Leveraging histone modifications to improve genome annotations

Abstract

Accurate genome annotations are essential to modern biology; however, they remain challenging to produce. Variation in gene structure and expression across species, as well as within an organism, make correctly annotating genes arduous; an issue exacerbated by pitfalls in current in-silico methods. These issues necessitate complementary approaches to add additional confidence and rectify potential misannotations. Integration of epigenomic data into genome annotation is one such approach. In this study, we utilized sets of histone modification data, which are precisely distributed at either gene bodies or promoters to evaluate the annotation of the Zea mays genome. We leveraged these data genome wide, allowing for identification of annotations discordant with empirical data. In total, 13,159 annotation discrepancies were found in Zea mays upon integrating data across three different tissues, which were corroborated using RNA-based approaches. Upon correction, genes were extended by an average of 2,128 base pairs, and we identified 2,529 novel genes. Application of this method to five additional plant genomes identified a series of misannotations, as well as identified novel genes, including 13,836 in Asparagus officinalis, 2,724 in Setaria viridis, 2,446 in Sorghum bicolor, 8,631 in Glycine max, and 2,585 in Phaseolous vulgaris. This study demonstrates that histone modification data can be leveraged to rapidly improve current genome annotations across diverse plant lineages.

Simple and accurate transcriptional start site identification using Smar2C2 and examination of conserved promoter features

“…Traditional annotations often cannot empirically define TSSs, instead estimating TSSs based on annotations from related organisms or RNA-seq. This has been shown to be potentially inaccurate (Mendieta et al, 2021), and lacks the resolution critical for the discovery of motifs outlined in this paper. Smar2C2 can both add novel TSS annotations and refine known gene TSS annotation.…”

Epigenome guided crop improvement: current progress and future opportunities

“…Recent innovations including CUT&RUN [32,33] and CUT&Tag [34] also facilitate profiling of chromatin modifications using lower input and less sequencing reads. These technologies enable co-localization of histone modification types with particular genomic sequences and features, including transcribed genes, promoters, transcription start sites (TSS), gene coding regions, as well as transcriptional repressed loci [35] (Figure 1). For example, Histone H3 Lysine 4 trimethylation (H3K4me3) is associated with transcriptional activation and is found at TSS, together with histones H3 acetylated at Lysine 9/27/56 positions; while gene bodies contain H3K4me1 and H3K36me3 (Figure 1) [16,[35][36][37].…”

“…These technologies enable co-localization of histone modification types with particular genomic sequences and features, including transcribed genes, promoters, transcription start sites (TSS), gene coding regions, as well as transcriptional repressed loci [35] (Figure 1). For example, Histone H3 Lysine 4 trimethylation (H3K4me3) is associated with transcriptional activation and is found at TSS, together with histones H3 acetylated at Lysine 9/27/56 positions; while gene bodies contain H3K4me1 and H3K36me3 (Figure 1) [16,[35][36][37]. In contrast, the presence of the H3K27me3 mark is indicative of transcriptional repression at a locus [38].…”

“…In particular, this information is useful not only to identify functional genes but also to refine gene boundaries and resolve inconsistencies in gene annotations. Mendieta et al [ 35 ], applied this histone code in maize and several other species, to enhance the existing genome annotations. In maize alone, thousands of new genes were identified as well as a total of 13 159 discrepancies pertaining to gene length, number and other mis-annotations [ 35 ].…”

“…Mendieta et al [ 35 ], applied this histone code in maize and several other species, to enhance the existing genome annotations. In maize alone, thousands of new genes were identified as well as a total of 13 159 discrepancies pertaining to gene length, number and other mis-annotations [ 35 ].…”