When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3' adapter. That adapter must be found and removed error-tolerantly from each read before read mapping. Previous solutions are either hard to use or do not offer required features, in particular support for color space data. As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features. Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/

https://journal.embnet.org/index.php/embnetjournal/article/download/200/458

Cutadapt removes adapter sequences from high-throughput sequencing reads

Genomic imprinting affects several dozen mammalian genes and results in the expression of those genes from only one of the two parental chromosomes. This is brought about by epigenetic instructions--imprints--that are laid down in the parental germ cells. Imprinting is a particularly important genetic mechanism in mammals, and is thought to influence the transfer of nutrients to the fetus and the newborn from the mother. Consistent with this view is the fact that imprinted genes tend to affect growth in the womb and behaviour after birth. Aberrant imprinting disturbs development and is the cause of various disease syndromes. The study of imprinting also provides new insights into epigenetic gene modification during development.

/pdf/genomic-imprinting-parental-influence-on-the-genome-3ft04w0kfl.pdf

Genomic imprinting: parental influence on the genome

Prader-Willi syndrome

Angelman syndrome (AS), characterized by mental retardation, seizures, frequent smiling and laughter, and abnormal gait, is one of the best examples of human disease in which genetic imprinting plays a role. In about 70% of cases, AS is caused by de novo maternal deletions at 15q11-q13 (ref. 2). Approximately 2% of AS cases are caused by paternal uniparental disomy (UPD) of chromosome 15 (ref. 3) and 2-3% are caused by "imprinting mutations'. In the remaining 25% of AS cases, no deletion, uniparental disomy (UPD), or methylation abnormality is detectable, and these cases, unlike deletions or UPD, can be familial. These cases are likely to result from mutations in a gene that is expressed either exclusively or preferentially from the maternal chromosome 15. We have found that a 15q inversion inherited by an AS child from her normal mother disrupts the 5' end of the UBE3A (E6-AP) gene, the product of which functions in protein ubiquitination. We have looked for novel UBE3A mutations in nondeletion/non-UPD/non-imprinting mutation (NDUI) AS patients and have found one patient who is heterozygous for a 5-bp de novo tandem duplication. We have also found in two brothers a heterozygous mutation, an A to G transition that creates a new 3' splice junction 7 bp upstream from the normal splice junction. Both mutations are predicted to cause a frameshift and premature termination of translation. Our results demonstrate that UBE3A mutations are one cause of AS and indicate a possible abnormality in ubiquitin-mediated protein degradation during brain development in this disease.

UBE3A/E6-AP mutations cause Angelman syndrome

https://birdlab.bio.ed.ac.uk/bird/sites/sbsweb2.bio.ed.ac.uk.bird/files/15.pdf

CpG islands--'a rough guide'.

A subset of patients with Angelman and Prader-Willi syndrome have apparently normal chromosomes of biparental origin, but abnormal DNA methylation at several loci within chromosome 15q11-13, and probably have a defect in imprinting. Using probes from a newly established 160-kb contig including D15S63 (PW71) and SNRPN, we have identified inherited microdeletions in two AS families and three PWS families. The deletions probably affect a single genetic element that we term the 15q11-13 imprinting centre (IC). In our model, the IC regulates the chromatin structure, DNA methylation and gene expression in cis throughout 15q11-13. Mutations of the imprinting centre can be transmitted silently through the germline of one sex, but appear to block the resetting of the imprint in the germline of the opposite sex.

Inherited microdeletions in the Angelman and Prader-Willi syndromes define an imprinting centre on human chromosome 15.

Recent case reports have suggested that infertility treatment with intracytoplasmic sperm injection (ICSI) may increase the risk of imprinting defects leading to Angelman syndrome (AS). Although imprinting defects account for only 4% of patients with AS, we have found four cases among 16 AS patients born to subfertile couples, who conceived with or without infertility treatment (25%; relative risk (RR) 6.25; 95% confidence interval (CI) 1.68 to 16.00). The risk in untreated couples with time to pregnancy (TTP) exceeding 2 years was identical to that of those treated by ICSI or by hormonal stimulation alone (RR 6.25; 95% CI 0.70 to 22.57). It was twice as high in couples who had received treatment and also had TTP >2 years (RR 12.5; 95% CI 1.40 to 45.13). Our findings suggest that imprinting defects and subfertility may have a common cause, and that superovulation rather than ICSI may further increase the risk of conceiving a child with an imprinting defect.

https://jmg.bmj.com/content/jmedgenet/42/4/289.full.pdf

Increased prevalence of imprinting defects in patients with Angelman syndrome born to subfertile couples

Using a test based on parent of origin specific DNA methylation at the D15S63 (PW71) locus, we studied 385 patients (aged 1 to 36 years) for diagnostic confirmation of Prader-Willi syndrome (PWS) and 65 infants (aged 0 to 12 months) with severe hypotonia of unknown cause. Fifty eight of 385 patients were examined personally; 28/58 patients had PWS and lacked the paternal PW71 band and 30/58 patients, who did not have PWS, had a normal methylation pattern. In five of these patients, a differential diagnosis was made (Ohdo-like blepharophimosis syndrome, Alstrom syndrome, Cohen syndrome, Bardet-Biedl syndrome, and pseudohypoparathyroidism). A total of 327/385 blood samples was sent to us from outside. The test confirmed the diagnosis of PWS in 112/327 patients. Most of the other 215 patients lacked the major diagnostic criteria such as neonatal hypotonia, feeding problems, characteristic facies, and hypogenitalism. On the other hand, 29/65 hypotonic infants tested positive for PWS. We conclude that the PW71 methylation test detects most, if not all, patients with typical PWS and that PWS is often not recognised in infants and wrongly suspected in obese and mentally retarded patients.

https://jmg.bmj.com/content/jmedgenet/32/2/88.full.pdf

DNA methylation based testing of 450 patients suspected of having Prader-Willi syndrome.

In adult human tissues, a HpaII and a CfoI restriction site at the PW71 (D15S63) locus in the Prader-Willi syndrome region on chromosome 15 are methylated on the maternal chromosome, but unmethylated on the paternal chromosome. The HpaII site is part of a sequence with high homology to the long terminal repeat of human endogenous retroviruses. Another HpaII site at the PW71 locus is methylated on both chromosomes. Sperm DNA carries the adult paternal methylation pattern. Oocyte DNA could not be studied. In chorion, placenta and tumor DNA, both HpaII sites are unmethylated. These findings suggest that the PW71 methylation imprint is established in the germline and that extraembryonic tissues and tumors are hypomethylated.

Characterization of a methylation imprint in the Prader — Willi syndrome chromosome region

Maternal uniparental disomy 14 [upd(14)mat] is associated with a recognizable phenotype that includes pre- and postnatal growth retardation, neonatal hypotonia, feeding problems and precocious puberty. Chromosome 14 contains an imprinted gene cluster, which is regulated by a differentially methylated region (IG-DMR) between DLK1 and GTL2. Here we report on four patients with clinical features of upd(14)mat who show a maternal-only methylation pattern, but biparental inheritance for chromosome 14. In three of the patients loss of paternal methylation appears to be a primary epimutation, whereas the other patient has a paternally derived deletion of -1 Mb that includes the imprinted DLK1-GTL2 gene cluster. These findings demonstrate that the upd(14)mat phenotype is caused by altered expression of genes within this cluster.

Stephanie Gross

Papers

Inherited microdeletions in the Angelman and Prader-Willi syndromes define an imprinting centre on human chromosome 15.

Increased prevalence of imprinting defects in patients with Angelman syndrome born to subfertile couples

DNA methylation based testing of 450 patients suspected of having Prader-Willi syndrome.

Characterization of a methylation imprint in the Prader — Willi syndrome chromosome region

Clinical features of maternal uniparental disomy 14 in patients with an epimutation and a deletion of the imprinted DLK1/GTL2 gene cluster.