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  • 1
    Online Resource
    Online Resource
    Inhibition of α-KG-dependent histone and DNA demethylases by fumarate and succinate that are accumulated in mutations of FH and SDH tumor suppressors
    Cold Spring Harbor Laboratory ; 2012
    In:  Genes & Development Vol. 26, No. 12 ( 2012-06-15), p. 1326-1338
    Details
    In: Genes & Development, Cold Spring Harbor Laboratory, Vol. 26, No. 12 ( 2012-06-15), p. 1326-1338
    Abstract: Two Krebs cycle genes, fumarate hydratase ( FH ) and succinate dehydrogenase ( SDH ), are mutated in a subset of human cancers, leading to accumulation of their substrates, fumarate and succinate, respectively. Here we demonstrate that fumarate and succinate are competitive inhibitors of multiple α-ketoglutarate (α-KG)-dependent dioxygenases, including histone demethylases, prolyl hydroxylases, collagen prolyl-4-hydroxylases, and the TET (ten-eleven translocation) family of 5-methlycytosine (5mC) hydroxylases. Knockdown of FH and SDH results in elevated intracellular levels of fumarate and succinate, respectively, which act as competitors of α-KG to broadly inhibit the activity of α-KG-dependent dioxygenases. In addition, ectopic expression of tumor-derived FH and SDH mutants inhibits histone demethylation and hydroxylation of 5mC. Our study suggests that tumor-derived FH and SDH mutations accumulate fumarate and succinate, leading to enzymatic inhibition of multiple α-KG-dependent dioxygenases and consequent alterations of genome-wide histone and DNA methylation. These epigenetic alterations associated with mutations of FH and SDH likely contribute to tumorigenesis.
    Type of Medium: Online Resource
    ISSN: 0890-9369 , 1549-5477
    URL: Article
    DOI: 10.1101/gad.191056.112
    RVK:
    WA 15000
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2012
    detail.hit.zdb_id: 1467414-2
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  • 2
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    Alternative splicing and trans -splicing events revealed by analysis of the Bombyx mori transcriptome
    Cold Spring Harbor Laboratory ; 2012
    In:  RNA Vol. 18, No. 7 ( 2012-07), p. 1395-1407
    Details
    In: RNA, Cold Spring Harbor Laboratory, Vol. 18, No. 7 ( 2012-07), p. 1395-1407
    Abstract: Alternative splicing and trans -splicing events have not been systematically studied in the silkworm Bombyx mori . Here, the silkworm transcriptome was analyzed by RNA-seq. We identified 320 novel genes, modified 1140 gene models, and found thousands of alternative splicing and 58 trans -splicing events. Studies of three SR proteins show that both their alternative splicing patterns and mRNA products are conserved from insect to human, and one isoform of Srsf6 with a retained intron is expressed sex-specifically in silkworm gonads. Trans -splicing of mod(mdg4) in silkworm was experimentally confirmed. We identified integrations from a common 5′-gene with 46 newly identified alternative 3′-exons that are located on both DNA strands over a 500-kb region. Other trans -splicing events in B. mori were predicted by bioinformatic analysis, in which 12 events were confirmed by RT-PCR, six events were further validated by chimeric SNPs, and two events were confirmed by allele-specific RT-PCR in F 1 hybrids from distinct silkworm lines of JS and L10, indicating that trans -splicing is more widespread in insects than previously thought. Analysis of the B. mori transcriptome by RNA-seq provides valuable information of regulatory alternative splicing events. The conservation of splicing events across species and newly identified trans -splicing events suggest that B. mori is a good model for future studies.
    Type of Medium: Online Resource
    ISSN: 1355-8382 , 1469-9001
    URL: Article
    DOI: 10.1261/rna.029751.111
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2012
    detail.hit.zdb_id: 1475737-0
    SSG: 12
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  • 3
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    The genome of the pear ( Pyrus bretschneideri Rehd.)
    Cold Spring Harbor Laboratory ; 2013
    In:  Genome Research Vol. 23, No. 2 ( 2013-02), p. 396-408
    Details
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 23, No. 2 ( 2013-02), p. 396-408
    Abstract: The draft genome of the pear ( Pyrus bretschneideri ) using a combination of BAC-by-BAC and next-generation sequencing is reported. A 512.0-Mb sequence corresponding to 97.1% of the estimated genome size of this highly heterozygous species is assembled with 194× coverage. High-density genetic maps comprising 2005 SNP markers anchored 75.5% of the sequence to all 17 chromosomes. The pear genome encodes 42,812 protein-coding genes, and of these, ∼28.5% encode multiple isoforms. Repetitive sequences of 271.9 Mb in length, accounting for 53.1% of the pear genome, are identified. Simulation of eudicots to the ancestor of Rosaceae has reconstructed nine ancestral chromosomes. Pear and apple diverged from each other ∼5.4–21.5 million years ago, and a recent whole-genome duplication (WGD) event must have occurred 30–45 MYA prior to their divergence, but following divergence from strawberry. When compared with the apple genome sequence, size differences between the apple and pear genomes are confirmed mainly due to the presence of repetitive sequences predominantly contributed by transposable elements (TEs), while genic regions are similar in both species. Genes critical for self-incompatibility, lignified stone cells (a unique feature of pear fruit), sorbitol metabolism, and volatile compounds of fruit have also been identified. Multiple candidate SFB genes appear as tandem repeats in the S -locus region of pear; while lignin synthesis-related gene family expansion and highly expressed gene families of HCT , C3′H , and CCOMT contribute to high accumulation of both G-lignin and S-lignin. Moreover, alpha-linolenic acid metabolism is a key pathway for aroma in pear fruit.
    Type of Medium: Online Resource
    ISSN: 1088-9051
    URL: Article
    DOI: 10.1101/gr.144311.112
    RVK:
    XA 10000
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2013
    detail.hit.zdb_id: 1483456-X
    SSG: 12
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  • 4
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    Topography of histone H3–H4 interaction with the Hat1–Hat2 acetyltransferase complex
    Cold Spring Harbor Laboratory ; 2022
    In:  Genes & Development Vol. 36, No. 7-8 ( 2022-04-01), p. 408-413
    Details
    In: Genes & Development, Cold Spring Harbor Laboratory, Vol. 36, No. 7-8 ( 2022-04-01), p. 408-413
    Abstract: Chaperones influence histone conformation and intermolecular interaction in multiprotein complexes, and the structures obtained with full-length histones often provide more accurate and comprehensive views. Here, our structure of the Hat1–Hat2 acetyltransferase complex bound to Asf1–H3–H4 shows that the core domains of H3 and H4 are involved in binding Hat1 and Hat2, and the N-terminal tail of H3 makes extensive interaction with Hat2. These findings expand the knowledge about histone–protein interaction and implicate a function of Hat2/RbAp46/48, which is a versatile histone chaperone found in many chromatin-associated complexes, in the passing of histones between chaperones.
    Type of Medium: Online Resource
    ISSN: 0890-9369 , 1549-5477
    URL: Article
    DOI: 10.1101/gad.349099.121
    RVK:
    WA 15000
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2022
    detail.hit.zdb_id: 1467414-2
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  • 5
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    Online Resource
    RePS: A Sequence Assembler That Masks Exact Repeats Identified from the Shotgun Data
    Cold Spring Harbor Laboratory ; 2002
    In:  Genome Research Vol. 12, No. 5 ( 2002-05-01), p. 824-831
    Details
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 12, No. 5 ( 2002-05-01), p. 824-831
    Abstract: We describe a sequence assembler, RePS (repeat-masked Phrap with scaffolding), that explicitly identifies exact 20mer repeats from the shotgun data and removes them prior to the assembly. The established software Phrap is used to compute meaningful error probabilities for each base. Clone-end-pairing information is used to construct scaffolds that order and orient the contigs. We show with real data for human and rice that reasonable assemblies are possible even at coverages of only 4× to 6×, despite having up to 42.2% in exact repeats. [The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: P. Green and A.F. Smit.]
    Type of Medium: Online Resource
    ISSN: 1088-9051 , 1549-5469
    URL: Article
    DOI: 10.1101/gr.165102
    RVK:
    XA 10000
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2002
    detail.hit.zdb_id: 1483456-X
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  • 6
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    Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma
    Cold Spring Harbor Laboratory ; 2013
    In:  Genome Research Vol. 23, No. 9 ( 2013-09), p. 1422-1433
    Details
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 23, No. 9 ( 2013-09), p. 1422-1433
    Abstract: Hepatocellular carcinoma (HCC) is one of the most deadly cancers worldwide and has no effective treatment, yet the molecular basis of hepatocarcinogenesis remains largely unknown. Here we report findings from a whole-genome sequencing (WGS) study of 88 matched HCC tumor/normal pairs, 81 of which are Hepatitis B virus (HBV) positive, seeking to identify genetically altered genes and pathways implicated in HBV-associated HCC. We find beta-catenin to be the most frequently mutated oncogene (15.9%) and TP53 the most frequently mutated tumor suppressor (35.2%). The Wnt/beta-catenin and JAK/STAT pathways, altered in 62.5% and 45.5% of cases, respectively, are likely to act as two major oncogenic drivers in HCC. This study also identifies several prevalent and potentially actionable mutations, including activating mutations of Janus kinase 1 ( JAK1 ), in 9.1% of patients and provides a path toward therapeutic intervention of the disease.
    Type of Medium: Online Resource
    ISSN: 1088-9051
    URL: Article
    DOI: 10.1101/gr.154492.113
    RVK:
    XA 10000
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2013
    detail.hit.zdb_id: 1483456-X
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  • 7
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    Online Resource
    Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
    Cold Spring Harbor Laboratory ; 2008
    In:  Genome Research Vol. 18, No. 3 ( 2008-03), p. 393-403
    Details
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 18, No. 3 ( 2008-03), p. 393-403
    Abstract: The most widely used method for detecting genome-wide protein–DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms, amplification procedures, and signal detection algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and “spike-ins” comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. We found that microarray platform choice is not the primary determinant of overall performance. In fact, variation in performance between labs, protocols, and algorithms within the same array platform was greater than the variation in performance between array platforms. However, each array platform had unique performance characteristics that varied with tiling resolution and the number of replicates, which have implications for cost versus detection power. Long oligonucleotide arrays were slightly more sensitive at detecting very low enrichment. On all platforms, simple sequence repeats and genome redundancy tended to result in false positives. LM-PCR and WGA, the most popular sample amplification techniques, reproduced relative enrichment levels with high fidelity. Performance among signal detection algorithms was heavily dependent on array platform. The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated.
    Type of Medium: Online Resource
    ISSN: 1088-9051
    URL: Article
    DOI: 10.1101/gr.7080508
    RVK:
    XA 10000
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2008
    detail.hit.zdb_id: 1483456-X
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  • 8
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    Online Resource
    A conserved intronic U1 snRNP-binding sequence promotes trans -splicing in Drosophila
    Cold Spring Harbor Laboratory ; 2015
    In:  Genes & Development Vol. 29, No. 7 ( 2015-04-01), p. 760-771
    Details
    In: Genes & Development, Cold Spring Harbor Laboratory, Vol. 29, No. 7 ( 2015-04-01), p. 760-771
    Abstract: Unlike typical cis -splicing, trans -splicing joins exons from two separate transcripts to produce chimeric mRNA and has been detected in most eukaryotes. Trans -splicing in trypanosomes and nematodes has been characterized as a spliced leader RNA-facilitated reaction; in contrast, its mechanism in higher eukaryotes remains unclear. Here we investigate mod(mdg4) , a classic trans -spliced gene in Drosophila , and report that two critical RNA sequences in the middle of the last 5′ intron, TSA and TSB, promote trans -splicing of mod(mdg4) . In TSA, a 13-nucleotide (nt) core motif is conserved across Drosophila species and is essential and sufficient for trans -splicing, which binds U1 small nuclear RNP (snRNP) through strong base-pairing with U1 snRNA. In TSB, a conserved secondary structure acts as an enhancer. Deletions of TSA and TSB using the CRISPR/Cas9 system result in developmental defects in flies. Although it is not clear how the 5′ intron finds the 3′ introns, compensatory changes in U1 snRNA rescue trans -splicing of TSA mutants, demonstrating that U1 recruitment is critical to promote trans -splicing in vivo. Furthermore, TSA core-like motifs are found in many other trans -spliced Drosophila genes, including lola. These findings represent a novel mechanism of trans -splicing, in which RNA motifs in the 5′ intron are sufficient to bring separate transcripts into close proximity to promote trans -splicing.
    Type of Medium: Online Resource
    ISSN: 0890-9369 , 1549-5477
    URL: Article
    DOI: 10.1101/gad.258863.115
    RVK:
    WA 15000
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2015
    detail.hit.zdb_id: 1467414-2
    SSG: 12
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  • 9
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    Mst1 shuts off cytosolic antiviral defense through IRF3 phosphorylation
    Cold Spring Harbor Laboratory ; 2016
    In:  Genes & Development Vol. 30, No. 9 ( 2016-05-01), p. 1086-1100
    Details
    In: Genes & Development, Cold Spring Harbor Laboratory, Vol. 30, No. 9 ( 2016-05-01), p. 1086-1100
    Abstract: Cytosolic RNA/DNA sensing elicits primary defense against viral pathogens. Interferon regulatory factor 3 (IRF3), a key signal mediator/transcriptional factor of the antiviral-sensing pathway, is indispensible for interferon production and antiviral defense. However, how the status of IRF3 activation is controlled remains elusive. Through a functional screen of the human kinome, we found that mammalian sterile 20-like kinase 1 (Mst1), but not Mst2, profoundly inhibited cytosolic nucleic acid sensing. Mst1 associated with IRF3 and directly phosphorylated IRF3 at Thr75 and Thr253. This Mst1-mediated phosphorylation abolished activated IRF3 homodimerization, its occupancy on chromatin, and subsequent IRF3-mediated transcriptional responses. In addition, Mst1 also impeded virus-induced activation of TANK-binding kinase 1 (TBK1), further attenuating IRF3 activation. As a result, Mst1 depletion or ablation enabled an enhanced antiviral response and defense in cells and mice. Therefore, the identification of Mst1 as a novel physiological negative regulator of IRF3 activation provides mechanistic insights into innate antiviral defense and potential antiviral prevention strategies.
    Type of Medium: Online Resource
    ISSN: 0890-9369 , 1549-5477
    URL: Article
    DOI: 10.1101/gad.277533.116
    RVK:
    WA 15000
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2016
    detail.hit.zdb_id: 1467414-2
    SSG: 12
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  • 10
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    The SPOROCYTELESS gene of Arabidopsis is required for initiation of sporogenesis and encodes a novel nuclear protein
    Cold Spring Harbor Laboratory ; 1999
    In:  Genes & Development Vol. 13, No. 16 ( 1999-08-15), p. 2108-2117
    Details
    In: Genes & Development, Cold Spring Harbor Laboratory, Vol. 13, No. 16 ( 1999-08-15), p. 2108-2117
    Type of Medium: Online Resource
    ISSN: 0890-9369
    URL: Article
    DOI: 10.1101/gad.13.16.2108
    RVK:
    WA 15000
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 1999
    detail.hit.zdb_id: 1467414-2
    SSG: 12
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