Transcriptomics

Dataset Information

37

Gene transcription profiles and potential transgenerational epigenetic effects related to Zn exposure history in Daphnia magna


ABSTRACT: A reduced level of DNA methylation has recently been described in both Zn-exposed and non-exposed offspring of Daphnia magna exposed to Zn. The hypothesis examined in this study is that DNA hypomethylation has an effect on gene transcription. A second hypothesis is that accumulative epigenetic effects can affect gene transcription in non-exposed offspring from parents with an exposure history of more than one generation. Transcriptional gene regulation was studied with a cDNA microarray. In the exposed and non-exposed hypomethylated daphnids, a large proportion of common genes were similarly up- or downregulated, indicating a possible effect of the DNA hypomethylation. Two of these genes can be mechanistically involved in DNA methylation reduction. The similar transcriptional regulation of two and three genes in the F0 and F1 exposed daphnids on one hand and their non-exposed offspring on the other hand, could be the result of a one-generation temporary transgenerational epigenetic effect, which was not accumulative. The experimental design used in the current study is as follows. A set of neonates (0-24h) taken from the laboratory culture was divided into two batches. One batch was transferred to modified standard M4 medium (Elendt and Bias, 1990) and cultured for three generations (CtrlF0–CtrlF2). A second batch of neonates was transferred into the same medium, with the Zn concentration adjusted to 388 µg/L. A group of F1 neonates born from this ZnF0 generation was then cultured in this Zn-contaminated medium [Zn(+)F1]. Another group of these F1 neonates was transferred back to the control medium [Zn(-)F1]. In this way, Zn(-)F1 daphnids were only briefly exposed to Zn during the first hours of their life-cycle. Offspring of the F1Zn(-) organisms were also cultured in the control medium [Zn(-/-)F2, which were named F2Zn(-) in Vandegehuchte et al. (2009))]. Offspring of the Zn(+)F1 daphnids were in turn divided in a similar manner into two batches, one of which was cultured further in Zn-contaminated medium [Zn(+)F2] while the other one was transferred to the control medium [Zn(+/-)F2]. Each combination of generation and exposure history is termed a ‘treatment’. Three replicates of ten adult daphnids each per treatment were sampled for RNA extraction on the day the next generation was started. In general, a universal reference design was used in which the reference sample was a pool composed of differently aged daphnids cultured in aerated carbon-filtered tap water, enriched with selenium (1 µg/L) and vitamins (7.5 mg/L thiamine, 100 µg/L cyanocobalamin and 75 µg/L biotin). Dye-bias effects were accounted for by regularly swapping Cy3 and Cy5 for labelling treatments/reference pool samples.

ORGANISM(S): Daphnia magna  

SUBMITTER: Colin R Janssen  Dieter De Coninck   Wim M De Coen   Tine Vandenbrouck   Michiel B Vandegehuchte   Michiel Vandegehuchte    

PROVIDER: E-GEOD-22805 | ArrayExpress | 2014-05-01

SECONDARY ACCESSION(S): GSE22805PRJNA127907

REPOSITORIES: GEO, ArrayExpress

altmetric image

Publications

Gene transcription profiles, global DNA methylation and potential transgenerational epigenetic effects related to Zn exposure history in Daphnia magna.

Vandegehuchte Michiel B MB   De Coninck Dieter D   Vandenbrouck Tine T   De Coen Wim M WM   Janssen Colin R CR  

Environmental pollution (Barking, Essex : 1987) 20100816 10


A reduced level of DNA methylation has recently been described in both Zn-exposed and non-exposed offspring of Daphnia magna exposed to Zn. The hypothesis examined in this study is that DNA hypomethylation has an effect on gene transcription. A second hypothesis is that accumulative epigenetic effects can affect gene transcription in non-exposed offspring from parents with an exposure history of more than one generation. Transcriptional gene regulation was studied with a cDNA microarray. In the  ...[more]

Similar Datasets

2010-07-23 | GSE22805 | GEO
| GSE53570 | GEO
2017-05-07 | E-GEOD-78120 | ArrayExpress
2012-09-26 | E-GEOD-40469 | ArrayExpress
| GSE98683 | GEO
| GSE85822 | GEO
2014-06-03 | E-GEOD-54738 | ArrayExpress
2014-06-03 | E-GEOD-54736 | ArrayExpress
| GSE100470 | GEO
2014-06-10 | E-GEOD-58091 | ArrayExpress