Regulation of Gene Expression Part I
Lehmann lab
FACs and RNA-seq to study germline transcription.
7K out 13.8K genes transcribed in germline.
Maternal to zygotic transition at stage 8-9 in germ cells.
Ovo motif C-GTTA
Zeba (dePace Lab)
quantitative input output.
Posterior stripe element conserved across species. D yakuba D. speudo
use linear weighting model for expression level of a cell. Really? Hb is linear in gt? HbCRM of different species driving LacZ inject into D mel.
Didn’t show sequence data (claim ‘different’)
Lilly (Stas)
2 enhancers for broad in FE.
Show by mitotic clones repressed by pointed and mirror.
Mirr required to express early enhancer and repress late enhancer.
Pointed effects only the late enhancer, leads to appendage fusion.
Rich Lusk
Testing enhancer grammar
count sites between species. Separate very weak, weak, strong, and very strong.
Neither mixed enhancer shows any expression. Mixed ‘word scrambling’ keeps most expression’ Keeps local correlation.
get str 7 and anterior headstripe (otd region). (gt no longer near bcd sites).
Homeodomain TFs
Same core for all homeodomain TFs TAT
overexpress msh and slouch, cell sort with Twi>GFP, genes respond differently to these two TFs.
Use microarray chips to find sequences TFs bind to. Find unique and common subsets of sites.
Look for enrichment of slo specific binding sites in slo specific genes (based on expression profiling).
Dissect slouch site in lbl enhancer, demonstrate cis and trans requirement for slo site to provide repression. Enhancer dosen’t work with a non-specific slouch site.
Rb regulation Longworth
repress etf mediated transcription in G1.
RBF1 interacts with promotes localization of condensin. Can loop DNA in vitro, necessary for ribosomal DNA in yeast. Colocalize on polytene chromosome, suggests non-mitotic role.
‘significance values’ for ven 109, 112, 458, overlap p=-103. Meaningless. Assert the genes are entirely independent.
Promote looping to bring common target genes into an expression factory of local active TF.
Ectdyosine hormone signaling.
Stimulates cell death during metamorphosis. Reaper and hid transcription lead to salvery gland destruction.
part II
Umulis (Purdue IN)
don’t measure biological output in fundamental units. Model data integration. Data integration tradoffs in model fitting.
Hard to compare quality of pattern quantitatively.
Model is very sensitive to parameters.
Lott / Eisen lab
early expression 2x greater for female X genes.
How does variation change throughout cycle 14
hb maternal levels remain constant through mid cc14. Some genes compensate, some don’t. Doesn’t correlate with strength.
Stowers (Jamie Dyer, Workman lab)
SAGA chromatin remodeling prior to PIC. Histone acytyl transferase contains deubiquitnation module, involved in initiated to elongating transition.
take neuronal and mesodermal tissues. Mudpit. Saga shows differential localization in muscle and nerve. Correlates with h3k9 ac.
mef2 interacts with saga so does MSL and Meso18e. MLF copurifies with most saga components. Meyloid leukemia factor.
White lab. Ctcf binding evo
Conserved insulator protein. Forms interchromosal loops. Pupa chip-seq in 4 species. Out to pseudo. Get same motif in all species. ~8bp. 20-70% binding sites diverged. Very reproducible replicates. Old binding sites subject to negative selection. Some rapid evolution of new sites (positive selection).
Tominick (Dresden max plank)
Live whole embryo gene expression at cell resolution. FlyFos gfp tag 960 genes with gfp including all TFs. Image with SPIM lightsheet imaging.
Need to reassemble image from many stacks from different angles. Correct for intensity differences (beads or nuclei) use yolk dynamics to align multiple embryos with different genes.
Software Fiji open source.
Mattias Alenius … Shadi Jaffari (Linkoping, Sweden)
How does one neuron find one receptor.
Find 7 relevant TFs expressed in different overlapping patterns in the antenna. Large differences between receptors in the number of factors. Small enhancer drags express in too many additional cells. Proximal activator enhancer modified by distal long range repressor. Also have promoter proximal short range dominant repression.