Finding function in mystery transcripts

Rae, Kelly

doi:10.1038/529423a

Cited by 10 publications

(7 citation statements)

References 10 publications

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“…Similarly, deep intronic variants not within the canonical splice acceptor or donor sequences can create strong pseudo exons that are included in the mature mRNA and disrupt reading frame [5]. To increase sensitivity and to gain understanding of the potential to increase diagnostic yield from WGS, we will augment DNA sequence with RNA analysis [17,18].For neurodevelopmental disorders, the affected tissue type isoften not available (i.e. brain).…”

Section: Aim 2: Augment Dna Sequencing With Normalized Transcriptome Analysismentioning

confidence: 99%

Al Mana Group and Ucla Research Project for Molecular Genetic Studies of Degenerative Disorders of Saudi Children

Bashir

2019

GJPNC

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Section: Aim 2: Augment Dna Sequencing With Normalized Transcriptome Analysismentioning

confidence: 99%

Al Mana Group and Ucla Research Project for Molecular Genetic Studies of Degenerative Disorders of Saudi Children

Bashir

2019

GJPNC

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“…Though the PacBio sequencing technology is limited by a lower throughput, higher error rate, and higher cost per base and complemented with RNA-seq to achieve better effects [13], the Iso-Seq still has obvious advantages in improving annotations in reference genomes and identifying gene isoforms, alternative splicing (AS), and gene fusion events. Additionally, it helps in complementing the short/incomplete transcripts for species without a reference genome [14, 15]. However, till date, there is no database that provides comprehensive resources for a complete transcript isoform obtained from Iso-Seq data.…”

Section: Introductionmentioning

confidence: 99%

ISOdb: A Comprehensive Database of Full-Length Isoforms Generated by Iso-Seq

Xie

Han

Chen

et al. 2018

International Journal of Genomics

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The accurate landscape of transcript isoforms plays an important role in the understanding of gene function and gene regulation. However, building complete transcripts is very challenging for short reads generated using next-generation sequencing. Fortunately, isoform sequencing (Iso-Seq) using single-molecule sequencing technologies, such as PacBio SMRT, provides long reads spanning entire transcript isoforms which do not require assembly. Therefore, we have developed ISOdb, a comprehensive resource database for hosting and carrying out an in-depth analysis of Iso-Seq datasets and visualising the full-length transcript isoforms. The current version of ISOdb has collected 93 publicly available Iso-Seq samples from eight species and presents the samples in two levels: (1) sample level, including metainformation, long read distribution, isoform numbers, and alternative splicing (AS) events of each sample; (2) gene level, including the total isoforms, novel isoform number, novel AS number, and isoform visualisation of each gene. In addition, ISOdb provides a user interface in the website for uploading sample information to facilitate the collection and analysis of researchers' datasets. Currently, ISOdb is the first repository that offers comprehensive resources and convenient public access for hosting, analysing, and visualising Iso-Seq data, which is freely available.

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“…Physiology of RNA has been generating more impact on modern biomedical sciences extending the previous views for the RNA metabolism that has been just oriented to steps of the process of the Central Dogma [1][2][3][4][5][6][7][8][9][10]. The intensive investigations on transcriptomes of the human genome-derived RNAs have uncovered enormous numbers of RNAs transcribed from the noncoding regions [11][12][13].…”

Section: Introductionmentioning

confidence: 99%

Affinity Profiles Categorize RNA-Binding Proteins into Distinctive Groups

Ueda¹

2018

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Recently, we have established a novel assay to detect interaction of RNA-binding proteins (RBPs) with RNA, using biotinylated RNA oligos to capture RBPs with Western blot of specific antibodies against RBPs. The assay detects RNA binding more confidently than the traditional gel shift assay. Starting with completely randomized RNA oligos from 5mer through 12mer length, their binding was examined with HeLa cell nuclear extract (NE). Coomassie brilliant blue-based (CBB) staining did not detect any strong signal. Western blot analysis of typical six RBP antibodies showed four RBPs bound with the random RNA oligos. hnRNPUL2 bound to all from 5mer to 12mer of RNA oligos, while no TLS and hnRNPH1 signal was detected in the random RNA oligo samples. Next, base specificity was examined using sets of oligos of RNA fixed at G, A, U, and C (GAUC RNA oliogs). The RNA oligos fixed at "G" (G RNA oligos) have the most prominent protein bands. A, U, and C of RNA oligos were shown to bind less numbers of protein. Western blot indicated that hnRNPUL2 and hnRNPU bind all four oligos of GAUC at the 10mer length. Contrarily, TLS and hnRNPH1 have no binding with these oligos of GAUC. Then, poly G, A, U and C of RNA at the length of 100mer were tested to see binding profile of RBPs. The CBB staining of the fractions bound with these four polymers of RNA showed that more bands were bound than GAUC RNA oligos. hnRNPU bound well to poly G, A, and, U, but slightly less to poly C. Intriguingly, TLS and hnRNPH1 have binding only to poly G, and also to their common specific sites consisting of GGUG motifs. These data demonstrate that RNA binding is regulated with three factors, length, base composition, and sequence. Furthermore, hnRNPU and hnRNPUL2 have low specificity binding to RNAs, while TLS and hnRNPH1 exert high specific binding. These different propensities in bindings of RBPs are supposed to support specific biological roles in living cells.

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Finding function in mystery transcripts

Cited by 10 publications

References 10 publications

Al Mana Group and Ucla Research Project for Molecular Genetic Studies of Degenerative Disorders of Saudi Children

Al Mana Group and Ucla Research Project for Molecular Genetic Studies of Degenerative Disorders of Saudi Children

ISOdb: A Comprehensive Database of Full-Length Isoforms Generated by Iso-Seq

Affinity Profiles Categorize RNA-Binding Proteins into Distinctive Groups

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