Evolution of MicroRNA Genes in Oryza sativa and Arabidopsis thaliana: An Update of the Inverted Duplication Model

The origin and evolution of microRNA (miRNA) genes, which are of significance in tuning and buffering gene expressions in a number of critical cellular processes, have long attracted evolutionary biologists. However, genome-wide perspectives on their origins, potential mechanisms of their de novo generation and subsequent evolution remain largely unsolved in flowering plants. Here, genome-wide analyses of Oryza sativa and Arabidopsis thaliana revealed apparently divergent patterns of miRNA gene origins. A large proportion of miRNA genes in O. sativa were TE-related and MITE-related miRNAs in particular, whereas the fraction of these miRNA genes much decreased in A. thaliana. Our results show that the majority of TE-related and pseudogene-related miRNA genes have originated through inverted duplication instead of segmental or tandem duplication events. Based on the presented findings, we hypothesize and illustrate the four likely molecular mechanisms to de novo generate novel miRNA genes from TEs and pseudogenes. Our rice genome analysis demonstrates that non-MITEs and MITEs mediated inverted duplications have played different roles in de novo generating miRNA genes. It is confirmed that the previously proposed inverted duplication model may give explanations for non-MITEs mediated duplication events. However, many other miRNA genes, known from the earlier proposed model, were rather arisen from MITE transpositions into target genes to yield binding sites. We further investigated evolutionary processes spawned from de novo generated to maturely-formed miRNA genes and their regulatory systems. We found that miRNAs increase the tunability of some gene regulatory systems with low gene copy numbers. The results also suggest that gene balance effects may have largely contributed to the evolution of miRNA regulatory systems

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Tailored thin film nanocomposite membrane incorporated with Noria for simultaneously overcoming the permeability-selectivity trade-off and the membrane fouling in nanofiltration process

Membrane fouling as well as the “trade-off effect” between water permeability and selectivity are the grand challenges for nanofiltration (NF) membranes. In this study, a macrocyclic molecule, Noria, was embedded in the polyamide layer to fabricate a thin film nanocomposite (TFN) membrane with high performances of separation and antifouling. Noria was first synthesized and dissolved in a piperazine (PIP) aqueous solution. Then the TFN membrane (i.e., PIP-Noria-TMC membrane, TMC is the abbreviation of 1,3,5-benzenetricarbonyl trichloride) was prepared by interfacial polymerization using PIP-Noria mixture as aqueous phase. The optimal PIP-Noria-TMC membrane reached 147.6 L m-2h-1MPa-1 of water permeability, which was almost twice that of the pristine NF membrane (i.e., PIP-TMC membrane). Meanwhile, the PIP-Noria-TMC membrane exhibited comparable Na2SO4 rejection (∼98%) to the PIP-TMC membrane and outstanding mono/divalent salt selectivity. Besides, static adsorption tests using E.coli and bovine serum albumin (BSA) as the model foulants revealed that the surface of PIP-Noria-TMC membranes with high hydrophilicity and electronegative charge could effectively resist foulant attachment, which was also exhibited in the dynamic BSA filtration tests. Therefore, this work provided a practicable pathway to simultaneously overcome the permeability-selectivity trade-off and membrane fouling problems for the NF process