Plasminogen activator urokinase expression reveals TRAIL responsiveness and supports fractional survival of cancer cells

Peer reviewe

Nucleic Acids Res

The absence of a quality control (QC) system is a major weakness for the comparative analysis of genome-wide profiles generated by next-generation sequencing (NGS). This concerns particularly genome binding/occupancy profiling assays like chromatin immunoprecipitation (ChIP-seq) but also related enrichment-based studies like methylated DNA immunoprecipitation/methylated DNA binding domain sequencing, global run on sequencing or RNA-seq. Importantly, QC assessment may significantly improve multidimensional comparisons that have great promise for extracting information from combinatorial analyses of the global profiles established for chromatin modifications, the bindings of epigenetic and chromatin-modifying enzymes/machineries, RNA polymerases and transcription factors and total, nascent or ribosome-bound RNAs. Here we present an approach that associates global and local QC indicators to ChIP-seq data sets as well as to a variety of enrichment-based studies by NGS. This QC system was used to certify >5600 publicly available data sets, hosted in a database for data mining and comparative QC analyses

Genes Dev

Multiple signaling pathways ultimately modulate the epigenetic information embedded in the chromatin of gene promoters by recruiting epigenetic enzymes. We found that, in estrogen-regulated gene programming, the acetyltransferase CREB-binding protein (CBP) is specifically and exclusively methylated by the coactivator-associated arginine methyltransferase (CARM1) in vivo. CARM1-dependent CBP methylation and p160 coactivators were required for estrogen-induced recruitment to chromatin targets. Notably, methylation increased the histone acetyltransferase (HAT) activity of CBP and stimulated its autoacetylation. Comparative genome-wide chromatin immunoprecipitation sequencing (ChIP-seq) studies revealed a variety of patterns by which p160, CBP, and methyl-CBP (meCBP) are recruited (or not) by estrogen to chromatin targets. Moreover, significant target gene-specific variation in the recruitment of (1) the p160 RAC3 protein, (2) the fraction of a given meCBP species within the total CBP, and (3) the relative recruitment of different meCBP species suggests the existence of a target gene-specific "fingerprint" for coregulator recruitment. Crossing ChIP-seq and transcriptomics profiles revealed the existence of meCBP "hubs" within the network of estrogen-regulated genes. Together, our data provide evidence for an unprecedented mechanism by which CARM1-dependent CBP methylation results in gene-selective association of estrogen-recruited meCBP species with different HAT activities and specifies distinct target gene hubs, thus diversifying estrogen receptor programming

The invasion history of Elodea canadensis and E. nuttallii (Hydrocharitaceae) in Italy from herbarium accessions, field records and historical literature

We analysed the invasion history of two North American macrophytes (Elodea canadensis and E. nuttallii) in Italy, through an accurate census of all available herbarium and field records, dating between 1850 and 2019, and a rich literature collection describing the initial introduction and naturalisation phase that supports the results obtained by the occurrence records. Elodea canadensis arrived in Italy before 1866 and had two invasion phases, between the 1890s and 1920s and between the 1990s and 2000s; E. nuttallii, probably arrived in the 1970s, started invading in 2000 and the invasion is still ongoing. Botanical gardens and fish farming played a crucial role in dispersal and naturalisation of both species. The current invasion range of both species is centred in northern Italy, with scattered occurrences of E. canadensis in central and southern regions. River Po represents a dispersal barrier to the Mediterranean region and a strategic monitoring site to prevent the invasion in the peninsula. The study detects differences in the niches of the two species during the introduction and naturalisation phase and a habitat switch occurred after 1980 in E. canadensis and after 2000 in E. nuttallii, during their expansion phases. For E. canadensis the switch corresponds to the second invasion round. Further research can clarify whether the second invasion round is due to confusion of the recently introduced E. nuttallii with E. canadensis, to a cryptic introduction of a new genotype, to post-introduction evolution, or just to an increased scientific interest in biological invasions

Notulae to the Italian alien vascular flora: 9

In this contribution, new data concerning the distribution of vascular flora alien to Italy are presented. It includes new records, confirmations, exclusions, and status changes for Italy or for Italian administrative regions. Furthermore, three new combinations are proposed. Nomenclatural and distribution updates published elsewhere are provided as Suppl. material 1

Floristic analysis of a high-speed railway embankment in a Mediterranean landscape

We analyzed the floristic composition of a 4.5 km-long segment of a high-speed railway in Lazio, central Italy, which travels on an artificial embankment through an intensively-farmed landscape. In total, 287 vascular plant species were recorded. The life-form distribution was found to be similar to that of the regional species pool, with high percentages of therophytes (38%) and phanerophytes (13%). In the chorological spectrum the Mediterranean floristic element prevailed (44%), while alien species were 8% of the flora. The phytosociological spectrum showed a high diversity of characteristic species from the class Stellarietea mediae or its subordinate syntaxa (26%), and in particular from the order Thero-Brometalia (Mediterranean, sub-nitrophilous annual communities). Species from forest syntaxa had a relatively high diversity (9%). These results suggest that the ecological filtering provided by the Mediterranean regional climate controlled species assemblage even in a completely artificial habitat, preventing floristic homogenization: the flora of the studied railway section is only partially »ruderalized«, while it keeps strong links with the regional (semi-) natural plant communities. However, in contrast to what is observed in central and north Europe, the railway sides studied in the present paper do not seem to represent a refugial habitat for rare species from grassland communities, mainly because in Italy semi-natural dry grasslands are still widely represented