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Digitale Medien

The MAT A locus of the dimorphic yeast Yarrowia lipolytica consists of two divergently oriented genes (1999)

Kurischko, C. ; Schilhabel, M. B. ; Kunze, I. ; [weitere]

Springer

Molecular genetics and genomics 262 (1999), S. 180-188

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ISSN: 1617-4623

Schlagwort(e): Key words Mating type ; Dimorphic yeast ; Sporulation ; HMG box

Quelle: Springer Online Journal Archives 1860-2000

Thema: Biologie

Notizen: Abstract The MAT A locus of Yarrowia lipolytica, which was on the basis of its ability to induce sporulation in a diploid B/B strain, represses the mating capacity of this strain. The gene functions required for induction of sporulation and repression of conjugation could be separated by subcloning. Sequence analysis revealed two ORFs in the MAT A locus. One of them (MAT A1) codes for a protein of 119 amino acids which is required to induce sporulation. The other (MAT A2) codes for a protein of 291 amino acids that is able to repress conjugation. Both genes are oriented divergently from a central promoter region, which possesses putative TATA and CAAT boxes for both genes. The product of MAT A1 shows no homology to any known protein and seems to represent a new class of mating-type genes. MAT A2 contains a HMG box with homology to other mating-type genes. Both MAT A1 and MAT A2 are mating-type specific. In cells of both mating types, the regions flanking the MAT A locus contain sequences with homology to either S. cerevisiae SLA2 and ORF YBB9, respectively. From hybridization and subcloning data we estimate that the MAT A region is approximately 2 kb long and is present only once in the genome.

Materialart: Digitale Medien

URL: http://dx.doi.org/10.1007/s004380051073

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Recent transfer of an iron-regulated gene from the plastid to the nuclear genome in an oceanic diatom adapted to chronic iron limitation (2010)

Lommer, Markus ; Roy, Alexandra-Sophie ; Schilhabel, M. ; [weitere]

BioMed Central

In: BMC Genomics, 11 . p. 718.

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Publikationsdatum: 2019-09-23

Beschreibung: Background Although the importance and widespread occurrence of iron limitation in the contemporary ocean is well documented, we still know relatively little about genetic adaptation of phytoplankton to these environments. Compared to its coastal relative Thalassiosira pseudonana, the oceanic diatom Thalassiosira oceanica is highly tolerant to iron limitation. The adaptation to low-iron conditions in T. oceanica has been attributed to a decrease in the photosynthetic components that are rich in iron. Genomic information on T. oceanica may shed light on the genetic basis of the physiological differences between the two species. Results The complete 141790 bp sequence of the T. oceanica chloroplast genome [GenBank: GU323224], assembled from massively parallel pyrosequencing (454) shotgun reads, revealed that the petF gene encoding for ferredoxin, which is localized in the chloroplast genome in T. pseudonana and other diatoms, has been transferred to the nucleus in T. oceanica. The iron-sulfur protein ferredoxin, a key element of the chloroplast electron transport chain, can be replaced by the iron-free flavodoxin under iron-limited growth conditions thereby contributing to a reduction in the cellular iron requirements. From a comparison to the genomic context of the T. pseudonana petF gene, the T. oceanica ortholog can be traced back to its chloroplast origin. The coding potential of the T. oceanica chloroplast genome is comparable to that of T. pseudonana and Phaeodactylum tricornutum, though a novel expressed ORF appears in the genomic region that has been subjected to rearrangements linked to the petF gene transfer event. Conclusions The transfer of the petF from the cp to the nuclear genome in T. oceanica represents a major difference between the two closely related species. The ability of T. oceanica to tolerate iron limitation suggests that the transfer of petF from the chloroplast to the nuclear genome might have contributed to the ecological success of this species.

Materialart: Article , PeerReviewed

Format: text

DOI: 10.1186/1471-2164-11-718

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Population connectivity and dispersal of vent mussels from the Mid-Atlantic Ridge (2015)

Breusing, Corinna ; Biastoch, Arne ; Drews, Annika ; [weitere]

In: [Talk] In: 14. Deep-Sea Biology Symposium, 31.08.-04.09.2015, Aveiro, Portugal .

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Publikationsdatum: 2019-09-23

Beschreibung: Knowledge about the genetic connectivity of populations is crucial for conserving biological diversity at hydrothermal vents. However, despite the paucity of such data for deep-sea biota, vent communities become increasingly threatened by anthropogenic pressures through resource extraction. Deep-sea mussels of the genus Bathymodiolus are key species in hydrothermal ecosystems worldwide. Using transcriptome sequencing we investigate migration and gene flow patterns among 10 Bathymodiolus populations of the Mid-Atlantic Ridge (37°N to 9°S). We combine outputs of particle tracking analyses using a 1/20° ocean model with genotypic data derived from 103 molecular markers that were designed from high-throughput transcriptomes. Multilocus assignment and differentiation tests indicated the presence of one southern and two northern genetic pools that become increasingly isolated with geographic distance. In spite of the relatively long pelagic duration of Bathymodiolus veligers, our analyses also show that dispersal of more than 100 km is unlikely and that connectivity between known vent populations can only be achieved via intermediate stepping stone habitats. These results have important ramifications for biodiversity conservation in Mid-Atlantic vents that might become targets for mineral extraction activities.

Materialart: Conference or Workshop Item , NonPeerReviewed

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MINCR is a MYC-induced lncRNA [Genetics] (2015)

Doose, G., Haake, A., Bernhart, S. H., Lopez, C., Duggimpudi, S., Woȷciech, F., Bergmann, A. K., Borkhardt, A., Burkhardt, B., Claviez, A., Dimitrova, L., Haas, S., Hoell, J. I., Hummel, M., Karsch, D., Klapper, W., Kleo, K., Kretzmer, H., Kreuz, M., Kuppers, R., Lawerenz, C., Lenze, D., Loeffler, M., Mantovani–Loffler, L., Moller, P., Ott, G., Richter, J., Rohde, M., Rosenstiel, P., Rosenwald, A., Schilhabel, M., Schneider, M., Scholz, I., Stilgenbauer, S., Stunnenberg, H. G., Szczepanowski, M., Trumper, L., Weniger, M. A., ICGC MMML–Seq Consortium, Hoffmann, S., Siebert, R., Iaccarino, I.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publikationsdatum: 2015-09-23

Beschreibung: Despite the established role of the transcription factor MYC in cancer, little is known about the impact of a new class of transcriptional regulators, the long noncoding RNAs (lncRNAs), on MYC ability to influence the cellular transcriptome. Here, we have intersected RNA-sequencing data from two MYC-inducible cell lines and a...

Print ISSN: 0027-8424

Digitale ISSN: 1091-6490

Thema: Biologie , Medizin , Allgemeine Naturwissenschaft

Publiziert von National Academy of Sciences

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The Transcriptome Analysis and Comparison Explorer--T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms (2012)

Philipp, E. E. R., Kraemer, L., Mountfort, D., Schilhabel, M., Schreiber, S., Rosenstiel, P.

Oxford University Press

In: Bioinformatics

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Publikationsdatum: 2012-03-20

Beschreibung: Motivation: Next generation sequencing (NGS) technologies allow a rapid and cost-effective compilation of large RNA sequence datasets in model and non-model organisms. However, the storage and analysis of transcriptome information from different NGS platforms is still a significant bottleneck, leading to a delay in data dissemination and subsequent biological understanding. Especially database interfaces with transcriptome analysis modules going beyond mere read counts are missing. Here, we present the Transcriptome Analysis and Comparison Explorer (T-ACE), a tool designed for the organization and analysis of large sequence datasets, and especially suited for transcriptome projects of non-model organisms with little or no a priori sequence information. T-ACE offers a TCL-based interface, which accesses a PostgreSQL database via a php-script. Within T-ACE, information belonging to single sequences or contigs, such as annotation or read coverage, is linked to the respective sequence and immediately accessible. Sequences and assigned information can be searched via keyword- or BLAST-search. Additionally, T-ACE provides within and between transcriptome analysis modules on the level of expression, GO terms, KEGG pathways and protein domains. Results are visualized and can be easily exported for external analysis. We developed T-ACE for laboratory environments, which have only a limited amount of bioinformatics support, and for collaborative projects in which different partners work on the same dataset from different locations or platforms (Windows/Linux/MacOS). For laboratories with some experience in bioinformatics and programming, the low complexity of the database structure and open-source code provides a framework that can be customized according to the different needs of the user and transcriptome project. Contact: e.philipp@ikmb.uni-kiel.de ; l.kraemer@ikmb.uni_kiel.de ; p.rosenstiel@mucosa.de Supplementary information: Supplementary data are available at Bioinformatics online.

Print ISSN: 1367-4803

Digitale ISSN: 1460-2059

Thema: Biologie , Informatik , Medizin

Publiziert von Oxford University Press

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Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution [METHOD] (2012)

Windhager, L., Bonfert, T., Burger, K., Ruzsics, Z., Krebs, S., Kaufmann, S., Malterer, G., L'Hernault, A., Schilhabel, M., Schreiber, S., Rosenstiel, P., Zimmer, R., Eick, D., Friedel, C. C., Dolken, L.

Cold Spring Harbor Laboratory Press

In: Genome Research

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Publikationsdatum: 2012-10-02

Beschreibung: RNA synthesis and decay rates determine the steady-state levels of cellular RNAs. Metabolic tagging of newly transcribed RNA by 4-thiouridine (4sU) can reveal the relative contributions of RNA synthesis and decay rates. The kinetics of RNA processing, however, had so far remained unresolved. Here, we show that ultrashort 4sU-tagging not only provides snapshot pictures of eukaryotic gene expression but, when combined with progressive 4sU-tagging and RNA-seq, reveals global RNA processing kinetics at nucleotide resolution. Using this method, we identified classes of rapidly and slowly spliced/degraded introns. Interestingly, each class of splicing kinetics was characterized by a distinct association with intron length, gene length, and splice site strength. For a large group of introns, we also observed long lasting retention in the primary transcript, but efficient secondary splicing or degradation at later time points. Finally, we show that processing of most, but not all small nucleolar (sno)RNA-containing introns is remarkably inefficient with the majority of introns being spliced and degraded rather than processed into mature snoRNAs. In summary, our study yields unparalleled insights into the kinetics of RNA processing and provides the tools to study molecular mechanisms of RNA processing and their contribution to the regulation of gene expression.

Digitale ISSN: 1549-5469

Thema: Biologie , Medizin

Publiziert von Cold Spring Harbor Laboratory Press

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Genetic Differentiation of Hypothalamus Parentally Biased Transcripts in Populations of the House Mouse Implicate the Prader-Willi Syndrome Imprinted Region as a Possible Source of Behavioral Divergence (2014)

Lorenc, A., Linnenbrink, M., Montero, I., Schilhabel, M. B., Tautz, D.

Oxford University Press

In: Molecular Biology and Evolution

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Publikationsdatum: 2014-11-28

Beschreibung: Parentally biased expression of transcripts (genomic imprinting) in adult tissues, including the brain, can influence and possibly drive the evolution of behavioral traits. We have previously found that paternally determined cues are involved in population-specific mate choice decisions between two populations of the Western house mouse ( Mus musculus domesticus ). Here, we ask whether this could be mediated by genomically imprinted transcripts that are subject to fast differentiation between these populations. We focus on three organs that are of special relevance for mate choice and behavior: The vomeronasal organ (VNO), the hypothalamus, and the liver. To first identify candidate transcripts at a genome-wide scale, we used reciprocal crosses between M. m. domesticus and M. m. musculus inbred strains and RNA sequencing of the respective tissues. Using a false discovery cutoff derived from mock reciprocal cross comparisons, we find a total of 66 imprinted transcripts, 13 of which have previously not been described as imprinted. The largest number of imprinted transcripts were found in the hypothalamus; fewer were found in the VNO, and the least were found in the liver. To assess molecular differentiation and imprinting in the wild-derived M. m. domesticus populations, we sequenced the RNA of the hypothalamus from individuals of these populations. This confirmed the presence of the above identified transcripts also in wild populations and allowed us to search for those that show a high genetic differentiation between these populations. Our results identify the Ube3a–Snrpn imprinted region on chromosome 7 as a region that encompasses the largest number of previously not described transcripts with paternal expression bias, several of which are at the same time highly differentiated. For four of these, we confirmed their imprinting status via single nucleotide polymorphism-specific pyrosequencing assays with RNA from reciprocal crosses. In addition, we find the paternally expressed Peg13 transcript within the Trappc9 gene region on chromosome 15 to be highly differentiated. Interestingly, both regions have been implicated in Prader–Willi nervous system disorder phenotypes in humans. We suggest that these genomically imprinted regions are candidates for influencing the population-specific mate-choice in mice.

Print ISSN: 0737-4038

Digitale ISSN: 1537-1719

Thema: Biologie

Publiziert von Oxford University Press

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The Magellania venosa Biomineralizing Proteome: A Window into Brachiopod Shell Evolution (2015)

Jackson, D. J., Mann, K., Haussermann, V., Schilhabel, M. B., Luter, C., Griesshaber, E., Schmahl, W., Worheide, G.

Oxford University Press

In: Genome Biology and Evolution

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Publikationsdatum: 2015-05-24

Beschreibung: Brachiopods are a lineage of invertebrates well known for the breadth and depth of their fossil record. Although the quality of this fossil record attracts the attention of paleontologists, geochemists, and paleoclimatologists, modern day brachiopods are also of interest to evolutionary biologists due to their potential to address a variety of questions ranging from developmental biology to biomineralization. The brachiopod shell is a composite material primarily composed of either calcite or calcium phosphate in close association with proteins and polysaccharides which give these composite structures their material properties. The information content of these biomolecules, sequestered within the shell during its construction, has the potential to inform hypotheses focused on describing how brachiopod shell formation evolved. Here, using high throughput proteomic approaches and next generation sequencing, we have surveyed and characterized the first shell-proteome and shell-forming transcriptome of any brachiopod, the South American Magellania venosa (Rhynchonelliformea: Terebratulida) . We find that the seven most abundant proteins present in the shell are unique to M. venosa , but that these proteins display biochemical features found in other metazoan biomineralization proteins. We can also detect some M. venosa proteins that display significant sequence similarity to other metazoan biomineralization proteins, suggesting that some elements of the brachiopod shell-forming proteome are deeply evolutionarily conserved. We also employed a variety of preparation methods to isolate shell proteins and find that in comparison to the shells of other spiralian invertebrates (such as mollusks) the shell ultrastructure of M. venosa may explain the effects these preparation strategies have on our results.

Digitale ISSN: 1759-6653

Thema: Biologie

Publiziert von Oxford University Press

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