Showing papers in "Trends in Genetics in 2021"

TL;DR: In this paper, the molecular mechanisms of DNA methylation abnormalities in cancer as well as their therapeutic potential are discussed, and the early findings that a variety of tumor suppressor genes (TSGs) are targets of DNA hypermethylation in cancer led to the proposal of a model in which aberrant DNA methylations promotes cellular oncogenesis through TSGs silencing.

TL;DR: It is discussed new technologies that can extend the standard regulatory mapping framework to more diverse, disease-relevant cell types and states and suggest an alternative strategy drawing on the dynamic and highly context-specific nature of gene regulation.

TL;DR: The importance of NMD for gene editing and tumor evolution, and how inhibiting NMD may be an effective strategy to increase the efficacy of cancer immunotherapy are discussed.

TL;DR: In this paper, the authors summarized recent findings of factors that can influence the choice of DNA repair pathway in response to Cas9-induced double-strand break (DSBs) induced by CRISPR-Cas9.

TL;DR: In this article, the authors dissect m6A-orchestrated feedback circuits that regulate histone modifications and the activity of regulatory RNAs, such as long noncoding (lnc)RNA and chromosome-associated regulatory RNA.

TL;DR: In this article, the authors review the current knowledge on specific low-abundant histone ubiquitination events that are highly regulated within the cellular DNA damage response (DDR), with particular emphasis on the latest discovery of Ub phosphorylation as a novel regulator of the DDR signaling pathway.

TL;DR: In this paper, the authors proposed an approach to accelerate the availability of beneficial alleles for breeding and research using genome sequencing technologies combined with efficient trait mapping procedures, and enhanced interoperability between different omics and phenotyping platforms.

TL;DR: In this paper, the authors discuss recent advances in understanding the structural architecture of PRC2, the regulation of its activity and chromatin recruitment, and the molecular mechanisms underlying Polycomb-mediated gene silencing.

TL;DR: The available data suggest that vertebrate NMD is a complex, branched pathway wherein individual branches regulate specific mRNA subsets to fulfill distinct physiological functions.

TL;DR: With further, more accurate human genome sequencing, additional mutation hotspots, mechanistic details of their formation, and the relevance of hotspots to evolution and disease are likely to be discovered.

TL;DR: The current principles of splicing regulation are summarized, including the impact of cis and trans regulatory elements, as well as the influence of chromatin structure, transcription, and RNA modifications.

TL;DR: Several approaches for increasing the amount of data used for phylogenetic inference are reviewed, focusing on methods that allow for the inclusion of duplicated genes (paralogs), suggesting a promising way to take full advantage of genomic data.

TL;DR: Monogenic lesions of IFN-I signalling pathways are reviewed and the organising principles which emerge are summarized to inform understanding of the place of the IFN system within the concerted antiviral response.

TL;DR: An updated overview of the main characteristics of the members of the FOX family, in terms of breadth of expression, protein domain composition, evolution, and function is provided.

TL;DR: The processes that lead to the retention of duplicated genes are not well understood as mentioned in this paper, but functional genomics approaches in model organisms, such as yeast, provide useful tools to test the mechanisms underlying retention with functional redundancy and divergence.

TL;DR: In this paper, the effects of DNA fragmentation factor B (DFFB), DNASE1L3, and DNase11 on cfDNA levels and their fragmentomic profiles are explored.

TL;DR: Current evidence for the potential contribution of epigenetic factors to heredity in humans is evaluated and the challenges and limitations of this fundamental biological process, its implications, and its societal relevance are discussed.

TL;DR: A historical review of the relevant literature and retraced numerous citation chains is performed to reveal the primary data that were used as the basis for the widely accepted conclusion that TADs are highly conserved across evolution.

TL;DR: The latest findings regarding piRNA/PIWI-dependent mRNA decay in germ cells and during the maternal-to-zygotic transition in embryos combined with new modes of action of PIWI proteins in mRNA stabilization and translational activation and piRNA-independent roles of PI WI proteins in cancer are discussed.

TL;DR: The Human Cell Atlas (HCA) as discussed by the authors is a global collaborative effort to create a reference map of all human cells as a basis for both understanding human health and diagnosing, monitoring, and treating disease.

TL;DR: In this article, a review provides a brief glimpse into how these new partners were discovered and their contribution to the mechanism and regulation of NHEJ, as well as a brief overview of their roles.

TL;DR: A comprehensive review of 46 methods for polygenic score (PGS) construction can be found in this article, where the authors connect the majority of these methods through a multiple linear regression framework which can be instrumental for understanding their prediction performance for traits with distinct genetic architectures.

TL;DR: What is currently known about chromatin status and the development of cells in the hematopoietic system under normal and abnormal conditions are brought together.

TL;DR: Those gene products involved in neurodegeneration that undergo liquid-liquid phase separation and their involvement in the DNA damage response are discussed.

TL;DR: In this paper, it was shown that the histone mark H3K27me3 is present on transposable elements in mutants and specific cell types devoid of DNA methylation.

TL;DR: In this article, the authors discuss the need for a unifying framework merging the fields of population genetics, quantitative genetics and systems biology to better understand the molecular bases of polygenic traits adaptation.

TL;DR: The current knowledge of the molecular genetics of replisome dysfunction disorders is reviewed and recent mechanistic insights into their pathogenesis are discussed, with a focus on the specific steps of DNA replication affected in these human diseases.

TL;DR: In this paper, the authors discuss how developments in machine learning methodologies contributed to more accurate base calling and lower error rates, and how these methods enable new biological discoveries, and highlight challenges and future directions for computational approaches to extract the additional information provided by nanopore signal data.

TL;DR: Silencers are regulatory DNA elements that reduce transcription from their target promoters; they are the repressive counterparts of enhancers as discussed by the authors, and despite evidence of their importance in development and disease, silencers have been much less studied than enhancers.

TL;DR: In this paper, the authors discuss potential speed-specificity trade-offs in the context of existing models and further discuss the recently described "distributed specificity" paradigm, suggesting that intrinsically disordered regions (IDRs) promote specificity while reducing the TF-target search time.