Human L1 Transposition Dynamics Unraveled with Functional Data Analysis

funBIalign: a hierachical algorithm for functional motif discovery based on mean squared residue scores

Motif discovery is gaining increasing attention in the domain of functional data analysis. Functional motifs are typical "shapes" or "patterns" that recur multiple times in different portions of a single curve and/or in misaligned portions of multiple curves. In this paper, we define functional motifs using an additive model and we propose funBIalign for their discovery and evaluation. Inspired by clustering and biclustering techniques, funBIalign is a multi-step procedure which uses agglomerative hierarchical clustering with complete linkage and a functional distance based on mean squared residue scores to discover functional motifs, both in a single curve (e.g., time series) and in a set of curves. We assess its performance and compare it to other recent methods through extensive simulations. Moreover, we use funBIalign for discovering motifs in two real-data case studies; one on food price inflation and one on temperature changes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11222-024-10537-y.

Noncanonical DNA structures are drivers of genome evolution

In addition to the canonical right-handed double helix, other DNA structures, termed 'non-B DNA', can form in the genomes across the tree of life. Non-B DNA regulates multiple cellular processes, including replication and transcription, yet its presence is associated with elevated mutagenicity and genome instability. These discordant cellular roles fuel the enormous potential of non-B DNA to drive genomic and phenotypic evolution. Here we discuss recent studies establishing non-B DNA structures as novel functional elements subject to natural selection, affecting evolution of transposable elements (TEs), and specifying centromeres. By highlighting the contributions of non-B DNA to repeated evolution and adaptation to changing environments, we conclude that evolutionary analyses should include a perspective of not only DNA sequence, but also its structure.

The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes

Transposable elements (TEs) are nearly ubiquitous in eukaryotes. The increase in genomic data, as well as progress in genome annotation and molecular biology techniques, have revealed the vast number of ways mobile elements have impacted the evolution of eukaryotes. In addition to being the main cause of difference in haploid genome size, TEs have affected the overall organization of genomes by accumulating preferentially in some genomic regions, by causing structural rearrangements or by modifying the recombination rate. Although the vast majority of insertions is neutral or deleterious, TEs have been an important source of evolutionary novelties and have played a determinant role in the evolution of fundamental biological processes. TEs have been recruited in the regulation of host genes and are implicated in the evolution of regulatory networks. They have also served as a source of protein-coding sequences or even entire genes. The impact of TEs on eukaryotic evolution is only now being fully appreciated and the role they may play in a number of biological processes, such as speciation and adaptation, remains to be deciphered.