ISSN / EISSN : 1087-0156 / 1546-1696
Published by: Springer Science and Business Media LLC (10.1038)
Total articles ≅ 17,053
Latest articles in this journal
Nature Biotechnology; doi:10.1038/d41587-021-00017-3
Following reports of collateral damage caused by CRISPR genome editing, now chromothripsis, a phenomenon associated with cancer, enters the spotlight. Following reports of collateral damage caused by CRISPR genome editing, now chromothripsis, a phenomenon associated with cancer, enters the spotlight.
Nature Biotechnology, Volume 39, pp 799-807; doi:10.1038/s41587-021-00970-z
A survey of patenting activity can facilitate coordination of R&D activities to fight emerging infectious diseases.
Nature Biotechnology pp 1-6; doi:10.1038/s41587-021-00984-7
With the risks of drug development prohibitive, repurposed or repositioned medicines appear the best hope against long-COVID, a condition that still raises many unanswered questions.
Nature Biotechnology pp 1-11; doi:10.1038/s41587-021-00968-7
MaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves deep proteome coverage with substantially better coefficients of variation in protein quantification than other software. MaxDIA is equipped with accurate false discovery rate (FDR) estimates on both library-to-DIA match and protein levels, including when using whole-proteome predicted spectral libraries. This is the foundation of discovery DIA—hypothesis-free analysis of DIA samples without library and with reliable FDR control. MaxDIA performs three- or four-dimensional feature detection of fragment data, and scoring of matches is augmented by machine learning on the features of an identification. MaxDIA’s bootstrap DIA workflow performs multiple rounds of matching with increasing quality of recalibration and stringency of matching to the library. Combining MaxDIA with two new technologies—BoxCar acquisition and trapped ion mobility spectrometry—both lead to deep and accurate proteome quantification.
Nature Biotechnology, Volume 39, pp 789-795; doi:10.1038/s41587-021-00973-w
China’s growing influence in biotech was underscored in 2020 during a record-breaking year for sector financing.
Nature Biotechnology pp 1-1; doi:10.1038/s41587-021-01003-5
Nature Biotechnology pp 1-10; doi:10.1038/s41587-021-00959-8
Histone exchange between histones carrying position-specific marks and histones bearing general marks is important for gene regulation, but understanding of histone exchange remains incomplete. To overcome the poor time resolution of conventional pulse–chase histone labeling, we present a genetically encoded histone exchange timer sensitive to the duration that two tagged histone subunits co-reside at an individual genomic locus. We apply these sensors to map genome-wide patterns of histone exchange in yeast using single samples. Comparing H3 exchange in cycling and G1-arrested cells suggests that replication-independent H3 exchange occurs at several hundred nucleosomes (<1% of all nucleosomes) per minute, with a maximal rate at histone promoters. We observed substantial differences between the two nucleosome core subcomplexes: H2A-H2B subcomplexes undergo rapid transcription-dependent replacement within coding regions, whereas H3-H4 replacement occurs predominantly within promoter nucleosomes, in association with gene activation or repression. Our timers allow the in vivo study of histone exchange dynamics with minute time scale resolution. The dynamics of histone exchange are measured with genetically encoded timers.
Published: 7 July 2021
Nature Biotechnology, Volume 39, pp 796-798; doi:10.1038/s41587-021-00976-7
Nature Biotechnology; doi:10.1038/d41587-021-00010-w
Ex vivo gene editing of hematopoietic stem cells using CRISPR–Cas9 and adeno-associated virus serotype 6 is ready for trials in people with sickle-cell disease. Ex vivo gene editing of hematopoietic stem cells using CRISPR–Cas9 and adeno-associated virus serotype 6 is ready for trials in people with sickle-cell disease.
Nature Biotechnology; doi:10.1038/s41587-021-00962-z
Single-cell combinatorial indexing (sci) with transposase-based library construction increases the throughput of single-cell genomics assays but produces sparse coverage in terms of usable reads per cell. We develop symmetrical strand sci ('s3'), a uracil-based adapter switching approach that improves the rate of conversion of source DNA into viable sequencing library fragments following tagmentation. We apply this chemistry to assay chromatin accessibility (s3-assay for transposase-accessible chromatin, s3-ATAC) in human cortical and mouse whole-brain tissues, with mouse datasets demonstrating a six- to 13-fold improvement in usable reads per cell compared with other available methods. Application of s3 to single-cell whole-genome sequencing (s3-WGS) and to whole-genome plus chromatin conformation (s3-GCC) yields 148- and 14.8-fold improvements, respectively, in usable reads per cell compared with sci-DNA-sequencing and sci-HiC. We show that s3-WGS and s3-GCC resolve subclonal genomic alterations in patient-derived pancreatic cancer cell lines. We expect that the s3 platform will be compatible with other transposase-based techniques, including sci-MET or CUT&Tag.