Genome-wide identification of novel long non-coding RNAs and their possible roles in hypoxic zebrafish brain

Bodhisattwa Banerjee; Debaprasad Koner; David Karasik; Nirmalendu Saha

doi:10.1016/j.ygeno.2020.11.023

Genome-wide identification of novel long non-coding RNAs and their possible roles in hypoxic zebrafish brain

Bodhisattwa Banerjee, Debaprasad Koner, David Karasik, Nirmalendu Saha

Bar-Ilan University - Azrieli Faculty of Medicine

North-Eastern Hill University India

Research output: Contribution to journal › Article › peer-review

13 Scopus citations

Abstract

Long non-coding RNAs (lncRNAs) are the master regulators of numerous biological processes. Hypoxia causes oxidative stress with severe and detrimental effects on brain function and acts as a critical initiating factor in the pathogenesis of Alzheimer's disease (AD). From the RNA-Seq in the forebrain (Fb), midbrain (Mb), and hindbrain (Hb) regions of hypoxic and normoxic zebrafish, we identified novel lncRNAs, whose potential cis targets showed involvement in neuronal development and differentiation pathways. Under hypoxia, several lncRNAs and mRNAs were differentially expressed. Co-expression studies indicated that the Fb and Hb regions' potential lncRNA target genes were involved in the AD pathogenesis. In contrast, those in Mb (cry1b, per1a, cipca) was responsible for regulating circadian rhythm. We identified specific lncRNAs present in the syntenic regions between zebrafish and humans, possibly functionally conserved. We thus identified several conserved lncRNAs as the probable regulators of AD genes (adrb3b, cav1, stat3, bace2, apoeb, psen1, s100b).

Original language	English
Pages (from-to)	29-43
Number of pages	15
Journal	Genomics
Volume	113
Issue number	1P1
DOIs	https://doi.org/10.1016/j.ygeno.2020.11.023
State	Published - Jan 2021

Bibliographical note

Publisher Copyright:
© 2020 Elsevier Inc.

Funding

This study was supported by a National Postdoctoral Fellowship project sanctioned to BB (PDF/2016/002013) by the Science and Engineering Research Board, New Delhi, India, and to NS by the National Agricultural Science Fund, Indian Council of Agricultural Research , New Delhi (ABA-7011/ 1018-19/240). NS acknowledges the FIST-II program (SR/FST/LS1-615/ 2014) by the DST, New Delhi. We thank Dr. Sumit Mukherjee, Bar-Ilan University, Israel, for his suggestions on bioinformatics works. This study was supported by a National Postdoctoral Fellowship project sanctioned to BB (PDF/2016/002013) by the Science and Engineering Research Board, New Delhi, India, and to NS by the National Agricultural Science Fund, Indian Council of Agricultural Research, New Delhi (ABA-7011/ 1018-19/240). NS acknowledges the FIST-II program (SR/FST/LS1-615/ 2014) by the DST, New Delhi. We thank Dr. Sumit Mukherjee, Bar-Ilan University, Israel, for his suggestions on bioinformatics works.

Funders	Funder number
National Agricultural Science Fund
Department of Science and Technology, Republic of South Africa
Department of Science and Technology, Ministry of Science and Technology, India
Indian Council of Agricultural Research	SR/FST/LS1-615/ 2014, ABA-7011/ 1018-19/240
Science and Engineering Research Board

Keywords

Alzheimer's disease
Brain regions
Hypoxia
Long non-coding RNAs
Zebrafish

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10.1016/j.ygeno.2020.11.023

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abstract = "Long non-coding RNAs (lncRNAs) are the master regulators of numerous biological processes. Hypoxia causes oxidative stress with severe and detrimental effects on brain function and acts as a critical initiating factor in the pathogenesis of Alzheimer's disease (AD). From the RNA-Seq in the forebrain (Fb), midbrain (Mb), and hindbrain (Hb) regions of hypoxic and normoxic zebrafish, we identified novel lncRNAs, whose potential cis targets showed involvement in neuronal development and differentiation pathways. Under hypoxia, several lncRNAs and mRNAs were differentially expressed. Co-expression studies indicated that the Fb and Hb regions' potential lncRNA target genes were involved in the AD pathogenesis. In contrast, those in Mb (cry1b, per1a, cipca) was responsible for regulating circadian rhythm. We identified specific lncRNAs present in the syntenic regions between zebrafish and humans, possibly functionally conserved. We thus identified several conserved lncRNAs as the probable regulators of AD genes (adrb3b, cav1, stat3, bace2, apoeb, psen1, s100b).",

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Genome-wide identification of novel long non-coding RNAs and their possible roles in hypoxic zebrafish brain

Abstract

Bibliographical note

Funding

Keywords

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