[閒聊] Campbell 沒教的事 研究新領域整理2

[snark (影燕)]

基因方面的研究
生物資訊  數學 物理學 開啟了許多重要的合作領域


Local RNA translation

1. genome 中大量的Intron Sequence 有何功能?
   ID elements 是老鼠基因中常見的序列

  在神經的突觸 有些蛋白是以mRNA運送的形式 來調控

  Cytoplasmic Intron Sequence-Retaining
Transcripts Can Be Dendritically Targeted
via ID Element Retrotransposons

Neuron 69, 877–884, March 10, 2011

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Network motifs
過去基因的研究注重在基因的功能還有整體的基因網路
但自從2001年開始 我們發現基因也像電路一樣 有常見的迴路架構
而不是形成隨機網路
Network motifs: theory and experimental approaches
Nature Reviews Genetics 8, 450-461 (June 2007)


這些不同型態的迴路之功能漸漸被解析

目前最重要的研究集中在訊號分析的調控
在動物與植物的發育上都有重要的成就

1. Pattern formation by dynamically interacting
   network motifs
 3213–3218 no. 9  vol. 106  March 3, 2009 PNAS


2. Filtering transcriptional noise during development: concepts
and mechanisms
Nat Rev Genet. 2006 Jan;7(1):34-44

3. Network Crosstalk Dynamically Changes
during Neutrophil Polarization
Cell 149, 1073–1083, May 25, 2012

4.Hox Genes Regulate Digit Patterning by Controlling the Wavelength
 of a Turing-Type Mechanism
Science 338, 1476 (2012)


這篇的數學難度比較高 討論我們熟知的植物根部發育
還有火紅的不對稱細胞分裂

還有生物現象中常見對於訊號的非線性反映
A Bistable Circuit Involving SCARECROWRETINOBLASTOMA
Integrates Cues to Inform Asymmetric Stem Cell Division

Cell 150, 1002–1015, August 31, 2012




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High through put sequencing
可以做甚麼?

重要的發展都在整合生物 已知的知識 改善統計方式
看到新的生物知識

1.Mapping mutations 突變劑是常用的研究手段 但是究竟哪個突變
造成我們想要的性狀呢

C. elegans Mutant Identification with a One-Step Whole-Genome-Sequencing
and SNP Mapping Strategy
PLoS ONE 5(11): e15435. doi:10.1371/journal.pone.0015435

A Strategy for Direct Mapping and Identification of Mutations
by Whole-Genome Sequencing
Genetics 186: 427-430 (September 2010)

The Impact of Whole Genome Sequencing on Model System Genetics:
Get Ready for the Ride
Genetics 184: 317-319 (February 2010)

2.
Next-generation sequencing technologies can be used to analyse genetically
heterogeneous samples at unprecedented detail.


Error correction of next-generation sequencing data and reliable estimation
of HIV quasispecies
Nucleic Acids Res. 2010 November; 38(21): 7400-7409.

Inferring Viral Quasispecies Spectra from Shotgun and Amplicon
Next-Generation Sequencing Reads, In Maria Poptsova, Genome Analysis:

Current Procedures and Applications,
Horizon Scientific Press, pp. to appear, 2013

Ultra-deep sequencing for the analysis of viral populations
Current Opinion in Virology 2011, 1:1-6


3. 核醣體在基因的哪裡終止轉譯?
 Analysis of translational pausing using ribosome profiling in bacteria.
        The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
Nature 484, 538-541  (26 April 2012)


4.  不是只有基因才會轉錄
   enhancer 也有明顯的轉錄活動 而且和chromatin modification 有關(尚未發表)

global run-on sequencing, GRO-seq

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters
Science 19 December 2008: Vol. 322 no. 5909 pp. 1845-1848

Defining the Status of RNA Polymerase at Promoters
Cell Reports 2, 1025-1035, October 25, 2012


5.  chromosome conformation capture

Methods for Identifying Higher-Order Chromatin Structure
Annu. Rev. Genomics Hum. Genet. 2012. 13:59-82


6.
Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing
Nature Methods(2013)doi:10.1038/nmeth.2408


7. complex disease研究

Nat Genet. 2011 Oct 9;43(11):1066-73. doi: 10.1038/ng.952.

Deep resequencing of GWAS loci identifies independent rare
variants associated with inflammatory bowel disease.



 Genome-wide association studies in mice

 Nature Reviews Genetics | AOP, published online 9 October 2012;
doi:10.1038/nrg3335



Finding the missing heritability of complex
diseases
Vol 461j8 October 2009jdoi:10.1038/nature08494

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