Abstract
Eukaryotic histone deacetylation, critical for maintaining nucleosome structure and regulating gene expression, is mediated by histone deacetylases (HDACs).
Analysis：
主語：Eucharyotic histone deacetylation
謂語：is mediated by
表語：histone deacetylase （HDACs）
句子critical for maintaining nucleosome structure and regulating gene expression 前面有先行詞histone deacetylation 因此是定語從句省略了which is
完整句子應該是：
Eukaryotic histone deacetylation which is critical for maintaining nucleosome structure and regulating gene expression, ......
這里的用法是：定語從句省略主格關系代詞的用法
即主格關系代詞+be+分詞省略主格關系代詞+be立宜，但是這里好像后面是critical for 其實這個是副詞修飾maintaing
所以我們可以去除ciritical for 在看這個句子：就是主格關系代詞which + be 動詞is的結構所以可以省略
Eukaryotic histone deacetylation which is maintaining nucleosome structure and regulating gene expression, ......
Although nucleosomes have been reported to regulate mRNA polyadenylation in humans, the role of HDACs in regulating polyadenylation has not been uncovered.
Although引導的讓步狀語從句崭添，Although nucleosomes（主語） have been reported to （謂語） regulate mRNA polyadenylation（賓語） in humans （地點狀語）。
the role of HDACs（主語）（which was省略） in regulating polyadenylation has not been（謂語） uncovered（表語）
Taking （現在分詞作狀語）advantage of phenotypic studies on Arabidopsis, HDA6 (one of HDACs) was found to be a critical part of many biological processes.
知識點：伴隨狀語
由于從句和主句主語一致墨辛，為了避免重復瘪吏，狀語從句主語省略癣防，同時動詞變成動名詞。
Because I felt tired掌眠， I went to bed ealier.
Feeling tired, I went to bed ealier
When she saw the dog蕾盯，she ran off
Seeing the dog，she ran off
這里乍看前后主語不一致后面好似HDA6蓝丙，前面從句好像是we级遭， 仔細觀察我們發(fā)現望拖，HDA6 是was found （by us省略），所以主語還是we 装畅，前后一致靠娱，只是科學描述為了避免主觀性，把主動變被動了掠兄。
Here, we report that HDA6 affects mRNA polyadenylation in Arabidopsis. Poly(A) sites of up-regulated transcripts are closer to the histone acetylation peaks in hda6 compared to the wild-type Col-0.
Here像云，地點狀語
we （主語）report（謂語） that （賓語從句） “HDA6 （主語）affects （謂語） mRNA polyadenylation （賓語）in Arabidopsis （地點狀語）.”
HDA6 is required for the deacetylation of histones around DNA on nucleosomes, which solely coincides with up-regulated or uniquely presented poly(A) sites in hda6.
主語: HDA6
謂語：is required for
賓語： the deacetylation of histones around DNA on nucleosomes（狀語）
which solely coincides with up-regulated or uniquely presented poly(A) sites in hda6. 非限制定語從句其中which為主語 solely狀語
coincide with 謂語
or 鏈接兩個同位語賓語
in hda6 狀語
Furthermore, defective HDA6 results in an overrepresentation of the canonical poly(A) signal (AAUAAA) usage.
Furthermore：狀語
主語：defective（定語） HDA6
位語：results in
賓語：an overrepresentation of the canonical poly(A) signal (AAUAAA) usage.
Chromatin loci for generating AAUAAA-type transcripts have a comparatively low H3K9K14ac around poly(A) sites when compared to other noncanonical poly(A) signal–containing transcripts.
主語：Chromatin loci
位語： have
賓語： a comparatively low H3K9K14ac around poly(A) sites
狀語：when compared to other noncanonical poly(A) signal–containing transcripts
其中 for generating AAUAAA-type transcripts=which is for generating AAUAAA-type transcripts
These results indicate that HDA6 regulates polyadenylation in a histone deacetylation–dependent manner in Arabidopsis.
主語：These results
位語：indicate
賓語：HDA6 （主語） regulates（謂語） polyadenylation （賓語） in a histone deacetylation–dependent manner in Arabidopsis （復合狀語）
Introduction
As one of the post-transcriptional modifications of mRNA, the polyadenylation process can critically regulate the gene expression in eukaryotes (Tian and Manley 2017).
主語： the polyadenylation process
謂語：regulate
賓語：the gene expression
狀語或賓補：in eukaryotes
知識點：賓補
所謂“補”就是補充說明，賓補呢蚂夕，就是對賓語的補充迅诬。英語中，做賓補的部分一把是名詞婿牍、形容詞侈贷、介詞短語和非謂語動詞。所謂的非謂語動詞等脂，就是分詞和不定式俏蛮，分詞又包括過去分詞和現在分詞。
1. 名詞做賓補：
We call her Goldilocks.
2. 形容詞的賓補：
My work keeps me busy.
3. 介詞短語的賓語補語：
I left a case on the train.
4. 動名詞短語的賓語補語：
Don't keep me waiting too long.
5. 不定式作賓補：
I asked him to help me.
6. 過去分詞作賓補：
Could you make yourself understood?
7. 除了以上情況上遥，有些副詞也可以做賓補：
Let me in.
Don't let your parents down.
Don't let the dog out.
Put your shoes away.
方式狀語：As one of the post-transcriptional modifications of mRNA,
知識點：
as 用作介詞搏屑，當它后面接名詞時，既可以表示“時間”粉楚，也可以“身份”辣恋。表示“時間”就是時間狀語，表示“身份”則是方式狀語模软，意為“以......身份（做某事）”伟骨。
例如：
1. 表示時間：
As a small boy, he was rather naughty.
She loved singing as a child and started vocal training at 12.
2. 表示身份：
As a teacher, you should be strict with your students.
He's not in the first grade as a musician.
as到底是表示“時間”還是“身份”，可以從后面接的名詞和語境上判斷出來燃异。
As a student, you should study hard. 在這個句子中携狭，as表示“身份”，意為“作為”特铝∈钪校“作為一名學生，你應該努力學習鲫剿■猓”
This universally required 3′ end processing for RNA polymerase II (Pol II)-dependent transcripts is mainly mediated by a protein complex which recognizes a poly(A) signal, cleavages the pre-mRNA, and synthesizes the poly(A) tail (Clerici et al. 2018).
主語：This 相當于it
謂語：required
賓語：3′ end processing
for RNA polymerase II (Pol II)-dependent transcripts is mainly mediated by a protein complex
for 引導的原因狀語從句，
知識點：
because 表示原因,回答why 的問句
比如： why are you absent?
Because i am ill.
for 一般不表示原因灵莲，表理由雕凹，一般不放句首
比較這兩個句子：
The day breaks, for the birds are singing.
The day breaks because the sun is rising.
鳥叫不是天亮的直接原因，只是因為鳥叫，而推斷天亮了．
而太陽出來了是直接原因枚抵，因為太陽出來了线欲，所以天亮了
which recognizes a poly(A) signal, cleavages the pre-mRNA, and synthesizes the poly(A) tail (Clerici et al. 2018).
which引導的限制性定語從句
主語：which
謂語：and 連接的復合謂語：recognizes，cleavages 汽摹，synthesizes
賓語：三個動詞后面的詞
Recent studies revealed that alternative polyadenylation (APA) sites can be positioned at either the 3′ untranslated region (UTR) or outside of the 3′ UTR (Deng and Cao 2017; Tian and Manley 2017).
主語：studies
謂語：revealed
賓語：that that alternative polyadenylation (APA) sites can be positioned at either the 3′ untranslated region (UTR) or outside of the 3′ UTR
APA results in increased diversity of transcripts and may affect mRNA stability, localization, and exportation.
主語：APA
謂語： results in 李丰， may affect
賓語： increased diversity of transcripts ，mRNA stability, localization, and exportation.
Consequently, the expression of these genes may be regulated by APA.
主語： the expression of these genes
謂語：may be regulated
賓語：by APA.
狀語：Consequently
By using high throughput sequencing approaches, it was found that over 50% of genes contain more than two poly(A) sites in eukaryotes (Xing and Li 2011; Tian and Manley 2017).
By using high throughput sequencing approaches
by+doing是“介詞by動名詞”逼泣，在句子中作狀語趴泌，可在在句尾，句首拉庶。如果在句中嗜憔，前后都要用逗號隔開。舉例說明:
He studied English by teaching himself when he was young.
By teaching himself he studied English when he was young.
He, by teaching himself, studied English when he was young.
主語：it（形式主語）氏仗，真正主語是that引導的名詞性從句（over 50% of genes（主語） contain （謂語）more than two poly(A) sites （賓語） in eukaryotes（狀語））
謂語：was
Poly(A) signal is mainly recognized by cleavage and polyadenylation specificity factors (CPSFs) (Clerici et al. 2018).
主語：Poly(A) signal
謂語：is mainly recognized by
賓語：cleavage and polyadenylation specificity factors (CPSFs)
Although CPSFs are highly conserved between mammals and plants (Zhang et al. 2008a; Hunt et al. 2012), the poly(A) signal
compositions are quite different.
主語：the poly(A) signal compositions
謂語：are
表語： quite （狀語） different.
讓步狀語從句：Although CPSFs are highly conserved between mammals and plants
More than 50% of transcripts from mammals use the canonical poly(A) signal AAUAAA for polyadenylation (Tian and Manley 2017), whereas the transcripts using AAUAAA only account for about 10% of plant transcripts (Wu et al. 2011b; Xing and Li 2011).
主語： 50% of transcripts from mammals （地點狀語）
謂語：use
賓語：the canonical poly(A) signal AAUAAA
賓補：for polyadenylation
The other 40% and 50% of plant transcripts contain 1-nt variations of AAUAAA and other poly(A) signals (Loke et al. 2005), respectively.
主語：The other 40% and 50% of plant transcripts
謂語：contain
賓語：1-nt variations of AAUAAA and other poly(A) signals
This distinguished characteristic of poly(A) signal reflects a more complex polyadenylation mechanism in plants that is not yet understood.
主語： characteristic of poly(A) signal
謂語：reflects
賓語： a more complex polyadenylation mechanism （in plants）
先行詞為mechanism的賓語從句： that is not yet understood.（主系表結構）
Nucleosomes are formed when histone proteins are wrapped with DNA.
主語：*Nucleosomes
謂語：are
表語：formed
狀語從句：when histone proteins are wrapped with DNA
These nucleosomes are then packed into highly condensed chromatins in the eukaryotic nucleus.
主語：These nucleosomes
謂語：are packed into
賓語：highly condensed chromatins
狀語：in the eukaryotic nucleus
It was reported that the nucleosome position affects the usage of proximal or distal poly(A) sites, suggesting the regulatory role of chromatin status in orchestrating mRNA polyadenylation (Huang et al. 2013; Lee and Chen 2013).
主語：形式主語it吉捶，真正主語是that引導的主語從句
謂語：was reported
suggestting （that）引導的結果狀語從句，解釋結果：suggesting the regulatory role of chromatin status in orchestrating mRNA polyadenylation
Overall, the compactness of chromatin is determined by histone modifications such as methylation and acetylation.
主語：the compactness of chromatin
謂語： is determined by
賓語：histone modifications
定語：such as methylation and acetylation解釋前面histone modification皆尔，定語前置后置的原則就是長的后面呐舔，短的前面，當時被動的后面慷蠕，比如a cake eaten by her
Within these modifications, histone acetylation is known to be associated with the accessibility of chromatin and the recruitment of DNA-binding proteins to activate gene expression.
主語： histone acetylation
謂語：is known to
賓語：be associated with the accessibility of chromatin and the recruitment of DNA-binding proteins
狀語：to activate gene expression 不定時作目的狀語
狀語：介詞短語作狀語滋早，修飾整個句子Within these modifications
However, acetylation of the histones can be erased by histone deacetylases (HDACs), resulting in structural changes to the chromatin. Thus, the dynamic acetylation of a histone is an epigenetic hallmark to gate transcription activation.
主語：acetylation of the histones
謂語： can be erased by
賓語：histone deacetylases (HDACs)
狀語1：resulting in structural changes to the chromatin （動名詞詞組作結果狀語）
插入語：however，
插入語：一般被逗號砌们，破折號，句子的其他成分隔開
類似的：
Frankly搁进，he is a good guy浪感，obviously，
HDA6 (encoded byAT5G63110), one of the HDACs, is associated with heterochromatin formation and gene repression (Tan et al. 2018).
主語： HDA6
謂語：is associated with
賓語：heterochromatin formation and gene repression
同位語：one of the HDACs
同樣還有：English饼问，a world wide language影兽，is playing a key role in our school
In addition, HDA6 is also involved in other biological processes, such as stress tolerance, flowering time, and circadian rhythm in Arabidopsis (Yuet al. 2011; Kim et al. 2017; Wang et al. 2017; Hung et al. 2018).
主語： HDA6
謂語： is also involved in
賓語：other biological processes
非限制性定語：such as stress tolerance, flowering time, and circadian rhythm
狀語：In addition，相當于additionally
例如 Your bonus this year is a one-week vacation in Hawaii. Additionally/In addition, you'll receive $3,000 in cash.
A recent study has revealed that nuclear retention of HDA6 results in gene silencing (Zhu et al. 2019).
主語：A recent study
謂語：has revealed
賓語：that nuclear retention of HDA6 results in gene silencing
Essentially, HDA6 deficiency could also result in a significant increase of histone H3K9ac, H3K14ac, (To et al. 2011), and gene activation (Earley et al. 2006; Tanaka et al. 2008; Yu et al. 2017).
主語：HDA6 deficiency
謂語：could also result in
賓語：a significant increase of histone H3K9ac, H3K14ac, (To et al. 2011), and gene activation（and 介導的多賓語）
狀語：Essentially莱革，副詞作狀語峻堰，修飾真?zhèn)€句子
It was reported that H3K9ac is required for the maximal Pol II pausing release to initiate and elongate transcription (Gates et al.
2017).
主語：it（形式主語）
謂語：reported
真在主語：that H3K9ac is required for the maximal Pol II pausing release to initiate and elongate transcription（目的狀語）
The hyperacetylation of H3K9ac in coding and intergenic regions is correlated with transcription, reflecting the global regulatory role of histone acetylation on gene expression (Kurdistani et al. 2004).
主語：The hyperacetylation of H3K9ac in coding and intergenic regions
謂語：is correlated with
賓語：transcription,
狀語： reflecting the global regulatory role of histone acetylation on gene expression（動名詞詞組作結果狀語）
By facing the challenge of environmental stress, H3K9ac is associated with the expression of induced stress response genes (Kim et al. 2008; Chinnusamy and Zhu 2009).
主語：H3K9ac
謂語： is associated with
賓語： the expression of induced stress response genes
狀語：By facing the challenge of environmental stress, by引導的方式狀語
The other type of histone acetylation, H3K14ac, co-occurs with H3K9ac at gene regulatory elements, suggesting their coordinated regulatory role in gene expression (Karmodiya et al. 2012).
主語：The other type of histone acetylation
同位語：H3K14ac
謂語： co-occurs with
賓語：H3K9ac
賓補： at gene regulatory elements
狀語：suggesting their coordinated regulatory role in gene expression（動名詞詞組作結果狀語）
Moreover, H3K14ac can crosstalk with H3K4 dimethylation during stress responses in soybeans (Wu et al. 2011a).
主語：H3K14ac
謂語： can crosstalk with
賓語：H3K4 dimethylation
狀語：during stress responses in soybeans
狀語2：Moreover
Together, these results indicate that H3K9ac and H3K14ac are important histone epigenetic hallmarks for regulating gene
expression.
主語：these results
謂語：indicate
賓語：that H3K9ac and H3K14ac are important histone epigenetic hallmarks for regulating gene
expression（由于前面主系表全有這里for是介詞短語做狀語）
狀語：Together，修飾整個句子
However, their roles in essential RNA maturation processes, polyadenylation, and APA are unknown.
主語：and 連接的多個主語their roles in essential RNA maturation processes, polyadenylation, and APA
謂語：are unknown
插入語：However盅视，一般被逗號捐名，破折號，句子的其他成分隔開
Thus, we carried out poly(A) tag sequencing (PAT-seq) and ChIP-seq of histone acetylation on wild type and HDA6 mutants
of Arabidopsis to uncover the crosstalk between histone deacetylation and mRNA 3′ end processing.
主語：we
謂語： carried out
賓語：poly(A) tag sequencing (PAT-seq) and ChIP-seq of histone acetylation
目的狀語： to uncover the crosstalk between histone deacetylation and mRNA 3′ end processing.
插入語或狀語：Thus
Results
PAT-seq, which uniquely sequences the 3′ end of mRNA, was applied for Col-0 and HDA6 mutants to uncover the effect of HDA6 on polyadenylation of Arabidopsis.
主語：PAT-seq
謂語：was applied for
賓語：Col-0 and HDA6 mutants
目的狀語：to uncover the effect of HDA6 on polyadenylation of Arabidopsis
非限制性定語從句：which uniquely sequences the 3′ end of mRNA
An overview of the experimental and computational analysis scheme is summarized in Supplemental Figure S1.
主語：overview
謂語： is summarized in
賓語：Supplemental Figure S1
It has been shown that mRNA polyadenylation sites are not exclusively positioned in the 3′ UTR (Wu et al.2011b).
主語：it（形式）
謂語：has been shown
主語從句：mRNA polyadenylation sites are not exclusively positioned in the 3′ UTR (Wu et al.2011b).
例子：Further, [狀語] it [形式主語] has recently been shown [謂語] something. [主語]
They can be located anywhere with a suitable poly(A) signal, resulting in truncated or prolonged mRNA isoforms (Supplemental Fig. S2A).
主語：They
謂語：can be
狀語：anywhere
伴隨狀語2：with a suitable poly(A) signal
resulting in truncated or prolonged mRNA isoforms （動名詞詞組作結果狀語）
About 50% of genes and intergenic loci were identified with more than two poly(A) sites (Fig. 1A).
主語：About 50% of genes and intergenic loci
謂語：were identified with
賓語：more than two poly(A) sites
Principle component analysis of PAT-seq data shows a good repeatability of this PAT-seq experiment (Supplemental Fig. S2B).
主語：Principle component analysis of PAT-seq data
謂語：shows
賓語：a good repeatability of this PAT-seq experiment
Furthermore, the percentage of reads clustered into each poly(A) site in a gene is calculated to represent the poly(A) site usage (PSU).
主語：the percentage of reads clustered into each poly(A) site in a gene（定語后置）
謂語： is calculated to
賓語：represent the poly(A) site usage (PSU)
By excluding intergenic poly(A) sites, we identified 10,681 genes with ≥2 poly(A) sites.
主語：we
謂語：identified
賓語：10,681 genes
方式狀語：By excluding intergenic poly(A) sites
定語：with ≥2 poly(A) sites
DESeq2 was used to calculate the p and adjusted P value (padj) of each poly(A) site.
主語：DESeq2
謂語：was used to
賓語（賓補）：calculate the p and adjusted P value (padj) of each poly(A) site.
To explore the effect of HDA6 on APA, different thresholds were used.
主語：different thresholds
謂語：were
表語：used
目的狀語： To explore the effect of HDA6 on APA
According to the published threshold of absolute value of PSU changes (|△PSU|≥0.05, P < 0.05) (Zheng et al. 2018), 1310 (978 + 279 + 53) genes were identified with significant APA events (Fig. 1B, red circle).
主語：1310 (978 + 279 + 53) genes
謂語：were identified with
賓語：significant APA events
狀語：條件狀語According to the published threshold of absolute value of PSU changes
Within these, about 25.34% (279 + 53) of genes have a larger (|△PSU|≥0.2) shift of poly(A) site usage (Fig. 1B, blue circle).
主語：25.34% (279 + 53) of genes
謂語：have
賓語： larger (|△PSU|≥0.2) shift of poly(A) site usage
條件狀語：Within these
However, if the threshold was set to |△PSU|≥0.2 and padj < 0.05, only 53 genes were identified with significant APA events (Fig. 1B, green circle; Supplemental Table S1).
插入語：However
主語：only 53 genes
謂語：were identified with
賓語：significant APA events
條件狀語從句： if the threshold was set to |△PSU|≥0.2 and padj < 0.05
These results indicate that HDA6 affects mRNA polyadenylation and APA of genes by different measures.
主語：These results
謂語：indicate
賓語：that HDA6 affects mRNA polyadenylation and APA of genes by different measures（方式狀語）.
The cumulative distribution curves present genome-wide polyadenylation profiles of hda6 and Col-0 and are folded at 50% cumulative frequency to show the median PSU (Supplemental Fig.S2C).
主語：The cumulative distribution curves
謂語：present 闹击；are folded at
賓語：genome-wide polyadenylation profiles of hda6 and Col-0镶蹋； 50% cumulative frequency
Although there is no large difference between the cumulative distribution curves of hda6 and Col-0, a Kolmogorov–Smirnov test (K-S test) shows a significant difference in the PSU profiles of hda6 and Col-0, reflecting that HDA6 has an impact on polyadenylation in Arabidopsis.
主語：a Kolmogorov–Smirnov test
謂語：shows
賓語：a significant difference in the PSU profiles of hda6 and Col-0
讓步狀語從句：Although there is no large difference between the cumulative distribution curves of hda6 and Col-0,
動名詞引導結果狀語從句：reflecting that HDA6 has an impact on polyadenylation in Arabidopsis
These results were further confirmed by the PAT-seq of another HDA6 mutant allele, sil1 (Liu et al. 2012) with a K-S test P value < 2.2 × 10?16 (Supplemental Fig. S2D).
主語：These results
謂語： were further confirmed by
賓語：the PAT-seq of another HDA6 mutant allele
Furthermore, by CDF plot again, we found that the PSU profile of DE poly(A) sites (n = 1387; threshold: padj < 0.05)
has a significant difference between hda6 and Col-0 (Fig. 1C).
主語：we
謂語：found
賓語：that the PSU profile of DE poly(A) sites (n = 1387; threshold: padj < 0.05) has a significant difference between hda6 and Col-0 (Fig. 1C)
狀語：Furthermore
狀語：by CDF plot again
**A heat map of these PSU profiles also illustrates that the PSUs of most DE poly(A) sites were varied between hda6 and Col-0, and this was consistent among replicates (Fig. 1D). **
主語：A heat map of these PSU profiles
謂語：illustrates
賓語：the PSUs of most DE poly(A) sites were varied between hda6 and Col-0
并列句：and this was consistent among replicates
To evaluate the potential that DE poly(A) sites resulted from the total gene expression variation, RT-qPCR was carried out
with a pair of primers which quantified the DE poly(A) sites and a pair of primers located on the 5′ end of genes which quantified
the total gene expression levels (Supplemental Fig. S3; Supplemental Table S2).
主語： RT-qPCR
謂語：was carried out with
賓語： a pair of primers which quantified the DE poly(A) sites（定語從句）
a pair of primers located on the 5′ end of genes（定語后置） which quantified the total gene expression levels （定語從句）
目的狀語從句： To evaluate the potential that DE poly(A) sites resulted from the total gene expression variation
Results showed that DE poly(A) sites identified by DESeq2 were validated by RT-qPCR, and variation of their corresponding total gene expression levels was neither significant (Supplemental Fig. S3A–D) nor in an opposite direction (Supplemental Fig. S3E–H).
主語：Results
謂語：showed
賓語：and 介導的雙賓語從句： DE poly(A) sites identified by DESeq2 were validated by RT-qPCR, and variation of their corresponding total gene expression levels was neither significant (Supplemental Fig. S3A–D) nor in an opposite direction
As a control, we selected AT1G35680 and AT2G38310 genes with non-DE poly(A) sites in the PAT-seq experiment.
As a control：as 用作介詞，當它后面接名詞時，既可以表示“時間”贺归，也可以“身份”淆两。表示“時間”就是時間狀語，表示“身份”則是方式狀語拂酣，意為“以......身份（做某事）”秋冰。
主語：we
謂語：selected
賓語： AT1G35680 and AT2G38310 genes
賓補： with non-DE poly(A) sites
定語：in the PAT-seq experiment
As shown in Supplemental Figure S3I, RT-qPCR confirmed that AT1G35680 was indeed not a DE poly(A) site gene.
方式狀語：As shown in Supplemental Figure S3I,
As shown=As it is shown or As is shown
- Enter the word as it is shown in the box below. 輸入下面顯示驗證字母。（方式狀語婶熬。as 從句不缺成分剑勾，主句是行為動詞enter）
可以省略為：Enter the word as shown in the box below.
- As is shown above, the laser beam is much more powerful.（比較狀語。as 充當從句主語尸诽，傳統(tǒng)語法叫“定語從句”甥材。）
如上所顯示，激光束比其他光束要強烈得多性含。
可以省略為：As shown above, the laser beam is much more powerful.
主語：RT-qPCR
謂語：confirmed
賓語：that AT1G35680 was indeed not a DE poly(A) site gene
For the second control gene AT2G38310, while its 3′ UTR was significantly down-regulated in hda6 by the RT-qPCR experiment, the total gene expression level also had the same trend (Supplemental Fig. S3J).
主語：the total gene expression level
謂語： had
賓語： the same trend
狀語：For the second control gene AT2G38310,
while引導的讓步狀語從句： while（=although） its 3′ UTR was significantly down-regulated in hda6 by the RT-qPCR experiment
It indicates that the variation of the 3′ UTR of AT2G38310 may be induced by the repression of gene expression in hda6, and it was not identified as a DE poly(A) site in the PAT-seq analysis.
主語：it
謂語：indicates
賓語： the variation of the 3′ UTR of AT2G38310 may be induced by the repression of gene expression in hda6, and it was not identified as a DE poly(A) site in the PAT-seq analysis
Taken together, DE poly(A) sites identified by PAT-seq were mainly contributed by the change in polyadenylation activity in
hda6, and these results suggest that HDA6 affects mRNA polyadenylation
主語：DE poly(A) sites identified by PAT-seq
謂語：were mainly contributed by
賓語：the change in polyadenylation activity in hda6
and 連接并列句：, （由于和前面不是并列關系洲赵，所以這個and前面加，如果不加商蕴，就是and連接的兩個并列賓語從句）and these results suggest that HDA6 affects mRNA polyadenylation
Histone acetyltransferase inhibitor minimizes the molecular effect of HDA6 mutation
主語：Histone acetyltransferase inhibitor
謂語：minimizes
賓語： the molecular effect of HDA6 mutation
It was demonstrated that defective HDA6 results in an increased gene expression (Earley et al. 2006; Tanaka et al. 2008; Yu et al.2017).
主語：it
謂語：was demonstrated
真正主語： that defective HDA6 results in an increased gene expression
Thus, we asked whether defective HDA6 causes differential expression of transcript isoforms.
主語：we
謂語：asked
賓語從句：whether defective HDA6 causes differential expression of transcript isoforms
狀語：Thus
We found that more differentially expressed transcripts are up-regulated in hda6 (Fig. 2A).
主語：We
謂語：found
賓語： that more differentially expressed transcripts are up-regulated in hda6
Within the 1387 transcripts with DE poly(A) sites, 882 are up-regulated and 505 are down-regulated.
主語：882 搂漠；505
謂語：are ；are
賓語：up-regulated锐秦；down-regulated.
狀語：Within the 1387 transcripts with DE poly(A) sites
Since HDA6 functions in deacetylation of chromatins, we asked whether the effects of HDA6 on polyadenylation can be minimized under a low histone acetylation level.
主語：we
謂語：asked
賓語： whether the effects of HDA6 on polyadenylation can be minimized under a low histone acetylation level （whether作引導詞不能省略耳璧，含義(是否)，有實際含義格郁。）
原因狀語從句：Since HDA6 functions in deacetylation of chromatins,
原因狀語從句引導詞：beacuse腹殿，for，as 例书，since
A histone acetyltransferase inhibitor, MB-3, was used to reduce the histone acetylation levels of hda6, sil1, and Col-0.
主語：A histone acetyltransferase inhibitor,
同位語：MB-3
謂語：was used to
賓語： reduce the histone acetylation levels of hda6, sil1, and Col-0
PAT-seq of MB-3-treated seedlings shows that the variances of those 1387 HDA6-dependent poly(A) sites are minimized (Fig.2B)
主語：PAT-seq of MB-3-treated seedlings
謂語：shows
賓語：that the variances of those 1387 HDA6-dependent poly(A) sites are minimized
Within those 1387 poly(A) sites, 929 show no significant difference after MB-3 treatment.
主語： 929
謂語：show
賓語：no significant difference
狀語1：Within those 1387 poly(A) sites
狀語2：after MB-3 treatment
The numbers of both up- and downregulated poly(A) sites are reduced a lot.
主語：The numbers of both up- and downregulated poly(A) sites
謂語：are reduced
狀語：a lot
Under normal conditions, the majority of DE poly(A) sites resided in protein coding genes (Fig. 2C, red boxes) and are mainly located in the 3′ UTR (Fig. 2D, red boxes).
主語：the majority of DE poly(A) sites锣尉；
謂語：resided in；are mainly located in
賓語： protein coding genes决采；3′ UTR
狀語：Under normal conditions
The interquartile ranges of boxplots and median values are minimized under MB-3 treatment, indicating that MB-3 treatment significantly reduces the variance of transcription expression levels among these three different gene types (Fig. 2C).
主語：The interquartile ranges of boxplots and median values
謂語： are minimized
狀語1：under MB-3 treatment
狀語2： indicating that MB-3 treatment significantly reduces the variance of transcription expression levels among these three different gene types （動名詞詞組引導結果狀語從句）
The median expression level (dashed lines in red boxes) of DE poly(A) sites is slightly down in the
3′ UTR (canonical poly(A) site), whereas it is up-regulated in most other noncanonical poly(A) sites, such as the intergenic regions and introns (Fig. 2D, red boxes).
主語：The median expression level (dashed lines in red boxes) of DE poly(A) sites
謂語： is
表語：down
狀語：in the 3′ UTR (canonical poly(A) site),
狀語從句： whereas it is up-regulated in most other noncanonical poly(A) site
whereas 為從屬連詞自沧，表示對比意義。從句位于主句之后時树瞭，分析為對比狀語從句（=while on the contrary)
非限制性定語：such as stress tolerance, flowering time, and circadian rhythm
The up-regulating pattern is also observed in sil1, although the expression pattern of CDS poly(A) transcripts is different from hda6 (Supplemental Fig. S2G).
主語：The up-regulating pattern
謂語： is also observed in
賓語：sil1
讓步狀語從句：although the expression pattern of CDS poly(A) transcripts is different from hda6 (Supplemental Fig. S2G).
MB-3 treatment also reduces the ΔPSU values of 1387 DE poly(A) sites (Fig. 2E), which reflects the assertion
that MB-3 partially patches the effect of mutated HDA6.
主語：*MB-3 treatment
謂語：reduces
賓語：ΔPSU values of 1387 DE poly(A) sites
非限制性定語從句：which reflects the assertion that MB-3 partially patches the effect of mutated HDA6（that引導的同位語從句）
This trend was also found in MB-3 treatment on sil1 (Supplemental Fig. S2H).
主語：This trend
謂語：as also found in
賓語：MB-3 treatment
Gene Ontology enrichment analyses show that genes with significant upand down- regulated poly(A) sites are
both enriched in terms related to stress response (Supplemental Fig. S4A,B, green dashed box).
主語：Gene Ontology enrichment analyses
謂語： show
賓語：that genes with significant upand down- regulated poly(A) sites are
both enriched in terms related to stress response
Genes with up-regulated poly(A) sites are also significantly enriched in translation-associated terms
(Supplemental Fig. S4A, red dashed box), whereas genes with down-regulated poly(A) sites are also enriched in light response-associated terms (Supplemental Fig. S4B, orange dashed box).
主語：Genes with up-regulated poly(A) sites
謂語：are also significantly enriched in
賓語： translation-associated terms
比較狀語從句：whereas genes with down-regulated poly(A) sites are also enriched in light response-associated terms
By checking the PAT-seq profiles, we found distinct APA on AT2G29500 encoding a HSP20-like protein, AT5G67300 encoding MYB DOMAIN PROTEIN 44 (MYB44), AT5G52882 encoding a Ploop protein in the nucleoside triphosphate hydrolases superfamily, and AT4G26090 encoding a leucine-rich repeat protein RPS2 (Supplemental Fig. S4C).
主語：we
謂語：found
賓語：and 引導的多個賓語
方式狀語從句：By checking the PAT-seq profiles
Under MB-3 treatment, poly(A) sites of these genes in hda6 and sil1 are similar to Col-0 but rather different in the nontreated samples, reflecting that the mutation effect of HDA6 is abolished under low chromatin acetylation level
主語：poly(A) sites of these genes in hda6 and sil1
謂語：are similar to
賓語： Col-0
狀語1：Under MB-3 treatment
but并列連詞拇厢，連接兩個句子，由于前面和后面句子主語謂語一致晒喷，為了避免重復孝偎，后面句子主語+謂語省略
伴隨狀語從句表示結果：reflecting that the mutation effect of HDA6 is abolished under low chromatin acetylation level
狀語從句變成伴隨狀語從句順序：1.去掉連詞，2.去掉主語厨埋，3.動詞變形
例如：Though he is young邪媳，he is very cute
Being young捐顷，he is very cute
After he finished his work，he went shopping
Finishing his work雨效，he went shopping
These distinct APA genes between hda6 and Col-0 may contribute to the phenotypic outcomes of hda6, such as affecting abiotic stress tolerance by AT5G52882 and MYB44 (Ali et al. 2013; Kim et al. 2017), altering heat shock tolerance by HSP20-like gene (Popova et al. 2013), and changing sensitivity to pathogen infection by RPS2 (Bhandari et al. 2019).
主語：These distinct APA genes between hda6 and Col-0
謂語：contribute to
賓語：the phenotypic outcomes of hda6
非限制性定語：such as affecting abiotic stress tolerance by AT5G52882 and MYB44 (Ali et al. 2013; Kim et al. 2017)迅涮， altering heat shock tolerance by HSP20-like gene (Popova et al. 2013), and changing sensitivity to pathogen infection by RPS2
One of the important effects of APA is changing the tandem 3′-UTR length of mRNA (Tian and Manley 2017; Chen et al. 2018;Srivastava et al. 2018).
主語：One of the important effects of APA
謂語：is changing
賓語：the tandem 3′-UTR length of mRNA
This molecular effect connects to various post-transcriptional regulations, including alteration of mRNA
stability, the gain or loss of miRNA, and/or RNA-binding protein targets (Mayr 2017).
主語：This molecular effect
謂語：connects to
賓語：various post-transcriptional regulations
狀語：including alteration of mRNA stability, the gain or loss of miRNA, and/or RNA-binding protein targets
By genome-wide calculation of the weighted 3′-UTR length of genes, we found that 3′ UTR lengthening events
(1157) are more abundant than 3′ UTR shortening events (373) in hda6 compared to Col-0 (Fig. 3A).
主語：we
謂語：found
賓語：that 3′ UTR lengthening events (1157) are more abundant than 3′ UTR shortening events (373) in hda6 compared to Col-0
These results suggest that HDA6 may play a role in ensuring proper 3′-UTR length for gene expression, indicating a connection between histone acetylation and 3′-UTR length control.
主語：These results
謂語：suggest
賓語：that HDA6 may play a role in ensuring proper 3′-UTR length for gene expression
動名詞引導結果狀語：indicating a connection between histone acetylation and 3′-UTR length control.
The length of the 3′ UTR was reported to be correlated with total gene expression (not at the individual transcript level) under certain conditions or in specific tissues (Zheng et al. 2018; Fu et al. 2019).
主語：The length of the 3′ UTR
謂語：was reported to
賓語：be correlated with total gene expression
狀語：under certain conditions or in specific tissues
RNA-seq data of the seedlings of hda6 and Col-0 from the NCBI Sequence Read Archive (SRA; https://www.ncbi.nlm.nih.gov/sra) database were downloaded to obtain complete gene expression profiles.
主語：RNA-seq data of the seedlings of hda6 and Col-0 from the NCBI Sequence Read Archive database
謂語：were downloaded to
賓語：obtain complete gene expression profiles
We did not observe a clear relationship between 3′-UTR length and gene expression.
主語：We
謂語：did not observe
賓語：a clear relationship between 3′-UTR length and gene expression
However, 3′ UTR lengthening and shortening events coincide with those of stable genes that are not significantly affected by the mutation of HDA6 (Fig. 3B).
主語：3′ UTR lengthening and shortening events
謂語： coincide with
賓語：those of stable genes
定語從句： that are not significantly affected by the mutation of HDA6
狀語：However
Figure 3C shows that decreased poly(A) site usage is coupled with an increase of another poly(A) site usage on the 3′ UTR of AT2G30720 and AT3G15518, which may explain the minor variance in total gene expression.
主語：Figure 3C
謂語：shows
賓語：that decreased poly(A) site usage is coupled with an increase of another poly(A) site usage on the 3′ UTR of AT2G30720 and AT3G15518
非限制性定語從句：which may explain the minor variance in total gene expression
Again, MB-3 treatment abolished the difference of poly(A) profile alteration of AT2G30720 and AT3G15518 between mutants and Col-0, reflecting that the 3′ UTR APA may depend on deacetylation by HDA6.
主語：MB-3 treatment
謂語：abolished
賓語：the difference of poly(A) profile alteration of AT2G30720 and AT3G15518 between mutants and Col-0
伴隨狀語：reflecting that the 3′ UTR APA may depend on deacetylation by HDA6.
狀語：Again
In general, these evidences indicate that defective HDA6 results in both gene expression activation and 3′-UTR length variance.
主語：these evidences
謂語：indicate
賓語：that defective HDA6 results in both gene expression activation and 3′-UTR length variance
狀語：In general,
However, 3′ UTR APA in hda6 is independent of the transcription activity but associated with histone acetylation status.
主語：3′ UTR APA in hda6
謂語：is independent of ；associated with
賓語： the transcription activity 徽龟； histone acetylation
狀語：However
Furthermore, tandem 3′ UTR sequences of genes with a switching of 3′-UTR length were submitted to the psRNATarget webserver (Dai et al. 2018) for identifying potential small RNA targets.
主語： tandem 3′ UTR sequences of genes with a switching of 3′-UTR length
謂語： were submitted to
賓語：the psRNATarget webserver (Dai et al. 2018)
狀語： for identifying potential small RNA targets
For lengthening events, psRNATarget reported 832 pairs of small RNAs interacting with said 3′ UTRs that may support cleavage inhibition, and 203 pairs of interactions that may be subject to translation inhibition (Supplemental Table S3).
主語：psRNATarget
謂語：reported
賓語：832 pairs of small RNAs (which were) interacting with 3′ UTRs
定語從句省略：主格關系代詞+be+分詞可以省略主格關系代詞+be
例如: The boy who is standing by the dor is my brother
The boy standing by the door is my brother
I received a letter which was written in English
I received a letter written in English
與此相同的還有伴隨狀語從句省略：
主句和從句主語相同時候可以省略連接詞和主語叮姑，同時謂語變成分詞形式
例如： Because I feel tired， I went to sleep
Feeling tired, I went to sleep
對于832 pairs of small RNAs (which were) interacting with 3′ UTRs 省略引導詞做主語据悔，因此是定語從句传透，狀語從句引導詞是連接副詞一般不做成分。
定語從句：that may support cleavage inhibition
狀語：For lengthening events
For shortening events, psRNATarget predicted 233 cleavage inhibition and 43 translation inhibition pairs (Supplemental Table S4).
主語：psRNATarget
謂語：predicted
賓語：233 cleavage inhibition and 43 translation inhibition pairs
目的狀語：For shortening events
These data suggest that the lengthening of the 3′ UTR in hda6 may increase possibilities of small RNA targeting for cleavage or translation inhibition, whereas the shortening of the 3′ UTR in hda6 may result in transcripts escaping from small RNA targeting.
主語：These data
謂語：suggest
賓語： that the lengthening of the 3′ UTR in hda6 may increase possibilities of small RNA targeting for cleavage or translation inhibition
非限制性定語從句:whereas the shortening of the 3′ UTR in hda6 may result in transcripts escaping from small RNA targeting
Thus, mRNA stability may be affected by the switch of 3′-UTR length.
主語：mRNA stability
謂語：may be affected by
賓語：the switch of 3′-UTR length
選自：http://www.genome.org/cgi/doi/10.1101/gr.255232.119.
