MicroRNAs: Genomics, Biogenesis, Mechanism, and Function

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

/pdf/initial-sequencing-and-analysis-of-the-human-genome-5dapk1rsx1.pdf

Initial sequencing and analysis of the human genome.

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

http://bartellab.wi.mit.edu/publication_reprints/Bartel_Cell09.pdf

MicroRNAs: Target Recognition and Regulatory Functions

A procedure for extracting plasmid DNA from bacterial cells is described. The method is simple enough to permit the analysis by gel electrophoresis of 100 or more clones per day yet yields plasmid DNA which is pure enough to be digestible by restriction enzymes. The principle of the method is selective alkaline denaturation of high molecular weight chromosomal DNA while covalently closed circular DNA remains double-stranded. Adequate pH control is accomplished without using a pH meter. Upon neutralization, chromosomal DNA renatures to form an insoluble clot, leaving plasmid DNA in the supernatant. Large and small plasmid DNAs have been extracted by this method.

A rapid alkaline extraction procedure for screening recombinant plasmid DNA

The intron separating the variable- and constant-region exons of the rearranged immunoglobulin heavy-chain locus contains a lymphocyte-specific transcriptional enhancer The enhancer is a member of a class of cis-acting, tissue-specific, transcriptional control elements which are characterized by orientation-independent and relatively position-independent function In vivo analysis of the position of DNA-binding factors, by assessing the availability of specific bases to chemical modification, has identified four sequence clusters within the heavy-chain enhancer, denoted E1 to E4 (refs 3, 4) These sites are protected (that is, occupied) only in B lymphocytes A consensus sequence relationship (consensus CAGGTGGC) between these four sites was suggested where three of the sites conformed to the consensus in seven of eight positions while the other was homologus in six of eight positions We proposed that a single trans-acting factor might recognize all four sites Using an assay involving gel electrophoresis of DNA-protein complexes to detect sequence-specific DNA binding factors that recognize these related motifs, we have now identified a mouse B-cell nuclear factor (NF-muE1) which binds specifically to one such motif within the mouse heavy-chain gene enhancer This factor binds poorly, if at all, to the other related motifs, and other factors have been identified which interact preferentially with some of these latter motifs Dimethyl sulphate interference experiments suggest that the NF-muE1 factor is in contact with at least the guanine residues in the sequence GATGGCCGATC This factor seems to be present in both lymphoid and non-lymphoid cell lines

Distinct factors bind to apparently homologous sequences in the immunoglobulin heavy-chain enhancer.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/S0014-5793%2801%2902953-2

Zinc regulates the function and expression of the iron transporters DMT1 and IREG1 in human intestinal Caco‐2 cells

Genetic screens are powerful tools for identifying genes responsible for diverse phenotypes. Here we describe a genome-wide CRISPR/Cas9-mediated loss-of-function screen in tumor growth and metastasis. We mutagenized a non-metastatic mouse cancer cell line using a genome-scale library with 67,405 single-guide RNAs (sgRNAs). The mutant cell pool rapidly generates metastases when transplanted into immunocompromised mice. Enriched sgRNAs in lung metastases and late-stage primary tumors were found to target a small set of genes, suggesting that specific loss-of-function mutations drive tumor growth and metastasis. Individual sgRNAs and a small pool of 624 sgRNAs targeting the top-scoring genes from the primary screen dramatically accelerate metastasis. In all of these experiments, the effect of mutations on primary tumor growth positively correlates with the development of metastases. Our study demonstrates Cas9-based screening as a robust method to systematically assay gene phenotypes in cancer evolution in vivo.

Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis

The next challenge for biomedical research will be to solve problems of highly complex and integrated biological systems within the human body. Predictive models of these systems in either normal or disease states are beyond the capability of current knowledge and technology.

http://science.sciencemag.org/content/sci/333/6042/527.full.pdf

Promoting Convergence in Biomedical Science

https://www.cell.com/cell/pdf/0092-8674(92)90084-P.pdf

Phillip A. Sharp

Papers

Distinct factors bind to apparently homologous sequences in the immunoglobulin heavy-chain enhancer.

Zinc regulates the function and expression of the iron transporters DMT1 and IREG1 in human intestinal Caco‐2 cells

Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis

Promoting Convergence in Biomedical Science

Promoter specificity of basal transcription factors