Detecting non-coding selective pressure in coding regions

被引:24
作者
Chen, Hui [1 ]
Blanchette, Mathieu [1 ]
机构
[1] McGill Univ, McGill Ctr Bioinformat, Montreal, PQ H3A 2B4, Canada
关键词
D O I
10.1186/1471-2148-7-S1-S9
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Background: Comparative genomics approaches, where orthologous DNA regions are compared and inter-species conserved regions are identified, have proven extremely powerful for identifying non-coding regulatory regions located in intergenic or intronic regions. However, non-coding functional elements can also be located within coding region, as is common for exonic splicing enhancers, some transcription factor binding sites, and RNA secondary structure elements affecting mRNA stability, localization, or translation. Since these functional elements are located in regions that are themselves highly conserved because they are coding for a protein, they generally escaped detection by comparative genomics approaches. Results: We introduce a comparative genomics approach for detecting non-coding functional elements located within coding regions. Codon evolution is modeled as a mixture of codon substitution models, where each component of the mixture describes the evolution of codons under a specific type of coding selective pressure. We show how to compute the posterior distribution of the entropy and parsimony scores under this null model of codon evolution. The method is applied to a set of growth hormone 1 orthologous mRNA sequences and a known exonic splicing elements is detected. The analysis of a set of CORTBP2 orthologous genes reveals a region of several hundred base pairs under strong non-coding selective pressure whose function remains unknown. Conclusion: Non-coding functional elements, in particular those involved in post-transcriptional regulation, are likely to be much more prevalent than is currently known. With the numerous genome sequencing projects underway, comparative genomics approaches like that proposed here are likely to become increasingly powerful at detecting such elements.
引用
收藏
页数:13
相关论文
共 50 条
  • [41] LeARN: a platform for detecting, clustering and annotating non-coding RNAs
    Céline Noirot
    Christine Gaspin
    Thomas Schiex
    Jérôme Gouzy
    BMC Bioinformatics, 9
  • [42] LeARN: a platform for detecting, clustering and annotating non-coding RNAs
    Noirot, Celine
    Gaspin, Christine
    Schiex, Thomas
    Gouzy, Jerome
    BMC BIOINFORMATICS, 2008, 9 (1)
  • [43] Coding non-coding human telomerase RNA
    Naraykina, Y.
    Rubtsova, M.
    Vasilkova, D.
    Meerson, M.
    Zvereva, M.
    Lazarev, V.
    Manuvera, V.
    Kovalchuk, S.
    Anikanov, N.
    Butenko, I.
    Pobeguts, O.
    Govorun, V.
    Dontsova, O.
    FEBS JOURNAL, 2017, 284 : 13 - 13
  • [44] Evolutionary dynamics of coding and non-coding transcriptomes
    Anamaria Necsulea
    Henrik Kaessmann
    Nature Reviews Genetics, 2014, 15 : 734 - 748
  • [45] Evolutionary dynamics of coding and non-coding transcriptomes
    Necsulea, Anamaria
    Kaessmann, Henrik
    NATURE REVIEWS GENETICS, 2014, 15 (11) : 734 - 748
  • [46] Coding genes join the non-coding world
    Manakov, Sergei A.
    Zhao, Jing Crystal
    PIGMENT CELL & MELANOMA RESEARCH, 2012, 25 (01) : 4 - 4
  • [47] Coding and non-coding RNAs & Mammalian development
    Sampath, Karuna
    SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY, 2015, 47-48 : 1 - 2
  • [48] A gradient measure to characterize the interface between non-coding and coding regions in genomic DNA sequences
    Goswami, P
    Raghavan, S
    CURRENT SCIENCE, 2001, 81 (08): : 1090 - 1099
  • [49] Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics
    Re, Matteo
    Pesole, Graziano
    Horner, David S.
    BMC BIOINFORMATICS, 2009, 10 : 282
  • [50] Assessing the effectiveness of coding and non-coding regions in antisense ribosome inhibition of gene expression in Tetrahymena
    Jacobs, ME
    Cortezzo, DE
    Klobutcher, LA
    JOURNAL OF EUKARYOTIC MICROBIOLOGY, 2004, 51 (05) : 536 - 541