1
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Abstract
Enhancer RNAs (eRNAs) are non-coding RNAs produced by transcriptional enhancers that are highly correlated with their activity. Using a capped nascent RNA sequencing (PRO-cap) dataset in human lymphoblastoid cell lines across 67 individuals, we identified inter-individual variation in the expression of over 80 thousand transcribed transcriptional regulatory elements (tTREs), in both enhancers and promoters. Co-expression analysis of eRNAs from tTREs across individuals revealed how enhancers are associated with each other and with promoters. Mid- to long-range co-expression showed a distance-dependent decay that was modified by TF occupancy. In particular, we found a class of "bivalent" TFs, including Cohesin, that both facilitate and isolate the interaction between enhancers and/or promoters, depending on their topology. At short distances, we observed strand-specific correlations between nearby eRNAs in both convergent and divergent orientations. Our results support a cooperative model of convergent eRNAs, consistent with eRNAs facilitating adjacent enhancers rather than interfering with each other. Therefore, our approach to infer functional interactions from co-expression analyses provided novel insights into the principles of enhancer interactions as a function of distance, orientation, and binding landscapes of TFs.
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Affiliation(s)
- Seungha Alisa Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Katla Kristjánsdóttir
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA.
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2
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Lee SA, Kristjánsdóttir K, Kwak H. Revealing eRNA interactions: TF dependency and convergent cooperativity. Res Sq 2023:rs.3.rs-2592357. [PMID: 36909657 PMCID: PMC10002804 DOI: 10.21203/rs.3.rs-2592357/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Enhancer RNAs (eRNAs) are non-coding RNAs produced from transcriptional enhancers that are highly correlated with their activities. Using capped nascent RNA sequencing (PRO-cap) dataset in human lymphoblastoid cell lines across individuals, we identified inter-individual variation of expression in over 80 thousand transcribed transcriptional regulatory elements (tTREs), in both enhancers and promoters. Co-expression analysis of eRNAs from tTREs across individuals revealed how enhancers interact with each other and with promoters. Mid-to-long range interactions showed distance-dependent decay, which was modified by TF occupancy. In particular, we found a class of 'bivalent' TFs, including Cohesin, which both facilitates and insulates the interaction between enhancers and/or promoters depending on the topology. In short ranges, we observed strand specific interactions between nearby eRNAs in both convergent or divergent orientations. Our finding supports a cooperative convergent eRNA model, which is compatible with eRNA remodeling neighboring enhancers rather than interfering with each other. Therefore, our approach to infer functional interactions from co-expression analyses provided novel insights into the principles of enhancer interactions depending on the distance, orientation, and the binding landscapes of TFs.
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3
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Bae S, Kim K, Kang K, Kim H, Lee M, Oh B, Kaneko K, Ma S, Choi JH, Kwak H, Lee EY, Park SH, Park-Min KH. RANKL-responsive epigenetic mechanism reprograms macrophages into bone-resorbing osteoclasts. Cell Mol Immunol 2023; 20:94-109. [PMID: 36513810 PMCID: PMC9794822 DOI: 10.1038/s41423-022-00959-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/03/2022] [Indexed: 12/15/2022] Open
Abstract
Monocyte/macrophage lineage cells are highly plastic and can differentiate into various cells under different environmental stimuli. Bone-resorbing osteoclasts are derived from the monocyte/macrophage lineage in response to receptor activator of NF-κB ligand (RANKL). However, the epigenetic signature contributing to the fate commitment of monocyte/macrophage lineage differentiation into human osteoclasts is largely unknown. In this study, we identified RANKL-responsive human osteoclast-specific superenhancers (SEs) and SE-associated enhancer RNAs (SE-eRNAs) by integrating data obtained from ChIP-seq, ATAC-seq, nuclear RNA-seq and PRO-seq analyses. RANKL induced the formation of 200 SEs, which are large clusters of enhancers, while suppressing 148 SEs in macrophages. RANKL-responsive SEs were strongly correlated with genes in the osteoclastogenic program and were selectively increased in human osteoclasts but marginally presented in osteoblasts, CD4+ T cells, and CD34+ cells. In addition to the major transcription factors identified in osteoclasts, we found that BATF binding motifs were highly enriched in RANKL-responsive SEs. The depletion of BATF1/3 inhibited RANKL-induced osteoclast differentiation. Furthermore, we found increased chromatin accessibility in SE regions, where RNA polymerase II was significantly recruited to induce the extragenic transcription of SE-eRNAs, in human osteoclasts. Knocking down SE-eRNAs in the vicinity of the NFATc1 gene diminished the expression of NFATc1, a major regulator of osteoclasts, and osteoclast differentiation. Inhibiting BET proteins suppressed the formation of some RANKL-responsive SEs and NFATc1-associated SEs, and the expression of SE-eRNA:NFATc1. Moreover, SE-eRNA:NFATc1 was highly expressed in the synovial macrophages of rheumatoid arthritis patients exhibiting high-osteoclastogenic potential. Our genome-wide analysis revealed RANKL-inducible SEs and SE-eRNAs as osteoclast-specific signatures, which may contribute to the development of osteoclast-specific therapeutic interventions.
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Affiliation(s)
- Seyeon Bae
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Kibyeong Kim
- Department of Biological Science, Ulsan National Institute of Science & Technology (UNIST), Ulsan, 44919, Republic of Korea
- Department of Life Science, College of Natural Sciences, Research Institute for Natural Sciences, Hanyang University, Seoul, Korea
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan, 3116, Republic of Korea
| | - Haemin Kim
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Minjoon Lee
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Brian Oh
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Kaichi Kaneko
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Sungkook Ma
- Department of Biological Science, Ulsan National Institute of Science & Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Jae Hoon Choi
- Department of Life Science, College of Natural Sciences, Research Institute for Natural Sciences, Hanyang University, Seoul, Korea
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, USA
| | - Eun Young Lee
- Division of Rheumatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.
| | - Sung Ho Park
- Department of Biological Science, Ulsan National Institute of Science & Technology (UNIST), Ulsan, 44919, Republic of Korea.
| | - Kyung-Hyun Park-Min
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.
- BCMB Allied Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, 10021, USA.
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4
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Kwak Y, Daly CWP, Fogarty EA, Grimson A, Kwak H. Dynamic and widespread control of poly(A) tail length during macrophage activation. RNA 2022; 28:947-971. [PMID: 35512831 PMCID: PMC9202586 DOI: 10.1261/rna.078918.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
The poly(A) tail enhances translation and transcript stability, and tail length is under dynamic control during cell state transitions. Tail regulation plays essential roles in translational timing and fertilization in early development, but poly(A) tail dynamics have not been fully explored in post-embryonic systems. Here, we examined the landscape and impact of tail length control during macrophage activation. Upon activation, more than 1500 mRNAs, including proinflammatory genes, underwent distinctive changes in tail lengths. Increases in tail length correlated with mRNA levels regardless of transcriptional activity, and many mRNAs that underwent tail extension encode proteins necessary for immune function and post-transcriptional regulation. Strikingly, we found that ZFP36, whose protein product destabilizes target transcripts, undergoes tail extension. Our analyses indicate that many mRNAs undergoing tail lengthening are, in turn, degraded by elevated levels of ZFP36, constituting a post-transcriptional feedback loop that ensures transient regulation of transcripts integral to macrophage activation. Taken together, this study establishes the complexity, relevance, and widespread nature of poly(A) tail dynamics, and the resulting post-transcriptional regulation during macrophage activation.
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Affiliation(s)
- Yeonui Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
- Graduate Field of Genetics, Genomics, and Development, Cornell University, Ithaca, New York 14853, USA
| | - Ciarán W P Daly
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
- Graduate Field of Biochemistry, Molecular, and Cell Biology, Cornell University, Ithaca, New York 14853, USA
| | - Elizabeth A Fogarty
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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5
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Kwak Y, Kwak H. Genome-Wide Identification of Polyadenylation Dynamics with TED-Seq. Methods Mol Biol 2022; 2404:281-298. [PMID: 34694615 DOI: 10.1007/978-1-0716-1851-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Polyadenylation and deadenylation of mRNA are major RNA modifications associated with nucleus-to-cytoplasm translocation, mRNA stability, translation efficiency, and mRNA decay pathways. Our current knowledge of polyadenylation and deadenylation has been expanded due to recent advances in transcriptome-wide poly(A) tail length assays. Whereas these methods measure poly(A) length by quantifying the adenine (A) base stretch at the 3' end of mRNA, we developed a more cost-efficient technique that does not rely on A-base counting, called tail-end-displacement sequencing (TED-seq). Through sequencing highly size-selected 3' RNA fragments including the poly(A) tail pieces, TED-seq provides accurate measure of transcriptome-wide poly(A)-tail lengths in high resolution, economically suitable for larger scale analysis under various biologically transitional contexts.
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Affiliation(s)
- Yeonui Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Graduate Field of Genetics, Genomics, and Developmental Biology, Cornell University, Ithaca, NY, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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6
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Park SR, Namkoong S, Friesen L, Cho CS, Zhang ZZ, Chen YC, Yoon E, Kim CH, Kwak H, Kang HM, Lee JH. Single-Cell Transcriptome Analysis of Colon Cancer Cell Response to 5-Fluorouracil-Induced DNA Damage. Cell Rep 2020; 32:108077. [PMID: 32846134 PMCID: PMC7486130 DOI: 10.1016/j.celrep.2020.108077] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 05/04/2020] [Accepted: 08/05/2020] [Indexed: 12/22/2022] Open
Abstract
DNA damage often induces heterogeneous cell-fate responses, such as cell-cycle arrest and apoptosis. Through single-cell RNA sequencing (scRNA-seq), we characterize the transcriptome response of cultured colon cancer cell lines to 5-fluorouracil (5FU)-induced DNA damage. After 5FU treatment, a single population of colon cancer cells adopts three distinct transcriptome phenotypes, which correspond to diversified cell-fate responses: apoptosis, cell-cycle checkpoint, and stress resistance. Although some genes are regulated uniformly across all groups of cells, many genes showed group-specific expression patterns mediating DNA damage responses specific to the corresponding cell fate. Some of these observations are reproduced at the protein level by flow cytometry and are replicated in cells treated with other 5FU-unrelated genotoxic drugs, camptothecin and etoposide. This work provides a resource for understanding heterogeneous DNA damage responses involving fractional killing and chemoresistance, which are among the major challenges in current cancer chemotherapy.
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Affiliation(s)
- Sung Rye Park
- Department of Molecular & Integrative Physiology and Institute for Gerontology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Sim Namkoong
- Department of Molecular & Integrative Physiology and Institute for Gerontology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Leon Friesen
- Department of Pathology and Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Chun-Seok Cho
- Department of Molecular & Integrative Physiology and Institute for Gerontology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Zac Zezhi Zhang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Yu-Chih Chen
- Department of Electrical Engineering and Computer Science, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA; Forbes Institute for Cancer Discovery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Euisik Yoon
- Department of Electrical Engineering and Computer Science, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA; Center for Nanomedicine, Institute for Basic Science (IBS), and Graduate Program of Nano Biomedical Engineering (Nano BME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
| | - Chang H Kim
- Department of Pathology and Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA.
| | - Jun Hee Lee
- Department of Molecular & Integrative Physiology and Institute for Gerontology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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7
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Woo YM, Kwak Y, Namkoong S, Kristjánsdóttir K, Lee SH, Lee JH, Kwak H. TED-Seq Identifies the Dynamics of Poly(A) Length during ER Stress. Cell Rep 2019; 24:3630-3641.e7. [PMID: 30257221 DOI: 10.1016/j.celrep.2018.08.084] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 07/02/2018] [Accepted: 08/28/2018] [Indexed: 12/31/2022] Open
Abstract
Post-transcriptional RNA processing is a core mechanism of gene expression control in cell stress response. The poly(A) tail influences mRNA translation and stability, but it is unclear whether there are global roles of poly(A)-tail lengths in cell stress. To address this, we developed tail-end displacement sequencing (TED-seq) for an efficient transcriptome-wide profiling of poly(A) lengths and applied it to endoplasmic reticulum (ER) stress in human cells. ER stress induced increases in the poly(A) lengths of certain mRNAs, including known ER stress regulators, XBP1, DDIT3, and HSPA5. Importantly, the mRNAs with increased poly(A) lengths are both translationally de-repressed and stabilized. Furthermore, mRNAs in stress-induced RNA granules have shorter poly(A) tails than in the cytoplasm, supporting the view that RNA processing is compartmentalized. In conclusion, TED-seq reveals that poly(A) length is dynamically regulated upon ER stress, with potential consequences for both translation and mRNA turnover.
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Affiliation(s)
- Yu Mi Woo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Yeonui Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Sim Namkoong
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katla Kristjánsdóttir
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Seung Ha Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jun Hee Lee
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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8
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Ries RJ, Zaccara S, Klein P, Olarerin-George A, Namkoong S, Pickering BF, Patil DP, Kwak H, Lee JH, Jaffrey SR. m 6A enhances the phase separation potential of mRNA. Nature 2019; 571:424-428. [PMID: 31292544 PMCID: PMC6662915 DOI: 10.1038/s41586-019-1374-1] [Citation(s) in RCA: 396] [Impact Index Per Article: 79.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/13/2019] [Indexed: 12/11/2022]
Abstract
N6-methyladenosine (m6A) is the most prevalent modified nucleotide in mRNA1,2, with ~25% of mRNAs containing at least one m6A. Methylation of mRNA to form m6A is required for diverse cellular and physiological processes3. Although the presence of m6A in an mRNA can affect its fate in different ways, it is unclear how m6A directs this process and why the effects of m6A can vary in different cellular contexts. Here we show that the cytosolic m6A-binding proteins, YTHDF1–3, undergo liquid-liquid phase separation (LLPS) in vitro and in cells. This LLPS is markedly enhanced by mRNAs that contain multiple, but not single, m6A residues. Polymethylated mRNAs act as a multivalent scaffold for binding YTHDF proteins, juxtaposing their low-complexity domains, leading to phase separation. The resulting mRNA-YTHDF complexes then partition into different endogenous phase-separated compartments, such as P-bodies, stress granules, or neuronal RNA granules. m6A-mRNA is subject to compartment-specific regulation, including reduced mRNA stability and translation. These studies reveal that the number and distribution of m6A sites in cellular mRNAs can regulate and influence the composition of the phase-separated transcriptome. Additionally, these findings indicate that the cellular properties of m6A-modified mRNAs are governed by liquid-liquid phase separation principles.
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Affiliation(s)
- Ryan J Ries
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
| | - Sara Zaccara
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
| | - Pierre Klein
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
| | - Anthony Olarerin-George
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
| | - Sim Namkoong
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Brian F Pickering
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
| | - Deepak P Patil
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Jun Hee Lee
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA.
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9
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Chu T, Rice EJ, Booth GT, Salamanca HH, Wang Z, Core LJ, Longo SL, Corona RJ, Chin LS, Lis JT, Kwak H, Danko CG. Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme. Nat Genet 2018; 50:1553-1564. [PMID: 30349114 PMCID: PMC6204104 DOI: 10.1038/s41588-018-0244-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 08/21/2018] [Indexed: 11/09/2022]
Abstract
The human genome encodes a variety of poorly understood RNA species that remain challenging to identify using existing genomic tools. We developed chromatin run-on and sequencing (ChRO-seq) to map the location of RNA polymerase for almost any input sample, including samples with degraded RNA that are intractable to RNA sequencing. We used ChRO-seq to map nascent transcription in primary human glioblastoma (GBM) brain tumors. Enhancers identified in primary GBMs resemble open chromatin in the normal human brain. Rare enhancers that are activated in malignant tissue drive regulatory programs similar to the developing nervous system. We identified enhancers that regulate groups of genes that are characteristic of each known GBM subtype and transcription factors that drive them. Finally we discovered a core group of transcription factors that control the expression of genes associated with clinical outcomes. This study characterizes the transcriptional landscape of GBM and introduces ChRO-seq as a method to map regulatory programs that contribute to complex diseases.
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Affiliation(s)
- Tinyi Chu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Graduate field of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Gregory T Booth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - H Hans Salamanca
- Department of Anesthesiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Zhong Wang
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Leighton J Core
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Sharon L Longo
- Department of Neurological Surgery, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Robert J Corona
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Lawrence S Chin
- Department of Neurological Surgery, SUNY Upstate Medical University, Syracuse, NY, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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10
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Johnson MB, Sun X, Kodani A, Borges-Monroy R, Girskis KM, Ryu SC, Wang PP, Patel K, Gonzalez DM, Woo YM, Yan Z, Liang B, Smith RS, Chatterjee M, Coman D, Papademetris X, Staib LH, Hyder F, Mandeville JB, Grant PE, Im K, Kwak H, Engelhardt JF, Walsh CA, Bae BI. Aspm knockout ferret reveals an evolutionary mechanism governing cerebral cortical size. Nature 2018; 556:370-375. [PMID: 29643508 PMCID: PMC6095461 DOI: 10.1038/s41586-018-0035-0] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 02/22/2018] [Indexed: 12/17/2022]
Abstract
The human cerebral cortex is distinguished by its large size and abundant
gyrification, or folding, yet the evolutionary mechanisms driving cortical size
and structure are unknown. While genes essential for cortical developmental
expansion have been identified from the genetics of human primary microcephaly
(“small head”, associated with reduced brain size and
intellectual disability)1,
studies of these genes in mice, whose smooth cortex is one thousand times
smaller than that of humans, have provided limited insight. Mutations of
abnormal spindle-like microcephaly-associated
(ASPM), the most common recessive microcephaly gene, reduce
cortical volume by ≥50% in humans2–4, but have little effect in mice5–9, likely reflecting evolutionarily divergent functions of
ASPM10,11. We used genome editing to
create a germline knockout (KO) of Aspm in the ferret
(Mustela putorius furo), a species with a larger, gyrified
cortex and greater neural progenitor cell (NPC) diversity12–14 than mice, and closer Aspm protein sequence homology to
human. Aspm KO ferrets exhibit severe microcephaly
(25–40% decreases in brain weight), reflecting reduced cortical
surface area without significant change in cortical thickness, as in human
patients3,4, suggesting loss of “cortical
units”. The mutant ferret fetal cortex displays a massive premature
displacement of ventricular radial glial cells (VRG) to the outer subventricular
zone (OSVZ), where many resemble outer radial glia (ORG), an NPC subtype
essentially absent in mice and implicated in cerebral cortical expansion in
primates12–16. These data suggest an
evolutionary mechanism whereby Aspm regulates cortical expansion by controlling
the affinity of VRG for the ventricular surface, thus modulating the ratio of
VRG, the most undifferentiated cell type, to ORG, a more differentiated
progenitor.
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Affiliation(s)
- Matthew B Johnson
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xingshen Sun
- Department of Anatomy and Cell Biology, Center for Gene Therapy, University of Iowa, Iowa City, IA, USA.,Center for Gene Therapy, University of Iowa, Iowa City, IA, USA.,National Ferret Resource and Research Center, University of Iowa, Iowa City, IA, USA
| | - Andrew Kodani
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rebeca Borges-Monroy
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kelly M Girskis
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Steven C Ryu
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter P Wang
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Komal Patel
- Department of Neurosurgery, School of Medicine, Yale University, New Haven, CT, USA
| | - Dilenny M Gonzalez
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yu Mi Woo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Ziying Yan
- Department of Anatomy and Cell Biology, Center for Gene Therapy, University of Iowa, Iowa City, IA, USA.,Center for Gene Therapy, University of Iowa, Iowa City, IA, USA.,National Ferret Resource and Research Center, University of Iowa, Iowa City, IA, USA
| | - Bo Liang
- Department of Anatomy and Cell Biology, Center for Gene Therapy, University of Iowa, Iowa City, IA, USA.,Center for Gene Therapy, University of Iowa, Iowa City, IA, USA.,National Ferret Resource and Research Center, University of Iowa, Iowa City, IA, USA
| | - Richard S Smith
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Manavi Chatterjee
- Department of Neurosurgery, School of Medicine, Yale University, New Haven, CT, USA
| | - Daniel Coman
- Magnetic Resonance Research Center (MRRC), Yale University, New Haven, CT, USA.,Quantitative Neuroscience with Magnetic Resonance (QNMR) Core Center, Yale University, New Haven, CT, USA.,Department of Radiology & Biomedical Imaging, Yale University, New Haven, CT, USA
| | - Xenophon Papademetris
- Quantitative Neuroscience with Magnetic Resonance (QNMR) Core Center, Yale University, New Haven, CT, USA.,Department of Radiology & Biomedical Imaging, Yale University, New Haven, CT, USA.,Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Lawrence H Staib
- Department of Radiology & Biomedical Imaging, Yale University, New Haven, CT, USA.,Department of Biomedical Engineering, Yale University, New Haven, CT, USA.,Department of Electrical Engineering, Yale University, New Haven, CT, USA
| | - Fahmeed Hyder
- Magnetic Resonance Research Center (MRRC), Yale University, New Haven, CT, USA.,Quantitative Neuroscience with Magnetic Resonance (QNMR) Core Center, Yale University, New Haven, CT, USA.,Department of Radiology & Biomedical Imaging, Yale University, New Haven, CT, USA.,Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Joseph B Mandeville
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
| | - P Ellen Grant
- Division of Newborn Medicine, Fetal Neonatal Neuroimaging and Developmental Science Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kiho Im
- Division of Newborn Medicine, Fetal Neonatal Neuroimaging and Developmental Science Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - John F Engelhardt
- Department of Anatomy and Cell Biology, Center for Gene Therapy, University of Iowa, Iowa City, IA, USA.,Center for Gene Therapy, University of Iowa, Iowa City, IA, USA.,National Ferret Resource and Research Center, University of Iowa, Iowa City, IA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. .,Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Byoung-Il Bae
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. .,Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. .,Department of Neurosurgery, School of Medicine, Yale University, New Haven, CT, USA.
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11
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Namkoong S, Ho A, Woo YM, Kwak H, Lee JH. Systematic Characterization of Stress-Induced RNA Granulation. Mol Cell 2018; 70:175-187.e8. [PMID: 29576526 DOI: 10.1016/j.molcel.2018.02.025] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/06/2017] [Accepted: 02/15/2018] [Indexed: 12/20/2022]
Abstract
Upon stress, cytoplasmic mRNA is sequestered to insoluble ribonucleoprotein (RNP) granules, such as the stress granule (SG). Partially due to the belief that translationally suppressed mRNAs are recruited to SGs in bulk, stress-induced dynamic redistribution of mRNA has not been thoroughly characterized. Here, we report that endoplasmic reticulum (ER) stress targets only a small subset of translationally suppressed mRNAs into the insoluble RNP granule fraction (RG). This subset, characterized by extended length and adenylate-uridylate (AU)-rich motifs, is highly enriched with genes critical for cell survival and proliferation. This pattern of RG targeting was conserved for two other stress types, heat shock and arsenite toxicity, which induce distinct responses in the total cytoplasmic transcriptome. Nevertheless, stress-specific RG-targeting motifs, such as guanylate-cytidylate (GC)-rich motifs in heat shock, were also identified. Previously underappreciated, transcriptome profiling in the RG may contribute to understanding human diseases associated with RNP dysfunction, such as cancer and neurodegeneration.
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Affiliation(s)
- Sim Namkoong
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Allison Ho
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yu Mi Woo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
| | - Jun Hee Lee
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA.
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12
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Wang IX, Grunseich C, Chung YG, Kwak H, Ramrattan G, Zhu Z, Cheung VG. RNA-DNA sequence differences in Saccharomyces cerevisiae. Genome Res 2016; 26:1544-1554. [PMID: 27638543 PMCID: PMC5088596 DOI: 10.1101/gr.207878.116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 09/15/2016] [Indexed: 01/06/2023]
Abstract
Alterations of RNA sequences and structures, such as those from editing and alternative splicing, result in two or more RNA transcripts from a DNA template. It was thought that in yeast, RNA editing only occurs in tRNAs. Here, we found that Saccharomyces cerevisiae have all 12 types of RNA–DNA sequence differences (RDDs) in the mRNA. We showed these sequence differences are propagated to proteins, as we identified peptides encoded by the RNA sequences in addition to those by the DNA sequences at RDD sites. RDDs are significantly enriched at regions with R-loops. A screen of yeast mutants showed that RDD formation is affected by mutations in genes regulating R-loops. Loss-of-function mutations in ribonuclease H, senataxin, and topoisomerase I that resolve RNA–DNA hybrids lead to increases in RDD frequency. Our results demonstrate that RDD is a conserved process that diversifies transcriptomes and proteomes and provide a mechanistic link between R-loops and RDDs.
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Affiliation(s)
- Isabel X Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Christopher Grunseich
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Youree G Chung
- College of Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Hojoong Kwak
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Girish Ramrattan
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Zhengwei Zhu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Vivian G Cheung
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Departments of Pediatrics and Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
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13
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Zhao Y, Liu Q, Acharya P, Stengel KR, Sheng Q, Zhou X, Kwak H, Fischer MA, Bradner JE, Strickland SA, Mohan SR, Savona MR, Venters BJ, Zhou MM, Lis JT, Hiebert SW. High-Resolution Mapping of RNA Polymerases Identifies Mechanisms of Sensitivity and Resistance to BET Inhibitors in t(8;21) AML. Cell Rep 2016; 16:2003-16. [PMID: 27498870 DOI: 10.1016/j.celrep.2016.07.032] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 12/17/2015] [Accepted: 07/13/2016] [Indexed: 02/07/2023] Open
Abstract
Bromodomain and extra-terminal domain (BET) family inhibitors offer an approach to treating hematological malignancies. We used precision nuclear run-on transcription sequencing (PRO-seq) to create high-resolution maps of active RNA polymerases across the genome in t(8;21) acute myeloid leukemia (AML), as these polymerases are exceptionally sensitive to BET inhibitors. PRO-seq identified over 1,400 genes showing impaired release of promoter-proximal paused RNA polymerases, including the stem cell factor receptor tyrosine kinase KIT that is mutated in t(8;21) AML. PRO-seq also identified an enhancer 3' to KIT. Chromosome conformation capture confirmed contacts between this enhancer and the KIT promoter, while CRISPRi-mediated repression of this enhancer impaired cell growth. PRO-seq also identified microRNAs, including MIR29C and MIR29B2, that target the anti-apoptotic factor MCL1 and were repressed by BET inhibitors. MCL1 protein was upregulated, and inhibition of BET proteins sensitized t(8:21)-containing cells to MCL1 inhibition, suggesting a potential mechanism of resistance to BET-inhibitor-induced cell death.
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MESH Headings
- Antineoplastic Agents/pharmacology
- Azepines/pharmacology
- Cell Line, Tumor
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Pair 8
- Clustered Regularly Interspaced Short Palindromic Repeats
- DNA-Directed RNA Polymerases/genetics
- DNA-Directed RNA Polymerases/metabolism
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Enhancer Elements, Genetic
- Gene Expression Regulation, Leukemic
- High-Throughput Nucleotide Sequencing/methods
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Multigene Family
- Myeloid Cell Leukemia Sequence 1 Protein/genetics
- Myeloid Cell Leukemia Sequence 1 Protein/metabolism
- Promoter Regions, Genetic
- Protein Isoforms/antagonists & inhibitors
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Proteins/antagonists & inhibitors
- Proteins/genetics
- Proteins/metabolism
- Proto-Oncogene Proteins c-kit/genetics
- Proto-Oncogene Proteins c-kit/metabolism
- Transcription, Genetic
- Translocation, Genetic
- Triazoles/pharmacology
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Affiliation(s)
- Yue Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Pankaj Acharya
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kristy R Stengel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Quanhu Sheng
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37212, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Melissa A Fischer
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Stephen A Strickland
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Sanjay R Mohan
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Michael R Savona
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Bryan J Venters
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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14
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Mahat DB, Kwak H, Booth GT, Jonkers IH, Danko CG, Patel RK, Waters CT, Munson K, Core LJ, Lis JT. Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nat Protoc 2016; 11:1455-76. [PMID: 27442863 PMCID: PMC5502525 DOI: 10.1038/nprot.2016.086] [Citation(s) in RCA: 275] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We provide a protocol for precision nuclear run-on sequencing (PRO-seq) and its variant, PRO-cap, which map the location of active RNA polymerases (PRO-seq) or transcription start sites (TSSs) (PRO-cap) genome-wide at high resolution. The density of RNA polymerases at a particular genomic locus directly reflects the level of nascent transcription at that region. Nuclei are isolated from cells and, under nuclear run-on conditions, transcriptionally engaged RNA polymerases incorporate one or, at most, a few biotin-labeled nucleotide triphosphates (biotin-NTPs) into the 3' end of nascent RNA. The biotin-labeled nascent RNA is used to prepare sequencing libraries, which are sequenced from the 3' end to provide high-resolution positional information for the RNA polymerases. PRO-seq provides much higher sensitivity than ChIP-seq, and it generates a much larger fraction of usable sequence reads than ChIP-seq or NET-seq (native elongating transcript sequencing). Similarly to NET-seq, PRO-seq maps the RNA polymerase at up to base-pair resolution with strand specificity, but unlike NET-seq it does not require immunoprecipitation. With the protocol provided here, PRO-seq (or PRO-cap) libraries for high-throughput sequencing can be generated in 4-5 working days. The method has been applied to human, mouse, Drosophila melanogaster and Caenorhabditis elegans cells and, with slight modifications, to yeast.
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Affiliation(s)
- Dig Bijay Mahat
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Gregory T Booth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Iris H Jonkers
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Charles G Danko
- The Baker Institute of Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Ravi K Patel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Colin T Waters
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Katie Munson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Leighton J Core
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
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15
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Welsh IC, Kwak H, Chen FL, Werner M, Shopland LS, Danko CG, Lis JT, Zhang M, Martin JF, Kurpios NA. Chromatin Architecture of the Pitx2 Locus Requires CTCF- and Pitx2-Dependent Asymmetry that Mirrors Embryonic Gut Laterality. Cell Rep 2015; 13:337-49. [PMID: 26411685 PMCID: PMC4617833 DOI: 10.1016/j.celrep.2015.08.075] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/20/2015] [Accepted: 08/24/2015] [Indexed: 11/24/2022] Open
Abstract
Expression of Pitx2 on the left side of the embryo patterns left-right (LR) organs including the dorsal mesentery (DM), whose asymmetric cell behavior directs gut looping. Despite the importance of organ laterality, chromatin-level regulation of Pitx2 remains undefined. Here, we show that genes immediately neighboring Pitx2 in chicken and mouse, including a long noncoding RNA (Pitx2 locus-asymmetric regulated RNA or Playrr), are expressed on the right side and repressed by Pitx2. CRISPR/Cas9 genome editing of Playrr, 3D fluorescent in situ hybridization (FISH), and variations of chromatin conformation capture (3C) demonstrate that mutual antagonism between Pitx2 and Playrr is coordinated by asymmetric chromatin interactions dependent on Pitx2 and CTCF. We demonstrate that transcriptional and morphological asymmetries driving gut looping are mirrored by chromatin architectural asymmetries at the Pitx2 locus. We propose a model whereby Pitx2 auto-regulation directs chromatin topology to coordinate LR transcription of this locus essential for LR organogenesis.
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Affiliation(s)
- Ian C Welsh
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Frances L Chen
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Melissa Werner
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Lindsay S Shopland
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA; Eastern Maine Medical Center Cancer Care, 33 Whiting Hill Road, Brewer, ME 04412, USA
| | - Charles G Danko
- Department of Biomedical Sciences, The Baker Institute for Animal Health, Cornell University, Ithaca, NY 14853, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Min Zhang
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James F Martin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Heart Institute, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Natasza A Kurpios
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
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16
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Park M, Ryu S, Kim Y, Kwak H. Development and Applicability Evaluation of the Foramen Ovale Puncture Guide. Skull Base Surg 2014. [DOI: 10.1055/s-0034-1383948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Abstract
Production of mRNA depends critically on the rate of RNA polymerase II (Pol II) elongation. To dissect Pol II dynamics in mouse ES cells, we inhibited Pol II transcription at either initiation or promoter-proximal pause escape with Triptolide or Flavopiridol, and tracked Pol II kinetically using GRO-seq. Both inhibitors block transcription of more than 95% of genes, showing that pause escape, like initiation, is a ubiquitous and crucial step within the transcription cycle. Moreover, paused Pol II is relatively stable, as evidenced from half-life measurements at ∼3200 genes. Finally, tracking the progression of Pol II after drug treatment establishes Pol II elongation rates at over 1000 genes. Notably, Pol II accelerates dramatically while transcribing through genes, but slows at exons. Furthermore, intergenic variance in elongation rates is substantial, and is influenced by a positive effect of H3K79me2 and negative effects of exon density and CG content within genes.DOI: http://dx.doi.org/10.7554/eLife.02407.001.
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Affiliation(s)
- Iris Jonkers
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Hojoong Kwak
- Howard Hughes Medical Institute, University of Michigan, Ann Harbor, United States
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
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18
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Satyaki PRV, Cuykendall TN, Wei KHC, Brideau NJ, Kwak H, Aruna S, Ferree PM, Ji S, Barbash DA. The Hmr and Lhr hybrid incompatibility genes suppress a broad range of heterochromatic repeats. PLoS Genet 2014; 10:e1004240. [PMID: 24651406 PMCID: PMC3961192 DOI: 10.1371/journal.pgen.1004240] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 01/30/2014] [Indexed: 11/19/2022] Open
Abstract
Hybrid incompatibilities (HIs) cause reproductive isolation between species and thus contribute to speciation. Several HI genes encode adaptively evolving proteins that localize to or interact with heterochromatin, suggesting that HIs may result from co-evolution with rapidly evolving heterochromatic DNA. Little is known, however, about the intraspecific function of these HI genes, the specific sequences they interact with, or the evolutionary forces that drive their divergence. The genes Hmr and Lhr genetically interact to cause hybrid lethality between Drosophila melanogaster and D. simulans, yet mutations in both genes are viable. Here, we report that Hmr and Lhr encode proteins that form a heterochromatic complex with Heterochromatin Protein 1 (HP1a). Using RNA-Seq analyses we discovered that Hmr and Lhr are required to repress transcripts from satellite DNAs and many families of transposable elements (TEs). By comparing Hmr and Lhr function between D. melanogaster and D. simulans we identify several satellite DNAs and TEs that are differentially regulated between the species. Hmr and Lhr mutations also cause massive overexpression of telomeric TEs and significant telomere lengthening. Hmr and Lhr therefore regulate three types of heterochromatic sequences that are responsible for the significant differences in genome size and structure between D. melanogaster and D. simulans and have high potential to cause genetic conflicts with host fitness. We further find that many TEs are overexpressed in hybrids but that those specifically mis-expressed in lethal hybrids do not closely correlate with Hmr function. Our results therefore argue that adaptive divergence of heterochromatin proteins in response to repetitive DNAs is an important underlying force driving the evolution of hybrid incompatibility genes, but that hybrid lethality likely results from novel epistatic genetic interactions that are distinct to the hybrid background. Sister species capable of mating often produce hybrids that are sterile or die during development. This reproductive isolation is caused by incompatibilities between the two sister species' genomes. Some hybrid incompatibilities involve genes that encode rapidly evolving proteins that localize to heterochromatin. Heterochromatin is largely made up of highly repetitive transposable elements and satellite DNAs. It has been hypothesized that rapid changes in heterochromatic DNA drives the changes in these HI genes and thus the evolution of reproductive isolation. In support of this model, we show that two rapidly evolving HI proteins, Lhr and Hmr, which reproductively isolate the fruit fly sister species D. melanogaster and D. simulans, repress transposable elements and satellite DNAs. These proteins also help regulate the length of the atypical Drosophila telomeres, which are themselves made of domesticated transposable elements. Our data suggest that these proteins are part of the adaptive machinery that allows the host to respond to changes and increases in heterochromatin and to maintain the activity of genes located within or adjacent to heterochromatin.
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Affiliation(s)
- P. R. V. Satyaki
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Tawny N. Cuykendall
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Kevin H-C. Wei
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Nicholas J. Brideau
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - S. Aruna
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Patrick M. Ferree
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Shuqing Ji
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Daniel A. Barbash
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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19
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Wang IX, Core LJ, Kwak H, Brady L, Bruzel A, McDaniel L, Richards AL, Wu M, Grunseich C, Lis JT, Cheung VG. RNA-DNA differences are generated in human cells within seconds after RNA exits polymerase II. Cell Rep 2014; 6:906-15. [PMID: 24561252 DOI: 10.1016/j.celrep.2014.01.037] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 12/27/2013] [Accepted: 01/28/2014] [Indexed: 10/25/2022] Open
Abstract
RNA sequences are expected to be identical to their corresponding DNA sequences. Here, we found all 12 types of RNA-DNA sequence differences (RDDs) in nascent RNA. Our results show that RDDs begin to occur in RNA chains ~55 nt from the RNA polymerase II (Pol II) active site. These RDDs occur so soon after transcription that they are incompatible with known deaminase-mediated RNA-editing mechanisms. Moreover, the 55 nt delay in appearance indicates that they do not arise during RNA synthesis by Pol II or as a direct consequence of modified base incorporation. Preliminary data suggest that RDD and R-loop formations may be coupled. These findings identify sequence substitution as an early step in cotranscriptional RNA processing.
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Affiliation(s)
- Isabel X Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Leighton J Core
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Lauren Brady
- Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alan Bruzel
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Lee McDaniel
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Allison L Richards
- Human Genetics Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ming Wu
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Christopher Grunseich
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
| | - Vivian G Cheung
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Departments of Pediatrics and Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
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20
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Abstract
The kinetics with which promoter-proximal paused RNA polymerase II (Pol II) undergoes premature termination versus productive elongation is central to understanding underlying mechanisms of metazoan transcription regulation. To assess the fate of Pol II quantitatively, we tracked photoactivatable GFP-tagged Pol II at uninduced Hsp70 on polytene chromosomes and showed that Pol II is stably paused with a half-life of 5 min. Biochemical analysis of short nascent RNA from Hsp70 reveals that this half-life is determined by two comparable rates of productive elongation and premature termination of paused Pol II. Importantly, heat shock dramatically increases elongating Pol II without decreasing termination, indicating that regulation acts at the step of paused Pol II entry to productive elongation.
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21
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Pagano JM, Kwak H, Waters CT, Sprouse RO, White BS, Ozer A, Szeto K, Shalloway D, Craighead HG, Lis JT. Defining NELF-E RNA binding in HIV-1 and promoter-proximal pause regions. PLoS Genet 2014; 10:e1004090. [PMID: 24453987 PMCID: PMC3894171 DOI: 10.1371/journal.pgen.1004090] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 11/22/2013] [Indexed: 11/22/2022] Open
Abstract
The four-subunit Negative Elongation Factor (NELF) is a major regulator of RNA Polymerase II (Pol II) pausing. The subunit NELF-E contains a conserved RNA Recognition Motif (RRM) and is proposed to facilitate Poll II pausing through its association with nascent transcribed RNA. However, conflicting ideas have emerged for the function of its RNA binding activity. Here, we use in vitro selection strategies and quantitative biochemistry to identify and characterize the consensus NELF-E binding element (NBE) that is required for sequence specific RNA recognition (NBE: CUGAGGA(U) for Drosophila). An NBE-like element is present within the loop region of the transactivation-response element (TAR) of HIV-1 RNA, a known regulatory target of human NELF-E. The NBE is required for high affinity binding, as opposed to the lower stem of TAR, as previously claimed. We also identify a non-conserved region within the RRM that contributes to the RNA recognition of Drosophila NELF-E. To understand the broader functional relevance of NBEs, we analyzed promoter-proximal regions genome-wide in Drosophila and show that the NBE is enriched +20 to +30 nucleotides downstream of the transcription start site. Consistent with the role of NELF in pausing, we observe a significant increase in NBEs among paused genes compared to non-paused genes. In addition to these observations, SELEX with nuclear run-on RNA enrich for NBE-like sequences. Together, these results describe the RNA binding behavior of NELF-E and supports a biological role for NELF-E in promoter-proximal pausing of both HIV-1 and cellular genes. RNA polymerase II (Pol II) is a molecular machine that is responsible for transcribing all protein coding genes in the eukaryotic genome. Transcription by Pol II is a highly regulated process consisting of several rate-limiting steps. During transcription elongation, a number of transcription factors are essential to modulate Pol II activity. One of these factors is the Negative Elongation Factor (NELF), and it plays a major role in promoter-proximal pausing, a widespread phenomenon during early transcription elongation. NELF-E, a protein subunit of the NELF complex contains a conserved RNA binding domain that is thought to regulate transcription through its interaction with newly transcribed RNA made by Pol II. However, the function of the RNA binding activity of NELF-E remains unresolved due to prior conflicting studies. Here, we clarify the RNA binding properties of NELF-E and provide insight into how this protein might facilitate promoter-proximal pausing of Pol II in transcription. Moreover, we identify the precise region of NELF-E binding in one of its known regulatory targets, HIV-1. Taken together, the results presented indicate a dynamic interplay between NELF and specific RNA sequences around the promoter pause region to modulate early transcription elongation.
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Affiliation(s)
- John M Pagano
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Colin T Waters
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Rebekka O Sprouse
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Brian S White
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Abdullah Ozer
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Kylan Szeto
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America
| | - David Shalloway
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Harold G Craighead
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
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22
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Abstract
Elongation is becoming increasingly recognized as a critical step in eukaryotic transcriptional regulation. Although traditional genetic and biochemical studies have identified major players of transcriptional elongation, our understanding of the importance and roles of these factors is evolving rapidly through the recent advances in genome-wide and single-molecule technologies. Here, we focus on how elongation can modulate the transcriptional outcome through the rate-liming step of RNA polymerase II (Pol II) pausing near promoters and how the participating factors were identified. Among the factors we describe are the pausing factors--NELF (negative elongation factor) and DSIF (DRB sensitivity-inducing factor)--and P-TEFb (positive elongation factor b), which is the key player in pause release. We also describe the high-resolution view of Pol II pausing and propose nonexclusive models for how pausing is achieved. We then discuss Pol II elongation through the bodies of genes and the roles of FACT and SPT6, factors that allow Pol II to move through nucleosomes.
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Affiliation(s)
- Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703; ,
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23
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Abstract
Transcription regulation occurs frequently through promoter-associated pausing of RNA polymerase II (Pol II). We developed a precision nuclear run-on and sequencing (PRO-seq) assay to map the genome-wide distribution of transcriptionally engaged Pol II at base pair resolution. Pol II accumulates immediately downstream of promoters, at intron-exon junctions that are efficiently used for splicing, and over 3' polyadenylation sites. Focused analyses of promoters reveal that pausing is not fixed relative to initiation sites, nor is it specified directly by the position of a particular core promoter element or the first nucleosome. Core promoter elements function beyond initiation, and when optimally positioned they act collectively to dictate the position and strength of pausing. This "complex interaction" model was tested with insertional mutagenesis of the Drosophila Hsp70 core promoter.
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Affiliation(s)
- Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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24
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Schaaf CA, Kwak H, Koenig A, Misulovin Z, Gohara DW, Watson A, Zhou Y, Lis JT, Dorsett D. Genome-wide control of RNA polymerase II activity by cohesin. PLoS Genet 2013; 9:e1003382. [PMID: 23555293 PMCID: PMC3605059 DOI: 10.1371/journal.pgen.1003382] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 01/30/2013] [Indexed: 11/22/2022] Open
Abstract
Cohesin is a well-known mediator of sister chromatid cohesion, but it also influences gene expression and development. These non-canonical roles of cohesin are not well understood, but are vital: gene expression and development are altered by modest changes in cohesin function that do not disrupt chromatid cohesion. To clarify cohesin's roles in transcription, we measured how cohesin controls RNA polymerase II (Pol II) activity by genome-wide chromatin immunoprecipitation and precision global run-on sequencing. On average, cohesin-binding genes have more transcriptionally active Pol II and promoter-proximal Pol II pausing than non-binding genes, and are more efficient, producing higher steady state levels of mRNA per transcribing Pol II complex. Cohesin depletion frequently decreases gene body transcription but increases pausing at cohesin-binding genes, indicating that cohesin often facilitates transition of paused Pol II to elongation. In many cases, this likely reflects a role for cohesin in transcriptional enhancer function. Strikingly, more than 95% of predicted extragenic enhancers bind cohesin, and cohesin depletion can reduce their association with Pol II, indicating that cohesin facilitates enhancer-promoter contact. Cohesin depletion decreases the levels of transcriptionally engaged Pol II at the promoters of most genes that don't bind cohesin, suggesting that cohesin controls expression of one or more broadly acting general transcription factors. The multiple transcriptional roles of cohesin revealed by these studies likely underlie the growth and developmental deficits caused by minor changes in cohesin activity.
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Affiliation(s)
- Cheri A. Schaaf
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Amanda Koenig
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Ziva Misulovin
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - David W. Gohara
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Audrey Watson
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Yanjiao Zhou
- The Genome Center, Department of Genetics, Washington University in St. Louis School of Medicine, Saint Louis, Missouri, United States of America
| | - John T. Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
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Core LJ, Waterfall JJ, Gilchrist DA, Fargo DC, Kwak H, Adelman K, Lis JT. Defining the status of RNA polymerase at promoters. Cell Rep 2012; 2:1025-35. [PMID: 23062713 DOI: 10.1016/j.celrep.2012.08.034] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 08/24/2012] [Accepted: 08/30/2012] [Indexed: 10/27/2022] Open
Abstract
Recent genome-wide studies in metazoans have shown that RNA polymerase II (Pol II) accumulates to high densities on many promoters at a rate-limited step in transcription. However, the status of this Pol II remains an area of debate. Here, we compare quantitative outputs of a global run-on sequencing assay and chromatin immunoprecipitation sequencing assays and demonstrate that the majority of the Pol II on Drosophila promoters is transcriptionally engaged; very little exists in a preinitiation or arrested complex. These promoter-proximal polymerases are inhibited from further elongation by detergent-sensitive factors, and knockdown of negative elongation factor, NELF, reduces their levels. These results not only solidify the notion that pausing occurs at most promoters, but demonstrate that it is the major rate-limiting step in early transcription at these promoters. Finally, the divergent elongation complexes seen at mammalian promoters are far less prevalent in Drosophila, and this specificity in orientation correlates with directional core promoter elements, which are abundant in Drosophila.
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Affiliation(s)
- Leighton J Core
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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26
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Kim S, Kim T, Kwak H, Song S, Sohn J, Yoon H, Shin D, Park S, Jeong J. Reference Values And Determinants Of Nasal Nitric Oxide In Healthy Adults. J Allergy Clin Immunol 2011. [DOI: 10.1016/j.jaci.2010.12.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Khoo KH, Zayak AT, Kwak H, Chelikowsky JR. First-principles study of confinement effects on the Raman spectra of Si nanocrystals. Phys Rev Lett 2010; 105:115504. [PMID: 20867585 DOI: 10.1103/physrevlett.105.115504] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 08/05/2010] [Indexed: 05/29/2023]
Abstract
The Raman spectra of Si nanocrystals are studied as a function of nanocrystal diameter using pseudopotential density functional theory and the Placzek approximation. Our calculations reproduce the redshift and broadening of the optical Raman peak with decreasing nanocrystal size, and calculated peak frequencies show good agreement with experimental values. We also find that a surface induced softening of vibrational modes is largely responsible for the Raman redshift, with relaxation of momentum conservation playing only a minor role.
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Affiliation(s)
- K H Khoo
- Center for Computational Materials, Institute for Computational Engineering and Sciences, University of Texas, Austin, Texas 78712, USA
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28
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Chae MJ, Sung HY, Kim EH, Lee M, Kwak H, Chae CH, Kim S, Park WY. Chemical inhibitors destabilize HuR binding to the AU-rich element of TNF-alpha mRNA. Exp Mol Med 2010; 41:824-31. [PMID: 19949288 DOI: 10.3858/emm.2009.41.11.088] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hu protein R (HuR) binds to the AU-rich element (ARE) in the 3UTR to stabilize TNF-alpha mRNA. Here, we identified chemical inhibitors of the interaction between HuR and the ARE of TNF-alpha mRNA using RNA electrophoretic mobility gel shift assay (EMSA) and filter binding assay. Of 179 chemicals screened, we identified three with a half-maximal inhibitory concentration (IC(50)) below 10 microM. The IC(50) of quercetin, b-40, and b-41 were 1.4, 0.38, and 6.21 microM, respectively, for binding of HuR protein to TNF-alpha mRNA. Quercetin and b-40 did not inhibit binding of tristetraprolin to the ARE of TNF-alpha mRNA. When LPS-treated RAW264.7 cells were treated with quercetin and b-40, we observed decreased stability of TNF-alpha mRNA and decreased levels of secreted TNF-alpha. From these results, we could find inhibitors for the TNF-alpha mRNA stability, which might be used advantageously for both the study for post-transcriptional regulation and the discovery of new anti-inflammation drugs.
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Affiliation(s)
- Min-Ju Chae
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
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29
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Abstract
Endoscopic duodenal polypectomy is a routine procedure particularly useful for obtaining histological diagnosis but it is not without serious complications. This is a case report of severe necrotising pancreatitis after duodenal polypectomy. We suggest that experienced endoscopists should carry out polypectomies and that clear guidelines for the management of duodenal polyps are required. Patients undergoing endoscopic duodenal polypectomies should be placed at the beginning of the endoscopy list and observed for at least 4 h.
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Affiliation(s)
- H Kwak
- Department of General Surgery, Royal Gwent Hospital, Newport, UK.
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30
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Dang TTN, Mahapatra SP, Sridhar V, Kim JK, Kim KJ, Kwak H. Dielectric properties of nanotube reinforced butyl elastomer composites. J Appl Polym Sci 2009. [DOI: 10.1002/app.30166] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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31
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Kwak H, Han Y. Abstract No. 68: Acute Stroke Associated with Obstruction of Proximal Internal Carotid Artery: Effect of Carotid Stent and Intraarterial Thrombolysis. J Vasc Interv Radiol 2009. [DOI: 10.1016/j.jvir.2008.12.403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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32
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Kwak H, Han Y. Abstract No. 316: Acute Upper Limb Ischemia: Usefulness of Aspiration Thrombectomy After Brachial Artery Puncture. J Vasc Interv Radiol 2009. [DOI: 10.1016/j.jvir.2008.12.311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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33
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Chung J, Kwak H, Jung S. POD-6.03: The Comparison of Efficacy and Side Effects Between M-VAC and GC Chemotherapy in Advanced and Metastatic Urothelial Carcinoma Patients with Good Performance Status. Urology 2008. [DOI: 10.1016/j.urology.2008.08.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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34
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Mahapatra SP, Sridhar V, Tripathy DK, Kim JK, Kwak H. Dynamic mechanical and dielectric relaxation characteristics of microcellular rubber composites. POLYM ADVAN TECHNOL 2008. [DOI: 10.1002/pat.1133] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Kwak H, Bae Y, Choo K, Lee S, Lee J, Park K. Differential control of alveolar and ductal development in grafts of rat mammary clonogenic epithelial cells. EJC Suppl 2008. [DOI: 10.1016/s1359-6349(08)70496-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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36
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37
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Kim JY, Kwak H, Choi KU, Chung J, Bae YT, Lee MK, Kim HW, Park DY, Lee CH, Huh KY, Sol MY. Array CGH analysisin neoadjuvant chemotherapy for breast cancer. J Clin Oncol 2005. [DOI: 10.1200/jco.2005.23.16_suppl.786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- J. Y. Kim
- Medcl Coll of Pusan National Univ, Busan, Republic of Korea
| | - H. Kwak
- Medcl Coll of Pusan National Univ, Busan, Republic of Korea
| | - K. U. Choi
- Medcl Coll of Pusan National Univ, Busan, Republic of Korea
| | - J. Chung
- Medcl Coll of Pusan National Univ, Busan, Republic of Korea
| | - Y. T. Bae
- Medcl Coll of Pusan National Univ, Busan, Republic of Korea
| | - M. K. Lee
- Medcl Coll of Pusan National Univ, Busan, Republic of Korea
| | - H. W. Kim
- Medcl Coll of Pusan National Univ, Busan, Republic of Korea
| | - D. Y. Park
- Medcl Coll of Pusan National Univ, Busan, Republic of Korea
| | - C. H. Lee
- Medcl Coll of Pusan National Univ, Busan, Republic of Korea
| | - K. Y. Huh
- Medcl Coll of Pusan National Univ, Busan, Republic of Korea
| | - M. Y. Sol
- Medcl Coll of Pusan National Univ, Busan, Republic of Korea
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38
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Kwak H. Breast conserving surgery by immediate repair of partial mastectomy defects. Eur J Cancer 2002. [DOI: 10.1016/s0959-8049(02)80337-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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39
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Kwak H. Stem cell characteristics of transplanted rat mammary clonogens. Eur J Cancer 2002. [DOI: 10.1016/s0959-8049(02)80151-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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40
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41
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Abstract
The effects of arginine on selective immune responses were investigated in a high arginine-requiring (HA) and low arginine-requiring (LA) strain of chickens. Female chickens from these strains were fed diet containing a nutritionally inadequate level of arginine (0.53% arginine diet) or a surfeit level of arginine (1.53% arginine diet) for 2 weeks. Compared to LA chickens, HA chickens showed a higher feed efficiency, body weight gain, and relative thymus and spleen weights with L-arginine supplementation (p < 0.05). In both HA and LA chickens, a deficiency of arginine significantly decreased the delayed-type hypersensitivity response (p < 0.05) and nitric oxide (NO) production from macrophages. Chickens of the HA strain had higher NO production than those of LA strain with E. coli lipopolysaccharide (LPS) activation. This study indicates that dietary arginine concentration influences the immune status of chickens and that strains that differ in arginine requirements for growth may differ in their arginine needs for immune function.
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Affiliation(s)
- H Kwak
- Department of Microbiology and Immunology, Cornell University, 14853, Ithaca, NY, USA
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42
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Kwak H, Bae M, Lee M, Sung H, Shin J, Ahn G, Kim Y, Lee C, Cho M. Effects of cartap on the early-life stages of medaka (Oryzias latipes). Bull Environ Contam Toxicol 2000; 65:717-723. [PMID: 11080351 DOI: 10.1007/s0012800182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Affiliation(s)
- H Kwak
- College of Veterinary Medicine, Seoul National University, Suwon 441-744, Korea
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43
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Kwak H, Lee M, Cho M. Interrelationship of apoptosis, mutation, and cell proliferation in N-methyl-N'-nitro-N-nitrosoguanidine (MNNG)-induced medaka carcinogenesis model. Aquat Toxicol 2000; 50:317-329. [PMID: 10967394 DOI: 10.1016/s0166-445x(00)00093-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The present study examined the interrelationship of GSH depletion, apoptosis, mutation, and cell proliferation following carcinogen exposure. Medaka (Oryzias latipes) were investigated following a 28 day, three times/week pulse exposure to N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). Fish (5 weeks old) were exposed to MNNG at concentrations of 0, 0.5, and 1 mg l(-1) and reared for 3, 5 and 7 more months after the last day of exposure. GSH levels were decreased in the higher concentration groups and longer-reared groups. Flow cytometric analysis revealed that fish from the groups reared 3 and 5 months showed active apoptotic changes in the dose- and time-dependent manner, but the group reared 7 months had fewer apoptotic, rather showed more necrotic and carcinogenic alterations. Mutational responses were detected by an arbitrarily primed polymerase chain reaction (AP-PCR) fingerprinting method using whole body DNA samples as templates and pBR primer. A mutational change was expressed by a loss or gain of a band. There was a time-dependent mutational change, but no distinctive concentration-dependent one. A band from normal fish sample that disappeared after treatment of MNNG was excised and sequenced. The band had an 869 base pair-long sequence, however, there was no putative protein-coding region based on an analysis by DNAsis. Spindle cell sarcomas invading muscle were detected on the whole body sections from three of ten fish examined, and immunohistochemical analysis with PCNA showed that tumor cells were actively proliferating. However, terminal deoxynucleotidyl transferase (TdT) assay showed that tumored fish still had active apoptotic cell changes in the tissues without tumor. This study shows not only the interrelationship of GSH depletion, apoptosis, mutation and cell proliferation, but also indicates that medaka is appropriate as a fish model for research on the passage of carcinogenesis.
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Affiliation(s)
- H Kwak
- Laboratory of Toxicology, College of Veterinary Medicine, Seoul National University, 441-744, Suwon, Korea
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44
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Shin M, Kim B, Mar W, Fang M, Son J, Kim M, Kwak H, Bae M, Byun T, Park S, Chun B, Byun J, An G, Lee B, Cho M. Mutagenicity of recombinant antihemophilic factor (GC-gamma AHF). Arzneimittelforschung 2000; 50:316-21. [PMID: 10758786 DOI: 10.1055/s-0031-1300207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
This study was carried out to evaluate the mutagenic potential of recombinant antihemophilic factor VIII (GC-gamma AHF). Salmonella typhimurium (S. typhimurium) reversion assay with/without histidine moiety, chromosomal aberration assay on Chinese hamster lung (CHL) fibroblast cells and in vivo micronucleus assay using mouse bone marrow cells and supravital micronucleus assay using peripheral blood were performed. GC-gamma AHF containing histidine did show inconsistent and irregular mutagenic effects on S. typhimurium TA98, TA100, TA1535 and TA1537 both in the absence and presence of the metabolic activation system, however, GC-gamma AHF without histidine showed no mutagenic effects regardless of the metabolic activation system, thus suggesting that the histidine moiety in GC-gamma AHF might cause inconsistent mutagenic effect. Also GC-gamma AHF did not increase the number of cells having structural or numerical chromosome aberration in the cytogenetic test. In classical and supravital micronucleus assay, no significant increases were observed in the occurrence of micronucleated polychromatic erythrocytes and micronucleated peripheral lymphocytes in male ICR mice. These results strongly indicate that GC-gamma AHF has no genetic toxicity under these experimental conditions.
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Affiliation(s)
- M Shin
- College of Veterinary Medicine, Seoul National University, Suwon, Korea
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45
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Abstract
In vivo effects of graded dietary levels of arginine on the body and lymphoid organs were investigated using Cornell K strain chickens of the B15/B15 haplotype. Two-week-old birds were fed an arginine-deficient basal diet (0.53% arginine) supplemented with additional arginine (up to 1.0% L-arginine to the diet). At four weeks of age, body weight, lymphoid organ weight, and concentrations of amino acids in plasma were measured. Arginine supplementation produced significant increases in plasma arginine (from 200 nM in chicks fed the basal diet to 2,000 nM in chicks receiving the 1.5% arginine diet) and ornithine concentrations (from 17 nM in chicks fed the basal diet to 500 nM in chicks receiving the 1.5% arginine diet). The arginine-deficient diet reduced body weight gain (P < 0.0001) and thymus, spleen, and bursa of Fabricius weights (P < 0.05). In contrast to the bursa weight, the thymus and spleen weights, as percentages of body weight, were also decreased (P < 0.05). This study suggests that arginine markedly influences lymphoid organ development, with a more pronounced effect on the thymus and spleen than on the bursa of Fabricius.
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Affiliation(s)
- H Kwak
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
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