Project description:A cascade of basic helix-loop-helix transcription factors guide tapetal cell development in maize anthers, using proteins conserved in Arabidopsis and rice but deployed with a distinctive timing. Anthers were dissected and staged to be 1500 μm in length (+/- 100 μm) and samples were compared between mutants and fertile siblings on an Agilent 4x44 custom microarray. Analysis included MS32 which is another basic helix-loop-helix factor that acts later during tapetal differentiation.
Project description:Supporting .raw data for "Functional conservation and divergence of the helix-turn-helix motif of E2 ubiquitin-conjugating enzymes", DOI: 10.15252/embj.2021108823
Related to Figure 1E and EV1A.
Project description:Improper regulation of translation initiation, a vital check-point of protein synthesis in the cell, has been linked to a number of cancers. Overexpression of protein subunits of eukaryotic translation initiation factor 3 (eIF3) has been associated with increased translation of mRNAs involved in cell proliferation. In addition to playing a major role in general translation initiation by serving as a scaffold for the assembly of translation initiation complexes, eIF3 regulates translation of specific cellular mRNAs and viral RNAs. Mutations in the N-terminal Helix-Loop-Helix (HLH) RNA-binding motif of the EIF3A subunit in eIF3 interfere with Hepatitis C Virus Internal Ribosome Entry Site (IRES) mediated translation initiation in vitro. Here we use RNA-seq and ribosome profiling of engineered lentiviral HEK293T cells to show that the EIF3A HLH motif controls translation of a small set of cellular transcripts enriched in oncogenic mRNAs, including MYC.
Project description:Basic helix-loop-helix (bHLH) transcription factors (TF) recognize E-boxes (CANNTG) and include over 100 members. Here we investigated how chromatinised E-boxes are engaged by two structurally diverse bHLH family members; the proto-oncogene MYC-MAX and the circadian TF, CLOCK-BMAL1. Both bind E-boxes preferentially near the nucleosomal entry/exit sites. Structural studies with artificial or endogenous nucleosome sequences illustrate that MYC-MAX/CLOCK-BMAL1 trigger DNA release from histones to gain access. The CLOCK-BMAL1 PAS dimerization domains engage the histone-octamer disc atop the H2A/H2B acidic patch, an interaction critical for circadian cycling. Binding of tandem E-boxes at endogenous DNA sequences is similarly achieved through direct interactions between two CLOCK-BMAL1 protomers and histones. At internal E-boxes, the MYC-MAX leucine zipper can also interact with histones H2B/H3, and its binding is indirectly enhanced by OCT4 elsewhere on the nucleosome. The nucleosomal E-box position and the type of bHLH dimerisation domain jointly determine the histone contact, the affinity, and the degree of competition/cooperativity with other nucleosome-bound factors.
