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A recent study has analysed publicly available long-read sequencing data to characterize human-specific variable number tandem repeats at high resolution.
A study in Current Biology reports the retrieval of genome-scale information for human, wolf (Canis lupus) and bison (Bison bonasus) by shotgun sequencing and genomic analysis of a sediment sample.
A new report introduces xPore, a computational method and statistical framework for the analysis of differential RNA modifications from nanopore direct RNA sequencing data.
A study in the American Journal of Human Genetics shows that using the GRCh37 versus GRCh38 version of the human reference genome makes a meaningful difference to the calling of human genetic variants, with implications for research-based and clinical-based human sequencing studies.
The RNA Atlas is reported in Nature Biotechnology. It provides a global view of human RNAs, including thousands of newly characterized non-coding RNAs.
In a paper in Nature, Hua et al. report the Micro-Capture-C method for near-base-pair resolution characterization of chromosomal interactions in mammalian cells.
During development, cell competition causes apoptosis of cells with abnormal ribosomal protein profiles. Ji et al. show that this same mechanism also deletes aneuploid cells and that the deleted cell populations mainly have altered ribosomal protein gene dosages.
Schep et al. show that non-homologous end joining is strongly favoured in euchromatin, whereas single-stranded template repair is moderately preferred in heterochromatin. Importantly, heterochromatin features that promote microhomology-mediated end joining also decrease Cas9 efficiency.
Human telomerase reverse transcriptase (hTERT) activity is tightly controlled. This report shows that hTERT is primarily regulated by alternative splicing; skipping of exon 2 triggers decay of TERT mRNA in differentiated cells and its retention promotes telomere maintenance in pluripotent cells.
In a study in Science, Lopatkin et al. identify mutations in metabolic genes of Escherichia coli that lead to antibiotic resistance. Functional analyses of the mutations support the view that metabolic dysfunction helps pathogens escape the lethal effects of antibiotics.
A paper published in Nature Methods describes integrative DNA and protein tagging (iDAPT). iDAPT is a new approach for analysing both genomic (iDAPT-seq) and proteomic (iDAPT-MS) components of accessible chromatin from a single nuclear lysate.
In a report in Molecular Cell, Wang et al. describe genome oligopaint via local denaturation fluorescence in situ hybridization (GOLD FISH). This Cas9-superhelicase-based DNA-FISH method locally denatures DNA at physiological temperatures and provides an improved signal-to-background ratio.
A study in Current Biology demonstrates the use of environmental DNA to monitor the abundance and composition of airborne grass pollen on a national scale. Integration with health data can infer the effects of specific pollen types on respiratory health.
In this paper, the authors present sequence data from ancient mammoth specimens, including samples more than 1 million years old. The sequences provide insights into mammoth evolution and reveal that distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene.
The TOPMed consortium report whole-genome sequencing data from 53,831 ethnically diverse participants. They describe the key features of the genetic variation and produce data resources for future medical research by the wider scientific community.
Park et al. describe in Cell how CRISPR–Cas9 genome editing can be used as a time recorder in mammalian cells in vitro and in vivo, including reporting the timescales of cellular events such as chemical exposure and inflammation.
In this paper in Nature Genetics, Atkinson et al. describe Tractor, a statistical framework and software package that enables admixed populations to be included in large-scale genomics studies.
Chew et al. report in Nature Communications that short histone H2A variants are upregulated in a wide range of cancers, indicating that they become oncohistones when aberrantly expressed.
