<i>HSPA1L</i> variants in the large GWAS data and their association to SPTB.

<p><i>HSPA1L</i> variants in the large GWAS data and their association to SPTB.</p

Genetic variants associated with chronotype (as either a continuous or binary trait) at <i>P</i><5x10^-8 in the UK Biobank study.

<p>Variants highlighted in bold were not identified by the 23andMe study, those in italic did not reach genome-wide significance on meta-analysis and those not highlighted replicate previously reported loci from 23andMe. Genes listed are candidate or nearest genes within 250Kb of the lead SNP. Odds ratios correspond to risk of morningness over eveningness. Beta, OR and frequency refers to A1. Replication data is based on continuous data and as the replication beta is in different units to the discovery GWAS beta, a P-value meta-analysis was performed.</p

Pathway results for Danish sister pairs (n = 93); showing only genes related to the Discovery findings.

<p>Pathway results for Danish sister pairs (n = 93); showing only genes related to the Discovery findings.</p

LocusZoom plot of chronotype associations in the <i>PER2</i> locus.

<p>Variants are coloured by their LD r² with lead variant rs75804782 and those with association <i>P</i>-values > 0.01 were omitted for clarity.</p

HSPA1L and GR protein levels in decidualized human endometrial stromal fibroblasts.

<p>Cultured ESFs were transfected with WT or Ala268Thr <i>HSPA1L</i>-pcDNA3.1 constructs or with empty pcDNA3.1 vector (control). Cells were treated with decidualization media supplemented with 100nM dexamethasone (glucocorticoids) for 72h. Both cytosolic and nuclear protein were extracted, and HSPA1L and GR protein levels were measured by Western blot. Band intensity of HSPA1L or GR was normalized to band intensity of the corresponding β-actin. Cytosolic (A) and nuclear (B) HSPA1L levels as well as cytosolic (C) and nuclear (D) GR levels are shown for control (empty vector), WT and Ala268Thr sample groups. Each experiment was performed as triplicates in three different passages (n = 9 each group, except n = 8 for nuclear control group) and bars represent mean + SEM. Significant p-value <0.05 is presented with an asterisk. Cytosolic GR levels were significantly higher (p = 0.04) in the WT compared to the Ala268Thr group as well as in the WT compared to the control group (p = 0.04).</p

Most significant pathway results for Finnish mothers with recurrent SPTB (n = 10).

<p>Most significant pathway results for Finnish mothers with recurrent SPTB (n = 10).</p

Effects of <i>HSPA1L</i> variants on protein sequence and structure.

<p>(A) HSPA1L is a 641-amino acid protein that consist of two major functional domains; an N-terminal nucleotide-binding domain and a C-terminal substrate-binding domain, that are connected with interdomain linker. Locations of four <i>HSPA1L</i> variants from whole exome sequencing (Discovery and Replication findings) are shown in the protein sequence. Purple diamonds represent ATP nucleotide-binding sites at positions 14−17, 204−206, 270−277 and 341−344. Green circles denote the additional phosphorylation site generated by Ala268Thr and the existing one T267-p. (B) <i>In silico</i> comparison of higher order assembly of reference and modified (Ala268Thr) HSPA1L protein models containing an ADP molecule. Overlayed reference and Ala268Thr molecules are presented as gold and light blue rounded ribbon structures, respectively. The interacting ADP molecule is shown as a stick model. (C) Closeup view of the intermolecular contact interface of HSPA1L bound to the ADP molecule. Key interacting residues (amino acids) are shown and their corresponding side chains are presented as stick molecules; nitrogen and oxygen atoms are indicated in blue and red, respectively. All interacting residues; THR16, TYR17, GLU270, LYS273, ARG274, SER277 (not shown in figure) and ASP368, that bind to the ADP ligand showed small changes in the chemical bond lengths. Only changes of ≥0.002Å are shown in the figure (+/- lenght of Ala268Thr structure in relation to reference structure).</p

Functional predictions for rare missense <i>HSPA1L</i> variants.

<p>Functional predictions for rare missense <i>HSPA1L</i> variants.</p

Overview of the whole exome sequencing study workflow.

<p>Abbreviations used QC; quality control, MAF; minor allele frequency, RD; read depth, GQ; genotype quality.</p

LocusZoom plots of sleep duration associations in the <i>VRK2</i> locus.

<p>Both plots show the same locus but each highlights a different lead variant: rs1380703 (left) and rs17190618 (right). Variants with association <i>P</i>-values > 0.01 were omitted for clarity. The two leads variants represent separate signals.</p