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Current Issue of Trends in Genetics


Issue: Trends in Genetics

Oct 01, 2021

Volume 37Issue 10p863-950, e1-e2
Leonardo Da Vinci was one of the earliest students of the internal form and function of the human body. In the notes accompanying one of his immortal sketches, Leonardo described his Vitruvian man as cosmografia del minor mondo, or cosmography of the microcosm, believing the workings of the human body to be analogous to the wider workings of the universe. While Leonardo knew naught of cells or evolution, we may well imagine that he would have been fascinated by the idea of human beings as mosaics of microscopic clones of cells, each contributing to a larger whole while at the same time ruthlessly competing to propagate itself at the expense of its neighbours. That within us is a microcosm of the evolutionary processes that shape all life on earth. On pages 872– 881, Olafsson and Anderson discuss somatic evolution within the body and what its study may teach us about common complex diseases other than cancer. Cover art: Sigurgeir Olafsson....
Leonardo Da Vinci was one of the earliest students of the internal form and function of the human body. In the notes accompanying one of his immortal sketches, Leonardo described his Vitruvian man as cosmografia del minor mondo, or cosmography of the microcosm, believing the workings of the human body to be analogous to the wider workings of the universe. While Leonardo knew naught of cells or evolution, we may well imagine that he would have been fascinated by the idea of human beings as mosaics of microscopic clones of cells, each contributing to a larger whole while at the same time ruthlessly competing to propagate itself at the expense of its neighbours. That within us is a microcosm of the evolutionary processes that shape all life on earth. On pages 872– 881, Olafsson and Anderson discuss somatic evolution within the body and what its study may teach us about common complex diseases other than cancer. Cover art: Sigurgeir Olafsson.

Science & Society

  • Research and leaders: a twisted tale!

    • Ashish Prasad,
    • Manoj Prasad
    Good leadership is important for the efficient functioning of an organization. PhD and postdoctoral research is a mentally challenging job, and a good mentor must be able to both treat students with compassion and provide motivation. Coronavirus disease 2019 (COVID-19) has resulted in the decline of the mental health of a large fraction of mentees.

Forum

  • Cats – telomere to telomere and nose to tail

    • Leslie A. Lyons
    Feline genomic medicine can decode human variants of uncertain significance (VUSs). Telomere-to-telomere genome assemblies are feasible for all felid species, supporting genetic evolution and speciation studies. Their highly conserved genomic organization compared to humans suggests cats may also decipher the intergenic variation affecting the 3D chromosome structures influencing gene regulation.
  • Quantitative genetics: pan-genomes, SVs, and k-mers for GWAS

    • Pushpendra K. Gupta
    For identification of marker–trait associations (MTAs) for complex traits in animals and plants, thousands of genome-wide association studies (GWAS) were conducted during the past two decades. This involved regular improvement in methodology. Initially, a reference genome and SNPs were used; more recently pan-genomes and the markers structural variations (SVs)/k-mers are also being used.

Opinions

  • Somatic mutations provide important and unique insights into the biology of complex diseases

    • Sigurgeir Olafsson,
    • Carl A. Anderson
    Open Access
    Somatic evolution of cells within the body is well known to lead to cancers. However, spread of somatic mutations within a tissue over time may also contribute to the pathogenesis of non-neoplastic diseases. Recent years have seen the publication of many studies aiming to characterize somatic evolution in healthy tissues. A logical next step is to extend such work to diseased conditions. As our understanding of the interplay between somatic mutations and non-neoplastic disease grows, opportunities for the joint study of germline and somatic variants will present themselves.
  • Role of Polycomb in the control of transposable elements

    • Angélique Déléris,
    • Frédéric Berger,
    • Sandra Duharcourt
    It is generally considered that Polycomb Repressive Complex (PRC)2 deposits the histone mark H3K27me3 on silent protein-coding genes, while transposable elements are repressed by DNA and/or H3K9 methylation. Yet, there is increasing evidence that PRC2 also targets and even silences transposable elements in representatives of several distantly related eukaryotic lineages. In plants and animals, H3K27me3 is present on transposable elements in mutants and specific cell types devoid of DNA methylation.

Reviews

  • Sperm mosaicism: implications for genomic diversity and disease

    • Martin W. Breuss,
    • Xiaoxu Yang,
    • Joseph G. Gleeson
    While sperm mosaicism has few consequences for men, the offspring and future generations are unwitting recipients of gonadal cell mutations, often yielding severe disease. Recent studies, fueled by emergent technologies, show that sperm mosaicism is a common source of de novo mutations (DNMs) that underlie severe pediatric disease as well as human genetic diversity. Sperm mosaicism can be divided into three types: Type I arises during sperm meiosis and is non-age dependent; Type II arises in spermatogonia and increases as men age; and Type III arises during paternal embryogenesis, spreads throughout the body, and contributes stably to sperm throughout life.
  • Evolutionary conservation in noncoding genomic regions

    • Nicole A. Leypold,
    • Michael R. Speicher
    Humans may share more genomic commonalities with other species than previously thought. According to current estimates, ~5% of the human genome is functionally constrained, which is a much larger fraction than the ~1.5% occupied by annotated protein-coding genes. Hence, ~3.5% of the human genome comprises likely functional conserved noncoding elements (CNEs) preserved among organisms, whose common ancestors existed throughout hundreds of millions of years of evolution. As whole-genome sequencing emerges as a standard procedure in genetic analyses, interpretation of variations in CNEs, including the elucidation of mechanistic and functional roles, becomes a necessity.

Series:Celebrating the Human Genome Project and its outcomes

  • Evolutionary cell type mapping with single-cell genomics

    • Amos Tanay,
    • Arnau Sebé-Pedrós
    A fundamental characteristic of animal multicellularity is the spatial coexistence of functionally specialized cell types that are all encoded by a single genome sequence. Cell type transcriptional programs are deployed and maintained by regulatory mechanisms that control the asymmetric, differential access to genomic information in each cell. This genome regulation ultimately results in specific cellular phenotypes. However, the emergence, diversity, and evolutionary dynamics of animal cell types remain almost completely unexplored beyond a few species.
  • From QTL to gene: C. elegans facilitates discoveries of the genetic mechanisms underlying natural variation

    • Kathryn S. Evans,
    • Marijke H. van Wijk,
    • Patrick T. McGrath,
    • Erik C. Andersen,
    • Mark G. Sterken
    Although many studies have examined quantitative trait variation across many species, only a small number of genes and thereby molecular mechanisms have been discovered. Without these data, we can only speculate about evolutionary processes that underlie trait variation. Here, we review how quantitative and molecular genetics in the nematode Caenorhabditis elegans led to the discovery and validation of 37 quantitative trait genes over the past 15 years. Using these data, we can start to make inferences about evolution from these quantitative trait genes, including the roles that coding versus noncoding variation, gene family expansion, common versus rare variants, pleiotropy, and epistasis play in trait variation across this species.

Genome of the Month

  • Callithrix jacchus (the common marmoset)

    • Chentao Yang,
    • Guojie Zhang
    The common marmoset (Callithrix jacchus) is an important primate model system widely used in biomedical research [1]. A recent study has produced the diploid genomes of this species with two sets of chromosomes fully phased using a trio binning approach [2]. Comparison of the paternal and maternal genomes has identified all spectra of heterozygosity and has shown that the heterozygosity level of the diploid genome is ten times higher than the traditional estimation with single nucleotide variations only.
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