Baris Tursun

Baris Tursun
University of Hamburg | UHH · Biocenter Grindel and Zoological Museum (BioZ Grindel)

Professor
Professor for Molecular Cell Biology of Animals

About

70
Publications
4,767
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
1,389
Citations
Citations since 2016
47 Research Items
760 Citations
2016201720182019202020212022020406080100120140
2016201720182019202020212022020406080100120140
2016201720182019202020212022020406080100120140
2016201720182019202020212022020406080100120140
Introduction
We use C. elegans as a genetic model organism to systematically study the molecular basis of Cell Fate Maintenance in the context of Development, cellular Reprogramming to Neurons, and Aging. We translate our findings derived from Systems Biology applications (ATAC-Seq, ChIP-Seq, RNA-Seq,) and genetic approaches in C. elegans also to human cells.
Additional affiliations
August 2021 - present
University of Hamburg
Position
  • Professor
Description
  • Professor for Molecular Cell Biology of Animals, Research Group Leader, Principal Investigator. Using C. elegans and human cells to study cell fate safeguarding in the context of reprogramming and aging.
June 2012 - March 2022
Max-Delbrück-Centrum für Molekulare Medizin
Position
  • Principal Investigator
Description
  • Research Group Leader, Principal Investigator. Using C. elegans and human cells to study cell fate safeguarding in the context of reprogramming and aging.

Publications

Publications (70)
Article
Epigenetic mechanisms control chromatin accessibility and gene expression to ensure proper cell fate specification. Histone proteins are integral chromatin components, and their modification promotes gene expression regulation. Specific proteins recognize modified histones such as the chromodomain protein MRG-1. MRG-1 is the Caenorhabditis elegans...
Article
Full-text available
Studying protein interactions in vivo can reveal key molecular mechanisms of biological processes. Co-immunoprecipitation with mass spectrometry detects protein–protein interactions with high throughput. The nematode Caenorhabditis elegans is a powerful genetic model organism for in vivo studies. Yet its rigid and complex tissues require optimizati...
Article
Full-text available
Cell fate conversion by the forced overexpression of transcription factors (TFs) is a process known as reprogramming. It leads to de-differentiation or trans- differentiation of mature cells, which could then be used for regenerative medicine applications to replenish patients suffering from, e.g., neurodegenerative diseases, with healthy neurons....
Preprint
Studying protein-protein interactions in vivo can reveal key molecular mechanisms of biological processes. Co-Immunoprecipitation followed by Mass Spectrometry (CoIP-MS) allows detection of protein-protein interactions in high-throughput. The nematode Caenorhabditis elegans (C. elegans) is a powerful genetic model organism for in vivo studies. Yet,...
Article
Full-text available
We recently identified FAcilitates Chromatin Transcription (FACT) as a reprogramming barrier of transcription factor (TF) mediated conversion of germ cells into neurons in C. elegans. FACT is a conserved heterodimer consisting of SPT16 and SSRP1 in mammals. Duplication events during evolution in C. elegans generated two SSRP1 homologs named HMG-3 a...
Preprint
Full-text available
Epigenetic mechanisms to control chromatin accessibility and structure is important for gene expression in eukaryotic cells. Chromatin regulation ensures proper development and cell fate specification but is also essential later in life. Modifications of histone proteins as an integral component of chromatin can promote either gene expression or re...
Article
Full-text available
Multiple gene activities control complex biological processes such as cell fate specification during development and cellular reprogramming. Investigating the manifold gene functions in biological systems requires also simultaneous depletion of two or more gene activities. RNA interference-mediated knockdown (RNAi) is commonly used in Caenorhabditi...
Article
Full-text available
The potential of a cell to produce all types of differentiated cells in an organism is termed totipotency. Totipotency is an essential property of germ cells, which constitute the germline and pass on the parental genetic material to the progeny. The potential of germ cells to give rise to a whole organism has been the subject of intense research f...
Preprint
Multiple gene activities control complex biological processes such as cell fate specification during development and cellular reprogramming. Investigating the manifold gene functions in biological systems requires also simultaneous depletion of two or more gene activities. RNA interference-mediated knockdown (RNAi) is commonly used in C. elegans to...
Article
Full-text available
Muscle atrophy is a physiological response to disuse and malnutrition, but hibernating bears are largely resistant to this phenomenon. Unlike other mammals, they efficiently reabsorb amino acids from urine, periodically activate muscle contraction, and their adipocytes differentially responds to insulin. The contribution of myocytes to the reduced...
Article
Full-text available
Whether extension of lifespan provides an extended time without health deteriorations is an important issue for human aging. However, to which degree lifespan and aspects of healthspan regulation might be linked is not well understood. Chromatin factors could be involved in linking both aging aspects, as epigenetic mechanisms bridge regulation of d...
Article
Full-text available
Reprogramming has the potential to provide specific cell types for regenerative medicine applications aiming at replacing tissues that have been lost or damaged due to degenerative diseases and injury. In this review we discuss the latest strategies and advances of in vivo reprogramming to convert cell identities in living organisms, including repr...
Article
Full-text available
High-occupancy target (HOT) regions are segments of the genome with unusually high number of transcription factor binding sites. These regions are observed in multiple species and thought to have biological importance due to high transcription factor occupancy. Furthermore, they coincide with house-keeping gene promoters and consequently associated...
Preprint
Whether extension of lifespan provides an extended time without health deteriorations is an important issue for human aging. However, to which degree lifespan and healthspan regulation might be linked is not well understood. Chromatin factors could be involved in linking both aging aspects, as epigenetic mechanisms bridge regulation of different bi...
Article
Full-text available
Chromatin regulators play important roles in the safeguarding of cell identities by opposing the induction of ectopic cell fates and, thereby, preventing forced conversion of cell identities by reprogramming approaches. Our knowledge of chromatin regulators acting as reprogramming barriers in living organisms needs improvement as most studies use t...
Article
Full-text available
Divergent transcription from promoters and enhancers is pervasive in many species, but it remains unclear if it is a general feature of all eukaryotic cis regulatory elements. To address this, here we define cis regulatory elements in C. elegans, D. melanogaster and H. sapiens and investigate the determinants of their transcription directionality....
Data
Table S5. ATAC-Seq Analysis of SSRP1 and SUPT16H Knockdown, Related to Figures 6 and S6
Data
Table S4. ChIP-Seq for SSRP1 and SUPT16H with RNA-Seq Analysis of SSRP1 and SUPT16H Knockdown, Related to Figures 6 and S6
Data
Table S2. Results of HMG-3 and HMG-4 Co-Immunoprecipitation with Subsequent Mass Spectrometry Analysis, Related to Figure S2 and STAR Methods
Data
Table S3. ChIP-Seq, ATAC-Seq, and RNA-Seq Analysis of hmg-3, hmg-4, and spt-16, Related to Figures 4, S3, and S4
Article
The chromatin regulator FACT (facilitates chromatin transcription) is essential for ensuring stable gene expression by promoting transcription. In a genetic screen using Caenorhabditis elegans, we identified that FACT maintains cell identities and acts as a barrier for transcription factor-mediated cell fate reprogramming. Strikingly, FACT's role a...
Article
Full-text available
The direct conversion of one differentiated cell fate into another identity is a process known as Transdifferentiation. During Transdifferentiation, cells pass through intermediate states that are not well understood. Given the potential application of transdifferentiation in regenerative medicine and disease modeling, a better understanding of int...
Article
Full-text available
Studying the cell biological processes during converting the identities of specific cell types provides important insights into mechanism that maintain and protect cellular identities. The conversion of germ cells into specific neurons in the nematode Caenorhabditis elegans (C. elegans) is a powerful tool for performing genetic screens in order to...
Chapter
Full-text available
In the nematode Caenorhabditis elegans PcG proteins forming the Polycomb repressive complex 2 (PRC2) are highly conserved while other PcG-related proteins mediate canonical PRC1 activities. PRC2 in C. elegans mediates histone H3K27 methylation and is mainly required for germline development. Animals without PRC2 lack a germline but are viable. Rece...
Preprint
Full-text available
Divergent transcription from promoters and enhancers is pervasive in many species, but it remains unclear if it is a general and passive feature of all eukaryotic cis regulatory elements. To address this, we define promoters and enhancers in C. elegans, D. melanogaster and H. sapiens using ATAC-Seq and investigate the determinants of their transcri...
Article
Autophagy is a ubiquitous catabolic process that causes cellular bulk degradation of cytoplasmic components and is generally associated with positive effects on health and longevity. Inactivation of autophagy has been linked with detrimental effects on cells and organisms. The antagonistic pleiotropy theory postulates that some fitness-promoting ge...
Preprint
The chromatin regulator FACT (Facilitates Chromatin Transcription) is essential for ensuring stable gene expression by promoting transcription. In a genetic screen using C. elegans we identified that FACT maintains cell identities and acts as a barrier for transcription factor-mediated cell fate reprogramming. Strikingly, FACTs role as a reprogramm...
Preprint
Autophagy is a ubiquitous catabolic process, which causes cellular bulk degradation of cytoplasmic components and thereby regulates cellular homeostasis. Inactivation of autophagy has been linked with detrimental effects to cells and organisms. The antagonistic pleiotropy theory postulates that fitness promoting genes during youth are harmful durin...
Data
Microarray results.(A) Microarray results of differentially expressed genes in Notch ON/OFF gonads. Figure 2—figure supplement 3 source data: Quantification of germlines with wild-type morphology versus germlines with tumors upon germline-autonomous RNAi against genetic interactors of PRC2. More details can be found in the corresponding figure lege...
Data
Information on used C. elegans strains, RNAi clones and primers. (A) Information on C. elegans strains used in the study. (B) Information on RNAi clones used in this study. (C) Information on primer design and sequences. DOI: http://dx.doi.org/10.7554/eLife.15477.025
Data
Quantification of GeCo in glp-1(gf) and lag-1 RNAi animals.(A) Quantification of GeCo+ phenotype upon RNAi against lin-53 in glp-1(ar202) mutants. (B) Quantification of GeCo dependency on LAG-1. (C) Quantification of germ cells in glp-1 (ar202) gonads with our without lag-1 RNAi treatment. (D) Quantification of GeCo in different genetic backgrounds...
Data
In situ hybridization patterns of Notch-activated genes. DOI: http://dx.doi.org/10.7554/eLife.15477.024
Data
Quantification of GeCo upon PRC2 depletion.(A) Quantification of GeCo+ phenotype upon RNAi against PRC2 subunits in glp-1(ar202) mutants. (B) Quantification of GeCo in different genetic backgrounds with highly proliferative germlines upon RNAi against PRC2 subunits. More details can be found in the corresponding figure legends.DOI: http://dx.doi.or...
Data
Quantification of GeCo upon double RNAi against lin-53 and Notch-activated genes.(A) Quantification of GeCo+ upon RNAi against lin-53 and Notch-activated genes. (B) Quantification of GeCo+ upon RNAi against lin-53 and Histone demethylases. Figure 4—figure supplement 1A source data: Quantification of GeCo+ upon RNAi against lin-53 and utx-1 with and...
Data
Enhancement or suppression of tumorous phenotypes. DOI: http://dx.doi.org/10.7554/eLife.15477.023
Article
Full-text available
Cell-fate reprograming is at the heart of development, yet very little is known about the molecular mechanisms promoting or inhibiting reprograming in intact organisms. In the C. elegans germline, reprograming germ cells into somatic cells requires chromatin perturbation. Here, we describe that such reprograming is facilitated by GLP-1/Notch signal...
Article
Full-text available
Background Affinity purification followed by mass spectrometry (AP/MS) is a widely used approach to identify protein interactions and complexes. In multicellular organisms, the accurate identification of protein complexes by AP/MS is complicated by the potential heterogeneity of complexes in different tissues. Here, we present an in vivo biotinylat...
Article
Full-text available
Left/right asymmetric features of animals are either randomly distributed on either the left or right side within a population ("antisymmetries") or found stereotypically on one particular side of an animal ("directional asymmetries"). Both types of asymmetries can be found in nervous systems, but whether the regulatory programs that establish thes...
Article
Full-text available
How specific cell types can be directly converted into other distinct cell types is a matter of intense investigation with wide-ranging basic and biomedical implications. Here, we show that removal of the histone 3 lysine 27 (H3K27) methyltransferase Polycomb repressor complex 2 (PRC2) permits ectopically expressed, neuron-type-specific transcripti...
Article
The identity of individual cell types in a multicellular organism appears to be continuously maintained through active processes but is not irreversible. Changes in the identity of individual cell types can be brought about through ectopic mis-expression of regulatory factors, but in a number of cases also occurs in normal development. I will revie...
Article
Full-text available
The ability of transcription factors to directly reprogram the identity of cell types is usually restricted and is defined by cellular context. Through the ectopic expression of single Caenorhabditis elegans transcription factors, we found that the identity of mitotic germ cells can be directly converted into that of specific neuron types: glutamat...
Article
Full-text available
Transcriptional co-repressors of the Groucho/TLE family are important regulators of development in many species. A subset of Groucho/TLE family members that lack the C-terminal WD40 domains have been proposed to act as dominant-negative regulators of Groucho/TLE proteins, yet such a role has not been conclusively proven. Through a mutant screen for...
Article
Full-text available
3' Untranslated region (UTR)-dependent post-transcriptional regulation has emerged as a critical mechanism of controlling gene expression in various physiological contexts, including cellular differentiation events. Here, we examine the regulation of the 3'UTR of the die-1 transcription factor in a single neuron of the nematode C. elegans. This 3'U...
Article
Full-text available
An understanding of the molecular mechanisms of cell fate determination in the nervous system requires the elucidation of transcriptional regulatory programs that ultimately control neuron-type-specific gene expression profiles. We show here that the C. elegans Tailless/TLX-type, orphan nuclear receptor NHR-67 acts at several distinct steps to dete...
Data
Comparison of our protocol to that of Dolphin and Hope (0.05 MB DOC)
Data
Example of extending a fosmid sequence. The goal was to extend a fosmid, WRM065cB03, to make it contain the full gcy-22 locus. This application is necessary in those relatively rare cases in which there is low fosmid coverage of a genomic region. pBALU-ext was used to amplify the kanamycin (Kan) resistance gene flanked by sequences homologous to th...
Data
Sequences of all pBALU cassettes (0.10 MB DOC)
Data
Example of sequence replacement by fosmid recombineering. The goal was to replace the miRNA-regulated 3′UTR from the cog-1 gene with that of 3′UTR from the unc-54 gene. Fosmid WRM067cF11 containing a yfp insertion in the cog-1 gene was used as the substrate for 3′ UTR replacement. pBALU 21 was used as template for amplification of the unc-54 3′ UTR...
Article
Full-text available
Mammary oncogenesis is profoundly influenced by signaling pathways controlled by estrogen receptor alpha (ERalpha). Although it is known that ERalpha exerts its oncogenic effect by stimulating the proliferation of many human breast cancers through the activation of target genes, our knowledge of the underlying transcriptional mechanisms remains lim...
Article
Full-text available
Engineering fluorescent proteins into large genomic clones, contained within BACs or fosmid vectors, is a tool to visualize and study spatiotemporal gene expression patterns in transgenic animals. Because these reporters cover large genomic regions, they most likely capture all cis-regulatory information and can therefore be expected to recapitulat...
Article
Full-text available
Complexes composed of multiple proteins regulate most cellular functions. However, our knowledge about the molecular mechanisms governing the assembly and dynamics of these complexes in cells remains limited. The in vivo activity of LIM homeodomain (LIM-HD) proteins, a class of transcription factors that regulates neuronal development, depends on t...
Article
The developmental regulation of LIM homeodomain transcription factors (LIM-HD) by the LIM domain-binding cofactors CLIM/Ldb/NLI and RLIM has been demonstrated. Whereas CLIM cofactors are thought to be required for at least some of the in vivo functions of LIM-HD proteins, the ubiquitin ligase RLIM functions as a negative regulator by its ability to...