Development of a transcription factor database useful for developmental biology, and decoding the maternal and zygotic transcriptome of the appendicularian, Oikopleura dioica
Year: 2015
Type: dissertation
Abstract: Genes encoding transcription factors that constitute gene-regulatory networks and maternal factors accumulating in egg cytoplasm are two classes of essential genes that play crucial roles in developmental processes.Transcription factors control the expression of their downstream target genes by interacting with cis-regulatory elements.Maternal factors initiate embryonic developmental programs by regulating the expression of zygotic genes and various other events during early embryogenesis.This manuscript documents the transcription factors of 77 metazoan species as well as human and mouse maternal factors.I improved the previous method for prediction of transcription factors using a statistical approach adding Gene Ontology information to Pfam based identification of transcription factors.This method detects previously un-discovered transcription factors.The novel features of this database are:1) It includes both transcription factors and maternal factors, although the number of species, in which maternal factors are listed, is limited at the moment.2) Ontological representation at the cell, tissue, organ, and system levels has been specially designed to facilitate developmental studies.This is the unique feature in our database and is not available in other transcription factor databases.I developed, a user-friendly web interface, REGULATOR (http://www.bioinformatics.org/regulator/),which can help researchers to efficiently identify, validate, and visualize the data in the database.Using this web interface, users can browse, search, and download detailed information on species of interest, genes, transcription factor families, or developmental ontology terms.In the second part of this thesis, I performed transcriptome analysis for the appendicularian, Oikopleura dioica (O.dioica), which is a planktonic chordate.It has been used as a novel model species in development biology and evolutionary studies.The most significant character of this species is rapid development and short life cycle (only 5 days).Recently, many bioinformatics resources are publicly available, such as the genome sequence and microarray data in the OikoBase.However, transcriptome information is still not complete, especially as to the next-generation sequencing data.In this study, we carried out transcriptome analysis using RNA sequencing data of a Japanese population collected from egg and larval stages.The major findings of this study are:1. Via mapping our reads (Japanese population) to the reference genome sequence deposited in the OikoBase (Norwegian population), an extreme low reads mapping rate were found, which due to the significant sequence variations between the Japanese population and the Norwegian population.2. After de novo transcriptome assembly, 16,423 proteins (belongs to 12,136 known unigenes) of Japanese population have homologies with that of the Norwegian population (OikoBase).These proteins corresponding to 95.4% of the protein-encoding genes deposited in OikoBase.3. Via comparing the 4,136 one-vs-one bidirectional best hits (BBH) at both the nucleotide and protein levels, the sequence similarity between Japanese and Norwegian population were estimated to be 91.0% in nucleotide level and 94.8% in amino acid level.4. Additional 175 novel protein-encoding genes were found.Among these novel genes, 144 of them were not predicted in the gene models deposited in OikoBase, but they can be II found in the Norwegian reference genome; whereas 31 unigenes were not found in the OikoBase reference genome due to the low sequence similarity.5. I found approximately 63% unigenes were expressed in egg-stage, whereas 99% were observed in larval-stage; Analysis of differentially expressed genes (DEG) using a fold change threshold of four for the total 12,311 unigenes, we found 3,772 of them were up-regulated and 1,336 were down-regulated.Gene ontology (GO) analyses showed distinct gene activities in these two developmental stages.6.The previously reported mRNA 5' trans-spliced leader was also detected by our method.While, it was observed in 40.8% of the total unique transcripts, which is much more frequently happed than the previous estimation.This trans-spliced leader showed preferential linkage to adenine at the 5' ends of the downstream exons.7. By comparing the trans-spliced mRNAs between egg and larval stage, as well as the down-regulated and up-regulated groups, we found trans-spliced mRNAs were more frequently observed in egg compared to larva.Our data of transcriptome assembly will provide an additional resource for studies of Japanese population.These findings would be useful for better understanding of the development as well as evolutionary history of O. dioica.
DOI: 10.18910/54035
Author: Kai Wang
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Awards: 個体発生および脳機能における平面内細胞極性因子の役割の解明, Development of forward gentics methods in appendicularians as a novel chordate model organism, G593849471, Specification mechanisms of three embryonic axes (animal-vegetal, anteior-posterior, and left-right axes) during ascidian embryogenesis, Developmental biology of the appendicularian, Oikopleura dioica: Tool development and study of developmental phenomena.
OpenAlex ID: W2561981149