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PubMed1998

Chromatin, TAFs, and a novel multiprotein coactivator are required for synergistic activation by Sp1 and SREBP-1a in vitro.

The promoter selectivity factor Sp1 often cooperates with other enhancer-binding proteins to activate transcription. To study the molecular underpinnings of these regulatory events, we have reconstituted in vitro the synergy observed in vivo between Sp1 and the sterol-regulated factor SREBP-1a at the low density lipoprotein receptor (LDLR) promoter. Using a highly purified human transcription system, we found that chromatin, TAFs, and a novel SREBP-binding coactivator activity, which includes CBP, are all required to mediate full synergistic activation by Sp1 and SREBP-1a. The SREBP-binding domain of CBP inhibits activation by SREBP-1a and Sp1 in a dominant-negative fashion that is both chromatin- and activator-specific. Whereas recombinant CBP alone is not sufficient to mediate activation, a human cellular fraction containing CBP can support high levels of chromatin-dependent synergistic activation. Purification of this activity to near homogeneity resulted in the identification of a multiprotein coactivator, including CBP, that selectively binds to the SREBP-1a activation domain and is capable of mediating high levels of synergistic activation by SREBP/Sp1 on chromatin templates. The development of a reconstituted chromatin transcription system has allowed us to isolate a novel coactivator that is recruited by the SREBP-1a activation domain and that functions in concert with TFIID to coordinate the action of multiple activators at complex promoters in the context of chromatin.

Animals↗
PubMed1992

Molecular dissection of a specific nuclear domain: the chromatin region of the ribosomal gene cluster in Xenopus laevis.

Molecular dissection of the nuclear domain corresponding to the ribosomal chromatin cluster was investigated. The experimental scheme was based on the ability of restriction enzymes to digest the whole genome without affecting this region (several megabases in length). Such a strategy involved the judicious choice of restriction enzymes, which is possible in Xenopus laevis, where the rDNA sequence is known and the repeated units are organized into one unique cluster. SalI, XhoI, and EcoRV digestion produced frequent cutting of the genome leaving the ribosomal cluster intact. Isolation of the rDNA cluster was confirmed by separation of the digested DNA by pulsed-field electrophoresis. When applied to purified nuclei, this approach allowed the isolation of the ribosomal chromatin cluster under very mild conditions: no cleavages (either enzymatic or mechanical) were detectable. Since the purification scheme depends only on the DNA sequence outside of the rDNA cluster, it permits the obtention of this domain in different functional states. Electron microscopic analysis demonstrated that the domain organization is substantially preserved and maintains its looped organization (the size and the full number of loops were preserved). This purification scheme provides a powerful tool for studying the structure-function relationships within the ribosomal nuclear domain.

Animals↗
PubMed1998

Sequence determinants of DNA binding by the hematopoietic helix-loop-helix transcription factor TAL1: importance of sequences flanking the E-box core.

TAL1 is a helix-loop-helix transcription factor that is essential for hematopoiesis. In vitro DNA binding site selection experiments have previously identified the preferred binding site for TAL1 heterodimers as AACAGATGGT. TAL1 homodimers do not bind DNA with significant affinity. A subset of other E-box sequences is also bound by TAL1 heterodimers. Here, we present an analysis of TAL1 heterodimer DNA binding specificity, using E-boxes derived from genomic clones, which were isolated by immunoadsorption of K562 erythroleukemia cell chromatin with a TAL1 antibody. We show that TAL1 heterodimer binding to a CAGATG E-box is strongly modulated by nucleotides flanking the E-box. A 10 base pair element consisting of the CAGATG E-box and two flanking nucleotides in both the 5' and 3' direction is sufficient for high-affinity binding. Certain mutations of nucleotides in either the 5' (-1 and -2) or 3' (+1 and +2) direction strongly inhibit binding. The importance of flanking nucleotides also exists in the context of nonpreferred E-boxes recognized by TAL1 heterodimers. Although there are no known target genes for TAL1, the regulatory regions of several genes involved in hematopoiesis contain the preferred E-box CAGATG. However, based on our results, the E-boxes in these potential target genes contain flanking sequences that would be expected to significantly reduce TAL1 heterodimer binding in vitro. Thus, additional stabilizing forces, such as protein-protein interactions between TAL1 heterodimers and accessory factors, may be required to confer high-affinity TAL1 heterodimer binding to such sequences.

Animals↗
PubMed1977

Regular folding chain conformation of the deoxyribonucleic acid in chromatin. X-ray diffraction and selforganization.

The following model is proposed for the structure of deoxyribonucleic acid (DNA) in chromatin: The DNA in a nucleosome is folded seven times to and fro on the surface of a cylindrical protein nucleus. There exist 3.5 DNA hairpins. The seven arms of the hairpins contain twenty DNA base pairs each. The six loops of the DNA hairpins contain ten DNA base pairs each. Consistently with the experiment, the model gives X-ray small-angle diffraction reflexes at 10.5 nm, 5.5 nm, 3.6 nm. The X-ray larg-angle diagram can also be interpreted by the model. Folding crystallization is the mechanism of supramolecular selfassembly giving condensation of DNA in the chromatin.

Chromatin↗
PubMed2003

Smooth muscle alpha-actin gene requires two E-boxes for proper expression in vivo and is a target of class I basic helix-loop-helix proteins.

Changes in the differentiated state of smooth muscle cells (SMCs) play a key role in vascular diseases, yet the mechanisms controlling SMC differentiation are still largely undefined. We addressed the role of basic helix-loop-helix (bHLH) proteins in SMC differentiation by first determining the role of two E-box (CAnnTG) motifs, binding sites for bHLH proteins, in the transcriptional regulation of the SMC differentiation marker gene, smooth muscle alpha-actin (SM alpha-actin), in vivo. Mutation of one or both E-boxes significantly reduced the expression of a -2560- to 2784-bp SM alpha-actin promoter/LacZ reporter gene in vivo in transgenic mice. We then determined the potential role of class I bHLH proteins, E12, E47, HEB, and E2-2, in SM alpha-actin regulation. In cotransfection experiments, E12, HEB, and E2-2 activated the SM alpha-actin promoter. Activation by HEB and E2-2 was synergistic with serum response factor. Additionally, the dominant-negative/inhibitory HLH proteins, Id2, Id3, and Twist, inhibited both the E12 and serum response factor-induced activations of the SM alpha-actin promoter. Finally, we demonstrated that E2A proteins (E12/E47) specifically bound the E-box-containing region of the SM alpha-actin promoter in vivo in the context of intact chromatin in SMCs. Taken together, these results provide the first evidence of E-box-dependent regulation of a SMC differentiation marker gene in vivo in transgenic mice. Moreover, they demonstrate a potential role for class I bHLH factors and their inhibitors, Id and Twist, in SM alpha-actin regulation and suggest that these factors may play an important role in control of SMC differentiation and phenotypic modulation.

3T3 Cells↗
PubMed2005

CLOCK is involved in the circadian transactivation of peroxisome-proliferator-activated receptor alpha (PPARalpha) in mice.

PPARalpha (peroxisome-proliferator-activated receptor alpha) is a member of the nuclear receptor superfamily of ligand-activated transcription factors that regulate the expression of genes associated with lipid metabolism. In the present study, we show that circadian expression of mouse PPARalpha mRNA requires the basic helix-loop-helix PAS (Per-Arnt-Sim) protein CLOCK, a core component of the negative-feedback loop that drives circadian oscillators in mammals. The circadian expression of PPARalpha mRNA was abolished in the liver of homozygous Clock mutant mice. Using wild-type and Clock-deficient fibroblasts derived from homozygous Clock mutant mice, we showed that the circadian expression of PPARalpha mRNA is regulated by the peripheral oscillators in a CLOCK-dependent manner. Transient transfection and EMSAs (electrophoretic mobility-shift assays) revealed that the CLOCK-BMAL1 (brain and muscle Arnt-like protein 1) heterodimer transactivates the PPARalpha gene via an E-box-rich region located in the second intron. This region contained two perfect E-boxes and four E-box-like motifs within 90 bases. ChIP (chromatin immunoprecipitation) also showed that CLOCK associates with this E-box-rich region in vivo. Circadian expression of PPARalpha mRNA was intact in the liver of insulin-dependent diabetic and of adrenalectomized mice, suggesting that endogenous insulin and glucocorticoids are not essential for the rhythmic expression of the PPARalpha gene. These results suggested that CLOCK plays an important role in lipid homoeostasis by regulating the transcription of a key protein, PPARalpha.

ARNTL Transcription Factors↗
PubMed2005

In vivo transcriptional regulation of N-Myc target genes is controlled by E-box methylation.

N-Myc is a transcription factor that forms heterodimers with the protein Max and binds gene promoters by recognizing a DNA sequence, CACGTG, called E-box. The identification of N-myc target genes is an important step for understanding N-Myc biological functions in both physiological and pathological contexts. In this study, we describe the identification of N-Myc-responsive genes through chromatin immunoprecipitation and methylation-sensitive restriction analysis. Results show that N-Myc is a direct regulator of several identified genes, and that methylation of the CpG dinucleotide within the E-box prevents the access of N-Myc to gene promoters in vivo. Furthermore, methylation profile of the E-box within the promoters of EGFR and CASP8, two genes directly controlled by Myc, is cell type-specific, suggesting that differential E-box methylation may contribute to generating unique patterns of Myc-dependent transcription. This study illuminates a central role of DNA methylation in controlling N-Myc occupancy at gene promoters and modulating its transcriptional activity in cancer cells.

Basic Helix-Loop-Helix Leucine Zipper Transcriptio↗
PubMed2007

Detection of chromatin-associated single-stranded DNA in regions targeted for somatic hypermutation.

After encounter with antigen, the antibody repertoire is shaped by somatic hypermutation (SHM), which leads to an increase in the affinity of antibodies for the antigen, and class-switch recombination (CSR), which results in a change in the effector function of antibodies. Both SHM and CSR are initiated by activation-induced cytidine deaminase (AID), which deaminates deoxycytidine to deoxyuridine in single-stranded DNA (ssDNA). The precise mechanism responsible for the formation of ssDNA in V regions undergoing SHM has yet to be experimentally established. In this study, we searched for ssDNA in mutating V regions in which DNA-protein complexes were preserved in the context of chromatin in human B cell lines and in primary mouse B cells. We found that V regions that undergo SHM were enriched in short patches of ssDNA, rather than R loops, on both the coding and noncoding strands. Detection of these patches depended on the presence of DNA-associated proteins and required active transcription. Consistent with this, we found that both DNA strands in the V region were transcribed. We conclude that regions of DNA that are targets of SHM assemble protein-DNA complexes in which ssDNA is exposed, making it accessible to AID.

Animals↗
PubMed2026

One chromatin, many structures: From ensemble contact maps to single-cell 3D organization.

Understanding how chromatin folds in three dimensions remains challenging because most experimental assays capture low-dimensional projections of an underlying, highly heterogeneous polymer. Here, we present an ensemble-based interpretive framework built on the previously introduced Self-Returning Excluded Volume (SR-EV) model, a minimal generator of chromatin conformations using a nucleosome-indexed coarse-grained representation based on stochastic return rules and excluded-volume geometry. Despite its simplicity, SR-EV recapitulates key experimental signatures across scales: heterogeneous nanoscale packing domains resembling ChromEMT and ChromSTEM observations, sparse and highly variable single-configuration contact patterns analogous to single-cell chromosome conformation capture (Hi-C), and robust ensemble-level contact enrichment consistent with topologically associating domains (TADs). In this framework, Hi-C loop and TAD signatures are interpreted as ensemble-level statistical enrichments rather than invariant features of single-cell conformations. SR-EV is explicitly designed to generate large ensembles of complete three-dimensional chromatin configurations that can be projected consistently onto two-dimensional contact maps and one-dimensional genomic profiles. By introducing architectural-protein effects only through ensemble selection rather than explicit forces, SR-EV supports a separation between intrinsic polymer geometry and regulatory bias and suggests that TAD-like features can emerge as statistical enrichments rather than deterministic three-dimensional structures. Coordination number and probe-based accessibility computed directly from SR-EV provide a unified link between three-dimensional packing, two-dimensional contact maps, and one-dimensional genomic profiles. The main contribution of this work is to show, within a single coarse-grained framework, how these multimodal observables arise as linked projections of the same heterogeneous chromatin ensemble through averaging and conditional sampling. Together, these results establish SR-EV as a minimal and geometrically grounded mesoscale reference framework for interpreting how heterogeneous chromatin ensembles give rise to multimodal experimental observables while remaining consistent with the fact that chromatin organization is realized in individual cells.

Chromatin↗
PubMed1997

V3 loop of human immunodeficiency virus type 1 suppresses interleukin 2-induced T cell growth.

We tested the effect of three linear or two loop peptides derived from the V3 region of the HTLV-III BH10 clone or the SF2 strain of human immunodeficiency virus type 1 on IL-2-driven T cell proliferation. V3-BH10, which consists of 42 amino acids and has a loop structure, suppressed IL-2-driven proliferation of all IL-2-dependent cells [Kit225, ED-40515(+), KT-3, 7-day PHA-blasts, and fresh peripheral blood mononuclear cells] tested, whereas it did not suppress the cell growth of IL-2-independent cell lines (Hut102, Molt-4, and Jurkat). This suppressive effect was also seen in IL-2-driven cell growth of CD8-positive lymphocytes purified from 7-day PHA-blasts, indicating that CD4 molecules were not required for the suppression. The treatment with anti-V3 loop monoclonal antibody (902 antibody) completely abolished the suppressive effect of V3-BH10. In addition, V3-BH10 generated the arrest of Kit225 cells and also purified CD8-positive lymphocytes in G1 phase in the presence of IL-2. Neither chromatin condensation nor DNA fragmentation was detected in Kit225 cells cultured with V3-BH10 and IL-2. V3-BH10 neither blocked radiolabeled IL-2 binding to IL-2 receptors nor affected tyrosyl phosphorylation of several cellular proteins (p120, p98, p96, p54, and p38), which is immediately induced by IL-2 stimulation. However, V3-BH10 enhanced IL-2-induced mRNA expression of c-fos but not c-myc or junB. Thus, the binding of V3 loop of gp120 to the cell surface molecule(s) appears to affect intracellular IL-2 signaling, which leads to the suppression of IL-2-induced T cell growth.

Amino Acid Sequence↗
PubMed2000

Uteroglobin gene transcription: what's the RUSH?

Prolactin enhances progesterone-dependent transcription of the rabbit uteroglobin gene. RUSH transcription factors are implicated in the signal transduction pathway. The RUSH acronym identifies key features of these nuclear phosphoproteins, that is, RING-finger motif, binds the uteroglobin promoter, structurally related to the SWI/SNF family of transcription factors, and helicase-like. Cloned by recognition site screening, RUSH proteins bind to an 85-bp region (-170/-85) of the uteroglobin promoter that was subsequently identified as a novel prolactin-responsive region by promoter deletion analysis. Gel shift and linker-scanning assays further reduced the RUSH target site to -160/-110. A hexameric core of MCWTDK was identified as the RUSH-specific DNA-binding site (-126/-121) by CASTing. This site overlaps authentic HNF3 beta and OCT-1 binding sites. A unique Type IV P-type ATPase that is embedded in the inner nuclear membrane binds the RING domain of RUSH. The conformationally flexible loop portion of this RING-finger binding protein (RFBP) extends into the nucleoplasm to contact euchromatin. The physical association of RFBP with transcriptionally active chromatin supports the speculation that RFBP targets RUSH transcription factors to the active uteroglobin promoter.

Animals↗
PubMedDate not supplied

Microscopic postmortem changes in kidneys of the domestic fowl.

Eighty-four male white leghorn chickens were killed by CO2 gas to determine the type, rate, and sequence of postmortem microscopic changes in the kidneys of dry and wet intact carcasses. They were held at 29 or 18 C with 50% relative humidity for different times postmortem. Microscopic postmortem changes in the different segments of the nephron underwent a different rate and sequence of cellular changes. Cellular changes occurred earlier at 29 C than at 18 C and earlier in chickens not wetted with detergent solution. The decrease in body temperature of wetted chickens over dry chickens was significant (P less than 0.05). The proximal convoluted tubule (PCT) underwent the earliest postmortem changes, followed by the distal convoluted tubule (DCT), collecting tubule (CT), medullary loop (ML), medullary collecting duct (MCD), and glomerulus. The PCT, DCT, and thin and thick segments of the ML underwent a sequential nuclear change of chromatin margination, progressive shrinkage, pyknosis, karyorrhexis, and karyolysis. Nuclei were pyknotic if cytoplasmic changes were severe. Primary karyorrhexis was the predominant feature of collecting tubules and ducts. As early as one hour after death, some PCT cells of all kidney sections were pyknotic, emphasizing that immediate tissue fixation was necessary for critical evaluation. By 9 and 18 hr postmortem, PCT of dry and wet chickens, respectively, held at 29 C had pyknotic and karyorrhectic nuclei with slight karyolysis and moderate to marked cytoplasmolysis that extended until 36 hr. At this time, DCT were hardly distinguishable because of loss of basophilia. Karyorrhectic nuclei were already evident in collecting tubules and ducts. At 48 hr postmortem, all tubular cells were non-nucleated with homogeneous, acidophilic cytoplasm. Basement membranes no longer stained with periodic acid-Schiff (PAS). Erythrocytes were pyknotic with unstained cytoplasm. Pyknotic glomeruli were first observed at 9 hr postmortem in dry chickens and 12 hr in wet chickens. Histologic appearance of dry chickens at 9 hr and wet chickens at 18 hr when held at 29 C was similar to that of dry chickens at 12 hr and wet chickens at 24 hr when held at 18 C, with minor differences in some tubular changes. At 18 C, pyknotic glomeruli appeared by 6 hr in dry chickens and 24 hr in wet chickens. Widespread bacterial invasion was noted at 72 hr in dry chickens and at 96 hr in wet chickens.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2006

KSHV RTA induces a transcriptional repressor, HEY1 that represses rta promoter.

Kaposi's sarcoma-associated herpesvirus (KSHV) is a gamma-herpesvirus that is frequently associated with the formation of tumors like Kaposi's sarcoma and primary effusion lymphomas. KSHV RTA is required for lytic replication/reactivation in KSHV-infected cells. We developed an inducible RTA expression cell line to search for RTA-inducible genes. Using DNA chip technology, we showed that hey1, a basic helix-loop-helix-containing transcription factor, increased three- to fourfold in this line. In a luciferase reporter system, RTA activated the hey1 promoter in several cell lines; conversely, HEY1 repressed the rta promoter. Chromatin immunoprecipitation assays indicated that HEY did not bind the rta promoter directly, although it may repress rta expression as part of a complex. Thus, hey1 may help to downregulate RTA after its burst of expression during lytic replication/reactivation. Similar repression mechanisms may downregulate immediate-early gene expression in other herpesviruses, although different transcription factors are probably involved.

Animals↗
PubMed2001

The Usf-1 transcription factor is a novel target for the stress-responsive p38 kinase and mediates UV-induced Tyrosinase expression.

The stress-activated signalling cascade leading to phosphorylation of the p38 family of kinases plays a crucial role during development and in the cellular response to a wide variety of stress-inducing agents. Although alterations in gene expression characteristic of the stress response require the regulation of key transcription factors by the p38 family, few downstream targets for this signalling pathway have been identified. By examining the ability of pigment cells to respond to UV irradiation as part of the UV-induced tanning response, we show that while the microphthalmia-associated transcription factor Mitf regulates basal Tyrosinase expression, it is the ubiquitous basic helix-loop-helix-leucine zipper transcription factor Usf-1 that is required for the UV activation of the Tyrosinase promoter. Consistent with this we demonstrate that Usf-1 is phosphorylated and activated by the stress-responsive p38 kinase. The results suggest that activation of Usf-1 by p38 at a wide variety of viral and cellular promoters will provide a link between stimuli as diverse as UV irradiation, glucose, viral infection and pro-inflammatory cytokines, and the changes in gene expression associated with the stress response.

3T3 Cells↗
PubMed1975

Observations on the male nucleus during fertilization in the fern Pteridium aquilinum.

Fertilization of eggs of Pteridium under controlled conditions has revealed that archegonia containing viable eggs require more than 30 min flooding before opening. Syngamy appears to take place by an engulfing action, and no evidence was found of a 'membrane-fusion' kind of conjugation. Although the gametic nucleus lacks a recognizable envelope, as soon as it comes into contact with the female cytoplasm an envelope is reconstituted from an opaque layer at the surface of its chromatin. This membrane also undergoes growth, the outer layer extending into the cytoplasm and surrounding spermatozoid mitochondria. The male envelope remains distinct from the female, and lacks evaginations and well defined pores. The male nucleus lies in irregular loops within a funnel, filled with egg cytoplasm, formed by the microtubular ribbon of the gamete. The mouth of the funnel is bordered by the multi-layered structure. Karyogamy is initiated at the anterior end of the male nucleus, the orifice connecting the 2 nuclei widening from about 0-1 to 2 mum in diameter during fusion. The contents of the male nucleus flow through the mouth of the funnel into the female, the chromatin relaxing locally, but retaining a rod-like form. The envelope of the male nucleus is probably resorbed at the site of junction. There is no evidence that it contributes significantly to the envelope of the zygotic nucleus.

Cell Nucleus↗
PubMed1993

Scanning electron microscopy of polytene chromosomes (I).

The structure of polytene chromosomes has been observed by conventional scanning electron microscopy and also with a high resolution 'in lens' field emission instrument. Surface imaging with secondary electron emission has characterized condensed chromatin and regions known for their RNA synthetic potential (nucleoli, Balbiani rings and puffs). In DNA-rich bands pairing of chromatids appears so perfect that individual chromomeres cannot be visualized as discrete units. In the interbands only chromatid bundles appear as elements, but not individual chromatids. High resolution scanning electron microscopy allows resolution at the nucleosome level. Improved localization of chromosomal structures is demonstrated, as in the case of the proposed separation of the prepupal 'Balbiani ring 1'. Surface images of the RNA synthetic centres of the salivary gland cell are presented. Transcripts of the Balbiani ring template can be observed in the condensed and gradually unfolded state, allowing measurement of unit ribonucleoparticles. The surfaces of puffs have been visualized and are characterized by multiple supercoiled loop structures, which are described according to size, conformation and distribution.

Animals↗
PubMed2005

Modulation of the expression and transactivation of androgen receptor by the basic helix-loop-helix transcription factor Pod-1 through recruitment of histone deacetylase 1.

Androgen receptor (AR) is important in male sexual differentiation and testicular function. Here, we demonstrate the regulation of AR expression and its transactivation by the basic helix-loop-helix (bHLH) transcription factor Pod-1, the expression of which in postnatal testis reciprocally coincides with the expression of AR. Pod-1 represses the promoter activity of AR, possibly through its E-box. An AR promoter region of 169 bp, which harbors one canonical E-box, is sufficient for the Pod-1-repression and bound by purified Pod-1 proteins. Pod-1 also suppresses the transactivation of AR. Transient transfection analyses of mammalian cells show that Pod-1 represses AR transactivation in a dose-dependent manner. Furthermore, yeast two-hybrid, glutathione-S-transferase-pull-down, and co-immunoprecipitation analyses reveal that Pod-1 directly associates with AR through its N-terminal region and through the DNA binding-hinge domain of AR. Interestingly, Pod-1 recruits histone deacetylase (HDAC)-1 to inhibit both promoter activity and transactivation of AR. Overexpression of HDAC1 further inhibits the Pod-1-mediated repressions and Pod-1 directly interacts with HDAC1. Furthermore, chromatin immunoprecipitation assay reveals that HDAC1 is recruited with Pod-1 to the endogenous AR promoter and the androgen-regulated Pem promoter. Taken together, these results suggest that Pod-1, which controls AR transcription and function, may play an important role in the development and function of the testis.

Animals↗
PubMed2004

The chromatin remodeler Mi-2beta is required for CD4 expression and T cell development.

Changes in chromatin structure underlie the activation or silencing of genes during development. The chromatin remodeler Mi-2beta is highly expressed in thymocytes and is presumed to be a transcriptional repressor because of its presence in the nucleosome remodeling deacetylase (NuRD) complex. Using conditional inactivation, we show that Mi-2beta is required at several steps during T cell development: for differentiation of beta selected immature thymocytes, for developmental expression of CD4, and for cell divisions in mature T cells. We further show that Mi-2beta plays a direct role in promoting CD4 gene expression. Mi-2beta associates with the CD4 enhancer as well as the E box binding protein HEB and the histone acetyltransferase (HAT) p300, enabling their recruitment to the CD4 enhancer and causing histone H3-hyperacetylation to this regulatory region. These findings provide important insights into the regulation of CD4 expression during T cell development and define a role for Mi-2beta in gene activation.

Acetyltransferases↗