Human Artificial Chromosomes that Bypass Centromeric DNA.

Recent breakthroughs with synthetic budding yeast chromosomes expedite the creation of synthetic mammalian chromosomes and genomes. Mammals, unlike budding yeast, depend on the histone H3 variant, CENP-A, to epigenetically specify the location of the centromere-the locus essential for chromosome segregation. Prior human artificial chromosomes (HACs) required large arrays of centromeric α-satellite repeats harboring binding sites for the DNA sequence-specific binding protein, CENP-B. We report the development of a type of HAC that functions independently of these constraints. Formed by an initial CENP-A nucleosome seeding strategy, a construct lacking repetitive centromeric DNA formed several self-sufficient HACs that showed no uptake of genomic DNA. In contrast to traditional α-satellite HAC formation, the non-repetitive construct can form functional HACs without CENP-B or initial CENP-A nucleosome seeding, revealing distinct paths to centromere formation for different DNA sequence types. Our developments streamline the construction and characterization of HACs to facilitate mammalian synthetic genome efforts.

The structure, function and evolution of a complete human chromosome 8.

The complete assembly of each human chromosome is essential for understanding human biology and evolution1,2. Here we use complementary long-read sequencing technologies to complete the linear assembly of human chromosome 8. Our assembly resolves the sequence of five previously long-standing gaps, including a 2.08-Mb centromeric α-satellite array, a 644-kb copy number polymorphism in the ß-defensin gene cluster that is important for disease risk, and an 863-kb variable number tandem repeat at chromosome 8q21.2 that can function as a neocentromere. We show that the centromeric α-satellite array is generally methylated except for a 73-kb hypomethylated region of diverse higher-order α-satellites enriched with CENP-A nucleosomes, consistent with the location of the kinetochore. In addition, we confirm the overall organization and methylation pattern of the centromere in a diploid human genome. Using a dual long-read sequencing approach, we complete high-quality draft assemblies of the orthologous centromere from chromosome 8 in chimpanzee, orangutan and macaque to reconstruct its evolutionary history. Comparative and phylogenetic analyses show that the higher-order α-satellite structure evolved in the great ape ancestor with a layered symmetry, in which more ancient higher-order repeats locate peripherally to monomeric α-satellites. We estimate that the mutation rate of centromeric satellite DNA is accelerated by more than 2.2-fold compared to the unique portions of the genome, and this acceleration extends into the flanking sequence.

3D-CLEM Reveals that a Major Portion of Mitotic Chromosomes Is Not Chromatin.

Recent studies have revealed the importance of Ki-67 and the chromosome periphery in chromosome structure and segregation, but little is known about this elusive chromosome compartment. Here we used correlative light and serial block-face scanning electron microscopy, which we term 3D-CLEM, to model the entire mitotic chromosome complement at ultra-structural resolution. Prophase chromosomes exhibit a highly irregular surface appearance with a volume smaller than metaphase chromosomes. This may be because of the absence of the periphery, which associates with chromosomes only after nucleolar disassembly later in prophase. Indeed, the nucleolar volume almost entirely accounts for the extra volume found in metaphase chromosomes. Analysis of wild-type and Ki-67-depleted chromosomes reveals that the periphery comprises 30%-47% of the entire chromosome volume and more than 33% of the protein mass of isolated mitotic chromosomes determined by quantitative proteomics. Thus, chromatin makes up a surprisingly small percentage of the total mass of metaphase chromosomes.

Actively transcribed rDNA and distal junction (DJ) sequence are involved in association of NORs with nucleoli.

Although they are organelles without a limiting membrane, nucleoli have an exclusive structure, built upon the rDNA-rich acrocentric short arms of five human chromosomes (nucleolar organizer regions or NORs). This has raised the question: what are the structural features of a chromosome required for its inclusion in a nucleolus? Previous work has suggested that sequences adjacent to the tandemly repeated rDNA repeat units (DJ, distal junction sequence) may be involved, and we have extended such studies by addressing several issues related to the requirements for the association of NORs with nucleoli. We exploited both a set of somatic cell hybrids containing individual human acrocentric chromosomes and a set of Human Artificial Chromosomes (HACs) carrying different parts of a NOR, including an rDNA unit or DJ or PJ (proximal junction) sequence. Association of NORs with nucleoli was increased when constituent rDNA was transcribed and may be also affected by the status of heterochromatin blocks formed next to the rDNA arrays. Furthermore, our data suggest that a relatively small size DJ region, highly conserved in evolution, is also involved, along with the rDNA repeats, in the localization of p-arms of acrocentric chromosomes in nucleoli. Thus, we infer a cooperative action of rDNA sequence-stimulated by its activity-and sequences distal to rDNA contributing to incorporation into nucleoli. Analysis of NOR sequences also identified LncRNA_038958 in the DJ, a candidate transcript with the region of the suggested promoter that is located close to the DJ/rDNA boundary and contains CTCF binding sites. This LncRNA may affect RNA Polymerase I and/or nucleolar activity. Our findings provide the basis for future studies to determine which RNAs and proteins interact critically with NOR sequences to organize the higher-order structure of nucleoli and their function in normal cells and pathological states.

Copper/Ruthenium Relay Catalysis for Stereodivergent Access to δ-Hydroxy α-Amino Acids and Small Peptides.

An atom- and step-economical and redox-neutral cascade reaction enabled by asymmetric bimetallic relay catalysis by merging a ruthenium-catalyzed asymmetric borrowing-hydrogen reaction with copper-catalyzed asymmetric Michael addition has been realized. A variety of highly functionalized 2-amino-5-hydroxyvaleric acid esters or peptides bearing 1,4-non-adjacent stereogenic centers have been prepared in high yields with excellent enantio- and diastereoselectivity. Judicious selection and rational modification of the Ru catalysts with careful tuning of the reaction conditions played a pivotal role in stereoselectivity control as well as attenuating undesired α-epimerization, thus enabling a full complement of all four stereoisomers that were otherwise inaccessible in previous work. Concise asymmetric stereodivergent synthesis of the key intermediates for biologically important chiral molecules further showcases the synthetic utility of this methodology.

Correction: An asymmetric metal-templated route to amino acids with an isoquinolone core via a Rh(III)-catalyzed coupling of aryl hydroxamates with chiral propargylglycine Ni(II) complexes.

Correction for 'An asymmetric metal-templated route to amino acids with an isoquinolone core via a Rh(III)-catalyzed coupling of aryl hydroxamates with chiral propargylglycine Ni(II) complexes' by Mikhail A. Arsenov et al., Org. Biomol. Chem., 2022, 20, 9385-9391, https://doi.org/10.1039/D2OB01970A.

A synthetic route to artificial chiral α-amino acids featuring a 3,4-dihydroisoquinolone core through a Rh(III)-catalyzed functionalization of allyl groups in chiral Ni(II) complexes.

Currently, non-proteinogenic α-amino acids (α-AAs) have attracted increasing interest in bio- and medicinal chemistry. In this context, the first protocol for the asymmetric synthesis of artificial α-AAs featuring a 3,4-dihydroisoquinolone core with two stereogenic centers was successfully elaborated. A straightforward Rh(III)-catalysed C-H activation/annulation reaction of various aryl hydroxamates with a set of robust and readily available chiral Ni(II) complexes, which have allylic appendages derived from glycine (Gly), alanine (Ala) and phenylalanine (Phe), allowed incorporation of a 3,4-dihydroisoquinolone scaffold into the chiral amino acid residue. The reaction was performed in methanol and under mild conditions (at room temperature under air atmosphere), providing separable diastereomeric complexes with up to 94% total yield. The target α-AA with a 3,4-dihydroisoquinolone core in an enantiopure form was subsequently released from the obtained chiral Ni(II) complexes via an acidic decomposition in aqueous HCl, along with the recovery of the chiral auxiliary ligand.

Synthesis, Characterization, and Study of Catalytic Activity of Chiral Cu(II) and Ni(II) Salen Complexes in the α-Amino Acid C-α Alkylation Reaction.

A new family of Cu(II) and Ni(II) salen complexes was synthesized and fully characterized through various physicochemical methods. Their catalytic activity was evaluated in the phase transfer Cα-alkylation reaction of the Schiff bases of D,L-alanine ester and benzaldehyde derivatives. It was found that the introduction of a chlorine atom into the ortho- and para-positions of the phenyl ring of the substrate resulted in an increase in both the chemical yield and the asymmetric induction (ee 66-98%). The highest enantiomeric excess was achieved in the case of a Cu(II) salen complex based on (S,S)-cyclohexanediamine and salicylaldehyde at -20 °C. The occurrence of a bulky substituent in the ligand present in the complexes led to a drastic decrease in ee and chemical yield. For instance, the introduction of bulky substituents at positions 3 and 5 of the phenyl ring of the catalyst resulted in a complete loss of the stereoselectivity control in the alkylation reaction.

H3K9me3 maintenance on a human artificial chromosome is required for segregation but not centromere epigenetic memory.

Most eukaryotic centromeres are located within heterochromatic regions. Paradoxically, heterochromatin can also antagonize de novo centromere formation, and some centromeres lack it altogether. In order to investigate the importance of heterochromatin at centromeres, we used epigenetic engineering of a synthetic alphoidtetO human artificial chromosome (HAC), to which chimeric proteins can be targeted. By tethering the JMJD2D demethylase (also known as KDM4D), we removed heterochromatin mark H3K9me3 (histone 3 lysine 9 trimethylation) specifically from the HAC centromere. This caused no short-term defects, but long-term tethering reduced HAC centromere protein levels and triggered HAC mis-segregation. However, centromeric CENP-A was maintained at a reduced level. Furthermore, HAC centromere function was compatible with an alternative low-H3K9me3, high-H3K27me3 chromatin signature, as long as residual levels of H3K9me3 remained. When JMJD2D was released from the HAC, H3K9me3 levels recovered over several days back to initial levels along with CENP-A and CENP-C centromere levels, and mitotic segregation fidelity. Our results suggest that a minimal level of heterochromatin is required to stabilize mitotic centromere function but not for maintaining centromere epigenetic memory, and that a homeostatic pathway maintains heterochromatin at centromeres.This article has an associated First Person interview with the first authors of the paper.

CENP-B creates alternative epigenetic chromatin states permissive for CENP-A or heterochromatin assembly.

CENP-B binds to CENP-B boxes on centromeric satellite DNAs (known as alphoid DNA in humans). CENP-B maintains kinetochore function through interactions with CENP-A nucleosomes and CENP-C. CENP-B binding to transfected alphoid DNA can induce de novo CENP-A assembly, functional centromere and kinetochore formation, and subsequent human artificial chromosome (HAC) formation. Furthermore, CENP-B also facilitates H3K9 (histone H3 lysine 9) trimethylation on alphoid DNA, mediated by Suv39h1, at ectopic alphoid DNA integration sites. Excessive heterochromatin invasion into centromere chromatin suppresses CENP-A assembly. It is unclear how CENP-B controls such different chromatin states. Here, we show that the CENP-B acidic domain recruits histone chaperones and many chromatin modifiers, including the H3K36 methylase ASH1L, as well as the heterochromatin components Suv39h1 and HP1 (HP1α, ß and γ, also known as CBX5, CBX1 and CBX3, respectively). ASH1L facilitates the formation of open chromatin competent for CENP-A assembly on alphoid DNA. These results indicate that CENP-B is a nexus for histone modifiers that alternatively promote or suppress CENP-A assembly by mutually exclusive mechanisms. Besides the DNA-binding domain, the CENP-B acidic domain also facilitates CENP-A assembly de novo on transfected alphoid DNA. CENP-B therefore balances CENP-A assembly and heterochromatin formation on satellite DNA.

A novel assay to screen siRNA libraries identifies protein kinases required for chromosome transmission.

One of the hallmarks of cancer is chromosome instability (CIN), which leads to aneuploidy, translocations, and other chromosome aberrations. However, in the vast majority of human tumors the molecular basis of CIN remains unknown, partly because not all genes controlling chromosome transmission have yet been identified. To address this question, we developed an experimental high-throughput imaging (HTI) siRNA assay that allows the identification of novel CIN genes. Our method uses a human artificial chromosome (HAC) expressing the GFP transgene. When this assay was applied to screen an siRNA library of protein kinases, we identified PINK1, TRIO, IRAK1, PNCK, and TAOK1 as potential novel genes whose knockdown induces various mitotic abnormalities and results in chromosome loss. The HAC-based assay can be applied for screening different siRNA libraries (cell cycle regulation, DNA damage response, epigenetics, and transcription factors) to identify additional genes involved in CIN. Identification of the complete spectrum of CIN genes will reveal new insights into mechanisms of chromosome segregation and may expedite the development of novel therapeutic strategies to target the CIN phenotype in cancer cells.

Family of Well-Defined Chiral-at-Cobalt(III) Complexes as Metal-Templated Hydrogen-Bond-Donor Catalysts: Effect of Chirality at the Metal Center on the Stereochemical Outcome of the Reaction.

A family of well-defined Λ- and Δ-diastereomeric octahedral cationic chiral-at-cobalt complexes were obtained by a simple two-step reaction of (R,R)-1,2-diaminocyclohexane, (R,R)-1,2-diphenylethylenediamine, or (S)-2-(aminomethyl)pyrrolidine and substituted salicylaldehydes with a cobalt(III) salt. It was observed for the first time that the use of an excess of cobalt(III) salt provides both the enantiopure Λ and Δ forms of the corresponding cobalt(III) complexes 1 and 2 in a ratio of diastereomers ranging from 1:1.6 to >20:1 (Λ/Δ) and in 31-95% combined yields. The obtained complexes were robust, air- and bench-stable, soluble in most of organic solvents, and insoluble in water. Through variation of the substituents in the phenyl ring of the salicylaldehyde moiety, it was shown that both steric and electronic effects of substituents have a significant impact on the formation of Λ and Δ isomers. Next, the efficacies of the enantiopure metal-templated complexes 1-3 were investigated in three benchmark asymmetric reactions in order to compare their catalytic activity. The chiral cobalt(III) complexes 1-3 were tested as enantioselective hydrogen-bond-donor catalysts in such important reactions as the Michael addition of the O'Donnell substrate to methyl acrylate, epoxidation of chalcone, and trimethylsilylcyanation of benzaldehyde. It was clearly demonstrated that the chirality at the cobalt center has an impact on the stereochemical outcome of the reactions. In particular, the Λ(R,R)-1 and Δ(R,R)-1 complexes acted as "pseudoenantiomeric" catalysts in the epoxidation and trimethylsilylcyanoation reactions, providing both enantiomers of the products with up to 57% enantiomeric excess.

An asymmetric metal-templated route to amino acids with an isoquinolone core via a Rh(III)-catalyzed coupling of aryl hydroxamates with chiral propargylglycine Ni(II) complexes.

A general protocol for the asymmetric synthesis of artificial amino acids (AAs) comprising an isoquinolone skeleton was successfully elaborated via a straightforward Rh(III)-catalyzed C-H activation/annulation of various aryl hydroxamates with a series of robust chiral propargylglycine Ni(II) complexes derived from glycine (Gly), alanine (Ala) and phenylalanine (Phe) in a green solvent (methanol) under mild conditions (at room temperature under air). Notably, in the case of phenylalanine-derived complexes, the formation of unfavorable 4-substituted isoquinolone regioisomers was achieved by a catalyst control for the first time. The subsequent acidic decomposition of the obtained Ni(II) complexes provides the target unnatural α- and α,α-disubstituted AAs with an isoquinolone core in an enantiopure form.

Enantioselective "organocatalysis in disguise" by the ligand sphere of chiral metal-templated complexes.

Asymmetric catalysis holds a prominent position among the important developments in chemistry during the 20th century. This was acknowledged by the 2001 Nobel Prize in chemistry awarded to Knowles, Noyori, and Sharpless for their development of chiral metal catalysts for organic transformations. The key feature of the catalysts was the crucial role of the chiral ligand and the nature of the metal ions, which promoted the catalytic conversions of the substrates via direct coordination. Subsequently the development of asymmetric organic catalysis opened new avenues to the synthesis of enantiopure compounds, avoiding any use of metal ions. Recently, an alternative approach to asymmetric catalysis emerged that relied on the catalytic functions of the ligands themselves boosted by coordination to metal ions. In other words, in these hybrid chiral catalysts the substrates are activated not by the metal ions but by the ligands. The activation and enantioselective control occurred via well-orchestrated and custom-tailored non-covalent interactions of the substrates with the ligand sphere of chiral metal complexes. In these metal-templated catalysts, the metal served either as a template (a purely structural role), or it constituted the exclusive source of chirality (metal-centred chirality due to the spatial arrangement of achiral or chiral bi-/tridentate ligands around an octahedral metal centre), and/or it increased the Brønsted acidity of the ligands. Although the field is still in its infancy, it represents an inspiring combination of both metal and organic catalysis and holds major unexplored potential to push the frontiers of asymmetric catalysis. Here we present an overview of this emerging field discussing the principles, applications and perspectives on the catalytic use of chiral metal complexes that operate as "organocatalysts in disguise". It has been demonstrated that these chiral metal complexes are efficient and provide high stereoselective control in asymmetric hydrogen bonding catalysis, phase-transfer catalysis, Brønsted acid/base catalysis, enamine catalysis, nucleophilic catalysis, and photocatalysis as well as bifunctional catalysis. Also, many of the catalysts have been identified as highly effective catalysts at remarkably low catalyst loadings. These hybrid systems offer many opportunities in the synthesis of chiral compounds and represent promising alternatives to metal-based and organocatalytic asymmetric transformations.

Synthesis and a Catalytic Study of Diastereomeric Cationic Chiral-at-Cobalt Complexes Based on (R,R)-1,2-Diphenylethylenediamine.

Here we report the first synthesis of two diastereomeric cationic octahedral Co(III) complexes based on commercially available (R,R)-1,2-diphenylethylenediamine and salicylaldehyde. Both diastereoisomers with opposite chiralities at the metal center (Λ and Δ configurations) were prepared. The new Co(III) complexes possessed both acidic hydrogen-bond donating (HBD) NH moieties and nucleophilic counteranions and operate as bifunctional chiral catalysts for the challenging kinetic resolution of terminal and disubstituted epoxides by the reaction with CO2 under mild conditions. The highest selectivity factor (s) of 2.8 for the trans-chalcone epoxide was achieved at low catalyst loading (2 mol %) in chlorobenzene, which is the best achieved result currently for this type of substrate.

A general asymmetric synthesis of artificial aliphatic and perfluoroalkylated α-amino acids by Luche's cross-electrophile coupling reaction.

Aliphatic artificial α-amino acids (α-AAs) have attracted great interest in biochemistry and pharmacy. In this context, we developed a promising practical protocol for the asymmetric synthesis of these α-AAs through the selective and efficient intermolecular cross-electrophile coupling of Belokon's chiral dehydroalanine Ni(ii) complex with different alkyl and perfluoroalkyl iodides mediated by a dual Zn/Cu system. The reaction afforded diastereomeric complexes with dr up to 21.3 : 1 in 24-95% yields (19 examples). Exemplarily, three enantiomerically pure aliphatic α-AAs were obtained through acidic decomposition of (S,S)-diastereomers of Ni(ii) complexes. Importantly, the chiral auxiliary ligand (S)-BPB ((S)-2-(N-benzylprolyl)aminobenzophenone) was easily recycled by simple filtration after acidic complex decomposition and reused for the synthesis of the initial dehydroalanine Ni(ii) complex.

Human artificial chromosome (HAC) for measuring chromosome instability (CIN) and identification of genes required for proper chromosome transmission.

Chromosomal instability (CIN) is one of the characteristics of cancer inherent for tumor initiation and progression, which is defined as a persistent, high rate of gain/loss of whole chromosomes. In the vast majority of human tumors the molecular basis of CIN remains unknown. The development of a conceptually simple colony color sectoring assay that measures yeast artificial chromosome (YAC) loss provided a powerful genetic tool to assess the rate of chromosome mis-segregation and also identified 937 yeast genes involved in this process. Similarly, a human artificial chromosome (HAC)-based assay has been recently developed and applied to quantify chromosome mis-segregation events in human cells. This assay allowed identification of novel human CIN genes in the library of protein kinases. Among them are PINK1, TRIO, IRAK1, PNCK, and TAOK1. The HAC-based assay may be applied to screen siRNA, shRNA and CRISPR-based libraries to identify the complete spectrum of CIN genes. This will reveal new insights into mechanisms of chromosome segregation and may expedite the development of novel therapeutic strategies to target the CIN phenotype in cancer cells.

Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing.

Despite the key role of the human ribosome in protein biosynthesis, little is known about the extent of sequence variation in ribosomal DNA (rDNA) or its pre-rRNA and rRNA products. We recovered ribosomal DNA segments from a single human chromosome 21 using transformation-associated recombination (TAR) cloning in yeast. Accurate long-read sequencing of 13 isolates covering ∼0.82 Mb of the chromosome 21 rDNA complement revealed substantial variation among tandem repeat rDNA copies, several palindromic structures and potential errors in the previous reference sequence. These clones revealed 101 variant positions in the 45S transcription unit and 235 in the intergenic spacer sequence. Approximately 60% of the 45S variants were confirmed in independent whole-genome or RNA-seq data, with 47 of these further observed in mature 18S/28S rRNA sequences. TAR cloning and long-read sequencing enabled the accurate reconstruction of multiple rDNA units and a new, high-quality 44 838 bp rDNA reference sequence, which we have annotated with variants detected from chromosome 21 of a single individual. The large number of variants observed reveal heterogeneity in human rDNA, opening up the possibility of corresponding variations in ribosome dynamics.

The charge-assisted hydrogen-bonded organic framework (CAHOF) self-assembled from the conjugated acid of tetrakis(4-aminophenyl)methane and 2,6-naphthalenedisulfonate as a new class of recyclable Brønsted acid catalysts.

The acid-base neutralization reaction of commercially available disodium 2,6-naphthalenedisulfonate (NDS, 2 equivalents) and the tetrahydrochloride salt of tetrakis(4-aminophenyl)methane (TAPM, 1 equivalent) in water gave a novel three-dimensional charge-assisted hydrogen-bonded framework (CAHOF, F-1). The framework F-1 was characterized by X-ray diffraction, TGA, elemental analysis, and 1H NMR spectroscopy. The framework was supported by hydrogen bonds between the sulfonate anions and the ammonium cations of NDS and protonated TAPM moieties, respectively. The CAHOF material functioned as a new type of catalytically active Brønsted acid in a series of reactions, including the ring opening of epoxides by water and alcohols. A Diels-Alder reaction between cyclopentadiene and methyl vinyl ketone was also catalyzed by F-1 in heptane. Depending on the polarity of the solvent mixture, the CAHOF F-1 could function as a purely heterogeneous catalyst or partly dissociate, providing some dissolved F-1 as the real catalyst. In all cases, the catalyst could easily be recovered and recycled.

Henry Reaction Revisited. Crucial Role of Water in an Asymmetric Henry Reaction Catalyzed by Chiral NNO-Type Copper(II) Complexes.

Chiral copper(II) and cobalt(III) complexes (1-5 and 6, respectively) derived from Schiff bases of (S)-2-(aminomethyl)pyrrolidine and salicylaldehyde derivatives were employed in a mechanistic study of the Henry reaction-type condensation of nitromethane and o-nitrobenzaldehyde in CH2Cl2 (CD2Cl2), containing different amounts of water. The reaction kinetics was monitored by 1H and 13C NMR. The addition of water had a different influence on the activity of the two types of complexes, ranging from a crucial positive effect in the case of the copper(II) complex 2 to insignificant in the case of the stereochemically inert cobalt(III) complex 6. No experimental support was found by 1H NMR studies for the classical Lewis acid complexation of the carbonyl group of the aldehyde by the central copper(II) ion, and, moreover, density functional theory (DFT) calculations support the absence of such coordination. On the other hand, a very significant complexation was found for water, and it was supported by DFT calculations. In fact, we suggest that it is the Brønsted acidity of the water molecule coordinated to the metal ion that triggers the aldehyde activation. The rate-limiting step of the reaction was the removal of an α-proton from the nitromethane molecule, as supported by the observed kinetic isotope effect equaling 6.3 in the case of the copper complex 2. It was found by high-resolution mass spectrometry with electrospray ionization that the copper(II) complex 2 existed in CH2Cl2 in a dimeric form. The reaction had a second-order dependence on the catalyst concentration, which implicated two dimeric forms of the copper(II) complex 2 in the rate-limiting step. Furthermore, DFT calculations help to generate a plausible structure of the stereodetermining transition step of the condensation.