Bioinformatic Methods to Discover Cis-regulatory Elements in mRNAs

Abstract

Cis-regulatory elements play a number of important roles in determining the fate of messenger RNAs (mRNAs). Due to these elements, mRNAs may be translated with remarkable efficiency, or destroyed with little translation. Untranslated regions cover over a third of a typical human mRNA and often contain a range of regulatory elements. Some elements along with their RNA or protein binding partners are well characterized, though many are not. These require different types of bioinformatic methods for identification and discovery. The most successful techniques combine a range of information and search strategies. Useful information may include conservation across species, prior biological knowledge, known false positives, or noisy high-throughput experimental data. This chapter focuses on current successful methods designed to discover elements with high sensitivity but low false-positive rates.

Abbreviations

3-D

three-dimensional

BLAST

basic local alignment search tool

CDS

coding sequence

CM

covariance model

ChIP

chromatin immunoprecipitation

DNA

deoxyribonucleic acid

EST

expressed sequence tag

FIRE

finding informative regulatory element

GEO

gene expression omnibus

HMM

hidden Markov model

IRE

iron responsive element

IUPAC

International Union of Pure and Applied Chemistry

KH

K homology

MAF

multiple alignment format

MEME

multiple expectation maximization for motif elicitation

MEMERIS

multiple EM for motif elucidation in RNAs including secondary structures

MFE

minimum free energy

NCBI

National Center for Biotechnology Information

PDB

protein data bank

PWM

position weight matrix

RBPDb

RNA-Binding Protein DataBase

RIP-chip

RNA immunoprecipitation chip

RNA

ribonucleic acid

RRM

RNA recognition motif

SCFG

stochastic context-free grammar

SCI

structure conservation index

SECIS

selenocysteine insertion sequence

SELEX

systematic evolution of ligands by exponential enrichment

TFBS

transcription factor binding site

UCSC

University of California Santa Cruz

UTR

untranslated regions

dsRNA

double-strand RNA

log

logistic regression

mRNA

messenger RNA

miRNA

microRNA

mirSVR

micro support vector regression

ncRNA

noncoding RNA

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Copyright information

© Springer-Verlag 2014

Authors and Affiliations

  1. 1.Department of BiochemistryUniversity of OtagoDunedinNew Zealand
  2. 2.Department of BiochemistryUniversity of OtagoDunedinNew Zealand

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