Evolutionarily Conserved Noncoding DNA

Abstract

Noncoding deoxyribonucleic acid (DNA), which includes all sequences within the genome except exon sequences that encode the protein‐reading frames, harbours a wide variety of regulatory genomic features and elements. The availability of increasingly complete and accurate genomic sequence data from evolutionarily separated species – as well as diverse strain and ethnic variants within species – is providing an unprecedented opportunity to identify potentially functional regions within the genomic noncoding DNA. A variety of computational approaches enable genome‐wide detection, characterisation and visualisation of highly conserved sequences and the occurrence of potentially functional elements within both the conserved and evolved elements. As a result of the continued discovery of these functional elements, the nongenic genetic neighbourhoods are now considered as keys to identifying regulatory elements that are essential for gene and chromosomal function. In this article is given an overview of the various known components of the noncoding DNA landscape and present some of the bioinformatic‐based approaches and resources to identify and analyse the potential regulatory regions in genomic sequences.

Key Concepts:

  • An indeterminate fraction of the noncoding proportion of the human genome has a decisive role in regulating gene expression.

  • Comparisons among genome sequences are keys to identifying the functional regions of noncoding DNA.

  • Identifying and analysing ‘phylogenetic footprints’ is a standard approach to examine for potential regulatory regions.

  • Two common features of long‐range regulatory elements are that they are frequently conserved in other mammals and are unique within the human genome.

  • It is not only the conservation of the noncoding DNA but also the loss of the same that holds some of the clues to understand our phenotypic complexity and diversity.

  • Post‐ENCODE, the genome is viewed as a network of collaborating RNA transcripts with many of the regulatory regions of proteins transcribed into RNA and serve as regulators (e.g., microRNAs and siRNAs).

Keywords: phylogenetic footprint; noncoding DNA ; regulatory region; cis elements; repetitive elements; promoter; enhancer

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Web Links

National Center for Biotechnology Information (NCBI): http://www.ncbi.nlm.nih.gov/gene/2821

National Center for Biotechnology Information (NCBI): http://www.ncbi.nlm.nih.gov/gene/3047

National Center for Biotechnology Information (NCBI): http://www.ncbi.nlm.nih.gov/gene/6029

National Center for Biotechnology Information (NCBI): http://www.ncbi.nlm.nih.gov/gene/7054

Online Mendelian Inheritance in Man (OMIM): http://omim.org/entry/172400

Online Mendelian Inheritance in Man (OMIM): http://omim.org/entry/142200

Online Mendelian Inheritance in Man (OMIM): http://omim.org/entry/191290

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Jegga, Anil G, and Aronow, Bruce J(Sep 2013) Evolutionarily Conserved Noncoding DNA . In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0006126.pub3]