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Krebs Group

Decoding gene regulation using single-molecule genomics

Publications

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 2020

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

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.


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