Publications

2019

High-throughput identification of human SNPs affecting regulatory element activity
van Arensbergen J, Pagie L, FitzPatrick VD, de Haas M, Baltissen MP, Comoglio F, van der Weide RH, Teunissen H, Vosa U, Franke L, de Wit E, Vermeulen M, Bussemaker HJ, van Steensel B.
Nature Genetics 2019, advance online.

Promoter-intrinsic and local chromatin features determine gene repression in LADs.
Leemans C, van der Zwalm M, Brueckner L, Comoglio F, van Schaik T, Pagie L, van Arensbergen J, van Steensel B.
Cell 2019. 177:852-864

Rapid Quantitative Evaluation of CRISPR Genome Editing by TIDE and TIDER.
Brinkman EK, van Steensel B.
Methods Mol Biol. 2019;1961:29-44. doi: 10.1007/978-1-4939-9170-9_3.

The role of transcription in shaping the spatial organization of the genome. Review.
van Steensel B, Furlong EEM.
Nat Rev Mol Cell Biol. 2019; 20:327-337

2018

Easy quantification of template-directed CRISPR/Cas9 editing.
Brinkman EK, Kousholt AN, Harmsen T, Leemans C, Chen T, Jonkers J, van Steensel B.
Nucleic Acids Res. 2018;46:e58

Scientific honesty and publicly shared lab notebooks.
Van Steensel B.
EMBO Rep. 2018;19:e46866

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler.
Chen Y, Zhang Y, Wang Y, Zhang L, Brinkman EK, Adam SA, Goldman R, van Steensel B, Ma J, and Belmont AS.
J Cell Biol 2018;217:4025-4048

The large fraction of heterochromatin in Drosophila neurons is bound by both B-type lamin and HP1a.
Pindyurin AV, Ilyin AA, Ivankin AV, Tselebrovsky MV, Nenasheva VV, Mikhaleva EA, Pagie L, van Steensel B, and Shevelyov YY.
Epigenetics Chromatin 2018;11;65

CHRAC/ACF contribute to the repressive ground state of chromatin.
Scacchetti A, Brueckner L, Jain D, Schauer T, Zhang X, Schnorrer F, van Steensel B, Straub T, and Becker PB.
Life Sci Alliance 2018;1, e201800024

Kinetics and fidelity of the repair of Cas9-induced double-strand DNA breaks.
Brinkman EK, Chen T, de Haas M, Holland HA, Akhtar W, van Steensel B.
Mol Cell, 2018;70:801-813

DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis.
La Fortezza M, Grigolon G, Cosolo A, Pinduyrin A, Breimann L, Blum H, van Steensel B, Classen AK. Epigenetics Chromatin 2018;11:27

2017

Genome-wide mapping of autonomous promoter activity in human cells
Van Arensbergen J*, FitzPatrick VD, de Haas M, Pagie L, Sluimer J, Bussemaker HJ*, van Steensel B*. *co-corresponding authors
Nature Biotechnol. 2017 Feb;35(2):145-153

Genome – nuclear lamina interactions: from cell populations to single cells
Yáñez-Cuna JO, van Steensel B.
Curr Opin Genet Dev. 2017 Jan 17;43:67-72

2016

High-throughput assessment of context-dependent effects of chromatin proteins.
Brueckner L, van Arensbergen J, Akhtar W, Pagie L, van Steensel B.
Epigenetics & Chromatin 2016;9:43

A single double-strand break system reveals repair dynamics and mechanisms in heterochromatin and euchromatin.
Janssen A, Breuer GA, Brinkman EK, van der Meulen AI, Borden SV, van Steensel B, Bindra RS, LaRocque JR, Karpen GH.
Genes Dev. 2016;30:1645-1657

Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila
Pindyurin AV*, Pagie L, Kozhevnikova EN, van Arensbergen J, van Steensel B* (*co-corresponding authors)
Nucleic Acids Res. 2016;44:5646-57

2015

GENE REGULATION. A HUSH for transgene expression.
Brummelkamp TR, van Steensel B.
Science 2015;348:1433-1434

Genome-wide maps of nuclear lamina interactions in single human cells.
Kind J, Pagie L, de Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, de Graaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny LA, Jalink K, Dekker J, van Oudenaarden A, van Steensel B.
Cell 2015;163:134-147

Nuclear lamins are not required for lamina-associated domain organization in mouse embryonic stem cells.
Amendola M, van Steensel B.
EMBO Rep. 2015 Mar 17. pii: e201439789

A short guide to technology development in cell biology.
van Steensel B.
J Cell Biol. 208:655-657

2014

Differential spatial and structural organization of the X chromosome underlies dosage compensation in C. elegans.
Sharma R, Jost D, Kind J, Gómez-Saldivar G, van Steensel B, Askjaer P, Vaillant C, Meister P.
Genes Dev. 28:2591-2596

Easy quantitative assessment of genome editing by sequence trace decomposition.
Brinkman EK, Chen T, Amendola M, van Steensel B
Nucleic Acids Res. 42:e168

In search of the determinants of enhancer-promoter interaction specificity.
van Arensbergen J, van Steensel B, Bussemaker HJ.
Trends Cell Biol. 24:695-702

Using TRIP for genome-wide position effect analysis in cultured cells.
Akhtar W, Pindyurin AV, de Jong J, Pagie L, Ten Hoeve J, Berns A, Wessels LF, van Steensel B, van Lohuizen M.
Nat Protoc. 9:1255-1281

Domains of genome-wide gene expression dysregulation in Down’s syndrome.
Letourneau A, Santoni FA, Bonilla X, Sailani MR, Gonzalez D, Kind J, Chevalier C, Thurman R, Sandstrom RS, Hibaoui Y, Garieri M, Popadin K, Falconnet E, Gagnebin M, Gehrig C, Vannier A, Guipponi M, Farinelli L, Robyr D, Migliavacca E, Borel C, Deutsch S, Feki A, Stamatoyannopoulos JA, Herault Y, van Steensel B, Guigo R, Antonarakis SE.
Nature 508:345-350

Stochastic genome-nuclear lamina interactions: Modulating roles of Lamin A and BAF.
van Steensel B, Kind J.
Nucleus 5(2)

Mechanisms and dynamics of nuclear lamina-genome interactions.
Amendola M, van Steensel B.
Curr Opin Cell Biol. 28C:61-68

2013

Chromatin position effects assayed by thousands of reporters integrated in parallel.
Akhtar W, de Jong J, Pindyurin AV, Pagie L, Meuleman W, de Ridder J, Berns A, Wessels LF, van Lohuizen M, van Steensel B.
Cell. 2013 Aug 15;154(4):914-27

Differential programming of B cells in AID deficient mice.
Hogenbirk MA, Heideman MR, Velds A, van den Berk PC, Kerkhoven RM, van Steensel B, Jacobs H.
PLoS One. 2013 Jul 29;8(7):e69815

The genomic landscape of the somatic linker histone subtypes H1.1 to H1.5 in human cells.
Izzo A, Kamieniarz-Gdula K, Ramírez F, Noureen N, Kind J, Manke T, van Steensel B, Schneider R.
Cell Rep. 2013 Jun 27;3(6):2142-54

Single-cell dynamics of genome-nuclear lamina interactions.
Kind J, Pagie L, Ortabozkoyun H, Boyle S, de Vries SS, Janssen H, Amendola M, Nolen LD, Bickmore WA, van Steensel B.
Cell. 2013 Mar 28;153(1):178-92

Genome architecture: domain organization of interphase chromosomes.
Bickmore WA, van Steensel B.
Cell. 2013 Mar 14;152(6):1270-84

A network model of the molecular organization of chromatin in Drosophila.
van Bemmel JG, Filion GJ, Rosado A, Talhout W, de Haas M, van Welsem T, van Leeuwen F, van Steensel B.
Mol Cell. 2013 Feb 21;49(4):759-71

Cromatin organization: form to function.
de Graaf CA, van Steensel B.
Curr Opin Genet Dev. 2013 Apr;23(2):185-90

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence.
Meuleman W, Peric-Hupkes D, Kind J, Beaudry JB, Pagie L, Kellis M, Reinders M, Wessels L, van Steensel B.
Genome Res. 2013 Feb;23(2):270-80

2012

Glucosylated hydroxymethyluracil, DNA base J, prevents transcriptional readthrough in Leishmania.
van Luenen HG, Farris C, Jan S, Genest PA, Tripathi P, Velds A, Kerkhoven RM, Nieuwland M, Haydock A, Ramasamy G, Vainio S, Heidebrecht T, Perrakis A, Pagie L, van Steensel B, Myler PJ, Borst P.
Cell. 2012 Aug 31;150(5):909-21

Mapping of lamin A- and progerin-interacting genome regions.
Kubben N, Adriaens M, Meuleman W, Voncken JW, van Steensel B, Misteli T.
Chromosoma. 2012 Oct;121(5):447-64

Hox in space: gene cluster regulation linked to folding of chromatin.
Pindyurin AV, van Steensel B.
Nucleus. 2012 Mar 1;3(2):118-22

The inner nuclear membrane proteins Man1 and Ima1 link to two different types of chromatin at the nuclear periphery in S. pombe.
Steglich B, Filion GJ, van Steensel B, Ekwall K
Nucleus. 2012 Jan-Feb;3(1):77-87

2011

Chromatin: constructing the big picture.
B van Steensel
EMBO J. May 18 2011, 30(10):1885-95

Interactions among Polycomb domains are guided by chromosome architecture.
B Tolhuis, M Blom, RM Kerkhoven, L Pagie, H Teunissen, M Nieuwland, M Simonis, W de Laat, M van Lohuizen, B van Steensel
PLoS Genet. Mar 2011, 7(3):e1001343

2010

Role of the nuclear lamina in genome organization and gene expression.
D Peric-Hupkes, B van Steensel
Cold Spring Harbor Symp. Quant. Biol. 2010, 75:517-24

The insulator protein SU(HW) fine-tunes nuclear lamina interactions of the Drosophila genome.
JG van Bemmel, L Pagie, U Braunschweig, W Brugman, W Meuleman, RM Kerkhoven, B van Steensel
PloS ONE. 2010, 5(11):e15013

Genomics tools for unraveling chromosome architecture.
B van Steensel, J Dekker
Nature Biotechnol. Oct 13 2010, 28(10):1089-1095

A direct role for cohesin in gene regulation and ecdysone response in Drosophila salivary glands.
A Pauli, JG van Bemmel, RA Oliveira, T Itoh, K Shirahige, B van Steensel, K Nasmyth
Current Biol. Oct 26 2010, 20(20):1787-98

Systematic protein location mapping reveals five principal chromatin types in Drosophila cells.
GJ Filion, JG van Bemmel, U Braunschweig, W Talhout, J Kind, LD Ward, W Brugman, IJ de Castro, RM Kerkhoven, HJ Bussemaker, B van Steensel
Cell. Oct 15 2010, 143(2):212-24

Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation.
D Peric-Hupkes, W Meuleman, L Pagie, SW Bruggeman, I Solovei, W Brugman, S Gräf, P Flicek, RM Kerkhoven, M van Lohuizen, M Reinders, L Wessels, B van Steensel
Mol. Cell. May 28 2010, 38(4):603-13

Genome-nuclear lamina interactions and gene regulation.
J Kind, B van Steensel
Current Opin. Cell Biol. Jun 2010, 22(3):320-5

Reassessing the abundance of H3K9me2 chromatin domains in embryonic stem cells.
GJ Filion, B van Steensel
Nature Genet. Jan 2010, 42(1):4; author reply 5-6

Bayesian network analysis of targeting interactions in chromatin.
B van Steensel, U Braunschweig, GJ Filion, M Chen, JG van Bemmel, T Ideker
Genome Res. Feb 2010, 20(2):190-200

2009

Histone H1 binding is inhibited by histone variant H3.3.
U Braunschweig, GJ Hogan, L Pagie, B van Steensel
EMBO J. Dec 2 2009, 28(23):3635-45

High-resolution mapping of heterochromatin redistribution in a Drosophila position-effect variegation model.
MJ Vogel, L Pagie, W Talhout, M Nieuwland, RM Kerkhoven, B van Steensel
Epigenetics & Chromatin. 2009, 2(1):1

Chromatin domains in higher eukaryotes: insights from genome-wide mapping studies.
E de Wit, B van Steensel
Chromosoma. Feb 2009, 118(1):25-36

2008

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions.
L Guelen, L Pagie, E Brasset, W Meuleman, MB Faza, W Talhout, BH Eussen, A de Klein, L Wessels, W de Laat, B van Steensel
Nature. Jun 12 2008, 453(7197):948-51

Global chromatin domain organization of the Drosophila genome.
E de Wit, U Braunschweig, F Greil, HJ Bussemaker, B van Steensel
PLoS Genet. Mar 2008, 4(3):e1000045

Linking cohesin to gene regulation.
D Peric-Hupkes, B van Steensel
Cell. Mar 21 2008, 132(6):925-8

2007

SUUR joins separate subsets of PcG, HP1 and B-type lamin targets in Drosophila.
AV Pindyurin, C Moorman, E de Wit, SN Belyakin, ES Belyaeva, GK Christophides, FC Kafatos, B van Steensel, IF Zhimulev
J. Cell Science. Jul 15 2007, 120(Pt 14):2344-51

Detection of in vivo protein-DNA interactions using DamID in mammalian cells.
MJ Vogel, D Peric-Hupkes, B van Steensel
Nature Protoc. 2007, 2(6):1467-78

High-resolution mapping reveals links of HP1 with active and inactive chromatin components.
E de Wit, F Greil, B van Steensel
PLoS Genet. Mar 2 2007, 3(3):e38

HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila.
F Greil, E de Wit, HJ Bussemaker, B van Steensel
EMBO J. Feb 7 2007, 26(3):741-51

2006

Prospero acts as a binary switch between self-renewal and differentiation in Drosophila neural stem cells.
SP Choksi, TD Southall, T Bossing, K Edoff, E de Wit, BE Fischer, B van Steensel, G Micklem, AH Brand
Dev. Cell. Dec 2006, 11(6):775-89

Human heterochromatin proteins form large domains containing KRAB-ZNF genes.
MJ Vogel, L Guelen, E de Wit, D Peric-Hupkes, M Lodén, W Talhout, M Feenstra, B Abbas, AK Classen, B van Steensel
Genome Res. Dec 2006, 16(12):1493-504

Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C).
M Simonis, P Klous, E Splinter, Y Moshkin, R Willemsen, E de Wit, B van Steensel, W de Laat
Nature Genet. Nov 2006, 38(11):1348-54

DamID: mapping of in vivo protein-genome interactions using tethered DNA adenine methyltransferase.
F Greil, C Moorman, B van Steensel
Meth. Enzymol. 2006, 410:342-59

Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster.
C Moorman, LV Sun, J Wang, E de Wit, W Talhout, LD Ward, F Greil, XJ Lu, KP White, HJ Bussemaker, B van Steensel
Proc. Nat. Acad. Sci. USA. Aug 8 2006, 103(32):12027-32

Characterization of the Drosophila melanogaster genome at the nuclear lamina.
H Pickersgill, B Kalverda, E de Wit, W Talhout, M Fornerod, B van Steensel
Nature Genet. Sep 2006, 38(9):1005-14

Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster.
B Tolhuis, E de Wit, I Muijrers, H Teunissen, W Talhout, B van Steensel, M van Lohuizen
Nature Genet. Jun 2006, 38(6):694-9

Chromosome-wide gene-specific targeting of the Drosophila dosage compensation complex.
GD Gilfillan, T Straub, E de Wit, F Greil, R Lamm, B van Steensel, PB Becker
Genes Dev. Apr 1 2006, 20(7):858-70

2005

Genome-wide HP1 binding in Drosophila: developmental plasticity and genomic targeting signals.
E de Wit, F Greil, B van Steensel
Genome Res. Sep 2005, 15(9):1265-73

Histone modifications: from genome-wide maps to functional insights.
F van Leeuwen, B van Steensel
Genome Biol. 2005, 6(6):113

Mapping of genetic and epigenetic regulatory networks using microarrays.
B van Steensel
Nature Genet. Jun 2005, 37 Suppl:S18-24

Whole-genome views of chromatin structure.
M Lodén, B van Steensel
Chromosome Res. 2005, 13(3):289-98

2003

Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location.
F Greil, I van der Kraan, J Delrow, JF Smothers, E de Wit, HJ Bussemaker, R van Driel, S Henikoff, B van Steensel
Genes Dev. Nov 15 2003, 17(22):2825-38

Epigenomic profiling using microarrays.
B van Steensel, S Henikoff
BioTechniques. Aug 2003, 35(2):346-50, 352-4, 356-7

Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila.
LV Sun, L Chen, F Greil, N Negre, TR Li, G Cavalli, H Zhao, B Van Steensel, KP White
Proc. Nat. Acad. Sci. USA. Aug 5 2003, 100(16):9428-33

Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network.
A Orian, B van Steensel, J Delrow, HJ Bussemaker, L Li, T Sawado, E Williams, LW Loo, SM Cowley, C Yost, S Pierce, BA Edgar, SM Parkhurst, RN Eisenman
Genes Dev. May 1 2003, 17(9):1101-14

Genomewide analysis of Drosophila GAGA factor target genes reveals context-dependent DNA binding.
B van Steensel, J Delrow, HJ Bussemaker
Proc. Nat. Acad. Sci. USA. Mar 4 2003, 100(5):2580-5

2002

Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing.
D Schübeler, D Scalzo, C Kooperberg, B van Steensel, J Delrow, M Groudine
Nature Genet. Nov 2002, 32(3):438-42

Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3.
R Tompa, CM McCallum, J Delrow, JG Henikoff, B van Steensel, S Henikoff
Current Biol. Jan 8 2002, 12(1):65-8

2001

Chromatin profiling using targeted DNA adenine methyltransferase.
B van Steensel, J Delrow, S Henikoff
Nature Genet. Mar 2001, 27(3):304-8