Not All H3K4 Methylations Are Created Equal: Mll2/COMPASS Dependency in Primordial Germ Cell Specification.

The spatiotemporal regulation of gene expression is central for cell-lineage specification during embryonic development and is achieved through the combinatorial action of transcription factors/co-factors and epigenetic states at cis-regulatory elements. Here, we show that in addition to implementing H3K4me3 at promoters of bivalent genes, Mll2 (KMT2B)/COMPASS can also implement H3K4me3 at a subset of non-TSS regulatory elements, a subset of which shares epigenetic signatures of active enhancers. Our mechanistic studies reveal that association of Mll2's CXXC domain with CpG-rich regions plays an instrumental role for chromatin targeting and subsequent implementation of H3K4me3. Although Mll2/COMPASS is required for H3K4me3 implementation on thousands of loci, generation of catalytically mutant MLL2/COMPASS demonstrated that H3K4me3 implemented by this enzyme was essential for expression of a subset of genes, including those functioning in the control of transcriptional programs during embryonic development. Our findings suggest that not all H3K4 trimethylations implemented by MLL2/COMPASS are functionally equivalent.

TmcA functions as a lysine 2-hydroxyisobutyryltransferase to regulate transcription.

Protein lysine 2-hydroxyisobutyrylation (Khib) has recently been shown to play a critical role in the regulation of cellular processes. However, the mechanism and functional consequence of Khib in prokaryotes remain unclear. Here we report that TmcA, an RNA acetyltransferase, functions as a lysine 2-hydroxyisobutyryltransferase in the regulation of transcription. We show that TmcA can effectively catalyze Khib both in vitro and intracellularly, and that R502 is a key site for the Khib catalytic activity of TmcA. Using quantitative proteomics, we identified 467 endogenous candidates targeted by TmcA for Khib in Escherichia coli. Interestingly, we demonstrate that TmcA can specifically modulate the DNA-binding activity of H-NS, a nucleoid-associated protein, by catalysis of Khib at K121. Furthermore, this TmcA-targeted Khib regulates transcription of acid-resistance genes and enhances E. coli survival under acid stress. Our study reveals transcription regulation mediated by TmcA-catalyzed Khib for bacterial acid resistance.

An Evolutionary Conserved Epigenetic Mark of Polycomb Response Elements Implemented by Trx/MLL/COMPASS.

Polycomb response elements (PREs) are specific DNA sequences that stably maintain the developmental pattern of gene expression. Drosophila PREs are well characterized, whereas the existence of PREs in mammals remains debated. Accumulating evidence supports a model in which CpG islands recruit Polycomb group (PcG) complexes; however, which subset of CGIs is selected to serve as PREs is unclear. Trithorax (Trx) positively regulates gene expression in Drosophila and co-occupies PREs to antagonize Polycomb-dependent silencing. Here we demonstrate that Trx-dependent H3K4 dimethylation (H3K4me2) marks Drosophila PREs and maintains the developmental expression pattern of nearby genes. Similarly, the mammalian Trx homolog, MLL1, deposits H3K4me2 at CpG-dense regions that could serve as PREs. In the absence of MLL1 and H3K4me2, H3K27me3 levels, a mark of Polycomb repressive complex 2 (PRC2), increase at these loci. By inhibiting PRC2-dependent H3K27me3 in the absence of MLL1, we can rescue expression of these loci, demonstrating a functional balance between MLL1 and PRC2 activities at these sites. Thus, our study provides rules for identifying cell-type-specific functional mammalian PREs within the human genome.

Epigenetics of hematopoiesis and hematological malignancies.

Hematological malignancies comprise a diverse set of lymphoid and myeloid neoplasms in which normal hematopoiesis has gone awry and together account for ∼10% of all new cancer cases diagnosed in the United States in 2016. Recent intensive genomic sequencing of hematopoietic malignancies has identified recurrent mutations in genes that encode regulators of chromatin structure and function, highlighting the central role that aberrant epigenetic regulation plays in the pathogenesis of these neoplasms. Deciphering the molecular mechanisms for how alterations in epigenetic modifiers, specifically histone and DNA methylases and demethylases, drive hematopoietic cancer could provide new avenues for developing novel targeted epigenetic therapies for treating hematological malignancies. Just as past studies of blood cancers led to pioneering discoveries relevant to other cancers, determining the contribution of epigenetic modifiers in hematologic cancers could also have a broader impact on our understanding of the pathogenesis of solid tumors in which these factors are mutated.

Antecubital Fossa Perforator Flaps for Soft-Tissue Defect Repair of the Anterior Elbow: Anatomical Study and Clinical Application.

BACKGROUND: The antecubital fossa is a main perforator cluster region located beside the anterior elbow defect, rendering it crucial to harvest the perforator pedicled flaps for the anterior elbow defects. PATIENTS AND METHODS: A total of 30 preserved cadaveric forearms were dissected in order to describe the perforator anatomy in the antecubital fossa. For each perforator, the number, the site of origin, the diameter at its origin, and the trajectory were recorded. In addition, all the patients treated for anterior elbow defects using inferior cubital artery (ICA) perforator pedicled flaps between June 2013 and June 2018 were reviewed in this retrospective study. RESULTS: A total of 85 perforators were dissected in the antecubital fossa area from the 30 specimens. Among these, 65 perforators originated from the radial artery, 6 from the recurrent radial artery, 13 from the brachial artery, and 1 from the ulnar artery. Each forearm specimen had a constant and large ICA perforator. All perforators originated from source vessels 2-5 cm distal from the interepicondylar line and could be harvested as perforator pedicled flap for anterior elbow reconstruction. In the clinical study, 11 patients with anterior elbow defects were treated with ICA perforator pedicled flaps with satisfactory functional and aesthetic outcomes. CONCLUSION: The antecubital fossa has a constant and dominant ICA perforator and many other perforators. The pedicled antecubital fossa perforator flaps could be harvested flexibly with a reliable blood supply for anterior elbow reconstruction.

Enhancer malfunction in cancer.

Why certain point mutations in a general transcription factor are associated with specific forms of cancer has been a major question in cancer biology. Enhancers are DNA regulatory elements that are key regulators of tissue-specific gene expression. Recent studies suggest that enhancer malfunction through point mutations in either regulatory elements or factors modulating enhancer-promoter communication could be the cause of tissue-specific cancer development. In this Perspective, we will discuss recent findings in the identification of cancer-related enhancer mutations and the role of Drosophila Trr and its human homologs, the MLL3 and MLL4/COMPASS-like complexes, as enhancer histone H3 lysine 4 (H3K4) monomethyltransferases functioning in enhancer-promoter communication. Recent genome-wide studies in the cataloging of somatic mutations in cancer have identified mutations in intergenic sequences encoding regulatory elements-and in MLL3 and MLL4 in both hematological malignancies and solid tumors. We propose that cancer-associated mutations in MLL3 and MLL4 exert their properties through the malfunction of Trr/MLL3/MLL4-dependent enhancers.

A role for H3K4 monomethylation in gene repression and partitioning of chromatin readers.

Monomethylation of lysine 4 on histone H3 (H3K4me1) is a well-established feature of enhancers and promoters, although its function is unknown. Here, we uncover roles for H3K4me1 in diverse cell types. Remarkably, we find that MLL3/4 provokes monomethylation of promoter regions and the conditional repression of muscle and inflammatory response genes in myoblasts. During myogenesis, muscle genes are activated, lose MLL3 occupancy, and become H3K4-trimethylated through an alternative COMPASS complex. Monomethylation-mediated repression was not restricted to skeletal muscle. Together with H3K27me3 and H4K20me1, H3K4me1 was associated with transcriptional silencing in embryonic fibroblasts, macrophages, and human embryonic stem cells (ESCs). On promoters of active genes, we find that H3K4me1 spatially demarcates the recruitment of factors that interact with H3K4me3, including ING1, which, in turn, recruits Sin3A. Our findings point to a unique role for H3K4 monomethylation in establishing boundaries that restrict the recruitment of chromatin-modifying enzymes to defined regions within promoters.

Integrator regulates transcriptional initiation and pause release following activation.

In unicellular organisms, initiation is the rate-limiting step in transcription; in metazoan organisms, the transition from initiation to productive elongation is also important. Here, we show that the RNA polymerase II (RNAPII)-associated multiprotein complex, Integrator, plays a critical role in both initiation and the release of paused RNAPII at immediate early genes (IEGs) following transcriptional activation by epidermal growth factor (EGF) in human cells. Integrator is recruited to the IEGs in a signal-dependent manner and is required to engage and recruit the super elongation complex (SEC) to EGF-responsive genes to allow release of paused RNAPII and productive transcription elongation.

Sequential posterior interosseous artery perforator flap for reconstruction of dorsal hand defects.

Dorsal hand defects accompanied by exposure of bones and tendons remain a huge challenge for plastic surgeons. The pedicled perforator flaps have unique advantages in resurfacing the defects. This study aimed to investigate the clinical efficacy of the sequential posterior interosseous artery perforator flap for repairing dorsal hand defects. This study was composed of an anatomical study and clinical application. Anatomically, 30 adult upper limb specimens injected with red latex were dissected, the perforators from the branches of the posterior interosseous artery were observed in the dorsal forearm, and the sequential flap based on them was designed based on the anatomical characteristics. Clinically, nine cases of soft tissue defects on the dorsum of the hand were treated by this flap. Anatomically, the posterior interosseous artery divided into an ascending branch and a descending branch, and the descending branch traveled 1.0 ± 0.3 cm down to divide into the ulnar and radial terminal branches. The ulnar terminal branch presented constantly, and the radial terminal branch had an occurrence rate of 93.33%. Clinically, all flaps survived completely and possessed a soft texture and satisfactory appearance, as well as a nonbloated pedicle, and the donor region had a natural color and appearance with only a linear scar left behind. The sequential posterior interosseous artery perforator flap could become a useful option for repairing dorsal hand defects, as it has the advantages of being easy to perform without sacrificing the main vessels and avoiding donor area skin grafting.

The little elongation complex functions at initiation and elongation phases of snRNA gene transcription.

The small nuclear RNA (snRNA) genes have been widely used as a model system for understanding transcriptional regulation due to the unique aspects of their promoter structure, selectivity for either RNA polymerase (Pol) II or III, and because of their unique mechanism of termination that is tightly linked with the promoter. Recently, we identified the little elongation complex (LEC) in Drosophila that is required for the expression of Pol II-transcribed snRNA genes. Here, using Drosophila and mammalian systems, we provide genetic and molecular evidence that LEC functions in at least two phases of snRNA transcription: an initiation step requiring the ICE1 subunit, and an elongation step requiring ELL.

ClusterMap: compare multiple single cell RNA-Seq datasets across different experimental conditions.

MOTIVATION: Single cell RNA-Seq (scRNA-Seq) facilitates the characterization of cell type heterogeneity and developmental processes. Further study of single cell profiles across different conditions enables the understanding of biological processes and underlying mechanisms at the sub-population level. However, developing proper methodology to compare multiple scRNA-Seq datasets remains challenging. RESULTS: We have developed ClusterMap, a systematic method and workflow to facilitate the comparison of scRNA-seq profiles across distinct biological contexts. Using hierarchical clustering of the marker genes of each sub-group, ClusterMap matches the sub-types of cells across different samples and provides 'similarity' as a metric to quantify the quality of the match. We introduce a purity tree cut method designed specifically for this matching problem. We use Circos plot and regrouping method to visualize the results concisely. Furthermore, we propose a new metric 'separability' to summarize sub-population changes among all sample pairs. In the case studies, we demonstrate that ClusterMap has the ability to provide us further insight into the different molecular mechanisms of cellular sub-populations across different conditions. AVAILABILITY AND IMPLEMENTATION: ClusterMap is implemented in R and available at https://github.com/xgaoo/ClusterMap. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The V-Y advancement flap based on the dorsal carpal perforators for dorsal metacarpal reconstruction: Anatomical and clinical study.

INTRODUCTION: Soft-tissue defects on the dorsal hand accompanied by exposed bone and tendon remain a challenge for plastic surgeons. The purpose of this study was to observe the morphological characteristics of the dorsal carpal perforators in the wrist and to design a V-Y advancement flap based on the dorsal carpal perforators. MATERIALS AND METHODS: Thirty cadaveric hand specimens were dissected to observe the origin, course, branches, and anastomoses of the dorsal carpal perforators, and a V-Y advancement flap was designed based on these perforators. Clinically, nine cases of dorsal hand defects were reconstructed with this flap. RESULTS: The dorsal carpal vascular network was formed by vascular anastomoses along the dorsal carpal branch of the radial artery, dorsal carpal branch of the anterior interosseous artery, ascending branch of the dorsal carpal perforator from the deep palmar arch, direct branch of the radial artery, dorsal carpal branch of the ulnar artery, posterior interosseous artery, and deep palmar branch of the ulnar artery; this network could be divided into a deep vascular network and superficial vascular network according to the anatomical plane. Among the perforators, the third and fourth perforators that pierce out bilaterally from the tendon of the extensor digitorium had a consistent occurrence rate (100%) with an outer diameter of 0.7 ± 0.3 mm and 0.6 ± 0.2 mm, respectively, and thus could be chosen as the vascular pedicle. In clinical applications, all flaps survived completely with excellent color and texture, a satisfactory appearance, and normal movement of the wrist joint. CONCLUSIONS: A V-Y advancement flap based on the dorsal carpal perforators can become a useful choice for the repair of dorsal metacarpal defects caused by trauma or dorsal metacarpal arterial flaps.

Anatomical Basis and Clinical Application of the First Metatarsal Proximal Perforator-Based Neurocutaneous Vascular Flap.

Forefoot defects caused by accidents are very common, but their reconstruction remains a substantial challenge for plastic surgeons. The purpose of this study is to determine the anatomical structure of the first metatarsal proximal perforator-based flap and to propose its clinical application. The study was divided into two parts: an anatomical study and a clinical application. Thirty preserved lower limbs injected with red latex were chosen for observation, and the following were recorded: the course and distribution of the medialis dorsalis pedis cutaneous nerve; the origin, course, branching and distribution of the first metatarsal proximal perforator; and the communication of the perforator and the dorsal medial vessels. Clinically, six cases of forefoot skin defects were reconstructed with the first metatarsal proximal perforator-based neurocutaneous vascular flap. The medialis dorsalis pedis cutaneous nerve mainly arose from the medial branch of the superficial peroneal nerve and proceeded forward for a distance of 2.5 ± 0.4 cm under the surface of the inferior extensor retinaculum; then, the nerve divided into the medial dorsal branch and the first and second dorsal metatarsal branches. The first metatarsal proximal perforator-based neurocutaneous vessels were multisegmented and multisourced, and the first branch was closely related to the operative procedure. In terms of the clinical application, all flaps of the six cases survived completely with good appearance, texture and elasticity. The first metatarsal proximal perforators present as constant. The first metatarsal proximal perforator-based neurocutaneous vascular flap may become a useful supplemental material for the reconstruction of forefoot defects. Clin. Anat., 33:653-660, 2020. © 2019 Wiley Periodicals, Inc.

Codependency of H2B monoubiquitination and nucleosome reassembly on Chd1.

Monoubiquitination of histone H2B on Lys 123 (H2BK123ub) is a transient histone modification considered to be essential for establishing H3K4 and H3K79 trimethylation by Set1/COMPASS and Dot1, respectively. Here, we identified Chd1 as a factor that is required for the maintenance of high levels of H2B monoubiquitination, but not for H3K4 and H3K79 trimethylation. Loss of Chd1 results in a substantial loss of H2BK123ub levels with little to no effect on the genome-wide pattern of H3K4 and H3K79 trimethylation. Our data show that nucleosomal occupancy is reduced in gene bodies in both chd1Δ and, as has been shown, K123A mutant backgrounds. We also demonstrated that Chd1's function in maintaining H2BK123ub levels is conserved from yeast to humans. Our study provides evidence that only small levels of H2BK123ub are necessary for full levels of H3K4 and H3K79 trimethylation in vivo and points to a possible role for Chd1 in positively regulating gene expression through promoting nucleosome reassembly coupled with H2B monoubiquitination.

Anatomical basis and clinical application of the dorsal perforator flap based on the palmar artery in the first web.

PURPOSE: Soft-tissue defects of the thumb and index finger remain a challenge for plastic surgeons. Our purpose was to observe the morphological characteristics of the cutaneous vessels in the first web, to design a dorsal perforator flap based on the palmar artery in the first web and to propose its clinical application. METHODS: Thirty preserved hand specimens were dissected to observe the origin, course, branch and anastomosis of the dorsal perforators in the first web, and the dorsal perforator flap based on the palmar artery in the first web was designed. Clinically, seven cases of hand defects were reconstructed using this flap. RESULTS: The blood supply for the dorsum of the first web comprised the dorsal perforators from both the dorsal artery (the branch of the first dorsal metacarpal artery) and palmar artery (the radial palmar digital artery of the index finger and the ulnar palmar digital artery of the thumb). The first dorsal metacarpal artery constantly arose from the radial artery and was divided into the radial, ulnar and medial branches. The palmar artery sent out 1-2 perforators and formed a constant anastomosis with the medial branch of the first dorsal metacarpal artery to supply the dorsal skin of the first web. In clinical application, all the flaps survived completely without contracture of the first web or other complications and the donor regions all healed at the first stage. CONCLUSION: The dorsal perforator flap based on the palmar artery in the first web is useful to repair soft-tissue defects of the thumb, the proximal phalanx of the index finger and thenar region, leading to a satisfactory appearance and good functional and sensory recovery.

The little elongation complex regulates small nuclear RNA transcription.

Eleven-nineteen lysine-rich leukemia (ELL) participates in the super elongation complex (SEC) with the RNA polymerase II (Pol II) CTD kinase P-TEFb. SEC is a key regulator in the expression of HOX genes in mixed lineage leukemia (MLL)-based hematological malignancies, in the control of induced gene expression early in development, and in immediate early gene transcription. Here, we identify an SEC-like complex in Drosophila, as well as a distinct ELL-containing complex that lacks P-TEFb and other components of SEC named the "little elongation complex" (LEC). LEC subunits are highly enriched at RNA Pol II-transcribed small nuclear RNA (snRNA) genes, and the loss of LEC results in decreased snRNA expression in both flies and mammals. The specialization of the SEC and LEC complexes for mRNA and snRNA-containing genes, respectively, suggests the presence of specific classes of elongation factors for each class of genes transcribed by RNA polymerase II.

Selective Late-Stage Oxygenation of Sulfides with Ground-State Oxygen by Uranyl Photocatalysis.

Oxygenation is a fundamental transformation in synthesis. Herein, we describe the selective late-stage oxygenation of sulfur-containing complex molecules with ground-state oxygen under ambient conditions. The high oxidation potential of the active uranyl cation (UO22+ ) enabled the efficient synthesis of sulfones. The ligand-to-metal charge transfer process (LMCT) from O 2p to U 5f within the O=U=O group, which generates a UV center and an oxygen radical, is assumed to be affected by the solvent and additives, and can be tuned to promote selective sulfoxidation. This tunable strategy enabled the batch synthesis of 32 pharmaceuticals and analogues by late-stage oxygenation in an atom- and step-efficient manner.

Anatomical Basis of the Intermediate Dorsal Pedal Neurocutaneous Perforator Pedicled Propeller Flap: A Cadaveric Dissection.

Soft tissue defects of the forefoot represent a challenging surgical modality to reconstructive microsurgeons. This study describes the anatomical basis and design of the perforator-based intermediate dorsal pedal neurocutaneous vascular flap. Thirty fresh human lower limb specimens were injected with red latex and used for dissection of the dorsal vascular and neural anatomy of the foot. The direction and distribution of the intermediate dorsal cutaneous nerve and the vascular anatomy of the third dorsal artery of the plantar arch, along with the intermediate dorsal neurocutaneous nutrient vessels, were mapped. A simulated flap elevation procedure was performed on one fresh cadaver specimen. A clinical series of five cases is presented to demonstrate the feasibility of using the perforator-based intermediate dorsal pedal neurocutaneous vascular flap to reconstruct soft-tissue defects of the forefoot. The intermediate dorsal cutaneous nerve usually originates from the lateral branch of the superficial peroneal nerve. Crossing the surface of the cruciate ligament, it descends distally to the proximal part of the fourth intermetatarsal space and divides into the third and fourth dorsal metatarsal branches. The intermediate dorsal cutaneous neural nutrient vessels, which are multi-segmental and polyphyletic, offer innervation to the skin paddle of the flap elevated on the basis of the third dorsal perforator of the plantar arch. This perforator occupies a relatively constant position in the proximal part of the intermetatarsal space. It sends multiple tiny branches toward the intermediate dorsal cutaneous neural or paraneural nutrient vessel chain. In terms of clinical application, all flaps survived completely; one patient had partial loss of the skin graft. The design and anatomical basis of the intermediate dorsal pedal neurocutaneous vascular flap based on the third dorsal perforator of the plantar arch is a reliable reconstructive option for reconstructing small soft tissue defects in the forefoot. Clin. Anat. 31:1077-1084, 2018. © 2018 Wiley Periodicals, Inc.

DOT1L/H3K79me2 represses HIV-1 reactivation via recruiting DCAF1.

DOT1L mediates the methylation of histone H3 at lysine 79 and, in turn, the transcriptional activation or repression in a context-dependent manner, yet the regulatory mechanisms and functions of DOT1L/H3K79me remain to be fully explored. Following peptide affinity purification and proteomic analysis, we identified that DCAF1-a component of the E3 ligase complex involved in HIV regulation-is associated with H3K79me2 and DOT1L. Interestingly, blocking the expression or catalytic activity of DOT1L or repressing the expression of DCAF1 significantly enhances the tumor necrosis factor alpha (TNF-α)/nuclear factor κB (NF-κB)-induced reactivation of the latent HIV-1 genome. Mechanistically, upon TNF-α/NF-κB activation, DCAF1 is recruited to the HIV-1 long terminal repeat (LTR) by DOT1L and H3K79me2. Recruited DCAF1 subsequently induces the ubiquitination of NF-κB and restricts its accumulation at the HIV-1 LTR. Altogether, our findings reveal a feedback modulation of HIV reactivation by DOT1L-mediated histone modification regulation and highlight the potential of targeting the DOT1L/DCAF1 axis as a therapeutic strategy for HIV treatment.

PRMT2 promotes HIV-1 latency by preventing nucleolar exit and phase separation of Tat into the Super Elongation Complex.

The HIV-1 Tat protein hijacks the Super Elongation Complex (SEC) to stimulate viral transcription and replication. However, the mechanisms underlying Tat activation and inactivation, which mediate HIV-1 productive and latent infection, respectively, remain incompletely understood. Here, through a targeted complementary DNA (cDNA) expression screening, we identify PRMT2 as a key suppressor of Tat activation, thus contributing to proviral latency in multiple cell line latency models and in HIV-1-infected patient CD4+ T cells. Our data reveal that the transcriptional activity of Tat is oppositely regulated by NPM1-mediated nucleolar retention and AFF4-induced phase separation in the nucleoplasm. PRMT2 preferentially methylates Tat arginine 52 (R52) to reinforce its nucleolar sequestration while simultaneously counteracting its incorporation into the SEC droplets, thereby leading to its functional inactivation to promote proviral latency. Thus, our studies unveil a central and unappreciated role for Tat methylation by PRMT2 in connecting its subnuclear distribution, liquid droplet formation, and transactivating function, which could be therapeutically targeted to eradicate latent viral reservoirs.