Loss of the abundant nuclear non-coding RNAMALAT1is compatible with life and development

Abstract

The metastasis-associated lung adenocarcinoma transcript 1, MALAT1, is a long non-coding RNA (lncRNA) that has been discovered as a marker for lung cancer metastasis. It is highly abundant, its expression is strongly regulated in many tumor entities including lung adenocarcinoma and hepatocellular carcinoma as well as physiological processes, and it is associated with many RNA binding proteins and highly conserved throughout evolution. The nuclear transcript MALAT-1 has been functionally associated with gene regulation and alternative splicing and its regulation has been shown to impact proliferation, apoptosis, migration and invasion. Here, we have developed a human and a mouse knockout system to study the loss-of-function phenotypes of this important ncRNA. In human tumor cells, MALAT1 expression was abrogated using Zinc Finger Nucleases. Unexpectedly, the quantitative loss of MALAT1 did neither affect proliferation nor cell cycle progression nor nuclear architecture in human lung or liver cancer cells. Moreover, genetic loss of Malat1 in a knockout mouse model did not give rise to any obvious phenotype or histological abnormalities in Malat1-null compared with wild-type animals. Thus, loss of the abundant nuclear long ncRNA MALAT1 is compatible with cell viability and normal development.

Long Noncoding RNAs: Past, Present, and Future

“…A most puzzling fact, however, is that in spite of their abundance and association with some of the most prominent subnuclear structures, knockouts of neither NEAT1 nor MALAT1 have robust phenotypes (Nakagawa et al , 2012Eissmann et al 2012;Zhang et al 2012). These recent observations add to the mystery surrounding lncRNAs and support the assertion that quantity and function do not necessarily correlate.…”

“…For instance, Kcnq1ot1 has a half-life of 1 hr (Clark et al 2012), the lncRNAs in the Xic are found only in placental mammals and have low conservation even within this taxon (Davidow et al 2007), and RepA exists at 5-10 copies per cell (Zhao et al 2008). Yet even fully processed transcripts that interact with protein factors might not be essential (Ponting and Belgard 2010;van Bakel et al 2010;Schorderet and Duboule 2011;Eissmann et al 2012). Ultimately, the true test for function lies in the detailed, mechanistic dissection of the genetic pathways and cellular activities for each individual putative lncRNA (see Figure 4).…”

Critical roles of long noncoding RNAs in Drosophila spermatogenesis

“…Those studies were generally conducted in cell-based in vitro systems; however, phenotypes at the cellular and organismal levels are frequently discrepant. For example, loss-of-function studies of Malat1 or Dlx6os1 in mouse revealed subtle or undetectable phenotypes (Bond et al 2009;Eißmann et al 2012), despite the fact that these lncRNAs appear to be important at the cellular level. Therefore, the gold standard in the field is the targeted in vivo silencing or deletion of specific lncRNAs (Mattick 2013).…”

Long non-coding RNA in health and disease

“…Various genetic model systems have to be established to understand the functional roles of lncRNAs:protein interactions that modulate chromatin remodeling complexes, gene and genome regulation to investigate lncRNA-associated pathogenesis of disease or developmental defects. In two different projects generating Malat1 knockout mice, any apparent phenotype or alteration of the murine development was observed [83,84]. Only in cis genes of Malat1 were differentially expressed [84].…”