Defining housekeeping genes suitable for RNA-seq analysis of the human allograft kidney biopsy tissue

Abstract Background Normalization of RNA-seq data aims at identifying biological expression differentiation between samples by removing the effects of unwanted confounding factors. Explicitly or implicitly, the justification of normalization requires a set of housekeeping genes. However, the existence of housekeeping genes common for a very large collection of samples, especially under a wide range of conditions, is questionable. Results We propose to carry out pairwise normalization with respect to multiple references, selected from representative samples. Then the pairwise intermediates are integrated based on a linear model that adjusts the reference effects. Motivated by the notion of housekeeping genes and their statistical counterparts, we adopt the robust least trimmed squares regression in pairwise normalization. The proposed method (MUREN) is compared with other existing tools on some standard data sets. The goodness of normalization emphasizes on preserving possible asymmetric differentiation, whose biological significance is exemplified by a single cell data of cell cycle. MUREN is implemented as an R package. The code under license GPL-3 is available on the github platform: github.com/hippo-yf/MUREN and on the conda platform: anaconda.org/hippo-yf/r-muren. Conclusions MUREN performs the RNA-seq normalization using a two-step statistical regression induced from a general principle. We propose that the densities of pairwise differentiations are used to evaluate the goodness of normalization. MUREN adjusts the mode of differentiation toward zero while preserving the skewness due to biological asymmetric differentiation. Moreover, by robustly integrating pre-normalized counts with respect to multiple references, MUREN is immune to individual outlier samples.

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Annotation of snoRNA abundance across human tissues reveals complex snoRNA-host gene relationships

Genome Biology ◽

10.1186/s13059-021-02391-2 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Étienne Fafard-Couture ◽

Danny Bergeron ◽

Sonia Couture ◽

Sherif Abou-Elela ◽

Michelle S. Scott

Keyword(s):

Housekeeping Genes ◽

Host Gene ◽

Rna Modification ◽

Human Tissues ◽

Rna Seq ◽

Healthy Human ◽

Protein Coding ◽

Conservation Level ◽

Nucleolar Rnas ◽

Host Genes

Abstract Background Small nucleolar RNAs (snoRNAs) are mid-size non-coding RNAs required for ribosomal RNA modification, implying a ubiquitous tissue distribution linked to ribosome synthesis. However, increasing numbers of studies identify extra-ribosomal roles of snoRNAs in modulating gene expression, suggesting more complex snoRNA abundance patterns. Therefore, there is a great need for mapping the snoRNome in different human tissues as the blueprint for snoRNA functions. Results We used a low structure bias RNA-Seq approach to accurately quantify snoRNAs and compare them to the entire transcriptome in seven healthy human tissues (breast, ovary, prostate, testis, skeletal muscle, liver, and brain). We identify 475 expressed snoRNAs categorized in two abundance classes that differ significantly in their function, conservation level, and correlation with their host gene: 390 snoRNAs are uniformly expressed and 85 are enriched in the brain or reproductive tissues. Most tissue-enriched snoRNAs are embedded in lncRNAs and display strong correlation of abundance with them, whereas uniformly expressed snoRNAs are mostly embedded in protein-coding host genes and are mainly non- or anticorrelated with them. Fifty-nine percent of the non-correlated or anticorrelated protein-coding host gene/snoRNA pairs feature dual-initiation promoters, compared to only 16% of the correlated non-coding host gene/snoRNA pairs. Conclusions Our results demonstrate that snoRNAs are not a single homogeneous group of housekeeping genes but include highly regulated tissue-enriched RNAs. Indeed, our work indicates that the architecture of snoRNA host genes varies to uncouple the host and snoRNA expressions in order to meet the different snoRNA abundance levels and functional needs of human tissues.

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Application of qRT-PCR and RNA-Seq analysis for the identification of housekeeping genes useful for normalization of gene expression values during Striga hermonthica development

Molecular Biology Reports ◽

10.1007/s11033-012-2417-y ◽

2012 ◽

Vol 40 (4) ◽

pp. 3395-3407 ◽

Cited By ~ 22

Author(s):

M. Fernández-Aparicio ◽

K. Huang ◽

E. K. Wafula ◽

L. A. Honaas ◽

N. J. Wickett ◽

...

Keyword(s):

Gene Expression ◽

Housekeeping Genes ◽

Striga Hermonthica ◽

Rna Seq ◽

Qrt Pcr

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The molecular mechanisms of inflammation and scarring in the kidneys of immunoglobulin A nephropathy

Seminars in Immunopathology ◽

10.1007/s00281-021-00891-8 ◽

2021 ◽

Author(s):

Francesco Paolo Schena ◽

Michele Rossini ◽

Daniela Isabel Abbrescia ◽

Gianluigi Zaza

Keyword(s):

Molecular Mechanisms ◽

Clinical Decision Making ◽

Kidney Biopsy ◽

Immunoglobulin A ◽

Renal Tissue ◽

Urinary Biomarkers ◽

Specific Gene ◽

Rna Seq ◽

Immunoglobulin A Nephropathy ◽

Renal Lesions

AbstractKidney biopsy is the cornerstone for the diagnosis of immunoglobulin A nephropathy (IgAN). The immunofluorescence technique evidences the IgA deposits in the glomeruli; the routine histology shows degree of active and chronic renal lesions. The spectrum of renal lesions is highly variable, ranging from minor or no detectable lesions to diffuse proliferative or crescentic lesions. Over the past three decades, renal transcriptomic studies have been performed on fresh or frozen renal tissue, and formalin-fixed paraffin-embedded kidney tissue specimens obtained from archival histological repositories. This paper aims to describe (1) the transcriptomic profiles of the kidney biopsy and (2) the potential urinary biomarkers that can be used to monitor the follow-up of IgAN patients. The use of quantitative Real-Time Polymerase Chain Reaction (qRT-PCR), microarrays and RNA-sequencing (RNA-seq) techniques on renal tissue and separated compartments of the nephron such as glomeruli and tubule-interstitium has clarified many aspects of the renal damage in IgAN. Recently, the introduction of the single-cell RNA-seq techniques has overcome the limitations of the previous methods, making that it is possible to study the whole renal tissue without the dissection of the nephron segments; it also allows better analysis of the cell-specific gene expression involved in cell differentiation. These gene products could represent effective candidates for urinary biomarkers for clinical decision making. Finally, some of these molecules may be the targets of old drugs, such as corticosteroids, renin–angiotensin–aldosterone blockers, and new drugs such as monoclonal antibodies. In the era of personalized medicine and precision therapy, high-throughput technologies may better characterize different renal patterns of IgAN and deliver targeted treatments to individual patients.

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HRT Atlas v1.1 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets

10.1101/787150 ◽

2019 ◽

Author(s):

Bidossessi Wilfried Hounkpe ◽

Francine Chenou ◽

Franciele Lima ◽

Erich Vinicius de Paula

Keyword(s):

Gene Expression ◽

Wild Type Mouse ◽

Housekeeping Genes ◽

Regulatory Elements ◽

Data Sets ◽

Rna Seq ◽

Cellular Functions ◽

Evolutionary Features ◽

Small Device ◽

Human And Mouse

AbstractHousekeeping (HK) genes are constitutively expressed genes that are required for the maintenance of basic cellular functions. Despite their importance in the calibration of gene expression, as well as the understanding of many genomic and evolutionary features, important discrepancies have been observed in studies that previously identified these genes. Here, we present Housekeeping Transcript Atlas (HRT Atlas v1.0, www.housekeeping.unicamp.br) a web-based database which addresses some of the previously observed limitations in the identification of these genes, and offers a more accurate database of human and mouse HK genes and transcripts. The database was generated by mining massive human and mouse RNA-seq data sets, including 12,482 and 507 high-quality RNA-seq samples from 82 human non-disease tissues/cells and 15 healthy tissues/cells of C57BL/6 wild type mouse, respectively. User can visualize the expression and download lists of 2,158 human HK transcripts from 2,176 HK genes and 3,024 mouse HK transcripts from 3,277 mouse HK genes. HRT Atlas also offers the most stable and suitable tissue selective candidate reference transcripts for normalization of qPCR experiments. Specific primers and predicted modifiers of gene expression for some of these HK transcripts are also proposed. HRT Atlas has also been integrated with regulatory elements from Epiregio server. All of these resources can be accessed and downloaded from any computer or small device web browsers.

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HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets

Nucleic Acids Research ◽

10.1093/nar/gkaa609 ◽

2020 ◽

Cited By ~ 3

Author(s):

Bidossessi Wilfried Hounkpe ◽

Francine Chenou ◽

Franciele de Lima ◽

Erich Vinicius De Paula

Keyword(s):

Gene Expression ◽

Wild Type Mouse ◽

Housekeeping Genes ◽

Regulatory Elements ◽

Data Sets ◽

Rna Seq ◽

Cellular Functions ◽

Evolutionary Features ◽

Reference Transcript ◽

Human And Mouse

Abstract Housekeeping (HK) genes are constitutively expressed genes that are required for the maintenance of basic cellular functions. Despite their importance in the calibration of gene expression, as well as the understanding of many genomic and evolutionary features, important discrepancies have been observed in studies that previously identified these genes. Here, we present Housekeeping and Reference Transcript Atlas (HRT Atlas v1.0, www.housekeeping.unicamp.br) a web-based database which addresses some of the previously observed limitations in the identification of these genes, and offers a more accurate database of human and mouse HK genes and transcripts. The database was generated by mining massive human and mouse RNA-seq data sets, including 11 281 and 507 high-quality RNA-seq samples from 52 human non-disease tissues/cells and 14 healthy tissues/cells of C57BL/6 wild type mouse, respectively. User can visualize the expression and download lists of 2158 human HK transcripts from 2176 HK genes and 3024 mouse HK transcripts from 3277 mouse HK genes. HRT Atlas also offers the most stable and suitable tissue selective candidate reference transcripts for normalization of qPCR experiments. Specific primers and predicted modifiers of gene expression for some of these HK transcripts are also proposed. HRT Atlas has also been integrated with a regulatory elements resource from Epiregio server.

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Endothelial Vesicles in an Allograft Kidney Biopsy: An Unusual Pattern of Biclonal Paraprotein Deposition

American Journal of Clinical Pathology ◽

10.1093/ajcp/142.suppl1.264 ◽

2014 ◽

Vol 142 (suppl_1) ◽

pp. A264-A264

Author(s):

Ellen Flatley ◽

Gerald Segal ◽

Thomas Batiuk ◽

William Bennett ◽

Donald Houghton ◽

...

Keyword(s):

Kidney Biopsy ◽

Unusual Pattern ◽

Allograft Kidney

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Improvement of allograft kidney biopsy yield by using a handheld smartphone microscope as an on-site evaluation device.

Heliyon ◽

10.1016/j.heliyon.2021.e07189 ◽

2021 ◽

pp. e07189

Author(s):

Wichien Sirithanaphol ◽

Natthida Incharoen ◽

Ukrit Rompsaithong ◽

Pakorn Kiatsopit ◽

Supanut Lumbiganon ◽

...

Keyword(s):

Kidney Biopsy ◽

Allograft Kidney ◽

Site Evaluation

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The Evolution of Sex Chromosome Dosage Compensation in Animals

10.1101/2020.07.04.187476 ◽

2020 ◽

Author(s):

Jiabi Chen ◽

Menghan Wang ◽

Xionglei He ◽

Jian-Rong Yang ◽

Xiaoshu Chen

Keyword(s):

Dosage Compensation ◽

Sex Chromosomes ◽

Sex Chromosome ◽

Housekeeping Genes ◽

Evolutionary Strategies ◽

Rna Seq ◽

Evolution Of Sex ◽

Computational Framework ◽

Multiple Species ◽

Transcriptional Output

ABSTRACTThe evolution of sex chromosomes in the XY or ZW systems shall lead to gene expression dosage problems, as in at least one of the sexes, the sex-linked gene dose has been reduced by half. It has been proposed, most notably by Susumu Ohno for mammals, that the transcriptional output of the whole sex chromosome should be doubled for a complete dosage compensation. However, due to the variability of the existing methods to determine the transcriptional differences between Sex chromosomes and Autosomes (S:A ratios) in different studies, whether clade-specific results are comparable and whether there is a more general model to explain dosage compensation states remain unanswered. In this study, we collected more than 500 public RNA-seq datasets from multiple tissues and species in major clades (including mammals, birds, fishes, insects, and worms) and proposed a unified computational framework for unbiased and comparable measurement of the S:A ratios of multiple species. We also tested the evolution of dosage compensation more directly by assessing changes in the expression levels of the current sex-linked genes relative to those of the ancestral sex-linked genes. We found that in mammals and birds, the S:A ratio is approximately 0.5, while in insects, fishes and flatworms, the S:A ratio is approximately 1. Further analysis showed that the fraction of dosage-sensitive housekeeping genes on the sex chromosome is significantly correlated with the S:A ratio. In addition, the degree of degradation of the Y chromosome may be responsible for the change in the S:A ratio in mammals without a dosage-compensation mechanism. Our observations offer unequivocal support for the sex chromosome insensitivity hypothesis in animals and suggest that the dosage sensitivity states of sex chromosomes is a major factor underlying different evolutionary strategies of dosage compensation.

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Systematic analysis of 1,298 RNA-Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas

10.1101/2019.12.23.886853 ◽

2019 ◽

Author(s):

Fabricio Brum Machado ◽

Kanhu C. Moharana ◽

Fabricio Almeida-Silva ◽

Rajesh K. Gazara ◽

Francisnei Pedrosa-Silva ◽

...

Keyword(s):

Glycine Max ◽

Animal Feed ◽

Expression Patterns ◽

Housekeeping Genes ◽

Transcript Level ◽

Rna Seq ◽

Systematic Analysis ◽

Expression Atlas ◽

Soybean Genetics ◽

Developmental Conditions

AbstractSoybean (Glycine max [L.] Merr.) is a major crop in animal feed and human nutrition, mainly for its rich protein and oil contents. The remarkable rise in soybean transcriptome studies over the past five years generated an enormous amount of RNA-seq data, encompassing various tissues, developmental conditions, and genotypes. In this study, we have collected data from 1,298 publicly available soybean transcriptome samples, processed the raw sequencing reads, and mapped them to the soybean reference genome in a systematic fashion. We found that 94% of the annotated genes (52,737/56,044) had detectable expression in at least one sample. Unsupervised clustering revealed three major groups, comprising samples from aerial, underground, and seed/seed-related parts. We found 452 genes with uniform and constant expression levels, supporting their roles as housekeeping genes. On the other hand, 1,349 genes showed heavily biased expression patterns towards particular tissues. A transcript-level analysis revealed that 95% (70,963/74,490) of the known transcripts overlap with those reported here, whereas 3,256 assembled transcripts represent potentially novel splicing isoforms. The dataset compiled here constitute a new resource for the community, which can be downloaded or accessed through a user-friendly web interface at http://venanciogroup.uenf.br/resources/. This comprehensive transcriptome atlas will likely accelerate research on soybean genetics and genomics.

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