Bergman Lab

Before embarking on any genome annotation effort, it is necessary to establish the best way to represent the biological feature under investigation. This post discusses how best to represent the annotation of transposable element (TE) insertions that are mapped to (but not present in) a reference genome sequence (e.g. from mutagenesis or re-sequencing studies), and how the standard coordinate system in use today causes problems for the annotation of TE insertions.

There are two major coordinate systems in genome bioinformatics, that differ primarily in whether they anchor genomic feature to (“base coordinate systems”) or between (“interbase coordinate systems”) nucleotide positions. Most genome annotation portals (e.g. NCBI or Ensembl), bioinformatics software (e.g. BLAST) and annotation file formats (e.g. GFF) use the base coordinate system, which represents a feature starting at the first nucleotide as position 1. In contrast, a growing number of systems (e.g. UCSC, Chado, DAS2) employ the interbase coordinate system, whereby a feature starting at the first nucleotide is represented as position 0. Note, the UCSC genome bioinformatics team actually use both systems and refer to the base coordinate system as “one-based, fully-closed” (used in the UCSC genome browser display) and interbase coordinate system as “zero-based, half-open” (used in their tools and file formats), leading to a FAQ about this issue by users. The interbase coodinate system is also referred to as “space-based” by some authors.

The differences between base (bottom) and interbase (top) coordinate system can be visualized in the following diagram (taken from the Chado wiki).

There are several advantage for using the interbase coordinate system including: (i) the ability to represent features that occur between nucleotides (like a splice site), (ii) simpler arithmetic for computing the length of features (length=end-start) and overlaps (max(start1,start2), min(end1,end2)) and (iii) more rational conversion of coordinates from the positive to the negative strand (see discussion here).

So why is the choice of coordinate system important for the annotation of TEs mapped to a reference sequence? The short answer is that TEs (and other insertions) that are not a part of the reference sequence occur between nucleotides in the reference coordinate system, and therefore it is difficult to accurately represent the location of a TE on base coordinates. Nevertheless, base coordinate systems dominate most of genome bioinformatics and are an established framework that one has to work within.

How then should we annotate TE insertions on base coordinates that are mapped precisely to a reference genome? If a TE insertion in reality occurs between positions X and X+1 in a genome, do we annotate the start and end position both at the same nucleotide? If so, do we annotate the start/stop coordinate at position X, or both at position X+1? If we chose to annotate the insertion at position X, then we need to invoke a rule that the TE inserts after nucleotide X. However this solution breaks down if the insertion is on the negative strand, since we either need to map a negative strand insertion to X+1 or have a different rule for interpreting the placement of the TE on positive and negative strands. Alternatively, do we annotate the TE as starting at X and ending at X+1, attempting to fake interbase coordinates on a base coordinate system, but at face value implying that the TE insertion is not mapped precisely and spans 2 bp in the genome.

After grappling with this issue for some time, it seems that neither of these solutions is sufficient to deal with the complexities of TE insertion and reference mapping. To understand why, we must consider the mechanisms of TE integration and how TE insertions are mapped to the genome. Most TEs create staggered cuts to the genomic DNA that are filled on integration into the genome leading to short target site duplications (TSDs). Most TEs also target a palindromic sequence, and insert randomly with respect to orientation. A new TE insertion is typically mapped to the genome by sequencing a fragment that spans the TE into unique flanking DNA, either by directed (e.g. inverse/linker PCR) or random (e.g. shotgun re-sequencing) approaches. The TE-flank fragment can be obtained from the 5′ or 3′ end of the TE. However, where one places the TE insertion depends on whether one uses the TE-flank from the 5′ or 3′ end and the orientation of the TE insertion in the genome. As shown in the following diagram, for an insertion on the positive strand (>>>), a TE-flank fragment from the 5′ end is annotated to occur at the 3′ end of the TSD (shown in bold), whereas a 3′ TE-flank fragment is placed at the 5′ end of the TSD.  For an insertion on the negative strand (<<<), the opposite effect occurs. In both cases, TE-flank fragments from the 5′ and 3′ end map the TE insertion to different locations in the genome.

Thus, where one chooses to annotate a TE insertion relative to the TSD is dependent on the orientation of the TE insertion and which end is mapped to the genome. As a consequence, both the single-base and two-base representations proposed above are flawed, since TE insertions into the same target site are annotated at two different locations on the positive and negative strand. This issue lead us (in retrospect) to misinterpret some aspects of the P-element target site preference in a recent paper, since FlyBase uses a single-base coordinate system to annotate TE insertions.

As an alternative, I propose that the most efficient and accurate way to represent TE insertions mapped to a reference genome on base coordinates is to annotate the span of the TSD and label the orientation of the TE in the strand field. This formulation allows one to bypass having to chose where to locate the TE relative to the TSD (5′ vs. 3′, as is required under the one-base/two-base annotation framework), and can represent insertions into the same target site that occur on different strands. Furthermore, this solution allows one to use both 5′ and 3′ TE-flank information. In fact, the overlap between coordinates from the 5′ and 3′ TE-flank fragments defines the TSD. Finally, this solution requires no prior information about TSD length for a given TE family, and also accommodates TE families that generate variable length TSDs since the TSD is annotated on a per TE basis.

The only problem left open by this proposed solution is for TEs that do not create a TSD, which have been reported to exist. Any suggestions for a general solution that also allows for annotation of TE insertions without TSDs would be much appreciated….