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1. Fragile DNA contributes to repeated evolution

Author:
Kratochwil, Claudius F.; Meyer, Axel
Source:
Genome biology 2019 v.20 no.1 pp. 39
ISSN:
1474-760X
Subject:
mutation,   etc   ; DNA; evolution; genomics;     Show all 4 Subjects
Abstract:
... Sequence features that affect DNA fragility might facilitate fast, repeated evolution by elevating mutation rates at genomic hotspots. ...
DOI:
10.1186/s13059-019-1655-x

2. Evolving Inversions

Author:
Faria, Rui; Johannesson, Kerstin; Butlin, Roger K.; Westram, Anja M.
Source:
Trends in ecology & evolution 2019 v.34 no.3 pp. 239-248
ISSN:
0169-5347
Subject:
mutation,   etc   ; genes; models;     Show all 3 Subjects
Abstract:
... Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polym ...
DOI:
10.1016/j.tree.2018.12.005

3. Interactions in the ESCRT-III network of the yeast Saccharomyces cerevisiae

Author:
Brune, Thomas; Kunze-Schumacher, Heike; Kölling, Ralf
Source:
Current genetics 2019 v.65 no.2 pp. 607-619
ISSN:
0172-8083
Subject:
mutation,   etc   ; Saccharomyces cerevisiae; phenotype; prediction; proteins; yeasts;     Show all 6 Subjects
Abstract:
... Here, we examine the genetic interactions between ESCRT-III mutations in the yeast Saccharomyces cerevisiae. From the obtained interaction network, we make predictions about alternative ESCRT-III complexes. By the successful generation of an octuple deletion strain using the CRISPR/Cas9 technique, we demonstrate for the first time that ESCRT-III activity as a whole is not essential for the life of ...
DOI:
10.1007/s00294-018-0915-8

4. π-π stacking interaction is a key factor for the stability of GH11 xylanases at low pH

Author:
Ge, Hui-Hua; Qiu, Yue; Yi, Zhi-Wei; Zeng, Run-Ying; Zhang, Guang-Ya
Source:
International journal of biological macromolecules 2019 v.124 pp. 895-902
ISSN:
0141-8130
Subject:
mutation,   etc   ; amino acids; engineering; equations; pH; xylanases;     Show all 6 Subjects
Abstract:
... Acidic xylanases possess the unique features necessary for the tolerance of acidic environments, which may have great potentials for industrial purposes. However, factors controlling the pH-dependent stability of xylanases are only partially known. Here we proposed a residue interaction networks based method to analyze the differences of residue interactions between 6 pairs of experimentally verif ...
DOI:
10.1016/j.ijbiomac.2018.11.282

5. “Top” or “bottom” switches of a cyclohexanone monooxygenase controlling the enantioselectivity of the sandwiched substrate

Author:
Hu, Yujing; Wang, Jie; Cen, Yixin; Zheng, He; Huang, Meilan; Lin, Xianfu; Wu, Qi
Source:
Chemical communications 2019 v.55 no.15 pp. 2198-2201
ISSN:
1364-548X
Subject:
mutation,   etc   ; cyclohexanones; enantioselectivity; enzymes; lactones; oxidation;     Show all 6 Subjects
Abstract:
... Single mutation at the switch residues F432 (F432I/L) or L435 (L435A/G) efficiently reversed the inherent enantiopreference of WT CHMOAcᵢₙₑₜₒ in the Baeyer–Villiger oxidation of various 4-phenyl-cyclohexanone derivatives and 4-alkyl-cyclohexanones, producing a series of substituted lactones with inversed configuration (up to 99% ee and 99% conversion). ...
DOI:
10.1039/c8cc09951k

6. Mosaicism in CRISPR/Cas9-mediated genome editing

Author:
Mehravar, Maryam; Shirazi, Abolfazl; Nazari, Mahboobeh; Banan, Mehdi
Source:
Developmental biology 2019 v.445 no.2 pp. 156-162
ISSN:
0012-1606
Subject:
mutation,   etc   ; animals; gene editing; genotyping; germ cells;     Show all 5 Subjects
Abstract:
... The CRISPR/Cas9 system is a rapid, simple, and often extremely efficient gene editing method. This method has been used in a variety of organisms and cell types over the past several years. However, using this technology for generating gene-edited animals involves a number of obstacles. One such obstacle is mosaicism, which is common in founder animals. This is especially the case when the CRISPR/ ...
DOI:
10.1016/j.ydbio.2018.10.008

7. A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions

Author:
Cheung, Rocky; Insigne, Kimberly D.; Yao, David; Burghard, Christina P.; Wang, Jeffrey; Hsiao, Yun-Hua E.; Jones, Eric M.; Goodman, Daniel B.; Xiao, Xinshu; Kosuri, Sriram
Source:
Molecular cell 2019 v.73 no.1 pp. 183-194.e8
ISSN:
1097-2765
Subject:
mutation,   etc   ; exons; genetic variation; humans; introns;     Show all 5 Subjects
Abstract:
... Mutations that lead to splicing defects can have severe consequences on gene function and cause disease. Here, we explore how human genetic variation affects exon recognition by developing a multiplexed functional assay of splicing using Sort-seq (MFASS). We assayed 27,733 variants in the Exome Aggregation Consortium (ExAC) within or adjacent to 2,198 human exons in the MFASS minigene reporter and ...
DOI:
10.1016/j.molcel.2018.10.037

8. Temporal evolution of Acinetobacter baumannii ST107 clone: conversion of blaOXA-143 into blaOXA-231 coupled with mobilization of ISAba1 upstream occAB1

Author:
Rodrigues-Costa, Fernanda; Cayô, Rodrigo; Matos, Adriana Pereira; Girardello, Raquel; Martins, Willames M.B.S.; Carrara-Marroni, Floristher Elaine; Gales, Ana Cristina
Source:
Research in microbiology 2019 v.170 no.1 pp. 53-59
ISSN:
0923-2508
Subject:
mutation,   etc   ; Acinetobacter baumannii; carbapenems; transcription (genetics);     Show all 4 Subjects
Abstract:
... Nine carbapenem-resistant Acinetobacter baumannii isolates carrying blaOXA-231 and an ISAba1 upstream occAB1 were evaluated. They were clonally related and belonged to ST107. An OXA-143-producing A. baumannii ST107 strain (Ac-148) that did not possess ISAba1 upstream occAB1 was included in the analysis. Reduction in the expression of occAB1 and a 4-fold increase of carbapenem MICs were observed fo ...
DOI:
10.1016/j.resmic.2018.07.001

9. Effects of molecular crowding on a bimolecular group I ribozyme and its derivative that self-assembles to form ribozyme oligomers

Author:
Rahman, Md Motiar; Matsumura, Shigeyoshi; Ikawa, Yoshiya
Source:
Biochemical and biophysical research communications 2018 v.507 no.1-4 pp. 136-141
ISSN:
0006-291X
Subject:
mutation,   etc   ; assays; ribozymes;     Show all 3 Subjects
Abstract:
... In the RNA world, enrichment of self-replicating RNAs would have been beneficial to their survival, amplification, and evolution. Self-assembly of RNAs may be a strategy by which they enrich themselves. We examined the effects of molecular crowding on the activity of a bimolecular group I ribozyme and its derivative that self-assembles to form ribozyme oligomers. In a comparative activity assay us ...
DOI:
10.1016/j.bbrc.2018.10.188

10. Do GWAS and studies of heterozygotes for NPC1 and/or NPC2 explain why NPC disease cases are so rare?

Author:
Erickson, Robert P.
Source:
Journal of applied genetics 2018 v.59 no.4 pp. 441-447
ISSN:
1234-1983
Subject:
mutation,   etc   ; alleles; heterozygosity;     Show all 3 Subjects
Abstract:
... Early onset Niemann-Pick C diseases are extremely rare, especially Niemann-Pick C2. Perhaps unusually for autosomal recessive diseases, heterozygotes for mutations in NPC1 manifest many biological variations. NPC2 deficiency has large effects on fertility. These features of NPC1 and NPC2 are reviewed in regard to possible negative selection for heterozygotes carrying null and hypomorphic alleles. ...
DOI:
10.1007/s13353-018-0465-2

11. Cancer Mutations in SPOP Put a Stop to Its Inter-compartmental Hops

Author:
Riley, Julia F.; Dao, Thuy P.; Castañeda, Carlos A.
Source:
Molecular cell 2018 v.72 no.1 pp. 1-3
ISSN:
1097-2765
Subject:
mutation,   etc   ; neoplasms; separation; ubiquitination;     Show all 4 Subjects
Abstract:
... In this issue of Molecular Cell, Bouchard et al. (2018) identify liquid-liquid phase separation as a mechanism for substrate-triggered localization of SPOP and ubiquitination machinery to different nuclear bodies and describe how cancer mutations disrupt this process. ...
DOI:
10.1016/j.molcel.2018.09.025

12. Self-Digestion for Lifespan Extension: Enhanced Autophagy Delays Aging

Author:
Arensman, Michael D.; Eng, Christina H.
Source:
Molecular cell 2018 v.71 no.4 pp. 485-486
ISSN:
1097-2765
Subject:
mutation,   etc   ; autophagy; longevity; mammals;     Show all 4 Subjects
Abstract:
... By systemically boosting autophagy with a knockin mutation that prevents binding of beclin 1 to BCL2, Fernández et al. (2018) demonstrate that enhanced autophagy prolongs lifespan in mammals. ...
DOI:
10.1016/j.molcel.2018.08.002

13. Detecting Rare Mutations and DNA Damage with Sequencing-Based Methods

Author:
Sloan, Daniel B.; Broz, Amanda K.; Sharbrough, Joel; Wu, Zhiqiang
Source:
Trends in biotechnology 2018 v.36 pp. 729-740
ISSN:
0167-7799
Subject:
mutation,   etc   ; DNA damage; tissues;     Show all 3 Subjects
Abstract:
... There is a great need in biomedical and genetic research to detect DNA damage and de novo mutations, but doing so is inherently challenging because of the rarity of these events. The enormous capacity of current DNA sequencing technologies has opened the door for quantifying sequence variants present at low frequencies in vivo, such as within cancerous tissues. However, these sequencing technologi ...
DOI:
10.1016/j.tibtech.2018.02.009

14. Phosphorylation alters Bim‐mediated Mcl‐1 stabilization and priming

Author:
Conage‐Pough, Jason E.; Boise, Lawrence H.
Source:
TheFEBS journal 2018 v.285 no.14 pp. 2626-2640
ISSN:
1742-464X
Subject:
mutation,   etc   ; apoptosis; phosphorylation; proteins;     Show all 4 Subjects
Abstract:
... Mcl‐1 is a highly labile protein, subject to extensive post‐translational regulation. This distinguishes Mcl‐1 from other antiapoptotic proteins and necessitates further study to better understand how interactions with proapoptotic Bcl‐2 proteins affect its regulation. One such protein, Bim, is known to stabilize Mcl‐1, and Bim phosphorylation has been associated with increased Mcl‐1 binding. Cons ...
DOI:
10.1111/febs.14505

15. Effects of mismatches distant from the target position on gene correction with a 5′-tailed duplex

Author:
Suzuki, Tetsuya; Yanai, Yuri; Nishigaki, Natsuki; Nakatsu, Yoshimichi; Tsuzuki, Teruhisa; Kamiya, Hiroyuki
Source:
Journal of bioscience and bioengineering 2018 v.125 no.5 pp. 619-623
ISSN:
1389-1723
Subject:
mutation,   etc   ; DNA; genes;     Show all 3 Subjects
Abstract:
... The introduction of a 5′-tailed duplex (5′-TD) fragment into cells corrects a base-substitution mutation in a target DNA. We previously reported that the gene correction efficiency was improved when a frameshift type of second mismatch was present ∼330 bases distant from the target position, between the target DNA and the 5′-TD fragment. In this study, the effects of the second mismatches on the g ...
DOI:
10.1016/j.jbiosc.2017.12.017

16. Interactions between BTB domain of CP190 and two adjacent regions in Su(Hw) are required for the insulator complex formation

Author:
Melnikova, Larisa; Kostyuchenko, Margarita; Molodina, Varvara; Parshikov, Alexander; Georgiev, Pavel; Golovnin, Anton
Source:
Chromosoma 2018 v.127 no.1 pp. 59-71
ISSN:
0009-5915
Subject:
mutation,   etc   ; Drosophila; chromatin; genomics;     Show all 4 Subjects
Abstract:
... The best-studied Drosophila insulator complex consists of two BTB-containing proteins, the Mod(mdg4)-67.2 isoform and CP190, which are recruited cooperatively to chromatin through interactions with the DNA-binding architectural protein Su(Hw). While Mod(mdg4)-67.2 interacts only with Su(Hw), CP190 interacts with many other architectural proteins. In spite of the fact that CP190 is critical for the ...
DOI:
10.1007/s00412-017-0645-6

17. Solving Mendelian Mysteries: The Non-coding Genome May Hold the Key

Author:
Valente, Enza Maria; Bhatia, Kailash P.
Source:
Cell 2018 v.172 pp. 889-891
ISSN:
0092-8674
Subject:
mutation,   etc   ; genes; genomics; transcriptomics;     Show all 4 Subjects
Abstract:
... Despite revolutionary advances in sequencing approaches, many mendelian disorders have remained unexplained. In this issue of Cell, Aneichyk et al. combine genomic and cell-type-specific transcriptomic data to causally link a non-coding mutation in the ubiquitous TAF1 gene to X-linked dystonia-parkinsonism. ...
DOI:
10.1016/j.cell.2018.02.022

18. Modeling double strand break susceptibility to interrogate structural variation in cancer

Author:
Ballinger, Tracy J.; Bouwman, Britta A. M.; Mirzazadeh, Reza; Garnerone, Silvano; Crosetto, Nicola; Semple, Colin A.
Source:
Genome biology 2019 v.20 no.1 pp. 28
ISSN:
1474-760X
Subject:
mutation,   etc   ; DNA; DNA damage; cell lines; chromatin; genes; models; neoplasms;     Show all 8 Subjects
Abstract:
... BACKGROUND: Structural variants (SVs) are known to play important roles in a variety of cancers, but their origins and functional consequences are still poorly understood. Many SVs are thought to emerge from errors in the repair processes following DNA double strand breaks (DSBs). RESULTS: We used experimentally quantified DSB frequencies in cell lines with matched chromatin and sequence features ...
DOI:
10.1186/s13059-019-1635-1

19. Cardiomyopathy Mutations in Metavinculin Disrupt Regulation of Vinculin-Induced F-Actin Assemblies

Author:
Sarker, Muzaddid; Lee, Hyunna T.; Mei, Lin; Krokhotin, Andrey; de los Reyes, Santiago Espinosa; Yen, Laura; Costantini, Lindsey M.; Griffith, Jack; Dokholyan, Nikolay V.; Alushin, Gregory M.; Campbell, Sharon L.
Source:
Journal of molecular biology 2019 v.431 no.8 pp. 1604-1618
ISSN:
0022-2836
Subject:
point mutation,   etc   ; actin; cardiomyopathy; dimerization; heart; microfilaments; models; mutants; tissues;     Show all 9 Subjects
Abstract:
... Debilitating heart conditions, notably dilated and hypertrophic cardiomyopathies (CMs), are associated with point mutations in metavinculin, a larger isoform of the essential cytoskeletal protein vinculin. Metavinculin is co-expressed with vinculin at sub-stoichiometric ratios in cardiac tissues. CM mutations in the metavinculin tail domain (MVt) occur within the extra 68-residue insert that diffe ...
DOI:
10.1016/j.jmb.2019.02.024

20. Target DNA mutagenesis-based fluorescence assessment of off-target activity of the CRISPR-Cas9 system

Author:
Wang, Dan; Niu, Cuili; Han, Jingxin; Ma, Dejun; Xi, Zhen
Source:
RSC advances 2019 v.9 no.16 pp. 9067-9074
ISSN:
2046-2069
Subject:
mutation,   etc   ; DNA; enzymes; fluorescence; gene editing; genomics; prediction;     Show all 7 Subjects
Abstract:
... The RNA-guided CRISPR/Cas9 system could cleave double-stranded DNA at the on-target sites but also induce off-target mutations in unexpected genomic regions. The base-pairing interaction of sgRNA with off-target DNA was still not well understood and also lacked a direct cell-based assay. Herein we developed a fast target DNA mutagenesis-based fluorescence assay to directly detect the Cas9 activity ...
DOI:
10.1039/c8ra10017a