Publications – Krebs Group

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Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II.

Chatsirisupachai K, Moene CJI, Kleinendorst R, Kreibich E, Molina N, Krebs A

Molecular systems biology, 2025

doi:10.1038/s44320-025-00094-5.

Identification of transcription factor co-binding patterns with non-negative matrix factorization.

Rauluseviciute I, Launay T, Barzaghi G, Nikumbh S, Lenhard B, Krebs AR, Castro-Mondragon JA, Mathelier A

Nucleic acids research, 2024

doi:10.1093/nar/gkae743.

Relevance of DNA methylation at enhancers for the acquisition of cell identities.

Kreibich E, Krebs AR

FEBS letters, 2023

doi:10.1002/1873-3468.14686.

Single-molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation.

Kreibich E, Kleinendorst R, Barzaghi G, Kaspar S, Krebs AR

Molecular cell, 2023

doi:10.1016/j.molcel.2023.01.017.

DNA sequence and chromatin modifiers cooperate to confer epigenetic bistability at imprinting control regions.

Butz S, Schmolka N, Karemaker ID, Villaseñor R, Schwarz I, Domcke S, Uijttewaal ECH, Jude J, Lienert F, Krebs AR, de Wagenaar NP, Bao X, Zuber J, Elling U, Schübeler D, Baubec T

Nature genetics, 2022

doi:10.1038/s41588-022-01210-z.

Cofactors: a new layer of specificity to enhancer regulation.

Kreibich E, Krebs AR

Trends in biochemical sciences, 2022

doi:10.1016/j.tibs.2022.07.008.

Single molecule multi-omics reveals context-dependent regulation of enhancers by DNA methylation.

Kreibich E, Kleinendorst R, Barzaghi G, Kaspar S, Krebs AR

bioRxiv.org, 2022

doi:10.1101/2022.05.19.492653.

Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting.

Kleinendorst RWD, Barzaghi G, Smith ML, Zaugg JB, Krebs AR

Nature protocols, 2021

doi:10.1038/s41596-021-00630-1.

BANP opens chromatin and activates CpG-island-regulated genes.

Grand RS, Burger L, Gräwe C, Michael AK, Isbel L, Hess D, Hoerner L, Iesmantavicius V, Durdu S, Pregnolato M, Krebs AR, Smallwood SA, Thomä N, Vermeulen M, Schübeler D

Nature, 2021

doi:10.1038/s41586-021-03689-8.

Studying transcription factor function in the genome at molecular resolution.

Krebs AR

Trends in genetics : TIG, 2021

doi:10.1016/j.tig.2021.03.008.

Molecular co-occupancy identifies transcription factor binding cooperativity in vivo.

Sönmezer C, Kleinendorst R, Imanci D, Barzaghi G, Villacorta L, Schübeler D, Benes V, Molina N, Krebs AR

Molecular cell, 2021

doi:10.1016/j.molcel.2020.11.015.

A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity.

Ginno PA, Gaidatzis D, Feldmann A, Hoerner L, Imanci D, Burger L, Zilbermann F, Peters AHFM, Edenhofer F, Smallwood SA, Krebs AR, Schübeler D

Nature communications, 2020

doi:10.1038/s41467-020-16354-x.

McQ – an open-source multiplexed SARS-CoV-2 quantification platform.

Vonesch SC, Bredikhin D, Dobrev N, Villacorta L, Kleinendorst R, Cacace E, Flock J, Frank M, Jung F, Kornienko J, Mitosch K, Osuna-Lopez M, Zimmermann J, Goettig S, Hamprecht A, Kraeusslich H, Knop M, Typas A, Steinmetz LM, Benes V, Remans K, Krebs AR

medRxiv, 2020

doi:10.1101/2020.12.02.20242628.

Targeting neuronal and glial cell types with synthetic promoter AAVs in mice, non-human primates and humans.

Jüttner J, Szabo A, Gross-Scherf B, Morikawa RK, Rompani SB, Hantz P, Szikra T, Esposti F, Cowan CS, Bharioke A, Patino-Alvarez CP, Keles Ö, Kusnyerik A, Azoulay T, Hartl D, Schübeler D, Krebs AR, Lukats A, Hajdu RI, Nagy ZZ, Nemeth J, Wu RH, Wu KC, Fang XL, Xiang L, Goldblum D, Jin ZB, Scholl HPN, Hasler PW, Roska B, Krol J

Nature neuroscience, 2019

doi:10.1038/s41593-019-0431-2.

Cis-regulatory landscapes of four cell types of the retina.

Hartl D, Krebs AR, Jüttner J, Roska B, Schübeler D

Nucleic acids research, 2017

doi:10.1093/nar/gkx923.

Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters.

Krebs AR, Imanci D, Hoerner L, Gaidatzis D, Burger L, Schübeler D

Molecular cell, 2017

doi:10.1016/j.molcel.2017.06.027.

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

Baubec T, Colombo DF, Wirbelauer C, Schmidt J, Burger L, Krebs AR, Akalin A, Schübeler D

Nature, 2015

doi:10.1038/nature14176.

Interpreting and visualizing ChIP-seq data with the seqMINER software.

Ye T, Ravens S, Krebs AR, Tora L

Methods in molecular biology (Clifton, N.J.), 2014

doi:10.1007/978-1-4939-0512-6_8.

High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions

Krebs AR, Dessus-Babus S, Burger L, Schübeler D

eLife, 2014

doi:10.7554/eLife.04094.

Tracking the evolution of cancer methylomes

Krebs AR, Schübeler D

Nature genetics, 2012

doi:10.1038/ng.2451.

SAGA and ATAC Histone Acetyl Transferase Complexes Regulate Distinct Sets of Genes and ATAC Defines a Class of p300-Independent Enhancers

Krebs AR, Karmodiya K, Lindahl-Allen M, Struhl K, Tora L

Molecular cell, 2011

doi:10.1016/j.molcel.2011.08.037.

seqMINER: an integrated ChIP-seq data interpretation platform

Ye T, Krebs AR, Choukrallah MA, Keime C, Plewniak F, Davidson I, Tora L

Nucleic acids research, 2011

doi:10.1093/nar/gkq1287.

Lessons from genome-wide studies: an integrated definition of the coactivator function of histone acetyl transferases

Anamika K, Krebs AR, Thompson J, Poch O, Devys D, Tora L

Epigenetics & chromatin, 2010

doi:10.1186/1756-8935-3-18.

Cell-specific occupancy of an extended repertoire of CREM and CREB binding loci in male germ cells

Martianov I, Choukrallah MA, Krebs A, Ye T, Legras S, Rijkers E, Van Ijcken W, Jost B, Sassone-Corsi P, Davidson I

BMC genomics, 2010

doi:10.1186/1471-2164-11-530.

The ATAC acetyl transferase complex controls mitotic progression by targeting non-histone substrates

Orpinell M, Fournier M, Riss A, Nagy Z, Krebs AR, Frontini M, Tora L

The EMBO journal, 2010

doi:10.1038/emboj.2010.125.

ATAC and Mediator coactivators form a stable complex and regulate a set of non-coding RNA genes

Krebs AR, Demmers J, Karmodiya K, Chang NC, Chang AC, Tora L

EMBO reports, 2010

doi:10.1038/embor.2010.75.

The metazoan ATAC and SAGA coactivator HAT complexes regulate different sets of inducible target genes

Nagy Z, Riss A, Fujiyama S, Krebs A, Orpinell M, Jansen P, Cohen A, Stunnenberg HG, Kato S, Tora L

Cellular and molecular life sciences : CMLS, 2010

doi:10.1007/s00018-009-0199-8.

Keys to Open Chromatin for Transcription Activation: FACT and Asf1

Krebs A, Tora L

Molecular cell, 2009

doi:10.1016/j.molcel.2009.05.004.

GPAT: Retrieval of genomic annotation from large genomic position datasets

Krebs A, Frontini M, Tora L

BMC bioinformatics, 2008

doi:10.1186/1471-2105-9-533.