exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling.

Small RNA sequencing has been widely adopted to study the diversity of extracellular RNAs (exRNAs) in biofluids; however, the analysis of exRNA samples can be challenging: they are vulnerable to contamination and artifacts from different isolation techniques, present in lower concentrations than cellular RNA, and occasionally of exogenous origin. To address these challenges, we present exceRpt, the exRNA-processing toolkit of the NIH Extracellular RNA Communication Consortium (ERCC). exceRpt is structured as a cascade of filters and quantifications prioritized based on one's confidence in a given set of annotated RNAs. It generates quality control reports and abundance estimates for RNA biotypes. It is also capable of characterizing mappings to exogenous genomes, which, in turn, can be used to generate phylogenetic trees. exceRpt has been used to uniformly process all ∼3,500 exRNA-seq datasets in the public exRNA Atlas and is available from genboree.org and github.gersteinlab.org/exceRpt.

Diverse human extracellular RNAs are widely detected in human plasma.

There is growing appreciation for the importance of non-protein-coding genes in development and disease. Although much is known about microRNAs, limitations in bioinformatic analyses of RNA sequencing have precluded broad assessment of other forms of small-RNAs in humans. By analysing sequencing data from plasma-derived RNA from 40 individuals, here we identified over a thousand human extracellular RNAs including microRNAs, piwi-interacting RNA (piRNA), and small nucleolar RNAs. Using a targeted quantitative PCR with reverse transcription approach in an additional 2,763 individuals, we characterized almost 500 of the most abundant extracellular transcripts including microRNAs, piRNAs and small nucleolar RNAs. The presence in plasma of many non-microRNA small-RNAs was confirmed in an independent cohort. We present comprehensive data to demonstrate the broad and consistent detection of diverse classes of circulating non-cellular small-RNAs from a large population.

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals.

Large-scale sequencing in the 1000 Genomes Project has revealed multitudes of single nucleotide variants (SNVs). Here, we provide insights into the functional effect of these variants using allele-specific behaviour. This can be assessed for an individual by mapping ChIP-seq and RNA-seq reads to a personal genome, and then measuring 'allelic imbalances' between the numbers of reads mapped to the paternal and maternal chromosomes. We annotate variants associated with allele-specific binding and expression in 382 individuals by uniformly processing 1,263 functional genomics data sets, developing approaches to reduce the heterogeneity between data sets due to overdispersion and mapping bias. Since many allelic variants are rare, aggregation across multiple individuals is necessary to identify broadly applicable 'allelic elements'. We also found SNVs for which we can anticipate allelic imbalance from the disruption of a binding motif. Our results serve as an allele-specific annotation for the 1000 Genomes variant catalogue and are distributed as an online resource (alleledb.gersteinlab.org).

Reads meet rotamers: structural biology in the age of deep sequencing.

Structure has traditionally been interrelated with sequence, usually in the framework of comparing sequences across species sharing a common fold. However, the nature of information within the sequence and structure databases is evolving, changing the type of comparisons possible. In particular, we now have a vast amount of personal genome sequences from human populations and a greater fraction of new structures contain interacting proteins within large complexes. Consequently, we have to recast our conception of sequence conservation and its relation to structure-for example, focusing more on selection within the human population. Moreover, within structural biology there is less emphasis on the discovery of novel folds and more on relating structures to networks of protein interactions. We cover this changing mindset here.

Geometric and electronic factors in the rational design of transition-metal-centered boron molecular wheels.

The effects of the electronic and geometric factors on the global minimum structures of MB9(-) (M = V, Nb, Ta) are investigated using photoelectron spectroscopy and ab initio calculations. Photoelectron spectra are obtained for MB9(-) at two photon energies, and similar spectral features are observed for all three species. The structures for all clusters are established by global minima searches and confirmed by comparison of calculated and experimental vertical electron detachment energies. The VB9(-) cluster is shown to have a planar C2v V©B9(-) structure, whereas both NbB9(-) and TaB9(-) are shown to have Cs M©B9(-) type structures with the central metal atom slightly out of plane. Theoretical calculations suggest that the V atom fits perfectly inside the B9 ring forming a planar D(9h) V©B9(2-) structure, while the lower symmetry of V©B9(-) is due to the Jahn-Teller effect. The Nb and Ta atoms are too large to fit in the B9 ring, and they are squeezed out of the plane slightly even in the M©B9(2-) dianions. Thus, even though all three M©B9(2-) dianions fulfill the electronic design principle for the doubly aromatic molecular wheels, the geometric effect lowers the symmetry of the Nb and Ta clusters.

Solid state adaptive natural density partitioning: a tool for deciphering multi-center bonding in periodic systems.

A new tool to elucidate chemical bonding in bulk solids, surfaces and nanostructures has been developed. Solid State Adaptive Natural Density Partitioning (SSAdNDP) is a method to interpret chemical bonding in terms of classical lone pairs and two-center bonds, as well as multi-center delocalized bonds. Here we extend the domain of AdNDP to bulk materials and interfaces, yielding SSAdNDP. We demonstrate the versatility of the method by applying it to several systems featuring both localized and many-center chemical bonding, and varying in structural complexity: boron α-sheet, magnesium diboride and the Na8BaSn6 Zintl phase.

Transition-metal-centered monocyclic boron wheel clusters (M©Bn): a new class of aromatic borometallic compounds.

Atomic clusters have intermediate properties between that of individual atoms and bulk solids, which provide fertile ground for the discovery of new molecules and novel chemical bonding. In addition, the study of small clusters can help researchers design better nanosystems with specific physical and chemical properties. From recent experimental and computational studies, we know that small boron clusters possess planar structures stabilized by electron delocalization both in the σ and π frameworks. An interesting boron cluster is B(9)(-), which has a D(8h) molecular wheel structure with a single boron atom in the center of a B(8) ring. This ring in the D(8h)-B(9)(-) cluster is connected by eight classical two-center, two-electron bonds. In contrast, the cluster's central boron atom is bonded to the peripheral ring through three delocalized σ and three delocalized π bonds. This bonding structure gives the molecular wheel double aromaticity and high electronic stability. The unprecedented structure and bonding pattern in B(9)(-) and other planar boron clusters have inspired the designs of similar molecular wheel-type structures. But these mimics instead substitute a heteroatom for the central boron. Through recent experiments in cluster beams, chemists have demonstrated that transition metals can be doped into the center of the planar boron clusters. These new metal-centered monocyclic boron rings have variable ring sizes, M©B(n) and M©B(n)(-) with n = 8-10. Using size-selected anion photoelectron spectroscopy and ab initio calculations, researchers have characterized these novel borometallic molecules. Chemists have proposed a design principle based on σ and π double aromaticity for electronically stable borometallic cluster compounds, featuring a highly coordinated transition metal atom centered inside monocyclic boron rings. The central metal atom is coordinatively unsaturated in the direction perpendicular to the molecular plane. Thus, chemists may design appropriate ligands to synthesize the molecular wheels in the bulk. In this Account, we discuss these recent experimental and theoretical advances of this new class of aromatic borometallic compounds, which contain a highly coordinated central transition metal atom inside a monocyclic boron ring. Through these examples, we show that atomic clusters can facilitate the discovery of new structures, new chemical bonding, and possibly new nanostructures with specific, advantageous properties.

Photoelectron spectroscopy and ab initio study of boron-carbon mixed clusters: CB9- and C2B8-.

We performed a joint photoelectron spectroscopy and ab initio study of two carbon-doped boron clusters, CB(9)(-) and C(2)B(8)(-). Unbiased computational searches revealed similar global minimum structures for both clusters. The comparison of the experimentally observed and theoretically calculated vertical detachment energies revealed that only the global minimum structure is responsible for the experimental spectra of CB(9)(-), whereas the two lowest-lying isomers of C(2)B(8)(-) contribute to the experimental spectra. The planar "distorted wheel" type structures with a single inner boron atom found for CB(9)(-) and C(2)B(8)(-) are different from the quasi-planar structure of B(10)(-), which consists of two inner atoms and eight peripheral boron atoms. The adaptive natural density partitioning chemical bonding analysis revealed that CB(9)(-) and C(2)B(8) clusters exhibit π aromaticity and σ antiaromaticity, which is consistent with their planar distorted structures.

Transition-metal-centered nine-membered boron rings: MⓒB9 and MⓒB9(-) (M = Rh, Ir).

We report the observation of two transition-metal-centered nine-atom boron rings, RhⓒB(9)(-) and IrⓒB(9)(-). These two doped-boron clusters are produced in a laser-vaporization supersonic molecular beam and characterized by photoelectron spectroscopy and ab initio calculations. Large HOMO-LUMO gaps are observed in the anion photoelectron spectra, suggesting that neutral RhⓒB(9) and IrⓒB(9) are highly stable, closed shell species. Theoretical calculations show that RhⓒB(9) and IrⓒB(9) are of D(9h) symmetry. Chemical bonding analyses reveal that these complexes are doubly aromatic, each with six completely delocalized π and σ electrons, which describe the bonding between the central metal atom and the boron ring. This work establishes firmly the metal-doped B rings as a new class of novel aromatic molecular wheels.

Valence isoelectronic substitution in the B8(-) and B9(-) molecular wheels by an Al dopant atom: umbrella-like structures of AlB7(-) and AlB8(-).

The structures and the electronic properties of two aluminum-doped boron clusters, AlB(7)(-) and AlB(8)(-), were investigated using photoelectron spectroscopy and ab initio calculations. The photoelectron spectra of AlB(7)(-) and AlB(8)(-) are both broad, suggesting significant geometry changes between the ground states of the anions and the neutrals. Unbiased global minimum searches were carried out and the calculated vertical electron detachment energies were used to compare with the experimental data. We found that the Al atom does not simply replace a B atom in the parent B(8)(-) and B(9)(-) planar clusters in AlB(7)(-) and AlB(8)(-). Instead, the global minima of the two doped-clusters are of umbrella shapes, featuring an Al atom interacting ionically with a hexagonal and heptagonal pyramidal B(7) (C(6v)) and B(8) (C(7v)) fragment, respectively. These unique umbrella-type structures are understood on the basis of the special stability of the quasi-planar B(7)(3-) and planar B(8)(2-) molecular wheels derived from double aromaticity.

Aluminum avoids the central position in AlB9- and AlB10-: photoelectron spectroscopy and ab initio study.

The structures and the electronic properties of two Al-doped boron clusters, AlB(9)(-) and AlB(10)(-), were investigated via joint photoelectron spectroscopy and high-level ab initio study. The photoelectron spectra of both anions are relatively broad and have no vibrational structure. The geometrical structures were established by unbiased global minimum searches using the Coalescence Kick method and comparison between the experimental and calculated vertical electron detachment energies. The results show that both clusters have quasi-planar structures and that the Al atom is located at the periphery. Chemical bonding analysis revealed that the global minimum structures of both anions can be described as doubly (σ- and π-) aromatic systems. The nona-coordinated wheel-type structure of AlB(9)(-) was found to be a relatively high-lying isomer, while a similar structure for the neutral AlB(9) cluster was previously shown to be either a global minimum or a low-lying isomer.

Planarity takes over in the C(x)H(x)P(6-x) (x = 0-6) series at x = 4.

In this work we examine a structural transition from non-planar three-dimensional structures to planar benzene-like structures in the C(x)H(x)P(6-x) (x = 0-6) series. The global minima of P(6), CHP(5), and C(2)H(2)P(4) species are benzvalene-like structures. The benzvalene and benzene-like structures of C(3)H(3)P(3) are close in energy with the former being slightly more stable at our best level of theory. The transition occurs at x = 4 (C(4)H(4)P(2)), where the benzene-like structures become significantly more stable than the benzvalene-like structures. We show that the pseudo Jahn-Teller effect, which is responsible for the deformation of planar P(6), CHP(5), and C(2)H(2)P(4) structures, is completely suppressed at x = 3 (benzene-like structures of C(3)H(3)P(3)). We present NICS(zz) values of all the benzene-like isomers in the series.

Deciphering the mystery of hexagon holes in an all-boron graphene α-sheet.

Boron could be the next element after carbon capable of forming 2D-materials similar to graphene. Theoretical calculations predict that the most stable planar all-boron structure is the so-called α-sheet. The mysterious structure of the α-sheet with peculiar distribution of filled and empty hexagons is rationalized in terms of chemical bonding. We show that the hexagon holes serve as scavengers of extra electrons from the filled hexagons. This work could advance rational design of all-boron nanomaterials.

Molecular wheel to monocyclic ring transition in boron-carbon mixed clusters C2B6⁻ and C3B5⁻.

In this joint experimental and theoretical work we present a novel type of structural transition occurring in the series of C(x)B(8-x)(-) (x=1-8) mixed clusters upon increase of the carbon content from x=2 to x=3. The wheel to ring transition is surprising because it is rather planar-to-linear type of transition to be expected in the series since B(8), B(8)(-), B(8)(2-) and CB(7)(-) are known to possess wheel-type global minimum structures while C(8) is linear.