Cancer stem cells in oesophageal squamous cell carcinoma: Identification, prognostic and treatment perspectives

Cancer stem cells (CSCs) are a vital subpopulation of cells to target for the treatment of cancers. In oesophageal squamous cell carcinoma (ESCC), there are several markers such as CD44, ALDH, Pygo2, MAML1, Twist1, Musashi1, Side population (SP), CD271 and CD90 that have been proposed to identify the cancer stem cells in individual cancer masses. It has also been demonstrated that stem cell markers like ALDH1, HIWI, Oct3/4, ABCG2, SOX2, SALL4, BMI-1, NANOG, CD133 and podoplanin are associated with patient's prognosis, pathological stages, cancer recurrence and therapy resistance. Finding new cancer stem cell targets or designing drugs to manipulate the known molecular targets in CSCs could be useful for improvements in clinical outcomes of the disease. To conclude, data suggest that CSCs in oesophageal squamous cell carcinoma are related to resistance to therapy and poor prognosis of patients with ESCC. Therefore, innovative insights into CSC biology and CSC-targeted therapies will help to achieve more effective management of patients with oesophageal squamous cell carcinoma.

MicroRNA-125a Reduces Proliferation and Invasion of Oral Squamous Cell Carcinoma Cells by Targeting Estrogen-related Receptor alpha IMPLICATIONS FOR CANCER THERAPEUTICS

Estrogen-related receptor (ESRRA) functions as a transcription factor and regulates the expression of several genes, such as WNT11 and OPN. Up-regulation of ESRRA has been reported in several cancers. However, the mechanism underlying its up-regulation is unclear. Furthermore, the reports regarding the role and regulation of ESRRA in oral squamous cell carcinoma (OSCC) are completely lacking. Here, we show that tumor suppressor miR-125a directly binds to the 3UTR of ESRRA and represses its expression. Overexpression of miR-125a in OSCC cells drastically reduced the level of ESRRA, decreased cell proliferation, and increased apoptosis. Conversely, the delivery of an miR-125a inhibitor to these cells drastically increased the level of ESRRA, increased cell proliferation, and decreased apoptosis. miR-125a-mediated down-regulation of ESRRA impaired anchorage-independent colony formation and invasion of OSCC cells. Reduced cell proliferation and increased apoptosis of OSCC cells were dependent on the presence of the 3UTR in ESRRA. The delivery of an miR-125a mimic to OSCC cells resulted in marked regression of xenografts in nude mice, whereas the delivery of an miR-125a inhibitor to OSCC cells resulted in a significant increase of xenografts and abrogated the tumor suppressor function of miR-125a. We observed an inverse correlation between the expression levels of miR-125a and ESRRA in OSCC samples. In summary, up-regulation of ESRRA due to down-regulation of miR-125a is not only a novel mechanism for its up-regulation in OSCC, but decreasing the level of ESRRA by using a synthetic miR-125a mimic may have an important role in therapeutic intervention of OSCC and other cancers.

Isolation of mineralizing Nestin+ Nkx6.1+ vascular muscular cells from the adult human spinal cord

Background: The adult central nervous system (CNS) contains different populations of immature cells that could possibly be used to repair brain and spinal cord lesions. The diversity and the properties of these cells in the human adult CNS remain to be fully explored. We previously isolated Nestin(+) Sox2(+) neural multipotential cells from the adult human spinal cord using the neurosphere method (i.e. non adherent conditions and defined medium). -- Results: Here we report the isolation and long term propagation of another population of Nestin(+) cells from this tissue using adherent culture conditions and serum. QPCR and immunofluorescence indicated that these cells had mesenchymal features as evidenced by the expression of Snai2 and Twist1 and lack of expression of neural markers such as Sox2, Olig2 or GFAP. Indeed, these cells expressed markers typical of smooth muscle vascular cells such as Calponin, Caldesmone and Acta2 (Smooth muscle actin). These cells could not differentiate into chondrocytes, adipocytes, neuronal and glial cells, however they readily mineralized when placed in osteogenic conditions. Further characterization allowed us to identify the Nkx6.1 transcription factor as a marker for these cells. Nkx6.1 was expressed in vivo by CNS vascular muscular cells located in the parenchyma and the meninges. -- Conclusion: Smooth muscle cells expressing Nestin and Nkx6.1 is the main cell population derived from culturing human spinal cord cells in adherent conditions with serum. Mineralization of these cells in vitro could represent a valuable model for studying calcifications of CNS vessels which are observed in pathological situations or as part of the normal aging. In addition, long term propagation of these cells will allow the study of their interaction with other CNS cells and their implication in scar formation during spinal cord injury.

Uso de células iPS en terapia regenerativa renal: obtención de células iPS mediante vector no integrativo y diferenciación hacia podocitos.

[ES]En las sociedades modernas existe una creciente preocupación por el aumento de la incidencia de la enfermedad renal crónica. Debido a la deficiencia de donantes de órganos y al elevado coste del tratamiento de diálisis, existe la necesidad de desarrollar nuevos tratamientos para estos pacientes. La medicina regenerativa basada en la aplicación de células iPS es una opción prometedora para el tratamiento de esta enfermedad. Sin embargo, la falta de conocimientos sobre el estado pluripotencial de las células y sobre su proceso de diferenciación, así como las limitaciones derivadas del propio procedimiento de reprogramación, impiden su aplicación clínica en un futuro inmediato. Para que se convierta en realidad, numerosas investigaciones se están llevando a cabo con el objetivo de mejorar el procedimiento y hacerlo adecuado para su aplicación clínica. En este trabajo se propone un método que permitiría obtener células iPS a partir de células mesangiales mediante la transfección con un vector no integrativo, el virus Sendai, portador de los genes Oct3/4, Sox2, Klf4 y c-Myc. Al tratarse de un vector no integrativo, se minimizaría el efecto del proceso de reprogramación sobre la estabilidad del genoma celular. Además, en este proyecto se estudiará la capacidad de las células iPS obtenidas para diferenciarse en células progenitoras de podocitos que puedan ser aplicadas específicamente en terapias regenerativas para enfermos renales crónicos.

Valoracion de alternativas en paneles vegetales prefabricados

En las sociedades modernas existe una creciente preocupación por el aumento de la incidencia de la enfermedad renal crónica. Debido a la deficiencia de donantes de órganos y al elevado coste del tratamiento de diálisis, existe la necesidad de desarrollar nuevos tratamientos para estos pacientes. La medicina regenerativa basada en la aplicación de células iPS es una opción prometedora para el tratamiento de esta enfermedad. Sin embargo, la falta de conocimientos sobre el estado pluripotencial de las células y sobre su proceso de diferenciación, así como las limitaciones derivadas del propio procedimiento de reprogramación, impiden su aplicación clínica en un futuro inmediato. Para que se convierta en realidad, numerosas investigaciones se están llevando a cabo con el objetivo de mejorar el procedimiento y hacerlo adecuado para su aplicación clínica. En este trabajo se propone un método que permitiría obtener células iPS a partir de células mesangiales mediante la transfección con un vector no integrativo, el virus Sendai, portador de los genes Oct3/4, Sox2, Klf4 y c-Myc. Al tratarse de un vector no integrativo, se minimizaría el efecto del proceso de reprogramación sobre la estabilidad del genoma celular. Además, en este proyecto se estudiará la capacidad de las células iPS obtenidas para diferenciarse en células progenitoras de podocitos que puedan ser aplicadas específicamente en terapias regenerativas para enfermos renales crónicos.

The Regulation of Sleep and Circadian Rhythms: The Role of Melatonin and Adenosine in Zebrafish

Sleep is a highly conserved behavioral state whose regulation is still unclear. In this thesis I initially briefly introduce the known sleep circuitry and regulation in vertebrates, and why zebrafish is seen as a good model to study sleep-regulation. I describe the existing two-process model of sleep regulation, which posits that the two processes C (circadian) and S (homeostatic) control timing of sleep-wake behavior. I then study the role melatonin plays in the circadian regulation of sleep using zebrafish. Firstly, we find that the absence of melatonin results in a reduction of sleep at night, establishing that endogenous melatonin is required for sleep at night. Secondly, melatonin mutants show a reduction in sleep in animals with no functional behavioral rhythms suggesting that melatonin does not require intact circadian rhythms for its effect on sleep. Thirdly, melatonin mutants do not exhibit any changes in circadian rhythms, suggesting that the circadian clock does not require melatonin for its function. Fourthly, we find that in the absence of melatonin, there is no rhythmic expression of sleep, suggesting that melatonin is the output molecule of process C. Lastly, we describe a connection between adenosine signaling (output molecules of process S), and melatonin. Following this we proceed to study the role adenosine signaling plays in sleep-wake behavior. We find that firstly, adenosine receptor A1 and A2 are involved in sleep- wake behavior in zebrafish, based on agonist/antagonist behavioral results. Secondly, we find that several brain regions such as PACAP cells in the rostral midbrain, GABAergic cells in the forebrain and hindbrain, Dopamine and serotonin cells in the caudal hypothalamus and sox2 cells lining the hindbrain ventricle are activated in response to the A1 antagonist and VMAT positive cells are activated in response to the A2A agonist, suggesting these areas are involved in adenosine signaling in zebrafish. Thirdly, we find that knocking out the zebrafish adenosine receptors has no effect on sleep architecture. Lastly, we find that while the A1 agonist phenotype requires the zfAdora1a receptor, the antagonist and the A2A agonist behavioral phenotypes are not mediated by the zfAdora1a, zfAdora1b and zfAdoraA2Aa, zfAdora2Ab receptors respectively.

Análise de polimorfismos e de expressão do gene p16INK4a em neoplasias cervicais

O câncer de colo do útero é o segundo carcinoma mais frequente em mulheres no mundo e um dos cânceres femininos mais incidentes no Brasil. Em lesões pré-malignas e malignas do colo uterino, a proteína p16INK4a, que participa do controle do ciclo celular, apresenta um aumento considerável de sua expressão, devido possivelmente à presença de oncoproteínas do papilomavírus humano (HPV). Dois polimorfismos no gene p16INK4a, p16 500C>G e p16 540C>T, estão localizados na região 3 não traduzida (3UTR), que está envolvida na regulação pós-transcricional da expressão gênica. O objetivo deste estudo foi avaliar possíveis associações entre os polimorfismos p16 500C>G e p16 540C>T e o desenvolvimento de neoplasias cervicais e/ou a severidade das lesões, considerando os níveis de expressão da proteína p16INK4a nas lesões cervicais e certos fatores de risco clássicos para o câncer cervical, incluindo a infecção pelo HPV. Para isso, foram selecionadas 567 mulheres residentes no Rio de Janeiro, 319 com citologia cervical alterada (grupo de casos) e 248 sem história prévia de alteração citológica do colo uterino (grupo de comparação). Amostras de sangue periférico de todas as participantes foram utilizadas na análise molecular dos polimorfismos p16 500C>G e p16 540C>T através da técnica de PCR-RFLP (reação em cadeia da polimerase - polimorfismo de comprimento de fragmento de restrição), usando as enzimas de restrição MspI e HaeIII, respectivamente. A expressão da proteína p16INK4a em 137 biópsias de mulheres pertencentes ao grupo de casos foi avaliada por imunohistoquímica. A detecção de DNA do HPV em células cervicais foi feita em todas as amostras do grupo de comparação e em 194 amostras do grupo de casos pela técnica de PCR, usando dois pares de oligonucleotídeos, MY09/MY11 e GP05+/GP06+. Os dois grupos de estudo se encontram em equilíbrio de Hardy-Weinberg. As distribuições genotípicas para p16 500C>G e p16 540C>T e as distribuições de combinações haplotípicas nos dois grupos não apresentaram diferenças significativas. A análise do subgrupo HSIL+câncer (casos com lesão intraepitelial de alto grau ou carcinoma invasivo) em comparação com o subgrupo LSIL (casos com lesão intraepitelial de baixo grau) revelou diferença significativa entre as distribuições das combinações haplotípicas (p = 0,036) e diferenças marginais entre as distribuições genotípicas para p16 500C>G (p = 0,071) e p16 540C>T (p = 0,051). O alelo p16 540G, em heterozigose ou homozigose (OR = 1,91, IC 95% = 1,08-3,37), e a combinação haplotípica p16 500C-540C 500G-540C (OR = 2,34, IC 95% = 1,202-4,555) mostraram-se associados com a severidade da lesões cervicais. Já o genótipo p16 540T/T (OR = 0,25, IC 95% = 0,08-0,79), e a combinação haplotípica p16 500C-540T 500C-540T (OR = 0,27, IC 95% = 0,088-0,827) exibiram papel protetor contra o desenvolvimento de lesões mais severas. As análises de interação entre os polimorfismos de p16INK4a e a expressão de p16 ou a infecção pelo HPV foram comprometidas pelo número reduzido de amostras analisadas. Não se observou qualquer interação entre os polimorfismos estudados e os fatores de risco clássicos para o câncer de colo uterino. Nossos resultados apontam para a importância dos polimorfismos do gene p16INK4a como marcadores de severidade da neoplasia cervical.

Fast and Efficient Neural Conversion of Human Hematopoietic Cells

Neurons obtained directly from human somatic cells hold great promise for disease modeling and drug screening. Available protocols rely on overexpression of transcription factors using integrative vectors and are often slow, complex, and inefficient. We report a fast and efficient approach for generating induced neural cells (iNCs) directly from human hematopoietic cells using Sendai virus. Upon SOX2 and c-MYC expression, CD133-positive cord blood cells rapidly adopt a neuroepithelial morphology and exhibit high expansion capacity. Under defined neurogenic culture conditions, they express mature neuronal markers and fire spontaneous action potentials that can be modulated with neurotransmitters. SOX2 and c-MYC are also sufficient to convert peripheral blood mononuclear cells into iNCs. However, the conversion process is less efficient and resulting iNCs have limited expansion capacity and electrophysiological activity upon differentiation. Our study demonstrates rapid and efficient generation of iNCs from hematopoietic cells while underscoring the impact of target cells on conversion efficiency.

PLOD3基因3'调控区的人类特异突变改变miR-124a对PLOD3的调控

microRNAs(miRNAs)是一类在转录后水平调控基因表达的不编码蛋白质的小RNA(长度20-24个碱基).其中,miR-124a是一个在哺乳动物中枢神经系统高度表达的miRNA,在神经前体细胞向神经元分化的过程中起着举足轻重的作用.由于miRNAs特异性地识别靶基因的3'端调控区(3'UTR)的靶序列,因此,在人类起源过程中基因3'UTR的单核苷酸序列变异有可能导致miRNA调控的改变.通过靶基因预测和3'UTR区在哺乳动物代表物种间的同源序列比较,我们发现miR-124a的靶基冈中有一个基因(PLOD3)3UTR的靶位点中存在人类特异突变位点.利用体外报告基因系统,发现PLOD3基因3'UTR靶位点中所含的一个人类特异的突变导致miR-124a对PLOD3的调控效率降低.研究表明,miRNAs靶基因3'UTR的序列变异具有功能效应,它有可能足人类中枢神经系统在起源和演化中发挥关键作用的重要遗传机制之一.

Temporal and Spatial Expression Patterns of Sox1 Gene in Xenopus laevis

克隆了非洲爪蟾的Sox1基因并研究了它在非洲爪蟾早期发育过程中的时空表达图式,比较了Sox1-3基因在发育的脑和眼中的表达图式.序列比对分析显示Sox1-3蛋白在其HMG框结构域具有高度的保守性.通过RT-PCR方法分析了Sox1基因在爪蟾早期不同发育时段的表达情况,结果显示Sox1基因从未受精卵到尾芽期均有表达,但表达强度有所差异.原位杂交结果显示,在早期卵裂阶段和囊胚期,Sox1基因主要在动物极表达;从神经板期开始,Sox1基因主要在中枢神经系统和眼原基中表达.在蝌蚪期,Sox1与Sox2、Sox3在脑部和眼睛的表达区域有所不同.对于爪蟾Sox1基因时空表达图式的研究将有助于阐明SoxB1基因家族在脊椎动物神经系统发生过程中的作用.

一个先天性小眼球家系致病基因的排除性定位

先天性小眼球是一种先天发育异常性眼科疾病.通过基因扫描和连锁分析对一个6代常染色体显性遗传先天性小眼球中国家系的疾病相关基因进行研究.根据已报道的与小眼球相关的5个基因座位(MITF,SOX2,PAX6,MCOP和NNO2),在3,11,14和15号染色体上选取了14个微卫星标记,以荧光标记引物的聚合酶链反应(PCR)扩增目的片段,用ABI 377 DNA遗传分析仪对该家系成员进行基因扫描和基因分型,并采用Linkage软件包对基因分型结果进行连锁分析.结果显示,该家系致病基因与这些已报道的座位均不连锁,即该家系致病基因不是已报道的座位,可能是一个尚未报道的对眼球发育至关重要的新基因座位.

饲养层FGF2表达量对猕猴胚胎干细胞自我更新及多能性的影响

用转基因和RNA干扰(RNAi)法建立5组不同成纤维细胞生长因子-2(fibroblast growth factor-2,FGF2)表达量的猕猴耳部皮肤成纤维细胞(MESF)系:过表达FGF2组(f1),过表达的阴性对照组(f2),FGF2 RNA干扰组(f3),RNA干扰的阴性对照组(f4)和未作任何处理的对照组(f5).5组MESF的FGF2表达量相对值为f1:f2:f3:f4:f5=4:2:1:2:2;c-fos,TGF-β1,INHBA,Gremlinl在f1中表达量上升,在f3中表达量下降;BMP4,TGF-β2在f1中表达量下降,在f3中表达量上升;表明内源FGF2能够作用于MESF的TGF-β信号通路,引起相关基因表达量的变化.用这砦细胞作为饲养层长期培养(10代)猕猴胚胎干细胞(RhESC),结果在f1上培养的RhESC增殖速度都比对照组快,并且c-fos,TGF-β1,INHBA,Gremlinl,Oct-4,Nanog,Sox2表达量均上升,BMP4表达下调;在f3上培养的RhESC增殖较慢,BMP4表达上调,c-fos,TGF-β1,INHBA,Gremlinl,Oct-4,Nanog,Sox2表达下调.5组MESF上培养的RhESC形成的EB均表达各胚层早期标记基因(marker),说明RhESC的多能性没有受到影响,但表达量有差异,f1上RhESC形成的EB所有marker都低表达.结果表明饲养层的FGF2含量不仅影响自身相关基凶的表达,还对RhESC的自我更新有一定的作用.

大脑表达 miRNA 在大脑进化中的作用及其遗传机制初步研究

人类区别于其它动物的最本质特征是其拥有其他动物所无法比拟的大脑容量及高 级的认知能力。即使与其近亲－非人灵长类相比，人也拥有比非人灵长类大好几倍的脑 容量和更为发达的认知能力。现在一般认为，人类大脑的形成是适应性选择(达尔文正 选择)的结果。但是到目前为止，对人类起源过程中大脑容量增大及认知能力提高的遗 传学机制却知之甚少。以前的研究表明，几个与大脑发育相关的蛋白质编码基因在人类 起源中受到了正向选择。同时，也有证据表明人类大脑的进化也可能是基因表达调控变 化的结果。因此寻找人与非人灵长类大脑表达基因的调控差异或许能够进一步为人与非 人灵长类为何有如此巨大的差异提供分子生物学水平上的解释。 MicroRNA(miRNA)是一类在转录后水平调控基因表达的不编码蛋白质的小 RNA(长度20－24个碱基)。通过调控靶基因的表达，miRNA参与了众多的生理过程。而 很多大脑表达的miRNA的表达量在大脑发育过程中呈显著的变化，这表明miRNA参与 了大脑的发育调控。由此可知，miRNA对其靶基因调控效率的改变很可能引起大脑发育 调控的改变。 本文通过寻找大脑表达的保守microRNA 及对其靶基因的预测，同时用比较基因组 学的方法发现：有很多microRNA 的靶基因3’UTR 的靶位点中存在人类特异突变位点。 我们推测这些人类特异突变位点可能改变microRNA 对其靶基因的表达调控效应，而调 控效应的改变可能在进化过程中对认知能力的提高发挥重要作用。利用体外报告基因系 统，我们发现有几个预测的靶基因是对应miRNA 的真实靶基因。其中，miR-127 的靶 基因（SEMA3F）3’UTR 的靶位点中所含的一个人类特有的突变增强了miR-127 对 SEMA3F 的调控效率。将该位点突变回复为黑猩猩的位点使得miR-127 对SEMA3F 的 调控效率降低到黑猩猩的水平。这表明miR-127 对SEMA3F 的调控效率的改变确实是 由该人类特异突变位点引起的。我们提供了人类特异突变位点能够引起miR-127 对SEMA3F 的调控效率的改变的体外证据，但是体内的调控模式是否如此尚需进一步的工 作。 总之，本文通过体外试验表明，miRNA靶基因3’UTR的序列变异具有功能效应，它 有可能是人类中枢神经系统在起源和演化中发挥关键作用的重要遗传机制之一。

非洲爪蟾Brunol1 基因的功能以及文昌鱼肌动蛋白基因家族扩增的研究

BRUNOL 蛋白又称CELF（CUG-BP and ETR3 like factor）是一种典型的RNA 结合蛋白，它的N 端含有两个连续的RNA 识别结构域（RNA recognition motif，RRM)， C 端有一个RRM 结构域。主要参与对可变剪切、翻译、降解和编辑等基因表达转录后水平的调节。迄今在人类中已发现6 个Brunol 基因家族成员，即Brunol1-6；在非洲爪蟾中已发现了5 个：Brunol1-5。近期，我们克隆了爪蟾的Brunol1-5 并研究了它们在非洲爪蟾早期胚胎发育过程中的时空表达图式。结果显示，与以往研究结果一致， Brunol1 基因高量、特异地在神经管中表达，提示Brunol1 基因可能对于爪蟾的神经系统的发生和发育发挥着重要的作用。本实验利用Morpholino 和过表达等手段研究了爪蟾Brunol1 基因对于爪蟾早期胚胎发育的影响。结果显示，在下调和过表达Brunol 1 基因的情况下都会导致胚胎出现体轴弯曲，眼睛和头部发育不全等表型。而将 Brunol1 基因特异的Morpholino 与它的mRNA 共注射时可以明显挽救这一表型。我们通过原位杂交实验，检测了一些爪蟾神经系统的标记基因在Brunol1 过表达胚胎中的表达情况，结果发现过表达Brunol1 基因能显著地下调Krox-20, N-tubulin, Lhx2, Pax6 等的表达，而Sox2 和Otx2 的表达却未受影响。这说明Brunol1 的异常表达确实影响到了神经系统发育过程的信号调控网络，导致胚胎发育的畸形。该结果将有助于阐述Brunol1 基因对于脊椎动物神经系统发生的意义。肌动蛋白是一种分布广泛而且在进化上十分保守的蛋白，它是构成细胞骨架的关键组分。通常人们将肌动蛋白分成肌肉型和胞质型两种类型，它们各自行使着不同的功能。在此，我们通过对古老的脊索动物文昌鱼的肌动蛋白基因家族进行系统的分析发现，文昌鱼中该基因家族成员多达30 多个，而且它们中很多都有连锁现象；进化分析的结果显示，文昌鱼的肌动蛋白基因家族通过串联重复序列的复制发生扩增；从结构上看，它们的基因结构多样化, 包含2-7 个外显子；同时，我们还克隆了两个不同的文昌鱼肌肉型的肌动蛋白基因，并进一步比较了它们在文昌鱼早期胚胎中的表达图式。结果显示，这两个基因在表达上有着细微的差别，这提示文昌鱼肌动蛋白基因家族成员在功能上的分化。该结论将有助于阐述肌动蛋白基因家族的进化以及它们在脊索动物发育的中所扮演的功能。

人类基因组中保守二级结构的纯净化选择及其在转录调控网络中的作用

保守序列是一种跨物种保守的基因组序列，而且绝大多数为非蛋白编码序 列。保守序列在人类遗传疾病中发挥着重要作用。其中，一部分保守序列能够 折叠形成二级结构。已鉴定的一些保守二级结构编码一些RNA 分子，如 microRNA、RNA 编辑序列和组蛋白mRNA 3’端非翻译区茎环结构等。但是，对 于绝大部分的保守二级结构，它们的生物学功能以及作用于它们上面的进化作 用力依然是未知的。 群体的SNP 数据在分析序列上的进化作用力时非常有效。SNP 在群体中的 频率会因为受到不同的进化作用力而表现出差异，而与其是否位于基因组中的 突变热点无关。对于受纯净化选择作用的SNP，它们的频率一般会比中性SNP 具有低的新生型等位基因频率（DAF）。我们运用生物信息学的方法，在人类基 因组保守二级结构中找到746 个SNP。这746 个SNP 与基因组其它区段的SNP 在突变模式上并不存在显著差异，在保守二级结构内同样存在突变热点。通过 与侧翼序列SNP 的分布比较发现，保守二级结构上SNP 密度约为其侧翼序列的 2/3。相比于侧翼序列SNP，有更高比例的保守二级结构SNP 具有低的DAF 值。 这些结果提示，有很多保守二级结构上的SNP 因为受到纯净化选择作用而在现 代人群中被剔除了。保守二级结构与侧翼序列在SNP 密度和DAF 上的差异要高 于保守序列与非保守序列之间的差异，提示保守二级结构是受到纯净化选择作 用最为严格的一类保守序列。我们发现，在保守二级结构内部，纯净化选择作 用的强度也有差异。茎区比环区具有更低的SNP 密度，而且有更高比例的茎区 SNP 具有低的DAF 值。这个结果提示，保守二级结构上的纯净化选择力主要作 用于茎区上的位点。我们推测，这可能是茎区上的突变往往比环区的突变对二级结构的造成更大的影响导致的。 我们通过寻找保守二级结构与转录因子SOX2、OCT4、NANOG、SUZ12 和C-MYC 结合位点之间的重叠，还分析了保守二级结构在转录调控网络中的作用。结果 显示，很多保守二级结构是作为转录因子的结合位点调控了许多与发育相关的 转录因子编码基因的表达。转录因子与保守二级结构之间的结合模式非常复杂， 可以有多个转录因子结合到同一个保守二级结构上，也可以是一个转录因子结 合到自身编码基因相关的保守二级结构上。不同的转录因子和保守二级结构结 合可以主导靶基因的特异模式，当绝大多数相关的保守二级结构与SUZ12 结合 时，基因表达受到抑制，而当绝大多数相关的保守二级结构不与SUZ12 结合时， 基因表达受到激活。在转录调控网络中，约有30%的保守二级结构是作为启动 子来调控基因的表达。因为转录因子SOX2、OCT4、NANOG、SUZ12 和C-MYC 仅仅 只结合到很小一部分保守二级结构上，提示可能还有更多的转录因子会结合到 保守二级结构上。因此，保守二级结构介导的转录调控网络要比目前已知的复 杂得多。