Transcriptomics

Dataset Information

300

Transcription profiling by high throughput sequencing of four tissues of maize B73 and Mo17 lines


ABSTRACT: Transposable elements (TEs) have the potential to act as controlling elements to influence the expression of genes and are often subject to heterochromatic silencing. The current paradigm suggests that heterochromatic silencing can spread beyond the borders of TEs and influence the chromatin state of neighboring low-copy sequences. This would allow TEs to condition obligatory or facilitated epialleles and act as controlling elements. The maize genome contains numerous families of class I TEs (retrotransposons) that are present in moderate to high copy numbers, and many are found in regions near genes, which provides an opportunity to test whether the spreading of heterochromatin from retrotransposons is prevalent. We have investigated the extent of heterochromatin spreading into DNA flanking each family of retrotransposons by profiling DNA methylation and di-methylation of lysine 9 of histone 3 (H3K9me2) in low-copy regions of the maize genome. RNA–seq was performed on three biological replicates of four tissues: 3rd leaf, immature ear (SRP013432), embryo and endosperm(SRP009313) for both B73 and Mo17.

INSTRUMENT(S): Illumina Genome Analyzer IIx

ORGANISM(S): Zea mays  

SUBMITTER: Nathan Springer  

PROVIDER: E-MTAB-4318 | ArrayExpress | 2012-09-04

SECONDARY ACCESSION(S): SRP009313SRP013432

REPOSITORIES: ArrayExpress, ENA

altmetric image

Publications


Transposable elements (TEs) have the potential to act as controlling elements to influence the expression of genes and are often subject to heterochromatic silencing. The current paradigm suggests that heterochromatic silencing can spread beyond the borders of TEs and influence the chromatin state of neighboring low-copy sequences. This would allow TEs to condition obligatory or facilitated epialleles and act as controlling elements. The maize genome contains numerous families of class I TEs (re  ...[more]

Similar Datasets

| GSE39460 | GEO
2012-11-26 | E-GEOD-39460 | ArrayExpress
2013-01-01 | E-GEOD-41183 | ArrayExpress
2014-03-11 | E-GEOD-55730 | ArrayExpress
| GSE70945 | GEO
| GSE61136 | GEO
2015-05-22 | E-GEOD-61688 | ArrayExpress
2015-10-25 | E-GEOD-71842 | ArrayExpress
2013-09-24 | E-GEOD-46430 | ArrayExpress
2014-09-04 | E-GEOD-61028 | ArrayExpress