@article {113, title = {A novel conserved enhancer at zebrafish zic3 and zic6 loci drives neural expression.}, journal = {Dev Dyn}, volume = {248}, year = {2019}, month = {2019 09}, pages = {837-849}, abstract = {

BACKGROUND: Identifying enhancers and deciphering their putative roles represent a major step to better understand the mechanism of metazoan gene regulation, development, and the role of regulatory elements in disease. Comparative genomics and transgenic assays have been used with some success to identify critical regions that are involved in regulating the spatiotemporal expression of genes during embryogenesis.

RESULTS: We identified two novel tetrapod-teleost conserved noncoding elements within the vicinity of the zic3 and zic6 loci in the zebrafish genome and demonstrated their ability to drive tissue-specific expression in a transgenic zebrafish assay. The syntenic analysis and robust green fluorescent expression in the developing habenula in the stable transgenic line were correlated with known sites of endogenous zic3 and zic6 expression.

CONCLUSION: This transgenic line that expresses green fluorescent protein in the habenula is a valuable resource for studying a specific population of cells in the zebrafish central nervous system. Our observations indicate that a genomic sequence that is conserved between humans and zebrafish acts as an enhancer that likely controls zic3 and zic6 expression.

}, keywords = {Animals, Animals, Genetically Modified, Conserved Sequence, Embryonic Development, Enhancer Elements, Genetic, Gene Expression Regulation, Developmental, Green Fluorescent Proteins, Habenula, Homeodomain Proteins, Humans, Nervous System, Repressor Proteins, Transcription Factors, Zebrafish, Zebrafish Proteins}, issn = {1097-0177}, doi = {10.1002/dvdy.69}, author = {Minhas, Rashid and Paterek, Aleksandra and {\L}api{\'n}ski, Maciej and Baza{\l}a, Micha{\l} and Korzh, Vladimir and Winata, Cecilia L} } @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} }