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Abstract Non-coding RNAs (ncRNAs) are transcribed throughout the genome and provide regulatory inputs to gene expression through their interaction with chromatin. Yet, the genomic targets and functions of most ncRNAs are unknown. Here we use chromatin-associated RNA sequencing (ChAR-seq) to map the global network of ncRNA interactions with chromatin in human embryonic stem cells and the dynamic changes in interactions during differentiation into definitive endoderm. We uncover general principles governing the organization of the RNA-chromatin interactome, demonstrating that nearly all ncRNAs exclusively interact with genes in close three-dimensional proximity to their locus and provide a model predicting the interactome. We uncover RNAs that interact with many loci across the genome and unveil thousands of unannotated RNAs that dynamically interact with chromatin. By relating the dynamics of the interactome to changes in gene expression, we demonstrate that activation or repression of individual genes is unlikely to be controlled by a single ncRNA.

Abstract Net photosynthetic CO2 assimilation rate (A n) decreases at leaf temperatures above a relatively mild optimum (T opt) in most higher plants. This decline is often attributed to reduced CO2 conductance, increased CO2 loss from photorespiration and respiration, reduced chloroplast electron transport rate (J), or deactivation of Ribulose-1,5-bisphosphate Carboxylase Oxygenase (Rubisco). However, it is unclear which of these factors can best predict species independent declines in A n at high temperature. We show that independent of species, and on a global scale, the observed decline in A n with rising temperatures can be effectively accounted for by Rubisco deactivation and declines in J. Our finding that A n declines with Rubisco deactivation and J supports a coordinated down-regulation of Rubisco and chloroplast electron transport rates to heat stress. We provide a model that, in the absence of CO2 supply limitations, can predict the response of photosynthesis to short-term increases in leaf temperature.

Measurement(s) plant trait Technology Type(s) various Factor Type(s) none Sample Characteristic - Organism Tracheophyta Sample Characteristic - Environment natural environment Sample Characteristic - Location global

Measurement(s) plant trait Technology Type(s) digital curation Sample Characteristic - Organism Viridiplantae Sample Characteristic - Location Australia Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.14545755

Objective: To describe the patient and cycle characteristics of women who undergo intrauterine insemination (IUI) immediately after an unsuccessful oocyte retrieval. Design: Retrospective case series. Setting: University-affiliated center. Patient(s): Women who underwent an oocyte retrieval procedure in which no oocytes were retrieved followed by an IUI on the same morning. Intervention(s): None. Main Outcome Measure(s): Live birth rate, subsequent live birth rate. Result(s): From 2011 to 2019, 63 cycles in 57 patients were identified. The mean (SD) age was 39.6 (4.6) years, and diminished ovarian reserve (94.7%) was the most common diagnosis. The median (IQR) number of previous IVF cycles in this cohort was 3 (1–7), with 56.1% having had at least one previous canceled IVF cycle. The majority of patients had undergone either controlled ovarian hyperstimulation (COH) (64.9%) or modified natural cycles (21.1%). The mean (SD) number of follicles >14 mm at the time of trigger was 1.9 (1.4), with 38.9% of patients manifesting a drop in their estradiol levels after the trigger. One pregnancy resulting in a live birth was identified (1.8%). For patients who underwent subsequent IVF cycles, 60.7% had at least one subsequent cancelled cycle. Three patients went on to achieve a live birth using autologous oocytes (6.5%). Conclusion(s): Same-day IUI for patients who have no oocytes retrieved is associated with a

ABSTRACT T cells must recognize pathogen-derived peptides bound to major histocompatibility complexes (MHCs) in order to initiate a cell-mediated immune response against an infection, or to support the development of high-affinity antibody responses. Identifying antigens presented on MHCs by infected cells and professional antigen-presenting cells (APCs) during infection may therefore provide a route toward developing new vaccines. Peptides bound to MHCs can be identified at whole-proteome scale using mass spectrometry—a technique referred to as “immunopeptidomics.” This technique has emerged as a powerful tool for identifying potential vaccine targets in the context of many infectious diseases. In this review, we discuss the contributions immunopeptidomic studies have made to understanding antigen presentation and T cell priming in the context of infection and the potential for immunopeptidomics to inform the development of vaccines to address pressing global health problems in infectious disease.

Morphogenesis of tissue sheets is well studied, but mechanisms that shape bulk tissues are unclear. Here, the authors show that mesenchymal cells intercalate in 3D to shape the mouse branchial arch, with cortical forces driving intercalations in a Wnt5a-, Yap/Taz- and Piezo1-dependent manner.

RepID has previously been shown to promote origin firing. Here the authors reveal that RepID regulates replication origins via the recruitment of the CRL4 complex, and prevents re-initiation and unscheduled DNA replication.

New global datasets of upper canopy vegetation respiration have become available and their impact on global carbon cycle models is unclear. Here, the authors show the implications of these parameterisations with a global gridded land model and report significantly higher global plant respiration estimates.

We updated the routines used to estimate leaf maintenance respiration (MR) in the Energy Land Model (ELM) using a comprehensive global respiration data base. The updated algorithm includes a temperature acclimating base rate, an updated instantaneous temperature response, and new plant functional type specific parameters. The updated MR algorithm resulted in a very large increase in global MR of 16.1 Pg (38%), but the signal was not geographically uniform. The increase was concentrated in the tropics and humid warm-temperate forests. The increase in MR led to large but proportionally smaller decreases in global net primary production (19%) and in average global leaf area index (15%). The effect on global gross primary production (GPP) was a more modest 5.7 Pg (4%). A detailed site level analysis also demonstrated a wide range of effects the updated algorithm can have on the seasonal cycle of GPP. Output from the updated and old models did not differ markedly in how closely they matched a suite of benchmarks. Given the substantial impact on the land surface carbon cycle, a neutral influence on model benchmarks, and better alignment with empirical evidence, an MR algorithm similar to the one presented here should be adopted into ELM.

Origins of mammalian DNA replication are poorly characterised because they lack an Identifiable consensus sequence. Here the authors identify RepID, a protein that binds to a subset of G-rich replication origins and facilitates initiation from those origins.

RNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here, we present a proximity ligation and sequencing method called Chromatin-Associated RNA sequencing (ChAR-seq) that maps all RNA-to-DNA contacts across the genome. Using Drosophila cells, we show that ChAR-seq provides unbiased, de novo identification of targets of chromatin-bound RNAs including nascent transcripts, chromosome-specific dosage compensation ncRNAs, and genome-wide trans-associated RNAs involved in co-transcriptional RNA processing.

Cape Espenberg is a sandy spit on the Chukchi Sea coast in northwestern Alaska, containing the remains of 4000 years of human occupation and climatic change. Archaeological and paleo-ecological research since 2009 as part of a large pluridisciplinary project provides new data on settlement chronology for the last thousand year of occupation and documents the emergence of the Thule culture which is directly ancestral to today’s Inuit/Inupiat in a context of increased storminess during the Little Ice Age. At the same time, this research raises the question of the nature of the Birnirk occupation identified on the low E-6 dune ridge, site KTZ-304, an archaeological complex which contributes to the emergence of the Thule culture between the 12th and 13th AD. This Birnirk mound at Cape Espenberg resembles in many aspects the type side named Birnirk in north Alaska (Barrow region). The excavation of house F12 uncovered a multi-room structure with overlain occupation levels and produced a collection of remains showing real architectural differences, signs of long distance raw material and object circulation and of mobility. All these elements suggest newcomers possibly of Chukotka origin and provides the opportunity to revisit an old research question in Arctic archaeology, that of the origin of Birnirk culture on the Alaska coast.

This paper provides an overview of the United States (US) Department of Energy's (DOE's) Energy Exascale Earth System Model version 2 (E3SMv2) fully coupled regionally refined model (RRM) and documents the overall atmosphere, land, and river results from the Coupled Model Intercomparison Project 6 (CMIP6) DECK (Diagnosis, Evaluation, and Characterization of Klima) and historical simulations - a first-of-its-kind set of climate production simulations using RRM. The North American (NA) RRM (NARRM) is developed as the high-resolution configuration of E3SMv2 with the primary goal of more explicitly addressing DOE's mission needs regarding impacts to the US energy sector facing Earth system changes. The NARRM features finer horizontal resolution grids centered over NA, consisting of 25→100¯km atmosphere and land, a 0.125 river-routing model, and 14→60¯km ocean and sea ice. By design, the computational cost of NARRM is 1/43× of the uniform low-resolution (LR) model at 100¯km but only 1/4¯10¯%-20¯% of a globally uniform high-resolution model at 25¯km. A novel hybrid time step strategy for the atmosphere is key for NARRM to achieve improved climate simulation fidelity within the high-resolution patch without sacrificing the overall global performance. The global climate, including climatology, time series, sensitivity, and feedback, is confirmed to be largely identical between NARRM and LR as quantified with typical climate metrics. Over the refined NA area, NARRM is generally superior to LR, including for precipitation and clouds over the contiguous US (CONUS), summertime marine stratocumulus clouds off the coast of California, liquid and ice phase clouds near the North Pole region, extratropical cyclones, and spatial variability in land hydrological processes. The improvements over land are related to the better-resolved topography in NARRM, whereas those over ocean are attributable to the improved air-sea interactions with finer grids for both atmosphere and ocean and sea ice. Some features appear insensitive to the resolution change analyzed here, for instance the diurnal propagation of organized mesoscale convective systems over CONUS and the warm-season land-atmosphere coupling at the southern Great Plains. In summary, our study presents a realistically efficient approach to leverage the fully coupled RRM framework for a standard Earth system model release and high-resolution climate production simulations.

Here we provide the 'Global Spectrum of Plant Form and Function Dataset', containing species mean values for six vascular plant traits. Together, these traits -plant height, stem specific density, leaf area, leaf mass per area, leaf nitrogen content per dry mass, and diaspore (seed or spore) mass - define the primary axes of variation in plant form and function. The dataset is based on ca. 1 million trait records received via the TRY database (representing ca. 2,500 original publications) and additional unpublished data. It provides 92,159 species mean values for the six traits, covering 46,047 species. The data are complemented by higher-level taxonomic classification and six categorical traits (woodiness, growth form, succulence, adaptation to terrestrial or aquatic habitats, nutrition type and leaf type). Data quality management is based on a probabilistic approach combined with comprehensive validation against expert knowledge and external information. Intense data acquisition and thorough quality control produced the largest and, to our knowledge, most accurate compilation of empirically observed vascular plant species mean traits to date.

Ground-penetrating radar (GPR) offers many advantages for assessing archaeological potential in frozen and partially frozen contexts in high latitude and alpine regions. These settings pose several challenges for GPR, including extreme velocity changes at the interface of frozen and active layers, cryogenic patterns resulting in anomalies that can easily be mistaken for cultural features, and the difficulty in accessing sites and deploying equipment in remote settings. In this study we discuss some of these challenges while highlighting the potential for this method by describing recent successful investigations with GPR in the region. We draw on cases from Bering Land Bridge National Preserve, Cape Krusenstern National Monument, Kobuk Valley National Park, and Gates of the Arctic National Park and Preserve. The sites required small aircraft accessibility with light equipment loads and minimal personnel. The substrates we investigate include coastal saturated active layer over permafrost, interior well-drained active layer over permafrost, a frozen thermo-karst lake, and an alpine ice patch. These examples demonstrate that GPR is effective at mapping semi-subterranean house remains in several contexts, including houses with no surface manifestation. GPR is also shown to be effective at mapping anomalies from the skeletal remains of a late Pleistocene mammoth frozen in ice. The potential for using GPR in ice and snow patch archaeology, an area of increasing interest with global environmental change exposing new material each year, is also demonstrated.

Although central to evolution, the causes of hybrid inviability that drive reproductive isolation are poorly understood. Embryonic lethality occurs when the eggs of the frog X. tropicalis are fertilized with either X. laevis or X. borealis sperm. We observed that distinct subsets of paternal chromosomes failed to assemble functional centromeres, causing their mis-segregation during embryonic cell divisions. Core centromere DNA sequence analysis revealed little conservation among the three species, indicating that epigenetic mechanisms that normally operate to maintain centromere integrity are disrupted on specific paternal chromosomes in hybrids. In vitro reactions combining X. tropicalis egg extract with either X. laevis or X. borealis sperm chromosomes revealed that paternally matched or overexpressed centromeric histone CENP-A and its chaperone HJURP could rescue centromere assembly on affected chromosomes in interphase nuclei. However, although the X. laevis chromosomes maintained centromeric CENP-A in metaphase, X. borealis chromosomes did not and also displayed ultra-thin regions containing ribosomal DNA. Both centromere assembly and morphology of X. borealis mitotic chromosomes could be rescued by inhibiting RNA polymerase I or preventing the collapse of stalled DNA replication forks. These results indicate that specific paternal centromeres are inactivated in hybrids due to the disruption of associated chromatin regions that interfere with CENP-A incorporation, at least in some cases due to conflicts between replication and transcription machineries. Thus, our findings highlight the dynamic nature of centromere maintenance and its susceptibility to disruption in vertebrate interspecies hybrids.

Studies of genome regulation routinely use high-throughput DNA sequencing approaches to determine where specific proteins interact with DNA, and they rely on DNA amplification and short-read sequencing, limiting their quantitative application in complex genomic regions. To address these limitations, we developed directed methylation with long-read sequencing (DiMeLo-seq), which uses antibody-tethered enzymes to methylate DNA near a target protein's binding sites in situ. These exogenous methylation marks are then detected simultaneously with endogenous CpG methylation on unamplified DNA using long-read, single-molecule sequencing technologies. We optimized and benchmarked DiMeLo-seq by mapping chromatin-binding proteins and histone modifications across the human genome. Furthermore, we identified where centromere protein A localizes within highly repetitive regions that were unmappable with short sequencing reads, and we estimated the density of centromere protein A molecules along single chromatin fibers. DiMeLo-seq is a versatile method that provides multimodal, genome-wide information for investigating protein-DNA interactions.

Centromeres play an essential function in cell division by specifying the site of kinetochore formation on each chromosome for mitotic spindle attachment. Centromeres are defined epigenetically by the histone H3 variant Centromere Protein A (Cenpa). Cenpa nucleosomes maintain the centromere by designating the site for new Cenpa assembly after dilution by replication. Vertebrate centromeres assemble on tandem arrays of repetitive sequences, but the function of repeat DNA in centromere formation has been challenging to dissect due to the difficulty in manipulating centromeres in cells. Xenopus laevis egg extracts assemble centromeres in vitro, providing a system for studying centromeric DNA functions. However, centromeric sequences in Xenopus laevis have not been extensively characterized. In this study, we combine Cenpa ChIP-seq with a k-mer based analysis approach to identify the Xenopus laevis centromere repeat sequences. By in situ hybridization, we show that Xenopus laevis centromeres contain diverse repeat sequences, and we map the centromere position on each Xenopus laevis chromosome using the distribution of centromere-enriched k-mers. Our identification of Xenopus laevis centromere sequences enables previously unapproachable centromere genomic studies. Our approach should be broadly applicable for the analysis of centromere and other repetitive sequences in any organism.

We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.

We present evidence for |$\gamma$| -ray emission from a stacked population of 39 high-latitude globular clusters (GCs) not detected in the Fermi Point Source Catalogue, likely attributable to populations of millisecond pulsars within them. In this work, we use 13 yr of data collected by the Large Area Telescope aboard the Fermi Gamma-Ray Space Telescope to search for a cumulative signal from undetected GCs and compared them to control fields (CFs), selected to match the celestial distribution of the target clusters so as to distinguish the |$\gamma$| -ray signal from background emission. The joint likelihood distribution of the GCs has a significant separation (⁠|$\sim 4\sigma$|⁠) from that of the CFs. We also investigate correlations between detected cluster luminosities and other cluster properties such as distance, the number of millisecond pulsars associated with each cluster, and stellar encounter rate but find no significant relationships. [ABSTRACT FROM AUTHOR]

Our ability to understand and predict the response of ecosystems to a changing environment depends on quantifying vegetation functional diversity. However, representing this diversity at the global scale is challenging. Typically, in Earth system models, characterization of plant diversity has been limited to grouping related species into plant functional types (PFTs), with all trait variation in a PFT collapsed into a single mean value that is applied globally. Using the largest global plant trait database and state of the art Bayesian modeling, we created fine-grained global maps of plant trait distributions that can be applied to Earth system models. Focusing on a set of plant traits closely coupled to photosynthesis and foliar respiration-specific leaf area (SLA) and dry mass-based concentrations of leaf nitrogen ([Formula: see text]) and phosphorus ([Formula: see text]), we characterize how traits vary within and among over 50,000 [Formula: see text]-km cells across the entire vegetated land surface. We do this in several ways-without defining the PFT of each grid cell and using 4 or 14 PFTs; each model's predictions are evaluated against out-of-sample data. This endeavor advances prior trait mapping by generating global maps that preserve variability across scales by using modern Bayesian spatial statistical modeling in combination with a database over three times larger than that in previous analyses. Our maps reveal that the most diverse grid cells possess trait variability close to the range of global PFT means.

Analysis of preserved lipids from archaeological sites in northwest Alaska indicates hunters exploited marine animal resources as early as 4500 years ago. Bone preservation at early prehistoric sites in northern Alaska is generally poor, contributing to uncertainty about the economic orientation of the earliest Arctic Small Tool tradition (ASTt) hunters. We used lipid analysis and compound specific stable isotope analysis (CSIA) of burned, cemented sand and organic residue features to detect the use of marine versus terrestrial animals at several coastal sites in northwest Alaska. Though the sample size for this initial study was small (n=5), comparisons among samples from early ASTt, and later Norton and Thule sites indicate all three groups made use of marine animals for food and/or fuel. Recently obtained radiocarbon dates suggest ASTt hunters settled coastal regions of Alaska prior to moving inland to exploit terrestrial habitats. Our results provide empirical evidence that suggests the economy of the early ASTt population included a maritime component. In Arctic settings where bone preservation is poor, lipid analysis of cemented sand and organic residue features can provide an effective alternative for detecting the use and processing of marine versus terrestrial animals.