Mus musculus
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ABSTRACT:
PROVIDER: PRJNA382711 | ENA |
REPOSITORIES: ENA
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Project description:Genome-wide binding reveals intrinsic specificity and regulatory function of lineage-specifying bHLH transcription factors
| PRJNA382708 | ENA
Project description:Genome-wide binding reveals intrinsic specificity and regulatory function of lineage-specifying bHLH transcription factors (RNA-Seq).
| PRJNA382709 | ENA
Project description:Genome-wide binding reveals intrinsic specificity and regulatory function of lineage-specifying bHLH transcription factors (ChIP-Seq).
| PRJNA382710 | ENA
Project description:Stomata are pores in the epidermis of plants that can open and close and allow for gas exchange vital for photosynthesis and regulate transpiration. Stomatal development is driven by a set of conserved bHLH transcription factors (SPCH, MUTE, FAMA, and their heterodimerization partners ICE1, SCRM2), that initiate and promote progression of cell fates in the stomatal lineage. Due to the shared ancestry of SPCH, MUTE and FAMA (subgroup Ia) and ICE1 and SCRM2 (subgroup IIIb) their DNA binding specificity is similar and there is some functional redundancy. However, individual bHLHs also have unique functions. For example, SPCH is required for initiation of the stomatal lineage, while FAMA is responsible for terminal differentiation of the guard cell pair. In grasses, the stomatal complex comprises the guard cell pair, and two flanking subsidiary cells. Recruitment of the latter from neighboring cell filed during development requires expression of MUTE. Remarkably, while MUTE is absolutely required for the promotion of guard mother cell fate in maize and rice, this is not the case in Brachypodium. This suggests that another TF can at least partially substitute for MUTE in this function. While different expression profiles of the bHLH dimers within the stomatal lineage may partially responsible for distinct functions of each pair, it is likely that each pair forms different transcriptional complexes and that interaction with other transcriptional regulators affects the dimer’s binding DNA binding and gene regulation properties. Given the differences in bHLH function between dicots and grasses and even within the grass family, we were interested in elucidating the protein interaction networks of the stomatal lineage regulators in Brachypodium. To this end, we performed co-immunoprecipitation coupled to LC-MS/MS of BdSPCH2-YFP, YFP-BdMUTE, YFP-BdFAMA, YFP-ICE1 and YFP-SCRM2 from the developmental zone of young B. distachyon leaves using GFP-Trap beads. All YFP-fusion proteins were expressed under the endogenous promoter in the Bd21-3 background. The only exception was BdICE1, which was expressed under the ZmUBI promoter, but was nevertheless mostly restricted to the stomatal lineage. As control lines we use the Bd21-3 wild type and a line expressing 3x YFPnls (nuclear YFP) under the MUTE promoter. Comparison of proteins enriched with the bHLH fusion proteins vs. the controls revealed overlapping and distinct putative interactors, which is in agreement with the assumption that these transcription factors have both shared and unique functions. Notably, in addition to the presumed hetero-dimerization partners, we found a number of other bHLH transcription factors that were identified with one or more of the bait proteins. This suggests the presence of a larger bHLH network acting in the stomatal lineage.
2023-03-11 | PXD035582 | Pride
Project description:Homotypic cooperativity and collective binding are determinants of bHLH specificity and function
| PRJNA555089 | ENA
Project description:Developmental mechanisms of lineage specification are crucial to tissue-specific gene regulation, and crucial lineage-specification factors are associated with developmental and oncogenic diseases. The mechanisms by which these factors regulate their distinct transcriptional profiles remains unclear. Comparison of their binding in a common context reveals that such specificity is intrinsic to these factors, and not simply a consequence of distinction in preference for, or availability of accessible chromatin at their respective binding sites.
2018-02-27 | GSE97714 | GEO
Project description:Developmental mechanisms of lineage specification are crucial to tissue-specific gene regulation, and crucial lineage-specification factors are associated with developmental and oncogenic diseases. The mechanisms by which these factors regulate their distinct transcriptional profiles remains unclear. Comparison of their binding in a common context reveals that such specificity is intrinsic to these factors, and not simply a consequence of distinction in preference for, or availability of accessible chromatin at their respective binding sites.
2018-02-27 | GSE97713 | GEO
Project description:Developmental mechanisms of lineage specification are crucial to tissue-specific gene regulation, and crucial lineage-specification factors are associated with developmental and oncogenic diseases. The mechanisms by which these factors regulate their distinct transcriptional profiles remains unclear. Comparison of their binding in a common context reveals that such specificity is intrinsic to these factors, and not simply a consequence of distinction in preference for, or availability of accessible chromatin at their respective binding sites.
2018-02-27 | GSE97712 | GEO
Project description:Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF cooperativity. Although in vitro studies suggest it may be common, examples of such cooperativity remain scarce in cellular contexts. Here, we demonstrate how ‘Coordinator’, a long DNA motif comprised of common motifs bound by many basic helix-loop-helix (bHLH) and homeodomain (HD) TFs, uniquely defines regulatory regions of embryonic face and limb mesenchyme. Coordinator guides cooperative and selective binding between the bHLH family mesenchymal regulator TWIST1 and a collective of HD factors associated with regional identities in the face and limb. TWIST1 is required for HD binding and open chromatin at Coordinator sites, while HD factors stabilize TWIST1 occupancy at Coordinator and titrate it away from HD-independent sites. This cooperativity results in shared regulation of genes involved in cell-type and positional identities, and ultimately shapes facial morphology and evolution.
2023-05-30 | GSE230318 | GEO
Project description:Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF cooperativity. Although in vitro studies suggest it may be common, examples of such cooperativity remain scarce in cellular contexts. Here, we demonstrate how ‘Coordinator’, a long DNA motif comprised of common motifs bound by many basic helix-loop-helix (bHLH) and homeodomain (HD) TFs, uniquely defines regulatory regions of embryonic face and limb mesenchyme. Coordinator guides cooperative and selective binding between the bHLH family mesenchymal regulator TWIST1 and a collective of HD factors associated with regional identities in the face and limb. TWIST1 is required for HD binding and open chromatin at Coordinator sites, while HD factors stabilize TWIST1 occupancy at Coordinator and titrate it away from HD-independent sites. This cooperativity results in shared regulation of genes involved in cell-type and positional identities, and ultimately shapes facial morphology and evolution.
2023-05-30 | GSE230317 | GEO