Biology subjects

Krause, K.

Publications and source records attributed to Krause, K..

15 recordsLinked to original sources

bioRxiv2025

Epigenetic gene regulation is controlled by distinct regulatory complexes utilizing specialized paralogs of TELOMERE REPEAT BINDING FACTORS

Epigenetic regulators shape chromatin landscapes, allowing cells to express distinct gene sets depending on cell-type, developmental stage or environmental cues. These regulatory complexes rely on interactions with sequence-specific DNA binding proteins, such as the small family of TELOMERE REPEAT BINDING FACTORS (TRBs). TRBs are components of chromatin regulatory complexes with opposing functions, such as the epigenetic repressors Polycomb Repressive Complex 2 (PRC2) and a JMJ14/NAC complex that respectively add and removes the repressive H3K27me3 and positive H3K4me3 modification, but also with the plant-specific PEAT complex that is linked to histone acetylation and gene activation. We dissected the partial redundancy between TRB1, TRB2 and TRB3 in target gene selection and interaction with different chromatin regulatory complexes. High redundancy of TRBs is suggested by major phenotypic changes that are only observed trb triple mutants; however, we found different target site preference between TRB1-3 and preferred partnership with chromatin complexes. Furthermore, TRB paralogs interacted with the NuA4 histone acetylation complex, both together with and in absence of PEAT. Among the three paralogs, TRB1 had more unique binding sites and correlated stronger with PEAT and NuA4 functions. In contrast, TRB2 and TRB3 were more dependent on the presence of bona fide telo-box motifs and were more likely to be found at PRC2 associated sites. Overall, we provide insight into the diverse roles of TRBs in epigenetic gene regulation and how their diversification contributes to their apparent redundancy, as well as their observed activating and repressing effects on gene expression.

plant biology↗

bioRxiv2025

Functional interrogation uncovers a critical role for a high-plasticity cell state in lung adenocarcinoma

Plasticity--the ability of cells to undergo phenotypic transitions--drives cancer progression and therapy resistance1-3. To date, strategies targeting cancer plasticity have not advanced to the clinic due to a lack of fundamental understanding of the underlying mechanisms. Recent studies have suggested that plasticity in solid tumors is concentrated in a minority subset of cancer cells4-6, yet functional studies interrogating this high plasticity cell state (HPCS) in situ are lacking. Here, we developed mouse models enabling detection, longitudinal lineage tracing, and ablation of the HPCS in autochthonous lung tumors in vivo. Using lineage tracing, we uncover the HPCS cells are dedifferentiated but possess high capacity for cell state transitions, giving rise to both early neoplastic (differentiated) and advanced lung cancer cell states in situ. Longitudinal lineage tracing using secreted luciferases reveals HPCS-derived cells harbor high capacity for growth when compared to bulk cancer cells or another defined cancer cell state with features of differentiated lung epithelium. Suicide gene-mediated ablation of the HPCS in early neoplasias abrogates tumor progression. Ablating HPCS cells in established tumors by suicide gene or HPCS-directed CAR T cells robustly reduces tumor burden, whereas ablation of a differentiated lung cancer cell state had no effect. We further demonstrate that the HPCS gives rise to therapy-resistant cell states, whereas ablation of the HPCS abrogates resistance to chemotherapy and oncoprotein-targeted therapy. Interestingly, an HPCS-like state is ubiquitous in regenerating epithelia and in carcinomas of multiple other tissues, revealing a convergence of plasticity programs. Our work establishes the HPCS as a critical hub enabling reciprocal transitions between cancer cell states, including acquisition of states adapted to cancer therapies. Targeting the HPCS in lung cancer and in other carcinomas may suppress cancer progression and eradicate treatment resistance.

cancer biology↗

bioRxiv2024

Sex-specific role of epigenetic modification of a leptin upstream enhancer in the adipose tissue

ObjectiveMaternal hormonal status can have long-term effects on offspring metabolic health, likely regulated via epigenetic mechanisms. We elucidated the effect of maternal thyroid hormones on epigenetic regulation of Leptin (Lep) transcription in adipose tissue (AT) and investigated the role of DNA methylation at a Lep upstream enhancer (UE) in adipocyte biology. MethodsPregnant mice were treated with Triiodothyronine (T3). Offspring body composition and adipose tissue were analysed at 6 months (treatment: N = 8, control: N = 12). DNA methylation at the Lep UE and Lep mRNA levels in gonadal white adipose tissue (gWAT) and leptin serum levels were measured. The Lep UE was hypomethylated in murine preadipocytes using a dCas9-SunTag-TET1 system, followed by differentiation. In human visceral AT samples (N = 52) from the Leipzig Obesity BioBank (LOBB) LEP UE methylation and LEP mRNA levels were assessed alongside leptin serum levels and correlated with body fat percentage. Causal relationships were explored using mediation analysis. ResultsHigh maternal T3 levels reduced offspring body weight, total fat, and gWAT mass. Female offspring of T3-treated mothers showed lower Lep mRNA levels and higher Lep UE methylation compared to controls. CRISPR/dCas9 editing reduced Lep UE methylation by [~]20% in preadipocytes without altering Lep expression or lipid accumulation after differentiation. In humans, a mediation of sex-specific difference in body fat percentage via Lep UE methylation was found. ConclusionMaternal thyroid hormones might affect offspring gWAT Lep expression in a sex-specific manner, potentially driven by DNA methylation at the Lep UE, influencing body fat percentage.

genetics↗

bioRxiv2024

Glia multitask to compensate for neighboring glial cell dysfunction

As glia mature, they undergo glial tiling to abut one another without invading each others boundaries. Upon the loss of the secreted neurotrophin Spatzle3 (Spz3), Drosophila cortex glia transform morphologically and lose their intricate interactions with neurons and surrounding glial subtypes. Here, we reveal that all neighboring glial cell types (astrocytes, ensheathing glia, and subperineurial glia) react by extending processes into the previous cortex glial territory to compensate for lost cortex glial function and reduce the buildup of neuronal debris. However, the loss of Spz3 alone is not sufficient for glia to cross their natural borders, as blocking CNS growth via nutrient-restriction blocks the aberrant infiltration induced by the loss of Spz3. Surprisingly, even when these neighboring glia divert their cellular resources beyond their typical borders to take on new compensatory roles, they are able to multitask to continue to preserve their own normal functions to maintain CNS homeostasis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/611719v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@1a1a884org.highwire.dtl.DTLVardef@3ea222org.highwire.dtl.DTLVardef@676b7org.highwire.dtl.DTLVardef@5c21d6_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

Novel RNA-binding protein YebC enhances translation of proline-rich amino acid stretches in bacteria

The ribosome employs a set of highly conserved translation factors to efficiently synthesise proteins. Some translation factors interact with the ribosome in a transient manner and are thus challenging to identify. However, proteins involved in translation can be specifically identified by their interaction with ribosomal RNAs. Using a combination of proteomics approaches, we identified novel RNA binding proteins in the pathogenic bacterium Streptococcus pyogenes. One of these, a universally conserved protein YebC, was shown to transiently interact with 23S rRNA near the peptidyl-transferase centre. Deletion of yebC moderately affected the physiology and virulence of S. pyogenes. We performed ribosome profiling and detected increased pausing at proline-rich amino acid stretches in the absence of functional YebC. Further results obtained with in vivo reporters and in vitro translation system suggest that YebC is a novel translation factor required for efficient translation of proteins with proline-rich motifs.

molecular biology↗

bioRxiv2024

Expression quantitative trait locus mapping in recombinant gametes using single nucleus RNA sequencing

Phenotypic differences between individuals of a species are often caused by differences in gene expression, which are in turn caused by genetic variation. Expression quantitative trait locus (eQTL) analysis is a methodology by which we can identify such causal variants. Scaling eQTL analysis is costly due to the expense of generating mapping populations, and the collection of matched transcriptomic and genomic information. We developed a rapid eQTL analysis approach using single-cell/nucleus RNA sequencing of gametes from a small number of heterozygous individuals. Patterns of inherited polymorphisms are used to infer the recombinant genomes of thousands of individual gametes and identify how different haplotypes correlate with variation in gene expression. Applied to Arabidopsis pollen nuclei, our approach uncovers both cis- and trans-eQTLs, ultimately mapping variation in a master regulator of sperm cell development that affects the expression of hundreds of genes. This establishes snRNA-sequencing as a powerful, cost-effective method for the mapping of meiotic recombination, addressing the scalability challenges of eQTL analysis and enabling eQTL mapping in specific cell-types.

bioinformatics↗

bioRxiv2024

The majority of somatic mutations in fruit trees are layer-specific

BackgroundAll plant tissues and organs develop from meristems. Plant meristems are structured organs consisting of distinct layers of stem cells. Somatic mutations occurring in one of these layers can propagate into large sectors of the plant. However, the frequency and characteristics of meristematic mutations that form the basis of somaclonal phenotypic variation remain unclear. ResultsHere, we analysed the frequency and distribution of somatic mutations in an individual Apricot tree. For this, we sequenced the genomes of fruit samples corresponding to distinct meristematic cell layers selected across the entire tree. Most somatic mutations (>90%) were specific to individual layers. Genotyping the somatic mutations in leaves sampled next to the fruits confirmed their meristematic origin. Interestingly, layer 1 (epidermis) had a higher mutation load than layer 2 (mesocarp), implying differential mutational dynamics between the layers. The somatic mutations followed the branching pattern of the tree. These factors led to the unexpected observation that the layer 1 samples from different branches were more similar to each other than to layer 2 samples of the same branch. Further, using single-cell RNA sequencing, we demonstrated that the layer-specific mutant alleles could only be found in the transcripts of the respective, layer-specific cell clusters and could form the basis for somaclonal phenotypic variation. ConclusionsHere, we analyzed the prevalence and distribution of somatic mutations with meristematic origin. Our insights into the yet unexplored layer-specificity of such somatic mutations outlined how they can be identified and how they impact the breeding of clonally propagated crops.

genomics↗

bioRxiv2023

DNA hypomethylation promotes the expression of CASPASE-4 which exacerbates neuroinflammation and amyloid-β deposition in Alzheimer's disease

Alzheimers Disease (AD) is the 6th leading cause of death in the US. It is established that neuroinflammation contributes to the synaptic loss, neuronal death, and symptomatic decline of AD patients. Accumulating evidence suggests a critical role for microglia, innate immune phagocytes of the brain. For instance, microglia release pro-inflammatory products such as IL-1{beta} which is highly implicated in AD pathobiology. The mechanisms underlying the transition of microglia to proinflammatory promoters of AD remain largely unknown. To address this gap, we performed Reduced Representation Bisulfite Sequencing (RRBS) to profile global DNA methylation changes in human AD brains compared to no disease controls. We identified differential DNA methylation of CASPASE-4 (CASP4), which when expressed, can be involved in generation of IL-1{beta} and is predominantly expressed in immune cells. DNA upstream of the CASP4 transcription start site was hypomethylated in human AD brains, which was correlated with increased expression of CASP4. Furthermore, microglia from a mouse model of AD (5xFAD) express increased levels of CASP4 compared to wild-type (WT) mice. To study the role of CASP4 in AD, we developed a novel mouse model of AD lacking the mouse ortholog of CASP4, CASP11, which is encoded by mouse Caspase-4 (5xFAD/Casp4-/-). The expression of CASP11 was associated with increased accumulation of pathologic protein aggregate amyloid-{beta} (A{beta}) and increased microglial production of IL-1{beta} in 5xFAD mice. Utilizing RNA sequencing, we determined that CASP11 promotes unique transcriptomic phenotypes in 5xFAD mouse brains, including alterations of neuroinflammatory and chemokine signaling pathways. Notably, in vitro, CASP11 promoted generation of IL-1{beta} from macrophages in response to cytosolic A{beta} through cleavage of downstream effector Gasdermin D (G SDMD). We describe a role for CASP11 and GSDMD in the generation of IL-1{beta} in response to A{beta} and the progression of pathologic inflammation in AD. Overall, our results demonstrate that overexpression of CASP4 due to differential methylation in AD microglia contributes to the progression of AD pathobiology, thus identifying CASP4 as a potential target for immunotherapies for the treatment of AD.

neuroscience↗

bioRxiv2023

The identification and analysis of meristematic mutations within the apple tree that developed the RubyMac sport mutation

Understanding the molecular basis of sport mutations in fruit trees can accelerate breeding of novel cultivars. For this, we analyzed the DNA of the apple tree that evolved the RubyMac phenotype through a sport mutation that introduced changes in fruit coloration in upper branches of the tree. Unexpectedly, we not only found 46 de novo mutations, but also 54 somatic gene conversions (i.e., loss-of-heterozygosity mutations) distinguishing the mutant and wild-type branches of the tree. Approximately 30% of the de novo mutations and 80% of the gene conversions were observed only in specific cells layers suggesting that they occurred in the corresponding meristematic layers. Interestingly, the de novo mutations were enriched for GC=>AT transitions, while the gene conversions showed the opposite bias for AT=>GC transitions suggesting that GC-biased gene conversions have the potential to counteract the AT-bias of de novo mutations. By comparing the gene expression patterns in fruit skins from mutant and wild-type branches, we found 56 differentially expressed genes including 18 that were involved in anthocyanin biosynthesis. While none of the differently expressed genes harbored a mutation, we found that some of the mutations affected the integrity of candidate genes in regions of the genome that were recently associated with natural variation in fruit coloration.

genomics↗

bioRxiv2022

Machine learning guided signal enrichment for ultrasensitive plasma tumor burden monitoring

In solid tumor oncology, circulating tumor DNA (ctDNA) is poised to transform care through accurate assessment of minimal residual disease (MRD) and therapeutic response monitoring. To overcome the sparsity of ctDNA fragments in low tumor fraction (TF) settings and increase MRD sensitivity, we previously leveraged genome-wide mutational integration through plasma whole genome sequencing (WGS). We now introduce MRD-EDGE, a composite machine learning-guided WGS ctDNA single nucleotide variant (SNV) and copy number variant (CNV) detection platform designed to increase signal enrichment. MRD-EDGE uses deep learning and a ctDNA-specific feature space to increase SNV signal to noise enrichment in WGS by 300X compared to our previous noise suppression platform MRDetect. MRD-EDGE also reduces the degree of aneuploidy needed for ultrasensitive CNV detection through WGS from 1Gb to 200Mb, thereby expanding its applicability to a wider range of solid tumors. We harness the improved performance to track changes in tumor burden in response to neoadjuvant immunotherapy in non-small cell lung cancer and demonstrate ctDNA shedding in precancerous colorectal adenomas. Finally, the radical signal to noise enrichment in MRD-EDGE enables de novo mutation calling in melanoma without matched tumor, yielding clinically informative TF monitoring for patients on immune checkpoint inhibition.

genomics↗

bioRxiv2021

Clostridium difficile Toxin B activates the NLRP3 inflammasome in human macrophages, demonstrating a novel regulatory mechanism for the Pyrin inflammasome

Pyrin is a cytosolic immune sensor that forms an inflammasome when bacterial virulence factors inhibit RhoA, triggering the release of inflammatory cytokines, including IL-1{beta}. Gain of function mutations in the MEFV gene encoding Pyrin cause auto-inflammatory disorders, such as familial Mediterranean fever (FMF) and Pyrin associated auto-inflammation with Neutrophilic Dermatosis (PAAND). To precisely define the role of Pyrin in detecting pathogen virulence factors in relevant human immune cells, we investigated how the Pyrin inflammasome response was initiated and regulated in monocyte-derived macrophages (hMDM) compared to human monocytes. Unlike monocytes and murine macrophages, we determined that hMDM failed to activate Pyrin in response to known Pyrin activators Clostridioides difficile (C. difficile) toxins A or B (TcdA or TcdB). In contrast, TcdB activated the NLRP3 inflammasome in hMDM. Notably, we ascertained that the Pyrin inflammasome response could be re-enabled in hMDM by prolonged priming with either LPS or type I or II interferons, and required an increase in Pyrin expression. These data demonstrate an unexpected redundancy in detecting these toxins by inflammasome sensors.

immunology↗

bioRxiv2021

Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

Potato is the most important tuber crop in the world. However, separate reconstruction of the four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report the 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the potato cultivar Otava using high-quality long reads coupled with single-cell sequencing of 717 pollen genomes and Hi-C data. Unexpectedly, almost 50% of the genome were found to be identical-by-descent due to recent inbreeding, which contrasted by highly abundant structural rearrangements involving around 20% of the genome. Among 38,214 genes, only 54% were present in four haplotypes with an average of 3.2 copies per gene. Analyzing the leaf transcriptome as example, we found that 11% of the genes featured differently expressed alleles in at least one of the haplotypes, of which 25% are likely regulated through allele-specific DNA methylation. Our work sheds light on the recent breeding history of potato, the functional organization of its tetraploid genome and has the potential to strengthen the future of genomics-assisted breeding.

genomics↗

bioRxiv2021

Mitochondrial genomes of two parasitic Cuscuta species show little evidence of horizontal gene transfer and retain unusually fragmented ccmFC genes

BackgroundThe intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus. ResultsThe mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with ten missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmFC gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT. ConclusionsThe lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of the Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences.

genomics↗

bioRxiv2020

A highly efficient protocol for transforming Cuscuta reflexa based on artificially induced infection sites

A current bottleneck in the functional analysis of the emerging parasitic model plant Cuscuta and the exploitation of its recently sequenced genomes is the lack of efficient transformation tools. Here, we describe the development of a novel highly efficient Agrobacterium-mediated transformation protocol for Cuscuta reflexa based on the parasitic structure referred to as adhesive disk. Both, Agrobacterium rhizogenes and Agrobacterium tumefaciens carrying binary transformation vectors with reporter fluorochromes yielded high numbers of transformation events. An overwhelming majority of transformed cells were observed in the cell layer below the adhesive disks epidermis, suggesting that these cells are particularly susceptible to infection. Co-transformation of these cells happens frequently when Agrobacterium strains carrying different constructs are applied together. Explants containing transformed tissue expressed the fluorescent markers in in vitro culture for several weeks, offering a possibility for development of transformed cells into callus. ONE SENTENCE SUMMARYA protocol that yields high numbers of transformed cells in the adhesive disks of Cuscuta reflexa upon exposure to agrobacteria brings closer the vision of generating genetically modified Cuscuta.

plant biology↗

bioRxiv2020

The chloroplast ribonucleoprotein CP33B quantitatively binds the psbA mRNA

Chloroplast RNAs are stabilized and processed by a multitude of nuclear-encoded RNA binding proteins, often in response to external stimuli like light and temperature. A particularly interesting RNA based regulation occurs with the psbA mRNA, which shows light-dependent translation. Recently, the chloroplast ribonucleoprotein CP33B was identified as a ligand of the psbA mRNA. We here characterized the interaction of CP33B with chloroplast RNAs in greater detail using a combination of RIP-chip, quantitative dot-blot, and RNA-Bind-n-Seq experiments. We demonstrate that CP33B prefers psbA over all other chloroplast RNAs and associates with vast majority of the psbA transcript pool. The RNA sequence target motif determined in vitro does not fully explain CP33Bs preference for psbA, suggesting that there are other determinants of specificity in vivo.

molecular biology↗