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Khazeem MM, Cowell IG, Harkin LF, Casement JW, Austin CA. Transcription of carbonyl reductase 1 is regulated by DNA topoisomerase II beta. FEBS Lett 2020; 594:3395-3405. [PMID: 32767399 DOI: 10.1002/1873-3468.13904] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 05/14/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/16/2022]
Abstract
DNA topoisomerase II beta (TOP2B) has a role in transcriptional regulation. Here, to further investigate transcriptional regulation by TOP2B, we used RNA-sequencing and real-time PCR to analyse the differential gene expression profiles of wild-type and two independent TOP2B-null pre-B Nalm-6 cell lines, one generated by targeted insertion and the other using CRISPR-Cas9 gene editing. We identified carbonyl reductase 1 (CBR1) among the most significantly downregulated genes in these TOP2B-null cells. Reduced CBR1 expression was accompanied by loss of binding of the transcription factors USF2 and MAX to the CBR1 promoter. We describe possible mechanisms by which loss of TOP2B results in CBR1 downregulation. To our knowledge, this is the first report of a link between TOP2B and CBR1.
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Affiliation(s)
- Mushtaq M Khazeem
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Ian G Cowell
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Lauren F Harkin
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - John W Casement
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Caroline A Austin
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
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Harkin LF, Lindsay SJ, Xu Y, Alzu'bi A, Ferrera A, Gullon EA, James OG, Clowry GJ. Corrigendum: Neurexins 1-3 Each Have a Distinct Pattern of Expression in the Early Developing Human Cerebral Cortex. Cereb Cortex 2019; 29:1705. [PMID: 30753338 DOI: 10.1093/cercor/bhz012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Indexed: 11/12/2022] Open
Affiliation(s)
- Lauren F Harkin
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne, UK.,Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne, UK
| | - Susan J Lindsay
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne, UK
| | - Yaobo Xu
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne, UK
| | - Ayman Alzu'bi
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne, UK.,Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne, UK
| | - Alexandra Ferrera
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne, UK.,Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne, UK
| | - Emily A Gullon
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne, UK.,Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne, UK
| | - Owen G James
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne, UK.,Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne, UK
| | - Gavin J Clowry
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
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Alzu'bi A, Lindsay SJ, Harkin LF, McIntyre J, Lisgo SN, Clowry GJ. The Transcription Factors COUP-TFI and COUP-TFII have Distinct Roles in Arealisation and GABAergic Interneuron Specification in the Early Human Fetal Telencephalon. Cereb Cortex 2017; 27:4971-4987. [PMID: 28922831 PMCID: PMC5903418 DOI: 10.1093/cercor/bhx185] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/12/2017] [Accepted: 07/03/2017] [Indexed: 12/13/2022] Open
Abstract
In human telencephalon at 8-12 postconceptional weeks, ribonucleic acid quantitative sequencing and immunohistochemistry revealed cortical chicken ovalbumin upstream promotor-transcription factor 1 (COUP-TFI) expression in a high ventro-posterior to low anterior gradient except for raised immunoreactivity in the anterior ventral pallium. Unlike in mouse, COUP-TFI and SP8 were extensively co-expressed in dorsal sensory neocortex and dorsal hippocampus whereas COUPTFI/COUPTFII co-expression defined ventral temporal cortex and ventral hippocampus. In the ganglionic eminences (GEs) COUP-TFI immunoreactivity demarcated the proliferative zones of caudal GE (CGE), dorsal medial GE (MGE), MGE/lateral GE (LGE) boundary, and ventral LGE whereas COUP-TFII was limited to ventral CGE and the MGE/LGE boundary. Co-labeling with gamma amino butyric acidergic interneuron markers revealed that COUP-TFI was expressed in subpopulations of either MGE-derived (SOX6+) or CGE-derived (calretinin+/SP8+) interneurons. COUP-TFII was mainly confined to CGE-derived interneurons. Twice as many GAD67+ cortical cells co-labeled for COUP-TFI than for COUP-TFII. A fifth of COUP-TFI cells also co-expressed COUP-TFII, and cells expressing either transcription factor followed posterior or anterio-lateral pathways into the cortex, therefore, a segregation of migration pathways according to COUP-TF expression as proposed in mouse was not observed. In cultures differentiated from isolated human cortical progenitors, many cells expressed either COUP-TF and 30% also co-expressed GABA, however no cells expressed NKX2.1. This suggests interneurons could be generated intracortically from progenitors expressing either COUP-TF.
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Affiliation(s)
- Ayman Alzu'bi
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Susan J Lindsay
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Lauren F Harkin
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
- Present address: School of Healthcare Science, Manchester Metropolitan University, UK
| | - Jack McIntyre
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Steven N Lisgo
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Gavin J Clowry
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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Harkin LF, Lindsay SJ, Xu Y, Alzu'bi A, Ferrara A, Gullon EA, James OG, Clowry GJ. Neurexins 1-3 Each Have a Distinct Pattern of Expression in the Early Developing Human Cerebral Cortex. Cereb Cortex 2017; 27:216-232. [PMID: 28013231 PMCID: PMC5654756 DOI: 10.1093/cercor/bhw394] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/16/2016] [Accepted: 12/02/2016] [Indexed: 12/17/2022] Open
Abstract
Neurexins (NRXNs) are presynaptic terminal proteins and candidate neurodevelopmental disorder susceptibility genes; mutations presumably upset synaptic stabilization and function. However, analysis of human cortical tissue samples by RNAseq and quantitative real-time PCR at 8-12 postconceptional weeks, prior to extensive synapse formation, showed expression of all three NRXNs as well as several potential binding partners. However, the levels of expression were not identical; NRXN1 increased with age and NRXN2 levels were consistently higher than for NRXN3. Immunohistochemistry for each NRXN also revealed different expression patterns at this stage of development. NRXN1 and NRXN3 immunoreactivity was generally strongest in the cortical plate and increased in the ventricular zone with age, but was weak in the synaptogenic presubplate (pSP) and marginal zone. On the other hand, NRXN2 colocalized with synaptophysin in neurites of the pSP, but especially with GAP43 and CASK in growing axons of the intermediate zone. Alternative splicing modifies the role of NRXNs and we found evidence by RNAseq for exon skipping at splice site 4 and concomitant expression of KHDBRS proteins which control this splicing. NRXN2 may play a part in early cortical synaptogenesis, but NRXNs could have diverse roles in development including axon guidance, and intercellular communication between proliferating cells and/or migrating neurons.
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Affiliation(s)
- Lauren F Harkin
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
- Present address: School of Healthcare Science, Manchester Metropolitan University, Manchester, M1 5GD, UK
| | - Susan J Lindsay
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
| | - Yaobo Xu
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
- Present address: Wellcome Trust, Sanger Institute, Cambridge, CB10 1SA, UK
| | - Ayman Alzu'bi
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
| | - Alexandra Ferrara
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
| | - Emily A Gullon
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
| | - Owen G James
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
- Present address: MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Gavin J Clowry
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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Lindsay SJ, Xu Y, Lisgo SN, Harkin LF, Copp AJ, Gerrelli D, Clowry GJ, Talbot A, Keogh MJ, Coxhead J, Santibanez-Koref M, Chinnery PF. HDBR Expression: A Unique Resource for Global and Individual Gene Expression Studies during Early Human Brain Development. Front Neuroanat 2016; 10:86. [PMID: 27833533 PMCID: PMC5080337 DOI: 10.3389/fnana.2016.00086] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/12/2016] [Indexed: 12/21/2022] Open
Affiliation(s)
- Susan J Lindsay
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | - Yaobo Xu
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | - Steven N Lisgo
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | - Lauren F Harkin
- Institute of Genetic Medicine, Newcastle UniversityNewcastle upon Tyne, UK; Institute of Neuroscience, Newcastle UniversityNewcastle upon Tyne, UK
| | - Andrew J Copp
- Institute of Child Health, University College London London, UK
| | - Dianne Gerrelli
- Institute of Child Health, University College London London, UK
| | - Gavin J Clowry
- Institute of Neuroscience, Newcastle University Newcastle upon Tyne, UK
| | - Aysha Talbot
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | - Michael J Keogh
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | - Jonathan Coxhead
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | | | - Patrick F Chinnery
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
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Harkin LF, Gerrelli D, Gold Diaz DC, Santos C, Alzu'bi A, Austin CA, Clowry GJ. Distinct expression patterns for type II topoisomerases IIA and IIB in the early foetal human telencephalon. J Anat 2015; 228:452-63. [PMID: 26612825 PMCID: PMC4832326 DOI: 10.1111/joa.12416] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2015] [Indexed: 01/16/2023] Open
Abstract
TOP2A and TOP2B are type II topoisomerase enzymes that have important but distinct roles in DNA replication and RNA transcription. Recently, TOP2B has been implicated in the transcription of long genes in particular that play crucial roles in neural development and are susceptible to mutations contributing to neurodevelopmental conditions such as autism and schizophrenia. This study maps their expression in the early foetal human telencephalon between 9 and 12 post‐conceptional weeks. TOP2A immunoreactivity was restricted to cell nuclei of the proliferative layers of the cortex and ganglionic eminences (GE), including the ventricular zone and subventricular zone (SVZ) closely matching expression of the proliferation marker KI67. Comparison with sections immunolabelled for NKX2.1, a medial GE (MGE) marker, and PAX6, a cortical progenitor cell and lateral GE (LGE) marker, revealed that TOP2A‐expressing cells were more abundant in MGE than the LGE. In the cortex, TOP2B is expressed in cell nuclei in both proliferative (SVZ) and post‐mitotic compartments (intermediate zone and cortical plate) as revealed by comparison with immunostaining for PAX6 and the post‐mitotic neuron marker TBR1. However, co‐expression with KI67 was rare. In the GE, TOP2B was also expressed by proliferative and post‐mitotic compartments. In situ hybridisation studies confirmed these patterns of expression, except that TOP2A mRNA is restricted to cells in the G2/M phase of division. Thus, during early development, TOP2A is likely to have a role in cell proliferation, whereas TOP2B is expressed in post‐mitotic cells and may be important in controlling expression of long genes even at this early stage.
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Affiliation(s)
- Lauren F Harkin
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Chloe Santos
- HDBR Resource, UCL Institute of Child Health, London, UK
| | - Ayman Alzu'bi
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Caroline A Austin
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Gavin J Clowry
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
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