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

Chromatin Modifications and Their Function

The X-ray crystal structure of the nucleosome core particle of chromatin shows in atomic detail how the histone protein octamer is assembled and how 146 base pairs of DNA are organized into a superhelix around it. Both histone/histone and histone/DNA interactions depend on the histone fold domains and additional, well ordered structure elements extending from this motif. Histone amino-terminal tails pass over and between the gyres of the DNA superhelix to contact neighbouring particles. The lack of uniformity between multiple histone/DNA-binding sites causes the DNA to deviate from ideal superhelix geometry.

Crystal structure of the nucleosome core particle at 2.8 Å resolution

Detection of protein families in large databases is one of the principal research objectives in structural and functional genomics. Protein family classification can significantly contribute to the delineation of functional diversity of homologous proteins, the prediction of function based on domain architecture or the presence of sequence motifs as well as comparative genomics, providing valuable evolutionary insights. We present a novel approach called TRIBE-MCL for rapid and accurate clustering of protein sequences into families. The method relies on the Markov cluster (MCL) algorithm for the assignment of proteins into families based on precomputed sequence similarity information. This novel approach does not suffer from the problems that normally hinder other protein sequence clustering algorithms, such as the presence of multi-domain proteins, promiscuous domains and fragmented proteins. The method has been rigorously tested and validated on a number of very large databases, including SwissProt, InterPro, SCOP and the draft human genome. Our results indicate that the method is ideally suited to the rapid and accurate detection of protein families on a large scale. The method has been used to detect and categorise protein families within the draft human genome and the resulting families have been used to annotate a large proportion of human proteins.

https://bioinformatics.cs.vt.edu/%7Eeasychair/multigenome_comparisons/EnrightEtAl_NAR_2002.pdf

An efficient algorithm for large-scale detection of protein families

http://www.people.vcu.edu/~mreimers/SysBio/Li%20-%20Role%20of%20chromatin%20in%20transcription.pdf

The Role of Chromatin during Transcription

ING tumor suppressor proteins are critical regulators of chromatin acetylation required for genome expression and perpetuation.

The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast. Its catalytic component, Esa1, is essential for cell cycle progression, gene-specific regulation and has been implicated in DNA repair. Almost all NuA4 subunits have clear homologues in higher eukaryotes, suggesting that the complex is conserved throughout evolution to metazoans. We demonstrate here that NuA4 complexes are indeed present in human cells. Tip60 and its splice variant Tip60b/PLIP were purified as stable HAT complexes associated with identical polypeptides, with 11 of the 12 proteins being homologs of yeast NuA4 subunits. This indicates a highly conserved subunit composition and the identified human proteins underline the role of NuA4 in the control of mammalian cell proliferation. ING3, a member of the ING family of growth regulators, links NuA4 to p53 function which we confirmed in vivo. Proteins specific to the human NuA4 complexes include ruvB-like helicases and a bromodomain-containing subunit linked to ligand-dependent transcription activation by the thyroid hormone receptor. We also demonstrate that subunits MRG15 and DMAP1 are present in distinct protein complexes harboring histone deacetylase and SWI2-related ATPase activities, respectively. Finally, analogous to yeast, a recombinant trimeric complex formed by Tip60, EPC1, and ING3 is sufficient to reconstitute robust nucleosomal HAT activity in vitro. In conclusion, the NuA4 HAT complex is highly conserved in eukaryotes, in which it plays primary roles in transcription, cellular response to DNA damage, and cell cycle control.

/pdf/structural-and-functional-conservation-of-the-nua4-histone-2q5cw0eh4f.pdf

Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeast to humans

Comparison of affinity tags for protein purification.

Promoter-specific recruitment of histone acetyltransferase activity is often critical for transcriptional activation. We present a detailed study of the interaction between the histone acetyltransferase complexes SAGA and NuA4, and transcription activators. We demonstrate by affinity chromatography and photo-cross-linking label transfer that acidic activators directly interact with Tra1p, a shared subunit of SAGA and NuA4. Mutations within the COOH-terminus of Tra1p disrupted its interaction with activators and resulted in gene-specific transcriptional defects that correlated with lowered promoter-specific histone acetylation. These data demonstrate that the essential Tra1 protein serves as a common target for activators in both SAGA and NuA4 acetyltransferases.

http://science.sciencemag.org/content/sci/292/5525/2333.full.pdf

Recruitment of HAT complexes by direct activator interactions with the ATM-related Tra1 subunit.

When fully extended, one copy of the three billion base pair human genome reaches a length of over two meters. Yet, it must be packaged into the nucleus of a cell with an average diameter of less than 10 μm. Within this context, specific segments of the genome must be transcriptionally active or repressed in a coordinated fashion to allow a cell to react to its ever-changing environment. This is akin to arranging 30 miles of thread inside a basketball such that at moment’s notice key segments can be accessed. To establish such compaction while maintaining coordinated accessibility, organisms ranging from yeast to man organize their genomes in a polymeric complex called chromatin. The fundamental unit of the chromatin polymer is the nucleosome, which repeats every 160 to 240 bp across the genome.1 Each nucleosome contains a nucleosome core, composed of an octameric complex of the core histone proteins, which forms a spool to wrap 145 to 147 bp of DNA. The nucleosome core is connected to the adjacent nucleosome core through a segment of linker DNA, which often associates with the linker histone protein (H1 or H5). The nucleosome core with ∼165 bp of DNA together with the linker histone is called the chromatosome.2 The chromatosome and the additional linker DNA constitutes a nucleosome.2 Despite these technical definitions, the nucleosome core particle is often colloquially referred to as the nucleosome.

The nucleosome serves three primary functions. First, it brings about the first level of genomic compaction, organizing ∼200 bp of DNA. Second, the nucleosome acts as a signaling hub for chromatin-templated processes by providing a scaffold for the binding of chromatin enzymes and displaying a combinatorial array of post-translational modifications (PTMs). This array of PTMs further regulates the recruitment of chromatin enzymes3 and tunes both nucleosome stability4 and the higher-order compaction of chromatin.5−7 Third, the nucleosome can self-assemble into higher-order chromatin structures, allowing for further compaction of the genome. The first level of higher-order compaction is the 30 nm chromatin fiber for which several models have been created based on experimental data using cryogenic-electron microscopy (cryo-EM) and X-ray crystallography.8

This review focuses on recent advances in our understanding of the structure and function of the nucleosome and is divided into four parts. First, we present a primer covering the fundamentals of the nucleosome core particle structure determined at atomic scale by X-ray crystallography in 1997.9 Next we discuss recent insights into the role of DNA sequence in the structure of nucleosomal DNA based on structure–function studies of nucleosome core particles containing derivatives of the Widom 601 nucleosome positioning sequence.10 We then introduce patterns of nucleosome recognition by chromatin factors using recent crystal structures and NMR and cryo-EM models of peptide and protein macromolecular chromatin factors bound to the nucleosome core particle. Finally, we will compare a recent cryo-EM model for the 30 nm chromatin fiber11 to two previous models based on crystallographic and cryo-EM data.12,13

Song Tan

Papers

ING tumor suppressor proteins are critical regulators of chromatin acetylation required for genome expression and perpetuation.

Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeast to humans

Comparison of affinity tags for protein purification.

Recruitment of HAT complexes by direct activator interactions with the ATM-related Tra1 subunit.

Nucleosome structure and function.