Principles of gene and regulatory evolution as inferred from cross-species comparisons in primates

Kliesmete, Zane (2024): Principles of gene and regulatory evolution as inferred from cross-species comparisons in primates. Dissertation, LMU München: Fakultät für Biologie

Abstract

The sequence contained in the 3.2 Gb long haploid stretches of our DNA has been registered but we are still far from having decoded the information that it contains. Among the approaches that facilitate a closer insight into the relevance of individual elements for existent phenotypes is the comparative approach. It extends beyond focusing solely on one species, instead exploiting the knowledge gained from investigating patterns of evolutionary change. Evolutionary comparisons have an advantage over other techniques that rely on genetic change, in that they inform on the types of changes that have evidently occurred in nature. In this thesis, I bridge advances made in gathering genetic information and in generating high-throughput functional assays in a cross-species context to answer fundamental questions in evolutionary genomics. To be able to rely on recently developed genome-wide functional assays like RNA-seq, we should know the amount of error that these measurements contain. Using genetic variation between species, I contribute to estimating the precision with which we measure expression. We further evaluate and compare computational methods that are designed to remove this noise, using our substitution-based error estimates as the ground truth. Then, I study multiple aspects of gene and regulatory evolution by leveraging cross-species data on DNA, expression, accessibility and the activity of regulatory and protein sequences. An important current task in genomics is to improve our ability to read and interpret the regulatory code that governs expression. Therefore, I study how constraint is reflected in a range of functional properties of cis-regulatory elements (CREs), using their tissue-specificity as a proxy for functional importance. Based on theoretical considerations and patterns seen in the case of genes, pleiotropic CREs that are utilized in all or the majority of tissues are expected to be under most constraint. This turns out to be true for the conservation patterns of transcription factor binding site repertoires, whereas the exact binding sites as well as the underlying sequences show even lower conservation than that of tissue-specific CREs. Considering the highly conserved accessibility of pleiotropic CREs and the conserved downstream gene expression, these findings suggest pervasive compensatory evolution acting within the sequences of pleiotropic CREs and, likely, across functionally orthologous tissue-specific CREs. This study underlines the importance to evaluate CRE conservation and functionality using metrics beyond simple sequence conservation. Further, I touch another currently highly debated aspect of genome evolution: The role of newly evolved elements in species-specific rewiring of gene regulatory networks. Transposable element-derived regulatory and gene sequences are gaining increasing attention due to their ability to expand the genome in a clade- or species-specific manner. In addition, some types of TEs, such as long terminal repeat (LTR) elements, carry binding sites for important transcription factors active in pluripotent stem or other cell types. This leads to new regulatory sequences and transcripts. While some of these have been proposed or indeed shown to contribute to the cellular phenotypes, in the current study we revisit one such candidate long non-coding gene, ESRG, and find that in spite of its high expression in human pluripotent stem cells, it is dispensable to the function of these cells. We also find no evidence for selection using sequence divergence and polymorphism-based analyses. This study is a reminder to be careful in interpreting expression as a sign of function. Finally, I combine evolutionary and functional measures to assess the association between genetic and phenotypic evolution. Specifically, I focus on the association between brain evolution and the evolution of a particular brain developmental gene TRNP1 across over 30 mammalian species. I find that TRNP1 coding sequence evolution, TRNP1-dependent proliferation rates and the activity of a cis-regulatory element of TRNP1 co-evolve with brain size and the degree of gyrification. These findings advance our evolutionary and neu- rodevelopmental understanding of how larger and more folded brains evolve. Moreover, with the increasing availability of high-quality genomes and possibilities to assay genetic variants in massively parallel assays, this and similar studies are demonstrations of how evolutionary information can be leveraged by combining phylogenetic approaches with functional assays.

• Dokumententyp: Dissertationen (Dissertation, LMU München)
• Keywords: Genome evolution, primate evolution, gene evolution, cis-regulatory element evolution, protein evolution, computational biology, genomics, multiomics, epigenetics, transcriptomics
• Themengebiete: 500 Naturwissenschaften und Mathematik ; 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie
• Fakultäten: Fakultät für Biologie
• Sprache der Hochschulschrift: Englisch
• Datum der mündlichen Prüfung: 5. Dezember 2024
• 1. Bericht­erstatter:in: Hellmann, Ines