Qing Dai - Academia.edu (original) (raw)

Papers by Qing Dai

Nature Biotechnology, 2024

Small, 2014

The blood‐brain barrier (BBB) remains a formidable obstacle in medicine, preventing efficient pen... more The blood‐brain barrier (BBB) remains a formidable obstacle in medicine, preventing efficient penetration of chemotherapeutic and diagnostic agents to malignant gliomas. Here, a transactivator of transcription (TAT) peptide‐modified gold nanoparticle platform (TAT‐Au NP) with a 5 nm core size is demonstrated to be capable of crossing the BBB efficiently and delivering cargoes such as the anticancer drug doxorubicin (Dox) and Gd3+ contrast agents to brain tumor tissues. Treatment of mice bearing intracranial glioma xenografts with pH‐sensitive Dox‐conjugated TAT‐Au NPs via a single intravenous administration leads to significant survival benefit when compared to the free Dox. Furthermore, it is demonstrated that TAT‐Au NPs are capable of delivering Gd3+ chelates for enhanced brain tumor imaging with a prolonged retention time of Gd3+ when compared to the free Gd3+ chelates. Collectively, these results show promising applications of the TAT‐Au NPs for enhanced malignant brain tumor th...

Human molecular genetics, Jun 9, 2016

Alzheimer's disease (AD) is a chronic neurodegenerative disorder characterized by progressive... more Alzheimer's disease (AD) is a chronic neurodegenerative disorder characterized by progressive deterioration of cognitive function. Pathogenesis of AD is incompletely understood; evidence suggests a role for epigenetic regulation, in particular the cytosine modifications 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). 5hmC is enriched in the nervous system and displays neurodevelopment and age-related changes. To determine the role of 5hmC in AD, we performed genome-wide analyses of 5hmC in DNA from prefrontal cortex of post-mortem AD patients, and RNA-Seq to correlate changes in 5hmC with transcriptional changes. We identified 325 genes containing differentially hydroxymethylated loci (DhMLs) in both discovery and replication datasets. These are enriched for pathways involved in neuron projection development and neurogenesis. Of these, 140 showed changes in gene expression. Proteins encoded by these genes form direct protein-protein interactions with AD-associated gen...

Nature, Jan 10, 2016

Gene expression can be regulated post-transcriptionally through dynamic and reversible RNA modifi... more Gene expression can be regulated post-transcriptionally through dynamic and reversible RNA modifications. A recent noteworthy example is N(6)-methyladenosine (m(6)A), which affects messenger RNA (mRNA) localization, stability, translation and splicing. Here we report on a new mRNA modification, N(1)-methyladenosine (m(1)A), that occurs on thousands of different gene transcripts in eukaryotic cells, from yeast to mammals, at an estimated average transcript stoichiometry of 20% in humans. Employing newly developed sequencing approaches, we show that m(1)A is enriched around the start codon upstream of the first splice site: it preferentially decorates more structured regions around canonical and alternative translation initiation sites, is dynamic in response to physiological conditions, and correlates positively with protein production. These unique features are highly conserved in mouse and human cells, strongly indicating a functional role for m(1)A in promoting translation of meth...

Journal of the American Chemical Society, Dec 15, 2017

RNA labeling is crucial for the study of RNA structure and metabolism. Herein we report N6-allyla... more RNA labeling is crucial for the study of RNA structure and metabolism. Herein we report N6-allyladenosine (a6A) as a new small molecule for RNA labeling through both metabolic and enzyme-assisted manners. a6A behaves like A and can be metabolically incorporated into newly synthesized RNAs inside mammalian cells. We also show that human RNA N6-methyladenosine (m6A) methyltransferases METTL3/METTL14 can work with a synthetic cofactor, namely allyl-SAM (S-adenosyl methionine with methyl replaced by allyl) in order to site-specifically install an allyl group to the N6-position of A within specific sequence to generate a6A-labeled RNAs. The iodination of N6-allyl group of a6A under mild buffer conditions spontaneously induces the formation of N1,N6-cyclized adenosine and creates mutations at its opposite site during complementary DNA synthesis of reverse transcription. The existing m6A in RNA is inert to methyltransferase-assisted allyl labeling, which offers a chance to differentiate m6...

Angewandte Chemie (International ed. in English), Jan 24, 2017

The abundant Watson-Crick face methylations in biological RNAs such as N(1) -methyladenosine (m(1... more The abundant Watson-Crick face methylations in biological RNAs such as N(1) -methyladenosine (m(1) A), N(1) -methylguanosine (m(1) G), N(3) -methylcytosine (m(3) C), and N(2) ,N(2) -dimethylguanosine (m(2)2 G) cause significant obstacles for high-throughput RNA sequencing by impairing cDNA synthesis. One strategy to overcome this obstacle is to remove the methyl group on these modified bases prior to cDNA synthesis using enzymes. The wild-type E. coli AlkB and its D135S mutant can remove most of m(1) A, m(1) G, m(3) C modifications in transfer RNA (tRNA), but they work poorly on m(2)2 G. Here we report the design and evaluation of a series of AlkB mutants against m(2)2 G-containing model RNA substrates that we synthesize using an improved synthetic method. We show that the AlkB D135S/L118V mutant efficiently and selectively converts m(2)2 G modification to N(2) -methylguanosine (m(2) G). We also show that this new enzyme improves the efficiency of tRNA sequencing.

Nucleic acids research, Jan 25, 2017

N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNA (... more N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA), and affects almost every stage of the mRNA life cycle. The YTH-domain proteins can specifically recognize m6A modification to control mRNA maturation, translation and decay. m6A can also alter RNA structures to affect RNA-protein interactions in cells. Here, we show that m6A increases the accessibility of its surrounding RNA sequence to bind heterogeneous nuclear ribonucleoprotein G (HNRNPG). Furthermore, HNRNPG binds m6A-methylated RNAs through its C-terminal low-complexity region, which self-assembles into large particles in vitro. The Arg-Gly-Gly repeats within the low-complexity region are required for binding to the RNA motif exposed by m6A methylation. We identified 13,191 m6A sites in the transcriptome that regulate RNA-HNRNPG interaction and thereby alter the expression and alternative splicing pattern of target mRNAs. Low-complexity regions are pervasive among mRNA bindin...

Human molecular genetics, Jun 22, 2016

Preeclampsia and gestational diabetes mellitus (GDM) are the most common clinical conditions in p... more Preeclampsia and gestational diabetes mellitus (GDM) are the most common clinical conditions in pregnancy that could result in adversein uteroenvironments. Fetal exposure to poor environments may raise the long-term risk of postnatal disorders, while epigenetic modifications could be involved. Recent research has implicated involvement of 5-hydroxymethylcytosine (5hmC), a DNA base derived from 5-methylcytosine (5mC), via oxidation by ten-eleven translocation (TET) enzymes, in DNA methylation-related plasticity. Here we show that the TET2 expression and 5hmC abundance are significantly altered in the umbilical veins of GDM and preeclampsia. Genome-wide profiling of 5hmC revealed its specific reduction on intragenic regions from both GDM and preeclampsia compared to healthy controls. Gene Ontology analysis using loci bearing unique GDM- and preeclampsia-specific loss-of-5hmC indicated its impact on several critical biological pathways. Interestingly, the substantial alteration of 5hmC...

Journal of Pharmacology and Experimental Therapeutics, 2008

British Journal of Pharmacology, 2011

BACKGROUND AND PURPOSE Potent synthetic nonsteroidal liver X receptor (LXR) agonists like T090131... more BACKGROUND AND PURPOSE Potent synthetic nonsteroidal liver X receptor (LXR) agonists like T0901317 induce triglyceridaemia and fatty liver, effects not observed with some natural and synthetic steroidal, relatively weak agonists of LXR. To determine if potency is responsible for the lack of side effects with some steroidal agonists, we investigated the in vivo effects of a novel steroidal LXR agonist, ATI-111, that is more potent than T0901317. EXPERIMENTAL APPROACH Eight week old male LDLR-/mice fed an atherogenic diet were orally treated with vehicle or ATI-111 at 3 and 5 mg•kg-1 •day-1 for 8 weeks, and effects on plasma and liver lipid levels, expression of genes involved in lipid metabolism and on atherogenesis were analysed. KEY RESULTS ATI-111 increased the expression of genes involved in lipid transport, such as ABCA1, ABCG1 and ABCG5/G8, in intestine and macrophages; decreased ABCG1, apoE; and slightly increased ABCA1 and ABCG5/G8 expression in liver. ATI-111 markedly increased sterol regulatory element-binding protein (SREBP)-1c mRNA in some tissues, whereas acetyl-coenzyme A carboxylase and fatty acid synthase expression was unaffected or only slightly increased in intestine and liver. ATI-111 inhibited the conversion of SREBP-1c precursor form to its active form. Compared with vehicle-treated mice, the levels of hepatic lipids and liver-secreted nascent lipoproteins were not altered, while a significant decrease in plasma cholesterol and triglyceride levels was observed in ATI-111-treated mice. ATI-111 significantly inhibited atherogenesis in three separate vascular sites. CONCLUSIONS AND IMPLICATIONS ATI-111 is a promising candidate for further development as a treatment of certain vascular diseases as it lacks the significant side effects associated with nonsteroidal LXR agonists, the induction of fatty liver and hypertriglyceridaemia.

Cell, 2016

Highlights d ALKBH1 catalyzes the demethylation of m 1 A in tRNA d The m 1 A demethylation affect... more Highlights d ALKBH1 catalyzes the demethylation of m 1 A in tRNA d The m 1 A demethylation affects the tRNA iMet level and translation initiation d The ALKBH1-mediated tRNA demethylation attenuates translation elongation d Reversible tRNA methylation dynamically regulates translation

ACS chemical biology, Jan 17, 2015

In the active cytosine demethylation pathway, 5-methylcytosine (5mC) is oxidized sequentially to ... more In the active cytosine demethylation pathway, 5-methylcytosine (5mC) is oxidized sequentially to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Thymine DNA glycosylase (TDG) selectively excises 5fC and 5caC but not cytosine (C), 5mC, and 5hmC. We propose that the electron-withdrawing properties of -CHO and -COOH in 5fC and 5caC increase N3 acidity, leading to weakened hydrogen bonding and reduced base pair stability relative to C, 5mC, and 5hmC, thereby facilitating the selective recognition of 5fC and 5caC by TDG. Through (13)C NMR, we measured the pKa at N3 of 5fC as 2.4 and the two pKa's of 5caC as 2.1 and 4.2. We used isotope-edited IR spectroscopy coupled with density functional theory (DFT) calculations to site-specifically assign the more acidic pKa of 5caC to protonation at N3, indicating that N3 acidity is increased in 5fC and 5caC relative to C. IR and UV melting studies of self-complementary DNA oligomers confirm reduced stabili...

Nature Biotechnology

Functional characterization of pseudouridine (Ψ) in mammalian mRNA has been hampered by the lack ... more Functional characterization of pseudouridine (Ψ) in mammalian mRNA has been hampered by the lack of a quantitative method that maps Ψ in the whole transcriptome. We report bisulfite-induced deletion sequencing (BID-seq), which uses a bisulfite-mediated reaction to convert pseudouridine stoichiometrically into deletion upon reverse transcription without cytosine deamination. BID-seq enables detection of abundant Ψ sites with stoichiometry information in several human cell lines and 12 different mouse tissues using 10–20 ng input RNA. We uncover consensus sequences for Ψ in mammalian mRNA and assign different ‘writer’ proteins to individual Ψ deposition. Our results reveal a transcript stabilization role of Ψ sites installed by TRUB1 in human cancer cells. We also detect the presence of Ψ within stop codons of mammalian mRNA and confirm the role of Ψ in promoting stop codon readthrough in vivo. BID-seq will enable future investigations of the roles of Ψ in diverse biological processes.

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Current protocols in nucleic acid chemistry / edited by Serge L. Beaucage ... [et al.], 2011

This unit describes procedures for preparation of two phosphoramidite building blocks III and IV,... more This unit describes procedures for preparation of two phosphoramidite building blocks III and IV, both containing a TBDMS as 5-CH(2)OH-protecting group. Phosphoramidites III and IV allow efficient incorporation of 5-hmC into DNA and a "one-step" deprotection procedure to cleanly remove all the protecting groups. A "two-step" deprotection strategy is compatible with ultramild DNA synthesis, which enables the synthesis of 5 hmC-containing DNA with additional modifications. Methods are also presented for their incorporation into oligonucleotides by solid-phase synthesis, subsequent deprotection, and HPLC analysis.

Nature Methods, 2011

We describe strand-specific, base-resolution detection of 5-hydroxymethylcytosine (5-hmC) in geno... more We describe strand-specific, base-resolution detection of 5-hydroxymethylcytosine (5-hmC) in genomic DNA with single-molecule sensitivity, combining a bioorthogonal, selective chemical labeling method of 5-hmC with single-molecule, real-time (SMRT) DNA sequencing. The chemical labeling not only allows affinity enrichment of 5-hmC-containing DNA fragments but also enhances the kinetic signal of 5-hmC during SMRT sequencing. We applied the approach to sequence 5-hmC in a genomic DNA sample with high confidence. The base 5-hydroxymethylcytosine (5-hmC) is a newly discovered DNA modification in mammalian cells and, along with 5-methylcytosine (5-mC), is believed to be an important epigenetic mark involved in many critical cellular functions, including embryonic stem cell differentiation, normal myelopoiesis as well as zygotic development 1-3. Understanding the biological functions of 5-hmC requires the development of sensitive sequencing methods to reveal locations of this base modification in the genome, as existing sequencing methods, such as bisulfite sequencing, cannot be used to differentiate 5-hmC from 5-mC (ref. 4). Recently, we developed a selective chemical labeling technology for 5-hmC, in which 5-hmC is first modified with an azide-substituted glucose using β-glucosyltransferase followed by a click chemistry reaction to install a biotin tag 5. Using this method, 5-hmC in genomic DNA has been enriched for deep sequencing to provide the genomic distribution of this base modification. However, this and other methods 5-11 do not currently give information about the exact genomic locations of 5-hmC. Progress in the understanding of 5-hmC biology has been hampered by the lack of a method for high-throughput, strandspecific, base-resolution sequencing of 5-hmC.

Nature, 2013

In nuclear pre-messenger RNA splicing, introns are excised by the spliceosome, a multimegadalton ... more In nuclear pre-messenger RNA splicing, introns are excised by the spliceosome, a multimegadalton machine composed of both proteins and small nuclear RNAs (snRNAs). Over thirty years ago, following the discovery of self-splicing group II intron RNAs, the snRNAs were hypothesized to catalyze splicing. However, no definitive evidence for a role of either RNA or protein in catalysis by the spliceosome has been reported to date. By using metal rescue strategies, here we show that the U6 snRNA catalyzes both splicing reactions by positioning divalent metals that stabilize the leaving groups during each reaction. Strikingly, all of the U6 catalytic metal ligands we identified correspond to the ligands observed to position catalytic, divalent metals in crystal structures of a group II intron RNA. These findings indicate that group II introns and the spliceosome share common catalytic mechanisms, and likely common evolutionary origins. Our results demonstrate that RNA mediates catalysis within the spliceosome. Nuclear pre-mRNA splicing (Fig. 1a) is a crucial determinant of the export, translation, stability, and diversity of eukaryotic messages 1 , but the spliceosome is the only major cellular machinery 2 required for gene expression for which the catalytic components remain undefined. Nevertheless, for three decades, there has been widespread speculation that nuclear pre-mRNA splicing is catalyzed by RNA. Users may view, print, copy, download and text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: