NATsDB: Natural Antisense Transcripts DataBase

Abstract

Natural antisense transcripts (NATs) are reverse complementary at least in part to the sequences of other endogenous sense transcripts. Most NATs are transcribed from opposite strands of their sense partners. They regulate sense genes at multiple levels and are implicated in various diseases. Using an improved whole-genome computational pipeline, we identified abundant cis-encoded exon-overlapping sense-antisense (SA) gene pairs in human (7356), mouse (6806), fly (1554), and eight other eukaryotic species (total 6534). We developed NATsDB (Natural Antisense Transcripts DataBase, http://natsdb.cbi.pku.edu.cn/) to enable efficient browsing, searching and downloading of this currently most comprehensive collection of SA genes, grouped into six classes based on their overlapping patterns. NATsDB also includes non-exon-overlapping bidirectional (NOB) genes and non-bidirectional (NBD) genes. To facilitate the study of functions, regulations and possible pathological implications, NATsDB includes extensive information about gene structures, poly(A) signals and tails, phastCons conservation, homologues in other species, repeat elements, expressed sequence tag (EST) expression profiles and OMIM disease association. NATsDB supports interactive graphical display of the alignment of all supporting EST and mRNA transcripts of the SA and NOB genes to the genomic loci. It supports advanced search by species, gene name, sequence accession number, chromosome location, coding potential, OMIM association and sequence similarity.

Figure 1

The browser interface of NATsDB: Limited by the criteria specified by the user in the top part of the page, the browser marks on the human chromosomes all SA pairs that involve coding genes on both strands, at least one of which has ‘kinase’ in its description, with overlapping length ≥100 bp. The x-axis of the figure at the bottom of the page shows the chromosomes. ‘+’ signs marked on the chromosome in different colors denote different classes of SA pairs.

Figure 2

Loci browser showing human SA gene pair, MKRN2/RAF1: The control panel on top allows users to interactively select all or subsets of all sequences. Below the control panel, the browser displays, from top to bottom, the chromosome coordination (‘Genome’), phastCons conservation score (‘Conservation Score’), selected supporting mRNA/EST sequences with representative sense and antisense transcripts marked in red, and links to expression profiles of the ESTs. Gene name, tissue information, Homologene link, OMIM link and sequence link appear on the right-hand side of each transcript. For more details, please refer to .

Figure 3

Expression profile of MKRN2/RAF1 is shown as bar plot, based on all spliced ESTs derived from the plus strand (MKRN2) and minus strand (RAF1) of this genomic locus. Users could change the criteria in the control panel on the loci page to select any other subsets of ESTs to profile the sense and antisense genes, such as only polyadenylated ESTs [with poly(A) tail or signal].

Figure 4

The search interface of NATsDB NATsDB supports multiple search methods including free text search, OMIM disease search, chromosomal location search and BLAST sequence search.