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Thangavel S, Mendoza-Maldonado R, Tissino E, Sidorova JM, Yin J, Wang W, Monnat RJ, Falaschi A, Vindigni A. Human RECQ1 and RECQ4 helicases play distinct roles in DNA replication initiation. Mol Cell Biol 2010; 30:1382-96. [PMID: 20065033 PMCID: PMC2832491 DOI: 10.1128/mcb.01290-09] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Revised: 10/26/2009] [Accepted: 12/29/2009] [Indexed: 11/20/2022] Open
Abstract
Cellular and biochemical studies support a role for all five human RecQ helicases in DNA replication; however, their specific functions during this process are unclear. Here we investigate the in vivo association of the five human RecQ helicases with three well-characterized human replication origins. We show that only RECQ1 (also called RECQL or RECQL1) and RECQ4 (also called RECQL4) associate with replication origins in a cell cycle-regulated fashion in unperturbed cells. RECQ4 is recruited to origins at late G(1), after ORC and MCM complex assembly, while RECQ1 and additional RECQ4 are loaded at origins at the onset of S phase, when licensed origins begin firing. Both proteins are lost from origins after DNA replication initiation, indicating either disassembly or tracking with the newly formed replisome. Nascent-origin DNA synthesis and the frequency of origin firing are reduced after RECQ1 depletion and, to a greater extent, after RECQ4 depletion. Depletion of RECQ1, though not that of RECQ4, also suppresses replication fork rates in otherwise unperturbed cells. These results indicate that RECQ1 and RECQ4 are integral components of the human replication complex and play distinct roles in DNA replication initiation and replication fork progression in vivo.
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Affiliation(s)
- Saravanabhavan Thangavel
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Ramiro Mendoza-Maldonado
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Erika Tissino
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Julia M. Sidorova
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Jinhu Yin
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Weidong Wang
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Raymond J. Monnat
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Arturo Falaschi
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Alessandro Vindigni
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
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Ying SY, Chang CP, Lin SL. Intron-mediated RNA interference, intronic microRNAs, and applications. Methods Mol Biol 2010; 629:205-37. [PMID: 20387152 DOI: 10.1007/978-1-60761-657-3_14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nearly 97% of the human genome is non-coding DNA. The intron occupies most of it around the gene-coding regions. Numerous intronic sequences have been recently found to encode microRNAs (miRNAs), responsible for RNA-mediated gene silencing through RNA interference (RNAi)-like pathways. miRNAs, small single-stranded regulatory RNAs capable of interfering with intracellular messenger RNAs (mRNAs) that contain either complete or partial complementarity, are useful for the design of new therapies against cancer polymorphism and viral mutation. This flexible characteristic differs from double-stranded siRNAs (small interfering RNAs) because more rigid complementarity is required for siRNA-induced RNAi gene silencing. miRNAs were firstly discovered in Caenorhabditis elegans as native RNA fragments that modulate a wide range of genetic regulatory pathways during embryonic development. Currently, varieties of miRNAs are widely reported in plants, animals, and even microorganisms. Intronic miRNA is a new class of miRNAs derived from the processing of gene introns. The intronic miRNAs differ from previously described intergenic miRNAs due to the requirement of type II RNA polymerases (Pol-II) and spliceosomal components for their biogenesis. Several kinds of intronic miRNAs have been identified in C. elegans, mouse, and human cells. However, neither function nor application has been reported. Here, we show that, for the first time, intron-derived miRNAs are able to induce RNA interference not only in human and mouse cell lines but also in zebrafish, chicken, and mouse, which demonstrates the evolutionary preservation of the intron-mediated gene silencing through miRNA functionality in cell and in vivo. Based on this novel mechanism, numerous biomedical applications have been developed, including cosmetic skin whitening, transgenic animal generation, anti-viral vaccination and therapy, and somatic cell reprogramming into induced pluripotent stem (iPS) cells. These findings suggest an important miRNA-mediated gene regulatory system, which fine-tunes a variety of cellular and developmental events through the mechanism of RNAi-like gene silencing.
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Affiliation(s)
- Shao-Yao Ying
- Department of Cell, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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