The Individual Gene in Relation to the Chromomere and the Chromosome

AbstractMolecular characterization of the individual cell types in human kidney as well as model organisms are critical in defining organ function and understanding translational aspects of biomedical research. Previous studies have uncovered gene expression profiles of several kidney glomerular cell types, however, important cells, including mesangial (MCs) and glomerular parietal epithelial cells (PECs), are missing or incompletely described, and a systematic comparison between mouse and human kidney is lacking. To this end, we use Smart-seq2 to profile 4332 individual glomerulus-associated cells isolated from human living donor renal biopsies and mouse kidney. The analysis reveals genetic programs for all four glomerular cell types (podocytes, glomerular endothelial cells, MCs and PECs) as well as rare glomerulus-associated macula densa cells. Importantly, we detect heterogeneity in glomerulus-associated Pdgfrb-expressing cells, including bona fide intraglomerular MCs with the functionally active phagocytic molecular machinery, as well as a unique mural cell type located in the central stalk region of the glomerulus tuft. Furthermore, we observe remarkable species differences in the individual gene expression profiles of defined glomerular cell types that highlight translational challenges in the field and provide a guide to design translational studies.

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Technical considerations when designing a gene expression panel for renal transplant diagnosis

Scientific Reports ◽

10.1038/s41598-020-74794-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

F. Toulza ◽

K. Dominy ◽

T. Cook ◽

J. Galliford ◽

J. Beadle ◽

...

Keyword(s):

Gene Expression ◽

Renal Transplant ◽

Biological Significance ◽

Tissue Sampling ◽

Individual Gene ◽

Antibody Mediated Rejection ◽

Gene Level ◽

Diagnostic Panel ◽

The Individual ◽

Gene Panels

Abstract Gene expression analysis is emerging as a new diagnostic tool in transplant pathology, in particular for the diagnosis of antibody-mediated rejection. Diagnostic gene expression panels are defined on the basis of their pathophysiological relevance, but also need to be tested for their robustness across different preservatives and analysis platforms. The aim of this study is the investigate the effect of tissue sampling and preservation on candidate genes included in a renal transplant diagnostic panel. Using the NanoString platform, we compared the expression of 219 genes in 51 samples, split for formalin-fixation and paraffin-embedding (FFPE) and RNAlater preservation (RNAlater). We found that overall, gene expression significantly correlated between FFPE and RNAlater samples. However, at the individual gene level, 46 of the 219 genes did not correlate across the 51 matched FFPE and RNAlater samples. Comparing gene expression results using NanoString and qRT-PCR for 18 genes in the same pool of RNA (RNAlater), we found a significant correlation in 17/18 genes. Our study indicates that, in samples from the same routine diagnostic renal transplant biopsy procedure split for FFPE and RNAlater, 21% of 219 genes of potential biological significance do not correlate in expression. Whether this is due to fixatives or tissue sampling, selection of gene panels for routine diagnosis should take this information into consideration.

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Deep transcriptomic profiling reveals the similarity between endothelial cells cultured under static and oscillatory shear stress conditions

Physiological Genomics ◽

10.1152/physiolgenomics.00025.2016 ◽

2016 ◽

Vol 48 (9) ◽

pp. 660-666 ◽

Cited By ~ 15

Author(s):

Congzhen Qiao ◽

Fan Meng ◽

Inhwan Jang ◽

Hanjoong Jo ◽

Y. Eugene Chen ◽

...

Keyword(s):

Endothelial Cells ◽

Shear Stress ◽

Endothelial Function ◽

Stress Conditions ◽

Individual Gene ◽

Gene Level ◽

The Individual ◽

Oscillatory Shear Stress ◽

Whole Transcriptome ◽

Transcriptome Level

Atherosclerosis is a multifactorial disease that preferentially develops in specific regions in the arterial tree. This characteristic is mainly attributed to the unique pattern of hemodynamic shear stress in vivo. High laminar shear stress (LS) found in straight lumen exerts athero-protective effects. Low or oscillatory shear stress (OS) present in regions of lesser curvature and arterial bifurcations predisposes arterial intima to atherosclerosis. Shear stress-regulated endothelial function plays an important role in the process of atherosclerosis. Most in vitro research studies focusing on the molecular mechanisms of endothelial function are performed in endothelial cells (ECs) under cultured static (ST) condition. Some findings, however, are not recapitulated in subsequent translational studies, mostly likely due to the missing biomechanical milieu. Here, we profiled the whole transcriptome of primary human coronary arterial endothelial cells (HCAECs) under different shear stress conditions with RNA sequencing. Among 16,313 well-expressed genes, we detected 8,177 that were differentially expressed in OS vs. LS conditions and 9,369 in ST vs. LS conditions. Notably, only 1,618 were differentially expressed in OS vs. ST conditions. Hierarchical clustering of ECs demonstrated a strong similarity between ECs under OS and ST conditions at the transcriptome level. Subsequent pairwise heat mapping and principal component analysis gave further weight to the similarity. At the individual gene level, expressional analysis of representative well-known genes as well as novel genes showed a comparable amount at mRNA and protein levels in ECs under ST and OS conditions. In conclusion, the present work compared the whole transcriptome of HCAECs under different shear stress conditions at the transcriptome level as well as at the individual gene level. We found that cultured ECs are significantly different from those under LS conditions. Thus using cells under ST conditions is unlikely to elucidate endothelial physiology. Given the revealed high similarities of the endothelial transcriptome under OS and ST conditions, it may be helpful to understand the underlying mechanisms of OS-induced endothelial dysfunction from static cultured endothelial studies.

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The good, the bad, and the ugly: Evolutionary and pathological aspects of gene dosage alterations

PLoS Genetics ◽

10.1371/journal.pgen.1009906 ◽

2021 ◽

Vol 17 (12) ◽

pp. e1009906

Author(s):

M. Felicia Basilicata ◽

Claudia Isabelle Keller Valsecchi

Keyword(s):

Developmental Disorders ◽

Common Ground ◽

Gene Dosage ◽

Paternal Genome ◽

Individual Gene ◽

Developmental Progression ◽

Gene Level ◽

Heteromorphic Sex Chromosomes ◽

Genetic Perturbations ◽

The Individual

Diploid organisms contain a maternal and a paternal genome complement that is thought to provide robustness and allow developmental progression despite genetic perturbations that occur in heterozygosity. However, changes affecting gene dosage from the chromosome down to the individual gene level possess a significant pathological potential and can lead to developmental disorders (DDs). This indicates that expression from a balanced gene complement is highly relevant for proper cellular and organismal function in eukaryotes. Paradoxically, gene and whole chromosome duplications are a principal driver of evolution, while heteromorphic sex chromosomes (XY and ZW) are naturally occurring aneuploidies important for sex determination. Here, we provide an overview of the biology of gene dosage at the crossroads between evolutionary benefit and pathogenicity during disease. We describe the buffering mechanisms and cellular responses to alterations, which could provide a common ground for the understanding of DDs caused by copy number alterations.

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Mobile-CRISPRi: Enabling Genetic Analysis of Diverse Bacteria

10.1101/315499 ◽

2018 ◽

Cited By ~ 3

Author(s):

Jason M. Peters ◽

Byoung-Mo Koo ◽

Ramiro Patino ◽

Gary E. Heussler ◽

Cameron C. Hearne ◽

...

Keyword(s):

Gene Networks ◽

Essential Genes ◽

Genetic Dissection ◽

Human Pathogens ◽

Major Barrier ◽

Bacterial Gene ◽

Bacterial Physiology ◽

Individual Gene ◽

Host Microbe Interactions ◽

The Individual

Introductory paragraphThe vast majority of bacteria, including human pathogens and microbiome species, lack genetic tools needed to systematically associate genes with phenotypes. This is the major impediment to understanding the fundamental contributions of genes and gene networks to bacterial physiology and human health. CRISPRi, a versatile method of blocking gene expression using a catalytically inactive Cas9 protein (dCas9) and programmable single guide RNAs (sgRNAs), has emerged as a powerful genetic tool to dissect the functions of essential and non-essential genes in species ranging from bacteria to human. However, the difficulty of establishing effective CRISPRi systems in non-model bacteria is a major barrier to its widespread use to dissect bacterial gene function. Here, we establish “Mobile-CRISPRi”, a suite of CRISPRi systems that combine modularity, stable genomic integration and ease of transfer to diverse bacteria by conjugation. Focusing predominantly on human pathogens associated with antibiotic resistance, we demonstrate the efficacy of Mobile-CRISPRi in Proteobacteria and Firmicutes at the individual gene scale by examining drug-gene synergies and at the library scale by systematically phenotyping conditionally essential genes involved in amino acid biosynthesis. Mobile-CRISPRi enables genetic dissection of non-model bacteria, facilitating analyses of microbiome function, antibiotic resistances and sensitivities, and comprehensive screens for host-microbe interactions.

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Concurrent up-regulation of guanine-nucleotide-binding proteins Gi1α, Gi2α and Gi3α in adipocytes of hypothyroid rats

Biochemical Journal ◽

10.1042/bj2700765 ◽

1990 ◽

Vol 270 (3) ◽

pp. 765-769 ◽

Cited By ~ 27

Author(s):

G Milligan ◽

E D Saggerson

Keyword(s):

Binding Proteins ◽

Nucleotide Binding ◽

Guanine Nucleotide ◽

Individual Gene ◽

White Adipocytes ◽

Guanine Nucleotide Binding ◽

The Individual ◽

Nucleotide Binding Proteins ◽

Guanine Nucleotide Binding Proteins ◽

Gs Alpha

Rat white adipocytes express three distinct ‘Gi-like’ guanine-nucleotide-binding proteins (G-proteins) [Mitchell, Griffiths, Saggerson, Houslay, Knowler & Milligan (1989) Biochem. J. 262, 403-408]. We have previously noted elevated levels of Gi in membranes of adipocytes from hypothyroid rats [Milligan, Spiegel, Unson & Saggerson (1987) Biochem. J. 247, 223-227]. Using a series of anti-peptide antisera able to discriminate between the individual gene products we have examined levels of each Gi-like G-protein in adipocyte membranes of hypothyroid rats compared with euthyroid controls. We demonstrate that up-regulation of Gi in adipocytes of hypothyroid rats is not restricted to a single subtype of Gi but that each of Gi1 alpha, Gi2 alpha and Gi3 alpha is present at markedly higher levels compared with euthyroid animals. In contrast, levels of both the 45 and 42 kDa forms of Gs alpha were not altered substantially in the hypothyroid state.

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Contribution of genetic and epigenetic changes to escape from X-chromosome inactivation

Epigenetics & Chromatin ◽

10.1186/s13072-021-00404-9 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Bradley P. Balaton ◽

Carolyn J. Brown

Keyword(s):

Dna Methylation ◽

X Chromosome ◽

Cpg Islands ◽

X Chromosome Inactivation ◽

Chromosome Inactivation ◽

Status Change ◽

Epigenetic Marks ◽

Individual Gene ◽

Inactive X Chromosome ◽

The Individual

Abstract Background X-chromosome inactivation (XCI) is the epigenetic inactivation of one of two X chromosomes in XX eutherian mammals. The inactive X chromosome is the result of multiple silencing pathways that act in concert to deposit chromatin changes, including DNA methylation and histone modifications. Yet over 15% of genes escape or variably escape from inactivation and continue to be expressed from the otherwise inactive X chromosome. To the extent that they have been studied, epigenetic marks correlate with this expression. Results Using publicly available data, we compared XCI status calls with DNA methylation, H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3 and H3K36me3. At genes subject to XCI we found heterochromatic marks enriched, and euchromatic marks depleted on the inactive X when compared to the active X. Genes escaping XCI were more similar between the active and inactive X. Using sample-specific XCI status calls, we found some marks differed significantly with variable XCI status, but which marks were significant was not consistent between genes. A model trained to predict XCI status from these epigenetic marks obtained over 75% accuracy for genes escaping and over 90% for genes subject to XCI. This model made novel XCI status calls for genes without allelic differences or CpG islands required for other methods. Examining these calls across a domain of variably escaping genes, we saw XCI status vary across individual genes rather than at the domain level. Lastly, we compared XCI status calls to genetic polymorphisms, finding multiple loci associated with XCI status changes at variably escaping genes, but none individually sufficient to induce an XCI status change. Conclusion The control of expression from the inactive X chromosome is multifaceted, but ultimately regulated at the individual gene level with detectable but limited impact of distant polymorphisms. On the inactive X, at silenced genes euchromatic marks are depleted while heterochromatic marks are enriched. Genes escaping inactivation show a less significant enrichment of heterochromatic marks and depletion of H3K27ac. Combining all examined marks improved XCI status prediction, particularly for genes without CpG islands or polymorphisms, as no single feature is a consistent feature of silenced or expressed genes.

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Variation Due to Change in the Individual Gene

The American Naturalist ◽

10.1086/279846 ◽

1922 ◽

Vol 56 (642) ◽

pp. 32-50 ◽

Cited By ~ 118

Author(s):

H. J. Muller

Keyword(s):

Individual Gene ◽

The Individual

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Characterization of a Major Cluster of nif,fix, and Associated Genes in a Sugarcane Endophyte,Acetobacter diazotrophicus

Journal of Bacteriology ◽

10.1128/jb.182.24.7088-7091.2000 ◽

2000 ◽

Vol 182 (24) ◽

pp. 7088-7091 ◽

Cited By ~ 44

Author(s):

Sunhee Lee ◽

Alexander Reth ◽

Dietmar Meletzus ◽

Myrna Sevilla ◽

Christina Kennedy

Keyword(s):

Rhodobacter Capsulatus ◽

Bacterial Species ◽

Promoter Sequence ◽

Gene Products ◽

Acetobacter Diazotrophicus ◽

Individual Gene ◽

Major Cluster ◽

Transcriptional Units ◽

The Individual

ABSTRACT A major 30.5-kb cluster of nif and associated genes ofAcetobacter diazotrophicus (syn. Gluconacetobacter diazotrophicus), a nitrogen-fixing endophyte of sugarcane, was sequenced and analyzed. This cluster represents the largest assembly of contiguous nif-fix and associated genes so far characterized in any diazotrophic bacterial species. Northern blots and promoter sequence analysis indicated that the genes are organized into eight transcriptional units. The overall arrangement of genes is most like that of the nif-fix cluster in Azospirillum brasilense, while the individual gene products are more similar to those in species of Rhizobiaceae or in Rhodobacter capsulatus.

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Molecular Phylogenetics of Candida albicans

Eukaryotic Cell ◽

10.1128/ec.00041-07 ◽

2007 ◽

Vol 6 (6) ◽

pp. 1041-1052 ◽

Cited By ~ 198

Author(s):

Frank C. Odds ◽

Marie-Elisabeth Bougnoux ◽

Duncan J. Shaw ◽

Judith M. Bain ◽

Amanda D. Davidson ◽

...

Keyword(s):

Candida Albicans ◽

Molecular Phylogenetics ◽

Univariate Analysis ◽

Antifungal Susceptibility ◽

Separate Analysis ◽

Individual Gene ◽

Susceptibility Data ◽

Strain Type ◽

The Individual ◽

Almost All

ABSTRACT We analyzed data on multilocus sequence typing (MLST), ABC typing, mating type-like locus (MAT) status, and antifungal susceptibility for a panel of 1,391 Candida albicans isolates. Almost all (96.7%) of the isolates could be assigned by MLST to one of 17 clades. eBURST analysis revealed 53 clonal clusters. Diploid sequence type 69 was the most common MLST strain type and the founder of the largest clonal cluster, and examples were found among isolates from all parts of the world. ABC types and geographical origins showed statistically significant variations among clades by univariate analysis of variance, but anatomical source and antifungal susceptibility data were not significantly associated. A separate analysis limited to European isolates, thereby minimizing geographical effects, showed significant differences in the proportions of isolates from blood, commensal carriage, and superficial infections among the five most populous clades. The proportion of isolates with low antifungal susceptibility was highest for MAT homozygous a/a types and then α/α types and was lowest for heterozygous a/α types. The tree of clades defined by MLST was not congruent with trees generated from the individual gene fragments sequenced, implying a separate evolutionary history for each fragment. Analysis of nucleic acid variation among loci and within loci supported recombination. Computational haplotype analysis showed a high frequency of recombination events, suggesting that isolates had mixed evolutionary histories resembling those of a sexually reproducing species.

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