Skip to content
Back to outputs

Phylogenetic footprinting: an evolutionary tool for the identification of cis-regulatory elements

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Standard

Phylogenetic footprinting : an evolutionary tool for the identification of cis-regulatory elements. / Castillo, Hozana A.; Grade, Carla V. C.; Dietrich, Susanne; Schubert, Frank; Salerno, Monica S.; Xavier-Neto, Jose; Alvares, Lucia E.

The analysis of regulatory DNA: current developments, knowledge and applications uncovering gene regulation. ed. / Kenneth W. Berendzen; Joachim Kilian; Dierk Wanke. Bentham Science, 2013. p. 101-123.

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Harvard

Castillo, HA, Grade, CVC, Dietrich, S, Schubert, F, Salerno, MS, Xavier-Neto, J & Alvares, LE 2013, Phylogenetic footprinting: an evolutionary tool for the identification of cis-regulatory elements. in KW Berendzen, J Kilian & D Wanke (eds), The analysis of regulatory DNA: current developments, knowledge and applications uncovering gene regulation. Bentham Science, pp. 101-123. https://doi.org/10.2174/97816080549231130101

APA

Castillo, H. A., Grade, C. V. C., Dietrich, S., Schubert, F., Salerno, M. S., Xavier-Neto, J., & Alvares, L. E. (2013). Phylogenetic footprinting: an evolutionary tool for the identification of cis-regulatory elements. In K. W. Berendzen, J. Kilian, & D. Wanke (Eds.), The analysis of regulatory DNA: current developments, knowledge and applications uncovering gene regulation (pp. 101-123). Bentham Science. https://doi.org/10.2174/97816080549231130101

Vancouver

Castillo HA, Grade CVC, Dietrich S, Schubert F, Salerno MS, Xavier-Neto J et al. Phylogenetic footprinting: an evolutionary tool for the identification of cis-regulatory elements. In Berendzen KW, Kilian J, Wanke D, editors, The analysis of regulatory DNA: current developments, knowledge and applications uncovering gene regulation. Bentham Science. 2013. p. 101-123 https://doi.org/10.2174/97816080549231130101

Author

Castillo, Hozana A. ; Grade, Carla V. C. ; Dietrich, Susanne ; Schubert, Frank ; Salerno, Monica S. ; Xavier-Neto, Jose ; Alvares, Lucia E. / Phylogenetic footprinting : an evolutionary tool for the identification of cis-regulatory elements. The analysis of regulatory DNA: current developments, knowledge and applications uncovering gene regulation. editor / Kenneth W. Berendzen ; Joachim Kilian ; Dierk Wanke. Bentham Science, 2013. pp. 101-123

Bibtex

@inbook{f6e189f8029844dea96a54f226c8b101,
title = "Phylogenetic footprinting: an evolutionary tool for the identification of cis-regulatory elements",
abstract = "Phylogenetic footprinting is an evolutionary tool used for the identification of functional elements in selected genomes. This method relies on the search for similarities among ancestrally related sequences and has been widely used to identify cis-regulatory elements in non-coding genomic regions. Conservednon-coding elements (CNEs) have been shown to be crucial for controlling gene transcription in vertebrate genomes. Here we present practical guidelines for discovering new cis-regulatory elements using phylogenetic footprinting and discuss pros and cons of different approaches for the functional characterization ofthese elements. In addition, we present two case studies to provide practical examples of how this powerful technique is used. The first case study illustrates the in silico identification of the Myostatin gene promoter conserved in vertebrates and its biological validation. The second case study describes the searchfor cis-regulatory elements of the Raldh2 gene and demonstrates the conserved biological function of an intronic CNE responsible for modulating the gene activity in the embryonic dorsal spinal cord in vertebrates. The comparison of these two case studies highlights the similarities and differences regarding bioinformaticstrategies and validation methods for the identification and functional characterization of promoters and distal cis-regulatory elements (enhancers/silencers).",
keywords = "Phylogenetic footprinting, Conserved non-coding elements, Enhancer, Myostatin, Retinaldehyde Dehydrogenase 2",
author = "Castillo, {Hozana A.} and Grade, {Carla V. C.} and Susanne Dietrich and Frank Schubert and Salerno, {Monica S.} and Jose Xavier-Neto and Alvares, {Lucia E.}",
year = "2013",
doi = "10.2174/97816080549231130101",
language = "English",
isbn = "9781608057115 ",
pages = "101--123",
editor = "Berendzen, {Kenneth W.} and Joachim Kilian and Dierk Wanke",
booktitle = "The analysis of regulatory DNA",
publisher = "Bentham Science",

}

RIS

TY - CHAP

T1 - Phylogenetic footprinting

T2 - an evolutionary tool for the identification of cis-regulatory elements

AU - Castillo, Hozana A.

AU - Grade, Carla V. C.

AU - Dietrich, Susanne

AU - Schubert, Frank

AU - Salerno, Monica S.

AU - Xavier-Neto, Jose

AU - Alvares, Lucia E.

PY - 2013

Y1 - 2013

N2 - Phylogenetic footprinting is an evolutionary tool used for the identification of functional elements in selected genomes. This method relies on the search for similarities among ancestrally related sequences and has been widely used to identify cis-regulatory elements in non-coding genomic regions. Conservednon-coding elements (CNEs) have been shown to be crucial for controlling gene transcription in vertebrate genomes. Here we present practical guidelines for discovering new cis-regulatory elements using phylogenetic footprinting and discuss pros and cons of different approaches for the functional characterization ofthese elements. In addition, we present two case studies to provide practical examples of how this powerful technique is used. The first case study illustrates the in silico identification of the Myostatin gene promoter conserved in vertebrates and its biological validation. The second case study describes the searchfor cis-regulatory elements of the Raldh2 gene and demonstrates the conserved biological function of an intronic CNE responsible for modulating the gene activity in the embryonic dorsal spinal cord in vertebrates. The comparison of these two case studies highlights the similarities and differences regarding bioinformaticstrategies and validation methods for the identification and functional characterization of promoters and distal cis-regulatory elements (enhancers/silencers).

AB - Phylogenetic footprinting is an evolutionary tool used for the identification of functional elements in selected genomes. This method relies on the search for similarities among ancestrally related sequences and has been widely used to identify cis-regulatory elements in non-coding genomic regions. Conservednon-coding elements (CNEs) have been shown to be crucial for controlling gene transcription in vertebrate genomes. Here we present practical guidelines for discovering new cis-regulatory elements using phylogenetic footprinting and discuss pros and cons of different approaches for the functional characterization ofthese elements. In addition, we present two case studies to provide practical examples of how this powerful technique is used. The first case study illustrates the in silico identification of the Myostatin gene promoter conserved in vertebrates and its biological validation. The second case study describes the searchfor cis-regulatory elements of the Raldh2 gene and demonstrates the conserved biological function of an intronic CNE responsible for modulating the gene activity in the embryonic dorsal spinal cord in vertebrates. The comparison of these two case studies highlights the similarities and differences regarding bioinformaticstrategies and validation methods for the identification and functional characterization of promoters and distal cis-regulatory elements (enhancers/silencers).

KW - Phylogenetic footprinting

KW - Conserved non-coding elements

KW - Enhancer

KW - Myostatin

KW - Retinaldehyde Dehydrogenase 2

U2 - 10.2174/97816080549231130101

DO - 10.2174/97816080549231130101

M3 - Chapter (peer-reviewed)

SN - 9781608057115

SP - 101

EP - 123

BT - The analysis of regulatory DNA

A2 - Berendzen, Kenneth W.

A2 - Kilian, Joachim

A2 - Wanke, Dierk

PB - Bentham Science

ER -

ID: 1263952