Wei Deng

NONCODE: an integrated knowledge database of non-coding RNAs.

NONCODE is an integrated knowledge database dedicated to non-coding RNAs (ncRNAs), that is to say, RNAs that function without being translated into proteins. All ncRNAs in NONCODE were filtered automatically from literature and GenBank, and were later manually curated. The distinctive features of NONCODE are as follows: (i) the ncRNAs in NONCODE include almost all the types of ncRNAs, except transfer RNAs and ribosomal RNAs. (ii) All ncRNA sequences and their related information (e.g. function, cellular role, cellular location, chromosomal information, etc.) in NONCODE have been confirmed manually by consulting relevant literature: more than 80% of the entries are based on experimental data. (iii) Based on the cellular process and function, which a given ncRNA is involved in, we introduced a novel classification system, labeled process function class, to integrate existing classification systems. (iv) In addition, some 1100 ncRNAs have been grouped into nine other classes according to whether they are specific to gender or tissue or associated with tumors and diseases, etc. (v) NONCODE provides a user-friendly interface, a visualization platform and a convenient search option, allowing efficient recovery of sequence, regulatory elements in the flanking sequences, secondary structure, related publications and other information. The first release of NONCODE (v1.0) contains 5339 non-redundant sequences from 861 organisms, including eukaryotes, eubacteria, archaebacteria, virus and viroids. Access is free for all users through a web interface at http://noncode.bioinfo.org.cn.

GJB2 mutation spectrum in 2063 Chinese patients with nonsyndromic hearing impairment

BackgroundMutations in GJB2 are the most common molecular defects responsible for autosomal recessive nonsyndromic hearing impairment (NSHI). The mutation spectra of this gene vary among different ethnic groups.MethodsIn order to understand the spectrum and frequency of GJB2 mutations in the Chinese population, the coding region of the GJB2 gene from 2063 unrelated patients with NSHI was PCR amplified and sequenced.ResultsA total of 23 pathogenic mutations were identified. Among them, five (p.W3X, c.99delT, c.155_c.158delTCTG, c.512_c.513insAACG, and p.Y152X) are novel. Three hundred and seven patients carry two confirmed pathogenic mutations, including 178 homozygotes and 129 compound heterozygotes. One hundred twenty five patients carry only one mutant allele. Thus, GJB2 mutations account for 17.9% of the mutant alleles in 2063 NSHI patients. Overall, 92.6% (684/739) of the pathogenic mutations are frame-shift truncation or nonsense mutations. The four prevalent mutations; c.235delC, c.299_c.300delAT, c.176_c.191del16, and c.35delG, account for 88.0% of all mutantalleles identified. The frequency of GJB2 mutations (alleles) varies from 4% to 30.4% among different regions of China. It also varies among different sub-ethnic groups.ConclusionIn some regions of China, testing of the three most common mutations can identify at least one GJB2 mutant allele in all patients. In other regions such as Tibet, the three most common mutations account for only 16% the GJB2 mutant alleles. Thus, in this region, sequencing of GJB2 would be recommended. In addition, the etiology of more than 80% of the mutant alleles for NSHI in China remains to be identified. Analysis of other NSHI related genes will be necessary.

Evolution and migration history of the Chinese population inferred from Chinese Y-chromosome evidence.

AbstractY-chromosomes from 76 Chinese men covering 33 ethnical minorities throughout China as well as the Han majority were collected as genetic material for the study of Chinese nonrecombinant Y-chromosome (NRY) phylogeny. Of the accepted worldwide NRY haplogroups, three (haplogroups D, C, O) were significant in this sample, extending previous assessments of Chinese genetic diversity. Based on geographic, linguistic, and ethnohistorical information, the 33 Chinese ethnical minorities in our survey were divided into the following four subgroups: North, Tibet, West, and South. Inferred from the distribution of the newfound immediate ancestor lineage haplogroup O*, which has M214 but not M175, we argue that the southern origin scenario of this most common Chinese Y haplogroup is not very likely. We tentatively propose a West/North-origin hypothesis, suggesting that haplogroup O originated in West/North China and mainly evolved in China and thence spread further throughout eastern Eurasia. The nested cladistic analysis revealed in detail a multilayered, multidirectional, and continuous history of ethnic admixture that has shaped the contemporary Chinese population. Our results give some new clues to the evolution and migration of the Chinese population and its subsequence moving about in this land, which are in accordance with the historical records.

Detecting chimeric 5′/3′UTRs with cross-chromosomal splicing by bioinformatics

The 5′/3′ UTRs of mRNA are crucial in translational regulation, and several serious diseases are believed to be associated with abnormal splicing of these parts of the mRNA sequence. In this work a novel method which uses sequence alignment database searching for detecting chimeric 5′3′ UTRs with cross-chromosomal splicing is reported. Eight highly credible instances of cross-chromosomal splicing have been found using this method, representing additional confirmation of the existence of cross-chromosomal splicing events provided by bioinformatics tools. Since no conserved motif has been found in any of the eight instances, and at the same time current prediction algorithms produce only trivial secondary structures at the “splicing sites”, it is not possible to identify any specific signal leading to the splicing.