Specific transcriptomic signatures and dual regulation of steroidogenesis between fetal and adult mouse Leydig cells

Leydig cells (LC) are the main testicular androgen-producing cells. In eutherian mammals, two types of LCs emerge successively during testicular development, fetal Leydig cells (FLCs) and adult Leydig cells (ALCs). Both display significant differences in androgen production and regulation. Using bulk RNA sequencing, we compared the transcriptomes of both LC populations to characterise their specific transcriptional and functional features. Despite similar transcriptomic profiles, a quarter of the genes show significant variations in expression between FLCs and ALCs. Non-transcriptional events, such as alternative splicing was also observed, including a high rate of intron retention in FLCs compared to ALCs. The use of single-cell RNA sequencing data also allowed the identification of nine FLC-specific genes and 50 ALC-specific genes. Expression of the corticotropin-releasing hormone 1 (Crhr1) receptor and the ACTH receptor melanocortin type 2 receptor (Mc2r) specifically in FLCs suggests a dual regulation of steroidogenesis. The androstenedione synthesis by FLCs is stimulated by luteinizing hormone (LH), CRH and ACTH whereas the testosterone synthesis by ALCs is dependent exclusively on LH. Overall, our study provides a useful database to explore LC development and function.

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Specific Transcriptomic Signatures and Dual Regulation of Steroidogenesis Between Fetal and Adult Mouse Leydig Cells

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.695546 ◽

2021 ◽

Vol 9 ◽

Author(s):

Pauline Sararols ◽

Isabelle Stévant ◽

Yasmine Neirijnck ◽

Diane Rebourcet ◽

Annalucia Darbey ◽

...

Keyword(s):

Rna Sequencing ◽

Leydig Cells ◽

Intron Retention ◽

High Rate ◽

Testicular Development ◽

Sequencing Data ◽

Releasing Hormone ◽

Genes Expression ◽

Acth Receptor ◽

Functional Features

Leydig cells (LC) are the main testicular androgen-producing cells. In eutherian mammals, two types of LCs emerge successively during testicular development, fetal Leydig cells (FLCs) and adult Leydig cells (ALCs). Both display significant differences in androgen production and regulation. Using bulk RNA sequencing, we compared the transcriptomes of both LC populations to characterize their specific transcriptional and functional features. Despite similar transcriptomic profiles, a quarter of the genes show significant variations in expression between FLCs and ALCs. Non-transcriptional events, such as alternative splicing was also observed, including a high rate of intron retention in FLCs compared to ALCs. The use of single-cell RNA sequencing data also allowed the identification of nine FLC-specific genes and 50 ALC-specific genes. Expression of the corticotropin-releasing hormone 1 (Crhr1) receptor and the ACTH receptor melanocortin type 2 receptor (Mc2r) specifically in FLCs suggests a dual regulation of steroidogenesis. The androstenedione synthesis by FLCs is stimulated by luteinizing hormone (LH), corticotrophin-releasing hormone (CRH), and adrenocorticotropic hormone (ACTH) whereas the testosterone synthesis by ALCs is dependent exclusively on LH. Overall, our study provides a useful database to explore LC development and functions.

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Rbm10 facilitates heterochromatin assembly via the Clr6 HDAC complex

10.1101/518936 ◽

2019 ◽

Author(s):

Martina Weigt ◽

Qingsong Gao ◽

Hyoju Ban ◽

Haijin He ◽

Guido Mastrobuoni ◽

...

Keyword(s):

Fission Yeast ◽

Intron Retention ◽

Splicing Factors ◽

Minor Effect ◽

Sequencing Data ◽

Chromatin Remodelers ◽

Heterochromatin Formation ◽

Proteomic Data ◽

Heterochromatin Silencing ◽

And Function

Splicing factors have recently been shown to be involved in heterochromatin formation, but their role in controlling heterochromatin structure and function remains poorly understood. In this study, we identified a fission yeast homologue of human splicing factor RBM10, which has been linked to TARP syndrome. Overexpression of Rbm10 in fission yeast leads to strong global intron retention. Rbm10 also interacts with splicing factors in a pattern resembling that of human RBM10, suggesting that the function of Rbm10 as a splicing regulator is conserved. Surprisingly, our deep-sequencing data showed that deletion of Rbm10 caused only minor effect on genome-wide gene expression and splicing. However, the mutant displays severe heterochromatin defects. Further analyses indicated that the heterochromatin defects in the mutant did not result from mis-splicing of heterochromatin factors. Our proteomic data revealed that Rbm10 associates with the histone deacetylase Clr6 complex and chromatin remodelers known to be important for heterochromatin silencing. Deletion of Rbm10 results in significant reduction of Clr6 in heterochromatin. Our work together with previous findings further suggests that different splicing subunits may play distinct roles in heterochromatin regulation.

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SNPlice: variants that modulate Intron retention from RNA-sequencing data

Bioinformatics ◽

10.1093/bioinformatics/btu804 ◽

2014 ◽

Vol 31 (8) ◽

pp. 1191-1198 ◽

Cited By ~ 12

Author(s):

Prakriti Mudvari ◽

Mercedeh Movassagh ◽

Kamran Kowsari ◽

Ali Seyfi ◽

Maria Kokkinaki ◽

...

Keyword(s):

Rna Sequencing ◽

Intron Retention ◽

Sequencing Data

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Detection of aberrant splicing events in RNA-seq data using FRASER

Nature Communications ◽

10.1038/s41467-020-20573-7 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Christian Mertes ◽

Ines F. Scheller ◽

Vicente A. Yépez ◽

Muhammed H. Çelik ◽

Yingjiqiong Liang ◽

...

Keyword(s):

Rna Sequencing ◽

Multiple Testing ◽

Intron Retention ◽

Rna Seq ◽

Sequencing Data ◽

Multiple Testing Correction ◽

Aberrant Splicing ◽

Count Distribution ◽

Disease Diagnostics ◽

A Minor

AbstractAberrant splicing is a major cause of rare diseases. However, its prediction from genome sequence alone remains in most cases inconclusive. Recently, RNA sequencing has proven to be an effective complementary avenue to detect aberrant splicing. Here, we develop FRASER, an algorithm to detect aberrant splicing from RNA sequencing data. Unlike existing methods, FRASER captures not only alternative splicing but also intron retention events. This typically doubles the number of detected aberrant events and identified a pathogenic intron retention in MCOLN1 causing mucolipidosis. FRASER automatically controls for latent confounders, which are widespread and affect sensitivity substantially. Moreover, FRASER is based on a count distribution and multiple testing correction, thus reducing the number of calls by two orders of magnitude over commonly applied z score cutoffs, with a minor loss of sensitivity. Applying FRASER to rare disease diagnostics is demonstrated by reprioritizing a pathogenic aberrant exon truncation in TAZ from a published dataset. FRASER is easy to use and freely available.

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Dynamic Expression of Imprinted Genes in the Developing and Postnatal Pituitary Gland

Genes ◽

10.3390/genes12040509 ◽

2021 ◽

Vol 12 (4) ◽

pp. 509

Author(s):

Valeria Scagliotti ◽

Ruben Costa Fernandes Esse ◽

Thea L. Willis ◽

Mark Howard ◽

Isabella Carrus ◽

...

Keyword(s):

Pituitary Gland ◽

Rna Sequencing ◽

Gene Networks ◽

Current Knowledge ◽

High Sensitivity ◽

Imprinted Genes ◽

Sequencing Data ◽

Dynamic Regulation ◽

Imprinted Gene ◽

And Function

In mammals, imprinted genes regulate many critical endocrine processes such as growth, the onset of puberty and maternal reproductive behaviour. Human imprinting disorders (IDs) are caused by genetic and epigenetic mechanisms that alter the expression dosage of imprinted genes. Due to improvements in diagnosis, increasing numbers of patients with IDs are now identified and monitored across their lifetimes. Seminal work has revealed that IDs have a strong endocrine component, yet the contribution of imprinted gene products in the development and function of the hypothalamo-pituitary axis are not well defined. Postnatal endocrine processes are dependent upon the production of hormones from the pituitary gland. While the actions of a few imprinted genes in pituitary development and function have been described, to date there has been no attempt to link the expression of these genes as a class to the formation and function of this essential organ. This is important because IDs show considerable overlap, and imprinted genes are known to define a transcriptional network related to organ growth. This knowledge deficit is partly due to technical difficulties in obtaining useful transcriptomic data from the pituitary gland, namely, its small size during development and cellular complexity in maturity. Here we utilise high-sensitivity RNA sequencing at the embryonic stages, and single-cell RNA sequencing data to describe the imprinted transcriptome of the pituitary gland. In concert, we provide a comprehensive literature review of the current knowledge of the role of imprinted genes in pituitary hormonal pathways and how these relate to IDs. We present new data that implicate imprinted gene networks in the development of the gland and in the stem cell compartment. Furthermore, we suggest novel roles for individual imprinted genes in the aetiology of IDs. Finally, we describe the dynamic regulation of imprinted genes in the pituitary gland of the pregnant mother, with implications for the regulation of maternal metabolic adaptations to pregnancy.

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Rbm10 facilitates heterochromatin assembly via the Clr6 HDAC complex

Epigenetics & Chromatin ◽

10.1186/s13072-021-00382-y ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Martina Weigt ◽

Qingsong Gao ◽

Hyoju Ban ◽

Haijin He ◽

Guido Mastrobuoni ◽

...

Keyword(s):

Fission Yeast ◽

Intron Retention ◽

Splicing Factors ◽

Minor Effect ◽

Sequencing Data ◽

Chromatin Remodelers ◽

Heterochromatin Formation ◽

Proteomic Data ◽

Heterochromatin Silencing ◽

And Function

AbstractSplicing factors have recently been shown to be involved in heterochromatin formation, but their role in controlling heterochromatin structure and function remains poorly understood. In this study, we identified a fission yeast homologue of human splicing factor RBM10, which has been linked to TARP syndrome. Overexpression of Rbm10 in fission yeast leads to strong global intron retention. Rbm10 also interacts with splicing factors in a pattern resembling that of human RBM10, suggesting that the function of Rbm10 as a splicing regulator is conserved. Surprisingly, our deep-sequencing data showed that deletion of Rbm10 caused only minor effect on genome-wide gene expression and splicing. However, the mutant displays severe heterochromatin defects. Further analyses indicated that the heterochromatin defects in the mutant did not result from mis-splicing of heterochromatin factors. Our proteomic data revealed that Rbm10 associates with the histone deacetylase Clr6 complex and chromatin remodelers known to be important for heterochromatin silencing. Deletion of Rbm10 results in significant reduction of Clr6 in heterochromatin. Our work together with previous findings further suggests that different splicing subunits may play distinct roles in heterochromatin regulation.

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Detection of aberrant splicing events in RNA-seq data with FRASER

10.1101/2019.12.18.866830 ◽

2019 ◽

Cited By ~ 1

Author(s):

Christian Mertes ◽

Ines Scheller ◽

Vicente A. Yépez ◽

Muhammed H. Çelik ◽

Yingjiqiong Liang ◽

...

Keyword(s):

Rna Sequencing ◽

Multiple Testing ◽

Intron Retention ◽

Sequencing Data ◽

Multiple Testing Correction ◽

Aberrant Splicing ◽

Sensitivity Loss ◽

Count Distribution ◽

Disease Diagnostics ◽

A Minor

AbstractAberrant splicing is a major cause of rare diseases, yet its prediction from genome sequence remains in most cases inconclusive. Recently, RNA sequencing has proven to be an effective complementary avenue to detect aberrant splicing. Here, we developed FRASER, an algorithm to detect aberrant splicing from RNA sequencing data. Unlike existing methods, FRASER captures not only alternative splicing but also intron retention events. This typically doubles the number of detected aberrant events and identified a pathogenic intron retention in MCOLN1. FRASER automatically controls for latent confounders, which are widespread and substantially affect sensitivity. Moreover, FRASER is based on a count distribution and multiple testing correction, reducing the number of calls by two orders of magnitude over commonly applied z score cutoffs, with a minor sensitivity loss. The application to rare disease diagnostics is demonstrated by reprioritizing a pathogenic aberrant exon truncation in TAZ from a published dataset. FRASER is easy to use and freely available.

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HEDGEHOG/GLI Modulates the PRR11-SKA2 Bidirectional Transcription Unit in Lung Squamous Cell Carcinomas

Genes ◽

10.3390/genes12010120 ◽

2021 ◽

Vol 12 (1) ◽

pp. 120

Author(s):

Yiyun Sun ◽

Dandan Xu ◽

Chundong Zhang ◽

Yitao Wang ◽

Lian Zhang ◽

...

Keyword(s):

Rna Sequencing ◽

Squamous Cell ◽

Gene Pair ◽

Gene List ◽

Ectopic Expression ◽

Lung Squamous Cell Carcinoma ◽

Gene Set Enrichment Analysis ◽

The Cancer Genome Atlas ◽

Sequencing Data ◽

Gene Set

We previously demonstrated that proline-rich protein 11 (PRR11) and spindle and kinetochore associated 2 (SKA2) constituted a head-to-head gene pair driven by a prototypical bidirectional promoter. This gene pair synergistically promoted the development of non-small cell lung cancer. However, the signaling pathways leading to the ectopic expression of this gene pair remains obscure. In the present study, we first analyzed the lung squamous cell carcinoma (LSCC) relevant RNA sequencing data from The Cancer Genome Atlas (TCGA) database using the correlation analysis of gene expression and gene set enrichment analysis (GSEA), which revealed that the PRR11-SKA2 correlated gene list highly resembled the Hedgehog (Hh) pathway activation-related gene set. Subsequently, GLI1/2 inhibitor GANT-61 or GLI1/2-siRNA inhibited the Hh pathway of LSCC cells, concomitantly decreasing the expression levels of PRR11 and SKA2. Furthermore, the mRNA expression profile of LSCC cells treated with GANT-61 was detected using RNA sequencing, displaying 397 differentially expressed genes (203 upregulated genes and 194 downregulated genes). Out of them, one gene set, including BIRC5, NCAPG, CCNB2, and BUB1, was involved in cell division and interacted with both PRR11 and SKA2. These genes were verified as the downregulated genes via RT-PCR and their high expression significantly correlated with the shorter overall survival of LSCC patients. Taken together, our results indicate that GLI1/2 mediates the expression of the PRR11-SKA2-centric gene set that serves as an unfavorable prognostic indicator for LSCC patients, potentializing new combinatorial diagnostic and therapeutic strategies in LSCC.

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