Identification of 4438 novel lincRNAs involved in mouse pre-implantation embryonic development

Abstract

Long intergenic non-coding RNAs (lincRNAs) as a key group of non-coding RNAs have gained substantial attention. Though lincRNAs have been systematically explored in various mouse tissues and cell lines, large-scale identification of lincRNAs in mouse pre-implantation embryonic development (PED) process has not be documented previously. Therefore, it is important to identify and characterize novel lincRNAs that may be involved in PED. In this paper, we performed transcriptome assembly based on published single-cell RNA-seq data during mouse PED and identified 4,438 putative lincRNAs. Combining these with Ensembl lincRNAs, we established a reference catalog of 5,808 transcribed lincRNAs in PED. We then systematically analyzed the lincRNAs in this reference catalog and revealed that the identified novel PED lincRNAs are generally comparable with known Ensembl lincRNAs in genomic aspects. In addition, the global expression patterns can be separated by zygote first cleavage division in clustering analysis and we further identified and analyzed differentially expressed lincRNAs involved in this process. The expression of lincRNAs involved in the process is negatively correlated with promoter methylation in trend. The identified lincRNAs involved in zygote first cleavage division could have important roles in mouse early embryonic development and need further functional studies. Altogether, a novel reference catalog of mouse PED lincRNAs is provided and characterized, which would be a valuable resource for further functional analyses and may help elucidate the pre-implantation regulatory mechanism.

Identification and functional analysis of long intergenic noncoding RNA genes in porcine pre-implantation embryonic development

“…Considering the incomplete annotation in pig, herein we performed genome-wide characterization of novel lincRNAs using two signature tools independent of known annotations. As results, our newly identified lincRNAs in pig shared many characteristics with those in other mammalian species31617272829. They are lower in exon number, longer in exon, shorter in whole transcripts, lower in expression level and more specific in expression patterns than protein coding transcripts.…”

“…To quantitatively assess the expression specificity of each transcript, we applied an entropy-based metric that relies on Jensen-Shannon distance-based algorithm to calculate expression specificity score of each transcript27. Consistent with our previous observation31617, we have also found that our predicted pig lincRNAs show higher JS scores on average than protein-coding genes (mean 0.83 and 0.76; Kolomogorv-Smirnov Test, P -value < 2.2 × 10 −16 ) (Fig. 3B).…”

“…Therefore, understanding the molecular mechanism underlying ZGA is required. Although the transcription of lincRNAs have been extensively investigated in mouse and human PED21617, little is known about its function. In pig, ZGA mainly occurs between the 4-cell and 8-cell stages18.…”

Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat

“…The identification and characterization of goat lncRNAs, particularly in fetal skeletal muscle development, have been very limited compared with lncRNAs in human [2, 48] and other model organisms [3, 49]. In goat skeletal muscle, the main focus has been on genes and miRNAs rather than on lncRNAs [44, 45, 50, 51].…”

“…Generally, ncRNAs shorter than 200 nucleotides are usually described as small/short ncRNA, such as microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), small interfering RNAs (siRNAs), and classical ncRNAs such as ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), and small nucleolar RNAs (snoRNAs), whereas ncRNAs longer than 200 nucleotides are described as long ncRNAs (lncRNAs). In the past few years, an increasing number of lncRNAs have been discovered in mammal, including Homo sapiens [1, 2], Mus musculus [3–7], Bos taurus [8, 9], Sus scrofa [10–13], and Ovis aries [14]. And accordingly unveiled that lncRNAs play critical roles in biological processes like transcriptional regulation [15–17], epigenetic modification [18–20], development [21–23], cell differentiation [24–26], as well as in some diseases [27–29].…”