TY - JOUR AB - Recent developments in low-input genomics techniques have greatly advanced the analysis of the order in which DNA is replicated in the genome - that is, replication timing (RT) - and its interrelationships with other processes. RT correlates or anticorrelates with genomic-specific parameters such as gene expression, chromatin accessibility, histone modifications, and the 3D structure of the genome, but the significance of how they influence each other and how they relate to biological processes remains unclear. In this review I discuss the results of recent analyses of RT, the time at which it is remodeled and consolidated during embryogenesis, how it influences development and differentiation, and the regulatory mechanisms and factors involved. AU - Nakatani, T. C1 - 73691 C2 - 57174 CY - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa SP - 568-576 TI - Dynamics of replication timing during mammalian development. JO - Trends Genet. VL - 41 IS - 7 PB - Cell Press PY - 2025 SN - 0168-9479 ER - TY - JOUR AB - Genome-wide association studies (GWAS) have provided insights into the genetic basis of complex diseases. In the next step, integrative multi-omics approaches can characterize molecular profiles in relevant primary tissues to reveal the mechanisms that underlie disease development. Here, we highlight recent progress in four examples of complex diseases generated by integrative studies: type 2 diabetes (T2D), osteoarthritis, Alzheimer's disease (AD), and systemic lupus erythematosus (SLE). High-resolution methodologies such as single-cell and spatial omics techniques will become even more important in the future. Furthermore, we emphasize the urgent need to include as yet understudied cell types and increase the diversity of studied populations. AU - Kreitmaier, P. AU - Katsoula, G. AU - Zeggini, E. C1 - 66297 C2 - 52772 CY - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa SP - 46-58 TI - Insights from multi-omics integration in complex disease primary tissues. JO - Trends Genet. VL - 39 IS - 1 PB - Cell Press PY - 2023 SN - 0168-9479 ER - TY - JOUR AB - The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics. AU - Theissinger, K.* AU - Fernandes, C.* AU - Formenti, G.* AU - Bista, I.* AU - Berg, P.R.* AU - Bleidorn, C.* AU - Bombarely, A.* AU - Crottini, A.* AU - Gallo, G.R.* AU - Godoy, J.A.* AU - Jentoft, S.* AU - Malukiewicz, J.* AU - Mouton, A.* AU - Oomen, R.A.* AU - Paez, S.* AU - Palsbøll, P.J.* AU - Pampoulie, C.* AU - Ruiz-López, M.J.* AU - Secomandi, S.* AU - Svardal, H.* AU - Theofanopoulou, C.* AU - de Vries, J.* AU - Waldvogel, A.M.* AU - Zhang, G.* AU - Jarvis, E.D.* AU - Bálint, M.* AU - Ciofi, C.* AU - Waterhouse, R.M.* AU - Mazzoni, C.J.* AU - Höglund, J.* AU - European Reference Genome Atlas Consortium (Urban, L.) C1 - 67755 C2 - 54117 SP - 545-559 TI - How genomics can help biodiversity conservation. JO - Trends Genet. VL - 39 IS - 7 PY - 2023 SN - 0168-9479 ER - TY - JOUR AB - Transposable elements are the largest individual constituent of mammalian genomes. These elements are highly diverse, a consequence of the multiplicity of genomic habitats that they inhabit and of the complex evolutionary histories that they have developed therein. Intriguingly, a surge of transposable element transcription occurs during mammalian preimplantation development, contributing to the establishment of totipotency and pluripotency and to the activation of the embryonic genome. However, it remains an open question how such an evolutionarily divergent set can mediate such conserved developmental processes. Here, we review transposable element diversity across mammals and their evolutionary significance. We also discuss the implications that their high evolutionary divergence has for the regulation of preimplantation development across mammals. AU - Rodriguez-Terrones, D. AU - Torres-Padilla, M.E. C1 - 54031 C2 - 45223 CY - 84 Theobalds Rd, London Wc1x 8rr, England SP - 806-820 TI - Nimble and ready to mingle: Transposon outbursts of early development. JO - Trends Genet. VL - 34 IS - 10 PB - Elsevier Science London PY - 2018 SN - 0168-9479 ER - TY - JOUR AB - Active transport and local translation of mRNAs ensure the appropriate spatial organization of proteins within cells. Recent work has shown that this process is intricately connected to membrane trafficking. Here, we focus on new findings obtained in fungal model systems. Important highlights are that RNA-binding proteins recognize cargo mRNA synergistically and that mRNAs are co-transported with membranous compartments such as the endoplasmic reticulum (ER) and endosomes. We further discuss a novel concept of endosome-coupled translation that loads shuttling endosomes with septin cargo, a process important for correct septin filamentation. Interestingly, evidence is accumulating that RNA and membrane trafficking are also tightly interwoven in higher eukaryotes, suggesting that this phenomenon is a common theme and not an exception restricted to fungi. AU - Jansen, R.P.* AU - Niessing, D. AU - Baumann, S.* AU - Feldbrügge, M.* C1 - 31906 C2 - 34872 SP - 408-417 TI - MRNA transport meets membrane traffic. JO - Trends Genet. VL - 30 IS - 9 PY - 2014 SN - 0168-9479 ER - TY - JOUR AB - In higher eukaryotes, an unusual C-terminal domain (CTD) is crucial to the function of RNA polymerase II in transcription. The CTD consists of multiple heptapeptide repeats; differences in the number of repeats between organisms and their degree of conservation have intrigued researchers for two decades. Here, we review the evolution of the CTD at the molecular level. Several primitive motifs have been integrated into compound heptads that can be readily amplified. The selection of phosphorylatable residues in the heptad repeat provided the opportunity for advanced gene regulation in eukaryotes. Current findings suggest that the CTD should be considered as a collection of continuous overlapping motifs as opposed to a specific functional unit defined by a heptad. AU - Chapman, R.D. AU - Heidemann, M. AU - Hintermair, C. AU - Eick, D. C1 - 2725 C2 - 25742 SP - 289-296 TI - Molecular evolution of the RNA polymerase II CTD. JO - Trends Genet. VL - 24 IS - 6 PB - Elsevier PY - 2008 SN - 0168-9479 ER - TY - JOUR AU - Pagel, P. AU - Mewes, H.-W. AU - Frishman, D. C1 - 5217 C2 - 22380 SP - 72-76 TI - Conservation of protein-protein interactions - lessons from ascomycota. JO - Trends Genet. VL - 20 PY - 2004 SN - 0168-9479 ER - TY - JOUR AU - Werner, T. C1 - 9832 C2 - 21696 SP - 467-469 TI - Yeast expression-array analysis goes molecular. JO - Trends Genet. VL - 19 PY - 2003 SN - 0168-9479 ER - TY - JOUR AU - Fessele, S.* AU - Maier, H. AU - Zischek, C.* AU - Nelson, P.J.* AU - Werner, T.* C1 - 9833 C2 - 20604 SP - 60-63 TI - Regulatory context is a crucial part of gene function. JO - Trends Genet. VL - 18 PY - 2002 SN - 0168-9479 ER - TY - JOUR AU - Marschall, S. AU - Hrabě de Angelis, M. C1 - 22324 C2 - 21151 SP - 128-131 TI - Cryopreservation of mouse spermatozoa : double your mouse space. JO - Trends Genet. VL - 15 PY - 1999 SN - 0168-9479 ER - TY - JOUR AU - Chatterjee, B. AU - Gimbel, W. AU - Görblich, T. AU - Werner, T. C1 - 40473 C2 - 40025 SP - 406 TI - HPLC purification of PCR products for direct sequencing. JO - Trends Genet. VL - 9 IS - 12 PY - 1993 SN - 0168-9479 ER -