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- Lysenkova Wiklander, Mariya, et al.
(författare)
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Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH
- 2023
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Ingår i: BMC Research Notes. - : BioMed Central (BMC). - 1756-0500. ; 16:1
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Tidskriftsartikel (refereegranskat)abstract
- ObjectivesThe aim of this data paper is to describe a collection of 33 genomic, transcriptomic and epigenomic sequencing datasets of the B-cell acute lymphoblastic leukemia (ALL) cell line REH. REH is one of the most frequently used cell lines for functional studies of pediatric ALL, and these data provide a multi-faceted characterization of its molecular features. The datasets described herein, generated with short- and long-read sequencing technologies, can both provide insights into the complex aberrant karyotype of REH, and be used as reference datasets for sequencing data quality assessment or for methods development.Data descriptionThis paper describes 33 datasets corresponding to 867 gigabases of raw sequencing data generated from the REH cell line. These datasets include five different approaches for whole genome sequencing (WGS) on four sequencing platforms, two RNA sequencing (RNA-seq) techniques on two different sequencing platforms, DNA methylation sequencing, and single-cell ATAC-sequencing.
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- Shao, Jingxia, et al.
(författare)
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Functional analysis of the HD-Zip transcription factor genes Oshox12 and Oshox14 in rice
- 2018
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Ingår i: PLOS ONE. - : PUBLIC LIBRARY SCIENCE. - 1932-6203. ; 13:7
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Tidskriftsartikel (refereegranskat)abstract
- The homeodomain-leucine zipper (HD-Zip) transcription factor family plays vital roles in plant development and morphogenesis as well as responses to biotic and abiotic stresses. In barley, a recessive mutation in Vrs1 (HvHox1) changes two-rowed barley to six-rowed barley, which improves yield considerably. The Vrs1 gene encodes an HD-Zip subfamily I transcription factor. Phylogenetic analysis has shown that the rice HD-Zip I genes Oshox12 and Oshox14 are the closest homologues of Vrs1. Here, we show that Oshox12 and Oshox14 are ubiquitously expressed with higher levels in developing panicles. Trans-activation assays in yeast and rice protoplasts demonstrated that Oshox12 and Oshox14 can bind to a specific DNA sequence, AH1 (CAAT(A/T)ATTG), and activate reporter gene expression. Overexpression of Oshox12 and Oshox14 in rice resulted in reduced panicle length and a dwarf phenotype. In addition, Oshox14 overexpression lines showed a deficiency in panicle exsertion. Our findings suggest that Oshox12 and Oshox14 may be involved in the regulation of panicle development. This study provides a significant advancement in understanding the functions of HD-Zip transcription factors in rice.
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- Övernäs, Elin, 1978-
(författare)
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Characterisation of Members of the HD-Zip I and DREB/ERF Transcription Factor Families and their Functions in Plant Stress Responses
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Plants have to adapt to various environmental conditions. In comparison with other eukaryotes, plant genomes encode relatively many transcription factors, and have families of transcription factors only found in plants, two such are the large AP2/ERF (APETALA2/Ethylene Responsive Factor) and HD-Zip (Homeodomain leucine zipper) families. Members of these families play roles in plant development, responses to stress and other environmental stimuli. This thesis describes the functions of members of both these families. Two AP2/ERF proteins of the DREB/ERF (Drought Responsive Element Binding/Ethylene Responsive Factor) subfamily, AtERF38 and AtERF39 show a negative effect on growth in transgenic over-expression lines. They are regulated by stress and confer stress tolerance, which suggests a function as negative growth regulators during stress. The 14 Oryza sativa (rice) HD-Zip I genes were described and a phylogenetic analysis of the HD-Zip I genes in Arabidopsis thaliana, rice and Craterostigma plantagineum defined four clades that were conserved between mono and dicots, but also showed that four clades had most likely been lost in either lineage. The phylogeny was supported by conserved intron/exon patterning and the duplication history of the rice genome. The expression patterns in different organs indicate a non-conserved regulation of genes within and between clades. Drought stress regulation was conserved within two clades, but not between the clades. Further analysis on the function of four HD-Zip I genes in Arabidopsis, ATHB5, -6, -7 and -12 showed an involvement in the transcriptional regulation of ABA receptors and signalling components. These are the first described direct target genes for ATHB7 and ATHB12. It was also shown that there exists a direct cross-regulation between these four HD-Zips. The effect of ATHB5, -6, -7 and -12 would be as negative regulators of ABA signalling, desensitising the plant to constant levels of ABA, and enabling sensitivity to changes in stress level.
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