Nature Communications

Identification of methylation-sensitive human transcription factors using meSMiLE-seq

A Antoni J. Gralak K Katerina Faltejskova A Ally W. H. Yang C Clemence Steiner J Julie Russeil N Nadia Grenningloh S Sachi Inukai M Mustafa Demir R Riccardo Dainese C Cooper Owen E Eugenia V. Pankevich P Philipp Bucher O Oriol Fornes J Jan Grau I Ivo Grosse A Arttu Jolma F Fedor A. Kolpakov V Vsevolod J. Makeev M Mihai Albu M Marjan Barazandeh A Alexander Brechalov Z Zhenfeng Deng A Ali Fathi C Chun Hu S Samuel A. Lambert K Kaitlin U. Laverty Z Zain M. Patel S Sara E. Pour R Rozita Razavi M Mikhail Salnikov I Isaac Yellan H Hong Zheng (Center of Nanomaterials for Renewable Energy, State Key Laboratory of Electrical Insulation and Power Equipment, School of Electrical Engineering) G Georgy Meshcheryakov G Giovanna Ambrosini M Marie-Luise Plescher S Semyon Kolmykov I Ivan Yevshin N Nikita Gryzunov I Ivan Kozin M Mikhail Nikonov V Vladimir Nozdrin A Arsenii Zinkevich P Pavel Kravchenko S Sergey Abramov A Alexandr Boytsov V Vasilii Kamenets D Dmitry Penzar A Anton Vlasov I Ilya E. Vorontsov A Aldo Hernandez-Corchado H Hamed S. Najafabadi Q Quaid Morris X Xiaoting Chen M Matthew T. Weirauch (Division of Gastroenterology, Hepatology & Nutrition, Cincinnati Children’s Hospital Medical Center) T Timothy R. Hughes I Ivan V. Kulakovskiy J Judith F. Kribelbauer-Swietek G Guido van Mierlo (Department of Medical BioSciences, Radboudumc) B Bart Deplancke

Abstract

Abstract Transcription factors (TFs) are key players in eukaryotic gene regulation, but the DNA binding specificity of many TFs remains unknown. Here, we assay 284 mostly uncharacterized putative human TFs using selective microfluidics-based ligand enrichment followed by sequencing (SMiLE-seq), revealing 74 new DNA binding motifs. To investigate whether TFs lacking detectable motifs preferably bind epigenetically modified DNA, we develop methylation-sensitive SMiLE-seq (meSMiLE-seq), a microfluidic assay that simultaneously probes binding to methylated and unmethylated DNA. Using meSMiLE-seq, we assay 114 TFs and identify DNA-binding models for 48 proteins, including known methylation-sensitive binding modes for POU5F1 and RFX5. 11 TFs prefer methylated DNA or display alternative methylation-dependent motifs (e.g. PRDM13), while 13 show aversion to methylated sequences (e.g. USF3). Finally, we identify ZHX2 as a putative Z-DNA binder. Altogether, our study significantly expands the human TF codebook, while providing a versatile platform to quantitatively assay the impact of DNA modifications on TF binding.

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Article Details

Volume / Issue Vol. 17, Issue 1
Published August 05, 2026
ISSN 2041-1723
Publisher Nature Portfolio

Journal Info

Nature Communications

Nature Portfolio
ISSN: 2041-1723 Open Access Life Sciences

Authors (59)

A

Antoni J. Gralak

K

Katerina Faltejskova

A

Ally W. H. Yang

C

Clemence Steiner

J

Julie Russeil

N

Nadia Grenningloh

S

Sachi Inukai

M

Mustafa Demir

R

Riccardo Dainese

C

Cooper Owen

E

Eugenia V. Pankevich

P

Philipp Bucher

O

Oriol Fornes

J

Jan Grau

I

Ivo Grosse

A

Arttu Jolma

F

Fedor A. Kolpakov

V

Vsevolod J. Makeev

M

Mihai Albu

M

Marjan Barazandeh

A

Alexander Brechalov

Z

Zhenfeng Deng

A

Ali Fathi

C

Chun Hu

S

Samuel A. Lambert

K

Kaitlin U. Laverty

Z

Zain M. Patel

S

Sara E. Pour

R

Rozita Razavi

M

Mikhail Salnikov

I

Isaac Yellan

H

Hong Zheng

Center of Nanomaterials for Renewable Energy, State Key Laboratory of Electrical Insulation and Power Equipment, School of Electrical Engineering

G

Georgy Meshcheryakov

G

Giovanna Ambrosini

M

Marie-Luise Plescher

S

Semyon Kolmykov

I

Ivan Yevshin

N

Nikita Gryzunov

I

Ivan Kozin

M

Mikhail Nikonov

V

Vladimir Nozdrin

A

Arsenii Zinkevich

P

Pavel Kravchenko

S

Sergey Abramov

A

Alexandr Boytsov

V

Vasilii Kamenets

D

Dmitry Penzar

A

Anton Vlasov

I

Ilya E. Vorontsov

A

Aldo Hernandez-Corchado

H

Hamed S. Najafabadi

Q

Quaid Morris

X

Xiaoting Chen

M

Matthew T. Weirauch

Division of Gastroenterology, Hepatology & Nutrition, Cincinnati Children’s Hospital Medical Center

T

Timothy R. Hughes

I

Ivan V. Kulakovskiy

J

Judith F. Kribelbauer-Swietek

G

Guido van Mierlo

Department of Medical BioSciences, Radboudumc

B

Bart Deplancke

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