Deep vertebrate roots for mammalian zinc finger transcription factor subfamilies.
Deep vertebrate roots for mammalian zinc finger transcription factor subfamilies.
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DOI：
10.1093/gbe/evu030
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发表时间：
2014-03
影响因子：
3.3
通讯作者：
Stubbs L
中科院分区：
文献类型：
--
作者：
Liu H;Chang LH;Sun Y;Lu X;Stubbs L
虽然许多脊椎动物转录因子（TF）家族是保守的，但C2 H2锌指（ZNF）家族是一个值得注意的例外。特别是，新的ZNF基因类型已经出现，复制，并在整个进化过程中独立分化，产生许多谱系特异性TF基因。这种进化动态不仅提出了许多有趣的问题，但也严重复杂的ZNF基因的识别仍然功能保守。为了解决这个问题，我们通过从8个测序的基因组中挖掘ZNF位点，然后比对从编码的ZNF基序中提取的DNA结合氨基酸或“指纹”的模式，来搜索脊椎动物的“DNA结合直系同源物”。使用这种方法，我们在每个物种中发现了数百个谱系特异性基因，也发现了数百个直链组。大多数组的直系同源物表现出一定程度的物种之间的指纹分歧，但174组显示指纹模式，已非常严格地保守。专注于动态KRAB-ZNF亚家族，包括近400个人类基因被认为具有强大的KRAB介导的表观遗传沉默活性，我们发现只有三个基因之间的哺乳动物和非哺乳动物群体保守。这三个基因是一个古老家族簇的成员，编码一个不寻常的KRAB结构域，作为转录激活因子发挥作用。进化分析证实了这种激活KRAB的古老起源，并揭示了KRAB-ZNF在每个脊椎动物谱系中的独立扩展。大多数人类ZNF基因，从最高度保守的灵长类动物特异性基因，在免疫和生殖组织中高度表达，表明它们已被招募来调节进化上不同的生物学性状。
While many vertebrate transcription factor (TF) families are conserved, the C2H2 zinc finger (ZNF) family stands out as a notable exception. In particular, novel ZNF gene types have arisen, duplicated, and diverged independently throughout evolution to yield many lineage-specific TF genes. This evolutionary dynamic not only raises many intriguing questions but also severely complicates identification of those ZNF genes that remain functionally conserved. To address this problem, we searched for vertebrate “DNA binding orthologs” by mining ZNF loci from eight sequenced genomes and then aligning the patterns of DNA-binding amino acids, or “fingerprints,” extracted from the encoded ZNF motifs. Using this approach, we found hundreds of lineage-specific genes in each species and also hundreds of orthologous groups. Most groups of orthologs displayed some degree of fingerprint divergence between species, but 174 groups showed fingerprint patterns that have been very rigidly conserved. Focusing on the dynamic KRAB-ZNF subfamily—including nearly 400 human genes thought to possess potent KRAB-mediated epigenetic silencing activities—we found only three genes conserved between mammals and nonmammalian groups. These three genes, members of an ancient familial cluster, encode an unusual KRAB domain that functions as a transcriptional activator. Evolutionary analysis confirms the ancient provenance of this activating KRAB and reveals the independent expansion of KRAB-ZNFs in every vertebrate lineage. Most human ZNF genes, from the most deeply conserved to the primate-specific genes, are highly expressed in immune and reproductive tissues, indicating that they have been enlisted to regulate evolutionarily divergent biological traits.
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DOI：
10.1111/j.1600-0897.2010.00860.x
发表时间：
2010-10
期刊：
American journal of reproductive immunology (New York, N.Y. : 1989)
影响因子：
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作者：
Black SG;Arnaud F;Palmarini M;Spencer TE
通讯作者：
Spencer TE
DOI：
10.1038/nsb1196-940
发表时间：
1996-11-01
期刊：
NATURE STRUCTURAL BIOLOGY
影响因子：
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作者：
Kim, CA;Berg, JM
通讯作者：
Berg, JM
影响因子：
11.4
作者：
BELLEFROID, EJ;MARINE, JC;MARTIAL, JA
通讯作者：
MARTIAL, JA
DOI：
10.1073/pnas.94.11.5617
发表时间：
1997-05-27
影响因子：
11.1
作者：
Isalan, M;Choo, Y;Klug, A
通讯作者：
Klug, A
影响因子：
30.8
作者：
通讯作者：
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