Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment

Kueh, Hao Yuan and Yui, Mary A. and Ng, Kenneth K. H. and Pease, Shirley S. and Zhang, Jingli A. and Damle, Sagar S. and Freedman, George and Siu, Sharmayne and Bernstein, Irwin D. and Elowitz, Michael B. and Rothenberg, Ellen V. (2016) Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment. Nature Immunology, 17 (8). pp. 956-965. ISSN 1529-2908. PMCID PMC4955789. doi:10.1038/ni.3514. https://resolver.caltech.edu/CaltechAUTHORS:20160613-162442836

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	Image (JPEG) (Supplementary Figure 1: Binding profiles of key transcription factors to the Bcl11b gene and enhancer) - Supplemental Material See Usage Policy. 347kB
	Image (JPEG) (Supplementary Figure 2: Generation and validation of Bcl11b-YFP knock-in reporter) - Supplemental Material See Usage Policy. 120kB
	Image (JPEG) (Supplementary Figure 3: Bcl11b-YFP levels are not affected by presence of the neomycin drug resistance cassette) - Supplemental Material See Usage Policy. 252kB
	Image (JPEG) (Supplementary Figure 4: Experimental and analysis workflow for time-lapse imaging of Bcl11b-YFP levels in progenitor cells) - Supplemental Material See Usage Policy. 151kB
	Image (JPEG) (Supplementary Figure 5: Notch signaling promotes all-or-none Bcl11b activation in a dose-dependent manner) - Supplemental Material See Usage Policy. 320kB
	Image (JPEG) (Supplementary Figure 6: shTcf7 constructs reduce Tcf7 transcript levels in ETP and DN2 cells) - Supplemental Material See Usage Policy. 136kB
	Image (JPEG) (Supplementary Figure 7: Effects of TCF-1 perturbation on Bcl11b activation in pro-T cells) - Supplemental Material See Usage Policy. 275kB
	Image (JPEG) (Supplementary Figure 8: Runx1, but not TCF-1 or GATA-3, controls Bcl11b expression amplitude in mature T cells) - Supplemental Material See Usage Policy. 143kB
	PDF (Supplementary Figures 1–8 and Supplementary Tables 3 and 4) - Supplemental Material See Usage Policy. 2MB
	MS Excel (Supplementary Table 1 - Transcript levels for genes differentially expressed in Bcl11b^-YFP– versus Bcl11b-YFP^+ cells) - Supplemental Material See Usage Policy. 50kB
	MS Excel (Supplementary Table 2 - Transcript levels for transcriptional regulators expressed in developing T cells) - Supplemental Material See Usage Policy. 249kB

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Abstract

During T cell development, multipotent progenitors relinquish competence for other fates and commit to the T cell lineage by turning on Bcl11b, which encodes a transcription factor. To clarify lineage commitment mechanisms, we followed developing T cells at the single-cell level using Bcl11b knock-in fluorescent reporter mice. Notch signaling and Notch-activated transcription factors collaborate to activate Bcl11b expression irrespectively of Notch-dependent proliferation. These inputs work via three distinct, asynchronous mechanisms: an early locus 'poising' function dependent on TCF-1 and GATA-3, a stochastic-permissivity function dependent on Notch signaling, and a separate amplitude-control function dependent on Runx1, a factor already present in multipotent progenitors. Despite their necessity for Bcl11b expression, these inputs act in a stage-specific manner, providing a multitiered mechanism for developmental gene regulation.

Item Type:

Article

Related URLs:

URL	URL Type	Description
http://dx.doi.org/10.1038/ni.3514	DOI	Article
http://rdcu.be/jbrX	Publisher	Free ReadCube access
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4955789/	PubMed Central	Article

ORCID:

Author	ORCID
Kueh, Hao Yuan	0000-0001-6272-6673
Yui, Mary A.	0000-0002-3136-2181
Bernstein, Irwin D.	0000-0003-0795-3392
Elowitz, Michael B.	0000-0002-1221-0967
Rothenberg, Ellen V.	0000-0002-3901-347X

Additional Information:

© 2016 Macmillan Publishers Limited. Received 26 January 2016; Accepted 14 June 2016; Published online 04 July 2016. We thank M. Lerica Gutierrez Quiloan for assistance with mouse genotyping and maintenance; N. Verduzco and I. Soto for animal husbandry; J. Longmate for help with statistical analysis of alternate-lineage-potential experiments; R.A. Diamond, K. Beadle, J. Grimm, D. Perez and J. Verceles for cell sorting; N. Feng for initial flow cytometric analysis; J. Hahn for advice on BAC recombineering; S. Qin for assistance with qPCR experiments; X.Wang for performing pilot studies with microwell arrays; and J. Ungerbäck for assistance with visualizing genome track data. We also thank A. Bhandoola, L. Xu and W. Pear (University of Pennsylvania); J. Telfer (University of Massachusetts) and N. Masuyama (University of Tokyo) for constructs. This work was funded by a CRI/Irvington Postdoctoral Fellowship and a US National Institutes of Health (NIH) K99/R00 Award (K99HL119638A) to H.Y.K.; a California Institute for Regenerative Medicine Bridges to Stem-Cell Research award to K.K.H.N. (TB1-01176); NIH grants to E.V.R. (R01 AI083514, R01 AI095943, RC2 CA148278, R33 HL089123, R01 CA90233 and R01 HL119102) and M.A.Y. (R01 AI064590); NIH/HHS grant U01HL100395 (I.D.B.); the Albert Billings Ruddock Professorship to E.V.R.; and the Al Sherman Foundation and the Louis A. Garfinkle Memorial Laboratory Fund to E.V.R.’s lab. Author Contributions: H.Y.K. designed research, performed experiments, analyzed data and wrote the paper. M.A.Y. designed research, performed experiments, analyzed data and wrote the paper. K.K.H.N., and S.S.P. performed experiments. S.S.D., G.F. and I.D.B. provided reagents. J.A.Z. performed experiments and analyzed data. S.S. analyzed data. M.B.E. designed research. E.V.R. designed research, analyzed data and wrote the paper. Code availability: Image analysis code is available upon request to H.Y.K. The authors declare no competing financial interests.

Funders:

Funding Agency	Grant Number
CRI/Irvington Postdoctoral Fellowship	UNSPECIFIED
NIH	K99HL119638A
California Institute for Regenerative Medicine (CIRM)	TB1-01176
NIH	R01 AI083514
NIH	R01 AI095943
NIH	RC2 CA148278
NIH	R33 HL089123
NIH	R01 CA90233
NIH	R01 HL119102
NIH	R01 AI064590
NIH	U01HL100395
Albert Billings Ruddock Professorship	UNSPECIFIED
Al Sherman Foundation	UNSPECIFIED
Louis A. Garfinkle Memorial Laboratory Fund	UNSPECIFIED

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PubMed Central ID:

PMC4955789

DOI:

10.1038/ni.3514

Record Number:

CaltechAUTHORS:20160613-162442836

Persistent URL:

https://resolver.caltech.edu/CaltechAUTHORS:20160613-162442836

Official Citation:

Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment Hao Yuan Kueh, Mary A Yui, Kenneth K H Ng, Shirley S Pease, Jingli A Zhang, Sagar S Damle, George Freedman, Sharmayne Siu, Irwin D Bernstein, Michael B Elowitz & Ellen V Rothenberg Nature Immunology 17, 956–965 (2016) doi:10.1038/ni.3514

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ID Code:

67892

Collection:

CaltechAUTHORS

Deposited By:

George Porter

Deposited On:

06 Jul 2016 20:43

Last Modified:

26 Apr 2022 17:42

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