Developmental changes in the accessible chromatin, transcriptome and Ascl1-binding correlate with the loss in Müller Glial regenerative potential.
Animals
Basic Helix-Loop-Helix Transcription Factors
/ metabolism
Cells, Cultured
Cellular Reprogramming
Chromatin
/ genetics
Ependymoglial Cells
/ cytology
Epigenomics
Gene Expression Profiling
/ methods
Gene Expression Regulation
Gene Expression Regulation, Developmental
Mice
Nerve Regeneration
Retina
Sequence Analysis, RNA
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
12 08 2020
12 08 2020
Historique:
received:
13
03
2020
accepted:
16
07
2020
entrez:
14
8
2020
pubmed:
14
8
2020
medline:
12
1
2021
Statut:
epublish
Résumé
Diseases and damage to the retina lead to losses in retinal neurons and eventual visual impairment. Although the mammalian retina has no inherent regenerative capabilities, fish have robust regeneration from Müller glia (MG). Recently, we have shown that driving expression of Ascl1 in adult mouse MG stimulates neural regeneration. The regeneration observed in the mouse is limited in the variety of neurons that can be derived from MG; Ascl1-expressing MG primarily generate bipolar cells. To better understand the limits of MG-based regeneration in mouse retinas, we used ATAC- and RNA-seq to compare newborn progenitors, immature MG (P8-P12), and mature MG. Our analysis demonstrated developmental differences in gene expression and accessible chromatin between progenitors and MG, primarily in neurogenic genes. Overexpression of Ascl1 is more effective in reprogramming immature MG, than mature MG, consistent with a more progenitor-like epigenetic landscape in the former. We also used ASCL1 ChIPseq to compare the differences in ASCL1 binding in progenitors and reprogrammed MG. We find that bipolar-specific accessible regions are more frequently linked to bHLH motifs and ASCL1 binding. Overall, our analysis indicates a loss of neurogenic gene expression and motif accessibility during glial maturation that may prevent efficient reprogramming.
Identifiants
pubmed: 32788677
doi: 10.1038/s41598-020-70334-1
pii: 10.1038/s41598-020-70334-1
pmc: PMC7423883
doi:
Substances chimiques
Ascl1 protein, mouse
0
Basic Helix-Loop-Helix Transcription Factors
0
Chromatin
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
13615Subventions
Organisme : NICHD NIH HHS
ID : T32 HD007183
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM007270
Pays : United States
Organisme : NEI NIH HHS
ID : R01 EY021482
Pays : United States
Références
Bringmann, A. et al. Cellular signaling and factors involved in Muller cell gliosis: neuroprotective and detrimental effects. Prog. Retin. Eye Res.28, 423–451 (2009).
pubmed: 19660572
Goldman, D. Müller glial cell reprogramming and retina regeneration. Nat. Rev. Neurosci.15, 431–442 (2014).
pubmed: 24894585
pmcid: 4249724
Gemberling, M., Bailey, T. J., Hyde, D. R. & Poss, K. D. The zebrafish as a model for complex tissue regeneration. Trends Genet.29, 611–620 (2013).
pubmed: 23927865
VandenBosch, L. S. & Reh, T. A. Epigenetics in neuronal regeneration. Semin. Cell Dev. Biol. https://doi.org/10.1016/J.SEMCDB.2019.04.001 (2019).
doi: 10.1016/J.SEMCDB.2019.04.001
pubmed: 30951894
Ramachandran, R., Fausett, B. V. & Goldman, D. Ascl1a regulates Müller glia dedifferentiation and retinal regeneration through a Lin-28-dependent, let-7 microRNA signalling pathway. Nat. Cell Biol.12, 1101–1107 (2010).
pubmed: 20935637
pmcid: 2972404
Fausett, B. V., Gumerson, J. D. & Goldman, D. The proneural basic helix-loop-helix gene ascl1a is required for retina regeneration. J. Neurosci.28, 1109–17 (2008).
pubmed: 18234889
pmcid: 2800945
Ohsawa, R. & Kageyama, R. Regulation of retinal cell fate specification by multiple transcription factors. Brain Res.1192, 90–98 (2008).
pubmed: 17488643
Ueki, Y. et al. Transgenic expression of the proneural transcription factor Ascl1 in Müller glia stimulates retinal regeneration in young mice. Proc. Natl. Acad. Sci.112, 13717–13722 (2015).
pubmed: 26483457
Jorstad, N. L. et al. Stimulation of functional neuronal regeneration from Müller glia in adult mice. Nature548, 103–107 (2017).
pubmed: 28746305
pmcid: 5991837
Arnold, K. et al. Sox2(+) adult stem and progenitor cells are important for tissue regeneration and survival of mice. Cell Stem Cell9, 317–329 (2011).
pubmed: 21982232
pmcid: 3538360
Young, R. W. Cell differentiation in the retina of the mouse. Anat. Rec.212, 199–205 (1985).
pubmed: 3842042
Blackshaw, S. et al. Genomic analysis of mouse retinal development. PLoS Biol.2, E247 (2004).
pubmed: 15226823
pmcid: 439783
Wilken, M. S. et al. DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements. Epigenet. Chromatin8, 8 (2015).
Neph, S. et al. BEDOPS: high-performance genomic feature operations. Bioinformatics28, 1919 (2012).
pubmed: 22576172
pmcid: 3389768
Nelson, B. R. et al. Genome-wide analysis of Müller glial differentiation reveals a requirement for Notch signaling in postmitotic cells to maintain the glial fate. PLoS ONE6, e22817 (2011).
pubmed: 21829655
pmcid: 3149061
Ueki, Y. et al. A transient wave of bmp signaling in the retina is necessary for muller glial differentiation. Dev.142, 533–543 (2015).
Wohl, S. G. & Reh, T. A. The microRNA expression profile of mouse Müller glia in vivo and in vitro. Sci. Rep.6, 35423 (2016).
pubmed: 27739496
pmcid: 5064377
Brzezinski, J. A., Kim, E. J., Johnson, J. E. & Reh, T. A. Ascl1 expression defines a subpopulation of lineage-restricted progenitors in the mammalian retina. Development138, 3519–3531 (2011).
pubmed: 21771810
pmcid: 3143566
Aydin, B. et al. Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes. Nat. Neurosci.22, 897–908 (2019).
pubmed: 31086315
pmcid: 6556771
Castro, D. S. et al. A novel function of the proneural factor Ascl1 in progenitor proliferation identified by genome-wide characterization of its targets. Genes Dev.25, 930–945 (2011).
pubmed: 21536733
pmcid: 3084027
Hägglund, A.-C., Dahl, L. & Carlsson, L. Lhx2 is required for patterning and expansion of a distinct progenitor cell population committed to eye development. PLoS ONE6, e23387 (2011).
pubmed: 21886788
pmcid: 3158764
de Melo, J., Clark, B. S. & Blackshaw, S. Multiple intrinsic factors act in concert with Lhx2 to direct retinal gliogenesis. Sci. Rep.6, 32757 (2016).
pubmed: 27605455
pmcid: 5015061
Gordon, P. J. et al. Lhx2 balances progenitor maintenance with neurogenic output and promotes competence state progression in the developing retina. J. Neurosci.33, 12197–12207 (2013).
pubmed: 23884928
pmcid: 3721834
Shu, T., Butz, K. G., Plachez, C., Gronostajski, R. M. & Richards, L. J. Abnormal development of forebrain midline glia and commissural projections in Nfia knock-out mice. J. Neurosci.23, 203–212 (2003).
pubmed: 12514217
pmcid: 6742120
Ninkovic, J. et al. The BAF complex interacts with Pax6 in adult neural progenitors to establish a neurogenic cross-regulatory transcriptional network. Cell Stem Cell13, 403–418 (2013).
pubmed: 23933087
pmcid: 4098720
Martynoga, B. et al. Epigenomic enhancer annotation reveals a key role for NFIX in neural stem cell quiescence. Genes Dev.27, 1769–1786 (2013).
pubmed: 23964093
pmcid: 3759694
Pollak, J. et al. ASCL1 reprograms mouse Müller glia into neurogenic retinal progenitors. Development140, 2619–2631 (2013).
pubmed: 23637330
pmcid: 3666387
Wapinski, O. L. et al. Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons. Cell155, 621–635 (2013).
pubmed: 24243019
Casey, B. H., Kollipara, R. K., Pozo, K. & Johnson, J. E. Intrinsic DNA binding properties demonstrated for lineage-specifying basic helix-loop-helix transcription factors. Genome Res.28, 484–496 (2018).
pubmed: 29500235
pmcid: 5880239
Hughes, A. E. O., Enright, J. M., Myers, C. A., Shen, S. Q. & Corbo, J. C. Cell type-specific epigenomic analysis reveals a uniquely closed chromatin architecture in mouse rod photoreceptors. Sci. Rep.7, 43184 (2017).
pubmed: 28256534
pmcid: 5335693
Omori, Y. et al. Analysis of transcriptional regulatory pathways of photoreceptor genes by expression profiling of the Otx2-deficient retina. PLoS ONE6, e19685 (2011).
pubmed: 21602925
pmcid: 3094341
Jadhav, A. P., Roesch, K. & Cepko, C. L. Development and neurogenic potential of Müller glial cells in the vertebrate retina. Prog. Retin. Eye Res.28, 249–262 (2009).
pubmed: 19465144
pmcid: 3233204
Aldiri, I. et al. The dynamic epigenetic landscape of the retina during development, reprogramming, and tumorigenesis. Neuron94, 550-568.e10 (2017).
pubmed: 28472656
pmcid: 5508517
Heng, Y. H. E. et al. NFIX regulates proliferation and migration within the murine SVZ neurogenic niche. Cereb. Cortex25, 3758–3778 (2015).
pubmed: 25331604
Deneen, B. et al. The transcription factor NFIA controls the onset of gliogenesis in the developing spinal cord. Neuron52, 953–968 (2006).
pubmed: 17178400
Clark, B. S. et al. Single-cell RNA-Seq analysis of retinal development identifies NFI factors as regulating mitotic exit and late-born cell specification. Neuron102, 1111-1126.e5 (2019).
pubmed: 31128945
pmcid: 6768831
Zibetti, C., Liu, S., Wan, J., Qian, J. & Blackshaw, S. Epigenomic profiling of retinal progenitors reveals LHX2 is required for developmental regulation of open chromatin. Commun. Biol.2, 142 (2019).
pubmed: 31044167
pmcid: 6484012
Wu, L. et al. The E2F1–3 transcription factors are essential for cellular proliferation. Nature414, 457–462 (2001).
pubmed: 11719808
Stevaux, O. & Dyson, N. J. A revised picture of the E2F transcriptional network and RB function. Curr. Opin. Cell Biol.14, 684–691 (2002).
pubmed: 12473340
Murphy, D., Hughes, A. E. O., Lawrence, K. A., Myers, C. A. & Corbo, J. C. Cis-regulatory basis of sister cell type divergence in the vertebrate retina. bioRxiv 648824 (2019) https://doi.org/10.1101/648824 .
Buenrostro, J. D., Wu, B., Chang, H. Y. & Greenleaf, W. J. ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr. Protoc. Mol. Biol.109, 21–29 (2015).
pubmed: 25559105
pmcid: 4374986
Krueger, F. Trim galore. A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ (2015).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods9, 357–359 (2012).
pubmed: 22388286
pmcid: 22388286
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics25, 2078–2079 (2009).
pubmed: 19505943
pmcid: 2723002
Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol.29, 24–26 (2011).
pubmed: 3346182
pmcid: 3346182
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell38, 576–589 (2010).
pubmed: 2898526
pmcid: 2898526
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics26, 139–140 (2010).
Liao, Y., Smyth, G. K. & Shi, W. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Res.47, e47 (2019).
pubmed: 30783653
pmcid: 6486549
McLean, C. Y. et al. GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol.28, 495–501 (2010).
pubmed: 20436461
pmcid: 4840234
Falcon, S. & Gentleman, R. Using GOstats to test gene lists for GO term association. Bioinformatics23, 257–258 (2007).
pubmed: 17098774
Ramírez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res.44, W160–W165 (2016).
pubmed: 27079975
pmcid: 27079975