74 research outputs found
The Alternative Choice of Constitutive Exons throughout Evolution
Alternative cassette exons are known to originate from two processes
exonization of intronic sequences and exon shuffling. Herein, we suggest an
additional mechanism by which constitutively spliced exons become alternative
cassette exons during evolution. We compiled a dataset of orthologous exons
from human and mouse that are constitutively spliced in one species but
alternatively spliced in the other. Examination of these exons suggests that
the common ancestors were constitutively spliced. We show that relaxation of
the 59 splice site during evolution is one of the molecular mechanisms by which
exons shift from constitutive to alternative splicing. This shift is associated
with the fixation of exonic splicing regulatory sequences (ESRs) that are
essential for exon definition and control the inclusion level only after the
transition to alternative splicing. The effect of each ESR on splicing and the
combinatorial effects between two ESRs are conserved from fish to human. Our
results uncover an evolutionary pathway that increases transcriptome diversity
by shifting exons from constitutive to alternative splicin
Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene
Background: Gene duplication and exonization of intronic transposed elements
are two mechanisms that enhance genomic diversity. We examined whether there is
less selection against exonization of transposed elements in duplicated genes
than in single-copy genes. Results: Genome-wide analysis of exonization of
transposed elements revealed a higher rate of exonization within duplicated
genes relative to single-copy genes. The gene for TIF-IA, an RNA polymerase I
transcription initiation factor, underwent a humanoid-specific triplication,
all three copies of the gene are active transcriptionally, although only one
copy retains the ability to generate the TIF-IA protein. Prior to TIF-IA
triplication, an Alu element was inserted into the first intron. In one of the
non-protein coding copies, this Alu is exonized. We identified a single point
mutation leading to exonization in one of the gene duplicates. When this
mutation was introduced into the TIF-IA coding copy, exonization was activated
and the level of the protein-coding mRNA was reduced substantially. A very low
level of exonization was detected in normal human cells. However, this
exonization was abundant in most leukemia cell lines evaluated, although the
genomic sequence is unchanged in these cancerous cells compared to normal
cells. Conclusion: The definition of the Alu element within the TIF-IA gene as
an exon is restricted to certain types of cancers; the element is not exonized
in normal human cells. These results further our understanding of the delicate
interplay between gene duplication and alternative splicing and of the
molecular evolutionary mechanisms leading to genetic innovations. This implies
the existence of purifying selection against exonization in single copy genes,
with duplicate genes free from such constrains
Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program
Summary Microglia, the brain-resident immune cells, are critically involved in many physiological and pathological brain processes, including neurodegeneration. Here we characterize microglia morphology and transcriptional programs across ten species spanning more than 450 million years of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to humans, including ligands and receptors associated with interactions between glia and neurons. In most species, microglia show a single dominant transcriptional state, whereas human microglia display significant heterogeneity. In addition, we observed notable differences in several gene modules of rodents compared with primate microglia, including complement, phagocytic, and susceptibility genes to neurodegeneration, such as Alzheimer’s and Parkinson’s disease. Our study provides an essential resource of conserved and divergent microglia pathways across evolution, with important implications for future development of microglia-based therapies in humans
Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma
Multiple myeloma, a plasma cell malignancy, is the second most common blood cancer. Despite extensive research, disease heterogeneity is poorly characterized, hampering efforts for early diagnosis and improved treatments. Here, we apply single cell RNA sequencing to study the heterogeneity of 40 individuals along the multiple myeloma progression spectrum, including 11 healthy controls, demonstrating high interindividual variability that can be explained by expression of known multiple myeloma drivers and additional putative factors. We identify extensive subclonal structures for 10 of 29 individuals with multiple myeloma. In asymptomatic individuals with early disease and in those with minimal residual disease post-treatment, we detect rare tumor plasma cells with molecular characteristics similar to those of active myeloma, with possible implications for personalized therapies. Single cell analysis of rare circulating tumor cells allows for accurate liquid biopsy and detection of malignant plasma cells, which reflect bone marrow disease. Our work establishes single cell RNA sequencing for dissecting blood malignancies and devising detailed molecular characterization of tumor cells in symptomatic and asymptomatic patients
Phosphatidylserine Increases IKBKAP Levels in Familial Dysautonomia Cells
Familial Dysautonomia (FD) is an autosomal recessive congenital neuropathy that results from abnormal development and progressive degeneration of the sensory and autonomic nervous system. The mutation observed in almost all FD patients is a point mutation at position 6 of intron 20 of the IKBKAP gene; this gene encodes the IκB kinase complex-associated protein (IKAP). The mutation results in a tissue-specific splicing defect: Exon 20 is skipped, leading to reduced IKAP protein expression. Here we show that phosphatidylserine (PS), an FDA-approved food supplement, increased IKAP mRNA levels in cells derived from FD patients. Long-term treatment with PS led to a significant increase in IKAP protein levels in these cells. A conjugate of PS and an omega-3 fatty acid also increased IKAP mRNA levels. Furthermore, PS treatment released FD cells from cell cycle arrest and up-regulated a significant number of genes involved in cell cycle regulation. Our results suggest that PS has potential for use as a therapeutic agent for FD. Understanding its mechanism of action may reveal the mechanism underlying the FD disease
Pre-mRNA splicing is a determinant of nucleosome organization.
Chromatin organization affects alternative splicing and previous studies have shown that exons have increased nucleosome occupancy compared with their flanking introns. To determine whether alternative splicing affects chromatin organization we developed a system in which the alternative splicing pattern switched from inclusion to skipping as a function of time. Changes in nucleosome occupancy were correlated with the change in the splicing pattern. Surprisingly, strengthening of the 5' splice site or strengthening the base pairing of U1 snRNA with an internal exon abrogated the skipping of the internal exons and also affected chromatin organization. Over-expression of splicing regulatory proteins also affected the splicing pattern and changed nucleosome occupancy. A specific splicing inhibitor was used to show that splicing impacts nucleosome organization endogenously. The effect of splicing on the chromatin required a functional U1 snRNA base pairing with the 5' splice site, but U1 pairing was not essential for U1 snRNA enhancement of transcription. Overall, these results suggest that splicing can affect chromatin organization
Caffeinated chewing gum as countermeasure to drivers' passive task-related fatigue caused by monotonous roadway
This study analyzed driver passive task-related fatigue caused by a monotonous environment and the effectiveness of caffeinated chewing gum as a countermeasure. Data collected by a driving simulator in the laboratory were used to measure changes in driving performance. A self-perceived measure of fatigue was also analyzed. Seventy-Two subjects were asked to drive for 70 min along a straight road after receiving one of the following substances (treatments): caffeinated chewing gum, a cup of coffee, or placebo chewing gum. The 72 subjects were subdivided into three groups of 24 each, and all participants were asked to take part in two driving sessions: one control drive without administration (no treatment) and one with administration (one of the treatments). The negative effects on driving performance of prolonged driving and the effectiveness of the standard deviation of the lateral position in representing worsening driving performance were demonstrated. This analysis indicated that intake of caffeine in the form of caffeinated chewing gum (100 mg caffeine) improved driving performance in less than 10 min. Drinking an ordinary cup of coffee (with the same caffeine content) did not improve driving performance in the same short time interval
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