Non-coding RNAs and disease: the classical ncRNAs make a comeback

Many human diseases have been attributed to mutation in the protein coding regions of the human genome. The protein coding portion of the human genome, however, is very small compared with the non-coding portion of the genome. As such, there are a disproportionate number of diseases attributed to the coding compared with the non-coding portion of the genome. It is now clear that the non-coding portion of the genome produces many functional non-coding RNAs and these RNAs are slowly being linked to human diseases. Here we discuss examples where mutation in classical non-coding RNAs have been attributed to human disease and identify the future potential for the non-coding portion of the genome in disease biology.

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Landscape of human miRNA variation and conservation using Annotative Database of miRNA Elements, ADmiRE

10.1101/177170 ◽

2017 ◽

Author(s):

Ninad Oak ◽

Rajarshi Ghosh ◽

Sharon E. Plon

Keyword(s):

Rare Variants ◽

Human Diseases ◽

Mirna Sequence ◽

Allele Frequency Distribution ◽

Genomic Context ◽

Protein Coding ◽

Variant Annotation ◽

Future Studies ◽

Coding Regions ◽

Non Coding Rnas

AbstractMicroRNAs (miRNAs) are the most abundant class of non-coding RNAs that regulate expression of >60% genes and are frequently deregulated in many human diseases. Sequence variants in miRNAs are expected to have a high impact on miRNA function. However, the lack of miRNA variant annotation and prioritization guidelines has hampered this analysis from whole genome/exome sequencing (WGS/WES) studies. Through the development of an Annotative Database of miRNA Elements, ADmiRE workflow, we re-annotated the publicly available population dataset of gnomAD 15,596 WGS and 123,136 WES and describe 26,094 precursor-miRNA variants. AdmiRE annotates twice the miRNA variants predicted by existing tools which prioritize variation relative to protein coding regions. We provide the allele frequency distribution of miRNA variation which is comparable to variation in exonic regions. This distribution is similar for miRNAs located in the intragenic and intergenic genomic context. Moreover, ‘high confidence’ miRNAs (designated by miRBase) harbor less variation (the majority contributed by rare variants) compared with the remaining miRNAs. We identify 279 miRNAs highly constrained with little or no variation in gnomAD. We further describe the evolutionary conservation of miRNAs across 100 vertebrates and identify 434 highly conserved miRNAs. We demonstrate that these constraint and conservation metrics (now incorporated into the ADmiRE workflow) characterize miRNAs previously implicated in human diseases. In conclusion, through the development of ADmiRE, we comprehensively analyze the landscape of miRNA sequence variation in large human population datasets and provide miRNA vertebrate conservation scores to aid future studies of miRNA variation in human diseases.

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Distinctive functional regime of endogenous lncRNAs in dark regions of human genome

10.1101/2020.12.06.413880 ◽

2020 ◽

Author(s):

Anyou Wang ◽

Rong Hai

Keyword(s):

Human Genome ◽

Rna Processing ◽

Self Regulation ◽

Post Translational Modification ◽

Protein Coding ◽

Noncoding Regions ◽

Coding Regions ◽

Rnaseq Data ◽

Response To Stress ◽

Eukaryotic Genomes

AbstractEukaryotic genomes gradually gain noncoding regions when advancing evolution and human genome actively transcribes >90% of its noncoding regions1, suggesting their criticality in evolutionary human genome. Yet <1% of them have been functionally characterized2, leaving most human genome in dark. Here we systematically decode endogenous lncRNAs located in unannotated regions of human genome and decipher a distinctive functional regime of lncRNAs hidden in massive RNAseq data. LncRNAs divergently distribute across chromosomes, independent of protein-coding regions. Their transcriptions barely initiate on promoters through polymerase II, but mostly on enhancers. Yet conventional enhancer activators(e.g. H3K4me1) only account for a small proportion of lncRNA activation, suggesting alternatively unknown mechanisms initiating the majority of lncRNAs. Meanwhile, lncRNA-self regulation also notably contributes to lncRNA activation. LncRNAs trans-regulate broad bioprocesses, including transcription and RNA processing, cell cycle, respiration, response to stress, chromatin organization, post-translational modification, and development. Overall lncRNAs govern their owned regime distinctive from protein’s.

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COMPARATIVE ANALYSIS OF DISEASE-ASSOCIATED MUTATIONS IN THE CODING REGIONS OF ALTERNATIVELY AND CONSTITUTIVELY SPLICED HUMAN GENES

Journal of Biological System ◽

10.1142/s0218339008002563 ◽

2008 ◽

Vol 16 (02) ◽

pp. 241-253

Author(s):

QIANLI HUANG ◽

YONG LI ◽

JESSE LI-LING ◽

HUIFANG HUANG ◽

XUEPING CHEN ◽

...

Keyword(s):

Alternative Splicing ◽

Codon Usage ◽

Codon Usage Bias ◽

Human Disease ◽

Molecular Mechanisms ◽

Human Diseases ◽

Disease Genes ◽

Single Mutation ◽

Coding Regions ◽

Human Disease Genes

To better understand the evolutionary and molecular mechanisms of alternative splicing causing human diseases, we have systematically compared the pattern, the distribution and the density of disease-associated mutations as well as the influence of codon usage bias on the single mutation between alternatively and constitutively spliced genes through analysis of the large datasets from human disease genes. The results indicated that: 1. The most common pattern of single mutation in alternatively and constitutively spliced genes are, respectively, C/T (25.17%), (22.81%) and G/A (21.54%), (22.73%), suggesting that the two types of disease genes are prone to C → T and G → A mutations. 2. There is an overall preponderance for transitions over transversions in alternatively (62.88% versus 37.12%) and constitutively (64.41% versus 35.59%) spliced disease genes. 3. For the second base of codons, there exist significant differences in transitions and transversions between the two types of genes. 4. Our data indicated that the single mutation tends to occur preferentially when the upstream neighboring-nucleotide is C or G in human disease genes. 5. Codon usage bias and synonymous codon usage have great influence on the single mutation in both alternatively and constitutively spliced genes. The GC content and gene length also have very evident influence on such mutations. Our results seem to imply that disease-associated mutations within the coding regions of alternatively spliced human disease genes have different mechanisms from constitutively spliced genes. Such findings may facilitate understanding the molecular mechanism of alternative splicing causing human diseases, and the development of gene therapies for such diseases.

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N6-Methyladenine DNA Modification in Human Genome

10.1101/176958 ◽

2017 ◽

Cited By ~ 1

Author(s):

Chuan-Le Xiao ◽

Song Zhu ◽

Minghui He ◽

De Chen ◽

Qian Zhang ◽

...

Keyword(s):

Human Genome ◽

Genomic Dna ◽

Human Cells ◽

Human Diseases ◽

Dna Modification ◽

Down Regulation ◽

Coding Regions

SummaryDNA N6-methyladenine (6mA) modification is the most prevalent DNA modification in prokaryotes, but whether it exists in human cells and whether it plays a role in human diseases remain enigmatic. Here, we showed that 6mA is extensively present in human genome, and we cataloged 881,240 6mA sites accounting for ∼0.051% of the total adenines. [G/C]AGG[C/T] was the most significantly associated motif with 6mA modification. 6mA sites were enriched in the coding regions and mark actively transcribed genes in human cells. We further found that DNA N6-methyladenine and N6-demethyladenine modification in human genome were mediated by methyltransferase N6AMT1 and demethylase ALKBH1, respectively. The abundance of 6mA was significantly lower in cancers, accompaning with decreased N6AMT1 and increased ALKBH1 levels, and down-regulation of 6mA modification levels promoted tumorigenesis. Collectively, our results demonstrate that DNA 6mA modification is extensively present in human cells and the decrease of genomic DNA 6mA promotes human tumorigenesis.

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Mutation severity spectrum of rare alleles in the human genome is predictive of disease type

10.1101/835462 ◽

2019 ◽

Author(s):

Jimin Pei ◽

Lisa Kinch ◽

Nick V. Grishin

Keyword(s):

Human Genome ◽

Genetic Disorders ◽

Single Amino Acid ◽

Missense Mutations ◽

Single Nucleotide ◽

Protein Coding ◽

Coding Regions ◽

Structural And Functional Properties ◽

Disease Associations ◽

Disease Associated Genes

AbstractThe human genome harbors a variety of genetic variations. Single-nucleotide changes that alter amino acids in protein-coding regions are one of the major causes of human phenotypic variation and diseases. These single-amino acid variations (SAVs) are routinely found in whole genome and exome sequencing. Evaluating the functional impact of such genomic alterations is crucial for diagnosis of genetic disorders. We developed DeepSAV, a deep-learning convolutional neural network to differentiate disease-causing and benign SAVs based on a variety of protein sequence, structural and functional properties. Our method outperforms most stand-alone programs and has similar predictive power as some of the best available. We transformed DeepSAV scores of rare SAVs observed in the general population into a mutation severity measure of protein-coding genes. This measure reflects a gene’s tolerance to deleterious missense mutations and serves as a useful tool to study gene-disease associations. Genes implicated in cancer, autism, and viral interaction are found by this measure as intolerant to mutations, while genes associated with a number of other diseases are scored as tolerant. Among known disease-associated genes, those that are mutation-intolerant are likely to function in development and signal transduction pathways, while those that are mutation-tolerant tend to encode metabolic and mitochondrial proteins.

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Building the vertebrate codex using the gene breaking protein trap library

eLife ◽

10.7554/elife.54572 ◽

2020 ◽

Vol 9 ◽

Author(s):

Noriko Ichino ◽

MaKayla R Serres ◽

Rhianna M Urban ◽

Mark D Urban ◽

Anthony J Treichel ◽

...

Keyword(s):

Human Disease ◽

Molecular Mechanisms ◽

Genetic Diseases ◽

Transgenic Zebrafish ◽

Protein Coding ◽

Coding Regions ◽

Disease Associated Genes ◽

Functional Genome Annotation ◽

Specific Mrna

One key bottleneck in understanding the human genome is the relative under-characterization of 90% of protein coding regions. We report a collection of 1200 transgenic zebrafish strains made with the gene-break transposon (GBT) protein trap to simultaneously report and reversibly knockdown the tagged genes. Protein trap-associated mRFP expression shows previously undocumented expression of 35% and 90% of cloned genes at 2 and 4 days post-fertilization, respectively. Further, investigated alleles regularly show 99% gene-specific mRNA knockdown. Homozygous GBT animals in ryr1b, fras1, tnnt2a, edar and hmcn1 phenocopied established mutants. 204 cloned lines trapped diverse proteins, including 64 orthologs of human disease-associated genes with 40 as potential new disease models. Severely reduced skeletal muscle Ca2+ transients in GBT ryr1b homozygous animals validated the ability to explore molecular mechanisms of genetic diseases. This GBT system facilitates novel functional genome annotation towards understanding cellular and molecular underpinnings of vertebrate biology and human disease.

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An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome

PLoS ONE ◽

10.1371/journal.pone.0008949 ◽

2010 ◽

Vol 5 (1) ◽

pp. e8949 ◽

Cited By ~ 24

Author(s):

Danny A. Bitton ◽

Duncan L. Smith ◽

Yvonne Connolly ◽

Paul J. Scutt ◽

Crispin J. Miller

Keyword(s):

Mass Spectrometry ◽

Human Genome ◽

Protein Coding ◽

Coding Regions ◽

Novel Protein

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Extreme purifying selection against point mutations in the human genome

10.1101/2021.08.23.457339 ◽

2021 ◽

Author(s):

Noah Dukler ◽

Mehreen R Mughal ◽

Ritika Ramani ◽

Yi-Fei Huang ◽

Adam Siepel

Keyword(s):

Human Genome ◽

De Novo ◽

Point Mutations ◽

Purifying Selection ◽

Selection Coefficient ◽

Sequencing Data ◽

Protein Coding ◽

Coding Regions ◽

Protein Coding Genes ◽

Selective Effects

Genome sequencing of tens of thousands of human individuals has recently enabled the measurement of large selective effects for mutations to protein-coding genes. Here we describe a new method, called ExtRaINSIGHT, for measuring similar selective effects at individual sites in noncoding as well as in coding regions of the human genome. ExtRaINSIGHT estimates the prevalance of strong purifying selection, or "ultraselection" (λs), as the fractional depletion of rare single-nucleotide variants (minor allele frequency <0.1%) in a target set of genomic sites relative to matched sites that are putatively neutrally evolving, in a manner that controls for local variation and neighbor-dependence in mutation rate. We show using simulations that, above an appropriate threshold, λs is closely related to the average site-specific selection coefficient against heterozygous point mutations, as predicted at mutation-selection balance. Applying ExtRaINSIGHT to 71,702 whole genome sequences from gnomAD v3, we find particularly strong evidence of ultraselection in evolutionarily ancient miRNAs and neuronal protein-coding genes, as well as at splice sites. Moreover, our estimated selection coefficient against heterozygous amino-acid replacements across the genome (at 1.4%) is substantially larger than previous estimates based on smaller sample sizes. By contrast, we find weak evidence of ultraselection in other noncoding RNAs and transcription factor binding sites, and only modest evidence in ultraconserved elements and human accelerated regions. We estimate that ~0.3-0.5% of the human genome is ultraselected, with one third to one half of ultraselected sites falling in coding regions. These estimates suggest ~0.3-0.4 lethal or nearly lethal de novo mutations per potential human zygote, together with ~2 de novo mutations that are more weakly deleterious. Overall, our study sheds new light on the genome-wide distribution of fitness effects for new point mutations by combining deep new sequencing data sets and classical theory from population genetics.

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ZC3H4 restricts non-coding transcription in human cells

eLife ◽

10.7554/elife.67305 ◽

2021 ◽

Vol 10 ◽

Author(s):

Chris Estell ◽

Lee Davidson ◽

Pieter C Steketee ◽

Adam Monier ◽

Steven West

Keyword(s):

Cell Proliferation ◽

Human Genome ◽

Substantial Reduction ◽

Human Cells ◽

Protein Coding ◽

Antisense Rnas ◽

Transcriptional Termination ◽

Non Coding Rnas

The human genome encodes thousands of non-coding RNAs. Many of these terminate early and are then rapidly degraded, but how their transcription is restricted is poorly understood. In a screen for protein-coding gene transcriptional termination factors, we identified ZC3H4. Its depletion causes upregulation and extension of hundreds of unstable transcripts, particularly antisense RNAs and those transcribed from so-called super-enhancers. These loci are occupied by ZC3H4, suggesting that it directly functions in their transcription. Consistently, engineered tethering of ZC3H4 to reporter RNA promotes its degradation by the exosome. ZC3H4 is predominantly metazoan - interesting when considering its impact on enhancer RNAs that are less prominent in single-celled organisms. Finally, ZC3H4 loss causes a substantial reduction in cell proliferation, highlighting its overall importance. In summary, we identify ZC3H4 as playing an important role in restricting non-coding transcription in multi-cellular organisms.

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ZC3H4 restricts non-coding transcription in human cells

10.1101/2021.02.10.430684 ◽

2021 ◽

Cited By ~ 1

Author(s):

Chris Estell ◽

Lee Davidson ◽

Pieter C. Steketee ◽

Adam Monier ◽

Steven West

Keyword(s):

Cell Proliferation ◽

Human Genome ◽

Substantial Reduction ◽

Human Cells ◽

Protein Coding ◽

Antisense Rnas ◽

Non Coding Rnas

SUMMARYThe human genome encodes thousands of non-coding RNAs. Many of these terminate early and are then rapidly degraded, but how their transcription is restricted is poorly understood. In a screen for protein-coding gene termination factors, we identified ZC3H4. However, its depletion causes upregulation and extension of hundreds of unstable transcripts, particularly antisense RNAs and those transcribed from so-called super-enhancers. These loci are occupied by ZC3H4, suggesting that it directly functions in their transcription. Consistently, engineered tethering of ZC3H4 to reporter RNA promotes its degradation by the exosome. ZC3H4 is metazoan-specific - interesting when considering its impact on enhancer RNAs that are less prominent in single-celled organisms. Finally, ZC3H4 loss causes a substantial reduction in cell proliferation, highlighting its overall importance. In summary, we identify ZC3H4 as a factor that plays an important role in restricting non-coding transcription in multi-cellular organisms.

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