MOSAIC enables in situ saturation mutagenesis of genes and CRISPR prime editing guide RNA optimization in human cells.

CRISPR prime editing offers unprecedented versatility and precision for the installation of genetic edits in situ . Here we describe the development and characterization of the Multiplexing Of Site-specific Alterations for In situ Characterization ( MOSAIC ) method, which leverages a non-viral PCR-based prime editing method to enable rapid installation of thousands of defined edits in pooled fashion. We show that MOSAIC can be applied to perform in situ saturation mutagenesis screens of: (1) the BCR-ABL1 fusion gene, successfully identifying known and potentially new imatinib drug-resistance variants; and (2) the IRF1 untranslated region (UTR), re-confirming non-coding regulatory elements involved in transcriptional initiation. Furthermore, we deployed MOSAIC to enable high-throughput, pooled screening of hundreds of systematically designed prime editing guide RNA ( pegRNA ) constructs for a large series of different genomic loci. This rapid screening of >18,000 pegRNA designs identified optimized pegRNAs for 89 different genomic target modifications and revealed the lack of simple predictive rules for pegRNA design, reinforcing the need for experimental optimization now greatly simplified and enabled by MOSAIC. We envision that MOSAIC will accelerate and facilitate the application of CRISPR prime editing for a wide range of high-throughput screens in human and other cell systems.

CRISPR PERSIST-On enables heritable and fine-tunable human gene activation.

Current technologies for upregulation of endogenous genes use targeted artificial transcriptional activators but stable gene activation requires persistent expression of these synthetic factors. Although general "hit-and-run" strategies exist for inducing long-term silencing of endogenous genes using targeted artificial transcriptional repressors, to our knowledge no equivalent approach for gene activation has been described to date. Here we show stable gene activation can be achieved by harnessing endogenous transcription factors ( EndoTF s) that are normally expressed in human cells. Specifically, EndoTFs can be recruited to activate endogenous human genes of interest by using CRISPR-based gene editing to introduce EndoTF DNA binding motifs into a target gene promoter. This Precision Editing of Regulatory Sequences to Induce Stable Transcription-On ( PERSIST-On ) approach results in stable long-term gene activation, which we show is durable for at least five months. Using a high-throughput CRISPR prime editing pooled screening method, we also show that the magnitude of gene activation can be finely tuned either by using binding sites for different EndoTF or by introducing specific mutations within such sites. Our results delineate a generalizable framework for using PERSIST-On to induce heritable and fine-tunable gene activation in a hit-and-run fashion, thereby enabling a wide range of research and therapeutic applications that require long-term upregulation of a target gene.

PrimeDesign software for rapid and simplified design of prime editing guide RNAs.

Prime editing (PE) is a versatile genome editing technology, but design of the required guide RNAs is more complex than for standard CRISPR-based nucleases or base editors. Here we describe PrimeDesign, a user-friendly, end-to-end web application and command-line tool for the design of PE experiments. PrimeDesign can be used for single and combination editing applications, as well as genome-wide and saturation mutagenesis screens. Using PrimeDesign, we construct PrimeVar, a comprehensive and searchable database that includes candidate prime editing guide RNA (pegRNA) and nicking sgRNA (ngRNA) combinations for installing or correcting >68,500 pathogenic human genetic variants from the ClinVar database. Finally, we use PrimeDesign to design pegRNAs/ngRNAs to install a variety of human pathogenic variants in human cells.

The NSL complex-mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise.

Nucleosomal organization at gene promoters is critical for transcription, with a nucleosome-depleted region (NDR) at transcription start sites (TSSs) being required for transcription initiation. How NDRs and the precise positioning of the +1 nucleosomes are maintained on active genes remains unclear. Here, we report that the Drosophila nonspecific lethal (NSL) complex is necessary to maintain this stereotypical nucleosomal organization at promoters. Upon NSL1 depletion, nucleosomes invade the NDRs at TSSs of NSL-bound genes. NSL complex member NSL3 binds to TATA-less promoters in a sequence-dependent manner. The NSL complex interacts with the NURF chromatin remodeling complex and is necessary and sufficient to recruit NURF to target promoters. Not only is the NSL complex essential for transcription, but it is required for accurate TSS selection for genes with multiple TSSs. Furthermore, loss of the NSL complex leads to an increase in transcriptional noise. Thus, the NSL complex establishes a canonical nucleosomal organization that enables transcription and determines TSS fidelity.

High-resolution TADs reveal DNA sequences underlying genome organization in flies.

Despite an abundance of new studies about topologically associating domains (TADs), the role of genetic information in TAD formation is still not fully understood. Here we use our software, HiCExplorer (hicexplorer.readthedocs.io) to annotate >2800 high-resolution (570 bp) TAD boundaries in Drosophila melanogaster. We identify eight DNA motifs enriched at boundaries, including a motif bound by the M1BP protein, and two new boundary motifs. In contrast to mammals, the CTCF motif is only enriched on a small fraction of boundaries flanking inactive chromatin while most active boundaries contain the motifs bound by the M1BP or Beaf-32 proteins. We demonstrate that boundaries can be accurately predicted using only the motif sequences at open chromatin sites. We propose that DNA sequence guides the genome architecture by allocation of boundary proteins in the genome. Finally, we present an interactive online database to access and explore the spatial organization of fly, mouse and human genomes, available at http://chorogenome.ie-freiburg.mpg.de .

High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila.

Dosage compensation mechanisms provide a paradigm to study the contribution of chromosomal conformation toward targeting and spreading of epigenetic regulators over a specific chromosome. By using Hi-C and 4C analyses, we show that high-affinity sites (HAS), landing platforms of the male-specific lethal (MSL) complex, are enriched around topologically associating domain (TAD) boundaries on the X chromosome and harbor more long-range contacts in a sex-independent manner. Ectopically expressed roX1 and roX2 RNAs target HAS on the X chromosome in trans and, via spatial proximity, induce spreading of the MSL complex in cis, leading to increased expression of neighboring autosomal genes. We show that the MSL complex regulates nucleosome positioning at HAS, therefore acting locally rather than influencing the overall chromosomal architecture. We propose that the sex-independent, three-dimensional conformation of the X chromosome poises it for exploitation by the MSL complex, thereby facilitating spreading in males.

The NSL complex regulates housekeeping genes in Drosophila.

MOF is the major histone H4 lysine 16-specific (H4K16) acetyltransferase in mammals and Drosophila. In flies, it is involved in the regulation of X-chromosomal and autosomal genes as part of the MSL and the NSL complexes, respectively. While the function of the MSL complex as a dosage compensation regulator is fairly well understood, the role of the NSL complex in gene regulation is still poorly characterized. Here we report a comprehensive ChIP-seq analysis of four NSL complex members (NSL1, NSL3, MBD-R2, and MCRS2) throughout the Drosophila melanogaster genome. Strikingly, the majority (85.5%) of NSL-bound genes are constitutively expressed across different cell types. We find that an increased abundance of the histone modifications H4K16ac, H3K4me2, H3K4me3, and H3K9ac in gene promoter regions is characteristic of NSL-targeted genes. Furthermore, we show that these genes have a well-defined nucleosome free region and broad transcription initiation patterns. Finally, by performing ChIP-seq analyses of RNA polymerase II (Pol II) in NSL1- and NSL3-depleted cells, we demonstrate that both NSL proteins are required for efficient recruitment of Pol II to NSL target gene promoters. The observed Pol II reduction coincides with compromised binding of TBP and TFIIB to target promoters, indicating that the NSL complex is required for optimal recruitment of the pre-initiation complex on target genes. Moreover, genes that undergo the most dramatic loss of Pol II upon NSL knockdowns tend to be enriched in DNA Replication-related Element (DRE). Taken together, our findings show that the MOF-containing NSL complex acts as a major regulator of housekeeping genes in flies by modulating initiation of Pol II transcription.

Synthesis, characterization, and laser flash photolysis reactivity of a carbonmonoxy heme complex.

We present here the synthesis, characterization, and flash photolysis study of [(F(8)TPP)Fe(II)(CO)(THF)] (1) [F(8)TPP = tetrakis(2,6-difluorophenyl)porphyrinate(2-)]. Complex 1 crystallizes from THF/heptane solvent system as a tris-THF solvate, [(F(8)TPP)Fe(II)(CO)(THF)].3THF (1.3THF), with ferrous ion in the porphyrin plane (C(61)H(52)F(8)FeN(4)O(5); a = 11.7908(2) A, b = 20.4453(2) A, c = 39.9423(3), alpha = 90 degrees, beta = 90 degrees, gamma = 90 degrees; orthorhombic, P2(1)2(1)2(1), Z = 8; Fe-N(4)(av) = 2.00 A; N-Fe-N (all) = 90.0 degrees ). This complex (as 1.THF) has also been characterized by (1)H NMR [six-coordinate, low-spin heme; CD(3)CN, RT, delta 8.82 (s, pyrrole-H, 8H), 7.89 (s, para-phenyl-H, 8H), 7.46 (s, meta-phenyl-H, 4H), 3.58 (s, THF, 8H), 1.73 (s, THF, 8H)], (2)H NMR (pyrrole-deuterated analogue) [(F(8)TPP-d(8))Fe(II)(CO)(THF)] [THF, RT, delta 8.78 ppm (s, pyrrole-D)], (13)C NMR (on (13)CO-enriched adduct) [THF-d(8), RT, delta 206.5 ppm; CD(2)Cl(2), RT, delta 206.1 ppm], UV-vis [THF, RT, lambda(max), 411 (Soret), 525 nm], and IR [293 K, solution, nu(CO) 1979 cm(-)(1) (THF), 1976 cm(-)(1) (acetone), 1982 cm(-)(1) (CH(3)CN)] spectroscopies. In order to more fully understand the intricacies of solvent-ligand binding (as compared to CO rebinding to the photolyzed heme), we have also synthesized the bis-THF adduct [(F(8)TPP)Fe(II)(THF)(2)]. Complex 2 also crystallizes from THF/heptane solvent system as a bis-THF solvate, [(F(8)TPP)Fe(II)(THF)(2)].2THF (2.2THF), with ferrous iron in the porphyrin plane (C(60)H(52)F(8)FeN(4)O(4); a = 21.3216(3) A, b = 12.1191(2) A, c = 21.0125(2) A, alpha = 90 degrees, beta = 105.3658(5) degrees, gamma = 90 degrees; monoclinic, C2/c, Z = 4; Fe-N(4)(av) = 2.07 A; N-Fe-N (all) = 90.0 degrees ). Further characterization of 2 includes UV-vis [THF, lambda(max), 421 (Soret), 542 nm] and (1)H NMR [six-coordinate, high spin heme; THF-d(8), RT, delta 56.7 (s, pyrrole-H, 8H), 8.38 (s, para-phenyl-H, 8H), 7.15 (s, meta-phenyl-H, 4H)] spectroscopies. Flash photolysis studies employing 1 were able to resolve the CO rebinding kinetics in both THF and cyclohexane solvents. In CO saturated THF [[CO] approximately 5 mM] and at [1] congruent with 5 microM, the conversion of [(F(8)TPP)Fe(II)(THF)(2)] (produced after photolytic displacement of CO) to [(F(8)TPP)Fe(II)(CO)(THF)] was monoexponential, with k(obs) = 1.6 (+/-0.2) x 10(4) s(-)(1). Reduction in [CO] by vigorous Ar purging gave k(obs) congruent with 10(3) s(-)(1) in cyclohexane. The study presented in this report lays the foundation for applying fast-time scale studies based on CO flash photolysis to the more complicated heterobimetallic heme/Cu systems.

Syntheses and structural characterizations of the unsymmetrical diphosphene DmpP=PMes* (Dmp =2,6-Mes(2)C(6)H(3), Mes* = 2,4,6-(t)Bu(3)C(6)H(2)) and the cyclotetraphosphane [DmpPPPh](2).

The new diphosphene DmpP=PMes* (Dmp = 2,6-Mes(2)C(6)H(3); Mes* = 2,4,6-(t)Bu(3)C(6)H(2), 1) having two different classes of sterically demanding aryls has been prepared and structurally characterized. This structure appears to be the first featuring both types of sterically demanding groups (a meta-terphenyl and Mes*) in a single molecule about a multiply bonded unit. Compound 1 features a P=P bond length of 2.024(13) A. The structure of 1 also allows comparisons to the two previously structurally characterized symmetric diphosphenes DmpP=PDmp and Mes*P=PMes*. The crystal structure of the cyclotetraphosphane [DmpPPPh](2) (3), the product of self-dimerization of the unstable diphosphene DmpP=PPh (2), has been determined. The structure of 3 demonstrates that a single bulky Dmp group is insufficient to prevent dimerization of 2. (31)P NMR data for all three compounds are also reported.

Synthesis and structural characterization of 2,6-dimesitylphenyl complexes of scandium, ytterbium, and yttrium.

The molecular structures of a number of 2,6-dimesitylphenyl-based (2,6-dimesitylphenyl = Dmp) complexes of the group 3 elements scandium and yttrium as well as of the lanthanide element ytterbium are reported. Reaction of 1 equiv of DmpLi with 1 equiv of MCl(3) (M = Sc, Yb, Y) in tetrahydrofuran at room temperature followed by crystallization from toluene/hexanes at -30 degrees C produces DmpMCl(2)(THF)(2) (M = Sc: 1; M = Yb: 2) and DmpMCl(2)(THF)(3) (M = Y: 3), respectively. The one-pot reaction of DmpLi with 1 equiv of YbCl(3) in tetrahydrofuran at room temperature followed by addition of 1 equiv of KO(t)Bu produces the heterobimetallic monoalkoxide complex DmpYb(THF)(O(t)Bu)(mu-Cl)(2)Li(THF)(2) (4), which was crystallized from toluene/tetrahydrofuran (20:1) at -30 degrees C. Crystal data for 1: monoclinic, P2(1)/n; T = 203 K; a = 10.178(3) A; b = 15.468(3) A; c = 20.132(5) A; beta = 101.85(3) degrees; V = 3102.0(17) A(3); Z' = 4; D(calcd) = 1.228 g cm(-3); R(1) = 5.89%. Crystal data for 2: monoclinic, P2(1)/n; T = 173 K; a = 10.2447(7) A; b = 15.5683(12) A; c = 20.0979(14) A; beta = 101.749(4) degrees; V = 3238.3(5) A(3); Z' = 4; D(calcd) = 1.485 g cm(-3); R(1) = 4.32%. Crystal data for 3: monoclinic, P2(1)/n; T = 203 K; a = 15.950(3) A; b = 11.865(2) A; c = 18.254(3) A; beta = 92.323(3) degrees; V = 3451.9(10) A(3); Z' = 4; D(calcd) = 1.327 g cm(-)(3); R(1) = 4.43%. Crystal data for 4: triclinic, P1; T = 193 K; a = 10.2252(2) A; b = 11.3497(2) A; c = 18.5814(2) A; alpha = 98.7353(6) degrees; beta = 102.8964(6) degrees; gamma = 94.8058(5) degrees; V = 2062.09(5) A(3); Z' = 2; D(calcd) = 1.375 g cm(-3); R(1) = 4.56%. The molecular structures of 1-3 feature monomeric complexes with distorted trigonal-bipyramidal (1 and 2) or octahedral (3) coordination geometry about the metal atom, with the two chlorine atoms occupying the axial positions. 4 represents the first example of an alkoxide derivative of a terphenyl lanthanide complex. The molecular structure of the ate complex 4 exhibits a heavily distorted trigonal-bipyramidal coordination polyhedron about the ytterbium atom, with one of the mu-chlorine atoms and the oxygen atom of the tetrahydrofuran ligand representing the axial positions of the trigonal-bipyramidal arrangement. A terminal alkoxide ligand is another main feature of the molecular structure of complex 4.

Tris[(alkylthio)methyl]silanes: Syntheses and Structures of Chromium, Molybdenum, and Tungsten Complexes with a Tripodal Thioether Ligand.

The first member of a new family of tripodal thioether ligands, the methyltris[(alkylthio)methyl]silanes MeSi(CH(2)SR)(3) (R = Me), has been synthesized and characterized. Reactivity studies lead to the isolation of the complete series of group 6 metal carbonyl derivatives {eta(3)-MeSi(CH(2)SMe)(3)}M(CO)(3) (M = Cr, Mo, W), whose structures have been determined by single-crystal X-ray diffraction. The three complexes are isomorphous and display distorted octahedral structures with face-capping tridentate thioether ligands. {eta(3)-MeSi(CH(2)SMe)(3)}Cr(CO)(3) is monoclinic, P2(1)/c, a = 8.1658(2) Å, b = 15.0563(2) Å, c = 26.5791(3) Å, beta = 90.3653(6) degrees, V = 3267.74(8) Å(3), Z = 8. {eta(3)-MeSi(CH(2)SMe)(3)}Mo(CO)(3) is monoclinic, P2(1)/c, a = 8.34630(6) Å, b = 15.2747(2) Å, c = 27.1865(4) Å, beta = 90.8987(9) degrees, V = 3465.44(10) Å(3), Z = 8. {eta(3)-MeSi(CH(2)SMe)(3)}W(CO)(3) is monoclinic, P2(1)/c, a = 8.1582(2) Å, b = 14.9903(2) Å, c = 26.7268(4) Å, beta = 90.6568(8) degrees, V = 3268.30(9) Å(3), Z = 8.