A high-resolution enhancer atlas of the developing telencephalon

Axel Visel, Leila Taher, Hani Girgis, Dalit May, Olga Golonzhka, Renee V. Hoch, Gabriel L. McKinsey, Kartik Pattabiraman, Shanni N. Silberberg, Matthew J. Blow, David V. Hansen, Alexander Nord, Jennifer A. Akiyama, Amy Holt, Roya Hosseini, Sengthavy Phouanenavong, Ingrid Plajzer-Frick, Malak Shoukry, Veena Afzal, Tommy KaplanArnold R. Kriegstein, Edward M. Rubin, Ivan Ovcharenko, Len A. Pennacchio, John L.R. Rubenstein

Research output: Contribution to journalArticle

133 Citations (Scopus)

Abstract

The mammalian telencephalon plays critical roles in cognition, motor function, and emotion. Though many of the genes required for its development have been identified, the distant-acting regulatory sequences orchestrating their in vivo expression are mostly unknown. Here, we describe a digital atlas of in vivo enhancers active in subregions of the developing telencephalon. We identified more than 4,600 candidate embryonic forebrain enhancers and studied the in vivo activity of 329 of these sequences in transgenic mouse embryos. We generated serial sets of histological brain sections for 145 reproducible forebrain enhancers, resulting in a publicly accessible web-based data collection comprising more than 32,000 sections. We also used epigenomic analysis of human and mouse cortex tissue to directly compare the genome-wide enhancer architecture in these species. These data provide a primary resource for investigating gene regulatory mechanisms of telencephalon development and enable studies of the role of distant-acting enhancers in neurodevelopmental disorders.

Original languageEnglish (US)
Pages (from-to)895-908
Number of pages14
JournalCell
Volume152
Issue number4
DOIs
StatePublished - Feb 14 2013
Externally publishedYes

Fingerprint

Telencephalon
Atlases
Genes
Prosencephalon
Regulator Genes
Epigenomics
Cognition
Transgenic Mice
Brain
Emotions
Embryonic Structures
Genome
Tissue

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Visel, A., Taher, L., Girgis, H., May, D., Golonzhka, O., Hoch, R. V., ... Rubenstein, J. L. R. (2013). A high-resolution enhancer atlas of the developing telencephalon. Cell, 152(4), 895-908. https://doi.org/10.1016/j.cell.2012.12.041

A high-resolution enhancer atlas of the developing telencephalon. / Visel, Axel; Taher, Leila; Girgis, Hani; May, Dalit; Golonzhka, Olga; Hoch, Renee V.; McKinsey, Gabriel L.; Pattabiraman, Kartik; Silberberg, Shanni N.; Blow, Matthew J.; Hansen, David V.; Nord, Alexander; Akiyama, Jennifer A.; Holt, Amy; Hosseini, Roya; Phouanenavong, Sengthavy; Plajzer-Frick, Ingrid; Shoukry, Malak; Afzal, Veena; Kaplan, Tommy; Kriegstein, Arnold R.; Rubin, Edward M.; Ovcharenko, Ivan; Pennacchio, Len A.; Rubenstein, John L.R.

In: Cell, Vol. 152, No. 4, 14.02.2013, p. 895-908.

Research output: Contribution to journalArticle

Visel, A, Taher, L, Girgis, H, May, D, Golonzhka, O, Hoch, RV, McKinsey, GL, Pattabiraman, K, Silberberg, SN, Blow, MJ, Hansen, DV, Nord, A, Akiyama, JA, Holt, A, Hosseini, R, Phouanenavong, S, Plajzer-Frick, I, Shoukry, M, Afzal, V, Kaplan, T, Kriegstein, AR, Rubin, EM, Ovcharenko, I, Pennacchio, LA & Rubenstein, JLR 2013, 'A high-resolution enhancer atlas of the developing telencephalon', Cell, vol. 152, no. 4, pp. 895-908. https://doi.org/10.1016/j.cell.2012.12.041
Visel A, Taher L, Girgis H, May D, Golonzhka O, Hoch RV et al. A high-resolution enhancer atlas of the developing telencephalon. Cell. 2013 Feb 14;152(4):895-908. https://doi.org/10.1016/j.cell.2012.12.041
Visel, Axel ; Taher, Leila ; Girgis, Hani ; May, Dalit ; Golonzhka, Olga ; Hoch, Renee V. ; McKinsey, Gabriel L. ; Pattabiraman, Kartik ; Silberberg, Shanni N. ; Blow, Matthew J. ; Hansen, David V. ; Nord, Alexander ; Akiyama, Jennifer A. ; Holt, Amy ; Hosseini, Roya ; Phouanenavong, Sengthavy ; Plajzer-Frick, Ingrid ; Shoukry, Malak ; Afzal, Veena ; Kaplan, Tommy ; Kriegstein, Arnold R. ; Rubin, Edward M. ; Ovcharenko, Ivan ; Pennacchio, Len A. ; Rubenstein, John L.R. / A high-resolution enhancer atlas of the developing telencephalon. In: Cell. 2013 ; Vol. 152, No. 4. pp. 895-908.
@article{5690ffd607a648eb988209ce5d44f6ab,
title = "A high-resolution enhancer atlas of the developing telencephalon",
abstract = "The mammalian telencephalon plays critical roles in cognition, motor function, and emotion. Though many of the genes required for its development have been identified, the distant-acting regulatory sequences orchestrating their in vivo expression are mostly unknown. Here, we describe a digital atlas of in vivo enhancers active in subregions of the developing telencephalon. We identified more than 4,600 candidate embryonic forebrain enhancers and studied the in vivo activity of 329 of these sequences in transgenic mouse embryos. We generated serial sets of histological brain sections for 145 reproducible forebrain enhancers, resulting in a publicly accessible web-based data collection comprising more than 32,000 sections. We also used epigenomic analysis of human and mouse cortex tissue to directly compare the genome-wide enhancer architecture in these species. These data provide a primary resource for investigating gene regulatory mechanisms of telencephalon development and enable studies of the role of distant-acting enhancers in neurodevelopmental disorders.",
author = "Axel Visel and Leila Taher and Hani Girgis and Dalit May and Olga Golonzhka and Hoch, {Renee V.} and McKinsey, {Gabriel L.} and Kartik Pattabiraman and Silberberg, {Shanni N.} and Blow, {Matthew J.} and Hansen, {David V.} and Alexander Nord and Akiyama, {Jennifer A.} and Amy Holt and Roya Hosseini and Sengthavy Phouanenavong and Ingrid Plajzer-Frick and Malak Shoukry and Veena Afzal and Tommy Kaplan and Kriegstein, {Arnold R.} and Rubin, {Edward M.} and Ivan Ovcharenko and Pennacchio, {Len A.} and Rubenstein, {John L.R.}",
year = "2013",
month = "2",
day = "14",
doi = "10.1016/j.cell.2012.12.041",
language = "English (US)",
volume = "152",
pages = "895--908",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "4",

}

TY - JOUR

T1 - A high-resolution enhancer atlas of the developing telencephalon

AU - Visel, Axel

AU - Taher, Leila

AU - Girgis, Hani

AU - May, Dalit

AU - Golonzhka, Olga

AU - Hoch, Renee V.

AU - McKinsey, Gabriel L.

AU - Pattabiraman, Kartik

AU - Silberberg, Shanni N.

AU - Blow, Matthew J.

AU - Hansen, David V.

AU - Nord, Alexander

AU - Akiyama, Jennifer A.

AU - Holt, Amy

AU - Hosseini, Roya

AU - Phouanenavong, Sengthavy

AU - Plajzer-Frick, Ingrid

AU - Shoukry, Malak

AU - Afzal, Veena

AU - Kaplan, Tommy

AU - Kriegstein, Arnold R.

AU - Rubin, Edward M.

AU - Ovcharenko, Ivan

AU - Pennacchio, Len A.

AU - Rubenstein, John L.R.

PY - 2013/2/14

Y1 - 2013/2/14

N2 - The mammalian telencephalon plays critical roles in cognition, motor function, and emotion. Though many of the genes required for its development have been identified, the distant-acting regulatory sequences orchestrating their in vivo expression are mostly unknown. Here, we describe a digital atlas of in vivo enhancers active in subregions of the developing telencephalon. We identified more than 4,600 candidate embryonic forebrain enhancers and studied the in vivo activity of 329 of these sequences in transgenic mouse embryos. We generated serial sets of histological brain sections for 145 reproducible forebrain enhancers, resulting in a publicly accessible web-based data collection comprising more than 32,000 sections. We also used epigenomic analysis of human and mouse cortex tissue to directly compare the genome-wide enhancer architecture in these species. These data provide a primary resource for investigating gene regulatory mechanisms of telencephalon development and enable studies of the role of distant-acting enhancers in neurodevelopmental disorders.

AB - The mammalian telencephalon plays critical roles in cognition, motor function, and emotion. Though many of the genes required for its development have been identified, the distant-acting regulatory sequences orchestrating their in vivo expression are mostly unknown. Here, we describe a digital atlas of in vivo enhancers active in subregions of the developing telencephalon. We identified more than 4,600 candidate embryonic forebrain enhancers and studied the in vivo activity of 329 of these sequences in transgenic mouse embryos. We generated serial sets of histological brain sections for 145 reproducible forebrain enhancers, resulting in a publicly accessible web-based data collection comprising more than 32,000 sections. We also used epigenomic analysis of human and mouse cortex tissue to directly compare the genome-wide enhancer architecture in these species. These data provide a primary resource for investigating gene regulatory mechanisms of telencephalon development and enable studies of the role of distant-acting enhancers in neurodevelopmental disorders.

UR - http://www.scopus.com/inward/record.url?scp=84874118170&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84874118170&partnerID=8YFLogxK

U2 - 10.1016/j.cell.2012.12.041

DO - 10.1016/j.cell.2012.12.041

M3 - Article

C2 - 23375746

AN - SCOPUS:84874118170

VL - 152

SP - 895

EP - 908

JO - Cell

JF - Cell

SN - 0092-8674

IS - 4

ER -