Dlk1-Dio3 locus-derived LncRNAs perpetuate postmitotic motor neuron cell fate and subtype identity

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Abstract

The mammalian imprinted Dlk1-Dio3 locus produces multiple long non-coding RNAs (lncRNAs) from the maternally inherited allele, including Meg3 (i.e., Gtl2) in the mammalian genome. Although this locus has well-characterized functions in stem cell and tumor contexts, its role during neural development is unknown. By profiling cell types at each stage of embryonic stem cell derived motor neurons (ESC~MNs) that recapitulate spinal cord development, we uncovered that lncRNAs expressed from the Dlk1-Dio3 locus are predominantly and gradually enriched in rostral motor neurons (MNs). Mechanistically, Meg3 and other Dlk1-Dio3 locus-derived lncRNAs facilitate Ezh2/Jarid2 interactions. Loss of these lncRNAs compromises the H3K27me3 landscape, leading to aberrant expression of progenitor and caudal Hox genes in postmitotic MNs. Our data thus illustrate that these lncRNAs in the Dlk1-Dio3 locus, particularly Meg3, play a critical role in maintaining postmitotic MN cell fate by repressing progenitor genes and they shape MN subtype identity by regulating Hox genes.

Data availability

All microarray, RNA-seq, ChIP-seq data have been deposited in GEO under accession codes GSE114283, GSE114285 and GSE114228.

The following data sets were generated

1. Chen J
2. Yen Y
(2018) Genome-wide maps of H3K27me3 in chromatin state in embryonic stem cells differentiated motor neurons
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE114283).

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE114283
1. Chen J
2. Lu Y
(2018) Next Generation Sequencing Facilitates Quantitative Analysis of ES, pMN, MN, and IN Transcriptomes
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE114285).

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE114285
1. Chen J
2. Yen Y
(2018) Transcriptome analysis of Meg3 KD and IG-DMR maternal deletion in ESC, pMN, and MN
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE114228).

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE114228

The following previously published data sets were used

1. Mazzoni et al
(2013) Induced V5-tagged Lhx3 (iLhx3-V5) in iNIL3-induced motor neurons (Day 4)
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM782847).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM782847
1. Mazzoni et al
(2013) Isl1/2 in iNIL3-induced motor neurons (Day 4)
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM782848).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi
1. Narendra et al
(2015) H3K4me3
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM1468401).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi
1. Rhee et al
(2016) H3K27ac_day6
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM2098385).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi
1. Rhee et al
(2016) ATAC_seq_day6
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM2098391).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi
1. Mahony et al
(2011) RAR_Day2+8hrsRA
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM482750).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi
1. Mahony et al
(2011) Pol2-S5P_Day2+8h
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM981593).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi
1. Li et al
(2017) ES-WT
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM2420680).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2420680
1. Li et al
(2017) AK4-WT
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM2420683).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2420683
1. Li et al
(2017) AK7-WT
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM2420684).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2420684

Article and author information

Author details

Ya-Ping Yen

Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China

Competing interests
The authors declare that no competing interests exist.
Wen-Fu Hsieh

Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China

Competing interests
The authors declare that no competing interests exist.
Ya-Yin Tsai

Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China

Competing interests
The authors declare that no competing interests exist.
Ya-Lin Lu

Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China

Competing interests
The authors declare that no competing interests exist.
Ee Shan Liau

Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China

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The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-4115-5573
Ho-Chiang Hsu

Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China

Competing interests
The authors declare that no competing interests exist.
Yen-Chung Chen

Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China

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The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-8529-1251
Ting-Chun Liu

Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China

Competing interests
The authors declare that no competing interests exist.
Mien Chang

Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China

Competing interests
The authors declare that no competing interests exist.
Joye Li

Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China

Competing interests
The authors declare that no competing interests exist.
Shau-Ping Lin

Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan, Republic of China

For correspondence
shaupinglin@ntu.edu.tw

Competing interests
The authors declare that no competing interests exist.
Jui-Hung Hung

Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China

For correspondence
juihunghung@gmail.com

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-2208-9213
Jun-An Chen

Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China

For correspondence
jachen@imb.sinica.edu.tw

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-9870-3203

Funding

Ministry of Science and Technology, Taiwan (RO1)

Jun-An Chen

National Health Research Institutes (CDG)

Jun-An Chen

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All of the live animals were kept in an SPF animal facility, approved and overseen by IACUC (12-07-389 ) Academia Sinica.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.