Screening for Gene Function Using the FOX (Full-Length cDNA OvereXpressor Gene) Hunting System

2013 ◽  
pp. 201-210 ◽  
Author(s):  
Mieko Higuchi-Takeuchi ◽  
Minami Matsui
Keyword(s):  
Gene Function ◽  
Full Length ◽  
Full Length Cdna ◽  
Gene Hunting

scholarly journals RiceFOX: A Database of Arabidopsis Mutant Lines Overexpressing Rice Full-Length cDNA that Contains a Wide Range of Trait Information to Facilitate Analysis of Gene Function

2010 ◽  
Vol 52 (2) ◽  
pp. 265-273 ◽  
Author(s):  
Tetsuya Sakurai ◽  
Youichi Kondou ◽  
Kenji Akiyama ◽  
Atsushi Kurotani ◽  
Mieko Higuchi ◽  
...  
Keyword(s):  
Gene Function ◽  
Full Length ◽  
Full Length Cdna ◽  
Wide Range ◽  
Arabidopsis Mutant ◽  
Mutant Lines

scholarly journals Identifying transcript 5′ capped ends in Plasmodium falciparum

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11983
Author(s):  
Philip J. Shaw ◽  
Jittima Piriyapongsa ◽  
Pavita Kaewprommal ◽  
Chayaphat Wongsombat ◽  
Chadapohn Chaosrikul ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Gene Function ◽  
Malaria Parasite ◽  
Full Length ◽  
Human Malaria Parasite ◽  
Full Length Cdna ◽  
Coding Regions ◽  
Sequence Patterns ◽  
Mrna Transcripts ◽  
Generation Sequencing

Background The genome of the human malaria parasite Plasmodium falciparum is poorly annotated, in particular, the 5′ capped ends of its mRNA transcripts. New approaches are needed to fully catalog P. falciparum transcripts for understanding gene function and regulation in this organism. Methods We developed a transcriptomic method based on next-generation sequencing of complementary DNA (cDNA) enriched for full-length fragments using eIF4E, a 5′ cap-binding protein, and an unenriched control. DNA sequencing adapter was added after enrichment of full-length cDNA using two different ligation protocols. From the mapped sequence reads, enrichment scores were calculated for all transcribed nucleotides and used to calculate P-values of 5′ capped nucleotide enrichment. Sensitivity and accuracy were increased by combining P-values from replicate experiments. Data were obtained for P. falciparum ring, trophozoite and schizont stages of intra-erythrocytic development. Results 5′ capped nucleotide signals were mapped to 17,961 non-overlapping P. falciparum genomic intervals. Analysis of the dominant 5′ capped nucleotide in these genomic intervals revealed the presence of two groups with distinctive epigenetic features and sequence patterns. A total of 4,512 transcripts were annotated as 5′ capped based on the correspondence of 5′ end with 5′ capped nucleotide annotated from full-length cDNA data. Discussion The presence of two groups of 5′ capped nucleotides suggests that alternative mechanisms may exist for producing 5′ capped transcript ends in P. falciparum. The 5′ capped transcripts that are antisense, outside of, or partially overlapping coding regions may be important regulators of gene function in P. falciparum.

scholarly journals Fox Hunting in Wild Apples: Searching for Novel Genes in Malus Sieversii

2020 ◽  
Vol 21 (24) ◽  
pp. 9516
Author(s):  
Michael Wisniewski ◽  
Timothy Artlip ◽  
Jia Liu ◽  
Jing Ma ◽  
Erik Burchard ◽  
...  
Keyword(s):  
Cdna Library ◽  
Gene Function ◽  
Full Length ◽  
Fruit Traits ◽  
Freezing Resistance ◽  
Malus Sieversii ◽  
Transgenic Seeds ◽  
Transgenic Lines ◽  
Gene Hunting ◽  
Full Length Gene

Malus sieversii is considered the progenitor of modern apple (Malus pumila) cultivars and to represent a valuable source of genetic diversity. Despite the importance of M. sieversii as a source of disease resistance, stress tolerance, and novel fruit traits, little is known about gene function and diversity in M. sieversii. Notably, a publicly annotated genome sequence for this species is not available. In the current study, the FOX (Full-length cDNA OvereXpressing) gene hunting system was used to construct a library of transgenic lines of Arabidopsis in which each transgenic line overexpresses a full-length gene obtained from a cDNA library of the PI619283 accession of M. sieversii. The cDNA library was constructed from mRNA obtained from bark tissues collected in late fall–early winter, a time at which many abiotic stress-adaptative genes are expressed. Over 4000 apple FOX Arabidopsis lines have been established from the pool of transgenic seeds and cDNA inserts corresponding to various Gene Ontology (GO) categories have been identified. A total of 160 inserts appear to be novel, with no or limited homology to M. pumila, Arabidopsis, or poplar. Over 1300 lines have also been screened for freezing resistance. The constructed library of transgenic lines provides a valuable genetic resource for exploring gene function and diversity in Malus sieversii. Notably, no such library of t-DNA lines currently exists for any Malus species.

Full-Length cDNA Overexpressor Gene Hunting System (FOX Hunting System)

2010 ◽  
pp. 77-89 ◽  
Author(s):  
Mieko Higuchi ◽  
Youichi Kondou ◽  
Takanari Ichikawa ◽  
Minami Matsui
Keyword(s):  
Full Length ◽  
Full Length Cdna ◽  
Gene Hunting

Establishment and Identification of a Normalized Full-Length cDNA Library of CCRI 36

2009 ◽  
Vol 35 (4) ◽  
pp. 602-607 ◽  
Author(s):  
Dong WU ◽  
Jun-Jie LIU ◽  
Shu-Xun YU ◽  
Shu-Li FAN ◽  
Mei-Zhen SONG
Keyword(s):  
Cdna Library ◽  
Full Length ◽  
Full Length Cdna

Full length cDNA cloning and tissue expression of PRLR in Cyprinus carpio var. jian

2013 ◽  
Vol 20 (4) ◽  
pp. 722-732
Author(s):  
Bing LI ◽  
Jie WANG ◽  
Chengfeng ZHANG ◽  
Jian ZHU
Keyword(s):  
Cdna Cloning ◽  
Cyprinus Carpio ◽  
Tissue Expression ◽  
Full Length ◽  
Full Length Cdna

The full length cDNA cloning and expression analysis of RXR from the Chinese mitten crab(Eriocheir sinensis)

2013 ◽  
Vol 37 (12) ◽  
pp. 1761 ◽  
Author(s):  
Yao WANG ◽  
Zhigang YANG ◽  
Zihao GUO ◽  
Qinqin YAO ◽  
Qitao ZENG ◽  
...  
Keyword(s):  
Cdna Cloning ◽  
Expression Analysis ◽  
Eriocheir Sinensis ◽  
Full Length ◽  
Cloning And Expression ◽  
Chinese Mitten Crab ◽  
Full Length Cdna ◽  
Mitten Crab
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