol. 2024;2694:235-265. doi: 10.1007/978-1-0716-3377-9_12.
Locus-specific proteome decoding reveals Fpt1 as a chromatin-associated negative regulator of RNA polymerase III assembly
van Breugel ME, van Kruijsbergen I, Mittal C, Lieftink C, Brouwer I, van den Brand T, Kluin RJC, Hoekman L, Menezes RX, van Welsem T, Del Cortona A, Malik M, Beijersbergen RL, Lenstra TL, Verstrepen KJ, Pugh BF, van Leeuwen F.
Mol Cell. 2023 Dec 7;83(23):4205-4221.e9. doi: 10.1016/j.molcel.2023.10.037. Epub 2023 Nov 22.
Transcription factor clusters enable target search but do not contribute to target gene activation
Meeussen JVW, Pomp W, Brouwer I, de Jonge WJ, Patel HP, Lenstra TL
Nucleic Acids Res. 2023 Jun 23;51(11):5449-5468. doi: 10.1093/nar/gkad227.
DNA supercoiling restricts the transcriptional bursting of neighboring eukaryotic genes
Patel HP, Stefano Coppola S, Pomp W, Aiello U, Brouwer I, Libri D,
Lenstra TL
Mol Cell. 2023 May 18;83(10):1573-1587.e8. doi: 10.1016/j.molcel.2023.04.015.
Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting
Brouwer I, Kerklingh E, van Leeuwen F, Lenstra TL
Nat Struct Mol Biol. 2023 May;30(5):692-702. doi: 10.1038/s41594-023-00981-1. Epub 2023 May 1.
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Competition between transcription and loop extrusion modulates promoter and enhancer dynamics
Platania A, Erb C, Barbieri M, Molcrette B, Grandgirard E, de Kort MA, Meaburn K, Taylor T, Shchuka VM, Kocanova S, Monteiro Oliveira G, Mitchell JA, Soutoglou E, Lenstra TL, Molina N, Papantonis A, Bystricky K, Sexton T.
bioRxiv. 2023 Apr 26:2023.04.25.538222. doi: 10.1101/2023.04.25.538222. Preprint.
Quantifying how post-transcriptional noise and gene copy number variation bias transcriptional parameter inference from mRNA distributions
Fu X*, Patel HP*, Coppola S, Xu L, Cao Z#, Lenstra TL#, Grima R#
Elife. 2022 Oct 17;11:e82493. doi: 10.7554/eLife.82493.
*Co-first #Co-last
Transcriptional regulation and chromatin architecture maintenance are decoupled functions at the Sox2 locus
Taylor T, Sikorska N, Shchuka VM, Chahar S, Ji C, Macpherson NN, Moorthy SD, de Kort MAC, Mullany S, Khader N, Gillespie ZE, Langroudi L, Tobias IC, Lenstra TL, Mitchell JA, Sexton T.
Genes Dev. 2022 Jun 1;36(11-12):699-717. doi: 10.1101/gad.349489.122. Epub 2022 Jun 16.
Following the tracks: How transcription factor binding dynamics control transcription
de Jonge WJ*, Patel HP*, Meeussen JVW, Lenstra TL
Biophys J. 2022 May 3;121(9):1583-1592. doi: 10.1016/j.bpj.2022.03.026. Epub 2022 Mar 23.
*These authors contributed equally
Transcription-replication coordination revealed in single live cells
Tsirkas I, Dovrat D, Thangaraj M, Brouwer I, Cohen A, Paleiov Z, Meijler MM, Lenstra TL, Aharoni A
Nucleic Acids Res. 2022 Feb 28;50(4):2143-2156. doi: 10.1093/nar/gkac069.
The Hda1 histone deacetylase limits divergent non-coding transcription and restricts transcription initiation frequency
Gowthaman U, Ivanov M, Schwarz I, Patel HP, Müller NA, García-Pichardo D, Lenstra TL, Marquardt S
EMBO J. 2021 Dec 1;40(23):e108903. doi: 10.15252/embj.2021108903. Epub 2021 Oct 18.
Optimized protocol for single-molecule RNA FISH to visualize gene expression in S. cerevisiae
Patel HP, Brouwer I, Lenstra TL
STAR Protoc. 2021 Jul 6;2(3):100647. doi: 10.1016/j.xpro.2021.100647. eCollection 2021 Sep 17.
Single-Molecule Fluorescence Imaging in Living Saccharomyces cerevisiae Cells
Brouwer I, Patel HP, Meeussen JVW, Pomp W, Lenstra TL
STAR Protoc. 2020 Oct 17;1(3):100142. doi: 10.1016/j.xpro.2020.100142. eCollection 2020 Dec 18.
RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting
Quintero-Cadena P, Lenstra TL, Sternberg PW
Mol Cell. 2020 Jul 16;79(2):207-220.e8. doi: 10.1016/j.molcel.2020.05.030. Epub 2020 Jun 15.
Live-cell imaging reveals the
interplay between transcription factors, nucleosomes, and bursting.
Donovan BT, Huynh A, Ball BA, Patel HP, Poirier MG, Larson DR, Ferguson ML*, Lenstra TL*.
EMBO J. 2019 Jun 17;38(12). pii: e100809. doi: 10.15252/embj.2018100809. Epub 2019 May 17.
*These
authors contributed equally
Dot1 promotes H2B ubiquitination
by a methyltransferase-independent mechanism.
van Welsem T, Korthout T, Ekkebus R, Morais D,
Molenaar TM, van Harten K, Poramba-Liyanage DW, Sun SM, Lenstra TL, Srivas R, Ideker T, Holstege FCP,
van Attikum H, El Oualid F, Ovaa H, Stulemeijer IJE, Vlaming H, van Leeuwen F.
Nucleic Acids Res.
2018 Nov 30;46(21):11251-11261. doi: 10.1093/nar/gky801.
Single-Molecule Imaging Reveals a
Switch between Spurious and Functional ncRNA Transcription.
Lenstra TL, Coulon A, Chow CC,
Larson DR.
Mol Cell. 2015 Nov 19;60(4):597-610. doi: 10.1016/j.molcel.2015.09.028. Epub 2015 Nov 5.
Transcription Dynamics in Living
Cells.
Lenstra TL, Rodriguez J, Chen H, Larson DR.
Annu Rev Biophys. 2016 Jul 5;45:25-47.
doi: 10.1146/annurev-biophys-062215-010838. Epub 2016 Apr 27.
Single-Molecule mRNA Detection in
Live Yeast.
Lenstra TL, Larson DR.
Curr Protoc Mol Biol. 2016;113:14.24.1-14.24.15. Epub
2016 Jan 4.
A high-resolution gene expression
atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic
interactions.
Sameith K, Amini S, Groot Koerkamp MJ, van Leenen D, Brok M, Brabers N, Lijnzaad
P, van Hooff SR, Benschop JJ, Lenstra TL, Apweiler E, van Wageningen S, Snel B, Holstege FC, Kemmeren P.
BMC Biol. 2015 Dec 23;13:112. doi: 10.1186/s12915-015-0222-5.
Cell cycle population effects in
perturbation studies.
O'Duibhir E, Lijnzaad P, Benschop JJ, Lenstra TL, van Leenen D, Groot
Koerkamp MJ, Margaritis T, Brok MO, Kemmeren P, Holstege FC.
Mol Syst Biol. 2014 Jun 21;10:732. doi:
10.15252/msb.20145172.
Large-scale genetic perturbations
reveal regulatory networks and an abundance of gene-specific repressors.
Kemmeren P*, Sameith
K*, van de Pasch LA*, Benschop JJ*, Lenstra TL*, Margaritis T*, O'Duibhir E, Apweiler E, van Wageningen
S, Ko CW, van Heesch S, Kashani MM, Ampatziadis-Michailidis G, Brok MO, Brabers NA, Miles AJ,
Bouwmeester D, van Hooff SR, van Bakel H, Sluiters E, Bakker LV, Snel B, Lijnzaad P, van Leenen D, Groot
Koerkamp MJ, Holstege FC.
Cell. 2014 Apr 24;157(3):740-52. doi: 10.1016/j.cell.2014.02.054.
*These
authors contributed equally
The role of Ctk1 kinase in
termination of small non-coding RNAs.
Lenstra TL*, Tudek A*, Clauder S, Xu Z, Pachis ST, van
Leenen D, Kemmeren P, Steinmetz LM, Libri D, Holstege FC.
PLoS One. 2013 Dec 4;8(12):e80495. doi:
10.1371/journal.pone.0080495. eCollection 2013.
*These authors contributed equally
Kinetochore function and chromosome
segregation rely on critical residues in histones H3 and H4 in budding yeast.
Ng TM, Lenstra TL,
Duggan N, Jiang S, Ceto S, Holstege FC, Dai J, Boeke JD, Biggins S.
Genetics. 2013
Nov;195(3):795-807. doi: 10.1534/genetics.113.152082. Epub 2013 Sep 13.
Systematic triple-mutant analysis
uncovers functional connectivity between pathways involved in chromosome regulation.
Haber JE,
Braberg H, Wu Q, Alexander R, Haase J, Ryan C, Lipkin-Moore Z, Franks-Skiba KE, Johnson T, Shales M,
Lenstra TL, Holstege FC, Johnson JR, Bloom K, Krogan NJ.
Cell Rep. 2013 Jun 27;3(6):2168-78. doi:
10.1016/j.celrep.2013.05.007. Epub 2013 Jun 6.
A novel role for Sem1 and TREX-2 in
transcription involves their impact on recruitment and H2B deubiquitylation activity of SAGA.
García-Oliver E, Pascual-García P, García-Molinero V, Lenstra TL, Holstege FC, Rodríguez-Navarro S.
Nucleic Acids Res. 2013 Jun;41(11):5655-68. doi: 10.1093/nar/gkt272. Epub 2013 Apr 17.
Dysregulated RasGRP1 responds to
cytokine receptor input in T cell leukemogenesis.
Hartzell C, Ksionda O, Lemmens E, Coakley K,
Yang M, Dail M, Harvey RC, Govern C, Bakker J, Lenstra TL, Ammon K, Boeter A, Winter SS, Loh M, Shannon
K, Chakraborty AK, Wabl M, Roose JP.
Sci Signal. 2013 Mar 26;6(268):ra21. doi:
10.1126/scisignal.2003848.
The discrepancy between chromatin
factor location and effect.
Lenstra TL, Holstege FC.
Nucleus. 2012 May-Jun;3(3):213-9. doi:
10.4161/nucl.19513. Epub 2012 May 1.
A barcode screen for epigenetic
regulators reveals a role for the NuB4/HAT-B histone acetyltransferase complex in histone
turnover.
Verzijlbergen KF, van Welsem T, Sie D, Lenstra TL, Turner DJ, Holstege FC, Kerkhoven
RM, van Leeuwen F.
PLoS Genet. 2011 Oct;7(10):e1002284. doi: 10.1371/journal.pgen.1002284. Epub 2011
Oct 6.
The specificity and topology of
chromatin interaction pathways in yeast.
Lenstra TL, Benschop JJ, Kim T, Schulze JM, Brabers NA,
Margaritis T, van de Pasch LA, van Heesch SA, Brok MO, Groot Koerkamp MJ, Ko CW, van Leenen D, Sameith
K, van Hooff SR, Lijnzaad P, Kemmeren P, Hentrich T, Kobor MS, Buratowski S, Holstege FC.
Mol Cell.
2011 May 20;42(4):536-49. doi: 10.1016/j.molcel.2011.03.026.
Gcn4 misregulation reveals a direct
role for the evolutionary conserved EKC/KEOPS in the t6A modification of tRNAs.
Daugeron MC*,
Lenstra TL*, Frizzarin M, El Yacoubi B, Liu X, Baudin-Baillieu A, Lijnzaad P, Decourty L, Saveanu C,
Jacquier A, Holstege FC, de Crécy-Lagard V, van Tilbeurgh H, Libri D.
Nucleic Acids Res. 2011
Aug;39(14):6148-60. doi: 10.1093/nar/gkr178. Epub 2011 Apr 1.
*These authors contributed
equally
Dot1 binding induces chromatin
rearrangements by histone methylation-dependent and -independent mechanisms.
Stulemeijer IJ,
Pike BL, Faber AW, Verzijlbergen KF, van Welsem T, Frederiks F, Lenstra TL, Holstege FC, Gasser SM, van
Leeuwen F.
Epigenetics Chromatin. 2011 Feb 3;4(1):2. doi: 10.1186/1756-8935-4-2.
Functional overlap and regulatory
links shape genetic interactions between signaling pathways.
van Wageningen S, Kemmeren P,
Lijnzaad P, Margaritis T, Benschop JJ, de Castro IJ, van Leenen D, Groot Koerkamp MJ, Ko CW, Miles AJ,
Brabers N, Brok MO, Lenstra TL, Fiedler D, Fokkens L, Aldecoa R, Apweiler E, Taliadouros V, Sameith K,
van de Pasch LA, van Hooff SR, Bakker LV, Krogan NJ, Snel B, Holstege FC.
Cell. 2010 Dec
10;143(6):991-1004. doi: 10.1016/j.cell.2010.11.021.