Alternative usage of 5′ exons in the chicken nerve growth factor gene: refined characterization of a weakly expressed gene

Bertaux, O; Toselli-Mollereau, Esther; Auffray, Charles; Devignes, Marie‐Dominique

doi:10.1016/j.gene.2004.02.052

Cited by 8 publications

(6 citation statements)

References 34 publications

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“…These studies, and others, have shown that alternate splicing is not only widespread and tissue specific, but is influenced by evolutionary forces and linked with levels of transcription. There have been a number of studies characterising specific AS events in chick (Mezquita et al, 2000; Zhong et al, 2004) including Fibronectin in the early embryo (Peters et al, 2002), β-crystallins in the lens (Wilmarth et al, 2004) and Nerve Growth Factor (Bertaux et al, 2004). As yet, there have been no comprehensive studies on the apparent level of alternate splicing in chickens, although there are tools developed to examine them (Kim P. et al, 2005; Kim N et al, 2005a, 2005b), and comparative analyses have examined various facets of conservation of splicing, exons, and exon symmetry across other eukaryotes (Kan et al, 2005; Magen & Ast, 2005; Nagasaki et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

Characterising alternate splicing and tissue specific expression in the chicken from ESTs

Tang¹,

Heeley²,

Morlec³

et al. 2007

Cytogenet Genome Res

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Alternate splicing is believed to produce the greatest diversity in transcriptional complexity and function in eukaryotic species. In this study, we present an analysis of alternative splicing events that occur in the chicken, using the recently sequenced genomic sequence and over 580,000 EST sequences mapped back to the genome. A carefully controlled EST-to-genome mapping pipeline is presented, based around the EXONERATE program using the est2genome model, which also considers several quality control steps to filter out erroneous matches. The data is then used to estimate the level of alternate splicing events with respect to Ensembl predicted transcripts. The EST-genome mappings are characterised at the exon level, in order to classify individual splicing events and provide estimates of novel transcripts not currently annotated by the Ensembl genome database. This is the first large scale analysis of this kind in an avian species, and suggests that chicken displays a similar level of alternate splicing as that found in other higher vertebrates such as human and mouse, both in terms of the number of genes that undergo alternate splicing events, and the average number of transcripts produced per gene. The EST data suggests alternate splicing may occur in some 50–60% of the chicken gene set and with an average of around 2.3 transcripts per gene which undergo this process. The EST data is also used to look at gene and transcript usage in the tissues sequenced in embryonic and adult libraries. Genes which display notable biases were analysed in more detail, including twinfilin-2 and embryonic heavy chain myosin. This also highlights several as yet functionally un-annotated genes which appear to be important in embryonic tissues and also undergo alternate splicing events. The analysis also demonstrates some of the difficulties involved in using EST-based data to annotate transcriptional activity in eukaryotic genes, where a broad spectrum of tissues and a large number of sequenced transcripts are required in order to fully characterise alternate splicing and differential expression.

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Section: Introductionmentioning

confidence: 99%

Characterising alternate splicing and tissue specific expression in the chicken from ESTs

Tang¹,

Heeley²,

Morlec³

et al. 2007

Cytogenet Genome Res

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“…BDNF is a neurotrophin and its gene contains a single coding exon with multiple promoter and alternative slicing transcripts (Bertaux et al, 2004). The binding between acetylated histone H3 and BDNF promoter IV was higher in the HC-DR group, although no changes in the mRNA levels were found.…”

Section: Discussionmentioning

confidence: 99%

Eating habits modulate short term memory and epigenetical regulation of brain derived neurotrophic factor in hippocampus of low- and high running capacity rats

Torma

Bori

Koltai

et al. 2014

Brain Research Bulletin

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Exercise capacity and dietary restriction (DR) are linked to improved quality of life, including enhanced brain function and neuro-protection. Brain derived neurotrophic factor (BDNF) is one of the key proteins involved in the beneficial effects of exercise on brain. Low capacity runner (LCR) and high capacity runner (HCR) rats were subjected to DR in order to investigate the regulation of BDNF. HCR-DR rats out-performed other groups in a passive avoidance test. BDNF content increased significantly in the hippocampus of HCR-DR groups compared to control groups (p<0.05). The acetylation of H3 increased significantly only in the LCR-DR group. However, Chip-assay revealed that the specific binding between acetylated histone H3 and BNDF promoter was increased in both LCR-DR and HCR-DR groups. In spite of these increases in binding, at the transcriptional level only, the LCR-DR group showed an increase in BDNF mRNA content. Additionally, DR also induced the activity of cAMP response element-binding protein (CREB), while the content of SIRT1 was not altered. Peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α) was elevated in HCR-DR groups. But, based on the levels of nuclear respiratory factor-1 and cytocrome c oxidase, it appears that DR did not cause mitochondrial biogenesis. The data suggest that DR-mediated induction of BDNF levels includes chromatin remodeling. Moreover, DR does not induce mitochondrial biogenesis in the hippocampus of LCR/HCR rats. DR results in different responses to a passive avoidance test, and BDNF regulation in LCR and HCR rats.

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“…The first cluster consists of three leader exons (1a, 1b, 1c) and the second cluster contains exons 2 and 3. Differential usage of leader and internal exons, alternative transcription start sites, alternative donor and acceptor sites generates at least 21 different transcripts (Bertaux et al, 2004). Comparison of the 6-exon chicken NGF with the 3-exon human NGFB gene reveals significant nucleotide alignment of chicken NGF exons 2 and 4 with human NGFB exons 2 and 3, with the chicken and human proteins showing 87% identity.…”

Section: Ngfmentioning

confidence: 99%

“…Comparison of the 6-exon chicken NGF with the 3-exon human NGFB gene reveals significant nucleotide alignment of chicken NGF exons 2 and 4 with human NGFB exons 2 and 3, with the chicken and human proteins showing 87% identity. There is no equivalent to chicken exon 3 in either the human or mouse genome (Bertaux et al, 2004).…”

Section: Ngfmentioning

confidence: 99%

Evolutionary conservation of alternative splicing in chicken

Katyal¹,

Gao²,

Liu³

et al. 2007

Cytogenet Genome Res

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Alternative splicing represents a source of great diversity for regulating protein expression and function. It has been estimated that one-third to two-thirds of mammalian genes are alternatively spliced. With the sequencing of the chicken genome and analysis of transcripts expressed in chicken tissues, we are now in a position to address evolutionary conservation of alternative splicing events in chicken and mammals. Here, we compare chicken and mammalian transcript sequences of 41 alternatively-spliced genes and 50 frequently accessed genes. Our results support a high frequency of splicing events in chicken, similar to that observed in mammals.

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Alternative usage of 5′ exons in the chicken nerve growth factor gene: refined characterization of a weakly expressed gene

Cited by 8 publications

References 34 publications

Characterising alternate splicing and tissue specific expression in the chicken from ESTs

Characterising alternate splicing and tissue specific expression in the chicken from ESTs

Eating habits modulate short term memory and epigenetical regulation of brain derived neurotrophic factor in hippocampus of low- and high running capacity rats

Evolutionary conservation of alternative splicing in chicken

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