The C. elegans pseudogene sspt-16 (F55A3.7) is required to safeguard germ cells against reprogramming.

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 and HMG-4, while SPT-16 is the only homolog of SPT16. Yet, the pseudogene F55A3.7 has nearly complete nucleotide sequence homology to the spt-16 gene. However, F55A3.7 lacks some spt-16 exons and DNA pieces so we named it sspt-16 (short spt-16). Surprisingly, the deletion mutant ok1829, which affects only the sspt-16 pseudogene, shows similar germ cell reprogramming effects as described previously for FACT-depleted animals. We examined whether lack of sspt-16 affects other genes or chromatin accessibility, which may explain the permissiveness for germ cell reprogramming.

The CONJUDOR pipeline for multiplexed knockdown of gene pairs identifies RBBP-5 as a germ cell reprogramming barrier in C. elegans.

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 Caenorhabditis elegans to assess essential genes, which otherwise lead to lethality or developmental arrest upon full knockout. RNAi application is straightforward by feeding worms with RNAi plasmid-containing bacteria. However, the general approach of mixing bacterial RNAi clones to deplete two genes simultaneously often yields poor results. To address this issue, we developed a bacterial conjugation-mediated double RNAi technique 'CONJUDOR'. It allows combining RNAi bacteria for robust double RNAi with high-throughput. To demonstrate the power of CONJUDOR for large scale double RNAi screens we conjugated RNAi against the histone chaperone gene lin-53 with more than 700 other chromatin factor genes. Thereby, we identified the Set1/MLL methyltransferase complex member RBBP-5 as a novel germ cell reprogramming barrier. Our findings demonstrate that CONJUDOR increases efficiency and versatility of RNAi screens to examine interconnected biological processes in C. elegans with high-throughput.

Strategies for in vivo reprogramming.

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 reprogramming induced by transcription factors (TFs) and CRISPR/dCas9 synthetic TFs, as well as by cell fusion and small molecules. We also provide a brief recap of reprogramming barriers, the effect of senescence on reprogramming efficiency, and strategies to deliver reprogramming factors in vivo. Because of the limited space, we omit dwelling on naturally occurring reprogramming phenomena such as developmentally programmed transdifferentiation found in the nematode Caenorhabditis elegans.

MRG-1/MRG15 Is a Barrier for Germ Cell to Neuron Reprogramming in Caenorhabditis elegans.

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 tissue culture. We used Caenorhabditis elegans as an in vivo gene discovery model and automated solid-phase RNA interference screening, by which we identified 10 chromatin-regulating factors that protect cells against ectopic fate induction. Specifically, the chromodomain protein MRG-1 safeguards germ cells against conversion into neurons. MRG-1 is the ortholog of mammalian MRG15 (MORF-related gene on chromosome 15) and is required during germline development in C. elegans However, MRG-1's function as a barrier for germ cell reprogramming has not been revealed previously. Here, we further provide protein-protein and genome interactions of MRG-1 to characterize its molecular functions. Conserved chromatin regulators may have similar functions in higher organisms, and therefore, understanding cell fate protection in C. elegans may also help to facilitate reprogramming of human cells.

FACT Sets a Barrier for Cell Fate Reprogramming in Caenorhabditis elegans and Human Cells.

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 as a barrier to cell fate conversion is conserved in humans as we show that FACT depletion enhances reprogramming of fibroblasts. Such activity is unexpected because FACT is known as a positive regulator of gene expression, and previously described reprogramming barriers typically repress gene expression. While FACT depletion in human fibroblasts results in decreased expression of many genes, a number of FACT-occupied genes, including reprogramming-promoting factors, show increased expression upon FACT depletion, suggesting a repressive function of FACT. Our findings identify FACT as a cellular reprogramming barrier in C. elegans and humans, revealing an evolutionarily conserved mechanism for cell fate protection.

Dewaxed ECM: A simple method for analyzing cell behaviour on decellularized extracellular matrices.

Decellularization techniques have been used on a wide variety of tissues to create cell-seedable scaffolds for tissue engineering. Finding a suitable decellularization protocol for a certain type of tissue can be laborious, especially when organ perfusion devices are needed. In this study, we report a quick and simple method for comparing decellularization protocols combining the use of paraffin slices and two-dimensional cell cultures. We developed three decellularization protocols for adult murine kidney that yielded decellularized extracellular matrices (ECMs) with varying histological properties. The resulting paraffin-embedded ECM slices were deparaffinized and reseeded with murine embryonic stem cells (mESCs). We analyzed cell attachment four days post seeding via determination of cell numbers, and used quantitative Real-Time PCR 13 days post seeding to measure gene expression levels of two genes associated with renal development, Pax2 and Pou3f3. The three decellularization protocols produced kidney-matrices that showed clearly distinguishable results. We demonstrated that formerly paraffin-embedded decellularized ECMs can effectively influence differentiation of stem cells. This method can be used to identify optimal decellularization protocols for recellularization of three-dimensional tissue-scaffolds with embryonic stem cells and other tissue-specific cell types.

ECM modulated early kidney development in embryonic organ culture.

The use of exogenous signals is gaining importance in renal regenerative therapies. We wanted to explore the role of extracellular matrix (ECM) constituents on renal structure formation during renal organogenesis. We used a recently established organ culture setup to expose embryonic kidney rudiments directly to a large set of surface-immobilized or dissolved ECM molecules and growth factors. Organ culture was also performed on immobilized adult kidney ECM extracts and on reactive polymer films without any biomolecular components. The applied conditions resulted in distinct differences of organ phenotypes, underlining the multifaceted role of exogenous signals during kidney development. Specific ECM components, including collagen I and laminin, supported nephronal and tubular structure formation of the developing organ. ECM biopolymers, e.g. hyaluronic acid, were found to determine the fate of developing explants in a concentration- and molecular weight-dependent manner. The organ culture system used was an effective and robust means to identify exogenous signals that direct kidney development. This system can provide valuable insight for future regenerative therapies of kidney diseases.

A novel, low-volume method for organ culture of embryonic kidneys that allows development of cortico-medullary anatomical organization.

Here, we present a novel method for culturing kidneys in low volumes of medium that offers more organotypic development compared to conventional methods. Organ culture is a powerful technique for studying renal development. It recapitulates many aspects of early development very well, but the established techniques have some disadvantages: in particular, they require relatively large volumes (1-3 mls) of culture medium, which can make high-throughput screens expensive, they require porous (filter) substrates which are difficult to modify chemically, and the organs produced do not achieve good cortico-medullary zonation. Here, we present a technique of growing kidney rudiments in very low volumes of medium-around 85 microliters-using silicone chambers. In this system, kidneys grow directly on glass, grow larger than in conventional culture and develop a clear anatomical cortico-medullary zonation with extended loops of Henle.