Circadian changes in long noncoding RNAs in the pineal gland

Coon, Steven L.; Munson, Peter J.; Cherukuri, Praveen F.; Sugden, David; Rath, Martin F.; Møller, Mette; Clokie, Samuel; Fu, Cong; Olanich, Mary E.; Rangel, Zoila G.; Werner, Thomas; Program, Nisc Comparative Sequencing; Mullikin, James C.; Klein, David C.

doi:10.1073/pnas.1207748109

Cited by 78 publications

(65 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Here, we found that RNA-sequencing coverage plots (Coon et al 2012) provide evidence that four Lhx9 transcripts, corresponding to those previously reported in mammals, exist in the embryonic rat pineal gland; in addition, a novel 3′-terminal exon was discovered (Fig. 3).…”

Section: Resultssupporting

confidence: 78%

The Lhx9 homeobox gene controls pineal gland development and prevents postnatal hydrocephalus

Yamazaki

Møller

et al. 2014

Brain Struct Funct

Self Cite

View full text Add to dashboard Cite

Lhx9 is a member of the LIM homeobox gene family. It is expressed during mammalian embryogenesis in the brain including the pineal gland. Deletion of Lhx9 results in sterility due to failure of gonadal development. The current study was initiated to investigate Lhx9 biology in the pineal gland. Lhx9 is highly expressed in the developing pineal gland of the rat with transcript abundance peaking early in development; transcript levels decrease postnatally to nearly undetectable levels in the adult, a temporal pattern that is generally similar to that reported for Lhx9 expression in other brain regions. Studies with C57BL/6J Lhx9−/− mutant mice revealed marked alterations in brain and pineal development. Specifically, the superficial pineal gland is hypoplastic, being reduced to a small cluster of pinealocytes surrounded by meningeal and vascular tissue. The deep pineal gland and the pineal stalk are also reduced in size. Although the brains of neonatal Lhx9−/− mutant mice appear normal, severe hydrocephalus develops in about 70 % of the Lhx9−/− mice at 5–8 weeks of age; these observations are the first to document that deletion of Lhx9 results in hydrocephalus and as such indicate that Lhx9 contributes to the maintenance of normal brain structure. Whereas hydrocephalus is absent in neonatal Lhx9−/−mutant mice, the neonatal pineal gland in these animals is hypoplastic. Accordingly, it appears that Lhx9 is essential for early development of the mammalian pineal gland and that this effect is not secondary to hydrocephalus.

show abstract

Section: Resultssupporting

confidence: 78%

The Lhx9 homeobox gene controls pineal gland development and prevents postnatal hydrocephalus

Yamazaki

Møller

et al. 2014

Brain Struct Funct

Self Cite

View full text Add to dashboard Cite

show abstract

“…The group identified 112 lncRNAs that were differentially expressed during day and night, which were named lncSNs (lncRNAs, Section on Neuroendocrinology), with 59% of them having their expression increased during the night. 90 Eight of these lnSNs, whose size ranged from <1 kb to >50 kb, were chosen for further analysis. The rhythmic oscillation of their expression depended on the suprachiasmatic nucleus (SCN)–pineal pathway, as this rhythmic oscillation was blocked after surgical removal of the SCN but not when the rats were housed in constant darkness.…”

Section: Lncrnas In Endocrine Physiology and Diseasementioning

confidence: 99%

Long non-coding RNAs as regulators of the endocrine system

Knoll¹,

Lodish²,

Sun³

2015

Nat Rev Endocrinol

196

147

View full text Add to dashboard Cite

Long non-coding RNAs (lncRNAs) are a large and diverse group of RNAs that are often lineage-specific and that regulate multiple biological functions. Many are nuclear and are essential parts of ribonucleoprotein complexes that modify chromatin segments and establish active or repressive chromatin states; others are cytosolic and regulate the stability of mRNA or act as microRNA sponges. This Review summarizes the current knowledge of lncRNAs as regulators of the endocrine system, with a focus on the identification and mode of action of several endocrine-important lncRNAs. We highlight lncRNAs that have a role in the development and function of pancreatic β cells, white and brown adipose tissue, and other endocrine organs, and discuss the involvement of these molecules in endocrine dysfunction (for example, diabetes mellitus). We also address the associations of lncRNAs with nuclear receptors involved in major hormonal signalling pathways, such as estrogen and androgen receptors, and the relevance of these associations in certain endocrine cancers.

show abstract

“…It is not yet fully understood how lincRNAs control gene expression, but case-specific studies suggest that they might act as scaffolds to target chromatin-modifying complexes and transcriptional regulatory proteins to the genome (20). Recently, circadian expression of long noncoding RNAs was reported (7,21).To identify and investigate cyclically expressed factors, we synchronized NIH 3T3 cells, a commonly used murine model system, in their circadian rhythm. We performed RNA-sequencing (RNA-seq) to derive an extensive time course data set and applied three established as well as one novel computational approach to identify a number of transcription factors, epigenetic regulators, and lincRNAs that show cyclical expression.…”

mentioning

confidence: 99%

mentioning

confidence: 99%

Identifying Novel Transcriptional Regulators with Circadian Expression

Schick

Becker

Thakurela

et al. 2016

Molecular and Cellular Biology

View full text Add to dashboard Cite

Organisms adapt their physiology and behavior to the 24-h day-night cycle to which they are exposed. On a cellular level, this is regulated by intrinsic transcriptional-translational feedback loops that are important for maintaining the circadian rhythm. These loops are organized by members of the core clock network, which further regulate transcription of downstream genes, resulting in their circadian expression. Despite progress in understanding circadian gene expression, only a few players involved in circadian transcriptional regulation, including transcription factors, epigenetic regulators, and long noncoding RNAs, are known. Aiming to discover such genes, we performed a high-coverage transcriptome analysis of a circadian time course in murine fibroblast cells. In combination with a newly developed algorithm, we identified many transcription factors, epigenetic regulators, and long intergenic noncoding RNAs that are cyclically expressed. In addition, a number of these genes also showed circadian expression in mouse tissues. Furthermore, the knockdown of one such factor, Zfp28, influenced the core clock network. Mathematical modeling was able to predict putative regulator-effector interactions between the identified circadian genes and may help for investigations into the gene regulatory networks underlying circadian rhythms.O rganisms adapt to the 24-h day-night cycle, which leads to oscillations in physiology and behavior. This is coordinated by an intrinsic molecular clock originating from the interplay of transcriptional-translational feedback loops (1). In mammals, the core loop consists of the transcriptional activators Clock and Bmal1 and the repressors Period (Per) and cryptochrome (Cry). In a second loop, retinoid-related orphan receptors (ROR) activate transcription while Rev-Erb factors (Nr1d1 and Nr1d2) repress transcription (2). These core clock components also regulate the expression of additional genes, possibly resulting in an oscillating transcription of these socalled clock-controlled genes and finally in the circadian phenotype.Recent genome-wide studies of circadian time courses in various mouse tissues indicated that each tissue expresses its own particular set of cyclical genes, which only partly overlap each other (3-7). Nearly half of all genes in the mouse genome show circadian oscillation in at least one tissue (7). The basic mechanisms causing transcriptional rhythms of the core clock components are similar among all tissues, but how tissue-specific circadian output is achieved remains unknown, although several mechanisms have been proposed (2). Among these are the use of tissue-specific transcription factors (TFs) or coregulators (6,8) and different temporal control of RNA polymerase II recruitment (9, 10), as well as defined rhythms in histone modifications accompanied by differential gene regulation (9-19).To gain further insight into the transcriptional control of the circadian rhythm, we aimed to identify novel factors, particularly transcription factors and epigenetic regula...

show abstract

Circadian changes in long noncoding RNAs in the pineal gland

Cited by 78 publications

References 47 publications

The Lhx9 homeobox gene controls pineal gland development and prevents postnatal hydrocephalus

The Lhx9 homeobox gene controls pineal gland development and prevents postnatal hydrocephalus

Long non-coding RNAs as regulators of the endocrine system

Identifying Novel Transcriptional Regulators with Circadian Expression

Contact Info

Product

Resources

About