Dataset Information

In silico finding of Putative Cis-Acting Elements for the Tethering of Polycomb Repressive Complex2 in Human Genome.

ABSTRACT: Polycomb Repressive Complex2 maintains a predetermined state of transcription which constitutes a cellular memory stable over many cell divisions. Since this complex acts through the regulation of chromatin structure, it is important to understand how it is recruited to chromatin. The specific target sequences of this complex such as PRE (polycomb repressive element) have not been completely recognized in human genome. In this study, we have compared the target sequences of this complex with non-target genes in tumor cell lines. Through in silico and statistical analyses, we have identified some motifs which are over-represented in target genes against non-target genes. Analyzing these motifs shows some transcription factors which are potential recruiters of Polycomb repressive complex2.

SUBMITTER: Hajjari M

PROVIDER: S-EPMC4070047 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

In silico finding of Putative Cis-Acting Elements for the Tethering of Polycomb Repressive Complex2 in Human Genome.

Hajjari Mohammadreza M Behmanesh Mehrdad M Jahani Mohammad Mehdi MM

Bioinformation 20140423 4

Polycomb Repressive Complex2 maintains a predetermined state of transcription which constitutes a cellular memory stable over many cell divisions. Since this complex acts through the regulation of chromatin structure, it is important to understand how it is recruited to chromatin. The specific target sequences of this complex such as PRE (polycomb repressive element) have not been completely recognized in human genome. In this study, we have compared the target sequences of this complex with non ...[more]

PMID: 24966518

Similar Datasets

Project description:BackgroundCryptosporidium parvum is a unicellular eukaryote in the phylum Apicomplexa. It is an obligate intracellular parasite that causes diarrhea and is a significant AIDS-related pathogen. Cryptosporidium parvum is not amenable to long-term laboratory cultivation or classical molecular genetic analysis. The parasite exhibits a complex life cycle, a broad host range, and fundamental mechanisms of gene regulation remain unknown. We have used data from the recently sequenced genome of this organism to uncover clues about gene regulation in C. parvum. We have applied two pattern finding algorithms MEME and AlignACE to identify conserved, over-represented motifs in the 5' upstream regions of genes in C. parvum. To support our findings, we have established comparative real-time -PCR expression profiles for the groups of genes examined computationally.ResultsWe find that groups of genes that share a function or belong to a common pathway share upstream motifs. Different motifs are conserved upstream of different groups of genes. Comparative real-time PCR studies show co-expression of genes within each group (in sub-sets) during the life cycle of the parasite, suggesting co-regulation of these genes may be driven by the use of conserved upstream motifs.ConclusionThis is one of the first attempts to characterize cis-regulatory elements in the absence of any previously characterized elements and with very limited expression data (seven genes only). Using de novo pattern finding algorithms, we have identified specific DNA motifs that are conserved upstream of genes belonging to the same metabolic pathway or gene family. We have demonstrated the co-expression of these genes (often in subsets) using comparative real-time-PCR experiments thus establishing evidence for these conserved motifs as putative cis-regulatory elements. Given the lack of prior information concerning expression patterns and organization of promoters in C. parvum we present one of the first investigations of gene regulation in this important human pathogen.

Dataset Information

In silico finding of Putative Cis-Acting Elements for the Tethering of Polycomb Repressive Complex2 in Human Genome.

Publications

In silico finding of Putative Cis-Acting Elements for the Tethering of Polycomb Repressive Complex2 in Human Genome.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets