Question

3. (10pt) Your colleague professor Stu Dentgenerated a genome-wide DNA methylation map for normal colon cells using MRE-seq (a restriction enzyme approach) and MeDIP-seq(an immunoprecipitation approach). In an intergenic region, he found an interesting locus. This locus is about 20kb. On one end of the locus, there is a 2kb CpG rich stretch that has both relatively lowMRE-seq and MeDIP-seq signals. The rest 18kb has high level of MeDIP-seq signals. (A) (3pt) Why might you suspect that this region encodes for a novel gene? (B) (4pt) You decide to look at histone modification patterns across this regionfor more evidence. There are several genome-wide datasets available for this cell type: H3K4me1, H3K4me3, H3K27me3, H3K9me3, H3K36me3, and H3K9Ac. Which histone mark would youinvestigatefor this locus and why? (C) (3pt) Suggestat least one other source of data (NOT annotation or bisulfide sequencing) that may help you confirm or refute your suspicion, and why you think it may help?

Answer 1

(A) intergonic region encoded for novel gene

Small, untranslated RNA molecules were identified initially in bacteria, but examples can be found in all kingdoms of life.

These RNAs carry out diverse functions, and many of them are regulators of gene expression.

Genes encoding small, untranslated RNAs are difficult to detect experimentally or to predict by traditional sequence analysis approaches.

Thus, in spite of the rising recognition that such RNAs may play key roles in bacterial physiology, many of the small RNAs known to date were discovered fortuitously.

( B )

Histone modifications could influence plant growth and development by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited.

Used chromatin immunoprecipitation followed by high-throughput sequencing, to investigate the genome-wide distribution of four histone modifications: di and trimethylation of H3K4 (H3K4me2 and H3K4me3) and acylation of H3K9 and H3K27 (H3K9ac and H3K27ac).

Explored DNase-Hypersensitive (DH) sites along the rice genome.

The histone marks appeared mainly in generic regions and were enriched around the transcription start sites (TSSs) of genes.

This analysis demonstrated that the four histone modifications and the DH sites were all associated with active transcription.

Furthermore, the four histone modifications were highly concurrent with transcript regions—a promising feature that was used to predict missing genes in the rice gene annotation.

The predictions were further validated by experimentally confirming the transcription of two predicted missing genes.

Moreover, a sequence motif analysis was constructed in order to identify the DH sites and many putative transcription factor binding sites.  

( C )

Many studies aimed at reconstructing the invasion history of a species rely, in part, on inferences based on patterns of genetic variation.

however, In particular, given the time scale of most invasions, the typical demography of invasive species in their invaded range, and the available molecular tools, the underlying assumptions of population genetic models will often be violated.

Given this fact, examined the potential of population genetic data for recon-structing the history of serial introductions of the small Indian mongoose, Herpestes auropunctatus.

Simulations to test the power of existing microsatellite data for testing the credibility of historical introduction records.

Although our results are generally consistent with most historical records for H.auropunctatus, the existing data have low power to reject alternative historical hypotheses.

Simulations of a wide range of founder population sizes show broadly overlapping results, making rather different historical.

Difficult to rule out with typical data sets.

Advocate caution in the use of molecular population genetics to interfer the history of invasive species, and extensive simulations as a tool to evaluate.