Schematic representation of clathrin-mediated endocytosis.

<p>Plasma membrane molecules (in this case the dopamine receptor) associate with nascent clathrin-coated pits which then mature invaginate and finally pinch off to form clathrin-coated vesicles. The shedding of the coat takes place after the vesicle buds from the plasma membrane. This process is driven by Hsc70 ATP hydrolysis activity which is recruited to clathrin coats by Auxilin. The uncoated vesicle fuses with the membrane of a target compartment and delivers its cargo. Clathrin molecules are directed to the plasma membrane for re-use.</p

The c.801 −2 A−>G mutation in the DNAJC6 gene.

<p>The green arrow points at the first nucleotide of exon 7 and the mutation affects the preceding AG splice acceptor site of intron 6 which is changed to GG in the patient (A). The sequence of an obligate heterozygote is shown in (B) and that of a control in (C). Schematic representation of the mutation site at the genomic level (D) and its impact on the cDNA (E). Chromatogram of cDNA from a patient encompassing the 3′ junction of exon 6 (F) and demonstrating a transcript lacking exon 7 and another transcript where nNext to the last base of exon 6 (blue arrow) overlapping exon 8 sequence is the intronic sequences from intron 6 (c.801 −91). The normal exon 6/exon 7 spliced form is undetectable.</p

RT-PCR results showing evidence of amplifiable splice forms across exons 32–33 of LRRK2 in selected brain regions, occipital cortex (OCTX), substantia nigra (SNIG), medulla (MEDU) and cerebellum (CRBL).

<p>(<b>A</b>) RT-PCR results confirming the splicing out of exons 32–33 in SNIG, compared with the other brain regions tested. The expected band size for the isoform with exon 32–33 included is 470 bps, whereas that for the isoform with exon 32 alone spliced out is 270 bps. These results show splicing out of exons 32–33 in substantia nigra and the existence of an isoform with exon 32 alone spliced out in OCTX, MEDU and CRBL. (<b>B</b>) RT-PCR results further confirm the splicing out of exon 33 in SNIG. While OCTX, MEDU and CRBL show the expected band size of 195 bps suggesting that exon 32–33 is not spliced out in these regions, SNIG does not.</p

List of identified <i>LRRK2</i> eQTLs in three gene expression datasets: brain (n = 134), liver (n = 970) and monocytes (n = 1,490).

<p>For the P-value computations in brain samples, <i>LRRK2</i> expression values are averaged across all 10 brain regions. MAF: minor allele frequency. ^a: See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070724#pone.0070724.s002" target="_blank">Figure S2</a>. ^b: See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070724#pone.0070724.s001" target="_blank">Figure S1</a>.</p

Common variant associations in the <i>LRRK2</i> region for PD, CD and leprosy.

<p>The CD GWAS results indicate a minimum of two independent associations. For each disease association we list the P-values in the expression datasets. NS: not-significant (<i>P</i>>0.001). (a): See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070724#pone.0070724.s003" target="_blank">Figure S3</a>.</p

Regional variability in LRRK2 expression.

<p>(<b>A</b>) Box plot of mRNA expression levels for <i>LRRK2</i> in 10 brain regions, based on microarray experiments and plotted on a log2 scale (y axis). Whiskers extend from the box to 1.5 times the inter-quartile range. (<b>B</b>) Box plot of mRNA expression levels for <i>LRRK2</i> in 4 brain regions, based on QuantiGene experiments. Whiskers extend to the maximum and minimum values. Stars indicate significant differences in expression between brain regions (p-value <0.01, Wilcoxon signed rank testing). (<b>C</b>) Dot plot of mRNA expression levels for <i>LRRK2</i> in 3 brain regions based on TaqMan Real Time PCR experiments. The expression levels were normalized to the geometric mean of 3 housekeeping genes. The graph shows higher expression in OCTX compared with other regions. Abbreviations: frontal cortex (FCTX), occipital cortex (specifically primary visual cortex, OCTX), temporal cortex (TCTX), intralobular white matter (WHMT), thalamus (THAL), putamen (PUTM), substantia nigra (SNIG), hippocampus (HIPP), medulla (specifically inferior olivary nucleus, MEDU) and cerebellum (CRBL).</p

Additional file 1: of Discovery and functional prioritization of Parkinson’s disease candidate genes from large-scale whole exome sequencing

Includes all 12 additional tables with every table on a separate spreadsheet. The file format is an Excel spreadsheet. (XLSX 183 kb