Full Text Journal Articles by
Author Peter B Becker


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Loss of nucleosome remodelers CHRAC/ACF does not sensitize early Drosophila embryos to X-rays.

Alessandro Scacchetti, Peter B Becker,

MicroPubl Biol (microPublication biology)
[2020, 2020:]

Cited: 0 times

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Two-step mechanism for selective incorporation of lncRNA into a chromatin modifier.

Marisa Müller, Tamas Schauer, Silke Krause, Raffaella Villa, Andreas W Thomae, Peter B Becker,

The MLE DExH helicase and the roX lncRNAs are essential components of the chromatin modifying Dosage Compensation Complex (DCC) in Drosophila. To explore the mechanism of ribonucleoprotein complex assembly, we developed vitRIP, an unbiased, transcriptome-wide in vitro assay that reveals RNA binding specificity. We found that MLE has intrinsic specificity ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2020, 48(13):7483-7501]

Cited: 0 times

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Beads on a string-nucleosome array arrangements and folding of the chromatin fiber.

Sandro Baldi, Philipp Korber, Peter B Becker,

Understanding how the genome is structurally organized as chromatin is essential for understanding its function. Here, we review recent developments that allowed the readdressing of old questions regarding the primary level of chromatin structure, the arrangement of nucleosomes along the DNA and the folding of the nucleosome fiber in nuclear ... Read more >>

Nat. Struct. Mol. Biol. (Nature structural & molecular biology)
[2020, 27(2):109-118]

Cited: 2 times

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Progressive dosage compensation during Drosophila embryogenesis is reflected by gene arrangement.

Khairunnadiya Prayitno, Tamás Schauer, Catherine Regnard, Peter B Becker,

In Drosophila melanogaster males, X-chromosome monosomy is compensated by chromosome-wide transcription activation. We found that complete dosage compensation during embryogenesis takes surprisingly long and is incomplete even after 10 h of development. Although the activating dosage compensation complex (DCC) associates with the X-chromosome and MOF acetylates histone H4 early, many genes ... Read more >>

EMBO Rep. (EMBO reports)
[2019, 20(8):e48138]

Cited: 1 time

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Structure, dynamics and roX2-lncRNA binding of tandem double-stranded RNA binding domains dsRBD1,2 of Drosophila helicase Maleless.

Pravin Kumar Ankush Jagtap, Marisa Müller, Pawel Masiewicz, Sören von Bülow, Nele Merret Hollmann, Po-Chia Chen, Bernd Simon, Andreas W Thomae, Peter B Becker, Janosch Hennig,

Maleless (MLE) is an evolutionary conserved member of the DExH family of helicases in Drosophila. Besides its function in RNA editing and presumably siRNA processing, MLE is best known for its role in remodelling non-coding roX RNA in the context of X chromosome dosage compensation in male flies. MLE and ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2019, 47(8):4319-4333]

Cited: 0 times

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Factor cooperation for chromosome discrimination in Drosophila.

Christian Albig, Evgeniya Tikhonova, Silke Krause, Oksana Maksimenko, Catherine Regnard, Peter B Becker,

Transcription regulators select their genomic binding sites from a large pool of similar, non-functional sequences. Although general principles that allow such discrimination are known, the complexity of DNA elements often precludes a prediction of functional sites. The process of dosage compensation in Drosophila allows exploring the rules underlying binding site selectivity. ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2019, 47(4):1706-1724]

Cited: 5 times

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Genome-wide Rules of Nucleosome Phasing in Drosophila.

Sandro Baldi, Dhawal S Jain, Lisa Harpprecht, Angelika Zabel, Marion Scheibe, Falk Butter, Tobias Straub, Peter B Becker,

Regular successions of positioned nucleosomes, or phased nucleosome arrays (PNAs), are predominantly known from transcriptional start sites (TSSs). It is unclear whether PNAs occur elsewhere in the genome. To generate a comprehensive inventory of PNAs for Drosophila, we applied spectral analysis to nucleosome maps and identified thousands of PNAs throughout ... Read more >>

Mol. Cell (Molecular cell)
[2018, 72(4):661-672.e4]

Cited: 3 times

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Genome-wide measurement of local nucleosome array regularity and spacing by nanopore sequencing.

Sandro Baldi, Stefan Krebs, Helmut Blum, Peter B Becker,

The nature of chromatin as regular succession of nucleosomes has gained iconic status. However, since most nucleosomes in metazoans are poorly positioned it is unknown to which extent bulk genomic nucleosome repeat length reflects the regularity and spacing of nucleosome arrays at individual loci. We describe a new approach to ... Read more >>

Nat. Struct. Mol. Biol. (Nature structural & molecular biology)
[2018, 25(9):894-901]

Cited: 9 times

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CHRAC/ACF contribute to the repressive ground state of chromatin.

Alessandro Scacchetti, Laura Brueckner, Dhawal Jain, Tamas Schauer, Xu Zhang, Frank Schnorrer, Bas van Steensel, Tobias Straub, Peter B Becker,

The chromatin remodeling complexes chromatin accessibility complex and ATP-utilizing chromatin assembly and remodeling factor (ACF) combine the ATPase ISWI with the signature subunit ACF1. These enzymes catalyze well-studied nucleosome sliding reactions in vitro, but how their actions affect physiological gene expression remains unclear. Here, we explored the influence of Drosophila ... Read more >>

Life Sci Alliance (Life science alliance)
[2018, 1(1):e201800024]

Cited: 2 times

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Ubiquitylation of the acetyltransferase MOF in Drosophila melanogaster.

Sarah Schunter, Raffaella Villa, Victoria Flynn, Jan B Heidelberger, Anne-Kathrin Classen, Petra Beli, Peter B Becker,

The nuclear acetyltransferase MOF (KAT8 in mammals) is a subunit of at least two multi-component complexes involved in transcription regulation. In the context of complexes of the 'Non-Specific-Lethal' (NSL) type it controls transcription initiation of many nuclear housekeeping genes and of mitochondrial genes. While this function is conserved in metazoans, ... Read more >>

PLoS ONE (PloS one)
[2017, 12(5):e0177408]

Cited: 2 times

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Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions.

Thomas Blasi, Christian Feller, Justin Feigelman, Jan Hasenauer, Axel Imhof, Fabian J Theis, Peter B Becker, Carsten Marr,

Post-translational modifications (PTMs) are pivotal to cellular information processing, but how combinatorial PTM patterns ("motifs") are set remains elusive. We develop a computational framework, which we provide as open source code, to investigate the design principles generating the combinatorial acetylation patterns on histone H4 in Drosophila melanogaster. We find that ... Read more >>

Cell Syst (Cell systems)
[2016, 2(1):49-58]

Cited: 5 times

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Splice variants of the SWR1-type nucleosome remodeling factor Domino have distinct functions during Drosophila melanogaster oogenesis.

Kenneth Börner, Peter B Becker,

SWR1-type nucleosome remodeling factors replace histone H2A by variants to endow chromatin locally with specialized functionality. In Drosophila melanogaster a single H2A variant, H2A.V, combines functions of mammalian H2A.Z and H2A.X in transcription regulation and the DNA damage response. A major role in H2A.V incorporation for the only SWR1-like enzyme ... Read more >>

Development (Development (Cambridge, England))
[2016, 143(17):3154-3167]

Cited: 7 times

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PionX sites mark the X chromosome for dosage compensation.

Raffaella Villa, Tamas Schauer, Pawel Smialowski, Tobias Straub, Peter B Becker,

The rules defining which small fraction of related DNA sequences can be selectively bound by a transcription factor are poorly understood. One of the most challenging tasks in DNA recognition is posed by dosage compensation systems that require the distinction between sex chromosomes and autosomes. In Drosophila melanogaster, the male-specific ... Read more >>

Nature (Nature)
[2016, 537(7619):244-248]

Cited: 28 times

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CMV promoter mutants with a reduced propensity to productivity loss in CHO cells.

Benjamin Moritz, Peter B Becker, Ulrich Göpfert,

The major immediate-early promoter and enhancer of the human cytomegalovirus (hCMV-MIE) is one of the most potent DNA elements driving recombinant gene expression in mammalian cells. Therefore, it is widely employed not only in research but also in large-scale industrial applications, e.g. for the production of therapeutic antibodies in Chinese ... Read more >>

Sci Rep (Scientific reports)
[2015, 5:16952]

Cited: 15 times

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High levels of histone H3 acetylation at the CMV promoter are predictive of stable expression in Chinese hamster ovary cells.

Benjamin Moritz, Laura Woltering, Peter B Becker, Ulrich Göpfert,

Chinese hamster ovary cells (CHO) are widely used in the production of glycosylated therapeutic proteins such as antibodies. During expansion and maintenance, CHO cell lines are prone to production instability, which may be caused by promoter silencing, loss of transgene copies, or post-transcriptional effects. Silencing of recombinant genes may be ... Read more >>

Biotechnol. Prog. (Biotechnology progress)
[2016, 32(3):776-786]

Cited: 7 times

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A role for tuned levels of nucleosome remodeler subunit ACF1 during Drosophila oogenesis.

Kenneth Börner, Dhawal Jain, Paula Vazquez-Pianzola, Sandra Vengadasalam, Natascha Steffen, Dmitry V Fyodorov, Pavel Tomancak, Alexander Konev, Beat Suter, Peter B Becker,

The Chromatin Accessibility Complex (CHRAC) consists of the ATPase ISWI, the large ACF1 subunit and a pair of small histone-like proteins, CHRAC-14/16. CHRAC is a prototypical nucleosome sliding factor that mobilizes nucleosomes to improve the regularity and integrity of the chromatin fiber. This may facilitate the formation of repressive chromatin. ... Read more >>

Dev. Biol. (Developmental biology)
[2016, 411(2):217-230]

Cited: 6 times

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Structure of the RNA Helicase MLE Reveals the Molecular Mechanisms for Uridine Specificity and RNA-ATP Coupling.

J Rajan Prabu, Marisa Müller, Andreas W Thomae, Steffen Schüssler, Fabien Bonneau, Peter B Becker, Elena Conti,

The MLE helicase remodels the roX lncRNAs, enabling the lncRNA-mediated assembly of the Drosophila dosage compensation complex. We identified a stable MLE core comprising the DExH helicase module and two auxiliary domains: a dsRBD and an OB-like fold. MLEcore is an unusual DExH helicase that can unwind blunt-ended RNA duplexes ... Read more >>

Mol. Cell (Molecular cell)
[2015, 60(3):487-499]

Cited: 23 times

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Computational study of remodeling in a nucleosomal array.

Raoul D Schram, Henrike Klinker, Peter B Becker, Helmut Schiessel,

Chromatin remodeling complexes utilize the energy of ATP hydrolysis to change the packing state of chromatin, e.g. by catalysing the sliding of nucleosomes along DNA. Here we present simple models to describe experimental data of changes in DNA accessibility along a synthetic, repetitive array of nucleosomes during remodeling by the ... Read more >>

Eur Phys J E Soft Matter (The European physical journal. E, Soft matter)
[2015, 38(8):85]

Cited: 0 times

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Active promoters give rise to false positive 'Phantom Peaks' in ChIP-seq experiments.

Dhawal Jain, Sandro Baldi, Angelika Zabel, Tobias Straub, Peter B Becker,

Chromatin immunoprecipitation (ChIP) is widely used to identify chromosomal binding sites. Chromatin proteins are cross-linked to their target sequences in living cells. The purified chromatin is sheared and the relevant protein is enriched by immunoprecipitation with specific antibodies. The co-purifying genomic DNA is then determined by massive parallel sequencing (ChIP-seq).We ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2015, 43(14):6959-6968]

Cited: 54 times

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Structural basis of X chromosome DNA recognition by the MSL2 CXC domain during Drosophila dosage compensation.

Sanduo Zheng, Raffaella Villa, Jia Wang, Yingang Feng, Jinfeng Wang, Peter B Becker, Keqiong Ye,

The male-specific lethal dosage compensation complex (MSL-DCC) selectively assembles on the X chromosome in Drosophila males and activates gene transcription by twofold through histone acetylation. An MSL recognition element (MRE) sequence motif nucleates the initial MSL association, but how it is recognized remains unknown. Here, we identified the CXC domain ... Read more >>

Genes Dev. (Genes & development)
[2014, 28(23):2652-2662]

Cited: 12 times

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Global and specific responses of the histone acetylome to systematic perturbation.

Christian Feller, Ignasi Forné, Axel Imhof, Peter B Becker,

Regulation of histone acetylation is fundamental to the utilization of eukaryotic genomes in chromatin. Aberrant acetylation contributes to disease and can be clinically combated by inhibiting the responsible enzymes. Our knowledge of the histone acetylation system is patchy because we so far lacked the methodology to describe acetylation patterns and ... Read more >>

Mol. Cell (Molecular cell)
[2015, 57(3):559-571]

Cited: 50 times

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Beads-on-a-string on a bead: reconstitution and analysis of chromatin on a solid support.

Raphael Sandaltzopoulos, Peter B Becker,

Complex experimental strategies involving in vitro reconstituted chromatin or simple chromatin interaction studies are much facilitated by immobilizing the nucleosomal arrays to paramagnetic beads. Chromatin-containing beads can be retrieved from a reaction mix solution on a magnet fast and quantitatively, effectively separating bound, loosely attached and unbound components efficiently. This ... Read more >>

Methods Mol. Biol. (Methods in molecular biology (Clifton, N.J.))
[2015, 1288:1-14]

Cited: 0 times

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UNR facilitates the interaction of MLE with the lncRNA roX2 during Drosophila dosage compensation.

Cristina Militti, Sylvain Maenner, Peter B Becker, Fátima Gebauer,

Dosage compensation is a regulatory process that balances the expression of X-chromosomal genes between males (XY) and females (XX). In Drosophila, this requires non-coding RNAs and RNA-binding proteins (RBPs) whose specific functions remain elusive. Here we show that the Drosophila RBP UNR promotes the targeting of the activating male-specific-lethal complex ... Read more >>

Nat Commun (Nature communications)
[2014, 5:4762]

Cited: 16 times

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The histone-fold protein CHRAC14 influences chromatin composition in response to DNA damage.

Veena Mathew, Anne-Laure Pauleau, Natascha Steffen, Andrea Bergner, Peter B Becker, Sylvia Erhardt,

Chromatin reorganization and the incorporation of specific histone modifications during DNA damage response are essential steps for the successful repair of any DNA lesion. Here, we show that the histone-fold protein CHRAC14 plays an essential role in response to DNA damage in Drosophila. Chrac14 mutants are hypersensitive to genotoxic stress ... Read more >>

Cell Rep (Cell Reports)
[2014, 7(2):321-330]

Cited: 14 times

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Nucleosome sliding mechanisms: new twists in a looped history.

Felix Mueller-Planitz, Henrike Klinker, Peter B Becker,

Nucleosomes, the basic organizational units of chromatin, package and regulate eukaryotic genomes. ATP-dependent nucleosome-remodeling factors endow chromatin with structural flexibility by promoting assembly or disruption of nucleosomes and the exchange of histone variants. Furthermore, most remodeling factors induce nucleosome movements through sliding of histone octamers on DNA. We summarize recent ... Read more >>

Nat. Struct. Mol. Biol. (Nature structural & molecular biology)
[2013, 20(9):1026-1032]

Cited: 47 times

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