53 research outputs found
Rapid Gene Expression Changes in Peripheral Blood Lymphocytes upon Practice of a Comprehensive Yoga Program
<div><p>One of the most common integrative medicine (IM) modalities is yoga and related practices. Previous work has shown that yoga may improve wellness in healthy people and have benefits for patients. However, the mechanisms of how yoga may positively affect the mind-body system are largely unknown. Here we have assessed possible rapid changes in global gene expression profiles in the peripheral blood mononuclear cells (PBMCs) in healthy people that practiced either a comprehensive yoga program or a control regimen. The experimental sessions included gentle yoga postures, breathing exercises, and meditation (Sudarshan Kriya and Related Practices – SK&P) compared with a control regimen of a nature walk and listening to relaxing music. We show that the SK&P program has a rapid and significantly greater effect on gene expression in PBMCs compared with the control regimen. These data suggest that yoga and related practices result in rapid gene expression alterations which may be the basis for their longer term cell biological and higher level health effects.</p></div
The top 20 ranked genes that are differentially expressed upon yoga (SK&P) or the control regimen.
<p>The ranks and the fold changes were determined as described in Materials and Methods. Values greater than 1.0 denote an increase and values smaller than –1.0 indicate a decrease in gene expression.</p
The mRNA expression of the indicated genes which are differentially expressed by the yoga (SK&P), but not the control regimen, according to the microarray data were subjected to qPCR analysis as described in Materials and Methods.
<p>Ctrl, control; yoga, SK&P. White and black bars represent samples collected before and after the interventions, respectively. Y axis denotes fold-change in expression. Results represent data from 8 different subjects for each group. Comparisons were made with the student’s T-test. *, <i>P</i><0.05.</p
Heatmaps of the differentially expressed genes induced by the yoga (A) and control (B) regimens.
<p>Genes were clustered as described in Materials and Methods. Letters in columns represent subjects and the numbers after the letters refer to the interventions (1 and 3  =  before yoga; 2 and 4  =  after yoga; 5 and 7 before the control regimen; 6 and 8, after the control regimen) (also see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061910#pone.0061910.s001" target="_blank">Figure S1</a>). C) Venn diagram indicating the overlap in the genes commonly regulated by the yoga and control regimens.</p
Same as in Figure 3, but a sample of the genes that are differentially expressed by both the control and the yoga regimens according to the microarray analysis were subjected to qPCR.
<p>White and black bars represent samples collected before and after the interventions, respectively.</p
Ectopic ALKBH4 expression does not change H3K79 methylation levels <i>in vivo</i>.
<p>As analyzed by Western blotting, all three methylation states (mono- di- and tri-methylation) of the H3K79 residue remained similar in histones purified from stable HEK293 transfectants after doxycycline-dependent over-expression of either ALKBH4 or an enzymatically inactive mutant (ALKBH4<sup>H169A/D171A</sup>), compared to the equivalent, non-induced cells. Signal intensities of bands corresponding to methylated histones were quantified using ImageJ <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049045#pone.0049045-Schneider1" target="_blank">[69]</a>, and normalized to the total histone H3 load, but no effect of ALKBH4 overexpression was detected (not shown).</p
Schematic representation of yeast two-hybrid high confidence hits involved in transcription.
<p>Individual prey fragment clones and the resulting selected interaction domains (SIDs) reported to bind ALKBH4 are indicated above each protein; black lines, placenta library; orange lines, fetal brain library; green lines, placenta library screened with ALKBH4<sup>H169A/D171A</sup>; red dashed lines, SIDs. Grey boxes indicate protein domains. Proteins and domains are drawn to scale according to the InterPro (version 4.8) and PROSITE (release 20.68) databases <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049045#pone.0049045-Hunter1" target="_blank">[73]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049045#pone.0049045-Sigrist1" target="_blank">[74]</a>.//indicates regions omitted for simplicity. ZnF, C<sub>2</sub>H<sub>2</sub> zinc finger; HD, homeodomain; YEATS, Yaf9 ENL AF9 Taf14 Sas5; TAZ, transcription adaptor putative zinc finger; BRD, bromodomain; PHD plant homeodomain; HAT histone acetyl transferase; DBD, DNA binding domain. Bar, 100 aa.</p
The genes most differentially expressed in either direction identified in ALKBH7 over-expressing cells compared to parental non over-expressing cells.
<p>The genes most differentially expressed in either direction identified in ALKBH7 over-expressing cells compared to parental non over-expressing cells.</p
High confidence<sup>a</sup> ALKBH4 interacting proteins identified by the yeast two-hybrid system.
a<p>PBS (predicted biological score) of A or B. PBS (calculated according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049045#pone.0049045-Formstecher1" target="_blank">[75]</a>) represents the probability of an interaction to be non-specific, and refers to an e-value with defined thresholds to rank the results in the high-to-low confidence categories A–D.</p>b<p>SID (selected interaction domain) refers to the amino acid region shared by all prey fragments matching the same reference protein,</p>c<p>(+) Low confidence hit (PBS D),</p>d<p>EIF3CL. Grey shade, transcription related interactants. YEATS, Yaf9 ENL AF9 TAF14 Sas5; DBD, DNA binding domain; PHD, plant homeodomain; PET, Prickle Espinas Testin; LIM, Lin-11 Isl-1 Mec-3; PCI, Proteasome, COP9, Initiation factor-3; PTP, protein tyrosine phosphatase.</p
Effects of ectopic expression of ALKBH4 or ALKBH7 on global gene expression.
<p>(<b>A</b>) Quantitative RT-PCR analysis of relative <i>ALKBH4</i> levels in HEK293 cells stably transfected with a construct for DOX-inducible over-expression of ALKBH4-FLAG, either treated with DOX (2 µg/ml) or untreated. Results are presented as mean fold change of three independent replicates normalized to <i>β-actin</i> ± S.D. (<b>B</b>) Ectopic ALKBH4 protein levels in DOX-induced and non-induced cells, as determined by Western blot analysis. Ectopic ALKBH4 was detected using an antibody against the FLAG-tag introduced at the C-terminus of ALKBH4. GAPDH expression levels are included as loading control. (<b>C</b>) Microarray analysis of gene expression in cells over-expressing either ALKBH4 or ALKBH7 vs. non-overexpressing cells. The number of genes whose expression is altered at least 2.0-fold (ALKBH7) or 1.35-fold (ALKBH4) is indicated (<b>D</b>) MetaCore (GeneGo Inc.) analysis of molecular pathways significantly (False discovery rate (FDR) <0.05) enriched with genes affected by ectopic ALKBH7 expression. DOX, doxycycline.</p
- …