RNA测序和目标长读测序揭示了一个内基转位子插入,导致异常拼接
Ryota Kawakami1, Takuya Hiraide1, Kazuki Watanabe2
1Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan.
Journal of human genetics
|December 15, 2023
概括
对罕见疾病的遗传分析往往仍未得到解决. 长读测序与RNA测序相结合,发现了一个复杂的插入,导致过早染色体分离综合征.
科学领域:
- 遗传学 遗传学 是一个
- 分子生物学分子生物学
- 基因组医学是基因组医学.
背景情况:
- 短读测序 (外基因组/基因组测序) 无法解决超过一半的疑似遗传疾病.
- RNA测序 (RNA-seq) 和长读测序 (LRS) 为变体解释和结构变体检测提供了互补的方法.
- 在纳米孔测序器上进行自适应采样,以促进针对性的LRS.
研究的目的:
- 为了调查一名被诊断为过早染色体分离 (PCS) /马赛克多彩形形 (MVA) 综合征的日本女孩的一个未解决的遗传疾病.
- 通过标准的短读测序方法来识别遗漏的致病变体.
- 为了证明结合RNA-seq和向LRS用于复杂变异检测的实用性.
主要方法:
- 进行了外基因组测序 (ES) 和基因组测序 (GS).
- 用RNA测序 (RNA-seq) 来检测转录组异常.
- 使用纳米孔LRS进行自适应采样,以调查内基变异.
- 为了功能验证,进行了微基因拼接试验和免疫血栓检测.
主要成果:
- 在母体中,ES鉴定了BUB1B (c.1402-5A>G) 中已知的异构生病变体,导致异常拼接.
- GS未能检测到第二种致病变体.
- RNA-seq显示了2号内中的异常读数,促使进一步调查.
- 向的LRS发现了新型的父性3.0kb插入在2号内突中,由Alu和SVA元素组成.
- 插入创建了一个新的拼接位置,导致异常的BUB1B mRNA拼接和降低蛋白质水平.
结论:
- RNA-seq可以作为确定转录组异常的关键第一步,以指导进一步的变体发现.
- 长读测序,特别是通过适应性采样,对于表征复杂的结构变异,包括插入,是非常有效的.
- RNA-seq和LRS的组合为解决以前未被诊断的遗传疾病提供了一个强大的策略.
相关概念视频
RNA Splicing
56.4K
Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
56.4K
Non-LTR Retrotransposons
11.5K
As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
11.5K
DNA-only Transposons
14.5K
DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
The donor site from where the transposon is excised is either degraded or...
14.5K
Alternative RNA Splicing
21.2K
Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
21.2K
piRNA - Piwi-interacting RNAs
6.9K
PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...
6.9K
Exon Recombination
3.6K
The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon...
Exon shuffling follows “splice frame rules.” Each exon...
3.6K


