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Article

The Genome-Wide Impact of Nipblb Loss-of-Function on Zebrafish Gene Expression

by
Marco Spreafico
1,†,
Eleonora Mangano
2,†,
Mara Mazzola
1,
Clarissa Consolandi
2,
Roberta Bordoni
2,
Cristina Battaglia
1,
Silvio Bicciato
3,
Anna Marozzi
1,† and
Anna Pistocchi
1,*,†
1
Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy
2
Institute of Biomedical Technologies, Italian National Research Council (ITB-CNR), Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy
3
Department of Life Sciences, University of Modena and Reggio-Emilia, Via G. Campi 287, 41125 Modena, Italy
*
Author to whom correspondence should be addressed.
†
The authors contributed equally to this work.
Int. J. Mol. Sci. 2020, 21(24), 9719; https://doi.org/10.3390/ijms21249719
Submission received: 7 November 2020 / Revised: 15 December 2020 / Accepted: 17 December 2020 / Published: 19 December 2020
(This article belongs to the Special Issue Epigenetics, Transcriptome and Proteome Analysis of Zebrafish)
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Abstract

Transcriptional changes normally occur during development but also underlie differences between healthy and pathological conditions. Transcription factors or chromatin modifiers are involved in orchestrating gene activity, such as the cohesin genes and their regulator NIPBL. In our previous studies, using a zebrafish model for nipblb knockdown, we described the effect of nipblb loss-of-function in specific contexts, such as central nervous system development and hematopoiesis. However, the genome-wide transcriptional impact of nipblb loss-of-function in zebrafish embryos at diverse developmental stages remains under investigation. By RNA-seq analyses in zebrafish embryos at 24 h post-fertilization, we examined genome-wide effects of nipblb knockdown on transcriptional programs. Differential gene expression analysis revealed that nipblb loss-of-function has an impact on gene expression at 24 h post fertilization, mainly resulting in gene inactivation. A similar transcriptional effect has also been reported in other organisms, supporting the use of zebrafish as a model to understand the role of Nipbl in gene regulation during early vertebrate development. Moreover, we unraveled a connection between nipblb-dependent differential expression and gene expression patterns of hematological cell populations and AML subtypes, enforcing our previous evidence on the involvement of NIPBL-related transcriptional dysregulation in hematological malignancies.
Keywords: NIPBL; RNA sequencing; zebrafish; gene expression regulation; acute myeloid leukemia NIPBL; RNA sequencing; zebrafish; gene expression regulation; acute myeloid leukemia

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MDPI and ACS Style

Spreafico, M.; Mangano, E.; Mazzola, M.; Consolandi, C.; Bordoni, R.; Battaglia, C.; Bicciato, S.; Marozzi, A.; Pistocchi, A. The Genome-Wide Impact of Nipblb Loss-of-Function on Zebrafish Gene Expression. Int. J. Mol. Sci. 2020, 21, 9719. https://doi.org/10.3390/ijms21249719

AMA Style

Spreafico M, Mangano E, Mazzola M, Consolandi C, Bordoni R, Battaglia C, Bicciato S, Marozzi A, Pistocchi A. The Genome-Wide Impact of Nipblb Loss-of-Function on Zebrafish Gene Expression. International Journal of Molecular Sciences. 2020; 21(24):9719. https://doi.org/10.3390/ijms21249719

Chicago/Turabian Style

Spreafico, Marco, Eleonora Mangano, Mara Mazzola, Clarissa Consolandi, Roberta Bordoni, Cristina Battaglia, Silvio Bicciato, Anna Marozzi, and Anna Pistocchi. 2020. "The Genome-Wide Impact of Nipblb Loss-of-Function on Zebrafish Gene Expression" International Journal of Molecular Sciences 21, no. 24: 9719. https://doi.org/10.3390/ijms21249719

APA Style

Spreafico, M., Mangano, E., Mazzola, M., Consolandi, C., Bordoni, R., Battaglia, C., Bicciato, S., Marozzi, A., & Pistocchi, A. (2020). The Genome-Wide Impact of Nipblb Loss-of-Function on Zebrafish Gene Expression. International Journal of Molecular Sciences, 21(24), 9719. https://doi.org/10.3390/ijms21249719

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