High-complexity regions in mammalian genomes are enriched for developmental genes.

ABSTRACT:

Motivation

Unique sequence regions are associated with genetic function in vertebrate genomes. However, measuring uniqueness, or absence of long repeats, along a genome is conceptually and computationally difficult. Here we use a variant of the Lempel-Ziv complexity, the match complexity, Cm, and augment it by deriving its null distribution for random sequences. We then apply Cm to the human and mouse genomes to investigate the relationship between sequence complexity and function.

Results

We implemented Cm in the program macle and show through simulation that the newly derived null distribution of Cm is accurate. This allows us to delineate high-complexity regions in the human and mouse genomes. Using our program macle2go, we find that these regions are twofold enriched for

SUBMITTER: Pirogov A 

PROVIDER: S-EPMC6546125 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature