Ultraconserved Enhancers Are Required for Normal Development
Abstract
Non-coding “ultraconserved” regions containing hundreds of consecutive bases of perfect sequence conservation across mammalian genomes can function as distant-acting enhancers. However, initial deletion studies in mice revealed that loss of such extraordinarily constrained sequences had no immediate impact on viability. We show that ultraconserved enhancers are required for normal development. Focusing on some of the longest ultraconserved sites genome wide, located near the essential neuronal transcription factor Arx, we used genome editing to create an expanded series of knockout mice lacking individual or combinations of ultraconserved enhancers. Mice with single or pairwise deletions of ultraconserved enhancers were viable and fertile but in nearly all cases showed neurological or growth abnormalities, including substantial alterations of neuron populations and structural brain defects. Our results demonstrate the functional importance of ultraconserved enhancers and indicate that remarkably strong sequence conservation likely results from fitness deficits that appear subtle in a laboratory setting.
- Authors:
- more »
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE; LBNL Laboratory Directed Research and Development (LDRD) Program; National Inst. of Health (NIH) (United States)
- OSTI Identifier:
- 1548828
- Alternate Identifier(s):
- OSTI ID: 1506293
- Grant/Contract Number:
- AC02-05CH11231; S10RR029668; S10RR027303; R01HG003988; R24HL123879; UM1HL098166; R01NS34661; R37MH049428
- Resource Type:
- Published Article
- Journal Name:
- Cell
- Additional Journal Information:
- Journal Name: Cell Journal Volume: 172 Journal Issue: 3; Journal ID: ISSN 0092-8674
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; enhancer; ultraconserved; gene regulation; brain development; Arx; noncoding; knockout; in vivo; hippocampus; neurons
Citation Formats
Dickel, Diane E., Ypsilanti, Athena R., Pla, Ramón, Zhu, Yiwen, Barozzi, Iros, Mannion, Brandon J., Khin, Yupar S., Fukuda-Yuzawa, Yoko, Plajzer-Frick, Ingrid, Pickle, Catherine S., Lee, Elizabeth A., Harrington, Anne N., Pham, Quan T., Garvin, Tyler H., Kato, Momoe, Osterwalder, Marco, Akiyama, Jennifer A., Afzal, Veena, Rubenstein, John L. R., Pennacchio, Len A., and Visel, Axel. Ultraconserved Enhancers Are Required for Normal Development. United States: N. p., 2018.
Web. doi:10.1016/j.cell.2017.12.017.
Dickel, Diane E., Ypsilanti, Athena R., Pla, Ramón, Zhu, Yiwen, Barozzi, Iros, Mannion, Brandon J., Khin, Yupar S., Fukuda-Yuzawa, Yoko, Plajzer-Frick, Ingrid, Pickle, Catherine S., Lee, Elizabeth A., Harrington, Anne N., Pham, Quan T., Garvin, Tyler H., Kato, Momoe, Osterwalder, Marco, Akiyama, Jennifer A., Afzal, Veena, Rubenstein, John L. R., Pennacchio, Len A., & Visel, Axel. Ultraconserved Enhancers Are Required for Normal Development. United States. https://doi.org/10.1016/j.cell.2017.12.017
Dickel, Diane E., Ypsilanti, Athena R., Pla, Ramón, Zhu, Yiwen, Barozzi, Iros, Mannion, Brandon J., Khin, Yupar S., Fukuda-Yuzawa, Yoko, Plajzer-Frick, Ingrid, Pickle, Catherine S., Lee, Elizabeth A., Harrington, Anne N., Pham, Quan T., Garvin, Tyler H., Kato, Momoe, Osterwalder, Marco, Akiyama, Jennifer A., Afzal, Veena, Rubenstein, John L. R., Pennacchio, Len A., and Visel, Axel. Mon .
"Ultraconserved Enhancers Are Required for Normal Development". United States. https://doi.org/10.1016/j.cell.2017.12.017.
@article{osti_1548828,
title = {Ultraconserved Enhancers Are Required for Normal Development},
author = {Dickel, Diane E. and Ypsilanti, Athena R. and Pla, Ramón and Zhu, Yiwen and Barozzi, Iros and Mannion, Brandon J. and Khin, Yupar S. and Fukuda-Yuzawa, Yoko and Plajzer-Frick, Ingrid and Pickle, Catherine S. and Lee, Elizabeth A. and Harrington, Anne N. and Pham, Quan T. and Garvin, Tyler H. and Kato, Momoe and Osterwalder, Marco and Akiyama, Jennifer A. and Afzal, Veena and Rubenstein, John L. R. and Pennacchio, Len A. and Visel, Axel},
abstractNote = {Non-coding “ultraconserved” regions containing hundreds of consecutive bases of perfect sequence conservation across mammalian genomes can function as distant-acting enhancers. However, initial deletion studies in mice revealed that loss of such extraordinarily constrained sequences had no immediate impact on viability. We show that ultraconserved enhancers are required for normal development. Focusing on some of the longest ultraconserved sites genome wide, located near the essential neuronal transcription factor Arx, we used genome editing to create an expanded series of knockout mice lacking individual or combinations of ultraconserved enhancers. Mice with single or pairwise deletions of ultraconserved enhancers were viable and fertile but in nearly all cases showed neurological or growth abnormalities, including substantial alterations of neuron populations and structural brain defects. Our results demonstrate the functional importance of ultraconserved enhancers and indicate that remarkably strong sequence conservation likely results from fitness deficits that appear subtle in a laboratory setting.},
doi = {10.1016/j.cell.2017.12.017},
journal = {Cell},
number = 3,
volume = 172,
place = {United States},
year = {Mon Jan 01 00:00:00 EST 2018},
month = {Mon Jan 01 00:00:00 EST 2018}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1016/j.cell.2017.12.017
https://doi.org/10.1016/j.cell.2017.12.017
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 99 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
ARX Regulates Cortical Intermediate Progenitor Cell Expansion and Upper Layer Neuron Formation Through Repression of Cdkn1c
journal, August 2013
- Colasante, Gaia; Simonet, Jacqueline C.; Calogero, Raffaele
- Cerebral Cortex, Vol. 25, Issue 2
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
journal, December 2004
- Pruitt, K. D.
- Nucleic Acids Research, Vol. 33, Issue Database issue
A Resource of Cre Driver Lines for Genetic Targeting of GABAergic Neurons in Cerebral Cortex
journal, September 2011
- Taniguchi, Hiroki; He, Miao; Wu, Priscilla
- Neuron, Vol. 71, Issue 6
Cutadapt removes adapter sequences from high-throughput sequencing reads
journal, May 2011
- Martin, Marcel
- EMBnet.journal, Vol. 17, Issue 1
NPAS1 Represses the Generation of Specific Subtypes of Cortical Interneurons
journal, December 2014
- Stanco, Amelia; Pla, Ramón; Vogt, Daniel
- Neuron, Vol. 84, Issue 5
Dispensability of mammalian DNA
journal, November 2008
- McLean, C.; Bejerano, G.
- Genome Research, Vol. 18, Issue 11
Developmental interneuron subtype deficits after targeted loss of Arx
journal, June 2016
- Marsh, Eric D.; Nasrallah, MacLean Pancoast; Walsh, Caroline
- BMC Neuroscience, Vol. 17, Issue 1
Postnatal development of cholinergic neurons in the rat: I. Forebrain
journal, December 1991
- Gould, Elizabeth; Woolf, Nancy J.; Butcher, Larry L.
- Brain Research Bulletin, Vol. 27, Issue 6
ROCR: visualizing classifier performance in R
journal, August 2005
- Sing, T.; Sander, O.; Beerenwinkel, N.
- Bioinformatics, Vol. 21, Issue 20
The development of parvalbumin-immunoreactivity in the neocortex of the mouse
journal, September 1994
- del Rio, JoséAntonio; de Lecea, L.; Ferrer, Isidro
- Developmental Brain Research, Vol. 81, Issue 2
MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
journal, December 2015
- Finak, Greg; McDavid, Andrew; Yajima, Masanao
- Genome Biology, Vol. 16, Issue 1
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
journal, November 2009
- Robinson, M. D.; McCarthy, D. J.; Smyth, G. K.
- Bioinformatics, Vol. 26, Issue 1
STAR: ultrafast universal RNA-seq aligner
journal, October 2012
- Dobin, Alexander; Davis, Carrie A.; Schlesinger, Felix
- Bioinformatics, Vol. 29, Issue 1
HTSeq--a Python framework to work with high-throughput sequencing data
journal, September 2014
- Anders, S.; Pyl, P. T.; Huber, W.
- Bioinformatics, Vol. 31, Issue 2
Deletion of Ultraconserved Elements Yields Viable Mice
journal, September 2007
- Ahituv, Nadav; Zhu, Yiwen; Visel, Axel
- PLoS Biology, Vol. 5, Issue 9
SC3: consensus clustering of single-cell RNA-seq data
journal, March 2017
- Kiselev, Vladimir Yu; Kirschner, Kristina; Schaub, Michael T.
- Nature Methods, Vol. 14, Issue 5
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
journal, May 2010
- Trapnell, Cole; Williams, Brian A.; Pertea, Geo
- Nature Biotechnology, Vol. 28, Issue 5
Functional analysis of limb transcriptional enhancers in the mouse: Mouse limb enhancers
journal, June 2014
- Nolte, Mark J.; Wang, Ying; Deng, Jian Min
- Evolution & Development, Vol. 16, Issue 4
Arx Is a Direct Target of Dlx2 and Thereby Contributes to the Tangential Migration of GABAergic Interneurons
journal, October 2008
- Colasante, G.; Collombat, P.; Raimondi, V.
- Journal of Neuroscience, Vol. 28, Issue 42
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
journal, May 2015
- Macosko, Evan Z.; Basu, Anindita; Satija, Rahul
- Cell, Vol. 161, Issue 5
In vivo enhancer analysis of human conserved non-coding sequences
journal, November 2006
- Pennacchio, Len A.; Ahituv, Nadav; Moses, Alan M.
- Nature, Vol. 444, Issue 7118
TopHat: discovering splice junctions with RNA-Seq
journal, March 2009
- Trapnell, Cole; Pachter, Lior; Salzberg, Steven L.
- Bioinformatics, Vol. 25, Issue 9
The mystery of extreme non-coding conservation
journal, December 2013
- Harmston, Nathan; Barešić, Anja; Lenhard, Boris
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 368, Issue 1632
Progressive Loss of Function in a Limb Enhancer during Snake Evolution
journal, October 2016
- Kvon, Evgeny Z.; Kamneva, Olga K.; Melo, Uirá S.
- Cell, Vol. 167, Issue 3
The UCSC Genome Browser database: 2015 update
journal, November 2014
- Rosenbloom, Kate R.; Armstrong, Joel; Barber, Galt P.
- Nucleic Acids Research, Vol. 43, Issue D1
Single-cell RNA sequencing identifies distinct mouse medial ganglionic eminence cell types
journal, March 2017
- Chen, Ying-Jiun J.; Friedman, Brad A.; Ha, Connie
- Scientific Reports, Vol. 7, Issue 1
MouseMine: a new data warehouse for MGI
journal, June 2015
- Motenko, H.; Neuhauser, S. B.; O’Keefe, M.
- Mammalian Genome, Vol. 26, Issue 7-8
Cis-element mutated in GATA2-dependent immunodeficiency governs hematopoiesis and vascular integrity
journal, October 2012
- Johnson, Kirby D.; Hsu, Amy P.; Ryu, Myung-Jeom
- Journal of Clinical Investigation, Vol. 122, Issue 10
Heavy metal intensification of DAB-based HRP reaction product.
journal, June 1981
- Adams, J. C.
- Journal of Histochemistry & Cytochemistry, Vol. 29, Issue 6
A High-Resolution Enhancer Atlas of the Developing Telencephalon
journal, February 2013
- Visel, Axel; Taher, Leila; Girgis, Hani
- Cell, Vol. 152, Issue 4
One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering
journal, May 2013
- Wang, Haoyi; Yang, Hui; Shivalila, Chikdu S.
- Cell, Vol. 153, Issue 4, p. 910-918
Mutation of ARX causes abnormal development of forebrain and testes in mice and X-linked lissencephaly with abnormal genitalia in humans
journal, October 2002
- Kitamura, Kunio; Yanazawa, Masako; Sugiyama, Noriyuki
- Nature Genetics, Vol. 32, Issue 3
GENCODE: The reference human genome annotation for The ENCODE Project
journal, September 2012
- Harrow, J.; Frankish, A.; Gonzalez, J. M.
- Genome Research, Vol. 22, Issue 9
RNA-Guided Human Genome Engineering via Cas9
journal, January 2013
- Mali, P.; Yang, L.; Esvelt, K. M.
- Science, Vol. 339, Issue 6121, p. 823-826
The UCSC Known Genes
journal, February 2006
- Hsu, F.; Kent, W. J.; Clawson, H.
- Bioinformatics, Vol. 22, Issue 9
One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering
journal, September 2013
- Yang, Hui; Wang, Haoyi; Shivalila, Chikdu S.
- Cell, Vol. 154, Issue 6
Ultraconservation identifies a small subset of extremely constrained developmental enhancers
journal, January 2008
- Visel, Axel; Prabhakar, Shyam; Akiyama, Jennifer A.
- Nature Genetics, Vol. 40, Issue 2
Inactivation of Arx, the Murine Ortholog of the X-Linked Lissencephaly with Ambiguous Genitalia Gene, Leads to Severe Disorganization of the Ventral Telencephalon with Impaired Neuronal Migration and Differentiation
journal, April 2007
- Colombo, E.; Collombat, P.; Colasante, G.
- Journal of Neuroscience, Vol. 27, Issue 17
Genome-wide compendium and functional assessment of in vivo heart enhancers
journal, October 2016
- Dickel, Diane E.; Barozzi, Iros; Zhu, Yiwen
- Nature Communications, Vol. 7, Issue 1
Inducible expression of an hsp68-lacZ hybrid gene in transgenic mice
journal, April 1989
- Kothary, R.; Clapoff, S.; Darling, S.
- Development, Vol. 105, Issue 4
Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
journal, December 2004
- Sandelin, Albin; Bailey, Peter; Bruce, Sara
- BMC Genomics, Vol. 5, Issue 1
Ultraconserved Elements in the Human Genome
journal, May 2004
- Bejerano, G.
- Science, Vol. 304, Issue 5675
NIH Image to ImageJ: 25 years of image analysis
journal, June 2012
- Schneider, Caroline A.; Rasband, Wayne S.; Eliceiri, Kevin W.
- Nature Methods, Vol. 9, Issue 7
Opposing actions of Arx and Pax4 in endocrine pancreas development
journal, October 2003
- Collombat, P.
- Genes & Development, Vol. 17, Issue 20
ARX: a gene for all seasons
journal, June 2006
- Gécz, Jozef; Cloosterman, Desiree; Partington, Michael
- Current Opinion in Genetics & Development, Vol. 16, Issue 3
Ultraconserved Elements: Analyses of Dosage Sensitivity, Motifs and Boundaries
journal, October 2008
- Chiang, Charleston W. K.; Derti, Adnan; Schwartz, Daniel
- Genetics, Vol. 180, Issue 4
Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning
journal, March 2017
- Wang, Bo; Zhu, Junjie; Pierson, Emma
- Nature Methods, Vol. 14, Issue 4