TY - JOUR
T1 - Integration of genomic and functional approaches reveals enhancers at LMX1A and LMX1B
AU - Burzynski, Grzegorz M.
AU - Reed, Xylena
AU - Maragh, Samantha
AU - Matsui, Takeshi
AU - McCallion, Andrew S.
N1 - Funding Information:
Acknowledgments The authors gratefully acknowledge the support of the McKusick Nathans Institute of Genetic Medicine Center for Functional Investigation in Zebrafish (FINZ). This research was supported in part by the National Institute of Neurological Disease and Stroke (R01 NS062972; NINDS, NIH) to ASM. XR was also supported by NIH pre-doctoral training grant 5T32GM07814. SM was supported by funds from the National Institute of Standards and Technology.
PY - 2013/11
Y1 - 2013/11
N2 - LMX1A and LMX1B encode two closely related members of the LIM homeobox family of transcription factors. These genes play significant, and frequently overlapping, roles in the development of many structures in the nervous system, including the cerebellum, hindbrain, spinal cord roof plate, sensory systems and dopaminergic midbrain neurons. Little is known about the cis-acting regulatory elements (REs) that dictate their temporal and spatial expression or about the regulatory landscape surrounding them. The availability of comparative sequence data and the advent of genomic technologies such as ChIP-seq have revolutionized our capacity to identify regulatory sequences like enhancers. Despite this wealth of data, the vast majority of loci lack any significant in vivo functional exploration of their non-coding regions. We have completed a significant functional screen of conserved non-coding sequences (putative REs) scattered across these critical human loci, assaying the temporal and spatial control using zebrafish transgenesis. We first identify and describe the LMX1A paralogs lmx1a and lmx1a-like, comparing their expression during embryogenesis with that in mammals, along with lmx1ba and lmx1bb genes. Consistent with their prominent neuronal expression, 47/71 sequences selected within and flanking LMX1A and LMX1B exert spatial control of reporter expression in the central nervous system (CNS) of mosaic zebrafish embryos. Upon germline transmission, we identify CNS reporter expression in multiple independent founders for 22 constructs (LMX1A, n = 17; LMX1B, n = 5). The identified enhancers display significant overlap in their spatial control and represent only a fraction of the conserved non-coding sequences at these critical genes. Our data reveal the abundance of regulatory instruction located near these developmentally important genes.
AB - LMX1A and LMX1B encode two closely related members of the LIM homeobox family of transcription factors. These genes play significant, and frequently overlapping, roles in the development of many structures in the nervous system, including the cerebellum, hindbrain, spinal cord roof plate, sensory systems and dopaminergic midbrain neurons. Little is known about the cis-acting regulatory elements (REs) that dictate their temporal and spatial expression or about the regulatory landscape surrounding them. The availability of comparative sequence data and the advent of genomic technologies such as ChIP-seq have revolutionized our capacity to identify regulatory sequences like enhancers. Despite this wealth of data, the vast majority of loci lack any significant in vivo functional exploration of their non-coding regions. We have completed a significant functional screen of conserved non-coding sequences (putative REs) scattered across these critical human loci, assaying the temporal and spatial control using zebrafish transgenesis. We first identify and describe the LMX1A paralogs lmx1a and lmx1a-like, comparing their expression during embryogenesis with that in mammals, along with lmx1ba and lmx1bb genes. Consistent with their prominent neuronal expression, 47/71 sequences selected within and flanking LMX1A and LMX1B exert spatial control of reporter expression in the central nervous system (CNS) of mosaic zebrafish embryos. Upon germline transmission, we identify CNS reporter expression in multiple independent founders for 22 constructs (LMX1A, n = 17; LMX1B, n = 5). The identified enhancers display significant overlap in their spatial control and represent only a fraction of the conserved non-coding sequences at these critical genes. Our data reveal the abundance of regulatory instruction located near these developmentally important genes.
KW - Enhancer
KW - Hindbrain
KW - LMX1A
KW - LMX1B
KW - Midbrain
KW - Zebrafish
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U2 - 10.1007/s00438-013-0771-7
DO - 10.1007/s00438-013-0771-7
M3 - Article
C2 - 23942840
AN - SCOPUS:84889879954
SN - 1617-4615
VL - 288
SP - 579
EP - 589
JO - Molecular Genetics and Genomics
JF - Molecular Genetics and Genomics
IS - 11
ER -