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Article ; Online: OCT4

Xuecong Wang / Ralf Jauch

Cell Regeneration, Vol 3, Iss

A penetrant pluripotency inducer

2014 Volume 1

Abstract: Native OCT4 protein has the intrinsic ability of crossing cellular membranes to enter cells. This finding could revive efforts to induce pluripotency with proteins replacing nucleic acid-based approaches, and raises the intriguing question as to whether ... ...

Abstract	Native OCT4 protein has the intrinsic ability of crossing cellular membranes to enter cells. This finding could revive efforts to induce pluripotency with proteins replacing nucleic acid-based approaches, and raises the intriguing question as to whether OCT4 can act non-cell-autonomously.
Keywords	OCT4 ; Cell penetrating peptide ; Induced pluripotent stem cells ; Reprogramming ; Pluripotency ; Medicine (General) ; R5-920 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	SpringerOpen
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Diversity among POU transcription factors in chromatin recognition and cell fate reprogramming

Malik, Vikas / Dennis Zimmer / Ralf Jauch

Cellular and molecular life sciences. 2018 May, v. 75, no. 9

2018

Abstract: The POU (Pit-Oct-Unc) protein family is an evolutionary ancient group of transcription factors (TFs) that bind specific DNA sequences to direct gene expression programs. The fundamental importance of POU TFs to orchestrate embryonic development and to ... ...

Abstract	The POU (Pit-Oct-Unc) protein family is an evolutionary ancient group of transcription factors (TFs) that bind specific DNA sequences to direct gene expression programs. The fundamental importance of POU TFs to orchestrate embryonic development and to direct cellular fate decisions is well established, but the molecular basis for this activity is insufficiently understood. POU TFs possess a bipartite ‘two-in-one’ DNA binding domain consisting of two independently folding structural units connected by a poorly conserved and flexible linker. Therefore, they represent a paradigmatic example to study the molecular basis for the functional versatility of TFs. Their modular architecture endows POU TFs with the capacity to accommodate alternative composite DNA sequences by adopting different quaternary structures. Moreover, associations with partner proteins crucially influence the selection of their DNA binding sites. The plentitude of DNA binding modes confers the ability to POU TFs to regulate distinct genes in the context of different cellular environments. Likewise, different binding modes of POU proteins to DNA could trigger alternative regulatory responses in the context of different genomic locations of the same cell. Prominent POU TFs such as Oct4, Brn2, Oct6 and Brn4 are not only essential regulators of development but have also been successfully employed to reprogram somatic cells to pluripotency and neural lineages. Here we review biochemical, structural, genomic and cellular reprogramming studies to examine how the ability of POU TFs to select regulatory DNA, alone or with partner factors, is tied to their capacity to epigenetically remodel chromatin and drive specific regulatory programs that give cells their identities.
Keywords	DNA ; DNA-binding domains ; binding sites ; cellular microenvironment ; chromatin ; embryogenesis ; gene expression ; genes ; genomics ; nucleotide sequences ; somatic cells ; transcription (genetics) ; transcription factors
Language	English
Dates of publication	2018-05
Size	p. 1587-1612.
Publishing place	Springer International Publishing
Document type	Article
Note	Review
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-018-2748-5
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Reprogramming cells with synthetic proteins

Xiaoxiao Yang / Vikas Malik / Ralf Jauch

Asian Journal of Andrology, Vol 17, Iss 3, Pp 394-

2015 Volume 402

Abstract: Conversion of one cell type into another cell type by forcibly expressing specific cocktails of transcription factors (TFs) has demonstrated that cell fates are not fixed and that cellular differentiation can be a two-way street with many intersections. ... ...

Abstract	Conversion of one cell type into another cell type by forcibly expressing specific cocktails of transcription factors (TFs) has demonstrated that cell fates are not fixed and that cellular differentiation can be a two-way street with many intersections. These experiments also illustrated the sweeping potential of TFs to "read" genetically hardwired regulatory information even in cells where they are not normally expressed and to access and open up tightly packed chromatin to execute gene expression programs. Cellular reprogramming enables the modeling of diseases in a dish, to test the efficacy and toxicity of drugs in patient-derived cells and ultimately, could enable cell-based therapies to cure degenerative diseases. Yet, producing terminally differentiated cells that fully resemble their in vivocounterparts in sufficient quantities is still an unmet clinical need. While efforts are being made to reprogram cells nongenetically by using drug-like molecules, defined TF cocktails still dominate reprogramming protocols. Therefore, the optimization of TFs by protein engineering has emerged as a strategy to enhance reprogramming to produce functional, stable and safe cells for regenerative biomedicine. Engineering approaches focused on Oct4, MyoD, Sox17, Nanog and Mef2c and range from chimeric TFs with added transactivation domains, designer transcription activator-like effectors to activate endogenous TFs to reprogramming TFs with rationally engineered DNA recognition principles. Possibly, applying the complete toolkit of protein design to cellular reprogramming can help to remove the hurdles that, thus far, impeded the clinical use of cells derived from reprogramming technologies.
Keywords	cellular reprogramming; protein design; protein engineering; synthetic transcription factors; transactivation ; Medicine ; R ; Diseases of the genitourinary system. Urology ; RC870-923
Language	English
Publishing date	2015-06-01T00:00:00Z
Publisher	Wolters Kluwer Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: The Crystal Structure of a Maxi/Mini-Ferritin Chimera Reveals Guiding Principles for the Assembly of Protein Cages

Cornell, Thomas A / Brendan P. Orner / Ralf Jauch / Rongli Fan / Yogesh Srivastava

Biochemistry. 2017 Aug. 01, v. 56, no. 30

2017

Abstract: Cage proteins assemble into nanoscale structures with large central cavities. They play roles, including those as virus capsids and chaperones, and have been applied to drug delivery and nanomaterials. Furthermore, protein cages have been used as model ... ...

Abstract	Cage proteins assemble into nanoscale structures with large central cavities. They play roles, including those as virus capsids and chaperones, and have been applied to drug delivery and nanomaterials. Furthermore, protein cages have been used as model systems to understand and design protein quaternary structure. Ferritins are ubiquitous protein cages that manage iron homeostasis and oxidative damage. Two ferritin subfamilies have strongly similar tertiary structure yet distinct quaternary structure: maxi-ferritins normally assemble into 24-meric, octahedral cages with C-terminal E-helices centered around 4-fold symmetry axes, and mini-ferritins are 12-meric, tetrahedral cages with 3-fold axes defined by C-termini lacking E-domains. To understand the role E-domains play in ferritin quaternary structure, we previously designed a chimera of a maxi-ferritin E-domain fused to the C-terminus of a mini-ferritin. The chimera is a 12-mer cage midway in size between those of the maxi- and mini-ferritin. The research described herein sets out to understand (a) whether the increase in size over a typical mini-ferritin is due to a frozen state where the E-domain is flipped out of the cage and (b) whether the symmetrical preference of the E-domain in the maxi-ferritin (4-fold axis) overrules the C-terminal preference in the mini-ferritin (3-fold axis). With a 1.99 Å resolution crystal structure, we determined that the chimera assembles into a tetrahedral cage that can be nearly superimposed with the parent mini-ferritin, and that the E-domains are flipped external to the cage at the 3-fold symmetry axes.
Keywords	capsid ; crystal structure ; drugs ; ferritin ; homeostasis ; iron ; models ; nanomaterials ; protein quaternary structure ; viruses
Language	English
Dates of publication	2017-0801
Size	p. 3894-3899.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.7b00312
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: glbase

Andrew Paul Hutchins / Ralf Jauch / Mateusz Dyla / Diego Miranda-Saavedra

Cell Regeneration, Vol 3, Iss

a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data

2014 Volume 1

Abstract: Genomic datasets and the tools to analyze them have proliferated at an astonishing rate. However, such tools are often poorly integrated with each other: each program typically produces its own custom output in a variety of non-standard file formats. ... ...

Abstract	Genomic datasets and the tools to analyze them have proliferated at an astonishing rate. However, such tools are often poorly integrated with each other: each program typically produces its own custom output in a variety of non-standard file formats. Here we present glbase, a framework that uses a flexible set of descriptors that can quickly parse non-binary data files. glbase includes many functions to intersect two lists of data, including operations on genomic interval data and support for the efficient random access to huge genomic data files. Many glbase functions can produce graphical outputs, including scatter plots, heatmaps, boxplots and other common analytical displays of high-throughput data such as RNA-seq, ChIP-seq and microarray expression data. glbase is designed to rapidly bring biological data into a Python-based analytical environment to facilitate analysis and data processing. In summary, glbase is a flexible and multifunctional toolkit that allows the combination and analysis of high-throughput data (especially next-generation sequencing and genome-wide data), and which has been instrumental in the analysis of complex data sets. glbase is freely available at http://bitbucket.org/oaxiom/glbase/.
Keywords	ChIP-seq ; RNA-seq ; Genomics ; Microarray ; Motifs ; Transcription factor ; Bioinformatics ; Medicine (General) ; R5-920 ; Biology (General) ; QH301-705.5
Subject code	005
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	SpringerOpen
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Directed Evolution of Reprogramming Factors by Cell Selection and Sequencing

Veeramohan Veerapandian / Jan Ole Ackermann / Yogesh Srivastava / Vikas Malik / Mingxi Weng / Xiaoxiao Yang / Ralf Jauch

Stem Cell Reports, Vol 11, Iss 2, Pp 593-

2018 Volume 606

Abstract: Summary: Directed biomolecular evolution is widely used to tailor and enhance enzymes, fluorescent proteins, and antibodies but has hitherto not been applied in the reprogramming of mammalian cells. Here, we describe a method termed directed evolution of ...

Abstract	Summary: Directed biomolecular evolution is widely used to tailor and enhance enzymes, fluorescent proteins, and antibodies but has hitherto not been applied in the reprogramming of mammalian cells. Here, we describe a method termed directed evolution of reprogramming factors by cell selection and sequencing (DERBY-seq) to identify artificially enhanced and evolved reprogramming transcription factors. DERBY-seq entails pooled screens with libraries of positionally randomised genes, cell selection based on phenotypic readouts, and genotyping by amplicon sequencing for candidate identification. We benchmark this approach using pluripotency reprogramming with libraries based on the reprogramming factor SOX2 and the reprogramming incompetent endodermal factor SOX17. We identified several SOX2 variants outperforming the wild-type protein in three- and four-factor cocktails. The most effective variants were discovered from the SOX17 library, demonstrating that this factor can be converted into a highly potent inducer of pluripotency with a range of diverse modifications. We propose DERBY-seq as a broad-based approach to discover reprogramming factors for any donor/target cell combination applicable to direct lineage reprogramming in vitro and in vivo. : Transcription factor-driven cell-fate conversions are powerful methods to turn one cell type into another but are typically slow and inefficient. In this article Jauch and Veerapandian et al. showed that naturally occurring factors are not optimally adapted for this feat but can be profoundly improved by artificially evolving the way they read and translate regulatory information stored in the genome. Keywords: directed evolution, protein engineering, cellular reprogramming, synthetic biology, deep mutational scanning, synthetic transcription factors, SOX2, SOX17, OCT4
Keywords	Medicine (General) ; R5-920 ; Biology (General) ; QH301-705.5
Subject code	306
Language	English
Publishing date	2018-08-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Correction

Jeroen Overman / Frank Fontaine / Mehdi Moustaqil / Deepak Mittal / Emma Sierecki / Natalia Sacilotto / Johannes Zuegg / Avril AB Robertson / Kelly Holmes / Angela A Salim / Sreeman Mamidyala / Mark S Butler / Ashley S Robinson / Emmanuelle Lesieur / Wayne Johnston / Kirill Alexandrov / Brian L Black / Benjamin M Hogan / Sarah De Val /

Robert J Capon / Jason S Carroll / Timothy L Bailey / Peter Koopman / Ralf Jauch / Matthew A Cooper / Yann Gambin / Mathias Francois

eLife, Vol

Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice

2023 Volume 12

Keywords	Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2023-08-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Exploring the utility of organo-polyoxometalate hybrids to inhibit SOX transcription factors

Kamesh Narasimhan / Kevin Micoine / Emmanuel Lacôte / Serge Thorimbert / Edwin Cheung / Bernold Hasenknopf / Ralf Jauch

Cell Regeneration, Vol 3, Iss

2014 Volume 1

Abstract: Background: SOX transcription factors constitute an attractive target class for intervention with small molecules as they play a prominent role in the field of regenerative biomedicine and cancer biology. However, rationally engineering specific ... ...

Abstract	Background: SOX transcription factors constitute an attractive target class for intervention with small molecules as they play a prominent role in the field of regenerative biomedicine and cancer biology. However, rationally engineering specific inhibitors that interfere with transcription factor DNA interfaces continues to be a monumental challenge in the field of transcription factor chemical biology. Polyoxometalates (POMs) are inorganic compounds that were previously shown to target the high-mobility group (HMG) of SOX proteins at nanomolar concentrations. In continuation of this work, we carried out an assessment of the selectivity of a panel of newly synthesized organo-polyoxometalate hybrids in targeting different transcription factor families to enable the usage of polyoxometalates as specific SOX transcription factor drugs. Results: The residual DNA-binding activities of 15 different transcription factors were measured after treatment with a panel of diverse polyoxometalates. Polyoxometalates belonging to the Dawson structural class were found to be more potent inhibitors than the Keggin class. Further, organically modified Dawson polyoxometalates were found to be the most potent in inhibiting transcription factor DNA binding activity. The size of the polyoxometalates and its derivitization were found to be the key determinants of their potency. Conclusion: Polyoxometalates are highly potent, nanomolar range inhibitors of the DNA binding activity of the Sox-HMG family. However, binding assays involving a limited subset of structurally diverse polyoxometalates revealed a low selectivity profile against different transcription factor families. Further progress in achieving selectivity and deciphering structure-activity relationship of POMs require the identification of POM binding sites on transcription factors using elaborate approaches like X-ray crystallography and multidimensional NMR. In summary, our report reaffirms that transcription factors are challenging molecular architectures and that future ...
Keywords	Medicine (General) ; R5-920 ; Biology (General) ; QH301-705.5
Subject code	540 ; 570
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	SpringerOpen
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Coop-Seq Analysis Demonstrates that Sox2 Evokes Latent Specificities in the DNA Recognition by Pax6

Hu, Caizhen / Vikas Malik / Yiming Kenny Chang / Veeramohan Veerapandian / Yogesh Srivastava / Yong-Heng Huang / Linlin Hou / Vlad Cojocaru / Gary D. Stormo / Ralf Jauch

Journal of molecular biology. 2017 Nov. 24, v. 429, no. 23

2017

Abstract: Sox2 and Pax6 co-regulate genes in neural lineages and the lens by forming a ternary complex likely facilitated allosterically through DNA. We used the quantitative and scalable cooperativity-by-sequencing (Coop-seq) approach to interrogate Sox2/Pax6 ... ...

Abstract	Sox2 and Pax6 co-regulate genes in neural lineages and the lens by forming a ternary complex likely facilitated allosterically through DNA. We used the quantitative and scalable cooperativity-by-sequencing (Coop-seq) approach to interrogate Sox2/Pax6 dimerization on a DNA library where five positions of the Pax6 half-site were randomized yielding 1024 cooperativity factors. Consensus positions normally required for the high-affinity DNA binding by Pax6 need to be mutated for effective dimerization with Sox2. Out of the five randomized bases, a 5′ thymidine is present in most of the top ranking elements. However, this thymidine maps to a region outside of the Pax half site and is not expected to directly interact with Pax6 in known binding modes suggesting structural reconfigurations. Re-analysis of ChIP-seq data identified several genomic regions where the cooperativity promoting sequence pattern is co-bound by Sox2 and Pax6. A highly conserved Sox2/Pax6 bound site near the Sprouty2 locus was verified to promote cooperative dimerization designating Sprouty2 as a potential target reliant on Sox2/Pax6 cooperativity in several neural cell types. Collectively, the functional interplay of Sox2 and Pax6 demands the relaxation of high-affinity binding sites and is enabled by alternative DNA sequences. We conclude that this binding mode evolved to warrant that a subset of target genes is only regulated in the presence of suitable partner factors.
Keywords	DNA ; DNA libraries ; binding sites ; dimerization ; genes ; genomics ; loci ; nucleotide sequences ; thymidine
Language	English
Dates of publication	2017-1124
Size	p. 3626-3634.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2017.10.013
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2

Vikas Malik / Laura V. Glaser / Dennis Zimmer / Sergiy Velychko / Mingxi Weng / Markus Holzner / Marius Arend / Yanpu Chen / Yogesh Srivastava / Veeramohan Veerapandian / Zahir Shah / Miguel A. Esteban / Huating Wang / Jiekai Chen / Hans R. Schöler / Andrew P. Hutchins / Sebastiaan H. Meijsing / Sebastian Pott / Ralf Jauch

Nature Communications, Vol 10, Iss 1, Pp 1-

2019 Volume 16

Abstract: Oct4, along with Sox2 and Klf4 can induce pluripotency, but structurally similar factors like Oct6 cannot. Here, using pluripotency competent and incompetent factors, the authors show that Sox2 plays a dominant role in facilitating chromatin opening at ... ...

Abstract	Oct4, along with Sox2 and Klf4 can induce pluripotency, but structurally similar factors like Oct6 cannot. Here, using pluripotency competent and incompetent factors, the authors show that Sox2 plays a dominant role in facilitating chromatin opening at Oct4 bound DNA early during reprogramming to pluripotency.
Keywords	Science ; Q
Language	English
Publishing date	2019-08-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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