Dataset creators: 
Michelle L. Brinkmeier, Akima S. George, Leonard Y. M. Cheung, Ryan E. Mills, Philippa Melamed, Sally A. Camper
 

Dataset contact: 
Sally A. Camper, PhD.  scamper@umich.edu
 

Funding: 
National Institutes of Health (R01HD034283, R01HD097096 to SAC) and 
United States - Israel Binational Science Foundation (#2023086 to PM and SAC). 
 

Key points:
-We identified lncRNA expressed in mouse pituitary glands from embryonic day 12.5-14.5.
-We identified protein coding transcripts and lncRNA expressed in whole adult (7-8 wk) pituitary glands and in specialized hormone producing cell types including thyrotropes, gonadotropes, and somatotropes.
-We identified protein coding transcripts and lncRNA expressed in whole pituitary glands from postnatal day 7 mice and in thyrotropes.
 

Research overview: Mammalian genomes contain thousands of genes for long non-coding RNA (lncRNAs), some of which have been shown to affect protein-coding gene expression through diverse mechanisms. The lncRNA transcripts are longer than 200 nucleotides and are often capped, spliced and polyadenylated, but not translated into protein.  Nuclear lncRNAs can modify chromatin structure and transcription in trans or cis by interacting with the DNA, forming R-loops, and recruiting regulatory proteins.  Not much is known about the role of lncRNA in pituitary gland differentiation and function.  We mined transcriptome data from mouse pituitary glands collected at embryonic days 12.5 and 14.5 and identified over 200 different lncRNA transcripts.  To develop a research resource for the study of lncRNA, we used pituitary cre transgenes to tag pituitary cell types in adult mice with fluorescent markers, and enriched for thyrotropes, gonadotropes, and somatotropes using fluorescence activated cell sorting.  We determined the transcriptome of each cell population using RNA sequencing and mined the data for lncRNA.  We detected hundreds of lncRNAs in adult pituitary cells, a few were located immediately nearby genes that encode pituitary hormones or lineage-specific transcription factors.  The location of these lncRNAs suggests the possibility of a cis-acting regulatory role in pituitary development or function, and we observe coordinated expression of two of them with their putative target genes in transgenic mice.  This research resource sets the foundation for examining the actions of lncRNAs on their putative target genes and determining whether they have roles during development and in response to physiological demand.
 

Methodology:
RNA was prepared from adult pituitary tissue or sorted cells and cDNA was prepared using ribo-depletion to capture both mRNA and lncRNA without relying on polyadenylylation.  Samples were barcoded and sequenced in a strand-specific manner, on the Illumina HiSeq4000.  The bioinformatics pipeline involved use of FastQC to trim poor quality reads and Tuxedo Suite, TopHat, and Bowtie for alignment.  Read counts are expressed in transcripts per kilobase million (TPM).  We used a cut-off of 3 TPM for comparing gene expression between samples.

 
Files included here:
-_Suppl_Table_1_lncRNA_mgi_filter_final.xlsx - Supplemental Table 1: lncRNA expressed in e12.5-e14.5 mouse pituitary gland
-Suppl_Table_2_LncRNA.xlsx - Supplemental Table 2: lncRNA expressed in 7-8 wk mouse pituitary gland
-Suppl_Table_3_lncRNA_Tshb-cre.xlsx - Supplemental Table 3: lncRNA Enriched in Tshb-cre labeled cells relative to nontransgenic mouse pituitary glands (TPM)
-Suppl_Endo_204-00287.xlsx - 
 
CSV versions of Excel sheets:
-All genes.csv
-All genes > 1 TPM.csv
-All genes > 3 TPM.csv
-All lncRNA adult.csv
-All lncRNA > 3 TPM.csv


NOTE: Bulk RNA seq data has been deposited in Geo (GSE277389).  Embryonic pituitary cDNA clone end sequences are deposited at https://fantom.gsc.riken.jp/data/.

Related publication:
Michelle L. Brinkmeier, Akima S. George, Leonard Y. M. Cheung, Ryan E. Mills, Philippa Melamed, Sally A. Camper.  Long non-coding RNAs expressed in mouse pituitary development and mature hormone-producing cells.  Endocrinology, 2024 Nov 2:bqae147. doi: 10.1210/endocr/bqae147. Online ahead of print.PMID: 39487735
 

Use and Access:
This data set is made available under a Creative Commons Attribution-Noncommercial license (CC BY-NC 4.0).
 

To Cite Data:
Michelle L. Brinkmeier, Akima S. George, Leonard Y. M. Cheung, Ryan E. Mills, Philippa Melamed, Sally A. Camper.  (2024). Long non-coding RNAs expressed in mouse pituitary development and mature hormone-producing cells.  [Data set]. University of Michigan - Deep Blue. https://deepblue.lib.umich.edu/data (https://doi.org/10.7302/pnpj-jg34)