@article {126, title = {Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish.}, journal = {Life Sci Alliance}, volume = {6}, year = {2023}, month = {2023 Jan}, abstract = {

Most mitochondrial proteins are encoded by nuclear genes, synthetized in the cytosol and targeted into the organelle. To characterize the spatial organization of mitochondrial gene products in zebrafish (), we sequenced RNA from different cellular fractions. Our results confirmed the presence of nuclear-encoded mRNAs in the mitochondrial fraction, which in unperturbed conditions, are mainly transcripts encoding large proteins with specific properties, like transmembrane domains. To further explore the principles of mitochondrial protein compartmentalization in zebrafish, we quantified the transcriptomic changes for each subcellular fraction triggered by the mutation, causing the disorders in the mitochondrial protein import. Our results indicate that the proteostatic stress further restricts the population of transcripts on the mitochondrial surface, allowing only the largest and the most evolutionary conserved proteins to be synthetized there. We also show that many nuclear-encoded mitochondrial transcripts translated by the cytosolic ribosomes stay resistant to the global translation shutdown. Thus, vertebrates, in contrast to yeast, are not likely to use localized translation to facilitate synthesis of mitochondrial proteins under proteostatic stress conditions.

}, keywords = {Animals, Genes, Mitochondrial, Mitochondria, Mitochondrial Proteins, Nuclear Proteins, RNA, Messenger, Saccharomyces cerevisiae, Zebrafish}, issn = {2575-1077}, doi = {10.26508/lsa.202201514}, author = {Uszczynska-Ratajczak, Barbara and Sugunan, Sreedevi and Kwiatkowska, Monika and Migdal, Maciej and Carbonell-Sala, Silvia and Sokol, Anna and Winata, Cecilia L and Chacinska, Agnieszka} } @article {74, title = {Impaired development of neural-crest cell-derived organs and intellectual disability caused by MED13L haploinsufficiency.}, journal = {Hum Mutat}, volume = {35}, year = {2014}, month = {2014 Nov}, pages = {1311-20}, abstract = {

MED13L is a component subunit of the Mediator complex, an important regulator of transcription that is highly conserved across eukaryotes. Here, we report MED13L disruption in a translocation t(12;19) breakpoint of a patient with Pierre-Robin syndrome, moderate intellectual disability, craniofacial anomalies, and muscular defects. The phenotype is similar to previously described patients with MED13L haploinsufficiency. Knockdown of MED13L orthologue in zebrafish, med13b, showed early defective migration of cranial neural crest cells (NCCs) that contributed to cartilage structure deformities in the later stage, recapitulating craniofacial anomalies seen in human patients. Notably, we observed abnormal distribution of developing neurons in different brain regions of med13b morphant embryos, which could be rescued upon introduction of full-length human MED13L mRNA. To compare with mammalian system, we suppressed MED13L expression by short-hairpin RNA in ES-derived human neural progenitors, and differentiated them into neurons. Transcriptome analysis revealed differential expression of components of Wnt and FGF signaling pathways in MED13L-deficient neurons. Our finding provides a novel insight into the mechanism of overlapping phenotypic outcome targeting NCCs derivatives organs in patients with MED13L haploinsufficiency, and emphasizes a clinically recognizable syndromic phenotype in these patients.

}, keywords = {Animals, Cell Differentiation, Cell Movement, Child, Preschool, Chromosome Breakpoints, Disease Models, Animal, Embryonic Stem Cells, Female, Gene Expression, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Knockdown Techniques, Genetic Association Studies, Haploinsufficiency, Humans, Intellectual Disability, Mediator Complex, Neural Crest, Neurons, Phenotype, RNA, Messenger, Sequence Analysis, DNA, Transcriptome, Translocation, Genetic, Zebrafish}, issn = {1098-1004}, doi = {10.1002/humu.22636}, author = {Utami, Kagistia Hana and Winata, Cecilia L and Hillmer, Axel M and Aksoy, Irene and Long, Hoang Truong and Liany, Herty and Chew, Elaine G Y and Mathavan, Sinnakaruppan and Tay, Stacey K H and Korzh, Vladimir and Sarda, Pierre and Davila, Sonia and Cacheux, Valere} } @article {32, title = {Normalization of RNA-sequencing data from samples with varying mRNA levels.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014}, pages = {e89158}, abstract = {

Methods for normalization of RNA-sequencing gene expression data commonly assume equal total expression between compared samples. In contrast, scenarios of global gene expression shifts are many and increasing. Here we compare the performance of three normalization methods when polyA(+) RNA content fluctuates significantly during zebrafish early developmental stages. As a benchmark we have used reverse transcription-quantitative PCR. The results show that reads per kilobase per million (RPKM) and trimmed mean of M-values (TMM) normalization systematically leads to biased gene expression estimates. Biological scaling normalization (BSN), designed to handle differences in total expression, showed improved accuracy compared to the two other methods in estimating transcript level dynamics. The results have implications for past and future studies using RNA-sequencing on samples with different levels of total or polyA(+) RNA.

}, keywords = {Animals, Base Sequence, Gene Expression, Gene Expression Profiling, Polymerase Chain Reaction, RNA, Messenger, Sequence Analysis, RNA, Zebrafish}, issn = {1932-6203}, doi = {10.1371/journal.pone.0089158}, author = {Aanes, H{\r a}vard and Winata, Cecilia L and Moen, Lars F and {\O}strup, Olga and Mathavan, Sinnakaruppan and Collas, Philippe and Rognes, Torbj{\o}rn and Alestr{\"o}m, Peter} } @article {36, title = {Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition.}, journal = {Genome Res}, volume = {21}, year = {2011}, month = {2011 Aug}, pages = {1328-38}, abstract = {

Maternally deposited mRNAs direct early development before the initiation of zygotic transcription during mid-blastula transition (MBT). To study mechanisms regulating this developmental event in zebrafish, we applied mRNA deep sequencing technology and generated comprehensive information and valuable resources on transcriptome dynamics during early embryonic (egg to early gastrulation) stages. Genome-wide transcriptome analysis documented at least 8000 maternal genes and identified the earliest cohort of zygotic transcripts. We determined expression levels of maternal and zygotic transcripts with the highest resolution possible using mRNA-seq and clustered them based on their expression pattern. We unravel delayed polyadenylation in a large cohort of maternal transcripts prior to the MBT for the first time in zebrafish. Blocking polyadenylation of these transcripts confirms their role in regulating development from the MBT onward. Our study also identified a large number of novel transcribed regions in annotated and unannotated regions of the genome, which will facilitate reannotation of the zebrafish genome. We also identified splice variants with an estimated frequency of 50\%-60\%. Taken together, our data constitute a useful genomic information and valuable transcriptome resource for gene discovery and for understanding the mechanisms of early embryogenesis in zebrafish.

}, keywords = {Animals, Base Sequence, Genome, RNA, Messenger, RNA, Messenger, Stored, Sequence Analysis, RNA, Transcriptome, Zebrafish, Zebrafish Proteins, Zygote}, issn = {1549-5469}, doi = {10.1101/gr.116012.110}, author = {Aanes, H{\r a}vard and Winata, Cecilia L and Lin, Chi Ho and Chen, Jieqi P and Srinivasan, Kandhadayar G and Lee, Serene G P and Lim, Adrian Y M and Hajan, Hajira Shreen and Collas, Philippe and Bourque, Guillaume and Gong, Zhiyuan and Korzh, Vladimir and Alestr{\"o}m, Peter and Mathavan, Sinnakaruppan} }